Mechanistic studies of a model reaction for enzymatic hydroxylation

A study has been made of the reaction mechanism of a model system for enzymatic hydroxylation. The results of a kinetic study of the hydroxylation of 2-hydroxyazobenzene derivatives by cupric ion and hydrogen peroxide are presented. An investigation of kinetic orders indicates that hydroxylation proceeds by way of a coordinated intermediate complex consisting of cupric ion and the mono anions of 2-hydroxyazobenzene and hydrogen peroxide. Studies with deuterated substrate showed the absence of a primary kinetic isotope effect and no evidence of an NIH shift. The effect of substituents on the formation of intermediate complexes and the overall rate of hydroxylation was studied quantitatively in aqueous solution. The combined results indicate that the hydroxylation step is only slightly influenced by ring substitution. The substituent effect is interpreted in terms of reaction by a radical path or a concerted mechanism in which the formation of ionic intermediates is avoided. The reaction mechanism is discussed as a model for enzymatic hydroxylation.

Heterometallic Complexes as Models of Enzymatic Active Sites

This dissertation describes studies on two multinucleating ligand architectures: the first scaffold was designed to support tricopper complexes, while the second platform was developed to support tri- and tetrametallic clusters.

In Chapter 2, the synthesis of yttrium (and lanthanide) complexes supported by a tripodal ligand framework designed to bind three copper centers in close proximity is described. Tricopper complexes were shown to react with dioxygen in a 1:1 [Cu₃]/O₂ stoichiometry to form intermediates in which the O–O bond was fully cleaved, as characterized via UV-Vis spectroscopy and determination of the reaction stoichiometry. Pre-arrangement of the three Cu centers was pivotal to cooperative O₂ activation, as mono-copper complexes reacted differently with dioxgyen. The reactivity of the observed intermediates was studied with various substrates (reductants, O-atom acceptors, H-atom donors, Brønsted acids) to determine their properties. In Chapter 3, the reactivity of the same yttrium-tricopper complex with nitric oxide was explored. Reductive coupling to form a trans-hyponitrite complex (characterized by X-ray crystallography) was observed via cooperative reactivity by an yttrium and a copper center on two distinct tetrametallic units. The hyponitrite complex was observed to release nitrous oxide upon treatment with a Brønsted acid, supporting its viability as an intermediate in nitric oxide reduction to nitrous oxide.

In Chapter 4, a different multinucleating ligand scaffold was employed to synthesize heterometallic triiron clusters containing one oxide and one hydroxide bridges. The effects of the redox-inactive, Lewis acidic heterometals on redox potential was studied by cyclic voltammetry, unveiling a linear correlation between redox potential and heterometal Lewis acidity. Further studies on these complexes showed that the Lewis acidity of the redox-inactive metals also affected the oxygen-atom transfer reactivity of these clusters. Comparisons of this reactivity with manganese systems, collaborative efforts to reassign the structures of related manganese oxo-hydroxo clusters, and synthetic attempts to access related dioxo clusters are also described.

In Appendix A, ongoing efforts to synthesize new clusters supported by the same multinucleating ligand platform are described. Studies of novel approaches towards ligand exchange in tetrametallic clusters and incorporation of new supporting and bridging ligand motifs in trinuclear complexes are presented.

Brain type II calcium and calmodulin-dependent protein kinase: characterization of a brain-region specific isozyme and regulation by autophosphorylation

A variety of molecular approaches have been used to investigate the structural and enzymatic properties of rat brain type ll Ca^(2+) and calmodulin-dependent protein kinase (type ll CaM kinase). This thesis describes the isolation and biochemical characterization of a brain-region specific isozyme of the kinase and also the regulation the kinase activity by autophosphorylation.

The cerebellar isozyme of the type ll CaM kinase was purified and its biochemical properties were compared to the forebrain isozyme. The cerebellar isozyme is a large (500-kDa) multimeric enzyme composed of multiple copies of 50-kDa α subunits and 60/58-kDa β/β’ subunits. The holoenzyme contains approximately 2 α subunits and 8 β subunits. This contrasts to the forebrain isozyme, which is also composed of and β/β'subunits, but they are assembled into a holoenzyme of approximately 9 α subunits and 3 β/β ' subunits. The biochemical and enzymatic properties of the two isozymes are similar. The two isozymes differ in their association with subcellular structures. Approximately 85% of the cerebellar isozyme, but only 50% of the forebrain isozyme, remains associated with the particulate fraction after homogenization under standard conditions. Postsynaptic densities purified from forebrain contain the forebrain isozyme, and the kinase subunits make up about 16% of their total protein. Postsynaptic densities purified from cerebellum contain the cerebellar isozyme, but the kinase subunits make up only 1-2% of their total protein.

The enzymatic activity of both isozymes of the type II CaM kinase is regulated by autophosphorylation in a complex manner. The kinase is initially completely dependent on Ca^(2+)/calmodulin for phosphorylation of exogenous substrates as well as for autophosphorylation. Kinase activity becomes partially Ca^(2+) independent after autophosphorylation in the presence of Ca^(2+)/calmodulin. Phosphorylation of only a few subunits in the dodecameric holoenzyme is sufficient to cause this change, suggesting an allosteric interaction between subunits. At the same time, autophosphorylation itself becomes independent of Ca^(2+) These observations suggest that the kinase may be able to exist in at least two stable states, which differ in their requirements for Ca^(2+)/calmodulin.

The autophosphorylation sites that are involved in the regulation of kinase activity have been identified within the primary structure of the α and β subunits. We used the method of reverse phase-HPLC tryptic phosphopeptide mapping to isolate individual phosphorylation sites. The phosphopeptides were then sequenced by gas phase microsequencing. Phosphorylation of a single homologous threonine residue in the α and β subunits is correlated with the production of the Ca^(2+) -independent activity state of the kinase. In addition we have identified several sites that are phosphorylated only during autophosphorylation in the absence of Ca^(2+)/ calmodulin.

Proton transfers at the air-water interface

Proton transfer reactions at the interface of water with hydrophobic media, such as air or lipids, are ubiquitous on our planet. These reactions orchestrate a host of vital phenomena in the environment including, for example, acidification of clouds, enzymatic catalysis, chemistries of aerosol and atmospheric gases, and bioenergetic transduction. Despite their importance, however, quantitative details underlying these interactions have remained unclear. Deeper insight into these interfacial reactions is also required in addressing challenges in green chemistry, improved water quality, self-assembly of materials, the next generation of micro-nanofluidics, adhesives, coatings, catalysts, and electrodes. This thesis describes experimental and theoretical investigation of proton transfer reactions at the air-water interface as a function of hydration gradients, electrochemical potential, and electrostatics. Since emerging insights hold at the lipid-water interface as well, this work is also expected to aid understanding of complex biological phenomena associated with proton migration across membranes.

Based on our current understanding, it is known that the physicochemical properties of the gas-phase water are drastically different from those of bulk water. For example, the gas-phase hydronium ion, H₃O⁺(g), can protonate most (non-alkane) organic species, whereas H₃O⁺(aq) can neutralize only relatively strong bases. Thus, to be able to understand and engineer water-hydrophobe interfaces, it is imperative to investigate this fluctuating region of molecular thickness wherein the ‘function’ of chemical species transitions from one phase to another via steep gradients in hydration, dielectric constant, and density. Aqueous interfaces are difficult to approach by current experimental techniques because designing experiments to specifically sample interfacial layers (< 1 nm thick) is an arduous task. While recent advances in surface-specific spectroscopies have provided valuable information regarding the structure of aqueous interfaces, but structure alone is inadequate to decipher the function. By similar analogy, theoretical predictions based on classical molecular dynamics have remained limited in their scope.

Recently, we have adapted an analytical electrospray ionization mass spectrometer (ESIMS) for probing reactions at the gas-liquid interface in real time. This technique is direct, surface-specific,and provides unambiguous mass-to-charge ratios of interfacial species. With this innovation, we have been able to investigate the following:

1. How do anions mediate proton transfers at the air-water interface?

2. What is the basis for the negative surface potential at the air-water interface?

3. What is the mechanism for catalysis ‘on-water’?

In addition to our experiments with the ESIMS, we applied quantum mechanics and molecular dynamics to simulate our experiments toward gaining insight at the molecular scale. Our results unambiguously demonstrated the role of electrostatic-reorganization of interfacial water during proton transfer events. With our experimental and theoretical results on the ‘superacidity’ of the surface of mildly acidic water, we also explored implications on atmospheric chemistry and green chemistry. Our most recent results explained the basis for the negative charge of the air-water interface and showed that the water-hydrophobe interface could serve as a site for enhanced autodissociation of water compared to the condensed phase.

Mathematical study of complex networks : brain, internet, and power grid

The dissertation is concerned with the mathematical study of various network problems. First, three real-world networks are considered: (i) the human brain network (ii) communication networks, (iii) electric power networks. Although these networks perform very different tasks, they share similar mathematical foundations. The high-level goal is to analyze and/or synthesis each of these systems from a “control and optimization” point of view. After studying these three real-world networks, two abstract network problems are also explored, which are motivated by power systems. The first one is “flow optimization over a flow network” and the second one is “nonlinear optimization over a generalized weighted graph”. The results derived in this dissertation are summarized below.

Brain Networks: Neuroimaging data reveals the coordinated activity of spatially distinct brain regions, which may be represented mathematically as a network of nodes (brain regions) and links (interdependencies). To obtain the brain connectivity network, the graphs associated with the correlation matrix and the inverse covariance matrix—describing marginal and conditional dependencies between brain regions—have been proposed in the literature. A question arises as to whether any of these graphs provides useful information about the brain connectivity. Due to the electrical properties of the brain, this problem will be investigated in the context of electrical circuits. First, we consider an electric circuit model and show that the inverse covariance matrix of the node voltages reveals the topology of the circuit. Second, we study the problem of finding the topology of the circuit based on only measurement. In this case, by assuming that the circuit is hidden inside a black box and only the nodal signals are available for measurement, the aim is to find the topology of the circuit when a limited number of samples are available. For this purpose, we deploy the graphical lasso technique to estimate a sparse inverse covariance matrix. It is shown that the graphical lasso may find most of the circuit topology if the exact covariance matrix is well-conditioned. However, it may fail to work well when this matrix is ill-conditioned. To deal with ill-conditioned matrices, we propose a small modification to the graphical lasso algorithm and demonstrate its performance. Finally, the technique developed in this work will be applied to the resting-state fMRI data of a number of healthy subjects.

Communication Networks: Congestion control techniques aim to adjust the transmission rates of competing users in the Internet in such a way that the network resources are shared efficiently. Despite the progress in the analysis and synthesis of the Internet congestion control, almost all existing fluid models of congestion control assume that every link in the path of a flow observes the original source rate. To address this issue, a more accurate model is derived in this work for the behavior of the network under an arbitrary congestion controller, which takes into account of the effect of buffering (queueing) on data flows. Using this model, it is proved that the well-known Internet congestion control algorithms may no longer be stable for the common pricing schemes, unless a sufficient condition is satisfied. It is also shown that these algorithms are guaranteed to be stable if a new pricing mechanism is used.

Electrical Power Networks: Optimal power flow (OPF) has been one of the most studied problems for power systems since its introduction by Carpentier in 1962. This problem is concerned with finding an optimal operating point of a power network minimizing the total power generation cost subject to network and physical constraints. It is well known that OPF is computationally hard to solve due to the nonlinear interrelation among the optimization variables. The objective is to identify a large class of networks over which every OPF problem can be solved in polynomial time. To this end, a convex relaxation is proposed, which solves the OPF problem exactly for every radial network and every meshed network with a sufficient number of phase shifters, provided power over-delivery is allowed. The concept of “power over-delivery” is equivalent to relaxing the power balance equations to inequality constraints.

Flow Networks: In this part of the dissertation, the minimum-cost flow problem over an arbitrary flow network is considered. In this problem, each node is associated with some possibly unknown injection, each line has two unknown flows at its ends related to each other via a nonlinear function, and all injections and flows need to satisfy certain box constraints. This problem, named generalized network flow (GNF), is highly non-convex due to its nonlinear equality constraints. Under the assumption of monotonicity and convexity of the flow and cost functions, a convex relaxation is proposed, which always finds the optimal injections. A primary application of this work is in the OPF problem. The results of this work on GNF prove that the relaxation on power balance equations (i.e., load over-delivery) is not needed in practice under a very mild angle assumption.

Generalized Weighted Graphs: Motivated by power optimizations, this part aims to find a global optimization technique for a nonlinear optimization defined over a generalized weighted graph. Every edge of this type of graph is associated with a weight set corresponding to the known parameters of the optimization (e.g., the coefficients). The motivation behind this problem is to investigate how the (hidden) structure of a given real/complex valued optimization makes the problem easy to solve, and indeed the generalized weighted graph is introduced to capture the structure of an optimization. Various sufficient conditions are derived, which relate the polynomial-time solvability of different classes of optimization problems to weak properties of the generalized weighted graph such as its topology and the sign definiteness of its weight sets. As an application, it is proved that a broad class of real and complex optimizations over power networks are polynomial-time solvable due to the passivity of transmission lines and transformers.

Phase behavior of complex superprotonic solid acids

Superprotonic phase transitions and thermal behaviors of three complex solid acid systems are presented, namely Rb3H(SO4)2-RbHSO4 system, Rb3H(SeO4)2-Cs3H(SeO4)2 solid solution system, and Cs6(H2SO4)3(H1.5PO4)4. These material systems present a rich set of phase transition characteristics that set them apart from other, simpler solid acids. A.C. impedance spectroscopy, high-temperature X-ray powder diffraction, and thermal analysis, as well as other characterization techniques, were employed to investigate the phase behavior of these systems.

Rb3H(SO4)2 is an atypical member of the M3H(XO4)2 class of compounds (M = alkali metal or NH4+ and X = S or Se) in that a transition to a high-conductivity state involves disproportionation into two phases rather than a simple polymorphic transition [1]. In the present work, investigations of the Rb3H(SO4)2-RbHSO4 system have revealed the disproportionation products to be Rb2SO4 and the previously unknown compound Rb5H3(SO4)4. The new compound becomes stable at a temperature between 25 and 140 °C and is isostructural to a recently reported trigonal phase with space group P3̅m of Cs5H3(SO4)4 [2]. At 185 °C the compound undergoes an apparently polymorphic transformation with a heat of transition of 23.8 kJ/mol and a slight additional increase in conductivity.

The compounds Rb3H(SeO4)2 and Cs3H(SeO4)2, though not isomorphous at ambient temperatures, are quintessential examples of superprotonic materials. Both adopt monoclinic structures at ambient temperatures and ultimately transform to a trigonal (R3̅m) superprotonic structure at slightly elevated temperatures, 178 and 183 °C, respectively. The compounds are completely miscible above the superprotonic transition and show extensive solubility below it. Beyond a careful determination of the phase boundaries, we find a remarkable 40-fold increase in the superprotonic conductivity in intermediate compositions rich in Rb as compared to either end-member.

The compound Cs6(H2SO4)3(H1.5PO4)4 is unusual amongst solid acid compounds in that it has a complex cubic structure at ambient temperature and apparently transforms to a simpler cubic structure of the CsCl-type (isostructural with CsH2PO4) at its transition temperature of 100-120 °C [3]. Here it is found that, depending on the level of humidification, the superprotonic transition of this material is superimposed with a decomposition reaction, which involves both exsolution of (liquid) acid and loss of H2O. This reaction can be suppressed by application of sufficiently high humidity, in which case Cs6(H2SO4)3(H1.5PO4)4 undergoes a true superprotonic transition. It is proposed that, under conditions of low humidity, the decomposition/dehydration reaction transforms the compound to Cs6(H2-0.5xSO4)3(H1.5PO4)4-x, also of the CsCl structure type at the temperatures of interest, but with a smaller unit cell. With increasing temperature, the decomposition/dehydration proceeds to greater and greater extent and unit cell of the solid phase decreases. This is identified to be the source of the apparent negative thermal expansion behavior.

References

[1] L.A. Cowan, R.M. Morcos, N. Hatada, A. Navrotsky, S.M. Haile, Solid State Ionics 179 (2008) (9-10) 305.

[2] M. Sakashita, H. Fujihisa, K.I. Suzuki, S. Hayashi, K. Honda, Solid State Ionics 178 (2007) (21-22) 1262.

[3] C.R.I. Chisholm, Superprotonic Phase Transitions in Solid Acids: Parameters affecting the presence and stability of superprotonic transitions in the MHnXO4 family of compounds (X=S, Se, P, As; M=Li, Na, K, NH4, Rb, Cs), Materials Science, California Institute of Technology, Pasadena, California (2003).

Catalytic conversion of nitrogen to ammonia by an iron model complex

Threefold symmetric Fe phosphine complexes have been used to model the structural and functional aspects of biological N₂ fixation by nitrogenases. Low-valent bridging Fe-S-Fe complexes in the formal oxidation states Fe(II)Fe(II), Fe(II)/Fe(I), and Fe(I)/Fe(I) have been synthesized which display rich spectroscopic and magnetic behavior. A series of cationic tris-phosphine borane (TPB) ligated Fe complexes have been synthesized and been shown to bind a variety of nitrogenous ligands including N₂H₄, NH₃, and NH₂-. These complexes are all high spin S = 3/2 and display EPR and magnetic characteristics typical of this spin state. Furthermore, a sequential protonation and reduction sequence of a terminal amide results in loss of NH₃ and uptake of N₂. These stoichiometric transformations represent the final steps in potential N₂ fixation schemes.

Treatment of an anionic FeN₂ complex with excess acid also results in the formation of some NH₃, suggesting the possibility of a catalytic cycle for the conversion of N₂ to NH₃ mediated by Fe. Indeed, use of excess acid and reductant results in the formation of seven equivalents of NH₃ per Fe center, demonstrating Fe mediated catalytic N₂ fixation with acids and protons for the first time. Numerous control experiments indicate that this catalysis is likely being mediated by a molecular species.

A number of other phosphine ligated Fe complexes have also been tested for catalysis and suggest that a hemi-labile Fe-B interaction may be critical for catalysis. Additionally, various conditions for the catalysis have been investigated. These studies further support the assignment of a molecular species and delineate some of the conditions required for catalysis.

Finally, combined spectroscopic studies have been performed on a putative intermediate for catalysis. These studies converge on an assignment of this new species as a hydrazido(2-) complex. Such species have been known on group 6 metals for some time, but this represents the first characterization of this ligand on Fe. Further spectroscopic studies suggest that this species is present in catalytic mixtures, which suggests that the first steps of a distal mechanism for N₂ fixation are feasible in this system.

A new high-order Fourier continuation-based elasticity solver for complex three-dimensional geometries

This thesis presents a new approach for the numerical solution of three-dimensional problems in elastodynamics. The new methodology, which is based on a recently introduced Fourier continuation (FC) algorithm for the solution of Partial Differential Equations on the basis of accurate Fourier expansions of possibly non-periodic functions, enables fast, high-order solutions of the time-dependent elastic wave equation in a nearly dispersionless manner, and it requires use of CFL constraints that scale only linearly with spatial discretizations. A new FC operator is introduced to treat Neumann and traction boundary conditions, and a block-decomposed (sub-patch) overset strategy is presented for implementation of general, complex geometries in distributed-memory parallel computing environments. Our treatment of the elastic wave equation, which is formulated as a complex system of variable-coefficient PDEs that includes possibly heterogeneous and spatially varying material constants, represents the first fully-realized three-dimensional extension of FC-based solvers to date. Challenges for three-dimensional elastodynamics simulations such as treatment of corners and edges in three-dimensional geometries, the existence of variable coefficients arising from physical configurations and/or use of curvilinear coordinate systems and treatment of boundary conditions, are all addressed. The broad applicability of our new FC elasticity solver is demonstrated through application to realistic problems concerning seismic wave motion on three-dimensional topographies as well as applications to non-destructive evaluation where, for the first time, we present three-dimensional simulations for comparison to experimental studies of guided-wave scattering by through-thickness holes in thin plates.

Intramolecular conflict : conformation and self-assembly of architecturally complex macromolecules in solution

The solution behavior of linear polymer chains is well understood, having been the subject of intense study throughout the previous century. As plastics have become ubiquitous in everyday life, polymer science has grown into a major field of study. The conformation of a polymer in solution depends on the molecular architecture and its interactions with the surroundings. Developments in synthetic techniques have led to the creation of precision-tailored polymeric materials with varied topologies and functionalities. In order to design materials with the desired properties, it is imperative to understand the relationships between polymer architecture and their conformation and behavior. To meet that need, this thesis investigates the conformation and self-assembly of three architecturally complex macromolecular systems with rich and varied behaviors driven by the resolution of intramolecular conflicts. First we describe the development of a robust and facile synthetic approach to reproducible bottlebrush polymers (Chapter 2). The method was used to produce homologous series of bottlebrush polymers with polynorbornene backbones, which revealed the effect of side-chain and backbone length on the overall conformation in both good and theta solvent conditions (Chapter 3). The side-chain conformation was obtained from a series of SANS experiments and determined to be indistinguishable from the behavior of free linear polymer chains. Using deuterium-labeled bottlebrushes, we were able for the first time to directly observe the backbone conformation of a bottlebrush polymer which showed self-avoiding walk behavior. Secondly, a series of SANS experiments was conducted on a homologous series of Side Group Liquid Crystalline Polymers (SGLCPs) in a perdeuterated small molecule liquid crystal (5CB). Monodomain, aligned, dilute samples of SGLCP-b-PS block copolymers were seen to self-assemble into complex micellar structures with mutually orthogonally oriented anisotropies at different length scales (Chapter 4). Finally, we present the results from the first scattering experiments on a set of fuel-soluble, associating telechelic polymers. We observed the formation of supramolecular aggregates in dilute (≤0.5wt%) solutions of telechelic polymers and determined that the choice of solvent has a significant effect on the strength of association and the size of the supramolecules (Chapter 5). A method was developed for the direct estimation of supramolecular aggregation number from SANS data. The insight into structure-property relationships obtained from this work will enable the more targeted development of these molecular architectures for their respective applications.

Complex behavior and perception in Drosophila emerges from iterative feedback-regulated reflexes

For a hungry fruit fly, locating and landing on a fermenting fruit where it can feed, find mates, and lay eggs, is an essential and difficult task requiring the integration of both olfactory and visual cues. Understanding how flies accomplish this will help provide a comprehensive ethological context for the expanding knowledge of their neural circuits involved in processing olfaction and vision, as well as inspire novel engineering solutions for control and estimation in computationally limited robotic applications. In this thesis, I use novel high throughput methods to develop a detailed overview of how flies track odor plumes, land, and regulate flight speed. Finally, I provide an example of how these insights can be applied to robotic applications to simplify complicated estimation problems. To localize an odor source, flies exhibit three iterative, reflex-driven behaviors. Upon encountering an attractive plume, flies increase their flight speed and turn upwind using visual cues. After losing the plume, flies begin zigzagging crosswind, again using visual cues to control their heading. After sensing an attractive odor, flies become more attracted to small visual features, which increases their chances of finding the plume source. Their changes in heading are largely controlled by open-loop maneuvers called saccades, which they direct towards and away from visual features. If a fly decides to land on an object, it begins to decelerate so as to maintain a stereotypical ratio of expansion to retinal size. Once they reach a stereotypical distance from the target, flies extend their legs in preparation for touchdown. Although it is unclear what cues they use to trigger this behavior, previous studies have indicated that it is likely under visual control. In Chapter 3, I use a nonlinear control theoretic analysis and robotic testbed to propose a novel and putative mechanism for how a fly might visually estimate distance by actively decelerating according to a visual control law. Throughout these behaviors, a common theme is the visual control of flight speed. Using genetic tools I show that the neuromodulator octopamine plays an important role in regulating flight speed, and propose a neural circuit for how this controller might be implemented in the flies brain. Two general biological and engineering principles are evident across my experiments: (1) complex behaviors, such as foraging, can emerge from the interactions of simple independent sensory-motor modules; (2) flies control their behavior in such a way that simplifies complex estimation problems.

Geological evolution of two crustal scale shear zones. Part I. The Rand thrust complex, northwestern Mojave Desert, California. Part II. The Magdalena metamorphic core complex, north central Sonora, Mexico

The geology and structure of two crustal scale shear zones were studied to understand the partitioning of strain within intracontinental orogenic belts. Movement histories and regional tectonic implications are deduced from observational data. The two widely separated study areas bear the imprint of intense Late Mesozoic through Middle Cenozoic tectonic activity. A regional transition from Late Cretaceous-Early Tertiary plutonism, metamorphism, and shortening strain to Middle Tertiary extension and magmatism is preserved in each area, with contrasting environments and mechanisms. Compressional phases of this tectonic history are better displayed in the Rand Mountains, whereas younger extensional structures dominate rock fabrics in the Magdalena area.

In the northwestern Mojave desert, the Rand Thrust Complex reveals a stack of four distinctive tectonic plates offset along the Garlock Fault. The lowermost plate, Rand Schist, is composed of greenschist facies metagraywacke, metachert, and metabasalt. Rand Schist is structurally overlain by Johannesburg Gneiss (= garnet-amphibolite grade orthogneisses, marbles and quartzites), which in turn is overlain by a Late Cretaceous hornblende-biotite granodiorite. Biotite granite forms the fourth and highest plate. Initial assembly of the tectonic stack involved a Late Cretaceous? south or southwest vergent overthrusting event in which Johannesburg Gneiss was imbricated and attenuated between Rand Schist and hornblende-biotite granodiorite. Thrusting postdated metamorphism and deformation of the lower two plates in separate environments. A post-kinematic stock, the Late Cretaceous Randsburg Granodiorite, intrudes deep levels of the complex and contains xenoliths of both Rand Schist and mylonitized Johannesburg? gneiss. Minimum shortening implied by the map patterns is 20 kilometers.

Some low angle faults of the Rand Thrust Complex formed or were reactivated between Late Cretaceous and Early Miocene time. South-southwest directed mylonites derived from Johannesburg Gneiss are commonly overprinted by less penetrative north-northeast vergent structures. Available kinematic information at shallower structural levels indicates that late disturbance(s) culminated in northward transport of the uppermost plate. Persistence of brittle fabrics along certain structural horizons suggests a possible association of late movement(s) with regionally known detachment faults. The four plates were juxtaposed and significant intraplate movements had ceased prior to Early Miocene emplacement of rhyolite porphyry dikes.

In the Magdalena region of north central Sonora, components of a pre-Middle Cretaceous stratigraphy are used as strain markers in tracking the evolution of a long lived orogenic belt. Important elements of the tectonic history include: (1) Compression during the Late Cretaceous and Early Tertiary, accompanied by plutonism, metamorphism, and ductile strain at depth, and thrust driven? syntectonic sedimentation at the surface. (2) Middle Tertiary transition to crustal extension, initially recorded by intrusion of leucogranites, inflation of the previously shortened middle and upper crustal section, and surface volcanism. (3) Gravity induced development of a normal sense ductile shear zone at mid crustal levels, with eventual detachment and southwestward displacement of the upper crustal stratigraphy by Early Miocene time.

Elucidation of the metamorphic core complex evolution just described was facilitated by fortuitous preservation of a unique assemblage of rocks and structures. The "type" stratigraphy utilized for regional correlation and strain analysis includes a Jurassic volcanic arc assemblage overlain by an Upper Jurassic-Lower Cretaceous quartz pebble conglomerate, in turn overlain by marine strata with fossiliferous Aptian-Albian limestones. The Jurassic strata, comprised of (a) rhyolite porphyries interstratified with quartz arenites, (b) rhyolite cobble conglomerate, and (c) intrusive granite porphyries, are known to rest on Precambrian basement north and east of the study area. The quartz pebble conglomerate is correlated with the Glance Conglomerate of southeastern Arizona and northeastern Sonora. The marine sequence represents part of an isolated arm? of the Bisbee Basin.

Crosscutting structural relationships between the pre-Middle Cretaceous supracrustal section, younger plutons, and deformational fabrics allow the tectonic sequence to be determined. Earliest phases of a Late Cretaceous-Early Tertiary orogeny are marked by emplacement of the 78 ± 3 Ma Guacomea Granodiorite (U/Pb zircon, Anderson et al., 1980) as a sill into deep levels of the layered Jurassic series. Subsequent regional metamorphism and ductile strain is recorded by a penetrative schistosity and lineation, and east-west trending folds. These fabrics are intruded by post-kinematic Early Tertiary? two mica granites. At shallower crustal levels, the orogeny is represented by north directed thrust faulting, formation of a large intermontane basin, and development of a pronounced unconformity. A second important phase of ductile strain followed Middle Tertiary? emplacement of leucogranites as sills and northwest trending dikes into intermediate levels of the deformed section (surficial volcanism was also active during this transitional period to regional extension). Gravitational instabilities resulting from crustal swelling via intrusion and thermal expansion led to development of a ductile shear zone within the stratigraphic horizon occupied by a laterally extensive leucogranite sill. With continued extension, upper crustal brittle normal faults (detachment faults) enhanced the uplift and tectonic denudation of this mylonite zone, ultimately resulting in southwestward displacement of the upper crustal stratigraphy.

Strains associated with the two ductile deformation events have been successfully partitioned through a multifaceted analysis. R_f/Ø measurements on various markers from the "type" stratigraphy allow a gradient representing cumulative strain since Middle Cretaceous time to be determined. From this gradient, noncoaxial strains accrued since emplacement of the leucogranites may be removed. Irrotational components of the postleucogranite strain are measured from quartz grain shapes in deformed granites; rotational components (shear strains) are determined from S-C fabrics and from restoration of rotated dike and vein networks. Structural observations and strain data are compatable with a deformation path of: (1) coaxial strain (pure shear?), followed by (2) injection of leucogranites as dikes (perpendicular to the minimum principle stress) and sills (parallel to the minimum principle stress), then (3) southwest directed simple shear. Modeling the late strain gradient as a simple shear zone permits a minimum displacement of 10 kilometers on the Magdalena mylonite zone/detachment fault system. Removal of the Middle Tertiary noncoaxial strains yields a residual (or pre-existing) strain gradient representative of the Late Cretaceous-Early Tertiary deformation. Several partially destrained cross sections, restored to the time of leucogranite emplacement, illustrate the idea that the upper plate of the core complex bas been detached from a region of significant topographic relief. 50% to 100% bulk extension across a 50 kilometer wide corridor is demonstrated.

Late Cenozoic tectonics of the Magdalena region are dominated by Basin and Range style faulting. Northeast and north-northwest trending high angle normal faults have interacted to extend the crust in an east-west direction. Net extension for this period is minor (10% to 15%) in comparison to the Middle Tertiary detachment related extensional episode.

Organotitanium and niobium chemistry. I. Structure and reactivity of a titanium ethylene complex. II. Reactivity of decamethyl niobocene derivatives

The synthesis and X-ray diffraction study of bis(pentamethylcyclopentadienyl) ethylene titanium (I) are reported. This complex represents the first example of an isolable ethylene adduct of a group IV metal, a key intermediate in Ziegler-Natta olefin polymerization schemes. While treatment of I with ethylene leads to only traces of polymer after months, I participates in a wide range of stoichiometric and catalytic reactions. These include the catalytic conversion of ethylene specifically to butadiene and ethane and the catalytic isomerization of alkenes. Detailed studies have been carried out on the stoichiometric reactions of I with nitriles and alkynes. At low temperatures, nitriles react to form metallacycloimine species which more slowly undergo a formal 1,3-hydrogen shift to generate metallacycloeneamines. The lowest energy pathway for this rearrangement is an intramolecular hydrogen shift which is sensitive to the steric bulk of the R substituent. The reactions of I with alkynes yield metallacyclopentene complexes with high regioisomer selectivity. Carbonylation of the metallacyclopentene (η-C₅Me₅5)₂TiC(CH₃)=C(CH₃)CH₂ under relatively mild conditions cleanly produces the corresponding cyclopentenone and [C₅(CH₃)₅]₂Ti(CO)₂. Compounds derived from CO₂ and acetaldehyde have also been isolated.

The synthesis and characterization of bis-(η-pentamethylcyclopentadienyl) niobium(III) tetrahydroborate (II) are described and a study of its temperature-dependent proton NMR spectroscopic behavior is reported. The complex is observed to undergo a rapid intramolecular averaging process at elevated temperatures. The free energy of activation, ΔG^≠ = 16.4 ± 0.4 kcal/mol, is calculated. The reinvestigation of a related compound, bis(η-cyclopentadienyl)niobium(III) tetrahydroborate, established ΔG^≠ = 14.6 ± 0.2 kcal/mol for the hydrogen exchange process. The tetrahydroborate complex, II reacts with pyridine and dihydrogen to yield (η-C₅Me₅5)₂NbH₃ (III). The reactivity of III with CO and ethylene is reported.

Random propagation in complex systems : nonlinear matrix recursions and epidemic spread

This dissertation studies long-term behavior of random Riccati recursions and mathematical epidemic model. Riccati recursions are derived from Kalman filtering. The error covariance matrix of Kalman filtering satisfies Riccati recursions. Convergence condition of time-invariant Riccati recursions are well-studied by researchers. We focus on time-varying case, and assume that regressor matrix is random and identical and independently distributed according to given distribution whose probability distribution function is continuous, supported on whole space, and decaying faster than any polynomial. We study the geometric convergence of the probability distribution. We also study the global dynamics of the epidemic spread over complex networks for various models. For instance, in the discrete-time Markov chain model, each node is either healthy or infected at any given time. In this setting, the number of the state increases exponentially as the size of the network increases. The Markov chain has a unique stationary distribution where all the nodes are healthy with probability 1. Since the probability distribution of Markov chain defined on finite state converges to the stationary distribution, this Markov chain model concludes that epidemic disease dies out after long enough time. To analyze the Markov chain model, we study nonlinear epidemic model whose state at any given time is the vector obtained from the marginal probability of infection of each node in the network at that time. Convergence to the origin in the epidemic map implies the extinction of epidemics. The nonlinear model is upper-bounded by linearizing the model at the origin. As a result, the origin is the globally stable unique fixed point of the nonlinear model if the linear upper bound is stable. The nonlinear model has a second fixed point when the linear upper bound is unstable. We work on stability analysis of the second fixed point for both discrete-time and continuous-time models. Returning back to the Markov chain model, we claim that the stability of linear upper bound for nonlinear model is strongly related with the extinction time of the Markov chain. We show that stable linear upper bound is sufficient condition of fast extinction and the probability of survival is bounded by nonlinear epidemic map.

Direct simulation of quantum dynamics in complex systems

Accurate simulation of quantum dynamics in complex systems poses a fundamental theoretical challenge with immediate application to problems in biological catalysis, charge transfer, and solar energy conversion. The varied length- and timescales that characterize these kinds of processes necessitate development of novel simulation methodology that can both accurately evolve the coupled quantum and classical degrees of freedom and also be easily applicable to large, complex systems. In the following dissertation, the problems of quantum dynamics in complex systems are explored through direct simulation using path-integral methods as well as application of state-of-the-art analytical rate theories.

Models of the Oxygen-Evolving Complex of Photosystem II

In the five chapters that follow, I delineate my efforts over the last five years to synthesize structurally and chemically relevant models of the Oxygen Evolving Complex (OEC) of Photosystem II. The OEC is nature’s only water oxidation catalyst, in that it forms the dioxygen in our atmosphere necessary for oxygenic life. Therefore understanding its structure and function is of deep fundamental interest and could provide design elements for artificial photosynthesis and manmade water oxidation catalysts. Synthetic endeavors towards OEC mimics have been an active area of research since the mid 1970s and have mutually evolved alongside biochemical and spectroscopic studies, affording ever-refined proposals for the structure of the OEC and the mechanism of water oxidation. This research has culminated in the most recent proposal: a low symmetry Mn₄CaO₅ cluster with a distorted Mn₃CaO₄ cubane bridged to a fourth, dangling Mn. To give context for how my graduate work fits into this rich history of OEC research, Chapter 1 provides a historical timeline of proposals for OEC structure, emphasizing the role that synthetic Mn and MnCa clusters have played, and ending with our Mn₃CaO₄ heterometallic cubane complexes.

In Chapter 2, the triarylbenzene ligand framework used throughout my work is introduced, and trinuclear clusters of Mn, Co, and Ni are discussed. The ligand scaffold consistently coordinates three metals in close proximity while leaving coordination sites open for further modification through ancillary ligand binding. The ligands coordinated could be varied, with a range of carboxylates and some less coordinating anions studied. These complexes’ structures, magnetic behavior, and redox properties are discussed.

Chapter 3 explores the redox chemistry of the trimanganese system more thoroughly in the presence of a fourth Mn equivalent, finding a range of oxidation states and oxide incorporation dependent on oxidant, solvent, and Mn salt. Oxidation states from Mn^II₄ to Mn^IIIMn^IV₃ were observed, with 1-4 O^2– ligands incorporated, modeling the photoactivation of the OEC. These complexes were studied by X-ray diffraction, EPR, XAS, magnetometry, and CV.

As Ca²⁺ is a necessary component of the OEC, Chapter 4 discusses synthetic strategies for making highly structurally accurate models of the OEC containing both Mn and Ca in the Mn₃CaO₄ cubane + dangling Mn geometry. Structural and electrochemical characterization of the first Mn₃CaO₄ heterometallic cubane complex— and comparison to an all-Mn Mn₄O₄ analog—suggests a role for Ca²⁺ in the OEC. Modification of the Mn₃CaO₄ system by ligand substitution affords low symmetry Mn₃CaO₄ complexes that are the most accurate models of the OEC to date.

Finally, in Chapter 5 the reactivity of the Mn₃CaO₄ cubane complexes toward O- atom transfer is discussed. The metal M strongly affects the reactivity. The mechanisms of O-atom transfer and water incorporation from and into Mn₄O₄ and Mn₄O₃ clusters, respectively, are studied through computation and ¹⁸O-labeling studies. The μ3-oxos of the Mn₄O₄ system prove fluxional, lending support for proposals of O^2– fluxionality within the OEC.