Vibrational spectroscopy of molecules chemically bound to electrodes

The atomic scale structures of the molecule-metal interfaces of single-molecule nanowires forming stable electrically conducting bridges between metal electrodes have been studied intensively for more than a decade but have remained elusive, and are still central to the field of single-molecule nanoelectronics. In this theoretical study, I show how inelastic tunneling spectroscopy experiments with the help of theory are now capable of determining the unknown bonding geometries between the molecule and electrodes, and thus resolving the long standing “contact problem" of molecular nanoelectronics. As an example I consider the propanedithiolate (PDT) molecules bridging gold nanocontacts in the recent experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] 1. Based on ab initio density functional and semi-empirical calculations, I find the relaxed geometries and vibrational modes of extended molecules each consisting of one or two PDT molecules connecting two gold nanoclusters and calculate their elastic conductances and inelastic tunneling spectra. Comparing my results with the data of Hihath et al., I find that the most frequently realized conformation in the experiment was trans molecules top-site bonded to both electrodes. I identify the features observed in the experimental inelastic electron tunneling spectroscopy (IETS) of these molecules at phonon energies near 46, 40 and 42 meV and show the switching from the 42 meV vibrational mode to the 46 meV mode observed in the experiment to be due to the transition of trans molecules from top-bridge to top-site bonding geometries. I extend my study to evaluating the effect of thiol hydrogen atoms in molecular junctions and show how IETS can be used to monitor gold-thiol bond formation and the cleavage of the S-H bond during this process. For pairs of PDT molecules connecting the gold electrodes in parallel, I find total elastic conductances close to twice those of single molecules bridging the contacts with similar bonding conformations and small splittings of the vi- brational mode energies for the modes that are the most sensitive to the molecule-electrode bonding geometries. I also describe the dependence of the transport properties of alkanedithiols molecular junctions on the length of the alkane chain.