Microscopic properties of thin oxynitrides are investigated using a combination of the infrared ATR and ab-initio electronic structure methods. We use a theoretical structural model based on the Si-SiO2 interface with the oxide thickness of 0.8 nm. The interfacial region amounts to about 0.4 nm (the total thickness of the oxygen containing layer is 1.2 nm). The Quantum Molecular Dynamics simulations suggest that N accumulates at the interface. We have generated samples with the nitrogen concentrations from 1.69 × 1014 cm−2 to 6.78 × 1014 cm−2. The structural analysis of nitrogen containing cells indicates a significant improvement of the oxide layer and the strain reduction at the interface. We have performed a calculation of the vibrational density of states. A N-localized mode at 809 cm-1 has been identified. The experimental ifnrared ATR data is in qualitative agreement with the calculation. The valence band offset calculations reveal a 0.3 eV increase of the offset due to nitrogen at the highest nitrogen concentration considered. The valence band offset increase comes mainly from the structural change in the oxide layer. The interfacial dipole contributes 0.12 eV to the increase, while the structural change in the oxide layer gives additional 0.2 eV.