Q-Chem Webinar 15

Exploring Reaction Pathways using QM/MM Free Energy Simulations: Application to Biochemical Reactions

Presented by Abir Ganguly on 2014-03-26

Abir Ganguly received his PhD from the Sharon Hammes-Schiffer research group at the University of Illinois at Urbana-Champaign as part of a team that has the general interest of understanding enzymatic processes with particular emphasis on the role of hydrogen bonding, hydrogen tunneling, electrostatics, and motion in enzyme reactions. Specifically, his graduate research focused on understanding the different aspects of chemistry of small, self-cleaving RNA enzymes, or ribozymes, using a variety of computational tools. He is now a research professor in the York Lab at Rutgers University.

Abstract

Characterizing the free energy pathway of a chemical reaction can provide valuable information related to the mechanism, kinetics and thermodynamics of the reaction. In the case of complex biological systems, this can be a challenging task due to the multi-dimensional nature of the reaction pathway and the lack of a priori knowledge of the relevant reaction coordinates. This webinar will discuss the characterization of the multidimensional free energy surfaces associated with biochemical reactions and the identification of favorable reaction pathways using quantum mechanical/molecular mechanical (QM/MM) free energy simulations with Q-Chem and CHARMM. The free energy surfaces are generated by combining a finite temperature string method with umbrella sampling simulations.