Direct Imaging of Individual Molecular Binding to Clean Nanopore Edges in 2D Monolayer MoS₂

We use annular dark-field scanning transmission electron microscopy (ADF-STEM) to study how solution-deposited molecules bind to the edges and surface regions around nanopores in MoS₂ monolayers. Nanopores with clean atomically flat edges and controllable mean diameter were generated by time-dependent large-area electron beam exposure during an in situ heating process, ready for subsequent molecular attachment. An organic molecule was designed to have a dithiolane end group that binds to Mo-terminated sites and a ligand structure that incorporates a single transition metal atom (Pt) marker for ADF-STEM detection. Pt atoms were used to track molecular binding around zigzag edges of MoS₂ and to predict the orientations and conformations of molecules upon binding. We found that the molecules preferred to reside on the surface of the MoS₂, pointing inward when attaching to the edge, rather than dangling out from the edge into free space, which is attributed to van der Waals interactions between the aromatic core of the molecule and the MoS₂ basal planes. These results help us understand the way solution-deposited single molecules attach to free-standing edges of 2D crystals and the influence of van der Waals forces in guiding molecular binding.