Precise determination of molecular adsorption geometries by room temperature non-contact atomic force microscopy

High resolution force measurements of molecules on surfaces, in non-contact atomic force microscopy, are often only performed at cryogenic temperatures, due to needing a highly stable system, and a passivated probe tip (typically via CO-functionalisation). Here we show a reliable protocol for acquiring three-dimensional force map data over both single organic molecules and assembled islands of molecules, at room temperature. Isolated cobalt phthalocyanine and islands of C₆₀ are characterised with submolecular resolution, on a passivated silicon substrate (B:Si(111)- \((\sqrt{3}\times \sqrt{3})R3{0}^{\circ }\) $\left(\sqrt{3}\times \sqrt{3}\right)R30^{\circ }$ ). Geometries of cobalt phthalocyanine are determined to a ~ 10 pm accuracy. For the C₆₀, the protocol is sufficiently robust that areas spanning 10 nm × 10 nm are mapped, despite the difficulties of room temperature operation. These results provide a proof-of-concept for gathering high-resolution three-dimensional force maps of networks of complex, non-planar molecules on surfaces, in conditions more analogous to real-world application.