Citation: WANG Chang-Sheng, LIU Peng, YU Nan. Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin[J]. Acta Physico-Chimica Sinica, ;2013, 29(06): 1173-1182. doi: 10.3866/PKU.WHXB201303153 shu

Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin

1.
School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, Liaoning Province, P. R. China

Received Date: 28 December 2012
Available Online: 15 March 2013
Fund Project: 国家自然科学基金(20973088, 21173109, 21133005) (20973088, 21173109, 21133005) 教育部高等学校博士学科点专项科研基金(20102136110001) (20102136110001)辽宁省优秀人才基金(LR2012037)资助项目 (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.
- Quercetin,
- Uracil,
- Thymine,
- Hydrogen bond,
- Binding energy,
- Natural bond orbital analysis,
- Atoms in molecules analysis
References
1. [1]
  
  (1) Trouillas, P.; Marsal, P.; Siri, D.; Lazzaroni, R.; Duroux, J. L.Food Chem. 2006, 97, 679. doi: 10.1016/j.foodchem.2005.05.042
2. [2]
  (2) Lespade, L.; Bercion, S. J. Phys. Chem. B 2010, 114, 921. doi: 10.1021/jp9041809
3. [3]
  (3) Guzzo, M. R.; Uemi, M.; Donate, P. M.; Nikolaou, S.; Machado,A. E. H.; Okano, L. T. J. Phys. Chem. A 2006, 110, 10545. doi: 10.1021/jp0613337
4. [4]
  (4) Chakraborty, S.; Biswas, P. K. J. Phys. Chem. A 2012, 116,8775. doi: 10.1021/jp303543z
5. [5]
  (5) Estévez, L.; Mosquera, R. A. J. Phys. Chem. A 2007, 111,11100. doi: 10.1021/jp074941a
6. [6]
  (6) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. Theor.Chem. Acc. 2004, 111, 210. doi: 10.1007/s00214-003-0544-1
7. [7]
  (7) Lee, S.; Shin, S. Y.; Lee, Y.; Park, Y.; Kim, B. G.; Ahn, J. H.;Chong, Y.; Lee, Y. H.; Lim, Y. Bioorg. Med. Chem. Lett. 2011,21, 3866. doi: 10.1016/j.bmcl.2011.05.043
8. [8]
  (8) Kang, J.W.; Zhuo, L.; Lu, X. Q.; Liu, H. D.; Zhang, M.;Wu, H.X. J. Inorg. Biochem. 2004, 98, 79. doi: 10.1016/j.jinorgbio.2003.08.015
9. [9]
  (9) Bhuva, H. A.; Kini, S. G. J. Mol. Graph. Model. 2010, 29, 32.doi: 10.1016/j.jmgm.2010.04.003
10. [10]
  (10) Zhang, M.; Lv, Q. L.; Yue, N. N.;Wang, H. Y. Spectrochim.Acta A 2009, 72, 572. doi: 10.1016/j.saa.2008.10.045
11. [11]
  (11) Cornard, J. P.; Merlin, J. C. J. Mol. Struct. 2003, 651-653, 381.
12. [12]
  (12) Mukai, K.; Oka,W.;Watanabe, K.; Egawa, Y.; Nagaoka, S. I.J. Phys. Chem. A 1997, 101, 3746. doi: 10.1021/jp9706745
13. [13]
  (13) Ni, Y. N.; Du, S.; Kokot, S. Anal. Chim. Acta 2007, 584, 19.doi: 10.1016/j.aca.2006.11.006
14. [14]
  (14) Ren, J.; Meng, S.; Lekka, C. E.; Kaxiras, E. J. Phys. Chem. B2008, 112, 1845. doi: 10.1021/jp076881e
15. [15]
  (15) Leopoldini, M.; Russo, N.; Chiodo, S.; Toscano, M. J. Agric.Food Chem. 2006, 54, 6343. doi: 10.1021/jf060986h
16. [16]
  (16) Lekka, C. E.; Ren, J.; Meng, S.; Kaxiras, E. J. Phys. Chem. B2009, 113, 6478. doi: 10.1021/jp807948z
17. [17]
  (17) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. J. Phys.Chem. A 2004, 108, 4916. doi: 10.1021/jp037247d
18. [18]
  (18) Lemańska, K.; Szymusiak, H.; Tyrakowska, B.; Zieliński, R.;Soffers, A. E. M. F.; Rietjens, I. M. C. M. Free Raobc. Med.2001, 7, 869.
19. [19]
  (19) Plaper, A.; lob, M.; Hafner, I.; Oblak, M.; Šolmajer, T.;Jerala, R. Biochem. Biophys. Res. Commun. 2003, 306, 530.doi: 10.1016/S0006-291X(03)01006-4
20. [20]
  (20) Solimani, R. Biochim. Biophys. Acta 1997, 1336, 281. doi: 10.1016/S0304-4165(97)00038-X
21. [21]
  (21) Zhang, C. S.; Lai, L. H. Acta Phys. -Chim. Sin. 2012, 28 (10),2363. [张长胜, 来鲁华. 物理化学学报, 2012, 28 (10), 2363.]doi: 10.3866/PKU.WHXB201209172
22. [22]
  (22) Huang, Y. Y.; Yang, X. F.; Li, H. T.; Ji, X. F.; Cheng, H. L.;Zhao, Y. J.; Guo, D. C.; Li, L.; Liu, S. Y. Acta Phys. -Chim. Sin.2012, 28 (10), 2390. [黄阳玉, 阳秀凤, 李昊田, 纪晓峰, 程洪礼, 赵蕴杰, 郭大川, 李林, 刘士勇. 物理化学学报, 2012, 28 (10), 2390.] doi: 10.3866/PKU.WHXB201209111
23. [23]
  (23) Zhang, M.; Zheng, Y. P.; Jiang, X. N.;Wang, C. S. ActaPhys. -Chim. Sin. 2010, 26 (3), 735. [张敏, 郑艳萍, 姜笑楠, 王长生. 物理化学学报, 2010, 26 (3), 735.] doi: 10.3866/PKU.WHXB20100235
24. [24]
  (24) Liu, D. J.;Wang, C. S. Acta Phys. -Chim. Sin. 2012, 28 (12),2809. [刘冬佳, 王长生. 物理化学学报, 2012, 28 (12), 2809.]doi: 10.3866/PKU.WHXB201209263
25. [25]
  (25) Dong, H.; Hua,W. J.; Li, S. H. J. Phys. Chem. A 2007, 111,2941. doi: 10.1021/jp0709860
26. [26]
  (26) Jiang, X. N.;Wang, C. S. Sci. China Ser. Chem. 2010, 8, 1754.
27. [27]
  (27) Li, Y.;Wang, C. S. Sci. China Ser. Chem. 2011, 54 (11), 1759.doi: 10.1007/s11426-011-4411-y
28. [28]
  (28) Kobko, R.; Dannenberg, J. J. J. Phys. Chem. A 2003, 107,10389. doi: 10.1021/jp0365209
29. [29]
  (29) Wu, Y. D.; Zhao, Y. L. J. Am. Chem. Soc. 2001, 123, 5313.doi: 10.1021/ja003482n
30. [30]
  (30) Frish, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gassian 03,Revision D.01; Gaussian Inc.: Pittsburgh, PA, 2003.
31. [31]
  (31) Biegler, K. F.; Schonbohm, J.; Bayles, D. J. Comput. Chem.2001, 22, 545.
32. [32]
  (32) Yang, Y. J. Phys. Chem. A 2012, 116, 10150. doi: 10.1021/jp304420c
33. [33]
  (33) Yang, Y. J. Phys. Chem. A 2011, 115, 9043. doi: 10.1021/jp204531e
34. [34]
  (34) Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J. Phys. Chem. B2007, 111, 8940.
35. [35]
  (35) Zhao, G. J.; Han, K. L. Accounts Chem. Res. 2012, 45, 404. doi: 10.1021/ar200135h
1. [1]
  
  (1) Trouillas, P.; Marsal, P.; Siri, D.; Lazzaroni, R.; Duroux, J. L.Food Chem. 2006, 97, 679. doi: 10.1016/j.foodchem.2005.05.042
2. [2]
  (2) Lespade, L.; Bercion, S. J. Phys. Chem. B 2010, 114, 921. doi: 10.1021/jp9041809
3. [3]
  (3) Guzzo, M. R.; Uemi, M.; Donate, P. M.; Nikolaou, S.; Machado,A. E. H.; Okano, L. T. J. Phys. Chem. A 2006, 110, 10545. doi: 10.1021/jp0613337
4. [4]
  (4) Chakraborty, S.; Biswas, P. K. J. Phys. Chem. A 2012, 116,8775. doi: 10.1021/jp303543z
5. [5]
  (5) Estévez, L.; Mosquera, R. A. J. Phys. Chem. A 2007, 111,11100. doi: 10.1021/jp074941a
6. [6]
  (6) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. Theor.Chem. Acc. 2004, 111, 210. doi: 10.1007/s00214-003-0544-1
7. [7]
  (7) Lee, S.; Shin, S. Y.; Lee, Y.; Park, Y.; Kim, B. G.; Ahn, J. H.;Chong, Y.; Lee, Y. H.; Lim, Y. Bioorg. Med. Chem. Lett. 2011,21, 3866. doi: 10.1016/j.bmcl.2011.05.043
8. [8]
  (8) Kang, J.W.; Zhuo, L.; Lu, X. Q.; Liu, H. D.; Zhang, M.;Wu, H.X. J. Inorg. Biochem. 2004, 98, 79. doi: 10.1016/j.jinorgbio.2003.08.015
9. [9]
  (9) Bhuva, H. A.; Kini, S. G. J. Mol. Graph. Model. 2010, 29, 32.doi: 10.1016/j.jmgm.2010.04.003
10. [10]
  (10) Zhang, M.; Lv, Q. L.; Yue, N. N.;Wang, H. Y. Spectrochim.Acta A 2009, 72, 572. doi: 10.1016/j.saa.2008.10.045
11. [11]
  (11) Cornard, J. P.; Merlin, J. C. J. Mol. Struct. 2003, 651-653, 381.
12. [12]
  (12) Mukai, K.; Oka,W.;Watanabe, K.; Egawa, Y.; Nagaoka, S. I.J. Phys. Chem. A 1997, 101, 3746. doi: 10.1021/jp9706745
13. [13]
  (13) Ni, Y. N.; Du, S.; Kokot, S. Anal. Chim. Acta 2007, 584, 19.doi: 10.1016/j.aca.2006.11.006
14. [14]
  (14) Ren, J.; Meng, S.; Lekka, C. E.; Kaxiras, E. J. Phys. Chem. B2008, 112, 1845. doi: 10.1021/jp076881e
15. [15]
  (15) Leopoldini, M.; Russo, N.; Chiodo, S.; Toscano, M. J. Agric.Food Chem. 2006, 54, 6343. doi: 10.1021/jf060986h
16. [16]
  (16) Lekka, C. E.; Ren, J.; Meng, S.; Kaxiras, E. J. Phys. Chem. B2009, 113, 6478. doi: 10.1021/jp807948z
17. [17]
  (17) Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M. J. Phys.Chem. A 2004, 108, 4916. doi: 10.1021/jp037247d
18. [18]
  (18) Lemańska, K.; Szymusiak, H.; Tyrakowska, B.; Zieliński, R.;Soffers, A. E. M. F.; Rietjens, I. M. C. M. Free Raobc. Med.2001, 7, 869.
19. [19]
  (19) Plaper, A.; lob, M.; Hafner, I.; Oblak, M.; Šolmajer, T.;Jerala, R. Biochem. Biophys. Res. Commun. 2003, 306, 530.doi: 10.1016/S0006-291X(03)01006-4
20. [20]
  (20) Solimani, R. Biochim. Biophys. Acta 1997, 1336, 281. doi: 10.1016/S0304-4165(97)00038-X
21. [21]
  (21) Zhang, C. S.; Lai, L. H. Acta Phys. -Chim. Sin. 2012, 28 (10),2363. [张长胜, 来鲁华. 物理化学学报, 2012, 28 (10), 2363.]doi: 10.3866/PKU.WHXB201209172
22. [22]
  (22) Huang, Y. Y.; Yang, X. F.; Li, H. T.; Ji, X. F.; Cheng, H. L.;Zhao, Y. J.; Guo, D. C.; Li, L.; Liu, S. Y. Acta Phys. -Chim. Sin.2012, 28 (10), 2390. [黄阳玉, 阳秀凤, 李昊田, 纪晓峰, 程洪礼, 赵蕴杰, 郭大川, 李林, 刘士勇. 物理化学学报, 2012, 28 (10), 2390.] doi: 10.3866/PKU.WHXB201209111
23. [23]
  (23) Zhang, M.; Zheng, Y. P.; Jiang, X. N.;Wang, C. S. ActaPhys. -Chim. Sin. 2010, 26 (3), 735. [张敏, 郑艳萍, 姜笑楠, 王长生. 物理化学学报, 2010, 26 (3), 735.] doi: 10.3866/PKU.WHXB20100235
24. [24]
  (24) Liu, D. J.;Wang, C. S. Acta Phys. -Chim. Sin. 2012, 28 (12),2809. [刘冬佳, 王长生. 物理化学学报, 2012, 28 (12), 2809.]doi: 10.3866/PKU.WHXB201209263
25. [25]
  (25) Dong, H.; Hua,W. J.; Li, S. H. J. Phys. Chem. A 2007, 111,2941. doi: 10.1021/jp0709860
26. [26]
  (26) Jiang, X. N.;Wang, C. S. Sci. China Ser. Chem. 2010, 8, 1754.
27. [27]
  (27) Li, Y.;Wang, C. S. Sci. China Ser. Chem. 2011, 54 (11), 1759.doi: 10.1007/s11426-011-4411-y
28. [28]
  (28) Kobko, R.; Dannenberg, J. J. J. Phys. Chem. A 2003, 107,10389. doi: 10.1021/jp0365209
29. [29]
  (29) Wu, Y. D.; Zhao, Y. L. J. Am. Chem. Soc. 2001, 123, 5313.doi: 10.1021/ja003482n
30. [30]
  (30) Frish, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gassian 03,Revision D.01; Gaussian Inc.: Pittsburgh, PA, 2003.
31. [31]
  (31) Biegler, K. F.; Schonbohm, J.; Bayles, D. J. Comput. Chem.2001, 22, 545.
32. [32]
  (32) Yang, Y. J. Phys. Chem. A 2012, 116, 10150. doi: 10.1021/jp304420c
33. [33]
  (33) Yang, Y. J. Phys. Chem. A 2011, 115, 9043. doi: 10.1021/jp204531e
34. [34]
  (34) Zhao, G. J.; Liu, J. Y.; Zhou, L. C.; Han, K. L. J. Phys. Chem. B2007, 111, 8940.
35. [35]
  (35) Zhao, G. J.; Han, K. L. Accounts Chem. Res. 2012, 45, 404. doi: 10.1021/ar200135h
1. [1]
  Huiying Xu , Minghui Liang , Zhi Zhou , Hui Gao , Wei Yi . Application of Quantum Chemistry Computation and Visual Analysis in Teaching of Weak Interactions. University Chemistry, 2025, 40(3): 199-205. doi: 10.12461/PKU.DXHX202407011
2. [2]
  Rong Tian , Yadi Yang , Naihao Lu . Comprehensive Experimental Design of Undergraduate Students Based on Interdisciplinarity: Study on the Effect of Quercetin on Chlorination Activity of Myeloperoxidase. University Chemistry, 2024, 39(8): 247-254. doi: 10.3866/PKU.DXHX202312064
3. [3]
  Yinglian LI , Chengcheng ZHANG , Xinyu ZHANG , Xinyi WANG . Spin crossover in [Co(pytpy)₂]²⁺ complexes modified by organosulfonate anions. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1162-1172. doi: 10.11862/CJIC.20240087
4. [4]
  Aidang Lu , Yunting Liu , Yanjun Jiang . Comprehensive Organic Chemistry Experiment: Synthesis and Characterization of Triazolopyrimidine Compounds. University Chemistry, 2024, 39(8): 241-246. doi: 10.3866/PKU.DXHX202401029
5. [5]
  Jiaxun Wu , Mingde Li , Li Dang . The R eaction of Metal Selenium Complexes with Olefins as a Tutorial Case Study for Analyzing Molecular Orbital Interaction Modes. University Chemistry, 2025, 40(3): 108-115. doi: 10.12461/PKU.DXHX202405098
6. [6]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
7. [7]
  Wenyan Dan , Weijie Li , Xiaogang Wang . The Technical Analysis of Visual Software ShelXle for Refinement of Small Molecular Crystal Structure. University Chemistry, 2024, 39(3): 63-69. doi: 10.3866/PKU.DXHX202302060
8. [8]
  Simin Fang , Hong Wu , Wei Liu , Wei Wei , Hongyan Feng , Wan Li . Construction and Application of Teaching Resources for Inorganic and Analytical Chemistry Experimental Course in the Context of Digital Empowerment. University Chemistry, 2024, 39(10): 156-163. doi: 10.3866/PKU.DXHX202402053
9. [9]
  Wanqun Hu , Pingping Zhu , Yuan Zheng , Wanqun Zhang , Wei Shao , Hong Wu , Qiang Zhou , Kaiping Yang , Xiang Sheng . Design and Practice of Ideological and Political Case Study in Instrumental Analysis Experiment Course: the Extraction and Structural Identification of Artemisinin. University Chemistry, 2024, 39(2): 203-207. doi: 10.3866/PKU.DXHX202310062
10. [10]
  Liwei Wang , Guangran Ma , Li Wang , Fugang Xu . A Comprehensive Analytical Chemistry Experiment: Colorimetric Detection of Vitamin C Using Nanozyme and Smartphone. University Chemistry, 2024, 39(8): 255-262. doi: 10.3866/PKU.DXHX202312094
11. [11]
  Linhan Tian , Changsheng Lu . Discussion on Sextuple Bonding in Diatomic Motifs of Chromium Family Elements. University Chemistry, 2024, 39(8): 395-402. doi: 10.3866/PKU.DXHX202401056
12. [12]
  Jiarong Feng , Yejie Duan , Chu Chu , Dezhen Xie , Qiu'e Cao , Peng Liu . Preparation and Application of a Streptomycin Molecularly Imprinted Electrochemical Sensor: A Suggested Comprehensive Analytical Chemical Experiment. University Chemistry, 2024, 39(8): 295-305. doi: 10.3866/PKU.DXHX202401016
13. [13]
  Jinghan Xu , Yang Wang , Donghui Wei . Drawing Cross-Sectional Contour Maps of π Molecular Orbitals. University Chemistry, 2025, 40(3): 23-29. doi: 10.12461/PKU.DXHX202403023
14. [14]
  Rui Li , Jiayu Zhang , Anyang Li . Two Levels of Understanding of Chemical Bonds: a Case of the Bonding Model of Hypervalent Molecules. University Chemistry, 2024, 39(2): 392-398. doi: 10.3866/PKU.DXHX202308051
15. [15]
  Yong Shu , Xing Chen , Sai Duan , Rongzhen Liao . How to Determine the Equilibrium Bond Distance of Homonuclear Diatomic Molecules: A Case Study of H₂. University Chemistry, 2024, 39(7): 386-393. doi: 10.3866/PKU.DXHX202310102
16. [16]
  Zhuomin Zhang , Hanbing Huang , Liangqiu Lin , Jingsong Liu , Gongke Li . Course Construction of Instrumental Analysis Experiment: Surface-Enhanced Raman Spectroscopy for Rapid Detection of Edible Pigments. University Chemistry, 2024, 39(2): 133-139. doi: 10.3866/PKU.DXHX202308034
17. [17]
  Zhenli Sun , Ning Wang , Kexin Lin , Qin Dai , Yufei Zhou , Dandan Cao , Yanfeng Dang . Visual Analysis of Hotspots and Development Trends in Analytical Chemistry Education Reform. University Chemistry, 2024, 39(11): 57-64. doi: 10.12461/PKU.DXHX202403095
18. [18]
  Zhaoyang Li , Haiyan Zhao , Yali Zhang , Yuan Zhang , Shiqiang Cui . Integration of Nobel Prize Achievements in Analytical Technology with College Instrumental Analysis Course. University Chemistry, 2025, 40(3): 269-276. doi: 10.12461/PKU.DXHX202405131
19. [19]
  Junjie Zhang , Yue Wang , Qiuhan Wu , Ruquan Shen , Han Liu , Xinhua Duan . Preparation and Selective Separation of Lightweight Magnetic Molecularly Imprinted Polymers for Trace Tetracycline Detection in Milk. University Chemistry, 2024, 39(5): 251-257. doi: 10.3866/PKU.DXHX202311084
20. [20]
  Zhening Lou , Quanxing Mao , Xiaogeng Feng , Lei Zhang , Xu Xu , Yuyang Zhang , Xueyan Liu , Hongling Kang , Dongyang Feng , Yongku Li . Practice of Implementing Blended Teaching in Shared Analytical Chemistry Course. University Chemistry, 2024, 39(2): 263-269. doi: 10.3866/PKU.DXHX202308089

Get Citation

PDF

XML

Metrics

PDF Downloads(612)
Abstract views(1052)
HTML views(39)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Site-Preference of Uracil and Thymine Hydrogen Bonding to Quercetin

References

Metrics

通讯作者: 陈斌, bchen63@163.com