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Theoretical Studies on Structural and Spectroscopic Properties of Photoelectrochemical Cell Ruthenium Sensitizers―the Derivatives of N3

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Chemical Research in Chinese Universities 2012年第4期28卷 696-702页

作者： CHEN Jie WANG Jian BAI Fu-quan zheng qing-chuan ZHANG Hong-xing State Key Laboratory of Theoretical and Computational Chemistry Institute of Theoretical ChemistryJilin UniversityChangchun 130021P.R.China

A series of dye molecules was designed ***,azoles and their derivatives were chosen as the modifying groups linking to ancillary ligands of [Ru（dcbpyH2）2（NCS）2]（N3,dcbpy=4,4＇-dicarboxy2,2＇-bipyridine;NCS=thiocyanato）.Density functional theory（DFT） based approaches were applied to exploring the electronic structures and properties of all these *** dye molecule with 1,2,4-triazole groups which exhibits a very high intensity of absorption in visible region,was ***-dependent DFT（TD-DFT） results indicate that the ancillary ligand dominates the molecular orbital（MO） energy levels and masters the absorption transition nature to a certain *** deprotonation of anchoring ligand not only affects the frontier MO energy levels but also controls the energy gaps of the highest occupied MO（HOMO） to the lowest unoccupied MO（LUMO） and LUMO to LUMO＋1 *** the gap between LUMO-LUMO＋1 is small enough,the higher efficiency of dye-sensitized solar cell（DSSC） should be expected.

关键词： Dye-sensitized solar cell Density functional theory(DFT) Frontier molecular orbital Absorption spectrum Deprotonation

Insight into Reaction Mechanism of Sirtuins via Molecular Simulation and Density Functional Theory Study

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Chemical Research in Chinese Universities 2010年第5期26卷 833-837页

作者： ZHAO Yong-shan HOU Rui-zhe ZHANG Hong-xing zheng qing-chuan SUN Chia-chung State Key Laboratory of Theoretical and Computational Chemistry Institute of Theoretical Chemistry Norman Bethune College of Medicine Jilin University Changchun 130021 P. R. China School of Life Sciences ＆ Biopharmaceutical Sciences Shenyang Pharmaceutical University Shenyang 110016 P R. China

With density functional theory（DFT） and molecular mechanics method, the catalytic mechanism of silent information regulator（sirtuins） has been investigated. The calculations support the SN2-1ike reaction of the initial step of the catalysis, and are consistent with experiment results. We further explored the second step of the catalysis and proposed that this step took place in a concerted reaction. In addition, the side chain of Phenylalanine33 may help to shield the glycosidic bond from water and be in a position to protect the developing oxacabenium transition state from hydrolysis. Our results of the calculations support this hypothesis that the phenylalanine33 plays a critical role in the sirtuins biology function.

关键词： Sirtuin NAD^+ p53 Model Density functional theory

Theoretical Study on GSH Activation Mechanism of a New Type of Glutathione Transferase Gtt2

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Chemical Research in Chinese Universities 2012年第3期28卷 500-502页

作者： LI Xue WU Yun-jian LI Zhuo CHU Wen-ting ZHANG Hong-xing zheng qing-chuan State Key Laboratory of Theoretical and Computational Chemistry Institute of Theoretical ChemistryJilin UniversityChangehun 130021P.R.China

Glutathione transferases（GSTs） play an important role in the detoxification of xenobiotic/endobiotic toxic compounds. The α-, π-, and/l-classes of cytosolic GSTs have been studied extensively, while Gtt2 from Saccharo- myces cerevisiae, a novel atypical GST, is still poorly understood. In the present study, we investigated the gluta- thione（GSH） activation mechanism of Gtt2 using the density functional theory（DFT） with the hybrid functional B3LYP. The computational results show that a water molecule could assist a proton transfer between the GSH thiol and the N atom of His133. The energy barrier of proton transfer is 46.0 kJ/mol. The GSH activation mechanism and the characteristics of active site are different from those of classic cytosolic GSTs.

关键词： Quantum chemistry Enzyme catalysis Reaction mechanism Glutathione transferase Glutathione(GSH)activation

Association of (S)-Isoserine Derivatives and 2,2,4-Trimethyl-3-hydroxy-4-cyclohexenecarboxylate

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Chemical Research in Chinese Universities 2007年第1期23卷 18-21页

作者： WANG Lei zheng qing-chuan SONG Zhi-guang FANG Wei-shuo LI Ye-zhi HUANG Hua-min College of Chemistry State Key Laboratory of Theoretical and Computational Chemistry Jilin University Changchun 130021 P. R. China Institute of Materia Medica Chinese Academy of Medical Sciences ＆ Peking Union Medical College Beijing 100050 P. R. China

Two novel compounds（4a and 4b） were obtained by the association of 2,2,4-trimethyl-3-hydroxy-5-cyclohexenecarboxylate with （S） -isoserine derivatives. The space location of the hydroxyl group of compound 1 was identified via the formation of lactone 6. Fe2 （SO4）3·xH2O was used as the catalyst for the synthesis of lactone 6. The carboxyl group was selectively protected with diazomethane. All the products were characterized via ^1H NMR and mass spectra. The Docking study showed that the associations have the potential therapeutic use of DPP-Ⅳ inhibitor.

关键词： (S) -Isoserine 2,2,4-Trimethyl-3-hydroxy-d-cyclohexenecarboxylate Association DPP- Ⅳ

Insight into the Docking Pose of Dehydroascorbate: A Molecular Docking and Molecular Dynamics Simulations Study on Human Omega-Class Glutathione Transferases

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Insight into the Docking Pose of Dehydroascorbate: A Molecul...

Molecular Docking of 3-Methylindole-containing Drugs Binding into CYP3A4

中国化学会第十二届全国量子化学会议

作者： Wang Yan zheng qing-chuan State Key Lab of Theoretical ＆ Computational Chemistry Institute of Theoretical ChemistryJilin University

The reduction of dehydroascorbate（DHA）to ascorbic acid（AA）is a vital cellular *** omega-class glutathione transferases（GSTs）catalyze several reductive reactions in cellular biochemistry,including DHA *** humans,GSTO1-1 and GSTO2-2 are proved to be significant DHA reductase（DHAR）*** structure of a human GSTO1-1（PDB ID:3VLN）has been determined at 1.7 resolution in complex with the reaction product AA,which unexpectedly binds in the G-site,where the glutamyl moiety of GSH *** this work,molecular docking and molecular dynamics simulations were carried out to obtain the complex of GSTO-GSH-DHA and explore the conformational change of this *** Dock4.2software package2 was used to dock DHA into the active site of *** 40ns MD simulation was carried out by employing ***99SB force field4 was used *** mean square deviation（RMSD）was shown in Figure *** using clustering analysis in Amber Tools1.5,the representative structure was obtained and was shown in Figure *** complex can be used as the starting structure of the reaction of reduction of dehydroascorbate（DHA）to ascorbic acid（AA）.

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Chemical Research in Chinese Universities 2012年第1期28卷 137-141页

作者： MENG Xuan-yu, LI Zhuo, NIU Rui-juan, ZHANG Hong-xing and zheng qing-chuan State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130021, P. R. China Institute of Theoretical Chemistry Jilin University State Key Laboratory of Theoretical and Computational Chemistry Changchun 130021

Drugs SPD-304（6,7-dimethyl-3-{[methyl-（2-{methyl-[1-（3-trifluoromethyl-phenyl）-1H-indol-3-ylme thyl]-amino}-ethyl）-amino]-methyl}-chromen-4-one） and zafirlukast contain a common structural element of 3-substituted indole moiety which closely relates to a dehydrogenated reaction catalyzed by cytochrome P450s（CYPs）. It was reported that the dehydrogenation can produce a reactive electrophilic intermediate which cause toxicities and inactivate CYPs. Drug L-745,870（3-{[4-（4-chlorophenyl）piperazin-1-yl]-methyl}-1H-pyrrolo 2,3-β-pyridine） might have similar effect since it contains the same structural element. We used molecular docking approach combined with molecular dynamics（MD） simulation to model three-dimensional（3D） complex structures of SPD-304, zafirlukast and L-745,870 into CYP3A4, respectively. The results show that these three drugs can stably bind into the active site and the 3-methylene carbons of the drugs keep a reasonable reactive distance from the heme iron. The complex structure of SPD-304-CYP3A4 is in agreement with experimental data. For zafirlukast, the calcu lation results indicate that 3-methylene carbon might be the dehydrogenation reaction site. Docking model of L-745,870-CYP3A4 shows a potential possibility of L-745,870 dehydrogenated by CYP3A4 at 3-methylene carbon which is in agreement with experiment in vivo. In addition, residues in the phenylalanine cluster as well as S119 and R212 play a critical role in the ligands binding based on our calculations. The docking models could provide some clues to understand the metabolic mechanism of the drugs by CYP3A4.

关键词： CYP3A4 Molecular docking Molecular dynamics(MD) simulation

C6H5N光谱性质的多组态二级微扰理论研究

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高等学校化学学报 2008年第7期29卷 1448-1451页

作者：侯春园郑清川赵增霞张红星吉林大学理论化学研究所、理论化学计算国家重点实验室长春130023

采用全活化空间自洽场方法(CASSCF)在C2v对称性和6-31g(d,p)基组水平下,研究了C6H5N自由基及其阴阳离子的基态和低激发态性质.为了进一步考察动态电子相关效应,采用多组态二级微扰理论(CASPT2)获得更加精确的能量值.计算得到13A2→13A1... 详细信息

采用全活化空间自洽场方法(CASSCF)在C2v对称性和6-31g(d,p)基组水平下,研究了C6H5N自由基及其阴阳离子的基态和低激发态性质.为了进一步考察动态电子相关效应,采用多组态二级微扰理论(CASPT2)获得更加精确的能量值.计算得到13A2→13A1和13A2→13B2在4303.1和4212.2kJ/mol处的激发可分别归因于π(b1)→ny和π(a2)→ny的跃迁,而13A2→13B1和13A2→11B1在2634.9和2700.4kJ/mol处的激发具有nx→π*(a2)和π(a2)→nx的混合跃迁特征,理论波长与紫外吸收光谱得到的实验数据一致.计算得到的电离能与实验值也非常接近.

关键词：苯基氮多组态自洽场理论多组态二级微扰理论光电子能谱

细胞色素p450 2s1(CYP2s1)三维结构模建及其与维甲酸分子的对接研究

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高等学校化学学报 2005年第4期26卷 689-692页

作者：孙苗李泽生张媛郑清川孙家锺吉林大学理论化学研究所理论化学计算国家重点实验室长春130023

利用同源模建和分子动力学模拟,模建了细胞色素P450(CYP2s1)的三维结构.在模建结构的基础上,分析了活性位点的组成和结构,并进行了与小分子(维甲酸)的分子对接研究.研究结果表明,在由维甲酸和CYP2s1形成的复合物中,非键相互作用较强,其... 详细信息

利用同源模建和分子动力学模拟,模建了细胞色素P450(CYP2s1)的三维结构.在模建结构的基础上,分析了活性位点的组成和结构,并进行了与小分子(维甲酸)的分子对接研究.研究结果表明,在由维甲酸和CYP2s1形成的复合物中,非键相互作用较强,其中,GLu411和Ala414是与维甲酸相互作用能最强的两个残基,对复合物的结合起重要作用.

关键词：同源模建细胞色素分子动力学

人类2-氨基3-羧基粘康酸6-半醛脱羧酶(ACMSD)与底物及抑制剂作用模型的理论研究

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高等学校化学学报 2008年第12期29卷 2398-2402页

作者：楚慧郢郑清川赵勇山张红星吉林大学理论化学研究所理论化学计算国家重点实验室长春130023

利用同源模建和分子动力学模拟方法构建了人类2-氨基3-羧基粘康酸6-半醛脱羧酶(hACMSD)的三维结构,并利用Profile-3D和Procheck等方法评估了模型的可靠性.在此基础上,用分子对接程序(Affinity),将其底物2-氨基3-羧基粘康酸6-半醛(ACMS)... 详细信息

利用同源模建和分子动力学模拟方法构建了人类2-氨基3-羧基粘康酸6-半醛脱羧酶(hACMSD)的三维结构,并利用Profile-3D和Procheck等方法评估了模型的可靠性.在此基础上,用分子对接程序(Affinity),将其底物2-氨基3-羧基粘康酸6-半醛(ACMS)和抑制剂喹啉酸(QA)分别与hACMSD进行对接,获得了复合物结构的理论模型.通过配体与受体之间相互作用能和结构分析给出了底物和抑制剂的具体结合方式,明确了hACMSD与底物和抑制剂结合时起重要作用的氨基酸残基.

关键词： 2-氨基3-羧基粘康酸6-半醛脱羧酶分子动力学模拟分子对接同源模建