Theoretical Study of Chloroperoxidase Catalyzed Chlorination of beta-Cyclopentanedione and Role of Water in the Chlorination Mechanism

Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate beta-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state

The Influence of the Proximal Amide Hydrogen Bonds and the Proximal Helix Dipole on the Catalytic Activity of Chloroperoxidase

Chloroperoxidase (CPO) is a heme-thiolate protein with exceptional versatility and great potential as a biocatalyst. The CPO reactive species, Compound I ( Cpd I) is of particular interest, as well as the Cytochrome P450 (P450) -type monoxygenase catalytic activity, which has significant biotechnological potential. Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH•••S) is a conserved feature of heme-thiolate enzymes. In CPO, the effect of NH•••S bonds is amplified by the dipole moment of the proximal helix. The role of the proximal region has been disputed as to whether it simply protects the axial sulfur, or whether it additionally influences catalysis via modulation of the push effect. The objective of the research presented herein is two-fold. First, the influence of the NH•••S bonds on Cpd I formation is determined by obtaining the reaction coordinate, starting from a peroxide bound heme, for two model systems (one with proximal residues providing NH•••S bonds and one without) and comparing the results. Secondly, the influence of the proximal region on the epoxidation of Cis-β-methylsterene is obtained. This is performed similarly to the first objective however, the reaction coordinate begins with a Cpd I-CBMS complex and the proximal contribution is extended to include the influence of the proximal helix dipole. Our findings show that the proximal region stabilizes Cpd 0 relative to all other minima and reduces the barrier for Cpd 0’s formation. The stability of protonated Compound 0 is reduced, favoring a hybrid homo-heterolytic relative to a classic heterolytic mechanism for O-O bond scission. Additionally, the proximal region significantly enhances CPO’s reactivity; the Cβ-O bond barrier is stabilized, while Cα-O-Cβ ring closure becomes barrierless. The stabilization of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket and involves a change in the electron transfer mechanism. These results can be traced to a reduction in the pKa of the heme-bound substrate and an increase in oxidation potential, a result of the proximal region reducing the “push effect”

Effects of solar ultraviolet radiation on biogeochemical dynamics in aquatic environments : report of a workshop, Marine Biological Laboratory, Woods Hole, Massachusetts, October 23-26, 1989

This workshop assembled a diverse group of experts, including atmospheric chemists and physicists and aquatic chemists, biochemists and biologists to address the possible ramifcations of changing Ultraviolet levels on biogeochemical dynamics of aquatic environments.Funding was provided by the Environmental Protection Agency through an Assistance Ageement (CR-816171-01-0) and the Office of Naval Research through Grant Number N00014-90-J-1154

10th Anniversary of Nanomaterials—Recent Advances in Environmental Nanoscience and Nanotechnology

This reprint contains contributions focusing on recent developments in the design, synthesis, and characterization of nanocatalysts intended for applications in environmental protection and low carbon footprint power generation processes thanks to the overall effort of scientists and researchers for a cleaner and more sustainable future. New synthetic approaches to the production and in-depth characterization of innovative nanostructured composites and hybrid materials with well-controlled textural and surface chemistry properties that give performance advantages in a variety of important environmental and energy applications such as CO2 utilization/recycling, hydrogen and syngas production, biosensing, and biocatalysis as well as in ways to obtain useful materials from waste are included, among others. This reprint is the result of one of the cutting-edge Special Issues in the field of Nanoscience and Nanotechnology organized by Nanomaterials to celebrate its 10th anniversary