A new 1:1 organic molecular adduct 2-aminopyrimidine: 3-nitrophthalic acid (APNP) was successfully synthesized and single crystals were grown by slow solvent evaporation technique at room temperature. The formation of the molecular adduct was confirmed by single crystal XRD analysis, which further reveals that the crystal belongs to the monoclinic crystal system with a centrosymmetric space group, P21/n. FT-IR spectrum was recorded to identify the functional groups present in the molecular adduct. The purity and stoichiometry of the molecular adduct were confirmed by CHN analysis. The presence of different kinds of protons and carbon atoms in the molecular adduct was confirmed by 1H and 13C NMR spectroscopic studies respectively. UV–Vis–NIR spectroscopic study was carried out to identify the transparency window of APNP crystal. The TG/DTA analyses were carried out simultaneously to establish the thermal stability of the adduct crystal. The computational studies including optimization of molecular geometry, natural bond orbital (NBO) and HOMO-LUMO analyses were performed by density functional theory at the B3LYP method at 6–21g basis set level using Gaussian 09 software. Hirshfeld surface analysis was carried out to know the influence of hydrogen bonding on the molecular properties of the adduct crystal. The third order nonlinear susceptibility of the APNP salt was established by the Z-Scan study. Moreover, the APNP crystal was subjected to antimicrobial activity against various bacterial and fungal species. In addition, the antioxidant activity of APNP adduct was evaluated by DPPH assay method. © 2019 Elsevier B.V.