铜锌金属天然酶活性中心量子化学计算

以菠菜叶中天然超氧化物歧化酶（SOD）铜锌活性中心及人为去掉金属锌的活 性中心为模板，运用Gaussian 94量子化学程序，在B3LYP/LANL2DZ基组水平上进行 了计算，获得了分子轨道能量、电荷分布以及原子轨道对前沿分子轨道贡献的信息 。结果表明，金属铜对于催化歧化超氧阴离子O_2~-具有至关重要的作用，而金属 锌起到稳定结构和促成构建活性中心的作用。     

Molecular Structures and Magnetic Properties of Strongly Antiferromagnetically Coupled Binuclear Copper(II) Complexes [CU2 REP(μ-X)(Y)2]

The molecular structures of binuclear copper(II) complexes [Cu₂REP(μ-OH)(ClO₄)₂] (4) and [Cu₂REP(μ-Cl)Cl₂] (5), in which REP = deprotonated 2,6-bis(1′-(4′-(2″-pyridyl)-2′-thiabutyl))-4-methylphenol, have been characterized by single-crystal X-ray diffraction. The former crystallizes in the triclinic space group Pl? with a = 10.156(3), b = 12.631(3), c = 25.128(10) Å, α = 92.03(3), β = 96.84(3), γ = 108.02(2),° and Z ? 2. Complex 5 crystallizes in the monoclinic space group C2/c with a = 12.166(2), b = 11.825(2), c = 18.240(4) Å, β = 100.97(2)°, and Z =4. All copper ions are pentacoordinated with ligation to a sulfur, a nitrogen, and the bridging phenolato oxygen of the REP ligand, the exogenous bridge, and a counteranion. The coordination geometry of each copper of the binuclear copper sites is square pyramidal in both 4 and 5. Magnetic susceptibility measurements in the temperature range 6–300 K reveal a strong antiferromagnetic spin exchange in 5 (exchange integral 2J = ?460 cm^?1). A diamagnetic behavior is observed for 4 according to a similar cryomagnetic investigation. The diamagnetism of 4 is further confirmed by measurements of magnetic susceptibility through Evan's method at room temperature. Complex 4 has no EPR signal. The powder EPR spectrum of 5 shows the typical triplet state characteristics with Δm = ±1 transitions at g = 2.15 and a weaker Δm = 2 transition at half field with g = 4.24.     

Recent Insights into Cu-Based Catalytic Sites for the Direct Conversion of Methane to Methanol

Direct conversion of methane to methanol is an effective and practical process to improve the efficiency of natural gas utilization. Copper (Cu)-based catalysts have attracted great research attention, due to their unique ability to selectively catalyze the partial oxidation of methane to methanol at relatively low temperatures. In recent decades, many different catalysts have been studied to achieve a high conversion of methane to methanol, including the Cu-based enzymes, Cu-zeolites, Cu-MOFs (metal-organic frameworks) and Cu-oxides. In this mini review, we will detail the obtained evidence on the exact state of the active Cu sites on these various catalysts, which have arisen from the most recently developed techniques and the results of DFT calculations. We aim to establish the structure–performance relationship in terms of the properties of these materials and their catalytic functionalities, and also discuss the unresolved questions in the direct conversion of methane to methanol reactions. Finally, we hope to offer some suggestions and strategies for guiding the practical applications regarding the catalyst design and engineering for a high methanol yield in the methane oxidation reaction.     

簇合物中锥形四重桥硫3d轨道成键的EHMO研究

运用EHMO方法对四个[M_4S_2]（M＝Co，Nb）型簇合物的电子结构进行了计算，通过对硫原子3d轨道引入前后体系总能量、轨道能级、电荷分布和Mulliken键级等性质的比较，发现簇合物中锥形四重桥硫原子的3d轨道参与了成键，对稳定[M_4S_2]结构单元有重要的作用．     

UV/VIS Spectral Studies of Catecholase Activity of Binuclear Copper(II) Complexes [Cu2REP(μ-X)(Y)2]

By means of ultraviolet and visible spectroscopy we have studied the catecholase activity of two binuclear copper(II) complexes of general formula [Cu₂REP(u-X)(Y)₂] (1, X=OH and Y=ClO₄; 2, X=Y=CI), REP =deprotonated 2, 6-bis(1′-(4′-(2″-pyridyl)-2′-thiabutyl))-4-methylphenol. Both complexes promote catalytic autoxidation of 3, 5-di-tert-butylcatechol (3, 5-DTBC) to 3, 5-di-tert-butylquinone (3, 5-DTBQ) in methanol, but not in acetonitrile.     

基于复小波能量谱的蛋白质活性位点识别新方法

蛋白质活性位点的识别对于理解蛋白质的功能及计算机辅助药物设计具有重要的意义. 基于复小波能量谱建立蛋白质活性位点识别新方法, 采用Morlet复小波对数字化的蛋白质序列进行一维连续小波变换. 结果表明, 通过时-频分析, 能量集中区域往往与蛋白质的活性位点具有密切联系, 并且同源蛋白质序列的复小波能量最大值通常分布于相同的频率处, 表明小波功率谱在预测蛋白质活性位点方面具有广阔的应用前景.     

铁超氧化物歧化酶活性中心结构研究

对氧化型、还原型及非活性形式铁超氧化物歧化酶Fe-SOD活性中心进行了量子化学计算和比较。在HF方法及LANL2DZ基组水平上获得了分子轨道能量、电荷分布以及原子轨道对前沿分子轨道贡献的信息。结果表明, Fe-SOD酶的活性形式的活性中心易于接受超氧自由基(O2- )的进攻而完成其生理功能。     

Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

Particulate methane monooxygenase (pMMO) is one of the few enzymes that can activate methane. The metal content of this enzyme has been highly controversial, with suggestions of a dinuclear Fe site or mono‐, di‐, or trinuclear Cu sites. Crystal structures have shown a mono‐ or dinuclear Cu site, but the resolution was low and the geometry of the dinuclear site unusual. We have employed quantum refinement (crystallographic refinement enhanced with quantum‐mechanical calculations) to improve the structure of the active site. We compared a number of different mono‐ and dinuclear geometries, in some cases enhanced with more protein ligands or one or two water molecules, to determine which structure fits two sets of crystallographic raw data best. In all cases, the best results were obtained with mononuclear Cu sites, occasionally with an extra water molecule. Thus, we conclude that there is no crystallographic support for a dinuclear Cu site in pMMO.     

多功能光学活性丁二醇衍生物的合成和结构

通过新的合成策略,以手性合成子3和具有生物活性的有机碱类化合物4为反应底物,利用Michael不对称加成反应,合成得到光学纯的5-(R)-［(1R,2S,5R)-(-)-氧基］-4-(R)-(杂环碱基)-2(5H)-呋喃酮(5). 加成物5通过还原反应得到了多功能光学活性的二醇类化合物6,产率为42%~82%,e.e.≥98%. 化合物6的化学结构得到了确认,其立体化学结构和绝对构型经X射线晶体学测定得到了确定.     

双原子位点M-N-C电催化剂在CO2还原反应中活性位点的最佳分布

双原子位点M-N-C催化剂是催化CO₂还原反应(CO₂RR)性能最佳的催化剂之一. 然而, 目前的研究主要集中于M-N-C活性中心原子类型的调控, 低估了活性位点的配位模式及分布对其催化性能的影响. 本文选取典型的双原子位点M-N-C催化剂(NiFe-N-C)为研究对象, 采用密度泛函理论方法探究了9种活性位点具有不同配位环境的NiFe-N-C催化剂电催化CO₂RR的反应机理. 结果表明, 随着金属原子配位数、 双原子位点间距离的增加, M-N-C催化剂的稳定性、 催化CO₂还原至CO的活性及抑制氢析出反应的选择性均呈现先升高后下降的趋势. 其中, 金属原子四配位且对称分布的NiFe-N-C-model 3催化剂, 因其双原子位点的强相互作用表现出最优的催化性能.     

Electronic Structures of Mono-and Bi-nuclear Benzene-Transition Metal Sandwich Complexes

We report here the calculations on electronic structures of mono- and bi-nuclear benzene - transition metal sandwich complexes by means of CNDO/2 program, on the basis of molecular orbital components, atomic net charges and bond orders, the bonding pictures are analysed and discussed.     

化学修饰法表征Bacillus smithii T7产耐热菊粉酶催化活性中心的必需氨基酸残基

采用化学修饰法研究了史氏芽胞杆菌Bacillus smithiiT7产耐热菊粉酶活性中心氨基酸残基,发现该酶活性中心存在一个组氨酸残基和一个谷氨酸(或天冬氨酸)残基.修饰前后的酶动力学参数变化表明组氨酸残基参与了底物的结合和催化过程,而谷氨酸(或天冬氨酸)的羧基亲核攻击促使底物分解.邹氏作图法证明酶活性中心存在两个必需的色氨酸残基,荧光和圆二色光谱研究表明色氨酸残基在酶的催化和酶的耐热性方面起重要作用.     

烯醇式异桥双铜配合物的合成及磁交换作用的研究

合成了２个异桥双铜配合物：［Ｃｕ２（ｐｆｈｍｐ）Ｂｒ］·２Ｈ２Ｏ（１）和［Ｃｕ２（ｐｆｈｍｐ）Ｃ３Ｈ３Ｎ２］·２Ｈ２Ｏ（２），经元素分析、红外及摩尔电导等手段推知两配合物均为烯醇式构型。变温磁化率测定结果表明，由于外源桥的影响，铜离子间的反铁磁相互作用有明显差别。     

高分散隔离活性位催化剂中过渡金属离子结构对丙烷选择氧化反应性能的影响

考察了碱金属K修饰的SiO2负载极低含量过渡金属的高分散隔离活性位系列催化剂(K-M/SiO2(n(K)∶n(M)∶n(Si)=10∶1∶1000),M=V,Cr,Mn,Fe,Co,Ni,Cu,Zn)的丙烷选择氧化催化性能,并运用UV-Raman和CO2-TPD等方法,对该系列催化剂进行了结构和物化性能表征,探讨了催化剂的表面离子结构与催化反应性能之间的关系。 发现钾修饰的SiO2负载过渡金属高分散隔离活性位催化剂上过渡金属离子的组态结构,对丙烷选择氧化反应性能有重要影响。相对稳定的全充满或无d电子的表面离子结构有利于选择氧化反应进行,而存在多种价态的相对不稳定的离子结构有利于深度氧化的进行。 这一离子结构与丙烷选择氧化催化性能的关系与前期乙烷选择氧化规律相似,进一步说明在高分散隔离活性位催化剂中,过渡金属离子的电子组态结构是影响低碳烷烃选择氧化反应性能的最重要因素。     

新型异桥烯醇式双铜配合物的合成及磁交换作用的研究

合成了2个含不同外源桥基的双铜配合物[Cu_2(pfhmp)OH]·2H_2O和[Cu_2(pfhmp)N_3]·H_2O,pfhmp~(3-)表明N,N′-二异烟酰基-2-羧基-4-甲基-1,3-苯二甲醛双腙的脱氢阴离子。经元素分析、红外光谱、摩尔电导等手段推知两配合物均为异桥结构与烯醇式构型,变温磁化率测定表明改变外源桥基会明显改变2个铜离子之间的磁交换作用。     

Influence of the Active Site Flexibility on the Efficiency of Substrate Activation in the Active Sites of Bi-Zinc Metallo-β-Lactamases

The influence of the active site flexibility on the efficiency of catalytic reaction is studied by taking two members of metallo-β-lactamases, L1 and NDM-1, with the same substrate, imipenem. Active sites of these proteins are covered by L10 loops, and differences in their amino acid compositions affect their rigidity. A more flexible loop in the NDM-1 brings additional flexibility to the active site in the ES complex. This is pronounced in wider distributions of key interatomic distances, such as the distance of the nucleophilic attack, coordination bond lengths, and covalent bond lengths in the substrate. Substrate activation, quantified by Fukui electrophilicity index of the carbonyl carbon atom of the substrate, is also sensitive to the active site flexibility. In the tighter and more rigid L1 enzyme-substrate complex, the substrate is activated more efficiently. In the NDM-1 containing system, only one third of the states are activated to the same extent. Other fractions demonstrate lower substrate activation. Efficiency of the substrate activation and rigidity of the ES complex influence the following chemical reaction. In the more rigid L1-containing system, the reaction barrier of the first step of the reaction is lower, and the first intermediate is more stabilized compared to the NDM-1 containing system.     

卤素氮氧化物的结构和光谱性质的理论研究

通过DFT/B3LYP计算,优化了卤素氮氧化物XNO_2及其异构体XONO（X = F,Cl ,Br,I）的平衡几何构型,预测了异构体的相对稳定性及其相互转化的活化能垒 。在B3LYP和QCISD（T）计算水平上,确定了X-NO_2键的解离能。应用与时间有关 的密度泛函理论（TD-B3LYP）计算了XNO_2低激发态的跃迁能,并讨论了这些激发 态与卤素氮氧化物光诱导解离过程的关联。     

A DFT Study of the Models of the Bronsted Acid Sites of Zeolite Catalysts

A systematic study of the different cluster models of the Bronsted site has been carried out in order to predict how the local structure influences the geometric parameters of the SiO(H)Al site and the harmonic frequencies of the characteristics vibrational modes of the bridging surface hydroxyl group. The performance of the B3LYP variant of the density functional theory (DFT) method is examined and compared with both SCF HF and MP2 approximations. In order to find the best molecular model for the Bronsted site, two series of derivatives based on the prototype model cores SiO(H)Al and HAlO₄ were considered. In the HAlO₄ series, H₃SiO(H)Al(OH)₂OSiH₃ and H₃SiO(H)Al(OSiH₃)₃ were investigated. Among the models in the SiO(H)Al series were H₃SiO(H)AlH₃, H₃SiO(H)Al(OH)₃, H₂(OH)SiO(H)Al(OH)₃, (OH)₃SiO(H)Al(OH)₃, and (H₃SiO)₃SiO(H)Al(OSiH₃)₃. The research reveals that the acidic OH bond length and its stretching frequency are greatly influenced by the H bond formed between the acidic proton and its next-nearest neighbor oxygen on the aluminum atom. The geometry and the frequencies for the larger models predicted at the B3LYP/D95(d,p) level are in good agreement with the experiments, suggesting that the B3LYP/D95(d,p) theory is reliable for a study of the Bronsted site. This study also suggests that the OH terminated models are not suitable as models for the SiO(H)Al site due to the strong dipole moment of the OH group, which strongly affects the acidic H.