Atomic vacancies with controlled depth and size are generated on a graphite surface by low-energy ion bombardment. The reactivity of vacancies towards an oxygen molecule is investigated by using scanning tunneling microscopy (STM) and density functional theory. An oxygen molecule (i) exothermally dissociates and then chemisorbs at the top sites and/or the bridge sites of a vacancy, or (ii) forms a precursor state of molecular oxygen at a bridge site. Reaction pathways for oxidative etching are proposed to interpret serpentine and circular etching patterns observed by STM.

Point defects at graphite surfaces are investigated by scanning tunneling microscopy (STM) under ultrahigh vacuum conditions. Graphite surfaces are bombarded with energy-selected beams of ${\mathrm{Ar}}^{+}$ and ${\mathrm{Kr}}^{+}$ ions at low energies (<100 eV) to generate the defects on atomic scale. The ion bombardment produces mostly carbon vacancy defects (VD’s) and interstitial defects (ID’s), the latter formed by trapping an incident ion beneath the surface carbon plane. A VD appears as a protrusion in STM image and so does an ID, but they can be distinguished from each other in the measurements of local tunneling barrier height (Φ) and tunneling spectroscopy $(I-V$ curve). They can also be physically separated by heating the defected surface to a temperature high enough to evaporate the noble-gas interstitials. By employing these methodologies, we are able to examine the electronic structure of individual VD’s and ID’s. A VD exhibits a Φ value substantially lower than an ID or a clean graphite. Both VD and ID increase the local charge density of states near the Fermi energy, but this effect is largest for a VD due to its dangling bonds. A $\sqrt{3}\times \sqrt{3}$ superlattice structure appears from an ID, but not from a VD. This observation disproves the existing theoretical interpretation that the superlattice structure results from electron scattering at a VD site. The absolute yield is measured for production of VD’s and ID’s at ion impact energies of 40–100 eV. The features of the yield curves, including the dependency on ion energy and the threshold energies for defect creation, provide reasonable explanations for the ion-surface collisional events leading to VD and ID creation in the low-energy regime.

Inelastic electron tunneling spectroscopy and microscopy with a scanning tunneling microscope revealed two vibrational modes showing a decrease in conductance at $\pm 82.0$ and $\pm 38.3\mathrm{mV}$ sample bias for single oxygen molecules chemisorbed on the fourfold hollow sites of Ag(110) surface at 13 K. The spatial distribution of the vibrational intensities exhibited ${\pi }_g$-orbital (perpendicular to surface) symmetry of ${\mathrm{O}}_2$ with the molecular axis along the [001] direction. These results are attributed to resonant inelastic electron tunneling.

A carbon monoxide molecule (CO) was positioned with a scanning tunneling microscope (STM) at various distances from an oxygen atom (O) on the Ag(110) surface at 13 K. At the closest separation, carbon dioxide ( ${\mathrm{CO}}_2$) production was induced by tunneling electrons. Direct reaction of a CO desorbed from the STM tip with an O atom on Ag(110) illustrates another catalytic oxidation mechanism. Inelastic electron tunneling spectroscopy with the STM was used to monitor the vibrations of CO in its different environment.

An atomic vacancy is produced on a graphite surface by bombarding it with low-energy (40-80 eV) beams of ${\mathrm{Ar}}^{+}$ ions, and its structure is examined by scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The atomic vacancy is imaged as a surface protrusion in STM, while it is transparent in AFM. These two contradictory results are explained by the vacancy-induced enhancement of the partial charge density of states at the carbon atoms near the vacancy. The charge enhancement can occur over tens of the surrounding carbon atoms for multiatom vacancy.