An atomic-scale perspective on individual thiol-terminated molecules anchored to single S vacancies in MoS$_2$

TL;DR

This study uses scanning tunneling microscopy and DFT calculations to explore how thiol molecules anchor to sulfur vacancies in MoS₂, revealing two reaction pathways and potential for defect functionalization with various functional groups.

Contribution

It demonstrates the atomic-scale mechanisms of thiol molecule anchoring at sulfur vacancies in MoS₂ and identifies two distinct reaction products, including catalytically activated dehydrogenation.

Findings

Both molecules are charge neutral.

One molecule remains intact, the other results from dehydrogenation.

Vacancies serve as effective anchoring sites for functionalization.

Abstract

Sulphur vacancies in 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 (CF$_3$-3P-SH) 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. One of them is an anchored intact CF$_3$-3P-SH molecule while the other one is the result of catalytically activated dehydrogenation to CF$_3$-3P-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.