Stochastic molecular dynamics study of t r a n s–g a u c h e isomerization processes in simple chain molecules

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Abstract
T r a n s–g a u c h eisomerization rates for n‐butane, n‐pentane, and n‐decane are determined from a stochastic molecular dynamics calculation of the reactive fluxes. Analysis of the deviations of these rates from the transition state theory predictions shows that the transmission coefficients differ markedly from unity for all physically realizable conditions. The dependence of the transmission coefficient on the collision frequency or friction constant parameterizing the stochastic element is discussed. A comparison between the stochastic dynamics and a true Newtonian molecular dynamics simulation of n‐butane in a simple liquidsolvent indicates that the reactive flux correlation function is significantly different than would be predicted by the high friction noninertial theory first discussed long ago by Kramers. For longer chain molecules, the isomerization rates depend upon which particular torsional angle is considered, and upon the configurational state of the neighboring angles. This dependence is analyzed. Finally, calculations are presented which address certain questions concerning the use of holonomic constraints in the dynamics of alkane chains.

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