Kinetic Analysis of a Reaction Path Network Including Ambimodal Transition States: A Case Study of an Intramolecular Diels–Alder Reaction

Abstract

This study proposes a methodology for the kinetic analysis of a reaction path network including ambimodal transition states (TSs), through which an ensemble of trajectories bifurcates to multiple minima in a phenomenon called dynamical bifurcation. The proposed methodology consists of three techniques: an automated reaction path search to construct a reaction path network including ambimodal TSs, an ab initio molecular dynamics simulation to evaluate the branching ratio, and the definition of rate constants incorporating this ratio. Applying the procedure to a Diels–Alder reaction, it was found that the inclusion of dynamical bifurcations is necessary to explain the experimental reaction yield of a byproduct. In addition, it was verified that the products take 1013 s to reach thermal equilibrium and that the experimental selectivity is determined by the dynamical bifurcations.

Exploring Downhill Bifurcations in [3,3]-Sigmatropic Rearrangement by Finding Transitions from an Uphill Bifurcation to a Downhill Bifurcation

“…Therefore, it would be interesting to investigate how much of the overall chemical reactions involves downhill bifurcations. Additionally, downhill bifurcations decrease the reaction yield of the target product. − Thus, exploring novel downhill bifurcations is also necessary from the viewpoint of achieving full control over chemical reactions.…”

Enhanced Sampling for Free Energy Profiles with Post-Transition-State Bifurcations

“…The occurrence of bifurcations on PESs means that intrinsic reaction coordinate (IRC) analysis, , which is commonly used to study reactions, is not sufficient to characterize reactive systems featuring PTSBs. Accordingly, molecular dynamics (MD) simulationsin particular, quasiclassical direct dynamics and quantum mechanics/molecular mechanics (QM/MM) simulationshave been utilized to understand reaction mechanisms and selectivity associated with PTSBs. − Although quasiclassical direct dynamics simulations account for product distributions and offer real-time trajectories from which mechanistic properties (e.g., synchronicity) can be probed, the results of such analyses are dependent on the starting TS structures. It has been reported that PESs in the vicinity of ambimodal transition states may possess a large number of saddle points because of the complexity of the chemical interactions and conformational flexibility of the reactants .…”