Intrinsic and extrinsic disorder from lattice imperfections, substrate and environment has a strong effect on the local electronic structure and hence the optical properties of atomically thin transition metal dichalcogenides that are determined by strong Coulomb interaction. Here, we examine the role of the substrate material and intrinsic defects in monolayer MoS2 crystals on SiO2 and hBN substrates using a combination of scanning tunneling spectroscopy, scanning tunneling microscopy, optical absorbance, and low-temperature photoluminescence measurements. We find that the different substrates significantly impact the optical properties and the local density of states near the conduction band edge observed in tunneling spectra. While the SiO2 substrates induce a large background doping with electrons and a substantial amount of band tail states near the conduction band edge of MoS2, such states as well as the high doping density are absent using high quality hBN substrates. By accounting for the substrate effects we obtain a quasiparticle gap that is in excellent agreement with optical absorbance spectra and we deduce an exciton binding energy of about 480 meV. We identify several intrinsic lattice defects that are ubiquitious in MoS2, but we find that on hBN substrates the impact of these defects appears to be passivated. We conclude that the choice of substrate controls both the effects of intrinsic defects and extrinsic disorder, and thus the electronic and optical properties of MoS2. The correlation of substrate induced disorder and defects on the electronic and optical properties of MoS2 contributes to an in-depth understanding of the role of the substrates on the performance of 2D materials and will help to further improve the properties of 2D materials based quantum nanosystems.
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