Effects of intrinsic defects on methanthiol monolayers on Cu(111): A density functional theory study

Density functional theory calculations were used to examine the effects of intrinsic surface defects of Cu(111) on the adsorption of methylthiol (CH ₃SH). The examination covers both the initial non-dissociative adsorption and the subsequent dissociation reaction pathways to form intermediate and final reaction products. By comparing the most probable adsorption structures likely formed after the adsorption of CH₃SH on Cu(111) with and without the presence of adatoms (Cu_ad) and vacancies, this computational work offers new insights about the geometry and thermodynamic stability of these structures. Particularly, it reveals a new type of surface complexes having two CH₃S bonding to one Cu_ad (referred therein as CH₃S-Cu_ad-CH₃S). In addition, this work also yields new reaction dynamics results on transition states and activation barriers. The results reveal that the presence of Cu _ad indeed significantly changes the kinetics of adsorption and dissociation of CH₃SH on Cu(111). The most kinetically favorable reaction pathway turns out to be that involving the formation of a special surface complex formed by one Cu_ad plus two CH₃S fragments from the dissociation of CH₃SH, with the two S atoms located at the bridge sites of Cu(111). Finally, this work also gives simulated scanning tunneling microscopic images for the most important adsorption species in the course of the transition from CH₃SHCu(111) to CH₃SCu(111), which may stimulate future experimental studies of self-assembled monolayers on practical metal substrates such as thiols on copper.