Chapters 1-6 describe studies of enzymes and their applications in biocatalysis. Biocatalysis, the use of natural enzymes or engineered enzymes to produce molecules of interest, has been an emerging and favorable approach to supplement or replace traditional organic synthesis. Enzymes are very efficient and selective in catalysis, and enzyme catalysis is also environmentally friendly. The first portion of this dissertation reports the theoretical study of several enzymes that catalyze very different reactions, including oxidation, halogenation as well as Diels–Alder reactions. The study reveals the mechanism behind each enzyme-catalyzed reaction in terms of efficiency, substrate specificity and regio-/stereo selectivity. In addition to the understanding of each enzyme, mutations are proposed based on the mechanism of the enzyme reactions to improve the natural enzymes for better catalysis.
Chapter 1 introduces a general strategy for synthesis of macrolactones using nickel catalyzed C-C coupling and a site-selective P450 C-H oxidations carried out at Michigan by the groups of Montgomery and Sherman. Quantum mechanical (QM) computations show the intrinsic energy barriers at different hydrogen atoms at different sites in a single substrate. Molecular dynamic (MD) simulations reproduce the site selectivity and stereoselectivity in the biocatalytic oxidations with the aid of QM results. Our results suggest the linker length and its interaction with the enzyme determines the reaction yield.
Chapter 2 presents a study of the first natural Diels–Alderase (DAase) and its mechanism for catalyzing a DA reaction. QM calculations suggest the reaction goes through an ambimodal TS leading to both [4+2] and [6+4] adducts. MD simulations show that trajectories pass through the TS and go to [4+2] adduct more in the enzyme than in gas phase or water. The enzyme influences the outcome of bifurcation dramatically, mainly through hydrophobic contact. The energy barrier of the enzymatic reaction is also reproduced accurately with our newly developed method: Environment Perturbed TS Sampling (EPTSS).
Chapter 3 studies the Cope rearrangement and cyclization in hapalindole biogenesis. The X-ray crystal structure of HpiC1 is reported in this study. Mutagenesis study as well as computational computations uncover the key residues for the enzymatic reaction. QM computations show the reaction goes through an acid-catalyzed [3,3]-sigmatropic rearrangement. The switch from hapalindole to fischerindole is explained by the position change of the terminal electrophilic aromatic substitution in MD simulations.
Chapter 4 describes the mechanism of Diels–Alderase PyrI4 in pyrroindomycins biosynthesis. Density functional theory (DFT) calculations and EPTSS calculations compare the energy barriers of the reaction in the gas phase, theozyme model, and in the enzyme. Hydrogen bonding has limited contribution to the TS stabilization in the enzyme. MD simulations show that hydrophobic interactions dominate in the catalysis of the enzyme catalyzed Diels–Alder reaction by fitting with the exo TS better than other TSs or the reactants.
Chapter 5 presents the study of a multifunctional P450 MycG and its substrate specificity. QM computations reveal the mechanism behind the MycG biopathway. MD simulations show that a hydrophobic cavity in MycG differentiates the three different substrates favors the binding of the natural substrate. Based on MD simulations, potential beneficial mutations are proposed and tested by the Sherman group at Michigan, and are proven to improve the enzyme performance in experiment.
Chapter 6 studies flavin dependent halogenase and its regioselectivity in directed evolution. The flavin dependent halogenase RebH was engineered to catalyze chlorination at different regioselective sites of tryptamine. QM calculations reveal that the intrinsic energy barriers at different sites are similar to each other. Docking and MD simulations show the different binding poses are favorable in WT and the mutants. Key mutations are identified through MD simulations and reverse mutations.
Chapters 7-9 are projects about molecular machines in solid state as well as solvent phase, studied experimentally by the Garcia-Garibay group. Ever since Prof. Feynman’s famous talk “There is plenty of room at the bottom”, nanotechnology has witnessed tremendous progress in the synthesis and design of molecular machines capable of mechanical movements. The early stage of molecular machine development was simply to mimic macroscopic designs. However, to succeed in building nanoscale versions of the mechanical world, more understanding is required, rather than simple mimicry. In these chapters, I have studied the dynamics of molecular rotation in dendrimetric materials, MOFs crystal and organic solvents. With computational study, the rotational process is revealed at nanosecond time scale. New designs of molecular machine are proposed to improve their performance in different environments.
Chapter 7 studies the rotation of phenyl rings at different parts in a dendrimeric material. Molecular dynamics study reveals the different dynamics of molecular rotations at the core, branches and peripheral ends. The energy surfaces of molecular rotation are scanned using umbrella sampling, and the energy barriers are computed.
In Chapter 8, the rotational dynamics of molecular rotors in amphidynamic crystals are studied. The energy barriers of the rotation are computed by QM study to be ~0.2 kcal/mol, consistent with the ultrafast rotation in the rigid BODCA-MOF crystals. MD simulations reveal the ultrafast rotation at different temperatures and find it to be diffusion-like at high temperature.
Chapter 9 compares and studies the gearing performance of different molecular spur gears. The gearing efficiency is affected by the distance between the two rotors in molecular gears. Solvent molecules are shown to interfere with the rotation of the molecular rotors and promote slippage rather than gearing. A new design of molecular spur gear is proposed and tested by MD simulations. With a macrocyclic structure, the solvent effect is eliminated and the molecular spur gear is able to gear in solvent phase.