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Computational modeling of (bio)chemical reactions has been around for decades using small gas-phase simulations on the quantum mechanical (QM) and large-scale simulations involving explicit solvent with combined quantum mechanical/molecular mechanical (QM/MM) techniques. Enzymes are powerful tools developed by nature to construct complex molecules that are bioactive. The reactions of enzymes can be difficult to study experimentally due to short lived intermediates, such as radicals. Computational modeling of reaction pathways of an enzyme, such as one- and two-electron mechanisms, and how the enzyme affects the reaction via active site interactions can help to guide enzyme redesign to alter the outcome or even chemistry of the enzyme. The thesis contained herein seeks to add to the computational tools available to study enzymatic and other condensed phase systems to gain insight into their mechanisms and the underlying chemical principles governing reactivity. The first goal of this thesis was to develop a new combined constrained density functional theory/molecular mechanics (CDFT/MM) tool to study reactions involving single-electron transfer (SET) in condensed phases. Specifically, the new CDFT/MM tool was tested on two well defined organic electron donors (OEDs). Tetrakis(dimethylamino)ethylene (TDAE) and tetrathiafulvene (TTF) are OEDs that have been extensively studied by the Murphy group since the 1990s and 2000s. Reactions involving TDAE and TTF begin with a SET and result in the formation of indoles and benzofuranyl alcohols, respectively. The CDFT/MM tool was able to describe known SET transfer processes, to identify known and unknown intermediates, and to replicate well defined chemistry. With the CDFT/MM tool being validated, it was then applied during the study of mechanisms for the enzyme TropC. TropC is an α-ketoglutarate (αKG) dependent non-heme iron (NHI) enzyme that catalyzes a ring expansion to produce a seven-membered aromatic ring known as a tropolone, which is a scaffold observed in bioactive natural products. Initially, three reaction pathways were studied using a QM model to gain insight into potential reactions. Results from the QM model revealed that the enzyme preferred a one-electron mechanism for production of tropolones. Specifically, radical- and SET-based mechanisms were determined to be most plausible for TropC. Using the insights gained from the QM model, QM/MM modeling of TropC and the three pathways was conducted. The new CDFT/MM tool was used to study the viability of a SET within the active site of TropC. Following SET from a radical intermediate, a barrierless ring expansion was observed with a large reorganization energy. It was subsequently found that the SET pathway was potentially viable, and further study of this possibility is merited. Based on the data herein the mechanism of TropC is suggested to proceed through a one-electron radical-based ring expansion. |
