%0 Journal Article
%A Zinovjev, Kirill
%A Martí, Sergi
%A Tuñón, Iñaki
%D 2012
%T A Collective Coordinate
to Obtain Free Energy Profiles
for Complex Reactions in Condensed Phases
%U https://acs.figshare.com/articles/journal_contribution/A_Collective_Coordinate_to_Obtain_Free_Energy_Profiles_for_Complex_Reactions_in_Condensed_Phases/2524312
%R 10.1021/ct300070b.s001
%2 https://acs.figshare.com/ndownloader/files/4167241
%K CO
%K Obtain Free Energy Profiles
%K chemical reactions
%K energy profiles
%X 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.
%I ACS Publications