Experimental Spectroscopic, Structural (Monomer and Dimer), Molecular Docking, Molecular Dynamics Simulation and Hirshfeld Surface Analysis of 2-Amino-6-Methylpyridine

Abstract

2-Amino-6-methylpyridine (2-AMP) was investigated experimentally using FT-IR, 1H, NMR, and UV-Vis spectra, as well as theoretically using DFT calculations. The quantum computational calculations (the optimized structure, FT-IR, NMR and UV-Vis.) to support experimental data were performed by DFT approach at B3LYP functional and 6–311 + +G(d,p) basis set. The optimized molecular geometry and wavenumber calculations were done in the gas phase, while theoretical NMR was performed in Chloroform (CHCL3) solvation. The “Potential Energy Distribution analysis” (PED) of the title compound was performed with VEDA analysis and these assignments were compared with the experimental FT-IR spectrum. Hirshfeld analysis was also performed and analyzed intermolecular interactions on the surface of crystal, However, the most significant contributions to the Hirshfeld surface come from N···H (17.3%), C···H/H···C (23%) and H···H (68.8%). Chemical reactivity studies, Molecular Electrostatic Potential (MEP) maps, and surface area maps were also conducted. To show electron delocalization in the molecule, researchers used the electron localization function (ELF). Other topics included topological and mulliken charge distribution studies. Natural Bond Order Analysis (NBO) was performed to interpret intermolecular charge transfer.The effect of temperature on thermodynamical parameters such as Gibbs free energy, enthalpy, and entropy was examined. TD-DFT analysis was also used to shed more light on how the electronic transitions in the UV–Vis spectra were estimated. For different solvents, the estimated maximum wavelength (λ) absorbance and the band-gap energy of 2-AMP were calculated and compared to experimental results. The molecule's bioactivity is described theoretically using the Electrophilicity index and the interaction between the ligand-protein is depicted using Molecular docking. The proteins 3DQS, 4UX6, 5ADF, 5TUD, and 6E9L were studied via molecular docking. The nature of the molecule was determined by its drug-likeness. A molecular dynamics simulation was used to explore biomolecular stability.

Keywords:

• DFT
• MEP
• TD-DFT
• Hirshfeld surface analysis
• molecular docking

Acknowledgements

We acknowledge Dr. B. R. Ambedkar University, Agra, India for providing necessary facilities. The authors appreciated Taif University Researchers Supporting Project number TURSP-2020/267, Taif University, Taif, Saudi Arabia.

Disclosure statement

No potential conflict of interest was reported by the authors.