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Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

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

Zhi-Xin Qin¹, Matthew Tremblay², Xin Hong¹

¹Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027, China.

The Journal of Physical Chemistry Letters

|October 28, 2021

Summary

This summary is machine-generated.

Fleeting intermediates in chemical reactions can have longer lifetimes due to entropy maxima, not free energy minima. This study clarifies the role of conformational flexibility in dynamic reaction pathways.

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Area of Science:

Chemical Kinetics
Computational Chemistry
Reaction Dynamics

Background:

Fleeting intermediates are key in stepwise reaction mechanisms.
Their characterization in molecular dynamics is established, but their nature as entropic intermediates (free energy minima) remains unclear.
Understanding intermediate behavior is crucial for predicting reaction outcomes.

Purpose of the Study:

To develop and apply a computational method, entropic path sampling, for evaluating entropic variations along reaction paths.
To investigate the presence and nature of entropic intermediates in the cyclopentadiene dimerization reaction.
To elucidate the relationship between entropy, energy, and intermediate lifetimes in dynamic reaction mechanisms.

Main Methods:

Developed entropic path sampling (EPS) computational protocol.
Utilized an ensemble of molecular dynamics trajectories.
Applied the protocol to the model reaction of cyclopentadiene dimerization.

Main Results:

Observed an entropy maximum along the reaction path for cyclopentadiene dimerization.
This maximum arises from increased conformational flexibility in a flat energy region.
No free energy minimum was found along the post-transition state pathway, despite an entropy maximum.
Dynamic intermediates with elongated lifetimes were identified, but they are not entropic intermediates.

Conclusions:

Cyclopentadiene dimerization proceeds via dynamic intermediates associated with an entropy maximum, not a free energy minimum.
Entropic path sampling provides a method to distinguish between dynamic and entropic intermediates.
The study clarifies the role of conformational entropy in reaction mechanisms and intermediate formation.