Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images atomic-scale features on surfaces, but resolving single atoms within an adsorbed molecule remains a great challenge because the tunneling current is primarily sensitive to the local electron density of states close to the Fermi level. We demonstrate imaging of molecules with unprecedented atomic resolution by probing the short-range chemical forces with use of noncontact atomic force microscopy. The key step is functionalizing the microscope's tip apex with suitable, atomically well-defined terminations, such as CO molecules. Our experimental findings are corroborated by ab initio density functional theory calculations. Comparison with theory shows that Pauli repulsion is the source of the atomic resolution, whereas van der Waals and electrostatic forces only add a diffuse attractive background.

Ultrathin insulating NaCl films have been employed to decouple individual pentacene molecules electronically from the metallic substrate. This allows the inherent electronic structure of the free molecule to be preserved and studied by means of low-temperature scanning-tunneling microscopy. Thereby direct images of the unperturbed molecular orbitals of the individual pentacene molecules are obtained. Elastic scattering quantum chemistry calculations substantiate the experimental findings.

Petroleum is one of the most precious and complex molecular mixtures existing. Because of its chemical complexity, the solid component of crude oil, the asphaltenes, poses an exceptional challenge for structure analysis, with tremendous economic relevance. Here, we combine atomic-resolution imaging using atomic force microscopy and molecular orbital imaging using scanning tunnelling microscopy to study more than 100 asphaltene molecules. The complexity and range of asphaltene polycyclic aromatic hydrocarbons are established in detail. Identifying molecular structures provides a foundation to understand all aspects of petroleum science from colloidal structure and interfacial interactions to petroleum thermodynamics, enabling a first-principles approach to optimize resource utilization. Particularly, the findings contribute to a long-standing debate about asphaltene molecular architecture. Our technique constitutes a paradigm shift for the analysis of complex molecular mixtures, with possible applications in molecular electronics, organic light emitting diodes, and photovoltaic devices.

The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules constitutes a two-level system that was manipulated and probed by low-temperature scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the molecules can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the molecule and is expressed as considerable changes in the conductivity of the molecule. We also demonstrated a coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule.