Date of Award

Winter 2014

Document Type


Degree Name

Doctor of Philosophy (PhD)


Micro and Nanoscale Systems

First Advisor

Daniela S. Mainardi


Enzymes have been considered as molecular electrocatalysts due to their extraordinary characteristics such as their ability to accelerate reactions enormously, to operate under physiological conditions, and to produce fewer by-products during a catalytic reaction. However, enzyme based fuel cells have been reported to have power output and stability limitations, which are restricting the use of this kind of fuel cell to small electronic devices. Methanol dehydrogenase (MDH) is one such enzyme, which oxidizes methanol and other primary alcohols to their corresponding aldehydes. The active site of MDH contains a divalent cation (Ca2+), a co-factor pyrrolo-quinoline quinone (PQQ), several amino acids, and water molecules. Ca2+ ion holds the PQQ in place, and also acts as a Lewis acid, contributing to the methanol electro-oxidation reaction mechanism by this enzyme. Among the proposed mechanisms for methanol oxidation by MDH in the literature, the Hydride Transfer (H-T) mechanism seems, to the best of our knowledge, to be the preferred one under normal conditions. Work reported in the literature shows that the binding of the substrate and the reaction energy barrier for substrate oxidation by dehydrogenase enzymes is influenced by the nature of the ion in the enzyme active site. Thus, understanding the role of the ion in the active site of MDH as well as the methanol oxidation mechanism may have major impacts on alternative power sources research as they could lead to the development of new bio-inspired synthetic catalysts that could impact the use of methanol as fuel.

In this study, the binding energy of methanol to the active site models of ion-modified MDH is determined and the effect of ion on methanol oxidation is investigated. It has been observed that the binding affinity of methanol and free energy barrier for the rate determining step of the H-T mechanism decreases as the ionic size increases. This shows that replacing the naturally occurring ion (Ca2+) with Mg2+, Sr2+ and Ba2+ affect the methanol oxidation process and binding of methanol to the active site of MDH. Density Functional Theory (DFT) calculations at BLYP/DNP theory level are performed using the DMOL3 module of the Materials Studio software to evaluate binding energies and investigate the reaction pathways. Furthermore, polarization curves corresponding to the electrochemical methanol oxidation in biofuel cell anodic chambers when MDH enzymes are used as the anode catalysts are obtained using the kinetic Monte Carlo approach. Microscopic reaction rates, obtained from free energy barriers evaluated using DFT and Transition State Theory (TST), are provided as inputs in a kinetic Monte Carlo (kMC) program (CARLOS 4.1) to model the oxidation process at macroscopic level. These simulations gave a better understanding of the catalytic methanol oxidation mechanism by MDH, helping evaluate the enzyme catalysis and their dependence on various factors like the nature of the ion in the MDH active site.