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.