Acta Phys. -Chim. Sin. ›› 2013, Vol. 29 ›› Issue (06): 1173-1182.doi: 10.3866/PKU.WHXB201303153


Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin

WANG Chang-Sheng, LIU Peng, YU Nan   

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China
  • Received:2012-12-28 Revised:2013-03-15 Published:2013-05-17
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (20973088, 21173109, 21133005), Specialized Research Fund for the Doctoral Program of Higher Education of China (20102136110001), and Program for Liaoning Excellent Talents in University, China (LR2012037).


Exploring the binding features between small drug molecules and biomolecules is particularly important because it can provide valuable information for understanding the interaction mechanism and therefore rationally designing, modifying and screening of new drugs. In this paper, the site-preference of the nucleic acid bases uracil and thymine hydrogen bonding to the small medical molecule quercetin is investigated using the density functional theory method. Thirty stable hydrogen-bonded complexes were located at the B3LYP/6-31G(d) level of theory. The binding energies for these complexes were further evaluated at the B3LYP/6-311++G(3df,2p) level of theory with the basis set superposition error corrections. The results indicate that quercetin can interact with uracil or thymine through five binding sites, which herein we refer to as Site qu1, Site qu2, Site qu3, Site qu4, and Site qu5, and uracil (or thymine) can interact with quercetin through three binding sites, which herein we refer to as Site u1, Site u2, and Site u3 (or Site t1, Site t2, and Site t3). We found that once the binding site of quercetin is fixed, the hydrogen bonds formed through uracil Site u1 and thymine Site t1 are the strongest, while those formed through uracil Site u2 and thymine Site t2 are the weakest. When the binding site of uracil or thymine is fixed, the hydrogen bonds formed through the quercetin Site qu1 are the strongest, followed by those formed through quercetin Site qu5, while those formed through quercetin Site qu3 are the weakest. Atoms in molecules (AIM) and natural bond orbital (NBO) analyses were also carried out to explore the interaction nature of these hydrogen-bonded complexes.

Key words: Quercetin, Uracil, Thymine, Hydrogen bond, Binding energy, Natural bond orbital analysis, Atoms in molecules analysis


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