Coulombic interactions and crystal packing effects in the folding of donor-acceptor oligorotaxanes

The folding of a series of donor-acceptor oligorotaxanes is studied by means of molecular dynamics simulations. The oligorotaxanes consist of tetracationic cyclobis(paraquat-p-phenylene) rings threaded onto oligomers of 1,5-dioxynaphthalene linked by polyethers. Minimum energy structures are isolated using simulated annealing from which insights into the interactions responsible for the folding are extracted. The folding in vacuum is primarily driven by Coulombic interactions between the ionic species. In turn, in a high dielectric medium, the folding is the result of a series of conflicting interactions primarily orchestrated by the rings. In both cases, folded globular structures result. The observed secondary structures extend a previously proposed pleated π-stacked model for the folding that has been, in fact, observed in crystal samples of a [3]Rotaxane, the smallest of the oligorotaxanes considered. Simulations using two different force fields in the crystal environment, in vacuum, and in explicit solvent indicate that the π-stacked conformation adopted by the [3]Rotaxane is stable due to crystal packing effects rather than intracomplex interactions. The π-stacked conformation is also shown to be thermodynamically improbable in longer oligomers.