Reversible Hydrogen-Bond Network Dynamics under external forces: Molecular Dynamics Simulations of Catenane structures

The unbinding of adhesion bonds in supramolecular assemblies can be triggered by the application of an external force. The reverse process of rebinding, however, often cannot be observed. Thus, for instance, the unfolding of proteins can be observed using force spectroscopy but the reverse process of refolding usually can not be followed. In the proposed project molecular dynamics (MD)-simulations under external force will be performed using entangled calixarene dimers as model systems. Here, the chemical bonding of the entangled loops provides a mechanical lock preventing the system from complete dissociation and thus enables reversible rebinding. The loop length can be tuned and for longer loops the opening transition is accomponied by the occurence of an intermediate structure. The impact of this intermediate on the kinetic rates and the relation between loop-length and reversibility will be studied in detail. Since bond breaking and bond formation are stochastic processes the respective rates are determined via a statistical analysis of a large number of MD-simulations. All systems studied are small enough (max. 10.000 particles) to allow to perform the large number of simulations needed. On the other hand, they are large enough to show a dynamic complexity in the hydrogen bond network that allows to generalize the results to chemically or biologically relevant systems. It is planned to perform MD-simulations using different protocols for the application of the external force and to compare the results for the kinetic rates and other structural and dynamic parameters. The results will allow for a detailed study of various force induced non-equilibrium effects.