Vibrational excitations in weakly coupled single-molecule junctions: a computational analysis.

In bulk systems, molecules are routinely identified by their vibrational spectrum using Raman or infrared spectroscopy. In recent years, vibrational excitation lines have been observed in low-temperature conductance measurements on single-molecule junctions, and they can provide a similar means of identification. We present a method to efficiently calculate these excitation lines in weakly coupled, gateable single-molecule junctions, using a combination of ab initio density functional theory and rate equations. Our method takes transitions from excited to excited vibrational state into account by evaluating the Franck-Condon factors for an arbitrary number of vibrational quanta and is therefore able to predict qualitatively different behavior from calculations limited to transitions from ground state to excited vibrational state. We find that the vibrational spectrum is sensitive to the molecular contact geometry and the charge state, and that it is generally necessary to take more than one vibrational quantum into account. Quantitative comparison to previously reported measurements on pi-conjugated molecules reveals that our method is able to characterize the vibrational excitations and can be used to identify single molecules in a junction. The method is computationally feasible on commodity hardware.