Value of Temporal Information When Analyzing Reaction Coordinates

Reaction coordinates chart pathways from reactants to products of chemical reactions. Determination of reaction coordinates from ensembles of molecular trajectories has thus been the focus of many studies. A widely used and insightful choice of a reaction coordinate is the committor function, define...

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Bibliographic Details
Published in:Journal of chemical theory and computation 2020-10, Vol.16 (10), p.6077-6090
Main Authors: Ma, Piao, Elber, Ron, Makarov, Dmitrii E
Format: Article
Language:English
Subjects:
Chemical reactions
Molecular trajectories
Statistical Mechanics
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Summary:Reaction coordinates chart pathways from reactants to products of chemical reactions. Determination of reaction coordinates from ensembles of molecular trajectories has thus been the focus of many studies. A widely used and insightful choice of a reaction coordinate is the committor function, defined as the probability that a trajectory will reach the product before the reactant. Here, we consider alternatives to the committor function that add useful mechanistic information, the mean first passage time, and the exit time to the product. We further derive a simple relationship between the functions of the committor, the mean first passage time, and the exit time. We illustrate the diversity of mechanisms predicted by alternative reaction coordinates with several toy problems and with a simple model of protein searching for a specific DNA motif.
ISSN:1549-9618
1549-9626
DOI:10.1021/acs.jctc.0c00678