The rotaxane formed by alpha-cyclodextrins (alpha-CDs) threaded onto a poly(ethylene glycol) (PEG) chain was investigated in the gas phase and in an aqueous solution by means of molecular dynamics simulations. The free-energy difference between the three possible spatial arrangements of consecutive alpha-CD-viz.. head-to-head (HH), head-to-tail (HT),. and tail-to-tail, was determined using free-energy perturbation calculations. These simulations reveal that the interaction of alpha-CD with the PEG chain is very similar in the two surroundings, whereas the mutual interaction of the macrocycles is stronger in the gas phase than in the aqueous solution. Moreover, difference in the overall interaction appears to stem primarily from changes in the electrostatic contribution. Analysis of intermolecular hydrogen bonds indicates that hydrogen bonds created between alpha-CD and water molecules weaken the hydrogen-bonding interaction of adjacent alpha-CDs. Comparison of the free-energy differences characteristic of the three possible spatial arrangements of contiguous alpha-CDs reveals that the HH motif of the rotaxane is the most stable in the gas phase due to the hydrogen-bond formation between the secondary hydroxyl groups of the two alpha-CDs, and the slight preference for the HT motif in aqueous solution, which can be related to the directionality of the dipole moment borne by the macrocycles in these two motifs.