Host-guest chemistry of rotaxanes and catenanes: application of a polarizable all-atom force field to cyclobis(paraquat-p-phenylene) complexes with disubstituted benzenes and biphenyls

Modeling of host-guest complexes of cyclobis(paraquat-p-phenylene) with ben ezidine, biphenol, 1,4-diaminobenzene, and benzohydroquinone in the gas-pha se and in liquid CH,CN solution with molecular mechanics and Monte Carlo st atistical mechanics has been performed. The complexes are important structu ral elements for a wide variety of self-assembling rotaxanes and catenanes with prospective use in nanoscale devices. However, their highly charged na ture presents potential challenges for accurate modeling. In particular, th e need for explicit polarization has been considered through computation of association energies using an all-atom force field with and without non-ad ditive electrostatic polarization terms. The effect of including PF6- count erions has also been addressed. Polarization generally strengthens the gas- phase interactions, but has modest effects on the structures of the complex es and on the relative free energies of binding in solution, which are in r easonable agreement with experimental data.