Decoding atomic landscapes: Integrating electronic structure theory and high-resolution atomic force microscopy

High-resolution atomic force microscopy (HR-AFM) has emerged as a transformative technique for imaging and manipulating matter with atomic precision. By functionalizing the scanning probe with a CO molecule, HR-AFM enables direct visualization of chemical bonds, intermolecular interactions, charged states, and electron orbital signatures. We provide an overview of HR-AFM from both experimental and theoretical perspectives. The operational principles of frequency-modulation AFM and the role of tip functionalization are described, together with methods that combine AFM and STM for enhanced imaging and spectroscopy. Theoretical approaches, such as the virtual tip method, full density functional theory, frozen density embedding theory, and tip-tilting correction methods, enable the quantitative interpretation of tip-sample interactions and image contrast. These developments support applications of HR-AFM in resolving bond orders, functional groups, heteroatoms, and orbital fingerprints in single molecules, as well as in characterizing complex industrial hydrocarbons. Beyond imaging, HR-AFM also serves as a platform for controlled bond rupture and manipulation at the atomic scale. The benchmark Si(111)-(7 × 7) surface is revisited with recent insights into tip-induced contrast dynamics arising from B doping. Extensions of HR-AFM to state-resolved imaging of quantum defects in two-dimensional materials are also discussed. By combining high-resolution imaging with first-principles modeling, HR-AFM demonstrates a unique capability to reveal previously inaccessible surface phenomena, thereby further decoding the atomic landscapes of matter at the single-atom and molecular scale.