The tip of a low-temperature scanning tunneling microscope is brought into contact with individual cobalt atoms adsorbed on Cu(100). A smooth transition from the tunneling regime to contact occurs at a conductance of $G\approx G_0$. Spectroscopy in the contact regime, i.e., at currents in a $\mu \mathrm{A}$ range, was achieved and indicated a significant change of the Kondo temperature $T_K$. Calculations indicate that the proximity of the tip shifts the cobalt $d$ band and thus affects $T_K$.

The tip of a low-temperature scanning tunneling microscope is approached towards a ${\mathrm{C}}_{60}$ molecule adsorbed at a pentagon-hexagon bond on Cu(100) to form a tip-molecule contact. The conductance rapidly increases to $\approx 0.25$ conductance quanta in the transition region from tunneling to contact. Ab-initio calculations within density functional theory and nonequilibrium Green’s function techniques explain the experimental data in terms of the conductance of an essentially undeformed ${\mathrm{C}}_{60}$. The conductance in the transition region is affected by structural fluctuations which modulate the tip-molecule distance.

Scanning tunneling spectroscopy of the differential conductance is performed at constant current and at constant distance. These modes of operation significantly affect peak positions and line shapes in spectra as well as patterns in spatial maps of the differential conductance. A normalization procedure for constant-current data, which relies on experimental current-distance data, is shown to yield spectral information on the local density of states.

Clusters containing a single magnetic impurity were investigated by scanning tunneling microscopy, spectroscopy, and ab initio electronic structure calculations. The Kondo temperature of a Co atom embedded in Cu clusters on Cu(111) exhibits a nonmonotonic variation with the cluster size. Calculations model the experimental observations and demonstrate the importance of the local and anisotropic electronic structure for correlation effects in small clusters.

Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure of the surface electrode. Nonequilibrium Green's function calculations reproduce the trend of the conductance and visualize the current flow through the junction, which is guided through molecule-electrode chemical bonds.