Transition between scanning tunneling microscopy images of alkane derivatives on graphite

•SAMs of dialkyl sulfides form at the liquid–graphite interface.•STM contrast of molecules change reversibly between zigzag and aligned bright spot patterns.•The free energy for contrast change is smaller than the thermal energy (RT).•STM contrast change is caused by electronic effects and registry of the alkyl chains. Self-assembled monolayers of alkylated sulfides containing two alkyl chains and a sulfur atom positioned at the center of the molecules were studied on a graphite surface using scanning tunneling microscopy (STM). STM images of the closed-packed alkyl chains that extend linearly from the sulfur atoms change reversibly between a zigzag pattern and an aligned bright spot pattern on a time scale of minutes. The observation times of the zigzag and aligned bright spot patterns indicate that the difference between the free energies of these two stable molecular configurations with respect to the graphite surface is smaller than their thermal energies in the presence of a solvent, and 10 times smaller than the theoretical free energy between parallel and perpendicular configurations of the alkyl chains on graphite under vacuum. The change in the contrast of the STM images occurred owing to the electronic effects that depend on the registry of the alkyl chains on the graphite surface, and not by the classical observation of transfer between parallel and perpendicular orientations of alkyl chains on the surface.