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;
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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
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