Collective variables
Presentations
14/03/2012, Cambridge, Cavendish Laboratory
Articles
Topologically Invariant Reaction Coordinates for Simulating Multistate Chemical ReactionsL Mones and G Csanyi
2012, The Journal of Physical Chemistry B 116 (51), 14876-14885
Abstract: Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.
The energy gap as a universal reaction coordinate for the simulation of chemical reactions
L Mones P Kulhanek, I Simon, A Laio and M Fuxreiter
2009, The Journal of Physical Chemistry B 113 (22), 7867-7873
Abstract: The selection of a proper reaction coordinate is a major bottleneck in simulations of chemical reactions in complex systems. Increasing the number of variables that are used to bias the reaction largely affects the convergence and leads to an unbearable increase in computational price. This problem can be overcome by employing a complex reaction coordinate that depends on many geometrical variables of the system, such as the energy gap (EGAP) in the empirical valence bond (EVB) method. EGAP depends on all of the coordinates of the system, and its robustness has been demonstrated for a variety of enzymatic reactions. In this work, we demonstrate that EGAP, derived from a classical representation, can be used as a reaction coordinate in systems described with any quantum chemistry Hamiltonian. Benefits of using EGAP as a reaction coordinate as compared to a traditional geometrical variable are illustrated in the case of a symmetric nucleophilic substitution reaction in water solution. EGAP is shown to provide a significantly more efficient sampling and allows a better localization of the transition state as compared to a geometrical reaction coordinate.