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A density functional theory study of the hydrolysis mechanism of phosphodiester catalyzed by a mononuclear Zn(II) complex
Zhang, Xuepeng1; Gao, Hui2; Xu, Huiying1; Xu, Jianqiao1; Chao, Hui1; Zhao, Cunyuan1
2013-03-01
Source PublicationJOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL
Volume368Pages:53-60
AbstractDensity functional theory (DFT) calculations were used to explore the hydrolysis mechanism of the DNA analog BNPP (BNPP= bis(4-nitrophenyl)phosphate) catalyzed by the mononuclear zinc(II):OH- complex of 1,5,9-triazacyclododecane (Zn:([12] aneN(3))). We present a binding mode in which one terminal phosphoryl oxygen atom as well as the nucleophilic group (hydroxyl anion) binds to zinc center. Two potential mechanisms were found as follows: one is a concerted mechanism with a reaction barrier of 18.1 kcal/mol in liquid phase of implicit solvent and 13.8 kcal/mol in liquid phase of explicit solvent of water molecules; the other is a stepwise mechanism with a hydroxylated phosphate reaction intermediate of a quasi-trigonal bipyramid configuration but is less feasible. Both the concerted reaction pathway and stepwise reaction pathway are S(N)2 manner of nucleophilic substitution reactions. Meanwhile polar protic solvents like water, methanol and ethanol are favored in the catalyst-assisted hydrolysis mechanism. We explore the rationality of deprotonation of mono-anionic phosphates in the transient products and find that it is difficult to dissociate a proton and the ultimate product is NPP- rather than NPP2-. These results are consistent with and systematically interpret the experimental observations, more importantly, provide useful suggestions in the catalyst design and solvent selection. (C) 2012 Elsevier B.V. All rights reserved.
SubtypeArticle
KeywordPhosphodiester Zinc Hydrolysis Solvent Effect s(n)2 Reaction Deprotonation
WOS HeadingsScience & Technology ; Physical Sciences
DOI10.1016/j.molcata.2012.11.025
WOS Subject ExtendedChemistry
WOS KeywordMETAL-IONS ; PHOSPHATE DIESTERS ; MODEL SYSTEM ; CLEAVAGE ; METHANOL ; ENZYMES ; BINDING ; SERIES ; ACIDS ; SET
Indexed BySCI
Language英语
WOS SubjectChemistry, Physical
WOS IDWOS:000315176600008
Citation statistics
Cited Times:7[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.giec.ac.cn/handle/344007/9142
Collection中国科学院广州能源研究所
Affiliation1.Sun Yat Sen Univ, MOE Key Lab Bioinorgan & Synthet Chem KLGHEI Envi, Sch Chem & Chem Engn, Guangzhou 510275, Guangdong, Peoples R China
2.Chinese Acad Sci, Key Lab Renewable Energy & Gas Hydrate, Guangzhou Inst Energy Convers, Guangzhou 510640, Peoples R China
Recommended Citation
GB/T 7714
Zhang, Xuepeng,Gao, Hui,Xu, Huiying,et al. A density functional theory study of the hydrolysis mechanism of phosphodiester catalyzed by a mononuclear Zn(II) complex[J]. JOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL,2013,368:53-60.
APA Zhang, Xuepeng,Gao, Hui,Xu, Huiying,Xu, Jianqiao,Chao, Hui,&Zhao, Cunyuan.(2013).A density functional theory study of the hydrolysis mechanism of phosphodiester catalyzed by a mononuclear Zn(II) complex.JOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL,368,53-60.
MLA Zhang, Xuepeng,et al."A density functional theory study of the hydrolysis mechanism of phosphodiester catalyzed by a mononuclear Zn(II) complex".JOURNAL OF MOLECULAR CATALYSIS A-CHEMICAL 368(2013):53-60.
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