Periodic DFT calculations have been performed on molybdenum(vi) oxide species supported on the hydroxylated amorphous silica surface. The Mo grafting site has been investigated systematically for the type of silanol (geminate, vicinal, isolated or in a nest) accessible on the surface, as well as its effect on H-bond formation and stabilization, with the Mo-oxide species. Different grafting geometries, combined with different degrees of hydration of the Mo species are investigated using atomistic thermodynamics. The most stable Mo(vi) oxide species resulting from these calculations are confronted with experiment. Finally, calculated vibrational frequencies confirm the experimental evidence of the dominant presence of di grafted di-oxo Mo(vi) species on silica up to 700 K.