The shuttling mechanism of foldaxanes: More than just the translocation and rotation
Tailoring structures of nanomachines to achieve specific functions is one of the major challenges in chemistry. Disentangling difference movements of nanomachines is critical to characterize their functions. Here, the motions within one kind of molecular machines, foldaxanes, composed of a foldamer with the spring-like conformation onto an axle have been examined at the molecular level. In the aid of molecular dynamics simulations and enhanced sampling methods, the free‒energy landscape characterizing the shuttling of the foldaxane has been drawn. The calculated free‒energy barrier, amounting to 20.7 kcal/mol, agrees well with experiment. Further analysis reveals that the predominant contribution to the free‒energy barrier stems from the disruption of hydrogen bonds between the foldamer and the thread. In the absence of hydrogen bonding interactions between terminals of the foldamer and the thread, the shrinkage and swelling movements of the foldamer have been identified and investigated in detail. By deciphering the intricate mechanism how the foldaxane shuttles, our understanding of motions within molecular machines is expected to be improved, helping in turn the construction of molecular machines with specific functions.