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This study systematically investigates the molecular structure and electronic properties of 2-methoxy-4,6-diphenylnicotinonitrile, employing X-ray diffraction (XRD) and sophisticated computational methodologies. XRD findings validate the compound’s orthorhombic crystallization in the P21212 space group, composed of a pyridine core flanked by two phenyl rings. Utilizing the three-dimensional Hirshfeld surface, the research decodes the molecule’s spatial attributes, further supported by exhaustive statistical assessments. Key interactions, such as π–π stacking and H⋯X contacts, are spotlighted, underscoring their role in the crystal’s inherent stability and characteristics. Energy framework computations and density functional theory (DFT) analyses elucidate the prevailing forces in the crystal and reveal geometric optimization facets and molecular reactivity descriptors. Emphasis is given to the exploration of frontier molecular orbitals (FMOs), aromaticity, and π–π stacking capacities. The research culminates in distinguishing electron density distributions, aromatic nuances, and potential reactivity hotspots, providing a holistic view of the compound’s structural and electronic landscape. Concurrently, molecular docking investigates its interaction with the lipoprotein-associated phospholipase A2 protein. Notably, the compound showcases significant interactions with the protein’s active site. Molecular dynamics simulations reveal the compound’s influence on protein stability and flexibility. Although the molecule exhibits strong inhibitory potential against Lp-PLA2, its drug development prospects face challenges related to solubility and interactions with drug transport proteins.

This study aims to synthesis 2-[(dipyrrolidin-1-yl)methylene] malononitrile 2 and identify its crystal structure by X-ray diffraction analysis. 2-[(dipyrrolidin-1-yl)methylene] malononitrile was prepared by a direct displacement of the methylthio group (SMe) in the 2-[bis(methylthio)methylene] malononitrile 1 with pyrrolidine as cyclic secondary amine by conjugating addition-elimination reaction under reflux conditions for two hours. The compound was obtained in high yield (80%). The structure of compound 2-[(dipyrrolidin-1-yl)methylene] malononitrile2 was identified by performing X-ray diffraction analysis. Suitable crystals of compound 2 were grown by slow evaporation of methanol solution of the compound. The compound 2 crystallized in an orthorhombic crystal system with a space group of Pbcn. In the title compound, the two cyanide groups and the two pyrrolidine rings adopted trans configurations across the C2=C3 bond. The bond lengths and angles of the two pyrrolidinyl rings in the compound are within the normal range. The maximum deviation of N5/C2/C3/C4/N5a/C4a is 0.002(1) around C4, and no deviation has been recorded for the fragment N1/N1a/C2/C3 (0.000 (1)°). The dihedral angle between the pyrrolidine ring and N1/N1a/C2/C3 is 33.06(8)°, and the dihedral angle between the pyrrolidine ring and N5/C2/C3/C4/N5a/C4a is 50.57(7)°. The crystal packing is stabilized by two intermolecular and one intramolecular C---H…N hydrogen bonds, which form a one-dimensional polymeric chain along the axis.