ArticleThe Journal of chemical physics2016
Reaction mechanism and reaction coordinates from the viewpoint of energy flow.
Article in The Journal of chemical physics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Reaction Coordinates Are Optimal Channels of Energy Flow.Annual review of physical chemistry · 2025Review
- Enhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation.Nature communications · 2025Article
- Exact reaction coordinates for flap opening in HIV-1 protease.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Reactive Vortexes in a Naturally Activated Process: Non-Diffusive Rotational Fluxes at Transition State Uncovered by Persistent Homology.The journal of physical chemistry. B · 2022Article
- Mechanism for the rare fluctuation that powers protein conformational change.The Journal of chemical physics · 2022Article
- Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology.The journal of physical chemistry. B · 2021Article
- A benchmark for reaction coordinates in the transition path ensemble.The Journal of chemical physics · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.
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