Atomic-scale perspective on individual thiol-terminated molecules anchored to single S vacancies in MoS2

Sulfur vacancies in ${\mathrm{MoS}}_2$ on Au(111) have been shown to be negatively charged as reflected by a Kondo resonance. Here, we use scanning tunneling microscopy to show that these vacancies serve as anchoring sites for thiol-based molecules $\left({\mathrm{CF}}_3\text{−}3\mathrm{P}\text{−}\mathrm{SH}\right)$ with two distinct reaction products, one of them showing a Kondo resonance. Based on comparisons with density-functional theory (DFT) calculations, including a random structure search and computation of energies and electronic properties at a hybrid exchange-correlation functional level, we conclude that both anchored molecules are charge neutral. We propose that one of them is an anchored intact ${\mathrm{CF}}_3\text{−}3\mathrm{P}\text{−}\mathrm{SH}$ molecule while the other one is the result of catalytically activated dehydrogenation to ${\mathrm{CF}}_3\text{−}3\mathrm{P}\text{−}\mathrm{S}$ with subsequent anchoring. Our investigations highlight a perspective of functionalizing defects with thiol-terminated molecules that can be equipped with additional functional groups, such as charge donor or acceptor moieties, switching units, or magnetic centers.