Acta Phys. -Chim. Sin. ›› 2013, Vol. 29 ›› Issue (12): 2551-2557.doi: 10.3866/PKU.WHXB201310293


Site Preferences of Adenine Hydrogen Bonding to Peptide Amides

LIU Shuai, LI Shu-Shi, LIU Dong-Jia, WANG Chang-Sheng   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China
  • Received:2013-08-11 Revised:2013-10-28 Published:2013-11-28
  • Contact: WANG Chang-Sheng
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (21173109), Specialized Research Fund for the Doctoral Program of Higher Education of China (20102136110001), Program for Liaoning Excellent Talents in University, China (LR2012037), and Program for Leading Figures in Dalian, China.


A detailed understanding of how nucleobases interact with protein peptides will allow us to gain valuable insights into how these interesting biological molecules could be used to construct complex nanostructures and materials. In this work, the optimal structures and binding energies of 20 hydrogenbonded complexes, which contained the nucleic acid base adenine, N-methylacetamide, a glycine dipeptide, and an alanine dipeptide, were obtained. The site preferences of adenine hydrogen bonding to peptide amides were explored. The calculation results show that adenine can use two binding sites (site A1 and site A2) to form N―H…N or N―H…O=C hydrogen-bonded complexes with N-methylacetamide; the N―H…N hydrogen-bonded complexes formed at site A1 of adenine are more stable. The calculation results also show that the glycine dipeptide can use either site Gly7 or site Gly5, and the alanine dipeptide can use either site Ala7 or site Ala5 to form hydrogen-bonded complexes with adenine; the hydrogenbonded complexes formed at site Gly7 of the glycine dipeptide and at site Ala7 of the alanine dipeptide are more stable. The hydrogen-bonded complexes formed by adenine and a dipeptide have larger negative binding energies than the complexes formed by adenine and N-methylacetamide, indicating that the interaction between adenine and the peptide is preferred to that between adenine and N-methylacetamide. The nature of the hydrogen bonding in these complexes was further explored based on the atoms in molecules calculations and the natural bond orbital analysis.

Key words: Adenine, N-methylacetamide, Glycine dipeptide, Alanine dipeptide, Hydrogen bond, Binding energy