Extraction of Chemical Reactivity and Structural Relaxations of an Organic Dye from the Short-Range Interaction with a Molecular Probe

Unveiling the nature of atomic defects in graphene on a metal surface

Low-energy argon ion bombardment of graphene on Ir(111) induces atomic-scale defects at the surface. Using a scanning tunneling microscope, the two smallest defects appear as a depression without discernible interior structure suggesting the presence of vacancy sites in the graphene lattice. With an atomic force microscope, however, only one kind can be identified as a vacancy defect with four missing carbon atoms, while the other kind reveals an intact graphene sheet. Spatially resolved spectroscopy of the differential conductance and the measurement of total-force variations as a function of the lateral and vertical probe-defect distance corroborate the different character of the defects. The tendency of the vacancy defect to form a chemical bond with the microscope probe is reflected by the strongest attraction at the vacancy center as well as by hysteresis effects in force traces recorded for tip approach to and retraction from the Pauli repulsion range of vertical distances.

Orbital and Skeletal Structure of a Single Molecule on a Metal Surface Unveiled by Scanning Tunneling Microscopy

Atomic-scale spatial characteristics of a phthalocyanine orbital and skeleton are obtained on a metal surface with a scanning tunneling microscope and a CO-functionalized tip. Intriguingly, the high spatial resolution of the intramolecular electronic patterns is achieved without resonant tunneling into the orbital and despite the hybridization of the molecule with the reactive Cu substrate. The resolution can be fine-tuned by the tip-molecule distance, which controls the p-wave and s-wave contribution of the molecular probe to the imaging process. The detailed structure is deployed to minutely track the translation of the molecule in a reversible interconversion of rotational variants and to quantify relaxations of the adsorption geometry. Entering into the Pauli repulsion imaging mode, the intramolecular contrast loses its orbital character and reflects the molecular skeleton instead. The assignment of pyrrolic-hydrogen sites becomes possible, which in the orbital patterns remains elusive.

Tracking the Interaction between a CO-Functionalized Probe and Two Ag-Phthalocyanine Conformers by Local Vertical Force Spectroscopy

Intentionally terminating scanning probes with a single atom or molecule belongs to a rapidly growing field in the quantum chemistry and physics at surfaces. However, the detailed understanding of the coupling between the probe and adsorbate is in its infancy. Here, an atomic force microscopy probe functionalized with a single CO molecule is approached with picometer control to two conformational isomers of Ag-phthalocyanine adsorbed on Ag(111). The isomer with the central Ag atom pointing to CO exhibits a complex evolution of the distance-dependent interaction, while the conformer with Ag bonded to the metal surface gives rise to a Lennard-Jones behavior. By virtue of spatially resolved force spectroscopy and the comparison with results obtained from microscope probes terminated with a single Ag atom, the mutual coupling of the protruding O atom of the tip and the Ag atom of the phthalocyanine molecule is identified as the cause for the unconventional variation of the force. Simulations of the entire junction within density functional theory unveil the presence of ample relaxations in the case of one conformer, which represents a rationale for the peculiar vertical-distance evolution of the interaction. The simulations highlight the role of physisorption, chemisorption, and unexpected junction distortions at the verge of bond formation in the interpretation of the distance-dependent force between two molecules.