Multi-scale Simulations of Dynamics of Chemical Reactions

The motions of the chemical environment, such as solvents and proteins, are closely connected to the kinetics and dynamics of reactions. The environment can either perturb reaction pathways by altering the free energy of activation and reaction, or exert a dynamical role by affecting the motions of reacting species during barrier-crossing and energy exchange processes. Theoretical calculations and molecular dynamics simulations have made it possible to obtain a direct evaluation of the effect of the chemical surroundings. Nevertheless, owing to the sophisticated interaction patterns and motions at different time scales, it is often a challenging task in computational chemistry to get a clear picture of how the surroundings are coupled to the reaction progress, and how they damp the nuclear dynamics. The main objective of this PhD thesis is to understand the effect of chemical environments (including solvents and protein) on reactions by developing efficient reactive force fields and using them in molecular dynamics simulations. This thesis has explored three classes of chemical phenomena, (i) energy relaxation of deuterium fluoride in deuterated acetonitrile and dichloromethane (Chapters 3 and 4), (ii) dynamics of the Diels-Alder reaction in organic solution (Chapter 5) and (iii) mutation effects on the Co—C bond cleavage step in adenosylcobalamin-dependent glutamate mutase (Chapter 6).