High resolution Atomic Force Microscopy (AFM) and Scanning Tunnelling Microscopy (STM) imaging with functionalized tips is well established, but a detailed understanding of the imaging mechanism is still missing. We present a numerical STM/AFM model, which takes into account the relaxation of the probe due to the tip-sample interaction. We demonstrate that the model is able to reproduce very well not only the experimental intra-and intermolecular contrasts, but also their evolution upon tip approach. At close distances, the simulations unveil a significant probe particle relaxation towards local minima of the interaction potential. This effect is responsible for the sharp sub-molecular resolution observed in AFM/STM experiments. In addition, we demonstrate that sharp apparent intermolecular bonds should not be interpreted as true hydrogen bonds, in the sense of representing areas of increased electron density. Instead they represent the ridge between two minima of the potential energy landscape due to neighbouring atoms.

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A scanning tunneling microscope (STM) has been equipped with a nanoscale force sensor and signal transducer composed of a single D2 molecule that is confined in the STM junction. The uncalibrated sensor is used to obtain ultrahigh geometric image resolution of a complex organic molecule adsorbed on a noble metal surface. By means of conductance-distance spectroscopy and corresponding density functional calculations the mechanism of the sensor and transducer is identified. It probes the short-range Pauli repulsion and converts this signal into variations of the junction conductance.

Local, noncovalent intermolecular interactions in organic monolayers have been directly imaged using scanning tunneling hydrogen microscopy (STHM). Unprecedented spatial resolution directly reveals the relation between the intermolecular interactions, the molecular chemical structure, and the ordering in the film.