This paper reports the working mechanism for a redox-responsive bistable [2]rotaxane incorporating an alpha-cyclodextrin (alpha-CD) ring (J. Am. Chem. Soc. 2008, 130, 11294-11296), based on free energy profiles obtained from all-atom molecular dynamics simulations. Employing an umbrella sampling technique, the free energy profiles (potential of mean force, PMF) were calculated for the shuttling motion of the alpha-CD ring between a tetrathiafulvalene (TTF) recognition site and a triazole (TZ) unit on the dumbbell of the rotaxane for three oxidation states (0, +1, +2) of the TTF unit. These calculated free energy profiles verified the experimentally observed binding preference for each state. Analysis of the free energy components reveals that, for these alpha-CD-based rotaxanes with charged TTF units, the real driving force for the shuttling in the oxidized states is actually the interactions between water and the rotaxane components, which overwhelms the attractive interactions between the alpha-CD ring and the charged dumbbell. In this work, we put forward a feasible approach to correctly describe the complexation behavior of CD with charged species, that is, free energy profiles obtained from all-atom molecular dynamics simulation.