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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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:10635", "collection": "thesis", "collection_id": "10635", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01102018-113108870", "primary_object_url": { "basename": "Montgomery_W_2000.pdf", "content": "final", "filesize": 6142493, "license": "other", "mime_type": "application/pdf", "url": "/10635/1/Montgomery_W_2000.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Equation of State for Polymethylmethacrylate (PMMA)", "author": [ { "family_name": "Montgomery", "given_name": "Wren Bowlan", "clpid": "Montgomery-Wren-Bowlan" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "None", "given_name": "None" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "With ever-increasing computing power, simulations of larger, more complex systems\r\nare becoming more and more feasible. The ability to model systems, especially those\r\nnot easily studied in the laboratory, is desired. But with these strictly computational\r\nproblem there comes a question of accuracy. In this paper, a well-studied polymer,\r\npolymethylmethacrylate (PMMA), will verify the computational results obtained for\r\npolymers which are less easily (if at all) studied experimentally. Assuming that a\r\nsmall sample accurately represents the system as a whole, energy calculations with\r\nthe simulation engine Cerius2 will be used to determine a cold compression curve,\r\nfollowed by a series of molecular dynamics calculations to determine the Griineisen\r\nparameter. These calculations may be compared with the ample experimental evidence\r\navailable for PMMA, providing a calibration for those substances (such as\r\nKel-F) which cannot be studied experimentally. Further basis for comparision can be\r\nobtained using various viscoelastic and thermodynamic properties. Additionally, the\r\nGriineisen parameter may be used to revese the traditional experimental approach to\r\ncalculate the Hugoniot data, providing further basis for comparision and an opportunity\r\nfor improving the accuracy of the model.", "doi": "10.7907/ADK8-TW81", "publication_date": "2000", "thesis_type": "senior_major", "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:5309", "collection": "thesis", "collection_id": "5309", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-095619938", "primary_object_url": { "basename": "Brameld_ka_1999.pdf", "content": "final", "filesize": 10630762, "license": "other", "mime_type": "application/pdf", "url": "/5309/1/Brameld_ka_1999.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Molecular modeling of biological systems : from chitinase A to Z-DNA", "author": [ { "family_name": "Brameld", "given_name": "Kenneth A.", "clpid": "Brameld-K-A" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Quantum chemical methods and molecular dynamics simulations are used herein to address interesting problems associated with chemical systems of biological relevance. Two such systems are investigated: The mechanisms of family 18 and family 19 chitinases and the development of a force field for simulations of nucleic acids from first principles calculations.
\r\n\r\nChitinases catalyze the hydrolysis of chitin, a \u03b2(1,4)-linked N-acetyl-glucosamine polymer. Family 18 and family 19 chitinases are glycosyl hydrolases with different structures and mechanisms. Using a combination of quantum chemical and molecular dynamics methods, several interesting and unexpected features of the hydrolysis mechanisms of chitinases were discovered. Family 18 chitinases induce substrate distortion forcing the N-acetyl-glucosamine sugar bound at subsite -1 to adopt a boat conformation. Protonation of the \u03b2(1,4)-anomeric oxygen leads to spontaneous bond cleavage and the formation of an oxazoline ion intermediate. The oxazoline ion is stabilized through anchimeric assistance from the neighboring N-acetyl group. In contrast, family 19 chitinases do not induce substrate distortion and utilize an oxocarbenium ion intermediate. The first of two acidic residues in the active site serves to protonate the \u03b2(1,4)-anomeric oxygen while the second acidic residue stabilizes the oxocarbenium ion through a conformational change within a flexible loop of the enzyme. The second acidic residue also coordinates with and activates a water molecule for nucleophilic attack at the Cl' anomeric carbon to complete the hydrolysis mechanism.
\r\n\r\nFor molecular dynamics simulations of biomolecules, it is desirable to use accurate potential energy functions (force fields) which are also generic enough to be parameterized for most any conceivable molecule. A hierarchical approach is undertaken herein to achieve this flexibility and accuracy. To begin, a rule based force field (UFF) forms the foundation upon which additional parameters are added so as to reproduce structural and energetic properties important for nucleic acids. The specific substructures within nucleic acids which require additional parameterization are the phosphodiester backbone, sugar ring pseudorotation, glycosidic bond and base pair hydrogen bonding. The potential energy surfaces for each of these substructures are determined from high level quantum mechanical calculations and the force field parameterized to reproduce these results.
\r\n", "doi": "10.7907/mvyy-4570", "publication_date": "1999", "thesis_type": "phd", "thesis_year": "1999" }, { "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: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:5306", "collection": "thesis", "collection_id": "5306", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-084600422", "primary_object_url": { "basename": "Bertsch_ra_1998.pdf", "content": "final", "filesize": 23644128, "license": "other", "mime_type": "application/pdf", "url": "/5306/1/Bertsch_ra_1998.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The early events of protein folding : Simulations of polyalanine folding into an alpha-helix", "author": [ { "family_name": "Bertsch", "given_name": "Ruth Ann", "clpid": "Bertsch-R-A" } ], "thesis_advisor": [ { "family_name": "Chan", "given_name": "Sunney I.", "clpid": "Chan-S-I" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The kinetics of \u03b1-helix formation in polyalanine and polyglycine eicosamers (20-mers) were examined using the Newton-Euler Inverse Mass Operator (NEIMO) method (Jain et al. (1993) J. Comp. Phys. 106: 258-268), a new type of torsional coordinate molecular dynamics (MD). One hundred fifty-five (155) different MD experiments were carried out on extended (Ala)_(20) under identical conditions for 0.5 ns each, and 129 of the simulations (83%) formed a persistent \u03b1-helix. In contrast, the extended state of (Gly)_(20) only formed a right-handed \u03b1-helix in two of the 20 MD experiments (10%), and these helices were not as long or as persistent as those of polyalanine. This is consistent with the helix propensities of the natural amino acids.\r\n\r\nThe analysis of all 155 simulations show helix formation to be a competition between the rates of \r\n\r\n\t(a) forming local hydrogen bonds (i.e., hydrogen bonds between any residue i and \r\n\t its i + 2, i + 3, i + 4, or i + 5th neighbor) and\r\n\r\n\t(b) forming nonlocal hydrogen bonds (HBs) between residues widely separated in sequence.\r\n\r\nLocal HBs grow rapidly into an \u03b1-helix; but, nonlocal HBs usually retard helix formation by \"trapping\" the polymer in irregular, \"balled-up\" structures. Most trajectories formed some nonlocal HBs, sometimes as many as eight. But, for (Ala)_(20), most of these eventually rearranged to form local HBs that lead to \u03b1-helices. A simple kinetic model describes the rate of converting nonlocal HBs into \u03b1-helices.\r\n\r\nTorsional coordinate MD speeds folding by eliminating bond and angle degrees of freedom and reducing dynamical friction. Thus, the observed times of 80 to 500 ps are likely to be lower bounds on real rates. However, we believe the sequential steps observed here mirror those of real systems. When compensating for the effect of dynamic friction, the half live for \u03b1-helix formation of (Ala)_(20) is estimated to be 209 ps.\r\n\r\nChapters 2 and 3 describe two trajectories of (Ala)_(20) folding into an \u03b1-helix. Different types of analyses are used to understand the process of formation and simplify the megabytes of information available in each trajectory. Chapter 2 illustrates a trajectory that forms an \u03b1-helix fast, whereas Chapter 3 describes a trajectory where helix formation was retarded by nonlocal HBs.\r\n\r\nThese simulations attempt to elucidate the early events of protein folding. As elaborated in Chapter 1, the early events may be vital to controlling folding yield and the folding/aggregation partition.\r\n", "doi": "10.7907/vewx-3f78", "publication_date": "1998", "thesis_type": "phd", "thesis_year": "1998" }, { "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: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: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: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: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:5351", "collection": "thesis", "collection_id": "5351", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-085123252", "primary_object_url": { "basename": "Takeuchi_t_1996.pdf", "content": "final", "filesize": 4217602, "license": "other", "mime_type": "application/pdf", "url": "/5351/1/Takeuchi_t_1996.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Electronic Structure of Distorted Porphyins and Cobalt Schiff Base Derivatives as Novel Enzyme Inhibitors", "author": [ { "family_name": "Takeuchi", "given_name": "Toshihiko", "clpid": "Takeuchi-Toshihiko" } ], "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" }, { "family_name": "Meade", "given_name": "Thomas J.", "clpid": "Meade-T-J" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Halogenated porphyrins, which are catalysts for the oxidation of alkanes, were studied by semiempirical AM 1 calculations. The calculations predicted the effects of halogenation of the porphyrin ring on UV-visible absorption spectra and electrochemical data. Predictions regarding the stability of catalysts were made, and have been experimentally verified. INDO/S semiempirical calculations were performed on a series of porphyrins to understand the effects of a highly disfavored distortion that is conserved in cytochromes c. The highest occupied molecular orbitals were destabilized, and the orbital energy of the metal and the lowest unoccupied orbitals change, causing a shift in the redox potential of the heme and a change in the electron transfer properties of cytochromes c.\r\n\r\nIn order to delineate the anti-enzymatic properties of Co(acacen) derivatives, which are potent inhibitors of the herpes virus, carbonic anhydrase (CA), thermolysin (TL), and thrombin (TH) were chosen as targets Inhibition of CA occurs upon incubation with the novel water-soluble Co(II)hydroxypropylacacen (Co(II)hpr) but not with [Co(III)hpr(NH_3)_2 ^+(OAc)^- . The difference in reactivity of the species is a consequence of the steric limitations imposed by the axial ligands bound to the Co(III) complex. [Co(III)acacen(NH_3)_2^+ irreversibly inhibits TL, and this inhibition was prevented by binding a strong reversible inhibitor to the active site of the enzyme before addition of the cobalt species, suggesting that cobalt-acacen derivatives can inhibit enzymes by binding to active site histidines. In an effort to develop more potent and selective enzyme inhibitors, active site-directed peptides were coupled via a peptide bond through a carboxylic acid, which is part of the acacen ligand framework. The peptide coupled derivatives rapidly and irreversibly inhibited TH, and the potency of inhibition was over an order of magnitude better than the uncoupled components.\r\n", "doi": "10.7907/py88-c390", "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: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: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: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:4113", "collection": "thesis", "collection_id": "4113", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10162007-105256", "primary_object_url": { "basename": "Kiang_ch_1995.pdf", "content": "final", "filesize": 12241703, "license": "other", "mime_type": "application/pdf", "url": "/4113/1/Kiang_ch_1995.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Physics and chemistry of advanced nanoscale materials : experiment, simulation, and theory", "author": [ { "family_name": "Kiang", "given_name": "Ching-Hwa", "clpid": "Kiang-C" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis discusses simulation and theory of lattice dynamics as well as experiments on novel forms of carbon.\n\nA new crystalline AgBr interaction potential was constructed by fitting literature experimental data. The shell model was successfully used to account for the polarizabilities of the ions. This approach overcame difficulties previous investigators faced in determining the AgBr potential.\n\nThe very useful shell model was generalized to allow, for the first time, its use in dynamical simulations. The rapid shell dynamics, simulating the electron polarization, were integrated out in a generalized Born-Oppenheimer-like approach. The effective Hamiltonians were derived for both quantum and classical descriptions of the shells.\n\nThe first crystallization and characterization of a metallofullerene were performed. Endohedral metallofullerenes were synthesized and characterized. Metals such as Sc, Y, and Er that formed stable compounds in fullerene cages were synthesized and products purified. The crystal structure of Sc2C84 was determined by transmission electron microscopy study.\n\nExperimental studies on fullerenes and related materials lead to the first example of a catalytically-grown, fullerene-like material. We discovered that single-layer carbon nanotubes can be produced by vaporizing cobalt and carbon with an electric arc in a helium atmosphere. Catalyst promoters such as sulfur, bismuth, and lead were found not only to enhance the yield of single-layer nanotubes but also to produce tubes in a diameter range not accessible with cobalt alone. Sulfur, bismuth, and tungsten were found to catalyze the formation of cobalt crystals encapsulated in graphitic polyhedra. Various carbon structures were also produced concurrently, e.g. multilayer nanotubes, strings of carbon nanocompartments, carbon nanofibers, and metal-filled nanomaterials. Nanotubes were observed to undergo real-time structural changes under electron beam heating.\n\nA growth model of single-layer nanotube was formulated based on the experimental results. The carbon ring is regarded as the nanotube precursor, and cobalt carbide is regarded as the catalytic species that efficiently supplies carbon clusters to the open end of tube. The catalyst promoter assists the reaction by keeping the growing end open.\n", "doi": "10.7907/4t4q-5805", "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: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:5365", "collection": "thesis", "collection_id": "5365", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11112009-144801757", "primary_object_url": { "basename": "Plaxco_kw_1994.pdf", "content": "final", "filesize": 12205625, "license": "other", "mime_type": "application/pdf", "url": "/5365/1/Plaxco_kw_1994.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Protein-DNA interactions : molecular modeling and energetics", "author": [ { "family_name": "Plaxco", "given_name": "Kevin W.", "clpid": "Plaxco-K-W" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The thesis deals with the structural elements involved in and the energetics of sequence specific recognition of DNA.\r\n\r\nChapter 1 of the thesis provides a brief overview on the mechanics and applicability of molecular dynamics based methods for studying the structure and function of molecules of proteins, DNA and other macromolecules of biological relevance.\r\n\r\nChapter 2 presents a constrained molecular dynamics derived model we have developed for the DNA binding domain of the protein Hin Recombinase. Based on a combination of homology modeling and experimentally derived placement constraints we used molecular dynamics to conduct a search of conformation space constrained to remain consistent with the then known experimental characterizations of the protein. The model generated by this approach allowed us to correctly predict the sequence selectivity of the Hin, and lead to a number of insights into the nature of its sequence selectivity.\r\n\r\nChapter 3 discusses a variety of experimental results that have been obtained on the structure of the Hin-hix complex. While these results primarily conform with model based predictions, others have pointed towards further refinements that are possible.\r\n\r\nChapter 4 of the thesis provides a brief overview of the methods and applicability of perturbation thermodynamic analysis as applied to the molecular dynamics based simulation of proteins and DNA in general and some specific issues of concern with regard to the simulations reported in this thesis.\r\n\r\nIn chapter 5 we report on our perturbation thermodynamic molecular dynamics analysis of the relative free energy of solvation of thymine and uricil. This work provides important insights into the role solvation plays in the formation of sequence specific protein-DNA complexes.\r\n\r\nFinally, chapter 6 is a report on our investigations into the mechanisms of sequence specific binding for the minor groove binding peptide Netropsin. Steric, electrostatic and solvation effects are all investigated using a perturbation thermodynamic approach to elucidate the mechanisms involved in complex formation for this important class of DNA binding ligands.\r\n", "doi": "10.7907/fdk3-5402", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "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:5371", "collection": "thesis", "collection_id": "5371", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-152204878", "primary_object_url": { "basename": "Perry_jk_1994.pdf", "content": "final", "filesize": 10382459, "license": "other", "mime_type": "application/pdf", "url": "/5371/1/Perry_jk_1994.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Alkane activation by first, second, and third row transition metal ions : organometallic chemistry in the gas plate", "author": [ { "family_name": "Perry", "given_name": "Jason Kendrick", "clpid": "Perry-J-K" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Reactions of the atomic transition metal cations, Co^+, Rh^+, and Ir^+, with H_2, CH_4, and C_2H_6 in the gas phase are considered using high level ab initio techniques. The nature of complexation and oxidative addition, in particular, are discussed. We find that the third row metal, Ir^+, is significantly more reactive toward these small molecules in comparison to the first and second row metals. Ir^+ is capable of inserting into the H\u2014H bond and leads to the facile dehydrogenation of CH_4 to form IrCH^+_2. Co^+ and Rh^+ form only molecular complexes with these molecules. All three metals exothermically dehydrogenate ethane but Co^+ has a barrier which prevents the reaction from being observed at room temperature. The mechanisms for dehydrogenation are distinctly different for each metal. For Co^+, the initial C\u2014H insertion to form Co(H)(C_2 H_5)^+ is rate limiting. This is followed by a multi-center elimination of H_2. For Rh^+, the concerted insertion into two C\u2014H bonds to form Rh(H)_2(C_2H_4)+ is seen without the intermediacy of Rh(H)(C_2H_5)^+. Reductive elimination ofH_2 follows. For Ir^+, a number of reaction pathways are viable with the most favorable being a stepwise oxidative addition/\u03b2-H shift mechanism. Much of the difference in the chemistry of these metals stems from two principal factors: the atomic state splittings and the orbital sizes. For Co^+ and Ir^+, both the s^1d^7 and d^8 valence electron configurations are accessible, providing the flexibility needed to adapt to the changing ligation of the reaction profile. For Rh^+, the s^1d^7 state is high in energy, limiting the efficiency of this metal in these reactions. In addition, the s and d orbitals have dramatically different sizes for Co^+, which diminishes the effectiveness of sd hybridization and leads to weaker bonds, particularly in highly ligated complexes. The s and d orbitals of Rh^+ and Ir^+ are more similar in size, providing strong sd hybrid bonds. These two factors compromise the reactivity of Co^+ and Rh^+, leaving only Ir^+ near the ideal.", "doi": "10.7907/cs1d-8f56", "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:5335", "collection": "thesis", "collection_id": "5335", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10292009-080702117", "primary_object_url": { "basename": "Muller_rp_1994.pdf", "content": "final", "filesize": 6059925, "license": "other", "mime_type": "application/pdf", "url": "/5335/1/Muller_rp_1994.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Development and implementation of ab initio methods for application to large molecules", "author": [ { "family_name": "Muller", "given_name": "Richard P.", "clpid": "Muller-R-P" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Chan", "given_name": "Sunney I.", "clpid": "Chan-S-I" }, { "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": "This thesis describes new methods for extending ab initio electronic structure theory calculations to larger molecules\u2014those requiring more than ~200 basis functions. These molecules are difficult to describe with standard methods in electronic structure theory because they require large amounts of CPU time, disk storage space, and physical memory. The work presented in this thesis develops the PS-GVB program that uses pseudospectral operator construction\u2014a faster method of constructing two electron operators\u2014to calculate the electronic structure of real chemical systems; and it outlines the procedure for using these operators to calculate the electronic structure of molecules with a variety of compositions, geometries, and wave functions. This thesis extends PS-GVB to metallic elements, which present particular problems for the pseudospectral method because the nature of the chemical bonding is qualitatively different between metallic elements than between non-metallic main group elements. This thesis also generalizes the Direct Inversion in the Iterative Subspace method to wave functions with arbitrary numbers of core, open-shell, and GVB natural orbitals. These wave functions are necessary to describe physical properties of chemical systems. Finally, this thesis applies these methods to study porphyrin excited states. Porphyrins appear in a variety of biological applications including the photosynthetic reaction center and the heme group, as well as applications in chemical catalysis. Semi-empirical electronic structure calculations have suggested that the porphyrin excited states are composed of coupled single excitations from the ground state. The combination of the large size of the porphyrins and the multi-configurational nature of the excited states have prevented ab initio calculations with quality basis sets on these states. Two different approaches are used: (i) Frozen Core-Four Orbital Excited States, which takes advantage of the planar geometry of many porphyrin rings to separate the \u03c3 and \u03c0orbitals of the molecules; and (ii) Self-Consistent-Four Orbital Excited States, which calculates explicitly the multi-configurational excited state energies and optimum orbitals. Both methods yield excellent agreement with experimental results suggesting that they may be used to analyze a wide variety of different porphyrin spectra.\r\n", "doi": "10.7907/gtra-9x03", "publication_date": "1994", "thesis_type": "phd", "thesis_year": "1994" }, { "id": "thesis:5337", "collection": "thesis", "collection_id": "5337", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10292009-110407804", "primary_object_url": { "basename": "Mathiowetz_am_1993.pdf", "content": "final", "filesize": 17219737, "license": "other", "mime_type": "application/pdf", "url": "/5337/1/Mathiowetz_am_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Dynamic and Stochastic Protein Simulations: from Peptides to Viruses", "author": [ { "family_name": "Mathiowetz", "given_name": "Alan Martin", "clpid": "Mathiowetz-Alan-Martin" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "In order to increase the efficiency of protein simulations, both deterministic and stochastic methods can be formulated in terms of the most important degrees of freedom in polypeptide and protein systems: the torsions. Two such methods are presented here. The first is Newton-Euler Inverse Mass Operator (NEIMO) Dynamics, an internal-coordinate molecular dynamics method originally designed to study the dynamics of general multibody systems. The second is the Probability Grid Monte Carlo (PGMC) method, developed for searching the conformational space of polypeptides using a weighted sampling of the most favorable dihedral angles.
\r\n\r\nThe first use of the NEIMO Dynamics method for studying molecular systems is reported here. The method is used to study the dynamics of a wide range of peptide and protein systems. These range from the pentapeptide Met-enkephalin to the crystallographic asymmetric unit of the tomato bushy stunt virus (TBSV), an assembly of three chains totaling 893 residues. Bond lengths and angles do not vary during the dynamics simulations; this enables timesteps larger than 10 femtoseconds to be used for small peptides, a substantial improvement over Cartesian coordinate molecular dynamics. Timesteps of 10 fs do not work well for NEIMO simulations of large proteins because of unacceptably large energy fluctuations. However, timesteps of 2-5 fs give acceptable results, even for very large systems. The NEIMO method is applied to TBSV coat proteins, in an investigation of the effect of Ca2+ ions on the coat stability.
\r\n\r\nThe PGMC method provides efficient conformational searches for polypeptide systems by assigning probabilities to different discrete values of the \u03c6, \u03c8, and \u03c7 dihedral angles. These probabilities were derived by investigation of the protein structures in the Brookhaven Protein Database. The PGMC method is applied successfully to several important problems in protein modeling: studies of the low-energy conformations of a peptide, prediction of the all-atom conformation of a protein from its C\u03b1 coordinates alone, and the prediction of antibody loop conformations. The success of the C\u03b1, modeling is further extended by its application to structures with coordinates constrained to a lattice, through the use of a simple C\u03b1 Forcefield.
\r\n", "doi": "10.7907/pe34-yy14", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:5363", "collection": "thesis", "collection_id": "5363", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11112009-114142428", "primary_object_url": { "basename": "Park_c_1993.pdf", "content": "final", "filesize": 6278652, "license": "other", "mime_type": "application/pdf", "url": "/5363/1/Park_c_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Protein design and simulation. Part I. Protein design. Part II. Protein simulation", "author": [ { "family_name": "Park", "given_name": "Changmoon", "clpid": "Park-C" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Since specific DNA binding proteins play many important roles in the regulation of cellular reactions including replication, transcription, and translation by the specific interactions of DNA binding proteins with DNA, the design and synthesis of sequence-specific DNA binding proteins is of great interest in modern chemistry and biology.\r\n\r\nChapter 1 introduces a strategy by which to design new protein structures recognizing new sequences of DNA. The results of experiments using new protein show that there is cooperation between the monomers in binding to DNA and each monomer recognizes the half-site of the dimer binding site.\r\n\r\nChapter 2 describes the advantage of palindromic sites and dimerization in DNA recognition according to the experimental results. The results also show that each monomer in a dimer recognizes one half-site of the dimer binding site irrespective of the relative orientation monomer in the dimer and the dimer binding site depends on the relative orientation of the two monomer in the dimer.\r\n\r\nChapter 3 shows that the monomer of DNA binding region of the v-Jun leucine zipper protein recognizes the dimer binding site. Our results support the possibility that two monomers of v-Jun might bind sequentially to the dimer site with dimerization of v-Jun occurring while bound.\r\n\r\nChapter 4 describes the design of a new protein recognizing a new 16 by site in DNA. Our results show that there is cooperation between monomers and all three monomers in the new peptide recognize unique half-sites in the proposed trimeric binding site.\r\n\r\nChapter 5 describes quantum mechanical calculations on the active site of cytochrome P-450cam to improve force constants for the molecular simulations of cytochrome P-450cam. Our results show that the size of iron ion is a function of its spin and oxidation state and plays a key role in the process of oxygenation.\r\n", "doi": "10.7907/sv6x-9s75", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "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:5323", "collection": "thesis", "collection_id": "5323", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10222009-160215418", "primary_object_url": { "basename": "Lang_ghw_1993.pdf", "content": "final", "filesize": 3423271, "license": "other", "mime_type": "application/pdf", "url": "/5323/1/Lang_ghw_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Auxiliary-field Monte Carlo methods for interacting fermions : application to the nuclear shell model", "author": [ { "family_name": "Lang", "given_name": "Gladys Hau-Wan", "clpid": "Lang-G-H-W" } ], "thesis_advisor": [ { "family_name": "Koonin", "given_name": "Steven E.", "clpid": "Koonin-S-E" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_pma" } ], "abstract": "This thesis presents the path-integral formulation of the nuclear shell model using the Hubbard-Stratonovich transformation, which linearizes the two-body interaction by auxiliary fields. The path-integral was evaluated via Monte Carlo. The method scales favorably with valence-nucleon number and shell-model basis: full-basis calculations can be done up to the rare-earth region, which cannot be treated by other methods. Observables are calculated for the ground state and in a thermal \r\nensemble. Dynamical correlations are obtained, from which strength functions are extracted through the Maximum Entropy method. Examples in the s-d shell, where exact diagonalization can be carried out, compare well with exact results. The \"sign problem\", which is generic to fermion Monte Carlo calculations, is proved to be absent in a wide class of interactions including the attractive pairing-plus-multipole interactions. The formulation is general for interacting fermion systems and is well suited for parallel computation. The method has been implemented on the Intel Touchstone Delta System, achieving better than 99% parallelization.\r\n", "doi": "10.7907/xh84-k642", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "id": "thesis:5310", "collection": "thesis", "collection_id": "5310", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-102157942", "primary_object_url": { "basename": "Coley_tr_1993.pdf", "content": "final", "filesize": 19371467, "license": "other", "mime_type": "application/pdf", "url": "/5310/1/Coley_tr_1993.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Prediction of scanning tunneling microscope images by computational quantum chemistry: chemical models and software design", "author": [ { "family_name": "Coley", "given_name": "Terry Ronald", "clpid": "Coley-T-R" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Baldeschwieler", "given_name": "John D.", "clpid": "Baldeschwieler-J-D" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We have created chemical models for predicting and interpreting STM images of several specific systems. Detailed studies are made of transition metal dichalcogenides (MoS_2 and MoTe_2), Xe on Ni (110), C_3H_4 on Ni (110) and n-butyl benzene on a graphite model (C_(42)O_6H_(12). In the case of MoS_2 we study the ambiguity in the STM images regarding the assignment of peaks to the subsurface metal or the surface chalcogenide. In the Ni models we study STM imaging mechanisms for cases where the adsorbate states lie far above and below the metal Fermi level. The large n-butyl on graphite system models a system where adsorbate states can play a direct role in the imaging. Results from the cluster studies are related to various STM imaging modes, including constant current mode, constant height mode, and barrier height imaging.\t\r\nTwo new procedures are developed to aid in computational prediction of STM images. First, we implement an algorithm for computing Bardeen-type tunneling matrix elements from ab initio wave functions in Gaussian basis sets. Second, we show how to obtain state densities as a function of energy for bulk substrate/adsorbate systems using only Fock matrix elements from cluster calculations. Initial results are presented for a linear chain of Ni atoms with a perturbing Xe atom.\r\nA software environment for computational chemistry developed in the course of performing these calculations is presented. Tools for creating computational servers to perform chemistry calculations are described. Embedded in each chemistry server is a public domain control language created by J. Ousterhout at the University of California, Berkeley. This allows the development of a variety of clients for controlling the servers using a common language. Clients can be simple text \"scripts\" that organize a calculation, graphical interfaces, or control streams from other programs. All software entities are designed in an object oriented fashion discussed in the text.\r\n", "doi": "10.7907/jey5-ex12", "publication_date": "1993", "thesis_type": "phd", "thesis_year": "1993" }, { "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: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: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:5334", "collection": "thesis", "collection_id": "5334", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10282009-111805575", "primary_object_url": { "basename": "Guo_y_1992.pdf", "content": "final", "filesize": 7667112, "license": "other", "mime_type": "application/pdf", "url": "/5334/1/Guo_y_1992.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "I. Molecular simulations of buckyball fullerenes. II. Quantum chemistry studies on high-T_c superconductors.", "author": [ { "family_name": "Guo", "given_name": "Yuejin", "clpid": "Guo-Y" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I. In order to interpret and predict the unusual chemical and physical properties of the C_(60) and related fullerenes, fullerites, and molecular/solid state derivatives, we started with the graphite force field (GraFF) developed for sp^2 carbon centers (based on fitting experimental lattice parameters, elastic constants, phonon frequencies for graphite and alkali-intercalated graphite), and successfully predicted vibrational frequencies, fullerite and alkali-doped fullerite crystal structure, density, heat of sublimation, and compressibility, etc., for C_(60), C_(70) and their derivatives. We also developed a highly accurate force field for C_(60) in excellent agreement with all 14 experimental frequencies within abs error 3.0 cm^(-1).\r\n\r\nPart II. We have applied ab initio electronic methods (GVB and CI) to various clusters representing La_2CUO_4, Nd_2CuO_4, YBa_2Cu_3O_7, and Bi and Tl containing high-Tc materials to study their basic electronic structure and magnetic interaction. Particularly, we develop the GVB superexchange CI (GVB - X - CI) method to study the superexchange coupling interaction. Using this method, we can calculate the J_(dd) from the first principle at about the same accuracy as experiment.\r\n\r\nOur results indicate that the superconductivity in Cu-0 plane of these cuprates arise from a essentially magnetically induced interaction, that is, (i) all Cu have a Cu^(II) d^9 oxidation state with one unpaired spin that is coupled antiferromagnetically to the spins of adjacent Cu^(II) sites; (ii) reduction below the cupric Cu^(II) state leads to Cu^I d^(10) sites with a highly mobile Cu(3d) electron, and these extra electrons hop from site to site (while the oxygen remains in the O^(2-) state). The hopping of these extra electrons causes the flipping of the local spin moment of the antiferromagnetic background; (iii) oxidation beyond the cupric Cu^(II) state leads not to Cu^(III) but rather to oxidized oxygen atoms with an highly mobile Op hole, which is ferromagnetically coupled to the adjacent Cu^(II) d electrons despite the fact that this is opposed by the direct dd exchange. This coupling induces an attractive interaction between conduction electrons that is responsible for the superconductivity\r\n", "doi": "10.7907/jvvc-ry41", "publication_date": "1992", "thesis_type": "phd", "thesis_year": "1992" }, { "id": "thesis:6702", "collection": "thesis", "collection_id": "6702", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10042011-094257165", "primary_object_url": { "basename": "Rico_rj_1992.pdf", "content": "final", "filesize": 19340835, "license": "other", "mime_type": "application/pdf", "url": "/6702/1/Rico_rj_1992.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Quantum-mechanical studies of vanadium oxides", "author": [ { "family_name": "Rico", "given_name": "Rudolph J.", "clpid": "Rico-R-J" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A variety of V-O systems were examined in order to model the catalytic site for VPO-catalyzed conversion of butane to maleic anhydride. All V-O systems examined could be described as a V-O triple bond, with a covalent \u03c3-bond and two \u03c0-bonds, and a bond length of approximately 1.56-1.60 \u00c5. The nature of the \u03c0-bonds varied. In VOCl_4^(3-) and VOCl_(2-), the \u03c0-bonds were both described as donor-acceptors. All other systems displayed one covalent bond and one donor-acceptor bond. Resonance between the two \u03c0-bonds was displayed for four-chloride C_(4v) VOCl_4^(2-/-). Optimized C_(2v) geometries for VOCl_4^(2-/-) appear to be the result of this resonance, in which the wavefunction and geometry represent one resonance state of the overall C_(4v) system, in which one \u03c0 -bond is highly covalent, and the other highly donor-acceptor. The C_(4v) system is lower in energy than the C_(2v) system at all levels of theory (HF, CASSCF, MRCI) except GVB(3/6)-PP. VOCl_2^(0/+) calculations show strong similarities to C_(2v) VOCl_4^(2-/-) in both V-O bond description and geometry, suggesting that these systems\r\ncan be described as C_(2v) VOCl_4^(2-/-) systems without the axial chlorides. VO+ and VOCl_3 results, for which experimental data exists, support the descriptions of geometry and bonding given. V(V) systems display a strong degree of covalent character to the chlorides (as does VO_3 to the bound oxygen molecule), but this effect decreases\r\nsignificantly as the V(3d\u03b4 )-orbitals are occupied. Snap bond calculations indicate that the V(V)-O bond is approximately 28 kcal/mol weaker than the V(lV)-O bond - this may be due to the increased V-C1 interaction in the products of the V(V) bondbreaking.\r\n", "doi": "10.7907/2set-6e48", "publication_date": "1992", "thesis_type": "masters", "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:2660", "collection": "thesis", "collection_id": "2660", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06202007-111048", "primary_object_url": { "basename": "Irikura_kk_1991.pdf", "content": "final", "filesize": 5090791, "license": "other", "mime_type": "application/pdf", "url": "/2660/1/Irikura_kk_1991.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Gas-Phase Chemistry of Organotransition Metal Ions", "author": [ { "family_name": "Irikura", "given_name": "Karl Kensuke Mason", "clpid": "Irikura-Karl-Kensuke-Mason" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The gas-phase chemistry of many transition metal ions has been investigated by Fourier transform ion cyclotron resonance spectrometry (FTICR). Emphasis is on organometallic chemistry, including an application to geochronology, but inorganic and bio-inorganic systems have also been investigated. Quantum chemical calculations have been performed to address problems in interstellar chemistry and also traditional physical organic chemistry.
\r\n\r\nChapter I is concerned with the chemistry of ions OsOn+(n=0-4) with several small molecules, including methane. A wide variety of reactions are observed, including many that are archetypes for fundamental mechanistic processes in organometallic chemistry. In Chapter II, the differences in the gas-phase chemistry of Os+ and Re+ are applied to analytical problems associated with the 187RE-187 dating method, which is important in geology.
\r\n\r\nChapter III is a survey of the reactivity of third-row transition metal ions, with emphasis on the unusual reactions involving methane. Fundamental concepts that have proven useful in the interpretation of chemistry in the first and second transition series are also applicable in the third row.
\r\n\r\nChapter IV describes the gas-phase synthesis of positive and negative metalloporphyrin ions by reactions of metal-containing ions with porphine vapor. Chapter V presents some possibilities for transition metal catalysis in interstellar clouds. A very low value is calculated for the rate of radiative association of Fe+ and hydrogen atoms, suggesting that transition metal chemistry is not important in these systems.
\r\n\r\nChapter VI involves scaling the results of ab initio calculations in order to predict accurate singlet-triplet energy gaps in many substituted carbenes. Observed trends are rationalized using a synergistic bonding model. A simple relationship based upon electronegativity is presented to permit carbene singlet-triplet gaps to be computed using minimal resources, such as a hand calculator.
\r\n\r\nChapter VII deals with five different experimental issues that have arisen during FTICR studies of reactive transition metal ions. Difficulties, helpful techniques, and data analysis are discussed.
", "doi": "10.7907/REZ3-DD85", "publication_date": "1991", "thesis_type": "phd", "thesis_year": "1991" }, { "id": "thesis:8806", "collection": "thesis", "collection_id": "8806", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03272015-161328191", "primary_object_url": { "basename": "Miller_gh_1990.pdf", "content": "final", "filesize": 7846556, "license": "other", "mime_type": "application/pdf", "url": "/8806/1/Miller_gh_1990.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "The Equation of State and Petrogenesis of Komatiite", "author": [ { "family_name": "Miller", "given_name": "Gregory Hale", "clpid": "Miller-G-H" } ], "thesis_advisor": [ { "family_name": "Ahrens", "given_name": "Thomas J.", "clpid": "Ahrens-T-J" }, { "family_name": "Stolper", "given_name": "Edward M.", "clpid": "Stolper-E-M" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "(1) Equation of State of Komatiite
\r\n\r\nThe equation of state (EOS) of a molten komatiite (27 wt% MgO) was detennined in the 5 to\r\n36 GPa pressure range via shock wave compression from 1550\u00b0C and 0 bar. Shock wave velocity,\r\nUS, and particle velocity, UP, in km/s follow the linear relationship US = 3.13(\u00b10.03) + 1.47(\u00b10.03)\r\nUP. Based on a calculated density at 1550\u00b0C, 0 bar of 2.745\u00b10.005 glee, this US-UP relationship\r\ngives the isentropic bulk modulus KS = 27.0 \u00b1 0.6 GPa, and its first and second isentropic pressure\r\nderivatives, K'S = 4.9 \u00b1 0.1 and K\"S = -0.109 \u00b1 0.003 GPa-1.
\r\n\r\nThe calculated liquidus compression curve agrees within error with the static compression\r\nresults of Agee and Walker [1988a] to 6 GPa. We detennine that olivine (FO94) will be neutrally\r\nbuoyant in komatiitic melt of the composition we studied near 8.2 GPa. Clinopyroxene would also\r\nbe neutrally buoyant near this pressure. Liquidus garnet-majorite may be less dense than this komatiitic\r\nliquid in the 20-24 GPa interval, however pyropic-garnet and perovskite phases are denser than\r\nthis komatiitic liquid in their respective liquidus pressure intervals to 36 GPa. Liquidus perovskite\r\nmay be neutrally buoyant near 70 GPa.
\r\n\r\nAt 40 GPa, the density of shock-compressed molten komatiite would be approximately equal\r\nto the calculated density of an equivalent mixture of dense solid oxide components. This observation\r\nsupports the model of Rigden et al. [1989] for compressibilities of liquid oxide components.\r\nUsing their theoretical EOS for liquid forsterite and fayalite, we calculate the densities of a spectrum\r\nof melts from basaltic through peridotitic that are related to the experimentally studied komatiitic\r\nliquid by addition or subtraction of olivine. At low pressure, olivine fractionation lowers the density\r\nof basic magmas, but above 14 GPa this trend is reversed. All of these basic to ultrabasic liquids\r\nare predicted to have similar densities at 14 GPa, and this density is approximately equal to the bulk\r\n(PREM) mantle. This suggests that melts derived from a peridotitic mantle may be inhibited from\r\nascending from depths greater than 400 km.
\r\n\r\nThe EOS of ultrabasic magmas was used to model adiabatic melting in a peridotitic mantle.\r\nIf komatiites are formed by >15% partial melting of a peridotitic mantle, then komatiites generated\r\nby adiabatic melting come from source regions in the lower transition zone (\u2248500-670 km) or the\r\nlower mantle (>670 km). The great depth of incipient melting implied by this model, and the melt\r\ndensity constraint mentioned above, suggest that komatiitic volcanism may be gravitationally hindered.\r\nAlthough komatiitic magmas are thought to separate from their coexisting crystals at a temperature\r\n=200\u00b0C greater than that for modern MORBs, their ultimate sources are predicted to be\r\ndiapirs that, if adiabatically decompressed from initially solid mantle, were more than 700\u00b0C hotter\r\nthan the sources of MORBs and derived from great depth.
\r\n\r\nWe considered the evolution of an initially molten mantle, i.e., a magma ocean. Our model\r\nconsiders the thermal structure of the magma ocean, density constraints on crystal segregation, and\r\napproximate phase relationships for a nominally chondritic mantle. Crystallization will begin at the\r\ncore-mantle boundary. Perovskite buoyancy at > 70 GPa may lead to a compositionally stratified\r\nlower mantle with iron-enriched mangesiowiistite content increasing with depth. The upper mantle\r\nmay be depleted in perovskite components. Olivine neutral buoyancy may lead to the formation of\r\na dunite septum in the upper mantle, partitioning the ocean into upper and lower reservoirs, but this\r\nseptum must be permeable.
\r\n\r\n(2) Viscosity Measurement with Shock Waves
\r\n\r\nWe have examined in detail the analytical method for measuring shear viscosity from the\r\ndecay of perturbations on a corrugated shock front The relevance of initial conditions, finite shock\r\namplitude, bulk viscosity, and the sensitivity of the measurements to the shock boundary conditions\r\nare discussed. The validity of the viscous perturbation approach is examined by numerically solving\r\nthe second-order Navier-Stokes equations. These numerical experiments indicate that shock instabilities\r\nmay occur even when the Kontorovich-D'yakov stability criteria are satisfied. The experimental\r\nresults for water at 15 GPa are discussed, and it is suggested that the large effective viscosity\r\ndetermined by this method may reflect the existence of ice VII on the Rayleigh path of the\r\nHugoniot This interpretation reconciles the experimental results with estimates and measurements\r\nobtained by other means, and is consistent with the relationship of the Hugoniot with the phase\r\ndiagram for water. Sound waves are generated at 4.8 MHz at in the water experiments at 15 GPa.\r\nThe existence of anelastic absorption modes near this frequency would also lead to large effective\r\nviscosity estimates.
\r\n\r\n(3) Equation of State of Molybdenum at 1400\u00b0C
\r\n\r\nShock compression data to 96 GPa for pure molybdenum, initially heated to 1400\u00b0C, are\r\npresented. Finite strain analysis of the data gives a bulk modulus at 1400\u00b0C, K'S. of 244\u00b12 GPa and\r\nits pressure derivative, K'OS of 4. A fit of shock velocity to particle velocity gives the coefficients of\r\nUS = CO+S UP to be CO = 4.77\u00b10.06 km/s and S = 1.43\u00b10.05. From the zero pressure sound speed, CO, a bulk modulus of 232\u00b16 GPa is calculated that is consistent with extrapolation of ultrasonic elasticity measurements. The temperature derivative of the bulk modulus at zero pressure, \u03b8KOS\u03b8T|P, is\r\napproximately -0.012 GPa/K. A thermodynamic model is used to show that the thermodynamic\r\nGr\u00fcneisen parameter is proportional to the density and independent of temperature. The Mie-Gr\u00fcneisen\r\nequation of state adequately describes the high temperature behavior of molybdenum\r\nunder the present range of shock loading conditions.
", "doi": "10.7907/r0pt-2227", "publication_date": "1990", "thesis_type": "phd", "thesis_year": "1990" }, { "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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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: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:5391", "collection": "thesis", "collection_id": "5391", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-140133915", "primary_object_url": { "basename": "Upton_th_1980.pdf", "content": "final", "filesize": 12345082, "license": "other", "mime_type": "application/pdf", "url": "/5391/1/Upton_th_1980.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Theoretical Studies of Chemisorption Processes on Nickel Surfaces", "author": [ { "family_name": "Upton", "given_name": "Thomas Hallworth", "clpid": "Upton-Thomas-Hallworth" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I: Generalized Valence Bond and Configuration Interaction calculations are reported for the zero valent nickel complexesNiC_2H_2, NiC_2H_4, Ni_2C_2H_4, and Ni_2C_2H_2. It is found that the NiC_2H_2 and NiC_2H_4 a coordination complex is formed in which the ligand \u03c0 orbital delocalizing into an empty Ni 4sp orbital. The 4s^13d^9 configuration of the Ni atom is stabilized. Bond energies of 16.7 and 14.2 kcal are found for the two complexes, respectively. In both complexes, the ligand is very weakly distorted, a result that is supported by complementary experimental data characterizing the IR and UV-visible spectral properties of NiC_2H_4 and thNi_2C_2H_4 \u03c0-complex.\r\n\r\nAcetylene is coordinated to Ni_2 in both di-\u03c3 and di-\u03c0 bonded form, for which bond energies of 23 and 60 kcal (relative to C_2H_2 + 2Ni) are found, respectively.\r\n\r\nConfiguration interaction calculations are also reported characterizing all ligand valence ionization levels for theNiC_2H_2, NiC_2H_4 and Ni_2C_2H_2 complexes. Excellent agreement is found between the UPS results for chemisorbed ethylene and the NiC_2H_4 calculated spectrum. \"Bonding shifts\" are found to result from a differential screening effect.\r\n\r\nPart II: Extensive generalized valence bond (GVB) and configuration interaction calculations (POL-CI) have been carried out for the lowest states of Ni_2 and Ni_2^+ for bond lengths from 1.6 to 4.0 \u00c5. The six lowest states of Ni_2 are found to be essentially degenerate with an average equilibrium bond length r_e = 2.04 \u00c5 and D_e = 2.92 eV. A ^4\u03a3^+_g ground state is found for the ion with a bond length R_e = 1.96 \u00c5 and dissociation energy D_e = 4.14 eV. The bonding of Ni is dominated by the interactions of the 4s orbital on each Ni with each Ni of Ni_2 corresponding to a (4s)^1(3d)^9 configuration. The lowest states lead to singly occupied \u03c3 orbitals on each center with other 3d occupations leading to 100 electronic states within about 1.0 eV of the ground state.\r\n\r\nHartree-Fock calculations are also reported, characterizing the low-lying states of an Ni_8 cluster. It is found that the 4s^13d^9 valence configuration of the Ni atom is strongly stabilized, and that here too, the 3d orbitals remain localized and are of secondary importance in the bonding.\r\n\r\nAs a result of these findings, further first principles calculations have been carried out characterizing the \"conduction band\" properties of high and low symmetry clusters up to Ni_(87). Macroscopic properties [ionization potential (IP), electron affinity (EA), bandwidth, and cohesive energies are not sensitive to cluster geometry, and except for EA, show definite convergence towards the bulk limit by Ni_(87) .\r\nEven for Ni_(87), the EA is over 2.5 eV smaller than the IP, and the origin of this effect is discussed.\r\n\r\nPart III: First Principles Hartree-Fock and Generalized Valence Bond Calculations are reported for the bonding of atomic H, Cl, Na, 0, and S on high symmetry sites of the Ni(100) face using an Ni_(20) cluster as a model. All of the adsorbates are found to prefer the fourfold site, with bond energies (D_e) of 3.04, 4.9, 1.3, 3.63, and 4.34 eV, respectively. Bond distances are 0.78, 1.38, 2.7, 0.88, and 1.24 \u00c5 above the surface, which are (except for Na) in excellent agreement with available experimental data. Vibrational frequencies of 73, 17, 30, 46, and 37 meV are found for each adsorbate, respectively. Decreasing site coordination is found to uniformly increase vibrational frequencies, and bond distances while decreasing bond energies. The data are analyzed through the introduction of the concepts of site acidity and basicity, and it is found that site basicity increases with increasing coordination. This trend is responsiale for the observed preference of each adsorbate for high coordinate sites, and it is expected that donor adsorbates (such as CO) would show a reverse trend. The data for Na are found to be in poor agreement with the analogous bulk data, confirming the prediction from Part II.0 that small particles should behave differently from the bulk when bonded to highly electropositive species.\r\n\r\nPart IV: A technique is presented for carrying out ab initio Hartree-Fock calculations on systems of infinite three-dimensional periodicity. The method represents an adaptation of standard molecular basis set expansion techniques and fully utilizes translational and point group symmetry to simplify the calculations. It is shown that the expression for total energy may be written as a sum of pairwise interactions between neutral charge units consisting of a nucleus and a localized compensating electronic charge. The resulting sums are rapidly convergent. The technique is illustrated with sample calculations on face-centered cubic lattices of hydrogen, lithium, and sodium. Generalization to systems of lower symmetry is discussed.\r\n", "doi": "10.7907/bvbb-m935", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:5389", "collection": "thesis", "collection_id": "5389", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-132537342", "primary_object_url": { "basename": "Harding_lb_1979.pdf", "content": "final", "filesize": 38179135, "license": "other", "mime_type": "application/pdf", "url": "/5389/1/Harding_lb_1979.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Ab Initio Studies of Excited States and Reactions of Organic Molecules", "author": [ { "family_name": "Harding", "given_name": "Lawrence Brook", "clpid": "Harding-Lawrence-Brook" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part A: Extensiveab initio calculations (double zeta, plus polarization function basis with correlated wave functions) on the addition of ^1O_2 ethylene are combined with standard thermochemical methods of estimating substituent effects to predict the energetics of the addition of ^1O_2 to substituted olefins. The results include estimates for peroxy biradical, open 1,4-zwitterion and perepoxide intermediates. It is concluded that only the first two play a role in this reaction. Detailed comparisons of the theoretical predictions with experimental results are also reported.It is shown that many aspects of the stereospecificity and regiospecificity can be understood assuming a biradical intermediate or transition state.\r\n\r\nPart B: Generalized valence bond (GVB) and configuration interaction (CI) calculations using an extensive basis [double zeta plus polarization functions (DZd)] have been carried out on peroxymethylene (H_2COO) often referred to as carbonyl oxide or as the Criegee intermediate), dioxirane, and dioxymethylene (OCH_2O). The ab initio thermochemical results are combined with existing thermochemical data to analyze possible modes of ozonolysis. The predicted heat of formation of peroxymethylene is 29.1 kcal, indicating that the dissociation of the primary ozonide to form peroxymethylene biradical and formaldehyde is 9 kcal endothermic. The ring state, dioxirane, is predicted to be 36 kcal below peroxymethylene with dioxymethylene lying 15 kcal above the ring state. Gas phase experimental results are shown to be consistent with the predicted thermochemistry. In addition, solution phase results on the stereospecificity of ozonolysis are shown to ae consistent with a biradical intermediate.\r\n\r\nPart C: Large basis set configuration interaction, bending potential curves for three states (^3B_1, ^1A_1, and ^B_1) of netural CH_2 and one state (^2B_1) of CH_2^- are reported. Vibronic calculations using these potential curves are found to lead to excellent agreement with the observed ^1B_1 - ^1A_1 spectrum. Similar calculations on the ^3B_1 - ^2B_1 and ^1A_1 - ^2B_1 photoelectron spectra indicate the presence of hot bands in the observed negative ion spectrum. Reassignment of the observed spectrum based on these calculations leads to the prediction of ^1A_1 - ^3B_1 splitting of O. 38 \u00b1 0.05 eV.\r\n\r\nPart D: The ground and valence excited states of ketene (H_2CCO) were studied using ab initio generalized valence bond (GVB) and configuration interaction (GVB-CI) wavefunctions. The character and properties of the states are analyzed in terms of the GVB wave- functions. The calculated vertical excitation energies (in eV) are 3.62 ^3(n \u2192 \u03c0*) or ^3A_2, 3.69 ^1(n \u2192 \u03c0*) or ^1A_2, 5.39 and 3(n \u2192 \u03c0*) or 1 ^3A_1, and 7.37 ^3(\u03c0 \u2192 \u03c0*) or 2^3A_1. (Here \u03c0 indicates a \u03c0-like orbital in the plane of the molecule.) These results are in excellent agreement with the observed electron impact excitation energies, 3.8 (^1A_2) and 5.35 ev (^3A_1). Note in particular the small separation (0.07 eV) of the ^3A_2 and ^1A_2 states (0.5 eV for H_2CO) and the 2-eV separation in the \u03c0 \u03c0* triplet states in the two planes. The calculated ground state dipole moment, 1.62 D, is in fair agreement with the experimental value of 1.41 D. The calculated dipole moments of the ^3A_2, ^1A_2, 1 ^3A_1, and 2 ^3A_1 excited states are 2.76, 3.43, 2.43 and 0.27 D respectively.\r\n\r\nPart E:\tAb inito configuration interaction (GVB-CI) methods are used to study the excited Rydberg states of formaldehyde formed by exciting out of either the n or \u03c0 orbital into the various 3s, 3p, and 3d-like Rydberg orbitals. The resulting excitation energies are in good agreement (within ~ 0.1 eV) with the available experimental results. Calculated oscillator strengths are in fair agreement with experiment. Two states ^1(\u03c0\u2192\u03c0*) and ^1(\u03c0\u21923s) are calculated to lie between 10.7 and 10.8 eV, corresponding closely to a broad unassigned peak in the electron impact spectrum (10.5-11.0 eV). We have assigned other peaks in the electron impact spectrum at 11.4-19.n eV and 12.5-12.8 eV as resulting from (\u03c0\u21923p) and (\u03c0\u21923d) transitions, respectively.\r\n", "doi": "10.7907/19z3-cp09", "publication_date": "1979", "thesis_type": "phd", "thesis_year": "1979" }, { "id": "thesis:5388", "collection": "thesis", "collection_id": "5388", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-093719542", "primary_object_url": { "basename": "Olafson_bd_1979.pdf", "content": "final", "filesize": 7587323, "license": "other", "mime_type": "application/pdf", "url": "/5388/1/Olafson_bd_1979.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "A Molecular Description of Oxygen Binding to Hemoglobin", "author": [ { "family_name": "Olafson", "given_name": "Barry Duane", "clpid": "Olafson-Barry-Duane" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We discuss the bonding of O_2 to hemoglobin (Hb) at the molecular level. The ideas presented here are the results of ab initio calculations on idealized portions of the Hb molecule.\r\n\r\nThe bond between Fe and O_2 is formed by coupling a triplet state of Fe to the triplet ground state of O_2. The electronic structure of the FeO_2 moiety is analogous to that of ozone. We show how the ozone model is in agreement with the EPR data for MnO_2 and CoO_2, predicting unpaired spin density on the Mn for the former molecule, and unpaired spin density on the O_2 ligand in CoO_2. Our calculations lead to a bound molecule with very little transfer of electron density onto the O_2 ligand. Valence bond ideas also indicate the similarity between HbO_2 and the formal Fe(III) complexes of HbOH and HbCN.\r\n\r\nThe heme plane and axial imidazole ligand are seen to play a key role in promoting reversible O_2 binding. The effective size of high- spin Fe is not found to play a major role in the O_2 binding process. The Fe remains in the heme plane for four-coordinate molecules, regardless of the local spin state about the Fe. The Fe moves out of the heme plane for five-coordinate complexes in order to keep a strong dative bond to the axial ligand while reducing the nonbonded repulsions between the heme plane and the axial ligand. The spin state change on Fe is found to occur, not because the Fe moves into the plane of the porphyrin, but because the formation of the FeO_2 bond reduces the number of local exchange interactions that stabilize the high-spin state. The role of the coordination sphere of Fe pertaining to the chemistry of the Hb molecule is to reduce the energy separation between the atomic states. It makes an intermediate-spin state accessible for bond formation and thereby provides a mechanism by which an O_2 molecule can easily and reversibly bind to Hb. Neither the diamagnetic (t_(2g))^6 excited state of Fe nor the excited singlet state of O_2 play a role in the formation of the FeO_2 bond.\r\n\r\nWe show how movement of the proximal imidazole, long thought to initiate the change in quaternary structure of Hb, is also responsible for the reduced O_2 affinity in the T quaternary form of Hb. Assuming that protein forces hinder the movement of the axial ligand leads to the calculation of protein forces in the T and R quaternary forms, and a prediction of the movement of Fe upon a change in the quaternary structure. This movement of the Fe center is found to be on the order of 0.05 \u00c5. Based upon the structural studies of Perutz and co-workers we show how the different protein forces in the T and R quaternary forms can be traced to a small number of hydrogen bonds and salt bridges. This allows us to present a model that displays the molecular origin for the cooperative binding effect. Transferring these protein forces to the coboglobin molecule allows us to calculate the magnitude of the cooperative effect in this metal-substituted Hb. The predicted cooperative effect is found to be in excellent agreement with the experimentally determined value.\r\n\r\nThe ozone model of transition metal-O_2 binding leads to the prediction of a second metal-O_2 stretching band between 1000-1200 cm^(-1). It has also been used to tentatively assign the near-infrared and z- polarized ultraviolet-visible spectra of HbO_2, HbCN, and HbCO.\r\n", "doi": "10.7907/7fss-rj50", "publication_date": "1979", "thesis_type": "phd", "thesis_year": "1979" }, { "id": "thesis:5336", "collection": "thesis", "collection_id": "5336", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10292009-093916795", "primary_object_url": { "basename": "Nascimento_mac_1978.pdf", "content": "final", "filesize": 5411302, "license": "other", "mime_type": "application/pdf", "url": "/5336/1/Nascimento_mac_1978.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "I. Theoretical studies of photoionization. II. The electronic structure of linear polyenes", "author": [ { "family_name": "Nascimento", "given_name": "Marco Antonio Chaer", "clpid": "Nascimento-M-A-C" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I:\r\nThe photoionization cross section is shown to be directly related to the imaginary part of the frequency dependent polarizability. Using this relation, an approximate representation of the frequency-dependent polarizability is constructed from a discrete set of transition frequencies and oscillator strengths. This approximate representation is used in an analytical continuation for complex values of the frequency using a sequence of (N+ J/N) Pade Approximants (with J \u2265 1). Once the representation of the frequency-dependent polarizability in the upper half part of the complex plane is known, we can calculate its value along the real axis and consequently the photo- ionization cross section. The great advantage of the method resides on the fact that the use of a discrete representation for the dynamic polarizability explicitly avoids the use of continuum functions. We have applied this method previously in the calculation of photoionization cross sections for the helium atom in its ground state and in the 2^1S and 2^3S metastable states. Calculations for the CO molecule are in progress. Here we present calculations for the H^- atom. For this system we also computed the dynamic polarizability in the normal dispersion region. A study of the basis set dependence is also presented.\r\n\r\nPart II:\r\nSelf-consistent ab initio generalized valence bond (GVB) and configuration interaction (CI) calculations are presented for the ground states, valence and non-valence states, Rydberg states and \u03c0 positive ion states of trans 1, 3-butadiene and all-trans 1, 3, 5-hexatriene molecules. It is shown that the electronic spectra of these molecules can be rationalized in terms of a few valence excited states and a series of Rydberg states. The first singlet excited states of these molecules (1^1B_u) correspond to non-valence, non-vertical states. It was found that to correctly describe the 1^1B_u and the 2^1A_g (valence) states of these molecules it is necessary to correlate not only the electrons of the \u03c0 system but also the electrons of the (C-C)_\u03c3 subspace. It is also shown that the first two bands of the photoelectron spectrum (PE) of the butadiene molecule and the first three bands of the PE spectrum of hexatriene correspond to ionization out of the occupied \u03c0 orbitals of these molecules. Another important conclusion from our studies is that for this type of system, good quality GVB (n/PP) wavefunctions with the 2n \u03c0 electrons correlated can be obtained by carrying out a Hartree-Fock calculation on the ground state followed by a GVB (n/PP) calculation on just the 2n\u03c0 orbitals (keeping the \u03c3 HF space fixed). From this wavefunction accurate values for the transition energies of the valence states can be obtained. Work on all-trans 1, 3, 5, 7-octatetraene now in progress will provide a good test for this scheme.\r\n", "doi": "10.7907/e7dw-3p39", "publication_date": "1978", "thesis_type": "phd", "thesis_year": "1978" }, { "id": "thesis:6970", "collection": "thesis", "collection_id": "6970", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04242012-160948000", "primary_object_url": { "basename": "Davis_jh_1977.pdf", "content": "final", "filesize": 23586493, "license": "other", "mime_type": "application/pdf", "url": "/6970/1/Davis_jh_1977.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical Studies of Organic Diradicals and the Thermal Rearrangement of Bicyclopropenyls", "author": [ { "family_name": "Davis", "given_name": "James Hubbard", "clpid": "Davis-James-Hubbard" } ], "thesis_advisor": [ { "family_name": "Bergman", "given_name": "Robert G.", "clpid": "Bergman-R-G" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part A. Generalized valence bond calculations on cyclopropene and vinylmethylene lead to the following conclusions: (1) the allyl-type \u03c0-system is strongly distorted by the presence of the unpaired sigma electron leading to a methylene-like triplet, ^3A^\", but a 1,3-diradical-like singlet state, ^1A^\"; (2) the lowest-lying singlet state of vinylmethylene has the form of a singlet methylene ^1A lying 12 kcal/mole above the triplet ground state, while the diradical singlet state lies at 14 kcal/mole.
\r\n\r\nPart B. Generalized valence bond calculations on trimethylenemethane indicate that the ground state is the planar triplet with the planar singlet state 26 kcal/mole higher. The rotational barrier for the triplet state is 18 kcal/mole, while one component of the planar singlet prefers the bisected geometry by 7 kcal/mole. Oscillator strengths for vertical transitions and ionization potentials are also reported.
\r\n\r\nPart C. Generalized valence bond calculations on vinylidene predict that the ground state is a singlet with a methylene-like triplet at 2 eV higher. With extensive CI calculations, we find CC bond energy of D_0(h_2C=C) = 150.1 kcal/mole and a heat of formation of 111.5 kcal/mole at 298\u00b0K. The dipole moment for the singlet is calculated to be 2.23D, while the dipole moment for the triplet is 0.55D.
\r\n\r\nPart D. Generalized valence bond calculations on aminonitrene indicate that the ground state is a singlet (^1A_1) with a low-lying triplet state (^3A_2) at 15 kcal/mole. We find the nitrogen-nitrogen bond dissociation energy for the singlet state is 70.4 kcal/mole. The dipole moment is found to be 4.036D for the ^1A_1 and 2.351D for the ^3A_2 state of aminonitrene. The ionization potential is calculated to be 9.4 eV.
\r\n\r\nPart E. The kinetic distribution of isomeric xylenes formed on the thermal aromatization of dl- and meso-1,1'-dimethyl-3,3'-bicylopropenyl and of 3,3'-dimethyl-3,3'-bicyclopropenyl has been determined by extrapolation of the time-dependent xylene percentages to zero percent conversion. The data is most consistent with a mechanism involving initial cleavage of one of the cyclopropene rings, followed by expansion of the other ring, closure to Dewar benzene and finally opening of the Dewar to form aromatic products.
", "doi": "10.7907/KZ6K-7P42", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" }, { "id": "thesis:6970", "collection": "thesis", "collection_id": "6970", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04242012-160948000", "primary_object_url": { "basename": "Davis_jh_1977.pdf", "content": "final", "filesize": 23586493, "license": "other", "mime_type": "application/pdf", "url": "/6970/1/Davis_jh_1977.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical Studies of Organic Diradicals and the Thermal Rearrangement of Bicyclopropenyls", "author": [ { "family_name": "Davis", "given_name": "James Hubbard", "clpid": "Davis-James-Hubbard" } ], "thesis_advisor": [ { "family_name": "Bergman", "given_name": "Robert G.", "clpid": "Bergman-R-G" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part A. Generalized valence bond calculations on cyclopropene and vinylmethylene lead to the following conclusions: (1) the allyl-type \u03c0-system is strongly distorted by the presence of the unpaired sigma electron leading to a methylene-like triplet, ^3A^\", but a 1,3-diradical-like singlet state, ^1A^\"; (2) the lowest-lying singlet state of vinylmethylene has the form of a singlet methylene ^1A lying 12 kcal/mole above the triplet ground state, while the diradical singlet state lies at 14 kcal/mole.
\r\n\r\nPart B. Generalized valence bond calculations on trimethylenemethane indicate that the ground state is the planar triplet with the planar singlet state 26 kcal/mole higher. The rotational barrier for the triplet state is 18 kcal/mole, while one component of the planar singlet prefers the bisected geometry by 7 kcal/mole. Oscillator strengths for vertical transitions and ionization potentials are also reported.
\r\n\r\nPart C. Generalized valence bond calculations on vinylidene predict that the ground state is a singlet with a methylene-like triplet at 2 eV higher. With extensive CI calculations, we find CC bond energy of D_0(h_2C=C) = 150.1 kcal/mole and a heat of formation of 111.5 kcal/mole at 298\u00b0K. The dipole moment for the singlet is calculated to be 2.23D, while the dipole moment for the triplet is 0.55D.
\r\n\r\nPart D. Generalized valence bond calculations on aminonitrene indicate that the ground state is a singlet (^1A_1) with a low-lying triplet state (^3A_2) at 15 kcal/mole. We find the nitrogen-nitrogen bond dissociation energy for the singlet state is 70.4 kcal/mole. The dipole moment is found to be 4.036D for the ^1A_1 and 2.351D for the ^3A_2 state of aminonitrene. The ionization potential is calculated to be 9.4 eV.
\r\n\r\nPart E. The kinetic distribution of isomeric xylenes formed on the thermal aromatization of dl- and meso-1,1'-dimethyl-3,3'-bicylopropenyl and of 3,3'-dimethyl-3,3'-bicyclopropenyl has been determined by extrapolation of the time-dependent xylene percentages to zero percent conversion. The data is most consistent with a mechanism involving initial cleavage of one of the cyclopropene rings, followed by expansion of the other ring, closure to Dewar benzene and finally opening of the Dewar to form aromatic products.
", "doi": "10.7907/KZ6K-7P42", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" }, { "id": "thesis:5361", "collection": "thesis", "collection_id": "5361", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11092009-084139276", "primary_object_url": { "basename": "Walch_sp_1977.pdf", "content": "final", "filesize": 9433116, "license": "other", "mime_type": "application/pdf", "url": "/5361/1/Walch_sp_1977.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical Studies of Chemisorption", "author": [ { "family_name": "Walch", "given_name": "Stephen Perry", "clpid": "Walch-Stephen-Perry" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "PART A: GVB and GVB-Cl wavefunctions (using a double zeta basis) have been obtained as a function of internuclear distance for the lowest three states of NiCO. The wavefunctions lead to a qualitative description in which the Ni atom is neutral with a (4s)^1(3d)^9 atomic configuration. The CO lone pair delocalizes slightly onto the Ni, leading to the 4s-like orbital hybridizing away from the CO. The dir pairs on the Ni are slightly back-bonding to the CO. The three bound states are ^3\u03a3^+, ^3\u220f, and ^3\u0394\r\nconsisting of the singly occupied 4s-like orbital plus a single d hole in a \u03c3, \u03c0, or \u03b4 orbital, respectively. The ground state is found to be ^3\u0394 with calculated R_e = 1.90 \u00c5, D_e = 1.15 eV = 26.5 kcal/mol, and \u03c9_c(Ni-C) = 428 cm^(-1), all reasonable values, although direct information on NiCO is not yet available. The adiabatic excitation energies are calculated as 0.240 eV to ^3\u03a3^+, and 0.293 eV to ^3\u220f. The states with (4s)^2(3d)^8 configurations on the Ni lead to repulsive potential curves with vertical excitation energies in the range of 3.0 to 5.0 eV.\r\n\r\nPART B:\tConfiguration interaction calculations have been carried out for a number of positive ion states of NiCO. These calculations indicate that there are two distinct groups of ionization potentials. The first group involves ionizations out of Ni-like orbitals. The lowest states of this group involve ionization out of a Ni 4s-like orbital leading to a 3d^9 configuration and states of symmetry ^2\u03a3^+, ^2\u220f, and ^2\u0394 depending on whether the 3d-hole is taken in a \u03c3 , \u03c0) or \u03b4 orbital. At the optimum geometry of NiCO, the dissociation energy of NiCO^+ to Ni^+(^2D) and CO is calculated to be 2.26, 2.03 and 2.50 eV for the ^2\u03a3^+, ^2\u220f, and ^2\u0394 states, respectively, in reasonable agreement with the value of 2.10 eV calculated from the experimental heat of formation of NiCO^+. Other states in the first group involve ionization out of Ni 3d orbitals leading to a group of ion states with a width of 3.1 eV. This is in good agreement with the Ni d bandwidth as observed in photoemission experiments. The second group of ion states correlates at large Ni-C separation with the ground state of the Ni atom and various states of CO^+. The principal change as compared with free CO is that the 5\u03c3 ionization (lone pair on the CO) increases in energy by about 2.5 eV, whereas the 4\u03c3 and 1\u03c0 ionizations change only slightly. This leads to the 5\u03c3 and 1\u03c0 ionizations being nearly degenerate, with the 4\u03c3 ionization about 3.0 eV higher, in agreement with the currently accepted interpretation of the photoelectron spectrum of CO chemisorbed on Ni.\r\n\r\nPART C: Geometries for 0 and S overlayers on the (100) and (110) surfaces of Ni have been calculated using ab initio wavefunctions for 0 and S bonded to small clusters of Ni atoms (1 to 5 Ni atoms). The calculated geometries are within 0.07\u00c5 of the results of dynamic LEED intensity calculations, indicating that accurate geometries\r\nof chemisorbed atoms may be obtained from calculations using clusters including only those metal atoms within bonding distance.\r\n\r\nPART D:\tElectronic wavefunctions have been obtained as a function of geometry fora S atom bonded to Ni clusters consisting of l to 4 atoms de-signed to model bonding to the Ni(100) and Ni(110) surfaces. Electron correlation effects were included using the generalized valence bond and configuration interaction methods. Modeling the (100) surface with four Ni atoms, we find the optimum S position to be 1.33\u00c5 above the surface, in good agreement with the value (1.30 \u00b1 0.10\u00c5) from dynamic LEED intensity calculations. The bonding is qualitatively like that in H_2S with two covalent bonds to one diagonal pair of Ni atoms. There is a S p\u03c0 pair overlapping the other diagonal pair of Ni atoms. [Deleting this pair the S moves in to a position 1.04\u00c5 from the surface.] There are two equivalent such structures, the resonance leading to equivalent S atoms and a c(2x2) structure for the S overlayer. The Ni in the layer beneath the surface seems to have little effect (~0.03\u00c5) on the calculated geometry.\r\nThe above model of the bonding suggests that for the (110) surface the S lies along the long edge of the rectangular unit cell (2 coordinate) rather than at the four coordinate site usually assumed. Our calculated position for the S of 1.04\u00c5 is in reasonable agreement with the value from dynamic LEED intensity calculations, 0.93 \u00b10.10\u00c5.\r\nBonding the S directly above a single Ni atom leads to a much weaker bond (D_e = 3.32 eV) than does bonding in a bridge position (D_e = 5.37 eV). \r\n\r\nPART E:\tElectronic wavefunctions have been obtained as a function of geometry for an 0 atom bonded to Ni clusters (consisting of 1 to 5 atoms) designed to model bonding to the Ni(100) and Ni(110) surfaces. Electron correlation effects were included using the generalized valence bond and configuration interaction methods. For the (100) surface, we find that the charge distribution for the full 0 overlayer is consistent with taking a positively charged cluster. The four surface atoms in the surface unit cell and the atom beneath the surface are important in determining the geometry, leading to a Ni^+_50 cluster as the model for the (100) surface. The optimum oxygen position with this model is 0.96\u00c5 above the surface (four-fold coordinate site) in good agreement with the value (0.90\u00b1 0.10\u00c5) from dynamic LEED intensity analysis. The atom beneath the surface allows important polarization effects for the positively charged cluster. The bonding to the surface involves bridging two diagonal surface Ni atoms. There is an 0(2p\u03c0)pair which overlaps the other diagonal pair of Ni atoms leading to nonbonded repulsions which increase the distance above the surface. There are two equivalent such structures, the resonance leading to a c(2 x 2) structure for the 0 over-layer. The above model suggests that for the (110) surface the 0 lies along the long edge of the rectangular unit cell. For this registry with the surface, calculations based on Ni_20 and Ni_30 models indicate that the oxygen is only 0.1\u00c5 above the plane of the surface.\r\n\r\nPART F:\tGeneralized valence bond and configuration interaction wave-functions have been obtained as a function of R for numerous electronic states of NiO. All the lower states are found to involve the (4s)^1(3d)^9 Ni atom configuration and 0 in the (2s)^2(2p)^4 configuration. There are two groups of states. The lower group of states involves pairing singly occupied Mi(4s).and 0(2p \u03c3) orbitals into a (somewhat ionic) sigma bond pair with various pairings of the Ni(3d)^9 and 0(2p\u03c0)^3 configurations. This leads to a number of states including the ground state which we find to be x^3\u03a3^-. (The electronic structure is analogous to that of O_2.) The calculated D_o and R_e for the x^3\u03a3^- state of Ni0 are 89.9 Kcal/mole and 1.60 \u00c5 respectively. The bond energy is in good agreement with the experimental value 86.5 \u00b15 Kcal/mole, while the R_e value is not known experimentally. The higher group of states involve a doubly occupied 0(2p \u03c3) orbital., The Ni(4s) orbital in this case is non-bonding and builds in\r\n4p character to move away from the oxygen orbitals. The bonding mainly involves stabilization of the oxygen orbitals by the Ni(3d)^9 core (somewhat analogously to the bonding in NiC0). Numerous allowed transitions between these states and the states of the lower group are calculated to be in the range 1.0 to 3.0 eV where numerous bands are seen in emission.\r\n\r\n", "doi": "10.7907/TDQT-V666", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" }, { "id": "thesis:5380", "collection": "thesis", "collection_id": "5380", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11182009-101146638", "primary_object_url": { "basename": "Redondo-Muino_a_1977.pdf", "content": "final", "filesize": 6937057, "license": "other", "mime_type": "application/pdf", "url": "/5380/1/Redondo-Muino_a_1977.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical Studies of Silicon Surfaces Using Finite Clusters", "author": [ { "family_name": "Redondo-Mui\u00f1o", "given_name": "Antonio", "clpid": "Redondo-Mui\u00f1o-Antonio" } ], "thesis_advisor": [ { "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" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "The objective of this thesis is to study the electronic structure, geometries and chemical binding characteristics of the surfaces of silicon and of the initial form of oxygenated Si. We examined the (111), (100), and (110) surfaces, relaxation on the (111) and (100) surfaces and reconstruction on the (100) surfaces. In addition we examined steps on the OM surfaces. In the oxygenated surface we considered the geometry, excited states and ion states of both 0 and 0_2 bonded to the perfect (111) surface.\r\n\r\nThese studies indicated that surfaces and chemisorption lead to localized electronic states for which explicit inclusion of electronic correlation (many body) effects is essential. These effects are included through use of generalized valence bond (GVB) and configuration interaction (CI) techniques. These techniques require use of a finite collection of Si atoms to represent the surface. We find that very small clusters lead to reliable results if the model system is properly tied off with SiH bonds (to represent internal Si-Si bonds).\r\nIn Chapter 1 we report an effective potential for replacing the ten core electrons in calculations involving the Si atom. The potential is obtained directly from ab initio calculations on the states of the Si atom and no empirical data or adjustable parameters are used. The ab initio effective potential is tested by carrying out Hartree-Fock generalized valence bond and configuration interaction calculations on various molecules. We considered Si, Si_2, SiH_3, Si_2H_6 and H_3S10_2 and calculated excitation energies, ionization potentials, and electron affinities both both using the effective potential and without it (ab initio). In essentially all cases the agreement is to better than 0.1 eV, providing strong evidence that the effective potential adequately represents the Si core. This potential is utilized in all of the calculations reported in subsequent chapters. \r\n\r\nIn Chapter 2 we consider clean (111), (100) and (110) silicon surfaces. For the (111) surface the relaxation of silicon surface atoms is studied by means of an Si(SiH_3)_3 cluster. We find that the surface state is accurately described as a dangling bond orbital with 93% p character. We determined the .optimum relaxation of the surface layer to be 0.08\u00c5 toward the second layer. For the positive ion we find that the surface atom relaxes toward the second layer by an additional 0.30\u00c5. Using an Si_3H_6 cluster we find that the interaction between adjacent dangling bond orbitals indicates that they are very weakly coupled (with a splitting of ~0.01 eV between the singlet and triplet spin couplings.) For the (100) surface we used an Si(SiH_3)_2 cluster. We find a relaxation distance of 0.10\u00c5 toward the vacuum. We also considered the 2x1 reconstruction of such surfaces using the results for Si_2H_4 and Si(SiH_3)_2 complexes. It is found that adjacent surface atoms form a bond (1.76 eV bond strength), leading to pairing up. of adjacent silicons with an optimum Si-Si bond length of 2.38\u00c5).\r\n\r\nIn Chapter 3 we consider the electronic structure of divalent steps on (111) silicon surfaces. We find three localized electronic states separated by less than 0.3 eV. These states have quite different electronic structure and are expected to be reactive toward a large range of chemical species.\r\n\r\nIn Chapter 4 we study the chemisorption of oxygen upon Si (111) surfaces. For single oxygen atoms we find an optimum Si-0 bond length of 1.63\u00c5. We also find ionization potentials in the range 11-16 eV. Then we consider a model in which an oxygen molecule chemisorbed onto the silicon surface has, an electronic structure corresponding to a peroxy radical. We find ionization potentials in the range 11-18 eV\r\nin agreement with experiment. We find an optimum 0-0 bond length of 1.37\u00c5 and a Si-0-0 bond angle of 126\u00b0 for the chemisorbed peroxy radical.\r\n", "doi": "10.7907/8M08-WC34", "publication_date": "1977", "thesis_type": "phd", "thesis_year": "1977" }, { "id": "thesis:5356", "collection": "thesis", "collection_id": "5356", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-153524672", "primary_object_url": { "basename": "Surratt_gt_1976.pdf", "content": "final", "filesize": 5093781, "license": "other", "mime_type": "application/pdf", "url": "/5356/1/Surratt_gt_1976.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "A Generalized Valence Bond Description of Vacancy and Impurity States in Diamond and Silicon", "author": [ { "family_name": "Surratt", "given_name": "Grover Timothy", "clpid": "Surratt-Grover-Timothy" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Generalized Valence Bond and Configuration Interaction calculations using a double zeta basis have been performed for the vacancy states of diamond and silicon and for the lithium and boron impurities in silicon. For the vacancy case it was found that the nature of the low-lying electronic states of the positive, negative and neutral charge species is easily understood in terms of simple valence bond concepts. Here the effect of symmetric distortion of the vacancy was included, but no other distortions were included. For those cases in which the ordering of the states is known, the experimental ordering is reproduced by the theoretical results. For the impurity case it is found that boron is strongly bound in a substitutional site whereas lithium is not. In both cases the states of the system can be predicted from a simple valence bond analysis. The calculated results are compared with experiment through the use of a dielectric continuum approximation to correct the energies of charged and ionic states.\r\n", "doi": "10.7907/YCT9-H995", "publication_date": "1976", "thesis_type": "phd", "thesis_year": "1976" }, { "id": "thesis:5383", "collection": "thesis", "collection_id": "5383", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11182009-145338541", "primary_object_url": { "basename": "Wadt_wr_1975.pdf", "content": "final", "filesize": 9533467, "license": "other", "mime_type": "application/pdf", "url": "/5383/1/Wadt_wr_1975.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. The Electronic Structure of the Criegee Intermediate. II. The Electronic Structure of Pyrazine. III. Approximate Integral Methods and Correlated Wavefunctions", "author": [ { "family_name": "Wadt", "given_name": "Willard Rogers", "clpid": "Wadt-Willard-Rogers" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part 1: The Electronic Structure of the Criegee Intermediate: Ramifications for the Mechanism of Ozonolysis. \r\nGeneralized valence bond (GVB) and configuration interaction (CI) calculations using a double zeta basis set have been carried out on methylene peroxide (H_2COOO), the reactive intermediate in the Criegee mechanism for ozonolysis of olefins. The ground state of methylene peroxide (using an open geometry) is shown to be a singlet biradical rather than a zwitterion. A strong analogy between methylene peroxide and its isoelectronic counterpart, ozone, is developed. The calculations also show that the ring state of methylene peroxide is 1 eV lower than the open form. Moreover, the ring state may reopen to give the dioxy-methane biradical. The ab initio results are combined with thermochemical data in order to analyze the stability of the Criegee intermediate as well as the possible modes of reaction in ozonolysis. With regard to ozonolysis in solution, the mechanism for epoxide formation is elucidated and the possible role of methylene peroxide rearrangement to dioxymethane is considered in interpreting the ^(13)O isotope experiments. With regard to ozonolysis in the gas phase, the production of many of the chemiluminescent species observed by Pitts and co-workers is explained. The production of reactive radicals such as OH and HO_2 in the course of ozonolysis, which may have important consequences for understanding the generation of photochemical air pollution, is also delineated.\r\n\r\nPart 2: The Electronic Structure of Pyrazine: A Valence Bond Model for Lone Pair Interaction.\r\nA valence bond (VB) model is developed to describe the interaction of the lone pair excitations in pyrazine. Extensive ab initio minimal basis set (MBS) configuration interaction (CI) calculations show that the description of the n cations and n\u03c0* states of pyrazine afforded by the VB model is more accurate than that afforded by the molecular orbital (MO) model proffered by Hoffmann. The VB picture of the n cations and n\u03c0* states involves the interaction (resonance) of two equivalent, localized excitations. The resultant splitting is large (1 to 2 eV) because of a light delocalization of the n orbitals induced by the Pauli principle. (The n orbitals are still 90% localized on the nitrogens.) The splitting of the n\u03c0* states is comparable to that of the n cations because the \u03c0* orbital is delocalized, even though the excitation process is localized on one nitrogen. The MBS CI calculations indicate that the lowest ionization potential of pyrazine corresponds to the ^2A_g (n) state. Calculations on the lowest Rydberg states indicate that they involve excitations out of an n orbital rather than a \u03c0 orbital, in opposition to earlier spectroscopic assignments. Finally, the calculations show that the forbidden 1 ^1B_2g (n\u03c0*) states is 1 eV higher than the allowed 1 ^1B_3u (n\u03c0*) state, so that the perturbations observed in the absorption spectrum must be ascribed to another source.\r\n\r\nPart 3: Comparison of INDO and Ab Initio Methods for the Correlated Wavefunctions of the Ground and Excited States of Ozone. \r\nThe validity of using integral approximation schemes in conjunction with correlated wavefunctions has been tested by performing generalized valence bond (GVB) and extensive configuration interaction (CI) calculations with INDO approximate integrals on the ground and excited states of ozone. High quality ab initio calculations have previously shown correlation effects to be extremely important for describing ozone. We find that for the CI wavefunctions the INDO approximation leads to vertical excitation energies- within about 30% [from 0.8 eV too low to 0. 6 eV too high with an RMS error of 0.5 eV], as compared with comparable ab initio calculations. We also found that the INDO GVB wavefunctions lead to bond angles in good agreement with experimental and ab initio calculations, but produced bond lengths that were too short. Most important was the discovery that INDO grossly favors closed geometries as opposed to open geometries, predicting the ground state of ozone to be an equilateral triangle state (even for correlated wavefunctions) with an energy 6 eV below the correct open state!\r\n\r\nPart 4: Comparison of INDO and Ab initio Methods for Correlated Wavefunctions of the Ground and Excited States of Methylene and Ethylene. \r\nThe usefulness of the INDO integral approximation for correlated wavefunctions was tested by carrying out GVB calculations on (1) the three lowest states of methylene as a function of bond angle and (2) the three lowest states of ethylene as a function of the dihedral twist angle. The methylene potential curves obtained with INDO were in good agreement (0.2 eV errors) with ab initio results, while the \r\nethylene curves were very poor (2 to 4 eV errors). Comparison with ab initio calculations revealed two major problems in the INDO method (1) the use of empirical values from atomic spectra for the one-center exchange integrals and (2) the use of only one resonance or \u03b2 parameter per atom.\r\n\r\nPart 5: Approximate Integral Methods and Correlated Wavefunctions\r\nAttempts to develop an approximate integral method that produces reliable results in conjunction with correlated wavefunctions are reported. Two basic lines of approach are pursued: (1) modification (or reparametrization) of INDO and (2) general investigation of truncated integral sets. The integral approximations were tested on the low-lying states of H_2, H_3, C_2, O_2, C_2H_4, O_3, and C_6H_6 using consistently correlated wavefunctions. No approximate method investigated gave satisfactory results on all the systems tested, with the O_3 and C_2 molecules presenting the greatest problems. However, good results, using approximate methods comparable in complexity with INDO, were obtained for describing the potential curves of the low-lying states of H_2, H_3, and C_2H_4. Finally, the calculations revealed two important guidelines for approximate integral methods. (1) Transformation to orthogonal atomic orbitals (especially the one-electron integrals) is necessary prior to any truncation of the integral set. Truncation of the standard nonorthogonal integral set leads to poor results, biasing the calculations toward short bond lengths and closed geometries, (2) Replacement of core electrons with local potentials rather than 2J-K potentials leads to better results, because the need to orthogonalize the valence orbitals to the core is obviated.\r\n", "doi": "10.7907/AKCY-N766", "publication_date": "1975", "thesis_type": "phd", "thesis_year": "1975" }, { "id": "thesis:3807", "collection": "thesis", "collection_id": "3807", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09272005-143127", "primary_object_url": { "basename": "Bobrowicz_fw_1974.pdf", "content": "final", "filesize": 9887836, "license": "other", "mime_type": "application/pdf", "url": "/3807/1/Bobrowicz_fw_1974.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Investigations of Spin-Eigenfunction Correlated Wavefunctions", "author": [ { "family_name": "Bobrowicz", "given_name": "Frank Wilhelm", "clpid": "Bobrowicz-Frank-Wilhelm" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "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\nPart I\r\n\r\nGeneralized Valence-Bond descriptions for the low-lying [...], [...], and [...] states of CH are presented. These wavefunctions are found to behave properly at all internuclear distances, giving a clear and consistent physical picture of formation of these molecules from their constituent atoms.\r\n\r\nPart II\r\n\r\nA procedure for calculating Spin-Eigenfunction Configuration Interaction matrices utilizing the U matrices which form the irreducible representations of [...] is presented. In addition, an improved determinant method is summarized. By combining both of these U-matrix and Determinant methods, it has been possible to formulate a practical and yet highly efficient procedure for generating such CI matrices.\r\n\r\nPart III\r\n\r\nEven for relatively simple Hartree-Fock (HF) or Perfect-Pairing Generalized Valence-Bond (PPGVB) many-electron wavefunctions, self-consistent calculations can be prohibitively expensive for, many chemically interesting systems. Considerable effort has been devoted toward developing highly efficient computational techniques for solving for such wavefunctions. The results of this research, as embodied in the GVBTWO program, have made such calculations on relatively large systems a practical reality.\r\n\r\nPart IV\r\n\r\nThe Generalized Valence-Bond (GVB) wavefunction has had considerable success in describing chemical reactions and molecular structure. Unfortunately, this method can only be applied to systems involving a few electrons. The Perfect-Pairing approximation to GVB (PPGVB) greatly simplifies the situation and is found to adequately describe the low-lying states of many molecules. However, in describing chemical reactions the restrictions of PPGVB are quite serious. The Strongly Orthogonal approximation (SOGVB) described here overcomes this problem by allowing the orbitals to recouple while still retaining the simplifying orbital restrictions of PPGVB. This intermediate method correctly describes many chemical reactions and is practical for treating relatively large systems.", "doi": "10.7907/2XSV-1F12", "publication_date": "1974", "thesis_type": "phd", "thesis_year": "1974" }, { "id": "thesis:5357", "collection": "thesis", "collection_id": "5357", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-154826608", "primary_object_url": { "basename": "Levin_gb_1974.pdf", "content": "final", "filesize": 10982336, "license": "other", "mime_type": "application/pdf", "url": "/5357/1/Levin_gb_1974.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "The Generalized Valence Bond Description of the Pi Electron States of Conjugated Molecules", "author": [ { "family_name": "Levin", "given_name": "George Benjamin", "clpid": "Levin-George-Benjamin" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Using the generalized valence bond (GVB) wave function, the pi electron systems of ethylene, allyl cation, allyl radical, s-trans-1,3- butadiene and benzene were examined. The results were in good agreement with full configuration interaction calculations demonstrating the quantitative accuracy of the GVB method. The GVB description of the valence states systems includes a description of resonance and provides a rigorous quantum mechanical description of resonance in terms of spin couplings. It was found that the resonance stabilization energy is due to two effects, delocalization of orbitals onto additional centers while still maintaining their basically localized nature, and spin coupling optimization in a manner identical to the valence bond description of resonance.
\r\n\r\nIt was found that the GVB wave function imposed restrictions upon the orbitals of excited states. To remove these restrictions the GVB wave function was generalized by including a spatial projection operator. The GVB(SP) wave function imposes no restrictions upon individual orbitals and represents the most general independent particle wave function as yet presented. The GVB(SP) method was used to examine allyl radical and butadiene. All states were described by localized orbitals and energies were in excellent agreement with configuration interaction results. A molecules-in-molecules model using ethylene pi electron states was found to provide a qualitative description of all the states of allyl radical and butadiene examined.
\r\n", "doi": "10.7907/n2qd-5z12", "publication_date": "1974", "thesis_type": "phd", "thesis_year": "1974" }, { "id": "thesis:6267", "collection": "thesis", "collection_id": "6267", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03042011-095512877", "primary_object_url": { "basename": "Carhart_re_1973.pdf", "content": "final", "filesize": 5319212, "license": "other", "mime_type": "application/pdf", "url": "/6267/1/Carhart_re_1973.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "A Detailed Theoretical Study of the Difluoromethane Molecule", "author": [ { "family_name": "Carhart", "given_name": "Raymond Edgar", "clpid": "Carhart-Raymond-Edgar" } ], "thesis_advisor": [ { "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" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The first chapter describes our theoretical investigation of\r\nthe potential energy surface of the difluoromethane molecule. The\r\nHartree-Fock (HF) method, with a 73/3 gaussian basis contracted\r\nto the double-zeta level, was used, and in many cases, CNOO/2\r\ncalculations were included for comparison.\r\n\r\nThe optimum HF geometry is found to be closer to experiment\r\nthan that reported by other workers using a minimum (STO-3G)\r\nbasis set, but it appears that our more flexible basis does little to\r\nimprove the computed general harmonic force constants, the complete\r\nset of which is considered. The stretching constants are found to be\r\nin error by +20% to +35%, the bending constants by -4% to +45%.\r\nIn comparison with HF, the CNOO/2 method grossly overestimates\r\nthe stretching constants, but mimics rather well the bending and\r\ninteraction constants.\r\n\r\nThe theoretical (HF) normal modes and observed vibration\r\nfrequencies are combined to give a set of semi-empirical force\r\nconstants (SEFC's) which are used to predict the vibration frequencies\r\nof the deuterated difluoromethanes. The synthesis and IR spectrum\r\nanalysis of these compounds is described, and the SEFC predictions\r\nare found to be superior to ones appearing previously in the literature.\r\n\r\nThe Urey-Bradley potential (UBP) model, with 1/r^6 steric\r\nterms, is fit to the HF constants and SEFC's. A comparison of the\r\ntwo UBP models indicates that the HF method consistently over\r\nestimates all parameters but the F-F steric term, which it underestimates.\r\n\r\nAnharmonicity in the angular coordinates for large molecular\r\ndistortions is investigated, and it is found that CNOO/2 mimics HF\r\nquite well, except that CNOO/2 under estimates the anharmonicity\r\nwhen the fluorines are quite close together. The UBP model derived\r\nfrom the HF force constants is found to account for most of the\r\nanharmonicity in the HF energy variation.\r\n\r\nThe second chapter describes our investigation of the electronic\r\nstructure of difluoromethane. The HF method, with the basis set\r\ndiscussed above, and certain configuration-interaction methods, were\r\nused.\r\n\r\nThe localized (HF) molecular orbitals (LMO's) were obtained\r\nfor the equilibrium geometry using a new, quadratically convergent\r\napproach which is useful for cases in which convergence of the\r\nEdmiston-Ruedenberg \"two-by-two\" method is slow. The LMO's are\r\nexamined in detail, and several methods are used to show that the\r\nfluorine lone pairs are delocalized toward carbon, a delocalization\r\nwhich represents an important stabilization in the molecule. It is\r\nnoted that this effect, which is most pronounced for lone pairs lying\r\nin the F-C-F plane, may be the molecular-orbital equivalent of the\r\n\"double bond-no bond\" resonance of valence-bond theory.\r\n\r\nAn analysis of the LMO's for distorted geometries indicates\r\nthat the \"orbital following\" concept does not apply to difluoromethane\r\nas the F-C-F angle is altered.\r\n\r\nAn economical approximation to the generalized valence-bond\r\n(GVB) method is developed and is used to give a more detailed picture\r\nof the electron pairs in the molecule. The GVB-like pairs are\r\nlocalized, but in this case the localization is a result of the variation\r\nprinciple rather than a physically meaningless localization criterion.\r\nThey are used to define (in an apprOXimate fashion) \"naturally\"\r\nlocalized Hartree- Fock orbitals (NLMO's) qualitatively similar to\r\nthe LMO's.\r\n\r\nAn analysis of the NLMO's supports the conclusions drawn\r\nfrom the LMO analysis concerning lone-pair delocalization and\r\n\"orbital following\".\r\n", "doi": "10.7907/0SRB-RQ87", "publication_date": "1973", "thesis_type": "phd", "thesis_year": "1973" }, { "id": "thesis:5395", "collection": "thesis", "collection_id": "5395", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11202009-152551437", "primary_object_url": { "basename": "Melius_cf_1973.pdf", "content": "final", "filesize": 6156463, "license": "other", "mime_type": "application/pdf", "url": "/5395/1/Melius_cf_1973.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. A Theoretical Investigation of the Charge Transfer Process in Alkali-Atom Alkali-Ion Collisions. II. Ab Initio Effective Potentials for Use in Molecular Calculations", "author": [ { "family_name": "Melius", "given_name": "Carl Frederick", "clpid": "Melius-Carl-Frederick" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "PART I. The charge transfer processes occurring in collisions of alkali atoms with alkali ions have been studied theoretically using the molecular wavefunction approach. In Part A, we discuss the coupling process between electronic states as exemplified in collisions of Li + Na^+ and Na + Li^+. We find that the total transition process can be decomposed into a succession of simple two-state transition processes. The \u03a3-\u03a3 two-state process can be described by a three-step process involving a coupling region, an uncoupled phase changing region, and a decoupling region. On the other hand, in the molecular wavefunction formulation, the \u03a3- II two-state transition involves a continuous coupling process. The resulting transition probabilities for \u03a3-II coupling differs from \u03a3- \u03a3 coupling leading to different cross sections. In Part B, the molecular wavefunction approach is used to calculate the charge transfer cross sections of alkali-atoms and alkali-ions involving Li, Na, and K.\r\n\r\nPART II. We have investigated the method of effective potentials in replacing the core electrons in molecular calculations. The effective potential method has been formulated in a way which will simplify computations while preserving ab initio quality results. The effective potential is expressed in an analytic form which represents the actual ab initio non-local potential (as defined by the matrix elements for a given basis set). Furthermore, this analytic form permits efficient computations of the effective potential integrals by incorporating the properties of Gaussian basis functions. To minimize the number of basis functions required in the molecular calculations, we define a new ab initio effective potential derived from a modified IMF orbital whose core character has been removed. The effective potential method as formulated becomes a very strong but reliable tool in attempting calculations on very large molecules.\r\n", "doi": "10.7907/8YKN-Z171", "publication_date": "1973", "thesis_type": "phd", "thesis_year": "1973" }, { "id": "thesis:5353", "collection": "thesis", "collection_id": "5353", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-132233582", "primary_object_url": { "basename": "Huestis_dl_1973.pdf", "content": "final", "filesize": 7697816, "license": "other", "mime_type": "application/pdf", "url": "/5353/1/Huestis_dl_1973.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "I. The Projected GI Method and the Excited States of H\u2082. II. A Superposition Principle for Siegert Resonant States", "author": [ { "family_name": "Huestis", "given_name": "David Lee", "clpid": "Huestis-David-Lee" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The simplest orbital wavefunction that adequately describes the dissociation of the excited states of homonuclear diatomic molecules must involve a spatial symmetry projection operator. The use of such a wavefunction has been developed in detail and applied to the excited states of the hydrogen molecule. It was found that the advantages of an independent-particle description are enhanced considerably by spatial projection. The low-lying \u03a3 states of H_2 are explained unambiguously and convincingly in terms of orbital character based on the model of the one-electron heteronuclear diatomics.\r\n\r\nRecent experimental work in electron impact spectroscopy has illustrated that short-lived negative-ion resonances must play an important role. In an attempt to show that such resonances form a natural and complete characterization of the scattering process, the properties of the resonant states defined by Siegert have been investigated. In specific, a superposition principle for Siegert states was found, which provides a complete description of any quantum mechanical event involving a potential of finite range.\r\n", "doi": "10.7907/zqek-hg39", "publication_date": "1973", "thesis_type": "phd", "thesis_year": "1973" }, { "id": "thesis:5320", "collection": "thesis", "collection_id": "5320", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10222009-105738617", "primary_object_url": { "basename": "Guberman_sl_1973.pdf", "content": "final", "filesize": 6823817, "license": "other", "mime_type": "application/pdf", "url": "/5320/1/Guberman_sl_1973.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "I. Projected G1 wavefunctions for He\u2082. II. Localized wavefunctions for H\u2082O, OH, and O", "author": [ { "family_name": "Guberman", "given_name": "Steven Lawrence", "clpid": "Guberman-Steven-Lawrence" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "I. The low-lying excited states of He_2 have been examined using projected Generalized Valence Bond wavefunctions. Two types of interactions are shown to be important in understanding the anomalous maxima \r\nand the general shapes of the curves. The interaction between core orbitals on opposite centers is important at small R whereas at large R the dominant interaction is between core and Rydberg orbitals on opposite centers. The latter effect is expressible in terms of the exchange kinetic energy and arises from the repulsion between singlet coupled pairs of orbitals. This is described simply in terms of the shapes of the Rydberg orbitals. The results in general agree favorably with experiment where such comparison can be made.\r\n\r\nII. Localized wavefunctions obtained from applying an external localization criterion to orbitals resulting from the GF method are reported for H_2O, OH, and 0. The shapes and angles between the orbitals \r\nare described in some detail. It is shown that the resulting GF orbitals change in a chemically reasonable manner as we proceed from 0 to OH to H_2O.\r\n", "doi": "10.7907/TA01-KS50", "publication_date": "1973", "thesis_type": "phd", "thesis_year": "1973" }, { "id": "thesis:6267", "collection": "thesis", "collection_id": "6267", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03042011-095512877", "primary_object_url": { "basename": "Carhart_re_1973.pdf", "content": "final", "filesize": 5319212, "license": "other", "mime_type": "application/pdf", "url": "/6267/1/Carhart_re_1973.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "A Detailed Theoretical Study of the Difluoromethane Molecule", "author": [ { "family_name": "Carhart", "given_name": "Raymond Edgar", "clpid": "Carhart-Raymond-Edgar" } ], "thesis_advisor": [ { "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" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The first chapter describes our theoretical investigation of\r\nthe potential energy surface of the difluoromethane molecule. The\r\nHartree-Fock (HF) method, with a 73/3 gaussian basis contracted\r\nto the double-zeta level, was used, and in many cases, CNOO/2\r\ncalculations were included for comparison.\r\n\r\nThe optimum HF geometry is found to be closer to experiment\r\nthan that reported by other workers using a minimum (STO-3G)\r\nbasis set, but it appears that our more flexible basis does little to\r\nimprove the computed general harmonic force constants, the complete\r\nset of which is considered. The stretching constants are found to be\r\nin error by +20% to +35%, the bending constants by -4% to +45%.\r\nIn comparison with HF, the CNOO/2 method grossly overestimates\r\nthe stretching constants, but mimics rather well the bending and\r\ninteraction constants.\r\n\r\nThe theoretical (HF) normal modes and observed vibration\r\nfrequencies are combined to give a set of semi-empirical force\r\nconstants (SEFC's) which are used to predict the vibration frequencies\r\nof the deuterated difluoromethanes. The synthesis and IR spectrum\r\nanalysis of these compounds is described, and the SEFC predictions\r\nare found to be superior to ones appearing previously in the literature.\r\n\r\nThe Urey-Bradley potential (UBP) model, with 1/r^6 steric\r\nterms, is fit to the HF constants and SEFC's. A comparison of the\r\ntwo UBP models indicates that the HF method consistently over\r\nestimates all parameters but the F-F steric term, which it underestimates.\r\n\r\nAnharmonicity in the angular coordinates for large molecular\r\ndistortions is investigated, and it is found that CNOO/2 mimics HF\r\nquite well, except that CNOO/2 under estimates the anharmonicity\r\nwhen the fluorines are quite close together. The UBP model derived\r\nfrom the HF force constants is found to account for most of the\r\nanharmonicity in the HF energy variation.\r\n\r\nThe second chapter describes our investigation of the electronic\r\nstructure of difluoromethane. The HF method, with the basis set\r\ndiscussed above, and certain configuration-interaction methods, were\r\nused.\r\n\r\nThe localized (HF) molecular orbitals (LMO's) were obtained\r\nfor the equilibrium geometry using a new, quadratically convergent\r\napproach which is useful for cases in which convergence of the\r\nEdmiston-Ruedenberg \"two-by-two\" method is slow. The LMO's are\r\nexamined in detail, and several methods are used to show that the\r\nfluorine lone pairs are delocalized toward carbon, a delocalization\r\nwhich represents an important stabilization in the molecule. It is\r\nnoted that this effect, which is most pronounced for lone pairs lying\r\nin the F-C-F plane, may be the molecular-orbital equivalent of the\r\n\"double bond-no bond\" resonance of valence-bond theory.\r\n\r\nAn analysis of the LMO's for distorted geometries indicates\r\nthat the \"orbital following\" concept does not apply to difluoromethane\r\nas the F-C-F angle is altered.\r\n\r\nAn economical approximation to the generalized valence-bond\r\n(GVB) method is developed and is used to give a more detailed picture\r\nof the electron pairs in the molecule. The GVB-like pairs are\r\nlocalized, but in this case the localization is a result of the variation\r\nprinciple rather than a physically meaningless localization criterion.\r\nThey are used to define (in an apprOXimate fashion) \"naturally\"\r\nlocalized Hartree- Fock orbitals (NLMO's) qualitatively similar to\r\nthe LMO's.\r\n\r\nAn analysis of the NLMO's supports the conclusions drawn\r\nfrom the LMO analysis concerning lone-pair delocalization and\r\n\"orbital following\".\r\n", "doi": "10.7907/0SRB-RQ87", "publication_date": "1973", "thesis_type": "phd", "thesis_year": "1973" }, { "id": "thesis:5971", "collection": "thesis", "collection_id": "5971", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07092010-164234058", "primary_object_url": { "basename": "Ladner_rc_1972.pdf", "content": "final", "filesize": 6352121, "license": "other", "mime_type": "application/pdf", "url": "/5971/1/Ladner_rc_1972.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Independent-Particle Potential-Energy Surfaces for Chemical Reactions", "author": [ { "family_name": "Ladner", "given_name": "Robert Charles", "clpid": "Ladner-Robert-Charles" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A new independent-particle method, the spin-coupling optimized GI (SOGI) method is described. This method removes many of the restrictions of the Hartree-Fock (HF), valence bond (VB), and GI methods. This method is applied to the two reactive systems of linear H_3 and linear LiH_2. The results of the H_3 calculations are carefully compared with CI results. The shapes of the potential energy surfaces (PES\u2019s) are explained in terms of the SOGI orbitals. Finally, the SOGI method is applied to the excited states of H_3, both linear and nonlinear.", "doi": "10.7907/4FTW-PJ83", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:5394", "collection": "thesis", "collection_id": "5394", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11202009-150548056", "primary_object_url": { "basename": "Kahn_lr_1972.pdf", "content": "final", "filesize": 5788503, "license": "other", "mime_type": "application/pdf", "url": "/5394/1/Kahn_lr_1972.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Ab-Initio Effective Potentials for Use in Molecular Calculations. II. The Sternheimer Correction, Perturbation Theory and Approximate Wavefunctions. III. The Theoretical Determination of the Li\u2082 B\u00b9\u03a0u Potential Energy Curve", "author": [ { "family_name": "Kahn", "given_name": "Luis Ricardo", "clpid": "Kahn-Luis-Ricardo" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I: We have investigated the efficacy of ab-initio effective potentials in replacing the core electrons of atoms for use in molecular calculations. The effective potentials are obtained from ab initio GI calculations on atoms and are unique and local. We find that the use of these effective potentials to replace the core orbitals of such molecules as LiH, Li_2, BH, or LiH_2, leads to wavefunctions in excellent agreement with all-electron ab-initio results. The use of such effective potentials should allow ab-initio quality wavefunctions to be obtained for systems too large for the ab-initio consideration of all the electrons.\r\n\r\nPart II: We have investigated the Sternheimer correction for the calculation of the nuclear quadrupole coupling constants and its relation to the approximate nature of the zero-order wave- function. The first-order perturbed Hartree-Fock equations, and some approximations to them, are solved for the 2^2P state of Li, and the resulting Sternheimer type corrections are compared with Sternheimeris approximate calculations and with results from non-perturbation theory approaches.\r\n\r\nPART III: The Li_2 B^1\u03c0_u potential energy curve has been calculated with a Multi-Configuration SCF (MCSCF) wavefunction. Several different types of wavefunctions and basis sets have been examined and their accuracy determined. The most accurate wavefunction used predicts a binding energy of 0.3015 e.V. (84% of the experimental value of 0.362 e.V.), and predicts a potential hump of 0.0724 e.V. with its maximum in the vicinity of 10.6 Bohr. It is argued that the theoretical value of the hump is an upper bound to the experimental value.\r\n", "doi": "10.7907/P3JP-H317", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:5333", "collection": "thesis", "collection_id": "5333", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10282009-093808296", "primary_object_url": { "basename": "Blint_rj_1972.pdf", "content": "final", "filesize": 5329122, "license": "other", "mime_type": "application/pdf", "url": "/5333/1/Blint_rj_1972.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Orbital Interpretation and Properties of the X\u00b9\u03a3\u207a, a\u00b3\u220f, A\u00b9\u220f and \u00b3\u03a3\u207a States of BH. II. Gas Phase Reactions of Fluoromethyl Cations with Ethylene and Benzene", "author": [ { "family_name": "Blint", "given_name": "Richard Joseph", "clpid": "Blint-Richard-Joseph" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "clpid": "Beauchamp-J-L" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "\"Ab initio\" calculations have been carried out on the states of BH(\u03c71\u03a3+, a3\u03a0, A1\u03a0, and 3\u03a3+) which dissociate to the ground states of B and H. The application of the Gl method (which is a special case of the GI method) was extended to handle five- and six-electron systems, and this method along with SOGI, CI and the GVB method was used to investigate the BH states. The effect of restricting the orbitals of the wave-function to be basis functions for the irreducible representations of the spatial symmetry group leads to noncontinuous changes in the orbitals as a function of internuclear distance. And further it is noted that the removal of this restriction on the atomic wavefunction of boron leads to simple predictions of the forms of the wavefunctions, geometries of the molecules and characteristics of the potential curves for the BHN molecules. On the basis of this the potential curves for the a3\u03a0 and\r\nA1\u03a0 states are correctly predicted to have humps and the 2A1 and 2B1 states of BH2 are predicted to be bent and linear, respectively. Molecular properties for many of these wavefunctions have been calculated and correlated with changes in the orbitals as a function of internuclear distance.
\r\n\r\nGas phase reactions and properties of fluoromethyl cations have been investigated using the techniques of ion cyclotron resonance spectroscopy (icr). Fluoride transfer reactions between substituted methyl cations are observed to be rapid and permit the determination of relative fluoride ion affinities, defined as the negative of the enthalpy change for the reaction CHNF+3-N + F- \u2192 CHNF4-N. By combining available thermochemical data and our experimental results the following order for the fluoride affinities of the methyl cations is constructed: CF+3 (256.3 kcal/mole) > CH+3 (252.0 kcal/mole) > CH2F+ (243.6 kcal/mole) > CF2H+ (242.8 kcal/mole). A measurement of the equilibrium constant for the reaction (CF2H+ + CH2F2 \u21cc CH2F+ + CF3H) between the latter two ions has permitted their relative fluoride ion affinities to be accurately determined. Fluoride ion affinities are a means of determining carbonium ion stabilities.
\r\n\r\nWith the general goal of understanding reactions involving electrophillic addition to \u03c0-systems the reactions of the fluoromethyl cations with ethylene, ethylene-d4 and benzene-d6 were investigated. The important process in each case involves addition of the fluoromethyl cation to the substrate to form a chemically activated intermediate which decomposes with loss of HF or H2. Rate constants for the reactions of the fluoromethyl cations with ethylene were determined using icr trapped ion techniques. In conjunction with ion ejection double resonance, product distributions for the reactions involving ethylene-d4 and benzene-d6 have been determined. Only in the case of the reactions of fluoromethyl cations with benzene-d6 is the possibility of a distinctive reaction mechanism revealed from the isotopic product distributions.
\r\n", "doi": "10.7907/KJ13-G054", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:5366", "collection": "thesis", "collection_id": "5366", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-074130644", "primary_object_url": { "basename": "Hunt_wj_1972.pdf", "content": "final", "filesize": 5679177, "license": "other", "mime_type": "application/pdf", "url": "/5366/1/Hunt_wj_1972.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Electronic Wavefunctions for Small Molecules", "author": [ { "family_name": "Hunt", "given_name": "William James", "clpid": "Hunt-William-James" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "PART I. A simple variationally-based method for calculating electronic wavefunctions of excited states, the improved virtual orbital (IVO) method, is developed in this work. Calculations are presented for H_2O, O_2, CO, and N_2. While the IVO method gives limited accuracy in the treatment of valence excited states, the description of Rydberg states is very useful. For O_2 the theoretical prediction of 8.70 eV (v' = 2) for the transition from the ^3\u03a3^-_g ground state to the ^3\u03c0_g (1\u03c0_g \u2192 3s\u03c3_g) Rydberg state facilitated discovery of this transition in electron impact spectra at 8.65 eV (v' = 2).\r\n\r\nPART II. The N, T, and V states of ethylene have been studied with the Hartree-Foci (H-F) and configuration interaction (CI) techniques as a function of C-C bond distance and the twist angle between methylene groups. The calculated rotational barrier for the N state is 67.2 Kcal/mole, in good agreement with the experimentally derived activation energy of 65 Kcal/mole for cis-trans isomerization of 1,2di-deutero ethylene. The maximum in the N state curve lies 1.4 Kcal/mole above the minimum of the triplet state (T) curve. Both H-F end CI calculations show that the V state of planar ethylene has a more extended charge distribution than the T state. This charge distribution contracts as the methylene groups are twisted from the -planar geometry. Correlation terms included in the CI calculations contract the charge distribution considerably from its H-F size. A modified Franck-Condon Principle for internal rotation suggests that the maximum absorption observed experimentally does not correspond to vertical excitation for the N \u2192 V transition. \r\n\r\nPART III. A Generalized Valence Bond method combining the computational tractability of the usual MO-SCF approach with the conceptual advantages of a valence bond picture is proposed. The GVB method has been applied to calculation of potential curves for CH_2 in the ^3B_1, ^1A_1, and ^1B_1 states. These calculations predict that the ^3B_1 curve may cross the ^1A_1 curve near the minimum for the^1A_1 state. A study of the ring opening of cycloprooane predicts a barrier height of 61 Kcal/mole for cis-trans isomerization, in good agreement with the experimentally determined activation energy of 65 Kcal/mole for 1,2 di-deutero cyclopropene. An investigation of diatomic hydrides and fluorides in the GVB picture gives a consistent view of the energy levels and one-electron energies of these molecules.\r\n", "doi": "10.7907/F5KA-3M29", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:5402", "collection": "thesis", "collection_id": "5402", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-083723341", "primary_object_url": { "basename": "Mortola_ap_1972.pdf", "content": "final", "filesize": 5264757, "license": "other", "mime_type": "application/pdf", "url": "/5402/1/Mortola_ap_1972.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Bonding in Transition Metal Compounds", "author": [ { "family_name": "Mortola", "given_name": "Albert Patrick", "clpid": "Mortola-Albert-Patrick" } ], "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": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The values of the Hartree-Fock (HF) and Generalized Valence Bond (GVB) Theories of molecular structure are considered by theoretical investigations of the MnO_4^-, TiO, TiCO, and TiCO^+ molecules. Results of these calculations are used in determining the nature of the bonding in these compounds. From the ideas generated, extensions are made to other oxygen and carbonyl transition metal compounds. The conclusion is reached that GVB theory provides more information but is limited to small model compounds. In larger, real compounds, HF theory must be used.", "doi": "10.7907/FJ5R-XJ04", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:5347", "collection": "thesis", "collection_id": "5347", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11042009-080816954", "primary_object_url": { "basename": "Hay_pj_1972.pdf", "content": "final", "filesize": 8008819, "license": "other", "mime_type": "application/pdf", "url": "/5347/1/Hay_pj_1972.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. The Generalized Valence Bond Theory of Electronic Structure. II. An Orbital Interpretation of Superexchange in Antiferromagnetic Insulators", "author": [ { "family_name": "Hay", "given_name": "Philip Jeffrey", "clpid": "Hay-Philip-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": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I: A discussion is given of the generalized valence bond (GVB) method--a multi-configuration approach to electronic structure that combines a valence bond interpretation with the self-consistent techniques of Hartree-Fock theory. Ab initio calculations on simple hydrocarbons give improved descriptions of bonding in terms of localized C-C and C-H bonds. The nine lowest states of the ozone molecule are treated by GVB and configuration interaction techniques and an assignment of the spectrum of O_3 is made. A metastable excited singlet state with an equilateral geometry and an energy 1.5 eV above the ground state is discovered.\r\nThe calculated energy barrier of 60.5 kcal for the cis-trans isomerization of cyclopropane is in good agreement with the experimental value of 64.2 kcal. No barrier to ring closure is found in the trimethylene biradical in contrast to commonly accepted biradical mechanisms. The ^1A_1 state of CH_2 is calculated to be 0.50 eV (11. 5 kcal) above the ground ^3B_1 state. The ^1B_1 \u2190 ^1A_1, transition\u2014calculated to be 1. 40 eV--agrees with the lowest observed ^1B_1 \u2190 ^1A_1 band and suggests a reinterpretation of this as a 0-0 band. A new ^1A_1 state at 3.2 eV is also discussed. Good values of the barrier to internal rotation in ethane and of the dissociation energy of O_2 are obtained.\r\n\r\nPart II: An orbital interpretation of superexchange suggests that anti-ferromagnetism arises from increased metal-metal overlap due to the ligand orbitals. A theoretical value of the exchange parameter from ab initio calculations on the Ni^(++)-F^- -Ni^(++) \"molecule\" is 10% of the experimental value in KNiF_3.\r\n", "doi": "10.7907/D2P6-BA46", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:5806", "collection": "thesis", "collection_id": "5806", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05132010-113849886", "primary_object_url": { "basename": "O'keefe_p_1971.pdf", "content": "final", "filesize": 7163785, "license": "other", "mime_type": "application/pdf", "url": "/5806/1/O'keefe_p_1971.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Applications of the GI Method to Incorporation of Many-Body Effects in Metals; The Band Structure and Resolution of Several Anomalous Properties of Lithium Metal", "author": [ { "family_name": "O'Keefe", "given_name": "Patricia Marie", "clpid": "O'Keefe-Patricia-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": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A new approach to studying the electronic energy band structure on solids has been developed and calculations are reported for lithium metal. This framework, the GI method, leads to one-electron orbitals which in general are singly occupied, have no orthogonality constraints, are no longer required to have the full symmetry of the system, and lead to a description which is valid at all internuclear distances. Yet they still retain an independent particle interpretation.
\r\n\r\nIn the application to solids, similar considerations apply. It is found that, for the alkalis, the resulting one-electron conduction orbitals can be taken to be Bloch functions for a smaller symmetry group than the bcc symmetry of the lattice. Thus, the resulting Brillouin zone (BZ) is smaller than that in Hartree-Fock (HF), and gaps can occur at the Fermi surface where none were previously permitted. For lithium these gaps are found to be sufficiently small so that many of the expected properties are not significantly affected and the resulting Fermi surface is found to be quite spherical in good agreement with, for example, position annihilation results. However, for such properties as the high field transverse magneto resistance, the soft X-ray emission spectrum, the optical absorption spectrum, the thermoelectric power, and the Hall coefficient, striking alterations in the description are obtained which lead to an appealing explanation of many of the anomalous properties of the alkalis, and seem to be in at least qualitative agreement with the experimental observations. The Mott paradox is also resolved; the metal is found to change continuously from a conductor to an insulator as the system is dilated.
", "doi": "10.7907/QN5M-CW17", "publication_date": "1971", "thesis_type": "phd", "thesis_year": "1971" }, { "id": "thesis:5754", "collection": "thesis", "collection_id": "5754", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-111816149", "primary_object_url": { "basename": "Surratt_gt_1971.pdf", "content": "final", "filesize": 1306349, "license": "other", "mime_type": "application/pdf", "url": "/5754/1/Surratt_gt_1971.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Minimum Kinetic Energy Orbital and the Band Structure of Sodium", "author": [ { "family_name": "Surratt", "given_name": "Grover Timothy", "clpid": "Surratt-Grover-Timothy" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "For calculations on molecules and solids it has proven \r\nuseful to replace the various core electrons with a pseudo-potential. The most common method for doing this, that of \r\nPhillips andKleinman, suffers from the disadvantage that\r\nthe pseudopotential obtained is not unique. It has previously \r\nbeen shown, however, th t the non-uniqueness problem can be \r\nresolved by the use of ab-initio GI orbitals as the basis\r\nfor the potential. Such potentials have proven quite \r\nsatisfactory in replacing the core electrons in molecular and \r\nsolid-state calculations. Unfortunately, systems of ten or \r\nmore electrons are not accessible to GI, so that the approach \r\ncannot be used for sodium, for example.\r\n\r\n We have examined the GI orbitals and effective potentials \r\nfor Li, Be+, B++ and compared these orbitals and potentials \r\nwith those obtained from the usual Hartree-Fock formalism,\r\nbut employing an extra condition on the orbitals to ensure \r\nuniqueness. It was found that a condition suggested (but \r\napparently never tried) by Cohen and Heine, that the Hartree-Fock core orbitals be allowed to mix with the valence\r\norbital in such a way as to minimize the kinetic energy, \r\nproduced orbitals and potentials nearly identical to those \r\nfrom the GI method.\r\n\r\n We then employed this method to obtain local potentials \r\nfor the ^2S, ^2P and ^2D states of sodium.. These potentials \r\nwere found to reproduce the spectrum of sodium quite well.\r\nThese potentials were then used to study the energy levels \r\nof sodium metal at the high symmetry points in the Brillouin \r\nzone, employing the GI band structure formalism.\r\n", "doi": "10.7907/2665-JE74", "publication_date": "1971", "thesis_type": "masters", "thesis_year": "1971" }, { "id": "thesis:5759", "collection": "thesis", "collection_id": "5759", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04302010-075156671", "primary_object_url": { "basename": "Frank_r_1970.pdf", "content": "final", "filesize": 736959, "license": "other", "mime_type": "application/pdf", "url": "/5759/1/Frank_r_1970.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Theoretical correlation of the geometry and magnetic hyperfine splittings of the methyl radical", "author": [ { "family_name": "Frank", "given_name": "Robert", "clpid": "Frank-R" } ], "thesis_advisor": [ { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Spin densities at carbon and hydrogen are calculated at several out of plane angles of the methyl radical. Comparison with temperature dependent ESR studies indicate that the GF method describes the variation adequately while Hartree-Fock, Unrestricted Hartree-Fock, and Valence-Bond treatments do not.", "doi": "10.7907/5YF2-J383", "publication_date": "1970", "thesis_type": "masters", "thesis_year": "1970" }, { "id": "thesis:6056", "collection": "thesis", "collection_id": "6056", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09272010-083324433", "type": "thesis", "title": "The Excitation Operator Method and the Valence Excited States of Ethylene", "author": [ { "family_name": "Dunning", "given_name": "Thomas Harold, Jr", "clpid": "Dunning-Thomas-Harold, Jr" } ], "thesis_advisor": [ { "family_name": "McKoy", "given_name": "Basil Vincent", "clpid": "McKoy-B-V" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": " The problem of describing the electronic excited states of an atomic or molecular system can be reduced to one of finding a form for an operator A^+(E) such that it satisfies the following equation:\r\n\r\n[\u0124, A^+(E)] | 0> = \u0394E A^+(E) | 0>.\r\n\r\nFour approximations to the excitation operator, A^+(E), have been considered: (a) the single transition approximation, corresponding to excitation into virtual orbitals, (b) the improved single transition approximation which allows for the self-consistent field adjustment of the virtual orbital, (c) the Tamm-Dancoff approximation, corresponding to selective configuration interaction in the excited state and (d) the random-phase approximation which attempts to take into account correlation in both ground and excited states.\r\n\r\n Analyzing the excitation operator method in terms of the approximations to the excitation operator listed above, we found that the correlation does not always enter in the ground and excited states in a particularly balanced manner and that self-consistent field changes in the core are neglected. In addition, the strong \"mixing\" of certain doubly excited configurations into the ground state wavefunction, such as (\u03c0*\u03b1\u03c0*\u03b2) in ethylene, is shown to lead to a number of problems in the random-phase approximation, e.g., an instability in the triplet equations.\r\n\r\n The excitation operator approach is illustrated by ab initio calculations on a number of valence excited states of the ethylene molecule. These calculations indicate that the lowest singlet \u03c0\u2192\u03c0* state of ethylene is not a valence state as previously assumed, but that it is significantly more diffuse, e.g., in the improved single transition approximation the