Kinetics and energetics of chemical reactions through intermediate states

We analyze the kinetics and the energetics of chemical reactions passing through an intermediate state. Two approaches are adopted. The first one is a mesoscopic description in which the state of the reaction undergoes a diffusion process in a tristable potential along a reaction coordinate which parametrizes different molecular configurations in the reaction pathway. The second consists of a two-level system model. We show that the reaction flux and the energy dissipated (lost work) depend significantly on the mean life of the intermediate state. It is found that the values of these quantities obtained through both approaches differ especially at early stages, in the presence of high chemical potential differences for low energies of the intermediate state. The analysis presented unifies kinetics and energetics of chemical reactions steps and can be applied to explain the mechanism of enzymatic and organic reactions, RNA and protein folding and sorption processes.