The recent breakthrough in wafer-scale single-crystal growth has positioned two-dimensional (2D) semiconducting molybdenum disulfide (MoS2) as a compelling candidate for beyond-silicon electronics. Nevertheless, the high defect density in epitaxially grown MoS2 severely hinders its lab-to-fab transition. While the so-called sulfur vacancy (VS) defects have been extensively studied, here we demonstrate through multiscale simulations that oxygen-for-sulfur substitutions (OS) constitute the dominant defect species in epitaxially grown MoS2. Our calculation show that the formation of VS defects, although thermodynamically possible, is endothermic (3.3 eV) and kinetically very easy to be healed by ambient sulfur. In contrast, the formation of oxygen-for-sulfur substitution (OS) defects are thermodynamically more favorable (3.9 eV) than VS defects and kinetically persistent. Simulated scanning tunneling microscopy (STM) images show nearly identical signatures for both defect types, explaining the frequent experimental misidentification of VS and OS defects in grown MoS2. We identify the chemical origin of OS defects as incomplete sulfurization of oxygen-containing precursors during MoS2 growth. Based on kinetic Monte Carlo (kMC) simulations, we propose a spatial separation strategy that decouples precursor sulfurization from nucleation zones for complete sulfurization of precursor and intermediate, thereby greatly suppressing the defect formation. Our work fundamentally revises the prevailing VS-centered understanding of defects in epitaxially grown MoS2 and provides a practical pathway toward wafer-scale production of low defect density 2D transition metal dichalcogenides.
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