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.

Molecular junctions have emerged as a powerful tool to investigate chemistry and physics at the single-molecule limit. However, their utility as a platform to develop spectroscopies and construct molecular devices is limited by the broad conductance dispersion typically encountered in experiments. The current view is that such broad dispersion arises because the detailed junction configuration is uncontrollable and varies in and between experiments. Contrary to conventional wisdom, through atomistic simulations and experiments, we show that even in ideal conditions, where the electrodes and electrode-molecule binding configurations are perfectly well-defined, measurements will still exhibit a broad conductance histogram. Such dispersion arises because of conductance changes as the junction is mechanically manipulated and the unavoidable stochastic nature of junction rupture. The results offer detailed atomistic insights into the factors that contribute to the broad conductance histograms and identify the key physical aspects that need to be controlled to narrow its width.

We demonstrate how simultaneous measurements of conductance and force can be used to monitor the step-by-step progress of a mechanically activated cis-to-trans isomerization single-molecule reaction, including events that cannot be distinguished using force or conductance alone.