title: 'Dynamic Distance' Reaction Coordinate for Competing Bonds:  Applications in Classical and Ab Initio Simulations.
abstract: A versatile reaction coordinate, the "dynamic distance", is introduced for the study of reactions involving the rupture and formation of a series of chemical bonds or contacts. The dynamic distance is a mass-weighted mean of selected distances. When implemented as a generalized constraint, the dynamic distance is particularly suited for driving activated processes by controlled increase during a simulation. As a single constraint acting upon multiple degrees of freedom, the sequence of events along the resulting reaction pathway is determined unambiguously by the underlying energy landscape. Free energy profiles can be readily obtained from the mean constraint force. In this paper both theoretical aspects and numerical implementation are discussed, and the unique and diverse properties of this reaction coordinate are demonstrated using three examples:  In the framework of Car-Parrinello molecular dynamics, we present results for the prototypical double proton-transfer reaction in formic acid dimer and the photocycle of the guanine-cytosine DNA base pair. As a classical mechanical example, the opening of the binding pocket of the enzyme rubisco is analyzed.
authors.affiliation: Lehrstuhl für Biophysik, Ruhr-Universität Bochum, ND 04, 44780 Bochum, Germany, Unité de Bioinformatique Structurale, Institut Pasteur, CNRS URA 2185, 25-28 Rue du Dr. Roux, 75015 Paris, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Burisch
authors.affiliation: Lehrstuhl für Biophysik, Ruhr-Universität Bochum, ND 04, 44780 Bochum, Germany, Unité de Bioinformatique Structurale, Institut Pasteur, CNRS URA 2185, 25-28 Rue du Dr. Roux, 75015 Paris, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
authors.forename: Phineus R L
authors.initials: PR
authors.lastname: Markwick
authors.affiliation: Lehrstuhl für Biophysik, Ruhr-Universität Bochum, ND 04, 44780 Bochum, Germany, Unité de Bioinformatique Structurale, Institut Pasteur, CNRS URA 2185, 25-28 Rue du Dr. Roux, 75015 Paris, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
authors.forename: Nikos L
authors.initials: NL
authors.lastname: Doltsinis
authors.affiliation: Lehrstuhl für Biophysik, Ruhr-Universität Bochum, ND 04, 44780 Bochum, Germany, Unité de Bioinformatique Structurale, Institut Pasteur, CNRS URA 2185, 25-28 Rue du Dr. Roux, 75015 Paris, France, and Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schlitter