The rotaxane synthesised as a single isomer constituted of two cyclodextrins (CDs) and an azobenzene chain [M.R. Craig, T.D.W. Claridge, M.G. Hutchings, H.L. Anderson, Synthesis of a cyclodextrin azo dye rotaxane as a single isomer, Chem. Commun. 16 (1999) 1537-1538] has been investigated using molecular mechanics (MM) and dynamics (MD) with the MM3 force field in order to evaluate the stability of various configurations of the complex in the isolated and solvated states. The influence of the blocking groups and the presence of energy barriers along the azo chain were first investigated through the calculation of an energy profile. It revealed that the CD could translate along the chain at room temperature without any decomplexation. Next, MD simulations of three different types of configurations, i.e., head-to-head, head-to-tail, and tail-to-tail, of the rotaxane were carried out. The non-solvated phase simulations showed structures with the CDs close to each other while the solvated ones showed structures with CDs separated by larger distances. This separation occurs due to the solute-solvent interactions. When the systems are in isolated state, the observed structure of the complexes are less stable due to an unfavourable arrangement of the hydroxyls groups of the adjacent CD faces. When considering solvation, energies of the three configurations are roughly identical due to the large distance between the faces of the CDs. © 2006 Elsevier Inc. All rights reserved.