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Progress in Chemistry 2012, Vol. 24 Issue (06): 1214-1226 Previous Articles   

Special Issue: 计算化学

• Special Issue of Quantum Chemistry •

Accurate and Rapid Calculation of the Hydrogen Bond Strengths and Hydrogen Bonding Potential Energy Curves for the Hydrogen-Bonded Complexes Containing Peptide Amides and/or Nucleic Acid Bases

Huang Cuiying, Li Yang, Wang Changsheng   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029
  • Received: Revised: Online: Published:
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N-H···OC、C-H···OC、N-H···N and C-H···N hydrogen bonds are the main factors for the formation of protein a-helices and b-sheets and for the formation of the double helices of the deoxyribonucleic acid. These hydrogen bonds also play important roles in the processes of the protein-nucleic acid recognition, in the processes of the protein replication, and in the processes of transcription and expression of genetic information from DNA to protein. Accurate and rapid determination of the strengths of the hydrogen bonds and their dynamic properties in DNA and protein systems is very important for correctly simulating and therefore deeply understanding the mechanism of protein folding processes and the formation mechanism of the double helices of the deoxyribonucleic acid and for designing new biomolecular materials possessing special function. In this review, a dipole-dipole hydrogen bonding model and its applications to the hydrogen-bonded complexes containing peptide amides and/or nucleic acid bases are introduced. Contents
1 Introduction
2 Hydrogen bond model and parameterization
2.1 The dipole-dipole hydrogen bonding model
2.2 Parameterization
3 Applications
3.1 Calculation of the hydrogen bond strengths and hydrogen bonding potential energy curves for amide-amide and amide-water hydrogen-bonded dimers
3.2 Calculation of the total binding energies and potential energy curves for hydrogen-bonded complexes made of peptide amides and nucleic acid bases
3.3 Calculation of the total binding energies and potential energy curves for protein β-sheets
4 Conclusion and outlook
Key words: protein peptide, nucleic acid bases, dipole-dipole interaction, hydrogen bond strength, hydrogen bonding potential energy curve, Binding energy

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[1]

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