Signatures of Conformational Dynamics and Electrode-Molecule Interactions in the Conductance Profile During Pulling of Single-Molecule Junctions.

We demonstrate that conductance can act as a sensitive probe of conformational dynamics and electrode-molecule interactions during the equilibrium and nonequilibrium pulling of molecular junctions. To do so, we use a combination of classical molecular dynamics simulations and Landauer electron transport computations to investigate the conductance of a family of Au-alkanedithiol-Au junctions as they are mechanically elongated. The simulations show an overall decay of the conductance during pulling that is due to a decrease in the through-space electrode-molecule interactions, and that sensitivity depends on the electrode geometry. In addition, characteristic kinks induced by level alignment shifts (and to a lesser extent by quantum destructive interference) were also observed superimposed to the overall decay during pulling simulations. The latter effect depends on the variation of the molecular dihedral angles during pulling and therefore offers an efficient solution to experimentally monitor conformational dynamics at the single-molecule limit.