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The thermodynamic driving force in the self-assembly of the secondarystructure of a class of donor-acceptor oligorotaxanes is elucidated by means ofmolecular dynamics simulations of equilibrium isometric single-molecule forcespectroscopy AFM experiments. The oligorotaxanes consist ofcyclobis(paraquat-\emph{p}-phenylene) rings threaded onto an oligomer of1,5-dioxynaphthalenes linked by polyethers. The simulations are performed in ahigh dielectric medium using MM3 as the force field. The resulting force vs.extension isotherms show a mechanically unstable region in which the moleculeunfolds and, for selected extensions, blinks in the force measurements betweena high-force and a low-force regime. From the force vs. extension data themolecular potential of mean force is reconstructed using the weighted histogramanalysis method and decomposed into energetic and entropic contributions. Thesimulations indicate that the folding of the oligorotaxanes is energeticallyfavored but entropically penalized, with the energetic contributions overcomingthe entropy penalty and effectively driving the self-assembly. In addition, ananalogy between the single-molecule folding/unfolding events driven by the AFMtip and the thermodynamic theory of first-order phase transitions is discussedand general conditions, on the molecule and the cantilever, for the emergenceof mechanical instabilities and blinks in the force measurements in equilibriumisometric pulling experiments are presented. In particular, it is shown thatthe mechanical stability properties observed during the extension areintimately related to the fluctuations in the force measurements.

AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation