Physico-chemical characterizations and biological evaluation of a new semiconducting metal–organic compound based on pyrimidine frameworks

[Display omitted] •Based on 2-amino-4-methylpyrimidin, a new centrosymmetric Nickel (II) complex has been successfully synthesized and structurally characterized.•Diffuse reflectance spectroscopy suggests a semiconducting behavior with a band gap of 3.34 eV.•In silico, findings showed potential biological activities and are supported by acceptable druglikeness and pharmacokinetic properties.•Magnetic data analysis and ab initio calculations suggests that compound 1 consists of anisotropic S = 1 FM chains with a strong influence of ZFS. A new complex with the formula (C5H8N3)2[NiCl2(C5H7N3)2(H2O)2].2Cl (1) was synthesized in good yields and fully characterized. X-ray diffraction analysis, suggests that 1 is mononuclear nickel(II) complex and exhibits distorted octahedral geometry. Each octahedron is building from nickel(II) ion presenting the center and two nitrogen atoms from two organic ligands, two chloride ions, and two oxygen coming from aqua molecules, which occupy the six vertices. The supramolecular architecture can be described essentially as an alternating distribution of nickel octahedra and pyrimidine rings, some are oriented along [011] direction and the others follow the orientation [01 1¯ ]. This network is linked by three types of hydrogen bonds, N–H…Cl, N–H…N, and OW–H…Cl. The optical properties of the crystal were studied using UV–visible spectroscopy and the gap energy value was estimated to be 3.34 eV. The docking simulation showed acceptable binding affinities (between –4.5 and –6.3 kcal/mol), which together with the druglikeness explain the possible biological activities of the compound and its promising effects. Further in vitro and/or in vivo analyses might confirm the in silico simulation results. The analysis of the magnetic properties and ab initio calculations suggest that 1 can be described as quasi-one-dimensional anisotropic S = 1 ferromagnet with zero-field splitting parameters D/kB = 6.3 K and in-chain exchange coupling J/kB = 4.3 K.