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The aim of this research was to investigate the mechanism of PdIn intermetallic nanoparticles formation and its applicability in the liquid-phase hydrogenation of substituted alkynes. This reaction is of significant importance because its products (cis-/trans-olefins) play a key role as source materials for the food and pharmaceutical industry, domestic chemicals, light-emitting diodes, liquid-crystal displays, etc. The metals were loaded as heterobimetallic Pd(μ-O2CMe)4In(O2CMe) complex to ensure intimate contact between Pd and In. Formation of PdIn intermetallic nanoparticles supported on α-Al2O3 was studied by a complex of physicochemical methods. Reduction in H2 at 200°C resulted in Pd-rich PdIn alloy as evidenced by XRD. A minor amount of PdIn intermetallic phase appeared after reduction at 200°C and its formation was accomplished at 400°C. Neither monometallic Pd and/or In were found after reduction at 400–600°C. Catalytic performance of PdIn/α-Al2O3 was studied in the selective liquid-phase hydrogenation of diphenylacetylene (DPA). It was found that the reaction rate of undesired alkene hydrogenation is strongly reduced on PdIn nanoparticles enabling effective kinetic control of the process. Excellent selectivity (>90%) of PdIn/α-Al2O3 catalyst can be explained by: (1) isolation of Pd sites by inactive In atoms, (2) modification of their electronic structure, and (3) suppression of Pd hydride formation.