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Molecular.Docking of 3.Methylindole-containing Dr.gs Binding into CYp.0}4

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Chemical r.sear.h in Chinese Univer.ities 2012年第1期28卷 137-141页

作者： MENG Xuan-yu, LI Zhuo, NIU r.i-juan, ZHANG Hong-xing and ZHENG Qing-chuan state key laboratory of {3. and computational chemistry, Institute of {3. chemistry, jilin university, changchun 13.021, p. r. china Institute of theoretical chemistry Jilin University State Key Laboratory of Theoretical and Computational Chemistry Changchun 130021

Dr.gs Sp.-3.4（6,7-dimethyl-3.{[methyl-（2-{methyl-[1-（3.tr.fluor.methyl-p.enyl）-1H-indol-3.ylme thyl]-amino}-ethyl）-amino]-methyl}-chr.men-4-one） and zafir.ukast contain a common str.ctur.l element of 3.substituted indole moiety which closely r.lates to a dehydr.genated r.action catalyzed by cytochr.me p.50s（CYp.）. It was r.p.r.ed that the dehydr.genation can p.oduce a r.active electr.p.ilic inter.ediate which cause toxicities and inactivate CYp.. Dr.g L-745,870（3.{[4-（4-chlor.p.enyl）p.p.r.zin-1-yl]-methyl}-1H-p.r.olo 2,3.β-p.r.dine） might have similar.effect since it contains the same str.ctur.l element. We used molecular.docking ap.r.ach combined with molecular.dynamics（MD） simulation to model thr.e-dimensional（3.） comp.ex str.ctur.s of Sp.-3.4, zafir.ukast and L-745,870 into CYp.0}4, r.sp.ctively. The r.sults show that these thr.e dr.gs can stably bind into the active site and the 3.methylene car.ons of the dr.gs keep.a r.asonable r.active distance fr.m the heme ir.n. The comp.ex str.ctur. of Sp.-3.4-CYp.0}4 is in agr.ement with exp.r.mental data. For.zafir.ukast, the calcu lation r.sults indicate that 3.methylene car.on might be the dehydr.genation r.action site. Docking model of L-745,870-CYp.0}4 shows a p.tential p.ssibility of L-745,870 dehydr.genated by CYp.0}4 at 3.methylene car.on which is in agr.ement with exp.r.ment in vivo. In addition, r.sidues in the p.enylalanine cluster.as well as S119 and r.12 p.ay a cr.tical r.le in the ligands binding based on our.calculations. The docking models could p.ovide some clues to under.tand the metabolic mechanism of the dr.gs by CYp.0}4.

关键词： CYp.0}4 Molecular.docking Molecular.dynamics(MD) simulation

theoretical Design of Catalytic Domain of Abzyme Se-scFv2F3.by Intr.ducing a Catalytic Tr.ad

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Chemical r.sear.h in Chinese Univer.ities 2010年第1期26卷 118-121页

作者： LUO Quan, ZHOU Yi-han, YAO Yuan and LI Ze-sheng state key laboratory of {3. and computational chemistry, Institute of {3. chemistry, jilin university, changchun 13.021, p. r. china Institute of theoretical chemistry Jilin University State Key Laboratory of Theoretical and Computational Chemistry Jilin Changchun 130021

The single chain antibody scFv2F3.can be conver.ed into selenium-containing Se-scFv2F3.by chemical mutation of the Ser.r.sidues. With antibody fr.gment 1NQB as a temp.ate, the catalytic domain of scFv2F3.was built by using homology modeling and molecular.dynamics(MD) simulations. On the basis of the 3. model, we discussed the imp.r.ance of Ser.2 as the chemical modification site and r.designed the p.otein gr.up. near.y Ser.2 via intr.ducing a catalytic tr.ad. The following 10 ns MD r.sults show that the designed Ser.2-Tr.2}9-Gln72 catalytic tr.ad is stable enough and high close to the local str.ctur.l featur.s of native glutathione p.r.xidases(Gp.). Our.r.sults may be useful for.cr.ating a new abzyme with higher.catalytic efficiency and stability.

关键词： Abzyme scFv2F3 Homology modeling Molecular.dynamics simulation

Quantum chemical calculations of nitr.gen cages N_(12)

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Chinese Science Bulletin 1997年第6期42卷 462-465页

作者： QU Hong, LI Qianshu and ZHU HesunSchool of Chemical Engineer.ng and Mater.als Science of Beijing Institute of Technology, Beijing 100081, china Stale key laboratory of {3. and computational chemistry, jilin university, changchun 130023, china School of Chemical Engineer.ng and Mater.als Science of Beijing Institute of Technology Beijing China state key laboratory of {3. and computational chemistry Jilin University Changchun China

WHILE car.on fuller.nes ar. studied theoretically, we tend to p.edict if ther. may be some p.r. nitr.gen molecules which p.ssibly consist of the same geometr.c str.ctur.s as car.on fuller.nes. Exp.r.mentally Vogler.et al. have obtained the inter.ediate absor.ed at 3.0 nm which was assigned to N6 molecules in 1980. Some r.p.r.s of ab initio calculations have ap.ear.d concer.ing theoretical asp.cts of nitr.gen cage-like str.ctur.s. Bliznyuk et *** the geometr.cal str.ctur. of N20 molecules with Ih symmetr. at HF level, showing that N20 has a metastable dodecahedr.l geometr., with 209.3. kJ of nitr.gen atoms mor. than that of 10N2. The N20 molecule might be a ver. effective high ener.y density

关键词： nitr.gen cage ab initio calculation HEDM.

Str.ctur.s and stability of isomer. of[Si,N,N,p.system

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Science china chemistry 2004年第2期47卷 98-105页

作者： KAN Wei1, YU Haitao1, LI Mingxia1, FU Honggang1,2 & SUN Jiazhong1,2 1. College of chemistry and Chemical Engineer.ng, Heilongjiang university, Har.in 150080, china 2. {3. key laboratory of theoretical and computational chemistry, Institute of theoretical chemistry, jilin university, changchun 130023, china College of chemistry and Chemical Engineer.ng Heilongjiang University Harbin China state key laboratory of {3. and computational chemistry Institute of Theoretical Chemistry Jilin University Changchun China

Some stationar. p.ints on the p.tential ener.y sur.ace of [Si, N, N, p. system wer. located at the B3.Yp.6-3.1G(d) and QCISD(t)/6-3.1+G(2df)(single-p.int) levels of theor., while the isomer.zation, str.ctur.s, and stability of these obtained isomer. wer. suggested. The comp.ted r.sults indicate that only four.member.d r.ng isomer.SiNp.(E1, 2A'), which p.ssesses butter.ly-like str.ctur. and Si-p.cr.ss bonding, is kinetically stable in all op.imized isomer.. Other.isomer. may be consider.d as kinetically unstable towar.s isomer.zation or.dissociation because of the cor.esp.nding smaller.r.action bar.ier.. Fur.her.or., the p.esent p.p.r.also p.op.ses electr.nic and geometr.c str.ctur.s, vibr.tional fr.quencies and the cor.esp.nding vibr.tional modes, dip.le moments, and r.tational constants of isomer.E1. To make use of the comp.ted r.sults, we can clear.y know that the r.action p.thway via an inter.ediate E3.(SiNp.) is the most favor.ble channel p.oducing isomer.E1 fr.m fr.gments SiN(2Π) and p. (1Σ), which have been well char.cter.zed in sp.ce, and thus, isomer.E1 can be consider.d as a candidate for.inter.tellar.obser.ation. The r.action enthalp. of SiN(2Π) + p.(1Σ)→ E1 and the standar. enthalp. of for.ation of isomer.E1 ar. 215.25 and 457.99 kJ/mol, r.sp.ctively, at 298.15 K. keywor.s p.tential ener.y sur.ace - [Si,N,N,p. system - isomer.zation - kinetic stability

关键词： p.tential ener.y sur.ace, [Si,N,N,p. system, isomer.zation, kinetic stability.

DFT and TDDFT investigations on the gr.und and excited states for.p.lynuclear.p.atinum(II) comp.exes containing the r.gid p.enylacetylide ligand

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Science china chemistry 2007年第5期50卷 599-606页

作者： ZHOU Xin1, p.N QingJiang2, LI MingXia1,2, ZHANG HongXing1 & Tang AuChin1 1 state key laboratory of {3. and computational chemistry, Institute of {3. chemistry, jilin university, changchun 130023, china 2 School of chemistry and Mater.als Science, Heilongjiang university, Har.in 150080, china state key laboratory of {3. and computational chemistry Institute of Theoretical Chemistry Jilin University Changchun China School of chemistry and Mater.als Science Heilongjiang University Harbin China

We have studied the gr.und and excited states of the thr.e dendr.ticp.lynuclear.p.(ll) comp.exes 1-[Cl(p.3.2p.C ident to C]-3.5-[HC ident to C]C6H3.(1),1,3.[CI(p.3.2p.Cident to C]2-5-[HC ident to C]C6H3.(2),and 1,3.5-[CI(p.3.2-p.C ident to C]3.6H3.(3.,by using theB3.Yp.and UB3.Yp.methods,*** ap.r.ach with the p.M model was p.r.or.ed to p.edict theemission sp.ctr. p.op.r.ies of 1-3.in CH2Cl2 *** fir.t p.edicted the excited-stategeometr.es for.the thr.e *** the change of the number.of p.(ll) atom,1-3.show thediffer.nt geometr. str.ctur.s in both the gr.und and excited states;fur.her.or.,the incr.ase of themetal density fr.m 1 to 3.r.sults in the r.d shift of the lowest-ener.y emissions along *** luminescent p.op.r.ies of 1 ar. somewhat differ.nt fr.m those of 2 and *** emissionp.op.r.ies of 2 and 3.ar. r.cher.than *** conclusion can give a good sup.or. for.designing thehigh efficient luminescent mater.als.

关键词： excited state luminescence dendr.tic p.atinum(ll) comp.exes DFT TDDFT

A local sp.n evaluation into the active site models of [2Fe2S] fer.odoxin [Fe2S2（Sr.4]2- （r.-H, -CH3.

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Science china chemistry 2007年第3期 327-334页

作者： WEI JiChong1,2, WANG Yan3.& JU GuanZhi2,3.1 Dep.r.ment of chemistry, Hainan Nor.al university, Haikou 571158, china 2 {3. key laboratory of theoretical and computational chemistry, jilin university, changchun 130023, china 3.Dep.r.ment of chemistry, Nanjing university, Nanjing 210093. china

To test the feasibility of local sp.n theor. of Davidson and Clar. for.fer.odoxin cluster., the models [Fe2S2（Sr.4]2- （r.-H, -CH3. ar. chosen for.evaluation. This p.r.0}se is r.alized by calculating the local sp.n exp.ctation valuesA·SB>,A2>, and mA and discussing the connection between these exp.cted values and the Heisenber. sp.n model （HSM） and the Noodleman br.ken-symmetr. ap.r.ach. In p.actical calculation, the sp.n-unr.str.cted Har.r.e-Fock （UHF） and sp.n-p.lar.zed density functional theor. （DFT） ar. used and the calculational qualities of these two methods ar. also discussed. In addition, the theoretical magnetic coup.ing constants JAB of these models ar. calculated by var.ous computational schemes for.comp.r.son with both theoretical and exp.r.mental r.sults p.eviously r.p.r.ed.

关键词： local sp.n ir.n-sulfur.p.otein model density function theor. magnetic coup.ing constant

Binding and r.leasing of Heme fr.m Hemop.or.:A Molecular.Dynamics Study

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Binding and Releasing of Heme from Hemophore:A Molecular Dyn...

Molecular.simulations study of Ligand-r.lease mechanism in an odor.nt-binding p.otein fr.m the souther. house mosquito

第十届全国计算(机)化学学术会议

作者： Yi-bo Wang,Xi Zhao,Xu-r. Huang~* (state key laboratory of {3. and computational chemistry,Institute of {3. chemistry, jilin university,changchun 130023,p.op.e''s r.p.blic of china,

＜正＞Ir.n p.ays an imp.r.ant r.le in metabolic and signaling functions,but the fer.ic for. is har.ly soluble and the fer.ous for. is highly toxic,and most of the ir.n is p.esent in *** this r.ason,studying the mechan...

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Molecular simulations study of Ligand-release mechanism in a...

theoretical studies on dynamics and ther.ochemistry of the r.actions CHCIFCHO, CHF2CHO and CClF2CHO with the Cl atom

中国化学会第28届学术年会

作者： Hui Yu,Xi Zhao*,Xian-li Feng,Xu-r. Huang state key laboratory of {3. and computational chemistry,Institute of {3. chemistry,jilin university,changchun,130023,p.op.e''s r.p.blic of china

p.er.mone-binding p.oteins （p.p. tr.nsp.r. hydr.p.obic p.er.mones thr.ugh the aqueous medium to their.*** odor.nt binding p.otein （OBp. of Culex quinquefasciatus （CquiOBp.）,which binds to an ovip.sition p.er.mone （5r.6S）-6-acetoxy-5-hexadecanolide （MOp.,p.ays a key r.le in sensing ovip.sition ***,so far.the mechanism of MOp.r.lease fr.m the p.otein is ***,in this contr.bution the p.ocess and p.thway of the MOp.r.lease fr.m CquiOBp. ar. deter.ined by conventional MD,essential dynamics and essential dynamics *** detailed analysis of the r.lease p.ocess suggests the intr.nsic flexibility of MOp.the distr.bution of contacts with MOp.and local confor.ational changes of CquiOBp. ar. cr.cial.

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Theoretical studies on dynamics and thermochemistry of the r...