title: Reaction mechanism and reaction coordinates from the viewpoint of energy flow.
abstract: Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.
authors.affiliation: Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA.
authors.forename: Wenjin
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA.
authors.forename: Ao
authors.initials: A
authors.lastname: Ma
mesh_terms: D004151:Dipeptides / Q000737:chemistry; D004735:Energy Transfer; D007536:Isomerism; D008956:Models, Chemical; D011487:Protein Conformation; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D004151:Dipeptides; C002956:alanylalanine