The adsorption and diffusion of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules on a nanostructured KBr (001) surface were investigated by combining noncontact atomic force microscopy (NC-AFM) and first-principles calculations. Atomically resolved measurements demonstrate trapping of PTCDA molecules in intentionally created rectangular monolayer-deep substrate pits and a preferential adsorption at kink sites. In order to understand the experimental results, we found that it was essential to include a first-principles treatment of the van der Waals interactions. We show that at some sites on the surface, 85% of the molecular binding is provided by van der Waals interactions, and in general it is always the dominant contribution to the adsorption energy. It also qualitatively changes molecular diffusion on the surface. Based on the specificity of the molecular interaction at kink sites, the species of the imaged ionic sublattice in the NC-AFM measurements could be identified.Peer reviewe