Electrochemical and electron transfer investigations of copper proteins

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.

I. Thermochemistry and reaction kinetics of disolvated protons by ion cyclotron resonance spectroscopy. II. Thermochemical studies of small fluorocarbons by photoionization mass spectrometry

The disolvated proton, H(OH₂)₂⁺ is employed as a chemical reagent in low pressure (˂ 10^-5 torr) investigations by ion cyclotron resonance spectroscopy. Since termolecular reactions are absent at low pressure, disolvated protons are not generally observed. However H(OH₂)₂⁺ is produced in a sequence of bimolecular reactions in mixtures containing H₂O and one of a small number of organohalide precursors. Then a series of hydrated Lewis bases is produced by H₃O⁺ transfer from H(OH₂)₂⁺. In Chapter II, the relative stability of hydrated bases containing heteroatoms of both first and second row elements is determined from the preferred direction of H₃O⁺ transfer between BH(OH₂)⁺ complexes. S and P containing bases are shown to bind H₃O⁺ more weakly than O and N bases with comparable proton affinities. A simple model of hydrogen bonding is proposed to account for these observations.

H⁺ transfer from H(OH₂)₂⁺ to several Lewis bases also occurs at low pressure. In Chapter III the relative importance of H₃O⁺ transfer and H⁺ transfer from H(OH₂)₂⁺ to a series of bases is observed to be a function of base strength. Beginning with CH₃COOH, the weakest base for which H⁺ transfer is observed, the importance of H⁺ transfer increases with increasing proton affinity of the acceptor base. The nature of neutral products formed from H(OH₂)₂⁺ by loss of H⁺ is also considered.

Chapters IV and V deal with thermochemistry of small fluorocarbons determined by photoionization mass spectrometry. The enthalpy of formation of CF₂ is considered in Chapter IV. Photoionization of perfluoropropylene, perfluorocyclopropane, and trifluoromethyl benzene yield onsets for ions formed by loss of a CF₂ neutral fragment. Earlier determinations of ΔH^°_f298 (CF₂) are reinterpreted using updated thermochemical values and compared with results of this study. The heat of formation of neutral perfluorocyclopropane is also derived. Finally, the energetics of interconversion of perfluoropropylene and perfluorocyclopropane are considered for both the neutrals and their molecular ions.

In Chapter V the heats of formation of CF₃⁺ and CF₃I⁺are derived from photoionization of CF₃I. These are considered with respect to ion-molecule reactions observed in CF₃I monitored by the techniques of ion cyclotron resonance spectroscopy. Results obtained in previous experiments are also compared.

Zirconocenes as models for homogeneous Ziegler-Natta olefin polymerization catalysts

Using density functional theory, we studied the fundamental steps of olefin polymerization for zwitterionic and cationic Group IV ansa-zirconocenes and a neutral ansa- yttrocene. Complexes [H₂E(C₅H₄)₂ZrMe]ⁿ (n = 0: E = BH₂ (1), BF₂ (2), AlH₂(3); n = +: E = CH₂(4), SiH₂(5)) and H₂Si(C₅H₄)₂YMe were used as computational models. The largest differences among these three classes of compounds were the strength of olefin binding and the stability of the β-agostic alkyl intermediate towards β-hydrogen elimination. We investigated the effect of solvent on the reaction energetics for land 5. We found that in benzene the energetics became very similar except that a higher olefin insertion barrier was calculated for 1. The calculated anion affinity of [CH₃BF₃]^- was weaker towards 1 than 5. The calculated olefin binding depended primarily on the charge of the ansa linker, and the olefin insertion barrier was found to decrease steadily in the following order: [H₂C(C₅H₄)₂ZrMe]⁺ > [F₂B(C₅H₄)₂ZrMe] ≈ [H₂B(C₅H₄)₂ZrMe] > [H₂Si(C₅H₄)₂ZrMe]⁺ > [H₂Al(C₅H₄)₂ZrMe].

We prepared ansa-zirconocene dicarbonyl complexes Me₂ECp₂Zr(CO)₂ (E = Si, C), and t-butyl substituted complexes (t-BuCp)₂Zr(CO)₂, Me₂E(t-BuCp)₂Zr(CO)₂ (E = Si, C), (Me₂Si)₂(t-BuCp)₂Zr(CO)₂ as well as analogous zirconocene complexes. Both the reduction potentials and carbonyl stretching frequencies follow the same order: Me₂SiCp₂ZrCl₂> Me₂CCp₂ZrCl₂> Cp₂ZrCl₂> (Me₂Si)₂Cp₂ZrCl₂. This ordering is a result of both the donating abilities of the cyclopentadienyl substituents and the orientation of the cyclopentadiene rings. Additionally, we prepared a series of analogous cationic zirconocene complexes [LZrOCMe₃][MeB(C₆F₅)₃] (L = CP₂, Me₂SiCp₂, Me₂CCP₂, (Me₂Si)₂Cp₂) and studied the kinetics of anion dissociation. We found that the enthalpy of anion dissociation increased from 10.3 kcal•mol^-1 to 17.6 kcal•mol^-1 as exposure of the zirconium center increased.

We also prepared series of zirconocene complexes bearing 2,2-dimethyl-2-sila-4-pentenyl substituents (and methyl-substituted olefin variants). Methide abstraction with B(C₆F₅) results in reversible coordination of the tethered olefin to the cationic zirconium center. The kinetics of olefin dissociation have been examined using NMR methods, and the effects of ligand variation for unlinked, singly [SiMe₂]-linked and doubly [SiMe₂]-linked bis(cyclopentadienyl) arrangements has been compared (ΔG‡ for olefin dissociation varies from 12.8 to 15.6 kcal•mol^-1). Methide abstraction from 1,2-(SiMe₂)₂(η⁵-C₅H₃)₂Zr(CH₃)-(CH₂CMe₂CH₂CH = CH₂) results in rapid β-allyl elimination with loss of isobutene yielding the allyl cation [{1,2-(SiMe₂)₂(η⁵-C₅H₃)₂Zr(η³-CH₂CH=CH₂)]⁺.

Zn-VI/Cu2O Heterojunctions for Earth-Abundant Photovoltaics

The need for sustainable energy production motivates the study of photovoltaic materials, which convert energy from sunlight directly into electricity. This work has focused on the development of Cu₂O as an earth-abundant solar absorber due to the abundance of its constituent elements in the earth's crust, its suitable band gap, and its potential for low cost processing. Crystalline wafers of Cu₂O with minority carrier diffusion lengths on the order of microns can be manufactured in a uniquely simple fashion — directly from copper foils by thermal oxidation. Furthermore, Cu₂O has an optical band gap of 1.9 eV, which gives it a detailed balance energy conversion efficiency of 24.7% and the possibility for an independently connected Si/Cu₂O dual junction with a detailed balance efficiency of 44.3%.

However, the highest energy conversion efficiency achieved in a photovoltaic device with a Cu₂O absorber layer is currently only 5.38% despite the favorable optical and electronic properties listed above. There are several challenges to making a Cu₂O photovoltaic device, including an inability to dope the material, its relatively low chemical stability compared to other oxides, and a lack of suitable heterojunction partners due to an unusually small electron affinity. We have addressed the low chemical stability, namely the fact that Cu₂O is an especially reactive oxide due to its low enthalpy of formation (ΔH_f⁰ = -168.7 kJ/mol), by developing a novel surface preparation technique. We have addressed the lack of suitable heterojunction partners by investigating the heterojunction band alignment of several Zn-VI materials with Cu₂O. Finally, We have addressed the typically high series resistance of Cu₂O wafers by developing methods to make very thin, bulk Cu₂O, including devices on Cu₂O wafers as thin as 20 microns. Using these methods we have been able to achieve photovoltages over 1 V, and have demonstrated the potential of a new heterojunction material, Zn(O,S).

Stability of Hypervelocity Boundary Layers

The early stage of laminar-turbulent transition in a hypervelocity boundary layer is studied using a combination of modal linear stability analysis, transient growth analysis, and direct numerical simulation. Modal stability analysis is used to clarify the behavior of first and second mode instabilities on flat plates and sharp cones for a wide range of high enthalpy flow conditions relevant to experiments in impulse facilities. Vibrational nonequilibrium is included in this analysis, its influence on the stability properties is investigated, and simple models for predicting when it is important are described.

Transient growth analysis is used to determine the optimal initial conditions that lead to the largest possible energy amplification within the flow. Such analysis is performed for both spatially and temporally evolving disturbances. The analysis again targets flows that have large stagnation enthalpy, such as those found in shock tunnels, expansion tubes, and atmospheric flight at high Mach numbers, and clarifies the effects of Mach number and wall temperature on the amplification achieved. Direct comparisons between modal and non-modal growth are made to determine the relative importance of these mechanisms under different flow regimes.

Conventional stability analysis employs the assumption that disturbances evolve with either a fixed frequency (spatial analysis) or a fixed wavenumber (temporal analysis). Direct numerical simulations are employed to relax these assumptions and investigate the downstream propagation of wave packets that are localized in space and time, and hence contain a distribution of frequencies and wavenumbers. Such wave packets are commonly observed in experiments and hence their amplification is highly relevant to boundary layer transition prediction. It is demonstrated that such localized wave packets experience much less growth than is predicted by spatial stability analysis, and therefore it is essential that the bandwidth of localized noise sources that excite the instability be taken into account in making transition estimates. A simple model based on linear stability theory is also developed which yields comparable results with an enormous reduction in computational expense. This enables the amplification of finite-width wave packets to be taken into account in transition prediction.

Dynamics of the East Asian Summer Monsoon in Present and Future Climates

This thesis aims at enhancing our fundamental understanding of the East Asian summer monsoon (EASM), and mechanisms implicated in its climatology in present-day and warmer climates. We focus on the most prominent feature of the EASM, i.e., the so-called Meiyu-Baiu (MB), which is characterized by a well-defined, southwest to northeast elongated quasi-stationary rainfall band, spanning from eastern China to Japan and into the northwestern Pacific Ocean in June and July.

We begin with an observational study of the energetics of the MB front in present-day climate. Analyses of the moist static energy (MSE) budget of the MB front indicate that horizontal advection of moist enthalpy, primarily of dry enthalpy, sustains the front in a region of otherwise negative net energy input into the atmospheric column. A decomposition of the horizontal dry enthalpy advection into mean, transient, and stationary eddy fluxes identifies the longitudinal thermal gradient due to zonal asymmetries and the meridional stationary eddy velocity as the most influential factors determining the pattern of horizontal moist enthalpy advection. Numerical simulations in which the Tibetan Plateau (TP) is either retained or removed show that the TP influences the stationary enthalpy flux, and hence the MB front, primarily by changing the meridional stationary eddy velocity, with reinforced southerly wind on the northwestern flank of the north Pacific subtropical high (NPSH) over the MB region and northerly wind to its north. Changes in the longitudinal thermal gradient are mainly confined to the near downstream of the TP, with the resulting changes in zonal warm air advection having a lesser impact on the rainfall in the extended MB region.

Similar mechanisms are shown to be implicated in present climate simulations in the Couple Model Intercomparison Project - Phase 5 (CMIP5) models. We find that the spatial distribution of the EASM precipitation simulated by different models is highly correlated with the meridional stationary eddy velocity. The correlation becomes more robust when energy fluxes into the atmospheric column are considered, consistent with the observational analyses. The spread in the area-averaged rainfall amount can be partially explained by the spread in the simulated globally-averaged precipitation, with the rest primarily due to the lower-level meridional wind convergence. Clear relationships between precipitation and zonal and meridional eddy velocities are observed.

Finally, the response of the EASM to greenhouse gas forcing is investigated at different time scales in CMIP5 model simulations. The reduction of radiative cooling and the increase in continental surface temperature occur much more rapidly than changes in sea surface temperatures (SSTs). Without changes in SSTs, the rainfall in the monsoon region decreases (increases) over ocean (land) in most models. On longer time scales, as SSTs increase, rainfall changes are opposite. The total response to atmospheric CO^2 forcing and subsequent SST warming is a large (modest) increase in rainfall over ocean (land) in the EASM region. Dynamic changes, in spite of significant contributions from the thermodynamic component, play an important role in setting up the spatial pattern of precipitation changes. Rainfall anomalies over East China are a direct consequence of local land-sea contrast, while changes in the larger-scale oceanic rainfall band are closely associated with the displacement of the larger-scale NPSH. Numerical simulations show that topography and SST patterns play an important role in rainfall changes in the EASM region.