Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme

Iron-peroxide intermediates are central in the reaction cycle of many iron-containing biomolecules. We trapped iron(III)-(hydro)peroxo species in crystals of superoxide reductase (SOR), a nonheme mononuclear iron enzyme that scavenges superoxide radicals. X-ray diffraction data at 1.95 angstrom resolution and Raman spectra recorded in crystallo revealed iron-(hydro)peroxo intermediates with the (hydro)peroxo group bound end-on. The dynamic SOR active site promotes the formation of transient hydrogen bond networks, which presumably assist the cleavage of the iron-oxygen bond in order to release the reaction product, hydrogen peroxide.     

Hydroxyl orientation in muscovite as indicated by electrostatic energy calculations

The electrostatic energy of the 2M(1) muscovite structure, KAl(2)(Si(3)Al)- O(10)(OH)(2), has been calculated as a function of the orientation of the hydroxyl group (O-H distance = 0.97 angstrom). The minimum in the electrostatic energy occurs when the OH bond makes an angle of 18 degrees with the cleavage plane and an angle of 31 degrees with the b-axis (in the a-b plane), which is 2.5 degrees away from the orientation of the transition moment as determined from infrared measurements on single crystals. If the K+ ion is excluded from the calculation, the O-H bond makes an angle of 53 degrees with the cleavage plane. This indicates the strong influence that the interlayer cation exerts on the hydroxyl hydrogen in mica structures.     

Hydrogen Cyanide Production During Reduction of Nitric Oxide over Platinum Catalysts: Transient Effects

The formation of hydrogen cyanide during the catalytic reduction of nitric oxide (NO) with carbon monoxide and hydrogen was studied with a bench-scale flow reactor. The previously reported inhibition by sulfur dioxide of the formation of hydrogen cyanide was found to be counteracted by transient admission of oxygen to the catalyst. These results are discussed in the context of the control of automotive emissions of NO and the prevention of hydrogen cyanide production during such control.     

Renewable hydrogen from nonvolatile fuels by reactive flash volatilization

Droplets of nonvolatile fuels such as soy oil and glucose-water solutions can be flash evaporated by catalytic partial oxidation to produce hydrogen in high yields with a total time in the reactor of less than 50 milliseconds. Pyrolysis, coupled with catalytic oxidation of the fuels and their fragments upon impact with a hot rhodium-cerium catalyst surface, avoids the formation of deactivating carbon layers on the catalyst. The catalytic reactions of these products generate approximately 1 megawatt of heat per square meter, which maintains the catalyst surface above 800 degrees C at high drop impact rates. At these temperatures, heavy fuels can be catalytically transformed directly into hydrogen, carbon monoxide, and other small molecules in very short contact times without the formation of carbon.     

Hydrogen-Bond Breaking and Proton Exchange in Collisions of Gaseous Formic Acid with Liquid Sulfuric Acid

Gas-liquid scattering experiments provide direct observations of the fate of hydrogen-bonding molecules striking the surfaces of acidic liquids. Collisions of gaseous formic acid with concentrated sulfuric acid show that impinging monomers (HCOOH and DCOOD) scatter inelastically from the interface or become trapped by surface H2SO4. Most trapped DCOOD molecules undergo proton exchange before desorbing from the acid, indicating that gas-surface accommodation almost always leads to reaction with H2SO4 molecules. This proton transfer is not inhibited by dimerization of the formic acid: The dimers readily undergo intramolecular hydrogen bond cleavage and D-H exchange before desorbing from the acid.     

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.     

Photolytic cleavage of sulfonamide bonds

It has been found that the sulfonamide bond is relatively susceptible to photolytic cleavage. The breakdown was effected either by irradiation with a source having a continuous emission above the wavelengths of 1800 angstroms or by another source emitting principally at 2537 angstroms. Less destruction of the amino acids was seen with the latter relative to the sulfonamide bond cleavage. The cleavage was not effected by irradiation at wavelengths greater than about 3000 angstroms. Side reactions were noted involving decarboxylation, demination, and destruction of certain susceptible amino acids such as tryptophan. In only one case was a product found that arose from cleavage of a carboxamide bond; glycyltyrosine gave glycine and tyrosine upon irradiation. A yield of 75 percent of the corresponding amino acid has been obtained by irradiation of tosylhistidine; yields of 75 to 100 percent have been obtained from sulfamic acid (NH(2)SO(3)H). A qualitative method for identifying sulfonylated amino acids is described.     

N₂reduction and hydrogenation to ammonia by a molecular iron-potassium complex

The most common catalyst in the Haber-Bosch process for the hydrogenation of dinitrogen (N(2)) to ammonia (NH(3)) is an iron surface promoted with potassium cations (K(+)), but soluble iron complexes have neither reduced the N-N bond of N(2) to nitride (N(3-)) nor produced large amounts of NH(3) from N(2). We report a molecular iron complex that reacts with N(2) and a potassium reductant to give a complex with two nitrides, which are bound to iron and potassium cations. The product has a Fe(3)N(2) core, implying that three iron atoms cooperate to break the N-N triple bond through a six-electron reduction. The nitride complex reacts with acid and with H(2) to give substantial yields of N(2)-derived ammonia. These reactions, although not yet catalytic, give structural and spectroscopic insight into N(2) cleavage and N-H bond-forming reactions of iron.     

Dinitrogen Cleavage by a Three-Coordinate Molybdenum(III) Complex

Cleavage of the relatively inert dinitrogen (N(2)) molecule, with its extremely strong N identical withN triple bond, has represented a major challenge to the development of N(2) chemistry. This report describes the reductive cleavage of N(2) to two nitrido (N(3-)) ligands in its reaction with Mo(NRAr)(3), where R is C(CD(3))(2)CH(3) and Ar is 3,5-C(6)H(3)(CH(3))(2'), a synthetic three-coordinate molybdenum(III) complex of known structure. The formation of an intermediate complex was observed spectroscopically, and its conversion (with N identical withN bond cleavage) to the nitrido molybdenum(VI) product N identical withMo(NRAr)(3) followed first-order kinetics at 30 degrees C. It is proposed that the cleavage reaction proceeds by way of an intermediate complex in which N(2) bridges two molybdenum centers.     

A molecular jump mechanism of water reorientation

Despite long study, a molecular picture of the mechanism of water reorientation is still lacking. Using numerical simulations, we find support for a pathway in which the rotating water molecule breaks a hydrogen bond (H-bond) with an overcoordinated first-shell neighbor to form an H-bond with an undercoordinated second-shell neighbor. The H-bond cleavage and the molecular reorientation occur concertedly and not successively as usually considered. This water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many experimental data wherein water rotational relaxation is assumed to be diffusive.     

An RNA processing activity that debranches RNA lariats

The excised introns of pre-messenger RNA's (pre-mRNA's) and intron-containing splicing intermediates are in a lariat configuration in which the 5' end of the intron is covalently joined by a 2',5'-phosphodiester bond to a specific adenosine residue near the 3' end of the intron. A 2',5'-phosphodiesterase activity in HeLa cell extracts has been detected that debranches RNA lariats, converting them to linear RNA molecules by specific cleavage of the 2',5'-phosphodiester bond. This lariat debranching activity is distinct from previously reported 2',5'-phosphodiesterases with regard to its biochemical and substrate requirements as well as its stringent cleavage specificity. The debranching activity is observed only if the RNA lariats generated during in vitro processing are deproteinized and added back to the extract. These results suggest that during the normal in vitro splicing reaction the 2',5'-phosphodiester bond of RNA lariats is protected from cleavage by the lariat debranching activity.     

Quantification of primary versus secondary C-h bond cleavage in alkane activation: propane on pt

The trapping-mediated dissociative chemisorption of three isotopes of propane (C(3)H(8), CH(3),CD(2)CH(3), and C(3)D(8)) has been investigated on the Pt(110)-(1 x 2) surface, and both the apparent activation energies and the preexponential factors of the surface reaction rate coefficients have been measured. In addition, the probabilities of primary and secondary C-H bond cleavage for alkane activation on a surface were evaluated. The activation energy for primary C-H bond cleavage was 425 calories per mole greater than that of secondary C-H bond cleavage, and the two true activation energies that embody the single measured activation energy were determined for each of the three isotopes. Secondary C-H bond cleavage is also preferred on entropic grounds, and the magnitude of the effect was quantified.     

Efficient oxidative dechlorination and aromatic ring cleavage of chlorinated phenols catalyzed by iron sulfophthalocyanine

An efficient method has been developed for the catalytic oxidation of pollutants that are not easily degraded. The products of the hydrogen peroxide (H(2)O(2)) oxidation of 2,4,6,-trichlorophenol (TCP) catalyzed by the iron complex 2,9,16,23-tetrasulfophthalocyanine (FePcS) were observed to be chloromaleic, chlorofumaric, maleic, and fumaric acids from dechlorination and aromatic cycle cleavage, as well as additional products that resulted from oxidative coupling. Quantitative analysis of the TCP oxidation reaction revealed that up to two chloride ions were released per TCP molecule. This chemical system, consisting of an environmentally safe oxidant (H(2)O(2)) and an easily accessible catalyst (FePcS), can perform several key steps in the oxidative mineralization of TCP, a paradigm of recalcitrant pollutants.     

Tyrosinase reactivity in a model complex: an alternative hydroxylation mechanism

The binuclear copper enzyme tyrosinase activates O2 to form a mu-eta2:eta2-peroxodicopper(II) complex, which oxidizes phenols to catechols. Here, a synthetic mu-eta2:eta2-peroxodicopper(II) complex, with an absorption spectrum similar to that of the enzymatic active oxidant, is reported to rapidly hydroxylate phenolates at -80 degrees C. Upon phenolate addition at extreme temperature in solution (-120 degrees C), a reactive intermediate consistent with a bis-mu-oxodicopper(III)-phenolate complex, with the O-O bond fully cleaved, is observed experimentally. The subsequent hydroxylation step has the hallmarks of an electrophilic aromatic substitution mechanism, similar to tyrosinase. Overall, the evidence for sequential O-O bond cleavage and C-O bond formation in this synthetic complex suggests an alternative intimate mechanism to the concerted or late stage O-O bond scission generally accepted for the phenol hydroxylation reaction performed by tyrosinase.     

Local anesthetics: significance of hydrogen bonding in mechanism of action

The action of local anesthetics is considered in terms of their ability to function as the donor in a hydrogen bond. The formation of a hydrogen-bonded complex between the drug and an acceptor group on the neural membrane is suggested as a feature in the action of local anesthetics.     

坛紫菜藻红蛋白分离纯化研究

[目的]建立一种新型、高效、快速的藻红蛋白分离纯化方法,并对其分离机理进行探讨。[方法]以坛紫菜的藻红蛋白搅切法提取物为原料,首先通过100和500 kDa的超滤离心管对其进行超滤分离,再在Superose 12色谱柱上以不同种类和不同浓度的流动相对藻红蛋白粗提物进行等度洗脱,分析其分离机理,并优化分离条件。[结果]在0.05 mol/L NaCl等度洗脱的条件下,藻红蛋白在Superose12色谱柱上表现为典型的氢键吸附模式;在优化的条件下,通过超滤-Superose 12氢键吸附分离的方法,可以使坛紫菜藻红蛋白提取物纯度(A565/A280)达到7.98,总回收率52.9%。[结论]该研究结果表明藻红蛋白在Superose 12色谱柱上存在氢键吸附作用,同时,该研究所建立的超滤-Superose 12氢键吸附分离方法是一种新型、高效、快速的藻红蛋白分离纯化方法。     

Metathesis of Alkanes Catalyzed by Silica-Supported Transition Metal Hydrides

The silica-supported transition metal hydrides (=Si-O-Si=)(=Si-O-)2Ta-H and (=Si-O-)xM-H (M, chromium or tungsten) catalyze the metathesis reaction of linear or branched alkanes into the next higher and lower alkanes at moderate temperature (25degrees to 200degreesC). With (=Si-O-Si=)(=Si-O-)2Ta-H, ethane was transformed at room temperature into an equimolar mixture of propane and methane. Higher and lower homologs were obtained from propane, butane, and pentane as well as from branched alkanes such as isobutane and isopentane. The mechanism of the step leading to carbon-carbon bond cleavage and formation likely involves a four-centered transition state between a tantalum-alkyl intermediate and a carbon-carbon final sigma-bond of a second molecule of alkane.     

氯代甲醛-次氯酸复合物的结构和热力学性质

在B3LYP/6-311＋＋G＊＊水平上对氯代甲醛HCOCl与次氯酸HOCl可能的复合物进行结构优化与频率计算。得到5个稳定异构体,其中形成ClO-H…O=C氢键的复合物最稳定,经基组重叠误差和零点振动能校正后的相互作用能为-11.92KJ/mol。氢键的形成导致H-O伸缩振动频率红移。在298.15K和标准状态下,稳定复合物的形成反应是一个放热的非自发过程。     

A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center

Biochemical and crystallographic evidence suggests that 23S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23S rRNA that may have a perturbed pKa (where Ka is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral pKa of 7.6 +/- 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation.     

黑根霉菌孢囊孢子形成的电镜观察

电镜观察发现,黑根霉菌的孢囊孢子是以原生质割裂的方式形成。在原生质割裂初期,细胞核核膜上形成了形状不同的泡囊,该孢囊的产生与割裂泡的产生可能密切相关。大量的割裂泡通过在细胞核外的有规律排列和相互间的接合,从而将孢囊的原生质割裂开来,并形成大量的无壁新细胞,该细胞的质膜来源于割裂泡的外膜。随着细胞壁的出现,这些无壁的细胞最终发育成为孢囊孢子。观察还发现,孢囊的囊轴与原生质割裂是同步的。