Mapping Atomic-Scale Metal–Molecule Interactions: Salient Feature Extraction through Autoencoding of Vibrational Spectroscopy Data

[Image: see text] Atomic-scale features, such as step edges and adatoms, play key roles in metal–molecule interactions and are critically important in heterogeneous catalysis, molecular electronics, and sensing applications. However, the small size and often transient nature of atomic-scale structures make studying such interactions challenging. Here, by combining single-molecule surface-enhanced Raman spectroscopy with machine learning, spectra are extracted of perturbed molecules, revealing the formation dynamics of adatoms in gold and palladium metal surfaces. This provides unique insight into atomic-scale processes, allowing us to resolve where such metallic protrusions form and how they interact with nearby molecules. Our technique paves the way to tailor metal–molecule interactions on an atomic level and assists in rational heterogeneous catalyst design.