Chalcogen vacancies are considered to be the most abundant point defects in two-dimensional (2D) transition-metal dichalcogenide (TMD) semiconductors, and predicted to result in deep in-gap states (IGS). As a result, important features in the optical response of 2D-TMDs have typically been attributed to chalcogen vacancies, with indirect support from Transmission Electron Microscopy (TEM) and Scanning Tunneling Microscopy (STM) images. However, TEM imaging measurements do not provide direct access to the electronic structure of individual defects; and while Scanning Tunneling Spectroscopy (STS) is a direct probe of local electronic structure, the interpretation of the chemical nature of atomically-resolved STM images of point defects in 2D-TMDs can be ambiguous. As a result, the assignment of point defects as vacancies or substitutional atoms of different kinds in 2D-TMDs, and their influence on their electronic properties, has been inconsistent and lacks consensus. Here, we combine low-temperature non-contact atomic force microscopy (nc-AFM), STS, and state-of-the-art ab initio density functional theory (DFT) and GW calculations to determine both the structure and electronic properties of the most abundant individual chalcogen-site defects common to 2D-TMDs. Surprisingly, we observe no IGS for any of the chalcogen defects probed. Our results and analysis strongly suggest that the common chalcogen defects in our 2D-TMDs, prepared and measured in standard environments, are substitutional oxygen rather than vacancies.
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