Crystal structure of a complex of acridine, cytosine and water (1:1:1)

X-ray structural analysis of a crystalline complex between acridine C(13)H(9)N, cytosine C(4)H(5)N(3)O, and water (1:1:1) has been completed. The cytosine and water molecules form a sheet-like structure through a series of hydrogen bonds. The acridine molecules are bound to this layer through a hydrogen bridge from the water to the ring nitrogen. The acridine molecules stack in a parallel fashion normal to the cytosine-water sheets, with an average interplanar spacing of 3.5 angstroms.     

Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution

The crystal structure of the complex between Eco RI endonuclease and the cognate oligonucleotide TCGCGAATTCGCG provides a detailed example of the structural basis of sequence-specific DNA-protein interactions. The structure was determined, to 3 A resolution, by the ISIR (iterative single isomorphous replacement) method with a platinum isomorphous derivative. The complex has twofold symmetry. Each subunit of the endonuclease is organized into an alpha/beta domain consisting a five-stranded beta sheet, alpha helices, and an extension, called the "arm," which wraps around the DNA. The large beta sheet consists of antiparallel and parallel motifs that form the foundations for the loops and alpha helices responsible for DNA strand scission and sequence-specific recognition, respectively. The DNA cleavage site is located in a cleft that binds the DNA backbone in the vicinity of the scissile bond. Sequence specificity is mediated by 12 hydrogen bonds originating from alpha helical recognition modules. Arg200 forms two hydrogen bonds with guanine while Glu144 and Arg145 form four hydrogen bonds to adjacent adenine residues. These interactions discriminate the Eco RI hexanucleotide GAATTC from all other hexanucleotides because any base substitution would require rupture of at least one of these hydrogen bonds.     

Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions

The crystal structure of a complex containing the DNA-binding domain of lambda repressor and a lambda operator site was determined at 2.5 A resolution and refined to a crystallographic R factor of 24.2 percent. The complex is stabilized by an extensive network of hydrogen bonds between the protein and the sugar-phosphate backbone. Several side chains form hydrogen bonds with sites in the major groove, and hydrophobic contacts also contribute to the specificity of binding. The overall arrangement of the complex is quite similar to that predicted from earlier modeling studies, which fit the protein dimer against linear B-form DNA. However, the cocrystal structure reveals important side chain-side chain interactions that were not predicted from the modeling or from previous genetic and biochemical studies.     

Interplay of intra- and intermolecular H-bonding in a progressively solvated macrocyclic peptide

Studying solvation of a large molecule on an atomic level is challenging because of the transient character and inhomogeneity of hydrogen bonding in liquid water. We studied water clusters of a protonated macrocyclic decapeptide, gramicidin S, which were prepared in the gas phase and then cooled to cryogenic temperatures. The experiment spectroscopically tracked fine structural changes of the clusters upon increasing the number of attached water molecules from 1 to 50 and distinguished vibrational fingerprints of different conformers. The data indicate that only the first two water molecules induce a substantial change of the gramicidin S structure by breaking two intramolecular noncovalent bonds. The peptide structure remains largely intact upon further solvation, reflecting the interplay between the strong intramolecular and weaker intermolecular hydrogen bonds.     

Water diffusion and clustering on Pd(111)

The adsorption, diffusion, and clustering of water molecules on a Pd(111) surface were studied by scanning tunneling microscopy. At 40 kelvin, low-coverage water adsorbs in the form of isolated molecules, which diffuse by hopping to nearest neighbor sites. Upon collision, they form first dimers, then trimers, tetramers, and so on. The mobility of these species increased by several orders of magnitude when dimers, trimers, and tetramers formed, and decreased again when the cluster contained five or more molecules. Cyclic hexamers were found to be particularly stable. They grow with further exposure to form a commensurate hexagonal honeycomb structure relative to the Pd(111) substrate. These observations illustrate the change in relative strength between intermolecular hydrogen bonds and molecule-substrate bonds as a function of water cluster size, the key property that determines the wetting properties of materials.     

Bond selectivity in silicon film growth

Hydrogen atoms can selectively eliminate strained bonds that form during the growth of amorphous silicon films. By periodically interrupting the growth and exposing the grown material to hydrogen, the film composition can be varied continuously from a non-equilibrium amorphous structure to that of a crystalline solid. Furthermore, by tuning the hydrogen exposure it is possible to discriminate between Si-Si bonds formed on different substrates, thereby allowing substrate-selective growth. The evolution of the film structure during hydrogen exposure is directly observed by scanning tunneling microscopy, and a model describing the role of hydrogen is presented.     

Potassium hydrogen malonate: remarkable crystal and molecular structure

X-ray crystallographic investigations of potassium hydrogen malonate crystals reveal a very unusual structure in which malonic acid molecules and doubly ionized malonate ions exist in equal numbers. These two species a nected by strong hydrogen bonds in one direction and by potassium ions in the other directions. This seems to be the first observation of the simultaneous ence in a crystal of the two species dicarboxylic acid molecules and their charged ions.     

Structure of a glycerol-conducting channel and the basis for its selectivity

Membrane channel proteins of the aquaporin family are highly selective for permeation of specific small molecules, with absolute exclusion of ions and charged solutes and without dissipation of the electrochemical potential across the cell membrane. We report the crystal structure of the Escherichia coli glycerol facilitator (GlpF) with its primary permeant substrate glycerol at 2.2 angstrom resolution. Glycerol molecules line up in an amphipathic channel in single file. In the narrow selectivity filter of the channel the glycerol alkyl backbone is wedged against a hydrophobic corner, and successive hydroxyl groups form hydrogen bonds with a pair of acceptor, and donor atoms. Two conserved aspartic acid-proline-alanine motifs form a key interface between two gene-duplicated segments that each encode three-and-one-half membrane-spanning helices around the channel. This structure elucidates the mechanism of selective permeability for linear carbohydrates and suggests how ions and water are excluded.     

The structure of a complex of recombinant hirudin and human alpha-thrombin

The crystallographic structure of a recombinant hirudin-thrombin complex has been solved at 2.3 angstrom (A) resolution. Hirudin consists of an NH2-terminal globular domain and a long (39 A) COOH-terminal extended domain. Residues Ile1 to Tyr3 of hirudin form a parallel beta-strand with Ser214 to Glu217 of thrombin with the nitrogen atom of Ile1 making a hydrogen bond with Ser195 O gamma atom of the catalytic site, but the specificity pocket of thrombin is not involved in the interaction. The COOH-terminal segment makes numerous electrostatic interactions with an anion-binding exosite of thrombin, whereas the last five residues are in a helical loop that forms many hydrophobic contacts. In all, 27 of the 65 residues of hirudin have contacts less than 4.0 A with thrombin (10 ion pairs and 23 hydrogen bonds). Such abundant interactions may account for the high affinity and specificity of hirudin.     

Nicarbazin complex yields dinitrocarbanilide as ultrafine crystals with improved anticoccidial activity

Nicarbazin, a drug used to control the protozoal disease coccidiosis in poultry, is a complex of the highly insoluble drug 4,4'-dinitrocarbanilide with 2-hydroxy-4,6-dimethylpyrimidine. The structures of this and other 4,4'-dinitrocarbanilide complexes have not been determined, but an analogous 2:1 complex of 4,4'-dinitrodiphenylamine with 1,4-diacetylpiperazine has been prepared in which the only possible bonds are hydrogen bonds between the amide carbonyls and amino hydrogens. Scanning electron microscopy revealed that micron-size crystals of nicarbazin disintegrate in water to form much smaller dinitrocarbanilide crystals. Similar complex dissolution in the gut of poultry may account for the greater effectiveness of dinitrocarbanilide when administered as complexed rather than uncomplexed drug. Particle size problems associated with other highly insoluble drugs and pesticides may be resolved by the use of nicarbazin-like complexes.     

杀虫晶体蛋白Cry1Ac与其配体N-已酰半乳糖胺的对接研究

利用同源建模得到杀虫晶体蛋白Cry1Ac的三维结构,之后模拟其与配体N-已酰半乳糖胺的对接,预测关键的氨基酸残基:N482、Q506、S501、L505和V483。Cry1Ac的虚拟突变体与N-已酰半乳糖胺之间的分子对接分析结果表明,R466、R468、R470和R472可能对维持Cry1Ac的DomainⅢ稳定构象起着重要作用。N482和Q506两个残基均含有酰氨基,在对接中易于形成多个氢键,这对稳定对接具有重要作用。研究结果可提供一些有用的信息,用于指导杀虫晶体蛋白的理性设计。     

4-氨基-3,5二-（4-吡啶基）-1,2,4三-氮唑-Cu（Ⅰ）配合物的溶剂热合成及结构表征

采用CuBr与4-氨基-3,5-二（4-吡啶基）-1,2,4-三氮唑配体（4-abpt）在溶剂热条件下合成了配合物[CuBr（4-abpt）],并用红外光谱、元素分析及X-射线单晶衍射对其进行了结构表征.结果表明,该配合物中Cu（Ⅰ）呈现四面体配位几何,4-abpt采取μ3-桥连模式与μ3-Cu（Ⅰ）在ab平面形成了具有（4.82）拓扑结构的[Cu-（4-abpt）]层,相邻层间通过N-H…Br氢键作用和π-π堆积构筑成三维超分子网络.配合物结晶于单斜晶系,P2（1）/n空间群,a=0.768 97（6）nm,b=1.332 70（10）nm,c=1.263 38（9）nm,β=91.388（2）,V=1.294 34（17）nm3,Z=4,S=1.050,R1=0.023 1,wR2=0.056 7[I〉2σ（I）].     

4-氨基-3,5二-（4-吡啶基）-1,2,4三-氮唑-Cu（Ⅰ）配合物的溶剂热合成及结构表征

采用CuBr与4-氨基-3,5-二（4-吡啶基）-1,2,4-三氮唑配体（4-abpt）在溶剂热条件下合成了配合物[CuBr（4-abpt）],并用红外光谱、元素分析及X-射线单晶衍射对其进行了结构表征.结果表明,该配合物中Cu（Ⅰ）呈现四面体配位几何,4-abpt采取μ3-桥连模式与μ3-Cu（Ⅰ）在ab平面形成了具有（4.82）拓扑结构的[Cu-（4-abpt）]层,相邻层间通过N-H…Br氢键作用和π-π堆积构筑成三维超分子网络.配合物结晶于单斜晶系,P2（1）/n空间群,a=0.768 97（6）nm,b=1.332 70（10）nm,c=1.263 38（9）nm,β=91.388（2）,V=1.294 34（17）nm3,Z=4,S=1.050,R1=0.023 1,wR2=0.056 7[I〉2σ（I）].     

Hydrogen as a Probe of Semiconductor Surface Structure: The Ge(111)-c(2 x 8) Surface

Hydrogen can be used as an effective probe of the structure of semiconductor surfaces. Such surfaces consist of bonds with varying degrees of bond strain, and hydrogen can react with each selectively depending on the reaction conditions. This selectivity is derived from a reduced barrier to reaction associated with strained bonds. In this manner, hydrogen can be used to pick apart the surface one bond type at a time, thereby revealing the structure of even complex multilayer reconstructions. This method is used to directly show that the rest-layer of the Ge(111)-c(2 x 8) surface has a bulk structure.     

花生蛋白高水分挤压组织化过程中的化学键变化

 【目的】从挤压产品微观结构、化学键变化和蛋白质酰化改性等方面，探讨花生蛋白高水分挤压组织化结构的形成机理。【方法】采用扫描电子显微镜观察挤压产品的微观结构，利用物性测定仪分析挤压产品的质构特性，用化学分析方法对蛋白质中的总巯基和二硫键含量进行分析，采用琥珀酰化的方法对花生蛋白进行酰化处理。【结果】蛋白质溶解度试验结果显示，随挤压温度的升高，花生蛋白的溶解度迅速降低，在含2%SDS和2%SDS+2%2-ME缓冲液中的溶解度显著增加，最高达76.89%（140℃），说明挤压产品中以非共价键结合的蛋白质含量显著增加。随挤压温度的增加，二硫键含量在140～150℃范围内呈缓慢下降趋势，在155℃时显著降低。花生蛋白质酰化后，挤压产品的硬度、咀嚼度和组织化度等显著降低，相应的微观结构也显示出显著的变化。【结论】在花生蛋白高水分挤压组织化过程中，疏水作用和氢键起主要作用，其次是二硫键。在挤压过程中，花生蛋白分子内原有的二硫键含量降低，可能发生了部分断裂，高温会加速该反应的进行。酰化改性明显干扰了蛋白质分子间的相互作用，不利于挤压产品良好组织化结构的形成。     

Selective, nickel-catalyzed hydrogenolysis of aryl ethers

Selective hydrogenolysis of the aromatic carbon-oxygen (C-O) bonds in aryl ethers is an unsolved synthetic problem important for the generation of fuels and chemical feedstocks from biomass and for the liquefaction of coal. Currently, the hydrogenolysis of aromatic C-O bonds requires heterogeneous catalysts that operate at high temperature and pressure and lead to a mixture of products from competing hydrogenolysis of aliphatic C-O bonds and hydrogenation of the arene. Here, we report hydrogenolyses of aromatic C-O bonds in alkyl aryl and diaryl ethers that form exclusively arenes and alcohols. This process is catalyzed by a soluble nickel carbene complex under just 1 bar of hydrogen at temperatures of 80 to 120°C; the relative reactivity of ether substrates scale as Ar-OAr>Ar-OMe>ArCH(2)-OMe (Ar, Aryl; Me, Methyl). Hydrogenolysis of lignin model compounds highlights the potential of this approach for the conversion of refractory aryl ether biopolymers to hydrocarbons.     

木材酸性液化条件下苯酚的作用机理

论述了酸性条件下木材液化中苯酚的作用机理.苯酚作为亲核试剂,引起了木材组分一些主要化学键的断裂,使得木材组分大分子降解为小分子;苯酚作为反应试剂,与其中一些降解生成的小分子反应生成具有酚类结构的化合物;苯酚作为溶剂,使生成的酚类结构化合物溶解,并减缓或阻止了已生成的活性小分子之间的缩聚反应.催化剂酸提供质子(H )以及酸性环境,使化学键的断裂更为容易,同时也改变了液化反应途径.     

含水率对樟子松细胞壁弹性模量和硬度的影响规律

为探明水分对木材细胞壁力学性能的影响，选取樟子松为对象，利用热水、1%氢氧化钠以及苯-乙醇溶液在80 ℃、6 h、固液比1:20的工艺条件下对试样进行抽提处理，抽提后的木材样品加工成金字塔形，然后对试样进行吸湿处理并且调控试样含水率，借助纳米压痕测试研究含水率对木材细胞壁力学性能的影响，并建立机理模型做进一步分析。结果表明，随着含水率的增加，木材的纵向弹性模量与硬度，均出现了一定程度的下降。分析发现，水分子进入细胞壁后与游离羟基形成氢键，随着含水率增加，会被部分原有的氢键破坏，并与之前进入的水分子形成氢键，在内部形成水分子簇，增大了细胞壁分子链之间的距离，使空隙增多，进而降低木材的弹性模量，且水分会使木材细胞壁主成分逐渐软化，硬度降低。     

Supramolecular Archimedean cages assembled with 72 hydrogen bonds

Self-assembly of multiple components into well-defined and predictable structures remains one of the foremost challenges in chemistry. Here, we report on the rational design of a supramolecular cage assembled from 20 ions of three distinct species through 72 hydrogen bonds. The cage is constructed from two kinds of hexagonal molecular tiles, a tris(guanidinium)nitrate cluster and a hexa(4-sulfonatophenyl)benzene, joined at their edges through complementary and metrically matched N-H···O-S hydrogen bonds to form a truncated octahedron, one of the Archimedean polyhedra. The truncated octahedron, with an interior volume of 2200 cubic angstroms, serves as the composite building unit of a body-centered cubic zeolite-like framework, which exhibits an ability to encapsulate a wide range of differently charged species, including organic molecules, transition metal complexes, and "ship-in-a-bottle" nanoclusters not observed otherwise.