Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path

23 September 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Fleeting intermediates constitute dynamically-stepwise mechanisms. They have been characterized in molecular dynamics trajectories, but whether these intermediates form a free energy minimum to become entropic intermediate remains elusively defined. We developed a computational protocol known as entropic path sampling to evaluate the entropic variation of reacting species along a reaction path based on an ensemble of trajectories. Using cyclopentadiene dimerization as a model reaction, we observed a shallow entropic trap (–T∆S = –0.8 kcal/mol) along the reaction path which originates from an enhanced conformational flexibility as the reacting species enter into a flat energy region. As the reacting species further approach product formation, unfavorable entropic restriction fails to offset the potential energy drop, resulting in no free energy minimum along the post-TS pathway. Our results show that cyclopentadiene dimerization involves an entropic trap that leads to dynamic intermediates with elongated lifetime, but the reaction does not involve entropic intermediates.

Keywords

Entropic Intermediate
Entropic trap
Reaction dynamics
Bifurcation

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Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path
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