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Large ordered islands of aluminum phthalocyanine (AlPc) molecules, which are unstable in air, are synthesized from ClAlPc on Pb(100) via dechlorination. Low-temperature scanning tunneling microscopy reveals that isolated AlPc molecules lose their spin moment on superconducting Pb(100). Molecular magnetism, which is detected via Yu-Shiba-Rusinov (YSR) resonances, may be restored by surrounding a molecule with an array of neighbor molecules in artificial arrays or in a self-assembled monolayer. Unlike phthalocyanine (H

Sub-monolayer amounts of trioxatriangulenium (TOTA) molecules functionalized with biphenyl on Ag(111) were investigated with scanning tunnelling microscopy. The molecule is comprised of a rod-shaped axial ligand and a triangular platform that tends to form hydrogen bonds in arrays. Two superstructures are observed, a hexagonal tiling and a phase of molecular double rows. While the former structure matches previous observations from other functionalized TOTA molecules the latter one was unexpected. Aided by density functional theory results, we analyse the observed intramolecular contrast and present a model of the new phase. We discuss possible interaction mechanisms underlying the molecular pattern.

Spin-flip excitations of iron porphyrin molecules on Au(111) are investigated with a low-temperature scanning tunneling microscope. The molecules adopt two distinct adsorption configurations on the surface that exhibit different magnetic anisotropy energies. Density functional theory calculations show that the different structures and excitation energies reflect unlike occupations of the Fe 3d levels. We demonstrate that the magnetic anisotropy energy can be controlled by changing the adsorption site, the orientation, or the tip-molecule distance.

Molecular vibrational spectroscopy with the scanning tunneling microscope is feasible but usually detects few vibrational modes. We harness sharp Yu-Shiba-Rusinov states observed from molecules on a superconductor to significantly enhance the vibrational signal. From a lead phthalocyanine 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 Yu-Shiba-Rusinov states. The method may help to further probe the interaction of molecules with their environment and to better understand selection rules for vibrational excitations.