The optimized molecular structures, vibrational frequencies, corresponding vibrational assignments and atomic NBO charges of a biologically important molecule namely, pyrazino[2,3-d] pyrimidine have been carried out through density functional theory (B3LYP) level employing several basis sets. The results of vibrational frequencies and optimized geometric parameters were found in good agreement with the experimental data, which indicate that is planar and more stable. Moreover, the possible electrophilic and nucleophilic reactive sites were predicted by local reactivity descriptors and MEP map to describe the presence of intermolecular bonding and the hydrogen bonding interaction. In addition, the design format of our molecule present an opportunity to reveal the electron density profile by using the FMOs analysis and other electronic structure parameters such as ionization energy (I), Electron affinity (A), Global hardness (η), Chemical potential (μ), Electrophilicity index(ω), Electronegativity (X), Softness (S).
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