KINETICS OF THE GEOMETRIC ISOMERIZATION OF CYCLOHEXENE IN A STOCHASTIC BATH

Rare-events molecular dynamics techniques are used to study the interc onversion between the two half-chair isomers of cyclohexene (C6H10), i n a solvent modelled through a stochastic bath, in order to investigat e dynamic solvent effects on the isomerization rate. Adopting the tors ional angle around the C-C sigma bond opposite to the double bond as t he reaction coordinate, we calculate the equilibrium distribution of t his coordinate (using umbrella sampling), and estimate the isomerizati on rate, including the transmission coefficient kappa. The paper also contains methodological developments. A variant of Andersen's stochast ic collision method (canonical ensemble sampling) is developed for mol ecules with constraints: by resampling Cartesian velocities of a local ized subgroup of atoms of the molecule and leaving all other atomic ve locity components unchanged, one mimics the collision of a virtual gas molecule with a subpart of the molecule of interest. To evaluate the transmission coefficient kappa, the initial conditions for trajectorie s 'crossing the top' are automatically generated during the run, using a biased potential to obtain the probability of being at the saddle p oint.