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Abstract <p>Complexes of the alanyl-L–tyrosine zwitterion with neutral nucleoside (uridine, cytidine, adenosine, and guanosine) molecules are modeled by the quantum chemical DFT method. Different coordination modes of the peptide to nucleosides are considered, and the optimized structures of the complexes characterized by the most favorable values of changes in the free Gibbs energy are found. Changes in the energy and the free Gibbs energy during complexation are decomposed into contributions from the intermolecular interaction and structural reorganization of the peptide and nucleoside. Based on changes in the free Gibbs energy, the stability order of the alanyl–tyrosine complexes with nucleosides is determined: cytidine&#xa0;&gt;&#xa0;adenosine&#xa0;&gt; &gt;&#xa0;guanosine&#xa0;&gt;&#xa0;uridine. The energies of intermolecular H-bonds vary insignificantly on passing from the complexes of nucleic bases to those of nucleosides. However, the number of H-bonds is increased in the nucleoside complexes due to additional interactions with OH groups of the ribose residue. Additional stabilization effect of the complexes caused by π–π stacking is detected in the alanyl–tyrosine complexes with cytidine.</p>

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Analysis of Configurations and RDG-Distributions in the Comlexes of Nucleosides with the Alanyl-L–Tyrosine Peptide

  • 期刊论文

  • 发表日期：

    2025年11月1日

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  • M. S. Kurbatova,
  • V. P. Barannikov

摘要

Abstract

Complexes of the alanyl-L–tyrosine zwitterion with neutral nucleoside (uridine, cytidine, adenosine, and guanosine) molecules are modeled by the quantum chemical DFT method. Different coordination modes of the peptide to nucleosides are considered, and the optimized structures of the complexes characterized by the most favorable values of changes in the free Gibbs energy are found. Changes in the energy and the free Gibbs energy during complexation are decomposed into contributions from the intermolecular interaction and structural reorganization of the peptide and nucleoside. Based on changes in the free Gibbs energy, the stability order of the alanyl–tyrosine complexes with nucleosides is determined: cytidine > adenosine > > guanosine > uridine. The energies of intermolecular H-bonds vary insignificantly on passing from the complexes of nucleic bases to those of nucleosides. However, the number of H-bonds is increased in the nucleoside complexes due to additional interactions with OH groups of the ribose residue. Additional stabilization effect of the complexes caused by π–π stacking is detected in the alanyl–tyrosine complexes with cytidine.