All material supplied via Aaltodoc is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user. The adsorption and diffusion of 3,4,9,10-perylene-tetracarboxylic-dianhydride ͑PTCDA͒ molecules on a nanostructured KBr ͑001͒ surface were investigated by combining noncontact atomic force microscopy ͑NC-AFM͒ 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 firstprinciples 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.