Unexpected synthesis of novel 2-pyrone derivatives: crystal structures, Hirshfeld surface analysis and computational studies

Abstract

Here we report synthesis of three new compounds namely, 1-acetyl-1H-benzimidazolo-2(3H)-one (I), N-(5-acetyl-6-methyl-2-oxo-2H-pyran-4-yl)-N-(2-acetamidophenyl)acetamide (II) and N-(2-acetamidophenyl)-N-2-oxo-2H-pyran-4-yl)acetamide (III) have been synthesized and characterized by single crystal X-ray diffraction. Compounds I and II crystallize in the monoclinic space groups P21/n, and P21/c, respectively, while III crystallizes in the triclinic space group P-1. The theoretical parameters of I–III have been calculated through density functional theory (DFT) by using the hybrid functional B3LYP and basis set 6-311++G**. These theoretical parameters have been compared with the experimental ones obtained by XRD. The significant intermolecular interactions arising in crystal packing are rationalized by means of the Hirshfeld surface analysis method. The major intermolecular contacts in the Hirshfeld surfaces of I–III are from H…H contacts. In addition, binding modes of I–III within Tyrosine-protein kinase JAK2 were investigated using molecular docking and molecular dynamics simulation studies.

Communicated by Ramaswamy H. Sarma

Keywords:

• Pyrane
• benzimidazole
• crystal structure
• DFT calculations
• molecular docking
• molecular dynamics simulation

Acknowledgements

The authors gratefully acknowledge Mohammed V University (Morocco) for the facility for this study. We also thank the National Center for High-Performance Computing (Taiwan) for providing computing time. Special thanks are also due to the reviewers and the editor for their helpful suggestions and comments.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The support of NSF-MRI Grant #1228232 for the purchase of the diffractometer and Tulane University for support of the Tulane Crystallography Laboratory are gratefully acknowledged.