Cobaloximes are macrocyclic complexes well-studied as homogeneous catalysts for hydrogen evolution, but they are also competent at the microscopic reverse reaction, hydrogen oxidation. Kinetic studies of Co(dmgBF2)2L2 reacting with hydrogen and base reveal a rate law that is second-order in cobalt and first-order in H2, indicating that the mechanism of H-H bond breaking is homolytic.
The reduction potentials of metal cyanide complexes can be tuned by appending boranes to the N-terminus. By boronating ruthenium cyanide complexes containing diimine ligands, the RuII/III couple can be tuned without drastic modification of the diimine0/- couple. A new member of the [Ru(dimmine)(CN)4]2- family is synthesized with the ligand 4,4’-bis(trifluoromethyl)-2,2’-bipyridine (CF3bpy) and boronated, resulting in a molecule with two reversible redox events separated by 3.2 V.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/1sew-r360, author = {McNicholas, Brendon James}, title = {New Electrolytic Media and Methods for Energy Storage and Conversion}, school = {California Institute of Technology}, year = {2020}, doi = {10.7907/1sew-r360}, url = {https://resolver.caltech.edu/CaltechTHESIS:06082020-143301441}, abstract = {New electrolytic media and methods for energy storage and conversion are needed to fully realize the sustained use of renewable energy and complete removal of dependence on fossil fuels. Motivated by this urgency, researchers today are heavily invested in developing new electrocatalytic systems for carbon dioxide sequestration to reduce greenhouse gas emissions and new battery architectures, such as non-aqueous redox flow batteries, to keep solar energy at our disposal during peak times of energy consumption. Chapter 1 provides an overview of the conceptual frameworks for these two alternative energy technologies and a literature review of relevant work and inspiration in these fields. Chapter 2 demonstrates one of the first examples of ionic liquid voltammetry of a molecular species, namely (tpfc)Mn, and its electron transfer reactivity in ionic liquids with varying solvent viscosity, effective electrolyte concentration, and donor strength. As well as showing the non-unity diffusional properties of molecular species in ionic liquids and the capability of ionic liquid anions to coordinate to molecular species, these studies suggest the viability of ionic liquids as conductive media for energy storage and conversion. Chapter 3 introduces methods for immobilization of molecular catalysts in polymeric ion gels, a general strategy that bridges the divide between homogeneous solution-state catalysis and heterogeneous solid-state catalysis. These results provide insight into how environment, catalyst concentration, catalyst mobility, substrate availability, and dielectric properties of a medium all affect the catalytic response and overpotential for CO2 reduction. Further implementation of these ion gel composites in solid-state devices, in aqueous environments, and in gas diffusion electrodes is also discussed. In Chapter 4, a brief overview of the use of boranes as capping ligands for cyanide is provided. The synthesis, electronic properties, and theoretical calculations of homoleptic, boronated Fe(II) hexacyanoferrates are reported. Addition of borane to cyanometallates dramatically alters electronic structures and is a novel method for permanent modification of formal potentials while simultaneously maintaining or improving electrochemical reversibility and ambient stability. These complexes are characterized and studied by cyclic and differential pulse voltammetry, UV-vis, IR, and Raman spectroscopy, and flash-quench photolysis. Chapter 5 extends the unique reactivity of borane adducts to the characterization of a full series of hexaisocyanoboratometallates (Cr, Mn, Fe, Ru, Os), compounds which demonstrate the concept of cyanide as a “variable-field” ligand, including magnetic circular dichroism spectroscopy, electron paramagnetic resonance spectroscopy, luminescence studies, excited-state lifetime studies, and electrochemistry. As electrolytes for non-aqueous redox flow batteries, these species exhibit excellent Coulombic and voltage efficiencies and fast electron transfer rates. The highly oxidizing species will also find use as reversible oxidants for chemical oxidations. Chapter 6 extends the concept of modifying formal potentials to heteroleptic cyanometallates (M = Fe, Ru) with diimine ligands (L = bipyridine, phenanthroline, 4,4’-trifluoromethylbipyridine). These species are shown to be potent excited-state reductants and oxidants, strong and long-lived phosphors, and promising electrolytes for symmetric, non-aqueous redox flow batteries. These data also demonstrate improved excited-state lifetimes for borane-appended species, likely due to inhibition of non-radiative decay pathways. Chapter 7 focuses on the generation of a solution stable, square pyramidal Co(II) species, which is studied by electrochemistry, UV-vis-NIR spectroscopy, X-band and Q-band CW EPR, and pulsed EPR techniques (HYSCORE, ENDOR). These studies demonstrate that boronation of cyanide differentially affects the energies of ligand field transitions based on π backbonding ability.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B. and Grubbs, Robert H.}, } @phdthesis{10.7907/0fgd-j835, author = {Fajardo, Javier, Jr.}, title = {Transition Metal Complexes for Challenging Reductive Transformations: From Nitrogen Fixation Catalysts to Photoreductants}, school = {California Institute of Technology}, year = {2020}, doi = {10.7907/0fgd-j835}, url = {https://resolver.caltech.edu/CaltechTHESIS:06082020-141438135}, abstract = {Transition metal complexes are routinely employed as catalysts for the reductive cleavage of a diverse array of strong chemical bonds. Two notable research areas that exemplify such utility are nitrogen fixation, involving cleavage of the notoriously unreactive triple bond of dinitrogen (N₂) to form ammonia (NH₃), and photoredox catalysis, wherein powerful photoreductants generated by visible light excitation facilitate challenging reduction steps in a host of synthetic organic transformations. This thesis focuses on a number of structure-function studies conducted on group 8 transition metal complexes that catalyze N₂-to-NH₃ conversion, commonly referred to as the nitrogen reduction reaction (N₂RR), and on homoleptic tungsten(0) arylisocyanides that, among their many attractive qualities, possess highly reducing electronically excited states. These comparative studies provide fundamental insight into critical design features which can guide efforts to improve existing N₂RR or photocatalysts or rationally tailor them for specific applications.
Chapter 2 details the effect apical Lewis acidic atom substitution in P₃XFe platforms (X = B, Al, Ga) has on structure, bonding, and N₂RR activity. Structural, spectroscopic, electrochemical, and computational studies reveal that all three P₃XFe systems possess similar electronic structures, degrees of N₂ activation, and geometric flexibility, but P₃AlFe and P₃GaFe display significantly lower N₂RR efficiencies than P₃BFe when treated with HBArF₄/KC₈ or [H₂NPh₂][OTf]/Cp*₂Co at –78 °C in Et₂O.
Chapter 3 reports on isostructural tris(phosphino)silyl Ru and Os complexes that mediate catalytic N₂RR. The study of the homologous, isostructural series of complexes P₃SiM (M = Fe, Ru, Os) helps delineate important factors for N₂RR catalyst design. Low-temperature protonation of P₃SiOs–N₂⁻ yields P₃SiOs=NNH₂⁺, representing the first instance of an Os–N₂ species being converted to a protonated Os–NxHy product.
Chapter 4 communicates a novel series of homoleptic tungsten(0) photoactive complexes supported by fused-ring (CN-1-(2-iPr)-Naph) or alkynyl-bridged (CNDippCCAr) arylisocyanide ligands. Systematic studies establish facile electronic variation of the CNDippCCAr platform as a straightforward method by which to rationally modulate the ground- and excited-state properties of W(CNDippCCAr)₆ complexes. The photophysical properties of W(CN-1-(2-iPr)-Naph)₆ reveal potential benefits of utilizing fused-ring arylisocyanide ligands in the design of this class of photosensitizers.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/aq89-jv13, author = {Lichterman, Michael Yang}, title = {Analysis of Metal-Oxide Protected Photoelectrochemical Systems for Water Splitting}, school = {California Institute of Technology}, year = {2018}, doi = {10.7907/aq89-jv13}, url = {https://resolver.caltech.edu/CaltechTHESIS:06122018-090745040}, abstract = {The photoelectrochemical splitting of water into oxygen and hydrogen gas is one pathway toward the renewable and economic generation of a fuel which is sufficiently scalable to power a large fraction, or even a majority, of the power requirements of modern society. In order to make such a device economically promising, it must be sufficiently cheap, have sufficiently high efficiency, or some combination thereof. In this work, two primary routes toward such a device are discussed; the first is the use of a cheaply prepared photoanode material, BiVO4, the interactions of this material with cobalt oxide based catalysts, and the use of such structures in more extreme pH ranges than have previous been reported. The second route details the application of a protective layer, TiO2, on otherwise unstable materials such as GaP and CdTe when operated as photoanodes in alkaline media. The further work herein applies operando ambientpressure x-ray photoelectron spectroscopy (AP-XPS) to understand the nature of the energetics which allow conduction in the aforementioned TiO2, as well as other energetics in the electrochemical double layer in the adjacent electrolyte. Further experiments using Raman spectroscopy on associated III-V photoanode devices are also described.}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/Z9FJ2DT7, author = {Blumenfeld, Carl Michael}, title = {Covalent Functionalization of Metal-Oxide Surfaces with Non-Traditional Ligands}, school = {California Institute of Technology}, year = {2017}, doi = {10.7907/Z9FJ2DT7}, url = {https://resolver.caltech.edu/CaltechTHESIS:06052017-104255604}, abstract = {Herein detailed are the syntheses, properties, and applications of metal-oxide nanosubstrates covalently functionalized with two classes of materials, inorganic macrocycles called corroles, and genomic deoxyribonucleic acid (DNA). These products have found biomedical applications in tumor imaging and chemotherapeutic sequestration, respectively. Both classes of prepared materials are the first of their kind.
Corroles are tetrapyrrolic macrocycles, which have found applications in tumor imaging and treatment, catalysis, solar fuels, and energy conversion. The direct functionalization of metal-oxides with inorganic macrocycles, including corroles, has largely revolved around the formation of hydrogen bonding type interactions between the substrate and the ligand. Hydrogen bonding motifs result in materials with only moderate stability due to solvent dissolution. In the first three chapters of this thesis, the scalable preparation of 5,10,15- (trispentafluorophenyl) corrole and its subsequent covalent functionalization of metal-oxide surfaces are discussed.
Chapter 1 details mechanistic elements of the oligomerization and oxidative cyclization of 5,10,15-(trispentafluorophenyl) corrole from pentafluorobenzaldehyde and pyrrole. Prior to this work the synthesis of triperfluoroaryl corroles was dangerously exothermic and could only be carried out on milligram scale. Mechanistic insights led to a safe and scalable synthesis of the desired corrole species, achieving a 17.0 % yield (4.58 g). A detailed discussion of the covalent functionalization of the surface of TiO2 with chlorosulfonated derivatives of 5,10,15-tris(pentafluorophenyl) corrole is presented in Chapter 2. The chlorosulfonated species investigated include the freebase, gallium, and aluminum corroles. Hydroxyl groups on the metal-oxide react with the chlorosulfonyl groups of the corrole ring via nucleophilic attack, resulting in the formation of sulfonic ester linkages. The aluminum species was further investigated as a potential near-infrared optical contrast agent. The details of this study, described in Chapter 3, include imaging experiments with immortalized human cancer lines and harvested mouse hepatocytes. This nanoconjugate exhibited low toxicity and efficient cellular uptake.
Conventional chemotherapy agents that target DNA are notorious for producing severe side-effects. Sequestering chemotherapeutics that enters systemic circulation, in a process deemed “ChemoFiltration,” is a strategy for reducing off-target toxicity. Materials capable of such activity have yet to be fully realized. Reported in Chapter 4 are the first methods covalent attachments of genomic DNA to surfaces, namely magnetite (Fe3O4) nanoparticles, via two separate strategies. These materials show efficacy in removing doxorubicin, cisplatin, and epirubicin from biologically relevant solutions. A device coated with this material demonstrated in vivo activity in a porcine model.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/Z9FQ9TNB, author = {Hunter, Bryan Michael}, title = {Fuels and Materials from Sunlight and Water}, school = {California Institute of Technology}, year = {2017}, doi = {10.7907/Z9FQ9TNB}, url = {https://resolver.caltech.edu/CaltechTHESIS:06022017-112043547}, abstract = {The urgency to develop new technologies that harness energy and natural feedstocks in a sustainable fashion has never been more apparent. With global power consumption growing at an exponential rate, only one resource is truly capable of powering the planet: the sun. Sunlight is reliable, clean, and free.
Significant resources have been pledged to develop and refine solar energy devices that convert photons into electricity (i.e. photovoltaics), but the sun’s intermittency and the poor overlap of solar irradiance with global power demand a different strategy. In light of these limitations, we have proposed a device which converts solar energy into reduced chemical fuels (e.g. dihydrogen or methane) that can be indefinitely stored and easily transported. In principle, the only required inputs are sunlight, an earth-abundant feedstock such as carbon dioxide, protons (H+), and reducing equivalents (e-). The source of these protons and electrons must be abundant and ubiquitous—we chose water.
Despite the 2-billion-year history of plants performing water oxidation to produce molecular oxygen, protons, and electrons (Photosystem II), our understanding of this complex 4H+/4e- process has been severely limited. Only recently have high-performing, earth-abundant heterogeneous electrocatalysts been reported that can be scaled up to make functioning devices.
This dissertation describes progress on both the synthetic and mechanistic fronts in developing earth-abundant heterogeneous water oxidation catalysts for solar-driven water splitting. We have synthesized nanoparticulate Ni-Fe catalysts with the highest measured activity on flat electrodes to date. We carefully characterized these materials spectroscopically to determine that edge-site iron was active in catalysis. We then undertook novel in-situ spectroelectrochemical techniques in non-aqueous media to identify the active iron species, which is surprisingly a cis-dioxo-iron(VI) corner site. The data also indicate that geminal iron-oxo coupling may be the operative mechanism of O-O bond formation, a new scheme with potential biological relevance.
Finally, we have expanded our goal to include sustainably reducing other feedstocks, such as carbon dioxide and hydrocarbons. In doing so, we aim to make pharmaceuticals, polymers, and other high-value products from sunlight and water.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/Z9NK3C2J, author = {Darnton, Tania Victoria}, title = {Structures and Reactions of Diplatinum Complexes}, school = {California Institute of Technology}, year = {2017}, doi = {10.7907/Z9NK3C2J}, url = {https://resolver.caltech.edu/CaltechTHESIS:04172017-185314743}, abstract = {A d8−d8 complex [Pt2(μ-P2O5(BF2)4]4− (abbreviated Pt(pop-BF2)4−) undergoes two 1e− reductions at E1/2 = −1.68 and Ep = −2.46 V (vs Fc+/Fc) producing reduced Pt(pop-B2)5− and superreduced Pt(pop-BF2)6− species, respectively. The EPR spectrum of Pt(pop-BF2)5− and UV−vis spectra of both the reduced and the superreduced complexes, together with TD-DFT calculations, reveal successive filling of the 6pσ orbital accompanied by gradual strengthening of Pt−Pt bonding interactions and, because of 6pσ delocalization, of Pt−P bonds in the course of the two reductions. Both reduction steps proceed without changing either d8 Pt electronic configuration, making the superreduced Pt(pop-BF2)6− a very rare 6p2 σ-bonded binuclear complex. However, the Pt−Pt σ bonding interaction is limited by the relatively long bridging-ligand-imposed Pt−Pt distance accompanied by repulsive electronic congestion. Pt(pop-BF2)4− is predicted to be a very strong photooxidant (potentials of +1.57 and +0.86 V are estimated for the singlet and triplet dσ*pσ excited states, respectively).
Further study of the electronic excited states of Pt(pop-BF2)4- in the presence of luminescence quenchers revealed Stern-Volmer type dynamic quenching of the triplet state by trialkyl and triaryl amines. Quenching of the singlet as well as the triplet was observed in the presence of CoII trisbipyridine complexes, but sample decomposition and the observed presence of simultaneous static and dynamic quenching behaviors hampered quantitative analysis.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/Z9NS0RWS, author = {Roske, Christopher William}, title = {Towards a Hydrobromic Acid Splitting Device Using Earth-Abundant Materials}, school = {California Institute of Technology}, year = {2017}, doi = {10.7907/Z9NS0RWS}, url = {https://resolver.caltech.edu/CaltechTHESIS:09062016-162323180}, abstract = {This thesis disembarks from the traditional approach of tailoring a system to the water splitting reaction. As detailed in Chapter 2, this thesis predicts that two silicon photoelectrons connected in parallel are ideally suited to electricity storage in an integrated light collector and chemical storage device driving the splitting of hydrobromic acid (2HBr -> H2 + Br2). The predicted dual photoelectrode system could potentially obtain high solar-to-hydrogen conversion efficiencies of up to an ηSTH, HBr of 12 %, whereas an equivalent water splitting system is not possible due to the small band gap of silicon. Unfortunately, silicon possesses low catalytic activity for both the hydrogen evolution half-reaction and the bromide oxidation half-reaction. In the past, the electrocatalysis of silicon has been aided by using Pt/Ir alloys to act as both a protective and electrocatalytic layer. Herein, efforts are detailed to replace these precious metals, where possible, by using only earth-abundant materials to decrease the cost of a module. Our hope is that efforts along this path will aid the field of artificial photosynthesis as a whole.
We begin by further testing a chemical insight previously noted within our group and discover a surprisingly high activity electrocatalyst for the hydrogen evolution reaction by cobalt phosphide (CoP) nanoparticles, detailed in Chapter 3. Falling on a traditional technique of increasing the surface area of particular facets, we nanostructured our crystalline CoP to increase its surface area of exposed (111) facets and hoped it would increase our catalytic activity; however, we found that simple structuring resulted in poor adhesion of nanostructures and poorer activity than our multi-faceted CoP nanocrystals (see the appendix to find out more). Our original catalysis efforts spurred a flurry of activity in the literature, and consequently, alternative devices that are more scalable arose. We detail the developments occurring since our work in the last appendix.
Now, with a potential catalyst in hand, comes the difficulty of balancing the delicate interplay between light absorption and catalysis, as detailed in Chapter 4. While CoP is active for HER, our particles possess a relatively low turnover frequency compared to hydrogenase or platinum, and thus require high mass loadings of material (2 mg/cm2) to obtain competitive extrinsic performance. Planar electrodes are incompatible with our particles because of substantial light absorption by the thick catalyst overlayer. By structuring our photoelectrode, we abnegate our catalyst limitations by exploiting the properties of microwires. High-aspect ratio microwires have shown promise as potentially low-cost materials for future photovoltaic applications as well as photocathodes functioning as part of an energy storage device. We discuss how to integrate our materials with silicon microwires (the wires were grown by an unscalable process to serve in place of functional CVD wires with radial emitters) to prototype a candidate photocathode. While a parasitic resistance limited the overall efficiency of the photocathode candidate, it still had promising stability. The parasitic resistance was addressed by electrodepositing the cobalt phosphide, thereby giving us a promising efficiency limited by the quality of the p-n junction.
While high-catalytic activity for the HER in acidic solutions using earth-abundant materials represents a significant advance, the photocathode is just one component of what is necessary for a complex system of splitting hydrobromic acid. Silicon, by its virtue of being a small band gap material, is easily passivated in aqueous solutions by the formation of a silicon oxide. In the past, our colleagues had shown that a monolayer of graphene could occasionally provide protection in a test solution, but batch-to-batch variability provided a considerable challenge. The putative hypothesis offered for the degradation argued defects in the crystalline graphene at grain-boundaries were the culprit. In Chapter 5 we present a method to passivate defects in the graphene crystal by light fluorination and observe a considerable enhancement in stability relative to typical graphene-protected silicon photoanodes. We had hoped that catalysis for bromide oxidation would be aided by the near-perfect graphene liquid junction, but electrodeposited Pt was required to effect photoxidation. A cursory stability test shows promising stability for one-half of an hour, but we would like to avoid using Pt. Finally, we also turned our attention to protecting silicon surfaces from oxidation by exploiting covalent silicon surface chemistry, accessible via a two-step chlorination/alkylation procedure, and explored the deposition of potentially protective thin-film metal oxides (see the appendix).
}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/Z98P5XGX, author = {Shafaat, Oliver Syed}, title = {Temporal Control of Ion Channel Activation}, school = {California Institute of Technology}, year = {2016}, doi = {10.7907/Z98P5XGX}, url = {https://resolver.caltech.edu/CaltechTHESIS:05122016-095434020}, abstract = {Ion channels are a large class of integral membrane proteins that allow for the diffusion of ions across a cellular membrane and are found in all forms of life. Pentameric ligand-gated ion channels (pLGICs) comprise a large family of proteins that include the nicotinic acetylcholine receptor (nAChR) and the γ-aminobutyric acid (GABA) receptor. These ion channels are responsible for the fast synaptic transmission that occurs in humans and as a result are of fundamental biological importance. pLGICs bind ligands (neurotransmitters), and upon ligand-binding undergo activation. The activation event causes an ion channel to enter a new physical state that is able to conduct ions. Ion channels allow for the flux of ions across the membrane through a pore that is formed upon ion channel activation. For pLGICs to function properly both ligand-binding and ion channel activation must occur. The ligand-binding event has been studied extensively over the past few decades, and a detailed mechanism of binding has emerged. During activation the ion channel must undergo structural rearrangements that allow the protein to enter a conformation in which ions can flow through. Despite this great and ubiquitous importance, a fundamental understanding of the ion channel activation mechanism and kinetics, as well as concomitant structural arrangements, remains elusive.
This dissertation describes efforts that have been made to temporally control the activation of ligand-gated ion channels. Temporal control of ion channel activation provides a means by which to activate ion channels when desired. The majority of this work examines the use of light to activate ion channels. Several photocages were examined in this thesis; photocages are molecules that release a ligand under irradiation, and, for the work described here, the released ligand then activates the ion channel. First, a new water-soluble photoacid was developed for the activation of proton-sensitive ion channels. Activation of acid-sensing ion channels, ASIC2a and GLIC, was observed only upon irradiation. Next, a variety of Ru2+ photocages were also developed for the release of amine ligands. The Ru2+ systems interacted in a deleterious manner with a representative subset of biologically essential ion channels. The rapid mixing of ion channels with agonist was also examined. A detection system was built to monitor ion channels activation in the rapid mixing experiments. I have shown that liposomes, and functionally-reconstituted ELIC, are not destroyed during the mixing process. The work presented here provides the means to deliver agonist to ligand-gated ion channels in a controlled fashion.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/Z9MK69TD, author = {Agbo, Peter Chukwudi Ifeanychukwu}, title = {Development of Metalloenzyme Dioxygen Reduction Cathodes}, school = {California Institute of Technology}, year = {2015}, doi = {10.7907/Z9MK69TD}, url = {https://resolver.caltech.edu/CaltechTHESIS:09192014-121956600}, abstract = {The prime thrust of this dissertation is to advance the development of fuel cell dioxygen reduction cathodes that employ some variant of multicopper oxidase enzymes as the catalyst. The low earth-abundance of platinum metal and its correspondingly high market cost has prompted a general search amongst chemists and materials scientists for reasonable alternatives to this metal for facilitating catalytic dioxygen reduction chemistry. The multicopper oxidases (MCOs), which constitute a class of enzyme that naturally catalyze the reaction O2 + 4H+ + 4e- → 2H2O, provide a promising set of biochemical contenders for fuel cell cathode catalysts. In MCOs, a substrate reduces a copper atom at the type 1 site, where charge is then transferred to a trinuclear copper cluster consisting of a mononuclear type 2 or “normal copper” site and a binuclear type 3 copper site. Following the reduction of all four copper atoms in the enzyme, dioxygen is then reduced to water in two two-electron steps, upon binding to the trinuclear copper cluster. We identified an MCO, a laccase from the hyperthermophilic bacterium Thermus thermophilus strain HB27, as a promising candidate for cathodic fuel cell catalysis. This protein demonstrates resilience at high temperatures, exhibiting no denaturing transition at temperatures high as 95°C, conditions relevant to typical polymer electrolyte fuel cell operation.
In Chapter I of this thesis, we discuss initial efforts to physically characterize the enzyme when operating as a heterogeneous cathode catalyst. Following this, in Chapter II we then outline the development of a model capable of describing the observed electrochemical behavior of this enzyme when operating on porous carbon electrodes. Developing a rigorous mathematical framework with which to describe this system had the potential to improve our understanding of MCO electrokinetics, while also providing a level of predictive power that might guide any future efforts to fabricate MCO cathodes with optimized electrochemical performance. In Chapter III we detail efforts to reduce electrode overpotentials through site-directed mutagenesis of the inner and outer-sphere ligands of the Cu sites in laccase, using electrochemical methods and electronic spectroscopy to try and understand the resultant behavior of our mutant constructs. Finally, in Chapter IV, we examine future work concerning the fabrication of enhanced MCO cathodes, exploring the possibility of new cathode materials and advanced enzyme deposition techniques.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/Z94J0C2D, author = {Lam, Yan Choi}, title = {Synthesis, Oxidation and Photophysics of Perfluoroborated Tetrakis(pyrophosphito)diplatinate (II) and Density Functional Theory (DFT) Study of Electrochemical CO2 Reduction by Mn Catalysts}, school = {California Institute of Technology}, year = {2015}, doi = {10.7907/Z94J0C2D}, url = {https://resolver.caltech.edu/CaltechTHESIS:05212015-155730829}, 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·Et2O). 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.
In 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)]-.
An 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.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B. and Goddard, William A., III}, } @phdthesis{10.7907/CFD7-DK06, author = {Ener, Maraia Emily}, title = {Electron Flow Through Cytochrome P450}, school = {California Institute of Technology}, year = {2014}, doi = {10.7907/CFD7-DK06}, url = {https://resolver.caltech.edu/CaltechTHESIS:03272014-175135389}, abstract = {The cytochromes P450 (P450s) are a remarkable class of heme enzymes that catalyze the metabolism of xenobiotics and the biosynthesis of signaling molecules. Controlled electron flow into the thiolate-ligated heme active site allows P450s to activate molecular oxygen and hydroxylate aliphatic C–H bonds via the formation of high-valent metal-oxo intermediates (compounds I and II). Due to the reactive nature and short lifetimes of these intermediates, many of the fundamental steps in catalysis have not been observed directly. The Gray group and others have developed photochemical methods, known as “flash-quench,” for triggering electron transfer (ET) and generating redox intermediates in proteins in the absence of native ET partners. Photo-triggering affords a high degree of temporal precision for the gating of an ET event; the initial ET and subsequent reactions can be monitored on the nanosecond-to-second timescale using transient absorption (TA) spectroscopies. Chapter 1 catalogues critical aspects of P450 structure and mechanism, including the native pathway for formation of compound I, and outlines the development of photochemical processes that can be used to artificially trigger ET in proteins. Chapters 2 and 3 describe the development of these photochemical methods to establish electronic communication between a photosensitizer and the buried P450 heme. Chapter 2 describes the design and characterization of a Ru-P450-BM3 conjugate containing a ruthenium photosensitizer covalently tethered to the P450 surface, and nanosecond-to-second kinetics of the photo-triggered ET event are presented. By analyzing data at multiple wavelengths, we have identified the formation of multiple ET intermediates, including the catalytically relevant compound II; this intermediate is generated by oxidation of a bound water molecule in the ferric resting state enzyme. The work in Chapter 3 probes the role of a tryptophan residue situated between the photosensitizer and heme in the aforementioned Ru-P450 BM3 conjugate. Replacement of this tryptophan with histidine does not perturb the P450 structure, yet it completely eliminates the ET reactivity described in Chapter 2. The presence of an analogous tryptophan in Ru-P450 CYP119 conjugates also is necessary for observing oxidative ET, but the yield of heme oxidation is lower. Chapter 4 offers a basic description of the theoretical underpinnings required to analyze ET. Single-step ET theory is first presented, followed by extensions to multistep ET: electron “hopping.” The generation of “hopping maps” and use of a hopping map program to analyze the rate advantage of hopping over single-step ET is described, beginning with an established rhenium-tryptophan-azurin hopping system. This ET analysis is then applied to the Ru-tryptophan-P450 systems described in Chapter 2; this strongly supports the presence of hopping in Ru-P450 conjugates. Chapter 5 explores the implementation of flash-quench and other phototriggered methods to examine the native reductive ET and gas binding events that activate molecular oxygen. In particular, TA kinetics that demonstrate heme reduction on the microsecond timescale for four Ru-P450 conjugates are presented. In addition, we implement laser flash-photolysis of P450 ferrous–CO to study the rates of CO rebinding in the thermophilic P450 CYP119 at variable temperature. Chapter 6 describes the development and implementation of air-sensitive potentiometric redox titrations to determine the solution reduction potentials of a series of P450 BM3 mutants, which were designed for non-native cyclopropanation of styrene in vivo. An important conclusion from this work is that substitution of the axial cysteine for serine shifts the wild type reduction potential positive by 130 mV, facilitating reduction by biological redox cofactors in the presence of poorly-bound substrates. While this mutation abolishes oxygenation activity, these mutants are capable of catalyzing the cyclopropanation of styrene, even within the confines of an E. coli cell. Four appendices are also provided, including photochemical heme oxidation in ruthenium-modified nitric oxide synthase (Appendix A), general protocols (Appendix B), Chapter-specific notes (Appendix C) and Matlab scripts used for data analysis (Appendix D).}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/5EJQ-5134, author = {Lattimer, Judith Rebecca Cabelli}, title = {Functionalization of Si(111) Surfaces and the Formation of Mixed Monolayers for the Covalent Attachment of Molecular Catalysts in Photoelectrochemical Devices}, school = {California Institute of Technology}, year = {2014}, doi = {10.7907/5EJQ-5134}, url = {https://resolver.caltech.edu/CaltechTHESIS:05022014-101347718}, abstract = {The functionalization of silicon surfaces with molecular catalysts for proton reduction is an important part of the development of a solar-powered, water-splitting device for solar fuel formation. The covalent attachment of these catalysts to silicon without damaging the underlying electronic properties of silicon that make it a good photocathode has proven difficult. We report the formation of mixed monolayer-functionalized surfaces that incor- porate both methyl and vinylferrocenyl or vinylbipyridyl (vbpy) moieties. The silicon was functionalized using reaction conditions analogous to those of hydrosilylation, but instead of a H-terminated Si surface, a chlorine-terminated Si precursor surface was used to produce the linked vinyl-modified functional group. The functionalized surfaces were characterized by time-resolved photoconductivity decay, X-ray photoelectron spectroscopy (XPS), electro- chemical, and photoelectrochemical measurements. The functionalized Si surfaces were well passivated, exhibited high surface coverage and few remaining reactive Si atop sites, had a very low surface recombination velocity, and displayed little initial surface oxidation. The surfaces were stable toward atmospheric and electrochemical oxidation. The surface coverage of ferrocene or bipyridine was controllably varied from 0 up to 30% of a monolayer without loss of the underlying electronic properties of the silicon. Interfacial charge transfer to the attached ferrocene group was relatively rapid, and a photovoltage of 0.4 V was generated upon illumination of functionalized n-type silicon surfaces in CH3CN. The immobilized bipyridine ligands bound transition metal ions, and thus enabled the assembly of metal complexes on the silicon surface. XPS studies demonstrated that [Cp∗Rh(vbpy)Cl]Cl, [Cp∗Ir(vbpy)Cl]Cl, and Ru(acac)2vbpy were assembled on the surface. For the surface prepared with iridium, x-ray absorption spectroscopy at the Ir LIII edge showed an edge energy and post-edge features virtually identical to a powder sample of [Cp∗Ir(bipy)Cl]Cl (bipy is 2,2 ́-bipyridyl). Electrochemical studies on these surfaces confirmed that the assembled complexes were electrochemically active.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/N8B5-4644, author = {Ford, Nicole Danielle Bouley}, title = {Capturing Protein Dynamics with Time-Resolved Luminescence Spectroscopy}, school = {California Institute of Technology}, year = {2013}, doi = {10.7907/N8B5-4644}, url = {https://resolver.caltech.edu/CaltechTHESIS:05302013-155904165}, abstract = {
The presented doctoral research utilizes time-resolved spectroscopy to characterize protein dynamics and folding mechanisms. We resolve millisecond-timescale folding by coupling time-resolved fluorescence energy transfer (trFRET) to a continuous flow microfluidic mixer to obtain intramolecular distance distributions throughout the folding process. We have elucidated the folding mechanisms of two cytochromes—one that exhibits two-state folding (cytochrome
We have also investigated intrachain contact dynamics in unfolded cytochrome
In addition, we have explored the pathway dependence of electron tunneling rates between metal sites in proteins. Our research group has converted cytochrome
A critical challenge for the 21st century is shifting from the predominant use of fossil fuels to renewables for energy. Among many options, sunlight is the only single renewable resource with sufficient abundance to replace most or all of our current fossil energy use. However, existing photovoltaic and solar thermal technologies cannot be scaled infinitely due to the temporal and geographic intermittency of sunlight. Therefore efficient and inexpensive methods for storage of solar energy in a dense medium are needed in order to greatly increase utilization of the sun as a primary resource. For this purpose we have proposed an artificial photosynthetic system consisting of semiconductors, electrocatalysts, and polymer membranes to carry out photoelectrochemical water splitting as a method for solar fuel generation.
This dissertation describes efforts over the last five years to develop critical semiconductor and catalyst components for efficient and scalable photoelectrochemical hydrogen evolution, one of the half reactions for water splitting. We identified and developed Ni–Mo alloy and Ni2P nanoparticles as promising earth-abundant electrocatalysts for hydrogen evolution. We thoroughly characterized Ni–Mo alloys alongside Ni and Pt catalysts deposited onto planar and structured Si light absorbers for solar hydrogen generation. We sought to address several key challenges that emerged in the use of non-noble catalysts for solar fuels generation, resulting in the synthesis and characterization of Ni–Mo nanopowder for use in a new photocathode device architecture. To address the mismatch in stability between non-noble metal alloys and Si absorbers, we also synthesized and characterized p-type WSe2 as a candidate light absorber alternative to Si that is stable under acidic and alkaline conditions.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/BRZJ-YZ76, author = {Williamson, Heather R.}, title = {Engineering Multi Step Electron Tunneling Systems in Proteins}, school = {California Institute of Technology}, year = {2013}, doi = {10.7907/BRZJ-YZ76}, url = {https://resolver.caltech.edu/CaltechTHESIS:06112013-202017350}, abstract = {Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.
The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/HBFQ-8V20, author = {Keller, Gretchen Eva}, title = {Phototriggering Nitric Oxide Synthase from Geobacillus stearothermophilus}, school = {California Institute of Technology}, year = {2013}, doi = {10.7907/HBFQ-8V20}, url = {https://resolver.caltech.edu/CaltechTHESIS:02052013-133909189}, abstract = {Nitric oxide synthases (NOS) produce L-citrulline and nitric oxide (NO) in two turnovers from L-arginine via the bound intermediate, N-hydroxy-L-arginine. NO is an important biological signaling molecule, and NOS-like enzymes have been identified in all kingdoms of life. NOS enzymes utilize electrons from a reductase domain as well as a unique redox-active cofactor, tetrahydrobiopterin, in the activation of dioxygen. The NOS catalytic mechanism is only partially known, with proposed hihg-valent oxygenating intermediates similar to those of other monooxygenases. In the continued effort to understand the mechanism by which NOS catalytically produces NO, we have chosen to study NOS from the thermostable, nonpathogenic bacterium Geobacillus stearothermophilus (gsNOS).
In this work, covalently modified gsNOS with a ruthenium(II) diimine photosensitizer has been prepared to circumvent the need for an external reductase domain, while maintaining access to the substrate-binding channel. In this way, we hoped to produce the NOS ferrous state by rapid electron injection and to be able to access intermediates that form downstream. Chapter two describes the engineered gsNOS for selective cysteine labeling with [Ru(bpy)2(IA-phen)]2+ (IA-phen = 5-iodoacetamido-1,10-phenanthroline) to form the conjugate Ru(II)K115C-gsNOS. The labeled protein was characterized by mass spectrometry, UV-visible absorbance, and circular dichroism spectroscopy. Ru(II)K115C-gsNOS was crystallized and its structure solved to 2.6 Å resolution. Chapter three details phototriggered reduction by laser flash-quench methodology using the reversible, reductive quencher p-methoxy-N,N-dimethylanaline. Transient absorption studies have shown that rapid phototriggered heme reduction occurs on the order of 625 ns. Binding of substrates and/or cofactor is known to alter the heme reduction potential in NOS. However, these observed reduction rates are independent of substrate/cofactor, suggesting that the system is driving force optimized. Studies performed in the presence of oxygen were complicated by side-reactions with the ruthenium label and small molecule quencher. Excitingly, enzymatic turnover was achieved by steady-state LED illumination at 470 nm using the irreversible reductive quencher diethyldithiocarbamate, and is described in chapter four. NO produced from light-driven Ru(II)K115C-gsNOS catalysis was measured by the Griess Assay and L-citrulline production confirmed by liquid chromatography-mass spectrometry. In chapter five, we show how phototriggered heme reduction can be used to monitor CO binding and potential studies of gas diffusion pathways, and substrate/cofactor effects are discussed. In all, the development of this ruthenium-modified gsNOS system has enabled preliminary studies of reduction kinetics, diatomic ligand binding, and light-driven catalysis and may provide a useful platform for further investigation into the catalytic cycle of NOS.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/91HV-2R03, author = {Durrell, Alec Charles}, title = {Electronic Structures and Reactivity Patterns of Dipalladium(11,11) and Diplatinum(11,11) Complexes}, school = {California Institute of Technology}, year = {2012}, doi = {10.7907/91HV-2R03}, url = {https://resolver.caltech.edu/CaltechTHESIS:05172012-112437443}, abstract = {This work explores the electronic structures and reactivity patterns of diplatinum(II, II) and dipalladium(II, II) complexes. Complexes containing metal-metal bonds play important roles in both inorganic and organometallic chemistry. Among the many examples of these complexes, dimers of square planar RhI, IrI, and PtII centers comprise a special class that feature attractive d8–d8 interactions. The unique electronic structure characteristic of these complexes gives rise to chemical, photochemical, and photophysical properties that have engaged researchers for the past 35 years.
One of the best-known examples of these compounds is tetrakis(µ-pyrophosphito)platinum(II), Pt(pop). Herein, the photophysical properties of Pt(pop) are compared with its fluoroborated analogue, Pt(pop-BF2). This complex possesses eight BF2 groups that replace the hydrogen atoms located between each “pop” ligand. When compared with Pt(pop), Pt(pop-BF2) has a much greater singlet lifetime (1.56 ns) and singlet quantum yield (0.27). The enhancement is the result of a drastically slower 1A2u → 3A2u intersystem crossing rate. In particular, the thermal barrier to intersystem crossing is significantly higher in Pt(pop-BF2) (2230 cm-1 vs. 1190 cm-1). We believe this is primarily the result of the increased rigidity of the complex afforded by the BF2 groups. The rigidity increases the energy of symmetry-lowering vibrational modes, which are necessary to promote spin-orbit mixing of the 1dσpσ and 3dσpσ states.
Despite the many examples of M-M bonded d8–d8 complexes of RhI, IrI, and PtII in the literature, until recently there were no PdII complexes fitting this description. Our investigations of clamshell-shaped PdII dimers [(2-phenylpyridine)Pd(µ-X)]2 and [(2-p-tolylpyridine)Pd(µ-X)]2 (X = OAc or TFA) revealed short Pd–Pd distances (~ 2.85 Å). The molecules adopt this unusual geometry in part because of a d8–d8 bonding interaction between the two Pd centers. Density functional theory (DFT) and ab initio (AI) analyses confirm the presence of a Pd–Pd bonding interaction in [(2-phenylpyridine)Pd(µ-X)]2 and show that the HOMO is a dz2 σ*Pd–Pd antibonding orbital, while the LUMO and proximal unoccupied orbitals are mainly located on the 2-phenylpyridine rings. Computational analyses of other PdII–PdII dimers that have short Pd–Pd distances yield an orbital ordering similar to that of [(2-phenylpyridine)Pd(µ-X)]2, but quite different from that found for d8–d8 dimers of Rh, Ir, and Pt. This difference in orbital ordering arises because of the unusually large energy gap between the 4d and 5p orbitals in Pd, and may explain why Pd d8–d8 dimers do not exhibit the distinctive photophysical properties of related Rh, Ir, and Pt species.
Our work on PdII–PdII electronic structures led us to employ these complexes as electrocatalysts in the regioselective chlorination of C–H bonds. Previous work on d8–d8 complexes has established that when treated with halogens (Cl2, Br2, or I2), the complex undergoes two-center oxidative addition to form an axially coordinated X–d7–d7–X species. Similar products are observed following electrochemical oxidation in the presence of a halide (Cl–, Br–, or I–). Recently, related PdII–PdII complexes were found to selectively chlorinate benzo[h]quinoline through reductive elimination from a Cl–PdIII–PdIII–Cl species. This led us to probe the viability of the analogous electrochemical route. Cyclic voltammetry, spectroelectrochemistry, and bulk electrolysis measurements confirm that electrochemical oxidation of PdII–PdII yields the identical Cl–PdIII–PdIII–Cl intermediate, which is capable of reductive chlorination of C–H bonds. Additional evidence for formation of axially coordinated bromide and acetate species is also presented. Over 10 turnovers of 10-chlorobenzo[h]quinoline were achieved at 80% isolated yield. Further research into the area may lead to a potentially versatile, useful, and green route for C–H bond functionalization reactions.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/ZEHM-9S69, author = {Oblad, Paul Frederick}, title = {Toward the Upgrading of Hydrocarbons: Synthesis, Characterization, and Reactivity of Platinum and Palladium Complexes}, school = {California Institute of Technology}, year = {2012}, doi = {10.7907/ZEHM-9S69}, url = {https://resolver.caltech.edu/CaltechTHESIS:08292011-105052667}, abstract = {Herein, hydroxyl-dimers of platinum and palladium supported by diimine ligands have been prepared and studied. It was found that they are capable of activating allylic, benzylic, and aromatic carbon-hydrogen bonds. The kinetics of the C-H activation of cyclohexene with the platinum system and of indene with the palladium system were studied. In each case the rate-limiting step was found to be associative substitution. The catalytic dehydrogenation of cyclohexene to benzene with the palladium hydroxyl-dimer was investigated. The chemical oxidation of the η3-organometallic products synthesized via C-H activation of cyclohexene and indene with platinum and palladium, respectively, was explored. Treatment of these products with strong halogenating oxidants resulted in the liberation of halogenated substrates and bridging halide metal complexes. Uncharged platinum and palladium polypyrazoleborate complexes were synthesized and characterized. The kinetics of the degenerative ligand exchange of DMSO with palladium methyl DMSO complexes ligated with a polypyrazoleborate or a diimine ligand were studied and it was found that the associative substitution mechanism through which the diimine ligated complexes proceeds was unavailable to the polypyrazoleborate palladium complex. In the polypyrazoleborate system ligand exchange proceeded through a dissociative mechanism. The C-H activation substrate scope of the platinum and palladium hydroxyl-dimers was further explored. The diimine platinum hydroxyl-dimer was found to activate an allylic C-H bond in cyclopentene and form an η3-cyclopentenyl complex when heated with acid and dilute stoichiometric amounts of cyclopentene. Conversely, dehydrogenation of cyclopentene to a platinum-bound η5-cyclopentadiene resulted from the treatment of the platinum hydroxyl-dimer with super-stoichiometric amounts of cyclopentene at room temperature. This difference in reactivity with the same substrate may be due to the relative reactivities of allylic versus homoallylic C-H bonds. Further evidence of a homoallylic C-H activation mechanism was demonstrated by treating the diimine platinum hydroxyl-dimer with neo-hexene to form a cyclometalated neo-hexenyl platinum complex. The diimine palladium hydroxyl-dimer was also found to catalytically oligomerize and isomerize olefins. Furthermore, the catalytic activity was supported by the presence of oxygen and stable in the presence of water. Most likely the oligomerization proceeded through a palladium hydride that can decompose to palladium(0) complex, which can be reoxidized by oxygen. The photochemical oxidation of platinum complexes with Ru(bipy)_3^(2+) was also investigated. Finally, the coordination chemistry of the tris(triphenylphosphino)silyl ligand was explored with cobalt, ruthenium, nickel, and platinum.}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/XK4M-DZ27, author = {Dempsey, Jillian Lee}, title = {Hydrogen Evolution Catalyzed by Cobaloximes}, school = {California Institute of Technology}, year = {2011}, doi = {10.7907/XK4M-DZ27}, url = {https://resolver.caltech.edu/CaltechTHESIS:01252011-134049886}, abstract = {Cobaloximes are among a promising class of small molecules which catalytically evolve hydrogen at modest overpotentials. Motivated by the imminent need to develop efficient solar energy conversion processes, a number of research groups have recently revisited the catalytic activity of cobaloximes, which was initially reported by Espenson almost three decades ago. Both Espenson’s seminal work and the studies reported during this recent resurgence are chronicled in the introductory Chapter 1. The next three chapters introduce photochemical methods for detecting catalytic intermediates and determining kinetics associated with the elementary steps of hydrogen evolution. Four catalytic pathways are considered; each beginning with the reduction of a CoII-diglyoxime to generate CoI, which reacts with a proton donor to produce a CoIII-hydride. In a homolytic pathway, two CoIII-hydrides react in a bimolecular step to eliminate H₂. Alternatively, in a heterolytic pathway, protonation of CoIII-hydride produces H₂ and CoIII. The CoIII-hydride may also be reduced further to a CoII-hydride, which can react via analogous heterolytic or homolytic pathways. In Chapter 2, kinetics of electron transfer reactions of a Co-diglyoxime complex are presented. These experimental results, along with a detailed thermodynamic analysis of proposed hydrogen evolution pathways, shed new light on the barriers and driving forces of the elementary reaction steps involved in proton reduction. A strong thermodynamic preference for a CoIII-hydride homolytic pathway over a CoIII-hydride heterolytic route is identified as the key finding from this work. In Chapter 3, phototriggered hydride generation utilized in conjunction with time-resolved spectroscopy is introduced as a novel method for mechanistic investigations. Here, excited-state proton transfer from an organic photoacid to a CoI-diglyoxime triggers the formation of the reactive CoIII-hydride. This and the subsequent reactivity of CoIII-hydride are monitored spectroscopically. The reaction kinetics are consistent with a heterolytic route for hydrogen evolution that proceeds via a CoII-hydride intermediate. Chapter 4 extends these mechanistic investigations to aqueous media by employing photoionization and pulse radiolysis methods to trigger CoII-diglyoxime reduction. Chapters 5 and 6 focus on the design and construction of second generation cobaloximes. In Chapter 5, the thermodynamic preference for bimolecular reactivity of two CoIII-hydrides is probed with a binuclear cobaloxime. A covalent alkyl tether is used to decrease the volume required for diffusional collisions. Electrocatalytic activity is consistent with a rate-limiting step associated with the formation of the hydride, as seen in mononuclear catalysts, and thus no enhancement of catalytic activity is observed. However, as an efficient water splitting device may require the tethering of catalysts to an electrode surface, this ligand should allow binuclear association of immobilized catalysts. A strategy for covalently grafting cobaloxime derivatives to silicon electrodes is introduced in Chapter 6. A terminal olefin is incorporated into a glyoxime backbone, a functionality amenable to surface-based coupling reactions. The bifunctional cobaloxime is an active catalyst, and initial efforts to prepare the chemically modified electrode are discussed. Three appendices are provided, including work on the photochemical generation of powerful OsII reductant, electron transfer reactions of N,N’,3,3’-tetramethyl-4,4’-bipyridinium, and annotated MATLAB scripts utilized for kinetics analysis.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, month = {July}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/XQBW-D585, author = {Walker, Don}, title = {Corrole Sensitized Solar Cells}, school = {California Institute of Technology}, year = {2011}, doi = {10.7907/XQBW-D585}, url = {https://resolver.caltech.edu/CaltechTHESIS:09282010-221227791}, abstract = {The performance of dye sensitized solar cells (DSSC) was investigated as a function of electrolyte composition and dye sensitizer. Electrolytes consisting of increasing concentrations of bromide and tri-bromide effectively increased the current of DSSCs while conserving an increase in open circuit voltage. Corroles were used to investigate their efficacy as light absorbers for DSSCs. Electronic spectroscopy of corroles demonstrated that the spectra of corroles could be red shifted through β substitution. Also, the changes in the electronic spectra of corroles was not affected by adsorption to TiO2. Electrochemical data concluded that the functionalization of the β positions of the corroles did not significantly affect the corrole’s redox potentials. FTIR spectroscopy confirmed that the corroles were chemically adsorbed onto TiO2. Photoelectrochemical measurements concluded that the corroles are efficient sensitizers for DSSCs. A highly efficient corrole utilizing sulfonic acid binding groups was discovered. Also, a corrole with a malonic acid binding group was 70% as efficient as one of the best performing dye sensitizers in DSSCs.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/7CAD-6P44, author = {Palmer, Joshua Henry}, title = {Iridium Corroles: Synthesis, Properties, and Electronic Structure}, school = {California Institute of Technology}, year = {2011}, doi = {10.7907/7CAD-6P44}, url = {https://resolver.caltech.edu/CaltechTHESIS:02152011-145456588}, abstract = {The synthesis, properties, and electronic structures of a family of iridium corrole complexes are discussed in detail. These compounds represent the first well-characterized examples of third-row metals being inserted successfully into the small corrole binding pocket; they possess a planar macrocycle, which neither saddles nor ruffles upon bromination, and are bound at the axial positions by either two amine ligands or one phosphine. Unlike their well-studied cobalt and rhodium analogues, whose redox activity is restricted primarily to the corrole ring, iridium corroles can be oxidized to produce an electron paramagnetic resonance spectrum that has extremely anisotropic g tensor components, implying mixing of the 5d orbitals into the oxidized ground state and opening the door to possible higher-valent iridium complexes. Detailed experimental and computational studies are presented showing that this oxidized ground state is actually mostly corrole-based, as has been found in the past for numerous other supposedly high-valent corrole compounds, but the percentage of iridium character varies from 10 to 18% and tracks with the electron-donating ability of the ligand. Additionally, the unique (among corrole complexes) near-IR phosphorescence of Ir(III) corroles is presented and discussed. Iridium(III) corroles phosphoresce with lifetimes ranging from hundreds of nanoseconds to a few microseconds at room temperature, with slightly longer lifetimes at low temperature. Unfortunately, the quantum yields of phosphorescence are low, 1% or less, and this appears to be due to an exceptionally slow set of radiative rates for the corroles. An examination of the reactivity of ammine-ligated Ir(III) corroles is also described. These compounds can be oxidized in the presence of an ammonia source to form novel six-coordinate iridium(III) azaporphyrins in an unprecedented chemical transformation. The characterization and properties of these iridium azaporphyrin complexes are detailed as well, with a focus on nuclear magnetic resonance characterization techniques and a discussion of the red phosphorescence of the azaporphyrins.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/9HZZ-XE74, author = {Lancaster, Kyle Matthew}, title = {Outer-Sphere Effects on the Copper Sites of Pseudomonas Aeruginosa Azurins}, school = {California Institute of Technology}, year = {2011}, doi = {10.7907/9HZZ-XE74}, url = {https://resolver.caltech.edu/CaltechTHESIS:09082010-131422449}, abstract = {This thesis describes structural, spectroscopic, and reactivity studies of mutants of the cupredoxin azurin from Pseudomonas aeruginosa. Emphasis is given to the effects of outer-sphere coordination on spectroscopic observables and reduction potentials. Among the key findings are that the characteristics of the classical “type 1” copper site can be largely reproduced in the absence of canonically necessary cysteine thiolate ligation. Mutants exhibiting this behavior have been classified as “type zero” copper proteins.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/PZAY-WQ64, author = {Whited, Charlotte A.}, title = {Tuning Nitric Oxide Synthase: Investigating the Thiolate “Push” and No Release}, school = {California Institute of Technology}, year = {2011}, doi = {10.7907/PZAY-WQ64}, url = {https://resolver.caltech.edu/CaltechTHESIS:05042011-174816761}, abstract = {All heme thiolate enzymes have conserved hydrogen bonding networks surrounding the axial thiolate ligand. In order to understand the role of this proximal hydrogen bonding network in nitric oxide synthases (NOS), three mutants of the NOS enzyme from Geobacillus stearothermophilus were expressed and characterized. The wild type enzyme has a tryptophan residue at position 70 that π-stacks with the porphyrin ring and donates a long hydrogen-bonding interaction to the thiolate ligand of the heme iron. The native Trp was replaced with His, Phe, and Tyr. These three residues were selected to investigate the two effects of the Trp, H-bonding and Pi-stacking. Several different spectroscopic techniques were used to investigate the stability and properties of these mutant enzymes. The identity of each mutant was confirmed by mass spectrometry. Both UV-visible absorption and circular dichroism spectroscopies were used to assess the stability of the new proteins. It was shown using binding assays, generation of the ferrous-CO species, and redox titrations that the σ-donating abilities of the thiolate are increased after removal of the hydrogen bonding group in the Trp. Finally, electron paramagnetic resonance spectroscopy and Evans method nuclear magnetic resonance spectroscopy were used to characterize the spin state of the iron center in each mutant, reflecting the increased σ-donating capabilities of the thiolate upon removal of the hydrogen bonding group. The reduction potential of wild type and W70H were determined by chemical titration to be -362 and -339 mV vs. NHE, respectively. This is the first report of the reduction potential of any bacterial nitric oxide synthase.
The reactivity of each the wild type enzyme and the three new mutants was tested using stopped-flow mixing coupled with UV-visible absorption spectroscopy and the Griess Assay. Autoxidation rates measured by stopped-flow suggest that the Tyr and Phe mutants do indeed have significantly more negative reduction potentials, but that the His mutant is particularly slow to oxidize. The Griess Assays showed that all four enzymes produce nitrite in solution, when provided with substrate, cofactor and hydrogen peroxide (as a source of reducing equivalents). In single turnover experiments, however, only three of the four enzymes showed evidence of ferric-NO production. The His mutant showed no intermediate absorbance near 440 nm (which would be indicative of ferric-NO formation), suggesting that it releases NO- rather than the radical species NO∙. The role of this hydrogen bond is concluded to be an electronic one, rather than playing any part in positioning the heme. It prevents formation of the inactive P420 species, and tunes the reduction potential to one high enough to be reduced by a reductase but low enough to still deliver an electron to the redox active cofactor, tetrahydrobiopterin, at the end of catalysis.
The rate at which NO is released by each NOS enzyme varies greatly among isoforms and species, over nearly two orders of magnitude. One residue (an isoleucine located above the heme in bacterial enzymes) involved in the gating of NO release has been previously identified by Stuehr. However, this single residue does not account for the entirety of the differences among the forms of NOS. Another residue, a histidine at position 134 in NOS from Geobacillus stearothermophilus (gsNOS), was hypothesized to also participate in gating NO release based on an observed correlation between rates of NO release and the bulk of side chains at this position. Each single point mutation, H134S and I223V, and the double mutant were expressed in gsNOS and their reactivity toward the diatomic molecules CO and NO were studied. CO rebinding was investigated using laser flash photolysis and NO release using stopped flow UV-visible spectroscopy. The presence of both monomer and dimer was observed in solution, and position 134 was shown to be another key residue in gating NO release. Wild type gsNOS contains both the bulkier Ile223 and His134 and has the slowest measured NO release (0.039 s-1) of all NOS enzymes. A new, more accurate kinetics model for turnover is proposed. Each single mutation increased NO release substantially, while the double mutant has a rate constant of 1.0 s-1, nearly as fast as mammalian iNOS at 2.3 s-1, identifying position 134 as another important factor determining rate constants for NO release.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/0NFE-Y329, author = {Cable, Morgan Leigh}, title = {Life in Extreme Environments: Lanthanide-Based Detection of Bacterial Spores and Other Sensor Design Pursuits}, school = {California Institute of Technology}, year = {2010}, doi = {10.7907/0NFE-Y329}, url = {https://resolver.caltech.edu/CaltechTHESIS:05102010-145436548}, abstract = {Bacterial spores, or endospores, are produced by certain genera of bacteria under stress and are considered to be one of the most resilient forms of life on Earth. Detection of endospores is vital in areas ranging from bioburden reduction to homeland security. Rapid bacterial spore detection is achieved by targeting dipicolinic acid (DPA), a chemical marker unique to endospores. An improvement on the current bacterial spore detection assay based on sensitized lanthanide luminescence is presented through the implementation of a dipicolinate-specific Tb3+ receptor site. The use of a chelating ligand such as DO2A (1,4,7,10-tetraazacyclododecane-1,7-bisacetate) can increase both the sensitivity and selectivity of the assay. The luminescent series of Ln(DO2A)(DPA)- complexes (Ln = Sm, Eu, Tb and Dy) is fully characterized in terms of structure, photophysics and stability, and the Tb(DO2A)+ binary complex in particular is investigated as a sensing complex for bacterial spores. The ‘ligand enhancement’ observed in all cases improves dipicolinate binding affinity by approximately one order of magnitude over the lanthanide ion alone. Binding of the DO2A ligand also appears to generate a ‘gadolinium break’ effect, creating a discrepancy in binding affinity in the lanthanide series and rendering the terbium complex the most effective dipicolinate receptor site of all investigated. We have also extended the application of this receptor site design technology to the targeted detection of other aromatic analytes of biological relevance, such as salicylates and catecholamines. Our work indicates that construction of effective receptor site complexes is not governed by net electrostatic considerations, and that local charge variations from the ligand-induced perturbation of lanthanide electron density may play a significant role. This work sets the stage for the development of the next-generation terbium(macrocycle) complex for bacterial spore detection, with the aim of constructing a solid-state endospore microsensor for applications ranging from sterilization validation to life detection in extreme environments.}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/WWS3-C929, author = {Pribisko Yen, Melanie Anne}, title = {Unfolded States of Heme Proteins}, school = {California Institute of Technology}, year = {2010}, doi = {10.7907/WWS3-C929}, url = {https://resolver.caltech.edu/CaltechTHESIS:06242011-125949350}, abstract = {Cytochromes adopt discrete structures when the heme cofactor is present. Since the heme provides crucial contacts in the native protein, this hydrophobic prosthetic group plays an important role in the folding mechanism and introduces interesting features into the folding landscape. Since the iron-porphyrin is sensitive to protein structure and environment, it also acts an optical probe and will be used in photophysical and photochemical studies of three alpha-helical proteins in the electron transport family of cytochromes: both horse heart and Saccharomyces cerevisiae iso-1 cytochrome c (cyt c), Rhodopseudomonas palustris cytochrome c’ (cyt c’), and the engineered cytochrome cb₅₆₂(cyt cb₅₆₂) from E. coli cytochrome b₅₆₂.
The work in this thesis expands upon previous research in the Gray Group that has shown heterogenous unfolded populations in these three alpha-helical proteins. Triplet state decay kinetics of Zn-substituted cytochrome c (Zn-cyt c) reveal the level of solvent exposure of the heme through an isotope effect and bimolecular quenching of lifetimes. Differences of the GuHCl, urea, and thermally-induced unfolded states between Zn- and Fe-cyt c, cyt c’ and cb₅₆₂ were uncovered, revealing a distinct hydrophobic effect. The inability of elevated temperature to disrupt hydrophobic pockets was studied further for DNS(C102)-cyt c through FET kinetics that reveal a significant compact population at high temperature. Finally, initial experiments on macromolecular crowding of cyt c revealed only a slight effect on the equilibrium unfolded states.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/EYKS-R134, author = {Leigh, Brian Scott}, title = {Electron Transfer Through Organic and Biological Molecules}, school = {California Institute of Technology}, year = {2009}, doi = {10.7907/EYKS-R134}, url = {https://resolver.caltech.edu/CaltechETD:etd-08042008-115533}, abstract = {The function of solvent in facilitating long-range coupling in donor/bridge/acceptor complexes is not well understood. There are exceptional challenges inherent to the measurement of the electron transfer coupling properties of solvents. By immobilizing the donor and acceptor in a glass to eliminate the effects of diffusion, statistical methods of analysis can be employed to study electron transfer between randomly dispersed donor and acceptor molecules over long distances. Toluene and 2-methyltetrahydrofuran form glasses that can solubilize donor and acceptor molecules at 77 K. Exponential decay constant of 1.23 per angstrom, for electron tunneling through a frozen toluene glass, and 1.62 per angstrom through 2-methyltetrahydrofuran glass have been found. Identification of the electronic coupling sites on the surfaces of proteins is usually achieved by inspection of a crystal structure. These coupling spots have been experimentally observed by employing mixed self-assembled monolayer electrodes and a variety of mutants. The electron transport protein azurin has a well defined reduction potential on self-assembled monolayer electrodes (0.16 V vs. saturated Ag/AgCl). When a point mutation is made at position 48, electron transfer ceases. This disruption of electron transfer occurs because the mutation forces conformational changes that disrupt a critical hydrogen bond between asparagine-47 and cysteine-112. This hydrogen bond is a key element for electron transfer into and out of the protein.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/ZWH6-3B84, author = {Lai, Bert Tsunyin}, title = {Characterizing α-Synuclein Membrane Bound Structure}, school = {California Institute of Technology}, year = {2008}, doi = {10.7907/ZWH6-3B84}, url = {https://resolver.caltech.edu/CaltechETD:etd-05062008-171457}, abstract = {A feature of Parkinson’s disease is the presence of fibrillar protein deposits composed mostly of α-synuclein and calcium ions in the brain’s substantia nigra region. Although α-synuclein is natively unfolded, the N-terminal region of the protein is highly helical in the presence of membrane mimics, such as acidic phospholipid vesicles and SDS micelles. The C-terminal region of α-synuclein is known to bind to calcium ions and modulates aggregation. In this thesis, the structure of α-synuclein variants, incorporated with tryptophan and 3-nitrotyrosine as donor and energy acceptor pairs, have been characterized in the presence of SDS micelles, small unilammelar vesicles, and calcium ions by various techniques. Distance distributions extracted from time-resolved fluorescence energy-transfer measurements provide site-specific information on the protein conformations. In addition, similar studies using mutants linked to early onset Parkinson’s disease were also performed to investigate the structural effect caused by these mutations. Furthermore, single tryptophan mutants have been designed as fluorescent reporters. The locations of these different tryptophan residues in the bilayer were probed by lipids labeled with bromine and dinitrophenol quenchers. Finally, preliminary studies of the intramolecular structure of α-synuclein aggregates have been carried out, while elucidation of intermolecular α-synuclein aggregate structures was made possible by the synthesis of new dyes that allow for long-range fluorescent energy transfer.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/0E5A-1W62, author = {Shih, Crystal}, title = {Electron Tunneling and Hopping Through Proteins}, school = {California Institute of Technology}, year = {2008}, doi = {10.7907/0E5A-1W62}, url = {https://resolver.caltech.edu/CaltechETD:etd-05122008-105452}, abstract = {Long-range electron tunneling is a central component of processes that are essential for biological function. While many studies have been made to understand electron transfer in proteins, biologically efficient electron transfer at distances exceeding 25 Å remains unobserved in these experiments and hence unresolved. It is proposed that long-range electron transfer is in actuality multistep electron tunneling. What is reported in this thesis is the design, synthesis, and study of many protein systems for the purpose of studying multistep electron tunneling in azurin.
In each system, a histidine has been introduced on the protein for attachment of a high-potential ruthenium or rhenium sensitizer ([Ru(trpy)(tfmbpy)]2+ or [Re(dmp)(CO)3]+); a nitrotyrosine, tryptophan, or tyrosine is placed between the two metal centers on the tunneling pathway. The electron transfer is triggered with the excitation of the metal label with laser light, and the kinetics are monitored, for the most part, by time-resolved UV-VIS spectroscopy.
The first system to empirically demonstrate multistep electron tunneling in proteins was discovered; ultrafast electron transfer is observed between the copper and rhenium centers in the Re124/W122 system; the system was structurally characterized and studied by time-resolved UV-VIS and IR spectroscopies. A two-step tunneling model is proposed; the data sets for the different methods utilized are all in excellent agreement with the model.
Systematic perturbations were made to the working hopping system. It was discovered that nitrotyrosine can participate as an intermediate, but studies to demonstrate its participation in multistep tunneling are not yet fully realized. A second hopping system was discovered in the development of the Re126/W122 system.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/4PSM-AS02, author = {Arjara, Gitrada}, title = {Refolding a β-Barrel Membrane Protein}, school = {California Institute of Technology}, year = {2007}, doi = {10.7907/4PSM-AS02}, url = {https://resolver.caltech.edu/CaltechETD:etd-05292007-061922}, abstract = {The field of membrane protein folding is relatively new compared to soluble protein folding. This thesis describes spectroscopy investigations of the refolding and dynamics of a β-barrel membrane protein. The amphiphilic, β-barrel outer membrane protein A (OmpA) refolds and inserts directly into a lipid vesicle or micelle from a denatured state in aqueous urea solution. Spectroscopic probes used to study this system are native tryptophans located at positions 7, 15, 57, 102, and 143. Steady-state and time-resolved fluorescence measurements were performed using single tryptophan mutants of full-length OmpA (325 residues) and the truncated, transmembrane domain (176 residues). Both full-length and truncated mutants exhibit similar tryptophan emission lifetimes, suggesting that the transmembrane microenvironment is not greatly perturbed by the presence of the C-terminus.
While the microenvironments of folded full-length and truncated OmpA appear similar, the dynamics of refolding at each tryptophan position exhibit subtle differences when the C-terminus is present. Specifically, we observe that tryptophan-102, which faces the pore interior, inserts and folds the fastest while tryptophan-7, which does not cross the bilayer, is the slowest. Fluorescence anisotropy decays also indicate that tryptophan-7 is the most flexible residue compared to the other tryptophans. Temperature studies below the lipid gel-liquid transition temperature have also been performed. In the lipid gel phase, OmpA adsorbs to the surface of the vesicles but contains immediate β-sheet structure upon folding as well as very hydrophobic tryptophan environments. It is still uncertain from ensemble measurements whether this species is a true intermediate.
Fluorescence energy transfer kinetics have successfully determined the intramolecular distance between tryptophan-7 and cysteine-175 labeled with a dansyl fluorophore. These results reveal that the barrel ends of OmpA come into contact early in the refolding process and remain close together up to the final assembly of the barrel. We also have evidence that the adsorbed species at low temperatures is not an intermediate in the folding pathway since no energy transfer is observed for this species. These spectroscopic investigations have provided the foundation for further fundamental studies to dissect the molecular mechanism of the folding pathway of OmpA as well as other integral membrane proteins.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, } @phdthesis{10.7907/fgsb-4m91, author = {Nguyen, Yen Hoang Le}, title = {Wiring Inducible Nitric Oxide Synthase}, school = {California Institute of Technology}, year = {2007}, doi = {10.7907/fgsb-4m91}, url = {https://resolver.caltech.edu/CaltechETD:etd-09262006-134259}, abstract = {The “wires project” in the Gray group has been focused on characterizing short-lived intermediates of Fe heme enzyme catalytic cycles by designing and synthesizing photosensitizers (wires) that bind to the protein active site with high affinity. The heart of this thesis is on rhenium channel binding and ruthenium surface binding wires for inducible nitric oxide synthase (iNOS). Binding and inhibition studies were conducted, electron transfer (ET) kinetics were studied, and iNOS catalytic activity was assayed for nitric oxide (NO) production.
Both channel and surface binding wires bind to iNOS with low micro molar affinity. Channel binding wires bind at the active site, closely interacting with the protoporphyrin IX iron heme (Fe heme). Characteristic spectral shifts of Fe heme perturbation were observed. The surface binding wires bind presumably at the hydrophobic patch of the oxygenase domain where the reductase domain was proposed to dock during electron transfer processes. The surface binding wire interacts closely with the Fe heme from the surface of the protein, but still close to where spectral shifts of the Fe heme were observed; however, the surface binding wire does not displace other channel binding wires, indicative of a second binding site.
Upon photo-excitation of all rhenium wires, the resting state Fe(III) heme is reduced to Fe(II) heme in less than 10 ns, characterized by transient absorption spectroscopy. This ET rate is orders of magnitude faster than Fe(III) reduction by the reductase domain (kET = 1 s-1) under biological conditions. In some cases, the wires were observed to ligate the Fe(II), creating a six-coordinate Fe(II) complex. The fully coordinated Fe(II) species is prevented from binding oxygen, and the catalytic mechanism is terminated. Another electron cannot be injected, and there is no production of NO. In the cases where the wire was shorter, ligation of the Fe(II) species was not observed. The Fe(II) remains five-coordinate, leaving room for oxygen to bind and for the mechanism to continue. In this case, NOS catalytic activity was assayed for the production of NO by photo-excitation of the wires. Complications of photodecomposition of NO indicators presented a challenge in data analysis. It is possible that a very small amount of NO was produced by photo-excitation of the wire; unfortunately, nothing definitely can be concluded. A new method to assay for NOS catalytic activity was proposed.
Both channel and surface binding wires led to many insights on substrate binding modes at the protein active site and on the surface; ET mechanisms were redefined, including amino acid radicals participating in electron transfer processes; and future directions for new wire were designed with hopes of accomplishing the long standing goal of characterizing high-valent Fe species.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/vc42-nh03, author = {Duimstra, Joseph Anthony}, title = {Modulation of Magnetic Properties in Magnetic Resonance Imaging Contrast Agents and Molecular Magnetic Materials}, school = {California Institute of Technology}, year = {2006}, doi = {10.7907/vc42-nh03}, url = {https://resolver.caltech.edu/CaltechETD:etd-04222006-220215}, abstract = {This dissertation focuses on fundamental research in two areas of magnetism, the technologically advanced field of magnetic resonance imaging (MRI) and the nascent discipline of molecular magnetic materials. Contrast agents for MRI based on the gadolinium(III) ion were designed and studied to gain insight into the parameters that may be modulated to control contrast agent efficacy. Two parameters in particular, the inner-sphere coordination environment and the electronic relaxation of the gadolinium(III) ion, were examined. Investigations into the electronic relaxation of the gadolinium(III) ion led to insights that were applied to the synthesis and evaluation of a low dimensional magnetic material based on ruthenium(III) and nickel(II) ions.
Manipulation of the gadolinium(III) coordination sphere provided the basis for an MRI contrast agent designed to be sensitive to the oncologically relevant enzyme beta-glucuronidase. This agent functions by restricting water access to the inner-sphere coordination sites of the gadolinium(III) ion. The design, synthesis, magnetic properties and biochemistry of the agent are described in detail. The agent displays good enzyme kinetics and complicated coordination equilibria with water and carbonate ion.
A second approach to modulating contrast agent efficacy consisted of varying the electronic relaxation time of the gadolinium(III) ion. Towards this goal, ligand frameworks were designed and synthesized to influence the relaxation time of the gadolinium(III) ion via remote redox activity. Structural characterization and in vitro assays of these ligand-metal constructs indicated more robust ligands were required for complex stability. Initial steps toward a ligand that fulfills these requirements proved successful.
The structural data from the electronic relaxation studies led to the synthesis of a one-dimensional coordination polymer comprised of chelated ruthenium(III) and nickel(II) ions bridged by cyanide ligands. The compound was studied by X-ray crystallography and its magnetic properties indicated that the ions were ferromagnetically coupled.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Meade, Thomas J. and Fraser, Scott E. and Gray, Harry B.}, } @phdthesis{10.7907/8DS8-QS11, author = {Weaver, Jeremy John}, title = {Corroles}, school = {California Institute of Technology}, year = {2005}, doi = {10.7907/8DS8-QS11}, url = {https://resolver.caltech.edu/CaltechETD:etd-04122005-152030}, abstract = {Corroles, porphyrin analogues, are the center of a rapidly growing field of research. By virtue of a missing meso-carbon, corroles retain the aromaticity of porphyrins, but become tribasic ligands in place of the dibasic porphyrin. This thesis is a study of synthetic methods for corroles, as well as their photophysical properties and potential applications.
New synthetic methodologies for the free-base molecules have been used to obtain corroles with pentafluorophenyl meso substituents in both water-soluble and non-water-soluble forms. Closed-shell metallocorrole complexes have been synthesized by introducing Ga(III) and Sn(IV) ions into the macrocycle. Likewise, an open shell transition metal corrole utilizing Mn(III) has been made. Problems arising from making a third type of closed shell metallocorrole by introduction of In(III) are also discussed. Among other characterizations of these complexes, Gouterman’s four-orbital model for porphyrins is reinterpreted under the reduced symmetry of the corrole macrocycle to explain the absorption and singlet emission spectra of the molecules. Evidence of a triplet excited state is also presented.
The application of corrole complexes to other aspects of chemistry is then examined in two different areas. The interactions of the water-soluble corroles with human serum albumin were investigated to assess their usefulness as diagnostic agents and drugs for cancer research. These highly colored compounds have also been introduced as the dye component of dye-sensitized solar cells, and various aspects of the cells, including overall efficiency, have been tested.
This thesis concludes with a summary of results obtained from collaborations on the interactions of corroles in cellular systems and synthetic attempts toward new types of water-soluble corroles, including an imidazole substituted chromium corrole and a sulfonated manganese nitrido corrole.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/1721, author = {Udit, Andrew K.}, title = {P450 BM3 Electrochemistry and Electrocatalysis}, school = {California Institute of Technology}, year = {2005}, url = {https://resolver.caltech.edu/CaltechETD:etd-05112005-100825}, abstract = {Cytochromes P450 catalyze monooxygenations of relatively inert substrates. The significance of this activity in physiology and industry has inspired many to capture this activity in vitro. However, practical applications of P450s will continue to be hindered by the need for reducing equivalents from NAD(P)H. While electrochemical methods provide a potential solution, the difficulty in achieving good electronic coupling to the heme remains an enormous obstacle.
Flavocytochrome P450 BM3 is soluble, well-characterized, and easily manipulated, making it a good target for in vitro applications. Bioelectrocatalysis was first attempted with holo BM3 using a novel electrochemical mediator, 1,1’-dicarboxycobaltocene (Mred). Absorption spectroscopy confirmed electron transfer (ET) from Mred to the cofactors, while electrolyses resulted in Mred-mediated hydroxylation of lauric acid by both the holo (16.5 nmol product / nmol enzyme / min) and heme proteins (hBM3) (1.8 nmol product / nmol enzyme / min).
Subsequent bioelectrocatalysis was attempted with the more stable hBM3. We achieved direct electrochemistry of hBM3 by wiring it through engineered surface Cys387 to a basal plane graphite electrode (BPG) with 1-pyreneiodoacetamide (Py). AFM images revealed that only pyrene-wired enzyme molecules adsorb to BPG. ko for the BPG-Py-hBM3 system was 650 ± 50/s. Rotated-disk electrode (RDE) experiments show that the BPG-Py-hBM3 system catalyzes the four-electron reduction of dioxygen to water. Analogous experiments were performed with enzyme labeled at Cys62, which is spatially adjacent to Cys387 but does not provide a similar well-coupled through-bond pathway to the heme. Surprisingly, the Cys62 mutant showed similar electrode kinetics, demonstrating that the pyrene tether does not provide a unique pathway, but probably anchors the protein onto the electrode surface in a favorable docking mode for ET.
Extensive electrochemical characterization of hBM3 was conducted in various surfactant films on BPG. Cyclic voltammetry of hBM3 in SDS films revealed the Fe(III/II) redox couple at -330 mV (vs. Ag/AgCl, pH 7.4), and ko of 40/s. Although voltammetry confirmed catalytic dioxygen reduction by Fe(II), substrate oxidation was not observed.
Voltammetry of hBM3 mutant 1-12G in DDAPSS films revealed Fe(III/II) (-202 mV) and Fe(II/I) (-1082 mV) redox couples of the heme (pH 7). Catalytic activity included dioxygen reduction by Fe(II), and reductive dehalogenation by Fe(I). Voltammetry on hBM3 in DDAPSS revealed that hBM3 and 1-12G display distinct redox properties. Absorption spectra in solution showed the Fe(III) Soret at 418 nm for hBM3, and a split Soret for 1-12G at 390 and 418 nm. Voltammetry of the proteins within DDAPSS films revealed nearly identical Fe(III/II) potentials (~ -200 mV), but significant differences in ko, 250 vs. 30 per second, and Fe(III/II) – CO potentials, -140 mV vs. -115 mV, for hBM3 vs. 1-12G. Catalytic dioxygen reduction by the proteins on RDEs was analyzed using Levich and Koutecky-Levich treatments. Calculated values of n, 2.7 vs. 4.7, and kobs, 1400000 vs. 100000/M/s, for hBM3 vs. 1-12G suggest that the two proteins differ strikingly in their reaction with dioxygen.
Using the prototypical cytochrome P450 CAM (CAM), we attempted to generate high-valent species of P450 in DDAB films. Performing rapid-scan (50 V/s) voltammetry revealed a couple (E) at 831 mV. E was not observed at scan rates less than 30 V/s at room temperature; however, at four degrees Celsius E could be reversibly generated at 1 V/s. E was found to be sensitive to imidazole in solution and to variations in pH, suggesting that the redox reaction is occurring at the metal center (i.e., Fe(IV/III)) rather than at the porphyrin macrocycle. Electrolyses revealed that the electrochemically generated high-valent species is only capable of performing S-oxidation, converting thioanisole to methyl phenyl sulfoxide.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Arnold, Frances Hamilton and Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/1875, author = {Bittner, Wendy Belliston}, title = {Ultrafast Photoreduction of Nitric Oxide Synthase by Electron Tunneling Wires}, school = {California Institute of Technology}, year = {2005}, url = {https://resolver.caltech.edu/CaltechETD:etd-05192005-234308}, abstract = {The Gray group has a long-standing interest in the study of methods for rapid delivery of electrons to enzyme active sites. This thesis describes picosecond to nanosecond reduction of the heme active site of the inducible nitric oxide synthase oxygenase domain (iNOSoxy) bound to Re- and Ru-diimine electron-tunneling wires. The Re wires have the form [(4,7-dimethylphenanthroline)ReI(CO)3L]+ where L is a perfluorinated biphenyl bridge connecting a rhenium-ligated imidazole or aminopropylimidazole to a distal imidazole (F8bp-im (1) and C3-F8bp-im (2)) or F (F9bp (3) and C3-F9bp (4)). All four bind tightly (micromolar to nanomolar Kd) in the active site channel of iNOSoxy. Upon excitation with 355 nm light, the bound rhenium of 1, 2, or 4 is quenched in fewer than 200 ps, possibly by electron donation from a nearby tryptophan residue. When a through-bond pathway from the rhenium to the heme iron exists, the active site Fe(III) is then reduced to Fe(II) within 300 ps, approximately ten orders of magnitude faster than the naturally occurring reduction. The Ru-diimine wire, [(4, 4’, 5, 5’-tetramethylbipyridine)2Ru(bpyF9bp)]2+ (5), also binds tightly to iNOSoxy. The binding of 5 is independent of tetrahydrobiopterin, arginine, imidazole, and 1, indicating that tmRu-F9bp resides on the surface of the enzyme. Reductive flash-quench studies have shown that the bound wire is capable of reducing the imidazole-bound active-site heme in approximately 50 ns, fully seven orders of magnitude faster than the comparable in vivo process. This work represents the first demonstration of electron-tunneling wires that specifically target and rapidly reduce an enzyme without blocking the active site channel.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/JHAP-JG47, author = {Robinson, Noah Edward}, title = {Investigations of Peptide and Protein Deamidation}, school = {California Institute of Technology}, year = {2004}, doi = {10.7907/JHAP-JG47}, url = {https://resolver.caltech.edu/CaltechETD:etd-09212004-154502}, abstract = {This work concerns the peptide and protein deamidation of asparaginyl, Asn, and glutaminyl, Gln, residues to aspartyl and glutamyl residues, respectively. This is accompanied by a change in charge and increase of one unit in mass. Isomerization also often takes place. This reaction–which occurs spontaneously and non-enzymatically in many proteins under physiological conditions–has been hypothesized to be a general molecular clock, which could be used as a timer for protein turnover, development, or aging, and for the controlled conversion of one protein into another. Since this hypothesis was first proposed, amide molecular clocks have been demonstrated in several biological systems. These include the timing of protein turnover in rat cytochrome c and aldolase; the counting of individual enzyme molecule catalytic cycles in triosephosphate isomerase; and the resetable time-dependent monitoring of DNA repair in Bcl-XL.
The objective of this work is to increase the understanding of peptide and protein deamidation, especially the prediction of deamidation rates for specific amides in proteins. This capability has been developed for Asn residues in proteins of known three-dimensional structure, and the sequence information required to do this for Gln residues has also been obtained. This work provides stability information to protein chemists and needed information to those who continue to investigate the molecular clock hypothesis.
The problem was attacked in two phases. The first consisted of experimental work to determine the rate of deamidation as a function of primary sequence near the amide. All 400 possible peptides of the type GlyXxxAsnYyyGly were synthesized and the deamidation rates of 323 of these were measured. An additional 67 asparaginyl containing peptides that had a variety of lengths and forms were also measured in order to assess the efficacy of pentapeptides in this work. Also, a similar set of 400 peptides were synthesized with Gln in place of Asn. The deamidation rates of 52 of the Gln peptides have been measured and, from these rates, the rates of the other Gln peptides have been inferred. With the addition of rates for 34 peptides with blocked Cys, a total of 476 individual rate experiments on peptides have been carried out in 0.15 M Tris buffer at pH 7.4, 37.00 [degrees]C. Additional rate experiments were conducted on solution effects and on properties of the experimental system.
The second phase involved using experimental data from the literature–on relative instabilities of specific amides in proteins under specified solvent conditions and on protein three-dimensional structures–to quantify the effect that secondary, tertiary, and quaternary protein structure has on primary structure deamidation rates.
Factors that determine deamidation rates include structural components as well as electronic effects. It happens that the primary sequence component is so large that it is possible to separate it from the rest of the problem and measure it alone. The secondary, tertiary, and quaternary effects were then considered. It was found that, on average, 60% of the rate is accounted for by primary sequence, while the remaining 40% is ascribable to secondary, tertiary, and quaternary structure in those proteins for which suitable deamidation observations are available. For all proteins, the estimated values are 50% and 50%. For individual amides, these percentages vary over a wide range.
A procedure was developed through which the quantitative deamidation rate of any amide in a protein for which the three-dimensional structure is known can be calculated. These estimated rates are accurate to within about a factor of two or better for most amides with half-times less than 100 days. They can be used to predict the fastest amides in a protein to greater than 95% reliability. This reliability is remarkable, considering the fact that deamidation half-times vary from less than 1 day to over 100 years in 37.00 [degrees]C, pH 7.4, 0.15 M Tris buffer. The procedure was calibrated with only relative amide instabilities. It was then evaluated with absolute deamidation rates.
Details of this work are given in the pages which follow. The result was a computerized procedure through which deamidation rates for every Asn of every protein in the PDB Protein Database were calculated and analyzed.
This work provides two discoveries of biological importance.
First, the assumption of genetic determination of deamidation rates, which has until now been dependent upon scattered and largely qualitative observations, has been placed upon firm quantitative foundation with a thorough understanding of the effects of primary, secondary, and tertiary structure.
Second, this quantitative understanding has permitted reliable estimation of the distribution functions of deamidation rates in thousands of proteins. These rates show that a substantial fraction of proteins are genetically programmed to deamidate in biologically relevant timed intervals even though most of the genetically available structures deamidate more slowly. This quantitative preference for fast deamidation times relative to slow deamidation times is an entirely new discovery. The fact that this property is present within the thousands of proteins of currently known three-dimensional structure markedly strengthens the molecular clock hypothesis.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/E9WY-1N05, author = {Mayo, Elizabeth Idonia}, title = {Kinetics and thermodynamics of dye (group VIII metal)-sensitized nanocrystalline titanium dioxide photoelectrodes}, school = {California Institute of Technology}, year = {2004}, doi = {10.7907/E9WY-1N05}, url = {https://resolver.caltech.edu/CaltechETD:etd-06042004-153530}, abstract = {This thesis reports a comprehensive series of experiments involving complementary kinetics and thermodynamic measurements directed at isolating the important individual reactions in dye-sensitized nanocrystalline titanium dioxide solar cells (DSSCs). These experiments were done in conjunction with steady-state photoelectrochemical measurements; a combination which allowed a greater understanding of the overall mechanisms and driving forces of these systems.
Alternative two-electron redox couples were studied and efficiency increases of >40% were achieved when compared to similar systems using iodide/triiodide. Surface treatment with carboxylic acids minimized direct reduction of the redox couple by electrons in the titanium dioxide, and interestingly, the photocurrent also increased resulting in overall efficiency increases as high as 20%. Bridging ligands were used in an attempt to minimize recombination of the injected electrons with the resulting oxidized dyes, but DSSCs with these sensitizers showed poor conversion efficiencies and no distance dependence for injection or recombination was observed. The lack of distance dependence was attributed to the flexible single carboxyl anchoring group. To further investigate the effect of binding mode, a series of carboxyl-modified ruthenium bipyridyl sensitizers were studied. A single carboxyl anchoring group resulted in unstable DSSCs due to enhanced desorption as well as poor photon-to-current conversion efficiencies. These dyes injected efficiently into TiO2 on the nanosecond timescale, and regeneration of the oxidized sensitizers competed effectively with recombination. Consequently, individual kinetics measurements could not explain the decreased steady-state performance. The regeneration rates of these dyes in solution were found to rapid, approaching the diffusion controlled limit. The regeneration rate was dependent on the number and electron-withdrawing nature of the pendant groups, with the rate decreasing with increasing number of electron withdrawing substituents. Iridium dyes with cyclometalating ligands were shown to be efficient sensitizers in DSSCs, with quantum yields on the order of a ruthenium analogue having similar spectral overlap. Overall, the repeated inconsistencies between the steady-state behavior and the measured individual kinetics processes indicate that the current kinetic model is insufficient to accurately predict photoelectrochemical behavior.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/HF8D-1W16, author = {Wehbi, William Amine}, title = {Amino acid radicals in rhenium-modified copper proteins}, school = {California Institute of Technology}, year = {2003}, doi = {10.7907/HF8D-1W16}, url = {https://resolver.caltech.edu/CaltechETD:etd-05302003-153624}, abstract = {Oxidative flash quench of [Re(CO)3(phen)(His)]+ generates a high-potential [Re]2+ oxidant (E° (Re2+/+) = 2 eV v. NHE), which has been used to obtain rates of electron transfer of Cu(I) oxidation in rhenium-modified azurins. These rates are enhanced over the [Ru(bpy)2(im)(His)]2+ analogues (E° Ru3+/2+ ~ 1 eV), suggesting an alternate mechanism from driving force optimized, singe-step electron tunneling. To test whether other intermediates can be involved, oxidative freeze flash quench of the zinc(II) derivatives were undertaken. These experiments reveal that [Re]2+ can produce the amino acid radicals of tyrosine and cysteine, as detected by EPR. The properties of these radicals in structurally well-defined protein microenvironments in Pseudomonas aeruginosa azurin mutants have focused, in particular, on the g1 component of the g-tensor, which is sensitive to the strength of the hydrogen bond to the radical. The g1 for Tyr48 radical, which resides in a completely hydrophobic pocket and is inaccessible to solvent, is found to be greater than the g1 for the solvent exposed Tyr108 radical. This comparison could not be made for the cysteine radicals as Cys108 formed a sulfenyl radical upon oxidation; the Cys48 radical has been demonstrated to be a thiyl radical species and provides the EPR spectroscopic benchmark for a non-hydrogen bonded thiyl radical.
In azurin mutants without any tyrosine, tryptophan, or cysteine residues, oxidative flash quench results in another organic based radical. This radical is located on the histidine imidazole ring that is coordinated to the rhenium atom. DFT calculations suggest that the spin density resides mainly on the imidazole ring when it is deprotonated. Corrected distances in the tunneling timetable to the imidazole ring from the copper atom predict an identical exponential decay in the electron transfer rates as for the ruthenium-labeled azurins. The rate enhancement is explained in terms of a “trivial hop” whereby Re2+ rapidly oxidizes the non-innocent histidine ligand in a proton dependent process; the histidine radical in turn oxidizes the copper atom or tyrosine, cysteine, or tryptophan when zinc is present. This model explains all of the enhanced Cu(I) oxidation rates by [Re]2+ and suggests that for Cu(I) oxidation in azurin, multistep electron tunneling through other amino acid radicals does not occur and that the observed radicals are generated in off-path processes.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/JAKV-8V97, author = {Meier, Alexandre Edouard}, title = {Gallium and chromium corroles}, school = {California Institute of Technology}, year = {2003}, doi = {10.7907/JAKV-8V97}, url = {https://resolver.caltech.edu/CaltechETD:etd-04082003-142034}, abstract = {We report on the synthesis and characterization of various chromium and gallium complexes of the corrole 1,5,15-trispentafluorophenylcorrole (tpfc)H3. We synthesized a chromium(V)oxo compound by reaction between (tpfc)H3 and Cr(CO)6 in refluxing toluene. Characterization of the compound via EPR and MS revealed a d1 metal species. Hyperfine splittings for the compound are A(53Cr) 1.64 mT, A(14N) 0.30 mT. Combined with the X-ray bond lengths (Cr-O, 1.545(2) ? Cr-N, 1.969/1.991 ? those data suggest that the stability of the Cr-O bond is mainly due to the strong N->Cr s donation. The compound (tpfc)Cr(O) provided the starting point for all other oxidation states we made and isolated.
By treatment with dioxinium hexachloroantimonate we were able to form the ligand radical chromium(V) oxo species, which was shown by EPR to be in its triplet ground state. By treatment with cobaltocene, we were able to isolate the chromium(IV) oxo species, which was proven diamagnetic via NMR. Reaction with phosphines, gave rise to the chromium(III) species, which is hexa-coordinated. The two axial ligands could be either pyridine, or triphenylphosphine oxide, and were readily exchanged with one another.
The reactivity of (tpfc)Cr(O) was found to be quite low, exhibiting a rate constant of 9.7 M-1s-1 for reaction with triphenylphosphine. The chromium(III) counterpart was readily reoxidized in air, with a mechanism involving a five coordinate intermediate as the reactive species.
In a bid to increase reactivity, we examined the effect of bromination at the b position on reactivity. To ascertain the electronic effects, we prepared a series of gallium corroles with various degrees of bromination. After characterization via MS and 2D NMR, electrochemical as well as UV-Vis measurements demonstrated that there is little steric deformation of the ligand framework upon increased bromination, which leads to a maximum of activity at maximum bromination.
We then successfully prepared the octabromo chromium corrole (Br8-tpfc)Cr(py)2. The oxidized compound (Br8-tpfc)Cr(O) was indeed reactive enough to oxidize various styrenes, albeit slowly (rates in the range:4.1?10-5-62 ?10-5 M-1 s-1). More surprisingly, the chromium(III) counterpart was found to oxidize in air, back to the oxo. The reoxidation is painfully slow, due in part to the difficulty in dissociating an axial ligand, and part to the low reactivity of the five-coordinate species. To speed up the reoxidation, we switched to adding TFA to (Br8-tpfc)Cr(py)2, in a bid to drive the ligand dissociation via trapping of the free pyridine.
The presence of an acid indeed leads to dramatically improved rates of air reoxidation of the compound, but at the same time, TFA was shown to play a non-innocent role in the process. We then proceeded to get rid of all the axial ligands altogether by treating the compound with HCl. The compound obtained displayed catalytic activity in the oxygenation of styrenes (~10 turnovers). The low turnover is due to product inhibition of the catalyst.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/8DNJ-GX96, author = {Quezada, Cindy Maria}, title = {Histidine phosphorylation in bacterial chemotaxis}, school = {California Institute of Technology}, year = {2003}, doi = {10.7907/8DNJ-GX96}, url = {https://resolver.caltech.edu/CaltechETD:etd-05302003-145522}, abstract = {Bacterial chemotaxis, the directed movement of bacteria in a chemical environment, represents one of the best biochemically and structurally characterized signal transduction pathways. The histidine kinase CheA is a central player in this two component regulatory system. Its active site is spread across two domains: the histidine phosphotransfer domain (P1) and the kinase domain (P4). Our efforts focus on elucidating the mechanistic contribution of P1 residues to the autophosphorylation reaction.
An atomic resolution structure (0.98 Å) of the Thermotoga maritima CheA histidine phosphotransfer domain was obtained, affording a unique opportunity to view the environment surrounding His45, the phosphoaccepting histidine, in detail. His45, participates in a hydrogen bonding network including three other residues: Glu67, Lys48, and His64, which are conserved in CheA. Employing a combination of site-directed mutagenesis studies, protein crystallography, and 2D heteronuclear NMR techniques, we explored the functional roles of these residues involved in the largely conserved hydrogen bonding network.
Our experiments revealed that the P1 domain provides the nucleophile for phosphate transfer (His45) and the activating glutamate (Glu67) completing a catalytic center observed in the GHL family of ATPases. Glu67 tunes the reactivity of His45 through a hydrogen bond. This interaction activates His45 to the normally unfavored N?1H tautomeric state. As a result, His45 possesses an altered pKa. Upon mutation of Glu67 to a Gln, the chemical properties of His45 change. When existing in the predominantly Nε2H tautomeric state, its pKa is similar to that of a solvent exposed histidine and its phosphorylation is dramatically reduced in vitro and in vivo.
Hence, the phosphoaccepting histidine must exist in the normally unfavored N?1H tautomeric state in order for CheA autophosphorylation to occur. The other two residues, Lys48 and His64, do not affect the reactivity of His45. Instead they contribute towards the structural integrity of the P1 active site. The results obtained in this thesis provide a solid structural and biochemical basis for further understanding the CheA phosphotransfer mechanism and may provide critical insight for the development of novel antibiotic agents.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/W2R9-Y195, author = {Lyubovitsky, Julia Gennadievna}, title = {Mapping the cytochrome c folding landscape}, school = {California Institute of Technology}, year = {2003}, doi = {10.7907/W2R9-Y195}, url = {https://resolver.caltech.edu/CaltechETD:etd-04102003-004657}, abstract = {The solution to the riddle of how a protein folds is encoded in the conformational energy landscape for the constituent polypeptide. Employing fluorescence energy transfer kinetics, we have mapped the S. cerevisiae iso-1 cytochrome c landscape by monitoring the distance between a C-terminal fluorophore and the heme during folding. Within 1 ms after denaturant dilution to native conditions, unfolded protein molecules have evolved into two distinct and rapidly equilibrating populations: a collection of collapsed structures with an average fluorophore-heme distance (r) of 27 A and a roughly equal population of extended polypeptides with r > 50 A. Molecules with the native fold appear on a timescale regulated by heme ligation events (~300 ms, pH 7). The experimentally derived landscape for folding has a narrow central funnel with a flat upper rim on which collapsed and extended polypeptides interchange rapidly in a search for the native structure.
Nonnative states of proteins are involved in a variety of cellular processes, including translocation of proteins across membranes and formation of amyloid fibrils. Probes that report on the structural heterogeneity of a polypeptide ensemble could resolve ambiguities in the classification of these states. We have shown that added anions shift the equilibrium between the compact and extended polypeptide structures that are present during refolding of Saccaromyces cerevisiae iso-1 cytochrome c. Specifically, at high salt concentrations (>= 700 mM), all the polypeptides are compact with a mean C-terminal fluorophore-heme separation quite close to that in the native protein (25 A). Addition of chemical detaturants, on the other hand, tends to shift the equilibrium towards unfolded structures.
Folding of modified Fe(II) cyt c was probed by fluorescence in presence of imidazole with NADH as photochemical sensitizer. At very high imidazole concentrations (400 mM), protein was still found to fold but the rate that coincides with Met80 ligation was slowed down significantly.
Reductive flash-quench/scavenge experiments, in which ascorbic acid was used to scavenge MeODMAA+, were shown to keep ferrocyt c reduced for up to 500 ms. Electron injection into unfolded modified yeast Fe(III)cyt c was fast in comparison to injection using NADH as photochemical sensitizer. The overall electron transfer process was reversible. This photoreduction system could be used to trigger folding of Fe(II) cyt c to monitor the changes in dansyl fluorescence intensity on ms time scales.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/V64A-V618, author = {Kent, David Randall}, title = {New quantum Monte Carlo algorithms to efficiently utilize massively parallel computers}, school = {California Institute of Technology}, year = {2003}, doi = {10.7907/V64A-V618}, url = {https://resolver.caltech.edu/CaltechETD:etd-02252003-134943}, 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.
A 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(N3) or better. This makes possible very high-level calculations on systems that are too large to be examined using standard high-level methods.
This 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.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/M27B-4W56, author = {Miller, Jeremiah Edward}, title = {Radical formation and electron transfer in biological molecules}, school = {California Institute of Technology}, year = {2003}, doi = {10.7907/M27B-4W56}, url = {https://resolver.caltech.edu/CaltechETD:etd-05292003-131114}, abstract = {Multi-step electron transfer is increasingly recognized as a means for moving charge in biological systems over long distances rapidly. Many postulated multi-step mechanisms rely on the formation of organic radicals (amino-acid radicals, nucleobase radicals) as intermediate electron or ?hole? carriers. In this thesis, the multi-step mechanism for electron transfer in both proteins and DNA is investigated. These two systems form a natural complement; the role of electron transfer in DNA with regard to lesion repair is still unknown, as are the electron transfer events in the proteins that mediate the repair. Rhenium-labeled mutant Pseudomonas aeruginosa azurins serve as model systems for this phenomenon in proteins. The photo-active rhenium label in these azurins can be oxidized by a flash/quench reaction to provide a potent oxidant capable of generating a variety of radicals in the protein matrix. Three mutants (with one tryptophan residue each) were constructed to investigate the effect of tryptophan radicals on charge transfer in proteins. The properties of tryptophan radicals in three protein environments have been investigated; including a kinetically stable tryptophan radical that persists for more than 5 hrs at room temperature. The variation in these radicals plays a significant role in their effect on the oxidation of the remote copper center in azurin. The stable radical greatly reduces the rate of electron transfer from copper relative to the rhenium-labeled wild-type analogs, while another radical plays no role in copper oxidation. In order to examine multi-step electron transfer in DNA, a series of photo-active ruthenium and rhenium-thymine complexes were constructed. By attaching the metal complexes at the sugar of the deoxyribonucleic acid, they were incorporated into DNA strands by solid-state synthetic techniques. Two different ruthenium-labeled DNA strands were produced in this way; one with a single guanine base and one with two side by side guanine bases. The strand containing a guanine-guanine sequence showed formation of a guanine radical by EPR under flash/quench conditions, while the strand containing a single guanine remained EPR silent. These strands represent an excellent template to examine a system which may or may not exhibit multi-step charge transfer.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/RW1J-6665, author = {Dunn, Alexander Robert}, title = {Sensitizer-linked substrates as probes of heme enzyme structure and catalysis}, school = {California Institute of Technology}, year = {2003}, doi = {10.7907/RW1J-6665}, url = {https://resolver.caltech.edu/CaltechETD:etd-05302003-172047}, abstract = {Ruthenium-diimine sensitizers (Ru-wires) with the structure [Ru(L2)L’]2+, where L’ is a perfluorobiphenyl bridge connecting 4,4’-dimethylbipyridine to the substrate adamantane or the heme ligand imidazole, bind to cytochrome P450cam with micromolar dissociation constants. Ru-wires can be used to trigger redox reactions on timescales faster than those achievable using conventional stopped-flow techniques: photoinduced heme reduction with an imidazole-terminated Ru-wire occurs in 40 ns. The large variation in ET rates among the Ru-diimine:P450 conjugates strongly supports a through-bonds model of Ru:heme electronic coupling.
The Ru-wires also bind the murine inducible nitric oxide synthase (NOS) oxidase domain, both in the active site and to the hydrophobic surface patch that interacts with the NOS reductase domain. Rhenium-diimine probes with the structure [Re(4,7-dimethyl phenanthroline)(CO)3L]+, where L = imidazole-C12F8-imidazole (Re-im) or imidazole-C12F9 (Re-F9bp), bind in the NOS active site. Re-im (Kd = 6 nM) ligates the heme iron. Re-F9bp (Kd = 3.4 micromolar) produces a partial low- to high-spin conversion of the heme. Compounds with properties similar to the Ru- and Re-diimine probes may provide novel means of NOS inhibition.
Luminescent dansyl probes were designed to target cytochrome P450cam. D-4-Ad (dansyl-C4-adamantane) luminescence is quenched by Forster energy transfer upon binding (Kd = 0.83 micromolar), but is restored when the probe is displaced from the active site by camphor. In contrast, D-8-Ad (Kd ~ 0.02 micromolar) is not displaced from the enzyme even in the presence of a large excess of camphor. Probes with properties similar to those of D-4-Ad potentially could be useful for screening P450 inhibitors.
Crystal structures of P450cam bound to ruthenium diimine and danysl probes reveal an open enzyme conformation that allows substrate access to the active center via a 22-A deep channel. Interactions of the probes with the channel illustrate the importance of exploiting protein dynamics in inhibitor design. Movements of the F, G and B’ helices couple to conformational changes in active site residues implicated in proton pumping and dioxygen activation. Common conformational states among P450cam and homologous enzymes indicate that the structural flexibility of the F/G helix region allows the 54 human P450s to oxidize diverse substrates.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/6WB9-2805, author = {Hoke, Kevin Richard}, title = {Electron Tunneling in Blue and Purple Copper Proteins}, school = {California Institute of Technology}, year = {2002}, doi = {10.7907/6WB9-2805}, url = {https://resolver.caltech.edu/CaltechTHESIS:01302012-102554225}, abstract = {The CU_A domain is the initial point of entry for electrons into cytochrome c oxidase. In order to explain fast rates of intramolecular electron transfer (ET) over long distances, it has been suggested that the ET reorganization energy is less than 0.6 eV. This issue was investigated by attaching a ruthenium(II)-bisbipyridyl-imidazole complex to a single surface histidine of the Thermus thermophilus CU_A domain. Photoexcitation results in rapid ET between the ruthenium complex and the copper site. This was done over a range of driving forces by employing a series of substituted bipyridines. An analysis of the driving force dependence of the ET rate suggests that the total reorganization energy for this CU_A fragment is about 0.7 eV, almost as high as for azurin. The degree of solvent exposure of the active site may be the factor responsible for the higher reorganization energy.
In addition, the effect of distance on ET rate was investigated. Two variants of ruthenium-modified CU_A were examined, in which the labeled sites are two positions apart. The observed ET rates only differ by an order of magnitude, drastically less than what theory would predict. It appears that geometric factors other than length influence ET coupled through hydrogen bonds.
The role of hydrogen bonds in ET was studied in more detail with ruthenium-modified azurin. Changes in the ET rate were observed for different degrees of deuterium incorporation in the system. For wild-type azurin, the greatest effect (k_H/k_D ≈ 0.7) is seen when the protein is subjected to rigorous exchange under denaturing conditions, then returned to a normal buffer as a control for the solvent isotope effect on the reorganization energy. This is the expected outcome if deuteration of internal, difficult to exchange hydrogen bonds results in improved coupling along the path.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/1968, author = {Villahermosa, Randy Michael}, title = {Electron tunneling through phenylene bridges}, school = {California Institute of Technology}, year = {2002}, url = {https://resolver.caltech.edu/CaltechETD:etd-05232005-084837}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
A series of donor-bridge-acceptor (D-B-A) complexes, […] (where n = 2 to 5, bpy = 2,2’-bipyridine, XY = 2,5-xylene, and G is 3-ethynyl-4-methoxy-N,N-dimethylaniline; abbreviated […]), were designed, synthesized, and characterized to study electron tunneling through phenylene bridges. […] is a versatile D-B-A scaffold that exhibits a strong correlation between xylene conformation and electron transfer properties.
[…] was assembled from three components in a convergent process. Stepwise oligomer growth produced the well-defined bridging ligand, […]; bipyridine was regioselectively functionalized with a xylene oligomer through multiple cycles of palladium-catalyzed cross-couplings. The donor, synthesized separately, was joined to […] using an alkyne linkage. Metalation with a […] fragment finished assembly of the D-B-A complex. The D-B-A series was analyzed with mass spectrometry and NMR.
Spectroscopic, electrochemical, and spectroelectrochemical characterizations of […] indicate no significant electronic or chemical difference among the members of the series. UV-visible absorption spectra, with a metal to ligand charge transfer (MLCT) band maximum of 460 nm, resemble the model complexes […] and […] (where TMS = trimethylsilyl). Representative cyclic voltammograms of […] contain reversible redox couples for Ru[…] and G[…], with potentials of 1.24 and 0.59 V (vs. Ag/AgCl). Spectroelectrochemical traces, displaying loss of MLCT intensity and increased absorption centered at 520 nm, indicate the formation of […].
The flash-quench technique was used to measure the electron transfer rates for […]. The rates, 9.0 ± 0.3 x 10[…], 2 ± 1 x 10[…], and 6 ± 1 10[…] for n = 3 through 5, have a strong dependence on donor-acceptor distance. Estimates of the donor-acceptor distance were used to determine a distance decay constant, […], of 0.84 […]. The typical [Beta]-value for electron tunneling through phenylenes is 0.4[…]. The unusually high [Beta]-value for […] is attributed to near-orthogonal dihedral angles between adjacent xylene rings. UV-visible spectra, cyclic voltammograms, and structural information, from molecular modeling calculations and a crystal structure, all support a near-orthogonal twist angle.
The versatility of […] as a molecular scaffold was demonstrated in studies on electron transfer reactions in nanocrystalline TiO2 solar cells. Modified to incorporate a terminal carboxyl group, […] (where BA = 4-ethynyl-benzoic acid) was synthesized and used as a TiO2 solar cell dye. Utilizing the flash-quench method, the second-order rate constant for dye regeneration with […], […] in homogenous fluid solution was 1.5 x […] for all three dyes in the series n=0 to 2.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/DCQ1-F958, author = {Lee, Jennifer Chen}, title = {Mapping heme protein folding landscapes}, school = {California Institute of Technology}, year = {2002}, doi = {10.7907/DCQ1-F958}, url = {https://resolver.caltech.edu/CaltechETD:etd-08202004-114236}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
The folding dynamics of two four-helix bundles, Fe’-cytochrome b[…] (E. coli) and Fe’-cytochrome c’ (R.palustris), have been investigated: in each case, folding was triggered by electron transfer (ET) to the unfolded Fe’-protein and probed by transient absorption spectroscopy. Although these two proteins are topologically homologous, they display strikingly different folding kinetics: for FE’-cyt […], the extrapolated time constant in the absence of denaturant […] is near the predicted value for intrachain diffusion; in contrast, Fe’-cyt c’ folding is heterogeneous over a ms-s time range.
Nonnative methionine ligands in Fe’-cyt c’ contribute to the complex folding kinetics. Removal of either Met-15 or Met-25 leads to simpler kinetics than found in the pseudo-wild-type (Q1A) protein. The amplitude of the intermediate folding phase ([…]) is diminished, suggesting that formation of near-native contacts may facilitate folding.
Cyt c’ has a wild-type Trp-72 residue that can be exploited in fluorescence energy transfer (FET) kinetics measurements. Also, we have crystallographically characterized […] a Trp-mutant, Q1A/F32W/W72F, in order to probe distances between position-32 and the heme during folding. Analysis of FET kinetics from Trp-72 and Trp-32 shows that there is structural heterogeneity in the denatured protein. Even at high guanidine hydrochloride (GuHCl) concentrations, 50% of the polypeptides adopt compact conformations (25-35A) in cyt c’. A burst phase […] is revealed when stopped-flow triggered refolding is probed by Trp fluorescence intensity: measurements on the Q1A protein show that 75% of the Trp-72 fluorescence (83% for Trp-32, Q1A/F32W/W72F) is quenched in the mixing deadtime, suggesting that most of the polypeptides have collapsed.
Electronically excited Zn-porphyrin in GuHCl-denatured Zn-substituted cytochrome c (Zn-cyt c) reduces […] about ten times faster than when embedded in the folded protein. Measurements of ET kinetics during folding reveal a burst intermediate in which one-third of the ensemble has a protected Zn-porphyrin and slow ET kinetics; the remaining fraction exhibits fast ET characteristic of a solvent-exposed cofactor. Importantly, our FET (cyt c’) and ET (Zn-cyt c) experiments show that collapsed nonnative structures are not substantially more stable than extended polypeptide conformations.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/2EYM-TW23, author = {Hess, Corinna Renate}, title = {Probing the Active Site of Amine Oxidase with Electron Tunneling Wires}, school = {California Institute of Technology}, year = {2002}, doi = {10.7907/2EYM-TW23}, url = {https://resolver.caltech.edu/CaltechTHESIS:01302012-150944800}, abstract = {Amine oxidases (AO) are copper-containing enzymes that catalyze the conversion of amines to aldehydes. The active site is deeply buried within the protein network, a factor which has precluded many investigations into the mechanism. A series of electron tunneling molecular wires has been synthesized, designed to access the cofactors of amine oxidase by means of the substrate channel. These wires are comprised of phenyl-ethynyl units and thus promote rapid rates of electron transfer to the active site. An amine group attached to one end of the oligomer serves as the channel-specific functionality, which binds within the channel. Binding of the oligomers to AO was demonstrated through inhibition and fluorescence quenching studies. A variety of reporter groups has been attached to the chain end opposite the amine group, allowing us to probe the enzyme using a variety of techniques. A Re terminated complex was designed for electron transfer studies with the enzyme. The photophysics of this complex were investigated in the presence of AO. A thiol terminated wire also has been synthesized, which was employed in electrochemical studies of the amine oxidase cofactors. These studies provide evidence for the ability to communicate with the active site using the molecular wires. In addition, these complexes fulfilled our primary goal and enabled us to determine a redox potential of the TPQ cofactor.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/8154, author = {Machczynski, Michael Christopher}, title = {Physical characterization of the rack effect and hydrogen bond networks in blue copper proteins}, school = {California Institute of Technology}, year = {2001}, url = {https://resolver.caltech.edu/CaltechTHESIS:03202014-144611863}, abstract = {A summary of previous research is presented that indicates that the purpose of a blue copper protein’s fold and hydrogen bond network, aka, the rack effect, enforce a copper(II) geometry around the copper(I) ion in the metal site. In several blue copper proteins, the C-terminal histidine ligand becomes protonated and detaches from the copper in the reduced forms. Mutants of amicyanin from Paracoccus denitrificans were made to alter the hydrogen bond network and quantify the rack effect by pKa shifts.
The pKa’s of mutant amicyanins have been measured by pH-dependent electrochemistry. P94F and P94A mutations loosen the Northern loop, allowing the reduced copper to adopt a relaxed conformation: the ability to relax drives the reduction potentials up. The measured potentials are 265 (wild type), 380 (P94A), and 415 (P94F) mV vs. NHE. The measured pKa’s are 7.0 (wild type), 6.3 (P94A), and 5.0 (P94F). The additional hydrogen bond to the thiolate in the mutants is indicated by a red-shift in the blue copper absorption and an increase in the parallel hyperfine splitting in the EPR spectrum. This hydrogen bond is invoked as the cause for the increased stability of the C-terminal imidazole.
Melting curves give a measure of the thermal stability of the protein. A thermodynamic intermediate with pH-dependent reversibility is revealed. Comparisons with the electrochemistry and apoamicyanin suggest that the intermediate involves the region of the protein near the metal site. This region is destabilized in the P94F mutant; coupled with the evidence that the imidazole is stabilized under the same conditions confirms an original concept of the rack effect: a high energy configuration is stabilized at a cost to the rest of the protein.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.1021/ja982536e, author = {Tezcan, Faik Akif}, title = {Reactions of Heme Proteins to Solutions and Crystals}, school = {California Institute of Technology}, year = {2001}, doi = {10.1021/ja982536e}, url = {https://resolver.caltech.edu/CaltechTHESIS:01312019-135136732}, abstract = {To assess the effects of heme solvation and iron ligation on reduction potentials in c-type cytochromes, we have examined the redox and ligand-binding properties of microperoxidase-8 (MP8). Methionine-, histidine- and amine-coordination to MP8 were found to account for 130, -40 and -10-mV shifts in the Fe(III/II)-potential, respectively. Our finding that reduction potentials increase with decreasing heme-surface exposure suggests that the protein matrix can further tune the reduction potential by 500 mV through water exclusion from the heme pocket.
The 410-mV upshift in the cytochrome c (cyt c) potential as the heme cofactor is moved from a highly-solvated environment to the protein interior signals a 10-kcal/mol greater stability of the reduced form. Consequently, there exists a range of denaturant concentrations where Fe(II)-cyt c is folded and Fe(III)-cyt c is unfolded. Electron injection into the oxidized protein in this range triggers the folding reaction. Using NADH as a redox photosensitizer, cyt c folding can be initiated within 100 µs. Our results suggest that the folding of cyt c is rate-limited by ligand-substitution events on the iron center.
Due to an increased barrier to ligand substitution, folding of Co(III)-substituted cyt cis 5 orders of magnitude slower than Fe-cyt c. The slow folding kinetics of Co(III)-cyt c have allowed the convenient study of protein dynamics with a variety of spectroscopic techniques, revealing previously unresolved folding pathways involving Lys- and His-misligated populations of the unfolded molecule and extremely long-lived folding intermediates.
Factors that control electron flow between proteins are not well understood, owing to uncertainties in the relative orientations and structures of the reactants during the short time that tunneling occurs. To circumvent this ambiguity, we have measured the kinetics of electron transfer (ET) between native and Zn-substituted tuna cyt c molecules in crystals of known structure. ET rates (320 s-1 for *Zn-cyt c → Fe(III)-cyt c; 2000 s-1 for Fe(II)-cyt c → Zn-cyt c+) over a Zn-Fe distance of 24.1 Å closely match those for intraprotein ET over similar donor-acceptor separations. Our results indicate that van der Waals interactions and water mediated H-bonds provide effective electronic coupling across a protein-protein interface.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/HABJ-3T48, author = {Szczepankiewicz, Steven Henry}, title = {Surface chemistry of titanium dioxide photocatalysts}, school = {California Institute of Technology}, year = {2001}, doi = {10.7907/HABJ-3T48}, url = {https://resolver.caltech.edu/CaltechETD:etd-05232006-094537}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
The surface chemistry of TiO2 photocatalysts have been characterized by infrared spectroscopy, alcalimetric titrations, and photocatalytic reactivity. The fundamental processes governing electron transfer at the surface were investigated by inhibiting the photocatalytic reactions.
Free and trapped charge carriers in polycrystalline TiO2 following bandgap irradiation are characterized by diffuse reflectance IR spectroscopy (DRIFTS). Irradiation of anatase in vacuo or in the presence of CD3OD leads to decreased overall reflectance, to an absorbance at 3717 cm(-1), and to the decline of a 3647 cm(-1) band. x persists for days in vacuum or dry O2 and is only bleached by the action of [O2 + H2O(g) + hv]. It is assigned to a Ti(III)O-H vibration ensuing electron trapping at the acidic Ti(IV)OH centers that absorb at 3647 cm(-1). Irradiation under O2 yields a band at 3683 cm(-1) (Y) that corresponds to bound OH radicals. These last indefinitely in vacuo, but decay in a few hours under O2. Since none of the above phenomena occur on defective TiO2-x, materials obtained by thermal annealing under vacuum, photochemical damage to actual catalysts involves concurrent surface reorganization. The presence of the 3717 cm(-1) band is used to confirm this reorganization.
The decreased reflectivity is due to a spectrum-wide absorption signal proportional to […]1.7 ([…] = wavelength/[…]), which indicates the presence of free conduction band electrons coupled with acoustic phonons in the lattice. Free electrons appear to decay according to saturation kinetics. The fitted parameters indicate a limited number of reversible trapping states. The concentration of these states appears to be diminished by sequential UV treatments. A broad IR absorption peak centered at 3380 cm(-1) is attributed to an electronic transition from an occupied surface electron trap 0.42 eV below the conduction band. The free carrier decay lifetime is lengthened as the samples are dehydrated.
Electric fields generated by photoexcited charge carriers in TiO2 (anatase) produce Stark effect intensity and wavelength shifts for surface TiO-H stretching vibrations. Shallow electron-trapping states, observed as broad absorption bands above 3000 cm(-1), produce an apparently homogeneous electric field. Intensity changes and corresponding wavelength shifts for v(TiO-H) are proportional to the magnitude and polarity of the electric field. O2 is shown to reversibly abstract electrons from shallow trapping states. These results suggest that shallow electron traps are not associated with localized structures, but rather are delocalized across the TiO2 surface.
The effect of poisoning the photocatayst is monitored during the oxidation of a phosphorous-containing organic substrate. The photoassisted oxidation of dimethyl-methyl-phosphonate (DMMP) over UV-irradiated TiO2 is investigated as a simulant for warfare nerve agent detoxification. Adsorption uptake measurements are performed by MS analysis of a fine DMMP aerosol up and downstream of an adsorbant TiO2 film. Photodesorption processes, gas phase intermediates and mineral products are quantified in situ by headspace GC-MS analysis of a static system. Non-volatile intermediates and products are analyzed by HPLC analysis of both aqueous and organic extractions from the Ti02 film. Adsorbed intermediates are characterized and quantified in situ by DRIFTS of Ti02 powders. Specific site binding of DMMIP and catalyst poisoning are observed in the DRIFT spectra. A proposed mechanism suggests rapid detoxification of DMMP as a simulant, but extensive poisoning of the catalyst by the end products.
In a comparative investigation of titania surface chemistry, TiO2 Q particles are synthesized and characterized by transmission electron microscopy, potentiometric titration, infrared analysis, and photocatalytic reactivity. TEM images show small individual particulates of anatase about 2 nm in diameter. Potentiometric titrations confirm the presence of a highly protonated gel layer on the surface of these particles. The infrared spectra indicate that this layer is amorphous. An autocatalytic enhancement of the photocatalysts during photooxidation of methyl orange suggests that reaction intermediates cause the collapse of the hydrated gel layer into a more active surface.
Two supplementary investigations are presented which confirm the previous results. MAS NMR data is presented which shows a paramagnetic influence from surface trapped electrons. The data also suggests localized trapping at a characteristic type of TiOH surface moiety. Theoretical calculations also confirm the band assignments presented in the previous chapters by reproducing the data with the predicted structural assignments.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Hoffmann, Michael R.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/8151, author = {Krider, Elizabeth Stratford}, title = {Synthesis and spectroscopy of ruthenium-modified nucleic acids}, school = {California Institute of Technology}, year = {2001}, url = {https://resolver.caltech.edu/CaltechTHESIS:03202014-093625161}, abstract = {Redox-active probes are designed and prepared for use in DNA-mediated electron transfer studies. These probes consist of ruthenium(II) complexes bound to nucleosides that possess metal-binding ligands. Low- and high-potential oxidants are synthesized from these modified nucleosides and display reversible one-electron electrochemical behavior. The ruthenium-modified nucleosides exhibit distinct charge-transfer transitions in the visible region that resemble those of appropriate model complexes. Resonance Raman and time-resolved emission spectroscopy are used to characterize the nature of these transitions.
The site-specific incorporation of these redox-active probes into oligonucleotides is explored using post-synthetic modification and solid-phase synthetic methods. The preparation of the metal-binding nucleosides, their incorporation into oligonucleotides, and characterization of the resulting oligonucleotides is described. Because the insertion of these probes into modified oligonucleotides using post-synthetic modification is unsuccessful, solid-phase synthetic methods are explored. These efforts lead to the first report of 3’-metallated oligonucleotides prepared completely by automated solid-phase synthesis. Preliminary efforts to prepare a bis-metallated oligonucleotide by automated synthesis are described.
The electrochemical, absorption, and emissive features of the ruthenium-modified oligonucleotides are unchanged from those of the precursor metallonucleoside. The absence of any change in these properties upon incorporation into oligonucleotides and subsequent hybridization suggests that the incorporated ruthenium(II) complex is a valuable probe for DNA-mediated electron transfer studies.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/8627, author = {Ponce, Adrian}, title = {Electron tunneling in proteins and water}, school = {California Institute of Technology}, year = {2000}, url = {https://resolver.caltech.edu/CaltechTHESIS:08062014-082923705}, abstract = {The subject of this thesis is electronic coupling in donor-bridge-acceptor systems. In Chapter 2, ET properties of cyanide-bridged dinuclear ruthenium complexes were investigated. The strong interaction between the mixed-valent ruthenium centers leads to intense metal-to-metal charge transfer bands (MMCT). Hush analysis of the MMCT absorption bands yields the electronic-coupling strength between the metal centers (H_(AB)) and the total reorganization energy (λ). Comparison of ET kinetics to calculated rates shows that classical ET models fail to account for the observed kinetics and nuclear tunneling must be considered.
In Chapter 3, ET rates were measured in four ruthenium-modified highpotential iron-sulfur proteins (HiPIP), which were modified at position His50, His81, His42 and His18, respectively. ET kinetics for the His50 and His81 mutants are a factor of 300 different, while the donor-acceptor separation is nearly identical. PATHWAY calculations corroborate these measurements and highlight the importance of structural detail of the intervening protein matrix.
In Chapter 4, the distance dependence of ET through water bridges was measured. Photoinduced ET measurements in aqueous glasses at 77 K show that water is a poor medium for ET. Luminescence decay and quantum yield data were analyzed in the context of a quenching model that accounts for the exponential distance dependence of ET, the distance distribution of donors and acceptors embedded in the glass and the excluded volumes generated by the finite sizes of the donors and acceptors.
In Chapter 5, the pH-dependent excited state dynamics of ruthenium-modified amino acids were measured. The [Ru(bpy)_(3)] ^(2+) chromophore was linked to amino acids via an amide linkage. Protonation of the amide oxygen effectively quenches the excited state. In addition. time-resolved and steady-state luminescence data reveal that nonradiative rates are very sensitive to the protonation state and the structure of the amino acid moiety.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/tzkw-0q94, author = {Bachrach, Max}, title = {Electron-Transfer in Covalently Coupled Donor-Acceptor Complexes}, school = {California Institute of Technology}, year = {1996}, doi = {10.7907/tzkw-0q94}, url = {https://resolver.caltech.edu/CaltechTHESIS:12152020-011716999}, abstract = {A picosecond transient absorption experiment has been constructed and used for the study of intramolecular electron-transfer (ET) in three molecular systems. The first of these is a donor-bridge-acceptor (D(br)A) complex composed of a d⁸-d⁸ iridium core covalently coupled to two pyridinium acceptors with flexible phosphonite spacers. Varying the pyridiniums’ substituents allows control of the driving-forces (ΔG°) of the photoinduced ET reactions from the core’s singlet and triplet states. The rates of these reactions have been determined from steady-state and time-resolved emission experiments. Picosecond transient absorption has been used to measure the rates of subsequent charge-recombination, and determine their dependencies on ΔG°. The reorganization energy accompanying intramolecular electron-transfer within this system (λ ≈ 0.86 eV) has been determined by fitting the rates of photoinduced and thermal reactions to a single-mode quantum-mechanical ET model.
The rates of all the photoinduced and thermal ET reactions have been measured as a function of temperature (200° K - 280° K). These data show that the charge-recombination reactions, which lie within the Marcus inverted region (ΔG° > λ), have rates (kBET) that are strongly dependent on temperature. Deuteration of the pyridinium acceptor has a temperature independent effect (kH/kD = 1.2) on kBET, indicating that, although the inverted region reactions within these complexes exhibit behavior that is remarkably classical, quantum-mechanical effects do need to be considered. Both temperature and isotope effects suggest that the molecules’ low internal reorganization energies (λin = 0.006 eV) account for their ET behavior.
Less comprehensive studies of two other electron-transfer systems are also reported. Unlike the iridium system, in which the donor-acceptor electronic coupling HAB is less than 100 cm-1, the couplings within these are over 2000 cm-1. It has been found that despite the large amount of coupling between the metals of [(bpy)(tpy)RuIICNRuII(NH3)5]2+ (bpy = 2,2’-bipyridine; tpy = 2,2’,2"-terpyridine), our transient absorption experiment is able to detect formation of a charge-separated state following excitation into the Ru → immine charge-transfer band. It is proposed that this species can be described as [(bpy)(tpy•-)RuIICNRuIII(NH3)5]2+ and that unusually low coupling between the tpy ligand and the oxidized ruthenium leads to slow (1 x 1010 s-1) charge-recombination.
The ground-state absorption features and excited-state decay kinetics of a series of ferrocene-based D(br)A complexes have also been measured. It is proposed that HAB is much larger than 2000 cm-1 for these complexes, and plays an important role in determining their nonlinear optical properties.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/4VTZ-PE72, author = {Mizoguchi, Tadashi Jack}, title = {Probing the role of the active-site Cysteine of Azurin by site-directed mutagenesis}, school = {California Institute of Technology}, year = {1996}, doi = {10.7907/4VTZ-PE72}, url = {https://resolver.caltech.edu/CaltechETD:etd-01162009-111204}, abstract = {The coordination chemistry and electron-transfer properties of a single-site mutant of the mononuclear copper electron-transfer protein azurin from Pseudomonas aeruginosa have been studied. The active-site cysteine at position 112 was replaced by an aspartate (Cys112Asp) to assess directly the importance of this ligand to the structure-function properties of azurin. Although the mutant protein retains a high-affinity copper-binding active site, the absorption and EPR spectra of Cu[superscript II]Cys112Asp azurin are quite distinct from those of the wild-type protein and indicate the presence of a normal (type 2) copper center. A Cu[superscript II/I] reduction potential of 180 mV vs. NHE (pH 7.0) was obtained through a redox titration experiment with cytochrome c[subscript 551]. The Co[superscript II] derivative of Cys112Asp azurin was prepared and found to be amenable to paramagnetic NMR spectroscopy. In conjunction with electronic absorption data, the NMR data were used to generate a computer model of the Co[superscript II] active-site structure in which the metal is coordinated by two histidines (His46 and His 117), a polypeptide backbone carbonyl oxygen (of Gly 45), and an out-of-plane, asymmetrically-bound bidentate aspartate (Asp 112) in an overall distorted square pyramidal geometry. The 2.4-Å resolution X-ray crystal structure of Cu[superscript II] Cys112Asp azurin is reported and confirms this ligand set and geometry. Ni[superscript II]-substituted Cys112Asp azurin was also made, but unlike Cu[superscript II] and Co[superscript II], the Ni[superscript II] ion is much less tightly bound by the protein. The electronic spectroscopy of Ni[superscript II] Cys112Asp azurin suggests the existence of some bonding interaction with the thioether sulfur atom of Met121. In contrast to Cys112-containing azurins, laser-induced intramolecular electron-transfer reactions from the reduced copper center of Asp 112-containing azurins to surface histidine-bound bis(bipyridy1)(imidazole) ruthenium(III) labels could not be observed. However, the kinetics of intermolecular protein-protein electron transfer between Cys112Asp and wild-type azurins were recorded by stopped-flow spectrophotometry. Analysis of the bimolecular kinetic data suggests that the Cys-to-Asp mutation has diminished significantly the electronic coupling between the copper and ruthenium centers in the intramolecular electron-transfer systems.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B. and Richards, John H.}, } @phdthesis{10.7907/D8HZ-E792, author = {Bren, Kara Lynne}, title = {Structurally Engineered Cytochromes c with Novel Ligand-Binding Properties}, school = {California Institute of Technology}, year = {1996}, doi = {10.7907/D8HZ-E792}, url = {https://resolver.caltech.edu/CaltechTHESIS:02042014-091755725}, abstract = {Semisynthesis of horse heart cytochrome c and site-directed mutagenesis of Saccharomyces cerevisiae (S. c.) iso-1-cytochrome c have been utilized to substitute Ala for the cytochrome c heme axial ligand Met80 to yield ligand-binding proteins (horse heart Ala80cyt c and S. c. Ala80cyt c) with spectroscopic properties remarkably similar to those of myoglobin. Both species of Fe(II)Ala80cyt c form exceptionally stable dioxygen complexes with autoxidation rates 10-30x smaller and O2 binding constants ~ 3x greater than those of myoglobin. The resistance of O2-Fe(II)Ala80cyt c to autoxidation is attributed in part to protection of the heme site from solvent as exhibited by the exceptionally slow rate of CO binding to the heme as well as the low quantum yield of CO photodissociation.
UV/vis, EPR, and paramagnetic NMR spectroscopy indicate that at pH 7 the Fe(III)Ala80cyt c heme is low-spin with axial His-OH- coordination and that below pH ~6.5, Fe(III)Ala80cyt c is high-spin with His-H2O heme ligation. Significant differences in the pH dependence of the 1H NMR spectra of S. c. Fe(III)Ala80cyt c compared to wild-type demonstrate that the axial ligands influence the conformational energetics of cytochrome c.
1H NMR spectroscopy has been utilized to determine the solution structure of the cyanide derivative of S. c. Fe(III)Ala80cyt c. 82% of the resonances in the 1H NMR spectrum of S. c. CN-Fe(III)Ala80cyt c have been assigned through 1D and 2D experiments. The RMSD values after restrained energy minimization of the family of 17 structures obtained from distance geometry calculations are 0.68 ± 0.11 Å for the backbone and 1.32 ± 0.14 Å for all heavy atoms. The solution structure indicates that a tyrosine in the “distal” pocket of CN-Fe(III)Ala80cyt c forms a hydrogen bond with the Fe(III)-CN unit, suggesting that it may play a role analogous to that of the distal histidine in myoglobin in stabilizing the dioxygen adduct.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/5351, author = {Takeuchi, Toshihiko}, title = {The electronic structure of distorted porphyins and cobalt schiff base derivatives as novel enzyme inhibitors}, school = {California Institute of Technology}, year = {1996}, url = {https://resolver.caltech.edu/CaltechTHESIS:11052009-085123252}, 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.
In 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.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/888, author = {Langen, Ralf}, title = {Electron transfer in proteins : theory and experiment}, school = {California Institute of Technology}, year = {1995}, url = {https://resolver.caltech.edu/CaltechETD:etd-03062006-091606}, abstract = {This thesis consists of two main parts and one appendix. The first part (Chapters 2 and 3) contains mainly experimental work on electron transfer in ruthenium-modified azurin mutants. The second part describes theoretical studies on the control of reduction potentials in cytochromes and feredoxins. The appendix presents calculations on the reaction mechanism for the GTP-hydrolysis in Ras p21.
In the experimental part electron tunneling through the beta-sheet in pseudomonas aeruginosa azurin is discussed. In agreement with theoretical consideration it is found that electron tunneling through a beta-strand is quite efficient. It is argued that the efficiency is due to the highly covalent nature of the bridge. Furthermore, the effects of the weakly coordinated M121 ligand and the strongly coordinated C112 ligand on the coupling are compared in Chapters 2 and 3. It is found that indeed the C112 ligand facilitates electron transfer, although the rate enhancement in the experiments does not appear to be much more than an order of magnitude.
The theoretical section (chapters 4-6) presents microscopical calculations of electrostatic effects found to be important for the control of reduction potentials. Chapter 4 analyzes the effect of the N521 mutation in cytochrome c. The calculations suggest that the change in reduction potential is due to an electrostatic effect and dominated by the loss of the N52 dipole, which compensates for the displacement of an internally bound water molecule. In chapter 5 it is concluded that the change in reduction potential for the M80H axial ligand replacement in cytochrome c is due to the effect of the ligand bonding rather than an electrostatic effect. The enormous variations in the reduction potentials of iron-sulfur clusters in several proteins are being investigated in chapter 6. The potentials mainly appear to be controlled by the number of hydrogen bonds. However, in some cases the effect of nearby water molecules need to be considered. The calculations presented in the appendix show that a previously proposed mechanism in Ras P21 does not appear energetically feasible (reprint 1). In reprint 2 an alternative mechanism is proposed.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B. and Richards, John H. and Warshel, Arieh}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/3999, author = {Hodge, Julia A.}, title = {Properties of distorted tetraphenylporphyrins}, school = {California Institute of Technology}, year = {1995}, url = {https://resolver.caltech.edu/CaltechETD:etd-10092007-082429}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
X-ray crystallographic structure determinations reveal that tetrakis(pentafluorophenyl)-porphyrin derivatives substituted with bulky [beta]-substituents undergo a tetrahedral distortion that reduces the macrocyclic symmetry from […] to […]. The nickel complex of [2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(pentafluorophenyl)porphyrin], […], has nitrogen atoms displaced ±0.192 […] and meso-carbons ±0.211 […] from the plane of the porphyrin. Despite large conformational changes, bond distances and angles are essentially conserved for all tetraphenylporphyrins. Electrochemical and UV-vis spectroelectrochemical experiments revealed a novel, ligand-centered two-electron (2e) oxidation for Zn and Mg derivatives. Values for the 1e potentials were calculated from […], the constant for the disproportionation of the singly oxidized product into the doubly oxidized and the neutral species, […], and the Nernst equation. The redox potentials are consistent with semiempirical AM1 calculations that indicate that […] distortion destabilizes the HOMOs […] preferentially over the […] LUMOs whereas halogen substitution lowers the energy of both the HOMO and the LUMO approximately equally. Consistent with the meso-substituent influencing relative ordering, EPR spectra of […], and […], and […] reveal […] and […] HOMOs, respectively. Furthermore, the [beta]-octaethyl and octamethyl tetrakis(pentafluorophenyl)porphyrins undergo a similar net 2e oxidation. Thus, the distortion observed in the neutral molecule appears to mirror an electronically favorable geometry for the doubly oxidized product. An understanding of the sterics and electronics that influence frontier orbital energy levels creates the possibility of tuning porphyrins for a variety of applications: light harvesting, electron transfer, and catalytic reactions involving 2e reductions.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/3473, author = {Birnbaum, Eva Rachel}, title = {The mechanism of catalytic hydrocarbon oxidation by molecular oxygen and halogenated ruthenium and iron porphyrins}, school = {California Institute of Technology}, year = {1995}, url = {https://resolver.caltech.edu/CaltechETD:etd-09112007-142146}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
Highly halogenated ruthenium and iron porphyrins are shown to be active catalysts for alkene oxidation with dioxygen or iodosobenzene. The synthesis and characterization of […]-octachloro-tetrakis(pentafluorophenyl)porphyrinato-ruthenium(II) carbonyl [RuTFPPCl…] and […]-octabromo-tetrakis(pentafluorophenyl)porphyrinato-iron(III) chloride [Fe(TIPPBr[…])Cl] are reported. Crystal structures of RuTFPPC1… and the zinc and free ligand precursor complexes show extensive distortion of the halogenated porphyrin macrocycles due to steric interactions between the b-chlorine atoms and the pentafluorophenyl rings. […]FNMR is developed as a method to characterize both paramagnetic and diamagnetic fluorinated porphyrins in solution. The anodically shifted reduction potentials and red shifted absorptions in the UV-Vis spectroscopy of the halogenated porphyrins are discussed in terms of steric and electronic effects on porphyrin frontier orbitals.
Both Fe(TFPPBr[…])Cl and RuTFPPCl… catalyze the oxidation of cyclohexene with dioxygen and without added coreductant, with 73 and 296 turnovers, respectively, in 24 hours. Although both porphyrins will catalyze reactions with iodosobenzene, showing selectivity consistent with high-valent metal-oxo formation, overall activity with dioxygen is much higher. In accord with earlier work, cyclohexene oxidation by Fe(TFPPBr[…])Cl is consistent with a mechanism involving porphyrin-mediated decomposition of alkyl peroxides, which generates free radicals in solution. Catalysis with RuTFPPCl… is shown to be of a photochemical nature, as irradiation with low energy light results in a dramatic increase in the reaction rate. A reaction mechanism involving olefin binding to the excited ruthenium porphyrin is suggested by laser photolysis experiments. This catalyst represents the first stable, effective metalloporphyrin catalyst for olefin oxidation with dioxygen and light.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Bercaw, John E. and Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/2948, author = {McCleskey, T. Mark}, title = {Design and applications of luminescent inorganic complexes}, school = {California Institute of Technology}, year = {1994}, url = {https://resolver.caltech.edu/CaltechETD:etd-07202005-153301}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
A series of Au(I) phosphine complexes were designed and synthesized to investigate the possibility of room temperature phosphorescence in solution from three different types of transitions: metal-to-ligand-charge-transfer in four coordinate monomers, […] in Au(I) dimers, and […] in two and three coordinate monomers. Solution emission was only observed from the three coordinate Au(I) complexes. The complex […] (dcpe = 1,2-bis-dicyclohexylphosphinoethane) has two isolated AuP3 units and emits at 508 nm in acetonitrile solution with a lifetime of 21 […] and a quantum yield of 0.8 (366 nm excitation). The emission has been assigned as a […] transition with the corresponding absorption band at 370 nm. The excited state is a powerful reductant capable of reducing aryl halides.
Electron transfer (ET) rates were studied from the excited […] to a series of substituted pyridiniums (py+). The low excited state reduction potential (Au(II)/Au(I)) of -2.3 V made it possible to study ET rates at driving forces as high as 2.1 eV. High driving force, bimolecular ET rates were also studied with [Ir(cod)(pz)]2 (IR2; cod = cyclooctadiene, pz = pyrazole). The forward ET rates from Ir2 to py+ increase to the diffusion limit and remain diffusion limited at driving forces as high as 1.60 eV. The recombination ET rates from py to Ir2+ show inverted behavior (rates decrease as the driving force increases) at driving forces > 0.85 eV, representing the first observation of inverted behavior for a bimolecular system. The discrepancy between the forward ET and recombination ET rates is explained by ET to low lying excited states.
On the basis of the emission observed from three coordinate Au(I) complexes, Au(I) was used as a probe for the coordination environment of the active site in Pseudomonas auruginosa azurin. The active site consists a copper center strongly bound to two histidines and a cysteine in a trigonal plane with a disputed axial interaction to […] away. The Au(I)-WT-azurin is stable and emits at 580 nm, indicating that there is little or no interaction with the Metl2l.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/7711, author = {Wuttke, Deborah Sharon}, title = {Preparation, characterization and intramolecular electron-transfer studies of ruthenium-modified cytochromes c}, school = {California Institute of Technology}, year = {1994}, url = {https://resolver.caltech.edu/CaltechTHESIS:05152013-095643991}, abstract = {Redox-active ruthenium complexes have been covalently attached to the surface of a series of natural, semisynthetic and recombinant cytochromes c. The protein derivatives were characterized by a variety of spectroscopic techniques. Distant Fe^(2+) - Ru^(3+) electronic couplings were extracted from intramolecular electron-transfer rates in Ru(bpy)_2(im)HisX (where X= 33, 39, 62, and 72) derivatives of cyt c. The couplings increase according to 62 (0.0060) < 72 (0.057) < 33 (0.097) < 39 (0.11 cm^(-1)); however, this order is incongruent with histidine to heme edge-edge distances [62 (14.8) > 39 (12.3) > 33 (11.1) > =72 (8.4 Å)]. These results suggest the chemical nature of the intervening medium needs to be considered for a more precise evaluation of couplings. The rates (and couplings) correlate with the lengths of a-tunneling pathways comprised of covalent bonds, hydrogen bonds and through-space jumps from the histidines to the heme group. Space jumps greatly decrease couplings: one from Pro71 to Met80 extends the σ-tunneling length of the His72 pathway by roughly 10 covalent bond units. Experimental couplings also correlate well with those calculated using extended Hiickel theory to evaluate the contribution of the intervening protein medium.
Two horse heart cyt c variants incorporating the unnatural amino acids (S)-2- amino-3-(2,2’-bipyrid-6-yl)-propanoic acid (6Bpa) and (S)-2-amino-3-(2,2’-bipyrid-4-yl)propanoic acid ( 4Bpa) at position 72 have been prepared using semisynthetic protocols. Negligible perturbation of the protein structure results from this introduction of unnatural amino acids. Redox-active Ru(2,2’-bipyridine)_2^(2+) binds to 4Bpa72 cyt c but not to the 6Bpa protein. Enhanced ET rates were observed in the Ru(bpy)_2^(2+)-modified 4Bpa72 cyt c relative to the analogous His72 derivative. The rapid (< 60 nanosecond) photogeneration of ferrous Ru-modified 4Bpa72 cyt c in the conformationally altered alkaline state demonstrates that laser-induced ET can be employed to study submicrosecond protein-folding events.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/7676, author = {Larson, Wayne E.}, title = {Synthesis, structure, and photophysics of polypyridophenazine transition-metal complexes}, school = {California Institute of Technology}, year = {1994}, url = {https://resolver.caltech.edu/CaltechTHESIS:05082013-114702641}, abstract = {The condensation of phenanthroline-5,6-dione (phendione) with polyamines is a versatile synthetic route to a wide variety of chelating ligands. Condensation with 2,3- napthalene diamine gives benzo[i]dipyrido[3,2-a:2’,3’-c]phenazine (bdppz) a ligand containing weakly-coupled orbitals of benzophenazine (bpz) and 2,2’ -bipyridinde(bpy) character. The bpy character gives Re and Ru complexes excited-state redox properties; intramolecular electron transfer (ET) takes place to the bpz portion of the ligand. The charge-separated state so produced has an extraordinarily-long 50 µs lifetime. The slow rate of charge recombination arises from a combination of extremely weak coupling between the metal center and the bpz acceptor orbital and Marcus “inverted region” behavior. Molecular orbital calculations show that only 3% the electron density in the lowest unoccupied molecular orbital lies on the bpy atoms of bdppz, effectively trapping the transferred electron on the bpz portion. The rate of charge recombination decreases with increasing driving force, showing that these rates lie in the inverted region. Comparison of forward and back ET rates shows that donor-acceptor coupling is four orders of magnitude greater for photoinduced electron transfer than it is for thermal charge recombination.
Condensation of phendione with itself or tetramines gives a series of binucleating tetrapyridophenazine ligands of incrementally-varying coordination-site separation. When a photoredox-active metal center is attached, excited-state energy and electron transfer to an acceptor metal center at the other coordination site can be studied as a function of distance. A variety of monometallic and homo- and heterodimetallic tetrapyridophenazine complexes has been synthesized. Electro- and magnetochemistry show that no ground-state interaction exists between the metals in bimetallic complexes. Excited-state energy and electron transfer, however, takes place at rates which are invariant with increasing donor-acceptor separation, indicating that a very efficient coupling mechanism is at work. Theory and experiment have suggested that such behavior might exist in extended π-systems like those presented by these ligands.
Condensation of three equivalents of 4,5-dimethyl-1,2-phenylenediamine with hexaketocyclohexane gives the trinucleating ligand hexaazahexamethyltrinapthalene (hhtn). Attaching two photredox-active metal centers and a third catalytic center to hhtn provides means by which multielectron photocatalyzed reactions might be carried out. The coordination properties of hhtn have been examined; X-ray crystallographic structure determination shows that the ligand’s constricted coordination pocket leads to distorted geometries in its mono- and dimetallic derivatives.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/2680, author = {Farid, Ramy Samir}, title = {Electron transfer in rigid and semi-rigid iridium d8-d8 donor-spacer-acceptor complexes}, school = {California Institute of Technology}, year = {1991}, url = {https://resolver.caltech.edu/CaltechETD:etd-06212007-154303}, abstract = {A series of rigid and semi-rigid donor-spacer-acceptor complexes, [Ir(µ-pz*)(CO)(Ph2P-O-C6H4-(CH2)n-py[superscript +]-R)]2(pz* = 3,5-dimethylpyrazolyl; C6H4 = phenylene; py[superscript +] = pyridinium; R = H, 4-tert-butyl, and 4-amide; and n = 0,1,2, and 3, has been synthesized for the purpose of studying photoinduced electron-transfer (ET) reactions. The spacers separating the iridium center (electron donor, Ir2) and pyridinium cation (electron acceptor, py[superscript +]) are based on terminal phosphinite ligands, consisting of a phenylene group and a number of methylene groups ranging from 0 to 3. Three distinct ET reactions can be studied in each complex: singles excited-state electron transfer ([superscript 1]ET), triplet excited-state electron transfer ([superscript 3]ET), and thermal back electron transfer (ET[superscript b]).
Atomic positions, obtained from the X-ray crystal structure of [Ir(µ-pz*)(CO)(Ph2P-O-C6H4-CH3]2 were used as a basis for molecular mechanics calculations, furnishing solution structures for the series of Ir2-py[superscript +] donor-acceptor complexes. These results revealed that the spacers in complexes where n = 0 and n =1 are rigid, and that in complexes where n = 2 and n = 3, the spacers are semi-rigid, taking on either folded or stretched conformations in fluid solution.
Steady-state and time-resolved emission and absorption experiments were employed to determine [superscript 1]ET, [superscript 3]ET, and ET[superscript b] rates in these complexes. The [superscript 1]ET and [superscript 3]ET rates for the n = 2 and n = 3 complexes exhibit Gaussian free-energy dependence, in excellent agreement with classical ET theory (n = 2: [lambda] = 1.10 eV, H[subscript DA] = 26 cm[superscript -1]; n = 3: [lambda] = 1.05 eV and H[subscript DA] = 7 cm[superscript -1]). However, the [superscript 1]ET and [superscript 3]ET rates in n = 0 and n = 1 complexes exhibit dramatically different behavior: the [superscript 3]ET rates in these rigid complexes are on the order of 10,000 times slower than the corresponding [superscript 1]ET rates. H[subscript DA]s for the ET[superscript b] reactions (n = 1,2) are similar to those of the corresponding [superscript 1]ET reactions. These results are discussed in terms of the solution structure parameters obtained for the series of donor-acceptor complexes. Evidence that through-bond and through-space couplings play different roles in singles and triplet electron transfer is presented for the first time.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/2596, author = {Chang, Thomas Kyu-Young}, title = {Gene synthesis, expression, and mutagenesis of azurin}, school = {California Institute of Technology}, year = {1991}, url = {https://resolver.caltech.edu/CaltechETD:etd-06142007-132218}, abstract = {A synthetic gene for the blue copper protein Pseudomonas aeruginosa azurin has been constructed using a novel, stepwise method. This method is designed to synthesize a gene of any size reliably by building only controlled amounts of the gene in each step. Another advantage of this method is that the intermediate plasmids, which are typically present in picomolar amounts, can be amplified through plasmid preparation for editing. Using this approach, the azurin gene was synthesized in five steps.
Both the synthetic genes for azurin and Populus nigra, var italica plastocyanin have been expressed in E. coli. These expressions have been achieved by using a synthetic Shine-Dalgano sequence and the signal sequence for azurin, which directs the transport of the expressed proteins to the periplasmic space of E. coli. The membrane translocation not only facilitates the purification of azurin and plastocyanin but also seems to be required for the proper folding of these proteins. In contrast to these successful expressions, earlier efforts to express plastocyanin in the cytoplasm of E. coli, either directly or as a fusion protein, have been unsuccessful at yielding folded plastocyanin.
Site-saturation cassette mutagenesis was performed in azurin at Methionine 121, one of the four ligands to the copper. Variants that contain each of the other nineteen amino acids as well as the amber stop codon have been identified. Surprisingly, all the variants are stable, as judged by Western blot. Furthermore, all mutants that have been isolated at this position (Asn, Asp, Gly, His, Ile, Leu, Val) have the characteristic blue absorption near 600 nm. Despite such similarity with the wild-type azurin, these mutants seem to have a more flexible copper center. They can lose or incorporate copper at a faster rate than the wild-type protein.
These results, along with those from EPR experiments, suggest that while Methionine 121 is important in giving stability to the copper center and in tuning the redox potential, its contribution to azurin’s spectroscopic properties is small when copper is coordinated to the site. Its spectroscopic contribution apparently becomes more significant when nickel or cobalt resides in the copper site, for the electronic spectra of these derivatives differ markedly from that of azurin with copper. It is likely that the copper centers of the mutants are flexible enough to accommodate the preferred geometries of nickel and cobalt, whereas it is more rigid in the wild-type. Finally, several mutants of azurin are proposed that are designed to probe systematically specific aspects of the biological electron transfer mechanism.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Richards, John H. and Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/2778, author = {Jacobs, Bradley Anson}, title = {Preparation, characterization, and intramolecular electron transfer in pentaammineruthenium-modified derivatives of cytochrome b5 and azurin}, school = {California Institute of Technology}, year = {1991}, url = {https://resolver.caltech.edu/CaltechETD:etd-06292007-133449}, abstract = {Wild-type, mutant, and deuteroporphyrin-substituted bovine cytochrome b5 have been modified with pentaammineruthenium (a5Ru) for intramolecular electron-transfer (ET) studies. The reactivity of the three surface histidines of the wild-type trypsinsolubilized protein (WT-b5) with [a5Ru(OH2)]2+ increases in the order His-15 < His-80 < His-26. Intramolecular ET rates from Fe(II) to Ru(IlI) have been measured by flash photolysis for a5Ru(His-26)-modified WT-b5, Ru(H26)WT-b5; mutant (asn-57 to Asp, Gln-13 to Glu, Glu-11 to Gln, His-15 to Asn, His-80 to Asn) lipase-solubilized cyt b5, Ru(H26)LM-b5; and deuteroporphyrin-substituted WT-b5, Ru(H26)DP-b5. The observed rates display a weak concentration dependence (0.5 - 3 µM protein, µ = 0.5 M sodium phosphate, ph 7.0 25°C): kET = 1.4(1)s[superscript-1], Ru(H26)WT-b5; 5.9(5) s[superscript-1], Ru(H26)LM-b5; and 0.2(1)s[superscript-1], Ru(H26)DP-b5. The rates do not directly correspond to differences in driving force (-0.08, -0.10, -0.13 eV) or edge-to-edge, donor-acceptor separation (12.1, 12, 12.9 A). Evaluation of the donor-acceptor electronic coupling (HAB) in terms of specific through-bond and through-space interactions in the intervening medium for Ru(H26)WT-b5 and Ru(H26)LM-b5 revealed a probable ET pathway consisting of eight covalent bonds from C[gamma] of His-26 to the end of the Leu-25 side chain, then a through-space jump (R = 3.8, 3.7 A) to the heme 2-vinyl. Ru(H26)DP-b5 lacks the 2-vinyl, requiring a longer jump (R = 4.5 A) to the heme 3-methyl. Because HAB is predicted to decay rapidly with R, the calculated rate constants (assuming [lambda] = 1.2 eV reflect the differences in R for the three derivatives: Ru(H26)WT-b5, 1.9 s[superscript-1]; Ru(H26)LM-b5, 4.4 s[superscript-1]; Ru(H26)DP-b5, 0.16 s[superscript-1]. The close agreement of calculated and observed rate constants indicates that the electronic coupling in this system is reasonably described by the (His-26)(Leu-25)(through-space jump to heme) pathway. The ET rate in a mutant (His-26 to Arg), trypsin-solubilized cyt b5 modified with a5Ru3+ at His-80 was also measured. As expected from the long donor-acceptor separation (21 A) and poor electronic coupling predicted by pathway analysis, kET was within experimental error of 0 s[superscript-1].
Azurin from Alcaligenes denitrificans was singly modified at His-83 with asRu3+; the other surface histidine (32) was not successfully modified. The intramolecular ET rate from Ru(II) to Cu(II) for Ru(H83)Az was measured (1.0(3) s[superscript-1]) and was found to be comparable to that reported for the analogous ruthenium-modified P. a. azurin. These rates are slower than would be expected for a similar distance in cytochrome c. The application of a pathway theoretical model to both the P. a. and A. d. azurin systems showed no evidence that the ß-sheet secondary structure of azurin precludes effective electronic coupling. This suggests that weak electronic coupling to the copper site itself is responsible for the low kET’s in azurin.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/2598, author = {Brewer, John C.}, title = {Syntheses, characterizations and reactivity of trans-dioxorhenium(V) and -(VI) complexes}, school = {California Institute of Technology}, year = {1991}, url = {https://resolver.caltech.edu/CaltechETD:etd-06142007-144656}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
The synthesis, electronic structure and reactivity of trans-dioxorhenium(V) and -(VI) complexes have been examined in detail. An improved general synthesis of trans-[ReO2(L)4]X complexes is presented. The amine complex [ReO2(en)2]I can be made in 90% yield from ReO2(PPh3)2I and ethylenediamine in less than 15 minutes at room temperature. Refluxing methanol suspensions of ReO2(PPh3)2I with 12-50 equivalents of electron-rich pyridines results in the formation of [ReO2L4]I compounds in 50 to 85% yield.
Systematic substituent studies reveal the influence of ancillary ligands on the physical properties of trans-[ReO2(L)4][PF6] compounds. The Re(VI)/Re(V) redox couple is a linear function of pyridine ligand […] (ReVI/Re/V) = (0.96 + […]) V vs. Fc+/Fc. The dxy/dxz,dyz energy gap is also a linear function of pyridine […]; increasing the pyridine basicity lowers the energy of the dxy […] dxz,dyz transition and the energy of the […] excited state. The excited-state properties of trans-[ReO2(L)4][PF6] pyridine complexes follow a trend consistent with the energy-gap law.
Strongly basic 4-dialkylaminopyridine ligands stabilize d(1) trans-dioxorhenium(VI) complexes. Analysis of the X-ray structure of trans-[…] shows that there is considerable shortening (0.04 A) in the Re-N bond lengths relative to Re(V) analogues, but the Re-oxo bond lengths are virtually the same in both oxidation states. The EPR spectrum of the d(1) ion trans-[…] (dmap = 4-dimethylaminopyridine) has been measured in a 50% DMSO/H2O glass at 7 K. Analysis of the spectrum gives g[…] = 1.91, A[…] = 0.031 cm(-1), g|| = 1.83, A|| = 0.060 cm(-1), and Qz = 0.0075 cm(-1). Because of the large quadrupole coupling, the forbidden ([…] = ±1, ±2) transitions are quite intense and some are stronger than the allowed ([…] = 0) transitions. Comparison of Qz values and dxy […] dxz,dyz transition energies for trans-reO2(dmap)4 and related monooxo and mononitrido complexes confirms that the ligand-field splitting associated with the multiply bonded units increases in the order ReO(4+) < ReN(3+) < ReO2(2+).
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/8790, author = {Zewert, Thomas Edward}, title = {Electron transfer in chemically and genetically modified myoglobins}, school = {California Institute of Technology}, year = {1990}, url = {https://resolver.caltech.edu/CaltechTHESIS:03182015-162901623}, abstract = {The temperature dependences of the reduction potentials (Eo’) of wildtype human myoglobin (Mb) and three site-directed mutants have been measured by using thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. At pH 7.0, reduction of the heme iron (III) in the former two proteins is accompanied by uptake of a proton by the protein. The changes in Eo’, and the standard entropy (ΔSo’) and enthalpy (ΔHo’) of reduction in the mutant proteins were determined relative to values for wild-type; the change in Eo’ at 25°C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. Reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues, and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.
Through analysis of the temperature dependence and shapes of NMR dispersion signals, it is determined that a water molecule is bound to the sixth coordination site of the ferric heme in the Val68Asp and in the Val68Asn recombinant proteins while the carboxyl group of the sidechain of Glu68 occupies this position in Val68Glu. The relative rhombic distortions in the ESR spectra of these mutant proteins combined with H217O and spin interconversion experiments performed on them confirm the conclusions of the NMRD study.
The rates of intramolecular electron transfer (ET) of (NH3)5Ru-His48 (Val68Asp, His81GIn, Cys110AIa)Mb and (NH3)5Ru-His48 (Val68GIu,His81GIn,Cys110Ala)Mb were measured to be .85(3)s-1 and .30(2)s-1, respectively. This data supports the hypothesis that entropy of 111 reduction and reorganization energy of ET are inversely related. The rates of forward and reverse ET for (NH3)5 Ru-His48 (Val68GIu, His81 GIn, Cys110AIa)ZnMb -7.2(5)•104s-1and 1.4(2)•105s-1, respectively- demonstrate that the placement of a highly polar residue nearby does not significantly change the reorganization energy of the photoactive Zn porphyrin.
The distal histidine imidazoles of (NH3)4isnRu-His48 SWMb and (NH3)5Ru-His48 SWMb were cyanated with BrCN. The intramolecular ET rates of these BrCN-modified Mb derivatives are 5.5(6)s-1 and 3.2(5)s-1, respectively. These respective rates are 20 and 10 times faster than those of their noncyanated counterparts after the differences in ET rate from driving force are scaled according to the Marcus equation. This increase in ET rate of the cyanated Mb derivatives is attributed to lower reorganization energy since the cyanated Mb heme is pentacoordinate in both oxidation states; whereas, the native Mb heme loses a water molecule upon reduction so that it changes from six to five coordinate. The reorganization energy from Fe-OH2 dissociation is estimated to be .2eV. This conclusion is used to reconcile data from previous experiments in our lab. ET in photoactive porphyrin-substituted myoglobins proceed faster than predicted by Marcus Theory when it is assumed that the only difference in ET parameters between photoactive porphyrins and native heme systems is driving force. However, the data can be consistently fit to Marcus Theory if one corrects for the smaller reorganization in the photoactive porphyrin systems since they do not undergo a coordination change upon ET.
Finally, the intramolecular ET rate of (NH3)4isnRu-His48 SWMb was measured to be 3.0(4)s-1. This rate is within experimental error of that for (NH3)4pyrRu-His48 SWMb even though the former has 80mV more driving force. One likely possibility for this observation is that the tetraamminepyridineruthenium group undergoes less reorganization upon ET than the tetraammineisonicotinamideruthenium group. Moreover, analysis of the (NH3)4isnRu-His48 SWMb experimental system gives a likely explanation of why ET was not observed previously in (NH3)4isnRu-Cytochrome C.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/8545, author = {Sweeney, Robert Joseph}, title = {Hydrogen-Atom Transfer Photochemistry of Tetrakis(µ-pyrophosphito)diplatinate(II)}, school = {California Institute of Technology}, year = {1990}, url = {https://resolver.caltech.edu/CaltechTHESIS:07162014-152027500}, abstract = {In many senses, the hydrogen-atom transfer reactions observed with the triplet excited state of pyrophosphito-bridged platinum(II) dimers resemble the reactions of organic ketone nπ* states. The first two chapters describe our attempts to understand the reactivity differences between these two chromophores. Reactivity of the metal dimers is strongly regulated by the detailed nature of the ligands that ring the axial site, the hydrogen-abstraction center. A hydrogen-bonded network linking the ligands facilitates H-atom transfer quenching with alcohols through the formation of a hydrogen-bonded complex between the alcohol and a dimer. For substrates of equal C-H bond strength that lack a hydroxyl group (e.g., benzyl hydrocarbons), the quenching rate is several orders of magnitude slower.
The shape and size of the axial site, as determined by the ligands, also discriminate among quenchers by their steric characteristics. Very small quenchers quench slowly because of high entropies of activation, while very large ones have large enthalpic barriers. The two effects find a balance with quenchers of “just the right size.”
The third chapter discusses the design of a mass spectrometer that uses positron annihilation to ionize neutral molecules. The mass spectrometer creates positron-molecule adducts whose annihilation produces fragmentation products that may yield information on the bonding of positrons in such complexes.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/2HE2-C733, author = {Harvey, Erica Lyn}, title = {Photochemical hydrogen atom transfer reactions of binuclear platinum complexes}, school = {California Institute of Technology}, year = {1990}, doi = {10.7907/2HE2-C733}, url = {https://resolver.caltech.edu/CaltechETD:etd-06112007-134908}, abstract = {This thesis focuses on hydrogen atom (H-atom) transfer reactions of the lowest electronic excited state of the d8 dimer [Pt2(P2O5H2)4]4- (the ground state is abbreviated Pt2]; the lowest excited state is a long-lived triplet, abbreviated 3Pt2). Factors that influence initial rates of reaction of the excited state with alcohol and hydrocarbon H-atom donors are examined in Chapter 2. Observation of a large kinetic deuterium isotope effect (kH/kD=4) for phosphorescence quenching by [alpha]-secphenethyl alcohol verifies the importance of bond strength in determining reaction rates. A plot of H-atom abstraction rates versus C-H bond strengths reveals that bond strength is not the sole determinant of abstraction rate, however. Faster rates are observed when an [alpha]-hydroxy functionality is present, and the size of the substrate also influences abstraction rates. Chapter 3 features characterization of a diplatinum dihydride complex (Pt2H2) that acts as a key intermediate in H-atom transfer reactions. 3Pt2 reacts with hydrogen-atom donors to give a complex characterized by strong absorption at 314 nm; NMR (1H and 31P) and IR spectroscopic studies show that the complex is an axial dihydride (Pt2H2). Reactions of Pt2H2 include photochemical release of H2, rapid thermal reduction of O2, and thermal reduction of HCl to H2. Chapter 4 describes synthesis and characterization of a derivative of Pt2 modified by substitution of electron-withdrawing BF2+ groups for ligand H+. The new compound exhibits photophysical properties (phosphorescence lifetime, quantum yield, absorption and emission maxima) virtually identical with those of 3Pt2*, but dramatically shifted ground-state electrochemical properties (peak potential for oxidation shifted +750 mV). Comparisons of thermal reactivity (preparation of axial dihalide and dihydride complexes) and photochemical reactivity (reductive quenching and H-atom transfer quenching) of the two platinum dimers, detailed in Chapter 5, provide further insight into the factors influencing H-atom transfer in binuclear d8-d8 compounds.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/8019, author = {Zietlow, Miriam Heinrichs}, title = {Chemistry of low-valent platinum dimers}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechTHESIS:10282013-161114555}, abstract = {Physical and chemical properties of low-valent platinum dimers, namely [Pt_2(P_2O_5H_2)4]^(4-) and Pt_2(µ-dppm)_2Cl_2, have been investigated using a variety of structural and spectroscopic techniques.
Platinum(II) d8-d8 dimers have been shown to exhibit much thermal and photochemical reactivity. Chapter 2 describes studies aimed at elucidating the excited state reduction potenetial of [Pt_2(P_2O_5H_2)4]^(4-), Pt_2, in organic media. By conducting excited state electron transfer studies using derivatized pyridiniums and benzophenones, the excited state reduction potential has been estimated to be ~2 V. The Pt_2 complex undergoes partial oxidation to form Pt(II,III) linear chains. Chapter 3 describes the structural and spectroscopic techniques used to determine the translational symmetries of these [Pt_2(P_2O_5H_2)4]^(4-) (X = Cl, Br), Pt_2X, chains. Pt_2Br has been found to be intermediate between (AAB)_n and (AABCCB)_n, while, Pt_2Cl is of (AABCCB)_n translational symmetry. Investigations into the electronic transitions of Pt_2Cl and Pt_2Br were conducted using high pressure techniques and are presented in Chapter 4. The Pt_2X electronic spectrum exhibits bands attributable to the reduced Pt2 complex and the oxidized Pt_2X_2 complex [Pt_2(P_2O_5H_2)4]^(4-) along with an intervalence charge-tranfer band characteristic of a mixed-valence solid.
Photophysical investigations of a new luminescent chromophore, Pt_2(µ-dppm)_2Cl_2, a d9-d9 dimer, and its analogs are described in Chapter 5. The absorption band directly responsible for the observed emission is believed to be very weak and, as of yet, unobserved. Attempts to determine the spin multiplicty and approximate energy of this unobserved transition are described in Chapter 6. Excited-state energy transfer studies indicate that this absorption band is a triplet transition at -13,000 cm^(-1). Although, the Pt_2(µ-dppm)_2Cl_2 excited state is non-luminescent in fluid solution, it has been shown to undergo thermal electron transfer to tetracyanoethylene and photoinduced electron transfer to methylviologen. These experiments are presented in Chapter 7. Preliminary studies, described in Chapter 8, of non-bridged d9-d9 platinum(I) dimers have shown that [Pt_2(CNCH_3)_6]^(2+) serves as a versatile precursor in the synthesis of new d8-d8 A-frame complexes.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/7943, author = {St. Clair, Cynthia Strong}, title = {Electrochemical and Electron Transfer Investigations of Copper Proteins}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechTHESIS:08262013-120637323}, abstract = {A study of the pH and temperature dependence of the redox potentials of azurins from five species of bacteria has been performed. The variations in the potentials with pH have been interpreted in terms of electrostatic interactions between the copper site and titrating histidine residues, including the effects of substitutions in the amino acid sequences of the proteins on the electrostatic interactions. A comparison of the observed pH dependences with predictions based on histidine pK_a values known for Pseudomonas aeruginosa (Pae), Alcaligenes denitrificans (Ade), and Alcaligenes faecalis (Afa) azurins indicates that the Pae and Ade redox potentials exhibit pH dependences in line with electrostatic arguments, while Afa azurin exhibits more complex behavior. Redox enthalpies and entropies for four of the azurins at low and high pH values have also been obtained. Based on these results in conjuction with the variable pH experiments, it appears that Bordetella bronchiseptica azurin may undergo a more substantial conformational change with pH than has been observed for other species of azurin.
The temperature dependence of the redox potential of bovine erythrocyte superoxide dismutase (SOD) has been determined at pH 7.0, with potassium ferricyanide as the mediator. The following thermodynamic parameters have been obtained (T = 25°C): E°’ = 403±5 mV vs. NHE, ΔG°’ = -9.31 kcal/mol, ΔH°’ = -21.4 kcal/mol, ΔS°’ = -40.7 eu, ΔS°’_(rc) = -25.1 eu. It is apparent from these results that ΔH°‘, rather than ΔS°’, is the dominant factor in establishing the high redox potential of SOD. The large negative enthalpy of reduction may also reflect the factors which give SOD its high specificity toward reduction and oxidation by superoxide.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/5355, author = {Smith, David Charles}, title = {Electronic structure and photochemical reactivity of binuclear metal complexes}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechTHESIS:11052009-142520920}, abstract = {A valence bond (VB) “weak coupling” model of the electronic structure for Ir_2(TMB)_4_2 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. Photophysical characterization of the ^(1,3)(dσpσ) excited state of Ir_2(TMB)4^(2+) finds a system quite comparable to other binuclear d^8 complexes. Both fluorescence (λ(max) 735 nm, τ ~ 70 ± 30 ps) and phosphorescence (λ_(max) 1080 nm, τ = 210 ± 20 ns) are observed. The relatively long lifetime of the ^3(dσpσ) excited state of Ir_2(TMB)_4^(2+) 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_2 unit (the dσ* orbital) and an electron localized in the interior of the dimer cage (the pσ 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^8 complexes. The ^3(dσ*pσ) excited state of Ir_2(TMB)_4^(2+) is found to be a powerful reductant, E^0(Ir_2(TMB)_4^(3+/3)(Ir_2(TMB)_4^(2+))*) ~ 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, K ~ 0.0001, because of the large donor-acceptor separation, ~ 8 Å. The results for Ir_2(TMB)_4^(2+) are discussed in comparison to those for [Ir(µ-pz)COD]_2. Ir_2(TMB)_4^(2+) is found to react photochemically with alkyl halides. Although the ^3(dσpσ) excited state is a good reductant, outer-sphere electron transfer seems unlikely (E^0(RX/RX-) < -1.5 V (SSCE)). An S_(RN)1 pathway has been suggested to explain the alkyl halide photoreduction reaction observed for metal complexes with E0(M_2+/3M_2) < -1.5 V (SSCE); however, atom transfer to the ^3(dσ*pσ) excited state is the favored reaction mechanism for the alkyl halide photoreduction reaction of Ir_2(TMB)_4^(2+). The generality of this reaction is discussed. While there is some ambiguity as to the primary photoprocess for alkyl halide photoreactivity, ^3(dσ*pσ) excited-state hydrogen-atom transfer has been established as the mechanism of the reaction of Ir_2(TMB)4^(2+) and a number of organic substrates. The atom-transfer reactivity of the ^3(dσpσ) excited state is attributed to the presence of a hole in the dσ orbital, analogous to the 3nπ* state of organic ketones. Interaction of the oxidizing hole with the electron pair of the C-H bond is the presumed pathway. Electrochemical oxidation of Rh2(TMB)_4^(2+) generates the d8-d7 species Rh_2(TMB)_4^(3+). This complex reacts with 1,4-cyclohexadiene to abstract a hydrogen atom mimicking the initial step of the ^3(dσ*pσ) 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^8 complexes. The d7-d7 dihydride product obtained from the photoreaction of Ir_2(TMB)_4^(2+) 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.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Goddard, William A., III}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/2499, author = {Fox, Lucius Seiberling}, title = {Intramolecular electron transfer in an iridium d [supercript 8]-d [superscript 8] donor-acceptor system}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechETD:etd-06072007-081509}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
A series of donor-acceptor complexes, […] 2,4,6-trimethylpyridinium, 4-methylpyridinium, pyridinium, and 4-phenylpyridinium; […], have been synthesized for studying the rate of photoinduced electron transfer from the metal localized […] excited states of […] chromophores. The pyridinium electron acceptors are covalently attached to the iridium metal centers (donor) via a three atom hydrocarbon linker bound to the terminal phosphine ligands. The x-ray crystallographic structure of […] reveals a metal-metal distance of 3.219(1) […] and a solid state donor-acceptor separation of 5.34(1) […]. Additional donor-acceptor separations and orientations are available to the compounds in fluid solution through rotations about the Ir-P and linker group C-O, C- N, and C-C bonds. Steady state emission spectra show that the fluoresence and phosphoresence quantum yields in these compounds are substantially reduced relative to a appropriate model complex. To date the excited state reactivity of […] metal dimers has been exclusively attributed to their […] states. These findings represent the first evidence for reactivity from a shorter lived […] state.
Picosecond and nanosecond laser flash-photolysis techniques were employed to measure the rates of photoinduced electron transfer and charge recombination in these systems. Values of […], obtained from these studies, vary between […] and […] as a function of reaction exoergicity […]. Clear evidence for the inverted behavior predicted by classical and semiclassical electron transfer models is seen at high driving force. Rate constants for reactions involving the […] and […] excited states, as well as the rates of charge recombination are characterized by very similar values of […] and […]. Our data are adequately modeled by the classical theory of electron transfer proposed by Marcus […] or by a semiclassical model for […] where nuclear tunneling involves a low frequency metal-ligand mode […]. These findings are explored with regard to utilizing the donor-acceptor complexes as molecular photochemical energy storage systems.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/2520, author = {Karas, Jennifer Lynn}, title = {Long-range electron transfer in ruthenium-labelled myoglobin}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechETD:etd-06082007-092426}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
The driving force dependence of electron-transfer (ET) reactions has been investigated in protein derivatives of the type trans-Ru(NH3)4L-myoglobin (L=NH3, pyridine, isonicotinamide). In these species, the labelling sites of the ruthenium moiety were determined by proton NMR spectroscopy. ET rates have been measured from the iron(II)-heme in myoglobin to both a5Ru (a=NH3) and a4pyRu (py=pyridine) acceptors bound to histidine 48 (kET=0.04 and 2.5 s-1; [delta]E°=0.02 and 0.275, respectively). These kinetic results demonstrate for the ruthenium-labelled Mb system that long-range ET is reversible and that the dependence of the ET rates on reaction free energy closely follows Marcus theory. ET rates were also determined for high driving-force systems that were prepared by substitution of palladium and zinc(mesoporphyrin IX), (PdP, ZnP) into the a4LRu(His-48) derivatives of Mb. ET from the excited state MbMP* (M=Pd or Zn) to the ruthenium acceptor was measured by transient spectroscopy. Reverse ET rates from the surface RuII to the ZnP radical cation, (RuII[…]ZnP+) were also determined. The ET rates range from 0.04 s-1 for FeII[…]RuIII ET in a5Ru(His-48)MbFe ([delta]E°=0.02 V), to 3x10(5) s-1 for ZnP*[…]RuIII in a4isnRu(His48)MbZn ([delta]E°=1.2 V). The driving force dependence of the ET rates in the ruthenium-labelled Fe, Zn and Pd(His-48)Mb derivatives has provided information on the reorganization energy. Using Marcus theory, a reorganization energy of 1.5(2) eV has been estimated.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/7946, author = {Selman, Mary}, title = {Preparation and characterization of an intramolecular electron transfer in a pentaammineruthenium derivative of Candida krisei cytochrome c}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechTHESIS:08262013-151906759}, abstract = {A semisynthetic binuclear metalloprotein has been prepared by appending the pentaammineruthenium moiety to histidine 39 of the cytochrome c from the yeast Candida krusei. The site of ruthenium binding was identified by peptide mapping. Spectroscopic and electrochemical properties of the derivative indicate the protein conformation is unperturbed by the modification. A preliminary (minimum) rate constant of 170s^(-1) has been determined for the intramolecular electron transfer from ruthenium(II) to iron(III), which occurs over a distance of at least 13Å (barring major conformational changes). Electrochemical studies indicate that this reaction should proceed with a driving force of ~170mV. The rate constant is an order of magnitude faster than that observed in horse heart cytochrome c for intramolecular electron transfer from pentaammineruthenium(II)(histidine 33) to iron(III) (over a similar distance, and with a similar driving force), suggesting a medium or orientation effect makes the Candida intramolecular electron transfer more favorable.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/1862, author = {Kormann, Claudius}, title = {Synthesis and characterization of quantum size metal oxide colloidal particles. Photocatalytic peroxide formation on ZnO and TiO2}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechETD:etd-05182007-110357}, abstract = {The syntheses of transparent colloidal solutions of extremely small ZnO (d< 5nm) and Ti02 (d< 3 nm) particles in water, alcohol, and acetonitrile are presented. Quantum size effects are observed during particle growth and at final stages of synthesis. They are qualitatively and quantitatively (TiO2) interpreted by using a simple molecular orbital (MO) picture and a quantum mechanical model developed by Brus. The optical absorption and fluorescence properties as well as the surface acid-base properties are characterized in detail. The two materials are shown to be active photocatalysts in the formation and degradation of H2O2 and organic peroxides and in the degradation of chlorinated hydrocarbons. Quantum yields and steady state concentrations are given as function of various reaction parameters such as the oxygen concentration, the nature and concentration of electron donor, pH, and charge of the electron donor. Rates of reaction are correlated with surface speciation as calculated by the SURFEQL computer code. Transparent colloidal solutions of Fe2O3 (hematite) have also been prepared, however only negligible photocatalytic activity is found when compared to ZnO and TiO2. Evidence is presented for OH radical activity when aqueous TiO2 suspensions are illuminated at high pH.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Hoffmann, Michael R.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/7949, author = {Thorp, H. Holden}, title = {The photochemistry of dioxorhenium(V)}, school = {California Institute of Technology}, year = {1989}, url = {https://resolver.caltech.edu/CaltechTHESIS:08272013-140559569}, abstract = {The excited-state properties of trans-ReO2(py)4+ (ReO2+) in acetonitrile solution have been investigated. The excited-state absorption spectrum of ReO2+ is dominated by bleaching of the ground state MLCT and d-d systems. The reduction potential of ReO22+/+* is estimated from emission and electrochemical data to be -0.7 V (SSCE). The ReO2+ excited state efficiently reduces methylviologen and other pyridinium and olefin acceptors. The resulting Re(VI) species oxidizes secondary alcohols and silanes. Acetophenone is the product of sec-phenethyl alcohol oxidation.
The emission properties of ReO2+ in aqueous solutions of anionic and nonionic surfactants have been investigated. The emission and absorption maxima of ReO2+ are dependent on the water content of its environment. Emission lifetimes vary over four orders of magnitude upon shifting from aqueous to nonaqueous environments. The emission lifetime has a large (8.6) isotope effect (k(H2O)/k(D2O)) that reflects its sensitivity towards the environment. These properties have been used to develop a model for the interactions of ReO2+ with sodium dodecyl sulfate (SDS). A hydrophobic ReO2+ derivative, ReO2(3-Ph-py)4+, has been used to probe micelles of nonionic surfactants, and these results are consistent with those obtained with SDS.
The emission properties of ReO2+ in Nafion perfluorosulfonated membranes have been investigated. Absorption and emission spectroscopy indicate that the interior of the membrane is quite polar, similar to ethylene glycol. Two well-resolved emission components show different lifetimes and different isotope effects, indicative of varying degrees of solvent accessibility. These components are taken as evidence for chemically distinct regions in the polymer film, assigned as the interfacial region and the ion cluster region.
The unsubstituted pyridine complex shows monophasic, τ = 1.7 µs, emission decay when bound to calf thymus DNA. Switching to the 3-Ph-py complex yields a biphasic emission decay (τ1 = 2.4 µs, τ2 = 10 µs) indicative of an additional, solvent-inaccessible binding mode. Photoinduced electron transfer to methylviologen leads to oxidative cleavage of the DNA as detected by gel electrophoresis. Electrochemical and spectrophotometric techniques used with organic substrates also can be used to monitor the oxidation of DNA. Abstraction of the ribose 4’ hydrogen by ReO22+ is a possible mechanism.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/YJKW-3133, author = {Mayo, Stephen Leon}, title = {Electron Transfer in Structurally Engineered Metalloproteins}, school = {California Institute of Technology}, year = {1988}, doi = {10.7907/YJKW-3133}, url = {https://resolver.caltech.edu/CaltechETD:etd-04292004-095332}, abstract = {This thesis is concerned with experimental approaches for studying electron transfer in metalloproteins. The material presented traces the development of experimental techniques aimed at elucidating the mechanism of intramolecular metalloprotein electron transfer. The first chapter includes a reprint of an Inorganic Chemistry paper that describes the bimolecular reaction of small inorganic redox complexes with blue-copper proteins. The second chapter illustrates the use of covalently attached redox probes for studying rate-distance relationships. And the third chapter documents our progress in using genetic methods to structurally engineer yeast iso-1 cytochrome c into an idealized system for studying the distance dependence of intramolecular electron-transfer events.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Campbell, Judith L.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11439, author = {Axup, Andrew William}, title = {Laser Flash Spectroscopy of Zinc/Ruthenium Myoglobins: An Investigation of Distance and Medium Effects on Photoinduced Long-Range Intraprotein Electron Transfers}, school = {California Institute of Technology}, year = {1987}, url = {https://resolver.caltech.edu/CaltechTHESIS:04052019-103258317}, abstract = {An experimental investigation of the distance dependence of long-range intramolecular electron transfer in ruthenium-modified zinc myoglobins has been performed. The zinc/ruthenium-modified metalloproteins were prepared by substitution of zinc-mesoporphyrin IX diacid (ZnP) into four previously characterized pentaammineruthenium(III) (a5Ru) derivatives of sperm whale myoglobin (Mb). The derivatives are a5Ru(His-48)Mb, a5Ru(His-12)Mb, a5Ru(His-116)Mb, and a5Ru(His-81)Mb. Pulsed laser excitation of the zinc myoglobin produces the long-lived and highly reducing triplet excited state (3ZnP). Electron transfer from this triplet to the ruthenium, 3znP-Ru3+ → ZnP+-Ru2+ (ΔE° ≅ 0.8 V), was measured by time-resolved transient absorption techniques. The observed electron-transfer rates are 7.0 x 104, 100, 89, and 85 s-1 for the His-48, -12, -116, and -81 derivatives, respectively, at 25°C The electron-transfer distances were evaluated using computer modelling in which rotation about the Cα-Cβ bond of the imidazole side chain in the ruthenium-modified histidines is restricted by nonbonded repulsions with atoms at the protein surface. Recent crystallographic results for a5Ru(His-48)Mb indicate that the histidine has considerable rotational flexibility. The estimated accessible distances, both heme edge to inner coordination sphere ligand (e-e) and metal-to-metal (m-m), are as follows. For the His-48 derivative, the e-e range is 13.4-16.6 Å and the m-m range is 18.6-24.1 Å; His-12 ranges are 22.1-22.4 Å and 28.8-30.4 Å; His-116 ranges are 18.9-20.4 Å and 23.1-27.8 Å; and His-81 ranges are 19.0-19.4 Å and 26.3-26.9 Å. In addition, the orientation angles (θ) of the electron-transfer pathways with relation to the heme plane at a position of closest approach are 25° (His-48), 20° (His-12), 35° (His-116), and 25° (His-81). Fitting the rate data to an exponential distance dependence yields the expression ket = 8 x 109 exp(-β(R-4)) s-1, where β = 1.2 Å-1 and R - 4 ≥ 0 (R is the minimum e-e distance in Å). The electron-transfer rate in a5Ru(His-12)Mb(ZnP) is anomalously high (100 vs. 2 s-1 predicted by the rate-distance equation), thereby indicating that the 3ZnP*-Ru3+ electronic coupling may be enhanced by an intervening tryptophan residue that lies parallel-planar to the heme along the reaction pathway. Activation enthalpies calculated from the temperature dependences of the electron-transfer rates over the range 5-40°C are 1.7 ± 1.6 (His-48), 4.7 ± 0.9 (His-12), 5.4 ± 0.4 (His-116), and 5.6 ± 2.5 (His-81) kcal mol-1. Dynamic flexibility of the protein region containing His-48 may reduce the activation enthalpy with respect to the other more rigidly located derivatives.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11397, author = {Marshall, Janet Layne}, title = {Spectroscopy and Photochemistry of Pyrazolyl-Bridged Binuclear Iridium(I) Complexes}, school = {California Institute of Technology}, year = {1987}, url = {https://resolver.caltech.edu/CaltechTHESIS:02192019-111735898}, abstract = {Spectroscopic studies of a series of pyrazolyl-bridged and substituted-pyrazolyl-bridged binuclear iridium(I) complexes indicate that the description of the metal-metal interactions in previously studied D4h d8-d8 rhodium(I), iridium(I), and platinum(II) species may be extended to these lower symmetry (C2v) d8-d8 molecules. Specifically, the 1A1(dσ)2 (dσ)2 ground state exhibits weak metal-metal bonding, and the lowest excited states are a singlet (1B2) and triplet (3B2) derived from the (dσ)2(dσ)1(pσ)1 electronic configuration. The 1B2 and 3B2 excited states, which are expected to feature strong metal-meta1 bonding, are 1uminescent at ambient temperature in fluid solution.
Electronic absorption and emission spectroscopic studies and photophysical investigations of the emissive singlet and triplet excited states of bis(1,5-cyclooctadiene)bis(µ-pyrazolyl)diiridium(I), [Ir(µ-pz)(COD)]2, and analogous substituted-pyrazolyl complexes are presented in Chapter 2. The absorption spectrum of [Ir(µ-pz)(COD)]2 exhibits an intense band attributable to 1A1 → 1B2 at 498 nm (ε = 8100 M-1cm-1). Both fluorescence (λmax = 558 nm, Φem = 0.0001, τ < 20 ps) and phosphorescence (λmax = 684 nm, Φem = 0.0078, τ = 250 ns) from the 1B2 and 3B2 excited states, respectively, are observed at ambient temperature for this complex. The absorption and emission spectra of the substituted-pyrazolyl complexes show similar features. In addition, ground-state resonance Raman studies of these complexes suggest the presence of a reasonable metal-metal bonding interaction in the formally nonbonded binuclear center; excitation into the bands corresponding to the metal-metal localized 1A1 → 1B2 transition results in resonance-enhancement of vibrations at frequencies of of 58 cm-1 to 80 cm-1 that are assigned to ν(Ir-Ir ).
The long lifetime of the 3B2(dσ*pσ) excited state of [Ir(µ-pz)-(COD)]2 implies that it should be able to participate in bimolecular reactions. The results presented in Chapter 3 show that this strongly reducing excited state undergoes photoinduced electron transfer with a variety of substrates including reversible electron transfer to one-electron acceptors such as methyl viologen and pyridinium monocations. For pyridinium acceptors with reduction potentials ranging from -0.67 V to -1.85 V vs. SSCE, the rates of electron-transfer quenching range from a diffusion-limited rate of 2.0 x 1010 M-1s-1 to 1.1 x 106 M-1s-1 and obey Marcus-theory predictions for outer-sphere electron transfer in the “normal free-energy region.” However, the rates do not decrease as predicted for the “inverted free-energy region.” With acceptors such as halocarbons, the unproductive back-electron-transfer reaction can be circumvented, and net two-electron, photoinduced electron transfer yields iridium(II)-iridium(II) oxidative addition products.
Chapter 4 focuses on spectroscopic and photophysical investigations of pyrazolyl-bridged binuclear iridium(I) complexes containing carbon monoxide ligands. Spectroscopic studies of tetracarbonylbis(µ-pyrazolyl)diiridium(I), tetracarbonylbis(µ-3-methylpyrazolyl)diiridium(I), and tetracarbonylbis(µ-3,5-dimethylpyrazolyl)diiridium(I) reveal interesting features in the electronic absorption spectra at ambient temperature and 77 K that may be assigned to dπ(xz,yz) → [σ(pz), π*(CO)] transitions and predominantly metal-metal localized σ(dz2) → [σ(pz),π* (CO)] transitions that reflect the degree of metal-meta1 interaction. Photophysical studies of the emissive 1,3B2(dσ pσ) excited states suggest that a higher-energy d-d excited state may provide a pathway for thermal deactivation of these states.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11878, author = {Chiang, Huey-jenn}, title = {Studies of the Thermodynamics of Some Native and Ruthenated Metalloproteins by Spectroelectrochemistry}, school = {California Institute of Technology}, year = {1987}, url = {https://resolver.caltech.edu/CaltechTHESIS:10312019-170145504}, abstract = {The thermodynamic parameters of redox centers in some metalloproteins have been investigated using spectroelectrochemical techniques, with the employment of an OTTLE (Optically Transparent Thin-Layer Electrode) cell. With the aid of various carefully selected mediators, the temperature dependence of the formal redox potentials of type I copper (blue copper) ions in Rhus vernicifera (tree) laccase, as well as in native and in pentaammineruthenium-modified azurins from Pseudomonas aeruginosa, have been measured. Similar experiments have been carried out for the heme site of cis-[Ru(en)2(OH)(His)]-horse heart cytochrome c (en: ethylenediamine; His: histidine). Cyclic voltammetry has been used to study the pH-dependence of the formal redox potentials of the appended ruthenium ion in cis-[Ru(en)2(OH)(His)]-horse heart cytochrome c. Finally, the synthesis and spectroelectrochemistry of sperm whale myoglobin reconstituted with [Ru(MpIX)(DMSO) dicarboxylic acid]- moiety (MpIX: mesoporphyrin IX; DMSO: dimethyl sulfoxide) have also been carried out.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11813, author = {Gelles, Jeff Daniel}, title = {The Cuᴀ Site in Cytochrome c Oxidase: Its Role in Coupling Electron Transport to Proton Pumping}, school = {California Institute of Technology}, year = {1986}, url = {https://resolver.caltech.edu/CaltechTHESIS:10112019-095757311}, abstract = {Cytochrome c oxidase contains a copper-ion electron transfer site, CuA, which has previously been found to be unreactive with externally added reagents under conditions in which the protein remains structurally intact. We have studied the reaction of cytochrome oxidase with sodium p-hydroxymercuribenzoate (pHMB) and found that the reaction proceeds, under appropriate conditions, to give an excellent yield of a particular derivative of the CuA center which has electron paramagnetic resonance and near-infrared absorption spectroscopic properties which are distinctly different from those of the unmodified center. Spectroscopic and chemical characterization of the other metal-ion sites of the enzyme reveals little or no effect of the pHMB modification on the structures of and reactions at those sites. Of particular interest is the observation that the modified enzyme still displays a substantial fraction of the native steady-state activity of electron transfer from ferrocytochrome c to O2. Although the modified copper center retains the ability to receive electrons from the powerful reductant Na2S2O4 and to transfer electrons to O2, it is not significantly reduced when the enzyme is treated with milder (higher potential) reductants such as NADH/phenazine methosulfate or the physiological substrate ferrocytochrome c.
CuA exhibits many spectroscopic and chemical properties which make it highly atypical of cuproprotein active sites; the singular nature of this site has prompted speculation about the importance of the structural peculiarities of this metal-ion center in the catalytic cycle of the enzyme. In this work, we demonstrate that the unusual features of this site are not prerequisites for competent catalysis of electron transfer and O2 reduction by the enzyme. These observations suggest that a secondary electron transfer pathway not involving CuA exists between the cytochrome c and oxygen binding sites which can function at a rate at least 20% of the total turnover rate of the native enzyme.
Cytochrome c oxidase converts free energy released in respiratory electron transport into a metabolically useful form by contributing to the potential gradient across the mitochondrial inner membrane. Both a process involving electron transfer linked proton pumping and a process involving electron transfer from ferrocytochrome c to O2 contribute to the potential gradient. Taken together with those from other recent studies, the results of the experiments support a model for electron transfer in cytochrome oxidase in which CuA and Fea are parts of separate, parallel electron transport pathways between cytochrome c and the cytochrome oxidase O2 reduction site. This model has important implications for the role of CuA in respiratory energy transduction by cytochrome oxidase. It suggests that CuA is the best candidate among the four metal center sites in cytochrome oxidase to be the site of redox-linked proton pumping.
In order to explore more fully the mechanistic aspects of energy transduction in cytochrome oxidase, we propose a complete chemical mechanism for the enzyme’s proton pump. The mechanism achieves pumping with chemical reaction steps localized at a single redox site within the enzyme; no indirect coupling through protein conformational changes is required. The proposed mechanism is based on a novel redox-linked transition metal ligand substitution reaction. The use of this reaction leads in a straightforward manner to explicit mechanisms for achieving all of the processes determined by Blair, et al. (D.F. Blair, J. Gelles, and S.I. Chan, Biophys. J., in press) to be needed to accomplish redox-linked proton pumping. These processes include: 1) modulation of the energetics of protonation/deprotonation reactions and modulation of the energetics of redox reactions by the structural state of the pumping site; 2) control of the rates of the pump’s redox reactions with its electron transfer partners during the turnover cycle (gating of electrons); and 3) regulation of the rates of the protonation/deprotonation reactions between the pumping site and the aqueous phases on the two sides of the membrane during the reaction cycle (gating of protons). The model is the first proposed for the cytochrome oxidase proton pump which is mechanistically complete and specific enough that a realistic assessment can be made of how well the model pump would function as a redox-linked energy transducer. This assessment is accomplished via analyses of the thermodynamic properties and steady-state kinetics expected of the model. These analyses demonstrate that the behavior of a pump based on the model would be very similar to that observed of cytochrome oxidase both in the mitochondrion and purified preparations. Specifically, calculation of the properties of the model pump at equilibrium demonstrates that the behavior expected of the model pump in an electrochemical titration is the same as that observed for the CuA center: a nearly pH-independent midpoint potential of approximately 290 mV. An analysis of the performance of the pump during steady-state turnover demonstrates that the model pump is expected to function efficiently and with good power output under physiological conditions, and that its properties under conditions of varying load are similar to those observed in experiments on respiring mitochondria and on purified cytochrome oxidase reconstituted into artificial lipid vesicles.
Although the analysis presented here concerns only a single model of a redox-linked proton pump, it leads to some important general conclusions regarding the mechanistic features of such pumps. The first is that a workable proton pump mechanism does not require large protein conformational changes. Another conclusion is that a redox-linked proton pump need not display a pH-dependent midpoint potential as has frequently been assumed. A final conclusion is that mechanisms for redox-linked proton pumps that involve transition metal ligand exchange reactions are quite attractive because such reactions readily lend themselves to the linked gating processes necessary for proton pumping.
Several of the results of this research form the basis of a new approach to studying the role of CuA in energy transduction by cytochrome oxidase. I describe several continuing experimental programs based on this method, and summarize the goals, experimental design, and progress of these studies. I conclude by considering the physiological significance of the new conceptions about the role of CuA in energy transduction by cytochrome oxidase arising from this research.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/DVSC-0Z70, author = {Hopkins, Michael David}, title = {The Energetics, Structures, and Dynamics of the δδ* Excited States of Quadrulpy Bonded Dimers}, school = {California Institute of Technology}, year = {1986}, doi = {10.7907/DVSC-0Z70}, url = {https://resolver.caltech.edu/CaltechETD:etd-03102005-131755}, abstract = {The results of an experimental investigation of the electronic structures of the M2X4L4 (M = Mo, W; X = Cl, Br I; L = uncharged σ-donor ligand) class of quadruply bonded metal dimers are reported. These results are interpreted within a theoretical framework that is general for all types of weakly interacting orbitals; this is set out in Chapter I. In Chapter II we lay the structural foundation for this investigation by presenting the crystal structures of Mo2Br4(PMe3)4 and Mo2I4(PMe3)4 and comparing their bonding parameters with those previously reported for Mo2Cl4(PMe3)4. Resonance Raman and far-infrared spectral data of these complexes are also reported; comparisons to the available structural data indicate that the metal-metal distance and diatomic force constants, which are fingerprint parameters for the characterization of metal-metal interactions, display different ligand sensitivities. This chapter concludes with a discussion of the energies and intensities of the 1(δ → δ) transitions of these complexes, cast both in terms of their molecular structures as well as within the framework of existing theories of the electronic structural significance of these latter two spectroscopic properties. The data for the M2X4L4 complexes lead to a reevaluation of these standard interpretations, and a new postulate, based on charge transfer mixing, is put forth that more adequately accounts for the energies and intensities of the 1(δ → δ) transitions of nearly all quadruply bonded dimers. The 3(δδ) state is discussed briefly in Chapter III, wherein it is shown that differing magnetic and spectroscopic properties of the Mo2X4(PMe3)4 and diphosphine-bridged β-Mo2X4(dmpe)2 dimers are readily accounted for by the simple theoretical framework set out in Chapter I. The analysis of these data leads to experimental estimates of the energies of the 3(δδ) states of these compounds: L = PMe3, E = 5200 c-1; L = dmpe, E = 500 cm-1. In Chapter IV we consider the photophysical properties of the 1(δδ) state in light of its energetics relative to the 3(δδ) and δ2 states. Of particular interest is the finding that the photophysical properties of these complexes are perturbed by the nature of the coordination sphere to a different extent than are their 1(δ → δ) energies and intensities. The extensive series of M2X4L4 complexes studied allows the estimation of the intrinsic radiative and nonradiative decay properties of this chromophore. Chapter V contains the main body of this thesis, namely the analysis of the high-resolution electronic spectra of the M2X4L4 complexes. The unprecedented vibronic detail revealed by these spectra is interpreted using the conceptual base developed over the preceding four chapters, and results in the proposal of a double-well potential energy surface for the 1(δδ) state along nontotally symmetric coordinates; this arises from sudden polarization. In the final chapter, the photochemical manifestations of this new excited state description are outlined. Material that supplements the discussion in Chapters I-VI is presented in the appendices.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.1063/1.437731, author = {Zinck, Jennifer Joanne}, title = {A Study of the Dynamics of the Interaction of CH₄ with the (111) Surface of Rh and the (110) Surface of Ir}, school = {California Institute of Technology}, year = {1985}, doi = {10.1063/1.437731}, url = {https://resolver.caltech.edu/CaltechTHESIS:01032019-120826233}, abstract = {A study of the dynamics associated with the activated dissociative adsorption of CH4 on the (111) surface of Rh and the (110) surface of Ir has been performed in ultrahigh vacuum (UHV), using laser excitation and molecular beam techniques.
Chapter 2 describes an experiment in which gas phase CH4 is laser excited to the ν3 excited vibrational state (8.63 kcal/mole) in a collisionless environment, and also, collisionally deactivated to the 2ν4 state (7.46 kcal/mole), in a He atmosphere. Hydrogen thermal desorption spectra from a Rh(111) surface exposed to the excited gas indicate that. within the experimental limits of detection, no enhancement of dissociative adsorption of CH4 is obtained by excitation to the ν3, 2ν4 (or ν4) vibrational states.
Chapter 3 consists of the description of an ultrahigh vacuum-molecular beam apparatus constructed for the study of gas-surface dynamics. The ultrahigh vacuum chamber is a three level system of custom design. Level I is a load lock for introducing and retrieving the sample, to and from the UHV chamber. The molecular beam axis crosses the UHV chamber at Level II, and also crosses the axis of the ionizer of a quadrupole mass spectrometer detector. Low-energy electron diffraction optics are also mounted at Level II. Auger electron spectroscopy may be performed at Level III. An extended travel UHV sample manipulator has been designed and constructed, which allows translation of the sample to all three levels of the UHV system. The molecular beam line is of a nozzle source design, with three separate chambers which are pumped differentially. A chopper motor, for incident beam modulation, is mounted in the third beam chamber directly adjacent to the UHV chamber, and allows time-of-flight measurements.
Chapter 4 describes an experiment in which the role of translational energy in the chemisorption of CH4 on Ir(110) is studied via the use of molecu1ar beams of CH4 seeded in H2 and He. A probability of dissociative adsorption below 10-4 is associated with a CH4 beam which has an average translational energy of approximately 10 kcal/mole.
The results of Chapters 2 and 4 point to the existence of a barrier to dissociative adsorption of CH4 that is greater than 10 kcal/mole of total energy, on the surfaces studied. A combination of vibrational and translational activation of CH4 may be required for dissociative adsorption on Rh(111) and Ir (110).
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11333, author = {Zietlow, Thomas Christopher}, title = {Photophysics and Electrochemistry of d⁴ Metal Clusters}, school = {California Institute of Technology}, year = {1985}, url = {https://resolver.caltech.edu/CaltechTHESIS:01042019-095546695}, abstract = {The metal-ligand and metal-metal interactions in d4 metal cluster systems have been examined using emission spectroscopy and electrochemical techniques. A detailed picture of the electronic structure of the hexanuclear molybdenum and tungsten clusters has not yet been achieved, but significant insight has been obtained through studying the effects of ligand, temperature, and molecular structure on the properties of the emissive excited state. Through these studies, and through analogy to the (d4)2 quadruply bonded molybdenum and tungsten dimers, the dynamics of the excited state, and its relevance to the chemistry out of that state, can be better understood.
The work done on the excited state properties of the Mo6X2-14 (X = Cl, Br, I) clusters is outlined in Chapter 2. The energy of the emissive excited state is independent of halide ligand and is best described as a metallocalized state with very little ligand character. Energy transfer quenching data have determined that the emissive excited states are spin triplets.
The unusual emissive behavior of the tungsten series W6X8Y2-6 (X, Y = Cl, Br, I) is discussed in Chapters 3 and 4. The energy of the emissive states order: W6Cl2-14 (1.83 eV) < W6Br2-14(1.85 eV) < W6I2-14(2.05 eV), the opposite trend from that expected by including charge transfer character into the transition. Variation of axial and facial halides leads to the conclusion that the µ3-bridging halides dominate the electronic structure of the cluster, but that the axial halides have a strong influence on the non-radiative rate. The structural studies show that the W-W bonds are longer in the W6I2-14 cluster than in the W6Cl2-14 structure, indicating that the metal-metal bond overlap is not the sole determining factor in the energy of the emitting excited states.
Chapters 5, 6, and 7 describe the chemistry and properties of derivatives of these hexanuclear clusters. The W6Br-14 anion has been synthesized and its crystal structure determined. The effect of alkylphosphine ligands on the electrochemistry and photophysics of the Mo6Cl12 cluster has been found to be very small. Although the Mo5Xn-13 (n = 1, 2, 3) clusters do not appear to have any interesting photochemical properties, the observation of the splitting between spin-orbit states in a high nuclearity cluster has implications in the photochemistry of the hexanuclear clusters.
Finally, the last two chapters describe work done on the electrochemistry of Mo2X4 (PR3) 4 dimers. An unexpected ordering of the redox potentials is ascribed to π-backbonding from the metal center to the halide ligand. Efficient electrogenerated chemiluininescence has been observed for several of these dimers.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Anson, Fred C.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11329, author = {Baar, Roger Bennett}, title = {Synthesis and Characterization of a Ruthenium-edta Dimer by Spectral and Electrochemical Techniques}, school = {California Institute of Technology}, year = {1985}, url = {https://resolver.caltech.edu/CaltechTHESIS:01022019-103725460}, abstract = {Section I
The synthesis of a ruthenium-edta dimer is described. The dimer is shown to be the one-electron oxidized product of two [Ru(III)edta(OH2)]- monomers. The dimer was shown to contain one unpaired spin by magnetic susceptibility and esr spectroscopy indicating spin pairing between the two ruthenium metal centers. A band was detected in the near infrared that analyzed for a Class III complex indicating that the dimer is truly delocalized and that the oxidation state on each ruthenium is 3.5. The band was much narrower than predicted for a delocalized, Class II complex and its position did not exhibit any solvent dependence. The optical spectrum indicated some similarity with other formally Ru(III)-Ru(IV) dimers indicating that the formation of this type of dimer is favored regardless of the type of auxiliary ligands attached to the ruthenium.
The change in the optical spectrum upon raising the pH indicated a pKa of 10.32 for the dimer. This, taken in conjunction with the infrared, the raman and the nmr results indicated that the dimer was µ-oxo bridged at low pH and was, most likely, µ-oxo, µ-hydroxo bridged at higher pH.
When an excess of Ce(IV) was added to a solution of the dimer the catalytic evolution of dioxygen was observed. The dimer also catalyzed the disproportionation of hydrogen peroxide.
Section II describes the electrochemistry of Ru(III)edta and the dimer. Cyclic voltammetry, polarography and rotating ring-disk electrode (RRDE) voltammetry were used to characterize the oxidation and reduction of each of the two complexes. The electrochemical oxidation of Ru3Y produced the dimer after one Faraday per two moles of ruthenium. The catalytic evolution of dioxygen was also observed at a platinum electrode. The step-wise reduction of the dimer to produce Ru(II)edta is also described. The combined use of the RRDE with digital simulations of the mechanism of reduction yielded the rate constants for the rate of breakup of the intermediates. A spectro-electrochemical experiment also showed that the dimer can be oxidized further to produce a Ru(IV)-Ru(IV) dimer.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11443, author = {Martin, Craig Timothy}, title = {The Structures of CuA and Cytochrome a in Cytochrome c Oxidase}, school = {California Institute of Technology}, year = {1985}, url = {https://resolver.caltech.edu/CaltechTHESIS:04052019-144431487}, abstract = {Cytochrome c oxidase contains four metal centers, two heme irons and two copper centers. The two low-potential centers, CuA and cytochrome a, function in the transfer of electrons from cytochrome c to the oxygen binding site within cytochrome oxidase. Although almost nothing is currently known about the mechanism of proton pumping in cytochrome oxidase, it is very likely that at least one of these low-potential metal centers is directly involved in the translocation of protons across the inner mitochondrial membrane. Essential to a complete understanding of the mechanisms of electron transfer and proton pumping in cytochrome oxidase is a knowledge of the structures of the involved metal centers.
In this work, the spectroscopic tool of electron nuclear double resonance (ENDOR) is used in conjunction with the direct incorporation of isotopically substituted amino acids into the yeast protein to determine the identities of ligands to CuA and cytochrome a in cytochrome oxidase. For cytochrome a, the incorporation of [1,3-15N2]histidine into the yeast protein results in the appearance of an ENDOR signal associated with hyperfine coupling to the histidine ring 15N, thereby unambiguously identifying histidine as an axial ligand to cytochrome a. Comparison of this result with similar results in the native and 15N-substituted bis-imidazole model compounds metmyoglobin-imidazole and bis-imidazole tetraphenyl porphyrin, provides strong evidence that cytochrome a is coordinated by two axial histidine ligands.
Similar studies on the effect of the incorporation of [1,3-15N2]histidine into yeast cytochrome oxidase demonstrate that histidine is a ligand to CuA. The incorporation of [β,β-2H2]cysteine into the protein reveals that the two strongly coupled protons previously observed in the ENDOR spectrum of CuA (H. L. Van Camp, et al. (1978) Biochim. Biophys. Acta 537, 238) can be assigned to the methylene protons on cysteine, proving conclusively that cysteine is a ligand to [β-13C]cysteine-substituted protein. These results, combined with the resolution in the native enzyme of a new hyperfine coupling to a third strongly coupled proton for CuA, provide strong evidence for the coordination of two cysteine ligands to CuA.
Armed with the identification of one histidine and two cysteine ligands to CuA, we present a model for the physical and electronic structure of the oxidized CuA center. This model is characterized by the delocalization of a substantial amount of unpaired spin density away from the copper atom and into an orbital between the two cysteine sulfur ligands. This model satisfactorily explains many of the unusual spectroscopic features of CuA and should prove to be of use in future studies of the nature of the CuA site.
With the positive identification of ligands to cytochrome a and CuA, we have analyzed the available protein sequence data for the subunits of cytochrome oxidase from a wide variety of organisms, and are able to reach some conclusions regarding the physical location of these metal centers in the subunit structure of the protein. The cysteine ligand(s) to CuA most certainly derive from the two conserved cysteine residues in subunit II. Furthermore, it is predicted that all of the metal centers in cytochrome oxidase cannot be located in subunit II, and are quite likely shared with subunit I. Finally, we present a model for the protein coordination of CuA in which the two cysteine sulfur ligands to CuA originate in two cysteine residues which are physically adjacent on the face of an α-helix in subunit II.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.1016/0021-9517(85)90242-8, author = {Allison, Janet Noel}, title = {Theoretical Studies of Heterogeneous Catalysis of Molybdates}, school = {California Institute of Technology}, year = {1985}, doi = {10.1016/0021-9517(85)90242-8}, url = {https://resolver.caltech.edu/CaltechTHESIS:10192009-083321412}, abstract = {Chapter 1: We use thermochemical results from ab initio quantum chemical calculations (generalized valence bond) to examine the reaction mechanism for
H3COH + ½ O2 → H2CO + H2O
as catalyzed by MoO3. We find that surface dioxo sites
[Chemical structure; see abstract in scanned thesis for details.]
are critical to activating the methanol, but we find that the Trifiro proposal of a single site-single step process
[Chemical structure; see abstract in scanned thesis for details.]
is not favorable (∆H ≃ +31.5 kcal). Our conclusion is that the catalytic site involves two adjacent surface dioxo units (the dual dioxo site), with each dioxo site extracting one H in a sequence of steps. The required dual dioxo site exists on the (010) surface of MoO3 but does not exist on the other low index surfaces. This mechanism is supported by atmospheric pressure experimental studies which indicate that MoO3 (010) is selective for CH2O products. A detailed sequence of reaction steps and the associated thermochemistry is proposed.
Chapter 2: Molybdates involving various metal additives play a dominant role in such industrially important catalytic processes as selective oxidation (propene to acrolein) and ammoxidation (propene to acrylonitrile); however, the details of the reaction mechanism and of the surface sites responsible are yet quite uncertain. In order to establish the thermo-chemistry and detailed mechanistic steps involved with such reactions, we have performed ab intitio quantum chemical calculations [generalized valence bond (GVB) and configuration interaction (CI)]. These studies indicate a special importance of multiple surface dioxo Mo sites (possessing two Mo-O double bonds and hence spectator oxo groups) arranged together so as to provide the means for promoting the sequence of transformations.
Chapter 3: Extensive ab initio calculations have been carried out on molybdenum (VI, V and IV) complexes containing oxygen and nitrogen. A detailed description of the bonding of oxo, nitrido and imido terminally attached ligands to molybdenum is presented. These results are used to explain the preferred geometries of complexes as well as the periodic trends as ligands to molybdenum are varied from O, N, NH.
Chapter 4: We find that the ground state of MoN (4∑-) has a covalent triple bond where the σ bond is dz2-like on the Mo, leading to a quartet state with unpaired electrons in the Mo 5s, Mo 4dδxy and Mo 4dδx2-y2 orbitals. The first excited state (4Π) corresponds to the 5pπ ← 5s excitation. The calculated properties of Re = 1.60 Å, ωe = 1100 cm-1, De = 4.07 eV, and ∆E (4Π-4∑- = 2.128 eV are in good agreement with recent experimental results (Re = 1.63 Å and ∆E = 2.011 eV). Particularly interesting is a dramatic nonmonotonic change of dipole moment with distance (µ = -3.123 D at Re = 1.60 Å, -5.982 D at R = 2.60 Å and µ = -0.176 D at R = 5.0 Å. This effect is explained.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/XR1N-CM33, author = {Low, John James}, title = {Theoretical Studies of Oxidative Addition and Reductive Elimination}, school = {California Institute of Technology}, year = {1985}, doi = {10.7907/XR1N-CM33}, url = {https://resolver.caltech.edu/CaltechTHESIS:10232009-095454256}, abstract = {Chapter 1: Ab initio calculations (Hartree-Fock, generalized valence bond, and configuration interaction), utilizing relativistic core potentials, have been used to follow the oxidative addition of H2 to Pt(PH3)2. We find an activation barrier of 2.3 kcal/mol and an exothermicity of 15.9 kcal/mol. From examination of the geometries and wavefunctions, we find that up to the transition state the H-H bond is still intact. The role of the Pt s1d9 and d10 states in oxidative addition is described, and the effects of including electronic correlation are discussed. The implications for reductive elimination of the dimethyl and hydridomethyl complexes are also discussed.
Chapter 2: Ab initio calculations have been carried out on MR2 complexes (where M = Pd or Pt and R = H or CH3) to model concerted reductive coupling from MR2L2 complexes (where L is a substituted phosphine). The results of these calculations support the following two conclusions. (1) The differences in the driving force for reductive elimination from Pd(II) and Pt(II) complexes with the same R groups is very close (0-4 kcal/mol) to the difference in the s1d9-d10 state splittings of these elements (32 kcal/mol). Thus reductive elimination is exothermic from Pd complexes (since Pd prefers d10) and endothermic from Pt complexes (since Pt prefers s1d9), where the metal product is in its d10 state. This supports the conclusion, derived from qualitative considerations of generalized valence bond wavefunctions, that Pt(II) and Pd(II) complexes have their metal atoms in a s1d9 configuration and the metal atoms in Pt(0) and Pd(0) complexes are in a d10 configuration. (2) The activation barriers for C-C coupling are approximately twice that for C-H coupling. There are essentially no barriers for processes involving H-H bonds. The origin of this trend is the directionality of the methyl sp3 orbital, which destabilizes the transition state for the case where an M-C bond is being converted to a C-C or C-H bond. Conversely, the spherical H 1s is orbital can form multicenter bonds easily, allowing it to break M-H bonds while forming an H-H bond and leading to low intrinsic barriers. These results are consistent with the experimentally observed trends.
Chapter 3: Ab initio calculations were carried out on Pt(CH3)2(Cl)2(PH3)2 and on various Mt(R1)(R2)(PH3)2 complexes (where Mt = Pd or Pt; R1, R2 = H or CH3) in order to elucidate the differences in reductive H-C and C-C coupling from Pd(II), Pt(II), and Pt(IV) complexes. These studies explain why (1) reductive C-C coupling is facile for Pd(II), favorable for Pt(IV), and unobserved for Pt(II) systems, while (2) reductive H-C coupling is facile for Pt(II) and Pd(II) systems, and (3) oxidative addition is favorable only for addition of H2 to Pt(0) systems.
Chapter 4: Ab initio calculations were carried out on CHx and NHx molecular fragments on small clusters of Ni atoms (Ni13 and Ni14), as a model for chemisorption on the Ni(100) surface. The results presented here show that these species make strong π bonds to the surface which cause methylidyne and imidogen to be the most stable CHx and NHx, species on this surface. The results have also been used to estimate ∆H0f for various intermedates important for methanation and ammonia decomposition on Ni surfaces.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/S0HZ-TF05, author = {Steigerwald, Michael Louis}, title = {2ₛ + 2ₛ Reactions at Transition Metals}, school = {California Institute of Technology}, year = {1984}, doi = {10.7907/S0HZ-TF05}, url = {https://resolver.caltech.edu/CaltechETD:etd-01032007-142600}, abstract = {A study of the suprafacial 2 + 2 reaction at transition metal centers is presented. It is demonstrated that this reaction is allowed and proceeds with a low activation energy if the reacting transition metal-to-substituent bond is covalent, nonpolar, and has a large component at transition nickel d-orbital character. These chains are evinced by examination of 2s + 2s reactions at M-H bonds. Those systems in which M can use d orbitals show lower barriers to the 2s + 2s reaction than those in which M cannot use d orbitals.
The importance of the electronic structure of the metal-to-substituent bond is highlighted by a study of dichorotitanacyclopropane. This molecule, being a metallacyclopropane, can undergo 2s + 2s reactions which one unavailable to a simple olefin.
Studies concerning the importance of 2s + 2s reactivity in the organic chemistry of nickel, and in the Ziegler-Natta polymerization of simple olefins are presented.
It is suggested that the principle of maximum bonding (the Woodward-Hoffmann rules) implies the conservation of transition metal covalency in low-energy catalytic cycles.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/11263, author = {Buttry, Daniel Alan}, title = {Effects of Electron Exchange on the Photochemical, Electrochemical and Electrocatalytic Responses of Polymer Modified Electrodes}, school = {California Institute of Technology}, year = {1984}, url = {https://resolver.caltech.edu/CaltechTHESIS:10312018-105602325}, abstract = {A spectroelectrochemical method is presented which may be used to measure the concentrations of the two oxidation states of a redox couple in a polymer film. The method is applied to Ru(bpy)32+ in Nafion films on transparent tin oxide electrodes. Measurements of the emission of this complex in Nafion films on graphite and tin oxide electrodes are used to obtain information about the quenching of Ru(bpy)32+* by Ru(bpy)33+. Features of the luminescence which yield insight into the structure of the Nafion film are discussed.
Experiments are described which bear on the question of when electron self-exchange reactions can contribute to the propagation of electrons through polymer films on electrodes. The results of experiments on the Co(bpy)32+/+ couple are discussed in terms of a theory derived by Dahms and Ruff et al. which describes the contribution of electron self-exchange reactions to diffusion in mixtures containing both halves of a redox couple.
The propagation of charge through polymer films by electron exchange cross-reactions between different redox couples which are co-incorporated into a polymer film on an electrode is discussed. Two experimental examples of this phenomenon are presented.
An electrocatalytic application of a polymer modified electrode is described. Cobalt tetraphenylporphyrin is incorporated into a Nafion film on a graphite electrode, and this porphyrin is used to catalyze the two-electron electroreduction of dioxygen. Enhanced catalytic currents are observed when an electron mediator (Ru(NH3)63+) is added to the film. This mediator serves to shuttle electrons between the electrode and the relatively immobile catalyst sites. The performance of electrocatalysts in polymer films is discussed with emphasis on ways to enhance stability without sacrificing efficiency.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/5327, author = {Goodgame, Marvin Mark}, title = {Exchange Forces in Transition-Metal Bonding}, school = {California Institute of Technology}, year = {1984}, url = {https://resolver.caltech.edu/CaltechTHESIS:10232009-150307132}, abstract = {We have examined multiple bonds (σ, π, and δ) to transition metals and find that intra-atomic exchange forces on these metals are crucial for correct prediction of ground states and that a proper description of these terms is required for a quantitative understanding of bond energies.
Our calculations on models for bridged Fe porphyrin dimers show that intra-atomic exchange forces on the Fe’s are critical to the explanation for the dramatic differences in the Fe-Fe coupling for µ-oxo and µ-nitrido bridged Fe porphyrin dimers. The qualitative bonding concepts obtained are used to predict properties of the µ-carbido bridged Fe porphyrin dimer.
In most cases, the interactions responsible for bonding lead to antifer’romagnetic coupling between the d orbitals localized on adjacent centers, resulting in overall low-spin couplings. However, some extended metal systems (eg. metallic Ni) lead to net ferromagnetic interactions between d orbitals localized on different centers. In order to elucidate these effects, we have examined the direct and indirect d-d couplings in the Ni4 cluster as a function of bond distance. We find that ferromagnetic coupling dominates in a region of bond distance around the bulk Ni value of 2.5 Å with antiferromagnetic coupling dominating for short R (by 2.0 Å) and for long R (by 3.5 Å). The dominant interactions responsible for ferromagnetic coupling involve spin polarization of the conduction band (s-like), supporting a model for ferromagnetism in bulk metallic systems very similar to the Ruderman-Kittel model for magnetic impurities.
The dimers Cr2 and Mo2 provide the most dramatic illustration of the importance of exchange forces in bonding. With six unpaired electrons on each atom, there is the potential for up to six covalent bonds. However, formation of d-d covalent bonds requires a concomitant loss in intra-atomic d-d exchange energy. The net result is a double well where the long-R minimum (3 Å is dominated by s-s pairing (no loss of intra-atomic d-d terms) while the short-R minimum (1.7 to 1.9 Å) involves a strong quintuple bond of d orbitals plus an antibonding s-s interaction. To properly handle the intra-atomic exchange terms during this transition from long R with local high-spin coupling to small R with dominant singlet pairing within bonding pairs presents a formidable challenge to ab initio computation. To carry out such studies, we have extended the GVB and related approaches of ab initio calculations and have also developed a simple approximate method of including the electron correlation missing in GVB wavefunctions that provides a quantitatively accurate description of these systems.
The effects studied here should be of comparable importance for multiple bonds involving transition metals, lanthanides, and actinides bonding to each other and to such ligands as CR2, CR, O, N, and NR. Correlation terms beyond GVB are most important for the least electronegative ligands. Thus, the proper treatment of intra-atomic exchange and of interatomic d-d coupling should be of considerable importance in studies of heterogeneous and homogeneous catalytic systems.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.1021/ja00342a025, author = {Paffett, Mark Thomas}, title = {Electrochemistry of Molybdenum Aquo Ions}, school = {California Institute of Technology}, year = {1983}, doi = {10.1021/ja00342a025}, url = {https://resolver.caltech.edu/CaltechTHESIS:11012019-171533510}, abstract = {The electrochemical behavior of selected molybdenum aquo ions in acidic media is examined in relation to solution structure.
The electrochemistry of Mo(VI) in non-complexing aqueous electrolytes is usually severely complicated by the oligomerization and subsequent adsorption of the reactant. This problem can be circumvented by employing dilute (≤ 10-4 M) solutions of Mo(VI) in 1 to 2 M trifluoromethanesulfonic acid. Under these conditions staircase voltammograms and pulse polarograms exhibit single, reversible waves that are consistent with the one-electron reduction of an unadsorbed, monomeric Mo(VI) species. The pH dependence of the reduction potentials suggests that two protons are consumed in the reduction of each Mo(VI). The monomeric Mo(V) reduction product undergoes spontaneous dimerization with a rate constant estimated as 103 M-1 s-1. It also reduces perchlorate and nitrate anions at a significant rate.
The Mo2(V)/Mo2(III) redox couple in acidic solution involves an overall four electron-six proton transfer connecting the two participants. This redox process is characterized by extreme electrochemical irreversibility. Reduction of the Mo2(V) aquo ion to the Mo2(III) aquo ion proceeds with αna equal to 0.73 and a proton reaction order of 1.4. A chemical step with an inverse dependence on proton concentration precedes the reoxidation of aquo Mo2(III) to aquo Mo2(V). Plausible mechanisms are given for these observations.
The trinuclear ions containing Mo(IV), Mo3O4(H2O)4+9(Mo3(IV)) and an oxalato derivative, Mo3O4(C2O4)3(H2O) 2-3, can be reversibly reduced in acidic media to trinuclear Mo(III) species. The reductions involve two sequential electron transfer steps with formal potentials that are pH dependent:
[chemical equations; see abstract in scanned thesis for details].
Two waves are evident in voltammograms and polarograms of Mo3O4(C2O4)3(H2O)2-3 but with Mo3(IV) the two formal potentials are too close together to observe separate waves. However, logarithmic analysis of the shapes of normal pulse polarograms allowed the two formal potentials to be evaluated. The reductions of both complexes are believed to be accompanied by protonation of the bridging and capping oxo-ligands. The new, trinuclear Mo3(III) species resulting from the three-electron reduction of Mo3(IV) exhibits a characteristic EPR spectrum. The mixed-valent intermediate, Mo3(III, III, IV), is diamagnetic. Possible structural changes that accompany the addition of electrons and protons to Mo3IV) are discussed.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @mastersthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/5678, author = {Kanne, Robert M.}, title = {Studies of the enzyme laccase}, school = {California Institute of Technology}, year = {1983}, url = {https://resolver.caltech.edu/CaltechTHESIS:04022010-090654360}, abstract = {Rhus Vernicifera laccase was purified to an A_(280)/A_(614) ratio of 15.2. A procedure was then used to selectively remove the Type 2 copper and 70% of it was removed as judged by EPR. The treated enzyme showed decreased absorbance in the 330 nm, region, which is associated with the Type 3 site, The blue color was observed to reversibly bleach on occasion, apparently due to autoreduction of the Type 1 copper. The fluorescence of the Type 2 depleted laccase was increased 60% over that of the native protein. Since fluorescence quenching is often associated with binding of a metal to a protein site, fluorescence was used to monitor the attempted substitution of cobalt and nickel into the Type 2 site, There is some evidence that cobalt can occupy the Type 2 site.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.1016/0301-0104(81)80206-6, author = {Voter, Arthur Ford}, title = {The Resonating Valence Bond Model of Molecules and Reactions}, school = {California Institute of Technology}, year = {1983}, doi = {10.1016/0301-0104(81)80206-6}, url = {https://resolver.caltech.edu/CaltechTHESIS:11132009-133042163}, abstract = {This thesis presents an ab initio generalization of Pauling’s theory of resonance, the generalized resonating valence bond (GRVB) method. In GRVB, we optimize a wavefunction of the form
ΨTOT = CA ΨA + CB ΨB
where ΨA and ΨB are multiconfigurational wavefunctions with arbitrary overlap. This type of wavefunction has been considered unfeasible for more than a few electrons due to the n! computational dependence of evaluating the matrix element < ΨA | H | ΨB >. We reduce this dependence to ~n5 by biorthogonalizing the orbitals in each determinant pair. GRVB is ideally suited to describing systems which require a resonance of more than one bonding structure, such as benzene, molecules with three-electron bonds, and reaction transition states. Besides yielding a conceptually simple avefunction, we find that GRVB yields quantitative results for processes in which the dominant differential correlation is a resonance effect. For example, the GRVB barrier heights for the HCl + H and HF + H exchange reactions are each within one kcal of the basis set limit, in contrast to the orthogonal configuration interaction (CI) approaches which require hundreds or thousands of configurations to achieve the same accuracy. We also present application to the three-electron bonding in noble gas dimer ions, and various other examples.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/10780, author = {Bair, Raymond Alan}, title = {Part A. Theoretical Studies of the X-Ray Absorption Edge in Copper Complexes. Part B. Electron Correlation Consistent Calculation of Bond Dissociation Energies}, school = {California Institute of Technology}, year = {1982}, url = {https://resolver.caltech.edu/CaltechTHESIS:03222018-144512817}, abstract = {Part A: In order to elucidate the nature of the transitions involved in the x-ray absorption edge of molecular systems, we have used ab initio methods to examine the discrete transitions corresponding to the atomic 1s → 3d, 4s, 4p, 5s, and 5p transitions and the corresponding shakeup processes for Cu atom and for a Cu(II) model system, CuCl2. The three common features of the K edge are described by the calculations. For CuCl2, the lowest strong transitions have the character 1s → 4p (f = 0.00133). About 7.5 eV lower is a group of transitions involving 1s → 4p simultaneous with ligand-to-metal shakedown. About 18.7 eV below the main peak is a weak (65 times weaker) quadrupole-allowed transition corresponding to 1s → 3d (i.e., 1s23d9 → 1s13d10. In each case the spectral feature has been assigned to an allowed transition. Previously, the middle transition was assigned as 1s → 4s, whereas in this study the 1s → 4s transition was calculated to be too weak to be observed. We propose that the observed peak is due to the allowed transition involving 1s → 4p plus shakedown.
Part B: Ab initio generalized valence bond (GVB) and configuration interaction (CI) methods have been used to develop a generally applicable method for directly calculating bond energies. Particular effort has been put into obtaining a scheme in which all correlation terms that change upon dissociation of a particular bond are included consistently. The method uses in an essential way the localized orbitals from a GVB calculations, and is readily applicable to large systems [e.g., (CH3)3C-C(CH3)3]. To test our method, we selected two benchmark series of compounds, where the experimental bond energies are well known. Calculated bond energies are reported for the R-H bonds of CH4, NH3, H2O, and HF, which are low by 3.5, 2.5, 3.0, and 2.7 .kcal/mol, respectively. We also report calculations of the R-R bond energies of C2H6, N2H4, H2O2, and F2, which are low by 0.1, -3.2, -1.8, and 0.8 kcal/mol, respectively. In the application of our method, we have calculated all of the O-O, O-C, and O-H bond energies of HOOH, CH3OOH, CH3OOCH3, CH3OH, C2H5OH (O-H only), and CH3O-. Finally, we obtain the electron affinities of F, OH, and CH3O with the same techniques.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/DYY3-MQ42, author = {Williams, Ellen D.}, title = {Studies of Chemical Adsorption Using Low-Energy Electron Diffraction}, school = {California Institute of Technology}, year = {1982}, doi = {10.7907/DYY3-MQ42}, url = {https://resolver.caltech.edu/CaltechETD:etd-09302005-132833}, abstract = {Both experimental and computational studies based on low-energy electron diffraction (LEED) have been performed to determine the nature of order in chemically adsorbed overlayers. These studies have been directed towards obtaining a better understanding of adatom-adatom interactions by measurement of their most obvious manifestations; change in overlayer order during adsorption and co-adsorption, island formation, and order-disorder phenomena.
The effect of the co-adsorption of hydrogen on the ordering of CO on Rh(111) has been studied using LEED and thermal desorption mass spectrometry. The results indicate that the adsorption of CO proceeds via a physically adsorbed intermediate. In addition, there is a strong repulsive interaction between CO molecules and hydrogen atoms co-adsorbed on Rh(111). This interaction is apparent at distances up to 2.7-3.1 Å indicating that it is a through-metal effect.
A series of LEED patterns has been observed during the adsorption of sulfur on the reconstructed IR(110)-(1x2) surface. The structure observed at lowest coverages has a p2mg symmetry. This allows a determination of the absolute coverage, and indicates a probable binding site for the sulfur atoms.
A Monte Carlo simulation of the order-disorder behavior of oxygen on W(110) has been performed. General expressions relating the values of the interaction energies to the transition temperatures for a lattice gas with first, second and third neighbor interactions have been determined. Symmetry considerations in selecting a model for the interaction energies are discussed.
The effect of the ordering of adsorbed molecules into small islands on the LEED beam profile has been determined. In the limit of a random distribution of island positions the overall intensity is shown to be the weighted sum of the intensities from the individual islands. Computer simulations of island-containing overlayers have been used to determine the effect on the beam profiles of deviations from a random distribution of islands.
Experimental studies of island formation for CO on Ru(001) have been performed. The finite size of the ordered islands has a strong effect on the order-disorder behavior. Quantitative measurements of this effect have allowed a determination of the island size distribution and thus, the mean island size as a function of coverage.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/10852, author = {Eidem, Penny Kristen}, title = {An Investigation of the Photochemistry and Structures of Selected Second and Third Row Transition Metal Complexes}, school = {California Institute of Technology}, year = {1981}, url = {https://resolver.caltech.edu/CaltechTHESIS:05072018-093217287}, abstract = {Examination of the electronic spectrum of IrCl3-6 has led to a reassignment of the electronic transitions involved. The band at 206 nm, formerly assigned as the spin allowed πL to metal eg transition, is shown to be 1t1u (σ) → 2eg(z2, x2 - y2) [1A1g → 1T1u]. Low temperature spectra revealed the presence of additional features at 250 and 278 nm. These are ascribed to the 1t2u (π) → 2eg(z2, x2 - y2) [1A1g → 1T1u] and 1t2u (π) → 2eg(z2, x2 - y2) [1A1g → 3T1u] transitions, respectively. Irradiation (λ = 254 nm) of 1-12 M HCl solutions of IrCl3-6 yields IrCl2-6 and H2. Since the excited state populated at this wavelength has been shown to be ligand to metal charge transfer in nature, the reactive intermediate is proposed to he an Ir(II) species with a chlorine atom still formally bound. Photolysis of the reaction product, IrCl2-6 in HCl results in the formation of IrCl3-6 and Cl2. This reaction prevails regardless of wavelength of excitation. The reactive state is again LMCT in nature. Coupling of these reactions effects a reversible photochemical hydrohalic acid splitting catalyst.
The photochemistry of Mo(III), Mo(IV), Mo(V) in aqueous solution was investigated, and these ions were shown to be photochemically inert. Structural characterizations via Raman spectroscopy and X-ray ahsorption edge and EXAFS were undertaken. The Mo(II) structure is shown to be q quadruply bound dinuclear species. The Mo(III) is singly bonded with hydroxy bridges. Data for the Mo(V) ion are typical for oxobridged dinuclear compounds. In strong acid, Mo(IV) is shown to exist as a trinuclear species. As the pH of the medium is increased, the Mo-Mo amplitude decreased, indicating possible cluster fragmentation. In basic solution, a major structural change occurs. The presence of halide ions had no effect on the spectra.
Ru3(CO)12 reacts photochemically in the presence of olefins, CO, and H2 to catalyze the hydroformylation reaction. Typical yields are 1.5 x 10-3 moles of aldehydes in a 2:1 linear to branched chain ratio. A heterogeneous catalyst can also be effected by photoinduced fragmentation of the cluster in the presence of PV4P. Attachment of a Ru-CO moiety was confirmed by IR and elemental analysis. The first step in catalyst activation was shown to be formation of Ru(CO)4 olefin with a quantum yield of 0.03 for 1-pentene. Subsequent steps involved formation of a hydride-olefin complex, rearrangement to a hydride alkyl, “CO insertion,” and reductive elimination of aldehyde. Olefin isomerization and alkane production are also seen under reaction conditions. Formation of larger ruthenium carbonyl clusters led to catalyst deactivation. Photolysis of Ru3(CO)12 in the presence of H2 led to the formation of αH4-Ru4(CO)12. This molecule can also effect catalysis of the hydroformylation reaction, although yields are an order of magnitude less than for the parent cluster.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/10855, author = {George, Patricia Margaret}, title = {Electron Attachment Reactions and Photochemistry of Transition Metal Carbonyls in the Gas Phase and on Surfaces}, school = {California Institute of Technology}, year = {1981}, url = {https://resolver.caltech.edu/CaltechTHESIS:05072018-173514299}, abstract = {Mechanistic studies of photoassisted and electron-assisted deposition of thin metal films, from organometallic compounds at low pressures have been carried out. Various types of spectroscopy and microscopy are used to characterize the complex processes occurring during film formation. Chapter I gives an introduction emphasizing the importance of such an approach.
Chapter II details some of the experimental methods used in this study. The three major techniques which were used to evaluate metal films deposited in this manner were Rutherford backscattering spectrometry, X-ray photoelectron spectroscopy and energy dispersive X-ray microprobe analysis. A summary of the methodology associated with each is given and background information is supplied for necessary measurements and calculations.
Chapter III details the photoassisted mechanism which involves three stages: initiation, propagation and termination of film growth. Initiation is thought to occur primarily by the formation and subsequent reaction of photoelectrons and by photodecomposition. At low pressures formation and reaction of photoelectrons probably dominates while at higher pressures photodecomposition becomes increasingly important. The organometallic compounds are thought to react with electrons by dissociative electron capture, forming negative ions that decompose further to produce thin metal films. Propagation appears to involve a thermally active catalyst capable of effecting a number of turnovers in the dark before termination occurs. The limiting step appears to be loss of remaining CO ligands and the metal species is on the surface.
Chapter IV examines the dissociative electron attachment reactions of transition metal carbonyls. Dissociative electron attachment rates are measured for the transition metal carbonyls V(CO)6, Cr(CO)6, Fe(CO)5, Ni(CO)4, Mo(CO)6 and W(CO)6. Rates are measured as a function of the pressure of CO2 added to relax epithermal electrons. Derived thermal rate constants for the process M(CO)n → M(CO)-n-1 + CO are 0.6, 3.0, 2.0, 2.0, 1.3 and 1.2 x 10-7 cm3 molecule-1 s-1, respectively. The differences in these rate constants may be attributed to the different stabilities of the molecular anion with regard to dissociation versus autodetachment. The measured rate of thermalization of electrons by CO2 varies with the metal carbonyl used and depends on the variation of the dissociative electron capture cross section with electron energy. Each system is thus tightly coupled in that the electron energy distribution is determined not only by collisional processes involving CO2 but varies as well with the energy dependent depletion of the distribution by reactant species.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/10775, author = {Stevens, Tom Hall}, title = {The Structure of the Metal Centers in Cytochrome c Oxidase}, school = {California Institute of Technology}, year = {1981}, url = {https://resolver.caltech.edu/CaltechTHESIS:03132018-142618023}, abstract = {Mitochondrial cytochrome c oxidase catalyzes the four-electron reduction of oxygen to water. The functional form of the protein contains two copper ions and two heme irons. Two of these metal centers, cytochrome a3 and Cua3, constitute the oxygen reduction site. The other two metal centers, cytochrome a and Cua, are involved in electron transfer from cytochrome c to the oxygen reduction site. It is the structure and function of these four metal centers in cytochrome c oxidase which is the subject of this thesis.
The metal centers constituting the oxygen reduction site of cytochrome c oxidase have traditionally been difficult to study because their coupled nature renders them EPR silent. It is shown that nitric oxide can uncouple these metal centers, and under appropriate conditions renders both metal centers observable by EPR. One of the nitric oxide complexes is an NO-bridge complex, demonstrating that the oxygen reduction site is between the two metal centers. Furthermore, this NO-bound complex allows us to calculate a distance between the metal centers of about 5 Å. Finally, with 15N-his isotopically labeled yeast oxidase it is shown that the fifth endogenous ligand to cytochrome a3 is a histidine.
The copper metal center involved in electron transfer, Cua, is shown to have a cysteine and a histidine as ligands. The substitution of 12CD2-cysteine into yeast oxidase does not perturb the eight line hyperfine pattern first seen on the Cua EPR signal at 3 GHz. This demonstrates that the S = 1/2 center interacting with Cua is probably cytochrome a at a distance of 10-13 Å. These studies represent the first time that ligands to any of the metal centers in cytochrome c oxidase have been unequivocally elucidated.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @mastersthesis{10.7907/YM4S-K662, author = {Lewis, Nathan Saul}, title = {The chemistry of rhodium and molybdenum isocyanide complexes}, school = {California Institute of Technology}, year = {1977}, doi = {10.7907/YM4S-K662}, url = {https://resolver.caltech.edu/CaltechETD:etd-09192007-110805}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
The rhodium isocyanide dimer, […], has been synthesized and characterized. Like monomeric rhodium isocyanide complexes, the dimer has a tendency to associate in solution and reversibly form oligomers. These oligomers have been detected spectroscopically, and concentration dependences verify their formulation as high aggregates. The dimer also undergoes two-center, two-electron oxidative addition with a variety of reagents, including the halogens, methyl iodide, ethyl iodide, and methyl tosylate. These oxidative adducts have been characterized and studied through a variety of techniques. The dimer, unlike rhodium isocyanide monomers, acts as a base and binds one proton in aqueous solution. Titration data are presented, and an approximate […] has been obtained. When treated with aqueous acid, visable light (546 nm) photolysis of solutions of […] yields molecular hydrogen with quantum yields as high as 0.04. The photochemistry is oxygen sensitive, as well as anion dependent. Possible means of exploiting the photoreaction in a solar energy storage scheme is also discussed. In order to better understand the metal-metal interactions in the dimeric species, extended-Huckel molecular orbital calculations were performed on the rhodium dimer, as well as on monomeric fragments with the four isoelectronic metals Ru(O), Pd(II), Co(I), and Ir(I). These results, and their relationship to observed physical properties of the rhodium dimer are discussed in detail.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/0P1Q-WM72, author = {Powers, Dana Auburn}, title = {Magnetic behavior of basic iron(III) compounds. I. Magnetic behavior of the basic iron sulphates and basic iron chromate. II. Magnetic behavior of delta ferric oxide hydroxide}, school = {California Institute of Technology}, year = {1975}, doi = {10.7907/0P1Q-WM72}, url = {https://resolver.caltech.edu/CaltechTHESIS:02112015-085855387}, abstract = {I. The thermomagnetic behavior and infrared spectroscopic features of KFe3(SO4)2(OH)6 (jarosite), (H3O)Fe3(SO4)2 (OH)6 (hydronium jarosite), KFe3(CrO4)2 (OH)6, Fe(OH)SO4 (basic iron sulfate), and Fe(OH)CrO4 (basic iron chromate) are reported. Fe(OH)CrO4 and KFe3(CrO4)2 (OH)6 are shown to be weak ferro magnets with Curie temperatures of 73 and 71 °K, respectively. This unusual magnetic behavior is rationalized in terms of the ionic spin configurations of the phases. Exchange coupling through chromate bridging groups is shown to be weak.
NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
A technique for growing thin film single crystals using tetra-n-butylammonium as a cation is detailed. The polarizations of both ligand field and charge transfer transitions were measured at 5[degrees]K for a number of transition metal monomeric and dimeric species. The polarized spectra for the […] square planar complexes […] and […] confirm the […] nature of the charge transfer bands. Spin orbit coupling was found to be important. The d orbital ordering […] was found. The absorption spectra of the planar chlorobridged species […] and […] were found to exhibit anomalously large intensities for the spin-forbidden bands in the in-plane direction perpendicular to the metal-metal axis. The observed splitting of the lowest spin allowed d-d transition confirms the existence of metal-metal interaction. The ligand field absorption spectra of the square pyramidal […] and […] species are dominated by the equatorial allowed […], dyz transition. Progressions of the totally symmetric metal-nitrogen stretch are observed on the transition. The observation of an axial polarized double progression of the metal-halogen symmetric stretch requires the inclusion of spin orbit coupling. The d orbital ordering […] is identical to that in vanadyl ion. The […] transition in the quadruply bonded […] and […]. species has been positively identified by the MCD and polarization data in the […] complexes, compared to the polarization of this band in the lower symmetry species […]. Progressions of the totally symmetric metal-metal stretch characterize the band envelope. The related […] and […] species also contain an analogous temperature independent band. The applicability of the molecular orbital scheme proposed by Cotton was confirmed. The polarized spectra of the […] anion suggest a […] structure related to the […] complex. The polarization of the absorption bands of […] were distinctly different; this species is known to have a […] confacial bioctahedral structure.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/5KPA-2F87, author = {Geoffroy, Gregory L.}, title = {An investigation of the photochemical and excited state properties of selected second and third row transition metal complexes}, school = {California Institute of Technology}, year = {1974}, doi = {10.7907/5KPA-2F87}, url = {https://resolver.caltech.edu/CaltechETD:etd-10132005-154007}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
The photochemical properties of several different types of 2nd and 3rd row transition metal complexes are discussed. Complexes of the type […] have been prepared and characterized by electronic and infrared absorption spectral measurements. The complexes are readily prepared by thermal anation reactions of [[…]], the aquo complexes being formed by uv irradiation of acidic solutions of […]. The lowest energy electronic absorption band in the […] complexes is assigned to the ligand field transition […], whereas in […] both […] and […] absorptions are observed. The position of the […] transition establishes the order of decreasing ligand field strength of X as […] for both Rh(III) and Ir(III) complexes. Halide-to-metal charge transfer bands are observed for […] complexes with X = […] and […].
Ultraviolet irradiation of H2 and O2 adducts of […], […], […], and […] has been found to induce reductive-elimination of molecular hydrogen and oxygen and regeneration of the square-planar complexes. The reactions occur in argon purged solutions and in frozen EPA solutions of the adducts at 77[degrees]K.
Absorption and emission spectra for the square planar complexes […] and […] have been measured in the solid state and in frozen EPA [ethyl ether-isopentane-ethyl alcohol (5:5:2)] solution at 77[degrees]K. Of the four complexes, only […] fails to luminesce in the solid state at room temperature. At 77[degrees]K in EPA the emission maxima fall in the range 16.8-18.4[…], and the emission lifetimes are between 8.2 and 20.8 […]; […] exhibits an unusually sharp, strongly overlapping emission/absorption system, with an emission quantum yield of 0.93 ± 0.07 It is suggested that in the Ir(I) cases emission occurs from a square planar […] charge transfer state of […] symmetry. The fact that the emission maxima of the two Rh(I) complexes are both red-shifted by about 4000 […] from the lowest absorption peak is discussed in terms of an admixture of ligand field character in the primarily […] emitting state, which could give rise to a distortion of the RhP4 core towards tetrahedral geometry. The absorption and emission spectra of several other Rh(I) complexes are also briefly discussed.
Irradiation of […] in CH3CN results in cleavage of the Re2 quadruple bond and formation of monomeric Re(III) products. The primary photoproduct is […], and this species can be further photolyzed in CH3CN to give […]. The quantum yield of disappearance of […] upon irradiation at 313 nm was found to be 0.017 ± 0.005. […] is also the primary photoproduct under 254 nm irradiation. Irradiation of […] in CH3CN with a He-Ne laser (632.8 nm) does not lead to reaction, indicating that the excited state derived from the […] transition is not photoactive. Cleavage of the Re2 unit is observed, however, when solutions are irradiated at 366 nm.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Hammond, George Simms and Gray, Harry B.}, } @phdthesis{10.7907/28F0-T511, author = {Grunthaner, Frank John}, title = {Electronic structure, surface reactivity and site analysis of transition metal complexes and metalloproteins by X-ray photoelectron spectroscopy}, school = {California Institute of Technology}, year = {1974}, doi = {10.7907/28F0-T511}, url = {https://resolver.caltech.edu/CaltechETD:etd-10282005-125333}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
High resolution x-ray photoelectron core level spectra for a variety of transition metal complexes and metalloproteins are presented and related to questions of surface reactivity, electronic structure and metal ion valency. Core level spectra of VOSO4, VB2, V2O3, V2O5, V, VN, Na3VO4, B2O3, B, H3BO3, […], Au, Laccase, Stellacyanin, Plastocyanin, Hemocyanin, Spinach Ferredoxin, High Potential Iron Protein, […], […], […], […], […], […], […], […], […], […] are reported.
Electron binding energies correlated by internal referencing are tabulated for the species studied.
Charging effects in insulating chemical species are quantified and used to examine the electronic and chemical properties of the compounds studied. It is demonstrated that charge neutralization in electron spectroscopy is primarily due to capture of secondary electrons in the sample chamber with average kinetic energies below 6 eV.
Data handling methods for noise removal based on Fourier methods are presented. Treatment of the observed photoelectron line shape is given and spectral deconvolution is employed in data analysis.
Passivation reactions on vanadium diboride in carboxylic acid attack are attributed to the formation of surface vanadium oxides. Quantitative aspects of the electron spectra are developed, together with observed charging phenomenon, to show the unperturbed observation of adsorbed species on catalytic vanadium oxides.
The valency of copper in Laccase is studied by means of new copper sulfo-complexes and the well-defined proteins Stellacyanin and Plastocyanin. Type 1 and Type 2 copper is observed and Type 3 copper is described by a […] model. Oxyhemocyanin is also studied and assigned in terms of a cupric model.
The […] cluster complex is examined and the mercaptyl and sulfido sulfurs are assigned. Only one iron state is observed, […], supporting the delocalized model of this species. It is suggested that the oxidized and reduced cluster species can be stabilized in the electron spectrometer. By comparison of the photoelectron spectra, the cluster complex is shown to be a reasonable model for 2-Fe and 4-Fe Ferredoxins and a discussion of the spectral differences is given.
The experimental parameters necessary for the successful study of metalloproteins by photoelectron spectroscopy are developed in terms of elemental sensitivity, decomposition profiling, photoreduction, energy reference standards, sample preparation and thermal effects.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/0R6K-3R44, author = {Ellern, James Bernard}, title = {I. Synthetic studies on tertiary vinylogous amides and related compounds. II. Cobalt(II) chloride complexes of tertiary vinylogous amides and related ligands}, school = {California Institute of Technology}, year = {1974}, doi = {10.7907/0R6K-3R44}, url = {https://resolver.caltech.edu/CaltechETD:etd-10132005-080720}, abstract = {NOTE: Text or symbols not renderable in plain ASCII are indicated by […]. Abstract is included in .pdf document.
Tertiary vinylogous amides, both open-chain and cyclic, were prepared by several routes with a view toward their use as ligands for metal ions. It is shown that the thermodynamically preferred isomer (functionality trans) is the exclusive product in the open chain case. A new convenient synthesis of [beta]-aminobutenones is described.
In contrast to previous studies, it was found that activated vinylidene chlorides (AVDC’s) with [alpha]-hydrogen (Cl2C=CH-L, L = carbonyl function or cyano), react with certain secondary amines to give acetylenes, […], either as intermediates or final products except with L = CHO. The mechanism of this reaction is discussed. A simple synthesis of 3,3-dichloropropenoic acid and its conversion to several functional derivatives are described. A case is presented for rotational isomerism in four [beta,beta]-dichlorovinyl carbonyl compounds.
Nuclear magnetic resonance and infrared spectral correlations were made for the compounds prepared. In particular, it is shown that nmr spectroscopy allows ready distinction of piperidino vinylogous ureas from the isomeric acyl ketenaminals of this amine.
Synthesis and partial characterization of complexes of some of the above polarized ethylenes and acetylenes with cobalt(II) chloride are reported. The polarized ethylenes behave somewhat like tertiary amides as ligands; in two cases, different forms of complex with same ligand were found. The “push-pull” acetylenes form 1:1 complexes in which the triple bond absorption(s) of the ligand is absent. The possible implications of this result are discussed.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/ZFYP-9D77, author = {Miskowski, Vincent Mark}, title = {Electronic Structure of Metal Ion-Dioxygen Complexes}, school = {California Institute of Technology}, year = {1973}, doi = {10.7907/ZFYP-9D77}, url = {https://resolver.caltech.edu/CaltechTHESIS:02022018-101456398}, abstract = {The electronic structures of cobalt complexes containing O2 units as ligands have been investigated, primarily by electronic spectroscopy. Various cobalt complexes containing, the structural units present in the O2 complexes were investigated, and a systematic and self-consistent classification of their ligand field electronic transitions, charge-transfer electronic transitions, and excited state reactivities developed, which provided a basis for understanding the O2 complexes.
The O2 complexes investigated were all found to contain low-spin d6 cobalt (III) central metal ions, by spectroscopic criteria, and either peroxide or superoxide ligands. The O2n- ligands have positions in the spectrochemical series between those of ammonia and water, and have characteristic charge-transfer transitions in their complexes, superoxide complexes showing low energy metal-to-ligand transitions, while both superoxide and peroxide complexes show characteristic ligand-to-metal transitions in the UV. Extensive comparisons were made to O2 complexes of other metal ions, and the binding of dioxygen to metal ions concluded to be oxidative addition in general. Autoxidation of metal ions and the structures and properties of oxymetalloproteins have been considered in the light of these results, and the formulation of addition of O2 to Cu(I) and Fe(II) as one- and two-electron oxidative addition, respectively, is discussed.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/XBQW-9V06, author = {Harris, Daniel Charles}, title = {More Fun Than Anything}, school = {California Institute of Technology}, year = {1973}, doi = {10.7907/XBQW-9V06}, url = {https://resolver.caltech.edu/CaltechTHESIS:10232017-110825526}, abstract = {An exhaustive study of piddling cyclopropenium salts is described. This includes synthesis, characterization and the study of ligand
(See PDF)
substitution reactions of the M2Cl62- anions. The electronic absorption spectra and vibrational spectra are interpreted. A normal coordinate analysis of the M2Cl62- anions are reported. Startling counterion effects in ligand substitution reactions in CH2Cl2 solvent were observed.
The transformation M-M → M-H-M+, in which a metal-metal bond is protonated by strong acid, has been studied in several organomettalic systems. Electronic spectra are tentatively interpreted in terms of three-center two-electron M-H-M bonding. The stretching vibrations associated with a W-H-W bridge are assigned. Infrared spectra indicate the presence of isomeric protonated species for several iron compounds. Base strength determination indicates that the replacement of Fe by Ru or replacement of CO by P(OCH3)3 both increase the basicity of [(π-C5H5)Fe(CO)2]2 by at least 2-3 orders of magnitude.
Ancillary chapters deal with the present state of π-cyclopropenium chemistry, predictions about the infrared spectra of π-cyclopropenium complexes and an original technique for graphical display of the concentrations of the various species present during an acid-base titration in acetic acid. A brief description of my advanced placement freshman chemistry course is included.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Rossman, George Robert}, } @phdthesis{10.7907/FJ5R-XJ04, author = {Mortola, Albert Patrick}, title = {Bonding in transition metal compounds}, school = {California Institute of Technology}, year = {1972}, doi = {10.7907/FJ5R-XJ04}, url = {https://resolver.caltech.edu/CaltechTHESIS:11242009-083723341}, 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.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Goddard, William A., III}, } @phdthesis{10.7907/SJD3-AV69, author = {Webb, John Mark}, title = {Structural studies of some polynuclear iron proteins}, school = {California Institute of Technology}, year = {1972}, doi = {10.7907/SJD3-AV69}, url = {https://resolver.caltech.edu/CaltechETD:etd-02042005-105229}, abstract = {The coordination structure and electronic configuration of iron(III) bound in a polynuclear fashion to a number of proteins have been investigated by a variety of physical methods. These have included the temperature dependence of the magnetic susceptibility, electron spin resonance spectroscopy, electronic absorption spectroscopy at low temperatures, vibrational spectroscopy, X-ray analysis, Mossbauer spectroscopy down to helium temperature, and electron spectroscopy for chemical analysis (ESCA). The proteins investigated included the iron transport protein transferrin, the phosphoglycoprotein phosvitin, the gastric juice glycoprotein gastroferrin, and the two iron storage proteins ferritin and hemosiderin. On the basis of the results obtained by these techniques the structural relationship of the iron to the protein and to other iron atoms present in the polynuclear complex was clarified. Structural models for these relationships were proposed for the proteins listed. The implications of these results for the biological role of iron have been considered.}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B. and Saltman, Paul David}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/10588, author = {Bernstein, Paula K.}, title = {Electronic Structure of Complexes of the Ligand o-Phenylenebisdimethylarsine}, school = {California Institute of Technology}, year = {1971}, url = {https://resolver.caltech.edu/CaltechTHESIS:12062017-085349488}, abstract = {Various studies have been carried out to elucidate the detailed electronic structure of the unusual spin doublet complex [Ni(diars)2X2]Y (X = Cl, Br, -NCS; Y = CL, Br, -NCS, ClO4-). An X-ray crystallographic study has been done which confirmed its coordination number of six. U.v. and visible spectra have been taken of it and of other closely related cobalt and nickel complexes. Assignments for the charge transfer and ligand field spectra are suggested. ESR studies have been done in solution, powder, and single crystal to extract the components of the ligand superhyperfine splitting tensors. A semi-quantitative MO scheme, consistent with these tensor values, has been used to explain some of the unusual properties of this complex.
We have concluded from these studies that the energy level ordering in Ni(diarsine)2X2+ is x2 - y- < xz, yz < z2 < xy and that the ground state is 2Ag. The ground state is highly delocalized, consisting of approximately 50% ligand character distributed over all six ligands. The tipping of the benzene rings and the distortion of the axial ligands permits an admixture of chlorine px orbitals into the ground state molecular orbital which serves to further stabilize this system.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/1K1S-M151, author = {Treitel, Irving Marvin}, title = {Electronic Structures of Ligand Bridged Ruthenium and Cobalt Binuclear Complexes}, school = {California Institute of Technology}, year = {1971}, doi = {10.7907/1K1S-M151}, url = {https://resolver.caltech.edu/CaltechTHESIS:12012017-104324366}, abstract = {Bridged superoxo and peroxodecaamminedicobalt complexes have been investigated using electronic room and low temperature spectroscopy. Assignments for these spectra have been proposed. The most important feature in the superoxo spectra is a low energy metal ligand, Co → O2-, charge transfer transition of moderate intensity. Both the superoxide and peroxide ions have been assigned positions in the spectrochemical series. The Dq of superoxide is very close to ammonia, while the Dq of peroxied is between NCS- and H2O. These results have been used to eliminate Fe(III) - O2- as possible model for oxyhemoglobin.
Cyano bridged dicobalt and mixed iron-cobalt dimers have been looked at, and their spectra assigned as simple super-positions of their component parts.
A series of 4+, 5+ and 6+ µ-pyrazinedecaamminediruthenium compounds have been investigated. Magnetic susceptibilities of the 5+ and 6+ compounds were measured and analyzed, assuming a tetragonally distorted d5 ion. Values for the tetragonal field, delocalization, and spin-orbit coupling parameters have been obtained. The 5+ compound gives an ESR signal at room temperature, a result not usually obtained for d5 Ru(III) salts.
Electronic spectra were looked at for the ruthenium pyrazine dimers. The interesting 1570 nm band was found to be temperature independent, indicating an orbitally allowed transition. The origin of this band is discussed. A molecular orbital description of these compounds is suggested. The near IR transition is explained as a b3u (xz + xz) → b2g (xz - xz) d-d transition. The applicability of the Marcus Hush theory of electron transfer to the 5+ cation is discussed.
The crystal structure of µ-nitrogendecaamminediruthemium(II) was determined. The Ru-N-N-Ru linkage is linear, and the N-N distance was found to be 1.124 Å, - only slightly longer than that in free nitrogen. An approximate molecular orbital scheme is given which assumes back donation of electrons from ruthenium d orbitals to the π*N2 orbital.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/JZTQ-Q938, author = {Rossman, George Robert}, title = {I. The heptacyanomolybdate (III) ion : spectroscopic and magnetic properties and chemical reactivity. II. Spectroscopic and magnetic studies of monomeric and dimeric d^5 systems. III. Spectroscopic and magnetic studies of polymeric oxo- and hydroxobridged systems}, school = {California Institute of Technology}, year = {1971}, doi = {10.7907/JZTQ-Q938}, url = {https://resolver.caltech.edu/CaltechTHESIS:12202016-092448657}, abstract = {Heptacyanomolybdate(III), isolated as the potassium salt, K4Mo(CN)7 · 2H2O has been studied by infrared, raman, ESR, magnetic susceptibility, optical spectral, and x-ray techniques. Solutions of the ion have been identified as having a seven-coordinate pentagonal bipyramidal structure, while the structure in the solid potassium salt has been proposed to be a capped trigonal prism. The anhydrous potassium salt, K4Mo(CN)7, and the hydrated cesium salt, Cs4Mo(CN)7 · xH2O also assume the pentagonal bi pyramidal geometry. The molecule is chemically reactive, combining readily in solution with oxygen to form [Mo(CN)7OH2]4- and with halogens to form products which when isolated are waxy and presumably polymeric.
Optical spectra have been obtained for four-, five-, six-, and seven-coordinate manganese(II) and iron(III) compounds. These are used as a basis of comparison for interpretation of the detailed optical and magnetic data obtained on the oxobridged iron(III) dimer enH2[(FeHEDT A)2O] · 6H2O.
The occurrence of simultaneous pair electronic excitations in the dimer is described, and evaluation of the relative merits of the spin-coupling and molecular orbital models for oxobridged dimers is presented. A dihydroxobridged ferric dimer is described as well as a series of dialkoxobridged iron(m) and aluminum dimers derived from metal acetylacetonate and dipivaloylmetane complexes. The extent of antiferromagnetic coupling between the two iron atoms in the dihydroxo- and the dialkoxobridged iron dimers has been found to be nearly identical through variable temperature magnetic susceptibility studies. The magnetic and infrared studies are extended to include a variety of metal oxides, oxy-hydroxides, and natural and synthetic minerals which have various forms of oxo- and hydroxobridging. The OH infrared bands are identified and in some instances, the LN2 temperature positions of the band are compared to the room temperature position. Ferritin models and ferritin micelles are compared to these iron polymers, and the similarity of the infrared spectrum of ferric hydroxide to ferritin micelles is discussed.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/YGXW-1222, author = {Upholt, William Boyce}, title = {Properties of Closed Circular DNA}, school = {California Institute of Technology}, year = {1971}, doi = {10.7907/YGXW-1222}, url = {https://resolver.caltech.edu/CaltechTHESIS:11302017-114639809}, abstract = {A method for the measurement of the superhelix density, σ0, of a closed circular DNA from separation between fluorescent buoyant bands of nicked and closed circular forms in an ethidium bromide-CsCl equilibrium gradient is presented. Nicked and closed circular DNA’s are banded together in a gradient formed by centrifuging a CsCl solution of density 1.56 gm/ml. containing 330 µg/ml ethidium bromide at 20°C for 48 hours in the preparative ultracentrifuge. The separation between the bands, normalized by the separation between the nicked and closed circular forms of a DNA of known superhelix density, is shown to be linearly related to the difference in superhelix density between the DNA’s of known and unknown superhelix densities according to the equation
Δσ0 = (0.115 ± 0.005)(Ωc - 1)
where
Δσ0 = σ0 - σ0* and Ωc = Δr/Δr* r/r (v1θ*-1)2/(v1θ-1)2
Δr is the separation between the bands, r is the average distance of the two bands from the center of rotation, θ is the buoyant density of the DNA and v1 is the partial specific volume of water. The asterisk refers to the reference DNA. A molecular weight dependence of the intercept is seen when λb2b5c DNA (molecular weight 25 x 106) is banded against a SV40 DNA (3 x 106 standard. The relationship was obtained by measuring the separations for DNA’s whose superhelix densities were determined by sedimentation velocity-dye titrations. Native SV40 viral DNA with a superhelix density of -0.039 was used as a standard in all cases. DNA’s with altered superhelix densities were prepared by closing nicked circular DNA’s with polynucleotide ligase under various conditions.
Ten closed SV40 DNA’s with superhelix densities ranging from -0.007 to -0.085 have been prepared. This family of DNA’s has been used to examine the effects of superhelix density on the sedimentation velocity behavior of closed SV40 DNA. The sedimentation coefficient increases as the absolute value of the superhelix density rises from a low value to 0.019, then decreases to a local minimum at 0.035 and finally increases steadily as |σ0| rises to 0.085.
The sedimentation velocity-ethidium bromide titrations of these DNA’s have been converted from the primary s020,* versus c data, in which s020,* is the standard sedimentation coefficient still uncorrected for the buoyant effect of bound ethidium chloride and c is the free ethidium bromide concentration, to the more meaningful s020,w versus σ0 form, with the aid of coefficients in the expression for the free energy of superhelix formation. The resultant curves form a family that is approximately superimposable on the curve for s020,w versus σ0 in the absence of ethidium bromide.
The dependence of the sedimentation coefficient of selected SV40 DNA’s upon ionic strength, the nature of the cation, and temperature is consistent with the previously reported effects of these variables on the rotation angle of the base pairs along the helix axis.
Separations between open and closed circular DNA’s in buoyant CsCl gradients containing the ethidium bromide analogue, propidium di-diodide, are shown to be 1.8 times larger than in ethidium bromide.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Vinograd, Jerome Rubin}, } @phdthesis{10.7907/G8JJ-JX74, author = {Titus, Donald Dean}, title = {Structural Studies of Diethylphenylphosphonite-Transition Metal Complexes}, school = {California Institute of Technology}, year = {1971}, doi = {10.7907/G8JJ-JX74}, url = {https://resolver.caltech.edu/CaltechTHESIS:08232017-162818079}, abstract = {The synthesis and spectral properties of several tetrakis (diethylphenylphosphonite) transition metal complexes are reported.
The crystal structures of the hydrido complexes H2Fe((C6H5)P(OC2H5)2)4 and HCo((C6H5)P(OC2H5)2)4 have been determined. The phosphorus ligands are disposed nearly tetrahedrally about the metal atoms, with the hydrogen ligands occupying faces of the tetrahedra.
Infrared and n.m.r. studies of the hydrido complexes in methylcyclohexane solution indicate that the molecules are stereochemically non-rigid. The classical coordination structures used in discussing rearrangements of five- and six-coordinate complexes (octahedron, square pyramid, and trigonal bipyramid) are found to be inadequate in the discussion of the present complexes. A structure based on a tetrahedral skeleton of phosphorus atoms is presented as an alternative.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/10564, author = {Ottesen, David Keith}, title = {The Vibrational and Electronic Spectrum, and the Potential Field of Various Manganese Carbonyl Complexes}, school = {California Institute of Technology}, year = {1971}, url = {https://resolver.caltech.edu/CaltechTHESIS:11202017-154553422}, abstract = {I. The infra-red and Raman spectra of Mn(CO)5Br as both solid and CH2Cl2 solution from 50 to 2150 cm-1 are presented for the normal isotopic compound, and the 13CO and C18O substituted molecules. The observed bands are assigned, and the force constants and compliance constants of a general quadratic potential field are calculated using the FG method of Wilson, Decius, and Cross.
I. ELECTRONIC STRUCTURE OF METALLOCENES
The electronic absorption spectra of various low-spin d5 and d6 metallocene complexes have been studied in different
environments (glasses, KBr pellets, and single crystals) and as a function of temperature. Ferrocene, phenylferrocene, ruthenocene, and cobalticenium ion were selected in the d6 study and several ferricenium, n-butylferricenium, and 1,1’ -di-n-butylferricenium salts were examined in the d5 case. The electronic spectra of ferrocene and phenylferrocene single crystals at 4.2°K clearly
indicate that the bands at 22,700 cm-1 and 22,400 cm-1, respectively, consist of two electronic transitions each. The corresponding band systems in ruthenocene and cobalticenium ion also exhibit asymmetry at 77 °K. Ligand field theory has been successfully applied to the above d6 metallocenes, utilizing the three observed spin-allowed d-d absorption band positions. Emission of ruthenocene has been observed at 23,300 cm-1 and discussed in conjunction with the reported ferrocene emission. The visible absorption spectra of the various ferricenium complexes show a low-energy charge transfer transition (16,200 cm-1 in the unsubstituted ion). Ring substitution and temperature effects have been used to assign this band to the ligand-to-metal 2E2g → 2E1u transition. The vibrational structure observed for this band at 77°K appears as a doubled progression of the lowest energy a1g vibration. The doubling has been attributed to splitting of the 2E1u excited state. Detailed assignments of this vibrational structure are given for [Fe(cp)2]PF6 and Fe(cp)23. The intense charge transfer band of ferrocene(~ 50,000 cm-1), as well as the corresponding bands in the other d6 metallocenes, have been assigned as ligand-to-metal transitions. A similar assignment has been proposed for the three strong (f ≈ 0.1) bands observed in the ferricenium ultraviolet absorption spectrum.
The ground electronic state [2E2g(a1g)2(e2g)3] of the ferricenium ion has been further characterized by a variable-temperature (40-300°K) magnetic susceptibility study of nine ferricenium and two analogous Fe(III) dicarbollide (1,2-B9C2H112- state. Solvent and counter ion effects on the magnetic properties of the ferricenium ion are appreciable.
Attempts to prepare ruthenicenium salts have resulted in the synthesis and characterization of several interesting ruthenocene derivatives. Contrary to a previous report, electrochemical oxidation of ruthenocene employing a mercury anode yields the mercury-bridged dimer (cp)2Ru-Hg-Ru(cp)22. Analytical, infrared, Raman, and electronic absorption spectral data were utilized in assigning the molecular structure. In particular, a Raman band at 110 cm-1 was assigned to the symmetrical Ru-Hg-Ru stretching mode. Preliminary X-ray crystallographic data for the hexafluorophosphate salt, which was obtained by anion exchange, are in agreement with the above dimeric formulation. Chemical oxidation of ruthenocene by iodine and bromine gives [Ru(cp)2I]I3 and [Ru(cp)2Br]Br3, respectively, as indicated by analytical and spectral data.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{CaltechTHESIS_https://thesis.library.caltech.edu/id/eprint/9143, author = {Preer, James Randolph}, title = {Electronic structure in five-coordinate complexes of nickel(II) with heavy-donor ligands}, school = {California Institute of Technology}, year = {1970}, url = {https://resolver.caltech.edu/CaltechTHESIS:09082015-093220306}, abstract = {I.
Various studies designed to elucidate the electronic structure of the arsenic donor ligand, o-phenylenebisdimethylarsine (diarsine), have been carried out. The electronic spectrum of diarsine has been measured at 300 and 77˚K. Electronic spectra of the molecular complexes of various substituted organoarsines and phosphines with tetracyanoethylene have been measured and used to estimate the relative ionization potentials of these molecules.
Uv photolysis of arsines in frozen solution (96˚K) has yielded thermally labile, paramagnetic products. These include the molecular cations of the photolyzed compounds. The species (diars)+ exhibits hyper-fine splitting due to two equivalent 75As(I=3/2) nuclei. Resonances due to secondary products are reported and assignments discussed.
Evidence is presented for the involvement of d-orbitals in the bonding of arsines. In (diars)+ there is mixing of arsenic “lone-pair” orbitals with benzene ring π-orbitals.
Detailed electronic spectral measurements at 300 and 77˚K have been carried out on five-coordinate complexes of low-spin nickel(II), including complexes of both trigonal bipyramidal (TBP) and square pyramidal (SPY) geometry. TBP complexes are of the form NiLX+ (X=halide or cyanide,
L = Qƭ(CH2)3As(CH3)2]3 or
P [hexagon - Q’CH3] , Q = P, As,
Q’=S, Se).
The electronic spectra of these compounds exhibit a novel feature at low temperature. The first ligand field band, which is asymmetric in the room temperature solution spectrum, is considerably more symmetrical at 77˚K. This effect is interpreted in terms of changes in the structure of the complex.
The SPY complexes are of the form Ni(diars)2Xz (X=CL, Br, CNS, CN, thiourea, NO2, As). On the basis of the spectral results, the d-level ordering is concluded to be xy ˂ xz, yz ˂ z2 ˂˂ x2 - y2. Central to this interpretation is identification of the symmetry-allowed 1A1 → 1E (xz, yz → x2 - y2) transition. This assignment was facilitated by the low temperature measurements.
An assignment of the charge-transfer spectra of the five-coordinate complexes is reported, and electronic spectral criteria for distinguishing the two limiting geometries are discussed.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Gray, Harry B.}, } @phdthesis{10.7907/09YE-YV13, author = {Trifunac, Natalia Pisker}, title = {Photochemical cis-trans isomerization of β-styrylferrocene}, school = {California Institute of Technology}, year = {1970}, doi = {10.7907/09YE-YV13}, url = {https://resolver.caltech.edu/CaltechTHESIS:08312015-100258588}, abstract = {The effect of metal atoms on photochemical transformations has been investigated by studies of the cis-trans isomerization of β-styrylferrocene.
The photostationary state lies entirely on the side of the trans isomer in the cases of direct irradiation at 3130 Å or at 3660 Å. The quantum yield at 3130 Å is 0.00650 and does not vary with concentration. In the presence of benzophenon as sensitizer the quantum yield is 0.00540. On the other hand, the quantum yield for direct irradiation at 3660 Å decreases with increasing concentration of cis β- styrylferrocene varying from 0.00365 to 0.00198.
These results lead to the suggestion that the isomerization takes place from a triplet state of β-styrylferrocene which probably has higher energy than the lowest triplet; reaction from the third triplet seems most likely.
}, address = {1200 East California Boulevard, Pasadena, California 91125}, advisor = {Richards, John H.}, }