Nature of bonding in nine planar hydrogen-bonded adenine...thymine base pairs.
In this work, we investigate the mode of binding of all nine hydrogen-bonded structures of the adenine...thymine base pair. The planar H-bonded structures were optimized at the MP2/cc-pVTZ level, and the respective interaction energies, corrected for the basis set superposition error, were determined with the aug-cc-pVDZ basis set. The energy components were obtained from the DFT-SAPT procedure using the aug-cc-pVDZ basis set. The charge-transfer character of the single structures was estimated using NBO characteristics. It was established that dipole-dipole interaction itself cannot explain the preferred structure of the pair. Of the various energy components, first-order electrostatic energy plays the most important role. Second-order energy (the sum of induction and dispersion energies) amounts to about 56% of the electrostatic energy. The delta(HF) term covering among others the charge-transfer energy is rather large. The importance of delta(HF) is reflected by the NBO characteristics and especially by the NBO charge-transfer energy. The sum of the second-order energy and the delta(HF) term is only slightly smaller than the electrostatic energy (75-77%), which reflects the importance of the nonelectrostatic terms even in the case of strong H-bonded complexes. The WC structure, which exists in DNA, represents the seventh local minimum, while the three most stable structures utilize the N9-H proton donor group of the five-membered ring.
Ran
Jiong
J
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
Hobza
Pavel
P
D000225:Adenine / Q000737:chemistry*; D000465:Algorithms; D020029:Base Pairing; D001703:Biophysics / Q000379:methods*; D004247:DNA / Q000737:chemistry; D004735:Energy Transfer; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D013055:Spectrophotometry, Infrared / Q000379:methods; D055672:Static Electricity; D013941:Thymine / Q000737:chemistry*
D004247:DNA; D000225:Adenine; D013941:Thymine