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Scanning tunneling microscope data from a dinuclear Co(II) complex adsorbed on Au(111) are analysed using density functional theory calculations. We find that the interaction with the substrate substantially changes the geometry of the non-planar molecule. Its electronic states, however, remain fairly similar to those calculated for a gas-phase molecule. The calculations reproduce intriguing contrasts observed in experimental maps of the differential conductance dI/dV and reveal the relative importance of geometric and electronic factors that impinge on the image contrasts. For a meaningful comparison, it is important that the calculations closely mimic the experimental mode of measurement., Comment: 9 pages, 7 figures

Lead phthalocyanine (PbPc), a non-planar molecule, is studied on Pb(100) using scanning tunneling spectroscopy. A rigid shift of the molecular orbitals is found between molecules with the central Pb ion pointing to (PbPc$\downarrow$) or away (PbPc$\uparrow$) from the substrate and understood from the interaction between the molecules and their image charges. Inside the superconducting energy gap, Yu-Shiba-Rusinov (YSR) resonances are observed for PbPc$\uparrow$ molecules in islands indicating the presence of a magnetic moment. Such bound states are neither present on PbPc$\downarrow$ molecules nor isolated PbPc$\uparrow$ or molecules that lost the Pb ion during deposition (H$_0$Pc). The YSR energies vary depending on the orientation and type of the molecular neighbors. We analyze the role of the out-of-plane dipole moment of PbPc.

The zero-bias anomaly in conductance spectra of single Co atoms on Cu(111) observed at $\approx$ 4 K, which has been interpreted as being due to a Kondo resonance, is strongly modified when the Co atoms are attached to monatomic Cu chains. Scanning tunneling spectra measured at 340 mK in magnetic fields exhibit all characteristics of spin-flip excitations. Their dependence on the magnetic field reveals a magnetic anisotropy and suggests a non-collinear spin state. This indicates that spin-orbit coupling (SOC), which has so far been neglected in theoretical studies of Co/Cu(111), has to be taken into account. According to our density functional theory and multi-orbital quantum Monte Carlo calculations SOC suppresses the Kondo effect for all studied geometries.

Molecular vibrational spectroscopy with the scanning tunneling microscope is feasible but usually detects few vibrational modes. We harness sharp Yu-Shiba-Rusinov (YSR) states observed from molecules on a superconductor to significantly enhance the vibrational signal. From a lead phthalocyanin molecule 46 vibrational peaks are resolved enabling a comparison with calculated modes. The energy resolution is improved beyond the thermal broadening limit and shifts induced by neighbor molecules or the position of the microscope tip are determined. Vice versa, spectra of vibrational modes are used to measure the effect of an electrical field on the energy of YSR states. The method may help to further probe the interaction of molecules with their environment and to better understand selection rules for vibrational excitations.

Single Fe atoms on Au(111) surfaces were hydrogenated and dehydrogenated with the Au tip of a low-temperature scanning tunneling microscope (STM). Fe and FeH$_2$ were contacted with the tip of the microscope and show distinctly different evolutions of the conductance with the tip-substrate distance. The current shot noise of these contacts has been measured and indicates a single relevant conductance channel with the spin-polarized transmission. For FeH$_2$ the spin polarization reaches values up to 80\% for low conductances and is reduced if the tip-surface distance is decreased. These observations are partially reproduced using density functional theory (DFT) based transport calculations. We suggest that the quantum motion of the hydrogen atoms, which is not taken into account in our DFT modeling, may have a significant effect on the results., Comment: 10 pages

The current $I$ through nickelocene molecules and its noise are measured with a low temperature scanning tunneling microscope on a Cu(100) substrate. Density functional theory calculations and many-body modeling are used to analyze the data. During contact formation, two types of current evolution are observed, an abrupt jump to contact and a smooth transition. These data along with conductance spectra ($dI/dV$) recorded deep in the contact range are interpreted in terms of a transition from a spin-1 to a spin-1/2 state that is Kondo screened. Many-body calculations show that the smooth transition is also consistent with a renormalization of spin excitations of a spin-1 molecule by Kondo exchange coupling. The shot noise is significantly reduced compared to the Schottky value of $2eI$ but no influence of the Kondo effect or spin excitations are resolved. The noise can be described in the Landauer picture in terms of spin-polarized transmission of $\approx$35% through two degenerate $d_\pi$-orbitals of the Nickelocene molecule., Comment: 10 pages, 10 figures; revised version published in Phys. Rev. B

The shot noise of the current $I$ through junctions to single trioxatriangulenium cations (TOTA$^+$) on Au(111) is measured with a low temperature scanning tunneling microscope using Au tips. The noise is significantly reduced compared to the Poisson noise power of $2eI$ and varies linearly with the junction conductance. The data are consistent with electron transmission through a single spin-degenerate transport channel and show that TOTA$^+$ in a Au contact does not acquire an unpaired electron. Ab initio calculations reproduce the observations and show that the current involves the lowest unoccupied orbital of the molecule and tip states close to the Fermi level., Comment: 5 pages, 5 figures

The light emission from a scanning tunneling microscope operated on a Ag(111) surface at 6 K is analyzed from low conductances to values approaching the conductance quantum. Optical spectra recorded at a sample voltages V reveal emission with photon energies hv> 2eV. A model of electrons interacting coherently via a localized plasmon-polariton mode reproduces the experimental data, in particular the kinks in the spectra at eV and 2eV as well as the scaling of the intensity at low and intermediate conductances., Comment: 5 pages, 4 figures

In the scanning tunnelling microscope, the many-body Kondo effect leads to a zero-bias feature of the differential conductance spectra of magnetic adsorbates on surfaces. The intrinsic line shape of this Kondo resonance and its temperature dependence in principle contain valuable information. We use measurements on a molecular Kondo system, all-trans retinoic acid on Au(111), and model calculations to discuss the role of instrumental broadening. The modulation voltage used for the lock-in detection, noise on the sample voltage, and the temperature of the microscope tip are considered. These sources of broadening affect the apparent line shapes and render difficult a determination of the intrinsic line width, in particular when variable temperatures are involved.

C60-functionalized tips are used to probe C60 molecules on Cu(111) with scanning tunneling and atomic force microscopy. Distinct and complex intramolecular contrasts are found. Maximal attractive forces are observed when for both molecules a [6,6] bond faces a hexagon of the other molecule. Density functional theory calculations including parameterized van der Waals interactions corroborate the observations., Comment: 6 pages, 3 figures

All-trans-retinoic acid (ReA), a closed-shell organic molecule comprising only C, H, and O atoms, is investigated on a Au(111) substrate using scanning tunneling microscopy and spectroscopy. In dense arrays single ReA molecules are switched to a number of states, three of which carry a localized spin as evidenced by conductance spectroscopy in high magnetic fields. The spin of a single molecule may be reversibly switched on and off without affecting its neighbors. We suggest that ReA on Au is readily converted to a radical by the abstraction of an electron., Comment: 5 pages, 3 figures, accepted for publication in Phys. Rev. Lett

A Mn-porphyrin was contacted on Au(111) in a low-temperature scanning tunneling microscope (STM). Differential conductance spectra show a zero-bias resonance that is due to an underscreened Kondo effect according to many-body calculations. When the Mn center is contacted by the STM tip, the spectrum appears to invert along the voltage axis. A drastic change in the electrostatic potential of the molecule involving a small geometric relaxation is found to cause this observation., Comment: 8 pages, 8 figures (including supplemental material); accepted in Phys. Rev. Lett

Nickel islands are grown on W(110) at elevated temperatures. Islands with a thickness of two layers are investigated with scanning tunneling microscopy. Spectroscopic measurements reveal that nanometer sized areas of the islands exhibit distinctly different apparent heights and dI/dV spectra. Spin polarized and paramagnetic band structure calculations indicate that the spectral features are due to fcc(111) and bcc(110) orientations of the Ni film, respectively., Comment: The final publication is available at http://www.springerlink.com

Force and conductance were simultaneously measured during the formation of Cu-C60 and C60-C60 contacts using a combined cryogenic scanning tunneling and atomic force microscope. The contact geometry was controlled with submolecular resolution. The maximal attractive forces measured for the two types of junctions were found to differ significantly. We show that the previously reported values of the contact conductance correspond to the junction being under maximal tensile stress.

Visible and infra-red light emitted at a Ag-Ag(111) junction has been investigated from tunneling to single atom contact conditions with a scanning tunneling microscope. The light intensity varies in a highly nonlinear fashion with the conductance of the junction and exhibits a minimum at conductances close to the conductance quantum. The data are interpreted in terms of current noise at optical frequencies, which is characteristic of partially open transport channels.

The charge flow from a single C60 molecule to another one has been probed. The conformation and electronic states of both molecules on the contacting electrodes have been characterized using a cryogenic scanning tunneling microscope. While the contact conductance of a single molecule between two Cu electrodes can vary up to a factor of three depending on electrode geometry, the conductance of the C60-C60 contact is consistently lower by two orders of magnitude. First-principles transport calculations reproduce the experimental results, allow a determination of the actual C60-C60 distances, and identify the essential role of the intermolecular link in bi- and trimolecular chains., Comment: 4 pages, 4 figures (+ suppl. material 2 pages, 1 figure)

Silver dimers were fabricated on Ag(111) by single-atom manipulation using the tip of a cryogenic scanning tunnelling microscope. An unoccupied electronic resonance was observed to shift toward the Fermi level with decreasing atom-atom distance as monitored by spatially resolved scanning tunnelling spectroscopy. Density functional calculations were used to analyse the experimental observations and revealed that the coupling between the adsorbed atoms is predominantly direct rather than indirect via the Ag(111) substrate., Comment: 9 pages, 3 figures

Low-temperature scanning tunneling spectroscopy reveals that the Kondo temperature T_K of Co atoms adsorbed on Cu/Co/Cu(100) multilayers varies between 60 K and 134 K as the Cu film thickness decreases from 20 to 5 atomic layers. The observed change of T_K is attributed to a variation of the density of states at the Fermi level \rho_F induced by quantum well states confined to the Cu film. A model calculation based on the quantum oscillations of \rho_F at the belly and the neck of the Cu Fermi surface reproduces most of the features in the measured variation of T_K., Comment: 5 pages, Nature of the changes: After our submission, Brovko et al. reported ab initio calculations addressing the exchange interaction of exactly the system we have investigated experimentally (arXiv:0804.3298). We have modified the manuscript to stress the significance of our paper that promises experimental feasibility of such a prediction

Ultraviolet and visible radiation is observed from the contacts of a scanning tunneling microscope with Si(100) and (111) wafers. This luminescence relies on the presence of hot electrons in silicon, which are supplied, at positive bias on n- and p-type samples, through the injection from the tip, or, at negative bias on p-samples, by Zener tunneling. Measured spectra reveal a contribution of direct optical transitions in Si bulk. The necessary holes well below the valence band edge are injected from the tip or generated by Auger processes.

Measurements of light emission from a scanning tunneling microscope probing a Na overlayer on the (111) surface of Cu are reported along with results of a model calculation that essentially agree with the experimental ones. The observed light emission spectra show two characteristic features depending on the bias voltage. When the bias voltage is smaller than the energy of the second quantum well state formed outside the Na overlayer the light emission is due to a plasmon-mediated process, while for larger biases light emission is mainly caused by quantum well transitions between the two levels., Comment: Corrected typos etc; 10 pages, 4 figures

Unusual emission of visible light is observed in scanning tunneling microscopy of the quantum well system Na on Cu(111). Photons are emitted at energies exceeding the energy of the tunneling electrons. Model calculations of two-electron processes which lead to quantum well transitions reproduce the experimental fluorescence spectra, the quantum yield, and the power-law variation of the intensity with the excitation current., Comment: revised version, as published; 4 pages, 3 figures

The electronic structure of artificial Mn atom arrays on Ag(111) is characterized in detail with scanning tunnelling spectroscopy and spectroscopic imaging at low temperature. We demonstrate the degree to which variations in geometry may be used to control spatial and spectral distributions of surface state electrons confined within the arrays, how these are influenced by atoms placed within the structure and how the ability to induce spectral features at specific energies may be exploited through lineshape analyses to deduce quasiparticle lifetimes near the Fermi level. Through extensive comparison of $dI/dV$ maps and spectra we demonstrate the utility of a model based upon two-dimensional s-wave scatterers for describing and predicting the characteristics of specific resonators.