Density functional study of adenine tetrads with N6-H6...N3 hydrogen bonds

J Phys Chem A. 2008 May 8;112(18):4336-41. doi: 10.1021/jp710242k. Epub 2008 Apr 2.


The structure and energy of A-tetrads with N6-H6...N3 H-bonds was studied using B3LYP and BH&H density functional theory. The planar A-tetrad with C(4h) symmetry is more stable than the nonplanar structures at C4 and S4 symmetry. This structure corresponds to a local energy minimum. The energies of the structures with N6-H6...N1 and N6-H6...N7 H-bonds studied previously are of similar magnitude. Structures of A-tetrad complexes with sodium and potassium were most stable at S4 symmetry, and similarly, sandwich complexes consisting of two tetrads and a single cation were most stable at S8 symmetry. Relative energies of sandwich complexes with different symmetries obtained with the B3LYP and BH&H methods were quite different. BH&H overestimates the interaction energies between hydrogen-bonded neighbor bases relative to B3LYP.

MeSH terms

  • Adenine / chemistry*
  • Hydrogen / chemistry*
  • Hydrogen Bonding
  • Intercalating Agents / chemistry
  • Nitrogen / chemistry*
  • Potassium / chemistry
  • Quantum Theory*
  • Sodium / chemistry


  • Intercalating Agents
  • Hydrogen
  • Sodium
  • Adenine
  • Nitrogen
  • Potassium