Memory kernel in liquid phase c i s–t r a n s isomerization

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Abstract
The memory kernel in liquid phase cis–trans isomerization is examined from the point of view of existing experimental data as well as MD simulations. In agreement with nonlinear system/bath coupling theories, when the generalized Langevin equation is written in the conventional way, we find that the ‘‘effective’’ memory kernel in this equation depends on the properties of the isomerizing particle, including the barrier height. In addition, it is found that the angular velocity distribution for the isomerizing molecule may be strongly influenced by ‘‘shape effects,’’ caused by actual molecular differences between the cis and trans configurations. This distribution may not be Maxwellian when considered over a partial angular range, e.g., the ‘‘barrier region.’’ If this is a general phenomenon, the selection of correct initial conditions in the reactive flux method would create uncertainties in the application of that method to the calculation of barrier crossing rates.