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Cadmium chalcogenide quantum dots (QDs) passivated by thiol-based ligands exhibit several advantages in their applications in lighting, sensing, and imaging technologies. However, their emission is sensitive to thiol concentrations, pH conditions, and temperatures. Using calculations based on the density functional theory, we identify conditions for thiol/thiolate equilibrium at the CdS QD surface that either eliminate or introduce optically inactive hole trap states favoring or disfavoring the emission. Our calculations indicate much weaker interactions between the QD and protonated species (thiols), compared to their deprotonated counterparts (thiolates). Additionally, the surface of CdS QD facilitates the partial deprotonation of thiols, leading tomore » the formation of an additional stable networking conformation where the proton is shared between the ligand and the QD surface. Thiolates strongly reduce the optical intensity of low-energy transitions in CdS QDs, contributing thiolate-localized hole trap states at the QD band gap. However, networking between the thiols and the surface, as well as the presence of native ligands such as primary amines, stabilize such trap states brightening the lowest optical transitions. This explains the increased emission of thiol-passivated QDs at lower concentrations in neutral or acidic solutions. Surface-mediated bias toward deprotonated species and their contribution to optically inactive states also rationalizes irreversible emission quenching and bleaching in the CdSe/CdS QDs exposed to high temperatures or intensive laser pulse.« less