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QM/MM方法的研究 被引量:1
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作者 刘景林 曹亚杰 吴云飞 《哈尔滨师范大学自然科学学报》 CAS 2015年第6期68-71,共4页
从理论上探讨了QM/MM方法在模拟计算生物大分子体系的运用,实践表明这种方法能提高计算结果的精确性,能有效地降低计算成本.
关键词 量子力学 分子动力学 qm/mm
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HIV-1蛋白酶与抑制剂结合中桥接水分子作用的QM/MM研究 被引量:4
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作者 张玉新 张少龙 张庆刚 《山东科学》 CAS 2010年第1期1-5,共5页
对HIV-1蛋白酶与抑制剂2AH和4AH结合的两个复合物体系进行了水溶液环境下量子力学分子力学混合方法(hybrid QM/MM)的1ns分子动力学模拟,用MM-GBSA方法得到桥接水分子W301与HIV-1蛋白酶和抑制剂结合体的结合自由能分别为-24.93 kJ/mol和-... 对HIV-1蛋白酶与抑制剂2AH和4AH结合的两个复合物体系进行了水溶液环境下量子力学分子力学混合方法(hybrid QM/MM)的1ns分子动力学模拟,用MM-GBSA方法得到桥接水分子W301与HIV-1蛋白酶和抑制剂结合体的结合自由能分别为-24.93 kJ/mol和-20.29 kJ/mol,表明W301在抑制剂和HIV-1蛋白酶结合的过程中起到了不能被忽略的作用。 展开更多
关键词 HYBRID qm/mm方法 AM1方法 W301水分子 结合自由能 mm-GBSA
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W301水分子在HIV-1蛋白酶和配体ABT-538结合中作用的QM/MM研究 被引量:4
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作者 刘宝山 张少龙 张庆刚 《山东师范大学学报(自然科学版)》 CAS 2008年第4期32-34,共3页
结晶水分子W301在几乎所有的HIV-1蛋白酶(HIV-1PR)和配体的晶体结构中出现.在HIV-1PR中A链天门冬氨酸残基Asp25质子化状态或B链Asp25质子化状态下,QM/MM模拟后MM-GBSA方法计算得到W301水分子在HIV-1PR/ABT-538结合中的自由能贡献分别为-... 结晶水分子W301在几乎所有的HIV-1蛋白酶(HIV-1PR)和配体的晶体结构中出现.在HIV-1PR中A链天门冬氨酸残基Asp25质子化状态或B链Asp25质子化状态下,QM/MM模拟后MM-GBSA方法计算得到W301水分子在HIV-1PR/ABT-538结合中的自由能贡献分别为-16.88kJ/mol、-17.63kJ/mol,W301水分子在HIV-1PR/ABT-538的结合中起到了关键的作用.进一步分析发现W301水分子与HIV-1PR和ABT-538分别形成了两个、四个氢键. 展开更多
关键词 qm/mm方法 HIV-1蛋白酶 结合自由能 mm—GBSA
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抗原肽与MHC分子相互作用QM/MM分子动力学模拟研究
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作者 冯石磊 胡墅 +1 位作者 刘兵 刘伟 《化学学报》 SCIE CAS CSCD 北大核心 2013年第9期1313-1320,共8页
在MHC I类(major histocompatibility complex class I)分子抗原加工提呈过程中抗原蛋白在抗原提呈细胞(antigen-presenting cells,APC)的胞浆中被蛋白酶体(proteasome)裂解成短肽peptide,由转运相关蛋白(transporter associated with a... 在MHC I类(major histocompatibility complex class I)分子抗原加工提呈过程中抗原蛋白在抗原提呈细胞(antigen-presenting cells,APC)的胞浆中被蛋白酶体(proteasome)裂解成短肽peptide,由转运相关蛋白(transporter associated with antigen processing,TAP)将蛋白酶体裂解产生的短肽片段从胞浆转运至内质网腔.短肽peptide在内质网中与新生成的MHC I类分子结合,形成peptide-MHC复合体被提呈到APC细胞表面,与T细胞表面抗原受体(T cell receptor,TCR)特异性识别结合,使得CTL细胞开始活化、增殖、分化,进而对肿瘤细胞进行特异性杀伤.目前对CTL细胞如何识别抗原肽-MHC复合物分子及抗原短肽peptide如何与主要组织相容性复合体MHC分子的相互作用识别结合的机理还不是很清楚.传统的预测CTL细胞表位的方法没有考虑受体与配体结合过程中电子结构的变化,电子结构的变化需要用量子力学方法来处理.本文采用QM/MM多尺度生物大分子的分子动力学模拟方法,以天然抗原肽TAX(LLFGYPVYVYU)与HLA-A*0201分子结合的晶体结构为模板,替换抗原肽"锚点"氨基酸,将口袋氨基酸残基的原子极化电荷在空间形成的静电势用电多极矩分量表示.用箱线图分析每个口袋氨基酸分子静电势变化和功能,确定Pocket B的Glu63和Lys66的功能是精细识别氨基酸和一级结合氨基酸,Pocket F的Asp77,Tyr84的功能是精细识别氨基酸,而Asp77,Lys146是一级结合氨基酸,表明QM/MM方法在提取抗原肽与MHC I类分子识别结合特异性信息是可行的,这对了解免疫识别机理和指导肿瘤疫苗的开发都具有指导意义. 展开更多
关键词 qm/mm分子动力学模拟 电多极矩 T细胞表位 外源性抗原 MHC I类分子
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烟酰胺酶催化水解脱氨反应的QM/MM分子动力学模拟
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作者 段新丽 张欣 雷鸣 《高等学校化学学报》 SCIE EI CAS CSCD 北大核心 2015年第12期2491-2496,共6页
采用QM(PM3)/MM分子动力学(MD)方法模拟了烟酰胺酶催化烟酰胺水解脱氨形成烟碱酸的反应过程.计算结果表明,硫的亲核进攻是整个反应的速率控制步骤.当改变Ala155所在Loop区的位置,在亲核进攻时,底物能够自由旋转,可以加速亲核进攻过程并... 采用QM(PM3)/MM分子动力学(MD)方法模拟了烟酰胺酶催化烟酰胺水解脱氨形成烟碱酸的反应过程.计算结果表明,硫的亲核进攻是整个反应的速率控制步骤.当改变Ala155所在Loop区的位置,在亲核进攻时,底物能够自由旋转,可以加速亲核进攻过程并降低整个催化反应的能垒.讨论了氨分子的离去过程和质子传递过程的相关细节.为烟酰胺酶的定点突变以及脱氨酶的设计提供了有益的参考. 展开更多
关键词 烟酰胺酶 脱氨 反应机理 qm/mm方法 分子动力学模拟
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Infrared spectroscopy of N-methylacetamide in water from high-level QM/MM calculations 被引量:1
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作者 Zhen Yang Hao Lin +2 位作者 Tian Gui Rong-Fei Zhou Xiang-Shu Chen 《Chinese Chemical Letters》 SCIE CAS CSCD 2014年第1期107-110,共4页
The infrared (IR) spectra of the N-methylacetamide molecule in water are calculated by using the MD simulation with high-level QM]MM corrections. The B3LYP and MP2 levels with 6-31 I++G** basis set are used for ... The infrared (IR) spectra of the N-methylacetamide molecule in water are calculated by using the MD simulation with high-level QM]MM corrections. The B3LYP and MP2 levels with 6-31 I++G** basis set are used for the QM region, respectively, Our results show all IR spectra at the B3LYP level are well consistent with the corresponding MP2 results. A dynamical charge fluctuation is observed for each atom along the simulation trajectories due to the electrostatic polarization (EP) effects from surrounding solvent environment, We find that the QM/MM corrected IR spectra satisfactorily reprodnce the experimental vibrational features of amide 1-11I modes. 展开更多
关键词 Electrostatic polarization IR spectra Molecular dynamics qm/mm
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QM/MM study on the O_(2)activation reaction of 4-hydroxylphenyl pyruvate dioxygenase reveals a common mechanism forα-ketoglutarate dependent dioxygenase
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作者 Linhui Li Suitian Lai +6 位作者 Hongyan Lin Xinyun Zhao Xin Li Xi Chen Junjun Liu Guangfu Yang Changguo Zhan 《Chinese Chemical Letters》 SCIE CAS CSCD 2023年第5期461-465,共5页
The dioxygen activation catalyzed by 4-hydorxylphenyl pyruvate dioxygenase(HPPD)were reinvestigated by using hybrid quantum mechanics/molecular mechanics(QM/MM)approaches at the B3LYP/6-311++G(d,p):AMBER level.These s... The dioxygen activation catalyzed by 4-hydorxylphenyl pyruvate dioxygenase(HPPD)were reinvestigated by using hybrid quantum mechanics/molecular mechanics(QM/MM)approaches at the B3LYP/6-311++G(d,p):AMBER level.These studies showed that this reaction consisted of two steps including the dioxygen addition/decarboxylation and hetero O-O bond cleavage,where the first step was found to be rate-determining.The former step initially runs on a septet potential energy surface(PES),then switches to a quintet PES after crossing a septet/quintet minimum energy crossing point(MECP)5-7M2,whereas the rest step runs on the quintet PES.The reliability of our theoretical predictions is supported by the excellent agreement of the calculated free-energy barrier value of 16.9 kcal/mol with available experimental value of 16-17 kcal/mol.The present study challenges the widely accepted view which holds that the O2activation catalyzed byα-keto glutamate(α-KG)dioxygenase mainly runs on the quintet PES and provides new insight into the catalytic mechanism ofα-KG dioxygenase and/or other related Fe(Ⅱ)-dependent oxygenase. 展开更多
关键词 4-Hydroxylphenyl pyruvate dioxygenase O_(2)activation qm/mm Mechanism Minimum energy crossing point
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Molecular Dynamics and Combined QM/MM Studies on the Deactivation of anti-Tubercular Drug Isoniazid by Arylamine N-Acetyltransferases
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作者 乔青安 马翠华 +3 位作者 宋慧玲 蔡红兰 蔡政亭 冯大诚 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 2012年第5期683-689,共7页
Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics(QM/MM) study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylam... Both a molecule dynamic study and a combined quantum mechanics and mole-cule mechanics(QM/MM) study on the acetylating deactivation mechanism of isoniazid were presented.This type of reaction was catalyzed by arylamine N-acetyltransferases(NATs) and the results strongly support a direct acetyl group transfer process rather than a stepwise one.The isoniazid was strictly restrained in proper relative position to accept the acetyl group by a Hydrogen-bond network formed by the residues at the active center.The residues,His110 and Cys70,would be functioned as 'general base' rather than 'general acid'.If all the residues(including H2O molecules) were removed from the system,the activation energy will be increased from 145.1 to 243.3 kJ/mol.The calculations met the experimental data with good agreement. 展开更多
关键词 NATs qm/mm method deactivation of isoniazid acetyl group transfer
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QM/MM and MD Studies of the First Proton Transfer for O2 Activation in the Catalytic Cycle of Cytochrome P450cin
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作者 LIU Feng-Jiao SONG Jin-Shuai +4 位作者 LU Qian-Qian WEI Jing ZHANG Min-Yi HUANG Jing LI Chun-Sen 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 2018年第12期1907-1915,1844,共10页
P450 cin(CYP176 A1) isolated from Citrobacter braakii is a biodegradation enzyme that catalyzes the enantiospecific conversion of 1,8-cineole to(1 R)-6β-hydroxycineole. In many P450 family members the mechanism of pr... P450 cin(CYP176 A1) isolated from Citrobacter braakii is a biodegradation enzyme that catalyzes the enantiospecific conversion of 1,8-cineole to(1 R)-6β-hydroxycineole. In many P450 family members the mechanism of proton delivery for O2activation is proposed to require a conserved acid-alcohol dyad in the active area, while P450 cin has no such residue with alcohol but asparagine instead. In the present work, the mechanism of the first proton transfer of O2activation in P450 cin has been investigated by molecular dynamics(MD) and hybrid quantum mechanics/molecular mechanics(QM/MM) techniques. The MD simulation suggests there are two hydrogen bonding networks around the active site, one involving Asp241 and the other involving Glu356. According to our MD and QM/MM calculations, this Asp241 channel is proposed to be the energy accessible. MD results show that the hydrogen bonds around the substrate may contribute to regio-and stereo-oxidation of the substrate. 展开更多
关键词 P450cin CYP176A1 qm/mm proton transfer
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QM/MM Study of the Second Harmonic Generation and Two-photon Absorption Properties of a Fluorescent Proteins-Dreiklang
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作者 张敏熠 魏婧 +2 位作者 宋金帅 吴鹏 李春森 《Chinese Journal of Structural Chemistry》 SCIE CAS CSCD 2018年第9期1393-1403,共11页
A new reversibly switchable fluorescent protein(RSFP), namely Dreiklang, exhibits prominent feature that the wavelengths for switching and fluorescence are decoupled due to its great different structures between bri... A new reversibly switchable fluorescent protein(RSFP), namely Dreiklang, exhibits prominent feature that the wavelengths for switching and fluorescence are decoupled due to its great different structures between bright and dark states. This feature might also induce some nonlinear optic(NLO) properties changing as switching between two states, which might promote new method of biological science. We employ the QM/MM method to simulate the structures of different states, and study their second harmonic generation(SHG) and two-photon absorption(TPA) properties. And we found different states of Dreiklang have different SHG and TPA responses. The SHG and TPA properties of Dreiklang are correlated to particularly geometrical structures of different states, especially the centrosymmetric or nocentrosymmetric π-stacking structures which are formed by chromophore and beside residue Tyr203, so the SHG and TPA responses could be changed as the light induces switching among different states of Dreiklang. This work would prospectively guide the application of Dreiklang on the NLO technology, and help the development of new RSFP with special NLO function. 展开更多
关键词 fluorescent proteins the second harmonic generation two-photon absorption qm/mm method
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Quantifying Electronic Effects in QM and QM/MM Biomolecular Modeling with the Fukui Function 被引量:1
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作者 QI Helena W. KARELINA Maria KULIK Heather J. 《物理化学学报》 SCIE CAS CSCD 北大核心 2018年第1期81-91,共11页
Multi-scale quantum-mechanical/molecular-mechanical(QM/MM) and large-scale QM simulation provide valuable insight into enzyme mechanism and structure-property relationships. Analysis of the electron density afforded t... Multi-scale quantum-mechanical/molecular-mechanical(QM/MM) and large-scale QM simulation provide valuable insight into enzyme mechanism and structure-property relationships. Analysis of the electron density afforded through these methods can enhance our understanding of how the enzyme environment modulates reactivity at the enzyme active site. From this perspective, tools from conceptual density functional theory to interrogate electron densities can provide added insight into enzyme function. We recently introduced the highly parallelizable Fukui shift analysis(FSA) method, which identifies how frontier states of an active site are altered by the presence of an additional QM residue to identify when QM treatment of a residue is essential as a result of quantum-mechanically affecting the behavior of the active site. We now demonstrate and analyze distance and residue dependence of Fukui function shifts in pairs of residues representing different non-covalent interactions. We also show how the interpretation of the Fukui function as a measure of relative nucleophilicity provides insight into enzymes that carry out S_N2 methyl transfer. The FSA method represents a promising approach for the systematic, unbiased determination of quantum mechanical effects in enzymes and for other complex systems that necessitate multi-scale modeling. 展开更多
关键词 《物理化学学报》 期刊 编辑工作 发行工作
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QM/MM自由能模拟3-吲哚乙酸甲基转移(IAMT):催化机理和底物特异性(英文)
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作者 YAO Jian-zhuang MINTA Chaiprasongsuk +2 位作者 ZHAO Nan CHEN Feng GUO Hong 《分子科学学报》 CAS CSCD 北大核心 2013年第6期515-522,共8页
3-吲哚乙酸甲基转移(IAMT)催化甲基化植物激素3-吲哚乙酸(IAA)的端位自由羧酸,被认为在叶片发育过程中起到了至关重要的作用.然而,目前对于酶催化机理的详尽过程尚未被研究。在这里本文对拟南芥的甲基转移过程(AtIAMT1)进行结合量子力... 3-吲哚乙酸甲基转移(IAMT)催化甲基化植物激素3-吲哚乙酸(IAA)的端位自由羧酸,被认为在叶片发育过程中起到了至关重要的作用.然而,目前对于酶催化机理的详尽过程尚未被研究。在这里本文对拟南芥的甲基转移过程(AtIAMT1)进行结合量子力学和分子力学(QM/MM)的自由能模拟,并确定了其催化机制及IAMTs的底物特异性根源.研究表明,从S腺苷L甲硫氨酸(AdoMet)到3-吲哚乙酸盐(IAA)的甲基转移自由能垒要比从AdoMet到水杨酸盐的自由能垒低很多,这与之前的实验发现以及酶的底物特异性完全一致.这表明,与水杨酸相比,IAA相对高效性的甲基化是由于一部分过渡态构型的稳定性可能通过底物结合反映在反应物里,本文研究支持了之前关于计算模拟可对SABATH系列中酶的底物特异性根源进行深入理解的设想,并且可用来帮助生成可控的并具其他底物特异性的酶的实验研究. 展开更多
关键词 3-吲哚乙酸甲基 催化机理 底物特异性 qm mm
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Catalytic Mechanism of Cytochrome P450 2D6 for 4-Hydroxylation of Aripiprazole: A QM/MM Study
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作者 Rongwei Shi Weihua Li +1 位作者 Guixia Liu Yun Tang 《Chinese Journal of Chemistry》 SCIE CAS CSCD 2013年第9期1219-1227,共9页
Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 (CYP2D6) is a key enzyme for d... Drug metabolism is an important issue in drug discovery. Understanding how a drug is metabolized in the body will provide helpful information for lead optimization. Cytochrome P450 2D6 (CYP2D6) is a key enzyme for drug metabolism and responsible for the metabolism of about one third marketed drugs. Aripiprazole is an atypical an- tipsychotic and metabolized by CYP2D6 to its hydroxylated form. In this study, a series of computational methods were performed to understand how CYP2D6 accomplishes the 4-hydroxylation of aripiprazole. Molecular docking and molecular dynamics simulations were first performed to prepare the initial conformations for QM/MM calcula- tions. The results revealed two possible conformations for the drug-CYP2D6 complex. The ONIOM method for QM/MM calculations was then carried out to show detailed reaction pathways for the CYP2D6-catalyzed aripipra- zole hydroxylation reaction, which demonstrated that the dominant reactive channel was electrophilic and involved an initial attack on the n-system of the dichlorophenyl group of aripiprazole to produce cation δ-complex. Further- more, the product complex for each conformation was thermodynamically stable, which is in good agreement with previous reports. 展开更多
关键词 ARIPIPRAZOLE CYP2D6 qm/mm hydroxylation reaction ONIOM method
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QM/MM在计算DNA与配体评分函数的准确性研究
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作者 冯荣楷 刘若云 +2 位作者 陈趣汶 林凯盈 许梦莹 《计算机与应用化学》 CAS 2017年第9期669-672,共4页
目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys... 目的:评估QM/MM方法和Surflex-Dock分子对接程序对DNA-配体复合物模拟的准确性。方法:从蛋白质数据库(Protein Data Bank)下载DNA-配体复合物的三维结构,利用计算机辅助药物设计的分子对接程序Surflex-Dock模拟出147个诱饵化合物(decoys)并计算其结合分数(binding score)。然后将得出的分数与从QM/MM计算的结合能力以Z-score和辨别力(DP)作比较。从而评估Surflex-Dock和QM/MM的准确性。结果:Surflex-Dock的DPi值比QM/MM高,显示Surflex-Dock的辨别力较低。结论:因QM/MM计算速度慢,本研究认为Surflex-Dock可用作快速虚拟筛选,而较准确的QM/MM则适合用于对拥有较高结合分数的化合物进行再评分(rescoring)。 展开更多
关键词 计算机辅助药物设计 评分函数 DNA-配体 Surflex-Dock qm/mm
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丝组二肽对DNA切割作用的QM-MM研究 被引量:4
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作者 钟儒刚 赵丽娇 赵玉芬 《化学学报》 SCIE CAS CSCD 北大核心 2004年第24期2444-2446,共3页
运用QM MM方法对丝组二肽切割DNA作用的机理进行了研究 .通过计算得到了丝组二肽与DNA形成多氢键作用的有效分子识别模型及相关分子结构参数 ,从理论上解释了丝组二肽与DNA通过形成五配位磷中间体而使磷酸二酯键发生水解 ,从而使得DNA... 运用QM MM方法对丝组二肽切割DNA作用的机理进行了研究 .通过计算得到了丝组二肽与DNA形成多氢键作用的有效分子识别模型及相关分子结构参数 ,从理论上解释了丝组二肽与DNA通过形成五配位磷中间体而使磷酸二酯键发生水解 ,从而使得DNA被切断的作用机理 . 展开更多
关键词 mm DNA 二肽 生水 酯键 作用 研究 上解 配位 分子识别
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应用QM与ABEEM/MM结合的方法研究NAMI-A的结构性质
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作者 邹惠园 赵东霞 杨忠志 《化学学报》 SCIE CAS CSCD 北大核心 2013年第11期1547-1552,共6页
应用量子力学(QM)与ABEEM浮动电荷力场(ABEEM/MM)相结合的方法研究了抗癌药物NAMI-A在水溶液中的结构性质.所有的结构优化都是在DFT的B3LYP方法下采用6-31G(d,p)和LanL2DZ基组完成的,没有加入任何限制性条件.结果表明,优化得到的NAMI-A... 应用量子力学(QM)与ABEEM浮动电荷力场(ABEEM/MM)相结合的方法研究了抗癌药物NAMI-A在水溶液中的结构性质.所有的结构优化都是在DFT的B3LYP方法下采用6-31G(d,p)和LanL2DZ基组完成的,没有加入任何限制性条件.结果表明,优化得到的NAMI-A构型受不同环境及方法的影响均有变化.与气相中得到的构型相比,QM/MM迭代优化得到构型要比PCM的构型变化更明显.QM/MM(ABEEM/MM)迭代优化得到的NAMI-A构型比QM/MM(OPLS-AA)的变化要小.总之,溶剂通过极化效应对NAMI-A结构、电荷分布及径向分布函数等性质均有影响,客观地处理极化效应才能正确地反映QM区的性质. 展开更多
关键词 ABEEM mm qm qm mm NAMI-A
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Theoretical mechanism and research progress of thermally activated delayed fluorescence and room temperature phosphorescence molecules
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作者 ZHAO Xin SONG Yuzhi +2 位作者 LIN Lili WANG Chuankui FAN Jianzhong 《分子科学学报》 2024年第6期471-487,共17页
Thermally activated delayed fluorescence(TADF)and room temperature phosphorescence(RTP)molecules hold promising application prospects in the field of organic light emitting diodes(OLEDs),primarily attributed to their ... Thermally activated delayed fluorescence(TADF)and room temperature phosphorescence(RTP)molecules hold promising application prospects in the field of organic light emitting diodes(OLEDs),primarily attributed to their significant advantages in enhancing device stability and lumines-cence efficiency.Notably,TADF and RTP molecules can achieve nearly 100%exciton utilization without necessitating costly and limited precious metal elements.However,the primary challenges confronting TADF and RTP molecules at present encompass limitations in emission color,low luminescence efficien-cy,severe efficiency roll-off and so on.Given these points,this paper presents a comprehensive overview of the latest research progress in TADF and RTP molecules.We delve into the mechanisms by which TADF molecules achieve efficient fluorescence emission through unique molecular structural designs,fre-quently involving sophisticated intramolecular charge transfer processes and precise energy level modula-tion.Simultaneously,we provide an in-depth analysis of the unique luminescence properties and photo-physical mechanisms of RTP molecules.Furthermore,the article focuses on the design strategies for TADF and RTP molecules,encompassing the manipulation of molecular structures,electronic structures and the enhancement of charge transfer effects.By examining these strategies,we aim to provide a com-prehensive perspective on the research of TADF and RTP molecules.We hope that through this review,it could offer some guidance for future research and inspire the exploration of more innovative TADF and RTP molecules. 展开更多
关键词 thermally activated delayed fluorescence room temperature phosphorescence excited state property TVCF method qm/mm method
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Mechanistic insights into the conversion of flavin adenine dinucleotide(FAD)to 8-formyl FAD in formate oxidase:a combined experimental and in-silico study
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作者 Kai Wen Sirui Wang +4 位作者 Yixin Sun Mengsong Wang Yingjiu Zhang Jingxuan Zhu Quanshun Li 《Bioresources and Bioprocessing》 2024年第1期909-921,共13页
Formate oxidase(FOx),which contains 8-formyl flavin adenine dinucleotide(FAD),exhibits a distinct advantage in utilizing ambient oxygen molecules for the oxidation of formic acid compared to other glucose-methanol-cho... Formate oxidase(FOx),which contains 8-formyl flavin adenine dinucleotide(FAD),exhibits a distinct advantage in utilizing ambient oxygen molecules for the oxidation of formic acid compared to other glucose-methanol-choline(GMC)oxidoreductase enzymes that contain only the standard FAD cofactor.The FOx-mediated conversion of FAD to 8-formyl FAD results in an approximate 10-fold increase in formate oxidase activity.However,the mechanistic details underlying the autocatalytic formation of 8-formyl FAD are still not well understood,which impedes further utilization of FOx.In this study,we employ molecular dynamics simulation,QM/MM umbrella sampling simulation,enzyme activity assay,site-directed mutagenesis,and spectroscopic analysis to elucidate the oxidation mechanism of FAD to 8-formyl FAD.Our results reveal that a catalytic water molecule,rather than any catalytic amino acids,serves as a general base to deprotonate the C8 methyl group on FAD,thus facilitating the formation of a quinone-methide tautomer intermediate.An oxygen molecule subsequently oxidizes this intermediate,resulting in a C8 methyl hydroperoxide anion that is protonated and dissociated to form OHC-RP and OH−.During the oxidation of FAD to 8-formyl FAD,the energy barrier for the rate-limiting step is calculated to be 22.8 kcal/mol,which corresponds to the required 14-hour transformation time observed experimentally.Further,the elucidated oxidation mechanism reveals that the autocatalytic formation of 8-formyl FAD depends on the proximal arginine and serine residues,R87 and S94,respectively.Enzymatic activity assay validates that the mutation of R87 to lysine reduces the kcat value to 75%of the wild-type,while the mutation to histidine results in a complete loss of activity.Similarly,the mutant S94I also leads to the deactivation of enzyme.This dependency arises because the nucleophilic OH−group and the quinone-methide tautomer intermediate are stabilized through the noncovalent interaction provided by R87 and S94.These findings not only explain the mechanistic details of each reaction step but also clarify the functional role of R87 and S94 during the oxidative maturation of 8-formyl FAD,thereby providing crucial theoretical support for the development of novel flavoenzymes with enhanced redox properties. 展开更多
关键词 Formate oxidase 8-Formyl flavin adenine dinucleotide Oxidative maturation Molecular dynamics simulation qm/mm umbrella sampling simulation
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HY分子筛催化异丁烷/丁烯烷基化反应中氢负离子转移过程的模拟 被引量:4
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作者 任奎 龙军 +2 位作者 任强 李永祥 代振宇 《石油学报(石油加工)》 EI CAS CSCD 北大核心 2017年第6期1061-1071,共11页
建立了120T HY分子筛模型,应用QM/MM方法,揭示了叔/仲丁基烷氧基团(t-butyl alkoxide/s-butyl alkoxide,TBA/SBA)与异丁烷分子发生氢负离子转移反应的机理,并分析比较了二者的异同。结果表明,碳正离子是氢负离子转移反应的过渡态。与TB... 建立了120T HY分子筛模型,应用QM/MM方法,揭示了叔/仲丁基烷氧基团(t-butyl alkoxide/s-butyl alkoxide,TBA/SBA)与异丁烷分子发生氢负离子转移反应的机理,并分析比较了二者的异同。结果表明,碳正离子是氢负离子转移反应的过渡态。与TBA相比,SBA与异丁烷分子发生氢负离子转移反应的能垒高出27.5kJ/mol。这是由于TBA的C—O键长大于SBA,因而C—O键断裂所需能量更低,导致反应能垒更低。C—O键断裂后,TBA生成叔丁基碳正离子,SBA生成仲丁基碳正离子,前者中心碳原子所带电荷大于后者,因而与仲丁基碳正离子相比,叔丁基碳正离子更容易与异丁烷分子形成C—H—C"三中心两电子"结构。 展开更多
关键词 HY分子筛 烷基化 分子模拟 qm/mm 氢负离子转移反应
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理论计算中溶剂效应模型的构建及应用 被引量:2
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作者 戚传松 邓兴旺 李巍 《北京石油化工学院学报》 2006年第3期30-33,共4页
目前计算溶剂效应的方法主要有两种:一种是自洽反应场(self-consistent reactionfield,SCRF)理论计算法,该方法从发展初期至今一直应用广泛;另一类是将量子力学(quantum mechan-ics,QM)和分子力学(molecular mechanics,MM)结合起来,分... 目前计算溶剂效应的方法主要有两种:一种是自洽反应场(self-consistent reactionfield,SCRF)理论计算法,该方法从发展初期至今一直应用广泛;另一类是将量子力学(quantum mechan-ics,QM)和分子力学(molecular mechanics,MM)结合起来,分别用量子力学和分子力学来计算化合物及所在溶剂的结构与性质,这种方法近几年发展较快。笔者通过大量的文献论证了加入溶剂效应所得出的计算结果更加接近真实的实验结果这一结论。 展开更多
关键词 溶剂效应 量子化学 自洽反应场(SCRF ) qm/mm模型
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