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Engineering catalytic sites at the atomic level provide an opportunity to understand the catalyst’s active sites, which is vital to the development of improved catalysts. Herein, we show a reliable and tunable polyoxometalate (POM) template-based synthetic strategy to atomically engineer metal doping sites onto metallic 1T-MoS2, using Anderson-type POMs (XMo6, X = FeIII, CoIII, or NiII) as precursors. Benefiting from the synergistic effect of doping metals into 1T-MoS2 and the possible tuning effect of the Ni-O-Mo bond, the optimized Ni and O incorporated 1T-MoS2 (NiO@1T-MoS2) catalyst excels in the hydrogen evolution reaction (HER). With a positive onset potential of ~ 0 V and a low overpotential of -46 mV in 1.0 M KOH, its results are comparable to 20% Pt/C. First-principles calculations reveal co-doping Ni and O into 1T-MoS2 assists the processes of both water dissociation and hydrogen generation from their intermediate states. This research will expand on the ability to improve the activities of various catalysts by precisely engineering atomic activation sites to achieve significant electronic modulations and improve atomic utilization efficiencies.