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A quantum chemical study of the interactions of uracil as a constituent of ribonucleic acid (RNA) with thiazolidinedione and rhodanine bioactive molecules: an insight into energetic and structural features

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Abstract

In this study, the biologically active configurations composed of Thiazolidinedione–Uracil (TU) and Rhodanine–Uracil (RU) have been fully investigated from the energetic and structural points of view, employing B3LYP and M062X functionals in combination with the different basis sets. Dispersion corrections to the interaction energy using M062X–GD3 and double hybrid density functionals (B2PLYP–GD2, B2PLYP–GD3 and mPW2PLYP–GD2) are also taking into account. The basis set superposition error-corrected interaction energy for hydrogen bonded configurations ranges from − 5.27 to − 13.53 and − 5.25 to − 12.93 kcal/mol for TU and RU complexes respectively as calculated at M062X/6–311++G(df,pd) level. The charge transfer process within all of the TU and RU configurations were analyzed using Natural Bond Orbital (NBO) calculations. The nature of the interactions is analyzed with NBO and Atoms in Molecules (AIM) analysis at M062X/6–311++G(df,pd) and energy decomposition analysis at BP86–D3/TZ2P(ZORA)//M062X/6–311++G(df,pd) level of theory. The results confirm that the nature of the interactions is nearly electrostatic, with a contribution of about 51–56% of the total interaction energy. The orbital interactions (ΔEorb) for the considered TU and RU complexes have a contribution of about 24–38% of the total interaction energy. Based on the AIM and NBO results, the interactions were defined as electrostatic H-bonds with partially covalent character. In addition, correlation between interaction energies and vibrational frequency changes was investigated.

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Acknowledgments

Support of this work from the Research Council of the University of Guilan is gratefully appreciated. We also thank Professor Rolf H. Prager for proof reading this article.

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

    Behzad Khalili

  2. Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran, Iran

    Mehdi Rimaz

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Correspondence to Behzad Khalili.

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Khalili, B., Rimaz, M. A quantum chemical study of the interactions of uracil as a constituent of ribonucleic acid (RNA) with thiazolidinedione and rhodanine bioactive molecules: an insight into energetic and structural features. Struct Chem 29, 681–702 (2018). https://doi.org/10.1007/s11224-017-1062-4

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