The structures of self-assembled monolayers (SAMs) of short (methyl) and long (hexyl) chain alkyl thiols on the clean gold(111) surface were modeled using for the Au – S interactions either the reactive ReaxFF potential or the well-known nonreactive Morse potential, while for the Au – Au interactions either the ReaxFF potential or an embedded-atom method (EAM). Analysis of the molecular dynamics (MD) trajectories of possible SAM structures suggests that disordering of interfacial Au atoms is definitely driven by the gold–sulphur interactions. Our MD results reveal a novel structure where two methanethiol molecules are bound to a gold adatom that has been lifted from the surface at 300 K, and the same kind of RS– Au –SR motif was also observed for hexanethiol at 600 K but not at 300 K. What is more, the above motif is only observed for the reactive ReaxFF potential. Moreover, these results are in clear agreement with recent experiments and more costly first principles-based MD simulations. These findings strongly support the use of reactive potentials such as ReaxFF for gathering an accurate description of Au – S interactions in inexpensive classical MD simulations.