固氮酶反应中铁蛋白与MgATP配位的化学模拟

以[Fe_4S_4(SCH_2Ph)_4]~(-2)作为氧化态铁蛋白4Fe-4S中心的模型化合物,化学模拟研究表明,ATP能与[Fe_4S_4(SCH_2Ph)_4]~(-2)原子簇结合,促进原子簇与亚甲蓝之间的氧化还原反应速率,并敏化原子簇中的Fe(Ⅱ),使其易与亚铁螯合剂反应,用正庚烧作萃取刑,在原子簇-ATP体系没有检测到游离的HSCH_2Ph,ATP没有置换原子簇中的—SCH_2Ph,这表明作为电子活化剂的ATP可能通过其磷酸根与Fe_4S_4原子簇结合。     

Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase

Membrane-bound respiratory [NiFe]-hydrogenase (MBH), a H(2)-uptake enzyme found in the periplasmic space of bacteria, catalyses the oxidation of dihydrogen: H(2)?→?2H(+)?+?2e(-) (ref. 1). In contrast to the well-studied O(2)-sensitive [NiFe]-hydrogenases (referred to as the standard enzymes), MBH has an O(2)-tolerant H(2) oxidation activity; however, the mechanism of O(2) tolerance is unclear. Here we report the crystal structures of Hydrogenovibrio marinus MBH in three different redox conditions at resolutions between 1.18 and 1.32??. We find that the proximal iron-sulphur (Fe-S) cluster of MBH has a [4Fe-3S] structure coordinated by six cysteine residues--in contrast to the [4Fe-4S] cubane structure coordinated by four cysteine residues found in the proximal Fe-S cluster of the standard enzymes--and that an amide nitrogen of the polypeptide backbone is deprotonated and additionally coordinates the cluster when chemically oxidized, thus stabilizing the superoxidized state of the cluster. The structure of MBH is very similar to that of the O(2)-sensitive standard enzymes except for the proximal Fe-S cluster. Our results give a reasonable explanation why the O(2) tolerance of MBH is attributable to the unique proximal Fe-S cluster; we propose that the cluster is not only a component of the electron transfer for the catalytic cycle, but that it also donates two electrons and one proton crucial for the appropriate reduction of O(2) in preventing the formation of an unready, inactive state of the enzyme.     

Probing the chemistry of thioredoxin catalysis with force

Thioredoxins are enzymes that catalyse disulphide bond reduction in all living organisms. Although catalysis is thought to proceed through a substitution nucleophilic bimolecular (S(N)2) reaction, the role of the enzyme in modulating this chemical reaction is unknown. Here, using single-molecule force-clamp spectroscopy, we investigate the catalytic mechanism of Escherichia coli thioredoxin (Trx). We applied mechanical force in the range of 25-600 pN to a disulphide bond substrate and monitored the reduction of these bonds by individual enzymes. We detected two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulphide bond, causing a shortening of the substrate polypeptide by 0.79 +/- 0.09 A (+/- s.e.m.), and the second elongating the substrate disulphide bond by 0.17 +/- 0.02 A (+/- s.e.m.). These results support the view that the Trx active site regulates the geometry of the participating sulphur atoms with sub-?ngstr?m precision to achieve efficient catalysis. Our results indicate that substrate conformational changes may be important in the regulation of Trx activity under conditions of oxidative stress and mechanical injury, such as those experienced in cardiovascular disease. Furthermore, single-molecule atomic force microscopy techniques, as shown here, can probe dynamic rearrangements within an enzyme's active site during catalysis that cannot be resolved with any other current structural biological technique.     

The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre

Hydrogenases are abundant enzymes that catalyse the reversible interconversion of H(2) into protons and electrons at high rates. Those hydrogenases maintaining their activity in the presence of O(2) are considered to be central to H(2)-based technologies, such as enzymatic fuel cells and for light-driven H(2) production. Despite comprehensive genetic, biochemical, electrochemical and spectroscopic investigations, the molecular background allowing a structural interpretation of how the catalytic centre is protected from irreversible inactivation by O(2) has remained unclear. Here we present the crystal structure of an O(2)-tolerant [NiFe]-hydrogenase from the aerobic H(2) oxidizer Ralstonia eutropha H16 at 1.5?? resolution. The heterodimeric enzyme consists of a large subunit harbouring the catalytic centre in the H(2)-reduced state and a small subunit containing an electron relay consisting of three different iron-sulphur clusters. The cluster proximal to the active site displays an unprecedented [4Fe-3S] structure and is coordinated by six cysteines. According to the current model, this cofactor operates as an electronic switch depending on the nature of the gas molecule approaching the active site. It serves as an electron acceptor in the course of H(2) oxidation and as an electron-delivering device upon O(2) attack at the active site. This dual function is supported by the capability of the novel iron-sulphur cluster to adopt three redox states at physiological redox potentials. The second structural feature is a network of extended water cavities that may act as a channel facilitating the removal of water produced at the [NiFe] active site. These discoveries will have an impact on the design of biological and chemical H(2)-converting catalysts that are capable of cycling H(2) in air.     

不同含硫化合物对酸性溶液中不锈钢阳极极化行为的影响

研究了不同含硫化合物对铁素体不锈钢和奥氏体不锈钢在０．５ｍｏｌ／ＬＨ２ＳＯ４溶液中阳极溶解行为的影响．结果表明，含有带孤对电子的硫原子的化合物都可以催化不锈钢的阳极溶解．然而不同含硫化合物的催化能力并不相同，对于无机含硫化合物，Ｎａ２Ｓ２Ｏ３，Ｈ２Ｓ，ＫＳＣＮ等的催化能力较强，而Ｎａ２ＳＯ３的催化能力较弱．对于有机含硫化合物，其催化能力随分子体积的增加而降低     

单水协同作用下苯丙氨酸分子的手性转变机制

基于密度泛函理论B3LYP/6\|311+G(2df)水平上的计算, 研究单水协同作用下的苯丙氨酸分子手性转变反应过程. 寻找得到反应过程中4个中间体与5个过渡态的各极值点结构, 绘制单水协同作用下完整的苯丙氨酸分子手性转变路径反应势能面, 并分析各极值点的几何与电子结构特性. 结果表明： 单水协同作用下S型苯 丙氨酸分子手性C上的H原子以羧基上的O原子为桥梁, 转移至手性C原子的另一侧, 实现了从S型到R型苯丙氨酸分子的手性转变; 单水协同作用下该路径有4个中间体和5个过渡态, 最大的反应能垒为200.588 2 kJ/mol, 来源于第四个过渡态TS₂-R-Phe&1H₂O-2.     

绿豆胰蛋白酶抑制剂和铁的配合物的研究

本文提供了一个研究蛋白质和金属配位的工作体系。用绿豆胰蛋白酶抑制剂为配体,铁为中心原子,采用三种反应体系进行配位,在最佳反应条件下,此蛋白质分子和Fe形成稳定的2Fe—2S~*簇状配合物,此配合物具有天然植物型铁氧迅蛋白的典型紫外吸收光谱,但不具有传递电子的活性。在不打开S—S键的条件下,Fe只和蛋白质分子的末端羧基有很弱的配位。     

双核Ag（Ⅰ）-8-（2-嘧啶巯甲基）喹啉配合物的合成与晶体结构（英文）

8-（2-嘧啶巯甲基）喹啉与六氟磷酸银反应生成了一个二重对称的二核银配合物,二（六氟磷酸）化双[8-（2-嘧啶巯甲基）喹啉-二（乙腈）合银]1,[Ag2（C14H11N3S）2（CH3CN）2]（PF6）2。晶体结构为四方晶系,I4（1）/a空间群,a=21.255（6）,b=21.255（6）,c=18.196（11）,α=90.00°,β=90.00°,γ=90.00°,C32H28Ag2F12N8P2S2,Mr=1 094.42,V=8 220（6）3,Z=8,Dc=1.769 g.cm-3,F（000）=4 320,μ=1.223 mm-1,R1=0.064 0,wR2=0.218 0。银中心的几何构型为变形的三角锥型,每个AgI中心与来自两个不同配体的一个喹啉氮原子与一个嘧啶氮原子、一个硫原子和一个乙腈分子的氮原子配位。AgI中心的键角范围从89.77（7）°到145.33（7）°,Ag-Ag相互作用存在配合物中。     

N2O binding at a [4Cu:2S] copper-sulphur cluster in nitrous oxide reductase

Nitrous oxide (N(2)O) is generated by natural and anthropogenic processes and has a critical role in environmental chemistry. It has an ozone-depleting potential similar to that of hydrochlorofluorocarbons as well as a global warming potential exceeding that of CO(2) 300-fold. In bacterial denitrification, N(2)O is reduced to N(2) by the copper-dependent nitrous oxide reductase (N(2)OR). This enzyme carries the mixed-valent Cu(A) centre and the unique, tetranuclear Cu(Z) site. Previous structural data were obtained with enzyme isolated in the presence of air that is catalytically inactive without prior reduction. Its Cu(Z) site was described as a [4Cu:S] centre, and the substrate-binding mode and reduction mechanism remained elusive. Here we report the structure of purple N(2)OR from Pseudomonas stutzeri, handled under the exclusion of dioxygen, and locate the substrate in N(2)O-pressurized crystals. The active Cu(Z) cluster contains two sulphur atoms, yielding a [4Cu:2S] stoichiometry; and N(2)O bound side-on at Cu(Z), in close proximity to Cu(A). With the substrate located between the two clusters, electrons are transferred directly from Cu(A) to N(2)O, which is activated by side-on binding in a specific binding pocket on the face of the [4Cu:2S] centre. These results reconcile a multitude of available biochemical data on N(2)OR that could not be explained by earlier structures, and outline a mechanistic pathway in which both metal centres and the intervening protein act in concert to achieve catalysis. This structure represents the first direct observation, to our knowledge, of N(2)O bound to its reductase, and sheds light on the functionality of metalloenzymes that activate inert small-molecule substrates. The principle of using distinct clusters for substrate activation and for reduction may be relevant for similar systems, in particular nitrogen-fixing nitrogenase.     

Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II

Oxygenic photosynthesis in plants, algae and cyanobacteria is initiated at photosystem II, a homodimeric multisubunit protein-cofactor complex embedded in the thylakoid membrane. Photosystem II captures sunlight and powers the unique photo-induced oxidation of water to atmospheric oxygen. Crystallographic investigations of cyanobacterial photosystem II have provided several medium-resolution structures (3.8 to 3.2 A) that explain the general arrangement of the protein matrix and cofactors, but do not give a full picture of the complex. Here we describe the most complete cyanobacterial photosystem II structure obtained so far, showing locations of and interactions between 20 protein subunits and 77 cofactors per monomer. Assignment of 11 beta-carotenes yields insights into electron and energy transfer and photo-protection mechanisms in the reaction centre and antenna subunits. The high number of 14 integrally bound lipids reflects the structural and functional importance of these molecules for flexibility within and assembly of photosystem II. A lipophilic pathway is proposed for the diffusion of secondary plastoquinone that transfers redox equivalents from photosystem II to the photosynthetic chain. The structure provides information about the Mn4Ca cluster, where oxidation of water takes place. Our study uncovers near-atomic details necessary to understand the processes that convert light to chemical energy.     

Synthesis,crystal structure of a novel yttrium (Ⅲ) coordination compound supported by typical plenary Dawson cluster

Asarichanddiverseclassofinorganicclustersytems,thepolyoxometalateions,whicharecharacterizedbyfascinatingstructural,electrochemical,catalytic,manetic,medicinal,andphotophysicalproperties,havebeenfoundtobeextremelyversatileinorganicbuildingblocksinthefieldsofdesigningandassemblingmolecule-basedmaterials[1].Basedoncoordinationcapabilityofthesufaceoxygenatoms(bridgingorterminaloxygenatoms)ofthepolyoxoanions,novelcomplexeswithadiscretecluter,1D,2Dor3Dstructurescanbesynthesizedthroughmetalunitsbeing…     

微生物Rieske型芳香环双加氧酶研究进展

Rieske型芳香环双加氧酶是含有Rieske[2Fe-2S]中心的多组分酶系统,能够催化多种反应,在有机污染物生物降解和化学品绿色合成领域具有广阔的开发应用前景。Rieske型芳香环双加氧酶依靠还原酶、铁硫还原蛋白及末端氧化酶的铁硫中心进行电子传递,利用氧气实现芳香烃类化合物的立体选择性羟化双加氧反应。该类酶具有广泛的底物谱、高度立体选择性等特点,在芳香族污染物降解、环境微生物修复以及手性化合物合成等方面发挥重要作用,是现代生物催化理论与应用热点研究对象之一。本文总结了微生物Rieske型芳香环双加氧酶的结构组成、催化机制和实际应用等方面的研究进展,以期为相关研究工作提供参考资料。     

Co[(C2H5O)2PS2]2(C12H8N2)的合成和晶体结构

为研究二烃基二硫代磷酸酯合过渡金属配合物与氮碱加合物的性能,合成了二乙基二硫代磷酸酯合钴(Ⅲ)配合物,利用其与邻菲咯啉的加合反应,得到了Co[(C2H5O)2PS2]2(C12H8N2)配合物并测定了它的晶体结构．Co(Ⅱ)与2个二硫代磷酸酯的4个硫原子和邻菲咯啉分子中的2个氮原子形成六配位的八面体结构,二硫代磷酸酯分子中的磷原子与2个硫原子2个氧原子形成四面体的结构．     

超低硫钢精炼工艺

在感应炉上进行了一系列对比实验,研究结果表明：顶渣＋喂线工艺比完全顶渣工艺具有更快的脱硫效果,含ＢａＯ精炼渣系比传统的ＣａＯ－ＣａＦ２渣系具有更强的脱硫能力;当钢中氧和硫都很低时,ＣａＳｉ合金能起到显著的深脱硫作用,由研究结果得出超低硫钢（ｗｓ〈０．００１０％）钢液精炼的主要工艺参数。     

由NBS引发的MMA的室温电子活化再生原子转移自由基聚合(AGET ATRP)

以N-溴代丁二酰亚胺(NBS)为引发剂、CuBr2/五甲基二亚乙基三胺(PMDETA)络合体系为催化剂、辛酸亚锡(Sn(EH)2)为还原剂、苯甲醚为溶剂,在室温(25℃)条件下实现了对甲基丙烯酸甲酯(MMA)的电子活化再生原子转移自由基聚合(AGET ATRP)。研究了反应温度、溶剂、单体及引发剂用量等因素对反应的影响。聚合过程中数均分子量随单体转化率提高而线性增长,得到的聚合物分子量分布指数(PDI)在1.15~1.31之间。进行了扩链以进一步验证聚合具有活性特征。     

非限域单体天冬酰胺分子的手性转变机制

基于密度泛函理论B3LYP,在6-311+G(2df)基组水平上研究非限域单体天冬酰胺(Asn)分子手性转变第二反应通道过程,寻找反应过程中各极值点结构,绘制完整的Asn分子手性转变路径反应势能面,并分析各极值点的几何和电子结构特性.结果表明:S型Asn分子手性C原子上的4H原子以羧基上的10O原子为桥梁,转移至手性C原子的另一侧,实现从S型到R型Asn分子的手性转变;该路径有2个中间体和3个过渡态,最大的反应能垒为313.222 1kJ/mol.     

苯并[1，2-b：4，5-b’]二噻吩-thieno[3，4-易]thiadiazole导电性的理论研究

采用密度泛函理论，在B3LYP／6—31G（d）水平下，对苯并[1，2-b：4，5-b’]二噻吩（BDT）-thieno[3，4-b]thiadiaz01e（TD）的低聚物和聚合物进行了理论计算．其中，BDT为电子供体，TD为电子受体，以1：2的方式结合形成化合物，并计算了二面角、分子内的电荷传输、桥键键长和中心键电荷密度．结果显示：随着聚合链增长，共轭程度增加．NICSs值显示：中心环比边环的共轭程度更大．聚合物的能带结构表明：该聚合物的带隙比较低（0．87eV），故其可以作为潜在的导电材料．     

Al含量对Fe-Al合金中微观缺陷和价电子密度的影响

测量Ｆｅ２８Ａｌ和Ｆｅ４０Ａｌ合金的正电子寿命谱参数,计算合金基体和缺陷处的价电子密度。Ｆｅ２８Ａｌ和Ｆｅ４０Ａｌ合金基体的价电子密度（ｎｂ）分别为４１０×１０－２ａｕ和２３６×１０－２ａｕ,表明当Ａｌ和Ｆｅ结合形成Ｆｅ２８Ａｌ或Ｆｅ４０Ａｌ合金时,Ａｌ原子提供价电子与Ｆｅ原子的３ｄ电子形成局域的共价键,Ｆｅ２８Ａｌ和Ｆｅ４０Ａｌ合金中金属键和共价键共存。两种合金均有开空间大的缺陷,晶界缺陷处价电子密度（ｎｄ）〔１３２×１０－３ａｕ（Ｆｅ２８Ａｌ）,４７０×１０－３ａｕ（Ｆｅ４０Ａｌ）〕比基体的低,表明晶界处的键合力较弱。Ｆｅ４０Ａｌ合金晶界缺陷的开空间比Ｆｅ２８Ａｌ的大。     

Co-Fe-B非晶态合金成键及电子性质的DFT研究

利用密度泛函理论(DFT),通过团簇Co2FeB2,CoFe2B2的优化和计算,研究Co-Fe-B非晶态合金成键及电子性质.结果表明:团簇Co2FeB2(富Co)中主要的电子流向为B→Co,B→Fe,而团簇CoFe2B2(富Fe)电子流向多样化,这导致富Co合金中键级比例分布不均匀,而富Fe合金中键级比例相对均匀;另外,金属与B原子成键对合金稳定性的贡献最大,而两种团簇的M(max)-B与Co-Fe键协同作用相反:富Co团簇中Co-B与Co-Fe成键强度同增同长,而富Fe团簇中Fe-B与Co-Fe成键强度相互抑制.以上结论在一定程度上解释了富Co合金热稳定性差的现象.另外,B原子使富Fe团簇空间结构、成键以及电子流动方向更加复杂,使合金非晶态化增加.Co-Fe-B非晶态合金中存在B原子之间近距离接触,希望此结论不久后得到实验验证.     

O_2在Pd_2@Au/Pd(100)表面上分解机理研究

采用密度泛函理论,在slab模型下,研究了O2分子在Pd2@Au/Pd(100)表面上的吸附与分解.结果表明:O2分子优先吸附于Pd-Pd桥位,O-O键轴平行于表面.O2分子通过其3σg和1πu轨道向表面转移电荷,又通过其1πg轨道接受来自表面的电子,净的结果是每个O原子得到了0.22e.合金表面暴露出来的Pd二聚体团簇为催化分解O2的活性中心.O2分子在Pd2@Au/Pd(100)表面上分解时,首先需要在扩散中断裂O-O键,然后经过一系列O原子的扩散过程,达到稳定的产物结构.