Performance of different force fields in force probe simulations.

We present detailed force probe molecular dynamic simulations of mechanically interlocked dimeric calix[4]arene-catenanes, comparing the results obtained using three different commonly used force fields (GROMOS G53a5, OPLS-AA, and AMBER GAFF). The model system is well characterized as a two-state system consisting of a closed compact and an elongated structure. Both states are stabilized by a different hydrogen-bond network, and complete separation of the dimer is prevented by the mechanical lock of the entangled aliphatic loops.

Reversible hydrogen bond network dynamics: molecular dynamics simulations of calix[4]arene-catenanes.

We present detailed molecular dynamics (MD) simulations of mechanically interlocked calix[4]arene-catenanes under external force. Single-molecule force spectroscopy experiments revealed that the separation of dimers with two aliphatic loops results in reversible hydrogen bond breakage through an intermediate in a triple-well potential, while the tetra-loop species separates in a one-step manner (Janke, M.; et al.

Statistics of reversible bond dynamics observed in force-clamp spectroscopy.

We present a detailed analysis of two-state trajectories obtained from force-clamp spectroscopy (FCS) of reversibly bonded systems. FCS offers the unique possibility to vary the equilibrium constant in two-state kinetics, for instance, the unfolding and refolding of biomolecules, over many orders of magnitude due to the force dependence of the respective rates. We discuss two different kinds of counting statistics, the event counting usually employed in the statistical analysis of two-state kinetics and additionally the so-called cycle counting.