The geometry, energetic, and spectroscopic properties of molecular structures of silica-supported niobium oxide catalysts are studied using periodic density functional calculations (DFT) and compared with experimental data. The calculations are done for Nb oxide species inserted or grafted in/on an amorphous hydroxylated silica surface. Different positions of the Nb atom/atoms in the silica structure have been investigated. By means of DFT calculations the geometry and the degree of hydration of Nb oxide species with oxidation state +5 have been studied. The local Nb geometry depends on different parameters such as the number of Nb–O–Si groups vs. Nb–O–H groups, the formation of H bonds and the distance between Nb atoms. The interaction between the oxide and silanol groups occurs by formation of Si–O–Nb bonds with chemically and thermally stable Brønsted and Lewis acid sites. UV-Vis, reflection absorption infrared vibrational spectra (RAIRS) as well as various thermodynamic properties have also been investigated in order to get a better insight into the system studied and to provide support to possible experimental studies.