Citation: Wang Yinghui, Wei Simin, Wang Kang, Xu Rongrong, Zhao Hongmei. A Theoretical Study of 8-Azaguanine Radical Cation Deprotonation[J]. Acta Chimica Sinica, ;2020, 78(3): 271-278. doi: 10.6023/A19120435 shu

A Theoretical Study of 8-Azaguanine Radical Cation Deprotonation

Wang Yinghui ^a,† ,
Wei Simin ^b,†,, ,
Wang Kang ^a ,
Xu Rongrong ^b ,
Zhao Hongmei ^c,†,,

a.
College of Science, Chang'an University, Xi'an 710064
b.
Shaanxi Collaborative Innovation Center of Chinese Medicine Resources Industrialization, Shaanxi University of Chinese Medicine, Xianyang 712083
c.
Beijing National Laboratory for Molecular Science(BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190

Corresponding author: Wei Simin, weisimin@iccas.ac.cn Zhao Hongmei, hmzhao@iccas.ac.cn

^†

Received Date: 18 December 2019
Available Online: 9 February 2020
Fund Project: Project supported by the National Natural Science Foundation of China (No. 21705029) and the Shaanxi Provincial Association for Science and Technology Young Talents Lifting Plan (No. 20190307)the National Natural Science Foundation of China 21705029the Shaanxi Provincial Association for Science and Technology Young Talents Lifting Plan 20190307

Figures(7)

Due to the lower redox potential comparing with guanine, it is the 8-azaguanine (8-AG) as the hole trap to form 8-azaguanine radical cation (8-AG^·+) after one-electron oxidation of DNA containing 8-azaguanine. In generally, the 8-AG^·+ may suffer from deprotonation to generate 8-AG(-H)·. In this text, we were stimulated to investigate the deprotonation reaction of 8-AG^·+ generating by one-electron oxidation at M06-2X/6-31+G(d) level with explicit water molecules and polarized continuum model (PCM) to simulate the solvent effect. By building deprotonation model with different number of explicit water molecules, we found that these four water molecules locating around N(1)-H, O(6), N(2)-H of 8-AG^·+ as well as the one locating in the second water shell which was hydrogen-bonding with the water around O(6) were necessary. If the water in the second water shell was not included, the imino proton (N(1)-H) would not transfer into the bulk water. In parallel, the N(1)-H would transfer to the O(6) of 8-AG^·+ by intramolecular proton transfer. If the water molecule locating around N(2)-H was removed, the 8-AG^·+ deprotonation would continue but the energy barrier would be lowered from 24.8 kJ/mol to 16.3 kJ/mol. In addition, the site of the water molecule in the second water shell was also studied. If putting the water in the second water shell around N(2)-H of 8-AG^·+, the proton would be stabilized between the N(1) of 8-AG^·+ and the oxygen of water molecule around N(1)-H meaning the proton would not be transferred into bulk water. Further, in order to test the influence of water number on 8-AG^·+ deprotonation, the fifth water molecule, which is hydrogen-bonding with the water molecule around N(2)-H and another N(2)-H, was added. The potential energy surface with 5H₂O revealed that it is almost no effect on the deprotonation pathway and energy barrier (25.5 kJ/mol). Lastly, so as to obtain the exact energy barrier of 8-AG^·+ deprotonation, the deprotonation model with more explicit water molecules (9H₂O) was proposed, where the additional water molecules were placed around N(2)-H, N(3), O(6), N(7) and N(8). From the potential energy surface, the deprotonation energy barrier of 8-AG^·+ was confirmed to be 19.5 kJ/mol. These theoretical results provide valuable dynamics information and mechanistic insights for further understanding the properties of nucleic acid base analogues and one-electron oxidation of DNA.
- 8-azaguanine,
- one-electron oxidation,
- deprotonation reaction,
- potential energy surface
1. [1]
  Seth, P. P.; Tanowitz, M.; Bennett, C. F. J. Clin. Invest. 2019, 129, 915. doi: 10.1172/JCI125228
2. [2]
  Zou, X.; Zhao, H.; Yu, Y.; Su, H. J. Am. Chem. Soc. 2013, 135, 4509. doi: 10.1021/ja400483j
3. [3]
  Zou, X.; Dai, X.; Liu, K.; Zhao, H.; Song, D.; Su, H. J. Phys. Chem. B 2014, 118, 5864. doi: 10.1021/jp501658a
4. [4]
  Jie, J.; Xia, Y.; Huang, C.-H.; Zhao, H.; Yang, C.; Liu, K.; Song, D.; Zhu, B.-Z.; Su, H. Nucleic Acids Res. 2019, 47, 11514.
5. [5]
  Kim, N.; Choi, J. W.; Song, A. Y.; Choi, W. S.; Park, H. R.; Park, S.; Kim, I.; Kim, H. S. Int. Immunopharmacol. 2019, 67, 152. doi: 10.1016/j.intimp.2018.12.020
6. [6]
  Kawada, M.; Amemiya, M.; Sakamoto, S.; Ohishi, T.; Yoshida, J.; Tatsuda, D. Cancer Sci. 2018, 109, 157.
7. [7]
  Folkes, L. K.; O'Neill, P. Free Radical Biol. Med. 2013, 58, 14. doi: 10.1016/j.freeradbiomed.2013.01.014
8. [8]
  de Araujo, A. V. S.; Borin, A. C. J. Phys. Chem. A 2019, 123, 3109. doi: 10.1021/acs.jpca.9b01397
9. [9]
  Zhou, Z. N.; Hu, Z. B.; Zhang, X. W.; Jia, M. H.; Wang, X. L.; Su, H. M.; Sun, H. T.; Chen, J. Q.; Xu, J. H. ChemPhysChem 2019, 20, 757. doi: 10.1002/cphc.201800969
10. [10]
  Wierzchowski, J.; Medza, G.; Szabelski, M.; Stachelska- Wierzchowska, A. J. Photochem. Photobiol. A-Chem. 2013, 265, 49. doi: 10.1016/j.jphotochem.2013.05.014
11. [11]
  Kawai, K.; Majima, T. Acc. Chem. Res. 2013, 46, 2616. doi: 10.1021/ar400079s
12. [12]
  Cadet, J.; Wagner, J. R.; Shafirovich, V.; Geacintov, N. E. Int. J. Radiat Biol. 2014, 90, 423. doi: 10.3109/09553002.2013.877176
13. [13]
  Wang, Y.; Zhao, H.; Yang, C.; Jie, J.; Dai, X.; Zhou, Q.; Liu, K.; Song, D.; Su, H. J. Am. Chem. Soc. 2019, 141, 1970. doi: 10.1021/jacs.8b10743
14. [14]
  Takada, T.; Kawai, K.; Fujitsuka, M.; Majima, T. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 14002. doi: 10.1073/pnas.0402756101
15. [15]
  Wu, L. D.; Jie, J. L.; Liu, K. H.; Su, H. M. Acta Chim. Sinica 2014, 72, 1182 (in Chinese).
16. [16]
  Yang, W. Y.; Lei, Z. C.; Hong, W. J.; Huang, F. Z. Acta Chim. Sinica 2019, 77, 951 (in Chinese).
17. [17]
  Kobayashi, K.; Tagawa, S. J. Am. Chem. Soc. 2003, 125, 10213. doi: 10.1021/ja036211w
18. [18]
  Wu, L. D.; Liu, K. H.; Jie, J. L.; Song, D.; Su, H. M. J. Am. Chem. Soc. 2015, 137, 259. doi: 10.1021/ja510285t
19. [19]
  Wang, Y.; Zhao, H.; Zhou, Q.; Dai, X.; Liu, K.; Song, D.; Su, H. J. Phys. Chem. B 2019, 123, 2853.
20. [20]
  Rokhlenko, Y.; Cadet, J.; Geacintov, N. E.; Shafirovich, V. J. Am. Chem. Soc. 2014, 136, 5956. doi: 10.1021/ja412471u
21. [21]
  Rokhlenko, Y.; Geacintov, N. E.; Shafirovich, V. J. Am. Chem. Soc. 2012, 134, 4955. doi: 10.1021/ja212186w
22. [22]
  Zhang, Q. H.; Wang, Y.; Liu, C.; Yang, Z. Z. Acta Chim. Sinica 2014, 72, 956 (in Chinese).
23. [23]
  Lonkar, P.; Dedon, P. C. Int. J. Cancer 2011, 128, 1999. doi: 10.1002/ijc.25815
24. [24]
  Wu, Y. J.; Zhai, S. G.; Lu, K.; Gao, L. J. Solid State Electrochem. 2014, 18, 1593. doi: 10.1007/s10008-014-2393-3
25. [25]
  Li, X.; Cai, Z.; Sevilla, M. D. J. Phys. Chem. B 2001, 105, 10115. doi: 10.1021/jp012364z
26. [26]
  Kumar, A.; Sevilla, M. D. J. Phys. Chem. B 2009, 113, 11359. doi: 10.1021/jp903403d
27. [27]
  Wang, Y. H.; Jie, J. L.; Zhao, H. M.; Bai, Y.; Qin, P. X.; Song, D. Acta Chim. Sinica 2018, 76, 475 (in Chinese). doi: 10.11862/CJIC.2018.063
28. [28]
  Zhao, Y.; Truhlar, D. G. Theor. Chem. Acc. 2008, 120, 215. doi: 10.1007/s00214-007-0310-x
29. [29]
  Wei, S. M.; Wang, Y. H.; Zhao, H. M. Acta Chim. Sinica 2019, 77, 278 (in Chinese).
30. [30]
  Zhao, Y.; Truhlar, D. G. J. Phys. Chem. A 2008, 112, 1095. doi: 10.1021/jp7109127
31. [31]
  Galano, A.; Alvarez-Idaboy, J. R. Phys. Chem. Chem. Phys. 2012, 14, 12476. doi: 10.1039/c2cp40799j
32. [32]
  Candeias, L. P.; Steenken, S. J. Am. Chem. Soc. 1989, 111, 1094. doi: 10.1021/ja00185a046
33. [33]
  Berkelbach, T. C.; Lee, H. S.; Tuckerman, M. E. Phys. Rev. Lett. 2009, 103, 238302 doi: 10.1103/PhysRevLett.103.238302
34. [34]
  Marx, D.; Tuckerman, M. E.; Hutter, J.; Parrinello, M. Nature 1999, 397, 601. doi: 10.1038/17579
35. [35]
  Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Ha-segawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 09, Revision A. 01, Gaussian, Inc., Wallingford, CT, 2009.
1. [1]
  Jia Zhou . Constructing Potential Energy Surface of Water Molecule by Quantum Chemistry and Machine Learning: Introduction to a Comprehensive Computational Chemistry Experiment. University Chemistry, 2024, 39(3): 351-358. doi: 10.3866/PKU.DXHX202309060
2. [2]
  Chunmei GUO , Weihan YIN , Jingyi SHI , Jianhang ZHAO , Ying CHEN , Quli FAN . Facile construction and peroxidase-like activity of single-atom platinum nanozyme. Chinese Journal of Inorganic Chemistry, 2024, 40(9): 1633-1639. doi: 10.11862/CJIC.20240162
3. [3]
  Chuanming GUO , Kaiyang ZHANG , Yun WU , Rui YAO , Qiang ZHAO , Jinping LI , Guang LIU . Performance of MnO₂-0.39IrO_x composite oxides for water oxidation reaction in acidic media. Chinese Journal of Inorganic Chemistry, 2024, 40(6): 1135-1142. doi: 10.11862/CJIC.20230459
4. [4]
  Tong Zhou , Jun Li , Zitian Wen , Yitian Chen , Hailing Li , Zhonghong Gao , Wenyun Wang , Fang Liu , Qing Feng , Zhen Li , Jinyi Yang , Min Liu , Wei Qi . Experiment Improvement of “Redox Reaction and Electrode Potential” Based on the New Medical Concept. University Chemistry, 2024, 39(8): 276-281. doi: 10.3866/PKU.DXHX202401005
5. [5]
  Ji-Quan Liu , Huilin Guo , Ying Yang , Xiaohui Guo . Calculation and Discussion of Electrode Potentials in Redox Reactions of Water. University Chemistry, 2024, 39(8): 351-358. doi: 10.3866/PKU.DXHX202401031
6. [6]
  Chi Li , Jichao Wan , Qiyu Long , Hui Lv , Ying Xiong . N-Heterocyclic Carbene (NHC)-Catalyzed Amidation of Aldehydes with Nitroso Compounds. University Chemistry, 2024, 39(5): 388-395. doi: 10.3866/PKU.DXHX202312016
7. [7]
  Kai CHEN , Fengshun WU , Shun XIAO , Jinbao ZHANG , Lihua ZHU . PtRu/nitrogen-doped carbon for electrocatalytic methanol oxidation and hydrogen evolution by water electrolysis. Chinese Journal of Inorganic Chemistry, 2024, 40(7): 1357-1367. doi: 10.11862/CJIC.20230350
8. [8]
  Fei Liu , Dong-Yang Zhao , Kai Sun , Ting-Ting Yu , Xin Wang . Comprehensive Experimental Design for Photochemical Synthesis, Analysis, and Characterization of Seleno-Containing Medium-Sized N-Heterocycles. University Chemistry, 2024, 39(3): 369-375. doi: 10.3866/PKU.DXHX202309047
9. [9]
  Endong YANG , Haoze TIAN , Ke ZHANG , Yongbing LOU . Efficient oxygen evolution reaction of CuCo₂O₄/NiFe-layered bimetallic hydroxide core-shell nanoflower sphere arrays. Chinese Journal of Inorganic Chemistry, 2024, 40(5): 930-940. doi: 10.11862/CJIC.20230369
10. [10]
  Kaihui Huang , Dejun Chen , Xin Zhang , Rongchen Shen , Peng Zhang , Difa Xu , Xin Li . Constructing Covalent Triazine Frameworks/N-Doped Carbon-Coated Cu₂O S-Scheme Heterojunctions for Boosting Photocatalytic Hydrogen Production. Acta Physico-Chimica Sinica, 2024, 40(12): 2407020-. doi: 10.3866/PKU.WHXB202407020
11. [11]
  Pingwei Wu . Application of Diamond Software in Simplex Teaching. University Chemistry, 2024, 39(3): 118-121. doi: 10.3866/PKU.DXHX202311043
12. [12]
  Guangming YIN , Huaiyao WANG , Jianhua ZHENG , Xinyue DONG , Jian LI , Yi'nan SUN , Yiming GAO , Bingbing WANG . Preparation and photocatalytic degradation performance of Ag/protonated g-C₃N₄ nanorod materials. Chinese Journal of Inorganic Chemistry, 2024, 40(8): 1491-1500. doi: 10.11862/CJIC.20240086
13. [13]
  Ping Song , Nan Zhang , Jie Wang , Rui Yan , Zhiqiang Wang , Yingxue Jin . Experimental Teaching Design on Synthesis and Antitumor Activity Study of Cu-Pyropheophorbide-a Methyl Ester. University Chemistry, 2024, 39(6): 278-286. doi: 10.3866/PKU.DXHX202310087
14. [14]
  Tengjiao Wang , Tian Cheng , Rongjun Liu , Zeyi Wang , Yuxuan Qiao , An Wang , Peng Li . Conductive Hydrogel-based Flexible Electronic System: Innovative Experimental Design in Flexible Electronics. University Chemistry, 2024, 39(4): 286-295. doi: 10.3866/PKU.DXHX202309094
15. [15]
  Rui Li , Huan Liu , Yinan Jiao , Shengjian Qin , Jie Meng , Jiayu Song , Rongrong Yan , Hang Su , Hengbin Chen , Zixuan Shang , Jinjin Zhao . 卤化物钙钛矿的单双向离子迁移. Acta Physico-Chimica Sinica, 2024, 40(11): 2311011-. doi: 10.3866/PKU.WHXB202311011
16. [16]
  Fei Xie , Chengcheng Yuan , Haiyan Tan , Alireza Z. Moshfegh , Bicheng Zhu , Jiaguo Yu . d带中心调控过渡金属单原子负载COF吸附O₂的理论计算研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2407013-. doi: 10.3866/PKU.WHXB202407013
17. [17]
  Yuping Wei , Yiting Wang , Jialiang Jiang , Jinxuan Deng , Hong Zhang , Xiaofei Ma , Junjie Li . Interdisciplinary Teaching Practice——Flexible Wearable Electronic Skin for Low-Temperature Environments. University Chemistry, 2024, 39(10): 261-270. doi: 10.12461/PKU.DXHX202404007
18. [18]
  Wentao Lin , Wenfeng Wang , Yaofeng Yuan , Chunfa Xu . Concerted Nucleophilic Aromatic Substitution Reactions. University Chemistry, 2024, 39(6): 226-230. doi: 10.3866/PKU.DXHX202310095
19. [19]
  Heng Zhang . Determination of All Rate Constants in the Enzyme Catalyzed Reactions Based on Michaelis-Menten Mechanism. University Chemistry, 2024, 39(4): 395-400. doi: 10.3866/PKU.DXHX202310047
20. [20]
  Yuting Zhang , Zhiqian Wang . Methods and Case Studies for In-Depth Learning of the Aldol Reaction Based on Its Reversible Nature. University Chemistry, 2024, 39(7): 377-380. doi: 10.3866/PKU.DXHX202311037

Get Citation

PDF

XML

Metrics

PDF Downloads(12)
Abstract views(2253)
HTML views(304)

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