From Transition Paths to Transition States and Reaction Coordinates

The molecular mechanism of a reaction in solution is reflected in its transition-state ensemble and transition paths. Equilibrium and transition-path ensembles are related through a Bayesian expression that can be used to identify transition states, optimize reaction coordinates, and estimate rate coefficients. The theory is illustrated with applications to protein folding and the dipole reorientation of an ordered water chain inside a carbon nanotube.