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The selective separation of chalcopyrite from galena (lead sulfide) through the flotation method is still a challenging task in the field of mineral engineering. Mercaptoacetic acid, though a common depressant of many gangue (commercially worthless) minerals, has shown to be less selective in the flotation separation of chalcopyrite and galena. This resent study therefore systematically investigated the selectivity of different mercapto acids (especially three types: 3-mercaptopropionic acid, 3-mercaptoisobutyric acid and mercaptoacetic acid) on the separation of chalcopyrite and galena by making the use of flotation experiments and first principle calculations. The calculation results demonstrated that the sulfhydryl and carboxyl groups existing on the molecular structure of three mercapto acids are the reactive and chelating centers to metal ions on sulfide mineral surfaces. Mercapto acids have higher binding energies to Cu²⁺ by 300−400 kJ/mol compared to Pb²⁺, indicating a higher affinity towards chalcopyrite. The order of reactivity and chelating ability noted was as follows: 3-mercaptopropionic acid > 3-mercaptoisobutyric acid > mercaptoacetic acid. Flotation results further showed that the selectivity of 3-mercaptopropionic acid or 3-mercaptoisobutyric acid was better than mercaptoacetic acid. The good agreement between the first principle calculations and the flotation results demonstrated that the former reagent could be served as a most selective depressant in the improved flotation separation of chalcopyrite and galena.