Synthesis, crystal structure, DFT, Hirshfeld surface, 3D energy frameworks analysis and molecular docking of pyrimidine derivative: A theoretical and experimental approach

Abstract

Using X-ray diffraction, FT-IR, 1H, 13C NMR, and UV–Vis spectra as well as theoretical DFT calculations, Ethyl-2-methyl-4-phenyl-3,4-dihydro-2H-benzo[4,5]thiazolo-[3,2-a]pyrimidine-3-carboxylate (T[3,2-a]P) has been synthesized and characterized. Physicochemical characteristics have been compared to examine stability. The most stable optimized structure was identified using the B3LYP/6–311++G(d,p) basis set, followed by UV–Vis and NMR analysis. TD-DFT analysis gave more information on how to estimate the electronic transitions in the UV–Vis spectra. In addition to the energy framework calculations, the Hirshfeld surface analyses have been demonstrated and discussed. The calculated band-gap energy of the pyrimidine derivative for various solvents and the estimated maximum wavelength (λ) absorbance were compared to the outcome of experiments. There were additional studies regarding the MEP map, surface area maps, and chemical reactivity. Additionally, topological and Mulliken charge distribution investigations were included. A pyrimidine derivative may be used as a chemotherapeutic and anticancer drug, according to docking experiments that were used to examine the interactions of the ligand (T[3,2-a]P]) with certain protein targets. The current study may lead to the identification of pyrimidine derivative as a possible therapeutic molecule. The practical and theoretical results were remarkably similar in terms of geometric and spectroscopic characteristics.

Keywords

• DFT
• Docking
• X-ray diffraction
• Hirshfeld surface
• Xanthene