Reaction Coordinates and Rates from Transition Paths

Reaction Coordinates and Rates from Transition Paths

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 int...

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Veröffentlicht in:Proceedings of the National Academy of Sciences of the United States of America. - National Academy of Sciences of the United States of America. - 102(2005), 19, Seite 6732-6737
1. Verfasser: Best, Robert B. (VerfasserIn)
Weitere Verfasser: Hummer, Gerhard, Berne, Bruce J.
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2005
Zugriff auf das übergeordnete Werk:Proceedings of the National Academy of Sciences of the United States of America
Schlagworte:Carbon nanotubes Chemical kinetics Protein folding Transition-state theory Grotthuss mechanism Mathematics Physical sciences Education Applied sciences
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520 |a 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. 
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