The present article describes the synthesis of the new compound 2-methylbenzimidazo[1,2-a]pyrimidin-4(1H)-one. The electronic and spatial structure of this molecule was studied theoretically and experimentally. The title molecule, C11H9N3O, is slightly twisted and bowed based on the recent crystallographic study, while the DFT-B3LYP study shows that the title compound is fully planar in the gas phase. This discrepancy between the experimentally determined geometry and the B3LYP optimized one may be due to the crystal packing. In the crystal, a layer structure is formed by N—H•••N and C—H•••O hydrogen bonds together with π-stacking and C—H•••π(ring) interactions. However, the Hirshfled surface analysis showed that the most important intermolecular interaction for the title compound is the H•••H contact. Based on the wide biological interest, molecular docking and molecular dynamics studies were performed for the above titled compound with the poly(ADP-ribose)polymerase (PARP) enzyme target and the result shows that there is a good binding affinity and stability in PARP complex system.
