We report the syntheses and characterizations, in the solid state and in solution, of three new cyclic polyoxothiomolybdates self-assembled around 2,5-dimethylterephthalate (DMT) and 2,5-bis(trifluoromethyl)terephthalate (DFMT) ligands, namely [Mo12DMT](2-), [Mo12DFMT](2-) and [Mo16DFMT](2-). A series of these two Mo12-compounds completed by the two Mo12-compounds obtained with 2,3,5,6-tetramethylterephthalate and trimesate ligands offer the opportunity to compare their electro-catalytic properties for reduction of protons into hydrogen. The ability of these compounds to promote the reduction of protons into hydrogen in aqueous medium is evidenced and the influence of the embedded ligand is highlighted, thus allowing proposal of a mechanism for the hydrogen evolution reaction catalyzed by these clusters.