Citation: CHEN Ze-Qin, HE Yun-Qing, GUO Lin-Feng, XUE Ying. Effects of Explicit and Implicit Solvent Models on the Hydrolysis Cleavage of N-Glycosidic Bond in 8-Oxo-7,8-dihydro-2'-deoxyguanosine[J]. Chinese Journal of Structural Chemistry, ;2014, 33(4): 505-512. shu

Effects of Explicit and Implicit Solvent Models on the Hydrolysis Cleavage of N-Glycosidic Bond in 8-Oxo-7,8-dihydro-2'-deoxyguanosine

a.
a. College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637002, China;
b.
b. Department of Chemistry and Engineering, Sichuan Key Laboratory of Exploitation and Study of Distinctive Plants, Sichuan University of Arts and Science, Dazhou 635000, China;
c.
c. College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, China

Received Date: 5 September 2013
Available Online: 9 February 2014
Fund Project: Department of Education (12ZA174) of Sichuan Province as well as China West Normal University (11B002) (2011JY0136)

8-Oxoguanine (8-oxoG), a critical mutagenic DNA lesion induced by reactive oxy-gen species, gives rise to a G·C→T·A transversion during replication and thereby must be repaired. The effects of explicit and implicit solvent molecules on the hydrolysis cleavage of N-Glycosidic bond in 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) have been systematically clarified in the present work based upon two types of computational models. Detailed potential energy surface (PES) scans and full unconstraint optimizations for all the representative points on PESs were carried out at the B3LYP/6-31+G(d) level of theory. The effect of implicit solvent was tested by single-point calculation at the SCRF/IEF-PCM model. The results illustrate that the direct hydrolysis model involving one explicit water molecule can't provide a complete depiction of the hydrolysis process of 8-oxo-dG, attributed to the insufficiency of nucleophile activation and leaving group stabilization. The expansion hydrolysis model involving four explicit water molecules, however, facilitates discrete proton transfer and therefore produces smooth reaction surfaces for both the dissociative (S_N1) and concerted (S_N2) pathways. The presence of the implicit solvent substantially lowers all activation energies and the S_N1 process is more favorable than the S_N2 process. The data and insights present here agree well with the experimental results and have given out a baseline for the enzymatic deglycosylation reaction of 8-oxo-dG.
- 8-oxo-7,8-dihydro-2'-deoxyguanosine,
- hydrolysis mechanism,
- potential energy surface scan,
- solvent effect
1. [1]
  Ping Wang , Tianbao Zhang , Zhenxing Li . Reconstruction mechanism of Cu surface in CO2 reduction process. Chinese Journal of Structural Chemistry, 2024, 43(8): 100328-100328. doi: 10.1016/j.cjsc.2024.100328
2. [2]
  Yuan Dong , Mutian Ma , Zhenyang Jiao , Sheng Han , Likun Xiong , Zhao Deng , Yang Peng . Effect of electrolyte cation-mediated mechanism on electrocatalytic carbon dioxide reduction. Chinese Chemical Letters, 2024, 35(7): 109049-. doi: 10.1016/j.cclet.2023.109049
3. [3]
  Jaeyong Ahn , Zhenping Li , Zhiwei Wang , Ke Gao , Huagui Zhuo , Wanuk Choi , Gang Chang , Xiaobo Shang , Joon Hak Oh . Surface doping effect on the optoelectronic performance of 2D organic crystals based on cyano-substituted perylene diimides. Chinese Chemical Letters, 2024, 35(9): 109777-. doi: 10.1016/j.cclet.2024.109777
4. [4]
  Bin Dong , Ning Yu , Qiu-Yue Wang , Jing-Ke Ren , Xin-Yu Zhang , Zhi-Jie Zhang , Ruo-Yao Fan , Da-Peng Liu , Yong-Ming Chai . Double active sites promoting hydrogen evolution activity and stability of CoRuOH/Co₂P by rapid hydrolysis. Chinese Chemical Letters, 2024, 35(7): 109221-. doi: 10.1016/j.cclet.2023.109221
5. [5]
  Hai-Ling Wang , Zhong-Hong Zhu , Hua-Hong Zou . Structure and assembly mechanism of high-nuclear lanthanide-oxo clusters. Chinese Journal of Structural Chemistry, 2024, 43(9): 100372-100372. doi: 10.1016/j.cjsc.2024.100372
6. [6]
  Yuexiang Liu , Xiangqiao Yang , Tong Lin , Guantian Yang , Xiaoyong Xu , Bubing Zeng , Zhong Li , Weiping Zhu , Xuhong Qian . Efficient continuous synthesis of 2-[3-(trifluoromethyl)phenyl]malonic acid, a key intermediate of Triflumezopyrim, coupling with esterification-condensation-hydrolysis. Chinese Chemical Letters, 2025, 36(1): 109747-. doi: 10.1016/j.cclet.2024.109747
7. [7]
  Weiping Guo , Ying Zhu , Hong-Hua Cui , Lingyun Li , Yan Yu , Zhong-Zhen Luo , Zhigang Zou . β-Pb₃P₂S₈: A new optical crystal with exceptional birefringence effect. Chinese Chemical Letters, 2025, 36(2): 110256-. doi: 10.1016/j.cclet.2024.110256
8. [8]
  Huanyu Liu , Gang Yu , Ruoyao Guo , Hao Qi , Jiayin Zheng , Tong Jin , Zifeng Zhao , Zuqiang Bian , Zhiwei Liu . Direct identification of energy transfer mechanism in Ce^Ⅲ-Mn^Ⅱ system by constructing molecular heteronuclear complexes. Chinese Chemical Letters, 2025, 36(2): 110296-. doi: 10.1016/j.cclet.2024.110296
9. [9]
  Dongmei Yao , Junsheng Zheng , Liming Jin , Xiaomin Meng , Zize Zhan , Runlin Fan , Cong Feng , Pingwen Ming . Effect of surface oxidation on the interfacial and mechanical properties in graphite/epoxy composites composite bipolar plates. Chinese Chemical Letters, 2024, 35(11): 109382-. doi: 10.1016/j.cclet.2023.109382
10. [10]
  Xiaoyao Ma , Jinling Zhang , Ge Fang , He Gao , Jie Gao , Li Fu , Yuanyuan Hou , Gang Bai . Förster resonance energy transfer reveals phillygenin and swertiamarin concurrently target AKT on different binding domains to increase the anti-inflammatory effect. Chinese Chemical Letters, 2024, 35(5): 108823-. doi: 10.1016/j.cclet.2023.108823
11. [11]
  Fanxin Kong , Hongzhi Wang , Huimei Duan . Inhibition effect of sulfation on Pt/TiO2 catalysts in methane combustion. Chinese Journal of Structural Chemistry, 2024, 43(5): 100287-100287. doi: 10.1016/j.cjsc.2024.100287
12. [12]
  Tiantian Man , Fulin Zhu , Yaqi Huang , Yuhao Piao , Yan Su , Shengyuan Deng , Ying Wan . Mobile mini-fluorimeter for antibiotic aptasensing based on surface-plasmonic effect of burlike nanogolds enhanced by digitized imaging diagnosis. Chinese Chemical Letters, 2024, 35(5): 109036-. doi: 10.1016/j.cclet.2023.109036
13. [13]
  Xingxing Jiang , Yuxin Zhao , Yan Kong , Jianju Sun , Shangzhao Feng , Xin Lu , Qi Hu , Hengpan Yang , Chuanxin He . Support effect and confinement effect of porous carbon loaded tin dioxide nanoparticles in high-performance CO₂ electroreduction towards formate. Chinese Chemical Letters, 2025, 36(1): 109555-. doi: 10.1016/j.cclet.2024.109555
14. [14]
  Yubang Li , Xixi Hu , Daiqian Xie . The microscopic formation mechanism of O + H2 products from photodissociation of H2O. Chinese Journal of Structural Chemistry, 2024, 43(5): 100274-100274. doi: 10.1016/j.cjsc.2024.100274
15. [15]
  Xin Li , Wanting Fu , Ruiqing Guan , Yue Yuan , Qinmei Zhong , Gang Yao , Sheng-Tao Yang , Liandong Jing , Song Bai . Nucleophiles promotes the decomposition of electrophilic functional groups of tetracycline in ZVI/H₂O₂ system: Efficiency and mechanism. Chinese Chemical Letters, 2024, 35(10): 109625-. doi: 10.1016/j.cclet.2024.109625
16. [16]
  Guang-Xu Duan , Queting Chen , Rui-Rui Shao , Hui-Huang Sun , Tong Yuan , Dong-Hao Zhang . Encapsulating lipase on the surface of magnetic ZIF-8 nanosphers with mesoporous SiO₂ nano-membrane for enhancing catalytic performance. Chinese Chemical Letters, 2025, 36(2): 109751-. doi: 10.1016/j.cclet.2024.109751
17. [17]
  Hao Lv , Zhi Li , Peng Yin , Ping Wan , Mingshan Zhu . Recent progress on non-metallic carbon nitride for the photosynthesis of H₂O₂: Mechanism, modification and in-situ applications. Chinese Chemical Letters, 2025, 36(1): 110457-. doi: 10.1016/j.cclet.2024.110457
18. [18]
  Chaochao Wei , Ru Wang , Zhongkai Wu , Qiyue Luo , Ziling Jiang , Liang Ming , Jie Yang , Liping Wang , Chuang Yu . Revealing the size effect of FeS₂ on solid-state battery performances at different operating temperatures. Chinese Chemical Letters, 2024, 35(6): 108717-. doi: 10.1016/j.cclet.2023.108717
19. [19]
  Ting-Ting Huang , Jin-Fa Chen , Juan Liu , Tai-Bao Wei , Hong Yao , Bingbing Shi , Qi Lin . A novel fused bi-macrocyclic host for sensitive detection of Cr₂O₇²⁻ based on enrichment effect. Chinese Chemical Letters, 2024, 35(7): 109281-. doi: 10.1016/j.cclet.2023.109281
20. [20]
  Liang Ma , Zhou Li , Zhiqiang Jiang , Xiaofeng Wu , Shixin Chang , Sónia A. C. Carabineiro , Kangle Lv . Effect of precursors on the structure and photocatalytic performance of g-C3N4 for NO oxidation and CO2 reduction. Chinese Journal of Structural Chemistry, 2024, 43(11): 100416-100416. doi: 10.1016/j.cjsc.2024.100416

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(1011)
HTML views(38)

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

Address：Zhongguancun North First Street 2,100190 Beijing, PR China Tel: +86-010-82449177-888

DownLoad: Full-Size Img PowerPoint

Return