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Journal Article

Reaction coordinates and rates from transition paths

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Best, R. B., & Hummer, G. (2005). Reaction coordinates and rates from transition paths. Proceedings of the National Academy of Sciences of the United States of America, 102(19), 6732-6737. doi:10.1073/pnas.0408098102.

Cite as: https://hdl.handle.net/21.11116/0000-0008-C845-9
The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. We use a Bayesian formula relating the equilibrium and transition-path ensembles to identify transition states, rank reaction coordinates, and estimate rate coefficients. We also introduce a variational procedure to optimize reaction coordinates. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube. To describe the folding of a simple model of a three-helix bundle protein, we variationally optimize the weights of a projection onto the matrix of native and nonnative amino acid contacts. The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding.