Phthalocyanine molecules have been adsorbed to Ir(111) and to graphene on Ir(111). From a comparison of scanning tunneling microscopy images of individual molecules adsorbed to the different surfaces alone it is difficult to discern potential differences in the molecular adsorption geometry. In contrast, vibrational spectroscopy using inelastic electron scattering unequivocally hints at strong molecule deformations on Ir(111) and at a planar adsorption geometry on graphene. The spectroscopic evidence for the different adsorption configurations is supported by density functional calculations.

A scanning tunneling microscope is used to explore the evolution of electron and Cooper-pair transport across single Mn-phthalocyanine molecules adsorbed on Pb(111) from tunneling to contact ranges. Normal-metal as well as superconducting tips give rise to a gradual transition of the Bardeen-Cooper-Schrieffer energy gap in the tunneling range into a zero-energy resonance close to and at contact. Supporting transport calculations show that in the normal-metal-superconductor junctions this resonance reflects the merging of in-gap Yu-Shiba-Rusinov states as well as the onset of Andreev reflection. For the superconductor-superconductor contacts, the zero-energy resonance is rationalized in terms of a finite Josephson current that is carried by phase-dependent Andreev and Yu-Shiba-Rusinov levels.