DataVXThe Journal of Physical Chemistry LettersPaper
journal article·2021-11-04

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

Zhi-Xin Qin, Matthew Tremblay, Xin Hong, Zhongyue J. Yang

The Journal of Physical Chemistry Letters· Volume 12· Issue 43
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Source abstract

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 intermediates 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 an entropy maximum 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 entropy maximum that leads to dynamic intermediates with elongated lifetimes, but the reaction does not involve entropic intermediates.
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Research context

OpenAlex topics: Spectroscopy and Quantum Chemical Studies · Advanced Chemical Physics Studies · Computational Drug Discovery Methods

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Affiliations

Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China

Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States

Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States

Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States

Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States

Funding

Department of Chemistry, Vanderbilt University · National Natural Science Foundation of China · National Science Foundation · Fundamental Research Funds for the Central Universities · the State Key Laboratory of Clean Energy Utilization

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