Determination of the Configuration of a Single Molecule Junction by Inelastic Electron Tunneling Spectroscopy

First-principles calculations for inelastic electron tunneling spectroscopy (IETS) of a single 1,3-propanedithiol molecule covalently bound to gold electrodes are presented. Inelastic electron tunneling spectra of the single molecule junction with different contact geometries and molecular orientations at the interface are simulated. It is demonstrated that the delicate variation in the configuration of the single molecule junction caused by separating the two electrodes can result in significant changes in the inelastic electron tunneling spectral profile of the junction. The two most probable configurations of the molecular junction formed in the experiment (Nano Lett. 2008, 8, 1673) are theoretically identified, and the experimental IET spectra are correctly assigned.