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

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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

The Quantum Scattering Study for Ion-pair Formation Reaction Na+I_2→Na^+I_2^- with the LCAC-SW method

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Chinese Chemical Letters 1999年第4期10卷 325-326页

作者： Wan Yong MA Da Cheng FENG Zheng Ting CAI Cong Hao DENG(institute of theoretical chemistry, Shandong University, Jinan 250100) institute of theoretical chemistry Shandong University Jinan 250100 China

The selected-state probabilities of collinear ion-pair formation process Na+I2→Na++I2-on Aten-Laming-Los two-State potential energy surface have been calculated by using LCAC-SW method. The results show that reaction probabilities are oscillatory with collision energy; the threshold energy of this ioniZation reaction is 2.8 ev, which is in modest agreement with experimental result.

关键词： Ion-pair formation reaction probability quantum scattering LCAC-SW method

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双波长双相角结构不变量的比邻原理

物理学报 1989年第5期38卷 824-828页

作者：孙宏林张纲郭东耀吉林大学理论化学研究所

本文得到双波长双相角结构不变量一级比邻(Neighborhood)的一个严格解.对比计算及加随机误差计算表明,文献[5]的初级近似方法是简明可靠的.Hauptman做出的双相角结构不变量只与化学组成有关的结论在双波长情况实际上仍然有效.提出一个... 详细信息

本文得到双波长双相角结构不变量一级比邻(Neighborhood)的一个严格解.对比计算及加随机误差计算表明,文献[5]的初级近似方法是简明可靠的.Hauptman做出的双相角结构不变量只与化学组成有关的结论在双波长情况实际上仍然有效.提出一个快速计算方案.

关键词：双波长双相角结构不变量

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三苯基氧膦钕盐配合物的振动光谱

高等学校化学学报 1989年第11期10卷 1105-1109页

作者：梁映秋徐蔚青黄春辉吉林大学理论化学研究所北京大学化学系

本文测定了Ph_3PO、Nd(NCS)_3·4Ph_3PO、[Nd(ClO_4)_2·4Ph_3PO]^+ClO_4^-·2CH_3COCH_3以及Nd(NO_3)_3·2Ph_3PO·C_2H_5OH在4000～100 cm^(-1)区域内的FT-IR和激光Raman光谱,分析和讨论了各主要谱带的性质和配位结构.

关键词：钕配合物三苯基氧膦振动光谱

Anharmonic oscillator model of overtone spectra for D_(3h) symmetry molecules

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Chinese Journal of chemistry 1991年第4期9卷 289-296页

作者： WANG,Yi-Fei LIANG,Ying-Qiu TANG,Ao-Qing institute of theoretical chemistry,Jilin University,Changchun,130023 institute of theoretical chemistry Jilin University Changchun 130023

The bond stretching vibrations of XF_5 molecules with D_(3h)symmetry are treated computa- tionally on the Morse oscillator model in which the bond oscillators are coupled *** calculation involves four parameters for two types of Morse potential and three parameters for the kinetic-energy,potontial coupling *** eigenvalue formula for overtone and combination states up to three are presented and can be used to predict all the vibrational energylevels from local mode molecules through normal mode *** PF_5,AsF_5 and VF_5,the coupled Morse oscillator model gives a prediction in good agreement with the experimental data.

关键词： mode Anharmonic oscillator model of overtone spectra for D symmetry molecules

Transition State and Catastrophe Set

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Chemical Research in Chinese Universities 1991年第1期7卷 65-66页

作者： Fang Jianyun Tang Auchin (institute of theoretical chemistry, Jilin University, Changchun)

The study on transition states is one of the most important pathways to understand the essence of chemical reactions. With the development of femtoseeond pulse technique, Zewail et al. have carried out a number of experimental studies on the transition states, while the theoretical chemists has a great interest in the topic. In the previous

关键词： Transition state Catastrophe set State variable

Ab Initio Studies on the [Os(PR_3)_4H(H_2)]^+ System

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Chemical Research in Chinese Universities 1993年第4期9卷 339-344页

作者： LI Xue-kui and SUN Chia-zhong (institute of theoretical chemistry, Jilin University, Changchun, 130023)Keiji Morokuma (institute for Molecular Science, Myodaiji, Okazaki 444. Japan)

The [Os(PH3)4H(H2)]+ system was studied using the Gaussian 88 and the energy gradient technique at the restricted Hartree-Fock level under the effective core potential (ECP) approximation. The two different isomers of complex [Os(PH3)4H (H2)] (cis and trans) were optimized, and several orientations of the hydrogen molecule were considered for the cis isomer. When the hydride is placed in the cis position and oriented suitably, there is a strongly attractive effect between it and the molecular hydrogen.

关键词： Dihydrogen complexes Isomer Effective core potential

GRAPHICAL-DELETING METHOD FOR COMPUTING CHARACTERISTIC POLYNOMIAL OF A GRAPH

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Science in China,Ser.B 1982年第7期25卷 681-689页

作者：江元生 institute of theoretical chemistry Jilin University Changchun

By means of partition technique, a graphical-deleting method for evaluating the char-acteristic polynomial of a graph is proposed in this paper. As colloraries, the Heilbron-ner-Schwenk’s formulas are performed. In comparison with those current methods, thepresent one prevents people from dealing with a lot of subgraphs which originate in delet-ing cycles from the parent graph, thus facilitating working out the characteristic polyno-mial for a polycyclic graph. This seems true even if no topological symmetry is available.

关键词： GRAPHICAL-DELETING METHOD FOR COMPUTING CHARACTERISTIC POLYNOMIAL OF A GRAPH

Studies on the Interaction of 12-Tungstophosphoric Acid and Diethylene Glycol

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Chemical Research in Chinese Universities 1993年第4期9卷 317-323页

作者： ZHAO Yu-sheng, HUA Shi-ying , WU Tong-hao and WEI Quan (Department of chemistry, Jilin University, Changchun, 130023) Worked in institute of theoretical chemistry, Jilin University, Changchun.

The homogeneous system of 12-tungstophosphoric acid and diethylene glycol was studied using IR and NMR spectra. It was found that the protons in 12-tungstophosphoric acid formed proton oxonium ions with the hydroxyl oxygen in diethylene glycol by hydrogen-bonds, and the formed proton oxonium ions could react with the terminal oxygens of heteropoly anions. The dehydration-cyclization mechanism of diethylene glycol in the presence of heteropoly acid was also proposed.

关键词： IR NMR Diethylene glycol Proton oxonium ions