Influence of vibrational energy flow on isomerization of flexible molecules: incorporating non-Rice-Ramsperger-Kassel-Marcus kinetics in the simulation of dipeptide isomerization.

The conformational isomerization of a dipeptide, N-acetyl-tryptophan methyl amide (NATMA), is studied computationally by including important dynamical corrections to Rice-Ramsperger-Kassel-Marcus (RRKM) theory for the transition rate between pairs of isomers. The dynamical corrections arise from incomplete or sluggish vibrational energy flow in the dipeptide, a property suggested by the mode-selective chemistry that has been observed by Dian et al. [J. Chem. Phys. 120, 133 (2004)]. We compute the extent and rate of vibrational energy flow in NATMA quantum mechanically using local random matrix theory, which we then use to correct the RRKM theory rates. The latter rates are then introduced into a master equation to study the population dynamics of the dipeptide. Incomplete or slow vibrational energy flow is found to enhance the conformational selectivity of NATMA over RRKM estimates.