Synthesis, X-ray Structure, DFT, Hirshfeld Surface, QTAIM/RDG and Molecular Docking Analysis of 3-methyl-4-nitro-1,1-biphenyl (3-MNB)

Abstract

The synthesis of 3-methyl-4-nitro-1,1-biphenyl (3-MNB) and its crystal structure elucidated using experimental and theoretical methods has been reported in this paper. It crystallizes in the orthorhombic crystal system (space group P2₁2₁2₁) with unit cell parameters: a = 7.2918(4) Å, b = 12.0928(6) Å and c = 12.6759(7) Å and Z = 4. The structure has been characterized by FT-IR, NMR (¹H and ¹³C) and X-ray diffraction methods. There exists two C—H⋯O intermolecular hydrogen bond and two π…π interactions. Density functional theory (DFT/B3LYP/6-311 + + G(d, p)) has been employed for the optimization of the structure and the same was compared with the X-ray structure. The HOMO-LUMO energy gap and molecular electrostatic potential maps have been computed. The energy gap of 4.06 eV indicates that the molecule is stable and less reactive. Besides this, the molecular electrostatic potential (MEP) help determine the reactive sites of the molecule. The Hirshfeld surface analysis and 2-D fingerprint plots help explore the nature and percentage contribution of intermolecular interactions. The highest contribution to the total Hirshfeld surface area is from H…H contacts (47.2%) while the contribution of O…H/H…O contacts is 26.4%. The strength and nature of interactions present in the molecule have been characterized by RDG-based NCI and QTAIM analysis. DOS analysis has been performed to investigate the contribution of various orbitals. The molecular docking analysis analysis was performed to determine the binding patterns of 3-MNB with 1CX2, revealing a binding energy of -7.3 Kcal/mol, suggesting its potential as a COX-2 inhibitor.