Abstract
Linear molecular motors have recently attracted considerable interest. In this paper weuse molecular dynamics simulations to investigate the structural and energeticproperties of neutral and oxidized [2]rotaxane motors. We first consider a neutralstructure to identify the stable configuration of a bistable [2]rotaxane whose ringcomponent is on the tetrathiafulvalene (TTF) recognition site, followed by a study ofthe dynamic switching process of an oxidized [2]rotaxane. The study shows thatfor a neutral structure the ring component stays at the TTF station in bothfree and constrained situations. When the station is oxidized, the ring is pushedto the other station and the dynamic switching process finishes in about 10 ns.By comparing the results for the cases of free and fixed ends, the simulationsshow that structural deformation plays an important role during the switchingprocess and can significantly affect the displacement output of molecular motors.
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