Entropic Path Sampling: Computational Protocol to Evaluate Entropic Profile along a Reaction Path
| Autor: | Zhi-Xin Qin, Xin Hong, Zhongyue Yang, Matthew Tremblay |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Physics
Quantitative Biology::Biomolecules Cyclopentadiene Drop (liquid) Sampling (statistics) Potential energy chemistry.chemical_compound Molecular dynamics Entropy (classical thermodynamics) chemistry Reaction dynamics Chemical physics Path (graph theory) General Materials Science Reaction path Physical and Theoretical Chemistry Bifurcation |
| Zdroj: | The Journal of Physical Chemistry Letters. 12:10713-10719 |
| ISSN: | 1948-7185 |
| DOI: | 10.1021/acs.jpclett.1c03116 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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