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An insight into interaction of the uracil, thymine and cytosine biomolecules with methimazole anti-thyroid drug: DFT and GD3‑DFT approaches

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Abstract

The biologically complex configurations paired of methimazole (MET) anti-thyroid drug with each of the three nucleic acid bases of single ring based on pyrimidine (uracil (U), thymine (T) and cytosine (C)) have been studied at different levels of density functional theory. Twelve double H-bonded complexes were proposed and designed stand on the data obtained from electrostatic potential (ESP) maps of the studied nucleic acid bases and MET drug. The interaction energies of the optimized structures of all three set of complexes (MET-U, MET-T and MET-C) were computed using M062X/AUG–cc–pVDZ computational level and then corrected using M062X–GD3 functional with the same basis sets. The corrected interaction energies for the of MET-U, MET-T and MET-C complex series range from −10.89 to −17.52, −11.31 to −17.62, and −12.33 to −19.54 kcal mol−1, respectively. The highest interaction energy has been calculated between C nucleobase and the MET drug. Structural geometries of the U, T and C nucleobases as well as MET drug show that they can act as H-bond donor and H-bond acceptor simultaneously. The existence, strength and nature of the hydrogen bond interactions in the complex were confirmed and investigated using vibrational frequency, natural bond orbital (NBO) and non-covalent interactions (NCI) analysis and also with quantum theory of atoms in molecules (QTAIM) analysis at M062X/AUG–cc–pVDZ level of theory. In the most stable complexes of each series, charge transfer occurs (CT) from MET drug to the U, T and C nucleobases. Analysis of the electron density property shows that the N1− H7···Sʹ6 hydrogen bond nature in the most stable MET-UR1R′1, MET-TR1R′1 and MET-CR1R′1 complexes is slightly covalent and the nature of other hydrogen bonds in three series of studied complexes is electrostatic.

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Acknowledgements

Support of this work from the Research Council of the University of Guilan is gratefully appreciated.

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  1. Department of Chemistry, Faculty of Sciences, University of Guilan, P.O. Box 41335‑1914, Rasht, Iran

    Behzad Khalili, Khatereh Ghauri, Neda Ghavidel & Narjes Pourhasan

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BK contributed to conceptualization and writing—review and editing; KG contributed to formal analysis and methodology; NG and NP contributed to the investigation and provided the resources.

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Khalili, B., Ghauri, K., Ghavidel, N. et al. An insight into interaction of the uracil, thymine and cytosine biomolecules with methimazole anti-thyroid drug: DFT and GD3‑DFT approaches. Struct Chem 34, 1021–1042 (2023). https://doi.org/10.1007/s11224-022-02059-y

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