The structural properties of Hypoxanthine compound related to molecular dynamic activity have been ornately interpreted in this methodical research work. The FT-IR, FT-Raman, NMR and UV-Visible spectral analysis has been carried out and the obtained results were validated using theoretical tools. The tautomerism of the compound has been monitored while analyzing the molecular structure regarding to describe unknown properties and applications. The displacement of chemical shift of core carbons in pyrimidine and Imidazole rings by the injection of @ O atom and the mechanism customized to induce chemical properties were interpreted. The electronic degeneracy pathway in the interaction orbitals was discussed by viewing the frontier molecular overlapping. The involvement of CT-complex transitions in non bonding molecular orbitals has been inspected. The QSAR properties, Ligand efficiency (LE), Lipophilic Efficiency (LipE), were calculated and reported for explaining biological activity of Hypoxanthine. The drug and biological activity of the present compound was interpreted and the capability of suitable applications has been interpreted. The VCD spectrum for the measurement of toxicity level was simulated and the rate of masking was examined.