Activation energies, Ea, measured from molecular exchange experiments are combined with atomic-scale calculations to describe the migration of bare Au atoms and Au–alkanethiolate species on gold nanoparticle surfaces during ligand exchange for the creation of metal–molecule–metal junctions. It is well-known that Au atoms and alkanethiol–Au species can diffuse on gold with sub-1 eV barriers, and surface restructuring is crucial for self-assembled monolayer (SAM) formation for interlinking nanoparticles and in contacting nanoparticles to electrodes. In the present work, computer simulations reveal that naturally occurring ridges and adlayers on Au(111) are etched and resculpted by migration of alkanethiolate–Au species toward high coordination kink sites at surface step edges. The calculated energy barrier, Eb, for diffusion via step edges is 0.4–0.7 eV, close to the experimentally measured Ea of 0.5–0.7 eV. By contrast, putative migration from isolated nine-coordinated terrace sites and complete Au unbinding from the surface incur significantly larger barriers of +1 and +3 eV, respectively. Molecular van der Waals packing energies are calculated to have negligible effect on migration barriers for typically used molecules (length < 2.5 nm), indicating that migration inside SAMs does not change the size of the migration barrier. We use the computational methodology to propose a means of creating Au nanoparticle arrays via selective replacement of citrate protector molecules by thiocyanate linker molecules on surface step sites. This work also outlines the possibility of using Au/Pt alloys as possible candidates for creation of contacts that are well-formed and long-lived because of the superior stability of Pt interfaces against atomic migration.