Effects of Intrinsic Surface Defects on Thiophenol Self-Assembly on Au(111): Surface Structures and Reaction Mechanisms

Density functional theory calculations were used to examine the effects of intrinsic surface defects of Au(111) on nondissociative thiophenol (PhSH) adsorption and the follow-up reaction pathways toward the dissociation of PhSH to form phenyl-thiolate (PhS) and then stable PhS adsorption structures. The calculations yielded the surface geometry of the most probable adsorption products, on Au(111) with and without the presence of adatoms (Au-ad) and vacancies, including the adsorption geometry of stable PhS-Au-ad-PhS surface complexes formed as the optimal products of dissociative adsorption toward the growth of a self-assembled monolayer of phenyl-thiolates. The validity of the computational adsorption geometries and our analysis of them are supported by the agreement between our simulated scanning tunneling microscopic images derived from these adsorption structures and the experimental images available in the literature. To elucidate further the adsorption reaction dynamics, we calculated the relevant reaction pathways and activation barriers and found that whereas the lowest energy barrier for the formation of the most stable PhS-PhS pair with the closest separation on clean Au(111) with no intrinsic defects is 0.68 eV, the counterpart with Au-ad is only 0.32 eV. This and our other calculated results highlight the facilitating role of intrinsic defects of Au(111) in driving the dissociative adsorption of thiophenol and articulate the reaction mechanism of the formation of the trans-PhS-Au-ad-PhS surface complex, which is the precursor to the final completion of a self-assembled monolayer of phenyl-thiols: the end product of thiophenol adsorption.