Science.gov

Sample records for c-c bond cleavage

  1. Synthesis of Biaryls via Benzylic C-C Bond Cleavage of Styrenes and Benzyl Alcohols.

    PubMed

    Kumar, Arvind; Shah, Bhahwal Ali

    2015-11-01

    A metal-free oxidative coupling of styrenes and benzyl alcohols with arenes has been developed for the synthesis of biaryls. The reaction features a conspicuous benzylic C-C bond cleavage of styrenes and benzyl alcohols. The reaction with both substrates proceeds through a common aldehydic intermediate formed through oxidative C-C bond cleavage of alkene and oxidation of benzyl alcohols. The reaction proceeds efficiently over a broad range of substrates with excellent functional group tolerance. PMID:26479321

  2. Organic chemistry. Rh-catalyzed C-C bond cleavage by transfer hydroformylation.

    PubMed

    Murphy, Stephen K; Park, Jung-Woo; Cruz, Faben A; Dong, Vy M

    2015-01-01

    The dehydroformylation of aldehydes to generate olefins occurs during the biosynthesis of various sterols, including cholesterol in humans. Here, we implement a synthetic version that features the transfer of a formyl group and hydride from an aldehyde substrate to a strained olefin acceptor. A Rhodium (Xantphos)(benzoate) catalyst activates aldehyde carbon-hydrogen (C-H) bonds with high chemoselectivity to trigger carbon-carbon (C-C) bond cleavage and generate olefins at low loadings (0.3 to 2 mole percent) and temperatures (22° to 80°C). This mild protocol can be applied to various natural products and was used to achieve a three-step synthesis of (+)-yohimbenone. A study of the mechanism reveals that the benzoate counterion acts as a proton shuttle to enable transfer hydroformylation. PMID:25554782

  3. Metal-free oxidative cleavage of the C-C bond in ?-hydroxy-?-oxophosphonates.

    PubMed

    Battula, Satyanarayana; Kumar, Atul; Ahmed, Qazi Naveed

    2015-10-21

    The potential of TBHP to promote oxidative hydroxylation of ?-hydroxy-?-oxophosphonates (HOPs) through C(CO)-C bond cleavage is described. This cleavage, as depicted in the mechanism is expected through an isomer of HOP that reacts with TBHP to generate acids. PMID:26365809

  4. Regiospecific Synthesis of Benzoxepines through Pd-Catalyzed Carbene Migratory Insertion and C-C Bond Cleavage.

    PubMed

    Xie, Yang; Zhang, Ping; Zhou, Lei

    2016-03-01

    A new method for the synthesis of benzoxepines via migratory insertion into a Pd carbene followed by C-C bond cleavage was developed. Various benzoxepines were constructed by the regioselective ring expansion concomitant with the introduction of an aryl group at their 5-position. PMID:26841938

  5. Unusual formation of a N-heterocyclic germylene via homolytic cleavage of a C-C bond.

    PubMed

    Li, Yan; Mondal, Kartik Chandra; Stollberg, Peter; Zhu, Hongping; Roesky, Herbert W; Herbst-Irmer, Regine; Stalke, Dietmar; Fliegl, Heike

    2014-03-28

    Reaction of the monoanionic radical salt IP˙(-)K(+) (IP = (Py)CH(=NR); Py = C5H4N, R = 2,6-iPr2C6H3; α-iminopyridine) with GeCl2(dioxane) afforded compound (IPGeCl)2 (1) which produced red blocks of IPGe: (2), when treated with KC8 in toluene. 1 is a digermylene formed via C-C coupling between two carbon-centered radicals. 2 can be considered as an analogue of a N-heterocyclic carbene, which exhibits a five-membered GeC2N2 ring with one C=C double bond. 2 is formed by two-electron reduction of 1 with cleavage of the two Ge-Cl bonds and the central C-C single bond. PMID:24549122

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

    PubMed

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

    2014-06-20

    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

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

    PubMed

    Wang, Teng; Jiao, Ning

    2014-04-15

    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

  8. Oxidative C(sp3)-H bond cleavage, C-C and C=C coupling at a boron center with O2 as the oxidant mediated by platinum(II).

    PubMed

    Pal, S; Zavalij, P Y; Vedernikov, A N

    2014-05-25

    Dimethyl- and diphenylplatinum(II) fragments Pt(II)R2 (R = Me, Ph) enable facile and efficient oxidative C(sp(3))-H bond cleavage and stepwise C-C and C=C coupling at the boron atom of a coordinated 1,5-cyclooctanediyldi(2-pyridyl)borato ligand with O2 as the sole oxidant. PMID:24287586

  9. Rh(III)-Catalyzed Synthesis of N-Unprotected Indoles from Imidamides and Diazo Ketoesters via C-H Activation and C-C/C-N Bond Cleavage.

    PubMed

    Qi, Zisong; Yu, Songjie; Li, Xingwei

    2016-02-19

    The synthesis of N-unprotected indoles has been realized via Rh(III)-catalyzed C-H activation/annulation of imidamides with α-diazo β-ketoesters. The reaction occurs with the release of an amide coproduct, which originates from both the imidamide and the diazo as a result of C═N cleavage of the imidamide and C-C(acyl) cleavage of the diazo. A rhodacyclic intermediate has been isolated and a plausible mechanism has been proposed. PMID:26824751

  10. Bond cleavage during isobutanol thermal decomposition and the breaking of C-C bonds in alcohols at high temperatures.

    PubMed

    Rosado-Reyes, Claudette; Tsang, Wing

    2013-10-10

    Isobutanol was thermally decomposed in a single pulse shock tube under conditions where chain processes were suppressed. The main reaction is the breaking of C-C bonds. Literature rate expressions, experimentally determined, are found in some cases to be in disagreement. The rate expressions for the decomposition processes at temperatures of 1090 to 1240 K and pressures of 1.5 and 6 atm are k(isobutanol ? isopropyl + hydroxymethyl) + k(isobutanol ? methyl + 1-hydroxypropyl-2) = 10(16.70.3) exp(-41097 750) s(-1), where k(isobutanol ? isopropyl + hydroxymethyl) = 10(16.45 0.3) exp(-40910 750/T) s(-1) and k(isobutanol ? methyl + 1-hydroxypropyl-2) = 10(16.380.3) exp(-41560 750/T) s(-1). These values permit comparisons with recent estimates including those from ab initio calculations. A new procedure is presented that uses information on the kinetics of bond breaking reactions of alkanes and the effect of OH substitution to derive rate coefficients for similar reactions of alcohols. This leads to the following rate expression for the smaller alcohols, at temperatures of 1090 to 1240 K and pressures of 1.5 and 6 atm, k(ethanol ? methyl + hydroxymethyl) = 10(16.420.3) exp(-43496 750 K/T) s(-1), k(isopropanol ? methyl + 1-hydroxyethyl) = 10(16.540.3) exp(-42495 750 K/T) s(-1), k(n-propanol ? ethyl + hydroxymethyl) = 10(16.430.3) exp(-41696 750 K/T) s(-1), and k(n-propanol ? methyl + 2-hydroxymethyl) = 10(16.530.3) exp(-42945 750 K/T) s(-1). Extension of this approach to other alcohols is straightforward. The resulting correlations along with the data on dehydration of alcohols provide novel information of the kinetic stability of alcohols. PMID:23968459

  11. Synthesis of Multiply Substituted Polycyclic Aromatic Hydrocarbons by Iridium-Catalyzed Annulation of Ring-Fused Benzocyclobutenol with Alkyne through C-C Bond Cleavage.

    PubMed

    Yu, Jiajia; Yan, Hong; Zhu, Chen

    2016-01-01

    The first iridium-catalyzed intermolecular cyclization between alkynes and ring-fused benzocyclobutenols (RBCB) through C-C bond cleavage is described. A variety of elusive polycyclic aromatic hydrocarbons (PAHs) with multiple substituents are obtained in good yields under mild conditions. This procedure provides a unique and expeditious tool for the synthesis of PAHs. PMID:26633241

  12. A facile C-C bond cleavage in the epoxides and its use for the synthesis of oxygenated heterocycles by a ring expansion strategy.

    PubMed

    Lakshmipathi, Pandarinathan; Grée, Danielle; Grée, René

    2002-02-01

    The bicyclic epoxy alcohols when treated with DAST gave a new class of rearranged organofluorine compounds, by a ring expansion via C-C bond cleavage of the oxirane ring. The outcome of this reaction with respect to ring size and stereochemical relation between the functionalities is presented here. PMID:11820902

  13. Factors That Control C-C Cleavage versus C-H Bond Hydroxylation in Copper-Catalyzed Oxidations of Ketones with O2.

    PubMed

    Tsang, Althea S-K; Kapat, Ajoy; Schoenebeck, Franziska

    2016-01-20

    The Cu-catalyzed oxidation of ketones with O2 has recently been extensively utilized to cleave the α-C-C bond. This report examines the selective aerobic hydroxylation of tertiary α-C-H bonds in ketones without C-C cleavage. We set out to understand the underlying mechanisms of these two possible reactivity modes. Using experimental, in situ IR spectroscopic, and computational studies, we investigated several mechanisms. Our data suggest that both C-C cleavage and C-H hydroxylation pathways proceed via a common key intermediate, i.e., an α-peroxo ketone. The fate of this peroxide dictates the ultimate product selectivity. Specifically, we uncovered the role of hppH [= 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine] to act not only as a base in the transformation but also as a reductant of the peroxide to the corresponding α-hydroxy ketone. This reduction may also be accomplished through exogenous phosphine additives, therefore allowing the tuning of reduction efficiency toward higher driving forces, if required (e.g., for more-activated substrates). The likely competitive pathway is the cleavage of peroxide to the α-oxy radical (likely catalyzed by Cu), which is computationally predicted to spontaneously trigger C-C bond cleavage. Increasing the susceptibility of this deperoxidation step via (i) the removal of reductant (use of different base, e.g., DBU) or the modulation of (ii) the substitution pattern toward greater activation (substrate control) and (iii) the nature of Cu catalyst (counterion and solvent dependence) will favor the C-C cleavage product. PMID:26675262

  14. Ruthenium-Catalyzed C-C Bond Cleavage of 2H-Azirines: A Formal [3+2+2] Cycloaddition to Fused Azepine Skeletons.

    PubMed

    Li, Tengfei; Xu, Fen; Li, Xincheng; Wang, Chunxiang; Wan, Boshun

    2016-02-01

    2H-azirines can serve as three-atom synthons by C-C bond cleavage, however, it involves a high energy barrier under thermal conditions (>50.0?kcal?mol(-1) ). Reported is a ruthenium-catalyzed [3+2+2] cycloaddition reaction of 2H-azirines with diynes, thus leading to the formation of fused azepine skeletons. This approach features an unprecedented metal-catalyzed C-C bond cleavage of 2H-azirines at room temperature, and the challenging construction of aza-seven-membered rings from diynes. The results of this study provide a new reaction pattern for constructing nitrogen-containing seven-membered rings and may find applications in the synthesis of other complex heterocycles. PMID:26800151

  15. Iridium-Catalyzed Formal [4 + 1] Cycloaddition of Biphenylenes with Alkenes Initiated by C-C Bond Cleavage for the Synthesis of 9,9-Disubstituted Fluorenes.

    PubMed

    Takano, Hideaki; Kanyiva, Kyalo Stephen; Shibata, Takanori

    2016-04-15

    An Ir-catalyzed intermolecular reaction of biphenylenes as a C4 unit with various alkenes as a C1 unit gave 9,9-disubstituted fluorenes in moderate to high yields. Preliminary mechanistic studies revealed that this formal [4 + 1] cycloaddition probably proceeds via C-C bond cleavage, alkene insertion, β-hydrogen elimination, intramolecular alkene insertion, and then reductive elimination. An example of enantioselective reaction was also disclosed. PMID:27031498

  16. Ring Expansion via Cleavage of Benzylic C-C Bonds Enabling Direct Synthesis of Medium Ring-Fused Benzocarbocycles.

    PubMed

    Rao, Bin; Tang, Jinghua; Wei, Yu; Zeng, Xiaoming

    2016-04-01

    A fluoride-anion-induced, regioselective ring expansion of benzocyclic ketones and α-aryl cycloketones has been developed via insertion of arynes into unactivated benzylic C-C bonds. This reaction provides a straightforward, transition-metal-free avenue to prepare medium ring-fused benzocarbocycles by creating "noble" seven-, eight-, and nine-membered rings. Applications of this method in the creation of medium-sized exocyclic and inner benzocyclic olefins, nine-membered lactones, and lactams are described. PMID:26970443

  17. Catalytic asymmetric [3+2] cycloaddition of aromatic aldehydes with oxiranes by C-C bond cleavage of epoxides: highly efficient synthesis of chiral 1,3-dioxolanes.

    PubMed

    Chen, Weiliang; Lin, Lili; Cai, Yunfei; Xia, Yong; Cao, Weidi; Liu, Xiaohua; Feng, Xiaoming

    2014-02-28

    A novel and efficient N,N'-dioxide-Gd(III) complex was developed for the highly diastereo- and enantioselective [3+2] cycloaddition of aryl oxiranyl diketones and aldehydes via C-C bond cleavage of oxiranes. The corresponding chiral 1,3-dioxolanes were obtained in excellent yields (up to 99%) with high diastereoselectivities (>95 : 5 dr) and enantioselectivities (up to 91% ee). Moreover, a possible transition model was proposed to explain the origin of the asymmetric induction. PMID:24430105

  18. Catalytic tandem C-C bond formation/cleavage of cyclopropene for allylzincation of aldehydes or aldimine using organozinc reagents.

    PubMed

    Nakano, Takeo; Endo, Kohei; Ukaji, Yutaka

    2014-03-01

    The tandem allylation of aldehydes or an aldimine with allylzinc intermediates derived from organozinc reagents and cyclopropenes is described. The present three-component reaction involves carbozincation of cyclopropene and sequential cleavage of a cyclopropylzinc intermediate in situ without a transition-metal catalyst. The allylzinc intermediates generated in situ, which is an α,β-unsaturated acylanion equivalent, gave the corresponding homoallylic alcohols or amine in good yields. PMID:24564424

  19. Simple Bond Cleavage

    SciTech Connect

    Gary S. Groenewold

    2005-08-01

    Simple bond cleavage is a class of fragmentation reactions in which a single bond is broken, without formation of new bonds between previously unconnected atoms. Because no bond making is involved, simple bond cleavages are endothermic, and activation energies are generally higher than for rearrangement eliminations. The rate of simple bond cleavage reactions is a strong function of the internal energy of the molecular ion, which reflects a loose transition state that resembles reaction products, and has a high density of accessible states. For this reason, simple bond cleavages tend to dominate fragmentation reactions for highly energized molecular ions. Simple bond cleavages have negligible reverse activation energy, and hence they are used as valuable probes of ion thermochemistry, since the energy dependence of the reactions can be related to the bond energy. In organic mass spectrometry, simple bond cleavages of odd electron ions can be either homolytic or heterolytic, depending on whether the fragmentation is driven by the radical site or the charge site. Simple bond cleavages of even electron ions tend to be heterolytic, producing even electron product ions and neutrals.

  20. Multinuclear silver(i) XPhos complexes with cyclooctatetraene: photochemical C-C bond cleavage of acetonitrile and cyanide bridged Ag cluster formation.

    PubMed

    Grirrane, A; Álvarez, E; Albero, J; García, H; Corma, A

    2016-04-01

    Cationic mono-, di-, tri- and tetra-nuclear silver complexes with Buchwald-type phosphane (XPhos) and cyclooctatetraene (COT) have been synthesized and characterized. Formation of [(XPhos-Ag)n(COT)][SbF6]n (n = 1 and 2) complexes was confirmed by single-crystal X-ray crystallography and multinuclear NMR spectroscopy. Variable-temperature NMR spectroscopy in CD2Cl2 solution shows the fluxionality of the COT ring in the mono-Ag(i) XPhos complex. Fluxionality of COT was also confirmed in the case of the di-Ag(i) XPhos complex by solid-state and solution (31)P NMR spectroscopy. The C-C bond cleavage of coordinated acetonitrile [XPhos-Ag(i)-NCCH3] resulting in cyanide bridged Ag cluster formation [(XPhos-Ag)2(μ-CN)n(μ-Ag)n-1] (n = 1, 2, 3 and 4) upon light excitation of [(XPhos-Ag)n(COT)] was confirmed by HRESI-MS, UV-Absorption and HR-TEM. PMID:26959701

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

    PubMed

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

    2014-10-01

    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

  2. Mechanistic studies of processes involving C-C bond cleavage in gas-phase organometallic reactions using product kinetic energy release distributions: Co sup + reacting with cyclopentane

    SciTech Connect

    van Koppen, P.A.M.; Bowers, M.T. ); Beauchamp, J.L. )

    1990-03-01

    A reverse-geometry mass spectrometer is used to obtain product ion kinetic energy release distributions to probe the energetics and mechanisms of several gas-phase organometallic reactions. In particular, we examine the mechanism for C{sub 2}H{sub 4} and C{sub 3}H{sub 6} elimination from Co(cyclopentane){sup +}. The kinetic energy release distribution associated with these processes can be modeled by using phase space calculations assuming, for the C{sub 3}H{sub 6} elimination process, propene rather than cyclopropane is being eliminated as the product neutral, and for the C{sub 2}H{sub 4} elimination process, Co(propene){sup +} rather than (cobaltacyclobutane){sup +} is being formed as the product ion. In addition, we obtain a heat of formation for the cobalt ethylene ion of 255 kcal/mol at 0 K, corresponding to a bond dissociation energy of 42 kcal/mol at 0 K, by fitting the theoretical results to the experimental distribution.

  3. Understanding Rotation about a C=C Double Bond

    ERIC Educational Resources Information Center

    Barrows, Susan E.; Eberlein, Thomas H.

    2005-01-01

    The study focuses on the process and energetic cost of twisting around a C=C double bond and provides instructors with a simple vehicle for rectifying the common misrepresentation of C=C double bonds as rigid and inflexible. Discussions of cis and trans isomers of cycloalkenes are a good entry point for introducing students to the idea of a

  4. Understanding Rotation about a C=C Double Bond

    ERIC Educational Resources Information Center

    Barrows, Susan E.; Eberlein, Thomas H.

    2005-01-01

    The study focuses on the process and energetic cost of twisting around a C=C double bond and provides instructors with a simple vehicle for rectifying the common misrepresentation of C=C double bonds as rigid and inflexible. Discussions of cis and trans isomers of cycloalkenes are a good entry point for introducing students to the idea of a…

  5. Alkali metal mediated C-C bond coupling reaction

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto

    2015-02-01

    Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2]- was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

  6. C-C bond-forming desulfurizations of sulfoximines.

    PubMed

    Reggelin, M; Slavik, S; Bühle, P

    2008-09-18

    Highly substituted, enantiomerically pure azaheterocyclic ring systems play an important role in medicinal chemistry as potential peptide mimetics. Metalated 2-alkenyl sulfoximines offer an efficient entry to this class of compounds. In this paper, we describe a new means to remove the sulfonimidoyl auxiliary with concomitant formation of a C-C double bond. PMID:18712875

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

    SciTech Connect

    Bausch, M.

    1991-01-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Hu, Shaowei; Shima, Takanori; Hou, Zhaomin

    2014-08-01

    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 β-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.

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

    PubMed

    Hu, Shaowei; Shima, Takanori; Hou, Zhaomin

    2014-08-28

    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 β-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. PMID:25164752

  10. Microbial cleavage of organic C-S bonds

    DOEpatents

    Kilbane, II, John J.

    1994-01-01

    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.

  11. Microbial cleavage of organic C-S bonds

    DOEpatents

    Kilbane, J.J. II.

    1994-10-25

    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.

  12. Reductive cleavage of the peptide bond

    NASA Technical Reports Server (NTRS)

    Holian, J.; Garrison, W. M.

    1973-01-01

    In many biological research efforts, long chain organic molecules are studied by breaking large molecules into smaller components. Cleavage technique of recent interest is the use of solvated electrons. These are formed when aqueous solutions are bombarded with gamma radiation. Solvated electron is very reactive and can reduce most any species present, even to form free radicals.

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

    SciTech Connect

    Bausch, M.

    1991-12-31

    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.

  14. C-C bond formation: Rethinking cross-coupling

    NASA Astrophysics Data System (ADS)

    Sun, Ho-Yan; Hall, Dennis G.

    2014-07-01

    The palladium-catalysed cross-coupling of aryl- or alkenylboronates and aryl halides has proved phenomenally successful for the formation of Csp2-Csp2 bonds. Now, an alternative non-transition-metal-mediated coupling using similar reactants has been reported for the stereo-controlled formation of Csp2-Csp3 bonds.

  15. Carbon-carbon bond cleavage and formation reactions in drug metabolism and the role of metabolic enzymes.

    PubMed

    Bolleddula, Jayaprakasam; Chowdhury, Swapan K

    2015-11-01

    Elimination of xenobiotics from the human body is often facilitated by a transformation to highly water soluble and more ionizable molecules. In general, oxidation-reduction, hydrolysis, and conjugation reactions are common biotransformation reactions that are catalyzed by various metabolic enzymes including cytochrome P450s (CYPs), non-CYPs, and conjugative enzymes. Although carbon-carbon (C-C) bond formation and cleavage reactions are known to exist in plant secondary metabolism, these reactions are relatively rare in mammalian metabolism and are considered exceptions. However, various reactions such as demethylation, dealkylation, dearylation, reduction of alkyl chain, ring expansion, ring contraction, oxidative elimination of a nitrile through C-C bond cleavage, and dimerization, and glucuronidation through C-C bond formation have been reported for drug molecules. Carbon-carbon bond cleavage reactions for drug molecules are primarily catalyzed by CYP enzymes, dimerization is mediated by peroxidases, and C-glucuronidation is catalyzed by UGT1A9. This review provides an overview of C-C bond cleavage and formation reactions in drug metabolism and the metabolic enzymes associated with these reactions. PMID:26390887

  16. Stereochemistry of enzymatic water addition to C=C bonds.

    PubMed

    Chen, Bi-Shuang; Otten, Linda G; Hanefeld, Ulf

    2015-01-01

    Water addition to carbon-carbon double bonds using hydratases is attracting great interest in biochemistry. Most of the known hydratases are involved in primary metabolism and to a lesser extent in secondary metabolism. New hydratases have recently been added to the toolbox, both from natural sources or artificial metalloenzymes. In order to comprehensively understand how the hydratases are able to catalyse the water addition to carbon-carbon double bonds, this review will highlight the mechanistic and stereochemical studies of the enzymatic water addition to carbon-carbon double bonds, focusing on the syn/anti-addition and stereochemistry of the reaction. PMID:25640045

  17. Building Giant Carbocycles by Reversible C-C Bond Formation.

    PubMed

    Beaudoin, Daniel; Levasseur-Grenon, Olivier; Maris, Thierry; Wuest, James D

    2016-01-01

    We describe a simple way to build giant macrocyclic hydrocarbons by the reversible formation of carbon-carbon bonds. Specifically, extended spirobifluorene-substituted derivatives of Wittig's hydrocarbon were synthesized and found to undergo oligomerization, giving the largest hydrocarbon that has been crystallized and characterized by X-ray diffraction to date. PMID:26597318

  18. Cu(II)-catalyzed esterification reaction via aerobic oxidative cleavage of C(CO)-C(alkyl) bonds.

    PubMed

    Ma, Ran; He, Liang-Nian; Liu, An-Hua; Song, Qing-Wen

    2016-02-01

    A novel Cu(II)-catalyzed aerobic oxidative esterification of simple ketones for the synthesis of esters has been developed with wide functional group tolerance. This process is assumed to go through a tandem sequence consisting of α-oxygenation/esterification/nucleophilic addition/C-C bond cleavage and carbon dioxide is released as the only byproduct. PMID:26698150

  19. Glutamic Acid Selective Chemical Cleavage of Peptide Bonds.

    PubMed

    Nalbone, Joseph M; Lahankar, Neelam; Buissereth, Lyssa; Raj, Monika

    2016-03-01

    Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis. PMID:26866465

  20. Copper-catalyzed C(sp3)-OH cleavage with concomitant C-C coupling: synthesis of 3-substituted isoindolinones.

    PubMed

    Rao, H Surya Prakash; Rao, A Veera Bhadra

    2015-02-01

    Copper(II) trifluoromethanesulfonate (Cu(OTf)2) efficiently catalyzes the C-C coupling of 3-hydoxyisoindolinones with a variety of aryl-, heteroaryl-, and alkenylboronic acids to furnish C(3) aryl-, heteroaryl-, and alkenyl-substituted isoindolinones. The coupling reactions work smoothly in 1,2-dicholoroethane (DCE) reflux, to effect both inter- and intramolecular versions. This is the first report on C(sp(3))-OH cleavage with concomitant C-C coupling. The photolabile 2-nitrobenzyl protecting group is most appropriate for promotion of the coupling reaction and for deprotection. The tetracyclic ring motif of the alkaloid neuvamine was prepared by applying the newly developed copper-catalyzed C-C coupling. PMID:25569689

  1. Unexpected copper-catalyzed aerobic oxidative cleavage of C(sp3)-C(sp3) bond of glycol ethers.

    PubMed

    Liu, Zhong-Quan; Zhao, Lixing; Shang, Xiaojie; Cui, Zili

    2012-06-15

    An unexpected Cu-catalyzed oxidative cleavage of the C(sp(3))-C(sp(3)) bond in glycol ethers by using air or molecular oxygen as the terminal stoichiometric oxidant is demonstrated. As a result, the corresponding α-acyloxy ethers and formates of 1,2-ethanediol are formed by direct coupling of carboxylic acids and aldehydes with glycol ethers under the reaction conditions. This method represents the first example of Cu-catalyzed aerobic cleavage of saturated C-C bond in ethers. PMID:22668348

  2. Site-selective chemical cleavage of peptide bonds.

    PubMed

    Elashal, Hader E; Raj, Monika

    2016-05-01

    Site-selective cleavage of extremely unreactive peptide bonds is a very important chemical modification that provides invaluable information regarding protein sequence, and it acts as a modulator of protein structure and function for therapeutic applications. For controlled and selective cleavage, a daunting task, chemical reagents must selectively recognize or bind to one or more amino acid residues in the peptide chain and selectively cleave a peptide bond. Building on this principle, we have developed an approach that utilizes a chemical reagent to selectively modify the serine residue in a peptide chain and leads to the cleavage of a peptide backbone at the N-terminus of the serine residue. After cleavage, modified residues can be converted back to the original fragments. This method exhibits broad substrate scope and selectively cleaves various bioactive peptides with post-translational modifications (e.g. N-acetylation and -methylation) and mutations (d- and β-amino acids), which are a known cause of age related diseases. PMID:27087443

  3. Development and application of bond cleavage reactions in bioorthogonal chemistry.

    PubMed

    Li, Jie; Chen, Peng R

    2016-02-16

    Bioorthogonal chemical reactions are a thriving area of chemical research in recent years as an unprecedented technique to dissect native biological processes through chemistry-enabled strategies. However, current concepts of bioorthogonal chemistry have largely centered on 'bond formation' reactions between two mutually reactive bioorthogonal handles. Recently, in a reverse strategy, a collection of 'bond cleavage' reactions has emerged with excellent biocompatibility. These reactions have expanded our bioorthogonal chemistry repertoire, enabling an array of exciting new biological applications that range from the chemically controlled spatial and temporal activation of intracellular proteins and small-molecule drugs to the direct manipulation of intact cells under physiological conditions. Here we highlight the development and applications of these bioorthogonal cleavage reactions. Furthermore, we lay out challenges and propose future directions along this appealing avenue of research. PMID:26881764

  4. Switching the Cleavage Sites in Palladium on Carbon-Catalyzed Carbon-Carbon Bond Disconnection.

    PubMed

    Hattori, Tomohiro; Takakura, Ryoya; Ichikawa, Tomohiro; Sawama, Yoshinari; Monguchi, Yasunari; Sajiki, Hironao

    2016-04-01

    We have demonstrated a palladium on carbon-catalyzed approach to regioselectively alter the cleavage sites of the C-C bonds of cinnamaldehyde derivatives by a slight change in the reaction conditions in isopropanol under an O2 atmosphere. Styrene derivatives could be selectively formed by the addition of Na2CO3 in association with the dissociation of carbon monoxide, while benzaldehyde derivatives were generated by the addition of CuCl and morpholine instead of Na2CO3. PMID:26944077

  5. Biotic and abiotic carbon to sulfur bond cleavage

    SciTech Connect

    Frost, J.W.

    1991-01-01

    Cleavage of aliphatic organosulfonate carbon to sulfur (C-S) bonds, a critical link in the global biogeochemical sulfur cycle, has been identified in Escherichia coli K-12. Enormous quantities of inorganic sulfate are continuously converted (Scheme I) into methanesulfonic acid 1 and acylated 3-(6-sulfo-{alpha}-D-quinovopyranosyl)-L-glycerol 2. Biocatalytic desulfurization (Scheme I) of 1 and 2, which share the structural feature of an aliphatic carbon bonded to a sulfonic acid sulfur, completes the cycle, Discovery of this desulfurization in E. coli provides an invaluable paradigm for study of a biotic process which, via the biogeochemical cycle, significantly influences the atmospheric concentration of sulfur-containing molecules.

  6. Iterative reactions of transient boronic acids enable sequential C-C bond formation

    NASA Astrophysics Data System (ADS)

    Battilocchio, Claudio; Feist, Florian; Hafner, Andreas; Simon, Meike; Tran, Duc N.; Allwood, Daniel M.; Blakemore, David C.; Ley, Steven V.

    2016-04-01

    The ability to form multiple carbon-carbon bonds in a controlled sequence and thus rapidly build molecular complexity in an iterative fashion is an important goal in modern chemical synthesis. In recent times, transition-metal-catalysed coupling reactions have dominated in the development of C-C bond forming processes. A desire to reduce the reliance on precious metals and a need to obtain products with very low levels of metal impurities has brought a renewed focus on metal-free coupling processes. Here, we report the in situ preparation of reactive allylic and benzylic boronic acids, obtained by reacting flow-generated diazo compounds with boronic acids, and their application in controlled iterative C-C bond forming reactions is described. Thus far we have shown the formation of up to three C-C bonds in a sequence including the final trapping of a reactive boronic acid species with an aldehyde to generate a range of new chemical structures.

  7. Gas-phase reaction of CeV2O7+ with C2H4: activation of C-C and C-H bonds.

    PubMed

    Ma, Jia-Bi; Yuan, Zhen; Meng, Jing-Heng; Liu, Qing-Yu; He, Sheng-Gui

    2014-12-15

    The reactivity of metal oxide clusters toward hydrocarbon molecules can be changed, tuned, or controlled by doping. Cerium-doped vanadium cluster cations CeV2O7(+) are generated by laser ablation, mass-selected by a quadrupole mass filter, and then reacted with C2H4 in a linear ion trap reactor. The reaction is characterized by a reflectron time-of-flight mass spectrometer. Three types of reaction channels are observed: 1) single oxygen-atom transfer , 2) double oxygen-atom transfer , and 3) C=C bond cleavage. This study provides the first bimetallic oxide cluster ion, CeV2O7(+), which gives rise to C=C bond cleavage of ethene. Neither Ce(x)O(y)(±) nor V(x)O(y)(±) alone possess the necessary topological and electronic properties to bring about such a reaction. PMID:25208512

  8. Selective carbon-carbon bond cleavage for the stereoselective synthesis of acyclic systems.

    PubMed

    Marek, Ilan; Masarwa, Ahmad; Delaye, Pierre-Olivier; Leibeling, Markus

    2015-01-01

    Most of the efforts of organic chemists have been directed to the development of creative strategies to build carbon-carbon and carbon-heteroatom bonds in a predictable and efficient manner. In this Review, we show an alternative approach where challenging molecular skeletons could be prepared through selective cleavage of carbon-carbon bonds. We demonstrate that it has the potential to be a general principle in organic synthesis for the regio-, diastereo-, and even enantioselective preparation of adducts despite the fact that C-C single bonds are among the least reactive functional groups. The development of such strategies may have an impact on synthesis design and can ultimately lead to new selective and efficient processes for the utilization of simple hydrocarbons. PMID:25266824

  9. Ruthenium-catalyzed conversion of sp3 C-O bonds in ethers to C-C bonds using triarylboroxines.

    PubMed

    Ogiwara, Yohei; Kochi, Takuya; Kakiuchi, Fumitoshi

    2011-06-17

    Catalytic conversion of unreactive sp(3) C-O bonds in alkyl ethers to C-C bonds is described. Alkyl ethers bearing 2- or 4-pyridyl groups were coupled with triarylboroxines in the presence of a ruthenium catalyst. Triarylboroxines bearing a variety of functional groups including electron-withdrawing and -donating groups can be used for the reaction. No additional base was required for the coupling with the organoboron reagents, and base-sensitive groups can be tolerated. The reaction is considered to proceed via dehydroalkoxylation followed by addition of triarylboroxines to form C-C bonds. PMID:21598994

  10. Synthesis of 2-Benzylphenyl Ketones by Aryne Insertion into Unactivated C-C Bonds.

    PubMed

    Rao, Bin; Tang, Jinghua; Zeng, Xiaoming

    2016-04-01

    A transition-metal-free procedure to access to functionalized 2-benzylphenyl ketones is described by direct insertion of arynes into benzylic C-C bonds. This reaction was promoted by cesium fluoride at room temperature, allowing the products to form in high selectivity and achieve good functional group tolerance. PMID:27004731

  11. Iterative reactions of transient boronic acids enable sequential C-C bond formation.

    PubMed

    Battilocchio, Claudio; Feist, Florian; Hafner, Andreas; Simon, Meike; Tran, Duc N; Allwood, Daniel M; Blakemore, David C; Ley, Steven V

    2016-04-01

    The ability to form multiple carbon-carbon bonds in a controlled sequence and thus rapidly build molecular complexity in an iterative fashion is an important goal in modern chemical synthesis. In recent times, transition-metal-catalysed coupling reactions have dominated in the development of C-C bond forming processes. A desire to reduce the reliance on precious metals and a need to obtain products with very low levels of metal impurities has brought a renewed focus on metal-free coupling processes. Here, we report the in situ preparation of reactive allylic and benzylic boronic acids, obtained by reacting flow-generated diazo compounds with boronic acids, and their application in controlled iterative C-C bond forming reactions is described. Thus far we have shown the formation of up to three C-C bonds in a sequence including the final trapping of a reactive boronic acid species with an aldehyde to generate a range of new chemical structures. PMID:27001732

  12. [Hydrogen induced C-C, C-N, and C-S bond activities on Pi and Ni surfaces]: Summary

    SciTech Connect

    Gland, J.L.

    1994-12-31

    This document summarizes research applied to chemical bond activation studies. Topics summarized include: Carbon nitrogen bonds experimentation with aniline on Ni(111), Mi(100), and Pt(111) surfaces; carbon sulfur bonds experimentation with methanethiol, phenylthiol, and dimethyl disulfide on Pt(111) and Ni(111) surfaces; carbon-carbon bonds experimentation on Ni(100), Ni(111) and Pt(111) surfaces; and in-situ fluorescence yield near edge spectroscopy.

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

    SciTech Connect

    Hanson, Susan K; Gordon, John C; Thorn, David L; Scott, Brian L; Baker, R Tom

    2009-01-01

    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}).

  14. Theoretical thermochemistry of homolytic C-C and C-Cl bond dissociations in unbranched perchloroalkanes

    SciTech Connect

    Cioslowski, J.; Liu, G.; Moncrieff, D.

    1998-11-26

    Proper description of the dispersion interactions that attenuate the closed-shell repulsions among chlorine atoms in n-perchloroalkanes requires an accurate treatment of long-range electron correlation effects. The presently known density functionals, which do not correctly account for such effects, grossly underestimate thermodynamic stability of these molecules, yielding the standard enthalpy {Delta}H{degree}{sub C-C} of C-C bond dissociation in n-C{sub 4}Cl{sub 10} as low as 20 kcal/mol. In contrast, the predictions of the CBS-4 scheme fail to reproduce the weakening of the C-C bonds that is experimentally observed in the higher members of the C{sub n}Cl{sub 2n+2} homologous series. For the CCl{sub 4} and C{sub 2}Cl{sub 6} the most reliable estimates of {Delta}H{degree}{sub C-C} and {Delta}H{degree}{sub C-Cl} are provided by the G2 And G2MP2 methods. The MP2/6-311G{sup **} level of theory (without ZPEs and finite-temperature corrections) appears at present to be the only viable, though quite inaccurate, theoretical approach to theoretical thermochemistry of larger chlorocarbons. At that level of theory, {Delta}H{degree}{sub C-C} is predicted to decrease by ca. 10 kcal/mol upon the addition of each -CCl{sub 2}- unit, convincingly explaining the thermal lability of higher n-perchloroalkanes. Similar conclusions are reached by examining the estimates of {Delta}H{degree}{sub C-C} derived from the CBS-4 standard enthalpies with the E{sub CBS} energy term excluded.

  15. Branched Intermediate Formation Stimulates Peptide Bond Cleavage in Protein Splicing

    PubMed Central

    Frutos, Silvia; Goger, Michael; Giovani, Baldissera; Cowburn, David; Muir, Tom W.

    2010-01-01

    Protein splicing is a posttranslational modification in which an intein domain excises itself out of a host protein. Here, we investigate how the steps in the splicing process are coordinated so as to maximize the production of the final splice products and minimize the generation of undesired cleavage products. Our approach has been to prepare a branched intermediate (and analogs thereof) of the Mxe GyrA intein using protein semi-synthesis. Kinetic analysis of these molecules indicates that the high fidelity of this protein splicing reaction results from the penultimate step in the process (intein-succinimide formation) being rate-limiting. NMR experiments indicate that formation of the branched intermediate affects the local structure around the amide bond cleaved during succinimide formation. We propose that this structural change reflects a re-organization of the catalytic apparatus to accelerate succinimide formation at the C-terminal splice junction. PMID:20495572

  16. Intramolecular Aminocyanation of Alkenes via N–CN Bond Cleavage**

    PubMed Central

    Pan, Zhongda; Pound, Sarah M.; Rondla, Naveen R.; Douglas, Christopher J.

    2014-01-01

    A metal-free, Lewis acid-promoted intramolecular aminocyanation of alkenes was developed. B(C6F5)3 activates N-sulfonyl cyanamides, leading an formal cleavage of the N-CN bonds in conjunction with vicinal addition of sulfonamide and nitrile groups across an alkene. This method enables atom-economical access to indolines and tetrahydroquinolines in excellent yields, and provides a complementary strategy for regioselective alkene difunctionalizations with sulfonamide and nitrile groups. Labeling experiments with 13C suggest a fully intramolecular cyclization pattern due to lack of label scrambling in double crossover experiments. Catalysis with Lewis acid is realized and the reaction can be conducted under air. PMID:24719371

  17. Cleavage of an amide bond by a ribozyme

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

    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.

  18. Bronsted-Evans-Polany relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory.

    SciTech Connect

    Assary, R. S.; Broadbelt, L. J.; Curtiss, L. A.

    2012-01-01

    The concept of generalized enzyme reactions suggests that a wide variety of substrates can undergo enzymatic transformations, including those whose biotransformation has not yet been realized. The use of quantum chemistry to evaluate kinetic feasibility is an attractive approach to identify enzymes for the proposed transformation. However, the sheer number of novel transformations that can be generated makes this impractical as a screening approach. Therefore, it is essential to develop structure/activity relationships based on quantities that are more efficient to calculate. In this work, we propose a structure/activity relationship based on the free energy of binding or reaction of non-native substrates to evaluate the catalysis relative to that of native substrates. While Broensted-Evans-Polanyi (BEP) relationships such as that proposed here have found broad application in heterogeneous catalysis, their extension to enzymatic catalysis is limited. We report here on density functional theory (DFT) studies for C-C bond formation and C-C bond cleavage associated with the decarboxylation of six 2-keto acids by a thiamine-containing enzyme (EC 1.2.7.1) and demonstrate a linear relationship between the free energy of reaction and the activation barrier. We then applied this relationship to predict the activation barriers of 17 chemically similar novel reactions. These calculations reveal that there is a clear correlation between the free energy of formation of the transition state and the free energy of the reaction, suggesting that this method can be further extended to predict the kinetics of novel reactions through our computational framework for discovery of novel biochemical transformations.

  19. Collision Induced Dissociation Products of Disulfide-Bonded Peptides: Ions Result from the Cleavage of More Than One Bond

    NASA Astrophysics Data System (ADS)

    Clark, Daniel F.; Go, Eden P.; Toumi, Melinda L.; Desaire, Heather

    2011-03-01

    Disulfide bonds are a post-translational modification (PTM) that can be scrambled or shuffled to non-native bonds during recombinant expression, sample handling, or sample purification. Currently, mapping of disulfide bonds is not easy because of various sample requirements and data analysis difficulties. One step towards facilitating this difficult work is developing a better understanding of how disulfide-bonded peptides fragment during collision induced dissociation (CID). Most automated analysis algorithms function based on the assumption that the preponderance of product ions observed during the dissociation of disulfide-bonded peptides result from the cleavage of just one peptide bond, and in this report we tested that assumption by extensively analyzing the product ions generated when several disulfide-bonded peptides are subjected to CID on a quadrupole time of flight (QTOF) instrument. We found that one of the most common types of product ions generated resulted from two peptide bond cleavages, or a double cleavage. We found that for several of the disulfide-bonded peptides analyzed, the number of double cleavage product ions outnumbered those of single cleavages. The influence of charge state and precursor ion size was investigated, to determine if those parameters dictated the amount of double cleavage product ions formed. It was found in this sample set that no strong correlation existed between the charge state or peptide size and the portion of product ions assigned as double cleavages. These data show that these ions could account for many of the product ions detected in CID data of disulfide bonded peptides. We also showed the utility of double cleavage product ions on a peptide with multiple cysteines present. Double cleavage products were able to fully characterize the bonding pattern of each cysteine where typical single b/ y cleavage products could not.

  20. C-S bond cleavage by a polyketide synthase domain

    PubMed Central

    Ma, Ming; Lohman, Jeremy R.; Liu, Tao; Shen, Ben

    2015-01-01

    Leinamycin (LNM) is a sulfur-containing antitumor antibiotic featuring an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. The 1,3-dioxo-1,2-dithiolane moiety is essential for LNM’s antitumor activity, by virtue of its ability to generate an episulfonium ion intermediate capable of alkylating DNA. We have previously cloned and sequenced the lnm gene cluster from Streptomyces atroolivaceus S-140. In vivo and in vitro characterizations of the LNM biosynthetic machinery have since established that: (i) the 18-membered macrolactam backbone is synthesized by LnmP, LnmQ, LnmJ, LnmI, and LnmG, (ii) the alkyl branch at C-3 of LNM is installed by LnmK, LnmL, LnmM, and LnmF, and (iii) leinamycin E1 (LNM E1), bearing a thiol moiety at C-3, is the nascent product of the LNM hybrid nonribosomal peptide synthetase (NRPS)-acyltransferase (AT)-less type I polyketide synthase (PKS). Sulfur incorporation at C-3 of LNM E1, however, has not been addressed. Here we report that: (i) the bioinformatics analysis reveals a pyridoxal phosphate (PLP)-dependent domain, we termed cysteine lyase (SH) domain (LnmJ-SH), within PKS module-8 of LnmJ; (ii) the LnmJ-SH domain catalyzes C-S bond cleavage by using l-cysteine and l-cysteine S-modified analogs as substrates through a PLP-dependent β-elimination reaction, establishing l-cysteine as the origin of sulfur at C-3 of LNM; and (iii) the LnmJ-SH domain, sharing no sequence homology with any other enzymes catalyzing C-S bond cleavage, represents a new family of PKS domains that expands the chemistry and enzymology of PKSs and might be exploited to incorporate sulfur into polyketide natural products by PKS engineering. PMID:26240335

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

    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.

  2. Rhodium-Catalyzed C-C Bond Formation via Heteroatom-Directed C-H Bond Activation

    SciTech Connect

    Colby, Denise; Bergman, Robert; Ellman, Jonathan

    2010-05-13

    Once considered the 'holy grail' of organometallic chemistry, synthetically useful reactions employing C-H bond activation have increasingly been developed and applied to natural product and drug synthesis over the past decade. The ubiquity and relative low cost of hydrocarbons makes C-H bond functionalization an attractive alternative to classical C-C bond forming reactions such as cross-coupling, which require organohalides and organometallic reagents. In addition to providing an atom economical alternative to standard cross - coupling strategies, C-H bond functionalization also reduces the production of toxic by-products, thereby contributing to the growing field of reactions with decreased environmental impact. In the area of C-C bond forming reactions that proceed via a C-H activation mechanism, rhodium catalysts stand out for their functional group tolerance and wide range of synthetic utility. Over the course of the last decade, many Rh-catalyzed methods for heteroatom-directed C-H bond functionalization have been reported and will be the focus of this review. Material appearing in the literature prior to 2001 has been reviewed previously and will only be introduced as background when necessary. The synthesis of complex molecules from relatively simple precursors has long been a goal for many organic chemists. The ability to selectively functionalize a molecule with minimal pre-activation can streamline syntheses and expand the opportunities to explore the utility of complex molecules in areas ranging from the pharmaceutical industry to materials science. Indeed, the issue of selectivity is paramount in the development of all C-H bond functionalization methods. Several groups have developed elegant approaches towards achieving selectivity in molecules that possess many sterically and electronically similar C-H bonds. Many of these approaches are discussed in detail in the accompanying articles in this special issue of Chemical Reviews. One approach that has seen widespread success involves the use of a proximal heteroatom that serves as a directing group for the selective functionalization of a specific C-H bond. In a survey of examples of heteroatom-directed Rh catalysis, two mechanistically distinct reaction pathways are revealed. In one case, the heteroatom acts as a chelator to bind the Rh catalyst, facilitating reactivity at a proximal site. In this case, the formation of a five-membered metallacycle provides a favorable driving force in inducing reactivity at the desired location. In the other case, the heteroatom initially coordinates the Rh catalyst and then acts to stabilize the formation of a metal-carbon bond at a proximal site. A true test of the utility of a synthetic method is in its application to the synthesis of natural products or complex molecules. Several groups have demonstrated the applicability of C-H bond functionalization reactions towards complex molecule synthesis. Target-oriented synthesis provides a platform to test the effectiveness of a method in unique chemical and steric environments. In this respect, Rh-catalyzed methods for C-H bond functionalization stand out, with several syntheses being described in the literature that utilize C-H bond functionalization in a key step. These syntheses are highlighted following the discussion of the method they employ.

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

    PubMed

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

    2013-07-22

    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

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    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.

  5. A Homogeneous, Recyclable Polymer Support for Rh(I)-Catalyzed C-C Bond Formation

    PubMed Central

    Jana, Ranjan; Tunge, Jon A.

    2011-01-01

    A robust and practical polymer-supported, homogeneous, recyclable biphephos rhodium(I) catalyst has been developed for C-C bond formation reactions. Control of polymer molecular weight allowed tuning of the polymer solubility such that the polymer-supported catalyst is soluble in nonpolar solvents and insoluble in polar solvents. Using the supported rhodium catalysts, addition of aryl and vinylboronic acids to the electrophiles such as enones, aldehydes, N-sulfonyl aldimines, and alkynes occurs smoothly to provide products in high yields. Additions of terminal alkynes to enones and industrially relevant hydroformylation reactions have also been successfully carried out. Studies show that the leaching of Rh from the polymer support is low and catalyst recycle can be achieved by simple precipitation and filtration. PMID:21895010

  6. Ping-pong protons: how hydrogen-bonding networks facilitate heterolytic bond cleavage in peptide radical cations.

    PubMed

    Zhurov, Konstantin O; Wodrich, Matthew D; Corminboeuf, Clémence; Tsybin, Yury O

    2014-03-13

    Electron capture and electron transfer dissociation (ECD/ETD) tandem mass spectrometry (MS/MS) are commonly employed techniques for biomolecular analysis. The ECD/ETD process predominately cleaves N-Cα peptide backbone bonds, leading to primary sequence information complementary to other mass spectrometry techniques. Despite frequent laboratory use, the mechanistic underpinnings surrounding N-Cα bond cleavage remain debated. While the majority of mechanisms assume a homolytic bond rupture, we recently showed that heterolytic cleavage is also thermodynamically viable. For a cleavage of this type to be feasible, the charge separation created upon breaking of the N-Cα backbone bond must be quickly annihilated. In this work, we show, using density functional computations, that specific hydrogen-bonding motifs and structural rearrangements involving proton transfers stabilize the transition state associated with heterolytic cleavage and eliminate the ensuing charge separation from the final product fragments. The movement of protons can occur either directly from the z- to c-fragment or in a more complex manner including a ping-pong-type mechanism. The nature of these diverse hydrogen-bonding motifs reveals that not only those functional groups proximate to the bond rupture site, but also the entire global chemical environment, play important roles in backbone cleavage characteristic of ECD/ETD MS/MS. For doubly charged systems, both conformation and electron localization site dictate which of the two fragments retains the final positive charge. PMID:24555737

  7. Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2'-deoxyguanosine and guanosine.

    PubMed

    Wu, R R; Chen, Yu; Rodgers, M T

    2016-01-20

    Experimental and theoretical investigations suggest that hydrolysis of N-glycosidic bonds generally involves a concerted SN2 or a stepwise SN1 mechanism. While theoretical investigations have provided estimates for the intrinsic activation energies associated with N-glycosidic bond cleavage reactions, experimental measurements to validate the theoretical studies remain elusive. Here we report experimental investigations for N-glycosidic bond cleavage of the protonated guanine nucleosides, [dGuo+H](+) and [Guo+H](+), using threshold collision-induced dissociation (TCID) techniques. Two major dissociation pathways involving N-glycosidic bond cleavage, resulting in production of protonated guanine or the elimination of neutral guanine are observed in competition for both [dGuo+H](+) and [Guo+H](+). The detailed mechanistic pathways for the N-glycosidic bond cleavage reactions observed are mapped via electronic structure calculations. Excellent agreement between the measured and B3LYP calculated activation energies and reaction enthalpies for N-glycosidic bond cleavage of [dGuo+H](+) and [Guo+H](+) in the gas phase is found indicating that these dissociation pathways involve stepwise E1 mechanisms in analogy to the SN1 mechanisms that occur in the condensed phase. In contrast, MP2 is found to significantly overestimate the activation energies and slightly overestimate the reaction enthalpies. The 2'-hydroxyl substituent is found to stabilize the N-glycosidic bond such that [Guo+H](+) requires ?25 kJ mol(-1) more than [dGuo+H](+) to activate the glycosidic bond. PMID:26740232

  8. Concerted heavy-atom bond cleavage and proton and electron transfers illustrated by proton-assisted reductive cleavage of an O–O bond

    PubMed Central

    Costentin, Cyrille; Hajj, Viviane; Robert, Marc; Savéant, Jean-Michel; Tard, Cédric

    2011-01-01

    Electron transfer may be concerted with proton transfer. It may also be concerted with the cleavage of a bond between heavy atoms. All three events may also be concerted. A model is presented to analyze the kinetics of these all-concerted reactions for homogeneous or electrochemical reduction or oxidation processes. It allows the estimation of the kinetic advantage that derives from the increase of the bond-breaking driving force resulting from the concerted proton transfer. Application of the model to the electrochemical reductive cleavage of the O–O bond of an organic peroxide in the presence of a proximal acid group illustrates the applicability of the model and provides an example demonstrating that electron transfer, heavy-atom bond breaking, and proton transfer may be all concerted. Such analyses are expected to be useful for the invention, analysis, and optimization of reactions involved in contemporary energy challenges as well as for the comprehension of major biochemical processes, a number of which involve electron and proton transfer together with cleavage of bonds between heavy atoms. PMID:21551101

  9. Catalytic cleavage of ether C-O bonds by pincer iridium complexes.

    PubMed

    Haibach, Michael C; Lease, Nicholas; Goldman, Alan S

    2014-09-15

    The development of efficient catalytic methods to cleave the relatively unreactive C-O bonds of ethers remains an important challenge in catalysis. Building on our group's recent work, we report the dehydroaryloxylation of aryl alkyl ethers using pincer iridium catalysts. This method represents a rare fully atom-economical method for ether C-O bond cleavage. PMID:25060043

  10. Cleavage enhancement of specific chemical bonds in DNA-Cisplatin complexes induced by X-rays

    NASA Astrophysics Data System (ADS)

    Zheng, Yi; Yao, Xiaobin; Luo, Xinglan; Fu, Xianzhi

    2014-04-01

    The chemical bond transformation of cisplatin-DNA complexes can be probed efficiently by XPS which provides a concomitant X-ray irradiation source as well. The presence to Pt could considerably increase formation of the SE induced by X-ray and that the further interaction of these LEE with DNA leads to the enhancement of bond cleavages.

  11. Carbon-Carbon Bond Cleavage in Activation of the Prodrug Nabumetone

    PubMed Central

    Varfaj, Fatbardha; Zulkifli, Siti N. A.; Park, Hyoung-Goo; Challinor, Victoria L.; De Voss, James J.

    2014-01-01

    Carbon-carbon bond cleavage reactions are catalyzed by, among others, lanosterol 14-demethylase (CYP51), cholesterol side-chain cleavage enzyme (CYP11), sterol 17β-lyase (CYP17), and aromatase (CYP19). Because of the high substrate specificities of these enzymes and the complex nature of their substrates, these reactions have been difficult to characterize. A CYP1A2-catalyzed carbon-carbon bond cleavage reaction is required for conversion of the prodrug nabumetone to its active form, 6-methoxy-2-naphthylacetic acid (6-MNA). Despite worldwide use of nabumetone as an anti-inflammatory agent, the mechanism of its carbon-carbon bond cleavage reaction remains obscure. With the help of authentic synthetic standards, we report here that the reaction involves 3-hydroxylation, carbon-carbon cleavage to the aldehyde, and oxidation of the aldehyde to the acid, all catalyzed by CYP1A2 or, less effectively, by other P450 enzymes. The data indicate that the carbon-carbon bond cleavage is mediated by the ferric peroxo anion rather than the ferryl species in the P450 catalytic cycle. CYP1A2 also catalyzes O-demethylation and alcohol to ketone transformations of nabumetone and its analogs. PMID:24584631

  12. Central C-C Bonding Increases Optical and Chemical Stability of NIR Fluorophores

    PubMed Central

    Hyun, Hoon; Owens, Eric A.; Narayana, Lakshminarayana; Wada, Hideyuki; Gravier, Julien; Bao, Kai; Frangioni, John V.; Choi, Hak Soo; Henary, Maged

    2014-01-01

    Functional near-infrared (NIR) fluorophores have played a major role in the recent advances in bioimaging. However, the optical and physicochemical stabilities of NIR fluorophores in the biological and physiological environment are still a challenge. Especially, the ether linkage on the meso carbon of heptamethine core is fragile when exposed to serum proteins or other amine-rich biomolecules. To solve such a structural limitation, a rigid carbon-carbon bond was installed onto the framework of ether-linked NIR fluorophores through the Suzuki coupling. The robust fluorophores replaced as ZW800-1C and ZW800-3C displayed enhanced optical and chemical stability in various solvents and a 100% warm serum environment (> 99%, 24 h). The biodistribution and clearance of C-C coupled ZW800 compounds were almost identical to the previously developed oxygen-substituted ZW800 compounds. When conjugated with a small molecule ligand, ZW800-1C maintained the identical stable form in warm serum (>98%, 24 h), while ZW800-1A hydrolyzed quickly after 4 h incubation (34%, 24 h). PMID:25530846

  13. An alternative synthesis of the breast cancer drug fulvestrant (Faslodex®): catalyst control over C-C bond formation.

    PubMed

    Caprioglio, Diego; Fletcher, Stephen P

    2015-10-14

    Fulvestrant (Faslodex®) was synthesized in four steps (35% overall yield) from 6-dehydronandrolone acetate. Catalyst controlled, room temperature, diastereoselective 1,6-addition of the zirconocene derived from commercially available 9-bromonon-1-ene was used in the key C-C bond forming step. PMID:26300021

  14. Copper-catalyzed aerobic radical C–C bond cleavage of N–H ketimines

    PubMed Central

    Tnay, Ya Lin; Ang, Gim Yean

    2015-01-01

    Summary We report herein studies on copper-catalyzed aerobic radical C–C bond cleavage of N–H ketimines. Treatment of N–H ketimines having an α-sp3 hybridized carbon under Cu-catalyzed aerobic reaction conditions resulted in a radical fragmentation with C–C bond cleavage to give the corresponding carbonitrile and carbon radical intermediate. This radical process has been applied for the construction of oxaspirocyclohexadienones as well as in the electrophilic cyanation of Grignard reagents with pivalonitrile as a CN source. PMID:26664613

  15. Enantioselective Rh-Catalyzed Carboacylation of C═N Bonds via C-C Activation of Benzocyclobutenones.

    PubMed

    Deng, Lin; Xu, Tao; Li, Hongbo; Dong, Guangbin

    2016-01-13

    Herein we describe the first enantioselective Rh-catalyzed carboacylation of oximes (imines) via C-C activation. In this transformation, the benzocyclobutenone C1-C2 bond is selectively activated by a low valent rhodium catalyst and subsequently the resulting two Rh-C bonds add across a C═N bond, which provides a unique approach to access chiral lactams. A range of polycyclic nitrogen-containing scaffolds were obtained in good yields with excellent enantioselectivity. Further derivatization of the lactam products led to a rapid entry to various novel fused heterocycles. PMID:26674855

  16. Novel Cβ-Cγ Bond Cleavages of Tryptophan-Containing Peptide Radical Cations

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

    In this study, we observed unprecedented cleavages of the Cβ-Cγ 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 α-carbon radical intermediate at the tryptophan residue for the subsequent Cβ-Cγ 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 [W1-CH3GGGH]•+; 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 Cβ-Cγ bond cleavage. Hydrogen atom transfer or proton transfer to the γ-carbon atom of the tryptophan residue weakens the Cβ-Cγ bond and, therefore, decreases the dissociation energy barrier dramatically.

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

    SciTech Connect

    John J. Kilbane II

    2005-10-01

    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.

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

    PubMed

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

    2011-06-28

    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 π 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

  19. Metal-catalyzed release of supported boronic acids for C-C bond formation.

    PubMed

    Pourbaix, C; Carreaux, F; Carboni, B

    2001-03-22

    The viability of solid-supported boronic acids as reagents for Suzuki couplings and nucleophilic additions to aldehydes and enones was successfully demonstrated. This metal-catalyzed cleavage strategy allows the synthesis of a series of functionalized biphenyl products, benzylic alcohols, and beta-substituted ketones. PMID:11263886

  20. Thermodynamic Strategies for C-O Bond Formation and Cleavage via Tandem Catalysis.

    PubMed

    Lohr, Tracy L; Li, Zhi; Marks, Tobin J

    2016-05-17

    To reduce global reliance on fossil fuels, new renewable sources of energy that can be used with the current infrastructure are required. Biomass represents a major source of renewable carbon based fuel; however, the high oxygen content (∼40%) limits its use as a conventional fuel. To utilize biomass as an energy source, not only with current infrastructure, but for maximum energy return, the oxygen content must be reduced. One method to achieve this is to develop selective catalytic methods to cleave C-O bonds commonly found in biomass (aliphatic and aromatic ethers and esters) for the eventual removal of oxygen in the form of volatile H2O or carboxylic acids. Once selective methods of C-O cleavage are understood and perfected, application to processing real biomass feedstocks such as lignin can be undertaken. This Laboratory previously reported that recyclable "green" lanthanide triflates are excellent catalysts for C-O bond-forming hydroalkoxylation reactions. Based on the virtues of microscopic reversibility, the same lanthanide triflate catalyst should catalyze the reverse C-O cleavage process, retrohydroalkoxylation, to yield an alcohol and an alkene. However, ether C-O bond-forming (retrohydroalkoxylation) to form an alcohol and alkene is endothermic. Guided by quantum chemical analysis, our strategy is to couple endothermic, in tandem, ether C-O bond cleavage with exothermic alkene hydrogenation, thereby leveraging the combined catalytic cycles thermodynamically to form an overall energetically favorable C-O cleavage reaction. This Account reviews recent developments on thermodynamically leveraged tandem catalysis for ether and more recently, ester C-O bond cleavage undertaken at Northwestern University. First, the fundamentals of lanthanide-catalyzed hydroelementation are reviewed, with particular focus on ether C-O bond formation (hydroalkoxylation). Next, the reverse C-O cleavage/retrohydroalkoxylation processes enabled by tandem catalysis are discussed for both ether and ester C-O bond cleavage, including mechanistic and computational analysis. This is followed by recent results using this tandem catalytic strategy toward biomass relevant substrates, including work deconstructing acetylated lignin models, and the production of biodiesel from triglycerides, while bypassing the production of undesired glycerol for more valuable C3 products such as diesters (precursors to diols) in up to 47% selectivity. This Account concludes with future prospects for using this tandem catalytic system under real biomass processing conditions. PMID:27078085

  1. Kinetic Measurements on Single-molecule Disulfide Bond Cleavage

    PubMed Central

    Liang, Jian; Fernández, Julio M.

    2011-01-01

    We use single-molecule force clamp spectroscopy (SMFCS) to explore the reactivity of tris(2-carboxyethyl)phosphine (TCEP), 1, 4-DL-dithiothreitol (DTT) and hydrosulfide anion (HS-) on disulfide bonds within a mechanically stretched polypeptide. The single-bond level bimolecular nucleophilic substitution (SN2) events are recorded at a series of precisely-controlled temperatures so that the Arrhenius kinetic parameters, i.e. the height of the activation energy barrier (Ea) and the attempting frequency (A) of the chemical reactions, can be determined. The values of A are typically at the order of 107 M-1s-1, which is far lower than that predicted by the transition-state theory, in which A is given by kBT/h and around 1012 M-1s-1 at room temperature. Furthermore, Ea is derived to be 30-40 kJ/mol, which can be lowered by ~6-8% with every 100 pN mechanical force applied. The correlation of the A and Ea with the molecular structures reveals that the relative magnitude of these two parameters cannot be simply judged from the size of the molecule or the nucleophilicity of the attacking atom. The comparison of the influences on the reaction rate induced by force and temperature indicates an equivalent accelerating effect by every 50 pN or 10 K increment, giving for the first time the relationship between mechanical and thermal effects on a single-molecule SN2 chemical reaction. PMID:21341766

  2. Biotic and abiotic carbon to sulfur bond cleavage. Final report

    SciTech Connect

    Frost, J.W.

    1994-05-01

    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.

  3. Gold-Catalyzed Oxidation of Propargylic Ethers with Internal C-C Triple Bonds: Impressive Regioselectivity Enabled by Inductive Effect

    PubMed Central

    Ji, Kegong; D’Souza, Brendan; Nelson, Jon; Zhang, Liming

    2014-01-01

    Inductive perturbations of C-C triple bonds are shown to dictate the regiochemistry of gold-catalyzed oxidation of internal C-C triple bonds in the cases of propargylic ethers, resulting in highly regioselective formation of β-alkoxy-α,β-unsaturated ketones (up to >50/1 selectivity) via α-oxo gold carbene intermediates. Ethers derived from primary propargylic alcohols can be reliably transformed in good yields, and various functional groups are tolerated. With substrates derived from secondary propargylic alcohols, the development of a new P,N-bidentate ligand enables the minimization of competing alkyl group migration to the gold carbene center over the desired hydride migration; the preferred migration of a phenyl group, however, results in efficient formation of a α-phenyl-β-alkoxy-α,β-unsaturated ketone. These results further advance the surrogacy of a propargyl moiety to synthetically versatile enone function with reliable and readily predictable regioselectivity. PMID:25284890

  4. Highly Selective Cascade C-C Bond Formation via Palladium- Catalyzed Oxidative Carbonylation-Carbocyclization-Carbonylation-Alkynylation of Enallenes.

    PubMed

    Zhu, Can; Yang, Bin; Bäckvall, Jan-E

    2015-09-23

    A highly efficient palladium-catalyzed oxidative cascade reaction of enallenes undergoing overall four C-C bond formations has been developed. The insertion cascade proceeds via carbonylation-carbocyclization-carbonylation-alkynylation involving sequential insertion of carbon monoxide, olefin, and carbon monoxide. Furthermore, different types of terminal alkynes and functionalized enallenes have been investigated and found to undergo the cascade reaction under mild reaction conditions. PMID:26356201

  5. Stereoselective total synthesis of (-)-nupharamine utilizing an α-chlorosulfide and a sulfinimine for C-C bond formation.

    PubMed

    Raghavan, Sadagopan; Rajendar, Sheelamanthula

    2016-01-01

    An efficient stereoselective synthesis of the nuphar alkaloid, (-)-nupharamine, is reported. The key features include the Lewis acid catalyzed reaction of an α-chlorosulfide with a silyl ketene acetal for C-C bond formation, creation of the stereocenter at C2 by a diastereoselective reaction of allyl indium with a sulfinimine and reductive amination for the introduction of the C6 stereocenter of the piperidine ring. PMID:26490750

  6. Carbon-fluorine bond cleavage by zirconium metal hydride complexes

    SciTech Connect

    Edelbach, B.L.; Rahman, A.K.F.; Lachicotte, R.J.; Jones, W.D.

    1999-08-02

    The use of transition metal complexes to cleave strong carbon-fluorine bonds has blossomed in the past several years. Many late transition metal complexes with electron-donating ligands are believed to undergo oxidative addition to the C-F bond of a fluorinated aromatic group. The zirconium hydride dimer [Cp{sub 2}ZrH{sub 2}]{sub 2} reacts with C{sub 6}F{sub 6} at ambient temperature to give Cp{sub 2}Zr(C{sub 6}F{sub 5})F as the major product along with Cp{sub 2}ZrF{sub 2}, C{sub 6}F{sub 5}H and H{sub 2}. Neither the reaction rate nor the product ratio is affected by changes in H{sub 2} pressure or the concentration of C{sub 6}F{sub 6}. The reaction follows zero-order kinetics. The new compound Cp{sub 2}Zr(C{sub 6}F{sub 5})F has been structurally characterized. [Cp{sub 2}ZrH{sub 2}]{sub 2} reacts with C{sub 6}F{sub 5}H to give Cp{sub 2}Zr(p-C{sub 6}F{sub 4}H)F, Cp{sub 2}ZrF{sub 2}, C{sub 6}F{sub 4}H{sub 2}, and H{sub 2}. The zirconium hydride Cp{sub 3}ZrH has been structurally characterized and also reacts with C{sub 6}F{sub 6}. The products of the reaction are CpH, Cp{sub 2}Zr(C{sub 6}F{sub 5})F, C{sub 6}F{sub 5}H, Cp{sub 2}ZrF{sub 2}, Cp{sub 4}Zr, and Cp{sub 3}ZrF. The reaction rate is first order in [Cp{sub 3}ZrH] and [C{sub 6}F{sub 6}], but the product ratio is unaffected by the concentration of C{sub 6}F{sub 6}. Possible mechanisms of these reactions are discussed.

  7. Reaction Pathways and Energetics of Etheric C−O Bond Cleavage Catalyzed by Lanthanide Triflates

    SciTech Connect

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

    2013-07-15

    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.

  8. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

    NASA Astrophysics Data System (ADS)

    Rožman, Marko

    2016-01-01

    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

  9. Phospholipase D-catalyzed hydrolysis of phosphatidylcholine occurs with P-O bond cleavage.

    PubMed

    Holbrook, P G; Pannell, L K; Daly, J W

    1991-07-01

    Mammalian phospholipase D has been implicated in signal-transduction mechanisms, most recently in association with stimuli that enhance phosphatidylcholine (PC) turnover. It was previously unknown whether hydrolysis of PC by phospholipase D proceeds via P-O or C-O bond cleavage. Commercially available phospholipase D isolated from Streptomyces chromofuscus was used to hydrolyse distearoyl phosphatidylcholine (PC) in a detergent-containing buffer consisting of 90% 18O-water. The product of hydrolysis, phosphatidic acid (PA), was purified by thin-layer chromatography and analyzed using californium-252 plasma desorption mass spectrometry. An increase of two mass units was observed, compared to a distearoyl PA control, consistent with a reaction mechanism involving cleavage of the P-O bond. PMID:1854800

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

    SciTech Connect

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

    2011-01-01

    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.

  11. Biodehalogenation: The kinetics and rates of the microbial cleavage of carbon-halogen bonds

    SciTech Connect

    Castro, C.E. . Nematology Dept.)

    1993-09-01

    Specific rate constants associated with defined molecular paths of carbon-halogen bond cleavage from a variety of alkyl halide substrates by six soil organisms are presented. Five aerobes (three pseudomonads, one methylotroph, and one flavobacterium) and one anaerobe (a methanogen) are compared. The rate constants were obtained with resting cells in phosphate buffer at pH 7.4 in the absence of nutrients or other substances. The observed general rate law is d(X[sup [minus

  12. Carbon–carbon bond cleavage for Cu-mediated aromatic trifluoromethylations and pentafluoroethylations

    PubMed Central

    Sugiishi, Tsuyuka; Aikawa, Kohsuke

    2015-01-01

    Summary This short review highlights the copper-mediated fluoroalkylation using perfluoroalkylated carboxylic acid derivatives. Carbon–carbon bond cleavage of perfluoroalkylated carboxylic acid derivatives takes place in fluoroalkylation reactions at high temperature (150–200 °C) or under basic conditions to generate fluoroalkyl anion sources for the formation of fluoroalkylcopper species. The fluoroalkylation reactions, which proceed through decarboxylation or tetrahedral intermediates, are useful protocols for the synthesis of fluoroalkylated aromatics. PMID:26734112

  13. Exploring Regioselective Bond Cleavage and Cross-Coupling Reactions using a Low-Valent Nickel Complex.

    PubMed

    Desnoyer, Addison N; Friese, Florian W; Chiu, Weiling; Drover, Marcus W; Patrick, Brian O; Love, Jennifer A

    2016-03-14

    Recently, esters have received much attention as transmetalation partners for cross-coupling reactions. Herein, we report a systematic study of the reactivity of a series of esters and thioesters with [{(dtbpe)Ni}2 (μ-η(2) :η(2) -C6 H6 )] (dtbpe=1,2-bis(di-tert-butyl)phosphinoethane), which is a source of (dtbpe)nickel(0). Trifluoromethylthioesters were found to form η(2) -carbonyl complexes. In contrast, acetylthioesters underwent rapid Cacyl -S bond cleavage followed by decarbonylation to generate methylnickel complexes. This decarbonylation could be pushed backwards by the addition of CO, allowing for regeneration of the thioester. Most of the thioester complexes were found to undergo stoichiometric cross-coupling with phenylboronic acid to yield sulfides. While ethyl trifluoroacetate was also found to form an η(2) -carbonyl complex, phenyl esters were found to predominantly undergo Caryl -O bond cleavage to yield arylnickel complexes. These could also undergo transmetalation to yield biaryls. Attempts to render the reactions catalytic were hindered by ligand scrambling to yield nickel bis(acetate) complexes, the formation of which was supported by independent syntheses. Finally, 2-naphthyl acetate was also found to undergo clean Caryl -O bond cleavage, and although stoichiometric cross-coupling with phenylboronic acid proceeded with good yield, catalytic turnover has so far proven elusive. PMID:26879766

  14. D-β-aspartyl residue exhibiting uncommon high resistance to spontaneous peptide bond cleavage

    PubMed Central

    Aki, Kenzo; Okamura, Emiko

    2016-01-01

    Although L-amino acids were selected as main constituents of peptides and proteins during chemical evolution, D-aspartyl (Asp) residue is found in a variety of living tissues. In particular, D-β-Asp is thought to be stable than any other Asp isomers, and this could be a reason for gradual accumulation in abnormal proteins and peptides to modify their structures and functions. It is predicted that D-β-Asp shows high resistance to biomolecular reactions. For instance, less reactivity of D-β-Asp is expected to bond cleavage, although such information has not been provided yet. In this work, the spontaneous peptide bond cleavage was compared between Asp isomers, by applying real-time solution-state NMR to eye lens αΑ-crystallin 51–60 fragment, S51LFRTVLD58SG60 and αΒ-crystallin 61–67 analog, F61D62TGLSG67 consisting of L-α- and D-β-Asp 58 and 62, respectively. Kinetic analysis showed how tough the uncommon D-β-Asp residue was against the peptide bond cleavage as compared to natural L-α-Asp. Differences in pKa and conformation between L-α- and D-β-Asp side chains were plausible factors to determine reactivity of Asp isomers. The present study, for the first time, provides a rationale to explain less reactivity of D-β-Asp to allow abnormal accumulation. PMID:26876027

  15. D-β-aspartyl residue exhibiting uncommon high resistance to spontaneous peptide bond cleavage

    NASA Astrophysics Data System (ADS)

    Aki, Kenzo; Okamura, Emiko

    2016-02-01

    Although L-amino acids were selected as main constituents of peptides and proteins during chemical evolution, D-aspartyl (Asp) residue is found in a variety of living tissues. In particular, D-β-Asp is thought to be stable than any other Asp isomers, and this could be a reason for gradual accumulation in abnormal proteins and peptides to modify their structures and functions. It is predicted that D-β-Asp shows high resistance to biomolecular reactions. For instance, less reactivity of D-β-Asp is expected to bond cleavage, although such information has not been provided yet. In this work, the spontaneous peptide bond cleavage was compared between Asp isomers, by applying real-time solution-state NMR to eye lens αΑ-crystallin 51-60 fragment, S51LFRTVLD58SG60 and αΒ-crystallin 61-67 analog, F61D62TGLSG67 consisting of L-α- and D-β-Asp 58 and 62, respectively. Kinetic analysis showed how tough the uncommon D-β-Asp residue was against the peptide bond cleavage as compared to natural L-α-Asp. Differences in pKa and conformation between L-α- and D-β-Asp side chains were plausible factors to determine reactivity of Asp isomers. The present study, for the first time, provides a rationale to explain less reactivity of D-β-Asp to allow abnormal accumulation.

  16. Biotic and abiotic carbon to sulfur bond cleavage. Technical report, July 1, 1991--September 30, 1991

    SciTech Connect

    Frost, J.W.

    1991-12-31

    Cleavage of aliphatic organosulfonate carbon to sulfur (C-S) bonds, a critical link in the global biogeochemical sulfur cycle, has been identified in Escherichia coli K-12. Enormous quantities of inorganic sulfate are continuously converted (Scheme I) into methanesulfonic acid 1 and acylated 3-(6-sulfo-{alpha}-D-quinovopyranosyl)-L-glycerol 2. Biocatalytic desulfurization (Scheme I) of 1 and 2, which share the structural feature of an aliphatic carbon bonded to a sulfonic acid sulfur, completes the cycle, Discovery of this desulfurization in E. coli provides an invaluable paradigm for study of a biotic process which, via the biogeochemical cycle, significantly influences the atmospheric concentration of sulfur-containing molecules.

  17. Selective cleavage of isoaspartyl peptide bonds by hydroxylamine after methyltransferase priming.

    PubMed

    Zhu, Jeff X; Aswad, Dana W

    2007-05-01

    Formation of atypical isoaspartyl (isoAsp) sites in peptides and proteins via the deamidation-linked isomerization of asparaginyl-Xaa bonds or direct isomerization of aspartyl-Xaa bonds is a major contributor to spontaneous protein damage under mild conditions. This nonenzymatic reaction reroutes the Asx-Xaa peptide bond through the beta-carbonyl of asparaginyl or aspartyl residues, thereby adding an extra carbon to the polypeptide backbone. Formation of isoAsp has been implicated in protein inactivation, aggregation, degradation, and autoimmunity. Knowing the location of isoAsp sites in proteins is important for understanding mechanisms of protein damage and for characterizing protein pharmaceuticals. Here we present a simple nonradioactive method for direct localization of isoAsp residues in peptides or proteins. Using three model peptides, we demonstrate that isoAsp linkages can be cleaved selectively and in high yield by a two-step process in which (i) the isoAsp linkage is converted into a succinimide on incubation with S-adenosyl-l-methionine and the commercially available enzyme, protein l-isoaspartyl-O-methyltransferase, and (ii) the succinimidyl bond is then cleaved by hydroxylamine under conditions that minimize cleavage of the traditional hydroxylamine-sensitive Asn-Gly and related peptide bonds. Location of the isoAsp linkage is then inferred by identifying the cleavage products by mass spectrometry or N-terminal sequencing. PMID:17376395

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

    SciTech Connect

    Li, Meng; Cullen, David A; Sasaki, Kotaro; Marinkovic, N.; More, Karren Leslie; Adzic, Radoslav R.

    2013-01-01

    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.

  19. Matching plasmon resonances to the C=C and C-H bonds in estradiol

    NASA Astrophysics Data System (ADS)

    Mbomson, Ifeoma G.; McMeekin, Scott; De La Rue, Richard; Johnson, Nigel P.

    2015-03-01

    We tune nanoantennas to resonate within mid-infrared wavelengths to match the vibrational resonances of C=C and C-H of the hormone estradiol. Modelling and fabrication of the nanoantennas produce plasmon resonances between 2 μm to 7 μm. The hormone estradiol was dissolved in ethanol and evaporated, leaving thickness of a few hundreds of nanometres on top of gold asymmetric split H-like shaped on a fused silica substrate. The reflectance was measured and a red-shift is recorded from the resonators plasmonic peaks. Fourier transform infrared spectroscopy is use to observe enhanced spectra of the stretching modes for the analyte which belongs to alkenyl biochemical group.

  20. Residue 345 of dibenzothiophene (DBT) sulfone monooxygenase is involved in C-S bond cleavage specificity of alkylated DBT sulfones.

    PubMed

    Konishi, Jin; Maruhashi, Kenji

    2003-07-01

    Rhodococcus erythropolis IGTS8 that possesses dibenzothiophene sulfone monooxygenase mutated at residue 345 (Q345A), can degrade octyl sulfide on which the wild strain cannot grow. Residue 345 and the neighbouring residues were changed by site-directed mutagenesis. Only DszA changed at residue 345 gave an altered C-S bond cleavage pattern of 3-methyl DBT sulfone. This residue is therefore involved in C-S bond cleavage specifically for alkylated DBT sulfone. PMID:12967013

  1. Moving towards strong-field femtosecond control of bond cleavage and charge localization in triatomic molecules

    NASA Astrophysics Data System (ADS)

    Jochim, Bethany; Ablikim, U.; Zohrabi, M.; Gaire, B.; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

    2012-06-01

    A 3-D momentum imaging technique is employed to study intense ultrafast laser-induced dissociation of triatomic molecular ions from an ion beam. Utilizing our measured kinetic energy release and angular distribution spectra along with the calculated electronic structure of these molecules, we elucidate possible dissociation pathways and anticipate and explore various laser parameters that could be used to drive transitions to specific final products. For example, we have studied N2O^+, in which we find that for typical intense IR laser pulses (˜30 fs, transform-limited, 800 nm, ˜10^15 W/cm^2 pulses), the preferred bond cleavage (i.e., breaking the N-N bond vs. the N-O bond) and charge localization patterns are those that are the most energetically favorable. We investigate laser parameters that could be used to steer this and other systems to less likely outcomes.

  2. Chemistry of oxygenates on transition metal surfaces: Activation of C- H, C-C, and C-O bonds

    SciTech Connect

    Not Available

    1991-01-01

    Goal is to understand the requirements for and competition between activation of C-H, C-C, and C-O bonds in the synthesis and decomposition of oxygenates on transition metal surfaces. Efforts during the past year was devoted primarily to the role of activation of {beta}-CH bonds in decarbonylation of higher oxygenates on surfaces of metals such as Rh and Pd; studies were completed of more than a dozen C{sub 1}-C{sub 3} oxygenates on Rh(111), and progress was made with reagents for which {beta}-CH scission is blocked. It is shown that alcohols and aldehydes do not react via a common pathway on on Rh(111). Ethanol and acetaldehyde are formed from CO + H{sub 2} by parallel routes on Rh catalysts which do not contain interacting supports or oxide promoters; i.e., the two compounds result from CO insertion into different metal-hydrocarbon bonds. Aldehydes decarbonylate via {alpha}-CH scission to form acyl, followed by C-C scission to release an alkyl ligand; this ligand undergoes hydrogenation and dehydrogenation steps. Alcohols form surface alkoxides, but these do not dehydrogenate further to the aldehydes, they release CO + H{sub 2} but no volatile hydrocarbon. These results indicate that {beta}-CH scissors to form a surface oxametallacycle intermediate; supporting evidence is spresented for this intermediate. Chemistry of alcohols blocked to different extends at the {beta}-position was also studied; complete blocking (CF{sub 3}CH{sub 2}OH) forces the reaction to follow the aldehyde-acyl path, while partial substitution at the {beta} position (branched alcohols) favors the oxametallacycle pathway. (DLC)

  3. Competition between covalent and noncovalent bond cleavages in dissociation of phosphopeptide-amine complexes.

    PubMed

    Laskin, Julia; Yang, Zhibo; Woods, Amina S

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature and have been extensively studied phenomenologically. However, little is known about the binding energies in non-covalent complexes containing these functional groups. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A(3)pXA(3)-NH(2) (X = S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. For systems examined in this study, covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel. PMID:21387029

  4. N-H bond cleavage of ammonia on graphene-like B36 borophene: DFT studies.

    PubMed

    Rostami, Zahra; Soleymanabadi, Hamed

    2016-04-01

    Ammonia N-H bond cleavage at metal-free substrates has attracted great attention because of its industrial importance. Here, we investigate the dissociative adsorption of ammonia onto the surface of a B36 borophene sheet by means of density functional theory calculations. We show that the N-H bond may be broken at the edges of B36 even at room temperature, regarding the small energy barrier of 14.1-19.3 kcal mol(-1) at different levels of theory, and more negative Gibbs free energy change. Unlike basis set size, the kind of exchange correlation functional significantly affects the electronic properties of the studied systems. Also, by increasing the percentage of Hartree Fock (HF) exchange of density functionals, the activation and adsorption energies are lowered. A linear relationship between the highest occupied molecular orbital or lowest unoccupied molecular orbital of B36 borophene and the %HF exchange of functionals is predicted. Our work reveals that pure whole boron nanosheets may be promising metal-free materials in N-H bond cleavage, which would raise the potential application of these sheets. PMID:26969676

  5. Competition between Covalent and Noncovalent Bond Cleavages in Dissociation of Phosphopeptide-Amine Complexes

    SciTech Connect

    Laskin, Julia; Yang, Zhibo; Woods, Amina S.

    2011-04-21

    Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A3pXA3-NH2 (X=S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. We demonstrate that covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel

  6. Transversely isotropic elastic properties of single-walled carbon nanotubes by a rectangular beam model for the C ?C bonds

    NASA Astrophysics Data System (ADS)

    Li, Haijun; Guo, Wanlin

    2008-05-01

    Continuum mechanics modeling of carbon nanotubes has long been an attractive issue, but how to reflect exactly the physics essential of the atomic bonds still remains to be a challenging problem. To capture the distinguishing in-plane ?-? and out-of-plane ?-? bond angle bending rigidities of C ?C bonds in carbon nanotubes, an equivalent beam element with rectangular section is proposed and a corresponding frame structure model for a single-walled carbon nanotube (SWNT) is developed. By using the model, the five independent elastic moduli of SWNTs with arbitrary chirality and diameter are evaluated systematically. It is found that the elastic properties of the SWNTs are transversely isotropic when the tube diameter is small. The smaller the tube diameter is, the stronger the dependence of the elastic properties on the tube size and chirality is, while when the tube diameter is large enough, the SWNTs degenerate from transversely isotropic to isotropic and the elastic moduli tend to that of a graphite sheet. The present model can be incorporated into any standard finite element software directly, providing an extremely versatile and powerful tool for the study of nanostructures that beyond the computational capability of current atomistic approaches.

  7. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond.

    PubMed

    Rožman, Marko

    2016-01-01

    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates. PMID:26297186

  8. Recombinant Cyanobacteria for the Asymmetric Reduction of C=C Bonds Fueled by the Biocatalytic Oxidation of Water.

    PubMed

    Köninger, Katharina; Gómez Baraibar, Álvaro; Mügge, Carolin; Paul, Caroline E; Hollmann, Frank; Nowaczyk, Marc M; Kourist, Robert

    2016-04-25

    A recombinant enoate reductase was expressed in cyanobacteria and used for the light-catalyzed, enantioselective reduction of C=C bonds. The coupling of oxidoreductases to natural photosynthesis allows asymmetric syntheses fueled by the oxidation of water. Bypassing the addition of sacrificial cosubstrates as electron donors significantly improves the atom efficiency and avoids the formation of undesired side products. Crucial factors for product formation are the availability of NADPH and the amount of active enzyme in the cells. The efficiency of the reaction is comparable to typical whole-cell biotransformations in E. coli. Under optimized conditions, a solution of 100 mg prochiral 2-methylmaleimide was reduced to optically pure 2-methylsuccinimide (99 % ee, 80 % yield of isolated product). High product yields and excellent optical purities demonstrate the synthetic usefulness of light-catalyzed whole-cell biotransformations using recombinant cyanobacteria. PMID:27029020

  9. METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

    SciTech Connect

    John J. Kilbane II

    2004-10-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Simons, Jack

    2010-01-01

    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.

  11. Rh-Catalyzed C–C Bond Cleavage by Transfer Hydroformylation

    PubMed Central

    Murphy, Stephen K.; Park, Jung-Woo; Cruz, Faben A.; Dong, Vy M.

    2015-01-01

    The dehydroformylation of aldehydes to generate olefins occurs during the biosynthesis of various sterols, including cholesterol in humans. Here, we implement a synthetic version that features the transfer of a formyl group and hydride from an aldehyde substrate to a strained olefin acceptor. A Rh(Xantphos)(benzoate) catalyst activates aldehyde C–H bonds with high chemoselectivity to trigger C–C bond cleavage and generate olefins at low loadings (0.3 to 2 mol%) and temperatures (22 to 80 °C). This mild protocol can be applied to various natural products and was used to achieve a three step synthesis of (+)-yohimbenone. A study of the mechanism reveals that the benzoate counterion acts as a proton-shuttle to enable transfer hydroformylation. PMID:25554782

  12. Molecular features in complex environment: Cooperative team players during excited state bond cleavage.

    PubMed

    Thallmair, Sebastian; Roos, Matthias K; de Vivie-Riedle, Regina

    2016-07-01

    Photoinduced bond cleavage is often employed for the generation of highly reactive carbocations in solution and to study their reactivity. Diphenylmethyl derivatives are prominent precursors in polar and moderately polar solvents like acetonitrile or dichloromethane. Depending on the leaving group, the photoinduced bond cleavage occurs on a femtosecond to picosecond time scale and typically leads to two distinguishable products, the desired diphenylmethyl cations (Ph2CH(+)) and as competing by-product the diphenylmethyl radicals ([Formula: see text]). Conical intersections are the chief suspects for such ultrafast branching processes. We show for two typical examples, the neutral diphenylmethylchloride (Ph2CH-Cl) and the charged diphenylmethyltriphenylphosphonium ions ([Formula: see text]) that the role of the conical intersections depends not only on the molecular features but also on the interplay with the environment. It turns out to differ significantly for both precursors. Our analysis is based on quantum chemical and quantum dynamical calculations. For comparison, we use ultrafast transient absorption measurements. In case of Ph2CH-Cl, we can directly connect the observed signals to two early three-state and two-state conical intersections, both close to the Franck-Condon region. In case of the [Formula: see text], dynamic solvent effects are needed to activate a two-state conical intersection at larger distances along the reaction coordinate. PMID:26958588

  13. Molecular features in complex environment: Cooperative team players during excited state bond cleavage

    PubMed Central

    Thallmair, Sebastian; Roos, Matthias K.; de Vivie-Riedle, Regina

    2016-01-01

    Photoinduced bond cleavage is often employed for the generation of highly reactive carbocations in solution and to study their reactivity. Diphenylmethyl derivatives are prominent precursors in polar and moderately polar solvents like acetonitrile or dichloromethane. Depending on the leaving group, the photoinduced bond cleavage occurs on a femtosecond to picosecond time scale and typically leads to two distinguishable products, the desired diphenylmethyl cations (Ph2CH+) and as competing by-product the diphenylmethyl radicals (Ph2CH•). Conical intersections are the chief suspects for such ultrafast branching processes. We show for two typical examples, the neutral diphenylmethylchloride (Ph2CH–Cl) and the charged diphenylmethyltriphenylphosphonium ions (Ph2CH−PPh3+) that the role of the conical intersections depends not only on the molecular features but also on the interplay with the environment. It turns out to differ significantly for both precursors. Our analysis is based on quantum chemical and quantum dynamical calculations. For comparison, we use ultrafast transient absorption measurements. In case of Ph2CH–Cl, we can directly connect the observed signals to two early three-state and two-state conical intersections, both close to the Franck-Condon region. In case of the Ph2CH−PPh3+, dynamic solvent effects are needed to activate a two-state conical intersection at larger distances along the reaction coordinate. PMID:26958588

  14. METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

    SciTech Connect

    John J. Kilbane III

    2003-12-01

    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.

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

    SciTech Connect

    Bausch, M.; Ho, K.K.

    1993-05-01

    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.

  16. Mechanism and Thermodynamics of Reductive Cleavage of Carbon-Halogen Bonds in the Polybrominated Aliphatic Electrophiles.

    PubMed

    Rosokha, Sergiy V; Lukacs, Emoke; Ritzert, Jeremy T; Wasilewski, Adam

    2016-03-17

    Quantum-mechanical computations revealed that, despite the presence of electron-withdrawing and/or π-acceptor substituents, the lowest unoccupied molecular orbitals (LUMO) of the polybromosubstituted aliphatic molecules R-Br (R-Br = C3Br2F6, CBr3NO2, CBr3CN, CBr3CONH2, CBr3CO2H, CHBr3, CFBr3, CBr4, CBr3COCBr3) are delocalized mostly over their bromine-containing fragments. The singly occupied molecular orbitals in the corresponding vertically excited anion radicals (R-Br(•-))* are characterized by essentially the same shapes and show nodes in the middle of the C-Br bonds. An injection of an electron into the antibonding LUMO results in the barrierless dissociation of the anion-radical species and the concerted reductive cleavages of C-Br bonds leading to the formation of the loosely bonded {R(•)···Br(-)} associates. The interaction energies between the fragments of these ion-radical pairs vary from ∼10 to 20 kcal mol(-1) in the gas phase and from 1 to 3 kcal mol(-1) in acetonitrile. In accord with the concerted mechanism of reductive cleavage, all R-Br molecules showed completely irreversible reduction waves in the voltammograms in the whole range of the scan rates employed (from 0.05 to 5 V s(-1)). Also, the transfer coefficients α, established from the width of these waves and dependence of reduction peak potentials Ep on the scan rates, were significantly lower than 0.5. The standard reduction potentials of the R-Br electrophiles, E(o)R-Br/R·+X(-), and the corresponding R(•) radicals, E(o)R(•)/R(-), were calculated in acetonitrile using the appropriate thermodynamic cycles. In agreement with these calculations, which indicated that the R(•) radicals resulting from the reductive cleavage of the R-Br molecules are stronger oxidants than their parents, the reduction peaks' currents in cyclic voltammograms were consistent with the two-electron transfer processes. PMID:26816138

  17. Tailoring Bond Cleavage in Gas-Phase Biomolecules by Low Energy Electrons

    NASA Astrophysics Data System (ADS)

    Ptasinska, Sylwia

    2014-10-01

    The high energy quanta of impinging radiation can generate a large number (about 5x104) of secondary electrons per 1 MeV of energy deposited. When ejected in condensed phase water, the kinetic energy distribution of these free or quasi-free electrons is peaked below 10 eV. Low energy electrons also dominate in the secondary emission from biomolecular targets exposed to different energies of primary radiation. Due to the complexity of the radiation-induced processes in the condensed-phase environment, mechanisms of secondary electrons induced damage in biomolecules (BM) still need to be investigated. However, based on results from theory and different experiments accumulated within the last decade, it is now possible to determine the fundamental mechanisms that are involved in many chemical reactions induced in isolated gas-phase biomolecules by low energy electrons. The central finding of earlier research was the discovery of the bond- and site- selectivity in the dissociative electron attachment (DEA) process to biomolecules. It has been demonstrated that by tuning the energy of the incoming electron we can gain control over the location of the bond cleavage. These studies showed the selectivity in single bond cleavage reactions leading to the formation of the dehydrogenated closed shell anion (BM-H)- or the complementary reaction leading to H-. The loss of a hydrogen atom or an anion is fast compared with ring cleavage and the excision of heavier fragments and, hence, this reaction can compete efficiently with autodetachment. Moreover, site selectivity has been also observed in the metastable anion formation via the DEA process. Such delayed fragmentation was studied recently for the dehydrogenated closed-shell anion conversion into NCO- upon DEA proceeded a few μ sec after electron attachment, indicating a rather slow unimolecular decomposition. Interestingly, site selectivity was observed in the prompt as well as the metastable NCO- formation in DEA. The research described herein was supported by the Division of Chemical Sciences, Geosciences and Biosciences, Basic Energy Sciences, Office of Science, United States Department of Energy through Grant Number DE-FC02-04ER15533.

  18. Sequential N-O and N-N bond cleavage of N-heterocyclic carbene-activated nitrous oxide with a vanadium complex.

    PubMed

    Tskhovrebov, Alexander G; Solari, Euro; Wodrich, Matthew D; Scopelliti, Rosario; Severin, Kay

    2012-01-25

    Chemically induced bond cleavage of nitrous oxide typically proceeds by rupture of the N-O bond with concomitant O-atom transfer and liberation of dinitrogen. On a few occasions, N-N bond scission has been observed instead. We report a reaction sequence involving an N-heterocyclic carbene and a vanadium complex that results in cleavage of both the N-O bond and the N-N bond. PMID:22276774

  19. Reversible O-O bond cleavage and formation between Mn(IV)-peroxo and Mn(V)-oxo corroles.

    PubMed

    Kim, Sun Hee; Park, Hyejin; Seo, Mi Sook; Kubo, Minoru; Ogura, Takashi; Klajn, Jan; Gryko, Daniel T; Valentine, Joan Selverstone; Nam, Wonwoo

    2010-10-13

    Mn(IV)-peroxo and Mn(V)-oxo corroles were synthesized and characterized with various spectroscopic techniques. The intermediates were directly used in O-O bond cleavage and formation reactions. Upon addition of proton to the Mn(IV)-peroxo corrole, the formation of the Mn(V)-oxo corrole was observed. Interestingly, addition of base to the Mn(V)-oxo corrole afforded the formation of the Mn(IV)-peroxo corrole. Thus, we were able to report the first example of reversible O-O bond cleavage and formation reactions using in situ generated Mn(IV)-peroxo and Mn(V)-oxo corroles. PMID:20845972

  20. A mechanistic study of Trichoderma reesei Cel7B catalyzed glycosidic bond cleavage.

    PubMed

    Zhang, Yu; Yan, Shihai; Yao, Lishan

    2013-07-25

    An ONIOM study is performed to illustrate the mechanism of Trichoderma reesei Cel7B catalyzed p-nitrophenyl lactoside hydrolysis. In both the glycosylation and deglycosylation steps, the reaction proceeds in a concerted way, meaning the nucleophilic attack and the glycosidic bond cleavage occur simultaneously. The glycosylation step is rate limiting with a barrier of 18.9 kcal/mol, comparable to the experimental value derived from the kcat measured in this work. The function of four residues R108, Y146, Y170, and D172, which form a hydrogen-bond network involving the substrate, is studied by conservative mutations. The mutants, including R108K, Y146F, Y170F, and D172N, decrease the enzyme activity by about 150-8000-fold. Molecular dynamics simulations show that the mutations disrupt the hydrogen-bond network, cause the substrate to deviate from active binding and hinder either the proton transfer from E201 to O4(+1) or the nucleophilic attack from E196 to C1(-1). PMID:23822607

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

    PubMed

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

    2010-10-28

    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)(κ(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

  2. A Substrate-Assisted Mechanism of Nucleophile Activation in a Ser-His-Asp Containing C-C Bond Hydrolase

    SciTech Connect

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

    2013-11-12

    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, which possesses 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 to 2-hydroxy-2,4-pentadienoic acid 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 pKa2nuc ~ 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.

  3. Efficient C-H Bond Activations via O2 Cleavage by a Dianionic Cobalt(II) Complex.

    PubMed

    Nguyen, Andy I; Hadt, Ryan G; Solomon, Edward I; Tilley, T Don

    2014-07-01

    A dianionic, square planar cobalt(II) complex reacts with O2 in the presence of acetonitrile to give a cyanomethylcobalt(III) complex formed by C-H bond cleavage. Interestingly, PhIO and p-tolylazide react similarly to give the same cyanomethylcobalt(III) complex. Competition studies with various hydrocarbon substrates indicate that the rate of C-H bond cleavage greatly depends on the p Ka of the C-H bond, rather than on the C-H bond dissociation energy. Kinetic isotope experiments reveal a moderate KIE value of ca. 3.5 using either O2 or PhIO. The possible involvement of a cobalt(IV) oxo species in this chemistry is discussed. PMID:25071930

  4. Competition between birch reduction and bond cleavage in 1,2-bis(4-methyl-1-naphthyl)ethane

    SciTech Connect

    Marcinow, Z.; Hull, C.E.; Rabideau, P.W. )

    1989-07-21

    The reaction of 1,2-bis(4-methyl-1-naphthyl)ethane with Li, Na, and K in ammonia, THF, and HMPA, or mixtures thereof, has been examined with respect to the factors favoring Birch reduction of the aromatic ring and cleavage of the ethane carbon-carbon bond. Bond cleavage was found to increase relative to ring reduction in the series Li < Na < K and with the solvents NH{sub 3} < THF < HMPA. However, the latter position of ammonia may be due to the necessarily restricted low-reaction temperature since only ring reduction was observed at temperatures at or below the boiling point of ammonia (-33{degree}C). A number of reduction and cleavage products were isolated and identified, and the mechanistic pathways for their formation is discussed.

  5. Heterobimetallic Ti/Co Complexes That Promote Catalytic N-N Bond Cleavage.

    PubMed

    Wu, Bing; Gramigna, Kathryn M; Bezpalko, Mark W; Foxman, Bruce M; Thomas, Christine M

    2015-11-16

    Treatment of the tris(phosphinoamide) titanium precursor ClTi(XylNP(i)Pr2)3 (1) with CoI2 leads to the heterobimetallic complex (η(2)-(i)Pr2PNXyl)Ti(XylNP(i)Pr2)2(μ-Cl)CoI (2). One-electron reduction of 2 affords (η(2)-(i)Pr2PNXyl)Ti(XylNP(i)Pr2)2CoI (3), which can be reduced by another electron under dinitrogen to generate the reduced diamagnetic complex (THF)Ti(XylNP(i)Pr2)3CoN2 (4). The removal of the dinitrogen ligand from 4 under vacuum affords (THF)Ti(XylNP(i)Pr2)3Co (5), which features a Ti-Co triple bond. Treatment of 4 with hydrazine or methyl hydrazine results in N-N bond cleavage and affords the new diamagnetic complexes (L)Ti(XylNP(i)Pr2)3CoN2 (L = NH3 (6), MeNH2 (7)). Complexes 4, 5, and 6 have been shown to catalyze the disproportionation of hydrazine into ammonia and dinitrogen gas through a mechanism involving a diazene intermediate. PMID:26492046

  6. An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis

    SciTech Connect

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

    2010-01-12

    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.

  7. Cleavage of carbon-sulfur bonds in coal and substituted dibenzyl sulfides

    SciTech Connect

    Green, T.K.; Wang, L.; Estill, W.J.; Bixler, B.

    1996-10-01

    S-methylation of a bituminous coal using {sup 13}C-enriched methyl iodide in the presence of silver tetrafluoroborate produces significant quantities of trimethylsulfonium ion as determined by {sup 13}C NMR. This result suggests that carbon-sulfur bonds in coal are being cleaved. In an effort to determine the types of structures in coal responsible for this ion, a series of model substituted dibenzyl sulfides were S-methylated. The substrates included 4,4{prime}dimethoxydibenzylsulfide (1), 4,4{prime}dimethyldibenzylsulfide (2), dibenzylsulfide (3), 4,4{prime}dichlorodibenzylsufide (4). All substrates are cleaved to varying degrees in refluxing DCE (83{degrees}C) to produce a mixture of methyldibenzyl-, dimethylbenzyl- and trimethylsulfonium ions. The relative amounts of these ions depends on the substituent, with the degree of C-S bond cleavage increasing with the electron-donating ability of the substituent in the order (1) > (2) > (3) > (4). A mechanism is proposed consistent with this substituent effect which involves an intermediate benzyl carbocation - sulfide ion-dipole complex.

  8. Dihydrogen bond interactions as a result of H2 cleavage at Cu, Ag and Au centres.

    PubMed

    Grabowski, Sławomir J; Ruipérez, Fernando

    2016-05-14

    A quantum chemical study of H2 activation at fluorides of coinage metals, MF (M = Cu, Ag and Au), and its splitting was performed. The following reaction path was analyzed: FMH2→ FHHM → HMFH, where both the molecular complexes and the corresponding transition states have been characterized at the CCSD(T)/aug-cc-pVQZ//MP2/aug-cc-pVQZ level of theory. Further single-point CASSCF/CASPT2 calculations, including spin-orbit coupling effects, were also performed to analyze the role of non-dynamic correlation. The scalar relativistic effects are included via aug-cc-pVQZ-PP basis sets used for the metals. The dihydrogen-bonded copper (FHHCu) and silver (FHHAg) complexes are observed as a result of H2 cleavage, while the corresponding FHHAu gold complex is not found but the HAuHF arrangement is observed, instead. The energetic and geometrical parameters of the complexes have been analyzed and both the Quantum Theory of Atoms in Molecules approach and the Natural Bond Orbitals method were additionally applied to analyze the intermolecular interactions. PMID:27101741

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

    SciTech Connect

    Bausch, M.

    1992-10-01

    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.

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

    PubMed

    Wu, Tao; Mu, Xin; Liu, Guosheng

    2011-12-23

    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

  11. Catalytic C-O bond cleavage of 2-aryloxy-1-arylethanols and its application to the depolymerization of lignin-related polymers.

    PubMed

    Nichols, Jason M; Bishop, Lee M; Bergman, Robert G; Ellman, Jonathan A

    2010-09-15

    A ruthenium-catalyzed, redox neutral C-O bond cleavage of 2-aryloxy-1-arylethanols was developed that yields cleavage products in 62-98% isolated yield. This reaction is applicable to breaking the key ethereal bond found in lignin-related polymers. The bond transformation proceeds by a tandem dehydrogenation/reductive ether cleavage. Initial mechanistic investigations indicate that the ether cleavage is most likely an organometallic C-O activation. A catalytic depolymerization of a lignin-related polymer quantitatively yields the corresponding monomer with no added reagent. PMID:20731348

  12. Stereoselective Halogenation of Integral Unsaturated C-C Bonds in Chemically and Mechanically Robust Zr and Hf MOFs.

    PubMed

    Marshall, Ross J; Griffin, Sarah L; Wilson, Claire; Forgan, Ross S

    2016-03-24

    Metal-organic frameworks (MOFs) containing Zr(IV) -based secondary building units (SBUs), as in the UiO-66 series, are receiving widespread research interest due to their enhanced chemical and mechanical stabilities. We report the synthesis and extensive characterisation, as both bulk microcrystalline and single crystal forms, of extended UiO-66 (Zr and Hf) series MOFs containing integral unsaturated alkene, alkyne and butadiyne units, which serve as reactive sites for postsynthetic modification (PSM) by halogenation. The water stability of a Zr-stilbene MOF allows the dual insertion of both -OH and -Br groups in a single, aqueous bromohydrination step. Quantitative bromination of alkyne- and butadiyne-containing MOFs is demonstrated to be stereoselective, as a consequence of the linker geometry when bound in the MOFs, while the inherent change in hybridisation and geometry of integral linker atoms is facilitated by the high mechanical stabilities of the MOFs, allowing bromination to be characterised in a single-crystal to single-crystal (SCSC) manner. The facile addition of bromine across the unsaturated C-C bonds in the MOFs in solution is extended to irreversible iodine sequestration in the vapour phase. A large-pore interpenetrated Zr MOF demonstrates an I2 storage capacity of 279 % w/w, through a combination of chemisorption and physisorption, which is comparable to the highest reported capacities of benchmark iodine storage materials for radioactive I2 sequestration. We expect this facile PSM process to not only allow trapping of toxic vapours, but also modulate the mechanical properties of the MOFs. PMID:26916707

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

    SciTech Connect

    Xia, Y.; Mirzai, B.; Chackalamannil, S.

    1995-12-31

    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.

  14. Mechanistic Examination of Cβ–Cγ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations

    SciTech Connect

    Song, Tao; Ma, Ching-Yung; Chu, Ivan K.; Siu, Chi-Kit; Laskin, Julia

    2013-02-14

    In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The Cβ–Cγ bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against Cβ–Cγ bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The Cβ–Cγ bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote Cβ–Cγ bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

  15. O-Glycosidic bond exocyclic cleavage of difructose led by acidic proton migration: Density functional theory calculation study

    NASA Astrophysics Data System (ADS)

    Chen, Po-Tuan; Chan, Tzu-Hsin; Wang, Juen-Kai; Wang, Yuh-Lin; Hayashi, Michitoshi

    2012-10-01

    We investigate proton migrations from (H2O)n (n = 1-3) to difructose, α-D-fructofuranose-β-D-fructofuranose-2,3', using density functional theory. The proton migrations result in O-glycosidic bond cleavage. The highest transition barrier for proton migrations taking place from (H2O)3 to difructose is 11.67 kcal mol-1. The barriers are much lower than those for the direct breaking of a covalent bond in a difructose linkage. In addition, an autocatalysis process is also studied. An excess proton can migrate from a fructose molecule to a difructose molecule, leading to O-glycosidic bond cleavage. The transition barrier energy for this proton migration is 5.35 kcal mol-1.

  16. Rhodium-catalyzed silylation and intramolecular arylation of nitriles via the silicon-assisted cleavage of carbon-cyano bonds.

    PubMed

    Tobisu, Mamoru; Kita, Yusuke; Ano, Yusuke; Chatani, Naoto

    2008-11-26

    A rhodium-catalyzed silylation reaction of carbon-cyano bonds using disilane has been developed. Under these catalytic conditions, carbon-cyano bonds in aryl, alkenyl, allyl, and benzyl cyanides bearing a variety of functional groups can be silylated. The observation of an enamine side product in the silylation of benzyl cyanides and related stoichiometric studies indicate that the carbon-cyano bond cleavage proceeds through the deinsertion of silyl isocyanide from eta(2)-iminoacyl complex B. Knowledge gained from these studies has led to the development of a new intramolecular biaryl coupling reaction in which aryl cyanides and aryl chlorides are cross-coupled. PMID:18975946

  17. Far-UV photochemical bond cleavage of n-amyl nitrite: bypassing a repulsive surface.

    PubMed

    Minitti, Michael P; Zhang, Yao; Rosenberg, Martin; Brogaard, Rasmus Y; Deb, Sanghamitra; Sølling, Theis I; Weber, Peter M

    2012-01-19

    We have investigated the deep-UV photoinduced, homolytic bond cleavage of amyl nitrite to form NO and pentoxy radicals. One-color multiphoton ionization with ultrashort laser pulses through the S(2) state resonance gives rise to photoelectron spectra that reflect ionization from the S(1) state. Time-resolved pump-probe photoionization measurements show that upon excitation at 207 nm, the generation of NO in the v = 2 state is delayed, with a rise time of 283 (16) fs. The time-resolved mass spectrum shows the NO to be expelled with a kinetic energy of 1.0 eV, which is consistent with dissociation on the S(1) state potential energy surface. Combined, these observations show that the first step of the dissociation reaction involves an internal conversion from the S(2) to the S(1) state, which is followed by the ejection of the NO radical on the predissociative S(1) state potential energy surface. PMID:22175717

  18. Bond cleavage reactions in the tripeptide trialanine upon free electron capture

    NASA Astrophysics Data System (ADS)

    Puschnigg, Benjamin; Huber, Stefan E.; Scheier, Paul; Probst, Michael; Denifl, Stephan

    2014-05-01

    In the present study we performed dissociative electron attachment (DEA) measurements with the tripeptide trialanine, C9H17N3O4, utilizing a crossed electron-molecular beam experiment with high electron energy resolution (~100 meV). Anion efficiency yields as a function of the incident electron energy are obtained for the most abundant anions up to electron energies of ~4 eV. Quantum chemical calculations are performed to determine the thermochemical thresholds for the anions observed in the measurements. There is no evidence of a molecular anion with lifetime of mass spectrometric timescales. The dehydrogenated closed shell anion (M-H)- is one of the fragment anions observed for which the calculations show that H-loss is energetically possible from carboxyl, as well as amide groups. In contrast to the dipeptide dialanine and monomer alanine the cleavage of the N-Cα bond in the peptide chain is already possible by attachment of electrons at ~0 eV. Contribution to the Topical Issue "Nano-scale Insights into Ion-beam Cancer Therapy", edited by Andrey V. Solov'yov, Nigel Mason, Paulo Limão-Vieira and Malgorzata Smialek-Telega.

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

    PubMed

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

    2013-05-17

    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

  20. Identification of Possible Pathways for C-C Bond Formation during Electrochemical Reduction of CO2: New Theoretical Insights from an Improved Electrochemical Model.

    PubMed

    Goodpaster, Jason D; Bell, Alexis T; Head-Gordon, Martin

    2016-04-21

    We have carried out a periodic Kohn-Sham density functional theory investigation of the pathways by which carbon-carbon bonds could be formed during the electrochemical reduction of CO2 on Cu(100) using a model that includes the effects of the electrochemical potential, solvent, and electrolyte. The electrochemical potential was set by relating the applied potential to the Fermi energy and then calculating the number of electrons required by the simulation cell for that specific Fermi energy. The solvent was included as a continuum dielectric, and the electrolyte was described using a linearized Poisson-Boltzmann model. The calculated potential of zero charge for a variety of surfaces agrees with experiment to within a mean average error of 0.09 V, thereby validating the assumptions of the model. Analysis of the mechanism for C-C bond formation revealed that at low-applied potential, C-C bond formation occurs through a CO dimer. However, at high applied potentials, a large activation barrier blocks this pathway; therefore, C-C bond formation occurs through reaction of adsorbed CHO and CO. Rate parameters determined from our calculations were used to simulate the kinetics of ethene formation during the electrochemical reduction of CO over a Cu(100) surface. An excellent match was observed between previously reported measurements of the partial current for ethene formation as a function of applied voltage and the variation in the partial current for C-C bond formation predicted by our microkinetic model. The electrochemical model reported here is simple, fairly easy to implement, and involves only a small increase in computational cost over calculations neglecting the effects of the electrolyte and the applied field. Therefore, it can be used to study the effects of applied potential and electrolyte composition on the energetics of surface reactions for a wide variety of electrochemical reactions. PMID:27045040

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

    PubMed

    Cornella, Josep; Zarate, Cayetana; Martin, Ruben

    2014-12-01

    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

  2. Cobalt(III)-Catalyzed Redox-Neutral Synthesis of Unprotected Indoles Featuring an N-N Bond Cleavage.

    PubMed

    Lerchen, Andreas; Vásquez-Céspedes, Suhelen; Glorius, Frank

    2016-02-01

    A redox-neutral cobalt(III)-catalyzed synthetic approach for the direct synthesis of unprotected indoles showcasing an N-N bond cleavage is reported. The herein newly introduced Boc-protected hydrazines establish a beneficial addition to the limited portfolio of oxidizing directing groups for cobalt(III) catalysis. Moreover, the developed catalytic methodology tolerates a good variety of functional groups. PMID:26836438

  3. Estimation of peptide N-Cα bond cleavage efficiency during MALDI-ISD using a cyclic peptide.

    PubMed

    Asakawa, Daiki; Smargiasso, Nicolas; De Pauw, Edwin

    2016-05-01

    Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) induces N-Cα bond cleavage via hydrogen transfer from the matrix to the peptide backbone, which produces a c'/z• fragment pair. Subsequently, the z• generates z' and [z + matrix] fragments via further radical reactions because of the low stability of the z•. In the present study, we investigated MALDI-ISD of a cyclic peptide. The N-Cα bond cleavage in the cyclic peptide by MALDI-ISD produced the hydrogen-abundant peptide radical [M + 2H](+) • with a radical site on the α-carbon atom, which then reacted with the matrix to give [M + 3H](+) and [M + H + matrix](+) . For 1,5-diaminonaphthalene (1,5-DAN) adducts with z fragments, post-source decay of [M + H + 1,5-DAN](+) generated from the cyclic peptide showed predominant loss of an amino acid with 1,5-DAN. Additionally, MALDI-ISD with Fourier transform-ion cyclotron resonance mass spectrometry allowed for the detection of both [M + 3H](+) and [M + H](+) with two (13) C atoms. These results strongly suggested that [M + 3H](+) and [M + H + 1,5-DAN](+) were formed by N-Cα bond cleavage with further radical reactions. As a consequence, the cleavage efficiency of the N-Cα bond during MALDI-ISD could be estimated by the ratio of the intensity of [M + H](+) and [M + 3H](+) in the Fourier transform-ion cyclotron resonance spectrum. Because the reduction efficiency of a matrix for the cyclic peptide cyclo(Arg-Gly-Asp-D-Phe-Val) was correlated to its tendency to cleave the N-Cα bond in linear peptides, the present method could allow the evaluation of the efficiency of N-Cα bond cleavage for MALDI matrix development. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27194516

  4. Relationship between C=C Bonds and Mechanical Properties of Carbon Rich Low-k Films deposited by Plasma Enhanced Chemical Vapor Deposition

    NASA Astrophysics Data System (ADS)

    Shim, Cheonman; Jung, Donggeun

    2004-03-01

    We have studied the relationship between C=C bonds and the mechanical properties of different low-k films deposited by plasma enhanced chemical vapor deposition (PECVD) using a p-xylene and/or hexamethyldisilane (HMDS) precursor. The three types of films were called plasma polymerized p-xylene (PPpX) using p-xylene only, plasma polymerized p-xylene:hexamethyldisilane (PPpX:HMDS) using a mixture of p-xylene and HMDS, and plasma polymerized hexamethyldisilane (PPHMDS) using HMDS only as precursors. The mechanical strengths such as Youngs modulus and hardness decreased as a function of annealing temperature, while C=C bonds increased in number. We suggest that the mechanical properties of low-k films containing a large amount of C and small amounts of Si and/or O are closely related to the generation of C=C bonds in the films after annealing, and not to the decrease in the film density. This was investigated by Fourier transform Raman (FT-Raman) spectroscopy.

  5. A Cobalt(I) Pincer Complex with an η(2) -Caryl -H Agostic Bond: Facile C-H Bond Cleavage through Deprotonation, Radical Abstraction, and Oxidative Addition.

    PubMed

    Murugesan, Sathiyamoorthy; Stöger, Berthold; Pittenauer, Ernst; Allmaier, Günter; Veiros, Luis F; Kirchner, Karl

    2016-02-01

    The synthesis and reactivity of a Co(I) pincer complex [Co(ϰ(3) P,CH,P-P(CH)P(NMe) -iPr)(CO)2 ](+) featuring an η(2) - Caryl -H agostic bond is described. This complex was obtained by protonation of the Co(I) complex [Co(PCP(NMe) -iPr)(CO)2 ]. The Co(III) hydride complex [Co(PCP(NMe) -iPr)(CNtBu)2 (H)](+) was obtained upon protonation of [Co(PCP(NMe) -iPr)(CNtBu)2 ]. Three ways to cleave the agostic C-H bond are presented. First, owing to the acidity of the agostic proton, treatment with pyridine results in facile deprotonation (C-H bond cleavage) and reformation of [Co(PCP(NMe) -iPr)(CO)2 ]. Second, C-H bond cleavage is achieved upon exposure of [Co(ϰ(3) P,CH,P-P(CH)P(NMe) -iPr)(CO)2 ](+) to oxygen or TEMPO to yield the paramagnetic Co(II) PCP complex [Co(PCP(NMe) -iPr)(CO)2 ](+) . Finally, replacement of one CO ligand in [Co(ϰ(3) P,CH,P-P(CH)P(NMe) -iPr)(CO)2 ](+) by CNtBu promotes the rapid oxidative addition of the agostic η(2) -Caryl -H bond to give two isomeric hydride complexes of the type [Co(PCP(NMe) -iPr)(CNtBu)(CO)(H)](+) . PMID:26823229

  6. Unusually short chalcogen bonds involving organoselenium: insights into the Se-N bond cleavage mechanism of the antioxidant ebselen and analogues.

    PubMed

    Thomas, Sajesh P; Satheeshkumar, K; Mugesh, Govindasamy; Guru Row, T N

    2015-04-27

    Structural studies on the polymorphs of the organoselenium antioxidant ebselen and its derivative show the potential of organic selenium to form unusually short Se⋅⋅⋅O chalcogen bonds that lead to conserved supramolecular recognition units. Se⋅⋅⋅O interactions observed in these polymorphs are the shortest such chalcogen bonds known for organoselenium compounds. The FTIR spectral evolution characteristics of this interaction from solution state to solid crystalline state further validates the robustness of this class of supramolecular recognition units. The strength and electronic nature of the Se⋅⋅⋅O chalcogen bonds were explored using high-resolution X-ray charge density analysis and atons-in-molecules (AIM) theoretical analysis. A charge density study unravels the strong electrostatic nature of Se⋅⋅⋅O chalcogen bonding and soft-metal-like behavior of organoselenium. An analysis of the charge density around Se-N and Se-C covalent bonds in conjunction with the Se⋅⋅⋅O chalcogen bonding modes in ebselen and its analogues provides insights into the mechanism of drug action in this class of organoselenium antioxidants. The potential role of the intermolecular Se⋅⋅⋅O chalcogen bonding in forming the intermediate supramolecular assembly that leads to the bond cleavage mechanism has been proposed in terms of electron density topological parameters in a series of molecular complexes of ebselen with reactive oxygen species (ROS). PMID:25766307

  7. Formation of C-C Bonds via Ruthenium Catalyzed Transfer Hydrogenation: Carbonyl Addition from the Alcohol or Aldehyde Oxidation Level

    PubMed Central

    Shibahara, Fumitoshi; Krische, Michael J.

    2011-01-01

    Under the conditions of ruthenium catalyzed transfer hydrogenation employing isopropanol as terminal reductant, π-unsaturated compounds (1,3-dienes, allenes, 1,3-enynes and alkynes) reductively couple to aldehydes to furnish products of carbonyl addition. In the absence of isopropanol, π-unsaturated compounds couple directly from the alcohol oxidation level to form identical products of carbonyl addition. Such “alcohol-unsaturate C-C couplings” enable carbonyl allylation, propargylation and vinylation from the alcohol oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. Thus, direct catalytic C-H functionalization of alcohols at the carbinol carbon is achieved. PMID:21927534

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

    NASA Technical Reports Server (NTRS)

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

    2008-01-01

    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.

  9. Electron Transfer Dissociation Reveals Changes in the Cleavage Frequencies of Backbone Bonds Distant to Amide-to-Ester Substitutions in Polypeptides

    NASA Astrophysics Data System (ADS)

    Hansen, Thomas A.; Jung, Hye R.; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization.

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

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

    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.

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

    PubMed

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

    2014-09-21

    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

  12. Aromatic Cations from Oxidative Carbon–Hydrogen Bond Cleavage in Bimolecular Carbon–Carbon Bond Forming Reactions

    PubMed Central

    Clausen, Dane J.

    2012-01-01

    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

  13. Regioselective carbon-oxygen bond cleavage reactions of aromatic ethers and esters with potassium metal/18-crown-6/THF as the electron-transfer reagent

    SciTech Connect

    Fish, R.H.; Dupon, J.W.

    1988-10-28

    The facile carbon-oxygen bond cleavage reactions of a variety of aromatic ethers and esters were studied with an electron-transfer reagent that consisted of potassium metal and 18-crown-6 in tetrahydrofuran (THF). The relative rates of carbon-oxygen bond cleavage, with these aromatic ethers and esters under electron-transfer conditions, was studied in competition with the standard, diphenyl ether. The order of relative reactivities was as follows: phenyl 2-hydroxybenzoate (10) (>2.0); phenyl 2-methoxybenzoate (11) (>2.0); phenyl 4-methoxybenzoate (12) (>2.0); 2-methoxyphenyl benzoate (13) (>2.0); 4-methoxyphenyl benzoate (14) (>2.0); 4-hydroxyphenyl benzoate (15) (1.6); benzyl benzoate (9) (1.3); 4-methoxyphenyl phenyl ether (5) (1.15); phenyl benzoate (8) (1.04); diphenyl ether (1) (1.0); dibenzyl ether (2) (0.98); 2-methoxyphenyl phenyl ether (6) (0.97); benzyl phenyl ether (3) (0.96); phenethyl phenyl ether (7) (0.77); and 4-hydroxyphenyl phenyl ether (4) (<0.1). From these relative rates, it is clear that electron-donating groups increase the relative rates of C-O bond cleavage in aromatic esters. Conversely, a methoxyl group has no apparent effect on the relative rates of aromatic ether C-O bond cleavage, while a hydroxyl group dramatically decreases the rate. Proton donors, tert-butyl alcohol and hydroquinone, decreased the rate of diphenyl ether cleavage. The regioselectivity for C-O bond cleavage of esters 8-15, i.e., carbonyl-oxygen versus carboxyl-carbon cleavage, showed selective carbonyl-oxygen bond cleavage.

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

    SciTech Connect

    Bausch, M.

    1992-08-01

    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.

  15. Competitive intramolecular C-C vs. C-O bond coupling reactions toward C6 ring-fused 2-pyridone synthesis.

    PubMed

    Lepitre, T; Pintiala, C; Muru, K; Comesse, S; Rebbaa, A; Lawson, A M; Daïch, A

    2016-04-14

    An interesting competitive C-C vs. C-O bond coupling reaction on N,3,5-trisubstituted pyridones is reported. These coupling reactions provided selective access to C- or O-ring-fused pyridones, both at the challenging C6-pyridone position. 1,6-C-Annulated pyridones were generally achieved in good yields with excellent chemoselectivity under Pd(0) conditions. On the other hand, full C6-regioselective Csp(2) aryloxylation was achieved under oxidative coupling promoted by silver salts to access 5,6-O-annulated pyridones. Based on various experiments and observations, mechanistic evidence of these competitive reactions was provided and it was proposed that C-O bond formation proceeded through radical cyclization. These processes were performed under mild reaction conditions and offer an efficient and attractive methodology to selectively access a large scope of C-arylated and O-arylated pyridones of biological interest. PMID:26976735

  16. Cu-catalyzed cross-dehydrogenative coupling: A versatile strategy for C-C bond formations via the oxidative activation of sp3 C-H bonds

    NASA Astrophysics Data System (ADS)

    Li, Zhiping; Bohle, D. Scott; Li, Chao-Jun

    2006-06-01

    Cu-catalyzed cross-dehydrogenative coupling (CDC) methodologies were developed based on the oxidative activation of sp3 C-H bonds adjacent to a nitrogen atom. Various sp, sp2, and sp3 C-H bonds of pronucleophiles were used in the Cu-catalyzed CDC reactions. Based on these results, the mechanisms of the CDC reactions also are discussed. C-H activation | catalysis | Baylis-Hillman reaction | Mannich reaction | Friedel-Crafts reaction

  17. A systematic density functional theory study of the C-N bond cleavage of methylamine on metals.

    PubMed

    Li, Jun; Li, Rui-Fang; Wang, Gui-Chang

    2006-07-27

    The C-N bond cleavage for the relative large molecule of methylamine on Cu(1111), Ag(111), Au(111), Ni(111), Rh(111), Pd(111), Pt(111), and Mo(100) has been systemically studied using the DFT-GGA method; the reaction energy changes and the activation energies were obtained. The calculated results show that the activation energy of C-N bond cleavage decreases as the metal element goes up and to the left across the periodic table, which is in general agreement with the experimental observation. Moreover, it was found that the steric effect should be considered for the metals with high activity and small radius such as Ni, which is much different from the case for the small molecule decomposition in which the steric effect may be ignored. The linear relationships between the activation energies and electronic properties (d-band center) are presented. It is expected that such a rule can be used to predict the reactivity of metal for other dissociative adsorption systems. PMID:16854136

  18. Selective scission of C-O and C-C bonds in ethanol using bimetal catalysts for the preferential growth of semiconducting SWNT arrays.

    PubMed

    Zhang, Shuchen; Hu, Yue; Wu, Juanxia; Liu, Dan; Kang, Lixing; Zhao, Qiuchen; Zhang, Jin

    2015-01-28

    For the application of single-walled carbon nanotubes (SWNTs) to electronic and optoelectronic devices, techniques to obtain semiconducting SWNT (s-SWNT) arrays are still in their infancy. We have developed herein a rational approach for the preferential growth of horizontally aligned s-SWNT arrays on a ST-cut quartz surface through the selective scission of C-O and C-C bonds of ethanol using bimetal catalysts, such as Cu/Ru, Cu/Pd, and Au/Pd. For a common carbon source, ethanol, a reforming reaction occurs on Cu or Au upon C-C bond breakage and produces C(ads) and CO, while a deoxygenating reaction occurs on Ru or Pd through C-O bond breaking resulting in the production of O(ads) and C2H4. The produced C2H4 by Ru or Pd can weaken the oxidative environment through decomposition and the neutralization of O(ads). When the bimetal catalysts with an appropriate ratio were used, the produced C(ads) and C2H4 can be used as carbon source for SWNT growth, and O(ads) promotes a suitable and durable oxidative environment to inhibit the formation of metallic SWNTs (m-SWNTs). Finally, we successfully obtained horizontally aligned SWNTs on a ST-cut quartz surface with a density of 4-8 tubes/μm and an s-SWNT ratio of about 93% using an Au/Pd (1:1) catalyst. The synergistic effects in bimetallic catalysts provide a new mechanism to control the growth of s-SWNTs. PMID:25585016

  19. Chemistry of oxygenates on transition metal surfaces: Activation of C- H, C-C, and C-O bonds. Progress report, December 15, 1991

    SciTech Connect

    Not Available

    1991-12-31

    Goal is to understand the requirements for and competition between activation of C-H, C-C, and C-O bonds in the synthesis and decomposition of oxygenates on transition metal surfaces. Efforts during the past year was devoted primarily to the role of activation of {beta}-CH bonds in decarbonylation of higher oxygenates on surfaces of metals such as Rh and Pd; studies were completed of more than a dozen C{sub 1}-C{sub 3} oxygenates on Rh(111), and progress was made with reagents for which {beta}-CH scission is blocked. It is shown that alcohols and aldehydes do not react via a common pathway on on Rh(111). Ethanol and acetaldehyde are formed from CO + H{sub 2} by parallel routes on Rh catalysts which do not contain interacting supports or oxide promoters; i.e., the two compounds result from CO insertion into different metal-hydrocarbon bonds. Aldehydes decarbonylate via {alpha}-CH scission to form acyl, followed by C-C scission to release an alkyl ligand; this ligand undergoes hydrogenation and dehydrogenation steps. Alcohols form surface alkoxides, but these do not dehydrogenate further to the aldehydes, they release CO + H{sub 2} but no volatile hydrocarbon. These results indicate that {beta}-CH scissors to form a surface oxametallacycle intermediate; supporting evidence is spresented for this intermediate. Chemistry of alcohols blocked to different extends at the {beta}-position was also studied; complete blocking (CF{sub 3}CH{sub 2}OH) forces the reaction to follow the aldehyde-acyl path, while partial substitution at the {beta} position (branched alcohols) favors the oxametallacycle pathway. (DLC)

  20. The cross-dehydrogenative coupling of C(sp3)-H bonds: a versatile strategy for C-C bond formations.

    PubMed

    Girard, Simon A; Knauber, Thomas; Li, Chao-Jun

    2014-01-01

    Over the last decade, substantial research has led to the introduction of an impressive number of efficient procedures which allow the selective construction of CC bonds by directly connecting two different CH bonds under oxidative conditions. Common to these methodologies is the generation of the reactive intermediates in situ by activation of both CH bonds. This strategy was introduced by the group of Li as cross-dehydrogenative coupling (CDC) and discloses waste-minimized synthetic alternatives to classic coupling procedures which rely on the use of prefunctionalized starting materials. This Review highlights the recent progress in the field of cross-dehydrogenative C sp 3C formations and provides a comprehensive overview on existing procedures and employed methodologies. PMID:24214829

  1. Cyclopentadienyl nickel(ii) N,C-chelating benzothiazolyl NHC complexes: synthesis, characterization and application in catalytic C-C bond formation reactions.

    PubMed

    Teo, Wei Jie; Wang, Zhe; Xue, Fei; Andy Hor, T S; Zhao, Jin

    2016-04-25

    Cyclopentadienyl (Cp) Ni(ii) complexes [CpNiL][PF6] containing hybrid N,C chelating benzothiazolyl NHC ligands (L1 = 1-(2-benzothiazolyl)-3-methylimidazol-2-ylidene, ; L2 = 1-(2-benzothiazolyl)-3-allylimidazol-2-ylidene, ; L3 = 1-(2-benzothiazolyl)-3-benzylimidazol-2-ylidene, ) have been synthesized and fully characterized. The catalytic activity of in some C-C bond formation reactions has been examined. They are efficient catalysts for the homo-coupling of benzyl bromide in the presence of MeMgCl at r.t. with good functional group tolerance. Complex is active in the catalytic oxidative homo-coupling of Grignard reagents with 1,2-dichloroethane as an oxidant at r.t. PMID:27011227

  2. Salt-Free Reduction of Nonprecious Transition-Metal Compounds: Generation of Amorphous Ni Nanoparticles for Catalytic C-C Bond Formation.

    PubMed

    Yurino, Taiga; Ueda, Yohei; Shimizu, Yoshiki; Tanaka, Shinji; Nishiyama, Haruka; Tsurugi, Hayato; Sato, Kazuhiko; Mashima, Kazushi

    2015-11-23

    A salt-free procedure for the generation of a wide variety of metal(0) particles, including Fe, Co, Ni, and Cu, was achieved using 2,3,5,6-tetramethyl-1,4-bis(trimethylsilyl)-1,4-diaza-2,5-cyclohexadiene (1), which reduced the corresponding metal precursors under mild conditions. Notably, Ni particles formed in situ from the treatment of Ni(acac)2 (acac = acetylacetonate) with 1 in toluene exhibited significant catalytic activity for reductive C-C bond-forming reactions of aryl halides in the presence of excess amounts of 1. By examination of high-magnification transmission electron microscopy images and electron diffraction patterns, we concluded that amorphous Ni nanoparticles (Ni aNPs) were essential for the high catalytic activity. PMID:26419693

  3. An Electron-Poor C64 Nanographene by Palladium-Catalyzed Cascade C-C Bond Formation: One-Pot Synthesis and Single-Crystal Structure Analysis.

    PubMed

    Seifert, Sabine; Shoyama, Kazutaka; Schmidt, David; Würthner, Frank

    2016-05-23

    Herein, we report the one-pot synthesis of an electron-poor nanographene containing dicarboximide groups at the corners. We efficiently combined palladium-catalyzed Suzuki-Miyaura cross-coupling and dehydrohalogenation to synthesize an extended two-dimensional π-scaffold of defined size in a single chemical operation starting from N-(2,6-diisopropylphenyl)-4,5-dibromo-1,8-naphthalimide and a tetrasubstituted pyrene boronic acid ester as readily accessible starting materials. The reaction of these precursors under the conditions commonly used for Suzuki-Miyaura cross-coupling afforded a C64 nanographene through the formation of ten C-C bonds in a one-pot process. Single-crystal X-ray analysis unequivocally confirmed the structure of this unique extended aromatic molecule with a planar geometry. The optical and electrochemical properties of this largest ever synthesized planar electron-poor nanographene skeleton were also analyzed. PMID:27058998

  4. Mechanisms of Selective Cleavage of C-O Bonds in Di-aryl Ethers in Aqueous Phase

    SciTech Connect

    He, Jiayue; Zhao, Chen; Mei, Donghai; Lercher, Johannes A.

    2014-01-02

    A novel route for cleaving the C-O aryl ether bonds of p-substituted H-, CH3-, and OH- diphenyl ethers has been explored over Ni/SiO2 catalysts at very mild conditions. The C-O bond of diphenyl ether is cleaved by parallel hydrogenolysis and hydrolysis (hydrogenolysis combined with HO* addition) on Ni. The rates as a function of H2 pressure from 0 to 10 MPa indicate that the rate-determining step is the C-O bond cleavage on Ni. H* atoms compete with the organic reactant for adsorption leading to a maximum in the rate with increasing H2 pressure. In contrast to diphenyl ether, hydrogenolysis is the exclusive route for cleaving an ether C-O bond of di-p-tolyl ether to form p-cresol and toluene. 4,4'-dihydroxydiphenyl ether undergoes sequential surface hydrogenolysis, first to phenol and HOC6H4O* (adsorbed), which is then cleaved to phenol (C6H5O* with added H*) and H2O (O* with two added H*) in a second step. Density function theory supports the operation of this pathway. Notably, addition of H* to HOC6H4O* is less favorable than a further hydrogenolytic C-O bond cleavage. The TOFs of three aryl ethers with Ni/SiO2 in water followed the order 4,4'-dihydroxydiphenyl ether (69 h-1) > diphenyl ether (26 h-1) > di-p-tolyl ether (1.3 h-1), in line with the increasing apparent activation energies, ranging from 93 kJ∙mol-1 (4,4'-dihydroxydiphenyl ether) < diphenyl ether (98 kJ∙mol-1) to di-p-tolyl ether (105 kJ∙mol-1). D.M. thanks the support from the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.

  5. Brønsted acid mediated N-O bond cleavage for α-amination of ketones through the aromatic nitroso aldol reaction.

    PubMed

    Ramakrishna, Isai; Sahoo, Harekrishna; Baidya, Mahiuddin

    2016-02-11

    A Brønsted acid mediated N-O bond cleavage for α-amination of ketones has been developed through the nitroso aldol reaction of less-reactive aromatic nitroso compounds and silyl enol ethers having a disilane (-SiMe2TMS) backbone. This transformation is operationally simple and scalable, offering structurally diverse α-amino ketones in high yields (up to 98%) with complete regioselectivity. It represents a mechanistically unique and rare example of a metal-free N-O bond cleavage process. PMID:26810365

  6. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin.

    PubMed

    Helmich, Kate E; Pereira, Jose Henrique; Gall, Daniel L; Heins, Richard A; McAndrew, Ryan P; Bingman, Craig; Deng, Kai; Holland, Keefe C; Noguera, Daniel R; Simmons, Blake A; Sale, Kenneth L; Ralph, John; Donohue, Timothy J; Adams, Paul D; Phillips, George N

    2016-03-01

    Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin. PMID:26637355

  7. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin*

    PubMed Central

    Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; Heins, Richard A.; McAndrew, Ryan P.; Bingman, Craig; Deng, Kai; Holland, Keefe C.; Noguera, Daniel R.; Simmons, Blake A.; Sale, Kenneth L.; Ralph, John; Donohue, Timothy J.; Adams, Paul D.; Phillips, George N.

    2016-01-01

    Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin. PMID:26637355

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

    PubMed Central

    Schwartz, Phillip A.; Frey, Perry A.

    2008-01-01

    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 μM) or potassium-bound dioldehydrase (Kd = 0.8 ± 0.2 μM), 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

  9. The Mukaiyama aldol reaction of in situ generated nitrosocarbonyl compounds: selective C-N bond formation and N-O bond cleavage in one-pot for α-amination of ketones.

    PubMed

    Ramakrishna, Isai; Grandhi, Gowri Sankar; Sahoo, Harekrishna; Baidya, Mahiuddin

    2015-09-21

    A practical protocol for the α-amination of ketones (up to 99% yield) has been developed via the Mukaiyama aldol reaction of in situ generated nitrosocarbonyl compounds. The reaction with silyl enol ethers having a disilane (-SiMe2TMS) backbone proceeded not only with perfect N-selectivity but concomitant N-O bond cleavage was also accomplished. Such a cascade of C-N bond formation and N-O bond cleavage in a single step was heretofore unknown in the field of nitrosocarbonyl chemistry. A very high diastereoselectivity (dr = 19 : 1) was accomplished using (-)-menthol derived chiral nitrosocarbonyl compounds. PMID:26245149

  10. Protocols for the selective cleavage of carbon-sulfur bonds in coal. Final technical report, September 1, 1992--December 31, 1993

    SciTech Connect

    Bausch, M.

    1993-12-31

    Results of research pertaining to chemical reactions that aim to selectively cleave C-S bonds in model compounds as well as Illinois coal are summarized. 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 ``Protocols for the Selective Cleavage of Carbon-Sulfur Bonds in Coal`` investigations of reactions in which organic sulfur-containing coal model compounds are subjected to different conditions of temperature, solvent mixtures, reagents, and radiation have been completed. A series of reactions have been undertaken 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 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 endeavors aimed at initiating C-S bond cleavage reactions using oxidation/chlorination/desulfurization protocols, and various tellurium reagents.

  11. Nickel-catalyzed alkynylation of anisoles via C-O bond cleavage.

    PubMed

    Tobisu, Mamoru; Takahira, Tsuyoshi; Ohtsuki, Akimichi; Chatani, Naoto

    2015-02-01

    A new cross-coupling reaction has been developed for the introduction of an alkyne moiety to an anisole derivative through C-O bond activation using an NHC ligand. This method has been used for direct alkynylation of a broad range of anisole derivatives and provided rapid access to compounds with potential applications in biological and materials science. PMID:25584633

  12. Electron transfer dissociation reveals changes in the cleavage frequencies of backbone bonds distant to amide-to-ester substitutions in polypeptides.

    PubMed

    Hansen, Thomas A; Jung, Hye R; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization. PMID:21952783

  13. Ionic SN i-Si Nucleophilic Substitution in N-Methylaniline-Induced Si-Si Bond Cleavages of Si2 Cl6.

    PubMed

    Zhang, Jie; Xie, Ju; Lee, Myong Euy; Zhang, Lin; Zuo, Yujing; Feng, Shengyu

    2016-03-24

    N-Methylaniline-induced Si-Si bond cleavage of Si2 Cl6 has been theoretically studied. All calculations were performed by using DFT at the MPWB1K/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) levels. An ionic SN i-Si nucleophilic substitution mechanism, which is a newly found nucleophilic substitution in silicon-containing compounds, is proposed in the N-methylaniline-induced Si-Si bond cleavage in Si2 Cl6 . Unlike general SN i-Si nucleophilic substitutions that go through a pentacoordinated silicon transition state, ionic nucleophilic substitution goes through a tetracoordinated silicon transition state, in which the Si-Si bond is broken and siliconium ions are formed. Special cleavage of the Si-Si bond is presumably due to the good bonding strength between Si and N atoms, which leads to polarization of the Si-Si bond and eventually to heterolytic cleavage. Calculation results show that, in excess N-methylaniline, the final products of the reaction, including (NMePh)3-n SiHCln (n=0-2) and (NMePh)4-n SiCln (n=2-3), are the Si-Si cleavage products of Si2 Cl6 and the corresponding amination products of the former. The ionic SN i-Si nucleophilic substitution mechanism can also be employed to describe the amination of chlorosilane by N-methylaniline. The suggested mechanisms are consistent with experimental data. PMID:26916362

  14. A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex.

    PubMed

    Borowski, Tomasz; Bassan, Arianna; Siegbahn, Per E M

    2004-05-17

    Density functional calculations using the B3LYP functional have been used to study the reaction mechanism of [Fe(Tp(Ph2))BF] (Tp(Ph2) = hydrotris(3,5-diphenylpyrazol-1-yl)borate; BF = benzoylformate) with dioxygen. This mononuclear non-heme iron(II) complex was recently synthesized, and it proved to be the first biomimetic complex reproducing the dioxygenase activity of alpha-ketoglutarate-dependent enzymes. Moreover, the enthalpy and entropy of activation for this biologically interesting process were derived from kinetic experiments offering a unique possibility for direct comparison of theoretical and experimental data. The results reported here support a mechanism in which oxidative decarboxylation of the keto acid is the rate-limiting step. This oxygen activation process proceeds on the septet potential energy surface through a transition state for a concerted O-O and C-C bond cleavage. In the next step, a high-valent iron-oxo species performs electrophilic attack on the phenyl ring of the Tp(Ph2) ligand leading to an iron(III)-radical sigma-complex. Subsequent proton-coupled electron-transfer yields an iron(II)-phenol intermediate, which can bind dioxygen and reduce it to a superoxide radical. Finally, the protonated superoxide radical leaves the first coordination sphere of the iron(III)-phenolate complex and dismutates to dioxygen and hydrogen peroxide. The calculated activation barrier (enthalpy and entropy) and the overall reaction energy profile agree well with experimental data. A comparison to the enzymatic process, which is suggested to occur on the quintet surface, has been made. PMID:15132638

  15. Characterization of carbon-sulfur bond cleavage by axenic and mixed cultures of Rhodococcus rhodochrous IGTS8

    SciTech Connect

    Kayser, K.J.; Bielaga, B.A.; Jackowski, K.; Oduson, O.; Kilbane, J. II

    1992-12-31

    Growth assays reveal that Rhodococcus rhodochrous IGTS8 can utilize a wide range of organosulfur compounds as the sole source of sulfur. Compounds that are utilized include thiophenes, sulfides, disulfides, mercaptans, sulfoxides, and sulfones. None of the organosulfur compounds tested can serve as a carbon source. A convenient spectrophotometric assay (Gibbs assay) based on the chromogenic reaction of 2,6-dichloroquinone-4-chloroimide with aromatic hydroxyl groups was developed and used in conjunction with GC/MS analysis to examine the kinetics of carbon-sulfur bond cleavage by axenic and mixed cell cultures of Rhodococcus rhodochrous IGTS8. The desulfurization trait is expressed at uniform levels during the mid-exponential phase, reaches a maximum during idiophase, and then declines in stationary-phase cells. Desulfurization rates for dibenzothiophene (DBT) range from 8 to 15 {mu}M of DBT/10{sup 12} cells/hour. Mixtures of genetically marked Rhodococcus rhodochrous IGTS8 and an organisms incapable of cleaning carbon-sulfur bonds in relevant test compounds, Enterobacter cloacae, were prepared in ratios that varied over six orders of magnitude. Growth studies revealed that Enterobacter cloacae was able to gain access to sulfur liberated from organosulfur compounds by IGTS8; however, cell-to-cell contact was required. These data also indicate that the desulfurization activity of IGTS8 cells in mixed cultures may be as much as 200-fold higher than in axenic cultures.

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

    PubMed

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

    2001-01-01

    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

  17. Copper-Promoted Tandem Reaction of Azobenzenes with Allyl Bromides via N═N Bond Cleavage for the Regioselective Synthesis of Quinolines.

    PubMed

    Yi, Xiangli; Xi, Chanjuan

    2015-12-01

    A copper-promoted tandem reaction of a variety of azobenzenes and allyl bromides via N═N bond cleavage to regioselectively construct quinoline derivatives has been developed. The azobenzenes act as not only construction units but also an oxidant for quinoline formation. PMID:26580318

  18. A cascade of acid-promoted C-O bond cleavage and redox reactions: from oxa-bridged benzazepines to benzazepinones.

    PubMed

    Zhang, Yuewei; Yang, Fengzhi; Zheng, Lianyou; Dang, Qun; Bai, Xu

    2014-12-01

    A sequence of C-O bond cleavage and redox reactions in oxa-bridged azepines was realized under acid promoted conditions. This protocol provides an atom-economical and straightforward approach to access benzo[b]azepin-5(2H)-ones in high yields. The formal synthesis of tolvaptan was achieved by exploiting this new transformation. PMID:25397583

  19. Cleavage of the interchain disulfide bonds in rituximab increases its affinity for Fc?RIIIA.

    PubMed

    Suzuki, Mami; Yamanoi, Ayaka; Machino, Yusuke; Kobayashi, Eiji; Fukuchi, Kaori; Tsukimoto, Mitsutoshi; Kojima, Shuji; Kohroki, Junya; Akimoto, Kazunori; Masuho, Yasuhiko

    2013-07-01

    The Fc region of human IgG1 mediates effector function via binding to Fc? receptors and complement activation. The H and L chains of IgG1 antibodies are joined by four interchain disulfide bonds. In this study, these bonds within the therapeutic IgG1 rituximab (RTX) were cleaved either by mild reduction followed by alkylation or by mild S-sulfonation; consequently, two modified RTXs - A-RTX (alkylated) and S-RTX (S-sulfonated) - were formed, and both were almost as potent as unmodified RTX when binding CD20 antigen. Unexpectedly, each modified RTX had a higher binding affinity for Fc?RIIIA (CD16A) than did unmodified RTX. However, S-RTX and A-RTX were each less potent than RTX in an assay of antibody-dependent cellular cytotoxicity (ADCC). In this ADCC assay, each modified RTX showed decreased secretion of granzyme B, but no change in perforin secretion, from effector cells. These results provide significant information on the structures within IgG1 that are involved in binding Fc?RIIIA, and they may be useful in the development of therapeutic antagonists for Fc?RIIIA. PMID:23764395

  20. Promotion of exocyclic bond cleavages in the decomposition of 1,3-disilacyclobutane in the presence of a metal filament.

    PubMed

    Badran, I; Shi, Y J

    2015-01-29

    The primary decomposition of 1,3-disilacyclobutane (DSCB) on a tungsten filament and its secondary gas-phase reactions in a hot-wire chemical vapor deposition (CVD) reactor have been studied using laser ionization mass spectrometry. Under the collision-free conditions, DSCB decomposes on the W filament to produce H2 molecules with an activation energy of 43.6 4.1 kJmol(-1). With the help of the isotope labeling and chemical trapping methods, the mechanistic details in the secondary gas-phase reactions important in the hot-wire CVD reactor setup have been examined. The dominant pathway has been demonstrated to be the insertion of the cyclic 1,3-disilacyclobut-1-ylidene, generated by exocyclic Si-H bond rupture, into the Si-H bond in DSCB to form 1,1'-bis(1,3-disilacyclobutane) (174 amu). The successful trapping of 1,3-disilacyclobut-1-ylidene by both 1,3-butadiene and trimethylsilane provides compelling evidence for the existence of this cyclic silylene species in the hot-wire CVD reactor with DSCB. Other reactions operating in the reactor include the DSCB cycloreversion to form silene and the ring opening of DSCB via 1,2-H shift to produce silene/methylsilylene and 1-methylsilene/silylene. The introduction of an additional Si atom in the four-membered ring monosilacyclobutane molecule has caused two major changes in the reaction chemistry assumed by DSCB: (1) The endocyclic cycloreversion reactions that dominate in the decomposition of monosilacyclobutane molecules only play a much less important role in the dissociation of DSCB; and (2) the exocyclic bond cleavages are promoted in DSCB due to the ring stabilization caused by the introduction of one additional Si atom. PMID:25560235

  1. Mass Spectrometry and Theoretical Studies on N-C Bond Cleavages in the N-Sulfonylamidino Thymine Derivatives

    NASA Astrophysics Data System (ADS)

    Kobetić, Renata; Kazazić, Snježana; Kovačević, Borislav; Glasovac, Zoran; Krstulović, Luka; Bajić, Miroslav; Žinić, Biserka

    2015-05-01

    The reactivity of new biologically active thymine derivatives substituted with 2-(arylsulfonamidino)ethyl group at N1 and N3 position was investigated in the gas phase using CID experiments (ESI-MS/MS) and by density functional theory (DFT) calculations. Both derivatives show similar chemistry in the negative mode with a retro-Michael addition (Path A-) being the most abundant reaction channel, which correlate well with the fluoride induced retro-Michael addition observed in solution. The difference in the fragmentation of N-3 substituted thymine 5 and N-1 substituted thymine 1 in the positive mode relates to the preferred cleavage of the sulfonyl group ( m/z 155, Path B) in N-3 isomer and the formation of the acryl sulfonamidine 3 ( m/z 309) via Path A in N-1 isomer. Mechanistic studies of the cleavage reaction conducted by DFT calculations give the trend of the calculated activation energies that agree well with the experimental observations. A mechanism of the retro-Michael reaction was interpreted as a McLafferty type of fragmentation, which includes Hβ proton shift to one of the neighboring oxygen atoms in a 1,5-fashion inducing N1(N3)-Cα bond scission. This mechanism was found to be kinetically favorable over other tested mechanisms. Significant difference in the observed fragmentation pattern of N-1 and N-3 isomers proves the ESI-MS/MS technique as an excellent method for tracking the fate of similar sulfonamidine drugs. Also, the observed N-1 and/or N-3 thymine alkylation with in situ formed reactive acryl sulfonamidine 3 as a Michael acceptor may open interesting possibilities for the preparation of other N-3 substituted pyrimidines.

  2. Mass spectrometry and theoretical studies on N-C bond cleavages in the N-sulfonylamidino thymine derivatives.

    PubMed

    Kobeti?, Renata; Kazazi?, Snjeana; Kova?evi?, Borislav; Glasovac, Zoran; Krstulovi?, Luka; Baji?, Miroslav; ini?, Biserka

    2015-05-01

    The reactivity of new biologically active thymine derivatives substituted with 2-(arylsulfonamidino)ethyl group at N1 and N3 position was investigated in the gas phase using CID experiments (ESI-MS/MS) and by density functional theory (DFT) calculations. Both derivatives show similar chemistry in the negative mode with a retro-Michael addition (Path A(-)) being the most abundant reaction channel, which correlate well with the fluoride induced retro-Michael addition observed in solution. The difference in the fragmentation of N-3 substituted thymine 5 and N-1 substituted thymine 1 in the positive mode relates to the preferred cleavage of the sulfonyl group (m/z 155, Path B) in N-3 isomer and the formation of the acryl sulfonamidine 3 (m/z 309) via Path A in N-1 isomer. Mechanistic studies of the cleavage reaction conducted by DFT calculations give the trend of the calculated activation energies that agree well with the experimental observations. A mechanism of the retro-Michael reaction was interpreted as a McLafferty type of fragmentation, which includes H? proton shift to one of the neighboring oxygen atoms in a 1,5-fashion inducing N1(N3)-C? bond scission. This mechanism was found to be kinetically favorable over other tested mechanisms. Significant difference in the observed fragmentation pattern of N-1 and N-3 isomers proves the ESI-MS/MS technique as an excellent method for tracking the fate of similar sulfonamidine drugs. Also, the observed N-1 and/or N-3 thymine alkylation with in situ formed reactive acryl sulfonamidine 3 as a Michael acceptor may open interesting possibilities for the preparation of other N-3 substituted pyrimidines. PMID:25762153

  3. Hydrazine N-N Bond Cleavage over Silica-Supported Tantalum-Hydrides.

    PubMed

    Jia, Hong-Peng; Gouré, Eric; Solans-Monfort, Xavier; Llop Castelbou, Jessica; Chow, Catherine; Taoufik, Mostafa; Eisenstein, Odile; Quadrelli, Elsje Alessandra

    2015-12-21

    Hydrazine reacts with silica-supported tantalum-hydrides [(≡SiO)2TaHx] (x = 1, 3), 1, under mild conditions (100 °C). The IR in situ monitoring of the reaction with N2H4 or (15)N2H4, and the solid-state MAS NMR spectra of the fully (15)N labeled compounds (CP (15)N, (1)H-(15)N HETCOR, (1)H-(1)H double-quantum, and (1)H-(1)H triple-quantum spectra) were used to identify stable intermediates and products. DFT calculations were used for determining the reaction pathway and calculating the (15)N and (1)H NMR chemical shifts. Combining the experimental and computational studies led to the following results. At room temperature, only hydrazine adducts, 1-N2H4, are formed. Upon heating at 100 °C, the hydrazine adducts are converted to several species among which [(≡SiO)2Ta(═NH)(NH2)], 2, [(≡SiO)2TaH(NH2)2], 3, and [(≡SiO)2TaH2(NH-NH2)], 4, were identified. The final product 2 is also formed in the reaction of N2 with the same silica-supported tantalum-hydride complexes, and the species identified as 3 and 4 had been previously suggested by DFT studies as intermediates on the reaction pathway for N-N cleavage in N2. The present computational studies (cluster models with M06 functional complemented by selected calculations with periodic calculations) show that 2 is formed via 3 and 4, with either N2 or N2H4. This strengthens the previous proposal of the existence of 3 and 4 as intermediates in the reaction of N2 with the tantalum-hydrides. However, the reaction of N2 does not imply the formation of N2H4 or its hydrazido monoanionic or dianionic ligand as an intermediate. For this reason, this study informs both on the similarities and differences of the reaction pathways involving N2 and N2H4 with tantalum-hydrides. PMID:26650850

  4. Aromaticity Changes along the Lowest-Triplet-State Path for C?C Bond Rotation of Annulenyl-Substituted Olefins Probed by the Electron Localization Function

    NASA Astrophysics Data System (ADS)

    Villaume, Sbastien; Ottosson, Henrik

    2009-10-01

    The ?-contribution to the electron localization function (ELF?) was used to analyze changes in the aromaticity of annulenyl-substituted olefins in their lowest triplet state (T1) when the structure around the olefin C?C bond is twisted from planar to a structure (3p*) at which the planes of the two RR'C units are perpendicular. The ring closure bifurcation value and the range in the bifurcation values of the ELF? basins serve as (anti)aromaticity indicators directly linked to the electronic structure. Both Hckel's 4n + 2 ?-electron rule for aromaticity in the singlet ground state (S0) and Baird's 4n ?-electron rule for aromaticity in the lowest ??* triplet state are applied. Three olefins with S0 aromatic (T1 antiaromatic) substituents and four olefins with T1 aromatic (S0 antiaromatic) substituents were studied using the ELF? topology at the OLYP/6-311G(d,p) density functional theory level. The changes in the substituent ELF? bifurcation values upon rotation about the olefin bond in the T1 state reveal that aromatic character is recovered for the first three olefins and that it is reduced for the latter ones. These changes in aromatic character are reflected in the shapes of the T1 potential energy surfaces as a twist away from planar structures in olefins with T1 antiaromatic substituents is energetically favorable, but that in olefins with T1 aromatic substituents is unfavorable. Hence, aromaticity change is a driver for a photochemical reaction as for many ground-state reactions.

  5. Acetaldehyde partial oxidation on the Au(111) model catalyst surface: C-C bond activation and formation of methyl acetate as an oxidative coupling product

    NASA Astrophysics Data System (ADS)

    Karatok, Mustafa; Vovk, Evgeny I.; Shah, Asad A.; Turksoy, Abdurrahman; Ozensoy, Emrah

    2015-11-01

    Partial oxidation of acetaldehyde (CH3CHO) on the oxygen pre-covered Au(111) single crystal model catalyst was investigated via Temperature Programmed Desorption (TPD) and Temperature Programmed Reaction Spectroscopy (TPRS) techniques, where ozone (O3) was utilized as the oxygen delivery agent providing atomic oxygen to the reacting surface. We show that for low exposures of O3 and small surface oxygen coverages, two partial oxidation products namely, methyl acetate (CH3COOCH3) and acetic acid (CH3COOH) can be generated without the formation of significant quantities of carbon dioxide. The formation of methyl acetate as the oxidative coupling reaction product implies that oxygen pre-covered Au(111) single crystal model catalyst surface can activate C-C bonds. In addition to the generation of these products; indications of the polymerization of acetaldehyde on the gold surface were also observed as an additional reaction route competing with the partial and total oxidation pathways. The interplay between the partial oxidation, total oxidation and polymerization pathways reveals the complex catalytic chemistry associated with the interaction between the acetaldehyde and atomic oxygen on catalytic gold surfaces.

  6. Mild and Selective Catalytic Hydrogenation of the C=C Bond in α,β-Unsaturated Carbonyl Compounds Using Supported Palladium Nanoparticles.

    PubMed

    Nagendiran, Anuja; Pascanu, Vlad; Bermejo Gómez, Antonio; González Miera, Greco; Tai, Cheuk-Wai; Verho, Oscar; Martín-Matute, Belén; Bäckvall, Jan-E

    2016-05-17

    Chemoselective reduction of the C=C bond in a variety of α,β-unsaturated carbonyl compounds using supported palladium nanoparticles is reported. Three different heterogeneous catalysts were compared using 1 atm of H2 : 1) nano-Pd on a metal-organic framework (MOF: Pd(0) -MIL-101-NH2 (Cr)), 2) nano-Pd on a siliceous mesocellular foam (MCF: Pd(0) -AmP-MCF), and 3) commercially available palladium on carbon (Pd/C). Initial studies showed that the Pd@MOF and Pd@MCF nanocatalysts were superior in activity and selectivity compared to commercial Pd/C. Both Pd(0) -MIL-101-NH2 (Cr) and Pd(0) -AmP-MCF were capable of delivering the desired products in very short reaction times (10-90 min) with low loadings of Pd (0.5-1 mol %). Additionally, the two catalytic systems exhibited high recyclability and very low levels of metal leaching. PMID:27111403

  7. Efficient multicomponent strategy to pentacyclic pyrazole-fused naphtho[1,8-fg]isoquinolines through cleavage of two carbon-carbon bonds.

    PubMed

    Hao, Wen-Juan; Xu, Xiao-Ping; Bai, Hui-Wen; Wang, Shun-Yi; Ji, Shun-Jun

    2012-09-21

    Multicomponent reactions of acenaphthylene-1,2-dione with diaroylmethanes and electron-rich pyrazol-5-amines have been discovered. A series of new and polyfunctionalized pentacyclic pyrazole-fused naphtho[1,8-fg]isoquinolines were regioselectively synthesized. The reactions were easy to perform simply by mixing three common reactants in AcOH. During these reaction processes, the insertion of active methylene of diaroylmethane into the sp(2)-sp(2) C-C bond of the cyclohexa-2,5-dienone ring was readily achieved and two C-C bonds were cleaved under transition-metal-free conditions. PMID:22967112

  8. Intramolecular Interaction, Photoisomerization, and Mechanical C-C Bond Dissociation of 1,2-Di(9-anthryl)benzene and Its Photoisomer: A Fundamental Moiety of Anthracene-Based π-Cluster Molecules.

    PubMed

    Nishiuchi, Tomohiko; Uno, Shin-Ya; Hirao, Yasukazu; Kubo, Takashi

    2016-03-01

    We report variable and unique properties of 1,2-di(9-anthryl)benzene 1 as a fundamental moiety of anthracene-based π-cluster molecules. Due to a through-space π-conjugation between anthracene units, excimer emission at room temperature and charge delocalized state in radical cation state of 1 could be observed. Photoirradiation to 1 afforded an intramolecular [4 + 4] cyclized anthracene dimer 1' having a high strain energy with long C-C bond that exceeded 1.68 Å, resulting in C-C bond dissociation by simple mechanical grinding. PMID:26828776

  9. Reductive cleavage of carbon-chlorine bonds at catalytic and non-catalytic electrodes in 1-butyl-3-methylimidazolium tetrafluoroborate.

    PubMed

    Isse, Abdirisak A; Scarpa, Ludovico; Durante, Christian; Gennaro, Armando

    2015-12-14

    Dissociative electron transfer (DET) to a series of organic chlorides at glassy carbon (GC), silver and copper electrodes has been studied in 1-butyl-3-methylimidazolium tetrafluoroborate. The overall results of this study show that the ionic liquid behaves like molecular solvents such as acetonitrile and dimethylfomamide. It is found that aromatic chlorides follow a stepwise mechanism, whereas concerted electron transfer/bond cleavage is the preferred reaction mechanism for alkyl and benzyl chlorides. Ag and Cu show catalytic effects only when the DET follows a concerted mechanism, but Ag proves to be a much better electrocatalyst than Cu. A series of substituted benzyl chlorides (Z-C6H4CH2Cl, Z = H, 3-OCH3, 3-F, 4-Cl, and 3-CF3) show interesting results providing some insight into the reaction dynamics. The process occurs by a concerted mechanism and, albeit a constant standard potential for the whole series, Ep on GC and Cu, which does not show catalytic activity, is significantly affected by the substituents. In contrast, Ag shows good catalytic activity and, as expected, Ep does not change with the substituent. This difference in behavior may be rationalized by considering ion-dipole interactions between R˙ and Cl(-) as opposed to adsorption of the fragments on the electrode surface. PMID:26549620

  10. Chlorine atom-initiated low-temperature oxidation of prenol and isoprenol: The effect of C=C double bonds on the peroxy radical chemistry in alcohol oxidation

    DOE PAGESBeta

    Welz, Oliver; Savee, John D.; Osborn, David L.; Taatjes, Craig A.

    2014-07-04

    The chlorine atom-initiated oxidation of two unsaturated primary C5 alcohols, prenol (3-methyl-2-buten-1-ol, (CH3)2CCHCH2OH) and isoprenol (3-methyl-3-buten-1-ol, CH2C(CH3)CH2CH2OH), is studied at 550 K and low pressure (8 Torr). The time- and isomer-resolved formation of products is probed with multiplexed photoionization mass spectrometry (MPIMS) using tunable vacuum ultraviolet ionizing synchrotron radiation. The peroxy radical chemistry of the unsaturated alcohols appears much less rich than that of saturated C4 and C5 alcohols. The main products observed are the corresponding unsaturated aldehydes – prenal (3-methyl-2-butenal) from prenol oxidation and isoprenal (3-methyl-3-butenal) from isoprenol oxidation. No significant products arising from QOOH chemistry are observed. Thesemore » results can be qualitatively explained by the formation of resonance stabilized allylic radicals via H-abstraction in the Cl + prenol and Cl + isoprenol initiation reactions. The loss of resonance stabilization upon O2 addition causes the energies of the intermediate wells, saddle points, and products to increase relative to the energy of the initial radicals and O2. These energetic shifts make most product channels observed in the peroxy radical chemistry of saturated alcohols inaccessible for these unsaturated alcohols. The experimental findings are underpinned by quantum-chemical calculations for stationary points on the potential energy surfaces for the reactions of the initial radicals with O2. Under our conditions, the dominant channels in prenol and isoprenol oxidation are the chain-terminating HO2-forming channels arising from radicals, in which the unpaired electron and the –OH group are on the same carbon atom, with stable prenal and isoprenal co-products, respectively. These results suggest that the presence of C=C double bonds in alcohols will reduce low-temperature reactivity during autoignition.« less

  11. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Quarterly report No. 6, January 1-March 31, 1980

    SciTech Connect

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

    1980-05-09

    Bituminous coal is assumed to consist mostly of an aggregate of condensed aromatic and aliphatic rings, connected and made insoluble (but swellable) by crosslinks containing only single bonds. The objective of this project is to determine the proportions of the various kinds of connecting links and how they can best be broken - in other words, to determine the structure of coal, with emphasis on the crosslinks and breakable single bond. This report summarizes progress during the past quarter of the following tasks: (1) cleavages and alkylations of pyridine TIPS 28-A which covers treatment with zinc chloride in THF, alkylation, fractionation with KOH/ETOH, and solubilization with KOH in toluene; (2) cleavages of pyridine-extracted coal 18-A which includes pyridine hydroiodide in pyridine, zinc chloride in THF; (3) cleavage of pyridine-extracted coal with phenol and p-toluene sulfonic acid; (4) oxidation of pyridine-extracted coal with nitric acid; and (5) cleavages of benzylamine extraction products. 5 references, 2 figures, 4 tables.

  12. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Quarterly report No. 5, October 1-December 31, 1979

    SciTech Connect

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

    1980-01-14

    Bituminous coal is assumed to consist mostly of an aggregate of condensed aromatic and aliphatic rings, connected and made insoluble (but swellable) by crosslinks containing only single bonds. The objective of this project is to determine the proportions of the various kinds of connecting links and how they can best be broken - in other words, to determine the structure of coal, with emphasis on the crosslinks and breakable single bonds. This report presents brief summaries and experimental details of the following tasks; acetylation of asphaltols and black acids; cleavages of asphatol 28-A; cleavages of benzylamine extraction products; investigations of black acids; oxidation and oxidation products of coal extracts and black acids; and gel permeation chromatography. 6 references, 1 figure, 5 tables.

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

    PubMed

    Williams, Renee T; Wang, Yinsheng

    2012-08-14

    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

  14. From polymer to monomer: cleavage and rearrangement of Si-O-Si bonds after oxidation yielded an ordered cyclic crystallized structure.

    PubMed

    Zuo, Yujing; Gou, Zhiming; Cao, Jinfeng; Yang, Zhou; Lu, Haifeng; Feng, Shengyu

    2015-07-27

    Polymerization reactions are very common in the chemical industry, however, the reaction in which monomers are obtained from polymers is rarely invesitgated. This work reveals for the first time that oxone can break the Si-O-Si bond and induce further rearrangement to yield an ordered cyclic structure. The oxidation of P1, which is obtained by reaction of 2,2'-1,2-ethanediylbis(oxy)bis(ethanethiol) (DBOET) with 1,3-divinyl-1,1,3,3-tetramethyldisiloxane (MM(Vi)), with oxone yielded cyclic crystallized sulfone-siloxane dimer (P1-ox) after unexpected cleavage and rearrangement of the Si-O-Si bond. PMID:26186500

  15. Degree of remaining C=C bonds, polymerization shrinkage and stresses of dual-cured core build-up resin composites.

    PubMed

    Stavridakis, Minos M; Kakaboura, Afrodite I; Krejci, Ivo

    2005-01-01

    This study measured the degree of remaining C=C bonds (RDB), linear polymerization shrinkage (LPS) and polymerization stresses (PS) of dual-cured resin composite build-up materials using a variety of light exposure scenarios. Four commercially available materials were used: Bis-Core, FluoroCore, Build-it! and Permalute. The RDB was measured using FTIR spectroscopy, and custom-made devices were used to measure LPS and PS values. Data were obtained using three different modes of photoactivation: NLC (No Light-Curing); ILC (Immediate Light-Curing, where 60 second light-curing was applied at the start of the observation period); and DLC (Delayed Light-Curing, where 60-second light-curing was applied 10 minutes from the start of the observation period). Statistical evaluation of the data at the end of the 13-minute observation period was performed with two-way analysis of variance (ANOVA), Tukey's Studentized Range (HSD) Test (p=0.05) and simple linear regression. Differences in the development of LPS and PS during the 13 minutes were studied using mathematical calculus. Bis-Core presented the highest RDB and Permalute the lowest when ILC was applied, while no differences were found between Build-it! and FluoroCore and NLC and DLC increased RDB for FluoroCore and Permalute compared to ILC; whereas, no differences were noted for Build-it! and Bis-Core. Using DLC, a decrease in RDB was found only for Build-it! FluoroCore and Permalute exhibited a reduction in LPS and PS using NLC relative to ILC. No differences in LPS and PS values were detected for the materials Bis-Core and Build-it! when subjected to NLC or DLC, compared to ILC. Simple linear regression showed that only the two polymerization shrinkage properties studied were highly correlated (LPS-PS r2=0.85). The RDB rate was not correlated with either polymerization shrinkage properties (RDB-LPS r2=0.40; RDB-PS r2=0.57). A study of the evolution of the real-time curves of percentage values of LPS and PS showed that these properties evolved in a similar exponential mode and that, most often, there was a delay in the development of PS. PMID:16130864

  16. Chlorine atom-initiated low-temperature oxidation of prenol and isoprenol: The effect of C=C double bonds on the peroxy radical chemistry in alcohol oxidation

    SciTech Connect

    Welz, Oliver; Savee, John D.; Osborn, David L.; Taatjes, Craig A.

    2014-07-04

    The chlorine atom-initiated oxidation of two unsaturated primary C5 alcohols, prenol (3-methyl-2-buten-1-ol, (CH3)2CCHCH2OH) and isoprenol (3-methyl-3-buten-1-ol, CH2C(CH3)CH2CH2OH), is studied at 550 K and low pressure (8 Torr). The time- and isomer-resolved formation of products is probed with multiplexed photoionization mass spectrometry (MPIMS) using tunable vacuum ultraviolet ionizing synchrotron radiation. The peroxy radical chemistry of the unsaturated alcohols appears much less rich than that of saturated C4 and C5 alcohols. The main products observed are the corresponding unsaturated aldehydes – prenal (3-methyl-2-butenal) from prenol oxidation and isoprenal (3-methyl-3-butenal) from isoprenol oxidation. No significant products arising from QOOH chemistry are observed. These results can be qualitatively explained by the formation of resonance stabilized allylic radicals via H-abstraction in the Cl + prenol and Cl + isoprenol initiation reactions. The loss of resonance stabilization upon O2 addition causes the energies of the intermediate wells, saddle points, and products to increase relative to the energy of the initial radicals and O2. These energetic shifts make most product channels observed in the peroxy radical chemistry of saturated alcohols inaccessible for these unsaturated alcohols. The experimental findings are underpinned by quantum-chemical calculations for stationary points on the potential energy surfaces for the reactions of the initial radicals with O2. Under our conditions, the dominant channels in prenol and isoprenol oxidation are the chain-terminating HO2-forming channels arising from radicals, in which the unpaired electron and the –OH group are on the same carbon atom, with stable prenal and isoprenal co-products, respectively. These results suggest that the presence of C=C double bonds in alcohols will reduce low-temperature reactivity during autoignition.

  17. Unified view of oxidative C-H bond cleavage and sulfoxidation by a nonheme iron(IV)-oxo complex via Lewis acid-promoted electron transfer.

    PubMed

    Park, Jiyun; Morimoto, Yuma; Lee, Yong-Min; Nam, Wonwoo; Fukuzumi, Shunichi

    2014-04-01

    Oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by a nonheme iron(IV)-oxo complex, [(N4Py)Fe(IV)(O)](2+) (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine), were remarkably enhanced by the presence of triflic acid (HOTf) and Sc(OTf)3 in acetonitrile at 298 K. All the logarithms of the observed second-order rate constants of both the oxidative C-H bond cleavage and sulfoxidation reactions exhibit remarkably unified correlations with the driving forces of proton-coupled electron transfer (PCET) and metal ion-coupled electron transfer (MCET) in light of the Marcus theory of electron transfer when the differences in the formation constants of precursor complexes between PCET and MCET were taken into account, respectively. Thus, the mechanisms of both the oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by [(N4Py)Fe(IV)(O)](2+) in the presence of HOTf and Sc(OTf)3 have been unified as the rate-determining electron transfer, which is coupled with binding of [(N4Py)Fe(IV)(O)](2+) by proton (PCET) and Sc(OTf)3 (MCET). There was no deuterium kinetic isotope effect (KIE) on the oxidative C-H bond cleavage of toluene via the PCET pathway, whereas a large KIE value was observed with Sc(OTf)3, which exhibited no acceleration of the oxidative C-H bond cleavage of toluene. When HOTf was replaced by DOTf, an inverse KIE (0.4) was observed for PCET from both toluene and [Ru(II)(bpy)3](2+) (bpy =2,2'-bipyridine) to [(N4Py)Fe(IV)(O)](2+). The PCET and MCET reactivities of [(N4Py)Fe(IV)(O)](2+) with Brønsted acids and various metal triflates have also been unified as a single correlation with a quantitative measure of the Lewis acidity. PMID:24605985

  18. KO(t)Bu-mediated synthesis of dimethylisoindolin-1-ones and dimethyl-5-phenylisoindolin-1-ones: selective C-C coupling of an unreactive tertiary sp3 C-H bond.

    PubMed

    Bhakuni, Bhagat Singh; Yadav, Abhimanyu; Kumar, Shailesh; Patel, Saket; Sharma, Shubham; Kumar, Sangit

    2014-04-01

    A new reaction for the synthesis of dimethylisoindolinones has been presented from 2-halo-N-isopropyl-N-alkylbenzamide substrates and KO(t)Bu by the selective C-C coupling of an unreactive tertiary sp(3) C-H bond. The reaction manifested an excellent selectivity toward a tertiary sp(3) C-H bond over primary or sec C-H bond. Moreover, biaryl C-C coupling along with alkyl-aryl C-C coupling can be achieved in one pot using dihalobenzamides for the synthesis of biaryl 5-phenylisoindolin-1-ones. It seems that the reaction proceeds via a radical pathway in which the aryl radical translocates via 1,5-hydrogen atom transfer (HAT), forming a tertiary alkyl carbon-centered radical. The generated tertiary alkyl radical could attack the benzamide ring in a 5-exo/endo-trig manner followed by the release of an electron and a proton, leading to a five-membered isoindolinone ring. HAT seems to be responsible for the selective functionalization of the tertiary alkyl group over primary and secondary C-H bonds. PMID:24597670

  19. 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)

    Bhaskaran, Renjith; Sarma, Manabendra

    2014-09-01

    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 π* shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π* orbital of the base to the σ* 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.

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

    SciTech Connect

    Bhaskaran, Renjith; Sarma, Manabendra

    2014-09-14

    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 π{sup *} shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π{sup *} orbital of the base to the σ{sup *} 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.

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

    SciTech Connect

    Bausch, M.

    1992-12-31

    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.``

  2. Discovery and synthetic applications of novel silicon-carbon bond cleavage reactions based on the coordination number change of organosilicon compounds

    PubMed Central

    TAMAO, Kohei

    2008-01-01

    Some synthetically useful transformations of organosilicon compounds have been developed since the mid 1970s, based on the new concept that the silicon-carbon bonds are activated toward electrophilic cleavage via the formation of penta- and hexa-coordinate species. This review mainly consists of the following aspects: (1) a general concept for the activation of the silicon-carbon bond via penta- and hexa-coordinate species, (2) synthetic application of hexa-coordinate organopentafluorosilicates, and (3) development of the H2O2 oxidation of the silicon-carbon bond and its synthetic applications via the intramolecular hydrosilylation, silicon-tethered intramolecular radical cyclization and Diels-Alder reaction, and some silicon-containing organometallic reagents for nucleophilic hydroxymethylation and hydroxyallylation synthons. PMID:18941292

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

    SciTech Connect

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

    2013-12-01

    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, to confirm a multi-track radiation-damage process and to develop a model of that process. 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.

  4. Photosensitized oxidation of aryl benzyl sulfoxides. Evidence for nucleophilic assistance to the C-s bond cleavage of aryl benzyl sulfoxide radical cations.

    PubMed

    Del Giacco, Tiziana; Lanzalunga, Osvaldo; Lapi, Andrea; Mazzonna, Marco; Mencarelli, Paolo

    2015-02-20

    The radical cations of a series of aryl benzyl sulfoxides (4-X-C6H4CH2SOC6H4Y(+)) have been generated by photochemical oxidation of the parent sulfoxides sensitized by 3-cyano-N-methylquinolinium perchlorate (3-CN-NMQ(+)ClO4(-)). Steady-state photolysis experiments showed the prevailing formation of benzylic products deriving from the C-S fragmentation in the radical cations, together with sulfur-containing products. Formation of sulfoxide radical cations was unequivocally established by laser flash photolysis experiments showing the absorption bands of 3-CN-NMQ() (?max = 390 nm) and of the radical cations (?max = 500-620 nm). The decay rate constants of radical cations, determined by LFP experiments, decrease by increasing the electron-donating power of the arylsulfinyl Y substituent and to a smaller extent by increasing the electron-withdrawing power of the benzylic X substituent. A solvent nucleophilic assistance to the C-S bond cleavage has been suggested, supported by the comparison of substituent effects on the same process occurring in aryl tert-butyl sulfoxide radical cations. DFT calculations, performed to determine the bond dissociation free energy in the radical cations, the transition state energies associated with the unimolecular C-S bond cleavage, and the charge and spin delocalized on their structures, were also useful to endorse the nucleophilic assistance to the C-S scission. PMID:25601185

  5. Metal ion-promoted cleavage of nucleoside diphosphosugars: a model for reactions of phosphodiester bonds in carbohydrates.

    PubMed

    Dano, Meisa; Elmeranta, Marjukka; Hodgson, David R W; Jaakkola, Juho; Korhonen, Heidi; Mikkola, Satu

    2015-12-01

    Cleavage of five different nucleoside diphosphosugars has been studied in the presence of Cu(2+) and Zn(2+) complexes. The results show that metal ion catalysts promote the cleavage via intramolecular transesterification whenever a neighbouring HO group can adopt a cis-orientation with respect to the phosphate. The HO group attacks the phosphate and two monophosphate products are formed. If such a nucleophile is not available, Cu(2+) complexes are able to promote a nucleophilic attack of an external nucleophile, e.g. a water molecule or metal ion coordinated HO ligand, on phosphate. With the Zn(2+) complex, this was not observed. PMID:26547748

  6. Copper(I)-catalyzed substitution reactions of propargylic amines: importance of C(sp)-C(sp3) bond cleavage in generation of iminium intermediates.

    PubMed

    Sugiishi, Tsuyuka; Kimura, Akifumi; Nakamura, Hiroyuki

    2010-04-21

    Substitution reactions of propargylic amines proceed in the presence of copper(I) catalysts. Mechanistic studies showed that C(sp)-C(sp(3)) bond cleavage assisted by nitrogen lone-pair electrons is essential for the reaction, and the resulting iminium intermediates undergo amine exchange, aldehyde exchange, and alkyne addition reactions. Because iminium intermediates are key to aldehyde-alkyne-amine (A(3)) coupling reactions, this transformation is effective not only for reconstruction of propargylic amines but also for chiral induction of racemic compounds in the presence of chiral catalysts. PMID:20353176

  7. Homolytic cleavage of the O-Cu(ii) bond: XAFS and EPR spectroscopy evidence for one electron reduction of Cu(ii) to Cu(i).

    PubMed

    Yi, Hong; Zhang, Guanghui; Xin, Jie; Deng, Yi; Miller, Jeffrey T; Kropf, Arthur J; Bunel, Emilio E; Qi, Xiaotian; Lan, Yu; Lee, Jyh-Fu; Lei, Aiwen

    2016-05-25

    The investigation into the active copper(i) catalysts from copper(ii) precursors has become a fundamental and important task in copper catalysis. In this work, we demonstrate that the (t)BuO(-) anion serves not only as a base but also as a mediator to promote the reduction of Cu(ii) to Cu(i) in copper catalysis. XAFS and EPR spectroscopy evidence the [Cu(O(t)Bu)3](-) ate complex as the key intermediate which undergoes homolytic-cleavage of the O-Cu(ii) bond generating [Cu(O(t)Bu)2](-) ate complex. PMID:27145712

  8. Visible-Light-Induced Alkoxyl Radical Generation Enables Selective C(sp(3))-C(sp(3)) Bond Cleavage and Functionalizations.

    PubMed

    Jia, Kunfang; Zhang, Fuyuan; Huang, Hanchu; Chen, Yiyun

    2016-02-10

    The alkoxyl radical is an important reactive intermediate in mechanistic studies and organic synthesis; however, its current generation from alcohol oxidation heavily relies on transition metal activation under strong oxidative conditions. Here we report the first visible-light-induced alcohol oxidation to generate alkoxyl radicals by cyclic iodine(III) reagent catalysis under mild reaction conditions. The β-fragmentation of alkoxyl radicals enables selective C(sp(3))-C(sp(3)) bond cleavage and alkynylation/alkenylation reactions with various strained cycloalkanols, and for the first time with linear alcohols. PMID:26829105

  9. Tomato carotenoid cleavage dioxygenases 1A and 1B: Relaxed double bond specificity leads to a plenitude of dialdehydes, mono-apocarotenoids and isoprenoid volatiles

    PubMed Central

    Ilg, Andrea; Bruno, Mark; Beyer, Peter; Al-Babili, Salim

    2014-01-01

    The biosynthetic processes leading to many of the isoprenoid volatiles released by tomato fruits are still unknown, though previous reports suggested a clear correlation with the carotenoids contained within the fruit. In this study, we investigated the activity of the tomato (Solanum lycopersicum) carotenoid cleavage dioxygenase (SlCCD1B), which is highly expressed in fruits, and of its homolog SlCCD1A. Using in vitro assays performed with purified recombinant enzymes and by analyzing products formed by the two enzymes in carotene-accumulating Escherichia coli strains, we demonstrate that SlCCD1A and, to a larger extent, SlCCD1B, have a very relaxed specificity for both substrate and cleavage site, mediating the oxidative cleavage of cis- and all-trans-carotenoids as well as of different apocarotenoids at many more double bonds than previously reported. This activity gives rise to a plenitude of volatiles, mono-apocarotenoids and dialdehyde products, including cis-pseudoionone, neral, geranial, and farnesylacetone. Our results provide a direct evidence for a carotenoid origin of these compounds and point to CCD1s as the enzymes catalyzing the formation of the vast majority of tomato isoprenoid volatiles, many of which are aroma constituents. PMID:25057464

  10. Substituent-Controlled Chemoselective Cleavage of C═C or Csp(2)-C(CO) Bond in α,β-Unsaturated Carbonyl Compounds with H-Phosphonates Leading to β-Ketophosphonates.

    PubMed

    Zhou, Yao; Rao, Changqing; Mai, Shaoyu; Song, Qiuling

    2016-03-01

    An unprecedented substituent-controlled chemoselective cleavage of C═C double bond or C(sp(2))-C(CO) bond along with aerobic phosphorylation of α,β-unsaturated carbonyl compounds with H-phosphonates through a radical process has been disclosed. The current strategy provides an access to β-ketophosphonates under mild conditions with a wide substrate scope. PMID:26829969

  11. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Annual report, October 1, 1980-September 30, 1981

    SciTech Connect

    Hirschon, A.S.; Zevely, J.; Mayo, F.R.

    1981-11-12

    The objective of this project is to determine the structure of bituminous coal by determining the proportions of the various kinds of connecting bonds and how they can best be broken. Results obtained during the past quarter are presented for the following tasks: (1) extractions and fractionations of coal products which covers pyridine extraction, fractionation of TIPS fractions, EDA extraction of Illinois No. 6 coal and swelling ratios of coal samples; (2) experiments on breakable single bonds which cover reactions of ethylenediamine and model ethers, reaction of pyridine-extracted coal with Me/sub 3/SiI, Baeyer-Villiger oxidations, reaction to diphenylmethane with 15% HNO/sub 3/, cleavage of TIPS with ZnI/sub 2/, and cleavage of black acids; and (3) oxygen oxidation No. 18. Some of the highlights of these studies are: (1) some model ethers are not cleaved by EDA under extraction conditions; (2) oxidation of diaryl ketones with m-chloroperbenzoic acid and saponification of the resulting esters in promising for identifying ketones, (3) treatment of a black acid with pyridine hydroiodide reduced the acid's molecular weight and increased its solubility in pyridine, but treatment with ZnI/sub 2/ was ineffective; (4) in comparison with 0.1 M K/sub 2/S/sub 2/O/sub 8/, 0.01 M persulfate is relatively ineffective in accelerating oxidation of BnNH/sub 2/-extracted coal in water suspension. 2 figures, 3 tables.

  12. Effect of thermal denaturation, inhibition, and cleavage of disulfide bonds on the low-frequency Raman and FTIR spectra of chymotrypsin and albumin

    NASA Astrophysics Data System (ADS)

    Brandt, Nikolay N.; Chikishev, Andrey Yu; Mankova, Anna A.; Sakodynskaya, Inna K.

    2015-05-01

    The analysis of the structure-function relationship is extremely important in the study of proteins. The importance of function-related motions of large parts or subglobules of protein molecules stimulates the spectroscopic study in the low-frequency (terahertz) domain. However, only tentative assignments are available and the spectroscopic data are insufficiently discussed in terms of structural changes. This work is aimed at the analysis of regularities of changes in the low-frequency (100 to 600 cm-1) FTIR and Raman spectra of proteins related to their structural modifications. We study the spectra of two proteins with substantially different structures (albumin and chymotrypsin) and the spectra of samples in which the structures of protein molecules are modified using inhibition, thermal denaturation, and cleavage of disulfide bonds. The results indicate that the low-frequency spectral interval can be used to characterize protein conformations. Correlated variations in the intensities of several low-frequency bands are revealed in the spectra of the modified proteins. The strongest spectral changes are caused by thermal denaturation of proteins, and the effect of cleavage of disulfide bonds is generally weaker. It is demonstrated that the inhibitor binding in the active site causes spectral changes that can be compared to the changes induced by thermal denaturation.

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

    SciTech Connect

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

    1986-03-15

    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.

  14. Transformations of X (C, O, N)-CN Bonds: Cases of Selective X (C, O, N)-C Activation.

    PubMed

    Wang, Rui; Falck, John Russell

    2014-01-01

    Activation of C-C, C-N, and C-O bonds has in recent decades been recognized as a valuable strategic objective. While considerable progress has been achieved, many of the more challenging issues, e.g., regioselective activation of specific C-X (C, O, N) bonds, chemoselective cleavage of C(sp3)-X bonds, enantioselective activation and even the successful application of solid catalysts in such transformations remain elusive. The research disclosed herein summarize recent advances in C-X bond cleavages, including regioselective processes, although the carbon is activated in the form of a cyano group. PMID:24660056

  15. Transformations of X (C, O, N)-CN Bonds: Cases of Selective X (C, O, N)-C Activation**

    PubMed Central

    Wang, Rui; Falck, John Russell

    2014-01-01

    Activation of C-C, C-N, and C-O bonds has in recent decades been recognized as a valuable strategic objective. While considerable progress has been achieved, many of the more challenging issues, e.g., regioselective activation of specific C-X (C, O, N) bonds, chemoselective cleavage of C(sp3)-X bonds, enantioselective activation and even the successful application of solid catalysts in such transformations remain elusive. The research disclosed herein summarize recent advances in C-X bond cleavages, including regioselective processes, although the carbon is activated in the form of a cyano group. PMID:24660056

  16. Resonance Raman spectroscopy reveals pH-dependent active site structural changes of lactoperoxidase compound 0 and its ferryl heme O-O bond cleavage products.

    PubMed

    Mak, Piotr J; Thammawichai, Warut; Wiedenhoeft, Dennis; Kincaid, James R

    2015-01-14

    The first step in the enzymatic cycle of mammalian peroxidases, including lactoperoxidase (LPO), is binding of hydrogen peroxide to the ferric resting state to form a ferric-hydroperoxo intermediate designated as Compound 0, the residual proton temporarily associating with the distal pocket His109 residue. Upon delivery of this "stored" proton to the hydroperoxo fragment, it rapidly undergoes O-O bond cleavage, thereby thwarting efforts to trap it using rapid mixing methods. Fortunately, as shown herein, both the peroxo and the hydroperoxo (Compound 0) forms of LPO can be trapped by cryoradiolysis, with acquisition of their resonance Raman (rR) spectra now permitting structural characterization of their key Fe-O-O fragments. Studies were conducted under both acidic and alkaline conditions, revealing pH-dependent differences in relative populations of these intermediates. Furthermore, upon annealing, the low pH samples convert to two forms of a ferryl heme O-O bond-cleavage product, whose ν(Fe═O) frequencies reflect substantially different Fe═O bond strengths. In the process of conducting these studies, rR structural characterization of the dioxygen adduct of LPO, commonly called Compound III, has also been completed, demonstrating a substantial difference in the strengths of the Fe-O linkage of the Fe-O-O fragment under acidic and alkaline conditions, an effect most reasonably attributed to a corresponding weakening of the trans-axial histidyl imidazole linkage at lower pH. Collectively, these new results provide important insight into the impact of pH on the disposition of the key Fe-O-O and Fe═O fragments of intermediates that arise in the enzymatic cycles of LPO, other mammalian peroxidases, and related proteins. PMID:25506715

  17. CO2 conversion to isocyanate via multiple N-Si bond cleavage at a bulky uranium(III) complex.

    PubMed

    Camp, Clément; Chatelain, Lucile; Kefalidis, Christos E; Pécaut, Jacques; Maron, Laurent; Mazzanti, Marinella

    2015-10-28

    The reaction of the sterically saturated uranium(III) tetrasilylamido complex [K(18c6)][U(N(SiMe3)2)4] with CO2 leads to CO2 insertion into the U-N bond affording the stable U(IV) isocyanate complex [K(18c6)][U(N(SiMe3)2)3(NCO)2]n that was crystallographically characterized. DFT studies indicate that the reaction involves the [2+2] cyclo-addition of a double bond of O=CO to the U-N(SiMe3)2 bond and proceeds to the final product through multiple silyl migration steps. PMID:26346380

  18. Rhodium-catalyzed cascade oxidative annulation leading to substituted naphtho[1,8-bc]pyrans by sequential cleavage of C(sp2)-H/C(sp3)-H and C(sp2)-H/O-H bonds.

    PubMed

    Tan, Xing; Liu, Bingxian; Li, Xiangyu; Li, Bin; Xu, Shansheng; Song, Haibin; Wang, Baiquan

    2012-10-01

    The cascade oxidative annulation reactions of benzoylacetonitrile with internal alkynes proceed efficiently in the presence of a rhodium catalyst and a copper oxidant to give substituted naphtho[1,8-bc]pyrans by sequential cleavage of C(sp(2))-H/C(sp(3))-H and C(sp(2))-H/O-H bonds. These cascade reactions are highly regioselective with unsymmetrical alkynes. Experiments reveal that the first-step reaction proceeds by sequential cleavage of C(sp(2))-H/C(sp(3))-H bonds and annulation with alkynes, leading to 1-naphthols as the intermediate products. Subsequently, 1-naphthols react with alkynes by cleavage of C(sp(2))-H/O-H bonds, affording the 1:2 coupling products. Moreover, some of the naphtho[1,8-bc]pyran products exhibit intense fluorescence in the solid state. PMID:22989331

  19. The nature of solid-state N-H triplebondO/O-H triplebond N tautomeric competition in resonant systems. Intramolecular proton transfer in low-barrier hydrogen bonds formed by the triplebond O=C-C=N-NH triple bond --> <-- triplebond HO-C=C-N=N triplebond Ketohydrazone-Azoenol system. A variable-temperature X-ray crystallographic and DFT computational study.

    PubMed

    Gilli, Paola; Bertolasi, Valerio; Pretto, Loretta; Lycka, Antonín; Gilli, Gastone

    2002-11-13

    The tautomeric.O=C-C=N-NH triplebond --> <-- HO-C=C-N=N triplebond ketohydrazone-azoenol system may form strong N-H triplebond O/O-H triplebond N intramolecular resonance-assisted H-bonds (RAHBs) which are sometimes of the low-barrier H-bond type (LBHB) with dynamic exchange of the proton in the solid state. The problem of the N-H triplebond O/O-H triplebond N competition in these compounds is studied here through variable-temperature (100, 150, 200, and 295 K) crystal-structure determination of pF = 1-(4-F-phenylazo)2-naphthol and oF = 1-(2-F-phenylazo)2-naphthol, two molecules that, on the ground of previous studies (Gilli, P; Bertolasi, V.; Ferretti, V.; Gilli, G. J. Am. Chem. Soc. 2000, 122, 10405), were expected to represent an almost perfect balance of the two tautomers. According to predictions, the two molecules form remarkably strong bonds (d(N triplebond O) = 2.53-2.55 A) of double-minimum or LBHB type with dynamic N-H triplebond O/ O-H triplebond N exchange in the solid state. The enthalpy differences between the two minima, as measured by van't Hoff methods from the X-ray-determined proton populations, are very small and amount to DeltaH degrees = -0.120 and DeltaH degrees = -0.156 kcal mol(-)(1) in favor of the N-H triplebond O form for pF and oF, respectively. Successive emulation of pF by DFT methods at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d,p) level has shown that both energetic and geometric experimental aspects can be almost perfectly reproduced. Generalization of these results was sought by performing DFT calculations at the same level of theory along the complete proton-transfer (PT) pathway for five test molecules designed in such a way that the RAHB formed changes smoothly from weak N-H triplebond O to strong O-H.N through very strong N-H triplebond O/O-H triplebond N bond of LBHB type. A systematic correlation analysis of H-bond energies, H-bond and pi-conjugated fragment geometries, and H-bond Bader's AIM topological properties performed along the PT-pathways leads to the following conclusions: (a) any X-H triplebond Y H-bonded system is fully characterized by its intrinsic PT-barrier, that is, the symmetric barrier occurring when the proton affinities of X and Y are identical; (b) the intrinsic X-H triplebond Y bond associated with the symmetric barrier is the strongest possible bond in that system and will be single-minimum (single-well, no-barrier) or double-minimum (double-well, low-barrier) according to whether the intrinsic PT-barrier is lower or slightly higher than the zero-point vibrational level of the proton; (c) with reference to the intrinsic H-bond, the effect of chemical substitution can only be that of making more and more dissymmetric the PT-barrier, while the two H-bonds split in a higher-energy bond which is stronger because closer to the transition-state structure and in a lower-energy one (the stable form) which is weaker because farther from it; (d) complete dissymmetrization of the PT-barrier will increasingly weaken the more stable H-bond until the formation of an extreme dissymmetric single-minimum or dissymmetric single-well H-bond. PMID:12418911

  20. Cleavage of the Nb=O bond of oxoniobium(V) porphyrins. Synthesis and characterization of novel niobium(V) porphyrins with two distinct catechols

    SciTech Connect

    Kurihara, Masato; Kotoh, Noriyuki; Kojima, Takahiko

    1995-09-13

    A novel catecholato complex, Nb{sup v}(tpp)(cat)(Hcat), where cat and Hcat are two distinct catechol ligands (a bidentate catecholate dianion and a monodentate catecholate monoanion, respectively) and tpp is 5, 10, 15, 20-tetaphenylporphyrin dianion, has been isolated in the reaction of Nb{sup v} (tpp)(O)(AcO) with catechol, where AcO is an acetatoligand. Its molecular structure has been determined by X-ray crystallography. Crystal data: monoclinic, space group P2{sub 1}/c, Z = 4, a = 14.592(3) {Angstrom}, b = 23.46(1) {Angstrom}, c = 14.415(4) {Angstrom}, {beta} = 100.95(2){degrees}, R = 0.079. The heptacoordinate niobium atom is displaced by 1.02 {Angstrom} from the mean plane of the four nitrogen atoms. The structure of the complex in solution and the mechanism of the Nb=O cleavage were investigated by means of {sup 1}H-NMR spectroscopy. The bidentate catechol is oriented in C{sub s} symmetry with respect to the porphyrin plane, and the monodentate catechol is located perpendicularly to both the bidentate catechol and the porphyrin plane. Two intermediates with the bidentate catechol were observed after addition of 2 equiv of catechol to Nb(tmp)(O)(AcO) at -30 {degrees}C, where tmp denotes the 5,10,15,20-tetramesitylporphyrin dianion. These intermediates were determined to be Nb(tmp)(cat)(OH) and Nb(tmp)(cat)(AcO). Thus, the Nb=O bond of Nb(tmp)(O)(AcO) was easily cleaved to create the two intermediates. The authors propose a unique route to the Nb=O cleavage that involves an intramolecular electron transfer from the catechol ligand coordinated at the first stage through a ligand exchange with AcO. Both protonation and electron transfer to the Nb=O moiety play important roles in the Nb=O cleavage.

  1. Does C-C bonding proceed during exposure of adequate metal surfaces to CH{sub 4}? Reply to {open_quotes}Comment by Z. Hlavathy, Z. Paal, and P. Tetenyi{close_quotes}

    SciTech Connect

    Amaraiglio, A.; Pareja, P.; Amariglio, H.

    1997-02-01

    The comments, results, and reflections presented by Hlavathy and co-workers in their Letter aim at demonstrating that C-C bonding between CH{sub x} adspecies, formed upon exposure of Pt to CH{sub 4}, can proceed as well during the exposure itself as during further exposure to H{sub 2}. This possibility was implicitly put forward because they thought that a tight parallelism exists between the interactions of CH{sub 4} and CO with a metal surface, provided that the exposure to CH{sub 4} is carried out at a high enough temperature (450{degrees}C). In both cases these authors assumed that three kinds of carbon, C{sub {alpha}}, C{sub {beta}}, and C{sub {gamma}}, can be formed, C{sub {alpha}} being the main species responsible for the production of CH{sub 4} and of the C{sub 2}, alkanes obtained when the metal was further contacted with H{sub 2} at 100{degrees}C. As they argued that C{sub {alpha}} (also named carbidic carbon) has only metal atoms in its first coordination shell, they were implicitly led it that C-C bonding must take place during the hydrogenation step. The authors have not denied this possibility, but they have suggested that different situations can result from exposures to CH{sub 4} conducted at temperatures much lower than those used by Koerts et al.. 13 refs.

  2. Protolytic Cleavage of Hg–C Bonds Induced by 1-Methyl-1,3-dihydro-2H-benzimidazole-2-selone: Synthesis and Structural Characterization of Mercury Complexes

    PubMed Central

    2016-01-01

    Multinuclear (1H, 77Se, and 199Hg) NMR spectroscopy demonstrates that 1-methyl-1,3-dihydro-2H-benzimidazole-2-selone, H(sebenzimMe), a structural analogue of the selenoamino acid, selenoneine, binds rapidly and reversibly to the mercury centers of HgX2 (X = Cl, Br, I), while X-ray diffraction studies provide evidence for the existence of adducts of composition [H(sebenzimMe)]xHgX2 (X = Cl, x = 2, 3, 4; X = I, x = 2) in the solid state. H(sebenzimMe) also reacts with methylmercury halides, but the reaction is accompanied by elimination of methane resulting from protolytic cleavage of the Hg–C bond, an observation that is of relevance to the report that selenoneine demethylates CysHgMe, thereby providing a mechanism for mercury detoxification. Interestingly, the structures of [H(sebenzimMe)]xHgX2 exhibit a variety of different hydrogen bonding patterns resulting from the ability of the N–H groups to form hydrogen bonds with chlorine, iodine, and selenium. PMID:25822075

  3. Catalysis and co-catalysis of bond cleavages in coal and coal analogs. Final report, August 1, 1990--January 31, 1994

    SciTech Connect

    Miller, B.

    1994-05-01

    In work prior to the inception of this project, the authors observed that mixtures of phenolic materials and polyalkoxyaromatic molecules were appreciably more effective in catalyzing the decompositions of di-2-naphthyl ether and of di-1-naphthyl sulfide in tetralin solutions at 450{degrees}C than were the phenols by themselves, even though the polyalkoxyaromatic molecules, in the absence of phenolic co- catalysts, show essentially no catalytic activity. This was of appreciable interest in coal research because dinapthyl ether and dinapthyl sulfide have been employed as model compounds for coals in studies aimed at cleaving ether and sulfide bonds similar to those in coals. The authors proposed (R. K. Sharma, K. P. Raman, and B. Miller) that the mixed catalysts used in these studies catalyze cleavages of ether and sulfide bonds by means of a mechanism involving electron transfer from the polyalkoxyaromatics to the substrates, which are activated as electron acceptors by hydrogen bonding to phenols. Since phenols themselves are electron donors, they also proposed that the well known effects of phenols in catalyzing the conversion of coals are due to similar electron transfer mechanisms.

  4. Peroxide-mediated selective cleavage of [60]fullerene skeleton bonds: towards the synthesis of open-cage fulleroid C55O5.

    PubMed

    Gan, Liangbing

    2015-02-01

    Replacement of a pentagon in [60]fullerene with five oxygen atoms yields the open-cage compound C55O5 with five carbonyl groups on the rim of the orifice. Our attempts to synthesize such a target molecule starting from C60 have led us to prepare the fullerene-mixed peroxides such as C60(OO-t-Bu)6 with all the peroxo addends surrounding the same pentagon. Further investigations of the peroxide chemistry have generated various open-cage fullerene derivatives, including the carbon monoxide encapsulated endohedral compound CO@C59O6. This Personal Account mainly discusses peroxide-based processes resulting in selective cleavage of the fullerene skeleton bonds. PMID:25345399

  5. Mechanistic aspects of dinitrogen cleavage and hydrogenation to produce ammonia in catalysis and organometallic chemistry: relevance of metal hydride bonds and dihydrogen.

    PubMed

    Jia, Hong-Peng; Quadrelli, Elsje Alessandra

    2014-01-21

    Dinitrogen cleavage and hydrogenation by transition-metal centers to produce ammonia is central in industry and in Nature. After an introductory section on the thermodynamic and kinetic challenges linked to N2 splitting, this tutorial review discusses three major classes of transition-metal systems (homogeneous, heterogeneous and biological) capable of achieving dissociation and hydrogenation of dinitrogen. Molecular complexes, solid-state Haber-Bosch catalytic systems, silica-supported tantalum hydrides and nitrogenase will be discussed. Emphasis is focused on the reaction mechanisms operating in the process of dissociation and hydrogenation of dinitrogen, and in particular on the key role played by metal hydride bonds and by dihydrogen in such reactions. PMID:24108246

  6. Methanol conversion to hydrocarbons over zeolite H-ZSM-5: Investigation of the role of CO and ketene in the formation of the initial C-C bond

    SciTech Connect

    Hutchings, G.J.; Johnston, P. ); Hunter, R. ); Van Rensburg, L.J. )

    1993-08-01

    Mechanistic studies concerning the formation of the initial carbon-carbon bond in the methanol conversion reaction over zeolite H-ZSM-5 are described and discussed. In particular, the possible roles of CO as a reaction intermediate or as a catalyst, via the formation of ketene, are evaluated. Experiments using [sup 13]CH[sub 3]OH/[sup 12]CO reactant mixtures demonstrate that no CO is incorporated into ethene, the primary product of this reaction. In addition, CO is found to have no significant effect on the induction period for this reaction. Model experiments for the methylation of ketene by reaction with Me[sub 2]SO[sub 4] and Me[sub 3]O[sup +]SbCl[sub 6][sup [minus

  7. Mechanistic Investigation of Phosphate Ester Bond Cleavages of Glycylphosphoserinyltryptophan Radical Cations under Low-Energy Collision-Induced Dissociation

    NASA Astrophysics Data System (ADS)

    Quan, Quan; Hao, Qiang; Song, Tao; Siu, Chi-Kit; Chu, Ivan K.

    2013-04-01

    Under the conditions of low-energy collision-induced dissociation (CID), the canonical glycylphosphoserinyltryptophan radical cation having its radical located on the side chain of the tryptophan residue ([G p SW]•+) fragments differently from its tautomer with the radical initially generated on the α-carbon atom of the glycine residue ([G• p SW]+). The dissociation of [G• p SW]+ is dominated by the neutral loss of H3PO4 (98 Da), with backbone cleavage forming the [b2 - H]•+/y1 + pair as the minor products. In contrast, for [G p SW]•+, competitive cleavages along the peptide backbone, such as the formation of [G p SW - CO2]•+ and the [c2 + 2H]+/[z1 - H]•+ pair, significantly suppress the loss of neutral H3PO4. In this study, we used density functional theory (DFT) to examine the mechanisms for the tautomerizations of [G• p SW]+ and [G p SW]•+ and their dissociation pathways. Our results suggest that the dissociation reactions of these two peptide radical cations are more efficient than their tautomerizations, as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. We also propose that the loss of H3PO4 from both of these two radical cationic tautomers is preferentially charge-driven, similar to the analogous dissociations of even-electron protonated peptides. The distonic radical cationic character of [G• p SW]+ results in its charge being more mobile, thereby favoring charge-driven loss of H3PO4; in contrast, radical-driven pathways are more competitive during the CID of [G p SW]•+.

  8. {{text{C}}_{α }} - {text{C}} Bond Cleavage of the Peptide Backbone in MALDI In-Source Decay Using Salicylic Acid Derivative Matrices

    NASA Astrophysics Data System (ADS)

    Asakawa, Daiki; Takayama, Mitsuo

    2011-07-01

    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}}_{α }} - {{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}}_{α }} - {{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.

  9. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Quarterly report No. 12, June 1-September 30, 1981

    SciTech Connect

    Hirschon, A.S.; Zevely, J.; Mayo, F.R.

    1981-11-12

    We assume that bituminous coal consists mostly of an aggregate of condensed aromatic and aliphatic rings, connected and made insoluble (but swellable) by crosslinks containing single bonds. The objective of this project is to determine the proportions of the various kinds of connecting links and how they can best be broken - in other words, to determine the structure of bituminous coal, with emphasis on the crosslinks and breakable single bonds. The program began with an investigation of the structure of the TIPS fraction of Illinois No. 6 coal, that is, the two-thirds of the 16% extracted by pyridine that is toluene-insoluble, pyridine-soluble, mostly through changes in molecular weight during cleavage reactions in pyridine solution. The most promising of these cleavage reactions are now being applied to the 84% of coal that is insoluble in pyridine and presents the main problem in coal liquefaction, following the progress of the reactions by formation of soluble material and swelling of the insoluble portion. We found that benzylamine (BnNH/sub 2/) would extract an additional 14% (of the original weight of coal) of material from pyridine-extracted coal, and later that an ethylenediamine/dimethyl sulfoxide (EDA/DMSO) mixture would dissolve another 21% of the original coal. The BnNH/sub 2/ extract is soluble in pyridine. Our best present guess is that the BnNH/sub 2/ extract cleaves most of the ester groups in coal and that EDA/DMSO cleaves the remaining ester and most of the ether groups.

  10. Carbon-oxygen bond cleavage reactions by electron transfer. 1. Electrochemical studies on the formation and subsequent reaction pathways of cyanoanisole radical anions

    SciTech Connect

    Koppang, M.D.; Woolsey, N.F.; Bartak, D.E.

    1984-05-16

    The radical anions of three isomers of cyanoanisole have been electrochemically generated and subsequently shown to react by at least three different reaction pathways in dry N,N-dimethylformamide (DMF). The o-cyanoanisole radical anion (E/sub pc/ = -2.3 V vs. SCE) dimerizes (k/sub 2/ = 3.2 X 10/sup 2/ M/sup -1/s/sup -1/) to form an intermediate dimeric dianion. The dianion, which can be oxidized (E/sub pa = 1.1 V vs. SCE), undergoes a slow intramolecular disproportionation reaction to form o-cyanophenoxide ion, methide ion, and unreduced substrate (k/sub 3/ = 1.9 X 10/sup -2/s/sup -1/). Subsequent protonation results in the formation of methane and p-cyanophenol in an overall two-electron process. The m-cyanoanisole radical anion (E/sub pc/ = -2.3 V vs. SCE) is very stable (t/sub 1/2/ > 10/sup 3/ s) under anhydrous DMF conditions. Overall, slow carbon-carbon bond cleavage with loss of cyanide occurs competitively with ..beta.. carbon-oxygen bond cleavage to produce anisole and m-cyanophenol, respectively. The final products of the reduction of p-cyanoanisole are p-cyanophenol and methane; however, the radical anion of p-cyanoanisole (E/sub pc/ = -2.5 V vs. SCE) undergoes a relatively rapid unimolecular fragmentation reaction (k/sub 1/ = 7 s/sup -1/). The initial products of the fragmentation are p-cyanophenoxide ion and the methyl radical, which is reduced further to methide ion. Hydrogen atom abstraction reactions by the methyl radical can also occur in the bulk solution to produce methane.

  11. The Mechanism of N-O Bond Cleavage in Rhodium-Catalyzed C-H Bond Functionalization of Quinoline N-oxides with Alkynes: A Computational Study.

    PubMed

    Li, Yingzi; Liu, Song; Qi, Zisong; Qi, Xiaotian; Li, Xingwei; Lan, Yu

    2015-07-01

    Metal-catalyzed C-H activation not only offers important strategies to construct new bonds, it also allows the merge of important research areas. When quinoline N-oxide is used as an arene source in C-H activation studies, the N-O bond can act as a directing group as well as an O-atom donor. The newly reported density functional theory method, M11L, has been used to elucidate the mechanistic details of the coupling between quinoline N-O bond and alkynes, which results in C-H activation and O-atom transfer. The computational results indicated that the most favorable pathway involves an electrophilic deprotonation, an insertion of an acetylene group into a Rh-C bond, a reductive elimination to form an oxazinoquinolinium-coordinated Rh(I) intermediate, an oxidative addition to break the N-O bond, and a protonation reaction to regenerate the active catalyst. The regioselectivity of the reaction has also been studied by using prop-1-yn-1-ylbenzene as a model unsymmetrical substrate. Theoretical calculations suggested that 1-phenyl-2-quinolinylpropanone would be the major product because of better conjugation between the phenyl group and enolate moiety in the corresponding transition state of the regioselectivity-determining step. These calculated data are consistent with the experimental observations. PMID:26059235

  12. 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

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

    2012-01-01

    The potentials of mean force (PMFs) 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 Mller-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 PMFs 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 PMFs 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 PMFs, 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

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

    PubMed Central

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

    2008-01-01

    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/τ1 ∼ 500 s−1) transforms HOPDA (λmax = 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/τ2 = 54 s−1, 1/τ3 = 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/τ1 and 1/τ2, but affected neither 1/τ3 nor kcat, suggesting that 1/τ2 may reflect diffusive HPD dissociation, while 1/τ3 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 (λmax = 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

  14. Ether complexes of tungsten with two different binding modes: An O-bound ether and an {eta}{sup 2}-(C=C) vinyl ether. Evidence for C-H...O hydrogen bonding of vinylic C-H groups

    SciTech Connect

    Song, J.S.; Szalda, D.J.; Bullock, R.M.

    1996-11-13

    The reaction of PhCH(OCH{sup 3}){sup 2} with Cp(CO){sup 3}WH and HOTf gives [Cp(CO){sup 3}W(PhCH{sup 2}OCH{sup 3})]{sup +}OTf{sup -}. The structure of this benzyl methyl ether complex was determined by single crystal X-ray diffraction and was shown to have the ether bonded to tungsten through the oxygen. This compound was isolated as a kinetic product of the reaction; it decomposes in solution by releasing free PhCH{sup 2}OCH{sup 3} and forming Cp(CO){sup 3}WOTf. An analog with the BAr`{sup 4}{sup -} counterion [Ar` = 3, 5-bis(trifluoromethyl)phenyl] is more stable. The reaction of the vinyl acetal CH{sup 2}=CHCH(OEt){sup 2} with Cp(CO){sup 3}WH and HOTf produces [Cp(CO){sup 3}W({eta}{sup 2}-EtOCH=CHCH{sup 3})]{sup +} OTf{sup -}, in which the ether is bonded to tungsten through the C=C bond of the vinyl ether. The crystal structure of this compound shows that the W-C(OEt) distance (2.69(3) A) is significantly longer than the W-C(CH{sup 3}) distance (2.37(3) A). There are weak C-H...O hydrogen bonds between both vinyl CH`s and oxygens of the triflate counterions. Evidence is presented that some of these weak hydrogen bonds are maintained in CD{sup 2}Cl{sup 2} solution but not in CD{sup 3}CN. 44 refs., 4 figs., 3 tabs.

  15. Enabling and Probing Oxidative Addition and Reductive Elimination at a Group 14 Metal Center: Cleavage and Functionalization of E-H Bonds by a Bis(boryl)stannylene.

    PubMed

    Protchenko, Andrey V; Bates, Joshua I; Saleh, Liban M A; Blake, Matthew P; Schwarz, Andrew D; Kolychev, Eugene L; Thompson, Amber L; Jones, Cameron; Mountford, Philip; Aldridge, Simon

    2016-04-01

    By employing strongly σ-donating boryl ancillary ligands, the oxidative addition of H2 to a single site Sn(II) system has been achieved for the first time, generating (boryl)2SnH2. Similar chemistry can also be achieved for protic and hydridic E-H bonds (N-H/O-H, Si-H/B-H, respectively). In the case of ammonia (and water, albeit more slowly), E-H oxidative addition can be shown to be followed by reductive elimination to give an N- (or O-)borylated product. Thus, in stoichiometric fashion, redox-based bond cleavage/formation is demonstrated for a single main group metal center at room temperature. From a mechanistic viewpoint, a two-step coordination/proton transfer process for N-H activation is shown to be viable through the isolation of species of the types Sn(boryl)2·NH3 and [Sn(boryl)2(NH2)](-) and their onward conversion to the formal oxidative addition product Sn(boryl)2(H)(NH2). PMID:26981766

  16. 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

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

    2013-01-01

    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

  17. Heterolytic Cleavage of Hydrogen by an Iron Hydrogenase Model: An Fe-H - - - H-N Dihydorgen Bond Characterized by Neutron Diffraction

    SciTech Connect

    Liu, Tianbiao L.; Wang, Xiaoping; Hoffmann, Christina; DuBois, Daniel L.; Bullock, R. Morris

    2014-05-19

    Use of hydrogen as a fuel by [FeFe]-hydrogenase enzymes in nature requires heterolytic cleavage of the H-H bond into a proton (H+) and hydride (H-), a reaction that is also a critical step in homogeneous catalysts for hydrogenation of C=O and C=N bonds. An understanding of the catalytic oxidation of H2 by hydrogenases provides insights into the design of synthetic catalysts that are sought as cost-effective alternatives to the use of the precious metal platinum in fuel cells. Crystallographic studies on the [FeFe]-hydrogenase enzyme were critical to understanding of its reactivity, but the key H-H cleavage step is not readily observed experimentally in natural hydrogenases. Synthetic biomimics have provided evidence for H2 cleavage leading to hydride transfer to the metal and proton transfer to an amine. Limitations on the precise location of hydrogen atoms by x-ray diffraction can be overcome by use of neutron diffraction, though its use is severely limited by the difficulty of obtaining suitable crystals and by the scarcity of neutron sources. Here we show that an iron complex with a pendant amine in the diphosphine ligand cleaves hydrogen heterolytically under mild conditions, leading to [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4-, [PtBu2NtBu2 = 1,5-di(tert-butyl)-3,7-di(tert-butyl)-1,5-diaza-3,7-diphosphacyclooctane; ArF = 3,5-bis(trifluoromethyl)phenyl]. The Fe-H- - - H-N moiety has a strong dihydrogen bond, with a remarkably short H • • • H distance of 1.489(10) Å between the protic N-Hδ+ and hydridic Fe-Hδ-. The structural data for [CpC5F4NFeH(PtBu2NtBu2H)]+ provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes, with the pendant amine playing a key role as a proton relay. The iron complex [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4- is an electrocatalyst for oxidation of H2 (1 atm) at 22 °C, so the structural data are obtained on a complex that is a functional model for catalysis by [FeFe]-hydrogenase enzymes. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  18. Primary photodissociation pathways of epichlorohydrin and analysis of the C-C bond fission channels from an O(3P)+allyl radical intermediate

    NASA Astrophysics Data System (ADS)

    FitzPatrick, Benjamin L.; Alligood, Bridget W.; Butler, Laurie J.; Lee, Shih-Huang; Lin, Jim-Min, Jr.

    2010-09-01

    This study initially characterizes the primary photodissociation processes of epichlorohydrin, c-(H2COCH)CH2Cl. The three dominant photoproduct channels analyzed are c-(H2COCH)CH2+Cl, c-(H2COCH)+CH2Cl, and C3H4O+HCl. In the second channel, the c-(H2COCH) photofission product is a higher energy intermediate on C2H3O global potential energy surface and has a small isomerization barrier to vinoxy. The resulting highly vibrationally excited vinoxy radicals likely dissociate to give the observed signal at the mass corresponding to ketene, H2CCO. The final primary photodissociation pathway HCl+C3H4O evidences a recoil kinetic energy distribution similar to that of four-center HCl elimination in chlorinated alkenes, so is assigned to production of c-(H2COC)=CH2; the epoxide product is formed with enough vibrational energy to isomerize to acrolein and dissociate. The paper then analyzes the dynamics of the C3H5O radical produced from C-Cl bond photofission. When the epoxide radical photoproduct undergoes facile ring opening, it is the radical intermediate formed in the O(P3)+allyl bimolecular reaction when the O atom adds to an end C atom. We focus on the HCO+C2H4 and H2CO+C2H3 product channels from this radical intermediate in this report. Analysis of the velocity distribution of the momentum-matched signals from the HCO+C2H4 products at m/e=29 and 28 shows that the dissociation of the radical intermediate imparts a high relative kinetic energy, peaking near 20 kcal/mol, between the products. Similarly, the energy imparted to relative kinetic energy in the H2CO+C2H3 product channel of the O(P3)+allyl radical intermediate also peaks at high-recoil kinetic energies, near 18 kcal/mol. The strongly forward-backward peaked angular distributions and the high kinetic energy release result from tangential recoil during the dissociation of highly rotationally excited nascent radicals formed photolytically in this experiment. The data also reveal substantial branching to an HCCH+H3CO product channel. We present a detailed statistical prediction for the dissociation of the radical intermediate on the C3H5O potential energy surface calculated with coupled cluster theory, accounting for the rotational and vibrational energy imparted to the radical intermediate and the resulting competition between the H+acrolein, HCO+C2H4, and H2CO+C2H3 product channels. We compare the results of the theoretical prediction with our measured branching ratios. We also report photoionization efficiency (PIE) curves extending from 9.25 to 12.75 eV for the signal from the HCO+C2H4 and H2CO+C2H3 product channels. Using the C2H4 bandwidth-averaged absolute photoionization cross section at 11.27 eV and our measured relative photoion signals of C2H4 and HCO yields a value of 11.6+1/-3 Mb for the photoionization cross section of HCO at 11.27 eV. This determination puts the PIE curve of HCO measured here on an absolute scale, allowing us to report the absolute photoionization efficiency of HCO over the entire range of photoionization energies.

  19. C-C and C-Heteroatom Bond Dissociation Energies in CH3R′C(OH)2: Energetics for Photocatalytic Processes of Organic Diolates on TiO2 Surfaces

    SciTech Connect

    Wang, Tsang-Hsiu; Dixon, David A.; Henderson, Michael A.

    2010-08-26

    The bond energies of a range of gem-diols, CH3R′C(OH)2 (R′ = H, F, Cl, Br, CN, NO2, CF3, CH3CH2, CH3CH2CH2, CH3CH2CH2CH2, ((CH3)2)CH, (CH3)3C, ((CH3)2CH)CH2, (CH3CH2)(CH3)CH, C6H5 (CH3CH2)(CH3)CH) which serve as models for binding to a surface have been studied with density functional theory (DFT) and the molecular orbital G3(MP2) methods to provide thermodynamic data for the analysis of the photochemistry of ketones on TiO2. The ultraviolet (UV) photon-induced photodecomposition of adsorbed acetone and 3,3-dimethylbutanone on the rutile TiO2 (110) surface have been investigated with photon stimulated desorption (PSD) and temperature programmed desorption (TPD). The C-CH3 and C-C(R′) bond dissociation energies in CH3R′C(OH)2 were predicted, and our calculated bond dissociation energies are in excellent agreement with the available experimental values. We used a series of isodemic reactions to provide small corrections to the various bond dissociation energies. The calculated bond dissociation energies are in agreement with the observed photodissociation processes except for R′ = CF3, suggesting that these processes are under thermodynamic control. For R′ = CF3, reaction dynamics also play a role in determining the photodissociation mechanism. The gas phase Brönsted acidities of the gem-diols were calculated. For three molecules, R′ = Cl, Br, and NO2, loss of a proton leads to the formation of a complex of acetic acid with the anion Cl-, Br-, and NO2-. The acidities of these three species are very high with the former two having acidities comparable to CF3SO3H. The ketones (R′RC(=O)) are weak Lewis acids except where addition of OH- leads to the dissociation of the complex to form an anion bonded to acetic acid, R' = NO2, Cl, and Br. The X-C bond dissociation energies for a number of X-CO2- species were calculated and these should be useful in correlating with photochemical reactivity studies.

  20. Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase.

    PubMed

    Isaksen, Geir Villy; Hopmann, Kathrin Helen; Åqvist, Johan; Brandsdal, Bjørn Olav

    2016-04-12

    Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides and 2'-deoxyribonucleosides, yielding the purine base and (2'-deoxy)ribose 1-phosphate as products. While this enzyme has been extensively studied, several questions with respect to the catalytic mechanism have remained largely unanswered. The role of the phosphate and key amino acid residues in the catalytic reaction as well as the purine ring protonation state is elucidated using density functional theory calculations and extensive empirical valence bond (EVB) simulations. Free energy surfaces for adenosine, inosine, and guanosine are fitted to ab initio data and yield quantitative agreement with experimental data when the surfaces are used to model the corresponding enzymatic reactions. The cognate substrates 6-aminopurines (inosine and guanosine) interact with PNP through extensive hydrogen bonding, but the substrate specificity is found to be a direct result of the electrostatic preorganization energy along the reaction coordinate. Asn243 has previously been identified as a key residue providing substrate specificity. Mutation of Asn243 to Asp has dramatic effects on the substrate specificity, making 6-amino- and 6-oxopurines equally good as substrates. The principal effect of this particular mutation is the change in the electrostatic preorganization energy between the native enzyme and the Asn243Asp mutant, clearly favoring adenosine over inosine and guanosine. Thus, the EVB simulations show that this particular mutation affects the electrostatic preorganization of the active site, which in turn can explain the substrate specificity. PMID:26985580

  1. Primary photodissociation pathways of epichlorohydrin and analysis of the C-C bond fission channels from an O({sup 3}P)+allyl radical intermediate

    SciTech Connect

    FitzPatrick, Benjamin L.; Alligood, Bridget W.; Butler, Laurie J.; Lee, Shih-Huang; Lin, Jim Jr-Min

    2010-09-07

    This study initially characterizes the primary photodissociation processes of epichlorohydrin, c-(H{sub 2}COCH)CH{sub 2}Cl. The three dominant photoproduct channels analyzed are c-(H{sub 2}COCH)CH{sub 2}+Cl, c-(H{sub 2}COCH)+CH{sub 2}Cl, and C{sub 3}H{sub 4}O+HCl. In the second channel, the c-(H{sub 2}COCH) photofission product is a higher energy intermediate on C{sub 2}H{sub 3}O global potential energy surface and has a small isomerization barrier to vinoxy. The resulting highly vibrationally excited vinoxy radicals likely dissociate to give the observed signal at the mass corresponding to ketene, H{sub 2}CCO. The final primary photodissociation pathway HCl+C{sub 3}H{sub 4}O evidences a recoil kinetic energy distribution similar to that of four-center HCl elimination in chlorinated alkenes, so is assigned to production of c-(H{sub 2}COC)=CH{sub 2}; the epoxide product is formed with enough vibrational energy to isomerize to acrolein and dissociate. The paper then analyzes the dynamics of the C{sub 3}H{sub 5}O radical produced from C-Cl bond photofission. When the epoxide radical photoproduct undergoes facile ring opening, it is the radical intermediate formed in the O({sup 3}P)+allyl bimolecular reaction when the O atom adds to an end C atom. We focus on the HCO+C{sub 2}H{sub 4} and H{sub 2}CO+C{sub 2}H{sub 3} product channels from this radical intermediate in this report. Analysis of the velocity distribution of the momentum-matched signals from the HCO+C{sub 2}H{sub 4} products at m/e=29 and 28 shows that the dissociation of the radical intermediate imparts a high relative kinetic energy, peaking near 20 kcal/mol, between the products. Similarly, the energy imparted to relative kinetic energy in the H{sub 2}CO+C{sub 2}H{sub 3} product channel of the O({sup 3}P)+allyl radical intermediate also peaks at high-recoil kinetic energies, near 18 kcal/mol. The strongly forward-backward peaked angular distributions and the high kinetic energy release result from tangential recoil during the dissociation of highly rotationally excited nascent radicals formed photolytically in this experiment. The data also reveal substantial branching to an HCCH+H{sub 3}CO product channel. We present a detailed statistical prediction for the dissociation of the radical intermediate on the C{sub 3}H{sub 5}O potential energy surface calculated with coupled cluster theory, accounting for the rotational and vibrational energy imparted to the radical intermediate and the resulting competition between the H+acrolein, HCO+C{sub 2}H{sub 4}, and H{sub 2}CO+C{sub 2}H{sub 3} product channels. We compare the results of the theoretical prediction with our measured branching ratios. We also report photoionization efficiency (PIE) curves extending from 9.25 to 12.75 eV for the signal from the HCO+C{sub 2}H{sub 4} and H{sub 2}CO+C{sub 2}H{sub 3} product channels. Using the C{sub 2}H{sub 4} bandwidth-averaged absolute photoionization cross section at 11.27 eV and our measured relative photoion signals of C{sub 2}H{sub 4} and HCO yields a value of 11.6+1/-3 Mb for the photoionization cross section of HCO at 11.27 eV. This determination puts the PIE curve of HCO measured here on an absolute scale, allowing us to report the absolute photoionization efficiency of HCO over the entire range of photoionization energies.

  2. Molecular basis of 1,6-anhydro bond cleavage and phosphoryl transfer by Pseudomonas aeruginosa 1,6-anhydro-N-acetylmuramic acid kinase.

    PubMed

    Bacik, John-Paul; Whitworth, Garrett E; Stubbs, Keith A; Yadav, Anuj K; Martin, Dylan R; Bailey-Elkin, Ben A; Vocadlo, David J; Mark, Brian L

    2011-04-01

    Anhydro-N-acetylmuramic acid kinase (AnmK) catalyzes the ATP-dependent conversion of the Gram-negative peptidoglycan (PG) recycling intermediate 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) to N-acetylmuramic acid-6-phosphate (MurNAc-6-P). Here we present crystal structures of Pseudomonas aeruginosa AnmK in complex with its natural substrate, anhMurNAc, and a product of the reaction, ADP. AnmK is homodimeric, with each subunit comprised of two subdomains that are separated by a deep active site cleft, which bears similarity to the ATPase core of proteins belonging to the hexokinase-hsp70-actin superfamily of proteins. The conversion of anhMurNAc to MurNAc-6-P involves both cleavage of the 1,6-anhydro ring of anhMurNAc along with addition of a phosphoryl group to O6 of the sugar, and thus represents an unusual enzymatic mechanism involving the formal addition of H3PO4 to anhMurNAc. The structural complexes and NMR analysis of the reaction suggest that a water molecule, activated by Asp-182, attacks the anomeric carbon of anhMurNAc, aiding cleavage of the 1,6-anhydro bond and facilitating the capture of the γ phosphate of ATP by O6 via an in-line phosphoryl transfer. AnmK is active only against anhMurNAc and not the metabolically related 1,6-anhydro-N-acetylmuramyl peptides, suggesting that the cytosolic N-acetyl-anhydromuramyl-l-alanine amidase AmpD must first remove the stem peptide from these PG muropeptide catabolites before anhMurNAc can be acted upon by AnmK. Our studies provide the foundation for a mechanistic model for the dual activities of AnmK as a hydrolase and a kinase of an unusual heterocyclic monosaccharide. PMID:21288904

  3. Carbon-carbon cleavage during Birch-Hueckel-type reductions

    SciTech Connect

    Collins, C.J.; Hombach, H.P.; Maxwell, B.; Woody, M.C.; Benjamin, B.M.

    1980-01-16

    Results of reactions of Na-K alloy in the solvent system glyme-triglyme on a series of compounds, bibenzyl, 1,2-diphenylpropane, diphenylmethane, and phenyl-p-tolylmethane, to determine whether the Birch-Hueckel reduction could be used in this solvent system to cleave C-C bonds are reported. Both methyl-/sup 14/C iodide and water were studied as quenchers, and the products from all reactions were analyzed by gas chromatography. The results indicated that coal can be efficiently degraded at low-temperatures by cleavage of aliphatic as well as aromatic-aliphatic C-C bonds by the action of Na-K alloy under conditions studied in this work. (BLM)

  4. Glycosidic bond cleavage in deoxynucleotides: effects of solvent and the DNA phosphate backbone in the computational model.

    PubMed

    Lenz, Stefan A P; Kellie, Jennifer L; Wetmore, Stacey D

    2012-12-13

    Density functional theory (B3LYP) was employed to examine the hydrolysis of the canonical 2'-deoxynucleotides in varied environments (gas phase or water) using different computational models for the sugar residue (methyl or phosphate group at C5') and nucleophile (water activated through full or partial proton abstraction). Regardless of the degree of nucleophile activation, our results show that key geometrical parameters along the reaction pathway are notably altered upon direct inclusion of solvent effects in the optimization routine, which leads to significant changes in the reaction energetics and better agreement with experiment. Therefore, despite the wide use of gas-phase calculations in the literature, small model computational work, as well as large-scale enzyme models, that strive to understand nucleotide deglycosylation must adequately describe the environment. Alternatively, although inclusion of the phosphate group at C5' also affects the geometries of important stationary points, the effects cancel to yield unchanged deglycosylation barriers, and therefore smaller computational models can be used to estimate the energy associated with nucleotide deglycosylation, with the 5' phosphate group included if full (geometric) details of the reaction are desired. Hydrogen-bonding interactions with the nucleobase can significantly reduce the barrier to deglycosylation, which supports suggestions that discrete hydrogen-bonding interactions with active-site amino acid residues can play a significant role in enzyme-catalyzed nucleobase excision. Taken together with previous studies, the present work provides vital clues about the components that must be included in future studies of the deglycosylation of isolated noncanonical nucleotides, as well as the corresponding enzyme-catalyzed reactions. PMID:23167947

  5. Synthesis of seco-B-ring bryostatin analogue WN-1 via C-C bond-forming hydrogenation: critical contribution of the B-ring in determining bryostatin-like and phorbol 12-myristate 13-acetate-like properties.

    PubMed

    Andrews, Ian P; Ketcham, John M; Blumberg, Peter M; Kedei, Noemi; Lewin, Nancy E; Peach, Megan L; Krische, Michael J

    2014-09-24

    The seco-B-ring bryostatin analogue, macrodiolide WN-1, was prepared in 17 steps (longest linear sequence) and 30 total steps with three bonds formed via hydrogen-mediated C-C coupling. This synthetic route features a palladium-catalyzed alkoxycarbonylation of a C2-symmetric diol to form the C9-deoxygenated bryostatin A-ring. WN-1 binds to PKCα (Ki = 16.1 nM) and inhibits the growth of multiple leukemia cell lines. Although structural features of the WN-1 A-ring and C-ring are shared by analogues that display bryostatin-like behavior, WN-1 displays PMA-like behavior in U937 cell attachment and proliferation assays, as well as in K562 and MV-4-11 proliferation assays. Molecular modeling studies suggest the pattern of internal hydrogen bonds evident in bryostatin 1 is preserved in WN-1, and that upon docking WN-1 into the crystal structure of the C1b domain of PKCδ, the binding mode of bryostatin 1 is reproduced. The collective data emphasize the critical contribution of the B-ring to the function of the upper portion of the molecule in conferring a bryostatin-like pattern of biological activity. PMID:25207655

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

    PubMed

    Huang, Jiansheng; Smith, Forrest; Panizzi, Peter

    2014-04-15

    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

  7. Surface phosphophilicity of aluminum-containing adjuvants probed by their efficiency for catalyzing the P--O bond cleavage with chromogenic and fluorogenic substrates.

    PubMed

    Zhao, Q; Sitrin, R

    2001-08-01

    Aluminum-containing adjuvants are widely used in a variety of vaccine products, such as recombinant proteins, virus-like particles, conjugated polysaccharides, and recently DNA vaccines. Aluminum-containing adjuvants are also known to have a high affinity to inorganic phosphate and its mono- or diesters. Since phosphate groups are present in many antigens as well as the natural physiological environment, a better understanding of the interactions between phosphate and phospho-containing species could help in the design of improved vaccines. This report describes a convenient and novel continuous procedure to measure the avidity denoted by the new term "phosphophilicity" of phosphate and phosphate esters to the surface of aluminum-containing adjuvants. The assay measures the rate of hydrolysis of a fluorogenic substrate-6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP)-with a microplate reader. This method was based on the fundamental bioorganic phenomenon that when a tight binding event occurs, the effective concentration of nucleophile(s) will be significantly increased in the proximity of the P atom for a nucleophilic reaction (i.e., the cleavage of the P&bond;O bond) to take place. A very good leaving group (pK(a) of DiFMU approximately 4.7) in the phosphate monoester substrate makes the assay highly sensitive. Top reading of the nascent fluorescence makes the assay very convenient with no need to separate the particulate adjuvants from the reaction mixtures. The results from this assay are consistent with catalysis of the chromogenic phosphate mono- or diesters. PMID:11476547

  8. The Molybdenum Active Site of Formate Dehydrogenase Is Capable of Catalyzing C-H Bond Cleavage and Oxygen Atom Transfer Reactions.

    PubMed

    Hartmann, Tobias; Schrapers, Peer; Utesch, Tillmann; Nimtz, Manfred; Rippers, Yvonne; Dau, Holger; Mroginski, Maria Andrea; Haumann, Michael; Leimkühler, Silke

    2016-04-26

    Formate dehydrogenases (FDHs) are capable of performing the reversible oxidation of formate and are enzymes of great interest for fuel cell applications and for the production of reduced carbon compounds as energy sources from CO2. Metal-containing FDHs in general contain a highly conserved active site, comprising a molybdenum (or tungsten) center coordinated by two molybdopterin guanine dinucleotide molecules, a sulfido and a (seleno-)cysteine ligand, in addition to a histidine and arginine residue in the second coordination sphere. So far, the role of these amino acids in catalysis has not been studied in detail, because of the lack of suitable expression systems and the lability or oxygen sensitivity of the enzymes. Here, the roles of these active site residues is revealed using the Mo-containing FDH from Rhodobacter capsulatus. Our results show that the cysteine ligand at the Mo ion is displaced by the formate substrate during the reaction, the arginine has a direct role in substrate binding and stabilization, and the histidine elevates the pKa of the active site cysteine. We further found that in addition to reversible formate oxidation, the enzyme is further capable of reducing nitrate to nitrite. We propose a mechanistic scheme that combines both functionalities and provides important insights into the distinct mechanisms of C-H bond cleavage and oxygen atom transfer catalyzed by formate dehydrogenase. PMID:27054466

  9. Experimental and theoretical investigations of copper (I/II) complexes with triazine-pyrazole derivatives as ligands and their in situ C-N bond cleavage

    NASA Astrophysics Data System (ADS)

    Wang, Ji-Xiao; Wang, Che; Wang, Xuan; Wang, Xin-Yu; Xing, Yong-Heng; Sun, Qiao

    2015-05-01

    Two copper complexes, Cu(SCN)(Mpz∗T-(EtO)2) (1) (Mpz∗T-(EtO)2 = L3) and CuCl(H2O)(Mpz∗T-O2) (2) (Mpz∗T-O2 = L4) were synthesized by the reaction of 2,4,6-tri(3,5-dimethylpyrazol-1-yl)-1,3,5-triazine (L1) or 2,4,6-tri(1H-pyrazol-1-yl)-1,3,5-triazine (L2) with CuCl2·2H2O in anhydrous ethanol and methanol, respectively. The complexes were characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single crystal X-ray diffraction and X-ray powder diffraction. The structural characterizations and quantum mechanical calculations of the two complexes were analyzed in detail. It was found that an in site reaction occurred during the synthesis process of complexes 1 and 2, likely due to catalytic property of copper ions which leads to the C-N bond cleavage to generate new organic species, namely, Mpz∗T-(EtO)2 (L3) and Mpz∗T-O2 (L4).

  10. Substrate-Triggered Activation of a Synthetic [Fe2(μ-O)2] Diamond Core for C–H Bond Cleavage

    PubMed Central

    Xue, Genqiang; Pokutsa, Alexander; Que, Lawrence

    2011-01-01

    An [FeIV2(μ-O)2] diamond core structure has been postulated for intermediate Q of soluble methane monooxygenase (sMMO-Q), the oxidant responsible for cleaving the strong C–H bond of methane and its hydroxylation. By extension, analogous species may be involved in the mechanisms of related diiron hydroxylases and desaturases. Due to the paucity of well-defined synthetic examples, there are few, if any, mechanistic studies on the oxidation of hydrocarbon substrates by complexes with high-valent [Fe2(μ-O)2] cores. We report here that water or alcohol substrates can activate synthetic [FeIIIFeIV(μ-O)2] complexes supported by tetradentate tris(pyridyl-2-methyl)amine ligands (1 and 2) by several orders of magnitude for C–H bond oxidation. On the basis of detailed kinetic studies, it is postulated that the activation results from Lewis base attack on the [FeIIIFeIV(μ-O)2] core, resulting in the formation of a more reactive species with a [X–FeIII–O–FeIV=O] ring-opened structure (1-X, 2-X, X = OH− or OR−). Treatment of 2 with methoxide at −80 °C forms the 2-methoxide adduct in high yield, which is characterized by an S = 1/2 EPR signal indicative of an antiferromagnetically coupled [S = 5/2 FeIII/S = 2 FeIV] pair. Even at this low temperature, the complex undergoes facile intramolecular C–H bond cleavage to generate formaldehyde, showing that the terminal high-spin FeIV=O unit is capable of oxidizing a C–H bond as strong as 96 kcal mol−1. This intramolecular oxidation of the methoxide ligand can in fact be competitive with intermolecular oxidation of triphenylmethane, which has a much weaker C–H bond (DC-H 81 kcal mol−1). The activation of the [FeIIIFeIV(μ-O)2] core is dramatically illustrated by the oxidation of 9,10-dihydroanthracene by 2-methoxide, which has a second order rate constant that is 3.6 x 107-fold larger than that for the parent diamond core complex 2. These observations provide strong support for the DFT-based notion that an S = 2 FeIV=O unit is much more reactive at H-atom abstraction than its S = 1 counterpart and suggest that core isomerization could be a viable strategy for the [FeIV2(μ-O)2] diamond core of sMMO-Q to selectively attack the strong C–H bond of methane in the presence of weaker C–H bonds of amino acid residues that define the diiron active site pocket. PMID:21899336

  11. N-Cα Bond Cleavage of Zinc-Polyhistidine Complexes in Electron Transfer Dissociation Mediated by Zwitterion Formation: Experimental Evidence and Theoretical Analysis of the Utah-Washington Model.

    PubMed

    Asakawa, Daiki; Yamashita, Asuka; Kawai, Shikiho; Takeuchi, Takae; Wada, Yoshinao

    2016-02-11

    Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of gas-phase ions are widely used for peptide/protein sequencing by mass spectrometry. To understand the general mechanism of ECD/ETD of peptides, we focused on the ETD fragmentation of metal-peptide complexes in the absence of remote protons. Since Zn(2+) strongly binds to neutral histidine residues in peptides, Zn(2+)-polyhistidine complexation does not generate any remote protons. However, in the absence of remote protons, electron transfer to the Zn(2+)-polyhistidine complex induced the N-Cα bond cleavage. The formation pathway for the ETD products was investigated by density functional theory calculations. The calculations showed that the charge-reduced zinc-peptide radical, [M + Zn](•+), can exist in the low-energy zwitterionic amide π* states, which underwent homolytic N-Cα bond dissociation. The homolytic cleavage resulted in the donation of an electron from the N-Cα bond to the nitrogen atom, producing an iminoenol c' anion. The counterpart z(•) radical contained a radical site on the α-carbon atom. The iminoenol c' anion then abstracted a proton to presumably form the more stable amide c' fragment. The current experimental and computational joint study strongly suggested that the N-Cα bond cleavage occurred through the aminoketyl radical-anion formation for Zn(2+)-polyhistidine complexes in ETD. PMID:26673038

  12. 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

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

    2007-01-01

    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.

  13. Reactivity of triruthenium thiophyne and furyne clusters: competitive S-C and P-C bond cleavage reactions and the generation of highly unsymmetrical alkyne ligands.

    PubMed

    Uddin, Md Nazim; Begum, Noorjahan; Hassan, Mohammad R; Hogarth, Graeme; Kabir, Shariff E; Miah, Md Arzu; Nordlander, Ebbe; Tocher, Derek A

    2008-11-28

    The synthesis and reactivity of the thiophyne and furyne clusters [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, O) is reported. Addition of P(C4H3E)3 to [Ru3(CO)10(mu-dppm)] (1) at room temperature in the presence of Me3NO gives simple substitution products [Ru3(CO)9(mu-dppm)(P(C4H3E)3)] (E = S, 2; E = O, 3). Mild thermolysis in the presence of further Me3NO affords the thiophyne and furyne complexes [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 4; E = O, 6) resulting from both carbon-hydrogen and carbon-phosphorus bond activation. In each the C4H2E (E = S, O) ligand donates 4-electrons to the cluster and the rings are tilted with respect to the mu-dppm and the phosphido-bridged open triruthenium unit. Heating 4 at 80 degrees C leads to the formation of the ring-opened cluster [Ru3(CO)5(mu-CO)(mu-dppm)(mu3-eta3-SC4H3)(mu-P(C4H3S)2)] (5) resulting from carbon-sulfur bond scission and carbon-hydrogen bond formation and containing a ring-opened mu3-eta3-1-thia-1,3-butadiene ligand. In contrast, a similar thermolysis of 3 affords the phosphinidene cluster [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2O)(mu3-P(C4H3O))] (7) resulting from a second phosphorus-carbon bond cleavage and (presumably) elimination of furan. Treatment of 4 and 6 with PPh3 affords the simple phosphine-substituted products [Ru3(CO)6(PPh3)(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 8; E = O, 9). Both thiophyne and furyne clusters 4 and 6 readily react with hydrogen bromide to give [Ru3(CO)6Br(mu-Br)(mu-dppm)(mu3-eta2-eta1-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 10; E = O, 11) containing both terminal and bridging bromides. Here the alkynes bind in a highly unsymmetrical manner with one carbon acting as a bridging alkylidene and the second as a terminally bonded Fisher carbene. As far as we are aware, this binding mode has only previously been noted in ynamine complexes or those with metals in different oxidation states. The crystal structures of seven of these new triruthenium clusters have been carried out, allowing a detailed analysis of the relative orientations of coordinated ligands. PMID:18985255

  14. Palladium-catalyzed synthesis of benzosilolo[2,3-b]indoles via cleavage of a C(sp3)-Si bond and consequent intramolecular C(sp2)-Si coupling.

    PubMed

    Liang, Yun; Zhang, Shaoguang; Xi, Zhenfeng

    2011-06-22

    An efficient process involving Pd-catalyzed selective cleavage of a C(sp(3))-Si bond and consequent intramolecular C(sp(2))-Si coupling has been developed, affording benzosilolo[2,3-b]indoles as a new type of silicon-bridged polyheteroarene in excellent yields. Aldehyde was found for the first time to be able to promote the efficiency of the catalytic process remarkably. PMID:21517096

  15. Aza-Quaternary Scaffolds from Selective Bond Cleavage of Bridgehead-Substituted 7-Azabicyclo[2.2.1]heptane: Total Synthesis of (+)-Cylindricines C-E and (-)-Lepadiformine A.

    PubMed

    Pandey, Ganesh; Janakiram, Vaitla

    2015-09-01

    A novel bridgehead-substituted aza-bicyclic framework has been designed and developed in both enantiomeric forms through an asymmetric desymmetrization reaction. Strategic exploitation of the ring strain in the aza-bicyclic framework has been utilized for the construction of the chiral aza-quaterenary scaffolds by selective bond fragmentation processes. Furthermore, a strategically designed precursor is employed for selective bond cleavage to initiate a cascade rearrangement for the total synthesis of the 1-azaspirotricyclic marine alkaloids (+)-cylindricines C, D, and E, as well as (-)-lepadiformine A. An oxidation/retro-aldol/aza-Michael sequence generated three new chiral centers with the required configuration in one pot. PMID:26220441

  16. Chemo- and Regioselective Hydrogenolysis of Diaryl Ether C-O Bonds by a Robust Heterogeneous Ni/C Catalyst: Applications to the Cleavage of Complex Lignin-Related Fragments.

    PubMed

    Gao, Fang; Webb, Jonathan D; Hartwig, John F

    2016-01-01

    We report the chemo- and regioselective hydrogenolysis of the C-O bonds in di-ortho-substituted diaryl ethers under the catalysis of a supported nickel catalyst. The catalyst comprises heterogeneous nickel particles supported on activated carbon and furnishes arenes and phenols in high yields without hydrogenation. The high thermal stability of the embedded metal particles allows C-O bond cleavage to occur in highly substituted diaryl ether units akin to those in lignin. Preliminary mechanistic experiments show that this catalyst undergoes sintering less readily than previously reported catalyst particles that form from a solution of [Ni(cod)2 ]. PMID:26666391

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

    SciTech Connect

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

    2014-09-03

    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 μ-(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 C{sub benzoyl}N 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 β = 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 (ε = 116 dm{sup 3} mol{sup −1} cm{sup −1}) supports the presence of Cu(II) centres.

  18. 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)

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

    2014-09-01

    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 μ-{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 β = 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 (ɛ = 116 dm3 mol-1 cm-1) supports the presence of Cu(II) centres.

  19. 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

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

    2012-04-07

    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.

  20. A study of the reactions of a methionine- and histidine-containing tetrapeptide with different Pd(II) and Pt(II) complexes: selective cleavage of the amide bond by platination of the peptide and steric modification of the catalyst.

    PubMed

    Rajković, Snezana; Zivković, Marija D; Kállay, Csilla; Sóvágó, Imre; Djuran, Milos I

    2009-10-21

    (1)H NMR spectroscopy was applied to the study of the reactions of [M(en)(H(2)O)(2)](2+) complexes (M = Pd(ii) and Pt(ii)) with the N-acetylated methionyl-glycyl-histidyl-glycineamide, MeCOMet-Gly-His-GlyNH(2). All reactions were performed in the pH range 1.5-2.0 with equimolar amounts of the [M(en)(H(2)O)(2)](2+) complex and the tetrapeptide at 60 degrees C. In all these reactions, a metal(ii) complex bound to a methionine residue affects the regioselective cleavage of the amide bond involving the carboxylic group of methionine. The priority in the cleavage of the Met-Gly amide bond in relation to the other amide bonds in this peptide is due to the high affinity of Pt(ii) and Pd(ii) ions for the sulfur donor atom. The mechanism of these hydrolytic reactions is discussed and, for its clarification, the reaction of the [Pd(en)(H(2)O)(2)](2+) complex with MeCOMet-Gly-His-GlyNH(2) was additionally investigated by potentiometric titration. The steric effects of the various palladium(ii) complexes of the type [Pd(L)(H(2)O)(2)](2+), in which L is a chelating diamine (ethylenediamine, en, 2-picolylamine, pic, or 2,2-dipyridylamine, dpa) on the hydrolytic cleavage of the amide bond involving the carboxylic group of histidine in the MeCOMet-Gly-His-GlyNH(2) tetrapeptide were also studied by (1)H NMR spectroscopy. All reactions were performed under the above-mentioned conditions and in the initial stage of these reactions, the MeCOMet-Gly-His-GlyNH(2) was reacted with an equimolar amount of the [Pt(dien)Cl](+) complex (dien is diethylenetriamine) and then the monoplatinated [Pt(dien)(MeCOMet-Gly-His-GlyNH(2)-S)](2+) complex was treated with an equimolar amount of [Pd(L)(H(2)O)(2)](2+). It was found that the rate of hydrolysis of the His-GlyNH(2) amide bond in [Pt(dien)(MeCOMet-Gly-His-GlyNH(2)-S)](2+) decreased from the en to the pic complex, with finally a total inhibition of this reaction with [Pd(dpa)(H(2)O)(2)](2+). These results are an important step in the study of the regioselective cleavage of peptides and proteins and in the development of new palladium(ii) complexes as artificial metallopeptidases. PMID:19789790

  1. The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase Kinetic and Structural Evidence Supporting a Key Role for Histidine 265 of the Catalytic triad

    SciTech Connect

    Horsman, Geoff P.; Bhowmik, Shiva; Seah, Stephen Y.K.; Kumar, Pravindra; Bolin, Jeffrey T.; Eltis, Lindsay D.

    2010-01-07

    BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to afford benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). An enol-keto tautomerization has been proposed to precede hydrolysis via a gem-diol intermediate. The role of the canonical catalytic triad (Ser-112, His-265, Asp-237) in mediating these two half-reactions remains unclear. We previously reported that the BphD-catalyzed hydrolysis of HOPDA ({lambda}{sub max} is 434 nm for the free enolate) proceeds via an unidentified intermediate with a red-shifted absorption spectrum ({lambda}{sub max} is 492 nm) (Horsman, G. P., Ke, J., Dai, S., Seah, S. Y. K., Bolin, J. T., and Eltis, L. D. (2006) Biochemistry 45, 11071-11086). Here we demonstrate that the S112A variant generates and traps a similar intermediate ({lambda}{sub max} is 506 nm) with a similar rate, 1/{tau} {approx} 500 s{sup -1}. The crystal structure of the S112A:HOPDA complex at 1.8-{angstrom} resolution identified this intermediate as the keto tautomer, (E)-2,6-dioxo-6-phenyl-hex-3-enoate. This keto tautomer did not accumulate in either the H265A or the S112A/H265A double variants, indicating that His-265 catalyzes tautomerization. Consistent with this role, the wild type and S112A enzymes catalyzed tautomerization of the product HPD, whereas H265A variants did not. This study thus identifies a keto intermediate, and demonstrates that the catalytic triad histidine catalyzes the tautomerization half-reaction, expanding the role of this residue from its purely hydrolytic function in other serine hydrolases. Finally, the S112A:HOPDA crystal structure is more consistent with hydrolysis occurring via an acyl-enzyme intermediate than a gem-diol intermediate as solvent molecules have poor access to C6, and the closest ordered water is 7{angstrom} away.

  2. Mechanistic study on the cleavage and reorganization of C(sp3)-H and C=N bonds in carbodiimides: synthesis of 1,2-dihydrothiopyrimidines and 2,3-dihydropyrimidinthiones through four-component coupling.

    PubMed

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

    2013-08-01

    This study sheds light on the cleavage and reorganization of C(sp(3))-H and C=N bonds of carbodiimides in a three-component reaction of terminal alkynes, sulfur, and carbodiimides by a combination of methods including 1) isolation and X-ray analysis of six-membered-ring lithium species 2-S, 2) trapping of the oxygen-analogues (B-O and D-O) of both four-membered-ring intermediate B-S and ring-opening intermediate D-S, 3) deuterium labeling studies, and 4) theoretical studies. These results show that 1) the reaction rate-determining step is [2+2] cycloaddition, 2) the C=N bond cleavage takes place before C(sp(3))-H bond cleavage, 3) the hydrogen attached to C6 in 2-S originates from the carbodiimide, and 4) three types of new aza-heterocycles, such as 1,2-dihydrothiopyrimidines, N-acyl 2,3-dihydropyrimidinthiones, and 1,2-dihydropyrimidinamino acids are constructed efficiently based on 2-S. All results strongly support the idea that the reaction proceeds through [2+2] cycloaddition/4π electrocyclic ring-opening/1,5-H shift/6π electrocyclic ring-closing as key steps. The research strategy on the synthesis, isolation, and reactivity investigation of important intermediates in metal-mediated reactions not only helps achieve an in-depth understanding of reaction mechanisms but also leads to the discovery of new synthetically useful reactions based on the important intermediates. PMID:23821475

  3. Regioselective alkene carbon-carbon bond cleavage to aldehydes and chemoselective alcohol oxidation of allylic alcohols with hydrogen peroxide catalyzed by [cis-Ru(II)(dmp)2(H2O)2]2+ (dmp = 2,9-dimethylphenanthroline).

    PubMed

    Kogan, Vladimir; Quintal, Miriam M; Neumann, Ronny

    2005-10-27

    [reaction: see text] [cis-Ru(II)(dmp)2(H2O)2]2+ (dmp = 2,9-dimethylphenanthroline) was found to be a selective oxidation catalyst using hydrogen peroxide as oxidant. Thus, primary alkenes were very efficiently oxidized via direct carbon-carbon bond cleavage to the corresponding aldehydes as an alternative to ozonolysis. Secondary alkenes were much less reactive, leading to regioselective oxidation of substrates such as 4-vinylcyclohexene and 7-methyl-1,6-octadiene at the terminal position. Primary allylic alcohols were chemoselectively oxidized to the corresponding allylic aldehydes, e.g., geraniol to citral. PMID:16235952

  4. Access to N-thioalkenyl and N-(o-thio)aryl-benzimidazol-2-ones by ring opening of thiazolobenzimidazolium and benzimidazobenzothiazolium salts and C-O bond cleavage of an alkoxide.

    PubMed

    Andreoli, Federico; Kaid-Slimane, Radia; Coppola, Fabien; Farran, Daniel; Roussel, Christian; Vanthuyne, Nicolas

    2015-03-20

    We report herein the synthesis of highly functionalized 1,3-dihydro-2H-benzimidazol-2-ones via a ring opening of thiazolo[3,2-a]benzimidazolium or benzimidazo[2,1-b][1,3]benzothiazol-6-ium salts and an unusual C-O bond cleavage of an alkoxide. A large variety of benzimidazolones bearing an original N-thioalkenyl or N-(o-thio)aryl group was obtained in high yields. The developed chemistry provides efficient and rapid access to the privileged benzimidazol-2-one scaffold. PMID:25723903

  5. Mechanism of the mutagenic action of hydroxylamine. IX. The UV-induced cleavage of the N-O bond in N4-hydroxy-and N4-methoxycytidine and N6-methoxyadenosine.

    PubMed Central

    Simukova, N A; Yakovlev, D Y; Budowsky, E I

    1975-01-01

    The principal UV-induced (lambda = 2546nm) reaction of N4-hydroxy- and N4methoxycytidines and N6-methoxyadenosine in neutral aqueous solutions is cleavage of the exocyclic N-O bond with the respective formation of cytidine and adenosine. Quantum yields are 2.8x10(-3) and 2.2x10(-3) M/E for the first two compounds and 9.1x10(-3) M/E for N6-methoxyadenosine. PMID:1052542

  6. Iron-catalyzed N-alkylation of azoles via cleavage of an sp3 C-H bond adjacent to a nitrogen atom.

    PubMed

    Xia, Qinqin; Chen, Wanzhi

    2012-10-19

    Iron-catalyzed direct C-N bond formation between azoles and amides is described. The oxidative coupling reactions of sp(3) C-H bonds adjacent to a nitrogen atom in amides and sulfonamides with the N-H bond in azoles proceeded smoothly in the presence of FeCl(2) and di-tert-butyl peroxide (DTBP). PMID:23025235

  7. Catalytic hydrogenolysis of an aryl-aryl carbon-carbon bond with a rhodium complex

    SciTech Connect

    Perthuisot, C.; Jones, W.D. )

    1994-04-20

    Recent publications have brought renewed interest to the quest for homogeneous catalytic activation of carbon-carbon bonds. However, except for a few reports of biphenylene cleavage, the mechanism and scope of aryl-aryl C-C bond activation remains relatively uninvestigated. In the hope of overcoming the obstacle of weak M-C bonds, we used a rhodium system that should provide a thermodynamically favored C-C cleaved complex by making strong metal-aryl bonds. Reaction of (C[sub 5]Me[sub 5])Rh(PMe[sub 3])(Ph)(H) (1) with 1.5 equiv of biphenylene in cyclohexane-d[sub 12] at 65[degree]C resulted in the quantitative formation of (CC[sub 5]Me[sub 5])Rh(PMe[sub 3]) (biphenylenyl(H)) (2), along with a small amount of a red complex. The cleavage of the well-hidden carbon-carbon bond of biphenylene described relies both on a strained four-membered ring and on the formation of a stable pentametallacycle. The results show that C-H activation and [eta][sup 2] coordination are probably involved in the process leading to C-C bond cleavage, and valuable information can be obtained from studies of this system. 21 refs., 1 fig.

  8. Theoretical and structural analysis of long C-C bonds in the adducts of polycyanoethylene and anthracene derivatives and their connection to the reversibility of Diels-Alder reactions.

    PubMed

    Hirsch, Anna K H; Reutenauer, Philippe; Le Moignan, Marc; Ulrich, Sébastien; Boul, Peter J; Harrowfield, Jack M; Jarowski, Peter D; Lehn, Jean-Marie

    2014-01-20

    X-ray structure determinations on four Diels-Alder adducts derived from the reactions of cyano- and ester-substituted alkenes with anthracene and 9,10-dimethylanthracene have shown the bonds formed in the adduction to be particularly long. Their lengths range from 1.58 to 1.62 Å, some of the longest known for Diels-Alder adducts. Formation of the four adducts is detectably reversible at ambient temperature and is associated with free energies of reaction ranging from -2.5 to -40.6 kJ  mol(-1). The solution equilibria have been experimentally characterised by NMR spectroscopy. Density-functional-theory calculations at the MPW1K/6-31+G(d,p) level with PCM solvation agree with experiment with average errors of 6 kJ  mol(-1) in free energies of reaction and structural agreement in adduct bond lengths of 0.013 Å. To understand more fully the cause of the reversibility and its relationship to the long adduct bond lengths, natural-bond-orbital (NBO) analysis was applied to quantify donor-acceptor interactions within the molecules. Both electron donation into the σ*-anti-bonding orbital of the adduct bond and electron withdrawal from the σ-bonding orbital are found to be responsible for this bond elongation. PMID:24339005

  9. 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

    SciTech Connect

    Gliniak, B.C.; Kabat, D. )

    1989-09-01

    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. The authors 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. They 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.

  10. Palladium-Catalyzed Deaminative Phenanthridinone Synthesis from Aniline via C-H Bond Activation.

    PubMed

    Yedage, Subhash L; Bhanage, Bhalchandra M

    2016-05-20

    This work reports palladium-catalyzed phenanthridinone synthesis using the coupling of aniline and amide by formation of C-C and C-N bonds in a one-pot fashion via dual C-H bond activation. It involves simultaneous cleavage of four bonds and the formation of two new bonds. The present protocol is ligand-free, takes place under mild reaction conditions, and is environmentally benign as nitrogen gas and water are the only side products. This transformation demonstrates a broad range of aniline and amide substrates with different functional groups and has been scaled up to gram level. PMID:27088815

  11. A Light/Ketone/Copper System for Carboxylation of Allylic C-H Bonds of Alkenes with CO2.

    PubMed

    Ishida, Naoki; Masuda, Yusuke; Uemoto, Sho; Murakami, Masahiro

    2016-05-01

    A photo-induced carboxylation reaction of allylic C-H bonds of simple alkenes with CO2 is prompted by means of a ketone and a copper complex. The unique carboxylation reaction proceeds through a sequence of an endergonic photoreaction of ketones with alkenes forming homoallyl alcohol intermediates and a thermal copper-catalyzed allyl transfer reaction from the homoallyl alcohols to CO2 through C-C bond cleavage. PMID:26998686

  12. In vitro mutagenesis of Caenorhabditis elegans cuticle collagens identifies a potential subtilisin-like protease cleavage site and demonstrates that carboxyl domain disulfide bonding is required for normal function but not assembly.

    PubMed Central

    Yang, J; Kramer, J M

    1994-01-01

    The importance of conserved amino acids in the amino and carboxyl non-Gly-X-Y domains of Caenorhabditis elegans cuticle collagens was examined by analyzing site-directed mutations of the sqt-1 and rol-6 collagen genes in transgenic animals. Altered collagen genes on transgenic arrays were shown to produce appropriate phenotypes by injecting in vivo cloned mutant alleles. Equivalent alterations in sqt-1 and rol-6 generally produced the same phenotypes, indicating that conserved amino acids in these two collagens have similar functions. Serine substitutions for either of two conserved carboxyl domain cysteines produced LRol phenotypes. Substitution for both cysteines in sqt-1 also resulted in an LRol phenotype, demonstrating that disulfide bonding is important for normal function but not required for assembly. Arg-1 or Arg-4 to Cys mutations in homology block A (HBA; consensus, 1-RXRRQ-5; in the amino non-Gly-X-Y domain) caused RRol phenotypes, while the same alteration at Arg-3 had no effect, indicating that Arg-3 is functionally different from Arg-1 and Arg-4. Substitutions of Arg-4 with Ser, Leu, or Glu also produced the RRol phenotype, while Lys substitutions for Arg-1 or Arg-4 did not generate any abnormal phenotypes. His substitutions for Arg-1 or Arg-4 caused somewhat less severe RRol phenotypes. Therefore, strong positively charged residues, Arg or Lys, are required at positions 1 and 4 for normal function. The conserved pattern of arginines in HBA matches the cleavage sites of the subtilisin-like endoproteinases. HBA may be a cleavage site for a subtilisin-like protease, and cleavage may be important for cuticle collagen processing. PMID:8139571

  13. 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

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

    2009-01-01

    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

  14. Using IR and Raman spectra to explain the catalytic activity of the Fe(II)/Fe(III) pair toward the cleavage of peptide bonds.

    PubMed

    Camacho, Felipe G; Alves, Wagner A

    2015-12-01

    IR and Raman experiments of formamide (FA) solutions containing variable amounts of Fe(II) and Fe(III) salts were carried out. The νCO vibration is downshifted whereas the νCN mode is upshifted in the presence of the divalent ion. As the trivalent ion is added to the solvent, upshifts of both νCO and νCN vibrations are observed. These spectral patterns are related to the distinct FA forms that are stabilized by each ion. Fe(II) is surrounded by 6 ionic FA species while neutral ones coordinate to the trivalent ion with formation of [Fe(FA)3Cl](2+) and [Fe(FA)2(Cl)2](+). In higher salt compositions [FeCl4](-) is also identified in the spectra. Our vibrational results are very well corroborated by biological studies on the catalytic activity of the Fe(II)/Fe(III) pair in oxidative cleavage processes of polypeptides and proteins. PMID:26117195

  15. The Specific Cleavage of Lactone Linkage to Open-Loop in Cyclic Lipopeptide during Negative ESI Tandem Mass Spectrometry: The Hydrogen Bond Interaction Effect of 4-Ethyl Guaiacol

    PubMed Central

    Guo, Mengzhe; Pan, Youlu; Zhang, Rong; Cao, Yang; Chen, Jianzhong; Pan, Yuanjiang

    2014-01-01

    Mass spectrometry is a valuable tool for the analysis and identification of chemical compounds, particularly proteins and peptides. Lichenysins G, the major cyclic lipopeptide of lichenysin, and the non-covalent complex of lichenysins G and 4-ethylguaiacol were investigated with negative ion ESI tandem mass spectrometry. The different fragmentation mechanisms for these compounds were investigated. Our study shows the 4-ethylguaiacol hydrogen bond with the carbonyl oxygen of the ester group in the loop of lichenysins G. With the help of this hydrogen bond interaction, the ring structure preferentially opens in lactone linkage rather than O-C bond of the ester-group to produce alcohol and ketene. Isothermal titration 1H-NMR analysis verified the hydrogen bond and determined the proportion of subject and ligand in the non-covalent complex to be 1∶1. Theoretical calculations also suggest that the addition of the ligand can affect the energy of the transition structures (TS) during loop opening. PMID:25144459

  16. Oxidative coupling of dichalcogenides with sodium sulfinates via copper-catalyzed cleavage of S-S and Se-Se bonds.

    PubMed

    Taniguchi, Nobukazu

    2015-02-01

    A copper-catalyzed sulfonylation of disulfides was achieved using sodium sulfinates in air. The reaction formed various sulfur-sulfone bonds efficiently and afforded thiosulfonates in good yields. Selenosulfonates could also be prepared with this procedure. Furthermore, both chalcogenide groups on the dichalcogenides were available in these reactions. PMID:25562106

  17. Cleavage of the phenacyl esters of carboxylic and thiocarboxylic acids by metal alkoxides

    SciTech Connect

    Morozov, A.A.

    1988-11-20

    During the cleavage of phenacyl esters with general formula XC/sub 6/H/sub 4/COCH/sub 2/OCOR by metal alkoxides in alcohols and in ether-alcohol solutions the acids, esters, and ethers are formed as a result of cleavage of the C-C bond. The solvent participates in the formation of the ether and gives rise to transesterification of RCOOCH/sub 3/ with catalytic participation of the metal alkoxide. The reactivity of the phenacyl esters of the thio acids is much higher. Before dissociation the esters of substituted benzoins C/sub 6/H/sub 5/COCH(OCOCH/sub 3/) /times/ C/sub 6/H/sub 4/X-4 undergo irreversible rearrangement with the formation of isomeric products.

  18. Samarium(III)-catalyzed C(sp3)-H bond activation: synthesis of indolizines via C-C and C-N coupling between 2-alkylazaarenes and propargylic alcohols.

    PubMed

    Wang, Xu; Li, Shen-yan; Pan, Ying-ming; Wang, Heng-shan; Liang, Hong; Chen, Zhen-feng; Qin, Xiao-huan

    2014-01-17

    A new rare earth metal and samarium-catalyzed C(sp(3))-H bond activation is reported in which 2-alkylazaarenes and propargylic alcohols were converted to indolizines. This process operates under mild conditions and solvent-free conditions. A broad scope of coupling partners has been established, and a likely mechanism has also been suggested. PMID:24359214

  19. Hydrodenitrogenation chemistry. I. Cleavage of alkylcarbon-nitrogen bonds, methane and ammonia formation in the HDN reaction of 1,2,3,4-tetrahydroquinoline with a nickel oxide catalyst supported on silica/alumina

    SciTech Connect

    Fish, R.H.; Thormodsen, A.D.; Moore, R.S.; Perry, D.L.; Heinemann, H.

    1986-11-01

    The hydrodenitrogenation reaction (HDN) is one of the most important industrial processes used in the refining of petroleum feedstocks and involves the removal of the nitrogen atom, as ammonia, from polynuclear heteroaromatic nitrogen compounds at high temperatures and high pressures of hydrogen gas (350-500/sup 0/C and 2000 psi). It is interesting to note that most of the reported heterogeneous catalysts require the complete hydrogenation of both the nitrogen heterocyclic ring and the aromatic ring before carbon-nitrogen bond cleavage can occur. A major breakthrough in the technical and economic aspects of the HDN reaction would take place if, in fact a catalyst could be found that would selectively cleave the C-N bond din the saturated nitrogen ring and subsequently produce ammonia, without substantial reduction of the aromatic rings, at lower temperatures as well as lower pressures of hydrogen gas. In this note, the authors report on a highly loaded nickel oxide catalyst (50% by weight Ni), supported on silica/alumina, that will effectively provide some of the criteria for an ideal HDN catalyst. 8 references.

  20. Homolytic Cleavage of a B-B Bond by the Cooperative Catalysis of Two Lewis Bases: Computational Design and Experimental Verification.

    PubMed

    Wang, Guoqiang; Zhang, Honglin; Zhao, Jiyang; Li, Wei; Cao, Jia; Zhu, Chengjian; Li, Shuhua

    2016-05-10

    Density functional theory (DFT) investigations revealed that 4-cyanopyridine was capable of homolytically cleaving the B-B σ bond of diborane via the cooperative coordination to the two boron atoms of the diborane to generate pyridine boryl radicals. Our experimental verification provides supportive evidence for this new B-B activation mode. With this novel activation strategy, we have experimentally realized the catalytic reduction of azo-compounds to hydrazine derivatives, deoxygenation of sulfoxides to sulfides, and reduction of quinones with B2 (pin)2 at mild conditions. PMID:27061603

  1. Activation of Homolytic Si-Zn and Si-Hg Bond Cleavage, Mediated by a Pt(0) Complex, via Novel Pt-Zn and Pt-Hg Compounds.

    PubMed

    Kratish, Yosi; Molev, Gregory; Kostenko, Arseni; Sheberla, Dennis; Tumanskii, Boris; Botoshansky, Mark; Shimada, Shigeru; Bravo-Zhivotovskii, Dmitry; Apeloig, Yitzhak

    2015-09-28

    The thermally stable [(tBuMe2 Si)2 M] (M=Zn, Hg) generate R3 Si(.) radicals in the presence of [(dmpe)Pt(PEt3 )2 ] at 60-80 °C. The reaction proceeds via hexacoordinate Pt complexes, (M=Zn (2 a and 2 b), M=Hg (3 a and 3 b)) which were isolated and characterized. Mild warming or photolysis of 2 or 3 lead to homolytic dissociation of the Pt-MSiR3 bond generating silyl radicals and novel unstable pentacoordinate platinum paramagnetic complexes (M=Zn (5), Hg (6)) whose structures were determined by EPR spectroscopy and DFT calculations. PMID:26288342

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

    PubMed

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

    2014-10-01

    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

  3. CO sub 2 ter dot minus radical induced cleavage of disulfide bonds in proteins. A gamma-ray and pulse radiolysis mechanistic investigation

    SciTech Connect

    Favaudon, V.; Tourbez, H.; Lhoste, J-M. ); Houee-Levin, C. )

    1990-12-01

    Disulfide bond reduction by the CO{sub 2}{sup {center dot}{minus}} radical was investigated in aponeocarzinostatin, aporiboflavin-binding protein, and bovine immunoglobulin. Protein-bound cysteine free thiols were formed under {gamma}-ray irradiation in the course of a pH-dependent and protein concentration dependent chain reaction. The chain efficiency increased upon acidification of the medium, with an apparent pK{sub a} around 5, and decreased abruptly below pH 3.6. It decreased also at neutral pH as cysteine accumulated. From pulse radiolysis analysis, CO{sub 2}{sup {center dot}{minus}} proved able to induce rapid one-electron oxidation of thiols and of tyrosine phenolic groups in addition to one-electron donation to exposed disulfide bonds. The bulk rate constant of CO{sub 2}{sup {center dot}{minus}} uptake by the native proteins was 5{minus} to 10-fold faster at pH 3 than at pH 8, and the protonated form of the disulfide radical anion, appeared to be the major protein radical species formed under acidic conditions. Formation of the disulfide radical cation, phenoxyl radical Tyr-O{sup {center dot}} disproportionation, and phenoxyl radical induced oxidation of preformed thiol groups should also be taken into consideration to explain the fate of the oxygen-centered phenoxyl radical.

  4. A theoretical study on the enthalpies of homolytic and heterolytic N-H bond cleavage in substituted melatonins in the gas-phase and aqueous solution.

    PubMed

    Najafi, Meysam; Farmanzadeh, Davood; Klein, Erik; Zahedi, Mansour

    2013-01-01

    In this paper, the study of melatonin and 60 meta- and ortho-substituted melatonins is presented. The reaction enthalpies related to the hydrogen atom transfer (HAT), single electron transfer - proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET) have been calculated using DFT/B3LYP method in gas-phase and water. Results show that electron-withdrawing substituents increase the bond dissociation enthalpy (BDE), ionization potential (IP) and electron transfer enthalpy (ETE), while electron-donating ones cause a rise in the proton dissociation enthalpy (PDE) and proton affinity (PA). In ortho position, substituents show larger effect on reaction enthalpies than in meta position. In comparison to gas-phase, water attenuates the substituent effect on all reaction enthalpies. Results show that IP and BDE values can be successfully correlated with the indolic N-H bond length after electron abstraction, R(N-H(+*)), and the partial charge on the indolyl radical nitrogen atom, q(N). Furthermore, calculated IP and PA values for meta and ortho substituted melatonins show linear dependence on the energy of the highest occupied molecular orbital (E(HOMO)) of studied molecules in the two environments. SPLET represents the thermodynamically preferred mechanism in water. PMID:23841331

  5. Effect of substituents on the preferred modes of one-electron reductive cleavage of N-Cl and N-Br bonds.

    PubMed

    O'Reilly, Robert J; Karton, Amir; Radom, Leo

    2013-01-17

    In this study, we investigate the effect of substituents in determining the modes of one-electron reductive cleavage of X-NRR' (X = Cl and Br) molecules. We achieve this through comparison of the calculated gas-phase electron affinities (EAs) and aqueous-phase one-electron reduction potentials (E°'s) for a range of nitrogen-centered radicals ((•)NRR') with the corresponding EA and E° values for (•)Cl and (•)Br. The gas-phase EAs have been obtained using the benchmark-quality W1w thermochemical protocol, whereas E° values have been obtained by additionally applying free energy of solvation corrections, obtained using the conductor-like polarizable continuum (CPCM) model. We find that the N-halogenated derivatives of amines and amides should generally cleave in such a way as to afford (•)NRR' and X(-). For the N-halogenated imides, on the other hand, the N-brominated derivatives are predicted to produce (•)Br in solution, whereas the N-chlorinated derivatives again would give Cl(-). Importantly, we predict that N-bromouracil is likely to afford (•)Br. This may have important implications in terms of inflammatory-related diseases, because (•)Br may damage biomolecules such as proteins and DNA. To assist in the determination of the gas-phase EAs of larger (•)NRR' radicals, not amenable to investigation using W1w, we have evaluated the performance of a wide range of lower-cost theoretical methods. Of the standard density functional theory (DFT) procedures, M06-2X, τ-HCTHh, and B3-LYP show good performance, with mean absolute deviations (MADs) from W1w of 4.8-6.8 kJ mol(-1), whereas ROB2-PLYP and B2-PLYP emerge as the best of the double-hybrid DFTs (DHDFTs), with MADs of 2.5 and 3.0 kJ mol(-1), respectively. Of the Gn-type procedures, G3X and G4 show very good performance (MADs = 2.4 and 2.6 kJ mol(-1), respectively). The G4(MP2)-6X+ procedure performs comparably, with an MAD of 2.7 kJ mol(-1), with the added advantage of significantly reduced computational expense. PMID:23282473

  6. Bioinformatic and Biochemical Characterizations of C–S Bond Formation and Cleavage Enzymes in the Fungus Neurospora crassa Ergothioneine Biosynthetic Pathway

    PubMed Central

    2015-01-01

    Ergothioneine is a histidine thiol derivative. Its mycobacterial biosynthetic pathway has five steps (EgtA-E catalysis) with two novel reactions: a mononuclear nonheme iron enzyme (EgtB) catalyzed oxidative C–S bond formation and a PLP-mediated C–S lyase (EgtE) reaction. Our bioinformatic and biochemical analyses indicate that the fungus Neurospora crassa has a more concise ergothioneine biosynthetic pathway because its nonheme iron enzyme, Egt1, makes use of cysteine instead of γ-Glu-Cys as the substrate. Such a change of substrate preference eliminates the competition between ergothioneine and glutathione biosyntheses. In addition, we have identified the N. crassa C–S lyase (NCU11365) and reconstituted its activity in vitro, which makes the future ergothioneine production through metabolic engineering feasible. PMID:25275953

  7. Synthesis and [2 + 2] cycloaddition of bimethyleneketene acetals. Reaction with C[sub 60] and facile hydrolysis of the C-C bond connected to C[sub 60

    SciTech Connect

    Yamago, Shigeru; Takeichi, Atsuo; Nakamura, Eiichi )

    1994-02-09

    We report here that the O-alkylated enolates of cyclopropanecarboxylates (dimethyleneketene acetals 3) can be prepared from readily available precursors, and that they are extemely reactive, serving as useful surrogates of the elusive parent enolates. Their utility is illustrated by the [2 + 2] cycloaddition to electron-deficient olefins, which, after hydrolytic workup, gives rise to the Michael addition products: a type of reaction product previously unavailable. We also found that 3 reacts smoothly with C[sub 60] to give the [2 + 2] adduct 5 and, most remarkably, that the asterisked C[minus]C [sigma] bond in 5 directly connected to the fullerene core is hydrolytically unstable and can be quantitatively cleaved with aqueous acid. 15 refs., 1 tab.

  8. Low-temperature N-O bond cleavage in nitrosyl ligands induced by the unsaturated dimolybdenum anion [Mo2(eta(5)-C5H5)2(mu-PPh2)(mu-CO)2]-.

    PubMed

    García, M Esther; García-Vivó, Daniel; Melón, Sonia; Ruiz, Miguel A; Graiff, Claudia; Tiripicchio, Antonio

    2009-10-01

    The unsaturated anion [Mo(2)Cp(2)(mu-PPh(2))(mu-CO)(2)](-) (1) (Na(+) salt) reacts with the nitrosyl complexes [MCp'(CO)(2)(NO)]BF(4) (M = Mn, Re; Cp' = eta(5)-C(5)H(4)Me) rapidly at about 193 K. Upon warming of the resulting mixtures up to 243 K orange solutions are obtained, shown to contain the corresponding oxo- and nitride-bridged tetracarbonyl complexes [Mo(2)MCp(2)Cp'(mu-N)(mu-O)(mu-PPh(2))(CO)(4)] as the major product, which could be isolated only for M = Re. Above 253 K, however, these compounds experience spontaneous decarbonylation to yield the unsaturated tricarbonyl derivatives [Mo(2)MCp(2)Cp'(mu-N)(mu-O)(mu-PPh(2))(CO)(3)] (Mo-Mo = 2.840 A for the Mn compound, according to density functional theory (DFT) calculations). These complexes in turn react rapidly with air to give the corresponding dioxodicarbonyl derivatives [Mo(2)MCp(2)Cp'(mu-N)(mu-O)(mu-PPh(2))(O)(CO)(2)] almost quantitatively. The structure of the latter product (M = Re) was determined by X-ray diffraction methods (Mo-Mo = 2.763(1) A). In contrast with the N-O bond cleavage easily taking place in the above reactions, the direct nitrosylation of 1 with N-methyl-N-nitroso-p-toluenesulfonamide induces no bond cleavage process in the nitrosyl ligand, but just gives the electron-precise tricarbonyl derivative [Mo(2)Cp(2)(mu-PPh(2))(CO)(3)(NO)] or, in the presence of CN(t)Bu, a mixture of the new isocyanide complexes [Mo(2)Cp(2)(mu-PPh(2))(CN(t)Bu)(CO)(2)(NO)] and [Mo(2)Cp(2)(mu-PPh(2))(mu-eta(1):eta(2)-CN(t)Bu)(CO)(NO)]. Separate experiments indicated that these isocyanide complexes cannot be converted one into each other, nor can they be obtained through thermal substitution reactions on the above tricarbonyl product. PMID:19746903

  9. Si-H and Si-C bond cleavage reactions of silane and phenylsilanes with Mo(PMe3)6: silyl, hypervalent silyl, silane, and disilane complexes.

    PubMed

    Zuzek, Ashley A; Parkin, Gerard

    2014-06-11

    Mo(PMe3)6 cleaves the Si-H bonds of SiH4, PhSiH3, and Ph2SiH2 to afford a variety of novel silyl, hypervalent silyl, silane, and disilane complexes, as respectively illustrated by Mo(PMe3)4(SiH3)2H2, Mo(PMe3)4(κ(2)-H2-H2SiPh2H)H, Mo(PMe3)3(σ-HSiHPh2)H4, and Mo(PMe3)3(κ(2)-H2-H2Si2Ph4)H2. Mo(PMe3)4(κ(2)-H2-H2SiPh2H)H and Mo(PMe3)3(κ(2)-H2-H2Si2Ph4)H2 are respectively the first examples of complexes that feature a hypervalent κ(2)-H2-H2SiPh2H silyl ligand and a chelating disilane ligand, and both compounds convert to the diphenylsilane adduct, Mo(PMe3)3(σ-HSiHPh2)H4, in the presence of H2. Mo(PMe3)4(SiH3)2H2 undergoes isotope exchange with SiD4, and NMR spectroscopic analysis of the SiHxD4-x isotopologues released indicates that the reaction does not occur via initial reductive elimination of SiH4, but rather by a metathesis pathway. PMID:24874576

  10. Cleavage of peptide bonds bearing ionizable amino acids at P{sub 1} by serine proteases with hydrophobic S{sub 1} pocket

    SciTech Connect

    Qasim, Mohammad A.; Song, Jikui; Markley, John L.; Laskowski, Michael

    2010-10-01

    Research highlights: {yields} Large pK shifts in ionizable groups when buried in the protein interior. {yields} Substrate dependent shifts in pH optimum for serine proteases. {yields} Lys side chain is a stronger acid in serine protease S{sub 1} pocket than Asp side chain. -- Abstract: Enzymatic hydrolysis of the synthetic substrate succinyl-Ala-Ala-Pro-Xxx-pNA (where Xxx = Leu, Asp or Lys) catalyzed by bovine chymotrypsin (CHYM) or Streptomyces griseus protease B (SGPB) has been studied at different pH values in the pH range 3-11. The pH optima for substrates having Leu, Asp, and Lys have been found to be 7.5-8.0, 5.5-6.0, and {approx}10, respectively. At the normally reported pH optimum (pH 7-8) of CHYM and SGPB, the substrate with Leu at the reactive site is more than 25,000-fold more reactive than that with Asp. However, when fully protonated, Asp is nearly as good a substrate as Leu. The pK values of the side chains of Asp and Lys in the hydrophobic S{sub 1} pocket of CHYM and SGPB have been calculated from pH-dependent hydrolysis data and have been found to be about 9 for Asp and 7.4 and 9.7 for Lys for CHYM and SGPB, respectively. The results presented in this communication suggest a possible application of CHYM like enzymes in cleaving peptide bonds contributed by acidic amino acids between pH 5 and 6.

  11. Temperature dependent structural variation from 2D supramolecular network to 3D interpenetrated metal–organic framework: In situ cleavage of S–S and C–S bonds

    SciTech Connect

    Ugale, Bharat; Singh, Divyendu; Nagaraja, C.M.

    2015-03-15

    Two new Zn(II)–organic compounds, [Zn(muco)(dbds){sub 2}(H{sub 2}O){sub 2}] (1) and [Zn(muco)(dbs)] (2) (where, muco=trans, trans-muconate dianion, dbds=4,4′-dipyridyldisulfide and dbs=4,4′-dipyridylsulfide) have been synthesized from same precursors but at two different temperatures. Both the compounds have been characterized by single-crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, IR spectroscopy, thermal analysis and photoluminescence studies. Compound 1 prepared at room temperature possesses a molecular structure extended to 2D supramolecular network through (H–O…H) hydrogen-bonding interactions. Compound 2, obtained at high temperature (100 °C) shows a 3-fold interpenetrating 3D framework constituted by an in situ generated dbs linker by the cleavage of S–S and C–S bonds of dbds linker. Thus, the influence of reaction temperature on the formation of two structural phases has been demonstrated. Both 1 and 2 exhibit ligand based luminescence emission owing to n→π⁎ and π→π⁎ transitions and also high thermal stabilities. - Graphical abstract: The influence of temperature on the formation of two structural phases, a 2D supramolecular network and a 3D 3-fold interpenetrating framework has been demonstrated and their luminescence emission is measured. - Highlights: • Two new Zn(II)–organic compounds were synthesized by tuning reaction temperatures. • Temperature induced in situ generation of dbs linker has been observed. • The compounds exhibit high thermal stability and luminescence emission properties. • The effect of temperature on structure, dimension and topology has been presented.

  12. In situ and theoretical studies for the dissociation of water on an active Ni/CeO2 catalyst: importance of strong metal-support interactions for the cleavage of O-H bonds.

    PubMed

    Carrasco, Javier; Lpez-Durn, David; Liu, Zongyuan; Ducho?, Tom; Evans, Jaime; Senanayake, Sanjaya D; Crumlin, Ethan J; Matoln, Vladimir; Rodrguez, Jos A; Ganduglia-Pirovano, M Vernica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Supported by experimental and density-functional theory results, the effect of the support on O?H bond cleavage activity is elucidated for nickel/ceria systems. Ambient-pressure O?1s photoemission spectra at low Ni loadings on CeO2 (111) reveal a substantially larger amount of OH groups as compared to the bare support. Computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO2 (111) compared with pyramidal Ni4 particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of this support effect is the ability of ceria to stabilize oxidized Ni(2+) species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO2 has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions. PMID:25651288

  13. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO₂ catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

    SciTech Connect

    Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; Liu, Zongyuan; Duchon, Tomas; Evans, Jaime; Senanayake, Sanjaya D.; Crumlin, Ethan J.; Matolin, Vladimir; Ganduglia-Pirovano, M. Veronica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO₂(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO₂(111) compared with pyramidal Ni₄ particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of this support effect is the ability of ceria to stabilize oxidized Ni²⁺ species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO₂ has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.

  14. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO? catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

    SciTech Connect

    Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; Liu, Zongyuan; Duchon, Tomas; Evans, Jaime; Senanayake, Sanjaya D.; Crumlin, Ethan J.; Matolin, Vladimir; Ganduglia-Pirovano, M. Veronica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO?(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO?(111) compared with pyramidal Ni? particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of this support effect is the ability of ceria to stabilize oxidized Ni? species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO? has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.

  15. In-situ and theoretical studies for the dissociation of water on an active Ni/CeO₂ catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

    DOE PAGESBeta

    Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; Liu, Zongyuan; Duchon, Tomas; Evans, Jaime; Senanayake, Sanjaya D.; Crumlin, Ethan J.; Matolin, Vladimir; Ganduglia-Pirovano, M. Veronica

    2015-03-23

    Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO₂(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO₂(111) compared with pyramidal Ni₄ particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of thismore » support effect is the ability of ceria to stabilize oxidized Ni²⁺ species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO₂ has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.« less

  16. Regioselective C-N bond cleavage in an {eta}{sup 2}(N,C)-coordinated pyridine and an {eta}{sup 1}(N) {r_arrow} {eta}{sup 2}(N,C) bonding rearrangement in coordinated quinoline: Models for hydrodenitrogenation catalysis

    SciTech Connect

    Gray, S.D.; Smith, D.P.; Bruck, M.A.; Wigley, D.E.

    1992-06-17

    The catalytic removal of sulfur and nitrogen from petroleum feedstocks and coal-derived liquids is essential to preclude the poisoning of hydrocracking and reforming catalysts and to reduce emissions of their oxides. Industrial hydrodenitrogenation (HDN) is typically effected over sulfided CoMo/Al{sub 2}O{sub 3} or NiMo/Al{sub 2}O{sub 3} under conditions which remove nitrogen as NH{sub 3}. The nitrogen-containing compounds which are most difficult to process are the aromatic heterocycles such as pyridine, quinoline, and indole derivatives. One central question in HDN catalysis which remains unresolved concerns how the strong C-N bonds in these heterocycles are cleaved. Herein the authors provide evidence for an {eta}{sup 1}(N){r_arrow}{eta}{sup 2}(N,C) bonding rearrangement in model HDN substrates and demonstrate that nucleophilic attack of an {eta}{sup 2}(N,C)-pyridine results in facile, regioselective C-N bond cleavage. 17 refs., 3 figs.

  17. Copper(II) complex of in situ formed 5-(2-pyridyl)-1,3,4-triazole through C-S bond cleavage in 1,2-bis(2-pyridylmethylthio)-bis-ethylsulphide: Synthesis, structural characterization and DNA binding study

    NASA Astrophysics Data System (ADS)

    Sarkar, Sandipan; Mukherjee, Titas; Sen, Supriti; Zangrando, Ennio; Chattopadhyay, Pabitra

    2010-09-01

    On reaction of 1,2-bis(2-pyridylmethylthio)-bis-ethylsulphide (L) with copper(II) chloride in presence of an excess of azide ions led to the formation of a new copper(II) complex formulated as [Cu(2-PTrz) 2(H 2O) 2] ( 1), where 2-PTrz = 5-(2-pyridyl)-1,3,4-triazole is formed through the cleavage of C-S bond in L promoted by copper(II) chloride. The precursor of 1 is the in situ formed Cu(pic) 2 derivative (pic = 2-picolinate), the existence of which has been established by separating out in pure form the complexes [Cu 2(pic) 3(H 2O)](ClO 4) ( 2), [Cu 2(pic) 3(H 2O](NO 3) ( 3) by using different anions. In addition [Cu(pyca)Cl] ( 4) (pyca = bis(pyridin-2-carbonyl)amine) was also obtained from 1 with a less quantity of azide. All the copper(II) complexes obtained in this study were characterized by physico-chemical tools as well as X-ray crystallographic studies. The 2-PTrz ligand separated out from 1 was used in the synthesis of the nickel(II) complex [Ni(2-PTrz) 2(H 2O) 2], 5. The complexes 1 and 5 are isomorphous and isostructural. In dimethylformamide solution, complex 1 was found to exhibit Cu II/Cu I quasi-reversible redox couple in cyclic voltammograms with E1/2 value of -340 mV (versus Ag/AgCl) at 298 K. The interaction of complex 1 with CT-DNA has been investigated spectroscopically. The results showed that the interaction mode between complex 1 and DNA might be groove binding.

  18. Origin of brittle cleavage in iridium.

    PubMed

    Cawkwell, Marc J; Nguyen-Manh, Duc; Woodward, Christopher; Pettifor, David G; Vitek, Vaclav

    2005-08-12

    Iridium is unique among the face-centered cubic metals in that it undergoes brittle cleavage after a period of plastic deformation under tensile stress. Atomistic simulation using a quantum-mechanically derived bond-order potential shows that in iridium, two core structures for the screw dislocation are possible: a glissile planar core and a metastable nonplanar core. Transformation between the two core structures is athermal and leads to exceptionally high rates of cross slip during plastic deformation. Associated with this athermal cross slip is an exponential increase in the dislocation density and strong work hardening from which brittle cleavage is a natural consequence. PMID:16099981

  19. Cleavage of nucleic acids

    SciTech Connect

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor L.; Brow, Mary Ann D.; Dahlberg, James E.

    2007-12-11

    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 structure-specific 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.

  20. Cleavage of nucleic acids

    SciTech Connect

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    2000-01-01

    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 structure-specific 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.

  1. Cleavage of nucleic acids

    SciTech Connect

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow; Mary Ann D.; Dahlberg, James E.

    2010-11-09

    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 structure-specific 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.

  2. Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

    PubMed

    Gao, Honghai; Huang, Jianmin; Barany, Francis; Cao, Weiguo

    2007-01-01

    Endonuclease V (endo V) recognizes a broad range of aberrations in DNA such as deaminated bases or mismatches. It nicks DNA at the second phosphodiester bond 3' to a deaminated base or a mismatch. Endonuclease V obtained from Thermotoga maritima preferentially cleaves purine mismatches in certain sequence context. Endonuclease V has been combined with a high-fidelity DNA ligase to develop an enzymatic method for mutation scanning. A biochemical screening of site-directed mutants identified mutants in motifs III and IV that altered the base preferences in mismatch cleavage. Most profoundly, a single alanine substitution at Y80 position switched the enzyme to essentially a C-specific mismatch endonuclease, which recognized and cleaved A/C, C/A, T/C, C/T and even the previously refractory C/C mismatches. Y80A can also detect the G13D mutation in K-ras oncogene, an A/C mismatch embedded in a G/C rich sequence context that was previously inaccessible using the wild-type endo V. This investigation offers insights on base recognition and active site organization. Protein engineering in endo V may translate into better tools in mutation recognition and cancer mutation scanning. PMID:17130153

  3. Development of degradative techniques for coal chemistry based on ether cleavage reactions and metal arene chemistry

    SciTech Connect

    Lemke, D.W.

    1988-01-01

    The degradation of C-O and C-C bonds have been examined using model compounds that are similar in structure to those found in coal and other natural products. The conditions to maximize ether cleavage and minimize the formation of undesirable side products were determined by varying the concentration of reagents, temperature, and reaction time. 2-Phenoxynaphthalene (1) and 1-methoxypyrene (2) were the compounds examined. The optimum conditions demonstrated complete disappearance of 1 and 2, mass recoveries were above 84%, and the formation of reduced dimers in less than 10 mole % yield. The possibility of cleaving a C-C bond by a (3+2) cycloaddition and subsequent cycloreversion reactions was examined by treating a variety of dipolarphiles with deprotonated (({eta}{sup 6}-arene)FeCp){sup +} complexes (arene = hexamethylbenzene or tetralin) Azides and ozone were found to add quantitatively to the metal-arene complexes. Upon decomplexation of the ring, moderated yields of benzyl substituted products were isolated. The mechanism of this reaction is yet unknown but is postulated to occur by direct nucleophilic addition of the complex anion to the most electropositive atom of the dipolarphile. Chemical and electrochemical oxidation techniques were applied to the deprotonated (({eta}{sup 6}-arene)FeCp){sup +} complexes. Only minor yields of benzylic oxidation products were observed.

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

    PubMed Central

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

    2013-01-01

    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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. Selective cleavage of pepsin by molybdenum metallopeptidase

    SciTech Connect

    Yenjai, Sudarat; Malaikaew, Pinpinat; Liwporncharoenvong, Teerayuth; Buranaprapuk, Apinya

    2012-03-02

    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.

  10. Measurements of ? (3686 )?K-? ? ++c .c . and ? (3686 )?? K-? ? ++c .c .

    NASA Astrophysics Data System (ADS)

    Ablikim, M.; Achasov, M. N.; Ai, X. C.; Albayrak, O.; Albrecht, M.; Ambrose, D. J.; Amoroso, A.; An, F. F.; An, Q.; Bai, J. Z.; Baldini Ferroli, R.; Ban, Y.; Bennett, D. W.; Bennett, J. V.; Bertani, M.; Bettoni, D.; Bian, J. M.; Bianchi, F.; Boger, E.; Bondarenko, O.; Boyko, I.; 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, H. Y.; Chen, J. C.; Chen, M. L.; Chen, S. J.; Chen, X.; Chen, X. R.; Chen, Y. B.; Cheng, H. P.; Chu, X. K.; Cibinetto, G.; Cronin-Hennessy, D.; Dai, H. L.; Dai, J. P.; Dbeyssi, A.; Dedovich, D.; Deng, Z. Y.; Denig, A.; Denysenko, I.; Destefanis, M.; de Mori, F.; Ding, Y.; Dong, C.; Dong, J.; Dong, L. Y.; Dong, M. Y.; Du, S. X.; Duan, P. F.; Fan, J. Z.; Fang, J.; Fang, S. S.; Fang, X.; Fang, Y.; Fava, L.; Feldbauer, F.; Felici, G.; Feng, C. Q.; Fioravanti, E.; Fritsch, M.; Fu, C. D.; Gao, Q.; Gao, X. Y.; Gao, Y.; Gao, Z.; Garzia, I.; 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, Y.; Guo, Y. P.; Haddadi, Z.; Hafner, A.; Han, S.; Han, Y. L.; Hao, X. Q.; Harris, F. A.; He, K. L.; He, Z. Y.; Held, T.; Heng, Y. K.; Hou, Z. L.; Hu, C.; Hu, H. M.; Hu, J. F.; Hu, T.; Hu, Y.; Huang, G. M.; Huang, G. S.; Huang, H. P.; Huang, J. S.; Huang, X. T.; Huang, Y.; Hussain, T.; Ji, Q.; Ji, Q. P.; Ji, X. B.; Ji, X. L.; Jiang, L. L.; Jiang, L. W.; Jiang, X. S.; Jiao, J. B.; Jiao, Z.; Jin, D. P.; Jin, S.; Johansson, T.; Julin, A.; Kalantar-Nayestanaki, N.; Kang, X. L.; Kang, X. S.; Kavatsyuk, M.; Ke, B. C.; Kliemt, R.; Kloss, B.; Kolcu, O. B.; Kopf, B.; Kornicer, M.; Khn, W.; Kupsc, A.; Lai, W.; Lange, J. S.; Lara, M.; Larin, P.; Leng, C.; Li, C. H.; Li, Cheng; Li, D. M.; Li, F.; Li, G.; Li, H. B.; Li, J. C.; Li, Jin; Li, K.; Li, K.; Li, Lei; Li, P. R.; Li, T.; Li, W. D.; Li, W. G.; Li, X. L.; Li, X. M.; Li, X. N.; Li, X. Q.; Li, Z. B.; Liang, H.; Liang, Y. F.; Liang, Y. T.; Liao, G. R.; Lin, D. X.; Liu, B. J.; Liu, C. X.; Liu, F. H.; Liu, Fang; Liu, Feng; Liu, H. B.; Liu, H. H.; Liu, H. H.; Liu, H. M.; Liu, J.; Liu, J. P.; Liu, J. Y.; Liu, K.; Liu, K. Y.; Liu, L. D.; Liu, P. L.; Liu, Q.; Liu, S. B.; Liu, X.; Liu, X. X.; Liu, Y. B.; Liu, Z. A.; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H.; Lou, X. C.; Lu, H. J.; Lu, J. G.; Lu, R. Q.; Lu, Y.; Lu, Y. P.; Luo, C. L.; Luo, M. X.; Luo, T.; Luo, X. L.; Lv, M.; Lyu, X. R.; Ma, F. C.; Ma, H. L.; Ma, L. L.; Ma, Q. M.; Ma, S.; Ma, T.; Ma, X. N.; Ma, X. Y.; Maas, F. E.; Maggiora, M.; Malik, Q. A.; Mao, Y. J.; Mao, Z. P.; Marcello, S.; Messchendorp, J. G.; Min, J.; Min, T. J.; Mitchell, R. E.; Mo, X. H.; Mo, Y. J.; Morales Morales, C.; Moriya, K.; Muchnoi, N. Yu.; Muramatsu, H.; Nefedov, Y.; Nerling, F.; Nikolaev, I. B.; Ning, Z.; Nisar, S.; Niu, S. L.; Niu, X. Y.; Olsen, S. L.; Ouyang, Q.; Pacetti, S.; Patteri, P.; Pelizaeus, M.; Peng, H. P.; Peters, K.; Pettersson, J.; Ping, J. L.; Ping, R. G.; Poling, R.; Pu, Y. N.; Qi, M.; Qian, S.; Qiao, C. F.; Qin, L. Q.; Qin, N.; Qin, X. S.; Qin, Y.; Qin, Z. H.; Qiu, J. F.; Rashid, K. H.; Redmer, C. F.; Ren, H. L.; Ripka, M.; Rong, G.; Ruan, X. D.; Santoro, V.; Sarantsev, A.; Savri, M.; Schoenning, K.; Schumann, S.; Shan, W.; Shao, M.; Shen, C. P.; Shen, P. X.; Shen, X. Y.; Sheng, H. Y.; Song, W. M.; Song, X. Y.; Sosio, S.; Spataro, S.; 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.; Tiemens, M.; Toth, D.; Ullrich, M.; Uman, I.; Varner, G. S.; Wang, B.; Wang, B. L.; 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.; Weber, T.; Wei, D. H.; Wei, J. B.; Weidenkaff, P.; Wen, S. P.; Wiedner, U.; Wolke, M.; Wu, L. H.; 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.; Yan, L.; Yan, W. B.; Yan, W. C.; Yan, Y. H.; Yang, H. X.; Yang, L.; Yang, Y.; Yang, Y. X.; Ye, H.; Ye, M.; Ye, M. H.; Yin, J. H.; Yu, B. X.; Yu, C. X.; Yu, H. W.; Yu, J. S.; Yuan, C. Z.; Yuan, W. L.; Yuan, Y.; Yuncu, A.; Zafar, A. A.; Zallo, A.; Zeng, Y.; Zhang, B. X.; Zhang, B. Y.; Zhang, C.; 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, K.; Zhang, L.; Zhang, S. H.; Zhang, X. Y.; Zhang, Y.; Zhang, Y. H.; Zhang, Y. T.; Zhang, Z. H.; Zhang, Z. P.; Zhang, Z. Y.; Zhao, G.; Zhao, H. S.; Zhao, J. W.; Zhao, J. Y.; Zhao, J. Z.; Zhao, Lei; Zhao, Ling; Zhao, M. G.; Zhao, Q.; Zhao, Q. W.; Zhao, S. J.; Zhao, T. C.; Zhao, Y. B.; Zhao, Z. G.; Zhemchugov, A.; Zheng, B.; Zheng, J. P.; Zheng, W. J.; 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, S.; Zhu, X. L.; Zhu, Y. C.; Zhu, Y. S.; Zhu, Z. A.; Zhuang, J.; Zotti, L.; Zou, B. S.; Zou, J. H.; Besiii Collaboration

    2015-05-01

    Using a sample of 1.06 1 08? (3686 ) events produced in e+e- collisions at ?{s }=3.686 GeV and collected with the BESIII detector at the BEPCII collider, we present studies of the decays ? (3686 )?K-? ? ++c .c . and ? (3686 )?? K-? ? ++c .c . . We observe two hyperons, ? (1690 )- and ? (1820 )- , in the K-? invariant mass distribution in the decay ? (3686 )?K-? ? ++c .c . with significances of 4.9 ? and 6.2 ? , respectively. The branching fractions of ? (3686 )?K-? ? ++c .c . , ? (3686 )?K-?0? ++c .c . , ? (3686 )?? ?c J?? K-? ? ++c .c . (J =0 , 1, 2), and ? (3686 )?? (1690 /1820 )-? ++c .c . with subsequent decay ? (1690 /1820 )-?K-? are measured for the first time.

  11. DNA cleavage by aromatic amines.

    PubMed

    Warner, Philip M; Qi, Jiwei; Meng, Bin; Li, Gang; Xie, Longfei; El-Shafey, Ahmed; Jones, Graham B

    2002-01-01

    A series of aryl amines was found to induce cleavage of DNA. Subsequent refinement led to an efficient family of dimeric derivatives capable of cleavage at low concentration. Initial investigations suggest this is an unprecedented mode of DNA cleavage, which may be ultimately applied to the development of sequence-specific agents. PMID:11738560

  12. 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.

    PubMed

    Vrkoslav, Vladimír; Háková, Martina; Pecková, Karolina; Urbanová, Klára; Cvačka, Josef

    2011-04-15

    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 α and ω ions has been introduced. Fragmentation of the α-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

  13. Mapping the Globe with C & C Technologies

    NASA Astrophysics Data System (ADS)

    Kleiner, A. A.

    2001-12-01

    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 3000ś 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.

  14. 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

  15. 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

  16. 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

  17. 1,3-Diazasilabicyclo[1.1.0]butane with a Long Bridging N-N Bond.

    PubMed

    Xiao, Xu-Qiong; Dong, Zhaowen; Li, Zhifang; Yan, Chenting; Lai, Guoqiao; Kira, Mitsuo

    2016-03-01

    A 1,3-diazasilabicyclo[1.1.0]butane (1) is synthesized as thermally stable crystals by using the cycloaddition reaction of an isolable dialkylsilylene with aziadamantane. The bridge N-N bond length of 1 (1.70 Å) is the longest among those of known N-N singly-bonded compounds, including side-on bridged transition-metal dinitrogen complexes. The compound 1 is intact in air but moisture sensitive. No reaction occurs with hydrogen, even under pressure at 0.5 MPa. Irradiation of 1 with light gives an isomer quantitatively by N-N and adamantyl C-C bond cleavage. The origin of the remarkable N-N bond elongation is ascribed to significant interaction between a Si-C σ* and Ν-Ν π and σ orbitals as determined by DFT calculations of model compounds. PMID:26855202

  18. Microscopic thermal characterization of C/C and C/C-SiC composites

    NASA Astrophysics Data System (ADS)

    Jumel, J.; Krapez, J. C.; Lepoutre, F.; Enguehard, F.; Rochais, D.; Neuer, G.; Cataldi, M.

    2002-05-01

    To measure the thermal properties of C/C and C/C-SiC composites constituents, photoreflectance microscopy is used. Specific methods are developed to cope with experimental artefacts (material semi-transparency, convolution effects), so as with fibers and matrix specificities (strong thermal anisotropy, geometric effects…). Experimental results are presented demonstrating the interest of photoreflectance microscopy for a quantitative determination of the microscopic thermal properties of these complex graphite materials.

  19. Hydrogen Induced C-C, C-N, & C-S Bond Activation on Pt & Ni Surfaces

    SciTech Connect

    Gland, J. L.

    2004-07-29

    The primary reactions investigated were chosen based on their importance in fuel and chemical production as well as in environmental remediation, and include reactions for hydrodesulfurization (HDS), hydrodenitrogenation (HDN), carbon-carbon hydrogenolysis, and hydrocarbon oxidation.

  20. Thermodynamic and kinetic study of cleavage of the N-O bond of N-oxides by a vanadium(III) complex: enhanced oxygen atom transfer reaction rates for adducts of nitrous oxide and mesityl nitrile oxide.

    PubMed

    Palluccio, Taryn D; Rybak-Akimova, Elena V; Majumdar, Subhojit; Cai, Xiaochen; Chui, Megan; Temprado, Manuel; Silvia, Jared S; Cozzolino, Anthony F; Tofan, Daniel; Velian, Alexandra; Cummins, Christopher C; Captain, Burjor; Hoff, Carl D

    2013-07-31

    Thermodynamic, kinetic, and computational studies are reported for oxygen atom transfer (OAT) to the complex V(N[t-Bu]Ar)3 (Ar = 3,5-C6H3Me2, 1) from compounds containing N-O bonds with a range of BDEs spanning nearly 100 kcal mol(-1): PhNO (108) > SIPr/MesCNO (75) > PyO (63) > IPr/N2O (62) > MesCNO (53) > N2O (40) > dbabhNO (10) (Mes = mesityl; SIPr = 1,3-bis(diisopropyl)phenylimidazolin-2-ylidene; Py = pyridine; IPr = 1,3-bis(diisopropyl)phenylimidazol-2-ylidene; dbabh = 2,3:5,6-dibenzo-7-azabicyclo[2.2.1]hepta-2,5-diene). Stopped flow kinetic studies of the OAT reactions show a range of kinetic behavior influenced by both the mode and strength of coordination of the O donor and its ease of atom transfer. Four categories of kinetic behavior are observed depending upon the magnitudes of the rate constants involved: (I) dinuclear OAT following an overall third order rate law (N2O); (II) formation of stable oxidant-bound complexes followed by OAT in a separate step (PyO and PhNO); (III) transient formation and decay of metastable oxidant-bound intermediates on the same time scale as OAT (SIPr/MesCNO and IPr/N2O); (IV) steady-state kinetics in which no detectable intermediates are observed (dbabhNO and MesCNO). Thermochemical studies of OAT to 1 show that the V-O bond in O≡V(N[t-Bu]Ar)3 is strong (BDE = 154 ± 3 kcal mol(-1)) compared with all the N-O bonds cleaved. In contrast, measurement of the N-O bond in dbabhNO show it to be especially weak (BDE = 10 ± 3 kcal mol(-1)) and that dissociation of dbabhNO to anthracene, N2, and a (3)O atom is thermodynamically favorable at room temperature. Comparison of the OAT of adducts of N2O and MesCNO to the bulky complex 1 show a faster rate than in the case of free N2O or MesCNO despite increased steric hindrance of the adducts. PMID:23805977

  1. Alpha and omega of carotenoid cleavage.

    PubMed

    Lakshman, M R

    2004-01-01

    In early 1900s, based on indirect evidence, Steenbock and Morton independently predicted that beta-carotene could be the biological precursor of vitamin A, although this notion was contested by others. In the 1930s, Thomas Moore showed the in vivo formation of vitamin A from beta-carotene. But it was not until Jim Olson and DeWitt Goodman independently showed in 1965 the formation of retinal, the aldehyde form of vitamin A from beta-carotene in cell-free extracts of liver and intestine, that this vital pathway of beta-carotene was recognized. Despite compelling evidence in several experimental systems for the central cleavage of beta-carotene to retinal by many investigators, there were some careful independent studies by Glover et al., Ganguly et al., Hansen and Meret and Krinsky et al. showing the eccentric cleavage of beta-carotene resulting in the formation of apocarotenoids both in vivo and in vitro. In an attempt to resolve this controversial issue, we revisited this problem in 1989 and showed beyond doubt the formation of retinal as the sole enzymatic product of a cytosolic enzyme from rabbit and rat intestinal mucosa by mass spectrometry and tracer analysis of the crystallized product. This was confirmed in 1996 by Nagao using the pig intestinal extract. Yeum et al. confirmed in 2000 that retinal is the sole product of beta-carotene cleavage in the presence of alpha-tocopherol, and that the observed formation of apocarotenoids occurs only in the absence of an antioxidant like alpha-tocopherol. In the same year, Barua and Olson also concluded from their in vivo studies in rats that central cleavage is by far the major pathway for the formation of vitamin A from beta-carotene. Beta, beta-carotene 15,15'-dioxygenase (EC 1.13.11.21) is the key enzyme that cleaves beta-carotene into two molecules of retinal. It is a cytosolic enzyme primarily localized in the duodenal mucosa although it has been found in liver. It is a 66 kDa sulfhydryl protein, requires molecular oxygen and is activated by ferrous ions. It is highly specific for 15:15' ethylenic bond of carotenoids although it has fairly broad specificity towards a number of carotenoids with at least one intact beta-ionone ring. The dioxygenase was recently cloned from Drosophila melanogaster and from the chicken intestine. The recombinant protein was found to form retinal as the sole cleavage product of beta-carotene. No apo-carotenoids were formed. Therefore, it is unequivocally proven that the major, if not the sole, pathway of beta-carotene cleavage to vitamin A is by oxidative cleavage of the central ethylenic bond of beta-carotene to yield two molecules of retinal. Most recently, human dioxygenase has also been cloned. Thus, the wisdom, vision and epoch-making mission of Jim Olson in the science of beta-carotene metabolism have been accomplished. I have no doubt that the impact of his original discovery of the dioxygenase and its importance in vitamin A nutriture should be forthcoming in the near future. PMID:14704327

  2. Electrochemical cleavage of aryl ethers promoted by sodium borohydride.

    PubMed

    Wu, Wen-Bin; Huang, Jing-Mei

    2014-11-01

    The NaBH4 (or TBABH4)-promoted electrochemically reductive cleavage of aryl C-O bonds in diaryl ethers to produce phenols and arenes with high yields and excellent selectivities at room temperature was reported. Air- and water-tolerable, this process also works on the cleavage of aryl alkyl and benzyl ethers. The application to break the β-O-4, α-O-4, and 4-O-5 lignin model compounds is also illustrated, which highlights the advance toward the goal of lignin conversion. PMID:25317950

  3. Ammonia cleaves polypeptides at asparagine proline bonds.

    PubMed

    Tarelli, E; Corran, P H

    2003-12-01

    Polypeptides that contain the sequence Asn-Pro undergo complete cleavage at this amide bond with ammonia. One cleavage product possesses Pro as the new amino terminus and the other Asn or isoAsn as the new C-terminus, the formation of the latter probably arising by way of a cyclic succinimide intermediate. Other Asn-X bonds where X = Tyr, Gln, Ile, Glu, Ala, Gly, Asn or Phe did not exhibit any peptide bond cleavage, whereas when X = Leu, Thr and Ser partial cleavage was observed. Asn residues not involved in chain-cleavage underwent deamidation to Asp as shown by MALDI-ToF mass spectrometry (MS) analysis. The partial conversion of in-chain Asp residues to isoAsp under the reaction conditions was inferred from RP-HPLC and MS analysis of reaction mixtures. PMID:14632927

  4. Invasive cleavage of nucleic acids

    SciTech Connect

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    2002-01-01

    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 structure-specific 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.

  5. Invasive cleavage of nucleic acids

    SciTech Connect

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

    1999-01-01

    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 structure-specific 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.

  6. Design and synthesis of quasi-diastereomeric molecules with unchanging central, regenerating axial and switchable helical chirality via cleavage and formation of Ni(II)–O and Ni(II)–N coordination bonds

    PubMed Central

    Aceña, José Luis; Ueki, Hisanori; Han, Jianlin

    2012-01-01

    Summary We describe herein the design and synthesis of asymmetric, pentadentate ligands, which are able to coordinate to Ni(II) cations leading to quasi-diastereomeric complexes displaying two new elements of chirality: stereogenic axis and helix along with configurational stabilization of the stereogenic center on the nitrogen. Due to the stereocongested structural characteristics of the corresponding Ni(II) complexes, the formation of quasi-diastereomeric products is highly stereoselective providing formation of only two, (R a*,M h*,R c*) and (R a*,P h*,R c*), out of the four possible stereochemical combinations. The reversible quasi-diastereomeric transformation between the products (R a*,M h*,R c*) and (R a*,P h*,R c*) occurs by intramolecular trans-coordination of Ni–NH and Ni–O bonds providing a basis for a chiral switch model. PMID:23209532

  7. Mutational analysis of a type II topoisomerase cleavage site: distinct requirements for enzyme and inhibitors.

    PubMed Central

    Freudenreich, C H; Kreuzer, K N

    1993-01-01

    We have analyzed the DNA sequence requirements for cleavage of a 30 bp oligonucleotide that contains a strong bacteriophage T4 type II topoisomerase site. A novel method was used to generate substrates with each of the four nucleotides at 10 positions surrounding the cleavage site, and mutant substrates were also prepared for the four internal positions of the staggered cleavage site. The substrates were tested for cleavage in the presence of several inhibitors that induce enzyme-mediated cleavage: four antitumor agents of different classes (an aminoacridine, a substituted anthraquinone, an ellipticine derivative and an epipodophyllotoxin) and one antibacterial quinolone. At eight nucleotide positions flanking the cleavage site, the same preferred bases were found regardless of which inhibitor was present. These preferred bases show dyad symmetry with respect to the cleavage site, indicating that both protomers of the topoisomerase homodimer interact with DNA in an analogous manner. In addition, we found that the preferred bases on the 5' side of each cleaved phosphodiester bond are highly specific to the inhibitor used in the cleavage reaction. These results strongly suggest that the inhibitors interact directly with the DNA bases at the cleavage site, placing the inhibitor binding site precisely at the site of DNA cleavage. Images PMID:8387918

  8. Binding of substrate in two conformations to human prothrombinase drives consecutive cleavage at two sites in prothrombin.

    PubMed

    Orcutt, Steven J; Krishnaswamy, Sriram

    2004-12-24

    Thrombin formation results from cleavage of prothrombin following Arg(271) and Arg(320). Both bonds are accessible for cleavage, yet the sequential action of prothrombinase on Arg(320) followed by Arg(271) is implied by the intermediate observed during prothrombin activation. We have studied the individual cleavage reactions catalyzed by prothrombinase by using a series of recombinant derivatives: wild type prothrombin (II(WT)) contained both cleavage sites; II(Q271) contained a single cleavable site at Arg(320); II(Q320) and II(A320) contained a single cleavable site at Arg(271); and II(QQ) was resistant to cleavage. Cleavage at Arg(320) in II(Q271) could account for the initial cleavage reaction leading to the consumption of either plasma prothrombin or II(WT), whereas cleavage at Arg(271) in either II(Q320) or II(A320) was found to be approximately 30-fold slower. Equivalent kinetic constants were obtained for three of the four possible half-reactions. Slow cleavage at Arg(271) in intact prothrombin resulted from an approximately 30-fold reduction in V(max). Thus, the observed pathway of bond cleavage by prothrombinase can be explained by the kinetic constants for the four possible individual cleavage reactions. II(Q320) was a competitive inhibitor of II(Q271) cleavage, and II(QQ) was a competitive inhibitor for each reaction with K(i) approximately K(m). The data are inconsistent with previous proposals and suggest a model in which substrates for each of the four possible half-reactions bind in a mutually exclusive manner and with equal affinity to prothrombinase in a cleavage site-independent way. Despite equivalent exosite binding interactions between all four possible substrates and the enzyme, we propose that ordered bond cleavage results from the constraints associated with the binding of substrates in one of two conformations to a single form of prothrombinase. PMID:15494418

  9. Densification Behavior and Performances of C/C Composites Derived from Various Carbon Matrix Precursors

    NASA Astrophysics Data System (ADS)

    Shao, H. C.; Xia, H. Y.; Liu, G. W.; Qiao, G. J.; Xiao, Z. C.; Su, J. M.; Zhang, X. H.; Li, Y. J.

    2014-01-01

    Three types of carbon/carbon (C/C) composites were manufactured by densifying the needled carbon fiber preform through resin and pitch impregnation/carbonization repeatedly, as well as propylene pyrolysis by chemical vapor infiltration plus carbonization after the resin impregnation/carbonization. The densification behavior and performances (involving electric, thermal, and mechanical properties, as well as impurity) of the C/C composites were investigated systematically. The results show that besides the processing and testing conditions, the electric resistivity, thermal conductivity (TC), coefficient of thermal expansion (CTE), strength, and fracture, as well as impurity content and composition of the C/C composites were closely related to the fiber orientation, interfacial bonding between carbon fiber and carbon matrix, material characteristics of the three precursors and the resulting matrix carbons. In particular, the resin-carbon matrix C/C (RC/C) composites had the highest electric resistivity, tensile, and flexural strength, as well as impurity content. Meanwhile, the pitch-carbon matrix C/C (PC/C) composites possessed the highest TC and CTE in the parallel and vertical direction. And most of the performances of pyro-carbon/resin carbon matrix C/C composites were between those of the RC/C and PC/C composites except the impurity content.

  10. Modeling the Active Sites in Metalloenzymes 5. The Heterolytic Bond Cleavage of H2 in the [NiFe] Hydrogenase of DesulfoWibrio gigas by a Nucleophilic Addition Mechanism

    SciTech Connect

    Niu, Shuqiang; Hall, Michael B.

    2001-11-19

    The H2 activation catalyzed by an Fe(II)-Ni(III) model of the [NiFe] hydrogenase of DesulfoVibrio gigas has been investigated by density functional theory (DFT/B3LYP) calculations on the neutral and anionic active site complexes, [(CO)(CN)2Fe(Mu-SH)2Ni(SH)(SH2)]0 and [(CO)(CN)2Fe(Mu-SH)2Ni(SH)2]-. The results suggest that the reaction proceeds by a nucleophilic addition mechanism that cleaves the H-H bond heterolytically. The terminal cysteine residue Cys530 in the [NiFe] hydrogenase active site of the D. gigas enzyme plays a crucial role in the catalytic process by accepting the proton. The active site is constructed to provide access by this cysteine residue, and this role explains the change in activity observed when this cysteine is replaced by a selenocysteine. Furthermore, the optimized geometry of the transition state in the model bears a striking resemblance to the geometry of the active site as determined by X-ray crystallography.

  11. Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

    PubMed

    Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

    2016-02-23

    In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL. PMID:26820485

  12. Selective cleavage enhanced by acetylating the side chain of lysine.

    PubMed

    Fu, Leixiaomeng; Chen, Tingting; Xue, Gaiqing; Zu, Lily; Fang, Weihai

    2013-01-01

    Selective cleavage is of great interest in mass spectrometry studies as it can help sequence identification by promoting simple fragmentation pattern of peptides and proteins. In this work, the collision-induced dissociation of peptides containing internal lysine and acetylated lysine residues were studied. The experimental and computational results revealed that multiple fragmentation pathways coexisted when the lysine residue was two amino acid residues away from N-terminal of the peptide. After acetylation of the lysine side-chain, b(n)+ ions were the most abundant primary fragment products and the Lys(Ac)-Gly amide bond became the dominant cleavage site via an oxazolone pathway. Acetylating the side-chain of lysine promoted the selective cleavage of Lys-Xxx amide bond and generated much more information of the peptide backbone sequence. The results re-evaluate the selective cleavage due to the lysine basic side-chain and provide information for studying the post-translational modification of proteins and other bio-molecules containing Lys residues. PMID:23303756

  13. Autyomatic Differentiation of C/C++

    Energy Science and Technology Software Center (ESTSC)

    2005-11-14

    Automatic differentiation (AD) tools mechanize the process of developing code for the computation of derivatives. AD avoids the inaccuracies inherent in numerical approximations. Furthermore, sophisticated AD algoirthms can often produce c ode that is more reliable and more efficient than code written by an expert programmer. ADIC is the first and only AD tool for C and C++ based on compiler technology. This compiler foundation makes possible analyses and optimizations not available in toos basedmore » on operator overloading. The earliest implementations of ADIC included support for ANSI C applications, ADIC 2.0 lverages EDG, a commercial C/C++ parser, to provide robust C++ differentiation support. Modern AD tools, including ADIC are implemented in a modular way, aiming to isolate language-dependent program analyses and semantic transformations. The component design leads to much higher implementation quality because the different components can be implemented by experts in each of the different domains involved. For example, a compiler expert can focus on parsing, canonicalizing, and unparising C and C++, while an expert in graph theory and algorithms can produce new differentiation modules without having to worry about the complexity of parsing and generating C++ code. Thsi separation of concerns was achieved through the use of language-independent program analysis interfaces (in collaboration with researcgers at Rice University) and a language-independent XML representation of the computational portions of programs (XAIF). In addition to improved robustness and faster development times, this design naturally enables the reuse of program analysis algorithms and differentiation modules in compiler-based AD tools for other languages. In fact, the analysis and differention components are used in both ADIC and the Open AD Fortran front-end (based on Rice's Open64 compiler.« less

  14. C-H bond activation as the initial step in the Co sup + -mediated demethanation of propane: The critical role of angular momentum at the rate-limiting transition state

    SciTech Connect

    van Koppen, P.A.M.; Brodbelt-Lustig, J.; Bowers, M.T. ); Dearden, D.V.; Beauchamp, J.L. ); Fisher, E.R.; Armentrout, P.B. )

    1990-07-04

    Exothermic reactions of transition-metal ions with alkanes have in many instances been shown to be facile in the gas phase. Reactions mainly result in the loss of molecular hydrogen and small alkanes to yield metal ion-olefin complexes. A variety of experimental techniques have provided thermochemical, kinetic, dynamic, and mechanistic information for these reactions, with an important focus being the identification of the initial activation step. The question of C-H versus C-C bond activation as the initial step in the formation of C-C bond cleavage products has yet to be resolved. The authors have measured reaction cross sections and kinetic energy release distributions for the exothermic reactions of Co{sup +} with propane, propane-2-d{sub 1}, propane-2,2-d{sub 2}, propane-1,1,1-d{sub 3}, propane-1,1,1,3,3,3-d{sub 6}, and propane-d{sub 8}.

  15. Rhodium-catalyzed C-C coupling reactions via double C-H activation.

    PubMed

    Li, Shuai-Shuai; Qin, Liu; Dong, Lin

    2016-05-18

    Various rhodium-catalyzed double C-H activations are reviewed. These powerful strategies have been developed to construct C-C bonds, which might be widely embedded in complex aza-fused heterocycles, polycyclic skeletons and heterocyclic scaffolds. In particular, rhodium(iii) catalysis shows good selectivity and reactivity to functionalize the C-H bond, generating reactive organometallic intermediates in most of the coupling reactions. Generally, intermolecular, intramolecular and multi-component coupling reactions via double C-H activations with or without heteroatom-assisted chelation are discussed in this review. PMID:27099126

  16. Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease

    PubMed Central

    Kuznetsova, Irina L.; Zenkova, Marina A.; Gross, Hans J.; Vlassov, Valentin V.

    2005-01-01

    Cleavage of phosphodiester bonds by small ribonuclease mimics within different bulge-loops of RNA was investigated. Bulge-loops of different size (1–7 nt) and sequence composition were formed in a 3′ terminal fragment of influenza virus M2 RNA (96 nt) by hybridization of complementary oligodeoxynucleotides. Small bulges (up to 4 nt) were readily formed upon oligonucleotide hybridization, whereas hybridization of the RNA to the oligonucleotides designed to produce larger bulges resulted in formation of several alternative structures. A synthetic ribonuclease mimic displaying Pyr–Pu cleavage specificity cleaved CpA motifs located within bulges faster than similar motifs within the rest of the RNA. In the presence of 10 mM MgCl2, 75% of the cleavage products resulted from the attack of this motif. Thus, selective RNA cleavage at a single target phosphodiester bond was achieved by using bulge forming oligonucleotides and a small ribonuclease A mimic. PMID:15731340

  17. Potential energy surfaces for CH bond cleavage reactions

    SciTech Connect

    Harding, L.B.

    1996-12-31

    Ab initio, multi-reference, configuration interaction calculations are reported for CH{sub 4}{leftrightarrow}CH{sub 3}+H, CH{sub 3}F{leftrightarrow}CH{sub 2}F+H, CH{sub 2}F{sub 2}{leftrightarrow}CHF{sub 2}+H, and CHF{sub 3}{leftrightarrow}CF{sub 3}+H. Two equivalent, barrier-less paths are found for the CH{sub 3}+H recombination, two inequivalent, barrier-less paths are found for the CH{sub 2}F+H and CHF{sub 2}+H recombinations (depending on which side of the radical the H atom approaches), and only one barrier-less path is found for the CF{sub 3}+H recombination. Minimum energy path for H atom approaching CF{sub 3} from the concave side is predicted to have a barrier of 27 kcal/mole. Both minimum energy path energies and transitional frequencies as function of R{sub CH} for all 4 reactions are predicted to be similar.

  18. The Chemical Bond in C2.

    PubMed

    Hermann, Markus; Frenking, Gernot

    2016-03-14

    Quantum chemical calculations using the complete active space of the valence orbitals have been carried out for Hn CCHn (n=0-3) and N2 . The quadratic force constants and the stretching potentials of Hn CCHn have been calculated at the CASSCF/cc-pVTZ level. The bond dissociation energies of the C-C bonds of C2 and HC≡CH were computed using explicitly correlated CASPT2-F12/cc-pVTZ-F12 wave functions. The bond dissociation energies and the force constants suggest that C2 has a weaker C-C bond than acetylene. The analysis of the CASSCF wavefunctions in conjunction with the effective bond orders of the multiple bonds shows that there are four bonding components in C2 , while there are only three in acetylene and in N2 . The bonding components in C2 consist of two weakly bonding σ bonds and two electron-sharing π bonds. The bonding situation in C2 can be described with the σ bonds in Be2 that are enforced by two π bonds. There is no single Lewis structure that adequately depicts the bonding situation in C2 . The assignment of quadruple bonding in C2 is misleading, because the bond is weaker than the triple bond in HC≡CH. PMID:26756311

  19. Zener relaxation strength in B.C.C. and F.C.C. alloys under torsional and longitudinal excitations

    SciTech Connect

    Povolo, F.; Mosca, H.O.

    1994-01-01

    Calculations of the intensity of the Zener relaxation strength in b.c.c. and f.c.c. alloys are presented. Welch and Le Claire theory for the relaxation strength of shear modulus in f.c.c. alloys is extended to include the relaxation strength of Young`s and bulk modulus. A complete set of equations is given to be used for calculation of the relaxation strength of all the moduli in b.c.c. alloys. Finally, some applications to experimental data in both alloys systems are presented.

  20. Zero Steric Potential and bond order

    NASA Astrophysics Data System (ADS)

    Ghasemi, S.; Noorizadeh, S.

    2016-05-01

    The variation of Zero Steric Potential (ZSP) through a C-C bond shows two maximums, which their values depend on the bond order (BO). A good relationship (R2 = 1) is observed between the mean values of maximum ZSPs and the bond orders of C-C bonds in ethane, ethylene and acetylene, as reference molecules (Ln BO = 1.956ZSP‾max - 0.898). The obtained equation is used to predict the C-C bond orders of more than twenty aromatic and aliphatic hydrocarbons. The results show that the obtained bond orders from ZSP‾max are more reliable than those which are evaluated using NBO and Laplacian methods.

  1. Mechanistic Analysis of Oxidative CH Cleavages Using Inter- and Intramolecular Kinetic Isotope Effects

    PubMed Central

    Jung, Hyung Hoon; Floreancig, Paul E.

    2009-01-01

    A series of monodeuterated benzylic and allylic ethers were subjected to oxidative carbonhydrogen bond cleavage to determine the impact of structural variation on intramolecular kinetic isotope effects in DDQ-mediated cyclization reactions. These values are compared to the corresponding intermolecular kinetic isotope effects that were accessed through subjecting mixtures of non-deuterated and dideuterated substrates to the reaction conditions. The results indicate that carbonhydrogen bond cleavage is rate determining and that a radical cation is most likely a key intermediate in the reaction mechanism. PMID:20640173

  2. Modelling of c-C2H4O formation on grain surfaces

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    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.

  3. Centralspindlin in Rappaport's cleavage signaling.

    PubMed

    Mishima, Masanori

    2016-05-01

    Cleavage furrow in animal cell cytokinesis is formed by cortical constriction driven by contraction of an actomyosin network activated by Rho GTPase. Although the role of the mitotic apparatus in furrow induction has been well established, there remain discussions about the detailed molecular mechanisms of the cleavage signaling. While experiments in large echinoderm embryos highlighted the role of astral microtubules, data in smaller cells indicate the role of central spindle. Centralspindlin is a constitutive heterotetramer of MKLP1 kinesin and the non-motor CYK4 subunit and plays crucial roles in formation of the central spindle and recruitment of the downstream cytokinesis factors including ECT2, the major activator of Rho during cytokinesis, to the site of division. Recent reports have revealed a role of this centralspindlin-ECT2 pathway in furrow induction both by the central spindle and by the astral microtubules. Here, a unified view of the stimulation of cortical contractility by this pathway is discussed. Cytokinesis, the division of the whole cytoplasm, is an essential process for cell proliferation and embryonic development. In animal cells, cytokinesis is executed using a contractile network of actin filaments driven by a myosin-II motor that constricts the cell cortex (cleavage furrow ingression) into a narrow channel between the two daughter cells, which is resolved by scission (abscission) [1-3]. The anaphase-specific organization of the mitotic apparatus (MA, spindle with chromosomes plus asters) positions the cleavage furrow and plays a major role in spatial coupling between mitosis and cytokinesis [4-6]. The nucleus and chromosomes are dispensable for furrow specification [7-10], although they contribute to persistent furrowing and robust completion in some cell types [11,12]. Likewise, centrosomes are not essential for cytokinesis, but they contribute to the general fidelity of cell division [10,13-15]. Here, classical models of cleavage furrow induction are outlined, and a unified view of the stimulation of cortical contractility by the centralspindlin-ECT2 pathway is discussed. PMID:26964770

  4. Luminescent (N^C^C) Gold(III) Complexes: Stabilized Gold(III) Fluorides.

    PubMed

    Kumar, Roopender; Linden, Anthony; Nevado, Cristina

    2015-11-23

    We report the design, synthesis, and application of a (N^C^C)-ligand framework able to stabilize highly electron-deprived gold(III) species. This novel platform enabled the preparation of C(sp(2) )-gold(III) fluorides for the first time in monomeric, easy-to-handle, bench-stable form by a Cl/F ligand-exchange reaction. Devoid of oxidative conditions or stoichiometric use of toxic Hg salts, this method was applied to the preparation of multiple [C(sp(2) )-Au(III) -F] complexes, which were used as mechanistic probes for the study of the unique properties and intrinsic reactivity of AuF bonds. The improved photophysical properties of [(N^C^C)Au(III) ] complexes compared to classical pincer (C^N^C)-Au systems paves the way for the design of new late-transition-metal-based OLEDs. PMID:26439538

  5. 7. Historic American Buildings Survey, C. C. Adams, Photographer August ...

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

    7. Historic American Buildings Survey, C. C. Adams, Photographer August 1931, SEED PACKING ROOM, Gift of New York State Department of Education. - Shaker North Family Washhouse (first), Shaker Road, New Lebanon, Columbia County, NY

  6. Photo-Fenton reaction of graphene oxide: a new strategy to prepare graphene quantum dots for DNA cleavage.

    PubMed

    Zhou, Xuejiao; Zhang, Yan; Wang, Chong; Wu, Xiaochen; Yang, Yongqiang; Zheng, Bin; Wu, Haixia; Guo, Shouwu; Zhang, Jingyan

    2012-08-28

    Graphene quantum dots (GQDs) are great promising in various applications owing to the quantum confinement and edge effects in addition to their intrinsic properties of graphene, but the preparation of the GQDs in bulk scale is challenging. We demonstrated in this work that the micrometer sized graphene oxide (GO) sheets could react with Fenton reagent (Fe(2+)/Fe(3+)/H(2)O(2)) efficiently under an UV irradiation, and, as a result, the GQDs with periphery carboxylic groups could be generated with mass scale production. Through a variety of techniques including atomic force microscopy, X-ray photoelectron spectroscopy, gas chromatography, ultraperformance liquid chromatography-mass spectrometry, and total organic carbon measurement, the mechanism of the photo-Fenton reaction of GO was elucidated. The photo-Fenton reaction of GO was initiated at the carbon atoms connected with the oxygen containing groups, and C-C bonds were broken subsequently, therefore, the reaction rate depends strongly on the oxidization extent of the GO. Given the simple and efficient nature of the photo-Fenton reaction of GO, this method should provide a new strategy to prepare GQDs in mass scale. As a proof-of-concept experiment, the novel DNA cleavage system using as-generated GQDs was constructed. PMID:22813062

  7. Does Electron Capture Dissociation Cleave Protein Disulfide Bonds?

    PubMed Central

    Ganisl, Barbara; Breuker, Kathrin

    2012-01-01

    Peptide and protein characterization by mass spectrometry (MS) relies on their dissociation in the gas phase into specific fragments whose mass values can be aligned as ‘mass ladders’ to provide sequence information and to localize possible posttranslational modifications. The most common dissociation method involves slow heating of even-electron (M+n H)n+ ions from electrospray ionization by energetic collisions with inert gas, and cleavage of amide backbone bonds. More recently, dissociation methods based on electron capture or transfer were found to provide far more extensive sequence coverage through unselective cleavage of backbone N–Cα bonds. As another important feature of electron capture dissociation (ECD) and electron transfer dissociation (ETD), their unique unimolecular radical ion chemistry generally preserves labile posttranslational modifications such as glycosylation and phosphorylation. Moreover, it was postulated that disulfide bond cleavage is preferred over backbone cleavage, and that capture of a single electron can break both a backbone and a disulfide bond, or even two disulfide bonds between two peptide chains. However, the proposal of preferential disulfide bond cleavage in ECD or ETD has recently been debated. The experimental data presented here reveal that the mechanism of protein disulfide bond cleavage is much more intricate than previously anticipated. PMID:24363980

  8. Copper-catalyzed, C-C coupling-based one-pot tandem reactions for the synthesis of benzofurans using o-iodophenols, acyl chlorides, and phosphorus ylides.

    PubMed

    Liu, Yunyun; Wang, Hang; Wan, Jie-Ping

    2014-11-01

    One-pot reactions involving acyl chlorides, phosphorus ylides, and o-iodophenols with copper catalysis have been established for the rapid synthesis of functionalized benzofurans. With all of these easily available and stable reactants, the construction of the target products has been accomplished via tandem transformations involving a key C-C coupling, leading to the formation of one C(sp(2))-C bond, one C(sp(2))-O bond, and one C ═ C bond. PMID:25279735

  9. Determination of the orientation of OH bond axes in layer silicates by infrared absorption

    USGS Publications Warehouse

    Serratosa, J.M.; Bradley, W.F.

    1958-01-01

    It is observed that, among the micas and related crystallizations, trioctahedral compositions exhibit an OH bond axis normal to the cleavage flake, with an infrared absorption frequency near 3700 cm.-1, but that dioctahedral compositions exhibit OH bond axes near the plane of the cleavage flake and of lesser absorption frequencies.

  10. Bent Bonds and Multiple Bonds.

    ERIC Educational Resources Information Center

    Robinson, Edward A.; Gillespie, Ronald J.

    1980-01-01

    Considers carbon-carbon multiple bonds in terms of Pauling's bent bond model, which allows direct calculation of double and triple bonds from the length of a CC single bond. Lengths of these multiple bonds are estimated from direct measurements on "bent-bond" models constructed of plastic tubing and standard kits. (CS)

  11. Testing of DLR C/C-SiC and C/C for HIFiRE 8 Scramjet Combustor

    NASA Technical Reports Server (NTRS)

    Glass, David E.; Capriotti, Diego P.; Reimer, Thomas; Kutemeyer, Marius; Smart, Michael K.

    2014-01-01

    Ceramic Matrix Composites (CMCs) have been proposed for use as lightweight hot structures in scramjet combustors. Previous studies have calculated significant weight savings by utilizing CMCs (active and passive) versus actively cooled metallic scramjet structures. Both a carbon/carbon (C/C) and a carbon/carbon-silicon carbide (C/C-SiC) material fabricated by DLR (Stuttgart, Germany) are being considered for use in a passively cooled combustor design for Hypersonic International Flight Research Experimentation (HIFiRE) 8, a joint Australia / Air Force Research Laboratory hypersonic flight program, expected to fly at Mach 7 for approximately 30 sec, at a dynamic pressure of 55 kilopascals. Flat panels of the DLR C/C and C/C-SiC materials were installed downstream of a hydrogen-fueled, dual-mode scramjet combustor and tested for several minutes at conditions simulating flight at Mach 5 and Mach 6. Gaseous hydrogen fuel was used to fuel the scramjet combustor. The test panels were instrumented with embedded Type K and Type S thermocouples. Zirconia felt insulation was used during some of the tests to reduce heat loss from the back surface and thus increase the heated surface temperature of the C/C-SiC panel approximately 177 C (350 F). The final C/C-SiC panel was tested for three cycles totaling over 135 sec at Mach 6 enthalpy. Slightly more erosion was observed on the C/C panel than the C/C-SiC panels, but both material systems demonstrated acceptable recession performance for the HIFiRE 8 flight.

  12. The mechanism of brittle fracture in a microalloyed steel: Part 1. Inclusion-induced cleavage

    SciTech Connect

    Fairchild, D.P.; Howden, D.G.; Clark, W.A.T.

    2000-03-01

    The cleavage resistance of two microalloyed steels (steels A and B) was studied using several tests, including the instrumented precracked Charpy and Charpy V-notch (CVN) techniques. Ductile-to-brittle transition temperatures were measured for the base-metal and simulated heat-affected zone (HAZ) microstructures. Steel B showed inferior cleavage resistance to steel A, and this could not be explained by differences in gross microstructure. Scanning electron fractography revealed that TiN inclusions were responsible for cleavage initiation in steel B. These inclusions were well bonded to the ferritic matrix. It is believed that a strong inclusion-matrix bond is a key factor in why TiN inclusions are potent cleavage initiators in steel. Strong bonding allows high stresses in a crack/notch-tip plastic zone to act on the inclusions without debonding the interface. Once an inclusion cleaves, the strong bond allows for transfer of the TiN crack into the ferritic matrix. It was estimated that only 0.0016 wt pct Ti was tied up in the offending inclusion in steel B. This indicates that extended times at high temperatures during the casting of such steels could produce TiN-related toughness deterioration at even modest Ti contents.

  13. Regioselective Lithium-Iodine Exchange-Initiated Cleavage of 2-Iodomethyl-1,3-dioxanes: A Complex-Induced Proximity Effect.

    PubMed

    Bailey, William F; Fair, Justin D

    2016-05-01

    Lithium-iodine exchange-initiated fragmentation of a series of 4-substituted 2-iodomethyl-1,3-dioxanes proceeds rapidly and regioselectively to afford enol ether alcohols by preferential cleavage of the less congested C(2)-O(1) bond. The results demonstrate that a complex-induced proximity effect (CIPE) is likely responsible for the selectivity of the cleavage. PMID:27074433

  14. Bismuth(iii)dichalcogenones as highly active catalysts in multiple C-C bond formation reactions.

    PubMed

    Srinivas, Katam; Sathyanarayana, Arruri; Naga Babu, Chatla; Prabusankar, Ganesan

    2016-03-15

    Thirteen new bismuth(iii) dichalcogenone derivatives of triflates and halides were synthesized and structurally characterized. The mono, di, tetra and heptanuclear complexes were isolated with different bismuth(iii) coordination environments. These newly isolated bismuth(iii)dichalcogenones were characterized by multinuclear NMR, FT-IR, UV-vis, TGA and single crystal X-ray diffraction techniques. These complexes were tested for the synthesis of symmetrical triaryl- or triheteroarylmethanes and the catalysts were found to be highly active. In particular, the selone complexes were relatively more active than thione complexes. Subsequently, the scope of the catalytic reactions was further explored with different substituents. PMID:26891252

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

    PubMed Central

    RajanBabu, T. V.

    2009-01-01

    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

  16. Characterization of Brazed Joints of C-C Composite to Cu-clad-Molybdenum

    NASA Technical Reports Server (NTRS)

    Singh, M.; Asthana, R.

    2008-01-01

    Carbon-carbon composites with either pitch+CVI matrix or resin-derived matrix were joined to copper-clad molybdenum using two active 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 de-lamination in resin-derived C-C composite due to its low inter-laminar shear strength. Extensive braze penetration of the inter-fiber channels in the pitch+CVI C-C composites was observed. The relatively low brazing temperatures (<950 C) precluded melting of the clad layer and restricted the redistribution of alloying elements but led to metallurgically sound composite joints. The Knoop microhardness (HK) distribution across the joint interfaces revealed sharp gradients at the Cu-clad-Mo/braze interface and higher hardness in Ticusil (approx.85-250 HK) than in Cusil-ABA (approx.50-150 HK). These C-C/Cu-clad-Mo joints with relatively low thermal resistance may be promising for thermal management applications.

  17. Rhodium-catalyzed C-H activation of phenacyl ammonium salts assisted by an oxidizing C-N bond: a combination of experimental and theoretical studies.

    PubMed

    Yu, Songjie; Liu, Song; Lan, Yu; Wan, Boshun; Li, Xingwei

    2015-02-01

    Rh(III)-catalyzed C-H activation assisted by an oxidizing directing group has evolved to a mild and redox-economic strategy for the construction of heterocycles. Despite the success, these coupling systems are currently limited to cleavage of an oxidizing N-O or N-N bond. Cleavage of an oxidizing C-N bond, which allows for complementary carbocycle synthesis, is unprecedented. In this article, α-ammonium acetophenones with an oxidizing C-N bond have been designed as substrates for Rh(III)-catalyzed C-H activation under redox-neutral conditions. The coupling with α-diazo esters afforded benzocyclopentanones, and the coupling with unactivated alkenes such as styrenes and aliphatic olefins gave ortho-olefinated acetophenoes. In both systems the reactions proceeded with a broad scope, high efficiency, and functional group tolerance. Moreover, efficient one-pot coupling of diazo esters has been realized starting from α-bromoacetophenones and triethylamine. The reaction mechanism for the coupling with diazo esters has been studied by a combination of experimental and theoretical methods. In particular, three distinct mechanistic pathways have been scrutinized by DFT studies, which revealed that the C-H activation occurs via a C-bound enolate-assisted concerted metalation-deprotonation mechanism and is rate-limiting. In subsequent C-C formation steps, the lowest energy pathway involves two rhodium carbene species as key intermediates. PMID:25569022

  18. Interstellar Detection of c-C3D2

    NASA Astrophysics Data System (ADS)

    Spezzano, S.; Brünken, S.; Schilke, P.; Caselli, P.; Menten, K. M.; McCarthy, M. C.; Bizzocchi, L.; Trevinõ-Morales, S. P.; Aikawa, Y.; Schlemmer, S.

    2013-06-01

    We report the first interstellar detection of c-C3D2. Doubly deuterated cyclopropenylidene, a carbene, has been detected toward the starless cores TMC-1C and L1544 using the IRAM 30 m telescope. The J_{K_a,K_c} = 3_{0,3} {--} 2_{1,2}, 31, 3-20, 2, and 22, 1-11, 0 transitions of this species have been observed at 3 mm in both sources. The expected 1:2 intensity ratio has been found in the 30, 3-21, 2 and 31, 3-20, 2 lines, belonging to the para and ortho species, respectively. We also observed lines of the main species, c-C3H2, singly deuterated c-C3HD, and the species with one 13C off of the principal axis of the molecule, c-H13CC2H. The lines of c-C3D2 have been observed with high signal-to-noise ratio, better than 7.5σ in TMC-1C and 9σ in L1544. The abundance of doubly deuterated cyclopropenylidene with respect to the normal species is found to be 0.4%-0.8% in TMC-1C and 1.2%-2.1% in L1544. The deuteration of this small hydrocarbon ring is analyzed with a comprehensive gas-grain model, the first including doubly deuterated species. The observed abundances of c-C3D2 can be explained solely by gas-phase processes, supporting the idea that c-C3H2 is a good indicator of gas-phase deuteration. Based on observations carried out with the IRAM 30 m Telescope. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).

  19. Aerobic Copper-Promoted Radical-Type Cleavage of Coordinated Cyanide Anion: Nitrogen Transfer to Aldehydes To Form Nitriles.

    PubMed

    Wu, Qian; Luo, Yi; Lei, Aiwen; You, Jingsong

    2016-03-01

    We have disclosed for the first time the copper-promoted C≡N triple bond cleavage of coordinated cyanide anion under a dioxygen atmosphere, which enables a nitrogen transfer to various aldehydes. Mechanistic study of this unprecedented transformation suggests that the single electron-transfer process could be involved in the overall course. This protocol provides a new cleavage pattern for the cyanide ion and would eventually lead to a more useful synthetic pathway to nitriles from aldehydes. PMID:26907853

  20. Autoactivation of mouse trypsinogens is regulated by chymotrypsin C via cleavage of the autolysis loop.

    PubMed

    Nmeth, Balzs Csaba; Wartmann, Thomas; Halangk, Walter; Sahin-Tth, Mikls

    2013-08-16

    Chymotrypsin C (CTRC) is a proteolytic regulator of trypsinogen autoactivation in humans. CTRC cleavage of the trypsinogen activation peptide stimulates autoactivation, whereas cleavage of the calcium binding loop promotes trypsinogen degradation. Trypsinogen mutations that alter these regulatory cleavages lead to increased intrapancreatic trypsinogen activation and cause hereditary pancreatitis. The aim of this study was to characterize the regulation of autoactivation of mouse trypsinogens by mouse Ctrc. We found that the mouse pancreas expresses four trypsinogen isoforms to high levels, T7, T8, T9, and T20. Only the T7 activation peptide was cleaved by mouse Ctrc, causing negligible stimulation of autoactivation. Surprisingly, mouse Ctrc poorly cleaved the calcium binding loop in all mouse trypsinogens. In contrast, mouse Ctrc readily cleaved the Phe-150-Gly-151 peptide bond in the autolysis loop of T8 and T9 and inhibited autoactivation. Mouse chymotrypsin B also cleaved the same peptide bond but was 7-fold slower. T7 was less sensitive to chymotryptic regulation, which involved slow cleavage of the Leu-149-Ser-150 peptide bond in the autolysis loop. Modeling indicated steric proximity of the autolysis loop and the activation peptide in trypsinogen, suggesting the cleaved autolysis loop may directly interfere with activation. We conclude that autoactivation of mouse trypsinogens is under the control of mouse Ctrc with some notable differences from the human situation. Thus, cleavage of the trypsinogen activation peptide or the calcium binding loop by Ctrc is unimportant. Instead, inhibition of autoactivation via cleavage of the autolysis loop is the dominant mechanism that can mitigate intrapancreatic trypsinogen activation. PMID:23814066

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

    NASA Technical Reports Server (NTRS)

    Chraska, P.; Mclellan, R. B.

    1971-01-01

    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.

  2. Biomass Oxidation: Formyl C-H Bond Activation by the Surface Lattice Oxygen of Regenerative CuO Nanoleaves.

    PubMed

    Amaniampong, Prince N; Trinh, Quang Thang; Wang, Bo; Borgna, Armando; Yang, Yanhui; Mushrif, Samir H

    2015-07-27

    An integrated experimental and computational investigation reveals that surface lattice oxygen of copper oxide (CuO) nanoleaves activates the formyl C-H bond in glucose and incorporates itself into the glucose molecule to oxidize it to gluconic acid. The reduced CuO catalyst regains its structure, morphology, and activity upon reoxidation. The activity of lattice oxygen is shown to be superior to that of the chemisorbed oxygen on the metal surface and the hydrogen abstraction ability of the catalyst is correlated with the adsorption energy. Based on the present investigation, it is suggested that surface lattice oxygen is critical for the oxidation of glucose to gluconic acid, without further breaking down the glucose molecule into smaller fragments, because of C-C cleavage. Using CuO nanoleaves as catalyst, an excellent yield of gluconic acid is also obtained for the direct oxidation of cellobiose and polymeric cellulose, as biomass substrates. PMID:26119659

  3. Pre-mRNA 3’ Cleavage is Reversibly Inhibited In Vitro by Cleavage Factor Dephosphorylation

    PubMed Central

    Ryan, Kevin

    2016-01-01

    During 3' end formation most pre-mRNAs undergo endonucleolytic cleavage and polyadenylation in the 3' untranslated region. Very little is known concerning the role that post-translational modifications play in the function and regulation of the factors required for 3' cleavage. Using the reconstituted pre-mRNA cleavage reaction, we find that non-specific dephosphorylation of HeLa cell nuclear extract leads to the loss of 3' cleavage activity. A variety of serine/threonine phosphatases inhibited cleavage activity, while a tyrosine phosphatase did not. When the three major cleavage factor activities—CPSF, CstF and CFm (containing CFIm and CFIIm)—were separated and dephosphorylated individually, only CFm was found to lose activity, indicating that the target of dephosphorylation resides within this fraction. In accordance with this result, only CFm was able to restore cleavage activity to HeLa nuclear extract whose 3' cleavage activity had been completely inactivated by dephosphorylation. We conclude that at least one subunit of either CFIm or CFIIm requires serine or threonine phosphorylation to function during 3' cleavage. Our data suggest that cleavage factor phosphorylation may serve as a regulatory on/off switch to control pre-mRNA 3' end formation. PMID:17585202

  4. [Recent knowledge about intestinal absorption and cleavage of carotenoids].

    PubMed

    Borel, P; Drai, J; Faure, H; Fayol, V; Galabert, C; Laromiguière, M; Le Moël, G

    2005-01-01

    Our knowledge about intestinal absorption and cleavage of carotenoids has rapidly grown during the last years. New facts about carotenoid absorption have emerged while some controversies about cleavage are close to end. The knowledge of the absorption and conversion processes is indispensable to understand and interpret the perturbations that can occur in the metabolism of carotenoids and vitamin A. Recently, it has been shown that the absorption of certain carotenoids is not passive - as believed for a long time - but is a facilitated process that requires, at least for lutein, the class B-type 1 scavenger receptor (SR-B1). Various epidemiological and clinical studies have shown wide variations in carotenoid absorption from one subject to another, such differences are now explained by the structure of the concerned carotenoid, by the nature of the food that is absorbed with the carotenoid, by diverse exogenous factors like the intake of medicines or interfering components, by diet factors, by genetic factors, and by the nutritional status of the subject. Recently, the precise mechanism of beta-carotene cleavage by betabeta-carotene 15,15' monooxygenase (EC 1.14.99.36) - formerly called beta-carotene 15,15' dioxygenase (ex EC 1.13.11.21) - has been discovered, and a second enzyme which cleaves asymmetrically the beta-carotene molecule has been found. beta-carotene 15,15' monooxygenase only acts on the 15,15' bond, thus forming two molecules of retinal from one molecule of beta-carotene by central cleavage. Even though the betabeta-carotene 15,15' monooxygenase is much more active on the beta-carotene molecule, a study has shown that it can act on all carotenoids. Searchers now agree that other enzymes that can catalyse an eccentric cleavage of carotenoids probably exist, but under physiological conditions the betabeta-carotene 15,15' monooxygenase is by far the most active, and it is mainly effective in the small bowel mucosa and in the liver. However the conversion of provitamin A carotenoids into vitamin A is only partial, and requires a satisfactory protein status. PMID:15771974

  5. Phosphino imidazoles and imidazolium salts for Suzuki C-C coupling reactions.

    PubMed

    Milde, Bianca; Schaarschmidt, Dieter; Rüffer, Tobias; Lang, Heinrich

    2012-05-01

    The consecutive syntheses of imidazoles 1-(4-X-C(6)H(4))-4,5-R(2)-(c)C(3)HN(2) (3a, X = Br, R = H; 3b, X = I, R = Me; 3c, X = H, R = Me; 5, X = Fc, R = H; 7, X = C≡CFc, R = H; 9, X = C(6)H(5), R = Me; Fc = Fe(η(5)-C(5)H(4))(η(5)-C(5)H(5))), phosphino imidazoles 1-(4-X-C(6)H(4))-2-PR'(2)-4,5-R(2)-(c)C(3)N(2) (11a-k; X = Br, I, Fc, FcC≡C, Ph; R = H, Me; R' = Ph, (c)C(6)H(11), (c)C(4)H(3)O), imidazolium salts [1-(4-X-C(6)H(4))-3-R''-4,5-R(2)-(c)C(3)HN(2)]I (16a; X = Br, R = H, R'' = n-Bu; 16b, X = Br, R = H, R'' = n-C(8)H(17); 16c, X = I, R = Me, R'' = n-C(8)H(17), 16d, X = H, R = Me, R'' = n-C(8)H(17)) and phosphino imidazolium salts [1-C(6)H(5)-2-PR'(2)-3-n-C(8)H(17)-4,5-Me(2)-(c)C(3)N(2)]PF(6) (17a, R' = C(6)H(5); 17b, R' = (c)C(6)H(11)) or [1-(4-P(C(6)H(5))(2)-C(6)H(4))-3-n-C(8)H(17)-4,5-Me(2)-(c)C(3)HN(2)]PF(6), (20) and their selenium derivatives 1-(4-X-C(6)H(4))-2-P([double bond, length as m-dash]Se)R'(2)-4,5-R(2)-(c)C(3)N(2) (11a-Se-f-Se; X = Br, I; R = H, Me; R' = C(6)H(5), (c)C(6)H(11), (c)C(4)H(3)O) are reported. The structures of 11a-Se and [(1-(4-Br-C(6)H(4))-(c)C(3)H(2)N(2)-3-n-Bu)(2)PdI(2)] (19) in the solid state were determined. Cyclovoltammetric measurements were performed with the ferrocenyl-containing molecules 5 and 7 showing reversible redox events at E(0) = 0.108 V (ΔE(p) = 0.114 V) (5) and E(0) = 0.183 V (ΔE(p) = 0.102 V) (7) indicating that 7 is more difficult to oxidise. Imidazole oxidation does not occur up to 1.3 V in dichloromethane using [(n-Bu)(4)N][B(C(6)F(5))(4)] as supporting electrolyte, whereas an irreversible reduction is observed between -1.2 - -1.5 V. The phosphino imidazoles 11a-k and the imidazolium salts 17a,b and 20, respectively, were applied in the Suzuki C-C cross-coupling of 2-bromo toluene with phenylboronic acid applying [Pd(OAc)(2)] as palladium source. Depending on the electronic character of 11a-k, 17a,b and 20 the catalytic performance of the in situ generated catalytic active species can be predicted. As assumed, more electron-rich phosphines with their higher donor capability show higher activity and productivity. Additionally, 11e was applied in the coupling of 4-chloro toluene with phenylboronic acid showing an excellent catalytic performance when compared to catalysts used by Fu, Beller and Buchwald. Furthermore, 11e is eligible for the synthesis of sterically hindered biaryls under mild reaction conditions. C-C Coupling reactions with the phosphino imidazolium salts 17b and 20 in ionic liquids [BMIM][PF(6)] and [BDMIM][BF(4)] were performed, showing less activity than in common organic solvents. PMID:22450875

  6. [Study on spectral emissivity of C/C composites].

    PubMed

    Zhu, Bo; Cao, Wei-Wei; Jing, Min; Dong, Xing-Guang; Wang, Cheng-Guo

    2009-11-01

    Different types of C/C composites were prepared by conventional molding, and the changes in normal spectral emissivity of samples were tested. The testing results show that spectral emissivity of C/C composite reinforced by short cut carbon fibers is generally higher than the sample reinforced by carbon cloth in the entire 2500-13000nm wavelength region. The structure of short cut carbon fibers is relatively loose and the number of material particles is less than other samples in unit volume, which increases the penetration depth of electromagnetic waves. This is the reason for higher normal spectral emissivity and better heat radiation property. Meanwhile, the test results of normal spectral emissivity for fiber perform and C/C composite samples show that the spectral emissivity of resin carbon is better than fiber carbon because of the difference in microstructure for the two kinds of carbon materials. Laser Raman spectroscopy was employed to analyze the microstructures of different carbon materials, and the results show that because sp3 and sp2 hybrid states of carbon atoms in resin carbon produced more vibration modes, the resin carbon also has higher normal spectral emissivity and better characteristics of heat radiation. PMID:20101951

  7. Copper-Catalyzed S-C/S-N Bond Interconversions.

    PubMed

    Wen, Jian; Cheng, Hanchao; Dong, Shunxi; Bolm, Carsten

    2016-04-11

    Under an atmosphere of dioxygen, copper-catalyzed de-alkylation/amination sequences provide sulfonimidamides from unprotected sulfoximines in moderate to good yields. Mechanistic studies suggest the involvement of radicals in both the C-S bond cleavage and the formation of the new N-S bond. PMID:26892735

  8. Proteolytic Cleavage Driven by Glycosylation.

    PubMed

    Ktzler, Miriam P; Withers, Stephen G

    2016-01-01

    Proteolytic processing of human host cell factor 1 (HCF-1) to its mature form was recently shown, unexpectedly, to occur in a UDP-GlcNAc-dependent fashion within the transferase active site of O-GlcNAc-transferase (OGT) (Lazarus, M. B., Jiang, J., Kapuria, V., Bhuiyan, T., Janetzko, J., Zandberg, W. F., Vocadlo, D. J., Herr, W., and Walker, S. (2013) Science 342, 1235-1239). An interesting mechanism involving formation and then intramolecular rearrangement of a covalent glycosyl ester adduct of the HCF-1 polypeptide was proposed to account for this unprecedented proteolytic activity. However, the key intermediate remained hypothetical. Here, using a model enzyme system for which the formation of a glycosyl ester within the enzyme active site has been shown unequivocally, we show that ester formation can indeed lead to proteolysis of the adjacent peptide bond, thereby providing substantive support for the mechanism of HCF-1 processing proposed. PMID:26515062

  9. Quantification of C=C and C=O Surface Carbons in Detonation Nanodiamond by NMR

    SciTech Connect

    Cui, J -F; Fang, X -W; Schmidt-Rohr, K

    2014-05-08

    The ability of solid-state 13C NMR to detect and quantify small amounts of sp2-hybridized carbon on the surface of ~5 nm diameter nanodiamond particles is demonstrated. The C=C carbon fraction is only 1.1 ± 0.4% in pristine purified detonation nanodiamond, while a full single-layer graphitic or “bucky diamond” shell would contain ca. 25% of all C in a 5 nm diameter particle. Instead of large aromatic patches repeatedly proposed in the recent literature, sp3-hybridized CH and COH carbons cover most of the nanodiamond particle surface, accounting for ~5% each. C=O and COO groups also seen in X-ray absorption near-edge structure spectroscopy (XANES) but not detected in previous NMR studies make up ca. 1.5% of all C. They are removed by heat treatment at 800 °C, which increases the aromatic fraction. 13C{1H} NMR demonstrates that the various sp2-hybridized carbons are mostly not protonated, but cross-polarization shows that they are separated from 1H by only a few bond lengths, which proves that they are near the protonated surface. Together, the observed C–H, C–OH, C=O, and C=C groups account for 12–14% of all C, which matches the surface fraction expected for bulk-terminated 5 nm diameter diamond particles.

  10. Sequence-specific cleavage of dsRNA by Mini-III RNase

    PubMed Central

    G?w, Dawid; Pianka, Dariusz; Sulej, Agata A.; Koz?owski, ?ukasz P.; Czarnecka, Justyna; Chojnowski, Grzegorz; Skowronek, Krzysztof J.; Bujnicki, Janusz M.

    2015-01-01

    Ribonucleases (RNases) play a critical role in RNA processing and degradation by hydrolyzing phosphodiester bonds (exo- or endonucleolytically). Many RNases that cut RNA internally exhibit substrate specificity, but their target sites are usually limited to one or a few specific nucleotides in single-stranded RNA and often in a context of a particular three-dimensional structure of the substrate. Thus far, no RNase counterparts of restriction enzymes have been identified which could cleave double-stranded RNA (dsRNA) in a sequence-specific manner. Here, we present evidence for a sequence-dependent cleavage of long dsRNA by RNase Mini-III from Bacillus subtilis (BsMiniIII). Analysis of the sites cleaved by this enzyme in limited digest of bacteriophage ?6 dsRNA led to the identification of a consensus target sequence. We defined nucleotide residues within the preferred cleavage site that affected the efficiency of the cleavage and were essential for the discrimination of cleavable versus non-cleavable dsRNA sequences. We have also determined that the loop ?5b-?6, a distinctive structural element in Mini-III RNases, is crucial for the specific cleavage, but not for dsRNA binding. Our results suggest that BsMiniIII may serve as a prototype of a sequence-specific dsRNase that could possibly be used for targeted cleavage of dsRNA. PMID:25634891

  11. Distinct mechanisms for DNA cleavage by myoglobin with a designed heme active center.

    PubMed

    Zhao, Yuan; Du, Ke-Jie; Gao, Shu-Qin; He, Bo; Wen, Ge-Bo; Tan, Xiangshi; Lin, Ying-Wu

    2016-03-01

    Heme proteins perform diverse biological functions, of which myoglobin (Mb) is a representative protein. In this study, the O2 carrier Mb was shown to cleave double stranded DNA upon aerobic dithiothreitol-induced reduction, which is fine-tuned by an additional distal histidine, His29 or His43, engineered in the heme active center. Spectroscopic (UV-vis and EPR) and inhibition studies suggested that free radicals including singlet oxygen and hydroxyl radical are responsible for efficient DNA cleavage via an oxidative cleavage mechanism. On the other hand, L29E Mb, with a distinct heme active center involving three water molecules in the met form, was found to exhibit an excellent DNA cleavage activity that was not depending on O2. Inhibition and ligation studies demonstrated for the first time that L29E Mb cleaves double stranded DNA into both the nicked circular and linear forms via a hydrolytic cleavage mechanism, which resembles native endonucleases. This study provides valuable insights into the distinct mechanisms for DNA cleavage by heme proteins, and lays down a base for creating artificial DNA endonucleases by rational design of heme proteins. Moreover, this study suggests that the diverse functions of heme proteins can be fine-tuned by rational design of the heme active center with a hydrogen-bonding network. PMID:26775281

  12. Sequence-specific cleavage of dsRNA by Mini-III RNase.

    PubMed

    Głów, Dawid; Pianka, Dariusz; Sulej, Agata A; Kozłowski, Łukasz P; Czarnecka, Justyna; Chojnowski, Grzegorz; Skowronek, Krzysztof J; Bujnicki, Janusz M

    2015-03-11

    Ribonucleases (RNases) play a critical role in RNA processing and degradation by hydrolyzing phosphodiester bonds (exo- or endonucleolytically). Many RNases that cut RNA internally exhibit substrate specificity, but their target sites are usually limited to one or a few specific nucleotides in single-stranded RNA and often in a context of a particular three-dimensional structure of the substrate. Thus far, no RNase counterparts of restriction enzymes have been identified which could cleave double-stranded RNA (dsRNA) in a sequence-specific manner. Here, we present evidence for a sequence-dependent cleavage of long dsRNA by RNase Mini-III from Bacillus subtilis (BsMiniIII). Analysis of the sites cleaved by this enzyme in limited digest of bacteriophage Φ6 dsRNA led to the identification of a consensus target sequence. We defined nucleotide residues within the preferred cleavage site that affected the efficiency of the cleavage and were essential for the discrimination of cleavable versus non-cleavable dsRNA sequences. We have also determined that the loop α5b-α6, a distinctive structural element in Mini-III RNases, is crucial for the specific cleavage, but not for dsRNA binding. Our results suggest that BsMiniIII may serve as a prototype of a sequence-specific dsRNase that could possibly be used for targeted cleavage of dsRNA. PMID:25634891

  13. Bond Issues.

    ERIC Educational Resources Information Center

    Pollack, Rachel H.

    2000-01-01

    Notes trends toward increased borrowing by colleges and universities and offers guidelines for institutions that are considering issuing bonds to raise money for capital projects. Discussion covers advantages of using bond financing, how use of bonds impacts on traditional fund raising, other cautions and concerns, and some troubling aspects of…

  14. Sticker Bonding.

    ERIC Educational Resources Information Center

    Frazier, Laura Corbin

    2000-01-01

    Introduces a science activity on the bonding of chemical compounds. Assigns students the role of either a cation or anion and asks them to write the ions they may bond with. Assesses students' understanding of charge, bonding, and other concepts. (YDS)

  15. Does Cleavage Work at Work? Men, but Not Women, Falsely Believe Cleavage Sells a Weak Product

    ERIC Educational Resources Information Center

    Glick, Peter; Chrislock, Karyna; Petersik, Korinne; Vijay, Madhuri; Turek, Aleksandra

    2008-01-01

    We examined whether men, but not women, would be distracted by a female sales representative's exposed cleavage, leading to greater perceived efficacy for a weak, but not for a strong product. A community sample of 88 men and 97 women viewed a video of a female pharmaceutical sales representative who (a) had exposed cleavage or dressed modestly

  16. Does Cleavage Work at Work? Men, but Not Women, Falsely Believe Cleavage Sells a Weak Product

    ERIC Educational Resources Information Center

    Glick, Peter; Chrislock, Karyna; Petersik, Korinne; Vijay, Madhuri; Turek, Aleksandra

    2008-01-01

    We examined whether men, but not women, would be distracted by a female sales representative's exposed cleavage, leading to greater perceived efficacy for a weak, but not for a strong product. A community sample of 88 men and 97 women viewed a video of a female pharmaceutical sales representative who (a) had exposed cleavage or dressed modestly…

  17. Structural basis of cohesin cleavage by separase.

    PubMed

    Lin, Zhonghui; Luo, Xuelian; Yu, Hongtao

    2016-04-01

    Accurate chromosome segregation requires timely dissolution of chromosome cohesion after chromosomes are properly attached to the mitotic spindle. Separase is absolutely essential for cohesion dissolution in organisms from yeast to man. It cleaves the kleisin subunit of cohesin and opens the cohesin ring to allow chromosome segregation. Cohesin cleavage is spatiotemporally controlled by separase-associated regulatory proteins, including the inhibitory chaperone securin, and by phosphorylation of both the enzyme and substrates. Dysregulation of this process causes chromosome missegregation and aneuploidy, contributing to cancer and birth defects. Despite its essential functions, atomic structures of separase have not been determined. Here we report crystal structures of the separase protease domain from the thermophilic fungus Chaetomium thermophilum, alone or covalently bound to unphosphorylated and phosphorylated inhibitory peptides derived from a cohesin cleavage site. These structures reveal how separase recognizes cohesin and how cohesin phosphorylation by polo-like kinase 1 (Plk1) enhances cleavage. Consistent with a previous cellular study, mutating two securin residues in a conserved motif that partly matches the separase cleavage consensus converts securin from a separase inhibitor to a substrate. Our study establishes atomic mechanisms of substrate cleavage by separase and suggests competitive inhibition by securin. PMID:27027290

  18. α-Cleavage of cellular prion protein

    PubMed Central

    Liang, Jingjing; Kong, Qingzhong

    2012-01-01

    The cellular prion protein (PrPC) is subjected to various processing under physiological and pathological conditions, of which the α-cleavage within the central hydrophobic domain not only disrupts a region critical for both PrP toxicity and PrPC to PrPSc conversion but also produces the N1 fragment that is neuroprotective and the C1 fragment that enhances the pro-apoptotic effect of staurosporine in one report and inhibits prion in another. The proteases responsible for the α-cleavage of PrPC are controversial. The effect of ADAM10, ADAM17, and ADAM9 on N1 secretion clearly indicates their involvement in the α-cleavage of PrPC, but there has been no report of direct PrPC α-cleavage activity with any of the three ADAMs in a purified protein form. We demonstrated that, in muscle cells, ADAM8 is the primary protease for the α-cleavage of PrPC, but another unidentified protease(s) must also play a minor role. We also found that PrPC regulates ADAM8 expression, suggesting that a close examination on the relationships between PrPC and its processing enzymes may reveal novel roles and underlying mechanisms for PrPC in non-prion diseases such as asthma and cancer. PMID:23052041

  19. Isomerization of the diphosphine ligand 3,4-bis(diphenylphosphino)-5-methoxy-2(5H)-furanone (bmf) at a triosmium cluster and P C bond cleavage in the unsaturated cluster 1,1-Os3(CO)9(bmf): Synthesis and X-ray diffraction structures of the isomeric Os3(CO)10(bmf) clusters and HOs3(CO)8( -C6H4)[ -PhPCC(Ph2P)CH(OMe)OC(O)

    SciTech Connect

    Kandala, Srikanth; Yang, Li; Campana, Charles F.; Nesterov, Vladimir; Richmond, Michael G.

    2010-07-01

    The labile cluster 1,2-Os3(CO)10(MeCN)2 (1) reacts with the chiral diphosphine ligand 3,4-bis(diphenylphosphino)-5-methoxy-2(5H)-furanone (bmf) to furnish 1,2-Os3(CO)10(bmf) (2a) in high yield. Heating cluster 2a over the temperature range 358 383 K under CO leads to isomerization of the bmf ligand and formation of the diphosphine-chelated cluster 1,1-Os3(CO)10(bmf) (2b) and an equilibrium mixture consisting of 2a and 2b in a 15:85 ratio. Extended thermolysis of an equilibrium mixture of Os3(CO)10(bmf) is accompanied by CO loss and ortho-metalation of an aryl ring to afford an inseparable mixture of three diastereomeric hydride clusters HOs3(CO)9(C29H23O3P2) (3a c). Thermolysis of HOs3(CO)9(C29H23O3P2) (3a c) in refluxing toluene leads to P C bond cleavage and formation of the benzyne-substituted clusters HOs3(CO)8( -C6H4)( -C23H19O3P2) (4a,b) as a 4:1 mixture of diastereomers. The unequivocal identity of the major benzyne-substituted cluster has been determined by X-ray diffraction analysis, where the activation of one of the phenyl groups situated to the furanone carbonyl group in the bmf ligand has been established. The isomerization and activation of the bmf ligand are contrasted with other Os3(CO)10(diphosphine) derivatives prepared by our groups.

  20. Nanomechanical cleavage of molybdenum disulphide atomic layers.

    PubMed

    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

    2014-01-01

    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

  1. Nanomechanical cleavage of molybdenum disulphide atomic layers

    NASA Astrophysics Data System (ADS)

    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

    2014-04-01

    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.

  2. Verification of 2A peptide cleavage.

    PubMed

    Szymczak-Workman, Andrea L; Vignali, Kate M; Vignali, Dario A A

    2012-02-01

    The need for reliable, multicistronic vectors for multigene delivery is at the forefront of biomedical technology. It is now possible to express multiple proteins from a single open reading frame (ORF) using 2A peptide-linked multicistronic vectors. These small sequences, when cloned between genes, allow for efficient, stoichiometric production of discrete protein products within a single vector through a novel "cleavage" event within the 2A peptide sequence. The easiest and most effective way to assess 2A cleavage is to perform transient transfection of 293T cells (human embryonic kidney cells) followed by western blot analysis, as described in this protocol. 293T cells are easy to grow and can be efficiently transfected with a variety of vectors. Cleavage can be assessed by detection with antibodies against the target proteins or anti-2A serum. PMID:22301658

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

    PubMed

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

    2014-06-01

    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

  4. THE BIOCHEMICAL CHARACTERIZATION OF FERRET CAROTENE-9', 10'-MONOOXYGENASE CATALYZING CLEAVAGE OF CAROTENOIDS IN VITRO AND IN VIVO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies have shown that beta -carotene 15,15'-monooxygenase (CMO1) catalyzes the cleavage of beta -carotene at the central carbon 15, 15’-double bond, but cleaves lycopene with much lower activity. However, expressing the mouse carotene-9’,10’-monooxygenase (CMO2) in beta-carotene/lycopene...

  5. Evidence of a long C-C attractive interaction in cerussite mineral: QTAIM and ELF analyses.

    PubMed

    Vidal, Isaac; Navas, Antonio Snchez

    2014-09-01

    Cerussite, an orthorhombic lead carbonate mineral, has a structure and physical properties that cannot be understood merely in terms of ionic anion-cation interactions. The nature of the chemical bonding in cerussite is analyzed by means of the quantum theory of atoms in molecules (QTAIM) and the analysis of the electron localization function (ELF). A long C-C attractive interaction (3.077 ) along the c axis of the cerussite structure is evidenced by the presence of bond critical points between the C atoms of the CO(3)(2-) molecular groups. It is proposed that the Pb-O interactions, which are mostly ionic in nature, disturb the structure of the CO(3)(2-) molecular groups and promote their interaction along the c axis. The importance of this long-range interaction in the high-pressure crystal chemistry of carbonate minerals and in the explanation of some crystal growth features observed for orthorhombic carbonates is also discussed in this work. PMID:25129662

  6. Cleavage of cytoplasm within the oligonucleate zoosporangia of allomyces macrogynus.

    PubMed

    Ji, Yunjeong; Song, Youngsun; Kim, Namhun; Youn, Hyunjoo; Kang, Minkook; Song, Yurim; Cho, Chungwon

    2014-01-01

    Allomyces macrogynus produces zoosporangia that discharge uninucleate zoospores after cleavage of multinucleate cytoplasm. Cleavage of cytoplasm within the oligonucleate zoosporangia of A. macrogynus was visualized by constructing three-dimensional models based on electron micrographs and confocal images. In oligonucleate zoosporangia, three adjacent nuclei can form three cleavage planes with a line of intersection of the planes. The position and boundary of the cleavage planes are thought to be determined by the relative positions of the nuclei. The establishment of three cleavage planes by cleavage membranes occurred sequentially, and the nuclear axis connecting the centers of two nuclei affected the development of cleavage membranes on each cleavage plane. In multinucleate zoosporangia, groups of three neighboring nuclei near the cell cortex may initiate the sequential establishment of cleavage planes and then may interact with the nuclei further from the cortex until the interactions of nuclei are propagated to the central region of the cytoplasm. PMID:24871589

  7. Silicon-Carbon Bond Formation via Nickel-Catalyzed Cross-Coupling of Silicon Nucleophiles with Unactivated Secondary and Tertiary Alkyl Electrophiles.

    PubMed

    Chu, Crystal K; Liang, Yufan; Fu, Gregory C

    2016-05-25

    A wide array of cross-coupling methods for the formation of C-C bonds from unactivated alkyl electrophiles have been described in recent years. In contrast, progress in the development of methods for the construction of C-heteroatom bonds has lagged; for example, there have been no reports of metal-catalyzed cross-couplings of unactivated secondary or tertiary alkyl halides with silicon nucleophiles to form C-Si bonds. In this study, we address this challenge, establishing that a simple, commercially available nickel catalyst (NiBr2·diglyme) can achieve couplings of alkyl bromides with nucleophilic silicon reagents under unusually mild conditions (e.g., -20 °C); especially noteworthy is our ability to employ unactivated tertiary alkyl halides as electrophilic coupling partners, which is still relatively uncommon in the field of cross-coupling chemistry. Stereochemical, relative reactivity, and radical-trap studies are consistent with a homolytic pathway for C-X bond cleavage. PMID:27187869

  8. Defect structures in deformed F.C.C. metals

    SciTech Connect

    Dai, Y.; Victoria, M.

    1997-08-01

    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.

  9. C,C-diacetylenic phosphaalkenes as heavy diethynylethene analogues.

    PubMed

    Oberg, Elisabet; Schäfer, Bernhard; Geng, Xue-Li; Pettersson, Jenny; Hu, Qi; Kritikos, Mikael; Rasmussen, Torben; Ott, Sascha

    2009-12-18

    A series of C,C-diacetylenic phosphaalkenes 1b-e has been prepared from 1-chloropenta-1,2-dien-4-ynes 6b-e in a reaction with Mes*PCl(2) (Mes* = 2,4,6-((t)Bu)(3)Ph) in the presence of LDA. Under identical conditions, isomeric butadiyne-substituted phosphaalkenes 2c-f can be obtained from 3-chloropenta-1,4-diynes 5c-f. The title compounds represent rare examples of diethynylethenes in which a constituting methylene has been replaced by a phosphorus center. The formation of both isomers can be rationalized by a common pathway that involves isomeric allenyllithium species. Spectroscopic, electrochemical, and theoretical investigations show that the phosphorus heteroatoms are an intrinsic part of the compounds' pi-systems and lead to decreased HOMO-LUMO gaps compared to those in all-carbon-based reference compounds. PMID:19911774

  10. The dual role of oxygen functions in coal pretreatment and liquefaction: Crosslinking and cleavage reactions. Seventh quarterly report, September 30, 1992--December 31, 1992

    SciTech Connect

    Serio, M.A.; Kroo, E.; Charpenay, S.; Solomon, P.R.

    1992-12-31

    The work during the past quarter under Task 2 has focused on the investigation of FT-IR methods for measuring carboxyl and phenolic functions. Fourier transform infrared (FT-IR) spectra of coal contain a wealth of information that can be utilized in the development of quantitative analysis routines based on least squares curvefitting. Because of the importance of the carboxylate groups in retrogressive reactions, recent efforts have focused on the C=O stretching region. Raw and modified coal samples (acid washed, demineralized, and cation exchanged) were analyzed in order to validate the proposed band assignments in the C=O stretching region. This parameter set differentiates free carbonyl (B2) and hydrogen-bonded carbonyl (B4) from carboxylic acid carbonyl (B3) and carboxylate (B7). One test of these assignments, which are based on literature data, is to plot B3 versus B7. This should be linear, assuming that the sum of the free carboxyl and carboxylate groups is constant and that the intensity of the overlapped aromatic ring band in B7 is also constant. This relationship was found to hold for a set of raw, acid washed, and acid washed/cation-exchanged Zap coals. The work under Task 3 has involved (1) completion of the synthesis of the -C-C-0- linked, methoxy substituted lignin-network polymer, -- C{sub 6}H{sub 3}(o-OMe)-O-CH{sub 2}CH{sub 2}]{sub {eta}} -- polymer, (2) Analysis of the polymer via depolymerization under pyrolysis-FIMS (Py-FIMS) conditions, and (3) testing of several routes to selective cleavage of the O-Methyl bond so that the relative crosslinking tendencies of the methylated and unmethylated versions of the polymer could be determined.

  11. Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad

    SciTech Connect

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

    2012-03-14

    Meta-cleavage product (MCP) hydrolases are members of the {alpha}/{beta}-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 {angstrom} 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 {sup 18}O into the benzoate produced during hydrolysis in H{sub 2}{sup 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{sup 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.

  12. 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)

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

    2006-01-01

    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.

  13. Surface-catalyzed C-C covalent coupling strategies toward the synthesis of low-dimensional carbon-based nanostructures.

    PubMed

    Fan, Qitang; Gottfried, J Michael; Zhu, Junfa

    2015-08-18

    Carbon-based nanostructures have attracted tremendous interest because of their versatile and tunable properties, which depend on the bonding type of the constituting carbon atoms. Graphene, as the most prominent representative of the π-conjugated carbon-based materials, consists entirely of sp(2)-hybridized carbon atoms and exhibits a zero band gap. Recently, countless efforts were made to open and tune the band gap of graphene for its applications in semiconductor devices. One promising method is periodic perforation, resulting in a graphene nanomesh (GNM), which opens the band gap while maintaining the exceptional transport properties. However, the typically employed lithographic approach for graphene perforation is difficult to control at the atomic level. The complementary bottom-up method using surface-assisted carbon-carbon (C-C) covalent coupling between organic molecules has opened up new possibilities for atomically precise fabrication of conjugated nanostructures like GNM and graphene nanoribbons (GNR), although with limited maturity. A general drawback of the bottom-up approach is that the desired structure usually does not represent the global thermodynamic minimum. It is therefore impossible to improve the long-range order by postannealing, because once the C-C bond formation becomes reversible, graphene as the thermodynamically most stable structure will be formed. This means that only carefully chosen precursors and reaction conditions can lead to the desired (non-graphene) material. One of the most popular and frequently used organic reactions for on-surface C-C coupling is the Ullmann reaction of aromatic halides. While experimentally simple to perform, the irreversibility of the C-C bond formation makes it a challenge to obtain long-range ordered nanostructures. With no postreaction structural improvement possible, the assembly process must be optimized to result in defect-free nanostructures during the initial reaction, requiring complete reaction of the precursors in the right positions. Incomplete connections typically result when mobile precursor monomers are blocked from reaching unsaturated reaction sites of the preformed nanostructures. For example, monomers may not be able to reach a randomly formed internal cavity of a two-dimensional (2D) nanostructure island due to steric hindrance in 2D confinement, leaving reaction sites in the internal cavity unsaturated. Wrong connections between precursor monomers, here defined as intermolecular C-C bonds forcing the monomer into a nonideal position within the structure, are usually irreversible and can induce further structural defects. The relative conformational flexibility of the monomer backbones permits connections between deformed monomers when they encounter strong steric hindrance. This, however, usually leads to heterogeneous structural motifs in the formed nanostructures. This Account reviews some of the latest developments regarding on-surface C-C coupling strategies toward the synthesis of carbon-based nanostructures by addressing the above-mentioned issues. The strategies include Ullmann coupling and other, "cleaner" alternative C-C coupling reactions like Glaser coupling, cyclo-dehydrogenation, and dehydrogenative coupling. The choice of substrate materials and precursor designs is crucial for optimizing substrate reactivity and precursor diffusion rates, and to reduce events of wrong linkage. Hierarchical polymerization is employed to steer the coupling route, which effectively improves the completeness of the reaction. Effects of byproducts on nanostructure formation is comprehended with both experimental and theoretical studies. PMID:26194462

  14. Institutional Bonding.

    ERIC Educational Resources Information Center

    Allard, M. June

    Institutional bonding was examined at a public, urban commuter college with exceptionally high attrition and visibly low morale. Changes in bonding and attrition were measured 6 years after a 2-year effort to develop school identity and student feelings of membership. It was found that a simple index of campus morale is provided by level of

  15. Spontaneous cleavage of proteins at serine and threonine is facilitated by zinc.

    PubMed

    Lyons, Brian; Kwan, Ann H; Truscott, Roger J W

    2016-04-01

    Old proteins are widely distributed in the body. Over time, they deteriorate and many spontaneous reactions, for example isomerisation of Asp and Asn, can be replicated by incubation of peptides under physiological conditions. One of the signatures of long-lived proteins that has proven to be difficult to replicate in vitro is cleavage on the N-terminal side of Ser residues, and this is important since cleavage at Ser, and also Thr, has been observed in a number of human proteins. In this study, the autolysis of Ser- and Thr-containing peptides was investigated with particular reference to discovering factors that promote cleavage adjacent to Ser/Thr at neutral pH. It was found that zinc catalyses cleavage of the peptide bond on the N-terminal side of Ser residues and further that this process is markedly accelerated if a His residue is adjacent to the Ser. NMR analysis indicated that the imidazole group co-ordinates zinc and that once zinc is co-ordinated, it can polarize the carbonyl group of the peptide bond in a manner analogous to that observed in the active site of the metalloexopeptidase, carboxypeptidase A. The hydroxyl side chain of Ser/Thr is then able to cleave the adjacent peptide bond. These observations enable an understanding of the origin of common truncations observed in long-lived proteins, for example truncation on the N-terminal side of Ser 8 in Abeta, Ser 19 in alpha B crystallin and Ser 66 in alpha A crystallin. The presence of zinc may therefore significantly affect the long-term stability of cellular proteins. PMID:26751411

  16. Cleavage of factor XIII by human neutrophil elastase results in a novel active truncated form of factor XIII A subunit.

    PubMed

    Bagoly, Zsuzsa; Fazakas, Ferenc; Komáromi, István; Haramura, Gizella; Tóth, Eszter; Muszbek, Lászlo

    2008-04-01

    The first step in the activation of plasma factor XIII (FXIII) is the cleavage of R37-G38 bond in FXIII-A subunit (FXIII-A) by thrombin, which makes the subsequent formation of an active transglutaminase possible. No active truncated form of FXIII-A, other than G38-FXIII-A, has been identified. In contrast to thrombin, which has a preference toward arginine residues, human neutrophil elastase (HNE) cleaves peptide bonds at small side-chain aliphatic amino acids, preferably at valine. As there are several valine residues close to the thrombin cleavage-site, we tested if an active truncated FXIII-A was formed during fragmentation of FXIII by HNE. It was demonstrated by Western blotting and transglutaminase assay that HNE induced a limited cleavage of FXIII-A resulting in the activation of both plasma and cellular FXIII; the maximal transglutaminase activities were 52.5% and 67.4% of thrombin-activated FXIII, respectively. After the relatively rapid activation a much slower inactivation occurred. HNE-activated FXIII cross-linked fibrin gamma- and alpha-chains in the clot formed by batroxobin moojeni. MALDI-TOF analysis of the cleaved fragments and N-terminal Edman degradation of the truncated protein identified V39-N40 as the primary cleavage-site and N40-FXIII-A as the active form. No primary cleavage occurred at V34, V35, V47, V50 residues. FXIII-A V34L polymorphism, which increases the rate of FXIII-A cleavage by thrombin, was without effect on FXIII activation by HNE. Molecular modeling located the primary HNE cleavage-site in the middle of the flexible and accessible Q32-L45 loop and showed that other neighboring valine residues were in less favorable position. PMID:18392324

  17. Cleavage crystallography of liquid metal embrittled aluminum alloys

    NASA Astrophysics Data System (ADS)

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

    1991-08-01

    Failure in aluminum alloys subjected to liquid metal embrittlement (LME) typically occurs by either intergranular (IG) fracture or transgranular (TG) cleavage. In this study, the crystallography of liquid metal-induced TG 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) in all cases. It was further determined that the cleavage crystallography was not influenced by alloy texture. Examination of the fracture surfaces indicated that there was not a unique direction of crack propagation. In addition, the existence of (100) 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.

  18. JMS Proxy and C/C++ Client SDK

    NASA Technical Reports Server (NTRS)

    Wolgast, Paul; Pechkam, Paul

    2007-01-01

    JMS Proxy and C/C++ Client SDK (JMS signifies "Java messaging service" and "SDK" signifies "software development kit") is a software package for developing interfaces that enable legacy programs (here denoted "clients") written in the C and C++ languages to communicate with each other via a JMS broker. This package consists of two main components: the JMS proxy server component and the client C library SDK component. The JMS proxy server component implements a native Java process that receives and responds to requests from clients. This component can run on any computer that supports Java and a JMS client. The client C library SDK component is used to develop a JMS client program running in each affected C or C++ environment, without need for running a Java virtual machine in the affected computer. A C client program developed by use of this SDK has most of the quality-of-service characteristics of standard Java-based client programs, including the following: Durable subscriptions; Asynchronous message receipt; Such standard JMS message qualities as "TimeToLive," "Message Properties," and "DeliveryMode" (as the quoted terms are defined in previously published JMS documentation); and Automatic reconnection of a JMS proxy to a restarted JMS broker.

  19. DNA cleavage induced by antitumor antibiotic leinamycin and its biological consequences.

    PubMed

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

    2012-07-15

    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 β-elimination reaction. However, methoxyamine modification of leinamycin-induced abasic sites was found to be refractory to the spontaneous β-elimination reaction. Furthermore, this complex was even resistant to the δ-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

  20. Fe-catalyzed cleavage of the α subunit of Na/K-ATPase: Evidence for conformation-sensitive interactions between cytoplasmic domains

    PubMed Central

    Goldshleger, Rivka; Karlish, Steven J. D.

    1997-01-01

    Incubation of Na/K-ATPase with ascorbate plus H2O2 produces specific cleavage of the α subunit. Five fragments with intact C termini and complementary fragments with intact N termini were observed. The β subunit is not cleaved. Cleavages depend on the presence of contaminant or added Fe2+ ions, as inferred by suppression of cleavages with nonspecific metal complexants (histidine, EDTA, phenanthroline) or the Fe3+-specific complexant desferrioxamine, or acceleration of cleavages by addition of low concentrations of Fe2+ but not of other heavy metal ions. Na/K-ATPase is inactivated in addition to cleavage, and both effects are insensitive to OH⋅ radical scavengers. Cleavages are sensitive to conformation. In low ionic strength media (E2) or media containing Rb ions [E2(Rb)], cleavage is much faster than in high ionic strength media (E1) or media containing Na ions (E1Na). N-terminal fragments and two C-terminal fragments (N-terminals E214 and V712) have been identified by amino acid sequencing. Approximate positions of other cleavages were determined with specific antibodies. The results suggest that Fe2+ (or Fe3+) ions bind with high affinity at the cytoplasmic surface and catalyze cleavages of peptide bonds close to the Fe2+ (or Fe3+) ion. Thus, cleavage patterns can provide information on spatial organization of the polypeptide chain. We propose that highly conserved regions of the α subunit, within the minor and major cytoplasmic loops, interact in the E2 or E2(Rb) conformations but move apart in the E1 or E1Na conformations. We discuss implications of domain interactions for the energy transduction mechanism. Fe-catalyzed cleavages may be applicable to other P-type pumps or membrane proteins. PMID:9275168

  1. Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.

    PubMed

    Edgell, David R; Stanger, Matthew J; Belfort, Marlene

    2004-11-01

    To maximize spread of their host intron or intein, many homing endonucleases recognize nucleotides that code for important and conserved amino acid residues of the target gene. Here, we examine the cleavage requirements for I-TevI, which binds a stretch of thymidylate synthase (TS) DNA that codes for functionally critical residues in the TS active site. Using an in vitro selection scheme, we identified two base-pairs in the I-TevI cleavage site region as important for cleavage efficiency. These were confirmed by comparison of I-TevI cleavage efficiencies on mutant and on wild-type substrates. We also showed that nicking of the bottom strand by I-TevI is not affected by mutation of residues surrounding the bottom-strand cleavage site, unlike other homing endonucleases. One of these two base-pairs is universally conserved in all TS sequences, and is identical with a previously identified cleavage determinant of I-BmoI, a related GIY-YIG endonuclease that binds a homologous stretch of TS-encoding DNA. The other base-pair is conserved only in a subset of TS genes that includes the I-TevI, but not the I-BmoI, target sequence. Both the I-TevI and I-BmoI cleavage site requirements correspond to functionally critical residues involved in an extensive hydrogen bond network within the TS active site. Remarkably, these cleavage requirements correlate with TS phylogeny in bacteria, suggesting that each endonuclease has individually adapted to efficiently cleave distinct TS substrates. PMID:15491609

  2. Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries

    PubMed Central

    Béliveau, François; Leduc, Richard; Overall, Christopher M.

    2014-01-01

    Background Type II transmembrane serine proteases (TTSPs) are a family of cell membrane tethered serine proteases with unclear roles as their cleavage site specificities and substrate degradomes have not been fully elucidated. Indeed just 52 cleavage sites are annotated in MEROPS, the database of proteases, their substrates and inhibitors. Methodology/Principal Finding To profile the active site specificities of the TTSPs, we applied Proteomic Identification of protease Cleavage Sites (PICS). Human proteome-derived database searchable peptide libraries were assayed with six human TTSPs (matriptase, matriptase-2, matriptase-3, HAT, DESC and hepsin) to simultaneously determine sequence preferences on the N-terminal non-prime (P) and C-terminal prime (P’) sides of the scissile bond. Prime-side cleavage products were isolated following biotinylation and identified by tandem mass spectrometry. The corresponding non-prime side sequences were derived from human proteome databases using bioinformatics. Sequencing of 2,405 individual cleaved peptides allowed for the development of the family consensus protease cleavage site specificity revealing a strong specificity for arginine in the P1 position and surprisingly a lysine in P1′ position. TTSP cleavage between R↓K was confirmed using synthetic peptides. By parsing through known substrates and known structures of TTSP catalytic domains, and by modeling the remainder, structural explanations for this strong specificity were derived. Conclusions Degradomics analysis of 2,405 cleavage sites revealed a similar and characteristic TTSP family specificity at the P1 and P1′ positions for arginine and lysine in unfolded peptides. The prime side is important for cleavage specificity, thus making these proteases unusual within the tryptic-enzyme class that generally has overriding non-prime side specificity. PMID:25211023

  3. Role of posttranslational cleavage in glycinin assembly.

    PubMed Central

    Dickinson, C D; Hussein, E H; Nielsen, N C

    1989-01-01

    Glycinin, like other 11S seed storage proteins, undergoes a complex series of posttranslational events between the time proglycinin precursors are synthesized in endoplasmic reticulum and the mature glycinin subunits are deposited in vacuolar protein bodies. According to the current understanding of this process, proglycinin subunits aggregate into trimers in endoplasmic reticulum, and then the trimers move to the vacuolar protein bodies where a protease cleaves them into acidic and basic polypeptide chains. Stable glycinin hexamers, rather than trimers, are isolated from mature seeds. We used a re-assembly assay in this study to demonstrate that proteolytic cleavage of the proglycinin subunits is required for in vitro assembly of glycinin oligomers beyond the trimer stage. The possibility that the cleavage is a regulatory step and that it triggers the deposition of 11S seed storage proteins as insoluble aggregates in vivo is considered. PMID:2562565

  4. Reaction between radicals and N-alkoxyamines As coordinated cleavage with fragmentation

    NASA Astrophysics Data System (ADS)

    Denisov, E. T.; Shestakov, A. F.

    2015-08-01

    Quantum chemical calculations of the enthalpy and activation energy of two reactions with MeO{2/⊙} attacking the CH- and CH2-groups of 2,2,6,6-tetramethylpiperidineoxy-2'-butane are performed. It is shown that the cleavage of hydrogen atoms is accompanied by coordinated breaking of N-O-bonds in the former case and C-O-bonds in the latter. Based on the obtained results, a new scheme is proposed for the cyclic mechanism behind the cleavage of chains on nitroxyl radicals in oxidizing hydrocarbons and polymers that agrees with experimental data. At the center of this cyclic mechanism lies the fast exothermic reaction between peroxyl radicals and N-alkoxyamine with the cleavage of H atoms and the coordinated fragmentation of molecules. Using the model of intersecting parabolas, an algorithm for calculating the enthalpies, activation energies, and rate constants of these reactions with the participation of alkyl, alkoxy, aminyl, peroxyl, phenoxyl, thiyl, and hydroxyl radicals is proposed.

  5. Calpain cleavage prediction using multiple kernel learning.

    PubMed

    DuVerle, David A; Ono, Yasuko; Sorimachi, Hiroyuki; Mamitsuka, Hiroshi

    2011-01-01

    Calpain, an intracellular Ca²⁺-dependent cysteine protease, is known to play a role in a wide range of metabolic pathways through limited proteolysis of its substrates. However, only a limited number of these substrates are currently known, with the exact mechanism of substrate recognition and cleavage by calpain still largely unknown. While previous research has successfully applied standard machine-learning algorithms to accurately predict substrate cleavage by other similar types of proteases, their approach does not extend well to calpain, possibly due to its particular mode of proteolytic action and limited amount of experimental data. Through the use of Multiple Kernel Learning, a recent extension to the classic Support Vector Machine framework, we were able to train complex models based on rich, heterogeneous feature sets, leading to significantly improved prediction quality (6% over highest AUC score produced by state-of-the-art methods). In addition to producing a stronger machine-learning model for the prediction of calpain cleavage, we were able to highlight the importance and role of each feature of substrate sequences in defining specificity: primary sequence, secondary structure and solvent accessibility. Most notably, we showed there existed significant specificity differences across calpain sub-types, despite previous assumption to the contrary. Prediction accuracy was further successfully validated using, as an unbiased test set, mutated sequences of calpastatin (endogenous inhibitor of calpain) modified to no longer block calpain's proteolytic action. An online implementation of our prediction tool is available at http://calpain.org. PMID:21559271

  6. Chemo-regioselectivity in heterogeneous catalysis: competitive routes for C = O and C = C hydrogenations from a theoretical approach.

    PubMed

    Loffreda, David; Delbecq, Françoise; Vigné, Fabienne; Sautet, Philippe

    2006-02-01

    The usual empirical rule stating that the C=C bond is more reactive than the C=O group for catalytic hydrogenations of unsaturated aldehydes is invalidated from the present study. Density functional theory calculations of all the competitive hydrogenation routes of acrolein on Pt(111) reveals conversely that the attack at the C=O bond is systematically favored. The explanation of such catalytic behavior is the existence of metastable precursor states for the O-H bond formation showing that the attack at the oxygen atom follows a new preferential mechanism where the C=O moiety is not directly bonded with the Pt surface atoms, hence yielding an intermediate pathway between Langmuir-Hinshelwood and Rideal-Eley general types of mechanisms. When the whole catalytic cycle is considered, our results reconcile with experimental studies devoted to hydrogenation of acrolein on Pt, since the desorption step of the partially hydrogenated product (unsaturated alcohol versus saturated aldehyde) plays a key role for the selectivity. PMID:16433550

  7. Luminescent Iridium(III) Complexes Supported by N-Heterocyclic Carbene-based C^C^C-Pincer Ligands and Aromatic Diimines

    PubMed Central

    Chung, Lai-Hon; Lo, Hoi-Shing; Ng, Sze-Wing; Ma, Dik-Lung; Leung, Chung-Hang; Wong, Chun-Yuen

    2015-01-01

    Iridium(III) hydrido complexes containing N-heterocyclic carbene (NHC)-based pincer ligand 1,3-bis(1-butylimidazolin-2-ylidene)phenyl anion (C1^C^C1) or 1,3-bis(3-butylbenzimidazolin-2-ylidene)phenyl anion (C2^C^C2) and aromatic diimine (2,2′-bipyridine (bpy), 1,10-phenanthroline (phen), 4,4′-dimethyl-2,2′-bipyridine (Me2bpy), or dipyrido-[3,2-f:2′,3′-h]-quinoxaline (dpq)) in the form of [Ir(C^C^C)(N^N)(H)]+ have been prepared. Crystal structures for these complexes show that the Ir–CNHC distances are 2.043(5)–2.056(5) Å. The hydride chemical shifts for complexes bearing C1^C^C1 (−20.6 to −20.3 ppm) are more upfield than those with C2^C^C2 (−19.5 and −19.2 ppm), revealing that C1^C^C1 is a better electron donor than C2^C^C2. Spectroscopic comparisons and time-dependent density functional theory (TD-DFT) calculations suggest that the lowest-energy electronic transition associated with these complexes (λ = 340–530 nm (ε ≤ 103 dm3 mol−1 cm−1)) originate from a dπ(IrIII) → π*(N^N) metal-to-ligand charge transfer transition, where the dπ(IrIII) level contain significant contribution from the C^C^C ligands. All these complexes are emissive in the yellow-spectral region (553–604 nm in CH3CN and CH2Cl2) upon photo-excitation with quantum yields of 10−3–10−1. PMID:26487542

  8. Luminescent Iridium(III) Complexes Supported by N-Heterocyclic Carbene-based C^C^C-Pincer Ligands and Aromatic Diimines

    NASA Astrophysics Data System (ADS)

    Chung, Lai-Hon; Lo, Hoi-Shing; Ng, Sze-Wing; Ma, Dik-Lung; Leung, Chung-Hang; Wong, Chun-Yuen

    2015-10-01

    Iridium(III) hydrido complexes containing N-heterocyclic carbene (NHC)-based pincer ligand 1,3-bis(1-butylimidazolin-2-ylidene)phenyl anion (C1^C^C1) or 1,3-bis(3-butylbenzimidazolin-2-ylidene)phenyl anion (C2^C^C2) and aromatic diimine (2,2‧-bipyridine (bpy), 1,10-phenanthroline (phen), 4,4‧-dimethyl-2,2‧-bipyridine (Me2bpy), or dipyrido-[3,2-f:2‧,3‧-h]-quinoxaline (dpq)) in the form of [Ir(C^C^C)(N^N)(H)]+ have been prepared. Crystal structures for these complexes show that the Ir-CNHC distances are 2.043(5)-2.056(5) Å. The hydride chemical shifts for complexes bearing C1^C^C1 (-20.6 to -20.3 ppm) are more upfield than those with C2^C^C2 (-19.5 and -19.2 ppm), revealing that C1^C^C1 is a better electron donor than C2^C^C2. Spectroscopic comparisons and time-dependent density functional theory (TD-DFT) calculations suggest that the lowest-energy electronic transition associated with these complexes (λ = 340-530 nm (ɛ ≤ 103 dm3 mol-1 cm-1)) originate from a dπ(IrIII) → π*(N^N) metal-to-ligand charge transfer transition, where the dπ(IrIII) level contain significant contribution from the C^C^C ligands. All these complexes are emissive in the yellow-spectral region (553-604 nm in CH3CN and CH2Cl2) upon photo-excitation with quantum yields of 10-3-10-1.

  9. Cleavage crystallography of liquid metal embrittled aluminum alloys

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

    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.

  10. Olefin cis-Dihydroxylation and Aliphatic C-H Bond Oxygenation by a Dioxygen-Derived Electrophilic Iron-Oxygen Oxidant.

    PubMed

    Chatterjee, Sayanti; Paine, Tapan Kanti

    2015-08-01

    Many iron-containing enzymes involve metal-oxygen oxidants to carry out O2-dependent transformation reactions. However, the selective oxidation of C-H and C=C bonds by biomimetic complexes using O2 remains a major challenge in bioinspired catalysis. The reactivity of iron-oxygen oxidants generated from an Fe(II)-benzilate complex of a facial N3 ligand were thus investigated. The complex reacted with O2 to form a nucleophilic oxidant, whereas an electrophilic oxidant, intercepted by external substrates, was generated in the presence of a Lewis acid. Based on the mechanistic studies, a nucleophilic Fe(II)-hydroperoxo species is proposed to form from the benzilate complex, which undergoes heterolytic O-O bond cleavage in the presence of a Lewis acid to generate an Fe(IV)-oxo-hydroxo oxidant. The electrophilic iron-oxygen oxidant selectively oxidizes sulfides to sulfoxides, alkenes to cis-diols, and it hydroxylates the C-H bonds of alkanes, including that of cyclohexane. PMID:26088714

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

    ERIC Educational Resources Information Center

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

    2008-01-01

    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

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

    ERIC Educational Resources Information Center

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

    2008-01-01

    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…

  13. Intramolecular Cleavage of the hASRGL1 Homodimer Occurs in Two Stages.

    PubMed

    Li, Wenzong; Irani, Seema; Crutchfield, Amanda; Hodge, Kristal; Matthews, Wendy; Patel, Pooja; Zhang, Yan Jessie; Stone, Everett

    2016-02-16

    The human asparaginase-like protein 1 (hASRGL1) is a member of the N-terminal nucleophile (Ntn) family that hydrolyzes l-asparagine and isoaspartyl-dipeptides. The nascent protein folds into an αβ-βα sandwich fold homodimer that cleaves its own peptide backbone at the G167-T168 bond, resulting in the active form of the enzyme. However, biophysical studies of hASRGL1 are difficult because of the curious fact that intramolecular cleavage of the G167-T168 peptide bond reaches only ≤50% completion. We capitalized upon our previous observation that intramolecular processing increases thermostability and developed a differential scanning fluorimetry assay that allowed direct detection of distinct processing intermediates for the first time. A kinetic analysis of these intermediates revealed that cleavage of one subunit of the hASRGL1 subunit drastically reduces the processing rate of the adjacent monomer, and a mutagenesis study showed that stabilization of the dimer interface plays a critical role in this process. We also report a comprehensive analysis of conserved active site residues and delineate their relative roles in autoprocessing and substrate hydrolysis. In addition to glycine, which was previously reported to selectively accelerate hASRGL1 cleavage, we identified several novel small molecule activators that also promote intramolecular processing. The structure-activity analysis supports the hypothesis that multiple negatively charged small molecules interact within the active site of hASRGL1 to act as a base in promoting cleavage. Overall, our investigation provides a mechanistic understanding of the maturation process of this Ntn hydrolase family member. PMID:26780688

  14. Cleavage of [4Fe-4S]-Type Clusters: Breaking the Symmetry

    SciTech Connect

    Niu, Shuqiang; Ichiye, Toshiko

    2009-05-14

    The cleavage of [4Fes4S]-type clusters is thought to be important in proteins such as FesS scaffold proteins and nitrogenase. However, most [4Fes4S]2+ clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe2.5+sFe2.5+ pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fes4S] core into two [2Fes2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe3+sFe2+ pairs. Cleavage first through the weak Fe2+sS bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe4S4L4]2- (L ) SCH3, Cl, H) and heteroligand [Fe4S4(SCH3)2L2]2- (L ) Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fes4S] cluster in their biological function might have spin-localized [4Fes4S] clusters.

  15. Cleavage of [4Fe--4S]-Type Clusters: Breaking the Symmetry

    SciTech Connect

    Niu, Shuqiang; Ichiye, Toshiko

    2009-05-14

    The cleavage of [4Fe--4S]-type clusters is thought to be important in proteins such as Fe--S scaffold proteins and nitrogenase. However, most [4Fe--4S]2⁺ clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe2.5⁺+--Fe2.5⁺ pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fe--4S] core into two [2Fe--2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe3⁺--Fe2⁺ pairs. Cleavage first through the weak Fe2⁺--S bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe₄S₄L₄]2⁻ (L = SCH3, Cl, H) and heteroligand [Fe₄S₄ (SCH3)2L2]2⁻ (L = Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fe--4S] cluster in their biological function might have spin-localized [4Fe--4S] clusters.

  16. Distinguishing Bonds.

    PubMed

    Rahm, Martin; Hoffmann, Roald

    2016-03-23

    The energy change per electron in a chemical or physical transformation, ΔE/n, may be expressed as Δχ̅ + Δ(VNN + ω)/n, where Δχ̅ is the average electron binding energy, a generalized electronegativity, ΔVNN is the change in nuclear repulsions, and Δω is the change in multielectron interactions in the process considered. The last term can be obtained by the difference from experimental or theoretical estimates of the first terms. Previously obtained consequences of this energy partitioning are extended here to a different analysis of bonding in a great variety of diatomics, including more or less polar ones. Arguments are presented for associating the average change in electron binding energy with covalence, and the change in multielectron interactions with electron transfer, either to, out, or within a molecule. A new descriptor Q, essentially the scaled difference between the Δχ̅ and Δ(VNN + ω)/n terms, when plotted versus the bond energy, separates nicely a wide variety of bonding types, covalent, covalent but more correlated, polar and increasingly ionic, metallogenic, electrostatic, charge-shift bonds, and dispersion interactions. Also, Q itself shows a set of interesting relations with the correlation energy of a bond. PMID:26910496

  17. Theoretical study of the bond dissociation energies of methanol

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

    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.

  18. Cleavage of benzylaryl ethers in the presence of zinc halides

    SciTech Connect

    Frederick, T.J.; Bell, A.T.

    1984-05-01

    Ether groups constitute one of the primary linkages between aromatic centers present in coal. During the liquefaction of coal under the influence of zinc halides, it is believed that these linkages are cleaved. The details of this process have been studied in the present investigation using benzylphenyl ether (BPE), benzyl-p-tolyl ether (BTE), and benzyl-l-naphthyl ether (BNE) to represent the ether structures present in coal. ZnCl/sub 2/ and ZnBr/sub 2/ were used as catalysts. ZnCl/sub 2/ was found to be catalytically inactive. However, in the presence of HCl it forms a stable adduct which is highly active. HBr/ZnBr/sub 2/ behaves in a manner analogous to HCl/ZnCl/sub 2/ but is tenfold more active. All three ethers react in a similar fashion. In each case cleavage occurs at the oxygen-methylene bond and is accompanied by a small degree of ether rearrangement to form the corresponding hydroxydiarylmethane. The reaction kinetics for BPE, BTE, and BNE can be described in terms of a carbocation mechanism. Rate coefficients for each of the elementary steps have been determined by simulation of the experimentally observed product concentration versus time profiles.

  19. Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement.

    PubMed Central

    Shih, I H; Been, M D

    1999-01-01

    The natural substrate cleaved by the hepatitis delta virus (HDV) ribozyme contains a 3',5'-phosphodiester linkage at the cleavage site; however, a 2',5'-linked ribose-phosphate backbone can also be cleaved by both trans-acting and self-cleaving forms of the HDV ribozyme. With substrates containing either linkage, the HDV ribozyme generated 2',3'-cyclic phosphate and 5'-hydroxyl groups suggesting that the mechanisms of cleavage in both cases were by a nucleophilic attack on the phosphorus center by the adjacent hydroxyl group. Divalent metal ion was required for cleavage of either linkage. However, although the 3',5'-linkage was cleaved slightly faster in Ca2+ than in Mg2+, the 2',5'-linkage was cleaved in Mg2+ (or Mn2+) but not Ca2+. This dramatic difference in metal-ion specificity is strongly suggestive of a crucial metal-ion interaction at the active site. In contrast to the HDV ribozymes, cleavage at a 2',5'-phosphodiester bond was not efficiently catalyzed by the hammerhead ribozyme. The relaxed linkage specificity of the HDV ribozymes may be due in part to lack of a rigid binding site for sequences 5' to the cleavage site. PMID:10496215

  20. Yankee bonds

    SciTech Connect

    Delaney, P. )

    1993-10-01

    Yankee and Euromarket bonds may soon find their way into the financing of power projects in Latin America. For developers seeking long-term commitments under build, own, operate, and transfer (BOOT) power projects in Latin America, the benefits are substantial.

  1. Bonds Boom.

    ERIC Educational Resources Information Center

    Reynolds, Cathryn

    1989-01-01

    The combined effect of the "Serrano" decision and Proposition 13 left California school districts with aging, overcrowded facilities. Chico schools won a $18.5 million general obligation bond election for facilities construction. With $11 billion needed for new school construction, California will need to tap local sources. A sidebar outlines…

  2. Application of C/C composites to the combustion chamber of rocket engines. Part 1: Heating tests of C/C composites with high temperature combustion gases

    NASA Astrophysics Data System (ADS)

    Tadano, Makoto; Sato, Masahiro; Kuroda, Yukio; Kusaka, Kazuo; Ueda, Shuichi; Suemitsu, Takeshi; Hasegawa, Satoshi; Kude, Yukinori

    1995-04-01

    Carbon fiber reinforced carbon composite (C/C composite) has various superior properties, such as high specific strength, specific modulus, and fracture strength at high temperatures of more than 1800 K. Therefore, C/C composite is expected to be useful for many structural applications, such as combustion chambers of rocket engines and nose-cones of space-planes, but C/C composite lacks oxidation resistivity in high temperature environments. To meet the lifespan requirement for thermal barrier coatings, a ceramic coating has been employed in the hot-gas side wall. However, the main drawback to the use of C/C composite is the tendency for delamination to occur between the coating layer on the hot-gas side and the base materials on the cooling side during repeated thermal heating loads. To improve the thermal properties of the thermal barrier coating, five different types of 30-mm diameter C/C composite specimens constructed with functionally gradient materials (FGM's) and a modified matrix coating layer were fabricated. In this test, these specimens were exposed to the combustion gases of the rocket engine using nitrogen tetroxide (NTO) / monomethyl hydrazine (MMH) to evaluate the properties of thermal and erosive resistance on the thermal barrier coating after the heating test. It was observed that modified matrix and coating with FGM's are effective in improving the thermal properties of C/C composite.

  3. The role of structural ledges at phase boundaries; 2: F. c. c. -b. c. c. interfaces in Nishiyama-Wasserman orientation

    SciTech Connect

    Shiflet, G.J.; Merwe, J.H. van der . Dept. of Physics)

    1994-04-01

    The ledge mode of misfit accommodation was first postulated for boundaries between b.c.c. and f.c.c metal phases; the interfaces being [111] f.c.c.-[110] b.c.c. planes and relative orientations varying from Nishiyama-Wassermann (NW) to Kurdjumov-Sachs (KS). Here the geometrical quantities are uniquely related by the misfit ratio r of atomic diameters. They consider the so-called NW-x configuration in which the orientation is imposed by close matching along the <[bar 2]11> f.c.c. and <[bar 1]10> b.c.c. (taken as x-) directions. From the fact that no net shear pattern displacements are present with x-ledges (ledges normal to the x-direction) it is concluded that they are energetically preferable to y-ledges and justifies the approach of an energetic comparison between stepped interfaces with x-ledges and a planar interface containing conventional misfit dislocations (MDs). The NW-x stepped configuration is at first subjected to a rigid model analysis, i.e. a model with rigid crystals and periodic (truncated Fourier representation) interfacial interaction. This analysis provides (1) energetic justification for a relation between terrace periodicity and misfit cancellation, (2) values of upper and lower average energy bounds, (3) a method for estimating interfacial shear moduli, and (4) a motivation for the suggestion that a relative rigid translation of the crystals is needed for energy minimization.

  4. Resistance of Actin to Cleavage during Apoptosis

    NASA Astrophysics Data System (ADS)

    Song, Qizhong; Wei, Tie; Lees-Miller, Susan; Alnemri, Emad; Watters, Dianne; Lavin, Martin F.

    1997-01-01

    A small number of cellular proteins present in the nucleus, cytosol, and membrane fraction are specifically cleaved by the interleukin-1β -converting enzyme (ICE)-like family of proteases during apoptosis. Previous results have demonstrated that one of these, the cytoskeletal protein actin, is degraded in rat PC12 pheochromocytoma cells upon serum withdrawal. Extracts from etoposide-treated U937 cells are also capable of cleaving actin. It was assumed that cleavage of actin represented a general phenomenon, and a mechanism coordinating proteolytic, endonucleolytic, and morphological aspects of apoptosis was proposed. We demonstrate here that actin is resistant to degradation in several different human cells induced to undergo apoptosis in response to a variety of stimuli, including Fas ligation, serum withdrawal, cytotoxic T-cell killing, and DNA damage. On the other hand, cell-free extracts from these cells and the ICE-like protease CPP32 were capable of cleaving actin in vitro. We conclude that while actin contains cleavage sites for ICE-like proteases, it is not degraded in vivo in human cells either because of lack of access of these proteases to actin or due to the presence of other factors that prevent degradation.

  5. The hammerhead cleavage reaction in monovalent cations.

    PubMed Central

    Curtis, E A; Bartel, D P

    2001-01-01

    Recently, Murray et al. (Chem Biol, 1998, 5:587-595) found that the hammerhead ribozyme does not require divalent metal ions for activity if incubated in high (> or =1 M) concentrations of monovalent ions. We further characterized the hammerhead cleavage reaction in the absence of divalent metal. The hammerhead is active in a wide range of monovalent ions, and the rate enhancement in 4 M Li+ is only 20-fold less than that in 10 mM Mg2+. Among the Group I monovalent metals, rate correlates in a log-linear manner with ionic radius. The pH dependence of the reaction is similar in 10 mM Mg2+, 4 M Li+, and 4 M Na+. The exchange-inert metal complex Co(NH3)3+ also supports substantial hammerhead activity. These results suggest that a metal ion does not act as a base in the reaction, and that the effects of different metal ions on hammerhead cleavage rates primarily reflect structural contributions to catalysis. PMID:11345433

  6. Activity dependent CAM cleavage and neurotransmission

    PubMed Central

    Conant, Katherine; Allen, Megan; Lim, Seung T.

    2015-01-01

    Spatially localized proteolysis represents an elegant means by which neuronal activity dependent changes in synaptic structure, and thus experience dependent learning and memory, can be achieved. In vitro and in vivo studies suggest that matrix metalloproteinase and adamalysin activity is concentrated at the cell surface, and emerging evidence suggests that increased peri-synaptic expression, release and/or activation of these proteinases occurs with enhanced excitatory neurotransmission. Synaptically expressed cell adhesion molecules (CAMs) could therefore represent important targets for neuronal activity-dependent proteolysis. Several CAM subtypes are expressed at the synapse, and their cleavage can influence the efficacy of synaptic transmission through a variety of non-mutually exclusive mechanisms. In the following review, we discuss mechanisms that regulate neuronal activity-dependent synaptic CAM shedding, including those that may be calcium dependent. We also highlight CAM targets of activity-dependent proteolysis including neuroligin and intercellular adhesion molecule-5 (ICAM-5). We include discussion focused on potential consequences of synaptic CAM shedding, with an emphasis on interactions between soluble CAM cleavage products and specific pre- and post-synaptic receptors. PMID:26321910

  7. Metal ion cooperativity in ribozyme cleavage of RNA

    PubMed Central

    Brännvall, Mathias; Kirsebom, Leif A.

    2001-01-01

    Combinations of chemical and genetic approaches were used to study the function of divalent metal ions in cleavage of RNA by the ribozyme RNase P RNA. We show that different divalent metal ions have differential effects on cleavage site recognition and rescue of cleavage activity by mixing divalent metal ions that do not promote cleavage by themselves. We conclude that efficient and correct cleavage is the result of cooperativity between divalent metal ions bound at different sites in the RNase P RNA-substrate complex. Complementation of a mutant RNase P RNA phenotype as a result of divalent metal ion replacement is demonstrated also. This finding together with other data indicate that one of the metal ions involved in this cooperativity is positioned near the cleavage site. The possibility that the Mg2+/Ca2+ ratio might regulate the activity of biocatalysts that depend on RNA for activity is discussed. PMID:11606743

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

    PubMed

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

    2014-10-20

    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

  9. Oxidative cleavage of olefins by in situ-generated catalytic 3,4,5,6-tetramethyl-2-iodoxybenzoic acid/oxone.

    PubMed

    Moorthy, Jarugu Narasimha; Parida, Keshaba Nanda

    2014-12-01

    Oxidative cleavage of a variety of olefins to the corresponding ketones/carboxylic acids is shown to occur in a facile manner with 3,4,5,6-tetramethyl-2-iodobenzoic acid (TetMe-IA)/oxone. The simple methodology involves mere stirring of the olefin and catalytic amount (10 mol %) of TetMe-IA and oxone in acetonitrile-water mixture (1:1, v/v) at rt. The reaction mechanism involves initial dihydroxylation of the olefin with oxone, oxidative cleavage by the in situ-generated 3,4,5,6-tetramethyl-2-iodoxybenzoic acid (TetMe-IBX), and oxidation of the aldehyde functionality to the corresponding acid with oxone. Differences in the reactivities of electron-rich and electron-poor double bonds have been exploited to demonstrate chemoselective oxidative cleavage in substrates containing two double bonds. PMID:25353314

  10. Mapping Homing Endonuclease Cleavage Sites Using In Vitro Generated Protein

    PubMed Central

    Belfort, Marlene

    2015-01-01

    Mapping the precise position of endonucleolytic cleavage sites is a fundamental experimental technique used to describe the function of a homing endonuclease. However, these proteins are often recalcitrant to cloning and over-expression in biological systems because of toxicity induced by spurious DNA cleavage events. In this chapter we outline the steps to successfully express a homing endonuclease in vitro and use this product in nucleotide-resolution cleavage assays. PMID:24510259

  11. Redox-triggered C-C coupling of alcohols and vinyl epoxides: diastereo- and enantioselective formation of all-carbon quaternary centers via tert-(hydroxy)-prenylation.

    PubMed

    Feng, Jiajie; Garza, Victoria J; Krische, Michael J

    2014-06-25

    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, premetalated reagents, and discrete alcohol-to-aldehyde redox manipulations. PMID:24915473

  12. Determination and interrelation of bond heterolysis and homolysis energies in solution. Final report, January 1988-August 1991

    SciTech Connect

    Arnett, E.M.

    1993-01-01

    Solution phase heats of heterolysis Delta H(sub(het)) and homolysis Delta H(sub(homo)) were determined for covalent bonds that can be cleaved to produce resonance-stabilized carbenium ions, anions, and radicals. Simple and broadly applicable correlation equations were developed which relate Delta H(sub(het)) to ion stabilization properties pK(sub(R+5)) and pK(sub a) and relate Delta H(sub(homo)) to radical stabilization properties (AOPs and CRPs). Important conclusions from the study are: (1) there is no general correlation between Delta H(sub(het)) and Delta H(sub(homo)) which implies that heterolytic bond cleavage pathways in coal will be quite different than the homolytic bond cleavage pathways associated with coal thermolysis; (2) many covalent bonds in coal which require high temperature for homolytic cleavage may be susceptible to heterolytic cleavage under mild conditions; and (3) coal conversion process chemistry based upon heterolytic bond cleavage may be more selective and controllable than homolytic bond cleavage associated with coal thermolysis.

  13. Mechanochemistry: One Bond at a Time

    PubMed Central

    Liang, Jian; Fernández, Julio M.

    2009-01-01

    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 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((FΔxr-Ea)/kBT)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate we measured the bond elongation parameter, Δxr, along the reaction coordinate to the transition state of the SN2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the Δxr 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 single-molecule force clamp spectroscopy approach in providing unprecedented access to chemical reactions. PMID:19572737

  14. Efficient Access to Multifunctional Trifluoromethyl Alcohols through Base-Free Catalytic Asymmetric C-C Bond Formation with Terminal Ynamides.

    PubMed

    Cook, Andrea M; Wolf, Christian

    2016-02-01

    The asymmetric addition of terminal ynamides to trifluoromethyl ketones with a readily available chiral zinc catalyst gives CF3 -substituted tertiary propargylic alcohols in up to 99?% yield and 96?%?ee. The exclusion of organozinc additives and base as well as the general synthetic utility of the products are key features of this reaction. The value of the ?-hydroxy-?-trifluoromethyl ynamides is exemplified by selective transformations to chiral Z- and E-enamides, an amide, and N,O-ketene acetals. The highly regioselective hydration, stereoselective reduction, and hydroacyloxylation reactions proceed with high yields and without erosion of the ee?value of the parent ?-hydroxy ynamides. PMID:26806871

  15. Palladium-catalyzed enolate arylation as a key C-C bond-forming reaction for the synthesis of isoquinolines.

    PubMed

    Pilgrim, Ben S; Gatland, Alice E; Esteves, Carlos H A; McTernan, Charlie T; Jones, Geraint R; Tatton, Matthew R; Procopiou, Panayiotis A; Donohoe, Timothy J

    2016-01-21

    The palladium-catalyzed coupling of an enolate with an ortho-functionalized aryl halide (an α-arylation) furnishes a protected 1,5-dicarbonyl moiety that can be cyclized to an isoquinoline with a source of ammonia. This fully regioselective synthetic route tolerates a wide range of substituents, including those that give rise to the traditionally difficult to access electron-deficient isoquinoline skeletons. These two synthetic operations can be combined to give a three-component, one-pot isoquinoline synthesis. Alternatively, cyclization of the intermediates with hydroxylamine hydrochloride engenders direct access to isoquinoline N-oxides; and cyclization with methylamine, gives isoquinolinium salts. Significant diversity is available in the substituents at the C4 position in four-component, one-pot couplings, by either trapping the in situ intermediate after α-arylation with carbon or heteroatom-based electrophiles, or by performing an α,α-heterodiarylation to install aryl groups at this position. The α-arylation of nitrile and ester enolates gives access to 3-amino and 3-hydroxyisoquinolines and the α-arylation of tert-butyl cyanoacetate followed by electrophile trapping, decarboxylation and cyclization, C4-functionalized 3-aminoisoquinolines. An oxime directing group can be used to direct a C-H functionalization/bromination, which allows monofunctionalized rather than difunctionalized aryl precursors to be brought through this synthetic route. PMID:26632484

  16. C-C Bond Formation via Copper-Catalyzed Conjugate Addition Reactions to Enones in Water at Room Temperature

    PubMed Central

    Lipshutz, Bruce H.; Huang, Shenlin; Leong, Wendy Wen Yi; Isley, Nicholas A.

    2013-01-01

    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

  17. Unraveling the Fischer-Tropsch mechanism: a combined DFT and microkinetic investigation of C-C bond formation on Ru.

    PubMed

    Mirwald, Jens W; Inderwildi, Oliver R

    2012-05-21

    A combined modelling study on the Fischer-Tropsch Mechanism on Ru(0001). The DFT results presented herein approve the idea that the carbide mechanism is not the main reaction path in the synthesis of liquid hydrocarbons on Ru{0001}. The direct reaction of a CH(x)(s) species with a CO(s) species is kinetically and thermochemically preferred over CO dissociation and the hydrogenation of carbon monoxide can be seen as the initiation reaction of the hydrocarbon polymerisation process. Moreover, this study shows that CO dissociation is favoured over desorption on Ru{0001}, while on the analogue Co facet desorption is clearly favoured. This study therefore is an important further confirmation on new thinking in the Fischer-Tropsch synthesis. The fundamental insight gained in these studies will be of paramount importance for engineers optimising the FT process. Optimisation will not only lower the cost of FT fuels but simultaneously lower energy consumption and emissions. PMID:22482113

  18. Acetylacetone-cleaving enzyme Dke1: a novel C-C-bond-cleaving enzyme from Acinetobacter johnsonii.

    PubMed Central

    Straganz, Grit D; Glieder, Anton; Brecker, Lothar; Ribbons, Douglas W; Steiner, Walter

    2003-01-01

    The toxicity of acetylacetone has been demonstrated in various studies. Little is known, however, about metabolic pathways for its detoxification or mineralization. Data presented here describe for the first time the microbial degradation of acetylacetone and the characterization of a novel enzyme that initiates the metabolic pathway. From an Acinetobacter johnsonii strain that grew with acetylacetone as the sole carbon source, an inducible acetylacetone-cleaving enzyme was purified to homogeneity. The corresponding gene, coding for a 153 amino acid sequence that does not show any significant relationship to other known protein sequences, was cloned and overexpressed in Escherichia coli and gave high yields of active enzyme. The enzyme cleaves acetylacetone to equimolar amounts of methylglyoxal and acetate, consuming one equivalent of molecular oxygen. No exogenous cofactor is required, but Fe(2+) is bound to the active protein and essential for its catalytic activity. The enzyme has a high affinity for acetylacetone with a K (m) of 9.1 microM and a k(cat) of 8.5 s(-1). A metabolic pathway for acetylacetone degradation and the putative relationship of this novel enzyme to previously described dioxygenases are discussed. PMID:12379146

  19. Topotactic elimination of water across a C-C ligand bond in a dense 3-D metal-organic framework.

    PubMed

    Yeung, Hamish H-M; Kosa, Monica; Griffin, John M; Grey, Clare P; Major, Dan T; Cheetham, Anthony K

    2014-11-11

    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

  20. Reversible Sigma C-C Bond Formation Between Phenanthroline Ligands Activated by (C5Me5)2Yb

    SciTech Connect

    Nocton, Gré gory; Lukens, Wayne W.; Booth, Corwin H.; Rozenel, Sergio S.; Medling, Scott A.; Maron, Laurent; Andersen, Richard A.

    2014-06-26

    The electronic structure and associated magnetic properties of the 1,10-phenanthroline adducts of Cp*2Yb are dramatically different from those of the 2,2?-bipyridine adducts. The monomeric phenanthroline adducts are ground state triplets that are based upon trivalent Yb(III), f13, and (phen ) that are only weakly exchange coupled, which is in contrast to the bipyridine adducts whose ground states are multiconfigurational, open-shell singlets in which ytterbium is intermediate valent ( J. Am. Chem. Soc 2009, 131, 6480; J. Am. Chem. Soc 2010, 132, 17537). The origin of these different physical properties is traced to the number and symmetry of the LUMO and LUMO+1 of the heterocyclic diimine ligands. The bipy has only one 1 orbital of b1 symmetry of accessible energy, but phen has two orbitals of b1 and a2 symmetry that are energetically accessible. The carbon p-orbitals have different nodal properties and coefficients and their energies, and therefore their populations change depending on the position and number of methyl substitutions on the ring. A chemical ramification of the change in electronic structure is that Cp 2Yb(phen) is a dimer when crystallized from toluene solution, but a monomer when sublimed at 180190 C. When 3,8-Me2phenanthroline is used, the adduct Cp*2Yb(3,8-Me2phen) exists in the solution in a dimer monomer equilibrium in which G is near zero. The adducts with 3-Me, 4-Me, 5-Me, 3,8-Me2, and 5,6-Me2-phenanthroline are isolated and characterized by solid state X-ray crystallography, magnetic susceptibility and LIII-edge XANES spectroscopy as a function of temperature and variable-temperature 1H NMR spectroscopy.

  1. Diffusion bonding

    DOEpatents

    Anderson, Robert C.

    1976-06-22

    1. A method for joining beryllium to beryllium by diffusion bonding, comprising the steps of coating at least one surface portion of at least two beryllium pieces with nickel, positioning a coated surface portion in a contiguous relationship with an other surface portion, subjecting the contiguously disposed surface portions to an environment having an atmosphere at a pressure lower than ambient pressure, applying a force upon the beryllium pieces for causing the contiguous surface portions to abut against each other, heating the contiguous surface portions to a maximum temperature less than the melting temperature of the beryllium, substantially uniformly decreasing the applied force while increasing the temperature after attaining a temperature substantially above room temperature, and maintaining a portion of the applied force at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions.

  2. C-H and C-C clumping in ethane by high-resolution mass spectrometry

    NASA Astrophysics Data System (ADS)

    Clog, M. D.; Eiler, J. M.

    2014-12-01

    Ethane (C2H6) is an important natural compound, and its geochemistry can be studied through 13C-13C, 13C-D and/or D-D clumping. Such measurements are potentially important both as a stepping stone towards the study of more complex organic molecules and, in its own regard, to understand processes controlling the generation, migration and destruction of natural gas. Isotopic clumping on C-C and C-H bonds could be influenced by thermodynamics, chemical kinetics, diffusion or gas mixing. Previous work showed that 13C-D clumping in methane generally reflects equilibrium and provides a measure of formation temperature (Stolper et al 2014a), whereas 13C-13C clumping in ethane is likely most controlled by chemical-kinetic processes and/or inheritance from the isotopic structure of source organic compounds (Clog et al 2014). 13C-D clumping in ethane has the potential to provide a thermometer for its synthesis, as it does for methane. However, the difference in C-H bond dissociation energy for these two compounds may suggest a lower 'blocking temperature' for this phenomenon in ethane (the blocking temperature for methane is ≥~250 C in geological conditions). We present analytical techniques to measure both 13C-13C and 13C-D clumping in ethane, using a novel two-instrument technique, including both the Thermo 253-Ultra and the Thermo DFS. In this method, the Ultra is used to measure the relative abundances of combinations nearly isobaric isotopologues: (13C12CH6 + 12C2DH5)/12C2H6 and (13C2H6 + 12C13CDH5)/12C2H6, free of other isobaric interferences like O2. The DFS, a very high resolution single-collector instrument, is then used to measure the ratios of isotopologues of ethane at a single cardinal mass: 12C2DH5/13C12CH6, and 12C13CDH5/13C2H6, with precisions of ~1 permil. Those 4 measurements allow us to calculate the bulk isotopic composition (D and 13C) as well as the abundance of 13C2H6 and 13C12CDH5. We also present progress on the development of software tools to use the data measured with the DFS efficiently.

  3. Two Spin-State Reactivity in the Activation and Cleavage of CO2 by [ReO2](.).

    PubMed

    Canale, Valentino; Robinson, Robert; Zavras, Athanasios; Khairallah, George N; d'Alessandro, Nicola; Yates, Brian F; O'Hair, Richard A J

    2016-05-19

    The rhenium dioxide anion [ReO2](-) reacts with carbon dioxide in a linear ion trap mass spectrometer to produce [ReO3](-) corresponding to activation and cleavage of a C-O bond. Isotope labeling experiments using [Re(18)O2](-) reveal that (18)O/(16)O scrambling does not occur prior to cleavage of the C-O bond. Density functional theory calculations were performed to examine the mechanism for this oxygen atom abstraction reaction. Because the spins of the ground states are different for the reactant and product ions ((3)[ReO2](-) versus (1)[ReO3](-)), both reaction surfaces were examined in detail and multiple [O2Re-CO2](-) intermediates and transition structures were located and minimum energy crossing points were calculated. The computational results show that the intermediate [O2Re(η(2)-C,O-CO2)](-) species most likely initiates C-O bond activation and cleavage. The stronger binding affinity of CO2 within this species and the greater instabilities of other [O2Re-CO2)](-) intermediates are significant enough that oxygen atom exchange is avoided. PMID:27193088

  4. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses.

    PubMed

    Eckhard, Ulrich; Huesgen, Pitter F; Schilling, Oliver; Bellac, Caroline L; Butler, Georgina S; Cox, Jennifer H; Dufour, Antoine; Goebeler, Verena; Kappelhoff, Reinhild; Keller, Ulrich Auf dem; Klein, Theo; Lange, Philipp F; Marino, Giada; Morrison, Charlotte J; Prudova, Anna; Rodriguez, David; Starr, Amanda E; Wang, Yili; Overall, Christopher M

    2016-01-01

    Secreted and membrane tethered matrix metalloproteinases (MMPs) are key homeostatic proteases regulating the extracellular signaling and structural matrix environment of cells and tissues. For drug targeting of proteases, selectivity for individual molecules is highly desired and can be met by high yield active site specificity profiling. Using the high throughput Proteomic Identification of protease Cleavage Sites (PICS) method to simultaneously profile both the prime and non-prime sides of the cleavage sites of nine human MMPs, we identified more than 4300 cleavages from P6 to P6' in biologically diverse human peptide libraries. MMP specificity and kinetic efficiency were mainly guided by aliphatic and aromatic residues in P1' (with a ~32-93% preference for leucine depending on the MMP), and basic and small residues in P2' and P3', respectively. A wide differential preference for the hallmark P3 proline was found between MMPs ranging from 15 to 46%, yet when combined in the same peptide with the universally preferred P1' leucine, an unexpected negative cooperativity emerged. This was not observed in previous studies, probably due to the paucity of approaches that profile both the prime and non-prime sides together, and the masking of subsite cooperativity effects by global heat maps and iceLogos. These caveats make it critical to check for these biologically highly important effects by fixing all 20 amino acids one-by-one in the respective subsites and thorough assessing of the inferred specificity logo changes. Indeed an analysis of bona fide MEROPS physiological substrate cleavage data revealed that of the 37 natural substrates with either a P3-Pro or a P1'-Leu only 5 shared both features, confirming the PICS data. Upon probing with several new quenched-fluorescent peptides, rationally designed on our specificity data, the negative cooperativity was explained by reduced non-prime side flexibility constraining accommodation of the rigidifying P3 proline with leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond. PMID:26407638

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

    SciTech Connect

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

    2008-01-01

    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.

  6. Sequence-specific cleavage of RNA by Type II restriction enzymes

    PubMed Central

    Murray, Iain A.; Stickel, Shawn K.; Roberts, Richard J.

    2010-01-01

    The ability of 223 Type II restriction endonucleases to hydrolyze RNA–DNA heteroduplex oligonucleotide substrates was assessed. Despite the significant topological and sequence asymmetry introduced when one strand of a DNA duplex is substituted by RNA we find that six restriction enzymes (AvaII, AvrII, BanI, HaeIII, HinfI and TaqI), exclusively of the Type IIP class that recognize palindromic or interrupted-palindromic DNA sequences, catalyze robust and specific cleavage of both RNA and DNA strands of such a substrate. Time-course analyses indicate that some endonucleases hydrolyze phosphodiester bonds in both strands simultaneously whereas others appear to catalyze sequential reactions in which either the DNA or RNA product accumulates more rapidly. Such strand-specific variation in cleavage susceptibility is both significant (up to orders of magnitude difference) and somewhat sequence dependent, notably in relation to the presence or absence of uracil residues in the RNA strand. Hybridization to DNA oligonucleotides that contain endonuclease recognition sites can be used to achieve targeted hydrolysis of extended RNA substrates produced by in vitro transcription. The ability to ‘restrict’ an RNA–DNA hybrid, albeit with a limited number of restriction endonucleases, provides a method whereby individual RNA molecules can be targeted for site-specific cleavage in vitro. PMID:20702422

  7. Design and Preparation of New Palladium Precatalysts for C-C and C-N Cross-Coupling Reactions

    PubMed Central

    Bruno, Nicholas C.

    2012-01-01

    A series of easily prepared, phosphine-ligated palladium precatalysts based on the 2-aminobiphenyl scaffold have been prepared. The role of the precatalyst-associated labile halide (or pseudohalide) in the formation and stability of the palladacycle has been examined. It was found that replacing the chloride in the previous version of the precatalyst with a mesylate leads to a new class of precatalysts with improved solution stability and that are readily prepared from a wider range of phosphine ligands. The differences between the previous version of precatalyst and that reported here are explored. In addition, the reactivity of the latter is examined in a range of C-C and C-N bond forming reactions. PMID:23667737

  8. Pd loaded amphiphilic COF as catalyst for multi-fold Heck reactions, C-C couplings and CO oxidation

    NASA Astrophysics Data System (ADS)

    Mullangi, Dinesh; Nandi, Shyamapada; Shalini, Sorout; Sreedhala, Sheshadri; Vinod, Chathakudath P.; Vaidhyanathan, Ramanathan

    2015-06-01

    COFs represent a class of polymers with designable crystalline structures capable of interacting with active metal nanoparticles to form excellent heterogeneous catalysts. Many valuable ligands/monomers employed in making coordination/organic polymers are prepared via Heck and C-C couplings. Here, we report an amphiphilic triazine COF and the facile single-step loading of Pd0 nanoparticles into it. An 18-20% nano-Pd loading gives highly active composite working in open air at low concentrations (Conc. Pd(0) <0.05 mol%, average TON 1500) catalyzing simultaneous multiple site Heck couplings and C-C couplings using ‘non-boronic acid’ substrates, and exhibits good recyclability with no sign of catalyst leaching. As an oxidation catalyst, it shows 100% conversion of CO to CO2 at 150 °C with no loss of activity with time and between cycles. Both vapor sorptions and contact angle measurements confirm the amphiphilic character of the COF. DFT-TB studies showed the presence of Pd-triazine and Pd-Schiff bond interactions as being favorable.

  9. Pd loaded amphiphilic COF as catalyst for multi-fold Heck reactions, C-C couplings and CO oxidation

    PubMed Central

    Mullangi, Dinesh; Nandi, Shyamapada; Shalini, Sorout; Sreedhala, Sheshadri; Vinod, Chathakudath P.; Vaidhyanathan, Ramanathan

    2015-01-01

    COFs represent a class of polymers with designable crystalline structures capable of interacting with active metal nanoparticles to form excellent heterogeneous catalysts. Many valuable ligands/monomers employed in making coordination/organic polymers are prepared via Heck and C-C couplings. Here, we report an amphiphilic triazine COF and the facile single-step loading of Pd0 nanoparticles into it. An 18–20% nano-Pd loading gives highly active composite working in open air at low concentrations (Conc. Pd(0) <0.05 mol%, average TON 1500) catalyzing simultaneous multiple site Heck couplings and C-C couplings using ‘non-boronic acid’ substrates, and exhibits good recyclability with no sign of catalyst leaching. As an oxidation catalyst, it shows 100% conversion of CO to CO2 at 150 °C with no loss of activity with time and between cycles. Both vapor sorptions and contact angle measurements confirm the amphiphilic character of the COF. DFT-TB studies showed the presence of Pd-triazine and Pd-Schiff bond interactions as being favorable. PMID:26057044

  10. A Dynamic Pathway for Stone-Wales Bond Rotation on Carbon Nanotubes through Diamond-Like Bonds

    NASA Technical Reports Server (NTRS)

    Wei, Chen-Yu; Srivastava, Deepak; Cho, Kyeong-Jae; Menon, Madhu

    2003-01-01

    A new lower energy barrier with a two-step pathway of Stone-Wales (SW) ,ond rotation on carbon nanotubes (CNTs) is found through molecular dynamics (MD) simulations of CNTs under tension. The first step involves going over to a stable sp3-like metastable configuration with half rotated and partially tilted C-C bond. The second step involves going over to the fully rotated C-C bond with the formation of a SW defect in the nanotube. The energy barrier for this two-step dynamic pathway is significantly lower than the previously known static barrier for in-plane rotation of the C-C bond on a tensile strained (> 4%) CNT.

  11. Measurement of the cleavage energy of graphite

    NASA Astrophysics Data System (ADS)

    Wang, Wen; Dai, Shuyang; Li, Xide; Yang, Jiarui; Srolovitz, David J.; Zheng, Quanshui

    2015-08-01

    The basal plane cleavage energy (CE) of graphite is a key material parameter for understanding many of the unusual properties of graphite, graphene and carbon nanotubes. Nonetheless, a wide range of values for the CE has been reported and no consensus has yet emerged. Here we report the first direct, accurate experimental measurement of the CE of graphite using a novel method based on the self-retraction phenomenon in graphite. The measured value, 0.37+/-0.01 J m-2 for the incommensurate state of bicrystal graphite, is nearly invariant with respect to temperature (22 °C<=T<=198 °C) and bicrystal twist angle, and insensitive to impurities from the atmosphere. The CE for the ideal ABAB graphite stacking, 0.39+/-0.02 J m-2, is calculated based on a combination of the measured CE and a theoretical calculation. These experimental measurements are also ideal for use in evaluating the efficacy of competing theoretical approaches.

  12. Testing of DLR C/C-SiC for HIFiRE 8 Scramjet Combustor

    NASA Technical Reports Server (NTRS)

    Glass, David E.; Capriotti, Diego P.; Reimer, Thomas; Kutemeyer, Marius; Smart, Michael

    2013-01-01

    Ceramic Matrix Composites (CMCs) have been proposed for hot structures in scramjet combustors. Previous studies have calculated significant weight savings by utilizing CMCs (active and passive) versus actively cooled metallic scramjet structures. Both a C/C and a C/C-SiC material system fabricated by DLR (Stuttgart, Germany) are being considered for use in a passively cooled combustor design for HIFiRE 8, a joint Australia / AFRL hypersonic flight program, expected to fly at Mach 7 for approximately 30 sec, at a dynamic pressure of 55 kPa. Flat panels of the DLR C/C and the C/C-SiC were tested in the NASA Langley Direct Connect Rig (DCR) at Mach 5 and Mach 6 enthalpy for several minutes. Gaseous hydrogen fuel was used to fuel the scramjet combustor. The test panels were instrumented with embedded Type K and Type S thermocouples. Zirconia felt insulation was used in some of the tests to increase the surface temperature of the C/C-SiC panel for approximately 350degF. The final C/C-SiC panel was tested for 3 cycles totaling over 135 sec at Mach 6 enthalpy. Slightly more erosion was observed on the C/C panel than the C/C-SiC panels, but both material systems demonstrated acceptable recession performance for the HIFiRE 8 flight.

  13. 77 FR 10004 - C$ cMoney, Inc.; Order of Suspension of Trading

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-21

    ... COMMISSION C$ cMoney, Inc.; Order of Suspension of Trading February 16, 2012. It appears to the Securities... securities of C$ cMoney, Inc. (``cMoney'') because of questions regarding the accuracy of assertions by c... in the securities of the above-listed company. Therefore, it is ordered, pursuant to Section 12(k)...

  14. Cleavage of nicotinamide adenine dinucleotide by the ribosome-inactivating protein from Momordica charantia.

    PubMed

    Vinkovic, M; Dunn, G; Wood, G E; Husain, J; Wood, S P; Gill, R

    2015-09-01

    The interaction of momordin, a type 1 ribosome-inactivating protein from Momordica charantia, with NADP(+) and NADPH has been investigated by X-ray diffraction analysis of complexes generated by co-crystallization and crystal soaking. It is known that the proteins of this family readily cleave the adenine-ribose bond of adenosine and related nucleotides in the crystal, leaving the product, adenine, bound to the enzyme active site. Surprisingly, the nicotinamide-ribose bond of oxidized NADP(+) is cleaved, leaving nicotinamide bound in the active site in the same position but in a slightly different orientation to that of the five-membered ring of adenine. No binding or cleavage of NADPH was observed at pH 7.4 in these experiments. These observations are in accord with current views of the enzyme mechanism and may contribute to ongoing searches for effective inhibitors. PMID:26323301

  15. Transition Metals Catalyzed Element-Cyano Bonds Activations

    PubMed Central

    Wang, Rui; Falck, John R.

    2014-01-01

    Cyano group as a versatile functionalized intermediate has been explored for several decades, as it readily transfers to many useful functionalization groups such as amine, amide, acid, etc., which make it possess high popularization and use value in organic synthesis. Reactions involved with element-cyano bond cleavage can provide not only a new cyano group but also a freshly functionalized skeleton in one-pot, consequently making it of high importance. The highlights reviewed herein include H-CN, Si-CN, C-CN, B-CN, Sn-CN, Ge-CN, S-CN, Halo-CN, N-CN, and O-CN bonds cleavages and will summarize progress in such an important research area. This review article will focus on transition metal catalyzed reactions involving element-cyano bond activation. PMID:25558119

  16. The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a

    PubMed Central

    Smith, M. Duane; Mehdizadeh, Reza; Olive, Joan E.; Collins, Richard A.

    2008-01-01

    Several small ribozymes employ general acid–base catalysis as a mechanism to enhance site-specific RNA cleavage, even though the functional groups on the ribonucleoside building blocks of RNA have pK a values far removed from physiological pH. The rate of the cleavage reaction is strongly affected by the identity of the metal cation present in the reaction solution; however, the mechanism(s) by which different cations contribute to rate enhancement has not been determined. Using the Neurospora VS ribozyme, we provide evidence that different cations confer particular shifts in the apparent pK a values of the catalytic nucleobases, which in turn determines the fraction of RNA in the protonation state competent for general acid–base catalysis at a given pH, which determines the observed rate of the cleavage reaction. Despite large differences in observed rates of cleavage in different cations, mathematical models of general acid–base catalysis indicate that k 1, the intrinsic rate of the bond-breaking step, is essentially constant irrespective of the identity of the cation(s) in the reaction solution. Thus, in contrast to models that invoke unique roles for metal ions in ribozyme chemical mechanisms, we find that most, and possibly all, of the ion-specific rate enhancement in the VS ribozyme can be explained solely by the effect of the ions on nucleobase pK a. The inference that k 1 is essentially constant suggests a resolution of the problem of kinetic ambiguity in favor of a model in which the lower pK a is that of the general acid and the higher pK a is that of the general base. PMID:18697921

  17. Autocatalytic Cleavage within Classical Swine Fever Virus NS3 Leads to a Functional Separation of Protease and Helicase

    PubMed Central

    Lamp, Benjamin; Riedel, Christiane; Wentz, Eveline; Tortorici, Maria-Alejandra

    2013-01-01

    Classical swine fever virus (CSFV) is a positive-stranded RNA virus belonging to the genus Pestivirus within the Flaviviridae family. Pivotal for processing of a large portion of the viral polyprotein is a serine protease activity within nonstructural protein 3 (NS3) that also harbors helicase and NTPase activities essential for RNA replication. In CSFV-infected cells, NS3 appears as two forms, a fully processed NS3 of 80 kDa and the precursor molecule NS2-3 of 120 kDa. Here we report the identification and mapping of additional autocatalytic intramolecular cleavages. One cleavable peptide bond occurs between Leu1781 and Met1782, giving rise to a helicase subunit of 55 kDa and, depending on the substrate, a NS2-3 fragment of 78 kDa (NS2-3p) or a NS3 protease subunit of 26 kDa (NS3p). In trans-cleavage assays using NS4-5 as a substrate, NS3p acts as a fully functional protease that is able to process the polyprotein. NS3p comprises the minimal essential protease, as deletion of Leu1781 results in inactivation. A second intramolecular cleavage was mapped to the Leu1748/Lys1749 peptide bond that yields a proteolytically inactive NS3 fragment. Deletion of either of the cleavage site residues resulted in a loss of RNA infectivity, indicating the functional importance of amino acid identity at the respective positions. Our data suggest that internal cleavage within the NS3 moiety is a common process that further extends the functional repertoires of the multifunctional NS2-3 or NS3 and represents another level of the complex polyprotein processing of Flaviviridae. PMID:23986594

  18. Trypanosome U-deletional RNA editing involves guide RNA-directed endonuclease cleavage, terminal U exonuclease, and RNA ligase activities.

    PubMed Central

    Cruz-Reyes, J; Sollner-Webb, B

    1996-01-01

    We have studied the mechanism of accurate in vitro RNA editing of Trypanosoma brucei ATPase 6 mRNA, using four mRNA-guide RNA (gRNA) pairs that specify deletion of 2, 3, or 4 U residues at editing site 1 and mitochondrial extract. This extract not only catalyzes deletion of the specified number of U residues but also exhibits a novel endonuclease activity that cleaves the input pre-mRNA in a gRNA-directed manner, precisely at the phosphodiester bond predicted in a simple enzymatic model of RNA editing. This cleavage site is inconsistent with a chimera-based editing mechanism. The U residues to be deleted, present at the 3' end of the upstream cleavage product, are then removed evidently by a 3' U-specific exonuclease and not by a reverse reaction of terminal U transferase. RNA ligase can then join the mRNA halves through their newly formed 5' P and 3' OH termini, generating mRNA faithfully edited at the first editing site. This resultant, partially edited mRNA can then undergo accurate, gRNA-directed cleavage at editing site 2, again precisely as predicted by the enzymatic editing model. All of these enzymatic activities cofractionate with the U-deletion activity and may reside in a single complex. The data imply that each round of editing is a four-step process, involving (i) gRNA-directed cleavage of the pre-mRNA at the bond immediately 5' of the region base paired to the gRNA, (ii) U deletion from or U addition to the 3' OH of the upstream mRNA half, (iii) ligation of the mRNA halves, and (iv) formation of additional base pairing between the correctly edited site and the gRNA that directs subsequent nuclease cleavage at the next editing site. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:8799125

  19. Pi Bond Orders and Bond Lengths

    ERIC Educational Resources Information Center

    Herndon, William C.; Parkanyi, Cyril

    1976-01-01

    Discusses three methods of correlating bond orders and bond lengths in unsaturated hydrocarbons: the Pauling theory, the Huckel molecular orbital technique, and self-consistent-field techniques. (MLH)

  20. Reinterpretation of the Vibrational Spectroscopy of the Medicinal Bioinorganic Synthon c,c,t-[Pt(NH3)2Cl2(OH)2]†

    PubMed Central

    Johnstone, Timothy C.

    2014-01-01

    The Pt(IV) complex c,c,t-[Pt(NH3)2Cl2(OH)2] is an important intermediate in the synthesis of Pt(IV) anticancer prodrugs and has been investigated as an anticancer agent in its own right. An analysis of the vibrational spectroscopy of this molecule was previously reported [Faggiani et al., 1982, Can. J. Chem. 60, 529] in which crystallographic determination of the structure of the complex permitted a site group approach. The space group, however, was incorrectly assigned. In the present study we have redetermined at high resolution crystal structures of c,c,t-[Pt(NH3)2Cl2(OH)2] and c,c,t-[Pt(NH3)2Cl2(OH)2]·H2O2, which enable discussion of the effect of hydrogen bonding on the N–H and O–H vibrational bands. The correct crystallographic site symmetry of the platinum complex in the c,c,t-[Pt(NH3)2Cl2(OH)2] structure is employed to conduct a new vibrational analysis using both group theoretical and modern DFT methods. This analysis reveals the nature and symmetry of the “missing band” described in the original publication and suggests a possible explanation for its disappearance. PMID:24515615

  1. Palladium-catalyzed oxidative insertion of carbon monoxide to N-sulfonyl-2-aminobiaryls through C-H bond activation: access to bioactive phenanthridinone derivatives in one pot.

    PubMed

    Rajeshkumar, Venkatachalam; Lee, Tai-Hua; Chuang, Shih-Ching

    2013-04-01

    Palladium-catalyzed oxidative carbonylation of N-sulfonyl-2-aminobiaryls through C-H bond activation and C-C, C-N bond formation under TFA-free and milder conditions has been developed. The reaction tolerates a variety of substrates and provides biologically important phenanthridinone derivatives in yields up to 94%. PMID:23477600

  2. Alkali metal control over N-N cleavage in iron complexes.

    PubMed

    Grubel, Katarzyna; Brennessel, William W; Mercado, Brandon Q; Holland, Patrick L

    2014-12-01

    Though N2 cleavage on K-promoted Fe surfaces is important in the large-scale Haber-Bosch process, there is still ambiguity about the number of Fe atoms involved during the N-N cleaving step and the interactions responsible for the promoting ability of K. This work explores a molecular Fe system for N2 reduction, particularly focusing on the differences in the results obtained using different alkali metals as reductants (Na, K, Rb, Cs). The products of these reactions feature new types of Fe-N2 and Fe-nitride cores. Surprisingly, adding more equivalents of reductant to the system gives a product in which the N-N bond is not cleaved, indicating that the reducing power is not the most important factor that determines the extent of N2 activation. On the other hand, the results suggest that the size of the alkali metal cation can control the number of Fe atoms that can approach N2, which in turn controls the ability to achieve N2 cleavage. The accumulated results indicate that cleaving the triple N-N bond to nitrides is facilitated by simultaneous approach of least three low-valent Fe atoms to a single molecule of N2. PMID:25412468

  3. Alkali Metal Control over NN Cleavage in Iron Complexes

    PubMed Central

    2015-01-01

    Though N2 cleavage on K-promoted Fe surfaces is important in the large-scale HaberBosch process, there is still ambiguity about the number of Fe atoms involved during the NN cleaving step and the interactions responsible for the promoting ability of K. This work explores a molecular Fe system for N2 reduction, particularly focusing on the differences in the results obtained using different alkali metals as reductants (Na, K, Rb, Cs). The products of these reactions feature new types of FeN2 and Fe-nitride cores. Surprisingly, adding more equivalents of reductant to the system gives a product in which the NN bond is not cleaved, indicating that the reducing power is not the most important factor that determines the extent of N2 activation. On the other hand, the results suggest that the size of the alkali metal cation can control the number of Fe atoms that can approach N2, which in turn controls the ability to achieve N2 cleavage. The accumulated results indicate that cleaving the triple NN bond to nitrides is facilitated by simultaneous approach of least three low-valent Fe atoms to a single molecule of N2. PMID:25412468

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

    PubMed

    Rodrigo, María J; Alquézar, Berta; Alós, Enriqueta; Medina, Víctor; Carmona, Lourdes; Bruno, Mark; Al-Babili, Salim; Zacarías, Lorenzo

    2013-11-01

    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 β-citraurin (3-hydroxy-β-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 β-citraurin content and CCD4b1 transcript levels. These results point to the involvement of CCD4b1 in β-citraurin formation and indicate that the accumulation of this compound is determined by the availability of the presumed precursors zeaxanthin and β-cryptoxanthin. Functional analysis of CCD4b1 by in vitro assays unequivocally demonstrated the asymmetric cleavage activity at the 7',8' double bond in zeaxanthin and β-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

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

    PubMed Central

    Rodrigo, María J.; Alquézar, Berta; Al-Babili, Salim

    2013-01-01

    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 β-citraurin (3-hydroxy-β-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 β-citraurin content and CCD4b1 transcript levels. These results point to the involvement of CCD4b1 in β-citraurin formation and indicate that the accumulation of this compound is determined by the availability of the presumed precursors zeaxanthin and β-cryptoxanthin. Functional analysis of CCD4b1 by in vitro assays unequivocally demonstrated the asymmetric cleavage activity at the 7′,8′ double bond in zeaxanthin and β-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

  6. Selective and Nonselective Cleavages in Positive and Negative CID of the Fragments Generated from In-Source Decay of Intact Proteins in MALDI-MS

    NASA Astrophysics Data System (ADS)

    Takayama, Mitsuo; Sekiya, Sadanori; Iimuro, Ryunosuke; Iwamoto, Shinichi; Tanaka, Koichi

    2014-01-01

    Selective and nonselective cleavages in ion trap low-energy collision-induced dissociation (CID) experiments of the fragments generated from in-source decay (ISD) with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) of intact proteins are described in both positive and negative ion modes. The MALDI-ISD spectra of the proteins demonstrate common, discontinuous, abundant c- and z'-ions originating from cleavage at the N-Cα bond of Xxx-Asp/Asn and Gly-Xxx residues in both positive- and negative-ion modes. The positive ion CID of the c- and z'-ions resulted in product ions originating from selective cleavage at Asp-Xxx, Glu-Xxx and Cys-Xxx residues. Nonselective cleavage product ions rationalized by the mechanism of a "mobile proton" are also observed in positive ion CID spectra. Negative ion CID of the ISD fragments results in complex product ions accompanied by the loss of neutrals from b-, c-, and y-ions. The most characteristic feature of negative ion CID is selective cleavage of the peptide bonds of acidic residues, Xxx-Asp/Glu/Cys. A definite influence of α-helix on the CID product ions was not obtained. However, the results from positive ion and negative ion CID of the MALDI-ISD fragments that may have long α-helical domains suggest that acidic residues in helix-free regions tend to degrade more than those in helical regions.

  7. Bonded Lubricants

    NASA Technical Reports Server (NTRS)

    1977-01-01

    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.

  8. Global analyses of endonucleolytic cleavage in mammals reveal expanded repertoires of cleavage-inducing small RNAs and their targets

    PubMed Central

    Cass, Ashley A.; Bahn, Jae Hoon; Lee, Jae-Hyung; Greer, Christopher; Lin, Xianzhi; Kim, Yong; Hsiao, Yun-Hua Esther; Xiao, Xinshu

    2016-01-01

    In mammals, small RNAs are important players in post-transcriptional gene regulation. While their roles in mRNA destabilization and translational repression are well appreciated, their involvement in endonucleolytic cleavage of target RNAs is poorly understood. Very few microRNAs are known to guide RNA cleavage. Endogenous small interfering RNAs are expected to induce target cleavage, but their target genes remain largely unknown. We report a systematic study of small RNA-mediated endonucleolytic cleavage in mouse through integrative analysis of small RNA and degradome sequencing data without imposing any bias toward known small RNAs. Hundreds of small cleavage-inducing RNAs and their cognate target genes were identified, significantly expanding the repertoire of known small RNA-guided cleavage events. Strikingly, both small RNAs and their target sites demonstrated significant overlap with retrotransposons, providing evidence for the long-standing speculation that retrotransposable elements in mRNAs are leveraged as signals for gene targeting. Furthermore, our analysis showed that the RNA cleavage pathway is also present in human cells but affecting a different repertoire of retrotransposons. These results show that small RNA-guided cleavage is more widespread than previously appreciated. Their impact on retrotransposons in non-coding regions shed light on important aspects of mammalian gene regulation. PMID:26975654

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

    PubMed Central

    Lidell, Martin E.; Hansson, Gunnar C.

    2006-01-01

    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

  10. Interplay of terminal amino group and coordinating side chains in directing regioselective cleavage of natural peptides and proteins with palladium(II) complexes.

    PubMed

    Milović, Nebojsa M; Kostić, Nenad M

    2002-12-30

    Palladium(II) ions anchored to side chains of histidine and methionine residues in peptides and proteins in weakly acidic aqueous solutions promote hydrolytic cleavage of proximate amide bonds in the backbone. In this study, we determine how attachment of Pd(II) ions to histidine and methionine anchors and also to the terminal amino group in six natural peptides (chains A and B of insulin, segment 11-14 of angiotensinogen, pentagastrin, angiotensin II, and segment 3-8 of angiotensin II) and two proteins (ubiquitin and cytochrome c) affects regioselectivity and rate of backbone cleavage. These Pd(II)-promoted reactions follow a clear pattern of regioselectivity, directed by the anchoring side chains. When the Pd(II) reagent is nonspecifically anchored to the terminal amino group, the ligating site that is present in almost all proteins, the cleavage is fortunately absent. When the reagent is anchored to a residue in positions 1, 2, or 3, cleavage is absent, because the terminal amino group and deprotonated amide nitrogen atom(s) interposed between it and the anchor "lock" the Pd(II) ion in hydrolytically inactive chelate complexes. When the reagent is anchored to residues in positions beyond 3, the second amide bond upstream from the anchor is regioselectively cleaved in all cases when the anchor was "isolated," that is, flanked by noncoordinating side chains. Segment 3-8 of angiotensin II undergoes additional cleavage, which we explain by determining the rate constants for the cleavage, identifying the rate-limiting displacement of ethylenediamine ligand from the Pd(II) ion, and detecting several intermediates. Experiments with cytochrome c demonstrate that the number of cleavage sites can be controlled by adjusting the mole ratio of the Pd(II) reagent to the substrate. Our inorganic peptidases are useful for biochemical applications because their regioselectivity and reactivity set them apart from proteolytic enzymes and organic chemical reagents. PMID:12495344

  11. Distinct oxidative cleavage and modification of bovine [Cu- Zn]-SOD by an ascorbic acid/Cu(II) system: Identification of novel copper binding site on SOD molecule.

    PubMed

    Uehara, Hiroshi; Luo, Shen; Aryal, Baikuntha; Levine, Rodney L; Rao, V Ashutosh

    2016-05-01

    We investigated the combined effect of ascorbate and copper [Asc/Cu(II)] on the integrity of bovine [Cu-Zn]-superoxide dismutase (bSOD1) as a model system to study the metal catalyzed oxidation (MCO) and fragmentation of proteins. We found Asc/Cu(II) mediates specific cleavage of bSOD1 and generates 12.5 and 3.2kDa fragments in addition to oxidation/carbonylation of the protein. The effect of other tested transition metals, a metal chelator, and hydrogen peroxide on the cleavage and oxidation indicated that binding of copper to a previously unknown site on SOD1 is responsible for the Asc/Cu(II) specific cleavage and oxidation. We utilized tandem mass spectrometry to identify the specific cleavage sites of Asc/Cu(II)-treated bSOD1. Analyses of tryptic- and AspN-peptides have demonstrated the cleavage to occur at Gly31 with peptide bond breakage with Thr30 and Ser32 through diamide and α-amidation pathways, respectively. The three-dimensional structure of bSOD1 reveals the imidazole ring of His19 localized within 5Å from the α-carbon of Gly31 providing a structural basis that copper ion, most likely coordinated by His19, catalyzes the specific cleavage reaction. PMID:26872685

  12. Cleavage of synthetic substrates containing non-nucleotide inserts by restriction endonucleases. Change in the cleavage specificity of endonuclease SsoII.

    PubMed Central

    Kubareva, E A; Petrauskene, O V; Karyagina, A S; Tashlitsky, V N; Nikolskaya, I I; Gromova, E S

    1992-01-01

    A study was made of the interaction between restriction endonucleases recognizing CCNGG (SsoII and ScrFI) or CCA/TGG (MvaI and EcoRII) DNA sequences and a set of synthetic substrates containing 1,3-propanediol, 1,2-dideoxy-D-ribofuranose or 9-[1'-hydroxy-2'-(hydroxymethyl)ethoxy] methylguanine (gIG) residues replacing either one of the central nucleosides or dG residues in the recognition site. The non-nucleotide inserts (except for gIG) introduced into the recognition site both increase the efficiency of SsoII and change its specificity. A cleavage at the noncanonical position takes place, in some cases in addition to the correct ones. Noncanonical hydrolysis by SsoII occurs at the phosphodiester bond adjacent to the point of modification towards the 5'-end. With the guanine base returned (the substrate with gIG), the correct cleavage position is restored. ScrFI specifically cleaves all the modified substrates. DNA duplexes with non-nucleotide inserts (except for the gIG-containing duplex) are resistant to hydrolysis by MvaI and EcoRII. Prompted by the data obtained we discuss the peculiarities of recognition by restriction endonucleases of 5-membered DNA sequences which have completely or partially degenerated central base pairs. It is suggested that SsoII forms a complex with DNA in an 'open' form. Images PMID:1408753

  13. Basics of Fidelity Bonding.

    ERIC Educational Resources Information Center

    Kahn, Steven P.

    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…

  14. H-H, C-H, and C-C NMR spin-spin coupling constants calculated by the FP-INDO method for aromatic hydrocarbons

    NASA Technical Reports Server (NTRS)

    Long, S. A. T.; Memory, J. D.

    1978-01-01

    The FP-INDO (finite perturbation-intermediate neglect of differential overlap) method is used to calculate the H-H, C-H, and C-C coupling constants in hertz for molecules of six different benzenoid hydrocarbons: benzene, naphthalene, biphenyl, anthracene, phenanthrene, and pyrene. The calculations are based on both the actual and the average molecular geometries. It is found that only the actual molecular geometries can always yield the correct relative order of values for the H-H coupling constants. For the calculated C-C coupling constants, as for the calculated C-H coupling constants, the signs are positive (negative) for an odd (even) number of bonds connecting the two nuclei. Agreements between the calculated and experimental values of the coupling constants for all six molecules are comparable to those reported previously for other molecules.

  15. Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation

    PubMed Central

    Rawlings, Neil D.

    2016-01-01

    One peptidase can usually be distinguished from another biochemically by its action on proteins, peptides and synthetic substrates. Since 1996, the MEROPS database (http://merops.sanger.ac.uk) has accumulated a collection of cleavages in substrates that now amounts to 66,615 cleavages. The total number of peptidases for which at least one cleavage is known is 1700 out of a total of 2457 different peptidases. This paper describes how the cleavages are obtained from the scientific literature, how they are annotated and how cleavages in peptides and proteins are cross-referenced to entries in the UniProt protein sequence database. The specificity profiles of 556 peptidases are shown for which ten or more substrate cleavages are known. However, it has been proposed that at least 40 cleavages in disparate proteins are required for specificity analysis to be meaningful, and only 163 peptidases (6.6%) fulfil this criterion. Also described are the various displays shown on the website to aid with the understanding of peptidase specificity, which are derived from the substrate cleavage collection. These displays include a logo, distribution matrix, and tables to summarize which amino acids or groups of amino acids are acceptable (or not acceptable) in each substrate binding pocket. For each protein substrate, there is a display to show how it is processed and degraded. Also described are tools on the website to help with the assessment of the physiological relevance of cleavages in a substrate. These tools rely on the hypothesis that a cleavage site that is conserved in orthologues is likely to be physiologically relevant, and alignments of substrate protein sequences are made utilizing the UniRef50 database, in which in each entry sequences are 50% or more identical. Conservation in this case means substitutions are permitted only if the amino acid is known to occupy the same substrate binding pocket from at least one other substrate cleaved by the same peptidase. PMID:26455268

  16. Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation.

    PubMed

    Rawlings, Neil D

    2016-03-01

    One peptidase can usually be distinguished from another biochemically by its action on proteins, peptides and synthetic substrates. Since 1996, the MEROPS database (http://merops.sanger.ac.uk) has accumulated a collection of cleavages in substrates that now amounts to 66,615 cleavages. The total number of peptidases for which at least one cleavage is known is 1700 out of a total of 2457 different peptidases. This paper describes how the cleavages are obtained from the scientific literature, how they are annotated and how cleavages in peptides and proteins are cross-referenced to entries in the UniProt protein sequence database. The specificity profiles of 556 peptidases are shown for which ten or more substrate cleavages are known. However, it has been proposed that at least 40 cleavages in disparate proteins are required for specificity analysis to be meaningful, and only 163 peptidases (6.6%) fulfil this criterion. Also described are the various displays shown on the website to aid with the understanding of peptidase specificity, which are derived from the substrate cleavage collection. These displays include a logo, distribution matrix, and tables to summarize which amino acids or groups of amino acids are acceptable (or not acceptable) in each substrate binding pocket. For each protein substrate, there is a display to show how it is processed and degraded. Also described are tools on the website to help with the assessment of the physiological relevance of cleavages in a substrate. These tools rely on the hypothesis that a cleavage site that is conserved in orthologues is likely to be physiologically relevant, and alignments of substrate protein sequences are made utilizing the UniRef50 database, in which in each entry sequences are 50% or more identical. Conservation in this case means substitutions are permitted only if the amino acid is known to occupy the same substrate binding pocket from at least one other substrate cleaved by the same peptidase. PMID:26455268

  17. Divalent metals can reside on bonds in fullerenes.

    PubMed

    Gao, Xuejiao; Sun, Baoyun; Zhao, Yuliang; Chen, Bo-Zhen; Gao, Xingfa

    2015-05-28

    DFT calculations consistently suggest that a lanthanide will sit on either the 6/6 bond inside C60 having a divalent state or the hexagonal center having a trivalent state. Some lanthanides can stay only above the 6/6 bond inside C60 to form stabilized structures, despite the greatly reduced metal-cage coordination numbers. The preference for C-C bonds by a divalent metal has been confirmed by revisiting the structures of Yb@C2v(3)-C80, Yb@Cs(6)-C82 and Yb@C2v(9)-C82, for which the calculations suggest that the Yb atoms are indeed situated above the C-C bonds, close to the reported structures obtained by single crystal XRD experiments. The result will guide the characterization of structures and electronic structures of endohedral metallofullerenes (EMFs), especially C60 mono-EMFs, in the future. PMID:25919542

  18. 3-Keto-5-aminohexanoate Cleavage Enzyme

    PubMed Central

    Bellinzoni, Marco; Bastard, Karine; Perret, Alain; Zaparucha, Anne; Perchat, Nadia; Vergne, Carine; Wagner, Tristan; de Melo-Minardi, Raquel C.; Artiguenave, François; Cohen, Georges N.; Weissenbach, Jean; Salanoubat, Marcel; Alzari, Pedro M.

    2011-01-01

    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

  19. A cleavage toughness master curve model

    NASA Astrophysics Data System (ADS)

    Odette, G. R.; He, M. Y.

    2000-12-01

    Development of fusion power will require a fracture toughness database, derived largely from small specimen tests, closely integrated with methods to assess first wall and blanket structural integrities. A master curve-shift (MC-ΔT) method has been proposed as an engineering expedient to treat the effects of structural geometry, irradiation, loading rates and safety margins. However, a number of issues related to the MC-ΔT method remain to be resolved, including the universality of MC shapes. A new micromechanical model of fracture toughness in the cleavage transition regime is proposed that combines analytical representations of finite element analysis simulations of crack-tip stress fields with a local critical stress-critical stressed area (σ∗-A∗) fracture criterion. This model, has been successful in predicting geometry effects, as well as high loading rate and irradiation hardening-induced Charpy shifts. By incorporating a modest temperature dependence in σ∗(T), an inconsistency between model predictions and an observed universal-type MC shape is resolved.

  20. Measurement of the cleavage energy of graphite.

    PubMed

    Wang, Wen; Dai, Shuyang; Li, Xide; Yang, Jiarui; Srolovitz, David J; Zheng, Quanshui

    2015-01-01

    The basal plane cleavage energy (CE) of graphite is a key material parameter for understanding many of the unusual properties of graphite, graphene and carbon nanotubes. Nonetheless, a wide range of values for the CE has been reported and no consensus has yet emerged. Here we report the first direct, accurate experimental measurement of the CE of graphite using a novel method based on the self-retraction phenomenon in graphite. The measured value, 0.37±0.01 J m(-2) for the incommensurate state of bicrystal graphite, is nearly invariant with respect to temperature (22 °C≤T≤198 °C) and bicrystal twist angle, and insensitive to impurities from the atmosphere. The CE for the ideal ABAB graphite stacking, 0.39±0.02 J m(-2), is calculated based on a combination of the measured CE and a theoretical calculation. These experimental measurements are also ideal for use in evaluating the efficacy of competing theoretical approaches. PMID:26314373

  1. Measurement of the cleavage energy of graphite

    PubMed Central

    Wang, Wen; Dai, Shuyang; Li, Xide; Yang, Jiarui; Srolovitz, David J.; Zheng, Quanshui

    2015-01-01

    The basal plane cleavage energy (CE) of graphite is a key material parameter for understanding many of the unusual properties of graphite, graphene and carbon nanotubes. Nonetheless, a wide range of values for the CE has been reported and no consensus has yet emerged. Here we report the first direct, accurate experimental measurement of the CE of graphite using a novel method based on the self-retraction phenomenon in graphite. The measured value, 0.37±0.01 J m−2 for the incommensurate state of bicrystal graphite, is nearly invariant with respect to temperature (22 °C≤T≤198 °C) and bicrystal twist angle, and insensitive to impurities from the atmosphere. The CE for the ideal ABAB graphite stacking, 0.39±0.02 J m−2, is calculated based on a combination of the measured CE and a theoretical calculation. These experimental measurements are also ideal for use in evaluating the efficacy of competing theoretical approaches. PMID:26314373

  2. Familial Alzheimer’s mutations within APPTM increase Aβ42 production by enhancing accessibility of ɛ-cleavage site

    NASA Astrophysics Data System (ADS)

    Chen, Wen; Gamache, Eric; Rosenman, David J.; Xie, Jian; Lopez, Maria M.; Li, Yue-Ming; Wang, Chunyu

    2014-01-01

    The high Aβ42/Aβ40 production ratio is a hallmark of familial Alzheimer’s disease, which can be caused by mutations in the amyloid precursor protein (APP). The C-terminus of Aβ is generated by γ-secretase cleavage within the transmembrane domain of APP (APPTM), a process that is primed by an initial ɛ-cleavage at either T48 or L49, resulting in subsequent production of Aβ42 or Aβ40, respectively. Here we solve the dimer structures of wild-type APPTM (AAPTM WT) and mutant APPTM (FAD mutants V44M) with solution NMR. The right-handed APPTM helical dimer is mediated by GXXXA motif. From the NMR structural and dynamic data, we show that the V44M and V44A mutations can selectively expose the T48 site by weakening helical hydrogen bonds and increasing hydrogen-deuterium exchange rate (kex). We propose a structural model in which FAD mutations (V44M and V44A) can open the T48 site γ-secretase for the initial ɛ-cleavage, and consequently shift cleavage preference towards Aβ42.

  3. Analysis of the recognition mechanism involved in the EcoRV catalyzed cleavage of DNA using modified oligodeoxynucleotides.

    PubMed Central

    Fliess, A; Wolfes, H; Seela, F; Pingoud, A

    1988-01-01

    We have prepared a series of undecadeoxynucleotides that contain changes in the functional group pattern present within the EcoRV recognition site - GATATC-. Oligonucleotides were synthesized on solid phase using normal and modified beta-cyanoethylphosphoramidites and analyzed in steady state cleavage experiments with the EcoRV restriction endonuclease. The following groups appear to interact strongly with the enzyme, since their modification or substitution renders the oligonucleotides refractory to cleavage: the exocyclic NH2-groups of both A residues, the N7 of the first A residue, the exocyclic NH2-group of the C residue and the CH3-groups of both T residues. The exocyclic NH-group of the G residue supports effective recognition, since its absence lowers the kcat of the cleavage reaction. The N7 of the second A residue and the C5 position of the C residue apparently are not recognized by EcoRV; their substitution by -CH- or modification with -Br or -CH3, resp., does not considerably change the rate of cleavage. All oligonucleotides investigated compete with the unmodified substrate for binding to the enzyme. We conclude that EcoRV recognizes its substrate presumably through hydrogen bonds to the exocyclic NH2-group and the N7 of the first A residue, the exocyclic NH2-groups of the second A and the C residue, as well as through hydrophobic interactions with both T residues. PMID:3062581

  4. Oxidative addition of methane and benzene C--H bonds to rhodium center: A DFT study

    NASA Astrophysics Data System (ADS)

    Bi, Siwei; Zhang, Zhenwei; Zhu, Shufen

    2006-11-01

    A density functional theory study on mechanisms of the oxidative addition of methane and benzene C-H bonds to the rhodium center containing Cp and PMe 3 ligands has been performed. Our calculated results confirm that the C-H bond cleavage from a sigma complex to a hydride alkyl complex is the rate-determining step. Compared with the case of methane C-H bond, the oxidative addition of benzene C-H bond is more favorable kinetically and thermodynamically. Stronger backdonation from metal center to the σ ∗ antibonding orbital of benzene C-H bond is responsible for the observations.

  5. Quantification of DNA cleavage specificity in Hi-C experiments

    PubMed Central

    Meluzzi, Dario; Arya, Gaurav

    2016-01-01

    Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonuclease. Although this cleavage should happen specifically at the enzyme's recognition sequence, an unknown proportion of cleavage events may involve other sequences, owing to the enzyme's star activity or to random DNA breakage. A quantitative estimation of these non-specific cleavages may enable simulating realistic Hi-C read pairs for validation of downstream analyses, monitoring the reproducibility of experimental conditions and investigating biophysical properties that correlate with DNA cleavage patterns. Here we describe a computational method for analyzing Hi-C read pairs to estimate the fractions of cleavages at different possible targets. The method relies on expressing an observed local target distribution downstream of aligned reads as a linear combination of known conditional local target distributions. We validated this method using Hi-C read pairs obtained by computer simulation. Application of the method to experimental Hi-C datasets from murine cells revealed interesting similarities and differences in patterns of cleavage across the various experiments considered. PMID:26264668

  6. [On the classification of the cleavage patterns in amphibian embryos].

    PubMed

    Desnitskiĭ, A G

    2014-01-01

    This paper presents a brief survey and preliminary classification of embryonic cleavage patterns in the class Amphibia. We use published data on 41 anuran and 22 urodele species concerning the character of the third cleavage furrow (latitudinal or longitudinal) and the stage of transition from synchronous to asynchronous blastomere divisions in the animal hemisphere (4-8-celled stage, 8-16-celled stage or later). Based on this, four patterns of amphibian embryonic cleavage are recognized, and an attempt to elucidate the evolutionary relationships among these patterns is undertaken. The so-called "standard" cleavage pattern (the extensive series of synchronous blastomere divisions including latitudinal furrows of the third cleavage) with the typical model species Ambystoma mexicanum and Xenopus laevis seems to be derived and probably originated independently in the orders Anura and Caudata. The ancestral amphibian cleavage pattern seems to be represented by species with longitudinal furrows of the third cleavage and the loss ofsynchrony as early as the 8-celled stage (such as in primitive urodele species from the family Cryptobranchidae). PMID:25720261

  7. Bundled slaty cleavage in laminated argillite, north-central minnesota

    USGS Publications Warehouse

    Southwick, D.L.

    1987-01-01

    Exceptional bundled slaty cleavage (defined herein) has been found in drill cores of laminated, folded, weakly metamorphosed argillite at several localities in the early Proterozoic Animikie basin of north-central Minnesota. The cleavage domains are more closely spaced within the cleavage bundles than outside them, the mean tectosilicate grain size of siltstone layers, measured normal to cleavage, is less in the cleavage bundles than outside them, and the cleavage bundles are enriched in opaque phases and phyllosilicates relative to extra-bundle segments. These facts suggest that pressure solution was a major factor in bundle development. If it is assumed that opaque phases have been conserved during pressure solution, the modal differences in composition between intra-bundle and extra-bundle segments of beds provide a means for estimating bulk material shortening normal to cleavage. Argillite samples from the central part of the Animikie basin have been shortened a minimum of about 22%, as estimated by this method. These estimates are similar to the shortening values derived from other strain markers in other rock types interbedded with the argillite, and are also consistent with the regional pattern of deformation. ?? 1987.

  8. Specific Cleavage of the Nucleoprotein of Fish Rhabdovirus.

    PubMed

    Zhou, G-Z; Yi, Y-J; Chen, Z-Y; Zhang, Q-Y

    2015-11-01

    Siniperca chuatsi rhabdovirus (SCRV) is one of myriad rhabdoviruses recorded in fish. Preliminary data show that inhibition of the SCRV nucleoprotein (N) could significantly reduce the progeny virus titers in infected Epithelioma papulosum cyprinid (EPC) cells. Here, the authors propose that cleavage of the viral 47-kDa N protein is caspase-mediated based on caspase inhibition experiments, transient expression in EPC transfection, and analysis of cleavage sites. Cleavage of the SCRV N protein in culture was prevented by a pan-caspase inhibitor, z-VAD-FMK (z-Val-Ala-DL-Asp-fluoromethyl ketone). Subsequently, N was transiently expressed in EPC cells, the results of which indicated that the specific cleavage of N also occurred in the cells transfected with N-GFP plasmid. Several truncated fragments of the N gene were constructed and transiently transfected into EPC cells. Immunoblotting results indicated that D324 and D374 are the cleavage sites of N by caspases. The authors also found that z-VAD-FMK could inhibit the cytopathic effect in SCRV-infected EPC cells but not affect the production of infectious progeny, suggesting that the caspase-mediated cleavage of N protein is not required for in vitro SCRV replication. To the authors' knowledge, this is the first report on the cleavage of rhabdovirus proteins. PMID:25689989

  9. Cleavage fracture properties of high strength steel weldments

    SciTech Connect

    Hughes, R.K.; Ritter, J.C.

    1996-12-31

    The qualification of consumables and welding of steels in critical naval applications, including submarine construction, is dependent upon the achievement of high levels of toughness at low temperature. The principal technique employed is the Charpy impact test at temperatures down to {minus}115 C ({minus}175 F). In the investigation described here, low temperature toughness properties were investigated by breaking notched specimens in slow four point bending and measuring the critical tensile stress for cleavage initiation. Multi-pass Flux Cored Arc (FCA) welds joining 690 MPa (100 ksi) yield strength, quenched and tempered steel were tested to identify cleavage fracture micromechanisms and to investigate the role of microstructural features in the cleavage fracture process. Cleavage fracture stress values in the range 2,018 to 2,381 MPa were recorded in weld metal when testing at sub-zero temperatures. Detailed examination of fracture surfaces by scanning electron microscope (SEM) revealed that weld metal inclusions play a critical role in acting as cleavage initiation sites. Changing welding position from downhand to vertical-up resulted in a small number of widely spaced inclusions approaching or exceeding 10 {micro}m in diameter but these were not observed to act as cleavage initiation sites. The cleavage fracture resistance of multi-pass Manual Metal Arc (MMA) welds which are currently under investigation is compared with FCA weldments.

  10. Universal Bronsted-Evans-Polanyi Relations for C-C, C-O, C-N, N-O, N-N, and O-O Dissociation Reactions

    SciTech Connect

    Wang, Shengguang

    2010-10-27

    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.

  11. Circularization and cleavage of guinea pig cytomegalovirus genomes.

    PubMed Central

    McVoy, M A; Nixon, D E; Adler, S P

    1997-01-01

    The mechanisms by which herpesvirus genome ends are fused to form circles after infection and are re-formed by cleavage from concatemeric DNA are unknown. We used the simple structure of guinea pig cytomegalovirus genomes, which have either one repeated DNA sequence at each end or one repeat at one end and no repeat at the other, to study these mechanisms. In circular DNA, two restriction fragments contained fused terminal sequences and had sizes consistent with the presence of single or double terminal repeats. This result implies a simple ligation of genomic ends and shows that circularization does not occur by annealing of single-stranded terminal repeats formed by exonuclease digestion. Cleavage to form the two genome types occurred at two sites, and homologies between these sites identified two potential cis elements that may be necessary for cleavage. One element coincided with the A-rich region of a pac2 sequence and had 9 of 11 bases identical between the two sites. The second element had six bases identical at both sites, in each case 7 bp from the termini. To confirm the presence of cis cleavage elements, a recombinant virus in which foreign sequences displaced the 6- and 11-bp elements 1 kb from the cleavage point was constructed. Cleavage at the disrupted site did not occur. In a second recombinant virus, restoration of 64 bases containing the 6- and 11-bp elements to the disrupted cleavage site restored cleavage. Therefore, cis cleavage elements exist within this 64-base region, and sequence conservation suggests that they are the 6- and 11-bp elements. PMID:9151807

  12. Specific oxidative cleavage of carotenoids by VP14 of maize

    SciTech Connect

    Schwartz, S.H.; Zeevaart, J.A.D.; Gage, D.A.; Tan, Bao Cai

    1997-06-20

    The plant growth regulator abscisic acid (ABA) is formed by the oxidative cleavage of an epoxy-carotenoid. The synthesis of other apocarotenoids, such as vitamin A in animals, may occur by a similar mechanism. In ABA biosynthesis, oxidative cleavage is the first committed reaction and is believed to be the key regulatory step. A new ABA-deficient mutant of maize has been identified and the corresponding gene, Vp14, has been cloned. The recombinant VP14 protein catalyzes the cleavage of 9-cis-epoxy-carotenoids to form C{sub 25} apo-aldehydes and xanthoxin, a precursor of ABA in higher plants.

  13. Detection of nucleic acid sequences by invader-directed cleavage

    DOEpatents

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    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.

  14. Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study.

    PubMed

    Qi, Yue; Lu, Jiarui; Lai, Wenzhen

    2016-05-26

    To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O-O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C2 hydroxyl group is not ionized (the nonionized pathway), the O-O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C2 hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C2 hydroxyl group is more likely to be nonionized. PMID:27119315

  15. C/C composite brake disk nondestructive evaluation by IR thermography

    NASA Astrophysics Data System (ADS)

    Chu, Tsuchin P.; Poudel, Anish; Filip, Peter

    2012-06-01

    This paper discusses the non-destructive evaluation of thick Carbon/Carbon (C/C) composite aircraft brake disks by using transient infrared thermography (IRT) approach. Thermal diffusivity measurement technique was applied to identify the subsurface anomalies in thick C/C brake disks. In addition, finite element analysis (FEA) modeling tool was used to determine the transient thermal response of the C/C disks that were subjected to flash heating. For this, series of finite element models were built and thermal responses with various thermal diffusivities subjected to different heating conditions were investigated. Experiments were conducted to verify the models by using custom built in-house IRT system and commercial turnkey system. The analysis and experimental results showed good correlation between thermal diffusivity value and anomalies within the disk. It was demonstrated that the step-heating transient thermal approach could be effectively applied to obtain the whole field thermal diffusivity value of C/C composites.

  16. A dense and strong bonding collagen film for carbon/carbon composites

    NASA Astrophysics Data System (ADS)

    Cao, Sheng; Li, Hejun; Li, Kezhi; Lu, Jinhua; Zhang, Leilei

    2015-08-01

    A strong bonding collagen film was successfully prepared on carbon/carbon (C/C) composites. The surface conditions of the modified C/C composites were detected by contact angle measurements, scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS) and Raman spectra. The roughness, optical morphology, bonding strength and biocompatibility of collagen films at different pH values were detected by confocal laser scanning microscope (CLSM), universal test machine and cytology tests in vitro. After a 4-h modification in 30% H2O2 solution at 100 °C, the contact angle on the surface of C/C composites was decreased from 92.3° to 65.3°. Large quantities of hydroxyl, carboxyl and carbonyl functional groups were formed on the surface of the modified C/C composites. Then a dense and continuous collagen film was prepared on the modified C/C substrate. Bonding strength between collagen film and C/C substrate was reached to 8 MPa level when the pH value of this collagen film was 2.5 after the preparing process. With 2-day dehydrathermal treatment (DHT) crosslinking at 105 °C, the bonding strength was increased to 12 MPa level. At last, the results of in vitro cytological test showed that this collagen film made a great improvement on the biocompatibility on C/C composites.

  17. Rubber oxygenase and latex clearing protein cleave rubber to different products and use different cleavage mechanisms.

    PubMed

    Birke, Jakob; Jendrossek, Dieter

    2014-08-01

    Two types of enzyme for oxidative cleavage of poly(cis-1,4-isoprene) are known. One is rubber oxygenase (RoxA) that is secreted by Xanthomonas sp. strain 35Y and a few other Gram-negative rubber-degrading bacteria during growth on polyisoprene. RoxA was studied in the past, and the recently solved structure showed a structural relationship to bacterial cytochrome c peroxidases (J. Seidel et al., Proc. Natl. Acad. Sci. U. S. A. 110:13833-13838, 2013, http://dx.doi.org/10.1073/pnas.1305560110). The other enzyme is latex-clearing protein (Lcp) that is secreted by rubber-degrading actinomycetes, but Lcp has not yet been purified. Here, we expressed Lcp of Streptomyces sp. strain K30 in a ΔroxA background of Xanthomonas sp. strain 35Y and purified native (untagged) Lcp. The specific activities of Lcp and RoxA were 0.70 and 0.48 U/mg, respectively. Lcp differed from RoxA in the absence of heme groups and other characteristics. Notably, Lcp degraded polyisoprene via endo-type cleavage to tetra-C20 and higher oligo-isoprenoids with aldehyde and keto end groups, whereas RoxA used an exo-type cleavage mechanism to give the main end product 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD). RoxA was able to cleave isolated Lcp-derived oligo-isoprenoid molecules to ODTD. Inhibitor studies, spectroscopic investigations and metal analysis gave no indication for the presence of iron, other metals, or cofactors in Lcp. Our results suggest that Lcp could be a member of the growing group of cofactor-independent oxygenases and differs in the cleavage mechanism from heme-dependent RoxA. In conclusion, RoxA and Lcp represent two different answers to the same biochemical problem, the cleavage of polyisoprene, a polymer that has carbon-carbon double bonds as the only functional groups for enzymatic attack. PMID:24907333

  18. Rubber Oxygenase and Latex Clearing Protein Cleave Rubber to Different Products and Use Different Cleavage Mechanisms

    PubMed Central

    Birke, Jakob

    2014-01-01

    Two types of enzyme for oxidative cleavage of poly(cis-1,4-isoprene) are known. One is rubber oxygenase (RoxA) that is secreted by Xanthomonas sp. strain 35Y and a few other Gram-negative rubber-degrading bacteria during growth on polyisoprene. RoxA was studied in the past, and the recently solved structure showed a structural relationship to bacterial cytochrome c peroxidases (J. Seidel et al., Proc. Natl. Acad. Sci. U. S. A. 110:13833–13838, 2013, http://dx.doi.org/10.1073/pnas.1305560110). The other enzyme is latex-clearing protein (Lcp) that is secreted by rubber-degrading actinomycetes, but Lcp has not yet been purified. Here, we expressed Lcp of Streptomyces sp. strain K30 in a ΔroxA background of Xanthomonas sp. strain 35Y and purified native (untagged) Lcp. The specific activities of Lcp and RoxA were 0.70 and 0.48 U/mg, respectively. Lcp differed from RoxA in the absence of heme groups and other characteristics. Notably, Lcp degraded polyisoprene via endo-type cleavage to tetra-C20 and higher oligo-isoprenoids with aldehyde and keto end groups, whereas RoxA used an exo-type cleavage mechanism to give the main end product 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD). RoxA was able to cleave isolated Lcp-derived oligo-isoprenoid molecules to ODTD. Inhibitor studies, spectroscopic investigations and metal analysis gave no indication for the presence of iron, other metals, or cofactors in Lcp. Our results suggest that Lcp could be a member of the growing group of cofactor-independent oxygenases and differs in the cleavage mechanism from heme-dependent RoxA. In conclusion, RoxA and Lcp represent two different answers to the same biochemical problem, the cleavage of polyisoprene, a polymer that has carbon-carbon double bonds as the only functional groups for enzymatic attack. PMID:24907333

  19. Mechanical properties of oxidation-resistant SiC/C compositionally graded graphite materials

    SciTech Connect

    Nakano, Junichi; Fujii, Kimio; Yamada, Reiji

    1997-11-01

    Mechanical properties of oxidation-resistant SiC/C compositionally graded graphite materials composed of a CVD SiC coating layer, a SiC/C graded layer, and a graphite substrate were studied by bending, compressive, and hardness tests at room temperature. CVD SiC coated graphite and graphite with a SiC/C graded layer alone were also examined. The bending strengths of oxidation-resistant SiC/C compositionally graded graphite materials as well as CVD SiC coated graphite were about twice as much as that of graphite. The bending and compressive strengths of graphite with the SiC/C graded layer along were almost the same as those of graphite. The higher strengths of graphite with the CVD SiC layer can be mainly due to the CVD SiC strength itself, and partly due to the smooth CVD surface. No effect of the SiC/C layer on the strengths was discussed in terms of porosity, surface morphology, and the strength of SiC.

  20. Detection and Formation of Interstellar c-C_3D_2

    NASA Astrophysics Data System (ADS)

    Spezzano, Silvia; Brunken, Sandra; Schilke, Peter; Menten, Karl M.; Caselli, Paola; McCarthy, Michael C.; Bizzocchi, Luca; Trevino, Sandra; Aikawa, Yuri; Schlemmer, Stephan

    2013-06-01

    Multiply deuterated molecules are unique observational probes for the earliest stages of star formation. Cyclopropenylidene, c-C_3H_2, is an ideal probe for deuterium chemistry. It is one of the most widespread molecules in our Galaxy and it has the possibility of double deuteration. Furthermore, since c-C_3H_2 is an "early-type" molecule, it is a particular useful tool to investigate early stages of a molecular cloud. This makes observations of its deuterated forms particularly important to test time-dependent chemical codes which include deuteration processes. The centimeter and millimeter wavelength spectra of doubly deuterated cyclopropenylidene have recently been measured in the laboratory, allowing for the first time a search for c-C_3D_2 in space. We report the detection of c-C_3D_2 in two starless cores, L1544 and TMC-1C. The deuteration of this small hydrocarbon ring is analysed with a comprehensive gas-grain model, the first including doubly deuterated species. The observed abundances of c-C_3D_2 can be explained solely by gas-phase processes, supporting the idea that c-C_3H_2 is a good indicator of gas-phase deuteration. S. Spezzano, F. Tamassia, S. Thorwirth, P. Thaddeus, C. A. Gottlieb, and M. C. McCarthy Astroph. J. Supp. Series {200}(1), 2012.