Theoretical Study of Reaction Dynamics in Gas and Condensed Phases

Abstract

Finding transition states are important for analyzing chemical reactions, but revealing the reaction dynamics can be also essential in understanding many realistic reactions. For instance, recent experiments have shed light on the importance of protein’s heterogeneous dynamics in the native state and during function, and ultrafast dynamics in photo-triggered chemical reactions have been studied over decades. However, most efforts in theoretical studies have been devoted to characterizing transition states and calculating ensemble-averaged properties, e.g. free energy profi les, whereas the dynamics have been of less focus. In this account, we review our recent efforts toward revealing the dynamics of reactions under diverse conditions from the theoretical perspective. We discuss three cases, i.e. photo-isomerization reaction in gas phase, and protein folding and enzyme catalysis in condensed phase. The key in these studies has been to shed light on the individual events occurring during reactions, rather than focusing only on the characteristic states and ensemble averages. These studies show that dynamics play a fundamental role in all three cases, and demonstrate how the dynamics analyses can deepen our understanding of the reactions under various conditions.