Firuz Demir

Identification of the atomic scale structures of the gold-thiol interfaces of molecular nanowires by inelastic tunneling spectroscopy

We examine theoretically the effects of the bonding geometries at the gold-thiol interfaces on the inelastic tunneling spectra of propanedithiolate (PDT) molecules bridging gold electrodes and show that inelastic tunneling spectroscopy combined with theory can be used to determine these bonding geometries experimentally. With the help of density functional theory, we calculate the relaxed geometries and vibrational modes of extended molecules each consisting of one or two PDT molecules connecting two gold nanoclusters. We formulate a perturbative theory of inelastic tunneling through molecules bridging metal contacts in terms of elastic transmission amplitudes, and use this theory to calculate the inelastic tunneling spectra of the gold-PDT-gold extended molecules. We consider PDT molecules with both trans and gauche conformations bound to the gold clusters at top, bridge, and hollow bonding sites. Comparing our results with the experimental data of Hihath et al. [Nano Lett. 8, 1673 (2008)], we identify the most frequently realized conformation in the experiment as that of trans molecules top-site bonded to both electrodes. We find 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 mixed top-bridge to pure top-site bonding geometries. Our results also indicate that gauche molecular conformations and hollow site bonding did not contribute significantly to the experimental inelastic tunneling spectra. For pairs of PDT molecules connecting the gold electrodes in parallel we find total elastic conductances close to twice those of single molecules bridging the contacts with similar bonding conformations and small splittings of the vibrational mode energies for the modes that are the most sensitive to the molecule-electrode bonding geometries.

Communication: Identification of the molecule–metal bonding geometries of molecular nanowires

Molecular nanowires in which a single molecule bonds chemically to two metal electrodes and forms a stable electrically conducting bridge between them have been studied intensively for more than a decade. However, the experimental determination of the bonding geometry between the molecule and electrodes has remained elusive. Here we demonstrate by means of ab initio calculations that inelastic tunneling spectroscopy (IETS) can determine these geometries. We identify the bonding geometries at the gold-sulfur interfaces of propanedithiolate molecules bridging gold electrodes that give rise to the specific IETS signatures that were observed in recent experiments.

Mechanism of the enhanced conductance of a molecular junction under tensile stress

Despite its fundamental importance for nano physics and chemistry and potential device applications, the relationship between atomic structure and electronic transport in molecular nanostructures is not well understood. Thus the experimentally observed increase of the conductance of some molecular nano junctions when they are stretched continues to be counterintuitive and controversial. Here we explore this phenomenon in propanedithiolate molecules bridging gold electrodes by means of {\em ab initio} computations and semi-empirical modeling. We show that in this system it is due to changes in Au-S-C bond angles and strains in the gold electrodes, rather than to the previously proposed mechanisms of Au-S bond stretching and an associated energy shift of the highest occupied molecular orbital and/or Au atomic chain formation. Our findings indicate that conductance enhancement in response to the application of tensile stress should be a generic property of molecular junctions in which the molecule is thiol-bonded in a similar way to gold electrodes.

On the Coulomb-Sturmian matrix elements of the Coulomb Green's operator

The two-body Coulomb Hamiltonian, when calculated in Coulomb-Sturmian basis, has an infinite symmetric tridiagonal--i.e., Jacobi-matrix form. This Jacobi-matrix structure involves a continued-fraction representation for the inverse of the Greens matrix. The continued fraction can be transformed to a ratio of two {sub 2}F{sub 1} hypergeometric functions. From this result we find an exact analytic formula for the matrix elements of the Greens operator of the Coulomb Hamiltonian.

Green's operator for Hamiltonians with Coulomb plus polynomial potentials

The Hamiltonian of a Coulomb plus polynomial potential in the Coulomb–Sturmian basis has an infinite symmetric band-matrix structure. A band matrix can always be considered as a block-tridiagonal matrix. So, the corresponding Greens operator can be given as a matrix-valued continued fraction. As examples, we calculate Greens operator for the Coulomb plus linear and quadratic confinement potential problems and determine the energy levels.

Controlling the thermoelectric effect by mechanical manipulation of the electron’s quantum phase in atomic junctions

The thermoelectric voltage developed across an atomic metal junction (i.e., a nanostructure in which one or a few atoms connect two metal electrodes) in response to a temperature difference between the electrodes, results from the quantum interference of electrons that pass through the junction multiple times after being scattered by the surrounding defects. Here we report successfully tuning this quantum interference and thus controlling the magnitude and sign of the thermoelectric voltage by applying a mechanical force that deforms the junction. The observed switching of the thermoelectric voltage is reversible and can be cycled many times. Our ab initio and semi-empirical calculations elucidate the detailed mechanism by which the quantum interference is tuned. We show that the applied strain alters the quantum phases of electrons passing through the narrowest part of the junction and hence modifies the electronic quantum interference in the device. Tuning the quantum interference causes the energies of electronic transport resonances to shift, which affects the thermoelectric voltage. These experimental and theoretical studies reveal that Au atomic junctions can be made to exhibit both positive and negative thermoelectric voltages on demand, and demonstrate the importance and tunability of the quantum interference effect in the atomic-scale metal nanostructures.

Inelastic tunneling spectroscopy of gold-thiol and gold-thiolate interfaces in molecular junctions: the role of hydrogen.

It is widely believed that when a molecule with thiol (S-H) end groups bridges a pair of gold electrodes, the S atoms bond to the gold and the thiol H atoms detach from the molecule. However, little is known regarding the details of this process, its time scale, and whether molecules with and without thiol hydrogen atoms can coexist in molecular junctions. Here, we explore theoretically how inelastic tunneling spectroscopy (IETS) can shed light on these issues. We present calculations of the geometries, low bias conductances, and IETS of propanedithiol and propanedithiolate molecular junctions with gold electrodes. We show that IETS can distinguish between junctions with molecules having no, one, or two thiol hydrogen atoms. We find that in most cases, the single-molecule junctions in the IETS experiment of Hihath et al. [Nano Lett. 8, 1673 (2008)] had no thiol H atoms, but that a molecule with a single thiol H atom may have bridged their junction occasionally. We also consider the evolution of the IETS spectrum as a gold STM tip approaches the intact S-H group at the end of a molecule bound at its other end to a second electrode. We predict the frequency of a vibrational mode of the thiol H atom to increase by a factor ~2 as the gap between the tip and molecule narrows. Therefore, IETS should be able to track the approach of the tip towards the thiol group of the molecule and detect the detachment of the thiol H atom from the molecule when it occurs.