Thermal curing of a self-assembled monolayer at the nanoscale

On fabrication by contact printing, a nanostructured self-assembled monolayer (SAM) of alkanethiol contains a substantial fraction of unbound molecules that are either inverted among other upright molecules or piled on top of the SAM. The molecular dynamics simulation in the present study demonstrates that thermal annealing cures these defects for a SAM island of octadecanethiol. The SAM island melted partially as a result of heating, so the unbound molecules that had piled on top of the SAM island penetrated down to make contact with the surface, and the inverted molecules flipped to achieve adsorption. With subsequent cooling, the packing of sulfur atoms and alignment of alkyl chains of the SAM island were recovered. The molecular pathways for the adsorption of the unbound molecules were unraveled. The transition state and activation energy, calculated for each pathway in the absence of annealing, showed that these defects are incurable without the help of annealing.