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Exploring chemical reactivity of complex systems with path‐based coordinates: Role of the distance metric
Author(s) -
Zinovjev Kirill,
Tuñón Iñaki
Publication year - 2014
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23673
Subject(s) - metric (unit) , metric tensor , tensor (intrinsic definition) , variable (mathematics) , path (computing) , work (physics) , mathematics , physics , computer science , mathematical analysis , geometry , thermodynamics , operations management , programming language , economics , geodesic
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. © 2014 Wiley Periodicals, Inc.