Seminar: Yiqin Gao (Peking University)

May 23, 2017 at - | Lynch Lecture Hall, Chemistry Complex

"Chemical Reaction Mechanisms in Solutions Studied by Enhanced Sampling Molecular Dynamics Simulations"





Chemical reactions in solution can have multiple reaction pathways and it is interesting to investigate the roles of solvent in affecting these reaction pathways. It is thus desirable to develop simulation methods to study chemical reactions in solution without pre-determined reaction pathways. A sampling strategy for rare events, enhanced sampling of reactive trajectories, was developed, in which an ensemble of chemical reaction trajectories were efficiently generated and collected with known thermal weights, thus allowing a statistical investigation of thermodynamics, kinetics, dynamics and mechanisms of the reaction event of interest. The post-analysis of reaction mechanisms is performed to gain knowledge on reaction coordinates, which were optimized optimized based on a Bayesian learning algorithm, and reaction mechanisms. As an example, the reaction coordinate(s) of a (retro-)Claisen rearrangement in bulk water was studied. The combinatorial relative atom position of the bond-forming/breaking site serves as a reasonable RC, which is also dynamically coupled with charge separation and dipole change of the reactant. The hydrogen-bonding of water molecule to the charge-enriched site of the reactant state, and the parallelization of neighboring solvent dipoles during the reaction progression was found to facilitate this in-water reaction. In addition, the solvent shell shrinks during the reaction, consistent with the “cage-effect”. The transition path time of the reaction and the rate constants for the forward and backward reaction were calculated independent of RCs, and we were able to self-consistently connect the kinetics to the thermodynamics. The diffusion coefficient over the energy barrier was also determined according to Kramers’ theory, showing the limitation of canonical transition state theory in dealing with the condensed phase reactions.

Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories, J. Phys. Chem. B 119, 14505-14514 (2015).
Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories, ACS Central Science, DOI: 10.1021/acscentsci.7b00037






Rosa Vargas; rvargas@sas.upenn.edu