Molecular dynamics study of rotational reorientation of tryptophan and several indoles in water

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Abstract
Molecular dynamics simulations of the rotational reorientation of tryptophan and a series of indole derivatives in water were carried out. The majority of the simulations used CHARMm and produced results that are quite similar to the experimental data on these systems. Decomposition of the calculated correlation functions shows that the indole reorientation is dominated by in‐plane spinning. For systems with side chains the motion is quite different and is dominated by motion around the side chain axis. The issue of solvent attachment is addressed and the origin of the stickier reorientation of tryptophan as compared to indole discussed. Finally memory functions are calculated and briefly discussed.