Rigid Molecular Model for the Assembly Characteristics and Optimal Structure in Molecular Monolayers of Alkanethiols on Au(111)

We present a simple molecular model for the self-assembly of alkanethiols on gold. The model, a rigid rod representation of a molecule which is constrained to a given distance from the gold surface, allows direct long-time simulations of large-scale molecular ensembles (104−105 molecules) on desktop workstations. As a result, the model allows for efficient studies of evolution and ordering of, for example, orientational order and domain patterns in a full range of monolayer coverages. The model is parametrized entirely by existing literature on atomic and molecular scale interactions. Extensive simulations of molecular self-assembled monolayer domain formation at optimal (packing commensurate with a gold surface (111) structure) and suboptimal packing are conducted and presented. The results show close correspondence between the model features and the existing, and emerging, picture observed through experimental characterization of self-assembled monolayers on Au(111). This strong experimental validation of the conformationally insensitive molecular model suggests that the conformational degrees of freedom are not essential for the self-assembly of alkanethiols on gold. It appears that the interplay between the substrate−headgroup and chain−chain interactions determines the self-assembly process and the emergent molecular structures. The presentation of simulation results for different molecular surface coverages is used to derive a primitive two-dimensional isothermal phase diagram. The latter was found to be in good general agreement with available experimental data and provides insight into the formation and growth mechanism of monolayers. The work suggests directions for a minimal approach to studying at least some of the complexity contained in molecular self-assembly processes.