(6o) Molecular Simulation As a Tool for Materials Synthesis, Catalysis, and Biocatalysis

The poster displays an overview of my PhD and postdoctoral computational research. Unifying themes include computational chemistry, molecular simulation, rare events, transition states, and structure-function predictions. Currently, at the Pacific Northwest National Laboratory my postdoctoral research is focused on materials and catalysis. In one project the mechanism of metal organic framework (MOF) synthesis is being investigated with computational chemistry focused on establishing detailed reaction schemes from metal ions and organic linkers to MOF building blocks. In a second project the kinetics and dynamics of water on metal oxide surfaces is studied. Using density functional theory (DFT) and ab initio molecular dynamics, energy barriers for individual adsorption, reaction, diffusion, and desorption events were obtained, and used in kinetic models, explaining experimental observables. My dissertation work at Iowa State University, as part of the Center for Biorenewable Chemicals, focused on enzymes. A bioinformatics approach was taken to find target enzymes with desired activities among the many ones existing in nature. To that end, a database that classified enzymes by structure was constructed. With experimental collaboration, a statistical approach identified enzymes with novel activity. Molecular dynamics and mixed quantum mechanics/molecular mechanics (QM/MM) simulations were done to understand in detail the mechanism of enzymatic catalysis; revealing transition state conformation, the roles of active site residues, and energy landscape.