These are representative sample records from related to your search topic.
For comprehensive and current results, perform a real-time search at

Novel C?-C? bond cleavages of tryptophan-containing peptide radical cations.  


In this study, we observed unprecedented cleavages of the C(?)-C(?) bonds of tryptophan residue side chains in a series of hydrogen-deficient tryptophan-containing peptide radical cations (M(•+)) during low-energy collision-induced dissociation (CID). We used CID experiments and theoretical density functional theory (DFT) calculations to study the mechanism of this bond cleavage, which forms [M - 116](+) ions. The formation of an ?-carbon radical intermediate at the tryptophan residue for the subsequent C(?)-C(?) bond cleavage is analogous to that occurring at leucine residues, producing the same product ions; this hypothesis was supported by the identical product ion spectra of [LGGGH - 43](+) and [WGGGH - 116](+), obtained from the CID of [LGGGH](•+) and [WGGGH](•+), respectively. Elimination of the neutral 116-Da radical requires inevitable dehydrogenation of the indole nitrogen atom, leaving the radical centered formally on the indole nitrogen atom ([Ind](•)-2), in agreement with the CID data for [WGGGH](•+) and [W(1-CH3)GGGH](•+); replacing the tryptophan residue with a 1-methyltryptophan residue results in a change of the base peak from that arising from a neutral radical loss (116 Da) to that arising from a molecule loss (131 Da), both originating from C(?)-C(?) bond cleavage. Hydrogen atom transfer or proton transfer to the ?-carbon atom of the tryptophan residue weakens the C(?)-C(?) bond and, therefore, decreases the dissociation energy barrier dramatically. PMID:22135037

Song, Tao; Hao, Qiang; Law, Chun-Hin; Siu, Chi-Kit; Chu, Ivan K



A general synthesis of ynones from aldehydes via oxidative C-C bond cleavage under aerobic conditions.  


We describe a direct synthesis of various ynones from readily available aldehydes and hypervalent alkynyl iodides. In this method, a gold catalyst and a secondary amine work synergistically to produce the trisubstituted allenyl aldehyde, which can be converted to the desired ynone through an in situ C-C bond oxidative cleavage using molecular oxygen. PMID:25133731

Wang, Zhaofeng; Li, Li; Huang, Yong



Metal-Free Tandem Oxidative Aryl Migration and C-C Bond Cleavage: Synthesis of ?-Ketoamides and Esters from Acrylic Derivatives.  


A novel tandem metal-free oxidative aryl migration/C-C bond-cleavage reaction, mediated by hypervalent iodine reagent, has been discovered. The presented transformation provided straightforward access to important ?-ketoamide and ?-ketoester derivatives from readily available acrylic derivatives via a concerted process of 1,2-aryl shift concomitant with C-C bond cleavage. PMID:25343425

Liu, Le; Du, Liang; Zhang-Negrerie, Daisy; Du, Yunfei; Zhao, Kang



Ceric ammonium nitrate (CAN) catalyzed modification of ketones via two C-C bond cleavages with the retention of the oxo-group.  


A simple ceric ammonium nitrate (CAN) catalyzed functionalization of ketones through double C-C bond cleavage strategy has been disclosed. This reaction provides a mild, practical method toward carbamoyl azides, which are versatile intermediates and building blocks in organic synthesis. Based on relevant mechanistic studies, a unique and plausible C-C bond and N-O bond cleavage process is proposed, where the oxyamination intermediate plays an important role in this reaction. PMID:24906031

Feng, Peng; Sun, Xiang; Su, Yijin; Li, Xinyao; Zhang, Li He; Shi, Xiaodong; Jiao, Ning



Direct approaches to nitriles via highly efficient nitrogenation strategy through C-H or C-C bond cleavage.  


Because of the importance of nitrogen-containing compounds in chemistry and biology, organic chemists have long focused on the development of novel methodologies for their synthesis. For example, nitrogen-containing compounds show up within functional materials, as top-selling drugs, and as bioactive molecules. To synthesize these compounds in a green and sustainable way, researchers have focused on the direct functionalization of hydrocarbons via C-H or C-C bond cleavage. Although researchers have made significant progress in the direct functionalization of simple hydrocarbons, direct C-N bond formation via C-H or C-C bond cleavage remains challenging, in part because of the unstable character of some N-nucleophiles under oxidative conditions. The nitriles are versatile building blocks and precursors in organic synthesis. Recently, chemists have achieved the direct C-H cyanation with toxic cyanide salts in the presence of stoichiometric metal oxidants. In this Account, we describe recent progress made by our group in nitrile synthesis. C-H or C-C bond cleavage is a key process in our strategy, and azides or DMF serve as the nitrogen source. In these reactions, we successfully realized direct nitrile synthesis using a variety of hydrocarbon groups as nitrile precursors, including methyl, alkenyl, and alkynyl groups. We could carry out C(sp(3))-H functionalization on benzylic, allylic, and propargylic C-H bonds to produce diverse valuable synthetic nitriles. Mild oxidation of C?C double-bonds and C?C triple-bonds also produced nitriles. The incorporation of nitrogen within the carbon skeleton typically involved the participation of azide reagents. Although some mechanistic details remain unclear, studies of these nitrogenation reactions implicate the involvement of a cation or radical intermediate, and an oxidative rearrangement of azide intermediate produced the nitrile. We also explored environmentally friendly oxidants, such as molecular oxygen, to make our synthetic strategy more attractive. Our direct nitrile synthesis methodologies have potential applications in the synthesis of biologically active molecules and drug candidates. PMID:24684545

Wang, Teng; Jiao, Ning



The benzoyl peroxide promoted dual C-C bond formation via dual C-H bond cleavage: ?-phenanthridinylation of ether by isocyanide.  


The benzoyl peroxide-promoted ?-phenanthridinylation of ether by isocyanide is developed, proceeding through dual C-H bond cleavage and dual C-C bond formation. The procedure tolerates a series of functional groups, such as methyl, fluoro, chloro, acetyl, methoxy carbonyl, cyano, and trifluoromethyl. Thus, it represents a facile pathway leading to 6-substituted phenanthridine derivatives. The addition of radical to the isonitrile followed by a radical aromatic cyclization is involved in this transformation. PMID:24684422

Wang, Lei; Sha, Wanxing; Dai, Qiang; Feng, Xiaomei; Wu, Wenting; Peng, Haibo; Chen, Bin; Cheng, Jiang



C?-C bond cleavage of the peptide backbone in MALDI in-source decay using salicylic acid derivative matrices.  


The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H](+). The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H](+) to that of non-oxidized protonated molecule [M + H](+) of peptide was of the order 5-NSA > 5-FSA > 5-aminosalicylic acid (5-ASA) ? 2,5-dihydroxyl benzoic acid (2,5-DHB) ? 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the C?-C bond, leading to the formation of a- and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the C?-C bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides. PMID:21953105

Asakawa, Daiki; Takayama, Mitsuo



Metal-catalyzed C-C bond cleavage in alkanes: effects of methyl substitution on transition-state structures and stability.  


Methyl substituents at C-C bonds influence hydrogenolysis rates and selectivities of acyclic and cyclic C2-C8 alkanes on Ir, Rh, Ru, and Pt catalysts. C-C cleavage transition states form via equilibrated dehydrogenation steps that replace several C-H bonds with C-metal bonds, desorb H atoms (H*) from saturated surfaces, and form ? H2(g) molecules. Activation enthalpies (?H(‡)) and entropies (?S(‡)) and ? values for (3)C-(x)C cleavage are larger than for (2)C-(2)C or (2)C-(1)C bonds, irrespective of the composition of metal clusters or the cyclic/acyclic structure of the reactants. (3)C-(x)C bonds cleave through ?,?,?- or ?,?,?,?-bound transition states, as indicated by the agreement between measured activation entropies and those estimated for such structures using statistical mechanics. In contrast, less substituted C-C bonds involve ?,?-bound species with each C atom bound to several surface atoms. These ?,? configurations weaken C-C bonds through back-donation to antibonding orbitals, but such configurations cannot form with (3)C atoms, which have one C-H bond and thus can form only one C-M bond. (3)C-(x)C cleavage involves attachment of other C atoms, which requires endothermic C-H activation and H* desorption steps that lead to larger ?H(‡) values but also larger ?S(‡) values (by forming more H2(g)) than for (2)C-(2)C and (2)C-(1)C bonds, irrespective of alkane size (C2-C8) or cyclic/acyclic structure. These data and their mechanistic interpretation indicate that low temperatures and high H2 pressures favor cleavage of less substituted C-C bonds and form more highly branched products from cyclic and acyclic alkanes. Such interpretations and catalytic consequences of substitution seem also relevant to C-X cleavage (X = S, N, O) in desulfurization, denitrogenation, and deoxygenation reactions. PMID:24961991

Flaherty, David W; Hibbitts, David D; Iglesia, Enrique



Brønsted acid promoted addition-cyclization and C-C bond cleavage: a convenient synthesis of 2-amino-5-aroylmethylthiazoles derivatives.  


A Brønsted acid promoted C-C bond cleavage method for the synthesis of novel 2-amino-5-aroylmethylthiazole derivatives has been directly developed from 1,4-enediones and thioureas through self-sequenced thio-Michael-addition, intramolecular selective cyclization, dehydration/aromatization, and C-C bond cleavage reactions. It is noteworthy that this reaction has significant advantages in simple reagents, under environmentally benign conditions and with excellent yields. This highly efficient method is also a highly attractive alternative for the preparation of PLTP, CETP inhibitors and novel biheterocycles. PMID:25327278

Ni, Fan; Yang, Yan; Shu, Wen-Ming; Ma, Jun-Rui; Wu, An-Xin



Biosynthetic pathway toward carbohydrate-like moieties of alnumycins contains unusual steps for C-C bond formation and cleavage  

PubMed Central

Carbohydrate moieties are important components of natural products, which are often imperative for the solubility and biological activity of the compounds. The aromatic polyketide alnumycin A contains an extraordinary sugar-like 4?-hydroxy-5?-hydroxymethyl-2?,7?-dioxane moiety attached via a carbon-carbon bond to the aglycone. Here we have extensively investigated the biosynthesis of the dioxane unit through 13C labeling studies, gene inactivation experiments and enzymatic synthesis. We show that AlnA and AlnB, members of the pseudouridine glycosidase and haloacid dehalogenase enzyme families, respectively, catalyze C-ribosylation conceivably through Michael-type addition of d-ribose-5-phosphate and dephosphorylation. The ribose moiety may be attached both in furanose (alnumycin C) and pyranose (alnumycin D) forms. The C1?-C2? bond of alnumycin C is subsequently cleaved and the ribose unit is rearranged into an unprecedented dioxolane (cis-bicyclo[3.3.0]-2?,4?,6?-trioxaoctan-3??-ol) structure present in alnumycin B. The reaction is catalyzed by Aln6, which belongs to a previously uncharacterized enzyme family. The conversion was accompanied with consumption of O2 and formation of H2O2, which allowed us to propose that the reaction may proceed via hydroxylation of C1? followed by retro-aldol cleavage and acetal formation. Interestingly, no cofactors could be detected and the reaction was also conducted in the presence of metal chelating agents. The last step is the conversion of alnumycin B into the final end-product alnumycin A catalyzed by Aln4, an NADPH-dependent aldo-keto reductase. This characterization of the dioxane biosynthetic pathway sets the basis for the utilization of C-C bound ribose, dioxolane and dioxane moieties in the generation of improved biologically active compounds. PMID:22474343

Oja, Terhi; Klika, Karel D.; Appassamy, Laura; Sinkkonen, Jari; Mantsala, Pekka; Niemi, Jarmo; Metsa-Ketela, Mikko



An asymmetric [3+2] cycloaddition of alkynes with oxiranes by selective C-C bond cleavage of epoxides: highly efficient synthesis of chiral furan derivatives.  


An efficient enantioselective [3+2] cycloaddition of alkynes with oxiranes via selective C-C bond cleavage of epoxides was developed. A number of optically active 2,5-dihydrofurans were obtained in excellent yields (up to 99%) and enantioselectivities (up to 95% ee) under mild reaction conditions. Moreover, chiral tetrahydrofuran could also be obtained by cycloaddition of alkene and oxirane or hydrogenation of chiral 2,5-dihydrofuran. PMID:25133274

Chen, Weiliang; Fu, Xuan; Lin, Lili; Yuan, Xiao; Luo, Weiwei; Feng, Juhua; Liu, Xiaohua; Feng, Xiaoming



The "excited state C-C bond cleavage-luminescence" phenomenon of a biphenyl-substituted methylenecyclopropane triggered by intermolecular energy transfer from triplet benzophenone.  


Existence of the "excited state C-C bond cleavage-luminescence" phenomenon was demonstrated by utilizing intermolecular energy transfer from the excited-triplet benzophenone to 2,2-di(4-biphenylyl)-1-methylenecyclopropane (3). An excellent linear relationship between the intensity of the excitation laser light and that of luminescence clearly shows that formation of the corresponding excited trimethylenemethane biradical (3)4??* proceeds via a one-photon route. PMID:25267075

Matsui, Yasunori; Kido, Taiki; Ohta, Eisuke; Ikeda, Hiroshi



Iron-promoted C-C bond cleavage of 1,3-diketones: a route to 1,2-diketones under mild reaction conditions.  


A conceptual method for the preparation of 1,2-diketones is reported. The selective C-C bond cleavage of 1,3-diketones affords the 1,2-diketones in high yields under mild reaction conditions in air by the use of FeCl(3) as the catalyst and tert-butyl nitrite (TBN) as the oxidant without the use of solvent. The possible reaction mechanism is discussed. This protocol provides an expeditious route to the useful 1,2-diketones. PMID:21627329

Huang, Lehao; Cheng, Kai; Yao, Bangben; Xie, Yongju; Zhang, Yuhong



Reactivity of biomimetic iron(II)-2-aminophenolate complexes toward dioxygen: mechanistic investigations on the oxidative C-C bond cleavage of substituted 2-aminophenols.  


The isolation and characterization of a series of iron(II)-2-aminophenolate complexes [(6-Me3-TPA)Fe(II)(X)](+) (X = 2-amino-4-nitrophenolate (4-NO2-HAP), 1; X = 2-aminophenolate (2-HAP), 2; X = 2-amino-3-methylphenolate (3-Me-HAP), 3; X = 2-amino-4-methylphenolate (4-Me-HAP), 4; X = 2-amino-5-methylphenolate (5-Me-HAP), 5; X = 2-amino-4-tert-butylphenolate (4-(t)Bu-HAP), 6 and X = 2-amino-4,6-di-tert-butylphenolate (4,6-di-(t)Bu-HAP), 7) and an iron(III)-2-amidophenolate complex [(6-Me3-TPA)Fe(III)(4,6-di-(t)Bu-AP)](+) (7(Ox)) supported by a tripodal nitrogen ligand (6-Me3-TPA = tris(6-methyl-2-pyridylmethyl)amine) are reported. Substituted 2-aminophenols were used to prepare the biomimetic iron(II) complexes to understand the effect of electronic and structural properties of aminophenolate rings on the dioxygen reactivity and on the selectivity of C-C bond cleavage reactions. Crystal structures of the cationic parts of 5·ClO4 and 7·BPh4 show six-coordinate iron(II) centers ligated by a neutral tetradentate ligand and a monoanionic 2-aminophenolate in a bidentate fashion. While 1·BPh4 does not react with oxygen, other complexes undergo oxidative transformation in the presence of dioxygen. The reaction of 2·ClO4 with dioxygen affords 2-amino-3H-phenoxazin-3-one, an auto-oxidation product of 2-aminophenol, whereas complexes 3·BPh4, 4·BPh4, 5·ClO4 and 6·ClO4 react with O2 to exhibit C-C bond cleavage of the bound aminophenolates. Complexes 7·ClO4 and 7(Ox)·BPh4 produce a mixture of 4,6-di-tert-butyl-2H-pyran-2-imine and 4,6-di-tert-butyl-2-picolinic acid. Labeling experiments with (18)O2 show the incorporation of one oxygen atom from dioxygen into the cleavage products. The reactivity (and stability) of the intermediate, which directs the course of aromatic ring cleavage reaction, is found to be dependent on the nature of ring substituent. The presence of two tert-butyl groups on the aminophenolate ring in 7·ClO4 makes the complex slow to cleave the C-C bond of 4,6-di-(t)Bu-HAP, whereas 4·BPh4 containing 4-Me-HAP displays fastest reactivity. Density functional theory calculations were conducted on [(6-Me3-TPA)Fe(III)(4-(t)Bu-AP)](+) (6(Ox)) to gain a mechanistic insight into the regioselective C-C bond cleavage reaction. On the basis of the experimental and computational studies, an iron(II)-2-iminobenzosemiquinonate intermediate is proposed to react with dioxygen resulting in the oxidative C-C bond cleavage of the coordinated 2-aminophenolates. PMID:24787025

Chakraborty, Biswarup; Bhunya, Sourav; Paul, Ankan; Paine, Tapan Kanti



Unstrained carbon?carbon bond cleavage.  


This Focus Review presents recent developments in the cleavage of C?C bonds in organic molecules. Significant progress in C?C activation, including the development of a variety of new synthetic strategies, has contributed to the development of this field over the past few decades. Transition-metal-mediated C?C bond cleavage has been shown to be a quite efficient process and several elegant metal-free methods have also recently been developed. Strained rings have been widely used in C?C cleavage transformations; however, unstrained C?C activation has increasingly caught the attention of organic researchers, which inspired us to clarify the developments in this field. PMID:25179561

Liu, Hui; Feng, Minghao; Jiang, Xuefeng



Density Functional Theory Calculations on Oxidative C?C Bond Cleavage and N?O Bond Formation of [Ru(II) (bpy)2 (diamine)](2+) via Reactive Ruthenium Imide Intermediates.  


DFT calculations are performed on [Ru(II) (bpy)2 (tmen)](2+) (M1, tmen=2,3-dimethyl-2,3-butanediamine) and [Ru(II) (bpy)2 (heda)](2+) (M2, heda=2,5-dimethyl-2,5-hexanediamine), and on the oxidation reactions of M1 to give the C?C bond cleavage product [Ru(II) (bpy)2 (NH=CMe2 )2 ](2+) (M3) and the N?O bond formation product [Ru(II) (bpy)2 (ONCMe2 CMe2 NO)](2+) (M4). The calculated geometrical parameters and oxidation potentials are in good agreement with the experimental data. As revealed by the DFT calculations, [Ru(II) (bpy)2 (tmen)](2+) (M1) can undergo oxidative deprotonation to generate Ru-bis(imide) [Ru(bpy)2 (tmen-4?H)](+) (A) or Ru-imide/amide [Ru(bpy)2 (tmen-3?H)](2+) (A') intermediates. Both A and A' are prone to C?C bond cleavage, with low reaction barriers (?G(?) ) of 6.8 and 2.9?kcal?mol(-1) for their doublet spin states (2) A and (2) A', respectively. The calculated reaction barrier for the nucleophilic attack of water molecules on (2) A' is relatively high (14.2?kcal?mol(-1) ). These calculation results are in agreement with the formation of the Ru(II) -bis(imine) complex M3 from the electrochemical oxidation of M1 in aqueous solution. The oxidation of M1 with Ce(IV) in aqueous solution to afford the Ru(II) -dinitrosoalkane complex M4 is proposed to proceed by attack of the cerium oxidant on the ruthenium imide intermediate. The findings of ESI-MS experiments are consistent with the generation of a ruthenium imide intermediate in the course of the oxidation. PMID:25267445

Guan, Xiangguo; Law, Siu-Man; Tse, Chun-Wai; Huang, Jie-Sheng; Che, Chi-Ming



Catalytic constructive deoxygenation of lignin-derived phenols: new C-C bond formation processes from imidazole-sulfonates and ether cleavage reactions.  


As part of a programme aimed at exploiting lignin as a chemical feedstock for less oxygenated fine chemicals, several catalytic C-C bond forming reactions utilising guaiacol imidazole sulfonate are demonstrated. These include the cross-coupling of a Grignard, a non-toxic cyanide source, a benzoxazole, and nitromethane. A modified Meyers reaction is used to accomplish a second constructive deoxygenation on a benzoxazole functionalised anisole. PMID:25130565

Leckie, Stuart M; Harkness, Gavin J; Clarke, Matthew L



Specific cleavage at peptide backbone C?-C and CO-N bonds during matrix-assisted laser desorption/ionization in-source decay mass spectrometry with 5-nitrosalicylic acid as the matrix.  


The use of 5-nitrosalicylic acid (5-NSA) as a matrix for in-source decay (ISD) of peptides during matrix-assisted laser desorption/ionization (MALDI) is described herein. Mechanistically, the decay process is initiated by a hydrogen abstraction from a peptide backbone amide nitrogen by 5-NSA. Hydrogen abstraction results in formation of an oxidized peptide containing a radical amide nitrogen. Subsequently, the C(?)-C bond N-terminal to the peptide bond is cleaved to form an a·/x fragment pair. The C(?)-C bonds C-terminal to Gly residues were less susceptible to cleavage than were those of other residues. C(?)-C bonds N-terminal to Pro and Sar residues were not cleaved by the aforementioned mechanism; instead, after hydrogen abstraction from a Pro or Sar C(?)-H bond, the peptide bond N-terminal to the Pro was cleaved yielding b- and y-series ions. We also show that fragments produced by MALDI 5-NSA-induced ISD were formed independently of the ionization process. PMID:21793066

Asakawa, Daiki; Takayama, Mitsuo



Molecular approach to the mechanisms of C-C bond formation and cleavage on metal surfaces: Hydrogenolysis, homologation, and dimerization of ethylene over Ru/SiO sub 2 catalysts  

SciTech Connect

At temperatures above ca. 50 C, over Ru/SiO{sub 2} catalysts and in the presence of hydrogen, ethylene undergoes hydrogenation, hydrogenolysis, homologation, and dimerization reactions. The influence of contact times and reaction temperatures on conversions and selectivities has been examined. At low temperatures (C-C bond cleavage and formation; two mechanisms are proposed which involve either metallocarbene insertion-elimination reactions or formation and decomposition of dimetallacyclic intermediates. Several mechanisms are envisioned for dimerization of ethylene; experimental data seem to support a mechanism which involves formation and coupling of two ethylidene species.

Rodriguez, E.; Leconte, M.; Basset, J.M.; Tanaka, K. (Institut de Recherches sur la Catalyse, Villeurbanne (France))



Mechanisms of C-C bond formation and cleavage on metal surfaces: Formation of butenes and hexenes from linear and branched pentenes over Ru/SiO sub 2 catalysts  

SciTech Connect

Over Ru/SiO{sub 2} catalyst, at temperatures above 100-150C and in the presence of hydrogen, linear and branched pentenes (1-pentene, cis- and trans-2-pentene, 2-methyl-2-butene, 3-methyl-1-butene, and 2-methyl-1-butene) undergo isomerization, hydrogenation, hydrogenolysis, and homologation. The main primary products of these last two reactions of C-C bond cleavage and formation are methane, butenes, and hexanes. At low temperature (100-150C), the formation of methane is reduced and the major products are C{sub 4} and C{sub 6} olefinic hydrocarbons, which are obtained in roughly comparable amounts. The distribution of the butenes isomers and of the hexenes isomers strongly depends on the structure of the starting pentene (linear or branched, terminal or internal). The results confirm that hydrogenolysis and homologation of a C{sub 5} olefinic hydrocarbon occur at comparable rates and involve: (1) cleavage of mainly a terminal C-C bond of the pentene isomer leading to C{sup 4} and C{sup 1} fragments, (2) reaction of this C{sup 1} fragment with the starting C{sup 5} to give C{sup 6} hydrocarbons, and (or) (3) hydrogenation of the C{sup 1} fragment to methane. Two mechanisms, based on concepts of organometallic chemistry, can account for the results (especially for the distribution of the C{sup 4} and C{sup 6} olefinic isomers): (1) a methylene insertion-deinsertion mechanism or (2) a mechanism that involves formation and decomposition of dimetallacyclic intermediates. Several experimental results seem to be in favor of the last proposed mechanism.

Rodriguez, E.; Leconte, M.; Basset, J. (Conventionne a l'Universite Claude-Bernard, Lyon (France))



Conversion of levulinate into succinate through catalytic oxidative carbon-carbon bond cleavage with dioxygen.  


Grand Cleft Oxo: Levulinate, available from biomass, is oxidized into succinate through manganese(III)-catalyzed selective cleavage of C?C bonds with molecular oxygen. In addition to levulinate, a wide range of aliphatic methyl ketones also undergo oxidative C?C bond cleavage at the carbonyl group. This procedure offers a route to valuable dicarboxylic acids from biomass resources by nonfermentive approaches. PMID:23922234

Liu, Junxia; Du, Zhongtian; Lu, Tianliang; Xu, Jie



Photochemical dynamics of Mg +-acetaldehyde: C-H vs. C-C bond activation pathways  

NASA Astrophysics Data System (ADS)

We have investigated the chemical dynamics of Mg +-acetaldehyde bimolecular complexes following Mg +-centered (3p?3s) excitation. Non-reactive dissociation to Mg + is the dominant decay channel. However, excitation in the 3p?(A ')?3s?(A ') band also results in reactive dissociation to MgH +, MgCHO +, and MgCH 3+ products, showing a clear ?-like electronic orbital alignment preference for chemical quenching. Isotope substitution shows reaction involves a direct attack on the aldehydic C-H or C-C bonds; the relative product branching indicates that the probabilities for C-H and C-C bond cleavage are comparable.

Lu, W.-Y.; Kleiber, P. D.



Carbon-carbon bond cleavage and rearrangement of benzene by a trinuclear titanium hydride  

NASA Astrophysics Data System (ADS)

The cleavage of carbon-carbon (C-C) bonds by transition metals is of great interest, especially as this transformation can be used to produce fuels and other industrially important chemicals from natural resources such as petroleum and biomass. Carbon-carbon bonds are quite stable and are consequently unreactive under many reaction conditions. In the industrial naphtha hydrocracking process, the aromatic carbon skeleton of benzene can be transformed to methylcyclopentane and acyclic saturated hydrocarbons through C-C bond cleavage and rearrangement on the surfaces of solid catalysts. However, these chemical transformations usually require high temperatures and are fairly non-selective. Microorganisms can degrade aromatic compounds under ambient conditions, but the mechanistic details are not known and are difficult to mimic. Several transition metal complexes have been reported to cleave C-C bonds in a selective fashion in special circumstances, such as relief of ring strain, formation of an aromatic system, chelation-assisted cyclometallation and ?-carbon elimination. However, the cleavage of benzene by a transition metal complex has not been reported. Here we report the C-C bond cleavage and rearrangement of benzene by a trinuclear titanium polyhydride complex. The benzene ring is transformed sequentially to a methylcyclopentenyl and a 2-methylpentenyl species through the cleavage of the aromatic carbon skeleton at the multi-titanium sites. Our results suggest that multinuclear titanium hydrides could serve as a unique platform for the activation of aromatic molecules, and may facilitate the design of new catalysts for the transformation of inactive aromatics.

Hu, Shaowei; Shima, Takanori; Hou, Zhaomin



Protocols for the selective cleavage of carbon-sulfur bonds in coal  

SciTech Connect

Removal of the organic sulfur in coal constitutes one of the major challenges facing fossil fuel scientists today. A cost--effective of desulfurizing Illinois coal is non-existent at the present time. Research in our group aims to develop a simple protocol for sulfur removal by gaining understanding of how various additives can enhance the rates of C-S bond cleavage in Illinois coal and coal model compounds, relative to fragmentation of the coal macromolecule via C-C, C-O, and C-N bond cleavage. During this funding period, we plan to carry out examinations of: (a) the effects of various reaction conditions on radical-initiated and Lewis acid-catalyzed C-S bond cleavages; (b) the effects of caustic impregnation and subsequent alcoholic reflux on C-S bond cleavage strategies; (c) the reactions of coal model compounds with electron-deficient substrates; (d) examinations of photooxidative C-S bond cleavage reactions; (e) the effects of moderate (300--400{degrees}C) temperatures and pressures as well as ultrasonic radiation on (a) - (c). Also planned are differential scanning calorimetric (DSC) examinations of selected C-S bond cleavage protocols, including those on Illinois coals that possess varying amounts of organic and inorganic sulfur.

Bausch, M.



Enantioselective C-C bond synthesis catalysed by enzymes.  


The enantioselective synthesis of C-C bonds is often the pivotal step of a synthesis. Nature has made a variety of versatile enzymes available that catalyse this type of reaction very selectively under mild conditions. Cyanohydrins, acyloins (alpha-hydroxy ketones), alpha-hydroxy acids and aldols (beta-hydroxy ketones) are very efficiently synthesised enantioselectively with the aid of C-C bond forming enzymes, which we discuss in this tutorial review. In the case of the alpha-hydroxy acids the applications of nitrilases in a synthetic dkr even allows a disconnection that has no enantioselective chemical equivalent. PMID:16137165

Sukumaran, Joly; Hanefeld, Ulf



Cerium-catalyzed oxidative C–C bond forming reactions  

Microsoft Academic Search

With respect to economical and ecological considerations, molecular oxygen is the oxidant of choice for functionalization of organic substrates. On the basis of our cerium-catalyzed ?-hydroxylation of ?-dicarbonyl compounds, we have developed an oxidative process for C–C bond formation in the presence of simple olefins like styrene. Products of these reactions, which are isolated as endoperoxidic 1,2-dioxane derivatives with potential

Jens Christoffers; Thomas Werner; Michael Rössle



Carbon-Selenium Bond Cleavage by a Rhodium Complex  

E-print Network

Carbon-Selenium Bond Cleavage by a Rhodium Complex David A. Vicic, Andrew W. Myers, and William D with tel- lophene.4,5 As Angelici has pointed out,3 selenium is an attractive sulfur analog because of its

Jones, William D.


Microbial cleavage of organic C-S bonds  


A microbial process is described for selective cleavage of organic C-S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials. Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C-S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Kilbane, J.J. II.



Microbial cleavage of organic C-S bonds  


A microbial process for selective cleavage of organic C--S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials, Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C--S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Kilbane, II, John J. (Woodstock, IL)



Protocols for the selective cleavage of carbon-sulfur bonds in coal. Quarterly report, September 1, 1991--November 30, 1991  

SciTech Connect

Removal of the organic sulfur in coal constitutes one of the major challenges facing fossil fuel scientists today. A cost--effective of desulfurizing Illinois coal is non-existent at the present time. Research in our group aims to develop a simple protocol for sulfur removal by gaining understanding of how various additives can enhance the rates of C-S bond cleavage in Illinois coal and coal model compounds, relative to fragmentation of the coal macromolecule via C-C, C-O, and C-N bond cleavage. During this funding period, we plan to carry out examinations of: (a) the effects of various reaction conditions on radical-initiated and Lewis acid-catalyzed C-S bond cleavages; (b) the effects of caustic impregnation and subsequent alcoholic reflux on C-S bond cleavage strategies; (c) the reactions of coal model compounds with electron-deficient substrates; (d) examinations of photooxidative C-S bond cleavage reactions; (e) the effects of moderate (300--400{degrees}C) temperatures and pressures as well as ultrasonic radiation on (a) - (c). Also planned are differential scanning calorimetric (DSC) examinations of selected C-S bond cleavage protocols, including those on Illinois coals that possess varying amounts of organic and inorganic sulfur.

Bausch, M.



Spectroscopic and structural evidence for the hydrogen bond nature of C?C?H…C?C contacts in ethynyl steroids  

NASA Astrophysics Data System (ADS)

Structural and IR-spectroscopic evidence is given that directed contacts from terminal alkynes to C?C double bonds possess the essential characteristics of weak hydrogen bonds. The contacts are directed at the center of the ?-bond rather than at one of the individual C-atoms. The contact distances from H to the center of the C?C bond are typically 2.8 Å, with the shortest distances being ˜2.5 Å. The interaction is of pronounced long-range nature and can be detected in the infrared spectrum even with a long H…? distance of almost 3.0 Å. The sample used is mainly composed of ethynyl steroids belonging to the progestine family.

Lutz, Bert; Kanters, Jan A.; van der Maas, John; Kroon, Jan; Steiner, Thomas



Disulfide bond cleavage: a redox reaction without electron transfer.  


By using Car-Parrinello molecular dynamics (CPMD) simulations we have simulated a mechanically induced redox reaction. Previous single-molecule atomic force microscopy (AFM) experiments demonstrated that the reduction of disulfide bonds in proteins with the weak reducing agent dithiothreitol depends on a mechanical destabilization of the breaking bond. With reactive molecular dynamics simulations the single steps of the reaction mechanism can be elucidated and the motion of the electrons can be monitored. The simulations show that the redox reaction consists of the heterolytic cleavage of the S--S bond followed by a sequence of proton transfers. PMID:20349464

Hofbauer, Florian; Frank, Irmgard



Bioluminescence detection of proteolytic bond cleavage by using recombinant aequorin.  


Detection of proteolytic bond cleavage was achieved by taking advantage of the bioluminescence emission generated by the photoprotein aequorin. A genetically engineered HIV-1 protease substrate was coupled with a cysteine-free mutant of aequorin by employing the polymerase chain reaction to produce a fusion protein that incorporates an optimum natural protease cleavage site. The fusion protein was immobilized on a solid phase and employed as the substrate for the HIV-1 protease. Proteolytic bond cleavage was detected by a decrease in the bioluminescence generated by the aequorin fusion protein on the solid phase. A dose-response curve for HIV-1 protease was constructed by relating the decrease in bioluminescence signal with varying amounts of the protease. The system was also used to evaluate two competitive and one noncompetitive inhibitor of the HIV-1 protease. Among the advantages of this assay is that by using recombinant methods a complete bioluminescently labeled protease recognition site can be designed and produced. The assay yields very sensitive detection limits, which are inherent to bioluminescence-based methods. An application of this system may be in the high-throughput screening of biopharmaceutical drugs that are potential inhibitors of a target protease. PMID:10847614

Deo, S K; Lewis, J C; Daunert, S



Borrowing hydrogen: a catalytic route to C-C bond formation from alcohols.  


Ruthenium complexes have been shown to perform efficient transfer hydrogenation reactions between alcohols and alkenes; in combination with an in situ Wittig reaction, indirect formation of C-C bonds has been achieved from alcohols. PMID:14737346

Edwards, Michael G; Jazzar, Rodolphe F R; Paine, Belinda M; Shermer, Duncan J; Whittlesey, Michael K; Williams, Jonathan M J; Edney, Dean D



Carbon-carbon bond cleavage of 1,2-hydroxy ethers b7 vanadium(V) dipicolinate complexes  

SciTech Connect

The development of alternatives to current petroleum-based fuels and chemicals is becoming increasingly important due to concerns over climate change, growing world energy demand, and energy security issues. Using non-food derived biomass to produce renewable feedstocks for chemicals and fuels is a particularly attractive possibility. However, the majority of biomass is in the form of lignocellulose, which is often not fully utilized due to difficulties associated with breaking down both lignin and cellulose. Recently, a number of methods have been reported to transform cellulose directly into more valuable materials such as glucose, sorbitol, 5-(chloromethyl)furfural, and ethylene glycol. Less progress has been made with selective transformations of lignin, which is typically treated in paper and forest industries by kraft pulping (sodium hydroxide/sodium sulfide) or incineration. Our group has begun investigating aerobic oxidative C-C bond cleavage catalyzed by dipicolinate vanadium complexes, with the idea that a selective C-C cleavage reaction of this type could be used to produce valuable chemicals or intermediates from cellulose or lignin. Lignin is a randomized polymer containing methoxylated phenoxy propanol units. A number of different linkages occur naturally; one of the most prevalent is the {beta}-O-4 linkage shown in Figure 1, containing a C-C bond with 1,2-hydroxy ether substituents. While the oxidative C-C bond cleavage of 1,2-diols has been reported for a number of metals, including vanadium, iron, manganese, ruthenium, and polyoxometalate complexes, C-C bond cleavage of 1,2-hydroxy ethers is much less common. We report herein vanadium-mediated cleavage of C-C bonds between alcohol and ether functionalities in several lignin model complexes. In order to explore the scope and potential of vanadium complexes to effect oxidative C-C bond cleavage in 1,2-hydroxy ethers, we examined the reactivity of the lignin model complexes pinacol monomethyl ether (A), 2-phenoxyethanol (B), and 1,2-diphenyl-2-methoxyethanol (C) (Figure 1). Reaction of (dipic)V{sup V}(O)O{sup i}Pr (1a) or (dipic)V{sup v}(O)OEt (lb) with A, B, or C in acetonitrile yielded new vanadium(V) complexes where the alcohol-ether ligand was bound in a chelating fashion. From the reaction of 1b with pinacol monomethyl ether (A) in acetonitrile solution, (dipic)V{sup v}(O)(pinOMe) (2) (PinOMe = 2,3-dimethyl-3-methoxy-2-butanoxide) was isolated in 61 % yield. Reaction of 1b with 2-phenoxyethanol (B) in acetonitrile gave the new complex (dipic)V{sup v}(O)(OPE) (3) (OPE = 2-phenoxyethoxide), which was isolated in 76% yield. In a similar fashion, 1a reacted with 1,2-diphenyl-2-methoxyethanol (C) to give (dipic)V(O)(DPME) (4) (DPME = 1,2-diphenyl-2-methoxyethoxide), which was isolated in 39% yield. Complexes 2, 3, and 4 were characterized by {sup 1}H NMR and IR spectroscopy, elemental analysis, and X-ray crystallography. Compared to the previously reported vanadium(V) pinacolate complex (dipic)V(O)(pinOH) the X-ray structure of complex 2 reveals a slightly shorter V = O bond, 1.573(2) {angstrom} vs 1.588(2) {angstrom} for the pinOH structure. Complexes 3 and 4 display similar vanadium oxo bond distances of 1.568(2) {angstrom} and 1.576(2) {angstrom}, respectively. All three complexes show longer bonds to the ether-oxygen trans to the oxo (2.388(2) {angstrom} for 2, 2.547(2) {angstrom} for 3, and 2.438(2) {angstrom} for 4) than to the hydroxy-oxygen in the pinOH structure (2.252(2) {angstrom}).

Hanson, Susan K [Los Alamos National Laboratory; Gordon, John C [Los Alamos National Laboratory; Thorn, David L [Los Alamos National Laboratory; Scott, Brian L [Los Alamos National Laboratory; Baker, R Tom [Los Alamos National Laboratory



Cleavage of an amide bond by a ribozyme  

NASA Technical Reports Server (NTRS)

A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

Dai, X.; De Mesmaeker, A.; Joyce, G. F.; Miller, S. L. (Principal Investigator)



Formation, preservation, and cleavage of the disulfide bond by vanadium.  


Reaction of the disulfide [HpicanS](2) (HpicanS is the carboxamide based on picolinate (pic) and o-mercaptoaniline (anS); the [] brackets are used to denote disulfides) with [VOCl(2)(thf)(2)] leads to reductive scission of the disulfide bond and formation of the mixed-valence (V(IV)/V(V)) complex anion [(OVpicanS)(2)mu-O](-) (1), with the dianionic ligand coordinating through the pyridine-N atom, the deprotonated amide-N atom, and thiophenolate-S atom. Reductive cleavage of the SbondS bond is also observed as [VCl(2)(tmeda)(2)] (tmeda=tetramethylethylenediamine) is treated with the disulfides [HsalanS](2) or [HvananS](2) (HsalanS and HvananS are the Schiff bases formed between o-mercaptoaniline and salicylaldehyde (Hsal) or vanillin (Hvan), respectively), yielding the V(III) complexes [VCl(tmeda)(salanS)] (2 a), or [VCl(tmeda)(vananS)] (2 b). The disulfide bond remains intact in the aerial reaction between [HsalanS](2) and [VCl(3)(thf)(3)] to yield the V(V) complex [VOCl[salanS](2)] (3), where (salanS)(2-) coordinates through the two phenolate and one of the imine functions. The S-S bond is also preserved as [VO(van)(2)] or [VO(nap)(2)] (Hnap=2-hydroxynaphthalene-1-carbaldehyde) is treated with bis(2-aminophenyl)disulfide, [anS](2), a reaction which is accompanied by condensation of the aldehyde and the diamine, and complexation of the resulting bis(Schiff bases) [HvananS](2) or [HnapanS](2) to form the complexes [VO[vananS](2)] (4 a) or [VO[napanS](2)] (4 b). In 4 a and 4 b, the phenolate and imine functions, and presumably also one of the disulfide-S atoms, coordinate to V(IV). 2-Mercaptophenyl-2'-pyridinecarboxamide (H(2)picanS) retains its identity in the presence of V(III); reaction between [VCl(3)(thf)(3)] and H(2)picanS yields [V[picanS](2)](-) (5). The dithiophenolate 2,6-bis(mercaptophenylthio)dimethylpyridine (6 a) is oxidized, mediated by VO(2+), to the bis(disulfide) octathiadiaza-cyclo-hexaeicosane 6 b. The relevance of these reactions for the speciation of vanadium under physiological conditions is addressed. [HNEt(3)]-1.0.5 NEt(3,) 3.3 CH(2)Cl(2), [HsalanS](2), [HNEt(3)]-5, and 6 b.4 THF have been characterized by X-ray diffraction analysis. PMID:12698438

Wang, Dongren; Behrens, Axel; Farahbakhsh, Mahin; Gätjens, Jessica; Rehder, Dieter



Formation of C–C Bonds via Iridium-Catalyzed Hydrogenation and Transfer Hydrogenation  

PubMed Central

The formation of C–C bonds via catalytic hydrogenation and transfer hydrogenation enables carbonyl and imine addition in the absence of stoichiometric organometallic reagents. In this review, iridium-catalyzed C–C bond-forming hydrogenations and transfer hydrogenations are surveyed. These processes encompass selective, atom-economic methods for the vinylation and allylation of carbonyl compounds and imines. Notably, under transfer hydrogenation conditions, alcohol dehydrogenation drives reductive generation of organoiridium nucleophiles, enabling carbonyl addition from the aldehyde or alcohol oxidation level. In the latter case, hydrogen exchange between alcohols and ?-unsaturated reactants generates electrophile–nucleophile pairs en route to products of hydro-hydroxyalkylation, representing a direct method for the functionalization of carbinol C–H bonds. PMID:21822399

Bower, John F.; Krische, Michael J.



The analysis and practical application about the effect of intra-vascular laser irradiation on C-C bond  

NASA Astrophysics Data System (ADS)

C-C bond is the most common kind of interactions in biological molecules. For example, the molecules of cholesterol and fibrinogen are connected with C-C bonds. We analysis the effect of Laser onto C-C bond in medical cure case by the method of Intra-vascular Laser Irradiation on blood (ILIB), and in theory a new model of "Laser-(C-C)" inharmonic oscillator is constructed on the base of quantum mechanics. Furthermore, we investigate the helpful influence of ILIB through sixty-two cases of brain-thrombus.

Zhang, Can-Bang; Dai, Zhi-Fu; Zhang, Li-Li; Tian, Jia-Jin; Zhou, Ling-Yun



Addition of C-C and C-H bonds by pincer-iridium complexes: a combined experimental and computational study.  


We report that pincer-ligated iridium complexes undergo oxidative addition of the strained C-C bond of biphenylene. The sterically crowded species ((tBu)PCP)Ir ((R)PCP = ?(3)-1,3-C6H3(CH2PR2)2) initially reacts with biphenylene to selectively add the C(1)-H bond, to give a relatively stable aryl hydride complex. Upon heating at 125 °C for 24 h, full conversion to the C-C addition product, ((tBu)PCP)Ir(2,2'-biphenyl), is observed. The much less crowded ((iPr)PCP)Ir undergoes relatively rapid C-C addition at room temperature. The large difference in the apparent barriers to C-C addition is notable in view of the fact that the addition products are not particularly crowded, since the planar biphenyl unit adopts an orientation perpendicular to the plane of the (R)PCP ligands. Based on DFT calculations the large difference in the barriers to C-C addition can be explained in terms of a "tilted" transition state. In the transition state the biphenylene cyclobutadiene core is calculated to be strongly tilted (ca. 50°-60°) relative to its orientation in the product in the plane perpendicular to that of the PCP ligand; this tilt results in very short, unfavorable, non-bonding contacts with the t-butyl groups in the case of the (tBu)PCP ligand. The conclusions of the biphenylene studies are applied to interpret computational results for cleavage of the unstrained C-C bond of biphenyl by ((R)PCP)Ir. PMID:25250874

Laviska, David A; Guan, Changjian; Emge, Thomas J; Wilklow-Marnell, Miles; Brennessel, William W; Jones, William D; Krogh-Jespersen, Karsten; Goldman, Alan S



Cleavage of aromatic carbon-carbon bonds. [Cleavage reactions with o-terphenyl  

SciTech Connect

The search for a model substrate to use in evaluating relative reactivity of H-donors, under coal liquefaction conditions has led to this study of o-terphenyl. Results of cleavage reaction studies with o-terphenyl show that o-terphenyl couples in the presence of model H-donors and many coal derived solvents to form triphenylene, and forms biphenyl by cleavage. The latter reaction is of more interest as the yields are substantial, and the yields have application to the study of properties of solvents. Attempts to elucidate the mechanism involved kinetic studies, and reaction with a deuterated H-donor. The best mechanism appears to be that in which the low steady-state concentration of reactive H-donor attacks either ipso position in o-terphenyl followed by cleavage. This mechanism is known to occur at high temperatures. 7 references, 3 tables.

Kline, E.A.; Teichert, W.P.; Farnum, B.W.



The computation of C-C and N-N bond dissociation energies for singly, doubly, and triply bonded systems  

NASA Technical Reports Server (NTRS)

The bond dissociation energies (D sub e) of C2H2, C2H4, C2H6, N2, N2H2, and N2H4 are studied at various levels of correlation treatment. The convergence of D sub e with respect to the one particle basis is studied at the single reference modified coupled-pair functional (MCPF) level. At all levels of correlation treatment, the errors in the bond dissociation energies increase with the degree of multiple bond character. The multireference configuration interaction (MRCI) D sub e values, corrected for an estimate of higher excitations, are in excellent agreement with those determined using the size extensive averaged coupled pair functional (ACPF) method. It was found that the full valence complete active space self consistent field (CASSCF)/MRCI calculations are reproduced very well by MRCI calculations based on a CASSCF calculation that includes in the active space only those electrons involved in the C-C or N-N bonds. To achieve chemical accuracy (1 kcal/mole) for the D sub e values of the doubly bonded species C2H4 and N2H2 requires one particle basis sets including up through h angular momentum functions (l = 5) and a multireference treatment of electron correlation: still higher levels of calculation are required to achieve chemical accuracy for the triply bonded species C2H2 and N2.

Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.; Taylor, Peter R.



Theoretical studies on Si-C bond cleavage in organosilane precursors during polycondensation to organosilica hybrids.  


Molecular orbital theory calculations were carried out to predict the occurrence of Si-C bond cleavage in various organosilane precursors during polycondensation to organosilica hybrids under acidic and basic conditions. On the basis of proposed mechanisms for cleavage of the Si-C bonds, the proton affinity (PA) of the carbon atom at the ipso-position and the PA of the carbanion generated after Si-C cleavage were chosen as indices for Si-C bond stability under acidic and basic conditions, respectively. The indices were calculated using a density functional theory (DFT) method for model compounds of organosilane precursors (R-Si(OH)(3)) having organic groups (R) of benzene (Ph), biphenyl (Bp), terphenyl (Tph), naphthalene (Nph), N-methylcarbazole (MCz), and anthracene (Ant). The orders for the predicted stability of the Si-C bond were Ph > Nph > Bp > Ant > Tph > MCz for acidic conditions and Ph > MCz > Bp > Nph > Tph > Ant for basic conditions. These behaviors were primarily in agreement with experimental results where cleavage of the Si-C bonds occurred for Tph (both acidic and basic), MCz (acidic), and Ant (basic). The Si-C bond cleavage of organosilane precursors during polycondensation is qualitatively predicted from these indices based on our theoretical approach. PMID:20429568

Shirai, Soichi; Goto, Yasutomo; Mizoshita, Norihiro; Ohashi, Masataka; Tani, Takao; Shimada, Toyoshi; Hyodo, Shi-aki; Inagaki, Shinji



The Transition State for Metal-Catalyzed Dehalogenation: C-I Bond Cleavage on Ag(111)  

E-print Network

is the dissociation of carbon-iodine bonds which is used to create stable alkyl groups on many metal surfaces.3 picture of the nature of the transition state for carbon-iodine and carbon-chlorine bond cleavage on both- fluorocarbons (CFCs) into hydrofluorocarbons (HFCs).1,2 The most commonly studied catalyst

Gellman, Andrew J.


The Janus-faced role of external forces in mechanochemical disulfide bond cleavage.  


Recent force microscopy measurements on the mechanically activated cleavage of a protein disulfide bond through reaction with hydroxide ions revealed that for forces greater than 0.5 nN, the acceleration of the reaction rate is substantially reduced. Here, using ab initio simulations, we trace this 'reactivity switch' back to a dual role played by the mechanical force, which leads to antagonistic effects. On the one hand, the force performs work on the system, and thereby accelerates the reaction. On the other hand, the force also induces a conformational distortion that involves the S-S-C-C dihedral angle, which drives the disulfide into a conformation that is shielded against nucleophilic attack because of steric hindrance. The discovery of force-induced conformational changes that steer chemical reactivity provides a new key concept that is expected to be relevant beyond this specific case, for example in understanding how 'disulfide switches' regulate protein function and for the rational design of mechanoresponsive materials. PMID:23881500

Dopieralski, Przemyslaw; Ribas-Arino, Jordi; Anjukandi, Padmesh; Krupicka, Martin; Kiss, Janos; Marx, Dominik



Formation of C–C bonds via ruthenium-catalyzed transfer hydrogenation*  

PubMed Central

Ruthenium-catalyzed transfer hydrogenation of diverse ?-unsaturated reactants in the presence of aldehydes provides products of carbonyl addition. Dehydrogenation of primary alcohols in the presence of the same ?-unsaturated reactants provides identical products of carbonyl addition. In this way, carbonyl addition is achieved from the alcohol or aldehyde oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. In this account, the discovery of ruthenium-catalyzed C–C bond-forming transfer hydrogenations and the recent development of diastereo- and enantioselective variants are discussed. PMID:23430602

Moran, Joseph; Krische, Michael J.



An erbium-based bifuctional heterogeneous catalyst: a cooperative route towards C-C bond formation.  


Heterogeneous bifuctional catalysts are multifunctional synthetic catalysts enabling efficient organic transformations by exploiting two opposite functionalities without mutual destruction. In this paper we report the first Er(III)-based metallorganic heterogeneous catalyst, synthesized by post-calcination MW-assisted grafting and modification of the natural aminoacid L-cysteine. The natural acid-base distance between sites was maintained to assure the cooperation. The applicability of this new bifunctional heterogeneous catalyst to C-C bond formation and the supposed mechanisms of action are discussed as well. PMID:25029070

Oliverio, Manuela; Costanzo, Paola; Macario, Anastasia; De Luca, Giuseppina; Nardi, Monica; Procopio, Antonio



Acetate C-C bond formation and decomposition in the anaerobic world: the structure of a central enzyme and its key active-site metal cluster.  


The structure of carbon monoxide dehydrogenase/acetyl-coenzyme A synthase (CODH/ACS), a central enzyme in the anaerobic metabolism of acetyl-coenzyme A (acetyl-CoA), has been solved to a resolution of 2.2A. The active-site metal cluster responsible for catalyzing acetyl C-C bond synthesis and cleavage, designated the A center, was identified as an Fe(4)S(4) iron sulfur cluster with one of its cysteine thiolates acting as a bridge to an adjacent binuclear metal site. Nickel was found at one position in the binuclear site and the other metal was indicated to be copper - a surprising result, implying a previously unrecognized role for copper. Details of the A center provided new insight into the unusual organometallic mechanism of acetyl C-C bond formation and cleavage, with substantial conformational changes indicated for binding of the large methylcorrinoid protein substrate, and a unique intramolecular channel acting to contain carbon monoxide within the protein and transfer it to the site needed for acetyl-CoA synthesis. PMID:12765830

Grahame, David A



Palladium(II)-catalyzed dehydrogenative cross-coupling between two C(sp3)-H bonds: unexpected C=C bond formation.  


C=C bond construction: A palladium-catalyzed oxidative C(sp3)-H/C(sp3)-H cross-coupling is shown to forge C=C bonds rather than C(sp3)-C(sp3) bonds through reactions of indolin-2-ones or benzofuran-2-ones with O-benzoyl hydroxylamines in the absence of an added oxidant. PMID:23780778

Li, Gaocan; Qian, Shengyou; Wang, Chunxia; You, Jingsong



Transition-metal-free C-C bond forming reactions of aryl, alkenyl and alkynylboronic acids and their derivatives.  


Investigation of new methods for the synthesis of C-C bonds is fundamental for the development of new organic drugs and materials. Aryl-, alkenyl- and alkynylboronic acids and their derivatives constitute attractive reagents towards this end, due to their stability, low toxicity and ease of handling. However, these compounds are only moderately nucleophilic. Consequently, the most popular C-C bond forming reactions of these boronic acids, such as the Suzuki-Miyaura, Heck, and Hayashi-Miyaura reactions, or additions to C[double bond, length as m-dash]O and C[double bond, length as m-dash]N bonds, require catalysis by transition metals. However, due to the toxicity and cost of transition metals, some new methods for C-C bond formation using aryl-, alkenyl- and alkynylboronic acids under transition-metal-free conditions are beginning to emerge. In this tutorial review, the recent synthetic advances in this field are highlighted and discussed. PMID:25181967

Roscales, S; Csákÿ, A G



The computation of C-C and N-N bond dissociation energies for singly, doubly, and triply bonded systems  

NASA Technical Reports Server (NTRS)

The bond dissociation energies (De) of C2H2, C2H4, C2H6, N2, N2H2, and N2H4 are studied at various levels of correlation treatment. The convergence of De with respect to the one-particle basis is studied at the single-reference modified coupled-pair-functional (MCPF)level. At all levels of correlation treatment, the errors in the bond dissociation energies increase with the degree of multiple bond character. The multireference configuration-interaction (MRCI) De values, corrected for an estimate of higher excitations, are in excellent agreement with those determined using the size-extensive averaged-coupled-pair-functional (ACPF) method. The full-valence complete-active-space self-consistent-field (CASSCF)/MRCI calculations are reproduced very well by MRCI calculations based on a CASSCF calculation that includes in the active space only those electrons involved in the C-C or N-N bonds.

Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.; Taylor, Peter R.



Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds  

SciTech Connect

The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.

John J. Kilbane II



Switchable conductance in functionalized carbon nanotubes via reversible sidewall bond cleavage.  


We propose several covalent functionalizations for carbon nanotubes that display switchable on/off conductance in metallic tubes. The switching action is achieved by reversible control of bond-cleavage chemistry in [1 + 2] cycloadditions via the sp(3) ? sp(2) rehybridization that it induces; this leads to remarkable changes of conductance even at very low degrees of functionalization. Reversible bond-cleavage chemistry is achieved by identifying addends that provide optimal compensation between the bond-preserving through-space ? orbital interactions with the tube against the bond-breaking strain energy of the cyclopropane moiety. Several strategies for real-time control, based on redox or hydrolysis reactions, cis-trans isomerization or excited-state proton transfer are proposed. Such designer functional groups would allow for the first time direct control of the electrical properties of metallic carbon nanotubes, with extensive applications in nanoscale devices. PMID:21591731

Li, Elise Y; Poilvert, Nicolas; Marzari, Nicola



Direct enantiospecific substitution of primary ?-aminoalkylferrocenes via Lewis acid-catalyzed C-N bond cleavage.  


Highly enantioenriched primary ?-aminoalkylferrocenes were found to undergo zinc chloride-catalyzed substitution with various carbon, nitrogen, and sulfur nucleophiles in an enantiospecific fashion through C-N bond cleavage. The reaction tolerates air and moisture and exhibits high atom-economy by releasing ammonia as the sole byproduct. PMID:25307165

Zhou, Meng-Guang; Zhang, Wen-Zhao; Tian, Shi-Kai



Cleavage of Carbon-Carbon Bonds in Alkyl Cyanides Using Nickel(0)  

E-print Network

Cleavage of Carbon-Carbon Bonds in Alkyl Cyanides Using Nickel(0) Juventino J. Garci´a,*, Alma Are of alkyl cyanides afforded nickel(0) compounds of the type [(dippe)Ni(2 -RCN)], where R ) Me, Et, Pr, i Pr, the use of alkyl and aryl cyanides as substrates has been scarcely studied. Relevant examples

Jones, William D.


Raman spectroscopic determination of the length, energy, Debye temperature, and compressibility of the C-C bond in carbon allotropes  

NASA Astrophysics Data System (ADS)

Raman phonon relaxation dynamics in carbon allotropes including graphene, carbon nanotube, C60, carbon nanobud, graphite, and diamond has been formulated in terms of the bond order-length-strength (BOLS) correlation. The length and energy responses of the representative bond to the change of coordination environment, pressure, and temperature determine intrinsically the Raman shifts. Reproduction of the measured results in quantitative information of the bond length, bond energy, mode cohesive energy, binding energy density, Debye temperature, and the compressibility of the C-C bond in each phase without needing involvement of the phonon scattering resonant processes or the mode Grüneisen constants.

Yang, X. X.; Zhou, Z. F.; Wang, Yan; Li, J. W.; Guo, N. G.; Zheng, W. T.; Peng, J. Z.; Sun, C. Q.



a Computational Investigation of c-C3H2...HX(X = F, Cl, Br) H-Bonded Complexes  

NASA Astrophysics Data System (ADS)

Cyclopropenylidene (c-C3H2) is of significant importance in interstellar chemistry and synthetic chemistry (e.g., transition metal and organic catalysis). Because of its peculiar structure, c-C3H2 can act as a hydrogen-bond donor or acceptor. In order to gain insight into this feature, the ground-state potential energy surfaces of singlet c-C3H2 complexed with hydrogen halides HX (X = F, Cl, Br) have been explored extensively by density-functional theory (B3LYP) and {ab initio} quantum chemistry (MP2) with a variety of basis sets, cc-pVxZ and aug-cc-pVxZ (x = D, T). The complexes characterized have the carbenic end of c-C3H2 H-bonded to HX, with some proton transfer occurring, the extent of which follows the order HF < HCl < HBr. Accompanying the complex formation are the dipole moment enhancement, the charge transfer, red shifts of the HX vibrational stretching frequencies together with the significant enhancement of band intensity and concomitant HX bond elongation. The nature of H-bonding in these complexes has been explored, based on energy decomposition schemes and the Bader's quantum theory of atoms-in-molecules, with the conclusion that c-C3H2 is a strong H-bond acceptor with respect to the hydrogen halides.

Varadwaj, Pradeep R.; Varadwaj, Arpita; Peslherbe, Gilles H.



Cleavage of NH bonds by active oxygen on Ag(110). II. Selective oxidation of ethylamine to acetonitrile  

NASA Astrophysics Data System (ADS)

The adsorption of ethylamine on Ag(110) and its reaction with adsorbed oxygen was studied with temperature programmed reaction spectroscopy (TPRS), X-ray photoelectron spectroscopy (XPS), and electron energy loss vibrational spectroscopy (EELS). Adsorption of ethylamine on the clean Ag(110) surface proceeds at 110 K without dissociation. Desorption from the multilayer occurs at 160 K, and a series of broader desorption peaks from monolayer states are observed from 150 to 400 K. The chemical shift of the N(1s) X-ray photoelectron spectrum indicates that ethylamine bonds through the nitrogen lone pair in the monolayer. The reaction of ethylamine with adsorbed oxygen starts with the formation of adsorbed CH 3CH 2NH and adsorbed hydroxyl groups upon adsorption at 110 K. These species undergo further reaction to yield water from 280 to 370 K, and hydrogen, acetonitrile, and regenerated ethylamine at 370 K. Acetonitrile is the only carbon-containing product observed (other than ethylamine), indicative of highly selective bond breaking processes. Deuterium labeling experiments showed that preadsorbed oxygen activates the N?H bonds, leading to water formation, while the hydrogen product evolved at higher temperatures originates from the carbon skeleton via C?H bond metallation by the silver surface. Disproportionation of CH 3CH 2NH groups was identified. Ethylamine is formed by rate-limiting C?H bond cleavage of adsorbed CH 3CH 2N. No evidence was found for the activation of either C?C or C?N bonds, and the surface metallation of N?H bonds does not occur.

Thornburg, D. M.; Madix, R. J.



Biotic and abiotic carbon to sulfur bond cleavage. Final report  

SciTech Connect

The microbial desulfurization of organosulfur compounds occurs by unprecedented and largely unexplored biochemical processes. A study of such biotic desulfurizations can be expected to give rise to new and useful chemistry and enzymology. The potential value of understanding and harnessing these processes is seen in relation to the need for methods for the removal of organically bound sulfur from coal and the degradation of organic sulfur-containing pollutants. This research effort has been directed towards an examination of desulfurization ability in well characterized microorganisms, the isolation of bacteria with desulfurization ability from natural sources, the characterization and mechanistic evaluation of the observed biocatalytic processes, the development of biomimetic synthetic organic chemistry based on biotic desulfurization mechanisms and the design and preparation of improved coal model compounds for use in microbial selection processes. A systematic approach to studying biodesulfurizations was undertaken in which organosulfur compounds have been broken down into classes based on the oxidation state of the sulfur atom and the structure of the rest of the organic material. Microbes have been evaluated in terms of ability to degrade organosulfur compounds with sulfur in its sulfonic acid oxidation state. These compounds are likely intermediates in coal desulfurization and are present in the environment as persistent pollutants in the form of detergents. It is known that oxygen bonded to sulfur lowers the carbon-sulfur bond energy, providing a thermodynamic basis for starting with this class of compounds.

Frost, J.W.



The mechanism of hydrocarbon oxygenate reforming: C-C bond scission, carbon formation, and noble-metal-free oxide catalysts.  


Towards a molecular understanding of the mechanism behind catalytic reforming of bioderived hydrocarbon oxygenates, we explore the C-C bond scission of C2 model compounds (acetic acid, ethanol, ethylene glycol) on ceria model catalysts of different complexity, with and without platinum. Synchrotron photoelectron spectroscopy reveals that the reaction pathway depends very specifically on both the reactant molecule and the catalyst surface. Whereas C-C bond scission on Pt sites and on oxygen vacancies involves intermittent surface carbon species, the reaction occurs without any carbon formation and deposition for ethylene glycol on CeO2(111). PMID:24203922

Lykhach, Yaroslava; Neitzel, Armin; Šev?íková, Klára; Johánek, Viktor; Tsud, Nataliya; Skála, Tomáš; Prince, Kevin C; Matolín, Vladimír; Libuda, Jörg



Reaction Pathways and Energetics of Etheric C?O Bond Cleavage Catalyzed by Lanthanide Triflates  

SciTech Connect

Efficient and selective cleavage of etheric C?O bonds is crucial for converting biomass into platform chemicals and liquid transportation fuels. In this contribution, computational methods at the DFT B3LYP level of theory are employed to understand the efficacy of lanthanide triflate catalysts (Ln(OTf)3, Ln = La, Ce, Sm, Gd, Yb, and Lu) in cleaving etheric C?O bonds. In agreement with experiment, the calculations indicate that the reaction pathway for C?O cleavage occurs via a C?H ? O?H proton transfer in concert with weakening of the C?O bond of the coordinated ether substrate to ultimately yield a coordinated alkenol. The activation energy for this process falls as the lanthanide ionic radius decreases, reflecting enhanced metal ion electrophilicity. Details of the reaction mechanism for Yb(OTf)3-catalyzed ring opening are explored in depth, and for 1-methyl-d3-butyl phenyl ether, the computed primary kinetic isotope effect of 2.4 is in excellent agreement with experiment (2.7), confirming that etheric ring-opening pathway involves proton transfer from the methyl group alpha to the etheric oxygen atom, which is activated by the electrophilic lanthanide ion. Calculations of the catalytic pathway using eight different ether substrates indicate that the more rapid cleavage of acyclic versus cyclic ethers is largely due to entropic effects, with the former C?O bond scission processes increasing the degrees of freedom/particles as the transition state is approached.

Assary, Rajeev S.; Atesin, Abdurrahman C.; Li, Zhi; Curtiss, Larry A.; Marks, Tobin J.



Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage  

SciTech Connect

In this chapter, we summarize recent work from our laboratory and provide new perspective on two important aspects of bacterial mercury resistance: the molecular mechanism of transcriptional regulation by MerR, and the enzymatic cleavage of the Hg-C bond in methylmercury by the organomercurial lyase, MerB. Molecular dynamics (MD) simulations of MerR reveal an opening-and-closing dynamics, which may be involved in initiating transcription of mercury resistance genes upon Hg(II) binding. Density functional theory (DFT) calculations on an active-site model of the enzyme reveal how MerB catalyzes the Hg-C bond cleavage using cysteine coordination and acid-base chemistry. These studies provide insight into the detailed mechanisms of microbial gene regulation and defense against mercury toxicity.

Guo, Hao-Bo [ORNL; Parks, Jerry M [ORNL; Johs, Alexander [ORNL; Smith, Jeremy C [ORNL



Observation and X-ray analysis of the microstructures for a bonding material of C\\/C composite and copper  

Microsoft Academic Search

The purpose of this study is to examine the microstructure of a bonding material of C\\/C composite and copper before and after thermal shock tests. Optical and scanning electron microscopy, and energy dispersive X-ray analysis were used to study the microstructures before and after thermal shock tests. In this study, the specimen were given thermal shock without an active cooling,

A. Kurumada; B. McEnaney; T. Oku; K. Kawamata; O. Motojima; N. Noda



From Ketones to Esters by a Cu-Catalyzed Highly Selective C(CO)-C(alkyl) Bond Cleavage: Aerobic Oxidation and Oxygenation with Air.  


The Cu-catalyzed aerobic oxidative esterification of simple ketones via C-C bond cleavage has been developed. Varieties of common ketones, even inactive aryl long-chain alkyl ketones, are selectively converted into esters. The reaction tolerates a wide range of alcohols, including primary and secondary alcohols, chiral alcohols with retention of the configuration, electron-deficient phenols, as well as various natural alcohols. The usage of inexpensive copper catalyst, broad substrate scope, and neutral and open air conditions make this protocol very practical. (18)O labeling experiments reveal that oxygenation occurs during this transformation. Preliminary mechanism studies indicate that two novel pathways are mainly involved in this process. PMID:25251943

Huang, Xiaoqiang; Li, Xinyao; Zou, Miancheng; Song, Song; Tang, Conghui; Yuan, Yizhi; Jiao, Ning



Entropic Origin of Cobalt-Carbon Bond Cleavage Catalysis in Adenosylcobalamin-Dependent Ethanolamine Ammonia-Lyase  

PubMed Central

Adenosylcobalamin-dependent enzymes accelerate the cleavage of the cobalt-carbon (Co-C) bond of the bound coenzyme by >1011-fold. The cleavage-generated 5?-deoxyadenosyl radical initiates the catalytic cycle by abstracting a hydrogen atom from substrate. Kinetic coupling of the Co-C bond cleavage and hydrogen atom transfer steps at ambient temperatures has interfered with past experimental attempts to directly address the factors that govern Co-C bond cleavage catalysis. Here, we use time-resolved, full-spectrum electron paramagnetic resonance spectroscopy, temperature-step reaction initiation, starting from the enzyme-coenzyme-substrate ternary complex, and 2H-labeled substrate, to study radical pair generation in ethanolamine ammonia-lyase from Salmonella typhimurium at 234-248 K in a dimethylsulfoxide/water cryosolvent system. The monoexponential kinetics of formation of the 2H- and 1H-substituted substrate radicals are the same, indicating that Co-C bond cleavage rate-limits radical pair formation. Analysis of the kinetics by using a linear, three-state model allows extraction of the microscopic rate constant for Co-C bond cleavage. Eyring analysis reveals that the activation enthalpy for Co-C bond cleavage is 32 ±1 kcal/mol, which is the same as for the cleavage reaction in solution. The origin of Co-C bond cleavage catalysis in the enzyme is, therefore, the large, favorable activation entropy of 61 ±6 cal/mol/K (relative to 7 ±1 cal/mol/K in solution). This represents a paradigm shift from traditional, enthalpy-based mechanisms that have been proposed for Co-C bond breaking in B12 enzymes. The catalysis is proposed to arise from an increase in protein configurational entropy along the reaction coordinate. PMID:24028405

Wang, Miao; Warncke, Kurt



Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase.  


Adenosylcobalamin-dependent enzymes accelerate the cleavage of the cobalt-carbon (Co-C) bond of the bound coenzyme by >10(10)-fold. The cleavage-generated 5'-deoxyadenosyl radical initiates the catalytic cycle by abstracting a hydrogen atom from substrate. Kinetic coupling of the Co-C bond cleavage and hydrogen-atom-transfer steps at ambient temperatures has interfered with past experimental attempts to directly address the factors that govern Co-C bond cleavage catalysis. Here, we use time-resolved, full-spectrum electron paramagnetic resonance spectroscopy, with temperature-step reaction initiation, starting from the enzyme-coenzyme-substrate ternary complex and (2)H-labeled substrate, to study radical pair generation in ethanolamine ammonia-lyase from Salmonella typhimurium at 234-248 K in a dimethylsulfoxide/water cryosolvent system. The monoexponential kinetics of formation of the (2)H- and (1)H-substituted substrate radicals are the same, indicating that Co-C bond cleavage rate-limits radical pair formation. Analysis of the kinetics by using a linear, three-state model allows extraction of the microscopic rate constant for Co-C bond cleavage. Eyring analysis reveals that the activation enthalpy for Co-C bond cleavage is 32 ± 1 kcal/mol, which is the same as for the cleavage reaction in solution. The origin of Co-C bond cleavage catalysis in the enzyme is, therefore, the large, favorable activation entropy of 61 ± 6 cal/(mol·K) (relative to 7 ± 1 cal/(mol·K) in solution). This represents a paradigm shift from traditional, enthalpy-based mechanisms that have been proposed for Co-C bond-breaking in B12 enzymes. The catalysis is proposed to arise from an increase in protein configurational entropy along the reaction coordinate. PMID:24028405

Wang, Miao; Warncke, Kurt



Base-promoted aryl-bromine bond cleavage with cobalt(II) porphyrins via a halogen atom transfer mechanism.  


Aryl-bromine bonds are successfully cleaved by cobalt(II) porphyrins in basic media to give Co(por)Ar (por = porphyrin) in good yields. Mechanistic studies suggested that the aryl-bromine bond is cleaved through a halogen atom transfer mechanism, which is different from the aryl-halogen bond cleavage mechanism with other group 9 metalloporphyrins. PMID:24699823

Liu, Chun Ran; Qian, Ying Ying; Chan, Kin Shing



Disulfide bond cleavage in TEMPO-free radical initiated peptide sequencing mass spectrometry.  


The gas-phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o-TEMPO-Bz-conjugated peptides with an intra- and intermolecular disulfide bond was investigated using MS(n) tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLCRIVVIRVCR), TGF-? (CHSGYVGVRC), MCH (DFDMLRCMLGRVFRPCWQY) and Adrenomedullin (16-31) (CRFGTCTVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o-TEMPO-Bz-conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the S-S or C-S bond was readily cleaved. The observed peptide backbone fragments included a-, c-, x- or z-types, which indicates that the radical-driven peptide fragmentation mechanism plays an important role in TEMPO-FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the S-S or C-S bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of •SH or •SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the S-S bond, the abstraction of a hydrogen atom at C(?) by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H-abstraction at C(?) is suggested to lead to C-S bond cleavage, which yields [ion ± S] fragments or the loss of •SH or •SSH. PMID:21834022

Lee, Minhee; Lee, Younjin; Kang, Minhyuk; Park, Hyeyeon; Seong, Yeonmi; Sung, Bong June; Moon, Bongjin; Oh, Han Bin



Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds  

SciTech Connect

The objective of the project was to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically, the development of a novel biochemical pathway for the selective cleavage of C-N bonds in carbazole was the focus of research in this project. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. Obtaining an enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl-2,3-diol was the focus of much of the research in this project, however; no suitable enzyme was found. Project accomplishments included expressing the genes for carbazole dioxygenase in Rhodococcus erythropolis and Escherichia coli, development of gene expression vectors for Rhodococcus, and isolation of a Pseudomonas sp. strain GTIN-G4 that has the novel biochemical ability to replace one of the nitrogen-associated hydrogen atoms in 2-aminobiphenyl with formaldehyde. Rhodococcus cultures are capable of metabolizing a wide range of substrates, including hydrophobic substrates like petroleum, and may find widespread use in the development of biotechnology processes in the future. The results of this project will directly benefit the development of future biotechnology processes/projects employing Rhodococcus hosts. Three manuscripts were prepared and submitted for publication based on the data obtained in this project: (1) ''Formylation of 2-aminobiphenyl by Pseudomonas sp. strain GTIN-G4''; (2) ''Screening and Analysis of DNA Fragments that Show Promoter Activities in Rhodococcus erythropolis''; and (3) ''Microbial Biocatalyst Developments to Upgrade Fossil Fuels''.

John J. Kilbane II



Chiral BINOL-derived phosphoric acids: privileged Brønsted acid organocatalysts for C-C bond formation reactions.  


BINOL-derived phosphoric acids have emerged during the last five years as powerful chiral Brønsted acid catalysts in many enantioselective processes. The most successful transformations carried out with chiral BINOL phosphates include C-C bond formation reactions. The recent advances have been reviewed in this article with a focus being placed on hydrocyanations, aldol-type, Mannich, Friedel-Crafts, aza-ene-type, Diels-Alder, as well as cascade and multi-component reactions. PMID:20820680

Zamfir, Alexandru; Schenker, Sebastian; Freund, Matthias; Tsogoeva, Svetlana B



A quantum chemical topological analysis of the C-C bond formation in organic reactions involving cationic species.  


ELF topological analysis of the ionic Diels-Alder (I-DA) reaction between the N,N-dimethyliminium cation and cyclopentadiene (Cp) has been performed in order to characterise the C-C single bond formation. The C-C bond formation begins in the short range of 2.00-1.96 Åvia a C-to-C pseudoradical coupling between the most electrophilic center of the iminium cation and one of the two most nucleophilic centers of Cp. The electron density of the pseudoradical center generated at the most electrophilic carbon of the iminium cation comes mainly from the global charge transfer which takes place along the reaction. Analysis of the global reactivity indices indicates that the very high electrophilic character of the iminium cation is responsible for the negative activation energy found in the gas phase. On the other hand, the analysis of the radical P(k)(o) Parr functions of the iminium cation, and the nucleophilic P(k)(-) Parr functions of Cp makes the characterisation of the most favourable two-center interaction along the formation of the C-C single bond possible. PMID:24901220

Domingo, Luis R; Pérez, Patricia



Cleavage of C-O bonds in lignin model compounds catalyzed by methyldioxorhenium in homogeneous phase.  


Methyldioxorhenium (MDO)-catalyzed C-O bond cleavage of a variety of lignin ?-O-4-model compounds yields phenolic and aldehydic compounds in homogeneous phase under mild reaction conditions. MDO is in situ generated by reduction of methyltrioxorhenium (MTO) and is remarkably stable under the applied reaction conditions allowing its reuse for least five times without significant activity loss. Based on the observed and isolated intermediates, 17 O- and 2 H-isotope labeling experiments, DFT calculations, and several spectroscopic studies, a reaction mechanism is proposed. PMID:24449501

Harms, Reentje G; Markovits, Iulius I E; Drees, Markus; Herrmann, H C Mult Wolfgang A; Cokoja, Mirza; Kühn, Fritz E



Mechanisms for S-S and N-C ? bond cleavage in peptide ECD and ETD mass spectrometry  

NASA Astrophysics Data System (ADS)

This Letter reviews efforts made to elucidate the mechanism by which electron-capture and electron-transfer dissociation bond cleavages occur in mass spectrometry. The primary issues include where in the parent ion the electron initially attaches, whether the energy released in this initial electron-capture step is key to determining which bonds will cleave, whether the electron can migrate from the site to which it initially attaches to other sites in the parent ion, and, if so, over what distances and at what rates, and why, in polypeptides, one finds disulfide and N-C ? bond cleavage primarily.

Simons, Jack




SciTech Connect

The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project was focused on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate deaminase. The objective of the final phase of the project will be to develop derivative C-N bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments resulted in the isolation of microbial cultures that utilize aromatic amides as sole nitrogen sources, several amidase genes were cloned and were included in directed evolution experiments to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. During the second year of the project (October, 2003-September, 2004) enrichment culture experiments succeeded in isolating a mixed bacterial culture that can utilize 2-aminobiphenyl as a sole nitrogen source, directed evolution experiments were focused on the aniline dioxygenase enzyme that is capable of deaminating aniline, and expression vectors were constructed to enable the expression of genes encoding C-N bond cleaving enzymes in Rhodococcus hosts. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum. Aromatic compounds such as carbazole are representative of the difficult-to-treat organonitrogen compounds most commonly encountered in petroleum. There are two C-N bonds in carbazole and the construction of a metabolic pathway for the removal of nitrogen from carbazole will require enzymes capable cleaving both C-N bonds. A multi-component enzyme, carbazole dioxygenase, which can selectively cleave the first C-N bond has been identified and the genes that encode this enzyme have been cloned, sequenced, and are being expressed in Rhodococcus erythropolis, a bacterial culture that tolerates exposure to petroleum. An enzyme capable of selectively cleaving the second C-N bond in carbazole has not yet been identified, but enrichment culture experiments have recently succeeded in isolating a bacterial culture that is a likely candidate and may possess a suitable enzyme. Research in the near future will verify if a suitable enzyme for the cleavage of the second C-N bond in carbazole has indeed been found, then the genes encoding a suitable enzyme will be identified, cloned, and sequenced. Ultimately genes encoding enzymes for selective cleavage of both C-N bonds in carbazole will be assembled into a new metabolic pathway and the ability of the resulting bacterial culture to remove nitrogen from petroleum will be determined.

John J. Kilbane II




SciTech Connect

The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project will focus on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate amidase. The objective of the final phase of the project will be to develop derivative CN bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. The project is on schedule and no major difficulties have been encountered. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments have resulted in the isolation of promising cultures that may be capable of cleaving C-N bonds in aromatic amides, several amidase genes have been cloned and are currently undergoing directed evolution to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. Future research will address expression of these genes in Rhodococcus erythropolis. Enrichment culture experiments and directed evolution experiments continue to be a main focus of research activity and further work is required to obtain an appropriate amidase that will selectively cleave C-N bonds in aromatic substrates. Once an appropriate amidase gene is obtained it must be combined with genes encoding an enzyme capable of converting carbazole to 2'aminobiphenyl-2,3-diol: specifically carA genes. The carA genes from two sources have been cloned and are ready for construction of C-N bond cleavage pathway. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum.

John J. Kilbane III



Unlocking Hydrogenation for C-C Bond Formation: A Brief Overview of Enantioselective Methods  

PubMed Central

Hydrogenation of ?-unsaturated reactants in the presence of carbonyl compounds or imines promotes reductive C-C coupling, providing a byproduct-free alternative to stoichiometric organometallic reagents in an ever-increasing range of C=X (X = O, NR) additions. Under transfer hydrogenation conditions, hydrogen exchange between alcohols and ?-unsaturated reactants triggers generation of electrophile-nucleophile pairs, enabling carbonyl addition directly from the alcohol oxidation level, bypassing discrete alcohol oxidation and generation of stoichiometric byproducts. PMID:22125398

Hassan, Abbas; Krische, Michael J.



Ternary Electrocatalysts for Oxidizing Ethanol to Carbon Dioxide: Making Ir Capable of Splitting C-C bond  

SciTech Connect

Splitting the C-C bond is the main obstacle to electroxidation of ethanol (EOR) to CO2. We recently demonstrated that the ternary PtRhSnO2 electrocatalyst can accomplish that reaction at room temperature with Rh having a unique capability to split the C-C bond. In this article we report the finding that Ir can be induced to split the C-C bond as a component of the ternary catalyst. We synthesized, characterized and compared the properties of several ternary electrocatalysts. Carbon-supported nanoparticle (NP) electrocatalysts comprising a SnO2 NP core decorated with multi-metallic nanoislands (MM = PtIr, PtRh, IrRh, PtIrRh) were prepared using a seeded growth approach. An array of characterization techniques were employed to establish the composition and architecture of the synthesized MM /SnO2 NPs, while electrochemical and in situ infrared reflection absorption spectroscopy studies elucidated trends in activity and the nature of the reaction intermediates and products. Both EOR reactivity and selectivity towards CO2 formation of several of these MM /SnO2/C electrocatalysts are significantly higher compared to conventional Pt/C and Pt/SnO2/C catalysts. We demonstrate that the PtIr/SnO2/C catalyst with high Ir content shows outstanding catalytic property with the most negative EOR onset potential and reasonably good selectivity towards ethanol complete oxidation to CO2. PtRh/SnO2/C catalysts with a moderate Rh content exhibit the highest EOR selectivity, as deduced from infrared studies.

Li, Meng [Brookhaven National Laboratory (BNL); Cullen, David A [ORNL; Sasaki, Kotaro [Brookhaven National Laboratory (BNL); Marinkovic, N. [University of Delaware; More, Karren Leslie [ORNL; Adzic, Radoslav R. [Brookhaven National Laboratory (BNL)



Protocols for the selective cleavage of carbon-sulfur bonds in coal. Technical report, December 1, 1992--February 28, 1993  

SciTech Connect

Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. Planned in the second year of our project Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal are investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures and radiation. Other investigations that will result in analyses of the likelihood of C-S bond cleavages resulting from various oxidative processes will also be undertaken. Summarized in this quarterly report are results of our investigations of the following topics: (a) desulfurization of coal model sulfones; (b) desulfurization of coal model sulfides; (c) photooxidation of organic sulfides; and (d) photolytic desulfurization of coal.

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States); Ho, K.K. [Illinois Clean Coal Inst., Carterville, IL (United States)



Online mass spectrometric analysis of proteins/peptides following electrolytic cleavage of disulfide bonds.  


The disulfide bond bridge is an important post-translational modification for proteins. This study presents a structural analysis of biologically active peptides and proteins containing disulfide bonds using electrochemistry (EC) online combined with desorption electrospray ionization mass spectrometry (DESI-MS), in which the sample undergoes electrolytic disulfide cleavage in an electrochemical flow cell followed by MS detection. Using this EC/DESI-MS method, the disulfide-containing peptides can be quickly identified from enzymatic digestion mixtures, simply based on the abrupt decrease in their relative ion abundances after electrolysis. Peptide mass mapping and tandem MS analysis of the ions of the resulting free peptide chains can possibly establish the disulfide linkage pattern and sequence the precursor peptides. In this regard, the method provides much more chemical information than previous analogous electrochemical analyses. In addition, derivatization of thiols by selective selenamide reagents is useful for easy recognition of reduced peptide ions and the number of their free thiols. Furthermore, electrolytic reduction of proteins (e.g., ?-lactalbumin) leads to increased charges on the detected protein ions, revealing the role of disulfide bonds on maintaining protein conformation. This electrochemical mass spectrometric method is fast (completed in few minutes) and does not need chemical reductants, potentially having valuable applications in proteomics research. PMID:21197958

Zhang, Yun; Dewald, Howard D; Chen, Hao



Controllable synthesis of silver and silver sulfide nanocrystals via selective cleavage of chemical bonds  

NASA Astrophysics Data System (ADS)

A one-step colloidal process has been adopted to prepare silver (Ag) and silver sulfide (Ag2S) nanocrystals, thus avoiding presynthesis of an organometallic precursor and the injection of a toxic phosphine agent. During the reaction, a layered intermediate compound is first formed, which then acts as a precursor, decomposing into the nanocrystals. The composition of the as-obtained products can be controlled by selective cleavage of S-C bonds or Ag-S bonds. Pure Ag2S nanocrystals can be obtained by directly heating silver acetate (Ag(OAc)) and n-dodecanethiol (DDT) at 200?° C without any surfactant, and pure Ag nanocrystals can be synthesized successfully if the reaction temperature is reduced to 190?° C and the amount of DDT is decreased to 1 ml in the presence of a non-coordinating organic solvent (1-octadecene, ODE). Otherwise, the mixture of Ag and Ag2S is obtained by directly heating Ag(OAc) in DDT by increasing the reaction temperature or in a mixture of DDT and ODE at 200?° C. The formation mechanism has been discussed in detail in terms of selective S-C and Ag-S bond dissociation due to the nucleophilic attack of DDT and the lower bonding energy of Ag-S. Interestingly, some products can easily self-assemble into two- or three-dimensional (2D or 3D) highly ordered superlattice structures on a copper grid without any additional steps. The excess DDT plays a key role in the superlattice structure due to the bundling and interdigitation of the thiolate molecules adsorbed on the as-obtained nanocrystals.

Tang, Aiwei; Wang, Yu; Ye, Haihang; Zhou, Chao; Yang, Chunhe; Li, Xu; Peng, Hongshang; Zhang, Fujun; Hou, Yanbing; Teng, Feng



Low-oxidation state indium-catalyzed C-C bond formation.  


The development of innovative metal catalysis for selective bond formation is an important task in organic chemistry. The group 13 metal indium is appealing for catalysis because indium-based reagents are minimally toxic, selective, and tolerant toward various functional groups. Among elements in this group, the most stable oxidation state is typically +3, but in molecules with larger group 13 atoms, the chemistry of the +1 oxidation state is also important. The use of indium(III) compounds in organic synthesis has been well-established as Lewis acid catalysts including asymmetric versions thereof. In contrast, only sporadic examples of the use of indium(I) as a stoichiometric reagent have been reported: to the best of our knowledge, our investigations represent the first synthetic method that uses a catalytic amount of indium(I). Depending on the nature of the ligand or the counteranion to which it is coordinated, indium(I) can act as both a Lewis acid and a Lewis base because it has both vacant p orbitals and a lone pair of electrons. This potential ambiphilicity may offer unique reactivity and unusual selectivity in synthesis and may have significant implications for catalysis, particularly for dual catalytic processes. We envisioned that indium(I) could be employed as a metallic Lewis base catalyst to activate Lewis acidic boron-based pronucleophiles for selective bond formation with suitable electrophiles. Alternatively, indium(I) could serve as an ambiphilic catalyst that activates both reagents at a single center. In this Account, we describe the development of low-oxidation state indium catalysts for carbon-carbon bond formation between boron-based pronucleophiles and various electrophiles. We discovered that indium(I) iodide was an excellent catalyst for ?-selective allylations of C(sp(2)) electrophiles such as ketones and hydrazones. Using a combination of this low-oxidation state indium compound and a chiral semicorrin ligand, we developed catalytic highly enantioselective allylation, crotylation, and ?-chloroallylation reactions of hydrazones. These transformations proceeded with rare constitutional selectivities and remarkable diastereoselectivities. Furthermore, indium(I) triflate served as the most effective catalyst for allylations and propargylations of C(sp(3)) electrophiles such as O,O-acetals, N,O-aminals, and ethers, and we applied this methodology to carbohydrate chemistry. In addition, a catalyst system composed of indium(I) chloride and a chiral silver BINOL-phosphate facilitated the highly enantioselective allylation and allenylation of N,O-aminals. Overall, these discoveries demonstrate the versatility, efficiency, and sensitivity of low-oxidation state indium catalysts in organic synthesis. PMID:22626010

Schneider, Uwe; Kobayashi, Shu



Palladium-catalyzed oxidative arylalkylation of activated alkenes: dual C-H bond cleavage of an arene and acetonitrile.  


Not one but two: The title reaction proceeds through the dual C-H bond cleavage of both aniline and acetonitrile. The reaction affords a variety of cyano-bearing indolinones in excellent yield. Mechanistic studies demonstrate that this reaction involves a fast arylation of the olefin and a rate-determining C-H activation of the acetonitrile. PMID:22076660

Wu, Tao; Mu, Xin; Liu, Guosheng



Protocols for the selective cleavage of carbon-sulfur bonds in coal. Technical report, March 1, 1992--May 30, 1992  

SciTech Connect

Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. Unfortunately, several classes of reactions that lead to carbon-sulfur bond cleavage are not well understood. Planned in ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal`` are reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures and radiation. Summarized in this quarterly report are results of our investigations of the following topics: (a) the reactions of coal model compounds, namely, benzyl phenyl sulfide (BPS), diphenyl sulfide (hereafter referred to as phenylsulfide, PS) and dibenzothiophene (DBT) with various reagents (Lewis acid catalysts, radical initiators, electron acceptors) using different solvents and temperature in an attempt to maximize the degree of carbon-sulfur (C-S) bond cleavage; and (b) the results of photooxidation of coal model compounds under controlled conditions. Quantitative product analyses are presented in this report.

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States)



An unusual carbon?carbon bond cleavage reaction during phosphinothricin biosynthesis  

SciTech Connect

Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine residues. Synthetic phosphinothricin (glufosinate) is a component of two top-selling herbicides (Basta and Liberty), and is widely used with resistant transgenic crops including corn, cotton and canola. Recent genetic and biochemical studies showed that during phosphinothricin tripeptide biosynthesis 2-hydroxyethylphosphonate (HEP) is converted to hydroxymethylphosphonate (HMP). Here we report the in vitro reconstitution of this unprecedented C(sp{sup 3})-C(sp{sup 3}) bond cleavage reaction and X-ray crystal structures of the enzyme. The protein is a mononuclear non-haem iron(II)-dependent dioxygenase that converts HEP to HMP and formate. In contrast to most other members of this family, the oxidative consumption of HEP does not require additional cofactors or the input of exogenous electrons. The current study expands the scope of reactions catalysed by the 2-His-1-carboxylate mononuclear non-haem iron family of enzymes.

Cicchillo, Robert M.; Zhang, Houjin; Blodgett, Joshua A.V.; Whitteck, John T.; Li, Gongyong; Nair, Satish K.; van derDonk, Wilfred A.; Metcalf, William W.; (UIUC)



Can metal ions be used as gas-phase disulfide bond cleavage reagents? A survey of coinage metal complexes of model peptides containing an intermolecular disulfide bond.  


The role that a metal ion can have in promoting disulfide bond cleavage has been assessed by surveying the tandem mass spectra of the following metal complexes of model peptides containing an intermolecular disulfide bond: [M--H+Cu(II)](+); [M--H+Cu(II)(bipy)](+); [M+Ag(I)](+); and [M+Au(I)(PMe(3))](+). In comparison to previously studied protonated peptides, these binary and ternary metal complexes generally yield more abundant S--S and/or C--S bond cleavage. In general, [M--H+Cu(II)](+) ions cleave the adjacent C--S bond more readily, while the [M+Au(I)(PMe(3))](+) ion cleaves the S--S bond more readily. The ternary metal complex [M--H+Cu(II)(bipy)](+), on the other hand, fragments by exclusive loss of the bipyridyl ligand for the larger model peptides studied. Of all coinage metal systems studied, Me(3)PAu(+) is superior in promoting disulfide bond cleavage. PMID:17654640

Lioe, Hadi; Duan, Mubing; O'Hair, Richard A J



Transition-metal-catalyzed aminations and aziridinations of C-H and C=C bonds with iminoiodinanes.  


Catalytic insertion or addition of a metal-imido/nitrene species, generated from reaction of a transition-metal catalyst with iminoiodanes, to C-H and C=C bonds offers a convenient and atom economical method for the synthesis of nitrogen-containing compounds. Following this groundbreaking discovery during the second half of the last century, the field has received an immense amount of attention with a myriad of impressive metal-mediated methods for the synthesis of amines and aziridines having been developed. This review will cover the significant progress made in improving the efficiency, versatility and stereocontrol of this important reaction. This will include the various iminoiodanes, their in situ formation, and metal catalysts that could be employed and new ligands, both chiral and non-chiral, which have been designed, as well as the application of this functional group transformation to natural product synthesis and the preparation of bioactive compounds of current therapeutic interest. PMID:22121122

Chang, Joyce Wei Wei; Ton, Thi My Uyen; Chan, Philip Wai Hong



Designing molecules for PDT: red light-induced DNA cleavage on disulfide bond activation in a dicopper(II) complex.  


The binuclear copper(II) complex [Cu)(RSSR)2](1), where RSSR is a dianionic Schiff base derived from 2-(thioethyl)salicylaldimine having a disulfide bond is prepared, structurally characterized by X-ray crystallography and its photo-induced DNA cleavage activity studied. The Schiff base ligand H2RSSR is also structurally characterized. The crystal structure of shows the discrete dimeric nature of the complex with each metal showing square-planar geometry with a CuN2O2 coordination (Cu...Cu, 5.011(1)A). The tetradentate Schiff base RSSR acts as a linker of two copper centers. The sulfur atoms in the disulfide unit do not show any apparent interaction with the metal ion. Complex 1, which is cleavage inactive in the dark in the presence of reducing agents, shows significant cleavage of supercoiled pUC19 DNA on exposure to UV light of 312 nm or visible light of different wavelengths under aerobic conditions, in the absence of any additives. DNA cleavage data from control experiments reveal involvement of the disulfide unit as a photosensitizer undergoing photo-induced S-S bond cleavage on exposure to UV light and the resulting species activates molecular oxygen to form singlet oxygen (1O2) that causes DNA cleavage following a type-II process. Photo-induced DNA cleavage by 1 on red-light exposure using a CW laser of 632.8 nm or a pulsed ruby laser of 694 nm is proposed to involve sulfide radicals in a type-I process and hydroxyl radicals as the reactive species. PMID:15616724

Dhar, Shanta; Nethaji, Munirathinam; Chakravarty, Akhil R



Effects of nucleophile, oxidative damage, and nucleobase orientation on the glycosidic bond cleavage in deoxyguanosine.  


Deglycosylation of nucleotides occurs during many essential biological processes, including DNA repair, and is initiated by a variety of nucleophiles. In the present work, density functional theory (B3LYP) was used to investigate the thermodynamics and kinetics of the glycosidic bond cleavage reaction in the model nucleoside forms of guanine and its major oxidation product, 8-oxoguanine. Base excision facilitated by four different nucleophiles (hydroxyl anion (fully activated water), formate-water complex (partially activated water), lysine, and proline) was considered, which spans nucleophiles involved in a collection of spontaneous and enzyme-catalyzed processes. Because some enzymes that catalyze deglycosylation can accommodate more than one orientation of the base with respect to the sugar moiety, the effects of the (anti/syn) base orientation on the barrier height were also considered. We find that the nucleophile has a very large effect on the overall (gas-phase) reaction energetics. Although this effect decreases in different (polar) environments, the nucleophile has the greatest influence on the overall reaction as compared to whether the base is damaged or to the base orientation. Furthermore, the effects are significant in environments that most closely resemble (nonpolar) enzymatic active sites. Our results provide a greater understanding of the relative effects of the nucleophile, damage to the nucleobase, and the nucleobase orientation with respect to the sugar moiety on the deglycosylation pathway, which provide qualitative explanations for relative base excision rates observed in some biological systems. PMID:20095611

Shim, Eun Jung; Przybylski, Jennifer L; Wetmore, Stacey D



Structural effects on the C-S bond cleavage in aryl tert-butyl sulfoxide radical cations.  


The oxidation of a series of aryl tert-butyl sulfoxides (4-X-C6H4SOC(CH3)3: 1, X = OCH3; 2, X = CH3; 3, X = H; 4, X = Br) photosensitized by 3-cyano-N-methylquinolinium perchlorate (3-CN-NMQ(+)) has been investigated by steady-state irradiation and nanosecond laser flash photolysis (LFP) under nitrogen in MeCN. Products deriving from the C-S bond cleavage in the radical cations 1(+•)-4(+•) have been observed in the steady-state photolysis experiments. By laser irradiation, the formation of 3-CN-NMQ(•) (?(max) = 390 nm) and 1(+•)-4(+•) (?(max) = 500-620 nm) was observed. A first-order decay of the sulfoxide radical cations, attributable to C-S bond cleavage, was observed with fragmentation rate constants (k(f)) that decrease by increasing the electron donating power of the arylsulfinyl substituent from 1.8 × 10(6) s(-1) (4(+•)) to 2.3 × 10(5) s(-1) (1(+•)). DFT calculations showed that a significant fraction of the charge is delocalized in the tert-butyl group of the radical cations, thus explaining the small substituent effect on the C-S bond cleavage rate constants. Via application of the Marcus equation to the kinetic data, a very large value for the reorganization energy (? = 62 kcal mol(-1)) has been calculated for the C-S bond scission reaction in 1(+•)-4(+•). PMID:23581281

Cavattoni, Tullio; Del Giacco, Tiziana; Lanzalunga, Osvaldo; Mazzonna, Marco; Mencarelli, Paolo



A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation.  


The gas-phase fragmentation mechanisms of small models for peptides containing intermolecular disulfide links have been studied using a combination of tandem mass spectrometry experiments, isotopic labeling, structural labeling, accurate mass measurements of product ions, and theoretical calculations (at the MP2/6-311 + G(2d,p)//B3LYP/3-21G(d) level of theory). Cystine and its C-terminal derivatives were observed to fragment via a range of pathways, including loss of neutral molecules, amide bond cleavage, and S-S and C-S bond cleavages. Various mechanisms were considered to rationalize S-S and C-S bond cleavage processes, including charge directed neighboring group processes and nonmobile proton salt bridge mechanism. Three low-energy fragmentation pathways were identified from theoretical calculations on cystine N-methyl amide: (1) S-S bond cleavage dominated by a neighboring group process involving the C-terminal amide N to form either a protonated cysteine derivative or protonated sulfenyl amide product ion (44.3 kcal mol(-1)); (2) C-S bond cleavage via a salt bridge mechanism, involving abstraction of the alpha-hydrogen by the N-terminal amino group to form a protonated thiocysteine derivative (35.0 kcal mol(-1)); and (3) C-S bond cleavage via a Grob-like fragmentation process in which the nucleophilic N-terminal amino group forms a protonated dithiazolidine (57.9 kcal mol(-1)). Interestingly, C-S bond cleavage by neighboring group processes have high activation barriers (63.1 kcal mol(-1)) and are thus not expected to be accessible during low-energy CID experiments. In comparison to the energetics of simple amide bond cleavage, these S-S and C-S bond cleavage reactions are higher in energy, which helps rationalize why bond cleavage processes involving the disulfide bond are rarely observed for low-energy CID of peptides with mobile proton(s) containing intermolecular disulfide bonds. On the other hand, the absence of a mobile proton appears to "switch on" disulfide bond cleavage reactions, which can be rationalized by the salt bridge mechanism. This potentially has important ramifications in explaining the prevalence of disulfide bond cleavage in singly protonated peptides under MALDI conditions. PMID:17462910

Lioe, Hadi; O'Hair, Richard A J



Metal-catalyzed activation of ethers via C-O bond cleavage: a new strategy for molecular diversity.  


In 1979, the seminal work of Wenkert set the standards for the utilization of aryl and vinyl ethers as coupling partners via C-O bond-cleavage. Although the topic remained dormant for almost three decades, the last few years have witnessed a renaissance in this area of expertise, experiencing an exponential growth and becoming a significant discipline within the cross-coupling arena. The means to utilize readily accessible aryl or vinyl ethers as counterparts does not only represent a practical, powerful and straightforward alternative to organic halides, but also constitutes an excellent opportunity to improve our chemical knowledge about a relatively unexplored area of expertise. This review summarizes the most significant developments in the area of C-O bond-cleavage when employing aryl or vinyl ethers, providing a detailed overview of the current state of the art and including future aspects, when applicable. PMID:25157613

Cornella, Josep; Zarate, Cayetana; Martin, Ruben



Unexpected activation of carbon-bromide bond promoted by palladium nanoparticles in Suzuki C-C couplings.  


Dihydroanthracene derivatives (1-6) containing imide (1-3) and amine (4-6) functions have been used for the stabilization of palladium nanoparticles, starting from Pd(0) and Pd(ii) organometallic precursors. Well-dispersed nanoparticles of mean size in the range ca. 1.9 to 3.6 nm could be obtained using Pd(0) precursors (PdLc and PdLd, where L = 1-6 and c and d mean the organometallic precursor involved, [Pd(2)(dba)(3)] and [Pd(ma)(nbd)] respectively). With the aim to evaluate the behaviour of homogeneous species and nanoparticles used as catalytic precursors, palladium complex coordinated to the diamine 6, [Pd(OAc)(2)(?(2)-N,N-6)], was prepared, reporting for the first time the X-ray diffraction structure of a metallic complex containing a ligand with a 9,10-dihydroanthracene backbone. Palladium systems were evaluated in Suzuki C-C coupling reactions and relevant differences were observed comparing the reactivity of the homogeneous systems in relation to that obtained using palladium nanoparticles as starting catalyst in relation to the activation of the C-Br bonds for deactivated substrates. PMID:20820601

Sanhes, Delphine; Raluy, Eva; Rétory, Stéphane; Saffon, Nathalie; Teuma, Emmanuelle; Gómez, Montserrat



Characterization of heme environment and mechanism of peroxide bond cleavage in human prostacyclin synthase.  


Prostacyclin is a potent mediator of vasodilation and anti-platelet aggregation. It is synthesized from prostaglandin H(2) by prostacyclin synthase (PGIS), a member of Family 8 in the cytochrome P450 superfamily. Unlike most P450s, which require exogenous reducing equivalents and an oxygen molecule for mono-oxygenation, PGIS catalyzes an isomerization with an initial step of endoperoxide bond cleavage of prostaglandin H(2) (PGH(2)). The low abundance of PGIS in natural tissues necessitates heterologous expression for studies of structure/function relationships and reaction mechanism. We report here a high-yield prokaryotic system for expression of enzymatically active human PGIS. The PGIS cDNA is modified by replacing the hydrophobic amino-terminal sequence with the more hydrophilic amino-terminal sequence from P450 2C5 and by adding a four-histidine tag at the carboxyl terminus. The resulting recombinant PGIS associates with host cell membranes and was purified to electrophoretic homogeneity by nickel affinity, hydroxyapatite and CM Sepharose column chromatography. The recombinant PGIS, with a heme:protein ratio of 0.9:1, catalyzes prostacyclin formation at a K(m) of 13.3 muM PGH(2) and a V(max) of 980 per min. The dithionite-reduced PGIS binds CO with an on-rate of 5.6 x 10(5) M(-1) s(-1) and an off-rate of 15 s(-1). The ferrous-CO complex of PGIS is very short-lived and decays at a rate of 0.7 s(-1). Spectral binding assays showed that imidazole binds weakly to PGIS (K(d) approximately 0.5 mM,) but clotrimazole, a bulky and rigid imidazole derivative, binds strongly (K(d) approximately 1 microM). The transient nature of the CO complex and the weak imidazole binding seem to support an earlier proposal that PGIS active site has a limited space, but the tight binding of clotrimazole argues against this view. It appears that the heme distal pocket of PGIS is fairly adaptable to ligands of various structures. UV-visible absorption, magnetic circular dichroism and electron paramagnetic resonance spectra indicate that PGIS has a typical low-spin heme with a hydrophobic active site. PGIS catalyzes homolytic scission of the peroxide bond of a test substrate, 10-hydroperoxyoctadeca-8,12-dienoic acid, accompanied by formation of a heme intermediate with a Compound II-like optical spectrum. PMID:16406803

Yeh, Hui-Chun; Hsu, Pei-Yung; Wang, Jinn-Shyan; Tsai, Ah-Lim; Wang, Lee-Ho



A substrate-assisted mechanism of nucleophile activation in a Ser-His-Asp containing C-C bond hydrolase  

PubMed Central

The meta-cleavage product (MCP) hydrolases utilize a Ser-His-Asp triad to hydrolyze a carbon-carbon bond. Hydrolysis of the MCP substrate has been proposed to proceed via an enol-to-keto tautomerization followed by a nucleophilic mechanism of catalysis. Ketonization involves an intermediate, ESred, possessing a remarkable bathochromically-shifted absorption spectrum. We investigated the catalytic mechanism of the MCP hydrolases using DxnB2 from Sphingomonas wittichii RW1. Pre-steady-state kinetic and LC ESI/MS evaluation of the DxnB2-mediated hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxy-2,4-pentadienoic acid (HPD) and benzoate support a nucleophilic mechanism catalysis. In DxnB2, the rate of ESred decay and product formation showed a solvent kinetic isotope effect of 2.5 indicating that a proton transfer reaction, assigned here to substrate ketonization, limits the rate of acylation. For a series of substituted MCPs, this rate was linearly dependent on MCP pKa2 (?nuc ~1). Structural characterization of DxnB2 S105A:MCP complexes revealed that the catalytic histidine is displaced upon substrate-binding. The results provide evidence for enzyme-catalyzed ketonization in which the catalytic His-Asp pair does not play an essential role. The data further suggest that ESred represents a dianionic intermediate that acts as a general base to activate the serine nucleophile. This substrate-assisted mechanism of nucleophilic catalysis distinguishes MCP hydrolases from other serine hydrolases. PMID:24067021

Ruzzini, Antonio C.; Bhowmik, Shiva; Ghosh, Subhangi; Yam, Katherine C.; Bolin, Jeffrey T.; Eltis, Lindsay D.



Lewis acid mediated intramolecular C-C bond formation of alkyne-epoxide leading to six-membered nitrogen and oxygen heterocycles.  


Intramolecular C-C bond formation of oxygen- and nitrogen-tethered alkynes and epoxide mediated by Lewis acid under ambient conditions is described. A simple procedure for the synthesis of 3,6- and 5,6-dihydropyrans and 3,4-dehydropiperidines from acyclic building blocks in good yields without using any transition metal is shown. PMID:24720735

Ghosh, Priya; Saha, Pipas; Bondalapati, Somasekhar; Indukuri, Kiran; Saikia, Anil K



Palladium-mediated C-C bond forming reactions: Cross-coupling reactions of organozinc and organotin reagents with purinones and triazines  

SciTech Connect

Palladium-mediated cross coupling reactions of organozinc and organotin reagents were used to form C-C bonds on heterocyclic substrates (8-bromopurin-6-ones and monochloro-1,3,5-triazines). These reactions represent the first examples of such coupling reactions on the above heterocyclic systems and they offer new ways to introduce a variety of carbon substituents into purinones and triazines.

Xia, Y.; Mirzai, B.; Chackalamannil, S. [Schering-Plough Research Institute, Kenilworth, NJ (United States)



Facile C-S, S-H, and S-S bond cleavage using a nickel(0) NHC complex.  


[Ni2(iPr2Im)4(COD)] 1 (iPr2Im = 1,3-di(isopropyl)-imidazol-2-ylidene) reacts at room temperature with the thioethers methyl para-tolyl sulfide, ethyl phenyl sulfide, benzothiophene and dibenzothiophene to afford the C-S bond cleavage products [Ni(iPr2Im)2(4-CH3-C6H4)(SMe)] 2, [Ni(iPr2Im)2(C6H5)(SEt)] 3, [Ni(iPr2Im)2(1,8-benzothiophenylato)] 4 and [Ni(iPr2Im)2(C,S-dibenzothiophenylato)] 5. In contrast to the reaction of thioethers or sulfoxides (reported earlier), no C-S bond cleavage was observed for the reaction of 1 with the sulfones bezothiophene-1,1-dioxide and methyl phenyl sulfone. In those cases the stable compounds [Ni(iPr2Im)2(eta2-2,3-benzothiophene-1,1-dioxide)] 6 and [Ni(iPr2Im)2(eta2-MeSO2C6H5)] 7 with a eta2-coordinated sulfone ligand have been isolated. Compound 6 has been structurally characterized. S-H bond cleavage was observed using 2-methyl-2-propanthiol to afford [Ni(iPr2Im)2(H)(StBu)] 8. The reaction of 1 with disulfides led to the dithiolato complexes [Ni(iPr2Im)2(SR)2] (R = tBu 9, Me 10, Ph 11) by S-S bond scission. PMID:20449150

Schaub, Thomas; Backes, Marc; Plietzsch, Oliver; Radius, Udo



Stepwise cycloreversion of oxetane radical cations with initial C-O bond cleavage.  


2,4,6-Triaryl(thia)pyrylium salts have been used as electron-transfer photosensitizers for the cycloreversion of the oxetane ring system. The radical cation of 2,3-diphenyl-4-hydroxymethyloxetane (1) undergoes stepwise splitting via initial O-C2 cleavage. Spin and charge in the resulting intermediate are located in the oxygen and carbon atoms, respectively. Subsequent intramolecular nucleophilic attack produces 2,3-diphenyl-4-hydroxytetrahydrofuran (4a). Formation of this product occurs in the submicrosecond time scale, competing with C3-C4 cleavage to the detectable (lambdamax = 470 nm) trans-stilbene radical cation. PMID:12047163

Miranda, Miguel A; Izquierdo, M Angeles



Theoretical study of the Diels-Alder reaction of C{sub 60}. Transition-state structures and reactivities of C-C bonds  

SciTech Connect

Chemical interactions between large species are not easy to look at by means of accurate MO calculations and by the usual orbital interaction scheme based on perturbation theory. By transforming the MO`s of the reagent and reactant parts into paired interacting orbitals, we have studied the Diels-Alder reaction of C{sub 60} with butadiene. The interaction involved in this system has been demonstrated to be almost completely localized on a C-C bond at the transition state, bearing a close resemblance to the orbital interactions between dienes and small dienophiles. The addition of butadiene to a C-C bond of C{sub 60} that is common to two annulated six-membered rings has been calculated to have a much lower activation energy than the addition to a C-C bond shared by a six-membered ring and a five-membered ring. The difference in reactivities has been shown to be related qualitatively to the local electron-donating potential and the electron-accepting capacitance of those bonds. The double addition of butadiene has been suggested to be not highly regioselective, both from these local reactivity scales and from the calculated heat of reactions. The possibility of C{sub 60} serving as a diene has also been studied. 98 refs., 6 figs., 9 tabs.

Chikama, Akirou; Fueno, Hiroyuki; Fujimoto, Hiroshi [Kyoto Univ. (Japan)



Protocols for the selective cleavage of carbon-sulfur bonds in coal. Technical report, December 1, 1991--February 29, 1992  

SciTech Connect

Planned in this project ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal`` are reactions in which organic free radicals and/or organic anions are allowed to react with physically cleaned Illinois coal and sulfur-containing coal model compounds. This quarterly report contains the results of photooxidation of coal model compounds, namely, benzyl phenyl sulfide, phenylsulfide, dibenzothiophene, benzothiophene and thiophene, in the presence of 9,10-dicyanoanthracene or anthracene. Quantitative product analysis for the matrix of reactions whereby the coal model compounds are subjected to various solvents and temperature changes is presented in this quarterly report. Further quantitative analyses of the products are being undertaken.

Bausch, M.



Aromatic Cations from Oxidative Carbon-Hydrogen Bond Cleavage in Bimolecular Carbon-Carbon Bond Forming Reactions  

PubMed Central

Chromenes and isochromenes react quickly with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) to form persistent aromatic oxocarbenium ions through oxidative carbon–hydrogen cleavage. This process is tolerant of electron-donating and electron-withdrawing groups on the benzene ring and additional substitution on the pyran ring. A variety of nucleophiles can be added to these cations to generate a diverse set of structures. PMID:22780559

Clausen, Dane J.



Protocols for the selective cleavage of carbon-sulfur bonds in coal. [Quarterly] technical report, March 1, 1993--May 31, 1993  

SciTech Connect

Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. Planned in the second year of our project ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal`` are investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures and radiation. other investigations that will result in analyses of the likelihood of C-S bond cleavages resulting from various oxidative processes will also be undertaken. Summarized in this quarterly report are results of our investigations of the following topics: (a) desulfurization of coal model sulfones and sulfides; (b) photolytic desulfurization of coal; (c) differential scanning calorimetric experiments on photooxidized coal; and (d) discussions on C-S bond strengths in radical cations.

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States)



N-N bond cleavage of hydrazines with a multiproton-responsive pincer-type iron complex.  


N-N bond cleavage of hydrazines on transition metals is of considerable importance in understanding the mechanism of biological nitrogen fixation under ambient conditions. We found that a metal-ligand-bifunctional complex of iron with a pincer-type ligand bearing two proton-responsive pyrazole arms catalyzes the disproportionation of hydrazine into ammonia and dinitrogen. The NH groups in the pyrazole ligands and hydrazines are crucial for the reaction, which most likely occurs through multiple and bidirectional proton-coupled electron transfer between the iron complex and hydrazine. The multiproton-responsive pincer-type ligand also stabilizes the intermediate diazene complex through a hydrogen-bonding network, as revealed by structural characterization of a ?(1)N-phenylhydrazine complex. PMID:23611139

Umehara, Kazuki; Kuwata, Shigeki; Ikariya, Takao



Raman spectroscopic determination of the length, strength, compressibility, Debye temperature, elasticity, and force constant of the C-C bond in graphene.  


From the perspective of bond relaxation and bond vibration, we have formulated the Raman phonon relaxation of graphene, under the stimuli of the number-of-layers, the uni-axial strain, the pressure, and the temperature, in terms of the response of the length and strength of the representative bond of the entire specimen to the applied stimuli. Theoretical unification of the measurements clarifies that: (i) the opposite trends of the Raman shifts, which are due to the number-of-layers reduction, of the G-peak shift and arises from the vibration of a pair of atoms, while the D- and the 2D-peak shifts involve the z-neighbor of a specific atom; (ii) the tensile strain-induced phonon softening and phonon-band splitting arise from the asymmetric response of the C(3v) bond geometry to the C(2v) uni-axial bond elongation; (iii) the thermal softening of the phonons originates from bond expansion and weakening; and (iv) the pressure stiffening of the phonons results from bond compression and work hardening. Reproduction of the measurements has led to quantitative information about the referential frequencies from which the Raman frequencies shift as well as the length, energy, force constant, Debye temperature, compressibility and elastic modulus of the C-C bond in graphene, which is of instrumental importance in the understanding of the unusual behavior of graphene. PMID:22105904

Yang, X X; Li, J W; Zhou, Z F; Wang, Y; Yang, L W; Zheng, W T; Sun, Chang Q



Design and Synthesis of Chiral Zn2+ Complexes Mimicking Natural Aldolases for Catalytic C-C Bond Forming Reactions in Aqueous Solution  

PubMed Central

Extending carbon frameworks via a series of C–C bond forming reactions is essential for the synthesis of natural products, pharmaceutically active compounds, active agrochemical ingredients, and a variety of functional materials. The application of stereoselective C–C bond forming reactions to the one-pot synthesis of biorelevant compounds is now emerging as a challenging and powerful strategy for improving the efficiency of a chemical reaction, in which some of the reactants are subjected to successive chemical reactions in just one reactor. However, organic reactions are generally conducted in organic solvents, as many organic molecules, reagents, and intermediates are not stable or soluble in water. In contrast, enzymatic reactions in living systems proceed in aqueous solvents, as most of enzymes generally function only within a narrow range of temperature and pH and are not so stable in less polar organic environments, which makes it difficult to conduct chemoenzymatic reactions in organic solvents. In this review, we describe the design and synthesis of chiral metal complexes with Zn2+ ions as a catalytic factor that mimic aldolases in stereoselective C–C bond forming reactions, especially for enantioselective aldol reactions. Their application to chemoenzymatic reactions in aqueous solution is also presented. PMID:24481060

Itoh, Susumu; Sonoike, Shotaro; Kitamura, Masanori; Aoki, Shin



Design and synthesis of chiral Zn2+ complexes mimicking natural aldolases for catalytic C-C bond forming reactions in aqueous solution.  


Extending carbon frameworks via a series of C-C bond forming reactions is essential for the synthesis of natural products, pharmaceutically active compounds, active agrochemical ingredients, and a variety of functional materials. The application of stereoselective C-C bond forming reactions to the one-pot synthesis of biorelevant compounds is now emerging as a challenging and powerful strategy for improving the efficiency of a chemical reaction, in which some of the reactants are subjected to successive chemical reactions in just one reactor. However, organic reactions are generally conducted in organic solvents, as many organic molecules, reagents, and intermediates are not stable or soluble in water. In contrast, enzymatic reactions in living systems proceed in aqueous solvents, as most of enzymes generally function only within a narrow range of temperature and pH and are not so stable in less polar organic environments, which makes it difficult to conduct chemoenzymatic reactions in organic solvents. In this review, we describe the design and synthesis of chiral metal complexes with Zn2+ ions as a catalytic factor that mimic aldolases in stereoselective C-C bond forming reactions, especially for enantioselective aldol reactions. Their application to chemoenzymatic reactions in aqueous solution is also presented. PMID:24481060

Itoh, Susumu; Sonoike, Shotaro; Kitamura, Masanori; Aoki, Shin



Cleavage of interchain disulfide bonds following matrix-assisted laser desorption  

NASA Astrophysics Data System (ADS)

The metastable decay of insulin produced by matrix-assisted laser desorption has been examined in a reflecting time-of-flight mass spectrometer. The [M-H]- molecular ion decays into negative A and B chain daughters with various numbers of sulfurs attached, corresponding to cleavage of the interchain disulfide bridges at different points. This type of decomposition can be identified by the characteristic 32 u spacing between the components.

Zhou, J.; Ens, W.; Poppe-Schriemer, N.; Standing, K. G.; Westmore, J. B.



The deep oxidation of chemical warfare agent models: facile catalytic oxidative cleavage of phosphorus-carbon and sulfur-carbon bonds using dioxygen  

Microsoft Academic Search

In water, metallic palladium on carbon was found to catalyze the deep oxidation of organophosphorus and organosulfur compounds\\u000a by dioxygen at 90C in the presence of carbon monoxide. This system presents the first examples of catalytic cleavage of phosphorus-carbon\\u000a bonds. Starting with trimethylphosphine oxide, the phosphorus-containing products formed by sequential P-C cleavage were dimethylphosphinic\\u000a acid, methylphosphonic acid, and phosphoric acid.

T. Hogan; R. Simpson; M. Lin; A. Sen



Chemistry of Materials 1989, 1,83-101 How C-C Bonds Are Formed and How They Influence  

E-print Network

properties. In the UC2structure, both uranium-carbon bonding and carbon-carbon bonding are enhanced upon,has a substantialgap between the valence and conduction bands. The pairingof carbon atoms in Dy, with late transition-metal elements. Early transition-metal carbides of the same composition do not exist

Li, Jing


Evidence that platelet glycoprotein IIIa has a large disulfide-bonded loop that is susceptible to proteolytic cleavage.  


The proteolytic digestion of GPIIIa on intact platelets by chymotrypsin, thrombin, plasmin, trypsin, and staphylococcal V8 protease was monitored in immunoblot studies employing three different antibodies to GPIIIa, one of which was made against a 13-residue synthetic peptide containing the amino terminus of GPIIIa. Chymotrypsin, plasmin, and trypsin gave similar patterns, from which it could be inferred that the major products after extensive digestion were two-chain molecules composed of amino-terminal fragments of Mr approximately 17,000-18,000 disulfide bonded to carboxyl-terminal remnants of Mr approximately 58,000-70,000. These patterns suggest that GPIIIa contains a large disulfide-bonded loop of at least 325 amino acids that is susceptible to proteolytic cleavage, and that the 4 cysteine residues between residues 177 and 273 bond with each other. Such a structure can also account for the presence of the PIA1 epitope, which has recently been localized to a polymorphism at position 33 on these late digestion products. Thrombin did not proteolyze GPIIIa even at 2.5 units/ml. Still to be resolved is whether the minor immunoreactive GPIIIa bands found on normal platelets are related to in vivo or in vitro proteolysis and whether GPIIIa proteolysis plays a role in chymotrypsin-induced exposure of the GPIIb/IIIa receptor. PMID:2529261

Beer, J; Coller, B S



Dioldehydrase: an Essential Role for Potassium Ion in the Homolytic Cleavage of the Cobalt-Carbon Bond in Adenosylcobalamin†  

PubMed Central

The complex of dioldehydrase with adenosylcobalamin (Coenzyme B12) and potassium ion reacts with molecular oxygen in the absence of a substrate to oxidize coenzyme and inactivate the complex. In this paper, high performance liquid chromatography and mass spectral analysis are used to identify the nucleoside products resulting from oxygen inactivation. The product profile indicates that oxygen inactivation proceeds by direct reaction of molecular oxygen with the 5?-deoxyadenosyl radical and cob(II)alamin. Formation of 5?-peroxyadenosine as the initial nucleoside product chemically correlates this reaction with aerobic, aqueous photoinduced homolytic cleavage of adenosylcobalamin (Schwartz, P. A. and Frey, P. A., (2007) Biochemistry, accompanying paper), indicating that both reactions proceed through similar chemical intermediates. The oxygen inactivation of the enzyme-coenzyme complex shows an absolute requirement for the same monocations required in catalysis by dioldehydrase. Measurements of the dissociation constants for adenosylcobalamin from potassium-free (Kd = 16 ± 2 ?M) or potassium-bound dioldehydrase (Kd = 0.8 ± 0.2 ?M), reveal that the effect of the monocation in stimulating oxygen sensitivity cannot be explained by an effect on the binding of coenzyme to the enzyme. Cross-linking experiments suggest that the full quaternary structure is assembled in the absence of potassium ion under the experimental conditions. The results indicate that dioldehydrase likely harvests the binding energy of the activating monocation to stimulate the homolytic cleavage of the Co-C5? bond in adenosylcobalamin. PMID:17516630

Schwartz, Phillip A.; Frey, Perry A.



Protocols for the selective cleavage of carbon-sulfur bonds in coal. Interim final technical report, September 1, 1992--August 31, 1993  

SciTech Connect

This report presents results of research pertaining to chemical reactions that aim to selectively cleave C-S bonds in model compounds as well as Illinois coal. Chemical reactions that result in carbon-sulfur bond cleavage are an essential aspect of any protocol designed to remove organic sulfur from coal. In the second year of the project {open_quotes}Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal, the author has completed investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures, reagents, and radiation. He has also undertaken a series of reactions in which physically cleaned Illinois coal has been subjected to many of the same reaction conditions that were shown, via the use of model sulfides, to result in substantial C-S bond cleavage and or sulfur oxidation. Therefore, summarized in this interim final report are results of the investigations of the photooxidation reactions of coal model sulfones and sulfides; the photolytic desulfurization of coal; and various other topics, including a summary of the endeavors aimed at initiating C-S bond cleavage reactions using oxidation/chlorination/desulfurization protocols, and various tellurium reagents. Important experiments remain to be completed on this project; therefore, efforts in these areas will continue through the end of calendar year 1993.

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States)



Efficient C-C bond splitting on Pt monolayer and sub-monolayer catalysts during ethanol electro-oxidation: Pt layer strain and morphology effects.  


Efficient catalytic C-C bond splitting coupled with complete 12-electron oxidation of the ethanol molecule to CO2 is reported on nanoscale electrocatalysts comprised of a Pt monolayer (ML) and sub-monolayer (sML) deposited on Au nanoparticles (Au@Pt ML/sML). The Au@Pt electrocatalysts were synthesized using surface limited redox replacement (SLRR) of an underpotentially deposited (UPD) Cu monolayer in an electrochemical cell reactor. Au@Pt ML showed improved catalytic activity for ethanol oxidation reaction (EOR) and, unlike their Pt bulk and Pt sML counterparts, was able to generate CO2 at very low electrode potentials owing to efficient C-C bond splitting. To explain this, we explore the hypothesis that competing strain effects due to the Pt layer coverage/morphology (compressive) and the Pt-Au lattice mismatch (tensile) control surface chemisorption and overall activity. Control experiments on well-defined model Pt monolayer systems are carried out involving a wide array of methods such as high-energy X-ray diffraction, pair-distribution function (PDF) analysis, in situ electrochemical FTIR spectroscopy, and in situ scanning tunneling microscopy. The vibrational fingerprints of adsorbed CO provide compelling evidence on the relation between surface bond strength, layer strain and morphology, and catalytic activity. PMID:25081353

Loukrakpam, Rameshwori; Yuan, Qiuyi; Petkov, Valeri; Gan, Lin; Rudi, Stefan; Yang, Ruizhi; Huang, Yunhui; Brankovic, Stanko R; Strasser, Peter



Imaging Adsorbate O-H Bond Cleavage: Methanol on TiO2(110)  

SciTech Connect

We investigated methanol adsorption and dissociation on bridge-bonded oxygen vacancies of TiO2(110) (1×1) surface using in situ scanning tunneling microscopy. We provide the first direct evidence that methanol dissociates on oxygen vacancies via O-H bond scission rather than C-O scission. For CH3OH coverages lower than the oxygen vacancy concentration, stationary methoxy-hydroxyl pairs form. At CH3OH coverages close to the oxygen vacancy concentration undissociated mobile CH3OH interacts with methoxy-hydroxyl pairs and facilitates the movement of hydroxyl away from the methoxy group

Zhang, Zhenrong; Bondarchuk, Olexsandr; White, J. M.; Kay, Bruce D.; Dohnalek, Zdenek



Effect of water on hydrolytic cleavage of non-terminal ?-glycosidic bonds in cyclodextrins to generate monosaccharides and their derivatives in a dimethyl sulfoxide-water mixture.  


Hydrolytic cleavage of the non-terminal ?-1,4-glycosidic bonds in ?-, ?-, and ?-cyclodextrins and the anomeric-terminal one in d-maltose was investigated to examine how the cleavage rate for ?-, ?-, and ?-cyclodextrins is slower than that for d-maltose. Effects of water and temperature were studied by applying in situ (13)C NMR spectroscopy and using a dimethyl sulfoxide (DMSO)-water mixture over a wide range of water mole fraction, xw = 0.004-1, at temperatures of 120-180 °C. The cleavage rate constant for the non-anomeric glycosidic bond was smaller by a factor of 6-10 than that of the anomeric-terminal one. The glycosidic-bond cleavage is significantly accelerated through the keto-enol tautomerization of the anomeric-terminal d-glucose unit into the d-fructose one. The smaller the size of the cyclodextrin, the easier the bond cleavage due to the ring strain. The remarkable enhancement in the cleavage rate with decreasing water content was observed for the cyclodextrins and d-maltose as well as d-cellobiose. This shows the important effect of the solitary water whose hydrogen bonding to other water molecules is prohibited by the presence of the organic dipolar aprotic solvent, DMSO, and which has more naked partial charges and higher reactivity. A high 5-hydroxymethyl-2-furaldehyde (5-HMF) yield of 64% was attained in a non-catalytic conversion by tuning the water content to xw = 0.30, at which the undesired polymerization by-paths can be most effectively suppressed. This study provides a step toward designing a new optimal, earth-benign generation process of 5-HMF starting from biomass. PMID:24527672

Kimura, Hiroshi; Hirayama, Masaki; Yoshida, Ken; Uosaki, Yasuhiro; Nakahara, Masaru



High resolution analysis of snake venom metalloproteinase (SVMP) peptide bond cleavage specificity using proteome based peptide libraries and mass spectrometry.  


Both serine and metalloproteinases have been shown to play the role of toxins in the venoms of many snakes. Determination of the natural protein substrates of these toxins is an important feature in the toxinological characterization of these proteinases. Furthermore, characterization of their peptide bond specificity is of value for understanding active site preference of the proteinase associated with effective proteolysis as well as of use in the design of peptide substrates and inhibitor lead compounds. Typically the determination of peptide bond cleavage specificity of snake venom serine proteinases (SVSPs) and snake venom metalloproteinases (SVMPs) has been performed using limited sets of peptides or small oligopeptides as experimental substrates. Although this approach has yielded valuable data it is generally limited in scope due to the relatively small sets of substrates used to generate the consensus specificity sequences for these proteinases. In this study we use a large, plasma based, proteome-derived peptide library as substrates along with mass spectrometry to explore the peptide bond specificity of three PI SVMPs and one PIII SVMP to determine their individual peptide cleavage consensus sequences. All of the proteinases assayed displayed a clear preference for a leucine residue in the P1' site. Careful analysis of the specificity profiles of the SVMPs examined showed interesting differences in the preferences at the other P and P' sites suggesting functional differences between these proteinases. The PI SVMPs, leucurolysin-a, atrolysin C, and BaP1, showed preferences across the full P4 to P4' range whereas the PIII SVMP bothropasin showed a narrower range of preferences across the sites. In silico docking experiments with the experimentally derived consensus sequences as well as with comparison of the results to those in the literature regarding peptide bond specificity based on both peptide and protein substrates give rise to a fresh understanding of the specificity of these SVMPS and may serve as a foundation for future experiments to better elucidate their mechanism of action in the complex pathophysiology of snakebite envenomation. PMID:21156218

Paes Leme, Adriana F; Escalante, Teresa; Pereira, Jose G C; Oliveira, Ana K; Sanchez, Eladio F; Gutiérrez, José M; Serrano, Solange M T; Fox, Jay W



Benzyl radical addition reaction through the homolytic cleavage of a benzylic C-H bond.  


Direct generation of a benzyl radical by C-H bond activation of toluenes and the addition reaction of the resulting radical to an electron deficient olefin were developed. The reaction of dimethyl fumarate with toluene in the presence of Et(3)B as a radical initiator at reflux afforded 2-benzylsuccinic acid dimethyl ester in good yield. PMID:21331427

Ueda, Masafumi; Kondoh, Eiko; Ito, Yuta; Shono, Hiroko; Kakiuchi, Maiko; Ichii, Yuki; Kimura, Takahiro; Miyoshi, Tetsuya; Naito, Takeaki; Miyata, Okiko



Oxidative addition of the C?-C? bond in ?-O-4 linkage of lignin to transition metals using a relativistic pseudopotential-based ccCA-ONIOM method.  


A multi-level multi-layer QM/QM method, the relativistic pseudopotential correlation-consistent composite approach within an ONIOM framework (rp-ccCA-ONIOM), was applied to study the oxidative addition of the C(?)-C(?) bond in an archetypal arylglycerol ?-aryl ether (?-O-4 linkage) substructure of lignin to Ni, Cu, Pd and Pt transition metal atoms. The chemically active high-level layer is treated using the relativistic pseudopotential correlation-consistent composite approach (rp-ccCA), an efficient methodology designed to reproduce an accuracy that would be obtained using the more computationally demanding CCSD(T)/aug-cc-pCV?Z-PP, albeit at a significantly reduced computational cost, while the low-level layer is computed using B3LYP/cc-pVTZ. The thermodynamic and kinetic feasibilities of the model reactions are reported in terms of enthalpies of reactions at 298 K (?H°(298)) and activation energies (?H-act). The results obtained from the rp-ccCA:B3LYP hybrid method are compared to the corresponding values using CCSD(T) and several density functionals including B3LYP, M06, M06 L, B2PLYP, mPWPLYP and B2GP-PLYP. The energetics of the oxidative addition of C?C bond in ethane to Ni, Cu, Pd and Pt atoms are also reported to demonstrate that the rp-ccCA method effectively reproduces the accuracy of the CCSD(T)/aug-cc-pCV?Z method. Our results show that in the catalytic activation of the C(?)-C(?) bond of ?-O-4, the use of platinum metal catalysts will lead to the most thermodynamically favored reaction with the lowest activation barrier. PMID:22144374

Oyedepo, Gbenga A; Wilson, Angela K



Bonding and Integration of C-C Composite to Cu-Clad-Molybdenum for Thermal Management Applications  

NASA Technical Reports Server (NTRS)

Two- and three-dimensional carbon-carbon composites with either resin-derived matrix or CVI matrix were joined to Cu-clad-Mo using active Ag-Cu braze alloys for thermal management applications. The joint microstructure and composition were examined using Field-Emission Scanning Electron Microscopy and Energy-Dispersive Spectroscopy, and the joint hardness was characterized using the Knoop microhardness testing. Observations on the infiltration of the composite with molten braze, dissolution of metal substrate, and solute segregation at the C-C surface have been discussed. The thermal response of the integrated assembly is also briefly discussed.

Asthana, R.; Singh, M.; Shpargel, T.P.



Active Metal Brazing and Adhesive Bonding of Titanium to C/C Composites for Heat Rejection System  

NASA Technical Reports Server (NTRS)

Robust assembly and integration technologies are critically needed for the manufacturing of heat rejection system (HRS) components for current and future space exploration missions. Active metal brazing and adhesive bonding technologies are being assessed for the bonding of titanium to high conductivity Carbon-Carbon composite sub components in various shapes and sizes. Currently a number of different silver and copper based active metal brazes and adhesive compositions are being evaluated. The joint microstructures were examined using optical microscopy, and scanning electron microscopy (SEM) coupled with energy dispersive spectrometry (EDS). Several mechanical tests have been employed to ascertain the effectiveness of different brazing and adhesive approaches in tension and in shear that are both simple and representative of the actual system and relatively straightforward in analysis. The results of these mechanical tests along with the fractographic analysis will be discussed. In addition, advantages, technical issues and concerns in using different bonding approaches will also be presented.

Singh, M.; Shpargel, Tarah; Cerny, Jennifer



Computational Study of Low-Temperature Catalytic C-C Bond Activation of Alkanes for Portable Power.  

National Technical Information Service (NTIS)

The development of a room temperature (<50 C) fuel cell that would use a generally available fuel such as JP8 would be most valuable. However there are no known catalysts that can selectively activate the CC bonds of such fuels at such temperature. The go...



Photodissociation Dynamics of 2-BROMOETHYLNITRITE at 351 NM and C-C Bond Fission in the ? - Radical Product  

NASA Astrophysics Data System (ADS)

We used a crossed laser-molecular beam scattering experiment to investigate the primary photodissociation channels of bromoethylnitrite at 351 nm. Only the O-NO bond fission channel forming the ? -bromoethoxy radical and NO, no HBr photoelimination, was detected upon 351 nm photoexcitation,. The subsequent decomposition of the highly vibrational excited ? -bromoethoxy radical to formaldehyde + CH{_2}Br was also investigated.

Wang, Lei; Chhantyal-Pun, Rabi; Brynteson, Matt D.; Miller, Terry A.; Butler, Laurie J.



Substituent-controlled selective synthesis of N-acyl 2-aminothiazoles by intramolecular zwitterion-mediated C-N bond cleavage.  


The cleavage of C-N bonds is an interesting and challenging subject in modern organic synthesis. We have achieved the first zwitterion-controlled C-N bond cleavage in the MCR reaction among lithium alkynethiolates, bulky carbodiimides, and acid chlorides to construct N-acyl 2-aminothiazoles. This is a simple, highly efficient, and general method for the preparation of N-acyl 2-aminothiazoles with a broad range of substituents. The selective synthesis of N-acyl 2-aminothiazoles significantly depends on the steric hindrance of carbodiimides. The result is in striking contrast with our previous convergent reaction giving 5-acyl-2-iminothiazolines via 1,5-acyl migration. It is indeed interesting that the slight change of the substituents on the carbodiimides can completely switch the product structure. Experimental and theoretical results demonstrate the reason why the C-N bond cleavage in the present system is prior to the acyl migration. The intramolecular hydrogen relay via unprecedented Hofmann-type elimination is essential for this totally new zwitterion-controlled C-N bond cleavage. PMID:25361067

Wang, Yang; Zhao, Fei; Chi, Yue; Zhang, Wen-Xiong; Xi, Zhenfeng



Palladium-catalyzed double alkylation of 3-aryl-2-fluoroallyl esters with malonate nucleophiles through the carbon-fluorine bond cleavage.  


The alkylation of (Z)-3-aryl-2-fluoroallyl acetate with the malonate anion by the [Pd(C3H5)(cod)]BF4/2,2'-bpy catalyst proceeds through the carbon-fluorine bond cleavage, and 2 equiv of the malonate nucleophile was introduced to the allyl substrate. PMID:24479838

Yamamoto, Mitsuaki; Hayashi, Shunsuke; Isa, Kazuki; Kawatsura, Motoi



Metal-free aerobic oxidative C-N bond cleavage of tertiary amines for the synthesis of N-heterocycles with high atom efficiency.  


An efficient metal-free aerobic oxidative C-N bond cleavage of tertiary amines has been developed to construct N-heterocycles using molecular oxygen as the sole oxidant with high atom efficiency, in which all of the three alkyl groups in tertiary amines can be utilized and transformed into N-heterocycles. PMID:24788750

Chen, Xiuling; Chen, Tieqiao; Zhou, Yongbo; Han, Daoqing; Han, Li-Biao; Yin, Shuang-Feng



Selective cleavage of the two CS bonds in asymmetrically alkylated dibenzothiophenes by Rhodococcus erythropolis KA2-5-1.  


The Rhodococcus erythropolis strain KA2-5-1 was characterized by its ability to cleave carbon-sulfur bonds in the dibenzothiophene (DBT) ring by asymmetrically alkyl substitution, such as C2-DBTs (e.g., dimethyl and ethyl DBTs) and C3-DBTs (e.g., trimethyl and propyl DBTs), which are known to remain in hydrodesulfurization-treated diesel fuels. After treatment by solid-phase extraction (SPE) of solvents from microbial reactions of alkylated DBTs (Cx-DBTs), we used gas chromatography (GC), GC-atomic emission detection, GC-mass spectrometry and 1H nuclear magnetic resonance spectroscopy to identify and quantitatively evaluate the Cx-DBT metabolites. Molar ratios of metabolic isomers of the desulfurization products suggested that resting-cell reactions of KA2-5-1 against these Cx-DBTs occurrs through specific carbon-sulfur-bond-targeted cleavages, yielding alkylated hydroxybiphenyls, and that the manner of the attack on the DBT skeleton is affected not only by the position but also by the number and length of the alkyl substituents. PMID:16233063

Onaka, T; Kobayashi, M; Ishii, Y; Konishi, J; Maruhashi, K



Low-energy (0.1 eV) electron attachment S?S bond cleavage assisted by Coulomb stabilization  

NASA Astrophysics Data System (ADS)

Electron capture by the ion H3C-S-S-CH2-CH2-NH +3 at either the -NH +3 site (to form the Rydberg radical H3C-S-S-CH2-CH2-NH3) or into the S-S antibonding ?* orbital is shown to be able to produce the same S-S bond fragmentation products H3C-S and HS-CH2-CH2-NH2, albeit by very different pathways. Capture into the S-S ?* orbital is, in the absence of the nearby positive site, endothermic by approximately 0.9 eV and leads to an electronically metastable anion that can undergo dissociation or autodetachment. In contrast, in the presence of the stabilizing Coulomb potential provided by the nearby NH +3 site, electron attachment into the S-S ?* orbital is rendered exothermic. As a result, as we have shown in this paper, the effective cross sections for forming the H3C-S and HS-CH2-CH2-NH2 products via attachment at the -NH +3 and S-S ?* sites are predicted to be comparable for our model compound. Moreover, we predict that the ?* site will become more amenable to electron attachment compared with the -NH +3 site for compounds in which the distance between the S-S bond and the protonated amine is larger than in our cation. These findings and insights should be of substantial value to workers studying bond cleavage rates and fragmentation patterns in gaseous positively charged samples of peptides and proteins.

Sawicka, Agnieszka; Berdys-Kocha?ska, Joanna; Skurski, Piotr; Simons, Jack


Mechanism of SN2 disulfide bond cleavage by phosphorus nucleophiles. Implications for biochemical disulfide reducing agents.  


The B3LYP variant of DFT has been used to study the mechanism of S-S bond scission in dimethyl disulfide by a phosphorus nucleophile, trimethylphospine (TMP). The reaction is highly endothermic in the gas phase and requires significant external stabilization of the charged products. DFT calculations (B3LYP) were performed with explicit (water molecules added) and implicit solvent corrections (COSMO model). The transition structures for this SN2 displacement reaction in a number of model systems have been located and fully characterized. The reaction barriers calculated with different approaches for different systems are quite close (around 11 kcal/mol). Remarkably, the calculations suggest that the reaction is almost barrierless with respect to the preorganized reaction complex and that most of the activation energy is required to rearrange the disulfide and TMP to its most effective orientation for the SMe group transfer way. Different reactivities of different phosphorus nucleophiles were suggested to be the result of steric effects, as manifested largely by varying amounts of hindrance to solvation of the initial product phosphonium ion. These data indicate that the gas-phase addition of a phosphine to the disulfide moiety will most likely form a phosphonium cation-thiolate anion salt, in the presence of four or more water molecules, that provide sufficient H-bonding stabilization to allow displacement of the thiolate anion, a normal uncomplicated SN2 transition state is to be expected. PMID:17914842

Dmitrenko, Olga; Thorpe, Colin; Bach, Robert D



Radical coupling for directed C-C/C-S bond formation in the reaction of Cp*IrS2C2B10H10 with 1-azido-3-nitrobenzene.  


Reactions of half-sandwich complex Cp*IrS2C2B10H10 (1) with 1-azido-3-nitrobenzene (3-NO2C6H4N3, L) upon heating or under light led to new complexes 2-6. Complexes 2 and 3 contain a five-membered cyclometalated ligand arising from C(sp(2))-H activation of the azide ligand L. Complex 4 is a 16 electron species containing a new-generated C-C bond between the azide ligand L and the Cp* unit where C(sp(3))-H activation of the methyl unit occurred. Complexes 5 and 6 contain two types of the ligand which appear in complexes 2, 3 and 4. Further reactions of complexes 5 and 6 with L under more harsh conditions gave rise to the nucleophilic addition products 7 and 8, where ring expansion of the azide ligand at the imido site of complexes 5 and 6 happened. Complexes 2-8 were characterized by NMR, MS, IR, and elemental analysis, and X-ray structural analyses were performed for complexes 2-4 and 6-8. The radical mechanisms for the formation of complexes 2-6 were proposed on the basis of capture experiments by EPR and ESI-MS. And the formation mechanism of complexes 7 and 8 was also suggested. PMID:24108087

Zhong, Wei; Jiang, Qibai; Zhang, Qian; Shang, Yi; Yan, Hong; Bregadze, Vladimir



Understanding the Mechanisms of Unusually Fast H?H, C?H, and C?C Bond Reductive Eliminations from Gold(III) Complexes.  


Carbon-carbon bond reductive elimination from gold(III) complexes are known to be very slow and require high temperatures. Recently, Toste and co-workers have demonstrated extremely rapid C?C reductive elimination from cis-[AuPPh3 (4-F-C6 H4 )2 Cl] even at low temperatures. We have performed DFT calculations to understand the mechanistic pathway for these novel reductive elimination reactions. Direct dynamics calculations inclusive of quantum mechanical tunneling showed significant contribution of heavy-atom tunneling (>25?%) at the experimental reaction temperatures. In the absence of any competing side reactions, such as phosphine exchange/dissociation, the complex cis-[Au(PPh3 )2 (4-F-C6 H4 )2 ](+) was shown to undergo ultrafast reductive elimination. Calculations also revealed very facile, concerted mechanisms for H?H, C?H, and C?C bond reductive elimination from a range of neutral and cationic gold(III) centers, except for the coupling of sp(3) carbon atoms. Metal-carbon bond strengths in the transition states that originate from attractive orbital interactions control the feasibility of a concerted reductive elimination mechanism. Calculations for the formation of methane from complex cis-[AuPPh3 (H)CH3 ](+) predict that at -52?°C, about 82?% of the reaction occurs by hydrogen-atom tunneling. Tunneling leads to subtle effects on the reaction rates, such as large primary kinetic isotope effects (KIE) and a strong violation of the rule of the geometric mean of the primary and secondary KIEs. PMID:25224135

Nijamudheen, A; Karmakar, Sharmistha; Datta, Ayan



Tight coupling of partial reactions in the acetyl-CoA decarbonylase/synthase (ACDS) multienzyme complex from Methanosarcina thermophila: acetyl C-C bond fragmentation at the a cluster promoted by protein conformational changes.  


Direct synthesis and cleavage of acetyl-CoA are carried out by the bifunctional CO dehydrogenase/acetyl-CoA synthase enzyme in anaerobic bacteria and by the acetyl-CoA decarbonylase/synthase (ACDS) multienzyme complex in Archaea. In both systems, a nickel- and Fe/S-containing active site metal center, the A cluster, catalyzes acetyl C-C bond formation/breakdown. Carbonyl group exchange of [1-(14)C]acetyl-CoA with unlabeled CO, a hallmark of CODH/ACS, is weakly active in ACDS, and exchange with CO(2) was up to 350 times faster, indicating tight coupling of CO release at the A cluster to CO oxidation to CO(2) at the C cluster in CO dehydrogenase. The basis for tight coupling was investigated by analysis of three recombinant A cluster proteins, ACDS beta subunit from Methanosarcina thermophila, acetyl-CoA synthase of Carboxydothermus hydrogenoformans (ACS(Ch)), and truncated ACS(Ch) lacking its 317-amino acid N-terminal domain. A comparison of acetyl-CoA synthesis kinetics, CO exchange, acetyltransferase, and A cluster Ni(+)-CO EPR characteristics demonstrated a direct role of the ACS N-terminal domain in promoting acetyl C-C bond fragmentation. Protein conformational changes, related to "open/closed" states previously identified crystallographically, were indicated to have direct effects on the coordination geometry and stability of the A cluster Ni(2+)-acetyl intermediate, controlling Ni(2+)-acetyl fragmentation and Ni(2+)(CO)(CH(3)) condensation. EPR spectral changes likely reflect variations in the Ni(+)-CO equatorial coordination environment in closed buried hydrophobic and open solvent-exposed states. The involvement of subunit-subunit interactions in ACDS, versus interdomain contacts in ACS, ensures that CO is not released from the ACDS beta subunit in the absence of appropriate interactions with the alpha(2)epsilon(2) CO dehydrogenase component. The resultant high efficiency CO transfer explains the low rate of CO exchange relative to CO(2). PMID:20202935

Gencic, Simonida; Duin, Evert C; Grahame, David A



Facile O-atom insertion into C-C and C-H bonds by a trinuclear copper complex designed to harness a singlet oxene.  


Two trinuclear copper [Cu(I)Cu(I)Cu(I)(L)](1+) complexes have been prepared with the multidentate ligands (L) 3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(dimethylamino)ethyl)(methyl)amino)propan-2-ol) (7-Me) and (3,3'-(1,4-diazepane-1,4-diyl)bis(1-((2-(diethylamino) ethyl)(ethyl) amino)propan-2-ol) (7-Et) as models for the active site of the particulate methane monooxygenase (pMMO). The ligands were designed to form the proper spatial and electronic geometry to harness a "singlet oxene," according to the mechanism previously suggested by our laboratory. Consistent with the design strategy, both [Cu(I)Cu(I)Cu(I)(L)](1+) reacted with dioxygen to form a putative bis(mu(3)-oxo)Cu(II)Cu(II)Cu(III) species, capable of facile O-atom insertion across the central C-C bond of benzil and 2,3-butanedione at ambient temperature and pressure. These complexes also catalyze facile O-atom transfer to the C-H bond of CH(3)CN to form glycolonitrile. These results, together with our recent biochemical studies on pMMO, provide support for our hypothesis that the hydroxylation site of pMMO contains a trinuclear copper cluster that mediates C-H bond activation by a singlet oxene mechanism. PMID:17804786

Chen, Peter P-Y; Yang, Richard B-G; Lee, Jason C-M; Chan, Sunney I



Room temperature C-N bond cleavage of anionic guanidinate ligand in rare-earth metal complexes.  


The dissociation of the anionic guanidinate ligand N=C(NMe2)2 promoted by rare-earth metal complexes at room temperature is described. Treatment of CpLnCl2(THF)3 with two equiv. of Li[N=C(NMe2)2] in THF at room temperature affords [Cp2Ln(?-?(1):?(2)-L2)]2 (Ln = Y; L = N=C(NMe2)N=C(NMe2)2) and CpLn[N=C(NMe2)2](?-?(1):?(2)-L)2LnCp2 (Ln = Dy) in moderated yields, respectively. YCl3 reacts with three equiv. of Li[N=C(NMe2)2] under the same conditions to give a trinuclear yttrium guanidinate [(Me2N)2C=N]5Y3[?-N=C(NMe2)2]2(?-?(1):?(2)-L)2 in 63% yield. These reactions show that rare-earth metals can promote a C-N bond cleavage of the guanidine anion [N=C(NMe2)2](-) at room temperature. All new complexes were characterized by elemental analysis and spectroscopic properties, and their solid-state structures were determined through single-crystal X-ray diffraction analysis. PMID:23456152

Zhang, Jie; Yi, Weiyin; Chen, Zhenxia; Zhou, Xigeng



3-Deoxy-D-manno-octulosonate-8-phosphate synthase catalyzes the C-O bond cleavage of phosphoenolpyruvate.  


The mechanism of 3-deoxy-D-manno-octulosonate-8-phosphate (KDO8P) synthase was investigated. When [18O]-PEP specifically labeled in the enolic oxygen is a substrate for KDO8P synthase, the 18O is recovered in Pi. This indicates that the KDO8P synthase reaction proceeds with C-O bond cleavage of PEP similar to that observed in the 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase catalyzed condensation of PEP and erythrose-4-phosphate (1). No evidence for a covalent enzyme-PEP intermediate could be obtained. No [32P]-Pi exchange into PEP nor scrambling of bridge 18O to non-bridging positions in [18O]-PEP was observed in the presence or absence of arabinose-5-phosphate or its analog ribose-5-phosphate. Bromopyruvate inactivated KDO8P synthase in a time dependent process. It is likely that bromopyruvate reacts with a functional group at the PEP binding site since PEP, but not arabinose-5-phosphate, protects against inactivation. PMID:2904815

Hedstrom, L; Abeles, R



Bis(trifluoromethyl)methylene addition to vinyl-terminated SAMs: a gas-phase C-C bond-forming reaction on a surface.  


Vinyl-terminated self-assembled monolayers (SAMs) on silicon oxide substrates were chemically modified by the addition of a bis(trifluoromethyl)methylene group in a rare gas-phase C-C bond-forming reaction to directly generate films carrying terminal CF3 groups. The vinyl-terminated films were treated with hexafluoroacetone azine (HFAA) for modification. The films were characterized with ellipsometry, contact angle measurements, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). In this study, we find that for optimized conditions clean reactions occur on a surface between SAMs with terminal olefins and HFAA, and the product is consistent with bis(trifluoromethyl)cyclopropanation formation after nitrogen extrusion. PMID:24806554

Adamkiewicz, Malgorzata; O'Hagan, David; Hähner, Georg



Tailored synthesis of various nanomaterials by using a graphene-oxide-based gel as a nanoreactor and nanohybrid-catalyzed c?c bond formation.  


New graphene oxide (GO)-based hydrogels that contain vitamin?B2 /B12 and vitamin?C (ascorbic acid) have been synthesized in water (at neutral pH value). These gel-based soft materials have been used to synthesize various metal nanoparticles, including Au, Ag, and Pd nanoparticles, as well as nanoparticle-containing reduced graphene oxide (RGO)-based nanohybrid systems. This result indicates that GO-based gels can be used as versatile reactors for the synthesis of different nanomaterials and hybrid systems on the nanoscale. Moreover, the RGO-based nanohybrid hydrogel with Pd nanoparticles was used as an efficient catalyst for C?C bond-formation reactions with good yields and showed high recyclability in Suzuki-Miyaura coupling reactions. PMID:25224859

Biswas, Abhijit; Banerjee, Arindam



Bis(trifluoromethyl)methylene Addition to Vinyl-Terminated SAMs: A Gas-Phase C-C Bond-Forming Reaction on a Surface  

PubMed Central

Vinyl-terminated self-assembled monolayers (SAMs) on silicon oxide substrates were chemically modified by the addition of a bis(trifluoromethyl)methylene group in a rare gas-phase C–C bond-forming reaction to directly generate films carrying terminal CF3 groups. The vinyl-terminated films were treated with hexafluoroacetone azine (HFAA) for modification. The films were characterized with ellipsometry, contact angle measurements, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). In this study, we find that for optimized conditions clean reactions occur on a surface between SAMs with terminal olefins and HFAA, and the product is consistent with bis(trifluoromethyl)cyclopropanation formation after nitrogen extrusion. PMID:24806554



High chemoselectivity of an advanced iron catalyst for the hydrogenation of aldehydes with isolated c?c bond: a computational study.  


Knölker's iron complex is a "green" catalyst that exhibits low toxicity and is abundant in nature. Density functional theory (DFT) was used to explore the highly chemoselective nature of the catalytic hydrogenation of CH2?CHCH2CHO. An outer-sphere concerted hydrogen transfer was found to be the most reasonable kinetic route for the hydrogenation of the olefin. However, the C?C hydrogenation reaction has a high free energy barrier of 28.1 kcal/mol, requiring a high temperature to overcome. By comparison, the CH?O bond concerted hydrogen-transfer reaction catalyzed using Knölker's iron catalyst has an energy barrier of only 14.0 kcal/mol. Therefore, only the CH?O of CH2?CHCH2CHO can be hydrogenated in the presence of Knölker's catalyst at room temperature, due to kinetic domination. All computational results were in good agreement with experimental results. PMID:25222376

Lu, Xi; Cheng, Runjiao; Turner, Nicholas; Liu, Qian; Zhang, Mingtao; Sun, Xiaomin



Novel enzymatic activity of cell free extract from thermophilic Geobacillus sp. UZO 3 catalyzes reductive cleavage of diaryl ether bonds of 2,7-dichlorodibenzo- p-dioxin  

Microsoft Academic Search

We characterized the ability of the cell free extract from polychlorinated dibenzo-p-dioxins degrading bacterium Geobacillus sp. UZO 3 to reduce even highly chlorinated dibenzo-p-dioxins such as octachlorodibenzo-p-dioxins in incineration fly ash. The degradation of 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD) as a model dioxin catalyzed by the cell free extract from this strain implicates that the ether bonds of 2,7-DCDD molecule undergo reductive cleavage,

Yuzoh Suzuki; Masaya Nakamura; Yuichiro Otsuka; Nao Suzuki; Keisuke Ohyama; Takeshi Kawakami; Kanna Sato; Shinya Kajita; Shojiro Hishiyama; Takeo Fujii; Atsushi Takahashi; Yoshihiro Katayama



A density functional theory study on the kinetics and thermodynamics of N-glycosidic bond cleavage in 5-substituted 2'-deoxycytidines.  


B3LYP/6-311+G(2d,p)//B3LYP/6-31+G(d) density functional theory calculations were employed to explore the kinetics and thermodynamics of gas-phase N-glycosidic bond cleavage induced by nucleophilic attack of C1' with a hydroxide ion in 5-substituted 2'-deoxycytidines. The results showed that, among the 5-substituted 2'-deoxycytidine derivatives examined [XdC, where X = H (dC), CH(3) (medC), CH(2)OH (hmdC), CHO (fmdC), COOH (cadC), F (FdC), or Br (BrdC)], fmdC and cadC exhibited the lowest energy barrier and largest exothermicity for N-glycosidic bond cleavage. These results paralleled previously reported nucleobase excision activities of human thymine DNA glycosylase (hTDG) toward duplex DNA substrates harboring a thymine and 5-substituted cytosine derivatives when paired with a guanine. Our study suggests that the inherent chemistry associated with the nucleophilic cleavage of N-glycosidic bond constitutes a major factor contributing to the selectivity of hTDG toward 5-substituted dC derivatives. These findings provided novel insights into the role of TDG in active cytosine demethylation. PMID:22809372

Williams, Renee T; Wang, Yinsheng



Iron dicarbonyl complexes featuring bipyridine-based PNN pincer ligands with short interpyridine C-C bond lengths: innocent or non-innocent ligand?  


A series of iron dicarbonyl complexes with bipyridine-based PNN pincer ligands were synthesized and characterized by multinuclear NMR spectroscopy ((1) H, (13) C, (15) N, (31) P), IR spectroscopy, cyclic voltammetry, (57) Fe Mössbauer spectroscopy, XPS spectroscopy, and single-crystal X-ray diffraction. The complexes with the general formula [(R-PNN)Fe(CO)2 ] (5: R-PNN=tBu-PNN=6-[(di-tert-butylphosphino)methyl]-2,2'-bipyridine, 6: R-PNN=iPr-PNN=6-[(diisopropylphosphino)methyl]-2,2'-bipyridine, and 7: R-PNN=Ph-PNN=6-[(diphenylphosphino)methyl]-2,2'-bipyridine) feature differently P-substituted PNN pincer ligands. Complexes 5 and 6 were obtained by reduction of the corresponding dihalide complexes [(R-PNN)Fe(X)2 ] (1: R=tBu, X=Cl; 2: R=tBu, X=Br; 3: R=iPr, X=Cl; 4: R=iPr, X=Br) in the presence of CO. The analogous Ph-substituted complex 7 was synthesized by a reaction of the free ligand with iron pentacarbonyl. The low-spin complexes 5-7 (S=0) are diamagnetic and have distorted trigonal bipyramidal structures in solution, whereas in the solid state the geometries around the iron are best described as distorted square pyramidal. Compared to other structurally characterized complexes with these PNN ligands, shortened interpyridine C?C bonds of about 1.43?Å were measured. A comparison with known examples, theoretically described as metal complexes bearing bipyridine ?-radical anions (bpy(.) (-) ), suggests that the complexes can be described as Fe(I) complexes with one electron antiferromagnetically coupled to the ligand-based radical anions. However, computational studies, at the NEVPT2/CASSCF level of theory, reveal that the shortening of the C?C bond is a result of extensive ?-backbonding of the iron center into the antibonding orbital of the bpy unit. Hence, the description of the complexes as Fe(0) complexes with neutral bipyridine units is the favorable one. PMID:24591249

Zell, Thomas; Milko, Petr; Fillman, Kathlyn L; Diskin-Posner, Yael; Bendikov, Tatyana; Iron, Mark A; Leitus, Gregory; Ben-David, Yehoshoa; Neidig, Michael L; Milstein, David



Low energy electron induced cytosine base release in 2'-deoxycytidine-3'-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study  

NASA Astrophysics Data System (ADS)

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2'-deoxycytidine-3'-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3' C-O bond cleavage from the lowest ?* shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the ?* orbital of the base to the ?* orbital of the glycosidic N-C bond. In addition, the metastable state formed after impinging LEE (0-1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N-C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ˜35-55 fs. Comparison of salient features of the two dissociation events, i.e., 3' C-O single strand break and glycosidic N-C bond cleavage in 3'-dCMPH molecule are also provided.

Bhaskaran, Renjith; Sarma, Manabendra



Regioselective functionalization of iminophosphoranes through Pd-mediated C-H bond activation: C-C and C-X bond formation.  


The orthopalladation of iminophosphoranes [R(3)P=N-C(10)H(7)-1] (R(3) = Ph(3) 1, p-Tol(3) 2, PhMe(2) 3, Ph(2)Me 4, N-C(10)H(7)-1 = 1-naphthyl) has been studied. It occurs regioselectively at the aryl ring bonded to the P atom in 1 and 2, giving endo-[Pd(?-Cl)(C(6)H(4)-(PPh(2=N-1-C(10)H(7))-2)-?-C,N](2) (5) or endo-[Pd(?-Cl)(C(6)H(3)-(P(p-Tol)(2)=N-C(10)H(7)-1)-2-Me-5)-?-C,N](2) (6), while in 3 the 1-naphthyl group is metallated instead, giving exo-[Pd(?-Cl)(C(10)H(6)-(N=PPhMe(2))-8)-?-C,N](2) (7). In the case of 4, orthopalladation at room temperature affords the kinetic exo isomer [Pd(?-Cl)(C(10)H(6)-(N=PPh(2)Me)-8)-?-C,N](2) (11exo), while a mixture of 11exo and the thermodynamic endo isomer [Pd(?-Cl)(C(6)H(4)-(PPhMe=N-C(10)H(7)-1)-2)-?-C,N](2) (11endo) is obtained in refluxing toluene. The heating in toluene of the acetate bridge dimer [Pd(?-OAc)(C(10)H(6)-(N=PPh(2)Me)-8)-?-C,N](2) (13exo) promotes the facile transformation of the exo isomer into the endo isomer [Pd(?-OAc)(C(6)H(4)-(PPhMe=N-C(10)H(7)-1)-2)-?-C,N](2) (13endo), confirming that the exo isomers are formed under kinetic control. Reactions of the orthometallated complexes have led to functionalized molecules. The stoichiometric reactions of the orthometallated complexes [Pd(?-Cl)(C(10)H(6)-(N=PPhMe(2))-8)-?-C,N](2) (7), [Pd(?-Cl)(C(6)H(4)-(PPh(2)[=NPh)-2)](2) (17) and [Pd(?-Cl)(C(6)H(3)-(C(O)N=PPh(3))-2-OMe-4)](2) (18) with I(2) or with CO results in the synthesis of the ortho-halogenated compounds [PhMe(2)P=N-C(10)H(6)-I-8] (19), [I-C(6)H(4)-(PPh(2)=NPh)-2] (21) and [Ph(3)P=NC(O)C(6)H(3)-I-2-OMe-5] (23) or the heterocycles [C(10)H(6)-(N=PPhMe(2))-1-(C(O))-8]Cl (20), [C(6)H(5)-(N=PPh(2)-C(6)H(4)-C(O)-2]ClO(4) (22) and [C(6)H(3)-(C(O)-1,2-N-PPh(3))-OMe-4]Cl (24). PMID:20927428

Aguilar, David; Navarro, Rafael; Soler, Tatiana; Urriolabeitia, Esteban P



Protocols for the selective cleavage of carbon-sulfur bonds in coal. Final technical report, September 1, 1991--August 31, 1992  

SciTech Connect

Summarized in the final technical report for our project ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal`` are results of research pertaining to chemical reactions that aim to selectively cleave C-S bonds in model compounds as well as Illinois coal. Removal of the organic sulfur in coal constitutes one of the major challenges facing fossil fuel scientists today. A cost-effective means of desulfurizing Illinois coal is, at present, non-existent. Research in our group aims to develop a simple protocol for sulfur removal by gaining understanding of how various additives and reaction conditions, including solvents, bases, added reagents, catalysts, oxidizing agents, electron acceptors, temperature, pressure, and light energy, can enhance the rates of C-S bond cleavage in Illinois coal and coal model compounds. These experiments have been at the focus of our research effort for the past twelve months. Previous quarterly reports described research results in which simple aromatic and aliphatic sulfides were allowed to react with (a) Lewis Acids such as zinc chloride and tin chloride; (b) electron accepting substrates such as 9-fluorenone and benzoquinone; (c) strong bases such as NaOH and KOH; (d) radical initiators such as AIBN; (e) neat solvents at reflux temperatures and higher temperatures; (f) molecular oxygen in the presence of dyes or sensitizers such as anthracene. In this final report, we report on additional experiments involving the photooxidation of organic sulfides, as well as some experiments aimed at evaluating and comparing the reactivities of simple organic sulfones with their sulfidyl analogues. Also contained in this final report is a brief summary of the research described in the previous three quarterly reports for ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal.``

Bausch, M. [Southern Illinois Univ., Carbondale, IL (United States)



Long live vinylidene! A new view of the H(2)C=C: --> HC triple bond CH rearrangement from ab initio molecular dynamics.  


We present complete active space self-consistent field (CASSCF) ab initio molecular dynamics (AIMD) simulations of the preparation of the metastable species vinylidene, and its subsequent, highly exothermic isomerization to acetylene, via electron removal from vinylidene anion (D(2)C=C(-) --> D(2)C=C: --> DC triple bond CD). After equilibrating vinylidene anion-d(2) at either 600 +/- 300 K (slightly below the isomerization barrier) or 1440 K +/- 720 K (just above the isomerization barrier), we remove an electron to form a vibrationally excited singlet vinylidene-d(2) and follow its dynamical evolution for 1.0 ps. Remarkably, we find that none of the vinylidenes equilibrated at 600 K and only 20% of the vinylidenes equilibrated at 1440 K isomerized, suggesting average lifetimes >1 ps for vibrationally excited vinylidene-d(2). Since the anion and neutral vinylidene are structurally similar, and yet extremely different geometrically from the isomerization transition state (TS), neutral vinylidene is not formed near the TS so that it must live until it has sufficient instantaneous kinetic energy in the correct vibrational mode(s). The origin of the delay is explained via both orbital rearrangement and intramolecular vibrational energy redistribution (IVR) effects. Unique signatures of the isomerization dynamics are revealed in the anharmonic vibrational frequencies extracted from the AIMD, which should be observable by ultrafast vibrational spectroscopy and in fact are consistent with currently available experimental spectra. Most interestingly, of those trajectories that did isomerize, every one of them violated conventional transition-state theory by recrossing back to vinylidene multiple times, against conventional notions that expect highly exothermic reactions to be irreversible. The dynamical motion responsible for the multiple barrier recrossings involves strong mode-coupling between the vinylidene CD(2) rock and a local acetylene DCC bend mode that has been recently observed experimentally. The multiple barrier recrossings can be used, via a generalized definition of lifetime, to reconcile extremely disparate experimental estimates of vinylidene's lifetime (differing by at least 6 orders of magnitude). Last, a caveat: These results are constrained by the approximations inherent in the simulation (classical nuclear motion, neglect of rotation-vibration coupling, and restriction to C(s) symmetry); refinement of these predictions may be necessary when more exact simulations someday become feasible. PMID:11456576

Hayes, R L; Fattal, E; Govind, N; Carter, E A



N-N bond cleavage of mid-valent Ta(IV) hydrazido and hydrazidium complexes relevant to the Schrock cycle for dinitrogen fixation.  


Chemical reduction of the Ta(V) hydrazido chloride 1 generates the open-shell, mononuclear Ta(IV) hydrazido complex 2, which upon N-methylation yields the corresponding structurally characterized Ta(IV) hydrazidium 6. Chemical reduction of 6 results in N-N bond cleavage to generate a cis/trans mixture of the [Ta(V),Ta(V)] bis(?-nitrido) product 7 in tetrahydrofuran and the mononuclear Ta(V) parent imide 8 in toluene. These results serve to establish an important foundation for the pursuit of a group-5 metal variant of the Schrock cycle for dinitrogen fixation. PMID:23725566

Keane, Andrew J; Zavalij, Peter Y; Sita, Lawrence R



Regioselective CC bond cleavage in arylhydrazones of 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-diones  

NASA Astrophysics Data System (ADS)

New (Z)-2-(2-(para-substituted phenyl)hydrazono)-4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-diones with chloro (1), bromo (2) and carboxy (3) substituents were synthesized and characterized by ESI-MS, IR, 1H and 13C NMR spectroscopies and elemental analysis. The regioselective carbon-carbon bond cleavage with the formation (E)-2-(2-(4-substituted phenyl) hydrazono)-1-(thiophen-2-yl)ethanones was achieved upon heating (80 °C) of 1-3 in methanol-water.

Solhnejad, Reza; Aliyeva, Farqana S.; Maharramov, Abel M.; Aliyeva, Rafiga A.; Chyragov, Famil M.; Gurbanov, Atash V.; Mahmudov, Kamran T.; Kopylovich, Maximilian N.



Cleavage of both C(sp3)-C(sp2) bonds of alkylidenecyclopropanes: formation of ethylene-osmium-vinylidene complexes.  


The complex [OsTp(kappa(1)-OCMe)(2)(P(i)Pr(3))]BF(4) [Tp = hydridotris(pyrazolyl)borate] promotes the cleavage of both C(sp(3))-C(sp(2)) bonds of benzylidenecyclopropane and 3-phenylpropylidenecyclopropane to yield the complexes [OsTp(=C=CHR)(eta(2)-CH(2)=CH(2))(P(i)Pr(3))]BF(4) (R = Ph, CH(2)CH(2)Ph). The process is proposed to take place via metallacyclopropene intermediates stabilized by an ethylene chelation assistant. The driving force for the fragmentation is the high stability of the resulting ethylene-Os-vinylidene species. PMID:20017552

Castro-Rodrigo, Ruth; Esteruelas, Miguel A; López, Ana M; López, Fernando; Mascareñas, José L; Oliván, Montserrat; Oñate, Enrique; Saya, Lucía; Villarino, Lara



Significant evidence of C···O and C···C long-range contacts in several heterodimeric complexes of CO with CH3-X, should one refer to them as carbon and dicarbon bonds!  


Noncovalent interactions in 18 weakly bound binary complexes formed between either of the two end-on orientations of the CO molecule and the methylated carbon positive ?-hole associated with the hydrophobic part of the CH3-X molecules are exploited using the density functional theory to examine the physical chemistry of the recently introduced 'carbon bonds' (Phys. Chem. Chem. Phys., 2013, 15, 14377), where X = -NO2, -CN, -F, -Cl, -Br, -OH, -CF3, -CCl3, and -NH2. The two important types of interactions are identified as C···O and C···C, the latter has probably never studied before, and are found to be stabilized by charge-transfer delocalizations between the electron-acceptor and -donor natural bond orbitals of the interacting partners involved, unveiled using natural bond orbital analysis. Application of atoms in molecular theory revealed preferable quantum mechanical exchange-correlation energy channels and (3, -1) bond critical points (bcps) between the atoms of noncovalently bonded pairs in these complexes, in excellent agreement with the results of the noncovalent-interaction reduced-density-gradient (NCI-RDG) theory that revealed expected isosurfaces and troughs in the low density region of the RDG vs. sign(?2)? plots. The dependencies of the C···O and C···C bcp charge densities on their corresponding local energy densities, as well as on their corresponding bond electron delocalization indices are found to exhibit nontrivial roles of these topological descriptors to explain the stabilities of the investigated binary complexes. Moreover, the vibrational red- and blue-shifts in the CO bond stretching frequencies, and concomitant elongations and contractions of the corresponding bond lengths, both with respect to the monomer values, are observed upon the formation of the C···O- and C···C-bonded complexes, respectively. The increase and decrease in the complex dipole moments, relative to the sum of their respective monomer values, are found to be a characteristic that separates the aforementioned red- and blue-shifted interactions. In analogy with dihydrogen bonding, as well as that with the charge and electrostatic surface potential model descriptions, we suggest the C···C interactions to be referred to as dicarbon bonds. PMID:25017184

Varadwaj, Pradeep R; Varadwaj, Arpita; Jin, Bih-Yaw



Reactions of rhenium and manganese carbonyl complexes with 1,8-bis(diphenylphosphino)naphthalene: Ligand chelation, C–H and C–P bond-cleavage reactions  

Microsoft Academic Search

Reaction of [Re2(CO)8(MeCN)2] with 1,8-bis(diphenylphosphino)naphthalene (dppn) afforded three mono-rhenium complexes fac-[Re(CO)3(?1:?1-PPh2C10H6)(PPh2H)] (1), fac-[Re(CO)3{?1:?1:?1-(O)PPh2C10H6(O)PPh(C6H4)}] (2) and fac-[ReCl(CO)3(?2-PPh2C10H6PPh2)] (3). Compounds 1–3 are formed by Re–Re bond cleavage and P–C and C–H bond activation of the dppn ligand. Each of these three complexes have three CO groups arranged in facial fashion. Compound 1 contains a chelating cyclometalated diphenylnaphthylphosphine ligand and a terminally coordinated

Shariff E. Kabir; Faruque Ahmed; Shishir Ghosh; Mohammad R. Hassan; Muhammad S. Islam; Ayesha Sharmin; Derek A. Tocher; Daniel T. Haworth; Sergey V. Lindeman; Tasneem A. Siddiquee; Dennis W. Bennett; Kenneth I. Hardcastle



Photoreactions of Ir/sub 8/(CO)/sub 22//sup 2/minus//. Homolytic cleavage of an unsupported metal-metal bond linking two tetrahedral iridium carbonyl clusters  

SciTech Connect

The photolysis of an anion, Ir/sub 8/(CO)/sub 22//sup 2/minus//, where the metal-metal bond links two polyhedral metal clusters is discussed herein. The photolytic reaction apparently leads to homolytic bond cleavage to yield the reactive anion Ir/sub 4/(CO)/sub 11//sup /minus//. The photolysis of a complex incorporating the named anion was studied in dichloromethane under N/sub 2/ and in tetrahydrofuran under CO. The relative reactivity of the intermediate, Ir/sub 4/(CO)/sub 11//sup /minus// is illustrated by its ability to extract a chlorine atom from dichloromethane. The results of the photolysis study indicated that the tetrairidium radical may be sufficiently reactive to abstract a hydrogen atom from tetrahydrofuran. 13 references, 1 figure.

Vandenberg, D.M.; Friedman, A.E.; Ford, P.C.



Lysine-146 of rabbit muscle aldolase is essential for cleavage and condensation of the C3-C4 bond of fructose 1,6-bis(phosphate).  


Lysine-146 of rabbit muscle aldolase (D-fructose-1,6-biphosphate aldolase, EC is absolutely conserved in class I (Schiff base) aldolases and has been implicated previously in catalysis by protein modification. Site-directed mutagenesis was used to change lysine-146 to alanine, glutamine, leucine, or histidine, creating the mutant enzymes K146A, K146Q, K146L, and K146H, respectively. These mutant proteins were expressed at high levels in bacteria and were purified by substrate affinity elution from CM-Sepharose, the same method that is used for the wild-type enzyme. The mutants K146A, K146Q, and K146L had substrate cleavage rates below standard detection levels. Modified cleavage assays indicated that these enzymes were (0.5-2) x 10(6)-fold decreased in the rate of catalysis of fructose 1,6-bis(phosphate) (Fru-1,6-Pa)cleavage. The K146H enzyme, however, was approximately 2000-fold slower than wild type in the rates of both cleavage and condensation of Fru-1,6-P2. In assays for the presence of enzymatic intermediates, all of the mutant enzymes were able to catalyze formation of the carbanion intermediate with dihydroxyacetone phosphate, whereas this intermediate was below the level of detection with Fru-1,6-P2. Single-turnover experiments with these enzymes in excess over radiolabeled Fru-1,6-P2 were used to measure the rates of Schiff base and product formation. The rate of Schiff base formation was decreased in each of the mutant enzymes, yet the magnitude of this decrease was less than the reduction in the respective kcat. These mutations had a much larger effect, however, on the rate of C3-C4 bond breaking, showing that Lys-146 is crucial at this step of the catalytic cycle. PMID:7918450

Morris, A J; Tolan, D R



Mechanism of ribonucleotide reductase from Herpes simplex virus type 1. Evidence for 3' carbon-hydrogen bond cleavage and inactivation by nucleotide analogs  

SciTech Connect

Isotope effects of 2.5, 2.1, and 1.0 were measured on the conversion of (3'-3H)ADP, (3'-H)UDP, and (5-3H) UDP to the corresponding 2'-deoxynucleotides by herpes simplex virus type 1 ribonucleotide reductase. These results indicate that the reduction of either purine or pyrimidine nucleotides requires cleavage of the 3' carbon-hydrogen bond of the substrate. The substrate analogs 2'-chloro-2'-deoxyuridine 5'-diphosphate (ClUDP), 2'-deoxy-2'-fluorouridine 5'-diphosphate, and 2'-azido-2'-deoxyuridine 5'-diphosphate were time-dependent inactivators of the herpes simplex virus type 1 ribonucleotide reductase. Incubation of (3'-3H)ClUDP with the enzyme was accompanied by time-dependent release of 3H to the solvent. Reaction of (beta-32P)ClUDP with the reductase resulted in the production of inorganic pyrophosphate. These results are consistent with the enzyme-mediated cleavage of the 3' carbon-hydrogen bond of ClUDP and the subsequent conversion of the nucleotide to 2-methylene-3(2H)furanone, as previously reported with the Escherichia coli ribonucleotide reductase.

Ator, M.A.; Stubbe, J.; Spector, T.



N-N bond cleavage of 1,2-diarylhydrazines and N-H bond formation via H-atom transfer in vanadium complexes supported by a redox-active ligand.  


Addition of stoichiometric quantites of 1,2-diarylhydrazines to the bis(imino)pyridine vanadium dinitrogen complex, [{((iPr)BPDI)V(THF)}2(?2-N2)] ((iPr)BPDI = 2,6-(2,6-iPr2-C6H3N?CPh)2C5H3N), resulted in N-N bond cleavage to yield the corresponding vanadium bis(amido) derivatives, ((iPr)BPDI)V(NHAr)2 (Ar = Ph, Tol). Spectroscopic, structural, and computational studies support an assignment as vanadium(III) complexes with chelate radical anions, [BPDI](•-). With excess 1,2-diarylhydrazine, formation of the bis(imino)pyridine vanadium imide amide compounds, ((iPr)BPDI)V(NHAr)NAr, were observed along with the corresponding aryldiazene and aniline. A DFT-computed N-H bond dissociation free energy of 69.2 kcal/mol was obtained for ((iPr)BPDI)V(NHPh)NPh, and interconversion between this compound and ((iPr)BPDI)V(NHPh)2 with (2,2,6,6-tetramethylpiperidin-1-yl)oxidanyl (TEMPO), 1,2-diphenylhydrazine, and xanthene experimentally bracketed this value between 67.1 and 73.3 kcal/mol. For ((iPr)BPDI)V(NHPh)2, the N-H BDFE was DFT-calculated to be 64.1 kcal/mol, consistent with experimental observations. Catalytic disproportionation of 1,2-diarylhydrazines promoted by ((iPr)BPDI)V(NHAr)NAr was observed, and crossover experiments established exchange of anilide (but not imido) ligands in the presence of free hydrazine. These studies demonstrate the promising role of redox-active active ligands in promoting N-N bond cleavage with concomitant N-H bond formation and how the electronic properties of the metal-ligand combination influence N-H bond dissocation free energies and related hydrogen atom transfer processes. PMID:25066657

Milsmann, Carsten; Semproni, Scott P; Chirik, Paul J



Metal coordination and in situ S-C bond cleavage of the bis(2-pyridylthio)methane ligand.  


The compound [2bpytmH](2)[I(3)](2)[I(2)], which contains protonated 2bpytm, and four neutral monomeric complexes [CoCl(2)(2bpytm)]·H(2)O (1), [CoBr(2)(2bpytm)] (2), [CoI(2)(2bpytm)]·1/2H(2)O (3) and [NiBr(2)(2bpytm)]·H(2)O (4) have been obtained during a study into the reactivity of the bis(2-pyridylthio)methane (2bpytm) ligand towards cobalt(II) and nickel(II) halides. Furthermore, a cyclic dimer [CuBr(2)(2bpytm)](2) (5) and a 1D polymer [CuBr(2)(2bpytm)](n)·CH(3)CN (6) have been obtained from copper(II)/(I) bromide salts. An unprecedented S-CH(2)-S activation and cleavage in 2bpytm has been observed on using copper(II) salts with organic and voluminous inorganic anions. The cleavage of 2bpytm enabled the isolation of copper(II) complexes containing the in situ generated ligands 2-pyridinethiolate, 2-pyridinesulfenate or 2-pyridinesulfonate. PMID:20882242

Belén Lago, Ana; Amoedo, Almudena; Carballo, Rosa; García-Martínez, Emilia; Vázquez-López, Ezequiel M



The mechanism of homogeneous CO2 reduction by Ni(cyclam): product selectivity, concerted proton-electron transfer and C-O bond cleavage.  


Homogeneous CO2 reduction catalyzed by [Ni(I)(cyclam)](+) (cyclam = 1,4,8,11-tetraazacyclotetradecane) exhibits high efficiency and selectivity yielding CO only at a relatively low overpotential. In this work, a density functional theory study of the reaction mechanism is presented. Earlier experiments have revealed that the same reaction occurring on mercury surfaces generates a mixture of CO and formate. According to the proposed mechanism, an ?(1)-CO2 adduct is the precursor for CO evolution, whereas formate is obtained from an ?(1)-OCO adduct. Our calculations show that generation of the ?(1)-CO2 adduct is energetically favored by ?14.0 kcal/mol relative to that of the ?(1)-OCO complex, thus rationalizing the product selectivity observed experimentally. Binding of ?(1)-CO2 to Ni(I) only leads to partial electron transfer from the metal center to CO2. Hence, further CO2 functionalization likely proceeds via an outer-sphere electron-transfer mechanism, for which concerted proton coupled electron transfer (PCET) is calculated to be the most feasible route. Final C-O bond cleavage involves rather low barriers in the presence of H3O(+) and H2CO3 and is therefore essentially concerted with the preceding PCET. As a result, the entire reaction mechanism can be described as concerted proton-electron transfer and C-O bond cleavage. On the basis of the theoretical results, the limitations of the catalytic activity of Ni(cyclam) are discussed, which sheds light on future design of more efficient catalysts. PMID:24957425

Song, Jinshuai; Klein, Eric L; Neese, Frank; Ye, Shengfa



Highly selective fluorescence turn-on sensing of gold ions by a nanoparticle generation/C-I bond cleavage sequence.  


We have developed a quickly responsive, and specific fluorescent assay for the detection of Au(III) on the basis of the formation of gold nanoparticles in the presence of HEPES, which cleave the C-I bond of I-BODIPY 1 to yield the highly fluorescent H-BODIPY 2. PMID:22866326

Park, Jihye; Choi, Sohee; Kim, Tae-Il; Kim, Youngmi



11704 J. Am. Chem. SOC.1995,117, 11704-11709 Regiochemical Selectivity in the Carbon-Sulfur Bond Cleavage  

E-print Network

11704 J. Am. Chem. SOC.1995,117, 11704- 11709 Regiochemical Selectivity in the Carbon- Sulfur Bond be an importantstep in the removal of sulfur from thiophene in the hydrodesulfur- ization (HDS) process.' Thiophene and its benzo derivatives represent abundant sulfur-containing impurities in coal and petroleum feedstocks

Jones, William D.


Cleavage of different ether bonds in butyl glycidyl ether and allyl glycidyl ether by K ?, K +(15-crown-5) 2  

Microsoft Academic Search

The kind of substituent in alkyl glycidyl ethers affects the course of their reaction with K?, K+(15-crown-5)2. The cyclic oxirane ring is exclusively cleaved in the case of butyl glycidyl ether whereas the presence of the unsaturated allyl group in the glycidyl ether molecule unexpectedly prefers the scission of the linear ether bond. In both the systems organometallic intermediates are

Zbigniew Grobelny; Andrzej Stolarzewicz; Adalbert Maercker; Stanis?aw Krompiec; Tadeusz Bieg



Folding of HIV-1 envelope glycoprotein involves extensive isomerization of disulfide bonds and conformation-dependent leader peptide cleavage.  


Human immunodeficiency virus binds and enters cells via the Envelope glycoprotein gp160 at its surface. In infected cells, gp160 is found not only on the plasma membrane but also in the endoplasmic reticulum (ER). Our aim was to establish rate-determining steps in the maturation process of gp160, using a radioactive pulse-chase approach. We found that gp160 has an intricate folding process: disulfide bonds start to form during synthesis but undergo extensive isomerization until the correct native conformation is reached. Removal of the leader peptide critically depends on formation of at least some disulfide bonds in subunit gp120 during folding. Envelope folds extremely slowly and therefore resides in the ER longer than other proteins, but the yield of properly folded molecules is high and degradation is undetectable. The large quantity of gp160 in the ER hence is a result of its slow transit through this compartment. We show here that newly synthesized HIV-1 Envelope glycoprotein apparently follows a slow but high-yield folding path in which co- and post-translational formation of disulfide bonds in gp120, disulfide isomerization and conformation dependent removal of the leader sequence are determining and intertwined events. PMID:12773488

Land, Aafke; Zonneveld, Duco; Braakman, Ineke



Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies  

PubMed Central

Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5–0.8?MGy, in contrast to the saturating dose of ?0.2?MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure. PMID:24311579

Sutton, Kristin A.; Black, Paul J.; Mercer, Kermit R.; Garman, Elspeth F.; Owen, Robin L.; Snell, Edward H.; Bernhard, William A.



Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH{sub 2}BrI  

SciTech Connect

It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (n{sub X}) to a carbon-halogen antibonding orbital (?*{sub C-X}). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH{sub 2}BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH{sub 2}BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH{sub 2}Br + I radical pairs, iso-CH{sub 2}Br-I, and iso-CH{sub 2}I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH{sub 2}Br-I. Both iso-CH{sub 2}Br-I and iso-CH{sub 2}I-Br are observed in cyclohexane with a ratio of ?2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH{sub 2}I-Br photoproduct as well as iso-CH{sub 2}Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH{sub 2}Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and ?1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH{sub 2}BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes.

Anderson, Christopher P.; Spears, Kenneth G.; Wilson, Kaitlynn R.; Sension, Roseanne J. [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)] [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)



Geometric and Electronic Structure of [{Cu(MeAN)}2(?-?2:?2(O22?))]2+ with an Unusually Long O–O Bond: O–O Bond Weakening vs Activation for Reductive Cleavage  

PubMed Central

Certain side-on peroxo dicopper(II) species with particularly low ?O–O (710–730 cm?1) have been found in equilibrium with their bis-?-oxo dicopper(III) isomer. An issue is whether such side-on peroxo bridges are further activated for O–O cleavage. In a previous study (Liang, H.-C., et al., J. Am. Chem. Soc. 2002, 124, 4170–4171), we showed that oxygenation of the three-coordinate complex [CuI(MeAN)]+ (MeAN=N-methyl-N,N-bis[3-(dimethylamino)propyl]amine) leads to a low-temperature stable [{CuII(MeAN)}2(?-?2:?2-O22?)]2+ peroxo species with low ?O–O (721 cm?1), as characterized by UV-Vis absorption and resonance Raman (rR) spectroscopies. Here, this complex has been crystallized as its SbF6? salt and an X-ray structure indicates the presence of an unusually long O–O bond (1.540(5) Å) consistent with the low ?O–O. EXAFS and rR spectroscopic and reactivity studies indicate the exclusive formation of [{CuII(MeAN)}2(?-?2:?2-O22?)]2+ without any bis-?-oxo-dicopper(III) isomer present. This is the first structure of a side-on peroxo dicopper(II) species with a significantly long and weak O–O bond. DFT calculations show that the weak O–O bond results from strong ? donation from the MeAN ligand to Cu that is compensated by a decrease in the extent of peroxo to Cu charge transfer. Importantly, the weak O–O bond does not reflect an increase in backbonding into the ?* orbital of the peroxide. Thus, although the O–O bond is unusually weak, this structure is not further activated for reductive cleavage to form a reactive bis-?-oxo-dicopper(III) species. These results highlight the necessity of understanding electronic structure changes associated with spectral changes for correlations to reactivity. PMID:22571744

Park, Ga Young; Qayyum, Munzarin F.; Woertink, Julia; Hodgson, Keith O.; Hedman, Britt; Narducci Sarjeant, Amy A.; Solomon, Edward I.; Karlin, Kenneth D.



Inhibitors of protein-disulfide isomerase prevent cleavage of disulfide bonds in receptor-bound glycoprotein 120 and prevent HIV-1 entry.  


We previously reported that monoclonal antibodies to protein-disulfide isomerase (PDI) and other membrane-impermeant PDI inhibitors prevented HIV-1 infection. PDI is present at the surface of HIV-1 target cells and reduces disulfide bonds in a model peptide attached to the cell membrane. Here we show that soluble PDI cleaves disulfide bonds in recombinant envelope glycoprotein gp120 and that gp120 bound to the surface receptor CD4 undergoes a disulfide reduction that is prevented by PDI inhibitors. Concentrations of inhibitors that prevent this reduction and inhibit the cleavage of surface-bound disulfide conjugate prevent infection at the level of HIV-1 entry. The entry of HIV-1 strains differing in their coreceptor specificities is similarly inhibited, and so is the reduction of gp120 bound to CD4 of coreceptor-negative cells. PDI inhibitors also prevent HIV envelope-mediated cell-cell fusion but have no effect on the entry of HIV-1 pseudo-typed with murine leukemia virus envelope. Importantly, PDI coprecipitates with both soluble and cellular CD4. We propose that a PDI.CD4 association at the cell surface enables PDI to reach CD4-bound virus and to reduce disulfide bonds present in the domain of gp120 that binds to CD4. Conformational changes resulting from the opening of gp120-disulfide loops may drive the processes of virus-cell and cell-cell fusion. The biochemical events described identify new potential targets for anti-HIV agents. PMID:12218051

Gallina, Angelo; Hanley, Timothy M; Mandel, Richard; Trahey, Meg; Broder, Christopher C; Viglianti, Gregory A; Ryser, Hugues J-P



Hydrogen bonding constrains free radical reaction dynamics at serine and threonine residues in peptides.  


Free radical-initiated peptide sequencing (FRIPS) mass spectrometry derives advantage from the introduction of highly selective low-energy dissociation pathways in target peptides. An acetyl radical, formed at the peptide N-terminus via collisional activation and subsequent dissociation of a covalently attached radical precursor, abstracts a hydrogen atom from diverse sites on the peptide, yielding sequence information through backbone cleavage as well as side-chain loss. Unique free-radical-initiated dissociation pathways observed at serine and threonine residues lead to cleavage of the neighboring N-terminal C?-C or N-C? bond rather than the typical C?-C bond cleavage observed with other amino acids. These reactions were investigated by FRIPS of model peptides of the form AARAAAXAA, where X is the amino acid of interest. In combination with density functional theory (DFT) calculations, the experiments indicate the strong influence of hydrogen bonding at serine or threonine on the observed free radical chemistry. Hydrogen bonding of the side-chain hydroxyl group with a backbone carbonyl oxygen aligns the singly occupied ? orbital on the ?-carbon and the N-C? bond, leading to low-barrier ?-cleavage of the N-C? bond. Interaction with the N-terminal carbonyl favors a hydrogen-atom transfer process to yield stable c and z(•) ions, whereas C-terminal interaction leads to effective cleavage of the C?-C bond through rapid loss of isocyanic acid. Dissociation of the C?-C bond may also occur via water loss followed by ?-cleavage from a nitrogen-centered radical. These competitive dissociation pathways from a single residue illustrate the sensitivity of gas-phase free radical chemistry to subtle factors such as hydrogen bonding that affect the potential energy surface for these low-barrier processes. PMID:24605822

Thomas, Daniel A; Sohn, Chang Ho; Gao, Jinshan; Beauchamp, J L



Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA.  


Type IIB restriction-modification systems, such as BcgI, feature a single protein with both endonuclease and methyltransferase activities. Type IIB nucleases require two recognition sites and cut both strands on both sides of their unmodified sites. BcgI cuts all eight target phosphodiester bonds before dissociation. The BcgI protein contains A and B polypeptides in a 2:1 ratio: A has one catalytic centre for each activity; B recognizes the DNA. We show here that BcgI is organized as A(2)B protomers, with B at its centre, but that these protomers self-associate to assemblies containing several A(2)B units. Moreover, like the well known FokI nuclease, BcgI bound to its site has to recruit additional protomers before it can cut DNA. DNA-bound BcgI can alternatively be activated by excess A subunits, much like the activation of FokI by its catalytic domain. Eight A subunits, each with one centre for nuclease activity, are presumably needed to cut the eight bonds cleaved by BcgI. Its nuclease reaction may thus involve two A(2)B units, each bound to a recognition site, with two more A(2)B units bridging the complexes by protein-protein interactions between the nuclease domains. PMID:23147005

Smith, Rachel M; Marshall, Jacqueline J T; Jacklin, Alistair J; Retter, Susan E; Halford, Stephen E; Sobott, Frank



Trend in the C C and C O bond hydrogenation of acrolein on Pt–M (M = Ni, Co, Cu) bimetallic surfaces  

Microsoft Academic Search

Acrolein, the smallest ?,?-unsaturated aldehyde, is used as a probe molecule to study the effect on the hydrogenation activity toward the CC and CO bonds due to the presence of a 3d transition metal either on the surface or in the subsurface region of a Pt(111) substrate. Temperature programmed desorption (TPD), high-resolution electron energy loss spectroscopy (HREELS), and density functional

Luis E. Murillo; Carl A. Menning; Jingguang G. Chen



Ordered cleavage of myeloperoxidase ester bonds releases active site heme leading to inactivation of myeloperoxidase by benzoic acid hydrazide analogs.  


Myeloperoxidase (MPO) catalyzes the breakdown of hydrogen peroxide and the formation of the potent oxidant hypochlorous acid. We present the application of the fluorogenic peroxidase substrate 10-acetyl-3,7-dihydroxyphenoxazine (ADHP) in steady-state and transient kinetic studies of MPO function. Using initial kinetic parameters for the MPO system, we characterized under the same conditions a number of gold standards for MPO inhibition, namely 4-amino benzoic acid hydrazide (4-ABAH), isoniazid and NaN3 before expanding our focus to isomers of 4-ABAH and benzoic acid hydrazide analogs. We determined that in the presence of hydrogen peroxide that 4-ABAH and its isomer 2-ABAH are both slow-tight binding inhibitors of MPO requiring at least two steps, whereas NaN3 and isoniazid-based inhibition has a single observable step. We also determined that MPO inhibition by benzoic acid hydrazide and 4-(trifluoromethyl) benzoic acid hydrazide was due to hydrolysis of the ester bond between MPO heavy chain Glu 242 residue and the heme pyrrole A ring, freeing the light chain and heme b fragment from the larger remaining MPO heavy chain. This new mechanism would essentially indicate that the benzoic acid hydrazide analogs impart inhibition through initial ejection of the heme catalytic moiety without prior loss of the active site iron. PMID:24632143

Huang, Jiansheng; Smith, Forrest; Panizzi, Peter



Unexpected multiple bond cleavage and rearrangement of organosulfide ligands in the presence of Cu(II) assisted by solvothermal and solvothermal-microwave conditions.  


An unprecedented in situ multiple bond cleavage of S-S, S-C(sp(2)) and C-N in the pyrimidinedisulfide (pym(2)S(2)) ligand is observed by the reaction of CuCl(2)·2H(2)O with this ligand under solvothermal and solvothermal-microwave conditions. In this process the formation of the compound [Cu(II)(?-Cl)(Cl)L](2), where L represents the new ligand (L = 2-(pyrimidin-2-ylamino)-1,3-thiazole-4-carbaldehyde), is observed. This ligand has been further isolated and X-ray characterized. The similar reaction carried out under solvothermal-microwave conditions gives, in addition to the latter compound, the complex {9·[Cu(pym(2)S(3))(?-Cl)(Cl)](2)·[Cu(pym(2)S(2))(?-Cl)(Cl)](2)}. Coordination of a pyrimidinetrisulfide ligand (pym(2)S(3)) is reported for the first time. This work represents an illustrative example of the novel synthetic perspectives attainable via solvothermal-microwave procedures. PMID:21140008

Delgado, Salomé; Gallego, Almudena; Castillo, Oscar; Zamora, Félix



Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Quarterly report No. 9, October 1-December 31, 1980  

SciTech Connect

Objective is to determine the structure of bituminous coal with emphasis on the crosslinks and breakable single bonds. Some of the highlights of this quarter are: (1) large-scale extraction of benzylamine-extracted coal with ethylene diamine-dimethyl sulfoxide (EDA-DMSO) led to 50.4% recovery of soluble material and 40.5% recovery of undissolved coal; (2) EDA-DMSO extraction appears to have removed essentially all of the ether and ester links in both fractions, leaving only hydrocarbon links; (3) extraction of whole coal by a mixture of N-methylpyrrolidinone (NMP) and EDA is no better than EDA-DMSO, even though NMP alone is a better solvent than DMSO alone; (4) investigators have no evidence that NaOCl will oxidize sulfide links to sulfuric acid and NaOCl appears to be unsuitable for determining sulfide links in coal; (5) black acid fraction from several NaOCl oxidations precipitated between pH 4.98 and 4.66 was characterized; (6) measurements of hydroxyl and carboxyl contents on pyridine and benzylamine extracts and extracted coal show increases in carboxyl content on reactions of these fractions with alcoholic KOH, and an increase in hydroxyl content on reactions of the pyridine-extracted coal with benzylamine, consistent with ester cleavage. 6 tables.

Pavelka, L.A.; Mayo, F.R.; Zevely, J.



Synthetic Approaches to (smif)2Ti (smif = 1,3-di-(2-pyridyl)-2-azaallyl) Reveal Redox Non-Innocence and C-C Bond-Formation  

PubMed Central

Attempted syntheses of (smif)2Ti (smif = 1,3-di-(2-pyridyl)-2-azaallyl) based on metatheses of TiClnLm (n = 2–4) with M(smif) (M = Li, Na), in the presence of a reducing agent (Na/Hg) when necessary, failed, but several apparent Ti(II) species were identified by X-ray crystallography and multidimensional NMR spectroscopy: (smif){Li(smif-smif)}Ti (1, X-ray), [(smif)Ti]2(?-?3,?3-N,N(py)2-smif,smif) (2), (smif)Ti(?3-N,N(py)2-smif,(smif)H) (3), and (smif)Ti(dpma) (4). NMR spectroscopy and K-edge XAS showed that each compound possesses ligands that are redox non-innnocent, such that d1 Ti(III) centers AF-couple to ligand radicals: (smif){Li(smif-smif)2?}TiIII (1), [(smif2?)TiIII]2(?-?3,?3-N,N(py)2-smif,smif) (2), [(smif2?)TiIII](?3-N,N(py)2-smif,(smif)H) (3), and (smif2?)TiIII(dpma) (4). The instability of the (smif)2Ti relative to its C-C coupled dimer, 2, is rationalized via the complementary nature of the amide and smif radical anion ligands, which are also common to 3 and 4. Calculations support this contention. PMID:22830452

Frazier, Brenda A.; Wolczanski, Peter T.; Keresztes, Ivan; DeBeer, Serena; Lobkovsky, Emil B.; Pierpont, Aaron W.; Cundari, Thomas R.



Determination of effective potentials for the stretching of C? ? C? virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine  

PubMed Central

The potentials of mean force (PMF’s) for the deformation of the C? ? C? virtual bonds in polypeptide chains were determined from the diabatic energy surfaces of N-methylacetamide (modeling regular peptide groups) and N-acetylpyrrolidine (modeling the peptide groups preceding proline), calculated at the Møller-Plesset (MP2) ab initio level of theory with the 6-31G(d,p) basis set. The energy surfaces were expressed in the C? ? C? virtual-bond length (d) and the H-N-C? ? C? improper dihedral angle (?) that describes the pyramidicity of the amide nitrogen, or in the C?-C?(O)-N-C? dihedral angle (?) and the angle ?. For each grid point, the potential energy was minimized with respect to all remaining degrees of freedom. The PMF’s obtained from the (d, ?) energy surfaces produced realistic free-energy barriers to the trans-cis transition (10 kcal/mol and 13 kcal/mol for the regular and proline peptide groups, respectively, compared to 12.6 – 13.9 kcal/mol and 17.3 – 19.6 kcal/mol determined experimentally for glycylglycine and N-acylprolines, respectively), while those obtained from the (?, ?) energy maps produced either low-quality PMF curves when direct Boltzmann summation was implemented to compute the PMF’s or too-flat curves with too-low free-energy barriers to the trans-cis transition if harmonic extrapolation was used to estimate the contributions to the partition function. An analytical bimodal logarithmic-Gaussian expression was fitted to the PMF’s, and the potentials were implemented in the UNRES force field. Test Langevin-dynamics simulations were carried out for the Gly-Gly and Gly-Pro dipeptides, which showed a 106-fold increase of the simulated rate of the trans-cis isomerization with respect to that measured experimentally; effectively the same result was obtained with the analytical Kramers theory of reaction rate applied to the UNRES representation of the peptide groups. Application of Kramers’ theory to compute the rate constants from the all-atom ab initio energy surfaces of the model compounds studied resulted in isomerization rates close to the experimental values, which demonstrates that the increase of the isomerization rate in UNRES simulations results solely from averaging out the secondary degrees of freedom. PMID:23087598

Sieradzan, Adam K.; Scheraga, Harold A.; Liwo, Adam



Radical reactions with double memory of chirality (2MOC) for the enantiospecific synthesis of adjacent stereogenic quaternary centers in solution: cleavage and bonding faster than radical rotation.  


The solution photochemistry of bis(phenylpyrrolidinonyl)ketones (R,R)-1b and (S,S)-1b exhibited a remarkably high memory of chirality. Stereospecific decarbonylation to products (R,R)-3b and (S,S)-3b, respectively, occurred with an ee of ca. 80%. The reaction is thought to occur along the single state manifold by sequential Norrish type-I alpha-cleavage, decarbonylation, and radical-radical combination in a time scale that is comparable to that required for the radical intermediate to expose its other enantiotopic face by rotation about an axis perpendicular to that of the p orbital (ca. 3-7 ps). The absolute configuration of a key intermediate and that of ketone (R,R)-1b were determined by single-crystal X-ray diffraction and the ee values of the photochemical products with the help of chiral shift reagent (+)-Eu(tfc)(3) and chiral LC-MS/MS. On the basis of the ee and de values at 25 degrees C, it could be determined that ca. 70% of the bond forming events occur with double memory of chirality, ca. 21% occur after rotation of one radical to form the meso product (R,S)-3b, and only 9% occur after double rotation to form the opposite enantiomer. This report represents the first example of a doubly enantiospecific Norrish type-I and decarbonylation reaction in solution and illustrates potentially efficient ways to obtain compounds with adjacent stereogenic quaternary centers. PMID:19473007

Resendiz, Marino J E; Family, Farnosh; Fuller, Kerrian; Campos, Luis M; Khan, Saeed I; Lebedeva, Natalia V; Forbes, Malcolm D E; Garcia-Garibay, Miguel A



Kinetic and Structural Insight into the Mechanism of BphD, a C-C Bond Hydrolase from the Biphenyl Degradation Pathway†  

PubMed Central

Kinetic and structural analyses of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) hydrolase from Burkholderia xenovorans LB400 (BphDLB400) provide insight into the catalytic mechanism of this unusual serine hydrolase. Single turnover stopped-flow analysis at 25 °C showed that the enzyme rapidly (1/?1 ? 500 s?1) transforms HOPDA (?max = 434 nm) to a species with electronic absorption maxima at 473 and 492 nm. The absorbance of this enzyme-bound species (E:S) decayed in a biphasic manner (1/?2 = 54 s?1, 1/?3 = 6 s?1 ? kcat) with simultaneous biphasic appearance (48 and 8 s?1) of an absorbance band at 270 nm characteristic of one of the products, 2-hydroxypenta-2,4-dienoic acid (HPD). Increasing solution viscosity with glycerol slowed 1/?1 and 1/?2, but affected neither 1/?3 nor kcat, suggesting that 1/?2 may reflect diffusive HPD dissociation, while 1/?3 represents an intramolecular event. Product inhibition studies suggested that the other product, benzoate, is released after HPD. Contrary to studies in a related hydrolase, we found no evidence that ketonized HOPDA is partially released prior to hydrolysis, and therefore postulate that the biphasic kinetics reflect one of two mechanisms, pending assignment of E:S (?max = 492 nm). Crystal structures of wild type, the S112C variant, and S112C incubated with HOPDA were each determined to 1.6 Å resolution. The latter reveals interactions between conserved active site residues and the dienoate moiety of the substrate. Most notably, the catalytic residue His265 is hydrogen-bonded to the 2-hydroxy/oxo substituent of HOPDA, consistent with a role in catalyzing ketonization. The data are more consistent with an acyl-enzyme mechanism than with the formation of a gem-diol intermediate. PMID:16964968

Horsman, Geoff P.; Ke, Jiyuan; Dai, Shaodong; Seah, Stephen Y. K.; Bolin, Jeffrey T.; Eltis, Lindsay D.



Rapid carbon-carbon bond formation and cleavage revealed by carbon isotope exchange between the carboxyl carbon and inorganic carbon in hydrothermal fluids  

NASA Astrophysics Data System (ADS)

The carbon isotopic composition of organic compounds in water-rock systems (e.g., hydrothermal vents, sedimentary basins, and carbonaceous meteorites) is generally interpreted in terms of the isotopic composition of the sources of such molecules, and the kinetic isotope effects of metabolic or abiotic reactions that generate or transform such molecules. This hinges on the expectation that the carbon isotopic composition of many organic compounds is conserved under geochemical conditions. This expectation is reasonable in light of the strength of carbon-carbon bonds (ca. 81 kcal/mol); in general, environmental conditions conducive to carbon-carbon bond cleavage typically lead to transformations of organic molecules (decarboxylation is a notable example). Geochemically relevant reactions that involve isotopic exchange between carbon atoms in organic molecules and inorganic forms of carbon with no change in molecular structure appear to be rare. Notwithstanding such rarity, there have been preliminary reports of relatively rapid carbon isotope exchange between the carboxyl group in carboxylic acids and carbon dioxide in hot water [1,2]. We have performed laboratory hydrothermal experiments to gain insights into the mechanism of this surprising reaction, using phenylacetate as a model structure. By mass spectrometry, we confirm that the carboxyl carbon undergoes facile isotopic exchange with 13C-labeled bicarbonate at moderate temperatures (i.e., 230 C). Detailed kinetic analysis reveals that the reaction rate is proportional to the concentrations of both reactants. Further experiments demonstrate that the exchange reaction only occurs if the carbon atom adjacent to the carboxyl carbon is bonded to a hydrogen atom. As an example, no carbon isotope exchange was observed for benzoate in experiments lasting up to one month. The requirement of an alpha C-H bond suggests that enolization (i.e., deprotonation of the H) is a critical step in the mechanism of the exchange reaction. We confirmed this by determining the exchange kinetics for various ring-substituted phenylacetates, and we find that the observed rate constants are consistent with the amount of negative charge that would be expected on the alpha carbon of the enolate. The emerging picture of the reaction mechanism is that enolization allows fixation of labeled carbon dioxide as a beta-carboxy group, where subsequent heterolytic decarboxylation of the unlabeled carboxy group completes the exchange process. Solvent stabilization of ionic reaction intermediates would lead to faster than expected rates of exchange, and ultimately to an isotopic equilibrium over even short geologic timescales. For enolizable carboxylic acids in natural systems, one has to consider this exchange mechanism when interpreting the carbon isotopic composition. [1] Dias R.F. (2000) Ph.D. Dissertation, Penn. State Univ. [2] Seewald J.S. & Boekelheide N. (2005) Goldschmidt Conf., A558.

Glein, C. R.; Cody, G. D.



Formation of a dinuclear copper(II) complex through the cleavage of CN bond of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole  

NASA Astrophysics Data System (ADS)

A simple mononuclear octahedral copper(II) complex was attempted from the reaction of three moles of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole and one mole of copper(II) perchlorate hexahydrate in methanol. However, the product of the reaction was confirmed to be a dinuclear copper(II) complex with ?-{3-(pyridin-2-yl)-pyrazolato} and 3-(pyridin-2-yl)-1H-pyrazole ligands attached to each of the Cu(II) centre atom. The copper(II) ion assisted the cleavage of the CbenzoylN bond afforded a 3-(pyridin-2-yl)-1H-pyrazole molecule. Deprotonation of the 3-(pyridin-2-yl)-1H-pyrazole gave a 3-(pyridin-2-yl)-pyrazolato, which subsequently reacted with the Cu(II) ion to give the {3-(pyridin-2-yl)-pyrazolato}{3-(pyridin-2-yl)-1H-pyrazole}Cu(II) product moiety. The structure of the dinuclear complex was confirmed by x-ray crystallography. The complex crystallized in a monoclinic crystal system with P2(1)/n space group and cell dimensions of a = 12.2029(8) Å, b = 11.4010(7) Å, c = 14.4052(9) Å and ? = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (? = 116 dm3 mol-1 cm-1) supports the presence of Cu(II) centres.

Shardin, Rosidah; Pui, Law Kung; Yamin, Bohari M.; Kassim, Mohammad B.



A Tungsten Complex with a Bidentate, Hemilabile N-Heterocyclic Carbene Ligand, Facile Displacement of the Weakly Bound W-(C=C) Bond, and the Vulnerability of the NHC Ligand Towards Catalyst Deactivation During Ketone Hydrogenation  

SciTech Connect

The initial reaction observed between the N-heterocyclic carbene IMes (IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene) and molybdenum and tungsten hydride complexes CpM(CO){sub 2}(PPh{sub 3})H (M = Mo, W) is deprotonation of the metal hydride by IMes, giving [(IMes)H]{sup +}[CpM(CO){sub 2}(PPh{sub 3})]{sup -}. At longer reaction times and higher temperatures, the reaction of IMes with CpM(CO){sub 2}(PR{sub 3})H (M = Mo, W; R = Me, Ph) produces CpM(CO){sub 2}(IMes)H. Hydride transfer from CpW(CO)2(IMes)H to Ph{sub 3}C{sub +}B(C{sub 6}F{sub 5}){sub 4}{sup -} gives CpW(CO){sub 2}(IMes){sup +}B(C{sub 6}F{sub 5}){sub 4}{sup -}, which was crystallographically characterized using X-ray radiation from a synchrotron. The IMes is bonded as a bidentate ligand, through the carbon of the carbene as well as forming a weak bond from the metal to a C=C bond of one mesityl ring. The weakly bound C=C ligand is hemilabile, being readily displaced by H{sub 2}, THF, ketones, or alcohols. Reaction of CpW(CO){sub 2}(IMes){sup +} with H{sub 2} gives the dihydride complex [CpW(CO){sub 2}(IMes)(H){sub 2}]{sup +}. Addition of Et{sub 2}CH-OH to CpW(CO){sub 2}(IMes){sup +}B(C{sub 6}F{sub 5}){sub 4}{sup -} gives the alcohol complex [CpW(CO){sub 2}(IMes)(Et{sub 2}CH-OH)]{sup +}[B(C{sub 6}F{sub 5}){sub 4}]{sup -}, which was characterized by crystallography and exhibits no evidence for hydrogen bonding of the bound OH group. Addition of H{sub 2} to the ketone complex [CpW(CO){sub 2}(IMes)(Et{sub 2}C=O)]{sup +}[B(C{sub 6}F{sub 5}){sub 4}]{sup -} produces an equilibrium with the dihydride [CpW(CO){sub 2}(IMes)(H){sub 2}]{sup +} (K{sub eq} = 1.1 x 10{sup 3} at 25 {sup o}C). The tungsten ketone complex [CpW(CO){sub 2}(IMes)(Et{sub 2}C=O)]{sup +}[B(C{sub 6}F{sub 5}){sub 4}]{sup -}- serves as a modest catalyst for hydrogenation of Et{sub 2}C=O to Et{sub 2}CH-OH in neat ketone solvent. Decomposition of the catalyst produces [H(IMes)]{sup +}B(C{sub 6}F{sub 5}){sub 4}{sup -}, indicating that these catalysts with N-heterocyclic carbene ligands are vulnerable to decomposition by a reaction that produces a protonated imidazolium cation.

Wu,F.; Dioumaev, V.; Szalda, D.; Hanson, J.; Bullock, R.



Synthesis and structure of cyclopropano-annelated homosesquinorbornene derivatives containing pyramidalized double bonds: evidence for the sterical effect of a cyclopropyl group on the degree of C=C double-bond pyramidalization.  


[reaction: see text] endo- and exo-2,3,4,7-tetrahydro-1H-1,4-methanobenzocycloheptene-7-carboxylic acid ethyl esters have been synthesized, and their Diels-Alder cycloaddition reactions with maleic anhydride, dimethyl acetylenedicarboxylate and singlet oxygen have been investigated. The X-ray analysis of four adducts indicated the pyramidalization of the central double bond. Density functional theory calculations on the isolated products and model compounds showed excellent agreement between the experimental and theoretical determined butterfly angles. Furthermore, it has been shown that a cyclopropyl group fused to [2.2.2] system decreases significantly the degree of the pyramidalization which is attributed to the steric interactions between the cyclopropyl group and ethano bridge of the norbornene systems. Due to the instability of the bicyclic endoperoxides, their X-ray analysis could not be carried out. DFT calculations on model compounds showed increased bending in the case of the product obtained by the addition of singlet oxygen to endo-2,3,4,7-tetrahydro-1H-1,4-methanobenzocycloheptene-7-carboxylic acid ethyl ester. PMID:15989319

Saracoglu, Nurullah; Talaz, Oktay; Azizoglu, Akín; Watson, William H; Balci, Metin



Leukemogenic membrane glycoprotein encoded by Friend spleen focus-forming virus: transport to cell surfaces and shedding are controlled by disulfide-bonded dimerization and by cleavage of a hydrophobic membrane anchor.  


The leukemogenic glycoprotein (gp55) encoded by Friend spleen focus-forming virus is predominantly retained in the rough endoplasmic reticulum (RER). However, a small proportion (ca. 5%) is processed to form a derivative that occurs on plasma membranes and causes mitosis of infected erythroblasts. We have now found that gp55 folds heterogeneously in the RER to form components with different disulfide bonds and that this difference may determine their processing fates. RER gp55 consists predominantly of monomers with intrachain disulfide bonds. In contrast, the processed molecules are disulfide-bonded dimers. These dimers are extensively modified in transit to cell surfaces by conversion of four N-linked high-mannose oligosaccharides to complex derivatives and by attachment of a sialylated O-linked oligosaccharide. The plasma membrane dimers are then slowly shed into the medium by a mechanism that involves proteolytic cleavage of approximately 25 membrane-anchoring hydrophobic amino acids from the carboxyl termini of the glycoproteins. Consequently, shed molecules have shorter polypeptide chains than cell-associated gp55. We conclude that gp55 folds into different disulfide-bonded components that do not substantially isomerize, and that only one specific dimer is competent for export from the RER. Mitogenic activity of gp55 could be caused by the cell surface dimers, by the shed derivative, or by the carboxyl-terminal hydrophobic anchors that remain in the membranes after the shedding reaction. PMID:2547985

Gliniak, B C; Kabat, D



Leukemogenic membrane glycoprotein encoded by Friend spleen focus-forming virus: transport to cell surfaces and shedding are controlled by disulfide-bonded dimerization and by cleavage of a hydrophobic membrane anchor.  

PubMed Central

The leukemogenic glycoprotein (gp55) encoded by Friend spleen focus-forming virus is predominantly retained in the rough endoplasmic reticulum (RER). However, a small proportion (ca. 5%) is processed to form a derivative that occurs on plasma membranes and causes mitosis of infected erythroblasts. We have now found that gp55 folds heterogeneously in the RER to form components with different disulfide bonds and that this difference may determine their processing fates. RER gp55 consists predominantly of monomers with intrachain disulfide bonds. In contrast, the processed molecules are disulfide-bonded dimers. These dimers are extensively modified in transit to cell surfaces by conversion of four N-linked high-mannose oligosaccharides to complex derivatives and by attachment of a sialylated O-linked oligosaccharide. The plasma membrane dimers are then slowly shed into the medium by a mechanism that involves proteolytic cleavage of approximately 25 membrane-anchoring hydrophobic amino acids from the carboxyl termini of the glycoproteins. Consequently, shed molecules have shorter polypeptide chains than cell-associated gp55. We conclude that gp55 folds into different disulfide-bonded components that do not substantially isomerize, and that only one specific dimer is competent for export from the RER. Mitogenic activity of gp55 could be caused by the cell surface dimers, by the shed derivative, or by the carboxyl-terminal hydrophobic anchors that remain in the membranes after the shedding reaction. Images PMID:2547985

Gliniak, B C; Kabat, D



C-C bond unsaturation degree in monosubstituted ferrocenes for molecular electronics investigated by a combined near-edge x-ray absorption fine structure, x-ray photoemission spectroscopy, and density functional theory approach.  


We present the results of an experimental and theoretical investigation of monosubstituted ethyl-, vinyl-, and ethynyl-ferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotron-radiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1s XPS) spectroscopies, and density functional theory (DFT) calculations. Such a combined study is aimed at elucidating the role played by the C-C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1s NEXAFS spectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFS spectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the ?/? hyperconjugation in EtFC and the ?-conjugation in VFC and EFC. PMID:22482553

Boccia, A; Lanzilotto, V; Marrani, A G; Stranges, S; Zanoni, R; Alagia, M; Fronzoni, G; Decleva, P



C-C bond unsaturation degree in monosubstituted ferrocenes for molecular electronics investigated by a combined near-edge x-ray absorption fine structure, x-ray photoemission spectroscopy, and density functional theory approach  

NASA Astrophysics Data System (ADS)

We present the results of an experimental and theoretical investigation of monosubstituted ethyl-, vinyl-, and ethynyl-ferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotron-radiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1s XPS) spectroscopies, and density functional theory (DFT) calculations. Such a combined study is aimed at elucidating the role played by the C-C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1s NEXAFS spectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFS spectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the ?/? hyperconjugation in EtFC and the ?-conjugation in VFC and EFC.

Boccia, A.; Lanzilotto, V.; Marrani, A. G.; Stranges, S.; Zanoni, R.; Alagia, M.; Fronzoni, G.; Decleva, P.



C-C bond unsaturation degree in monosubstituted ferrocenes for molecular electronics investigated by a combined near-edge x-ray absorption fine structure, x-ray photoemission spectroscopy, and density functional theory approach  

SciTech Connect

We present the results of an experimental and theoretical investigation of monosubstituted ethyl-, vinyl-, and ethynyl-ferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotron-radiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1s XPS) spectroscopies, and density functional theory (DFT) calculations. Such a combined study is aimed at elucidating the role played by the C-C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1s NEXAFS spectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFS spectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the {sigma}/{pi} hyperconjugation in EtFC and the {pi}-conjugation in VFC and EFC.

Boccia, A.; Lanzilotto, V.; Marrani, A. G.; Zanoni, R. [Dipartimento di Chimica, Universita degli Studi di Roma ''La Sapienza'', piazzale Aldo Moro 5, I-00185 Rome (Italy); Stranges, S. [Dipartimento di Chimica, Universita degli Studi di Roma ''La Sapienza'', piazzale Aldo Moro 5, I-00185 Rome (Italy); IOM-CNR, Laboratorio TASC, I-34149 Basovizza, Trieste (Italy); Alagia, M. [IOM-CNR, Laboratorio TASC, I-34149 Basovizza, Trieste (Italy); Fronzoni, G.; Decleva, P. [Dipartimento di Scienze Chimiche, Universita di Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy and IOM-CNR Democritos, Trieste (Italy)



Three new phosphoric triamides with a [C(O)NH]P(O)[N(C)(C)]2 skeleton: a database analysis of C-N-C and P-N-C bond angles.  


In N,N,N',N'-tetraethyl-N''-(4-fluorobenzoyl)phosphoric triamide, C15H25FN3O2P, (I), and N-(2,6-difluorobenzoyl)-N',N''-bis(4-methylpiperidin-1-yl)phosphoric triamide, C19H28F2N3O2P, (II), the C-N-C angle at each tertiary N atom is significantly smaller than the two P-N-C angles. For the other new structure, N,N'-dicyclohexyl-N''-(2-fluorobenzoyl)-N,N'-dimethylphosphoric triamide, C21H33FN3O2P, (III), one C-N-C angle [117.08?(12)°] has a greater value than the related P-N-C angle [115.59?(9)°] at the same N atom. Furthermore, for most of the analogous structures with a [C(=O)NH]P(=O)[N(C)(C)]2 skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B58, 380-388], the C-N-C angle is significantly smaller than the two P-N-C angles; exceptions were found for four structures with the N-methylcyclohexylamide substituent, similar to (III), one structure with the seven-membered cyclic amide azepan-1-yl substituent and one structure with an N-methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linked via pairs of N-H...O=P hydrogen bonds to form dimers. PMID:25279604

Pourayoubi, Mehrdad; Tarahhomi, Atekeh; Rheingold, Arnold L; Golen, James A



Palladium-catalyzed one-pot three- or four-component coupling of aryl iodides, alkynes, and amines through C-N bond cleavage: efficient synthesis of indole derivatives.  


An efficient synthesis of N-substituted indole derivatives was realized by combining the Pd-catalyzed one-pot multicomponent coupling approach with cleavage of the C(sp(3))-N bonds. Three or four components of aryl iodides, alkynes, and amines were involved in this coupling process. The cyclopentadiene-phosphine ligand showed high efficiency. A variety of aryl iodides, including cyclic and acyclic tertiary amino aryl iodides, and substituted 1-bromo-2-iodobenzene derivatives could be used. Both symmetric and unsymmetric alkynes substituted with alkyl, aryl, or trimethylsilyl groups could be applied. Cyclic secondary amines such as piperidine, morpholine, 4-methylpiperidine, 1-methylpiperazine, 2-methylpiperidine, and acyclic amines including secondary and primary amines all showed good reactivity. Further application of the resulting indole derivatives was demonstrated by the synthesis of benzosilolo[2,3-b]indole. PMID:24449487

Hao, Wei; Geng, Weizhi; Zhang, Wen-Xiong; Xi, Zhenfeng



Emergent mechanistic diversity of enzyme-catalysed ?-diketone cleavage  

PubMed Central

The enzymatic cleavage of C–C bonds in ?-diketones is, comparatively, a little studied biochemical process, but one that has important relevance to human metabolism, bioremediation and preparative biocatalysis. In recent studies, four types of enzymes have come to light that cleave C–C bonds in the ?-diketone functionality using different chemical mechanisms. OPH [oxidized poly(vinyl alcohol) hydrolase from Pseudomonas sp. strain VM15C], which cleaves nonane-4,6-dione to butyrate and pentan-2-one is a serine-triad hydrolase. Dke1 (diketone-cleaving enzyme from Acinetobacter johnsonii) is a dioxygenase, cleaving acetylacetone to methylglyoxal and acetate. Fumarylacetoacetate hydrolase cleaves fumarylacetoacetate to fumarate and acetoacetate using a water molecule, activated by a catalytic His/Asp dyad, aided by a calcium ion that both chelates the enol acid form of the substrate and indirectly positions the water for nucleophilic attack at a carbonyl group. 6-Oxocamphor hydrolase cleaves nonenolizable cyclic ?-diketones and is a homologue of the crotonase superfamily, employing a catalytic His/Asp dyad to activate a water molecule for nucleophilic attack at a carbonyl group on one prochiral face of the diketone substrate, effecting desymmetrizations of symmetrical substrates. PMID:15934927



Is the 2,3-carbon-carbon bond of indole really inert to oxidative cleavage by Oxone?--synthesis of isatoic anhydrides from indoles.  


A recent report has indicated that the oxidizing agent Oxone does not possess the ability to cleave the 2,3-carbon-carbon bond of indole. Work in our laboratory shows that this is not the case. Indole and a variety of aryl ring substituted derivatives readily react to form synthetically important isatoic anhydrides. PMID:24089031

Nelson, Amber C; Kalinowski, Emily S; Czerniecki, Nikolas J; Jacobson, Taylor L; Grundt, Peter



Applications of bis(1-R-imidazol-2-yl)disulfides and diselenides as ligands for main-group and transition metals: kappa2-(N,N) coordination, S-S bond cleavage, and S-S/E-E (E = S, Se) bond metathesis reactions.  


Bis(1-R-imidazol-2-yl)disulfides, (mim(R))2 (R = Ph, Bu(t)), and diselenides, (seim(Mes))2, serve as bidentate N,N-donor ligands for main-group and transition metals. For example, [kappa2-(mim(Bu)(t))2]MCl2 (M = Fe, Co, Ni, Zn), [kappa2-(mim(Ph))2]MCl2 (M = Co, Zn), [kappa2-(mim(Bu)(t))2]CuX (X = Cl, I), and [kappa2-(seim(Mes))2]MCl2 (M = Fe, Co, Ni) are obtained by treatment of (mim(Bu)(t))2 or (seim(Mes))2 with the respective metal halide and have been structurally characterized by X-ray diffraction. On the other hand, the zerovalent nickel complex Ni(PMe3)4 effects cleavage of the disulfide bond of (mim(Bu)(t))2 to give square-planar trans-Ni(PMe3)2(mim(Bu)(t))2 in which the (mim(Bu)(t)) ligands coordinate via nitrogen rather than sulfur, a most uncommon coordination mode for this class of ligands. Although [kappa2-(mim(R))2]MCl2 (M = Fe, Co, Ni, Zn) are not subject to homolytic cleavage of the S-S bond because the tetravalent state is not readily accessible, the observation that [kappa2-(mimPh)2]CoCl2 and [kappa2-(mim(Bu)(t))2]CoCl2 form an equilibrium mixture with the asymmetric disulfide [kappa2-(mim(Ph))(mim(Bu)(t))]CoCl2 indicates that S-S bond cleavage via another mechanism is possible. Likewise, metathesis between disulfide and diselenide ligands is observed in the formation of [kappa2-(mim(Bu)(t))(seim(Mes))]CoCl2 upon treatment of [kappa2-(mim(Bu)(t))2]CoCl2 with [kappa2-(seim(Mes))2]CoCl2. PMID:17900186

Figueroa, Joshua S; Yurkerwich, Kevin; Melnick, Jonathan; Buccella, Daniela; Parkin, Gerard



Ultrasonic cleavage of thioethers.  


The rates of DPPH (diphenylpicrylhydrazyl) trapping and the sonolytical products obtained during the sonolysis of thioethers at normal and low temperature are reported. CS2, lower sulfides, thiophene, and sulfurized species are the common products during the ultrasonic irradiations. Hydrocarbons are also obtained during the sonolysis of diallyl sulfide, diethyl disulfide, and dipropyl disulfide. Furthermore, aldehydes are obtained as oxidized species; SO2 is found at 208 K. The principal sonochemical process appears to be the cleavage of C-S or S-S bond with secondary combinations and rearrangements. DPPH has been used to probe the sonolytical potential of thioethers. The results show a good correlation between the rates of DPPH trapping and the vapor pressures of thioethers. In conclusion, a lower vapor pressure results in a higher sonolytical rate. The sonochemical behaviors of thioethers have strong qualitative similarities to the pyrolysis. PMID:16839045

Wu, Zhilin; Ondruschka, Bernd; Stark, Annegret



Silicon–Carbon bond cleavage reactions of Ansa tungstenocene compounds: The [Me2Si] bridge as a site for metallocene functionalization  

PubMed Central

[Me2Si(CpMe2)2]W(H)Cl is obtained via reaction of WCl6 with a mixture of [Me2Si(CpMe2)2]Li2 and NaBH4, from which the dichloride [Me2Si(CpMe2)2]WCl2 is obtained via treatment with CHCl3. [Me2Si(CpMe2)2]WCl2 provides a means to access other ansa tungstenocene compounds, such as [Me2Si(CpMe2)2]WH2, [Me2Si(CpMe2)2]WMe2, and [Me2Si(CpMe2)2]WCO. Of most interest, the reactions of [Me2Si(CpMe2)2]W(H)Cl with organolithium reagents do not yield simple ansa tungstenocene derivatives. Specifically, the reactions of [Me2Si(CpMe2)2]W(H)Cl with MeLi, BunLi, or PhLi result in the formation of mixed-ring tungstenocene compounds resulting from C–Si cleavage and functionalization of the ansa bridge, namely (CpMe2)(?5,?1–C5H2Me2SiMe2CH2)WH, (CpMe2)[?5,?1–C5H2Me2Si(Me)(Bun)CH2]WH, and (CpMe2)[?5,?1–C5H2Me2SiMe2(C6H4)]WH, respectively. In contrast to the C–Si cleavage achieved by MeLi, BunLi, and PhLi, the ansa bridge of [Me2Si(CpMe2)2]W(H)Cl is inert to ButLi and the product obtained is the fulvene (“tuck-in”) complex [Me2Si(CpMe2)(?6–C5MeH2CH2)]WH derived from dehydrohalogenation. PMID:18635687

Zachmanoglou, Cary E.; Lee, Hyosun; Jang, Seung Ho; Pang, Keliang; Parkin, Gerard



Cleavage of S-S bond by nitric oxide (NO) in the presence of oxygen: a disproportionation reaction of two disulfides.  


Disulfide bond was cleaved by a catalytic amount of nitric oxide in the presence of oxygen, which was confirmed by experiments employing two symmetrical disulfides. The reaction resulted in the formation of unsymmetrical disulfides in nearly 50% yields. The steric hindrance of alkyl disulfide slowed the reaction rate, and an electron-donating group on the aryl disulfide promoted the reaction. The substituent and S-nitrosothiol effects suggested that the reaction was initialized with an oxidative process by NO+. PMID:11045462

Tsutsumi, N; Itoh, T; Ohsawa, A



Unusual carbon-sulfur bond cleavage in the reaction of a new type of bulky hexathioether with a zerovalent palladium complex.  


The reaction of a bulky hexathioether, TbtS(o-Phen)S(o-Phen)SS(o-Phen)S(o-Phen)STbt (o-Phen = o-phenylene, Tbt = 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl) (1), with 3 molar amounts of Pd(PPh3)4 afforded trinuclear palladium complex bridged by two benzenedithiolato ligands via a three-step palladium insertion reaction into one sulfur-sulfur and two carbon-sulfur bonds of 1. PMID:16372097

Shimizu, Daisuke; Takeda, Nobuhiro; Tokitoh, Norihiro



Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins.  


Heme-nitric oxide/oxygen (H-NOX) binding domains are a recently discovered family of heme-based gas sensor proteins that are conserved across eukaryotes and bacteria. Nitric oxide (NO) binding to the heme cofactor of H-NOX proteins has been implicated as a regulatory mechanism for processes ranging from vasodilation in mammals to communal behavior in bacteria. A key molecular event during NO-dependent activation of H-NOX proteins is rupture of the heme-histidine bond and formation of a five-coordinate nitrosyl complex. Although extensive biochemical studies have provided insight into the NO activation mechanism, precise molecular-level details have remained elusive. In the present study, high-resolution crystal structures of the H-NOX protein from Shewanella oneidensis in the unligated, intermediate six-coordinate and activated five-coordinate, NO-bound states are reported. From these structures, it is evident that several structural features in the heme pocket of the unligated protein function to maintain the heme distorted from planarity. NO-induced scission of the iron-histidine bond triggers structural rearrangements in the heme pocket that permit the heme to relax toward planarity, yielding the signaling-competent NO-bound conformation. Here, we also provide characterization of a nonheme metal coordination site occupied by zinc in an H-NOX protein. PMID:25253889

Herzik, Mark A; Jonnalagadda, Rohan; Kuriyan, John; Marletta, Michael A



Homolytic cleavage and aggregation processes in cyclopentadienylchromium chemistry.  


The reactivity of the cyclopentadienylchromium tricarbonyl dimer [CpCr(CO)3]2 (Cp = C5H5, 1) toward several classes of organo-P-, -S- and -N-compounds will be described. The organic substrates include the following: (i) bis(diphenylthiophosphinyl)disulfane, R2P(S)SSP(S)R2; (ii) bis(thiophosphoryl)disulfane, (RO)2P(S)SSP(S)(OR)2; (iii) tetraalkylthiuram disulfides, R2NC(S)SSC(S)NR2; (iv) tetraalkyldiphosphine disulfides, R2P(S)P(S)R2; (v) dibenzothiazolyl disulfide, (C6H4NSC)2; and (vi) Lawesson's reagent, (CH3OC6H4)2P2S4. The primary products, namely, the complexes CpCr(CO)2(SPR2), CpCr(CO)2)(S2CNR2), CpCr(CO)2(SCSN(C6H4)), and CpCr(CO)2(SPC6H4OCH3), containing the thiophosphinito, dithiocarbamate, 2-mercaptobenzothiazole, and dithiophosphorane ligands, respectively, arise from facile cleavage of the S-S, P-P, and P-S bonds in the organic substrates. Further treatment of these complexes with 1 under thermal activation results in cleavage of C-X (X = N, S), P-S, and Cr-E (E = C, N, P, S) bonds, accompanied by C-C and P-P bond formation in some cases, generating a variety of organometallic compounds belonging to the phosphido, phosphinidene, thiocarbenoid, dithiooxamide, aminocarbyne, aminoalkenylacyl, and cuboidal types. PMID:15023086

Weng, Zhiqiang; Goh, Lai Yoong



Novel Enterokinase Cleavage Sequences.  

National Technical Information Service (NTIS)

Novel enterokinase cleavage sequences are provided. Also disclosed are methods for the rapid isolation of a protein of interest present in a fusion protein construct including a novel enterokinase cleavage sequence of the present invention and a ligand re...

A. C. Ley, C. J. Luneau, R. C. Ladner



Solar Photochemical Oxidation of Alcohols using Catalytic Hydroquinone and Copper Nanoparticles under Oxygen: Oxidative Cleavage of Lignin Models.  


Alcohols are converted into to their corresponding carbonyl compounds using catalytic amounts of 1,4-hydroquinone with a copper nanoparticle electron transfer mediator with oxygen as the terminal oxidant in acetone as solvent under visible light irradiation. These conditions employing biorenewable hydroquinone as reagent were developed from initial experiments using stoichiometric amounts of 1,4-benzoquinone as oxidant. A range of benzylic and aliphatic primary and secondary alcohols are oxidized, affording the corresponding aldehydes or ketones in moderate to excellent yields. The methodology is also applicable to the oxidative degradation of lignin model compounds that undergo C-C bond cleavage to give simple aromatic compounds. PMID:25322456

Mitchell, Lorna J; Moody, Christopher J



Elucidation of the Double-Bond Position of Long-Chain Unsaturated Fatty Acids by Multiple-Stage Linear Ion-Trap Mass Spectrometry with Electrospray Ionization  

PubMed Central

Linear ion-trap (LIT) MS2 mass spectrometric approach toward locating the position of double bond(s) of unsaturated long-chain fatty acids and toward discerning among isomeric unsaturated fatty acids as dilithiated adduct ([M ? H + 2Li]+) ions are described in this report. Upon resonance excitation in a LIT instrument, charge-remote fragmentation that involves ?-cleavage with ?-H shift (McLafferty rearrangement) is the predominant fragmentation pathway seen for the [M ? H + 2Li]+ ions of monoenoic long-chain fatty acids. The fragmentation process results in a dilithiated product ion of terminally unsaturated fatty acid, which undergoes consecutive McLafferty rearrangement to eliminate a propylene residue, and gives rise to another dilithiated adduct ion of terminally unsaturated fatty acid. In addition to the above-cited fragmentation process, the [M ? H + 2Li]+ ions of homoconjugated dienoic long-chain fatty acids also undergo ?-cleavage(s) with shift of the allylic hydrogen situated between the homoconjugated double bonds to the unsaturated site. These fragmentation pathways lead to two types of C—C bond cleavages that are allylic (?-cleavage) or vinylic, respectively, to the proximal C—C double bond, resulting in two distinct sets of ion series, in which each ion series is separated by a —CH2CH=CH— (40 Da) residue. These latter fragmentations are the predominant processes seen for the polyunsaturated long-chain fatty acids. The spectrum feature dependent on the position of unsaturated double bond(s) affords unambiguous assignment of the position of double bond(s) of long-chain unsaturated fatty acids. PMID:18692406

Hsu, Fong-Fu; Turk, John



Protonation of a Peroxodiiron(III) Complex and Conversion to a Diiron(III/IV) Intermediate: Implications for Proton-assisted O-O Bond Cleavage in Nonheme Diiron Enzymes  

PubMed Central

Oxygenation of a diiron(II) complex,[FeII2(?-OH)2(BnBQA)2(NCMe)2]2+ (2) (where BnBQA is N-benzyl-N,N-bis(2-quinolinylmethyl)amine) results in the formation of a metastable peroxodiferric intermediate (3). Treatment of 3 with strong acid affords its conjugate acid 4 in which the (?-oxo)(?-1,2-peroxo)diiron(III) core of 3 is protonated at the oxo bridge. The core structures of 3 and 4 are characterized in detail by UV-vis, Mössbauer, resonance Raman, and X-ray absorption spectroscopies. Complex 4 is shorter lived than 3 and decays to generate in 20–25% yield a diiron(III/IV) species (5) that can be identified by EPR and Mössbauer spectroscopy. This reaction sequence demonstrates for the first time that protonation of the oxo bridge of a (?-oxo)(?-1,2-peroxo)diiron(III) complex leads to the cleavage of the peroxo O–O bond and formation of a high-valent diiron complex, thereby mimicking the steps involved in the formation of intermediate X in the activation cycle of ribonucleotide reductase. PMID:22971084

Cranswick, Matthew A.; Meier, Katlyn K.; Shan, Xiaopeng; Stubna, Audria; Kaizer, Joszef; Mehn, Mark P.; Munck, Eckard; Que, Lawrence



Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c2 from Rhodopseudomonas palustris and its ammonia complex  

PubMed Central

The three-dimensional structures of the native cytochrome c2 from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 ? and in the reduced state at 1.95 ? resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c2 with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 310-helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c2 with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles ? and ? of approximately ?140 and ?130°, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 ? resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c2 of the rare six-residue insertion in the helix 310 conformation that increases Met loop flexibility. PMID:11742117

Geremia, Silvano; Garau, Gianpiero; Vaccari, Lisa; Sgarra, Riccardo; Viezzoli, Maria Silvia; Calligaris, Mario; Randaccio, Lucio



Catalytic Carbonyl Allylation, Propargylation and Vinylation from the Alcohol or Aldehyde Oxidation Level via C-C Bond Forming Hydrogenation and Transfer Hydrogenation: A Departure from Preformed Organometallic Reagents**  

PubMed Central

Classical protocols for carbonyl allylation, propargylation and vinylation typically rely upon the use of preformed allyl metal, allenyl metal and vinyl metal reagents, respectively, mandating stoichiometric generation of metallic byproducts. Through transfer hydrogenative C-C coupling, carbonyl addition may be achieved from the aldehyde or alcohol oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. Here, we review transfer hydrogenative methods for carbonyl addition, which encompass the first cataltyic protocols enabling direct C–H functionalization of alcohols. PMID:19040235

Bower, John F.; Kim, In Su; Patman, Ryan L.; Krische, Michael J.



A DFT study on the interaction between adsorbed silver on C?? and disulfide bond.  


Adsorption of a silver atom on the surface of Buckyball (C??) was investigated using density functional theory (DFT). The Ag atom tends to occupy the bridge site over C--C bond in pentagon-hexagon ring junction with the binding energy of -38.33 kcal mol?¹. The capability of destroying S--S bond by both a single silver atom and the silver atom adsorbed on C?? was also investigated by DFT calculations using dimethyl disulfide as the molecular model. The results of the natural bond orbital (NBO) and population analysis indicate that the cleavage of the S--S bond effectively occurs by the silver atom adsorbed on C??. Since denaturation of disulfide bonds of envelope glycoprotein (gp) 120 is a key step in the prevention of the spread of HIV-1, the development of the proposed study is promised to HIV-1 research field. PMID:23085174

Azizi, Khaled; Sohrabinia, Ali



Metallacyclocumulenes: a theoretical perspective on the structure, bonding, and reactivity.  


Conspectus Transition metals help to stabilize highly strained organic fragments. Metallacycles, especially unsaturated ones, provide much variety in this area. We had a sustained interest in understanding new C-C bond formation reactions affected by binuclear transition metal fragments Cp2M. One such study led to the exploration of the bimetallic C-C cleavage and coupled complexes, where the acetylide ligands bridge two metal atoms. The underlying M-C interaction in these complexes inspired the synthesis of a five-membered cyclocumulene complex, which opened a new phase in organometallic chemistry. The metallacyclocumulene produces a variety of C-C cleavage and coupled products including a radialene complex. Group 4 metallocenes have thus unlocked a fascinating chemistry by stabilizing strained unsaturated C4 organic fragments in the form of five-membered metallacyclocumulenes, metallacyclopentynes, and metallacycloallenes. Over the years, we have carried out a comprehensive theoretical study to understand the unusual stability and reactivity of these metallacycles. The unique (M-C?) interaction of the internal carbon atoms with the metal atom is the reason for unusual stability of the metallacycles. We have also shown that there is a definite dependence of the C-C coupling and cleavage reactions on the metal of metallacyclocumulenes. It demonstrates unexpected reaction pathways for these reactions. Based on this understanding, we have predicted and unraveled the stabilization factors of an unusual four-membered metallacycloallene complex. Indeed, our prediction about a four-membered heterometallacycle has led to an interesting bonding situation, which is experimentally realized. This type of M-C bonding is intriguing from a fundamental perspective and has great relevance in synthesizing unusual structures with interesting properties. In this Account, we first give a short prologue of what led to the present study and describe the salient features of the structure and bonding of the metallacyclocumulenes. The unusual reaction pathway of this metallacycle is explored next. Similar features of the metallacyclopentynes and metallacycloallenes are briefly mentioned. Then, we discuss the exploitation of the unique M-C bonding to design some exotic molecules such as a four-membered metallacycloallene complex. Our efforts to build a conceptual framework to understand these metallacycles and to exploit their chemistry continue. PMID:25171518

Roy, Subhendu; Rosenthal, Uwe; Jemmis, Eluvathingal D



C. C. Jones: Scientific Photographs  

NSDL National Science Digital Library

This image gallery, by C. C. Jones of Union College, contains many examples of physical optics and also x-ray diffraction. Several images of diffraction show how the pattern changes when the wavelength, the distance between light sources, and the aperture is varied. Also included are pinhole photos and comparisons of emission spectra of various elements and the absorption spectrum of the sun. Captions provide background information.



Palladium-catalyzed C-C, C-N and C-O bond formation  

E-print Network

New methods for Pd-catalyzed cross-coupling reactions of aryl halides or arenesulfonates are described. Key to the success of these transformations is the proper choice of ligand and reaction conditions. Palladium catalysts ...

Huang, Xiaohua, 1973-



Photoinduced C-C reactions on insulators toward photolithography of graphene nanoarchitectures.  


On-surface chemistry for atomically precise sp(2) macromolecules requires top-down lithographic methods on insulating surfaces in order to pattern the long-range complex architectures needed by the semiconductor industry. Here, we fabricate sp(2)-carbon nanometer-thin films on insulators and under ultrahigh vacuum (UHV) conditions from photocoupled brominated precursors. We reveal that covalent coupling is initiated by C-Br bond cleavage through photon energies exceeding 4.4 eV, as monitored by laser desorption ionization (LDI) mass spectrometry (MS) and X-ray photoelectron spectroscopy (XPS). Density functional theory (DFT) gives insight into the mechanisms of C-Br scission and C-C coupling processes. Further, unreacted material can be sublimed and the coupled sp(2)-carbon precursors can be graphitized by e-beam treatment at 500 °C, demonstrating promising applications in photolithography of graphene nanoarchitectures. Our results present UV-induced reactions on insulators for the formation of all sp(2)-carbon architectures, thereby converging top-down lithography and bottom-up on-surface chemistry into technology. PMID:24524804

Palma, Carlos-Andres; Diller, Katharina; Berger, Reinhard; Welle, Alexander; Björk, Jonas; Cabellos, Jose Luis; Mowbray, Duncan J; Papageorgiou, Anthoula C; Ivleva, Natalia P; Matich, Sonja; Margapoti, Emanuela; Niessner, Reinhard; Menges, Bernhard; Reichert, Joachim; Feng, Xinliang; Räder, Hans Joachim; Klappenberger, Florian; Rubio, Angel; Müllen, Klaus; Barth, Johannes V



Selective cleavage of pepsin by molybdenum metallopeptidase  

SciTech Connect

Graphical abstract: Molybdenum metallopeptidase: the Mo(VI) cluster with six molybdenum cations has the ability to cleave protein under mild conditions (37 Degree-Sign C, pH 7) without reducing agents. The reaction required only low concentration of ammonium heptamolybdatetetrahydrate ((NH{sub 4}){sub 6}Mo{sub 7}O{sub 24}{center_dot}4H{sub 2}O) (0.125 mM). The reaction undergoes possibly via a hydrolytic mechanism. This is the first demonstration of protein cleavage by a molybdenum cluster. Highlights: Black-Right-Pointing-Pointer This is the first demonstration of protein cleavage by a Mo(VI) cluster with six molybdenum cations. Black-Right-Pointing-Pointer The cleavage reaction undergoes at mild conditions. Black-Right-Pointing-Pointer No need of reducing agents. Black-Right-Pointing-Pointer Only low concentration of Mo(VI) cluster and short time of incubation are needed. -- Abstract: In this study, the cleavage of protein by molybdenum cluster is reported for the first time. The protein target used is porcine pepsin. The data presented in this study show that pepsin is cleaved to at least three fragments with molecular weights of {approx}23, {approx}19 and {approx}16 kDa when the mixture of the protein and ammonium heptamolybdate tetrahydrate ((NH{sub 4}){sub 6}Mo{sub 7}O{sub 24}{center_dot}4H{sub 2}O) was incubated at 37 Degree-Sign C for 24 h. No self cleavage of pepsin occurs at 37 Degree-Sign C, 24 h indicating that the reaction is mediated by the metal ions. N-terminal sequencing of the peptide fragments indicated three cleavage sites of pepsin between Leu 112-Tyr 113, Leu 166-Leu 167 and Leu 178-Asn 179. The cleavage reaction occurs after incubation of the mixture of pepsin and (NH{sub 4}){sub 6}Mo{sub 7}O{sub 24}{center_dot}4H{sub 2}O) only for 2 h. However, the specificity of the cleavage decreases when incubation time is longer than 48 h. The mechanism for cleavage of pepsin is expected to be hydrolytic chemistry of the amide bonds in the protein backbone.

Yenjai, Sudarat; Malaikaew, Pinpinat; Liwporncharoenvong, Teerayuth [Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110 (Thailand)] [Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110 (Thailand); Buranaprapuk, Apinya, E-mail: [Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110 (Thailand)] [Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110 (Thailand)



Enzymatic enantioselective C-C-bond formation in microreactors.  


We have demonstrated that multiple crude enzyme lysates containing a hydroxynitrile lyase can be used for the enantioselective synthesis of cyanohydrins from aldehydes in microchannels. Using a microreactor setup, two important parameters were efficiently screened consuming only minute amounts of reagents. More importantly, results from the continuous flow reaction were fully consistent with results obtained from larger batchwise processes in which a stable emulsion was formed. PMID:17879309

Koch, K; van den Berg, R J F; Nieuwland, P J; Wijtmans, R; Schoemaker, H E; van Hest, J C M; Rutjes, F P J T



Primary crenulation pencil cleavage  

NASA Astrophysics Data System (ADS)

Previous pencil cleavage models rely on either pressure solution or independent grain rotation as the principal shortening mechanism. In contrast, samples from the Rose Hill Formation and the Marcellus Shale from the Central Appalachians show a primary tectonic crenulation fabric dominated by domainal grain rotation in microfold limbs. The crenulations are identified in crossed-polarized light where they appear as alternating light and dark bands of optically aligned phyllosilicates in the microfold limbs. Relatively rare pressure solution developed concentrations of insoluble residue and thinned bedding laminae within microfold limbs. A systematic relationship of pressure solution to microfold limbs in more deformed samples indicates that microfolding preceded pressure solution. Shortening, in six samples without pressure solution, ranges from 9.2 to 20.4% and exhibits no direct relationship to the length/width ratios for the pencils. A new model for pencil cleavage begins with compacted shale having a strong bedding-parallel alignment of inequant grains. Compression causes microfolding, developing a primary crenulation pencil cleavage fabric. Pressure solution is then initiated within the microfold limbs and continues as a major shortening mechanism which overprints bedding to form planar cleavage.

Ferrill, David A.


Cleavage and Fracture  

NSDL National Science Digital Library

In this activity, students will learn the properties of cleavage and fracture (how minerals break when struck with a hammer), and will use these properties as a diagnostic test for identifying minerals. Working in small groups, they will break a selection of specimens with a hammer, observe the results, and record their observations. A student worksheet and discussion questions are provided.



Conformational changes of 1-4-glucopyranosyl residues of a sulfated C-C linked hexasaccharide.  


This work describes the structure of a fully sulfated maltotriose alpha-beta C-C linked dimer, where a central glycosidic bond was substituted by a non natural, hydrolase-resistant C-C bond. Such compound shows anti-metastatic properties being an inhibitor of the heparanase enzymatic activity and of P-selectin-mediated cell-cell interactions. NMR spectroscopy was applied to investigate the structure and conformational properties of this C-C linked hexasaccharide. The presence of sulfate substituents and the internal C-C bond drives the two internal rings in an unusual (1)C(4) chair conformation, while the external rings linked by glycosidic bonds retain the typical (4)C(1) conformation. The NMR results were confirmed by molecular mechanics calculations using structure corresponding di- and tetrasaccharides as models. PMID:24680506

Coletti, Alessia; Elli, Stefano; Macchi, Eleonora; Galzerano, Patrizia; Zamani, Leila; Guerrini, Marco; Torri, Giangiacomo; Vismara, Elena



Homolytic bond dissociation energies for C-H bonds adjacent to sulfur and aromatic moieties: The effects of substituents of C-H bond strengths of the benzylic positions in coal model compounds  

SciTech Connect

Sulfur-containing compounds are precursors for thiyl radicals at coal liquefaction temperatures due to the weakness of The and S-S bonds. Thiyl radicals play important roles in hydrogen atom shuttling between benzylic positions and catalyze the cleavage and the formation of strong C-C bonds. Although many reactions of thiyl and other sulfur-containing radicals are qualitatively understood, the homolytic bond dissociation energies (EDE`s) and the thermochemistry associated with many key high molecular weight hydrocarbon and sulfur-containing organic structures important to coal is lacking because they are inappropriate for gas-phase techniques. The measurement of BDE`s has been proven to be difficult even in the simplest of molecules.

Alnajjar, M.S.; Franz, J.A. [Pacific Northwest Lab., Richland, WA (United States); Gleicher, G.J.; Truksa, S. [Oregon State Univ., Corvallis, OR (United States). Dept. of Chemistry; Bordwell, F.; Zhang, Xian-Man [Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry



Localization of double bonds in wax esters by high-performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry utilizing the fragmentation of acetonitrile-related adducts.  


Unsaturated wax esters (WEs) provided molecular adducts with C(3)H(5)N ([M + 55](+•)) in APCI sources in the presence of acetonitrile. CID MS/MS of [M + 55](+•) yielded fragments allowing the localization of double bond(s) in the hydrocarbon chains of the WEs. These fragments were formed by a cleavage on each side of the double bond. In methylene-interrupted polyunsaturated WEs, diagnostic fragments related to each double bond were detected; the most abundant were those corresponding to the cleavage of the C-C bond next to the first and the last double bond. To differentiate between those fragments differing in their structure or origin, a simple nomenclature based on ? and ? ions has been introduced. Fragmentation of the ?-type ions (fragments containing an ester bond) provided information on the occurrence of a double bond in the acid or alcohol part of the WEs. While no significant differences between the spectra of the WEs differing by cis/trans isomerism were found, the isomers were separated chromatographically. A data-dependent HPLC/APCI-MS(2) method for the comprehensive characterization of WEs in their complex mixtures has been developed and applied to natural mixtures of WEs isolated from jojoba oil and beeswax. More than 50 WE molecular species were completely identified, including the information on the acid and alcohol chain length and the position of the double bonds. PMID:21428309

Vrkoslav, Vladimír; Háková, Martina; Pecková, Karolina; Urbanová, Klára; Cva?ka, Josef



Facilitating room-temperature Suzuki coupling reaction with light: Mott-Schottky photocatalyst for C-C-coupling  

NASA Astrophysics Data System (ADS)

The Suzuki coupling reaction is one of the most practiced classes of catalytic C-C bond formation. The development of new means of activating molecules and bonds over old catalysts for C-C bond formation is a fundamental objective for chemists. Here, we report the room-temperature C-C bond formation over heterogeneous Pd catalysts by light-mediated catalyst activation. We employ stimulated electron transfer at the metal-semiconductor interface from optically active mesoporous carbon nitride nanorods to Pd nanoparticles. This photocatalytic pathway is highly efficient for coupling aryl halides with various coupling partners with high activity and selectivity under photo irradiation and very mild conditions.

Li, Xin-Hao; Baar, Moritz; Blechert, Siegfried; Antonietti, Markus



Facilitating room-temperature Suzuki coupling reaction with light: Mott-Schottky photocatalyst for C-C-coupling  

PubMed Central

The Suzuki coupling reaction is one of the most practiced classes of catalytic C-C bond formation. The development of new means of activating molecules and bonds over old catalysts for C-C bond formation is a fundamental objective for chemists. Here, we report the room-temperature C-C bond formation over heterogeneous Pd catalysts by light-mediated catalyst activation. We employ stimulated electron transfer at the metal-semiconductor interface from optically active mesoporous carbon nitride nanorods to Pd nanoparticles. This photocatalytic pathway is highly efficient for coupling aryl halides with various coupling partners with high activity and selectivity under photo irradiation and very mild conditions.

Li, Xin-Hao; Baar, Moritz; Blechert, Siegfried; Antonietti, Markus



Palladium-catalyzed allylic alkylation via decarboxylative and retro-Claisen C-C cleavage methods  

E-print Network

Presented herein is the development of new methods for Pd-catalyzed allylic alkylation with a central focus on reactions that generate molecular complexity rapidly with little waste byproduct. With this simply stated, yet ...

Grenning, Alexander James



N-O Cleavage reactions of heterobicycloalkene-fused 2-isoxazolines  

PubMed Central

Summary Transition metal-mediated N–O bond cleavage reactions of heterobicycloalkene-fused 3-methyl-2-isoxazolines were investigated. Optimal cleavage conditions were found with Raney nickel/AlCl3 mediation in aqueous methanol. The reaction provided a diverse collection of novel heterobicycle-fused ?-hydroxyketones with good to excellent yields (66–95%) and without the need for chromatographic purification.

Nagireddy, Jaipal R; Tranmer, Geoffrey K; Carlson, Emily



Coupling insertion reactions of diphenylbuta-1, 4-diyne into iron-carbene bonds of [Fe 2 (CO) 7 {?-C(Ph)C(NEt 2 }]. Syntheses and reactivities of the ferracyclopentadiene [Fe 2 (CO) 6 {C(Ph)C(NEt 2 )C(Ph)C(C 2 Ph)}] with [Fe 2 (CO) 9  

Microsoft Academic Search

The diiron ynamine complex [Fe2(CO)7{µ-C(Ph)C(NEt2)}] (1) reacts with the diphenylbuta-1, 4-diyne, PhC=C-C=CPh, in refluxing hexane to yield three isomer complexes [Fe2(CO)6{C(Ph)C(NEt2)C(Ph)C(C2Ph}] (2a), [Fe2(CO)6{C(Ph)C(NEt2)C(C2Ph)C(Ph)}] (2b), and [Fe2(CO)6{NEt2)C(Ph)C(C2)C(Ph)}] (2c) All three compounds were identified by their1H NMR spectra. Compounds2a and2c were characterized by single crystal X-ray diffraction analyses. Crystal data: for2a: space group = P21\\/n,a = 17.873(1) Å,ß = 18.388(6) Å,c =

J. C. Daran; E. Gilbert; M. Gouygou; S. Halut; B. Heim; Y. Jeannin



Acyclic carotenoid and cyclic apocarotenoid cleavage by an orthologue of lignostilbene-?,?-dioxygenase in Rhodopseudomonas palustris.  


Carotenoid cleavage oxygenases catalyse formation of apocarotenoids and the precursors of phytohormones, abscisic acid and strigolactones through oxidative cleavage at specific double bonds of carotenoids. A gene encoding a presumed bacterial oxygenase homologous to lignostilbene-?,?-dioxygenases has been found in the genome of Rhodopseudomonas palustris. By analysing apocarotenoids in recombinant Escherichia coli strains, it was found that the presumed oxygenase catalyses the 15,15' double bond cleavage of lycopene and neurosporene. Cell lysate containing the recombinant protein cleaved all-trans-?-apo-8'-carotenal at the 15,15' double bond into retinal and apo-8',15'-apocarotene-dial. These data demonstrate for the first time that the orthologue of lignostilbene-?,?-dioxygenase found in the carotenogenic phototrophic bacterium has the 15,15' double bond cleavage activity towards both the acyclic carotenoids and cyclic apocarotenoid. PMID:23946507

Maeda, Isamu; Inaba, Atsushi; Koike, Hiroyuki; Yoneyama, Koichi; Ueda, Shunsaku; Yoshida, Kazuyuki



Temperature effects on adsorption and diffusion dynamics of CH3CH2(ads) and H3C-C?C(ads) on Ag(111) surface and their self-coupling reactions: Ab initio molecular dynamics approach  

NASA Astrophysics Data System (ADS)

Density functional theory (DFT)-based molecular dynamics (DFTMD) simulations in combination with a Fourier transform of dipole moment autocorrelation function are performed to investigate the adsorption dynamics and the reaction mechanisms of self-coupling reactions of both acetylide (H3C-C(?)?C(?) (ads)) and ethyl (H3C(?)-C(?)H2(ads)) with I(ads) coadsorbed on the Ag(111) surface at various temperatures. In addition, the calculated infrared spectra of H3C-C(?)?C(?)(ads) and I coadsorbed on the Ag(111) surface indicate that the active peaks of -C(?)?C(?)- stretching are gradually merged into one peak as a result of the dominant motion of the stand-up -C-C(?)?C(?)- axis as the temperature increases from 200 K to 400 K. However, the calculated infrared spectra of H3C(?)-C(?)H2(ads) and I coadsorbed on the Ag(111) surface indicate that all the active peaks are not altered as the temperature increases from 100 K to 150 K because only one orientation of H3C(?)-C(?)H2(ads) adsorbed on the Ag(111) surface has been observed. These calculated IR spectra are in a good agreement with experimental reflection absorption infrared spectroscopy results. Furthermore, the dynamics behaviors of H3C-C(?)?C(?)(ads) and I coadsorbed on the Ag(111) surface point out the less diffusive ability of H3C-C(?)?C(?)(ads) due to the increasing s-character of C? leading to the stronger Ag-C? bond in comparison with that of H3C(?)-C(?)H2(ads) and I coadsorbed on the same surface. Finally, these DFTMD simulation results allow us to predict the energetically more favourable reaction pathways for self-coupling of both H3C-C(?)?C(?)(ads) and H3C(?)-C(?)H2(ads) adsorbed on the Ag(111) surface to form 2,4-hexadiyne (H3C-C?C-C?C-CH3(g)) and butane (CH3-CH2-CH2-CH3(g)), respectively. The calculated reaction energy barriers for both H3C-C?C-C?C-CH3(g) (1.34 eV) and CH3-CH2-CH2-CH3(g) (0.60 eV) are further employed with the Redhead analysis to estimate the desorption temperatures approximately at 510 K and 230 K, respectively, which are in a good agreement with the experimental low-coverage temperature programmed reaction spectroscopy measurements.

Lu, Shao-Yu; Lin, Jyh-Shing



98. Catalog HHistory 1, C.C.C., 19 Tree Planting, Negative No. ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

98. Catalog H-History 1, C.C.C., 19 Tree Planting, Negative No. P 474c (Photographer and date unknown) TRANSPLANTING TREE. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA


101. Catalog HHistory 1, C.C.C., 34 Landscaping, Negative No. 1340 ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

101. Catalog H-History 1, C.C.C., 34 Landscaping, Negative No. 1340 (Photographer and date unknown) BANK BLENDING WORK BY CCC. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA


100. Catalog HHistory 1, C.C.C., 34 Landscaping, Negative No. P ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

100. Catalog H-History 1, C.C.C., 34 Landscaping, Negative No. P 733c (Photographer and date unknown) SLOPE MAINTENANCE WORK BY CCC. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA


99. Catalog HHistory 1, C.C.C., 23 Guard Rail Construction, Negative ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

99. Catalog H-History 1, C.C.C., 23 Guard Rail Construction, Negative No. P455e (Photographer and date unknown) GUARD RAIL INSTALLATION. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA


Anti-metastatic Semi-synthetic Sulfated Maltotriose C-C Linked Dimers. Synthesis and Characterisation  

PubMed Central

This manuscript describes the preparation and the spectroscopic characterisation of semi-synthetic sulfated maltotriose C-C linked dimers (SMTCs) where the natural C-O-C anomeric bond was substituted by one direct central C-C bond. This C-C bond induces conformation and flexibility changes with respect to the usual anomeric bond. SMTCs neutral precursors came from maltotriosyl bromide electroreduction through maltotriosyl radical intermediate dimerisation. The new C-C bond configuration, named for convenience ?,?, ?,? and ?,? as the natural anomeric bond, dictated the statistic ratio formation of three diastereoisomers. They were separated by silica gel flash chromatography followed by semi preparative HPLC chromatography. Each diastereoisomer was exhaustively sulfated to afford the corresponding SMTCs. SMTCs were huge characterised by NMR spectroscopy which provided the sulfation degree, too. ?,? and ?,? were found quite homogeneous samples with a high degree of sulfation (85–95%). ?,? appeared a non-homogeneous sample whose average sulfation degree was evaluated at around 78%. Mass spectroscopy experiments confirmed the sulfation degree range. Some considerations were proposed about SMTCs structure-biological properties. PMID:22902885

Vismara, Elena; Coletti, Alessia; Valerio, Antonio; Naggi, AnnaMaria; Urso, Elena; Torri, Giangiacomo



Mild P-P Bond Cleavage in the Methyldiphosphenyl Complex [Mo2Cp2(?-PCy2)(?-?(2):?(2)-P2Me)(CO)2] To Give Novel Phosphide-Bridged Trinuclear Derivatives.  


Reactions of the title diphosphenyl complex with [Fe2(CO)9] and [W(CO)4(THF)2] gave the trinuclear species [Mo2FeCp2(?3-P)(?-PCy2)(?3-PMe)(CO)5] and [Mo2WCp2(?3-P)(?-PCy2)(?3-PMe)(CO)6] following from formal insertion of the 14-electron fragments Fe(CO)3 and W(CO)4, respectively, in the P-P bond of the diphosphenyl ligand and formation of a new heterometallic bond [Mo-Fe = 2.9294(6) Å and Mo-W = 3.146(1) Å]. Reactions of the diphosphenyl complex with the tetrahydrofuran adducts [MLn(THF)] (MLn = MnCp'(CO)2, W(CO)5) led instead to trinuclear diphosphenyl complexes [Mo2MCp2(?-PCy2)(?3-?(2):?(2):?(1)-P2Me)(CO)2Ln] following from coordination in each case of the corresponding 16-electron fragment MLn to the lone-pair-bearing P atom of the P2Me ligand. However, these diphosphenyl complexes were unstable and decomposed at room temperature or under mild heating by the release of methylphosphinidene (PMe), to give the corresponding derivatives [Mo2MCp2(?3-P)(?-PCy2)(CO)2Ln] displaying trigonal-planar phosphide ligands, giving rise to strongly deshielded (31)P NMR resonances (?P ca. 1100 ppm), while being involved in strong ? bonding with the unsaturated Mo2 center of these molecules [Mo-Mo = 2.749(1) Å and Mo-P = ca. 2.30 Å when M = W]. An isolobal analogy could be established between the P?MLn fragments in these products and a carbyne ligand (CR), supported by density functional theory calculations on the tungsten compound, which also enabled an easy interpretation and prediction of their chemical behavior. Thus, the manganese complex could be reversibly carbonylated (pCO = ca. 3 atm, 293 K) to give the corresponding electron-precise pentacarbonyl [MnMo2Cp2Cp'(?3-P)(?-PCy2)(CO)5] [Mo-Mo = 3.1318(7) Å], a process also involving a trans-to-cis rearrangement of the Mo2Cp2 subunit. On the other hand, decarbonylation of the tungsten complex was accomplished in a refluxing toluene solution to give the hexacarbonyl [Mo2WCp2(?3-P)(?-PCy2)(?-CO)(CO)5], a derivative containing an unsaturated 30-electron dimolybdenum center with an intermetallic triple bond. PMID:25300937

Alvarez, M Angeles; García, M Esther; García-Vivó, Daniel; Lozano, Raquel; Ramos, Alberto; Ruiz, Miguel A



Joining C/C composite to copper using active Cu-3.5Si braze  

NASA Astrophysics Data System (ADS)

A simple technique was developed to join C/C composite to Cu using active Cu-3.5Si braze for nuclear thermal applications. The brazing alloy exhibited good wettability on C/C substrate due to the reaction layer formed at the interface. A strong interfacial bond of the brazing alloy on C/C with the formation of TiC + SiC + Ti 5Si 3 reaction layer was obtained. The produced CC/Cu/CuCrZr joint exhibited shear strength as high as 79 MPa and excellent thermal resistance during the thermal shock tests.

Shen, Yuanxun; Li, Zhenglin; Hao, Chuanyong; Zhang, Jinsong



Organohelium compounds: structures, stabilities and chemical bonding analyses.  


This paper deals with the possibility of forming short and relatively strong carbon-helium bonds in small typical organic molecules through substitution of one or several H atoms by He(+). A structural and energetics study (based on high-level calculations) of this unusual bonding, as well as a topological characterization of the resulting cations, is undertaken. Stable species generally requires substitution of about half of the hydrogen atoms for formation. Under these conditions, the number of such species appears to be potentially unlimited. "True" C-He bonds exhibit equilibrium distances ranging from 1.327 (C2H2He2(2+)) to 1.129 Å (He2CO(2+)). The energies of neutral He releasing range from approximately 5 kcal?mol(-1) [He2CO(2+), (Z)-C2H2He2(2+)] to 25 kcal?mol(-1) (C2HHe3(3+)), but remain most frequently around 10 kcal?mol(-1). However, most of He(+)-substituted hydrocarbons are metastable with respect to C-C cleavage, except derivatives of ethene. Atoms in molecules (AIM) and electron localization function (ELF) topological descriptors classify the C-He bond as a weak charge-shift interaction [S. Shaik, D. Danovich, B. Silvi, D. L. Lauvergnat, P. C. Hiberty, Chem. Eur. J. 2005, 11, 6358-6371] in agreement with a recent publication by Rzepa [S. H. Rzepa, Nat. Chem. 2010, 2, 390-393]. He2CO(2+) is the only investigated compound that presents a C-He bonding ELF basin, which indicates a non-negligible covalent contribution to the bond. Other modifications in the electronic structure, such as the breaking of the triple bond in ethyne derivatives or the loss of aromaticity in C6H3He3(3+), are also nicely revealed by the ELF topology. PMID:24488791

Fourré, Isabelle; Alvarez, Elsa; Chaquin, Patrick



Mapping the Globe with C & C Technologies  

NASA Astrophysics Data System (ADS)

C & C Technologies is an international survey and mapping company with an entrepreneurial spirit that is evident throughout. C & C was recently awarded the MTS (Marine Technology Society) ROV Committee Corporate Excellence Award in recognition of their pioneering spirit displayed by the introduction of the HUGIN 3000 Autonomous Underwater Vehicle (AUV) to the offshore industry. This presentation will outline the wide variety of global mapping projects that C & C has performed for government, private sector, and academia. These include high-resolution mapping of Cater Lake, the Panama Canal, Antarctica, Lake Tahoe, and the HUGIN 3000? discovery of the German submarine U-166 in 5000 feet of water in the Gulf of Mexico. Adacemic disciplines required to support these technical challenges will be characterized and job opportunities in this emerging field will be addressed.

Kleiner, A. A.



Cleavage of Prolactin by Its Target Organs and the Possible Significance of this Process  

Microsoft Academic Search

An enzymatically cleaved form of rat prolactin (rPRL) was first described in 1980. This cleavage produces a molecule that consists of two chains of amino acids linked by a disulfide bond between two Cys residues. Reduction of that bond produces two fragments of 6 and 16 Kd. A considerable amount of information has accrued in recent years about the cleaved

Charles S. Nicoll



New Insight into the Cleavage Reaction of Nostoc sp. Strain PCC 7120 Carotenoid Cleavage Dioxygenase in Natural and Nonnatural Carotenoids  

PubMed Central

Carotenoid cleavage dioxygenases (CCDs) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. In this study, we investigated the activity and substrate preferences of NSC3, a CCD of Nostoc sp. strain PCC 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. NSC3 cleaved ?-apo-8?-carotenal at 3 positions, C-13C-14, C-15C-15?, and C-13?C-14?, revealing a unique cleavage pattern. NSC3 cleaves the natural structure of carotenoids 4,4?-diaponeurosporene, 4,4?-diaponeurosporen-4?-al, 4,4?-diaponeurosporen-4?-oic acid, 4,4?-diapotorulene, and 4,4?-diapotorulen-4?-al to generate novel cleavage products (apo-14?-diaponeurosporenal, apo-13?-diaponeurosporenal, apo-10?-diaponeurosporenal, apo-14?-diapotorulenal, and apo-10?-diapotorulenal, respectively). The study of carotenoids with natural or nonnatural structures produced by using synthetic modules could provide information valuable for understanding the cleavage reactions or substrate preferences of other CCDs in vivo and in vitro. PMID:23524669

Heo, Jinsol; Kim, Se Hyeuk



104. Catalog HHistory 1, C.C.C., 73 Picnic Furniture Construction, Negative ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

104. Catalog H-History 1, C.C.C., 73 Picnic Furniture Construction, Negative No. 8821 ca. 1936 WOOD UTILIZATION. COMPLETED RUSTIC BENCH MADE BY CCC ENROLLEES AT CAMP NP-3 FOR USE AT PARKING OVERLOOKS AND PICNIC GROUNDS. NOTE SAW IN BACKGROUND USED FOR HALVING CHESTNUT. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA


103. Catalog HHistory 1, C.C.C., 58 Landscaping, Negative No. 870 ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

103. Catalog H-History 1, C.C.C., 58 Landscaping, Negative No. 870 10 ca. 1936 PROPAGATION AND PLANTING. ROOTED PLANTS TRANSPLANTED FROM HOT BEDS TO CANS TO SHADED BEDS IN PREPARATION FOR PLANTING ON ROAD SLOPES. NURSERY AT NORTH ENTRANCE. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA


102. Catalog HHistory 1, C.C.C., 34 Landscaping, Negative No. 6040a ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

102. Catalog H-History 1, C.C.C., 34 Landscaping, Negative No. 6040a (Photographer and date unknown) BEAUTIFICATION PROGRAM STARTED AS SOON AS GRADING ALONG THE DRIVE WAS COMPLETED. CCC CAMP 3 SHOWN PLANTING LAUREL. - Skyline Drive, From Front Royal, VA to Rockfish Gap, VA , Luray, Page County, VA


Photodegradation of human growth hormone: a novel backbone cleavage between Glu-88 and Pro-89.  


The exposure of protein pharmaceuticals to light can cause loss of potency, oxidation, structural changes and aggregation. To elucidate the chemical pathways of photodegradation, we irradiated human growth hormone (hGH) at ? = 254 nm, ? ? 265-340 nm, and ? ? 295-340 nm (using the spectral cutoff of borosilicate glass) and analyzed the products by mass spectrometry. By means of LC-MS/MS analysis, we observed an unusual peptide backbone cleavage between Glu-88 and Pro-89. The crystal structure of hGH indicates that these residues are in proximity to Trp-86, which likely mediates this backbone cleavage. The two cleavage fragments observed by MS/MS analysis indicate the loss of CO from the amide bond and replacement of the Glu-C(? O)Pro bond with a Glu-H bond, accompanied by double bond formation on proline. The reaction is oxygen-independent and likely involves hydrogen transfer to the C? of Glu-88. To probe the influence of the protein fold, we irradiated hGH in its unfolded state, in 1:1 (v/v) acetonitrile/water, and also the isolated tryptic peptide Ile-78-Arg-90, which contains the Glu-88-Pro-89 sequence. In both cases, the cleavage between Glu-88 and Pro-89 was largely suppressed, while other cleavage pathways became dominant, notably between Gln-84 and Ser-85, as well as Ser-85 and Trp-86. PMID:23721578

Steinmann, Daniel; Ji, J Andrea; Wang, Y John; Schöneich, Christian




E-print Network

biochemistry and genetics of chromatin. 7. Kitsis Lab: Micrograph of pancreatic islet from normal mouse blood cells (ESEP) and malignant erythroleukemia cells (MEL). 5. Birshtein/Scharff Labs: Mouse DEPARTMENT OF CELL BIOLOGY 2011-2012 3'5' L V DJ C C C3 C1 C2b C2aC C 3'EnhEnh intronic **** 1. 2

Jenny, Andreas


Evaluation by Rocket Combustor of C/C Composite Cooled Structure Using Metallic Cooling Tubes  

NASA Astrophysics Data System (ADS)

In this study, the cooling performance of a C/C composite material structure with metallic cooling tubes fixed by elastic force without chemical bonding was evaluated experimentally using combustion gas in a rocket combustor. The C/C composite chamber was covered by a stainless steel outer shell to maintain its airtightness. Gaseous hydrogen as a fuel and gaseous oxygen as an oxidizer were used for the heating test. The surface of these C/C composites was maintained below 1500 K when the combustion gas temperature was about 2800 K and the heat flux to the combustion chamber wall was about 9 MW/m2. No thermal damage was observed on the stainless steel tubes that were in contact with the C/C composite materials. The results of the heating test showed that such a metallic tube-cooled C/C composite structure is able to control the surface temperature as a cooling structure (also as a heat exchanger) as well as indicated the possibility of reducing the amount of coolant even if the thermal load to the engine is high. Thus, application of this metallic tube-cooled C/C composite structure to reusable engines such as a rocket-ramjet combined-cycle engine is expected.

Takegoshi, Masao; Ono, Fumiei; Ueda, Shuichi; Saito, Toshihito; Hayasaka, Osamu


Dinitrogen cleavage and hydrogenation by a trinuclear titanium polyhydride complex.  


Both the Haber-Bosch and biological ammonia syntheses are thought to rely on the cooperation of multiple metals in breaking the strong N?N triple bond and forming an N-H bond. This has spurred investigations of the reactivity of molecular multimetallic hydrides with dinitrogen. We report here the reaction of a trinuclear titanium polyhydride complex with dinitrogen, which induces dinitrogen cleavage and partial hydrogenation at ambient temperature and pressure. By (1)H and (15)N nuclear magnetic resonance, x-ray crystallographic, and computational studies of some key reaction steps and products, we have determined that the dinitrogen (N2) reduction proceeds sequentially through scission of a N2 molecule bonded to three Ti atoms in a ?-?(1):?(2):?(2)-end-on-side-on fashion to give a ?2-N/?3-N dinitrido species, followed by intramolecular hydrogen migration from Ti to the ?2-N nitrido unit. PMID:23812710

Shima, Takanori; Hu, Shaowei; Luo, Gen; Kang, Xiaohui; Luo, Yi; Hou, Zhaomin



Observation of the decay ?(3686)???¯±??+c.c.  

NASA Astrophysics Data System (ADS)

Using a sample of 1.06×108 ?(3686) events collected with the BESIII detector, we present the first observation of the decays of ?(3686)???¯+?-+c.c. and ?(3686)???¯-?++c.c. The branching fractions are measured to be B(?(3686)???¯+?-+c.c.)=(1.40±0.03±0.13)×10-4 and B(?(3686)???¯-?++c.c.)=(1.54±0.04±0.13)×10-4, where the first errors are statistical and the second ones systematic.

Ablikim, M.; Achasov, M. N.; Ai, X. C.; Albayrak, O.; Ambrose, D. J.; An, F. F.; An, Q.; Bai, J. Z.; Baldini Ferroli, R.; Ban, Y.; Bennett, J. V.; Bertani, M.; Bian, J. M.; Boger, E.; Bondarenko, O.; Boyko, I.; Braun, S.; Briere, R. A.; Cai, H.; Cai, X.; Cakir, O.; Calcaterra, A.; Cao, G. F.; Cetin, S. A.; Chang, J. F.; Chelkov, G.; Chen, G.; Chen, H. S.; Chen, J. C.; Chen, M. L.; Chen, S. J.; Chen, X.; Chen, X. R.; Chen, Y. B.; Cheng, H. P.; Chu, X. K.; Chu, Y. P.; Cronin-Hennessy, D.; Dai, H. L.; Dai, J. P.; Dedovich, D.; Deng, Z. Y.; Denig, A.; Denysenko, I.; Destefanis, M.; Ding, W. M.; Ding, Y.; Dong, C.; Dong, J.; Dong, L. Y.; Dong, M. Y.; Du, S. X.; Fang, J.; Fang, S. S.; Fang, Y.; Fava, L.; Feng, C. Q.; Fu, C. D.; Fu, J. L.; Fuks, O.; Gao, Q.; Gao, Y.; Geng, C.; Goetzen, K.; Gong, W. X.; Gradl, W.; Greco, M.; Gu, M. H.; Gu, Y. T.; Guan, Y. H.; Guo, A. Q.; Guo, L. B.; Guo, T.; Guo, Y. P.; Guo, Y. P.; Han, Y. L.; Harris, F. A.; He, K. L.; He, M.; He, Z. Y.; Held, T.; Heng, Y. K.; Hou, Z. L.; Hu, C.; Hu, H. M.; Hu, J. F.; Hu, T.; Huang, G. M.; Huang, G. S.; Huang, J. S.; Huang, L.; Huang, X. T.; Hussain, T.; Ji, C. S.; Ji, Q.; Ji, Q. P.; Ji, X. B.; Ji, X. L.; Jiang, L. L.; Jiang, X. S.; Jiao, J. B.; Jiao, Z.; Jin, D. P.; Jin, S.; Jing, F. F.; Johansson, T.; Kalantar-Nayestanaki, N.; Kang, X. L.; Kavatsyuk, M.; Kloss, B.; Kopf, B.; Kornicer, M.; Kuehn, W.; Kupsc, A.; Lai, W.; Lange, J. S.; Lara, M.; Larin, P.; Leyhe, M.; Li, C. H.; Li, Cheng; Li, Cui; Li, D.; Li, D. M.; Li, F.; Li, G.; Li, H. B.; Li, J. C.; Li, K.; Li, K.; Li, Lei; Li, P. R.; Li, Q. J.; Li, T.; Li, W. D.; Li, W. G.; Li, X. L.; Li, X. N.; Li, X. Q.; Li, X. R.; Li, Z. B.; Liang, H.; Liang, Y. F.; Liang, Y. T.; Liao, G. R.; Lin, D. X.; Liu, B. J.; Liu, C. L.; Liu, C. X.; Liu, F. H.; Liu, Fang; Liu, Feng; Liu, H. B.; Liu, H. H.; Liu, H. M.; Liu, J.; Liu, J. P.; Liu, K.; Liu, K. Y.; Liu, P. L.; Liu, Q.; Liu, S. B.; Liu, X.; Liu, Y. B.; Liu, Z. A.; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H.; Lou, X. C.; Lu, G. R.; Lu, H. J.; Lu, H. L.; Lu, J. G.; Lu, X. R.; Lu, Y.; Lu, Y. P.; Luo, C. L.; Luo, M. X.; Luo, T.; Luo, X. L.; Lv, M.; Ma, F. C.; Ma, H. L.; Ma, Q. M.; Ma, S.; Ma, T.; Ma, X. Y.; Maas, F. E.; Maggiora, M.; Malik, Q. A.; Mao, Y. J.; Mao, Z. P.; Messchendorp, J. G.; Min, J.; Min, T. J.; Mitchell, R. E.; Mo, X. H.; Moeini, H.; Morales Morales, C.; Moriya, K.; Muchnoi, N. Yu.; Nefedov, Y.; Nikolaev, I. B.; Ning, Z.; Nisar, S.; Niu, X. Y.; Olsen, S. L.; Ouyang, Q.; Pacetti, S.; Pelizaeus, M.; Peng, H. P.; Peters, K.; Ping, J. L.; Ping, R. G.; Poling, R.; Prencipe, E.; Qi, M.; Qian, S.; Qiao, C. F.; Qin, L. Q.; Qin, X. S.; Qin, Y.; Qin, Z. H.; Qiu, J. F.; Rashid, K. H.; Redmer, C. F.; Ripka, M.; Rong, G.; Ruan, X. D.; Sarantsev, A.; Schoenning, K.; Schumann, S.; Shan, W.; Shao, M.; Shen, C. P.; Shen, X. Y.; Sheng, H. Y.; Shepherd, M. R.; Song, W. M.; Song, X. Y.; Spataro, S.; Spruck, B.; Sun, G. X.; Sun, J. F.; Sun, S. S.; Sun, Y. J.; Sun, Y. Z.; Sun, Z. J.; Sun, Z. T.; Tang, C. J.; Tang, X.; Tapan, I.; Thorndike, E. H.; Toth, D.; Ullrich, M.; Uman, I.; Varner, G. S.; Wang, B.; Wang, D.; Wang, D. Y.; Wang, K.; Wang, L. L.; Wang, L. S.; Wang, M.; Wang, P.; Wang, P. L.; Wang, Q. J.; Wang, S. G.; Wang, W.; Wang, X. F.; Wang, Y. D.; Wang, Y. F.; Wang, Y. Q.; Wang, Z.; Wang, Z. G.; Wang, Z. H.; Wang, Z. Y.; Wei, D. H.; Wei, J. B.; Weidenkaff, P.; Wen, S. P.; Werner, M.; Wiedner, U.; Wolke, M.; Wu, G. G.; Wu, L. H.; Wu, N.; Wu, W.; Wu, Z.; Xia, L. G.; Xia, Y.; Xiao, D.; Xiao, Z. J.; Xie, Y. G.; Xiu, Q. L.; Xu, G. F.; Xu, L.; Xu, Q. J.; Xu, Q. N.; Xu, X. P.; Xue, Z.; Yan, L.; Yan, W. B.; Yan, W. C.; Yan, Y. H.; Yang, H. X.; Yang, Y.; Yang, Y. X.; Ye, H.; Ye, M.; Ye, M. H.; Yu, B. X.; Yu, C. X.; Yu, H. W.; Yu, J. S.; Yu, S. P.; Yuan, C. Z.; Yuan, W. L.; Yuan, Y.; Zafar, A. A.; Zallo, A.; Zang, S. L.; Zeng, Y.; Zhang, B. X.; Zhang, B. Y.; Zhang, C.; Zhang, C. B.; Zhang, C. C.; Zhang, D. H.; Zhang, H. H.; Zhang, H. Y.; Zhang, J. J.; Zhang, J. L.; Zhang, J. Q.; Zhang, J. W.; Zhang, J. Y.; Zhang, J. Z.; Zhang, S. H.; Zhang, X. J.; Zhang, X. Y.; Zhang, Y.; Zhang, Y. H.; Zhang, Z. H.; Zhang, Z. P.; Zhang, Z. Y.; Zhao, G.; Zhao, J. W.; Zhao, Lei; Zhao, Ling; Zhao, M. G.; Zhao, Q.; Zhao, Q. W.; Zhao, S. J.; Zhao, T. C.; Zhao, X. H.; Zhao, Y. B.; Zhao, Z. G.; Zhemchugov, A.; Zheng, B.; Zheng, J. P.; Zheng, Y. H.; Zhong, B.; Zhou, L.; Zhou, Li; Zhou, X.; Zhou, X. K.; Zhou, X. R.; Zhou, X. Y.; Zhu, K.; Zhu, K. J.; Zhu, X. L.; Zhu, Y. C.; Zhu, Y. S.; Zhu, Z. A.; Zhuang, J.; Zou, B. S.; Zou, J. H.



Novel carbon-carbon bond formations for biocatalysis  

PubMed Central

Carbon–carbon bond formation is the key transformation in organic synthesis to set up the carbon backbone of organic molecules. However, only a limited number of enzymatic C–C bond forming reactions have been applied in biocatalytic organic synthesis. Recently, further name reactions have been accomplished for the first time employing enzymes on a preparative scale, for instance the Stetter and Pictet–Spengler reaction or oxidative C–C bond formation. Furthermore, novel enzymatic C–C bond forming reactions have been identified like benzylation of aromatics, intermolecular Diels-Alder or reductive coupling of carbon monoxide. PMID:21354781

Resch, Verena; Schrittwieser, Joerg H; Siirola, Elina; Kroutil, Wolfgang



A tandem in situ peptide cyclization through trifluoroacetic acid cleavage.  


We present a new approach for peptide cyclization during solid phase synthesis under highly acidic conditions. Our approach involves simultaneous in?situ deprotection, cyclization and trifluoroacetic acid (TFA) cleavage of the peptide, which is achieved by forming an amide bond between a lysine side chain and a succinic acid linker at the peptide N-terminus. The reaction proceeds via a highly active succinimide intermediate, which was isolated and characterized. The structure of a model cyclic peptide was solved by NMR spectroscopy. Theoretical calculations support the proposed mechanism of cyclization. Our new methodology is applicable for the formation of macrocycles in solid-phase synthesis of peptides and organic molecules. PMID:24827640

Chandra, Koushik; Roy, Tapta Kanchan; Shalev, Deborah E; Loyter, Abraham; Gilon, Chaim; Gerber, R Benny; Friedler, Assaf



Intermolecular interactions in the N?C C?C H dimer  

NASA Astrophysics Data System (ADS)

Ab initio calculations on N?C-C?C-H and its anti-parallel dimer are reported, with a view to studying the intermolecular interactions present. Following initial optimisation of the monomer at the MP2/6-311+G(d,p) level, the PES of the dimer corresponding to variations in chain separation and overlap was explored. Two minima on this surface were found, varying in their degree of overlap, but both having C 2 h symmetry. Topological charge density analysis shows these two arrangements to have qualitatively different structures. Atoms in Molecules decomposition shows the origin of the dimer stabilisation to lie in an increase in nitrogen's population and self-stabilisation.

Platts, James A.; Howard, Sean T.; Fallis, Ian. A.



Organometallics 1987, 6, 1301-1311 1301 Preparation, Dynamic Behavior, and C-H and C-C Cleavage  

E-print Network

of cyclopentadiene at 0 "C for short periods of time. Continued photolysis results in the formation of CpRe(PPh3)H4 cyclopentadiene and a rhenium phosphine polyhydride. After the discovery of ferrocene, a number of other cy- clopentadienyl derivativeswere synthesized from reactions of metals with cyclopentadiene. In several instances

Jones, William D.


Failure mechanisms in wood joints bonded with urea-formaldehyde adhesives  

Microsoft Academic Search

Wood joints bonded with urea-formaldehyde (UF) are weakened by cyclic swelling and shrinking. To study the failure mecha- nisms in UF-bonded joints, specimens were bonded with unmod- ified, modified (amine), or phenol formaldehyde adhesive and subjected to accelerated aging. Modification of the adhesive properties increased the cleavage fracture toughness and shear strength of bonded joints and improved the resistance of

B. H. River; R. O. Ebewele; G. E. Myers



Cleavage of ?-dicarbonyl compounds by terpene hydroperoxide.  


The highly reactive ?-dicarbonyl compounds, glyoxal, methylglyoxal (MGO), and 3-deoxyglucosone, react with the amino groups of proteins to form advanced glycation end-products (AGEs) which have been implicated in diabetic complications, aging, and Alzheimer's disease. We found that a test sample of terpinen-4-ol (T4) containing hydroperoxides showed cleaving activity toward an ?-dicarbonyl compound, but that the freshly isolated pure sample did not. Prepared terpinen-4-ol hydroperoxide (T4-H) also efficiently cleaved the C-C bond of the ?-dicarbonyl compounds via Baeyer-Villiger-like rearrangement and subsequent hydrolysis of an acid anhydride moiety in the rearranged product to give carboxylic acids. Other terpene hydroperoxides, as well as T4-H, showed significant cleaving activities, and all these hydroperoxides protected RNase A from the lowering of enzyme activity induced by MGO. The cleaving mechanism via Baeyer-Villiger-like rearrangement was confirmed by time-interval NMR measurements of the reaction mixture of the symmetrical ?-dicarbonyl compound, diacetyl with T4-H. PMID:23047102

Nagamatsu, Ryu-ichiro; Mitsuhashi, Shinya; Shigetomi, Kengo; Ubukata, Makoto



Structural basis of carotenoid cleavage: from bacteria to mammals.  


Carotenoids and their metabolic derivatives serve critical functions in both prokaryotic and eukaryotic cells, including pigmentation, photoprotection and photosynthesis as well as cell signaling. These organic compounds are also important for visual function in vertebrate and non-vertebrate organisms. Enzymatic transformations of carotenoids to various apocarotenoid products are catalyzed by a family of evolutionarily conserved, non-heme iron-containing enzymes named carotenoid cleavage oxygenases (CCOs). Studies have revealed that CCOs are critically involved in carotenoid homeostasis and essential for the health of organisms including humans. These enzymes typically display a high degree of regio- and stereo-selectivity, acting on specific positions of the polyene backbone located in their substrates. By oxidatively cleaving and/or isomerizing specific double bonds, CCOs generate a variety of apocarotenoid isomer products. Recent structural studies have helped illuminate the mechanisms by which CCOs mobilize their lipophilic substrates from biological membranes to perform their characteristic double bond cleavage and/or isomerization reactions. In this review, we aim to integrate structural and biochemical information about CCOs to provide insights into their catalytic mechanisms. PMID:23827316

Sui, Xuewu; Kiser, Philip D; Lintig, Johannes von; Palczewski, Krzysztof



An Unbiased Proteomic Screen Reveals Caspase Cleavage Is Positively and Negatively Regulated by Substrate Phosphorylation*  

PubMed Central

Post-translational modifications of proteins regulate diverse cellular functions, with mounting evidence suggesting that hierarchical cross-talk between distinct modifications may fine-tune cellular responses. For example, in apoptosis, caspases promote cell death via cleavage of key structural and enzymatic proteins that in some instances is inhibited by phosphorylation near the scissile bond. In this study, we systematically investigated how protein phosphorylation affects susceptibility to caspase cleavage using an N-terminomic strategy, namely, a modified terminal amino isotopic labeling of substrates (TAILS) workflow, to identify proteins for which caspase-catalyzed cleavage is modulated by phosphatase treatment. We validated the effects of phosphorylation on three of the identified proteins and found that Yap1 and Golgin-160 exhibit decreased cleavage when phosphorylated, whereas cleavage of MST3 was promoted by phosphorylation. Furthermore, using synthetic peptides we systematically examined the influence of phosphoserine throughout the entirety of caspase-3, -7, and -8 recognition motifs and observed a general inhibitory effect of phosphorylation even at residues considered outside the classical consensus motif. Overall, our work demonstrates a role for phosphorylation in controlling caspase-mediated cleavage and shows that N-terminomic strategies can be tailored to study cross-talk between phosphorylation and proteolysis. PMID:24556848

Turowec, Jacob P.; Zukowski, Stephanie A.; Knight, James D. R.; Smalley, David M.; Graves, Lee M.; Johnson, Gary L.; Li, Shawn S. C.; Lajoie, Gilles A.; Litchfield, David W.



Lysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism.  

PubMed Central

LexA repressor of Escherichia coli is inactivated in vivo by a specific cleavage reaction requiring activated RecA protein. In vitro, cleavage requires activated RecA at neutral pH and proceeds spontaneously at alkaline pH. These two cleavage reactions have similar specificities, suggesting that RecA acts indirectly to stimulate self-cleavage, rather than directly as a protease. We have studied the chemical mechanism of cleavage by using site-directed mutagenesis to change selected amino acid residues in LexA, chosen on the basis of kinetic data, homology to other cleavable repressors, and potential similarity of the mechanism to that of proteases. Serine-119 and lysine-156 were changed to alanine, a residue with an unreactive side chain, resulting in two mutant proteins that had normal repressor function and apparently normal structure, but were completely deficient in both types of cleavage reaction. Serine-119 was also changed to cysteine, another residue with a nucleophilic side chain, resulting in a protein that was cleaved at a significant rate. These and other observations suggest that hydrolysis of the scissile peptide bond proceeds by a mechanism similar to that of serine proteases, with serine-119 being a nucleophile and lysine-156 being an activator. Possible roles for RecA are discussed. Images PMID:3108885

Slilaty, S N; Little, J W



Formation and cleavage of aromatic disulfide radical anions.  


The electron transfer (ET) to a series of para-substituted diaryl disulfides, having the general formula (X-C(6)H(4)S-)(2), has been studied. The X groups were selected as to have a comprehensive variation of the substituent effect, being X = NH(2), MeO, H, F, Cl, CO(2)Et, CN, and NO(2). The reduction was carried out experimentally, using N,N-dimethylformamide as the solvent, and by molecular orbital (MO) ab initio calculations. The ET was studied heterogeneously, by voltammetric reduction and convolution analysis, and homogeneously, by using electrogenerated radical anions as the solution electron donors. The reduction is dissociative, leading to the cleavage of the S-S bond in a stepwise manner. Both experimental approaches led us to estimate the E degrees and the intrinsic barrier values for the formation of the radical anions. Comparison of the independently obtained results allowed obtaining, for the first time, a quantitative description of the correlation between heterogeneous and homogeneous rate constants of ETs associated with significant inner reorganization energy. The experimental outcome was fully supported by the theoretical calculations, which provided information about the disulfide lowest unoccupied MOs (LUMOs) and singly occupied MO (SOMO), the bond dissociation energies, and the most significant structural modifications associated with radical anion formation. With disulfides bearing electron-donating or mildly electron-withdrawing groups, the inner reorganization is particularly large, which reflects the significant stretching of the S-S bond experienced by the molecule upon ET. The process entails formation of loose radical anion species in which the SOMO is heavily localized, as the LUMO, onto the frangible bond. As a consequence of the formation of these sigma-radical anions, the S-S bond energy of the latter is rather small and the cleavage rate constant is very large. With electron-withdrawing groups, the extent of delocalization of the SOMO onto the aryl system increases, leading to a decrease of the reorganization energy for radical anion formation. Interestingly, while the LUMO now has pi character, the actual reduction intermediate (and thus the SOMO) is still a sigma-type radical anion. With the nitro-substituted disulfide, very limited inner reorganization is required and a pi-radical anion initially forms. A nondissociative type intramolecular ET then ensues, leading to the formation of a new radical anion whose antibonding orbital has similar features as those of the SOMO of the other diaryl disulfides. Therefore, independently of the substituent, the actual S-S bond cleavage occurs in a quite similar way along the series investigated. The S-S bond cleavage rate, however, tends to decrease as the Hammett sigma increases, which would be in keeping with an increase of both the electronic and solvent reorganization energies. PMID:14640668

Antonello, Sabrina; Daasbjerg, Kim; Jensen, Henrik; Taddei, Ferdinando; Maran, Flavio



Electron Transfer Dissociation (ETD) of Peptides Containing Intrachain Disulfide Bonds  

NASA Astrophysics Data System (ADS)

The fragmentation chemistry of peptides containing intrachain disulfide bonds was investigated under electron transfer dissociation (ETD) conditions. Fragments within the cyclic region of the peptide backbone due to intrachain disulfide bond formation were observed, including: c (odd electron), z (even electron), c-33 Da, z + 33 Da, c + 32 Da, and z-32 Da types of ions. The presence of these ions indicated cleavages both at the disulfide bond and the N-C? backbone from a single electron transfer event. Mechanistic studies supported a mechanism whereby the N-C? bond was cleaved first, and radical-driven reactions caused cleavage at either an S-S bond or an S-C bond within cysteinyl residues. Direct ETD at the disulfide linkage was also observed, correlating with signature loss of 33 Da (SH) from the charge-reduced peptide ions. Initial ETD cleavage at the disulfide bond was found to be promoted amongst peptides ions of lower charge states, while backbone fragmentation was more abundant for higher charge states. The capability of inducing both backbone and disulfide bond cleavages from ETD could be particularly useful for sequencing peptides containing intact intrachain disulfide bonds. ETD of the 13 peptides studied herein all showed substantial sequence coverage, accounting for 75%-100% of possible backbone fragmentation.

Cole, Scott R.; Ma, Xiaoxiao; Zhang, Xinrong; Xia, Yu



Electron transfer dissociation (ETD) of peptides containing intrachain disulfide bonds.  


The fragmentation chemistry of peptides containing intrachain disulfide bonds was investigated under electron transfer dissociation (ETD) conditions. Fragments within the cyclic region of the peptide backbone due to intrachain disulfide bond formation were observed, including: c (odd electron), z (even electron), c-33 Da, z+33 Da, c+32 Da, and z-32 Da types of ions. The presence of these ions indicated cleavages both at the disulfide bond and the N-C? backbone from a single electron transfer event. Mechanistic studies supported a mechanism whereby the N-C? bond was cleaved first, and radical-driven reactions caused cleavage at either an S-S bond or an S-C bond within cysteinyl residues. Direct ETD at the disulfide linkage was also observed, correlating with signature loss of 33 Da (SH) from the charge-reduced peptide ions. Initial ETD cleavage at the disulfide bond was found to be promoted amongst peptides ions of lower charge states, while backbone fragmentation was more abundant for higher charge states. The capability of inducing both backbone and disulfide bond cleavages from ETD could be particularly useful for sequencing peptides containing intact intrachain disulfide bonds. ETD of the 13 peptides studied herein all showed substantial sequence coverage, accounting for 75%-100% of possible backbone fragmentation. PMID:22161508

Cole, Scott R; Ma, Xiaoxiao; Zhang, Xinrong; Xia, Yu



A single operon-encoded form of the acetyl-CoA decarbonylase/synthase multienzyme complex responsible for synthesis and cleavage of acetyl-CoA in Methanosarcina thermophila.  


Methanogens growing on C-1 substrates synthesize 2-carbon acetyl groups in the form of acetyl-CoA for carbon assimilation using the multienzyme complex acetyl-CoA decarbonylase/synthase (ACDS) which contains five different subunits encoded within an operon. In species growing on acetate ACDS also functions to cleave the acetate C-C bond for energy production by methanogenesis. A number of species of Methanosarcina that are capable of growth on either C-1 compounds or acetate contain two separate ACDS operons, and questions have been raised about whether or not these operons play separate roles in acetate synthesis and cleavage. Methanosarcina thermophila genomic DNA was analyzed for the presence of two ACDS operons by PCR amplifications with different primer pairs, restriction enzyme analyses, DNA sequencing and Southern blot analyses. A single ACDS operon was identified and characterized, with no evidence for more than one. MALDI mass spectrometric analyses were carried out on ACDS preparations from methanol- and acetate-grown cells. Peptide fragmentation patterns showed that the same ACDS subunits were present regardless of growth conditions. The evidence indicates that a single form of ACDS is used both for acetate cleavage during growth on acetate and for acetate synthesis during growth on C-1 substrates. PMID:16044263

Grahame, David A; Gencic, Simonida; DeMoll, Edward



Modelling of c-C2H4O formation on grain surfaces  

NASA Astrophysics Data System (ADS)

Despite its potential reactivity due to ring strain, ethylene oxide (c-C2H4O) is a complex molecule that seems to be stable under the physical conditions of an interstellar dense core; indeed, it has been detected towards several high-mass star-forming regions with a column density of the order of 1013 cm-2. To date, its observational abundances cannot be reproduced by chemical models and this may be due to the significant contribution played by its chemistry on grain surfaces. Recently, Ward & Price have performed experiments in order to investigate the surface formation of ethylene oxide starting with oxygen atoms and ethylene ice as reactants. We present a chemical model which includes the most recent experimental results from Ward & Price on the formation of c-C2H4O. We study the influence of the physical parameters of dense cores on the abundances of c-C2H4O. We verify that ethylene oxide can indeed be formed during the cold phase (when the interstellar medium dense cores are formed), via addition of an oxygen atom across the C=C double bond of the ethylene molecule, and released by thermal desorption during the hot core phase. A qualitative comparison between our theoretical results and those from the observations shows that we are able to reproduce the abundances of ethylene oxide towards high-mass star-forming regions.

Occhiogrosso, A.; Viti, S.; Ward, M. D.; Price, S. D.



A large and accurate collection of peptidase cleavages in the MEROPS database  

PubMed Central

Peptidases are enzymes that hydrolyse peptide bonds in proteins and peptides. Peptidases are important in pathological conditions such as Alzheimer's disease, tumour and parasite invasion, and for processing viral polyproteins. The MEROPS database is an Internet resource containing information on peptidases, their substrates and inhibitors. The database now includes details of cleavage positions in substrates, both physiological and non-physiological, natural and synthetic. There are 39 118 cleavages in the collection; including 34 606 from a total of 10 513 different proteins and 2677 cleavages in synthetic substrates. The number of cleavages designated as ‘physiological’ is 13 307. The data are derived from 6095 publications. At least one substrate cleavage is known for 45% of the 2415 different peptidases recognized in the MEROPS database. The website now has three new displays: two showing peptidase specificity as a logo and a frequency matrix, the third showing a dynamically generated alignment between each protein substrate and its most closely related homologues. Many of the proteins described in the literature as peptidase substrates have been studied only in vitro. On the assumption that a physiologically relevant cleavage site would be conserved between species, the conservation of every site in terms of peptidase preference has been examined and a number have been identified that are not conserved. There are a number of cogent reasons why a site might not be conserved. Each poorly conserved site has been examined and a reason postulated. Some sites are identified that are very poorly conserved where cleavage is more likely to be fortuitous than of physiological relevance. This data-set is freely available via the Internet and is a useful training set for algorithms to predict substrates for peptidases and cleavage positions within those substrates. The data may also be useful for the design of inhibitors and for engineering novel specificities into peptidases. Database URL: PMID:20157488



Copper(II)-catalyzed disulfide scission--stepwise aerobic oxidative cleavage to sulfinate and sulfonate and reductive anaerobic cleavage to thiols.  


The Cu(II)-catalyzed oxidative and reductive cleavage of the disulfide bond of N-(2-(2-(2-picolinamido)phenyl)disulfanyl)phenyl)picolinamide, L, is reported for the first time. Aerobic oxidation with Cu(II) gives complete oxidation of S-S bond to sulfonates, whereas Ag(I) gives only partial oxidation up to sulfinates, in the absence of any other oxidizing agent, in tetrahydrofuran/water solution. The in situ generated sulfonate product forms a thermally stable, two-dimensional H-bonded polymeric complex with Cu(II) ions in two polymorphic forms. L in the presence of Cu(II), in an inert atmosphere, results in a reductive cleavage of the disulfide bond and an in situ formation of a new C-S bond. The latter forms a unique tetranuclear complex with Cu(II) employing deprotonated amide groups and bridging thiol and chloride atoms. The disulfide precursor and the products were characterized by X-ray crystallography and spectroscopic techniques. PMID:24979501

Lumb, Isha; Hundal, Maninder Singh; Hundal, Geeta



Selective Inhibition of Carotenoid Cleavage Dioxygenases  

PubMed Central

Members of the carotenoid cleavage dioxygenase family catalyze the oxidative cleavage of carotenoids at various chain positions, leading to the formation of a wide range of apocarotenoid signaling molecules. To explore the functions of this diverse enzyme family, we have used a chemical genetic approach to design selective inhibitors for different classes of carotenoid cleavage dioxygenase. A set of 18 arylalkyl-hydroxamic acids was synthesized in which the distance between an iron-chelating hydroxamic acid and an aromatic ring was varied; these compounds were screened as inhibitors of four different enzyme classes, either in vitro or in vivo. Potent inhibitors were found that selectively inhibited enzymes that cleave carotenoids at the 9,10 position; 50% inhibition was achieved at submicromolar concentrations. Application of certain inhibitors at 100 ?m to Arabidopsis node explants or whole plants led to increased shoot branching, consistent with inhibition of 9,10-cleavage. PMID:19098002

Sergeant, Martin J.; Li, Jian-Jun; Fox, Christine; Brookbank, Nicola; Rea, Dean; Bugg, Timothy D. H.; Thompson, Andrew J.



Dissociation Channels of c-C4F8 to CF2 Radical in Reactive Plasma  

NASA Astrophysics Data System (ADS)

It has been generally assumed that octafluorocyclobutane (c-C4F8) is mainly decomposed to CF2 via C2F4 in etching process plasma. However, the detailed mechanism for the dissociations is yet ambiguous. In this paper we have calculated the probable dissociation pathways by using ab initio molecular orbital method. The results show that c-C4F8 is dissociated via the first triplet excited state T1(3A2), the fourth triplet excited state T4(32E) and the fourth singlet excited state S4(12E). One of the degenerate excited states of T4 and S4 is constituted by antibonding combination of two ? bonding orbital of C2F4. T1 state is constituted by antibonding combination of b1u antibonding ? orbital of C2F4. Therefore, in the case of the dissociation via S4 and T4 excited states c-C4F8 may dissociate to two C2F4, and in the case of the dissociation via T1 excited state c-C4F8 may dissociate to four CF2 radicals. It is also found that C3F5+ ion observed as the main peak in c-C4F8 process plasma is produced by electron collision with the slightly larger energy than the ionization threshold value. The main dissociation path of C2F4 is a vertical electron attachment. However, it is also found that dissociation pathways via 1B2g, 3B1u, and 3B2g excited states are very important and should not be ignored.

Hayashi, Toshio; Ishikawa, Kenji; Sekine, Makoto; Hori, Masaru; Kono, Akihiro; Suu, Koukou



A new paradigm for enzymatic control of ?-cleavage and ?-cleavage of the prion protein.  


The cellular form of the prion protein (PrP(C)) is found in both full-length and several different cleaved forms in vivo. Although the precise functions of the PrP(C) proteolytic products are not known, cleavage between the unstructured N-terminal domain and the structured C-terminal domain at Lys-109?His-110 (mouse sequence), termed ?-cleavage, has been shown to produce the anti-apoptotic N1 and the scrapie-resistant C1 peptide fragments. ?-Cleavage, residing adjacent to the octarepeat domain and N-terminal to the ?-cleavage site, is thought to arise from the action of reactive oxygen species produced from redox cycling of coordinated copper. We sought to elucidate the role of key members of the ADAM (a disintegrin and metalloproteinase) enzyme family, as well as Cu(2+) redox cycling, in recombinant mouse PrP (MoPrP) cleavage through LC/MS analysis. Our findings show that although Cu(2+) redox-generated reactive oxygen species do produce fragmentation corresponding to ?-cleavage, ADAM8 also cleaves MoPrP in the octarepeat domain in a Cu(2+)- and Zn(2+)-dependent manner. Additional cleavage by ADAM8 was observed at the previously proposed location of ?-cleavage, Lys-109?His-110 (MoPrP sequencing); however, upon addition of Cu(2+), the location of ?-cleavage shifted by several amino acids toward the C terminus. ADAM10 and ADAM17 have also been implicated in ?-cleavage at Lys-109?His-110; however, we observed that they instead cleaved MoPrP at a novel location, Ala-119?Val-120, with additional cleavage by ADAM10 at Gly-227?Arg-228 near the C terminus. Together, our results show that MoPrP cleavage is far more complex than previously thought and suggest a mechanism by which PrP(C) fragmentation responds to Cu(2+) and Zn(2+). PMID:24247244

McDonald, Alex J; Dibble, Jessie P; Evans, Eric G B; Millhauser, Glenn L



Promiscuous esterase activities of the C-C hydrolases from Dyella ginsengisoli.  


A C-C hydrolase gene (bphD(LA-4)) from strain Dyella ginsengisoli LA-4 was cloned and expressed in Escherichia coli BL21 (DE3). BphD(LA-4) together with another hydrolase MfphA(LA-4), which derived from the same strain, possessed esterase activities. p-Nitrophenyl butyrate was the best substrate for both enzymes. BphD(LA-4) had high catalytic efficiency to p-nitrophenyl benzoate, whereas MfphA(LA-4) had no activity. Homology modeling and docking studies demonstrated that the proper hydrogen bond interaction was important for the reactivity of specific substrate. PMID:22361962

Zhou, Hao; Qu, Yuanyuan; Kong, Chunlei; Wu, Yingge; Zhu, Kang; Yang, Jie; Zhou, Jiti



Control of blood proteins by functional disulfide bonds  

PubMed Central

Most proteins in nature are chemically modified after they are made to control how, when, and where they function. The 3 core features of proteins are posttranslationally modified: amino acid side chains can be modified, peptide bonds can be cleaved or isomerized, and disulfide bonds can be cleaved. Cleavage of peptide bonds is a major mechanism of protein control in the circulation, as exemplified by activation of the blood coagulation and complement zymogens. Cleavage of disulfide bonds is emerging as another important mechanism of protein control in the circulation. Recent advances in our understanding of control of soluble blood proteins and blood cell receptors by functional disulfide bonds is discussed as is how these bonds are being identified and studied. PMID:24523239

Butera, Diego; Cook, Kristina M.; Chiu, Joyce; Wong, Jason W. H.



Directed protein replacement in recombination full sites reveals trans-horizontal DNA cleavage by Flp recombinase.  

PubMed Central

One round of site-specific recombination between two DNA partners mediated by the Flp recombinase requires the breakage and reformation of four phosphodiester bonds. The reaction is accomplished by the combined action of four Flp monomers. Within the recombination complex, what is the relative disposition of a Flp monomer with respect to the target diester that it cleaves? To address this question, we have devised a strategy for the targeted orientation of Flp monomers within full-site recombination substrates. Our experimental design is not dependent on 'altered binding specificity' of the recombinase. Analysis of the pattern of DNA cleavage by this method reveals no evidence for DNA cleavage in cis. A Flp monomer bound to its recognition element within the full site does not cleave the scissile phosphodiester bond adjacent to it. Our results are most consistent with 'trans-horizontal cleavage'. Cleavage by Flp occurs at the scissile phosphodiester distal to it, but within the same full site. The general experimental design employed here will be of widespread utility in mechanistic analyses of nucleic acid transactions involving multimeric DNA-protein assemblies. Images PMID:7957100

Lee, J; Whang, I; Lee, J; Jayaram, M



Cleavage kinetics and anchor linked intermediates in solid phase peptide amide synthesis.  


Kinetics and cleavage conditions of peptide amide synthesis were studied using the anchor molecules 5-(4'-aminomethyl-3',5'-dimethoxyphenoxy)valeric acid (4-ADPV-OH) and 5-(2'-aminomethyl-3'-5'-dimethoxyphenoxy) valeric acid (2-ADPV-OH). Unexpectedly the anchor amide alanyl-4-ADPV-NH2 was isolated and characterized as an intermediate during the cleavage with trifluoroacetic acid (TFA) of alanyl-4-ADPV-alanyl-aminomethyl-polystyrene to yield the alanine amide. As a matter of fact the NH--CH alpha bond of the alanyl spacer has to be cleaved to form this intermediate. Using TFA-dichloromethane (1:9) alanyl-4-ADPV-NH2 was obtained as a cleavage product in 50% yield within 60 min, whereas the isomeric alanyl-2-ADPV-NH2 was formed more slowly under these mild conditions. At high TFA concentration no difference between the 2- and 4-ADPV anchor was observed in the rate of formation of the free alanine amide. The presence of tryptophan amide in the cleavage mixture resulted in an anchor alkylated tryptophan amide, which remains stable in acidic solution but disappears rapidly in the presence of the resin. A low TFA/high TFA cleavage procedure is recommended for peptide amid synthesis applying the ADPV anchor. PMID:1783490

Dürr, H; Beck-Sickinger, A G; Schnorrenberg, G; Rapp, W; Jung, G



Unexpected relationship between interlayer distances and surface/cleavage energies in ?-TiAl: density functional study.  


Density functional calculations were performed to study the ?-TiAl (001), (100), (110) and (111) surfaces. The (100) surface is the most stable under Ti-rich conditions, while the Al-termination (110) surface becomes the most stable with the increase of Al chemical potential. We calculate that in ?-TiAl intermetallic compound the larger the interlayer distance, the larger the surface energy and cleavage energy. This is different from the situation in a pure metal. This phenomenon can be explained by the analysis of the bonding characteristics in ?-TiAl. In particular there are both metallic and covalent bonds in ?-TiAl, and the strongest covalent bonds mainly focus on the center of three Ti-Al-Ti atoms. It is the covalent bonds that affect greatly the cleavage energy, the surface energy and the surface stability. PMID:21673399

Wang, Lu; Shang, Jia-Xiang; Wang, Fu-He; Zhang, Yue; Chroneos, Alexander



OH-induced oxidative cleavage of dimethyl disulfide in the presence of NO.  


We report the results of the theoretical study of (•)OH-induced oxidative cleavage of dimethyl disulfide (DMDS) and the experimental study of the CH3SSCH3 + (•)OH reaction in the presence of (•)NO. Infrared low temperature argon matrix studies combined with ab initio calculations allowed us to identify cis-CH3SONO, which evidences the formation of the CH3SO(•) and CH3SH molecules in the course of the CH3SSCH3 + (•)OH reaction. Ab initio/quantum chemical topology calculations revealed details of the oxidative cleavage of dimethyl disulfide, which is a complex multistep process involving an alteration of S-O and S-S covalent bonds as well as a hydrogen atom transfer. The ability of delocalization of the unpaired electron density by sulfur atoms and a formation of a hydrogen bond by CH3SO(•) and CH3SH are the factors which seem to explain antiradical properties of DMDS. PMID:23947660

Bil, Andrzej; Grzechnik, Katarzyna; Mierzwicki, Krzysztof; Mielke, Zofia



Synthesis of tertiary alkyl fluoride centers by asymmetric C?C(F) bond formation  

Microsoft Academic Search

Asymmetric alkylation of pseudoephedrine ?-fluoropropionamide (1) affords ?-alkylated products efficiently and with excellent stereocontrol at the newly formed tertiary alkyl fluoride center. Mild alkaline hydrolysis of the products provides the corresponding carboxylic acids with high enantiomeric excess.

Andrew G. Myers; Lydia McKinstry; James L. Gleason



Total Synthesis of 6-Deoxyerythronolide B via C-C Bond-Forming Transfer Hydrogenation  

PubMed Central

The 14-membered macrolide 6-deoxyerythronolide B is prepared in 14 steps (longest linear sequence) and 20 total steps. Two different methods for alcohol CH-crotylation via transfer hydrogenation are deployed for the first time in target-oriented synthesis. Enyne metathesis is used to form the 14-membered ring. The present approach represents the most concise construction of any erythronolide reported, to date. PMID:23464668

Gao, Xin; Woo, Sang Kook; Krische, Michael J.



In Pursuit of an Ideal C-C Bond-Forming Reaction  

PubMed Central

Attempts to introduce the highly versatile vinyl group into other organic molecules in a chemo-, regio- and stereoselective fashion via catalytic activation of ethylene provided challenging opportunities to explore new ligand and salt effects in homogeneous catalysis. This review provides a personal account of the development of enantioselective reactions involving ethylene. PMID:19606231

RajanBabu, T. V.



Phosphaannulation by palladium-catalyzed carbonylation of C-H bonds of phosphonic and phosphinic acids.  


An efficient phosphaannulation by Pd-catalyzed carbonylation of C-H bonds of phosphonic and phosphinic acids for the synthesis of oxaphosphorinanone oxides is reported. These compounds are novel phosphorus heterocyclic scaffolds, thus opening a new avenue to sequential C-C/C-O bond formation in one pot. PMID:24856076

Shin, Seohyun; Jeong, Yeonseok; Jeon, Woo Hyung; Lee, Phil Ho



The Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix Provides a Rationale for the Sequential Cleavage Mechanism of ?-Secretase  

PubMed Central

The etiology of Alzheimer’s disease depends on the relative abundance of different amyloid-? (A?) peptide species. These peptides are produced by sequential proteolytic cleavage within the transmembrane helix of the 99 residue C-terminal fragment of the amyloid precursor protein (C99) by the intramembrane protease ?-secretase. Intramembrane proteolysis is thought to require local unfolding of the substrate helix, which has been proposed to be cleaved as a homodimer. Here, we investigated the backbone dynamics of the substrate helix. Amide exchange experiments of monomeric recombinant C99 and of synthetic transmembrane domain peptides reveal that the N-terminal Gly-rich homodimerization domain exchanges much faster than the C-terminal cleavage region. MD simulations corroborate the differential backbone dynamics, indicate a bending motion at a di-glycine motif connecting dimerization and cleavage regions, and detect significantly different H-bond stabilities at the initial cleavage sites. Our results are consistent with the following hypotheses about cleavage of the substrate. First, the GlyGly hinge may precisely position the substrate within ?-secretase such that its catalytic center must start proteolysis at the known initial cleavage sites. Second, the ratio of cleavage products formed by subsequent sequential proteolysis could be influenced by differential extents of solvation and by the stabilities of H-bonds at alternate initial sites. Third, the flexibility of the Gly-rich domain may facilitate substrate movement within the enzyme during sequential proteolysis. Fourth, dimerization may affect substrate processing by decreasing the dynamics of the dimerization region and by increasing that of the C-terminal part of the cleavage region. PMID:23265086

Pester, Oxana; Barrett, Paul J.; Hornburg, Daniel; Hornburg, Philipp; Probstle, Rasmus; Widmaier, Simon; Kutzner, Christoph; Durrbaum, Milena; Kapurniotu, Aphrodite; Sanders, Charles R.; Scharnagl, Christina; Langosch, Dieter



Class 5, fertilization and onset of cleavage September 23, 2009 Fertilization and Cleavage: the start of making a new organism  

E-print Network

Class 5, fertilization and onset of cleavage September 23, 2009 1 Fertilization and Cleavage, fertilization and onset of cleavage September 23, 2009 2 7.4 Structure of the sea urchin egg at fertilization, fertilization and onset of cleavage September 23, 2009 3 7.11 The acrosome reaction in sea urchin sperm 7

Devoto, Stephen H.


Changing cleavage structure in new democracies: An empirical analysis of political cleavages in Korea  

Microsoft Academic Search

Cleavage structure cuts across the members of a state and affects the electorate's choice of parties and candidates. Social cleavage structure can be stable or go through changes depending on on-going social change as well as political parties' electoral strategies. With the collapse of communism and the advent of the third wave of democracy, many countries in Eastern Europe, Latin

HeeMin Kim; Jun Young Choi; Jinman Cho



Structural basis of carotenoid cleavage: From bacteria to mammals Xuewu Sui, Philip D. Kiser, Johannes von Lintig, Krzysztof Palczewski  

E-print Network

for the health of organisms including humans. These enzymes typically display a high degree of regio- and ste bond cleavage and/or isomerization reactions. In this review, we aim to integrate structural.). Such coloring improves the chance of reproductive success by attracting insects to disperse pollen in plants

Palczewski, Krzysztof


Nanomechanical cleavage of molybdenum disulphide atomic layers.  


The discovery of two-dimensional materials became possible due to the mechanical cleavage technique. Despite its simplicity, the as-cleaved materials demonstrated surprising macro-continuity, high crystalline quality and extraordinary mechanical and electrical properties that triggered global research interest. Here such cleavage processes and associated mechanical behaviours are investigated by a direct in situ transmission electron microscopy probing technique, using atomically thin molybdenum disulphide layers as a model material. Our technique demonstrates layer number selective cleavage, from a monolayer to double layer and up to 23 atomic layers. In situ observations combined with molecular dynamics simulations reveal unique layer-dependent bending behaviours, from spontaneous rippling (<5 atomic layers) to homogeneous curving (~ 10 layers) and finally to kinking (20 or more layers), depending on the competition of strain energy and interfacial energy. PMID:24698887

Tang, Dai-Ming; Kvashnin, Dmitry G; Najmaei, Sina; Bando, Yoshio; Kimoto, Koji; Koskinen, Pekka; Ajayan, Pulickel M; Yakobson, Boris I; Sorokin, Pavel B; Lou, Jun; Golberg, Dmitri



Kinetic analysis of delta ribozyme cleavage.  


The ability of delta ribozyme to catalyze the cleavage of an 11-mer RNA substrate was examined under both single- and multiple-turnover conditions. In both cases only small differences in the kinetic parameters were observed in the presence of either magnesium or calcium as cofactor. Under multiple-turnover conditions, the catalytic efficiency of the ribozyme (kcat/KM) was higher at 37 degreesC than at 56 degreesC. The cleavage reaction seems to be limited by the product release step at 37 degreesC and by the chemical cleavage step at 56 degreesC. We observed substrate inhibition at high concentrations of the 11-mer substrate. Cleavage rate constants were determined with a structural derivative characterized by an ultrastable L4 tetraloop. The kinetic parameters (kcat and KM) and dissociation constant (Kd) were almost identical for both ribozymes, suggesting that the stability of the L4 loop has a negligible impact on the catalytic activities of the examined ribozymes. Various cleavage inhibition and gel-shift assays with analogues, substrate, and both active and inactive ribozymes were performed. The 2'-hydroxyl group adjacent to the scissile phosphate was shown to be involved in binding with the ribozyme, while the essential cytosine residue of the J4/2 junction was shown to contribute to substrate association. We clearly show that substrate binding to the delta ribozyme is not restricted to the formation of a helix located downstream of the cleavage site. Using these results, we postulate a kinetic pathway involving a conformational transition step essential for the formation of the active ribozyme/substrate complex. PMID:9836591

Mercure, S; Lafontaine, D; Ananvoranich, S; Perreault, J P



Identification of an acyl-enzyme intermediate in a meta-cleavage product hydrolase reveals the versatility of the catalytic triad.  


Meta-cleavage product (MCP) hydrolases are members of the ?/?-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 Å resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of (18)O into the benzoate produced during hydrolysis in H(2)(18)O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ES(red), previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad. PMID:22339283

Ruzzini, Antonio C; Ghosh, Subhangi; Horsman, Geoff P; Foster, Leonard J; Bolin, Jeffrey T; Eltis, Lindsay D



Photochemical DNA Cleavage by the Antitumor Agent  

E-print Network

provided evidence that 2 undergoes frag- mentation to yield the potent DNA-damaging agent hydroxyl radicalPhotochemical DNA Cleavage by the Antitumor Agent 3-Amino-1,2,4-benzotriazine 1,4-Dioxide to derive its therapeutic activity by selectively damaging DNA in oxygen-poor (hypoxic) tumor cells.1,2 DNA

Gates, Kent. S.


Cleavage oriented iron single crystal fracture toughness  

NASA Astrophysics Data System (ADS)

Fundamental understanding of atomic level mechanisms controlling cleavage fracture in bcc metals, and the corresponding brittle to ductile transition (BDT) has been a long sought, 'grand challenge' of science. This is particularly true for the BDT in Fe, which is among vital elements that underpin our technological civilization. A key obstacle to developing an understanding of the BDT in Fe is the absence of a reliable database on the temperature dependence of toughness in Fe. In ferritic alloys, the micro-arrest toughness of ferrite, Kmu(T), is hypothesized to control macroscopic cleavage. As a surrogate for Kmu(T), special techniques were developed to measure the arrest toughness, Ka(T), for cleavage oriented, Fe single crystals. Further, the mechanisms controlling cleavage and the BDT should be reflected in the loading rate dependence of static-dynamic initiation toughness, K Ic and KId. Thus KIc/d(T) were also measured for K-rate from 10-1 to 104 MPa?m/s. These studies led to the following conclusions: (1) Ka is semi-brittle, increasing from an average of ? 3.5 MPa?m at -196°C to ? 9 MPa?m at 0°C. (2) The (100) Ka are similar in the [010] and [011] and orientations, but cleavage does not occur on (110) planes. (3) The Ka for unalloyed Fe is about 150°C lower than that for Fe-3wt%Si, suggesting that equivalent Ka may occur at equivalent lattice sigmay. (4) Higher K-rate shift K Ic/d(T) curves to higher T. (5) The shifts of the KIc/d(T) and Ka(T) curves can be understood and modeled based on dislocation dynamics concepts for the glide of screw dislocations with a stress (and T) controlled activation energy, Ea, with a maximum value of about ? 0.5 eV. (6) This Ea is consistent with a double kink nucleation mechanism. Etch pit, slip trace and ledge patterns on side, fracture and sectioned surfaces of the crystals were characterized to study dislocation activity associated with cleavage and the BDT. The results showed extensive dislocation activity on {110}<111> and {211}<111> slip systems. Consistent with its semi-brittle nature, there is evidence of significant dislocation glide and multiplication during cleavage, perhaps associated with pre-existing dislocations.

Hribernik, Michael Louis


Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages  

PubMed Central

This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MALDI-TOF and LC-ESI-MS to identify the peptide products. RNase A and B each contain four disulfide bonds, and the addition of a reducing reagent, such as dithiothreitol, was found to be required to achieve efficient acidic proteolysis. The linkage of the glycosidic group to the asparagine side-chain in ribonuclease B was found not to be cleaved by brief microwave treatment in 12.5 % acetic acid. The distribution of the heterogeneous carbohydrate side chain in the glycopeptide products of acid cleavage was compared to that of the glycopeptide products of tryptic digestion. Hydrolysis within the carbohydrate chain itself is minimal under the conditions used. The O-linked side-chain on alpha crystalline A was found to be cleaved during acid cleavage of the protein. PMID:19956338

Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine



One-Electron-Transfer Reactions of Polychlorinated Ethylenes: Concerted and Stepwise Cleavages  

SciTech Connect

Reaction barriers were calculated by using ab initio electronic structure methods for the reductive dechlorination of the polychlorinated ethylenes: C2CL4, C2Cl4, C2HCl3, trans-1,2-C2H2Cl2, cis-1,2-C2H2Cl2, 1,1-C2H2Cl2, and C2HCl3. Concerted and stepwise cleavages of R-Cl bonds were considered. Stepwise cleavages yielded lower activation barriers than concerted cleavages for the reduction of C2Cl4, C2HCl3, and trans-1,2-C2H2Cl2 via strong reducing agents. However, for typical ranges of reducing strength concerted cleavages were found to be favored. Both gas-phase and aqueous-phase calculations predicted C2Cl4 to have the lowest reaction barrier. Additionally, the reduction of C2HCl3 was predicted to have a significant amount of selectivity of cis-1,2-C2HCl2 over the corresponding reactions leading to the trans-1,2-C2HCl2, and 1,1-C2HCl2 radicals. These results illustrate how ab initio electronic structure methods, by providing experimentally inaccessible thermodynamics properties and activation energies, are able to sort out possible reactions mechanisms of reactions that have broad relevance in environmental chemistry.

Bylaska, Eric J.; Dupuis, Michel; Tratnyek, Paul G.



DNA cleavage induced by antitumor antibiotic leinamycin and its biological consequences  

PubMed Central

The natural product leinamycin has been found to produce abasic sites in duplex DNA through the hydrolysis of the glycosidic bond of guanine residues modified by this drug. In the present study, using a synthetic oligonucleotide duplex, we demonstrate spontaneous DNA strand cleavage at leinamycin-induced abasic sites through a -elimination reaction. However, methoxyamine modification of leinamycin-induced abasic sites was found to be refractory to the spontaneous -elimination reaction. Furthermore, this complex was even resistant to the -elimination reaction with hot piperidine treatment. Bleomycin and methyl methanesulfonate also induced strand cleavage in a synthetic oligonucleotide duplex even without thermal treatment. However, methoxyamine has a negligible effect on DNA strand cleavage induced by both drugs, suggesting that the mechanism of DNA cleavage induced by leinamycin might be different from those induced by bleomycin or methyl methanesulfonate. In this study, we also assessed the cytotoxicity of leinamycin against a collection of mammalian cell lines defective in various repair pathways. The mammalian cell line defective in the nucleotide excision repair (NER) or base excision repair (BER) pathways was about 3 to 5 times more sensitive to leinamycin as compared to the parental cell line. In contrast, the radiosensitive mutant xrs-5 cell line deficient in V(D)J recombination showed similar sensitivity towards leinamycin compared to the parental cell line. Collectively, our findings suggest that both NER and BER pathways play an important role in the repair of DNA damage caused by leinamycin. PMID:22682923

Viswesh, Velliyur; Hays, Allison M.; Gates, Kent; Sun, Daekyu



Thermodynamic properties of carbon in b.c.c. and f.c.c. iron-silicon-carbon solid solutions.  

NASA Technical Reports Server (NTRS)

The equilibrium between hydrogen-methane gas mixtures and Fe-Si-C solid solutions has been investigated both as a function of temperature and carburizing gas composition. The thermodynamic properties of the carbon atoms in both b.c.c. and f.c.c. solid solution have been derived from the equilibrium measurements. The results found have been compared with those of earlier investigations and with the predictions of recent theoretical models on ternary solid solutions containing both substitutional and interstitial solute atoms.

Chraska, P.; Mclellan, R. B.



Photonics Integration for THz Generation , C.C. Renaud  

E-print Network

Photonics Integration for THz Generation F. Pozzi , C.C. Renaud , D.C. Rogers , I.F. Lealman. The concept of a photonic THz generator is introduced, focusing on the optical part of the phase locking section of the photonic system. Different approaches to the integration of this element of the THz source

Haddadi, Hamed


Enhancing Security Check in Visual Studio C\\/C++ Compiler  

Microsoft Academic Search

Buffer overflow exploitation is a major threat to software security. To reduce the threat, Visual studio C\\/C++compiler enables to randomize the addresses of the compiled program in initialization time, and to embed security stack guards by the compiled program in run time. The present paper upgrades the compiler by increasing the compiled program's capabilities in the following aspects: (1) protects

Yongdong Wu



Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII.  

PubMed Central

Each of four possible sets of mismatches (G.A/C.T, C.C/G.G, A.A/T.T, and C.A/G.T) containing the 8 possible single-base-pair mismatches derived from isolated mutations were examined to test the ability of T4 endonuclease VII to consistently detect mismatches in heteroduplexes. At least two examples of each set of mismatches were studied for cleavage in the complementary pairs of heteroduplexes formed between normal and mutant DNA. Four deletion mutations were also included in this study. The various PCR-derived products used in the formation of heteroduplexes ranged from 133 to 1502 bp. At least one example of each set showed cleavage of at least one strand containing a mismatch. Cleavage of at least one strand of the pairs of heteroduplexes occurred in 17 of the 18 known single-base-pair mutations tested, with an A.A/T.T set not being cleaved in any mismatched strand. We propose that this method may be effective in detecting and positioning almost all mutational changes when DNA is screened for mutations. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:7816853

Youil, R; Kemper, B W; Cotton, R G



Catalytic C-CN bond activation.  


Synthetic organic reactions through C-CN activation by transition metal catalysis are reviewed. C-CN bond activation by metal complexes proceeds mainly via two pathways; oxidative addition and C-CN cleavage accompanied by silylisonitrile formation. Both the elemental reactions have been successfully applied to the catalytic reactions, including hydrodecyanation of nitriles, cross-coupling using nitriles as electrophiles, cyanation of aryl halides and arenes using organic nitriles as cyanating agents, and carbocyanation of unsaturated compounds. PMID:24549840

Nakao, Yoshiaki




E-print Network

CLEAVAGE FRACTURE MICROMECHANISMS RELATED TO WPS EFFECT IN RPV STEEL S. R. Bordet1 , B. Tanguy1 , S by warm pre-stress (WPS) on the cleavage fracture micromechanisms of a 18MND5 (A533B) reactor pressure, and a change in the cleavage fracture micromechanisms induced by plastic deformation. While all these factors

Boyer, Edmond


Failure mechanisms in wood joints bonded with urea-formaldehyde adhesives  

Microsoft Academic Search

Wood joints bonded with urea-formaldehyde (UF) are weakened by cyclic swelling and shrinking. To study the failure mechanisms\\u000a in UF-bonded joints, specimens were bonded with unmodified, modified (amine), or phenol formaldehyde adhesive and subjected\\u000a to accelerated aging. Modification of the adhesive properties increased the cleavage fracture toughness and shear strength\\u000a of bonded joints and improved the resistance of joints to

B. H. River; R. O. Ebewele; G. E. Myers



On the Relative Merits of Non-Orthogonal and Orthogonal Valence Bond Methods Illustrated on the Hydrogen Molecule  

ERIC Educational Resources Information Center

Valence bond (VB) is one of the cornerstone theories of quantum chemistry. Even if in practical applications the molecular orbital (MO) approach has obtained more attention, some basic chemical concepts (such as the nature of the chemical bond and the failure of the single determinant-based MO methods in describing the bond cleavage) are normally…

Angeli, Celestino; Cimiraglia, Renzo; Malrieu, Jean-Paul



Regulation of APP cleavage by ?-, ?- and ?-secretases  

Microsoft Academic Search

Proteolytic cleavage of the amyloid protein from the amyloid protein precursor (APP) by APP secretases is a key event in Alzheimer’s disease (AD) pathogenesis. ?-Secretases cleave APP within the amyloid sequences, whereas ?- and ?-secretases cleave on the N- and C-terminal ends respectively. The transmembrane aspartyl protease BACE has been identified as ?-secretase and several proteases (ADAM-10, TACE, PC7) may

Janelle Nunan; David H Small



Theoretical study of the bond dissociation energies of methanol  

NASA Technical Reports Server (NTRS)

A theoretical study of the bond dissociation energies for H2O and CH3OH is presented. The C-H and O-H bond energies are computed accurately with the modified coupled-pair functional method using a large basis set. For these bonds, an accuracy of +/- 2 kcal/mol is achieved, which is consistent with the C-H and C-C single bond energies of other molecules. The C-O bond is much more difficult to compute accurately because it requires higher levels of correlation treatment and more extensive one-particle basis sets.

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Walch, Stephen P.



Modulation of ascorbic acid-induced DNA cleavage by polyamide: cleavage manner, kinetics and mechanism.  


Manipulation of DNA presents a great interest in biotechnology and therapeutics. The molecules that damage DNA selectively offer new prospects for controlled manipulation of DNA. The conjugations of DNA-code reading molecules such as polyamides to reagents that induce DNA damages provide an approach to reach this goal. In this work, a new compound which contained polyamide and ascorbic acid conjugated by flexible linker (polyamide-Vc), was successfully synthesized, characterized, and evaluated as DNA cleavage agent, compared with that by using ascorbic acid molecule. The kinetics data showed that polyamide-Vc successfully promoted the cleavage of plasmid DNA, with k(max) of 0.314 h(-1) and K(d) of 0.105 mM. The evaluation of DNA linearization elicited that the activity of cleaving double-strand in the supercoiled pUC18 plasmid DNA by polyamide-Vc was enhanced remarkably, achieving n1/n2 ratio of 13.9 at 1.2 mM for 1 h. The introduction of polyamide to Vc could also partially weaken the inhibition of hydrogen radical to double-strand cleavage process because of its good binding activity to DNA. We anticipate that this work could provide a method for improving the efficiency of double-strand cleavage, especially to oxidative cleavage agents. PMID:22214457

Li, C; Duan, S; Xu, J; Qiao, R; Xu, P; Zhao, Y



Cleavage crystallography of liquid metal embrittled aluminum alloys  

NASA Technical Reports Server (NTRS)

The crystallography of liquid metal-induced transgranular cleavage in six aluminum alloys having a variety of microstructures has been determined via Laue X-ray back reflection. The cleavage crystallography was independent of alloy microstructure, and the cleavage plane was 100-plane oriented in all cases. It was further determined that the cleavage crystallography was not influenced by alloy texture. Examination of the fracture surface indicated that there was not a unique direction of crack propagation. In addition, the existence of 100-plane cleavage on alloy 2024 fracture surfaces was inferred by comparison of secondary cleavage crack intersection geometry on the 2024 surfaces with the geometry of secondary cleavage crack intersections on the test alloys.

Reynolds, A. P.; Stoner, G. E.



The Turbulent Alfvenic Aurora C. C. Chaston,1  

E-print Network

The Turbulent Alfve´nic Aurora C. C. Chaston,1 C. Salem,1 J. W. Bonnell,1 C. W. Carlson,1 R. E) It is demonstrated from observations that the Alfve´nic aurora may be powered by a turbulent cascade transverse acceleration of electrons from near-Earth space to form the aurora. We find that regions of Alfve´n wave

California at Berkeley, University of


Cleavage duplexes in the Marcellus Shale of the Appalachian foreland  

NASA Astrophysics Data System (ADS)

Cleavage duplexes are zones of platy, spaced cleavage, that either parallel bedding or ramp through shale sections. Examples are 2-60 m thick. The cleavage within the zones is generally subperpendicular to the zone boundaries but sigmoidally dragged against floor, roof and internal thrusts. Between the well-developed floor thrust and the more obscure roof thrusts of the duplexes the shale has been shortened >30% perpendicular to cleavage. The thrusts are sharp strain discontinuities because both overlying and underlying shale is uncleaved and less deformed (<10% layer parallel shortening). Cleavage in the duplexes was initiated perpendicular to bedding by pure shear in front of a propagating tip line. Cleavage halos at the ends of associated stiff carbonate concretions are small scale models illustrating initiation of cleavage. The cleavage is a primary crenulation cleavage with dissolution of limbs indicated by clay carbon partings. Transfer of thrusting from the floor to the roof of the cleavage duplex proceeded incrementally toward the foreland, imposing the simple shear that led to sigmoidal cleavage traces as the cleavage continuously evolved. Environmental conditions for formation of cleavage duplexes during the Alleghanian Orogeny are estimated as temperature 200-250°C, and pressure 1.1-1.3 kb, based upon conodont coloration (CA1 4), fluid inclusions and restored stratigraphic thicknesses. Cleavage duplexes or similar fold duplexes have been recognized in suitable black shales of Ordovician to Carboniferous age. They are manifestations of the progressive transfer of slip from floor to roof through a disturbed zone that serves as a shear boundary between large, more internally passive, thrust sheets.

Nickelsen, Richard P.


Small molecule activators of pre-mRNA 3? cleavage  

PubMed Central

3? Cleavage and polyadenylation are obligatory steps in the biogenesis of most mammalian pre-mRNAs. In vitro reconstitution of the 3? cleavage reaction from human cleavage factors requires high concentrations of creatine phosphate (CP), though how CP activates cleavage is not known. Previously, we proposed that CP might work by competitively inhibiting a cleavage-suppressing serine/threonine (S/T) phosphatase. Here we show that fluoride/EDTA, a general S/T phosphatase inhibitor, activates in vitro cleavage in place of CP. Subsequent testing of inhibitors specific for different S/T phosphatases showed that inhibitors of the PPM family of S/T phosphatases, which includes PP2C, but not the PPP family, which includes PP1, PP2A, and PP2B, activated 3? cleavage in vitro. In particular, NCI 83633, an inhibitor of PP2C, activated extensive 3? cleavage at a concentration 50-fold below that required by fluoride or CP. The testing of structural analogs led to the identification of a more potent compound that activated 3? cleavage at 200 ?M. While testing CP analogs to understand the origin of its cleavage activation effect, we found phosphocholine to be a more effective activator than CP. The minimal structural determinants of 3? cleavage activation by phosphocholine were identified. Our results describe a much improved small molecule activator of in vitro pre-mRNA cleavage, identify the molecular determinants of cleavage activation by phosphoamines such as phosphocholine, and suggest that a PPM family phosphatase is involved in the negative regulation of mammalian pre-mRNA 3? cleavage. PMID:19155323

Ryan, Kevin; Khleborodova, Asya; Pan, Jingyi; Ryan, Xiaozhou P.



902 SULFAPYRIDINE Fig. 2. Packing diagram of SP IV, showing the hydrogen bonds. For  

E-print Network

902 SULFAPYRIDINE C C A Fig. 2. Packing diagram of SP IV, showing the hydrogen bonds. For clarity, thus leading to the proliferation of polymorphic structures. The hydrogen-bonding motifs of polymorphs distinguish the current structure is a pair of hydrogen bonds of the type N(3)-H(N3)...N(1) forming a cyclic

Paris-Sud XI, Université de


Disulfide bond assignments by mass spectrometry of native natural peptides: cysteine pairing in disulfide bonded conotoxins.  


The critical, and often most difficult, step in structure elucidation of diverse classes of natural peptides is the determination of correct disulfide pairing between multiple cysteine residues. Here, we present a direct mass spectrometric analytical methodology for the determination of disulfide pairing. Protonated peptides, having multiple disulfide bonds, fragmented under collision induced dissociation (CID) conditions and preferentially cleave along the peptide backbone, with occasional disulfide fragmentation either by C(?)-S bond cleavage through H(?) abstraction to yield dehydroalanine and cysteinepersulfide, or by S-S bond cleavage through H(?) abstraction to yield the thioaldehyde and cysteine. Further fragmentation of the initial set of product ions (MS(n)) yields third and fourth generation fragment ions, permitting a distinction between the various possible disulfide bonded structures. This approach is illustrated by establishing cysteine pairing patterns in five conotoxins containing two disulfide bonds. The methodology is extended to the Conus araneosus peptides Ar1446 and Ar1430, two 14 residue sequences containing 3 disulfide bonds. A distinction between 15 possible disulfide pairing schemes becomes possible using direct mass spectral fragmentation of the native peptides together with fragmentation of enzymatically nicked peptides. PMID:20843009

Gupta, Kallol; Kumar, Mukesh; Balaram, Padmanabhan




Microsoft Academic Search

Fatigue (slow) crack growth in silane bonded epoxy\\/glass interfaces was studied under static and cyclic loading at 23 'C, 95% RH using the double cleavage drilled compression test. Crack growth rates under cyclic loading were significantly greater than under static loading, in contrast to crack growth results in monolithic glass. In addition, cyclic crack growth rate data after aging up




A Simple Test to Determine the Effectiveness of Different Braze Compositions for Joining Ti-Tubes to C/C Composite Plates  

NASA Technical Reports Server (NTRS)

A simple tube-plate joint tensile test was implemented to compare the effectiveness of commercial brazes, namely, TiCuNi, TiCuSil, and Cu-ABA, used for bonding Ti-tubes joined to C-C composite plates. The different braze systems yielded different; yet, repeatable results. The Cu-ABA system proved to have about twice the load-carrying ability of the other two systems due to the fact that the bonded area between the braze material and the C-C plate was largest for this system. The orientation of the surface fiber tows also had a significant effect on load-carrying ability with tows oriented perpendicular to the tube axis displaying the highest failure loads. Increasing the process load and modifying the surface of the C-C plate by grooving out channels for the Ti-Tube to nest in resulted in increased load-carrying ability for the TiCuSil and Cu-ABA systems due to increased bonded area and better penetration of the braze material into the C-C composite.

Morscher, Gregory N.; Singh, Mrityunjay; Shpargel, Tarah; Asthana, Rajiv



In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.  


Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-Å crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modelled 2'-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5' bond. Both an invariant guanosine and a Mg(2+) are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site. PMID:25410397

Ren, Aiming; Košuti?, Marija; Rajashankar, Kanagalaghatta R; Frener, Marina; Santner, Tobias; Westhof, Eric; Micura, Ronald; Patel, Dinshaw J



Mechanochemistry: one bond at a time.  


Single-molecule force-clamp spectroscopy offers a novel platform for mechanically denaturing proteins by applying a constant force to a polyprotein. A powerful emerging application of the technique is that, by introducing a disulfide bond in each protein module, the chemical kinetics of disulfide bond cleavage under different stretching forces can be probed at the single-bond level. Even at forces much lower than that which can rupture the chemical bond, the breaking of the S-S bond at the presence of various chemical reducing agents is significantly accelerated. Our previous work demonstrated that the rate of thiol/disulfide exchange reaction is force-dependent and well-described by an Arrhenius term of the form r = A(exp((F?x(r) - E(a))/k(B)T)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate, we measured the bond elongation parameter, ?x(r), along the reaction coordinate to the transition state of the S(N)2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the ?x(r) value can help depicting the energy landscapes and elucidating the mechanisms of the reactions at the single-molecule level. Small nucleophiles, such as 1,4-dl-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP), and l-cysteine, react with the S-S bond with monotonically increasing rates under the applied force, while thioredoxin enzymes exhibit both stretching-favored and -resistant reaction-rate regimes. These measurements demonstrate the power of the single-molecule force-clamp spectroscopy approach in providing unprecedented access to chemical reactions. PMID:19572737

Liang, Jian; Fernández, Julio M



Atomically Smooth Stress-Corrosion Cleavage of a Hydrogen-Implanted Crystal  

NASA Astrophysics Data System (ADS)

We present a quantum-accurate multiscale study of how hydrogen-filled discoidal “platelet” defects grow inside a silicon crystal. Dynamical simulations of a 10-nm-diameter platelet reveal that H2 molecules form at its internal surfaces, diffuse, and dissociate at its perimeter, where they both induce and stabilize the breaking up of highly stressed silicon bonds. A buildup of H2 internal pressure is neither needed for nor allowed by this stress-corrosion growth mechanism, at odds with previous models. Slow platelet growth up to micrometric sizes is predicted as a consequence, making atomically smooth crystal cleavage possible in implantation experiments.

Moras, Gianpietro; Ciacchi, Lucio Colombi; Elsässer, Christian; Gumbsch, Peter; de Vita, Alessandro



Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine.  


The N?N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. PMID:25214300

Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki



Unprecedented in situ oxidative ring cleavage of isoxazolidines: diastereoselective transformation of nitronic acids and derivatives into 3-hydroxymethyl 4-nitro tetrahydrofurans and pyrrolidines.  


[reaction: see text] Nitronic acids undergo an intramolecular 1,3-dipolar cycloaddition to unactivated double bonds, and the resulting isoxazolidines spontaneously evolve by an unprecedented in situ oxidative ring cleavage. The extension of this transformation to silyl nitronates results in a general diastereoselective construction of hydroxymethyl nitro functionalized tetrahydro-furans and -pyrrolidine having up to four consecutive stereogenic centers. PMID:15176810

Roger, Pierre-Yves; Durand, Anne-Catherine; Rodriguez, Jean; Dulcère, Jean-Pierre



Direct femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO to 2CH3 CO: Resolving  

E-print Network

devoted to answer such a question, and the issue in different reactions pericyclic, SN2, elimination, etcDirect femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO, California 91125 Received 17 April 1995; accepted 2 May 1995 When a reaction involving two equivalent bonds

Kim, Sang Kyu


DFT studies on the mechanism of palladium-catalyzed carbon-silicon cleavage for the synthesis of benzosilole derivatives.  


DFT calculations have been carried out to study the detailed mechanism of Pd-catalyzed intermolecular coupling reactions of 2-silylaryl bromides with alkynes via selective cleavage of C(sp(3))-Si bonds. Through our calculations, we found that, starting from the alkenylpalladium intermediate derived from oxidative addition of the substrate C-Br bond followed by alkyne insertion, there are two possible pathways leading to the formation of the benzosilole product. Furthermore, these two pathways were found to be competitive. In this paper, we will present the detailed mechanistic study and analyze the results we have obtained. PMID:24573107

Chen, Wen-Jie; Lin, Zhenyang



DNA Recognition, Strand Selectivity, and Cleavage Mode during Integrase Family Site-specific Recombination*  

PubMed Central

We have probed the association of Flp recombinase with its DNA target using protein footprinting assays. The results are consistent with the domain organization of the Flp protein and with the general features of the protein-DNA interactions revealed by the crystal structures of the recombination intermediates formed by Cre, the Flp-related recombinase. The similarity in the organization of the Flp and Cre target sites and in their recognition by the respective recombinases implies that the overall DNA-protein geometry during strand cleavage in the two systems must also be similar. Within the functional recombinase dimer, it is the interaction between two recombinase monomers bound on either side of the strand exchange region (or spacer) that provides the allosteric activation of a single active site. Whereas Cre utilizes the cleavage nucleophile (the active site tyrosine) in cis, Flp utilizes it in trans (one monomer donating the tyrosine to its partner). By using synthetic Cre and Flp DNA substrates that are geometrically restricted in similar ways, we have mapped the positioning of the active and inactive tyrosine residues during cis and trans cleavage events. We find that, for a fixed substrate geometry, Flp and Cre cleave the labile phosphodiester bond at the same spacer end, not at opposite ends. Our results provide a model that accommodates local heterogeneities in peptide orientations in the two systems while preserving the global functional architecture of the reaction complex. PMID:10748094

Tribble, Gena; Ahn, Yong-Tae; Lee, Jehee; Dandekar, Thomas; Jayaram, Makkuni



Oxidative modification of von Willebrand factor by neutrophil oxidants inhibits its cleavage by ADAMTS13.  


Elevated plasma von Willebrand factor (VWF) and low ADAMTS13 activity have been reported in several inflammatory states, including sepsis and acute respiratory distress syndrome. One hallmark of inflammation is neutrophil activation and production of reactive oxygen species, including superoxide radical, hydrogen peroxide, and hypochlorous acid (HOCl). HOCl is produced from hydrogen peroxide and chloride ions through the action of myeloperoxidase. HOCl can oxidize methionine to methionine sulfoxide and tyrosine to chlorotyrosine. This is of interest because the ADAMTS13 cleavage site in VWF, the Tyr(1605)-Met(1606) peptide bond, contains both oxidation-prone residues. We hypothesized that HOCl would oxidize either or both of these residues and possibly inhibit ADAMTS13-mediated cleavage. We therefore treated ADAMTS13 substrates with HOCl and examined their oxidative modification by mass spectrometry. Met(1606) was oxidized to the sulfoxide in a concentration-dependent manner, with complete oxidation at 75muM HOCl, whereas only a miniscule percentage of Tyr(1605) was converted to chlorotyrosine. The oxidized substrates were cleaved much more slowly by ADAMTS13 than the nonoxidized substrates. A similar result was obtained with multimeric VWF. Taken together, these findings indicate that reactive oxygen species released by activated neutrophils have a prothrombotic effect, mediated in part by inhibition of VWF cleavage by ADAMTS13. PMID:19812385

Chen, Junmei; Fu, Xiaoyun; Wang, Yi; Ling, Minhua; McMullen, Brad; Kulman, John; Chung, Dominic W; López, José A



Structural Basis for Accelerated Cleavage of Bovine Pancreatic Trypsin Inhibitor (BPTI) by Human Mesotrypsin  

SciTech Connect

Human mesotrypsin is an isoform of trypsin that displays unusual resistance to polypeptide trypsin inhibitors and has been observed to cleave several such inhibitors as substrates. Whereas substitution of arginine for the highly conserved glycine 193 in the trypsin active site has been implicated as a critical factor in the inhibitor resistance of mesotrypsin, how this substitution leads to accelerated inhibitor cleavage is not clear. Bovine pancreatic trypsin inhibitor (BPTI) forms an extremely stable and cleavage-resistant complex with trypsin, and thus provides a rigorous challenge of mesotrypsin catalytic activity toward polypeptide inhibitors. Here, we report kinetic constants for mesotrypsin and the highly homologous (but inhibitor sensitive) human cationic trypsin, describing inhibition by, and cleavage of BPTI, as well as crystal structures of the mesotrypsin-BPTI and human cationic trypsin-BPTI complexes. We find that mesotrypsin cleaves BPTI with a rate constant accelerated 350-fold over that of human cationic trypsin and 150,000-fold over that of bovine trypsin. From the crystal structures, we see that small conformational adjustments limited to several side chains enable mesotrypsin-BPTI complex formation, surmounting the predicted steric clash introduced by Arg-193. Our results show that the mesotrypsin-BPTI interface favors catalysis through (a) electrostatic repulsion between the closely spaced mesotrypsin Arg-193 and BPTI Arg-17, and (b) elimination of two hydrogen bonds between the enzyme and the amine leaving group portion of BPTI. Our model predicts that these deleterious interactions accelerate leaving group dissociation and deacylation.

Salameh,M.; Soares, A.; Hockla, A.; Radisky, E.



Chymase Cleavage of Stem Cell Factor Yields a Bioactive, Soluble Product  

NASA Astrophysics Data System (ADS)

Stem cell factor (SCF) is produced by stromal cells as a membrane-bound molecule, which may be proteolytically cleaved at a site close to the membrane to produce a soluble bioactive form. The proteases producing this cleavage are unknown. In this study, we demonstrate that human mast cell chymase, a chymotrypsin-like protease, cleaves SCF at a novel site. Cleavage is at the peptide bond between Phe-158 and Met-159, which are encoded by exon 6 of the SCF gene. This cleavage results in a soluble bioactive product that is 7 amino acids shorter at the C terminus than previously identified soluble SCF. This research shows the identification of a physiologically relevant enzyme that specifically cleaves SCF. Because mast cells express the KIT protein, the receptor for SCF, and respond to SCF by proliferation and degranulation, this observation identifies a possible feedback loop in which chymase released from mast cell secretory granules may solubilize SCF bound to the membrane of surrounding stromal cells. The liberated soluble SCF may in turn stimulate mast cell proliferation and differentiated functions; this loop could contribute to abnormal accumulations of mast cells in the skin and hyperpigmentation at sites of chronic cutaneous inflammation.

Longley, B. Jack; Tyrrell, Lynda; Ma, Yongsheng; Williams, David A.; Halaban, Ruth; Langley, Keith; Lu, Hsieng S.; Schechter, Norman M.



Gold-catalyzed C(sp3)-H bond functionalization.  


C-H bonds are ubiquitous in organic molecules. Homogenous gold-catalyzed direct functionalization of unsaturated C-H bonds has emerged as a powerful method in our synthetic toolbox. However, Csp(3)-H bonds have larger dissociation energy and lower proton acidity, and thus the efficient and exquisitely selective cleavage of this kind of chemical bonds for the formation of new carbon-carbon and carbon-heteroatom bonds is still a great challenge. In this tutorial review, we will highlight the recent achievements of gold-catalyzed oxidative and redox-neutral Csp(3)-H bond functionalization, which opens new avenues for economical and sustainable construction of fine chemicals. PMID:24853478

Xie, Jin; Pan, Changduo; Abdukader, Ablimit; Zhu, Chengjian



Bonded Lubricants  

NASA Technical Reports Server (NTRS)

Another spinoff to the food processing industry involves a dry lubricant developed by General Magnaplate Corp. of Linden, N.J. Used in such spacecraft as Apollo, Skylab and Viking, the lubricant is a coating bonded to metal surfaces providing permanent lubrication and corrosion resistance. The coating lengthens equipment life and permits machinery to be operated at greater speed, thus increasing productivity and reducing costs. Bonded lubricants are used in scores of commercia1 applications. They have proved particularly valuable to food processing firms because, while increasing production efficiency, they also help meet the stringent USDA sanitation codes for food-handling equipment. For example, a cookie manufacturer plagued production interruptions because sticky batter was clogging the cookie molds had the brass molds coated to solve the problem. Similarly, a pasta producer faced USDA action on a sanitation violation because dough was clinging to an automatic ravioli-forming machine; use of the anti-stick coating on the steel forming plates solved the dual problem of sanitation deficiency and production line downtime.



Defect structures in deformed F.C.C. metals  

SciTech Connect

A high density of small defect clusters, similar to those observed in irradiated or quenched metals, has been observed in the deformed f.c.c. metals Cu, Au and Ni. The preliminary results show that the defect clusters are predominantly stacking fault tetrahedral (SFT). The SFT number density, rather than the size distribution, is deformation dependent. The defect cluster density is greater in the vicinities of dislocation tangles and grain boundaries. Their size distribution is wider than that produced by irradiation with an important number of larger clusters being formed. It is argued that these deformation-produced clusters may play a role in determining the flow stress and work hardening at low deformations.

Dai, Y.; Victoria, M. [Ecole Polytechnique Federale de Lausanne, Villigen PSI (Switzerland). CRPP-Fusion Technology Div.] [Ecole Polytechnique Federale de Lausanne, Villigen PSI (Switzerland). CRPP-Fusion Technology Div.



Basics of Fidelity Bonding.  

ERIC Educational Resources Information Center

Fidelity bonds are important for an agency to hold to protect itself against any financial loss that can result from dishonest acts by its employees. Three types of fidelity bonds are available to an agency: (1) public official bonds; (2) dishonesty bonds; and (3) faithful performance bonds. Public official bonds are required by state law to be…

Kahn, Steven P.


Bonding and reactivity of cyclopentene on Pt(111)  

NASA Astrophysics Data System (ADS)

The adsorption and thermal reactivity of c-C 5H 8 on a Pt(111) surface has been studied by quantitative thermal desorption spectroscopy, high resolution electron energy loss spectroscopy and work function changes, and the bonding configurations and reactivity compared and contrasted with the linear olefins. At < 250 K, associative ?-donor-acceptor bonding in the Dewar-Chatt-Duncanson sense has been rejected. Instead, the vibrational data are more consistent with extensive sp 2 ? sp 3 rehybridization of the olefinic bond leading to a bonding configuration designated ?2(di- ?)- c-C 5H 8. Steric considerations suggest that there is a tilting of the C 5 ring which manifests itself in a soft CH stretch near 2750 cm -1 attributed to additional hydrogen-bonding interaction with the surface. At 250-300 K the partial dehydrogenation pathway of the linear olefins to an adsorbed alkylidyne is inhibited by the inherent stability of the C 5 ring. Instead, three hydrogen atoms from ?2(di- ?)- c-C 5H 8 are dissociated to produce a new adsorbed species identified as a pentahapto-cyclopentadienyl, ? 5-Cp, which is covalently ?-bonded to the surface in a manner analogous to the inorganic metallocenes like ferrocene, FeCp 5. Under these conditions, ? 5-Cp essentially saturates the surface with a coverage estimated at 1.5 ± 0.5×10 10 molecules cm -1. With the surface saturated with ?2(di- ?)- c-C 5H 8 the onset of hydrogen desorption at 250 K is accompanied by the desorption of excess parent c-C 5H 8. It is proposed that c-C 5H 8 is sterically displaced from the surface by the greater Van der Waals dimensions of the more strongly bound ? 5-Cp. c-C 5H 8 is not evolved from submonolayer coverages. Desorption of both hydrogen and c-C 5H 8 occurs with a common reaction-limited onset at 250 K. However, whereas c-C 5H 8 desorption occurs with a peak at 285 K, hydrogen may, with increasing conversion, be accommodated on the surface and subsequently desorbs in a ? 2 desorption-limited step at 305 K. ? 5-Cp is stable to 480 K when it dehydrogenates leaving, at 750 K, carbon on the surface. Decomposition is complex with the vibrational data suggesting a methylidyne stable to 600 K and a MCH?CHM species which is somewhat less stable.

Avery, Neu R.



Modeling and Inferring Cleavage Patterns in Proliferating Epithelia  

PubMed Central

The regulation of cleavage plane orientation is one of the key mechanisms driving epithelial morphogenesis. Still, many aspects of the relationship between local cleavage patterns and tissue-level properties remain poorly understood. Here we develop a topological model that simulates the dynamics of a 2D proliferating epithelium from generation to generation, enabling the exploration of a wide variety of biologically plausible cleavage patterns. We investigate a spectrum of models that incorporate the spatial impact of neighboring cells and the temporal influence of parent cells on the choice of cleavage plane. Our findings show that cleavage patterns generate “signature” equilibrium distributions of polygonal cell shapes. These signatures enable the inference of local cleavage parameters such as neighbor impact, maternal influence, and division symmetry from global observations of the distribution of cell shape. Applying these insights to the proliferating epithelia of five diverse organisms, we find that strong division symmetry and moderate neighbor/maternal influence are required to reproduce the predominance of hexagonal cells and low variability in cell shape seen empirically. Furthermore, we present two distinct cleavage pattern models, one stochastic and one deterministic, that can reproduce the empirical distribution of cell shapes. Although the proliferating epithelia of the five diverse organisms show a highly conserved cell shape distribution, there are multiple plausible cleavage patterns that can generate this distribution, and experimental evidence suggests that indeed plants and fruitflies use distinct division mechanisms. PMID:19521504

Patel, Ankit B.; Gibson, William T.; Gibson, Matthew C.; Nagpal, Radhika



A nematode kinesin required for cleavage furrow advancement  

Microsoft Academic Search

Dividing cells need to coordinate the separation of chromosomes with the formation of a cleavage plane. There is evidence that microtubule bundles in the interzone region of the anaphase spindle somehow control both the location and the assembly of the cleavage furrow [1–3]. A microtubule motor that concentrates in the interzone, MKLP1, has previously been implicated in the assembly of

James Powers; Olaf Bossinger; Debra Rose; Susan Strome; William Saxton



A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigments  

PubMed Central

Citrus is the first tree crop in terms of fruit production. The colour of Citrus fruit is one of the main quality attributes, caused by the accumulation of carotenoids and their derivative C30 apocarotenoids, mainly ?-citraurin (3-hydroxy-?-apo-8?-carotenal), which provide an attractive orange-reddish tint to the peel of oranges and mandarins. Though carotenoid biosynthesis and its regulation have been extensively studied in Citrus fruits, little is known about the formation of C30 apocarotenoids. The aim of this study was to the identify carotenoid cleavage enzyme(s) [CCD(s)] involved in the peel-specific C30 apocarotenoids. In silico data mining revealed a new family of five CCD4-type genes in Citrus. One gene of this family, CCD4b1, was expressed in reproductive and vegetative tissues of different Citrus species in a pattern correlating with the accumulation of C30 apocarotenoids. Moreover, developmental processes and treatments which alter Citrus fruit peel pigmentation led to changes of ?-citraurin content and CCD4b1 transcript levels. These results point to the involvement of CCD4b1 in ?-citraurin formation and indicate that the accumulation of this compound is determined by the availability of the presumed precursors zeaxanthin and ?-cryptoxanthin. Functional analysis of CCD4b1 by in vitro assays unequivocally demonstrated the asymmetric cleavage activity at the 7?,8? double bond in zeaxanthin and ?-cryptoxanthin, confirming its role in C30 apocarotenoid biosynthesis. Thus, a novel plant carotenoid cleavage activity targeting the 7?,8? double bond of cyclic C40 carotenoids has been identified. These results suggest that the presented enzyme is responsible for the biosynthesis of C30 apocarotenoids in Citrus which are key pigments in fruit coloration. PMID:24006419

Rodrigo, Maria J.; Alquezar, Berta; Al-Babili, Salim



Cleavage in the GDPH sequence of the C-terminal cysteine-rich part of the human MUC5AC mucin  

PubMed Central

MUC5AC is the main gel-forming mucin expressed by goblet cells of the airways and stomach where it protects the underlying epithelia. We expressed the C-terminal cysteine-rich part of the human MUC5AC mucin in CHO-K1 cells (Chinese-hamster ovary K1 cells) where it formed disulfide-linked dimers in the ER (endoplasmic reticulum). After reducing the disulfide bonds of these dimers, not only the expected monomers were found, but also two smaller fragments, indicating that the protein was partially cleaved. The site of cleavage was located at an Asp–Pro bond situated in a GDPH (Gly-Asp-Pro-His) sequence found in the vWD4 (von Willebrand D4) domain. This sequence is also found in the human MUC2 mucin, previously shown to be cleaved at the same site by a slow, non-enzymatic process triggered by a pH below 6 [Lidell, Johansson and Hansson (2003) J. Biol. Chem. 278, 13944–13951]. In contrast with this, the cleavage of MUC5AC started already in the neutral ER. However, it continued and was slightly accelerated at a pH below 6.5, a pH found in the later parts of the secretory pathway. The cleavage generated a reactive group in the new C-terminus that could link the protein to a primary amine. No cleavage of MUC5AC has so far been reported. By using an antibody reacting with the C-terminal cleavage fragment, we could verify that the cleavage occurs in wild-type MUC5AC produced by HT-29 cells. The cleavage of MUC5AC and the generation of the reactive new C-terminus could contribute to the adherent and viscous mucus found at chronic lung diseases such as asthma and cystic fibrosis, characterized by mucus hypersecretion and lowered pH of the airways. PMID:16787389

Lidell, Martin E.; Hansson, Gunnar C.



Water-stabilized three- and four-atom palladium clusters as highly active catalytic species in ligand-free C-C cross-coupling reactions.  


Elite cliques: Palladium clusters with three and four atoms were found to be the catalytically active species for ligand-free palladium-catalyzed C?C bond-forming reactions. These palladium cluster species could be stabilized in water and stored for long periods of time for use on demand with no loss of activity. High yields of products and turnover frequencies (TOFs) of up to 10(5) ?h(-1) were observed. PMID:24038914

Leyva-Pérez, Antonio; Oliver-Meseguer, Judit; Rubio-Marqués, Paula; Corma, Avelino



Selective activation of carbon-carbon bonds next to a carbonyl group  

NASA Astrophysics Data System (ADS)

ORGANOMETALLIC complexes are used to effect a wide range of catalytic transformations in organic synthesis, such as the activation of C-H bonds1,2. Carbon-carbon bonds, however, are generally unreactive towards transition metals under homogeneous conditions. C-C bond activation by a process of oxidative addition to soluble transition-metal complexes has been limited mostly to stoichiometric (not catalytic) reactions1,3-7,18, to highly strained substrates such as cyclopropane and cubane1,8-11 or to chelating ketones19. Here we present a synthetically useful process of selective C-C bond activation in which the C-C bond adjacent to a carbonyl group is opened by insertion of a soluble rhodium(I) complex. The resulting organometallic intermediate can be transformed to a variety of products in a way that regenerates the rhodium complex. We anticipate that this catalytic scheme will have considerable utility in organic synthesis.

Murakami, Masahiro; Amii, Hideki; Ito, Yoshihiko



Site specificity of DSP-PP cleavage by BMP1.  


Bone morphogenic protein 1 (BMP1), a metalloproteinase, is known to cleave a wide variety of extracellular matrix proteins, suggesting that a consensus substrate cleavage amino acid sequence might exist. However, while such a consensus sequence has been proposed based on P4 to P4' (i.e. the four amino acids flanking either side of the BMP1 cleavage site; P4P3P2P1|P1'P2'P3'P4') sequence homologies between two BMP1 substrates, dentin matrix protein 1 and dentin sialoprotein phosphophoryn (DSP-PP) (i.e. xMQx|DDP), no direct testing has so far been attempted. Using an Sf9 cell expression system, we have been able to produce large amounts of uncleaved DSP-PP. Point mutations introduced into this recombinant DSP-PP were then tested for their effects on DSP-PP cleavage by either Sf9 endogenous tolloid-related protein 1 (TLR-1) or by its human homolog, BMP1. Here, we have measured DSP-PP cleavage efficiencies after modifications based on P4-P4' sequence comparisons with dentin matrix protein 1, as well as for prolysyl oxidase and chordin, two other BMP1 substrates. Our results demonstrate that any mutations within or outside of the DSP-PP P4 to P4' cleavage site can block, impair or accelerate DSP-PP cleavage, and suggest that its BMP1 cleavage site is highly conserved in order to regulate its cleavage efficiency, possibly with additional assistance from its conserved exosites. Thus, BMP1 cleavage cannot be based on a consensus substrate cleavage site. PMID:25158199

Yang, Robert T; Lim, Glendale L; Yee, Colin T; Fuller, Robert S; Ritchie, Helena H



Methodology for hardware\\/software co-verification in C\\/C++ (short paper)  

Microsoft Academic Search

In this paper we present our C\\/C++-based design envi- ronment for hardware\\/software co-verification. Our approach is to use C\\/C++ to describe both hardware and software throughout the design flow. Our methodology supports the efficient mapping of C\\/ C++ functional descriptions directly into hardware and software. The advantages of a C\\/C++-based flow from the verification point of view are presented. The

Luc Séméria; Abhijit Ghosh



functions of APH-1 and PEN-2 are the same in Notch cleavage as in APP cleavage. This is  

E-print Network

functions of APH-1 and PEN-2 are the same in Notch cleavage as in APP cleavage. This is important--affect the expression and processing of APP and Notch9,10 ,wedonotyetknowifandhowsuch signals affect -secretase activity to be the enzyme that actually cleaves APP and Notch2 . If so, then nicastrin, APH-1 and PEN-2 might regulate

Blatt, Rainer


Determination of the Proteolytic Cleavage Sites of the Amyloid Precursor-Like Protein 2 by the Proteases ADAM10, BACE1 and ?-Secretase  

PubMed Central

Regulated intramembrane proteolysis of the amyloid precursor protein (APP) by the protease activities ?-, ?- and ?-secretase controls the generation of the neurotoxic amyloid ? peptide. APLP2, the amyloid precursor-like protein 2, is a homolog of APP, which shows functional overlap with APP, but lacks an amyloid ? domain. Compared to APP, less is known about the proteolytic processing of APLP2, in particular in neurons, and the cleavage sites have not yet been determined. APLP2 is cleaved by the ?-secretase BACE1 and additionally by an ?-secretase activity. The two metalloproteases ADAM10 and ADAM17 have been suggested as candidate APLP2 ?-secretases in cell lines. Here, we used RNA interference and found that ADAM10, but not ADAM17, is required for the constitutive ?-secretase cleavage of APLP2 in HEK293 and SH-SY5Y cells. Likewise, in primary murine neurons knock-down of ADAM10 suppressed APLP2 ?-secretase cleavage. Using mass spectrometry we determined the proteolytic cleavage sites in the APLP2 sequence. ADAM10 was found to cleave APLP2 after arginine 670, whereas BACE1 cleaves after leucine 659. Both cleavage sites are located in close proximity to the membrane. ?-secretase cleavage was found to occur at different peptide bonds between alanine 694 and valine 700, which is close to the N-terminus of the predicted APLP2 transmembrane domain. Determination of the APLP2 cleavage sites enables functional studies of the different APLP2 ectodomain fragments and the production of cleavage-site specific antibodies for APLP2, which may be used for biomarker development. PMID:21695060

Hogl, Sebastian; Kuhn, Peer-Hendrik; Colombo, Alessio; Lichtenthaler, Stefan F.



3-Keto-5-aminohexanoate Cleavage Enzyme  

PubMed Central

The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long known as being involved in the anaerobic fermentation of lysine but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn2+ cation reminiscent of metal-dependent class II aldolases, our results based on a combination of x-ray snapshots and molecular modeling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the “domain of unknown function” DUF849. PMID:21632536

Bellinzoni, Marco; Bastard, Karine; Perret, Alain; Zaparucha, Anne; Perchat, Nadia; Vergne, Carine; Wagner, Tristan; de Melo-Minardi, Raquel C.; Artiguenave, Francois; Cohen, Georges N.; Weissenbach, Jean; Salanoubat, Marcel; Alzari, Pedro M.



Detection of nucleic acid sequences by invader-directed cleavage  


The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

Brow, Mary Ann D. (Madison, WI); Hall, Jeff Steven Grotelueschen (Madison, WI); Lyamichev, Victor (Madison, WI); Olive, David Michael (Madison, WI); Prudent, James Robert (Madison, WI)



Redox-Triggered C-C Coupling of Alcohols and Vinyl Epoxides: Diastereo- and Enantioselective Formation of All-Carbon Quaternary Centers via tert-(Hydroxy)-Prenylation  

PubMed Central

Iridium catalyzed primary alcohol oxidation triggers reductive C-O bond cleavage of isoprene oxide to form aldehyde-allyliridium pairs that combine to form products of tert-(hydroxy)-prenylation, a motif found in >2000 terpenoid natural products. Curtin-Hammett effects are exploited to enforce high levels of anti-diastereo- and enantioselectivity in the formation of an all-carbon quaternary center. The present redox-triggered carbonyl additions occur in the absence of stoichiometric byproducts, premetallated reagents and discrete alcohol-to-aldehyde redox manipulations. PMID:24915473

Feng, Jiajie; Garza, Victoria J.; Krische, Michael J.



Mechanistic Investigation of Catalytic Carbon-Carbon Bond Activation and Formation by Platinum and Palladium Phosphine  

E-print Network

Mechanistic Investigation of Catalytic Carbon-Carbon Bond Activation and Formation by Platinum). The breaking of C-C bonds is also crucial in coal liquefaction processes such as the Exxon Donor Solvent process or the Microcat Coal Liquefaction process. Presently cracking is achieved with heterogeneous

Jones, William D.


Diffusion Bonding of Metals.  

National Technical Information Service (NTIS)

The need to reduce the cost and weight of aerospace metallic structures has led to increased interest in solid state and liquid phase diffusion bonding processes, especially in combination with superplastic forming. The bonding mechanisms and bonding tech...

P. G. Partridge



Transsynaptic signaling by activity-dependent cleavage of neuroligin-1.  


Adhesive contact between pre- and postsynaptic neurons initiates synapse formation during brain development and provides a natural means of transsynaptic signaling. Numerous adhesion molecules and their role during synapse development have been described in detail. However, once established, the mechanisms of adhesive disassembly and its function in regulating synaptic transmission have been unclear. Here, we report that synaptic activity induces acute proteolytic cleavage of neuroligin-1 (NLG1), a postsynaptic adhesion molecule at glutamatergic synapses. NLG1 cleavage is triggered by NMDA receptor activation, requires Ca2+ /calmodulin-dependent protein kinase, and is mediated by proteolytic activity of matrix metalloprotease 9 (MMP9). Cleavage of NLG1 occurs at single activated spines, is regulated by neural activity in vivo, and causes rapid destabilization of its presynaptic partner neurexin-1? (NRX1?). In turn, NLG1 cleavage depresses synaptic transmission by abruptly reducing presynaptic release probability. Thus, local proteolytic control of synaptic adhesion tunes synaptic transmission during brain development and plasticity. PMID:23083741

Peixoto, Rui T; Kunz, Portia A; Kwon, Hyungbae; Mabb, Angela M; Sabatini, Bernardo L; Philpot, Benjamin D; Ehlers, Michael D



Cleavages, social engagement and trust in post-communist euroupe  

E-print Network

This dissertation addresses generalized trust in Post-Communist Europe. I examine trust stressing two sets of factors: the impact of attitudes associated with cleavages coming out of transition to democracy, and the importance of informal...

Rossbach, David Otto



Modular functionalized polyphosphines for supported materials: previously unobserved (31)P-NMR «through-space» ABCD spin systems and heterogeneous palladium-catalysed C-C and C-H arylation.  


The modular design of polyphosphines, diversely functionalized for facile immobilization on virtually any kind of support, is reported. Previously unobserved ABCD (31)P NMR spin-spin systems evidence the control exercised on the polyphosphines conformation. We illustrate the catalytic performance at low Pd loading of the recyclable immobilized polyphosphines in C-C bond formation reactions. PMID:25008866

Beaupérin, Matthieu; Smaliy, Radomyr; Cattey, Hélène; Meunier, Philippe; Ou, Jun; Toy, Patrick H; Hierso, Jean-Cyrille



Carbon-Sulfur Bond Cleavage of Methyl-Substituted Thiophenes with Iridium(III)  

E-print Network

pollution and a poison for precious metal catalysts. Currently catalytic HDS is carried out using than one metal center is likely involved on the catalyst surface. [Cp*IrH3]2 was initially examined a heterogeneous Mo-Co sulfide catalyst (supported on Al2O3). This industrial process works well in removing

Jones, William D.


Bonded half planes containing an arbitrarily oriented crack  

NASA Technical Reports Server (NTRS)

The plane elastostatic problem for two bonded half planes containing an arbitrarily oriented crack in the neighborhood of the interface is considered. Using Mellin transforms, the problem is formulated as a system of singular integral equations. The equations are solved for various crack orientations, material combinations, and external loads. The numerical results given include the stress intensity factors, tHe strain energy release rates, and tHe probable cleavage angles giving the direction of crack propagation.

Erdogan, F.; Aksogan, O.



29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.  

Code of Federal Regulations, 2013 CFR

...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...



29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.  

Code of Federal Regulations, 2010 CFR

...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...



29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.  

Code of Federal Regulations, 2011 CFR

...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...



29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.  

Code of Federal Regulations, 2012 CFR

...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...



Total synthesis of (+)-trienomycins A and F via C-C bond-forming hydrogenation and transfer hydrogenation.  


The triene-containing C17-benzene ansamycins trienomycins A and F were prepared in 16 steps (longest linear sequence, LLS) and 28 total steps. The C11-C13 stereotriad was generated via enantioselective Ru-catalyzed alcohol CH syn crotylation followed by chelation-controlled carbonyl dienylation. Enantioselective Rh-catalyzed acetylene-aldehyde reductive coupling mediated by gaseous H2 was used to form a diene that ultimately was subjected to diene-diene ring closing metathesis to form the macrocycle. The present approach is 14 steps shorter (LLS) than the prior syntheses of trienomycins A and F, and 8 steps shorter than any prior synthesis of a triene-containing C17-benzene ansamycin. PMID:23862627

Del Valle, David J; Krische, Michael J



C-C Bond Formation via Copper-Catalyzed Conjugate Addition Reactions to Enones in Water at Room Temperature  

PubMed Central

Conjugate addition reactions to enones can now be done in water at room temperature with in situ-generated organocopper reagents. Mixing an enone, zinc powder, TMEDA, and an alkyl halide in a micellar environemnt containing catalytic amounts of Cu(I), Ag(I), and Au(III), leads to 1,4-adducts in good isolated yields: no organometallic precursor is involved. PMID:23190029

Lipshutz, Bruce H.; Huang, Shenlin; Leong, Wendy Wen Yi; Isley, Nicholas A.



Expanding the substrate scope in palladium-catalyzed C-N and C-C bond-forming reactions  

E-print Network

Chapter 1. The first detailed study of the palladium-catalyzed amination of aryl nonaflates is reported. Use of bulky electron-rich monophosphinobiaryl ligands or BINAP allow for the catalytic amination of electron-rich ...

Anderson, Kevin William



Topotactic elimination of water across a C-C ligand bond in a dense 3-D metal-organic framework.  


Upon heating, lithium l-malate undergoes topotactic dehydration to form a phase containing the unsaturated fumarate ligand, in which the original 3-D framework remains intact. Insight into this unusual transformation has been obtained by single crystal X-ray diffraction, MAS-NMR, in situ powder X-ray diffraction and DFT calculations. PMID:25232700

Yeung, Hamish H-M; Kosa, Monica; Griffin, John M; Grey, Clare P; Major, Dan T; Cheetham, Anthony K



Cyanide-catalyzed C-C bond formation: synthesis of novel compounds, materials and ligands for homogeneous catalysis  

E-print Network

Cyanide-catalyzed aldimine coupling was employed to synthesize compounds with 1,2-ene-diamine and �±-imine-amine structural motifs: 1,2,N,N'- tetraphenyletheylene-1,2-diamine (13) and (+/-)-2,3-di-(2-hydroxyphenyl)-1,2- dihydroquinoxaline (17...

Reich, Blair Jesse Ellyn



Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.  


We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ?15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ?1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction. PMID:21539371

Rosta, Edina; Nowotny, Marcin; Yang, Wei; Hummer, Gerhard



Hydrogen bonding in molecular recognition by HIV-1 protease  

NASA Astrophysics Data System (ADS)

Molecular recognition of the cleavage sites of the substrates by HIV-1 protease is analyzed in terms of hydrogen bonding. Crystal structures of an inactive enzyme complexed with six different substrates were used as reference structures. Applying molecular mechanics calculations it can be shown that the interaction energies between the real substrate and the enzyme are larger than with other peptides. From the analysis, it can be concluded that water molecules are essential in the recognition process. Moreover, the hydrogen bonds between the protease and various substrates are characterized in detail.

Aruksankunwong, O.; Hannongbua, S.; Wolschann, Peter



IBM XL C/C++ Advanced Edition V8.0 for Linux Programming Guide  

E-print Network

IBM XL C/C++ Advanced Edition V8.0 for Linux Programming Guide SC09-8014-00 #12;#12;IBM XL C/C++ Advanced Edition V8.0 for Linux Programming Guide SC09-8014-00 #12;Note! Before using this information) This edition applies to version 8.0 of IBM XL C/C++ Advanced Edition V8.0 for Linux (product number 5724-M16

Hickman, Mark


IBM XL C/C++ Advanced Edition V8.0 for Linux Compiler Reference  

E-print Network

IBM XL C/C++ Advanced Edition V8.0 for Linux Compiler Reference SC09-8013-00 #12;#12;IBM XL C/C++ Advanced Edition V8.0 for Linux Compiler Reference SC09-8013-00 #12;Note! Before using this information 2005 ) This edition applies to XL C/C++ Advanced Edition V8.0 for Linux (Program number 5724-M16

Hickman, Mark


IBM XL C/C++ Advanced Edition V8.0 for Linux Language Reference  

E-print Network

IBM XL C/C++ Advanced Edition V8.0 for Linux Language Reference SC09-8016-00 #12;#12;IBM XL C/C++ Advanced Edition V8.0 for Linux Language Reference SC09-8016-00 #12;Note! Before using this information (November, 2005) This edition applies to Version 8.0 of IBM XL C/C++ Advanced Edition for Linux (product

Hickman, Mark


Leukocyte proteases cleave von Willebrand factor at or near the ADAMTS13 cleavage site  

PubMed Central

The function of von Willebrand factor (VWF) is regulated by proteolysis, which limits its multimeric size and ability to tether platelets. The importance of ADAMTS13 metalloprotease in VWF regulation is demonstrated by the association between severe deficiency of ADAMTS13 and thrombotic thrombocytopenic purpura (TTP). However, ADAMTS13 activity levels do not always correlate with the clinical course of TTP, suggesting that other proteases could be important in regulating VWF. We identified 4 leukocyte proteases that cleave the synthetic VWF substrate FRETS-VWF73 and multimeric VWF. Elastase and proteinase 3 (PR3) cleave multimeric VWF and FRETS-VWF73 at the V1607-T1608 peptide bond; cathepsin G and matrix metalloprotease 9 cleave VWF substrates at the Y1605-M1606 and M1606-V1607 bonds, respectively. Isolated intact human neutrophils cleave FRETS-VWF73 at the V1607-T1608 peptide bond, suggesting that elastase or PR3 expressed on leukocyte surfaces might cleave VWF. In the presence of normal or ADAMTS13-deficient plasma, cleavage of FRETS-VWF73 by resting neutrophils is abolished. However, activated neutrophils retain proteolytic activity toward FRETS-VWF73 in the presence of plasma. Although the in vivo relevance remains to be established, these studies suggest the existence of a “hot spot” of VWF proteolysis in the VWF A2 domain, and support the possibility that activated leukocytes may participate in the proteolytic regulation of VWF. PMID:19541819

Cao, Wenjing; Atkinson, Bonnie S.; Bedell, Bruce; Montgomery, Robert R.; Lentz, Steven R.; Johnson, George F.



Survey of amino-terminal proteolytic cleavage sites in mitochondrial precursor proteins: leader peptides cleaved by two matrix proteases share a three-amino acid motif.  

PubMed Central

We have compiled sequences of precursor proteins for 50 mitochondrial proteins for which the mature amino terminus has been determined by amino acid sequence analysis. Included in this set are 8 precursors that have leader peptides that are cleaved in two places by mitochondrial matrix proteases. When these eight leader peptides are aligned and compared, a highly conserved three-amino acid motif is identified as being common to this class of leader peptides. This motif includes an arginine at position -10, a hydrophobic residue at position -8, and serine, threonine, or glycine at position -5 relative to the mature amino terminus. The initial cleavage of these peptides by matrix processing protease occurs within the motif, between residues at -9 and -8, such that arginine at position -10 is at position -2 relative to the cleaved bond. The rest of the motif is within the octapeptide removed by subsequent cleavage catalyzed by intermediate-specific protease. An additional 14 leader peptides in this collection (all of those that contain an arginine at -10) conform to this motif. Assuming that these 14 precursors are matured in two steps, we compared the internal cleavage sites at position -8 with the ends of the other 30 leader peptides in the collection. We find that 74% of matrix processing protease cleavage sites follow an arginine at position -2 relative to cleavage. PMID:2657736

Hendrick, J P; Hodges, P E; Rosenberg, L E



Anaerobic and aerobic cleavage of the steroid core ring structure by Steroidobacter denitrificans[S  

PubMed Central

The aerobic degradation of steroids by bacteria has been studied in some detail. In contrast, only little is known about the anaerobic steroid catabolism. Steroidobacter denitrificans can utilize testosterone under both oxic and anoxic conditions. By conducting metabolomic investigations, we demonstrated that S. denitrificans adopts the 9,10-seco-pathway to degrade testosterone under oxic conditions. This pathway depends on the use of oxygenases for oxygenolytic ring fission. Conversely, the detected degradation intermediates under anoxic conditions suggest a novel, oxygenase-independent testosterone catabolic pathway, the 2,3-seco-pathway, which differs significantly from the aerobic route. In this anaerobic pathway, testosterone is first transformed to 1-dehydrotestosterone, which is then reduced to produce 1-testosterone followed by water addition to the C-1/C-2 double bond of 1-testosterone. Subsequently, the C-1 hydroxyl group is oxidized to produce 17-hydroxy-androstan-1,3-dione. The A-ring of this compound is cleaved by hydrolysis as evidenced by H218O-incorporation experiments. Regardless of the growth conditions, testosterone is initially transformed to 1-dehydrotestosterone. This intermediate is a divergence point at which the downstream degradation pathway is governed by oxygen availability. Our results shed light into the previously unknown cleavage of the sterane ring structure without oxygen. We show that, under anoxic conditions, the microbial cleavage of steroidal core ring system begins at the A-ring. PMID:23458847

Wang, Po-Hsiang; Leu, Yann-Lii; Ismail, Wael; Tang, Sen-Lin; Tsai, Ching-Yen; Chen, Hsing-Ju; Kao, Ann-Tee; Chiang, Yin-Ru



Naturally Occurring Eccentric Cleavage Products of Provitamin A ?-Carotene Function as Antagonists of Retinoic Acid Receptors*  

PubMed Central

?-Carotene is the major dietary source of provitamin A. Central cleavage of ?-carotene catalyzed by ?-carotene oxygenase 1 yields two molecules of retinaldehyde. Subsequent oxidation produces all-trans-retinoic acid (ATRA), which functions as a ligand for a family of nuclear transcription factors, the retinoic acid receptors (RARs). Eccentric cleavage of ?-carotene at non-central double bonds is catalyzed by other enzymes and can also occur non-enzymatically. The products of these reactions are ?-apocarotenals and ?-apocarotenones, whose biological functions in mammals are unknown. We used reporter gene assays to show that none of the ?-apocarotenoids significantly activated RARs. Importantly, however, ?-apo-14?-carotenal, ?-apo-14?-carotenoic acid, and ?-apo-13-carotenone antagonized ATRA-induced transactivation of RARs. Competitive radioligand binding assays demonstrated that these putative RAR antagonists compete directly with retinoic acid for high affinity binding to purified receptors. Molecular modeling studies confirmed that ?-apo-13-carotenone can interact directly with the ligand binding site of the retinoid receptors. ?-Apo-13-carotenone and the ?-apo-14?-carotenoids inhibited ATRA-induced expression of retinoid responsive genes in Hep G2 cells. Finally, we developed an LC/MS method and found 3–5 nm ?-apo-13-carotenone was present in human plasma. These findings suggest that ?-apocarotenoids function as naturally occurring retinoid antagonists. The antagonism of retinoid signaling by these metabolites may have implications for the activities of dietary ?-carotene as a provitamin A and as a modulator of risk for cardiovascular disease and cancer. PMID:22418437

Eroglu, Abdulkerim; Hruszkewycz, Damian P.; dela Sena, Carlo; Narayanasamy, Sureshbabu; Riedl, Ken M.; Kopec, Rachel E.; Schwartz, Steven J.; Curley, Robert W.; Harrison, Earl H.



Disulphide bond assignment in human tissue inhibitor of metalloproteinases (TIMP).  

PubMed Central

Disulphide bonds in human recombinant tissue inhibitor of metalloproteinases (TIMP) were assigned by resolving proteolytic digests of TIMP on reverse-phase h.p.l.c. and sequencing those peaks judged to contain disulphide bonds by virtue of a change in retention time on reduction. This procedure allowed the direct assignment of Cys-145-Cys-166 and the isolation of two other peptides containing two disulphide bonds each. Further peptide cleavage in conjunction with fast-atom-bombardment m.s. analysis permitted the assignments Cys-1-Cys-70, Cys-3-Cys-99, Cys-13-Cys-124 and Cys-127-Cys-174 from these peptides. The sixth bond Cys-132-Cys-137 was assigned by inference, as the native protein has no detectable free thiol groups. Images Fig. 1. PMID:2163605

Williamson, R A; Marston, F A; Angal, S; Koklitis, P; Panico, M; Morris, H R; Carne, A F; Smith, B J; Harris, T J; Freedman, R B



Savings Bonds Value Calculator  

NSDL National Science Digital Library

From the Federal Reserve Bank of New York, this site computes the redemption value of users's US savings bonds. Easy-to-use pull-down menus allow visitors to enter information such as the date of issue and face value of their Series E bonds, Series EE bonds, and Series S bonds. After entering the information, the Calculator will then show a chart of issue dates and denominations and actual worth of the bonds, if cashed within a set period of time.


High resolution reaction intermediates of rabbit muscle fructose-1,6-bisphosphate aldolase: substrate cleavage and induced fit.  


Crystal structures were determined to 1.8 A resolution of the glycolytic enzyme fructose-1,6-bis(phosphate) aldolase trapped in complex with its substrate and a competitive inhibitor, mannitol-1,6-bis(phosphate). The enzyme substrate complex corresponded to the postulated Schiff base intermediate and has reaction geometry consistent with incipient C3-C4 bond cleavage catalyzed Glu-187, which is adjacent by to the Schiff base forming Lys-229. Atom arrangement about the cleaved bond in the reaction intermediate mimics a pericyclic transition state occurring in nonenzymatic aldol condensations. Lys-146 hydrogen-bonds the substrate C4 hydroxyl and assists substrate cleavage by stabilizing the developing negative charge on the C4 hydroxyl during proton abstraction. Mannitol-1,6-bis(phosphate) forms a noncovalent complex in the active site whose binding geometry mimics the covalent carbinolamine precursor. Glu-187 hydrogen-bonds the C2 hydroxyl of the inhibitor in the enzyme complex, substantiating a proton transfer role by Glu-187 in catalyzing the conversion of the carbinolamine intermediate to Schiff base. Modeling of the acyclic substrate configuration into the active site shows Glu-187, in acid form, hydrogen-bonding both substrate C2 carbonyl and C4 hydroxyl, thereby aligning the substrate ketose for nucleophilic attack by Lys-229. The multifunctional role of Glu-187 epitomizes a canonical mechanistic feature conserved in Schiff base-forming aldolases catalyzing carbohydrate metabolism. Trapping of tagatose-1,6-bis(phosphate), a diastereoisomer of fructose 1,6-bis(phosphate), displayed stereospecific discrimination and reduced ketohexose binding specificity. Each ligand induces homologous conformational changes in two adjacent alpha-helical regions that promote phosphate binding in the active site. PMID:15870069

St-Jean, Miguel; Lafrance-Vanasse, Julien; Liotard, Brigitte; Sygusch, Jurgen



Synthesis of Sulfur-Containing Heterocycles through Oxidative Carbon-Hydrogen Bond Functionalization  

PubMed Central

Vinyl sulfides react rapidly and efficiently with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) to form ?,?-unsaturated thiocarbenium ions through oxidative carbon–hydrogen bond cleavage. These electrophiles couple with appended ?-nucleophiles to yield sulfur-containing heterocycles through carbon–carbon bond formation. Several nucleophiles are compatible with the procedure and the reactions generally proceed through readily-predictable transition states. PMID:22420412

Cui, Yubo; Floreancig, Paul E.



Analysis of RNA cleavage by MALDI-TOF mass spectrometry.  


A method of analysis is presented that utilizes matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to monitor the kinetics and products of RNA cleavage, by use of a program designed to mass-match observed MS peaks with predicted RNA cleavage products. The method is illustrated through application to the study of targeted oxidation of RNA stem loops from HIV-1 Rev Response Element mRNA (RRE RNA) and ribosomal 16S A-site RNA (16S RNA) by metallonucleases. Following incubation of each RNA with catalysts and/or redox co-reactants, reaction mixtures were desalted, and MALDI-TOF MS was used to monitor both time-resolved formation of cleavage products and disappearance of full-length RNA. For each RNA, a unique list was generated that contained the predicted masses of both the full-length, and all of the possible RNA cleavage fragments that resulted from the combination of all possible cleavage sites and each of the six expected overhangs formed at nascent termini adjacent to the cleavage sites. The overhangs corresponded to 2',3'-cyclic phosphate, 3'-phosphate, 3'-phosphoglycolate, 5'- hydroxyl and 5'- phosphate, which corresponded to differing oxidative, hydrolytic, and/or 2'-OH-mediated-endonucleolytic modes of scission. Each mass spectrum was compared with a corresponding list of predicted masses, and peaks were rapidly assigned by use of a Perl script, with a mass-matching tolerance of 200 ppm. Both time-dependent cleavage mediated by metallonucleases and MALDI-TOF-induced fragmentation were observed, and these were distinguished by time-dependent experiments. The resulting data allowed a semi-quantitative assessment of the rate of formation of each overhang at each nucleotide position. Limitations included artifactual skewing of quantification by mass bias, a limited mass range for quantification, and a lack of detection of secondary cleavage products. Nevertheless, the method presented herein provides a rapid, accurate, highly-detailed and semi-quantitative analysis of RNA cleavage that should be widely applicable. PMID:22941655

Joyner, Jeff C; Keuper, Kevin D; Cowan, J A



LET'S BOND! A Chemical Bonding Webquest  

NSDL National Science Digital Library

Today we are going to use the internet to explore chemical bonding! Even though there are just a few questions for each website, you need to read the entire content. Don't worry about understanding all of it, but make sure that you are familiar with it! Stay on task and have fun! Let's start with some basics. Click on the link below and answer the questions on your worksheet under "Bonding Basics". Bonding Basics Good job! Lets move on and talk about ions. Ions are a big part of bonding, so make sure you get this section down pat! Click on the ...

Hicken, Mrs.



Cleavage Entropy as Quantitative Measure of Protease Specificity  

PubMed Central

A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. PMID:23637583

Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Margreiter, Michael A.; Spitzer, Gudrun M.; Wallnoefer, Hannes G.; Liedl, Klaus R.



The cleavage pattern in the leech Theromyzon tessulatum (Hirudinea, Glossiphoniidae).  


In order to evaluate the differences in the cleavage patterns of the glossiphoniid leeches Glossiphonia complanata and Theromyzon tessulatum, previously studied by Müller ('32) and Schmidt ('17, '41), the cleavage of Theromyzon tessulatum was reexamined. For the period of the first 29 hours of development embryos were observed, photographed, and serially sectioned for light microscopy at each developmental stage. The exact cell lineage until completion of teloblast formation is reported. Besides some other not previously reported features, we show that the mesoteloblast precursor cell in the glossiphoniid leeches, as probably in most Annelida, is not the cell 3D, but cell 4d formed by an additional division of cell 3D. The results further indicate that all glossiphoniid leeches likely share a common cleavage pattern, and that major differences between Glossiphonia complanata and Theromyzon tessulatum do not exist. A comparison between the cleavage patterns of some Oligochaeta and Hirudinea is made, and plesiomorphic characters in the cleavage of a clitellate ancestor species and their deviations in present day species are discussed. PMID:3385778

Sandig, M; Dohle, W



Morphological aspects of in vivo cleavage in Myocastor coypus (coypu).  


The objective of the present work was to characterize the in vivo cleavage stage of Myocastor coypus embryos. For this purpose a colpocytological follow-up and controlled mating of 18 females were performed. Specimens from the beginning of the first cleavage to the acquisition of a morula appearance were considered to be in cleavage stage. Embryos in cleavage were collected between days 3 and 6 post-coitus. Of the collected embryos, 80% presented an even number of blastomeres and the remaining 20% an odd number. Embryos from 3 to 7 cells were blastomere associations in a spherical disposition within the zona pellucida. Blastomeres were spherical or ovoid, presenting slight flattening in areas contacting with other blastomeres. Embryos of 8 and 9 cells were as a group of blastomeres slightly elongated, surrounded by a spherical zona pellucida. The percentage of peri-vitelline space occupied by the embryonic mass ranged from 74.1 to 95.8% for all the substages. The cleavage pattern, developed in the oviduct, was of a rotational holoblastic type and asynchronic. PMID:15027947

Felipe, A E; Teruel, M T; Cabodevila, J A; Callejas, S S



Investing in  

NSDL National Science Digital Library

Investing in Bonds was created by the Bond Market Association to educate investors about the benefits of bonds investing. The Investor's Guide to Bond Basics educates investors about the types of bonds available, criteria for evaluating a bond, a guide to buying bonds, bond investment strategies and a glossary of bond market terms. The Bond Market section provides an overview of the U.S. bond market while the Investor's Checklist section takes the investor step-by-step through the bond investment decision process. Investors will also find sections with information on municipal bonds, corporate bonds, mortgage securities and U.S. Inflation-Indexed Securities.


Biosynthetic labeling of hypusine in mammalian cells. Carbon-hydrogen bond fissions revealed by dual labeling  

SciTech Connect

Using a dual-label technique in which /sup 3/H- and /sup 14/C-labeled forms of putrescine and of spermidine were employed as biosynthetic precursors of hypusine, two -C-H bond cleavages were detected during production of this unique amino acid in Chinese hamster ovary cells. One of these cleavages occurs at C-1 of the 4-aminobutyl group during its transfer from the secondary amine nitrogen of spermidine to the nitrogen at the epsilon-position of a specific lysine residue in the polypeptide precursor of eukaryotic initiation factor 4D. Breakage of the other -C-H bond takes place at C-2 in this aminobutyl segment after it has been coupled to lysine to form the intermediate deoxyhypusine residue. Hydroxylation at this carbon atom, which constitutes the last step in hypusine biosynthesis, is the cause of bond cleavage. The data obtained are consistent with a notion that no additional -C-H bond fissions occur during hypusine biosynthesis. Our findings permit suggestion of a mechanism for enzymic aminobutyl group transfer in which 4-aminobutyraldehyde produced by oxidative cleavage of spermidine is coupled with the epsilon-amino group of a specific lysine residue to form an enzyme-bound imine intermediate.

Park, M.H.; Folk, J.E.




E-print Network

brakes are frequently made of carbon/carbon (C=C) compos- ites. To deposit the composite interphaseINTERACTION BETWEEN GAS DIFFUSION AND MULTISTABLE HETEROGENEOUS CHEMICAL KINETICS IN C=C COMPOSITE PROCESSING G#19;erard L. VIGNOLES Universit#19;e Bordeaux 1, Laboratoire des Composites ThermoStructuraux 3

Recanati, Catherine


The University of Texas at Dallas Erik Jonsson School c C. D. Cantrell (06/1997)  

E-print Network

The University of Texas at Dallas Erik Jonsson School PhoTEC c C. D. Cantrell (06/1997) FRESNEL analytical solution Numerical solution #12;The University of Texas at Dallas Erik Jonsson School PhoTEC c C negligible except for very small aper- tures or obstacles · In a uniform dielectric and in Cartesian

Hart, Gus


Abnormal Early Cleavage Events Predict Early Embryo Demise: Sperm Oxidative Stress and Early Abnormal Cleavage  

PubMed Central

Human embryos resulting from abnormal early cleavage can result in aneuploidy and failure to develop normally to the blastocyst stage. The nature of paternal influence on early embryo development has not been directly demonstrated although many studies have suggested effects from spermatozoal chromatin packaging, DNA damage, centriolar and mitotic spindle integrity, and plasma membrane integrity. The goal of this study was to determine whether early developmental events were affected by oxidative damage to the fertilizing sperm. Survival analysis was used to compare patterns of blastocyst formation based on P2 duration. Kaplan-Meier survival curves demonstrate that relatively few embryos with short (<1?hr) P2 times reached blastocysts, and the two curves diverged beginning on day 4, with nearly all of the embryos with longer P2 times reaching blastocysts by day 6 (p < .01). We determined that duration of the 2nd to 3rd mitoses were sensitive periods in the presence of spermatozoal oxidative stress. Embryos that displayed either too long or too short cytokineses demonstrated an increased failure to reach blastocyst stage and therefore survive for further development. Although paternal-derived gene expression occurs later in development, this study suggests a specific role in early mitosis that is highly influenced by paternal factors. PMID:25307782

Burruel, Victoria; Klooster, Katie; Barker, Christopher M.; Pera, Renee Reijo; Meyers, Stuart



Abnormal early cleavage events predict early embryo demise: sperm oxidative stress and early abnormal cleavage.  


Human embryos resulting from abnormal early cleavage can result in aneuploidy and failure to develop normally to the blastocyst stage. The nature of paternal influence on early embryo development has not been directly demonstrated although many studies have suggested effects from spermatozoal chromatin packaging, DNA damage, centriolar and mitotic spindle integrity, and plasma membrane integrity. The goal of this study was to determine whether early developmental events were affected by oxidative damage to the fertilizing sperm. Survival analysis was used to compare patterns of blastocyst formation based on P2 duration. Kaplan-Meier survival curves demonstrate that relatively few embryos with short (<1?hr) P2 times reached blastocysts, and the two curves diverged beginning on day 4, with nearly all of the embryos with longer P2 times reaching blastocysts by day 6 (p < .01). We determined that duration of the 2nd to 3rd mitoses were sensitive periods in the presence of spermatozoal oxidative stress. Embryos that displayed either too long or too short cytokineses demonstrated an increased failure to reach blastocyst stage and therefore survive for further development. Although paternal-derived gene expression occurs later in development, this study suggests a specific role in early mitosis that is highly influenced by paternal factors. PMID:25307782

Burruel, Victoria; Klooster, Katie; Barker, Christopher M; Pera, Renee Reijo; Meyers, Stuart



A Common Eurozone Bond  

Microsoft Academic Search

Introduction\\u000aThe sovereign bond yields of the Eurozone, or more correctly the euro area, have since the introduction of the Euro undergone a bond yield compression. However, as can be seen in table 1, these bond yields started to diverge considerably around mid 2008 following the recent financial crisis and increased sovereign risk. Yields on Greek, Irish, and Portuguese bond

Erik Welin



Rapid adhesive bonding concepts  

NASA Technical Reports Server (NTRS)

Adhesive bonding in the aerospace industry typically utilizes autoclaves or presses which have considerable thermal mass. As a consequence, the rates of heatup and cooldown of the bonded parts are limited and the total time and cost of the bonding process is often relatively high. Many of the adhesives themselves do not inherently require long processing times. Bonding could be performed rapidly if the heat was concentrated in the bond lines or at least in the adherends. Rapid adhesive bonding concepts were developed to utilize induction heating techniques to provide heat directly to the bond line and/or adherends without heating the entire structure, supports, and fixtures of a bonding assembly. Bonding times for specimens are cut by a factor of 10 to 100 compared to standard press bonding. The development of rapid adhesive bonding for lap shear specimens (per ASTM D1003 and D3163), for aerospace panel bonding, and for field repair needs of metallic and advanced fiber reinforced polymeric matrix composite structures are reviewed.

Stein, B. A.; Tyeryar, J. R.; Hodges, W. T.



Making and Breaking Bonds  

NSDL National Science Digital Library

Atoms collide and, under certain circumstances, react to form bonds with one another. The process of association is the bonding of atoms into a molecule while dissociation is the process by which a molecule breaks apart into simpler groups of atoms, individual atoms, or ions. Students interact with a molecular dynamics model to explore the making and breaking of bonds.

Consortium, The C.



Mapping of nuclease-sensitive sites in native reticulocyte ribosomes--an analysis of the accessibility of ribosomal RNA to enzymatic cleavage.  


Treatment of ribosomes in reticulocyte lysates with low concentrations of the calcium-dependent nuclease from Staphylococcus aureus resulted in cleavage of rRNA. The positions of the cleaved phosphodiester bonds were localised by primer extension and polyacrylamide gel electrophoresis. S. aureus nuclease-induced strand scissions were found in the 5'-domain of 18S rRNA and in domains II, IV and VI of 28S rRNA. The majority of the cleavage sites were located in eukaryote-specific expansion segments and only one cleavage site was found in a region suggested to be directly involved in ribosomal function. Treatment of the reticulocyte lysate with increasing amounts of S. aureus nuclease resulted in the introduction of new cleavage sites. However, even at the highest nuclease concentration used, large parts of the rRNAs were protected from nuclease digestion. Removal of translational components, by salt wash of isolated reticulocyte polysomes, exposed additional rRNA sequences to S. aureus nuclease cleavage. These sequences were found in the 3'-major domain of 18S rRNA and in domains II, IV, and V of 28S rRNA. These sites are located at the putative translational surface of the ribosome. The translational activity of the S. aureus nuclease-treated ribosomes, determined after addition of exogenous mRNA, was directly correlated to the extent of nuclease digestion of the ribosomes. However, the decrease in translational activity observed in lysates treated with low amounts of S. aureus nuclease was not due to a preferential exclusion of damaged ribosomes from polysome formation. This suggests that the induced cleavages were not detrimental to ribosomal function but could influence the rate of ribosomal movement along the mRNA. PMID:9249022

Holmberg, L; Nygård, O



The SIZE OF THINGS H-BOND = 2-5 kcal/mol  

E-print Network

C H 1.1 � C C 1.5 � C C 1.3 � C C 1.2 � The SIZE OF THINGS H-BOND = 2-5 kcal/mol FREE ENERGY AND Keq G = ­RT ln Keq Naphthalene: 6.1 x 5.1 � DNA helix: Protein: (300 aa) 50 � diameter Lipid bilayer: 50 � across (5 nm) Red blood cell: Thymus cell: Liver cell: Let's call an average cell 20 µm diam

Gates, Kent. S.


Oxidative DNA Cleavage by the Antitumor Antibiotic Leinamycin and Simple  

E-print Network

-dependent Fenton reaction10 (Figure 1). Addition of the enzyme superoxide dismutase (SOD) stimulates DNA cleavage The natural product leinamycin (1),1 thought to derive its antitumor activity through reactions with DNA, is of interest because of its potent biological activity and because it represents a new chemical class of DNA

Gates, Kent. S.


Exoproteolytic cleavage of N-terminal His tags QIAGEN Distributors  

E-print Network

June 2001 TAGZymeTM Handbook For Exoproteolytic cleavage of N-terminal His tags #12;QIAGEN Distributors Please see the last page for contact information for your local QIAGEN distributor. Australia QIAGEN Pty Ltd PO Box 25 · Clifton Hill · Victoria 3068 ABN 75 072 382 944 Orders 03-9489-3666 · Fax 03

Lebendiker, Mario


Scientific Correspondence Cleavage of Bipartite Substrates by Rice and Maize  

E-print Network

Scientific Correspondence Cleavage of Bipartite Substrates by Rice and Maize Ribonuclease P III, George Thomas, and Venkat Gopalan* Departments of Biochemistry (M.L.S.R., D.K.P., J.F.R., V with rice (Oryza sativa) and maize (Zea mays) nuclear RNase P. By successively employing ion

Gopalan, Venkat



E-print Network

) is generated by the first step of spliceosomal splicing. The cis- and trans- acting factors that distinguish the single step spliceosomal cleavage in TER1 from the two-step splicing reaction that removes introns in other genes are being investigated. We now...




Social identities and political cleavages: the role of political context  

Microsoft Academic Search

Using a novel method, the paper investigates the influence of social group identities on attitudes and on voting in a variety of political contexts. Examining the major regions of Britain, Canada and the USA, we find considerable national and regional diversity in the nature of social cleavages. For example, social class and race had widely different effects across societies, but

Robert Andersen; Anthony Heath



Crosstalk between transposase subunits during cleavage of the mariner transposon  

PubMed Central

Mariner transposition is a complex reaction that involves three recombination sites and six strand breaking and joining reactions. This requires precise spatial and temporal coordination between the different components to ensure a productive outcome and minimize genomic instability. We have investigated how the cleavage events are orchestrated within the mariner transpososome. We find that cleavage of the non-transferred strand is completed at both transposon ends before the transferred strand is cleaved at either end. By introducing transposon-end mutations that interfere with cleavage, but leave transpososome assembly unaffected, we demonstrate that a structural transition preceding transferred strand cleavage is coordinated between the two halves of the transpososome. Since mariner lacks the DNA hairpin intermediate, this transition probably reflects a reorganization of the transpososome to allow the access of different monomers onto the second pair of strands, or the relocation of the DNA within the same active site between two successive hydrolysis events. Communication between transposase subunits also provides a failsafe mechanism that restricts the generation of potentially deleterious double-strand breaks at isolated sites. Finally, we identify transposase mutants that reveal that the conserved WVPHEL motif provides a structural determinant of the coordination mechanism. PMID:24623810

Claeys Bouuaert, Corentin; Walker, Neil; Liu, Danxu; Chalmers, Ronald



Crosstalk between transposase subunits during cleavage of the mariner transposon.  


Mariner transposition is a complex reaction that involves three recombination sites and six strand breaking and joining reactions. This requires precise spatial and temporal coordination between the different components to ensure a productive outcome and minimize genomic instability. We have investigated how the cleavage events are orchestrated within the mariner transpososome. We find that cleavage of the non-transferred strand is completed at both transposon ends before the transferred strand is cleaved at either end. By introducing transposon-end mutations that interfere with cleavage, but leave transpososome assembly unaffected, we demonstrate that a structural transition preceding transferred strand cleavage is coordinated between the two halves of the transpososome. Since mariner lacks the DNA hairpin intermediate, this transition probably reflects a reorganization of the transpososome to allow the access of different monomers onto the second pair of strands, or the relocation of the DNA within the same active site between two successive hydrolysis events. Communication between transposase subunits also provides a failsafe mechanism that restricts the generation of potentially deleterious double-strand breaks at isolated sites. Finally, we identify transposase mutants that reveal that the conserved WVPHEL motif provides a structural determinant of the coordination mechanism. PMID:24623810

Claeys Bouuaert, Corentin; Walker, Neil; Liu, Danxu; Chalmers, Ronald



Surface atomic geometry and electronic structure of II--VI cleavage faces  

SciTech Connect

Recent models of the electronic structure and surface atomic geometries on wurtzite-structure CdS and CdSe have been extended to encompass zinc-blende structure CdTe. The driving force for the surface reconstruction of the cleavage faces of all these materials is the lowering in energy of a band of anion dangling bond surface states accompanied by their acquisition of back-bonding character. The resulting reconstructed surface is characterized by the eigenvalue spectrum associated with this band of states as well as the atomic geometries. The predicted geometries for CdTe(110), CdSe(101-bar0), and CdSe(112-bar0) are in good correspondence with low-energy electron diffraction (LEED) and low-energy positron diffraction intensity analyses. The calculated surface state eigenvalue spectra are compared with recent angle-resolved photoemission spectra (ARPES) for CdTe(110) and CdSe(101-bar0). The main features of the ARPES measurements are reproduced by the calculated eigenvalue spectra. The predicted atomic geometry for CdTe(110) corresponds well both with prior predictions for ZnSe(110) and ZnS(110), and with LEED experimental surface structures indicating that these surfaces exhibit a universal structure in which the independent surface structural parameters scale linearly with the bulk lattice constant.

Duke, C.B.; Wang, Y.R.



Analysis of carotenoid isomerase activity in a prototypical carotenoid cleavage enzyme, apocarotenoid oxygenase (ACO).  


Carotenoid cleavage enzymes (CCEs) constitute a group of evolutionarily related proteins that metabolize a variety of carotenoid and non-carotenoid substrates. Typically, these enzymes utilize a non-heme iron center to oxidatively cleave a carbon-carbon double bond of a carotenoid substrate. Some members also isomerize specific double bonds in their substrates to yield cis-apocarotenoid products. The apocarotenoid oxygenase from Synechocystis has been hypothesized to represent one such member of this latter category of CCEs. Here, we developed a novel expression and purification protocol that enabled production of soluble, native ACO in quantities sufficient for high resolution structural and spectroscopic investigation of its catalytic mechanism. High performance liquid chromatography and Raman spectroscopy revealed that ACO exclusively formed all-trans products. We also found that linear polyoxyethylene detergents previously used for ACO crystallization strongly inhibited the apocarotenoid oxygenase activity of the enzyme. We crystallized the native enzyme in the absence of apocarotenoid substrate and found electron density in the active site that was similar in appearance to the density previously attributed to a di-cis-apocarotenoid intermediate. Our results clearly demonstrated that ACO is in fact a non-isomerizing member of the CCE family. These results indicate that careful selection of detergent is critical for the success of structural studies aimed at elucidating structures of CCE-carotenoid/retinoid complexes. PMID:24648526

Sui, Xuewu; Kiser, Philip D; Che, Tao; Carey, Paul R; Golczak, Marcin; Shi, Wuxian; von Lintig, Johannes; Palczewski, Krzysztof



Design of controlled drug delivery system based on disulfide cleavage trigger.  


The disulfide bond has drawn increasing attention for the application on controlled drug delivery systems (CDDSs) due to its high redox sensibility, which is derived from the fact that the concentration of glutathione (GSH), a disulfide-bond-breaking agent, in the tumor tissue is 1000-fold higher than that in the blood plasma and the normal tissue. Thus, a disulfide is an ideal candidate for serving as the drug release trigger of CDDSs, which would be stable in the blood circulation and be broken when it reached the tumor tissue. However, improvements are still required in designing the structure of CDDSs and the drug loading patterns for CDDSs, which are important to the performance of CDDSs. This Feature Article briefly summarizes our recent research progress on the design and construction of CDDSs based on disulfide cleavage triggers, with different drug loading strategies (covalent and noncovalent) and carriers (copolymer and mesoporous silica nanoparticle). The controlled drug release mechanism and behaviors of these CDDSs are also discussed. PMID:25320865

Yang, Dong; Chen, Wulian; Hu, Jianhua



General Education Coursework: Credits General Education Coursework: Credits ENGL 110C (C or better) 3 ENGL 211C, 221C or 231C ( C or better) 3  

E-print Network

General Education Coursework: Credits General Education Coursework: Credits ENGL 110C (C or better: Credits General Education Coursework: Credits Information Literacy and Research 3 Human Creativity 3 BIOL SEMESTER (17 credits) SPRING SEMESTER (18 Major Coursework: Major Coursework: Major Coursework: Credits


Prospective bonding applications  

NASA Astrophysics Data System (ADS)

Adhesive bonding in industry and in the laboratory is surveyed and prospects for its wider utilization are assessed. The economic impact of bonding technology on industry is discussed. Research is reviewed, centering on the development of nondestructive testing and inspection techniques. Traditional (wood) as well as new materials susceptible to bonding are considered. Applications in construction and civil engineering, in aeronautics, and in the automobile industry are covered. The use of glues in mechanical constructions, in assembling cylindrical parts, and in metal-metal bonding are examined. Hybrid assembling and bonding of composite materials are included.

Ancenay, H.; Benazet, D.



Universal Bronsted-Evans-Polanyi Relations for C-C, C-O, C-N, N-O, N-N, and O-O Dissociation Reactions  

SciTech Connect

It is shown that for all the essential bond forming and bond breaking reactions on metal surfaces, the reactivity of the metal surface correlates linearly with the reaction energy in a single universal relation. Such correlations provide an easy way of establishing trends in reactivity among the different transition metals.

Wang, Shengguang



Brazing of C/C composites and Ni-based alloy using interlayer  

NASA Astrophysics Data System (ADS)

The brazing of C/C composites and Inconel-600 Ni-based heat resistant alloy was conducted using Fe-Ni-Cr-P-Si brazing filler alloy with inserting various thickness of Nb foil as stress relief interlayer. SEM observation of cross section of brazing interface revealed that Nb foil was resolved into the brazing filler layer on C/C composites side. Nb diffused to the surface of C/C composites and acted as the active metal element to enhance the wettability of molten metal on graphite matrix of C/C composites during the brazing process. The variation in shear strength values of the brazed joint with Nb layer thickness suggested that the Nb layer should be remained at least 100 ?m.

Ikeshoji, Toshi-Taka; Tokunaga, Tatsuya; Suzumura, Akio; Yamazaki, Takahisa



Cinematographic observation of “surface contraction waves” (SCW) during the early cleavage of axolotl eggs  

Microsoft Academic Search

Prior to the appearance of the cleavage furrows circular or semicircular zones suggesting surface contraction originate at the future initiation point of the cleavage furrow. They expand and travel in animal-vegetative direction.

K. Hara



Active Metal Brazing and Characterization of Brazed Joints in C-C and C-SiC Composites to Copper-Clad-Molybdenum System  

NASA Technical Reports Server (NTRS)

Carbon/carbon composites with CVI and resin-derived matrices, and C/SiC composites reinforced with T-300 carbon fibers in a CVI SiC matrix were joined to Cu-clad Mo using two Ag-Cu braze alloys, Cusil-ABA (1.75% Ti) and Ticusil (4.5% Ti). The brazed joints revealed good interfacial bonding, preferential precipitation of Ti at the composite/braze interface, and a tendency toward delamination in resin-derived C/C composite. Extensive braze penetration of the inter-fiber channels in the CVI C/C composites was observed. The Knoop microhardness (HK) distribution across the C/C joints indicated sharp gradients at the interface, and a higher hardness in Ticusil than in Cusil-ABA. For the C/SiC composite to Cu-clad-Mo joints, the effect of composite surface preparation revealed that ground samples did not crack whereas unground samples cracked. Calculated strain energy in brazed joints in both systems is comparable to the strain energy in a number of other ceramic/metal systems. Theoretical predictions of the effective thermal resistance suggest that such joined systems may be promising for thermal management applications.

Singh, M.; Asthana, R.



The Binding Orientation of a Norindenoisoquinoline in the Topoisomerase I-DNA Cleavage Complex Is Primarily Governed by ?-? Stacking Interactions  

PubMed Central

High level ab initio quantum chemical studies have shown that the binding orientations of topoisomerase I (Top1) inhibitors such as camptothecins and indenoisoquinolines are primarily governed by ?-? stacking. However, a recently discovered norindenoisoquinoline antitumor compound was observed by X-ray crystallography to adopt a “flipped” orientation (relative to indenoisoquinolines), which facilitates the formation of a characteristic hydrogen bond with the Arg364 of Top1 in its binding with the Top1-DNA complex. This observation raises the possibility that hydrogen bonding between the norindenoisoquinoline nitrogen and the Arg364 side chain of Top1 might be responsible for the “flip”. It also brings into question whether ?-? stacking, as opposed to hydrogen bonding, is primarily responsible for the binding orientations of indenoisoquinolines and norindenoisoquinolines. In this study, the forces responsible for the binding orientation of a norindenoisoquinoline in the DNA cleavage site were systematically investigated using MP2 methods. The theoretical calculation of the preferred binding orientation based solely on ?-? stacking was completely consistent with the actual orientation observed by X-ray crystallography, indicating that the binding of the norindenoisoquinoline in the Top1-DNA complex is mainly governed by ?-? stacking forces and that the “flip” can occur independently from hydrogen bonding. PMID:18636761

Song, Yunlong; Cushman, Mark



Cleavage specificity of a proteolytic antibody light chain and effects of the heavy chain variable domain.  


The recombinant light chain (L chain) of an antibody raised by immunization with vasoactive intestinal polypeptide (VIP) cleaved this peptide on the C-terminal side of basic residues. The major sites of cleavage in VIP were two adjacent peptide bonds, Lys20-Lys21 and Lys21-Tyr22. Lower levels of cleavage were evident at Arg14-Lys15 and Lys15-Gln16. Hydrolysis of radiolabeled VIP by the L chain was inhibited by two serine protease inhibitors, diisopropylfluorophosphate and aprotinin, but not by soybean or lima bean trypsin inhibitors or inhibitors of other classes of proteases. To probe the role of the VH domain, single chain Fv constructs composed of the VL domain of the anti-VIP L chain linked via a 14-residue peptide to its natural VH domain partner or an irrelevant anti-lysozyme VH domain (hybrid Fv) were prepared. The anti-VIP Fv hydrolyzed VIP with Ks 21.4-fold lower than the L chain and 250-fold lower than the hybrid Fv, suggesting increased affinity for the substrate ground state due to the anti-VIP VH domain. The kinetic efficiency (kcat/Ks) of the anti-VIP Fv was 6.6-fold greater compared to the L chain and 29.4-fold greater compared to the hybrid Fv. Peptide-MCA substrates unrelated in sequence to VIP were hydrolyzed by the anti-VIP Fv and L chain at equivalent rates. These observations lead to a model of catalysis by the anti-VIP Fv in which the essential catalytic residues are located in the VL domain and additional residues from the VH domain are involved in high affinity binding of the substrate. PMID:9268666

Sun, M; Gao, Q S; Kirnarskiy, L; Rees, A; Paul, S



Proteolytic cleavage of Ser52Pro variant transthyretin triggers its amyloid fibrillogenesis.  


The Ser52Pro variant of transthyretin (TTR) produces aggressive, highly penetrant, autosomal-dominant systemic amyloidosis in persons heterozygous for the causative mutation. Together with a minor quantity of full-length wild-type and variant TTR, the main component of the ex vivo fibrils was the residue 49-127 fragment of the TTR variant, the portion of the TTR sequence that previously has been reported to be the principal constituent of type A, cardiac amyloid fibrils formed from wild-type TTR and other TTR variants [Bergstrom J, et al. (2005) J Pathol 206(2):224-232]. This specific truncation of Ser52Pro TTR was generated readily in vitro by limited proteolysis. In physiological conditions and under agitation the residue 49-127 proteolytic fragment rapidly and completely self-aggregates into typical amyloid fibrils. The remarkable susceptibility to such cleavage is likely caused by localized destabilization of the ?-turn linking strands C and D caused by loss of the wild-type hydrogen-bonding network between the side chains of residues Ser52, Glu54, Ser50, and a water molecule, as revealed by the high-resolution crystallographic structure of Ser52Pro TTR. We thus provide a structural basis for the recently hypothesized, crucial pathogenic role of proteolytic cleavage in TTR amyloid fibrillogenesis. Binding of the natural ligands thyroxine or retinol-binding protein (RBP) by Ser52Pro variant TTR stabilizes the native tetrameric assembly, but neither protected the variant from proteolysis. However, binding of RBP, but not thyroxine, inhibited subsequent fibrillogenesis. PMID:24474780

Mangione, P Patrizia; Porcari, Riccardo; Gillmore, Julian D; Pucci, Piero; Monti, Maria; Porcari, Mattia; Giorgetti, Sofia; Marchese, Loredana; Raimondi, Sara; Serpell, Louise C; Chen, Wenjie; Relini, Annalisa; Marcoux, Julien; Clatworthy, Innes R; Taylor, Graham W; Tennent, Glenys A; Robinson, Carol V; Hawkins, Philip N; Stoppini, Monica; Wood, Stephen P; Pepys, Mark B; Bellotti, Vittorio



The Role of Multiple, Reformable Parallel Bonds on the Self-healing Behavior of Dual Crosslinked Nanogel Materials  

NASA Astrophysics Data System (ADS)

Using computational modeling, we design novel self-healing materials composed of nanoscopic polymer gel particles, or nanogels. The particles are interconnected via both labile bonds (e.g., disulfide bonds) and stronger, less reactive bonds (e.g, C-C bonds) and therefore the nanogels form a "dual crosslinked" network. The stable bonds provide a rigid backbone while the labile bonds allow the material to undergo a dynamic reconfiguration in response to stress. We adapt the Hierarchical Bell Model (HBM) to describe the labile bonding interactions. The HBM effectively allows us to model cases where the ligands on neighboring nanogels interact through multiple sites. We show that the introduction of a small number of labile bonds that lie in parallel significantly increases the strength of the material relative to samples crosslinked solely by the stable bonds. We also isolate an optimal range of labile interconnections that provide high-strength, tough materials that are capable of self-repair.

Salib, Isaac G.; Kolmakov, German V.; Gnegy, Chet N.; Matyjaszewski, Krzysztof; Balazs, Anna C.



A pathway sensor for genome-wide screens of intracellular proteolytic cleavage  

Microsoft Academic Search

Protein cleavage is a central event in many regulated biological processes. We describe a system for detecting intracellular proteolysis based on non-conventional secretion of Gaussia luciferase (GLUC). GLUC exits the cell without benefit of a secretory leader peptide, but can be anchored in the cell by fusion to ?-actin. By including protease cleavage sites between GLUC and ?-actin, proteolytic cleavage

Robin Ketteler; Zairen Sun; Karl F Kovacs; Wei-Wu He; Brian Seed



Computational Study of Bond Dissociation Enthalpies for Lignin Model Compounds. Substituent Effects in Phenethyl Phenyl Ethers  

SciTech Connect

Lignin is an abundant natural resource that is a potential source of valuable chemicals. Improved understanding of the pyrolysis of lignin occurs through the study of model compounds for which phenethyl phenyl ether (PhCH2CH2OPh, PPE) is the simplest example representing the dominant -O-4 ether linkage. The initial step in the thermal decomposition of PPE is the homolytic cleavage of the oxygen-carbon bond. The rate of this key step will depend on the bond dissociation enthalpy, which in turn will depend on the nature and location of relevant substituents. We used modern density functional methods to calculate the oxygen-carbon bond dissociation enthalpies for PPE and several oxygen substituted derivatives. Since carbon-carbon bond cleavage in PPE could be a competitive initial reaction under high temperature pyrolysis conditions, we also calculated substituent effects on these bond dissociation enthalpies. We found that the oxygen-carbon bond dissociation enthalpy is substantially lowered by oxygen substituents situated at the phenyl ring adjacent to the ether oxygen. On the other hand, the carbon-carbon bond dissociation enthalpy shows little variation with different substitution patterns on either phenyl ring.

Beste, Ariana [ORNL; Buchanan III, A C [ORNL



Brittle cleavage fracture: An overview of some historical aspects  

SciTech Connect

Many aspects of cleavage fracture were not well understood by the mid-1950s when George R. Irwin coined the term Fracture Mechanics. This discussion will attempt to relate some of the common concepts and misconceptions of that period. The leadership of Dr. Irwin in developing new concepts and methods for clarifying the understanding of brittle fracture will be emphasized here. An essential part of the progress made was to bring together the Engineering Mechanics, Metallurgy, and Physics of the subject into a reasoned balance in trying to further understand the nature of the phenomena. This is illustrated by recalling some of the personalities of that time period and their concepts and claims and how they interacted to make progress toward today`s state of knowledge. Indeed today`s closer ties between fields such as mechanics and metallurgy were in part caused by these requirements of analysis of Brittle Cleavage Fracture.

Paris, P.C. [Washington Univ., St. Louis, MO (United States). Dept. of Mechanical Engineering



Cleavage of bleomycin hydrolase by caspase-3 during apoptosis.  


Bleomycin hydrolase (BLH) affects bleomycin chemotherapy through inactivation of bleomycin with deamination. As a neutral cysteine protease, it also plays various roles in physiological conditions and diseases. However, its mechanism of degradation remains unclear. In the present study, we showed that the levels of BLH were significantly reduced during apoptosis induced by the antitumor agents bleomycin, etoposide and hydroxycamptothecin, and inhibited by the caspase inhibitors Q-VD-oph and Z-DEVD-FMK. Furthermore, the caspase-dependent cleavage of BLH was confirmed by cleavage of partly-purified human BLH with caspase-3 and caspase-9 in vitro. The stability of BLH at normal culture conditions was analyzed with the protein synthesis inhibitor cycloheximide and the proteasome inhibitor MG132. BLH was degraded at a rate lower than that of cyclin D1. This is the first report to demonstrate that BLH is cleaved by caspase-3 during apoptosis. PMID:23708668

Chen, Yang; Xu, Rong; Chen, Jianguo; Li, Xiaoyu; He, Qiyang



Energy pulse bonding  

NASA Technical Reports Server (NTRS)

To eliminate many of the present termination problems a technique called energy pulse bonding (EPB) was developed. The process demonstrated the capability of: (1) joining conductors without prior removal of insulations, (2) joining conductors without danger of brittle intermetallics, (3) increased joint temperature capability, (4) simultaneous formation of several bonds, (5) capability of higher joint density, and (6) a production oriented process. The following metals were successfully bonded in the solid state: copper, beryllium copper, phosphor bronze, aluminum, brass, and Kovar.

Smith, G. C.



Chemical bonding technology  

NASA Technical Reports Server (NTRS)

Primers employed in bonding together the various material interfaces in a photovoltaic module are being developed. The approach develops interfacial adhesion by generating actual chemical bonds between the various materials bonded together. The current status of the program is described along with the progress toward developing two general purpose primers for ethylene vinyl acetate (EVA), one for glass and metals, and another for plastic films.

Plueddemann, E.



Stepwise cyclopalladation of 2-phenacylthiopyridine to give C,C,N-pincer complexes.  


Orthopalladation of the phenyl ring in the cyclopalladated complex [Pd{C,N-pyl-SCHC(O)Ph}(?-X)]2 (pyl = 2-pyridyl, X = Cl; 1·Cl) occurs upon reacting it with AgOAc (1?:?2) in MeCN to give the pincer complex [Pd{C,C,N-pyl-SCHC(O)C6H4-2}(NCMe)] (2). The nature of the base and X plays a key role because palladation neither occurs with other bases nor when AgOAc is the base and X is Br, in which case 1·OAc is obtained. In addition, complex 2 is not obtained upon refluxing 1·OAc in MeCN. Complex 2 affords complexes [Pd{C,C,N,S-pyl-SCHC(O)C6H4-2}]n, [Pd{C,C,N-pyl-SCHC(O)C6H4-2}L] (L = PPh3, (t)BuNC, XyNC) or Me4N[Pd{C,C,N-pyl-SCHC(O)C6H4-2}Cl] upon acetonitrile loss, or its replacement by neutral or anionic ligands, respectively. Some such complexes act as metallaligands towards AgClO4 or [PdCl2(NCPh)2] giving rise to heterodinuclear [{Pd{C,C,N-pyl-SCHC(O)C6H4-2}(PPh3)}{Ag(PPh3)}]ClO4 or homodinuclear [{Pd{C,C,N-pyl-SCHC(O)C6H4-2}(Cl)}{Pd(?-Cl)}]2, [{Pd{C,C,N-pyl-SCHC(O)C6H4-2}(Cl)}{Pd(Cl)(PPh3}] complexes. Some derivatives of complexes 1 were also obtained. PMID:25182692

Chicote, María-Teresa; Rubio, Concepción; Bautista, Delia; Vicente, José



Model for an inductively coupled Ar/c-C4F8 plasma discharge  

NASA Astrophysics Data System (ADS)

This article describes a two-dimensional model for an inductively coupled Ar/c-C4F8 plasma discharge, which is widely used in the microelectronics industry for dielectric etching and polymerization. The chemical mechanism for c-C4F8 incorporates known information about electron impact dissociation, ionization, and attachment processes. Unknown details such as neutral dissociation byproducts have been empirically inferred using energetics analysis or diagnostic experiments. The mechanism also considers electron impact processes for neutral radicals (e.g., CF, CF2, CF3) and stable molecules (e.g., C2F4) produced in a c-C4F8 plasma. It is demonstrated in the article that the resulting neutral species densities, ion flux to the wafer, and electron characteristics are in good agreement with experiments in the Gaseous Electronics Conference reference cell. The validated model is used to understand the dynamics of an inductively coupled Ar/c-C4F8 plasma discharge, and the impact of various control parameters on plasma characteristics. Results indicate that CF2 is the dominant CFx radical in the c-C4F8 discharge and the plasma is mildly electronegative. Enhanced ionization and dissociation of c-C4F8 with increasing inductive power deposition leads to an increase in electron and CFx radical densities, and total ion flux to the wafer. Enhanced dissociative attachment at higher gas pressure decreases the electron density and increases the negative ion density. The plasma becomes more electropositive with decreasing c-C4F8 concentration in the gas mixture, which increases the total positive ion flux to the wafer.

Rauf, Shahid; Ventzek, Peter L. G.



Etheric C-O bond hydrogenolysis using a tandem lanthanide triflate/supported palladium nanoparticle catalyst system.  


Selective hydrogenolysis of cyclic and linear ether C-O bonds is accomplished by a tandem catalytic system consisting of lanthanide triflates and sinter-resistant supported palladium nanoparticles in an ionic liquid. The lanthanide triflates catalyze endothermic dehydroalkoxylation, while the palladium nanoparticles hydrogenate the resulting intermediate alkenols to afford saturated alkanols with high overall selectivity. The catalytic C-O hydrogenolysis is shown to have significant scope, and the C-O bond cleavage is turnover-limiting. PMID:22889142

Atesin, Abdurrahman C; Ray, Natalie A; Stair, Peter C; Marks, Tobin J



Borylation and silylation of C-H bonds: a platform for diverse C-H bond functionalizations.  


Methods that functionalize C-H bonds can lead to new approaches for the synthesis of organic molecules, but to achieve this goal, researchers must develop site-selective reactions that override the inherent reactivity of the substrates. Moreover, reactions are needed that occur with high turnover numbers and with high tolerance for functional groups if the C-H bond functionalization is to be applied to the synthesis of medicines or materials. This Account describes the discovery and development of the C-H bond functionalization of aliphatic and aromatic C-H bonds with borane and silane reagents. The fundamental principles that govern the reactivity of intermediates containing metal-boron bonds are emphasized and how an understanding of the effects of the ligands on this reactivity led us to broaden the scope of main group reagents that react under mild conditions to generate synthetically useful organosilanes is described. Complexes containing a covalent bond between a transition metal and a three-coordinate boron atom (boryl complexes) are unusually reactive toward the cleavage of typically unreactive C-H bonds. Moreover, this C-H bond cleavage leads to the formation of free, functionalized product by rapid coupling of the hydrocarbyl and boryl ligands. The initial observation of the borylation of arenes and alkanes in stoichiometric processes led to catalytic systems for the borylation of arenes and alkanes with diboron compounds (diborane(4) reagents) and boranes. In particular, complexes based on the Cp*Rh (in which Cp is the cyclopentadienyl anion) fragment catalyze the borylation of alkanes, arenes, amines, ethers, ketals, and haloalkanes. Although less reactive toward alkyl C-H bonds than the Cp*Rh systems, catalysts generated from the combination of bipyridines and iridium(I)-olefin complexes have proven to be the most reactive catalysts for the borylation of arenes. The reactions catalyzed by these complexes form arylboronates from arenes with site-selectivity for C-H bond cleavage that depends on the steric accessibility of the C-H bonds. These complexes also catalyze the borylation of heteroarenes, and the selectivity for these substrates is more dependent on electronic effects than the borylation of arenes. The products from the borylation of arenes and heteroarenes are suitable for a wide range of subsequent conversions to phenols, arylamines, aryl ethers, aryl nitriles, aryl halides, arylboronic acids, and aryl trifluoroborates. Studies of the electronic properties of the ancillary ligand on the rate of the reaction show that the flat structure and the strong electron-donating property of the bipyridine ligands, along with the strong electron-donating property of the boryl group and the presence of a p-orbital on the metal-bound atom, lead to the increased reactivity of the iridium catalysts. Based on this hypothesis, we studied catalysts containing substituted phenanthroline ligands for a series of additional transformations, including the silylation of C-H bonds. A sequence involving the silylation of benzylic alcohols, followed by the dehydrogenative silylation of aromatic C-H bonds, leads to an overall directed silylation of the C-H bond ortho to hydroxyl functionality. PMID:22075137

Hartwig, John F



Hydrogen bonding and anaesthesia  

NASA Astrophysics Data System (ADS)

General anaesthetics act by perturbing intermolecular associations without breaking or forming covalent bonds. These associations might be due to a variety of van der Waals interactions or hydrogen bonding. Neurotransmitters all contain OH or NH groups, which are prone to form hydrogen bonds with those of the neurotransmitter receptors. These could be perturbed by anaesthetics. Aromatic rings in amino acids can act as weak hydrogen bond acceptors. On the other hand the acidic hydrogen in halothane type anaesthetics are weak proton donors. These two facts together lead to a probable mechanism of action for all general anaesthetics.

Sándorfy, C.



Numerical modeling of ductile tearing effects on cleavage fracture toughness  

SciTech Connect

Experimental studies demonstrate a significant effect of specimen size, a/W ratio and prior ductile tearing on cleavage fracture toughness values (J{sub c}) measured in the ductile-to-brittle transition region of ferritic materials. In the lower-transition region, cleavage fracture often occurs under conditions of large-scale yielding but without prior ductile crack extension. The increased toughness develops when plastic zones formed at the crack tip interact with nearby specimen surfaces which relaxes crack-tip constraint (stress triaxiality). In the mid-to-upper transition region, small amounts of ductile crack extension (often < 1-2 mm) routinely precede termination of the J-{Delta}a curve by brittle fracture. Large-scale yielding, coupled with small amounts of ductile tearing, magnifies the impact of small variations in microscale material properties on the macroscopic fracture toughness which contributes to the large amount scatter observed in measured J{sub c}-values. Previous work by the authors described a micromechanics fracture model to correct measured J{sub c}-values for the mechanistic effects of large-scale yielding. This new work extends the model to also include the influence of ductile crack extension prior to cleavage. The paper explores development of the new model, provides necessary graphs and procedures for its application and demonstrates the effects of the model on fracture data sets for two pressure vessel steels (A533B and A515).

Dodds, R.H. Jr.; Tang, M. [Univ. of Illinois, Urbana (United States); Anderson, T.L. [Texas A& M Univ., College Station, TX (United States)



Failure of cell cleavage induces senescence in tetraploid primary cells.  


Tetraploidy can arise from various mitotic or cleavage defects in mammalian cells, and inheritance of multiple centrosomes induces aneuploidy when tetraploid cells continue to cycle. Arrest of the tetraploid cell cycle is therefore potentially a critical cellular control. We report here that primary rat embryo fibroblasts (REF52) and human foreskin fibroblasts become senescent in tetraploid G1 after drug- or small interfering RNA (siRNA)-induced failure of cell cleavage. In contrast, T-antigen-transformed REF52 and p53+/+ HCT116 tumor cells rapidly become aneuploid by continuing to cycle after cleavage failure. Tetraploid primary cells quickly become quiescent, as determined by loss of the Ki-67 proliferation marker and of the fluorescent ubiquitination-based cell cycle indicator/late cell cycle marker geminin. Arrest is not due to DNA damage, as the ?-H2AX DNA damage marker remains at control levels after tetraploidy induction. Arrested tetraploid cells finally become senescent, as determined by SA-?-galactosidase activity. Tetraploid arrest is dependent on p16INK4a expression, as siRNA suppression of p16INK4a bypasses tetraploid arrest, permitting primary cells to become aneuploid. We conclude that tetraploid primary cells can become senescent without DNA damage and that induction of senescence is critical to tetraploidy arrest. PMID:25143403

Panopoulos, Andreas; Pacios-Bras, Cristina; Choi, Justin; Yenjerla, Mythili; Sussman, Mark A; Fotedar, Rati; Margolis, Robert L




PubMed Central

Cadherins are initially synthesized bearing a prodomain that is thought to limit adhesion during early stages of biosynthesis. Functional cadherins lack this prodomain, raising the intriguing possibility that cells may utilize prodomain cleavage as a means to temporally or spatially regulate adhesion after delivery of cadherin to the cell surface. In support of this idea, immunostaining for the prodomain of zebrafish N-cadherin revealed enriched labeling at neuronal surfaces at the soma and along axonal processes. To determine whether post-translational cleavage of the prodomain affects synapse formation, we imaged Rohon-Beard cells in zebrafish embryos expressing GFP-tagged wild-type N-cadherin (NCAD-GFP) or a GFP-tagged N-cadherin mutant expressing an uncleavable prodomain (PRON-GFP) rendering it non-adhesive. NCAD-GFP accumulated at synaptic microdomains in a developmentally regulated manner, and its overexpression transiently accelerated synapse formation. PRON-GFP was much more diffusely distributed along the axon and its overexpression delayed synapse formation. Our results support the notion that N-cadherin serves to stabilize pre- to postsynaptic contacts early in synapse development and suggests that regulated cleavage of the N-cadherin prodomain may be a mechanism by which the kinetics of synaptogenesis are regulated. PMID:19365814

Latefi, Nazlie S.; Pedraza, Liliana; Schohl, Anne; Li, Ziwei; Ruthazer, Edward S.



Specific cleavage of hyper-edited dsRNAs  

PubMed Central

Extended double-stranded DNA (dsRNA) duplexes can be hyper-edited by adenosine deaminases that act on RNA (ADARs). Long uninterrupted dsRNA is relatively uncommon in cells, and is frequently associated with infection by DNA or RNA viruses. Moreover, extensive adenosine to inosine editing has been reported for various viruses. A number of cellular antiviral defence strategies are stimulated by dsRNA. An additional mechanism to remove dsRNA from cells may involve hyper-editing of dsRNA by ADARs, followed by targeted cleavage. We describe here a cytoplasmic endonuclease activity that specifically cleaves hyper-edited dsRNA. Cleavage occurs at specific sites consisting of alternating IU and UI base pairs. In contrast, unmodified dsRNA and even deaminated dsRNAs that contain four consecutive IU base pairs are not cleaved. Moreover, dsRNAs in which alternating IU and UI base pairs are replaced by isomorphic GU and UG base pairs are not cleaved. Thus, the cleavage of deaminated dsRNA appears to require an RNA structure that is unique to hyper-edited RNA, providing a molecular target for the disposal of hyper-edited viral RNA. PMID:11483527

Scadden, A.D.J.; Smith, Christopher W.J.



Mechanism of metabolic cleavage of a furan ring  

SciTech Connect

We studied the mechanism of metabolic cleavage of a furan ring, using a new hypolipidemic agent, ethyl 2-(4-chlorophenyl)-5-(2-furyl)oxazole-4-acetate (TA-1801), as a model compound. A TA-1801 analogue labeled with deuterium at the 5-position of its furan ring was administered orally to rats. The analysis of urinary metabolites by GC/MS revealed that the deuterium of the furan was retained in the ring-opened metabolite (M3). Metabolic cleavage of furan has been generally considered to proceed by hydroxylation of the 5-position followed by tautomerism and hydrolysis of the resulting 5-hydroxyfuran derivative. However, if the cleavage proceeded by this pathway, the deuterium of the 5-position would be eliminated during hydroxylation. Therefore, we propose that the ring was cleaved directly to form an unsaturated aldehyde, considering the mechanism of oxidation by cytochrome P-450. Although this intermediate was not detected in the biological specimens, a synthetic unsaturated aldehyde was transformed to the actual urinary metabolites M2 and M3 (major ring-opened metabolites) in the isolated rat liver.

Kobayashi, T.; Sugihara, J.; Harigaya, S.



Carotenoid-Cleavage Activities of Crude Enzymes from Pandanous amryllifolius.  


Carotenoid degradation products, known as norisoprenoids, are aroma-impact compounds in several plants. Pandan wangi is a common name of the shrub Pandanus amaryllifolius. The genus name 'Pandanus' is derived from the Indonesian name of the tree, pandan. In Indonesia, the leaves from the plant are used for several purposes, e.g., as natural colorants and flavor, and as traditional treatments. The aim of this study was to determine the cleavage of ?-carotene and ?-apo-8'-carotenal by carotenoid-cleavage enzymes isolated from pandan leaves, to investigate dependencies of the enzymatic activities on temperature and pH, to determine the enzymatic reaction products by using Headspace Solid Phase Microextraction Gas Chromatography/Mass Spectrophotometry (HS-SPME GC/MS), and to investigate the influence of heat treatment and addition of crude enzyme on formation of norisoprenoids. Crude enzymes from pandan leaves showed higher activity against ?-carotene than ?-apo-8'-carotenal. The optimum temperature of crude enzymes was 70°, while the optimum pH value was 6. We identified ?-ionone as the major volatile reaction product from the incubations of two different carotenoid substrates, ?-carotene and ?-apo-8'-carotenal. Several treatments, e.g., heat treatment and addition of crude enzymes in pandan leaves contributed to the norisoprenoid content. Our findings revealed that the crude enzymes from pandan leaves with carotenoid-cleavage activity might provide a potential application, especially for biocatalysis, in natural-flavor industry. PMID:25408328