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 benzidine, biphenol, 1,4-diaminobenzene, and benzohydroquinone in the gas-phase and in liquid CH3CN solution with molecular mechanics and Monte Carlo statistical mechanics has been performed. The complexes are important structural elements for a wide variety of self-assembling rotaxanes and catenanes with prospective use in nanoscale devices. However, their highly charged nature presents potential challenges for accurate modeling. In particular, the need for explicit polarization has been considered through computation of association energies using an all-atom force field with and without non-additive electrostatic polarization terms. The effect of including PF6– counterions has also been addressed. Polarization generally strengthens the gas-phase interactions, but has modest effects on the structures of the complexes and on the relative free energies of binding in solution, which are in reasonable agreement with experimental data.