A multiscale molecular switch model

Research paper by A. M. Popov, G. N. Shumkin

Indexed on: 20 Aug '10Published on: 20 Aug '10Published in: Moscow University Computational Mathematics and Cybernetics


A first-principles mathematical simulation of molecular switching of the isomerization reaction in a naphthalocyanine molecule on the basis of a current-induced tunnel microscope is presented. The Gibbs free energy surface and the reaction pathway are analyzed in terms of metadynamics using the numerical quantum mechanical Car-Parrinello molecular dynamics (CPMD) code. The calculations were performed on an IBM Blue Gene/P supercomputer at Moscow State University’s Faculty of Computational Mathematics and Cybernetics. The height of the energy barrier that must be overcome to achieve the isomerization reaction is found along an introduced coordination variable. A multiscale model of Ehrenfest molecular dynamics states is proposed on the basis of an excited electron. The model uses the coordination direction of the reaction on the free energy surface obtained in calculations for a complete molecule.