[en] Ion irradiation of α-quartz renders the crystal SiO₂ structure amorphous. The enormous amount of structural defects produced after ion irradiation give a chance for photoactive intrinsic defects to be formed. These may be responsible for the photoluminescence in irradiated α-quartz. On the other hand, the radiation defects are not stable, and thus, an alternative structure where the defects of interest can be stabilized is required. The stabilization of the defects can be achieved in the structures of amorphous silica with embedded Si nanocrystals (NC), thanks to the unique structure of the formed interface. By means of Molecular Dynamics (MD), we analyze defects in both amorphized α-quartz and Si-NC/a-SiO₂ interfaces formed by 1.1, 2.4 and 4 nm diameter NC's. In the simulation, we employ a classical interatomic potential and a potential, which takes into consideration a charge transfer between Si and O atoms. We show that although the number of silanone bonds Si=O in irradiated quartz is higher, they are also found in a Si-NC/a-SiO₂ interface without the necessity of preceding irradiation of the sample. We also compare the defects in irradiation-amorphized quartz and the three sizes of Si-NC/a-SiO₂ interfaces. Analysis of the charges showed that the charge state of coordination defects depends on the type of atoms in the near neighborhood.