| Chapter 1 In this chapter, extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are coupled with previous EPR and 57Fe Mossbauer spectroscopy to postulate structures for two cofactors. Fe and Mn K-edge EXAFS data yield intermetallic distances for the Mn(IV)/Fe(III) and Mn(IV)/Fe(IV) cofactors of ~2.9 and ~2.8A, respectively. The Mn data also suggest the presence of a short 1.74 A Mn-O bond for the Mn(IV)/Fe(III) cofactor. These metrics are compared to the results of DFT calculations on 16 cofactor models derived from the crystal structure of the inactive Fe2(III/III) form of the protein.;Chapter 2 It is hypothesized that the ability of metal-O(H) complexes to abstract hydrogen is directly related to the strength of the O-H bond formed in the resulting metal complex. For P450s, this Fe(IV)-OH species is called compound-II (P450-II). It is also hypothesized that P450s utilize an axial sulfur in order to increase the driving force to oxidize hydrocarbons. The sulfur increases the basicity of the Fe(IV)-O cofactor, making it basic under biological conditions. Thermodynamically, the metal O-H strength is directly dependent on the pKa of P450-II. Peroxidases, which usually possess an axial nitrogen, are incapable of performing alkane hydroxylations and are deprotonated at neutral pH. DFT calculated O-H bond strengths in P450 and peroxidase models are nearly identical, which is contrary to the aforementioned hypotheses.;Chapter 3 This chapter documents the development of the author's optimization code and will be utilized throughout the rest of the dissertation (Chapters 4-5). The motivation for development of the code stemmed from a desire to include chemically intuitive constraints in nonlinear regression problems. Regression is frequently used to fit theoretical models to experimental data by minimizing the difference between the actual experimental results and the predictive model. The fitting of rate constants to kinetic traces is a typical chemical example. As will be seen in the subsequent chapters, constraints range from experimentally obtained molecular expectation values to the fact that absorption spectra cannot be negative. The versatility of the method is seen in the wide range of problems it allows the researcher to address.;Chapter 4 Chloroperoxidase (CPO) is frequently studied to understand the important alkane-hydroxylating enzyme P450 (see Chapter 2). One intermediate of interest is compound-II (CPO-II). Compound-II is the Fe(IV)-OH species which immediately follows hydrogen atom transfer. The major species' splitting was accurately predicted with DFT, but the identity of the minority species has remained enigmatic. In order to find a model consistent with the minority species, a spectroscopically constrained geometry optimization is developed and employed. A model which is consistent with the experimental Fe(IV)-OH quadrupole splitting of 1.59 mm/s, as well as the Fe-O Raman stretch at 565 cm--1, is found. As a proof of concept, said quadrupole-constrained geometry optimization is shown to transition between different configurations of Fe(CO)42-- and Fe(CO)5. The constrained optimization approach developed here has potential to be used whenever a molecular expectation value is known experimentally which is not reproduced by the minimum energy model.;Chapter 5 In this chapter, Adomian decomposition methods (ADM) are used to obtain the solutions of chemical rate equations. The Adomian method outlined here outperforms high-order RK routines in the arenas of accuracy and truncation error. Additionally, four modifications are introduced that place the Adomian integration on par with RK in terms of speed (a primary reason for which Adomian decomposition methods are currently underemployed). This increase in computational performance is highly significant to kinetic inversion and global analysis problems where rate constants are obtained via the fitting of experimental data and hundreds of numerical integrations are needed. The inclusion of up to the fifth term in the Adomian expansion gives a truncation error of order O(h10 ). The method as presented yields solutions which are step-size independent in the non-stiff regime. The problem of rapid polynomial divergence is addressed through discretizing the time axis. (Abstract shortened by UMI.)... |
