title: Exploring chemical reactivity of complex systems with path-based coordinates: role of the distance metric.
abstract: Path-based reaction coordinates constitute a valuable tool for free-energy calculations in complex processes. When a reference path is defined by means of collective variables, a nonconstant distance metric that incorporates the nonorthonormality of these variables should be taken into account. In this work, we show that, accounting for the correct metric tensor, these kind of variables can provide iso-hypersurfaces that coincide with the iso-committor surfaces and that activation free energies equal the value that would be obtained if the committor function itself were used as reaction coordinate. The advantages of the incorporation of the variable metric tensor are illustrated with the analysis of the enzymatic reaction catalyzed by isochorismate-pyruvate lyase. Hybrid QM/MM techniques are used to obtain the free energy profile and to analyze reactive trajectories initiated at the transition state. For this example, the committor histogram is peaked at 0.5 only when a variable metric tensor is incorporated in the definition of the path-based coordinate.
authors.affiliation: Departament de Química Física, Universitat de València, 46100, Burjassot, Spain.
authors.forename: Kirill
authors.initials: K
authors.lastname: Zinovjev
authors.forename: Iñaki
authors.initials: I
authors.lastname: Tuñón
keywords: QM/MM; collective variables; free energy; minimum free energy path; reaction coordinate; transition state theory