The Site-preference Of Base Adenine Hydrogen Bonding To Peptide Amides

The ability to deeply understand how nucleobases interact with protein peptides will allowus to gain valuable insights into how we might be able to harness these interesting biologicalmolecules to construct complex nanostructures and materials. In this work, the optimalstructures and binding energies of twenty hydrogen-bonded complexes, which contain nucleicacid base adenine, N-methylacetamide, glycine dipeptide and alanine dipepetide, have beenobtained. The site-preferences of adenine hydrogen bonding to peptide amides are explored.The calculation results show that adenine may use two binding sites (Site A1and Site A2) toform N-H···N or N-H···O=C hydrogen-bonded complexes with N-methylacetamide and theN-H···N hydrogen-bonded complexes formed through Site A1of adenine are more stable. Thecalculation results also show that, for example, glycine dipeptide can use either Site Gly7orSite Gly5and alanine dipeptide can use either Site Ala7or Ala5to form hydrogen-bondedcomplexes with adenine, the hydrogen-bonded complexes formed through Site Gly7ofglycine dipeptide, and Site Ala7of alanine dipeptide, and Site Ser7of serine, and Site Cys7ofcysteine are more stable. The hydrogen-bonded complexes formed by adenine and dipeptidepossess larger negative binding energy than the complexes formed by adenine andN-methylacetamide, indicating that the interaction between adenine and peptide is ofpreference to that between adenine and N-methylacetamide. When the water molecule isadded to the side of N-methylacetamide, the hydrogen bond strength between base adenineand N-methylacetamide is slightly strengthened. However when the water molecule is addedto the side of adenine, the hydrogen bond strength between base adenine andN-methylacetamide is slightly weakened. The natures of hydrogen bonding in thesecomplexes are further discussed based on the atoms in molecules calculations and the naturalbond orbital analysis.