Shuttling Process in [2]Rotaxanes. Modeling by Molecular Dynamics and Free Energy Perturbation Simulations

The first application of a methodology previously developed and tested on pseudorotaxanes is presented here in the study of the structure and the energetics of [2]rotaxane 1. The approach is based on the AMBER force field with RESP charges, and on an explicit solvent model for acetonitrile. With this model, the experimentally observed free energy difference (0.98 kcal mol-1) between the two translational isomers of 1 (computed ΔG = 1.06 ± 0.04 kcal mol-1) was correctly reproduced. The linear component of the suprastructure adopts an extended conformation, as suggested by the free energy perturbation simulations.

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