A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases.

Exploration of chemical reactions in complex explicit environments has become an affordable task with the use of hybrid quantum mechanics/molecular mechanics potentials which allow calculating free energy profiles of chemical reactions under the influence of the surroundings. Tracing these free energy profiles requires the selection of a reaction coordinate, which can be cumbersome for those processes involving more than a single chemical event in a concerted step. We here propose a collective coordinate to be used in the calculation of free energy profiles for complex reactions in condensed phases. This coordinate is based in the definition of the advance along a path introduced by Branduardi et al. (J. Chem. Phys.2007, 126, 054103) but modified to use internal coordinates which are more adequate for the description of chemical reactions. The coordinate is tested with the analysis of the isochorismate transformation to pyruvate and salycilate in aqueous solution and in the active site of PchB, a reaction that involves a CO bond breaking simultaneously with a proton transfer between two carbon atoms. The coordinate introduced here allows obtaining smooth and meaningful free energy profiles of the reaction.