We investigated the structure of pure and Sc-doped synthetic diopside (a monoclinic single-chain silicate nominally CaMgSi2O6); in Sc-doped diopside, Sc3+ substitutes Mg2+ in the structure and, to achieve charge balance, vacancies form at the expense of Ca2+. We compared the structure obtained from ab initio modelling techniques at the density functional theory (DFT) level with the structure solved by employing single crystal X-ray diffraction. Furthermore, we compared IR and Raman spectroscopy experiments with vibrational density of states (VDOS) calculated from the Fourier transform of the velocity autocorrelation function obtained using ab initio (DFT) molecular dynamics simulations. In this framework, we developed a computational tool to assign the vibrational mode associated with a specific frequency. This method consists of projecting velocities along a specific set of internal coordinates such as stretching or bending, in cases involving defects or vacancies, to calculate a partial VDOS (pVDOS) that takes into account only the vibrations associated with selected internal modes, aiding the interpretation of the total VDOS and the experimental spectra in a relevant way. The computed data were validated with the experiments and we observed that doping the diopside structure with Sc produces peak broadening and the occurrence of new peaks in the Raman spectra and that site vacancies are associated with the nearby Sc site. The present work constitutes an interesting starting point to exploit the calculated VDOS/pVDOS to characterize experimental vibrational spectra of complex systems containing local vacancies, substitutions or defects as the Sc-doped diopside.