Reaction mechanism.pdf (3.61 MB)
Download file

Reaction mechanism and reaction coordinates from the viewpoint of energy flow.

Download (3.61 MB)
journal contribution
posted on 14.03.2017, 00:00 by WJ Li, A Ma
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 energyflows 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 energyflows 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.


Funding support from the National Institutes of Health (No. R01 GM086536) is acknowledged.


Publisher Statement

Copyright (2016) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Li, W., & Ma, A. (2016). Reaction mechanism and reaction coordinates from the viewpoint of energy flow. The Journal of chemical physics, 144(11), 114103 and may be found at


American Institute of Physics





Issue date


Usage metrics