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Thermochemistry and NBO analysis of peptide bond: Investigation of basis sets and binding energy

Russian Journal of Physical Chemistry A volume 83, pages 587–597 (2009)Cite this article

Abstract

Ab initio methods were used to analyze the structure, energetic and binding energy of the five began dipeptides with methionine, Met-Gly, Met-Ala, Met-Ser, Met-Cys, and Met-Thr dipeptides, in gas phase. The structures of the dipetides and involved amino acids in them were optimized by using Hartree-Fock and DFT methods and 3-21G(d), 6-31G(d), 6-311G, 6-311G(d), and 6-311+G(d) basis sets. The effect of basis sets and electron correlations were analyzed with special emphasis on the calculated binding energies and thermodynamic functions. All used methods revealed that Met-Thr has the highest binding energy among all of the five dipeptide molecules. These numerical results suggest that Thr donates the proton easier than other four amino acids and it has the most tendency to join with methionine and it forms the most strong bond with methionine. This fact may be the reason behind the obtained high binding energies for Met-Thr at all levels. From comparison of the values of binding energy for dipeptides in different levels of theory, we could identify that the order of tendency for joint with methionine is Thr > Gly > Ala > Cys > Ser. Also, these data represented that the highest binding energy provide in HF/6-311G level for all of the dipeptides (14.4202, 11.2387, 8.3267, 9.8853, 17.3362 kcal mol−1 for dipeptides 1–5, respectively). Moreover, natural bond orbital (NBO) analysis demonstrated that the effect of basis sets and electron correlations on σN1-C2 bonding orbital occupancy is the same as the basis set and electron correlation effects on binding energy of dipeptides in all cases. The obtained results from studying the effect of basis sets and electron correlations on binding energy, NMR and NBO properties showed that the effect of basis sets is almost independent of molecular structure and computational method, while electron correlation effects are relatively dependent to molecular structure and basis set type. In investigating the effect of basis sets and electron correlations on binding properties, the NBO results are in good agreement with the energetic and thermochemistry data at all levels of calculations.

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Authors and Affiliations

  1. Department of Chemistry, Science and Research Campus, Islamic Azad University, Tehran, Iran P.O.

    A. Tahan & M. Monajjemi

  2. Department of Chemistry, Qom Branch, Islamic Azad University, Qom, Iran

    F. Mollaamin

Authors
  1. A. Tahan
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  2. F. Mollaamin
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  3. M. Monajjemi
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Correspondence to M. Monajjemi.

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Tahan, A., Mollaamin, F. & Monajjemi, M. Thermochemistry and NBO analysis of peptide bond: Investigation of basis sets and binding energy. Russ. J. Phys. Chem. 83, 587–597 (2009). https://doi.org/10.1134/S003602440904013X

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  • DOI: https://doi.org/10.1134/S003602440904013X

Keywords

  • Dipeptide
  • Natural Bond Orbital
  • Electron Correlation
  • High Binding Energy
  • Natural Bond Orbital Analysis