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Submonolayer amounts of chloroaluminum-phthalocyanine on Cu(100) were studied with scanning tunneling spectroscopy. The molecule can be prepared in a fourfold symmetric state whose conductance spectrum exhibits a zero-bias feature similar to a Kondo resonance. In magnetic fields, however, this resonance splits far more than expected from the spin of a single electron. Density functional theory calculations reveal a charge transfer of 1.3 electrons to the degenerate lowest unoccupied molecular orbitals. These orbitals are mixed by the orbital momentum operator L[over ^]_{z} with a large matrix element corresponding to m_{L}≈2.7. Dehydrogenation of a ligand lifts the degerenracy of the lowest unoccupied molecular orbital, reduces the splitting in magnetic fields, and induces a polarity dependence of the spectra. Using model calculations of the spin, orbital, and vibrational degrees of freedom we show that a dynamical Jahn-Teller effect reproduces the main experimental observations.

Scanning tunneling spectroscopy measurements of Mn phthalocyanine (MnPc) molecules adsorbed on (sqrt[3]×sqrt[3]) surface alloys show single inelastic steps at exclusively positive or negative bias strongly depending on the tip position. This is in contrast to conventional molecular excitation thresholds, which are independent of the current direction and therefore always occur at both positive and negative bias. This polarity selectivity is found to coincide with the spatial distribution of occupied and empty orbitals. Because of the interaction with the substrate, charge transfer into the doubly degenerate d_{π} orbitals of MnPc takes place. The resulting Jahn-Teller effect lifts the degeneracy and leads to an isospin- or pseudospin-flip excitation, the inelastic analogue of an orbital Kondo resonance.

We show that the magnetic ordering of coupled atomic dimers on a superconductor is revealed by their intragap spectral features. Chromium atoms on the superconductor β-Bi_{2}Pd surface display Yu-Shiba-Rusinov bound states, detected as pairs of intragap excitations in tunneling spectra. By means of atomic manipulation with a scanning tunneling microscope's tip, we form Cr dimers with different arrangements and find that their intragap features appear either shifted or split with respect to single atoms. These spectral variations are associated with the magnetic coupling, ferromagnetic or antiferromagnetic, of the dimer, as confirmed by density functional theory simulations. The striking qualitative differences between the observed tunneling spectra prove that intragap Shiba states are extremely sensitive to the magnetic ordering on the atomic scale.

The controlled switching between two quasistable Néel states in adsorbed antiferromagnetic Fe chains has recently been achieved by Loth et al. [Science 335, 196 (2012)] using tunneling electrons from an STM tip. In order to rationalize their data, we evaluate the rate of tunneling electron-induced switching between the Néel states. Good agreement is found with the experiment, permitting us to identify three switching mechanisms: (i) low STM voltage direct electron-induced transitions, (ii) intermediate STM voltage switching via spin-wave-like excitation, and (iii) high STM voltage transitions mediated by domain-wall formation. Spin correlations in the antiferromagnetic chains are the switching driving force, leading to a marked chain-size dependence.

Density functional theory simulations of the vibrational inelastic electron tunneling spectroscopy (IETS) of O2 on Ag(110) permits us to solve its unexplained IETS data [Hahn, Phys. Rev. Lett. 85, 1914 (2000)]. When semilocal density functional theory is corrected by including static intra-atomic correlations, the IETS simulations are in excellent agreement with the experiment. The unforeseen consequence of our calculations is that when adsorbed along the [001] direction, molecular O2 on Ag(110) is a mixed-valent system. This analysis of IETS unambiguously reveals the paramagnetic nature of O2 on Ag(110).

The excitation of the spin degrees of freedom of an adsorbed atom by tunneling electrons is computed using strong coupling theory. Recent measurements [Heinrich, Science 306, 466 (2004)] reveal that electron currents in a magnetic system efficiently excite its magnetic moments. Our theory shows that the incoming electron spin strongly couples with that of the adsorbate so that memory of the initial spin state is lost, leading to large excitation efficiencies. First-principles transmissions are evaluated in quantitative agreement with the experiment.

We present a method to analyze the results of first-principles based calculations of electronic currents including inelastic electron-phonon effects. This method allows us to determine the electronic and vibrational symmetries in play, and hence to obtain the so-called propensity rules for the studied systems. We show that only a few scattering states--namely those belonging to the most transmitting eigenchannels--need to be considered for a complete description of the electron transport. We apply the method on first-principles calculations of four different systems and obtain the propensity rules in each case.

Codeposition of C60 and the three-dimensional molecular hydrocarbon 1,3,5,7-tetraphenyladamantane (TPA) on Au(111) leads to the spontaneous formation of molecular nanostructures in which each fullerene is locked into a specific orientation by three surrounding TPA. Scanning tunneling spectroscopy shows that the electronic coupling of C60 with the surface is significantly reduced in these nanostructures, enhancing the free-molecule properties. As evidenced by density functional theory simulations, the nanostructures are stabilized by 18 local electrostatic forces between C60 and TPA, resulting in a lifting of the C60 cage from the surface.

We present a method for including inelastic scattering in a first-principles density-functional computational scheme for molecular electronics. As an application, we study two geometries of four-atom gold wires corresponding to two different values of strain and present results for nonlinear differential conductance vs device bias. Our theory is in quantitative agreement with experimental results and explains the experimentally observed mode selectivity. We also identify the signatures of phonon heating.