Research in the Stoltz lab is focused on the synergistic development of novel methodologies for the asymmetric formation of congested stereocenters and natural product total synthesis, while employing computations to aid mechanistic understanding. This thesis describes the development and mechanistic studies of novel asymmetric reactions from Pd enolates and progress toward the total synthesis of hypermoin A.
\r\n\r\nThe first chapter details the development of an enantioselective intramolecular [4+2] cycloaddition from a chiral Pd enolate, allowing formation of highly stereoenriched polycyclic structures. Quantum mechanics calculations, Eyring analysis, and KIE studies allowed further mechanistic understanding of the reaction. The [4+2] cycloaddition was further investigated through molecular dynamics simulations, and studies of cyclohexenone-derived substrates are reported in chapter 2.
\r\n\r\nChapter 3 describes the application of a chiral Pd enolate in an asymmetric intramolecular Michael spirocyclization, forging vicinal quaternary and tertiary stereocenters in a single step. Computational investigations provide mechanistic insights to the stereoselectivity of the process. In chapter 4, a branched-selective asymmetric decarboxylative allylic alkylation reaction is reported. The hypotheses informed by quantum mechanics calculations allow rational ligand design to achieve high regio-, diastereo-, and enantioselectivity in forming vicinal quaternary and tertiary stereocenters.
\r\n\r\nChapter 5 outlines the ongoing progress toward the asymmetric total synthesis of hypermoin A. [2.2.2] bicycle formation through [4+2] cycloaddition or reductive Heck cyclization followed by ring expansion allows formation of a key [3.2.2] bicyclic core, and current efforts are focused on extending this approach to more elaborate substrates.
", "doi": "10.7907/war0-n433", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:18610", "collection": "thesis", "collection_id": "18610", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05222026-182628481", "type": "thesis", "title": "The Total Synthesis of Aleutianamine, (\u2013)-Crotonolide D, and (\u2013)-Crotonine G", "author": [ { "family_name": "Yu", "given_name": "Hao", "orcid": "0009-0008-6002-6276", "clpid": "Yu-Hao" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Fu", "given_name": "Gregory C.", "orcid": "0000-0002-0927-680X", "clpid": "Fu-G-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Robb", "given_name": "Maxwell J.", "orcid": "0000-0002-0528-9857", "clpid": "Robb-M-J" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The first chapter describes the total synthesis of aleutianamine, a pyrroloiminoquinone alkaloid that displays potent and selective cytotoxicity towards pancreatic cancer PANC-1 cell line (IC\u2085\u2080 = 25 nM). An initial a-thioketone derivatization approach was thwarted by a failed enolate functionalization. A second-generation approach employing palladium-\r\ncatalyzed Barbier addition enabled the successful construction of the [3.3.1]bicyclononane moiety of the natural product, but unsuccessful downstream functionalization and poor material throughput led to the abandonment of this approach. Along the way, a one-pot Larock indolization/Buchwald\u2013Hartwig amination cascade was developed for the synthesis of tricyclic diaminoindole derivatives. Eventually, the total synthesis was accomplished via a\r\nnovel dearomative arylation of an aminothiophene, which allowed rapid access to the molecular skeleton of aleutianamine including the challenging bridgehead sulfide. Following construction of the core, cerium-mediated oxidative amination and palladium-catalyzed decarboxylative pinacol-type rearrangement enabled chemoselective introduction of the C10 aniline and alkenyl bromide, leading to the total synthesis of aleutianamine.
\r\n\r\nThe second chapter details the total synthesis of crotonolide D and crotonine G. The synthetic approach employs a SmI\u2082 mediated ketyl radical cyclization to form the highly congested quaternary carbon at the center of these complex molecules. Following the furan introduction, the core structure of the natural product is constructed via oxidative olefin cleavage to install the unusual C19 and C20 oxidation. Finally, palladium-catalyzed carbonylation, furan oxidation and acid mediated condensation/epimerization completes the synthesis.
", "doi": "10.7907/cn84-6g19", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17616", "collection": "thesis", "collection_id": "17616", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08122025-011509478", "primary_object_url": { "basename": "Samkian_2026 Thesis.pdf", "content": "final", "filesize": 50130987, "license": "other", "mime_type": "application/pdf", "url": "/17616/4/Samkian_2026 Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Total Synthesis of Hypersampsone M and Studies of Related Polycyclic Polyprenylated Acylphloroglucinol Systems", "author": [ { "family_name": "Samkian", "given_name": "Adrian Eduard", "orcid": "0000-0002-0068-3572", "clpid": "Samkian-Adrian-Eduard" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Fu", "given_name": "Gregory C.", "orcid": "0000-0002-0927-680X", "clpid": "Fu-G-C" }, { "family_name": "Reisman", "given_name": "Sarah E.", "orcid": "0000-0001-8244-9300", "clpid": "Reisman-S-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Virgil", "given_name": "Scott C.", "orcid": "0000-0001-8586-5641", "clpid": "Virgil-S-C" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Research in the Stoltz group is primarily focused on the total synthesis of complex, bioactive natural products and on the development of reaction methodologies to enable these synthetic endeavors. This thesis focuses on the homoadamantane polycyclic polyprenylated acylphloroglucinol (PPAP) class of natural products, our efforts toward their synthesis, and discoveries made along the way. Chapter 1 describes the completed synthesis of hypersampsone M, while Chapter 2 describes ongoing efforts toward wilsonglucinol G and hypersampsone A. Appendix 5 presents the culmination of optimization studies and unsuccessful routes toward these natural products. Chapter 3 describes selective fragmentations of a-bromocaranones, reactions that were tailored to the synthesis of PPAPs. Chapter 4 discloses the synthesis and characterization of an unexpected, caged side product isolated during an unsuccessful route to the homoadamantane PPAPs. Chapter 5 discusses the development and scope of the key cyclopentene annulation methodology that enabled the installation of the challenging, hindered 5-membered ring on the homoadamantane PPAPs.", "doi": "10.7907/hd4h-sk15", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17800", "collection": "thesis", "collection_id": "17800", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12152025-200604749", "type": "thesis", "title": "Towards Sustainable, Scalable, Low-Cost InP Space Solar Power", "author": [ { "family_name": "Anjum", "given_name": "Sara", "orcid": "0009-0006-6639-4710", "clpid": "Anjum-Sara" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Schwab", "given_name": "Keith C.", "orcid": "0000-0001-8216-4815", "clpid": "Schwab-K-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "local_group": [ { "literal": "Space Solar Power Project" }, { "literal": "div_eng" } ], "abstract": "The world needs clean, sustainable, and consistent sources of power. Solar energy is an attractive source of renewable power, but energy storage is a challenge for intermittent sources like solar and wind. The massive reduction in space launch costs now makes the prospect of space solar power as a 24/7, consistent baseline source of clean power more of a viable possibility than before. Solar cells designed\r\nto provide power for Earth while in space must not only be low cost and efficient but also light and maintain their performance in harsh space environments, especially in extreme temperature conditions while being subject to damaging space radiation.
\r\n\r\nThis thesis explores two different approaches to achieving radiation hardness: using nanowire solar cells instead of planar cells and using thin-film diffusion-doped cells. It does so with cells made of indium phosphide (InP), which is inherently more resilient to damage from space radiation than materials like silicon (Si) and gallium arsenide (GaAs). The performance of diffusion-doped planar cells is compared to\r\nepitaxially-grown solar cells as a baseline.
\r\n\r\nNanowire cells were simulated in Lumerical to understand the light-trapping properties compared to planar cells with and without surface texturing that also enhances light absorption. The nanowires were simulated with and without hemispherical nanoparticles to enhance light absorption while maintaining a transparent conducting top layer to adequately transport the generated electricity. Nanowire and planar\r\ncells were further simulated in Sentaurus to predict their electrical performance. Nanowire fabrication was attempted as well, but reliable, consistent fabrication was challenging. Given the cost and scalability challenges of this approach, the rest of the work pivots to planar cells.
\r\n\r\nEpitaxially-grown InP cells optimized using Sentaurus were fabricated as a baseline and to work out fabrication challenges adjacent to the p-n junction formation itself. Then, diffusion-doped InP cells were fabricated using Cd\u2083P\u2082 and Zn\u2083P\u2082 as p-type dopants on undoped InP substrates. Preliminary cell performance optimzation was conducted by adjusting diffusion temperatures and times as well as thinning the emitter layer. Efficiencies of up to 4.94% were achieved in Cd-doped cells and up to 3.85% were achieved in Zn-doped cells without anti-reflection coatings, with a maximum JSC of 11.33 mA/cm\u00b2 and a maximum VOC of 778.1 mV in 100 nm thinned Zn-doped cells.
", "doi": "10.7907/rhn1-n250", "publication_date": "2026", "thesis_type": "engd", "thesis_year": "2026" }, { "id": "thesis:17530", "collection": "thesis", "collection_id": "17530", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07162025-124644565", "primary_object_url": { "basename": "Rezgui_Thesis.pdf", "content": "final", "filesize": 22197861, "license": "other", "mime_type": "application/pdf", "url": "/17530/1/Rezgui_Thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Development of Synthetic Methods to Enable the Synthesis of Pyrroloiminoquinone Alkaloids", "author": [ { "family_name": "Rezgui", "given_name": "Samir Peter", "orcid": "0000-0003-4080-9835", "clpid": "Rezgui-Samir-Peter" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Reisman", "given_name": "Sarah E.", "orcid": "0000-0001-8244-9300", "clpid": "Reisman-S-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Fu", "given_name": "Gregory C.", "orcid": "0000-0002-0927-680X", "clpid": "Fu-G-C" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Natural product total synthesis continues to serve as a driving force for inventions in organic chemistry, and is an essential paradigm in the Stoltz group. The content of this thesis reflects this central objective. Chapter 1 focuses on the total synthesis of aleutianamine\u2014 a new pyrroloiminoquinone alkaloid natural product that possesses an unprecedented structure and potent anti-tumor activity. Herein is described a non-biomimetic synthesis that hinges upon the development of a dearomative thiophene arylation to construct the unique [3.3.1] ring system of the natural product. An unconventional ketone installation was then developed to install the alkenyl bromide, and finally, an oxidative amination/thioaminal formation protocol was developed to complete the synthesis. Additionally, a novel Larock/Buchwald\u2013Hartwig annulation/cyclization was developed to access the core of the natural product.
\r\n\t\t\r\nChapter 2 focuses on leveraging the Larock/Buchwald\u2013Hartwig annulation/cyclization developed en route to aleutianamine to access several pyrroloiminoquinone alkaloids in a divergent manner. This strategy led to the shortest synthetic sequences at the time of four pyrroloiminoquinone alkaloids, and the first synthesis of another.
\r\n\t\t\r\nChapter 3 describes the progress toward the total synthesis of atkamine, another pyrroloiminoquinone that has yet to be synthesized, by further leveraging of the Larock/Buchwald\u2013Hartwig annulation/cyclization. The development of additional reaction methodologies were investigated to try and rapidly access the complex bicyclic ring system of this natural product.
\r\n\t\t\r\nFinally, Chapter 4 describes the synthesis of authentic standards to enable investigations of pinene secondary organic aerosols. Access to these standards allowed for the identification and formation mechanism of dimer esters in pinene organic aerosols, which has been a long-standing challenge in the field.
", "doi": "10.7907/xmbz-by61", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:18553", "collection": "thesis", "collection_id": "18553", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05112026-234054998", "type": "thesis", "title": "Efficient Evaluation of Coulomb Interactions for Large-Scale Quantum Chemistry", "author": [ { "family_name": "Li", "given_name": "Rui", "orcid": "0009-0002-9029-6847", "clpid": "Li-Rui" } ], "thesis_advisor": [ { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-Garnet-K-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-G-K" }, { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Sharma", "given_name": "Sandeep", "orcid": "0000-0002-6598-8887", "clpid": "Sharma-Sandeep" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Evaluating the Coulomb interaction remains a fundamental computational bottleneck in electronic structure theory, dictating the scaling and efficiency of quantum chemical simulations. While recent advancements in graphics processing units (GPUs) offer immense theoretical peak performance, translating traditional, memory-intensive CPU algorithms for evaluating electron repulsion integrals to GPU architectures presents significant challenges due to memory bandwidth limitations and warp divergence.
\r\n\r\nThis thesis presents the development of algorithms to efficiently evaluate Coulomb interactions across diverse chemical systems. Chapter 2 describes the GPU implementation of Coulomb interaction for molecular systems at Hartree-Fock level of theory. Chapter 3 shows how multigrid Gaussian-Plane-Wave algorithm can better utilize GPU compute performance by a two-level parallelization scheme and grid-based screening of orbital pairs in the real space. Chapter 4 illustrates the issues of the original modified Coulomb potential from GFN-xTB in periodic systems, and the effectiveness of a new generalized Ewald summation scheme for the potential in X23 molecular crystal dataset and a range of prototypical bulk semiconductors.
", "doi": "10.7907/vj28-vh82", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:18518", "collection": "thesis", "collection_id": "18518", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04282026-002052552", "type": "thesis", "title": "Enantioselective Reactions of Palladium Enolates and Progress Toward Mitomycin B", "author": [ { "family_name": "Strong", "given_name": "Christian Santiago", "orcid": "0000-0003-1349-302X", "clpid": "Strong-Christian-Santiago" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Fu", "given_name": "Gregory C.", "orcid": "0000-0002-0927-680X", "clpid": "Fu-G-C" }, { "family_name": "Reisman", "given_name": "Sarah E.", "orcid": "0000-0001-8244-9300", "clpid": "Reisman-S-E" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "orcid": "0000-0001-5661-1714", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Research within the Stoltz group encompasses the total synthesis of natural products and the development of useful enantioselective transformations. This thesis overlaps with these domains in that it describes: 1) the development of several stereoselective reactions of Pd enolates and 2) progress toward the total synthesis of mitomycin B. Specifically, Chapter 1 provides historical context for the development of enantioselective reactions of Pd enolates beyond allylic alkylation within our group. Chapter 2 details the development of an enantioselective [4+2] cycloaddition of Pd enolates generated from prenyl \u03b2-ketoesters. Additionally, it describes experimental and computational mechanistic investigations related to the origins of stereoselectivity and the mechanism of catalyst turnover in this transformation. Chapter 3 discloses an enantioselective Michael spirocyclization reaction of Pd enolates as well as a stereoselective intramolecular enone difunctionalization. This method leverages lessons learned from the [4+2] cycloaddition and enables access to a diverse library of stereochemically rich polycycles. Chapter 4 presents our ongoing progress toward the total synthesis of mitomycin B via an isomitomycin approach. Our current strategy involves a key intramolecular nitrile oxide cycloaddition that rapidly constructs a complex framework en route to mitomycin B.", "doi": "10.7907/gwac-qk95", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:17764", "collection": "thesis", "collection_id": "17764", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11172025-045827404", "type": "thesis", "title": "Methodological Development and Computational Investigations of Metal-Catalyzed Coupling Reactions", "author": [ { "family_name": "Anderson", "given_name": "Robert Lon", "orcid": "0009-0000-5568-7768", "clpid": "Anderson-Robert-Lon" } ], "thesis_advisor": [ { "family_name": "Fu", "given_name": "Gregory C.", "orcid": "0000-0002-0927-680X", "clpid": "Fu-G-C" } ], "thesis_committee": [ { "family_name": "Reisman", "given_name": "Sarah E.", "orcid": "0000-0001-8244-9300", "clpid": "Reisman-S-E" }, { "family_name": "Agapie", "given_name": "Theodor", "orcid": "0000-0002-9692-7614", "clpid": "Agapie-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Fu", "given_name": "Gregory C.", "orcid": "0000-0002-0927-680X", "clpid": "Fu-G-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter One describes the computational study of the asymmetric arylation of propargylic electrophiles. While previous mechanistic experiments have verified the general scheme of the catalytic cycle, it was still not known what the enantiodetermining step is, or how factors of the ligand and substrate influence reactivity. To answer these questions, a computational study to emulate the entire catalytic cycle was performed. It was determined that radical addition to the nickel catalyst was likely the enantiodetermining step. While the standard substrate and ligand combinations result was well predicted, the computational method was not widely applicable to different ligands. This implies that the catalytic cycle may not go through a discrete radical capture and reductive elimination step, but instead a more concerted process may be operating.
\r\n\r\nChapter Two details the development of the asymmetric cross-coupling between tertiary nucleophiles and secondary electrophiles. Specifically, \u03b1-zincated benzylic nitriles are asymmetrically coupling with secondary alkyl iodides under the influence of a nickel catalyst and iminopyrox ligand. This study represents the first report of such a ligand being use for any asymmetric nickel-catalyzed cross-couplings.
\r\n\r\nChapter Three describes computational work on three separate projects published by coworkers in the Fu lab.
\r\n1) The first section details work on the nickel-catalyzed asymmetric coupling of enynes with secondary racemic electrophiles to accomplish for the first time the simultaneous control of axial and point chirality. The computational work probed the possible steps of rearrangement of the putative nickel-propargyl species into nickel allenyl species, as well as rationalized the different reactivity of the catalyst towards different electrophiles.
\r\n2) The second project was investigations into the photocatalytic coupling of secondary and tertiary electrophiles with secondary amines by copper and a dual-ligand system. The computations shed light on possible C\u2014N coupling mechanisms, as well as rationalized the differing photoactivity of the two CuI complexes present in the system.
\r\n3) The final work supported mechanistic studies into the photocatalytic asymmetric azidation of \u03b1-bromoamides by a copper-phosphine complex. DFT studies were performed to predict EPR spectra which were used to disambiguate the possible CuII species present in solution.
Much of the universe is partially ionized by stellar radiation, x-rays, or cosmic rays, forming weakly-ionized plasma. Many of these environments are also extremely cold, from Earth\u2019s upper atmosphere to planetary rings, protoplanetary disks, and interstellar clouds. Within these conditions, small grains of ice and dust can form and acquire electric charge by collecting free electrons and ions from the plasma.
\r\n \r\nThis thesis investigates these ice-dusty plasmas in the laboratory, observing the nucleation, growth, and dynamics of water-ice grains within extremely cold plasma. It details the construction and operation of a steady-state radio-frequency plasma in which the electrodes are cryogenically cooled by tandem cryostats; water vapor injected into the plasma spontaneously nucleates into ice grains which grow in dendritic fractal shapes to millimeters in length. Their electric charges confine them to the plasma, where they exhibit complex dynamics such as vortices, lattices, and instabilities.
\r\n\r\nNotably, ice grains nucleate homogeneously within the plasma: OH\u207b and H\u2083O\u207a ions, formed by reactions between water vapor and free electrons, attract water molecules via ion-dipole interactions to produce stable, electrically-charged molecule clusters that rapidly grow into ice grains. This process occurs regardless of the ice phase: amorphous ice forms at lower temperatures and transitions irreversibly to crystalline ice at higher temperatures or over time, mirroring processes seen in solar system ices. Further experiments reveal that the complex dynamics of the cloud of ice grains are strongly influenced by their fractal morphology, as the scaling laws of their masses, surface areas, and electric charges are vastly different during fractal growth. This allows them to strongly couple with ambient gas, enhancing momentum transfer between the grains and their surroundings and significantly increasing their charge-to-mass ratio.
\r\n\r\nThis research offers critical insights into the formation and behavior of ice grains in ionized environments, with wide-ranging implications across astrophysics, materials science, and plasma technology. Understanding these processes in a controlled laboratory setting offers a window into complex phenomena across the cosmos.
", "doi": "10.7907/adns-n036", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:16689", "collection": "thesis", "collection_id": "16689", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09022024-211742520", "primary_object_url": { "basename": "Thesis_Sun_Jiace.pdf", "content": "final", "filesize": 9182063, "license": "other", "mime_type": "application/pdf", "url": "/16689/4/Thesis_Sun_Jiace.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Classical and Quantum Simulation of Chemical and Physical Systems", "author": [ { "family_name": "Sun", "given_name": "Jiace", "orcid": "0000-0002-0566-2084", "clpid": "Sun-Jiace" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-G-K" }, { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Chen", "given_name": "Xie", "orcid": "0000-0003-2215-2497", "clpid": "Chen-Xie" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Various quantum mechanics effects have been found and widely studied in different microscopic systems, such as quantum nuclear effects and electron correlation in molecular systems, electron-phonon coupling in crystal systems, and quantum Zeno effects in open quantum systems. However, exact numerical simulations require exponentially scaled classical resources. In this thesis, we study these quantum systems by a series of classical or quantum methods, which include semiclassical, ab initio, machine learning, and quantum computing approaches.
\r\n\r\nIn Chapter 2, we develop the molecular-orbital-based machine learning (MOB-ML) method as a general-purpose method to learn molecular electronic structure properties. By preserving physical constraints, including invariance conditions and size consistency, MOB-ML is shown to be able to capture both weak and strong interactions. Furthermore, the Gaussian Process framework is extended for learning both scalar properties such as energies, and linear-response properties like dipole moments with the rotationally equivariant derivative kernel. With these improvements, MOB-ML shows not only significantly higher learning rates for organic molecules, non-covalent interactions, and transition states but also excellent transferability from small systems to large systems.
\r\n\r\nIn Chapter 3, we develop a generalized class of integrators in the thermostatted ring-polymer molecular dynamics (T-RPMD) method, which is a semi-classical quantum dynamics method to capture various types of molecular nuclear quantum effects, including zero point energy, quantum tunneling, and kinetic isotopic effects. Such generalized integrators are carefully designed to be strong stable and dimension-free, which are essential for robust numerical computations. In particular, a so-called \"BCOCB\" integrator is proved to be superior in terms of accuracy and efficiency in the harmonic limit. Such superiority is further verified in strongly anharmonic systems featured by liquid water.
\r\n\r\nIn Chapter 4, we develop an ab initio-based semi-analytical model of electron-phonon scattering to describe the transport and noise behavior in GaAs, which is a widely-used semiconductor. Such a semi-analytical model lifts a few approximations in the standard ab initio calculation of intervalley scatterings, which were believed to be the origin of the failure to capture the nonmonotonic noise phenomena. We find qualitatively unchanged transport and noise properties and agreements on the scattering rates between the photoluminescence experiments. These results indicate the most probable origin of the nonmonotonic noise behavior is the formation of space-charge domains rather than the intervalley scattering.
\r\n\r\nIn Chapter 5, we simulate the challenging measurement-induced phase transitions (MIPT) behavior in quantum many-body systems on a superconducting quantum processor. Due to the intrinsic exponential scaling of the quantum state tomography and post-selection process, traditional simulations of MIPT were limited to a few qubits. With the recently introduced linear cross-entropy benchmarking, such exponential overhead is eliminated, and the correct critical behavior of MIPT is observed on a 22-qubit system. Our work paves the way for the studies of open quantum systems on large-scale near-term quantum devices.
", "doi": "10.7907/3qp8-q490", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16680", "collection": "thesis", "collection_id": "16680", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08282024-022514845", "primary_object_url": { "basename": "Bruch_Dorian_2025.pdf", "content": "final", "filesize": 11174069, "license": "other", "mime_type": "application/pdf", "url": "/16680/1/Bruch_Dorian_2025.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical Modeling of Interactions Between Electrolytes and Surfaces", "author": [ { "family_name": "Bruch", "given_name": "Dorian Wayne", "orcid": "0000-0002-3983-4841", "clpid": "Bruch-Dorian-Wayne" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Electrolytes are ubiquitous in science and engineering and are of active interest, owing to their applications biology, energy storage, colloidal suspensions, and even climate. Near a surface, electrolyte solutions exhibit a plethora of rich thermodynamic and structural phenomena, owing to the interplay of long-ranged electrostatics and nonelectrostatic interactions between ionic species, solvent, and the surface. In this thesis, we present a pedagogical formulation for the thermodynamics of electrolyte solutions near charged surfaces, followed by an examination of interactions and structure of different types of electrolytes near surfaces. Specifically, we investigate the difference between constant surface charge and constant surface potential boundaries in electrolyte solutions, the capacitance applications, double-layer structure, and screening behavior of a zwitterionic polymers, as well as the effect of image charge on structure, capacitance, and forces in simple electrolytes near metal, dielectric, and dielectrically-saturated metal surfaces. We conclude with a Gaussian-fluctuation model for ions with soft-core excluded volume interactions.", "doi": "10.7907/eey8-et93", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16530", "collection": "thesis", "collection_id": "16530", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06292024-045659387", "type": "thesis", "title": "Computational Design of Wearable Chemical Sensors for Personalized Healthcare", "author": [ { "family_name": "Mukasa", "given_name": "Daniel", "orcid": "0000-0001-8379-3648", "clpid": "Mukasa-Daniel" } ], "thesis_advisor": [ { "family_name": "Gao", "given_name": "Wei", "orcid": "0000-0002-8503-4562", "clpid": "Gao-Wei" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Schwab", "given_name": "Keith C.", "orcid": "0000-0001-8216-4815", "clpid": "Schwab-K-C" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Gao", "given_name": "Wei", "orcid": "0000-0002-8503-4562", "clpid": "Gao-Wei" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Wearable sweat sensors have the potential to revolutionize precision medicine as they can non-invasively collect molecular information closely associated with an individual\u2019s health status. However, the majority of clinically relevant biomarkers cannot be continuously detected in situ using existing wearable approaches. Molecularly imprinted polymers (MIPs) are a promising candidate to address this challenge but haven\u2019t yet gained widespread use due to their complex design and optimization process yielding variable selectivity. Despite their promise, MIPs have historically been known to be exceedingly difficult to optimize. Changes in the monomer/monomers used, polymerization solvent, and crosslinking agent have been shown to change the performance of MIP sensors significantly. This is particularly a concern in sweat-based sensors where the concentration of analytes is very low and chemical diversity is very high as a drop of sweat can contain vitamins, hormones, and amino acids. Consequentially, any sweat based sensor must exhibit high sensitivity (ability to detect low analyte concentrations) and selectivity (ability to distinguish one analyte from another). Computational methods have been introduced to design MIP sensitivity alone, however these prior methods do not cover all aspects essential for using a sensor in a wearable device such as selectivity optimization, detection of non-electroactive analytes, and scalable manufacturing. Here, we introduce a full computational method that allows for high throughput materials discovery for wearable devices. We will describe how to design novel sensing materials with QuantumDock, an automated computational framework for universal MIP development toward wearable applications. Then we delve into further technical details on signal transduction and scalable manufacturing approaches for these wearable devices. We present a number of novel devices designed with these computational methods including a wearable non-invasive phenylalanine monitoring system (the first of its kind), a wearable nutritional tracker \u2018Nutritrek\u2019 capable of monitoring a range of metabolic disorders, and an implantable pharmaceutical drug monitoring system for cancer patients.", "doi": "10.7907/r46k-sw73", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17006", "collection": "thesis", "collection_id": "17006", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02192025-011837407", "type": "thesis", "title": "Development and Characterization of a Table-Top Laser-Produced Plasma Source for In-Situ and Time-Resolved Soft X-Ray Absorption Spectroscopy", "author": [ { "family_name": "Nimlos", "given_name": "Danika Katherine", "orcid": "0000-0002-5414-0039", "clpid": "Nimlos-Danika-Katherine" } ], "thesis_advisor": [ { "family_name": "Cushing", "given_name": "Scott K.", "orcid": "0000-0003-3538-2259", "clpid": "Cushing-Scott-K" } ], "thesis_committee": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Cushing", "given_name": "Scott K.", "orcid": "0000-0003-3538-2259", "clpid": "Cushing-Scott-K" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "X-ray absorption spectroscopy (XAS) has emerged as an indispensable tool in the fields of carbon capture and conversion, providing element-specific insights into electronic structure, oxidation states, and chemical bonding. Of particular interest are soft X-rays (SXRs), which can probe the X-ray water window, enabling detailed studies of carbon, nitrogen, and transition metal L-edges in aqueous environments. Traditionally, access to this technique and this energy range has been limited to large- scale facilities like synchrotrons and XFELs, which can only serve a small population of users in a given year. Furthermore, more complex techniques such as time-resolved and in-situ XAS are practically inaccessible to the majority of users. This thesis explores the development of a table-top laser-produced plasma (LPP) source based on a gaseous target to extend the reach of XAS techniques into laboratory settings. Such sources offer significant advantages in accessibility, flexibility, and cost, while advances in X-ray optics and detection systems have further enhanced their utility. The research presented here focuses on the utilization of gaseous LPP sources for both in-situ and time-resolved XAS, pushing the boundaries of table-top soft X-ray absorption capabilities.
\r\n\r\nKey achievements include exploration of the lower temporal limit of LPP sources for SXR emission, and the first demonstration of liquid-phase XAS measurements using a gaseous LPP source. Gas-phase measurements were also achieved using the system built in this work. Additionally, a novel UV-pump/SXR-probe technique was developed, enabling future time-resolved studies of charge transfer dynamics in transition metal oxides. These advances pave the way for detailed investigations of photodriven processes, interfaces, and catalytic mechanisms critical to carbon capture and conversion. By improving temporal resolution and expanding the scope of in-situ XAS techniques, this work addresses fundamental challenges in the field, bringing the power of synchrotron-like spectroscopy into everyday laboratories. Ultimately, the results presented here aim to democratize XAS, fostering a broader adoption of this technique in catalysis and materials research.
", "doi": "10.7907/3e9t-xr72", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16544", "collection": "thesis", "collection_id": "16544", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07092024-152839479", "primary_object_url": { "basename": "Musgrave_thesis.pdf", "content": "final", "filesize": 38709982, "license": "other", "mime_type": "application/pdf", "url": "/16544/1/Musgrave_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Computational Approaches to Problems in Energy and Sustainability", "author": [ { "family_name": "Musgrave", "given_name": "Charles Bruce, III", "orcid": "0000-0002-5732-3180", "clpid": "Musgrave-Charles-Bruce-III" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Manthiram", "given_name": "Karthish", "orcid": "0000-0001-9260-3391", "clpid": "Manthiram-Karthish" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The rapid development of modern society has been met by a fierce and overwhelming increase in fossil fuel utilization and the mass production of nonrenewable/recyclable materials. The escalating usage of fossil fuels results in rising greenhouse gas (GHG) emissions, while mass production of non-recyclable materials has led to unimaginable amounts of waste, which ultimately ends up in landfills or in the ocean. If we seek a sustainable future, it is imperative that we develop methods that can harness \u201cgreen\u201d electrons to generate power, particularly synthetic routes that selectively generate renewable materials via these electrons.
\r\n\r\nIn this thesis, we leverage theoretical methods to investigate several platforms for the conversion of GHGs to value-added products such as methanol, ethylene, methylacetic acid, styrene, etc. To generate these products, we use heterogeneous and homogeneous catalysts, with and without the assistance of an applied potential. The overarching goal of these methods is to remediate carbon and nitrogen cycles, such that generation of harmful carbon and nitrogen-based products is immediately followed by conversion of said products back to useful reactant species.
\r\n\r\nIn summation, this thesis provides several catalytic platforms for the selective and efficient production of useful fuels and feedstocks from harmful GHGs.
", "doi": "10.7907/hnc1-je90", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:17232", "collection": "thesis", "collection_id": "17232", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05152025-170540802", "type": "thesis", "title": "Computational Methods for Nucleic Acid Structure Prediction and G Protein-Coupled Receptor Mechanism Investigation", "author": [ { "family_name": "Gonzalvo i Ulla", "given_name": "Marta", "orcid": "0009-0005-4235-4282", "clpid": "Gonzalvo-Ulla-Marta" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Shan", "given_name": "Shu-ou", "orcid": "0000-0002-6526-1733", "clpid": "Shan-Shu-ou" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Molecular dynamics (MD) simulation is a powerful tool to characterize molecular structure. In this thesis, we use MD to solve three problems in biological chemistry: the prediction of secondary nucleic acid structure, the prediction of the structure of a siRNA-based tool, and the understanding of the activation mechanism of the sweet taste receptor.
\r\n\r\nFirst, we use MD to computationally parameterize nucleic acid secondary structure models. Current models are parameterized using experimental data that was limited and time consuming to generate. In this work, we present a workflow to select an ensemble of base pairing reactions using machine learning, perform MD simulations to obtain their free energy and enthalpy profiles, and perform nonlinear regression on the energies and enthalpies to yield thermodynamic nearest neighbor parameters. This computational framework parameterizes secondary structure models with comparable accuracy to experimental data, and can be used to expand the current models to a range of materials and experimental conditions beyond the specific experimental conditions the parameters were originally generated in.
\r\n\r\nNext, we predict the structure of a RNA therapeutic tool, conditionally activated small interfering RNAs (Cond-siRNAs). We evaluate how two structural modifications to the two double helix topology affect the ability of the construct to perform its function in the RNAi pathway, finding that a short sensor overhang and a carbon chain linker between the two duplexes reduce undesired interactions in the structure. We also characterize the structure for a new topology with a single linker between the duplexes, and show how the position of terminal modifiers causes structural distortions and can disrupt its function. These insights will guide the design of Cond-siRNAs and other RNA tools with similar non-canonical modifications.
\r\n\r\nLastly, we investigate the mechanism of activation of the TAS1R2/TAS1R3 sweet taste receptor, coupled to the G protein gustducin. We use metadynamics simulations to estimate the reduction of the free energy of opening the G alpha subunit in the presence of a positive allosteric modulator and steviol glycosides of varying sweetness. We also uncover insights into how the modulator induces the activation of the G alpha, leading to the partial release of GDP; and how the steviol glycosides RebM, RebD and IsoRebM of high sweetness induce an interdomain twist in the Venus Fly Trap domains. These results further our understanding of the activation mechanism of the class C sweet taste receptor and can be used for the development of new sweeteners.
", "doi": "10.7907/bxdy-5x58", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16545", "collection": "thesis", "collection_id": "16545", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07092024-204040190", "type": "thesis", "title": "Part I: Multi-Valent Ion Effects on Polyelectrolyte Structure and Thermodynamics & Part II: Hydrodynamic Self-Propulsion", "author": [ { "family_name": "Glisman", "given_name": "Alec Gregory", "orcid": "0000-0001-9677-1958", "clpid": "Glisman-Alec-Gregory" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Brady", "given_name": "John F.", "orcid": "0000-0001-5817-9128", "clpid": "Brady-J-F" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I: Polyelectrolytes are a class of charged polymers that have found widespread utility in water treatment, drug delivery, and scale inhibition, among other applications. For many of these applications, it is crucial to control the phase stability of the polyelectrolyte solution. The long-ranged nature of the electrostatic interactions in polyelectrolyte solutions and the polyelectrolyte's connectivity lead to a rich phase behavior that can be challenging to study, especially in the presence of other ions or surfaces. In scale inhibition applications, polyelectrolytes such as poly(acrylic acid) (PAA) are used to prevent the dissolution of sparingly soluble salts, such as calcium carbonate, in water. While the significant influence of small ions on polyelectrolyte solution phase behavior is recognized, the precise molecular mechanisms driving the resulting phase stability remain largely elusive.
\r\n\r\nPolyelectrolyte theory suggests that a polyelectrolyte's behavior and adsorption properties in solution are strongly tied to the polymer chain conformation and charge distribution, which in turn is influenced by solution ionic strength and ionic valency. Consequently, we expect the polyelectrolyte performance to be highly dependent on the solution conditions and the molecular features of the polyelectrolyte. Previous computational studies have studied general polyelectrolytes in solution with coarse-grained and implicit solvent models and provided insights into the chain conformational transitions. However, they disagree on the mechanisms underlying aqueous polyelectrolytes salting out of suspension and are unable to yield chemically specific insights. We seek to better understand the antiscalant mechanisms of polyelectrolytes using all-atom molecular dynamics to capture solvation and polymer chemistry effects on the mechanisms of polyelectrolytes preventing scale nucleation and slowing growth.
\r\n\r\nThe current work investigates the structure and thermodynamics of polyelectrolytes in bulk solution and at crystalline interfaces with added multi-valent ions. The presence of multi-valent ions, such as Ca2+, can significantly influence polyelectrolyte conformation via ion bridging non-neighboring charged monomers as well as screening the electrostatic interactions. We employ all-atom molecular dynamics simulations to investigate the binding modes of Ca2+ onto a PAA chain, Ca2+\u2013PAA complex aqueous stability, and PAA adsorption onto a crystalline CaCO3 surface. In each of these cases, we find that the balance between ion bridging, electrostatic screening, and water-mediated interactions plays a crucial role in determining the polyelectrolyte's behavior in solution and at an interface.
\r\n\r\n\r\nPart II: Active bodies undergo self-propulsive motion in a fluid medium and span a broad range of length and time scales. Many active systems spontaneously self-organize into visually striking structures: fish schooling, birds flocking, and bacterial colonies growing. Current models of this emergent behavior in the inertial regime are mainly phenomenological and lack consideration of the fluid-mediated interactions between bodies.
\r\n\r\nTo address this limitation, we seek to advance physics-based models of swimmers by explicitly incorporating the fluid mechanical interactions between bodies. We aim to discern the fluid medium's role in group dynamics and determine whether it can reproduce the observed emergent phenomenon without resorting to phenomenologically based interaction rules. To that end, we focus specifically on swimming in high Reynolds number flows, where inertial forces dominate, and draw comparisons to the well-studied low Reynolds number (Stokes) regime. We begin by deriving the equations of motion for a collection of unconstrained spherical particles in potential flow and extend the model to include viscous dissipation and rigid body motion constraints for many bodies with arbitrary kinematics.
\r\n\r\nWe then consider the case of a single swimmer consisting of three linked spheres in potential flow. Through this, we find self-propulsion without needing external forces or momentum transfer via vortex shedding. We compare the inertial swimmer to an identical swimmer in the Stokes regime\u2014where fluid inertia is neglected\u2014and find that the structure of the equations of motion is identical in both flow regimes. Notably, the Stokes hydrodynamics are longer-ranged at leading order, leading to a more significant net displacement of the swimmer after one period of articulation. Finally, our study provides analytical insight into the swimming of a deformable body through an expansion of the non-linear spatial dependence of the hydrodynamic interactions.
", "doi": "10.7907/gf6m-gs53", "publication_date": "2025", "thesis_type": "phd", "thesis_year": "2025" }, { "id": "thesis:16375", "collection": "thesis", "collection_id": "16375", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05082024-165921385", "type": "thesis", "title": "Measuring Charge Carrier and Structural Photodynamics at Solar Energy Material Surfaces Using Transient Extreme Ultraviolet Reflection Spectroscopy", "author": [ { "family_name": "Michelsen", "given_name": "Jonathan Malte Zschiegner", "orcid": "0000-0002-7420-5610", "clpid": "Michelsen-Jonathan-Malte-Zschiegner" } ], "thesis_advisor": [ { "family_name": "Cushing", "given_name": "Scott K.", "orcid": "0000-0003-3538-2259", "clpid": "Cushing-Scott-K" } ], "thesis_committee": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Cushing", "given_name": "Scott K.", "orcid": "0000-0003-3538-2259", "clpid": "Cushing-Scott-K" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Electronic and vibrational degrees of freedom, and their interactions, control the chemical and physical properties of solids. Core-level spectroscopies, such as transient extreme ultraviolet (XUV) spectroscopy, provide detailed information on the electronic structure and local coordination environment of a material. In this work, we employ transient XUV reflection spectroscopy to measure surface carrier and structural dynamics in solar energy materials. To interpret experimental spectra, excited state valence effects are incorporated into the OCEAN code (Obtaining core excitations from ab initio electronic structure and the NIST Bethe-Salpeter equation solver). The modeling of core-level spectra from first principles enables the extraction of carrier kinetics via the robust assignment of spectral features. Moreover, this thesis explores experimental and theoretical methods for understanding carrier-structural coupling in solids relevant to solar energy applications.
\r\n\r\nSpecifically, we explore the chemical and physical information contained in core-level spectra for various solar energy material systems and present guiding principles for designing a core-level electronic spectroscopy experiments to determine photoexcited carrier and structural dynamics. We report on experimental measurements of ultrafast surface carrier and structural dynamics in photocathodes zinc telluride and copper iron oxide. Further, complementary excited state theory is presented to extract excited state valence dynamics from experimental core-level spectra based on ground state implementations of the Bethe-Salpeter equation.
", "doi": "10.7907/73h7-kg35", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16274", "collection": "thesis", "collection_id": "16274", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01082024-171459002", "primary_object_url": { "basename": "Lin_Haw_Wei_2024_Thesis.pdf", "content": "final", "filesize": 21762497, "license": "other", "mime_type": "application/pdf", "url": "/16274/1/Lin_Haw_Wei_2024_Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Nonlinear and Multidimensional Terahertz Spectroscopy of Liquids and Crystalline Solids", "author": [ { "family_name": "Lin", "given_name": "Haw-Wei", "orcid": "0000-0002-5208-7385", "clpid": "Lin-Haw-Wei" } ], "thesis_advisor": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" } ], "thesis_committee": [ { "family_name": "Cushing", "given_name": "Scott K.", "orcid": "0000-0003-3538-2259", "clpid": "Cushing-Scott-K" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Hadt", "given_name": "Ryan G.", "orcid": "0000-0001-6026-1358", "clpid": "Hadt-Ryan-G" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The delocalized and correlated nuclear degrees of freedom in the terahertz (THz) regime strongly influences the room temperature chemical and physical properties of condensed matter systems, yet detailed understanding of the photo-induced dynamics and anharmonicities of the vibrational modes have remained elusive. In hydrogen-bonded liquids, these information facilitates the development of accurate force field models to aid simulations of biological processes of proteins and DNAs. In the field of nonlinear phononics, anharmonic lattice vibrations form the foundation for ultrafast coherent control of material properties, which has become an indispensable technique in the engineering toolbox for quantum materials. In this thesis, we demonstrate the development and application of nonlinear 1D THz Kerr effect (TKE) and 2D THz-THz-Raman (2D-TTR) ultrafast THz spectroscopies, which are specially designed to induce resonant coherent excitations of the correlative nuclear degrees of freedom in liquids and crystalline solids. By analyzing the temporal evolution of the nuclear THz-driven dynamics, insights into the excitation mechanisms, nonlinear coupling interactions, and the dominant source(s) of anharmonicity may be determined. Specifically, we developed a nonlinear imaging method based on the third-order response of electro-optic crystal GaP, which significantly improved the alignment consistency and the signal strength of 2D-TTR spectroscopy. Further, we extended an echelon-based single-shot detection scheme, originally developed in 1D TKE spectroscopy, to 2D-TTR spectroscopy, which led to up to two orders-of-magnitude reduction in acquisition time. Armed with these instrument advancements, we measured 2D-TTR spectra of liquid halogenated methanes with significantly improved signal-to-noise and a larger temporal window, which led to the identification of a novel competing sum-frequency THz excitation pathway. On the other hand, we investigated resonant driven-dynamics of the phonon-polariton modes in semiconductor LiNbO$_3$, which revealed nonlinear coupling interactions between two phonon branches that are attributed to mechanical anharmonicity. In addition, we directly observed photo-induced coherent phonon wavepackets for the layered semiconductors transition metal dichalcogenide using 1D TKE spectroscopy, which are attributed to the sum-frequency excitation pathway. These works highlight the rigorous experimental considerations and careful spectral analysis required to extract essential insight into excitation mechanisms and anharmonic contributions, while avoiding spectral artifacts due to the instrument response function. In order to provide clarity to these often misunderstood spectroscopies in the THz regime, this thesis further summaries the theories behind 1D TKE and 2D-TTR spectroscopies and the lessons we have learned from experimental realization of these exotic instruments and the analysis of complex spectral features.", "doi": "10.7907/2qt0-mg05", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16260", "collection": "thesis", "collection_id": "16260", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12112023-043755538", "primary_object_url": { "basename": "JonesGregory2024Thesis.pdf", "content": "final", "filesize": 8591022, "license": "other", "mime_type": "application/pdf", "url": "/16260/1/JonesGregory2024Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "From Venus to Mars: Spectroscopy and Kinetics of Reactive Intermediates in Planetary Atmospheres", "author": [ { "family_name": "Jones", "given_name": "Gregory Harrison", "orcid": "0000-0003-3275-1661", "clpid": "Jones-Gregory-Harrison" } ], "thesis_advisor": [ { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-G-K" }, { "family_name": "Yung", "given_name": "Yuk L.", "orcid": "0000-0002-4263-2562", "clpid": "Yung-Y-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The spectroscopy and kinetics of reactive intermediates in the atmospheres of Venus, Earth, and Mars were investigated through a combination of experimental and theoretical methods. Vibrational progressions in the A- and B-bands of ClSO were assigned, and predicted spectra matched well with experiment. A new unimolecular mechanism for 3-hydroxy-substituted Criegee intermediates was proposed, and predicted to be competitive with known isomerization pathways. The kinetic isotope effect and temperature dependence of the H + HO\u2082 reaction was calculated using high-level ab initio methods, with implications for the understanding of water loss on Mars.", "doi": "10.7907/7010-fc76", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16242", "collection": "thesis", "collection_id": "16242", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11082023-043634180", "primary_object_url": { "basename": "thesis v2.5 Chen-Hsuan Lu.pdf", "content": "final", "filesize": 11189287, "license": "other", "mime_type": "application/pdf", "url": "/16242/16/thesis v2.5 Chen-Hsuan Lu.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Strategic Advances in 2D Materials: Low-Temperature Plasma-Enhanced Chemical Vapor Deposition Growth of Graphene and Complementary Insights into MoS\u2082", "author": [ { "family_name": "Lu", "given_name": "Chen-Hsuan", "orcid": "0000-0002-4802-1332", "clpid": "Lu-Chen-Hsuan" } ], "thesis_advisor": [ { "family_name": "Yeh", "given_name": "Nai-Chang", "orcid": "0000-0002-1826-419X", "clpid": "Yeh-Nai-Chang" } ], "thesis_committee": [ { "family_name": "Fabe", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Falso", "given_name": "Joseph", "orcid": "0000-0003-3183-9864", "clpid": "Falson-Joseph" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Yeh", "given_name": "Nai-Chang", "orcid": "0000-0002-1826-419X", "clpid": "Yeh-Nai-Chang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis explores the intricate details of the plasma-enhanced chemical vapor deposition (PECVD) technique for growing graphene on various substrates at low temperatures. The research begins by finely optimizing the PECVD growth conditions to produce high-quality graphene on copper ink, which can potentially be used in a wide range of flexible electronics and Internet of Things (IoT) devices. The study also showcases that PECVD is an effective technique for growing graphene directly on electroplated copper over polyimide substrates, which greatly improves the resilience and environmental stability of copper circuits.
\r\n\r\nFurthermore, the research investigates the possibility of using PECVD to grow graphene on gold, which can be a game-changer in anti-corrosion applications and increase the longevity of gold electrode-based biosensors. The study also makes a significant breakthrough by growing nanocrystalline multilayer graphene on silver in a single step, which demonstrates exceptional oxidation resistance and opens new opportunities for hybrid graphene-silver plasmonic technologies.
\r\n\r\nLastly, the thesis examines the potential and complexities of using electrodeposited (ED) copper foil as a graphene growth substrate, showing significant transformations in the properties of the ED copper foil post PECVD process. Towards the latter part of this work, attention is briefly shifted to explore the unique dipole ordering properties of monolayer molybdenum disulfide (MoS2) single crystals, which are synthesized using high-temperature chemical vapor deposition (CVD) and are van der Waals materials like graphene. Although not the main focus, this inclusion offers valuable insights into contrasting attributes and functionalities of graphene and MoS2, especially in areas like high-density data storage and non-volatile memories, and also compares the status of synthesis methods of these two types of van der Waals materials.
\r\n\r\nAlongside these investigations, the thesis also touches upon the prospects of both large-area PECVD graphene growth and interfacial graphene growth, identifying future paths for research and innovation. This comprehensive study highlights the versatility of low-temperature PECVD for graphene synthesis and provides insights that may reshape research and applications in flexible electronics, biosensing, and beyond. The findings of this research therefore pave ways for researchers, technology developers, and businesses to explore realistic technological applications of graphene and two-dimensional materials in various industries.
", "doi": "10.7907/cetf-ns02", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16488", "collection": "thesis", "collection_id": "16488", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-222110855", "type": "thesis", "title": "Low-Energy Plasma\u2013Surface Interactions at Airless Icy Bodies", "author": [ { "family_name": "Grayson", "given_name": "Robert Wall", "orcid": "0000-0002-8044-9654", "clpid": "Grayson-Robert-Wall" } ], "thesis_advisor": [ { "family_name": "Giap", "given_name": "Konstantinos P.", "orcid": "0000-0002-7393-298X", "clpid": "Giapis-K-P" } ], "thesis_committee": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "orcid": "0000-0002-7393-298X", "clpid": "Giapis-K-P" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Nordheim", "given_name": "Thomas A.", "orcid": "0000-0001-5888-4636", "clpid": "Nordheim-Thomas-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Low-energy plasma surface interactions occur in many solar system environments and are especially important in the magnetospheres of gas giants. Within these magnetospheres orbit a catalogue of icy moons, some of which famously host interior liquid-water oceans. They are continuously exposed to a cold, corotating plasma \u201cwind,\u201d resulting in bombardment by heavy reactive ions, with peak number fluxes in the hyperthermal energy regime (10s to 100s of eV). Despite their abundance, these low-energy ions have been mostly overlooked in planetary science because they are poor drivers of radiolysis. In this thesis we take a combined experimental-theoretical approach to understanding the interaction of hyperthermal water group molecules/ions with relevant surfaces, motivated by some specific solar system observations, mostly from the Saturn system.
\r\n \r\nWe begin with experimental case studies of water-group ion scattering on carbonaceous (Chapter 2) and chloride-salt surfaces (Chapter 3), focusing on the emission of secondary negative ions. For carbonaceous surfaces, we detect surprisingly energetic carbon fragments, apparently emitted by near-threshold sputtering processes. The most abundant products (O\u207b, C2\u207b, C2H\u207b) are consistent with mass range for negative PUIs of unknown origin observed near Dione and Rhea. The reported mass ranges, however, have been estimated for pick-up of initially stationary ions, which is a poor assumption for the products we observe. Our experiments with chloride salts (relevant to Jupiter\u2019s moon Europa) are complicated by surface charging but provide kinematic evidence of reactive scattering and single knock-on sputter processes. Specifically, we observe abstraction of Cl from Pt to form chlorine monoxide anions. We then describe a modification of our scattering apparatus to enable exposure of ice targets, developing a one-of-a-kind experimental facility (Chapter 6). Some limited and preliminary results for Ar\u207a and O\u207a bombardment of amorphous water ice follow, which are more revealing of experimental challenges than of surface chemistry and dynamics.
\r\n \r\nOur theoretical efforts include Reactive Molecular Dynamics simulations of collision-induced chemistry in ices using the ReaxFF formalism. These reveal a novel non-radiolytic process (an Eley-Rideal reaction) for formation of molecular oxygen in low-energy (2\u221250 eV) water-group molecule bombardment of crystalline water ice, relevant to the maintenance of O\u2082 exospheres at Saturn\u2019s moons Dione and Rhea (Chapter 4). With the addition of CH\u2084 to the ice (as a clathrate), bombardment results in formation of methanol and formaldehyde at yields as great as 10% and 5%, respectively (Chapter 5). Two mechanisms are observed for methanol synthesis: one a typical radiolysis process and the second a two-step non-radiolytic mechanism. We provide preliminary results for an HCN/CH\u2084/H\u2082O ice target in Chapter 8 to motivate further study of the role that hyperthermal reactive ions play in synthesis of prebiotic organics. Finally, in Chapter 7, we describe a Monte-Carlo model for the production and transport of H\u2082 in the Enceladus due to plasma-surface interactions. Radiolysis by suprathermal electrons is the primary contributor, but the calculated mixing ratio falls several orders of magnitude short of the reported ~1%, which lends credibility to the notion that H\u2082 is being emitted from Enceladus\u2019 internal ocean.
", "doi": "10.7907/fn7c-k591", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16487", "collection": "thesis", "collection_id": "16487", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-221310680", "primary_object_url": { "basename": "WRPalfey_Thesis.pdf", "content": "final", "filesize": 9003394, "license": "other", "mime_type": "application/pdf", "url": "/16487/3/WRPalfey_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Hydrogen Incorporation in Rutile- and Perovskite-Structured Minerals and Their Analogues", "author": [ { "family_name": "Palfey", "given_name": "William Richard", "orcid": "0000-0002-9555-7877", "clpid": "Palfey-William-Richard" } ], "thesis_advisor": [ { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" } ], "thesis_committee": [ { "family_name": "Asimow", "given_name": "Paul David", "orcid": "0000-0001-6025-8925", "clpid": "Asimow-P-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Jackson", "given_name": "Jennifer M.", "orcid": "0000-0002-8256-6336", "clpid": "Jackson-J-M" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "For several decades now, it has been known that large quantities of hydrogen can be stored in the earth\u2019s mantle. This hydrogen, which is disseminated as defect components in nominally anhydrous minerals (NAMs), can have an outsized influence on minerals\u2019 bulk properties, potentially impacting planetary-scale processes. However, a description of how this hydrogen is sequestered in NAMs \u2014 its distribution between phases, its inhomogeneity between different mantle regimes, and the variety of defects involved \u2014 has evolved significantly with time. Deciphering hydrogen\u2019s role in the deep earth requires a detailed understanding of how hydrogen incorporates into mantle phases, beginning at an atomistic and structural level. Unfortunately, for a variety of reasons, directly measuring the crystallographic positions of hydrogen in most NAMs represents an exceptionally high technical barrier. Thus, hydrogen\u2019s structural state is, in many phases, incompletely understood. One approach for addressing this is to incorporate the use of computational methods like density functional theory (DFT) in the interpretation of analytical methods that can provide indirect structural information, like Fourier transform infrared spectroscopy (FTIR). This is the methodology employed by the work outlined in subsequent chapters.
\r\n\r\nThis thesis focuses on two specific mineral structures found within the deep earth \u2014 the rutile and perovskite structures \u2014 and explores some of the many possible hydrogen defect states in these phases. These include not only the conventionally considered hydroxyl (OH\u207b) group, but also hydride (H\u207b), an anionic form of hydrogen whose role in the mantle has yet to be considered in detail. The predictive and interpretive capabilities of DFT are utilized in studies on stishovite, rutile-type TiO\u2082, SrTiO\u2083, and davemaoite to both elucidate hydrogen\u2019s incorporated state in these phases and make predictions about yet-to-be-observed hydrogen defects. Detailed spectroscopic studies on rutile-type TiO\u2082 and SrTiO\u2083 perovskite provide new insights into both hydrogen and non-hydrogen related defect structures in these materials, with implications for future studies of NAMs.
", "doi": "10.7907/nbyx-6446", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16162", "collection": "thesis", "collection_id": "16162", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08212023-205141057", "primary_object_url": { "basename": "Korol_Roman_2024.pdf", "content": "final", "filesize": 12254981, "license": "other", "mime_type": "application/pdf", "url": "/16162/2/Korol_Roman_2024.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Development and Applications of Imaginary Time Path Integral Methods", "author": [ { "family_name": "Korol", "given_name": "Roman", "orcid": "0000-0001-9307-6351", "clpid": "Korol-Roman" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-G-K" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Recent engineering advances have opened up avenues to novel technologies that bridge the gap between the quantum and the classical. In order to understand large-scale quantum systems, a variety of approximate theoretical treatments have been proposed. This thesis focuses on development and applications of path-integral methods, which have enjoyed broad applicability in recent years for exploring nuclear quantum effects in the domains that span physical, bio-, geo-, and materials chemistry.
\r\n\r\nFeynman's path-integral formulation of quantum statistical mechanics offers powerful and widely used strategies for including nuclear quantum effects in complex chemical systems. These strategies are based on the observation that the quantum Boltzmann statistical mechanics of a quantum system is exactly reproduced by the classical Boltzmann statistical mechanics of an isomorphic ring-polymer system. For the numerically exact calculation of quantum Boltzmann statistical properties, the classical Boltzmann distribution of the ring-polymer system can be sampled using Monte Carlo (i.e., path-integral Monte Carlo, or PIMC) or molecular dynamics (PIMD).
\r\n\r\nChapters 1 and 2 of this thesis identify and — with no computational overhead — eliminate the issues in virtually all previous numerical implementations of PIMD that stem from time discretization. The resultant integration scheme requires only a small modification to existing PIMD algorithms and provides accurate statistical and dynamical data in a single-shot simulation with an up to 3-fold increase in the timestep duration.
\r\n\r\nChapter 3 transitions from the PIMD method development to the applications of the related PIMC method to understand equilibrium of stable heavy isotopes (D, 13C, 17, and 18O in small gaseous molecules. We present a collaborative experiment-theory calibration of the temperature dependence of the clumped isotope effect in methane in Chapter 4. We continue in Chapter 5, adding the study of isotopic fractionation between methane, water, and molecular hydrogen. Here we present the first concrete example of the effect of Born-Oppenheimer approximation on PI calculations. Finally, Chapter 6 extends our treatment to ethane and propane. For propane, in addition to multiple clumped isotope effects, there is also a strong site preference for the heavy isotopes to occupy the central (methylene) group.
\r\n\r\nAll the isotopic equilibrium calculations utilize accurate potential energy surfaces and are validated against experimental data in close collaboration with Daniel Stolper's experimental group at Berkeley, representing (to the best of our knowledge) the most accurate reference data available to date.
", "doi": "10.7907/jy10-rf87", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16131", "collection": "thesis", "collection_id": "16131", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06222023-231753197", "primary_object_url": { "basename": "AQC_Thesis_Final.pdf", "content": "final", "filesize": 81763761, "license": "other", "mime_type": "application/pdf", "url": "/16131/1/AQC_Thesis_Final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Asymmetric Pericyclic Transformations from Reactive Palladium Intermediates", "author": [ { "family_name": "Cusumano", "given_name": "Alexander Quinn", "orcid": "0000-0002-2914-2008", "clpid": "Cusumano-Alexander-Quinn" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Fu", "given_name": "Gregory C.", "clpid": "Fu-G-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Agapie", "given_name": "Theodor", "orcid": "0000-0002-9692-7614", "clpid": "Agapie-T" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The Pd-catalyzed decarboxylative asymmetric allylic alkylation of enolate nucleophiles is a cornerstone of our groups\u2019 efforts to develop methodologies that directly facilitate the synthesis of stereochemically complex molecular building blocks. This thesis first focuses on our efforts to deepen our mechanistic understanding of these transformations. We then employ our insights as a base from which we expand the scope of the decarboxylative asymmetric allylic alkylation reaction, as well as develop entirely novel reaction paradigms.", "doi": "10.7907/b0wn-wt67", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16131", "collection": "thesis", "collection_id": "16131", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06222023-231753197", "primary_object_url": { "basename": "AQC_Thesis_Final.pdf", "content": "final", "filesize": 81763761, "license": "other", "mime_type": "application/pdf", "url": "/16131/1/AQC_Thesis_Final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Asymmetric Pericyclic Transformations from Reactive Palladium Intermediates", "author": [ { "family_name": "Cusumano", "given_name": "Alexander Quinn", "orcid": "0000-0002-2914-2008", "clpid": "Cusumano-Alexander-Quinn" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Fu", "given_name": "Gregory C.", "clpid": "Fu-G-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Agapie", "given_name": "Theodor", "orcid": "0000-0002-9692-7614", "clpid": "Agapie-T" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The Pd-catalyzed decarboxylative asymmetric allylic alkylation of enolate nucleophiles is a cornerstone of our groups\u2019 efforts to develop methodologies that directly facilitate the synthesis of stereochemically complex molecular building blocks. This thesis first focuses on our efforts to deepen our mechanistic understanding of these transformations. We then employ our insights as a base from which we expand the scope of the decarboxylative asymmetric allylic alkylation reaction, as well as develop entirely novel reaction paradigms.", "doi": "10.7907/b0wn-wt67", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16410", "collection": "thesis", "collection_id": "16410", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05222024-182628149", "primary_object_url": { "basename": "Thesis_Boehme_final.pdf", "content": "final", "filesize": 154143801, "license": "other", "mime_type": "application/pdf", "url": "/16410/1/Thesis_Boehme_final.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Observation of the Microenvironment Around CO\u2082 Reduction Electrodes via Fluorescent Confocal Laser-Scanning Microscopy", "author": [ { "family_name": "B\u00f6hme", "given_name": "Annette Ellen", "orcid": "0000-0003-1109-3428", "clpid": "B\u00f6hme-Annette-Ellen" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" }, { "family_name": "Ardo", "given_name": "Shane", "orcid": "0000-0001-7162-6826", "clpid": "Ardo-Shane" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Electrochemical carbon dioxide reduction (CO\u2082R) is compelling because it enables the storage of renewable energy in the form of chemical bonds and offers the possibility to make carbon-based chemicals and fuels from a sustainable feedstock. A solid understanding of and control over the local microenvironment in and around CO\u2082R electrodes is crucial to optimize the device performance.
\r\n\r\nIn this work, we develop and refine a technique to observe the microenvironment around CO\u2082R electrodes via fluorescent confocal laser scanning microscopy with three-dimensional sub-micrometer spatial as well as temporal resolution. We combine two fluorescent pH probes, DHPDS and APTS, to resolve the local pH value around operando CO\u2082R electrodes. The pH plays an important role in determining the CO\u2082R activity and selectivity. In a first step, we image the local pH value in and around CO\u2082R GDEs with a random pattern of trenches and find that the pH is locally enhanced inside trenches. This effect becomes more pronounced for narrower trenches, reaching a maximum at a trench width of 5 \u00b5m. With the help of multiphysics simulations we can show that the high pH inside trenches is closely related to an enhanced C\u2082\u208a Faradaic efficiency. We harness this effect and fabricate CO\u2082R GDEs with tailored patterns of holes and trenches that allow a more systematic study of the influence of various micromorphology geometry parameters. We confirm experimentally that narrow holes and trenches exhibit a locally enhanced CO\u2082R selectivity and determine the most beneficial geometry parameters. We further use the developed technique to investigate the influence of a GDE's pore size on the local pH and with it, on the CO\u2082R selectivity. We observe that CO\u2082 transport is slower through smaller pores which can lead to switching of the reaction pathway and significantly alter the selectivity. We further investigate the importance of the microenvironment pH for CO\u2082R in acidic bulk electrolytes with the result that a non-acidic microenvironment pH, that can be reached at sufficiently high current densities, is required for the onset of CO\u2082R. Finally, we aim to extend the sensing capabilities and detect the local CO concentration in electrochemical devices but identify several challenges, including the probe reduction at the cathode.
\r\n\r\nOverall, we utilized fluorescent confocal laser-scanning microscopy to observe the microenvironment around CO\u2082R electrodes and correlate it with the CO\u2082R performance to gain a better mechanistic understanding of CO\u2082R and inform the design of future CO\u2082R electrodes.
", "doi": "10.7907/ceqb-ew84", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16391", "collection": "thesis", "collection_id": "16391", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05192024-000137690", "primary_object_url": { "basename": "KVirgil_Thesis_2023.pdf", "content": "final", "filesize": 2810434, "license": "other", "mime_type": "application/pdf", "url": "/16391/1/KVirgil_Thesis_2023.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Polarization-Resolved, Oblique Incidence Terahertz Spectroscopy of Highly Uniform 2D Hybrid Perovskite Films", "author": [ { "family_name": "Virgil", "given_name": "Kyle Allan", "clpid": "Virgil-Kyle-Allan" } ], "thesis_advisor": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Cushing", "given_name": "Scott K.", "orcid": "0000-0003-3538-2259", "clpid": "Cushing-Scott-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dabiri", "given_name": "John O.", "orcid": "0000-0002-6722-9008", "clpid": "Dabiri-J-O" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis details the development and optimization of thin film THz transmission measurements to extract spectrally resolved vibrational anisotropy in high quality layered hybrid perovskite materials. After an introduction in Chapter 1, Chapter 2 details the design, construction, and characterization of a terahertz time-domain spectrometer from scratch. Generalized THz propagation models are presented which enable accurate and diverse implementation of THz analysis. In Chapter 3, hybrid perovskite materials are introduced and our efforts towards reliably synthesizing high quality thin film perovskites using spin coating techniques are discussed. We find that optimized thin films are achieved from tailored synthetic conditions which depend on perovskite composition. In Chapter 4, we present our investigation into the elusive yet highly influential THz vibrational properties of 2D hybrid perovskite systems. A novel implementation of oblique-incidence THz transmission measurements reveals previously unseen vibrational excitations which provide valuable insight into the fundamental photodynamics that govern perovskite optoelectronics. We conclude in Chapter 5. This thesis serves to enhance the accessibility of powerful THz spectroscopic techniques as well as support the realization of promising perovskite renewable energy technologies.", "doi": "10.7907/cr97-p373", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:15181", "collection": "thesis", "collection_id": "15181", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162023-225200255", "primary_object_url": { "basename": "Thesis_Ziyi_0522.pdf", "content": "final", "filesize": 12313820, "license": "other", "mime_type": "application/pdf", "url": "/15181/1/Thesis_Ziyi_0522.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Temperature Dependence of Gas Physisorption Energy: Experimental and Computational Studies of Krypton on Porous Carbon", "author": [ { "family_name": "Wang", "given_name": "Ziyi", "orcid": "0000-0003-0811-921X", "clpid": "Wang-Ziyi" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Stadie", "given_name": "Nicholas", "orcid": "0000-0002-1139-7846", "clpid": "Stadie-P-Nicholas" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This work comprehensively investigated the temperature dependence of physical adsorption energy, combining theoretical, computational, and experimental approaches. A thermodynamic analysis of the 2D ideal gas and the slit-pore models highlighted the role of van der Waal potentials in the adsorption energy and isotherm fitting methods, especially Henry's law. Experimental data of krypton adsorption on CNS-201 and MSC-30 porous carbon materials revealed a significant weakening in the isosteric adsorption energy with temperatures from 250 K to 330 K. Using the zero-coverage Henry's constants and Clausius\u2013Clapeyron equation, the adsorption energies weaken for 13% and 15% for CNS-201 and MSC-30. The corresponding changing rates are 4.35k_B for CNS-201 and 3.65k_B for MSC-30.
\r\n\r\nThe DFT-based computational study with the slit-pore model showed the van der Waal potentials of different-sized pores. Then it showed how the structures of the pores significantly influence the surface dynamics and the internal energies of the adsorbates at different temperatures. Gas molecules adsorbed in pores of different sizes have different heat capacities larger than the gas phase, leading to a temperature dependence of adsorption energy. Monte Carlo calculation indicated that displacements of adsorbent atoms caused by thermal vibration slightly weaken the van der Waal potentials but have a negligible effect on the temperature dependence of the adsorption energy.
\r\n\r\nThe distribution of pore sizes plays a crucial role in the temperature dependence of the overall adsorption energy. With increasing temperature, the pores with higher energy states become more accessible due to the Boltzmann distribution, weakening the statistically averaged internal energy. Adsorption energy weakening of 5% and 15% for CNS-201 and MSC-30 are given by combining the computational van der Waal potentials and experimentally measured pore sizes. The changing rates are 0.62k_B and 2.03k_B.
", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15143", "collection": "thesis", "collection_id": "15143", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04252023-051729803", "primary_object_url": { "basename": "Maureen_Morla_PhD_thesis_final.pdf", "content": "final", "filesize": 8237030, "license": "other", "mime_type": "application/pdf", "url": "/15143/1/Maureen_Morla_PhD_thesis_final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Redox-Activated Covalent Functionalization of Semiconductor Surfaces", "author": [ { "family_name": "Morla", "given_name": "Maureen Baradi", "orcid": "0000-0002-2520-9543", "clpid": "Morla-Maureen-Baradi" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Semiconducting materials are those with a band gap across which electrons can be excited when the material absorbs photons with sufficient energy. Surface functionalization of semiconductors involves manipulation of the properties of the material by attaching organic small molecules through a surficial covalent bond. By controlling the surface properties of the material, functionalization has enabled the application of semiconductors in a myriad of fields, prompting a highly active field of research. To aid in this effort, we explore a new reaction methodology based on redox-mediated surface functionalization, where an outer-sphere, one-electron metallocene reductant or oxidant is added to the solution medium containing the semiconductor and the small molecule to be added to its surface. Using density functional theory, we elucidated the thermodynamic and kinetic factors that limit the experimentally observed upper coverage bound of reductant-activated methylation of 1T\u2032-molybdenum disulfide by determining two governing factors: 1) sulfur sites with longer Mo\u2013S bonds are more thermodynamically favorable for methyl addition, and 2) sulfur sites with fewer adjacent methylated sulfur sites are preferentially functionalized due to steric hindrance. We then expanded this reductant-activated reaction methodology to silicon(111) surfaces and demonstrated that the reductant solution potential must lie near or above the silicon(111) conduction band edge to observe reactivity. By extending this study to silicon nanocrystals of different sized diameters and different conduction band edges, we found that the extent of surface reactivity relied heavily on reductant strength, but the energy difference between the conduction band edges was too small to observe a distinct dependency on nanocrystal size. The work encompassed in this thesis expanded our understanding of redox-mediated reactions on semiconductor surfaces, providing a new avenue for attaining atomic-level control of the surficial properties of the material using mild reaction conditions and no specialized equipment. Furthermore, redox-activated addition enables the use of new functional groups that would otherwise be reactive in other functionalization methods, promoting an abundance of opportunities to explore new applications of semiconductor materials.", "doi": "10.7907/1exn-0t72", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15109", "collection": "thesis", "collection_id": "15109", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02162023-233344819", "type": "thesis", "title": "Advancement of Asymmetric Bipolar Membranes for Tailoring Chemical Environments in Electrochemical Systems", "author": [ { "family_name": "Lucas", "given_name": "\u00c9owyn", "orcid": "0000-0002-8743-5722", "clpid": "Lucas-\u00c9owyn" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Xiang", "given_name": "Chengxiang", "orcid": "0000-0002-1698-6754", "clpid": "Xiang-Chengxiang" }, { "family_name": "Manthiram", "given_name": "Karthish", "orcid": "0000-0001-9260-3391", "clpid": "Manthiram-Karthish" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Under reverse bias, bipolar membranes (BPMs) enhance water dissociation (WD) at the junction between a cation exchange layer (CEL) and an anion exchange layer (AEL), often with additional improvement from an integrated WD catalyst. Recent research has shown promise for developing and implementing BPMs in renewable energy systems, such as carbon removal, water and CO\u2082 electrolysis, and energy storage. The economic feasibility of these carbon capture and conversion systems with incorporated BPMs, however, relies on BPMs to maintain stable operation at high current densities (>100 mA cm\u207b\u00b2) and low overpotentials. Existing commercial BPMs are limited to current densities of \u2264100 mA cm\u207b\u00b2 as water transport through the CEL and AEL cannot keep up with the increased rate of WD at the junction at higher current densities. In this work, we present a freestanding, high current density BPM (HCD-BPM) with a thin AEL (15 \u03bcm, PiperION 15R), a graphene oxide (GrOx) catalyst layer, and a mechanically supportive CEL (50 \u03bcm, Nafion 212) specifically designed to overcome water transport limitations. When tested under reverse bias in a custom electrodialysis cell with Luggin capillaries, this HCD-BPM demonstrates the lowest published overpotentials up to 1 A cm\u207b\u00b2. Furthermore, the HCD-BPM exhibits stabilities of >1000 hour at 80 mA cm\u207b\u00b2, >100 hours at 500 mA cm\u207b\u00b2, and >60 hours at 1 A cm\u207b\u00b2, Faradaic efficiencies for H\u207a and OH\u207b of >95%, and successful implementation into a multi-cell electrodialysis stack designed for integration into a DOC system. Additional characterization, such as SEM, Confocal microscopy, and titration, was performed to understand the structure and performance of the HCD-BPM. Additionally, the BPM was tested in forward bias to investigate its use for acid/base flow batteries. Overall, this thesis presents a novel BPM with record performance in multiple electrochemical systems that mitigate anthropogenic CO\u2082 emissions.
", "doi": "10.7907/jken-ty64", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15077", "collection": "thesis", "collection_id": "15077", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12102022-055022458", "type": "thesis", "title": "Physics-Informed Neural Approaches for Multiscale Molecular Modeling and Design", "author": [ { "family_name": "Qiao", "given_name": "Zhuoran", "orcid": "0000-0002-5704-7331", "clpid": "Qiao-Zhuoran" } ], "thesis_advisor": [ { "family_name": "Anandkumar", "given_name": "Anima", "orcid": "0000-0003-0097-5716", "clpid": "Anandkumar-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Anandkumar", "given_name": "Anima", "orcid": "0000-0002-6974-6797", "clpid": "Anandkumar-A" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Wei", "given_name": "Lu", "orcid": "0000-0001-9170-2283", "clpid": "Wei-Lu" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chemical processes in nature span multiple characteristic length and time scales, and the computational simulation for systems at the intersection of different scales is highly challenging with far-reaching implications for numerous scientific and industrial problems. To facilitate the computational modeling and design for large molecular systems and address the cost-resolution tradeoffs in conventional strategies, in this dissertation we introduce a series of physics-informed machine learning methods for the efficient computational modeling of chemical systems and the accurate prediction of their properties such as energetics, structures, and dynamics. In Chapters 2-3, we introduce a family of orbital-based geometric deep learning methods for the prediction of quantum chemical properties while adhering to the scaling and symmetry constraints of electronic structure theory. The presented methods achieve a chemical accuracy on community-wide benchmarks for molecular property prediction, and are shown to be transferable among diverse main-group molecular systems. In Chapter 4, we introduce a method for the prediction of protein-ligand complex structures based on a finite-time stochastic process parameterized by deep equivariant neural networks. The presented method achieves improved structure prediction accuracy against existing approaches, and is able to rapidly sample protein structures for folding landscapes that are modulated by inter-molecular interactions.
", "doi": "10.7907/48d1-ja21", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14992", "collection": "thesis", "collection_id": "14992", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08042022-183527205", "primary_object_url": { "basename": "JJL_Thesis_2022.pdf", "content": "final", "filesize": 19424322, "license": "other", "mime_type": "application/pdf", "url": "/14992/1/JJL_Thesis_2022.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Computational Investigations of Organometallic Catalysis", "author": [ { "family_name": "Lawniczak", "given_name": "James Joseph", "orcid": "0000-0003-1898-9809", "clpid": "Lawniczak-James-Joseph" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Fu", "given_name": "Gregory C.", "orcid": "0000-0002-0927-680X", "clpid": "Fu-G-C" }, { "family_name": "Robb", "given_name": "Maxwell J.", "orcid": "0000-0002-0528-9857", "clpid": "Robb-M-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Organometallic catalysis facilitates the synthesis of diverse products ranging from polyolefin materials to pharmaceutical compounds, and catalyst performance depends in part on the design of the ligand scaffold. Towards computational ligand design, quantum mechanical methods more fully capture chemical reactivity in comparison to classical methods, but are more computationally demanding. Free energy calculations of key elementary steps of the catalytic cycle permit the computational prediction of catalyst performance and allow modifications of the ligand structure to be explored. In the dissertation, experimental and computational investigations of organometallic catalysis focuses on rational ligand design. Embedding techniques such as embedded mean field theory (EMFT) and quantum mechanics/molecular mechanics (QM/MM) are leveraged in free energy calculations to allow for the reduction of wall-clock times of energy calculations and trajectory sampling. The organometallic systems investigated include Group IV polyolefin catalysts capable of co-polymerization and enantioselective cross-coupling nickel catalysts. Additionally, experimental methodology development is discussed for a nickel-catalyzed cross-coupling of alkynyl nucleophiles to tertiary electrophiles.
", "doi": "10.7907/aepb-jm46", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14550", "collection": "thesis", "collection_id": "14550", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04142022-025410011", "type": "thesis", "title": "Aqueous Aerosols in Atmospheric Chemistry and Airborne Diseases", "author": [ { "family_name": "Gu", "given_name": "Alan Yalun", "orcid": "0000-0001-8095-3634", "clpid": "Gu-Alan-Yalun" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Wennberg", "given_name": "Paul O.", "orcid": "0000-0002-6126-3854", "clpid": "Wennberg-P-O" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "COVID-19" }, { "literal": "Resnick Sustainability Institute" }, { "literal": "div_chem" } ], "abstract": "Aqueous atmospheric aerosols are small droplets (typically smaller than 5 \u03bcm) suspended in the air that are comprised of water and water-soluble components. These aerosols provide an air-water interfacial reaction environment on their surfaces, and act as a medium for airborne disease transmission. In this thesis, Chapters II and V explore atmospherically relevant reactions on the aqueous aerosol surface using an online mass spectrometry, while Chapter III investigates the SARS-CoV-2 airborne transmission considering suspended virus-laden aerosols as the transmission media. Spinning off this SARS-CoV-2 work, Chapter IV describes a newly developed quantitative RNA amplification test kit for COVID-19, with an emphasis on the amplification result photo recognition component.", "doi": "10.7907/4spy-az88", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14545", "collection": "thesis", "collection_id": "14545", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04132022-221839497", "primary_object_url": { "basename": "1 Sydney_Lea_Corona_Thesis.pdf", "content": "final", "filesize": 14989938, "license": "other", "mime_type": "application/pdf", "url": "/14545/17/1 Sydney_Lea_Corona_Thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Emerging Evidence of a Second Glass Phase in Strong to Ultra-Fragile Bulk Metallic Glass-Forming Liquids", "author": [ { "family_name": "Corona", "given_name": "Sydney Lea", "orcid": "0000-0002-4962-619X", "clpid": "Corona-Sydney-Lea" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Samwer", "given_name": "Konrad", "orcid": "0000-0003-4266-449X", "clpid": "Samwer-K" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Samwer", "given_name": "Konrad", "orcid": "0000-0003-4266-449X", "clpid": "Samwer-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Schwab", "given_name": "Keith C.", "orcid": "0000-0001-8216-4815", "clpid": "Schwab-K-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis compiles three experimental works that provide evidence for distinct bulk metallic glass (BMG) phases across a range of kinetic fragilities. Motivated by An et al.\u2019s computational discovery of a secondary heterogeneous glass phase in pure Ag and binary AgCu and CuZr, the thesis reports the distinct glass phases in the high and ultra-high fragile regime with a tunable Pt80-XCuXP20 system, and the\r\nkinetically strong Ni71.4Cr5.64Nb3.46P16.5B3 (Ni208) BMG.
\r\n\r\n\r\nThe high-fragility work utilizes direct measurement techniques for liquid configurational enthalpy as a function of temperature on anneal-equilibrated samples (Chapter 2). An apparent first-order glass-melting transition is revealed across kinetic fragilities ranging from m = 60 to over 90. The glass-melting temperature, Tgm, traverses up the\u2000\u2206T region with increasing Cu content, X. A further experimental study of PtCuP explored the traditional and second glass phases to determine if they are in fact equivalent to the two glasses of An et al. (Chapter 3). Hardness data reveal that while the high-fragility samples grow the second glass during anneal, it forms in the ultra-fragile samples on quenching. Further, this apparent glass-melting transition is visible via traditional thermodynamic methods in ultra-fragile samples. For X = 20, where Tgm is in the inaccessible \u2206T region, rapid capacitive discharge heating visualizes Tgm as well.
\r\n\r\nInvestigation of a kinetically stronger Ni-based BMG connects the presence of the secondary glass to the embrittlement transition in Ni208 (Chapter 4). Inclusions are only present in embrittled samples, and are suppressed to lower temperatures when the initial melt is overheated above a critical toughening temperature. The inclusions show a heterogeneous structure and 30% increased hardness, similar to the computational Ag secondary glass phase.
\r\n\r\nThese works provide compelling evidence for the existence of a secondary glass phase across the spectrum from strong to ultra-fragile glasses, and validates the initial computational discovery. This proves to be a significant work, as it presents direct experimental evidence of a novel phenomenon in metallic liquids, and presents a new solid-like glass phase.
", "doi": "10.7907/9bvb-2d78", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14545", "collection": "thesis", "collection_id": "14545", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04132022-221839497", "primary_object_url": { "basename": "1 Sydney_Lea_Corona_Thesis.pdf", "content": "final", "filesize": 14989938, "license": "other", "mime_type": "application/pdf", "url": "/14545/17/1 Sydney_Lea_Corona_Thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Emerging Evidence of a Second Glass Phase in Strong to Ultra-Fragile Bulk Metallic Glass-Forming Liquids", "author": [ { "family_name": "Corona", "given_name": "Sydney Lea", "orcid": "0000-0002-4962-619X", "clpid": "Corona-Sydney-Lea" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Samwer", "given_name": "Konrad", "orcid": "0000-0003-4266-449X", "clpid": "Samwer-K" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Samwer", "given_name": "Konrad", "orcid": "0000-0003-4266-449X", "clpid": "Samwer-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Schwab", "given_name": "Keith C.", "orcid": "0000-0001-8216-4815", "clpid": "Schwab-K-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis compiles three experimental works that provide evidence for distinct bulk metallic glass (BMG) phases across a range of kinetic fragilities. Motivated by An et al.\u2019s computational discovery of a secondary heterogeneous glass phase in pure Ag and binary AgCu and CuZr, the thesis reports the distinct glass phases in the high and ultra-high fragile regime with a tunable Pt80-XCuXP20 system, and the\r\nkinetically strong Ni71.4Cr5.64Nb3.46P16.5B3 (Ni208) BMG.
\r\n\r\n\r\nThe high-fragility work utilizes direct measurement techniques for liquid configurational enthalpy as a function of temperature on anneal-equilibrated samples (Chapter 2). An apparent first-order glass-melting transition is revealed across kinetic fragilities ranging from m = 60 to over 90. The glass-melting temperature, Tgm, traverses up the\u2000\u2206T region with increasing Cu content, X. A further experimental study of PtCuP explored the traditional and second glass phases to determine if they are in fact equivalent to the two glasses of An et al. (Chapter 3). Hardness data reveal that while the high-fragility samples grow the second glass during anneal, it forms in the ultra-fragile samples on quenching. Further, this apparent glass-melting transition is visible via traditional thermodynamic methods in ultra-fragile samples. For X = 20, where Tgm is in the inaccessible \u2206T region, rapid capacitive discharge heating visualizes Tgm as well.
\r\n\r\nInvestigation of a kinetically stronger Ni-based BMG connects the presence of the secondary glass to the embrittlement transition in Ni208 (Chapter 4). Inclusions are only present in embrittled samples, and are suppressed to lower temperatures when the initial melt is overheated above a critical toughening temperature. The inclusions show a heterogeneous structure and 30% increased hardness, similar to the computational Ag secondary glass phase.
\r\n\r\nThese works provide compelling evidence for the existence of a secondary glass phase across the spectrum from strong to ultra-fragile glasses, and validates the initial computational discovery. This proves to be a significant work, as it presents direct experimental evidence of a novel phenomenon in metallic liquids, and presents a new solid-like glass phase.
", "doi": "10.7907/9bvb-2d78", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14538", "collection": "thesis", "collection_id": "14538", "cite_using_url": "https://resolver.caltech.edu/CaltechThesis:04012022-153013173", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 9969368, "license": "other", "mime_type": "application/pdf", "url": "/14538/1/Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Accurate and Transferable Molecular-Orbital-Based Machine Learning for Molecular Modeling", "author": [ { "family_name": "Cheng", "given_name": "Lixue", "orcid": "0000-0002-7329-0585", "clpid": "Cheng-Lixue" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Garnet K.", "orcid": "0000-0001-8009-6038", "clpid": "Chan-G-K" }, { "family_name": "Anandkumar", "given_name": "Anima", "orcid": "0000-0002-6974-6797", "clpid": "Anandkumar-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Quantum simulation is a powerful tool for chemists to understand the chemical processes and discover their nature accurately by expensive wavefunction theory or approximately by cheap density function theory (DFT)\\nomenclature{DFT}{Density Functional Theory}. However, the cost-accuracy trade-offs in electronic structure methods limit the application of quantum simulation to large chemical and biological systems. In this thesis, an accurate, transferable, and physical-driven molecular modelling framework, i.e., molecular-orbital-based machine learning (MOB-ML), is introduced to provide accurate wavefunction-quality molecular descriptions with at most mean-field level computational cost. Instead of directly predicting the total molecular energies, MOB-ML describes the post-Hartree-Fock correlation energy from molecular orbital information at the cost of Hartree-Fock computations. \r\nPreserving all the physical constraints, molecular orbital based (MOB) features represent the chemical space faithfully in both supervised clustering and unsupervised learning for chemical space explorations. The development of local regressions with scalable exact Gaussian processes within clusters further allows MOB-ML to provide the most accurate approach in both low and big data regimes. As exciting and general new tool to tackle various problems in chemistry, MOB-ML offers great accuracies of predicting total energies and serves as a universal density functional for organic molecules and non-covalent interactions in various chemical systems. With the availability of analytical nuclear gradients, MOB-ML is also capable of generating accurate PESs with few reference high-level electronic structure computations in the diffusion Monte Carlo accurately and efficiently for computational spectroscopy.
", "doi": "10.7907/cjak-4x38", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14625", "collection": "thesis", "collection_id": "14625", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262022-015714738", "type": "thesis", "title": "Thermal Behavior of Cuprous Oxide: a Comprehensive Study of Three-Body Phonon Effects and Beyond", "author": [ { "family_name": "Saunders", "given_name": "Claire Nicole", "orcid": "0000-0001-7973-3722", "clpid": "Saunders-Claire-Nicole" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Schwab", "given_name": "Keith C.", "orcid": "0000-0001-8216-4815", "clpid": "Schwab-K-C" }, { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Granroth", "given_name": "Garrett", "orcid": "0000-0002-7583-8778", "clpid": "Granroth-Garrett" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Phonons, or quantized normal modes of crystal vibrations, are responsible for much of the thermophysical behavior in solid-state systems. This behavior includes properties like thermal expansion, defined as the change in material volume in response to temperature. Typically, materials expand upon heating and contract upon cooling; however, some undergo anomalous or negative thermal expansion (NTE). This study focuses on a material with NTE, cuprous oxide (Cu2O), commonly known as cuprite. Using computational and experimental methods, we identify the underlying mechanisms of the NTE and how these mechanisms relate to temperature-dependent phonon behavior with temperature, using both computational and experimental methods.
\r\n\r\nComputationally, we interpret temperature-dependent changes in phonon energies with perturbation theory. Assuming that the bonds between atoms behave like simple harmonic oscillators, we model the observed random motion of the atoms around their equilibrium positions with quasi-harmonic (QH) and anharmonic (AH) approximations. Furthermore, the perturbations in the atom position allow us to model phonon energy changes in response to temperatures.
\r\n\r\nWhile these models, particularly AH models, have proven accurate in predicting the phonon behavior, experimental methods, like inelastic neutron scattering (INS), remain the gold standard for validation. This study presents INS data from single-crystal cuprite measured on the Wide-Angular Range Chopper Spectrometer (ARCS) at the Oak Ridge National Laboratory (ORNL) Spallation Neutron Source (SNS). We present INS data collected at 10 K, 300 K, 700 K, and 900 K. The post-processing workflow included: (1) binning with the software package Mantid, (2) reducing with a multiphonon background correction for polyatomic crystals, and (3) condensing into a single irreducible wedge in the first Brillouin zone (BZ). From this, we obtain a four-dimensional scattering function S(Q, E). Our AH calculations use the stochastic-Temperature Dependent Effective Potential (sTDEP) and the Machine Learning Interatomic Potential (MLIP) methods. The former method uses perturbation theory to include cubic and quartic AH contributions. The latter uses machine learning (ML), which in principle, includes all orders of AH terms.
\r\n\r\nThis investigation of the NTE of cuprite demonstrates that QH and AH models successfully predict anomalous NTE behavior. However, only AH calculations show the temperature-dependent phonon behavior seen in INS results. This discrepancy likely stems from a fortuitous cancellation of cubic and quartic AH terms giving an apparent success of QH models for the NTE. Ultimately, a correct prediction of thermal expansion with incorrect phonons reinforces the need to look at the role of higher-order terms in the temperature-dependent behavior of this material.
\r\n\r\nDespite the success of sTDEP at predicting phonon frequency shifts, it could not account for the newly observed diffuse inelastic intensity (DII) in the INS phonon spectra. For this, MLIP was more effective.
\r\n\r\nThis work provides complementary models to explain the origins of the DII, which is likely an emerging category of AH feature best described as a local nonlinear many-body process. We investigate phonon dissipation, the dynamics of systems coupled to their environments, Brownian motion, and discontinuities due to impulse transfer effects. We conclude by addressing the potential applications of the results and their role in future work on thermal lattice dynamics.
", "doi": "10.7907/mate-2v65", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14420", "collection": "thesis", "collection_id": "14420", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11062021-151820825", "primary_object_url": { "basename": "Welch_thesis_final_8Dec2021.pdf", "content": "final", "filesize": 110423776, "license": "other", "mime_type": "application/pdf", "url": "/14420/5/Welch_thesis_final_8Dec2021.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Understanding and Optimizing the Local Catalyst Environment in CO\u2082 Reduction Electrodes", "author": [ { "family_name": "Welch", "given_name": "Alexandra Justine", "orcid": "0000-0003-2132-9617", "clpid": "Welch-Alexandra-Justine" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Understanding and managing the local microenvironments in carbon dioxide reduction catalysts is crucial for optimizing device performance. In particular a locally high pH can increase catalyst selectivity and activity, as well as indicate which part of the catalyst is most active. In this thesis we begin by studying how nanoporous catalysts can induce this locally high pH in an aqueous system. We observe an increase in both Faradaic efficiency and partial current density for carbon monoxide in the nanoporous system relative to a planar metal film. We then show that this same nanoporous architecture can be used for improved device performance in a gas diffusion electrode configuration. We also perform copper underpotential deposition and secondary ion mass spectroscopy to show that almost half of the catalyst is not in contact with the electrolyte in this configuration. Then we use confocal fluorescent microscopy to image the local pH in a gas diffusion electrode to determine which parts of the electrode are most active. Through a combination of experiment and simulations we find that the catalyst within thin cracks of the microporous layer is most active for carbon dioxide reduction. While the study of local pH and wetting is the main focus of this thesis, we also explore how light can be used to improve selectivity and activity. In particular we study gold nanoparticles on p-type gallium nitride and copper nanoparticles on p-type nickel oxide. Finally, this thesis also explores how carbon dioxide conversion can actually be deployed. We discuss opportunities for combining carbon dioxide capture and conversion, as well as evaluate different pathways for renewable methane generation.
\r\n\r\nThis thesis gives in depth analysis of electrochemical carbon dioxide reduction catalysts as well as putting this research into the larger context of how such devices can be deployed. We hope that by combining systems level thinking and specific device studies better carbon dioxide conversion systems can be realized.
", "doi": "10.7907/4s78-cq55", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14616", "collection": "thesis", "collection_id": "14616", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252022-162959411", "primary_object_url": { "basename": "Seungkyeum Kim Ph.D. Thesis Ver 2.pdf", "content": "final", "filesize": 2442673, "license": "other", "mime_type": "application/pdf", "url": "/14616/1/Seungkyeum Kim Ph.D. Thesis Ver 2.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Development of Electrochemical Processes for More Practical and Effective Onsite Wastewater Treatment", "author": [ { "family_name": "Kim", "given_name": "Seungkyeum", "orcid": "0000-0002-0948-6452", "clpid": "Kim-Seungkyeum" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In spite of the lack of safely managed sanitation and water supply systems, developing countries with rapid urbanization cannot afford to implement advanced treatment technologies that are highly centralized, calling for the development of practical onsite wastewater treatment. As effective yet practical solutions to the water crisis, I have developed high-performance earth-abundant electrocatalysts and an uncoupled electro-peroxone (E-peroxone) prototype reactor that can be applied in and as decentralized wastewater treatment systems. A series of conductive TiO\u2082 nanotube array electrodes are known to be effective for chlorine evolution reaction (CER) for wastewater treatment and oxygen evolution reaction (OER) for water splitting. In order to further enhance their electrocatalytic activities, an ultrathin layer of Al\u2082O\u2083 was deposited onto TiO\u2082 nanotube arrays via atomic layer deposition (ALD). Due to the facilitated formation of Ti\u00b3\u207a and oxygen vacancies by Al\u2082O\u2083 ALD, black TiO\u2082 nanotube arrays with 8 ALD cycles achieved up to 30% enhancement in CER and OER overpotentials in comparison to those without Al\u2082O\u2083 coating. Moreover, the ultrathin Al\u2082O\u2083 overlayer (~2 nm) reduced the charge transfer resistance and increased the electrochemical chemical surface area (ECSA) 3-fold for both reactions. Black TiO\u2082 nanotube arrays with 8 cycles were applied for toilet wastewater treatment and outperformed a dimensionally stable anode (DSA) in terms of chemical oxygen demand (COD) and ammonia reductions. The simplicity of the synthetic procedures and the use of inexpensive metal oxides suggest that Al\u2082O\u2083-deposited TiO\u2082 nanotube arrays can provide a promising approach to wastewater treatment and water splitting as practical alternatives for costly DSAs.
\r\n\r\nThe uncoupled E-peroxone reactor system integrates ozonation with in situ hydrogen peroxide (H\u2082O\u2082) production to generate hydroxyl radicals for wastewater treatment. The E-peroxone process variables such as H2O2 concentration and ozone dose were optimized to maximize the treatment efficiency. Consequently, the system succeeded in reducing COD by 89%, total organic carbon (TOC) by 91%, biochemical oxygen demand (BOD) by 86%, and turbidity by 95% after 90-minute treatment of synthetic graywater. Moreover, the system reclaimed treated wastewater as an electrolyte for H\u2082O\u2082 production for subsequent treatment and maintained over 80% and 70% reductions in COD and TOC, respectively, over four consecutive treatment cycles. This system does not need any chemical additive, utilizes the energy-efficient E-peroxone process, and comprises inexpensive, accessible components. As a result, these advantages significantly reduce the system\u2019s capital and operational costs. The promising results and cost-effectiveness show that it can provide a viable solution for the treatment of graywater and human wastewater in low-resource settings.
", "doi": "10.7907/ab1v-he77", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14578", "collection": "thesis", "collection_id": "14578", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05142022-060038327", "type": "thesis", "title": "Photovoltaic Technologies Developed for Space-Based Solar Power", "author": [ { "family_name": "Loke", "given_name": "Samuel Pei Hao", "orcid": "0000-0003-1856-3605", "clpid": "Loke-Samuel- Pei-Hao" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Hajimiri", "given_name": "Ali", "orcid": "0000-0001-6736-8019", "clpid": "Hajimiri-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this thesis, photovoltaic technologies were developed for space-based solar power. Two methods of realizing SBSP were introduced, namely concentrated photovoltaics (CPV) and radiation hard flat panel photovoltaics. Both techniques are instrumental to realizing SBSP as they are pathways to realizing high specific power and lower launch costs. Technologies developed to support these two forms of SBSP were then reported.
\r\n\r\nIn support of CPV, ultralight broadband mid-infrared coatings were developed for the concentrating mirrors used in our project. This was done to create radiative pathways for heat loss to ensure that the solar cells do not overheat. Using the rigorous coupled wave analysis technique, we optimized a backside single-layer coating using 2nm Cr/ 2\u03bcm CP1/ 500nm Ag that had an mIR emissivity of 0.6. Adding a second layer of this coating, we predicted that a 0.5nm Cr/ 1.9\u00b5m CP1/ 3nm Cr/ 2\u00b5m CP1/ 500nm Ag screen could achieve an emissivity of 0.8. We also optimized a 10nm ITO/ 2 \u03bcm CP1/ 500nm Ag frontside emitter which had a visible reflectivity of 0.896 and a mIR emissivity of 0.554. A backside emitter coating that was 0.927 emissive in the mIR with areal density 6.0 gm\u207b\u00b2 was successfully fabricated, as was a frontside mirror emitter coating with visible reflectivity of 0.896 and a mIR emissivity of 0.582 with areal density 4.1 gm\u207b\u00b2.
\r\n\r\nIn support of radiation hard photovoltaics, organo-lead halide perovskites (OHLP) were investigated. Challenges facing their fabrication were explored, with special focus on the electron transport layer PCBM as well as OHLP formulation. It was found that doping PCBM with a surfactant CTAB was beneficial, but did not work with all surfaces. An ITO/NiOx/MAPbI3/CTAB+PCBM/Cu device with in-house champion efficiency of 12.41% was achieved, and an ITO/NiOx/FA0.85Cs0.15PbI3/PCBM/Cu device with in-house champion efficiency of 11.81% was achieved. Time-dependant drift diffusion modelling was employed to account for the S-kink arising from poor PCBM carrier concentration.
\r\n\r\nFinally, the proton degradation of OHLP devices and constituent transport layers were investigated to shed better light on how OHLP devices degrade under proton irradiation. Films of ITO, PEDOT, NiOx, PCBM, and PTCDi were found to degrade under 30keV and 75keV protons of up to 1.4 x 10\u00b9\u2074 p\u207acm\u207b\u00b2 fluence, but their electrical resistivity and optical transmissivity were not found to impact the cell as much as the OHLP absorber layer itself. Observing the light IV and EQE degradation of OHLP cells, it is evident that proton deposition in the OHLP layer itself causes the most damage, especially at 30keV and 75keV protons with fluences from 4.3 x 10\u00b9\u00b3 p\u207acm\u207b\u00b2 to 1.7 x 10\u00b9\u2074 p\u207acm\u207b\u00b2. By considering the discrepancy in trends between Jsc and EQE, we concluded that the protons much accelerate intensity-based metastable photodegradation. Finally, by observing their anneal recovery, we concluded that it was temperature dependant and that maximum irrecoverable damage occurs at the OHLP/HTL interface.
", "doi": "10.7907/6jhy-2623", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14032", "collection": "thesis", "collection_id": "14032", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12152020-221422639", "primary_object_url": { "basename": "Yalu_Chen_Thesis_2021.pdf", "content": "final", "filesize": 17479467, "license": "other", "mime_type": "application/pdf", "url": "/14032/1/Yalu_Chen_Thesis_2021.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Computational Investigation of Nanoscale Electrocatalysts for Clean Energy Conversion", "author": [ { "family_name": "Chen", "given_name": "Yalu", "orcid": "0000-0002-0589-845X", "clpid": "Chen-Yalu" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Electrocatalysis provides a practical solution to the increasing global energy demand while maintaining a sustainable environment. Recently nanoscale catalysts (nanoparticles, nanowires, and dealloyed surfaces) have been shown to have experimentally far superior performance than metallic crystals at sustainable energy conversion. However, the surface feature of these improved catalysts is still unknown, as the detection of the active sites directly from experiment has not been possible.
\r\n\r\nIn this thesis work, we discuss using the quantum mechanics based muitiscale simulations and machine learning to understand the nature of these superior materials. We first studied jagged Pt nanowire (J-PtNW), which was shown to have performance at oxygen reduction reactions (ORR) 50 times better than Pt/C. We used multiscale simulations (reactive force field, and density functional theory) to explain this remarkably accelerated ORR activity from an atomistic perspective. Next, we looked into the irregular gold surfaces and copper surfaces (nanoparticles and dealloyed surfaces), which showed dramatically improved performance at CO2 reduction reactions (CO2RR) and CO reduction reactions (CORR). We developed the strategy to combine the reactive force field, density functional theory, and machine learning to identify the active sites responsible for their improved performance. This approach provided the possibility to understand the highly irregular and disordered surface, which is impossible with surface science experiments or with quantum mechanics. The identification of the active sites provides insights into new design concepts (alloys, NP, NW, and electrolytes such as ionic liquids) aimed at increasing product selectivity and rates simultaneously with reducing energy requirements.
", "doi": "10.7907/tgw8-c485", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14211", "collection": "thesis", "collection_id": "14211", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312021-211620881", "primary_object_url": { "basename": "Buabthong_thesis_Final.pdf", "content": "final", "filesize": 14890977, "license": "other", "mime_type": "application/pdf", "url": "/14211/1/Buabthong_thesis_Final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Stability and Protective Coatings of Semiconductor Electrodes for Solar Fuel Devices", "author": [ { "family_name": "Buabthong", "given_name": "Pakpoom (Pai)", "orcid": "0000-0001-5538-138X", "clpid": "Buabthong-Pakpoom-Pai" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Faber", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Climate change and increasing global energy consumption drive the need for clean and renewable alternatives to fossil fuels. Photoelectrochemical solar fuel devices offer a potential solution to capture and store clean and renewable solar energy in chemical bonds. Nevertheless, degradation of semiconductor electrodes is one of the major impediments to the implementation of practical stable solar fuels systems.
\r\n\r\nerein, we investigate the corrosion mechanisms and the corrosion kinetics of CdTe and ZnTe cathodes under the conditions for hydrogen-evolution reaction in strong acid and strong alkaline media. The effects of catalyst over-layer on CdTe\u2019s and ZnTe\u2019s corrosion pathways are discussed as well as potential protective coatings for ZnTe cathodes. Then, we address the original physical pinhole defects in amorphous a TiO\u2082 grown by atomic-layer deposition (ALD) on GaAs anodes. In addition, we explore new pinhole formation during electrochemical experiments and provide simulation for the propagation of the corroding GaAs substrate after new exposure to the electrolyte through microscopic pinholes. Finally, we develop a fabrication procedure for GaAs micro-island structures to provide defect isolation on the a TiO\u2082 film. The micro-island structures combined with dissolution measurements of the ALD a TiO\u2082 films were used to study the distribution and the evolution of pinholes from pre-existing defect spots in the protective coatings.
", "doi": "10.7907/dx7s-fh20", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14123", "collection": "thesis", "collection_id": "14123", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04192021-200916929", "type": "thesis", "title": "Controlling the Dynamics of Microstructure Formation in Mixed-Matrix Polymeric-Particle Membranes", "author": [ { "family_name": "Ford", "given_name": "Rachel Rae", "orcid": "0000-0001-9844-1557", "clpid": "Ford-Rachel-Rae" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Diallo", "given_name": "Mamadou S.", "clpid": "Diallo-Mamadou-S" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Wei", "given_name": "Lu", "clpid": "Wei-Lu" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" }, { "family_name": "Diallo", "given_name": "Mamadou S.", "clpid": "Diallo-Mamadou-S" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_chem" } ], "abstract": "Polymer membranes are increasingly important in energy generation, water purification, and resource recovery. Control over chemistry, morphology, and mechanical properties gives organic polymers unparalleled advantages for membrane technology\u2014but only if these complementary functions can be married into a cohesive material. Herein I have sought to expand upon the chemical tools for integrating diverse polymers into multifunctional membrane materials, making them easily tunable to various applications. To overcome a fundamental challenge in polymer science\u2014namely, that polymers with different functions often do not mix\u2014the functional polymer is grown in situ in a solution containing a preformed scaffold polymer, a method pioneered by co-advisor Mamadou Diallo. The hierarchical structure of the resulting mixed matrix polymeric-particle (M2P2) membrane is governed by the kinetic competition between polymerization and phase separation of the functional polymer from the scaffold polymer. This competition is quenched by immersion in a nonsolvent, which rapidly solidifies the material to trap the metastable structure formed during synthesis.
\r\n\r\nIn my quest to understand how these competing processes interact to inform multifunctional membrane design, I developed a general method for studying transient structure using ultra-small angle neutron scattering (Chapter II), working closely with Kornfield Group alumnus Dr. Joey Kim. I then investigated the synergistic effects of incorporating different functional polymer architectures in M2P2 membranes (Chapter III), working with fellow graduate student Orland Bateman. By combining low-generation dendrimers with randomly hyperbranched oligomers bearing similar chemical functionality, we can systematically tune the characteristic length of domains formed during synthesis. In the final chapter I discuss the main conclusions and describe future directions for understanding structure during processing in M2P2 membranes. My thesis ultimately provides a broadly relevant platform for membrane design and synthesis, one in which the favorable properties of different polymers may be combined to strike a balance between function, stability, and ease of fabrication.
", "doi": "10.7907/fqgq-vd04", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14069", "collection": "thesis", "collection_id": "14069", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02012021-171503477", "primary_object_url": { "basename": "JacobBagley_ThesisPDF.pdf", "content": "final", "filesize": 11019676, "license": "other", "mime_type": "application/pdf", "url": "/14069/1/JacobBagley_ThesisPDF.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Fabrication of Pristine and Doped Graphene Nanostripes and their Application in Energy Storage", "author": [ { "family_name": "Bagley", "given_name": "Jacob David", "orcid": "0000-0001-9490-1341", "clpid": "Bagley-Jacob-David" } ], "thesis_advisor": [ { "family_name": "Yeh", "given_name": "Nai-Chang", "orcid": "0000-0002-1826-419X", "clpid": "Yeh-Nai-Chang" } ], "thesis_committee": [ { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Yeh", "given_name": "Nai-Chang", "orcid": "0000-0002-1826-419X", "clpid": "Yeh-Nai-Chang" }, { "family_name": "Cushing", "given_name": "Scott K.", "orcid": "0000-0003-3538-2259", "clpid": "Cushing-Scott-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Fossil fuel usage causing rising CO2 levels and leading to climate change is, perhaps, the most pressing issue of our time. However, our economic dependence on energy necessitates its usage such that reducing energy usage is not possible leaving transitioning to renewable energy technologies as the only sustainable option. Currently, the largest barrier to large scale incorporation of renewable energy sources (e.g., solar, wind) is the high cost of energy storage technologies. Electrochemical energy storage technologies (e.g., lithium-ion batteries and supercapacitors) have been identified as a key approach for enabling the transition to renewable energy technologies.
\r\n\r\nGraphene is a material with exceptional properties that is receiving much attention for application in various energy storage technologies and could help reduce the cost of energy storage technologies. This thesis describes a novel fabrication procedure for low-cost and efficient synthesis of high-quality graphene nanostripes (GNSPs) and their application in lithium-ion battery and supercapacitor electrodes.
\r\n\r\nThis thesis is structured as follows. Chapter 1 outlines the motivation and technical background of this research. Chapter 2 describes the instrumentation and procedures for fabricating GNSPs. Chapter 3 describes in situ exfoliation of GNSPs as electrodes in supercapacitors to increase the capacitance. Chapter 4 describes synthesis and application of pyridinic-type nitrogen-doped GNSPs as a lithium-ion battery anode. Chapter 5 describes the synthesis and application of silicon-, germanium-, and tin-doped GNSPs and their application in lithium-ion battery anodes. Chapter 6 concludes and synthesizes the findings of the thesis holistically. Additionally, future outlook and potential research objectives are presented.
", "doi": "10.7907/hfdw-fs13", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13959", "collection": "thesis", "collection_id": "13959", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09202020-194859590", "primary_object_url": { "basename": "KLThesisPDF.pdf", "content": "final", "filesize": 913068, "license": "other", "mime_type": "application/pdf", "url": "/13959/1/KLThesisPDF.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "2-D Material Sensors on the Electronic Nose for the Sensitive Detection of VOCs", "author": [ { "family_name": "Lee", "given_name": "Kyra SoHyun", "orcid": "0000-0002-2100-1534", "clpid": "Lee-Kyra-SoHyun" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1
\r\n\r\nWhen coated with a polymer surface layer and suspended on 3-D textured glass electrodes, the hybrid combination of polymer and graphene yields sensitive chemiresistive vapor sensors. The expansion and contraction of the polymer layer when it absorbs/reacts with the VOCs, is proposed to produce tremendous train on the suspended graphene. Hence, when VOCs permeates into the polymer layer, sizable electrical resistive changes as folds and creases is induced in the graphene due to its high gauge factor. The hybrid suspended polymer/Gr sensor exhibits substantial responses to polar organic vapors, especially pyridine, while also exhibiting reversibility and the potential future tunability in the types of polymers used as the reactive surface layer.
\r\n\r\nChapter 2
\r\n\r\nVarious polar and non-polar functional groups were covalently bonded onto MoS2 yielding incredibly sensitive chemiresistive vapor sensors. The VOCs' interaction to the functional end groups produced tremendous signal, while also exhibiting reproducibility and reversibility. Future work will further standardize the sensors while also exploring tunability in the types of groups used.
\r\n\r\nChapter 3
\r\n\r\nThis chapter reflects the very start of my PhD research, and one of the important lessons to learn about the electronic nose. It is an example that I wish my predecessors taught me (all had graduated by the time I began my research) that I hope to pass onto future nose users. It is just one example of many projects that had similar end result. Many key lessons can be learned for future nose users. Readers can choose to skip reading this.
", "doi": "10.7907/j5e1-k535", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13731", "collection": "thesis", "collection_id": "13731", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282020-183139057", "primary_object_url": { "basename": "Sophia_thesis_final.pdf", "content": "final", "filesize": 45582784, "license": "other", "mime_type": "application/pdf", "url": "/13731/21/Sophia_thesis_final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Towards High Solar to Fuel Efficiency: From Photonic Design, Interface Study, to Device Integration", "author": [ { "family_name": "Cheng", "given_name": "Wen-Hui (Sophia)", "orcid": "0000-0003-3233-4606", "clpid": "Cheng-Wen-Hui-Sophia" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Houle", "given_name": "Frances A.", "orcid": "0000-0001-5571-2548", "clpid": "Houle-Frances-A" } ], "local_group": [ { "literal": "JCAP" }, { "literal": "div_eng" } ], "abstract": "Efficient unassisted solar fuel generation, a pathway to storable renewable energy in the form of chemical bonds, requires optimization of a photoelectrochemical device based on photonic design and interface study. We first focused on enhancing absorption via nanophotonic design of light absorbers. Near-unity, broadband absorption in sparse InP nanowire arrays with multi-radii and tapered nanowire array designs are simulated and experimentally demonstrated. Later, a few strategies are introduced to achieved high solar-to-fuel efficiency.
\r\n\r\nOptically, photoelectrochemical device would require the catalyst ensembles to be highly transparent. We report a record solar-to-hydrogen efficiency by integrating Rh nanoparticle catalysts onto photocathodes with minimal parasitic absorption and reflection losses in the visible range. The other two light management strategies have been developed and experimentally verified to create highly active and effectively transparent catalyst structures: i) arrays of mesophotonic dielectric cone structures that serve as tapered waveguide light couplers to efficiently guide incident light through apertures in an opaque catalyst into the light absorber, and ii) an effectively transparent catalyst consisting of arrays of micron-scale triangular cross-sectional metal grid fingers, which are capable of redirecting the incoming light to the open areas of the PEC cell without shadow loss.
\r\n\r\nThe electronic properties of the surface films exposed to the electrolyte are also critical. The anatase TiO\u2082 protection layer on the photocathode creates a favorable internal band alignment for hydrogen evolution, promoting the transport of the excess electrons and inhibiting voltage drops. The interfacial conduction mechanism between the defected TiO\u2082 and metal catalysts is investigated. A combinatorial approach of electrochemistry, X-ray photoelectron spectroscopy, and resonant X-ray spectroscopy reveals the correlation between the interfacial quasi-metal phase with TiO\u2082 properties. By careful control of gas diffusion electrode assembling to maintain appropriate wetted catalyst interface, another record solar-to-CO efficiency with extended stability can be realized.
", "doi": "10.7907/kd6a-xt88", "publication_date": "2020", "thesis_type": "phd", "thesis_year": "2020" }, { "id": "thesis:11429", "collection": "thesis", "collection_id": "11429", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12072018-215548214", "type": "thesis", "title": "From Quantum Mechanics to Experimental Observables: Computational Investigations of Energy-Related Heterogeneous Catalysts", "author": [ { "family_name": "Qian", "given_name": "Jin", "orcid": "0000-0002-0162-0477", "clpid": "Qian-Jin" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Soriaga", "given_name": "Manuel P.", "clpid": "Soriaga-M-P" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "One of the most severe challenges in this decade is assuring more secure, more efficient, cleaner, and more sustainable energy to power our world. This work takes a catalytic approach to help overcome this challenge.
\r\n\r\nThe Haber Bosch process is one of the towering achievements of industrial chemistry. It consumes a huge amount of energy due to the high temperature and high pressure reaction condition, and in turn, has enabled us to produce enough nitrogen fertilizer to feed the current world population. An essential goal of present research is therefore to dramatically reduce Haber Bosch energy cost by improving the catalytic performance of the presently used Fe-based heterogeneous catalysts. We use quantum mechanics (QM) and kinetic Monte Carlo (kMC) to predict reaction mechanisms and kinetics for NH3 synthesis on Fe(111) \u2013 the best Fe single crystal surface for NH3 synthesis. We find excellent agreement with a predicted turnover frequency (TOF) of 17.7 sec-1 per 2x2 site (5.3 x 10-9 moles/cm2/sec) compared to TOF=10 sec-1 per site from experiment, and we further predict that top-layer Co doping leads to an acceleration by a factor of 2.3 in reaction rates of ammonia synthesis.
\r\n\r\nCompared to the industrialized Haber Bosch reaction, renewable energy technologies are still in their infancy with a great deal of questions unanswered, as well as a lot of barriers to overcome. Here we report our atomistic understanding of how CO2 and H2O molecules adsorb on the catalyst surface and interact to initiate CO2 dissociation and subsequent product formation. Using synergistic experimental and theoretical analyses, we show that Cu and Ag operate entirely differently for the first step of activating CO2. We develop a method of predicting the ambient pressure XPS spectrum in an ab-initio multiscale fashion: from electronic structure, to atomic picture, to chemical reaction network (CRN), and eventually to the experimental observable. We bridge both the qualitative and quantitative gap from quantum mechanics to XPS, and demonstrate our approach by decoding the initial H2O adsorption and complex formation on Ag(111) surface, which we encourage to be the new standard protocol in this field.
\r\n", "doi": "10.7907/SPEJ-5X35", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11697", "collection": "thesis", "collection_id": "11697", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06062019-155629104", "type": "thesis", "title": "Light Emission and Ultrafast Carrier Dynamics in III-V Semiconductors from First Principles", "author": [ { "family_name": "Jhalani", "given_name": "Vatsal A.", "orcid": "0000-0003-0866-0858", "clpid": "Jhalani-Vatsal-A" } ], "thesis_advisor": [ { "family_name": "Bernardi", "given_name": "Marco", "orcid": "0000-0001-7289-9666", "clpid": "Bernardi-Marco" } ], "thesis_committee": [ { "family_name": "Minnich", "given_name": "Austin J.", "orcid": "0000-0002-9671-9540", "clpid": "Minnich-A-J" }, { "family_name": "Bernardi", "given_name": "Marco", "orcid": "0000-0001-7289-9666", "clpid": "Bernardi-Marco" }, { "family_name": "Faraon", "given_name": "Andrei", "orcid": "0000-0002-8141-391X", "clpid": "Faraon-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_eng" } ], "abstract": "The III-V semiconductors are a broad class of technologically important materials which have seen immense research interest in academia and industry due to their electronic, optoelectronic, and photovoltaic properties. In particular, GaN and the III-nitride family of wide bandgap semiconductors have emerged as promising candidates for the next generation of high-efficiency power electronics and light-emitting devices. Their device operation and macroscopic properties are governed by the dynamics of charge carriers and their microscopic scattering processes. Near room temperature, the carriers are scattered by lattice vibrations (phonons) at ultrafast timescales of order fs-ps. Microscopic understanding of carrier dynamics is challenging due to both the ultrafast time scale at play and to the presence of defects, interfaces, and impurities affecting transport and spectroscopy measurements. Typical theoretical treatments of carrier dynamics and light emission employ empirical models to interpret and fit experimental results. Over the last few years, so-called first-principles (or \"ab initio\") methods to accurately compute ultrafast carrier dynamics, transport, and light emission have seen a rapid rise. These approaches do not employ parameters from experiments, and using only the structure of the material as input, together with quantum mechanics and condensed matter theory, are enabling accurate predictions of carrier dynamics in a wide range of materials and are shedding light on microscopic details such as which electronic states, phonon modes and dissipative processes are responsible for the observed charge transport and light emission properties.
\r\n\r\n\r\nHere, we present first-principles calculations of different aspects of ultrafast carrier dynamics and light emission in III-V semiconductors of technological relevance, focusing on GaN, a key material for solid-state light emission technology. We first present a study of the ultrafast nonequilibrium dynamics of excited (so-called \"hot\") carriers in GaN, with a focus on electron-phonon scattering and the nanometer scale transport of carriers in GaN light emitting devices (LEDs). Using cutting-edge first-principles methods developed in this work, we find an asymmetry between the time scale of hot electron and hole thermalization which provides a possible explanation on a major open problem in the efficiency and energy losses of GaN LEDs. We then develop and apply a new rigorous first-principles approach for computing light emission and the radiative recombination lifetimes in bulk crystals, nanomaterials and isolated systems. Our approach is based on the Bethe-Salpeter equation (BSE), and it accurately includes excitons, namely electron-hole states bound by the Coulomb interaction that play a key role in light-matter interactions. Using this method, we carry out benchmark calculations of radiative lifetimes in GaAs and GaN. In GaN, our computed radiative lifetimes are in excellent agreement with experiment (within a factor of two), and our calculations further highlight the importance of including excitonic effects and spin-orbit coupling to obtain accurate radiative. We also employ a model to account for exciton thermal dissociation at high temperature, finding excellent agreement with spectroscopic measurements. Lastly, we discuss ongoing work on computing the intrinsic (phonon-limited) mobility in bulk GaN from first principles, focusing on efforts to include piezoelectric electron-phonon interactions, which are important for acoustic phonon modes in GaN. We compute the electron and hole mobilities in GaN and obtain excellent agreement with experiment. Our calculations shed light on which phonon modes scatter the carriers, providing new microscopic insight into charge carrier dynamics in GaN and related III-V semiconductors.
", "doi": "10.7907/9E0D-KX54", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11701", "collection": "thesis", "collection_id": "11701", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-011829568", "primary_object_url": { "basename": "Haemin_Paik_2019_Thesis_Final.pdf", "content": "final", "filesize": 5231750, "license": "other", "mime_type": "application/pdf", "url": "/11701/1/Haemin_Paik_2019_Thesis_Final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Development of Electrocatalysts in Solid Acid Fuel Cells", "author": [ { "family_name": "Paik", "given_name": "Haemin", "orcid": "0000-0001-8358-6067", "clpid": "Paik-Haemin" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Solid acid fuel cells (SAFCs) can operate at intermediate temperature (near 250 \u00baC) using a non-toxic, solid proton-conducting electrolyte, CsH2PO4, which allows for fuel flexibility, high efficiency, inexpensive auxiliary components, and easy on-off cycling. Despite these features, large activation overpotentials at the electrodes require high Pt loadings in order to achieve acceptable power output. Few alternatives to Pt have emerged for either the hydrogen oxidation reaction or the oxygen reduction reaction in SAFCs. This thesis explores the use of Pd and Pd-containing alloys for electrocatalysis in SAFCs to reduce overall precious metal loading and therefore reduce cost to commercialization.
\r\n\r\nFirst, this work explores the use of Pd at the SAFC anode, assessing both catalytic activity for hydrogen electro-oxidation and reactivity with the CsH2PO4 electrolyte. A thin film geometry, in which nanometric layers of metal were deposited onto a polycrystalline disk of CsH2PO4 was used to simplify the device and facilitate interpretation electrochemical behavior. Using a symmetric geometry, the cells were examined under a uniform hydrogen-rich gas. It was found that Pd reacts with CsH2PO4, forming palladium phosphide (Pd-P) at the metal-electrolyte interface. With the aim studying the behavior of Pd in the absence of this reactivity, Pd overlain on Pt was examined in a bilayer geometry of Pd | Pt | CsH2PO4 | Pt | Pd. The bilayer Pt | Pd films show much higher activity for hydrogen electro-oxidation than films of Pt alone, as measured by AC impedance spectroscopy. Ex-situ low energy ion scattering and scanning transmission electron microscopy revealed that Pd diffused into the Pt layer under operating conditions. The extremely high activity of the interdiffused films suggest that Pd catalyzes reactions at both the metal-gas and metal-electrolyte interfaces, and furthermore facilitates rapid hydrogen diffusion rates through the films.
\r\n\r\nThe high activity of Pt | Pd films, in which Pd eventually contacts the underlying electrolyte due to interdiffusion of the metals, motivates an investigation of Pd-based catalysts (Pd and Pd-P) for hydrogen electro-oxidation in a fuel cell relevant configuration. Working electrodes were formed from a mixture of Pd on carbon and the electrolyte material. The hydrogen oxidation kinetics from Pd, Pd6P, and Pd3P0.8 were observed to be comparable. The result is consistent with the observation that Pd catalyst reacts with CsH2PO4 and converts into Pd-P during cell operation. Both Pd and Pd-P appear to be more effective electrocatalysts for hydrogen oxidation than the equivalent mole percent of Pt supported on carbon. Further enhancement of Pd catalytic activity is achieved by reducing its crystallite size.
\r\n\r\nLastly, this work examines the catalytic activity of Pd for oxygen reduction at the SAFC cathode. Evaluation of this system is complicated by the instability of Pd on CsH2PO4 under oxidizing conditions, which causes microstructure collapse and performance degradation. A SnO2 thin film was introduced as a barrier layer to inhibit Pd reactivity with CsH2PO4 and as a structural support for the catalyst. Employing atomic layer deposition, a SnO2 thin film was deposited either between the Pd and CsH2PO4 interface, or over the Pd catalyst. Both Pd-SnO2 bilayers show improved fuel cell performance stability compared to a Pd-only control, forming Pd-Sn alloys under cathode conditions. This suggests that the formation of Pd-Sn alloy stabilizes the metallic phase of Pd, improving catalytic activity. This work presents a new approach for designing the cathode materials for SAFCs.
", "doi": "10.7907/C96K-Z389", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11092", "collection": "thesis", "collection_id": "11092", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06252018-172548450", "type": "thesis", "title": "Microstructure and Small-Scale Deformation of Al\u2080.\u2087CoCrFeNi High-Entropy Alloy", "author": [ { "family_name": "Giwa", "given_name": "Adenike Monsurat", "orcid": "0000-0002-1229-7505", "clpid": "Giwa-Adenike-Monsurat" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Faber", "given_name": "Katherine T.", "clpid": "Faber-K-T" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "Kavli Nanoscience Institute" }, { "literal": "div_eng" } ], "abstract": "Novel engineering materials are continuously being designed for structural applications, particularly for improved mechanical properties such as high strength, enhanced ductility, and great thermal stability. High entropy alloys (HEAs) as an emerging material can be distinguished from other metal systems as a five-or-more-component alloy in which the constituents are in equiatomic or near equiatomic proportions, thereby maximizing the configurational entropy.
\r\n\r\nThis thesis is focused on understanding the microstructure of an aluminum-containing HEA in relation to its small-scale mechanical properties. Physical phenomena such as size-effect, slip sizes, temperature effect, crystallographic orientation effect, influence of interface, and small perturbations in atom motions are studied.
\r\n\r\nUniaxial compression experiments were conducted on nanopillars fabricated from the individual phases (i.e. Face Centered Cubic (FCC) and Body Cubic Centered (BCC) present in the Al0.7CoCrFeNi HEA. We observed the presence of a size-effect in both phases, with smaller pillars having substantially greater strengths compared with bulk and with larger sized samples. The size-effect power law exponent m in \u03c4y \u03b1 D-m for the BCC phase was \u2212 0.28, which is lower than that of most pure BCC metals, and the FCC phase had m = \u2212 0.66, which is equivalent to most pure FCC metals. These results are discussed in the framework of nano-scale plasticity and the intrinsic lattice resistance through the interplay of the internal (microstructural) and external (dimensional) size effects.
\r\n\r\nIn addition to higher stresses observed at cryogenic temperature in both phases, the microstructural analysis of the deformed pillar via Transmission Electron Microscopy (TEM) showed that FCC pillars undergo deformation by planar-slip dislocation activities even at temperatures of 40 K. Bulk FCC HEAs have been studied to deform via twinning mechanism at low temperatures. The BCC phase, however, confirms dislocation\u2013driven plasticity and twinning at 40 K. These results are explained from the intrinsic nature of the dislocation structure of both phases at low temperatures.
\r\n\r\nThe effect of an 'interphase' in micron-sized HEA pillars was studied from different orientation configurations of the BCC | FCC phases. Slip transmission across the phases was observed in high symmetry orientation combination of both phases. Configurations having a mixture of both low and high symmetry orientations vary in deformation mechanisms. We explain these findings in relation to crystal orientation effect of the combining half pillars, competing plastic mechanisms, dislocation \u2013 boundary interactions and how these findings correlate with their mechanical response.
\r\n\r\nAlso, we conducted dynamic mechanical analysis on the FCC and BCC HEA nanopillars to reveal their damping properties. Higher storage modulus and damping factor values were observed in FCC and BCC the nanopillars. Storage Moduli in the nano-sized HEAs are a factor of 2 greater than both bulk BCC and FCC HEA counterparts. The difference is due to greater surface contribution of the external atoms in the small-sized HEAs.
", "doi": "10.7907/PSWX-RY20", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11320", "collection": "thesis", "collection_id": "11320", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12182018-111020369", "type": "thesis", "title": "Light Management in Photovoltaics and Photoelectrochemical Cells using Tapered Micro and Nano Structures", "author": [ { "family_name": "Yalamanchili", "given_name": "Sisir", "clpid": "Yalamanchili-Sisir" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "Kavli Nanoscience Institute" }, { "literal": "div_eng" } ], "abstract": "Enhancing the efficiency and reducing the cost of solar photovoltaic (PV) systems is critical for increasing their penetration into energy generation market. The intermittency of energy generation from such systems due to diurnal, seasonal, and weather-related variation of sunlight limits them to low capacity factors (typically ~ 25%). Therefore, despite the cost of electricity from solar PV systems being cost competitive, further reductions are necessary to incorporate storage and increase the fraction of solar energy in total energy generation. An integrated photoelectrochemical (PEC) system that can generate fuel directly from sunlight could potentially reduce the balance of systems cost that dominates current PV systems, and provide an alternative way for energy storage. PEC systems are currently in research stage.
\r\n\r\nIn this work conical and triangular micro-nano structures are utilized to explore optical solutions for maximizing the light absorption and therefore enhancing the efficiencies of both PV and PEC systems. Silicon (Si) based micro conical arrays demonstrate < 1 % Spectrum-and-Angle-Averaged reflection, and absorption nearing ray optic light trapping limit in a 20 \u00b5m effectively thick Si substrates. Si microcone based photocathodes prepared for performing hydrogen evolution reaction (HER) show that thick layers of light blocking Pt and Co-P catalysts can be incorporated with only a 6 % photocurrent loss. The light trapping properties of Si micro-cones are a result of efficient coupling of light to available waveguide modes in a conical geometry. Alternatively, TiO2 based dielectric nano-conical arrays are shown to couple the light to waveguide modes and transmit the light into a planar Si substrate despite covering 54 % of the planar front surface with a light blocking Ni catalyst as an alternative way of light trapping without texturing the light absorber.
\r\n\r\nTriangular silver (Ag) front contacts in place of conventional flat contacts over PV cells are shown as another alternative for reducing front contact reflection losses and enhancing the efficiency by ~ 1% in Si heterojunction solar cells. These structures are implemented using a polymer stamp prepared from a Si master with triangular groves, and by flowing Ag ink through them. A Si master fabrication method is shown for fabrication of multiple configurations of triangular Ag contacts which can potentially be applied to other PV and PEC systems to enhance their efficiency.
\r\n", "doi": "10.7907/RRYM-VK03", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11328", "collection": "thesis", "collection_id": "11328", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12232018-185711169", "type": "thesis", "title": "Computational Heterogeneous Electrochemistry \u2013 From Quantum Mechanics to Machine Learning", "author": [ { "family_name": "Huang", "given_name": "Yufeng", "orcid": "0000-0002-0373-2210", "clpid": "Huang-Yufeng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Because of coulomb interactions and complex surface morphologies, rigorous methods for heterogeneous electrochemical catalysis were not well-established. Thus, for different types of electrochemical systems, a specific strategy must be adapted. In this thesis, we first used the cluster model to study the chemistry on a 1D chain of MoS2 edges. Then, a rigorous grand canonical potential kinetics (GCP-K) method was developed for general crystalline systems. Starting from quantum mechanical calculations, the method gave rise to a different picture from the traditional description given by the Butler-Volmer kinetics. Next, we studied the chemical selectivity of CO2 reduction on polycrystalline copper nanoparticles. Because of the complexity of the reaction sites, we combined the reactive force field, density functional theory, and machine learning method to predict the reactive sites on 20,000 sites on a roughly 200,000-atom nanoparticle. Such a strategy opens up new way to understand chemistries on a much wider range of complex structures that were impossible to study theoretically. Lastly, we formulated a machine learning force field strategy using atomic energies for amorphous systems. We have shown that such a method can be used to reproduce quantum mechanical accuracies for molecular dynamics. This method will enable the accurate study of the dynamics of heterogeneous systems during electrochemical reactions. In summary, we have developed quantum chemical methods and machine learning strategies to reformulate rigorous ways to study a wide range of heterogeneous electrochemical catalysts.
", "doi": "10.7907/MCGV-Y790", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:11009", "collection": "thesis", "collection_id": "11009", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012018-190621868", "primary_object_url": { "basename": "Gethers_Matthew_2018_Thesis.pdf", "content": "final", "filesize": 24092782, "license": "other", "mime_type": "application/pdf", "url": "/11009/1/Gethers_Matthew_2018_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Therapeutic Opportunities and Approaches to Sequence Control for Nucleic Acids", "author": [ { "family_name": "Gethers", "given_name": "Matthew Leroy, III", "orcid": "0000-0001-7455-4709", "clpid": "Gethers-Matthew-Leroy-III" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Weiss", "given_name": "Paul S.", "orcid": "0000-0001-5527-6248", "clpid": "Weiss-P-S" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Rothemund", "given_name": "Paul W. K.", "orcid": "0000-0002-1653-3202", "clpid": "Rothemund-P-W-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Weiss", "given_name": "Paul S.", "orcid": "0000-0001-5527-6248", "clpid": "Weiss-P-S" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "RNA interference (RNAi) is a powerful mechanism to regulate gene expression. A key feature of RNAi is its sequence specificity: a short interfering RNA (siRNA) assembles into the RNA induced silencing complex (RISC) and then targets cellular transcripts complementary to the siRNA for degradation. RNAi has been adapted for therapeutic applications, but is challenged by the need to identify unique target transcripts for each disease that are both effective and result in few off-target effects. This challenge could be eased if siRNAs could be activated only and specifically in diseased cells. If this were the case, rather than targeting a new transcript for each new disease, the same cellular housekeeping genes could be reused. Targeting housekeeping genes would result in greater potency, both effectively treating the disease and requiring less drug for treatment, alleviating problems associated with toxicity and delivery. A new class of nucleic acid therapeutics called conditional siRNAs (Cond-siRNA) is designed to act in this environment-specific manner. The first part of this thesis uses molecular dynamics simulations to understand the structure of Cond-siRNA and to suggest improvements in future designs.
\r\n\r\nBioengineering like the work done in the development of Cond-siRNAs depends on the existence of tools that make work simple, fast, cheap, and reproducible. In the case of nucleic acids, de novo synthesis of custom constructs is a fundamental tool. While approaches to synthesis have improved immensely since their inception, increasing ambition demands increasingly powerful tools. As target constructs get longer, the synthesis can become intractably complicated, slowing the process, increasing costs, and making it less likely to be replicated by others. The source of complexity in nucleic acid synthesis is the inability to directly synthesize long fragments without errors. Finding a new means of sequence-controlled synthesis that results in fewer errors and perhaps allows for correction could address this challenge. The second part of this thesis looks at using graphene as a mask for patterning the deposition of molecules on a surface with an eye towards arranging and coupling reactants in a sequence-specific way.
", "doi": "10.7907/WE1E-EZ49", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10851", "collection": "thesis", "collection_id": "10851", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05062018-164727269", "type": "thesis", "title": "Performance and Stability Optimization of Solar Fuel Devices", "author": [ { "family_name": "Zhou", "given_name": "Xinghao", "orcid": "0000-0001-9229-7670", "clpid": "Zhou-Xinghao" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Faber", "given_name": "Katherine T.", "clpid": "Faber-K-T" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "JCAP" }, { "literal": "div_eng" } ], "abstract": "Fossil fuels enabled the Industrial Revolution, and have been the most important power for promoting the world's economic growth ever since. However, burning fossil fuels have also been causing severe air pollution, and global warming is also related to excessive use of fossil fuels. Solar energy is considered to be the largest renewable clean energy resource. The principal problems of solar energy are low energy concentration and intermittency. Storing solar energy in chemical bonds, similar to photosynthesis in nature, is a possible way to overcome these two problems. Carbon-free chemicals, like hydrogen gas produced by solar-driven water splitting, or carbon-neutral chemicals, like methane, ethylene, formic acid, carbon monoxide, etc. produced from solar-driven CO2 reduction, are all promising clean fuels for solar storage, as they feature high energy/power intensity, are easy and cheap to store and transport, and have direct interface with existing infrastructures.
\r\n\r\nIn this thesis, we focus on improving the efficiency and stability of the solar-driven fuel generation devices, which consist of (photo-)anode and (photo-)cathode. For the anode part, cobalt oxide Co3O4 ultrathin (2 nm) films by atomic layer deposition (ALD) were deposited onto silicon photoanode prior to deposition of thick nickel oxide (NiOx) layers. The photovoltage of the photoanode increased from 200 mV to 580 mV after including the interfacial Co3O4 layer, and the anode was stable in 1.0 M KOH(aq) for 1700 hours, which was equivalent to one year of operation in the field at a maximum photocurrent density of 30 mA/cm2 assuming a 20% solar capacity factor. Furthermore, the non-uniform sputtered (NiOx) layer of the n-Si/SiOx/Co3O4/NiOx photoanode was removed, and the 2 nm Co3O4 film was thickened to 50 nm, and the stability of n-Si/SiOx/50 nm-Co3O4 was improved to 2500 hours with lower efficiency decay rate. For the cathode part, an optimized Pd/C nanoparticle coated Ti mesh cathode exhibited < 100 mV overpotential at 8.5 mA/cm2 current density, and > 94% Faradaic efficiency for the reduction of 1 atm of CO2(g) to formate in 2.8 M KHCO3. A solar-driven CO2 reduction (CO2R) cell was constructed with this cathode, showing 10% solar-to-fuels conversion efficiency.
\r\n\r\nThis thesis can be divided into three parts. The first part discusses importance of solar fuels, as well as gives an introduction of solar-fuel generators. The second part includes Chapter II and Chapter III, which deal with performance improvement of silicon photoanode with ALD Co3O4 thin films. The third part is Chapter IV, in which we study the cathode for CO2 reduction to formate, and demonstrate a 10% efficiency solar-driven CO2 reduction cell with the cathode.
", "doi": "10.7907/SSNP-XW29", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10794", "collection": "thesis", "collection_id": "10794", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04052018-112428695", "type": "thesis", "title": "Coarse-Grained Simulation Approaches for Protein Integration and Translocation via the Sec Translocon", "author": [ { "family_name": "Niesen", "given_name": "Michiel Jacobus Maria", "orcid": "0000-0002-9255-6203", "clpid": "Niesen-Michiel-Jacobus-Maria" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Shan", "given_name": "Shu-ou", "clpid": "Shan-Shu-ou" }, { "family_name": "Clemons", "given_name": "William M.", "clpid": "Clemons-W-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes coarse-grained approaches for simulating the co-translational integration and translocation of proteins via the Sec translocon, which is a key step in the biogenesis of membrane and secretory proteins. We present a coarse-grained simulation approach that is capable of simulating minute-timescale dynamics while retaining sufficient chemical and structural detail to capture sequence-specific interactions. The model is validated through comparison to existing experimental data and applied to characterize the forces that act on nascent proteins and drive successful integration and translocation. We also apply coarse-grained simulations of the integration of multi-spanning membrane proteins to understand the effect of sequence modifications on expression levels. We uncover the link between integration efficiency and observed expression levels for membrane proteins, and utilize coarse-grained simulations to predict sequence modifications that improve heterologous overexpression.
", "doi": "10.7907/Z91N7ZBS", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:11069", "collection": "thesis", "collection_id": "11069", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06112018-181603942", "type": "thesis", "title": "Interrogating the Structural Landscape of Malaria Biomarkers with Epitope Targeted Peptide Capture Agents", "author": [ { "family_name": "Liang", "given_name": "JingXin", "orcid": "0000-0001-6600-8409", "clpid": "Liang-JingXin" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Shan", "given_name": "Shu-ou", "clpid": "Shan-Shu-ou" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Antibodies have conventionally been used as molecular recognition agents against epitopes, or antigenic regions, for protein capture and detection. The ability of monoclonal and polyclonal antibodies to selectively bind their targets with high affinities makes them excellent agents for specific protein recognition. However, as large proteins themselves (~150 kDa), antibodies are susceptible to changes in pH, temperature, and biochemical environment, particularly proteolytic cleavage. Additionally, epitope binding on antibodies is reliant on their rigid tertiary structure to position key functional groups that facilitation antigen recognition. Retaining the integrity of the protein structure creates rigid limitations against chemical modifications of antibodies to suit unique needs.
\r\n\r\nProtein-catalyzed capture agents (PCCs) developed within the Heath group at Caltech address the limitation of antibodies as affinity agents. Using epitope-targeted in situ click screening methodology, the Heath group has developed peptidomimetic molecules that offer an alternative solution to antibodies. These PCCs exhibit high affinity and selectivity for their protein targets. As peptide-based molecules, PCCs can be engineered to be biochemically stable and resistant to changes in their chemical environment. Their peptide-based structures are readily amenable to chemical modifications and allow for adaptation to a range of applications.
\r\n\r\nThis thesis describes the development of PCCs against unique protein biomarkers for the detection of the most lethal species of malaria infection, Plasmodium falciparum. Malaria is a global health epidemic and its eradication is reliant on rapid and accurate diagnostics for prompt treatment. We targeted the P. falciparum specific biomarkers lactate dehydrogenase (LDH) and Histidine-rich protein 2 (HRP2), both of which present unique challenges for protein capture. The LDH biomarker is homologous across malaria species, whereas HRP2 is highly polymorphic and lacks distinct secondary structure. The variation in sensitivity of HRP2 detection by antibody-based tests has been attributed to the genetic polymorphism of the biomarker.
\r\n\r\nIn Chapter 1, we describe the development of high affinity PCCs that bind selectively to the LDH biomarker. We targeted an epitope that was highly homologous across LDH species. This chapter also details the expansion of mono-valent PCC agents into bivalent ligands using the protein architecture to select secondary ligands for binding improvement. For the HRP2 biomarker, we developed a multiple epitope targeting strategy to address protein polymorphism. We targeted for epitopes in HRP2 and developed PCCs that bind in the range of monoclonal antibodies.
\r\n\r\nChapter 2 details the expansion of PCC agents developed against HRP2 into multivalent molecules for improved binding. The development of bivalent ligands from combinatorial screening of linker libraries is presented. The optimal linker lengths determined by the screens are described.
\r\n\r\nIn Chapter 3, a general strategy for targeting the protein landscape to inhibit formation of a protein and biomolecule complex with PCCs against HRP2 is demonstrated. Specifically, the inhibition of heme sequestration by HRP2 is shown. A bivalent ligand that targets two epitopes on HRP2 is shown to have enhanced inhibitory potency over any single or cocktail combination of PCCs.
\r\n\r\nAltogether, the studies herein demonstrate the utility of peptidomimetic molecules as agents for protein capture and detection as well as a generalizable strategy of functional inhibition through epitope-targeting.
", "doi": "10.7907/rxtr-6152", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:11068", "collection": "thesis", "collection_id": "11068", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06112018-153323554", "primary_object_url": { "basename": "Thesis_Jiang_Interfacial and Stability Studies of Photocathodes for Hydrogen Evolution_v4.pdf", "content": "final", "filesize": 4577599, "license": "other", "mime_type": "application/pdf", "url": "/11068/8/Thesis_Jiang_Interfacial and Stability Studies of Photocathodes for Hydrogen Evolution_v4.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Interfacial and Stability Studies of Photocathodes for Hydrogen Evolution", "author": [ { "family_name": "Jiang", "given_name": "Jingjing", "orcid": "0000-0002-3109-229X", "clpid": "Jiang-Jingjing" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "JCAP" }, { "literal": "div_eng" } ], "abstract": "Photoelectrochemical (PEC) water splitting is a promising way to generate clean hydrogen fuel from water and sunlight. The ideal photocathodes for hydrogen evolution reaction (HER) should have good electrical contact and mechanical adhesion on the interface between the semiconductor and the catalyst, and be stable during operation. However, the interfacial properties and the stability have not been intensively studied. We investigated the electrical and mechanical properties on the nanoscale of the interface of commonly used Si/Pt nanoparticles (Pt-NPs) electrodes with Pt-NPs as a catalyst, and showed that the Pt-NPs have a weaker adhesion in electrolyte than in air, and less than half of the Pt-NPs carry high currents, limiting the performance of the common Si/Pt-NPs electrodes. Furthermore, we explored the interfacial engineering of using TiO2 deposited by atomic layer deposition (ALD), and showed that annealed TiO2 led to higher open circuit voltages than the as grown ones by the possible formation of an interfacial Si-O-Ti mixture layer. Besides, the stability and corrosion behavior of CdTe electrodes for HER in the dark was studied in 1.0 M H2SO4(aq) and 1.0 M KOH(aq). The conditions studied herein include the electrochemical corrosion when biased at -100 mV vs. the reversible hydrogen electrode (RHE), the chemical corrosion when left at open circuit voltage (OCV), and the electrochemical corrosion with an active HER Pt catalyst overlayer when biased at -100 mV vs. RHE. The corrosion comes mostly from chemical corrosion and is reduced at negative bias in electrochemical condition. With a Pt catalyst overlayer at -100 mV vs. RHE, the corrosion rate is further reduced, indicating the promising utilization of CdTe for HER in PEC cells.
", "doi": "10.7907/SBJ9-D062", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10995", "collection": "thesis", "collection_id": "10995", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012018-042437640", "primary_object_url": { "basename": "brooks_thesis_6_1_18.pdf", "content": "final", "filesize": 4977239, "license": "other", "mime_type": "application/pdf", "url": "/10995/5/brooks_thesis_6_1_18.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Computational Investigation of Ionic Diffusion in Polymer Electrolytes for Lithium-Ion Batteries", "author": [ { "family_name": "Brooks", "given_name": "Daniel James", "clpid": "Brooks-Daniel-James" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bernardi", "given_name": "Marco", "orcid": "0000-0001-7289-9666", "clpid": "Bernardi-Marco" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" }, { "family_name": "Wise", "given_name": "Mark B.", "orcid": "0000-0002-9125-801X", "clpid": "Wise-M-B" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Energy storage is a critical problem in the 21st century and improvements in battery technology are required for the next generation of electric cars and electronic devices. Solid polymer electrolytes show promise as a material for use in long-lifetime, high energy density lithium-ion batteries. Improvements in ionic conductivity, however, for the development of commercially viable materials, and, to this end, a series of computational studies of ionic diffusion were performed. First, pulsed charging is examined as a technique for inhibiting the growth of potentially dangerous lithium dendrites. The effective timescale for pulse lengths is determined as a function of cell geometry. Next, the atomistic diffusion mechanism in the leading polymer electrolyte, PEO-LiTFSI, is characterized as a function of temperature, molecular weight, and ionic concentration using molecular dynamics simulations. A novel model for describing coordination of lithium to the polymer structure is developed which describes two types of interchain motion \"hops\" and \"shifts,\" the former of which is shown to contribute significantly to ionic diffusion. The methodology developed in this study is then applied to a new problem \u2013 the adsorption of CO2 at the surface of semi-permeable polymer membranes. Finally, a new method, PQEq, is developed, which provides an improved description of electrostatic interactions with the inclusion of explicit polarization, Gaussian shielding, and charge equilibration. The dipole interaction energies obtained from PQEq are shown to be in excellent agreement with QM and a preliminary application of PQEq to a polymer electrolyte suggest that it can provide an improved description of ionic diffusion. Taken as a whole, these techniques show promise as tools to explore and characterize novel materials for lithium-ion batteries. ", "doi": "10.7907/ZE9T-V407", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10967", "collection": "thesis", "collection_id": "10967", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292018-232454800", "type": "thesis", "title": "Synthesis, NMR Solution Structure, and Neuritogenic Activity of Chondroitin Sulfate D and E", "author": [ { "family_name": "Yang", "given_name": "Kuang-Wei", "clpid": "Yang-Kuang-Wei" } ], "thesis_advisor": [ { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Reisman", "given_name": "Sarah E.", "clpid": "Reisman-S-E" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chondroitin sulfate are ubiquitously expressed linear, sulfated polysaccharides that play critical roles in neuronal development and regeneration growth factor signaling, morphogenesis, and virus invasion. The diverse sulfation patterns presented by chondroitin sulfate has been suggested to regulate its activity, but the structural complexity and heterogeneity have hampered the understanding of structure-activity relationship. Therefore, we envisioned that chemically synthesized chondroitin sulfate oligosaccharide may provide a unique opportunity to specifically study the functions of sulfation patterns.
\r\n\r\nHere, we report the synthesis of a CS-D and CS-E tetrasaccharide in a step-efficient manner. By generating a disaccharide precursor from hydrolysis of polysaccharides, we were able to streamline the synthesis and reduce the number of steps by one-third comparing to the traditional synthesis without losing versatility of the synthetic route and functionality of the final product. With the structurally defined molecules, we were able to determine the NMR solution structure of CS-D and CS-E. In this work, we accomplished the first structural study of CS-D tetrasaccharide and the most thorough study of CS-E to date. Furthermore, we also discovered the existence of a second conformer in CS-D, which is the first time for such behavior to be observed experimentally in chondroitin sulfate. The electrostatic potential surface constructed based on the NMR structure presented unique structural features that may allow proteins to interact specifically.
\r\n\r\nThe CS-D and CS-E tetrasaccharide, along with a CS-D disaccharide, was\r\ninvestigated for their neuritogenic activity. We discovered that the CS-D tetrasaccharide specifically stimulates dendritic growth whereas the CS-E tetrasaccharide preferentially promoted axonal growth, revealing the potential critical role chondroitin sulfate with specific sulfation patterns may play in the nervous system. The lack of activity of the CS-D disaccharide suggested that the minimum motif required for activity of CS-D is a tetrasaccharide.
\r\n", "doi": "10.7907/TPD7-FB87", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10723", "collection": "thesis", "collection_id": "10723", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02152018-165139157", "type": "thesis", "title": "Development, Implementation, and Improvements on an Effective Electrochemical Wastewater Treatment and Recycling Unit as a Sustainable Sanitation Solution for the Developing World", "author": [ { "family_name": "Cid", "given_name": "Cl\u00e9ment Antoine Fran\u00e7ois", "orcid": "0000-0002-7293-035X", "clpid": "Cid-Cl\u00e9ment-Antoine-Fran\u00e7ois" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Diallo", "given_name": "Mamadou S.", "clpid": "Diallo-Mamadou-S" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this thesis, I present my work on the development of a self-contained toilet wastewater treatment and recycling system, the \u201cCaltech Solar Toilet\u201d. The Caltech Solar Toilet technology is based on electrolysis of toilet wastewater with TiO2-coated semiconductor anodes and stainless steel cathodes. This is a potentially viable onsite sanitation solution in parts of the world that lack the needed infrastructure for centralized wastewater treatment.
\r\n\r\nPrototypes of Caltech Solar Toilets were designed to fit in shipping containers in order to provide toilets and onsite wastewater treatment with clean water recycling. Units were designed to handle the waste of 25 users per day (or 130 L of toilet wastewater). The various prototypes were able to provide for the disinfection of pathogens, reduction of chemical oxygen demand (COD), [NH3], and color at an average energy consumption of 35 Wh L-1. The treated wastewater was recycled for use as toilet flushing water.
\r\n\r\nThe addition of a microbial fuel cell system for urine pre-treatment was investigated to lower the overall energy consumption of the Solar Toilets. The microbial fuel cell system used consisted of two stacks of 32 cells connected in parallel. An average power density of 23 mW m\u20112 was produced at an effective current density of 65\u00a0mA\u00a0m\u20112 for more than 120 days. [NH3], total inorganic carbon, COD, and total organic carbon levels were monitored frequently to understand the chemical energy conversion to electricity as well as to determine the best electrical configuration of the stacks. Archaeal and bacterial population on selected anode felts and in the anolyte of both stacks were investigated as well.
\r\n\r\nIn addition to treating toilet wastewater, pilot-scale and bench-scale experiments demonstrated that electrolysis can remove phosphate by cathodic precipitation as hydroxyapatite at no additional energy cost. Phosphate removal could be predicted based on initial phosphate and calcium concentrations, and up to 80% total phosphate removal was achieved. While calcium was critical for phosphate removal, magnesium and bicarbonate had only minor impacts on phosphate removal rates at concentrations typical of toilet wastewater.
", "doi": "10.7907/Z9BG2M61", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10962", "collection": "thesis", "collection_id": "10962", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292018-142628914", "type": "thesis", "title": "The Discovery of Novel Materials for the Electrocatalytic Reduction of Carbon Dioxide", "author": [ { "family_name": "Torelli", "given_name": "Daniel Anthony", "orcid": "0000-0002-6222-817X", "clpid": "Torelli-Daniel-Anthony" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "JCAP" }, { "literal": "div_chem" } ], "abstract": "The removal of atmospheric carbon dioxide is likely the only route to mitigating the effects of decades of increased fossil fuel combustion. Artificial photosynthesis presents one method for removal and conversion of problematic carbon dioxide into chemically useful products. By coupling electrochemical CO2 reduction (CO2R) to a renewable energy source atmospheric CO2 could be converted back into a fuel such as ethanol, or a commodity chemical such as ethylene. These products could then be consumed for energy or used to generate plastics effectively removing CO2 from the atmosphere. Significant advances in current electrocatalysts are needed in order for large scale CO2R to become a reality. Most known catalysts are only capable of transferring 2 electrons with needed protons to CO2 producing either carbon monoxide or formic acid. Copper is the only known metal capable of reducing CO2 to hydrocarbons at appreciable rates and low overpotentials. This work aims to find new materials that produce similar hydrocarbons, but at lower overpotentials with higher rates and greater selectivity than current copper catalysts. By implementing a cyclic process referred to as the Catalyst Discovery Cycle (CDC) iterations between predications, catalyst testing, and active site characterization allow for the rational design and discovery of new and improved catalysts. This methodology led to the discovery of nickel-gallium bimetallics as low overpotential catalysts for CO2R to methane, ethylene, and ethane. In addition, theoretical and experimental observations have determined a proposed active site and side reactions detrimental to their activity. ", "doi": "10.7907/RBD5-B141", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10624", "collection": "thesis", "collection_id": "10624", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01082018-142110350", "primary_object_url": { "basename": "Final thesis Shi Luo.pdf", "content": "final", "filesize": 5695075, "license": "other", "mime_type": "application/pdf", "url": "/10624/1/Final thesis Shi Luo.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Microstructural Effects on Diffusion and Mechanical Properties in Different Material Systems", "author": [ { "family_name": "Luo", "given_name": "Shi", "clpid": "Luo-Shi" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Faber", "given_name": "Katherine T.", "clpid": "Faber-K-T" }, { "family_name": "Daraio", "given_name": "Chiara", "clpid": "Daraio-C" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Material microstructures is a very broad subject that encompasses most of the field of materials science. Advances in materials characterization and small scale mechanical experiments have brought about progress in the understanding of microstructural features and mechanisms down to the nanometer scale. In contrast to bulk features and properties, the small length scale of these microstructures lead to many interesting properties, and often requires a material-by-material, and even localized region-by-region study. While a thorough understanding of microstructural effects even in one material system is way beyond the scope of this thesis, there are nonetheless many common themes and properties that link together microstructures and their effects on different materials, especially in terms of mechanical properties.
\r\n\r\nIn this thesis, the effects of microstructural features such as grain boundaries, surface modification and structural hierarchy are investigated using two sample material systems: Cu-In-Ga-Se (CIGS) thin films and marine diatom frustules. We find that grain structures (or a lack there of) play a major role in both systems, and lead to differences in material stiffness, strength, and diffusion of species. The latter is also significantly affected by material defects across length scales, exemplified in CIGS by both microscopic voids and pores, and atomic scale like substitutional point defects. On the other hand, in diatoms, a low flaw density combined with an effective hierarchical design can propel the mechanical property of relatively simple ingredients like amorphous silica, to achieve extraordinary mechanical strength. We will conclude by showcasing that we can generalize some of these knowledge on microstructural effects across material systems, to help designing manmade structures that fully capture the material-level and structural-level properties of natural marine diatoms.
", "doi": "10.7907/Z90G3HBV", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10717", "collection": "thesis", "collection_id": "10717", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02132018-133402404", "primary_object_url": { "basename": "GMM_Thesis.pdf", "content": "final", "filesize": 8654115, "license": "other", "mime_type": "application/pdf", "url": "/10717/1/GMM_Thesis.pdf", "version": "v16.0.0" }, "type": "thesis", "title": "Eph Receptor Clustering by Chondroitin Sulfate Inhibits Axon Regeneration", "author": [ { "family_name": "Miller", "given_name": "Gregory Martin", "clpid": "Miller-Gregory-Martin" } ], "thesis_advisor": [ { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "thesis_committee": [ { "family_name": "Hoelz", "given_name": "Andre", "clpid": "Hoelz-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chondroitin sulfate proteoglycans (CSPGs) play important roles in the developing and mature nervous system, where they guide axons, maintain stable connections, restrict synaptic plasticity, and prevent axon regeneration following CNS injury. The chondroitin sulfate glycosaminoglycan (CS GAG) chains that decorate CSPGs are essential for their functions. Through these sugar chains, CSPGs are able to bind and regulate the activity of a diverse range of proteins and through these interactions can regulate neuronal growth. These CS-protein interactions depend on specific sulfation patterns within the CS GAG chains, and accordingly, particular CS sulfation motifs are upregulated during development, in the mature nervous system, and in response to CNS injury. Thus, spatiotemporal regulation of CS GAG biosynthesis may provide an important mechanism to control the functions of CSPGs and modulate intracellular signaling pathways. Here, we will discuss these sulfation-dependent processes and highlight how the CS sugars on CSPGs contribute to neuronal growth, axon guidance, and plasticity in the nervous system.
\r\n\r\nChondroitin sulfate proteoglycans (CSPGs) are a major barrier to regenerating axons in the central nervous system (CNS), exerting their inhibitory effect through their polysaccharide side chains. Chondroitin sulfate (CS) potently inhibits axon regeneration through modulation of inhibitory signaling pathways induced by carbohydrate binding to protein ligands and receptors. Here, we identify a novel carbohydrate-protein interaction between CS and EphA4 that inhibits axon regrowth. We characterize the mechanism of activation and demonstrate how carbohydrate binding induces phosphorylation of the intracellular kinase domain through clustering of cell surface EphA4. Collectively, our studies present a novel mechanism of EphA4 activation by CS independent of the canonical ephrin ligands and uncover the role of this interaction in inhibition of neurite regrowth after injury. Our results underscore a mechanism of action by which carbohydrates can function as direct, activating ligands for protein receptors and provide mechanistic insights into the inhibition of axon growth by CS following injury to the CNS.
\r\n\r\nChondroitin sulfate proteoglycans (CSPGs) regulate neuronal plasticity, as well as axon regeneration and guidance through their ability to bind protein ligands and cell surface receptors. In this way, extracellular CSPGs can modulate the activity of intracellular signaling pathways. Here, a computational analysis of EphA4-CS interactions is performed to characterize the importance of key arginine and lysine residues towards CS binding, and to identify structural differences in CS-A, CS-C, CS-D, and CS-E docking to EphA4. Carbohydrate-induced Eph receptor clustering could be a general mechanism of Eph receptor activation. To identify additional Eph receptors that interact with CS, CS-E was docked to all EphA and EphB family members to predict relative binding affinities. The relative strengths of the predicted binding energies are: EphB4 > EphA8 > EphA1 > EphA3 > EphB1 > EphB3 > EphA7 > EphA5 > EphA4 > EphA6 > EphB2 > EphB6 > EphA2. In addition, the arginine and lysine residues that mediate CS binding are identified for each Eph receptor. These computational predictions provide mechanistic insights into Eph receptor activation by chondroitin sulfate and have implications for inhibition of axon regeneration following injury to the nervous system and axon guidance during development.
", "doi": "10.7907/Z9RJ4GPT", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:9907", "collection": "thesis", "collection_id": "9907", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08292016-233907648", "primary_object_url": { "basename": "Murialdo_Maxwell_FullThesis (Final Complete).pdf", "content": "final", "filesize": 25505593, "license": "other", "mime_type": "application/pdf", "url": "/9907/85/Murialdo_Maxwell_FullThesis (Final Complete).pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Anomalous Thermodynamics of Nonideal Gas Physisorption on Nanostructured Carbons", "author": [ { "family_name": "Murialdo", "given_name": "Maxwell Robert", "clpid": "Murialdo-Maxwell-Robert" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Bernardi", "given_name": "Marco", "orcid": "0000-0001-7289-9666", "clpid": "Bernardi-Marco" }, { "family_name": "Faber", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Mesoporous and microporous adsorbents play critical roles in gas storage and separation applications. This thesis describes previously unexplored anomalous thermodynamics in the field of gas physisorption and their impact on energy relevant gases including methane, ethane, krypton and carbon dioxide. Physisorption occurs when an adsorbent induces gas molecules to form a locally densified layer at its surface due to physical interactions. This increases gas storage capacity over pure compression and its efficacy is dependent on the surface area of the adsorbent and the isosteric heat of adsorption. The isosteric heat of adsorption is the molar change in the enthalpy of the adsorptive species upon adsorption and serves as a measure of adsorbent-adsorbate binding strength.
\r\n\r\nUnlike conventional adsorbate-adsorbent systems, which have isosteric heats of adsorption that decrease with surface loading, zeolite-templated carbon is shown to have isosteric heats of methane, ethane and krypton adsorption that increase with surface loading. This is a largely beneficial effect that can enhance gas storage and separation. The unique nanostructure and uniform pore periodicity of the zeolite-templated carbon promote lateral interactions among the adsorbed molecules that cause the isosteric heats of adsorption to increase with loading. These results have been tested and corroborated by developing robust fitting techniques and thermodynamics analyses. The anomalous thermodynamics are shown to result from cooperative adsorbate-adsorbate interactions among the nonideal species and are modeled with an Ising-type model.
\r\n\r\nAs a second theme of this thesis, the study of nonideal gas adsorption has enabled the development of a Generalized Law of Corresponding States for Physisorption. A predictive understanding of high-pressure physisorption on a variety of adsorbents would facilitate the further development of tailored adsorbents and adsorption analysis. Prior attempts at developing a predictive understanding, however, have been hindered by nonideal gas effects.
\r\n\r\nBy approaching physisorption from both empirical and fundamental perspectives, a Generalized Law of Corresponding States for Physisorption was established that accounts for a number of nonideal effects. This new Law of Corresponding States allows one to predict adsorption isotherms for a variety of classical gases from data measured with a single gas. In brief: \"At corresponding conditions on the same adsorbent, classical gases physisorb to the same fractional occupancy.\"
\r\n\r\nCorresponding conditions are met when the reduced variables of each nonideal gas are equivalent, and fractional occupancy gives the fraction of occupied adsorption sites. This Law of Corresponding States for Physisorption is determined using monolayer, BET and Dubinin-Polanyi adsorption theories along with measured adsorption isotherms across a number of conditions and adsorbents. Furthermore, the anomalous cooperative adsorbate-adsorbate interactions discussed in this thesis are shown to be consistent with the Generalized Law of Corresponding States for Physisorption.
\r\n", "doi": "10.7907/Z9GH9FXM", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10001", "collection": "thesis", "collection_id": "10001", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01032017-003321706", "type": "thesis", "title": "First-Principles-Based Simulations for G Protein-Coupled Receptor Activation and for Large-Scale Nonadiabatic Electron Dynamics", "author": [ { "family_name": "Dong", "given_name": "Sijia S.", "orcid": "0000-0001-8182-6522", "clpid": "Dong-Sijia-S" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis focuses on simulating large molecular systems within and beyond the Born-Oppenheimer framework from first principles. Two approaches have been developed for very different but important applications.
\r\n\r\nThe first one is a hybrid method based on classical force fields that predicts the high-energy ensemble of three-dimensional structures of a class of proteins critical in human physiology: the G protein-coupled receptors (GPCRs). GPCRs' functions rely on their activation marked by a series of conformational changes related to binding of certain ligands, but the short of experimental structures has hampered the study of their activation mechanism and drug discovery. Our method, combining homology modeling, hierarchical sampling, and nanosecond-scale molecular dynamics, is one of the very few computational methods that can predict their active-state conformations and is one of the most computationally inexpensive. It enables the conformational landscape and the first quantitative energy landscape of GPCR activation to be efficiently mapped out.
\r\n\r\nThis method, named ActiveGEnSeMBLE, allows the inactive- and active-state conformations of GPCRs without an experimental structure to be systematically predicted. We have validated the method with one of the most well-studied GPCRs, human β2 adrenergic receptor (hβ2AR), and applied the method on a GPCR without an experimental structure, human somatostatin receptor 5 (hSSTR5). Insights on GPCR activation as well as structure prediction methods are discussed.
\r\n\r\nThe second one is a semiclassical approach for large-scale nonadiabatic dynamics of condensed systems in extreme conditions, termed Gaussian Hartree Approximated Quantum Mechanics (GHA-QM). Many nonadiabatic processes related to important applications (e.g. renewable energy) happen in large systems, but existing excited state dynamics methods are too computationally demanding for their long timescale simulations. GHA-QM is based on the electron force field (eFF) framework where we model electrons as Gaussian wavepackets and nuclei as classical point charges, and obtain a simplified solution to the time-dependent Schr\u00f6dinger equation as the equation of motion. We employ a force field philosophy approximating the total energy as a sum of electronic kinetic energies, electrostatic energies and a Pauli correction, which corrects for the lack of explicit antisymmetry in the wavefunctions. New designs of the Pauli potential and preliminary results on hydrogen systems are discussed. With the new development, we hope to improve the accuracy and range of applications of eFF to simulate the nonadiabatic dynamics of hundreds of thousands of electrons on nanosecond timescale.
", "doi": "10.7907/Z98C9T8D", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10335", "collection": "thesis", "collection_id": "10335", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06122017-230026717", "type": "thesis", "title": "DarwinDock and GAG-Dock: Methods and Applications for Small Molecule Docking", "author": [ { "family_name": "Griffith", "given_name": "Adam Reid", "clpid": "Griffith-Adam-Reid" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Computational modeling is an effective tool in studying complex biological systems. Docking of small molecule ligands in particular is useful both in understanding the functioning of proteins as well as in the development of pharmaceuticals. Together with experiment, modeling can often provide a thorough picture of a given system. Computation can often provide details that are difficult or impossible to determine experimentally, while experiments provide guidance on what calculations are useful or interesting. Our goal is to extend computational modeling, specifically ligand docking, to systems not previously possible, such as the challenging glycosaminoglycan (GAG) systems. In order to do this it was first necessary to develop an automatic way of performing docking without extensive user input and experimental knowledge to narrow the list of candidate poses. DarwinDock represents our efforts in this respect. It is a method for small-molecule docking that separates pose generation and scoring into separate stages, which allows for complete binding site sampling followed by efficient, hierarchical sampling. Our convergence criteria for complete sampling allows for diverse systems to be studied without prior knowledge of how large a set of poses needs to be to span a given binding site, making the procedure more automatic. We also replace bulky, nonpolar residues with alanine, which we refer to as \"alanization\". This allows the ligand to interact more closely with polar sidechains, which help to orient the ligand. Additionally, alanization reduces the impact of incorrect sidechain placement on ligand placement, a concern that sometimes requires user intervention. With DarwinDock working for standard small molecules, it was then necessary to modify the procedure to work on challenging GAG ligands, which are large and have strong negative charges. A modification to DarwinDock \u2013 GAG-Dock \u2013 allows the method to be applied to GAGs and protein surface interactions. GAGs are large, linear polysaccharides with strong negative charge. They typically interact with the surfaces of proteins, rather than the cavities favored by most small-molecule drugs. GAG-Dock systematically samples the protein surface for unknown binding sites and modifies the pose generation to allow for large, surface-interacting ligands. GAG-Dock allowed us to study several systems important for neuronal development and answer interesting questions posed by experiment. Finally, we needed a way to validate our predictions for GAG binding sites. We used a systematic approach to identify sets of beneficial mutations to the GAG binding sites by building up from individual in silico mutations. Standard mutation experiments typically employ large mutations, such as arginine to alanine, which decrease or destroy binding. However, such information is not always definitive, as large mutations can have wide-ranging effects beyond direct protein-ligand interactions. Mutations that increase binding, however, are less ambiguous because they must form new interactions with the ligand in order to affect binding energies or affinity. Therefore, we have identified and proposed sets of mutations for our GAG predictions for PTPs, NgR1, NgR3, and EphB3. We encourage our experimentalist colleagues to try these mutations and validate our predictions.
", "doi": "10.7907/Z91Z42GS", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9916", "collection": "thesis", "collection_id": "9916", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09062016-162323180", "type": "thesis", "title": "Towards a Hydrobromic Acid Splitting Device Using Earth-Abundant Materials", "author": [ { "family_name": "Roske", "given_name": "Christopher William", "clpid": "Roske-Christopher-William" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Agapie", "given_name": "Theodor", "clpid": "Agapie-T" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis disembarks from the traditional approach of tailoring a system to the water splitting reaction. As detailed in Chapter 2, this thesis predicts that two silicon photoelectrons connected in parallel are ideally suited to electricity storage in an integrated light collector and chemical storage device driving the splitting of hydrobromic acid (2HBr -> H2 + Br2). The predicted dual photoelectrode system could potentially obtain high solar-to-hydrogen conversion efficiencies of up to an \u03b7STH, HBr of 12 %, whereas an equivalent water splitting system is not possible due to the small band gap of silicon. Unfortunately, silicon possesses low catalytic activity for both the hydrogen evolution half-reaction and the bromide oxidation half-reaction. In the past, the electrocatalysis of silicon has been aided by using Pt/Ir alloys to act as both a protective and electrocatalytic layer. Herein, efforts are detailed to replace these precious metals, where possible, by using only earth-abundant materials to decrease the cost of a module. Our hope is that efforts along this path will aid the field of artificial photosynthesis as a whole.
\r\n\r\nWe begin by further testing a chemical insight previously noted within our group and discover a surprisingly high activity electrocatalyst for the hydrogen evolution reaction by cobalt phosphide (CoP) nanoparticles, detailed in Chapter 3. Falling on a traditional technique of increasing the surface area of particular facets, we nanostructured our crystalline CoP to increase its surface area of exposed (111) facets and hoped it would increase our catalytic activity; however, we found that simple structuring resulted in poor adhesion of nanostructures and poorer activity than our multi-faceted CoP nanocrystals (see the appendix to find out more). Our original catalysis efforts spurred a flurry of activity in the literature, and consequently, alternative devices that are more scalable arose. We detail the developments occurring since our work in the last appendix.
\r\n\r\nNow, with a potential catalyst in hand, comes the difficulty of balancing the delicate interplay between light absorption and catalysis, as detailed in Chapter 4. While CoP is active for HER, our particles possess a relatively low turnover frequency compared to hydrogenase or platinum, and thus require high mass loadings of material (2 mg/cm2) to obtain competitive extrinsic performance. Planar electrodes are incompatible with our particles because of substantial light absorption by the thick catalyst overlayer. By structuring our photoelectrode, we abnegate our catalyst limitations by exploiting the properties of microwires. High-aspect ratio microwires have shown promise as potentially low-cost materials for future photovoltaic applications as well as photocathodes functioning as part of an energy storage device. We discuss how to integrate our materials with silicon microwires (the wires were grown by an unscalable process to serve in place of functional CVD wires with radial emitters) to prototype a candidate photocathode. While a parasitic resistance limited the overall efficiency of the photocathode candidate, it still had promising stability. The parasitic resistance was addressed by electrodepositing the cobalt phosphide, thereby giving us a promising efficiency limited by the quality of the p-n junction.
\r\n\r\nWhile high-catalytic activity for the HER in acidic solutions using earth-abundant materials represents a significant advance, the photocathode is just one component of what is necessary for a complex system of splitting hydrobromic acid. Silicon, by its virtue of being a small band gap material, is easily passivated in aqueous solutions by the formation of a silicon oxide. In the past, our colleagues had shown that a monolayer of graphene could occasionally provide protection in a test solution, but batch-to-batch variability provided a considerable challenge. The putative hypothesis offered for the degradation argued defects in the crystalline graphene at grain-boundaries were the culprit. In Chapter 5 we present a method to passivate defects in the graphene crystal by light fluorination and observe a considerable enhancement in stability relative to typical graphene-protected silicon photoanodes. We had hoped that catalysis for bromide oxidation would be aided by the near-perfect graphene liquid junction, but electrodeposited Pt was required to effect photoxidation. A cursory stability test shows promising stability for one-half of an hour, but we would like to avoid using Pt. Finally, we also turned our attention to protecting silicon surfaces from oxidation by exploiting covalent silicon surface chemistry, accessible via a two-step chlorination/alkylation procedure, and explored the deposition of potentially protective thin-film metal oxides (see the appendix).
", "doi": "10.7907/Z9NS0RWS", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9978", "collection": "thesis", "collection_id": "9978", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11062016-204445939", "primary_object_url": { "basename": "plymale_noah_2016_thesis.pdf", "content": "final", "filesize": 9293100, "license": "other", "mime_type": "application/pdf", "url": "/9978/49/plymale_noah_2016_thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Spectroscopic, Electronic, and Mechanistic Studies of Silicon Surfaces Chemically Modified with Short Alkyl Chains", "author": [ { "family_name": "Plymale", "given_name": "Noah Thomas", "orcid": "0000-0003-2564-8009", "clpid": "Plymale-Noah-Thomas" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Brunschwig", "given_name": "Bruce S.", "clpid": "Brunschwig-B-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The chemical, structural, and electronic properties of semiconductor surfaces are known to strongly influence the energetics at semiconductor interfaces. Inexpensive and scalable wet chemical modification of semiconductor surfaces provides a means to impart a desired functionality at semiconductor interfaces for the development of new devices based on precise and cost-effective chemistry. This thesis is composed of three studies that focused on identifying the spectroscopic, electronic, and mechanistic properties of reactions at Si surfaces. First, ethynyl- and propynyl-terminated Si(111) surfaces were prepared and characterized by vibrational and photoelectron spectroscopy as well as electrochemical scanning-tunneling microscopy. Ethynyl-terminated Si(111) exhibited \u2261C\u2212H, C\u2261C, Si\u2212C stretching signals and a fractional monolayer (ML) coverage (\u03a6) of \u03a6Si\u2212CCH = 0.63 \u00b1 0.08 ML and \u03a6Si\u2212OH = 0.35 \u00b1 0.03 ML. Propynyl-terminated Si(111) showed (C\u2212H)CH3 bending, Si\u2212C stretching, and C\u2261C stretching with \u03a6Si\u2212CCCH3 = 1.05 \u00b1 0.06 ML. Deprotonation of ethynyl-terminated Si(111) surfaces formed a unique surface-bound lithium acetylide that acted as nucleophile. This work provides definitive spectroscopic and microscopic evidence for the covalent attachment of ethynyl and propynyl groups to the Si(111) surface. \r\n
\r\n\r\nSecond, Si(111) surfaces were modified with 3,4,5-trifluorophenylacetylene (TFPA) groups to impart a positive dipole at the Si(111) surface. This negative surface dipole provides the necessary band-edge shift at the Si surface to maximize the interface between p-type Si and the proton reduction half reaction. Vibrational and photoelectron spectroscopy provided evidence for the attachment of TFPA groups to the Si(111) surface. Mixed methyl/TFPA monolayers were prepared and characterized using electrochemical and photoelectrochemical methods to show that the band-edge positions and open-circuit voltages were shifted positive with increasing fractional TFPA coverage on the surface. This work demonstrates that monolayer chemistry can be used to manipulate the band-edge positions of Si surfaces as a function of surface composition.\r\n
\r\n\r\nFinally, mechanistic studies of the reaction of liquid methanol with hydride-terminated Si(111) surfaces in the presence of an oxidant were carried out. Vibrational and photoelectron spectroscopy showed that acetylferrocenium, ferrocenium, and dimethyl-ferrocenium could serve as oxidants to promote an increased rate of methoxylation of the H\u2013Si(111) surface in the dark. Illumination of intrinsic and n-type surfaces resulted in an increased rate of methoxylation, resulting from a positive shift in energy of the electron quasi-Fermi level in the presence of light. The results are described in the context of a kinetic charge transfer formalism that is consistent with the experimentally observed results. This work provides a general framework to describe the kinetics of charge transfer reactions that occur on semiconductor surfaces.
", "doi": "10.7907/Z9FF3QB1", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9991", "collection": "thesis", "collection_id": "9991", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12082016-154933538", "primary_object_url": { "basename": "Small_Molecule_Catalysis_SJIJohnson_Final.pdf", "content": "final", "filesize": 17748756, "license": "other", "mime_type": "application/pdf", "url": "/9991/60/Small_Molecule_Catalysis_SJIJohnson_Final.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Computational Investigation of Small Molecule Catalysis by Cobalt, Rhodium, and Iridium Molecular Catalysts ", "author": [ { "family_name": "Johnson", "given_name": "Samantha Jo Iva", "orcid": "0000-0001-6495-9892", "clpid": "Johnson-Samantha-Jo-Iva" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Faber", "given_name": "Katherine T.", "clpid": "Faber-K-T" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Persson", "given_name": "Petter", "clpid": "Persson-Petter" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_eng" } ], "abstract": "Global energy demands are predicted to increase through 2040. In the spirit of meeting these demands, work focusing on increasing the efficiency of existing energy technologies, as well as improving energy storage is necessary. This work takes a catalytic approach to these challenges, focusing on Co, Rh, and Ir catalysts with pincer and bipyridine ligands. Density functional theory (DFT) can be used in order to gain a deeper understanding of how these catalysts behave. In the realm of improving existing technologies, the mechanism for oxidation of methane to methanol by Phebox Ir (Phebox = bis(oxazolinyl)phenyl) is investigated with a focus on understanding how subtle substitutions to the ligand can help or hinder this reaction. It is shown that in this catalyst, two unwanted intermediates on the potential energy surface (an IrIV state leading to catalyst deactivation and an IrV state leading to over-oxidation) can potentially be avoided by adding trifluoromethyl groups to the ligand. For production of fuels from solar energy, two reactions are studied. Experimentally, CO2 reduction to formate by (POCOP)Ir (POCOP = C6H3-2,6-[OP(tBu)2]2) has been shown to selectively occur at moderate potentials. The mechanism by which this catalyst reduces CO2 is elucidated. In particular, the impressive product selectivity afforded this catalyst for formate over hydrogen production is rooted in kinetics: high barriers for protonation inhibit the creation of H2 adducts. In addition to this, substitutions to the ligand and metal center are investigated to further illuminate the relationship between kinetics and thermodynamics. Hydrogen evolution in Cp*Rh(bpy) (bpy = 2,2'-bipyridine, Cp* = pentamethylcyclopentadienyl) is investigated, centering on unexpected protonation at the Cp* ligand rather than the metal center. This state is on the path for hydrogen evolution in the case of using weak acids, but in the presence of strong acids, the path through the traditional hydride is most likely. Finally, the attachment of these catalysts to electrode surfaces is discussed with the aim of making molecular catalysts a more viable option in industry It is shown that chlorine present in the attachment process enables easy catalyst dissociation from the surface. Several non-halogen options are discussed as replacements. Throughout the thesis two themes emerge: the constant interaction between thermodynamics and kinetics to control mechanistic paths and products, and the ability of small modifications to have huge impacts on catalytic cycles. ", "doi": "10.7907/Z9TD9V9K", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10184", "collection": "thesis", "collection_id": "10184", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182017-225415095", "primary_object_url": { "basename": "Thesis_Ho-Il_Ji_2017_v4_final.pdf", "content": "final", "filesize": 24616947, "license": "other", "mime_type": "application/pdf", "url": "/10184/1/Thesis_Ho-Il_Ji_2017_v4_final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Redox Kinetics of Nonstoichiometric Oxides", "author": [ { "family_name": "Ji", "given_name": "Ho-Il", "orcid": "0000-0002-6194-991X", "clpid": "Ji-Ho-Il" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Cerium oxide (CeO2-\u03b4) and its derivatives are the most attractive materials under consideration for solar-driven thermochemical production of chemical fuels. Understanding the rate-limiting factors in fuel production is essential for maximizing the efficacy of the thermochemical process.
\r\n\r\nThe rate of response of the porous ceria structured with architectural features typical of those employed in solar reactors was measured via electrical conductance relaxation methods. A transition from behavior controlled by material surface reaction kinetics to that controlled by sweep-gas supply rates is observed on increasing temperature, increasing volume specific surface area, and decreasing normalized gas flow rate. The transition behavior is relevant not only for optimal reactor operation and architectural design of material, but also for accurate measurement of material properties.
\r\n\r\nThe redox kinetics of undoped ceria, CeO2-\u03b4 at extreme high temperature (1400 \u00b0C) was investigated using the electrical conductivity relaxation method, and those of 10% Pr doped ceria at low temperature (700 \u00b0C) were done using the mass relaxation method. It was demonstrated under sufficiently high gas flow rates relative to the mass of the oxide, which is required in order to overcome gas phase limitations and access the material kinetic properties. Furthermore, the surface reaction rate constant of undoped ceria, ,kChem, was investigated at high temperature (1400 \u00b0C) in humidified gas atmosphere, in consideration of the operating conditions in thermochemical fuel production system. It was demonstrated that H2O potentially plays a role of oxidants as increasing temperature and/or decreasing oxygen partial pressure; thus in such thermodynamic conditions, pH2O, besides temperature and pO2, needs to be carefully considered in surface reaction study.
\r\n\r\nIn addition to relaxation experiments under small driving force for redox reaction, the kinetics of surface related oxidation reaction under large chemical driving force (large \u0394pO2 change) was investigated by mass relaxation method. Based on the normalized reaction rates of several possible rate determining steps, the relaxation behavior in oxygen concentration for all possible rate determining steps was computed. On the comparison with the experimental results, the most probable rate determining step was suggested (reduction of diatomic oxygen from neutral oxygen molecule to superoxide), and the oxidation kinetics under large driving force was explained.
\r\n", "doi": "10.7907/Z98913W2", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10245", "collection": "thesis", "collection_id": "10245", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012017-152250262", "primary_object_url": { "basename": "VERLAGE_Thesis_final.pdf", "content": "final", "filesize": 26764930, "license": "other", "mime_type": "application/pdf", "url": "/10245/1/VERLAGE_Thesis_final.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "High-Efficiency Solar Fuel Devices: Protection and Light Management Utilizing TiO2", "author": [ { "family_name": "Verlage", "given_name": "Erik A.", "orcid": "0000-0001-5940-0859", "clpid": "Verlage-Erik-A" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "JCAP" }, { "literal": "div_eng" } ], "abstract": "Global climate change coupled with increasing global energy consumption drives the need for renewable and carbon-neutral alternatives to fossil fuels. Photoelectrochemical devices store solar energy in chemical bonds, and have the potential to provide cost-effective fuel for grid-scale energy storage as well as to serve as a feedstock for the production of carbon-neutral transportation fuels. A widely recognized goal is the demonstration of a monolithically-integrated solar-fuels system that is simultaneously efficient, stable, intrinsically safe, and scalably manufacturable. This thesis presents the development of three separate high-efficiency solar fuel devices protected by thin films of amorphous TiO2, and develops light management strategies to increase the performance of these devices.
\r\n\r\nFirst, high-efficiency monolithic cells were designed to perform solar water-splitting and CO2 reduction. These designs are driven by high-quality single-crystalline III-V semiconductors that are unstable when placed in direct contact with aqueous electrolytes but can be protected against corrosion by hole-conducting amorphous films. Experimental fabrication and characterization of this tandem device was realized in the form of a fully-integrated water-splitting prototype with a solar-to-hydrogen efficiency of 10% showing stability for over 80 hours of operation. This was followed by the demonstration of water-splitting and CO2 reduction devices enabled by bipolar membranes, which increased stability and alleviated materials-compatibility constraints by creating a pH difference between the anolyte and catholyte, maintained at steady-state. Finally, universal light management strategies were developed using high-aspect-ratio TiO2 nanocones, resulting in an increase in catalyst loading with ultrahigh broadband transmission.
", "doi": "10.7907/Z9MC8X2P", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:10012", "collection": "thesis", "collection_id": "10012", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01132017-091611769", "primary_object_url": { "basename": "Saadi_Dissertation.pdf", "content": "final", "filesize": 13658760, "license": "other", "mime_type": "application/pdf", "url": "/10012/103/Saadi_Dissertation.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Acid-Stable Electrocatalysts for the Solar Production of Fuels", "author": [ { "family_name": "Saadi", "given_name": "Fadl Hussein", "orcid": "0000-0003-3941-0464", "clpid": "Saadi-Fadl-Hussein" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Soriaga", "given_name": "Manuel", "clpid": "Soriaga-M-P" } ], "local_group": [ { "literal": "JCAP" }, { "literal": "div_eng" } ], "abstract": "Sunlight is one of the few renewable resources that can meet global energy demand. Unfortunately, while solar energy has grown in the past few years, several economic and scientific constraints have hindered mass adoption. One of the main obstacles solar energy faces is the lack of economically competitive storage technologies. Artificial photosynthesis is a potential solution in which solar energy is directly converted into energy dense chemical bonds that can be easily stored and transported.
\r\n\r\nOne impediment facing the commercialization of artificial photosynthesis is the use of expensive and rare precious metals as catalysts. This dissertation focuses on the achievements of the past five years in characterizing novel, earth-abundant, acid-stable hydrogen evolution catalysts. While nickel alloys have long been known as catalysts for the hydrogen evolution reaction in basic media, it has only been in the past decade that earth abundant catalysts that are stable in acidic media have been reported. These discoveries are critically important as the many proposed artificial photosynthetic devices require the use of acidic media.
\r\n\r\nIn this dissertation we examine two families of hydrogen evolution catalysts: transition metal chalcogenides (namely molybdenum and cobalt selenide) as well as transition metal phosphides (cobalt phosphide). In addition to the electrochemical characterization of these catalysts, spectroscopic characterizations were performed in order to carefully examine the chemical compositions of these catalysts before, after and during the hydrogen evolution reaction. This analysis elucidated both chemical, and structural changes that occurred after the catalysts had been subject to the hydrogen evolution reaction conditions.
\r\n\r\nThe final chapter in this thesis delves into the techno-economic realities of energy transportation via different fuels. Due to the strong interest in renewable energy, several future energy transportation scenarios, including 100% grid electrification and widespread installation of hydrogen pipelines, have been proposed. In order to get a fuller understanding of such potential infrastructure alternatives, we report their differing energy transportation costs.
", "doi": "10.7907/Z9QF8QV4", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9233", "collection": "thesis", "collection_id": "9233", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212015-101150451", "type": "thesis", "title": "Phase Diagrams and Defect Thermodynamics to Devise Doping Strategies in Lead Chalcogenide Thermoelectric Materials and its Alloys", "author": [ { "family_name": "Bajaj", "given_name": "Saurabh", "orcid": "0000-0003-0216-9697", "clpid": "Bajaj-Saurabh" } ], "thesis_advisor": [ { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis discusses the application of phase diagrams and the associated thermodynamics to semiconductor materials through theoretical computational calculations. The majority of work is focused on thermoelectric semiconducting materials that enable direct inter-conversion between electrical and thermal energy. First, one of the most efficient thermoelectric material, PbTe, is picked to demonstrate the assessment of unknown phase diagrams by combining two methods - DFT and CALPHAD. Since there had been no previous investigations of defect stability in this material using computations, DFT is used to deduce the stability of various intrinsic point defects, and in turn attribute origins of n- and p-type conductivity to the most stable defects. Then, the calculated defect formation energies are used in the Pb-Te thermodynamic model built using the CALPHAD method to compare the estimated solubility lines and non-stoichiometric range of the PbTe phase with experimental data. Next, another lead chalcogenide, PbSe, is picked to explore the phase stability of the PbSe phase upon the addition of dopants (Br, Cl, I, Na, Sb, Bi, In), which is a common strategy to make thermoelectric materials and devices more efficient. The range of efficiencies and thermoelectric properties as functions of composition and temperature that can be achieved depends on the amount of dopant that can be added without precipitating secondary phases. Also, depending on the system and its phase diagram, there can be more than one way of doping a material. To help detail which method(s) of doping into PbSe will result in maximum dopant solubility, a procedure similar to the above for PbTe is followed by using DFT in combination with Boltzmann statistics to map solvus boundaries of the PbSe phase, but now in the ternary phase space of composition and temperature. This method also helps predict electrical conductivity, n- or p-type, in each region of the phase diagrams that represent different doping methods.
\r\n\r\nLastly, the role of surface energy contributions in changing phase stability at nano-dimensions is explored. The CALPHAD approach is employed to investigate these changes in three systems by calculating their phase diagrams at nano dimensions and comparing them with their bulk counterparts.
", "doi": "10.7907/Z9DF6P6N", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9849", "collection": "thesis", "collection_id": "9849", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06062016-153802648", "type": "thesis", "title": "Classical Force Field Simulations of Biological Processes and Quantum Chemical Computations of Homogeneous Catalysts", "author": [ { "family_name": "Liu", "given_name": "Fan", "orcid": "0000-0001-5650-2809", "clpid": "Liu-Fan" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Computational chemistry methods and tools have enabled studies of biological processes and chemical reactions to get insights from detailed atomic structures and reaction mechanisms. In this thesis, two biological problems are attacked by the classical force fields simulations and two homogeneous catalysis problems are studied by quantum chemical calculations. In all four problems, new insights have been revealed by the computational results.
\r\n\r\nChapter 1 briefly reviews the computational chemistry theories and methods developed and popularized in the past few decades. Chapter 2 addresses the protein-protein interaction problem in the onset of meningitis where E. coli OmpA interacts with Fc\u03b3RI \u03b1-chain (Fc\u03b3RIa) to invade macrophages. Computationally predicted three-dimensional structure of the OmpA-Fc\u03b3RIa complex showed the role of three N-glycans in Fc\u03b3RIa in the interaction. Chapter 3 studies the molecular origin of the bitter aftertaste of a kind of natural sweetener called steviol glycosides. By examining the predicted binding complexes between the human bitter taste receptors 2R4 and 2R14 which could be activated by steviol glycosides, a general activation model is proposed to explain the structure-function relationship and to predict new natural sweeteners with less bitterness. Chapter 4 investigated the reaction mechanisms of methane to methanol conversion by a biomimetic tricopper cluster compound. An unusual exchange-stabilized multiradical state is found to be responsible for the hydrogen abstraction reactivity and a methyl radical rebound mechanism is proposed for methane oxidation. Calculations also show interesting spin crossing during the reaction cycle with high spin state forbidden for methyl rebound. Chapter 5 examines the reaction mechanisms in olefin hydrosilylation by the Pt-based Karstedt\u2019s catalyst. An unexpected rate-determining step of agostic bond dissociation is found in between the elementary reaction steps proposed previously. The regioselectivity of the products are studied. An alternative reaction cycle which is kinetically unflavored is proposed. Oxygen stability is studied.
", "doi": "10.7907/Z94M92J2", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9815", "collection": "thesis", "collection_id": "9815", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312016-081457742", "primary_object_url": { "basename": "Crowley_Jason_2016.pdf", "content": "final", "filesize": 1949076, "license": "other", "mime_type": "application/pdf", "url": "/9815/1/Crowley_Jason_2016.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Resolution of the Band Gap Prediction Problem for Materials Design", "author": [ { "family_name": "Crowley", "given_name": "Jason Michael", "clpid": "Crowley-Jason-Michael" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An important property with any new material is the band gap. In order to design new materials in silico, it is critical to have an accurate and computationally inexpensive tool for predicting band gaps. Standard density functional theory (DFT) methods are computationally efficient, but grossly underestimate band gaps. Hybrid density functionals are known to improve band gap predictions, but the computational cost in the overwhelmingly popular plane-wave basis set codes used for solids is a serious drawback. Exact exchange can be evaluated much more efficiently using localized Gaussian basis functions; however, the most readily available Gaussian basis periodic quantum chemistry code lacked spin-orbit coupling. This seriously limited the range of compounds that can be studies. In this thesis, spin-orbit coupling was implemented in the periodic, Gaussian basis set code CRYSTAL. Using the modified code, band gaps were computed using the B3PW91 hybrid density functional for 70 compounds spanning the entire periodic table and a factor of 500 in band gap (0.014 - 15 eV). To benchmark the quality of the hybrid method, we compared to the rigorous GW many-body perturbation theory method. Surprisingly, the MAD for B3PW91 is about 1.5 times smaller than the MAD for GW. Furthermore, B3PW91 is three to four orders of magnitude faster computationally. We also show that increasing (decreasing) the amount of exact exchange compared to B3PW91 leads to systematic overestimates (underestimates) of band gaps. Finally, we show that the pathological vanishing of the density of states at the Fermi level of a metal cannot be observed in practical calculations of real metals. Thus, we believe that B3PW91 is a practical tool for predicting the band gaps of materials before they are synthesized while being computationally efficient enough for high-throughput applications and represents a solution to the band gap prediction problem for materials design.", "doi": "10.7907/Z9D21VKZ", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9801", "collection": "thesis", "collection_id": "9801", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272016-161721247", "primary_object_url": { "basename": "Shing_Amanda_Thesis_2016.pdf", "content": "final", "filesize": 12770609, "license": "other", "mime_type": "application/pdf", "url": "/9801/1/Shing_Amanda_Thesis_2016.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Development of Zn-IV-Nitride Semiconductor Materials and Devices", "author": [ { "family_name": "Shing", "given_name": "Amanda M.", "clpid": "Shing-Amanda-M" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Faber", "given_name": "Katherine T.", "clpid": "Faber-K-T" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis details explorations of the materials and device fabrication of Zn-IV-Nitride thin-films. Motivation in studying this materials series originates from its analgous properties to the III-Nitride semiconductor materials and its potential applications in photonic devices such as solar cells, light emitting diodes, and optical sensors. Building off of initial fabrication work from Coronel, Lahourcade et al., ZnSnxGe1-xN2 thin-films have shown to be a non-phase-segregating, tunable alloy series and a possible earth-abundant alternative to InxGa1-xN alloys. This thesis discusses further developments in fabrication of ZnSnxGe1-xN2 alloys by three-target co-sputtering and molecular beam epitaxy, and the resulting structural and optoelectronic characterization. Devices from these developed alloys are also highlighted.
\r\n\r\nInitial fabrication was based on the reactive radio-frequency (RF) sputtering technique and was limited to two-target sources and produced nanocrystalline films. Progression to three-target reactive RF co-sputtering for ZnSnxGe1-xN2 (x < 1) alloys is presented, where three-target co-sputtered alloys follow the structural and optoelectronic trends of the initial alloy series. However, three-target co-sputtering further enabled synthesis of alloys having < 10% atomic composition (x < 0.4) of tin, exhibiting non-degenerate doping. The electronic structure of sputtered thin-film surfaces for the alloy series were also characterized by photoelectron spectroscopy to measure their work functions and relative band alignment for device implementation.
\r\n\r\nLow electronic mobilities, degenerate carrier concentrations, and limited photoresponse may stem from the defective and nanocrystalline nature of the sputtered films. To improve crystalline quality, films were grown by molecular beam epitaxy (MBE). MBE ZnSnxGe1-xN2 films on sapphire and GaN were epitaxially grown, overall displaying single-crystalline quality films, higher electronic mobilities, and lower carrier concentrations. Througout experimentation, devices from both sputter deposited and MBE ZnSnxGe1-xN2 alloys films were constructed. Attempts at solid-state and electrochemical devices are described. Devices exhibited some photoresponse, providing a positive outlook for employment of ZnSnxGe1-xN2 alloys in solar cells or photon sensors.
\r\n", "doi": "10.7907/Z94Q7RXJ", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9780", "collection": "thesis", "collection_id": "9780", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262016-230647147", "primary_object_url": { "basename": "Kim_Hyun-Sik_2016_Thesis_Final.pdf", "content": "final", "filesize": 4367145, "license": "other", "mime_type": "application/pdf", "url": "/9780/1/Kim_Hyun-Sik_2016_Thesis_Final.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Thermoelectric Properties of Bismuth Antimony Telluride Alloys", "author": [ { "family_name": "Kim", "given_name": "Hyun-Sik", "orcid": "0000-0001-8934-4042", "clpid": "Kim-Hyun-Sik" } ], "thesis_advisor": [ { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William L.", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Minnich", "given_name": "Austin J.", "clpid": "Minnich-A-J" }, { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Commonly used ozone-depleting refrigerants in refrigerators will be completely phased out in less than 15 years according to the Montreal Protocol. This imminent challenge can be tackled effectively by replacing the current vapor-compression cooling with environmentally sustainable thermoelectric cooling. P-type (Bi0.25Sb0.75)2Te3 alloys have been intensively studied over the past 50 years for cooling applications because of their high thermoelectric performance near room temperature. However, the electronic origin of the high thermoelectric efficiency of (Bi0.25Sb0.75)2Te3 alloys is often understated or ignored completely. In this thesis, the underlying physics of high electronic performance observed in the particular alloy composition, (Bi2Te3).25\u2013(Sb2Te3).75, is investigated. It was demonstrated with two-band transport calculation that the convergence of bands occurred at (Bi2Te3).25\u2013(Sb2Te3).75. A zT improvement of 17 % was also achieved in zone-levelled (Bi0.25Sb.75)2Te3 crystals by controlling their carrier concentration while using the two-band model as a guide. With the optimum electronic efficiency theoretically calculated and achieved experimentally, the thesis moves on to minimize lattice thermal conductivity of (Bi0.25Sb.75)2Te3 for the maximum zT. A new liquid compaction method was devised to produce dense arrays of dislocations in grain boundaries of nanostructured (Bi0.25Sb.75)2Te3. The grain boundary dislocations were found to be highly effective in scattering phonons and a substantial improvement in zT was possible (zT = 1.86 at 320 K). The understanding of phonon scattering by dislocations was in turn applied to phonon scattering at grain boundaries of polycrystalline materials. By demonstrating that the frequency-dependent dislocation scattering can replace the commonly used frequency-independent boundary scattering by Casimir, this thesis suggests that the grain boundary dislocation scattering may be responsible for the mechanism of phonon scattering at grain boundaries. ", "doi": "10.7907/Z9RN35V0", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9759", "collection": "thesis", "collection_id": "9759", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-155624343", "primary_object_url": { "basename": "Chen_David_2016_Caltech_Thesis.pdf", "content": "", "filesize": 9910115, "license": "other", "mime_type": "application/pdf", "url": "/9759/1/Chen_David_2016_Caltech_Thesis.pdf", "version": "v1.0.0" }, "type": "thesis", "title": "Atomic-Level Structure and Deformation in Metallic Glasses", "author": [ { "family_name": "Chen", "given_name": "David Zhaoyue", "orcid": "0000-0001-5732-5015", "clpid": "Chen-David-Zhaoyue" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Metallic glasses (MGs) are a relatively new class of materials discovered in 1960\r\nand lauded for its high strengths and superior elastic properties. Three major obstacles\r\nprevent their widespread use as engineering materials for nanotechnology and\r\nindustry: 1) their lack of plasticity mechanisms for deformation beyond the elastic\r\nlimit, 2) their disordered atomic structure, which prevents effective study of their\r\nstructure-to-property relationships, and 3) their poor glass forming ability, which\r\nlimits bulk metallic glasses to sizes on the order of centimeters. We focused on\r\nunderstanding the first two major challenges by observing the mechanical properties\r\nof nanoscale metallic glasses in order to gain insight into its atomic-level structure\r\nand deformation mechanisms. We found that anomalous stable plastic flow emerges\r\nin room-temperature MGs at the nanoscale in wires as little as ~100 nanometers\r\nwide regardless of fabrication route (ion-irradiated or not). To circumvent experimental\r\nchallenges in characterizing the atomic-level structure, extensive molecular\r\ndynamics simulations were conducted using approximated (embedded atom\r\nmethod) potentials to probe the underlying processes that give rise to plasticity in\r\nnanowires. Simulated results showed that mechanisms of relaxation via the sample\r\nfree surfaces contribute to tensile ductility in these nanowires. Continuing with characterizing\r\nnanoscale properties, we studied the fracture properties of nano-notched\r\nMGnanowires and the compressive response of MG nanolattices at cryogenic (~130\r\nK) temperatures. We learned from these experiments that nanowires are sensitive\r\nto flaws when the (amorphous) microstructure does not contribute stress concentrations,\r\nand that nano-architected structures with MG nanoribbons are brittle at low\r\ntemperatures except when elastic shell buckling mechanisms dominate at low ribbon\r\nthicknesses (~20 nm), which instead gives rise to fully recoverable nanostructures regardless\r\nof temperature. Finally, motivated by understanding structure-to-property\r\nrelationships in MGs, we studied the disordered atomic structure using a combination\r\nof in-situ X-ray tomography and X-ray diffraction in a diamond anvil cell\r\nand molecular dynamics simulations. Synchrotron X-ray experiments showed the\r\nprogression of the atomic-level structure (in momentum space) and macroscale volume\r\nunder increasing hydrostatic pressures. Corresponding simulations provided\r\ninformation on the real space structure, and we found that the samples displayed\r\nfractal scaling (rd ∝ V, d < 3) at short length scales (< ~8 \u00c5), and exhibited a\r\ncrossover to a homogeneous scaling (d = 3) at long length scales. We examined\r\nthis underlying fractal structure of MGs with parallels to percolation clusters and\r\ndiscuss the implications of this structural analogy to MG properties and the glass\r\ntransition phenomenon.", "doi": "10.7907/Z95Q4T2B", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9718", "collection": "thesis", "collection_id": "9718", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05122016-150703449", "type": "thesis", "title": "Investigation of Capacitive Discharge Heating of Metallic Glasses", "author": [ { "family_name": "Kaltenboeck", "given_name": "Georg", "clpid": "Kaltenboeck-Georg" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Faber", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Demetriou", "given_name": "Marios D.", "clpid": "Demetriou-M-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In recent years, the discovery of bulk metallic glasses with exceptional properties has generated much interest. One of their most intriguing features is their capacity for viscous flow above the glass transition temperature. This characteristic allows metallic glasses to be formed like plastics at modest temperatures. However, crystallization of supercooled metallic liquids in the best bulk metallic glass-formers is much more rapid than in most polymers and silicate glass-forming liquids. The short times to crystallization impairs experimentation on and processing of supercooled glass-forming metallic liquids. A technique to rapidly and uniformly heat metallic glasses at rates of 105 to 106 kelvin per second is presented. A capacitive discharge is used to ohmically heat metallic glasses to temperatures in the super cooled liquid region in millisecond time-scales. By heating samples rapidly, the most time-consuming step in experiments on supercooled metallic liquids is reduced orders of magnitude in length. This allows for experimentation on and processing of metallic liquids in temperature ranges that were previously inaccessible because of crystallization.
\r\n\r\nA variety of forming techniques, including injection molding and forging, were coupled with capacitive discharge heating to produce near net-shaped metallic glass parts. In addition, a new forming technique, which combines a magnetic field with the heating current to produce a forming force, was developed. Viscosities were measured in previously inaccessible temperature ranges using parallel plate rheometry combined with capacitive discharge heating. Lastly, a rapid pulse calorimeter was developed with this technique to investigate the thermophysical behavior of metallic glasses at these rapid heating rates.
", "doi": "10.7907/Z9251G5Z", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9718", "collection": "thesis", "collection_id": "9718", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05122016-150703449", "type": "thesis", "title": "Investigation of Capacitive Discharge Heating of Metallic Glasses", "author": [ { "family_name": "Kaltenboeck", "given_name": "Georg", "clpid": "Kaltenboeck-Georg" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Faber", "given_name": "Katherine T.", "orcid": "0000-0001-6585-2536", "clpid": "Faber-K-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Demetriou", "given_name": "Marios D.", "clpid": "Demetriou-M-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In recent years, the discovery of bulk metallic glasses with exceptional properties has generated much interest. One of their most intriguing features is their capacity for viscous flow above the glass transition temperature. This characteristic allows metallic glasses to be formed like plastics at modest temperatures. However, crystallization of supercooled metallic liquids in the best bulk metallic glass-formers is much more rapid than in most polymers and silicate glass-forming liquids. The short times to crystallization impairs experimentation on and processing of supercooled glass-forming metallic liquids. A technique to rapidly and uniformly heat metallic glasses at rates of 105 to 106 kelvin per second is presented. A capacitive discharge is used to ohmically heat metallic glasses to temperatures in the super cooled liquid region in millisecond time-scales. By heating samples rapidly, the most time-consuming step in experiments on supercooled metallic liquids is reduced orders of magnitude in length. This allows for experimentation on and processing of metallic liquids in temperature ranges that were previously inaccessible because of crystallization.
\r\n\r\nA variety of forming techniques, including injection molding and forging, were coupled with capacitive discharge heating to produce near net-shaped metallic glass parts. In addition, a new forming technique, which combines a magnetic field with the heating current to produce a forming force, was developed. Viscosities were measured in previously inaccessible temperature ranges using parallel plate rheometry combined with capacitive discharge heating. Lastly, a rapid pulse calorimeter was developed with this technique to investigate the thermophysical behavior of metallic glasses at these rapid heating rates.
", "doi": "10.7907/Z9251G5Z", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:9681", "collection": "thesis", "collection_id": "9681", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04192016-013400484", "primary_object_url": { "basename": "Tang_Yinglu_2015_thesis_04212016.pdf", "content": "final", "filesize": 6246192, "license": "other", "mime_type": "application/pdf", "url": "/9681/55/Tang_Yinglu_2015_thesis_04212016.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Thermoelectric Skutterudites: Why and How High zT Can Be Achieved", "author": [ { "family_name": "Tang", "given_name": "Yinglu", "clpid": "Tang-Yinglu" } ], "thesis_advisor": [ { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William L.", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Minnich", "given_name": "Austin J.", "clpid": "Minnich-A-J" }, { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Thermoelectric materials have been widely studied over the past few decades due to their ability to convert waste heat into useful electricity. Among various thermoelectric materials, skutterudite distinguishes itself in both space and terrestrial applications with its excellent thermoelectric performance, robust mechanical properties, and thermal stability. The thermoelectric excellence of skutterudites is mostly attributed to the low thermal conductivity due to the addition of filler atoms (R) into the void (one per primitive cell Co4Sb12). Essential though this is to high zT, the importance of the intrinsic electronic structure in skutterudites is often understated or ignored completely. In this thesis, by combining experimental and computational studies, the electronic origin of high thermoelectric performance of CoSb3-based skutterudites is investigated. The high zT was shown to be a direct result of the high valley degeneracy inherent to CoSb3, which is further enhanced by band convergence at high temperatures. This successfully explains why the optimum doping carrier concentration in n-CoSb3 skutterudites is independent on the type of fillers. With the electronic origin of high thermoelectric performance clarified, the thesis moves on to elaborate how to achieve high zT in skutterudite with the aid of phase diagram study. By mapping out the phase regions near the skutterudite phase on the isothermal section of the R-Co-Sb ternary phase diagram, the solubility region of the CoSb3 skutterudite phase can be determined along with the solubility limit of R, both of which are often determined in stable compositions resulting in a synthesis window. The temperature dependence of the filler solubility is also demonstrated experimentally. This overturns the general understanding that the filler solubility is a single value only dependent on the filler type. The temperature dependence of stable compositions enables easy carrier concentration tuning which allows the optimization of thermoelectric performance. High zT values are achieved in single In, Yb, Ce-CoSb3 skutterudites. The methodology applied here are not confined to n-CoSb3, but can be generalized to any other ternary systems.", "doi": "10.7907/Z9TD9VB1", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:8820", "collection": "thesis", "collection_id": "8820", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04132015-220841374", "primary_object_url": { "basename": "Kirkpatrick_A_thesis.pdf", "content": "final", "filesize": 7598765, "license": "other", "mime_type": "application/pdf", "url": "/8820/1/Kirkpatrick_A_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Computational Predictions of G Protein-Coupled Receptor Structures and Binding Sites", "author": [ { "family_name": "Kirkpatrick", "given_name": "Andrea", "orcid": "0000-0002-7212-7946", "clpid": "Kirkpatrick-Andrea" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "G protein-coupled receptors (GPCRs) are the largest family of proteins within the human genome. They consist of seven transmembrane (TM) helices, with a N-terminal region of varying length and structure on the extracellular side, and a C-terminus on the intracellular side. GPCRs are involved in transmitting extracellular signals to cells, and as such are crucial drug targets. Designing pharmaceuticals to target GPCRs is greatly aided by full-atom structural information of the proteins. In particular, the TM region of GPCRs is where small molecule ligands (much more bioavailable than peptide ligands) typically bind to the receptors. In recent years nearly thirty distinct GPCR TM regions have been crystallized. However, there are more than 1,000 GPCRs, leaving the vast majority of GPCRs with limited structural information. Additionally, GPCRs are known to exist in a myriad of conformational states in the body, rendering the static x-ray crystal structures an incomplete reflection of GPCR structures. In order to obtain an ensemble of GPCR structures, we have developed the GEnSeMBLE procedure to rapidly sample a large number of variations of GPCR helix rotations and tilts. The lowest energy GEnSeMBLE structures are then docked to small molecule ligands and optimized. The GPCR family consists of five subfamilies with little to no sequence homology between them: class A, B1, B2, C, and Frizzled/Taste2. Almost all of the GPCR crystal structures have been of class A GPCRs, and much is known about their conserved interactions and binding sites. In this work we particularly focus on class B1 GPCRs, and aim to understand that family\u2019s interactions and binding sites both to small molecules and their native peptide ligands. Specifically, we predict the full atom structure and peptide binding site of the glucagon-like peptide receptor and the TM region and small molecule binding sites for eight other class B1 GPCRs: CALRL, CRFR1, GIPR, GLR, PACR, PTH1R, VIPR1, and VIPR2. Our class B1 work reveals multiple conserved interactions across the B1 subfamily as well as a consistent small molecule binding site centrally located in the TM bundle. Both the interactions and the binding sites are distinct from those seen in the more well-characterized class A GPCRs, and as such our work provides a strong starting point for drug design targeting class B1 proteins. We also predict the full structure of CXCR4 bound to a small molecule, a class A GPCR that was not closely related to any of the class A GPCRs at the time of the work.", "doi": "10.7907/Z9NG4NJG", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8765", "collection": "thesis", "collection_id": "8765", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02042015-031802985", "type": "thesis", "title": "Structure Prediction of G-Protein Coupled Receptors", "author": [ { "family_name": "Cvicek", "given_name": "Vaclav", "clpid": "Cvicek-Vaclav" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Pine", "given_name": "Jerome", "clpid": "Pine-J" }, { "family_name": "Abrol", "given_name": "Ravinder", "clpid": "Abrol-R" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "G-protein coupled receptors (GPCRs) form a large family of proteins and are very important drug targets. They are membrane proteins, which makes computational prediction of their structure challenging. Homology modeling is further complicated by low sequence similarly of the GPCR superfamily.
\r\n\r\nIn this dissertation, we analyze the conserved inter-helical contacts of recently solved crystal structures, and we develop a unified sequence-structural alignment of the GPCR superfamily. We use this method to align 817 human GPCRs, 399 of which are nonolfactory. This alignment can be used to generate high quality homology models for the 817 GPCRs.
\r\n\r\nTo refine the provided GPCR homology models we developed the Trihelix sampling method. We use a multi-scale approach to simplify the problem by treating the transmembrane helices as rigid bodies. In contrast to Monte Carlo structure prediction methods, the Trihelix method does a complete local sampling using discretized coordinates for the transmembrane helices. We validate the method on existing structures and apply it to predict the structure of the lactate receptor, HCAR1. For this receptor, we also build extracellular loops by taking into account constraints from three disulfide bonds. Docking of lactate and 3,5-dihydroxybenzoic acid shows likely involvement of three Arg residues on different transmembrane helices in binding a single ligand molecule.
\r\n\r\nProtein structure prediction relies on accurate force fields. We next present an effort to improve the quality of charge assignment for large atomic models. In particular, we introduce the formalism of the polarizable charge equilibration scheme (PQEQ) and we describe its implementation in the molecular simulation package Lammps. PQEQ allows fast on the fly charge assignment even for reactive force fields.
", "doi": "10.7907/Z9S46PVG", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8655", "collection": "thesis", "collection_id": "8655", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09082014-140216721", "primary_object_url": { "basename": "CKY20140916-updatedversion.pdf", "content": "final", "filesize": 10704397, "license": "other", "mime_type": "application/pdf", "url": "/8655/7/CKY20140916-updatedversion.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "An Exploration of Perovskite Materials for Thermochemical Water Splitting", "author": [ { "family_name": "Yang", "given_name": "Chih-Kai", "clpid": "Yang-Chih-Kai" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Two-step thermochemical water splitting is a promising technology for the hydrogen production of solar energy. This process possesses the advantages of utilizing the full solar spectrum, producing flexible fuels, and requiring no precious metal catalysts. It furthermore temporally separates the oxygen release and hydrogen production steps, eliminating the possibility of O2 and H2 recombination. Ceria, which undergoes non-stoichiometric changes in oxygen content, has been demonstrated as an effective material for solar-driven thermochemical fuel production, but the process requires extremely high temperatures (~ 1600 degrees C), leading to efficiency penalties and challenges in reactor design and construction. Accordingly, the objective of this work is the development of new thermochemical reaction substrate materials which enable operation at lower temperatures and ideally increase fuel productivity and efficiency. Here we explore perovskite systems, specifically La1-xSrxMnO3-\u03b4, La0.8Sr0.2Mn1-yFeyO3-\u03b4, and La0.8Sr0.2Mn1-yAlyO3-\u03b4. The link between the solid-state chemistry, redox properties, hydrogen production, and reaction kinetic limitations will be discussed. This study aims to learn how to design and tailor the good catalytic oxides for solar-driven thermochemical water splitting application.", "doi": "10.7907/Z91834GB", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8962", "collection": "thesis", "collection_id": "8962", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012015-203513094", "primary_object_url": { "basename": "Ho Cheng Tsai PhD-Thesis.pdf", "content": "final", "filesize": 6859056, "license": "other", "mime_type": "application/pdf", "url": "/8962/1/Ho Cheng Tsai PhD-Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Quantum Mechanics Studies of Fuel Cell Catalysts and Proton Conducting Ceramics with Validation by Experiment", "author": [ { "family_name": "Tsai", "given_name": "Ho-Cheng", "clpid": "Tsai-Ho-Cheng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "We carried out quantum mechanics (QM) studies aimed at improving the performance of hydrogen fuel cells. This led to predictions of improved materials, some of which were subsequently validated with experiments by our collaborators.
\r\n\r\nIn part I, the challenge was to find a replacement for the Pt cathode that would lead to improved performance for the Oxygen Reduction Reaction (ORR) while remaining stable under operational conditions and decreasing cost. Our design strategy was to find an alloy with composition Pt3M that would lead to surface segregation such that the top layer would be pure Pt, with the second and subsequent layers richer in M. Under operating conditions we expect the surface to have significant O and/or OH chemisorbed on the surface, and hence we searched for M that would remain segregated under these conditions. Using QM we examined surface segregation for 28 Pt3M alloys, where M is a transition metal. We found that only Pt3Os and Pt3Ir showed significant surface segregation when O and OH are chemisorbed on the catalyst surfaces. This result indicates that Pt3Os and Pt3Ir favor formation of a Pt-skin surface layer structure that would resist the acidic electrolyte corrosion during fuel cell operation environments. We chose to focus on Os because the phase diagram for Pt-Ir indicated that Pt-Ir could not form a homogeneous alloy at lower temperature. To determine the performance for ORR, we used QM to examine all intermediates, reaction pathways, and reaction barriers involved in the processes for which protons from the anode reactions react with O2 to form H2O. These QM calculations used our Poisson-Boltzmann implicit solvation model include the effects of the solvent (water with dielectric constant 78 with pH 7 at 298K). We found that the rate determination step (RDS) was the Oad hydration reaction (Oad + H2Oad -> OHad + OHad) in both cases, but that the barrier for pure Pt of 0.50 eV is reduced to 0.48 eV for Pt3Os, which at 80 degrees C would increase the rate by 218%. We collaborated with the Pu-Wei Wu\u2019s group to carry out experiments, where we found that the dealloying process-treated Pt2Os catalyst showed two-fold higher activity at 25 degrees C than pure Pt and that the alloy had 272% improved stability, validating our theoretical predictions.
\r\n\r\nWe also carried out similar QM studies followed by experimental validation for the Os/Pt core-shell catalyst fabricated by the underpotential deposition (UPD) method. The QM results indicated that the RDS for ORR is a compromise between the OOH formation step (0.37 eV for Pt, 0.23 eV for Pt2ML/Os core-shell) and H2O formation steps (0.32 eV for Pt, 0.22 eV for Pt2ML/Os core-shell). We found that Pt2ML/Os has the highest activity (compared to pure Pt and to the Pt3Os alloy) because the 0.37 eV barrier decreases to 0.23 eV. To understand what aspects of the core shell structure lead to this improved performance, we considered the effect on ORR of compressing the alloy slab to the dimensions of pure Pt. However this had little effect, with the same RDS barrier 0.37 eV. This shows that the ligand effect (the electronic structure modification resulting from the Os substrate) plays a more important role than the strain effect, and is responsible for the improved activity of the core- shell catalyst. Experimental materials characterization proves the core-shell feature of our catalyst. The electrochemical experiment for Pt2ML/Os/C showed 3.5 to 5 times better ORR activity at 0.9V (vs. NHE) in 0.1M HClO4 solution at 25 degrees C as compared to those of commercially available Pt/C. The excellent correlation between experimental half potential and the OH binding energies and RDS barriers validate the feasibility of predicting catalyst activity using QM calculation and a simple Langmuir\u2013Hinshelwood model.
\r\n\r\nIn part II, we used QM calculations to study methane stream reforming on a Ni-alloy catalyst surfaces for solid oxide fuel cell (SOFC) application. SOFC has wide fuel adaptability but the coking and sulfur poisoning will reduce its stability. Experimental results suggested that the Ni4Fe alloy improves both its activity and stability compared to pure Ni. To understand the atomistic origin of this, we carried out QM calculations on surface segregation and found that the most stable configuration for Ni4Fe has a Fe atom distribution of (0%, 50%, 25%, 25%, 0%) starting at the bottom layer. We calculated that the binding of C atoms on the Ni4Fe surface is 142.9 Kcal/mol, which is about 10 Kcal/mol weaker compared to the pure Ni surface. This weaker C binding energy is expected to make coke formation less favorable, explaining why Ni4Fe has better coking resistance. This result confirms the experimental observation. The reaction energy barriers for CHx decomposition and C binding on various alloy surface, Ni4X (X=Fe, Co, Mn, and Mo), showed Ni4Fe, Ni4Co, and Fe4Mn all have better coking resistance than pure Ni, but that only Ni4Fe and Fe4Mn have (slightly) improved activity compared to pure Ni.
\r\n\r\nIn part III, we used QM to examine the proton transport in doped perovskite-ceramics. Here we used a 2x2x2 supercell of perovskite with composition Ba8X7M1(OH)1O23 where X=Ce or Zr and M=Y, Gd, or Dy. Thus in each case a 4+ X is replace by a 3+ M plus a proton on one O. Here we predicted the barriers for proton diffusion allowing both includes intra-octahedron and inter-octahedra proton transfer. Without any restriction, we only observed the inter-octahedra proton transfer with similar energy barrier as previous computational work but 0.2 eV higher than experimental result for Y doped zirconate. For one restriction in our calculations is that the Odonor-Oacceptor atoms were kept at fixed distances, we found that the barrier difference between cerates/zirconates with various dopants are only 0.02~0.03 eV. To fully address performance one would need to examine proton transfer at grain boundaries, which will require larger scale ReaxFF reactive dynamics for systems with millions of atoms. The QM calculations used here will be used to train the ReaxFF force field.
\r\n \r\n", "doi": "10.7907/Z9P55KFW", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8798", "collection": "thesis", "collection_id": "8798", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03202015-113328412", "type": "thesis", "title": "First Principles Based Multiparadigm Modeling of Electronic Structures and Dynamics", "author": [ { "family_name": "Xiao", "given_name": "Hai", "orcid": "0000-0001-9399-1584", "clpid": "Xiao-Hai" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Electronic structures and dynamics are the key to linking the material composition and structure to functionality and performance.
\r\n\r\nAn essential issue in developing semiconductor devices for photovoltaics is to design materials with optimal band gaps and relative positioning of band levels. Approximate DFT methods have been justified to predict band gaps from KS/GKS eigenvalues, but the accuracy is decisively dependent on the choice of XC functionals. We show here for CuInSe2 and CuGaSe2, the parent compounds of the promising CIGS solar cells, conventional LDA and GGA obtain gaps of 0.0-0.01 and 0.02-0.24 eV (versus experimental values of 1.04 and 1.67 eV), while the historically first global hybrid functional, B3PW91, is surprisingly the best, with band gaps of 1.07 and 1.58 eV. Furthermore, we show that for 27 related binary and ternary semiconductors, B3PW91 predicts gaps with a MAD of only 0.09 eV, which is substantially better than all modern hybrid functionals, including B3LYP (MAD of 0.19 eV) and screened hybrid functional HSE06 (MAD of 0.18 eV).
\r\n\r\nThe laboratory performance of CIGS solar cells (> 20% efficiency) makes them promising candidate photovoltaic devices. However, there remains little understanding of how defects at the CIGS/CdS interface affect the band offsets and interfacial energies, and hence the performance of manufactured devices. To determine these relationships, we use the B3PW91 hybrid functional of DFT with the AEP method that we validate to provide very accurate descriptions of both band gaps and band offsets. This confirms the weak dependence of band offsets on surface orientation observed experimentally. We predict that the CBO of perfect CuInSe2/CdS interface is large, 0.79 eV, which would dramatically degrade performance. Moreover we show that band gap widening induced by Ga adjusts only the VBO, and we find that Cd impurities do not significantly affect the CBO. Thus we show that Cu vacancies at the interface play the key role in enabling the tunability of CBO. We predict that Na further improves the CBO through electrostatically elevating the valence levels to decrease the CBO, explaining the observed essential role of Na for high performance. Moreover we find that K leads to a dramatic decrease in the CBO to 0.05 eV, much better than Na. We suggest that the efficiency of CIGS devices might be improved substantially by tuning the ratio of Na to K, with the improved phase stability of Na balancing phase instability from K. All these defects reduce interfacial stability slightly, but not significantly.
\r\n\r\nA number of exotic structures have been formed through high pressure chemistry, but applications have been hindered by difficulties in recovering the high pressure phase to ambient conditions (i.e., one atmosphere and room temperature). Here we use dispersion-corrected DFT (PBE-ulg flavor) to predict that above 60 GPa the most stable form of N2O (the laughing gas in its molecular form) is a 1D polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03-0.10 eV/molecular unit less stable. Upon relaxation to ambient conditions both polymers relax below 14 GPa to the same stable non-planar trans-polymer, accompanied by possible electronic structure transitions. The predicted phonon spectrum and dissociation kinetics validate the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a new type of conducting polymer with all-nitrogen chains and as a high-energy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions.
\r\n\r\nModeling non-adiabatic electron dynamics has been a long-standing challenge for computational chemistry and materials science, and the eFF method presents a cost-efficient alternative. However, due to the deficiency of FSG representation, eFF is limited to low-Z elements with electrons of predominant s-character. To overcome this, we introduce a formal set of ECP extensions that enable accurate description of p-block elements. The extensions consist of a model representing the core electrons with the nucleus as a single pseudo particle represented by FSG, interacting with valence electrons through ECPs. We demonstrate and validate the ECP extensions for complex bonding structures, geometries, and energetics of systems with p-block character (C, O, Al, Si) and apply them to study materials under extreme mechanical loading conditions.
\r\n\r\nDespite its success, the eFF framework has some limitations, originated from both the design of Pauli potentials and the FSG representation. To overcome these, we develop a new framework of two-level hierarchy that is a more rigorous and accurate successor to the eFF method. The fundamental level, GHA-QM, is based on a new set of Pauli potentials that renders exact QM level of accuracy for any FSG represented electron systems. To achieve this, we start with using exactly derived energy expressions for the same spin electron pair, and fitting a simple functional form, inspired by DFT, against open singlet electron pair curves (H2 systems). Symmetric and asymmetric scaling factors are then introduced at this level to recover the QM total energies of multiple electron pair systems from the sum of local interactions. To complement the imperfect FSG representation, the AMPERE extension is implemented, and aims at embedding the interactions associated with both the cusp condition and explicit nodal structures. The whole GHA-QM+AMPERE framework is tested on H element, and the preliminary results are promising.
", "doi": "10.7907/Z94747T1", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8896", "collection": "thesis", "collection_id": "8896", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282015-121920930", "primary_object_url": { "basename": "PhDthesis_final_Chenguang Ji_05182015.pdf", "content": "final", "filesize": 3357230, "license": "other", "mime_type": "application/pdf", "url": "/8896/1/PhDthesis_final_Chenguang Ji_05182015.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Design of Antenna-Coupled Lumped-Element Titanium Nitride KIDs for LongWavelength Multi-Band Continuum Imaging", "author": [ { "family_name": "Ji", "given_name": "Chenguang", "clpid": "Ji-Chenguang" } ], "thesis_advisor": [ { "family_name": "Golwala", "given_name": "Sunil", "clpid": "Golwala-S-R" } ], "thesis_committee": [ { "family_name": "Golwala", "given_name": "Sunil", "clpid": "Golwala-S-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William L.", "clpid": "Johnson-W-L" }, { "family_name": "Rutledge", "given_name": "David B.", "clpid": "Rutledge-D-B" }, { "family_name": "Zmuidzinas", "given_name": "Jonas", "clpid": "Zmuidzinas-J" } ], "local_group": [ { "literal": "Astronomy Department" }, { "literal": "div_eng" } ], "abstract": "Many applications in cosmology and astrophysics at millimeter wavelengths including CMB polarization, studies of galaxy clusters using the Sunyaev-Zeldovich effect (SZE), and studies of star formation at high redshift and in our local universe and our galaxy, require large-format arrays of millimeter-wave detectors. Feedhorn and phased-array antenna architectures for receiving mm-wave light present numerous advantages for control of systematics, for simultaneous coverage of both polarizations and/or multiple spectral bands, and for preserving the coherent nature of the incoming light. This enables the application of many traditional \"RF\" structures such as hybrids, switches,\r\nand lumped-element or microstrip band-defining filters.
\r\n\r\nSimultaneously, kinetic inductance detectors (KIDs) using high-resistivity materials like titanium nitride are an attractive sensor option for large-format arrays because they are highly multiplexable and because they can have sensitivities reaching the condition of background-limited detection. A\r\nKID is a LC resonator. Its inductance includes the geometric inductance and kinetic inductance of the inductor in the superconducting phase. A photon absorbed by the superconductor breaks a Cooper pair into normal-state electrons and perturbs its kinetic inductance, rendering it a detector\r\nof light. The responsivity of KID is given by the fractional frequency shift of the LC resonator per unit optical power.
\r\n\r\nHowever, coupling these types of optical reception elements to KIDs is a challenge because of the impedance mismatch between the microstrip transmission line exiting these architectures and the high resistivity of titanium nitride. Mitigating direct absorption of light through free space coupling to the inductor of KID is another challenge. We present a detailed titanium nitride KID\r\ndesign that addresses these challenges. The KID inductor is capacitively coupled to the microstrip in such a way as to form a lossy termination without creating an impedance mismatch. A parallel plate capacitor design mitigates direct absorption, uses hydrogenated amorphous silicon, and yields acceptable noise. We show that the optimized design can yield expected sensitivities very close to\r\nthe fundamental limit for a long wavelength imager (LWCam) that covers six spectral bands from 90 to 400 GHz for SZE studies.
\r\n\r\nExcess phase (frequency) noise has been observed in KID and is very likely caused by two-level systems (TLS) in dielectric materials. The TLS hypothesis is supported by the measured dependence of the noise on resonator internal power and temperature. However, there is still a lack of a unified microscopic theory which can quantitatively model the properties of the TLS noise. In this thesis we\r\nderive the noise power spectral density due to the coupling of TLS with phonon bath based on an existing model and compare the theoretical predictions about power and temperature dependences with experimental data. We discuss the limitation of such a model and propose the direction for future study.
", "doi": "10.7907/Z9W66HQ7", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8705", "collection": "thesis", "collection_id": "8705", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10262014-094813435", "primary_object_url": { "basename": "Fathima_Kameel_2015_Thesis1.pdf", "content": "final", "filesize": 3011282, "license": "other", "mime_type": "application/pdf", "url": "/8705/1/Fathima_Kameel_2015_Thesis1.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Oxidation of Volatile Organic Compounds in Aqueous Solution and at the Air-water Interface of Aqueous Microdroplets", "author": [ { "family_name": "Kameel", "given_name": "Fathima Rifkha", "clpid": "Kameel-Fathima-Rifkha" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Wennberg", "given_name": "Paul O.", "clpid": "Wennberg-P-O" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Isoprene (ISO),the most abundant non-methane VOC, is the major contributor to secondary organic aerosols (SOA) formation. The mechanisms involved in such transformation, however, are not fully understood. Current mechanisms, which are based on the oxidation of ISO in the gas-phase, underestimate SOA yields. The heightened awareness that ISO is only partially processed in the gas-phase has turned attention to heterogeneous processes as alternative pathways toward SOA.
\r\n\r\nDuring my research project, I investigated the photochemical oxidation of isoprene in bulk water. Below, I will report on the \u03bb > 305 nm photolysis of H2O2 in dilute ISO solutions. This process yields C10H15OH species as primary products, whose formation both requires and is inhibited by O2. Several isomers of C10H15OH were resolved by reverse-phase high-performance liquid chromatography and detected as MH+ (m/z = 153) and MH+-18 (m/z = 135) signals by electrospray ionization mass spectrometry. This finding is consistent with the addition of ·OH to ISO, followed by HO-ISO· reactions with ISO (in competition with O2) leading to second generation HO(ISO)2· radicals that terminate as C10H15OH via \u03b2-H abstraction by O2.
\r\n\r\nIt is not generally realized that chemistry on the surface of water cannot be deduced, extrapolated or translated to those in bulk gas and liquid phases. The water density drops a thousand-fold within a few Angstroms through the gas-liquid interfacial region and therefore hydrophobic VOCs such as ISO will likely remain in these relatively 'dry' interfacial water layers rather than proceed into bulk water. In previous experiments from our laboratory, it was found that gas-phase olefins can be protonated on the surface of pH < 4 water. This phenomenon increases the residence time of gases at the interface, an event that makes them increasingly susceptible to interaction with gaseous atmospheric oxidants such as ozone and hydroxyl radicals.
\r\n\r\nIn order to test this hypothesis, I carried out experiments in which ISO(g) collides with the surface of aqueous microdroplets of various compositions. Herein I report that ISO(g) is oxidized into soluble species via Fenton chemistry on the surface of aqueous Fe(II)Cl2 solutions simultaneously exposed to H2O2(g). Monomer and oligomeric species (ISO)1-8H+ were detected via online electrospray ionization mass spectrometry (ESI-MS) on the surface of pH ~ 2 water, and were then oxidized into a suite of products whose combined yields exceed ~ 5% of (ISO)1-8H+. MS/MS analysis revealed that products mainly consisted of alcohols, ketones, epoxides and acids. Our experiments demonstrated that olefins in ambient air may be oxidized upon impact on the surface of Fe-containing aqueous acidic media, such as those of typical to tropospheric aerosols.
\r\n\r\nRelated experiments involving the reaction of ISO(g) with ·OH radicals from the photolysis of dissolved H2O2 were also carried out to test the surface oxidation of ISO(g) by photolyzing H2O2(aq) at 266 nm at various pH. The products were analyzed via online electrospray ionization mass spectrometry. Similar to our Fenton experiments, we detected (ISO)1-7H+ at pH < 4, and new m/z+ = 271 and m/z- = 76 products at pH > 5.
\r\n", "doi": "10.7907/Z9MP5174", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8721", "collection": "thesis", "collection_id": "8721", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11092014-074023936", "primary_object_url": { "basename": "Thesis_Hong.pdf", "content": "final", "filesize": 19969471, "license": "other", "mime_type": "application/pdf", "url": "/8721/1/Thesis_Hong.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Methods for Melting Temperature Calculation", "author": [ { "family_name": "Hong", "given_name": "Qi-Jun", "clpid": "Hong-Qi-Jun" } ], "thesis_advisor": [ { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Melting temperature calculation has important applications in the theoretical study of phase diagrams and computational materials screenings. In this thesis, we present two new methods, i.e., the improved Widom's particle insertion method and the small-cell coexistence method, which we developed in order to capture melting temperatures both accurately and quickly.
\r\n\r\nWe propose a scheme that drastically improves the efficiency of Widom's particle insertion method by efficiently sampling cavities while calculating the integrals providing the chemical potentials of a physical system. This idea enables us to calculate chemical potentials of liquids directly from first-principles without the help of any reference system, which is necessary in the commonly used thermodynamic integration method. As an example, we apply our scheme, combined with the density functional formalism, to the calculation of the chemical potential of liquid copper. The calculated chemical potential is further used to locate the melting temperature. The calculated results closely agree with experiments.
\r\n\r\nWe propose the small-cell coexistence method based on the statistical analysis of small-size coexistence MD simulations. It eliminates the risk of a metastable superheated solid in the fast-heating method, while also significantly reducing the computer cost relative to the traditional large-scale coexistence method. Using empirical potentials, we validate the method and systematically study the finite-size effect on the calculated melting points. The method converges to the exact result in the limit of a large system size. An accuracy within 100 K in melting temperature is usually achieved when the simulation contains more than 100 atoms. DFT examples of Tantalum, high-pressure Sodium, and ionic material NaCl are shown to demonstrate the accuracy and flexibility of the method in its practical applications. The method serves as a promising approach for large-scale automated material screening in which the melting temperature is a design criterion.
\r\n\r\nWe present in detail two examples of refractory materials. First, we demonstrate how key material properties that provide guidance in the design of refractory materials can be accurately determined via ab initio thermodynamic calculations in conjunction with experimental techniques based on synchrotron X-ray diffraction and thermal analysis under laser-heated aerodynamic levitation. The properties considered include melting point, heat of fusion, heat capacity, thermal expansion coefficients, thermal stability, and sublattice disordering, as illustrated in a motivating example of lanthanum zirconate (La2Zr2O7). The close agreement with experiment in the known but structurally complex compound La2Zr2O7 provides good indication that the computation methods described can be used within a computational screening framework to identify novel refractory materials. Second, we report an extensive investigation into the melting temperatures of the Hf-C and Hf-Ta-C systems using ab initio calculations. With melting points above 4000 K, hafnium carbide (HfC) and tantalum carbide (TaC) are among the most refractory binary compounds known to date. Their mixture, with a general formula TaxHf1-xCy, is known to have a melting point of 4215 K at the composition Ta4HfC5, which has long been considered as the highest melting temperature for any solid. Very few measurements of melting point in tantalum and hafnium carbides have been documented, because of the obvious experimental difficulties at extreme temperatures. The investigation lets us identify three major chemical factors that contribute to the high melting temperatures. Based on these three factors, we propose and explore a new class of materials, which, according to our ab initio calculations, may possess even higher melting temperatures than Ta-Hf-C. This example also demonstrates the feasibility of materials screening and discovery via ab initio calculations for the optimization of \"higher-level\" properties whose determination requires extensive sampling of atomic configuration space.
\r\n", "doi": "10.7907/Z98C9T6H", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8727", "collection": "thesis", "collection_id": "8727", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05012015-161434189", "type": "thesis", "title": "Dendrites Inhibition in Rechargeable Lithium Metal Batteries", "author": [ { "family_name": "Aryanfar", "given_name": "Asghar", "orcid": "0000-0002-8890-077X", "clpid": "Aryanfar-Asghar" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Andrade", "given_name": "Jose E.", "clpid": "Andrade-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Minnich", "given_name": "Austin J.", "clpid": "Minnich-A-J" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The specific high energy and power capacities of rechargeable lithium metal (Li0) batteries are ideally suited to portable devices and are valuable as storage units for intermittent renewable energy sources. Lithium, the lightest and most electropositive metal, would be the optimal anode material for rechargeable batteries if it were not for the fact that such devices fail unexpectedly by short-circuiting via the dendrites that grow across electrodes upon recharging. This phenomenon poses a major safety issue because it triggers a series of adverse events that start with overheating, potentially followed by the thermal decomposition and ultimately the ignition of the organic solvents used in such devices.
\r\n\r\nIn this thesis, we developed experimental platform for monitoring and quantifying the dendrite populations grown in a Li battery prototype upon charging under various conditions. We explored the effects of pulse charging in the kHz range and temperature on dendrite growth, and also on loss capacity into detached \u201cdead\u201d lithium particles.
\r\n\r\nSimultaneously, we developed a computational framework for understanding the dynamics of dendrite propagation. The coarse-grained Monte Carlo model assisted us in the interpretation of pulsing experiments, whereas MD calculations provided insights into the mechanism of dendrites thermal relaxation. We also developed a computational framework for measuring the dead lithium crystals from the experimental images.
\r\n", "doi": "10.7907/Z9ZK5DMP", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8876", "collection": "thesis", "collection_id": "8876", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05212015-155730829", "primary_object_url": { "basename": "Merged Revised.pdf", "content": "final", "filesize": 4223072, "license": "other", "mime_type": "application/pdf", "url": "/8876/1/Merged Revised.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Synthesis, Oxidation and Photophysics of Perfluoroborated Tetrakis(pyrophosphito)diplatinate (II) and Density Functional Theory (DFT) Study of Electrochemical CO2 Reduction by Mn Catalysts", "author": [ { "family_name": "Lam", "given_name": "Yan Choi", "orcid": "0000-0001-7809-4471", "clpid": "Lam-Yan-Choi" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Labinger", "given_name": "Jay A.", "clpid": "Labinger-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In the first part of this thesis (Chapters I and II), the synthesis, characterization, reactivity and photophysics of per(difluoroborated) tetrakis(pyrophosphito)diplatinate(II) (Pt(POPBF2)) are discussed. Pt(POP-BF2) was obtained by reaction of [Pt2(POP)4]4- with neat boron trifluoride diethyl etherate (BF3\u00b7Et2O). While Pt(POP-BF2) and [Pt2(POP)4]4- have similar structures and absorption spectra, they differ in significant ways. Firstly, as discussed in Chapter I, the former is less susceptible to oxidation, as evidenced by the reversibility of its oxidation by I2. Secondly, while the first excited triplet states (T1) of both Pt(POP-BF2) and [Pt2(POP)4]4- exhibit long lifetimes (ca. 0.01 ms at room temperature) and substantial zero-field splitting (40 cm-1), Pt(POP-BF2) also has a remarkably long-lived (1.6 ns at room temperature) singlet excited state (S1), indicating slow intersystem crossing (ISC). Fluorescence lifetime and quantum yield (QY) of Pt(POP-BF2) were measured over a range of temperatures, providing insight into the slow ISC process. The remarkable spectroscopic and photophysical properties of Pt(POP-BF2), both in solution and as a microcrystalline powder, form the theme of Chapter II.
\r\n\r\nIn the second part of the thesis (Chapters III and IV), the electrochemical reduction of CO2 to CO by [(L)Mn(CO)3]- catalysts is investigated using density functional theory (DFT). As discussed in Chapter III, the turnover frequency (TOF)-limiting step is the dehydroxylation of [(bpy)Mn(CO)3(CO2H)]0/- (bpy = bipyridine) by trifluoroethanol (TFEH) to form [(bpy)Mn(CO)4]+/0. Because the dehydroxylation of [(bpy)Mn(CO)3(CO2H)]- is faster, maximum TOF (TOFmax) is achieved at potentials sufficient to completely reduce [(bpy)Mn(CO)3(CO2H)]0 to [(bpy)Mn(CO)3(CO2H)]-. Substitution of bipyridine with bipyrimidine reduces the overpotential needed, but at the expense of TOFmax. In Chapter IV, the decoration of the bipyrimidine ligand with a pendant alcohol is discussed as a strategy to increase CO2 reduction activity. Our calculations predict that the pendant alcohol acts in concert with an external TFEH molecule, the latter acidifying the former, resulting in a ~ 80,000-fold improvement in the rate of TOF-limiting dehydroxylation of [(L)Mn(CO)3(CO2H)]-.
\r\n\r\nAn interesting strategy for the co-upgrading of light olefins and alkanes into heavier alkanes is the subject of Appendix B. The proposed scheme involves dimerization of the light olefin, operating in tandem with transfer hydrogenation between the olefin dimer and the light alkane. The work presented therein involved a Ta olefin dimerization catalyst and a silica-supported Ir transfer hydrogenation catalyst. Olefin dimer was formed under reaction conditions; however, this did not undergo transfer hydrogenation with the light alkane. A significant challenge is that the Ta catalyst selectively produces highly branched dimers, which are unable to undergo transfer hydrogenation.
", "doi": "10.7907/Z94J0C2D", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:9004", "collection": "thesis", "collection_id": "9004", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06052015-164458210", "primary_object_url": { "basename": "PrinehaNarang-Thesis.pdf", "content": "updated", "filesize": 19829149, "license": "other", "mime_type": "application/pdf", "url": "/9004/9/PrinehaNarang-Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Light-Matter Interactions in Semiconductors and Metals: From Nitride Optoelectronics to Quantum Plasmonics", "author": [ { "family_name": "Narang", "given_name": "Prineha", "orcid": "0000-0003-3956-4594", "clpid": "Narang-Prineha" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Refael", "given_name": "Gil", "clpid": "Refael-G" }, { "family_name": "Schwab", "given_name": "Keith C.", "clpid": "Schwab-K-C" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "JCAP" }, { "literal": "div_eng" } ], "abstract": "This thesis puts forth a theory-directed approach coupled with spectroscopy aimed at the discovery and understanding of light-matter interactions in semiconductors and metals.
\r\n\r\nThe first part of the thesis presents the discovery and development of Zn-IV nitride materials.The commercial prominence in the optoelectronics industry of tunable semiconductor alloy materials based on nitride semiconductor devices, specifically InGaN, motivates the search for earth-abundant alternatives for use in efficient, high-quality optoelectronic devices. II-IV-N2 compounds, which are closely related to the wurtzite-structured III-N semiconductors, have similar electronic and optical properties to InGaN namely direct band gaps, high quantum efficiencies and large optical absorption coefficients. The choice of different group II and group IV elements provides chemical diversity that can be exploited to tune the structural and electronic properties through the series of alloys. The first theoretical and experimental investigation of the ZnSnxGe1\u2212xN2 series as a replacement for III-nitrides is discussed here.
\r\n\r\nThe second half of the thesis shows ab\u2212initio calculations for surface plasmons and plasmonic hot carrier dynamics. Surface plasmons, electromagnetic modes confined to the surface of a conductor-dielectric interface, have sparked renewed interest because of their quantum nature and their broad range of applications. The decay of surface plasmons is usually a detriment in the field of plasmonics, but the possibility to capture the energy normally lost to heat would open new opportunities in photon sensors, energy conversion devices and switching. A theoretical understanding of plasmon-driven hot carrier generation and relaxation dynamics in the ultrafast regime is presented here. Additionally calculations for plasmon-mediated upconversion as well as an energy-dependent transport model for these non-equilibrium carriers are shown.
\r\n\r\nFinally, this thesis gives an outlook on the potential of non-equilibrium phenomena in metals and semiconductors for future light-based technologies.
", "doi": "10.7907/Z9513W4S", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8841", "collection": "thesis", "collection_id": "8841", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04302015-143917971", "primary_object_url": { "basename": "zachary_aitken_2015_thesis.pdf", "content": "final", "filesize": 3688241, "license": "other", "mime_type": "application/pdf", "url": "/8841/1/zachary_aitken_2015_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Effect of Microstructural Interfaces on the Mechanical Response of Crystalline Metallic Materials", "author": [ { "family_name": "Aitken", "given_name": "Zachary Howard", "clpid": "Aitken-Zachary-Howard" } ], "thesis_advisor": [ { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "thesis_committee": [ { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Kochmann", "given_name": "Dennis M.", "clpid": "Kochmann-D-M" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" } ], "local_group": [ { "literal": "Kavli Nanoscience Institute" }, { "literal": "div_eng" } ], "abstract": "Advances in nano-scale mechanical testing have brought about progress in the understanding of physical phenomena in materials and a measure of control in the fabrication of novel materials. In contrast to bulk materials that display size-invariant mechanical properties, sub-micron metallic samples show a critical dependence on sample size. The strength of nano-scale single crystalline metals is well-described by a power-law function, \u03c3\u03b1D-n, where D is a critical sample size and n is a experimentally-fit positive exponent. This relationship is attributed to source-driven plasticity and demonstrates a strengthening as the decreasing sample size begins to limit the size and number of dislocation sources. A full understanding of this size-dependence is complicated by the presence of microstructural features such as interfaces that can compete with the dominant dislocation-based deformation mechanisms. In this thesis, the effects of microstructural features such as grain boundaries and anisotropic crystallinity on nano-scale metals are investigated through uniaxial compression testing. We find that nano-sized Cu covered by a hard coating displays a Bauschinger effect and the emergence of this behavior can be explained through a simple dislocation-based analytic model. Al nano-pillars containing a single vertically-oriented coincident site lattice grain boundary are found to show similar deformation to single-crystalline nano-pillars with slip traces passing through the grain boundary. With increasing tilt angle of the grain boundary from the pillar axis, we observe a transition from dislocation-dominated deformation to grain boundary sliding. Crystallites are observed to shear along the grain boundary and molecular dynamics simulations reveal a mechanism of atomic migration that accommodates boundary sliding. We conclude with an analysis of the effects of inherent crystal anisotropy and alloying on the mechanical behavior of the Mg alloy, AZ31. Through comparison to pure Mg, we show that the size effect dominates the strength of samples below 10 \u03bcm, that differences in the size effect between hexagonal slip systems is due to the inherent crystal anisotropy, suggesting that the fundamental mechanism of the size effect in these slip systems is the same.", "doi": "10.7907/Z9C24TCP", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8625", "collection": "thesis", "collection_id": "8625", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07312014-164509193", "primary_object_url": { "basename": "Kangwoo Cho_2015_thesis_entire.pdf", "content": "final", "filesize": 5122341, "license": "other", "mime_type": "application/pdf", "url": "/8625/33/Kangwoo Cho_2015_thesis_entire.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Wastewater Electrolysis Cell for Environmental Pollutants Degradation and Molecular Hydrogen Generation\r ", "author": [ { "family_name": "Cho", "given_name": "Kangwoo", "orcid": "0000-0002-1819-7687", "clpid": "Cho-Kangwoo" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Seinfeld", "given_name": "John H.", "clpid": "Seinfeld-J-H" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "This study proposes a wastewater electrolysis cell (WEC) for on-site treatment of human waste coupled with decentralized molecular H2 production. The core of the WEC includes mixed metal oxides anodes functionalized with bismuth doped TiO2 (BiOx/TiO2). The BiOx/TiO2 anode shows reliable electro-catalytic activity to oxidize Cl- to reactive chlorine species (RCS), which degrades environmental pollutants including chemical oxygen demand (COD), protein, NH4+, urea, and total coliforms. The WEC experiments for treatment of various kinds of synthetic and real wastewater demonstrate sufficient water quality of effluent for reuse for toilet flushing and environmental purposes. Cathodic reduction of water and proton on stainless steel cathodes produced molecular H2 with moderate levels of current and energy efficiency. This thesis presents a comprehensive environmental analysis together with kinetic models to provide an in-depth understanding of reaction pathways mediated by the RCS and the effects of key operating parameters. The latter part of this thesis is dedicated to bilayer hetero-junction anodes which show enhanced generation efficiency of RCS and long-term stability.
\r\n\r\nChapter 2 describes the reaction pathway and kinetics of urea degradation mediated by electrochemically generated RCS. The urea oxidation involves chloramines and chlorinated urea as reaction intermediates, for which the mass/charge balance analysis reveals that N2 and CO2 are the primary products. Chapter 3 investigates direct-current and photovoltaic powered WEC for domestic wastewater treatment, while Chapter 4 demonstrates the feasibility of the WEC to treat model septic tank effluents. The results in Chapter 2 and 3 corroborate the active roles of chlorine radicals (Cl\u2022/Cl2-\u2022) based on iR-compensated anodic potential (thermodynamic basis) and enhanced pseudo-first-order rate constants (kinetic basis). The effects of operating parameters (anodic potential and [Cl-] in Chapter 3; influent dilution and anaerobic pretreatment in Chapter 4) on the rate and current/energy efficiency of pollutants degradation and H2 production are thoroughly discussed based on robust kinetic models. Chapter 5 reports the generation of RCS on Ir0.7Ta0.3Oy/BixTi1-xOz hetero-junction anodes with enhanced rate, current efficiency, and long-term stability compared to the Ir0.7Ta0.3Oy anode. The effects of surficial Bi concentration are interrogated, focusing on relative distributions between surface-bound hydroxyl radical and higher oxide.
\r\n", "doi": "10.7907/Z9DZ0676", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8826", "collection": "thesis", "collection_id": "8826", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04212015-084744168", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 2536526, "license": "other", "mime_type": "application/pdf", "url": "/8826/1/Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Development and Application of Embedding Methods for the Simulation of Large Chemical Systems", "author": [ { "family_name": "Barnes", "given_name": "Taylor Arnold", "clpid": "Barnes-Taylor-Arnold" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The high computational cost of correlated wavefunction theory (WFT) calculations has motivated the development of numerous methods to partition the description of large chemical systems into smaller subsystem calculations. For example, WFT-in-DFT embedding methods facilitate the partitioning of a system into two subsystems: a subsystem A that is treated using an accurate WFT method, and a subsystem B that is treated using a more efficient Kohn-Sham density functional theory (KS-DFT) method. Representation of the interactions between subsystems is non-trivial, and often requires the use of approximate kinetic energy functionals or computationally challenging optimized effective potential calculations; however, it has recently been shown that these challenges can be eliminated through the use of a projection operator. This dissertation describes the development and application of embedding methods that enable accurate and efficient calculation of the properties of large chemical systems.
\r\n\r\nChapter 1 introduces a method for efficiently performing projection-based WFT-in-DFT embedding calculations on large systems. This is accomplished by using a truncated basis set representation of the subsystem A wavefunction. We show that naive truncation of the basis set associated with subsystem A can lead to large numerical artifacts, and present an approach for systematically controlling these artifacts.
\r\n\r\nChapter 2 describes the application of the projection-based embedding method to investigate the oxidative stability of lithium-ion batteries. We study the oxidation potentials of mixtures of ethylene carbonate (EC) and dimethyl carbonate (DMC) by using the projection-based embedding method to calculate the vertical ionization energy (IE) of individual molecules at the CCSD(T) level of theory, while explicitly accounting for the solvent using DFT. Interestingly, we reveal that large contributions to the solvation properties of DMC originate from quadrupolar interactions, resulting in a much larger solvent reorganization energy than that predicted using simple dielectric continuum models. Demonstration that the solvation properties of EC and DMC are governed by fundamentally different intermolecular interactions provides insight into key aspects of lithium-ion batteries, with relevance to electrolyte decomposition processes, solid-electrolyte interphase formation, and the local solvation environment of lithium cations.
\r\n", "doi": "10.7907/Z9KK98P1", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8451", "collection": "thesis", "collection_id": "8451", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302014-220000101", "type": "thesis", "title": "Density Functional Theory Embedding for Correlated Wavefunctions", "author": [ { "family_name": "Goodpaster", "given_name": "Jason Daniel", "clpid": "Goodpaster-Jason-Daniel" } ], "thesis_advisor": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" } ], "thesis_committee": [ { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Methods that exploit the intrinsic locality of molecular interactions show significant promise in making tractable the electronic structure calculation of large-scale systems. In particular, embedded density functional theory (e-DFT) offers a formally exact approach to electronic structure calculations in which the interactions between subsystems are evaluated in terms of their electronic density. In the following dissertation, methodological advances of embedded density functional theory are described, numerically tested, and applied to real chemical systems.
\r\n\r\nFirst, we describe an e-DFT protocol in which the non-additive kinetic energy component of the embedding potential is treated exactly. Then, we present a general implementation of the exact calculation of the non-additive kinetic potential (NAKP) and apply it to molecular systems. We demonstrate that the implementation using the exact NAKP is in excellent agreement with reference Kohn-Sham calculations, whereas the approximate functionals lead to qualitative failures in the calculated energies and equilibrium structures.
\r\n\r\nNext, we introduce density-embedding techniques to enable the accurate and stable calculation of correlated wavefunction (CW) in complex environments. Embedding potentials calculated using e-DFT introduce the effect of the environment on a subsystem for CW calculations (WFT-in-DFT). We demonstrate that WFT-in-DFT calculations are in good agreement with CW calculations performed on the full complex.
\r\n\r\nWe significantly improve the numerics of the algorithm by enforcing orthogonality between subsystems by introduction of a projection operator. Utilizing the projection-based embedding scheme, we rigorously analyze the sources of error in quantum embedding calculations in which an active subsystem is treated using CWs, and the remainder using density functional theory. We show that the embedding potential felt by the electrons in the active subsystem makes only a small contribution to the error of the method, whereas the error in the nonadditive exchange-correlation energy dominates. We develop an algorithm which corrects this term and demonstrate the accuracy of this corrected embedding scheme.
", "doi": "10.7907/RX3S-GH65", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8234", "collection": "thesis", "collection_id": "8234", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05142014-120832065", "primary_object_url": { "basename": "Thesis_Tian - v1.pdf", "content": "final", "filesize": 4393060, "license": "other", "mime_type": "application/pdf", "url": "/8234/1/Thesis_Tian - v1.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Studies of Phonon Anharmonicity in Solids", "author": [ { "family_name": "Lan", "given_name": "Tian", "clpid": "Lan-Tian" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Schwab", "given_name": "Keith C.", "clpid": "Schwab-K-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Today our understanding of the vibrational thermodynamics of materials at low temperatures is emerging nicely, based on the harmonic model in which phonons are independent. At high temperatures, however, this understanding must accommodate how phonons interact with other phonons or with other excitations. We shall see that the phonon-phonon interactions give rise to interesting coupling problems, and essentially modify the equilibrium and non-equilibrium properties of materials, e.g., thermodynamic stability, heat capacity, optical properties and thermal transport of materials. Despite its great importance, to date the anharmonic lattice dynamics is poorly understood and most studies on lattice dynamics still rely on the harmonic or quasiharmonic models. There have been very few studies on the pure phonon anharmonicity and phonon-phonon interactions. The work presented in this thesis is devoted to the development of experimental and computational methods on this subject.
\r\n\r\nModern inelastic scattering techniques with neutrons or photons are ideal for sorting out the anharmonic contribution. Analysis of the experimental data can generate vibrational spectra of the materials, i.e., their phonon densities of states or phonon dispersion relations. We obtained high quality data from laser Raman spectrometer, Fourier transform infrared spectrometer and inelastic neutron spectrometer. With accurate phonon spectra data, we obtained the energy shifts and lifetime broadenings of the interacting phonons, and the vibrational entropies of different materials. The understanding of them then relies on the development of the fundamental theories and the computational methods.
\r\n\r\nWe developed an efficient post-processor for analyzing the anharmonic vibrations from the molecular dynamics (MD) calculations. Currently, most first principles methods are not capable of dealing with strong anharmonicity, because the interactions of phonons are ignored at finite temperatures. Our method adopts the Fourier transformed velocity autocorrelation method to handle the big data of time-dependent atomic velocities from MD calculations, and efficiently reconstructs the phonon DOS and phonon dispersion relations. Our calculations can reproduce the phonon frequency shifts and lifetime broadenings very well at various temperatures.
\r\n\r\nTo understand non-harmonic interactions in a microscopic way, we have developed a numerical fitting method to analyze the decay channels of phonon-phonon interactions. Based on the quantum perturbation theory of many-body interactions, this method is used to calculate the three-phonon and four-phonon kinematics subject to the conservation of energy and momentum, taking into account the weight of phonon couplings. We can assess the strengths of phonon-phonon interactions of different channels and anharmonic orders with the calculated two-phonon DOS. This method, with high computational efficiency, is a promising direction to advance our understandings of non-harmonic lattice dynamics and thermal transport properties.
\r\n\r\nThese experimental techniques and theoretical methods have been successfully performed in the study of anharmonic behaviors of metal oxides, including rutile and cuprite stuctures, and will be discussed in detail in Chapters 4 to 6. For example, for rutile titanium dioxide (TiO2), we found that the anomalous anharmonic behavior of the B1g mode can be explained by the volume effects on quasiharmonic force constants, and by the explicit cubic and quartic anharmonicity. For rutile tin dioxide (SnO2), the broadening of the B2g mode with temperature showed an unusual concave downwards curvature. This curvature was caused by a change with temperature in the number of down-conversion decay channels, originating with the wide band gap in the phonon dispersions. For silver oxide (Ag2O), strong anharmonic effects were found for both phonons and for the negative thermal expansion.
", "doi": "10.7907/AB7A-FP25", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8112", "collection": "thesis", "collection_id": "8112", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03062014-172332538", "primary_object_url": { "basename": "Wei_Wei_2014_thesis.pdf", "content": "final", "filesize": 10594762, "license": "other", "mime_type": "application/pdf", "url": "/8112/1/Wei_Wei_2014_thesis.pdf", "version": "v10.0.0" }, "type": "thesis", "title": "Microfluidics-Based Single-Cell Functional Proteomics Microchip for Portraying Protein Signal Transduction Networks within the Framework of Physicochemical Principles, with Applications in Fundamental and Translational Cancer Research", "author": [ { "family_name": "Wei", "given_name": "Wei", "orcid": "0000-0002-1018-7708", "clpid": "Wei-Wei" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William L.", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Single-cell functional proteomics assays can connect genomic information to biological function through quantitative and multiplex protein measurements. Tools for single-cell proteomics have developed rapidly over the past 5 years and are providing unique opportunities. This thesis describes an emerging microfluidics-based toolkit for single cell functional proteomics, focusing on the development of the single cell barcode chips (SCBCs) with applications in fundamental and translational cancer research.
\r\n\r\nThe microchip designed to simultaneously quantify a panel of secreted, cytoplasmic and membrane proteins from single cells will be discussed at the beginning, which is the prototype for subsequent proteomic microchips with more sophisticated design in preclinical cancer research or clinical applications. The SCBCs are a highly versatile and information rich tool for single-cell functional proteomics. They are based upon isolating individual cells, or defined number of cells, within microchambers, each of which is equipped with a large antibody microarray (the barcode), with between a few hundred to ten thousand microchambers included within a single microchip. Functional proteomics assays at single-cell resolution yield unique pieces of information that significantly shape the way of thinking on cancer research. An in-depth discussion about analysis and interpretation of the unique information such as functional protein fluctuations and protein-protein correlative interactions will follow.
\r\n\r\nThe SCBC is a powerful tool to resolve the functional heterogeneity of cancer cells. It has the capacity to extract a comprehensive picture of the signal transduction network from single tumor cells and thus provides insight into the effect of targeted therapies on protein signaling networks. We will demonstrate this point through applying the SCBCs to investigate three isogenic cell lines of glioblastoma multiforme (GBM).
\r\n\r\nThe cancer cell population is highly heterogeneous with high-amplitude fluctuation at the single cell level, which in turn grants the robustness of the entire population. The concept that a stable population existing in the presence of random fluctuations is reminiscent of many physical systems that are successfully understood using statistical physics. Thus, tools derived from that field can probably be applied to using fluctuations to determine the nature of signaling networks. In the second part of the thesis, we will focus on such a case to use thermodynamics-motivated principles to understand cancer cell hypoxia, where single cell proteomics assays coupled with a quantitative version of Le Chatelier's principle derived from statistical mechanics yield detailed and surprising predictions, which were found to be correct in both cell line and primary tumor model.
\r\n\r\nThe third part of the thesis demonstrates the application of this technology in the preclinical cancer research to study the GBM cancer cell resistance to molecular targeted therapy. Physical approaches to anticipate therapy resistance and to identify effective therapy combinations will be discussed in detail. Our approach is based upon elucidating the signaling coordination within the phosphoprotein signaling pathways that are hyperactivated in human GBMs, and interrogating how that coordination responds to the perturbation of targeted inhibitor. Strongly coupled protein-protein interactions constitute most signaling cascades. A physical analogy of such a system is the strongly coupled atom-atom interactions in a crystal lattice. Similar to decomposing the atomic interactions into a series of independent normal vibrational modes, a simplified picture of signaling network coordination can also be achieved by diagonalizing protein-protein correlation or covariance matrices to decompose the pairwise correlative interactions into a set of distinct linear combinations of signaling proteins (i.e. independent signaling modes). By doing so, two independent signaling modes \u2013 one associated with mTOR signaling and a second associated with ERK/Src signaling have been resolved, which in turn allow us to anticipate resistance, and to design combination therapies that are effective, as well as identify those therapies and therapy combinations that will be ineffective. We validated our predictions in mouse tumor models and all predictions were borne out.
\r\n\r\nIn the last part, some preliminary results about the clinical translation of single-cell proteomics chips will be presented. The successful demonstration of our work on human-derived xenografts provides the rationale to extend our current work into the clinic. It will enable us to interrogate GBM tumor samples in a way that could potentially yield a straightforward, rapid interpretation so that we can give therapeutic guidance to the attending physicians within a clinical relevant time scale. The technical challenges of the clinical translation will be presented and our solutions to address the challenges will be discussed as well. A clinical case study will then follow, where some preliminary data collected from a pediatric GBM patient bearing an EGFR amplified tumor will be presented to demonstrate the general protocol and the workflow of the proposed clinical studies.
\r\n", "doi": "10.7907/Z9WS8R7G", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8033", "collection": "thesis", "collection_id": "8033", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11222013-151337813", "primary_object_url": { "basename": "Xiao Liu_11_20_2013.pdf", "content": "final", "filesize": 27249590, "license": "other", "mime_type": "application/pdf", "url": "/8033/13/Xiao Liu_11_20_2013.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "A Study on Iron-Based Amorphous Alloys: Alloy Development, Thermodynamics and Soft Magnetism", "author": [ { "family_name": "Liu", "given_name": "Xiao", "clpid": "Liu-Xiao" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Metallic glass has since its debut been of great research interest due to its profound scientific significance. Magnetic metallic glasses are of special interest because of their promising technological applications. In this thesis, we introduced a novel series of Fe-based alloys and offer a holistic review of the physics and properties of these alloys. A systematic alloy development and optimization method was introduced, with experimental implementation on transition metal based alloying system. A deep understanding on the influencing factors of glass forming ability was brought up and discussed, based on classical nucleation theory. Experimental data of the new Fe-based amorphous alloys were interpreted to further analyze those influencing factors, including reduced glass transition temperature, fragility, and liquid-crystal interface free energy. Various treatments (fluxing, overheating, etc.) were discussed for their impacts on the alloying systems' thermodynamics and glass forming ability. Multiple experimental characterization methods were discussed to measure the alloys' soft magnetic properties. In addition to theoretical and experimental investigation, we also gave a detailed numerical analysis on the rapid-discharge-heating-and-forming platform. It is a novel experimental system which offers extremely fast heating rate for calorimetric characterization and alloy deformation. ", "doi": "10.7907/X2WM-RA54", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8032", "collection": "thesis", "collection_id": "8032", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11202013-144350295", "primary_object_url": { "basename": "GleasonRohrer2013thesis.pdf", "content": "final", "filesize": 2166776, "license": "other", "mime_type": "application/pdf", "url": "/8032/1/GleasonRohrer2013thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Measurement of the Band Bending and Surface Dipole at Chemically Functionalized Si(111)/Vacuum Interfaces", "author": [ { "family_name": "Gleason-Rohrer", "given_name": "David Charles", "clpid": "Gleason-Rohrer-David-Charles" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Brunschwig", "given_name": "Bruce S.", "clpid": "Brunschwig-B-S" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si-Br, Si-H, and Si-CH3 groups, respectively. The surface termination influenced the band bending, with the Si 2p3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)-Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)-H, followed by Si(111)-CH3 (whose Fermi level was positioned near mid-gap at the surface). Si(111)-CH3 surfaces exposed to Br2(g) yielded the lowest binding energies, with the Fermi level positioned between mid-gap and the valence band. The Fermi level position of Br2(g)-exposed Si(111)-CH3 was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.
", "doi": "10.7907/PD7F-P488", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7976", "collection": "thesis", "collection_id": "7976", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10082013-111509695", "primary_object_url": { "basename": "Thesis_SeokminJeon-131008-w_ack.pdf", "content": "final", "filesize": 6321158, "license": "other", "mime_type": "application/pdf", "url": "/7976/1/Thesis_SeokminJeon-131008-w_ack.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Structure, Chemistry, and Energetics of Organic and Inorganic Adsorbates on Ga-rich GaAs and GaP(00l) Surfaces", "author": [ { "family_name": "Jeon", "given_name": "Seokmin", "clpid": "Jeon-Seokmin" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The work described in this dissertation includes fundamental investigations into three surface processes, namely inorganic film growth, water-induced oxidation, and organic functionalization/passivation, on the GaP and GaAs(001) surfaces. The techniques used to carry out this work include scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. Atomic structure, electronic structure, reaction mechanisms, and energetics related to these surface processes are discussed at atomic or molecular levels.
\r\n\r\nFirst, we investigate epitaxial Zn3P2 films grown on the Ga-rich GaAs(001)(6\u00d76) surface. The film growth mechanism, electronic properties, and atomic structure of the Zn3P2/GaAs(001) system are discussed based on experimental and theoretical observations. We discover that a P-rich amorphous layer covers the crystalline Zn3P2 film during and after growth. We also propose more accurate picture of the GaP interfacial layer between Zn3P2 and GaAs, based on the atomic structure, chemical bonding, band diagram, and P-replacement energetics, than was previously anticipated.
\r\n\r\nSecond, DFT calculations are carried out in order to understand water-induced oxidation mechanisms on the Ga-rich GaP(001)(2\u00d74) surface. Structural and energetic information of every step in the gaseous water-induced GaP oxidation reactions are elucidated at the atomic level in great detail. We explore all reasonable ground states involved in most of the possible adsorption and decomposition pathways. We also investigate structures and energies of the transition states in the first hydrogen dissociation of a water molecule on the (2\u00d74) surface.
\r\n\r\nFinally, adsorption structures and thermal decomposition reactions of 1-propanethiol on the Ga-rich GaP(001)(2\u00d74) surface are investigated using high resolution STM, XPS, and DFT simulations. We elucidate adsorption locations and their associated atomic structures of a single 1-propanethiol molecule on the (2\u00d74) surface as a function of annealing temperature. DFT calculations are carried out to optimize ground state structures and search transition states. XPS is used to investigate variations of the chemical bonding nature and coverage of the adsorbate species.
\r\n", "doi": "10.7907/1T2B-J793", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8390", "collection": "thesis", "collection_id": "8390", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05232014-150103448", "primary_object_url": { "basename": "Wei-Guang_Liu_thesis_2014.pdf", "content": "final", "filesize": 2701449, "license": "other", "mime_type": "application/pdf", "url": "/8390/1/Wei-Guang_Liu_thesis_2014.pdf", "version": "v10.0.0" }, "type": "thesis", "title": "First-Principle Studies of the Initiation Mechanism of Energetic Materials", "author": [ { "family_name": "Liu", "given_name": "Wei-Guang", "orcid": "0000-0002-6633-7795", "clpid": "Liu-Wei-Guang" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "It is important to understand the initiation mechanism of energetic materials to improve and engineer them. In this thesis first-principle calculation is used to study the initiation of several explosives and propellants.
\r\n\r\nThe second chapter is focused on a new energetic material, silicon pentaerythritol tetranitrate (Si-PETN), DFT calculations have identified the novel rearrangement that explains the very dramatic increase in sensitivity observed experimentally. The critical difference is that Si-PETN allows a favorable five-coordinate transition state in which the new Si\u2212O and C\u2212O bonds form simultaneously, leading to a transition state barrier of 33 kcal/mol (it is 80 kcal/mol for PETN) and much lower than the normal O\u2212NO2 bond fission observed in other energetic materials (40 kcal/mol). In addition this new mechanism is very exothermic (45 kcal/mol) leading to a large net energy release at the very early stages of Si-PETN decomposition.
\r\n\r\nThe third chapter is about nitrogen-rich compounds, which has high heat of formation and releases the energy by decomposing into stable N2 molecules. Two families of compounds, azobistetrazoles and azobistriazoles, were studied. Based on the calculated mechanisms, for azobistetrazoles with four N atoms in the five-member ring, a clearly-defined N=N fragment can always be found in the ring, and its decomposition starts with ring-opening to free one end of N=N followed by N2 dissociation and heat generation. This barrier is around 28-35 kcal/mol, which is low enough to dominate the sensitivity of material. For azobistriazoles, only 1,1\u2019-azobis-1,2,3-triazole has a N=N fragment in the original 5-member ring and similar ring-opening - N2 dissociation pathway is favored. For the remaining compounds, an additional isomerization is necessary to release N2, which gives the barrier around 55~60 kcal/mol, making these compound less sensitive.
\r\n\r\nThe fourth chapter shifts focus to hypergolic propellants. DFT calculations with B3LYP functional was applied to study the hypergolic reaction between N,N,N',N'-tetramethylethylenediamine (TMEDA), N,N,N',N'-Tetramethylmethylenediamine (TMMDA) and HNO3. Bond energies in TMEDA and TMMDA were calculated and compared with their alkane analogues to demonstrate that the lone-pair electrons on N atoms plays the role of activating adjacent chemical bonds. Two key factors relating to the ignition delay were calculated at atomistic level. The first factor is the exothermicity of the formation of the dinitrate salt of TMEDA and TMMDA. Because of the shorter distance between basic amines in TMMDA, it is more difficult to protonate both amines for the stronger electrostatic repulsion, resulting in the smaller heat of dinitrate salt formation by 6.3kcal/mol. The second factor is the reaction rate of TMEDA and TMMDA reacting with NO2 to the step that releases enough heat and more reactive species to propagate reaction. In TMEDA, the formation of the intermediate with C-C double bond and the low bond energy of C-C single bond provide a route with low barrier to oxidize C. Both factors can contribute to the shorter ignition delay of TMEDA.
\r\n\r\nThe fifth chapter is about the other pair of hypergolic propellant, monomethylhydrazine (MMH) with oxidizers NO2/N2O4. Experimentally several IR-active species were identified in the early reactions, including HONO, monomethylhydrazinium nitrite (MMH\u2022HONO), methyl diazene (CH3N=NH), methyl nitrate (CH3ONO2), methyl nitrite (CH3ONO), nitromethane (CH3NO2), methyl azide (CH3N3), H2O, N2O and NO. In order to elucidate the mechanisms by which these observed products are formed, we carried out quantum mechanics calculations (CCSD(T)/6-31G**//M06-2X/6-311G**++) for the possible reaction pathways. Based on these studies, we proposed that the oxidation of MMH in an atmosphere of NO2 occurs via two mechanisms: (1) sequential H-abstraction and HONO formation, and (2) reaction of MMH with asymmetric ONONO2, leading to formation of methyl nitrate. These mechanisms successfully explain all intermediates observed experimentally. We concluded that the formation of asymmetric ONONO2 is assisted by an aerosol formed by HONO and MMH that provides a large surface area for ONONO2 to condense, leading to the generation of methyl nitrate. Thus we proposed that the overall pre-ignition process involves both gas-phase and aerosol-phase reactions.
\r\n\r\nThe sixth chapter is about another pair of hypergolic propellant, unsymmetrical dimethylhydrazine (UDMH) with oxidizers NO2/N2O4. We carried out the same level of quantum mechanics calculations as MMH to study this pair. We proposed that the oxidation of UDMH in an atmosphere of NO2 occurs via two mechanisms, similar with MMH: (1) sequential H-abstraction and HONO formation in gas phase, which has no more than 20 kcal/mol barrier and leads to the production of (CH3)2NNO and HONO. (2)UDMH reacts with asymmetric ONONO2 in aerosol phase, leading to formation of CH3N3 and then CH3ONO2, with a 26.8 kcal/mol enthalpic barrier, which is 10 kcal/mol higher than the corresponding reaction barrier for MMH. Thus we predicted the low production rate of CH3ONO2 for UDMH/NO2 pair. Experimental evidences support our mechanisms for both MMH and UDMH reacting with NO2.
\r\n", "doi": "10.7907/Z9445JGM", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8452", "collection": "thesis", "collection_id": "8452", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312014-002701930", "primary_object_url": { "basename": "Scott-C-E_thesis2014.pdf", "content": "final", "filesize": 30657742, "license": "other", "mime_type": "application/pdf", "url": "/8452/1/Scott-C-E_thesis2014.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Role of Conformational Changes in G Protein-Coupled Receptor Activation", "author": [ { "family_name": "Scott", "given_name": "Caitlin Eileen", "clpid": "Scott-Caitlin-Eileen" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Clemons", "given_name": "William M.", "clpid": "Clemons-W-M" }, { "family_name": "Shan", "given_name": "Shu-ou", "clpid": "Shan-Shu-ou" }, { "family_name": "Abrol", "given_name": "Ravinder", "clpid": "Abrol-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Transmembrane signal transduction is achieved by activation of G protein-coupled receptors (GPCRs) like the human cannabinoid type 1 (CB1) receptor, the human cannabinoid type 2 (CB2) receptor, and the human mu-opioid receptor. These receptors exist in the membrane in an ensemble of conformations each of which might bind to different signaling molecules and cause different physiological effects. Understanding the structural basis of their activation will eventually help us in designing drugs that target these receptors with potentially minimal undesirable side effects. CB1 is of particular interest because it is located in the central nervous system and modulates hunger, making it an attractive anti-obesity drug target. In this receptor, mutating a single residue, threonine 210, to isoleucine in the third transmembrane (TM3) domain makes it far more active than the wild-type (WT) receptor, whereas mutating it to alanine makes it fully inactive. CB1 is difficult to model because it has a small sequence identity with the receptors that have been crystallized. We used the first principles-based GEnSeMBLE method to predict 3D structures of these receptors representing the fully inactive to highly constitutively active states. With this software, we quickly found a set of low energy receptor conformations by sampling trillions of helix orientations. Differences in the intracellular surface explain experimental differences in activation for the CB1 receptor and its mutants. These predictions were validated by designing double mutants that were expected to switch the inactive T210A to WT levels of activation and expected to switch the very active L207A to T210A levels of activation. These predictions were first verified computationally then experimentally with GTPgammaS assays. The accuracy of our predictions indicate that the GEnSeMBLE method is a useful procedure for predicting GPCR structures at various activation states. Known inverse agonists were docked to these predicted CB1 receptor structures, and the resulting complexes were inserted into a solvated lipid bilayer for 50 ns of NPT molecular dynamics with NAMD software. The inverse agonist preferentially binds to a pre-activated CB1 state, but during MD, traits of the inactive structure start to form suggesting that the ligand induces conformational changes.", "doi": "10.7907/Z94747VG", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8502", "collection": "thesis", "collection_id": "8502", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072014-074257676", "type": "thesis", "title": "Protein Structure Refinement Algorithms", "author": [ { "family_name": "Chitsaz", "given_name": "Mohsen", "clpid": "Chitsaz-Mohsen" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bjorkman", "given_name": "Pamela Jane", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Umans", "given_name": "Christopher M.", "orcid": "0000-0002-6390-9401", "clpid": "Umans-C-M" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.
\r\n\r\nDifficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.
\r\n", "doi": "10.7907/7731-QM74", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:8255", "collection": "thesis", "collection_id": "8255", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05212014-155104252", "primary_object_url": { "basename": "rf-thesis.pdf", "content": "final", "filesize": 36271797, "license": "other", "mime_type": "application/pdf", "url": "/8255/1/rf-thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Iridium and Rhodium Analogues of the Shilov Cycle Catalyst; and The Investigation and Applications of the Reduction-Coupled Oxo Activation (ROA) Mechanistic Motif towards Alkane Upgrading", "author": [ { "family_name": "Fu", "given_name": "Ross", "clpid": "Fu-Ross" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Agapie", "given_name": "Theodor", "clpid": "Agapie-T" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation will cover several disparate topics, with the overarching theme centering on the investigation of organometallic C-H activation and hydrocarbon transformation and upgrading. Chapters 2 and 3 discuss iridium and rhodium analogues of the Shilov cycle catalyst for methane to methanol oxidation, and Chapter 4 on the recently discovered ROA mechanistic motif in catalysts for various alkane partial oxidation reactions. In addition, Chapter 5 discusses the mechanism of nickel pyridine bisoxazoline Negishi catalysts for asymmetric and stereoconvergent C-C coupling, and the appendices discuss smaller projects on rhodium H/D exchange catalysts and DFT method benchmarking.", "doi": "10.7907/WY3F-DZ94", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7752", "collection": "thesis", "collection_id": "7752", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252013-065528171", "primary_object_url": { "basename": "GRG_Full_Thesis.pdf", "content": "final", "filesize": 23139681, "license": "other", "mime_type": "application/pdf", "url": "/7752/49/GRG_Full_Thesis.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Study of the Origins of Toughness in Amorphous Metals", "author": [ { "family_name": "Garrett", "given_name": "Glenn Robert", "clpid": "Garrett-Glenn-Robert" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Demetriou", "given_name": "Marios D.", "clpid": "Demetriou-M-D" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Amorphous metals that form fully glassy parts over a few millimeters in thickness are still relatively new materials. Their glassy structure gives them particularly high strengths, high yield strains, high hardness values, high resilience, and low damping losses, but this can also result in an extremely low tolerance to the presence of flaws in the material. Since this glassy structure lacks the ordered crystal structure, it also lacks the crystalline defect (dislocations) that provides the micromechanism of toughening and flaw insensitivity in conventional metals. Without a sufficient and reliable toughness that results in a large tolerance of damage in the material, metallic glasses will struggle to be adopted commercially. Here, we identify the origin of toughness in metallic glass as the competition between the intrinsic toughening mechanism of shear banding ahead of a crack and crack propagation by the cavitation of the liquid inside the shear bands. We present a detailed study over the first three chapters mainly focusing on the process of shear banding; its crucial role in giving rise to one of the most damage-tolerant materials known, its extreme sensitivity to the configurational state of a glass with moderate toughness, and how the configurational state can be changed with the addition of minor elements. The last chapter is a novel investigation into the cavitation barrier in glass-forming liquids, the competing process to shear banding. The combination of our results represents an increased understanding of the major influences on the fracture toughness of metallic glasses and thus provides a path for the improvement and development of tougher metallic glasses. ", "doi": "10.7907/Z9JD4TRM", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7439", "collection": "thesis", "collection_id": "7439", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01252013-135311552", "primary_object_url": { "basename": "Pomrehn_Thesis_2013_Final.pdf", "content": "final", "filesize": 14384837, "license": "other", "mime_type": "application/pdf", "url": "/7439/1/Pomrehn_Thesis_2013_Final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Phase Stability and Defect Behavior in Complex Thermoelectric Zinc-Antimonides", "author": [ { "family_name": "Pomrehn", "given_name": "Gregory Schoelerman", "clpid": "Pomrehn-Gregory-Schoelerman" } ], "thesis_advisor": [ { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" }, { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" }, { "family_name": "Snyder", "given_name": "G. Jeffrey", "clpid": "Snyder-G-J" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The Zn-Sb binary phase system has been of interest for many years in the search for efficient and low-cost thermoelectric materials. Of primary interest has been the Zn4Sb3 phase which exhibits a thermoelectric figure of merit, zT, in excess of 1 in an intermediate temperature range. In this study, Zn4Sb3 is shown to be entropically stabilized with respect to decomposition to Zn and ZnSb through the effects of configurational disorder and phonon free energy. Single-phase stability is predicted for a range of compositions and temperatures. Retrograde solubility of Zn is predicted on the two-phase boundary region between Zn4Sb3 and Zn. The complex temperature-dependent solubility can be used to explain the variety of nanoparticle formation observed in the system: formation of ZnSb on the Sb-rich side, Zn on the far Zn-rich side, and nano-void formation due to Zn precipitates being reabsorbed at lower temperatures.
\r\n\r\nA new binary compound, Zn8Sb7, known only in nanoparticulate form, is also studied using density functional calculations. The free energies of formation, including effects from vibrations and configurational disorder, are calculated to compare with the relevant phases ZnSb, Zn, and Zn4Sb3, yielding insight into the phase stability of Zn8Sb7. Band structure calculations predict Zn8Sb7, much like ZnSb and Zn4Sb3, to be an intermetallic semiconductor with similar thermoelectric properties. If sufficient entropy or surface energy exists to stabilize the bulk material, it would be stable in a limited temperature window at high temperature.
\r\n\r\nIn the AZn2Sb2 series of materials—A = Ca, Sr, Yb, and Eu—I show that a large concentration of thermodynamically stable cation vacancies leads to high extrinsic carrier concentrations. The stable defect level depends on the choice of A, and is consistent with experimentally observed carrier concentrations in these materials. These results demonstrate that point defects are the primary mechanism by which the covalency of the cation bond can influence carrier concentration in nominally valence-precise AZn2Sb2compounds. This mechanism may be generally applicable to other Zintl phases, perhaps explaining similar trends seen in A14MSb11, A2MSb2 (A=2+ cation, M = 2+ or 3+ metal),and similar materials.
", "doi": "10.7907/0AWH-4P69", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7882", "collection": "thesis", "collection_id": "7882", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06102013-114658448", "type": "thesis", "title": "Molecular Design of Side-Group Liquid Crystalline Polymers: Understanding Their Interactions with Small Molecule Liquid Crystal Solvent", "author": [ { "family_name": "Kurji", "given_name": "Zuleikha", "clpid": "Kurji-Zuleikha" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Liquid crystal (LC) gels \u2013 the combination of macromolecules with small molecule LCs \u2013 couple the\r\nelasticity and mechanical strength of polymers to the order inherent to LCs and are attractive to many\r\nresearchers hoping to marry liquid crystals' optical and electro-optical responsiveness with polymers'\r\nmechanical strength and ease of processing. In particular, side-group liquid crystal polymers (SGLCPs)\r\nare flexible-chain polymers that are functionalized with LC side-groups. Here we introduce the concept\r\nof polymer dopants: homogenously dissolved LC-containing SGLCP homopolymers that are molecularly\r\ndesigned for solubility in and coupling to small molecule LC solvents. Using polymer analogous\r\nchemistry (changing the molecular makeup of the side groups and their linkers, while keeping backbone\r\nmolecular weight, polydispersity index, and degree of polymerization constant), we\u2019ve targeted the effect\r\nof side-group orientation, dipole position and strength, spacer length and linking-group type on\r\npolymer solubility and bulk material properties. We've shown that, at low concentration, these dopants\r\ncan have significant effects on the bulk material properties of two types of LCs: ferroelectric and vertically\r\naligned nematic LCs.", "doi": "10.7907/Z9WH2N6R", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7865", "collection": "thesis", "collection_id": "7865", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-111912342", "primary_object_url": { "basename": "Kiwook_Hwang_2013_thesis_final.pdf", "content": "final", "filesize": 24703251, "license": "other", "mime_type": "application/pdf", "url": "/7865/49/Kiwook_Hwang_2013_thesis_final.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Biotechnologies for Cancer Diagnostics: Cell Sorting, Protein Analysis and Imaging of Cellular Metabolism", "author": [ { "family_name": "Hwang", "given_name": "Kiwook", "clpid": "Hwang-Kiwook" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Cai", "given_name": "Long", "clpid": "Cai-Long" }, { "family_name": "Shan", "given_name": "Shu-ou", "clpid": "Shan-Shu-ou" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called \u201cNucleic Acid Cell Sorting (NACS)\u201d, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.
\r\n \r\nSecondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called \u201cRadiopharmaceutical Imaging Chip\u201d (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.
\r\n \r\nThe last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.
\r\n", "doi": "10.7907/Z6DN-0483", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7838", "collection": "thesis", "collection_id": "7838", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06052013-080936057", "primary_object_url": { "basename": "Complete.pdf", "content": "final", "filesize": 33403272, "license": "other", "mime_type": "application/pdf", "url": "/7838/1/Complete.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Advancing Electrocatalysis in Solid Acid Fuel Cells", "author": [ { "family_name": "Varga", "given_name": "Aron", "clpid": "Varga-Aron" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "clpid": "Giapis-K-P" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Solid acid fuel cells are currently performance limited by the electrochemical reaction kinetics at the electrodes. For acceptable power output, precious metal catalysts such as platinum, are required, rendering the technology too expensive for commercialization in all but niche applications. This thesis explores new approaches to solid acid fuel cell electrodes with the aim of reducing the catalyst loading or even eliminating precious metals entirely, without sacrificing performance. Two broad approaches are pursued: nanostructuring for enhanced catalyst utilization and incorporation of carbon-based materials for enhanced electrical transport and even electrocatalysis.
\r\n\r\nElectrospray deposition is shown to be a viable technique to produce nanoparticles of the solid acid fuel cell electrolyte material CsH2PO4. In situ aerosol particle size measurements using a differential mobility analyzer and a condensation particle counter allowed the characterization of the electrospray parameter space, resulting in CsH2PO4 particle size control between 10 and 50 nm. Co-deposition of the CsH2PO4 nanoparticles together with a stabilizing surfactant polyvinylpyrrolidone (PVP) and platinum catalyst nanoparticles allows the creation of highly active, porous, interconnected electrode nanostructures. These nanostructures directly deposited onto fuel cell components, either the carbon paper current collector or the thin film electrolyte layer, serve as electrodes. A 30-fold reduction of platinum loading, without sacrificing electrode performance as compared to mixed powder-electrodes, is demonstrated.
\r\n\r\nThe direct deposition of CsH2PO4 nanoparticles with the stabilizing surfactant PVP onto a prefabricated CsH2PO4 electrolyte layer and subsequent magnetron sputtering of a nanometer thin platinum film lead to surprising catalyst-mass normalized electrode activities for solid acid fuel cell anodes. Specifically, a 25-fold increase in the mass normalized activity is shown as compared to the predicted values from analysis\r\nof platinum thin films with a controlled geometry.
\r\n\r\nThe second part of the thesis deals with the introduction of carbon nanotubes to the solid acid fuel cell electrodes. Three types of carbon nanotubes (CNTs) were grown directly onto the carbon paper current collector, in all cases using a chemical vapor deposition method and nickel catalyst nanoparticles.
\r\n\r\n(i) Conventional CNTs were shown to act as effective current collectors for electrosprayed composite electrode structures, containing platinum nanoparticles. Matching of scales between the current collector and the electrosprayed structure leads to improved interconnectivity of the platinum catalyst nanoparticles and a higher density of electrochemically active triple phase boundaries.
\r\n\r\n(ii) Nitrogen doped carbon nanotubes (NCNTs) were shown to actively catalyze oxygen electroreduction in solid acid fuel cells, with no platinum present.
\r\n\r\n(iii) Undoped but defective carbon nanotubes (dCNTs) were shown to be highly efficient catalysts of the oxygen electroreduction reaction, surpassing the activity of the state of the art, platinum containing electrodes. This is the first time undoped carbon nanotubes have been reported to be catalytically active for electroreduction of oxygen.
In addition, catalytically active carbon nanotubes show excellent catalysis of the water splitting reaction, creating the opportunity for new applications of these solid state electrochemical devices.
", "doi": "10.7907/Z9RX992C", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7198", "collection": "thesis", "collection_id": "7198", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09092012-010239493", "primary_object_url": { "basename": "Stadie_N_2013_Thesis.pdf", "content": "updated", "filesize": 7810642, "license": "other", "mime_type": "application/pdf", "url": "/7198/83/Stadie_N_2013_Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Synthesis and Thermodynamic Studies of Physisorptive Energy Storage Materials", "author": [ { "family_name": "Stadie", "given_name": "Nicholas P.", "clpid": "Stadie-Nicholas-P" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ahn", "given_name": "Channing C.", "clpid": "Ahn-C-C" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ahn", "given_name": "Channing C.", "clpid": "Ahn-C-C" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Physical adsorption of hydrogen or other chemical fuels on the surface of carbonaceous materials offers a promising avenue for energy storage applications. The addition of a well-chosen sorbent material to a compressed gas tank increases the volumetric energy density of the system while still permitting fast refueling, simplicity of design, complete reversibility, high cyclability, and low overall cost of materials. While physical adsorption is most effective at temperatures below ambient, effective storage technologies are possible at room temperature and modestly high pressure. A volumetric Sieverts apparatus was designed, constructed, and commissioned to accurately measure adsorption uptake at high pressures and an appropriate thermodynamic treatment of the experimental data is presented.
\r\n\r\nIn Chapter 1, the problem of energy storage is introduced in the context of hydrogen as an ideal alternative fuel for future mobile vehicle applications, and with methane in mind as a near-term solution. The theory of physical adsorption that is relevant to this work is covered in Chapter 2. In-depth studies of two classes of materials are presented in the final chapters. Chapter 3 presents a study of the dissociative \u201chydrogen spillover\u201d effect in the context of its viability as a practical hydrogen storage solution at room temperature. Chapters 4-5 deal with zeolite-templated carbon, an extremely high surface-area material which shows promise for hydrogen and methane storage applications. Studies of hydrogen adsorption at high pressure (Chapter 4) and anomalous thermodynamic properties of methane adsorption (Chapter 5) on ZTCs are presented. The concluding chapter discusses the impact of and possible future directions for this work.
", "doi": "10.7907/ZK3P-CV60", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7285", "collection": "thesis", "collection_id": "7285", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11262012-160659812", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 39470329, "license": "other", "mime_type": "application/pdf", "url": "/7285/1/thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Plasmonics and Electron Optics in Graphene", "author": [ { "family_name": "Jang", "given_name": "Min Seok", "clpid": "Jang-Min-Seok" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Vahala", "given_name": "Kerry J.", "clpid": "Vahala-K-J" }, { "family_name": "Scherer", "given_name": "Axel", "clpid": "Scherer-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The field of plasmonics has been attracting wide interest because it has provided routes to guide and localize light at nanoscales by utilizing metals as its major building block. Meanwhile, graphene, a two-dimensional lattice of carbon atoms, has been regarded as an ideal material for electronic applications owing to its remarkably high carrier mobility and superior thermal properties. Both research fields have been growing rapidly, but quite independently. However, a closer look reveals that there are actually numerous similarities between them, and it is possible to extract useful applications from these analogies. Even more interestingly, these research fields are recently overlapping to create a new field of research, namely graphene plasmonics.
\r\n\r\nIn this thesis, we present a few examples of these intertwined topics. First, we investigate \"rainbow trapping\" structures, broadband plasmonic slow light systems composed of single or double negative materials. We clarify the mode-conversion mechanism and the light-trapping performance by analyzing the dispersion relation. We then show that electrons in graphene exhibit photonlike dynamics including Goos-Hanchen effect and the rainbow trapping effect, but quantitatively differently. To study the dynamics of graphene electrons numerically, we develop a finite-difference time domain simulator. We also present a way to enhance electron backscattering in graphene by engineering the dispersion of electron eigenmodes in a Kronig-Penney potential. Finally, we discuss physics of graphene plasmon cavities. We report the resonant mid-infrared transmission across a plasmonic waveguide gap that is governed by the Fano interference between transmission through plasmon modes in graphene and nonresonant background transmission. An ultracompact graphene plasmon cavity, which resonates at near-infrared telecommunication frequencies, is also proposed.
", "doi": "10.7907/59RB-9653", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7527", "collection": "thesis", "collection_id": "7527", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03192013-100649773", "type": "thesis", "title": "Single Cell Proteomics Microchip to Profile Immune Function, with Applications in Stem Cell Biology, Translational Disease Mechanism Study and Clinical Therapeutics Monitoring", "author": [ { "family_name": "Ma", "given_name": "Chao", "clpid": "Ma-Chao" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Pine", "given_name": "Jerome", "clpid": "Pine-J" }, { "family_name": "Braun", "given_name": "Jonathan", "clpid": "Braun-J" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.
\r\n\r\nTo study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor \u2013 killer immunoglobulin-like receptor (KIR) \u2013 has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.
\r\n\r\nIn all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-\u03b1, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-\u03b1, IL-6 and GM-CSF. TLR stimulation activated the NF-\u03baB signaling in HSCs.\r\nSingle cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.
\r\n", "doi": "10.7907/2M7E-0P25", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7693", "collection": "thesis", "collection_id": "7693", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05092013-220921048", "primary_object_url": { "basename": "Mishra_CalTech_Thesis_130509.pdf", "content": "final", "filesize": 7189688, "license": "other", "mime_type": "application/pdf", "url": "/7693/1/Mishra_CalTech_Thesis_130509.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Proton Transfers at the Air-Water Interface", "author": [ { "family_name": "Mishra", "given_name": "Himanshu", "clpid": "Mishra-Himanshu" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Proton transfer reactions at the interface of water with hydrophobic media, such as air or lipids, are ubiquitous on our planet. These reactions orchestrate a host of vital phenomena in the environment including, for example, acidification of clouds, enzymatic catalysis, chemistries of aerosol and atmospheric gases, and bioenergetic transduction. Despite their importance, however, quantitative details underlying these interactions have remained unclear. Deeper insight into these interfacial reactions is also required in addressing challenges in green chemistry, improved water quality, self-assembly of materials, the next generation of micro-nanofluidics, adhesives, coatings, catalysts, and electrodes. This thesis describes experimental and theoretical investigation of proton transfer reactions at the air-water interface as a function of hydration gradients, electrochemical potential, and electrostatics. Since emerging insights hold at the lipid-water interface as well, this work is also expected to aid understanding of complex biological phenomena associated with proton migration across membranes.
\r\n\r\nBased on our current understanding, it is known that the physicochemical properties of the gas-phase water are drastically different from those of bulk water. For example, the gas-phase hydronium ion, H3O+(g), can protonate most (non-alkane) organic species, whereas H3O+(aq) can neutralize only relatively strong bases. Thus, to be able to understand and engineer water-hydrophobe interfaces, it is imperative to investigate this fluctuating region of molecular thickness wherein the \u2018function\u2019 of chemical species transitions from one phase to another via steep gradients in hydration, dielectric constant, and density. Aqueous interfaces are difficult to approach by current experimental techniques because designing experiments to specifically sample interfacial layers (< 1 nm thick) is an arduous task. While recent advances in surface-specific spectroscopies have provided valuable information regarding the structure of aqueous interfaces, but structure alone is inadequate to decipher the function. By similar analogy, theoretical predictions based on classical molecular dynamics have remained limited in their scope.
\r\n\r\nRecently, we have adapted an analytical electrospray ionization mass spectrometer (ESIMS) for probing reactions at the gas-liquid interface in real time. This technique is direct, surface-specific,and provides unambiguous mass-to-charge ratios of interfacial species. With this innovation, we have been able to investigate the following:
\r\n\r\n1. How do anions mediate proton transfers at the air-water interface?
\r\n\r\n2. What is the basis for the negative surface potential at the air-water interface?
\r\n\r\n3. What is the mechanism for catalysis \u2018on-water\u2019?
\r\n\r\nIn addition to our experiments with the ESIMS, we applied quantum mechanics and molecular dynamics to simulate our experiments toward gaining insight at the molecular scale. Our results unambiguously demonstrated the role of electrostatic-reorganization of interfacial water during proton transfer events. With our experimental and theoretical results on the \u2018superacidity\u2019 of the surface of mildly acidic water, we also explored implications on atmospheric chemistry and green chemistry. Our most recent results explained the basis for the negative charge of the air-water interface and showed that the water-hydrophobe interface could serve as a site for enhanced autodissociation of water compared to the condensed phase.
", "doi": "10.7907/A9HR-PN89", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:7810", "collection": "thesis", "collection_id": "7810", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05312013-184738559", "primary_object_url": { "basename": "JAMunoz_thesis.pdf", "content": "final", "filesize": 4251866, "license": "cc_by_sa", "mime_type": "application/pdf", "url": "/7810/1/JAMunoz_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Electronic Structure and Phonon Thermodynamics of Iron Alloys", "author": [ { "family_name": "Mu\u00f1oz", "given_name": "Jorge Alberto", "clpid": "Mu\u00f1oz-Jorge-Alberto" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Inelastic neutron scattering (INS) and nuclear-resonant inelastic x-ray scattering (NRIXS) were used to measure phonon spectra of FeV as a B2- ordered compound and as a bcc solid solution. Contrary to the behavior of ordering alloys studied to date, the phonons in the B2-ordered phase are softer than in the solid solution. Ordering increases the vibrational entropy, which stabilizes the ordered phase to higher temperatures. Ab initio calculations show that the number of electronic states at the Fermi level increases upon ordering, enhancing the screening between ions, and reducing the interatomic force constants. The effect of screening is larger at the V atomic sites than at the Fe atomic sites.
\r\n\r\nThe phonon spectra of Au-rich alloys of fcc Au-Fe were also measured. The main effect on the vibrational entropy of alloying comes from a stiffening of the Au partial phonon density of states (DOS) with Fe concentration that increases the miscibility gap temperature. The magnitude of the effect is non- linear and it is reduced at higher Fe concentrations. Force constants were calculated for several compositions and show a local stiffening of Au\u2013Au bonds close to Fe atoms, but Au\u2013Au bonds that are farther away do not show this effect. Phonon DOS curves calculated from the force constants reproduced the experimental trends. The Au\u2013Fe bond is soft and favors ordering, but a charge transfer from the Fe to the Au atoms stiffens the Au\u2013Au bonds enough to favor unmixing. The stiffening is attributed to two main effects comparable in magnitude: an increase in electron density in the free-electron-like states, and stronger sd-hybridization.
\r\n\r\nINS and NRIXS measurements were performed at elevated temperatures on B2-ordered FeTi and NRIXS measurements were performed at high pressures. The high-pressure behavior is quasi- harmonic. The softening of the phonon DOS curves with temperature is strongly nonharmonic. Calculations of the force constants and Born-von Karman fits to the experimental data show that the bonds between second nearest neighbors (2nn) are much stiffer than those between 1nn, but fits to the high temperature data show that the former softens at a faster rate with temperature. The Fe\u2013Fe bond softens more than the Ti\u2013Ti bond. The unusual stiffness of the 2nn bond is explained by the calculated charge distribution, which is highly aspherical and localized preferentially in the t2g orbitals. Ab initio molecular dynamics (AIMD) simulations show a charge transfer from the t2g orbitals to the eg orbitals at elevated temperatures. The asphericity decreases linearly with temperature and is more severe at the Fe sites.
", "doi": "10.7907/7EJD-RP70", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:6732", "collection": "thesis", "collection_id": "6732", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11092011-100634353", "primary_object_url": { "basename": "PMT_Thesis_2012_Open_File.pdf", "content": "final", "filesize": 64438814, "license": "other", "mime_type": "application/pdf", "url": "/6732/1/PMT_Thesis_2012_Open_File.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Exploiting the Reactivity of Arynes in the Total Synthesis of Natural Products", "author": [ { "family_name": "Tadross", "given_name": "Pamela Michele", "clpid": "Tadross-Pamela-Michele" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Reisman", "given_name": "Sarah E.", "clpid": "Reisman-S-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Virgil", "given_name": "Scott C.", "clpid": "Virgil-S-C" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Within 14 years of the seminal experiments of J. D. Roberts leading to the first proposal of the structure of benzyne, synthetic organic chemists recognized the potential to exploit this highly reactive intermediate (and its substituted variants) in the synthesis of natural products. More specifically, it was recognized that arynes offered the strategic advantage of rapidly functionalizing an aromatic ring by forming multiple carbon\u2013carbon or carbon\u2013heteroatom bonds in a single operation, often in a regioselective manner. Herein are reported three separate efforts aimed at constructing natural products by aryne-based methodologies. In each of the studies described in the following chapters, the implementation of new aryne technologies developed in our group to natural product synthesis has resulted in concise, convergent, and general strategies to our targets.
\r\n\r\nThe first project discussed in this work is the enantioselective total synthesis of (\u2013)-curvularin by an acyl-alkylation reaction of a protected resorcinylic silyl aryl triflate aryne precursor with a \u03b2-ketolactone. Application of this strategic disconnection resulted in a six-step convergent synthesis of the polyketide natural product, the shortest to date. These efforts also resulted in the syntheses of curvulin and diplodialide C.
\r\n\r\nIn our efforts toward the total synthesis of two naturally occurring HIV integrase inhibitors, integrastatins A and B, we attempted to utilize a sequence involving an acyl-alkylation followed by an ortho-Fries-type rearrangement to access the tetracyclic core of the natural products. However, this proved to be a significant challenge and led to the development of an alternative route to the tetracyclic integrastatin core by a Wacker cyclization of a diol onto a pendant olefin.
\r\n\r\nFinally, ongoing progress toward the synthesis of the bis-tetrahydroisoquinoline natural product jorumycin is detailed. In a departure from the efforts toward curvularin and the integrastatins, jorumycin has been targeted through the application of a combination of aryne annulation and acyl-alkylation/condensation methodologies aimed at the synthesis of a functionalized bis-isoquinoline intermediate. Reduction of this key bis-isoquinoline to a bis-tetrahydroisoquinoline and subsequent lactamization provided the pentacyclic core of jorumycin and related natural products in only two steps from simple isoquinoline building blocks.
", "doi": "10.7907/0HAZ-QF41", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7104", "collection": "thesis", "collection_id": "7104", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302012-182258575", "primary_object_url": { "basename": "pt_thesis.pdf", "content": "final", "filesize": 4354641, "license": "other", "mime_type": "application/pdf", "url": "/7104/1/pt_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Atomistic Simulations of Materials: Methods for Accurate Potentials and Realistic Time-Scales", "author": [ { "family_name": "Tiwary", "given_name": "Pratyush", "clpid": "Tiwary-Pratyush" } ], "thesis_advisor": [ { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "van de Walle", "given_name": "Axel", "clpid": "van-de-Walle-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales.
\r\n\r\nI develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies.
\r\n\r\nA hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well. The robustness of the algorithm with respect to the only free parameter it involves is ascertained.
\r\n\r\nThe method is then applied to perform tensile tests on gold nanopillars on strain rates as low as 100/s, bringing out the perils of high strain-rate molecular dynamics calculations. We also calculate temperature and stress dependence of activation free energy for surface nucleation of dislocations in pristine gold nanopillars under realistic loads. While maintaining fully atomistic resolution, we reach the fraction-of-a-second time scale regime. It is found that the activation free energy depends significantly and nonlinearly on the driving force (stress or strain) and temperature, leading to very high activation entropies for surface dislocation nucleation.
", "doi": "10.7907/J8W9-XS70", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6865", "collection": "thesis", "collection_id": "6865", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03252012-235254880", "primary_object_url": { "basename": "Full.pdf", "content": "final", "filesize": 40574665, "license": "other", "mime_type": "application/pdf", "url": "/6865/21/Full.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Nanostructured Silicon Thermoelectrics", "author": [ { "family_name": "Yu", "given_name": "Jen-Kan", "clpid": "Yu-Jen-Kan" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The thesis discusses the thermoelectric properties of silicon nanostructures with a particular focus on their heat transport phenomenon. The aim of this thesis work is to design ultra-low thermal conductivity materials based on fundamental phonon physics. Silicon nanowires and silicon nanomeshes are the model nanostructure systems investigated in this thesis.
\r\n \r\nDegenerately boron-doped silicon nanowires (20 nm x 20 nm cross section) exhibit thermal conductivity, depending on the temperature of interest, roughly two orders of magnitude smaller than bulk silicon with similar impurity concentration. The reduction in thermal conductivity is presumably from increased boundary scattering of the thermal phonons. For smaller nanowire systems (e.g., 10 nm x 20 nm cross section), thermal conductivity lower than the amorphous limit is also observed. Dimensional crossover of the thermal phonons in these ultra-small nanowire systems is proposed to explain the thermal conductivity reduction. Thermoelectric figure-of-merit ZT~1, a two order of magnitude improvement is achieved in 20 nm x 20 nm silicon nanowires at 200K.
\r\n\r\nSilicon nanomeshes are designed to further reduce the thermal conductivity of silicon. The 2-D hole-array is patterned on the silicon nanomesh film as Bragg reflectors to slow down the phonon group velocity. From the direct thermal conductivity measurement via suspended microstructure platform, the coherent scattering mechanism effectively reduces the thermal conductivity of silicon by a factor of two from the nanowire value. In essence, the phononic metamaterial approach essentially creates a new class of silicon-based material with distinct phonon properties, in other words, the theoretical lower limit of thermal conductivity of silicon based on bulk dispersions no longer applies to the phononic nanomeshes. In addition, silicon nanomeshes exhibit bulk-like electrical conductivity rendering them potential high efficiency thermoelectrics.
\r\n\r\nIn Chapter 1, an introduction to the lattice thermal conductivity is given to point out the key parameters affecting the phonon transport, e.g., scattering mechanisms, phonon dispersions and phonon density-of-states. The thermoelectrics fundamentals are given in Chapter 2, as are the experimental results on silicon nanowires. The fabrication and measurement methodologies are also explained in this chapter. In Chapter 3, the phonon transport mechanism of the silicon nanomesh, a new class of phononic metamaterial, is investigated. A coherent phonon scattering mechanism is used to explain the unexpected phonon behaviors. A complete fabrication process flow is also developed in this chapter in order to fully release the nanostructure from the substrate for precise and accurate thermal conductivity measurement. In the last part of the thesis (Chapter 4), the phononic nanomesh approach is extended to a nanomesh superlattice structure. The architectural design is to incorporate interfacial thermal resistance or the Kapitza resistance to further reduce the thermal conductivity of silicon. In addition, device architecture consisting of self-assembled quantum dots is proposed to enhance the thermoelectric efficiency by energy-filtering mechanism.
\r\n", "doi": "10.7907/HPEF-BM21", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6891", "collection": "thesis", "collection_id": "6891", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04042012-095544878", "primary_object_url": { "basename": "yu_ted_2012_thesis.pdf", "content": "final", "filesize": 3137304, "license": "other", "mime_type": "application/pdf", "url": "/6891/1/yu_ted_2012_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Degradations and Improvements in PEM Fuel Cell Materials: A Computational Study\r ", "author": [ { "family_name": "Yu", "given_name": "Ted H.", "clpid": "Yu-Ted-H" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The advantages of Proton Exchange Membrane (PEM) fuel cells include lower operating temperature than other fuel cells and size small enough to fit into a car. Improving the cost and durability of PEM fuel cell materials is a hot topic of research today.
\r\n\r\nThe Nafion membrane and cathode catalysts are two areas where PEM fuel cells have issues of cost, durability, and efficiency. In order to improve these materials, researchers need a better understanding of the detailed mechanisms for basic operation and degradation. Computational quantum mechanics has improved in recent years to the point where it can provide accurate potential energy maps of reactions that are difficult to determine by laboratory experiments alone. With the basic understanding of mechanisms, experimentalists can make educated predictions of ways to improve fuel cell materials.
\r\n\r\nExperimental studies suggest that Nafion degradation is caused by generation of trace radical species (such as OH\u25cf, H\u25cf) when in the presence of H2, O2, and Pt. We use density functional theory (DFT) to construct the potential energy surfaces for various plausible reactions involving intermediates that might be formed when Nafion is exposed to H2 (or H+) and O2 in the presence of the Pt catalyst. We find that OH\u25cf can be generated in trace amounts on the Pt surface from HOOH and OOHad. Next, we look at various ways in which the OH\u25cf can attack the Nafion sidechains or endgroups on the backbone.
\r\n\r\nResearchers are looking for ways to replace the Pt cathode catalyst, due to the preciousness of Pt and the low efficiency of the oxygen reduction reaction (ORR) on Pt, among other things. Alloying Pt with non-precious Co greatly increases the ORR efficiency. However, Pt3Co was reported to not withstand long-cycle testing due to the migration of Co metals onto the catalyst surface and leaching of Co into the electrolyte. To overcome these challenges, we first study Pt3Co to find out what makes these alloys so special in improving fuel cell efficiency, as well as what causes degradation to occur. Then, we apply the principles we learned in proposing improved fuel cell alloy catalysts.
", "doi": "10.7907/0CYM-2B74", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7049", "collection": "thesis", "collection_id": "7049", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182012-130227746", "primary_object_url": { "basename": "qi_an_2012_thesis.pdf", "content": "final", "filesize": 5460155, "license": "other", "mime_type": "application/pdf", "url": "/7049/1/qi_an_2012_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Atomistic Simulations of Material Properties under Extreme Conditions", "author": [ { "family_name": "An", "given_name": "Qi", "orcid": "0000-0003-4838-6232", "clpid": "An-Qi" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Extreme conditions involve low or high temperatures (> 1500 K), high pressures (> 30 MPa), high strains or strain rates, high radiation fluxes (> 100 dpa), and high electromagnetic fields (> 15T). Material properties under extreme conditions can be extremely different from those under normal conditions. Understanding material properties and performance under extreme conditions, including their dynamic evolution over time, plays an essential role in improving material properties and developing novel materials with desired properties.
\r\n\r\nTo understand material properties under extreme conditions, we use molecular dynamics (MD) simulations with recently developed reactive force fields (ReaxFF) and traditional embedded atom methods (EAM) potentials to examine various materials (e.g., energetic materials and binary liquids) and processes. The key results from the simulations are summarized below.
\r\n\r\nAnisotropic sensitivity of RDX crystals: Based on the compress-and-shear reactive dynamics (CS-RD) simulations of cyclotrimethylene trinitramine (RDX) crystals, we predict that for mechanical shocks between 3 and 7 GPa, RDX is the most sensitive to shocks perpendicular to the (100) and (210) planes, while it is insensitive to those perpendicular to the (120), (111), and (110) planes. The simulations demonstrate that the molecular origin of anisotropic shock sensitivity is the steric hindrance to shearing of adjacent slip planes.
\r\n\r\nMechanisms of hotspot formation in polymer bonded explosives (PBXs): The simulations of a realistic model of PBXs reveal that hotspots may form at the nonplanar interfaces where shear relaxation leads to a dramatic temperature increase that persists long after the shock front has passed the interface. For energetic materials this temperature increase is coupled to chemical reactions that eventually lead to detonation. We show that decreasing the density of the binder eliminates the hotspots or reduces the sensitivity.
\r\n\r\nCavitation in binary metallic liquids: We demonstrate the stochastic nature of the cavitation process in binary metallic liquids, and that classical nucleation theory can predict the cavitation rate if we incorporate the Tolman length derived from the MD simulations.
\r\n\r\nSynthesis the single metallic glass on amorphous substrate: We show that single component metallic glasses (SCMGs) can be synthesized by thermal spray coating of nanodroplets onto an amorphous substrate (ND-AS). The key requirements to form the SCMGs are the rapid cooling rates and the amorphous substrates.
\r\n\r\nCarbon and hydrogen phases under extreme conditions: we report on the use of electron force fields (eFF) in characterizing the Hugoniot relationships of carbon, which includes consecutive phase transitions also captured by experiments, as well as the Hugonoit states of hydrogen centered at various initial densities compared to experiments and the predictions of other theories.
\r\n", "doi": "10.7907/E3Z0-1A27", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6977", "collection": "thesis", "collection_id": "6977", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04262012-115237724", "primary_object_url": { "basename": "PLT_thesis.pdf", "content": "final", "filesize": 172102892, "license": "other", "mime_type": "application/pdf", "url": "/6977/1/PLT_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Quantum Electron Dynamics of Materials Subjected to Extreme Environments", "author": [ { "family_name": "Theofanis", "given_name": "Patrick Lauren", "clpid": "Theofanis-Patrick-Lauren" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Quantum wavepacket molecular dynamics simulations are used to study the effects of extreme environments on materials. The electron forcefield (eFF) method provides energies and forces from which wavepackets can be propagated in time under conditions ranging from standard temperature and pressure to tens of thousands of Kelvin and hundreds of GPa of pressure with strain rates as high as 1 km per second. Using this technique nanometer scale systems with hundreds of thousands of particles can be simulated for up to hundreds of picoseconds.
\r\n\r\nHigh strain rate fracture in solids is accompanied by the emission of electrons and photons, though atomistic simulations have thus far been unable to capture such processes. The eFF method for nonadiabatic dynamics accounts for electron emission and large potential differences consistent with the experiments, providing the first atomistic description of the origin of these effects. The effects that we explain are (1) loading of a crack leads to a sudden onset of crack propagation at 7 GPa followed by uniform velocity of the crack at 2500 km/sec after initiation, and (2) voltage fluctuations in the 10\u2013400 mV range, charge creation (up to 1011 carriers/cm2), and current production (up to 1.3 mA). The development of an effective core potential for eFF enabled this large scale study.
\r\n\r\nUsing the eFF wavepacket molecular dynamics method, simulations of the single shock Hugoniot are reported for crystalline polyethylene (PE). The eFF results are in good agreement with previous DFT theories and experimental data which is available up to 80 GPa. We predict shock Hugoniots for PE up to 350 GPa. In addition, we analyze the phase transformations that occur due to heating. Our analysis includes ionization fraction, molecular decomposition, and electrical conductivity during isotropic compression. We find that above a compression of 2.4 g/cc the PE structure transforms into a Lennard-Jones fluid, leading to a sharp increase in electron ionization and a significant increase in system conductivity. eFF accurately reproduces shock pressures and temperatures for PE along the single shock Hugoniot.
", "doi": "10.7907/BJ5N-QV45", "publication_date": "2012-06-15", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7096", "collection": "thesis", "collection_id": "7096", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05302012-122930768", "primary_object_url": { "basename": "master.pdf", "content": "final", "filesize": 10961399, "license": "other", "mime_type": "application/pdf", "url": "/7096/1/master.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "I. Quantal Effects in Biochemical Cooperativity and a Proposed Mechanism for the Differentiation of Calcium Signaling in Synaptic Plasticity. II. Evolutionary Algorithms for the Optimization of Methods in Computational Chemistry", "author": [ { "family_name": "Ford", "given_name": "William Chastang", "clpid": "Ford-William-Chastang" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Elowitz", "given_name": "Michael B.", "clpid": "Elowitz-M-B" }, { "family_name": "Abrol", "given_name": "Ravinder", "clpid": "Abrol-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In Part 1 of this thesis, we propose that biochemical cooperativity is a fundamentally non-ideal process. We show quantal effects underlying biochemical cooperativity and highlight apparent ergodic breaking at small volumes. The apparent ergodic breaking manifests itself in a divergence of deterministic and stochastic models. We further predict that this divergence of deterministic and stochastic results is a failure of the deterministic methods rather than an issue of stochastic simulations.
\r\n\r\nErgodic breaking at small volumes may allow these molecular complexes to function as switches to a greater degree than has previously been shown. We propose that this ergodic breaking is a phenomenon that the synapse might exploit to differentiate Ca2+ signaling that would lead to either the strengthening or weakening of a synapse. Techniques such as lattice-based statistics and rule-based modeling are tools that allow us to directly confront this non-ideality. A natural next step to understanding the chemical physics that underlies these processes is to consider in silico specifically atomistic simulation methods that might augment our modeling efforts.
\r\n\r\nIn the second part of this thesis, we use evolutionary algorithms to optimize in silico methods that might be used to describe biochemical processes at the subcellular and molecular levels. While we have applied evolutionary algorithms to several methods, this thesis will focus on the optimization of charge equilibration methods. Accurate charges are essential to understanding the electrostatic interactions that are involved in ligand binding, as frequently discussed in the first part of this thesis.
", "doi": "10.7907/Z9HH6H1Z", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7066", "collection": "thesis", "collection_id": "7066", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05222012-224148199", "type": "thesis", "title": "Mechanistic Insights into Alkane C-H Activation and Functionalization by Metal Oxide Surfaces and Organometallic Complexes", "author": [ { "family_name": "Cheng", "given_name": "Mu-Jeng", "clpid": "Cheng-Mu-Jeng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Alkanes are the major components of natural gas and petroleum; however, there are only few practical processes that can functionalize them into more valuable products such as alkene or alcohols. The reason for this difficulty is because alkanes possess strong and inert C-H bonds. The development of such a process that can convert alkanes to other more valuable functionalized hydrocarbons in a catalytic fashion would produce enormous economic benefits. The key to achieve this goal is to develop a proper catalyst. The catalysts can be organometallic complexes or metal oxide surfaces that catalyze alkane C-H activation and functionalization in homogeneous or heterogeneous conditions.
\r\n\r\nIn this thesis, we apply quantum mechanics to study the known alkane functionalization reactions to provide more insight into those catalytic processes, and we further utilize our computational results to design new reaction pathways for alkane functionalization. Each chapter presented herein constitutes an independent publication focusing on different aspects of the problem.
\r\n\r\nChapter 1: Single-Site Vanadyl Activation, Functionalization, and Reoxidation Reaction Mechanism for Propane Oxidative Dehydrogenation on the Cubic V4O10 Cluster: Vanadium oxide is a powerful heterogeneous catalyst that can convert oxidative dehydrogenation (ODH) of propane. Despite numerous studies, either computational or experimental, on this topic, no complete catalytic cycle is provided. In this paper, we examined the detailed mechanism for propane reacting with a V4O10 cluster to model the catalytic oxidative dehydrogenation (ODH) of propane on the V2O5(001) surface. We reported the mechanism of the complete catalytic cycle, including the regeneration of the reduced catalyst using gaseous O2, in which only a single vanadyl site is involved. This mechanism is applicable to propane ODH on the supported vanadium oxide catalysts where only monovanadate (O=V-(O)4-) species is present.
\r\n \r\nChapter 2: The Magnetic and Electronic Structure of Vanadyl Pyrophosphate from Density Functional Theory: We have studied the magnetic structure of the high-symmetry vanadyl pyrophosphate, focusing on the spin exchange couplings, applying density functional theory with exact exchange and the full three-dimensional periodicity to this system for the first time. Based on the local density of states and the response of spin couplings to varying the cell parameter a, we found that two major types of spin exchange couplings originate from different mechanisms: one from a super-exchange interaction and the other from a direct exchange interaction. Based on the variations in V\u2013O bond length as a function of strain along a, we found that the V\u2013O bonds of V\u2013(OPO)2\u2013V are covalent and rigid, whereas the bonds of V\u2013(O)2\u2013V are fragile and dative.
\r\n\r\nChapter 3: The Para-Substituent Effect and pH-Dependence of the Organometallic Baeyer-Villiger Oxidation of Rhenium-Carbon Bonds: Organometallic Baeyer-Villiger represents another means of oxidizing M-R to M-OR. In this work, we conducted a series of calculations with the goal of providing more insights into the reaction. We find that during this organometallic BV oxidation, the migrating phenyl plays the role of a nucleophile and the leaving group OH is nucleophile. Moreover, we also find that for R = Ph the reaction rate is much faster than that for R = Me, which is later confirmed by experiments.
\r\n\r\nChapter 4: Carbon-Oxygen Bond-Forming Mechanisms in Rhenium Oxo-Alkyl Complexes: Intramolecular 1,2-migration of hydrocarbyl across metal-oxo bonds is one of the few means of oxy-functionalizing M-R to M-OR bonds. This strategy works for R = Ph, but fails for R = Me and Et. In this work, we study these systems with the goal of understanding the reason. We find that when R = Me and Et the \u03b1-hydrogen is very acidic and easy to abstract even with weak base, such as the counter ion of the complex, leading to unwanted by-products. We find that these side reactions can be avoided by two means: (1) use counter ions with weaker basicity to increase proton abstraction barriers, and (2) use R = iPr, which has a higher migratory aptitude, to accelerate the 1,2-migration rate.
\r\n \r\nChapter 5: A Homolytic Oxy-Functionalization Mechanism: Intermolecular Hydrocarbyl Migration from M-R to Vanadyl Oxo: Oxy-functionalization M\u03b4+-R\u03b4- to M-OR bonds is one of the key challenges in the development of hydrocarbon hydroxylation catalysts. This can be achieved by limited means: (1) organometallic Baeyer-Villiger oxidation, and (2) intramolecular 1,2-migration of hydrocarbyl across metal-oxo bonds. In this work, we have examined C-O bond formation in the reaction of OVCl3 with Ph2Hg to generate phenol using quantum mechanics. Surprisingly, we find this reaction is through an unprecedented bimolecular, one-electron oxidation of the V-Ph bond by a second V=O moiety, not through the experimentally proposed intramolecular phenyl 1,2-migration across V=O bonds. Our calculations on the oxidation of Rh-CH3 and Ir-CH3 complexes by OVCl3 further suggest that the possibility of integrating this new oxidation mechanism into alkane oxidation catalytic cycles. We also give guidelines to choose the systems in which this oxidation mechanism may play an important role.
", "doi": "10.7907/K4XH-V434", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6997", "collection": "thesis", "collection_id": "6997", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05012012-155623422", "primary_object_url": { "basename": "chen_li_2012_thesis.pdf", "content": "final", "filesize": 12515166, "license": "other", "mime_type": "application/pdf", "url": "/6997/1/chen_li_2012_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Phonon Anharmonicity of Ionic Compounds and Metals", "author": [ { "family_name": "Li", "given_name": "Chen W.", "orcid": "0000-0002-0758-5334", "clpid": "Li-Chen-W" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" }, { "family_name": "Minnich", "given_name": "Austin J.", "clpid": "Minnich-A-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Vibrational studies of materials at elevated temperatures are relatively rare, and most phonon work also has emphasized harmonic behavior. Non-harmonic effects are often unexplored. These non-harmonic effects can be important for many properties of the material, such as thermal transport and phase stability.
\r\n\r\nPhonon theory and computational methods are briefly reviewed, and the experimental techniques for phonon study, such as Raman spectroscopy and inelastic neutron scattering, are discussed. Several experiments on phonon anharmonicity were performed, and interpreted with these computational methods.
\r\n\r\nIn Raman spectroscopy studies on the phonon dynamics of hafnia and zirconia, Raman line positions, and shapes of temperatures to 1000 K were measured and the types of modes that exhibit the most anharmonicity were characterized and correlated to the vibrational displacements of individual atoms in the unit cell. It was found that anharmonicity in these systems is rich in information and strongly mode dependent.
\r\n\r\nUsing time-of-flight inelastic neutron scattering, we found purely quartic transverse modes with an anomalous mode stiffening with temperature, and related these modes to the enormous negative thermal expansion of the DO9 structure of scandium fluoride.
\r\n\r\nUsing second-order perturbation theory, phonon linewidths from the third-order anharmonicity were calculated from first-principles density functional theory with the supercell finite-displacement method. For face-centered cubic aluminum, the good agreement between calculations and the phonon density of states up to 750 K indicates that the third-order phonon-phonon interactions calculated can account for the lifetime broadenings of phonons in aluminum to at least 80% of its melting temperature.
", "doi": "10.7907/7VS5-0F52", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:7091", "collection": "thesis", "collection_id": "7091", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292012-220632933", "primary_object_url": { "basename": "JoseMendozaCortes_Thesis.pdf", "content": "final", "filesize": 57334900, "license": "other", "mime_type": "application/pdf", "url": "/7091/1/JoseMendozaCortes_Thesis.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Design of Molecules and Materials for Applications in Clean Energy, Catalysis and Molecular Machines Through Quantum Mechanics, Molecular Dynamics and Monte Carlo Simulations", "author": [ { "family_name": "Mendoza-Cortes", "given_name": "Jose Luis", "orcid": "0000-0001-5184-1406", "clpid": "Mendoza-Cortes-Jose-Luis" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Agapie", "given_name": "Theodor", "orcid": "0000-0002-9692-7614", "clpid": "Agapie-T" }, { "family_name": "Greer", "given_name": "Julia R.", "orcid": "0000-0002-9675-1508", "clpid": "Greer-J-R" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "We use a multiparadigm, multiscale strategy based on quantum mechanics (QM), first-principles QM-based molecular mechanics (MD) and grand canonical Monte Carlo (GCMC) to rationally design new molecules and materials for clean energy (H2 and CH4 storage), catalysis (O2 evolution, metal organic complexes) and molecular architectures (rotaxanes, hydrogels). This thesis is organized in seven chapters and shows that it is crucial to understand the scale of the system to be studied, the insight obtained can be used to rationally design new molecules and materials for desirable applications; as well as to guide and complement experimental studies. Chapter 1 discusses the specific details of the proposed methodology, including the theoretical underpinning of each modeling paradigm, potential limitations, and how we use these for in silico characterization and design optimization. Chapter 2 covers the structure prediction and characterization of metal-organic complex arrays (MOCA) through QM and force-field-based molecular mechanics. The methodology is inspired by the approach used for enzymatic systems, considering that experimentally determining their three-dimensional structure remains an open challenge. Chapter 3 describes the use of transition state theory for the calculation of reaction rates in polymer hydrogel network formation. This enables the determination of optimum concentrations for polymerization reactions and preparation of coarse-grained force elds. Chapter 4 describes the work performed on Stoddard's rotaxane dumbbells, where we explained origin for the template-directed synthesis through QM-derived free energies. We also give a consistent explanation for the role of the counter anion. Chapter 5 presents the simulation results for a tetranuclear cluster model for O2 evolution, based on CaMn304 and Mn4O4 clusters. We demonstrate how to calculate their oxidation potentials and propose new molecular designs that resemble the oxygen evolution complex (OEC) both structurally and electronically. Chapter 6 presents our findings for CH4 storage. Using a second-order Moller-Plesset perturbation theory force field and GCMC we propose a framework for optimal delivery. Chapter 7 presents our designed materials for hydrogen storage and the validation of our methodology against experimental results. We based our predictions in QM and GCMC calculations through the development of our own first-principles vdW force eld. Our results demonstrate novel frameworks capable of achieving the DOE energy density target for 2015. Finally, we show the generalization of adsorption phenomena for any porous material based on topological constraints.", "doi": "10.7907/PQ74-HK88", "publication_date": "2012", "thesis_type": "phd", "thesis_year": "2012" }, { "id": "thesis:6451", "collection": "thesis", "collection_id": "6451", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262011-123505549", "primary_object_url": { "basename": "ECBrown_Thesis_FINAL.pdf", "content": "final", "filesize": 33348428, "license": "other", "mime_type": "application/pdf", "url": "/6451/7/ECBrown_Thesis_FINAL.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Electrochemically Deposited Ceria Structures for Advanced Solid Oxide Fuel Cells", "author": [ { "family_name": "Brown", "given_name": "Evan Cornell", "clpid": "Brown-Evan-Cornell" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "As the pursuit towards emissions reduction intensifies with growing interest and nascent technologies, solid oxide fuel cells (SOFCs) remain an illustrious candidate for achieving our goals. Despite myriad advantages, SOFCs are still too costly for widespread deployment, even as unprecedented materials developments have recently emerged. This suggests that, in addition to informed materials selection, the necessary power output\u2014and, thereby, cost-savings\u2014gains must come from the fuel cell architecture. The work presented in this manuscript primarily investigates cathodic electrochemical deposition (CELD) as a scalable micro-/nanoscale fabrication tool for engineering ceria-based components in a SOFC assembly. Also, polymer sphere lithography was utilized to deposit fully connected, yet fully porous anti-dot metal films on yttira-stabilized zirconia (YSZ) with specific and knowable geometries, useful for mechanistic studies. Particular attention was given to anode structures, for which anti-dot metal films on YSZ served as composite substrates for subsequent CELD of doped ceria. By tuning the applied potential, a wide range of microstructures from high surface area coatings to planar, thin films was possible. In addition, definitive deposition was shown to occur on the electronically insulating YSZ surfaces, producing quality YSZ|ceria interfaces. These CELD ceria deposits exhibited promising electrochemical activity, as probed by A.C. Impedance Spectroscopy. In an effort to extend its usefulness as a SOFC fabrication tool, the CELD of ceria directly onto common SOFC cathode materials without a metallic phase was developed, as well as templated deposition schemes producing ceria nanowires and inverse opals.", "doi": "10.7907/93NE-TG09", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6385", "collection": "thesis", "collection_id": "6385", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05112011-205842246", "primary_object_url": { "basename": "Thesis-YaoSha.pdf", "content": "final", "filesize": 1619430, "license": "other", "mime_type": "application/pdf", "url": "/6385/1/Thesis-YaoSha.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Mechanisms of the Fuel Cell Oxygen Reduction Reaction on Pt and Other 8-11 Column Metal Surfaces", "author": [ { "family_name": "Sha", "given_name": "Yao", "clpid": "Sha-Yao" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "To better understand and improve the cathode process for Proton exchange membrane fuel cell, we studied systematically the mechanism of oxygen reduction reaction (ORR) on group 8\u201311 metals and their alloys using density functional theory calculations. To address the contribution of solvent effect, we developed a practical implicit solvation model based on Poisson-Boltzmann equation. We discovered that solvation changed greatly the reaction barriers and hence the pathways preferences. The two well known mechanisms O2-diss and OOH-form mechanisms become impossible with water solvation. Instead, we found three new alternative mechanisms, namely, O2-diss-hydr, OOH-form-hydr, and high-H mechanisms. We showed that the oxygen hydrolysis Oad + H2Oad -> 2OHad plays an important role in the ORR which leads to the preferred O2-diss-hydr mechanism. We also developed a method to study the processes involving electron transfer between the solvent and the electrode. We found that direct OH formation from Oad and H3O+ has a high barrier of 0.70eV and is hence unlikely to be the dominant way of forming OHad at the operating potential of 0.8V. The potential dependent barrier leads to an overall optimal operating potential of 0.68V. We also studied the ORR on Pt3Ni alloys and found that the sublayer Ni atoms imposes an inhomogeneity in surface binding sites. The different binding energies make the barriers coverage dependent. Pt3Ni can only outperform Pt at higher coverage. We also showed the general approach of studying an unknown alloying system using Pd-Cu system as an example. We studied the structural, surface cleavage, and binding site preferences for various types of PdCu alloys. We predicted that 1:1 PdCu alloy with L11 structure and layered surface is a better catalyst than pure Pd and Cu, which agrees with later experiments. ", "doi": "10.7907/7VD4-FY21", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6420", "collection": "thesis", "collection_id": "6420", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05232011-144137426", "primary_object_url": { "basename": "Louie-completeThesis.pdf", "content": "final", "filesize": 16789004, "license": "other", "mime_type": "", "url": "/6420/5/Louie-completeThesis.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Electrocatalysis in Solid Acid Fuel Cells", "author": [ { "family_name": "Louie", "given_name": "Mary W. C.", "clpid": "Louie-Mary-W-C" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "clpid": "Giapis-K-P" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Solid state electrochemical reactions play a crucial role in many energy conversion devices, yet the pathways of many reactions remain unknown. The elusiveness of the reaction mechanisms is due, in part, to the complexity of electrochemical reactions; because electrochemical reactions require the interaction of many species (e.g., ions, electrons, and adsorbates) across multiple phases (e.g., electrolyte, catalyst, and gas phases), elucidation of the reaction pathway can quickly become complicated. In this work, we develop and utilize model catalyst | electrolyte systems, that is, structures of reduced complexity, to study electrode reactions in solid acid fuel cells which operate at intermediate temperatures of ~ 250 \u00baC. We employ AC impedance spectroscopy to explore the reaction pathway for hydrogen electro-oxidation over Pt thin films sputter-deposited atop the proton-conducting solid acid electrolyte CsH2PO4. We observed that hydrogen electro-oxidation occurs by diffusion of hydrogen through Pt, taking advantage of the entire Pt | CsH2PO4 interfacial area rather than being confined to the triple-phase sites. This insight opens up new avenues for developing high performance electrodes with low Pt loadings by eliminating the requirement that Pt-based electrodes be comprised of high triple-phase site densities long considered to be critical for Pt electrocatalysis. Indeed, even for flat, planar electrodes of very thin Pt films, we obtained a Pt utilization that is significantly higher than in typical composite electrodes.
\r\n\r\nWe also demonstrate the efficacy of a new tool for probing the spatial heterogeneity of electrochemical reactions at the metal | electrolyte interface. We characterized oxygen electro-reduction kinetics at the nanoscale Pt | CsHSO4 interface at ~ 150 \u00baC using conducting atomic force microscopy in conjunction with cyclic voltammetry and AC impedance spectroscopy. Not only did we find the electrochemical activity for oxygen electro-reduction to vary dramatically across the electrolyte surface but the current-voltage data, when analyzed in the Butler-Volmer framework, exhibited a strong counter-correlation between two key kinetic parameters, the exchange coefficient and exchange current. Specifically, the exchange current spanned five orders of magnitude while the exchange coefficient ranged between 0.1 and 0.6. Such a correlation has not been observed before and points to the power of atomic force microscopy for electrochemical characterization at electrolyte | metal | gas boundaries in general.
\r\n\r\nAs reduction in microstructural complexity is a key advantage in model electrode | electrolyte systems, we also sought to understand the bulk properties of solid acid compounds, specifically, the relationship between microstructure and the superprotonic phase transition, the latter of which lends solid acid compounds their high proton conductivities at intermediate temperatures. We found a correlation between phase transformation hysteresis and crystallographic compatibility of the high- and low-temperature phases of the Cs1\u2013xRbxH2PO4 solid solution series. Therefore, it is to be expected that hysteresis, and therefore microcrack formation, can be minimized during phase transformation via the principle of crystallographic compatibility. This is confirmed in single crystals of CsHSO4, which was found to have higher crystallographic compatibility, lower hysteresis, and significantly fewer microcracks formed during phase transition compared to CsH2PO4. The apparent applicability of the theory of crystallographic compatibility implies a new tool for identifying solid acid compounds with suitable microstructures for fuel cell application and for model electrode | electrolyte systems.\r\n
\r\n", "doi": "10.7907/1HK1-2M22", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6214", "collection": "thesis", "collection_id": "6214", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12162010-142822030", "primary_object_url": { "basename": "Si-ping_Han_PhD_Thesis_version_4_Dec_16_2010.pdf", "content": "final", "filesize": 5652113, "license": "other", "mime_type": "application/pdf", "url": "/6214/1/Si-ping_Han_PhD_Thesis_version_4_Dec_16_2010.pdf", "version": "v10.0.0" }, "type": "thesis", "title": "DNA Directed Self-Assembly of Carbon Nanotube Structures", "author": [ { "family_name": "Han", "given_name": "Si-ping", "orcid": "0000-0002-2213-4953", "clpid": "Han-Si-ping" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Bockrath", "given_name": "Marc William", "clpid": "Bockrath-M-W" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Production of pure carbon nanotube species and organization of nanoscale structure are two fundamental barriers to the utilization of CNTs in nanoelectronics. We have developed new methods to characterize double walled carbon nanotube (DWNT) structure by Raman spectroscopy and organize single walled carbon nanotube (SWNT) constructs using DNA.
\r\n\r\nFirst, using atomistic force fields calculations, we have shown that the radial breathing modes (RBM) of double walled carbon nanotubes can be accurately modeled as two uniform concentric cylindrical elastic shells coupled by a van der Waals interaction. This model leads to a simple equation which can be solved to give accurate RBMs (given diameters) or diameters (given RBMs).
\r\n\r\nSecondly, we have developed a method for using DNA origami to template the assembly of complex SWNT structures. In this process, SWNTs are modified with non-covalently attached DNA linkers that present duplex labeling domains for base pairing to complementary single stranded hooks on customized DNA origami. We show that the SWNTs attach at positions and in orientations specified by their labeling sequence, and that nanotube cross-junctions assembled from two different SWNTs in this manner can behave as field effect transistors.
\r\n\r\nFinally, we have devised a method for using DNA linkers to organize arrays of parallel SWNTs with uniform and selectable inter-nanotube separation of <20 nm. SWNTs are first dispersed in aqueous solution with DNA linkers-spacers that non-covalently anchor onto their sidewalls. When the modified SWNTs are then deposited on mica or polar lipid bilayers and allowed to diffuse on the surface, they form parallel arrays of SWNTs in which different domains of the DNA linker-spacers act to maintain array cohesion and enforce uniform separation. Thus, the use of 7 bp, 20 bp, and 60 bp DNA spacer domains result in ~3 nm, ~8.5 nm, and ~22 nm inter-nanotube separations. We further use the spacer domains as rigid scaffolds for the positioning of Streptavidin proteins between adjacent nanotubes, and give a simple method for transfer of intact arrays onto adhesive glass substrates. Further development of this technology could lead to wafer scale organization of dense parallel SWNT decorated with heterogeneous nanoscale objects.
", "doi": "10.7907/3ZN9-T618", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:6072", "collection": "thesis", "collection_id": "6072", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09282010-221227791", "type": "thesis", "title": "Corrole Sensitized Solar Cells", "author": [ { "family_name": "Walker", "given_name": "Don", "clpid": "Walker-Don" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The performance of dye sensitized solar cells (DSSC) was investigated as a function of electrolyte composition and dye sensitizer. Electrolytes consisting of increasing concentrations of bromide and tri-bromide effectively increased the current of DSSCs while conserving an increase in open circuit voltage. Corroles were used to investigate their efficacy as light absorbers for DSSCs. Electronic spectroscopy of corroles demonstrated that the spectra of corroles could be red shifted through \u03b2 substitution. Also, the changes in the electronic spectra of corroles was not affected by adsorption to TiO2. Electrochemical data concluded that the functionalization of the \u03b2 positions of the corroles did not significantly affect the corrole's redox potentials. FTIR spectroscopy confirmed that the corroles were chemically adsorbed onto TiO2. Photoelectrochemical measurements concluded that the corroles are efficient sensitizers for DSSCs. A highly efficient corrole utilizing sulfonic acid binding groups was discovered. Also, a corrole with a malonic acid binding group was 70% as efficient as one of the best performing dye sensitizers in DSSCs.\r\n", "doi": "10.7907/XQBW-D585", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "id": "thesis:5319", "collection": "thesis", "collection_id": "5319", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-213942982", "primary_object_url": { "basename": "Revised_Thesis_Ying_Wang.pdf", "content": "final", "filesize": 4389057, "license": "other", "mime_type": "application/pdf", "url": "/5319/1/Revised_Thesis_Ying_Wang.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Equilibrium \u00b2H/\u00b9H Fractionations in Organic Molecules ", "author": [ { "family_name": "Wang", "given_name": "Ying", "clpid": "Wang-Ying" } ], "thesis_advisor": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" } ], "thesis_committee": [ { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "\r\nCompound-specific H isotope analysis has become widespread over the past decade and stimulated a variety of studies using the H isotopic composition (\u03b4\u00b2H values) of sedimentary organic molecules as paleoenvironmental proxies. Since alkyl H can be affected by a variety of exchange processes that lead to \u03b4\u00b2H changes on geological timescales, interpretation of empirical \u03b4\u00b2H data must account for these changes, which requires quantitative knowledge regarding the endpoint of the isotopic exchange, i.e., equilibrium fractionation factor (\u03b1eq). Nevertheless, to date relevant data have been lacking for molecules larger than methane. This is because the conventional isotope exchange experiments suffer from the slow exchange rates of C-bound H (half-life ~ 105\u2013106 years), whereas theoretical calculations \u2014 a convenient way to cover many organic structures over wide temperature ranges \u2014 are restricted by systematic biases for the H isotope system.
\r\n\r\nTo remedy the situation, this project was proposed to use experimental equilibration data to calibrate ab initio calculations of \u03b1eq. To accurately measure the value of \u03b1eq within reasonable experimental timescale, I utilized the keto-enol tautomerism that leads to fast equilibration between H positions adjacent to carbonyl groups (denoted as H\u03b1) and water. By equilibrating ketones with waters of varying \u03b4\u00b2H values, the values of \u03b1eq were measured for H\u03b1 positions in a variety of acyclic and cyclic molecular structures at different temperatures. On the other hand, statistical thermodynamics and ab initio QM computations (B3LYP/6-311G**) were applied to calculate \u03b1eq values for the same ketone molecules. Comparison between experimental and theoretical results yields a temperature-dependent linear calibration curve for linear molecules with slope = 1.081\u22120.00376T and intercept = 8.404\u22120.387T (T is temperature in degrees Celsius). For cyclic structures, the calibration is slightly different with slope of 1.44\u00b10.05 and intercept of 32.8\u00b15.1. Application of these calibration curves to more ab initio calculations generates the \u03b1eq values for various H sites in alkanes, alkenes, ketones, carboxylic acids, esters, alcohols, and ethers, with the uncertainties estimated to be 10\u201325\u2030. The effects of functional groups were found to increase the value of \u03b1eq for H next to electron-donating groups, e.g., \u2212OR, \u2212OH or \u2212O(C=O)R, and to decrease the value of \u03b1eq for H next to electron-withdrawing groups, e.g., \u2212(C=O)R or \u2212(C=O)OR. It is analogous to the well-known substituent effects in the aromatic ring system.
\r\n\r\nOur results provide a modular dataset to calculate equilibrium \u00b2H/\u00b9H fractionations for common molecules found in sediments and oils. By summing over individual H positions, the equilibrium fractionation relative to water between 0 and 100\u00b0C is estimated to be \u221270\u2030 to \u221290\u2030 for n-alkanes, around \u2212100\u2030 for acyclic isoprenoids and \u221275 to \u2212100\u2030 for steroids and hopanoids. The temperature dependence of these molecular fractionations is very weak within the relevant temperature range. The results agree well with field data for thermally mature hydrocarbons (\u03b4\u00b2H values between -80\u2030 and -110\u2030 relative to water; Schimmelmann et al., 2006), suggesting that the observed \u03b4\u00b2H changes in sedimentary organic matter can be confidently attributed to H exchange towards an equilibrium state.
\r\n\r\nBecause of the need to accurately measure the widely-ranging \u03b4\u00b2H values encountered in natural and isotopically-exchanged samples, a side project was conducted to quantitatively investigate the isotopic memory effects in compound-specific \u00b2H/\u00b9H analysis by gas chromatography/pyrolysis/isotope-ratio mass spectrometry (GC/P/IRMS), i.e., the situation in which the \u00b2H/\u00b9H ratio of a given chromatographic peak affects that of the following peak(s). Through a series of experiments that employed synthesized esters with \u03b4\u00b2H varying by up to 1000\u2030, we were able to estimate the isotopic memory to be typically 2\u20134% of the nominal \u03b4\u00b2H difference between two adjacent peaks. It increases with decreasing time separation, increasing analyte abundance of the preceding peak, or increasing age of the pyrolysis reactor. Roughly half of the memory effect can be attributed to the H2-adsorption process in the pyrolytic reactor, and the other half to unknown processes within the GC. Finally, based on our experimental and model study, modifications in routine analyses were proposed to mitigate memory effects.
", "doi": "10.7907/4MPX-MF10", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5278", "collection": "thesis", "collection_id": "5278", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09032009-105125", "primary_object_url": { "basename": "thesis_jenelle_bray.pdf", "content": "final", "filesize": 3782190, "license": "other", "mime_type": "application/pdf", "url": "/5278/1/thesis_jenelle_bray.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Development and Application of Computational Methods for the Prediction of G Protein-Coupled Receptor Structures", "author": [ { "family_name": "Bray", "given_name": "Jenelle Kiara", "clpid": "Bray-Jenelle-Kiara" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Clemons", "given_name": "William M.", "clpid": "Clemons-W-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Computational methods for the prediction of G protein-coupled receptor (GPCR) structures were applied to serotonin receptors, and new methods were developed to predict an orphan GPCR structure. First, the MembStruk procedure was used to predict the structures of the serotonin 2b and 2c receptors. Ligand binding sites for agonists and antagonists were predicted for both receptors. In addition, the SAR data for a series of psilocybin analogs bound to serotonin 2c were predicted. There was good agreement with binding and mutagenesis experiments.
\r\n\r\nA new structure prediction procedure called SuperBiHelix was developed to predict an ensemble of low-lying structures. SuperBiHelix samples the tilt and sweep angles of the transmembrane helices along with the rotation of the helices along the helical axes. The procedure was validated on the \u03b22-adrenergic receptor and A2A adenosine receptor crystal structures. This procedure was then used to predict the structure of GPR88, an orphan receptor. GPR88 has been identified as a novel target for psychiatric disorders. Three lipids were predicted to bind to GPR88. The head group of a lipid would bind to R113(3) and R116(3) at the extracellular side of the receptor. The lipid tail would bind in an aliphatic pocket in the TM2-TM3-TM6-TM7 region. The predicted bound complexes offer good suggestions for binding and mutagenesis experiments that could help validate the proposed structures.
\r\n", "doi": "10.7907/1655-ES74", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5332", "collection": "thesis", "collection_id": "5332", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10262009-204842274", "primary_object_url": { "basename": "tpascal_thesis.pdf", "content": "final", "filesize": 11748720, "license": "other", "mime_type": "application/pdf", "url": "/5332/1/tpascal_thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "New Approaches to Accurate Predictions of Free Energies: From Proteins to Organic Nanostructures", "author": [ { "family_name": "Pascal", "given_name": "Tod Augustin", "orcid": "0000-0003-2096-1143", "clpid": "Pascal-Tod-Augustin" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Winfree", "given_name": "Erik", "orcid": "0000-0002-5899-7523", "clpid": "Winfree-E" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Although computer simulations have been applied to the calculation of solvation free energies for a wide range of molecules, reliable calculations including explicit consideration of entropy and quantum effects (zero-point energy corrections) are less common, owing to the enormous computational effort required by standard perturbation methods. Accurate calculations of entropies are essential if computer simulations are to become more useful tools for obtaining molecular insights into solvation and ligand binding phenomena.
\r\n\r\nWe report on the extension of a method of calculating exact entropies and quantum effects from standard MD simulations. This novel method is applied to the investigation of three model cases: 1) the folding of a DNA three-way junction 2) the efficacy of binding in a protein-protein interaction, critical in the pathogenesis of bacterial meningitis in neonates and 3) the free energy of water molecules at two extreme surfaces, as model systems for an investigation of the hydrophobic effect. We develop a scheme to partition the free energy into the per-atom components, and show that the water molecules in the first hydration shell have unique character. Understanding their nature is critical to discovering the underlying physics in these systems.
", "doi": "10.7907/P0JH-QM60", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5844", "collection": "thesis", "collection_id": "5844", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262010-132424180", "primary_object_url": { "basename": "thesis_jmueller_final.pdf", "content": "final", "filesize": 3921784, "license": "other", "mime_type": "application/pdf", "url": "/5844/1/thesis_jmueller_final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Structures, Energetics and Reactions of Hydrocarbons on Nickel", "author": [ { "family_name": "Mueller", "given_name": "Jonathan Edward", "orcid": "0000-0001-8811-8799", "clpid": "Mueller-Jonathan-Edward" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "To better understand and improve reactive processes on nickel surfaces such as the catalytic steam reforming of hydrocarbons, the decomposition of hydrocarbons at fuel cell anodes, and the growth of carbon nanotubes, we have performed atomistic studies of hydrocarbon adsorption and decomposition on low index nickel surfaces and nickel catalyst nanoparticles. Quantum mechanics (QM) calculations utilizing the PBE flavor of density functional theory (DFT) were performed on all CHx and C2Hy species to determine their structures and energies on Ni(111). In good agreement with experiments, we find that CH is the most stable form of CHx on Ni(111). It is a stable intermediate in both methane dehydrogenation and CO methanation, while CH(2,ad) is only stable during methanation. We also find that nickel surface atoms play an important catalytic role in C-H bond formation and cleavage. For the C2Hy species we find a low surface coverage decomposition pathway proceeding through CHCHad, the most stable intermediate, and a high surface coverage pathway which proceeds through CCH3,ad, the next most stable intermediate. Our enthalpies along these pathways are consistent with experimental observations.
\r\n\r\nTo extend our study to larger systems and longer time scales, we have developed the ReaxFF reactive force field to describe hydrocarbon decomposition and reformation on nickel catalyst surfaces. The ReaxFF parameters were fit to geometries and energy surfaces from DFT calculations involving a large number of reaction pathways and equations of state for nickel, nickel carbides, and various hydrocarbon species chemisorbed on Ni(111), Ni(110) and Ni(100). The resulting ReaxFF description was validated against additional DFT data to demonstrate its accuracy, and used to perform reaction dynamics (RD) simulations on methyl decomposition for comparison with experiment. Finally ReaxFF RD simulations were applied to the chemisorption and decomposition of six different hydrocarbons (methane, acetylene, ethylene, benzene, cyclohexane and propylene) on a 468 atom nickel nanoparticle. These simulations realistically model hydrocarbon feedstock decomposition and provide reaction pathways relevant to this part of the carbon nanotube growth process. They show that C-C \u03c0 bonds provide a low barrier pathway for chemisorption, and that the low energy of subsurface C is an important driving force in breaking C-C bonds.
", "doi": "10.7907/RVXX-Z341", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5270", "collection": "thesis", "collection_id": "5270", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06262009-144008", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 4996181, "license": "other", "mime_type": "application/pdf", "url": "/5270/11/thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Biochemical Reactions in Confined Space", "author": [ { "family_name": "Liu", "given_name": "Yu", "clpid": "Liu-Yu" } ], "thesis_advisor": [ { "family_name": "Collier", "given_name": "C. Patrick", "orcid": "0000-0002-8198-793X", "clpid": "Collier-C-P" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Collier", "given_name": "C. Patrick", "orcid": "0000-0002-8198-793X", "clpid": "Collier-C-P" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The understanding of biological systems relies on the accurate description of the interaction among biomolecules. This knowledge can be obtained by in vitro assays involving interacting partners with well-defined compositional, spatial, and temporal constraints. The distinguishing features of living systems, namely, low copy number, crowded environment, and spatial compartmentalization, are usually absent in most in vitro experiments reported in the literature. This thesis discusses the implications of low copy number and spatial constraints using theoretical and computational methods in some model systems. Furthermore, two experimental platforms, based on the recent development of microfluidic techniques, are described in detail. In the first implementation, micronsized chambers fabricated using soft lithography provide a high-throughput reactor array whose size and composition can be configured to mimic the in vivo environment. The second design reports the generation and manipulation of femtoliter-volume water-in-oil droplets. A model biochemical reaction catalyzed by beta-galactosidase is observed in both reactors with precisely defined initiation time, opening the way to monitor transient kinetics in addition to steady-state behavior. Additionally, the enzymatic activity exhibits a negative correlation with the size of water-in-oil droplets when the nominal concentrations of reagents are kept the same. This surprising result is analyzed in detail by carefully designed control experiments, and attributed to the shear-induced redistribution of surfactant employed to stabilize the water/oil interface. Specifically, smaller droplets experience bigger shear stress, which change the surface concentration of surfactant and allow for the nonspecific binding of proteins to the interface. Surface-bound enzymes are denatured, leading to reduced catalytic activity. This highly dynamic process is hardly detectable by other methods such as tensiometry or direct fluorescence imaging of the interface.", "doi": "10.7907/W9H8-8T44", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5276", "collection": "thesis", "collection_id": "5276", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08122009-151332", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 1729685, "license": "other", "mime_type": "application/pdf", "url": "/5276/1/thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Quantum Monte Carlo: Faster, More Reliable, and More Accurate", "author": [ { "family_name": "Anderson", "given_name": "Amos Gerald", "clpid": "Anderson-Amos-Gerald" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Miller", "given_name": "Thomas F.", "clpid": "Miller-T-F" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The Schroedinger Equation has been available for about 83 years, but today, we still strain to apply it accurately to molecules of interest. The difficulty is not theoretical in nature, but practical, since we're held back by lack of sufficient computing power. Consequently, effort is applied to find acceptable approximations to facilitate real time solutions. In the meantime, computer technology has begun rapidly advancing and changing the way we think about efficient algorithms. For those who can reorganize their formulas to take advantage of these changes and thereby lift some approximations, incredible new opportunities await.
\r\n\r\nOver the last decade, we've seen the emergence of a new kind of computer processor, the graphics card. Designed to accelerate computer games by optimizing quantity instead of quality in processor, they have become of sufficient quality to be useful to some scientists. In this thesis, we explore the first known use of a graphics card to computational chemistry by rewriting our Quantum Monte Carlo software into the requisite \"data parallel\" formalism. We find that notwithstanding precision considerations, we are able to speed up our software by about a factor of 6.
\r\n\r\nThe success of a Quantum Monte Carlo calculation depends on more than just processing power. It also requires the scientist to carefully design the trial wavefunction used to guide simulated electrons. We have studied the use of Generalized Valence Bond wavefunctions to simply, and yet effectively, captured the essential static correlation in atoms and molecules. Furthermore, we have developed significantly improved two particle correlation functions, designed with both flexibility and simplicity considerations, representing an effective and reliable way to add the necessary dynamic correlation. Lastly, we present our method for stabilizing the statistical nature of the calculation, by manipulating configuration weights, thus facilitating efficient and robust calculations.
\r\n\r\nOur combination of Generalized Valence Bond wavefunctions, improved correlation functions, and stabilized weighting techniques for calculations run on graphics cards, represents a new way for using Quantum Monte Carlo to study arbitrarily sized molecules.
", "doi": "10.7907/KVTV-N754", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5791", "collection": "thesis", "collection_id": "5791", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05102010-145436548", "primary_object_url": { "basename": "Thesis_Morgan_L_Cable_2010.pdf", "content": "final", "filesize": 10854325, "license": "other", "mime_type": "application/pdf", "url": "/5791/1/Thesis_Morgan_L_Cable_2010.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Life in Extreme Environments: Lanthanide-Based Detection of Bacterial Spores and Other Sensor Design Pursuits", "author": [ { "family_name": "Cable", "given_name": "Morgan Leigh", "orcid": "0000-0002-3680-302X", "clpid": "Cable-Morgan-Leigh" } ], "thesis_advisor": [ { "family_name": "Ponce", "given_name": "Adrian", "clpid": "Ponce-A" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Ponce", "given_name": "Adrian", "clpid": "Ponce-A" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Bacterial spores, or endospores, are produced by certain genera of bacteria under stress and are considered to be one of the most resilient forms of life on Earth. Detection of endospores is vital in areas ranging from bioburden reduction to homeland security. Rapid bacterial spore detection is achieved by targeting dipicolinic acid (DPA), a chemical marker unique to endospores. An improvement on the current bacterial spore detection assay based on sensitized lanthanide luminescence is presented through the implementation of a dipicolinate-specific Tb3+ receptor site. The use of a chelating ligand such as DO2A (1,4,7,10-tetraazacyclododecane-1,7-bisacetate) can increase both the sensitivity and selectivity of the assay. The luminescent series of Ln(DO2A)(DPA)- complexes (Ln = Sm, Eu, Tb and Dy) is fully characterized in terms of structure, photophysics and stability, and the Tb(DO2A)+ binary complex in particular is investigated as a sensing complex for bacterial spores. The \u2018ligand enhancement\u2019 observed in all cases improves dipicolinate binding affinity by approximately one order of magnitude over the lanthanide ion alone. Binding of the DO2A ligand also appears to generate a \u2018gadolinium break\u2019 effect, creating a discrepancy in binding affinity in the lanthanide series and rendering the terbium complex the most effective dipicolinate receptor site of all investigated. We have also extended the application of this receptor site design technology to the targeted detection of other aromatic analytes of biological relevance, such as salicylates and catecholamines. Our work indicates that construction of effective receptor site complexes is not governed by net electrostatic considerations, and that local charge variations from the ligand-induced perturbation of lanthanide electron density may play a significant role. This work sets the stage for the development of the next-generation terbium(macrocycle) complex for bacterial spore detection, with the aim of constructing a solid-state endospore microsensor for applications ranging from sterilization validation to life detection in extreme environments.", "doi": "10.7907/0NFE-Y329", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5447", "collection": "thesis", "collection_id": "5447", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12152009-120706357", "type": "thesis", "title": "Development and Applications of Quantum Monte Carlo", "author": [ { "family_name": "Fisher", "given_name": "Daniel Ross", "clpid": "Fisher-Daniel-Ross" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "clpid": "Blake-G-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Quantum Monte Carlo is a relatively new class of electronic structure methods that has the potential to calculate expectation values for atomic, molecular, and materials systems to within chemical accuracy. QMC scales as (ON3 or better with the size of the system, which is much more favorable than traditional electronic structure methods capable of comparable accuracy. In addition, the stochastic nature of QMC makes it relatively easy to parallelize over multiple processors.
\r\n \r\nQMC calculations use the Metropolis algorithm to sample the electron density of the system. This method has an inherent equilibration phase, during which the configurations do not represent the desired density and must be discarded. Because the time spent on equilibration increases linearly with the number of processors, this phase limits the efficiency of parallel calculations, making it impossible to use large numbers of processors to speed convergence.
\r\n \r\nThis thesis presents an algorithm that generates statistically independent walker configurations in regions of high probability density, shortening the length of the equilibration phase and ensuring the accuracy of calculations. Shortening the length of the equilibration phase greatly improves the efficiency of large parallel calculations, which will allow QMC calculations to use the next generation of homogeneous, heterogeneous, and distributed computing resources to conduct highly accurate simulations on large systems.
\r\n\r\nThe most common formulation of diffusion Monte Carlo has two sources of error: the time step used to propagate the walkers and the nodes of the trial function. In order to explore these sources of error, DMC calculations were carried out on three pericyclic hydrocarbon reactions using Hartree-Fock, generalized valence bond, and multiconfiguration self-consistent field trial functions and time steps ranging from 10-4 to 10-2 au. The results are compared to values from experiment and high quality ab initio calculations, as well as the recently developed X3LYP, M06, and XYG3 density functionals. The appropriate time step and trial functions for the reactants, transition states, and products are identified to begin to develop guidelines for researchers carrying out calculations on larger systems.
\r\n", "doi": "10.7907/4YCS-9T88", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:3041", "collection": "thesis", "collection_id": "3041", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08072008-103726", "primary_object_url": { "basename": "MMT_Thesis.pdf", "content": "final", "filesize": 4162643, "license": "other", "mime_type": "application/pdf", "url": "/3041/8/MMT_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Chemical-Scale Studies of the Nicotinic and Muscarinic Acetylcholine Receptors", "author": [ { "family_name": "Torrice", "given_name": "Michael McCann", "clpid": "Torrice-Michael-McCann" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation describes three chemical-scale studies of neuroreceptor structure and function. Incorporation of unnatural amino acids into two acetylcholine receptors\u2014the nicotinic acetylcholine receptor (nAChR) and the M\u2082 muscarinic acetylcholine receptor (M\u2082AChR)\u2014and an electrophysiology assay of receptor function were performed in each of the studies. The nAChR is a ligand-gated ion channel (LGIC) and the M\u2082AChR is a G-protein-coupled receptor (GPCR).
\r\n\r\nIn Chapter 2, a highly conserved aspartate residue (D89) that is near the agonist binding site of the nAChR was probed for its role in agonist binding. We found that the side chain of D89 establishes a redundant network of hydrogen bonds and preorganizes the agonist binding site by positioning a critical agonist-binding residue, tryptophan 149 (W149). Previous studies of a D89N mutant led to the proposal that a negative charge at D89 was essential for receptor function. However, our studies show that neutral side chains at position 89 function well, only if an unfavorable electrostatic clash is avoided.
\r\n\r\nChapter 3 describes our attempts to incorporate unnatural amino acids into the M\u2082AChR, a GPCR. GPCR activity is assayed through second messenger signaling pathways, unlike the direct readout assays of LGICs. These second messenger pathways require significant amounts of optimization to create assays that produce reliable and robust data. In our experiments, variability of dose-response relationship data between batches of cells was the most significant concern. Several factors were investigated to reduce this batch-to-batch variability. After a reliable means to assay M\u2082AChR function was found, we performed a preliminary search for tryptophan residues in the agonist binding site that form a cation-pi interaction with acetylcholine.
\r\n\r\nFinally, in Chapter 4, we discuss the use of hydroxy acids to scan the \u03b1-M1 transmembrane helix of the nAChR for residues that undergo structural rearrangements during gating. Hydroxy acids disrupt hydrogen bonding in protein backbones and thus provide a means to detect backbone interactions that form or break during gating. The hydroxy acid analog of valine, valic acid (Vah), was incorporated at ten positions along the \u03b1-M1 helix. Backbone mutations at five residues on the intracellular side of a conserved proline (P221) produced shifts in dose-response relationships.
\r\n", "doi": "10.7907/4WKT-NB09", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:5196", "collection": "thesis", "collection_id": "5196", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05232009-204358", "primary_object_url": { "basename": "00CompleteThesis.pdf", "content": "final", "filesize": 23112891, "license": "other", "mime_type": "", "url": "/5196/1/00CompleteThesis.pdf", "version": "v12.0.0" }, "type": "thesis", "title": "Discovery of Aminoacyl-tRNA Synthetase Mutants for the Incorporation of Non Canonical Amino Acids into Proteins", "author": [ { "family_name": "Tanrikulu", "given_name": "Ismet \u00c7ag\u02d8ler", "orcid": "0000-0002-7165-0399", "clpid": "Tanrikulu-Ismet-\u00c7ag\u02d8ler" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Efficient in vivo incorporation of a noncanonical amino acid into proteins often requires engineering new aminoacyl-tRNA synthetase (AARS) activity into the cell, usually by modifying a natural aaRS. Although experimental methods, relying on mutagenesis and library screening, have identified many successful mutant aaRS-substrate pairs in the recent years, computational approaches have reported only a few successes. Here we compare the results of computational and experimental screens of an E. coli methionyl-tRNA synthetase (MetRS) saturation-mutagenesis library for binding (in silico), and activation and cell-surface display (in vivo) of azidonorleucine (Anl).
\r\n\r\nThree positions (L13, Y260, and H301) in the methionine binding pocket of E. coli MetRS were randomized, and the resulting library was screened for MetRS activity toward Anl, based on a screening strategy previously established in our group. This strategy relies on the introduction of reactive side chains into surface-exposed sites on outer-membrane protein C (OmpC), and their subsequent labeling with reactive, fluorescent probes. We have discovered a large diversity of MetRS mutants that allow the incorporation of Anl into proteins in vivo. The extent of OmpC expression and the amount of available Anl during the screen have substantial effects on the outcome of the screens. In addition to displaying improved activities toward Anl, identified mutants also show an improved discrimination against Met. We have shown that the degree of cell-surface labeling in vivo correlates well with the measured rates of Anl activation in vitro, which reflects the success of the screen design.
\r\n\r\nComputational analysis of the experimentally identified mutants revealed a good agreement between computed binding energies and in vitro activation data. To better test the computation model, we performed an in silico screen for Anl binding on a saturation-mutagenesis library comparable to the experimental library. Computational screen predominantly selects mutants that interact with Anl through hydrogen bonds, whereas the hydrophobic residues are selected more often by the experimental screen. We identify that experimental mutants try to optimize packing at the Y260 and H301 sites, but not at the L13 site. We discuss possible explanations for these results. Combined results from computation and experiments suggest the importance of various factors in ligand recognition and in vivo selection of MetRS mutants. We explore the implications of these factors to the future efforts in the engineering of new MetRS activities.
\r\n", "doi": "10.7907/E7D5-HN96", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:5239", "collection": "thesis", "collection_id": "5239", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07222008-023323", "primary_object_url": { "basename": "Thesis_YukiMatsuda.pdf", "content": "final", "filesize": 2985544, "license": "other", "mime_type": "application/pdf", "url": "/5239/1/Thesis_YukiMatsuda.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ab Initio Quantum Mechanical Studies in Electronic and Structural Properties of Carbon Nanotubes and Silicon Nanowires", "author": [ { "family_name": "Matsuda", "given_name": "Yuki", "clpid": "Matsuda-Yuki" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Bockrath", "given_name": "Marc William", "clpid": "Bockrath-M-W" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This dissertation focuses on ab-initio quantum mechanical calculations of nanoelectronics in three research topics: contact resistance properties of carbon nanotubes and graphenes (Chapters 1 through 3), electrical properties of carbon nanotubes (Chapter 4) and silicon nanowires (Chapter 5). Through all the chapters, the aim of the research is to provide useful guidelines for experimentalists.
\r\n\r\nChapter 1 presents the contact resistance of metal electrode\u2212carbon nanotube and metal electrode\u2212graphene interfaces for various deposited metals, based on first-principles quantum mechanical density functional and matrix Green\u2019s function methods. Chapters 2 and 3 describe inventive ways to enhance contact resistance properties as well as mechanical stabilities using \u201cmolecular anchors\u201d (Chapter 2) or using \"end-contacted\" (or end-on) electrodes (Chapter 3). Chapters 1 through 3 also provide useful guidelines for nanotube assembly process which is one of the main obstacles in nanoelectronics. Chapter 4 shows accurate and detailed band structure properties of single-walled carbon nanotubes using B3LYP hybrid functional, which are critical parameters in determining the electronic properties such as small band gaps (~0.1 eV) and effective masses. Chapter 5 details both structural and electronic properties of silicon nanowires. These results lead to the findings controlling the diameter and surface coverage by adsorbates (e.g., hydrogen) of silicon nanowires can be effectively used to optimize their properties for various applications.
\r\n\r\nAll the theoretical results are compared with other theoretical studies and experimental data. Notably, electronic studies using B3LYP show excellent agreement with experimental studies quantitatively, which previous quantum mechanical calculations had failed.
\r\n\r\nThese studies show how quantum mechanical predictions of complex phenomena can be effectively investigated computationally in nanomaterials and nanodevices. Given the difficulty, expense, and time required for experiments, theory may now be useful for high-throughout screening to identify the best conditions and materials before performing experiments.
\r\n", "doi": "10.7907/7FXD-ZQ68", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2371", "collection": "thesis", "collection_id": "2371", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012009-162039", "primary_object_url": { "basename": "Thesis-2.pdf", "content": "final", "filesize": 1664355, "license": "other", "mime_type": "application/pdf", "url": "/2371/1/Thesis-2.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Study of Liquid Metals by Electrostatic Levitation", "author": [ { "family_name": "Li", "given_name": "John Jian-Zhong", "clpid": "Li-John-Jian-Zhong" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Rhim", "given_name": "Won-Kyu", "clpid": "Rhim-W" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Painter", "given_name": "Oskar J.", "clpid": "Painter-O" }, { "family_name": "Rhim", "given_name": "Won-Kyu", "clpid": "Rhim-Won-Kyu" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "With the development of bulk metallic glasses (BMG) in recent years, more and more scientists in solid state physics are trying to understand the mechanism of glass-formation in terms of thermodynamics and kinetics, while engineers in metallurgy are trying different compositions and processes to improve the mechanical properties of BMGs and their composites.
\r\n\r\nGlasses are nothing but frozen liquids. So far most of the studies of metallic glasses have been below the glass transition temperature because molten metallic liquids are chemically reactive with the container walls. For this reason, we used the Electrostatic Levitation (ESL) method that was developed by Dr. Won-Kyu Rhim.
\r\n\r\nIn this thesis, the instrumentation of the ESL is described. Discussion on the advantages and disadvantages of ESL is given by comparing with the other levitation methods. Because of the advantage in sample position stability over all the other levitation methods, the ESL facility at Caltech is uniquely capable of measuring the viscosity and thermophysical properties of liquid metals in the undercooled temperature range. The ESL was further improved at Caltech to reduce temperature gradients on a sample and increase the stability of the sample positioning with a tetrahedral laser heating system.
\r\n\r\nUsing such an improved ESL, thermophysical properties of some evaporative metallic liquids such as Ti and silicon-germanium alloys have been successfully studied and mass loss as well as composition changes could be accounted for.
\r\n\r\nSeveral BMGs developed at Johnson group at Caltech have been studied using ESL. Among the liquid thermodynamics and kinetic properties of interest, special attention has been paid on to measurements of the TTT curve, viscosity, and volume changes with temperature. These data give useful insight on the glass-forming mechanism. Through these studies, guidelines in the search for good ductile metallic glass-formers have emerged. Discussing these guidelines is an important part of this thesis.
\r\n\r\nFinally, we discuss an investigation to understand observed hysteresis in the viscosity and the so-called threshold temperature that has been observed in some of the best glass-forming metallic liquids. We conclude this investigation with a hypothesis of a liquid-to-liquid phase transition that occurs above liquidus temperatures in several systems that we have studied.
\r\n", "doi": "10.7907/JY7J-Q837", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2467", "collection": "thesis", "collection_id": "2467", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06052009-140716", "primary_object_url": { "basename": "Ian_Shapiro_PhD_thesis.pdf", "content": "final", "filesize": 10319534, "license": "other", "mime_type": "application/pdf", "url": "/2467/1/Ian_Shapiro_PhD_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Observation of Single-Molecule Rotational Diffusion at Microsecond Timescale by Polarized Fluorescence Correlation Spectroscopy", "author": [ { "family_name": "Shapiro", "given_name": "Ian Ross McKay", "clpid": "Shapiro-Ian-Ross-McKay" } ], "thesis_advisor": [ { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" } ], "thesis_committee": [ { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This work presents a series of experimental and numerical studies of macromolecular organic, inorganic and biological structures, in all instances focusing on the behavior characteristic of individual discrete molecular elements. Chapters 1 and 2, beginning on pages 1 and 31, respectively, describe fabrication, use and numerical analysis of of single-walled carbon nanotube probes for amplitude-modulation atomic force microscopy. These studies reach the conclusion that the molecular structure and nanoscale surface interaction potential unique to carbon nanotubes collectively give rise to atomic force microscopy imaging artifacts manifesting as apparent lateral topographic resolution signi\ufb01cantly better than that predicted by the probe and sample structures.
\r\n\r\nChapter 3 (p. 61) presents a brief review of single-molecule microscopy, describes a generalized mathematical formalism for focusing polarized visible-spectrum electromagnetic radiation, and delineates the construction of a custom two-channel scanning confocal \ufb02uorescence microscope system with single-photon detection capability for spectral- and polarization-resolved studies of individual mobile \ufb02uorophores. This Chapter includes a theory-based optical analysis of the confocal probe volume structure and photoluminescence collection efficiency from 3D-polarized single-dipole emitters. The latter analysis was aided by introducing a modi\ufb01ed Jones formalism using non-square matrix representation for polarization state changes in the speci\ufb01c context of confocal optics. Proper calculation of the expected confocal probe volume dimensions was essential for accurately interpreting experimental data in the following chapter. Additionally, the quantitative understanding that followed from analysis of 3D polarization state measurement by orthogonally polarized detection channels was critical to both the interpretation of experimental data and the numerical generation of simulated data in Chapter 5.
\r\n\r\nChapter 4 (p. 125) presents a generalized formalism for correlation analysis of the \ufb02uorescence signal collected using the two-channel microscopy system described in Chapter 3. Particular focus was directed toward the theoretical auto- and cross-correlation traces anticipated from polarization-sensitive bivariate time series of photoluminescence emission from freely-rotating transition dipoles. Chapter 4 also presents population-resolved data collected from single F\u00a8orster resonance energy transfer \ufb02uorphore pairs conjugated to DNA oligomers as they undergo cleavage by restriction endonucleases. The endonuclease enzyme Michaelis constants KM measured for EcoRI and BglI via \ufb02uorescence burst analysis were in agreement with prior literature. The success of these experiments provide concrete con\ufb01rmation of the microscope\u2019s \ufb02uorescence emission sensitivity and detection channel selectivity in the context of single-molecule experiments.
\r\n\r\nChapter 5 describes a polarized \ufb02uorescence correlation spectroscopy (PFCS) investigation of liquid phase rotational diffusion by colloidal CdSe semiconductor nanocrystals possessing two-dimensional nondegenerate photoluminescence transition dipoles, as well as red \ufb02uorescent protein (monomeric DsRed) and rhodamine-labeled phospholipids that possess more conventional one-dimensional \ufb02uorescence transition dipoles. The experimental PFCS data collected from these samples is in close agreement with simulated PFCS data produced by a Monte Carlo rotational diffusion numerical routine that incorporates the microscope 3D polarization state sensitivity calculated in Chapter 3.
\r\n\r\nAppendices beginning on page 221 include a matrix-based description of arbitrary 3D rotation that was used in the rotational diffusion simulations, Matlab code transcripts (p. 227), and an additional mathematical formalism based on information theoretic precepts (p. 242) for assessing directed causal relationships in bivariate time series data.
\r\n", "doi": "10.7907/KVDR-9429", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:1930", "collection": "thesis", "collection_id": "1930", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05212009-221851", "primary_object_url": { "basename": "FinalThesis.pdf", "content": "final", "filesize": 20402703, "license": "other", "mime_type": "application/pdf", "url": "/1930/1/FinalThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems", "author": [ { "family_name": "Kim", "given_name": "Hyungjun", "orcid": "0000-0001-8261-9381", "clpid": "Kim-Hyungjun" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Multiscale and multiphysics simulation strategy is important to investigate complex problems in nature because it provides a systematic method to understand underpinning physics of the systems depending on the size. In this thesis, we discuss how such multiscale and multiphysics simulation framework can explain and rationalize the experimental observations in several nano- and biosystems. Furthermore, we exhibit the computational simulation methods that play major roles to rationally design novel materials with desired properties in next generation nano electronic devices, alternative energy materials, life science, and so on.
\r\n\r\nChapter 1 reviews the significance of multiscale and multiphysics simulation strategy. In this chapter, we briefly discuss the multiscale and multiphysics natures in nano- and bio-systems, and detailed examples are contained in the next chapters. Chapter 2 introduces an electric field induced conformational change mechanism, which is responsible for the unique current-voltage (I-V) behavior of nano device, negative differential resistance (NDR). In Chapter 3, the on/off kinetics of the Stoddart-Heath rotaxane-based programmable molecular electronic switch is discussed in terms of the free energy quantities. Chapter 4 explores sodium diffusion through the aluminum-doped zeolite BEA system, and the effect of water uptake amount is thoroughly discussed. This has importance for the application of zeolite to proton exchange membranes for fuel cells (PEMFC). In Chapters 5 and 6, the ion mobilities of tertiary and quaternary ammonium cations (precursors for lipids), and phosphatidylcholine (PC) lipid cations are investigated, respectively. In order to compute the ion mobilities of the precursors and entire lipids, we develop a modified trajectory (TJ) method dealing with the complicated integrals of interaction terms. QM and MD simulations are performed to determine the structures and charge distributions. In Chapter 7, we study how the model lung system of lipid monolayer with surfactant protein B (SP-B) responds to ozone introduction. In parallel with the field induced droplet ionization (FIDI) mass spectrometry study, MD simulations identify the distinct ozone reaction mechanism at the interface, and the role of SP-B at the pulmonary surfactant (PS) system on the oxidative stresses.
\r\n\r\nFrom these studies, we suggest various multiscale and multiphysics modeling approaches depending on the characteristics of systems and objectives. These efforts allow us to overcome the limited time- and length-scales of the monoscale simulations. In addition, we expect that an establishment of such multiscale modeling procedures will invoke interdisciplinary studies by tightly combining the developments occurring independently across fields.
\r\n", "doi": "10.7907/0PFF-R531", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2791", "collection": "thesis", "collection_id": "2791", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06302008-165534", "primary_object_url": { "basename": "BAS_complete_thesis.pdf", "content": "final", "filesize": 3881276, "license": "other", "mime_type": "application/pdf", "url": "/2791/1/BAS_complete_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Silicon Nanowires and Silicon/Molecular Interfaces for Nanoscale Electronics", "author": [ { "family_name": "Sheriff", "given_name": "Bonnie Ann", "clpid": "Sheriff-Bonnie-Ann" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the utilization of silicon nanowires and molecular films towards the realization of nanoscale electronics. The key enabling technology is the method in which the silicon nanowires are produced\u2014the superlattice nanowire pattern transfer (SNAP) method. The SNAP method allows for the simultaneous formation and alignment of metal or semiconducting nanowires using a template-mediated approach.
\r\n\r\nHigh-performance n- and p-type silicon nanowire field-effect transistors (FETs) were demonstrated. These FETs exhibited consistent performance and strong performance metrics such as high on/off ratios, high on-currents, high mobilities and low subthreshold swings. Due to the nanowire\u2019s large surface-area-to-volume ratio, surface states were shown to dominate performance, especially for the n-type FETs. Reducing the number of surface states improved performance significantly.
\r\n\r\nN- and p-type silicon nanowire FETs were integrated into complementary symmetry (CS) logic circuits. This required the development of a pattern doping technique that allowed for spatial control of doped regions. The inverter circuit was fabricated and tested. A gain of ~ 5 was consistently measured from 7 working inverter circuits. This demonstration provided the foundation for the eventual fabrication and characterization of the other Boolean logic functions.
\r\n\r\nA methodology was developed that optimizes the design of high-performance logic circuits constructed from Si NW p- and n-type FETs. Circuit performance can be predicted from individual fabricated NW FETs before prototype circuits are manufactured, resulting in a faster and more efficient design process. These results suggest design options for fabricating high performance NW circuits, which can then be implemented experimentally. The effectiveness of this methodology is shown by optimizing the gain of Si NW complementary symmetry inverter from an initially measured value of 8 to a gain of 45.
\r\n\r\nLastly, methods to covalently attach electronically interesting molecules via microcontact printing onto gold and silicon substrates were developed. In these studies, the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction was used to form the covalent attachment. It was observed that the reaction would proceed readily by replacing the Cu catalyst in the stamp ink by a Cu coating on the stamp directly. This reaction proceeded quickly on both azide-terminated monolayers on Au and Si(111) substrates.
", "doi": "10.7907/Q13E-NB40", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2268", "collection": "thesis", "collection_id": "2268", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292009-094239", "primary_object_url": { "basename": "1-FullThesis.pdf", "content": "final", "filesize": 3698531, "license": "other", "mime_type": "application/pdf", "url": "/2268/1/1-FullThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Adrenergic Receptors: Model Systems for Investigation of GPCR Structure and Function", "author": [ { "family_name": "Wiencko", "given_name": "Heather L.", "clpid": "Wiencko-Heather-L" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Membrane proteins mediate intercellular communication, resulting in changes in the membrane and within the cell itself. One superfamily of integral membrane proteins, G-protein coupled receptors (GPCRs), are responsible for a vast diversity of processes. Their conformational flexibility and membrane environment pose challenges for direct structural characterization, and to date only five of the more than 1,000 known GPCRs have been characterized by high-resolution crystallography.
\r\n\r\nThe nine adrenergic GPCRs mediate the stress response throughout the body, and are implicated in diseases including hypertension and asthma. While they are among the best studied families of GPCRs, much remains to be learned about selectivity and activation. The first section of this work describes the ab initio structure prediction of the turkey beta-1 receptor and validation using a series of stabilizing mutations. This work preceded the currently available turkey beta-1 structure but shows good agreement, especially in the binding site. It validates the latest methods developed for GPCR structure prediction, emphasizes the role of a neutral charge scheme in energy determination, and explores a structure validation strategy based on stabilizing mutations rather than ligand docking. The next section uses the experimental beta-1 crystal structure as a starting point for nanosecond timescale molecular dynamics, exploring the roles of ligand binding in helix movement that contribute to the transition to an active state. These simulations reveal the early steps in receptor activation, beginning with tilting motions of transmembrane helices 5 and 6 and movement of transmembrane helix 1 closer into the protein core. The last section presents homology models of the human adrenergic receptors for which there are not yet crystal structures. The receptors most closely related to the target structures show the best results, while the less related ones will require further refinement. The best structures provide insight into the binding site of subtype selective antagonists, and can serve as the foundation for future studies. Over the course of these explorations, new subtleties in adrenergic structure have been illuminated, and may drive further exploration into selective binding and the activation mechanism of these and other receptors.
", "doi": "10.7907/S3RC-RZ59", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2222", "collection": "thesis", "collection_id": "2222", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282009-131419", "primary_object_url": { "basename": "main.pdf", "content": "final", "filesize": 4341788, "license": "other", "mime_type": "application/pdf", "url": "/2222/1/main.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "A Monte Carlo-Based Torsion Construction Algorithm for Ligand Design", "author": [ { "family_name": "Kekenes-Huskey", "given_name": "Peter Michael", "orcid": "0000-0001-7286-3022", "clpid": "Kekenes-Huskey-Peter-Michael" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A wealth of computational strategies [1,2,3,4,] is available for predicting the binding site and affinities of a putative ligand inside a target receptor. Although numerous techniques focus on the orientation of ligands or fragments thereof, few methods have delved into improving the accuracy of generating reliable ligand conformations within predicted binding modes. In an effort to comprehensively sample the torsion space available to a flexible ligand and focus on low-energy conformations, a recursive, Metropolis Monte Carlo (MC)-based rotamer design protocol has been developed. This approach recursively samples adjacent rotatable bonds from a defined anchor and directs the search along low-energy pathways, such that high-affinity conformations of the ligand can be identified. Furthermore, this program applies spatial constraints within the search that restrict the solutions to structurally dissimilar conformations, thus encouraging a diverse solution set. The performance of moleculeGL has been evaluated for a set of 55 co-crystals, for which the number of rotatable bonds ranged from 2 to 32. Approximately 80 percent of the structures are predicted within 2.0 A2 root mean square deviations (RMSD) with respect to the crystal structure, starting from an arbitrary ligand conformation. This level of accuracy suggests the program's applicability to the design of pharmacaphore substituents, for which the position of a chemically active pharmacaphore is well-known.", "doi": "10.7907/A1MQ-3116", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2220", "collection": "thesis", "collection_id": "2220", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282009-112657", "primary_object_url": { "basename": "APH_thesis.pdf", "content": "final", "filesize": 8082715, "license": "other", "mime_type": "application/pdf", "url": "/2220/2/APH_thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Chemical-Scale Investigations of Cys-Loop Neurotransmitter Gated Ion Channels", "author": [ { "family_name": "Hanek", "given_name": "Ariele Patrice", "clpid": "Hanek-Ariele-Patrice" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Cys-loop ligand gated ion channels mediate rapid synaptic transmission in the mammalian central and peripheral nervous system. Proper functioning of this superfamily of receptors is critical to brain function and as such the proteins are implicated in a number of neuropathies and are a target for many pharmaceuticals. A central concern is how these receptors recognize and bind their neurotransmitter agonists as well as how these binding events lead to a conformational change spanning a distance of at least 50 \u00c5. Using the nonsense suppression methodology, we are able to incorporate unnatural amino acids into these proteins and identify the precise molecular interactions involved in neurotransmitter binding and the conformational changes that take place during channel activation.
\r\n\r\nIn chapters two through four we investigate the role of the nicotinic acetylcholine receptor (nAChR) \u03b11 loop 2 residues in channel activation. Using conventional mutagenesis, we have identified several residues that are part of a global electrostatic network. This is the first study to present an element of activation that is universal to the entire Cys-loop superfamily. Using unnatural amino acids, we identify the pro-S methyl group of \u03b1Val46 as a critical element in the activation pathway of the muscle type nicotinic acetylcholine receptor, thereby validating a proposed the pin-into-socket mechanism for this residue.
\r\n\r\nWe switch our focus from the excitatory nAChR to the inhibitory glycine (Gly) and \u03b3-aminobutyric acid type A (GABAA) receptors in chapter 5. By incorporating successively fluorinated phenylalanine analogs into the binding site of both the GlyR and GABAAR we were able to identify a cation-\u03c0 interaction at \u03b11Phe159 of the GlyR and \u03b22Tyr97 of the GABAAR, providing further evidence that the cation-\u03c0 interaction is conserved across the superfamily.
\r\n\r\nFinally we investigate the mechanisms of GABA activation and flurazepam (FLZM) potentiation in the GABAAR. Incorporation of a photo-activated backbone cleaving unnatural amino acid reveals that an unstructured linker connecting loops A and E of the GABAAR \u03b11 subunit is critical to GABA but not pentobarbital activation. We further investigate this region of the receptor and its role in GABA activation and flurazepam potentiation using conventional mutagenesis and incorporation of \u03b1-hydroxy acids. The data indicate that GABA activation and FLZM potentiation are differentially affected by side chain mutations in this region, but not by backbone mutations. Loss-of-function due to incorporation of alpha-hydroxy acids strongly suggests the unstructured linker becomes more structured during channel activation.
\r\n", "doi": "10.7907/FSYX-Y861", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:2120", "collection": "thesis", "collection_id": "2120", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262009-145437", "primary_object_url": { "basename": "FinalThesisDocumentIII.pdf", "content": "final", "filesize": 9966032, "license": "other", "mime_type": "application/pdf", "url": "/2120/1/FinalThesisDocumentIII.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Synthesis and Proton Conductivity Studies of Mesostructured Organosilicates and Bitriazole-Polymer Composites. II. Targeted Nanoparticles for siRNA Delivery", "author": [ { "family_name": "Alabi", "given_name": "Christopher Akinleye", "orcid": "0000-0003-2654-018X", "clpid": "Alabi-Christopher-Akinleye" } ], "thesis_advisor": [ { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Davis", "given_name": "Mark E.", "clpid": "Davis-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The underlying theme of the research outlined in both parts of this report is centered on the ability to use synthetic design as a probe to investigate and answer fundamental mechanistic questions in an effort to improve the function of materials employed in energy and biological research. Specifically in the field of energy research, we have designed a new strategy aimed at improving the proton conductivity of organically modified silica-based polymer electrolyte membranes for use in direct methanol fuel cells. Our design involves the incorporation of the desired organic functional group into a siloxane-modified polymerizable surfactant that can be used in mesoporous silicate synthesis. This approach takes advantage of the silicate assembly mechanism, which places surfactants exclusively within the pores of the silicate at high loadings. The desired functional group is revealed upon selective cleavage after hydrothermal silicate synthesis. We have used this approach to synthesize organosilicates with different sized organic groups displaying high organic acid densities and have studied their proton conductivity under fully hydrated conditions. Under these conditions, structural diffusion via a percolated water network is the dominant mechanism of proton transport.
\r\n\r\nWith regards to membranes for use in hydrogen fuel cells that operate best at temperatures above the dew point of water, the need for an alternative to water as the proton conducting medium is desired. Towards this end, we designed a new nitrogen-containing heterocycle (NCH), 4,4-1H-1H-bi-1,2,3-triazole (bitriazole) capable of mimicking water in the solid state and have investigated its ability to conduct protons in the presence of polyethylene oxides under anhydrous conditions. With numerous chemical tools at our disposal, we probed the mechanism of proton conduction and confirmed the bitriazole proton to be the source of anhydrous proton conductivity. Our data suggests structural diffusion as the dominant transport mechanism via synergistic interactions between bitriazole and polyethylene oxides in the polymer-rich region of the composite material that is encapsulated by a crystalline nonconductive bitriazole framework.
\r\n\r\nIn the second part of this report, we shift our focus to the investigation of antibody-mediated targeting, using our well-established cyclodextrin polycation (CDP) nanoparticles containing therapeutic oligonuleotides, to epitopes expressed at the surface of cancer cells as a means of increasing site-specific therapeutic delivery. To do this, we synthesized fragments of anti-CD20 (rituximab) and conjugated them to flexible poly(ethylene glycol) (PEG) linkers with terminal adamantane groups that can interact with the cyclodextrins on the surface of the CDP nanoparticle via the formation of an inclusion complex. With the PEGylated antibody fragments in hand, we investigate, via a B-cell lymphoma model, the binding characteristics of the targeting ligands as well as their effect on the binding, internalization, and efficacy of the targeted CDP-nucleic acid therapeutic nanoparticles.
\r\n", "doi": "10.7907/9SNH-2A91", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:3588", "collection": "thesis", "collection_id": "3588", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09172007-160334", "primary_object_url": { "basename": "ch1_title_introduction.pdf", "content": "final", "filesize": 385123, "license": "other", "mime_type": "application/pdf", "url": "/3588/1/ch1_title_introduction.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Thermodynamic Modeling of Organic Aerosol", "author": [ { "family_name": "Tong", "given_name": "Chinghang", "clpid": "Tong-Chinghang" } ], "thesis_advisor": [ { "family_name": "Seinfeld", "given_name": "John H.", "clpid": "Seinfeld-J-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Seinfeld", "given_name": "John H.", "clpid": "Seinfeld-J-H" }, { "family_name": "Blanco", "given_name": "Mario", "clpid": "Blanco-M" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Modeling atmospheric aerosols containing a large organic fraction with unknown chemical composition and properties has been a constant challenge. The dissertation focuses on the theoretical treatment of the thermodynamic equilibrium of atmospheric aerosol involving organic species.
\r\n\r\nWe present a vapor pressure estimation method, based on quantum chemistry methods, to predict the liquid vapor pressure, enthalpies of vaporization, and heats of sublimation of atmospheric organic compounds. Predictions are compared to literature data, and the overall accuracy is considered satisfactory given the simplicity of the equations. Quantum mechanical methods were also used to investigate the thermodynamic feasibility of various acid-catalyzed aerosol-phase heterogeneous chemical reactions. A stepwise procedure is presented to determine physical properties such as heats of formation, standard entropies, Gibbs free energies of formation, and solvation energies from quantum mechanics, for various short-chain aldehydes and ketones. Equilibrium constants of hydration reactions and aldol condensation are then reported; predictions are in qualitatively agreement with previous studies. We have shown that quantum methods can serve as useful tools for first approximation, especially for species with no available data, in determining the thermodynamic properties of multifunctional oxygenates.
\r\n\r\nWe also present an atmospheric aerosol phase equilibrium model to determine the aerosol phase equilibrium of aqueous systems. Phase diagrams for a number of organic/water systems characteristic of both primary and secondary organic aerosols are computed. Effects of organics on the deliquescence behavior of electrolytes are also shown in the inorganic/organic/water phase diagrams.
\r\n\r\nFinally, we evaluate the performance of four recent activity coefficient models developed for inorganic-organic-water mixtures typical of atmospheric aerosols. Based on the comparison on water activities, it is found that models that include ion-organic mixture parameters (referred to as coupled models) do not necessarily produce more accurate predictions than those models that utilizes additive approaches (referred to as decoupled models). Since the chemical composition and physical properties of the organic fraction is largely unknown, the additive approaches of the decoupled models are more feasible than the coupled model.
\r\n", "doi": "10.7907/3M7R-9620", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2169", "collection": "thesis", "collection_id": "2169", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272008-095638", "primary_object_url": { "basename": "jasonkeith_thesis_final.pdf", "content": "final", "filesize": 2467428, "license": "other", "mime_type": "application/pdf", "url": "/2169/1/jasonkeith_thesis_final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Palladium Mediated Activation of Molecular Oxygen", "author": [ { "family_name": "Keith", "given_name": "Jason M.", "orcid": "0000-0002-5292-397X", "clpid": "Keith-Jason-M" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In developing environmentally benign chemistries, it is most important to use dioxygen directly in lieu of toxic and/or corrosive stoichiometric oxidants. Unfortunately, for many processes such as direct oxidations this has not yet become practical. To help develop such processes, we elucidate here the mechanism for the reaction of molecular oxygen with palladium-hydride complexes in nonpolar solvent using quantum mechanics for several PdII complexes, specifically focusing on the pathways proceeding through Pd0 and on the direct insertion of oxygen into the Pd-H bond. All the chapters presented herein focus on different aspects of the total problem as follows:
\r\n\r\nChapter 1: Activation of Molecular Oxygen by ((\u2012)-Sparteine)PdHCl: Direct Insertion presents the first proposal of a hydrogen atom abstraction from a palladium-hydride complex by triplet oxygen that demonstrates the feasibility of this mechanism.
\r\n\r\nChapter 2: Activation of Molecular Oxygen by [1,3-(CH2PtBu2)2-C6H3]PdH examines the reaction of an experimentally isolated palladium-hydride complex from which formation of Pd0 has been deemed unlikely, thus proving the previously predicted insertion mechanism to be active in a known system.
\r\n\r\nChapter 3: Activation of Molecular Oxygen by ((\u2012)-Sparteine)PdHCl: Pd0 presents a thorough investigation of possible base-assisted reductive elimination pathways that can lead to the formation of Pd0 in the ((\u2012)-Sparteine)PdHCl system, and it demonstrates that the direct insertion mechanism is in fact the process involved in this system.
\r\n\r\nChapter 4: Activation of Molecular Oxygen by ((\u2012)-Sparteine)Pd(OAc)H: Pd0 vs. Direct Insertion examines the substitution of the OAc ion for Cl in ((\u2012)-Sparteine)PdH system. The acetate ligand\u2019s ability to act as a base while chelating the Pd significantly lowers the energy involved in the Pd0 pathway, switching the calculated preference to the Pd0 pathway.
\r\n\r\nChapter 5: Activation of Molecular Oxygen by (Pyridine)2Pd(OAc)H: Pd0 vs. Direct Insertion examines the reaction of (Pyridine)2Pd(OAc)H with O2. The calculated mechanisms present feasible cis/trans isomerisation and demonstrate that the Pd0 pathway is the favored pathway for both the cis and the trans cases.
\r\n\r\nAppendix: Enantioselective Oxidations of Secondary Alcohols by (\u2013)-Sparteine-PdII Complexes examines the mechanism of specific Pd oxidation catalysis focusing on alcohol binding, deprotonation to form the corresponding alkoxide and the subsequent beta-hydride elimination.
\r\n", "doi": "10.7907/K4AY-P498", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2927", "collection": "thesis", "collection_id": "2927", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07182007-154911", "primary_object_url": { "basename": "Complete_Thesis.pdf", "content": "final", "filesize": 4829848, "license": "other", "mime_type": "application/pdf", "url": "/2927/9/Complete_Thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Development of Water-Soluble Olefin Metathesis Catalysts Containing an N-Heterocyclic Carbene Ligand", "author": [ { "family_name": "Jordan", "given_name": "Jason Paul", "clpid": "Jordan-Jason-Paul" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This research describes the development of new olefin metathesis catalysts that are stable and active in water. Earlier water-soluble metathesis catalysts rely on phosphine ligands functionalized with ionic groups. In contrast to these bis(phosphine) complexes, the catalysts reported in this research harness the increased stability and activity provided by N-heterocyclic carbene (NHC) ligands. As a result, these catalysts display an activity and stability that are unprecedented in aqueous olefin metathesis.
\r\n\r\nInitial efforts to produce the desired water-soluble metathesis catalysts employed poly(ethylene glycol) (PEG) to generate a complex that was soluble in water (Chapter 2). This catalyst was capable of the ring-opening metathesis polymerization (ROMP) of a challenging endo-norbornene monomer, which an earlier bis(phosphine) complex catalyzed poorly. While demonstrating the potential of NHC ligands to improve the activity of water-soluble metathesis catalysts, this catalyst was not sufficiently stable to mediate metathesis transformations involving acyclic olefins in water.
\r\n\r\nA careful examination of the described PEG catalyst inspired a few strategies to produce olefin metathesis catalysts with improved activities in water (Chapter 3). This strategic vision was honed by studies examining the effect of water on the decomposition of catalysts that contain an NHC ligand (Chapter 4). These studies indicated that phosphine ligands play an active role in the aqueous decomposition of ruthenium methylidene complexes, which are vital complexes for metathesis reactions involving terminal olefins. With these results in hand, incorporating NHC ligands into phosphine-free ruthenium complexes was pursued as a promising approach to producing active metathesis catalysts that are stable in water.
\r\n\r\nCatalysts supported by both isopropoxybenzylidene and NHC ligands were modified to include ammonium salts (Chapter 5). The water-soluble catalysts produced were stable in water and competently initiated aqueous ROMP. More importantly, these catalysts readily catalyzed the ring-closing metathesis of [alpha],[omega]-dienes in water. The described catalysts were also able to homodimerize allyl alcohol and homoallyl alcohol in water, which are among the few known examples of cross metathesis in neat water.
", "doi": "10.7907/B57A-ZS49", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:217", "collection": "thesis", "collection_id": "217", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01172008-141725", "primary_object_url": { "basename": "Boukai_Thesis.pdf", "content": "final", "filesize": 1836812, "license": "other", "mime_type": "application/pdf", "url": "/217/1/Boukai_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Thermoelectric Properties of Bismuth and Silicon Nanowires", "author": [ { "family_name": "Boukai", "given_name": "Akram Issam", "clpid": "Boukai-Akram-Issam" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Thermoelectric materials convert temperature differences into electricity and vice versa. Such materials utilize the Seebeck effect for power generation and the Peltier effect for refrigeration. In the Seebeck effect, a temperature gradient across a material causes the diffusion of charged carriers across that gradient, thus creating a voltage difference between the hot and cold ends of the material. Conversely, the Peltier effect explains the fact that when current flows through a material a temperature gradient arises because the charged carriers exchange thermal energy at the contacts. Thermoelectrics perform these functions without moving parts and they do not pollute. This makes them highly reliable and more importantly attractive as renewable energy sources, especially at a time when global warming is a growing concern. However, thermoelectrics find only limited use because of their poor efficiency.
\r\n \t\r\nThe efficiency of a thermoelectric material is determined by the dimensionless figure of merit,ZT = S\u00b2\u03c3T/\u03ba , where S is the thermoelectric power, defined as the thermoelectric voltage, V, produced per degree temperature difference \u0394T , \u03c3 is the electrical conductivity, \u03ba is the thermal conductivity, and T is the temperature. To maximize ZT, S must be large so that a small temperature difference can create a large voltage, \u03c3 must be large in order to minimize joule heating losses, and \u03ba must be small to reduce heat leakage and maintain a temperature difference. Maximizing ZT is challenging because optimizing one physical parameter often adversely affects another. The best commercially available thermoelectric devices are alloys of Bi2Te3 and have a ZT of 1 which corresponds to a carnot efficiency of ~10%. My research has focused on achieving efficient thermoelectric performance from the single component systems of bismuth and silicon nanowires.
\r\n\r\nBismuth nanowires are predicted to undergo a semi-metal to semiconductor transition below a size of 50 nm which should increase the thermopower and thus ZT. Limited experimental evidence by other groups has been acquired to support this claim. Through electric field gating measurements and by tuning the nanowire size, we have shown that no such transition occurs. Instead, surface states dominate the electric transport at a size smaller than 50 nm and bismuth remains a semimetal.
\r\n\r\nBulk silicon is a poor thermoelectric due to its large thermal conductivity. However, silicon nanowires may have a dramatically reduced thermal conductivity. By varying the nanowire size and impurity doping levels, ZT values representing an approximately 100-fold improvement over bulk silicon are achieved over a broad temperature range, including a ZT ~ 1 at 200K. Independent measurements of S, \u03c3, and \u03ba, combined with theory, indicate that the improved efficiency originates from phonon effects. The thermal conductivity is reduced and the thermopower is enhanced. These results are expected to apply to other classes of semiconductor nanomaterials.
\r\n", "doi": "10.7907/QEE9-4H11", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:3765", "collection": "thesis", "collection_id": "3765", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09252007-100851", "primary_object_url": { "basename": "01TitlePage_Ack.pdf", "content": "final", "filesize": 195001, "license": "other", "mime_type": "application/pdf", "url": "/3765/1/01TitlePage_Ack.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Simulations, Modeling, and Designs of Bulk Metallic Glasses", "author": [ { "family_name": "Duan", "given_name": "Gang", "clpid": "Duan-Gang" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Samwer", "given_name": "Konrad", "clpid": "Samwer-K" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Bulk metallic glasses usually have very high yield strength, at least double that of ordinary commercially used crystalline materials, and high elastic strain limit, roughly 2% in tension or compression, due to their disordered atomic structure. Unfortunately, the Achilles heel of metallic glasses is their rather limited ductility and low resistance to the propagation of a crack especially in tension. Many research efforts have been devoted to understanding the deformation and fracture behavior of bulk metallic glasses. One interesting observation is that the properties of metallic glasses are well correlated with each other. The challenge is to understand these correlations, and to utilize such understanding to design novel glasses with good glass forming ability and mechanical toughness.
\r\n\r\nFollowing the Cooperative Shear Model, we investigated the temperature, volume, and configurational dependence of elastic properties by constructing an effective tight-binding force field for a Cu-Zr binary alloy system, and carrying out molecular dynamics simulations. We determined the isothermal Equation of State in a wide range of temperatures and pressures. Pressure-induced cavitation was observed and negative pressure is critical for triggering cavitation. The cavitation barrier height was estimated from the classical nucleation theory. The intrinsic origin of cavitation and its connection to Poisson\u2019s ratio or the ratio of G/B are investigated. The relationship to the deformation and fracture behavior of glasses is discussed.
\r\n\r\nWe designed several novel bulk metallic-glass-forming systems using the link between fragility, elastic properties, and glass forming ability as a guiding tool. The compositional dependence of thermal and elastic properties of Cu-Zr-Be ternary bulk-metallic-glass forming alloys was systematically studied. Lightweight Ti-based bulk amorphous structural metals with more than double the specific strength of conventional titanium alloys have been discovered. We report a novel class of bulk amorphous alloys with benchmark thermoplastic processability, having good glass forming ability, exceptional thermal stability, unexpectedly large Angell fragility number, and good mechanical toughness. Starting from the two binary bulk glass formers in the Cu-Zr system, we systematically investigated the compositional dependence of glass formation, thermal, elastic, and mechanical properties in the Cu-Zr-Ag ternary alloys.
\r\n", "doi": "10.7907/ZH3G-JF43", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:1565", "collection": "thesis", "collection_id": "1565", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05012008-092352", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 2091246, "license": "other", "mime_type": "application/pdf", "url": "/1565/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computational Insight into Homogeneous Organopalladium Catalysis", "author": [ { "family_name": "Keith", "given_name": "John Andrew", "orcid": "0000-0002-6583-6322", "clpid": "Keith-John-A" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An investigation of modern computational simulation techniques and their results in describing two notable organopalladium reactions are discussed. First, a methodology for computational quantum chemistry simulations of homogeneous catalysis is presented. We find that through careful consideration of electronic and thermodynamic energy contributions, practical methods are available to accurately study complicated reaction mechanisms and to make educated predictions about their chemistry. We apply this technique to develop the first full analysis of the Wacker Process, olefin oxidation by PdCl2 catalysts, effectively uniting nearly 50 years of research into one mechanistic model. Key findings include the identification of competitive rate determining steps that are dependent on ion concentrations and the inaccessibility of [beta]-hydride elimination during product formation. The second analysis addresses the unique performance of the enantioselective Tsuji-allylation reaction, a reaction the great potential in the fields of asymmetric catalysis and natural product synthesis. In this reaction, calculations point towards enantioselectivity determined after the rate determining step. Intriguingly, we find that C-C coupling is facile in a variant to canonical reductive elimination containing characteristics of both reductive cheletropic and Claisen rearrangements. Lastly, a model is presented to direct improved catalyst design. In total, this dissertation presents an outline for practical quantum chemical simulation of complicated and elaborate organopalladium reactions.\r\n", "doi": "10.7907/FAS9-DV26", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:4269", "collection": "thesis", "collection_id": "4269", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10262007-104725", "primary_object_url": { "basename": "Thesis-MLL_2.pdf", "content": "final", "filesize": 1845146, "license": "other", "mime_type": "application/pdf", "url": "/4269/1/Thesis-MLL_2.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Ultrasonic Investigation of the Elastic Properties and Liquid Fragility of Bulk Metallic Glasses in the Supercooled Liquid Region", "author": [ { "family_name": "Lind", "given_name": "Mary Laura", "orcid": "0000-0001-8585-8054", "clpid": "Lind-Mary-Laura" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Greer", "given_name": "Julia R.", "clpid": "Greer-J-R" }, { "family_name": "Conner", "given_name": "Robert Dale", "clpid": "Conner-R-D" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this thesis new methods for accessing the ultrasonic properties of supercooled liquid region in bulk metallic glass forming liquids were developed. An extensive examination of the relationship between the elastic properties of metallic glasses and liquid fragility has been undertaken. Three experimental techniques were created/modified to access the Supercooled Liquid Region of the glass: annealing relaxation measurements, delay line measurements, and long notched-rod measurements. The methods as well as the limitations are discussed.
\r\n\r\nUltrasonic contact methods with measurement frequencies of 25MHz have been used for in situ and ex situ examination of the elastic properties of the supercooled liquid region (SCLR) in bulk metallic glasses (BMGs). Ex situ relaxation experiments in Vitreloy-4 (Zr46.75Ti8.25Cu7.5Ni10Be27.5) were performed that demonstrated that in the glassy state, the low-temperature dependence (from 78K to 298K) of the elastic modulii is linear as expected from Debye-Gruneisen theory. In the liquid state, the temperature dependence of the shear modulus was found to be stronger than that of the bulk modulus. The strong temperature dependence of G is found to be an important aspect of the recently developed Cooperative Shear Model. Additionally, this temperature dependence of the shear modulus in the liquid state was found to directly relate to the viscosity (or fragility) of the liquid. In situ experiments, utilizing delay lines and notched-rods, were performed on BMGs with a range of fragilities. Improvements to the model relating viscosity, shear modulus, and liquid fragility are presented. The results from both types of measurement (in and ex situ) compared favorably; thus supporting the claim that we are measuring the properties of the equilibrium supercooled liquid. Additionally, these results are used support the idea that the shear modulus relates to a unique potential energetic state of the glass.
\r\n", "doi": "10.7907/3B4B-ZV48", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:4105", "collection": "thesis", "collection_id": "4105", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10152007-175458", "primary_object_url": { "basename": "Beginning.pdf", "content": "final", "filesize": 161532, "license": "other", "mime_type": "application/pdf", "url": "/4105/2/Beginning.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Alpha-Diaminobutyric Acid-Linked Hairpin Polyamide-Alklylator Conjugates ", "author": [ { "family_name": "Tsai", "given_name": "Sherry Mon-Yue", "clpid": "Tsai-Sherry-Mon-Yue" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The ability to control gene expression through the use of DNA sequence-specific, cell-permeable molecules holds therapeutic promise. Pyrrole-imidazole polyamides are a class of synthetic ligands that can be programmed to bind a broad repertoire of DNA sequences with affinities and specificities comparable to natural DNA-binding proteins. These ligands are generally linked via a turn moiety, resulting in a \u2018hairpin\u2019 structure. Conjugation of polyamides to the non-specific DNA alkylator chlorambucil produces molecules capable of the sequence-specific alkylation of DNA that can arrest gene transcription. We have identified \u03b1-diaminobutyric acid (\u03b1-DABA) as a new turn moiety that can give polyamide-chlorambucil conjugates distinctive biological properties in cellular and small animal models; this may be due to their increased DNA alkylation specificities relative to the standard \u03b3-DABA-linked conjugates. A general characterization of \u03b1-DABA-linked polyamides and their conjugates is reported.
\r\n\r\nAlso described is the development of a modular synthesis of chondroitin sulfate (CS) glycosaminoglycans \u2014 a class of linear, sulfated oligosaccharides that play critical roles in neuronal development, cell division, and spinal cord injury. CS structure in vivo is complex and heterogeneous, hampering efforts to understand its precise biological roles. Access to CS molecules of precisely defined structures is critical to understanding their structure-function relationships. The reported synthetic route is capable of accessing CS structures of defined lengths and sulfation motifs, providing a new approach to understanding these important molecules.
\r\n", "doi": "10.7907/3S8Y-YD79", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:706", "collection": "thesis", "collection_id": "706", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02212008-145524", "primary_object_url": { "basename": "Full.Thesis.Caspi.pdf", "content": "final", "filesize": 37238324, "license": "other", "mime_type": "application/pdf", "url": "/706/15/Full.Thesis.Caspi.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "The Adaptive Nature of Palladium Reactivity in Synthesis", "author": [ { "family_name": "Caspi", "given_name": "Daniel David", "clpid": "Caspi-Daniel-David" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Both Pd(0) and Pd(II) have had, and continue to have, far-reaching impacts on organic synthesis. The versatile nature of palladium, in conjunction with the mechanistic understanding and predictive models that have been elucidated, has permitted a wealth of exploration into the seemingly endless potential of this metal. The utility of palladium is described in the context of the syntheses of the pharmaceutical agents Prozac\u00ae, and Singulair\u00ae, as well as the natural products dragmacidin F and telomestatin.
\r\n\r\nFirst, the palladium-catalyzed aerobic oxidative kinetic resolution for the enantioselective preparation of a variety of pharmaceutical substances, including Prozac\u00ae, and Singulair\u00ae is described. In this regard, the versatility of this resolution is further demonstrated by the diversity of the substrates chosen for this study, and for the first time this work extends the utility of the resolution to include amino alcohol derivatives and highly functionalized benzylic alcohols.
\r\n\r\nSecondly, an enantiodivergent strategy for the total chemical synthesis of both (+)- and (\u2013)-dragmacidin F from a single enantiomer of quinic acid has been developed and successfully implemented. Although unique, the synthetic routes to these antipodes share a number of key features, including novel Pd(0) reductive isomerization reactions, Pd(II)-mediated oxidative carbocyclization reactions, halogen-selective Suzuki couplings, and high-yielding late-stage Neber rearrangements.
\r\n\r\nFinally, progress toward the total synthesis of the potent telomerase inhibitor telomestatin is described. Palladium-mediated cross-coupling reactions are employed to assemble oligooxazole intermediates from oxazole building blocks. Additionally, this strategy utilizes a minimum number of protecting groups, and proposes a unique aryl\u2013aryl macrocyclization as the last step of the synthesis. In addition to the biological relevance of the desired target, a successful total synthesis of telomestatin would also enable rapid access to the preparation of telomestatin analogs. This would allow for the investigation of key interactions between telomestatin and the G-quadruplex.
\r\n", "doi": "10.7907/N37A-5970", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:3367", "collection": "thesis", "collection_id": "3367", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09062007-233423", "primary_object_url": { "basename": "MeherAyalasomayajulaThesis.pdf", "content": "final", "filesize": 1225851, "license": "other", "mime_type": "application/pdf", "url": "/3367/1/MeherAyalasomayajulaThesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Theoretical Studies of Single Molecule Biophysical Systems and Photochemical Ensembles", "author": [ { "family_name": "Ayalasomayajula", "given_name": "Meher Kiran Prakash", "clpid": "Ayalasomayajula-Meher-Kiran-Prakash" } ], "thesis_advisor": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" } ], "thesis_committee": [ { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe focus of the present thesis is on theoretical analysis to understand the experimental results from three quite different systems - enzymes, RNA hairpins and nitrous oxide (N2O). Some experiments on single enzymes showed very unusual data: in separate experiments the fluctuations in catalysis rate ([...]) and fluorescence lifetime ([...]) of chromophore in single enzymes showed long-lasting autocorrelations, represented by a stretched exponential and power-law, respectively. With the aim of interpreting the origin of these fluctuations, we proposed a formulation based on fluctuations in electrostatic interaction energy ([...]) at the active site in the enzyme leading to the fluctuations in the various observables. We developed relations between the autocorrelation functions of [...], [...], spectral diffusion ([...]) and the radiative component of fluorescence lifetime ([...]). It was pointed out that the relation between [...] and [...], seen experimentally and modeled theoretically by using the relation noted above, is a dynamic analog of the solvatochromism concept used in the catalysis of organic reactions by solvent. The estimation of fluctuations in electrostatic interactions on the milliseconds to seconds time scale by computational methods is not possible, which are typically limited to tens of nanoseconds. To calculate the autocorrelation of electrostatic interactions and to compare them with experiments, we used the frequency dependent dielectric response of proteins and related it to the autocorrelation of [...]. Based on this formulation, we find a good agreement between the single molecule data on the enzyme candida antarctica lipase B and the calculation using dielectric response data on the enzyme. In single molecule data from other enzymes for which [...] is not yet available, we have predictions based on a commonly observed functional form of [...] for other proteins.\r\n\r\nSingle molecule experiments on RNA hairpins were used to test a nonequilibrium statistical physics result - Crooks' theorem. Crooks' theorem is about an exact equality relating the probability distributions of work done (W) on a system by varying an external parameter in the forward and reverse directions in a predetermined way. Usually in the single molecule experiments this predetermined variation is a constant rate ([...]) of increase or decrease of the external force for all runs of the experiment. Our study focuses on the relevance of the RNA hairpin unfolding experiments to the theorem. The unfolding of the molecule leads to a drop in the externally controlled force on the molecule, a condition which is not suited to the existing derivations of Crooks' theorem. An alternative interpretation of the experimental unfolding and refolding data using a phenomenological force-dependent distortion of activation barriers is provided to gain insight into the data on the probability distribution of work done during unfolding, refolding corresponding to different rates of change of force. This interpretation shows that the crossing of the unfolding and refolding work distributions which happens at the same value of W for all [... is a necessary but not sufficient condition to verify the theorem.\r\n\r\nThe experimental data on UV photodissociation of the greenhouse gas N2O and the associated isotope effects are important from the perspective of atmospheric interest. The calculations in the literature to model the photodissociation observations are of two kinds - some are computationally intensive quantum mechanical methods using wave packet propagation and the others are based on empirical calculations. The two different calculations we present, based on two different variants of the 'multidimensional reflection principle' maintain the simplicity of computation, while using the available ab initio data on the molecule for the potential energy surfaces and the transition dipole moments. In one of the calculations, the absorption cross section was broadened empirically to get agreement with the absorption data and the results were then used to make calculations of isotopologue fractionation. This broadening was also needed in a wave packet propagation calculation. In a later calculation, without introducing the broadening factor, the results were compared only on one side of the absorption cross section, where the isotopic fractionation measurements are available. Using these two methods, the fractionation of heavier isotopologues of N2O with respect to the most abundant isotopologue [...] were calculated and compared with the experiments. A simple relation between the fractionations of [...] and [...] was observed in the results from our calculations. A perturbation theoretical result was used to derive this relationship, which is independent of the detailed calculations required for each of the isotopologues individually.", "doi": "10.7907/5D2K-7H81", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:5035", "collection": "thesis", "collection_id": "5035", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12172007-134752", "primary_object_url": { "basename": "(Full)RMMThesis.pdf", "content": "final", "filesize": 45005243, "license": "other", "mime_type": "application/pdf", "url": "/5035/11/(Full)RMMThesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Applications of Palladium-Catalyzed Enantioselective Decarboxylative Alkylation in Natural Products Total Synthesis", "author": [ { "family_name": "McFadden", "given_name": "Ryan Michael", "clpid": "McFadden-Ryan-Michael" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The catalytic enantioselective preparation of all-carbon quaternary stereocenters within rings via alkylation is a major challenge in synthetic organic chemistry. Many important natural products and biologically active pharmaceuticals contain this motif. We have developed palladium-catalyzed decarboxylative alkylations capable of generating all-carbon quaternary stereocenters in good yield with high enantioselectivity.
\r\n\r\nAlkylated products are readily elaborated to synthetically useful cyclic scaffolds. The enantioselective decarboxylative alkylation is thus utilized to prepare intermediates previously reported in the total syntheses of classic natural products. Herein, we disclose modern formal syntheses of (\u2013)-Thujopsene, (-\u2013)-Dysidiolide, and (\u2013)-Aspidospermine.
\r\n\r\nThe longer-term goal was to apply this new enantioselective catalysis to the total syntheses of natural products with novel carbocyclic architectures. Our methodology is demonstrated during the first protecting group-free enantioselective total synthesis of (+)-dichroanone, a 4a-methyltetrahydrofluorene. The [6-5-6] tricyclic natural products family has members with important biological activity, and our route to (+)-dichroanone may provide general access to related compounds. During our synthetic endeavors, a novel Kumada-benzannulation approach to the aromatic portion of (+)-dichroanone was developed, along with a unique synthesis of a hydroxy-p-benzoquinone from a phenol. The absolute stereochemistry of the natural product was verified for the first time during our total synthesis.
\r\n\r\nSignificant progress has been made toward the total synthesis of the marine meroterpenoid liphagal, a potent and selective phosphatidylinositol 3-kinase alpha inhibitor. The enantioselective decarboxylative alkylation has been employed, and an acetylene [2 + 2] photoaddition / ring-opening sequence is used to construct the 7-membered ring. New understanding about the reactivity of [6-7] bicyclic scaffolds has been gathered, and the information applied during preparation of liphagal\u2019s benzofuran motif. Our efforts have led to a functionally diverse array of liphagal analogues, which may be used for structure-activity-relationship studies with phosphatidylinositol 3-kinases.
\r\n", "doi": "10.7907/GQ1E-RW28", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:2323", "collection": "thesis", "collection_id": "2323", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05302008-164022", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 5547848, "license": "other", "mime_type": "application/pdf", "url": "/2323/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Methods in Computational Protein Design", "author": [ { "family_name": "Kam", "given_name": "Victor Wai Tak", "clpid": "Kam-Victor-Wai-Tak" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In silico design of protein has generated enormous interest with the rapid advances in computational power. Biological systems are known for their complexity, and we have made a series of computational developments that allow us to perform computational protein design. In this work we present a methodology for the design and prediction of protein active sites.
\r\n\r\nWe begin by presenting SCREAM, a program developed to accurately position sidechains in proteins. We show how using an improved scoring function and placement algorithm allow us to achieve better accuracy in the placement and prediction of sidechains in proteins compared to other methods.
\r\n\r\nWe then describe the development of an accurate treatment for describing hydrogen bonding. This is done by refining the hydrogen bond term in the force field DREIDING. We also need to properly describe electrostatics effects in proteins, and to this end, we introduce neutralized residues for proteins. We found that this improves the variance in our predictions dramatically.
\r\n\r\nFinally, having established the components described above, we describe a protein design methodology encompassing the above methods and tools. We show predictions we made and those having been verified by experiments.
\r\n", "doi": "10.7907/S7KW-0M44", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:4497", "collection": "thesis", "collection_id": "4497", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11102006-144154", "primary_object_url": { "basename": "07jheo-Thesis.pdf", "content": "final", "filesize": 6981489, "license": "other", "mime_type": "application/pdf", "url": "/4497/8/07jheo-Thesis.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Computational Studies of Orphan G Protein-Coupled Receptors", "author": [ { "family_name": "Heo", "given_name": "Jiyoung", "orcid": "0000-0001-9953-6400", "clpid": "Heo-Jiyoung" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "G protein-coupled receptors (GPCRs) play an essential role in cell communications and sensory functions. Consequently, they are involved in wide variety of diseases and are targets for many drug therapies. Particularly important is the large number of orphan GPCRs, which may play important, albeit unknown, functions in various cells. To understand their respective physiological roles, it is important to identify their endogenous ligands, and to find small molecule ligands that would serve as selective agonists or antagonists. The mas-related gene G protein-coupled receptors (Mrg receptors) belong to the orphan GPCR family, which is expressed in a specific subset of sensory neurons known to detect painful stimuli, suggesting that they could be involved in pain sensation or modulation.
\r\n\r\nThe primary focus of this thesis is to predict the 3D structure and binding site of Mrg receptors and to identify novel ligands that would be potential agonists or antagonists. We predict the 3D structure for the mouse MrgC11 (mMrgC11) and the binding site for five chiral FMRF-NH2 ligands. We correctly predict the relative binding observed for these five ligands. We find that Tyr110 (TM3), Asp161 (TM4), and Asp179 (TM5) are particularly important to binding the ligands. Subsequently, we carry out mutagenesis experiments followed by intracellular calcium release assays that demonstrate the dramatic decrease in activity for the Y110A, D161A, and D179A mutants predicted by our model.
\r\n\r\nThe all-atom molecular dynamics simulation of the mMrgC11/F-(D)M-R-F-NH2 complex structure in explicit water and infinite lipid membrane system shows that some conformational fluctuations are present, but no significant instability is detected, thus validating our structure prediction method.
\r\n\r\nThe virtual screening with the combination of QSPR and docking methods is carried out for the predicted mMrgC11 receptor. The compounds showing the antagonistic effect are identified by competitive functional assays. These hit compounds are certainly good staring points in designing better agonists or antagonists.
\r\n\r\nThe binding site of rat MrgA receptor that shows differential binding between adenine and guanine is also predicted. The predicted binding affinity correlates with the availability of the hydrogen bonds to two Asn residues, which would be primary mutation candidates to validate the structure.
", "doi": "10.7907/rmmr-sj52", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2341", "collection": "thesis", "collection_id": "2341", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05312007-142846", "primary_object_url": { "basename": "JE_Green_Thesis.pdf", "content": "final", "filesize": 13833237, "license": "other", "mime_type": "application/pdf", "url": "/2341/7/JE_Green_Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ultra-Dense Nano- and Molecular-Electronic Circuits", "author": [ { "family_name": "Green", "given_name": "Jonathan Earl", "clpid": "Green-Jonathan-Earl" } ], "thesis_advisor": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes research towards the realization of large-scale, ultra-dense nanowire-based circuits. The primary means for the construction of such circuits is the superlattice nanowire pattern transfer (SNAP) technique. This technique was optimized for the fabrication of large nanowire arrays containing over 1000 nanowires at narrow pitch and aligned over millimeter length scales. Silicon nanowire arrays were fabricated with wire widths down to ten nanometers, and with precisely-controlled electronic properties and bulk-like resistivity values through the use of diffusion doping and the selection of high-quality silicon-on-insulator substrates.
\r\n\r\nA binary tree demultiplexer circuit allows the unique addressing of N nanowires from within an ultra-dense array using of order 2xlog2(N) control wires. An implementation of this circuit was experimentally demonstrated to bridge from the submicrometer dimensions of lithographic patterning to the nanometer-scale dimensions of SNAP patterning. This circuit utilized field-effect gating by relatively large control wires to address individual nanowires from within a 150-nanowire array patterned at a wire width and pitch of 13 and 34 nanometers, respectively.
\r\n\r\nSilicon- and metal-nanowire arrays were integrated with [2]rotaxane molecular materials for the fabrication of an ultra-dense, 160,000-bit crosspoint molecular electronic memory circuit. This circuit is patterned at a record density of 1x10^11 bits per square centimeter (device-pitch of 33 nanometers), and contains bistable, electrochemically addressable [2]rotaxane switching molecules as the data storage elements within the individual crosspoint junctions. Defective junctions could be readily identified through electronic testing and isolated through software coding. The working bits could then be configured to form a functional memory circuit. The molecular-mechanical nature of the switching mechanism was confirmed through volatility measurements.
\r\n\r\nAn optimized two-step chlorination/methylation protocol was used to methyl passivate thin (~20-nanometer) silicon(111)-on-insulator microelectronic device surfaces, that were then demonstrated to be stable in air for arbitrarily long periods, and to resist oxidation due to common microelectronic fabrication procedures and wet-chemical treatments. Additionally, temperature-dependent mobility data showed that methylated silicon-on-insulator surfaces can be prepared with bulk-like mobility characteristics through careful optimization of the methylation reaction protocol.
\r\n", "doi": "10.7907/HCQH-2S48", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1364", "collection": "thesis", "collection_id": "1364", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04122007-134232", "primary_object_url": { "basename": "JianThesisA.pdf", "content": "final", "filesize": 2205494, "license": "other", "mime_type": "application/pdf", "url": "/1364/1/JianThesisA.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Microfluidic Devices for Genetic Analysis and Gene Expression Studies", "author": [ { "family_name": "Liu", "given_name": "Jian", "orcid": "0000-0002-0095-8978", "clpid": "Liu-Jian" } ], "thesis_advisor": [ { "family_name": "Quake", "given_name": "Stephen R.", "clpid": "Quake-S-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Quake", "given_name": "Stephen R.", "clpid": "Quake-S-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Microfluidic devices hold the promise of becoming the next-generation laboratory platforms by offering many possible benefits in chemistry, biology, and medicine. However, microfluidics is still in its infancy at present, requiring a great deal of work before it can become more than an active research field in academia. This thesis describes efforts by the author in developing microfluidic technologies for applications in genetics. Section I describes the development of miniaturized devices for genetic analysis. Successful nucleic acid amplifications by polymerase chain reaction (PCR) have been demonstrated within a reaction volume as small as 700 picoliters. In section II, the concept of a microfluidic matrix chip is described and has been experimentally realized to solve the \"macroscopic/microfluidic\" interface problem. The matrix chip also provides a flexible platform to perform combinatorial tests with high throughput performance. Section III presents an application example of the microfluidic matrix chip in gene expression studies, providing quantitative profiles of gene isoforms by alternative splicing in a high throughput manner. In the section IV, a microfluidic chaotic mixer has been developed to accelerate the process and enhance the hybridization signals of DNA microarray experiments. These devices represent significant advances in microfluidics, with the following goals achieved: improved sensitivity and reliability of assays, reduction of consumption of reagents or analytes into desired economies of scale, and dramatic reduction of the time and complexity of \"hands-on\" manipulations, therefore providing experimental results in a high throughput manner.", "doi": "10.7907/xnm0-4a75", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:190", "collection": "thesis", "collection_id": "190", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01152007-080704", "primary_object_url": { "basename": "CompleteThesis.pdf", "content": "final", "filesize": 4146525, "license": "other", "mime_type": "application/pdf", "url": "/190/5/CompleteThesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Chemical Scale Investigations of the Gating Mechanism of Ion Channels", "author": [ { "family_name": "Lee", "given_name": "Lori Wai Hang", "clpid": "Lee-Lori-Wai-Hang" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Lester", "given_name": "Henry A.", "clpid": "Lester-H-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The studies contained in this dissertation are aimed at utilizing chemistry to understand neurobiology and neuronal communication. Chapters 2 and 3 both address the gating of ion channels, describing structure-function studies to shed light on the gating mechanisms of two classes of ion channels. Chapter 2 studies the gating mechanism of the mechanosensitive channel of small conductance (MscS), which is voltage modulated. Elucidating the mechanism of voltage sensation in MscS may provide insight into how voltage-gated channels translate a change in membrane potential to channel gating. The research discussed in Chapter 2 is aimed at elucidating the role of two arginine residues, in the TM1 and TM2 of MscS, in voltage sensing. We generated two MscS mutants, Arg46Ala and Arg74Ala, to evaluate the effects of \"neutralizing\" the charged side chain on the voltage sensing ability of the channel. The mutants were evaluated using single channel analysis in E. coli spheroplasts. Our preliminary results indicated a potentially significant role for Arg46 in the voltage sensitivity of MscS, however this data set is not extensive due to inconsistency in the spheroplasts preparation.
\r\n\r\nIn Chapter 3, we utilized nonsense suppression to incorporate unnatural amino acids to study the gating of the cation-selective Cys-loop family of ion channel receptors. Specifically, it describes work aimed at elucidating the role of cis-trans isomerization of a proline residue in the gating mechanism of the serotonin-gated 5-hydroxy-tryptamine receptor 3A (5-HT3A) and the nicotinic acetylcholine receptor. A series of proline analgues, of varying cis preference were incorporated at proline 308 in the M2-M3 loop of the 5-HT3A receptor using in vivo nonsense suppression methodology in a Xenopus oocyte expression system. Electrophysiological analysis of the mutant channels revealed a linear relationship between the cis preference of the proline analog and the EC50 of the mutant channel\u2014suggesting that proline 308 may serve as a hinge during the gating 5-HT3A. From these data, we proposed a model of gating for the 5-HT3A receptor. Initial results from similar studies in nAChR suggests that the analogous proline does not play a role in its gating.
\r\n\r\nLastly, Chapter 4 addresses the role of fucose-galactose carbohydrates in learning and memory. It aims to identify lectins to fucose-alpha(1-2)-galactose as well as identify the corresponding glycoproteins bearing fucose-alpha(1-2)-galactose. Chemical probes were synthesized and used to study fucose-alpha(1-2)-galactose binding proteins. One of the probes was used to demonstrate the existence of fucose-alpha(1-2)-galactose binding proteins in hippocampal neurons. Furthermore, initial results from experiments with a photoreactive probe suggested that the design of our probe is sufficient to isolate fucose-alpha(1-2)-galactose binding proteins from the brain. Additionally, we were able to use antibodies specific to fucose-alpha(1-2)-galactose epitopes to examine fucose-alpha(1-2)-galactose bearing glycoproteins in the brain. Overall, results from both studies utilizing chemical probes and molecular probes strongly suggest that the modifications of proteins with fucose-alpha(1-2)-galactose epitopes and the expression of fucose-alpha(1-2)-galactose binding proteins are developmentally regulated.
", "doi": "10.7907/bv54-5p15", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1989", "collection": "thesis", "collection_id": "1989", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05232007-142037", "primary_object_url": { "basename": "LisaCowanThesis.pdf", "content": "final", "filesize": 3982785, "license": "other", "mime_type": "application/pdf", "url": "/1989/1/LisaCowanThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Superprotonic Solid Acid Phase Transitions and Stability", "author": [ { "family_name": "Cowan", "given_name": "Lisa", "clpid": "Cowan-Lisa" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "orcid": "0000-0002-5293-6252", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "orcid": "0000-0002-5293-6252", "clpid": "Haile-S-M" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Solid acid proton conductors are viable alternatives to current fuel cell electrolytes. Incorporating solid acid electrolytes, next generation fuel cells would not require humidification of the electrolyte, as in proton exchange membrane fuel cells, and could operate at higher temperatures which would improve catalysis rates. Engineering the properties of these materials for fuel cell electrolyte applications requires an understanding of the structural and chemical parameters that support superprotonic phase transitions over melting or decomposition.
\r\n\r\nIn this thesis, the structures of three superprotonic solid acids are presented, and for the first time, a distinction is possible between local versus average structure. An adapted model for configurational entropy based on Pauling\u2019s entropy rules for ice is incorporated to describe the entropy of superprotonic solid acids. Insights from local structural information alleviate discrepancies between this model and experimentally determined entropy values. With clarifications from this work, the calculated configurational entropy of the superprotonic structures of CsD2PO4, RbDSeO4, and CsDSO4, agree well with experimentally determined entropy values.
\r\n\r\nA study of chemical intermediates, CsxRb1-xH2PO4, provides valuable insight into the nature of the cation size effect on superprotonic phase transitions within an isostructural system. For compounds in the series that do exhibit a superprotonic phase, CsH2PO4 \u2013 Cs0.3Rb0.7H2PO4, the magnitude of proton conductivity remains neutral to rubidium incorporation. Altering the effective cation size shows a profound impact on transition temperature for compounds with high rubidium content (x < 0.5) while preserving the overall conductivity of the high-temperature and low-temperature phases. X-ray diffraction, thermal analysis, Raman, IR, 133Cs, 87Rb and 1H-NMR spectroscopy all attest to the gradual variation in structural properties across the composition range.
\r\n\r\nThe complicated high-temperature properties of Rb3H(SO4)2 have been misinterpreted in earlier literature as a superprotonic phase transition. This work presents a careful analysis of a conglomeration of data from different techniques which definitively conclude that at ambient pressure, Rb3H(SO4)2 degrades via phase separation, Rb3H(SO4)2 \u2192 RbHSO4 + Rb2SO4.
", "doi": "10.7907/30RE-XG95", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:5258", "collection": "thesis", "collection_id": "5258", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10312006-164725", "primary_object_url": { "basename": "DCB_Thesis_Full.pdf", "content": "final", "filesize": 40165419, "license": "other", "mime_type": "application/pdf", "url": "/5258/17/DCB_Thesis_Full.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Progress Toward the Synthesis of (+)-Zoanthenol and the Development of an Asymmetric Tsuji Allylation Reaction", "author": [ { "family_name": "Behenna", "given_name": "Douglas Carl", "clpid": "Behenna-Douglas-Carl" } ], "thesis_advisor": [ { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The stereoselective synthesis of all carbon quaternary stereocenters is an important problem in synthetic chemistry due to their common occurrence in bioactive compounds. The zoanthamine class of marine natural products highlights the challenge in constructing such stereocenters. After a summary of the isolation, structure determination, and biological activities of the zoanthamine natural products, published approaches toward their chemical synthesis are reviewed.
\r\n\r\nSynthetic strategies toward the carbocyclic portion of zoanthenol focus on the synthesis of the three challenging quaternary stereocenters located on the central C ring. An unusual acid-mediated SN' cyclization of a nucleophilic arene with an allylic alcohol forms the B ring and diastereoselectively constructs the benzylic C(12) quaternary stereocenter. However, difficulties with late-stage installation of the remaining C(9) quaternary stereocenter compelled the use of C ring synthons containing the vicinal C(9) and C(22) stereocenters installed at an early stage in the synthesis. Desymmetrization of a meso-anhydride containing vicinal quaternary stereocenters accomplishes this goal in an enantioselective fashion. Several C ring synthons bearing the vicinal quaternary stereocenters are elaborated with A ring fragments, and several methods for the formation of the C(11)-C(12) bond in these systems are explored. Ultimately, a radical conjugate addition strategy provides the carbocyclic core of zoanthenol with the correct relative configuration of all three quaternary stereocenters.
\r\n\r\nThese efforts toward the synthesis of zoanthenol highlight the difficulty in generating enantioenriched alpha-quaternary cycloalkanones derived from ketones with multiple acidic alpha-hydrogens. The first direct catalytic enantioselective access to such products is achieved by the application of chiral bidentate phosphinooxazoline (PHOX) ligands to Tsuji\u2019s non-enantioselective allylation reactions. Cyclic allyl enol carbonates, silyl enol ethers, and allyl beta-ketoesters all provide uniformly excellent yields and high enantioselectivity in the reaction. The limitations on the substrate scope of the reaction are discussed. Preliminary studies into the mechanism of these allylation reactions with prochiral enolate fragments suggest that they occur by a different mechanism than the outer-sphere nucleophilic attack commonly proposed in the alkylation of prochiral allyl fragments.
\r\n", "doi": "10.7907/46KF-QE46", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1598", "collection": "thesis", "collection_id": "1598", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05032007-151410", "primary_object_url": { "basename": "FinalThesis.pdf", "content": "final", "filesize": 12879814, "license": "other", "mime_type": "application/pdf", "url": "/1598/1/FinalThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "An Electron Force Field for Simulating Large Scale Excited Electron Dynamics", "author": [ { "family_name": "Su", "given_name": "Julius Tsu-li", "clpid": "Su-Julius-Tsu-li" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We introduce an electron force field (eFF) that makes simulation of large scale excited electron dynamics possible and practical. The forces acting on thousands of electrons and nuclei can be computed in less than a second on a single modern processor.
\r\n\r\nJust as conventional force fields parameterize the ground state potential between nuclei, with electrons implicitly included, electron force fields parameterize the potential between nuclei and simplified electrons, with more detailed degrees of freedom implicitly included. The electrons in an electron force field are Gaussian wave packets whose only parameters are its position and its size.
\r\n\r\nUsing a simple version of the electron force field, we compute the dissociation and ionization behavior of dense hydrogen, and obtain equations of state and shock Hugoniot curves that are in agreement with results obtained from vastly more expensive path integral Monte Carlo methods. We also compute the Auger dissociation of hydrocarbons, and observe core hole decays, valence electron ionizations, and nuclear fragmentation patterns consistent with experiment.
\r\n\r\nWe show we can describe p-like valence electrons using spherical Gaussian functions, enabling us to compute accurate ionization potentials and polarizabilities for first row atoms, and accurate dissociation energies and geometries of atom hydrides and hydrocarbons.
\r\n\r\nWe show also that we can describe delocalized electrons in a uniform electron gas using localized eFF orbitals. We reproduce the energy of a uniform electron gas, including correlation effects; and following the historical development of density functional theory, we develop a preliminary eFF that can compute accurate exchange and correlation energies of atoms and simple molecules.
", "doi": "10.7907/d8a3-e876", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2244", "collection": "thesis", "collection_id": "2244", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292007-060906", "primary_object_url": { "basename": "CH0.pdf", "content": "final", "filesize": 133765, "license": "other", "mime_type": "application/pdf", "url": "/2244/2/CH0.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Computational Studies of the Structure and Function of Two Lipid-Activated G Protein-Coupled Receptors", "author": [ { "family_name": "Niemer", "given_name": "Rachel K.", "orcid": "0000-0002-6238-8544", "clpid": "Niemer-Rachel-K" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Vaidehi", "given_name": "Nagarajan", "clpid": "Vaidehi-N" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Vaidehi", "given_name": "Nagarajan", "clpid": "Vaidehi-N" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Phospholipids are pleiotropic intercellular signaling molecules that have been implicated in various pathologies, including tumorigenesis. Both lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P), among other phospholipids, use G protein coupled receptors (GPCRs) to transduce extracellular signals. Other families of GPCRs have successfully been utilized by the pharmaceutical industry, and further understanding of the phospholipid-receptor interaction can highlight potential therapeutic targets in these signaling pathways.
\r\n\r\nThis thesis presents research into the interaction between specific G protein-coupled receptors, lysophosphatidic acid receptor-2 (LPA2) and sphingosine-1-phosphate receptor 1 (S1P1), and their ligands, in an attempt to further validate our method of GPCR structure prediction and to understand subtype specificity within this family of lipid receptors. Although the first principles method of GPCR structure prediction has quite successfully predicted the protein structure of small molecule receptors, lipid receptors create a unique challenge. The surface area on the inside of a small molecule receptor contains a large percentage of polar groups, easily differentiating the inner surface from the highly hydrophobic outer surface. Lipid receptors do not show as dramatic a distinction, as the inner surface is significantly hydrophobic to bind the lipid ligand.
\r\n\r\nHerein we propose and test a new method of orienting the seven transmembrane helices of a GPCR relative to one another through an analysis of the lipid solubility of each residue in conjunction with an optimization of the inter-helical hydrogen bonding associations. We predict structures for LPA2 and S1P1 that replicate the relative binding of different lipids within the LPA and S1P lipid families. The interaction energies between the receptors and the tested ligands correlates well with ligand efficacy, and qualitative analysis of functional group-residue interactions further validates our model for both LPA2 an S1P.
", "doi": "10.7907/djy6-nw49", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1662", "collection": "thesis", "collection_id": "1662", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05072007-184544", "primary_object_url": { "basename": "JoannaDodd_thesis.pdf", "content": "final", "filesize": 26747721, "license": "other", "mime_type": "application/pdf", "url": "/1662/1/JoannaDodd_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Phase Composition and Dynamical Studies of Lithium Iron Phosphate", "author": [ { "family_name": "Dodd", "given_name": "Joanna Lynn", "clpid": "Dodd-Joanna-Lynn" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Yazami", "given_name": "Rachid", "clpid": "Yazami-R" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Yazami", "given_name": "Rachid", "clpid": "Yazami-R" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The olivine phase of lithium iron phosphate (Li\u2093FePO\u2084) is a promising cathode material for lithium-ion batteries. Some of its advantages are that it is nontoxic, highly stable, and inexpensive, but its low intrinsic electrical conductivity is a major disadvantage. Li\u2093FePO\u2084 has generally been described as a two-phase system as lithium is removed from or inserted into the material. However, the mechanism of lithium removal and the system's phase composition is still not fully understood, and is an area of interest.
\r\n\r\nThe two low-temperature phases, heterosite and triphylite, have previously been shown to transform to a single-phase disordered solid solution at temperatures above 200\u00b0C. Here, the phase diagram for Li\u2093FePO\u2084 has been determined for different lithium concentrations and temperatures. This disordered phase is stable at relatively low temperatures. The proposed phase diagram resembles a eutectoid system, with eutectoid point at around x = 0.6 and 200\u00b0C. The kinetics of mixing and unmixing transformations, including the hysteresis between heating and cooling, will be shown. The enthalpy of this transition is at least 700 J/mol. Further thermostability studies of the material up to temperatures of 800\u00b0C will also be discussed.
\r\n\r\nSolid solution regions have also been indicated near the end compositions of x = 0 and 1 at room temperature. Measurements of the entropy (\u0394S(x)) and enthalpy (\u0394H(x)) of lithiation were performed, indicating the ranges of solid solution regions to be x < 0.05 and x > 0.85. In addition, the entropy of lithiation in between (0.05 < x < 0.85) changes gradually with x. This is unexpected, since \u0394S(x)) should be constant in a two-phase region. There are several alternatives which could be causing this result. Further clarification of this topic could give additional information about the phase transformation occurring as LiFePO4 is delithiated.
\r\n\r\nThe topic of dynamics in Li\u2093FePO\u2084 is also very relevant, especially since this material is now touted as an important high-rate capability cathode. The electronic and ionic conductivity of the new disordered solid-solution phase has generated widespread interest. The local electronic structure around iron ions in Li0.6FePO\u2084 was studied by 57Fe Mossbauer spectrometry at temperatures from 25 to 240\u00b0C. The equilibrium two-phase triphylite plus heterosite material was compared to a disordered solid solution that was obtained by quenching from a high temperature. Substantial electronic relaxations were found in the disordered solid solution compared to the two-phase material at temperatures of 130\u00b0C and above. Fluctuations in the electric field gradient and the isomer shift showed activation energies of 335 +- 25 meV and 600 +- 100 meV, respectively. It is suggested that these spectral relaxations are caused by the motions of Li\u207a ions. The activation energies from the isomer shift can be related to the material conductivity, giving values of 10-6 to 10-4 S/cm; 3 to 5 orders of magnitude higher than the measured value of 10-9 for fully lithiated LiFePO\u2084. A slight relaxation at 180\u00b0C in 10% of the two-phase material can be attributed to defects in the heterosite and triphylite phases. Overall, the disordered solid-solution phase shows faster electronic dynamics than the two-phase material.
\r\n\r\nAdditional studies on the dynamics of the disordered solid solution, along with attempts to stabilize this phase at lower temperatures, should be a topic of further work.
", "doi": "10.7907/0B7N-ZF63", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:1661", "collection": "thesis", "collection_id": "1661", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05072007-150354", "primary_object_url": { "basename": "01_Title.pdf", "content": "final", "filesize": 21885, "license": "other", "mime_type": "application/pdf", "url": "/1661/1/01_Title.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Experimental Studies of Elasticity, Plastic Flow, and Anelasticity in Metallic-Glass-Forming-Liquids", "author": [ { "family_name": "Harmon", "given_name": "John Shelby, III", "clpid": "Harmon-John-Shelby-III" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A rheological law based on the concept of cooperatively-sheared flow zones is presented, in which the thermodynamic state variable controlling flow is identified to be the isoconfigurational shear modulus of the liquid. The law captures Newtonian as well as non-Newtonian viscosity data for glass-forming metallic liquids over a broad range of fragility. Acoustic measurements on specimens deformed at constant strain rates correlate with the measured steady-state viscosities, and define the relative effects of the \u201celastic\u201d and \u201ccooperative volume\u201d indices on the liquid fragility. The steady state deformation material properties are evaluated to obtain a relationship between the shear modulus and configurational enthalpy. Furthermore, the material properties are evaluated through steady state in an effort to probe the relaxation mechanisms governing flow.", "doi": "10.7907/53AD-3G15", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2362", "collection": "thesis", "collection_id": "2362", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012006-103350", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 6264655, "license": "other", "mime_type": "application/pdf", "url": "/2362/1/thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Development and Applications of Computational Protein Design", "author": [ { "family_name": "Choi", "given_name": "Eun Jung", "clpid": "Choi-Eun-Jung" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Chan", "given_name": "David C.", "orcid": "0000-0002-0191-2154", "clpid": "Chan-D-C" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Success in computational design of proteins requires a good understanding of the physical properties that determine the protein structure. However, computational protein design also provides us the opportunities to test and improve our current knowledge of protein structure. In our lab, the \"protein design cycle\" is used to improve the energy function and increase our knowledge of protein chemistry. This strategy utilizes a cyclic protocol where first, a modification that is predicted to improve the result is applied to the energy function. Next, proteins are simulated using this modified function. These molecules are then synthesized and analyzed to see if our simulation results correlate with the physical properties of the molecules. The new knowledge from the analysis is incorporated into the next design in the form of a new modification and the whole cycle starts again. Using this technique, an energy function highly successful in designing protein stability has been acquired in our lab.
\r\n\r\nA similar approach was used to determine whether the introduction of a backbone entropy term allows us to incorporate proline into the pool of amino acids we consider in designs. Using ORBIT, several proline mutants of protein G were simulated and synthesized. The correlation between the experimental results and computational results was analyzed. From this analysis, we learned that the entropic benefit of a proline mutation is usually small compared to the enthalpic disadvantages. However, including a backbone entropy term did increase the correlation between the rank order of the experimental stabilities and computational energies.
\r\n\r\nThe ultimate test of our protein design protocol is its application to biological systems of interest. We have applied ORBIT to three different design problems, increasing the affinity of peptide-protein interaction of TRAF6, the elimination of disulfide bonds for biosensor design and enhancement of solubility and stability of an anti-htt antibody fragment. The results provided here show that protein design protocol is a fast and efficient way to manipulate and study biological systems.
", "doi": "10.7907/ZNED-BV38", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:3265", "collection": "thesis", "collection_id": "3265", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08292005-210930", "primary_object_url": { "basename": "TW_Thesis.pdf", "content": "final", "filesize": 2367366, "license": "other", "mime_type": "application/pdf", "url": "/3265/1/TW_Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Chemical-Scale Study on the Ligand-Binding Site of a Serotonin-Gated Ion Channel", "author": [ { "family_name": "Mu", "given_name": "Tingwei", "orcid": "0000-0002-6419-9296", "clpid": "Mu-Tingwei" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Signal transmission is a combination of electrical and chemical processes. Upon binding neurotransmitters, ligand-gated ion channels open to allow ion flux, which converts chemical signals to electrical signals. In this thesis, experiments in conjunction with computations are utilized to study the mechanism of the ligand-binding process.
\r\n \r\nThe target receptor is a serotonin-gated chloride channel, the MOD-1 receptor. From the viewpoint of a chemist, we explore the specific orientation of the agonist inside the binding pocket and the specific non-covalent interactions responsible for binding. In Chapter 3, computational chemistry is used to build a homology model of MOD-1 using the acetylcholine binding protein template. We proceed to dock the agonist into the binding pocket. The binding pattern from the model provides guidance for the ensuing experimental studies.
\r\n\r\nUnnatural amino acid mutagenesis is a powerful tool to modify the structure of the protein at the chemical level. Systematic perturbations can be introduced at a specific amino acid. Therefore, specific non-covalent interactions, such as hydrogen bonding and cation-pi interactions can be probed. In Chapter 2, we prove that cation-pi interactions between the agonist serotonin and Trp 226 in loop C of MOD-1 play a key role in binding the ligand. Surprisingly, this cation-pi site in MOD-1 is different from that in the serotonin type 3 receptor although these two receptors both bind serotonin, and they are highly homologous. In Chapter 4, we further show that hydrogen bonds between serotonin and Gln 228 and Asn 223 in MOD-1 are important in the binding process. Both conventional and unnatural amino acid mutagenesis are used in conjunction with serotonin analogues. The results from these thorough structure-function studies confirm aspects of the hydrogen bond pattern described in the model.
\r\n\r\nIn Chapter 5, we apply another strategy called the tethered agonist approach to further probe the agonist binding site. This is another elegant example of the effectiveness of the nonsense suppression method.
", "doi": "10.7907/VSEF-4856", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2364", "collection": "thesis", "collection_id": "2364", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012006-151944", "primary_object_url": { "basename": "CCL_Thesis_Corrected.pdf", "content": "final", "filesize": 3466451, "license": "other", "mime_type": "application/pdf", "url": "/2364/1/CCL_Thesis_Corrected.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Chemistry of Tris(phosphino)borate Manganese and Iron Platforms", "author": [ { "family_name": "Lu", "given_name": "Connie Chih", "orcid": "0000-0002-5162-9250", "clpid": "Lu-Connie-Chih" } ], "thesis_advisor": [ { "family_name": "Peters", "given_name": "Jonas C.", "clpid": "Peters-J-C" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Peters", "given_name": "Jonas C.", "clpid": "Peters-J-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The coordination chemistry of monovalent and divalent manganese complexes supported by the anionic tris(phosphino)borate ligand [PhBPiPr3] is presented. The halide complexes, [PhBPiPr3]MnCl and [PhBPiPr3]MnI, have been characterized by XRD, SQUID magnetometry, and EPR spectroscopy. The halide [PhBPiPr3]MnI serves as a precursor to manganese azide, alkyl, and amide species: [PhBPiPr3]Mn(N3), [PhBPiPr3]Mn(CH2Ph), [PhBPiPr3]Mn(Me), [PhBPiPr3]Mn(NH(2,6-iPr2Ph)), [PhBPiPr3]Mn(dbabh), and [PhBPiPr3]Mn(1-Ph(isoindolate)). Collectively, they represent an uncommon motif of low-coordinate polyphosphine-supported manganese species. Some of our synthetic efforts to generate [PhBPiPr3]Mn?Nx species are described, as are theoretical DFT studies that probe the electronic viability of these multiply bonded target structures.
\r\n\r\nTwo tris(phosphino)borate ligands, [PhBPter3] and [PhBPCH2Cy3] are introduced that feature terphenyl and methylcyclohexyl groups on the phosphine arms, respectively. The iron chlorides, [PhBPter3]FeCl and [PhBPCH2Cy3]FeCl, have been prepared as precursors to iron nitrides. Addition of the nitride transfer reagent Li(dbabh) to [PhBPCH2Cy3]FeCl produced the terminal nitride, [PhBPCH2Cy3]Fe(N). The 15N NMR spectrum of the labeled species, [PhBPCH2Cy3]Fe(15N), contains a peak at 929 ppm, consistent with a terminal nitride functionality. Mossbauer spectroscopy of the nitride shows a low isomer shift value of 0.34(1) mm/s and an exceptionally large quadrupole splitting of 6.01(1) mm/s.
\r\n\r\nReduction of [PhBPCH2Cy3]FeCl generates a masked iron(I) species that is highly reactive. Combustion analysis of this species is consistent with \"[PhBPCH2Cy3]Fe.\" Other physical methods including VT NMR, EPR, and IR spectroscopies suggest the presence of a paramagnetic species in equilibrium with a diamagnetic species. The paramagnetic component is postulated to be an Fe(III) hydride, wherein a ligand C-H bond has been cyclometalated at the metal center. The reactivity of \"[PhBPCH2Cy3]Fe\" is consistent with iron(I). For example, its reaction with PMe3 and 1-adamantylazide affords the phosphine adduct, [PhBPCH2Cy3]Fe(PMe3), and the iron imide, [PhBPCH2Cy3]Fe(NAd), respectively. Interestingly, \"[PhBPCH2Cy3]Fe\" undergoes redox reactions with benzene to give initially a benzene adduct, {[PhBPCH2Cy3]Fe}2(mu-eta3:eta3-C6H6), which decomposes to {[PhBPCH2Cy3]Fe}2(mu-eta5:eta5-6,6'-bicyclohexadienyl) via radical C-C bond coupling. Finally, \"[PhBPCH2Cy3]Fe\" readily reduces CO2 at rt to give as the major product {[PhBPCH2Cy3]Fe}2(mu-CO)(mu-O), wherein a C=O bond has been cleaved. The minor product has not been definitively established, but one possibility is the oxalate-bridged dimer {[PhBPCH2Cy3]Fe}2(mu-eta2:eta2-O2CCO2) that results from reductive coupling of two CO2 molecules.
\r\n", "doi": "10.7907/0DND-1J03", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2333", "collection": "thesis", "collection_id": "2333", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05312006-163455", "primary_object_url": { "basename": "Julie_Biteen_PhD_Thesis_2006.PDF", "content": "final", "filesize": 42282605, "license": "other", "mime_type": "application/pdf", "url": "/2333/1/Julie_Biteen_PhD_Thesis_2006.PDF", "version": "v2.0.0" }, "type": "thesis", "title": "Plasmon-Enhanced Silicon Nanocrystal Luminescence for Optoelectronic Applications", "author": [ { "family_name": "Biteen", "given_name": "Julie Suzanne", "orcid": "0000-0003-2038-6484", "clpid": "Biteen-Julie-Suzanne" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "On the path toward the realization of silicon-based optical emitters for integrated microelectronics, this thesis studies the optoelectronic properties of silicon nanocrystals as a function of their surface passivation and their interactions with plasmonic materials. The first part of the thesis utilizes controlled oxidation exposures and photoluminescence spectroscopy to verify previous theoretical and computational predictions of oxygen-related surface states that effectively narrow the energy band gap of small silicon nanocrystals. The focus of the second half of the thesis is on experimental and computational studies of enhanced luminescence from silicon nanocrystals in the near field of noble metal nanostructures.
\r\n\r\nSurface plasmon enhancement is a technique that has only recently been applied to semiconductor nanocrystal luminescence. This thesis thoroughly investigates the emission of silicon nanocrystals coupled to gold and silver nanostructures to achieve a new level of understanding of the enhancement effect. By pairing silicon nanocrystals to metal nanostructures, up to ten-fold increases in the luminescence intensity are realized, concomitant with enhancements of the radiative decay rate, the absorbance cross section, and the quantum efficiency. Moreover, coupling at the plasmon resonance frequency is used to tune the nanocrystal emission spectrum. A computational exploration of these experimental observations indicates that the enhancement effects can be ascribed to emission in the concentrated local field that results from the excitation of metal particle plasmon modes. Finally, the process of coupling silicon nanocrystal emitters to plasmonic metals is applied to a silicon-nanocrystal light-emitting diode, and enhanced electroluminescence is realized.
", "doi": "10.7907/B77G-WS08", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:1756", "collection": "thesis", "collection_id": "1756", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05122006-102528", "primary_object_url": { "basename": "Santiago_Solares_PhD_Dissertation_2006.pdf", "content": "final", "filesize": 10261219, "license": "other", "mime_type": "application/pdf", "url": "/1756/1/Santiago_Solares_PhD_Dissertation_2006.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Multi-Scale Simulations of Single-Walled Carbon Nanotube Atomic Force Microscopy and Density Functional Theory Characterization of Functionalized and Non-Functionalized Silicon Surfaces", "author": [ { "family_name": "Solares", "given_name": "Santiago de Jesus", "orcid": "0000-0003-0895-8160", "clpid": "Solares-Santiago-de-Jesus" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Collier", "given_name": "C. Patrick", "clpid": "Collier-C-P" }, { "family_name": "Giapis", "given_name": "Konstantinos P.", "clpid": "Giapis-K-P" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation focuses on two theoretical research topics: Multiscale Simulations of Single-Walled Carbon Nanotube Atomic Force Microscopy (AFM, chapters 1 through 3) and Density Functional Theory Characterization of Functionalized and non-functionalized Silicon Surfaces (chapters 4 through 8). The first topic presents the development of an AFM simulation methodology, based on first principles, which incorporates the atomistic details of probe, sample, and impurities in the construction of the images. It also includes studies of the influence of common artifacts (such as elastic deformations and imaging multistability) and probe structure (tilt angle and number of walls in the carbon nanotube probe) on image quality. The second topic concerns the structure and energetics of reconstructed and unreconstructed silicon (111) surfaces (either functionalized with groups such as methoxy and methyl or without functionalization) and non-functionalized copper-silicon surfaces and crystals. These studies lead to novel findings such as the formation of a full stacking fault on the methylated Si(111) surface in the presence of large etch pits and the quantification of the surface energy path of the Si(111) 1x1 \u2192 DAS 7x7 reconstruction. Most of this work was done in collaboration with experimental groups and is in agreement with the most current experimental results.", "doi": "10.7907/XZR1-C472", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2113", "collection": "thesis", "collection_id": "2113", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262006-160244", "primary_object_url": { "basename": "ODelaire_Thesis.pdf", "content": "final", "filesize": 6881032, "license": "other", "mime_type": "application/pdf", "url": "/2113/1/ODelaire_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The Phonon Entropy of Transition Metals and Alloys: Effects of Impurities and of a Martensitic Phase Transition", "author": [ { "family_name": "Delaire", "given_name": "Olivier", "orcid": "0000-0003-1230-2834", "clpid": "Delaire-Olivier" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Halevy", "given_name": "Itzhak", "clpid": "Halevy-I" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "For a fixed configuration of ions on a given crystalline lattice, low energy excitations around the static average configuration can be thermally activated and will contribute to the entropy of the system. As such, phonons, spin-waves or electronic excitations have their own entropic contribution. This thesis investigates the entropic effects of lattice vibrations in transition metal alloys, both from experimental and computational points of view.
\r\n\r\nUsing inelastic neutron scattering, it is shown that a few percent of substitutional impurities from the transition metal series strongly affect the phonon density of states (DOS) of pure vanadium. Alloying with 6% Pt solutes produces a strong stiffening of the phonon DOS, inducing a large and negative vibrational entropy of mixing, which overcomes the increase in configurational entropy. A systematic study of chemical trends for different transition metal impurities was conducted. A previously unknown correlation is established between the vibrational entropy of alloying and the difference in electronegativity of the solute and the host. Density-functional theory calculations were conducted and confirmed the occurrence of systematic charge-transfers correlating with the electronegativity, which affect the interatomic force-constants and the phonons.
\r\n\r\nThe effect of impurities on the anomalous temperature-dependence of phonons in vanadium is investigated. It is found that the solutes which affect the phonon density of states most strongly at room temperature also suppress the anomalous temperature behavior. Electron-phonon and phonon-phonon couplings are examined as potential sources of this effect, through a careful accounting of their contributions to the heat capacity, based on inelastic neutron scattering experiments, calorimetry measurements and electronic structure calculations.
\r\n\r\nFinally, the changes in the phonon DOS and the vibrational entropy across the low-temperature martensitic phase transformation in Fe71Ni29 are investigated. The respective contributions of the phonons and magnetism to the entropy of the direct and reverse transformation are evaluated from neutron scattering and differential scanning calorimetry measurements. A significant magnetic entropy is found in the reverse transformation, which is not present in the direct transformation. This result stresses the necessity to account for the respective contributions of all microscopic degrees of freedom in evaluating entropy changes in solid-solid phase transitions.
", "doi": "10.7907/SDJF-E025", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:4746", "collection": "thesis", "collection_id": "4746", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12032005-115154", "primary_object_url": { "basename": "Thesis-Derek_Thurman.pdf", "content": "final", "filesize": 8030245, "license": "other", "mime_type": "application/pdf", "url": "/4746/1/Thesis-Derek_Thurman.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Molecular Aspects of Flow-Induced Crystallization of Polypropylene", "author": [ { "family_name": "Thurman", "given_name": "Derek Wade", "clpid": "Thurman-Derek-Wade" } ], "thesis_advisor": [ { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Polyolefins, semicrystalline polymers also known as thermoplastics, are highly desirable because of their material properties, low cost, and ease in processing. The flow and thermal history experienced during processing are known to affect dramatic changes in crystalline kinetics and morphology, dictating the final material properties of solidified products. However, the underlying physics that control crystalline orientation and kinetics is not well understood. To optimize processing conditions and maximize material performance, it is desirable to understand how the interplay of molecular character and flow conditions shape crystalline microstructure.
\r\n\r\nIn the last decade, advances in catalyst technology have produced well defined materials enabling the systematic study of molecular influences on flow-induced crystallization. We investigate bimodal blends of polypropylenes (PP) in which we vary the molecular character (concentration, molecular weight, regularity) of the high molecular weight mode. We apply a number of in situ characterization tools (rheo-optics, rheo-WAXD) to the development of transient structure and interpret our findings in light of ex situ examination (polarized light microscopy, TEM) of the final morphology.
\r\n\r\nBlending a well-characterized high molecular weight isotactic polypropylene into a \"base iPP\" at various concentrations (c), we determined that blends with less than 1% of chains with Mw five times larger than the Mw of the base resin profoundly affected the crystallization kinetics and crystalline morphology of a sheared melt. Beyond unambiguously demonstrating the important role of long chains in the formation of anisotropic crystallization under flow, this approach allowed us to be specific about the length that is meant by \"long chains\" and the concentration of these chains in the melt. Varying the concentration from below to above c* revealed that the effect of the long chains involves cooperative interactions, evident in the non-linear relationship of the long chain concentration, particularly as c approaches the long chain-long chain overlap concentration. The long chains greatly enhance the formation of threadlike precursors but only mildly enhance the formation of pointlike precursors.
\r\n\r\nIn studying a series of blends in which the Mw of the long chain mode was varied, we found that increasing the Mw of the long chain portion of a bimodal blend increased the tendency to form threadlike precursors to oriented crystallization. This was highlighted by a marked decrease in the threshold stress necessary to induce oriented crystalline growth and is related to the separation in time scales between the slowest relaxing chains and the average. Thus, the propagation of shish varies strongly with the separation in time scales between the slowest relaxing chains and the average. Below a threshold ratio of relaxation times (tau_L/tau_S ~ 100) addition of long chains did not change the behavior from that of Base-PP itself.
\r\n\r\nOur analysis of real-time rheo-optical and rheo-WAXD experiments combined with depth dependent information from a novel \"depth sectioning\" analysis technique uncovers several keys to understanding how anisotropic crystallization is induced by flow. Threads first form near the channel wall, where stress is highest, and grow in length with prolonged flow. After sufficient time, thread length per unit volume saturates, perhaps due to collisions with other threads or crystalline overgrowth from those threads. Prior to saturation, when crystalline overgrowth is negligible, the thread propagation appears to be linear with shearing time. The propagation of threads varies in a nonlinear manner with stress. Finally, we identify a promising set of conditions that can be used to measure the thread propagation velocity for this material if the appropriate length scale can be assigned by microscopy.
\r\n\r\nWe examined the effects of long chain regularity on the formation of threadlike precursors, showing that addition of molecular level defects to the high end of the molecular weight distribution effectively raises the threshold stress and mitigates the formation of oriented precursors induced by flow. Our study included a model bimodal blend of isotactic and atactic polypropylene as well as large scale bimodal blends of isotactic polypropylene and a propylene-ethylene copolymer fit for pilot-scale production of nonwoven fabrics. It is noteworthy that the qualitative behavior observed in the melt-spinning process accords well with the trends evident in isothermal shear-induced crystallization. This has value in two respects. Scientifically, it is significant that idealized flow and thermal conditions may well reveal the physics relevant to polymer processing, which involves mixed shear and extension under non-isothermal conditions. Technologically, the ability to screen different resin compositions on a small scale can be used to optimize flow-induced crystallization characteristics prior to scale up.
", "doi": "10.7907/wew1-af68", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:2327", "collection": "thesis", "collection_id": "2327", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05312005-114949", "primary_object_url": { "basename": "FinalThesisJoyce.pdf", "content": "final", "filesize": 22064932, "license": "other", "mime_type": "application/pdf", "url": "/2327/1/FinalThesisJoyce.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structure and Function Prediction of Human Muscarinic Acetylcholine Receptor 1, Cation-\u03c0 Studies, and Protein Design", "author": [ { "family_name": "Peng", "given_name": "Joyce Yaochun", "clpid": "Peng-Joyce-Yaochun" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Vaidehi", "given_name": "Nagarajan", "orcid": "0000-0001-8100-8132", "clpid": "Vaidehi-N" } ], "thesis_committee": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Bronner", "given_name": "Marianne E.", "orcid": "0000-0003-4274-1862", "clpid": "Bronner-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "(1) Muscarinic acetylcholine receptors, a G protein-coupled receptor, are responsible for a wide range of diseases. We predicted the 3D structure of the human M1 muscarinic receptor using the MembStruk method and validated its binding sites for 10 agonists and antagonists using the HierDock method. The predicted binding sites, the intramolecular contacts that stabilize the receptor conformation, and the in silico mutagenesis results, agree well with mutagenesis data. The calculated relative binding energies correlate well with measured binding affinities. In addition, the predicted binding sites provide a structural basis for the large reduction in ligand binding affinity and signaling efficacy by Trp 157 and Pro 159 mutations, which was not previously explained by homology models. The predicted binding sites illustrate the importance of aromatic residues in ligand binding through extensive cation-pi and aromatic-aromatic interactions, with new mutation candidates suggested. The predicted M1 structure improves our understanding of the muscarinic receptors, offers a basis for structure based drug design, and is a successful step toward applying these procedures in predicting the structures of other muscarinic receptor subtypes.
\r\n\r\n(2) We used high-level quantum mechanics to quantify cation-pi interactions in the crystal structure of carbamylcholine binding to Acetylcholine-binding Protein, a nicotinic receptor homolog. The calculated effects of fluorinated unnatural amino acid substitutions also correlate excellently with experimental EC50 data, suggesting that quantum mechanics can accurately predict cation-pi binding in a protein environment and provides a good model system in developing force fields to better describe cation-pi interactions.
\r\n\r\n(3) Histidines are known to modulate pH responsive binding. We designed a series of histidine derivatives by substituting its imidazole ring with functional groups that are small in size and lack the ability to form hydrogen bonds. Quantum mechanical calculations of the acid dissociation constants (pKa) show that these substitutions shift the histidine pKa upward or downward. We report a list of histidine derivatives and their corresponding pKa values that can be used in designing tumor specific drugs (e.g. HER2-Herceptin antibody), drug delivery through pH sensitive hydrogels, drug recycling, catalysis, and biosensors development. An example of how these unnatural histidines can be used is illustrated with 2-methyl histidine incorporated in a c-Myc-Max heterodimer.
", "doi": "10.7907/XVJR-RN32", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:1998", "collection": "thesis", "collection_id": "1998", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-133116", "primary_object_url": { "basename": "dirks05.pdf", "content": "final", "filesize": 20545101, "license": "other", "mime_type": "application/pdf", "url": "/1998/1/dirks05.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Analysis, Design, and Construction of Nucleic Acid Devices", "author": [ { "family_name": "Dirks", "given_name": "Robert Michael", "clpid": "Dirks-Robert- Michael" } ], "thesis_advisor": [ { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Nucleic acids present great promise as building blocks for nanoscale devices. To achieve this potential, methods for the analysis and design of DNA and RNA need to be improved. In this thesis, traditional algorithms for analyzing nucleic acids at equilibrium are extended to handle a class of pseudoknots, with examples provided relevant to biologists and bioengineers. With these analytical tools in hand, nucleic acid sequences are designed to maximize the equilibrium probability of a desired fold. Upon analysis, it is concluded that both affinity and specificity are important when choosing a sequence; this conclusion holds for a wide range of target structures and is robust to random perturbations to the energy model. Applying the intuition gained from these studies, a process called hybridization chain reaction (HCR) is invented, and sequences are chosen that experimentally verify this phenomenon. In HCR, a small number of DNA or RNA molecules trigger a system wide configurational change, allowing the amplification and detection of specific, nucleic acid sequences. As an extension, HCR is combined with a pre-existing aptamer domain to successfully construct an ATP sensor, and the groundwork is laid for the future development of sensors for other small molecules. In addition, recent studies on multi-stranded algorithms and improvements to HCR are included in the appendices. Not only will these advancements increase our understanding of biological RNAs, but they will also provide valuable tools for the future development of nucleic acid nanotechnologies.", "doi": "10.7907/VZ43-FM66", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:1999", "collection": "thesis", "collection_id": "1999", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-143543", "primary_object_url": { "basename": "SS_Preface.pdf", "content": "final", "filesize": 140358, "license": "other", "mime_type": "application/pdf", "url": "/1999/7/SS_Preface.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Prediction of Structure and Antagonist Binding Site in Human and Rodent Chemokine Receptor 1", "author": [ { "family_name": "Sharma", "given_name": "Shantanu", "clpid": "Sharma-Shantanu" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chemoattractant cytokines (chemokines) are small proteins that are known to play a key role in the development of numerous autoimmune and inflammatory diseases. The signal transduction cascade responsible for this pathology is initiated by chemokine binding to a G-protein coupled receptor (GPCR). Since therapeutic intervention would involve inhibition of ligand binding, it follows that detailed understanding of the structures and binding sites of these receptors would lead to the rational design of such drugs. However, GPCRs are a class of integral membrane proteins whose structures are extremely difficult to determine via the conventional method of X-ray crystallography. Additionally, homology models based on the crystal structure of bovine rhodopsin (BR) have offered little structural insight into the remotely homologous chemokine receptors. In light of this information, our laboratory has developed a novel computational approach to predicting the structures and ligand binding sites of GPCRs with no information from the atomic coordinates of the crystal structure of BR.
\r\n\r\nIn this thesis we describe the use of the MembStruk procedure to predict the structure of human, mouse, and rat chemokine receptor 1 (CCR1). Interhelical interactions that stabilize the conformation of each receptor are discussed in detail, and where appropriate comparisons are made to information gleaned from the crystal structure of BR. The side chain placements of conserved residues are found to be different across the human and rodent species, accounting for binding differentials not previously explained by homology models. To improve the binding of a low affinity small molecule antagonist, point mutation candidates in human CCR1 are predicted.
\r\n\r\nValidation of the human CCR1 structure is achieved through prediction of the antagonist binding site, to which a series of known antagonists are docked and scored for comparison to experimental structure-activity data. The ligand binding energies are in excellent agreement with the experimentally known trend in binding affinities, and results from a virtual ligand screening calculation (Dr. Sabine Schlyer, Berlex/Schering AG) also support the validity of the structural model. This work in this thesis provides the basis for the design of receptor-specific antagonists to human and rodent CCR1, thus accelerating the drug discovery process.
", "doi": "10.7907/j4zd-ny21", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2005", "collection": "thesis", "collection_id": "2005", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-172213", "primary_object_url": { "basename": "00_Introduction.pdf", "content": "final", "filesize": 126053, "license": "other", "mime_type": "application/pdf", "url": "/2005/1/00_Introduction.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Investigations of Ion Channel Structure and Function. I. Studies of Nicotine Binding to the Acetylcholine Receptor. II. Development of Tools for Studying Learning and Memory with Unnatural Amino Acids", "author": [ { "family_name": "Petersson", "given_name": "Ernest James", "orcid": "0000-0003-3854-9210", "clpid": "Petersson-Ernest-James" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Lester", "given_name": "Henry A.", "clpid": "Lester-H-A" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation can be divided into two main sections:
\r\n\r\nI. In previous studies, we have used fluorinated tryptophan derivatives to conclusively identify a cation-pi interaction with Trp 149 in the binding of acetylcholine (ACh) to the muscle-type nicotinic acetylcholine receptor (nAChR). We have incorporated mimics of ACh, termed tethered agonists, in the binding site to produce self-activating channels. Using tertiary tethered agonists that would only become cations and activate the channel when protonated, we identified a perturbed pKa for the binding pocket, which has implications for the binding of tertiary agonists like nicotine (Nic). It has been shown that Nic does not participate in a straight-forward cation-pi interaction as ACh does. We have examined a hydrogen bond between the Nic pyrrolidine N-H and the backbone carbonyl of Trp149 by introducing an ester linkage at this point, weakening the carbonyl H-bond accepting ability. Calculations performed on hydrogen bound complexes of ACh, Nic, and the Nic analog epibatidine (Epi) explain the trends observed for ligand activation of the nAChR. Expanding upon this study, we have performed molecular dynamics (MD) simulations of models of the ligand binding domain of the nAChR. Ligand-bound structures from these simulations have been taken on to quantum mechanical/molecular mechanical (QMMM) calculations to model the effects of unnatural amino acid mutations in an environment that simulates the full nAChR binding pocket.
\r\n\r\nII. The nAChR is essential to neurotransmission at the junction between nerve and muscle cells, and it plays an important role in many central nervous system processes. However, its role in learning and memory is limited, at least in our current molecular models of these events. In a sense, the formation of a memory consists of the strengthening of some synaptic connections and the weakening of others. These processes, termed long term potentiation (LTP) and depression (LTD) respectively, are primarily governed by modifications to glutamate receptors (GluRs). We have developed tools for studying the mechanism and timecourse of these modifications (of phosphorylation in particular), and we have demonstrated the first incorporation of unnatural amino acids into a GluR.
", "doi": "10.7907/yhty-re87", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2158", "collection": "thesis", "collection_id": "2158", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-160315", "primary_object_url": { "basename": "01_preliminary_pages.pdf", "content": "final", "filesize": 129155, "license": "other", "mime_type": "application/pdf", "url": "/2158/1/01_preliminary_pages.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Development of Novel Binary and Multi-Component Bulk Metallic Glasses", "author": [ { "family_name": "Xu", "given_name": "Donghua", "orcid": "0000-0001-5018-5603", "clpid": "Xu-Donghua" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "orcid": "0000-0003-2908-5469", "clpid": "Bhattacharya-K" }, { "family_name": "Conner", "given_name": "Robert Dale", "clpid": "Conner-R-D" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "orcid": "0000-0002-2912-0001", "clpid": "Ravichandran-G" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Bulk Metallic Glasses (BMGs) have been drawing increasing attention in recent years due to their scientific and engineering significance. A great deal of effort in this area has been devoted to developing BMGs in different alloy systems. BMGs based on certain late transition metals (e.g. Fe, Co, Ni, Cu) have many potential advantages over those based on early transition metals. These include even higher strength and elastic modulii, and lower materials cost, to name a few, which are highly preferable for a broad application of BMGs as engineering materials. Nevertheless, these ordinary-late-transition-metal-based BMGs generally have quite limited glass-forming ability (GFA). In particular, for the Ni-based and Cu-based alloys reported prior to this research, the maximum casting thickness allowed to retain their amorphous structures is only ~2 mm (or lower) and ~5 mm (or lower), respectively.
\r\n\r\nDuring this research it was first found that certain quinary Ni-based alloys in the Ni-Cu-Ti-Zr-Al system can be cast into 5 mm diameter amorphous rods. This critical casting thickness is the highest for any reported Ni-based BMG\u2019s indicating that these alloys are the easiest metallic glass formers based on Ni discovered to date. Secondly, certain binary alloys in the Cu-Zr and Cu-Hf systems were found to form bulk glasses with casting thickness as high as 2 mm. The discovery of these binary BMGs was very surprising since it had been widely considered that only multi-component (containing at least three elements) alloys could form bulk metallic glasses. These new binary BMGs provide interesting subjects for future theoretical studies such as molecular dynamics simulations since they possess both the simplicity of binary alloys and the good GFA of multi-component BMGs. In fact, these binary BMGs have led to the third but perhaps the most significant progress during this research, i.e., the discovery of a family of Cu-based BMGs in the Cu-Zr-Al-Y system which possess a critical casting thickness up to 1 cm. These quaternary Cu-based alloys, together with some complicated Fe-based alloys reported by two other groups during the course of this research, are the first centimeter level BMGs based on the ordinary late transition metals.
\r\n\r\nThis thesis first reviews the fundamentals related to BMG development, then reports in detail the formation and properties of the above-mentioned binary and multi-component BMGs based on Ni and Cu. A generalized geometric model for the critical-value problem of nucleation developed in this research is also presented.
", "doi": "10.7907/XD2M-WW51", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2158", "collection": "thesis", "collection_id": "2158", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-160315", "primary_object_url": { "basename": "01_preliminary_pages.pdf", "content": "final", "filesize": 129155, "license": "other", "mime_type": "application/pdf", "url": "/2158/1/01_preliminary_pages.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Development of Novel Binary and Multi-Component Bulk Metallic Glasses", "author": [ { "family_name": "Xu", "given_name": "Donghua", "orcid": "0000-0001-5018-5603", "clpid": "Xu-Donghua" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "orcid": "0000-0003-2908-5469", "clpid": "Bhattacharya-K" }, { "family_name": "Conner", "given_name": "Robert Dale", "clpid": "Conner-R-D" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "orcid": "0000-0002-2912-0001", "clpid": "Ravichandran-G" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Bulk Metallic Glasses (BMGs) have been drawing increasing attention in recent years due to their scientific and engineering significance. A great deal of effort in this area has been devoted to developing BMGs in different alloy systems. BMGs based on certain late transition metals (e.g. Fe, Co, Ni, Cu) have many potential advantages over those based on early transition metals. These include even higher strength and elastic modulii, and lower materials cost, to name a few, which are highly preferable for a broad application of BMGs as engineering materials. Nevertheless, these ordinary-late-transition-metal-based BMGs generally have quite limited glass-forming ability (GFA). In particular, for the Ni-based and Cu-based alloys reported prior to this research, the maximum casting thickness allowed to retain their amorphous structures is only ~2 mm (or lower) and ~5 mm (or lower), respectively.
\r\n\r\nDuring this research it was first found that certain quinary Ni-based alloys in the Ni-Cu-Ti-Zr-Al system can be cast into 5 mm diameter amorphous rods. This critical casting thickness is the highest for any reported Ni-based BMG\u2019s indicating that these alloys are the easiest metallic glass formers based on Ni discovered to date. Secondly, certain binary alloys in the Cu-Zr and Cu-Hf systems were found to form bulk glasses with casting thickness as high as 2 mm. The discovery of these binary BMGs was very surprising since it had been widely considered that only multi-component (containing at least three elements) alloys could form bulk metallic glasses. These new binary BMGs provide interesting subjects for future theoretical studies such as molecular dynamics simulations since they possess both the simplicity of binary alloys and the good GFA of multi-component BMGs. In fact, these binary BMGs have led to the third but perhaps the most significant progress during this research, i.e., the discovery of a family of Cu-based BMGs in the Cu-Zr-Al-Y system which possess a critical casting thickness up to 1 cm. These quaternary Cu-based alloys, together with some complicated Fe-based alloys reported by two other groups during the course of this research, are the first centimeter level BMGs based on the ordinary late transition metals.
\r\n\r\nThis thesis first reviews the fundamentals related to BMG development, then reports in detail the formation and properties of the above-mentioned binary and multi-component BMGs based on Ni and Cu. A generalized geometric model for the critical-value problem of nucleation developed in this research is also presented.
", "doi": "10.7907/XD2M-WW51", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2457", "collection": "thesis", "collection_id": "2457", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06052005-221223", "primary_object_url": { "basename": "00Chapters123.pdf", "content": "final", "filesize": 8257006, "license": "other", "mime_type": "application/pdf", "url": "/2457/1/00Chapters123.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computational Strategy in Catalyst Design", "author": [ { "family_name": "Nielsen", "given_name": "Robert J.", "orcid": "0000-0002-7962-0186", "clpid": "Nielsen-Robert-J" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Peters", "given_name": "Jonas C.", "clpid": "Peters-J-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The strategy and efficacy of applying computational tools to the development of new catalytic cycles is discussed using the enantioselective palladium-catalyzed aerobic oxidation of secondary alcohols as a model case. The key interactions responsible for the unique reactivity of ((\u2013)-sparteine)PdX2 complexes (X = chloride, acetate) in kinetic resolutions of secondary alcohols are elucidated using density functional theory with the Poisson-Boltzmann polarizable continuum solvent model. Enantioselectivities in these reactions are found to follow directly from calculated energies of diastereomeric beta-hydride elimination transition states incorporating (R) and (S) substrates. This relationship reveals an important role of the anion, namely to communicate the steric interaction of the ligand on one side of the PdII square plane and the substrate on the other side. When no anion is included, no enantioselectivity is predicted. Locating these transition states in different solvents shows that higher dielectrics stabilize the charge separation between the anion and metal and draw the anion farther into solution. Thus the solvent influences the barrier height (rate) and selectivity of the oxidation.
\r\n\r\nBased on this understanding, computational assays for selectivity, reaction rate and stability are developed and used to screen possible mimics of the natural product (\u2013)-sparteine which could be synthesized in both antipodes. Derivatives of the bispidine and bispidinone structures are predicted to have high selectivity but poor stability on palladium. Experimental results verify that catalytically active (bispidine)PdX2 complexes do not form.
\r\n\r\nMechanisms by which palladium diacetate complexes of N-heterocyclic carbenes may oxidize alcohols (a reaction known to occur with no enantioselectivity) are examined computationally. The strong trans effect of the carbene distinguishes the behavior of these complexes from other palladium catalysts. No traditional beta-hydride elimination is predicted to be capable of generating the high deuterium kinetic isotope effect measured using this catalyst. Instead, the low-energy pathway consistent with previous experimental observations (KIE, activation parameters, kinetics) is a \"reductive\" beta-hydride elimination, in which the beta-hydrogen of the alcohol is transferred directly to a bound acetate ligand. Assuming that relative energies of transition states of this type will determine enantioselectivity, new, chiral carbene ligands are hypothesized and screened. Careful placement of stereocenters and steric bulk has led to ligands with high predicted enantioselectivity and stability.
\r\n\r\nRecurring factors in the induction of selectivity by asymmetric ligands are observed. Strengths and weaknesses of quantum chemistry as applied to catalytic cycles are discussed, along with the synergy of theory and experiment. Common pitfalls and areas in need of improvement are highlighted.
", "doi": "10.7907/60VH-AQ40", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2301", "collection": "thesis", "collection_id": "2301", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05302005-112828", "primary_object_url": { "basename": "TOC.pdf", "content": "final", "filesize": 36456, "license": "other", "mime_type": "application/pdf", "url": "/2301/5/TOC.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical Study of the Mechanism of Olefin Metathesis and Synthesis of Cyclic Polymers", "author": [ { "family_name": "Benitez", "given_name": "Diego", "orcid": "0000-0003-1212-6957", "clpid": "Benitez-Diego" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Peters", "given_name": "Jonas C.", "clpid": "Peters-J-C" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The research presented in this thesis focuses on the study of the metathesis reaction and applications to synthetic polymeric structures. More specifically, how targeted changes in the polymerization reactants and catalyst provide very unique and useful macromolecular architectures.
\r\n\r\nChapter 1 describes the synthesis of acetoxy end-functionalized polynorbornenes. By introducing 1,4-bis(acetoxy)-2-butene as chain transfer agent (CTA) during a Ruthenium mediated ring opening metathesis polymerization (ROMP) of norbornene (NBE), the respective end-functionalized polymers with molecular weights controllable up to 30 kDa could be obtained in high yield.
\r\n\r\nChapter 2 describes a new synthetic route to cyclic polymers and their characterization. In this approach, the ends of growing polymer chains remain attached to a cyclic Ru catalyst throughout the entire polymerization process. This effectively excludes all types of linear intermediates, which were a major drawback of previous approaches to cyclic polymers.
\r\n\r\nChapter 3 describes the synthesis of cyclic poly-butadiene and the importance of the monomer purity. Techniques for characterizing and determining the purity of cyclic polymers are also discussed.
\r\n\r\nChapter 4 describes a quantum mechanical (QM) study of the mechanism of chloride isomerization of a ruthenium metathesis catalyst with density functional theory (DFT) with the B3LYP hybrid functional. This isomerization is relevant to the mechanism of metathesis and it serves as validation to further studies of the mechanism with the same method.
", "doi": "10.7907/eas9-x408", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2327", "collection": "thesis", "collection_id": "2327", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05312005-114949", "primary_object_url": { "basename": "FinalThesisJoyce.pdf", "content": "final", "filesize": 22064932, "license": "other", "mime_type": "application/pdf", "url": "/2327/1/FinalThesisJoyce.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structure and Function Prediction of Human Muscarinic Acetylcholine Receptor 1, Cation-\u03c0 Studies, and Protein Design", "author": [ { "family_name": "Peng", "given_name": "Joyce Yaochun", "clpid": "Peng-Joyce-Yaochun" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Vaidehi", "given_name": "Nagarajan", "orcid": "0000-0001-8100-8132", "clpid": "Vaidehi-N" } ], "thesis_committee": [ { "family_name": "Kennedy", "given_name": "Mary B.", "orcid": "0000-0003-1369-0525", "clpid": "Kennedy-M-B" }, { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Bronner", "given_name": "Marianne E.", "orcid": "0000-0003-4274-1862", "clpid": "Bronner-M-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "(1) Muscarinic acetylcholine receptors, a G protein-coupled receptor, are responsible for a wide range of diseases. We predicted the 3D structure of the human M1 muscarinic receptor using the MembStruk method and validated its binding sites for 10 agonists and antagonists using the HierDock method. The predicted binding sites, the intramolecular contacts that stabilize the receptor conformation, and the in silico mutagenesis results, agree well with mutagenesis data. The calculated relative binding energies correlate well with measured binding affinities. In addition, the predicted binding sites provide a structural basis for the large reduction in ligand binding affinity and signaling efficacy by Trp 157 and Pro 159 mutations, which was not previously explained by homology models. The predicted binding sites illustrate the importance of aromatic residues in ligand binding through extensive cation-pi and aromatic-aromatic interactions, with new mutation candidates suggested. The predicted M1 structure improves our understanding of the muscarinic receptors, offers a basis for structure based drug design, and is a successful step toward applying these procedures in predicting the structures of other muscarinic receptor subtypes.
\r\n\r\n(2) We used high-level quantum mechanics to quantify cation-pi interactions in the crystal structure of carbamylcholine binding to Acetylcholine-binding Protein, a nicotinic receptor homolog. The calculated effects of fluorinated unnatural amino acid substitutions also correlate excellently with experimental EC50 data, suggesting that quantum mechanics can accurately predict cation-pi binding in a protein environment and provides a good model system in developing force fields to better describe cation-pi interactions.
\r\n\r\n(3) Histidines are known to modulate pH responsive binding. We designed a series of histidine derivatives by substituting its imidazole ring with functional groups that are small in size and lack the ability to form hydrogen bonds. Quantum mechanical calculations of the acid dissociation constants (pKa) show that these substitutions shift the histidine pKa upward or downward. We report a list of histidine derivatives and their corresponding pKa values that can be used in designing tumor specific drugs (e.g. HER2-Herceptin antibody), drug delivery through pH sensitive hydrogels, drug recycling, catalysis, and biosensors development. An example of how these unnatural histidines can be used is illustrated with 2-methyl histidine incorporated in a c-Myc-Max heterodimer.
", "doi": "10.7907/XVJR-RN32", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2361", "collection": "thesis", "collection_id": "2361", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06012005-235052", "primary_object_url": { "basename": "Thesis-TOC.pdf", "content": "final", "filesize": 57256, "license": "other", "mime_type": "application/pdf", "url": "/2361/10/Thesis-TOC.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Development of a Structure Prediction Method for G-Protein Coupled Receptors", "author": [ { "family_name": "Hall", "given_name": "Spencer Eugene", "clpid": "Hall-Spencer-Eugene" } ], "thesis_advisor": [ { "family_name": "Vaidehi", "given_name": "Nagarajan", "orcid": "0000-0001-8100-8132", "clpid": "Vaidehi-N" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Campbell", "given_name": "Judith L.", "orcid": "0000-0001-8291-5551", "clpid": "Campbell-J-L" }, { "family_name": "Vaidehi", "given_name": "Nagarajan", "orcid": "0000-0001-8100-8132", "clpid": "Vaidehi-N" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "G-Protein Coupled Receptors (GPCRs) form a major target class of membrane proteins for therapeutic drug design, and the challenge is to design subtype specific drugs. Hence the knowledge of three-dimensional structure is critical to drug design for GPCRs. Since GPCRs are membrane bound proteins, there is only one crystal structure for a GPCR, namely bovine rhodopsin. The prediction of structure and function of G-protein-coupled receptors will allow for designing drugs with minimal side effects.
\r\n\r\nThe focus of my thesis is the development of computational methods for prediction of structure of GPCRs and application of these methods (MembStruk) for a class of important drug targets such as chemokine receptors. MembStruk method is a hierarchical method ranging from coarse grain optimization of the trans-membrane helices to fine grain optimization of the structure in explicit lipid bilayer. The first two chapters of the thesis details the computational steps involved in MembStruk and its application to validating the method for bovine rhodopsin. The first chapter presents the method development in the most current version of the MembStruk method, version 4.30, and its application to bovine rhodopsin. The final predicted structure for bovine rhodopsin deviates from the crystal structure trans-membrane main chain atoms by 2.66 A coordinate root mean square deviation (CRMSD), and the residues in the binding site of 11cis-retinal is only 1.37 A CRMSD from the crystal structure for the main chain atoms. The second chapter of this thesis details the computational methods for optimization of the rotation and translation of the trans-membrane regions. These methods of rotation and translation of transmembrane helices has been further extended to the comparison of structures of two membrane proteins, and applied to the comparison of crystal structures of bovine rhodopsin and bacteriorhodopsin. The third chapter details the graphical user interface that has been developed to automate the various steps of the MembStruk method.
\r\n\r\nOlfactory receptors are GPCRs and the molecular analysis for the recognition of odorants is very important in understanding the mechanism of olfaction. In a blind study prior to experiments, in collaboration with Dr. Bozza of Rockefeller University, I applied the MembStruk method to understanding the binding of odorants to rat and mouse olfactory receptor I7. Chapter 4 describes the application of the MembStruk method to rat and mouse I7 olfactory receptor and the binding of 65 odorants to this receptor. The last chapter describes the use of MembStruk method in predicting the structure and function of important drug targets, namely chemokine receptors CCR5 and CXCR4.
\r\n", "doi": "10.7907/JN28-5F55", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2086", "collection": "thesis", "collection_id": "2086", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262005-004951", "primary_object_url": { "basename": "Staneff_g_2005.pdf", "content": "final", "filesize": 32208062, "license": "other", "mime_type": "application/pdf", "url": "/2086/1/Staneff_g_2005.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "High-Pressure Synthesis of Thermoelectric Materials", "author": [ { "family_name": "Staneff", "given_name": "Geoffrey D.", "clpid": "Staneff-Geoffrey-D" } ], "thesis_advisor": [ { "family_name": "Asimow", "given_name": "Paul David", "orcid": "0000-0001-6025-8925", "clpid": "Asimow-P-D" } ], "thesis_committee": [ { "family_name": "Asimow", "given_name": "Paul David", "orcid": "0000-0001-6025-8925", "clpid": "Asimow-P-D" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "New thermoelectric materials were synthesized using high-pressure techniques. The synthetic limits of cerium filling in cobalt triantimonide were explored and a model for successful synthesis conditions was generated. The high-pressure technique expanded the practical filling limit from x=0.07 to x=0.5 in the CexCo4Sb12 system. Explorations of cerium filled ruthenium-rhodium triantimonide were also undertaken, using our previous work to guide the synthesis attempt. This material was predicted to have outstanding thermoelectric properties, but our investigations did not confirm this result. The filled skutterudite, Ce(Ru0.67Rh0.33)4Sb12, exhibited the low thermal conductivity anticipated, approximately half the total thermal conductivity of a binary CoSb3 skutterudite over a wide range in temperatures. The electrical properties were insufficient to produce a high efficiency thermoelectric, but these results did suggest incorporated rare earth filling atoms do not fully ionize when incorporated into the skutterudite structure. Modification of the carrier type should therefore be investigated by solid solution on the transition metal or pnictide sites and not the filling ion.
\r\n\r\nThe high-pressure synthesis techniques developed for skutterudite synthesis were then employed to sinter nano-scale silicon-germanium compounds. A sintering figure of merit was created to justify the use of high-pressure synthesis, which later proved to be a useful tool for planning subsequent experiments. Sintered silicon, germanium, and silicon-germanium composites were obtained, with the nano-scale grain structure and chemical heterogeneity of the starting powder aggregate intact.
\r\n\r\nFuture work in high-pressure synthesis should be undertaken to quantify the sintering figure of merit presented in this work. The ability to produce a dense multiphase material with a controlled nano-structure should provide a great boon to thermoelectrics research. The high-pressure synthesis technique provides an method to mix two thermoelectric materials without homogenizing them. Both the two-phased solid and the network of nano-scale grains provide powerful tools for minimizing the thermal conductivity of a thermoelectric device component.
", "doi": "10.7907/HWWN-NS80", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:639", "collection": "thesis", "collection_id": "639", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02152005-125249", "primary_object_url": { "basename": "th_shell_sub.pdf", "content": "final", "filesize": 5720663, "license": "other", "mime_type": "application/pdf", "url": "/639/1/th_shell_sub.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computational Optimization of Chemical Vapor Detector Arrays", "author": [ { "family_name": "Sisk", "given_name": "Brian Christopher", "orcid": "0000-0003-3156-9673", "clpid": "Sisk-Brian-Christopher" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "clpid": "Blake-G-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Arrays of broadly responsive, chemically sensitive detectors have been used for many years as a means of detecting a wide array of vapors. These systems have been used in fields ranging from analysis of wines and coffees to land mine and nerve agent detection to disease diagnosis. Despite their successes, these systems have been plagued by problems, namely a lack of sensor diversity, miniscule libraries of previously-recognized analytes, significant sensor drift, and weak signal processing capabilities compared to the mammalian olfactory system.
\r\n\r\nThis work details progress toward the alleviation of those problems with regard to arrays of polymer/carbon-black composite chemiresistor detectors developed at Caltech. Specifically, it has been determined that larger sensor arrays allow the suitable recognition of more analytes, and a greater chance of successful discrimination between a given analyte others to which it is similar. Additionally, new classes of percolative, low carbon-black sensors have been developed that yield far higher sensitivities and stronger responses than traditional sensors, as well as responses that are exponential with concentration. Such sensors allow for recognition of analytes using lower precision electronics than was previously realizable. A method for calibrating the system with few analyte exposures has also been developed from an analysis of the correlations between sensor/analyte response changes with time over groups of analytes and sensors.
\r\n\r\nFurther work has allowed algorithmic optimizations to assign functional group identities and certain physiochemical information such as molar volume and octanol/water partition coefficients to analytes that are completely unknown to the system, using a model built upon other known analytes. Additionally, a comparison of linear and nonlinear classifiers is performed to identify data characteristics that might be more suited to linear classifiers such as Fisher's Linear Discriminant or nonlinear ones such as Artificial Neural Networks.
\r\n\r\nThese improvements to chemical vapor detector arrays and the processing of their data allow the extraction of more useful information and the minimization of time spent training and calibrating the system. By constructing more appropriate sensor arrays, establishing non-comprehensive but extensive analyte response libraries, choosing useful algorithmic classifiers, and performing timely and mimimal calibration, the utility of detector systems can be maximized while minimizing maintenance.
", "doi": "10.7907/Z3K5-C749", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:388", "collection": "thesis", "collection_id": "388", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01282005-111916", "primary_object_url": { "basename": "Thesis_Chapters.pdf", "content": "final", "filesize": 1487780, "license": "other", "mime_type": "application/pdf", "url": "/388/1/Thesis_Chapters.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Study of Crystallization Behavior, Kinetics and Thermodynamics of Bulk Metallic Glasses Using Noncontact Electrostatic Levitation Technique", "author": [ { "family_name": "Mukherjee", "given_name": "Sundeep", "orcid": "0000-0002-1954-0045", "clpid": "Mukherjee-Sundeep" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Rhim", "given_name": "Won-Kyu", "clpid": "Rhim-Won-Kyu" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The exceptional stability against crystallization of recently developed bulk metallic glasses, together with the non-contact measurement techniques to investigate their thermophysical properties, have opened the doors for detailed studies of these systems in the deep undercooled liquid state. The primary objective of this thesis is identification of reliable predictive indicators of glass-forming ability based on the measured thermophysical properties and intrinsic crystallization behavior of bulk metallic glasses. A number of bulk metallic glass-forming alloys having widely different glass-forming abilities are chosen for this investigation. All of the measurements are carried out using the noncontact high vacuum electrostatic levitation technique to avoid any heterogeneous nucleation effects from container walls or environment.
\r\n\r\nThe measured kinetic properties, viscosity, and free volume are found to have the most pronounced influence on glass-forming ability, while the thermodynamics show weak correlation with the trends in glass-formation. The glass-forming melts show orders of magnitude higher viscosity compared to pure metals. Among the glass-forming alloys, better glass formers have higher melting temperature viscosity, higher fragility, and show a smaller change in volume upon crystallization compared to poor glass formers. The melting temperature viscosity is correlated with volume change upon crystallization in accordance with Cohen-Grest free-volume theory for a wide variety of alloys.
\r\n\r\nTo quantify the glass-forming ability, Time-Temperature-Transformation (TTT) curves of a number of glass-forming melts are measured over a wide temperature range between their glass-transition and melting temperatures. A pronounced effect of overheating is observed on the undercooling levels and crystallization time scales. This is attributed to oxide particles acting as heterogeneous nucleation sites unless dissolved by overheating above their melting points. The TTT curves, obtained after eliminating the heterogeneous influences, are found to scale with their respective glass transition temperatures. The TTT curves are analyzed within the framework of nucleation theory to obtain a quantitative correlation between crystal-melt interfacial tension, melt viscosity, and glass forming ability.
\r\n\r\nFinally, the crystallization behavior, microstructure, and melt viscosity of an in situ ductile phase reinforced amorphous matrix composite is investigated as a function of the processing temperature. The results for the in situ composite are compared with those of the monolithic bulk metallic glasses.
", "doi": "10.7907/33FY-8482", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:3107", "collection": "thesis", "collection_id": "3107", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08132004-132724", "primary_object_url": { "basename": "IMR_thesis_final_copy.pdf", "content": "final", "filesize": 2271401, "license": "other", "mime_type": "application/pdf", "url": "/3107/1/IMR_thesis_final_copy.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Functionalized Polymers and Surfaces via Ring-Opening Metathesis Polymerization", "author": [ { "family_name": "Rutenberg", "given_name": "Isaac Michael", "orcid": "0000-0003-0969-4523", "clpid": "Rutenberg-Isaac-Michael" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Heath", "given_name": "James R.", "clpid": "Heath-J-R" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The research presented in this thesis focuses on the preparation of functionalized polymers using olefin metathesis polymerization methods. A portion of this research is also devoted to the development of applications for metathesis-derived polymers.
\r\n\r\nThree distinct types of olefin metathesis polymerizations can be recognized within this work. Ring-opening metathesis polymerization (ROMP) is the most prevalent type, followed by acyclic diene metathesis (ADMET) polymerization and a hybrid of the ROMP and ADMET mechanisms known as ring-opening-insertion metathesis polymerization (ROIMP).
\r\n\r\nMany of the concepts that appear throughout this thesis are introduced in Chapter 1. Olefin metathesis occupies a central role in each of the subsequent chapters; detailed descriptions of the mechanism and important olefin metathesis catalysts are provided. The chapter also includes background information regarding polymers, polymer properties and the application of ROMP in the construction of electronic devices.
\r\n\r\nAlthough the utility of ADMET does not yet seem to match that of ROMP, valuable information can be obtained from ADMET polymerizations. In an effort to elucidate catalytic activity, Chapter 2 details a comparison of the ADMET polymerizations of terminal and non-terminal dienes.
\r\n\r\nExperimental investigations involving ROIMP, a novel method for the production of A,B-alternating copolymers, is presented in Appendix A. The mechanism of ROIMP is conceptually very different from the mechanisms of either step growth or chain growth polymerizations. Efforts toward understanding the mechanism of ROIMP using a mathematical model are discussed in Chapter 3.
\r\n\r\nPolymeric chain transfer agents (PCTAs) suitable for ROMP reactions are polymers that contain a single, metathesis-active olefin. These polymers are the focus of Chapter 4 and can be used in the preparation of novel block copolymers. As an example, Appendix B presents the preparation of block copolymers consisting of polyacetylene and various commodity polymers.
\r\n\r\nFinally, the development of applications for surface-initiated ROMP (SI-ROMP) is discussed in Chapter 5 and Appendix C. Polymer films prepared using SI-ROMP are shown to be viable dielectric layers in thin-film transistors, and research is presented involving microcontact printing and dip pen nanolithography as methods for forming patterned SI-ROMP polymer films.
\r\n", "doi": "10.7907/5Z6Y-G191", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:4822", "collection": "thesis", "collection_id": "4822", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12072004-021118", "primary_object_url": { "basename": "YouyongLi_Thesis.pdf", "content": "final", "filesize": 3996304, "license": "other", "mime_type": "application/pdf", "url": "/4822/1/YouyongLi_Thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Atomistic Simulation of Macromolecules", "author": [ { "family_name": "Li", "given_name": "Youyong", "orcid": "0000-0002-5248-2756", "clpid": "Li-Youyong" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis focuses on the atomistic simulation of polymers/dendrimers material properties and development/applications of Monte Carlo methods for macromolecules. The main topics and their outlines are listed as following.
\r\n\r\n1) Structures and properties of crystalline polymers from theory. Although crystalline polymers such as nylon are important industrial materials, it is difficult to get the details of the various structures/properties and the conversion between them from the experiment. Using molecular modeling, we successfully predicted the complicated structures/properties and illustrated the process of forming the polymer crystal and conversion mechanism among those structures.
\r\n\r\n2) Packing mechanism of self-assembly dendrimer balls with soft coronas. Using the vibrational density of state (DoS) derived from molecular dynamic simulations, we investigate the free energy of the liquid crystal formed by soft dendrimer balls. We find that the preferred lattice for soft balls is different from the hard balls and illustrate the mechanism.
\r\n\r\n3) Development of CCBTX Monte Carlo method for polymer and dendrimer. Although computer simulation has developed as a powerful research tool to study polymer/dendrimer materials properties recently, it has been hampered by the difficulties of sampling amorphous polymer/dendrimer configurations efficiently. We develop the efficient Continuous Configurational Biased TX (CCBTX) method to generate high-quality amorphous polymer and dendrimer atomistic structures directly. The code is implemented in C++ and ported in python environment, which provides friendly interface.
\r\n\r\n4) Thermodynamic functions, critical exponents, and theta temperatures of polymer chains from CCBB Monte Carlo method. We examine the thermodynamic properties (entropy, energy, end-to-end distance) of isolated polymer chains with the Monte Carlo method.
", "doi": "10.7907/NW1Q-1E81", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:4303", "collection": "thesis", "collection_id": "4303", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10292004-152709", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 2303147, "license": "other", "mime_type": "application/pdf", "url": "/4303/1/thesis.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Atomistic Simulation of Barium Titanate", "author": [ { "family_name": "Zhang", "given_name": "Qingsong", "clpid": "Zhang-Qingsong" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Ravichandran", "given_name": "Guruswami", "clpid": "Ravichandran-G" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Bhattacharya", "given_name": "Kaushik", "clpid": "Bhattacharya-K" }, { "family_name": "Ortiz", "given_name": "Michael", "clpid": "Ortiz-M" }, { "family_name": "Cagin", "given_name": "Tahir", "clpid": "Cagin-Tahir" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "We present the Polarizable Charge Equilibration (P-QEq) force field to include self-consistent atomic polarization and charge transfer in molecular dynamics of materials. The short-range Pauli repulsion effects are described by two body potentials without exclusions. A linear self-consistent field solution to the charge transfer is proposed for charge transfer in large systems. The P-QEq is parameterized for BaTiO\u2083 based on quantum mechanics calculations (DFT with GGA) and applied to the study of the phase transitions, domain walls and oxygen vacancies.
\r\n\r\nFrozen phonon analysis reveals that the three high-temperature BaTiO\u2083 phases in the displacive model are unstable. Within their corresponding macroscopic phase symmetries, the smallest stable phase structures are achieved by antiferroelectric distortions from unstable phonons at the Brillouin zone boundaries. The antiferroelectric distortions soften phonons, reduce zero point energies and increase vibrational entropies. A correct BaTiO\u2083 phase transition sequence and comparable transition temperatures are obtained by free energy calculations. The inelastic coherent scattering functions of these phases agree with X-ray diffraction experiments.
\r\n\r\nBaTiO\u2083 180\u00b0 domain wall is Ba-centered with abrupt polarization switching across the wall. The center of BaTiO\u2083 90\u00b0 domain wall is close to its orthogonal phase. There are transition layers from the wall centers to the internal domains in the types of domain walls. Polarization variation in these transition layers induces polarization charge and free charge transfer. This effect causes a strong bipolar electric field in BaTiO\u2083 90\u00b0 domain wall.
\r\n\r\nOxygen vacancies are frozen at room temperature, and mobile near the Curie temperature. In the tetragonal phase, the broken Ti-O chains are frozen, reducing switchable polarization. Due to charge redistribution and local relaxation, oxygen vacancy interaction is short-range and anisotropic. Two oxygen vacancies can form a stable pair state, where two broken Ti-O chains are aligned parallel. Oxygen vacancy clusters can form dendritic structures as a result of local relaxation and charge interaction.
", "doi": "10.7907/SQ9J-4H73", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:4814", "collection": "thesis", "collection_id": "4814", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-232639", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 3454192, "license": "other", "mime_type": "application/pdf", "url": "/4814/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Defect Chemistry and Proton Conductivity in Ba-based Perovskites", "author": [ { "family_name": "Wu", "given_name": "Jian", "clpid": "Wu-Jian" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The site incorporation mechanism of M\u00b3\u207a dopants into A\u00b2\u207aB\u2074\u207aO\u2083 perovskites controls the overall defect chemistry and thus their transport properties. For charge balance reasons, incorporation onto the A\u00b2\u207a site would require the creation of negatively charged point defects, such as cation vacancies, whereas incorporation onto the B\u2074\u207a site is accompanied by the generation of positively charged defects, typically oxygen vacancies. Oxygen vacancy content, in turn, is relevant to proton conducting oxides in which protons are introduced via the dissolution of hydroxyl ions at vacant oxygen sites.
\r\n\r\nThis work proposes that, on the basis of X-ray powder diffraction studies, electron microscopy, chemical analysis, thermal gravimetric analysis, AC impedance spectroscopy, extended X-ray fine structure (EXAFS) and atomistic simulation, that nominally B-site doped barium cerate can exhibit dopant partitioning partially as a consequence of barium evaporation at elevated temperatures. Such partitioning and the presence of significant dopant concentrations on the A-site negatively impact proton conductivity. As a consequence of the greater ability of larger cations to exist on the Ba site, the H\u2082O adsorption and proton conductivities of large-cation doped barium cerates are lower than those of small-cation doped analogs.
\r\n\r\nA series of dopants, La, Nd, Sm, Gd and Yb are adopted in doped BaCeO\u2083 with the composition BaCe0.85M0.15O3-\u03b4. Yb doped BaCeO\u2083 yields the highest proton conductivity among all the doped samples. Compositional non-stoichiometry, which is closely tied to sample processing, is studied in a Bax0.85M0.15O3\u00b1\u03b4 series. It is indicated that low temperature synthesis is beneficial to reduce barium evaporation at elevated temperatures and in turn increase the proton conductivity. The chemical stability of BaCeO\u2083 is investigated and Zr is used to stabilize BaCeO\u2083 in CO\u2082-rich atmosphere effectively. This result helps to commercialize doped BaCeO\u2083 as the electrolyte material for SOFCs.
", "doi": "10.7907/VTCG-T978", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" }, { "id": "thesis:2196", "collection": "thesis", "collection_id": "2196", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282004-161503", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 13394896, "license": "other", "mime_type": "application/pdf", "url": "/2196/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computation Aided Design in Molecular Nanotechnology", "author": [ { "family_name": "Deng", "given_name": "Wei-Qiao", "orcid": "0000-0002-3671-5951", "clpid": "Deng-Wei-Qiao" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We use multi-scale simulation strategy to understand, improve and rationally design novel materials with desired properties in molecular nanotechnology. The areas we have studied cover from molecular electronics, nano-structured materials to carbon nanotube technology.
\r\n\r\nIn term of molecular and nano-electronics, first we used quantum mechanics to characterize the structure and current-voltage (I-V) performance of the Stoddart-Heath rotaxane-based programmable electronic switch. This methodology established a basis for iterative experimental-theoretical efforts to optimize systems for molecule-based electronics. We extended this switch principle and rationally designed an ultrafast molecular switch, proton-hopping molecular switch. Second we developed a kinetic model to study the hole mobility in organic semiconductor. After screening several designs, we presented a nano-bracelet as a competitive organic semiconductor.
\r\n\r\nWe studied several topics related to the applications of nano-structured materials in fuel cell technology. Based on our simulation, we proposed a new kind of carbon-based materials for hydrogen storage. It can satisfy the target set up by the Department of Energy, USA. We develop a kinetic model to study the proton diffusion in proton exchange membrane of hydrogen fuel cell. We validated our proposed system, fluorinated imidazole impregnated nafion, as the candidate that can transfer proton above 100 0C at water-free media.
\r\n\r\nIn term of carbon nanotube technology, we explored the reason why bimetallic catalysts are 10-100 times better than mono-metals at assisting single wall carbon nanotube growth. Based on our proposed two-stage growth mechanism, we screened and designed a better catalysis.
", "doi": "10.7907/3EKY-3J53", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:2195", "collection": "thesis", "collection_id": "2195", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05282004-155105", "primary_object_url": { "basename": "thesis.pdf", "content": "final", "filesize": 29865064, "license": "other", "mime_type": "application/pdf", "url": "/2195/1/thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Superprotonic Solid Acids: Structure, Properties, and Applications", "author": [ { "family_name": "Boysen", "given_name": "Dane Andrew", "clpid": "Boysen-Dane-Andrew" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Asimow", "given_name": "Paul David", "clpid": "Asimow-P-D" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this work, the structure and properties of superprotonic MH\u2099XO\u2084-type solid acids (where M = monovalent cation, X = S, Se, P, As, and n = 1, 2) have been investigated and, for the first time, applied in fuel cell devices. Several MH\u2099XO\u2084-type solid acids are known to undergo a \"superprotonic\" solid-state phase transition upon heating, in which the proton conductivity increases by several orders of magnitude and takes on values of ~ 0.01 S/cm. The presence of superprotonic conductivity in fully hydrogen bonded solid acids, such as CsH\u2082PO\u2084, has long been disputed. In these investigations, through the use of pressure, the unequivocal identification of superprotonic behavior in both RbH\u2082PO\u2084 and CsH\u2082PO\u2084 has been demonstrated, whereas for chemically analogous compounds with smaller cations, such as KH\u2082PO\u2084 and NaH\u2082PO\u2084, superprotonic conductivity was notably absent. Such observations have led to the adoption of radius ratio rules, in an attempt to identify a critical ion size effect on the presence of superprotonic conductivity in solid acids. It has been found that, while ionic size does play a prominent role in the presence of superprotonic behavior in solid acids, equally important are the effects of ionic and hydrogen bonding. Next, the properties of superprotonic phase transition have been investigated from a thermodynamic standpoint. With contributions from this work, a formulation has been developed that accounts for the entropy resulting from both the disordering of both hydrogen bonds and oxy-anion librations in the superprotonic phase of solid acids. This formulation, fundamentally derived from Linus Pauling's entropy rules for ice, accurately accounts for the change in entropy through a superprotonic phase transition. Lastly, the first proof-of-principle fuel cells based upon solid acid electrolytes have been demonstrated. Initial results based upon a sulfate electrolyte, CsHSO\u2084, demonstrated the viability of solid acids, but poor chemical stability under the highly reducing H\u2082 gas environment of the fuel cell anode. Later experiments employing a CsH\u2082PO\u2084 electrolyte proved quite successful. The results of these solid acid-based fuel cell measurements suggest solid acids could serve as an alternative to current state-of-the-art fuel cell electrolytes.", "doi": "10.7907/41BQ-3R07", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:1912", "collection": "thesis", "collection_id": "1912", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05212004-144036", "primary_object_url": { "basename": "Elmore_Thesis.pdf", "content": "final", "filesize": 16831479, "license": "other", "mime_type": "application/pdf", "url": "/1912/8/Elmore_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Investigations of Ion Channel Structure-Function Relationships Using Molecular Modeling and Experimental Biochemistry", "author": [ { "family_name": "Elmore", "given_name": "Donald Eugene, Jr.", "orcid": "0000-0002-8723-8710", "clpid": "Elmore-Donald-Eugene-Jr" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Lester", "given_name": "Henry A.", "clpid": "Lester-H-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Ion channels are integral membrane proteins found in all cells that mediate the selective passage of specific ions or molecules across a cell membrane. These channels are important in a diverse range of physiological processes, including signal transmission in the nervous system, sensory perception, and regulation of vital systems, such as circulation. This thesis discusses the use of computational chemistry methods, such as molecular dynamics (MD) and ab initio calculations, and experimental biochemical techniques, such as site-directed mutagenesis, in vivo bacterial assays, chemical cross-linking, and circular dichroism spectroscopy, in tandem to elucidate ion channel structure-function relationships. This research was catalyzed by the solving of atomic resolution crystal structures of the mechanosensitive channels of large and small conductance (MscL and MscS) by the Rees group. Although interesting themselves, these bacterial channels also provide good model systems for considering more complex eukaryotic channels.
\r\n\r\nMscL is an ion channel gated only by membrane tension. Initial studies of MscL verified the relevance of the crystal structure conformation under physiological conditions and compared different MscL homologues. Other work began to elucidate potentially unique structural and functional roles of the M. tuberculosis MscL C-terminal helical bundle. As well, interactions between the MscL channel protein and surrounding lipid and the potential relevance of helical kinking in MscL gating pathways were investigated. MscS is also gated by membrane tension, but its gating can be modulated by changes in transmembrane potential. Thus, studies on MscS began to identify the specific amino acid residues that are responsible for giving the channel its voltage sensitivity. Finally, computations predicting the conformation of nicotine in different solvent environments are discussed. Nicotine is a small molecule ligand that binds to and gates nicotinic acetylcholine receptors, and a thorough understanding of nicotine structure could aid efforts to elucidate receptor structure-function relationships and design new pharmaceuticals.
", "doi": "10.7907/47GW-HT46", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:729", "collection": "thesis", "collection_id": "729", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02242004-181514", "primary_object_url": { "basename": "thesis_final_version2.pdf", "content": "final", "filesize": 3417275, "license": "other", "mime_type": "application/pdf", "url": "/729/1/thesis_final_version2.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Electron-Transfer Processes at Semiconductor/Liquid Interfaces and Metal/Nanogap Junctions", "author": [ { "family_name": "Gstrein", "given_name": "Florian", "clpid": "Gstrein-Florian" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Roukes", "given_name": "Michael Lee", "clpid": "Roukes-M-L" }, { "family_name": "Hone", "given_name": "James C.", "clpid": "Hone-J-C" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Roukes", "given_name": "Michael Lee", "clpid": "Roukes-M-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "It is shown that n-ZnO/H\u2082O-A/A\u207b junctions (A/A\u207b = [Co(bpy)\u2083]\u00b3\u207a/\u00b2\u207a or [OsL\u2082L']\u00b3\u207a/\u00b2\u207a) display energetic and kinetic behavior of unprecedented ideality. The rate constant of the junction with the highest driving force increased when the driving force was lowered, which indicates that the junction operated in the inverted regime. The driving force was varied by shifting the conduction-band edge of the semiconductor with pH. The contact with the lowest driving force was found to operate in the normal regime of charge transfer. These results provide the first experimental indication that semiconductor/liquid contacts can operate in the inverted regime. Junctions having a similar driving force but different reorganization energies show the expected dependence of the rate constant on the reorganization energy.
\r\n\r\nLow surface-recombination velocities (SRVs) were observed for systems with an accumulation of holes or electrons at the Si surface. Formation of the charge-carrier accumulation layer was confirmed by a solution-gated transistor method. Digital simulations revealed that SRVs < 10 cm s\u207b\u00b9 can be produced by surfaces with trap densities as large as 10\u00b9\u00b2 cm\u207b\u00b2 provided that the surface is in accumulation or inversion. The degree of band bending and SRVs of Si(111) in contact with a variety of aqueous fluoride solutions were determined for the first time at open circuit. An accumulation of electrons at the surface is responsible for the low effective SRVs in NH\u2084F and buffered HF solutions. The protonation of basic defect sites is important for the low SRV of Si(111)/H\u2082SO4(aq) and Si(111)/HF(aq) contacts.
\r\n\r\nThe J-E characteristics of electron-tunnel junctions formed by the electromigration of metal nanowires without a molecule bridging the gap were explored in detail. The low-temperature J-E curves of some junctions showed regions of zero conductivity near zero bias, while such features were absent in the data collected for other junctions. A common pattern was discerned in that the low-bias resistances of all junctions decreased by at least an order of magnitude with increasing temperature according to Abeles' model for electron tunneling in granular metal junctions. These findings were consistent with the Coulomb blockade effect and can be attributed to metal islands in the gap.
", "doi": "10.7907/1NT2-FB12", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:998", "collection": "thesis", "collection_id": "998", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03182004-221215", "primary_object_url": { "basename": "MSMThesisfinal.pdf", "content": "final", "filesize": 68941944, "license": "other", "mime_type": "application/pdf", "url": "/998/1/MSMThesisfinal.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Synthesis of Large-Grained Polycrystalline Silicon by Hot-Wire Chemical Vapor Deposition for Thin Film Photovoltaic Applications", "author": [ { "family_name": "Mason", "given_name": "Maribeth Swiatek", "clpid": "Mason-Maribeth-Swiatek" } ], "thesis_advisor": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" } ], "thesis_committee": [ { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Bockrath", "given_name": "Marc William", "clpid": "Bockrath-M-W" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In this study, we investigate the fabrication of large-grained polycrystalline silicon by hot-wire chemical vapor deposition (HWCVD) and its suitability for thin-film photovoltaic applications. We have devised two strategies for the fast, low-temperature growth of thin polycrystalline silicon films on glass substrates. The first is the direct growth of polycrystalline silicon on SiO\u2082 by HWCVD. We use atomic force microscopy (AFM) to characterize fully continuous polycrystalline silicon films grown by HWCVD on SiO\u2082, as well as the nucleation density of silicon islands formed in the early stages of HWCVD growth, as a function of temperature and hydrogen dilution (H\u2082:SiH\u2084). Our observations of the nucleation kinetics of Si on SiO\u2082 can be explained by a rate-equation pair-binding model, from which we derive an estimate for the prefactor and activation energy for surface diffusion of Si on SiO\u2082 during HWCVD growth and assess the viability of this method for the rapid growth of large-grained polycrystalline silicon on SiO\u2082.
\r\n\r\nThe second strategy uses large-grained (~100 \u00b5m) polycrystalline silicon layers fabricated by selective nucleation and solid-phase epitaxy (SNSPE) on SiO\u2082 substrates as templates for epitaxial growth by HWCVD. Using reflection high-energy electron diffraction (RHEED) and transmission electron microscopy (TEM), we have derived a phase diagram for Si on Si(100) consisting of epitaxial, twinned epitaxial, mixed epitaxial/polycrystalline, and polycrystalline phases of growth on Si(100) in the 50 nm-2 \u00b5m thickness regime. Evidence is also presented for epitaxial growth on SNSPE templates, which use nickel nanoparticles as nucleation sites for the solid-phase crystallization of phosphorus-doped amorphous silicon on SiO\u2082. Minority carrier lifetimes for films on Si(100), as measured by resonant-coupled photoconductive decay experiments, range from 5.7 to 14.8 microseconds while those for films on SNSPE templates range from 5.9 to 19.3 microseconds. Residual nickel present in the SNSPE templates does not significantly affect the lifetime of films grown on SNSPE templates, making the growth of epitaxial layers by HWCVD on SNSPE templates a possible strategy for the fabrication of thin-film photovoltaics.
", "doi": "10.7907/7K9R-VX22", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:1599", "collection": "thesis", "collection_id": "1599", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05042004-203854", "primary_object_url": { "basename": "Preface.pdf", "content": "final", "filesize": 277016, "license": "other", "mime_type": "application/pdf", "url": "/1599/8/Preface.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Structure and Function Studies of the Human Dopamine Receptors", "author": [ { "family_name": "Kalani", "given_name": "M. Yashar S.", "orcid": "0000-0002-5923-1255", "clpid": "Kalani-M-Yashar-S" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Vaidehi", "given_name": "Nagarajan", "clpid": "Vaidehi-N" }, { "family_name": "Patterson", "given_name": "Paul H.", "clpid": "Patterson-P-H" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Dopamine neurotransmitter and its receptors play a critical role in cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's and schizophrenia would be significantly enhanced with the availability of the three-dimensional (3-D) structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. In this thesis, I report the 3-D structures of the 5 subtypes of the human dopamine receptors, predicted from primary sequence using first principles theoretical and computational techniques. I use the term \"first principles\" to mean that we do not use the high resolution crystal structure of rhodopsin as a template, nor do we use homology modeling or threading of any kind to determine the structure. Predicting the binding sites, and the relative binding affinities of endogenous ligands and various pharmaceuticals to the 5 receptors validates the predicted structures. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies and give relative binding affinities that correlate well with experiment. The predicted binding site for dopamine and agonists is located between transmembrane helices (TM) 3, 4, 5, and 6, while the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM 5. We identify characteristic differences between the binding sites of agonists and antagonists, as well as factors that cause differential binding to the 5 subtypes of the human dopamine receptors.
\r\n\r\nThis thesis consists of five chapters that have, or will shortly result in publications. The first chapter is a brief introduction to the field, the motivation for the project, my scientific contributions, and contribution of others on the team. Chapter two introduces the methods and their successes at reproducing experimentally known results for the human D2 dopamine receptor; it discusses, in great detail, the active site of pharmaceutical agonists and antagonists to the human D2 dopamine receptor, and highlights the strengths and shortcomings of homology modeling for membrane bound proteins; this chapter will be submitted for publication to the Journal of Molecular Biology. Chapter three reports the results of a blind study performed in collaboration with Aventis Pharmaceuticals. For this study, we were provided with the two-dimensional structure of 9 antagonists and were asked to predict their binding sites, binding affinities, and to explain the differential binding of the ligands to the human D2 and D3 dopamine receptors and the human a1A adrenergic receptor. The results of this study are in preparation for submission to the Journal of Medicinal Chemistry. Chapters four and five of the thesis give preliminary results of comparative studies of the agonist and antagonist binding sites of the five subtypes of the human dopamine receptors. Chapter 6 contains results of another blind study on the G2A receptor with Professor Owen Witte.
\r\n\r\nIn addition to the six main chapters, this thesis contains 6 independent appendices that report results of similar studies in other systems. The first 2 appendices are work that has already been published. The remaining 4 appendices will shortly result in publications, but at this time, they are not publication worthy; these appendices represent data that has been analyzed but has not been written in paper format.
\r\n\r\nIn addition, I would like to make note of the studies that I have conducted on the 9 subtypes of the human adrenergic receptors with Mr. Peter Freddolino, the 4 human histamine receptors that were conducted with Mr. Freddolino and Mr. Maziyar Kalani, and the 4 G2A-like lipid receptors conducted with Mr. Rene Trabanino, Dr. Radu, Dr. Yang, and Professor Owen Witte of the Howard Hughes Medical Institute at the David Geffen School of Medicine at the University of California, Los Angeles.
", "doi": "10.7907/T6NV-7W30", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:5029", "collection": "thesis", "collection_id": "5029", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12172003-140435", "primary_object_url": { "basename": "toc.pdf", "content": "final", "filesize": 627204, "license": "other", "mime_type": "application/pdf", "url": "/5029/9/toc.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Expanding the Biosynthetic Capacity of the Aminoacyl-tRNA Synthetases", "author": [ { "family_name": "Wang", "given_name": "Pin", "clpid": "Wang-Pin" } ], "thesis_advisor": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Davis", "given_name": "Mark E.", "orcid": "0000-0001-8294-1477", "clpid": "Davis-M-E" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Incorporation of non-natural amino acids into proteins in vivo can provide biological materials with new chemical functions and improved physical properties. Examples include new posttranslational modification chemistry by introducing azide and ketone moieties into recombinant proteins, and novel strategies for engineering hyper-stable proteins by incorporating fluorinated side chains. Implementing such methods requires manipulation of protein biosynthesis to specifically alter the genetic code. The rules of the genetic code are established by the aminoacylation reaction, where the aminoacyl-tRNA synthetases (aaRS) catalyze the attachment of the amino acids to their cognate tRNAs. Thus manipulation of cellular aminoacylation reactions could potentially expand the available set of amino acid building blocks for protein engineering and biomaterials engineering.
\r\n\r\nBy simple depletion of the cellular pool of isoleucine and utilization of isoleucine auxotrophic hosts, we were able to force the endogenous isoleucyl-tRNA synthetase to join 5,5,5-trifluoroisoleucine (5TFI) to tRNAIle and assign it to isoleucine codons in vivo. Murine interleukin 2 containing 5TFI retains its biological activity. We showed that engineering of bacterial expression hosts can allow a single RNA message to be read in different ways, depending on the relative rates of competing aminoacylation reactions. Specifically, we showed that the 2S,3R-form of 4,4,4-trifluorovaline can be assigned either to isoleucine or to valine codons, depending on whether the bacterial host overexpresses the isoleucyl- or the valyl-tRNA synthetase. When an amino acid analog of interest is not recognized by the corresponding wild-type aaRS, we can either identify the appropriate modification of the amino acid as a promising ligand or design new synthetase activity. We describe an attempt to develop a virtual ligand screening method to find non-natural amino acids that can serve as ligands for the phenylalanyl-tRNA synthetase and our computational results correlate well with experimental results in vitro and in vivo. We also present a computational method for identifying the sites of mutations to relax the substrate specificity of the E. coli phenylalanyl-tRNA synthetase (ePheRS). One designed variant of ePheRS allows the efficient in vivo incorporation of aryl ketone functionality into proteins in vivo. Proteins outfitted with ketone functionality can be chemoselectively ligated with hydrazide reagents under mild conditions. Three designed mutants of ePheRS were subjected to extensive examination, and a broad activation profile toward many non-natural aromatic amino acids was observed. E. coli host strains were established to over-express these mutant ePheRSs, enabling the re-assignment of the Phe codons to many non-natural amino acids. By rational attenuation of the editing function of a leucyl-tRNA synthetase, oxonorvaline was incorporated into a recombinant protein in Escherichia coli.
\r\n\r\nThe work described above addresses the multi-site incorporation of new amino acids into proteins in vivo, which can be utilized to engineer the overall properties of biomacromolecules such as protein stability. The second component of this thesis focused on the site-specific incorporation of novel amino acids into proteins in vivo, which can be applied to problems that require local change of protein behavior. We have refined a previously described system, where we introduce a mutant form of yeast PheRS co-transformed with a cognate suppressor tRNA, allowing incorporation of several aromatic amino acids into proteins in response to an amber codon. The results firmly demonstrate the general strategy of importing an exogenous synthetase/tRNA pair to achieve site-specific incorporation of non-natural amino acids into proteins in vivo.
", "doi": "10.7907/99W6-8F08", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:2442", "collection": "thesis", "collection_id": "2442", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06042004-153530", "primary_object_url": { "basename": "Elizabeth_I_Mayo.pdf", "content": "final", "filesize": 7155748, "license": "other", "mime_type": "application/pdf", "url": "/2442/1/Elizabeth_I_Mayo.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Kinetics and Thermodynamics of Dye (Group VIII Metal)\u2013Sensitized Nanocrystalline Titanium Dioxide Photoelectrodes", "author": [ { "family_name": "Mayo", "given_name": "Elizabeth Idonia", "clpid": "Mayo-Elizabeth-Idonia" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis reports a comprehensive series of experiments involving complementary kinetics and thermodynamic measurements directed at isolating the important individual reactions in dye-sensitized nanocrystalline titanium dioxide solar cells (DSSCs). These experiments were done in conjunction with steady-state photoelectrochemical measurements; a combination which allowed a greater understanding of the overall mechanisms and driving forces of these systems.
\r\n\r\nAlternative two-electron redox couples were studied and efficiency increases of >40% were achieved when compared to similar systems using iodide/triiodide. Surface treatment with carboxylic acids minimized direct reduction of the redox couple by electrons in the titanium dioxide, and interestingly, the photocurrent also increased resulting in overall efficiency increases as high as 20%. Bridging ligands were used in an attempt to minimize recombination of the injected electrons with the resulting oxidized dyes, but DSSCs with these sensitizers showed poor conversion efficiencies and no distance dependence for injection or recombination was observed. The lack of distance dependence was attributed to the flexible single carboxyl anchoring group. To further investigate the effect of binding mode, a series of carboxyl-modified ruthenium bipyridyl sensitizers were studied. A single carboxyl anchoring group resulted in unstable DSSCs due to enhanced desorption as well as poor photon-to-current conversion efficiencies. These dyes injected efficiently into TiO\u2082 on the nanosecond timescale, and regeneration of the oxidized sensitizers competed effectively with recombination. Consequently, individual kinetics measurements could not explain the decreased steady-state performance. The regeneration rates of these dyes in solution were found to rapid, approaching the diffusion controlled limit. The regeneration rate was dependent on the number and electron-withdrawing nature of the pendant groups, with the rate decreasing with increasing number of electron withdrawing substituents. Iridium dyes with cyclometalating ligands were shown to be efficient sensitizers in DSSCs, with quantum yields on the order of a ruthenium analogue having similar spectral overlap. Overall, the repeated inconsistencies between the steady-state behavior and the measured individual kinetics processes indicate that the current kinetic model is insufficient to accurately predict photoelectrochemical behavior.
", "doi": "10.7907/E9WY-1N05", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:1893", "collection": "thesis", "collection_id": "1893", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05202004-174324", "primary_object_url": { "basename": "ALL_THESIS_2.pdf", "content": "final", "filesize": 8738128, "license": "other", "mime_type": "application/pdf", "url": "/1893/1/ALL_THESIS_2.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Prediction of Structure, Function, and Spectroscopic Properties of G-Protein-Coupled Receptors: Methods and Applications", "author": [ { "family_name": "Trabanino", "given_name": "Rene Jouvanni", "clpid": "Trabanino-Rene-Jouvanni" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Hsieh-Wilson", "given_name": "Linda C.", "clpid": "Hsieh-Wilson-L-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "G-protein-coupled receptors are of great pharmaceutical interest, comprising the majority of targets for currently marketed drugs. The theme of my thesis is the development of the structure prediction method, MembStruk, for the superfamily of G-protein-coupled receptors. The first part of this thesis focuses on the methods and their validation. There are several steps involved in MembStruk that are detailed and tested for membrane proteins with known structures in the first few chapters (Chapters 2-6). Specifically, the first principles methods for predicting the transmembrane helical ranges and the helix hydrophobic centers are tested. The program for predicting the transmembrane helical ranges, TM2ndS, ranks in the top two when comparing performance with other top prediction methods. And because it is based on general principles, it can be applied robustly for membrane protein families for which little structural information is available. The simulation of the EC-II closing is also tested on bovine rhodopsin. The use of the MembStruk method on bovine rhodopsin as a validation case is presented in detail (Chapter 2). The large majority (71%) of the residues involved in binding in rhodopsin are predicted and the protein structure itself is 2.84 \u00c5 coordinate root mean square error in the transmembrane main chain atoms from the crystal structure.
\r\n\r\nThe second part of the thesis discusses applications on various G-protein-coupled receptor systems. The application of the MembStruk method to other peptide chemokine G-protein-coupled receptors like CCR1 and CCR5 is discussed in Chapter 9. The fundamental scientific problems of G-protein-coupled receptor modulation of absorption and relaxation properties of a bound chromophore (retinal) are addressed and results are presented for the predictions of these properties.
\r\n\r\nThe prediction of structure and function of G-protein-coupled receptors would allow for structure-based drug design and a rational approach to reducing drug cross-reactivity across receptor families.
", "doi": "10.7907/VHED-4063", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:778", "collection": "thesis", "collection_id": "778", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02272004-034648", "primary_object_url": { "basename": "oren_full_thesis.pdf", "content": "final", "filesize": 4303633, "license": "other", "mime_type": "application/pdf", "url": "/778/13/oren_full_thesis.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Enhancing Materials Through Controlled Architectures with Ring-Opening Metathesis Polymerization", "author": [ { "family_name": "Scherman", "given_name": "Oren Alexander", "orcid": "0000-0001-8032-7166", "clpid": "Scherman-Oren-Alexander" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Stoltz", "given_name": "Brian M.", "clpid": "Stoltz-B-M" }, { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The focus of the research presented in this thesis is the synthesis of functional polymers and construction of controlled molecular architectures through a polymerization process referred to as ring-opening metathesis polymerization (ROMP). A brief overview of polymer chemistry as well as ring-olefin metathesis polymerization is discussed in introductory Chapter 1.
\r\n\r\nChapters 2 and 3 discuss new synthetic routes to polyacetylene and polyacetylene block-copolymers from cyclooctatetraene and a new ruthenium olefin metathesis catalysts. Polyacetylene is an intractable material, as are most organic conducting polymers. Chapter 3, however, introduces a novel route to soluble telechelic polyenes and polyacetylene block-copolymers.
\r\n\r\nThe construction of organic overlayers on semiconductor surfaces is important in the area of anti-fouling coatings as well as in organic electronic applications. Chapter 4 introduces a new route to polymer-covered silicon surfaces through a covalent Si-C linkage. ROMP of norbornene from a surface-attached ruthenium catalyst produces uniform polynorbornene overlayers with controlled thickness ranging from 10 \u00c5 to 5.5 \u00b5m. The work discussed in Chapter 5 elaborates on surface-initiated ROMP by constructing thin-film top-contact field effect transistors with a polynorbornene dielectric layer.
\r\n\r\nChapter 6 explores the synthesis of polar-functionalized linear polymers from cyclopentene and cycloheptene derivatives. The challenge of polymerizing low-ring strain monomers via ROMP is also discussed. A method to a priori discern a monomer's ability to undergo ROMP is outlined in this chapter as well.
\r\n\r\nChapters 7 and 8 describe the synthesis of both regioregular and stereoregular polar-functionalized linear ethylene vinyl alcohol (EVOH) co-polymers by the ROMP of rationally designed, symmetric monomers. These polymers were made with the goal of producing materials with enhanced oxygen barrier properties. Controlling material architecture imparts a dramatic effect on both the solution and solid state morphologies of EVOH and the synthetic challenges and results are discussed.
\r\n\r\nFinally, Chapter 9 complements Chapters 7 and 8, and investigates the reason behind enhanced oxygen barrier properties of EVOH through molecular dynamics simulations. For EVOH polymers that differs only by the syn or anti orientation of neighboring diols, a clear difference is observed for the hydrogen bonding clusters. Moreover, the free volume accessible to any solute molecules is extremely low identified by a probe radius of less than 0.6 \u00c5.
", "doi": "10.7907/E1BS-HG72", "publication_date": "2004", "thesis_type": "phd", "thesis_year": "2004" }, { "id": "thesis:4433", "collection": "thesis", "collection_id": "4433", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11072002-184043", "primary_object_url": { "basename": "bielawski.pdf", "content": "final", "filesize": 3979707, "license": "other", "mime_type": "application/pdf", "url": "/4433/1/bielawski.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Tailoring Polymer Synthesis with Designer Ruthenium Catalysts", "author": [ { "family_name": "Bielawski", "given_name": "Christopher William", "orcid": "0000-0002-0520-1982", "clpid": "Bielawski-Christopher-William" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Tirrell", "given_name": "David A.", "clpid": "Tirrell-D-A" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The research presented in this thesis focuses on applying ring-opening metathesis polymerization (ROMP) toward the synthesis of advanced macromolecular architectures. Chapter 1 provides an overview of the olefin metathesis reaction and evaluates the various synthetic tools currently employed for preparing complex polymeric structures.
\r\n\r\nChapters 2 and 3 summarize the performance of various Ru-based catalysts in ROMP. Chapter 2 focuses on complexes coordinated with various N-heterocyclic carbene ligands while Chapter 3 focuses on their phosphine ligated analogs and methods to improve their initiation efficiency. The scope and utility of these catalysts in various ROMP reactions are discussed.
\r\n\r\nChapters 4 and 5 describe the synthesis of acetoxy, hydroxy, and vinyl end-functionalized polybutadienes (PBDs) and polynorbornenes. By including allyl acetate, 1,4-bis(acetoxy)-2-butene, or 2-butene-1,4-diol as chain transfer agents (CTAs) during a Ru mediated ROMP of cyclooctadiene (COD) or norbornene (NBE), the respective end-functionalized polymers with molecular weights controllable up to 30 kDa could be obtained in high yield.
\r\n\r\nChapter 6 describes a one-pot synthesis of triblock copolymers composed of mechanistically incompatible segments. Bis(allyl chloride) and bis(2-bromopropionate) end-functionalized telechelic PBDs were synthesized by the ROMP of COD in the presence of the corresponding difunctional CTAs. These telechelic PBDs were subsequently used as difunctional macroinitiators for the atom transfer radical polymerization (ATRP) of styrene or methyl methacrylate (MMA) to form the respective block copolymers.
\r\n\r\nChapter 7 describes the synthesis of a multifunctional Ru complex which was found to be capable of mediated both the ROMP of COD and the ATRP of MMA to form diblock copolymers. Depending on the reaction conditions, the complex was found to catalyze both polymerizations either in tandem or simultaneously. Introduction of hydrogen at the conclusion of the polymerizations resulted in quantitative saturation of the polymer backbone.
\r\n\r\nChapters 8 and 9 describe a new synthetic route to cyclic polymers. In this approach, the ends of growing polymer chains remain attached to a cyclic Ru catalyst throughout the entire polymerization process. This effectively excludes all types of linear intermediates, which were a major drawback of previous approaches to cyclic polymers. Techniques for characterizing and determining the purity of cyclic polymers are also discussed.
", "doi": "10.7907/X0T4-9940", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:1086", "collection": "thesis", "collection_id": "1086", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03242003-111426", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 15104657, "license": "other", "mime_type": "application/pdf", "url": "/1086/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Protein-Ligand Interactions: Docking, Design and Conformation Change", "author": [ { "family_name": "Datta", "given_name": "Deepshikha", "clpid": "Datta-Deepshikha" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Roberts", "given_name": "Richard W.", "orcid": "0000-0002-8587-5097", "clpid": "Roberts-R-W" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Virtual ligand screening has proven to be a successful strategy in drug design. An in house-developed procedure (HierDock), a coarse grain docking method followed by a fine grain search procedure, was used to determine the binding site for sugars in the outer membrane protein A in E.coli, a key interaction in the pathogenesis of neonatal meningitis. These results are being further extended in suggesting possible peptide antagonists and drugs for therapeutic strategies.
\r\n\r\nPrediction of binding site of ligands in proteins, starting with the apo-protein is one of the challenges in the field of virtual ligand screening. HeirDock was modified for accurately predicting the ligand binding sites in apo-proteins that undergoes significant structural changes on binding to a ligand. The method was evaluated for finding the binding site for methionine in methionyl tRNA synthetase. We followed up on our understanding of binding mechanism in aminoacyl tRNA synthetases by attempting to design these enzymes to bind to non-natural amino acids. Using the computational protein design software (ORBIT), a phenylalanyl-tRNA synthetase variant that allows efficient in vivo incorporation of aryl ketone functionality into proteins was designed.
\r\n\r\nLigand-induced conformation changes are commonly seen in proteins. We have developed a procedure by combining computational protein design with methods from mean-field theory to design protein sequences capable of switching between two completely different protein folds on chelating to metal. This method is potentially useful in characterizing protein sequence-structure relationships.
", "doi": "10.7907/36FS-2262", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:2237", "collection": "thesis", "collection_id": "2237", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05292003-165018", "primary_object_url": { "basename": "chapter_0.pdf", "content": "final", "filesize": 12494, "license": "other", "mime_type": "application/pdf", "url": "/2237/1/chapter_0.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Molecular Dynamics Studies of Metallic Glasses", "author": [ { "family_name": "Lee", "given_name": "Hyon-Jee", "clpid": "Lee-Hyon-Jee" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Ustundag", "given_name": "Ersan", "clpid": "Ustundag-E" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The thermodynamic, structural, and mechanical properties of metallic glasses are studied using molecular dynamics simulations. Molecular dynamics provides a computational framework to simulate the movement of interacting atoms in response to external perturbations, such as changes in temperature or pressure. In this thesis, a Sutton-Chen potential was chosen to describe the many-body interactions in metals and alloys. Our first application for this approach is to develop a simple model to derive the thermodynamic properties of metallic alloys (Chapter 2). Based on this model, we demonstrate that the glass transition is thermodynamically sensitive to differences between atomic radii and that there is an optimal difference for glass formation. Next, we extend these simulations to elucidate the details of structural organization in the glass (Chapter 3). We find that the liquid phase is characterized by a local five-fold symmetry, which becomes more prominent as the glass phase forms. This five-fold symmetry is related to the formation of icosahedral structures. The mechanical properties of glasses are also investigated and it is found that shear localization, which accompanies a sharp drop in the stress-strain curve, occurs at 45 degree with respect to the loading axis (Chapter 4). The generation of free volume is found to be the dominant mechanism that leads to shear localization, rather than adiabatic heating. Finally, generic first principle potentials are constructed to guide the experimental development of AlTiNi based metallic glasses (Chapter 5). Together, the results from these simulations improve our understanding of the thermodynamic, structural, and mechanical properties of metallic glasses and will aid computer-driven materials design.\r\n", "doi": "10.7907/ZE5V-VZ33", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:1302", "collection": "thesis", "collection_id": "1302", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04082003-142034", "primary_object_url": { "basename": "01tableofcontent.pdf", "content": "final", "filesize": 407220, "license": "other", "mime_type": "application/pdf", "url": "/1302/1/01tableofcontent.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Gallium and Chromium Corroles", "author": [ { "family_name": "Meier", "given_name": "Alexandre Edouard", "clpid": "Meier-Alexandre-Edouard" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Peters", "given_name": "Jonas C.", "clpid": "Peters-J-C" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We report on the synthesis and characterization of various chromium and gallium complexes of the corrole 1,5,15-trispentafluorophenylcorrole (tpfc)H3. We synthesized a chromium(V)oxo compound by reaction between (tpfc)H3 and Cr(CO)6 in refluxing toluene. Characterization of the compound via EPR and MS revealed a d1 metal species. Hyperfine splittings for the compound are A(53Cr) 1.64 mT, A(14N) 0.30 mT. Combined with the X-ray bond lengths (Cr-O, 1.545(2) \u00c5 Cr-N, 1.969/1.991 \u00c5 those data suggest that the stability of the Cr-O bond is mainly due to the strong N->Cr s donation. The compound (tpfc)Cr(O) provided the starting point for all other oxidation states we made and isolated.
\r\n\r\nBy treatment with dioxinium hexachloroantimonate we were able to form the ligand radical chromium(V) oxo species, which was shown by EPR to be in its triplet ground state. By treatment with cobaltocene, we were able to isolate the chromium(IV) oxo species, which was proven diamagnetic via NMR. Reaction with phosphines, gave rise to the chromium(III) species, which is hexa-coordinated. The two axial ligands could be either pyridine, or triphenylphosphine oxide, and were readily exchanged with one another.
\r\n\r\n\r\nThe reactivity of (tpfc)Cr(O) was found to be quite low, exhibiting a rate constant of 9.7 M-1s-1 for reaction with triphenylphosphine. The chromium(III) counterpart was readily reoxidized in air, with a mechanism involving a five coordinate intermediate as the reactive species.
\r\n\r\n\r\nIn a bid to increase reactivity, we examined the effect of bromination at the b position on reactivity. To ascertain the electronic effects, we prepared a series of gallium corroles with various degrees of bromination. After characterization via MS and 2D NMR, electrochemical as well as UV-Vis measurements demonstrated that there is little steric deformation of the ligand framework upon increased bromination, which leads to a maximum of activity at maximum bromination.
\r\n\r\n\r\nWe then successfully prepared the octabromo chromium corrole (Br8-tpfc)Cr(py)2. The oxidized compound (Br8-tpfc)Cr(O) was indeed reactive enough to oxidize various styrenes, albeit slowly (rates in the range:4.1?10-5-62 ?10-5 M-1 s-1). More surprisingly, the chromium(III) counterpart was found to oxidize in air, back to the oxo. The reoxidation is painfully slow, due in part to the difficulty in dissociating an axial ligand, and part to the low reactivity of the five-coordinate species. To speed up the reoxidation, we switched to adding TFA to (Br8-tpfc)Cr(py)2, in a bid to drive the ligand dissociation via trapping of the free pyridine.
\r\n\r\n\r\nThe presence of an acid indeed leads to dramatically improved rates of air reoxidation of the compound, but at the same time, TFA was shown to play a non-innocent role in the process. We then proceeded to get rid of all the axial ligands altogether by treating the compound with HCl. The compound obtained displayed catalytic activity in the oxygenation of styrenes (~10 turnovers). The low turnover is due to product inhibition of the catalyst.
", "doi": "10.7907/JAKV-8V97", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:398", "collection": "thesis", "collection_id": "398", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01292003-150309", "primary_object_url": { "basename": "Final4.pdf", "content": "final", "filesize": 6445713, "license": "other", "mime_type": "application/pdf", "url": "/398/1/Final4.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Superprotonic Phase Transitions in Solid Acids: Parameters Affecting the Presence and Stability of Superprotonic Transitions in the MH\u2099XO\u2084 Family of Compounds (X=S,Se,P,As; M=Li,Na,K,NH\u2084,Rb,Cs)", "author": [ { "family_name": "Chisholm", "given_name": "Calum Ronald Inneas", "clpid": "Chisholm-Calum-Ronald-Inneas" } ], "thesis_advisor": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" } ], "thesis_committee": [ { "family_name": "Haile", "given_name": "Sossina M.", "clpid": "Haile-S-M" }, { "family_name": "Ustundag", "given_name": "Ersan", "clpid": "Ustundag-E" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The present work attempted to uncover the structural and chemical parameters that favor superprotonic phase transitions over melting or decomposition in the MHXO\u2084, MH\u2082ZO\u2084, and mixed MHXO\u2084-MH\u2082ZO\u2084 classes of compounds (X=S, Se; Z=P, As; M=Li, Na, K, NH\u2084, Rb, Cs) and to thereby gain some ability to \"engineer\" the properties of solid acids for applications. Three approaches are described. First, the general observation that larger cations enable superprotonic transitions was investigated in both the isostructural M\u2082(HSO\u2084)(H\u2082PO\u2084) and non-isostructural MHSO\u2084 family of compounds. The results of these studies confirmed and explained such a cation size effect, and also supplied a crystal-chemical measure for determining the likelihood of a compound undergoing a phase transition. Second, the entropic driving force behind the transitions was explored in the mixed CsHSO\u2084-CsH\u2082PO\u2084 system of compounds. From these investigations, a general set of rules for calculating the entropy change of a superprotonic transition was established and the role of entropy in the transitions illuminated. Finally, the superprotonic phase transition of CsHSO4 was simulated by molecular dynamics, with which means the transition was probed in ways not possible through experimental methods. A sufficiently general approach was utilized so as to be applicable to other (as yet un-synthesized) compounds, thereby speeding up the process of discovering novel superprotonic solid acids. All three approaches increase the fundamental understanding of which chemical/structural features facilitate superprotonic transitions and should aid attempts to create new solid acids with properties ideal for application.", "doi": "10.7907/FYTW-7G64", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:748", "collection": "thesis", "collection_id": "748", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02252003-134943", "primary_object_url": { "basename": "david_randall_kent_iv-dissertation.pdf", "content": "final", "filesize": 627928, "license": "other", "mime_type": "application/pdf", "url": "/748/1/david_randall_kent_iv-dissertation.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "New Quantum Monte Carlo Algorithms to Efficiently Utilize Massively Parallel Computers", "author": [ { "family_name": "Kent", "given_name": "David Randall, IV", "clpid": "Kent-David-Randall-IV" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "clpid": "Blake-G-A" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Bruck", "given_name": "Jehoshua", "clpid": "Bruck-J" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The exponential growth in computer power over the past few decades has been a huge boon to computational chemistry, physics, biology, and materials science. Now, a standard workstation or Linux cluster can calculate semi-quantitative properties of moderately sized systems. The next step in computational science is developing better algorithms which allow quantitative calculations of a system's properties.
\r\n\r\nA relatively new class of algorithms, known collectively as Quantum Monte Carlo (QMC), has the potential to quantitatively calculate the properties of molecular systems. Furthermore, QMC scales as O(N\u00b3) or better. This makes possible very high-level calculations on systems that are too large to be examined using standard high-level methods.
\r\n\r\nThis thesis develops (1) an efficient algorithm for determining \"on-the-fly\" the statistical error in serially correlated data, (2) a manager-worker parallelization algorithm for QMC that allows calculations to run on heterogeneous parallel computers and computational grids, (3) a robust algorithm for optimizing Jastrow functions which have singularities for some parameter values, and (4) a proof-of-concept demonstrating that it is possible to find transferable parameter sets for large classes of compounds.
", "doi": "10.7907/V64A-V618", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:5036", "collection": "thesis", "collection_id": "5036", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12182002-190040", "primary_object_url": { "basename": "zhangdq-thesis.pdf", "content": "final", "filesize": 6745389, "license": "other", "mime_type": "application/pdf", "url": "/5036/1/zhangdq-thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Structure-Based Design of Mutant Proteins: I. Molecular Docking Studies of Amino Acid Binding to Wild-Type Aminoacyl-tRNA Synthetases. II. Structure-Based Design of Mutant Aminoacyl-tRNA Synthetases for Non-Natural Amino Acid Incorporation", "author": [ { "family_name": "Zhang", "given_name": "Deqiang", "clpid": "Zhang-Deqiang" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Roberts", "given_name": "Richard W.", "clpid": "Roberts-R-W" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Chan", "given_name": "Sunney I.", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Protein biosynthesis has precisely controlled accuracy, and aminoacyl-tRNA synthetases (AARSs) play an important role in charging amino acids to their cognate tRNAs with high fidelity. In some cases the misactivation of non-natural amino acids by the wild-type or mutant AARS can be utilized to incorporate these non-natural amino acids into proteins in vivo. Such technique has tremendous potentials in protein engineering and other applications. Therefore, it is essential to understand the amino acid recognition mechanism displayed by AARSs.
\r\n\r\nIn this thesis, computational studies of the selection of natural and non-natural amino acids by AARSs at the binding stage have been conducted for methionyl-tRNA synthetase (Chapter 2), histidyl-tRNA synthetases (Chapter 3), and isoleucyl-tRNA synthetase (Chapter 4). In these chapters, molecular docking and ligand perturbation are used to elucidate the binding discrimination showed by these AARSs.
\r\n\r\nBecause many non-natural amino acids carrying interesting physical and chemical properties on their side chains cannot be incorporated by using the wild-type AARSs, it is necessary to manipulate the activity of AARSs by making mutations in the binding site of amino acids. To this end, we have developed a Clash Opportunity Progressive (COP) protein design tool to redesign the binding site of AARSs. Chapter 5 describes the main steps in COP. Chapters 6 to 8 present the application of COP to different AARSs. In Chapter 6, COP has been applied to design mutant tyrosyl-tRNA synthetase (TyrRS) for recognizing Ome-Tyr, Naph-Ala, and p-keto-Tyr. In Chapter 7, COP has been used to design mutant phenylalanyl-tRNA synthetase for p-keto-Phe. In Chapter 8, tryptophanyl-tRNA synthetase is used as a template to design mutant AARS to recognize NBD-Ala, bpy-Ala, and DAN-Ala.
\r\n\r\nThe appendices are some publications and manuscripts on various other projects. Appendix I is a molecular dynamics study of laboratory-evolved pNBE enzymes with different thermostability. The findings presented here will help us to better understand the determinants in protein stability evolution. Appendix II contains experimental work I have done in the Chan group. Unfolding experiments revealed the existence of intermediates in the equilibration unfolding of RdPf. In Appendix III, femtosecond time-resolved spectroscopy was used to study the fluorescence resonance energy transfer and tryptophan solvation dynamics in RdPf.
", "doi": "10.7907/CN3G-JH45", "publication_date": "2003", "thesis_type": "phd", "thesis_year": "2003" }, { "id": "thesis:6344", "collection": "thesis", "collection_id": "6344", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04212011-075629318", "primary_object_url": { "basename": "Sobrero_ac_2002.pdf", "content": "final", "filesize": 27921469, "license": "other", "mime_type": "application/pdf", "url": "/6344/1/Sobrero_ac_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Surface Structure Determination by Low-Energy Electron Diffraction", "author": [ { "family_name": "Sobrero", "given_name": "Aquiles Carlos", "clpid": "Sobrero-Aquiles-Carlos" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Four aspects of low-energy electron diffraction (LEED) have been investigated: interpretation of spot patterns to determine the surface unit cell and possible ambiguities, development of a photographic method for measuring angles of incidence and determining alignment of the LEED instrument, study of reliability factors used for intensity analysis, and justification for equivalent beam averaging.
\r\n\r\nThe interpretation of LEED spot patterns to determine the geometry of the surface unit cell can be involved when there are several symmetrically equivalent structural domains contributing to the pattern. Complex patterns can be deciphered by the algorithm described in Chapter II. The algorithm determines a surface unit cell that is often unique but not always, as where a p(2 x 2) pattern from a fcc(111) surface can be produced by a true (2 x 2) overlayer or by three domains of a (2 x 1) structure. This ambiguity arises on surfaces with 6m symmetry, such as fcc(111) and hcp(0001), for spot patterns with threefold rotational symmetry.
\r\n\r\nIn Chapter III, a broadly applicable photographic method for measuring angles of incidence and determining the alignment of the LEED instruments is described. Two published methods for determining the angle of incidence are special cases of this general procedure. The procedure extends the photographic methods and facilitates the verification of the alignment of the components of the LEED instrument.
\r\n\r\nReliability factors are used to evaluate correspondence between computed and observed LEED intensity spectra. Zanazzi and Jona, Pendry, and Sobrero and Weinberg have proposed reliability factors that are examined in Chapter IV. Chapter V provides a theoretical analysis and shows that averaging over momentum space gives the best resolution of the surface structure while energy averaging smears out information in the intensity spectra.
\r\n\r\nChapter VI provides a theoretical basis for the procedure of equivalent beam averaging, which provides a first-order correction to LEED intensities for systematic error due to angular misalignment of the incident beam and corrects for misorientation (where the actual surface plane is at a slight angle to the desired crystal plane). The potential of higher-order corrections is discussed.
", "doi": "10.7907/9b54-km20", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:6344", "collection": "thesis", "collection_id": "6344", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04212011-075629318", "primary_object_url": { "basename": "Sobrero_ac_2002.pdf", "content": "final", "filesize": 27921469, "license": "other", "mime_type": "application/pdf", "url": "/6344/1/Sobrero_ac_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Surface Structure Determination by Low-Energy Electron Diffraction", "author": [ { "family_name": "Sobrero", "given_name": "Aquiles Carlos", "clpid": "Sobrero-Aquiles-Carlos" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Seinfeld", "given_name": "John H.", "orcid": "0000-0003-1344-4068", "clpid": "Seinfeld-J-H" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Four aspects of low-energy electron diffraction (LEED) have been investigated: interpretation of spot patterns to determine the surface unit cell and possible ambiguities, development of a photographic method for measuring angles of incidence and determining alignment of the LEED instrument, study of reliability factors used for intensity analysis, and justification for equivalent beam averaging.
\r\n\r\nThe interpretation of LEED spot patterns to determine the geometry of the surface unit cell can be involved when there are several symmetrically equivalent structural domains contributing to the pattern. Complex patterns can be deciphered by the algorithm described in Chapter II. The algorithm determines a surface unit cell that is often unique but not always, as where a p(2 x 2) pattern from a fcc(111) surface can be produced by a true (2 x 2) overlayer or by three domains of a (2 x 1) structure. This ambiguity arises on surfaces with 6m symmetry, such as fcc(111) and hcp(0001), for spot patterns with threefold rotational symmetry.
\r\n\r\nIn Chapter III, a broadly applicable photographic method for measuring angles of incidence and determining the alignment of the LEED instruments is described. Two published methods for determining the angle of incidence are special cases of this general procedure. The procedure extends the photographic methods and facilitates the verification of the alignment of the components of the LEED instrument.
\r\n\r\nReliability factors are used to evaluate correspondence between computed and observed LEED intensity spectra. Zanazzi and Jona, Pendry, and Sobrero and Weinberg have proposed reliability factors that are examined in Chapter IV. Chapter V provides a theoretical analysis and shows that averaging over momentum space gives the best resolution of the surface structure while energy averaging smears out information in the intensity spectra.
\r\n\r\nChapter VI provides a theoretical basis for the procedure of equivalent beam averaging, which provides a first-order correction to LEED intensities for systematic error due to angular misalignment of the incident beam and corrects for misorientation (where the actual surface plane is at a slight angle to the desired crystal plane). The potential of higher-order corrections is discussed.
", "doi": "10.7907/9b54-km20", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:6777", "collection": "thesis", "collection_id": "6777", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01252012-135136531", "primary_object_url": { "basename": "Feldmann_mt_2002.pdf", "content": "final", "filesize": 53221379, "license": "other", "mime_type": "application/pdf", "url": "/6777/1/Feldmann_mt_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Quantum Monte Carlo: Quest to Get Bigger, Faster, and Cheaper", "author": [ { "family_name": "Feldmann", "given_name": "Michael Todd", "clpid": "Feldmann-Michael-Todd" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Bruck", "given_name": "Jehoshua", "orcid": "0000-0001-8474-0812", "clpid": "Bruck-J" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We reexamine some fundamental Quantum Monte Carlo (QMC) algorithms with the goal of making QMC more mainstream and efficient. Two major themes exist: (1) Make QMC faster and cheaper, and (2) Make QMC more robust and easier to use. A fast \"on-the-fly\" algorithm to extract uncorrelated estimators from serially correlated data on a huge network is presented, DDDA. A very efficient manager-worker algorithm for QMC parallelization is presented, QMC-MW. Reduced expense VMC optimization procedure is presented to better guess initial Jast row parameter sets for hydrocarbons, GJ. I also examine the formation and decomposition of aminomethanol using a variety of methods including a test of the hydrocarbon GJ set on these oxygen- and nitrogen-containing systems. The QMC program suite QMcBeaver is available from the authors in its entirety while a user's and developer's manual is attached as supplementary material.", "doi": "10.7907/4D4F-WZ34", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:6777", "collection": "thesis", "collection_id": "6777", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01252012-135136531", "primary_object_url": { "basename": "Feldmann_mt_2002.pdf", "content": "final", "filesize": 53221379, "license": "other", "mime_type": "application/pdf", "url": "/6777/1/Feldmann_mt_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Quantum Monte Carlo: Quest to Get Bigger, Faster, and Cheaper", "author": [ { "family_name": "Feldmann", "given_name": "Michael Todd", "clpid": "Feldmann-Michael-Todd" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Bruck", "given_name": "Jehoshua", "orcid": "0000-0001-8474-0812", "clpid": "Bruck-J" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Pierce", "given_name": "Niles A.", "orcid": "0000-0003-2367-4406", "clpid": "Pierce-N-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We reexamine some fundamental Quantum Monte Carlo (QMC) algorithms with the goal of making QMC more mainstream and efficient. Two major themes exist: (1) Make QMC faster and cheaper, and (2) Make QMC more robust and easier to use. A fast \"on-the-fly\" algorithm to extract uncorrelated estimators from serially correlated data on a huge network is presented, DDDA. A very efficient manager-worker algorithm for QMC parallelization is presented, QMC-MW. Reduced expense VMC optimization procedure is presented to better guess initial Jast row parameter sets for hydrocarbons, GJ. I also examine the formation and decomposition of aminomethanol using a variety of methods including a test of the hydrocarbon GJ set on these oxygen- and nitrogen-containing systems. The QMC program suite QMcBeaver is available from the authors in its entirety while a user's and developer's manual is attached as supplementary material.", "doi": "10.7907/4D4F-WZ34", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:5145", "collection": "thesis", "collection_id": "5145", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12272005-154952", "primary_object_url": { "basename": "Bogdanoff_pd_2002.pdf", "content": "final", "filesize": 4489294, "license": "other", "mime_type": "application/pdf", "url": "/5145/1/Bogdanoff_pd_2002.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Phonon Entropy of Metals and Alloys: The Effects of Thermal and Chemical Disorder", "author": [ { "family_name": "Bogdanoff", "given_name": "Peter David", "clpid": "Bogdanoff-Peter-David" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Haile", "given_name": "Sossina M.", "orcid": "0000-0002-5293-6252", "clpid": "Haile-S-M" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Phillips", "given_name": "Robert B.", "orcid": "0000-0003-3082-2809", "clpid": "Phillips-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Vibrational entropy is important for the thermodynamics of alloying, alloy formation, phase transitions and phase stability at high temperature. Vibrational entropies of alloying and alloy formation were calculated for 32 binary alloys and intermetallic compounds using phonon DOS curves taken from the literature. The vibrational entropies of formation span a wide range from -0.64 to +0.55 kB/atom, and the vibrational entropies of alloying ranged from -0.39 to +1.0 kB/atom. This range exceeds the range of configurational entropy of a binary alloy, which reaches a maximum value of +0.69 kB/atom and a minimum value of 0 kB/atom.
\r\n\r\nThe vibrational entropy of the NiTi martensitic transition was measured using low-temperature calorimetry and inelastic neutron-scattering. The high-temperature B2 phase of NiTi has a vibrational entropy 0.5 kB/atom larger than the low-temperature martensitic phase. The difference in vibrational entropy accounts for the total entropy of the austenitic-martensitic phase transition.
\r\n\r\nInelastic neutron scattering was used to show that the phonon DOS of V is unchanged between 20 and 1000\u00b0C, inconsistent with the phonon softening expected from thermal expansion. It is found that the effects of volume expansion and rising temperature exert equal and opposite shifts on the phonon DOS. The pure temperature dependence of the phonon DOS is due to strong phonon-phonon scattering, which in turn leads to a large anharmonic vibrational entropy contribution at high temperature.
\r\n\r\nThe vibrational entropy of eight chemically disordered Cu-Au alloys was measured using inelastic neutron scattering. The analysis of the phonon entropy of a disordered alloy was performed in a novel way by modeling the partial vibrational entropies of Cu and Au. The partial vibrational entropies of Cu and Au were shown to be slowly varying and smooth functions of composition. The vibrational entropy of disordering in Cu3Au is calculated as 0.24 \u00b1 0.02 kB/atom, substantially larger than results predicted from recent theoretical work.
", "doi": "10.7907/045G-6426", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:5374", "collection": "thesis", "collection_id": "5374", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-112545862", "type": "thesis", "title": "First Principles Based Multiscale Modeling of Single Crystal Plasticity: Application to BCC Tantalum", "author": [ { "family_name": "Wang", "given_name": "Guofeng", "orcid": "0000-0001-8249-4101", "clpid": "Wang-Guofeng" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Cagin", "given_name": "Tahir", "clpid": "Cagin-Tahir" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Haile", "given_name": "Sossina M.", "orcid": "0000-0002-5293-6252", "clpid": "Haile-S-M" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "In principle, the macroscopic plasticity properties of crystalline materials are derivable from the physical processes involving dislocations and interactions between dislocations with other defects. However, a quantitative theory of plasticity based on the dislocation mechanism requires crossing multiple length and time scales. To accommodate these requirements, we developed a multiscale approach for modeling crystalline solids. In this thesis, to establish the connections between simulations in different length and time scales, I mainly focus on identifying and determining the importance and influence of various unit processes involving the dislocations through atomic level simulations. These unit processes in turn play a major role in modeling the single crystal plasticity.
\r\n\r\nKey Results from Atomistic Simulations
\r\n\r\nDislocation core structure and core energy: Using the first-principles qEAM force field (FF), we determine the core energy for 1/2a<111> screw dislocation and 1/2a<111> edge dislocation in bcc Ta. We find that the core energy of edge dislocation is 1.77 times higher than that of screw dislocation. This ratio (1.77) is a fundamental material property used as input to the macroscopic model. Furthermore, we find that the central 12 atoms closest to the 1/2a<111> screw dislocation line have distinguishably higher atomistic strain energy than the other atoms. Thus, we arrive at a physical definition of dislocation core.
\r\n\r\nScrew dislocation mobility: In this thesis, we proposed a new method to investigate dislocation mobility by analyzing the process of migration of a screw dislocation dipole. The new method is based on the energy distribution at the atomistic scale and is used to calculate the Peierls potential barrier and Peierls stress for dislocation continuous motion. The calculated Peierls stress is in good agreement with results obtained using other method. Simulating dislocation motion at finite temperatures (from 20 K to 300 K), we find that the activation energy for dislocation motion is about 6 times lower than computed at 0.001 K. Our results suggest that the decrease in the correlation between neighboring segments in the dislocation line accounts for the decrease of activation energy. We observe that the formation of kink pair along the dislocation line enhances the dislocation mobility. This verifies the traditional belief that the screw dislocation in bcc metals moves by first kink pair nucleation and subsequently lateral movements of kinks along the dislocation.
\r\n\r\nKinks in screw dislocations: To bridge the atomistic process of dislocation motion with continuum model, we accurately calculate the material properties, such as kink pair formation energy and effective kink pair length, using atomic level simulations. In detailed structural analysis, we discover the substructures of different kinks when the screw dislocation core is asymmetric. There are only two kinds of elementary kinks in the dislocation and the others are the composite kinks consisting of an elementary kink and one or two flips. Based on these findings, we further explain the observed trend of the formation energy and mobility of different classes of kinks. (Note: Similar trend and conclusion could have been found in earlier studies but not mentioned by the authors of those papers.)
\r\n\r\nIn summary, we have used quantum mechanics based interaction potentials to investigate the unit processes that play important role in single crystal plasticity and verified the findings using the quantitative results obtained from the atomic level simulation in a macroscopic model for single crystal plasticity.
", "doi": "10.7907/5nyn-ct36", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:330", "collection": "thesis", "collection_id": "330", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01252002-100801", "primary_object_url": { "basename": "bolon_thesis.pdf", "content": "final", "filesize": 4053155, "license": "other", "mime_type": "application/pdf", "url": "/330/1/bolon_thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computational Enzyme Design", "author": [ { "family_name": "Bolon", "given_name": "Daniel N.", "orcid": "0000-0001-5857-6676", "clpid": "Bolon-Daniel-N" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The long-term objective of computational enzyme design is the ability to generate efficient protein catalysts for any chemical reaction. This thesis develops and experimentally validates a general computational approach for the design of enzymes with novel function.
\r\n \r\nIn order to include catalytic mechanism in protein design, a high-energy state (HES) rotamer (side chain representation) was constructed. In this rotamer, substrate atoms are in a HES. In addition, at least one amino acid side chain is positioned to interact favorably with substrate atoms in their HES and facilitate the reaction. Including an amino acid side chain in the HES rotamer automatically positions substrate relative to a protein scaffold and allows protein design algorithms to search for sequences capable of interacting favorably with the substrate. Because chemical similarity exists between the transition state and the high-energy state, optimizing the protein sequence to interact favorably with the HES rotamer should lead to transition state stabilization. In addition, the HES rotamer model focuses the subsequent computational active site design on a relevant phase space where an amino acid is capable of interacting in a catalytically active geometry with substrate.
\r\n\r\nUsing a HES rotamer model of the histidine mediated nucleophilic hydrolysis of p-nitrophenyl acetate, the catalytically inert 108 residue E. coli thioredoxin as a scaffold, and the ORBIT protein design software to compute sequences, an active site scan identified two promising active site designs. Experimentally, both candidate ?protozymes? demonstrated catalytic activity significantly above background. In addition, the rate enhancement of one of these ?protozymes? was the same order of magnitude as the first catalytic antibodies.
\r\n\r\nBecause polar groups are frequently buried at enzyme-substrate interfaces, improved modeling of buried polar interactions may benefit enzyme design. By studying native protein structures, rules have been developed within the scope of protein design that require core polar residues to largely satisfy their hydrogen bonding potential. Using this polar strategy to design the core of thioredoxin resulted in a protein that was thermodynamically stabilized relative to both the wt protein and a protein designed without core polar residues.
\r\n\r\nThe enzyme design procedures presented here may serve as a platform to develop more detailed methods. It is hoped that the development and experimental testing of more detailed methods will continue to improve our understanding of enzyme mechanism and lead to the long-term goal of designing highly efficient enzymes.
", "doi": "10.7907/W7F3-DS14", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:6971", "collection": "thesis", "collection_id": "6971", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04252012-084159781", "primary_object_url": { "basename": "Amashukeli_x_2002.pdf", "content": "final", "filesize": 33072066, "license": "other", "mime_type": "application/pdf", "url": "/6971/1/Amashukeli_x_2002.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Electron-Transfer Reorganization Energies of Isolated Molecules", "author": [ { "family_name": "Amashukeli", "given_name": "Xenia", "clpid": "Amashukeli-Xenia" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Winkler", "given_name": "Jay Richmond", "orcid": "0000-0002-4453-9716", "clpid": "Winkler-J-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Electron-transferreorganization energies of isolated organic molecules and biologically relevant porphyrins are obtained from analyses of their photoelectron spectra. The\r\nassignments of experimental ionization energies are aided by ab initio calculations, and comparisons between He I and He II ionization data. It is established that in unsymmetrically substituted metalloporphyrins, i.e., Zn(II) protoporphyrin IX, the highest occupied molecular orbital has appreciable nitrogen character (Chapter 3).Quantum-mechanical and semiclassical analyses of vibrational progressions observed in photoelectron spectra yield\r\ngas-phase reorganization energies. Favorable agreement is reached between experimental and calculated values of reorganization energies (Chapters 2 and 3). This observation is not surprising, however, since density functional theory calculations, employed in this thesis, are successful at reproducing experimental molecular geometries. Indeed, X-ray structural parameters of dibenzo[a,c]phenazine are in excellent agreement with calculated results (Chapter 6). Vibrational frequencies of organic molecules are also calculated (Chapter 5) to aid mode-specific quantum mechanical analyses of fine structure observed in photoelectron spectra. Given the success of ab initio calculations of reorganization energies of organic\r\nmolecules, the same computational approach is employed to obtain reorganization energies of six-coordinate metalloporphyrin model systems (Chapter 4). The results show that large reorganization energies are associated with charged ligands, which are most frequently found in protein redox catalytic sites; small reorganization energies, on the other hand, are calculated for the molecules with neutral ligands, commonly located in the protein active\r\nsites that facilitate electron transfer.
\r\n", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:1277", "collection": "thesis", "collection_id": "1277", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04062005-082441", "primary_object_url": { "basename": "Zamanakos_g_2002.pdf", "content": "final", "filesize": 12924872, "license": "other", "mime_type": "application/pdf", "url": "/1277/1/Zamanakos_g_2002.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Fast and Accurate Analytical Method for the Computation of Solvent Effects in Molecular Simulations", "author": [ { "family_name": "Zamanakos", "given_name": "Georgios", "clpid": "Zamanakos-Georgios" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Barr", "given_name": "Alan H.", "clpid": "Barr-A-H" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Quake", "given_name": "Stephen R.", "orcid": "0000-0002-1613-0809", "clpid": "Quake-S-R" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "The solvent environment of molecules plays a very important role in their structure and function. In biological systems it is well known that water has profound effects in the functions of proteins. Simulations assist us in microscopic studies of chemical and biological phenomena. It is important then to include solvation effects accurately and efficiently in molecular simulations. In this work we present a novel approximate analytical method for calculating the solvation energy for every atom of a molecular system and the forces that act on each atom because of the solvent. The solvation energy is partitioned into long-range and short-range contributions. The longrange contributions are due to polar interactions between the solvent and the solute and the short-range are due to van der Waals and entropic effects. We show how the calculation of these effects, under certain approximations, can be reduced to the calculation of the volume and exposed area of each atom, assuming a fused-sphere model for the solute. We demonstrate a fast method for the exact, analytical calculation of the volume and area of each atom in the fused-sphere model and their gradients with respect to the atom's position. We incorporate the fast geometric algorithms into the approximate formulas we derived for the calculation of the solvation energy, to get our solvation model, the Analytical Volume Generalized Born - Solvent Accessible Surface (AVGBSAS) model.
\r\n\r\nThe predictions of the polar part of the method (AVGB) are very good as compared to numerical solutions of the underlying physical model, the Poisson-Boltzman equation, for small and large molecular systems. AVGB does not depend on any fitting parameters, which is common in the literature for such approximate methods. It is very fast compared to numerical solutions of the PB equation or other Generalized Born methods. Also, the method is parallelizable which allows us to study much larger systems. The AVGB-SAS method has been implemented in a parallel molecular dynamics software package and a molecular docking software package. We have demonstrated the quality of the results of the AVGB-SAS model in the dynamics of DNA and in rational drug design applications.
", "doi": "10.7907/B7W8-N760", "publication_date": "2002", "thesis_type": "phd", "thesis_year": "2002" }, { "id": "thesis:5372", "collection": "thesis", "collection_id": "5372", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-154318044", "primary_object_url": { "basename": "Debe_da_2001.pdf", "content": "final", "filesize": 6323465, "license": "other", "mime_type": "application/pdf", "url": "/5372/1/Debe_da_2001.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Shaving Levinthal with Occam's Razor: Understanding the Rate Limiting Step in Protein Folding", "author": [ { "family_name": "Debe", "given_name": "Derek Anthony", "clpid": "Debe-Derek-Anthony" } ], "thesis_advisor": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "How do proteins fold? This thesis addresses this simple yet important question by developing a first principles theoretical framework that accurately describes the experimentally observed protein folding rate data. The success of the new theory suggests that single domain proteins fold according two a two- state mechanism consisting of
\r\n(i)\ta random, diffusive search for the native topology, followed by
\r\n(ii)\tnon-random, local conformation changes within the native topology to find the unique native state.
In chapter 1, a popular analogy between protein folding and the game of golf is used to qualitatively illustrate the most important aspects of the new theory. In chapter 2, mean-field computational methods are developed that allow the time involved in the rate limiting diffusive search for the native state to be calculated. Chapters 3 and 4 remove the mean-field restriction from the methods of chapter 2, allowing the folding rate for an arbitrary two-state folding protein to be calculated. Chapter 5 then explores how real proteins deviate from this ideal model by examining the roles that non-random mechanisms such as helix, hydrophobic core, and 13-turn formation play in the early folding process. Finally, chapter 6 develops an empirical model that also capably predicts protein folding rates, adding further support to the proposed folding mechanism.
", "doi": "10.7907/p4yc-y834", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:1979", "collection": "thesis", "collection_id": "1979", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05232006-094537", "primary_object_url": { "basename": "Szczepankiewicz_sh_2001.pdf", "content": "final", "filesize": 6977318, "license": "other", "mime_type": "application/pdf", "url": "/1979/1/Szczepankiewicz_sh_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Surface Chemistry of TiO\u2082 Photocatalysts", "author": [ { "family_name": "Szczepankiewicz", "given_name": "Steven Henry", "clpid": "Szczepankiewicz-Steven-Henry" } ], "thesis_advisor": [ { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The surface chemistry of TiO\u2082 photocatalysts have been characterized by infrared spectroscopy, alcalimetric titrations, and photocatalytic reactivity. The fundamental processes governing electron transfer at the surface were investigated by inhibiting the photocatalytic reactions.
\r\n\r\nFree and trapped charge carriers in polycrystalline TiO\u2082 following bandgap irradiation are characterized by diffuse reflectance IR spectroscopy (DRIFTS). Irradiation of anatase in vacuo or in the presence of CD\u2083OD leads to decreased overall reflectance, to an absorbance at 3717 cm\u207b\u00b9, and to the decline of a 3647 cm\u207b\u00b9 band. x persists for days in vacuum or dry O\u2082 and is only bleached by the action of [O\u2082 + H\u2082O(g) + hv]. It is assigned to a Ti(III)O-H vibration ensuing electron trapping at the acidic Ti(IV)OH centers that absorb at 3647 cm\u207b\u00b9. Irradiation under O\u2082 yields a band at 3683 cm\u207b\u00b9 (Y) that corresponds to bound OH radicals. These last indefinitely in vacuo, but decay in a few hours under O\u2082. Since none of the above phenomena occur on defective TiO\u2082-x, materials obtained by thermal annealing under vacuum, photochemical damage to actual catalysts involves concurrent surface reorganization. The presence of the 3717 cm\u207b\u00b9 band is used to confirm this reorganization.
\r\n\r\nThe decreased reflectivity is due to a spectrum-wide absorption signal proportional to \u03bb1.7 (\u03bb = wavelength/\u00b5m), which indicates the presence of free conduction band electrons coupled with acoustic phonons in the lattice. Free electrons appear to decay according to saturation kinetics. The fitted parameters indicate a limited number of reversible trapping states. The concentration of these states appears to be diminished by sequential UV treatments. A broad IR absorption peak centered at 3380 cm\u207b\u00b9 is attributed to an electronic transition from an occupied surface electron trap 0.42 eV below the conduction band. The free carrier decay lifetime is lengthened as the samples are dehydrated.
\r\n\r\nElectric fields generated by photoexcited charge carriers in TiO\u2082 (anatase) produce Stark effect intensity and wavelength shifts for surface TiO-H stretching vibrations. Shallow electron-trapping states, observed as broad absorption bands above 3000 cm\u207b\u00b9, produce an apparently homogeneous electric field. Intensity changes and corresponding wavelength shifts for v(TiO-H) are proportional to the magnitude and polarity of the electric field. O\u2082 is shown to reversibly abstract electrons from shallow trapping states. These results suggest that shallow electron traps are not associated with localized structures, but rather are delocalized across the TiO\u2082 surface.
\r\n\r\nThe effect of poisoning the photocatayst is monitored during the oxidation of a phosphorous-containing organic substrate. The photoassisted oxidation of dimethyl-methyl-phosphonate (DMMP) over UV-irradiated TiO\u2082 is investigated as a simulant for warfare nerve agent detoxification. Adsorption uptake measurements are performed by MS analysis of a fine DMMP aerosol up and downstream of an adsorbant TiO\u2082 film. Photodesorption processes, gas phase intermediates and mineral products are quantified in situ by headspace GC-MS analysis of a static system. Non-volatile intermediates and products are analyzed by HPLC analysis of both aqueous and organic extractions from the Ti02 film. Adsorbed intermediates are characterized and quantified in situ by DRIFTS of TiO\u2082 powders. Specific site binding of DMMIP and catalyst poisoning are observed in the DRIFT spectra. A proposed mechanism suggests rapid detoxification of DMMP as a simulant, but extensive poisoning of the catalyst by the end products.
\r\n\r\nIn a comparative investigation of titania surface chemistry, TiO\u2082 Q particles are synthesized and characterized by transmission electron microscopy, potentiometric titration, infrared analysis, and photocatalytic reactivity. TEM images show small individual particulates of anatase about 2 nm in diameter. Potentiometric titrations confirm the presence of a highly protonated gel layer on the surface of these particles. The infrared spectra indicate that this layer is amorphous. An autocatalytic enhancement of the photocatalysts during photooxidation of methyl orange suggests that reaction intermediates cause the collapse of the hydrated gel layer into a more active surface.
\r\n\r\nTwo supplementary investigations are presented which confirm the previous results. MAS NMR data is presented which shows a paramagnetic influence from surface trapped electrons. The data also suggests localized trapping at a characteristic type of TiOH surface moiety. Theoretical calculations also confirm the band assignments presented in the previous chapters by reproducing the data with the predicted structural assignments.
", "doi": "10.7907/HABJ-3T48", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:3597", "collection": "thesis", "collection_id": "3597", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09172008-112120", "primary_object_url": { "basename": "Qi_y_2001.pdf", "content": "final", "filesize": 10701193, "license": "other", "mime_type": "application/pdf", "url": "/3597/1/Qi_y_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Molecular dynamics (MD) studies on phase transformation and deformation behaviors in FCC metals and alloys", "author": [ { "family_name": "Qi", "given_name": "Yue", "clpid": "Qi-Yue" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Ortiz", "given_name": "Michael", "clpid": "Ortiz-M" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis focused on the phase transformation and deformation in face center cubic (FCC) metals and alloys. These studies use the new quantum modified Sutton-Chen (QMSC) many-body potentials for Cu, Ni, Ag, and Au and for their alloys through simple combination rules. Various systems and processes are simulated by standard equilibrium molecular dynamics (MD), quasi-static equilibrium MD and non-equilibrium MD (NEMD), cooperated with different periodic boundary conditions. The main topics and their outlines are listed as the following:\r\n\r\n1) Melting, glass formation, and crystallization processes in bulk alloys: Using cooling rates in the range of 2*10[superscript 12] to 4*10[superscript 14]K/s, we find that CuNi and pure Cu always form an FCC crystal while Cu[subscript 4]Ag[subscript 6] always forms a glass (with Tg decreasing as the quench rate increases), which confirms the role of size mismatch in glass formability and validates the accuracy of the force field.\r\n\r\n2) The size effects in melting and crystallization in Ni nano clusters, ranging 100 to 8007 atoms: We find a transition from cluster or molecular behavior below ~500 atoms to a mesoscale nanocrystal regime (with well-defined bulk and surface properties and surface melting processes, which leads to T[subscript m,N] = T[subscript m,bulk] - \u03b1 N[superscript -1/3]) above ~750 atoms. Cooling from the melt leads first to supercooled clusters with icosahedral local structure, then for N>500 the supercooled clusters transform to FCC grains, while clusters with N<500 form icosahedral structures.\r\n\r\n3) The deformation behavior of metallic nanowires of pure Ni, NiCu and NiAu alloys, under high rates of uniaxial tensile strain, ranging from 5*10[superscript 8]/s to 5*10[superscript 10]/s: These nanowires are too small to sustain dislocations; instead we find that deformation proceeds through twinning and coherent slipping mechanisms at low strain rate, and amorphization at high strain rate. We find that critical strain rate, beyond which the crystal transformed into glassy state, for NiAu (13% size mismatch) is 100 times slower than that for NiCu (2.5% size mismatch). Thus the critical strain rate also depends on the glass formability.\r\n\r\n4) The calculation of the 1/2<110> screw dislocation in nickel (Ni): From a quadrupolar dislocation system with 3-D periodic boundary conditions, we found the screw dislocation dissociated into two partials on {111} planes, and the core energy is 0.5 eV/b. We also studied motion and annihilation process of opposite signed dislocations with different configurations of dissociation planes. On two intersecting or parallel dissociation planes, a cross-slip process is captured and the energy barriers is 0.1eV/b in our simulations.\r\n\r\n5) Friction Anisotropy at Ni(100)/(100) interface: We carried out a series of NEMD simulations for sliding of Ni(100) interfaces under a constant force. We found that the clean, flat, and incommensurate interface has a very small static friction coefficient, as analytical theory predicted. However surface roughness can increase the static friction on the incommensurate interfaces dramatically, and increase the friction on the commensurate interfaces to a lesser extent. The dynamic frictional coefficients are comparable to the experimental values and show the same anisotropic behavior, thus explaining the difference between theory and experiment.\r\n", "doi": "10.7907/9NXP-E603", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:1979", "collection": "thesis", "collection_id": "1979", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05232006-094537", "primary_object_url": { "basename": "Szczepankiewicz_sh_2001.pdf", "content": "final", "filesize": 6977318, "license": "other", "mime_type": "application/pdf", "url": "/1979/1/Szczepankiewicz_sh_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Surface Chemistry of TiO\u2082 Photocatalysts", "author": [ { "family_name": "Szczepankiewicz", "given_name": "Steven Henry", "clpid": "Szczepankiewicz-Steven-Henry" } ], "thesis_advisor": [ { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The surface chemistry of TiO\u2082 photocatalysts have been characterized by infrared spectroscopy, alcalimetric titrations, and photocatalytic reactivity. The fundamental processes governing electron transfer at the surface were investigated by inhibiting the photocatalytic reactions.
\r\n\r\nFree and trapped charge carriers in polycrystalline TiO\u2082 following bandgap irradiation are characterized by diffuse reflectance IR spectroscopy (DRIFTS). Irradiation of anatase in vacuo or in the presence of CD\u2083OD leads to decreased overall reflectance, to an absorbance at 3717 cm\u207b\u00b9, and to the decline of a 3647 cm\u207b\u00b9 band. x persists for days in vacuum or dry O\u2082 and is only bleached by the action of [O\u2082 + H\u2082O(g) + hv]. It is assigned to a Ti(III)O-H vibration ensuing electron trapping at the acidic Ti(IV)OH centers that absorb at 3647 cm\u207b\u00b9. Irradiation under O\u2082 yields a band at 3683 cm\u207b\u00b9 (Y) that corresponds to bound OH radicals. These last indefinitely in vacuo, but decay in a few hours under O\u2082. Since none of the above phenomena occur on defective TiO\u2082-x, materials obtained by thermal annealing under vacuum, photochemical damage to actual catalysts involves concurrent surface reorganization. The presence of the 3717 cm\u207b\u00b9 band is used to confirm this reorganization.
\r\n\r\nThe decreased reflectivity is due to a spectrum-wide absorption signal proportional to \u03bb1.7 (\u03bb = wavelength/\u00b5m), which indicates the presence of free conduction band electrons coupled with acoustic phonons in the lattice. Free electrons appear to decay according to saturation kinetics. The fitted parameters indicate a limited number of reversible trapping states. The concentration of these states appears to be diminished by sequential UV treatments. A broad IR absorption peak centered at 3380 cm\u207b\u00b9 is attributed to an electronic transition from an occupied surface electron trap 0.42 eV below the conduction band. The free carrier decay lifetime is lengthened as the samples are dehydrated.
\r\n\r\nElectric fields generated by photoexcited charge carriers in TiO\u2082 (anatase) produce Stark effect intensity and wavelength shifts for surface TiO-H stretching vibrations. Shallow electron-trapping states, observed as broad absorption bands above 3000 cm\u207b\u00b9, produce an apparently homogeneous electric field. Intensity changes and corresponding wavelength shifts for v(TiO-H) are proportional to the magnitude and polarity of the electric field. O\u2082 is shown to reversibly abstract electrons from shallow trapping states. These results suggest that shallow electron traps are not associated with localized structures, but rather are delocalized across the TiO\u2082 surface.
\r\n\r\nThe effect of poisoning the photocatayst is monitored during the oxidation of a phosphorous-containing organic substrate. The photoassisted oxidation of dimethyl-methyl-phosphonate (DMMP) over UV-irradiated TiO\u2082 is investigated as a simulant for warfare nerve agent detoxification. Adsorption uptake measurements are performed by MS analysis of a fine DMMP aerosol up and downstream of an adsorbant TiO\u2082 film. Photodesorption processes, gas phase intermediates and mineral products are quantified in situ by headspace GC-MS analysis of a static system. Non-volatile intermediates and products are analyzed by HPLC analysis of both aqueous and organic extractions from the Ti02 film. Adsorbed intermediates are characterized and quantified in situ by DRIFTS of TiO\u2082 powders. Specific site binding of DMMIP and catalyst poisoning are observed in the DRIFT spectra. A proposed mechanism suggests rapid detoxification of DMMP as a simulant, but extensive poisoning of the catalyst by the end products.
\r\n\r\nIn a comparative investigation of titania surface chemistry, TiO\u2082 Q particles are synthesized and characterized by transmission electron microscopy, potentiometric titration, infrared analysis, and photocatalytic reactivity. TEM images show small individual particulates of anatase about 2 nm in diameter. Potentiometric titrations confirm the presence of a highly protonated gel layer on the surface of these particles. The infrared spectra indicate that this layer is amorphous. An autocatalytic enhancement of the photocatalysts during photooxidation of methyl orange suggests that reaction intermediates cause the collapse of the hydrated gel layer into a more active surface.
\r\n\r\nTwo supplementary investigations are presented which confirm the previous results. MAS NMR data is presented which shows a paramagnetic influence from surface trapped electrons. The data also suggests localized trapping at a characteristic type of TiOH surface moiety. Theoretical calculations also confirm the band assignments presented in the previous chapters by reproducing the data with the predicted structural assignments.
", "doi": "10.7907/HABJ-3T48", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:8137", "collection": "thesis", "collection_id": "8137", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03142014-154815404", "primary_object_url": { "basename": "Chang 2001.pdf", "content": "final", "filesize": 16564703, "license": "other", "mime_type": "application/pdf", "url": "/8137/1/Chang 2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Cleavage of DNA by Polamide-Seco-CB1 Conjugates", "author": [ { "family_name": "Chang", "given_name": "Aileen Yulin", "clpid": "Chang-Aileen-Yulin" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Small molecules that bind to any predetermined DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) N-methylpyrrole (Py) are cell permeable small molecules that bind DNA according to a set of \"pairing rules\" with affinities and specificities similar to many naturally occurring DNA binding proteins. Py-Im polyamides offer a general approach to the chemical regulation of gene expression. We demonstrate here that polyamide containing a DNA alkylating moiety seco-CBI can specifically direct sequence specific DNA alkylation. We can also control the strand of DNA that is alkylated, depending on the enantiomer of seco-CBI used and the orientation of the polyamide relative to the alkylation site (Chapter 2). This class of molecules has been applied to a gene repair system in collaboration with the Baltimore group at Caltech (Chapter 3). Also reported are additional seco-CBI polyamide conjugates synthesized to study other systems (HIV-1 and COX-2) (Appendix 1).\r\n", "doi": "10.7907/FY0F-DW57", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:6203", "collection": "thesis", "collection_id": "6203", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12142010-083329053", "primary_object_url": { "basename": "Manley_me_2001.pdf", "content": "final", "filesize": 6056869, "license": "other", "mime_type": "application/pdf", "url": "/6203/1/Manley_me_2001.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "From Elementary Excitations to Microstructures: the Thermodynamics of Metals and Alloys Across Length Scales", "author": [ { "family_name": "Manley", "given_name": "Michael Edward", "clpid": "Manley-Michael-Edward" } ], "thesis_advisor": [ { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Ortiz", "given_name": "Michael", "clpid": "Ortiz-M" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "An experimental investigation has been made into the components that determine the phase stability of metals and alloys. Contributions were found to be important across many length scales from electronic excitations to atomic vibrations and finally microstructural strains at the continuum level. The metals and alloy that have been studied are U, Ce, and Pd3V.
\r\n\r\nTime-of-flight (TOF) inelastic neutron scattering spectra were measured on the three crystalline phases of uranium at temperatures from 50 K to 1213 K. Phonon density of states (DOS) curves were obtained from these spectra. For the \u03b1-phase, a large decrease in phonon energies with increasing temperature was observed over the entire temperature range. Analysis of the vibrational power spectrum showed that the phonon softening originates with continuous softening of a harmonic solid, as opposed to vibrations in anharmonic potentials. Without anharmonicty, it must be that thermal excitations of the electronic structure are changing the interatomic forces. State-of-the-art electronic band structure calculations are based on the assumption that temperature effects on the electronic structure can be neglected when compared to volume effects (where the volume effects are just a manifestation of anharmonicity). The present results turn that problem upside down by showing that temperature effects are actually more important than volume effects. Vibrational entropies of the phase transitions were (S\u03b2-S\u03b1)vib = (0.15\u00b10.1) kB/atom and (S\u03b3 -S\u03b2)vib = (0.36\u00b10.1) kB/atom.The former accounts for about 35% and the latter 65% of the total entropy of the phase transition. The remaining entropy must be electronic.
\r\n\r\nTOF inelastic neutron scattering spectra were measured on cerium at temperatures near the fcc (\u03b3) to bcc (\u03b4) transition temperature. Phonon DOS curves were extracted from data acquired over a wide range of momentum transfers. A large softening of the phonon DOS was found in going from \u03b3-cerium to \u03b4-cerium, and this accounts for an increase in vibrational entropy of (0.71 \u00b1 0.05) kB/atom. To be consistent with the latent heat of the \u03b3-\u03b4 transition, this increase in vibrational entropy must be accompanied by a large decrease in electronic entropy. The results not only confirm the recent discovery of a significant electronic contribution to the \u03b3-\u03b4 transition but also suggest that it may be twice as large as previously reported.
\r\n\r\nTOF inelastic neutron scattering spectra were measured on \u03b2-cerium (dhcp) and \u03b3-cerium (fcc) near the phase transition temperature. Phonon densities of states (DOS) were extracted from the TOF spectra. A softening of the phonon DOS occurs in the transition from \u03b2-cerium to \u03b3-cerium, accounting for an increase in vibrational entropy of \u0394S\u03b3-\u03b2vib = (0.09 \u00b10.05) kB/atom. Crystal field levels were extracted from the magnetic scattering for both\r\nphases. The entropy calculated from the crystal field levels and a fit to calorimetry data from the literature was significantly larger in \u03b2-cerium than \u03b3-cerium below room temperature. The difference was found to be negligible at the experimental phase transition temperature. There was a contribution to the specific heat from Kondo spin fluctuations that was consistent with the quasielastic magnetic scattering, but the difference between phases was negligible. To be consistent with the latent heat of the \u03b2-\u03b3 transition, the increase in vibrational entropy at the phase transition may be accompanied by a decrease in electronic entropy not associated with the crystal field splitting or spin fluctuations. At least three sources of entropy need to be considered for the \u03b2-\u03b3 transition in cerium.
\r\n\r\nDifferences in the heat capacity and thermal expansion of cubic (fcc-disordered) and tetragonal (DO22-ordered) Pd3V were measured from 40 K to 315 K. Below 100 K the heatcapacity difference was consistent with harmonic vibrations. At higher temperatures, however, the data show significant anharmonic effects. Measurements of elastic constants, densities, and thermal expansion showed that the anharmonic volume expansion contribution (Cp \u2013 Cv) could account for only about one-third of this anharmonic heat capacity difference. The remainder may originate with elastic and plastic deformation of the polycrystalline microstructure. Strain energy from anisotropic thermal contractions of grains in the tetragonal ordered phase contributes to the heat capacity, but some of this strain energy is eliminated by plastic deformation. The vibrational entropy difference of disordered and ordered Pd3V was estimated to be Sdis \u2013 Sord = (+0.035\u00b1 0.001) kB//atom at 300 K, with 70% of this coming from anharmonic effects.
\r\n\r\nThe microstructural contribution to the heat capacity of \u03b1-uranium was determined bymeasuring the heat capacity difference between polycrystalline and single crystal samples from 77 K to 320 K. When cooled to 77 K and then heated to about 280 K, the uranium microstructure released (3\u00b12) J/mol of strain energy. On further heating to 300 K the microstructure absorbed energy as the microstructure began to redevelop microstrains. Neutron diffraction measurements on polycrystals predicted the total strain energy stored in the microstructure to be (3.7\u00b10.5) J/mol at 77 K and (1\u00b10.5) J/mol at room temperature in good agreement with the calorimetry.
", "doi": "10.7907/WECC-4662", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:5387", "collection": "thesis", "collection_id": "5387", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-085252318", "primary_object_url": { "basename": "Kua_j_2001.pdf", "content": "final", "filesize": 7674564, "license": "other", "mime_type": "application/pdf", "url": "/5387/1/Kua_j_2001.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Computational Studies of Heterogeneous and Homogeneous Catalysis by Late Transition Metals", "author": [ { "family_name": "Kua", "given_name": "Jeremy Soo Pin", "orcid": "https://orcid.org/0000-0002-2472-1887", "clpid": "Kua-Jeremy-Soo-Pin" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Myers", "given_name": "Andrew G.", "clpid": "Myers-A-G" } ], "thesis_committee": [ { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Davis", "given_name": "Mark E.", "orcid": "0000-0001-8294-1477", "clpid": "Davis-M-E" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "To design new catalysts that meet the environmental, materials and energy concerns of modern society, it is vital to understand the fundamental mechanisms involved in catalytic reactions. This thesis focuses on using quantum mechanical methods to determine the mechanisms for several critical catalytic processes in chemical industry.
\r\n\r\nLate transition metals are widely used as heterogeneous catalysts involving organic substrates. To lay a foundation for developing an orbital view useful for reasoning about surface reactions, we have developed the interstitial electron model (IEM) for bonding in platinum described in Chapter 1. To test the validity of the model cluster chosen to represent the surface, we studied the chemistry of C\u2081 and C\u2082 hydrocarbons, for which the most single-crystal experimental data is available, as described in Chapter 2.
\r\n\r\nIn Chapter 3, we extend this model to the second and third row Group VIII transition metals (Ir, Os, Pd, Rh, Ru) and develop a thermochemical group additivity framework for hydrocarbons on metal surfaces similar to the Benson scheme so useful for gas phase hydrocarbons. This provides a potentially powerful technique for deriving a mechanistic understanding on complex hydrocarbon reactions on catalytic surfaces, applicable to hydrocarbon reforming processes.
\r\n\r\nAn advantage of direct methanol fuel cells (DMFCs) over the internal combustion engines is to avoid the environmental damage caused by the latter. Chapter 4 describes our studies on electrocatalysis of methanol oxidation in direct methanol fuel cells. In particular, we focus on the role of different metals at the anode as alloys and as promoters for various aspects of the reaction converting methanol and water to CO\u2082 and energy.
\r\n\r\nOne of the most important challenges is to find ways to utilize the enormous resources in methane around the world as the fundamental feedstock for the chemical and energy industries. Perhaps the most promising progress in developing low-temperature highly selective homogeneous catalysts have been the Hg and PtCl\u2082 catalysts from Catalytica. Chapter 5 reports our studies on the stability, thermodynamics, and reaction mechanism of the PtCl\u2082 catalysts, with suggestions of possible modifications necessary to make this process economic.
", "doi": "10.7907/M9WN-7M53", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:8148", "collection": "thesis", "collection_id": "8148", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03192014-141855635", "primary_object_url": { "basename": "Brandow_cg_2001.pdf", "content": "final", "filesize": 38024719, "license": "other", "mime_type": "application/pdf", "url": "/8148/1/Brandow_cg_2001.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Zirconocenes as Models for Homogeneous Ziegler-Natta Olefin Polymerization Catalysts", "author": [ { "family_name": "Brandow", "given_name": "Christopher Graham", "clpid": "Brandow-Christopher-Graham" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Using density functional theory, we studied the fundamental steps of olefin \r\npolymerization for zwitterionic and cationic Group IV ansa-zirconocenes and a neutral ansa-\r\nyttrocene. Complexes [H2E(C5H4)2ZrMe]n (n = 0: E = BH2 (1), BF2 (2), AlH2(3); n = +: E = CH2(4), SiH2(5)) and \r\nH2Si(C5H4)2YMe were used as computational models. The largest\r\ndifferences among these three classes of compounds were the strength of olefin binding and the \r\nstability of the \u03b2-agostic alkyl intermediate towards \u03b2-hydrogen elimination. We investigated \r\nthe effect of solvent on the reaction energetics for land 5. We found that in benzene the \r\nenergetics became very similar except that a higher olefin insertion barrier was\r\ncalculated for 1. The calculated anion affinity of [CH3BF3]- was weaker towards 1 than 5. The\r\ncalculated olefin binding depended primarily on the charge of the ansa linker, and the olefin \r\ninsertion barrier was found to decrease steadily in the following order: [H2C(C5H4)2ZrMe]+ > [F2B(C5H4)2ZrMe] \u2248 [H2B(C5H4)2ZrMe] > [H2Si(C5H4)2ZrMe]+ > \r\n[H2Al(C5H4)2ZrMe].
\r\n\r\n\r\nWe prepared ansa-zirconocene dicarbonyl complexes Me2ECp2Zr(CO)2 (E = Si, C), and\r\nt-butyl substituted complexes (t-BuCp)2Zr(CO)2, Me2E(t-BuCp)2Zr(CO)2 (E = Si, C),\r\n(Me2Si)2(t-BuCp)2Zr(CO)2 as well as analogous zirconocene complexes. Both the reduction\r\npotentials and carbonyl stretching frequencies follow the same order: Me2SiCp2ZrCl2>\r\nMe2CCp2ZrCl2> Cp2ZrCl2> (Me2Si)2Cp2ZrCl2. This ordering is a result of both the donating\r\nabilities of the cyclopentadienyl substituents and the orientation of the cyclopentadiene rings.\r\nAdditionally, we prepared a series of analogous cationic zirconocene complexes\r\n[LZrOCMe3][MeB(C6F5)3] (L = CP2, Me2SiCp2, Me2CCP2, (Me2Si)2Cp2) and studied the kinetics of anion dissociation. We found that the enthalpy of anion dissociation increased from 10.3 kcal\u2022mol-1 to 17.6 kcal\u2022mol-1 as exposure of the zirconium center increased.
\r\n\r\nWe also prepared series of zirconocene complexes bearing 2,2-dimethyl-2-sila-4-pentenyl substituents (and methyl-substituted olefin variants). Methide abstraction with B(C6F5) results in reversible coordination of the tethered olefin to the cationic zirconium center. The kinetics of olefin dissociation have been examined using NMR methods, and the effects of ligand variation for unlinked, singly [SiMe2]-linked and doubly [SiMe2]-linked bis(cyclopentadienyl) arrangements has been compared (\u0394G\u2021 for olefin dissociation varies from 12.8 to 15.6 kcal\u2022mol-1). Methide abstraction from 1,2-(SiMe2)2(\u03b75-C5H3)2Zr(CH3)-(CH2CMe2CH2CH = CH2) results in rapid \u03b2-allyl elimination with loss of isobutene yielding the allyl cation [{1,2-(SiMe2)2(\u03b75-C5H3)2Zr(\u03b73-CH2CH=CH2)]+.
\r\n", "doi": "10.7907/kxb2-wp19", "publication_date": "2001", "thesis_type": "phd", "thesis_year": "2001" }, { "id": "thesis:5386", "collection": "thesis", "collection_id": "5386", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-084608026", "primary_object_url": { "basename": "Carlson_mj_2000.pdf", "content": "final", "filesize": 9021815, "license": "other", "mime_type": "application/pdf", "url": "/5386/1/Carlson_mj_2000.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "BUFF: A Biological Universal Forcefield Derived from Quantum Mechanics", "author": [ { "family_name": "Carlson", "given_name": "Matt Jeffrey", "clpid": "Carlson-Matt-Jeffrey" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Molecular mechanical simulations of biomolecules require an accurate potential energy function (forcefield) in order to produce meaningful results. Most current forcefields are highly parameterized in order to correctly reproduce high level theory and experiment. Increasingly, new biomolecules are designed and studied that have atypical configurations such as metal centers and nonstandard amino acids. To avoid a lengthy process to develop new parameters for each new system encountered, a generic forcefield is desired. A hierarchical approach is undertaken herein to achieve this flexibility and accuracy.\r\n\r\nBuilding upon the rule based generic forcefields UFF and Dreiding, a new biological universal forcefield, BUFF, is presented for the simulation of proteins and other biological molecules. In addition to its UFF and Dreiding based terms, the BUFF has additional hydrogen bond terms, specialized protein backbone torsions, and a process for deriving charges for amino acids that is independent of other parameterization. These additional parameters have been fit to ab initio quantum mechanical calculations carried out on model systems.\r\n\r\nValidation studies of peptide trimers demonstrate that the BUFF accurately reproduces the quantum mechanical torsional energies. Several other common, highly parameterized forcefields are also applied to the same tripeptide systems, as well as short \u03b1-helical chains and other model systems in order to make a comparison to the BUFF. These studies show that while the BUFF is universal and can be quickly deployed on new systems, such as unnatural amino acids or metal containing systems, it is also at least as accurate as other commonly employed, but highly parameterized, forcefields. The biological universal forcefield described herein is presented as complementary to the MSC forcefield derived for simulations of DNA and other nucleic acids.", "doi": "10.7907/5kyh-4402", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:5386", "collection": "thesis", "collection_id": "5386", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-084608026", "primary_object_url": { "basename": "Carlson_mj_2000.pdf", "content": "final", "filesize": 9021815, "license": "other", "mime_type": "application/pdf", "url": "/5386/1/Carlson_mj_2000.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "BUFF: A Biological Universal Forcefield Derived from Quantum Mechanics", "author": [ { "family_name": "Carlson", "given_name": "Matt Jeffrey", "clpid": "Carlson-Matt-Jeffrey" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Molecular mechanical simulations of biomolecules require an accurate potential energy function (forcefield) in order to produce meaningful results. Most current forcefields are highly parameterized in order to correctly reproduce high level theory and experiment. Increasingly, new biomolecules are designed and studied that have atypical configurations such as metal centers and nonstandard amino acids. To avoid a lengthy process to develop new parameters for each new system encountered, a generic forcefield is desired. A hierarchical approach is undertaken herein to achieve this flexibility and accuracy.\r\n\r\nBuilding upon the rule based generic forcefields UFF and Dreiding, a new biological universal forcefield, BUFF, is presented for the simulation of proteins and other biological molecules. In addition to its UFF and Dreiding based terms, the BUFF has additional hydrogen bond terms, specialized protein backbone torsions, and a process for deriving charges for amino acids that is independent of other parameterization. These additional parameters have been fit to ab initio quantum mechanical calculations carried out on model systems.\r\n\r\nValidation studies of peptide trimers demonstrate that the BUFF accurately reproduces the quantum mechanical torsional energies. Several other common, highly parameterized forcefields are also applied to the same tripeptide systems, as well as short \u03b1-helical chains and other model systems in order to make a comparison to the BUFF. These studies show that while the BUFF is universal and can be quickly deployed on new systems, such as unnatural amino acids or metal containing systems, it is also at least as accurate as other commonly employed, but highly parameterized, forcefields. The biological universal forcefield described herein is presented as complementary to the MSC forcefield derived for simulations of DNA and other nucleic acids.", "doi": "10.7907/5kyh-4402", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:13596", "collection": "thesis", "collection_id": "13596", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11222019-095315401", "primary_object_url": { "basename": "scholl-m-2000.pdf", "content": "final", "filesize": 4431025, "license": "other", "mime_type": "application/pdf", "url": "/13596/1/scholl-m-2000.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Expanding the Scope of Ruthenium-Based Olefin Metathesis Catalysts", "author": [ { "family_name": "Scholl", "given_name": "Matthias", "clpid": "Scholl-Matthias" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "clpid": "Barton-J-K" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Peters", "given_name": "Jonas C.", "clpid": "Peters-J-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The development of well-defined ruthenium alkylidene (PCy\u2083)\u2082Cl\u2082Ru=CHPh brought about a revolution in the area of olefin metathesis. The objective of the work presented here is to expand the scope of ruthenium-based olefin metathesis catalysts such as (PCy\u2083)\u2082Cl\u2082Ru=CHPh through the development of novel synthetic organic methods for ring-closing metathesis as well as through modification of the ligand sphere of the ruthenium complexes.
\r\n\r\nChapter 2 describes the application of ruthenium alkylidenes to the catalysis of polycyclization reactions. Several acyclic precursors have been synthesized and reacted with (PCy\u2083)\u2082Cl\u2082Ru=CHPh. These precursors vary in topology and contain acetylenic and/or cycloolefinic metathesis relays. The cyclization reactions proceed in good yields to produce polycyclic polyenes.
\r\n\r\nChapter 3 focuses on the synthesis of racemic and enantiopure targets containing the 6,8-dioxabicycIo [3.2.1]octane skeleton using an intramolecular ruthenium-catalyzed ring-closing metathesis reaction as the key step. The natural product frontalin is synthesized in racemic and enantiopure forms and in excellent yields using this methodology.
\r\n\r\nChapter 4 outlines the preparation of a novel imidazolylidene-substituted ruthenium-based complex starting from (PCy\u2083)\u2082RuCl\u2082(=CHPh). The N-heterocyclic carbene-substituted olefin metathesis initiator exhibits increased ring-closing metathesis activity at elevated temperature compared to that of the parent complex (PCy\u2083)\u2082Cl\u2082Ru(=CHPh). Di-, tri-, and tetra-substituted cycloolefins are successfully prepared from corresponding diene precursors in moderate to excellent yields.
\r\n\r\nChapter 5 describes the preparation of a new family of 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene-substituted ruthenium-based complexes. These air and water tolerant systems exhibit an increased ring-closing metathesis activity at elevated temperature when compared to that of the parent complex (PCy\u2083)\u2082Cl\u2082Ru(=CHPh) as well as to the complexes disclosed previously in Chapter 4. In many instances the activity of these new complexes also rivals or exceeds that of the alkoxy-imido molybdenum-based olefin metathesis catalysts. Applications of chiral N-heterocyclic carbene ruthenium complexes to asymmetric ring-closing metathesis are also briefly discussed.
\r\n\r\nFinally, the synthesis of the Schiff base-substituted ruthenium carbene complexes on a solid support is described in Chapter 6. The activities of the supported complexes are compared to those of their unsupported counterparts. The newly prepared systems are found to be highly stable to air, moisture, and temperature, and exhibit increased catalytic activity in acidic media.
", "doi": "10.7907/55x3-h359", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:16683", "collection": "thesis", "collection_id": "16683", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08292024-181421142", "type": "thesis", "title": "Expanding the Applications of Transition Metal Alkylidenes and Alkylidynes to Organic Synthesis", "author": [ { "family_name": "Kirkland", "given_name": "Thomas Andrew", "clpid": "Kirkland-Thomas-Andrew" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The application of olefin and acetylene metathesis to organic synthesis has\r\nincreased greatly since its introduction. The research in this thesis describes the Ring-Closing\r\nMetathesis (RCM) of substituted olefins and enynes, the metathesis of internal\r\nacyclic olefins and the conversion of acid chlorides to acetylenes with tungsten\r\nalkylidynes.
\r\n\r\nIn Chapter 1, the activity of ruthenium alkylidenes and molybdenum alkylidenes\r\nfor the RCM of dienes containing gem-disubstituted olefins was investigated. Dienes\r\nwith sterically-demanding and/or electron-withdrawing substituents were cyclized\r\nsuccessfully with only the molybdenum alkylidene. Dienes with allylic functional groups\r\nyielded functionalized cyclic olefins when treated with either alkylidene.
\r\n\r\nIn Chapter 2 the cyclization of enyne and endiyne substrates using ruthenium\r\nalkylidenes was discussed. The effects of ring size and methyl substitution on the\r\nconversion were determined. A mechanism in which the alkylidene reacts with the olefin\r\nfirst, followed by an intramolecular reaction with the acetylene on an enyne substrate is\r\ndescribed.
\r\n\r\nThe RCM of acyclic dienes containing vicinally substituted olefins was described\r\nin Chapter 3. Water-soluble ruthenium alkylidenes did not cyclize \u03b1,\u03c9-dienes due to the\r\ninstability of the resulting methylidene. The incorporation of a phenyl substituent\r\nresulted in nearly quantitative cyclization. RCM of a water-soluble diene has been\r\nachieved in aqueous solution using this methodology. This methodology has also been\r\nsuccessfully applied to increase RCM yields in organic solvents.
\r\n\r\nThe stereoselectivity of metathesis of acyclic olefins was investigated for several\r\nruthenium alkylidenes in Chapter 4. This was primarily done using cis-2-pentene\r\nmetathesis. Data from cis-2-pentene metathesis was also used to determine relative\r\nmetathesis rates for various alkylidenes and reaction conditions. An alkylidene bearing\r\ntricyclopentyl phosphines (13) was significantly more cis selective than one with\r\ntricyclohexyl phosphines (8). Alkylidene 8 was moderately cis selective for cis-2-pentene \r\nmetathesis and slightly cis selective for trans-2-pentene metathesis.
\r\n\r\nAn investigation into the conversion of acid chlorides to substituted acetylenes\r\nusing tungsten alkylidynes is discussed in Chapter 5. A new route to DIPP tungsten\r\nalkylidynes is described. Several aromatic acid chlorides were converted into acetylenes\r\nusing these alkylidynes in good yields. Finally, attempts at the synthesis of W2(DIPP)6\r\nare described.
", "doi": "10.7907/w770-7r65", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:6085", "collection": "thesis", "collection_id": "6085", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10012010-103544088", "primary_object_url": { "basename": "Lu_d_2000.pdf", "content": "final", "filesize": 40344265, "license": "other", "mime_type": "application/pdf", "url": "/6085/1/Lu_d_2000.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Theoretical Studies of the Nonlinear Optical Properties of Organic Materials", "author": [ { "family_name": "Lu", "given_name": "Daqi", "clpid": "Lu-Daqi" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "No abstract.", "doi": "10.7907/myx9-7278", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:11451", "collection": "thesis", "collection_id": "11451", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04092019-114920250", "primary_object_url": { "basename": "Morgan_CS_2000.pdf", "content": "final", "filesize": 45223607, "license": "other", "mime_type": "application/pdf", "url": "/11451/1/Morgan_CS_2000.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Full Sequence Design of an Alpha-Helical Protein and Investigation of the Importance of Helix Dipole and Capping Effects in Helical Protein Design", "author": [ { "family_name": "Morgan", "given_name": "Chantal Smith", "clpid": "Morgan-Chantal-Smith" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bjorkman", "given_name": "Pamela J.", "orcid": "0000-0002-2277-3990", "clpid": "Bjorkman-P-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Our goal is an objective, quantitative design algorithm based on the\r\nphysical chemical forces which determine protein structure and stability. To\r\nthis end, we have developed a cyclical protein design strategy which utilizes\r\ntheory, computation, and experimentation using a variety of protein systems.\r\nWe address the inverse folding problem using a protein design algorithm\r\nwhich objectively predicts protein sequences which are compatible with a\r\ngiven fold.
\r\n\r\nOur protein design methodology was developed using a variety of\r\nproteins, and therefore should be generalizable to many folds and motifs. To\r\ntest the generalizability and expand the size of proteins we have designed,\r\nengrailed homeodomain (enh), a 51-residue helix-turn-helix motif, was used\r\nas a target motif.
\r\n\r\nA series of design calculations and experiments on the thirty surface\r\npositions of enh were performed to probe the importance of the helix dipole\r\nand capping effects in protein design. Rules for which types of residues were\r\nallowed at the helix termini were introduced systematically, resulting in\r\nprogressively more stable proteins. The first design in the series, which had\r\nno considerations for the helix dipole or capping effects, was shown to have\r\nthe same thermal stability as wild-type enh and the protein with the most\r\nstringent rules has a Tm of 75 \u00b0C, 32\u00b0 higher than wild-type and the first\r\ndesign. Therefore, helix dipole and capping effects have a large impact on\r\nour ability to design stable proteins. The ten core residues of enh were\r\nincluded in the design calculation. The resulting protein, a 29-fold mutant of\r\nwild-type, has a Tm of 81 \u00b0C.
\r\n\r\nThe full sequence design of enh was computed stepwise. The eleven\r\nboundary residues were designed in the context of the surface-core design.\r\nThe resulting protein, a 39-fold mutant of wild-type enh, has a melting\r\ntemperature of 114 \u00b0C and is 4.7 kcal/mol more stable than wild-type. The\r\nstructure of the boundary-surface-core design was solved by NMR\r\ntechniques and found to be in excellent agreement with the target structure.\r\nThe top 10 structure have a backbone root-mean-square standard deviation of\r\n0.45 \u00c5 and the root-mean-square standard deviation between the model\r\nstructure and experimental backbones is 1.25 \u00c5.
\r\n\r\nThe side chain selection algorithm was also extended to the design of\r\npeptides to bind tightly to MHC class I proteins. A circular dichroism\r\nspectrometry assay was developed to determine the peptide dissociation\r\nconstants. Three designed peptides were bound more tightly to the MHC\r\nclass I molecule H-2Kd than known peptides. In addition, an investigation of\r\nthe removal of disulfide bonds from toxin folds is discussed.
\r\n\r\n", "doi": "10.7907/8wn3-cv27", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:17577", "collection": "thesis", "collection_id": "17577", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07312025-172124033", "primary_object_url": { "basename": "Gordon_DB_2000.pdf", "content": "final", "filesize": 40103293, "license": "other", "mime_type": "application/pdf", "url": "/17577/1/Gordon_DB_2000.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Combinatorial Optimization in Computational Protein Design", "author": [ { "family_name": "Gordon", "given_name": "David Benjamin", "clpid": "Gordon-David-Benjamin" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The central objective of computational protein design is to develop computational\r\ntechniques for selecting amino acid sequences that fold into proteins with desired\r\nstructures and functions. The work described here is directed toward addressing issues\r\nthat arise in the development of computational methods for the design of solvent-exposed\r\nportions of beta-sheets. However, it is also demonstrated that the results of these\r\ninvestigations extend beyond specific secondary structures and in fact provide a means to\r\naddress a broad spectrum of design problems. Computational issues arise from the fact\r\nthat when constructing a representation of protein sequence space for analysis, significant\r\nconcessions must be made with respect to the physical model and the search criteria in\r\norder to ensure that the calculation remains tractable. One of the limiting factors driving\r\nthese concessions is the sheer number of combinations of amino acid identities and\r\nconfigurations that must be evaluated. We have therefore pursued the development and\r\nrefinement of high-performance combinatorial search algorithms in order to better enable\r\nimprovement of computational methods. The consequent algorithmic work consists of\r\nenhancement strategies based on combining optimization methods and instilling within\r\nthem heuristics that manifest specialized knowledge of protein design problems. The\r\nresults are significant performance enhancements for the well-established Dead-End\r\nElimination algorithm, as well as two new algorithmic approaches, dubbed Branch and\r\nTerminate and Hybrid Rotamer Optimization.", "doi": "10.7907/fzxm-d394", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:1843", "collection": "thesis", "collection_id": "1843", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05172004-054229", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 3788034, "license": "other", "mime_type": "application/pdf", "url": "/1843/1/Thesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Metallocene-mediated olefin polymerization : the effects of distal ligand perturbations on polymer stereochemistry", "author": [ { "family_name": "Miller", "given_name": "Stephen Albert", "clpid": "Miller-S-A" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "New group IV compounds containing a 9-dialkylaminofluorenide ligand have been prepared. Their properties and reactivity have been investigated. For example, single crystal X-ray analysis of the metallocene (9-(N,N-dimethylamino)fluorenyl)2ZrCl2 (4) reveals a bonding mode that includes a zirconium-nitrogen bond. In combination with methylaluminoxane (MAO), several aminofluorenide complexes afford atactic polypropylene.\n\nA statistical model has been developed that quantifies the unidirectional site epimerization probability, e, for singly- and doubly-bridged C1- symmetric metallocene polymerization catalysts. The unidirectional site epimerization model allows deconvolution of the site sequence probability and the stereochemical probability for producing a given pentad.\n\nHighly stereoregular syndiotactic polypropylene is obtained with the catalyst systems Ph2C(Oct)(C5H4)ZrCl2/MAO (8/MAO) (Oct = octamethyloctahydrodibenzofluorenyl, C-29H36) and Me2C(Oct)(C5H4)ZrCl2/MAO (12/MAO). Melting temperatures as high as 153?C or 154?C are found for the thermally quenched polymers. Distal ligand perturbations are demonstrated to have a dramatic effect on polymer stereochemistry.\n\nPolypropylenes that are isotactic-hemiisotactic or syndiotactic-hemiisotactic can be made with proper R substituent selection in the catalyst system Me2C(Flu)(3-R-C5H3)ZrCl2/MAO or Me2C(Oct)(3-R-C5H3)ZrCl2/MAO, where Flu = fluorenyl (C13H8). The prepared polymers have been subjected to a statistical model which suggests that the metallocenes have one highly selective site (99%) and one site of variable selectivity which is highly dependent on the nature of the R substituent and whether the metallocene contains the Flu or Oct ligand.\n\nControl of the tacticity of isotactic-hemiisotactic polypropylene, as quantified by the parameter a, is achieved by proper R substituent selection in the catalyst system R'2C(3-R-C5H3)(C13H8)MCl2/MAO. For R = 2-adamantyl, R' = Ph, and M = Zr or Hf, a is approximately 0.60 and the polypropylene obtained is elastomeric. Its properties are rationalized by the statistical existence of isotactic stereoblocks among an otherwise amorphous hemiisotactic medium.\n\nFor the C1-symmetric polymerization catalyst Me2C(3-t-butyl-C5H3)(9-C13H8)ZrCl2/MAO, evidence gathered here supports an alternating mechanism in which both sites of the metallocene wedge are utilized for monomer insertion. For an Oct-containing catalyst system with a cyclopentadienyl substituent of R = 2-methyl-2-adamantyl, unprecedentedly high isotacticity (>99% [mmmm]) is observed for a fluorenyl-based metallocene catalyst. Melting temperatures for such isotactic polymers can be as high as 167?C (Tp = 0?C).", "doi": "10.7907/51r0-km07", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:17577", "collection": "thesis", "collection_id": "17577", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07312025-172124033", "primary_object_url": { "basename": "Gordon_DB_2000.pdf", "content": "final", "filesize": 40103293, "license": "other", "mime_type": "application/pdf", "url": "/17577/1/Gordon_DB_2000.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Combinatorial Optimization in Computational Protein Design", "author": [ { "family_name": "Gordon", "given_name": "David Benjamin", "clpid": "Gordon-David-Benjamin" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The central objective of computational protein design is to develop computational\r\ntechniques for selecting amino acid sequences that fold into proteins with desired\r\nstructures and functions. The work described here is directed toward addressing issues\r\nthat arise in the development of computational methods for the design of solvent-exposed\r\nportions of beta-sheets. However, it is also demonstrated that the results of these\r\ninvestigations extend beyond specific secondary structures and in fact provide a means to\r\naddress a broad spectrum of design problems. Computational issues arise from the fact\r\nthat when constructing a representation of protein sequence space for analysis, significant\r\nconcessions must be made with respect to the physical model and the search criteria in\r\norder to ensure that the calculation remains tractable. One of the limiting factors driving\r\nthese concessions is the sheer number of combinations of amino acid identities and\r\nconfigurations that must be evaluated. We have therefore pursued the development and\r\nrefinement of high-performance combinatorial search algorithms in order to better enable\r\nimprovement of computational methods. The consequent algorithmic work consists of\r\nenhancement strategies based on combining optimization methods and instilling within\r\nthem heuristics that manifest specialized knowledge of protein design problems. The\r\nresults are significant performance enhancements for the well-established Dead-End\r\nElimination algorithm, as well as two new algorithmic approaches, dubbed Branch and\r\nTerminate and Hybrid Rotamer Optimization.", "doi": "10.7907/fzxm-d394", "publication_date": "2000", "thesis_type": "phd", "thesis_year": "2000" }, { "id": "thesis:16203", "collection": "thesis", "collection_id": "16203", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10062023-220054560", "primary_object_url": { "basename": "Wilhelm_TE_1999.pdf", "content": "final", "filesize": 70575762, "license": "other", "mime_type": "application/pdf", "url": "/16203/1/Wilhelm_TE_1999.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Easier and More Efficient Methods for the Generation of Metathesis Catalysts: Investigations into Group VI and VII", "author": [ { "family_name": "Wilhelm", "given_name": "Thomas Edward", "clpid": "Wilhelm-Thomas-Edward" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1:
\r\n\r\nA high yield procedure for generating the ruthenium hydride complexes\r\nRu(H)(H2)Cl(PR3)2 (R=Cyclohexyl, cyclopentyl, isopropyl) in very high yield is\r\npresented. Following a novel insertion-elimination pathway, these hydrides can\r\nreact with propargyl or vinyl halides to make metathesis active vinyl and alkyl\r\ncarbene species with the general formulas (PR3)2Cl2Ru=CH-CH=CR'2 and\r\n(PR3)2Cl2Ru=CHR', respectively. Tertiary propargyl chlorides like 3-chloro-3-\r\nmethyl-1-butyne work best, yielding Ru-vinyl carbenes in extremely high yield.\r\nAn alternate route is to first add an alkyne, and then add HCl to give similar\r\nspecies.
\r\n\r\nIn attempting to learn about the insertion-elimination mechanism, the\r\ncompounds M(H)Cl(CO)(PR3)2 (M=Ru, Os; R=cyclohexyl, isopropyl) were found\r\nto react with 3-chloro-3-methyl-1-butyne to produce the metathesis inactive\r\ncarbenes with general formula cis-Cl2-trans(PCy3)2(CO)M=CHCH=CMe2. Kinetics\r\nofRu(H)Cl(CO)(PiPr3)2 can only be analyzed qualitatively, but from all of\r\nthe available data a mechanism is proposed for the insertion of hydrides into\r\nalkynes and rearrangement to give carbenes. The compounds\r\nM(H)Cl(CO)2(PR3)2 (M=Ru, Os; R=cyclohexyl, isopropyl) show no alkyne insertion.
\r\n\r\nThe osmium analogs Os(H)3Cl(PCy3)2 and (PCy3)2Cl2Os=CH=CH=CMe2\r\nwere investigated for the ability to generate carbenes. The osmium carbene,\r\nhowever, rapidly transforms to the hydrido-carbyne species (PCy3)2Cl2Os(H)(=CCH=\r\nCMe2). It appears that additional stabilization of the osmium system will\r\nbe necessary to prevent such rearrangement.
\r\n\r\nIt is also presented that (PCy3)2Cl2Ru=CHR' reacts with dihydrogen to\r\ngive H3CR', Ru(H)2(C1)2(PCy3)2, and Ru(H)(H2)Cl(PCy3)2. Theoretically, all\r\nRu(H)2(Cl)2(PCy3)2 can be converted to Ru(H)(H2)Cl(PCy3)2. It is thus possible\r\nto go from hydrides to carbenes, and back to hydrides.
\r\n\r\nChapter 2:
\r\n\r\nComplexes of the type M(O)Cl2(PR3)3 (M=W, Mo; R3=PMePh2, PMe2Ph) were\r\nsynthesized using literature procedures, and shown to react with 3,3-\r\ndiphenylcyclopropene to give the \u03b72-olefin complexes M(O)Cl2(PR3)2(\u03b72-\r\ndiphenylcyclopropene). Spectroscopic data suggest a distorted octahedral structure\r\nfor both, with the oxo ligand in the axial position with the olefin cis to it\r\nand the two mutually trans phosphines in the equatorial plane, which was confirmed\r\nfor M=W with an x-ray diffraction study. The olefin complexes react\r\nwith suitable alkoxides to give the oxo-carbene species M(O)(OR)2(PR3)(=CHCH=\r\nCPh2), the first known single component tungsten and molybdenum oxo-alkylidene\r\nmetathesis catalysts, in which the phosphine is readily displaced\r\nwith THF. For these complexes, spectroscopic data suggest a distorted trigonal\r\nbipyramid with the oxo, alkylidene, and one alkoxide ligand in the equatorial\r\nplane, which was confirmed for M=W by a diffraction experiment. These\r\nalkylidene species are active in olefin metathesis reactions, showing comparable\r\nactivity to similar arylimido complexes previously described; polymerization\r\ndata is presented for norbornene and cyclooctene. In addition, the olefin\r\ncomplexes were shown to be active in olefin metathesis at elevated temperatures.
", "doi": "10.7907/3d4p-py55", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:17842", "collection": "thesis", "collection_id": "17842", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01282026-190810142", "type": "thesis", "title": "Advances in High-Resolution Probes for Scanning Probe Microscopy", "author": [ { "family_name": "Unger", "given_name": "Marc Alexander", "clpid": "Unger-Marc-Alexander" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Quake", "given_name": "Stephen R.", "orcid": "0000-0002-1613-0809", "clpid": "Quake-S-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes work designed to improve the resolution of Scanned Probe\r\nMicroscopy (SPM). The work falls into three main sections. Sections I and III are both\r\naimed towards making scanned probes with atomic resolution by attaching a single sharp\r\nmolecule to the end of a tip. Section II is aimed towards making a near-field \"optical\"\r\nprobe in the infrared wavelengths.
\r\n\r\nThe first section centers on the Touchdown Scheme, a path towards attachment of a\r\nsingle sharp molecule at the end of a conventional atomic force microscope (AFM) tip.\r\nThe ability to derivatize the tip with a good monolayer was required. Chapters 2 and 3\r\ndescribe the development and optimization of surface chemistry for this purpose.\r\nIncluded in this development were methods for making chemically patterned surfaces\r\nwith simple photolithography techniques. Chapter 1 describes mathematical methods to\r\nextract intermolecular pair potentials from AFM force measurements.
\r\n\r\nThe second section describes a technique for etching infrared-transmitting fibers to very\r\nsharp points. These sharpened fibers serve as probes in a Near-field Scanning Infrared\r\nMicroscope (NSIM). Making tips by chemical etching is far easier than heat-pulling, and\r\nthe etched probes have a power throughput several orders of magnitude higher than\r\npulled probes.
\r\n\r\nThe third section centers on attempts to attach a single molecule to the end of a single\r\ncarbon nanotube for use as an ultrasharp AFM tip. Bulk derivatization and labeling\r\nchemistry of carbon nanotubes was developed and successfully applied to single mounted\r\nnanotubes. Along the way, several new methods for handling nanotubes were developed.\r\nThese include methods for non-oxidative cleaning, making stable suspensions,\r\nfluorescence staining, and removal from solution without coalescence.
", "doi": "10.7907/xqdw-8009", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:5304", "collection": "thesis", "collection_id": "5304", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-081325550", "primary_object_url": { "basename": "Claypool_cl_1999.pdf", "content": "final", "filesize": 20223689, "license": "other", "mime_type": "application/pdf", "url": "/5304/1/Claypool_cl_1999.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Why molecules look the way they do in STM : a systematic functional group approach", "author": [ { "family_name": "Claypool", "given_name": "Christopher L.", "clpid": "Claypool-C-L" } ], "thesis_advisor": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A series of functionalized alkanes and/or alkyl alcohols have been prepared and imaged by scanning tunneling microscopy (STM) methods on graphite surfaces. The stability of these ordered overlayers has facilitated reproducible collection of STM images at room temperature with sub-molecular resolution, in most cases allowing identification of individual hydrogen atoms in the alkane chains, but in all cases allowing identification of molecular length features and other aspects of the image that can be unequivocally related to the presence of functional groups in the various molecules of concern. Functional groups imaged in this study include halides (X=F, Cl, Br, I), amines, alcohols, nitriles, alkenes, alkynes, ethers, thioethers, allenes, and disulfides. The dominance of molecular topography in producing the STM images of alkanes and alkanols was established experimentally and also was consistent with quantum chemistry calculations. For molecules in which electronic effects overwhelmed topographic effects in determining the image contrast, a simple model is presented to explain the variation in the electronic coupling component that produces the contrast between the various functional groups observed in the STM images. Additionally, a theoretical model based on perturbation theory has been developed to predict the scanning tunneling microscopy (STM) images of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort and provides images that are in qualitative agreement with experimental results. The computations correlate well with the STM data of functionalized alkanes and allow assessment of the structure and orientation of most of the functionalized alkanes that have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals of the adsorbed molecules, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals, may play an important role in determining e STM image contrast of such systems.\r\n", "doi": "10.7907/AAWF-HM84", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:16203", "collection": "thesis", "collection_id": "16203", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10062023-220054560", "primary_object_url": { "basename": "Wilhelm_TE_1999.pdf", "content": "final", "filesize": 70575762, "license": "other", "mime_type": "application/pdf", "url": "/16203/1/Wilhelm_TE_1999.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Easier and More Efficient Methods for the Generation of Metathesis Catalysts: Investigations into Group VI and VII", "author": [ { "family_name": "Wilhelm", "given_name": "Thomas Edward", "clpid": "Wilhelm-Thomas-Edward" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1:
\r\n\r\nA high yield procedure for generating the ruthenium hydride complexes\r\nRu(H)(H2)Cl(PR3)2 (R=Cyclohexyl, cyclopentyl, isopropyl) in very high yield is\r\npresented. Following a novel insertion-elimination pathway, these hydrides can\r\nreact with propargyl or vinyl halides to make metathesis active vinyl and alkyl\r\ncarbene species with the general formulas (PR3)2Cl2Ru=CH-CH=CR'2 and\r\n(PR3)2Cl2Ru=CHR', respectively. Tertiary propargyl chlorides like 3-chloro-3-\r\nmethyl-1-butyne work best, yielding Ru-vinyl carbenes in extremely high yield.\r\nAn alternate route is to first add an alkyne, and then add HCl to give similar\r\nspecies.
\r\n\r\nIn attempting to learn about the insertion-elimination mechanism, the\r\ncompounds M(H)Cl(CO)(PR3)2 (M=Ru, Os; R=cyclohexyl, isopropyl) were found\r\nto react with 3-chloro-3-methyl-1-butyne to produce the metathesis inactive\r\ncarbenes with general formula cis-Cl2-trans(PCy3)2(CO)M=CHCH=CMe2. Kinetics\r\nofRu(H)Cl(CO)(PiPr3)2 can only be analyzed qualitatively, but from all of\r\nthe available data a mechanism is proposed for the insertion of hydrides into\r\nalkynes and rearrangement to give carbenes. The compounds\r\nM(H)Cl(CO)2(PR3)2 (M=Ru, Os; R=cyclohexyl, isopropyl) show no alkyne insertion.
\r\n\r\nThe osmium analogs Os(H)3Cl(PCy3)2 and (PCy3)2Cl2Os=CH=CH=CMe2\r\nwere investigated for the ability to generate carbenes. The osmium carbene,\r\nhowever, rapidly transforms to the hydrido-carbyne species (PCy3)2Cl2Os(H)(=CCH=\r\nCMe2). It appears that additional stabilization of the osmium system will\r\nbe necessary to prevent such rearrangement.
\r\n\r\nIt is also presented that (PCy3)2Cl2Ru=CHR' reacts with dihydrogen to\r\ngive H3CR', Ru(H)2(C1)2(PCy3)2, and Ru(H)(H2)Cl(PCy3)2. Theoretically, all\r\nRu(H)2(Cl)2(PCy3)2 can be converted to Ru(H)(H2)Cl(PCy3)2. It is thus possible\r\nto go from hydrides to carbenes, and back to hydrides.
\r\n\r\nChapter 2:
\r\n\r\nComplexes of the type M(O)Cl2(PR3)3 (M=W, Mo; R3=PMePh2, PMe2Ph) were\r\nsynthesized using literature procedures, and shown to react with 3,3-\r\ndiphenylcyclopropene to give the \u03b72-olefin complexes M(O)Cl2(PR3)2(\u03b72-\r\ndiphenylcyclopropene). Spectroscopic data suggest a distorted octahedral structure\r\nfor both, with the oxo ligand in the axial position with the olefin cis to it\r\nand the two mutually trans phosphines in the equatorial plane, which was confirmed\r\nfor M=W with an x-ray diffraction study. The olefin complexes react\r\nwith suitable alkoxides to give the oxo-carbene species M(O)(OR)2(PR3)(=CHCH=\r\nCPh2), the first known single component tungsten and molybdenum oxo-alkylidene\r\nmetathesis catalysts, in which the phosphine is readily displaced\r\nwith THF. For these complexes, spectroscopic data suggest a distorted trigonal\r\nbipyramid with the oxo, alkylidene, and one alkoxide ligand in the equatorial\r\nplane, which was confirmed for M=W by a diffraction experiment. These\r\nalkylidene species are active in olefin metathesis reactions, showing comparable\r\nactivity to similar arylimido complexes previously described; polymerization\r\ndata is presented for norbornene and cyclooctene. In addition, the olefin\r\ncomplexes were shown to be active in olefin metathesis at elevated temperatures.
", "doi": "10.7907/3d4p-py55", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "id": "thesis:5314", "collection": "thesis", "collection_id": "5314", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10202009-133456579", "primary_object_url": { "basename": "Gao_g_1998.pdf", "content": "final", "filesize": 9785256, "license": "other", "mime_type": "application/pdf", "url": "/5314/1/Gao_g_1998.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Large Scale Molecular Simulations with Application to Polymers and Nano-Scale Materials", "author": [ { "family_name": "Gao", "given_name": "Guanghua", "clpid": "Gao-Guanghua" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Frautschi", "given_name": "Steven C.", "clpid": "Frautschi-S-C" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Yeh", "given_name": "Nai-Chang", "orcid": "0000-0002-1826-419X", "clpid": "Yeh-Nai-Chang" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "There remain practical problems to predicting structures and properties of materials from first principles, though the foundation, quantum mechanics, has been established for many years. The goals of this research are to develop methods and tools that are accurate and practical, and apply them to important problems. Two aspects of the methodology are focused.\r\n\r\n1. The development of accurate force fields based on ab initio quantum mechanical calculations on prototype systems. Procedures were developed on polyvinyl chloride (PVC) and successfully applied on other types of polymers. They are very important to studying of amorphous polymers materials, for which current methods have not been useful in predicting important properties (e.g. moduli and glass temperature).\r\n\r\n2. The development of Massive Parallel Simulation (MPSim) Software. MPSim is suitable for large systems (millions of atoms). It has the ability of including environmental variables (temperature, pressure, tension, and shear) and extracting physical properties (moduli and glass temperatures). The theories and algorithms implemented are summarized in the Appendix.\r\n\r\nThese methods and tools are applied to the accurate simulation of structures and properties of amorphous polymer materials and nano-materials.\r\n\r\nMolecular dynamics (MD) simulation on polyethylene (chapter 6) was used to develop a general strategy for predicting glass transition temperatures which is expected to be very important in polymer industry. In chapter 7, these strategies were successfully applied to three important fluoro polymers.\r\n\r\nSingle-walled carbon nanotubes (SWNT), recently discovered but not very well characterized, is an interesting new class of materials. Using an accurate force field, structures and mechanical properties of these systems are studied. Chapter 2 shows that the dominating factor for deciding stable structures and mechanical properties is the tube size, not chirality. The behavior of (10, 10) nano-tube under bending are studied (chapter 3) based on energy of hypothetical toroids with different radii. Yielding curvature of 1/R_s (R_s = 183.3 (\u00c5)) where elastic bending becomes plastic response is found. In chapter 4, closest packing of K_5C_(80) with the distribution of K atoms along tube surface similar to the stacking of stage one K_1C_8 is established as the optimum structure of K-doped SWNT crystal.\r\n", "doi": "10.7907/69rm-7y79", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:17792", "collection": "thesis", "collection_id": "17792", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12102025-233557591", "primary_object_url": { "basename": "Lim_AC_1998.pdf", "content": "final", "filesize": 60742266, "license": "other", "mime_type": "application/pdf", "url": "/17792/1/Lim_AC_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Investigation of RNA Tertiary Structure and Function by Transition Metal Complexes", "author": [ { "family_name": "Lim", "given_name": "Ai Ching", "clpid": "Lim-Ai-Ching" } ], "thesis_advisor": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Parker", "given_name": "Carl Stevens", "orcid": "0000-0001-9795-4211", "clpid": "Parker-C-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Phenanthrenequinone diimine (phi) complexes of rhodium(III) were employed to\r\nprobe RNA secondary and tertiary structure. These complexes bind via intercalation in\r\nopen major grooves of RNA and upon irradiation promote strand scission. By probing\r\nboth synthetic and natural molecules containing a variety of tertiary motifs, a systematic and\r\npredictive understanding of the factors involved in RNA recognition by these complexes is\r\nsought. The metal complex Rh(phen)2phi3+ (phen = 1,10-phenanthroline) recognizes and\r\ncleaves synthetic triple helices selectively over double helices. The cleavage sites are\r\ndependent upon maximizing overlap between the phi ligand and the basepairs, and\r\nminimizing charge repulsion between the metal complex and protonated bases. These\r\ncleavage sites have proven useful in explaining rhodium complex cleavage in natural\r\nsystems such as tRNAPhe. With these complexes, we also seek to investigate the\r\ndifferences and similarities in RNA and DNA secondary and tertiary folding, by probing\r\nthe tertiary structure of tDNAPhe compared to tRNAPhe. These complexes have elucidated\r\nthe B-form nature of the DNA duplex as well as the tertiary folding of the DNA molecule,\r\nthus shedding light on the feasibility of using DNA analogs of RNA for structural studies.\r\nThese shape selective probes have also been applied to probe the tertiary structure of HIV\r\nand BIV (TAR (trans-activation response) RNAs. \u0394-Rh(phen)2phi3+ binds with high\r\naffinity (Kb= 6.1 \u00b1 1.3 x 105 M-1) and specificity to sites at and across from a bulge\r\nregion which is the recognition element for the binding of the Tat (trans-activating) peptide.\r\nImportantly, the metal complex recognizes an RNA base-triple the formation of which is\r\nnecessary for transactivation. Derivatives of Rh(phen)2phi3+, Rh(MGP)2phi5+(MGP = 4-\r\nguanidylmethy 1-1, 10-phenanthroline) and Rh(GEB)2phi5+ (GEB = 4-(2-guanidylethyl)-4'methy\r\n1-2,2'-bipyridine) where guanidinium moieties have been added to the ancillary\r\nligands of the rhodium complex, show enhanced affinity and selectivity for HIV and BIV\r\nRNA sequences. This is due to the guanidinium moieties mimicking the arginine side\r\nchains on the native Tat peptide, and making non-specific contacts with the phosphate\r\nbackbone of the RNA. However, even without these functionalities, shape-selection,\r\nmatching the shape of the small metal complex to its nucleic acid target, provides sufficient\r\nselective stabilization for RNA site discrimination. Indeed, these complexes compete\r\neffectively with the specific Tat peptides for their binding sites on their respective TAR\r\nRNAs. These complexes therefore employ shape selection to recognize structural\r\nvariations along the RNA polymer which are important for protein recognition. Shape-selective\r\nrecognition could also be applied to the design of novel small molecules to target\r\nnucleic acid sites with high site-selectivity, in the development of molecules to inhibit\r\nprotein recognition, and, potentially, in the design of new chemotherapeutics.", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:1785", "collection": "thesis", "collection_id": "1785", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05132009-113001", "primary_object_url": { "basename": "Dahiyat_bi_1998.pdf", "content": "final", "filesize": 7405459, "license": "other", "mime_type": "application/pdf", "url": "/1785/1/Dahiyat_bi_1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Protein Design Automation : Principles and Practice", "author": [ { "family_name": "Dahiyat", "given_name": "Bassil I.", "clpid": "Dahiyat-Bassil-I" } ], "thesis_advisor": [ { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Mayo", "given_name": "Stephen L.", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-S-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We have conceived and implemented a cyclical protein design strategy that couples theory, computation and experimental testing. Our goal is an objective, quantitative design algorithm that is based on the physical properties that determine protein structure and stability and which is not limited to specific folds or motifs. Such a method should escape the lack of generality that has resulted from design approaches based on system-specific heuristics and/or subjective considerations. A critical component of the development of our methods has been their experimental testing and validation. The use of a design cycle coupling theory, computation, and experiment has improved our understanding of the physical chemistry governing protein design and hence enhanced the performance of the design algorithm.\r\n\r\nOur protein design automation algorithm objectively predicts protein sequences likely to achieve a desired fold by using a side-chain selection algorithm that explicitly and quantitatively considers specific side-chain to backbone and side-chain to side-chain interactions. Using a rotamer description of the side chains, we implemented a fast discrete search algorithm based on the Dead End Elimination Theorem to rapidly find the globally optimal sequence in its optimal geometry. We subdivided the sequence selection problem into regions of proteins expected to be dominated by different factors: the tightly packed buried core, the solvent exposed surface, and the boundary between core and surface. We assessed the accuracy of a scoring function or combination of scoring functions by experimentally testing their sequence predictions. Improvements to the scoring function were derived from the experimental data and incorporated into the design algorithm. In this manner, we developed a scoring function for the core of a protein that considers packing interactions and hydrophobic solvation energy. In order to design boundary residues effectively, the usually neglected effect of exposed hydrophobic surface area was addressed. Scoring functions for the design of surface residues were developed that account for hydrogen bonding interactions and secondary structure propensities of amino acids. These potential functions were used to successfully redesign several proteins. The integration of these scoring functions was tested by designing the sequence for an entire protein and solving the NMR solution structure of the designed protein. This work reports the first successful automated design and experimental validation of a novel sequence for an entire protein.", "doi": "10.7907/08j5-w532", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:17605", "collection": "thesis", "collection_id": "17605", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08082025-165811908", "primary_object_url": { "basename": "Hastings_CA_1998.pdf", "content": "final", "filesize": 79636336, "license": "other", "mime_type": "application/pdf", "url": "/17605/1/Hastings_CA_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Part A. Studies Directed Toward the Total Synthesis of Chebulagic Acid. Part B. DNA Recognition by Metallointercalator-Peptide Conjugates", "author": [ { "family_name": "Hastings", "given_name": "Curtis Asa", "clpid": "Hastings-Curtis-Asa" } ], "thesis_advisor": [ { "family_name": "Carreira", "given_name": "Erick Moran", "orcid": "0000-0003-1472-490X", "clpid": "Carreira-E-M" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Carreira", "given_name": "Erick Moran", "orcid": "0000-0003-1472-490X", "clpid": "Carreira-E-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part A. The development of asymmetric allene/enone and allene/enoate\r\nintramolecular [2+2]-photocycloadditions is described. Irradiation of optically active\r\nallenes (89-92% ee) appended to enones and enoates afforded alkylidenecyclobutane\r\nphotoadducts with high levels of asymmetric induction (83 -100%) derived exclusively\r\nfrom the allene fragment. Substrates examined include allenyl alcohols appended to 1,3-\r\ncyclopentanedione, 1,3-cyclohexanedione, and 4-hydroxycoumarin. The absolute sense of\r\ninduction in these reactions was determined by photocycloaddition of an allene containing\r\nan internal stereochemical label. The exa-methylenecyclobutanes obtained upon irradiation\r\nof allene-coumarins were isolated as single olefin diastereomers. A model for the high\r\nlevels of enantioinduction observed in these transformations is presented.
\r\n\r\nThe asymmetric intramolecular allene/enoate [2+2]-photocycloaddition was applied\r\nto the synthesis of the topoisomerase I inhibitor chebulagic acid. The synthetic utility of\r\nthis reaction was demonstrated by the preparation of an advanced intermediate containing\r\nall of the stereochemical information present in the chebulic acid fragment of chebulagic\r\nacid. In the course of these synthetic studies an unusual 8-alkynyl lactone photoproduct\r\nwas obtained upon photocyloaddition of a substrate that was expected to afford a [7.6.6.4]tetracyclic\r\nsystem. A 1,5-hydrogen shift in a biradical intermediate was implicated in the\r\nformation of this product by isotopic labeling studies; the mechanistic implications of these\r\nresults for enantioselectivity in photochemical reactions of optically active allenes tethered\r\nto enones and enoates are discussed.
\r\n\r\nPart B. The DNA recognition properties of peptide conjugates of\r\nphenenthrenequinone diimine complexes of rhodium(III) have been studied. The structural\r\nand thermodynamic basis for the 5'-CCA-3'-selectivity of the metallointercalator-peptide\r\nconjugate [Rh(phi)2(phen')]3+ -AANVAIAAWERAA-CONH2 was investigated. A protocol\r\nfor measuring dissociation constants of DNA cleaving ligands by cleavage titration is\r\ndescribed. Using this protocol, the energetic contribution of the peptide to sequenceselective\r\nbinding was assessed, and evidence for the origin of the enhanced sequenceselectivity\r\nobserved at elevated temperature was obtained. Micromolar quantities of [\u0394Rh-(phi)2(phen')]3+-AANVAIAAWERAA-CONH2 were synthesized to examine the\r\nstructure of the metallointercalator-peptide conjugate and the metallointercalator-peptide\r\nconjugate\u2022DNA complex by NMR. NMR results for the metallointercalator-peptide\r\nconjugate in the absence of DNA are reported.
\r\n\r\nA family of peptide conjugates of [Rh(phi)2(phen')]3+(phi = 9, 10-\r\nphenanthrenequinone diimine, phen' = 5-(amidoglutaryl)-1,10-phenanthroline) was also\r\nsynthesized. The peptide sequences were obtained by single amino acid modification of the\r\n5'-CCA-3'-selective metallointercalator-peptide conjugate [Rh(phi)2(phen')]3+-\r\nAANVAIAAWERAA-CONH2 to explore the correlation between the amino acid sequence\r\nof the peptide and the nucleotide sequence of the DNA target. Changing the position of the\r\nglutamate at position 10 in the sequence of the appended peptide resulted in the\r\nidentification of a 5'-ACA-3'-selective metallointercalator-peptide conjugate,\r\n[Rh(phi)2(phen')3+-AANVAEAAWARAA-CONH2. Locating the glutamate on one face of\r\na putative \u03b1-helix was found to be essential for sequence specificity; peptide conjugates\r\nwith the glutamate at positions 7, 8, 12, and 13 did not afford sequence-selective DNA\r\nrecognition. Further amino acid substitutions were made at positions 6 and 10. Mutating\r\nthe glutamate at position 6 to arginine caused complex changes in the recognition\r\ncharacteristics of the resulting conjugate. To probe the interactions that give rise to\r\nsequence specificity, we have measured thermodynamic dissociation constants for these\r\nsequence-selective metallointercalator-peptide conjugates and [Rh(phi)2(phen')]3+.
\r\n\r\nThe observed sequence preferences are consistent with the model of Sardesai et al.\r\nfor the sequence selectivity of Rh(phi)2(phen')]3+-AANVAIAAWERAA-CONH2. This\r\nmodel states that sequence-specific DNA recognition requires the peptide to adopt an \u03b1-helical\r\nconformation, and that Glu10 makes a critical base-specific contact with the 5'-\r\nterminal cytosine of the recognition sequence. Using the additional sequence-selectivity\r\ndata, this model is refined. This refined model suggests that recognition of the central C\u2022G\r\nbase pair of the 5'-CCA-3' recognition sequence of [Rh]-E10 is accomplished by Ile6\r\nthrough shape-selection, and that recognition of the 5' -terminal A\u2022T base pair of the 5' -\r\nACA-3' recognition sequence of [Rh]-E6 is accomplished by van der Waals contacts\r\nbetween alanine and thymine methyl groups. The implications of these results for the de\r\nnova design of sequence-selective DNA binding peptides are discussed.
", "doi": "10.7907/e4be-bd57", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:17585", "collection": "thesis", "collection_id": "17585", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-174712767", "primary_object_url": { "basename": "Martin_JI_1998.pdf", "content": "final", "filesize": 35602016, "license": "other", "mime_type": "application/pdf", "url": "/17585/1/Martin_JI_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Statistical Mechanics of End-Attached Polymer Interfaces", "author": [ { "family_name": "Martin", "given_name": "Jeremy Isaac", "orcid": "0000-0001-7233-7217", "clpid": "Martin-Jeremy-Isaac" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation discusses several closely related problems involving end attached polymers\r\nat interfaces. The studies share a numerical self-consistent field approach which is described\r\nin detail in Chapter 1.
\r\n\r\nIn Chapter 2, we consider irreversible polymer brushes (polymers densely end tethered\r\nto a surface). First, we discuss the adequacy of second virial treatments of interchain\r\ninteractions. Next we examine the extent of interbrush penetration between compressed\r\npolymer brushes, and its effect on the interactions between them. Then we identify scaling\r\nvariables which control the behavior of polymer brushes in polymeric solvents. Finally we\r\ninvestigate brush configurations and interactions in mixed solvents, where nonmonotonic\r\ninteraction profiles are predicted with a longer range weak attraction, and strong repulsion\r\nat shorter separations.
\r\n\r\nIn Chapter 3, we discuss the modification of spreading properties of a liquid on a solid\r\nsurface by the addition of end-adsorbing polymers. An end-adsorption polymer additive\r\ncan lead an otherwise non-spreading liquid to spread. A phase diagram for spreading of a\r\nliquid drop of fixed volume as a function of the concentration of end-adsorbing polymers\r\nand the energy of end-adsorption to the surface is obtained. The equilibrium thickness of\r\na spread film is also calculated, and is shown to be closely related to the thickness of a\r\nself-assembled polymer brush in an unbounded fluid and relatively insensitive to the bare\r\nspreading power of the liquid or the Hamaker constant, which determine the equilibrium\r\nthickness of a film of a simple liquid.
\r\n\r\nFinally, in Chapter 4, we study the interaction forces between two plates in a semi-dilute\r\nsolution of polymers each having one weakly adsorbing end-group. This system exhibits\r\nboth repulsive and attractive interactions of comparable magnitude and well-separated\r\nlength scales. The repulsion has a length scale of the end-to-end distance of the endadsorbed\r\npolymer, and a magnitude which is proportional to the end-adsorption energy\r\nand the volume fraction of the polymer, and inversely proportional the chain molecular\r\nweight. At plate separations of order the correlation length of the solution, a depletion\r\nattraction sets in with a magnitude that scales with the bulk osmotic pressure.
", "doi": "10.7907/4pc9-vz14", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:17585", "collection": "thesis", "collection_id": "17585", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-174712767", "primary_object_url": { "basename": "Martin_JI_1998.pdf", "content": "final", "filesize": 35602016, "license": "other", "mime_type": "application/pdf", "url": "/17585/1/Martin_JI_1998.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Statistical Mechanics of End-Attached Polymer Interfaces", "author": [ { "family_name": "Martin", "given_name": "Jeremy Isaac", "orcid": "0000-0001-7233-7217", "clpid": "Martin-Jeremy-Isaac" } ], "thesis_advisor": [ { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "orcid": "0000-0002-3361-6114", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This dissertation discusses several closely related problems involving end attached polymers\r\nat interfaces. The studies share a numerical self-consistent field approach which is described\r\nin detail in Chapter 1.
\r\n\r\nIn Chapter 2, we consider irreversible polymer brushes (polymers densely end tethered\r\nto a surface). First, we discuss the adequacy of second virial treatments of interchain\r\ninteractions. Next we examine the extent of interbrush penetration between compressed\r\npolymer brushes, and its effect on the interactions between them. Then we identify scaling\r\nvariables which control the behavior of polymer brushes in polymeric solvents. Finally we\r\ninvestigate brush configurations and interactions in mixed solvents, where nonmonotonic\r\ninteraction profiles are predicted with a longer range weak attraction, and strong repulsion\r\nat shorter separations.
\r\n\r\nIn Chapter 3, we discuss the modification of spreading properties of a liquid on a solid\r\nsurface by the addition of end-adsorbing polymers. An end-adsorption polymer additive\r\ncan lead an otherwise non-spreading liquid to spread. A phase diagram for spreading of a\r\nliquid drop of fixed volume as a function of the concentration of end-adsorbing polymers\r\nand the energy of end-adsorption to the surface is obtained. The equilibrium thickness of\r\na spread film is also calculated, and is shown to be closely related to the thickness of a\r\nself-assembled polymer brush in an unbounded fluid and relatively insensitive to the bare\r\nspreading power of the liquid or the Hamaker constant, which determine the equilibrium\r\nthickness of a film of a simple liquid.
\r\n\r\nFinally, in Chapter 4, we study the interaction forces between two plates in a semi-dilute\r\nsolution of polymers each having one weakly adsorbing end-group. This system exhibits\r\nboth repulsive and attractive interactions of comparable magnitude and well-separated\r\nlength scales. The repulsion has a length scale of the end-to-end distance of the endadsorbed\r\npolymer, and a magnitude which is proportional to the end-adsorption energy\r\nand the volume fraction of the polymer, and inversely proportional the chain molecular\r\nweight. At plate separations of order the correlation length of the solution, a depletion\r\nattraction sets in with a magnitude that scales with the bulk osmotic pressure.
", "doi": "10.7907/4pc9-vz14", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:5032", "collection": "thesis", "collection_id": "5032", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12172004-155023", "primary_object_url": { "basename": "Belmares_mp_1998.pdf", "content": "final", "filesize": 9509084, "license": "other", "mime_type": "application/pdf", "url": "/5032/1/Belmares_mp_1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Molecular Origins of the Thermophysical Properties of Polymers and Modeling of Polymer Permeation by Large Molecules", "author": [ { "family_name": "Belmares", "given_name": "Michael Paul", "clpid": "Belmares-Michael-Paul" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The molecular origins of the phase transitions of polymers have not been completely understood. The molecular level understanding of polymer behavior is of great technological and scientific value. For example, the melt to glass transition of a polymer Tg is perhaps its most useful quantity describing it. A low Tg polymer will be a useful elastomer and a high Tg polymer will serve for structural purposes. Additionally, sub-glass relaxations are related to polymer aging.
\r\n\r\nBased on a simple poly (ethylene) model, the intramolecular and intermolecular factors governing polymer melting, the glass transition and subglass transitions were investigated through a careful and systematic variation of the torsional potential as well as the cohesive energy of the polymer. The model polymers were studied using constant pressure canonical (Gibbs) dynamics of a system of four polymer chains with one hundred and fifty beads per chain. The advantage of varying systematically the torsional potential is that the morphology of the polymer is controlled, ranging from highly amorphous to highly crystalline, depending on the gauche-trans conformational energy differences. The effect of cohesive energy on the various transitions may also be studied by changing the Van der Waals well depth of each bead in the polymer chain.
\r\n\r\nThe first study presented in this chapter is a semi-crystalline case where the gauche energy was +1.14 kcal/mol more stable than the trans energy, and the trans-gauche barrier was 3.01 kcal/mol. A melting point, a glass transition and a tentatively assigned gamma relaxation were characterized.
\r\n\r\nIn a second study, the effect of the trans-gauche barrier on the phase transitions of a semi-crystalline polymer (gauche energy=+1.14 kcal/mol) was investigated.
\r\n\r\nIn a third study, the effect of the torsional barrier on the glass transition of amorphous polymers (gauche energy=trans energy) was investigated.
\r\n\r\nIn a fourth study, the effects of crystallinity on the phase transitions of polymers was investigated by varying the trans-gauche energy differences while maintaining the trans-gauche barrier constant at 4.03 kcal/mol.
\r\n\r\nIn the fifth and final study, the effect of the cohesive energy on the polymer phase transitions was investigated by changing the Lennard Jones well depth of each bead while maintaining the torsional potential fixed with a gauche energy of 1.14 kcal/mol relative to the trans energy, and a trans-gauche barrier of 4.03 kcal/mol.
\r\n\r\nBased on these studies, new insights on the general thermo-physical properties of polymers were obtained. A summary of the molecular interpretations of the melting point, glass transition, and sub-glass transitions is provided at the conclusion of this study.
\r\n\r\nTherefore, the strength of this study is its ability to produce numerous phase transitions within a single structural polymer model by a systematic variation of the intermolecular and intramolecular forcefield parameters. This allows an effective comparison of the thermodynamics, the kinetics and morphology of each of the polymer cases.
", "doi": "10.7907/vnw1-8367", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:5325", "collection": "thesis", "collection_id": "5325", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10232009-112246663", "primary_object_url": { "basename": "Iotov_ms_1998.pdf", "content": "final", "filesize": 4895839, "license": "other", "mime_type": "application/pdf", "url": "/5325/1/Iotov_ms_1998.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Diffusion in Amorphous Media", "author": [ { "family_name": "Iotov", "given_name": "Mihail S.", "clpid": "Iotov-Mihail-S" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Blandford", "given_name": "Roger D.", "clpid": "Blandford-R-D" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Frautschi", "given_name": "Steven C.", "clpid": "Frautschi-S-C" }, { "family_name": "Kornfield", "given_name": "Julia A.", "orcid": "0000-0001-6746-8634", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "The goals of this research are twofold: First, to develop methods and tools for studying problems in chemistry, material science and biology, as well as accurate prediction of the properties of structures and materials of importance to those fields. Second, use those tools to apply the methods to practical problems. In terms of methodology development this thesis focuses on two topics: One: Development of a massively parallel computer program to perform electronic, atomic, molecular levels simulations of problems in chemistry, material science and biology. This computer program uses existing and emerging hardware platforms and parallel tools and is based on decades long research in computer modeling and algorithms. We report on that development in Chapter 3. Two: Development of tools for Molecular Dynamics simulation and methods and tools for course-grained meso-scale modeling of transport properties and especially diffusion of gas penetrants in polymers. We have formulated a new method for extracting coarse-grained information from short (0.2-0.5 nanoseconds [ns]) MD simulations and use this in a meso-scale simulation to calculate diffusion constants in polymer matrices. This is a grid-based method, which calculates the average probability of each grid point of being a void and performs constrained and biased Monte Carlo (MC) dynamics to reach much longer time regimes than possible in MD. The MC method mimics the three regimes of mean square deviation (MSD) behavior seen in MD, thus accounting for the proper mobility of the voids and the compressibility of the polymer matrix. Theoretical discussions and justification for the method is presented in chapter 6. Initial results on He diffusion in a low-density polyethylene (PE) matrix are presented in chapter 7. The behavior at different temperatures follows closely the trend observed from calibrating long term MD for this particular system.\r\n", "doi": "10.7907/9b0m-2j57", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:14280", "collection": "thesis", "collection_id": "14280", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06182021-193858046", "primary_object_url": { "basename": "Kuwata_Keith_1998_Thesis_Scan.pdf", "content": "final", "filesize": 11155550, "license": "other", "mime_type": "application/pdf", "url": "/14280/1/Kuwata_Keith_1998_Thesis_Scan.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Spectroscopic and Computational Studies of Ionic Clusters as Models of Solvation and Atmospheric Reactions", "author": [ { "family_name": "Kuwata", "given_name": "Keith Tadao", "orcid": "0000-0002-3542-2081", "clpid": "Kuwata-Keith-Tadao" } ], "thesis_advisor": [ { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Yung", "given_name": "Yuk L.", "clpid": "Yung-Y-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Ionic clusters are useful as model systems for the study of fundamental processes in solution and in the atmosphere. Their structure and reactivity can be studied in detail using vibrational predissociation spectroscopy, in conjunction with high level ab initio calculations. This thesis presents the applications of infrared spectroscopy and computation to a variety of gas-phase cluster systems.
\r\n\r\nA crucial component of the process of stratospheric ozone depletion is the action\r\nof polar stratospheric clouds (PS Cs) to convert the reservoir species HCl and chlorine\r\nnitrate (CIONO\u2082) to photochemically labile compounds. Quantum chemistry was used to\r\nexplore one possible mechanism by which this activation is effected:
\r\nCI\u207b + CIONO\u2082 \u2192 CI\u2082 + NO\u2083\u207b (1)
\r\nCorrelated ab initio calculations predicted that the direct reaction of chloride ion with CIONO\u2082 is facile, which was confirmed in an experimental kinetics study. In the reaction a weakly bound intermediate Cl\u2082--NO\u2083\u207b is formed, with ~70% of the charge localized on the nitrate moiety. This enables the Cl\u2082--NO\u2083\u207b cluster to be well solvated even in bulk solution, allowing (1) to be facile on PSCs.
Quantum chemistry was also applied to the hydration of nitrosonium ion (NO\u207a), an important process in the ionosphere. The calculations, in conjunction with an infrared spectroscopy experiment, revealed the structure of the gas-phase clusters NO\u207a(H\u2082O)\u2099. The large degree of covalent interaction between NO\u207a and the lone pairs of the H\u2082O ligands is contrasted with the weak electrostatic bonding between iodide ion and H\u2082O.
\r\n\r\nFinally, the competition between ion solvation and solvent self-association is explored for the gas-phase clusters CI\u207b(H\u2082O)\u2099, and CI\u207b(NH\u2083)\u2099. For the case of water, vibrational predissociation spectroscopy reveals less hydrogen bonding among H\u2082O ligands than predicted by ab initio calculations. Nevertheless, for n\u22655, cluster structure is dominated by water-water interactions, with CI\u207b only partially solvated by the water cluster. Preliminary infrared spectra and computations on CI\u207b(NH\u2083)\u2099 indicate that NH\u2083 preferentially binds to CI\u207b ion instead of forming inter-solvent networks.
", "doi": "10.7907/27ng-zt31", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:5313", "collection": "thesis", "collection_id": "5313", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10202009-092753223", "primary_object_url": { "basename": "Faglioni_f_1998.pdf", "content": "final", "filesize": 4545332, "license": "other", "mime_type": "application/pdf", "url": "/5313/1/Faglioni_f_1998.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Quantum chemical computations of heterogeneous selective oxidation, STM images, and multiple bond reactions", "author": [ { "family_name": "Faglioni", "given_name": "Francesco", "clpid": "Faglioni-F" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter one of this thesis describes first principles electronic structure computations performed to understand the mechanism of molecular oxygen activation by vanadyl pyrophosphate. The process is believed to play a key role in the catalytic oxidation of n-butane to maleic anhydride. The results obtained demonstrate that the mechanism involves at least two layers of vanadyl pyrophosphate crystal. Based on the computed energetics for small clusters, we propose an activation mechanism which involves the transfer of one oxygen atom from the first to the second layer of the crystal concerted with dioxygen activation by the first layer.\r\n\r\nChapter two describes a novel ab-initio computational technique, called GVB-RCI, which correctly describes the stretching and dissociation of multiple bonds and provides smooth potential energy surfaces for most chemical reactions. The technique is a special case of Multi Configuration SCF that does not have the Perfect Pairing restriction and still scales well with the size of the system. The capabilities and limitations of GVB-RCI are illustrated in the case of a few simple chemical reactions.\r\n\r\nChapter three contains a theoretical model describing the Scanning Tunneling Microscopy (STM) imaging of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort, and provides images that are in qualitative agreement with experimental results. The model predicts that topographic effects will dominate the STM images of alkanes on graphite surfaces. The computations correlate well with the STM data of functionalized alkanes, and allow assessment of the structure and orientation of most of the functionalized alkanes \r\nthat have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals of the adsorbed molecules, may play an important role in determining the STM \r\nimage contrast of such systems.", "doi": "10.7907/ksr7-qk84", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:13589", "collection": "thesis", "collection_id": "13589", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11212019-142607353", "primary_object_url": { "basename": "zuercher-wj-1998.pdf", "content": "final", "filesize": 4896812, "license": "other", "mime_type": "application/pdf", "url": "/13589/1/zuercher-wj-1998.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ruthenium-Catalyzed Polycyclization Reactions", "author": [ { "family_name": "Zuercher", "given_name": "William John", "clpid": "Zuercher-William-John" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Myers", "given_name": "Andrew G.", "clpid": "Myers-A-G" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Ruthenium carbene Cl\u2082(PCy\u2083)\u2082Ru=CHCH=CPh\u2082 mediates the efficient and selective conversion of acyclic dienynes to fused bicyclic [n.m.0] dienes containing five-, six- and seven-membered rings. Studies with various X-substituted acetylenes (X = H, alkyl, Ph, CO\u2082Me, SnBu\u2083, SiMe\u2083, halogen) suggest that the dienyne metathesis is not only sensitive to these substituents but also to the catalysts employed. Among the various metal alkylidenes examined, only the ruthenium catalyst I exhibited metathesis activity for a range of substrates. In no case, however, were acetylenes with heteroatomic substituents metathesized; these substrates either underwent simple diene RCM or failed to react with the catalyst in a productive fashion. These observations further expand the scope of catalytic RCM for the construction of complex organic compounds.
\r\n\r\nRuthenium alkylidene Cl\u2082(PCy\u2083)\u2082Ru=CHPh has been utilized in the tandem ring-opening/ring-closing metathesis of cycloolefins. This reaction produces a bicyclic molecules conatining nonconjugated dienes. Reactivity of the precursors is dependent upon strain, and thus ring size, of the cycloolefins. Competing oligomerization is observed in substrates having low ring strain; this process is inhibited by increasing dilution of the reaction or by adding alkyl substitution to the acyclic olefins.
\r\n\r\nThe application of ruthenium alkylidene Cl\u2082(PCy\u2083)\u2082Ru=CHPh to the catalysis of polycyclization reactions is detailed. Several acyclic precursors have been synthesized and reacted with the ruthenium alkylidene. These precursors vary in topology and contain either acetylenic or cyclic olefin metathesis relays or both. The cyclization reactions proceed in moderate to good yield to produce polycyclic polyenes when the precursors are subjected to catalytic amounts of the ruthenium complex. Precursors bearing n relay units generate polycycles containing (n + 1) rings.
", "doi": "10.7907/2857-9b48", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:5375", "collection": "thesis", "collection_id": "5375", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-113407018", "primary_object_url": { "basename": "Ramirez_be_1998.pdf", "content": "final", "filesize": 10289035, "license": "other", "mime_type": "application/pdf", "url": "/5375/1/Ramirez_be_1998.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The CU\u2090 center of cytochrome oxidase : electronic structure calculations and electron-tunneling pathways", "author": [ { "family_name": "Ramirez", "given_name": "Benjamin E.", "clpid": "Ramirez-Benjamin-E" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The Cu_A center is a mixed valence, dithoilate-bridged, binuclear copper center that is found in cytochrome oxidase. It serves as the initial acceptor of electrons from cytochrome c. The Cu_A center has distinct UV/Vis and EPR spectroscopic features. It is likely that this site has an extremely low inner-sphere reorganization energy because it very efficiently transfer electrons st low reaction driving forces over long distances (~15-20 \u00c5) in less than a millisecond. We undertook DFT calculations on a Cu_A model complex to examine the structure, spectroscopic assignments and reorganization energy of the center. The optimized structure of the Cu_A model complex closely resembles the structure determined from x-ray diffraction studies. The rms overlap of the optimized structure with the structure derived from EXAFS data is 0.16 \u00c5. Based on the calculated MO diagram, we assign the bands in the UV/Vis absorption spectrum to transitions originating from lower lying doubly-filled orbitals into a \u03c3_(Cu)* singly-occupied HOMO that is primarily Cu d_(x2-y2)/S p_x in character. We find that the character of the HOMO as well as the transition energies and intensities are extremely sensitive to the Cu-S-Cu angle. We also calculated the optimized structure of the reduced center to examine the role of the protein in reducing the inner-sphere reorganization energy. The following picture emerges from the calculations of the coordination geometry: the protein framework imposes a structure, with a low dielectric cavity in which the trigonal geometry of the oxidized form is optimal. In addition, this framework prevents the reduced structure from distorting to its optimal (linear, two-coordinate) structure. This so-called rack effect of the folded protein enables Cu_A and blue copper centers to function as very efficient electron-transfer agents.", "doi": "10.7907/r7t8-xt78", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "id": "thesis:4805", "collection": "thesis", "collection_id": "4805", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-112630", "primary_object_url": { "basename": "Tsai_bl_1997.pdf", "content": "final", "filesize": 5952071, "license": "other", "mime_type": "application/pdf", "url": "/4805/1/Tsai_bl_1997.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "First principles studies of semiconductor epitaxial growth", "author": [ { "family_name": "Tsai", "given_name": "Bao-Liang", "clpid": "Tsai-B" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis conducts investigations mainly on the structures, energetics, and reactions of semiconductor as well as oxide surfaces using first principles cluster model approach.
\r\n\r\nThe first part of the research work addresses the issues in the epitaxial growth of Hg1-xCdxTe (MCT) materials. Hg divalent compounds were studied thoroughly using a variety of quantum chemical methods in order to understand the energetics of Hg precursors for growth. The (001) growth surfaces were then examined in detail using cluster model calculations. Based on these results, a novel metal-organic molecular beam epitaxial (MOMBE) growth strategy with favorable energetics for growing MCT using H2C=CH-CH2-Hg-C=C-CH3 is proposed. It is hoped that with this new growth strategy, the Hg vacancy and p-doping problems that currently exist in growth can be avoided.
\r\n\r\nThe second part of the thesis discusses the molecular beam epitaxial (MBE) growth of cubic GaN on the (001) surface using various N sources. Surface reconstructions and the interactions of gas-phase atomic and molecular nitrogens with the surface were elucidated using cluster models. Using these results an energy phase diagram for the growth of GaN has been constructed. It suggests that excited state molecular N2 (3\u03a3u+) is the most favorable of all N species for growth of high quality GaN because it can undergo a dissociative chemisorption process. Ground state atomic N (4S) is also good for growth. The doublet excited states N (2D and 2P) might cause surface N abstraction, leading to N vacancies in the material.
\r\n\r\nFinally, a Fe(OH)3(H20)3 GVB cluster model of crystalline \u03b1-Fe203 was developed. This simple model can describe the local geometry and bonding of Fe in the bulk oxide. Using quantum mechanical calculations, the orientation of the oleic imidazoline (OI) molecule bonding to the oxide surface has been determined. OI class of molecules are used extensively for corrosion inhibitor in oil field pipeline applications. It is found in this work that OI can make very strong bonding to the Fe of the iron oxide. In aqueous environments they can replace water on the pipe surface to form a protective layer to prevent corrosion.
\r\n", "doi": "10.7907/2CV3-2A62", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:170", "collection": "thesis", "collection_id": "170", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01142008-075423", "primary_object_url": { "basename": "Jonscher_kr_1997.pdf", "content": "final", "filesize": 8993313, "license": "other", "mime_type": "application/pdf", "url": "/170/1/Jonscher_kr_1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Quadrupole Ion Trap Mass Spectrometry of Peptides", "author": [ { "family_name": "Jonscher", "given_name": "Karen Rae", "orcid": "0000-0002-7929-4886", "clpid": "Jonscher-Karen-Rae" } ], "thesis_advisor": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Biological mass spectrometry addresses the challenging unsolved structural issues surrounding biopolymers of fundamental importance to the biomedical sciences. Key to this discipline is the ability to extract useful information from complex peptide mixtures. Several approaches were developed to analyze peptides utilizing the unique capabilities of the quadrupole ion trap mass spectrometer. An external matrix-assisted laser desorption ionization source was constructed. Detection of peptides in the mid-femtomole range and of proteins in the low-femtomole range was reported. Singly-charged molecules with molecular weights in excess of 34,000 u were observed. Peptides generated by enzymatic digestion of the P protein of Sendai virus were separated by HPLC and the technique was successfully applied to locate phosphorylation sites.\r\n\r\nA hybrid quadrupole mass filter/quadrupole ion trap mass spectrometer was assembled. Peptide mixtures were separated by sequentially transmitting one value of m/z into the ion trap for mass analysis. The sequential injection technique served to significantly reduce space charge-induced suppression effects and improved resolution and fragmentation efficiency when compared to results obtained using an ion trap. A novel method of scanning afforded the ability to perform neutral loss experiments for the identification of phosphopeptides in a mixture. A long duty cycle, due to acquisition hardware, limited the utility of this approach for continuous ionization techniques.\r\n\r\nA low flowrate ionization source was constructed and interfaced to the hybrid and to an ion trap. A unique needle configuration provided a detection limit of 75 attomole of a peptide mixture infused into the source. A new type of liquid junction was developed to apply voltage to the sample consisting of a platinum wire inserted into the sidewall of a length of Teflon tubing. The junction was versatile, robust, and easy to use and performance compared well with other types of junctions. Capillary electrophoresis and hydrophobic membranes were used to separate peptide mixtures. Detection limits of the techniques were 1 femtomole and 10 femtomoles, respectively, for angiotensin. Differential release of peptides using step elutions from the hydrophobic membrane was demonstrated, providing a sensitive, high throughput means of mixture simplification prior to separation by capillary electrophoresis.", "doi": "10.7907/9btc-bk47", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:17528", "collection": "thesis", "collection_id": "17528", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07152025-200013414", "primary_object_url": { "basename": "Mines_GA_1997.pdf", "content": "final", "filesize": 47880549, "license": "other", "mime_type": "application/pdf", "url": "/17528/1/Mines_GA_1997.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Cytochrome c : Folding Triggered by Electron Transfer. Rates of Heme Oxidation and Reduction at High Driving Forces", "author": [ { "family_name": "Mines", "given_name": "Gary Alan", "clpid": "Mines-Gary-Alan" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" } ], "thesis_committee": [ { "family_name": "Barton", "given_name": "Jacqueline K.", "orcid": "0000-0001-9883-1600", "clpid": "Barton-J-K" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Rates of various intramolecular heme oxidations and reductions in a series of\r\nclosely related RuL2(X)(His33)cytochromes c [L = bipyridine or phenanthroline\r\nderivatives; X = imidazole (im) or cyanide (CN-)] have been measured over a freeenergy\r\nrange of 0.54 to 1.89 eV. The driving-force dependence of Fe2+\u2192Ru3+ electron\r\ntransfer (ET) is well described by semiclassical ET theory with a coupling-limited rate\r\n(kmax) of 2.8 x 106 s-1 and a reorganization energy of 0.74 eV. As predicted by theory,\r\nthe rate of an exergonic (-\u0394G\u00b0 = 1.3 eV) heme reduction reaction,\r\n*Ru2+(bpy)2(im)(His)\u2192Fe3+, falls in the inverted region (k = 2.0 x 105 s-1). In contrast,\r\nthe rates of three highly exergonic heme reductions, *Ru2+(phen)2(CN)(His)\u2192Fe3+ (3.1\r\nx 105 s-1; 1.4 eV), Ru+(4,4'-(CONH(C2H5))2-bpy)2(im)(His)\u2192Fe3+ (2.3 x 105 s-1; 1.44\r\neV), and Ru+(phen)2(CN)(His)\u2192Fe3+ (4.5 x 105 s-1; 1.89 eV), are much higher than\r\nexpected for reactions directly to ground-state products. Agreement with theory is\r\ngreatly improved by assuming that an electronically excited ferroheme\r\n(Fe2+\u2192*Fe2+ ~ 1.05 eV) is the initial product in each of these reactions.
\r\n\r\nIn a separate investigation, rates of folding of ferrocytochromes c from horse\r\n(h-cyt c) and yeast (y-cyt c) were measured over a range of denaturant concentrations\r\n(guanidine hydrochloride, GuHCl) and folding free energies (\u0394Gf) using a new ET\r\ntriggering technique. The backbone structures of the two homologs are similar, but y-cyt\r\nc is ~ 15 kJ mol-1 less stable than h-cyt c and is unfolded at concentrations of GuHCl ~ 1.5\r\nM lower than for h-cyt c. Activation free energies exhibit a linear dependence on GuHCl\r\nand \u0394Gf for both proteins, with folding rates decreasing with increasing concentration of\r\nGuHCl (less negative \u0394Gf). At a given denaturant concentration, the folding rates for y-cyt\r\nc are about an order of magnitude slower than those for h-cyt c, but when the folding\r\nfree energies are matched, folding rates of the two homologs are comparable.
", "doi": "10.7907/rtx8-jn96", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:13580", "collection": "thesis", "collection_id": "13580", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192019-173846004", "primary_object_url": { "basename": "herzog-ta-1997.pdf", "content": "final", "filesize": 8743116, "license": "other", "mime_type": "application/pdf", "url": "/13580/1/herzog-ta-1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Deuterium Isotope Effects as Evidence for \u03b1-Agostic Assistance in Ziegler-Natta Catalysts. Design, Synthesis, and Reactivity of a New Class of Highly Syndiospecific Ziegler-Natta Polymerization Catalysts", "author": [ { "family_name": "Herzog", "given_name": "Timothy Allan", "clpid": "Herzog-Timothy-Allan" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "By applying the concept of \"isotopic perturbation of stereochemistry\" to a number of Group III metallocene catalysts, further evidence for an \u03b1-agostic interaction in the chain propagation step of Ziegler-Natta polymerization has been obtained. These results are in accord with the \"modified Green-Rooney\" mechanism. An \u03b1-agostic interaction in the transition state of olefin insertion may contribute to the remarkable stereoselectivities of many Ziegler-Natta catalyst systems since it may restrict the possible orientations of the polymer chain such that it has a more significant impact on the orientation of the inserting olefin.
\r\n\r\nA new class of Group IV metallocene catalysts is presented for the syndiospedfic polymerization of propylene. These catalysts incorporate what are thought to be the key characteristics of syndiospedfic metallocene catalysts: Cs symmetry and rigidly linked cyclopentadienyls of greatly differing size. However, preliminary attempts to develop new syndioselective catalysts have suggested another important characteristic: a pocket in the larger moiety to avoid undesirable steric interactions between the ligand framework and coordinated olefin. In order to accommodate this constraint, a ligand system with a 1,3-dialkylcyclopentadienyl doubly linked to a singly substititued cydopentadienyl was chosen. Group IV metallocenes with these new ligands, in the presence of a cocatalyst (MAO), react rapidly with neat propylene to form highly syndiotactic polypropylene. This is the first example of a stereospecific doubly bridged olefin polymerization catalyst and is the first example of a highly syndiospedfic polymerization catalyst not based on a fluorenyl like ligand. This catalyst system is also very versatile since straightforward changes in the alkyl group of the singly substituted cydopentadienyl and in the reaction conditions lead to dramatic changes in the polymer microstructure. These catalysts should provide an excellent platform for mechanistic study and may be important industrially.
", "doi": "10.7907/tv4y-w681", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:198", "collection": "thesis", "collection_id": "198", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01162008-075117", "primary_object_url": { "basename": "Melnik_ms_1997.pdf", "content": "final", "filesize": 9091280, "license": "other", "mime_type": "application/pdf", "url": "/198/1/Melnik_ms_1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Diamond surfaces : interactions with hydrogen and halogens", "author": [ { "family_name": "Melnik", "given_name": "M. Susan", "clpid": "Melnik-M-Susan" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Atwater", "given_name": "Harry Albert", "clpid": "Atwater-H-A" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nAbsolute deuterium coverage on the diamond C(100) surface has been measured under a variety of dosing conditions by nuclear reaction analysis (NRA) using [...]. The (2x1) surface with ~1.0 D per surface C is produced under typical dosing conditions. However, at unusually high filament temperatures circa 2000\u00b0C, coverages up to 1.34 \u00b1 0.09 D per surface C are observed. Coverage is calibrated by comparing to a standard containing 1.5x[...] D/[...]. Signal from subsurface deuterium is estimated to be negligible by comparison to previous scattering experiments and by secondary-ion mass spectroscopy of a homoepitaxial CVD (100) sample. D breakage of surface dimer bonds at high filament temperature is proposed as a mechanism to generate surface dideuterides. The relevance of dimer breakage and dihydride formation to recent experiments on surface degradation is briefly discussed.\r\n\r\nPrevious models of hydrogen reactions with C(100) are substantially revised to include all types of sites on the reconstructed terrace, and it is shown that saturation coverage determines the ratio of site-averaged abstraction rate to site-averaged recombination rate, [...]. NRA coverage measurements of 0.95 \u00b1 0.04 D per surface C imply a [...] of 0.06 \u00b1 0.04 at 1800\u00b0C gas temperature and 360\u00b0C surface temperature. Results indicate that thermochemical kinetic models overpredict by a factor of ~20 the fraction of sites available for growth during diamond CVD.\r\n\r\nIn a separate issue, C(110) surface mobility is demonstrated by calculating activation energies for the migrations of H, F, and Cl with quantum chemical methods using hydrocarbon cluster models. The calculations included extensive basis sets with many-body effects at the level of single and double excitations from Hartree-Fock and Complete-Active-Space wavefunctions. Intra-chain migrations of H along [...] carbon chains and nearest-neighbor F migration are found to be too slow to compete with thermal desorption. However, inter-chain migrations of H and Cl are calculated to be sufficiently fast to compete with thermal desorption under ultrahigh vacuum conditions and with gas-surface reactions under typical diamond growth conditions. This was the first study to consider migration rates as well as barriers, establishing mobility's competitiveness during diamond growth. [...]/[...] is estimated to be [...]. Finally, a kinetic Monte-Carlo algorithm is presented to directly combine mobility with gas-surface reactions in the same iteration step when simulating hydrogen processing of diamond.\r\n", "doi": "10.7907/gdrt-7n92", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:173", "collection": "thesis", "collection_id": "173", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01142008-080911", "primary_object_url": { "basename": "McClurg_rb_1997.pdf", "content": "final", "filesize": 5159350, "license": "other", "mime_type": "application/pdf", "url": "/173/1/McClurg_rb_1997.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Homogeneous nucleation theory", "author": [ { "family_name": "McClurg", "given_name": "Richard Beatty", "clpid": "McClurg-R-B" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" } ], "thesis_committee": [ { "family_name": "Flagan", "given_name": "Richard C.", "clpid": "Flagan-R-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis thesis is composed of a brief preface followed by six chapters addressing various aspects of homogeneous nucleation theory. In the preface, I motivate the need for improved theoretical approaches to resolve the discrepancies between current theory and experiment. The remaining chapters are collected research papers which are in print, in press, or to be submitted as of the writing of the thesis. They were written in collaboration with one or both of my advisors. In Chapter 2, we review current nucleation theories in a statistical mechanical framework. This framework allows us to identify the errors of the various models and to point out internal inconsistencies in some of them. In Chapters 3 and 4, we develop methods to calculate the partition function and thermodynamic properties for noble gas clusters. The methods allow us to describe the asymptotic approach of cluster properties toward the bulk limit with increasing cluster size and to calculate the nucleation rate for supersaturated noble gas vapors. We then apply the methods to the homogeneous nucleation of condensed mercury from a supersaturated vapor in Chapter 5. Chapters 6 and 7 contain portions of the theoretical groundwork needed to extend atomistic nucleation theories to molecular systems. Chapter 6 is a development of a one-dimensional hindered rotor partition function. It sets the stage for the two and three-dimensional hindered rotor partition functions needed to model molecular solids. In Chapter 7 we construct a model for the charge distribution of [...]. We chose this icosahedral molecule as an ideal plastic crystalline substances. The plastic crystals are solids with translational symmetry, but having weak orientational symmetry due largely to their highly symmetric molecular charge distributions. Thus, plastic crystals are ideal hindered rotors in multiple dimensions. I conclude the thesis with some brief comments on my assertion that molecules which form plastic crystals will provide a fruitful common ground for theoretical and experimental investigations of homogeneous nucleation phenomena.\r\n", "doi": "10.7907/Z011-9767", "publication_date": "1997", "thesis_type": "phd", "thesis_year": "1997" }, { "id": "thesis:5317", "collection": "thesis", "collection_id": "5317", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-150813700", "primary_object_url": { "basename": "Gerdy_jj_1996.pdf", "content": "final", "filesize": 6054761, "license": "other", "mime_type": "application/pdf", "url": "/5317/1/Gerdy_jj_1996.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Accurate Interatomic Potentials for Simulations", "author": [ { "family_name": "Gerdy", "given_name": "James Joseph", "clpid": "Gerdy-James-Joseph" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis develops a rational foundation for the application of long-range forces to atomistic simulations. This area has lagged behind the other components \r\nof simulations because of two factors. First, the nonbond forces are difficult to probe experimentally. There are only a few materials for which properties clearly \r\nand directly correlate with van der Waals forces (such as molecular crystals) and then some of these cases are not relevant to common modeling applications (e.g. the \r\nhydrogen van der Waals forces in H_(2(xtl)) to are different from those in hydrocarbons). Second, more than for valence force field terms, van der Waals forces are difficult to determine by calculation. The forces are weak and require a large number of basis functions per atom to treat properly.\r\n\r\nThis thesis contains a method which has optimized a level of ab initio calculation on small clusters in order to extract a van der Waals potential. The size of \r\nthe calculation is controlled by carefully optimizing the basis set. Moreover, unlike for previous calculations of this sort, it was recognized that the repulsive and attractive potentials (the monotonic potentials) which constitute the van der Waals potential can be calculated optimally with different basis sets, further accelerating the calculation for a given level of accuracy. Also the use of diffuse basis sets off of the atom centers is used here to make the basis sets more efficient. The method \r\nhas been optimized for the case of nitrogen because it is both a closed shell case and relatively common in simulations. What results is a computational method \r\nwhich produces pair potentials for use in force field simulations. This is called the combination of monotonic potentials (COMP) method.\r\n\r\nSubsequently, potentials have been calculated for the atoms H, He, C, N, 0, F, Ne, Si, P, S, Cl, and Ar. In order to test the accuracy, the potentials are \r\napplied to test cases of molecular crystals and compared to other commonly used potentials. Important issues that are addressed are standard combination rules and \r\nthe accuracy of using isotropic pair potentials. COMP potentials give a measure of accuracy of van der Waals potentials for any atom. This research has also yielded an\r\naccurate functional form, a variant of the Morse potential, which has not been used in simulations but provides very accurate fits to the ab initio data. The relationships between different functional forms are analyzed so that the designer of force fields can make a judicious choice of both ab initio calculations to determine potentials and the appropriate functions with which to fit them.\r\n", "doi": "10.7907/g2gs-kv14", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:13677", "collection": "thesis", "collection_id": "13677", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04202020-161109407", "type": "thesis", "title": "Spectroscopy of Reactive Molecules and Clusters", "author": [ { "family_name": "Johnson", "given_name": "Matthew Stanley", "clpid": "Johnson-Matthew-Stanley" } ], "thesis_advisor": [ { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Chan", "given_name": "Sunney I.", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis presents spectroscopic investigations of reactive molecules and clusters. The techniques of laser excited fluorescence, infrared predissociation spectroscopy, and photoelectron spectroscopy were employed to investigate systems relating to fundamental cluster chemistry, ion solvation, and atmospheric ozone depletion.
\r\n\r\nAn instrument was developed to investigate van der Waals complexes of refractory elements. A pulsed laser ablation cluster source harnessed the cooling power of a supersonic free jet to condense weakly bound neutral clusters. Laser excited fluorescence was used to characterize the products of the source, which included adducts of aluminum atoms with water molecules, hydrogen, and argon. The species Al(H\u2082O), AlAr and AlH were identified.
\r\n\r\nThe infrared predissociation spectra of positive and negative cluster ions were investigated using a tandem time-of-flight instrument. In this work the photofragment yield spectrum of mass-selected I\u207b(H\u2082O) and I\u207b(H\u2082O)\u2082 complexes was measured between 3170 and 3800 cm\u207b\u00b9. The dominant features in the I\u207b(H\u2082O) spectra were assigned as a hydrogen bonded OH stretch and a free OH stretch. Ab initio calculations were used to aid in spectral assignment and for geometrical information concerning I\u207b(H\u2082O). Absorptions in the iodide water dimer cluster are attributed to a symmetric and an antisymmetric bonded OH stretch, and a free OH stretch.
\r\n\r\nChlorine nitrate is a key reservoir of stratospheric chlorine, and as such its photolysis branching ratio is crucial to partitioning of species involved with stratospheric ozone depletion. The He(I) photoelectron spectrum of chlorine nitrate was measured and assigned in order to understand the photodissociation behavior of chlorine nitrate. The results include the ionization potential of the molecule (10.86 eV), and the assignment of the first ionization peak to a nonbonding chlorine atomic orbital.
", "doi": "10.7907/ta23-4185", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:59", "collection": "thesis", "collection_id": "59", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01072008-115130", "primary_object_url": { "basename": "Hua_x_1996.pdf", "content": "final", "filesize": 17825179, "license": "other", "mime_type": "application/pdf", "url": "/59/1/Hua_x_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "First principles simulations : development of new density functionals and pseudopotentials and formation mechanism of fullerenes", "author": [ { "family_name": "Hua", "given_name": "Xinlei", "clpid": "Hua-X" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThis thesis consists of two parts. Part I deals with the development of first principles methodologies. Part II deals with applications of atomistic simulations, i.e. quantum mechanics and molecular dynamics simulations.\n\nPart I includes two topics. One is generalized gradient correction for the density functional theory which constitutes Chapter 2. The other is first principle pseudopotentials which is covered in Chapter 3 and 4. Chapter 3 develops the density functional theory version used mostly in solid state physics, while Chapter 4 develops the Ab initio version used mostly in chemistry. Part II also includes two topics. One is the fullerenes formation mechanism which is covered in Chapter 5 and 6. Chapter 5 deals with their thermodynamical properties and Chapter 6 discusses their formation processes. The other is the lattice properties for the [...], superconductor which is covered by Chapter 7. Also, in Chapter 1 we summarize the hierarchy models for materials simulations and review the state-of-the-art tools at various levels of that hierarchy.\n\nPredicting the band gap from first principles has been hindered by the complexity of the systems and the flaws in the simplified theories. The most successful first principle theory, i.e. DFT, gives a value about the 2/3 of the measured one. [...] This is partly due to the approximate nature of the functionals used in DFT calculations. It has long been known that HOMOs calculated with LDA, the most commonly used DFT, is far from ionization potential. [...] In Chapter 2, after analyzing the nature of gradient corrected functional for DFT, we proposed a new exchange energy functional. The new functional is tested on several atoms and molecules and found to reproduce the Hartree-Fock eigenvalues to a good accuracy. With the incorporation of correlation energy in DFT, we can hope that the new functional would lead to a new and efficient way of predicting energy band gaps for all the materials from first principles.\n\nAll chemistries involve mainly valence electrons. The effect of inner shells, shielding the nucleus Coulomb potential and providing Pauli repulsions to support the valence electrons, can be implemented by a potential called effective core potential (ECP). Since valence electrons of different angular momentum would experience different Pauli repulsion of the core electrons, this ECP is angular momentum dependent. This leads to a nonlocal potential and requires three-center integrals, which scales quadratically with the size of the system. On the other hand, the wave nature of electrons allows us to lower the resolution in describing the potential. By using a set of Gaussian functions to replace real-space grid in representing the ECP, we factorized the three-center integral into a sum of products of two-center integrals. We have found a set of Gaussian functions that gives accuracy of better than [...] for all the elements in the periodic table, sufficient for all ECP calculations. The new method scales linearly with the system size. At 128 atoms, the cost is 1/15 of the old ECP method. This cleared a bottleneck for first principle programs that use ECP to study heavy elements.\n\nWhy [...] fullerenes are so stable and how this highly symmetric molecule is formed in the super-heated vapor is the two most fundamental questions in fullerene research. Prompted by the recent observations of the monocyclic ring and bycyclic rings as intermediates, we performed DFT calculations on the ring isomers and fullerene isomers of carbon clusters of various sizes. From it we extracted a force field (FF) for molecular dynamics simulations. This FF is used to calculate the free-energies at different temperatures. Based on our analysis of the physical forces that drive the carbon clustering and isomerization, we describe an evolution process for fullerene formation that is consistent with all the observations so far. With a combined DFT/MD method we are able to provide the energetics for a complete path of fullerene formation. Hint for synthesis improvement are suggested.\n\nHigh-Tc superconductors are ceramics. To improve their mechanical and electrical properties, we conducted a molecular dynamics simulation for the [...] superconductor. We derived a ionic-covalent force field from fitting the experimental data. Our FF is able to reproduce the structure and Raman modes accurately. The FF predictions of isotope shifts of Raman frequencies, phonon dispersion spectra, phonon density of states, elastic stiffness constants, and volume thermal expansion are all in fairly good agreement with experiments.", "doi": "10.7907/r7qa-wt76", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:14038", "collection": "thesis", "collection_id": "14038", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12222020-002250563", "primary_object_url": { "basename": "colocci-n_1996.pdf", "content": "final", "filesize": 65451588, "license": "other", "mime_type": "application/pdf", "url": "/14038/1/colocci-n_1996.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Cooperative Oligonucleotide-Directed Triple Helix Formation at Adjacent DNA Sites", "author": [ { "family_name": "Colocci", "given_name": "Natalia", "clpid": "Colocci-Natalia" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Myers", "given_name": "Andrew G.", "clpid": "Myers-A-G" }, { "family_name": "Carreira", "given_name": "Erick Moran", "clpid": "Carreira-E-M" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Cooperative interactions between DNA-binding ligands are essential for their sequence specificity, binding affinity, and biological activity. Oligonucleotides can bind cooperatively to adjacent sites on double-helical DNA by triple helix formation. The study of the cooperative binding of oligonucleotides to DNA by triple helix formation is important as it provides useful information for the development of new methods leading to the sequence-specific recognition of DNA. As a first step towards this goal, the thermodynamics of the cooperative binding of oligodeoxyribonucleotides to adjacent DNA sites by triple helix formation have been determined by quantitative affinity cleavage titrations (Chapter Two). A 20-fold enhancement in equilibrium association constant is realized for an 11mer pyrimidine oligonucleotide binding in the presence of a neighboring bound site at 24 \u00b0C and pH 7.0 (25 mM TrisOAc, 10 mM NaCl, 1 mM spermine). This corresponds to an increase in binding free energy of 1.8 kcal\u2022mol\u207b\u00b9. This cooperativity is not observed when the two binding sites are separated by one base pair. The observed cooperative energy likely arises from favorable polarization and charge-charge interactions between the terminal bases at the triple-helical junction.
\r\n\r\nIn addition, the energetics of cooperative binding by oligodeoxyribonucleotides to adjacent sites by triple helix formation have been determined as a function of sequence composition at the junction (Chapter Three). The binding affinity of an 11mer in the presence of a neighboring bound oligonucleotide is enhanced by a factor of 12, 17, 61, and 127 when a 5'-TT-3', 5'-\u1d50C\u1d50C-3', 5'-T\u1d50C-3', and 5'-\u1d50CT-3' stack, respectively, is formed at the junction (10 mM Bis-Tris\u2022HCl at pH 7.0, 10 mM NaCl, 250 \u00b5M spermine, 24 \u00b0C) (\u1d50C designates 5-methyl-2'-deoxycytidine). These binding enhancements correspond to an interaction energy between the two oligonucleotides of 1.5, 1.7, 2.5, and 2.9 kcal\u2022mol\u207b\u00b9, respectively. The energetic penalties for a single-base mismatch differ depending on sequence and the location of the mismatch with respect to the 5'- or 3'-side of the junction. In the case of a 5'-TT-3' stack, a T\u2022GC mismatch on the 5'- side of the junction decreases the interaction energy from 1.5 kcal\u2022mol\u207b\u00b9 to 0.6 kcal\u2022mol\u207b\u00b9, whereas a T\u2022GC mismatch on the 3'- side destroys cooperativity. For a 5'-\u1d50CT-3' stack, a \u1d50C\u2022AT mismatch on the 5'-side of the junction decreases the cooperative interaction energy from 2.9 kcal\u2022mol\u207b\u00b9 to 1.7 kcal\u2022mol\u207b\u00b9, whereas a T\u2022GC mismatch on the 3'-side of the junction destroys cooperativity. Most importantly, two 11mer oligonucleotides interacting through a 5'-TT -3' stack binding to adjacent sites on DNA are significantly more sensitive to single-base mismatches than the corresponding 22mer binding to the same two abutting sites.
\r\n\r\nThe use of modified bases, such as 5-(1-propynyl)-2'-deoxyuridine, increases cooperativity between oligonucleotides bound to adjacent sites on DNA, presumably due to an increased stacking energy between the modified bases at the triplex junction (Chapter Four). Oligodeoxyribonucleotides containing 5-(1-propynyl)-2'-deoxyuridine and 5-methyl-2'-deoxycytidine as short as 8 nucleotides in length bind at micromolar concentrations to adjacent 8-bp sites on double-helical DNA at 24 \u00b0C and pH 7.0 (10 mM Bis-Tris\u2022HCl, 10 mM NaCl, 1 mM spermine). Quantitative affinity cleavage titrations reveal that the binding affinity of an 8mer in the presence of a neighboring bound 8mer is enhanced by a factor of at least 40. This corresponds to a remarkable cooperative interaction energy of > 4.5 kcal\u2022mol\u207b\u00b9. In addition, these cooperative interactions allow oligonucleotides as short as 6mers to bind to three adjacent sites on double-helical DNA at near micromolar concentrations (10 mM Bis-Tris\u2022HCl at pH 7.0, 10 mM NaCl, 1 mM spermine, 24 \u00b0C).
\r\n\r\nCooperativity is also observed between purine-rich oligonucleotides (Chapter Five). Quantitative DNase footprinting titration experiments show that the binding affinity of an 11mer purine-rich oligonucleotide in the presence of a neighboring bound oligonucleotide is enhanced by a factor of 81 when a 5'-GG-3' stack is formed at the junction (50 mM TrisOAc at pH 7.0, 10 mM NaCl, 10 mM MgCl\u2082, 24 \u00b0C). This binding enhancement corresponds to an interaction energy between the two oligonucleotides of 2.7 kcal\u2022mol\u207b\u00b9, and is abolished when the two binding sites are separated by one base pair.
\r\n\r\nThe synthesis of pyrimidine oligonucleotide analogs containing 5-(1-propynyl)- and 2'-O-allyl-modified nucleosides (Chapter Six), and the progress towards the synthesis of a novel base, N7-2'-deoxyisoinosine, designed for the recognition of AT base pairs within a parallel isomorphous purine motif (Chapter Seven), are described.
", "doi": "10.7907/08j6-sd37", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:3387", "collection": "thesis", "collection_id": "3387", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09082006-140314", "primary_object_url": { "basename": "Demiralp_e_1996.pdf", "content": "final", "filesize": 9701253, "license": "other", "mime_type": "application/pdf", "url": "/3387/1/Demiralp_e_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Prediction of structures and properties for organic superconductors", "author": [ { "family_name": "Demiralp", "given_name": "Ersan", "clpid": "Demiralp-E" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe main contributions of this thesis to the field of organic superconductors are basically (a) the band structure calculations for the investigations of the conduction properties of [...] using 2-D Hubbard Model with Unrestricted Hartree-Fock (UHF) theory, (b) ab initio quantum mechanical calculations for the structural characterizations and the properties of the donors of the organic superconductors, (c) electron-transfer boat-vibration (ET-BV) mechanism for the superconductivity of these materials, (d) developing force fields for BEDT-TTF and BEDT-TTF+.\n\nTo provide a basis for understanding the puzzling electronic properties of the organic superconductor [...] (with Tc=10.4K), we carried out band calculations using the 2-D Hubbard Model with Unrestricted Hartree-Fock (UHF) theory. The electron transfer hopping interactions are from ab initio calculations and the Hubbard parameter (Uopt=0.678950 eV) is adjusted to fit Shubnikov-de Haas and magnetic breakdown experiments. The calculations lead to a two-band semi-metal with a momentum gap separating the electron and the hole bands. The anomalous experimental observations are explained in terms of BEDT-TTF related phonons coupling these two bands (lower temperature) and by anion related phonons (higher temperature). These results also provide a framework for describing the conduction properties of other such complexes.\n\nThe donors of all known one- or two-dimensional organic superconductors, X, are based on a core organic molecule that is either tetrathiafulvalene (denoted as TTF) or tetraselenafulvalene (denoted as TSeF) or some mixture of these two molecules. Coupling X, with appropriate acceptors, Y, leads to superconductivity. The oxidized form of X may be X+ or X2+ species in the crystal. Using ab initio Hartree-Fock (HF) calculations (6-31G** basis set), we show that BEDT-TTF deforms to a boat structure (C2 symmetry) with an energy 28 meV (0.65 kcal/mol) lower than planar BEDT-TTF (D2 Symmetry). On the other hand BEDT-TTF+ is planar. Performing ab initio quantum mechanical calculations (HF/6-31G**) also on the other donors of organic superconductors, we find that all known organic superconductors involve an X that deforms to a boat structure while X+ is planar. This leads to a coupling between charge transfer and the boat deformation phonon modes. We propose that this electron-phonon coupling is responsible for the superconductivity and predict the isotope shifts [...] for experimental tests of the electron-transfer boat-vibration (ET-BV) mechanism. We suggest that new higher temperature organic donors can be sought by finding modifications that change the frequency and stability of this boat distortion mode. Based on this idea we have developed similar organic donors having the same properties and have suggested that with appropriate electron acceptors they will also lead to superconductivity.\n\nThe highest transition temperature Tc organic superconductors all involve molecule BEDT-TTF coupled with an appropriate acceptor. The experimental structures exhibit considerable disorder in the outer rings and concomitant uncertainty in the structures of BEDT-TTF. We find that Hartree-Fock (6-31G** basis set) calculations leads to results within 0.01\u00c5 and 1\u00b0 of experiment for the ordered regions allowing us to predict to composite structures expected to have this accuracy. We report optimized geometries and atomic charges for BEDT-TTF, BEDT-TTF+, and BEDT-TTF+1/2 that should be useful for atomistic simulations.\n\nThe vibrational levels of BEDT-TTF and BEDT-TTF+ have been only partially observed and assigned. In order to provide a complete consistent description of all levels, we carried out HF calculations for all fundamental vibrational frequencies of BEDT-TTF and BEDT-TTF+ and obtained the Hessians for these structures. With these Hessians and available experimental frequencies, we developed the force fields for the neutral and cation BEDT-TTF molecules by using Hessian-biased method.\n", "doi": "10.7907/7p7g-sm17", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:8124", "collection": "thesis", "collection_id": "8124", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03112014-150124711", "type": "thesis", "title": "Binding site size limitations of imidazole-pyrrole polyamides for recognition in the minor groove of DNA", "author": [ { "family_name": "Kelly", "given_name": "James J.", "clpid": "Kelly-J-J" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Rees", "given_name": "Douglas C.", "clpid": "Rees-D-C" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The discovery that the three ring polyamide Im-Py-Py-Dp containing imidazole\r\n(Im) and pyrrole (Py) carboxamides binds the DNA sequence 5'-(A,T)G(A,T)C(A,T)-3'\r\nas an antiparallel dimer offers a new model for the design of ligands for specific\r\nrecognition of sequences in the minor groove containing both G,C and A,T base pairs. In\r\nChapter 2, experiments are described in which the sequential addition of five N-\r\nmethylpyrrolecarboxamides to the imidazole-pyrrole polyamide Im-Py-Py-Dp affords a\r\nseries of six homologous polyamides, Im-(Py)2-7-Dp, that differ in the size of their binding\r\nsite, apparent first order binding affinity, and sequence specificity. These results\r\ndemonstrate that DNA sequences up to nine base pairs in length can be specifically\r\nrecognized by imidazole-pyrrole polyamides containing three to seven rings by 2:1\r\npolyamide-DNA complex formation in the minor groove. Recognition of a nine base pair\r\nsite defines the new lower limit of the binding site size that can be recognized by\r\npolyamides containing exclusively imidazole and pyrrolecarboxamides. The results of this\r\nstudy should provide useful guidelines for the design of new polyamides that bind longer\r\nDNA sites with enhanced affinity and specificity.
\r\n\r\nIn Chapter 3 the design and synthesis of the hairpin polyamide Im-Py-Im-Py-\u03b3-Im-\r\nPy-Im-Py-Dp is described. Quantitative DNase I footprint titration experiments reveal\r\nthat Im-Py-Im-Py-\u03b3-Im-Py-Im-Py-Dp binds six base pair 5'-(A,T)GCGC(A,T)-3'\r\nsequences with 30-fold higher affinity than the unlinked polyamide Im-Py-Im-Py-Dp. The\r\nhairpin polyamide does not discriminate between A\u2022T and T\u2022A at the first and sixth\r\npositions of the binding site as three sites 5'-TGCGCT-3', 5'-TGCGCA-3', and 5 'AGCGCT-\r\n3' are bound with similar affinity. However, Im-Py-Im-Py-\u03b3-Im-Py-Im-PyDp\r\nis specific for and discriminates between G\u2022C and C\u2022G base pairs in the 5'-GCGC-3'\r\ncore as evidenced by lower affinities for the mismatched sites 5'-AACGCA-3', 5'-\r\nTGCGTT-3', 5'-TGCGGT-3', and 5'-ACCGCT-3'.
\r\n\r\nIn Chapter 4, experiments are described in which a kinetically stable hexa-aza\r\nSchiff base La3+ complex is covalently attached to a Tat(49-72) peptide which has been\r\nshown to bind the HIV-1 TAR RNA sequence. Although these metallo-peptides cleave\r\nTAR site-specifically in the hexanucleotide loop to afford products consistent with\r\nhydrolysis, a series of control experiments suggests that the observed cleavage is not\r\ncaused by a sequence-specifically bound Tat(49-72)-La(L)3+ peptide.
", "doi": "10.7907/jc2t-pr07", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:11896", "collection": "thesis", "collection_id": "11896", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11052019-172741776", "primary_object_url": { "basename": "claverie-jp-1996.pdf", "content": "final", "filesize": 7479662, "license": "other", "mime_type": "application/pdf", "url": "/11896/1/claverie-jp-1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ring-Opening Metathesis Polymerization with Tungsten Based Catalysts: Kinetics, Thermodynamics and Mechanism", "author": [ { "family_name": "Claverie", "given_name": "J\u00e9r\u00f4me", "clpid": "Claverie-J\u00e9r\u00f4me" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Myers", "given_name": "Andrew G.", "clpid": "Myers-A-G" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Kornfield", "given_name": "Julia A.", "clpid": "Kornfield-J-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Ring-opening metathesis polymerization (ROMP) is instrumental in the synthesis of a variety of polymers. Since the appearance of well defined metathesis catalysts, the synthesis and characterization of ROMP polymers has been greatly improved.
\r\n\r\nIn the first chapter, the kinetics and the thermodynamics of such polymerizations are presented. When a living ROMP polymerization is effected in the presence of a chain transfer-agent, the molecular weight distribution is governed by the kinetics of the polymerization. The molecular weight distribution has been evaluated numerically, and the numerical results have been compared to experimental ones. The living polymerization of norbornene by Mo(=CHR)(=N-1,3-i-Pr-C6H3)(O-t-Bu)2 (R = -t-Bu, -C(CH3)2Ph) in the presence of neohexene and styrene has been used as a model experiment. When the ROMP catalyst is too active, chain transfer to the polymer occurs, and the molecular weight distribution is dependent upon the thermodynamics of the polymerization. The theoretical thermodynamic product distribution has been predicted, and compared to experimental results for the polymerization of 1,5-cyclooctadiene (COD) and cyclooctene. The results have been applied to the synthesis of short polyacetylene oligomers by ROMP of sec-butylcyclooctatetraene.
\r\n\r\nIn the second chapter, the synthesis of monodisperse substituted polyacetylenes is described. For this synthesis, one has to use very active ROMP catalysts which appreciably initiate the polymerization. The new class of tungsten vinyl alkylidenes allows such a polymerization. Synthesis, characterization and catalytic properties of tungsten imido and oxo vinyl alkylidenes is described.
\r\n\r\nIn the third chapter, reactivity of tertiary alcohols with tungsten vinyl alkylidenes and neopentylidenes is examined. These alcohols are found in trace amounts in all the samples of these tungsten carbenes. The role of the alcohols in ROMP is studied for polynorbornene, polycyclooctadiene and polyacetylene. Activation of these catalysts has been observed, even by trace amounts of alcohol, and has important consequences in the microstructure of the resulting polymer. Mechanistic implications toward a general scheme of acid activation of the well defined tungsten carbenes is proposed.
", "doi": "10.7907/h6fj-1t43", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:5072", "collection": "thesis", "collection_id": "5072", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12192007-150129", "primary_object_url": { "basename": "Heikal_aa_1996.pdf", "content": "final", "filesize": 10725002, "license": "other", "mime_type": "application/pdf", "url": "/5072/1/Heikal_aa_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ultrafast molecular dynamics in complexed trans-stilbene", "author": [ { "family_name": "Heikal", "given_name": "Ahmed Abdou", "clpid": "Heikal-A-A" } ], "thesis_advisor": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Culick", "given_name": "Fred E. C.", "clpid": "Culick-F-E-C" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nUltrafast molecular dynamics in large molecular systems have been studied using either pump/probe time-of-flight mass spectrometry, or laser-induced fluorescence with time-correlated single photon counting technique. Intramolecular vibrational energy redistribution (IVR) and photoisomerization reaction in alkane-solvated and substituted trans-stilbenes are presented. Absent, restricted, and dissipative IVR were identified in stilbene-hexane[...] van der Waals complex. The dramatic increase of the density of states upon hexane solvation shifts the threshold for an efficient IVR to much lower excess-energy (~300 [...] for the dissipative regime) in comparison with the bare molecule (~1170 [...]). The effects of symmetry, density of states, and number of atoms on IVR were studied by using 4-methoxystilbene, 4,4'-dimethoxystilbene, and 2-phenylindene as model systems. The solvation and structural effects on the isomerization reaction in trans-stilbene is even more dramatic. For the first time, the lowering of the isomerization barrier (~700\u00b1100 [...]) in trans-stilbene upon one-hexane complexation is observed experimentally upon and compared with that in the bare molecule (~1250\u00b1100 [...]). Furthermore, the isomerization rate above the barrier in stilbene-(hexane)[...] complex is slightly slower than that in bare trans-stilbene. As the excess-vibrational energy exceeds the calculated binding energy of the (1:1) complex, the vibrational predissociation channel become open and was accounted for by using a simple kinetic model. Further decrease in the isomerization rate in stilbene-hexane[...] clusters was observed as the number of solvent molecules [...] increases. As the cluster size increases, the rate becomes less dependent on the excess energy in the [...]-state and the separation of the barrier must await theoretical calculations. The solvent polarity (in stilbene-hexanenitrile[...] complexes) and isotope effects (in stilbene-hexane-[...] complex) on the overall isomerization reaction were also examined. Similar studies were carried out on stilbene-(ethane)[...] clusters which has a lower binding energy than stilbene-(hexane)[...] clusters which, in turn, make the fragmentation of the cluster more severe. On the other hand, interesting observations were made on the reaction dynamics in a designed set of substituted stilbenes. 4-Methoxystilbene, 4,4'-dimethoxystilbene, 4,4'-dihydroxystilbene, trans-[beta]-1-cyclohexene-styrene and 2-phenylindene were used as model systems to study the role of electron conjugation and the torsional motion around [...]-[...] single bond in the isomerization reaction in trans-stilbene.\n", "doi": "10.7907/p3gz-kj57", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:11894", "collection": "thesis", "collection_id": "11894", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11052019-113518368", "primary_object_url": { "basename": "Blake_RE_1996.pdf", "content": "final", "filesize": 43955318, "license": "other", "mime_type": "application/pdf", "url": "/11894/1/Blake_RE_1996.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Synthesis, Characterization and Study of Transition Metal Complexes for the Oxidation and Activation of Hydrocarbons", "author": [ { "family_name": "Blake", "given_name": "Robert Edward, Jr.", "clpid": "Blake-Robert-Edward-Jr" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Anson", "given_name": "Fred C.", "clpid": "Anson-F-C" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The reaction of previously characterized ruthenium oxo complex, [LOEtRuV(O)(\u00b5-O)]2 with alcohol substrates was undertaken to elucidate the mechanism of the oxidation reaction. Unfortunately, an autocatalytic reaction between the organometallic product, [LOEtRuIV(OH)(\u00b5-O)]2 and the reactant alcohol, as well as catalyst decomposition made exact determinations of rate constants impossible. During the course of this investigation, the free acid form of the ligand, LOEtH, was isolated as a viscous oil. Subsequent investigation of the reactions of [LOEtRuV(O)(\u00b5-O)]2 with other species such as acids, salts and bases demonstrated the inherent instability of the complex. In several cases, initial products were spectroscopically characterized, but isolation of pure compounds was not achieved.
\r\n\r\nGiven the problems with the decomposition of ruthenium complexes which utilized the Klaui ligand, trimetaphosphate was studied as a potentially oxidation-resistant alternative for the development of oxidation catalysts. Attempts were made to prepare salts of the trimetaphosphate ligand which are soluble in nonpolar media and free of water of hydration. Coordination complexes of the trimetaphosphate anion and transition elements were synthesized. The mode of coordination and stability of the ligand was examined by infrared and visible spectroscopy. In all cases, the very weakly coordinating trimetaphosphate anion failed to displace other weakly associated ligands from the metal, failed to adopt the proper coordination geometry or was easily removed from the metal center by water.
\r\n\r\nHexabenzyloxycyclotriphosphatriene was synthesized and thermally rearranged to 1,3,5 - tribenzyl - 2,4,6 tribenzyloxy - 2,4,6 trioxocyclotriphosphazane as per published procedures. Characterization of the rearranged product by NMR techniques revealed the previously undetermined stereochemistry of the product. This ligand precursor has been shown to react with trialkyl silyl chlorides, although the products have not been characterized.
\r\n\r\nCp*2Ta(=NtBu)(THF)[B(C6F5)4] (1) was synthesized according to the method developed previously in our group. A cationic analog to Bergman's Cp2Zr(=NtBu), the reactivity of this complex to hydrocarbon substrates was studied. Contrary to previous reports, this complex does not react with methane, but C-H activation reactions were observed for propyne and phenyl acetylene. In the propyne case, an initial mixture of the [2+2] and C-H activation products was driven to exclusively the C-H activation product thermally. An interesting intramolecular activation of a Cp* methyl group precludes much of the desired C-H activation chemistry. The steric demands of the active site was demonstrated by the observed reaction with ethylene, but the lack of reactivity towards propene. A very interesting dealkylation of the imido group was observed upon reaction with carbon dioxide, which is proposed to involve the intermediacy of a coordinated isocyanate. Cp*2Ta(=NtBu)(THF)[B(C6F5)4] reacts as expected with water, HCl and dihydrogen, and reacts cleanly with methylene chloride to give Cp*2Ta(NHtBu)Cl[B(C6F5)4]. Many of the new compounds have been crystallographically and spectroscopically characterized. The reactivity of this complex can be rationalized in terms of the presence of both electrophilic and nucleophilic sites in the same molecule.
", "doi": "10.7907/s731-np77", "publication_date": "1996", "thesis_type": "phd", "thesis_year": "1996" }, { "id": "thesis:3469", "collection": "thesis", "collection_id": "3469", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09112007-104050", "primary_object_url": { "basename": "Bierwagen_ep_1995.pdf", "content": "final", "filesize": 8110671, "license": "other", "mime_type": "application/pdf", "url": "/3469/1/Bierwagen_ep_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computational Studies of Ziegler-Natta Catalysis and Concurrent Resonance Computations", "author": [ { "family_name": "Bierwagen", "given_name": "Erik Paul", "clpid": "Bierwagen-Erik-Paul" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Myers", "given_name": "Andrew G.", "clpid": "Myers-A-G" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis thesis discusses work on two different subjects. First, results from computational studies of Ziegler-Natta catalysts are presented. Quantum mechanical calculations of model Ziegler-Natta catalysts [...] are described, where X is either Cl or the cyclopentadienyl (Cp) ligand, M is a group three transition metal or group four transition metal cation, and R is a hydrogen or alkyl group. It is found that complexes based on group four cations have pyramidal structures (the R group is not in the [...] plane), whereas group three neutral complexes have planar structures. This difference in structure is considered in the context of syndiodirecting polymerization, leading to the conclusion that the group three metals are expected to show little, if any, syndiodirecting capabilities, while the group four cations, including thorium, are expected to show large syndiodirecting capabilities, in accord with experiments. Results from molecular mechanics simulations of zirconocene-based catalysts follow. These calculations are used to assess the steric demands of different ligand environments during propylene polymerization, to determine the relative importance of site and chain end control on the enantioface selectivity, both of which are found to be operative.\r\n\r\nThe second part of the thesis describes the development of concurrent algorithms for the computation of resonance matrix elements. The algorithms are described for two different models of concurrent computing: parallel and distributed. A general program design and architecture that facilitate the program development are described. The scaling of both algorithms with the number of processors is found to be nearly ideal.", "doi": "10.7907/3w1m-hk72", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4103", "collection": "thesis", "collection_id": "4103", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10152007-143016", "primary_object_url": { "basename": "Lim_kt_1995.pdf", "content": "final", "filesize": 6156345, "license": "other", "mime_type": "application/pdf", "url": "/4103/1/Lim_kt_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Mega-molecular dynamics on highly parallel computers : methods and applications", "author": [ { "family_name": "Lim", "given_name": "Kian-Tat", "clpid": "Lim-K" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Large-scale systems of thousands and millions of atoms are of great interest in many areas of chemistry, biochemistry, and materials science. Atomic-level simulations of such systems can provide increased accuracy and especially enhanced insight and understanding when compared with either smaller-scale model calculations or grossly-averaged macroscopic models.\n\nMegamolecular simulations require large amounts of memory and computation, far more than can be provided by the typical scientific workstation. These resources can be most cost-effectively provided at this time by scalable massively parallel computers.\n\nThis thesis presents a large-scale, parallel, distributed-memory, general-purpose molecular dynamics code. The most time-consuming portion of the calculation, the computation of the nonbonded forces, is handled by the Cell Multipole Method, which was developed to overcome the speed and accuracy limitations of standard techniques for handling long-range power-law interactions in large molecular systems. Versions of the code for the KSR-1 and Intel Delta and Paragon parallel supercomputers are described, and performance, accuracy, and scalability results are given.\n\nThe applications section begins with a discussion of computational experiments leading to a prescription for choosing the value of the free timescale parameter in Nose-Hoover constant-volume, constant-temperature (NVT) canonical dynamics. This is followed by several applications of the above megamolecular dynamics codes to interesting chemical applications in the areas of argon cluster structure, polymer structure, surface tension of water drops, diffusion of gases through polymers, and viral structure.\n", "doi": "10.7907/e3qc-t131", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4182", "collection": "thesis", "collection_id": "4182", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10192007-104223", "type": "thesis", "title": "Molecular Mechanics and Ab Initio Simulations of Silicon (111) Surface Reconstructions, Semiconductors and Semiconductor Superlattices, H Abstraction for Nanotechnology, Polysilane, and Growth of CVD Diamond", "author": [ { "family_name": "Musgrave", "given_name": "Charles Bruce", "orcid": "0000-0002-5732-3180", "clpid": "Musgrave-Charles-Bruce" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Goodwin", "given_name": "David G.", "clpid": "Goodwin-D-G" }, { "family_name": "Johnson", "given_name": "William L.", "clpid": "Johnson-W-L" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis describes the application of ab initio and molecular mechanics quantum chemical methods to several problems in the materials and surface sciences. Chapter 1 reviews these methods. Chapter 2 details the application of these methods to study the reaction rate of a proposed mechanism for growth of CVD diamond. Chapter 3 uses high level ab initio methods to study the feasibility of a hydrogen abstraction tool for nanotechnology. Chapter 4 uses ab initio methods together with experimental data to develop a force field potential to model polysilane polymers. Chapter 5 is comprised of the development of atomistic potentials to describe semiconductors and their superlattices and interfaces. The approach of Chapter 5 is extended in Chaper 6 by combining the bulk force field with force field parameters developed from the Biased Hessian Method applied to unique clusters to model the reconstructions of the Si (111) surface. Chapter 7 concludes this thesis with a description of the Generalized London Potential which was developed to accurately model chemical reactions at the accuracy of high level configuration interaction methods, but with the practicality of molecular mechanics.
", "doi": "10.7907/7khv-pb17", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4305", "collection": "thesis", "collection_id": "4305", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10292007-104923", "primary_object_url": { "basename": "Wang_n_1995.pdf", "content": "final", "filesize": 1237235, "license": "other", "mime_type": "application/pdf", "url": "/4305/1/Wang_n_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Studies in dynamics", "author": [ { "family_name": "Wang", "given_name": "Neng E.", "clpid": "Wang-Neng-E" } ], "thesis_advisor": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wang", "given_name": "Zhen-Gang", "clpid": "Wang-Zhen-Gang" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nIn this thesis, three parts of my work are reported. The first part of the work was done with Prof. Rudy Marcus, the second and third parts of the work were done with Prof. Bill Goddard. Here I would like to summarize the results from each part briefly.\r\n\r\nIn the first part, we propose doing Scanning Tunneling Microscopy(STM) current calculations with a new model in the spheroidal coordinate system. The tip is modeled as a hyperboloid. The electrostatic potential part of this model is solved exactly. The free electron model of the whole system is also solved exactly.\r\n\r\nIn the second part, we found that the Nose Canonical Molecular Dynamics, the most commonly used CMD method, leads to the wrong heat capacity for the system and hence is inconsistent with the thermodynamics. To solve this problem, we propose Two Nose variable Dynamics by changing the dimensionality of the Nose variable s and its conjugate [...] from one- to two-dimension.\r\n\r\nIn the third part, The exact expression for the quantum statistical partition function in the canonical ensemble is given. The physical interpretation of each term for N-particle system is discussed. The new formula is applied to the weakly degenerate quantum ideal case. By analyzing each term in the expansion, it is possible that this canonical partition function can be applied to cases where both quantum correlation effects and particle interactions are important.\r\n", "doi": "10.7907/j1ch-3v41", "publication_date": "1995", "thesis_type": "masters", "thesis_year": "1995" }, { "id": "thesis:3469", "collection": "thesis", "collection_id": "3469", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09112007-104050", "primary_object_url": { "basename": "Bierwagen_ep_1995.pdf", "content": "final", "filesize": 8110671, "license": "other", "mime_type": "application/pdf", "url": "/3469/1/Bierwagen_ep_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Computational Studies of Ziegler-Natta Catalysis and Concurrent Resonance Computations", "author": [ { "family_name": "Bierwagen", "given_name": "Erik Paul", "clpid": "Bierwagen-Erik-Paul" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Myers", "given_name": "Andrew G.", "clpid": "Myers-A-G" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Lewis", "given_name": "Nathan Saul", "orcid": "0000-0001-5245-0538", "clpid": "Lewis-N-S" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis thesis discusses work on two different subjects. First, results from computational studies of Ziegler-Natta catalysts are presented. Quantum mechanical calculations of model Ziegler-Natta catalysts [...] are described, where X is either Cl or the cyclopentadienyl (Cp) ligand, M is a group three transition metal or group four transition metal cation, and R is a hydrogen or alkyl group. It is found that complexes based on group four cations have pyramidal structures (the R group is not in the [...] plane), whereas group three neutral complexes have planar structures. This difference in structure is considered in the context of syndiodirecting polymerization, leading to the conclusion that the group three metals are expected to show little, if any, syndiodirecting capabilities, while the group four cations, including thorium, are expected to show large syndiodirecting capabilities, in accord with experiments. Results from molecular mechanics simulations of zirconocene-based catalysts follow. These calculations are used to assess the steric demands of different ligand environments during propylene polymerization, to determine the relative importance of site and chain end control on the enantioface selectivity, both of which are found to be operative.\r\n\r\nThe second part of the thesis describes the development of concurrent algorithms for the computation of resonance matrix elements. The algorithms are described for two different models of concurrent computing: parallel and distributed. A general program design and architecture that facilitate the program development are described. The scaling of both algorithms with the number of processors is found to be nearly ideal.", "doi": "10.7907/3w1m-hk72", "publication_date": "1995", "thesis_type": "phd", "thesis_year": "1995" }, { "id": "thesis:4780", "collection": "thesis", "collection_id": "4780", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12042007-081615", "primary_object_url": { "basename": "Langlois_jm_1994.pdf", "content": "final", "filesize": 5970314, "license": "other", "mime_type": "application/pdf", "url": "/4780/1/Langlois_jm_1994.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "New methods for ab initio quantum mechanical calculations in molecular and crystalline systems", "author": [ { "family_name": "Langlois", "given_name": "Jean-Marc", "clpid": "Langlois-J" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThis thesis deals with the development of new methods for doing ab initio quantum mechanical calculations of electronic wavefunctions of large molecules and crystalline systems with the emphasis on inclusion of electronic correlation or many body effects using generalized valence-bond (GVB) wavefunctions.\n\nChapters 1 and 2 describe two necessary steps for using the generalized valence-bond (GVB) formalism in large molecular systems. In Chapter 1 a fast method for generating GVB trial wavefunctions is described. The method is based on piecewise atomic and diatomic localization and makes possible calculations with large numbers of GVB pairs. The efficacy of the method is illustrated by application to several cases including GVB wavefunctions with up to 26 pairs. In Chapter 2 the pseudospectral (PS) method for self-consistent-field calculations is applied to the GVB formalism. In the GVB perfect pairing approximation, the PS method is shown to reduce the scaling cost of the calculation from [...] to [...], where N is the number of basis functions. This makes possible the calculation of GVB wavefunctions for large molecular systems.\n\nChapter 3 describes a density-functional method for calculations on crystalline systems using Gaussian type orbitals. Accurate and efficient strategies were developed for computing both the Hamiltonian matrix elements and the Coulomb field. The Hamiltonian matrix elements are computed by decomposing the multicenter numerical integrations into single-center integrations via a projection technique and the Coulomb field is evaluated analytically using a dual-space approach based on the Ewald method. The self-consistent field is obtained by a fast conjugate gradient method which uses both first and second derivative information and an efficient preconditioning strategy. Illustrative calculations are performed on two allotropes of carbon: diamond and [...] crystals.\n", "doi": "10.7907/j75s-5f43", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:3923", "collection": "thesis", "collection_id": "3923", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10052004-121305", "primary_object_url": { "basename": "Li_m_1994.pdf", "content": "final", "filesize": 7296753, "license": "other", "mime_type": "application/pdf", "url": "/3923/1/Li_m_1994.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Crystal to Glass Transition and its Relation to Melting", "author": [ { "family_name": "Li", "given_name": "Mo", "orcid": "0000-0002-0139-5839", "clpid": "Li-Mo-1994" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Fultz", "given_name": "Brent T.", "clpid": "Fultz-B-T" }, { "family_name": "Goodstein", "given_name": "David L.", "clpid": "Goodstein-D-L" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This work contributes to the understanding of thermodynamic aspects and microscopic mechanisms of the crystal to glass transition and its relationship to melting. The topological order to disorder transition was investigated primarily in a model system consisting of Lennard-Jones binary solid solutions via molecular dynamics simulations. Under constant temperature and pressure, thermodynamic properties and structures of the solid solutions are mainly determined by solute/solvent atomic size difference and solute concentration. At a critical atomic size difference and/or concentration, the transition was found to occur with extremely small latent heat and density change, but large softening of shear elastic constants. Microscopic details such as atomic configuration show that the transition is induced by collective topological defects created by differences in atomic sizes of the solute and solvent atoms. The inhomogeneity in atomic displacements caused by these defects was shown to be directly responsible for crossover of the transition from a first order transition to a continuous one. The fundamental difference between melting and the crystal to glass transition was demonstrated by their thermodynamic, dynamic, and structural behavior under different kinetic environments. It was shown that melting is intrinsically a first order transition, whereas crystal to glass transition can occur in a variety of forms that are crucially dependent on the kinetic constraints imposed on the solid phases.\r\n", "doi": "10.7907/a2hw-gm49", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:3327", "collection": "thesis", "collection_id": "3327", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09042007-152645", "primary_object_url": { "basename": "Miller_a_1993.pdf", "content": "final", "filesize": 6275718, "license": "other", "mime_type": "application/pdf", "url": "/3327/1/Miller_a_1993.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ab initio calculations in heterogeneous and homogeneous catalysis : I. Methanol to gasoline with ZSM-5. II. Carbonyl ligand effects on metal-metal bonds", "author": [ { "family_name": "Miller", "given_name": "Ann Elizabeth", "clpid": "Miller-Ann-Elizabeth" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis is composed of two studies in catalysis. The first is an exploration, using computational techniques, of the mechanism for the first carbon-carbon bond formation in the Methanol to Gasoline (MTG) reaction. The second is a study of the factors important to the understanding of ligand effects on metal-metal bonds, and in particular, to metal clusters.\r\n\r\nThree possibilities were considered as ways to activate a carbon in the MTG process prior to formation of C2 or higher hydrocarbons. These were a free radical mechanism, a surface ylide mechanism, and a possible defect site which might lead to steric crowding of CH2 groups.\r\n\r\nAlthough the free radical mechanism was found to be thermodynamically within the parameters of the MTG process, it contained a high transition state. Consideration of the molecules available prior to hydrocarbon build-up and their specific electronic structure, led to the view that the available carbon atoms (methanol, dimethyl ether, etc.) were unlikely to be activated by a free radical intermediate. \r\n\r\nThe surface-stabilized ylide which has been proposed as an intermediate by many was studied to determine if in fact the ylide was stabilized. The total energy of the ylide was compared to that of the naked site on the zeolite and free methylene. Free methylene ranged, depending on the geometry of the ylide, between 50 and 80 kcal more stable. These numbers are qualitatively correct, but more electron correlation would have to be incorporated in the calculation to get an accurate value for the destabilization.\r\n\r\nStarting from a defect site, two CH2 groups were each attached to two oxygen atoms. It was thought that two CH2 groups would take up considerably more space than either the original Al atom or the four hydrogens. Molecular Mechanics calculations showed the zeolite to be sufficiently flexible to prevent crowding of the CH2's.\r\n\r\nThe second study involved determining the effects of colinear carbonyl ligands on osmium-osmium bonds. Calculations at the Dissociation Consistent Cl level showed that the ligands were weakening the metal-metal [pi]-bonds through back-donation.\r\n", "doi": "10.7907/WRBP-E952", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:1057", "collection": "thesis", "collection_id": "1057", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03222005-105400", "primary_object_url": { "basename": "Baselt_dr_1993.pdf", "content": "final", "filesize": 14972657, "license": "other", "mime_type": "application/pdf", "url": "/1057/1/Baselt_dr_1993.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The Tip-Sample Interaction in Atomic Force Microscopy and its Implications for Biological Applications", "author": [ { "family_name": "Baselt", "given_name": "David Randall", "clpid": "Baselt-David-Randall" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Okumura", "given_name": "Mitchio", "orcid": "0000-0001-6874-1137", "clpid": "Okumura-M" }, { "family_name": "Revel", "given_name": "Jean-Paul", "clpid": "Revel-J-P" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the construction of an atomic force microscope and its application to the study of tip-sample interactions, primarily through the use of friction and hardness (elasticity) imaging.\r\n\r\nPart one describes the atomic force microscope, which consists of a scanned-cantilever stage (chapter 2); a versatile digital signal processor-based control system with self-optimizing feedback, lock-in amplifier emulation (for hardness imaging), and macro programmability (chapter 3); and image processing software (chapter 4).\r\n\r\nPart two describes a number of results that have helped to characterize the tip-sample interaction and the contact imaging modes used for its study. Meniscus forces act laterally as well as normally, and that they vary with position (chapter 5). Friction measurements couple with scanner position quid feedback, and the meniscus effects friction images (chapter 6). Sliding of the tip over the sample surface introduces slope-dependence into hardness measurements (chapter 7). Dull tips can create prominent topography artifacts even on very flat surfaces (chapter 8).\r\n\r\nIn an investigation of collagen fibrils, AFM has revealed die characteristic 65 nm banding pattern, a second, minor banding pattern, and microfibrils that run along the fibril axis. The distribution of proteoglycans along the fibrils creates a characteristic pattern in friction images. Although imaging in water reduces interaction forces, water can also make biological samples more sensitive to force. However, for robust biological samples imaged in air, tip shape presents a greater obstacle than tip-sample interaction forces to obtaining high-resolution images. Tip contamination increases tip-sample friction and can occasionally improve resolution (chapter 9).\r\n\r\nFor a separate project I have designed a general-purpose nearfield scanning optical microscope (chapter 10).", "doi": "10.7907/5ZMM-7Q64", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:5318", "collection": "thesis", "collection_id": "5318", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-152426877", "primary_object_url": { "basename": "Evans_js_1993.pdf", "content": "final", "filesize": 17040139, "license": "other", "mime_type": "application/pdf", "url": "/5318/1/Evans_js_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "NMR and Computational Studies on the Conformational Folding of the Biomineralization Template, Posphophoryn", "author": [ { "family_name": "Evans", "given_name": "John Spencer", "orcid": "0000-0002-9565-7296", "clpid": "Evans-John-Spencer" } ], "thesis_advisor": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" } ], "thesis_committee": [ { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Bovine Dentine Phosphophoryn (BDPP) is a member of the \"Asp-rich\" superfamily of template macromolecules known as polyelectrolyte mineral matrix proteins (PMMPs). Using 1-D and 2-D NMR multinuclear spectroscopy, protein sequencing, solid-phase peptide synthesis, and molecular modeling, we investigated the capacity of BDPP to fold in solution under certain conditions. It is believed that the folding properties of a template macromolcule are important in the formation of n inorganic mineral phase. In this report, we have established the following regarding BDPP structure:\r\n\r\nI. BDPP sequence organization can be conceptualized as three types of domains: polyelectrolyte calcium binding domains (PCBD), hinge \r\ndomains (HD), and the hydrophobic domains (HC). The PCBD regions can be further subdivided into (Asp)_n, (PSer)_n, and (PSerAsp)_n-containing\r\nhomopolymer and heteropolymer sequence stretches. The HD contain predominantly neutral or uncharged amino acids such as Ser, Gly, and \r\nPro. These HD domain sequences are flanked on either side by PCBD regions.\r\n\r\nII. BDPP contains a number of Lys sidechains (44/1000 residues) which are believed to form ion pairs with either Asp, Glu, or PSer residues \r\nin the protein. The function of this salt-bridging is not understood at this time, but it may be responsible for maintaining the protein template molecule in a conformation that retains a high negative charge density.\r\n\r\nIII. At low pH, or in the presence of divalent cations, BDPP assumes a global conformation that is condensed in particle size. At neutral pH \r\nunder conditions of low ionic strength and in the absence of divalent cations, this global conformation converts to an extended form. The \r\nfolding transition between these two conformers is mediated by conformational change in the BD regions which are flanked by specific \r\nPCBD sequence regions.\r\n\r\nIV. The PCBD regions possess some degree of tertiary and secondary structural organization in the absence of divalent cations at low ionic \r\nstrength. This folding permits the surface charge density of these regions to remain high, relative to that of a random coil conformer.\r\n\r\nV. BDPP exhibits a selectivity in terms of divalent cation binding sites. Under conditions of low ionic strength and divalent cation depletion, the addition of Cd (II) to BDPP leads to binding at various PCBD sequence stretches, according to the following order:\r\n(PSer)_n > (PserAsp)_n > (Asp)_n\r\n\r\nVI. Modeling studies conducted on PCBD sequence peptides [(Asp)_(20), (PSer)_(20), and (PSerAsp)_(10)] indicate that there is a sequence preference for certain conformers in the presence of Na^+, i.e., (Asp)_(20) forms \"supercoils\", (PSer)_(20) forms \"hairpins\", and (PSerAsp)_(10) forms \"spirals\" or \"distorted\" hairpins. Each of these conformers features some degree of sidechain folding and/or peptide backbone secondary structure, in support of Mann's hypothesis, as well as the experimental data obtained for BDPP.\r\n\r\nVII. A peptide mimetic which represents a PCBD-Hinge-PCBD motif of rat \u03b1-phosphophoryn, was constructed using FMOC solid-phase peptide \r\nsynthesis. Using 2-D NMR spectroscopy and monitoring \u03b1-CH and sidechain \u03b2-CH_2 proton chemical shifts, we can demonstrate that this \r\npeptide mimetic folds or collapses under conditions of low pH and divalent cation addition, in a manner similar to that observed for intact \r\nBDPP.\r\n", "doi": "10.7907/ky1z-w552", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:6644", "collection": "thesis", "collection_id": "6644", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09012011-151648229", "primary_object_url": { "basename": "Baker_sm_1992.pdf", "content": "final", "filesize": 52406562, "license": "other", "mime_type": "application/pdf", "url": "/6644/1/Baker_sm_1992.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Scanning Tunneling Microscopy and Spectroscopy of Silicon and Carbon Surfaces", "author": [ { "family_name": "Baker", "given_name": "Shenda Mary", "orcid": "0000-0002-9985-473X", "clpid": "Baker-Shenda-Mary" } ], "thesis_advisor": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Scanning Tunneling Microscopy (STM) investigations and additional surface analyses were performed on carbon and silicon surfaces. A number of anomalies have been observed on highly oriented pyrolytic graphite (HOPG), including large corrugations, distorted images, large range of tip motion and the absence of defects. A mechanism involving direct contact between tip and sample or contact through a contamination layer to provide an additional conduction pathway is proposed. This model of point-contact imaging provides an explanation for added stability of the STM system, a mechanism for producing multiple tips or sliding graphite planes and an explanation for the observed anomalies. These observations indicate that the use of HOPG for testing and calibration of STM instrumentation may be misleading. Designs for the atmospheric STM used in this study are also presented.
\r\n\r\nThe conditions necessary for preparing a dean silicon(111) (7x7) surface are discussed. The design and analysis of heaters necessary to prepare the silicon reconstructed surface at ultrahigh vacuum (UHV) are described. Results from both radiatively and resistively heated samples are shown in addition to a comparision of topographic and barrier height images of the boron (\u221a3 x\u221a3) reconstructed surfaces. A spectroscopic distinction between sites of boron, silicon or contaminants is demonstrated.
\r\n\r\nA synthetic boron-doped diamond was examined by a number of analytical techniques in order to determine its composition and surface morphology. Current-voltage spectroscopy taken with the STM indicates that the diamond Fermi level can be pinned in atmospheric conditions. In ultrahigh vacuum, band bending is observed, but the strength of the electric field experienced by the diamond semiconductor is less than expected; introduction of surface charges is shown to account for the field screening.
\r\n\r\nPresentation of an STM study of a protein-antibody complex on a gold surface illustrates the requirements for and difficulties of imaging large biomolecules. A flat, conducting substrate and sample stability on the surface\r\nare shown and discussed. Molecular manipulation by the STM tip is also presented. Although routine imaging of large adsorbates on surfaces is not yet possible, this study presents the obstacles and the potential afforded by the STM in attaining this goal.
\r\n", "doi": "10.7907/5JGQ-4X60", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:6668", "collection": "thesis", "collection_id": "6668", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09132011-160134197", "primary_object_url": { "basename": "Sun_y_1992.pdf", "content": "final", "filesize": 60630395, "license": "other", "mime_type": "application/pdf", "url": "/6668/1/Sun_y_1992.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "NMR Studies of Protein-DNA Interactions: Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions", "author": [ { "family_name": "Sun", "given_name": "Yun", "clpid": "Sun-Yun" } ], "thesis_advisor": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The solution structures of two DNA oligomers were determined by the 2-D NMR method. These 14-base-pair DNA molecules contain the recognition sites for Hin recombinase. In spite of the differences in their sequences, the two structures are remarkably similar. The refined DNA structures possess a significant bend (25-32\u00b0) in the middle of the helices. As a result of the bending, the nearby major groove is compressed at almost exactly the position where the recombinase binds. The DNA molecules were also found to have a deepened and narrowed minor groove near the continuous dA tracts, where the minor groove contact happens between the N-terminal residues of the recombinase binding domain and the DNA molecules. Such pre-existing unique features of the free DNA molecules are likely to contribute to the specific interaction of the protein and the DNA tracts. Structure determinations by the NMR method were preceded with the use of complete relaxation matrix analysis and restrained molecular dynamics. A data processing system were developed which allowed us to simulate the NMR spectra and quantifying intensities from an overlapped data set. A complete system for high-resolution structure determinations in solution were set up and evaluated.
\r\n\r\nThe conformation of the Hin 52mer peptide-the binding domain of the Hin recombinase-and its binding interactions with the DNA oligomers are studied by NMR, circular dichroism and chromatographic methods. The conclusion is that the peptide does not have a unique and stable conformation alone as a single monomer in solution. The Hin peptide can be prevented from being aggregated by adjusting to acidic conditions, and it can be folded to a stable tertiary structure in an artificial environment with small amounts of trifluoroethanol. The Hin 52mer peptide conformation is greatly stabilized or induced by the presence of the DNA bearing specific binding sequences. The DNA binding activities of the peptide may be assayed by a chromatographic method. The behavior of the peptide in the binding complex and the characteristic structural features of the DNA molecules suggest the active role of the DNA in protein-DNA interactions providing complementary interactions with the peptide and stabilizing the peptide conformation upon its binding.
\r\n", "doi": "10.7907/em1y-p761", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:1605", "collection": "thesis", "collection_id": "1605", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05042006-112846", "primary_object_url": { "basename": "Tahir-Kheli_thesis_final.pdf", "content": "final", "filesize": 659758, "license": "other", "mime_type": "application/pdf", "url": "/1605/1/Tahir-Kheli_thesis_final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The infinite range Heisenberg model and high temperature superconductivity", "author": [ { "family_name": "Tahir-Kheli", "given_name": "Jamil", "clpid": "Tahir-Kheli-J" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Goodstein", "given_name": "David L.", "clpid": "Goodstein-D-L" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Frautschi", "given_name": "Steven C.", "clpid": "Frautschi-S-C" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe thesis deals with the theory of high temperature superconductivity from the standpoint of three-band Hubbard models.\n\nChapter 1 of the thesis proposes a strongly coupled variational wavefunction that has the three-spin system of an oxygen hole and its two neighboring copper spins in a doublet and the background Cu spins in an eigenstate of the infinite range antiferromagnet. This wavefunction is expected to be a good \"zeroth order\" wavefunction in the superconducting regime of dopings. The three-spin polaron is stabilized by the hopping terms rather than the copper-oxygen antiferromagnetic coupling Jpd. Considering the effect of the copper-copper antiferromagnetic coupling Jdd, we show that the three-spin polaron cannot be pure Emery (Dg), but must have a non-negligible amount of doublet-u (Du) character for hopping stabilization. Finally, an estimate is made for the magnitude of the attractive coupling of oxygen holes.\n\nChapter 2 presents an exact solution to a strongly coupled Hamiltonian for the motion of oxygen holes in a 1-D Cu-O lattice. The Hamiltonian separates into two pieces: one for the spin degrees of freedom of the copper and oxygen holes, and the other for the charge degrees of freedom of the oxygen holes. The spinon part becomes the Heisenberg antiferromagnet in 1-D that is soluble by the Bethe Ansatz. The holon piece is also soluble by a Bethe Ansatz with simple algebraic relations for the phase shifts.\n\nFinally, we show that the nearest neighbor Cu-Cu spin correlation increases linearly with doping and becomes positive at x [...] 0.70.", "doi": "10.7907/9JDD-4P11", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:5316", "collection": "thesis", "collection_id": "5316", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-105855010", "primary_object_url": { "basename": "Donnelly_re_1992.pdf", "content": "final", "filesize": 8172581, "license": "other", "mime_type": "application/pdf", "url": "/5316/1/Donnelly_re_1992.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Modeling and visualizing surfaces", "author": [ { "family_name": "Donnelly", "given_name": "Robert Edward", "clpid": "Donnelly-R-E" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "\"Modeling and Visualizing Surfaces\" denotes several developments aimed at increasing our ability to model and understand molecular surfaces. The Generalized London Potential is a new method of modeling potential energy surfaces of reactions. The London Equation assumptions of zero overlap and no three-body interactions are discarded and a more general potential is derived via valence bond theory and careful substitution of two-body terms into three-body energy expressions. Three-body corrections for dispersion energy are also introduced. Using the lowest order forms of overlap and dispersion corrections, a much improved potential energy surface is found for H_3. Input is limited to H_2 potentials and information only about the H_3 saddle point region, the latter determining the two or three parameters used. The predicted surface is shown to be stable with respect to varied input. A straightforward method of extending the method to make use of additional input is discussed. The method is applied to hydrogen abstraction from terminal carbons. The development of a stable model of exchange reactions will greatly increase the complexity of systems which can be studied with the increasingly accurate force fields of molecular modeling techniques by providing the means of handling reactive dynamics at polymer and crystalline surfaces. This introduces the second major theme of modeling and visualizing molecular surfaces.\r\n\r\nCommon to most definitions of a molecule's surface and, in fact, many calculations involving local spherical symmetry is the use of spherical meshes. A method of systematically creating spherical meshes of various sizes is presented. Degrees of freedom built into the mesh design can be optimized for a variety of problems. The meshes are used in calculating molecular surfaces and determining surface area. They are separately optimized for the integration of spherical harmonics and provide lower error for integration of higher angular momentum functions than previous quadratures. Finally, methods of visualizing molecular surfaces that allow real-time manipulation of complex molecules and yield a better understanding of surface properties are presented.\r\n", "doi": "10.7907/1d15-vv30", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:5296", "collection": "thesis", "collection_id": "5296", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10132009-131816426", "primary_object_url": { "basename": "Chen_g_1992.pdf", "content": "final", "filesize": 3615547, "license": "other", "mime_type": "application/pdf", "url": "/5296/1/Chen_g_1992.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Superconductivities of high-T_c materials and alkali compounds of Buckminsterfullerene", "author": [ { "family_name": "Chen", "given_name": "Guanhua", "clpid": "Chen-G" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "This thesis is composed of two chapters. Chapter I is an investigation of the spin wave spectrum of the two-dimensional spin-1/2 Heisenberg model and its relevance to high-T_c superconducting materials. Chapter II is a study on another interesting family of superconductors, the alkali compounds of Buckyminsterfullerene A_xC_(60). The electron-phonon coupling constant of one member of these compounds, K_3C_(60), has been calculated and discussed in the context of the phonon-mediated superconducting mechanism.\r\n\r\nChapter 1 consists of two projects. The first project is an exact diagonalization of a 4 x 4 S = 1/2 Heisenberg model. \r\nEnergy vs. momentum spectra is derived and compared with the dynamic structure factors. The comparison shows that spin wave or magnon of a certain momentum corresponds to the lowest spin triplet state of that particular momentum. The second project, an extension of the first, is a Projector Monte Carlo simulation of 2D S = 1/2 Heisenberg square lattices of size 4 x 4, 6 x 6, 8 x 8 and 12 x 12. The lowest lying spin wave spectrum has been obtained for each of the above lattices, and the extrapolation to the infinitely large 2D square lattice has been derived. These results suggest that the exact spectrum for the infinite lattice is that of linear magnon with an overall renormalization factor. These results are also used to infer the value of the exchange energy from inelastic neutron scattering experiments of a high-T_c superconductor La_2CuO_4.\r\n\r\nThe first part of Chapter 2 is a MNDO study of the electronic structure of a C_(60) molecule; this study excludes a proposed mechanism for the superconductivity in A_xC_(60), namely, Stability of Molecular Singlets (\"SMS\"). Secondly, Chapter II describes an investigation of the electron-phonon interaction caused by the changes of the electron-ion coulomb interactions, i.e., the static electron-phonon coupling. An accurate formalism based on the force field and phonon spectrum available is established to calculate the electron-phonon coupling matrix. This formalism includes exactly the available information about the phonon eigenvectors and eigenenergies and about the localized Wannier orbital for electrons in the conduction bands. The major contributions to the static electron-phonon coupling is found from the low frequency intermolecular phonon modes. Thirdly, a study on the electron-phonon coupling caused by the responses of the local electronic states to the vibrations of a C_(60) molecule (i.e., dynamic electron-phonon coupling) is presented. The study concludes that the dynamic coupling is strong enough to be relevant to the superconductivity in \r\nA_xC_(60). Finally, various properties related to the superconducting phase have been calculated, and are compared with the experimental results. On the basis of all these, an experiment is proposed to confirm our findings, and to determine the superconductivity mechanism in A_xC_(60) systems.\r\n", "doi": "10.7907/chz3-cq25", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:6668", "collection": "thesis", "collection_id": "6668", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09132011-160134197", "primary_object_url": { "basename": "Sun_y_1992.pdf", "content": "final", "filesize": 60630395, "license": "other", "mime_type": "application/pdf", "url": "/6668/1/Sun_y_1992.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "NMR Studies of Protein-DNA Interactions: Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions", "author": [ { "family_name": "Sun", "given_name": "Yun", "clpid": "Sun-Yun" } ], "thesis_advisor": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Arnold", "given_name": "Frances Hamilton", "orcid": "0000-0002-4027-364X", "clpid": "Arnold-F-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The solution structures of two DNA oligomers were determined by the 2-D NMR method. These 14-base-pair DNA molecules contain the recognition sites for Hin recombinase. In spite of the differences in their sequences, the two structures are remarkably similar. The refined DNA structures possess a significant bend (25-32\u00b0) in the middle of the helices. As a result of the bending, the nearby major groove is compressed at almost exactly the position where the recombinase binds. The DNA molecules were also found to have a deepened and narrowed minor groove near the continuous dA tracts, where the minor groove contact happens between the N-terminal residues of the recombinase binding domain and the DNA molecules. Such pre-existing unique features of the free DNA molecules are likely to contribute to the specific interaction of the protein and the DNA tracts. Structure determinations by the NMR method were preceded with the use of complete relaxation matrix analysis and restrained molecular dynamics. A data processing system were developed which allowed us to simulate the NMR spectra and quantifying intensities from an overlapped data set. A complete system for high-resolution structure determinations in solution were set up and evaluated.
\r\n\r\nThe conformation of the Hin 52mer peptide-the binding domain of the Hin recombinase-and its binding interactions with the DNA oligomers are studied by NMR, circular dichroism and chromatographic methods. The conclusion is that the peptide does not have a unique and stable conformation alone as a single monomer in solution. The Hin peptide can be prevented from being aggregated by adjusting to acidic conditions, and it can be folded to a stable tertiary structure in an artificial environment with small amounts of trifluoroethanol. The Hin 52mer peptide conformation is greatly stabilized or induced by the presence of the DNA bearing specific binding sequences. The DNA binding activities of the peptide may be assayed by a chromatographic method. The behavior of the peptide in the binding complex and the characteristic structural features of the DNA molecules suggest the active role of the DNA in protein-DNA interactions providing complementary interactions with the peptide and stabilizing the peptide conformation upon its binding.
\r\n", "doi": "10.7907/em1y-p761", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:3027", "collection": "thesis", "collection_id": "3027", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08062007-104316", "primary_object_url": { "basename": "Karasawa_n_1992.pdf", "content": "final", "filesize": 21061567, "license": "other", "mime_type": "application/pdf", "url": "/3027/1/Karasawa_n_1992.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Simulations of polymer crystals : new methods and applications", "author": [ { "family_name": "Karasawa", "given_name": "Naoki", "clpid": "Karasawa-N" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The most important applications for simulations of polymers involve composites or blends with extensive, amorphous regions. To simulate such materials we use a very large unit cell, so that the polymer can have random behavior within the cell, but periodic boundary conditions to keep the problem tractable. The major difficulties in carrying out such calculations are: (a) accurate calculation of the lattice sums for the nonbond interactions (electrostatic and dispersion), which converge very slowly; (b) computational time for systems large enough to simulate real materials (1 million atoms); (c) procedures for calculating the properties of interest (energy, force, stress, curvature, phonons, elastic constants, dielectric constants, and piezoelectric constants).\n\nWe describe herein significant progress on each of these three issues. Concerning (a) we developed the Accuracy-Bounded Convergence Acceleration (ABCA) procedure, which finds the optimal Ewald parameters to achieve a given accuracy in minimum computation time. Concerning (b) the critical bottleneck in atomic-level simulations of the structure and dynamics of very large molecules is the calculation of N2 nonbond interactions. Here a major advance is the development of the Cell Multipole Method (CMM), which involves no steps scaling a higher order than N. CMM treats the interactions in terms of a far field (which is evaluated in terms of multipole expansions) and a near field (which involves only approximately 50 near neighbors). The far field can be evaluated infrequently so that the full calculation for a million-atom system involves only the effort of calculation to interactions of each atom with about 50 near neighbors. This leads to a dramatic increase in efficiency, and systematic calculations have been carried out in realistic polymers with up to 1 million atoms (on a workstation). The CMM is 1500 times faster than the exact method for 1 million atoms. For periodic systems the cell multipole method is extended, using a reduced set that reproduces low-order multipoles of an original unit cell (CMMX). For a polymer with 1 million atoms, the C calculation is 1000 times faster than either the Ewald or Minimum Image Methods (the standards currently in use).\n\nA major issue in carrying out simulations for materials is the force field. We have developed general procedures for obtaining empirical force fields and have applied this to systematic development of force-field parameters for polyethylene and poly (vinylidene fluoride) crystals. Van der Waals parameters for carbon and hydrogen are empirically determined from experimental lattice constants, elastic constants and lattice frequencies utilizing Ewald/ABCA procedures. Various mechanical properties are calculated and compared with experimental data. For polyethylene, valence terms are determined by a biased- Hessian method for n-butane, and yield stress and surface energy are obtained from calculations of stress-strain relations in directions perpendicular to polymer chains. For poly (vinylidene fluoride) crystals, a shell model is introduced to include atomic polarizabilities into the simulation. Properties of five different forms (including a new form suggested by Lovinger) are computed using the same parameter sets. We find that using the shell model leads to significant improvement in the agreement between calculated and experimental piezoelectric and dielectric constants. In addition we find that the new form (not yet observed form) is mechanically stable with comparable energy with other forms.", "doi": "10.7907/mjj7-qt65", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:4660", "collection": "thesis", "collection_id": "4660", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11252003-112746", "type": "thesis", "title": "Real-Time Observation and Analysis of Coherence and Alignment in Molecular Systems: Isolated Molecules and Chemical Reactions", "author": [ { "family_name": "Baskin", "given_name": "John Spencer", "clpid": "Baskin-John-Spencer" } ], "thesis_advisor": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Gould", "given_name": "Roy Walter", "clpid": "Gould-R-W" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Picosecond time-resolved rotational coherence spectroscopy is developed as a probe of excited state rotational level structure and alignment. The measurement technique employs a combination of supersonic cooling by molecular beam expansion, coherent picosecond pulsed laser excitation, and time-resolved and polarization-analyzed detection of spectrally dispersed fluorescence. The requisite measurement system response time of approximately 50 picoseconds is attained using time-correlated single photon counting and a microchannel plate detector.
\r\n\r\nIn the case of purely rotational coherence (PRC), i.e., when rotation may be treated in the rigid rotor approximation, analysis of the polarization-analyzed fluorescence provides direct information about the rotational constants and structure of the molecule's excited vibronic state. This method of structural determination of excited states has the inherent advantages over conventional frequency-domain spectroscopy of sub-Doppler resolution and insensitivity to ground state structure. As a result, it is particularly valuable in investigations of large molecules and complexes. Analyses of PRC measurements on eight different molecular systems are detailed in this thesis. These provide illustrative examples of various aspects of the technique while permitting the derivation of new information about the excited states of six of the eight molecules or complexes studied. Principal among the findings are values of the sum of rotational constants B' and C' of the t-stilbene S\u2081 electronic state (B'+ C' = 0.5132 \u00b1 .0008 GHz) and of all three S\u2081 rotational constants of anthracene.
\r\n\r\nWe also report measurements of time-resolved and polarization-analyzed fluorescence as a function of excess vibrational energy in the S\u2081 electronic states of both t-stilbene and anthracene. We are able to distinguish the contribution of purely rotational coherence from the contributions of purely vibrational (or rovibrational) coherence to the evolution of fluorescence from the vibrationally excited molecule. Our results provide a test of the extent of coupling between vibrational and rotational motion and its influence on intramolecular vibrational energy redistribution.
\r\n\r\nMeasurements of polarization-analyzed fluorescence of dissociation products demonstrate that rotational coherence of the reagent can be transferred to its fragments. In order to interpret the results of these and related experiments, a classical model of fluorescence anisotropy in prompt, impulsive dissociation reactions is developed.
", "doi": "10.7907/H8TF-EE69", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:4660", "collection": "thesis", "collection_id": "4660", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11252003-112746", "type": "thesis", "title": "Real-Time Observation and Analysis of Coherence and Alignment in Molecular Systems: Isolated Molecules and Chemical Reactions", "author": [ { "family_name": "Baskin", "given_name": "John Spencer", "clpid": "Baskin-John-Spencer" } ], "thesis_advisor": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Gould", "given_name": "Roy Walter", "clpid": "Gould-R-W" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Picosecond time-resolved rotational coherence spectroscopy is developed as a probe of excited state rotational level structure and alignment. The measurement technique employs a combination of supersonic cooling by molecular beam expansion, coherent picosecond pulsed laser excitation, and time-resolved and polarization-analyzed detection of spectrally dispersed fluorescence. The requisite measurement system response time of approximately 50 picoseconds is attained using time-correlated single photon counting and a microchannel plate detector.
\r\n\r\nIn the case of purely rotational coherence (PRC), i.e., when rotation may be treated in the rigid rotor approximation, analysis of the polarization-analyzed fluorescence provides direct information about the rotational constants and structure of the molecule's excited vibronic state. This method of structural determination of excited states has the inherent advantages over conventional frequency-domain spectroscopy of sub-Doppler resolution and insensitivity to ground state structure. As a result, it is particularly valuable in investigations of large molecules and complexes. Analyses of PRC measurements on eight different molecular systems are detailed in this thesis. These provide illustrative examples of various aspects of the technique while permitting the derivation of new information about the excited states of six of the eight molecules or complexes studied. Principal among the findings are values of the sum of rotational constants B' and C' of the t-stilbene S\u2081 electronic state (B'+ C' = 0.5132 \u00b1 .0008 GHz) and of all three S\u2081 rotational constants of anthracene.
\r\n\r\nWe also report measurements of time-resolved and polarization-analyzed fluorescence as a function of excess vibrational energy in the S\u2081 electronic states of both t-stilbene and anthracene. We are able to distinguish the contribution of purely rotational coherence from the contributions of purely vibrational (or rovibrational) coherence to the evolution of fluorescence from the vibrationally excited molecule. Our results provide a test of the extent of coupling between vibrational and rotational motion and its influence on intramolecular vibrational energy redistribution.
\r\n\r\nMeasurements of polarization-analyzed fluorescence of dissociation products demonstrate that rotational coherence of the reagent can be transferred to its fragments. In order to interpret the results of these and related experiments, a classical model of fluorescence anisotropy in prompt, impulsive dissociation reactions is developed.
", "doi": "10.7907/H8TF-EE69", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:841", "collection": "thesis", "collection_id": "841", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03022007-090722", "primary_object_url": { "basename": "Nikzad_s_1990.pdf", "content": "final", "filesize": 4708078, "license": "other", "mime_type": "application/pdf", "url": "/841/1/Nikzad_s_1990.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Study of Ion Beam Sputtering of Compound Materials with Laser Spectroscopy", "author": [ { "family_name": "Nikzad", "given_name": "Shouleh", "orcid": "0009-0004-1255-1018", "clpid": "Nikzad-Shouleh" } ], "thesis_advisor": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Bellan", "given_name": "Paul Murray", "clpid": "Bellan-P-M" } ], "thesis_committee": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Pellin", "given_name": "Michael J.", "orcid": "0000-0002-8149-9768", "clpid": "Pellin-M-J" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_eng" } ], "abstract": "Single crystal metal sulfides of ZnS, CdS, and FeS\u2082 were bombarded with a 3 keV Ar\u207a beam. The secondary neutrals sputtered from the surface of the target were interrogated by laser ionization mass spectrometry and laser fluorescence spectroscopy.
\r\n\r\nThe velocity distribution and yield of sputtered Fe from a FeS\u2082 sample were measured. The velocity distribution of Fe sputtered from the sulfide is qualitatively the same as that of Fe sputtered from the pure metal. The yield of Fe from the sulfide target, after prolonged bombardment, was at most 20% of the yield from the metal. The results are compared with Monte Carlo calculations using the TRIM (transfer of ion in matter) code. Total sputtering yields of ZnS, CdS, and FeS\u2082 were measured by profilometry and were compared with the same measurements of sputtered metal targets.
\r\n\r\nWe have demonstrated the necessity of measuring sputtered molecules and excited state neutrals for accurate yield evaluation. The population distribution of ground state multiplets of sputtered Fe from FeS\u2082 is compared with that measured from an Fe target. The excited state population of sputtered Fe is slightly higher in the FeS\u2082 target (~10%). Molecular yields have also been measured by laser ionization mass spectrometry from ZnS, CdS, and FeS\u2082. S is sputtered predominantly as S\u2082 from all three crystals. Metals are sputtered as the atom, metal sulfide, and metal dimer (except in the case of Fe\u2082). The yield of the metal sulfidemolecules is about 10% of the yield of the metal. Plausible formation mechanisms of molecules and excited state neutrals are discussed.
", "doi": "10.7907/kgvz-n067", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:841", "collection": "thesis", "collection_id": "841", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03022007-090722", "primary_object_url": { "basename": "Nikzad_s_1990.pdf", "content": "final", "filesize": 4708078, "license": "other", "mime_type": "application/pdf", "url": "/841/1/Nikzad_s_1990.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Study of Ion Beam Sputtering of Compound Materials with Laser Spectroscopy", "author": [ { "family_name": "Nikzad", "given_name": "Shouleh", "orcid": "0009-0004-1255-1018", "clpid": "Nikzad-Shouleh" } ], "thesis_advisor": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Bellan", "given_name": "Paul Murray", "clpid": "Bellan-P-M" } ], "thesis_committee": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Atwater", "given_name": "Harry Albert", "orcid": "0000-0001-9435-0201", "clpid": "Atwater-H-A" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Pellin", "given_name": "Michael J.", "orcid": "0000-0002-8149-9768", "clpid": "Pellin-M-J" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_eng" } ], "abstract": "Single crystal metal sulfides of ZnS, CdS, and FeS\u2082 were bombarded with a 3 keV Ar\u207a beam. The secondary neutrals sputtered from the surface of the target were interrogated by laser ionization mass spectrometry and laser fluorescence spectroscopy.
\r\n\r\nThe velocity distribution and yield of sputtered Fe from a FeS\u2082 sample were measured. The velocity distribution of Fe sputtered from the sulfide is qualitatively the same as that of Fe sputtered from the pure metal. The yield of Fe from the sulfide target, after prolonged bombardment, was at most 20% of the yield from the metal. The results are compared with Monte Carlo calculations using the TRIM (transfer of ion in matter) code. Total sputtering yields of ZnS, CdS, and FeS\u2082 were measured by profilometry and were compared with the same measurements of sputtered metal targets.
\r\n\r\nWe have demonstrated the necessity of measuring sputtered molecules and excited state neutrals for accurate yield evaluation. The population distribution of ground state multiplets of sputtered Fe from FeS\u2082 is compared with that measured from an Fe target. The excited state population of sputtered Fe is slightly higher in the FeS\u2082 target (~10%). Molecular yields have also been measured by laser ionization mass spectrometry from ZnS, CdS, and FeS\u2082. S is sputtered predominantly as S\u2082 from all three crystals. Metals are sputtered as the atom, metal sulfide, and metal dimer (except in the case of Fe\u2082). The yield of the metal sulfidemolecules is about 10% of the yield of the metal. Plausible formation mechanisms of molecules and excited state neutrals are discussed.
", "doi": "10.7907/kgvz-n067", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "id": "thesis:5355", "collection": "thesis", "collection_id": "5355", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-142520920", "type": "thesis", "title": "Electronic Structure and Photochemical Reactivity of Binuclear Metal Complexes", "author": [ { "family_name": "Smith", "given_name": "David Charles", "clpid": "Smith-David-Charles" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "orcid": "0000-0001-6547-1469", "clpid": "Marcus-R-A" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Anson", "given_name": "Fred C.", "clpid": "Anson-F-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A valence bond (VB) \"weak coupling\" model of the electronic structure for [Ir\u2082(TMB)\u2084](B(C\u2086H\u2085)\u2084)\u2082 is developed and generalized to the class of dimeric systems in which the metals are nonbonded, in a formal sense, and can be viewed as weakly coupled. With the VB model, the energies and widths of the previously observed optical absorption bands can be rationalized; in addition, plausible assignments are made for bands that were not interpreted satisfactorily or not observed in earlier work. The VB model does not change any of the molecular orbital-based interpretations of the thermal chemistry, photochemistry, or photophysics of these systems.
\r\n\r\nPhotophysical characterization of the 1,3(d\u03c3*p\u03c3) excited state of Ir\u2082(TMB)\u2084\u00b2\u207a finds a system quite comparable to other binuclear d\u2078 complexes. Both fluorescence (\u03bb\u2098\u2090\u2093 735 nm, \u03c4 ~ 70 \u00b1 30 ps) and phosphorescence (\u03bb\u2098\u2090\u2093 1080 nm, \u03c4 = 210 \u00b1 20 ns) are observed.
\r\n\r\nThe relatively long lifetime of the \u00b3(d\u03c3*p\u03c3) excited state of Ir\u2082(TMB)\u2084\u00b2\u207a suggests that it should be able to participate in bimolecular photochemical reactions. The diradical-like structure of the excited state, an electron (or oxidizing hole) localized on the exterior of the M\u2082 unit (the d\u03c3* orbital) and an electron localized in the interior of the dimer cage (the p\u03c3 orbital), implies that one-electron chemistry will be observed. Reactions of the ground state follow two-electron pathways, similar to those observed for mononuclear d\u2078 complexes.
\r\n\r\nThe \u00b3(d\u03c3*p\u03c3) excited state of Ir\u2082(TMB)\u2084\u00b2\u207a is found to be a powerful reductant, E\u2070(Ir\u2082(TMB)\u20843+/3(Ir\u2082(TMB)\u2084\u00b2\u207a)*) ~ 1.0 V (SSCE). Excited-state electron- transfer quenching by pyridinium acceptors is observed to follow classical Marcus theory for outer-sphere electron transfer. No \"inverted\" behavior is found. The bimolecular electron-transfer reaction is highly nonadiabatic, \u03ba ~ 0.0001, because of the large donor-acceptor separation, ~ 8 \u00c5. The results for Ir\u2082(TMB)\u2084\u00b2\u207a are discussed in comparison to those for [Ir(\u00b5-pz)COD]\u2082.
\r\n\r\nIr\u2082(TMB)\u2084\u00b2\u207a is found to react photochemically with alkyl halides. Although the \u00b3(d\u03c3*p\u03c3) excited state is a good reductant, outer-sphere electron transfer seems unlikely (E\u2070(RX/RX\u2022-) < -1.5 V (SSCE)). An SRN1 pathway has been suggested to explain the alkyl halide photoreduction reaction observed for metal complexes with E\u2070(M\u2082+/3M\u2082*) < -1.5 V (SSCE); however, atom transfer to the \u00b3(d\u03c3*p\u03c3) excited state is the favored reaction mechanism for the alkyl halide photoreduction reaction of Ir\u2082(TMB)\u2084\u00b2\u207a. The generality of this reaction is discussed.
\r\n\r\nWhile there is some ambiguity as to the primary photoprocess for alkyl halide photoreactivity, \u00b3(d\u03c3*p\u03c3) excited-state hydrogen-atom transfer has been established as the mechanism of the reaction of Ir\u2082(TMB)\u2084\u00b2\u207a and a number of organic substrates. The atom-transfer reactivity of the \u00b3(d\u03c3*p\u03c3) excited state is attributed to the presence of a hole in the d\u03c3* orbital, analogous to the \u00b3n\u03c0* state of organic ketones. Interaction of the oxidizing hole with the electron pair of the C-H bond is the presumed pathway.
\r\n\r\nElectrochemical oxidation of Rh\u2082(TMB)\u2084\u00b2\u207a generates the d\u2078-d\u2077 species Rh\u2082(TMB)\u2084\u00b3\u207a. This complex reacts with 1,4-cyclohexadiene to abstract a hydrogen atom mimicking the initial step of the \u00b3(d\u03c3*p\u03c3) photoreaction. The importance of this result is discussed in terms of energy storage systems and extension of the range of hydrocarbon oxidations with binuclear d\u2078 complexes.
\r\n\r\nThe d\u2077-d\u2077 dihydride product obtained from the photoreaction of Ir\u2082(TMB)\u2084\u00b2\u207a and 1,4-cyclohexadiene is isolated and characterized. In addition to NMR, UV-Vis, IR, and Raman spectra, the complex is characterized crystallographically. The reactivity of this complex is also discussed.
", "doi": "10.7907/q1gz-dn84", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:1955", "collection": "thesis", "collection_id": "1955", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05222007-110626", "type": "thesis", "title": "Polyacetylene and Novel Conjugated Derivatives through the Metathesis Polymerization of 1,3,5,7-Cyclooctatetraenes", "author": [ { "family_name": "Klavetter", "given_name": "Floyd L.", "clpid": "Klavetter-Floyd-L" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A Diels-Alder adduct of cyclooctatetraene and benzyne has been polymerized through ring-opening metathesis by titanium methylidene sources to produce a soluble polyacetylene precursor. The polymerization proceeds through first order kinetics and linear increase in molecular weight, providing a route into conjugated polyene segments of various and controlled length.
\r\n\r\nA versatile and convenient route to polyacetylene has been developed through the condensed phase metathesis polymerization of cyclooctatetraene. Dissolution of catalyst in \"neat\" cyclooctatetraene provides a means of transforming the liquid into a highly lustrous film at ambient temperature and pressure. These films have physical and spectral properties very similar to films prepared by the Shirakawa methodology. Iodine-doped films exhibit conductivities greater than 300 \u03a9\u207b\u00b9/cm. New processing modes and novel morphologies for polyacetylene have been discovered. Novel polyacetylene derivatives have been prepared to demonstrate the versatility of the method. Both electron-releasing and electron-withdrawing groups have been attached to carbons in the \u03c0-conjugated system. These organic materials have been used in the fabrication of solid state devices.
\r\n\r\nThe mechanism of metathesis polymerization with a well-defined tungsten carbene catalyst has been explored, using cyclooctatetraene and its soluble analogue 1,5-cyclooctadiene as monomers. A new phenomenon referred to as \"cycloextrusion\" has been discovered, and its influence upon the statistical distribution of isomers and the cis-trans polymer stereochemistry delineated. Cycloextrusion is a dilute solution phenomenon, limited to cycloolefins containing an unhindered diene moeity in the ring. The thermodynamics and kinetics of the catalyst in the presence of a reversibly binding ligand have been intensively researched. Tetrahydrofuran serves as the reversibly binding ligand which deactivates the catalyst to an extent dependent upon concentration of tetrahydrofuran present. The metathesis of cyclooctadiene with this tungsten carbene can thus be sufficiently retarded to show that the polymerization kinetics involves a catalyst-monomer bound complex, followed by regeneration of catalyst.
\r\n\r\nLinear copolymers are prepared in both random and block form from the metathesis polymerization of 1,5-cyclooctadiene/cyclooctatetraene and norbornene/cyclooctatetraene solutions, respectively. The average conjugation length in the random copolymers can be varied systematically by varying the mole fraction of cyclooctatetraene in the copolymerization solution. Raman spectroscopy, UV-Vis, NMR, electrical conductivity, and non-linear optical measurements all indicate a progression of conjugation length in the copolymer with increasing mole fraction cyclooctatetraene.
", "doi": "10.7907/wqc2-mk42", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:7937", "collection": "thesis", "collection_id": "7937", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08232013-142740600", "primary_object_url": { "basename": "Pranata_j_1989.pdf", "content": "final", "filesize": 64719543, "license": "other", "mime_type": "application/pdf", "url": "/7937/1/Pranata_j_1989.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theoretical Studies of Novel Organic Systems: Biradicals, Polyradicals, and Conducting Polymers", "author": [ { "family_name": "Pranata", "given_name": "Julianto", "clpid": "Pranata-Julianto" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1
\r\n\r\nCyclobutanediyl has been studied in both its singlet and triplet states by ab initio electronic structure theory. The triplet, which is the ground state of the molecule, exists in both C2h and C2v forms, which interconvert via a Cs transition state. For the singlet, only a C2h form is found. It passes, via a Cs transition state, onto the C2v surface on which bicyclobutane is the only minimum. The ring-flipping (inversion) process in bicyclobutane includes the singlet biradical as an intermediate, and involves a novel, nonleast motion pathway. Semiclassical periodic orbit theory indicates that the various minima on both the singlet and triplet surfaces can interconvert via quantum mechanical tunneling.
\r\n\r\nChapter 2
\r\n\r\nThe dimethylenepolycyclobutadienes (n) are the non-Kekul\u00e9 analogues of the classical acenes. Application of a variety of theoretical methods reveals several novel features of such structures. Most interesting is the emergence of a parity rule. When n is even, n is predicted to be a singlet, with n disjoint NBMOs. When n is odd, theory predicts a triplet ground state with (n+1) NBMOs that are not fully disjoint.
\r\n\r\nChapter 3
\r\n\r\nBi(cyclobutadienyl) (2), the cyclobutadiene analogue of biphenyl, and its homologues tri- (3) and tetra(cyclobutadienyl) (4) have been studied using electronic structure theory. Ab initio calculations on 2 reveal that the central bond is a true double bond, and that the structure is best thought of as two allyl radicals plus an ethylene. The singlet and triplet states are essentially degenerate. Trimer 3 is two allyls plus a dimethylenecyclobutanediyl, while 4 is two coplanar bi(cyclobutadienyl) units connected by a single bond. For both 3 and 4, the quintet, triplet, and singlet states are essentially degenerate, indicating that they are tetraradicals. The infinite polymer, polycyclobutadiene, has been studied by HMO, EHCO, and VEH methods. Several geometries based on the structures of 3 and 4 have been studied, and the band structures are quite intriguing. A novel crossing between the valence and conduction bands produces a small band gap and a high density of states at the Fermi level.
\r\n\r\nChapter 4
\r\n\r\nAt the level of H\u00fcckel theory, polyfulvene has a HOCO-LUCO degeneracy much like that seen in polyacetylene. Higher levels of theory remove the degeneracy, but the band gap (Eg) is predicted to be significantly smaller than analogous structures such as polythiophene and polypyrrole at the fulvenoid geometry. An alternative geometry, which we have termed quinoid, is also conceivable for polyfulvene, and it is predicted to have a much larger Eg. The effects of benzannelation to produce analogues of polyisothianaphthene have been evaluated. We propose a new model for such structures based on conventional orbital mixing arguments. Several of the proposed structures have quite interesting properties, which suggest that they are excellent candidates for conducting polymers.
\r\n\r\nChapter 5
\r\n\r\nTheoretical studies of polydimethylenecyclobutene and polydiisopropylidene-cyclobutene reveal that, because of steric crowding, they cannot achieve a planar, fully conjugated structure in either their undoped or doped states. Rather, the structure consists of essentially orthogonal hexatriene units. Such a structure is incompatible with conventional conduction mechanisms involving polarons and bipolarons.
", "doi": "10.7907/x0ka-7s95", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:5370", "collection": "thesis", "collection_id": "5370", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-115104264", "type": "thesis", "title": "Experimental and Theoretical Studies of Silylenes, Silicenium Ions, and Organometallic Reactive Intermediates", "author": [ { "family_name": "Shin", "given_name": "Seung Koo", "clpid": "Shin-Seung-Koo" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Fourier transform ion cyclotron resonance spectroscopy has been used to investigate thermochemistry and relative stabilities of silylenes, silaethylene, and silicenium ions in the gas phase. Proton affinities of silylene, methylsilylene and silaethylene have been derived from studies of kinetics and thermochemistry of proton transfer from the corresponding silicenium ions to a series of n-donor bases with well-established gas-phase base strengths. Values of proton affinities combined with the known heats of formation of the corresponding silicenium ions yield heats of formation of silylene, methylsilylene, and silaethylene. Experimental results for the relative stability between methylsilylene and silaethylene are corroborated by ab initio generalized valence bond (GVB)-configuration interaction (CI) calculations which indicate that silaethylene is more stable than methylsilylene. Hydride affinities of the methyl-substituted silicenium ions have been precisely determined from examination of kinetics and equilibria of hydride-transfer reactions of methyl-substituted silanes with various hydrocarbons having well-established gas-phase hydride affinities. The result shows that the silicenium ions are significantly more stable than the corresponding carbonium ions in the gas phase with H\u207b as a reference base.
\r\n\r\nPhotoelectron spectroscopy and mass spectrometry have been employed to identify the gas-phase reactive intermediate in the chiorosilane chemical vapor deposition under the heterogeneous flash vacuum pyrolytic condition. The result indicates that dichlorosilylene and hydrogen chloride are the major gas-phase products and monochlorosilylene is not an abundant gas-phase intermediate.
\r\n\r\nThe ab initio theoretical methods have been used to calculate the equlibrium ge-ometries and singlet-triplet splittings of chlorine- and fluorine-substituted silylenes and methylenes. The GVB-dissociation consistent CI (DCCI) method has been developed to accurately predict singlet-triplet energy gaps within 1 kcal/mol error.
\r\n\r\nFinally, we have employed Fourier transform ion cyclotron resonance spec-troscopy combined with a line tunable CW CO\u2082 laser to isolate the coordinatively unsaturated organometallic intermediates and examine structures, reactivities, and spectroscopic properties of the isolated intermediates for the methyl-migratory decarbonylation reaction and ligand displacement reaction. The results show that the CF\u2083 group is an ideal infrared chromophore to investigate the infrared photochemistry of organometallic complexes, L\u2099M-CF\u2083, structures, and reaction mechanisms of their coordinatively unsaturated intermediates containing metal-bonded CF\u2083 groups. The infrared multiphoton dissociation spectra of the isolated intermediates containing metal-bonded CF\u2083 group are presented.
", "doi": "10.7907/sdj1-2y57", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:5377", "collection": "thesis", "collection_id": "5377", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-134341582", "type": "thesis", "title": "Insights on Enzymes and Polymers from Molecular Dynamics Simulations: Applications to Dihydrofolate Reductase Complexes and Starburst Dendrimers", "author": [ { "family_name": "Naylor", "given_name": "Adel Marie", "clpid": "Naylor-Adel-Marie" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Examples are given for the role of simulation and theory in designing artificial biomimetic and biocatalytic systems. Simulations on the \u03b2-alanine starburst dendrimer polymers indicate that, for the higher generation systems: (1) ~50% of the surface area is internal, and (ii) ~50% of the spheroidal volume is solvent- filled. These studies suggest a design for encapsulating and delivering dopamine to the kidney for cardiovascular therapies. Investigations of the penta-erythritol based polyether starburst dendrimers show that: (i) the later generations lack any internal surface area or volume and (ii) the dense-packed limit for these polymers to be the third generation, consistent with experiment. For Dihydrofolate Reductase (DHFR), the modeling and simulations: (i) explain the high degree of kinetic similarity between two dissimilar forms of DHFR; (ii) indicate why site specific mutation (Phe-31\u2192Tyr-31, Leu-54\u2192Ile-54, or Leu-54\u2192Gly-54) causes a significant change in the catalytic rate; and (iii) suggest modifications to engineer E. coli Chicken hybrid proteins capable of reducing folate.
", "doi": "10.7907/0789-jw44", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:5377", "collection": "thesis", "collection_id": "5377", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-134341582", "type": "thesis", "title": "Insights on Enzymes and Polymers from Molecular Dynamics Simulations: Applications to Dihydrofolate Reductase Complexes and Starburst Dendrimers", "author": [ { "family_name": "Naylor", "given_name": "Adel Marie", "clpid": "Naylor-Adel-Marie" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Examples are given for the role of simulation and theory in designing artificial biomimetic and biocatalytic systems. Simulations on the \u03b2-alanine starburst dendrimer polymers indicate that, for the higher generation systems: (1) ~50% of the surface area is internal, and (ii) ~50% of the spheroidal volume is solvent- filled. These studies suggest a design for encapsulating and delivering dopamine to the kidney for cardiovascular therapies. Investigations of the penta-erythritol based polyether starburst dendrimers show that: (i) the later generations lack any internal surface area or volume and (ii) the dense-packed limit for these polymers to be the third generation, consistent with experiment. For Dihydrofolate Reductase (DHFR), the modeling and simulations: (i) explain the high degree of kinetic similarity between two dissimilar forms of DHFR; (ii) indicate why site specific mutation (Phe-31\u2192Tyr-31, Leu-54\u2192Ile-54, or Leu-54\u2192Gly-54) causes a significant change in the catalytic rate; and (iii) suggest modifications to engineer E. coli Chicken hybrid proteins capable of reducing folate.
", "doi": "10.7907/0789-jw44", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:552", "collection": "thesis", "collection_id": "552", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02082007-095349", "type": "thesis", "title": "Molecular Dynamics Simulation of Sputtering", "author": [ { "family_name": "Lo", "given_name": "Davy", "clpid": "Lo-Davy" } ], "thesis_advisor": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" } ], "thesis_committee": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Housley", "given_name": "Robert M.", "clpid": "Housley-Robert-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The sputtering of metals by low-energy (keV) ion bombardment has been investigated with the molecular dynamics technique. This study, based on computer simulations, aims to elucidate experimental observations and to provide valuable theoretical insight. The systems studied include Ar+ ion bombardment of metals, alloys, and isotopic mixtures in either the solid or liquid state. Effects of many-body interactions on the spectrum of sputtered atoms were also examined. Simulation results generally support experimental findings and render many basic assumptions of analytic sputtering theory dubious.
\r\n\r\nThis thesis consists of molecular dynamics studies of several sputtering topics not directly related to each other and is organized accordingly into separate chapters. Each of these chapters will be a summary of corresponding publications published by the author during the course of his graduate study. Reprints of publications are included as appendices at the end of each chapter.
", "doi": "10.7907/EVKV-AW57", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:552", "collection": "thesis", "collection_id": "552", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02082007-095349", "type": "thesis", "title": "Molecular Dynamics Simulation of Sputtering", "author": [ { "family_name": "Lo", "given_name": "Davy", "clpid": "Lo-Davy" } ], "thesis_advisor": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" } ], "thesis_committee": [ { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Bellan", "given_name": "Paul Murray", "orcid": "0000-0002-0886-8782", "clpid": "Bellan-P-M" }, { "family_name": "Fultz", "given_name": "Brent T.", "orcid": "0000-0002-6364-8782", "clpid": "Fultz-B-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Housley", "given_name": "Robert M.", "clpid": "Housley-Robert-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The sputtering of metals by low-energy (keV) ion bombardment has been investigated with the molecular dynamics technique. This study, based on computer simulations, aims to elucidate experimental observations and to provide valuable theoretical insight. The systems studied include Ar+ ion bombardment of metals, alloys, and isotopic mixtures in either the solid or liquid state. Effects of many-body interactions on the spectrum of sputtered atoms were also examined. Simulation results generally support experimental findings and render many basic assumptions of analytic sputtering theory dubious.
\r\n\r\nThis thesis consists of molecular dynamics studies of several sputtering topics not directly related to each other and is organized accordingly into separate chapters. Each of these chapters will be a summary of corresponding publications published by the author during the course of his graduate study. Reprints of publications are included as appendices at the end of each chapter.
", "doi": "10.7907/EVKV-AW57", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:7948", "collection": "thesis", "collection_id": "7948", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08272013-134530519", "primary_object_url": { "basename": "Vogelaar 1989.pdf", "content": "final", "filesize": 28258634, "license": "other", "mime_type": "application/pdf", "url": "/7948/1/Vogelaar 1989.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Structural and Mechanistic Motifs in Membrane Proteins: The Three-Dimensional Modelling of Rhodopsin, Band 3, and the Nicotinic Acetylcholine Receptor", "author": [ { "family_name": "Vogelaar", "given_name": "Nancy Swick", "clpid": "Vogelaar-Nancy-Swick" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Chan", "given_name": "Sunney I.", "clpid": "Chan-S-I" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Marsh", "given_name": "Richard Edward", "clpid": "Marsh-R-E" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, \u03b2-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.
\r\n\r\nSpecific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and \u03b2-adrenergic receptors.
\r\n\r\nThe nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.
\r\n\r\nBand 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.
", "doi": "10.7907/mgah-n841", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:5370", "collection": "thesis", "collection_id": "5370", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-115104264", "type": "thesis", "title": "Experimental and Theoretical Studies of Silylenes, Silicenium Ions, and Organometallic Reactive Intermediates", "author": [ { "family_name": "Shin", "given_name": "Seung Koo", "clpid": "Shin-Seung-Koo" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Weitekamp", "given_name": "Daniel P.", "clpid": "Weitekamp-D-P" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Fourier transform ion cyclotron resonance spectroscopy has been used to investigate thermochemistry and relative stabilities of silylenes, silaethylene, and silicenium ions in the gas phase. Proton affinities of silylene, methylsilylene and silaethylene have been derived from studies of kinetics and thermochemistry of proton transfer from the corresponding silicenium ions to a series of n-donor bases with well-established gas-phase base strengths. Values of proton affinities combined with the known heats of formation of the corresponding silicenium ions yield heats of formation of silylene, methylsilylene, and silaethylene. Experimental results for the relative stability between methylsilylene and silaethylene are corroborated by ab initio generalized valence bond (GVB)-configuration interaction (CI) calculations which indicate that silaethylene is more stable than methylsilylene. Hydride affinities of the methyl-substituted silicenium ions have been precisely determined from examination of kinetics and equilibria of hydride-transfer reactions of methyl-substituted silanes with various hydrocarbons having well-established gas-phase hydride affinities. The result shows that the silicenium ions are significantly more stable than the corresponding carbonium ions in the gas phase with H\u207b as a reference base.
\r\n\r\nPhotoelectron spectroscopy and mass spectrometry have been employed to identify the gas-phase reactive intermediate in the chiorosilane chemical vapor deposition under the heterogeneous flash vacuum pyrolytic condition. The result indicates that dichlorosilylene and hydrogen chloride are the major gas-phase products and monochlorosilylene is not an abundant gas-phase intermediate.
\r\n\r\nThe ab initio theoretical methods have been used to calculate the equlibrium ge-ometries and singlet-triplet splittings of chlorine- and fluorine-substituted silylenes and methylenes. The GVB-dissociation consistent CI (DCCI) method has been developed to accurately predict singlet-triplet energy gaps within 1 kcal/mol error.
\r\n\r\nFinally, we have employed Fourier transform ion cyclotron resonance spec-troscopy combined with a line tunable CW CO\u2082 laser to isolate the coordinatively unsaturated organometallic intermediates and examine structures, reactivities, and spectroscopic properties of the isolated intermediates for the methyl-migratory decarbonylation reaction and ligand displacement reaction. The results show that the CF\u2083 group is an ideal infrared chromophore to investigate the infrared photochemistry of organometallic complexes, L\u2099M-CF\u2083, structures, and reaction mechanisms of their coordinatively unsaturated intermediates containing metal-bonded CF\u2083 groups. The infrared multiphoton dissociation spectra of the isolated intermediates containing metal-bonded CF\u2083 group are presented.
", "doi": "10.7907/sdj1-2y57", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:1955", "collection": "thesis", "collection_id": "1955", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05222007-110626", "type": "thesis", "title": "Polyacetylene and Novel Conjugated Derivatives through the Metathesis Polymerization of 1,3,5,7-Cyclooctatetraenes", "author": [ { "family_name": "Klavetter", "given_name": "Floyd L.", "clpid": "Klavetter-Floyd-L" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A Diels-Alder adduct of cyclooctatetraene and benzyne has been polymerized through ring-opening metathesis by titanium methylidene sources to produce a soluble polyacetylene precursor. The polymerization proceeds through first order kinetics and linear increase in molecular weight, providing a route into conjugated polyene segments of various and controlled length.
\r\n\r\nA versatile and convenient route to polyacetylene has been developed through the condensed phase metathesis polymerization of cyclooctatetraene. Dissolution of catalyst in \"neat\" cyclooctatetraene provides a means of transforming the liquid into a highly lustrous film at ambient temperature and pressure. These films have physical and spectral properties very similar to films prepared by the Shirakawa methodology. Iodine-doped films exhibit conductivities greater than 300 \u03a9\u207b\u00b9/cm. New processing modes and novel morphologies for polyacetylene have been discovered. Novel polyacetylene derivatives have been prepared to demonstrate the versatility of the method. Both electron-releasing and electron-withdrawing groups have been attached to carbons in the \u03c0-conjugated system. These organic materials have been used in the fabrication of solid state devices.
\r\n\r\nThe mechanism of metathesis polymerization with a well-defined tungsten carbene catalyst has been explored, using cyclooctatetraene and its soluble analogue 1,5-cyclooctadiene as monomers. A new phenomenon referred to as \"cycloextrusion\" has been discovered, and its influence upon the statistical distribution of isomers and the cis-trans polymer stereochemistry delineated. Cycloextrusion is a dilute solution phenomenon, limited to cycloolefins containing an unhindered diene moeity in the ring. The thermodynamics and kinetics of the catalyst in the presence of a reversibly binding ligand have been intensively researched. Tetrahydrofuran serves as the reversibly binding ligand which deactivates the catalyst to an extent dependent upon concentration of tetrahydrofuran present. The metathesis of cyclooctadiene with this tungsten carbene can thus be sufficiently retarded to show that the polymerization kinetics involves a catalyst-monomer bound complex, followed by regeneration of catalyst.
\r\n\r\nLinear copolymers are prepared in both random and block form from the metathesis polymerization of 1,5-cyclooctadiene/cyclooctatetraene and norbornene/cyclooctatetraene solutions, respectively. The average conjugation length in the random copolymers can be varied systematically by varying the mole fraction of cyclooctatetraene in the copolymerization solution. Raman spectroscopy, UV-Vis, NMR, electrical conductivity, and non-linear optical measurements all indicate a progression of conjugation length in the copolymer with increasing mole fraction cyclooctatetraene.
", "doi": "10.7907/wqc2-mk42", "publication_date": "1989", "thesis_type": "phd", "thesis_year": "1989" }, { "id": "thesis:7522", "collection": "thesis", "collection_id": "7522", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03182013-115728432", "primary_object_url": { "basename": "Parmeter 1988.pdf", "content": "final", "filesize": 55219935, "license": "other", "mime_type": "application/pdf", "url": "/7522/1/Parmeter 1988.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Organometallic Chemistry of the Ru(001) Surface", "author": [ { "family_name": "Parmeter", "given_name": "John Ethan", "clpid": "Parmeter-John-Ethan" } ], "thesis_advisor": [ { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The organometallic chemistry of the hexagonally close-packed Ru(001) surface has been studied using electron energy loss spectroscopy and thermal desorption mass spectrometry. The molecules that have been studied are acetylene, formamide and ammonia. The chemistry of acetylene and formamide has also been investigated in the presence of coadsorbed hydrogen and oxygen adatoms.
\r\n\r\nAcetylene is adsorbed molecularly on Ru(001) below approximately 230 K, with rehybridization of the molecule to nearly sp\u00b3 occurring. The principal decomposition products at higher temperatures are ethylidyne (CCH\u2083) and acetylide (CCH) between 230 and 350 K, and methylidyne (CH) and surface carbon at higher temperatures. Some methylidyne is stable to approximately 700 K. The preadsorption of hydrogen does not alter the decomposition products of acetylene, but reduces the saturation coverage and also leads to the formation of a small amount of ethylene (via an \u03b7\u00b2-CHCH\u2082 species) which desorbs molecularly near 175 K. Preadsorbed oxygen also reduces the saturation coverage of acetylene but has virtually no effect on the nature of the molecularly chemisorbed acetylene. It does, however, lead to the formation of an sp\u00b2-hybridized vinylidene (CCH\u2082) species in the decomposition of acetylene, in addition to the decomposition products that are formed on the clean surface. There is no molecular desorption of chemisorbed acetylene from clean Ru(001), hydrogen-presaturated Ru(001), or oxygen-presaturated Ru(001).
\r\n\r\nThe adsorption and decomposition of formamide has been studied on clean Ru(001), hydrogen-presaturated Ru(001), and Ru(001)-p(1x2)-O (oxygen adatom coverage = 0.5). On clean Ru(001), the adsorption of low coverages of formamide at 80 K results in CH bond cleavage and rehybridization of the carbonyl double bond to produce an \u03b7\u00b2(C,O)-NH\u2082CO species. This species is stable to approximately 250 K at which point it decomposes to yield a mixture of coadsorbed carbon monoxide, ammonia, an NH species and hydrogen adatoms. The decomposition of NH to hydrogen and nitrogen adatoms occurs between 350 and 400 K, and the thermal desorption products are NH\u2083 (-315 K), H\u2082 (-420 K), CO (-480 K) and N\u2082 (-770 K). At higher formamide coverages, some formamide is adsorbed molecularly at 80 K, leading both to molecular desorption and to the formation of a new surface intermediate between 300 and 375 K that is identified tentatively as \u03b7\u00b9(N)-NCHO. On Ru(001)-p(1x2)-O and hydrogen-presaturated Ru(001), formamide adsorbs molecularly at 80 K in an \u03b7\u00b9(O)-NH\u2082CHO configuration. On the oxygen-precovered surface, the molecularly adsorbed formamide undergoes competing desorption and decomposition, resulting in the formation of an \u03b7\u00b2(N,O)-NHCHO species (analogous to a bidentate formate) at approximately 265 K. This species decomposes near 420 K with the evolution of CO and H\u2082 into the gas phase. On the hydrogen precovered surface, the \u0397\u00b9(O)-NH\u2082CHO converts below 200 K to \u03b7\u00b2(C,O)-NH\u2082CHO and \u03b7\u00b2(C,O)-NH\u2082CO, with some molecular desorption occurring also at high coverage. The \u03b7\u00b2(C,O)-bonded species decompose in a manner similar to the decomposition of \u03b7\u00b2(C,O)-NH\u2082CO on the clean surface, although the formation of ammonia is not detected.
\r\n\r\nAmmonia adsorbs reversibly on Ru(001) at 80 K, with negligible dissociation occurring as the surface is annealed The EEL spectra of ammonia on Ru(001) are very similar to those of ammonia on other metal surfaces. Off-specular EEL spectra of chemisorbed ammonia allow the \u03bd(Ru-NH\u2083) and \u03c1(NH\u2083) vibrational loss features to be resolved near 340 and 625 cm\u207b\u00b9), respectively. The intense \u03b4g(NH\u2083) loss feature shifts downward in frequency with increasing ammonia coverage, from approximately 1160 cm\u207b\u00b9 in the low coverage limit to 1070 cm\u207b\u00b9 at saturation. In coordination compounds of ammonia, the frequency of this mode shifts downward with decreasing charge on the metal atom, and its downshift on Ru(001) can be correlated with the large work function decrease that the surface has previously been shown to undergo when ammonia is adsorbed. The EELS data are consistent with ammonia adsorption in on-top sites. Second-layer and multilayer ammonia on Ru(001) have also been characterized vibrationally, and the results are similar to those obtained for other metal surfaces.
", "doi": "10.7907/xv82-qr39", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:5339", "collection": "thesis", "collection_id": "5339", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10302009-113153689", "type": "thesis", "title": "New Concepts of Metallic Bonding", "author": [ { "family_name": "McAdon", "given_name": "Mark Herbert", "clpid": "McAdon-Mark-Herbert" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis presents results derived from ab initio wavefunctions, leading to new concepts of metallic bonding \u2014 real-space concepts that do not require \"thinking in reciprical (k) space.\" As the first step in this study of metallic bonding, Hartree-Fock and generalized valence bond wavefunctions are presented for ring clusters composed of monovalent atoms (Cu, Ag, Au, Li, and Na). These results show that one-dimensional metals need not exhibit Peierls instabilities, charge density waves, or spin density waves. In addition, magnon spectra calculated using various wavefunctions are compared with each other and with magnon spectia obtained with simple nearest-neighbor Ising and Heisenberg hamiltonians.
\r\n\r\nGeneralized valence bond wavefunctions for small metal clusters lead to the conclusion that, for metallic systems, the valence electrons occupy interstitial regions \u2014 bond midpoints for one-dimensional systems, triangular hollows for two-dimensional systems, and tetrahedral hollows for three-dimensional systems. The new concepts of metallic bonding are summarized by a set of rules for the valence sp electrons of metallic systems. These rules are used to derive the low-lying isomers of small metal clusters, and are expected to prove useful in predicting the chemistry and catalytic properties of such systems. Applying these rules to bulk metals leads to a new explanation of the solubility limits governing alloys of monovalent, divalent, trivalent, and tetravalent atoms. These rules are expected to prove valuable in describing the localized states in metals and alloys such as defects or interfaces.
\r\n", "doi": "10.7907/jtpr-6m88", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:6062", "collection": "thesis", "collection_id": "6062", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09272010-145542274", "type": "thesis", "title": "Icosahedral Order in Metastable Metallic Alloys", "author": [ { "family_name": "Anlage", "given_name": "Steven Mark", "clpid": "Anlage-Steven-Mark" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Bellan", "given_name": "Paul Murray", "clpid": "Bellan-P-M" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Cross", "given_name": "Michael Clifford", "clpid": "Cross-M-C" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Bellan", "given_name": "Paul Murray", "clpid": "Bellan-P-M" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "We examine the consequences of short-range icosahedral order in metastable metallic alloys. There is evidence, both direct and indirect, for the existence of atomic clustering with icosahedral symmetry in supercooled liquid metals, metastable metallic alloys, and large-unit-cell intermetallic compounds. It is observed that a variety of metallic alloys can exhibit a long-range ordered structure with icosahedral point group symmetry upon rapid quenching from the liquid. We have carefully examined one of these icosahedral phase-forming systems in an effort to understand how the long-range ordered solid develops from the liquid phase. Our studies show that the icosahedral phase nucleates homogeneously from the liquid during the rapid quenching process.
\r\n\r\nWe have developed a theory to explain qualitatively this observation. A model material is proposed, which is endowed with short-range icosahedral order broken up by defect structures. The thermodynamics of this model are described by a Ginzburg-Landau theory. The model displays a strong first-order phase transition from a high-temperature, heavily defected phase to a low-temperature phase with enhanced short-range icosahedral order. This transition is compared to our observations of icosahedral phase formation to fix the values of the theoretical parameters.
\r\n", "doi": "10.7907/mjqp-qr45", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:7501", "collection": "thesis", "collection_id": "7501", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03062013-161416978", "primary_object_url": { "basename": "Klippenstein 1988.pdf", "content": "final", "filesize": 37105558, "license": "other", "mime_type": "application/pdf", "url": "/7501/1/Klippenstein 1988.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theoretical Studies of Chemical Reaction Dynamics", "author": [ { "family_name": "Klippenstein", "given_name": "Stephen Jacob", "clpid": "Klippenstein-Stephen-Jacob" } ], "thesis_advisor": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this thesis theoretical models a.re developed and/or applied to the study of the dynamics of a variety of chemical reactions. First, a semiclassical model is developed to describe the effect of mutual orientation of the donor and acceptor on the rate of electron transfer between two large aromatic groups. The next reaction considered is that of gas phase H-atom transfer reactions. In this case a comparison is made of two previously developed approximations for the treatment of the particular case of H-atom transfer between two heavy particles.
\r\n\r\nThe next topic involves the study of the rate of intramolecular vibrational redistribution of energy. First, an iterative procedure is developed for determining more and more accurate effective Hamiltonians for the description of the dynamics. The foundation of this method is the separation of the basis states into resonant and nonresonant sets followed by an adiabatic approximation for the dynamics of the off-resonant set. A second study involves the application of artificial intelligence techniques to the choice of a small set of basis states which are the states of greatest importance to the redistribution dynamics.
\r\n\r\nThe remainder of the thesis is devoted to the study of those unimolecular dissociation/free radical recombination reactions which contain highly flexible transition states. For these reactions, a method for determining the quantum partition function for the transition state in terms of path integral ratios is developed and applied to the study of the thermally activated methyl radical recombination. Subsequently, a method is developed for determining the number of states, for the transition state, at a given energy and angular momentum. The basis of the method is the use of conventional Euler angle coordinates in the Monte Carlo evaluation of phase space integrals. This method is applied to the NCNO, CH\u2082CO, and H\u2082O\u2082 photodissociation processes. Also presented is a discussion of both the trend of the location of the transition state with increasing energy and the possible influence of excited potential energy surfaces.
\r\n", "doi": "10.7907/dbrd-wj15", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:3126", "collection": "thesis", "collection_id": "3126", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08152005-160834", "type": "thesis", "title": "Precursor Routes to Conducting Polymers from the Ring-Opening Metathesis Polymerization of Cyclic Olefins", "author": [ { "family_name": "Swager", "given_name": "Timothy Manning", "orcid": "0000-0002-3577-0510", "clpid": "Swager-Timothy-Manning" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_chem" } ], "abstract": "Chapter 1 provides an introduction to the field of conductive polymers. The perspective is that of a chemist who is also interested in the physics of conductive polymers. The concepts discussed in this chapter are referred to throughout the other chapters, and should be a good primer for newcomers to this field as well as a reference to the literature for others. This chapter sets the stage for the theme of this thesis, which is the use of soluble precursor polymers in the synthesis of conductive polymers. Recent work was cited in this chapter which is not available in existing reviews of conductive polymers.
\r\n \r\nThe method of ring-opening metathesis polymerization (ROMP) is discussed in Chapter 2. The concepts discussed therein are again referred to throughout the following chapters. The ideas of catalyst matching for different monomers are discussed, and particular emphasis is given to the steric requirements of the catalysts.
\r\n\r\nThe ROMP of derivatives of dimethylene cyclobutene is discussed in Chapter 3. However, the primary focus of the chapter is on the polymer polydiisopropylidenecyclobutene. This material is distinctly different from other conductive polymers in the fact that it has a structure consisting of triene units that are mutually orthogonal to each other. A detailed study of this material with a variety of spectroscopies and measurements is presented.
\r\n \r\nThe synthesis of polybenzvalene, and the isomerization of this material to polyacetylene, is discussed in Chapter 4. This work constitutes a new precursor method to this fundamentally important polymer, as well as a demonstration of the far reaching scope of ROMP. Polybenzvalene is also a high energy material and has unusual explosive properties which are also discussed.
\r\n\r\nIn Chapter 5, new precursor routes to conductive polymers based on the elimination and hydrolysis of ketals are presented. This work has been primarily focused on structural chemistry and how to best transform the precursor polymers into conductive polymers. The majority of the effort has been focused on the, poly (quinone bisketals); however, another example of this concept is presented briefly.
\r\n", "doi": "10.7907/KF6P-FC76", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:1542", "collection": "thesis", "collection_id": "1542", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04292004-095332", "type": "thesis", "title": "Electron Transfer in Structurally Engineered Metalloproteins", "author": [ { "family_name": "Mayo", "given_name": "Stephen Leon", "orcid": "0000-0002-9785-5018", "clpid": "Mayo-Stephen-Leon" } ], "thesis_advisor": [ { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Campbell", "given_name": "Judith L.", "clpid": "Campbell-J-L" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis is concerned with experimental approaches for studying electron transfer in metalloproteins. The material presented traces the development of experimental techniques aimed at elucidating the mechanism of intramolecular metalloprotein electron transfer. The first chapter includes a reprint of an Inorganic Chemistry paper that describes the bimolecular reaction of small inorganic redox complexes with blue-copper proteins. The second chapter illustrates the use of covalently attached redox probes for studying rate-distance relationships. And the third chapter documents our progress in using genetic methods to structurally engineer yeast iso-1 cytochrome c into an idealized system for studying the distance dependence of intramolecular electron-transfer events.
", "doi": "10.7907/YJKW-3133", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:5307", "collection": "thesis", "collection_id": "5307", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-085412529", "type": "thesis", "title": "Theoretical Insights into the Bonding in Thorium Organometallic Complexes: A Comparison with Group IV Transition Metal Chemistry", "author": [ { "family_name": "Brusich", "given_name": "Mark John", "clpid": "Brusich-Mark-John" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this thesis a detailed ab initio theoretical study of organothorium chemistry is presented. The first part is devoted to examining both the bonding in and the reaction chemistry of various substituted thorium complexes. Using the chlorine ligand as a model for the usual cyclopentadienyl groups found in these systems, we examine the bonding of hydrogen and methyl ligands to thorium. Frequent comparisons with the experimental results on similar species are made. In addition, by contrasting the bonding in the thorium complexes with the bonding in the analogous Group IVB systems, a qualitative and quantitative picture of bonding, as the atomic number of the metal becomes larger, can be obtained. The reaction chemistry is studied via two different sets of processes. In the first, the deuterium (D2) exchange reaction with a thorium-hydrogen bond is examined. Several studies have been done previously, both experimentally and theoretically, on the Group IVB exchange reactions. Hence, there is enough information to see trends and to make predictions about relative reaction rates. Also, from our investigation the effect that different types of ligands have on the activation barrier to reaction can be ascertained.
\r\n\r\nIn the second part of the thesis, the factors that go into stabilizing bond formation are discussed concerning both main group elements and transition metals, including actinides. In particular, the process of bond formation between hydrogen atom and the alkali metals is compared with the same process in the Group IVB-hydrogen and thorium-hydrogen saturated complexes. The main difference between the alkali metal and the transition metal bonds with hydrogen is the bond strength trends with increasing atomic number. For the alkali metals the bond energies decrease down the column, yet for the transition metals and thorium it is the reverse. The conclusion is that the shape of the mostly d in character transition metal bonding orbitals is such that better overlap can be achieved with hydrogen as the orbitals become more diffuse. In the alkali metals the bonds can be described as s\u2014s bonds whose overlap decreases with increasing diffuseness.
\r\n", "doi": "10.7907/89jn-7f38", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:7531", "collection": "thesis", "collection_id": "7531", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03202013-082024971", "primary_object_url": { "basename": "Snyder-gj-1988.pdf", "content": "final", "filesize": 74761861, "license": "other", "mime_type": "application/pdf", "url": "/7531/1/Snyder-gj-1988.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "2,4-Dimethylene-1,3-Cyclobutanediyl and 2,4-Dimethylenebicyclobutane. Synthesis, Spectroscopy, and Reactivity of a Triplet Biradical and Its Covalent Isomer", "author": [ { "family_name": "Snyder", "given_name": "\u200cGary James", "clpid": "Snyder-\u200cGary-James" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The preparation and direct observation of triplet 2,4-dimethylene-1,3-cyclobutanediyl (1), the non-Kekul\u00e9 isomer of benzene, is described. The biradical was generated by photolysis of 5,6-dimethylene-2,3-diazabicyclo[2.1.1]hex-2-ene (2) (which was synthesized in several steps from benzvalene) under cryogenic, matrix-isolation conditions. Biradical 1 was characterized by EPR spectroscopy (\u200c\u200c\u200c\u200c\u200c\u2502D/hc\u2502 = 0.0204 cm\u207b\u00b9, \u2502E/hc\u2502 = 0.0028 cm\u207b\u00b9) and found to have a triplet ground state. The \u0394ms = 2 transition displays hyperfine splitting attributed to a 7.3-G coupling to the ring methine and a 5.9-G coupling to the exocyclic methylene protons. Several experiments, including application of the magnetophotoselection (mps) technique in the generation of biradical 1, have allowed a determination of the zero-field triplet sublevels as x = -0.0040, y = +0.0136, and z = -0.0096 cm\u207b\u00b9), where x and y are respectively the long and short in-plane axes and z the out-of-plane axis of 1.
\r\n\r\nTriplet 1 is yellow-orange and displays highly structured absorption (\u03bbmax = 506 nm) and fluorescence (\u03bbmax = 510 nm) spectra, with vibronic spacings of 1520 and 620 cm\u207b\u00b9 for absorption and 1570 and 620 cm\u207b\u00b9 for emission. The spectra were unequivocally assigned to triplet 1 by the use of a novel technique that takes advantage of the biradical's photolability. The absorption \u0454 = 7200 M\u207b\u00b9 cm\u207b\u00b9 and f = 0.022, establishing that the transition is spin-allowed. Further use of the mps technique has demonstrated that the transition is x-polarized, and the excited state 1s therefore of B1g symmetry, in accord with theoretical predictions.
\r\n\r\nThermolysis or direct photolysis of diazene 2 in fluid solution produces 2,4-dimethylenebicyclo[l.l.0]butane (3), whose \u00b9H NMR spectrum (-80\u00b0C, CD\u2082Cl\u2082) consists of singlets at \u03b4 4.22 and 3.18 in a 2:1 ratio. Compound 3 is thermally unstable and dimerizes with second-order kinetics between -80 and -25\u00b0C (\u2206H\u2021 = 6.8 kcal mol\u207b\u00b9), (\u2206S\u2021 = -28 eu) by a mechanism involving direct combination of two molecules of 3 in the rate-determining step. This singlet-manifold reaction ultimately produces a mixture of two dimers, 3,8,9-trimethylenetricyclo[5.1.1.02,5]non-4-ene (75) and trans-3,10-dimethylenetricyclo[6.2.0.02,5]deca-4,8-diene (76t), with the former predominating. In contrast, triplet-sensitized photolysis of 2, which leads to triplet 1, provides, in addition to 75 and 76t, a substantial amount of trans-5,10-dimethylenetricyclo[6.2.0.03,6]deca-3,8-diene (77t) and small amounts of two unidentified dimers.
\r\n\r\nIn addition, triplet biradical 1 ring-closes to 3 in rigid media both thermally (77-140 K) and photochemically. In solution 3 forms triplet 1 upon energy transfer from sensitizers having relatively low triplet energies. The implications of the thermal chemistry for the energy surfaces of the system are discussed.
\r\n", "doi": "10.7907/4ftp-kr64", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:7509", "collection": "thesis", "collection_id": "7509", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03112013-144406216", "type": "thesis", "title": "Design, Synthesis and Characterization of Sequence Specific DNA Cleaving Agents", "author": [ { "family_name": "Sluka", "given_name": "James P.", "clpid": "Sluka-James-P" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter I: Synthetic, Sequence Specific DNA Cleaving Peptides
\r\n\r\nSynthetic peptides based on the sequence specific DNA binding domain of Hin recombinase have been prepared which are equiped with ethylenediaminetetraacetic acid (EDTA) at the amino terminus. Covalent attachment of EDTA converts the sequence specific DNA binding pep tides into peptides which are capable of DNA strand scission in the presence of iron II, a reducing agent and molecular oxygen. The EDTA-equiped peptides cleave DNA at Hin binding sites and provide information on the nucleotide postion and groove identity of the modified amino acid residue when bound to DNA. The EDTA-peptides were also competent at DNA double strand cleavage, which is a useful characteristic for identifying binding sites on large DNA fragments (>5000 base pairs). A general procedure for the incorporation of an EDTA equiped lysine residue at any position in a synthetic peptide is also described.
\r\n\r\nResults with 22 synthetic peptides indicate that Hin specifically recognizes a minor groove 5'-AAA sequence in its binding site with the peptide sequence Arg-Pro-Arg. Furthermore, the minor groove recognition event contributes substantially to the overall binding affinity. The possibility that minor groove recognition of tracks of A's by the peptide sequence Arg-Pro- Arg (and similar sequences), may be a common recognition motif in sequence specific DNA binding proteins is discussed.
\r\n\r\nChapter II: Distamycin-Actinomycin Hybrid Affinity Cleaving Molecules
\r\n\r\nOne approach to the design of sequence specific DNA binding molecules that read large sequences of double helical DNA is to couple DNA binding units of similar or diverse base pair specificities. Covalent attachment of his- and tris-N-methylpyrrolecarboxamides (based on the sequence specific DNA binding antibiotics Netropsin and Distamycin) and an aromatic phenoxazone intercalator (based on the sequence specific DNA intercalator Actinomycin) creates hybrid DNA binding minor groove and intercalation compounds. Using the affinity cleaving method we find that a first generation hybrid, bis-(EDTA-distamycin-glycyl)phenoxazone, binds the sequence 5'-TTATGGTTAA-3' which is consistent with simultaneous minor groove binding of the two tripyrrolecarboxamide units and intercalation of the phenoxazone moeity. Along with the targeted trimeric binding, the first generation hybrid also gave substantial monomeric/ dimeric binding, and exihibited only modest sequence specificity on large DNA fragments.
\r\n\r\nIn an attempt to reduce monomeric and dimeric binding, a second generation hybrid was prepared. Replacement of one pyrrolecarboxamide with a \u03b3 aminobutyric acid moeity, bis(EDTA-netropsin-glycyl)phenoxazone, generated a hybrid molecule which showed a reduced tendency for monomeric and dimeric DNA binding modes. The second generation hybrid binds to sequences of the form 5'-(A/T)\u2084GT(A/T)\u2084-3' and 5'-(A/T)\u2084CT(A/T)\u2084-3' and showed substantially improved sequence specificity on large DNA fragments relative to the first generation hybrid.
\r\n\r\nChapter III: Bleomycin-Distamycin Hybrid Affinity Cleaving Molecules
\r\n\r\nHybrids of the sequence specific DNA binding bithiazole domain of Bleomycin and tris-N-methylpyrrolecarboxamide of Distamycin are described. The hybrids address the issue of whether or not the bithiazole unit of the GC specific Bleomycin is a minor groove binding function. By the affinity cleaving method we find that hybrids in which the bithiazole is attached to either the amino or carboxy terminus of the tris-N-methylpyrrolecarboxamide, do not significantly alter the sequence specificity of the pyrrolecarboxamide domain. The results indicate that either the bithiazole unit is not a minor groove binding function in the same sense as the tripyrrolecarboxamide, or, alternatively, the bithiazole does not include all of the required sequence specific DNA recognition elements of Bleomycin.
\r\n\r\nChapter IV: Studies in Metalloporphyrin Mediated Affinity Cleaving
\r\n\r\nMetalloporphyrins are known to cause DNA strand scission using a variety of central metals, and various reducing and oxidizing cofactors. To investigate if a metalloporphyrin can replace an EDTA\u2022Fe chelate in an affinity cleaving molecule, a metalloporphyrin-Distamycin (PD) was prepared. PD\u2022Fe showed very inefficient DNA cleavage compared to EDTA\u2022Fe equiped affinity cleaving compounds. Additionally, PD\u2022Fe showed no detectable sequence specific DNA cleaving ability. PD\u2022Fe was also less efficient at DNA strand scission than ferriprotoporphyrin itself, which indicates that the DNA binding domain (tripyrrolecarboxamide) and cleaving domain (metalloporphyrin) are interfering with each other\u2019s function in the affinity cleaving compounds.
\r\n", "doi": "10.7907/4mj0-ec33", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:1524", "collection": "thesis", "collection_id": "1524", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04272006-160954", "type": "thesis", "title": "Studies in Molecular Recognition", "author": [ { "family_name": "Petti", "given_name": "Michael Anthony", "clpid": "Petti-Michael-Anthony" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A new class of water-soluble organic molecules containing hydrophobic binding sites is described. These host molecules, macrocycles assembled from 2,6-dihydroxy-9,10-dihydro-9,10-(1,2-dicarbomethoxy)-ethenoanthracene 8, can possess a hydrophobic cavity having a grossly right- (or left-)handed sense of twist. We believe this dissymmetric helical cavity could provide a means for chiral discrimination between the enantiomers of a racemate in aqueous solution.
\r\n\r\nBy varying the shape and size of the hydrophobic receptor site, such questions as the the roles of \u03c0-stacking, hydrophobicity and rigidity in molecular recognition are examined. The physical properties of these structures and their binding affinities for various guest molecules in aqueous solution are presented.
\r\n\r\nThese molecules have an especially high affinity for the aliphatic guest adamantyltrimethylammonium iodide (ATMA). In addition, this guest is an elegant probe of host geometry in the binding event. Several lines of evidence indicate that ATMA associates with these hosts in different geometries. Variable-temperature binding studies indicate that the binding of ATMA to hosts 4CMESO and 5CMESO displays a \"non-classical hydrophobic effect.\"
\r\n\r\nFurther studies with other alkyltrimethylammonium salts explore the role of guest shape, size, rigidity and charge on Ka. Studies involving variations of host structure suggest that rigidity, hydrophobicity, charge and donor-acceptor effects can significantly affect Ka.
\r\n\r\nTwo hosts of very similar structure, a p-xylyl-linked macrocycle (P-D) and a trans-1,4-dimethylenecyclohexyl-linked macrocycle (C6-L) are compared. Evidence for a new host geometry, efficient at encapsulating flat aromatic molecules, similar in shape to a naphthalene, is presented. These hosts efficiently bind aromatic heterocyclic guests (e.g., indole, quinoline, isoquinoline) and the N-methyl analogues. In this study, P-D displays an added affinity for the cationic guests. This additional ion-dipole effect is worth at least 1 kcal/mol in binding free energy. The binding of aromatic heterocycles is shown to be driven by donor-acceptor \u03c0-stacking interactions and hydrophobic effects.
\r\n\r\nThus, high binding affinities are achieved by a combination of forces without resorting to the use of highly lipophilic guests. These hosts maintain a clear separation of hydrophilic and hydrophobic groups, thereby eliminating the generally quite strong electrostatic interactions seen in other synthetic host systems.
\r\n\r\nSynthetic strategies to novel building blocks for new host structures are presented. These strategies could allow for the preparation of hosts having different solubility profiles, different aggregation properties and enhanced binding characteristics.
", "doi": "10.7907/wvhj-nb98", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:5308", "collection": "thesis", "collection_id": "5308", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-094841353", "type": "thesis", "title": "Mechanistic, Synthetic and Theoretical Studies of High Valent Metallacycles and metal Alkylidenes", "author": [ { "family_name": "Anslyn", "given_name": "Eric Van", "orcid": "0000-0002-5137-8797", "clpid": "Anslyn-Eric-Van" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The primary focus of this thesis is on the mechanism of olefin metathesis and ring opening metathesis polymerizations. In addition, several reactions of metal alkylidenes and metallacycles which are not traditionally viewed as part of the olefin metathesis reaction are presented. Olefin metathesis involves the 2+2 cycloaddition of metal alkylidenes with olefins and the 2+2 cycloreversion of metallacyclobutanes. These reactions are becoming common place in organometallic reaction mechanisms and join the traditional oxidative additions, reductive eliminations, ligand substitutions, intramolecular insertions, nucleophilic attacks on coordinated ligands and ligand fluxtionalities as the commonly sited organometallic reactions. A current goal of organometallic chemistry is to understand the influence of oxidation state, electron count, ligand sterics, ligand electronics and substituent effects upon each of these reactions.
\r\n\r\nThe knowledge of mechanisms is essential to be able to understand and rationally manipulate chemical processes. The knowledge also allows for the capability to catagorize mechanistic theories as an organizing device for understanding organometallic chemistry as a whole. Organometallic chemistry, however, is not easily catagorized due to the large complexity of bonding types and structures that inorganic chemistry produces. The work in this thesis has utilized some techniques of physical organic chemistry to study mechanisms and reactive intermediates. These techniques include kinetics, substituent effects, isotope effects, stereochemical studies and theoretical calculations.
\r\n\r\nOrganic chemistry has greatly benefited from the advent and subsequent development of the pericyclic theory for the understanding of covalent bonding, frontier orbitals and symmetry. These same notions have met with various levels of success in organometallic chemistry. The success of theoretical studies in organometallic systems very often depends upon the level of electron correlation and the extent to which the exchange integrals are calculated. The theory presented in this thesis utilizes a fully ab initio method with electron correlation. The structure of organometallic complexes is examined as a function of the nodal planes of the individual metal ligand bonds and their influence on the bonding of other ligands within the same complex. In addition, reactivity of the complexes are probed as a function of the symmetry and energy of the bonding and empty orbitals.
\r\n\r\nIn chapter one, data and speculations relating to the mechanism of cleavage of titanocene metallacyclobutanes is presented. The reactive intermediate is postulated to be a titanocene methylidene-olefin adduct. Chapter two further expands upon these mechanistic studies by presenting the kinetics and polydispersities of the ring opening metathesis polymerizations of slightly strained olefins. Chapter three presents work which utilizes ab initio electronic structure theory calculations to determine the energetics of the 2+2 cycloaddition of molybdenum alkylidene and imido complexes with olefins. In chapters 4, 5 and 6, reactivity different than the normal cycloadditions of metal alkylidenes and cycloreversions of metallacycles is examined. In chapter 4, an electron transfer mechanism for the reaction of titanocene methylidene with activated halides is presented. Chapter 5 discusses the reactivity of titanocene methylidene with inorganic carbonyls. The titanocene methylidene does not perform methylene transfer as is seen with organic carbonyls, but instead, the resultant oxametallacycle rearranges to yield a titanocene ketene complex. Finally, in chapter six, ab initio electronic structure theory calculations are again presented. They are used to explore the interconversion of a metallacyclobutadiene to a metallatetrahedrane. The two complexes are found to be energetically similar due to a balance between the strength of \u03c3 and \u03c0 bonds and the role of strain and resonance effects. Each chapter was written as an individual study and thus includes an Abstract, Introduction, Results and Discussion section and a Summary or Conclusion. Thus, this thesis presents work that attempts to add a little more knowledge to the mechanistic and theoretical understanding of organometallic reaction mechanisms.
\r\n", "doi": "10.7907/m7kp-4g32", "publication_date": "1988", "thesis_type": "phd", "thesis_year": "1988" }, { "id": "thesis:11469", "collection": "thesis", "collection_id": "11469", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04152019-173425189", "type": "thesis", "title": "Mechanistic Studies of Heterogeneously Catalyzed Reactions of Ammonia and Acetic Acid on Platinum Surfaces", "author": [ { "family_name": "Vajo", "given_name": "John J.", "clpid": "Vajo-John-J" } ], "thesis_advisor": [ { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The design and operation of a versatile microreactor capable of studying the rates of both steady-state and batch heterogeneous reactions on a wire, a foil or a single crystalline surface at pressures between 10-7 and 1000 Torr are described. The residence time distribution of the microreactor was characterized in order to evaluate the validity of using the continuous stirred tank reactor approximation to calculate reaction rates.
\r\n\r\nAbsolute reaction rates (i.e. the rate-per-unit catalyst surface area) have been measured for both the catalytic decomposition of NH3 and ND3 and the NH3 + D2 exchange reaction over a polycrystalline platinum wire. The pressure was varied between 5 x 10-7 and 0.5 Torr, and the temperature ranged from 400 to 1200 K. At relatively low pressures and/or high temperatures, the order of the decomposition reaction is unity with respect to ammonia, and the reaction rate is dictated by a competition between the surface reaction and the desorption of molecularly adsorbed ammonia. Under these conditions a primary isotope effect was observed for the decomposition of ND3. At relatively high pressures and/or low temperatures, the reaction rate is independent of ammonia pressure, and the recombinative desorption of nitrogen controls the rate of ammonia decomposition. The measured kinetics of the NH3 + D2 exchange reaction were employed together with adsorption-desorption parameters of NH3, N2 and H2 to develop a mechanistic model that describes the reaction rate over the entire (wide) range of conditions studied.
\r\n\r\nSteady-state absolute reaction rates are reported also for the catalytic decomposition of NH3 on the Pt(110)-(1x2) single crystalline surface at pressures between 1 x 10-6 and 2.6 x 10-6 Torr and at temperatures between 400 and 1000 K. Qualitatively, the kinetics is similar to those observed for ammonia decomposition on the polycrystalline platinum surface. Thermal desorption measurements conducted during the steady-state decomposition reaction demonstrate directly that nitrogen adatoms are the predominant surface species, and that the recombinative desorption of nitrogen is the major elementary reaction that produces molecular nitrogen.
\r\n\r\nThe decomposition of CH313COOH at 7 x 10-4 Torr on a polycrystalline platinum wire at temperatures between 300 and 900 K was examined in the microreactor. The major reaction products on the initially clean surface are 13CO, CO, 13CO2, H2 and adsorbed carbon-12. The adsorbed carbon accumulates on the surface until the reactions that produce these products are poisoned by the graphitic overlayer that is formed. On the graphitized platinum surface, acetic acid dehydrates catalytically to ketene and water. The relative quantities of 13CO and 13CO2 that are formed depend both on the surface temperature and on the surface carbon coverage.
\r\n\r\nThe catalytic dehydration of acetic acid to ketene was investigated over a graphitized polycrystalline platinum surface at pressures between 8 x 10-7 and 7 x 10-4 Torr and temperatures between 500 and 800 K. Steady-state absolute reaction rates, thermal desorption measurements, and the reactivities of functionally related compounds suggest that the reaction proceeds via an irreversibly adsorbed intermediate, which is formed by dissociation of the oxygen-hydrogen bond of acetic acid. For temperatures below 540 K at pressures of 3.5 x 10-4 Torr and above, the rate of decomposition of the surface intermediate controls the overall rate of the reaction. At 675 K or above for the entire range of pressures studied, the rate of dehydration is determined by a competition between the rates of desorption and surface reaction of molecularly adsorbed acetic acid.
", "doi": "10.7907/vayx-4k53", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:11410", "collection": "thesis", "collection_id": "11410", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02252019-123337280", "type": "thesis", "title": "Direct Observation and Reactions of Organic Biradicals Generated from Novel Bicyclic Azoalkanes", "author": [ { "family_name": "Jain", "given_name": "Rakesh", "clpid": "Jain-Rakesh" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Thermolysis of 2,3-diazabicyclo[2.1.1]hex-2-ene (14) in the gas phase produces highly vibrationally excited (chemically activated) bicyclo[1.1.0]butane (30). The excited 30 rearranges to butadiene, in competition with collisional deactivation by a bath gas. Quantitative modeling using RRKM theory and a stepladder model for collisional deactivation indicates that of the substantial amount of excess energy available to the products of thermolysis of 14, the great majority lies in the hydrocarbon fragment (30). Within the framework of a mechanistic criterion developed previously by Bauer, this result suggests that 14 decomposes by a stepwise, one-bond cleavage involving an intermediate diazenyl biradical. We have also synthesized 16, the dimethyl derivative of 14, and studied its thermal decomposition. As predicted by RRKM calculations, gas phase thermolysis of 16 does not produce chemically activated 1,3-dimethylbicyclobutane (31).
\r\n\r\nIrradiation of frozen solutions of 1,4-dialkyl-2,3-diazabicyclo[2.1.1]hex-2-enes (16-19) in the cavity of an ESR spectrometer between 4 and 25 K produces the corresponding triplet 1,3-dialkyl-1,3-cyclobutanediyls (20-23). The spectra display zero-field splitting parameters, |D/hc| = 0.112 cm-1 and |E/hc| = 0.005 cm-1. Hyperfine coupling can be resolved in some of these spectra and can be simulated using a computer program which has been developed for the purpose. The decay of the ESR signals between 4 and 25 K is nonexponential and shows very little dependence on temperature. A novel approach for analyzing the matrix-site effect is used and evidence is provided for quantum-mechanical tunneling in the decay process.
\r\n\r\nMatrix isolation photolysis of 2,3-diazabicyclo[2.2.1]hept-2-ene-7 \u2013spiro-cyclopropane (24) and 2,3 diazabicyclo[2.2.1]hept-2-ene-7,5'-spirobicyclo[2.1.0]pentane (25) between 4 and 35 K produces triplet ESR signals which are thermally stable up to 150 K. Independent generation from direct precursors 7-ethylidene-2,3-diazabicyclo[2.2.1 ]hept-2-ene (71) and 7-cyclobutylidene-2,3-diazabicyclo[2.2.1]hept-2-ene (72) confirms the assignment of the ESR signals to triplet biradicals 2-ethylidene-1,3-cyclopentanediyl (28) and 2-cyclobutylidene-1,3-cyclopentanediyl (29), respectively. Interpretable hyperfine coupling is observed and can be simulated, providing direct information about the electronic structures of these biradicals. The mechanism proposed for the formation of 28 and 29 from 24 and 25 involves two biradical rearrangements; a cyclopropylcarbinyl-type ring opening followed by a 1,2-H shift. Neither of these rearrangements can occur via thermal activation at such low temperatures. Chemical activation and quantum-mechanical tunneling are proposed to explain the reactivity of the intermediary biradicals.
\r\n", "doi": "10.7907/z16r-7e62", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:9279", "collection": "thesis", "collection_id": "9279", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132015-131516478", "primary_object_url": { "basename": "Holden_pj_1987.pdf", "content": "final", "filesize": 9097371, "license": "other", "mime_type": "application/pdf", "url": "/9279/1/Holden_pj_1987.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Extension Theorems for Functions of Vanishing Mean Oscillation", "author": [ { "family_name": "Holden", "given_name": "Peter James", "clpid": "Holden-Peter-James" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Wolff", "given_name": "Thomas H.", "clpid": "Wolff-T-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Wolff", "given_name": "Thomas H.", "clpid": "Wolff-T-H" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "A locally integrable function is said to be of vanishing mean oscillation (VMO) if its mean oscillation over cubes in Rd converges to zero with the volume of the cubes. We establish necessary and sufficient conditions for a locally integrable function defined on a bounded measurable set of positive measure to be the restriction to that set of a VMO function.
\r\n\r\nWe consider the similar extension problem pertaining to BMO(\u03c1) functions; that is, those VMO functions whose mean oscillation over any cube is O (\u03c1(\u2113(Q))) where \u2113(Q) is the length of Q and \u03c1 is a positive, non-decreasing function with \u03c1(0+) = 0.
\r\n\r\nWe apply these results to obtain sufficient conditions for a Blaschke sequence to be the zeros of an analytic BMO(\u03c1) function on the unit disc.
", "doi": "10.7907/f7k9-rh88", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:17606", "collection": "thesis", "collection_id": "17606", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08082025-174515566", "primary_object_url": { "basename": "Sponsler_MB_1987.pdf", "content": "final", "filesize": 81417123, "license": "other", "mime_type": "application/pdf", "url": "/17606/1/Sponsler_MB_1987.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Synthesis, EPR Spectroscopy, and Matrix-Isolation Decay Kinetics of Triplet Cyclobutanediyls", "author": [ { "family_name": "Sponsler", "given_name": "Michael Bradley", "orcid": "0000-0001-7181-1650", "clpid": "Sponsler-Michael-Bradley" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Roberts", "given_name": "John D.", "clpid": "Roberts-J-D" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1
\r\n\r\nBicyclo[1.1.1]pentanone (11) has been prepared in two\r\nsteps, the key reaction being the ozonolysis of\r\n2-phenylbicyclo[1.1.1)pentan-2-ol (24). The microwave\r\nspectra of five isotopic species of 11 have been obtained,\r\nallowing a complete rs structure determination for the heavy\r\natoms. Analysis of Stark-effect measurements has shown the\r\ndipole moment to be along the a principle inertial axis with\r\na magnitude of 3.164(5) D. These results are compared with\r\nthose obtained using molecular mechanics (MM2), MNDO, and\r\nHartree-Fock ab initio theory with STO-3G and 3-21G basis\r\nsets. On heating, 11 undergoes cycloreversion to allylketene\r\n(31). The activation parameters and solvent effects for this\r\nprocess suggest that the reaction is concerted and that the\r\ntransition state is relatively nonpolar. The predominant\r\nphotochemical pathway for 11 is decarbonylation to\r\nbicyclobutane (34). Cycloreversion to 31 is a minor\r\nreaction mode. Both the thermal and photochemical results\r\nare rationalized by considering the high strain energy and\r\nnovel geometrical features of 11 and, in the latter case, the\r\nunusually high energy of its 1(n\u03c0*) state.
\r\n\r\nChapter 2
\r\n\r\nAb initio theoretical methods have been applied to\r\ncyclobutanediyl. The geometry of the triplet biradical was\r\noptimized under the constraints of D2h symmetry. At the\r\noptimum geometry, the singlet-triplet energy gap was found to\r\nbe 1.74 kcal/mol, with the ground state being the triplet.\r\nThe closure reaction to bicyclo[1.1.0]butane (34) was\r\ninvestigated using a linear synchronous transit reaction\r\ncoordinate. A barrier of 6.6 kcal/mol was obtained for the\r\nsinglet surface, representing an upper limit to the actual\r\nbarrier. Calculations on 1,3-dimethylcyclobutanediyl (12)\r\nshow that the methyl groups do not strongly affect the\r\nsinglet-triplet gap, reducing it to 1.47 kcal/mol.
\r\n\r\nChapter 3
\r\n\r\nThe synthesis and EPR spectroscopy of 1,3-divinyl- and\r\n3-ethyl-1-vinylcyclobutanediyl (46-Vin and -EV) are\r\ndescribed and compared with results for other\r\ncyclobutanediyls. The triplet biradicals were generated by\r\nphotolysis of the appropriate 2,3-diazabicyclo[2.1.1]hex-\r\n2-enes (47) in frozen-solvent matrices at cryogenic\r\ntemperatures. A general synthetic scheme allowing the\r\npreparation of many diazenes has been developed. The key\r\nstep is the photochemical addition of methyltriazolinedione\r\nto 1,3-dicarbomethoxybicyclo[1.1.0]butane (49), giving the\r\ndicarbomethoxyurazole 15. The triplet EPR spectra offer\r\nvaluable insights into the electronic structure of the\r\ncyclobutanediyls and the role played by the substituents.\r\nBoth zero-field splitting and hyperfine coupling emerge as\r\nsensitive gauges for determining the distribution of spin\r\ndensity in the biradicals.
\r\n\r\nChapter 4
\r\n\r\nThe nonexponential decay kinetics of 1,3-divinyl- and\r\n3-ethyl-1-vinylcyclobutanediyl (46-Vin and -EV) has been\r\nquantitatively analyzed in the 20-54 K temperature range\r\nusing two methods based upon a distribution of first-order\r\nrate constants. A numerical procedure for fitting of decay\r\ntraces based upon an assumption of distribution shape has\r\nbeen modified to allow fitting of the signal growth during\r\nphotolysis as well as the decay. This method successfully\r\nreproduced our data using a variety of distribution shapes.\r\nA new method for analysis of dispersive kinetics, called\r\ndistribution slicing, has been developed. This method allows\r\ndetailed determination of distribution shapes and is\r\ncomplementary to decay-trace fitting in several other ways.\r\nThe two methods have been combined to eliminate several\r\nproblems encountered in the separate methods, allowing the\r\ndetermination of approximate activation parameters. An\r\napproximate log A value of 7.5 was determined for the decay\r\nof 46-Vin along with most-probable activation energies in\r\nthe range 1.2 to 1.7 kcal/mol, depending on the matrix\r\nmaterial. Using the same log A value, 46-EV gives\r\nmost-probable activation energies of 1.4 and 0.9 kcal/mol in\r\nMTHF and heptane, respectively. The stability of these\r\nbiradicals relative to the dialkyl cyclobutanediyls was\r\nrationalized in terms of hypothetical potential energy\r\nsurfaces.
", "doi": "10.7907/me26-sd58", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:2584", "collection": "thesis", "collection_id": "2584", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06142006-100902", "type": "thesis", "title": "Interactions of Ammonia with Platinum and Ruthenium Surfaces", "author": [ { "family_name": "Tsai", "given_name": "Wilman", "clpid": "Tsai-Wilman" } ], "thesis_advisor": [ { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "thesis_committee": [ { "family_name": "Bailey", "given_name": "James E.", "clpid": "Bailey-J-E" }, { "family_name": "Gavalas", "given_name": "George R.", "clpid": "Gavalas-G-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Specific reaction rates (cm-2-s-1) of the catalytic decomposition of ammonia, the isotopic exchange between ammonia and deuterium, and the inhibition of the decomposition of ammonia by hydrogen (with ammonia to hydrogen partial pressure ratios varying from 1:1 to 1:4) on a polycrystalline platinum wire have been measured in a continuous stirred tank microreactor at pressures between 5 x 10-7 and 0.6 Torr and temperatures between 400 and 1200 K. At relatively low temperatures and/or high pressures, nitrogen adatoms are the dominant surface species, and the recombinative desorption of nitrogen controls the rate of decomposition of ammonia. At relatively high temperatures and/or low pressures, the surface coverage of all species is low, and a competition between the desorption of molecular ammonia and the cleavage of an N-H bond of molecularly adsorbed ammonia controls the rate of reaction. The kinetics of decomposition of ammonia as well as the results for the NH3 + D2 exchange reaction are described quantitatively by a mechanistic model employing independently measured adsorption-desorption parameters of NH3 and H2, and desorption parameters of N2. The model was extended to incorporate the nitrogen coverage-dependence of the rate coefficient of hydrogen desorption to describe the inhibition of the decomposition by hydrogen. The hydrogenation of NH2(a) to produce molecularly adsorbed ammonia is predicted to be the dominant factor in the inhibition of the decomposition of ammonia.
\r\n\r\nThe kinetics of adsorption and desorption of deuterium have been studied on Pt(110)-(1x2) surfaces on which various fractional coverages of nitrogen adatoms were deposited via the decomposition of ammonia at 400 K. Nitrogen selectively blocks the high temperature \u03b22-state of deuterium prior to poisoning the low temperature \u03b21-state. No evidence of a 'long-range' electronic perturbation of the surface by the nitrogen adatoms was found. The adsorption kinetics of deuterium on both clean and nitrogen-precovered Pt(110)-(1x2) surfaces were Langmuirian. Nitrogen modifies the preexponential factor and the activation energy of desorption of deuterium on Pt(110)-(1x2) by essentially rescaling the effective coverage of the deuterium. The results are consistent with findings from previous studies of the inhibition of the decomposition of ammonia by hydrogen on polycrystalline platinum.
\r\n\r\nSteady-state specific reaction rates have also been measured for the catalytic decomposition of ammonia on a Ru(001) surface at pressures of 10-6 and 2 x 10-6 Torr and temperatures between approximately 500 and 1250 K. Qualitatively, the kinetics are similar to those observed for ammonia decomposition on the polycrystalline platinum surface. Based on thermal desorption measurements during the steady-state decomposition of ammonia at 2 x 10-6 Torr, nitrogen adatoms are the dominant surface species, and the recombinative desorption of nitrogen is the major (and probably the only) elementary reaction that produces molecular nitrogen. The mechanistic model developed previously describes accurately the pressure and temperature dependence of both the decomposition kinetics and the measured steady-state coverage of nitrogen adatoms.
\r\n\r\nThe isotopic exchange reaction between 15NH3 and deuter m at steady-state has been studied on Ru(001) for a partial pressure ratio of ammonia to deuterium of 4:1 with a total pressure of 2.5 x 10-6 Torr at temperatures between 380 and 720 K. All three exchange products were observed, and a dissociative exchange mechanism was found to describe quantitatively the experimental data. This mechanistic model is discussed in terms of a potential energy diagram that describes the catalytic decomposition (or synthesis) of ammonia on Ru(001). The energy levels of and the activation barriers separating the chemisorbed intermediates in the ammonia decomposition and synthesis reactions, namely, NH3, NH2+H, NH+2H, N+3H are determined, and the dissociative chemisorption of molecular nitrogen on Ru(001) is found to be activated with an activation energy estimated to be approximately 5 kcal-mol-1 in the limit of zero surface coverage of nitrogen adatoms. Direct comparsion between the estimated barrier for the dissociative adsorption of nitrogen on polycrystalline platinum and Ru(001) surfaces indicates clearly that ruthenium is a superior catalyst to platinum for the synthesis of ammonia.
", "doi": "10.7907/4Y3N-2321", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:11837", "collection": "thesis", "collection_id": "11837", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212019-165401033", "primary_object_url": { "basename": "Meinhart_JD_1987.pdf", "content": "final", "filesize": 44365681, "license": "other", "mime_type": "application/pdf", "url": "/11837/1/Meinhart_JD_1987.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Synthesis and Reactivity of Titanocene Methylene Complexes and Bis(\u03b7\u2075-Cyclopentadienyl) Titanacyclobutenes", "author": [ { "family_name": "Meinhart", "given_name": "James Douglas", "clpid": "Meinhart-James-Douglas" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "clpid": "Dervan-P-B" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Syntheses of several bis(\u03b75-cyclopentadienyl) titanium methylene phosphine complexes are reported. The titanium methylene phosphine complexes are generated from themolysis of titanacyclobutanes in the presence of excess phosphine. Spectral data and reactivity are consistent with a methylene phosphine complex rather than an ylide complex.
\r\n\r\nBis(\u03b75-cyclopentadienyl) titanacyclobutenes are readily synthesized by treatment of sources of \"Cp2TiCH2\" with disubstituted alkynes. A variety of stable titanacyclobutenes were synthesized containing aryl, alkyl, and etherial substituents. Titanacyclobutenes, unlike the related titanacyclobutanes, do not reform \"Cp2TiCH2\" thermally.
\r\n\r\nTitanacyclobutenes insert carbon monoxide, forming an acyl intermediate which rearranges to a titanocene vinyl ketene complex. A trimethylphosphine adduct of one of the ketene complexes was characterized by x-ray diffraction techniques. The carbonylation mechanism involves insertion of carbon monoxide into the more accessible titanium-carbon bond, followed by intra-molecular attack of the vinyl group to the acyl. Insertion of t-butyl isocyanide into a titanacyclobutene yields a cyclic imino-acyl complex, which was also characterized by x-ray diffraction. The vinyl ketene complexes react with many unsaturated substrates (alkynes, ethylene, and aldehydes) to form new organotitanium species.
\r\n\r\nTitanacyclobutenes react with ketones and aldehydes via 1,2-addition to yield titanium oxacyclohexenes. Aldehydes form both titanium-oxygen and titanium-carbon regioisomers. The organic ligand may be removed from the titanium to give homo-allylic alcohols in good yield. Nitriles also insert into titancyclobutenes to roduce titanium imidocyclohexenes.
", "doi": "10.7907/16dt-2465", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:739", "collection": "thesis", "collection_id": "739", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02242006-162144", "primary_object_url": { "basename": "Onuchic_jn_1987.pdf", "content": "final", "filesize": 13970390, "license": "other", "mime_type": "application/pdf", "url": "/739/1/Onuchic_jn_1987.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "New aspects of the theory of electron transfer reaction dynamics", "author": [ { "family_name": "Onuchic", "given_name": "Jos\u00e9 Nelson", "orcid": "0000-0002-9448-0388", "clpid": "Onuchic-Jos\u00e9-Nelson" } ], "thesis_advisor": [ { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis deals basically with some new aspects of the electron transfer theory. It is divided into four parts: (1) Chapter I gives an introduction to the electron transfer problem; (2) Chapter II addresses the subject of how nuclear dynamics influences the electron transfer rate; (3) Chapter III explains how to calculate electron transfer matrix elements for non-adiabatic electron transfer systems, in particular protein systems; and (4) Chapter IV discusses some preliminary ideas about new problems I intend to work on the future.
\r\n\r\nIn Chapter II the following dynamical problems are addressed. For the case of one overdamped reaction coordinate, the problem of adiabaticity and non-adiabaticity is considered in details. For an underdamped reaction coordinate, a preliminary discussion is given. All this formalism is developed using a density matrix formalism and path integral techniques. One of the advantages of using this formalism is that, by analyzing the spectral density, we can connect our microscopic Hamiltonian with macroscopic quantities. It also gives us a natural way of including friction in the problem. We also determine when the Hopfield semiclassical or the Jortner \"quantum\" models are good approximations to the \"complete\" Hamiltonian. In the limit that the reaction coordinates are \"classical,\" we discuss how we can obtain the Fokker-Planck equation associated with the Hamiltonian.
\r\n\r\nBy adding more than one reaction coordinate to the problem (normally two), several other problems are studied. The separation of \"fast\" quantum modes from \"slow\" semiclassical modes, where the fast modes basically renormalize the electronic matrix element and the driving force of the electron transfer reaction, is discussed. Problems such as exponential and non-exponential decay in time of the donor survival probability, and the validity of the Born-Oppenheimer and Condon approximations are also carefully addressed. This chapter is concluded with a calculation of the reaction rate in the inverted region for the extreme adiabatic limit.
\r\n\r\nIn Chapter III we discuss calculations of electronic matrix elements, which are essential for the calculation of non-adiabatic rates. It starts with a discussion of why, through bond rather than through space, electron transfer is the important mechanism in model compounds. Also, it explains why tight-binding Huckel calculations are reasonable for evaluating these matrix elements, and why, through space and through bond, matrix element decays with distance have a different functional dependence on energy. Bridge effects due to different hydrocarbon linkers are also calculated.
\r\n\r\nThis chapter concludes with a model for the calculation of matrix elements in proteins. The model assumes that the important electron transfer \"pathways\" are composed of both, through bond and through space parts. Finally, we describe how medium (bridge) fluctuations may introduce a new form of temperature dependence by modulating the matrix element.
\r\n\r\nIn Chapter IV we discuss some experimental results obtained for electron transfer in the porphyrin-phenyl-(bicyclo[2.2.2]octane)n-quinone molecule, and we propose some new experiments that should help to clarify our interpretation. It concludes with some preliminary discussions of how we can include entropy in the finite mode formalism described in Chapter II, and how we intend to use the formalism described in Chapter III in order to understand electron transfer in real protein systems.
", "doi": "10.7907/hcep-rh59", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:826", "collection": "thesis", "collection_id": "826", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03012008-133433", "primary_object_url": { "basename": "Cheng_yt_1987.pdf", "content": "final", "filesize": 4557577, "license": "other", "mime_type": "application/pdf", "url": "/826/1/Cheng_yt_1987.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ion-Beam Mixing and the Formation of Amorphous Alloys", "author": [ { "family_name": "Cheng", "given_name": "Yang-Tse", "clpid": "Cheng-Yang-Tse" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Ion beam interactions with solids have been of significant interest to both academic and industrial researchers for more than half a century. Looking back into the history of its development, one finds prominent names such as Bohr, Fermi, and Bethe, closely associated with the early development of this area of scientific research. Their efforts in understanding the interatomic potential of ions and atoms have led to the knowledge of ion penetration depth and energy loss in solids. It was also one of the early successful applications of the newly born quantum mechanics.
\r\n\r\nThe subsequent development of the range theory by Lindhard, Scharff, and Schioff in the early sixties (LSS theory) enables one to calculate the ion penetration depth in elemental solids to even greater accuracy and provides the basis for the realization of ion implantation technology.
\r\n\r\nSwelling of reactor materials, caused by ion irradiation, was first observed in austenitic steel in 1967 by a group of British scientists. Such radiation damage drew unprecedented attention of people from both academia and industry to the problem of ion-solid interactions. Irradiation-induced structural and phase changes in materials have since become a major part of the active research in ion beam interactions with solids.
\r\n\r\nIon implantation, which originated in the early 1960s, revolutionized the microelectronics industry. Because of the development of the range theory, ion implantation offered precise control over the number and depth of dopant atoms in semiconductor materials, making possible the miniaturization of electronic devices. Meanwhile, various ion beam analysis techniques, such as RBS (Rutherford Backscattering Spectrometry), developed rapidly and were applied to study problems ranging from Moon rocks to electronic devices.
\r\n\r\nAround 1972, while studying ion implantation in Si through an Al overlayer, D. H. Lee, O. J. Marsh, and R. R. Hart of the Hughes Research Laboratories observed coloration of the surface layer. Using RBS and optical reflectance measurements, they determined that the coloration was due to the migration of Si to the surface of the sample under the influence of ion bombardment. In another case, they observed Pt2Si formation due to mixing of the Si and the Pt overlayer caused by ion implantation. Soon it was found that metastable phases as well as equilibrium phases could be obtained by this type of ion beam-induced mixing phenomena, more commonly called ion mixing processes.
\r\n\r\nToday, ion implantation has found further applications in areas such as corrosion resistance, reduction of wear and friction, and improvement of adhesion. Ion mixing has been viewed as a powerful extension of the traditional ion implantation technology. It provides new challenges to fundamental research in ion-solid interactions and offers new promises to further industrial applications.
\r\n\r\nTwo issues are considered of fundamental importance and are treated in this thesis:
\r\n\r\nI. Mechanisms of ion-beam-induced mixing in solids.
\r\n\r\nII. The formation of amorphous alloys.
\r\n\r\nIn Part I, several aspects of the mixing mechanisms, such as the influence of chemical driving force, the influence of cohesive energy, a newly developed phenomenological model of ion mixing, and a correlation between the cohesive energy and the onset of radiation-enhanced diffusion will be discussed. Also in this part, the evolution of collisional cascades will be studied by using a fractal geometry approach. In Part II, mechanisms of amorphous alloy formation are discussed. Comparisons between amorphous alloy formation by ion mixing and by solid-state reaction illustrate various aspects of glass formation.
", "doi": "10.7907/W1Y4-0347", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:5359", "collection": "thesis", "collection_id": "5359", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11062009-094101367", "primary_object_url": { "basename": "Schilling_jb_1987.pdf", "content": "final", "filesize": 7602622, "license": "other", "mime_type": "application/pdf", "url": "/5359/1/Schilling_jb_1987.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Experimental and Theoretical Aspects of Hydrocarbon Activation by Transition Metal Ions in the Gas Phase", "author": [ { "family_name": "Schilling", "given_name": "Jerald Bruce", "clpid": "Schilling-Jerald-Bruce" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kechris", "given_name": "Alexander S.", "clpid": "Kechris-A-S" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Luxemburg", "given_name": "W. A. J.", "clpid": "Luxemburg-W-A-J" }, { "family_name": "Taylor", "given_name": "Hugh P.", "clpid": "Taylor-H-P" }, { "family_name": "Anderson", "given_name": "David J.", "clpid": "Anderson-D-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The reactions of several gas-phase metal cations with small hydrocarbons have been studied using ion beam mass spectrometric techniques. We also present several theoretical studies into the sigma bonding between the first and second row transition metal ions and H and CH3.
\r\n\r\nChapter II discusses the three cations, europium, praseodymium, and gadolinium in an attempt to understand the role of f electrons in the reactivity of gas-phase lanthanide ions. Eu+ and Pr+ are found to be unreactive with alkanes while Gd+ readily activates both C\u2014H and C\u2014C bonds. The unreactive metals have only one non-4f valence electron. Oxidative addition of a C\u2014H bond to these metals requires a strong bond to an f electron. Gd+, with two non-4f valence electrons need not use the 4f electrons and is seen to be very reactive. This reactivity behavior indicates that the 4f electrons of the lanthanides play little role in alkane activation due to the formation of weak sigma bonds.
\r\n\r\nIn Chapter III and VI, we discuss the reasons for the unreactivity of gas-phase chromium ions. Molybdenum ions which have a very similar electrons structure are found to activate C\u2014H bonds of alkanes. The metal ions are studied from the standpoint of gas-phase reactivity as well as the theoretical description of the bonding in the hydride and dihydride ions. The two metals are found to differ greatly in the strength of the sigma bonds that they form to hydrogen. The oxidative addition of C\u2014H and C\u2014C bonds to Cr+ is endothermic due to the extremely weak bonds formed to the metal ion.
\r\n\r\nChapters IV and V report systematic, ab initio, generalized valence bond and configuration interaction calculations on the first and second row transition metal hydrides. The bonding in these systems is seen to depend on a number of factors including: (1) the electronic structure of the metal ions; (2) the sizes of the metal s and d orbitals and the effect on the intrinsic strength of the metal\u2014hydrogen bond; and (3) the mediation of the intrinsic bond strengths by the loss of high spin exchange energy.
\r\n\r\nChapter VII presents a theoretical comparison between the metal hydride ions and metal methyl ions. The present theoretical study indicates that for a variety of metal systems, the metal\u2014hydrogen and metal\u2014carbon bonds are very similar, both from the standpoint of metal orbital hybridization as well as bond dissociation energy.
\r\n", "doi": "10.7907/vazp-zt83", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:4613", "collection": "thesis", "collection_id": "4613", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11212003-111159", "type": "thesis", "title": "Finesse in Quantum Chemistry: Accurate Energetics Relevant for Reaction Mechanisms", "author": [ { "family_name": "Carter", "given_name": "Emily Ann", "clpid": "Carter-Emily-Ann" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_chem" } ], "abstract": "A general, systematic approach for calculating accurate energetics for chemical processes within the framework of ab initio electronic structure theory is presented. The correlation-consistent configuration interaction (CCCI) method utilizes generalized valence bond wavefunctions as the starting point for the CI, which emphasizes the inclusion of only the dominant correlations dictated by the physics of the problem. The CI expansion truncates quickly, so that processes involving polyatomic molecules, which could not be addressed with conventional CI methodology, may now be treated easily.
\r\n\r\nA variety of applications of the method are presented, including the prediction of bond energies, electronic excitation energies, and energetics of chemical reactions, for both organic and transition metal-containing molecules. In cases where experimental data are available, the agreement is generally excellent (within 1-5 kcal/mol). We have used these quantitative results, along with qualitative aspects of the wavefunctions, to assess the bonding in and reactivity of a series of organic, organometallic, and inorganic molecules. These studies have produced a number of simple concepts useful for predicting the stability and reactivity of ligands attached to transition metals. Finally, key mechanistic pathways in two transition metal-catalyzed reactions have been examined using the CCCI approach: (i) the chain initiation step for the Fischer-Tropsch synthesis of hydrocarbons; and (ii) the Ag-catalyzed olefin epoxidation reaction.
\r\n", "doi": "10.7907/GVJQ-6Y71", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:826", "collection": "thesis", "collection_id": "826", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03012008-133433", "primary_object_url": { "basename": "Cheng_yt_1987.pdf", "content": "final", "filesize": 4557577, "license": "other", "mime_type": "application/pdf", "url": "/826/1/Cheng_yt_1987.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ion-Beam Mixing and the Formation of Amorphous Alloys", "author": [ { "family_name": "Cheng", "given_name": "Yang-Tse", "clpid": "Cheng-Yang-Tse" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Ion beam interactions with solids have been of significant interest to both academic and industrial researchers for more than half a century. Looking back into the history of its development, one finds prominent names such as Bohr, Fermi, and Bethe, closely associated with the early development of this area of scientific research. Their efforts in understanding the interatomic potential of ions and atoms have led to the knowledge of ion penetration depth and energy loss in solids. It was also one of the early successful applications of the newly born quantum mechanics.
\r\n\r\nThe subsequent development of the range theory by Lindhard, Scharff, and Schioff in the early sixties (LSS theory) enables one to calculate the ion penetration depth in elemental solids to even greater accuracy and provides the basis for the realization of ion implantation technology.
\r\n\r\nSwelling of reactor materials, caused by ion irradiation, was first observed in austenitic steel in 1967 by a group of British scientists. Such radiation damage drew unprecedented attention of people from both academia and industry to the problem of ion-solid interactions. Irradiation-induced structural and phase changes in materials have since become a major part of the active research in ion beam interactions with solids.
\r\n\r\nIon implantation, which originated in the early 1960s, revolutionized the microelectronics industry. Because of the development of the range theory, ion implantation offered precise control over the number and depth of dopant atoms in semiconductor materials, making possible the miniaturization of electronic devices. Meanwhile, various ion beam analysis techniques, such as RBS (Rutherford Backscattering Spectrometry), developed rapidly and were applied to study problems ranging from Moon rocks to electronic devices.
\r\n\r\nAround 1972, while studying ion implantation in Si through an Al overlayer, D. H. Lee, O. J. Marsh, and R. R. Hart of the Hughes Research Laboratories observed coloration of the surface layer. Using RBS and optical reflectance measurements, they determined that the coloration was due to the migration of Si to the surface of the sample under the influence of ion bombardment. In another case, they observed Pt2Si formation due to mixing of the Si and the Pt overlayer caused by ion implantation. Soon it was found that metastable phases as well as equilibrium phases could be obtained by this type of ion beam-induced mixing phenomena, more commonly called ion mixing processes.
\r\n\r\nToday, ion implantation has found further applications in areas such as corrosion resistance, reduction of wear and friction, and improvement of adhesion. Ion mixing has been viewed as a powerful extension of the traditional ion implantation technology. It provides new challenges to fundamental research in ion-solid interactions and offers new promises to further industrial applications.
\r\n\r\nTwo issues are considered of fundamental importance and are treated in this thesis:
\r\n\r\nI. Mechanisms of ion-beam-induced mixing in solids.
\r\n\r\nII. The formation of amorphous alloys.
\r\n\r\nIn Part I, several aspects of the mixing mechanisms, such as the influence of chemical driving force, the influence of cohesive energy, a newly developed phenomenological model of ion mixing, and a correlation between the cohesive energy and the onset of radiation-enhanced diffusion will be discussed. Also in this part, the evolution of collisional cascades will be studied by using a fractal geometry approach. In Part II, mechanisms of amorphous alloy formation are discussed. Comparisons between amorphous alloy formation by ion mixing and by solid-state reaction illustrate various aspects of glass formation.
", "doi": "10.7907/W1Y4-0347", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:17606", "collection": "thesis", "collection_id": "17606", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08082025-174515566", "primary_object_url": { "basename": "Sponsler_MB_1987.pdf", "content": "final", "filesize": 81417123, "license": "other", "mime_type": "application/pdf", "url": "/17606/1/Sponsler_MB_1987.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Synthesis, EPR Spectroscopy, and Matrix-Isolation Decay Kinetics of Triplet Cyclobutanediyls", "author": [ { "family_name": "Sponsler", "given_name": "Michael Bradley", "orcid": "0000-0001-7181-1650", "clpid": "Sponsler-Michael-Bradley" } ], "thesis_advisor": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Roberts", "given_name": "John D.", "clpid": "Roberts-J-D" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1
\r\n\r\nBicyclo[1.1.1]pentanone (11) has been prepared in two\r\nsteps, the key reaction being the ozonolysis of\r\n2-phenylbicyclo[1.1.1)pentan-2-ol (24). The microwave\r\nspectra of five isotopic species of 11 have been obtained,\r\nallowing a complete rs structure determination for the heavy\r\natoms. Analysis of Stark-effect measurements has shown the\r\ndipole moment to be along the a principle inertial axis with\r\na magnitude of 3.164(5) D. These results are compared with\r\nthose obtained using molecular mechanics (MM2), MNDO, and\r\nHartree-Fock ab initio theory with STO-3G and 3-21G basis\r\nsets. On heating, 11 undergoes cycloreversion to allylketene\r\n(31). The activation parameters and solvent effects for this\r\nprocess suggest that the reaction is concerted and that the\r\ntransition state is relatively nonpolar. The predominant\r\nphotochemical pathway for 11 is decarbonylation to\r\nbicyclobutane (34). Cycloreversion to 31 is a minor\r\nreaction mode. Both the thermal and photochemical results\r\nare rationalized by considering the high strain energy and\r\nnovel geometrical features of 11 and, in the latter case, the\r\nunusually high energy of its 1(n\u03c0*) state.
\r\n\r\nChapter 2
\r\n\r\nAb initio theoretical methods have been applied to\r\ncyclobutanediyl. The geometry of the triplet biradical was\r\noptimized under the constraints of D2h symmetry. At the\r\noptimum geometry, the singlet-triplet energy gap was found to\r\nbe 1.74 kcal/mol, with the ground state being the triplet.\r\nThe closure reaction to bicyclo[1.1.0]butane (34) was\r\ninvestigated using a linear synchronous transit reaction\r\ncoordinate. A barrier of 6.6 kcal/mol was obtained for the\r\nsinglet surface, representing an upper limit to the actual\r\nbarrier. Calculations on 1,3-dimethylcyclobutanediyl (12)\r\nshow that the methyl groups do not strongly affect the\r\nsinglet-triplet gap, reducing it to 1.47 kcal/mol.
\r\n\r\nChapter 3
\r\n\r\nThe synthesis and EPR spectroscopy of 1,3-divinyl- and\r\n3-ethyl-1-vinylcyclobutanediyl (46-Vin and -EV) are\r\ndescribed and compared with results for other\r\ncyclobutanediyls. The triplet biradicals were generated by\r\nphotolysis of the appropriate 2,3-diazabicyclo[2.1.1]hex-\r\n2-enes (47) in frozen-solvent matrices at cryogenic\r\ntemperatures. A general synthetic scheme allowing the\r\npreparation of many diazenes has been developed. The key\r\nstep is the photochemical addition of methyltriazolinedione\r\nto 1,3-dicarbomethoxybicyclo[1.1.0]butane (49), giving the\r\ndicarbomethoxyurazole 15. The triplet EPR spectra offer\r\nvaluable insights into the electronic structure of the\r\ncyclobutanediyls and the role played by the substituents.\r\nBoth zero-field splitting and hyperfine coupling emerge as\r\nsensitive gauges for determining the distribution of spin\r\ndensity in the biradicals.
\r\n\r\nChapter 4
\r\n\r\nThe nonexponential decay kinetics of 1,3-divinyl- and\r\n3-ethyl-1-vinylcyclobutanediyl (46-Vin and -EV) has been\r\nquantitatively analyzed in the 20-54 K temperature range\r\nusing two methods based upon a distribution of first-order\r\nrate constants. A numerical procedure for fitting of decay\r\ntraces based upon an assumption of distribution shape has\r\nbeen modified to allow fitting of the signal growth during\r\nphotolysis as well as the decay. This method successfully\r\nreproduced our data using a variety of distribution shapes.\r\nA new method for analysis of dispersive kinetics, called\r\ndistribution slicing, has been developed. This method allows\r\ndetailed determination of distribution shapes and is\r\ncomplementary to decay-trace fitting in several other ways.\r\nThe two methods have been combined to eliminate several\r\nproblems encountered in the separate methods, allowing the\r\ndetermination of approximate activation parameters. An\r\napproximate log A value of 7.5 was determined for the decay\r\nof 46-Vin along with most-probable activation energies in\r\nthe range 1.2 to 1.7 kcal/mol, depending on the matrix\r\nmaterial. Using the same log A value, 46-EV gives\r\nmost-probable activation energies of 1.4 and 0.9 kcal/mol in\r\nMTHF and heptane, respectively. The stability of these\r\nbiradicals relative to the dialkyl cyclobutanediyls was\r\nrationalized in terms of hypothetical potential energy\r\nsurfaces.
", "doi": "10.7907/me26-sd58", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:11823", "collection": "thesis", "collection_id": "11823", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10172019-161305619", "type": "thesis", "title": "Calculation of e\u207b-H Atom Scattering Processes Using Hyperspherical Coordinates", "author": [ { "family_name": "Hood", "given_name": "Diane Marie", "clpid": "Hood-Diane-Marie" } ], "thesis_advisor": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A method is presented for accurately solving the Schr\u00f6dinger equation for the scattering of an electron from a hydrogen atom in three dimensions, which uses hyperspherical coordinates. Our motivation for using this new technique is that previous methods -- coupled channel expansions using target atom eigenfunctions,1 polarization functions and pseudostates,2 and variational methods3 -- have all proven unsatisfactory. The coupled channel calculations tend to have difficulty obtaining convergence with respect to basis set size, and the variational method interjects spurious resonances. Previous applications of hyperspherical coordinates4 have used methods that, while adequate for computing the energy level of the bound state of H-, are not appropriate to full scattering calculations.
\r\n\r\nWe have obtained converged surface functions at a set of discrete values of the hyperradius, which acts as a parameter. The surface functions are further expanded in a basis set that involves 1-dimensional functions of the hyperspherical angle, which are obtained by a finite difference method.
\r\n\r\nThe surface functions have been used to expand the scattering functions. The resulting coupled equations are solved numerically. The wavefunctions are obtained separately at each energy and are converged with respect to the number of basis functions used. Calculations performed so far give converged results for J = 0 through J = 5 up to the n = 4 threshold. The method is both accurate and efficient, and has been implemented on a VAX 11/780 with an FPS164 attached processor.
\r\n\r\nBoth the magnitude and phase of elements of the scattering matrix have converged. Integral cross sections have been obtained for energies up to the n = 4 threshold of hydrogen. Feshbach resonances have been detected below each threshold, and they have been characterized and classified.
\r\n\r\n1P. G. Burke, S. Ormonde, and W. Whitaker, Proc. Phys. Soc. 92, 319, (1967).
\r\n2S. Geltman and P. G. Burke, J. Phys. B 3, 1062, (1970).
\r\n3J. Callaway, Phys. Rev. A 26, 199, (1982).
\r\n4C. D. Lin, Phys. Rev. A 23, 1585, (1981).
\r\n\r\n", "doi": "10.7907/xj5h-me61", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11868", "collection": "thesis", "collection_id": "11868", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10282019-140307646", "primary_object_url": { "basename": "Tolbert_MA_1986.pdf", "content": "final", "filesize": 44351249, "license": "other", "mime_type": "application/pdf", "url": "/11868/1/Tolbert_MA_1986.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Mechanisms and Energetics of Alkane Activation by Transition Metal Ions in the Gas Phase", "author": [ { "family_name": "Tolbert", "given_name": "Margaret A.", "clpid": "Tolbert-Margaret-A" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The mechanisms and energetics of alkane activation by transition metal ions in the gas phase are studied using an ion beam apparatus. These investigations concentrate on the reactivity of several early first row transition metal ions (Sc+, Ti+, V+) and the second row group 8-10 metal ions (Ru+, Rh+, Pd+). The reaction mechanisms are probed using deuterium labelled alkanes. Experimental and theoretical metal-ligand bond dissociation energies are used to help interpret the observed metal ion reactivities.
\r\n\r\nChapter II provides a detailed study of the reactions of Ru+, Rh+ and Pd+ with alkanes. The reactivity observed is contrasted to that of their first row congeners Fe+, Co+ and Ni+.
\r\n\r\nChapter III presents a determination of the heterolytic, M+-H-, and homolytic, M-H, bond dissociation energies for the first and second row group 8-10 metals. A correlation is found between the homolytic bond energies and the metal atom promotion energy to a state derived from an s1dn electronic configuration.
\r\n\r\nChapter IV examines the reactions of Ti+ and V+ with alkanes and deuterium labelled alkanes. Dehydrogenation mechanisms and deuterium isotope effects are explored.
\r\n\r\nChapter V reports the unusual reactivity of Sc+ with alkanes. The ability of Sc+ to form two strong metal-ligand sigma bonds results in alkane activation processes which are not observed for most other transition metal ions.
", "doi": "10.7907/3047-z490", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11868", "collection": "thesis", "collection_id": "11868", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10282019-140307646", "primary_object_url": { "basename": "Tolbert_MA_1986.pdf", "content": "final", "filesize": 44351249, "license": "other", "mime_type": "application/pdf", "url": "/11868/1/Tolbert_MA_1986.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Mechanisms and Energetics of Alkane Activation by Transition Metal Ions in the Gas Phase", "author": [ { "family_name": "Tolbert", "given_name": "Margaret A.", "clpid": "Tolbert-Margaret-A" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The mechanisms and energetics of alkane activation by transition metal ions in the gas phase are studied using an ion beam apparatus. These investigations concentrate on the reactivity of several early first row transition metal ions (Sc+, Ti+, V+) and the second row group 8-10 metal ions (Ru+, Rh+, Pd+). The reaction mechanisms are probed using deuterium labelled alkanes. Experimental and theoretical metal-ligand bond dissociation energies are used to help interpret the observed metal ion reactivities.
\r\n\r\nChapter II provides a detailed study of the reactions of Ru+, Rh+ and Pd+ with alkanes. The reactivity observed is contrasted to that of their first row congeners Fe+, Co+ and Ni+.
\r\n\r\nChapter III presents a determination of the heterolytic, M+-H-, and homolytic, M-H, bond dissociation energies for the first and second row group 8-10 metals. A correlation is found between the homolytic bond energies and the metal atom promotion energy to a state derived from an s1dn electronic configuration.
\r\n\r\nChapter IV examines the reactions of Ti+ and V+ with alkanes and deuterium labelled alkanes. Dehydrogenation mechanisms and deuterium isotope effects are explored.
\r\n\r\nChapter V reports the unusual reactivity of Sc+ with alkanes. The ability of Sc+ to form two strong metal-ligand sigma bonds results in alkane activation processes which are not observed for most other transition metal ions.
", "doi": "10.7907/3047-z490", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:1047", "collection": "thesis", "collection_id": "1047", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03212008-081007", "primary_object_url": { "basename": "Atzmon_m_1986.pdf", "content": "final", "filesize": 4573964, "license": "other", "mime_type": "application/pdf", "url": "/1047/1/Atzmon_m_1986.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Study of Bulk Amorphous Alloys Formed by Solid-State Reaction in Elemental Composites", "author": [ { "family_name": "Atzmon", "given_name": "Michael", "orcid": "0000-0002-7055-1313", "clpid": "Atzmon-Michael" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Ahrens", "given_name": "Thomas J.", "clpid": "Ahrens-T-J" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Bulk amorphous Zr- and Er- based alloys have been synthesized by solid-state reaction in elemental composites prepared by mechanical deformation. For the Er- based composites, complete amorphization was achieved by near- isothermal rolling near room temperature. The driving force for the reaction was found to be a large negative enthalpy of mixing between the constituent elements. Strain and interfacial energies have been estimated and found to modify the driving force only slightly. X-ray diffraction and differential scanning calorimetry have been used to characterize the structure and crystallization behavior of the alloys obtained. Comparison to corresponding amorphous alloys prepared by liquid quenching and sputtering gave good agreement.
\r\n\r\nThe diffusion of Au in amorphous Au-Y and Au-La thin films produced by co-evaporation has been studied by means of X-ray diffraction and Rutherford backscattering. An estimated diffusion coefficient agrees with those obtained by other authors for diffusion of Au in several amorphous alloys. The results confirm that there can be bulk self-diffusion in an amorphous alloy without crystallization. Thus, one does not need to assume short-circuit diffusion during the growth of an amorphous phase by solid-state reaction.
", "doi": "10.7907/5M6N-SK53", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11777", "collection": "thesis", "collection_id": "11777", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08302019-110545286", "type": "thesis", "title": "A Theoretical Model for Orientation Effects in Electron Transfer Reactions", "author": [ { "family_name": "Cave", "given_name": "Robert J.", "clpid": "Cave-Robert-J" } ], "thesis_advisor": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" } ], "thesis_committee": [ { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Marcus", "given_name": "Rudolph A.", "clpid": "Marcus-R-A" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this thesis, the development and application of a model for the examination of orientation effects in electron transfer reactions are considered. The model is designed to describe broad features of the electronic interactions between large molecules, where the transferred electron is delocalized in both reactant and product.
\r\n\r\nThe model employs spherical or oblate-spheroidal potentials of constant depth for the donor and acceptor sites. The Schrodinger equation is solved for the exact eigenfunctions of such a potential, and the electron transfer matrix element, TBA, is calculated us1ng these wavefunctions. TBA is the principal distance and orientation dependent quantity in current theories of nonadiabatic electron transfer. By comparison of results obtained using spherical and spheroidal wells, il was determined that both orbital shape and well shape (i.e., molecular shape) effects are important in determining the magnitude and orientation dependence of TBA.
\r\n\r\nThe model was used to examine orientation dependence in electron transfer reactions between porphyrins and porphyrin derivatives. TBA was examined for a variety of mutual orientations, including: 1) face-to-face transfers, where it was found that TBA for forward transfer from photoexcited reactants was considerably larger than Lhat for back transfer to yield ground state products, 2) edge-to-edge orientations, and 3) models of possible initial donor-acceptor pairs in a bacterial photosynthetic electron transfer system (Rhodopseudomonas viridis). It was observed that TBA was a sensitive function of orbital shape and orientation.
\r\n\r\nIn order to simplify the model, a semiclassical approximation was examined for the donor and acceptor wavefunctions, for both the spherical- and spheroidal-well states. The accuracy of the approximation supports the interpretations of the results obtained from the exact calculations. It also substantially reduced the calculational time involved.
", "doi": "10.7907/s9zp-mj05", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11412", "collection": "thesis", "collection_id": "11412", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02272019-121930852", "primary_object_url": { "basename": "Varney_MD_1986.pdf", "content": "final", "filesize": 42124809, "license": "other", "mime_type": "application/pdf", "url": "/11412/1/Varney_MD_1986.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Approach to the Synthesis of Chlorothricolide: Synthesis of (\u00b1)-19,20-Dihydro-24-O-methylchlorotricolide, methyl ester, ethyl carbonate", "author": [ { "family_name": "Varney", "given_name": "Michael David", "clpid": "Varney-Michael-David" } ], "thesis_advisor": [ { "family_name": "Ireland", "given_name": "Robert E.", "clpid": "Ireland-R-E" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Ireland", "given_name": "Robert E.", "clpid": "Ireland-R-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An approach to the total synthesis of the 14-membered macrolide antibiotic aglycon chlorothricolide is presented. Key steps from the two halves to (\u00b1)-19,20-Dihydro-24-O methylchlorothricolide, methyl ester, ethyl carbonate include initial esterification across the C1 and C25 carbons followed by macrodilactonization across the C17 and C14 carbons. Ester enolate Claisen rearrangement and subsequent decarboxylation afforded the intact lactone. Functionalization of the top half is explored.
\r\n\r\nThe ester enolate Claisen rearrangement of propionate derivatives of resolved 1-(t-butyldimethylsilyl)-trans-2-butene-1-ol is reported. Subsequent protiodesilation of the reduced and protected Claisen products resulted in the formation of 2,3-dimethyl-4-pentenyl ethers. Thus, the secondary \u03b1-silyl alcohol has functioned as a chiral primary alcohol equivalent.
\r\n\r\nThe Claisen rearrangement of vinyl ethyl derivatives of 5-tert-butyl-1-(hydroxymethyl)-1-cyclohexene is reported. The standard allyl vinyl ether conditions as well as the triethyl orthoacetate and ester enolate variants of the Claisen rearrangement all resulted in the formation of cis(axial)-4-tert-butylcyclohexyl-substituted systems. Thus, in sterically unbiased cases, this [3.3] sigmatropic process results in the axial attachment of the side chain in a cyclohexyl system.
", "doi": "10.7907/h9ke-rp15", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:1047", "collection": "thesis", "collection_id": "1047", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03212008-081007", "primary_object_url": { "basename": "Atzmon_m_1986.pdf", "content": "final", "filesize": 4573964, "license": "other", "mime_type": "application/pdf", "url": "/1047/1/Atzmon_m_1986.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "A Study of Bulk Amorphous Alloys Formed by Solid-State Reaction in Elemental Composites", "author": [ { "family_name": "Atzmon", "given_name": "Michael", "orcid": "0000-0002-7055-1313", "clpid": "Atzmon-Michael" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Ahrens", "given_name": "Thomas J.", "clpid": "Ahrens-T-J" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Bulk amorphous Zr- and Er- based alloys have been synthesized by solid-state reaction in elemental composites prepared by mechanical deformation. For the Er- based composites, complete amorphization was achieved by near- isothermal rolling near room temperature. The driving force for the reaction was found to be a large negative enthalpy of mixing between the constituent elements. Strain and interfacial energies have been estimated and found to modify the driving force only slightly. X-ray diffraction and differential scanning calorimetry have been used to characterize the structure and crystallization behavior of the alloys obtained. Comparison to corresponding amorphous alloys prepared by liquid quenching and sputtering gave good agreement.
\r\n\r\nThe diffusion of Au in amorphous Au-Y and Au-La thin films produced by co-evaporation has been studied by means of X-ray diffraction and Rutherford backscattering. An estimated diffusion coefficient agrees with those obtained by other authors for diffusion of Au in several amorphous alloys. The results confirm that there can be bulk self-diffusion in an amorphous alloy without crystallization. Thus, one does not need to assume short-circuit diffusion during the growth of an amorphous phase by solid-state reaction.
", "doi": "10.7907/5M6N-SK53", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:1011", "collection": "thesis", "collection_id": "1011", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03192008-084757", "primary_object_url": { "basename": "Hetzler_sr_1986.pdf", "content": "final", "filesize": 4686121, "license": "other", "mime_type": "application/pdf", "url": "/1011/1/Hetzler_sr_1986.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Infrared Optical Studies of HgTe-CdTe Superlattices and GaAs", "author": [ { "family_name": "Hetzler", "given_name": "Steven Robert", "clpid": "Hetzler-Steven-Robert" } ], "thesis_advisor": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "thesis_committee": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents two different studies of the infrared optical properties of two different semiconductors. Chapter 2 describes the results of the first infrared photoluminescence (IRPL) measurements of a HgTe-CdTe superlattice. IRPL spectra of two different HgTe-CdTe superlattices from two different sources were measured from 100 to 270K. Sample 1 was grown on (111) Cd0.96Zn0.04Te, and was grown to have 250 repeats of 38 - 40 \u00c5 of HgTe followed by 18 - 20 \u00c5 of CdTe. Sample 2 was grown on (111) CdTe and was grown to have 75 repeats of 50 \u00c5 of HgTe followed by 50 \u00c5 of CdTe. Sample 1 exhibited a single asymmetrical luminescence line at all temperatures studied. (Low signal-to-noise ratio from sample 2 prevented detailed analysis of the lineshape.) The luminescence from both samples occured at significantly lower energies than that from Hg1-xCdxTe alloys with the same Cd concentrations as the average Cd concentrations of the superlattices. At 240 K, the luminescence peak from sample 1 was near 148 meV, with a full width at half-maximum intensity of 42 meV, while the peak from sample 2 was near 242 meV, with a full width at half-maximum intensity of 69 meV. Analysis of the luminescence lineshape from sample 1 showed it to be consistent with wave-vector conserving band-to-band recombination. In this case, the band-gap energy of the superlattice would be near the low energy threshold of the luminescence peak. This study therefore represents the first direct determination of the band gap of an HgTe-CdTe superlattice. A comparison of the lineshapes from both samples with those measured in GaAs-Ga1-xAlxAs super-lattices showed evidence for fluctuations in the layer thicknesses of both the HgTe-CdTe superlattice samples. A comparison was made between the data and a simple theory of the band gaps of HgTe-CdTe superlattices. The theory was shown to be consistent with the experiments, if there were small errors in the measurements of the superlattice layer thicknesses of each sample. The differences in the luminescence properties of the two samples show that it is possible to tailor the band gaps of HgTe-CdTe superlattices.
\r\n\r\nChapter 3 describes the first observation of s-like excited states of a double acceptor in a semiconductor. Two experiments were performed to study the s-like excited states of the 78-meV acceptor in GaAs. The techniques used, selective excitation scattering (SEL) and electronic Raman scattering (ERS), are both sensitive to the detection of s-like excited states of single acceptors in semiconductors. Measurements on two different liquid encapsulated Czochralski GaAs samples showed two s-like excited state transitions of equal magnitude, separated by 4.0 meV. Only one s-like transition is expected in the energy range measured for a single acceptor. A simple effective mass-like model of a double acceptor was developed to account for the two s-like excited states. This model predicted a splitting of the 1s12s1 excited state of a double acceptor to be 2.6 meV, in good agreement with the observed value of 4.0meV. This proved that the 78-meV acceptor in GaAs is due to the first ionization of a double acceptor, the first such identification to be made based on the s-like excited state spectrum. It is therefore possible to identify the valency of an acceptor in a semiconductor by measuring the s-like excited state spectrum.
\r\n\r\nAppendix A describes a novel technique for performing infrared photoluminescence measurements using a Fourier transform infrared spectrophotometer. This technique was developed to perform the experiments described in Chapter 2.
", "doi": "10.7907/5ptm-z449", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11412", "collection": "thesis", "collection_id": "11412", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02272019-121930852", "primary_object_url": { "basename": "Varney_MD_1986.pdf", "content": "final", "filesize": 42124809, "license": "other", "mime_type": "application/pdf", "url": "/11412/1/Varney_MD_1986.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Approach to the Synthesis of Chlorothricolide: Synthesis of (\u00b1)-19,20-Dihydro-24-O-methylchlorotricolide, methyl ester, ethyl carbonate", "author": [ { "family_name": "Varney", "given_name": "Michael David", "clpid": "Varney-Michael-David" } ], "thesis_advisor": [ { "family_name": "Ireland", "given_name": "Robert E.", "clpid": "Ireland-R-E" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Ireland", "given_name": "Robert E.", "clpid": "Ireland-R-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An approach to the total synthesis of the 14-membered macrolide antibiotic aglycon chlorothricolide is presented. Key steps from the two halves to (\u00b1)-19,20-Dihydro-24-O methylchlorothricolide, methyl ester, ethyl carbonate include initial esterification across the C1 and C25 carbons followed by macrodilactonization across the C17 and C14 carbons. Ester enolate Claisen rearrangement and subsequent decarboxylation afforded the intact lactone. Functionalization of the top half is explored.
\r\n\r\nThe ester enolate Claisen rearrangement of propionate derivatives of resolved 1-(t-butyldimethylsilyl)-trans-2-butene-1-ol is reported. Subsequent protiodesilation of the reduced and protected Claisen products resulted in the formation of 2,3-dimethyl-4-pentenyl ethers. Thus, the secondary \u03b1-silyl alcohol has functioned as a chiral primary alcohol equivalent.
\r\n\r\nThe Claisen rearrangement of vinyl ethyl derivatives of 5-tert-butyl-1-(hydroxymethyl)-1-cyclohexene is reported. The standard allyl vinyl ether conditions as well as the triethyl orthoacetate and ester enolate variants of the Claisen rearrangement all resulted in the formation of cis(axial)-4-tert-butylcyclohexyl-substituted systems. Thus, in sterically unbiased cases, this [3.3] sigmatropic process results in the axial attachment of the side chain in a cyclohexyl system.
", "doi": "10.7907/h9ke-rp15", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:4890", "collection": "thesis", "collection_id": "4890", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12092003-145807", "primary_object_url": { "basename": "Blake_ga_1986.pdf", "content": "final", "filesize": 18425174, "license": "other", "mime_type": "application/pdf", "url": "/4890/1/Blake_ga_1986.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "On the Chemical Composition of Interstellar Molecular Clouds: A Millimeter and Submillimeter Spectral Line Survey of OMC-1", "author": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-Geoffrey-A" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Thomas G.", "clpid": "Phillips-T-G" }, { "family_name": "Pickett", "given_name": "Herbert M.", "clpid": "Pickett-Herbert-M" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Phillips", "given_name": "Thomas G.", "clpid": "Phillips-T-G" }, { "family_name": "Pickett", "given_name": "Herbert M.", "clpid": "Pickett-H-M" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Scoville", "given_name": "Nicholas Zabriskie", "orcid": "0000-0002-0438-3323", "clpid": "Scoville-N-Z" } ], "local_group": [ { "literal": "Astronomy Department" }, { "literal": "div_chem" } ], "abstract": "The same basic principles govern the chemical and physical evolution of systems throughout the universe. However, the dissimilar conditions on the Earth and in the interstellar medium lead to remarkably different chemical compositions for these two environments. While less familiar than terrestrial chemistry, the study of the chemical composition of the interstellar medium is important because it bears directly on the understanding of phenomena as diverse as star formation, galactic structure and dynamics, and the cosmological origin of the universe, in addition to providing a unique opportunity to investigate a number of fundamental chemical and physical processes.
\r\n\r\nWe present here results from a millimeter and submillimeter spectral line survey of the core of the Orion molecular cloud (OMC-1). The millimeter-wave survey, conducted at the Owens Valley Radio Observatory (OVRO), covers a 55 GHz interval in the 1.3 mm (230 GHz) atmospheric window and contains emission from 29 molecules. Together with the frequency selective submillimeter observations of H2D+ (372.4 GHz), Cl (492.2 GHz), NH3 (572.5 GHz), and HCl (625.9 GHz) performed aboard NASA's Kuiper Airborne Observatory, over 800 emission lines have been detected from 33 chemically distinct species during the course of this work. The uniformly calibrated results from the unique and extensive OVRO spectral line survey place significant constraints on models of interstellar chemistry, and have allowed the chemical composition of the various regions in OMC-1 to be definitively characterized.
\r\n\r\nA global analysis of the observed abundances has shown that the markedly different chemical compositions of the kinematically distinct Orion subsources may be simply interpreted in the framework of an evolving, initially quiescent, gas-phase chemistry influenced by the process of massive star formation. The chemical composition of the extended Orion cloud complex is similar to that found in a number of other objects, but the central regions of OMC-1 have had their chemistry selectively altered by the high velocity outflow from the young star(s) embedded deep within the interior of the molecular cloud. Detailed arguments are presented in this thesis which relate the seemingly disparate chemical compositions of the individual regions to each other and to the expected physical manifestations of the circumstellar mass loss, and which suggest that similar mechanisms may operate in other molecular clouds as well.
\r\n\r\nBy performing supporting laboratory spectroscopy to supplement existing millimeter-wave catalogues only 33 of the over 800 lines remain unidentified, in contradiction to earlier expectations which had predicted that the near millimeter-wave spectrum of molecular clouds would contain hundreds of strong, unidentifiable emission features. It is probable that a number of the unidentified lines left in the OVRO survey are due to transitions between states of either isotopically substituted or highly excited abundant and complex molecules such as CH3OH, CH3OCH3, and HCOOCH3 whose rotational spectra are poorly known at present. The very small percentage and weak strength of the unidentified lines implies that the dominant chemical constituents visible at millimeter wavelengths have been identified in the Orion molecular cloud.
\r\n\r\nAlso presented are high resolution laboratory millimeter, submillimeter, and far-infrared absorption spectra of the transient molecular species OH, CN, HOC+, and HCO, The zero-field pure rotational spectrum of the OH radical was observed, for the first time, with a frequency agile far-infrared laser sideband spectrometer which promises to revolutionize high resolution spectroscopy at submillimeter and far-infrared wavelengths, while the HOC+ molecular ion was synthesized in a novel glow discharge cell that increases ion abundances by roughly two orders of magnitude as compared with those produced by previously reported methods. Studies of several ions produced in the new discharge cell have provided a theory of the mechanism responsible for the ion enhancement. Sixty-five transitions of CN in its first four vibrational states have been observed, allowing a detailed examination of vibrational and electronic effects in this astrophysically important free radical. The investigation of HCO is the first extensive zero-field analysis of the formyl radical, and is one of the very few millimeter and submillimeter laboratory studies of a non-linear free radical performed to date.
", "doi": "10.7907/0F73-PJ76", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:1011", "collection": "thesis", "collection_id": "1011", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03192008-084757", "primary_object_url": { "basename": "Hetzler_sr_1986.pdf", "content": "final", "filesize": 4686121, "license": "other", "mime_type": "application/pdf", "url": "/1011/1/Hetzler_sr_1986.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Infrared Optical Studies of HgTe-CdTe Superlattices and GaAs", "author": [ { "family_name": "Hetzler", "given_name": "Steven Robert", "clpid": "Hetzler-Steven-Robert" } ], "thesis_advisor": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "thesis_committee": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis presents two different studies of the infrared optical properties of two different semiconductors. Chapter 2 describes the results of the first infrared photoluminescence (IRPL) measurements of a HgTe-CdTe superlattice. IRPL spectra of two different HgTe-CdTe superlattices from two different sources were measured from 100 to 270K. Sample 1 was grown on (111) Cd0.96Zn0.04Te, and was grown to have 250 repeats of 38 - 40 \u00c5 of HgTe followed by 18 - 20 \u00c5 of CdTe. Sample 2 was grown on (111) CdTe and was grown to have 75 repeats of 50 \u00c5 of HgTe followed by 50 \u00c5 of CdTe. Sample 1 exhibited a single asymmetrical luminescence line at all temperatures studied. (Low signal-to-noise ratio from sample 2 prevented detailed analysis of the lineshape.) The luminescence from both samples occured at significantly lower energies than that from Hg1-xCdxTe alloys with the same Cd concentrations as the average Cd concentrations of the superlattices. At 240 K, the luminescence peak from sample 1 was near 148 meV, with a full width at half-maximum intensity of 42 meV, while the peak from sample 2 was near 242 meV, with a full width at half-maximum intensity of 69 meV. Analysis of the luminescence lineshape from sample 1 showed it to be consistent with wave-vector conserving band-to-band recombination. In this case, the band-gap energy of the superlattice would be near the low energy threshold of the luminescence peak. This study therefore represents the first direct determination of the band gap of an HgTe-CdTe superlattice. A comparison of the lineshapes from both samples with those measured in GaAs-Ga1-xAlxAs super-lattices showed evidence for fluctuations in the layer thicknesses of both the HgTe-CdTe superlattice samples. A comparison was made between the data and a simple theory of the band gaps of HgTe-CdTe superlattices. The theory was shown to be consistent with the experiments, if there were small errors in the measurements of the superlattice layer thicknesses of each sample. The differences in the luminescence properties of the two samples show that it is possible to tailor the band gaps of HgTe-CdTe superlattices.
\r\n\r\nChapter 3 describes the first observation of s-like excited states of a double acceptor in a semiconductor. Two experiments were performed to study the s-like excited states of the 78-meV acceptor in GaAs. The techniques used, selective excitation scattering (SEL) and electronic Raman scattering (ERS), are both sensitive to the detection of s-like excited states of single acceptors in semiconductors. Measurements on two different liquid encapsulated Czochralski GaAs samples showed two s-like excited state transitions of equal magnitude, separated by 4.0 meV. Only one s-like transition is expected in the energy range measured for a single acceptor. A simple effective mass-like model of a double acceptor was developed to account for the two s-like excited states. This model predicted a splitting of the 1s12s1 excited state of a double acceptor to be 2.6 meV, in good agreement with the observed value of 4.0meV. This proved that the 78-meV acceptor in GaAs is due to the first ionization of a double acceptor, the first such identification to be made based on the s-like excited state spectrum. It is therefore possible to identify the valency of an acceptor in a semiconductor by measuring the s-like excited state spectrum.
\r\n\r\nAppendix A describes a novel technique for performing infrared photoluminescence measurements using a Fourier transform infrared spectrophotometer. This technique was developed to perform the experiments described in Chapter 2.
", "doi": "10.7907/5ptm-z449", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11464", "collection": "thesis", "collection_id": "11464", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04152019-124552652", "type": "thesis", "title": "An Inelastic Electron Tunneling Spectroscopic Investigation of Inorganic and Organometallic Molybdenum Complexes Adsorbed on Aluminum Oxide Surfaces", "author": [ { "family_name": "Gajda", "given_name": "Gregory Joseph", "clpid": "Gajda-Gregory-Joseph" } ], "thesis_advisor": [ { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The design, construction and operation of an integrated glove box-based tunnel\r\njunction fabrication system are described. This versatile, all stainless steel,\r\nultrahigh vacuum compatible system provides both vapor and liquid phase\r\nadsorption capabilities with a wide variety of molecules. The differences between\r\nadsorption from the liquid phase under an inert atmosphere and in the laboratory\r\natmosphere are illustrated by spectra from junctions prepared with\r\nethanolamine (2-amino-ethanol). A rapid (~ 10 s) and accurate (~ 1%) constant\r\nmodulation current tunnel junction spectrometer displays the obtained spectrum\r\non a storage oscilloscope. The design of these electronics is discussed, and\r\nthe ability to rapidly optimize the lock-in detector phase setting simplifies the\r\nmeasurement of inelastic electron tunneling spectra. The use of a numerical\r\nfirst derivative routine to remove the linear background slope in tunneling spectra\r\nis described, and its ability to determine peak positions in the processed\r\nspectra is discussed.
\r\n\r\nMolybdenum hexacarbonyl adsorbs reversibly on hydroxylated alumina surfaces\r\nat 22\u00b0C to form a carboxylic acid-type adspecies . An estimate of the heat\r\nof adsorption energy, 15 \u00b1 3 kcal/mole, is derived from the desorption kinetics.\r\nHeating the alumina surface to 140 \u00b1 2\u00b0C during adsorption produces thick\r\n(> 500 \u00c5) molybdenum films. Heating the surface to 100\u00b0C during adsorption\r\nproduces decomposition products which consist of molybdenum oxides and subcarbonyls,\r\ndepending on the decomposition parameters (time and post-heating\r\nsequence). The decomposition products show no reaction with 2 Torr of\r\nethylene at 100\u00b0C even after one hour.
\r\n\r\nAt 22\u00b0C, molybdenum oxytetrachloride adsorbs and reacts with the surface\r\nhydroxyl groups on the alumina to form a dioxo-bridged molybdenum dichloro\r\ncomplex, which desorbs slowly at 295 K. Heating during the adsorption produces\r\npoorly reproducible molybdenum suboxide compounds. At 22\u00b0C molybdenum\r\ndioxodichloride adsorbs from the vapor phase and reacts with surface\r\nhydroxyl groups on the alumina to form a molybdenum oxide which reacts\r\nreadily with background water vapor. Heating the surface during exposure produces\r\na partially polymerized oxide which still reacts with background water\r\nvapor. Heating the exposed surfaces in vacuum dehydrates the oxide and\r\nincreases the extent of oligomerization. The oxides show no reaction with 2 Torr\r\nof ethylene at 100\u00b0C after 30 minutes, or with acetic acid at 10-1 Torr after five\r\nminutes at 22\u00b0C. Exposure to 5 x 10-2 Torr of 4-t-butylpyridine for 100 s at 22\u00b0C\r\nresults in complete desorption of the oxide.
", "doi": "10.7907/2evk-b965", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:4890", "collection": "thesis", "collection_id": "4890", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12092003-145807", "primary_object_url": { "basename": "Blake_ga_1986.pdf", "content": "final", "filesize": 18425174, "license": "other", "mime_type": "application/pdf", "url": "/4890/1/Blake_ga_1986.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "On the Chemical Composition of Interstellar Molecular Clouds: A Millimeter and Submillimeter Spectral Line Survey of OMC-1", "author": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-Geoffrey-A" } ], "thesis_advisor": [ { "family_name": "Phillips", "given_name": "Thomas G.", "clpid": "Phillips-T-G" }, { "family_name": "Pickett", "given_name": "Herbert M.", "clpid": "Pickett-Herbert-M" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Phillips", "given_name": "Thomas G.", "clpid": "Phillips-T-G" }, { "family_name": "Pickett", "given_name": "Herbert M.", "clpid": "Pickett-H-M" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Scoville", "given_name": "Nicholas Zabriskie", "orcid": "0000-0002-0438-3323", "clpid": "Scoville-N-Z" } ], "local_group": [ { "literal": "Astronomy Department" }, { "literal": "div_chem" } ], "abstract": "The same basic principles govern the chemical and physical evolution of systems throughout the universe. However, the dissimilar conditions on the Earth and in the interstellar medium lead to remarkably different chemical compositions for these two environments. While less familiar than terrestrial chemistry, the study of the chemical composition of the interstellar medium is important because it bears directly on the understanding of phenomena as diverse as star formation, galactic structure and dynamics, and the cosmological origin of the universe, in addition to providing a unique opportunity to investigate a number of fundamental chemical and physical processes.
\r\n\r\nWe present here results from a millimeter and submillimeter spectral line survey of the core of the Orion molecular cloud (OMC-1). The millimeter-wave survey, conducted at the Owens Valley Radio Observatory (OVRO), covers a 55 GHz interval in the 1.3 mm (230 GHz) atmospheric window and contains emission from 29 molecules. Together with the frequency selective submillimeter observations of H2D+ (372.4 GHz), Cl (492.2 GHz), NH3 (572.5 GHz), and HCl (625.9 GHz) performed aboard NASA's Kuiper Airborne Observatory, over 800 emission lines have been detected from 33 chemically distinct species during the course of this work. The uniformly calibrated results from the unique and extensive OVRO spectral line survey place significant constraints on models of interstellar chemistry, and have allowed the chemical composition of the various regions in OMC-1 to be definitively characterized.
\r\n\r\nA global analysis of the observed abundances has shown that the markedly different chemical compositions of the kinematically distinct Orion subsources may be simply interpreted in the framework of an evolving, initially quiescent, gas-phase chemistry influenced by the process of massive star formation. The chemical composition of the extended Orion cloud complex is similar to that found in a number of other objects, but the central regions of OMC-1 have had their chemistry selectively altered by the high velocity outflow from the young star(s) embedded deep within the interior of the molecular cloud. Detailed arguments are presented in this thesis which relate the seemingly disparate chemical compositions of the individual regions to each other and to the expected physical manifestations of the circumstellar mass loss, and which suggest that similar mechanisms may operate in other molecular clouds as well.
\r\n\r\nBy performing supporting laboratory spectroscopy to supplement existing millimeter-wave catalogues only 33 of the over 800 lines remain unidentified, in contradiction to earlier expectations which had predicted that the near millimeter-wave spectrum of molecular clouds would contain hundreds of strong, unidentifiable emission features. It is probable that a number of the unidentified lines left in the OVRO survey are due to transitions between states of either isotopically substituted or highly excited abundant and complex molecules such as CH3OH, CH3OCH3, and HCOOCH3 whose rotational spectra are poorly known at present. The very small percentage and weak strength of the unidentified lines implies that the dominant chemical constituents visible at millimeter wavelengths have been identified in the Orion molecular cloud.
\r\n\r\nAlso presented are high resolution laboratory millimeter, submillimeter, and far-infrared absorption spectra of the transient molecular species OH, CN, HOC+, and HCO, The zero-field pure rotational spectrum of the OH radical was observed, for the first time, with a frequency agile far-infrared laser sideband spectrometer which promises to revolutionize high resolution spectroscopy at submillimeter and far-infrared wavelengths, while the HOC+ molecular ion was synthesized in a novel glow discharge cell that increases ion abundances by roughly two orders of magnitude as compared with those produced by previously reported methods. Studies of several ions produced in the new discharge cell have provided a theory of the mechanism responsible for the ion enhancement. Sixty-five transitions of CN in its first four vibrational states have been observed, allowing a detailed examination of vibrational and electronic effects in this astrophysically important free radical. The investigation of HCO is the first extensive zero-field analysis of the formyl radical, and is one of the very few millimeter and submillimeter laboratory studies of a non-linear free radical performed to date.
", "doi": "10.7907/0F73-PJ76", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11823", "collection": "thesis", "collection_id": "11823", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10172019-161305619", "type": "thesis", "title": "Calculation of e\u207b-H Atom Scattering Processes Using Hyperspherical Coordinates", "author": [ { "family_name": "Hood", "given_name": "Diane Marie", "clpid": "Hood-Diane-Marie" } ], "thesis_advisor": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" } ], "thesis_committee": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A method is presented for accurately solving the Schr\u00f6dinger equation for the scattering of an electron from a hydrogen atom in three dimensions, which uses hyperspherical coordinates. Our motivation for using this new technique is that previous methods -- coupled channel expansions using target atom eigenfunctions,1 polarization functions and pseudostates,2 and variational methods3 -- have all proven unsatisfactory. The coupled channel calculations tend to have difficulty obtaining convergence with respect to basis set size, and the variational method interjects spurious resonances. Previous applications of hyperspherical coordinates4 have used methods that, while adequate for computing the energy level of the bound state of H-, are not appropriate to full scattering calculations.
\r\n\r\nWe have obtained converged surface functions at a set of discrete values of the hyperradius, which acts as a parameter. The surface functions are further expanded in a basis set that involves 1-dimensional functions of the hyperspherical angle, which are obtained by a finite difference method.
\r\n\r\nThe surface functions have been used to expand the scattering functions. The resulting coupled equations are solved numerically. The wavefunctions are obtained separately at each energy and are converged with respect to the number of basis functions used. Calculations performed so far give converged results for J = 0 through J = 5 up to the n = 4 threshold. The method is both accurate and efficient, and has been implemented on a VAX 11/780 with an FPS164 attached processor.
\r\n\r\nBoth the magnitude and phase of elements of the scattering matrix have converged. Integral cross sections have been obtained for energies up to the n = 4 threshold of hydrogen. Feshbach resonances have been detected below each threshold, and they have been characterized and classified.
\r\n\r\n1P. G. Burke, S. Ormonde, and W. Whitaker, Proc. Phys. Soc. 92, 319, (1967).
\r\n2S. Geltman and P. G. Burke, J. Phys. B 3, 1062, (1970).
\r\n3J. Callaway, Phys. Rev. A 26, 199, (1982).
\r\n4C. D. Lin, Phys. Rev. A 23, 1585, (1981).
\r\n\r\n", "doi": "10.7907/xj5h-me61", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11464", "collection": "thesis", "collection_id": "11464", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04152019-124552652", "type": "thesis", "title": "An Inelastic Electron Tunneling Spectroscopic Investigation of Inorganic and Organometallic Molybdenum Complexes Adsorbed on Aluminum Oxide Surfaces", "author": [ { "family_name": "Gajda", "given_name": "Gregory Joseph", "clpid": "Gajda-Gregory-Joseph" } ], "thesis_advisor": [ { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The design, construction and operation of an integrated glove box-based tunnel\r\njunction fabrication system are described. This versatile, all stainless steel,\r\nultrahigh vacuum compatible system provides both vapor and liquid phase\r\nadsorption capabilities with a wide variety of molecules. The differences between\r\nadsorption from the liquid phase under an inert atmosphere and in the laboratory\r\natmosphere are illustrated by spectra from junctions prepared with\r\nethanolamine (2-amino-ethanol). A rapid (~ 10 s) and accurate (~ 1%) constant\r\nmodulation current tunnel junction spectrometer displays the obtained spectrum\r\non a storage oscilloscope. The design of these electronics is discussed, and\r\nthe ability to rapidly optimize the lock-in detector phase setting simplifies the\r\nmeasurement of inelastic electron tunneling spectra. The use of a numerical\r\nfirst derivative routine to remove the linear background slope in tunneling spectra\r\nis described, and its ability to determine peak positions in the processed\r\nspectra is discussed.
\r\n\r\nMolybdenum hexacarbonyl adsorbs reversibly on hydroxylated alumina surfaces\r\nat 22\u00b0C to form a carboxylic acid-type adspecies . An estimate of the heat\r\nof adsorption energy, 15 \u00b1 3 kcal/mole, is derived from the desorption kinetics.\r\nHeating the alumina surface to 140 \u00b1 2\u00b0C during adsorption produces thick\r\n(> 500 \u00c5) molybdenum films. Heating the surface to 100\u00b0C during adsorption\r\nproduces decomposition products which consist of molybdenum oxides and subcarbonyls,\r\ndepending on the decomposition parameters (time and post-heating\r\nsequence). The decomposition products show no reaction with 2 Torr of\r\nethylene at 100\u00b0C even after one hour.
\r\n\r\nAt 22\u00b0C, molybdenum oxytetrachloride adsorbs and reacts with the surface\r\nhydroxyl groups on the alumina to form a dioxo-bridged molybdenum dichloro\r\ncomplex, which desorbs slowly at 295 K. Heating during the adsorption produces\r\npoorly reproducible molybdenum suboxide compounds. At 22\u00b0C molybdenum\r\ndioxodichloride adsorbs from the vapor phase and reacts with surface\r\nhydroxyl groups on the alumina to form a molybdenum oxide which reacts\r\nreadily with background water vapor. Heating the surface during exposure produces\r\na partially polymerized oxide which still reacts with background water\r\nvapor. Heating the exposed surfaces in vacuum dehydrates the oxide and\r\nincreases the extent of oligomerization. The oxides show no reaction with 2 Torr\r\nof ethylene at 100\u00b0C after 30 minutes, or with acetic acid at 10-1 Torr after five\r\nminutes at 22\u00b0C. Exposure to 5 x 10-2 Torr of 4-t-butylpyridine for 100 s at 22\u00b0C\r\nresults in complete desorption of the oxide.
", "doi": "10.7907/2evk-b965", "publication_date": "1986", "thesis_type": "phd", "thesis_year": "1986" }, { "id": "thesis:11383", "collection": "thesis", "collection_id": "11383", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02052019-112244749", "primary_object_url": { "basename": "Flanagan_DJ_1985.pdf", "content": "final", "filesize": 85214194, "license": "other", "mime_type": "application/pdf", "url": "/11383/1/Flanagan_DJ_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Angular Resolved Photoelectron Spectroscopy of Various Polyatomic Molecular Systems", "author": [ { "family_name": "Flanagan", "given_name": "Dorothy Jean", "clpid": "Flanagan-Dorothy-Jean" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the study of the angular resolved photoelectron spectroscopy of a series of polyatomic molecules. The spectrometer consists of a He I radiation source, a scattering chamber, and a rotatable detection system which includes a set of electrostatic lenses, a hemispherical electrostatic kinetic energy analyzer and an electron multiplier. Angular distributions are determined from the variation in intensity as the detection system is rotated about the center of the scattering chamber.
\r\n\r\nThe theory of photoionization is discussed semiclassically, as the interaction of an atom or molecule treated quantum mechanically with a classical radiation field. Some recent calculations of the asymmetry parameter for valence electrons are briefly reviewed.
\r\n\r\nPhotoelectron angular distributions were measured for acetylene, propyne, 1-butyne, and 2-butyne. The asymmetry parameters of propyne, 1-butyne, and 2-butyne have been determined for the first time. Trends in the asymmetry parameter, ionization potentials and band shapes were studied. It was determined that the parity favoredness rules of Chang failed to account for the behavior of the asymmetry parameter of the molecule despite the symmetry of the molecule. Instead, acetylene and its alkylated analogs follow the trends in \u03b2 observed in studies of the methylated ethenes.
\r\n\r\nAdditionally, the semi-empirical rule that the \u03b2 values of \u03c0 orbitals are higher than for \u03c3 orbitals was violated in this series. Acetylene and propyne possess \u03c3 orbital with \u03b2 values significantly higher than the \u03c0 orbitals.
\r\n\r\nTwo principal substituent effects were observed: 1) a systematic decrease in the first ionization potential and 2) a similar decrease in the asymmetry parameter of the X̃ band with increasing alkylation.
\r\n\r\nThe photoelectron angular distributions were measured for formaldehyde, acetaldehyde, and acetone. The asymmetry parameter has been determined for the first time for acetaldehyde, and, with the exception of the first band, for acetone.
\r\n\r\nThis study has shown that the beta values of the X̃ nO bands of these molecules are, within experimental error, invariant with respect to methyl substitution, results that are consistent with the nonbonding characteristics of the molecular orbitals. The à \u03c0C = O bands, however, show a strong decrease in the asymmetry parameter of approximately 0.2 per methylation in a manner similar to that observed previously in the methylated ethenes and ethynes. The expected systematic decrease in first ionization potential with substitution was also observed.
\r\n\r\nLastly, HAM/3 calculations were performed to determine the ionization potentials of some substituted carbonyls and to examine the excitation energies of ethylene and its methyl and fluoro derivatives to evaluate the method's usefulness to studies in electron impact spectroscopy.
\r\n\r\nThere was generally good agreement between the ionization potential calculated by this method and experimentally determined values. Agreement between the calculated values of the excitation energies and the experimental were reasonable but the method was not sensitive enough to reproduce the trends observed with increasing substitution of the chromophore.
", "doi": "10.7907/f9mq-vz30", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:1161", "collection": "thesis", "collection_id": "1161", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03262008-142511", "primary_object_url": { "basename": "Collins_rt_1985.pdf", "content": "final", "filesize": 5903929, "license": "other", "mime_type": "application/pdf", "url": "/1161/1/Collins_rt_1985.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Electronic Properties of Heterostructures and Defects in Compound Semiconductors", "author": [ { "family_name": "Collins", "given_name": "Reuben Theodore", "orcid": "0000-0001-7910-3819", "clpid": "Collins-Reuben-Theodore" } ], "thesis_advisor": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "thesis_committee": [ { "family_name": "Lambe", "given_name": "John", "clpid": "Lambe-John" }, { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis deals with the electronic characteristics of semiconductor heterostructures and with the electrical properties of semiconductors which are used in the growth of heterostructures. Chapter 2 describes electrical measurements which were made on heterostructures composed of the compound semiconductors AlAs and GaAs. Specifically, the mechanisms for current transport perpendicular to one or more AlAs layers sandwiched between two degenerate GaAs layers were studied, with an emphasis on elastic and inelastic tunneling through the AlAs layers at low temperatures. Tunneling currents occur because the conduction band offset between AlAs and GaAs causes the AlAs to act as a barrier to electrons in the GaAs. Samples composed of single or multiple layers of AlAs sandwiched between GaAs layers were grown by metal organic chemical vapor deposition (MOCVD) and by molecular beam epitaxy (MBE). Electron transport perpendicular to the AlAs barriers was studied as a function of temperature, doping, and layer thickness by making I-V, first derivative (dI/dV), and second derivative d2I/dV2 measurements on these samples. The I-V curves give information about current transport mechanisms. If the dominant mechanism is tunneling, the I-V curves reflect mostly elastic tunneling currents, Structure in the derivatives of the I-V curves indicates the presence of inelastic and resonant tunneling processes. The elastic tunneling measurements give an understanding of the structure of the barriers since these measurements depend on barrier thickness, barrier spacings, and barrier height. Inelastic tunneling measurements can be used to identify the fundamental excitations in the tunneling barrier which can couple to the tunneling electrons; thus, inelastic measurements give additional information about the properties of the barrier. First and second derivatives were measured using modulation techniques.
\r\n\r\nThe main results of this study were the identification of the dominant current transport mechanisms across the AlAs barriers as a function of temperature and AlAs layer thickness, the observation of inelastic tunneling currents due to the excitation of phonons, and the observation of resonant tunneling currents. Measurements on MOCVD grown samples with a single p-type AlAs barrier indicated that thermionic emission was the dominant mechanism for current transport over the barrier at room temperature. At low temperatures, leakage currents dominated if the barrier was thicker than approximately 100 \u00c5, while tunneling currents were dominant in the samples with thinner AlAs barriers. Electron self-energy effects due to the coupling of electrons and optical phonons in the GaAs, and the inelastic-excitation of longitudinal optical phonons in the AlAs were observed in the tunneling current through samples with 50 \u00c5 thick AlAs barriers. This was the first observation of these effects in the AlAs/GaAs system. Measurements were also made on MOCVD grown samples with a single, n-type AlAs barrier. I-V curves for these samples did not have the expected dependence on AlAs layer width. Reproducible structure was still present in the second derivative spectra. A possible explanation for the differences between samples with n-type and p-type barriers which is based on band bending in the AlAs barrier is given. Measurements on MOCVD grown samples with AlxGa1-xAs barriers were made with results similar to those for pure AlAs barriers. Negative resistance regions were observed in the I-V curves of samples with multiple AlAs layers, indicating the presence of resonant tunneling effects. Tunneling measurements on MBE grown structures with a single AlAs barrier did not give reproducible or consistent results.
\r\n\r\nChapter 3 presents an investigation of the deep-level defect structure of CdTe using the technique of deep-level transient spectroscopy (DLTS). Layered structures composed of the compound semiconductors CdTe and HgTe or of the alloy Hg1-xCdxTe may have interesting properties. To realize these properties it is important to understand the electrical characteristics of CdTe and HgTe.The electronic properties of CdTe and HgTe are complicated by the fact that native defects may dominate the electrical characteristics of the crystals. An understanding of the deep-level defect structure of CdTe is, thus, important. DLTS measurements can be used to determine the energy of a deep-level with respect to the band edges, the concentration of the level, and its carrier capture cross section. DLTS measurements are made by monitoring changes in the capacitance of a diode caused by capturing carriers at levels in the depletion region of the diode and then thermally emitting the carriers back to the conduction and valence edges.
\r\n\r\nMeasurements were made on a variety of CdTe crystals. Nominally undoped, Cu-doped and In-doped CdTe crystals were studied. Some of the crystals were observed before and after anneals in Cd-vapor, Te-vapor, or in a purified H2 ambient. Characteristics of deep levels which are seen in all of the n-type CdTe samples are presented. These levels were attributed to native crystal defects or to impurities which are commonly incorporated into CdTe. Levels were also observed which were common to all of the p-type crystals. The same explanation was given for the origin of these traps. A few levels which were specific to certain crystals were also observed and were attributed to unidentified impurities. Deep states were present in the In-doped CdTe which were not observed until the sample was illuminated with above band gap light at low temperatures. Other levels were induced to appear by stressing the CdTe crystals. In general, anneal conditions had a large effect on the concentrations of both shallow and deep levels in the crystals, but did not alter which deep levels were present and their relative concentrations. Modest sample heating (400K) during the process of making DLTS measurements could change the amplitude of levels, sometimes causing new levels to appear or previously observed levels to no longer be observed.
", "doi": "10.7907/pg8h-k549", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:1161", "collection": "thesis", "collection_id": "1161", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03262008-142511", "primary_object_url": { "basename": "Collins_rt_1985.pdf", "content": "final", "filesize": 5903929, "license": "other", "mime_type": "application/pdf", "url": "/1161/1/Collins_rt_1985.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Electronic Properties of Heterostructures and Defects in Compound Semiconductors", "author": [ { "family_name": "Collins", "given_name": "Reuben Theodore", "orcid": "0000-0001-7910-3819", "clpid": "Collins-Reuben-Theodore" } ], "thesis_advisor": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "thesis_committee": [ { "family_name": "Lambe", "given_name": "John", "clpid": "Lambe-John" }, { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis deals with the electronic characteristics of semiconductor heterostructures and with the electrical properties of semiconductors which are used in the growth of heterostructures. Chapter 2 describes electrical measurements which were made on heterostructures composed of the compound semiconductors AlAs and GaAs. Specifically, the mechanisms for current transport perpendicular to one or more AlAs layers sandwiched between two degenerate GaAs layers were studied, with an emphasis on elastic and inelastic tunneling through the AlAs layers at low temperatures. Tunneling currents occur because the conduction band offset between AlAs and GaAs causes the AlAs to act as a barrier to electrons in the GaAs. Samples composed of single or multiple layers of AlAs sandwiched between GaAs layers were grown by metal organic chemical vapor deposition (MOCVD) and by molecular beam epitaxy (MBE). Electron transport perpendicular to the AlAs barriers was studied as a function of temperature, doping, and layer thickness by making I-V, first derivative (dI/dV), and second derivative d2I/dV2 measurements on these samples. The I-V curves give information about current transport mechanisms. If the dominant mechanism is tunneling, the I-V curves reflect mostly elastic tunneling currents, Structure in the derivatives of the I-V curves indicates the presence of inelastic and resonant tunneling processes. The elastic tunneling measurements give an understanding of the structure of the barriers since these measurements depend on barrier thickness, barrier spacings, and barrier height. Inelastic tunneling measurements can be used to identify the fundamental excitations in the tunneling barrier which can couple to the tunneling electrons; thus, inelastic measurements give additional information about the properties of the barrier. First and second derivatives were measured using modulation techniques.
\r\n\r\nThe main results of this study were the identification of the dominant current transport mechanisms across the AlAs barriers as a function of temperature and AlAs layer thickness, the observation of inelastic tunneling currents due to the excitation of phonons, and the observation of resonant tunneling currents. Measurements on MOCVD grown samples with a single p-type AlAs barrier indicated that thermionic emission was the dominant mechanism for current transport over the barrier at room temperature. At low temperatures, leakage currents dominated if the barrier was thicker than approximately 100 \u00c5, while tunneling currents were dominant in the samples with thinner AlAs barriers. Electron self-energy effects due to the coupling of electrons and optical phonons in the GaAs, and the inelastic-excitation of longitudinal optical phonons in the AlAs were observed in the tunneling current through samples with 50 \u00c5 thick AlAs barriers. This was the first observation of these effects in the AlAs/GaAs system. Measurements were also made on MOCVD grown samples with a single, n-type AlAs barrier. I-V curves for these samples did not have the expected dependence on AlAs layer width. Reproducible structure was still present in the second derivative spectra. A possible explanation for the differences between samples with n-type and p-type barriers which is based on band bending in the AlAs barrier is given. Measurements on MOCVD grown samples with AlxGa1-xAs barriers were made with results similar to those for pure AlAs barriers. Negative resistance regions were observed in the I-V curves of samples with multiple AlAs layers, indicating the presence of resonant tunneling effects. Tunneling measurements on MBE grown structures with a single AlAs barrier did not give reproducible or consistent results.
\r\n\r\nChapter 3 presents an investigation of the deep-level defect structure of CdTe using the technique of deep-level transient spectroscopy (DLTS). Layered structures composed of the compound semiconductors CdTe and HgTe or of the alloy Hg1-xCdxTe may have interesting properties. To realize these properties it is important to understand the electrical characteristics of CdTe and HgTe.The electronic properties of CdTe and HgTe are complicated by the fact that native defects may dominate the electrical characteristics of the crystals. An understanding of the deep-level defect structure of CdTe is, thus, important. DLTS measurements can be used to determine the energy of a deep-level with respect to the band edges, the concentration of the level, and its carrier capture cross section. DLTS measurements are made by monitoring changes in the capacitance of a diode caused by capturing carriers at levels in the depletion region of the diode and then thermally emitting the carriers back to the conduction and valence edges.
\r\n\r\nMeasurements were made on a variety of CdTe crystals. Nominally undoped, Cu-doped and In-doped CdTe crystals were studied. Some of the crystals were observed before and after anneals in Cd-vapor, Te-vapor, or in a purified H2 ambient. Characteristics of deep levels which are seen in all of the n-type CdTe samples are presented. These levels were attributed to native crystal defects or to impurities which are commonly incorporated into CdTe. Levels were also observed which were common to all of the p-type crystals. The same explanation was given for the origin of these traps. A few levels which were specific to certain crystals were also observed and were attributed to unidentified impurities. Deep states were present in the In-doped CdTe which were not observed until the sample was illuminated with above band gap light at low temperatures. Other levels were induced to appear by stressing the CdTe crystals. In general, anneal conditions had a large effect on the concentrations of both shallow and deep levels in the crystals, but did not alter which deep levels were present and their relative concentrations. Modest sample heating (400K) during the process of making DLTS measurements could change the amplitude of levels, sometimes causing new levels to appear or previously observed levels to no longer be observed.
", "doi": "10.7907/pg8h-k549", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:1180", "collection": "thesis", "collection_id": "1180", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03272008-090442", "primary_object_url": { "basename": "Dolgin_bp_1985.pdf", "content": "final", "filesize": 5427276, "license": "other", "mime_type": "application/pdf", "url": "/1180/1/Dolgin_bp_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Kinetics of the Formation of an Amorphous Layer During a Solid State Reaction", "author": [ { "family_name": "Dolgin", "given_name": "Benjamin Paul", "clpid": "Dolgin-Benjamin-Paul" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Vreeland", "given_name": "Thad", "clpid": "Vreeland-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Solid state reaction as a new method of amorphous film fabrication was introduced by R. Schwartz and W. L. Johnson in 1983. A thermodynamic explanation for the process given by the original article provides a clue to understanding the forces making the reaction possible. This thesis emphasizes the kinetic approach to the description of the reaction. The movements of the interfaces as a fundamental mechanism of the reaction is suggested. The reaction in La-Au and Ni-Hf multilayers is described. Resistance measurements, TEM and SIMS techniques, and Rutherford backscattering are used to study the process.
\r\n\r\nThe thesis contains a proof that the final product of the solid state reaction is amorphous. It describes the morphology of the reacting multilayers. The one-dimensional and multi-dimensional processes taking place during the growth are separated. The thesis connects the properties of the reaction with known properties of the \"fast diffusion.\" The phenomenological model for the reaction is introduced. The model consists of a diffusion equation with a new set of boundary conditions. The amorphous layer growth rate in the limit of short time is found to be X = 1 - exp(-At) and X = -1/(A - 1) + (2at)1/2 in the limit of long time. The \"steady state\" approximation as a solution to the diffusion equations in the limit of long time is found to be incorrect. The model shows excellent agreement with the experimental data.
", "doi": "10.7907/n0qt-h472", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:1180", "collection": "thesis", "collection_id": "1180", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03272008-090442", "primary_object_url": { "basename": "Dolgin_bp_1985.pdf", "content": "final", "filesize": 5427276, "license": "other", "mime_type": "application/pdf", "url": "/1180/1/Dolgin_bp_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Kinetics of the Formation of an Amorphous Layer During a Solid State Reaction", "author": [ { "family_name": "Dolgin", "given_name": "Benjamin Paul", "clpid": "Dolgin-Benjamin-Paul" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Corngold", "given_name": "Noel Robert", "clpid": "Corngold-N-R" }, { "family_name": "Vreeland", "given_name": "Thad", "clpid": "Vreeland-T" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Solid state reaction as a new method of amorphous film fabrication was introduced by R. Schwartz and W. L. Johnson in 1983. A thermodynamic explanation for the process given by the original article provides a clue to understanding the forces making the reaction possible. This thesis emphasizes the kinetic approach to the description of the reaction. The movements of the interfaces as a fundamental mechanism of the reaction is suggested. The reaction in La-Au and Ni-Hf multilayers is described. Resistance measurements, TEM and SIMS techniques, and Rutherford backscattering are used to study the process.
\r\n\r\nThe thesis contains a proof that the final product of the solid state reaction is amorphous. It describes the morphology of the reacting multilayers. The one-dimensional and multi-dimensional processes taking place during the growth are separated. The thesis connects the properties of the reaction with known properties of the \"fast diffusion.\" The phenomenological model for the reaction is introduced. The model consists of a diffusion equation with a new set of boundary conditions. The amorphous layer growth rate in the limit of short time is found to be X = 1 - exp(-At) and X = -1/(A - 1) + (2at)1/2 in the limit of long time. The \"steady state\" approximation as a solution to the diffusion equations in the limit of long time is found to be incorrect. The model shows excellent agreement with the experimental data.
", "doi": "10.7907/n0qt-h472", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11336", "collection": "thesis", "collection_id": "11336", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01072019-124055656", "primary_object_url": { "basename": "Szuromi_PD_1985.pdf", "content": "final", "filesize": 43256100, "license": "other", "mime_type": "application/pdf", "url": "/11336/1/Szuromi_PD_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Studies of Hydrocarbon Reactions on Low-Index Iridium and Platinum Surfaces", "author": [ { "family_name": "Szuromi", "given_name": "Phillip David", "clpid": "Szuromi-Phillip-David" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Collins", "given_name": "Terrence J.", "clpid": "Collins-T-J" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The interaction of hydrocarbons with the (110)-(1x2) and (111) surfaces of iridium and the (110)-(1x2) surface of platinum has been studied under ultrahigh vacuum conditions. The principle experimental techniques employed were thermal desorption mass spectrometry and low energy electron diffraction.
\r\n\r\nChapter 2 describes the extension of previous studies of the adsorption and reaction of ethane and propane on the Ir(110)-(1x2) surface to the normal isomers of butane, pentane, hexane and heptane. At low coverages, each of these alkanes undergoes dissociative chemisorption at 130 K. At higher coverages, molecular adsorption occurs as well. Thermal desorption spectra of hydrogen are similar in many respects for the dissociatively adsorbed overlayers of all six of these paraffins. Both desorption-limited and reaction-limited adstates of hydrogen are observed, the latter being associated with the dehydrogenation of hydrocarbon fragments on the surface. Ethane, butane and hexane form high temperature adstates, the associated fragments of which are low in hydrogen content, while those for propane, pentane and heptane contain relatively more hydrogen. This difference may be explained by extending a model for dehydrogenation which has been proposed previously [T. S. Wittrig, P. D. Szuromi and W. H. Weinberg, J. Chem. Phys. (76), 3305 (1982)] for understanding the dissociative adsorption of other saturated hydrocarbons on this surface.
\r\n\r\nChapter 3 discusses cyclopropane, propylene, propyne and allene on the reconstructed Ir(110)-(1x2) surface. Annealing adlayers of these hydrocarbons (at low coverages) leads to the formation of surface hydrogen and hydrocarbon fragments of approximate stoichiometry C3H2. The importance of the \u03b22 adsite of hydrogen on this surface of iridium has been demonstrated further by inhibition studies with hydrogen, CO and surface carbon. The close-packed Ir(111) surface dehydrogenates propylene, but neither propane nor cyclopropane adsorb dissociately under the same reaction conditions, indicating a strong effect for the activation of carbon-hydrogen bonds of alkanes.
\r\n\r\nChapter 4 describes the investigation of this strong effect of surface geometry on the dissociative adsorption of alkanes on surfaces of platinum. Previous work (L. E. Firment, Ph.D. Thesis, Univ. of California, Berkeley, 1976) shows that the close-packed Pt(111) surface does not dehydrogenate the normal alkanes through octane under ultrahigh vacuum conditions. On the reconstructed Pt(110)-(1x2) surface, low coverages of n-butane and n-pentane adsorb dissociatively at approximately 200 K to form surface hydrogen and hydrocarbon fragments, whereas only molecular adsorption is observed for ethane and propane. Inhibition of this reaction by precoverages of hydrogen suggests strongly that carbon-hydrogen bond activation is the initial reaction step, and occurs at the same adsite as for the adsorption of hydrogen at lower coverages. Thus for both iridium and platinum the availability of high coordination adsites on the (110)-(1x2) surface appears to lower the kinetic barriers that must be overcome to activate carbon-hydrogen bonds in alkanes. Differences in the electronic structure of the two metals manifest themselves in such details as the magnitude of that kinetic barrier.
", "doi": "10.7907/ndxy-rb82", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:5305", "collection": "thesis", "collection_id": "5305", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-083321412", "primary_object_url": { "basename": "Allison_jn_1985.pdf", "content": "final", "filesize": 3603329, "license": "other", "mime_type": "application/pdf", "url": "/5305/1/Allison_jn_1985.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Theoretical Studies of Heterogeneous Catalysis of Molybdates", "author": [ { "family_name": "Allison", "given_name": "Janet Noel", "clpid": "Allison-Janet-Noel" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Sparks", "given_name": "Randal K.", "clpid": "Sparks-Randal-K" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1: We use thermochemical results from ab initio quantum chemical calculations (generalized valence bond) to examine the reaction mechanism for
\r\n\r\nH3COH + \u00bd O2 \u2192 H2CO + H2O
\r\n\r\nas catalyzed by MoO3. We find that surface dioxo sites
\r\n\r\n[Chemical structure; see abstract in scanned thesis for details.]
\r\n\r\nare critical to activating the methanol, but we find that the Trifiro proposal of a single site-single step process
\r\n\r\n[Chemical structure; see abstract in scanned thesis for details.]
\r\n\r\nis not favorable (\u2206H \u2243 +31.5 kcal). Our conclusion is that the catalytic site involves two adjacent surface dioxo units (the dual dioxo site), with each dioxo site extracting one H in a sequence of steps. The required dual dioxo site exists on the (010) surface of MoO3 but does not exist on the other low index surfaces. This mechanism is supported by atmospheric pressure experimental studies which indicate that MoO3 (010) is selective for CH2O products. A detailed sequence of reaction steps and the associated thermochemistry is proposed.
\r\n\r\nChapter 2: Molybdates involving various metal additives play a dominant role in such industrially important catalytic processes as selective oxidation (propene to acrolein) and ammoxidation (propene to acrylonitrile); however, the details of the reaction mechanism and of the surface sites responsible are yet quite uncertain. In order to establish the thermo-chemistry and detailed mechanistic steps involved with such reactions, we have performed ab intitio quantum chemical calculations [generalized valence bond (GVB) and configuration interaction (CI)]. These studies indicate a special importance of multiple surface dioxo Mo sites (possessing two Mo-O double bonds and hence spectator oxo groups) arranged together so as to provide the means for promoting the sequence of transformations.
\r\n\r\nChapter 3: Extensive ab initio calculations have been carried out on molybdenum (VI, V and IV) complexes containing oxygen and nitrogen. A detailed description of the bonding of oxo, nitrido and imido terminally attached ligands to molybdenum is presented. These results are used to explain the preferred geometries of complexes as well as the periodic trends as ligands to molybdenum are varied from O, N, NH.
\r\n\r\nChapter 4: We find that the ground state of MoN (4\u2211-) has a covalent triple bond where the \u03c3 bond is dz2-like on the Mo, leading to a quartet state with unpaired electrons in the Mo 5s, Mo 4d\u03b4xy and Mo 4d\u03b4x2-y2 orbitals. The first excited state (4\u03a0) corresponds to the 5p\u03c0 \u2190 5s excitation. The calculated properties of Re = 1.60 \u00c5, \u03c9e = 1100 cm-1, De = 4.07 eV, and \u2206E (4\u03a0-4\u2211- = 2.128 eV are in good agreement with recent experimental results (Re = 1.63 \u00c5 and \u2206E = 2.011 eV). Particularly interesting is a dramatic nonmonotonic change of dipole moment with distance (\u00b5 = -3.123 D at Re = 1.60 \u00c5, -5.982 D at R = 2.60 \u00c5 and \u00b5 = -0.176 D at R = 5.0 \u00c5. This effect is explained.
\r\n", "doi": "10.7907/wpmx-ff05", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11383", "collection": "thesis", "collection_id": "11383", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02052019-112244749", "primary_object_url": { "basename": "Flanagan_DJ_1985.pdf", "content": "final", "filesize": 85214194, "license": "other", "mime_type": "application/pdf", "url": "/11383/1/Flanagan_DJ_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Angular Resolved Photoelectron Spectroscopy of Various Polyatomic Molecular Systems", "author": [ { "family_name": "Flanagan", "given_name": "Dorothy Jean", "clpid": "Flanagan-Dorothy-Jean" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the study of the angular resolved photoelectron spectroscopy of a series of polyatomic molecules. The spectrometer consists of a He I radiation source, a scattering chamber, and a rotatable detection system which includes a set of electrostatic lenses, a hemispherical electrostatic kinetic energy analyzer and an electron multiplier. Angular distributions are determined from the variation in intensity as the detection system is rotated about the center of the scattering chamber.
\r\n\r\nThe theory of photoionization is discussed semiclassically, as the interaction of an atom or molecule treated quantum mechanically with a classical radiation field. Some recent calculations of the asymmetry parameter for valence electrons are briefly reviewed.
\r\n\r\nPhotoelectron angular distributions were measured for acetylene, propyne, 1-butyne, and 2-butyne. The asymmetry parameters of propyne, 1-butyne, and 2-butyne have been determined for the first time. Trends in the asymmetry parameter, ionization potentials and band shapes were studied. It was determined that the parity favoredness rules of Chang failed to account for the behavior of the asymmetry parameter of the molecule despite the symmetry of the molecule. Instead, acetylene and its alkylated analogs follow the trends in \u03b2 observed in studies of the methylated ethenes.
\r\n\r\nAdditionally, the semi-empirical rule that the \u03b2 values of \u03c0 orbitals are higher than for \u03c3 orbitals was violated in this series. Acetylene and propyne possess \u03c3 orbital with \u03b2 values significantly higher than the \u03c0 orbitals.
\r\n\r\nTwo principal substituent effects were observed: 1) a systematic decrease in the first ionization potential and 2) a similar decrease in the asymmetry parameter of the X̃ band with increasing alkylation.
\r\n\r\nThe photoelectron angular distributions were measured for formaldehyde, acetaldehyde, and acetone. The asymmetry parameter has been determined for the first time for acetaldehyde, and, with the exception of the first band, for acetone.
\r\n\r\nThis study has shown that the beta values of the X̃ nO bands of these molecules are, within experimental error, invariant with respect to methyl substitution, results that are consistent with the nonbonding characteristics of the molecular orbitals. The à \u03c0C = O bands, however, show a strong decrease in the asymmetry parameter of approximately 0.2 per methylation in a manner similar to that observed previously in the methylated ethenes and ethynes. The expected systematic decrease in first ionization potential with substitution was also observed.
\r\n\r\nLastly, HAM/3 calculations were performed to determine the ionization potentials of some substituted carbonyls and to examine the excitation energies of ethylene and its methyl and fluoro derivatives to evaluate the method's usefulness to studies in electron impact spectroscopy.
\r\n\r\nThere was generally good agreement between the ionization potential calculated by this method and experimentally determined values. Agreement between the calculated values of the excitation energies and the experimental were reasonable but the method was not sensitive enough to reproduce the trends observed with increasing substitution of the chromophore.
", "doi": "10.7907/f9mq-vz30", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11381", "collection": "thesis", "collection_id": "11381", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02012019-115455977", "primary_object_url": { "basename": "Hanratty_MA_1985.pdf", "content": "final", "filesize": 62055541, "license": "other", "mime_type": "application/pdf", "url": "/11381/1/Hanratty_MA_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Investigations of the Mechanisms and Energetics for Transition Metal Ion Mediated Reactions", "author": [ { "family_name": "Hanratty", "given_name": "Maureen Alice", "clpid": "Hanratty-Maureen-Alice" } ], "thesis_advisor": [ { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "thesis_committee": [ { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Multiphoton infrared activation has been used to probe the potential energy surfaces for the reactions of stable Co(C5H10)+ adducts, formed by ligand exchange reactions in an ion cyclotron resonance spectrometer. These investigations are discussed in Chapter II. Infrared activation effected with a cw CO2 laser is highly selective, with dissociation occurring only by the lowest energy pathway.
\r\n\r\nChapter III describes the use of product translational energy release distributions to investigate the potential energy surfaces for elimination of H2 and small hydrocarbons from ionic cobalt and nickel complexes with alkanes. The measurements were made using a reverse geometry double focusing mass spectrometer. For dehydrogenation reactions, both the shape of the kinetic energy release distribution and the maximum kinetic energy release appear to be correlated with the reaction mechanism. Statistical RRKM theory is used to model the observed kinetic energy release distributions.
\r\n\r\nThe kinetic energy release distributions associated with loss of H2 and small hydrocarbons from Co(C5H10)+ complexes are presented in Chapter IV. The results from the ionic cobalt-alkene adducts are compared with the kinetic energy release distributions for the ionic cobalt-alkane complexes discussed in Chapter III. Collision induced dissociation is also employed to characterize the Co(C5H10)+ adducts.
\r\n\r\nThe formation and reactions of iron and nickel clusters containing up to four metal atoms with a varying number of CO ligands are discussed in Chapter V. Ion-molecule condensation reactions result in the rapid formation of polynuclear metal carbonyl clusters which lose CO when exposed to infrared or visible radiation. The reactivity of these ligated species is markedly different from that of the bare metal ion. The potential of this method for generating very specific unsaturated cluster compounds is demonstrated.
\r\n\r\n", "doi": "10.7907/6mqm-3w23", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11381", "collection": "thesis", "collection_id": "11381", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02012019-115455977", "primary_object_url": { "basename": "Hanratty_MA_1985.pdf", "content": "final", "filesize": 62055541, "license": "other", "mime_type": "application/pdf", "url": "/11381/1/Hanratty_MA_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Investigations of the Mechanisms and Energetics for Transition Metal Ion Mediated Reactions", "author": [ { "family_name": "Hanratty", "given_name": "Maureen Alice", "clpid": "Hanratty-Maureen-Alice" } ], "thesis_advisor": [ { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "thesis_committee": [ { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Multiphoton infrared activation has been used to probe the potential energy surfaces for the reactions of stable Co(C5H10)+ adducts, formed by ligand exchange reactions in an ion cyclotron resonance spectrometer. These investigations are discussed in Chapter II. Infrared activation effected with a cw CO2 laser is highly selective, with dissociation occurring only by the lowest energy pathway.
\r\n\r\nChapter III describes the use of product translational energy release distributions to investigate the potential energy surfaces for elimination of H2 and small hydrocarbons from ionic cobalt and nickel complexes with alkanes. The measurements were made using a reverse geometry double focusing mass spectrometer. For dehydrogenation reactions, both the shape of the kinetic energy release distribution and the maximum kinetic energy release appear to be correlated with the reaction mechanism. Statistical RRKM theory is used to model the observed kinetic energy release distributions.
\r\n\r\nThe kinetic energy release distributions associated with loss of H2 and small hydrocarbons from Co(C5H10)+ complexes are presented in Chapter IV. The results from the ionic cobalt-alkene adducts are compared with the kinetic energy release distributions for the ionic cobalt-alkane complexes discussed in Chapter III. Collision induced dissociation is also employed to characterize the Co(C5H10)+ adducts.
\r\n\r\nThe formation and reactions of iron and nickel clusters containing up to four metal atoms with a varying number of CO ligands are discussed in Chapter V. Ion-molecule condensation reactions result in the rapid formation of polynuclear metal carbonyl clusters which lose CO when exposed to infrared or visible radiation. The reactivity of these ligated species is markedly different from that of the bare metal ion. The potential of this method for generating very specific unsaturated cluster compounds is demonstrated.
\r\n\r\n", "doi": "10.7907/6mqm-3w23", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11350", "collection": "thesis", "collection_id": "11350", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01222019-123545387", "primary_object_url": { "basename": "Winniczek_JW_1985.pdf", "content": "final", "filesize": 110565437, "license": "other", "mime_type": "application/pdf", "url": "/11350/1/Winniczek_JW_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Anisotropic Interaction Potentials between Helium and Linear Molecules from Crossed Beam Experiments", "author": [ { "family_name": "Winniczek", "given_name": "Jaroslaw W.", "clpid": "Winniczek-Jaroslaw-W" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Anson", "given_name": "Fred C.", "clpid": "Anson-F-C" }, { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Anisotropic interaction potentials between helium and linear molecules have been studied experimentally and theoretically to examine the relationship between the potential and the scattering differential cross-section, and to extract these potentials from crossed-molecular beam data.
\r\n\r\nChapter 2 presents the measurement of total (elastic and inelastic) differential scattering cross sections for He + CO2, CS2, OCS at a relative collision energy of about 65 meV with a crossed molecular beam apparatus. Anisotropic interaction potentials were extracted from these data, by way of an infinite order sudden approximation analysis. Several different anisotropic potential models were used in this analysis. The necessity for considering the anisotropy in the position of the well minimum as well as of its depth is demonstrated. A potential is proposed for He + OCS that reflects the symmetry of OCS, with a minimum number of modeling parameters.
\r\n\r\nIn Chapter 3 a detailed sensitivity analysis of the total and rotational state-to-state differential cross-section (DCS) is performed on an empirical potential energy surface for He + CO2. The infinite order sudden approximation is used to calculate the cross-sections. The sensitivity analysis consists of: 1) a large scale modification of the parameters that determine the anisotropic potential, and 2) an infinitesimal variation of these parameters to obtain a relative sensitivity function for the DCS. From these we demonstrate the effect each potential parameter has on the cross-sections. Despite the fact that this highly quantum system displays no classical effects such as rainbow scattering, we have shown that the quantal DCS oscillations contain significant information regarding the depth and width of the potential well and its anisotropy. Much of this information can be extracted from total-DCS scattering data. However the rotationally inelastic DCS contain a substantial amount of additional information regarding the shape of the potential energy surface.
\r\n\r\nSome of the conclusions reached in Chapter 3 indicate that the measuring of rotationally inelastic differential cross-sections can provide significantly greater insight into the nature of the potential than does the total DCS. In Chapter 4 we develop the means for simulating experimentally observable data from the potential for a given set of apparatus conditions. In Chapter 5 we describe modifications made to the crossed-beam apparatus in order to observe this inelasticity and present preliminary results for He + CO2.
", "doi": "10.7907/5nvw-ym37", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11346", "collection": "thesis", "collection_id": "11346", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01182019-103133548", "primary_object_url": { "basename": "Spies_GH_1985.pdf", "content": "final", "filesize": 81270769, "license": "other", "mime_type": "application/pdf", "url": "/11346/1/Spies_GH_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Studies on the Coordination of Bis-hydroxybenzamido Chelating Ligations to Chromium, Iron, and Osmium. II. A Survey of the Organometallic Chemistry of Osmium Tetraoxide", "author": [ { "family_name": "Spies", "given_name": "George Harlan", "clpid": "Spies-George-Harlan" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Collins", "given_name": "Terrence J.", "clpid": "Collins-T-J" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Collins", "given_name": "Terrence J.", "clpid": "Collins-T-J" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The coordination chemistry of chromium, iron, and osmium with bis-hydroxybenzamido chelating ligands was investigated. Two types of complexes were obtained on reacting CrCl3 \u2022 6H2O with 1,2-bis(3,5-dichloro-2-hydroxybenzanido)-ethane ((H)4CHBA-Et). A neutral dimeric complex, in which two chelates bridge two metal centers, was discovered and characterized by X-ray crystallography. This is the first molecule in which both forms of monodentate organic amide coordination (i.e., O-bound and N-bound coordination) have been found. The N-bound amide was shown to be a better \u03c3-donor. This is the first well-characterized example of N-coordination to chromium(III).
\r\n\r\nA second complex, which is a precursor to the neutral dimer, has not been fully characterized. It may also be dimeric. Similar complexes, with different bis-hydroxybenzamido ligands, have been examined. Iron(III) species, synthesized from these ligands and FeCl3, appear to be analogous to the latter chromium(III) compounds.
\r\n\r\nX-ray crystallographic studies have complemented investigations into the coordination chemistry of these bis-hydroxybenzamido ligands with several transition metals. In addition to the dimeric chromium(III) complex, in which the ligand bridges two metal centers, many osmium(IV) complexes were found with the bis-hydroxybenzamido ligands coordinated to one metal center as a planar tetradentate tetraanion. These structures exhibited the first examples of bonds between osmium(IV) and an N-coordinated organic amide ligand and a phenoxide ligand. One such complex, a \u00b5-oxo dimer, was found with potassium ions in unusually low coordination environments (i.e., four- and five-coordinate). Oxidation of trans-Os( CHBA-Et)(py)2 subsequently resulted in crystals of a new con1plex with a hydroxy and a methoxy group on the ethylene unit bridging the amide nitrogen atoms of the chelated ligand. The bond distances and angles for this molecule are very similar to those of its precursor, trans-Os(CHBA-Et)(py)2. The ligand, (H)4 CHBA-Et, was found to cocrystallize with pyridinium chloride. This structure has provided a benchmark for comparison with complexed chelates; few significant differences were observed.
\r\n\r\nThe fusion of 2,3-bis(2-hydroxy-benzamido)-2,3-butane with (NH4)2OsCl6 (T > 300\u00b0C) resulted in the formation of an osmium(IV)-imidazoline complex.
\r\n\r\nAlso examined was the organometallic chemistry of osmium tetraoxide. Oxidation of low valent carbonyl complexes with the quinuclidine adduct of osmium tetraoxide resulted in attack of both the low valent metal and a carbonyl ligand with the formation of \u00b5-CO2 mixed-valent complexes. The surprising stability of this new type of CO2 complex is kinetic in origin as den1onstrated by the chemistry of a series of compounds. Decomposition with loss of CO2 was observed for more labile metal complexes. In the absence of nitrogenous bases, oxidation of Ru(CO)3(PPh3)2 with osmium tetraoxide resulted in the formation of what is believed to be a tetranuclear complex. The low valent metal center and a coordinated carbonyl ligand were oxidized.
\r\n\r\nOne other mode of reactivity was discovered. Oxidative addition of osmium tetraoxide to Pt(PPh3)2(C2H4) displaced the ethylene ligand with the formation of a \u00b5-oxo bridged tetranuclear complex. These and other potential modes of OsO4 reactivity with organometallic and inorganic complexes are discussed.
", "doi": "10.7907/s19j-2033", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11346", "collection": "thesis", "collection_id": "11346", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01182019-103133548", "primary_object_url": { "basename": "Spies_GH_1985.pdf", "content": "final", "filesize": 81270769, "license": "other", "mime_type": "application/pdf", "url": "/11346/1/Spies_GH_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Studies on the Coordination of Bis-hydroxybenzamido Chelating Ligations to Chromium, Iron, and Osmium. II. A Survey of the Organometallic Chemistry of Osmium Tetraoxide", "author": [ { "family_name": "Spies", "given_name": "George Harlan", "clpid": "Spies-George-Harlan" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Collins", "given_name": "Terrence J.", "clpid": "Collins-T-J" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Collins", "given_name": "Terrence J.", "clpid": "Collins-T-J" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The coordination chemistry of chromium, iron, and osmium with bis-hydroxybenzamido chelating ligands was investigated. Two types of complexes were obtained on reacting CrCl3 \u2022 6H2O with 1,2-bis(3,5-dichloro-2-hydroxybenzanido)-ethane ((H)4CHBA-Et). A neutral dimeric complex, in which two chelates bridge two metal centers, was discovered and characterized by X-ray crystallography. This is the first molecule in which both forms of monodentate organic amide coordination (i.e., O-bound and N-bound coordination) have been found. The N-bound amide was shown to be a better \u03c3-donor. This is the first well-characterized example of N-coordination to chromium(III).
\r\n\r\nA second complex, which is a precursor to the neutral dimer, has not been fully characterized. It may also be dimeric. Similar complexes, with different bis-hydroxybenzamido ligands, have been examined. Iron(III) species, synthesized from these ligands and FeCl3, appear to be analogous to the latter chromium(III) compounds.
\r\n\r\nX-ray crystallographic studies have complemented investigations into the coordination chemistry of these bis-hydroxybenzamido ligands with several transition metals. In addition to the dimeric chromium(III) complex, in which the ligand bridges two metal centers, many osmium(IV) complexes were found with the bis-hydroxybenzamido ligands coordinated to one metal center as a planar tetradentate tetraanion. These structures exhibited the first examples of bonds between osmium(IV) and an N-coordinated organic amide ligand and a phenoxide ligand. One such complex, a \u00b5-oxo dimer, was found with potassium ions in unusually low coordination environments (i.e., four- and five-coordinate). Oxidation of trans-Os( CHBA-Et)(py)2 subsequently resulted in crystals of a new con1plex with a hydroxy and a methoxy group on the ethylene unit bridging the amide nitrogen atoms of the chelated ligand. The bond distances and angles for this molecule are very similar to those of its precursor, trans-Os(CHBA-Et)(py)2. The ligand, (H)4 CHBA-Et, was found to cocrystallize with pyridinium chloride. This structure has provided a benchmark for comparison with complexed chelates; few significant differences were observed.
\r\n\r\nThe fusion of 2,3-bis(2-hydroxy-benzamido)-2,3-butane with (NH4)2OsCl6 (T > 300\u00b0C) resulted in the formation of an osmium(IV)-imidazoline complex.
\r\n\r\nAlso examined was the organometallic chemistry of osmium tetraoxide. Oxidation of low valent carbonyl complexes with the quinuclidine adduct of osmium tetraoxide resulted in attack of both the low valent metal and a carbonyl ligand with the formation of \u00b5-CO2 mixed-valent complexes. The surprising stability of this new type of CO2 complex is kinetic in origin as den1onstrated by the chemistry of a series of compounds. Decomposition with loss of CO2 was observed for more labile metal complexes. In the absence of nitrogenous bases, oxidation of Ru(CO)3(PPh3)2 with osmium tetraoxide resulted in the formation of what is believed to be a tetranuclear complex. The low valent metal center and a coordinated carbonyl ligand were oxidized.
\r\n\r\nOne other mode of reactivity was discovered. Oxidative addition of osmium tetraoxide to Pt(PPh3)2(C2H4) displaced the ethylene ligand with the formation of a \u00b5-oxo bridged tetranuclear complex. These and other potential modes of OsO4 reactivity with organometallic and inorganic complexes are discussed.
", "doi": "10.7907/s19j-2033", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:5324", "collection": "thesis", "collection_id": "5324", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10232009-095454256", "primary_object_url": { "basename": "Low_jj_1985.pdf", "content": "final", "filesize": 7245483, "license": "other", "mime_type": "application/pdf", "url": "/5324/1/Low_jj_1985.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Theoretical Studies of Oxidative Addition and Reductive Elimination", "author": [ { "family_name": "Low", "given_name": "John James", "orcid": "0000-0001-6598-5347", "clpid": "Low-John-James" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Chapter 1: Ab initio calculations (Hartree-Fock, generalized valence bond, and configuration interaction), utilizing relativistic core potentials, have been used to follow the oxidative addition of H2 to Pt(PH3)2. We find an activation barrier of 2.3 kcal/mol and an exothermicity of 15.9 kcal/mol. From examination of the geometries and wavefunctions, we find that up to the transition state the H-H bond is still intact. The role of the Pt s1d9 and d10 states in oxidative addition is described, and the effects of including electronic correlation are discussed. The implications for reductive elimination of the dimethyl and hydridomethyl complexes are also discussed.
\r\n\r\nChapter 2: Ab initio calculations have been carried out on MR2 complexes (where M = Pd or Pt and R = H or CH3) to model concerted reductive coupling from MR2L2 complexes (where L is a substituted phosphine). The results of these calculations support the following two conclusions. (1) The differences in the driving force for reductive elimination from Pd(II) and Pt(II) complexes with the same R groups is very close (0-4 kcal/mol) to the difference in the s1d9-d10 state splittings of these elements (32 kcal/mol). Thus reductive elimination is exothermic from Pd complexes (since Pd prefers d10) and endothermic from Pt complexes (since Pt prefers s1d9), where the metal product is in its d10 state. This supports the conclusion, derived from qualitative considerations of generalized valence bond wavefunctions, that Pt(II) and Pd(II) complexes have their metal atoms in a s1d9 configuration and the metal atoms in Pt(0) and Pd(0) complexes are in a d10 configuration. (2) The activation barriers for C-C coupling are approximately twice that for C-H coupling. There are essentially no barriers for processes involving H-H bonds. The origin of this trend is the directionality of the methyl sp3 orbital, which destabilizes the transition state for the case where an M-C bond is being converted to a C-C or C-H bond. Conversely, the spherical H 1s is orbital can form multicenter bonds easily, allowing it to break M-H bonds while forming an H-H bond and leading to low intrinsic barriers. These results are consistent with the experimentally observed trends.
\r\n\r\nChapter 3: Ab initio calculations were carried out on Pt(CH3)2(Cl)2(PH3)2 and on various Mt(R1)(R2)(PH3)2 complexes (where Mt = Pd or Pt; R1, R2 = H or CH3) in order to elucidate the differences in reductive H-C and C-C coupling from Pd(II), Pt(II), and Pt(IV) complexes. These studies explain why (1) reductive C-C coupling is facile for Pd(II), favorable for Pt(IV), and unobserved for Pt(II) systems, while (2) reductive H-C coupling is facile for Pt(II) and Pd(II) systems, and (3) oxidative addition is favorable only for addition of H2 to Pt(0) systems.
\r\n\r\nChapter 4: Ab initio calculations were carried out on CHx and NHx molecular fragments on small clusters of Ni atoms (Ni13 and Ni14), as a model for chemisorption on the Ni(100) surface. The results presented here show that these species make strong \u03c0 bonds to the surface which cause methylidyne and imidogen to be the most stable CHx and NHx, species on this surface. The results have also been used to estimate \u2206H0f for various intermedates important for methanation and ammonia decomposition on Ni surfaces.
", "doi": "10.7907/XR1N-CM33", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:6819", "collection": "thesis", "collection_id": "6819", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02132012-111043915", "type": "thesis", "title": "The Production and Characterization of an Intense Hyperthermal Beam of H\u2083 Molecules and of H Atoms", "author": [ { "family_name": "Garvey", "given_name": "James F.", "clpid": "Garvey-James-F" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The simplest bimolecular reaction involving neutral reagents is the reaction
\r\n\r\nH + H2 \u2192 H2 + H.
\r\n\r\nThis system, because of its simplicity and fundamental significance in chemical dynamics, has been the subject of extensive accurate ab initio theoretical quantum mechanical calculations and the results obtained have been used to test approximate theories of reaction dynamics. However, this system has proved difficult to study experimentally due to its high activation barrier (~ .33 eV) and its small reactive cross section (~ 1 x 10-16 cm2. Because of these factors, state-to-state reaction dynamics have only become feasible recently.
\r\n\r\nIn order to study this reaction in a crossed molecular beam experiment, a means of generating an intense beam of H atoms is essential. This thesis documents the design and operation of a hydrogen arc discharge for generating such a beam. The method consists of using a high power arc discharge to create a high temperature (~ 12,000 K) plasma in which H2 molecules can be dissociated into atoms. By using an arc source of the type developed by Kunth, a stable, intense, hyperthermal H atom beam has been successfully produced. Section 2 of this thesis discusses the design and operation of the apparatus and Section 3 of the thesis discusses the characterization of the hydrogen atoms within the beam. The laboratory energy distribution function of these atoms was determined approximately, and spans the range from 0.5 eV to about 12 eV. The total intensity of this beam is of the order of ~1022 atoms/sterad/sec. With such an intense and energetic beam, a wealth of chemical dynamical experiments may now become feasible.
\r\n\r\nIn the course of developing this intense beam of hydrogen atoms, the source was found to also produce metastable H3 molecules. This is the first direct, unambiguous observation of such a specie in a molecular beam, and is discussed in Section 4. Translational energy analysis of this H3 molecule indicates an energy distribution similar to that of the H atoms, suggesting that the lifetime of H3 is of the order of 40 \u00b5sec or longer. We also observed emission spectra from the Rydberg states of H3 identified previously by Herzberg. This is spectroscopic evidence for the presence of this neutral molecule in our beam. The only know state of H3 capable of having the long lifetime observed is 2p 2A\"2, the second excited state of this species.
\r\n\r\nIn addition, we detected this molecule by a variety of other independent techniques. It has long been known that alkali metal atoms with low ionization potential will ionize upon collision with a metal surface having a high work function. The 2p 2A\"2 state of H3 has an IP of ~ 3.7 eV and is expected to behave in a similar way. As a result, surface ionization of metastable 3 has been observed for for a variety of metals and is reported in this thesis. From that low IP one would also expect that the metastable H3 should be photoionizable using an appropriate light source. In this thesis we report the generation of H+3 through irradiation of the beam with the light from a high intensity mercury lamp. Lastly, since the metastable H3 is in a Rydberg state, it would be expected to exhibit a large total scattering cross section due to the diffuse nature of the Rydberg orbital. Such cross sections were measured by the attenuation of the H3 beam as it passed through a gas cell.
\r\n\r\nSection 5 describes the first observation of the electronic spectrum of WH. This emission spectrum was due to WH formed by the presence of the tungsten anode and cathode which are heated too close to its melting point by the arc discharge. Analysis of this spectrum has given rotational constants and bond distances for the electronic states of the mono-hydride involved in the observed transisiton. Due to relativistic terms in the potential, the theoretical calculation of WH has proved difficult to date. Recently a reliable potential for W has been generated such that our experimental bond distances will provide an important empirical check for any further theoretical calculations performed on this system. Likewise, the arc source may be employed in the future as a means of generating new metal hydride emission spectra.
\r\n\r\nAppendix A of the thesis details the design and construction of the inhomogeneous magnet to serve in the future as a velocity selector for the hyperthermal hydrogen beam in our crossed beam experiment. Using such a Stern-Gerlach magnet as a velocity selector, the dynamics of the H + H2 reaction can be probed as a function of translational energy of the reactants. Appendix B grew out of an interesting Ch 227 project and will now become a theoretical paper. Exact quantum mechanical calculations of the collinear reaction Be + FH (\u03bd = 0, 1) have been performed and the effects of reagent translational and vibrational excitation on reaction probabilities and product state distributions are examined. These quantum mechanical results are compared with those of quasi-classical trajectory calculations reported previously.
", "doi": "10.7907/r4n1-8762", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:6819", "collection": "thesis", "collection_id": "6819", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02132012-111043915", "type": "thesis", "title": "The Production and Characterization of an Intense Hyperthermal Beam of H\u2083 Molecules and of H Atoms", "author": [ { "family_name": "Garvey", "given_name": "James F.", "clpid": "Garvey-James-F" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The simplest bimolecular reaction involving neutral reagents is the reaction
\r\n\r\nH + H2 \u2192 H2 + H.
\r\n\r\nThis system, because of its simplicity and fundamental significance in chemical dynamics, has been the subject of extensive accurate ab initio theoretical quantum mechanical calculations and the results obtained have been used to test approximate theories of reaction dynamics. However, this system has proved difficult to study experimentally due to its high activation barrier (~ .33 eV) and its small reactive cross section (~ 1 x 10-16 cm2. Because of these factors, state-to-state reaction dynamics have only become feasible recently.
\r\n\r\nIn order to study this reaction in a crossed molecular beam experiment, a means of generating an intense beam of H atoms is essential. This thesis documents the design and operation of a hydrogen arc discharge for generating such a beam. The method consists of using a high power arc discharge to create a high temperature (~ 12,000 K) plasma in which H2 molecules can be dissociated into atoms. By using an arc source of the type developed by Kunth, a stable, intense, hyperthermal H atom beam has been successfully produced. Section 2 of this thesis discusses the design and operation of the apparatus and Section 3 of the thesis discusses the characterization of the hydrogen atoms within the beam. The laboratory energy distribution function of these atoms was determined approximately, and spans the range from 0.5 eV to about 12 eV. The total intensity of this beam is of the order of ~1022 atoms/sterad/sec. With such an intense and energetic beam, a wealth of chemical dynamical experiments may now become feasible.
\r\n\r\nIn the course of developing this intense beam of hydrogen atoms, the source was found to also produce metastable H3 molecules. This is the first direct, unambiguous observation of such a specie in a molecular beam, and is discussed in Section 4. Translational energy analysis of this H3 molecule indicates an energy distribution similar to that of the H atoms, suggesting that the lifetime of H3 is of the order of 40 \u00b5sec or longer. We also observed emission spectra from the Rydberg states of H3 identified previously by Herzberg. This is spectroscopic evidence for the presence of this neutral molecule in our beam. The only know state of H3 capable of having the long lifetime observed is 2p 2A\"2, the second excited state of this species.
\r\n\r\nIn addition, we detected this molecule by a variety of other independent techniques. It has long been known that alkali metal atoms with low ionization potential will ionize upon collision with a metal surface having a high work function. The 2p 2A\"2 state of H3 has an IP of ~ 3.7 eV and is expected to behave in a similar way. As a result, surface ionization of metastable 3 has been observed for for a variety of metals and is reported in this thesis. From that low IP one would also expect that the metastable H3 should be photoionizable using an appropriate light source. In this thesis we report the generation of H+3 through irradiation of the beam with the light from a high intensity mercury lamp. Lastly, since the metastable H3 is in a Rydberg state, it would be expected to exhibit a large total scattering cross section due to the diffuse nature of the Rydberg orbital. Such cross sections were measured by the attenuation of the H3 beam as it passed through a gas cell.
\r\n\r\nSection 5 describes the first observation of the electronic spectrum of WH. This emission spectrum was due to WH formed by the presence of the tungsten anode and cathode which are heated too close to its melting point by the arc discharge. Analysis of this spectrum has given rotational constants and bond distances for the electronic states of the mono-hydride involved in the observed transisiton. Due to relativistic terms in the potential, the theoretical calculation of WH has proved difficult to date. Recently a reliable potential for W has been generated such that our experimental bond distances will provide an important empirical check for any further theoretical calculations performed on this system. Likewise, the arc source may be employed in the future as a means of generating new metal hydride emission spectra.
\r\n\r\nAppendix A of the thesis details the design and construction of the inhomogeneous magnet to serve in the future as a velocity selector for the hyperthermal hydrogen beam in our crossed beam experiment. Using such a Stern-Gerlach magnet as a velocity selector, the dynamics of the H + H2 reaction can be probed as a function of translational energy of the reactants. Appendix B grew out of an interesting Ch 227 project and will now become a theoretical paper. Exact quantum mechanical calculations of the collinear reaction Be + FH (\u03bd = 0, 1) have been performed and the effects of reagent translational and vibrational excitation on reaction probabilities and product state distributions are examined. These quantum mechanical results are compared with those of quasi-classical trajectory calculations reported previously.
", "doi": "10.7907/r4n1-8762", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:751", "collection": "thesis", "collection_id": "751", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02252004-105813", "primary_object_url": { "basename": "gurer_c_1984.pdf", "content": "final", "filesize": 2554329, "license": "other", "mime_type": "application/pdf", "url": "/751/1/gurer_c_1984.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Time Dependent and Equilibrium Stress-Strain Behavior of Rubbers in Moderately Large Deformations", "author": [ { "family_name": "Gurer", "given_name": "Cigdem", "clpid": "Gurer-Cigdem" } ], "thesis_advisor": [ { "family_name": "Leal", "given_name": "L. Gary", "clpid": "Leal-L-G" } ], "thesis_committee": [ { "family_name": "Tschoegl", "given_name": "Nicholas W.", "clpid": "Tschoegl-N-W" }, { "family_name": "Stephanopoulos", "given_name": "Gregory N.", "clpid": "Stephanopoulos-G-N" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Leal", "given_name": "L. Gary", "clpid": "Leal-L-G" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this work, time dependent and equilibrium stress-strain properties of elastomeric networks are investigated for moderately large deformation. A two network potential is proposed, which constitutively describes stress-strain behavior at elastic equilibrium. The potential is applied to time dependent deformations thorough a molecular model.
\r\n", "doi": "10.7907/e0xe-8w83", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:781", "collection": "thesis", "collection_id": "781", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02272006-082939", "primary_object_url": { "basename": "Winkler_jr_1984.pdf", "content": "final", "filesize": 5584065, "license": "other", "mime_type": "application/pdf", "url": "/781/1/Winkler_jr_1984.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Spectroscopy and Photochemistry of Metal-Oxo Complexes", "author": [ { "family_name": "Winkler", "given_name": "Jay Richmond", "orcid": "0000-0002-4453-9716", "clpid": "Winkler-Jay-Richmond" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Anson", "given_name": "Fred C.", "clpid": "Anson-F-C" }, { "family_name": "Collins", "given_name": "Terrence J.", "clpid": "Collins-T-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Electronic spectroscopic, photophysical, and photochemical investigations of two types of metal-oxo complexes are described. The electronic absorption spectra of various molybdenyl ions (MoO3+ were measured in crystals and solutions. These spectra clearly support 2B1(x2-y2) \u2190 2B2(xy) and 2E(xz, yz) \u2190 2B2(xy) assignments for the two weak bands near 25,000 and 14,000 cm-1, respectively, in these molecules. A Franck-Condon analysis of the 2B1 \u2190 2B2 band in the 5 K single crystal absorption spectrum of (Ph4As)MoOCl4 indicated a 0.07(1) \u00c5 elongation of the metal-chloride bond in the excited state. Crystalline (Ph4As)MoOCl4 luminesces from the lower energy component of a split 2E(xz, yz) state with a lifetime of 160 ns at 300 K, increasing to 1.4 \u00b5s at 5 K. No luminescence was detected from any molybdenyl ion in solution.
\r\n\r\nThe electronic absorption and emission spectra of trans-ReO2L4z (L = CN-, z = 3-; L = 1/2(ethylenediamine), z = +; L = pyridine, z = +; L = 4-picoline, z = +; L = 4-t-butylpyridine, z = +) were also measured in crystals and solutions. The lowest energy absorption bands are assigned to components of a split 3Eg[(eg)1(b2g)1] state (ground state 1Ag1g[(b2g)2]). Emission from at least two of these components was identified in the cyanide and pyridine complexes and only the ethylenediamine complex failed to luminesce. Franck-Condon analyses of the emission spectra indicated ca. 0.1 \u00c5 elongations of each Re-O bond in the 3Eg excited states. The lifetime of the 3Eg state varies from 10 to 300 \u00b5s in crystals and is ca. 10 \u00b5s for trans-ReO2L4z species in aprotic solvents. Protons efficiently quench the luminescence of these molecules. Experiments directed toward photoinduced oxygen atom transfer chemistry are also described.
\r\n", "doi": "10.7907/DE5E-2Y69", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:5327", "collection": "thesis", "collection_id": "5327", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10232009-150307132", "primary_object_url": { "basename": "Goodgame_mm_1984.pdf", "content": "final", "filesize": 6367738, "license": "other", "mime_type": "application/pdf", "url": "/5327/1/Goodgame_mm_1984.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Exchange Forces in Transition-Metal Bonding", "author": [ { "family_name": "Goodgame", "given_name": "Marvin Mark", "clpid": "Goodgame-Marvin-Mark" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We have examined multiple bonds (\u03c3, \u03c0, and \u03b4) to transition metals and find that intra-atomic exchange forces on these metals are crucial for correct prediction of ground states and that a proper description of these terms is required for a quantitative understanding of bond energies.
\r\n\r\nOur calculations on models for bridged Fe porphyrin dimers show that intra-atomic exchange forces on the Fe's are critical to the explanation for the dramatic differences in the Fe-Fe coupling for \u00b5-oxo and \u00b5-nitrido bridged Fe porphyrin dimers. The qualitative bonding concepts obtained are used to predict properties of the \u00b5-carbido bridged Fe porphyrin dimer.
\r\n\r\nIn most cases, the interactions responsible for bonding lead to antifer'romagnetic coupling between the d orbitals localized on adjacent centers, resulting in overall low-spin couplings. However, some extended metal systems (eg. metallic Ni) lead to net ferromagnetic interactions between d orbitals localized on different centers. In order to elucidate these effects, we have examined the direct and indirect d-d couplings in the Ni4 cluster as a function of bond distance. We find that ferromagnetic coupling dominates in a region of bond distance around the bulk Ni value of 2.5 \u00c5 with antiferromagnetic coupling dominating for short R (by 2.0 \u00c5) and for long R (by 3.5 \u00c5). The dominant interactions responsible for ferromagnetic coupling involve spin polarization of the conduction band (s-like), supporting a model for ferromagnetism in bulk metallic systems very similar to the Ruderman-Kittel model for magnetic impurities.
\r\n\r\nThe dimers Cr2 and Mo2 provide the most dramatic illustration of the importance of exchange forces in bonding. With six unpaired electrons on each atom, there is the potential for up to six covalent bonds. However, formation of d-d covalent bonds requires a concomitant loss in intra-atomic d-d exchange energy. The net result is a double well where the long-R minimum (3 \u00c5 is dominated by s-s pairing (no loss of intra-atomic d-d terms) while the short-R minimum (1.7 to 1.9 \u00c5) involves a strong quintuple bond of d orbitals plus an antibonding s-s interaction. To properly handle the intra-atomic exchange terms during this transition from long R with local high-spin coupling to small R with dominant singlet pairing within bonding pairs presents a formidable challenge to ab initio computation. To carry out such studies, we have extended the GVB and related approaches of ab initio calculations and have also developed a simple approximate method of including the electron correlation missing in GVB wavefunctions that provides a quantitatively accurate description of these systems.
\r\n\r\nThe effects studied here should be of comparable importance for multiple bonds involving transition metals, lanthanides, and actinides bonding to each other and to such ligands as CR2, CR, O, N, and NR. Correlation terms beyond GVB are most important for the least electronegative ligands. Thus, the proper treatment of intra-atomic exchange and of interatomic d-d coupling should be of considerable importance in studies of heterogeneous and homogeneous catalytic systems.
", "doi": "10.7907/xs72-nm31", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:5331", "collection": "thesis", "collection_id": "5331", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10262009-151524640", "primary_object_url": { "basename": "McElweeWhite_la_1984.pdf", "content": "final", "filesize": 3310412, "license": "other", "mime_type": "application/pdf", "url": "/5331/1/McElweeWhite_la_1984.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Theoretical and Experimental Assessment of the Viability of 1,4,6,9-Spiro[4.4]Nonatetrayl as a Reactive Intermediate", "author": [ { "family_name": "McElwee-White", "given_name": "Lisa Ann", "clpid": "McElwee-White-Lisa-Ann" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "thesis_committee": [ { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Qualitative molecular orbital (MO) theory predicts that 1,4,6,9-spiro[4.4]nonatetrayl (7) should be stabilized via spiroconjugative interaction of the four radical p orbitals. In addition to this thermodynamic stabilization, energetic barriers are predicted for closure to either of the closed shell forms.
\r\n\r\nThe electronic structure of 7 has been investigated using ab initio electronic structure theory. The spiro-conjugative interaction of the four radical centers is evidenced by a large orbital splitting. However, spiroconjugation does not confer upon the structure the electronic properties of a biradical, contrary to qualitative MO considerations. Structure 7 possesses the six, low-lying (covalent) states that characterize a tetraradical. Spiroconjugation does strongly influence the relative energies of these six states, and does lead to a small but significant stabilization of the molecule. Possible modes of ring closure and closed shell isomers of 7 are also discussed.
\r\n\r\nDirect photolysis of spiro[bis(2,3-diazabicyclo[2.2.1]-hept-2-ene)-7,7'] (17) leads to loss of a single equivalent of N2 and ring closure of the resulting biradical to 2,3-diazabicyclo[2.2.11hept-2-ene-7,5'-spirobicyclo[2.1.0]-pentane (19). Generation of the triplet biradical by sensitized photolysis results in a competition between ring closure to 19 and a 1,2-alkyl shift to ,9-diazatricyclo-[5.2.2.02,6)]undeca-2,8-diene (23). While direct photolysis and thermolysis of 19 yield primarily ring closure product, sensitized photolysis leads to a series of biradical-to-biradical rearrangements that ultimately produce 2,3-divinyl-cyclopentene (24). Deuterium labeling studies indicate competing mechanistic pathways for this reaction. Rationalization of the label distribution requires one of two unprecedented processes: frontside radical attack on a C-C bond or intermediacy of 1,4,6,9-spiro[4.4]nonatetrayl.
", "doi": "10.7907/nytz-bf09", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:276", "collection": "thesis", "collection_id": "276", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01222007-152908", "primary_object_url": { "basename": "Zur_a_1984.pdf", "content": "final", "filesize": 17755605, "license": "other", "mime_type": "application/pdf", "url": "/276/1/Zur_a_1984.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theoretical Investigations of Solid Interfaces: 1. The Position of the Fermi Level at a Metal-Semiconductor Interface. 2. Geometric Lattice Match and Its Application to Heteroepitaxy. 3. Ab-Initio Calculation of the Elastic Properties of Silicon, Using Small Clusters", "author": [ { "family_name": "Zur", "given_name": "Amikam", "clpid": "Zur-Amikam" } ], "thesis_advisor": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The work presented in this thesis is concerned with theoretical investigations of the electronic, geometric, and elastic properties of solid interfaces. The interfacial electronic property studied was the effect of doping on the Fermi-level position at a metal-semiconductor interface. Geometric lattice match in heteroepitaxy was studied using a novel method of systematically determining every possible orientation of the two crystals which would result in lattice match at the interface between the two crystals. Finally, the parameters of several elastic models that can be used in calculating the elastic properties of silicon interfaces were computed, using ab-initio quantum-chemistry methods. The predictions of these models to bulk elastic properties were compared to experimental results to test the models.
\r\n\r\n(1) Chapter 1 presents the effect of semiconductor doping on the Fermi-level position at a metal-semiconductor interface. A model based on the concept of a dipole layer was used. The number of chargeable defects at the interface required to pin the Fermi level was determined in the limits of thin and thick metallic coverages. The calculations included the metal response to large charge transfer at the interface, using a jellium model for the metal.
\r\n\r\nThe major findings of this chapter are:
\r\n\r\n\u2022 It takes about 1014defects \u2022 cm-2 to pin the Fermi level in a bulk metal-semiconductor interface, but only about 1012defects \u2022 cm-2 during the initial stages of metallization.
\r\n\r\n\u2022 The Fermi-level position at the metal-semiconductor interface may be very different for n- and p- type semiconductors during the initial steps of metallization. These Fermi-level positions seem to stabilize after the creation of about 1012defects \u2022 cm-2 (which usually corresponds to less than a monolayer of metallic coverage). However, as the metallization proceeds, the two Fermi-level positions on n- and p-type semiconductors should merge to within 0.05 eV at the interface (for doping not exceeding 1017 cm-3).
\r\n\r\n\u2022 During the initial steps of metallization most of the carriers required to charge the defects come from the semiconductor. When the metallic overlayer is fully grown, it is the metal that contributes most of the charge.
\r\n\r\n\u2022 The potential difference between the metal surface and bulk, in the jellium model, changes quadratically with charge removed or added to the surface. For a charge density of 1014 electrons/cm2 removed from the surface, the slope of the potential vs. charge removed is of the order of 1V per 1014e \u2022 cm-2 or less.
\r\n\r\n(2) In Chapter 2 the relevance of lattice mismatch to heteroepitaxiall growth was investigated. A novel method to determine all the possible lattice matches between any two given materials, with any given crystal structure, has been developed. This method allows for an arbitrary periodic reconstruction of the interface. Such reconstruction results in two-dimensional superlattices on both sides of the interface, that have to be similar to each other. The input parameters to these calculations, besides the crystal structure of both materials, are the upper bound on the superlattice unit cell areas, and the maximum allowed mismatch in unit cell dimensions. This method was applied to study known heteroepitaxial interfaces of CdTe on GaAs, CdTe on sapphire, silicon on sapphire, and transition-metal silicides on silicon, to determine the relevance of lattice match in heteroepitaxy. For the last class of materials, namely, silicides on silicon, we list many possible lattice matches, including many that have not been grown so far.
\r\n\r\nThe principal results described in Chapter 2 are:
\r\n\r\n\u2022 A good lattice match is not necessary for epitaxial growth of a single crystal on another.
\r\n\r\n\u2022 In those cases checked in which the epitaxial layer is metallic (silicide on silicon) and a single crystal, there is a good lattice match (bulk mismatch of 2.5% or less).
\r\n\r\n\u2022 Even a polycrystalline epitaxial layer may have some epitaxial relations, that is, some preferred orientations of the crystallites with respect to the substrate. In this case mismatches of up to 15% may be present; this means that the lattice match requirement is probably irrelevant.
\r\n\r\n(3) In Chapter 3 the elastic properties of silicon are calculated using four models. The parameters of these models were calculated from the elastic constants of a small silicon cluster (Si5H12) using ab-initio quantum-chemistry methods. The calculated elastic properties were compared to experimental results to assess the quality of the models.
\r\n\r\nThe main findings are:
\r\n\r\n\u2022 All four different models yield a phonon-band structure which is qualitatively correct but not very accurate numerically.
\r\n\r\n\u2022 The deviations of the model predictions from experimental results were attributed to the models and not to the quantum-chemistry methods used to obtain their parameters.
\r\n\r\n\u2022 The LA branch of the phonon-band structure agreed very well with experiment in all the different models used.
\r\n\r\n\u2022 The TA branch of the phonon-band structure was in poor agreement with experiment in all the four models; in particular, the slopes of the TA branch near the \u0393 point (which determine the elastic constants c12 and c44) were inaccurate.
\r\n\r\n\u2022 The accuracy of the calculated optical phonons varied among the four models.
\r\n\r\n\u2022 Elastic properties associated with bond stretching were calculated much more accurately than elastic properties associated with bond bending.
", "doi": "10.7907/w8vp-2g07", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:751", "collection": "thesis", "collection_id": "751", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02252004-105813", "primary_object_url": { "basename": "gurer_c_1984.pdf", "content": "final", "filesize": 2554329, "license": "other", "mime_type": "application/pdf", "url": "/751/1/gurer_c_1984.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Time Dependent and Equilibrium Stress-Strain Behavior of Rubbers in Moderately Large Deformations", "author": [ { "family_name": "Gurer", "given_name": "Cigdem", "clpid": "Gurer-Cigdem" } ], "thesis_advisor": [ { "family_name": "Leal", "given_name": "L. Gary", "clpid": "Leal-L-G" } ], "thesis_committee": [ { "family_name": "Tschoegl", "given_name": "Nicholas W.", "clpid": "Tschoegl-N-W" }, { "family_name": "Stephanopoulos", "given_name": "Gregory N.", "clpid": "Stephanopoulos-G-N" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Leal", "given_name": "L. Gary", "clpid": "Leal-L-G" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In this work, time dependent and equilibrium stress-strain properties of elastomeric networks are investigated for moderately large deformation. A two network potential is proposed, which constitutively describes stress-strain behavior at elastic equilibrium. The potential is applied to time dependent deformations thorough a molecular model.
\r\n", "doi": "10.7907/e0xe-8w83", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:11296", "collection": "thesis", "collection_id": "11296", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12072018-114316546", "type": "thesis", "title": "The Total Synthesis of the Enantiomer of Lasalocid A", "author": [ { "family_name": "Fitzsimmons", "given_name": "Brian Joseph", "clpid": "Fitzsimmons-Brian-Jopseph" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Ireland", "given_name": "Robert E.", "clpid": "Ireland-R-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Anson", "given_name": "Fred C.", "clpid": "Anson-F-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A convergent total synthesis of the enantiomer of the\r\nnaturally occurring polyether antibiotic Lasalocid A (X-537A) and preliminary results of the biological testing of this compound are reported.
\r\n", "doi": "10.7907/w5gn-5650", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:11296", "collection": "thesis", "collection_id": "11296", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12072018-114316546", "type": "thesis", "title": "The Total Synthesis of the Enantiomer of Lasalocid A", "author": [ { "family_name": "Fitzsimmons", "given_name": "Brian Joseph", "clpid": "Fitzsimmons-Brian-Jopseph" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Ireland", "given_name": "Robert E.", "clpid": "Ireland-R-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Anson", "given_name": "Fred C.", "clpid": "Anson-F-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A convergent total synthesis of the enantiomer of the\r\nnaturally occurring polyether antibiotic Lasalocid A (X-537A) and preliminary results of the biological testing of this compound are reported.
\r\n", "doi": "10.7907/w5gn-5650", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:4440", "collection": "thesis", "collection_id": "4440", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11072005-153348", "primary_object_url": { "basename": "Baxter_dv_1984.pdf", "content": "final", "filesize": 4083120, "license": "other", "mime_type": "application/pdf", "url": "/4440/1/Baxter_dv_1984.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "EXAFS Studies of La-Ga Metallic Glasses", "author": [ { "family_name": "Baxter", "given_name": "David Verge", "orcid": "0000-0003-2812-0904", "clpid": "Baxter-David-Verge" } ], "thesis_advisor": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Tombrello", "given_name": "Thomas A.", "clpid": "Tombrello-T-A" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Extended X-ray Absorption Fine Structure ( EXAFS ) measurements have been performed on the Ga edge of several La-Ga metallic glasses, using an in-lab spectrometer. The results obtained are compared with earlier experiments on the same materials where X-ray diffraction and isomorphous substitution were used to determine partial pair correlation functions. This is, therefore, a rigorous test of the EXAFS technique when applied to strongly disordered systems, such as metallic glasses. It is found that the glass La80Ga20 has a comparatively simple local Ga environment and that the EXAFS for this glass can be described very well with a single asymmetric shell of La atoms surrounding the Ga. As the Ga concentration is increased, however, it is found that the local Ga environment becomes more complicated. Traditional methods of EXAFS analysis, based on nonlinear least squares curve fitting, are then unable to distinguish between several different possible local Ga environments. Finally a new, essentially non-parametric, method of analyzing EXAFS data is discussed and tests are conducted to demonstrate the circumstances under which this new method could prove advantageous over the more traditional methods.
\r\n", "doi": "10.7907/NHED-5T47", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:127", "collection": "thesis", "collection_id": "127", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01112007-111123", "primary_object_url": { "basename": "Mailhiot_c_1984.pdf", "content": "final", "filesize": 10061455, "license": "other", "mime_type": "application/pdf", "url": "/127/1/Mailhiot_c_1984.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Theoretical Investigations of Electron States in Small-Scale Semiconductor Structures", "author": [ { "family_name": "Mailhiot", "given_name": "Christian", "clpid": "Mailhiot-Christian" } ], "thesis_advisor": [ { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The work presented here is concerned with theoretical investigations of electronic states in small-scale semiconductor structures. This last term encompasses layered structures made up of two dissimilar, but lattice-matched, semiconductors. The semiconductors of interest here are mostly the tetrahedrally bonded zincblende semiconductors GaAs and the alloy Ga1-xAlxAs. The thesis is subdivided in three major chapters. The first chapter is concerned with electrical doping of Ga1-xAlxAs-GaAs-Ga1-xAlxAs quantum well structures. The second chapter addresses the question of the transport of electrons through GaAs-Ga1-xAlxAs double heterojunction structures. In the final chapter, we develop a theory of the electronic structure of semiconductor superlattices particularly suitable for the study of the optical properties and the recombination mechanisms.
\r\n\r\nIn Chapter 2, we study the energy spectrum of ground state and excited states of shallow donor states in Ga1-xAlxAs-GaAs-Ga1-xAlxAs quantum well structures. In this system, an impurity atom is located within a GaAs slab of finite thickness. The GaAs slab is, in turn, centered between two semi-infinite layers of Ga1-xAlxAs. We use a variational method to solve the effective mass equation for the donor envelope function. We study the variation of the binding energy as a function of
\r\n\r\n\u2218 thickness of the GaAs containing the impurity,
\r\n \r\n\u2218 alloy composition x in Ga1-xAlxAs, and
\r\n \r\n\u2218 position of the impurity in the GaAs slab.
\r\n \r\nTwo cases are treated:
\r\n\r\n(i) In the first case we assume that the potential well is formed by finite conduction band offsets at the GaAs-Ga1-xAlxAs interface (imperfect confinement).
\r\n\r\n(ii) In the second case we consider infinite confining potential at the GaAs-Ga1-xAlxAs interface (perfect confinement).
\r\n\r\nThe major result of this study is that the binding energy of the donor ground state is considerably modified as the thickness of the GaAs slab containing the impurity is varied. At large GaAs slab thicknesses, the binding energy is that of shallow donors in bulk GaAs. At small GaAs slab thicknesses, the binding energy is that of shallow donors in bulk Ga1-xAlxAs for the case of imperfect confinement, but corresponds to the two-dimensional Coulomb limit in the case of perfect confinement. It is also found that the binding energy depends on the position of the impurity atom within the GaAs slab. Thus, we have a confinement-induced lifting of the Coulomb energy levels.
\r\n\r\nIn Chapter 3, we study the transport characteristics of electrons through GaAs-Ga1-xAlxAs-GaAs double heterojunction structures. In this system, a Ga1-xAlxAs slab of finite thickness is centered between two semi-infinite layers of GaAs. An electron is incoming from the GaAs onto the Ga1-xAlxAs barrier. Transport coefficients are calculated using the formalism of the complex-k energy band structure within the empirical tight-binding method. Transmission into states derived from different energy extrema of the GaAs lowest conduction band obtained. We consider both the (111) and the (100) GaAs-Ga1-xAlxAs interfaces. Transport coefficients are calculated as a function of
\r\n\r\n\u2218 GaAs conduction band minimum from which the electron state is derived,
\r\n \r\n\u2218 energy of the electron incoming on the Ga1-xAlxAs barrier,
\r\n \r\n\u2218 thickness of the Ga1-xAlxAs barrier, and
\r\n \r\n\u2218 alloy composition x in the Ga1-xAlxAs.
\r\n\r\nThe major result of the study is that states derived from different energy extrema of the GaAs lowest conduction band appear to couple weakly across the GaAs-Ga1-xAlxAs interface. Thus, if we consider the (111) interface, is seems possible to reflect the L-point component of the current while transmitting the \u0393-point component. There exists two regimes of transport: tunneling transport and propagating transport. In the case where the energy incoming electron is below the energy barrier, transmission is small and the transport occurs via a tunneling process. However, in the case where the energy incoming electron is above the energy barrier, transmission is large and the transport occurs via a propagating process. Depending on the Ga1-xAlxAs slab thickness, it is possible to induce resonances whereby the transmission coefficient is unity.
\r\n\r\nIn Chapter 4, we develop a theoretical framework to investigate the electronic structure of semiconductor superlattices. The theoretical formulation is based on the k \u2022 p method derived from an accurate local pseudopotential method. The formalism developed is particularly well suited for the study of the optical properties and the investigation of the recombination mechanisms in semiconductor superlattices. Here again, we make extensive use of the complex-k energy band structure obtained via the k \u2022 p method. Realistic boundary conditions are imposed on the multi-component superlattice envelope function. From these boundary conditions, the energy spectrum of the superlattice is deduced. For the first time, we develop a scheme whereby the superlattice state function in both solids is expanded in terms of the same set of basis functions. By doing so, we relax the often used approximation that assumed that the basis functions are the same for all zincblende semiconductors.
", "doi": "10.7907/0470-nf89", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:12", "collection": "thesis", "collection_id": "12", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01032007-142600", "primary_object_url": { "basename": "Steigerwald_ml_1984.pdf", "content": "final", "filesize": 11811901, "license": "other", "mime_type": "application/pdf", "url": "/12/1/Steigerwald_ml_1984.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "2\u209b + 2\u209b Reactions at Transition Metals", "author": [ { "family_name": "Steigerwald", "given_name": "Michael Louis", "orcid": "0000-0001-6337-2707", "clpid": "Steigerwald-Michael-Louis" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A study of the suprafacial 2 + 2 reaction at transition metal centers is presented. It is demonstrated that this reaction is allowed and proceeds with a low activation energy if the reacting transition metal-to-substituent bond is covalent, nonpolar, and has a large component at transition nickel d-orbital character. These chains are evinced by examination of 2s + 2s reactions at M-H bonds. Those systems in which M can use d orbitals show lower barriers to the 2s + 2s reaction than those in which M cannot use d orbitals.
\r\n\r\nThe importance of the electronic structure of the metal-to-substituent bond is highlighted by a study of dichorotitanacyclopropane. This molecule, being a metallacyclopropane, can undergo 2s + 2s reactions which one unavailable to a simple olefin.
\r\n\r\nStudies concerning the importance of 2s + 2s reactivity in the organic chemistry of nickel, and in the Ziegler-Natta polymerization of simple olefins are presented.
\r\n\r\nIt is suggested that the principle of maximum bonding (the Woodward-Hoffmann rules) implies the conservation of transition metal covalency in low-energy catalytic cycles.
", "doi": "10.7907/S0HZ-TF05", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:3292", "collection": "thesis", "collection_id": "3292", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08312006-081008", "primary_object_url": { "basename": "Moody_dm_1983.pdf", "content": "final", "filesize": 4377047, "license": "other", "mime_type": "application/pdf", "url": "/3292/1/Moody_dm_1983.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Numerical Solution of the Superfluid Shock Jump Conditions. II. Experimental Investigation of the Liquid Helium II-Vapor Interface", "author": [ { "family_name": "Moody", "given_name": "Douglas Marion, Jr.", "clpid": "Moody-Douglas-Marion" } ], "thesis_advisor": [ { "family_name": "Goodstein", "given_name": "David L.", "clpid": "Goodstein-D-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Goodstein", "given_name": "David L.", "clpid": "Goodstein-D-L" }, { "family_name": "Liepmann", "given_name": "Hans Wolfgang", "clpid": "Liepmann-H-W" }, { "family_name": "Sturtevant", "given_name": "Bradford", "clpid": "Sturtevant-B" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Numerical Solution of the Superfluid Shock Jump Conditions
\r\n\r\nThe four fundamental conservation equations of superfluid mechanics may be integrated across a one-dimensional discontinuity (shock wave) propagating into undisturbed helium II to yield a set of four algebraic equations (jump conditions) which, when supplemented by thermodynamic state information, establish the equilibrium flow state behind the shock wave for a given wave speed and undisturbed flow state ahead of the shock. These jump conditions have been solved numerically for 19 points on the helium II p-T diagram with upstream Mach number as the independent parameter. Representative results of the calculations are presented for pressure shocks, temperature raising shocks, and temperature lowering shock. The results are compared to previous analytical approximate solutions to test the validity of those approximation. They are also compared to experimental data for shock waves in helium II as a means of testing the correctness of the full, nonlinear two-fluid equations.
\r\n\r\nExperimental Investigation of the Liquid Helium II-Vapor Interface
\r\n\r\nAn apparatus was designed and constructed to measure the linear reflection and transmission coefficients for weak second sound shocks impinging upon the liquid-vapor interface of helium II. The measured reflection coefficients reproduce the work of previous authors, giving values which are roughly 20% higher than those predicted by thermodynamic equilibrium theory. The transmitted pressure wave speed was measured, and was found to be sonic within the limits of experimental precision. Therefore strength could not be deduced from time of flight measurements. Direct amplitude measurements of this weak wave were prevented by the film which coats the sensors in the vapor. For these reasons, the attempted transmission coefficient measurements were unsuccessful.
\r\n", "doi": "10.7907/387M-V435", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:11786", "collection": "thesis", "collection_id": "11786", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-103344869", "primary_object_url": { "basename": "Duan_DC_1983.pdf", "content": "final", "filesize": 20555302, "license": "other", "mime_type": "application/pdf", "url": "/11786/1/Duan_DC_1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Evidence for a Stereospecific 1,2-Elimination Reaction in a 1,1-Diazene. Synthesis and Decomposition of [N-Phenyl-(Threo-(and Erythro)-2-Deuterio-1-Methylpropl)Amino]Nitrene", "author": [ { "family_name": "Duan", "given_name": "Daniel C.", "clpid": "Duan-Daniel-C" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Evans", "given_name": "David A.", "clpid": "Evans-David-A" }, { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "CHAPTER 1:
\r\n\r\nThe mechanism of the formal 1,2-elimination reaction of 1,1-diazenes to alkenes is examined. 'fue syntheses and decomposition of [N-phenyl-(1-methylpropyl)amino]nitrene (6), [N-phenyl(erythro-2-deuterio-1-methylpropyl)amino]nitrene (7) and [N-phenyl-(threo-2-deuterio-1-methylpropyl)amino]nitrene (8) are reported. Oxidation of 1-(1-methylpropyl)-1-phenylhydrazine (9) with nickel peroxide at 100\u00b0C affords 1-butene, trans-2-butene, cis-2-butene, butane and benzene in ratios of 0.59:0.30:0.097:0.005:1.00. Reaction of the corresponding benzenesulfonamide 10 with base at 100\u00b0C affords similar ratios. Oxidation of 1-(erythro-2-deuterio-1-methylpropyl)-1-phenylhydrazine (14) at 100\u00b0C affords 1-butene, trans-2-butene (100\u00b12% d1) and cis-2-butene (2.8\u00b12% d1), and butane in ratios of 0.67:0.30:0.03:0.004. Oxidation of 1-(threo-2-deuterio-1-methylpropyl)-1-phenylhydrazine (20) at 100\u00b0C affords 1-butene, trans-2-butene (1.8\u00b12% d1) and cis-2-butene (97.9\u00b12% d1) and butane in ratios of 0.77:0.11:0.11:0.009. Reaction of the corresponding benzenesulfonamides 15 and 21 with base at 100\u00b0C affords similar results. Primary kinetic isotope effects for 2-butene formation from the erythro and threo 1,1-diazene diastereomers were 3.5 and 3.4, respectively. The 1,1-diazene 1,2-elimination reaction studied here is a stereospecific cis elimination process.
\r\n\r\nCHAPTER 2:
\r\n\r\nAn attempt was made to observe chiral induction in a gas phase IR multiphoton photolysis using a circularly polarized output from a TEA CO2 laser. The molecule studied was trans-1,2-divinylcyclobutane (1) in the gas phase at 0.6 torr. Racemic samples were photolyzed at 977 cm-1 (=CHR bending) with 75 focused (0.8-0.9J) pulses. This resulted in about 33% conversion to 1,3-butadiene (2), 4-vinylcyclohexene (3) and 1.5-cyclooctadiene (4). A large number of samples were combined and the 1 (44mg) and 3 (6mg) were isolated by VPC. Neither showed optical activity.
\r\n\r\nCHAPTER 3:
\r\n\r\nThe possibility that triazolenitrenes (2) are involved in the photodecomposition of s-tetrazines (1) is considered. It was found that oxidation of 1-amino-2,5-diphenyl-1,3,4-triazole (5) in the presence of tetramethylethylene gave a high yield of triazolenitrene trapping product 6. Photolysis of 3,6-diphenyl-1,2,4,5-tetrazine (4) under these conditions failed to yield the adduct 6. Unsuccessful attempts were also made to prepare (2,5-di-tert-butyl-1,3,4-triazolidyl)nitrene (7) as a persistent species at low temperatures.
", "doi": "10.7907/zbfn-1t36", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:11788", "collection": "thesis", "collection_id": "11788", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-124939824", "primary_object_url": { "basename": "Ennis_MD_1983.pdf", "content": "final", "filesize": 82653053, "license": "other", "mime_type": "application/pdf", "url": "/11788/1/Ennis_MD_1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "I. Asymmetric Alkylation Reactions of Chiral Imide Enolates. II. Efforts Directed Toward the Total Synthesis of (+)-Macbecin I", "author": [ { "family_name": "Ennis", "given_name": "Michael Dalton", "clpid": "Ennis-Michael-Dalton" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Evans", "given_name": "David A.", "clpid": "Evans-David-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The preparation of chiral N-acyl oxazolidones 6 and 7 from readily available amino acid precursors is described. Reaction of the alkali metal enolates derived from these chiral imides with alkyl halides and acid chlorides exhibit high levels of kinetic diastereoselection. Chromatographic enrichment
\r\n\r\n[chemical structure; see abstract in scanned thesis for details]
\r\n\r\naffords alkylated and acylated products of \u2265 99:1 diastereomeric purity. Non-destructive cleavage of the chiral auxiliary is accomplished by a variety of means to afford optically active products.
\r\n\r\nThe use of chiral imides 6 and 7 in the synthesis of the ansa-antibiotic macbecin-I (1) is described. The synthesis makes use of the iterative application of highly stereoregulated aldol condensations of N-acyl oxazolidones for the construction of the ansa-bridge of 1. This project has culminated in the preparation of the advanced acyclic intermediate 46.
\r\n\r\n[Chemical structures; see abstract in scanned thesis for details.]
", "doi": "10.7907/pqm8-7286", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:1809", "collection": "thesis", "collection_id": "1809", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05152003-105639", "type": "thesis", "title": "Solid-State Proton Nuclear Magnetic Resonance Studies of Hydrogen Site Occupancies, Electronic Structure Properties, and Diffusion Behavior in Transition Metal Hydrides", "author": [ { "family_name": "Bowman", "given_name": "Robert Clark, Jr.", "orcid": "0000-0002-2114-1713", "clpid": "Bowman-Robert-Clark" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Rhim", "given_name": "Won-Kyu", "clpid": "Rhim-Won-Kyu" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Solid-state NMR techniques have been used to measure the proton lineshapes, Knight shifts, and relaxation times in several transition metal hydrides. The objective of these studies is to obtain a better understanding of the roles of host metal structure and substitutional alloying on the hydrogen site occupancy, the electronic structure properties, and diffusion mechanisms.
\r\n\r\nAn improved method for observing the rigid-lattice proton lineshapes and extracting the second moments has been developed. Comparisons of the experimental second moments for polycrystalline samples with the values calculated from Van Vleck formulas for nuclear dipolar interactions have indicated that only tetrahedral interstitial sites are occupied by the protons in TiHx, ZrHx, crystalline TiCuH0.94, Ti2CuH1.9, and Zr2PdHx (with x < 2) while both tetrahedral and octahedral sites can be occupied in amorphous a-TiCuH1.4, Ti2CuH2.6, and Zr2PdHx (x > 2).
\r\n\r\nThe proton Knight shifts and low-temperature spin-lattice relaxation times have been related to the local densities of electron states at the Fermi levels N(EF) in Ti1-yVyHx, TiCr1.8Hx, TiCr1.9Hx, TiCuHx, Ti2CuHx, ZrHx, and Zr2PdHx. The dominant conduction electron hyperfine interaction for protons is a transferred \"core-polarization\" of the paired hydrogen 1s electrons through spin exchange with the unpaired metal d electrons. The proton NMR parameters have confirmed that decreases in N(EF) through a Jahn-Teller type mechanism are associated with the temperature and composition dependent tetragonal distortions in Ti1-yVyH1.95 and ZrHx (where 1.75 \u2264 x \u2264 2.0). The proton NMR results are consistent with recent band theory calculations and photoemission spectra. Unusual N(EF) increases with hydrogen content, which are supported by independent magnetic susceptibility data, have been observed in TiCr1.8Hx, TiCr1.9Hx, and Ti2CuHx. The proton parameters suggest that significant differences in N(EF) for the crystalline and amorphous phases of TiCuHx and Zr2PdHx may reflect a smearing of energy levels in the disordered phases.
\r\n\r\nThe proton rotating-frame relaxation times for Ti1-yCuyHx indicate both crystal structure and hydrogen site occupancies greatly influence diffusion behavior. A significant enhancement in hydrogen mobility for amorphous a-TiCuH1.4 has been confirmed; but, short range order is probably retained in the structure of a-TiCuH1.4. Reductions in activation energies are observed when octahedral sites exist in the diffusion paths between tetrahedral sites.
", "doi": "10.7907/w68b-2750", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:8035", "collection": "thesis", "collection_id": "8035", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12022013-142422017", "type": "thesis", "title": "Synthesis and Characterization of 1,1-Di-Tert-Butyldiazene", "author": [ { "family_name": "McIntyre", "given_name": "Daniel Keith", "clpid": "McIntyre-Daniel-Keith" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The synthesis and direct observation of 1,1-di-tert-butyldiazene (16) at -127\u00b0C is described. The absorption spectrum of a red solution of 1,1-diazene 16 reveals a structured absorption band with \u03bbmax at 506 nm (Me2O, -125\u00b0C). The vibrational spacing in S1 is about 1200 cm-1. The excited state of 16 emits weakly with a single maximum at 715 nm observed in the fluorescence spectrum (Me2O:CD2Cl2, -196\u00b0C). The proton NMR spectrum of 16 occurs as a singlet at 1.41 ppm. Monitoring this NMR absorption at -940 \u00b1 2\u00b0C shows that 1,1-diazene 16 decomposes with a first-order rate of 1.8 x 10-3 sec-1 to form isobutane, isobutylene and hexarnethylethane. This rate is 108 and 1034 times faster than the thermal decomposition of the corresponding cis and trans 1,2-di-tert-butyldiazene isomers. The free energy of activation for decomposition of 1,1-diazene 16 is found to be 12.5 \u00b1 0.2 kcal/mol at -94\u00b0C which is much lower than the values of 19.1 and 19.4 kcal/lmole calculated at -94\u00b0C for N-(2,2,6,6-tetramethylpiperidyl)nitrene (3) and N-(2,2,5,5-tetramethylpyrrolidyl)nitrene (4), respectively. This difference between 16 and the cyclic-1,1-diazenes 3 and 4 can be attributed to a large steric interaction between the tert-butyl groups in 1,1-diazene 16.
\r\n\r\nIn order to investigate the nature of the singlet-triplet gap in 1,1-diazenes, 2,5-di-tert-butyl-N-pyrrolynitrene (22) was generated but was found to be too reactive towards dimerization to be persistent. In the presence of dimethylsulfoxide, however, N-pyrrolynitrene (22) can be trapped as N-(2,5-di-tert-butyl-N'-pyrrolyl)dimethylsulfoximine (38). N-(2,5-di-tert-butyl-N'-pyrrolyl)-d6-dimethylsulfoximine (38-d6) exchanges with free dimethylsulfoxide at 50\u00b0C in solution, presumably by generation and retrapping of pyrrolynitrene 22.
\r\n", "doi": "10.7907/y54d-s069", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:5376", "collection": "thesis", "collection_id": "5376", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-133042163", "primary_object_url": { "basename": "Voter_af_1983.pdf", "content": "final", "filesize": 8936590, "license": "other", "mime_type": "application/pdf", "url": "/5376/1/Voter_af_1983.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Resonating Valence Bond Model of Molecules and Reactions", "author": [ { "family_name": "Voter", "given_name": "Arthur Ford", "clpid": "Voter-Arthur-Ford" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis presents an ab initio generalization of Pauling's theory of resonance, the generalized resonating valence bond (GRVB) method. In GRVB, we optimize a wavefunction of the form
\r\n\r\n\u03a8TOT = CA \u03a8A + CB \u03a8B
\r\n\r\nwhere \u03a8A and \u03a8B are multiconfigurational wavefunctions with arbitrary overlap. This type of wavefunction has been considered unfeasible for more than a few electrons due to the n! computational dependence of evaluating the matrix element < \u03a8A | H | \u03a8B >. We reduce this dependence to ~n5 by biorthogonalizing the orbitals in each determinant pair. GRVB is ideally suited to describing systems which require a resonance of more than one bonding structure, such as benzene, molecules with three-electron bonds, and reaction transition states. Besides yielding a conceptually simple avefunction, we find that GRVB yields quantitative results for processes in which the dominant differential correlation is a resonance effect. For example, the GRVB barrier heights for the HCl + H and HF + H exchange reactions are each within one kcal of the basis set limit, in contrast to the orthogonal configuration interaction (CI) approaches which require hundreds or thousands of configurations to achieve the same accuracy. We also present application to the three-electron bonding in noble gas dimer ions, and various other examples.
", "doi": "10.7907/d754-h174", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:3292", "collection": "thesis", "collection_id": "3292", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08312006-081008", "primary_object_url": { "basename": "Moody_dm_1983.pdf", "content": "final", "filesize": 4377047, "license": "other", "mime_type": "application/pdf", "url": "/3292/1/Moody_dm_1983.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Numerical Solution of the Superfluid Shock Jump Conditions. II. Experimental Investigation of the Liquid Helium II-Vapor Interface", "author": [ { "family_name": "Moody", "given_name": "Douglas Marion, Jr.", "clpid": "Moody-Douglas-Marion" } ], "thesis_advisor": [ { "family_name": "Goodstein", "given_name": "David L.", "clpid": "Goodstein-D-L" } ], "thesis_committee": [ { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Goodstein", "given_name": "David L.", "clpid": "Goodstein-D-L" }, { "family_name": "Liepmann", "given_name": "Hans Wolfgang", "clpid": "Liepmann-H-W" }, { "family_name": "Sturtevant", "given_name": "Bradford", "clpid": "Sturtevant-B" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Numerical Solution of the Superfluid Shock Jump Conditions
\r\n\r\nThe four fundamental conservation equations of superfluid mechanics may be integrated across a one-dimensional discontinuity (shock wave) propagating into undisturbed helium II to yield a set of four algebraic equations (jump conditions) which, when supplemented by thermodynamic state information, establish the equilibrium flow state behind the shock wave for a given wave speed and undisturbed flow state ahead of the shock. These jump conditions have been solved numerically for 19 points on the helium II p-T diagram with upstream Mach number as the independent parameter. Representative results of the calculations are presented for pressure shocks, temperature raising shocks, and temperature lowering shock. The results are compared to previous analytical approximate solutions to test the validity of those approximation. They are also compared to experimental data for shock waves in helium II as a means of testing the correctness of the full, nonlinear two-fluid equations.
\r\n\r\nExperimental Investigation of the Liquid Helium II-Vapor Interface
\r\n\r\nAn apparatus was designed and constructed to measure the linear reflection and transmission coefficients for weak second sound shocks impinging upon the liquid-vapor interface of helium II. The measured reflection coefficients reproduce the work of previous authors, giving values which are roughly 20% higher than those predicted by thermodynamic equilibrium theory. The transmitted pressure wave speed was measured, and was found to be sonic within the limits of experimental precision. Therefore strength could not be deduced from time of flight measurements. Direct amplitude measurements of this weak wave were prevented by the film which coats the sensors in the vapor. For these reasons, the attempted transmission coefficient measurements were unsuccessful.
\r\n", "doi": "10.7907/387M-V435", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:11788", "collection": "thesis", "collection_id": "11788", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-124939824", "primary_object_url": { "basename": "Ennis_MD_1983.pdf", "content": "final", "filesize": 82653053, "license": "other", "mime_type": "application/pdf", "url": "/11788/1/Ennis_MD_1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "I. Asymmetric Alkylation Reactions of Chiral Imide Enolates. II. Efforts Directed Toward the Total Synthesis of (+)-Macbecin I", "author": [ { "family_name": "Ennis", "given_name": "Michael Dalton", "clpid": "Ennis-Michael-Dalton" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Evans", "given_name": "David A.", "clpid": "Evans-David-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The preparation of chiral N-acyl oxazolidones 6 and 7 from readily available amino acid precursors is described. Reaction of the alkali metal enolates derived from these chiral imides with alkyl halides and acid chlorides exhibit high levels of kinetic diastereoselection. Chromatographic enrichment
\r\n\r\n[chemical structure; see abstract in scanned thesis for details]
\r\n\r\naffords alkylated and acylated products of \u2265 99:1 diastereomeric purity. Non-destructive cleavage of the chiral auxiliary is accomplished by a variety of means to afford optically active products.
\r\n\r\nThe use of chiral imides 6 and 7 in the synthesis of the ansa-antibiotic macbecin-I (1) is described. The synthesis makes use of the iterative application of highly stereoregulated aldol condensations of N-acyl oxazolidones for the construction of the ansa-bridge of 1. This project has culminated in the preparation of the advanced acyclic intermediate 46.
\r\n\r\n[Chemical structures; see abstract in scanned thesis for details.]
", "doi": "10.7907/pqm8-7286", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:11784", "collection": "thesis", "collection_id": "11784", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-095416829", "primary_object_url": { "basename": "Daub_JP_1983.pdf", "content": "final", "filesize": 68627940, "license": "other", "mime_type": "application/pdf", "url": "/11784/1/Daub_JP_1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Total Synthesis of Macrolide Antibiotics", "author": [ { "family_name": "Daub", "given_name": "John Powell", "clpid": "Daub-John-Powell" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Evans", "given_name": "David A.", "clpid": "Evans-David-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An approach to the total synthesis of macrolide antibiotics via the key spiroketal intermediates i and ii, which possess all of the stereochemistry for the macrolides 10-deoxymethynolide (iii) and methynolide (iv), is described. Initially, the exocyclic enol ether v, which through hetero-Diels-Alder condensation with an \u03b1,\u03b2-unsaturated carbonyl compound would lead to these spiroketals i and ii, was prepared stereoselectively in optically pure form from 4,6-O-benzylidene-D-allal and was converted into the Prelog-Djerassi lactone (vi) by way of stereochemical confirmation. The low reactivity of this sensitive enol ether v toward hetero-Diels-Alder condensation led to the development of a new, high yield spiroketal synthesis through hetero-Diels-Alder condensation of the keto-enol ether vii with hetero-dienes; and, in this manner, the spiroketals i and ii were prepared stereoselectively. Cleavage of these spiroketals i and ii by thioketal exchange with 1,2-ethanedithiol led to seco-acid derivatives for the synthesis of the macrolides iii and iv. Additionally, a formal total synthesis of the antibiotic methymycin is achieved.
\r\n\r\n[See abstract in scanned thesis for chemical diagrams referenced above.]
", "doi": "10.7907/87f1-5d52", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:3948", "collection": "thesis", "collection_id": "3948", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10072002-110622", "primary_object_url": { "basename": "Speriosu_vs_1983.pdf", "content": "final", "filesize": 5683280, "license": "other", "mime_type": "application/pdf", "url": "/3948/1/Speriosu_vs_1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "X-ray Rocking Curve and Ferromagnetic Resonance Investigations of Ion-Implanted Crystals", "author": [ { "family_name": "Speriosu", "given_name": "Virgil Simon", "clpid": "Speriosu-Virgil-Simon" } ], "thesis_advisor": [ { "family_name": "Wilts", "given_name": "Charles H.", "clpid": "Wilts-C-H" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Johnson", "given_name": "William Lewis", "clpid": "Johnson-W-L" }, { "family_name": "Vreeland", "given_name": "Thad", "clpid": "Vreeland-T" }, { "family_name": "Wilts", "given_name": "Charles H.", "clpid": "Wilts-C-H" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "A kinematical model for general Bragg case x-ray diffraction in nonuniform films is presented. The model incorporates depth-dependent strain and structure factor. For ion-implanted crystals the change in structure factor attributed to damage is calculated using a spherically symmetric Gaussian distribution of incoherent atomic displacements. Profiles of strain and structure factor are obtained by fitting experimental rocking curves. The method is applicable to ion-implanted, diffused and multilayer crystalline structures such as heterojunctions and superlattices.
\r\n\r\nA comparison is made between profiles of strain and incoherent atomic displacements obtained from rocking curves and from Rutherford backscattering spectrometry in a Gd3Ga5O12 crystal implanted with 100 keV Ne+. The ranges of sensitivity of the two techniques-overlap for about one decade in implantation dose up to the amorphous threshold. Xray diffraction was found to be most sensitive to low damage levels while backscattering was found to be most sensitive to high damage levels. The two techniques are in excellent agreement on the near-surface strain, but differ significantly at depths below \u2243 500A. The discrepancy is attributed to errors caused by steering of channelled particles in backscattering spectrometry. The profiles of number of displaced atoms agree within a factor of two.
\r\n\r\nThe rocking curve method is combined with analysis of ferromagnetic resonance (FMR) spectra for characterization of crystalline and magnetic properties of [111]-oriented Gd,Tm,Ga:YIG films implanted with Ne+, He+, and H2+. For each implanted species the range of doses begins with easily-analyzed effects and ends with paramagnetism or amorphousness. Profiles of normal strain, lateral strain and damage were obtained. For maximum strains up to 1.3% the behavior of the strain with annealing is nearly independent of implanted species or dose. Magnetic profiles obtained before and after annealing were compared with the strain profiles. The local change in uniaxial anisotropy field \u0394Hk with increasing strain shows an initially linear rise for both He+ and Ne+, in quantitative agreement with the magnetostriction effect estimated from the composition. For strain values between 1% and 1.5%, \u0394Hk saturates and for increasing strain, \u0394Hk decreases to nearly zero when the material becomes paramagnetic. For peak strains greater than 1.3% for He+ and 1.1% for Ne+ the relation between uniaxial anisotropy and strain is not unique. Behavior of the saturation magnetization 4\u03c0M, the exchange constant A and the cubic anisotropy H1 was elucidated. For H2+ implantation the total \u0394Hk consists of a magnetostrictive contribution due to strain and of a comparable excess contribution associated with the local concentration of hydrogen. The profile of excess \u0394Hk agrees with calculated LSS range. The presence of hydrogen results in a reduction of 4\u03c0M not attributable to strain or damage. With increasing annealing temperature the excess \u0394Hk diminishes and above 400\u00b0C the only component of \u0394Hk is magnetostrictive.
\r\n\r\nCrystalline properties of Si-implanted [100] GaAs, Si, and Ge were studied by the rocking curve method. Sharp qualitative and quantitative differences were found between the damage in GaAs on one hand and Si and Ge on the other. At a moderate damage level the GaAs crystal undergoes a transition from elastic to plastic behavior. The plastically deformed region presents a barrier to epitaxial regrowth and is consistent with the well-known high defect density in regrown GaAs.
", "doi": "10.7907/BET3-1831", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:5390", "collection": "thesis", "collection_id": "5390", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-134206825", "type": "thesis", "title": "Electronic Transitions of Molecules by Electron Impact and Multiphoton Ionization Spectroscopy", "author": [ { "family_name": "Rianda", "given_name": "Ronald", "clpid": "Rianda-Ronald" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Sparks", "given_name": "Randal K.", "clpid": "Sparks-Randal-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The experimental work discussed in this thesis is concerned primarily with the detection of electric dipole forbidden transitions of molecules in the gas phase. The thesis is divided into two parts. The first part describes measurements made using the technique of low-energy, variable-angle, electron impact spectroscopy. The second part describes investigations performed using resonance enhanced multiphoton ionization (REMPI) spectroscopy.
\r\n\r\nThe low-energy variable-angle electron impact technique has been used to study the electronic spectroscopy of molecules. Both dipole allowed and dipole forbidden transitions have been investigated. Transitions having excitation energies from 0 eV to 20 eV have been studied using incident electron beam energies ranging from 25 eV to 75 eV and scattering angles from 0\u00b0 to 80\u00b0. Molecules studied included nitric oxide (NO), uranium hexafluoride (UF6), tungsten hexafluoride (WF6), nitrogen dioxide (NO2), hydrogen cyanide (HCN), acetonitrile (CH3CN), propionitrile (C2H5CN), butyronitrile (C3H7CN), and malononitrile (CH2(CN)2).
\r\n\r\nWeak structure was observed in the spectrum of nitric oxide between 5.22 eV and 5.60 eV. These bands have been assigned as vibronic bands belonging to the X2\u03c0 \u2192 a4\u03c0 transition. Additional structure extending from 5.7 eV to about 7 eV was assigned to the X2\u03c0 \u2192 b4\u03a3- transition. Several higher lying transitions were observed which have been tentatively assigned as doublet \u2192 quartet in nature.
\r\n\r\nIn order to elucidate the electronic structure of uranium hexafluoride the electron impact spectra at UF6 and WF6 were determined. Eleven features were observed in UF6 with intensity maxima at 3.26, 4.2, 4.7, 5.8, 7.0, 7.86, 9.26, 11.01, 11.75, 12.5 and 13.2 eV. Features were observed in the spectrum at 7.25, 7.9, 8.5, 9.85, 11.75, 12.6 and 13.5 eV. Comparison of the spectra indicate that the primary contribution to transition intensity in UF6 above 5.8 eV and in WF6 results form charge transfer excitations from fluorine p orbitals to metal d orbitals. Tentative assignments based on previous theoretical studies are made.
\r\n\r\nA previously unreported doublet \u2192 quartet transition was observed at 4.49 eV in the electron impact spectrum of NO2, in excellent agreement with theoretical calculations. Doublet \u2192 doublet transitions were observed with maxima at 2.95, 5.81, 7.48, 8.64, 9.69, 10.52, 10.68, 10.94 and 11.20 eV in agreement with previous studies.
\r\n\r\nThe series of C \u039e N containing molecules, Aydrogen cyanide, acetonitrile, malononitrile, propionitrile and butyronitrile, have also been studied using the electron impact technique. Results for hydrogen cyanide are in excellent agreement with previous work. Previously undetected singlet \u2192 triplet transitions of acetonitrile, propionitrile and butyronitrile are reported. In addition the first study of the electronic spectrum of malononitrile is reported.
\r\n\r\nTwo appendices to Part One are included. The first of these reports the results of generalized valence bond and configuration interaction studies of the low lying states of ammonia. The second appendix discusses an electron impact study of the electronically excited states of 1,3,5-cycloheptatriene.
\r\n\r\nPart Two of this thesis describes the theory of multiphoton ionization and reports results obtained using this technique. The application of REMPI spectroscopy to the detection of spin forbidden transitions is examined. It is shown in a study of the X1\u03a3+g \u2192 a3A2 state of CS2 to offer potential for the detection of spin forbidden transitions at high resolution and with great sensitivity.
\r\n\r\nFinally a preliminary study of the two-photon resonance enhanced multiphoton ionization of p-xylene is reported. Several elements of the X1Ag \u2192 1B2u transition observed previously in benzene and p-difluorobenzene are reported.
\r\n", "doi": "10.7907/b7ed-jg16", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:10912", "collection": "thesis", "collection_id": "10912", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05172018-114924220", "primary_object_url": { "basename": "Wight_CA_1982.pdf", "content": "final", "filesize": 53430349, "license": "other", "mime_type": "application/pdf", "url": "/10912/1/Wight_CA_1982.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Chemical Applications of Infrared Laser Photochemistry", "author": [ { "family_name": "Wight", "given_name": "Charles Albert", "clpid": "Wight-Charles-Albert" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Infrared multiphoton electron detachment reactions of gas phase carbanions are investigated using the techniques of ion cyclotron resonance spectroscopy. Ions are spatially confined in a low pressure environment for up to several seconds during irradiation with the unfocused output of a line tunable continuous wave CO2 laser. Analysis of the photodetachment yields as a function of irradiation time, neutral gas pressure, laser intensity and laser wavelength have revealed details of the multiphoton excitation process as well as radiative and collisional relaxation mechanisms. The emphasis for many of these studies is on the wavelength dependence of multiphoton electron detachment yields since the resulting infrared spectra are sensitive probes of molecular structure for distinguishing and identifying isomeric anions. An introduction to low power infrared photochemistry of ions is given in Chapter I.
\r\n\r\nIn Chapter II this technique is used to obtain infrared multiphoton electron detachment spectra of two C7H7- isomers, benzyl and cycloheptatrienyl anions. In the first known example where infrared spectra have been used to probe mechanistic details of an ion-molecule reaction, deprotonation of norbornadiene by CH3O- is shown to yield a mixture of benzyl and cycloheptatrienyl anions.
\r\n\r\nA closer examination of multiphoton electron detachment kinetics is the subject of Chapter III. The results are interpreted in terms of a kinetic model which is developed to describe low power multiphoton excitation and vibrational relaxation. Radiative relaxation of benzyl anion does not appear to be significant at laser intensities greater than 10 W /cm2 and collisions with neutral molecules are only moderately effective in deactiviating vibrationally excited anions.
\r\n\r\nIdentification of cis and trans butenyl anions in Chapter IV demonstrates the sensitivity of this technique for differentiating molecular structures. Deprotonation of cis-2-butene by NH2- forms the cis anion while deprotonation of trans-2-butene results in a mixture of cis and trans C4H7-. The multiphoton electron detachment spectrum of a third isomer, 2-methylallyl anion, is also presented.
\r\n\r\nVibrational relaxation of allyl anion, C3H5- is probed by infrared laser photodetachment techniques in Chapter V. In contrast to the results for benzyl anion in Chapter III, the radiative relaxation of 53 s-1 for allyl anion shows this to be the dominant mechanism for relaxation at pressures below 10-5 torr.
", "doi": "10.7907/gskp-8c88", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:10780", "collection": "thesis", "collection_id": "10780", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03222018-144512817", "type": "thesis", "title": "Part A. Theoretical Studies of the X-Ray Absorption Edge in Copper Complexes. Part B. Electron Correlation Consistent Calculation of Bond Dissociation Energies", "author": [ { "family_name": "Bair", "given_name": "Raymond Alan", "clpid": "Bair-Raymond-Alan" } ], "thesis_advisor": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part A: In order to elucidate the nature of the transitions involved in the x-ray absorption edge of molecular systems, we have used ab initio methods to examine the discrete transitions corresponding to the atomic 1s \u2192 3d, 4s, 4p, 5s, and 5p transitions and the corresponding shakeup processes for Cu atom and for a Cu(II) model system, CuCl2. The three common features of the K edge are described by the calculations. For CuCl2, the lowest strong transitions have the character 1s \u2192 4p (f = 0.00133). About 7.5 eV lower is a group of transitions involving 1s \u2192 4p simultaneous with ligand-to-metal shakedown. About 18.7 eV below the main peak is a weak (65 times weaker) quadrupole-allowed transition corresponding to 1s \u2192 3d (i.e., 1s23d9 \u2192 1s13d10. In each case the spectral feature has been assigned to an allowed transition. Previously, the middle transition was assigned as 1s \u2192 4s, whereas in this study the 1s \u2192 4s transition was calculated to be too weak to be observed. We propose that the observed peak is due to the allowed transition involving 1s \u2192 4p plus shakedown.
\r\n\r\nPart B: Ab initio generalized valence bond (GVB) and configuration interaction (CI) methods have been used to develop a generally applicable method for directly calculating bond energies. Particular effort has been put into obtaining a scheme in which all correlation terms that change upon dissociation of a particular bond are included consistently. The method uses in an essential way the localized orbitals from a GVB calculations, and is readily applicable to large systems [e.g., (CH3)3C-C(CH3)3]. To test our method, we selected two benchmark series of compounds, where the experimental bond energies are well known. Calculated bond energies are reported for the R-H bonds of CH4, NH3, H2O, and HF, which are low by 3.5, 2.5, 3.0, and 2.7 .kcal/mol, respectively. We also report calculations of the R-R bond energies of C2H6, N2H4, H2O2, and F2, which are low by 0.1, -3.2, -1.8, and 0.8 kcal/mol, respectively. In the application of our method, we have calculated all of the O-O, O-C, and O-H bond energies of HOOH, CH3OOH, CH3OOCH3, CH3OH, C2H5OH (O-H only), and CH3O-. Finally, we obtain the electron affinities of F, OH, and CH3O with the same techniques.
", "doi": "10.7907/ez8r-aj04", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:905", "collection": "thesis", "collection_id": "905", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03092005-130854", "type": "thesis", "title": "Spectroscopy and Photochemistry of Polynuclear Metal Complexes", "author": [ { "family_name": "Maverick", "given_name": "Andrew William", "clpid": "Maverick-Andrew-William" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Marsh", "given_name": "Richard Edward", "clpid": "Marsh-R-E" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The photochemical and spectroscopic properties of two classes of polynuclear metal complexes have been studied.
\r\n\r\nMolybdenum and Tungsten Cluster Halides: The cubic ions Mo6Cl142-, Mo6Br142-, and W6Cl142- are luminescent, with lifetimes approaching 200 \u03bcs in solution at room temperature. The luminescent excited state of Mo6Cl142- is probably associated with a transition localized on the central Mo6 core. Both this excited state and the corresponding ground state undergo facile one electron oxidation. These features make the cluster ions attractive for experiments in photochemical energy storage. Also discussed is evidence from magnetic and spectroscopic studies bearing on the electronic structures of the cluster ions.
\r\n\r\nRhodium Isocyanide Complexes: Various thermal and photochemical reactions in the system Rh2b42+ - Rh4b86+ - Rh2b44+ (b = 1,3-diisocyanopropane) have been examined. The possibility of photocatalytic hydrogen production sensitized by Rh2b42+ and Rh4b86+, previously shown to produce H2 stoichiometrically on irradiation in strongly acidic solution, was explored. Experiments were also conducted with Rh2(TMB)42+ (TMB = 2,5-diisocyano-2,5-dimethylhexane) in the hopes of accomplishing similar energy storage reactions. The equilibria in acidic aqueous solution involving these species as well as oligomers of intermediate oxidation state were also studied. Kinetic studies of the reduction of Rh2b44+ by H2 and of thermal and photochemical oxidation of Rh4b86+ by O2 were inconclusive.
\r\n", "doi": "10.7907/PBEA-8W62", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:905", "collection": "thesis", "collection_id": "905", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-03092005-130854", "type": "thesis", "title": "Spectroscopy and Photochemistry of Polynuclear Metal Complexes", "author": [ { "family_name": "Maverick", "given_name": "Andrew William", "clpid": "Maverick-Andrew-William" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "thesis_committee": [ { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Marsh", "given_name": "Richard Edward", "clpid": "Marsh-R-E" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The photochemical and spectroscopic properties of two classes of polynuclear metal complexes have been studied.
\r\n\r\nMolybdenum and Tungsten Cluster Halides: The cubic ions Mo6Cl142-, Mo6Br142-, and W6Cl142- are luminescent, with lifetimes approaching 200 \u03bcs in solution at room temperature. The luminescent excited state of Mo6Cl142- is probably associated with a transition localized on the central Mo6 core. Both this excited state and the corresponding ground state undergo facile one electron oxidation. These features make the cluster ions attractive for experiments in photochemical energy storage. Also discussed is evidence from magnetic and spectroscopic studies bearing on the electronic structures of the cluster ions.
\r\n\r\nRhodium Isocyanide Complexes: Various thermal and photochemical reactions in the system Rh2b42+ - Rh4b86+ - Rh2b44+ (b = 1,3-diisocyanopropane) have been examined. The possibility of photocatalytic hydrogen production sensitized by Rh2b42+ and Rh4b86+, previously shown to produce H2 stoichiometrically on irradiation in strongly acidic solution, was explored. Experiments were also conducted with Rh2(TMB)42+ (TMB = 2,5-diisocyano-2,5-dimethylhexane) in the hopes of accomplishing similar energy storage reactions. The equilibria in acidic aqueous solution involving these species as well as oligomers of intermediate oxidation state were also studied. Kinetic studies of the reduction of Rh2b44+ by H2 and of thermal and photochemical oxidation of Rh4b86+ by O2 were inconclusive.
\r\n", "doi": "10.7907/PBEA-8W62", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:5390", "collection": "thesis", "collection_id": "5390", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-134206825", "type": "thesis", "title": "Electronic Transitions of Molecules by Electron Impact and Multiphoton Ionization Spectroscopy", "author": [ { "family_name": "Rianda", "given_name": "Ronald", "clpid": "Rianda-Ronald" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Dougherty", "given_name": "Dennis A.", "orcid": "0000-0003-1464-2461", "clpid": "Dougherty-D-A" }, { "family_name": "Sparks", "given_name": "Randal K.", "clpid": "Sparks-Randal-K" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The experimental work discussed in this thesis is concerned primarily with the detection of electric dipole forbidden transitions of molecules in the gas phase. The thesis is divided into two parts. The first part describes measurements made using the technique of low-energy, variable-angle, electron impact spectroscopy. The second part describes investigations performed using resonance enhanced multiphoton ionization (REMPI) spectroscopy.
\r\n\r\nThe low-energy variable-angle electron impact technique has been used to study the electronic spectroscopy of molecules. Both dipole allowed and dipole forbidden transitions have been investigated. Transitions having excitation energies from 0 eV to 20 eV have been studied using incident electron beam energies ranging from 25 eV to 75 eV and scattering angles from 0\u00b0 to 80\u00b0. Molecules studied included nitric oxide (NO), uranium hexafluoride (UF6), tungsten hexafluoride (WF6), nitrogen dioxide (NO2), hydrogen cyanide (HCN), acetonitrile (CH3CN), propionitrile (C2H5CN), butyronitrile (C3H7CN), and malononitrile (CH2(CN)2).
\r\n\r\nWeak structure was observed in the spectrum of nitric oxide between 5.22 eV and 5.60 eV. These bands have been assigned as vibronic bands belonging to the X2\u03c0 \u2192 a4\u03c0 transition. Additional structure extending from 5.7 eV to about 7 eV was assigned to the X2\u03c0 \u2192 b4\u03a3- transition. Several higher lying transitions were observed which have been tentatively assigned as doublet \u2192 quartet in nature.
\r\n\r\nIn order to elucidate the electronic structure of uranium hexafluoride the electron impact spectra at UF6 and WF6 were determined. Eleven features were observed in UF6 with intensity maxima at 3.26, 4.2, 4.7, 5.8, 7.0, 7.86, 9.26, 11.01, 11.75, 12.5 and 13.2 eV. Features were observed in the spectrum at 7.25, 7.9, 8.5, 9.85, 11.75, 12.6 and 13.5 eV. Comparison of the spectra indicate that the primary contribution to transition intensity in UF6 above 5.8 eV and in WF6 results form charge transfer excitations from fluorine p orbitals to metal d orbitals. Tentative assignments based on previous theoretical studies are made.
\r\n\r\nA previously unreported doublet \u2192 quartet transition was observed at 4.49 eV in the electron impact spectrum of NO2, in excellent agreement with theoretical calculations. Doublet \u2192 doublet transitions were observed with maxima at 2.95, 5.81, 7.48, 8.64, 9.69, 10.52, 10.68, 10.94 and 11.20 eV in agreement with previous studies.
\r\n\r\nThe series of C \u039e N containing molecules, Aydrogen cyanide, acetonitrile, malononitrile, propionitrile and butyronitrile, have also been studied using the electron impact technique. Results for hydrogen cyanide are in excellent agreement with previous work. Previously undetected singlet \u2192 triplet transitions of acetonitrile, propionitrile and butyronitrile are reported. In addition the first study of the electronic spectrum of malononitrile is reported.
\r\n\r\nTwo appendices to Part One are included. The first of these reports the results of generalized valence bond and configuration interaction studies of the low lying states of ammonia. The second appendix discusses an electron impact study of the electronically excited states of 1,3,5-cycloheptatriene.
\r\n\r\nPart Two of this thesis describes the theory of multiphoton ionization and reports results obtained using this technique. The application of REMPI spectroscopy to the detection of spin forbidden transitions is examined. It is shown in a study of the X1\u03a3+g \u2192 a3A2 state of CS2 to offer potential for the detection of spin forbidden transitions at high resolution and with great sensitivity.
\r\n\r\nFinally a preliminary study of the two-photon resonance enhanced multiphoton ionization of p-xylene is reported. Several elements of the X1Ag \u2192 1B2u transition observed previously in benzene and p-difluorobenzene are reported.
\r\n", "doi": "10.7907/b7ed-jg16", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:10897", "collection": "thesis", "collection_id": "10897", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162018-103306929", "type": "thesis", "title": "The Application of Metallated Enamines to the Synthesis of Morphine Alkaloids", "author": [ { "family_name": "Mitch", "given_name": "Charles Howard", "clpid": "Mitch-Charles-Howard" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Evans", "given_name": "David A.", "clpid": "Evans-David-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Metallated enamines have been used to prepare a number of morphine-based analgesics, including efficient entry to the 4a-phenylisoquinolines and morphinans. Stereocontrolled formation of both cis and trans-fused perhydroisoquinolines has been accomplished by either kinetic or thermodynamic protonation of the corresponding octahydroisoquinoline. Reaction of 4a-phenyloctahydroisoquinolinium perchlorates with diazomethane afforded the expected aziridinium perchlorate with a component of direct cyclization to the morphinan structure also observed. Kornbloom oxidation to the \u03b1-amino-aldehyde was accomplished on treatment of the aziridinium salts with dimethyl-sulfoxide. The aldehydes were cyclized to the morphinan structure on reaction with boron trifluoride etherate, providing ready access to intermediates used by Gates in his pioneering total synthesis of morphine.
", "doi": "10.7907/vf0x-tn08", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:1273", "collection": "thesis", "collection_id": "1273", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04042008-131831", "type": "thesis", "title": "Picosecond Studies of Molecular Energy Transfer, Reorientation, and Internal Motion Dynamics", "author": [ { "family_name": "Millar", "given_name": "David Philip", "clpid": "Millar-David-Philip" } ], "thesis_advisor": [ { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the development and characterization of mode- locked CW dye lasers and their application to time-resolved studies of molecular reorientation in liquids, electronic energy transfer in solution, and the internal motions of nucleic acids. Both passive and synchronous mode-locking are found to produce slightly structured pulses with coherence times \u0394tc ~ 0.8 psec, and pulse envelope widths \u0394tp ~ 2 to 3 psec.
\r\n\r\nThe dynamics of reorientation of cresyl violet in alcohol solvents is directly studied on the picosecond time scale. The observed rotational correlation function decays as a single exponential, with a rotational relaxation time that is linearly dependent on solvent viscosity. Rotation times calculated from hydrodynamics are a factor of 2 smaller than observed. The discrepancy is attributed to hydrogen-bonding interactions with the solvent that cause additional friction.
\r\n\r\nElectronic energy transfer between cresyl violet donors and azulene acceptors in solution is studied. The excited donor decay is in excellent agreement with the Rirster dipole-dipole model over the time range from 2 psec to 10 nsec. The critical transfer distance inferred from the decay Ro = 26\u00c5 agrees well with the value calculated from the spectral properties, Ro = 27\u00c5. The increased energy transfer rate in fluid solutions due to translational motion is accurately predicted by the approximate solution to a diffusion equation for the donor excitation. However, the energy transport due to donor-donor transfer was nondiffusive on the picosecond time scale.
\r\n\r\nThe dynamics of the torsional and bending motions of nucleic acids are studied by sub nanosecond time-dependent fluorescence depolarization of intercalated ethidium bromide. The non exponential relaxation behavior is observed for the first time, and is in excellent agreement with the theoretical predictions of an elastic model for DNA internal motions. The intrinsic torsional rigidity of calf thymus DNA is C = 1.43 \u00b1 0.11 x 10-19 erg.cm. The torsional rigidity is shown to be sensitive to details of primary, secondary, and tertiary nucleic acid structure. The polyelectrolyte contribution to the torsional rigidity of DNA has been measured for the first time.
", "doi": "10.7907/NSA9-8028", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:6823", "collection": "thesis", "collection_id": "6823", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02152012-151600900", "type": "thesis", "title": "Theoretical Studies of Chemical Reaction Dynamics", "author": [ { "family_name": "Kaye", "given_name": "Jack Alan", "clpid": "Kaye-Jack-Alan" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Sparks", "given_name": "Randal K.", "clpid": "Sparks-Randal-K" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The collinear collision of an atom with a diatomic molecule has been studied within the frameworks of quantum and classical mechanics. Three major topics have been investigated.
\r\n\r\nIn part I, the collinear collision of hydrogen atoms with hydrogen fluoride (and singly deuterium substituted variants of this system) have been studied in the exchange channel by coupled-channel quantum mechanical calculations using a realistic (high barrier) potential energy surface. We have also investigated the effect on the dynamics of varying the barrier height of the potential energy surface.
\r\n\r\nIn part II, we consider the characterization of low energy resonances in the collinear H + H2 and F + H2(HD, DH, D2) systems. A variety of characterization techniques are used; the most useful proves to be the variation with energy of the eigenvalues of the collision lifetime matrix.
\r\n\r\nIn part III, we develop the method of hyperspherical coordinates for the study of collinear reactive atom-diatomic molecule collisions. The method is tested for the H + H2 system, and is applied to a model system above the threshhold for collision-induced dissociation and to reactions in which a light atom (hydrogen) is transferred between two heavy ones. Systems of this type studied include I + HI and Br + HCl; we also consider some aspects of the dynamics in the Cl + HCl system. We develop the formalism to extract the physical scattering wave function from the method and present preliminary results of probability densities and probability current densities on the H + H2 system. We also consider the formulation of the method in the adiabatic representation and examine both numerically and analytically the behavior of the coupling matrices at large values of the propagation variable. Convergence properties of the method are investigated in detail for the H + H2 and F + H2 systems. Quasi-classical trajectory calculations have been used to help understand the results obtained and to determine the importance of quantum mechanical effects.
\r\n", "doi": "10.7907/vkds-vb56", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:7227", "collection": "thesis", "collection_id": "7227", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10082012-092613083", "primary_object_url": { "basename": "Yocom_km_1982.pdf", "content": "final", "filesize": 36939408, "license": "other", "mime_type": "application/pdf", "url": "/7227/1/Yocom_km_1982.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Synthesis and Characterization of Inorganic Redox Reagent-Modified Cytochromes C", "author": [ { "family_name": "Yocom", "given_name": "Kathryn Mary", "clpid": "Yocom-Kathryn-Mary" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" }, { "family_name": "Grubbs", "given_name": "Robert H.", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A stable complex is formed between pentaammineruthenium(III) and the imidazole moiety of histidine-33 in cytochrome c. This complex is the major mono-substituted product of the reaction between aquopentaammineruthenium(II) and horse heart cytochrome c at pH 7. It is isolated and purified by ion exchange chromatography on CM-cellulose. High-pressure liquid chromatography of the tryptic hydrosylate of the modified cytochrome c is shown to be an effective method for the identification of the pentaammineruthenium binding site. The spectrum of the modified peptide mimics that of the pentaamminehistidineruthenium(III) model complex. Spectro-electrochemical and optical absorption measurements show that the integrity of the native structure in the vicinity of the heme c group is maintained in the ruthenium-modified protein. The reduction potentials of the two redox sites of the modified protein, derived from cyclic voltammetric measurements at a gold electrode in the presence of 4,4'-bipyridyl, are: heme c (Fe3+/2+), 0.26 V; Ru(NH3)5(His-33)3+/2+, 0.15 V (vs. NHE). A-15 \u00c5 separation between the two redox sites in this system is estimated from molecular models of cytochrome c. It is suggested that the specificity, stability, and redox properties exhibited by aquopentaammineruthenium(II) render it an ideal protein modification reagent for the production of \"synthetic\" multisite metalloproteins.
\r\n\r\nThe criterion of product stability is not met by the aquopentacyanoferrate(II) ion. The products isolated from the reaction of this reagent with cytochrome c are believed to be a mixture of histidine and methionine substitution products, and ionic association complexes. The relatively rapid dissociation of the pentacyanoferrate(II) moiety from the protein severely limits the extent to which the products can be characterized.
\r\n\r\nThe synthesis of a cobalt(III)-cytochrome c complex is described. Tetrachloroplatinate(II) reacts specifically with methionine-65. Pyridine-4-carboxylatopentaamminecobalt(III) is subsequently reacted with the platinum center. Unfortunately, the cobalt(II) form of the derivative is substitution labile, and the redox properties of the cobalt complex are highly unfavorable.
\r\n\r\nIntermolecular reductions of horse heart cytochrome c, Pseudomonas aeruginosa cytochrome c(551), Pseudomonas aeruginosa azurin, and Rhus verniaifera stellacyanin by hexaammineruthenium(II) are reported. Rate constants and activation parameters are presented. The results are discussed in terms of electron transfer distances for metalloprotein redox reactions.
", "doi": "10.7907/5tfv-gx02", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:10897", "collection": "thesis", "collection_id": "10897", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162018-103306929", "type": "thesis", "title": "The Application of Metallated Enamines to the Synthesis of Morphine Alkaloids", "author": [ { "family_name": "Mitch", "given_name": "Charles Howard", "clpid": "Mitch-Charles-Howard" } ], "thesis_advisor": [ { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "thesis_committee": [ { "family_name": "Evans", "given_name": "David A.", "clpid": "Evans-David-A" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Metallated enamines have been used to prepare a number of morphine-based analgesics, including efficient entry to the 4a-phenylisoquinolines and morphinans. Stereocontrolled formation of both cis and trans-fused perhydroisoquinolines has been accomplished by either kinetic or thermodynamic protonation of the corresponding octahydroisoquinoline. Reaction of 4a-phenyloctahydroisoquinolinium perchlorates with diazomethane afforded the expected aziridinium perchlorate with a component of direct cyclization to the morphinan structure also observed. Kornbloom oxidation to the \u03b1-amino-aldehyde was accomplished on treatment of the aziridinium salts with dimethyl-sulfoxide. The aldehydes were cyclized to the morphinan structure on reaction with boron trifluoride etherate, providing ready access to intermediates used by Gates in his pioneering total synthesis of morphine.
", "doi": "10.7907/vf0x-tn08", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:1273", "collection": "thesis", "collection_id": "1273", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04042008-131831", "type": "thesis", "title": "Picosecond Studies of Molecular Energy Transfer, Reorientation, and Internal Motion Dynamics", "author": [ { "family_name": "Millar", "given_name": "David Philip", "clpid": "Millar-David-Philip" } ], "thesis_advisor": [ { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis describes the development and characterization of mode- locked CW dye lasers and their application to time-resolved studies of molecular reorientation in liquids, electronic energy transfer in solution, and the internal motions of nucleic acids. Both passive and synchronous mode-locking are found to produce slightly structured pulses with coherence times \u0394tc ~ 0.8 psec, and pulse envelope widths \u0394tp ~ 2 to 3 psec.
\r\n\r\nThe dynamics of reorientation of cresyl violet in alcohol solvents is directly studied on the picosecond time scale. The observed rotational correlation function decays as a single exponential, with a rotational relaxation time that is linearly dependent on solvent viscosity. Rotation times calculated from hydrodynamics are a factor of 2 smaller than observed. The discrepancy is attributed to hydrogen-bonding interactions with the solvent that cause additional friction.
\r\n\r\nElectronic energy transfer between cresyl violet donors and azulene acceptors in solution is studied. The excited donor decay is in excellent agreement with the Rirster dipole-dipole model over the time range from 2 psec to 10 nsec. The critical transfer distance inferred from the decay Ro = 26\u00c5 agrees well with the value calculated from the spectral properties, Ro = 27\u00c5. The increased energy transfer rate in fluid solutions due to translational motion is accurately predicted by the approximate solution to a diffusion equation for the donor excitation. However, the energy transport due to donor-donor transfer was nondiffusive on the picosecond time scale.
\r\n\r\nThe dynamics of the torsional and bending motions of nucleic acids are studied by sub nanosecond time-dependent fluorescence depolarization of intercalated ethidium bromide. The non exponential relaxation behavior is observed for the first time, and is in excellent agreement with the theoretical predictions of an elastic model for DNA internal motions. The intrinsic torsional rigidity of calf thymus DNA is C = 1.43 \u00b1 0.11 x 10-19 erg.cm. The torsional rigidity is shown to be sensitive to details of primary, secondary, and tertiary nucleic acid structure. The polyelectrolyte contribution to the torsional rigidity of DNA has been measured for the first time.
", "doi": "10.7907/NSA9-8028", "publication_date": "1982", "thesis_type": "phd", "thesis_year": "1982" }, { "id": "thesis:10755", "collection": "thesis", "collection_id": "10755", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03062018-120827730", "primary_object_url": { "basename": "Highe_AJ_1981.pdf", "content": "final", "filesize": 50340096, "license": "other", "mime_type": "application/pdf", "url": "/10755/1/Highe_AJ_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ionic Motion in Solid Electrolytes: A Solid State NMR Study of Sodium and Lithium in \u03b2-Alumina", "author": [ { "family_name": "Highe", "given_name": "Albert John", "clpid": "Highe-Albert-John" } ], "thesis_advisor": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Cole", "given_name": "Terry", "clpid": "Cole-Terry" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Solid state NMR techniques have been used as a microscopic probe of the structural and dynamical properties of the mobile cations in the solid electrolyte \u03b2-alumina. The first order quadrupole shifts in the (\u00b13/2 \u2194 \u00b11/2) transitions in the spin 3/2 nuclei sodium and lithium have allowed the electric field gradients (EFG) for the nominal Beevers and Ross (BR) and mid-oxygen (MO) sites to be characterized. The details of the EFG's for and the distribution of cations among BR and MO sites reflect the differences in the potential wells for lithium and sodium in \u03b2-alumina. In particular, unlike sodium, the MO site for lithium is lower in energy than the BR site which results in a different structural arrangement of lithium ions. In sodium \u03b2-alumina, the equilibrium position for sodium in the BR site is displaced from the three-fold symmetry axis. It is believed that this is due to the presence of nearby MO-MO pairs. Furthermore, an activation energy of 0.04 eV is observed for the motion of sodium ions among the displaced BR sites which is associated with the correlated motion of MO-MO pairs. The effects of a second motional process with an activation energy of 0.08 eV are observed in both lithium and sodium spectra which are associated with the motion of cations among BR and MO sites. The interaction of cations in MO-MO pairs was further investigated by observing the effect of varying the ratio of lithium and sodium in mixed lithium-sodium \u03b2-alumina on the distribution of cations among the available sites. The results were interpreted using a theory previously developed to explain the mixed-alkali effect in glasses and indicate that there is a strong interaction between unlike MO-MO pairs which governs the cation site distribution and raises the activation energy for conduction.
", "doi": "10.7907/w0cr-8h87", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:122", "collection": "thesis", "collection_id": "122", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01112005-143434", "type": "thesis", "title": "I. Electrophilic Reactions of p-Toluenesulfonyl Azide. II. \u00b9\u2075N and \u00b9\u00b3C Nuclear Magnetic Studies of Aryldiazonium Compounds Effect of Substituent, Solvent and 18-Crown-6", "author": [ { "family_name": "Casewit", "given_name": "Carla Jutta", "clpid": "Casewit-Carla-Jutta" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Roberts", "given_name": "John D.", "clpid": "Roberts-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I
\r\n\r\nElectrophilic Reactions of p-Toluenesulfonyl Azide
\r\n\r\nSection 1. Review of Electrophilic Reactions of p-Toluenesulfonyl Azide
\r\n\r\nThe electrophilic reactions of p-toluenesulfonyl azide are reviewed using the principles of hard and soft acids and bases (HSAB).
\r\n\r\nSection 2. The Reaction of p-Toluenesulfonyl Azide with the Sodium Salt of p-Toluenesulfonamide
\r\n\r\nA number of concurrent reactions of p-toluenesulfonyl azide-3-15N (I-3-15N) with the sodium salt of p-toluenesulfonamide were followed by 15N NMR. I-2-15N is formed as a result of a degenerate diazo transfer by I-3-15N to p-toluenesulfonamide anion. p-Toluenesulfonamide anion also reacts with 1-3-15N to give di-p-toluenesulfonamide and azide ion. The 15-N-labeled azide ion exchanges with I to give I-1-15N. I also reacts with azide ion, yielding dinitrogen and p-toluenesulfinate anion. The sulfinate salt reacts readily and reversibly with I to give 1,3-di-p-toluenesulfontriazene anion, which provides another pathway for interconversion of 1-3-15N and I-1-15N.
\r\n\r\nSection 3. The Reaction of p-Toluenesulfonyl Azide with Potassium Azide
\r\n\r\nThe reaction of p-toluenesulfonyl azide with potassium azide-1-15N has been examined in toluene and dichloromethane by 15N NMR. In addition to azide-ion exchange leading to 1-1-15N and I-3-15N, the formation of 1-2-15N is indicated. Two mechanisms for this novel scrambling are proposed. Azide-ion metathesis involving reversible formation of an N-Pentazole derivative from I and azide ion, followed by azide exchange could account for the formation of 1-2-15N. Alternatively, a scrambling route involving the reversible addition of p-toluenesulfonylnitrene to 1-3-15N can be envisioned. The inhibition of scrambling in dichloromethane by addition of iodide ion suggests that a discrete p-toluenesulfonyl azide \u2013 azide ion intermediate is involved in any case.
\r\n\r\nPart II
\r\n\r\n15N and 13C Nuclear Magnetic Resonance Studies of Aryldiazonium Compounds. Effect of Substituent, Solvent and 18-Crown-6.
\r\n\r\n15N and 13C shifts induced by addition of one equivalent of 18-crown-6 have been determined for several para-substituted aryldiazonium fluoborates in dimethylformamide. The \u03b1-nitrogen (N1) and para carbon (C4) shift upfield and the \u03b2-nitrogen (N2) and C1 shift downfield on complexation. The effect of solvent on the positions of the 15N and 13C resonances of p-(n-butyl)benzenediazonium fluoborate are small. The influence of substituents on the 15N chemical shifts is relatively large and comparable to the effect of 18-crown-6. These 13C and 15N results, in conjunction with previous spectroscopic studies indicate that the crown ether complexed aryldiazonium cation is electronically more diazonium-like and less diazo-like than the uncomplexed form.
", "doi": "10.7907/nyft-yr23", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:10778", "collection": "thesis", "collection_id": "10778", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03222018-134525550", "primary_object_url": { "basename": "Thiel_PA_1981.pdf", "content": "final", "filesize": 148736950, "license": "other", "mime_type": "application/pdf", "url": "/10778/1/Thiel_PA_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Adsorption, Co-Adsorption and Catalytic Reactions on Rh(111) and Ru(001) Surfaces", "author": [ { "family_name": "Thiel", "given_name": "Patricia Ann", "clpid": "Thiel-Patricia-Ann" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The adsorption of oxygen, hydrogen, carbon monoxide , nitric oxide and water on Rh(111) and Ru(001) surfaces has been studied using the techniques of high-resolution electron energy loss spectroscopy, low-energy electron diffraction, Auger electron spectroscopy, ultraviolet photoelectron spectroscopy and thermal desorption mass spectrometry. In many cases co-adsorption experiments have provided insight into the nature of interaction between different adsorbates, with potential implications for heteroqeneous catalytic reaction mechanisms.
\r\n\r\nThe interaction of oxygen with Rh(111) consists of adsorption, irreversible thermally induced ordering and disordering phenomena, dissolution into the subsurface region and desorption. The thermodynamic parameters which describe these phenomena have been investigated. The forms of the kinetic rate expressions for the catalytic reaction of adsorbed oxygen with hydrogen are different for ordered and disordered arrays of oxygen adatoms. In agreement with co-adsorption studies of hydrogen and oxygen, and supported by studies of hydrogen chemisorption on clean Rh(111), this implies that the rate of adsorption of hydrogen is sensitive to the structure of the adsorbed oxygen lattice.
\r\n\r\nTwo forms of molecularly adsorbed NO are readily distinguished on a Ru(001) surface by the frequencies of the nitrogen-oxygen stretching vibrations, which can then be used to observe the influence of co-adsorbates. Oxygen, nitrogen and hydrogen adatoms compete selectively for the adsites which are occupied by multiply-coordinated NO, whereas CO competes for adsites occupied by the singly-coordinated molecular NO. Carbon monoxide can even induce conversion of adsorbed molecular NO from sites of single coordination to sites of multiple coordination with the metal substrate.
\r\n\r\nWater interacts with the Ru(001) surface to form chemisorption bonds, but it also forms intermolecular hydrogen bonds which are of comparable strength. This leads to formation of layered, hydrogen bonded aggregates at all coverages. The properties of the first two layers are distinct from those of the subsequent ice multilayers, and a specific structural model for the hydrogen bonded lattices is proposed. A thermally induced ordering effect is observed which is analogous to the vitreous-to-cubic phase transformation of bulk ice.
", "doi": "10.7907/8m9w-p414", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:10755", "collection": "thesis", "collection_id": "10755", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03062018-120827730", "primary_object_url": { "basename": "Highe_AJ_1981.pdf", "content": "final", "filesize": 50340096, "license": "other", "mime_type": "application/pdf", "url": "/10755/1/Highe_AJ_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Ionic Motion in Solid Electrolytes: A Solid State NMR Study of Sodium and Lithium in \u03b2-Alumina", "author": [ { "family_name": "Highe", "given_name": "Albert John", "clpid": "Highe-Albert-John" } ], "thesis_advisor": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" } ], "thesis_committee": [ { "family_name": "Zewail", "given_name": "Ahmed H.", "clpid": "Zewail-A-H" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Cole", "given_name": "Terry", "clpid": "Cole-Terry" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Solid state NMR techniques have been used as a microscopic probe of the structural and dynamical properties of the mobile cations in the solid electrolyte \u03b2-alumina. The first order quadrupole shifts in the (\u00b13/2 \u2194 \u00b11/2) transitions in the spin 3/2 nuclei sodium and lithium have allowed the electric field gradients (EFG) for the nominal Beevers and Ross (BR) and mid-oxygen (MO) sites to be characterized. The details of the EFG's for and the distribution of cations among BR and MO sites reflect the differences in the potential wells for lithium and sodium in \u03b2-alumina. In particular, unlike sodium, the MO site for lithium is lower in energy than the BR site which results in a different structural arrangement of lithium ions. In sodium \u03b2-alumina, the equilibrium position for sodium in the BR site is displaced from the three-fold symmetry axis. It is believed that this is due to the presence of nearby MO-MO pairs. Furthermore, an activation energy of 0.04 eV is observed for the motion of sodium ions among the displaced BR sites which is associated with the correlated motion of MO-MO pairs. The effects of a second motional process with an activation energy of 0.08 eV are observed in both lithium and sodium spectra which are associated with the motion of cations among BR and MO sites. The interaction of cations in MO-MO pairs was further investigated by observing the effect of varying the ratio of lithium and sodium in mixed lithium-sodium \u03b2-alumina on the distribution of cations among the available sites. The results were interpreted using a theory previously developed to explain the mixed-alkali effect in glasses and indicate that there is a strong interaction between unlike MO-MO pairs which governs the cation site distribution and raises the activation energy for conduction.
", "doi": "10.7907/w0cr-8h87", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:10772", "collection": "thesis", "collection_id": "10772", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03132018-112023831", "primary_object_url": { "basename": "Morse_RH_1981.pdf", "content": "final", "filesize": 75197056, "license": "other", "mime_type": "application/pdf", "url": "/10772/1/Morse_RH_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "EPR Spectroscopic Studies of the Active Sites of Some Heme- and Copper-Containing, Oxygen-Binding Proteins", "author": [ { "family_name": "Morse", "given_name": "Randall Heywood", "orcid": "ORCID ID\tFirst Name\tLast Name\tOther Names\tAffiliations 0000-0003-0000-8718", "clpid": "Morse-Randall-Heywood" } ], "thesis_advisor": [ { "family_name": "Roberts", "given_name": "John D.", "clpid": "Roberts-J-D" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Gray", "given_name": "Harry B.", "orcid": "0000-0002-7937-7876", "clpid": "Gray-H-B" }, { "family_name": "Roberts", "given_name": "John D.", "clpid": "Roberts-J-D" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "All oxygen-utilizing proteins contain copper, iron, or both, at the oxygen-bonding sites. The ligand environment and geometry about the metal centers in these proteins must be crucial in determining their individual functions. This thesis reports studies in which the ligand nitric oxide is used as a spin probe to investigate the structure of the oxygen-binding sites of myoglobin and some inorganic heme analogues, and of tree and fungal laccase and cytochrome c oxidase.
\r\n\r\nNitric oxide reacts with heme iron in ferrous hemeproteins such as hemoglobin and myoglobin, to form six-coordinate paramagnetic complexes. Chapter II reports investigations on the EPR spectra of the nitric oxide complexes of ferrous myoglobin, cytochrome c, and Fe(II) protoporphyrin IX-imidazole, which change with temperature over the range 30-180 K. This temperature dependence could be due to motional/relaxation effects or to a chemical equilibrium. To resolve this matter, the technique of factor analysis was used to deconvolute the temperature-dependent EPR spectra. By this method it has been found that all of the spectra for any given complex can be reproduced by adding together varied amounts of two signals, demonstrating that the variation of the EPR spectra with temperature is due to an equilibrium between two species. The two species differ in enthalpy by no more than about 2 kcal/mol. The observed signals are interpreted as arising from two six-coordinate conformers of the nitrosylheme\u2219nitrogen base complexes, differing primarily in the position of the iron with respect to the ligands and to the heme plane. The anomalous behavior of the terminal respiratory enzyme cytochrome c oxidase, which exhibits only one EPR signal independent of temperature, suggests that the NO-oxygen may interact with the cuprous ion at the cytochrome a3-Cua3 site of the enzyme. These results have implications for studies in general on oxygen-carrying proteins.
\r\n\r\nIn addition to being a strong-field ligand, NO is also a reactive molecule which can be oxidized to NO-2 and NO-3, and reduced to N2O, N2 and NH3. Chapter III details investigations of the reactions of NO with the copper-containing oxidases tree and fungal laccase, as well as with tree laccase depleted in type 2 copper. The oxidation states of the enzymes were monitored by EPR and optical spectroscopy, and the reaction products of NO were determined by NMR and mass spectroscopy. These studies show that NO reduces all three copper sites of fungal laccase. In addition, NO forms a specific complex with the reduced type 2 copper. NO similarly reduces all of the copper sites in tree laccase, but it also oxidizes the reduced sites produced by ascorbate or NO reduction. A catalytic cycle is set up in which N2O, NO-2 and various forms of the enzyme are produced. On freezing of fully reduced tree laccase in the presence of NO, the type 1 copper becomes reoxidized. This reaction does not occur with the enzyme depleted in type 1 copper, suggesting that it involves intramolecular electron transfer from the type 1 copper to NO bound to the type 2 copper. When the half-oxidized tree laccase is formed in the presence of NO, a population of molecules exists which exhibits a type 3 EPR signal. A triplet EPR signal is also seen in the same preparation, and is attributed to a population of the enzyme molecules in which NO is bound to the reduced copper of a half-oxidized type 3 copper site. The implications of these results towards the structures of tree and fungal laccase are discussed.
\r\n\r\nNitric oxide has also been used to probe the structure of the metal centers of cytochrome c oxidase, resulting in the discovery of three stable conformations of the oxidized enzyme [G. W. Brudvig, T. H. Stevens, R. H. Morse and S. I. Chan (1981) Biochemistry 20, in press]. These conformat1onsdiffer in the structure of the cytochrome a3-Cua3 site, which is the site of oxygen reduction, and are distinguishable by EPR spectroscopy. Two of the diagnostic EPR signals are unusual in that they cannot be interpreted simply in terms of normal Cu(II) or Fe(III) EPR signals. The \"g5\" conformation identified as a transient species occurring upon reoxidation of the reduced enzyme by O2 [R. W. Shaw, R. E. Hansen and H. Beinert (1978) J. Biol. Chem. 253, 6637-6640] similarly exhibits an EPR signal not subject to simple interpretation. In view of the complexity of these three EPR signals, they are most likely due to the coupled cytochrome a3+3-Cua3+2 site of the oxidized enzyme. Chapter IV describes calculations of the energy levels of, and allowed EPR transitions from, the cytochrome a3-Cua3 site under various conditions of exchange coupling and dipolar coupling, as a function of other parameters such as the magnitude of the rhombic zero-field splitting of the heme iron and distance between the two metal ions. On the basis of these calculations, one of the three unusual EPR signals from oxidized cytochrome c oxidase is deduced to arise from a strongly exchange-coupled (|J| > 200 cm-1) cytochrome a3+3-Cua3+2 site, one from a weakly exchange-coupled (|J| > 0.25 cm-1) cytochrome a3+3-Cua3+2 site, and one from an admixture of S = 5/2 and S = 3/2 states of the cytochrome a3+3 site.
", "doi": "10.7907/7cva-0k93", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:122", "collection": "thesis", "collection_id": "122", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01112005-143434", "type": "thesis", "title": "I. Electrophilic Reactions of p-Toluenesulfonyl Azide. II. \u00b9\u2075N and \u00b9\u00b3C Nuclear Magnetic Studies of Aryldiazonium Compounds Effect of Substituent, Solvent and 18-Crown-6", "author": [ { "family_name": "Casewit", "given_name": "Carla Jutta", "clpid": "Casewit-Carla-Jutta" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Roberts", "given_name": "John D.", "clpid": "Roberts-J-D" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I
\r\n\r\nElectrophilic Reactions of p-Toluenesulfonyl Azide
\r\n\r\nSection 1. Review of Electrophilic Reactions of p-Toluenesulfonyl Azide
\r\n\r\nThe electrophilic reactions of p-toluenesulfonyl azide are reviewed using the principles of hard and soft acids and bases (HSAB).
\r\n\r\nSection 2. The Reaction of p-Toluenesulfonyl Azide with the Sodium Salt of p-Toluenesulfonamide
\r\n\r\nA number of concurrent reactions of p-toluenesulfonyl azide-3-15N (I-3-15N) with the sodium salt of p-toluenesulfonamide were followed by 15N NMR. I-2-15N is formed as a result of a degenerate diazo transfer by I-3-15N to p-toluenesulfonamide anion. p-Toluenesulfonamide anion also reacts with 1-3-15N to give di-p-toluenesulfonamide and azide ion. The 15-N-labeled azide ion exchanges with I to give I-1-15N. I also reacts with azide ion, yielding dinitrogen and p-toluenesulfinate anion. The sulfinate salt reacts readily and reversibly with I to give 1,3-di-p-toluenesulfontriazene anion, which provides another pathway for interconversion of 1-3-15N and I-1-15N.
\r\n\r\nSection 3. The Reaction of p-Toluenesulfonyl Azide with Potassium Azide
\r\n\r\nThe reaction of p-toluenesulfonyl azide with potassium azide-1-15N has been examined in toluene and dichloromethane by 15N NMR. In addition to azide-ion exchange leading to 1-1-15N and I-3-15N, the formation of 1-2-15N is indicated. Two mechanisms for this novel scrambling are proposed. Azide-ion metathesis involving reversible formation of an N-Pentazole derivative from I and azide ion, followed by azide exchange could account for the formation of 1-2-15N. Alternatively, a scrambling route involving the reversible addition of p-toluenesulfonylnitrene to 1-3-15N can be envisioned. The inhibition of scrambling in dichloromethane by addition of iodide ion suggests that a discrete p-toluenesulfonyl azide \u2013 azide ion intermediate is involved in any case.
\r\n\r\nPart II
\r\n\r\n15N and 13C Nuclear Magnetic Resonance Studies of Aryldiazonium Compounds. Effect of Substituent, Solvent and 18-Crown-6.
\r\n\r\n15N and 13C shifts induced by addition of one equivalent of 18-crown-6 have been determined for several para-substituted aryldiazonium fluoborates in dimethylformamide. The \u03b1-nitrogen (N1) and para carbon (C4) shift upfield and the \u03b2-nitrogen (N2) and C1 shift downfield on complexation. The effect of solvent on the positions of the 15N and 13C resonances of p-(n-butyl)benzenediazonium fluoborate are small. The influence of substituents on the 15N chemical shifts is relatively large and comparable to the effect of 18-crown-6. These 13C and 15N results, in conjunction with previous spectroscopic studies indicate that the crown ether complexed aryldiazonium cation is electronically more diazonium-like and less diazo-like than the uncomplexed form.
", "doi": "10.7907/nyft-yr23", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:8984", "collection": "thesis", "collection_id": "8984", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06042015-131748215", "primary_object_url": { "basename": "Berman_dw_1981.pdf", "content": "final", "filesize": 16620458, "license": "other", "mime_type": "application/pdf", "url": "/8984/1/Berman_dw_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "I. Thermochemistry and Reaction Kinetics of Disolvated Protons by Ion Cyclotron Resonance Spectroscopy. II. Thermochemical Studies of Small Fluorocarbons by Photoionization Mass Spectrometry", "author": [ { "family_name": "Berman", "given_name": "D. Wayne", "clpid": "Berman-D-Wayne" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Janda", "given_name": "Kenneth C.", "clpid": "Janda-K-C" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The disolvated proton, H(OH2)2+ is employed as a chemical reagent in low pressure (\u02c2 10-5 torr) investigations by ion cyclotron resonance spectroscopy. Since termolecular reactions are absent at low pressure, disolvated protons are not generally observed. However H(OH2)2+ is produced in a sequence of bimolecular reactions in mixtures containing H2O and one of a small number of organohalide precursors. Then a series of hydrated Lewis bases is produced by H3O+ transfer from H(OH2)2+. In Chapter II, the relative stability of hydrated bases containing heteroatoms of both first and second row elements is determined from the preferred direction of H3O+ transfer between BH(OH2)+ complexes. S and P containing bases are shown to bind H3O+ more weakly than O and N bases with comparable proton affinities. A simple model of hydrogen bonding is proposed to account for these observations.
\r\n\r\nH+ transfer from H(OH2)2+ to several Lewis bases also occurs at low pressure. In Chapter III the relative importance of H3O+ transfer and H+ transfer from H(OH2)2+ to a series of bases is observed to be a function of base strength. Beginning with CH3COOH, the weakest base for which H+ transfer is observed, the importance of H+ transfer increases with increasing proton affinity of the acceptor base. The nature of neutral products formed from H(OH2)2+ by loss of H+ is also considered.
\r\n\r\nChapters IV and V deal with thermochemistry of small fluorocarbons determined by photoionization mass spectrometry. The enthalpy of formation of CF2 is considered in Chapter IV. Photoionization of perfluoropropylene, perfluorocyclopropane, and trifluoromethyl benzene yield onsets for ions formed by loss of a CF2 neutral fragment. Earlier determinations of \u0394H\u00b0f298 (CF2) are reinterpreted using updated thermochemical values and compared with results of this study. The heat of formation of neutral perfluorocyclopropane is also derived. Finally, the energetics of interconversion of perfluoropropylene and perfluorocyclopropane are considered for both the neutrals and their molecular ions.
\r\n\r\nIn Chapter V the heats of formation of CF3+ and CF3I+are derived from photoionization of CF3I. These are considered with respect to ion-molecule reactions observed in CF3I monitored by the techniques of ion cyclotron resonance spectroscopy. Results obtained in previous experiments are also compared.
\r\n", "doi": "10.7907/grqm-wy30", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:483", "collection": "thesis", "collection_id": "483", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02032005-112022", "type": "thesis", "title": "Theoretical Studies of Homogeneous Catalysis by Transition Metal Complexes", "author": [ { "family_name": "Rapp\u00e9", "given_name": "Anthony Kay", "clpid": "Rapp\u00e9-Anthony-Kay" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Grubbs", "given_name": "Robert H.", "orcid": "0000-0002-0057-7817", "clpid": "Grubbs-R-H" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "CHAPTER 1: Extensive ab initio calculations (double zeta plus polarization function basis with correlated wavefunctions) on the oxidation of hydrocarbons by chromyl chloride are combined with standard thermochemical methods to predict the energetics for oxidation of alkanes, alcohols, and alkenes. Additional results are presented on the analogous oxidations by molybdyl chloride. A common feature of all these reactions is identified and explained.
\r\n\r\nCHAPTER 2: Extensive ab initio calculations (double zeta plus polarization function basis with correlated wavefunctions) on the olefin metathesis reaction with high valent Mo and W catalysts are combined with standard thermochemical methods to predict the energetics of potential intermediates. The active catalyst is identified and explained together with several subsidiary features of the reaction manifold.
\r\n\r\nCHAPTER 3: A unifying generalized valence bond view of transition metal ligand bonding is presented as well as the energetics and structural characteristics of several ligand types. Additionally, the energetics for several ligand exchange reactions of potential synthetic utility are presented.
", "doi": "10.7907/8kc4-gq42", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:4964", "collection": "thesis", "collection_id": "4964", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12122006-090129", "type": "thesis", "title": "Investigations of Schottky Barrier Structures in Compound Semiconductors: I. HgTe on CdTe: a Lattice Matched Schottky Barrier. II. Au-Cd Barriers to CdTe. III. AAu Barriers on In\u2093Ga\u2081\u208b\u2093P", "author": [ { "family_name": "Kuech", "given_name": "Thomas Francis", "clpid": "Kuech-Thomas-Francis" } ], "thesis_advisor": [ { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" } ], "thesis_committee": [ { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Rutledge", "given_name": "David B.", "clpid": "Rutledge-D-B" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "i) The Au Schottky barrier height to n - InxGa1-xP was measured as a function of alloy composition. The Au barrier, \u03c6p, to p - InxGa1-xP was found to be independent of composition. The barrier, \u03c6p, was determined by the relation \u03c6p + \u03c6n = \u03c6g where \u03c6g is the band gap energy and \u03c6n is the measured barrier height to n - InxGa1-xP. It has been observed that the Au barrier height to p-type material for most compound semiconductors is determined by the anion. This dependence on the anion of the compound has now been seen to extend to the alloy system InxGa1-xP measured here.
\r\n\r\nii) The Schottky barrier height of Cd, Au, and Au-Cd alloys was determined on vacuum cleaved surfaces of n-CdTe. A large barrier of 0.92 eV was found in the case of the Au-Cd alloy contacts. Contacts made with elemental Cd or Au gave barrier heights of 0.45 and 0.65 eV, respectively. The increased barrier height found on Au-Cd alloy contacts may be related to recent UHV observations on Schottky barrier formation where crystal defects play a role in determining the observed barrier height.
\r\n\r\niii) HgTe-CdTe lattice matched heterojunctions were formed by the epitaxial growth of HgTe on CdTe substrates using a new low temperature metal organic chemical vapor deposition (MOCVD) technique. These heterojunctions combine features of the Schottky barrier structure, due to the high carrier concentrations found in the semi-metallic HgTe, with the structural perfection present in a lattice matched heterojunction. The measured Schottky barrier height varied from 0.65 to 0.90 eV depending on the details of the HgTe growth procedure used. Two models of the HgTe-CdTe heterojunction are presented which account for the observed variation in barrier height.
", "doi": "10.7907/8hcw-7421", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:4964", "collection": "thesis", "collection_id": "4964", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12122006-090129", "type": "thesis", "title": "Investigations of Schottky Barrier Structures in Compound Semiconductors: I. HgTe on CdTe: a Lattice Matched Schottky Barrier. II. Au-Cd Barriers to CdTe. III. AAu Barriers on In\u2093Ga\u2081\u208b\u2093P", "author": [ { "family_name": "Kuech", "given_name": "Thomas Francis", "clpid": "Kuech-Thomas-Francis" } ], "thesis_advisor": [ { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" } ], "thesis_committee": [ { "family_name": "McCaldin", "given_name": "James Oeland", "clpid": "McCaldin-J-O" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "McGill", "given_name": "Thomas C.", "clpid": "McGill-T-C" }, { "family_name": "Rutledge", "given_name": "David B.", "clpid": "Rutledge-D-B" }, { "family_name": "Nicolet", "given_name": "Marc-Aurele", "clpid": "Nicolet-M-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "i) The Au Schottky barrier height to n - InxGa1-xP was measured as a function of alloy composition. The Au barrier, \u03c6p, to p - InxGa1-xP was found to be independent of composition. The barrier, \u03c6p, was determined by the relation \u03c6p + \u03c6n = \u03c6g where \u03c6g is the band gap energy and \u03c6n is the measured barrier height to n - InxGa1-xP. It has been observed that the Au barrier height to p-type material for most compound semiconductors is determined by the anion. This dependence on the anion of the compound has now been seen to extend to the alloy system InxGa1-xP measured here.
\r\n\r\nii) The Schottky barrier height of Cd, Au, and Au-Cd alloys was determined on vacuum cleaved surfaces of n-CdTe. A large barrier of 0.92 eV was found in the case of the Au-Cd alloy contacts. Contacts made with elemental Cd or Au gave barrier heights of 0.45 and 0.65 eV, respectively. The increased barrier height found on Au-Cd alloy contacts may be related to recent UHV observations on Schottky barrier formation where crystal defects play a role in determining the observed barrier height.
\r\n\r\niii) HgTe-CdTe lattice matched heterojunctions were formed by the epitaxial growth of HgTe on CdTe substrates using a new low temperature metal organic chemical vapor deposition (MOCVD) technique. These heterojunctions combine features of the Schottky barrier structure, due to the high carrier concentrations found in the semi-metallic HgTe, with the structural perfection present in a lattice matched heterojunction. The measured Schottky barrier height varied from 0.65 to 0.90 eV depending on the details of the HgTe growth procedure used. Two models of the HgTe-CdTe heterojunction are presented which account for the observed variation in barrier height.
", "doi": "10.7907/8hcw-7421", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:10778", "collection": "thesis", "collection_id": "10778", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03222018-134525550", "primary_object_url": { "basename": "Thiel_PA_1981.pdf", "content": "final", "filesize": 148736950, "license": "other", "mime_type": "application/pdf", "url": "/10778/1/Thiel_PA_1981.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Adsorption, Co-Adsorption and Catalytic Reactions on Rh(111) and Ru(001) Surfaces", "author": [ { "family_name": "Thiel", "given_name": "Patricia Ann", "clpid": "Thiel-Patricia-Ann" } ], "thesis_advisor": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" } ], "thesis_committee": [ { "family_name": "Bercaw", "given_name": "John E.", "clpid": "Bercaw-J-E" }, { "family_name": "Weinberg", "given_name": "William Henry", "clpid": "Weinberg-W-H" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Kuppermann", "given_name": "Aron", "clpid": "Kuppermann-A" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The adsorption of oxygen, hydrogen, carbon monoxide , nitric oxide and water on Rh(111) and Ru(001) surfaces has been studied using the techniques of high-resolution electron energy loss spectroscopy, low-energy electron diffraction, Auger electron spectroscopy, ultraviolet photoelectron spectroscopy and thermal desorption mass spectrometry. In many cases co-adsorption experiments have provided insight into the nature of interaction between different adsorbates, with potential implications for heteroqeneous catalytic reaction mechanisms.
\r\n\r\nThe interaction of oxygen with Rh(111) consists of adsorption, irreversible thermally induced ordering and disordering phenomena, dissolution into the subsurface region and desorption. The thermodynamic parameters which describe these phenomena have been investigated. The forms of the kinetic rate expressions for the catalytic reaction of adsorbed oxygen with hydrogen are different for ordered and disordered arrays of oxygen adatoms. In agreement with co-adsorption studies of hydrogen and oxygen, and supported by studies of hydrogen chemisorption on clean Rh(111), this implies that the rate of adsorption of hydrogen is sensitive to the structure of the adsorbed oxygen lattice.
\r\n\r\nTwo forms of molecularly adsorbed NO are readily distinguished on a Ru(001) surface by the frequencies of the nitrogen-oxygen stretching vibrations, which can then be used to observe the influence of co-adsorbates. Oxygen, nitrogen and hydrogen adatoms compete selectively for the adsites which are occupied by multiply-coordinated NO, whereas CO competes for adsites occupied by the singly-coordinated molecular NO. Carbon monoxide can even induce conversion of adsorbed molecular NO from sites of single coordination to sites of multiple coordination with the metal substrate.
\r\n\r\nWater interacts with the Ru(001) surface to form chemisorption bonds, but it also forms intermolecular hydrogen bonds which are of comparable strength. This leads to formation of layered, hydrogen bonded aggregates at all coverages. The properties of the first two layers are distinct from those of the subsequent ice multilayers, and a specific structural model for the hydrogen bonded lattices is proposed. A thermally induced ordering effect is observed which is analogous to the vitreous-to-cubic phase transformation of bulk ice.
", "doi": "10.7907/8m9w-p414", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:14025", "collection": "thesis", "collection_id": "14025", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12112020-012735380", "type": "thesis", "title": "NMR Studies of Cooperativity in Hemoglobin", "author": [ { "family_name": "Adler", "given_name": "George", "clpid": "Adler-George" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Raftery", "given_name": "Michael A.", "clpid": "Raftery-M-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "PART I
\r\n\r\nIn this part the binding of ligands, like oxygen and carbonmonoxide to hemoglobin and myoglobin, and the connection between the physiological functions and the structure of these proteins are discussed. The allosteric models, which have been proposed to explain the cooperative binding of oxygen, and the effect of single residue mutations on the structure of hemoglobin are reviewed. Finally, questions which have not yet been satisfactorily answered are raised about the structure and function of hemoglobin.
\r\n\r\nPART II
\r\n\r\nThe binding of carbon monoxide to rabbit hemoglobin and to trifluoroacetonylated rabbit hemoglobin has been studied by \u00b9\u00b3C NMR and by \u00b9\u2079F NMR. The \u00b9\u00b3C NMR studies show that CO binds preferentially to the \u03b2 chains of rabbit hemoglobin in the absence of effectors such as 2,3-diphosphoglycerate (DPG) and inositol hexaphosphate.
\r\n\r\nThe \u00b9\u2079F spectrum of trifluoroacetonylated human adult hemoglobin, at low CO or O\u2082 ligation, indicated preferential a chain ligation (Huestis and Raftery, 1973, Biochemistry 12, 2531). There is a linear relationship between the fraction of the ligated signal of trifluoroacetonylated rabbit hemoglobin as monitored by \u00b9\u2079F NMR and the overall ligation detected by optical density measurements at 650 nm. Therefore, the trifluoroacetonyl label does not, in the case of rabbit hemoglobin, distinguish initial \u03b2 ligation from random ligation.
\r\n\r\nBoth in the absence of and in the presence of DPG, the \u00b9\u2079F spectra of partially ligated trifluoroacetonylated rabbit hemoglobin reveal only two significant resonances. These two resonances, which correspond to the deoxy (tense) and ligated (relaxed) structures of hemoglobin, are joined by two additional resonances when inositol hexaphosphate is added to the solution. The new resonances are presumably due to hemoglobin in intermediate structures between the relaxed and tense states.
\r\n\r\nThe \u00b9\u2079F chemical shifts of the deoxy and ligated TF labelled hemoglobin change due to the addition of organic phosphates. This observation implies that the organic phosphates bind to hemoglobin in both the deoxy and the ligated states.
\r\n\r\nPART III
\r\n\r\nTitrations of trifluoroacetonyl labelled human deoxy-, oxy-, carbonmonoxy-, nitrosylhemoglobin, aquamethemoglobin and cyanomethemoglobin have been followed by \u00b9\u2079F NMR. The titration curve of trifluoroacetonyl human deoxyhemoglobin (HbTF) in the presence or absence of 2,3-diphosphoglycerate (DPG) is similar to that found by Huestis and Raftery (Proc. Natl. Acad. Sci. USA (1972) 69, 1887). Nitrosyl-, oxy-, and carbonmonoxy-HbTF in the absence of effectors exhibit pH dependence only below pH 5.5. The addition of inositol hexaphosphate (IHP) resulted in large upfield shifts of the fluorine resonance of HbTF(NO)\u2084, HbTF(O\u2082)\u2084. In addition, the fluorine signal of HbTF(CO)\u2084 and HbTF(O\u2082) exhibited large linewidths which is evidence for the exchange between two structures. The addition of DPG to HbTF(NO)\u2084 below pH 7.4 results in the appearance of a second resonance which indicates the presence of two different protein structures.
\r\n\r\nThe titration of the labelled aquarnethemoglobin in the presence or in the absence of DPG supports the results of Huestis and Raftery (1972). In the presence of IHP trifluoroacetonyl Hb\u207a(CN\u207b)\u2084 shows a complicated \u00b9\u2079F spectra which suggests that cyanornethernoglobin can have three different structures. The implication of these results on the mechanism of cooperativity and on the two state model is discussed.
\r\n\r\nPART IV
\r\n\r\nThe intracellular pH, and the binding of intracellular 2,3-diphosphoglycerate (2,3-DPG) to hemoglobin are studied in AA and SS blood. There is no significant difference in the intracellular pH of AA and SS erythrocytes in the fully oxygenated state. However, in the \u00b3\u00b9P spectrum of deoxygenated AA blood the resonance due to 2-P of 2,3-DPG is downfield, while in the \u00b3\u00b9P spectrum of deoxygenated SS blood this resonance is upfield, from the chemical shift of the same phosphorous signal in oxygenated blood. This difference in \u00b3\u00b9P chemical shifts is likely due to a lower intracellular pH of the SS erythrocytes relative to the AA erythrocytes.
", "doi": "10.7907/089e-bj69", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:14025", "collection": "thesis", "collection_id": "14025", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12112020-012735380", "type": "thesis", "title": "NMR Studies of Cooperativity in Hemoglobin", "author": [ { "family_name": "Adler", "given_name": "George", "clpid": "Adler-George" } ], "thesis_advisor": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" } ], "thesis_committee": [ { "family_name": "Dervan", "given_name": "Peter B.", "orcid": "0000-0001-8852-7306", "clpid": "Dervan-P-B" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Raftery", "given_name": "Michael A.", "clpid": "Raftery-M-A" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "PART I
\r\n\r\nIn this part the binding of ligands, like oxygen and carbonmonoxide to hemoglobin and myoglobin, and the connection between the physiological functions and the structure of these proteins are discussed. The allosteric models, which have been proposed to explain the cooperative binding of oxygen, and the effect of single residue mutations on the structure of hemoglobin are reviewed. Finally, questions which have not yet been satisfactorily answered are raised about the structure and function of hemoglobin.
\r\n\r\nPART II
\r\n\r\nThe binding of carbon monoxide to rabbit hemoglobin and to trifluoroacetonylated rabbit hemoglobin has been studied by \u00b9\u00b3C NMR and by \u00b9\u2079F NMR. The \u00b9\u00b3C NMR studies show that CO binds preferentially to the \u03b2 chains of rabbit hemoglobin in the absence of effectors such as 2,3-diphosphoglycerate (DPG) and inositol hexaphosphate.
\r\n\r\nThe \u00b9\u2079F spectrum of trifluoroacetonylated human adult hemoglobin, at low CO or O\u2082 ligation, indicated preferential a chain ligation (Huestis and Raftery, 1973, Biochemistry 12, 2531). There is a linear relationship between the fraction of the ligated signal of trifluoroacetonylated rabbit hemoglobin as monitored by \u00b9\u2079F NMR and the overall ligation detected by optical density measurements at 650 nm. Therefore, the trifluoroacetonyl label does not, in the case of rabbit hemoglobin, distinguish initial \u03b2 ligation from random ligation.
\r\n\r\nBoth in the absence of and in the presence of DPG, the \u00b9\u2079F spectra of partially ligated trifluoroacetonylated rabbit hemoglobin reveal only two significant resonances. These two resonances, which correspond to the deoxy (tense) and ligated (relaxed) structures of hemoglobin, are joined by two additional resonances when inositol hexaphosphate is added to the solution. The new resonances are presumably due to hemoglobin in intermediate structures between the relaxed and tense states.
\r\n\r\nThe \u00b9\u2079F chemical shifts of the deoxy and ligated TF labelled hemoglobin change due to the addition of organic phosphates. This observation implies that the organic phosphates bind to hemoglobin in both the deoxy and the ligated states.
\r\n\r\nPART III
\r\n\r\nTitrations of trifluoroacetonyl labelled human deoxy-, oxy-, carbonmonoxy-, nitrosylhemoglobin, aquamethemoglobin and cyanomethemoglobin have been followed by \u00b9\u2079F NMR. The titration curve of trifluoroacetonyl human deoxyhemoglobin (HbTF) in the presence or absence of 2,3-diphosphoglycerate (DPG) is similar to that found by Huestis and Raftery (Proc. Natl. Acad. Sci. USA (1972) 69, 1887). Nitrosyl-, oxy-, and carbonmonoxy-HbTF in the absence of effectors exhibit pH dependence only below pH 5.5. The addition of inositol hexaphosphate (IHP) resulted in large upfield shifts of the fluorine resonance of HbTF(NO)\u2084, HbTF(O\u2082)\u2084. In addition, the fluorine signal of HbTF(CO)\u2084 and HbTF(O\u2082) exhibited large linewidths which is evidence for the exchange between two structures. The addition of DPG to HbTF(NO)\u2084 below pH 7.4 results in the appearance of a second resonance which indicates the presence of two different protein structures.
\r\n\r\nThe titration of the labelled aquarnethemoglobin in the presence or in the absence of DPG supports the results of Huestis and Raftery (1972). In the presence of IHP trifluoroacetonyl Hb\u207a(CN\u207b)\u2084 shows a complicated \u00b9\u2079F spectra which suggests that cyanornethernoglobin can have three different structures. The implication of these results on the mechanism of cooperativity and on the two state model is discussed.
\r\n\r\nPART IV
\r\n\r\nThe intracellular pH, and the binding of intracellular 2,3-diphosphoglycerate (2,3-DPG) to hemoglobin are studied in AA and SS blood. There is no significant difference in the intracellular pH of AA and SS erythrocytes in the fully oxygenated state. However, in the \u00b3\u00b9P spectrum of deoxygenated AA blood the resonance due to 2-P of 2,3-DPG is downfield, while in the \u00b3\u00b9P spectrum of deoxygenated SS blood this resonance is upfield, from the chemical shift of the same phosphorous signal in oxygenated blood. This difference in \u00b3\u00b9P chemical shifts is likely due to a lower intracellular pH of the SS erythrocytes relative to the AA erythrocytes.
", "doi": "10.7907/089e-bj69", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:747", "collection": "thesis", "collection_id": "747", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02242009-110155", "primary_object_url": { "basename": "Freiser_bs_1977.pdf", "content": "final", "filesize": 5683247, "license": "other", "mime_type": "application/pdf", "url": "/747/1/Freiser_bs_1977.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Photochemical Investigations of Ions in the Gas Phase Utilizing Ion Cyclotron Resonance Spectroscopy", "author": [ { "family_name": "Freiser", "given_name": "Ben Sherman", "clpid": "Freiser-Ben-Sherman" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Hammond", "given_name": "George Simms", "clpid": "Hammond-G-S" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The photochemistry and photophysical processes of a broad range of ions have been studied in the gas phase using ion cyclotron resonance techniques. A discussion summarizing much of this work, and two papers on related topics are presented.\r\n\r\nIn paper I, \"Acid-Base Properties of Molecules in Excited Electronic States Utilizing Ion Cyclotron Resonance Spectroscopy\", a general method is described for obtaining excited state acid-base properties of molecules and ions in the gas Phase which utilizes ion cyclotron resonance spectroscopy for studying photochemical processes involving ions. These processes, including photodissociation and photodetachment, yield in favorable instances, electronic excitation energies of ions. A comparison of the excitation energies of a base B with the corresponding acid-base complex AB yields the excited state basicity of B. Similarly, a comparison of the excitation energies of a chromophoric acid A with the complex AB yields information about the excited state acidity of A. Studies of the first type are described using the reference acids H[superscript +] and Li[superscript +] with the bases C6H5X (X = H, CN, NH2, CHO, COCH3, NO2, OCH3, O[superscript -], and S[superscript -) pyridine, and ferrocene. In several instances photodissociation spectra of solvated acid-base complexes of the type BLib[with a + above the L] have been obtained and analyzed to determine the effects of further solvation on the excitation spectra of these complexes. A comparison of the gas phase excitation spectra of a number of ions to their solution absorption is made.\r\n\r\nStudies of the second type (excited state acidities) are described using the reference base H[superscript -] with the acids C6H5CO[superscript +] and C6H5CHOH[superscript +]. Calculated changes in acidity and basicity are used to infer changes in electron distributions and dipole moments for excited states, and yield insight into the types of transitions involved. In particular, these studies are used to assess the controversial role played by intra-molecular charge transfer in the lowest two singlet \u03c0\u2192\u03c0* transitions of monosubstituted benzenes. These results are compared with findings from related experiments and calculations when available.\r\n\r\nPaper II, entitled \"Electron Impact Dissociation of Cyanobenzene Radical Cations by Ion Cyclotron Resonance Spectroscopy\", describes using trapped ion cyclotron resonance spectroscopy for the first time to study the electron impact dissociation of ions. Fragmentation of C6H5CN[superscript +] to produce C6H4[superscript +] and HCN is observed to occur at low electron energies (3-9 eV). The extent of dissociation is observed to be linear in emission current, rising from a threshold at 3.0 \u00b1 0.5 eV to a maximum cross section estimated to be 6 \u00c5[superscript 2] at 7.5 \u00b1 0.5 eV. The implications of these results are discussed.\r\n", "doi": "10.7907/HMVE-Q508", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" }, { "id": "thesis:747", "collection": "thesis", "collection_id": "747", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02242009-110155", "primary_object_url": { "basename": "Freiser_bs_1977.pdf", "content": "final", "filesize": 5683247, "license": "other", "mime_type": "application/pdf", "url": "/747/1/Freiser_bs_1977.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Photochemical Investigations of Ions in the Gas Phase Utilizing Ion Cyclotron Resonance Spectroscopy", "author": [ { "family_name": "Freiser", "given_name": "Ben Sherman", "clpid": "Freiser-Ben-Sherman" } ], "thesis_advisor": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" }, { "family_name": "Hammond", "given_name": "George Simms", "clpid": "Hammond-G-S" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The photochemistry and photophysical processes of a broad range of ions have been studied in the gas phase using ion cyclotron resonance techniques. A discussion summarizing much of this work, and two papers on related topics are presented.\r\n\r\nIn paper I, \"Acid-Base Properties of Molecules in Excited Electronic States Utilizing Ion Cyclotron Resonance Spectroscopy\", a general method is described for obtaining excited state acid-base properties of molecules and ions in the gas Phase which utilizes ion cyclotron resonance spectroscopy for studying photochemical processes involving ions. These processes, including photodissociation and photodetachment, yield in favorable instances, electronic excitation energies of ions. A comparison of the excitation energies of a base B with the corresponding acid-base complex AB yields the excited state basicity of B. Similarly, a comparison of the excitation energies of a chromophoric acid A with the complex AB yields information about the excited state acidity of A. Studies of the first type are described using the reference acids H[superscript +] and Li[superscript +] with the bases C6H5X (X = H, CN, NH2, CHO, COCH3, NO2, OCH3, O[superscript -], and S[superscript -) pyridine, and ferrocene. In several instances photodissociation spectra of solvated acid-base complexes of the type BLib[with a + above the L] have been obtained and analyzed to determine the effects of further solvation on the excitation spectra of these complexes. A comparison of the gas phase excitation spectra of a number of ions to their solution absorption is made.\r\n\r\nStudies of the second type (excited state acidities) are described using the reference base H[superscript -] with the acids C6H5CO[superscript +] and C6H5CHOH[superscript +]. Calculated changes in acidity and basicity are used to infer changes in electron distributions and dipole moments for excited states, and yield insight into the types of transitions involved. In particular, these studies are used to assess the controversial role played by intra-molecular charge transfer in the lowest two singlet \u03c0\u2192\u03c0* transitions of monosubstituted benzenes. These results are compared with findings from related experiments and calculations when available.\r\n\r\nPaper II, entitled \"Electron Impact Dissociation of Cyanobenzene Radical Cations by Ion Cyclotron Resonance Spectroscopy\", describes using trapped ion cyclotron resonance spectroscopy for the first time to study the electron impact dissociation of ions. Fragmentation of C6H5CN[superscript +] to produce C6H4[superscript +] and HCN is observed to occur at low electron energies (3-9 eV). The extent of dissociation is observed to be linear in emission current, rising from a threshold at 3.0 \u00b1 0.5 eV to a maximum cross section estimated to be 6 \u00c5[superscript 2] at 7.5 \u00b1 0.5 eV. The implications of these results are discussed.\r\n", "doi": "10.7907/HMVE-Q508", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" } ]