HYDROGEN-BONDING INTERACTION OF UREA WITH DNA BASES: A DENSITY FUNCTIONAL THEORY STUDY
Z. Qiu1, YO. Xia2, H. Wang2, K. Diao2
1 Henan Quality Polytechnic
2 State Key Laboratory of Food Science and Technology, Jiangnan University
chengq26@163.com
Keywords: DFT, urea, hydrogen bond, interaction energy
Pages: 478-486
Abstract
This work deals with the interaction between urea and DNA bases (adenine, thymine, guanine, and cytosine). The optimized geometries, binding energies, and harmonic vibrational frequencies are calculated using the DFT/B3LYP functional combined with the 6-31+G(d,p) basis set. Their interactions are studied aiming to understand more about the nature of the intercalation binding forces between urea and DNA. Fourteen stable complexes are found on the potential energy surface. The structures are cyclic; they are stabilized by NH…O/N and CH…O interactions. The binding energies range from -19.9 kJ·mol-1 to -74.0 kJ·mol-1. The obtained formation energies indicate that Urea:G and Urea:C are more favorable than Urea:T and Urea:A.
In addition, the Atoms in Molecules theory is performed to study the hydrogen bonds in the complexes.
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