  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.
