We conduct a first-principles total energy calculation of the atomic and electronic structures of the N defects near the Si(001)/alpha-quartz interface. We find that the N atoms preferentially form a pair structure at the Si surface immediately below the interface to minimize the system energy. A silicon-induced gap state (SIGS), which is predominantly localized at the interface, is formed just above the valence band edge of bulk Si. The energy level of the SIGS shifts toward the bulk Si valence band edge as the N pairs accumulate at the interface, indicating that the energy gap in the system increases. The atomic and electronic structures of the N-p defects is consistent with the previous core-level spectroscopy and spectroscopic charge pumping results. (C) 2016 Elsevier B.V. All rights reserved.