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. 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

  3. Structure sensitivity of hydrogenolytic cleavage of endocyclic and exocyclic C-C bonds in methylcyclohexane over supported iridium particles

    SciTech Connect

    Shi, Hui; Gutierrez, Oliver Y.; Haller, Gary L.; Mei, Donghai; Rousseau, Roger J.; Lercher, Johannes A.

    2013-01-02

    Structure sensitivities, H2 pressure effects and temperature dependencies for rates and selectivities of endo- and exocyclic CC bond cleavage in methylcyclohexane were studied over supported Ir catalysts. The rate of endocyclic CC bond cleavage first decreased and then increased with declining Ir dispersion from 0.65 to 0.035. The ring opening (RO) product distribution remained unchanged with varying H2 pressure on small Ir particles, while further shifting to methylhexanes with increasing H2 pressure on large particles. In contrast, the rate and selectivity of exocyclic CC bond cleavage decreased monotonically with increasing H2 pressure and decreasing Ir particle size. The distinct dependencies of endocyclic and exocyclic CC bond cleavage pathways on Ir dispersion and H2 pressure suggest that they are mediated by surface species with different ensemble size requirements. DFT calculations were performed on an Ir50 cluster and an Ir(111) surface, with or without pre-adsorbed hydrogen atoms, to provide insight into the observed effects of particle size and H2 pressure on RO pathways. On small Ir particles, the calculated dehydrogenation enthalpies for all endocyclic bonds were similar and affected to similar extents by H2 pressure; on large particles, the selectivity to n-heptane (via substituted C-C bond cleavage) was even lower than on small particles as a result of the least favorable adsorption and dehydrogenation energetics for hindered bonds. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences under Contract DE-AC05-76RL01830. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. The computing time is provided by the user project from EMSL, a national scientific user facility sponsored by the US Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

  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. Alkynylation of Tertiary Cycloalkanols via Radical C-C Bond Cleavage: A Route to Distal Alkynylated Ketones.

    PubMed

    Wang, Shun; Guo, Li-Na; Wang, Hua; Duan, Xin-Hua

    2015-10-01

    An efficient Na2S2O8-promoted radical coupling of tertiary cycloalkanols with alkynyl hypervalent iodide reagents via C-C bond cleavage was developed. This tandem ring-opening/alkynylation procedure showed some advantages, including mild conditions and wide substrate scope, thus providing a simple synthetic method for ?-, ?- and ?-alkynylated ketones. PMID:26378463

  6. Aryl Nitriles from Alkynes Using tert-Butyl Nitrite: Metal-Free Approach to C?C Bond Cleavage.

    PubMed

    Dutta, Uttam; Lupton, David W; Maiti, Debabrata

    2016-02-19

    Alkyne C?C bond breaking, outside of alkyne metathesis, remains an underdeveloped area in reaction discovery. Recently, nitrogenation has been reported to allow nitrile formation from alkynes. A new protocol for the metal-free C?C bond cleavage of terminal alkynes to produce nitriles is reported. This method provides an opportunity to synthesize a vast range of nitriles containing aryl, heteroaryl, and natural product derivatives (38 examples). In addition, the potential of (t)BuONO to act as a powerful nitrogenating agent for terminal aryl alkynes is demonstrated. PMID:26849380

  7. Copper-catalyzed oxidative cyclization of 1,5-enynes with concomitant C-C bond cleavage: an unexpected access to 3-formyl-1-indenone derivatives.

    PubMed

    Zhang, Jian; Wu, Degui; Chen, Xiaoling; Liu, Yunkui; Xu, Zhenyuan

    2014-06-01

    A Cu(0)/Selectfluor system-mediated oxidative cyclization of 1,5-enynes with concomitant C-C bond cleavage to access 3-formyl-1-indenone derivatives is described. Preliminary mechanistic investigations disclosed that the C-C bond cleavage involved a novel water-participated oxygen-insertion ?-carbon elimination through double oxycuprations. PMID:24807823

  8. Phenyliodonium diacetate mediated direct synthesis of benzonitriles from styrenes through oxidative cleavage of C?C bonds.

    PubMed

    Xu, Jin-Hui; Jiang, Qing; Guo, Can-Cheng

    2013-12-01

    A metal-free PhI(OAc)2 mediated nitrogenation of alkenes through C?C bond cleavage using inorganic ammonia salt as nitrogen source under mild conditions was developed, affording nitriles in moderate to good yields. The advantages of this reaction are mild reaction conditions, operational simplicity, and use of an ammonium salt as nitrogen source. Based upon experimental observations, a plausible reaction mechanism is proposed. PMID:24171555

  9. Deamination, oxidation, and C-C bond cleavage reactivity of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine.

    PubMed

    Schiesser, Stefan; Pfaffeneder, Toni; Sadeghian, Keyarash; Hackner, Benjamin; Steigenberger, Barbara; Schrder, Arne S; Steinbacher, Jessica; Kashiwazaki, Gengo; Hfner, Georg; Wanner, Klaus T; Ochsenfeld, Christian; Carell, Thomas

    2013-10-01

    Three new cytosine derived DNA modifications, 5-hydroxymethyl-2'-deoxycytidine (hmdC), 5-formyl-2'-deoxycytidine (fdC) and 5-carboxy-2'-deoxycytidine (cadC) were recently discovered in mammalian DNA, particularly in stem cell DNA. Their function is currently not clear, but it is assumed that in stem cells they might be intermediates of an active demethylation process. This process may involve base excision repair, C-C bond cleaving reactions or deamination of hmdC to 5-hydroxymethyl-2'-deoxyuridine (hmdU). Here we report chemical studies that enlighten the chemical reactivity of the new cytosine nucleobases. We investigated their sensitivity toward oxidation and deamination and we studied the C-C bond cleaving reactivity of hmdC, fdC, and cadC in the absence and presence of thiols as biologically relevant (organo)catalysts. We show that hmdC is in comparison to mdC rapidly oxidized to fdC already in the presence of air. In contrast, deamination reactions were found to occur only to a minor extent. The C-C bond cleavage reactions require the presence of high concentration of thiols and are acid catalyzed. While hmdC dehydroxymethylates very slowly, fdC and especially cadC react considerably faster to dC. Thiols are active site residues in many DNA modifiying enzymes indicating that such enzymes could play a role in an alternative active DNA demethylation mechanism via deformylation of fdC or decarboxylation of cadC. Quantum-chemical calculations support the catalytic influence of a thiol on the C-C bond cleavage. PMID:23980549

  10. The role of the steps in the cleavage of the C-C bond during ethanol oxidation on platinum electrodes.

    PubMed

    Colmati, Flavio; Tremiliosi-Filho, Germano; Gonzalez, Ernesto R; Bern, Antonio; Herrero, Enrique; Feliu, Juan M

    2009-10-28

    Ethanol oxidation has been studied on stepped platinum single crystal electrodes in acid media using electrochemical and Fourier transform infrared (FTIR) techniques. The electrodes used belong to two different series of stepped surfaces: those having (111) terraces with (100) monoatomic steps and those with (111) terraces with (110) monoatomic steps. The behaviors of the two series of stepped surfaces for the oxidation of ethanol are very different. On the one hand, the presence of (100) steps on the (111) terraces provides no significant enhancement of the activity of the surfaces. On the other hand, (110) steps have a double effect on the ethanol oxidation reaction. At potentials below 0.7 V, the step catalyzes the C-C bond cleavage and also the oxidation of the adsorbed CO species formed. At higher potentials, the step is not only able to break the C-C bond, but also to catalyze the oxidation of ethanol to acetic acid and acetaldehyde. The highest catalytic activity from voltammetry for ethanol oxidation was obtained with the Pt(554) electrode. PMID:19812831

  11. Intramolecular Cooperative C-C Bond Cleavage Reaction of 1,3-Dicarbonyl Compounds with 2-Iodoanilines to Give o-(N-Acylamino)aryl Ketones and Multisubstituted Indoles.

    PubMed

    Xing, Qi; Lv, Hui; Xia, Chungu; Li, Fuwei

    2015-06-01

    A copper-catalyzed C-C bond cleavage reaction of 1,3-dicarbonyl compounds with 2-iodoanilines was developed. In this process, the ortho effect played an important role in the reactivity and a new reaction pathway that involved a (2-aminophenyl)-bis-(1,3-dicarbonyl) copper species was clearly observed by a time-course HRMS analysis of the reaction mixture. Unlike the previous reports, both the nucleophilic and electrophilic parts of the 1,3-dicarbonyl compound were coupled with 2-iodoaniline by C-C bond cleavage to form o-(N-acylamino)aryl ketones, which could be efficiently converted into multisubstituted indoles. PMID:25940404

  12. 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

  13. 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

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

    PubMed

    Oja, Terhi; Klika, Karel D; Appassamy, Laura; Sinkkonen, Jari; Mntsl, Pekka; Niemi, Jarmo; Mets-Ketel, Mikko

    2012-04-17

    Carbohydrate moieties are important components of natural products, which are often imperative for the solubility and biological activity of the compounds. The aromatic polyketide alnumycin A contains an extraordinary sugar-like 4'-hydroxy-5'-hydroxymethyl-2',7'-dioxane moiety attached via a carbon-carbon bond to the aglycone. Here we have extensively investigated the biosynthesis of the dioxane unit through (13)C labeling studies, gene inactivation experiments and enzymatic synthesis. We show that AlnA and AlnB, members of the pseudouridine glycosidase and haloacid dehalogenase enzyme families, respectively, catalyze C-ribosylation conceivably through Michael-type addition of d-ribose-5-phosphate and dephosphorylation. The ribose moiety may be attached both in furanose (alnumycin C) and pyranose (alnumycin D) forms. The C(1')-C(2') bond of alnumycin C is subsequently cleaved and the ribose unit is rearranged into an unprecedented dioxolane (cis-bicyclo[3.3.0]-2',4',6'-trioxaoctan-3'?-ol) structure present in alnumycin B. The reaction is catalyzed by Aln6, which belongs to a previously uncharacterized enzyme family. The conversion was accompanied with consumption of O(2) and formation of H(2)O(2), which allowed us to propose that the reaction may proceed via hydroxylation of C1' followed by retro-aldol cleavage and acetal formation. Interestingly, no cofactors could be detected and the reaction was also conducted in the presence of metal chelating agents. The last step is the conversion of alnumycin B into the final end-product alnumycin A catalyzed by Aln4, an NADPH-dependent aldo-keto reductase. This characterization of the dioxane biosynthetic pathway sets the basis for the utilization of C-C bound ribose, dioxolane and dioxane moieties in the generation of improved biologically active compounds. PMID:22474343

  15. 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

  16. Ab initio calculations on a novel mode for storing and releasing electrons via C-C bond formation and cleavage

    SciTech Connect

    Cambi, R.; Nottoli, R.; Rosi, M.; Sgamellotti, A. ); Floriani, C. )

    1992-12-23

    Ab initio Hartree-Fock and second-order Moeller-Plesset calculations have been performed on systems which can be viewed as models for [Ni(salophen)] and its reductive product. The results indicate that the metal does not change its oxidation state in the reductive process because no orbitals, localized on nickel and at low energy, are available to accept electrons, except the in-plane d orbital, whose occupation would imply a large increase in the repulsion. The added electrons prefer to form a C-C bond, which can be cleaved restoring the original product. Ni[sup 2+] is electrostatically bonded to the ligand and acts as a shield among the negative charges of the ligand itself. Correlation effects influence the energetic balance of the reductive process but not as heavily as expected for transition metal systems because the electronic distribution at the transition metal ion does not change in the reaction. 17 refs., 2 figs., 2 tabs.

  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. 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.

  19. 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

  20. Iron-catalyzed aerobic oxidative cleavage of the C-C ?-bond using air as the oxidant: chemoselective synthesis of carbon chain-shortened aldehydes, ketones and 1,2-dicarbonyl compounds.

    PubMed

    Xing, Qi; Lv, Hui; Xia, Chungu; Li, Fuwei

    2016-01-11

    A simple iron-catalyzed aerobic oxidative C-C ?-bond cleavage of ketones has been developed. Readily available and environmentally benign air is used as the oxidant. This reaction avoids the use of noble metal catalysts or specialized oxidants, chemoselectively yielding carbon chain-shortened aldehydes, ketones and 1,2-dicarbonyl compounds without overoxidation. PMID:26529597

  1. DMSO/I2 mediated C-C bond cleavage of ?-ketoaldehydes followed by C-O bond formation: a metal-free approach for one-pot esterification.

    PubMed

    Venkateswarlu, Vunnam; Aravinda Kumar, K A; Gupta, Sorav; Singh, Deepika; Vishwakarma, Ram A; Sawant, Sanghapal D

    2015-08-01

    A novel and efficient I2/DMSO mediated metal-free strategy is presented for the direct C-C bond cleavage of aryl-/heteroaryl- or aliphatic ?-ketoaldehydes by C2-decarbonylation and C1-carbonyl oxidation to give the corresponding carboxylic acids followed by esterification in one pot, offering excellent yields in both the steps. Here, DMSO acts as the oxygen source/oxidant and this reaction works very well under both conventional heating and microwave irradiation. This is a very simple and convenient protocol. PMID:26110656

  2. 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

  3. Hydrogenolysis and homologation of linear and branched pentenes on Ru/SiO/sub 2/ catalysts: implication in the mechanism of C-C bond formation and cleavage on metal surfaces

    SciTech Connect

    Rodriguez, E.; Leconte, M.; Basset, J.M.; Tanaka, K.; Tanaka, K.I.

    1988-01-06

    Hydrogenolysis and homologation of 1-pentene to butenes and hexenes take place simultaneously and at the same rate over a Ru/SiO/sub 2/ catalysts at 110/sup 0/C, suggesting that these two reactions are mechanistically related. /sup 13/C labeling experiments indicate that C-C cleavage occurs at the double bond of 1-pentene-1-/sup 13/C leading to unlabeled 1-butene and labeled hexenes. The product distribution in the hydrogenolysis of 1-pentene, 2-pentenes, 3-methyl-1-butene, 2-methyl-2-butene, and 2-methyl-1-butene is accounted for by a carbene-olefin mechanism, which can therefore be considered as a reasonable common path for the formation and cleavage of carbon-carbon bonds on metal surfaces.

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

    SciTech Connect

    Rodriguez, E.; Leconte, M.; Basset, J.M.; Tanaka, K. )

    1989-09-01

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

  5. 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…

  6. 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

  7. 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.

  8. Silver(I) NHC mediated C-C bond activation of alkyl nitriles and catalytic efficiency in oxazoline synthesis.

    PubMed

    Heath, Rachael; Mller-Bunz, Helge; Albrecht, Martin

    2015-05-21

    Preparation of silver triazolylidene (trz) species from triazolium salts and Ag2O in refluxing MeCN leads to a selective C-C bond cleavage and the formation of complexes of general formula [(trz)Ag(CN)] from Calkyl-CN bond activation. Moreover, these silver carbene complexes are precursors of highly active catalysts for oxazoline formation via aldol condensation. PMID:25913007

  9. 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

  10. Can laccases catalyze bond cleavage in lignin?

    PubMed

    Munk, Line; Sitarz, Anna K; Kalyani, Dayanand C; Mikkelsen, J Dalgaard; Meyer, Anne S

    2015-01-01

    Modification of lignin is recognized as an important aspect of the successful refining of lignocellulosic biomass, and enzyme-assisted processing and upcycling of lignin is receiving significant attention in the literature. Laccases (EC 1.10.3.2) are taking the centerstage of this attention, since these enzymes may help degrading lignin, using oxygen as the oxidant. Laccases can catalyze polymerization of lignin, but the question is whether and how laccases can directly catalyze modification of lignin via catalytic bond cleavage. Via a thorough review of the available literature and detailed illustrations of the putative laccase catalyzed reactions, including the possible reactions of the reactive radical intermediates taking place after the initial oxidation of the phenol-hydroxyl groups, we show that i) Laccase activity is able to catalyze bond cleavage in low molecular weight phenolic lignin model compounds; ii) For laccases to catalyze inter-unit bond cleavage in lignin substrates, the presence of a mediator system is required. Clearly, the higher the redox potential of the laccase enzyme, the broader the range of substrates, including o- and p-diphenols, aminophenols, methoxy-substituted phenols, benzenethiols, polyphenols, and polyamines, which may be oxidized. In addition, the currently available analytical methods that can be used to detect enzyme catalyzed changes in lignin are summarized, and an improved nomenclature for unequivocal interpretation of the action of laccases on lignin is proposed. PMID:25560931

  11. Metal-Free Oxidative C-C Bond Formation through C-H Bond Functionalization.

    PubMed

    Narayan, Rishikesh; Matcha, Kiran; Antonchick, Andrey P

    2015-10-12

    The formation of C-C bonds embodies the core of organic chemistry because of its fundamental application in generation of molecular diversity and complexity. C-C bond-forming reactions are well-known challenges. To achieve this goal through direct functionalization of C-H bonds in both of the coupling partners represents the state-of-the-art in organic synthesis. Oxidative C-C bond formation obviates the need for prefunctionalization of both substrates. This Minireview is dedicated to the field of C-C bond-forming reactions through direct C-H bond functionalization under completely metal-free oxidative conditions. Selected important developments in this area have been summarized with representative examples and discussions on their reaction mechanisms. PMID:26239615

  12. 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 ?-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.

  13. 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.

  14. Activation of Propane C-H and C-C Bonds by Gas-Phase Pt Atom: A Theoretical Study

    PubMed Central

    Li, Fang-Ming; Yang, Hua-Qing; Ju, Ting-Yong; Li, Xiang-Yuan; Hu, Chang-Wei

    2012-01-01

    The reaction mechanism of the gas-phase Pt atom with C3H8 has been systematically investigated on the singlet and triplet potential energy surfaces at CCSD(T)//BPW91/6-311++G(d, p), Lanl2dz level. Pt atom prefers the attack of primary over secondary C-H bonds in propane. For the Pt + C3H8 reaction, the major and minor reaction channels lead to PtC3H6 + H2 and PtCH2 + C2H6, respectively, whereas the possibility to form products PtC2H4 + CH4 is so small that it can be neglected. The minimal energy reaction pathway for the formation of PtC3H6 + H2, involving one spin inversion, prefers to start at the triplet state and afterward proceed along the singlet state. The optimal C-C bond cleavages are assigned to C-H bond activation as the first step, followed by cleavage of a C-C bond. The C-H insertion intermediates are kinetically favored over the C-C insertion intermediates. From C-C to C-H oxidative insertion, the lowering of activation barrier is mainly caused by the more stabilizing transition state interaction ?E?int, which is the actual interaction energy between the deformed reactants in the transition state. PMID:22942766

  15. 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 ?-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

  16. S? Chalcogen Bonds between SF2 or SF4 and C-C Multiple Bonds.

    PubMed

    Nziko, Vincent de Paul N; Scheiner, Steve

    2015-06-01

    SF2 and SF4 were each paired with a series of unsaturated hydrocarbons including ethene, ethyne, 1,3-butadiene, and benzene, in each case forming a chalcogen bond between the S atom and the carbon ?-system. MP2 ab initio calculations reveal that the S atom is situated directly above one specific C?C bond, even when more than one are present. The binding energies range between 3.3 and 6.6 kcal/mol. SF2 engages in a stronger, and shorter, noncovalent bond than does SF4 for all systems with the exception of benzene, to which SF4 is more tightly bound. cis-Butadiene complexes contain the shortest chalcogen bond, even if not necessarily the strongest. The internal S-F covalent bonds elongate upon formation of each chalcogen bond. The molecules are held together largely by charge transfer forces, particularly from the C?C ?-bonds to the ?*(SF) antibonding orbitals. In the case of SF2, a sulfur lone pair can transfer charge into the ?* MOs of the alkene, a back-transfer which is more difficult for SF4. PMID:25970139

  17. Hydrogen induced C-C, C-N, and C-S bond activation on Pt and Ni surfaces

    SciTech Connect

    Gland, J.L.

    1992-01-01

    The work has focussed on hydrogen induced bond activation in adsorbed organic molecules and intermediates containin C-S and C-N and C-C bonds on Ni(100), Ni(111), and Pt(111) surfaces. Fluorescence Yield Near Edge Spectroscopy (FYNES) above the carbon K edge was used for adsorbed organic reactants and in-situ kinetic studies of bond activation. Results indicate that the activation is enhanced on Ni relative to Pt. Methylthiolate and methylamine adsorbed on Pt(111) were studied.

  18. Hydrogen induced C-C, C-N, and C-S bond activation on Pt and Ni surfaces

    SciTech Connect

    Gland, J.L.

    1992-12-01

    The work has focussed on hydrogen induced bond activation in adsorbed organic molecules and intermediates containin C-S and C-N and C-C bonds on Ni(100), Ni(111), and Pt(111) surfaces. Fluorescence Yield Near Edge Spectroscopy (FYNES) above the carbon K edge was used for adsorbed organic reactants and in-situ kinetic studies of bond activation. Results indicate that the activation is enhanced on Ni relative to Pt. Methylthiolate and methylamine adsorbed on Pt(111) were studied.

  19. Intramolecular, Pd/Cu-Co-catalyzed P-C Bond Cleavage and Addition onto an Alkyne: A Route to Benzophospholes.

    PubMed

    Zhou, Yang; Gan, Zhenjie; Su, Bo; Li, Jun; Duan, Zheng; Mathey, Franois

    2015-11-20

    Under Pd(II)/CuI cocatalysis, o-diarylphosphinophenylalkynes cyclize in boiling toluene via C-P bond cleavage and arylphosphination of the C?C bond. This protocol provides an unprecedented atom- and step-efficient access to optoelectronically and biologically interesting benzophospholes. PMID:26561234

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

    2016-01-26

    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 ?-oxygenation/esterification/nucleophilic addition/C-C bond cleavage and carbon dioxide is released as the only byproduct. PMID:26698150

  8. 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

  9. Linear alkane C-C bond chemistry mediated by metal surfaces.

    PubMed

    Cai, Zeying; Liu, Meizhuang; She, Limin; Li, Xiaoli; Lee, Jason; Yao, Dao-Xin; Zhang, Haiming; Chi, Lifeng; Fuchs, Harald; Zhong, Dingyong

    2015-05-18

    Linear alkanes undergo different C-C bond chemistry (coupling or dissociation) thermally activated on anisotropic metal surfaces depending on the choice of the substrate material. Owing to the one-dimensional geometrical constraint, selective dehydrogenation and C-C coupling (polymerization) of linear alkanes take place on Au(110) surfaces with missing-row reconstruction. However, the case is dramatically different on Pt(110) surfaces, which exhibit similar reconstruction as Au(110). Instead of dehydrogenative polymerization, alkanes tend to dehydrogenative pyrolysis, resulting in hydrocarbon fragments. Density functional theory calculations reveal that dehydrogenation of alkanes on Au(110) surfaces is an endothermic process, but further C-C coupling between alkyl intermediates is exothermic. On the contrary, due to the much stronger C-Pt bonds, dehydrogenation on Pt(110) surfaces is energetically favorable, resulting in multiple hydrogen loss followed by C-C bond dissociation. PMID:25752674

  10. Density Functional Theory Study of Selectivity Considerations for CC Versus CO Bond Scission in Glycerol Decomposition on Pt(111)

    SciTech Connect

    Liu, Bin; Greeley, Jeffrey P.

    2012-05-01

    Glycerol decomposition via a combination of dehydrogenation, CC bond scission, and CO bond scission reactions is examined on Pt(111) with periodic Density Functional Theory (DFT) calculations. Building upon a previous study focused on CC bond scission in glycerol, the current work presents a ?rst analysis of the competition between CO and CC bond cleavage in this reaction network. The thermochemistry of various species produced from CO bond breaking in glycerol dehydrogenation intermediates is estimated using an extension of a previously introduced empirical correlation scheme, with parameters ?t to DFT calculations. BrnstedEvansPolanyi (BEP) relationships are then used to estimate the kinetics of CO bond breaking. When combined with the previous results, the thermochemical and kinetic analyses imply that, while CO bond scission may be competitive with CC bond scission during the early stages of glycerol dehydrogenation, the overall rates are likely to be very low. Later in the dehydrogenation process, where rates will be much higher, transition states for CC bond scission involving decarbonylation are much lower in energy than are the corresponding transition states for CO bond breaking, implying that the selectivity for CC scission will be high for glycerol decomposition on smooth platinum surfaces. It is anticipated that the correlation schemes described in this work will provide an ef?cient strategy for estimating thermochemical and kinetic energetics for a variety of elementary bond breaking processes on Pt(111) and may ultimately facilitate computational catalyst design for these and related catalytic processes.

  11. Low temperature C?C bond scission during ethanol decomposition on Pt(331)

    NASA Astrophysics Data System (ADS)

    Cong, Y.; van Spaendonk, V.; Masel, R. I.

    1997-08-01

    The adsorption and decomposition of ethanol was studied on clean, and oxygen pre-covered Pt(331) surface by using mainly TPD, LEED and AES. It was found that ethanol adsorbed molecularly on the Pt(331) surface at low temperature. Upon heating, part of the ethanol desorbed molecularly from surface at 220 K, and part of the ethanol underwent C?C bond scission to form methane and a variety of other products. There are two distinct methane peaks at 240 K and 310 K in the desorption spectrum suggesting that there are two different pathways for ethanol decomposition on this surface; both pathways involve C?C bond scission since methane is a major desorption product. CO adsorption experiments as well as experiments with H (ad) and O (ad) suggest that the lower temperature pathway involves C?C bond scission at temperatures below that where the ethanol appreciably dehydrogenates, while the high temperature pathway involves dehydrogenation of the ethanol followed by C?C bond scission. O (ad) additions suppress the low temperature pathway and enhances the high temperature pathway presumably by speeding the dehydrogenation of the ethanol. H (ad) additions slightly enhance the low temperature pathway. We also observe hydrogenolysis of the ethanol to yield methanol at 180 K and methane at 240 K in the presence of excess hydrogen. These results show that the step sites on the Pt(331) surface have unusual activity for C?C bond scission in ethanol.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. Total synthesis of bryostatin 7 via C-C bond-forming hydrogenation.

    PubMed

    Lu, Yu; Woo, Sang Kook; Krische, Michael J

    2011-09-01

    The marine macrolide bryostatin 7 is prepared in 20 steps (longest linear sequence) and 36 total steps with five C-C bonds formed using hydrogenative methods. This approach represents the most concise synthesis of any bryostatin reported, to date. PMID:21780806

  17. Photoinduced C-S Bond Cleavage of Thioglycosides and Glycosylation.

    PubMed

    Mao, Run-Ze; Guo, Fan; Xiong, De-Cai; Li, Qin; Duan, Jinyou; Ye, Xin-Shan

    2015-11-20

    A glycosyl coupling reaction via photoinduced direct activation of thioglycosides and subsequent O-glycosylation in the absence of photosensitizer was developed for the first time. This reaction underwent a selectively homolytic cleavage of a C-S bond to generate a glycosyl radical, which was oxidized to an oxacarbenium ion by Cu(OTf)2, and a sequential O-glycosylation. A wide range of glycosides were synthesized in moderate to excellent yield using sugars, amino acids, or cholesterol as the acceptors. PMID:26540490

  18. Formation of CC Bonds via Iridium-Catalyzed Hydrogenation and Transfer Hydrogenation

    PubMed Central

    Bower, John F.; Krische, Michael J.

    2011-01-01

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

  19. [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.

  20. 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

  1. Mechanisms of photoinduced C??C? bond breakage in protonated aromatic amino acids

    NASA Astrophysics Data System (ADS)

    Lucas, B.; Barat, M.; Fayeton, J. A.; Perot, M.; Jouvet, C.; Grgoire, G.; Brndsted Nielsen, S.

    2008-04-01

    Photoexcitation of protonated aromatic amino acids leads to C??C? bond breakage among other channels. There are two pathways for the C??C? bond breakage, one is a slow process (microseconds) that occurs after hydrogen loss from the electronically excited ion, whereas the other is a fast process (nanoseconds). In this paper, a comparative study of the fragmentation of four molecules shows that the presence of the carboxylic acid group is necessary for this fast fragmentation channel to occur. We suggest a mechanism based on light-induced electron transfer from the aromatic ring to the carboxylic acid, followed by a fast internal proton transfer from the ammonium group to the negatively charged carboxylic acid group. The ion formed is a biradical since the aromatic ring is ionized and the carbon of the COOH group has an unpaired electron. Breakage of the weak C??C? bond gives two even-electron fragments and is expected to quickly occur. The present experimental results together with the ab initio calculations support the interpretation previously proposed.

  2. 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.

  3. 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}).

  4. 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.

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

    PubMed

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

    2014-11-21

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

  6. 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.

  7. Collision Induced Dissociation Products of Disulfide-bonded Peptides: Ions Result from the Cleavage of More than One Bond

    PubMed Central

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

    2012-01-01

    Disulfide bonds are a posttranslational 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 difficult due, to 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 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. This data shows 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. PMID:21472567

  8. Metalloenzyme-Like Zeolites as Lewis Acid Catalysts for C-C Bond Formation.

    PubMed

    Van de Vyver, Stijn; Romn-Leshkov, Yuriy

    2015-10-19

    The use of metalloenzyme-like zeolites as Lewis acid catalysts for C-C bond formation reactions has received increasing attention over the past few years. In particular, the observation of direct aldol condensation reactions enabled by hydrophobic zeolites with isolated framework metal sites has encouraged the development of catalytic approaches for producing chemicals from biomass-derived compounds. The discovery of new Diels-Alder cycloaddition/dehydration routes and experimental and computational studies of Lewis acid catalyzed carbonyl-ene reactions have given a further boost to this rapidly evolving field. PMID:26465652

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. Mass spectrometric and theoretical studies on dissociation of the Ssbnd S bond in the allicin: Homolytic cleavage vs heterolytic cleavage

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang

    2012-08-01

    On the basis of the tandem mass spectrometry (ESI-MS/MS) technique and DFT calculations, an experimental and theoretical investigation has been conducted into the gas-phase dissociation of the S1sbnd S1' bond in the allicin as well as that of the Ssbnd C (S1sbnd C2, S1'sbnd C2') bond. Meanwhile, the influence of protonation, alkali metal ion and electron transfer on the dissociation of the S1sbnd S1' bond has been taken into account. ESI-MS/MS experiments and DFT calculations show that in the neutral allicin, [allicin + Li]+ and [allicin + Na]+, the S1sbnd S1' bond favors homolytic cleavage, while in the allicin radical cation and protonated allicin, the S1sbnd S1' bond prefers heterolytic cleavage. In addition, alkali metal ions can strengthen the S1sbnd S1' bond in the allicin, while protonation or the loss of an electron will weaken the S1sbnd S1' bond.

  15. Application of a C-C Bond-Forming Conjugate Addition Reaction in Asymmetric Dearomatization of ?-Naphthols.

    PubMed

    Yang, Dongxu; Wang, Linqing; Kai, Ming; Li, Dan; Yao, Xiaojun; Wang, Rui

    2015-08-10

    A C-C bond-forming conjugate reaction was successfully applied to the enantioselective dearomatization of ?-naphthols. A C(sp2)-C(sp3) bond is formed by using propargylic ketones as reactive partners. Good to excellent Z/E?ratios and ee?values were obtained by employing an in?situ generated magnesium catalyst. Further transformations of the Z-configured C-C double bond in the products were achieved under mild reaction conditions. Moreover, the stereocontrolling element of this magnesium-catalyzed dearomatization reaction was explored by computational chemistry. PMID:26173841

  16. Quantification of primary versus secondary C-H bond cleavage in alkane activation: Propane on Pt

    SciTech Connect

    Weinberg, W.H.; Sun, Yongkui )

    1991-08-02

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

  17. 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

  18. Concerted heavy-atom bond cleavage and proton and electron transfers illustrated by proton-assisted reductive cleavage of an OO bond

    PubMed Central

    Costentin, Cyrille; Hajj, Viviane; Robert, Marc; Savant, Jean-Michel; Tard, Cdric

    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 OO 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

  19. 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

  20. 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.

  1. 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

  2. Efficient synthesis of ?-tertiary ?-silylamines from aryl sulfonylimidates via one-pot, sequential C-Si/C-C bond formations.

    PubMed

    Han, Xiao-Jun; Yao, Ming; Lu, Chong-Dao

    2012-06-01

    An efficient and flexible route for the synthesis of ?-tertiary (?,?-dibranched) ?-silylamines via sequential reactions of sulfonylimidates using readily available phenyldimethylsilyllithium and Grignard reagents is described. The procedure allows successive formation of C-Si/C-C bonds in a single flask. PMID:22621235

  3. 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

  4. Bond cleavage, fragment modification and reassembly in enantioselective three-component reactions

    PubMed Central

    Zhang, Dan; Zhou, Jun; Xia, Fei; Kang, Zhenghui; Hu, Wenhao

    2015-01-01

    Chemical bond cleavage and reconstruction are common processes in traditional rearrangement reactions. In contrast, the process that involves bond cleavage, fragment modification and then reconstruction of the modified fragment provides an efficient way to build structurally diversified molecules. Here, we report a palladium(II)/chiral phosphoric acid catalysed three-component reaction of aryldiazoacetates, enamines and imines to afford ?-amino-?-oxo pentanoic acid derivatives in good yields with excellent diastereoselectivities and high enantioselectivities. The stereoselective reaction went through a unique process that involves cleavage of a CN bond, modification of the resulting amino fragment and selective reassembly of the modified fragment. This innovative multi-component process represents a highly efficient way to build structurally diversified polyfunctional molecules in an atom and step economic fashion. A keto-iminium is proposed as a key intermediate and a chiral palladium/phosphate complex is proposed as an active catalyst. PMID:25586817

  5. 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

  6. 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

  7. 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.

  8. Stereoselective total synthesis of (-)-nupharamine utilizing an ?-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 ?-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

  9. Conceptual Basis for Understanding C-C Bond Activation in Ethane by Second Row Transition Metal Carbides.

    PubMed

    Sahoo, Sanjubala; Reber, Arthur C; Khanna, Shiv N

    2015-12-24

    It has been suggested that the addition of carbon to Mo and W may improve their catalytic properties and even grant these metal carbides behaviors similar to those of late transition metals such as Pd and Pt. First-principles studies on the C-C bond activation of ethane by 4d transition metal (TM) atoms and TMC molecules have been carried out to develop a conceptual model underlying the changes. We find that the addition of carbon to TM atoms leads to large variations in the activation barrier depending on the metal, and that MoC indeed reveals a pronounced reduction in the C-C bond activation energy. A critical examination of molecular orbitals shows that the changes in reactivity are not linked to a dramatic increase in the filling of 4d states as implied by the analogy with Pd. The reactivity is governed by the location and filling of the 5s and 4d orbitals, with the different orbitals controlling different facets of reactivity. The 5s state controls the initial binding of ethane, with a strong anticorrelation between the ethane binding energy and the 5s occupation, while the location of the 4dz(2) orbital controls the reaction barrier that controls the activation energy for cleaving the C-C bond. PMID:26616749

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Roman, Marko

    2015-08-01

    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.

  15. Synthesis of aromatic compounds by catalytic C-C bond activation of biphenylene or angular [3]phenylene.

    PubMed

    Korotvi?ka, Ale; Csa?ov, Ivana; Roithov, Jana; Kotora, Martin

    2012-04-01

    Substituted phenanthrenes and picenes were easily prepared by reaction of biphenylene or angular [3]phenylene with various alkynes in the presence of a catalytic amount of [IrCl(cod)](2) /dppe (cod=1,5-cyclooctadiene, dppe=1,2-bis(diphenylphosphino)ethane). The reaction is based on C-C bond activation of the cyclobutane ring. The reaction tolerates the presence of bulky groups on the alkyne, such as the ferrocene moiety. In addition, a catalytic system based on [RhCl(cod)](2)/dppe enabled the, hitherto unreported, reaction of biphenylene with nitriles to provide phenanthridines. PMID:22407483

  16. 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.

  17. Carboncarbon 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. Carboncarbon bond cleavage of perfluoroalkylated carboxylic acid derivatives takes place in fluoroalkylation reactions at high temperature (150200 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

  18. 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.

  19. 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

  20. 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

  1. Fine-tuning the energy barrier for metal-mediated dinitrogen N?N bond cleavage.

    PubMed

    Keane, Andrew J; Yonke, Brendan L; Hirotsu, Masakazu; Zavalij, Peter Y; Sita, Lawrence R

    2014-07-16

    Experimental data support a mechanism for N?N bond cleavage within a series of group 5 bimetallic dinitrogen complexes of general formula, {Cp*M[N((i)Pr)C(R)N((i)Pr)]}2(?-N2) (Cp* = ?(5)-C5Me5) (M = Nb, Ta), that proceeds in solution through an intramolecular "end-on-bridged" (?-?(1):?(1)-N2) to "side-on-bridged" (?-?(2):?(2)-N2) isomerization process to quantitatively provide the corresponding bimetallic bis(?-nitrido) complexes, {Cp*M[N((i)Pr)C(R)N((i)Pr)](?-N)}2. It is further demonstrated that subtle changes in the steric and electronic features of the distal R-substituent, where R = Me, Ph and NMe2, can serve to modulate the magnitude of the free energy barrier height for N?N bond cleavage as assessed by kinetic studies and experimentally derived activation parameters. The origin of the contrasting kinetic stability of the first-row congener, {Cp*V[N((i)Pr)C(Me)N((i)Pr)]}2(?-?(1):?(1)-N2) toward N?N bond cleavage is rationalized in terms of a ground-state electronic structure that favors a significantly less-reduced ?-N2 fragment. PMID:24960112

  2. Cyanoalkylation: Alkylnitriles in Catalytic C-C Bond-Forming Reactions.

    PubMed

    Lpez, Rosa; Palomo, Claudio

    2015-11-01

    Alkylnitriles are one of the most ubiquitous nitrogen-containing chemicals and are widely employed in reactions which result in nitrile-group conversion into other functionalities. Nevertheless, their use as carbon pronucleophiles in carbon-carbon bond-forming reactions has been hampered by difficulties associated mainly with the catalytic generation of active species, that is, ?-cyano carbanions or metalated nitriles. Recent investigations have addressed this challenge and have resulted in different modes of alkylnitrile activation. This review illustrates these findings, which have set the foundation for the development of practical and conceptually new catalytic, direct cyanoalkylation methodologies. PMID:26387483

  3. Nickel-Catalyzed Borylation of Aryl- and Benzyltrimethylammonium Salts via C-N Bond Cleavage.

    PubMed

    Hu, Jiefeng; Sun, Heqing; Cai, Wangshui; Pu, Xinghui; Zhang, Yemin; Shi, Zhuangzhi

    2016-01-01

    By developing a mild Ni-catalyzed system, a method for direct borylation of sp(2) and sp(3) C-N bonds has been established. The key to this hightly efficient C-N bond borylative cleavage depends on the appropriate choice of the nickel catalyst Ni(COD)2, ICyHCl as a ligand, and the use of 2-ethoxyethanol as the cosolvent. This transformation shows good functional group compatibility and can serve as a powerful synthetic tool for gram-scale synthesis and late-stage C-N borylation of complex compounds. PMID:26628255

  4. 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.

  5. 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

  6. Selective Cleavage of Isoaspartyl Peptide Bonds by Hydroxylamine after Methyltransferase Priming

    PubMed Central

    Zhu, Jeff X.; Aswad, Dana W.

    2007-01-01

    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 ?-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

  7. Short Access to Belt Compounds with Spatially Close C=C Bonds and Their Transannular Reactions.

    PubMed

    Camps, Pelayo; Gmez, Tnia; Otermin, Ane; Font-Bardia, Merc; Estarellas, Carolina; Luque, Francisco Javier

    2015-09-28

    Two domino Diels-Alder adducts were obtained from 3,7-bis(cyclopenta-2,4-dien-1-ylidene)-cis-bicyclo[3.3.0]octane and dimethyl acetylenedicarboxylate or N-methylmaleimide under microwave irradiation. From the first adduct, a C20H24 diene with C2v symmetry was obtained by Zn/AcOH reduction, hydrolysis, oxidative decarboxylation, and selective hydrogenation. Photochemical [2+2] cycloaddition of this diene gave a thermally unstable cyclobutane derivative, which reverts to the diene. However, both the diene and the cyclobutane derivatives could be identified by X-ray diffraction analysis upon irradiation of the diene crystal. New six-membered rings are formed upon the transannular addition of bromine or iodine to the diene. The N-type selectivity of the addition was examined by theoretical calculations, which revealed the distinct susceptibility of the doubly bonded carbon atoms to the bromine attack. PMID:26376331

  8. 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)

  9. Brnsted acid mediated N-O bond cleavage for ?-amination of ketones through the aromatic nitroso aldol reaction.

    PubMed

    Ramakrishna, Isai; Sahoo, Harekrishna; Baidya, Mahiuddin

    2016-02-11

    A Brnsted acid mediated N-O bond cleavage for ?-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 ?-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

  10. 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.

  11. 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

  12. 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

  13. First principles study of the electronic and magnetic structures and bonding properties of UCoC2 ternary, characteristic of C-C units

    NASA Astrophysics Data System (ADS)

    Matar, Samir F.

    2013-03-01

    The electronic structure of UCoC2, a di-carbide with the C-C units is examined from ab initio with an assessment of the properties of chemical bonding. The energy-volume equation of state shows large anisotropy effects due to C-C alignment along tetragonal c-axis leading to high linear incompressibility. Relevant features of selective bonding of uranium and cobalt with carbon at two different Wyckoff sites and strong C-C interactions are remarkable. The vibrational frequencies for C⋯C stretching modes indicate closer behavior to aliphatic C-C rather than Cdbnd C double bond. A ferromagnetic ground state is proposed from the calculations.

  14. Decomposition Pathways of Glycerol via CH, OH, and CC Bond Scission on Pt(111): A Density Functional Theory Study

    SciTech Connect

    Liu, Bin; Greeley, Jeffrey

    2011-09-01

    Glycerol decomposition on Pt(111) via dehydrogenation or CC bond scission is examined with periodic density functional theory (DFT) calculations. The thermochemistry of dehydrogenation intermediates is first estimated using an empirical correlation scheme with parameters fit to selected DFT calculations; the resulting estimates for the more stable intermediates are refined with full DFT calculations. BrnstedEvansPolanyi (BEP) relationships for dehydrogenation and CC bond scission reactions are developed and used to estimate the kinetics of elementary dehydrogenation and CC bond scission steps in the reaction network. The combined thermochemical and kinetic analysis implies that glycerol dehydrogenation products at intermediate levels of dehydrogenation are the most thermochemically stable. Additionally, although CC bond scission transition state energies are high for glycerol and for intermediates at early stages of dehydrogenation, these energies decrease as the intermediates are successively dehydrogenated, reaching a minimum after the removal of several hydrogen atoms from glycerol. At these levels of dehydrogenation, the CC scission transition state energies become comparable to those of OH or CH scission. These results suggest that CC bonds are only broken after glycerol has been significantly dehydrogenated and demonstrate that DFT-based analyses, combined with simple correlation schemes, can be effective for elucidating general features of complex biomassic reaction networks.

  15. Decomposition Pathways of Glycerol via CH, OH, and CC Bond Scission on Pt(111): A Density Functional Theory Study

    SciTech Connect

    Liu, Bin; Greeley, Jeffrey P.

    2011-10-13

    Glycerol decomposition on Pt(111) via dehydrogenation or CC bond scission is examined with periodic density functional theory (DFT) calculations. The thermochemistry of dehydrogenation intermediates is first estimated using an empirical correlation scheme with parameters fit to selected DFT calculations; the resulting estimates for the more stable intermediates are refined with full DFT calculations. BrnstedEvansPolanyi (BEP) relationships for dehydrogenation and CC bond scission reactions are developed and used to estimate the kinetics of elementary dehydrogenation and CC bond scission steps in the reaction network. The combined thermochemical and kinetic analysis implies that glycerol dehydrogenation products at intermediate levels of dehydrogenation are the most thermochemically stable. Additionally, although CC bond scission transition state energies are high for glycerol and for intermediates at early stages of dehydrogenation, these energies decrease as the intermediates are successively dehydrogenated, reaching a minimum after the removal of several hydrogen atoms from glycerol. At these levels of dehydrogenation, the CC scission transition state energies become comparable to those of OH or CH scission. These results suggest that CC bonds are only broken after glycerol has been significantly dehydrogenated and demonstrate that DFT-based analyses, combined with simple correlation schemes, can be effective for elucidating general features of complex biomassic reaction networks.

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

    PubMed

    Roman, 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. Graphical Abstract ?. PMID:26297186

  17. 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.

  18. 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

  19. 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.

  20. Amide Bond Cleavage: The Acceleration Due to a 1,3-Diaxial Interaction with a Carboxylic Acid

    PubMed Central

    Gerschler, Jared J.; Wier, Kevin A.; Hansen, David E.

    2008-01-01

    To independently assess the contribution of ground-state pseudoallylic strain to the enormous rates of amide bond cleavage in tertiary amide derivatives of Kemps triacid, we have studied four amide derivatives of (1?-3?-5?)-5-t-butyl-1,3-cyclohexanedicarboxylic acid. Our results confirm that absent pseudoallylic strain, a 1,3-diaxial interaction of an amide with a carboxylic acid leads to only a 2,400-fold increase in the rate of amide bond cleavage as compared with the rate of hydrolysis of an unactivated peptide bond. PMID:17221991

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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 ? 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.

  8. 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

  9. The role of alkane coordination in CH bond cleavage at a Pt(II) center

    PubMed Central

    Chen, George S.; Labinger, Jay A.; Bercaw, John E.

    2007-01-01

    The rates of CH bond activation for various alkanes by [(NN)Pt(Me)(TFEd3)]+ (N N = ArNC(Me)C(Me)NAr; Ar = 3,5-di-tert-butylphenyl; TFE-d3 = CF3CD2OD) were studied. Both linear and cyclic alkanes give the corresponding alkene-hydride cation [(NN)Pt(H)(alkene)]+ via (i) rate determining alkane coordination to form a CH ? complex, (ii) oxidative cleavage of the coordinated CH bond to give a platinum(IV) alkyl-methyl-hydride intermediate, (iii) reductive coupling to generate a methane ? complex, (iv) dissociation of methane, and (v) ?-H elimination to form the observed product. Second-order rate constants for cycloalkane activation (CnH2n), are proportional to the size of the ring (k ? n). For cyclohexane, the deuterium kinetic isotope effect (kH/kD) of 1.28 (5) is consistent with the proposed rate determining alkane coordination to form a CH ? complex. Statistical scrambling of the five hydrogens of the Pt-methyl and the coordinated methylene unit, via rapid, reversible steps ii and iii, and interchange of geminal CH bonds of the methane and cyclohexane CH ? adducts, is observed before loss of methane. PMID:17416678

  10. 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

  11. Biomimetic oxidation with molecular oxygen. Selective carbon-carbon bond cleavage of 1,2-diols by molecular oxygen and dihydropyridine in the presence of iron-porphyrin catalysts

    SciTech Connect

    Okamoto, T.; Sasaki, K.; Oka, S.

    1988-02-17

    The selective carbon-carbon bond cleavage of 1,2-diols in the presence of an iron-porphyrin complex, molecular oxygen, and 1-benzyl-3-carbamoyl-1,4-dihydropyridine is reported. The C-C bonds of aryl-substituted ethane-1,2-diols were cleaved exclusively to aldehydes or ketones as the oxidation products at room temperature. The reaction rates were influenced by the steric hindrance of the substituents both in the catalysts and diols, but no differences in the reactivities were observed between the two stereo isomers (meso and dl) of diols. A kinetic analysis of this bond cleavage reaction is consistent with the reaction mechanism consisting of the initial binding of diol on the active catalyst forming an intermediate complex and its subsequent breakdown in the rate-determining step of the catalytic cycle. The initial binding step is favorable for electron-deficient diols and is influenced by steric hindrance, whereas the rate-determining bond cleavage step is accelerated by electron-rich diols and unaffected by the steric effect. The mechanism of this diol cleavage reaction is discussed on the basis of these observations.

  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. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. Nickel-Catalyzed Formal Homocoupling of Methoxyarenes for the Synthesis of Symmetrical Biaryls via C-O Bond Cleavage.

    PubMed

    Nakamura, Keisuke; Tobisu, Mamoru; Chatani, Naoto

    2015-12-18

    A new method has been developed for the nickel-catalyzed homocoupling of methoxyarenes via C-O bond cleavage using a diboron reagent. The use of 1,3-dicyclohexylimidazol-2-ylidene as a ligand was found to be critical to the success of the reaction. This new method allows the synthesis of a wide range of biaryl compounds. PMID:26624568

  20. 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

  1. 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.

  2. Proton-coupled electron transfer cleavage of heavy-atom bonds in electrocatalytic processes. Cleavage of a C-O bond in the catalyzed electrochemical reduction of CO2.

    PubMed

    Costentin, Cyrille; Drouet, Samuel; Passard, Guillaume; Robert, Marc; Savant, Jean-Michel

    2013-06-19

    Most of the electrocatalytic processes of interest in the resolution of modern energy challenges are associated with proton transfer. In the cases where heavy atom bond cleavage occurs concomitantly, the question arises of the exact nature of its coupling with proton-electron transfer within the catalytic cycle. The cleavage of a C-O bond in the catalyzed electrochemical conversion of CO2 to CO offers the opportunity to address this question. Electrochemically generated iron(0) porphyrins are efficient, specific, and durable catalysts provided they are coupled with Lewis or Brnsted acids. The cocatalyst properties of four Brnsted acids of increasing strength, water, trifluoroethanol, phenol, and acetic acid, have been systematically investigated. Preparative-scale electrolyses showed that carbon monoxide is the only product of the catalytic reaction. Methodic application of a nondestructive technique, cyclic voltammetry, with catalyst and CO2 concentrations, as well as H/D isotope effect, as diagnostic parameters allowed the dissection of the reaction mechanism. It appears that the key step of the reaction sequence consists of an electron transfer from the catalyst concerted with the cleavage of a C-O bond and the transfer of one proton. This is the second example, and an intermolecular version of such a concerted proton-electron bond-breaking reaction after a similar electrochemical process involving the cleavage of O-O bonds has been identified. It is the first time that a proton-electron transfer concerted with bond breaking has been uncovered as the crucial step in a catalytic multistep reaction. PMID:23692448

  3. Mapping disulfide bonds in insulin with the Route 66 Method: selective cleavage of S-C bonds using alkali and alkaline earth metal enolate complexes.

    PubMed

    Kim, Hugh I; Beauchamp, J L

    2009-01-01

    Simple and fast identification of disulfide linkages in insulin is demonstrated with a peptic digest using the Route 66 method. This is accomplished by collisional activation of singly and doubly charged cationic Na(+) and Ca(2+) complexes generated using electrospray ionization mass spectrometry (ESI-MS). Collisional activation of doubly charged metal complexes of peptides with intermolecular disulfide linkages yields two sets of singly charged paired products separated by 66 mass units resulting from selective SC bond cleavages. Highly selective elimination of 66 mass units, which corresponds to the molecular weight of hydrogen disulfide (H(2)S(2)), is observed from singly charged metal complexes of peptides with disulfide linkages. The mechanism proposed for these processes is initiated by formation of a metal-stabilized enolate at Cys, followed by cleavage of the S-C bond. Further activation of the products yields sequence information that facilitates locating the position of the disulfide linkages in the peptic digest fragments. For example, the doubly charged Ca(2+) complex of the peptic digest product GIVEQCCASVCSL/FVNQHLCGSHL yields paired products separated by 66 mass units resulting from selective SC bond cleavages at an intermolecular disulfide linkage under low-energy collision-induced dissociation. Further activation of the product comprising the A chain reveals the presence of a second disulfide bridge, an intramolecular linkage. Experimental and theoretical studies of the disulfide linked model peptides provide mechanistic details for the selective cleavage of the S-C bond. PMID:18990587

  4. Luminescent pincer platinum(II) complexes with emission quantum yields up to almost unity: photophysics, photoreductive C-C bond formation, and materials applications.

    PubMed

    Chow, Pui-Keong; Cheng, Gang; Tong, Glenna So Ming; To, Wai-Pong; Kwong, Wai-Lun; Low, Kam-Hung; Kwok, Chi-Chung; Ma, Chensheng; Che, Chi-Ming

    2015-02-01

    Luminescent pincer-type Pt(II) ?complexes supported by C-deprotonated ?-extended tridentate R?C^N^N?R' ligands and pentafluorophenylacetylide ligands show emission quantum yields up to almost unity. Femtosecond time-resolved fluorescence measurements and time-dependent DFT calculations together reveal the dependence of excited-state structural distortions of [Pt(R?C^N^N?R')(C?C-C6 F5 )] on the positional isomers of the tridentate ligand. Pt?complexes [Pt(R-C^N^N?R')(C?C-Ar)] are efficient photocatalysts for visible-light-induced reductive C?C bond formation. The [Pt(R-C^N^N?R')(C?C-C6 F5 )] complexes perform strongly as phosphorescent dopants for green- and red-emitting organic light-emitting diodes (OLEDs) with external quantum efficiency values over 22.1?%. These complexes are also applied in two-photon cellular imaging when incorporated into mesoporous silica nanoparticles (MSNs). PMID:25581564

  5. 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, ?-D-fructofuranose-?-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.

  6. Mechanisms for enzymatic cleavage of the N-glycosidic bond in DNA

    PubMed Central

    Drohat, Alexander C.; Maiti, Atanu

    2014-01-01

    DNA glycosylases remove damaged or enzymatically modified nucleobases from DNA, thereby initiating the base excision repair (BER) pathway, which is found in all forms of life. These ubiquitous enzymes promote genomic integrity by initiating repair of mutagenic and/or cytotoxic lesions that arise continuously due to alkylation, deamination, or oxidation of the normal bases in DNA. Glycosylases also perform essential roles in epigenetic regulation of gene expression, by targeting enzymatically-modified forms of the canonical DNA bases. Monofunctional DNA glycosylases hydrolyze the N-glycosidic bond to liberate the target base, while bifunctional glycosylases mediate glycosyl transfer using an amine group of the enzyme, generating a Schiff base intermediate that facilitates their second activity, cleavage of the DNA backbone. Here we review recent advances in understanding the chemical mechanism of monofunctional DNA glycosylases, with an emphasis on how the reactions are influenced by properties of the nucleobase leaving-group, the moiety that varies across the vast range of substrates targeted by these enzymes. PMID:25181003

  7. 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-C? 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 Limo-Vieira and Malgorzata Smialek-Telega.

  8. Mechanisms for enzymatic cleavage of the N-glycosidic bond in DNA.

    PubMed

    Drohat, Alexander C; Maiti, Atanu

    2014-11-14

    DNA glycosylases remove damaged or enzymatically modified nucleobases from DNA, thereby initiating the base excision repair (BER) pathway, which is found in all forms of life. These ubiquitous enzymes promote genomic integrity by initiating repair of mutagenic and/or cytotoxic lesions that arise continuously due to alkylation, deamination, or oxidation of the normal bases in DNA. Glycosylases also perform essential roles in epigenetic regulation of gene expression, by targeting enzymatically-modified forms of the canonical DNA bases. Monofunctional DNA glycosylases hydrolyze the N-glycosidic bond to liberate the target base, while bifunctional glycosylases mediate glycosyl transfer using an amine group of the enzyme, generating a Schiff base intermediate that facilitates their second activity, cleavage of the DNA backbone. Here we review recent advances in understanding the chemical mechanism of monofunctional DNA glycosylases, with an emphasis on how the reactions are influenced by the properties of the nucleobase leaving-group, the moiety that varies across the vast range of substrates targeted by these enzymes. PMID:25181003

  9. Intramolecular C-C Bond Coupling of Nitriles to a Diimine Ligand in Group 7 Metal Tricarbonyl Complexes.

    PubMed

    Yempally, Veeranna; Fan, Wai Yip; Arndtsen, Bruce A; Bengali, Ashfaq A

    2015-12-01

    Dissolution of M(CO)3(Br)(L(Ar)) [L(Ar) = (2,6-Cl2-C6H3-NCMe)2CH2] in either acetonitrile [M = Mn, Re] or benzonitrile (M = Re) results in C-C coupling of the nitrile to the diimine ligand. When reacted with acetonitrile, the intermediate adduct [M(CO)3(NCCH3)(L(Ar))]Br forms and undergoes an intramolecular C-C coupling reaction between the nitrile carbon and the methylene carbon of the ?-diimine ligand. PMID:26554575

  10. 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

  11. A metal-free tandem C-C/C-O bond formation approach to densely functionalized indolyl 4H-chromenes catalyzed by polystyrene-supported p-toluenesulfonic acid under solvent-free conditions.

    PubMed

    Shinde, Vijay Vilas; Jeong, Yong Seok; Jeong, Yeon Tae

    2015-05-01

    A new environmentally benign and highly convergent protocol for the synthesis of indolyl 4H-chromene derivatives has been developed. This one-pot three-component condensation reaction of salicylaldehyde, cyclic 1,3-diketones, and indole is promoted by PS-PTSA as a reusable heterogeneous acid catalyst under solvent-free conditions. This protocol demonstrates several notable advantages such as that the catalyst is readily available and can be recovered and reused for at least five runs without any significant impact on product yields, high atom economy, excellent yields, and efficiency of producing three new bonds (two C-C and one C-O) and one stereo center in a single operation. PMID:25802172

  12. Design and Synthesis of Chiral Zn2+ Complexes Mimicking Natural Aldolases for Catalytic CC Bond Forming Reactions in Aqueous Solution

    PubMed Central

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

    2014-01-01

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

  13. 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.

  14. 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.

  15. Templated C-C and C-N Bond Formation Facilitated by a Molybdenum(VI) Metal Center.

    PubMed

    Zwettler, Niklas; Dup, Antoine; Schachner, Jrg A; Belaj, Ferdinand; Msch-Zanetti, Nadia C

    2015-12-21

    Preparation of molybdenum dioxido complexes with novel iminophenolate ligands bearing pendant secondary amide functionalities led to unprecedented C-C and C-N coupling reactions of two ?-iminoamides upon coordination. The diastereoselective cyclization to asymmetric imidazolidines occurs at the metal center in two consecutive steps via a monocoupled intermediate. A meaningful mechanism is proposed on the basis of full characterization of intermediate and final molybdenum-containing products by spectroscopic means and by single-crystal X-ray diffraction analyses. This process constitutes the first example of a diastereoselective self-cyclization of two ?-iminoamides. PMID:26646158

  16. Pathways and kinetics of methane and ethane C-H bond cleavage on PdO(101)

    NASA Astrophysics Data System (ADS)

    Antony, Abbin; Asthagiri, Aravind; Weaver, Jason F.

    2013-09-01

    We used conventional density functional theory (DFT) and dispersion-corrected DFT (DFT-D3) calculations to investigate C-H bond activation pathways for methane and ethane ?-complexes adsorbed on the PdO(101) surface. The DFT-D3 calculations predict lower and more physically realistic values of the apparent C-H bond cleavage barriers, which are defined relative to the gas-phase energy level, while giving nearly the same energy differences between stationary states as predicted by conventional DFT for a given reaction pathway. For the stable CH4 ?2 complex on PdO(101), DFT-D3 predicts that the C-H bond cleavage barriers are 55.2 and 16.1 kJ/mol relative to the initial molecularly adsorbed and gaseous states, respectively. We also predict that dehydrogenation of the resulting CH3 groups and conversion to CH3O species are significantly more energetically demanding than the initial C-H bond activation of CH4 on PdO(101). Using DFT-D3, we find that an ?2 and an ?1 ethane complex can undergo C-H bond cleavage on PdO(101) with intrinsic energy barriers that are similar to that of the methane complex, but with apparent barriers that are close to zero. We also investigated the dissociation kinetics of methane and ethane on PdO(101) using microkinetic models, with parameters derived from the DFT-D3 relaxed structures. We find that a so-called 3N - 2 model, in which two frustrated adsorbate motions are treated as free motions, predicts desorption pre-factors and alkane dissociation probabilities that agree well with estimates obtained from the literature. The microkinetic simulations demonstrate the importance of accurately describing entropic contributions in kinetic simulations of alkane dissociative chemisorption.

  17. 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.

  18. 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

  19. 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

  20. 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

  1. Synthesis of Indolizines through Oxidative Linkage of C-C and C-N Bonds from 2-Pyridylacetates.

    PubMed

    Mohan, Darapaneni Chandra; Ravi, Chitrakar; Pappula, Venkatanarayana; Adimurthy, Subbarayappa

    2015-07-01

    Synthesis of indolizine-1-carboxylates through the Ortoleva-King reaction of 2-pyridylacetate followed by the Aldol condensation under mild reaction conditions has been described. This protocol is compatible with a broad range of functional groups, and it has been also successfully extended to unsaturated ketones, bringing about the regioselective formation of benzoyl-substituted indolizines through Michael addition followed by C-N bond formation, which are difficult to prepare by previous methods in a single step. PMID:26044904

  2. Dynamics of vibrational relaxation in the S 1 state of carotenoids having 11 conjugated C?C bonds

    NASA Astrophysics Data System (ADS)

    Hrvin Billsten, Helena; Zigmantas, Donatas; Sundstrm, Villy; Polvka, Tom

    2002-04-01

    Transient absorption spectra and kinetics in the 470-650 nm region were recorded for lycopene, ?-carotene and zeaxanthin, all carotenoids with 11 conjugated double bonds, in two solvents with different polarity. Analysis of the red wing of the carotenoid S 1-S n transition revealed presence of a pronounced shoulder at early delay times. The kinetics recorded at this low-energy shoulder of the S 1-S n transition yields an additional decay component of 500-800 fs in addition to the main S 1 decay. This dynamics is ascribed to a vibrational relaxation in the S 1 state of the carotenoids.

  3. Organolanthanide-induced C-C bond formation. Preparation and properties of monomeric lanthanide aldolates and enolates

    SciTech Connect

    Heeres, H.J.; Maters, M.; Teuben, J.H.

    1992-01-01

    The reactivity of early-lanthanide carbyls Cp* {sub 2}LnCH(SiMe{sub 3}){sub 2} (1, Ln = La; 2, Ln = Ce) toward ketones has been studied. No reaction was observed with the bulky di-tert-butyl ketone. The corresponding lanthanum hydride [Cp* {sub 2}LaH]{sub 2} (3) is more reactive and afforded the addition product Cp*{sub 2}LaOCH(t-Bu){sub 2}{sup center-dot}O=C(t-Bu){sub 2} (4). Hydrogen transfer and formation of lanthanide aldolates Cp* {sub 2}LnOCMe{sub 2}C(=O)Me (5, Ln = Ce; 6, Ln =La) together with the protonated carbyl CH{sub 2}(SiMe{sub 3}){sub 2} were observed when 1 or 2 was treated with acetone. The molecular structure of the cerium analogue 5 was determined by X-ray diffraction and was found to be a monomeric bent metallocene compound with a {eta}{sup 2}-coordinated aldol fragment. Addition of 3-pentanone to the carbyls 1 and 2 did not result in C-C coupling but provided enolate-ketone adducts Cp*{sub 2}LnOC(Et)=C(H)MeO=CEt{sub 2} (7, Ln = La; 8, Ln = Ce). Reactions of the carbyls 1 and 2 with 4-methyl-5-hydroxy-5ethyl-3-heptanone yielded the enolate-ketone adducts as well and suggest that the differences in reactivity between acetone and 3-pentanone are thermodynamic and not kinetic in origin. 32 refs., 2 figs., 5 tabs.

  4. 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

  5. Synthesis of Silaphenalenes by Ruthenium-Catalyzed Annulation between 1-Naphthylsilanes and Internal Alkynes through C-H Bond Cleavage.

    PubMed

    Tokoro, Yuichiro; Sugita, Kengo; Fukuzawa, Shin-ichi

    2015-09-14

    Ruthenium-catalyzed annulation of 1-naphthylsilanes with internal alkynes afforded silaphenalenes through cleavage of the C-H bond at the 8-position of the naphthalene. [RuH2 (CO){P(p-FC6 H4 )3 }3 ] efficiently catalyzed the reaction. The use of 1-naphthyldiphenylsilane as a substrate resulted in a better yield of the annulation product compared to the use of silanes with alkyl groups on the silicon atom. Internal alkynes with both aryl and alkyl groups were tolerated in this reaction. PMID:26235840

  6. Selective cleavage of the C-O bonds in alcohols and asymmetric ethers by dissociative electron attachment

    NASA Astrophysics Data System (ADS)

    Ibanescu, Bogdan C.; Allan, Michael

    2009-11-01

    We present a comparative study of dissociative electron attachment for 20 saturated compounds containing ether and hydroxyl groups. We have discovered an unexpected case of selectivity for the cleavage of the C-O bonds in asymmetrical ethers R1-O-R2, within the range of the ?-Feshbach resonances, where a neutral alkyl group R1 is lost at a given energy, independent of R2. This empirical rule indicates that the excitation of Feshbach resonances responsible for the fragmentation is spatially localized on one or the other alkyl group. A number of other observations are also presented.

  7. 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)

  8. Understanding the mechanisms of unusually fast H-H, C-H, and C-C bond reductive eliminations from gold(III) complexes.

    PubMed

    Nijamudheen, A; Karmakar, Sharmistha; Datta, Ayan

    2014-11-01

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

  9. Oxidative bond formation and reductive bond cleavage at main group metal centers: reactivity of five-valence-electron MX? radicals.

    PubMed

    Protchenko, Andrey V; Dange, Deepak; Blake, Matthew P; Schwarz, Andrew D; Jones, Cameron; Mountford, Philip; Aldridge, Simon

    2014-08-01

    Monomeric five-valence-electron bis(boryl) complexes of gallium, indium, and thallium undergo oxidative M-C bond formation with 2,3-dimethylbutadiene, in a manner consistent with both the redox properties expected for M(II) species and with metal-centered radical character. The weaker nature of the M-C bond for the heavier two elements leads to the observation of reversibility in M-C bond formation (for indium) and to the isolation of products resulting from subsequent B-C reductive elimination (for both indium and thallium). PMID:25036798

  10. How to optimize a C bond H cleavage with a mononuclear copper-dioxygen adduct?

    NASA Astrophysics Data System (ADS)

    Lande, A. De La; Grard, H.; Parisel, O.

    We here report the investigations on the role of the charge transfer (CT) from copper toward dioxygen on the activation barrier of the C bond H bond breaking in a model [Cu(trenCH3)(O2)]+ adduct. By playing on the donating capability of the trenCH3 ligand, by means of a supplementary pseudopotential applied on the apical nitrogen atom, the existence of an optimum CT to achieve the rupture of the C bond H bond is revealed. When considering the dioxygen/superoxide/peroxide range in its whole, it appears that both dioxygen- and peroxide-type complexes are poor oxidant toward the C bond H bond. At variance, superoxide dominant complexes are confirmed to be better suited for a reactive purpose.

  11. Net heterolytic cleavage of B-H and B-B bonds across the N-Pd bond in a cationic (PNP)Pd fragment.

    PubMed

    Zhu, Yanjun; Chen, Chun-Hsing; Fafard, Claudia M; Foxman, Bruce M; Ozerov, Oleg V

    2011-09-01

    The use of weakly coordinating anions BAr(F)(4) (where Ar(F) = 3,5-(CF(3))(2)C(6)H(3)) and CB(11)H(12) allows one to access clean reactions of the [(PNP)Pd](+) fragment (PNP = bis(2-(i)Pr(2)P4-Me-phenyl)amido) with the B-H bond in catecholborane (CatBH) and catecholdiboron (CatBBCat). In both cases, a net heterolytic cleavage of B-H or B-B takes place, with the nitrogen atom of PNP being a recipient of a boryl fragment. The resultant products [(PN(BCat)P)PdH](+) (2) and [(PN(BCat)P)PdBCat](+) (3) were isolated as either BAr(F)(4) or CB(11)H(12) salts and fully characterized. They are susceptible to hydrolysis, with the B-N bond hydrolyzing selectively and rapidly at RT to give [(PN(H)P)PdH](+) (1) and [(PN(H)P)PdBCat](+) (4). Notably, 4 and 2 are isomers, but they do not interconvert even under thermolysis at 90 C. The Pd-B bond in 4 can be further hydrolyzed more slowly, to give 1. On the other hand, a Pd-B bond was formed from the Pd-H bond in 2 by reaction with excess CatBH (and evolution of H(2)), producing 3. PMID:21819075

  12. Importance of Protein Dynamics during Enzymatic CH Bond Cleavage Catalysis

    PubMed Central

    Klinman, Judith P.

    2014-01-01

    Quantum tunneling and protein dynamics have emerged as important components of enzyme function. This review focuses on soybean lipoxygenase-1, to illustrate how the properties of enzymatic CH bond activation link protein motions to the fundamental bond makingbreaking processes. PMID:23373460

  13. 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

  14. Formation of C?C bond via knoevenagel reaction between aromatic aldehyde and barbituric acid at liquid/HOPG and vapor/HOPG interfaces.

    PubMed

    Geng, Yanfang; Dai, Hongliang; Chang, Shaoqing; Hu, Fangyun; Zeng, Qingdao; Wang, Chen

    2015-03-01

    Controlling chemical reactions on surface is of great importance to constructing self-assembled covalent nanostructures. Herein, Knoevenagel reaction between aromatic aldehyde compound 2,5-di(5-aldehyde-2-thienyl)-1,4-dioctyloxybenzene (PT2) and barbituric acid (BA) has been successfully performed for the first time at liquid/HOPG interface and vapor/HOPG interface. The resulting surface nanostructures and the formation of C?C bond are recorded through scanning tunneling microscopy (STM), and confirmed by attenuated total reflectance Fourier-transform infrared (ATR/FT-IR) spectrometer and UV-vis absorption. The obtained results reveal that Knoevenagel condensation reaction can efficiently occur at both interfaces. This surface reaction would be an important step toward further reaction to produce innovative conjugated nanomaterial on the surface. PMID:25664650

  15. Glycosidic Bond Cleavage in DNA Nucleosides: Effect of Nucleobase Damage and Activation on the Mechanism and Barrier.

    PubMed

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

    2015-12-24

    Although DNA damage can have a variety of deleterious effects on cells (e.g., senescence, death, and rapid growth), the base excision repair (BER) pathway combats the effects by removing several types of damaged DNA. Since the first BER step involves cleavage of the bond between the damaged nucleobase and the DNA sugar-phosphate backbone, we have used density functional theory to compare the intrinsic stability of the glycosidic bond in a number of common DNA oxidation, deamination, and alkylation products to the corresponding natural nucleosides. Our calculations predict that the dissociative (SN1) and associative (SN2) pathways are nearly isoenergetic, with the dissociative pathway only slightly favored on the Gibbs reaction surface for all canonical and damaged nucleosides, which suggests that DNA damage does not affect the inherently most favorable deglycosylation pathway. More importantly, with the exception of thymine glycol, all DNA lesions exhibit reduced glycosidic bond stability relative to the undamaged nucleosides. Furthermore, the trend in the magnitude of the deglycosylation barrier reduction directly correlates with the relative nucleobase acidity (at N9 for purines or N1 for pyrimidines), which thereby provides a computationally efficient, qualitative measure of the glycosidic bond stability in DNA damage. The effect of nucleobase activation (protonation) at different sites predicts that the positions leading to the largest reductions in the deglycosylation barrier are typically used by DNA glycosylases to facilitate base excision. Finally, deaza purine derivatives are found to have greater glycosidic bond stability than the canonical counterparts, which suggests that alterations to excision rates measured using these derivatives to probe DNA glycosylase function must be interpreted in reference to the inherent differences in the nucleoside reactivity. Combined with previous studies of the deglycosylation of DNA nucleosides, the current study provides a greater fundamental understanding about the reactivity of the glycosidic bond in damaged DNA, which has direct implications to the function of critical DNA repair enzymes. PMID:26618397

  16. 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.

  17. 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

  18. 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

  19. 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

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

    PubMed

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

    2015-09-21

    A practical protocol for the ?-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

  1. 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.

  2. 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

  3. Selective Bond Cleavage in Potassium Collisions with Pyrimidine Bases of DNA

    NASA Astrophysics Data System (ADS)

    Almeida, Diogo; Ferreira da Silva, Filipe; Garca, Gustavo; Limo-Vieira, Paulo

    2013-01-01

    Electron transfer in alkali-molecule collisions to gas phase thymine and uracil yielding H- formation is selectively controlled in the energy range between 5.3 and 66.1 eV. By tuning the collision energy, electron transfer from the alkali to partly deuterated thymine, methylated thymine at the N1 and methylated uracil at the N3 positions, H- loss proceeds not only through the breaking of the (C-H) against (N-H) bonds but also through N1 against N3 sites. Such selectivity, as far as bond and site are concerned, is here reported for the first time by electron transfer induced dissociation experiments in alkali-molecule collisions.

  4. 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

  5. Atomic force microscopy imaging of TiO{sub 2} surfaces active for C-C bond formation reactions in ultrahigh vacuum

    SciTech Connect

    Watson, B.A.; Barteau, M.A.

    1994-06-01

    TiO{sub 2}(001) single crystal surfaces active for a variety of different chemistries were examined using atomic force microscopy (AFM). C-C bond forming reactions previously identified on these surfaces include carboxylic acid ketonization, aldol condensation, reductive carbonyl coupling, and alkyne cyclotrimerization. The surfaces were prepared in ultrahigh vacuum (UHV) and examined by AFM in air. Surfaces examined included the (011)-faceted surface, (114)-faceted surface, and argon-ion-bombarded surfaces, as well as the mechanically polished single-crystal surface prior to treatment in UHV. The one unifying feature of all the images was their extreme flatness. Root-mean-square roughnesses were routinely less than 10 {Angstrom} in 500 x 500 nm scans. These same scans showed the surfaces to have surface areas exceeding that of an ideal flat surface by no more than 1.2%. Images of the polished surface revealed a variety of surface features, including polishing scratches and particle-like features. The argon-ion-bombarded surface and the faceted surfaces were composed of large flat plateaus ranging in size from 21 to 75 nm. The size of the plateaus was essentially the same for the ion bombarded surface and the (011)-faceted surface. The (114)-faceted surfaced exhibited slightly smaller plateau regions than the other surfaces. The images indicate that argon-ion bombardment, while disordering the surface and causing significant composition changes, does not lead to observable morphological changes on this scale. The relative uniformity of the surfaces examined is consistent with the selectivity of carbon-carbon bond-forming reactions that have been shown to take place on these surfaces. The images also reveal how the surface topography on the scale of the plateau structures observed is only slightly changed during the transformation of the surface unit cell structure from the (011)- to the (114)-faceted surface. 29 refs., 6 figs., 1 tab.

  6. 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.

  7. 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.

  8. Palladium-catalyzed carbonation-diketonization of terminal aromatic alkenes via carbon-nitrogen bond cleavage for the synthesis of 1,2-diketones.

    PubMed

    Wang, Azhong; Jiang, Huanfeng; Li, Xianwei

    2011-08-19

    A palladium-catalyzed carbonation-diketonization reaction of terminal alkenes via carbon-nitrogen bond cleavage under an atmosphere of oxygen has been developed. A series of 1,2-diketones were readily prepared from the reaction of aromatic terminal alkenes with nitroalkanes. PMID:21732586

  9. Designed synthesis of size-tunable Ag2S nanoclusters via distinguishable C-S bond cleavage reaction of alkyl- and aryl-thiolates.

    PubMed

    Chen, Hang-Qing; He, Xin; Guo, Hui; Fu, Nan-Yan; Zhao, Liang

    2015-03-01

    We report herein the synthesis of two different silver clusters of aryl- and alkyl-thiolates. These two cluster complexes exhibited biased C-S bond cleavage reaction rates upon removing protective hexamethylazacalix[6]pyridine (Py[6]) ligands, which was applied in the fabrication of silver sulfide nanoclusters with variable and controllable sizes. PMID:25652650

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    Jia, Hong-Peng; Gour, 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

  17. Intermediate in the O?O Bond Cleavage Reaction of an Extradiol Dioxygenase

    SciTech Connect

    Kovaleva, Elena G.; Lipscomb, John D.

    2009-02-16

    The reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and O{sub 2} in adjacent ligand positions of the active site metal [usually Fe(II)]. This intermediate and the following Fe(II)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (HPCD). Here a subsequent intermediate in which the O-O bond is broken to yield a gem diol species is structurally characterized. This new intermediate is stabilized in the crystal by using the alternative substrate, 4-sulfonylcatechol, and the Glu323Leu variant of HPCD, which alters the crystal packing.

  18. On the radical scavenging activity of isoflavones: thermodynamics of O-H bond cleavage.

    PubMed

    Lengyel, Jozef; Rimar?k, Jn; Vagnek, Adam; Klein, Erik

    2013-07-14

    We have performed Density Functional Theory B3LYP/6-311++G** calculations of reaction enthalpies of antioxidant action mechanisms for nine isoflavones. O-H bond dissociation enthalpies, ionization potentials, proton dissociation enthalpies, proton affinities and electron transfer enthalpies related to Hydrogen Atom Transfer (HAT), Single Electron Transfer-Proton Transfer (SET-PT) and Sequential Proton-Loss Electron-Transfer (SPLET) mechanisms were investigated in gas- and solution-phases. Studies on the radical scavenging ability of isoflavones, contrary to various flavonoids, are still scarce. Thus, understanding of its thermodynamics can be considered beneficial. The selection of isoflavones (daidzein, formononetin, genistein, biochanin A, prunetin, 6-hydroxydaidzein, glycitein, orobol and santal) enables us to evaluate the effects of various structural features, such as the presence of methoxy (4'-OMe, 6-OMe, 7-OMe) and hydroxy (3'-OH, 5-OH, 6-OH) groups, on studied reaction enthalpies. The obtained results show that HAT can be attributed predominantly to the B ring, while SPLET takes place preferentially in the A ring, as was also indicated in experimental works. PMID:23698223

  19. 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

  20. Reactions of isocyanides with rhodium porphyrins. Formation of formimidoyl and carbamoyl complexes and CN-R bond cleavage

    SciTech Connect

    Poszmik, G.; Carroll, P.J.; Wayland, B.B. )

    1993-09-01

    Reactions of alkyl and aryl isocyanides with (octaethylporphyrinato)rhodium hydride, (OEP)Rh-H, (octaethylporphyrinato)rhodium(II) dimer, [(OEP)Rh][sub 2] and (tetramesitylporphyrinato)rhodium(II), (TMP)Rh, have been investigated for comparison with CO reactivity. Alkyl and aryl isocyanides interact with (OEP)Rh-H to form 1:1 adducts, (OEP)Rh(H)(CNR), which react further to produce formimidoyl complexes, (OEP)Rh-CH=NR, in analog with the reaction of (OEP)Rh-H with CO that produces a formyl complex, (OEP)Rh-CHO. [(OEP)Rh][sub 2] forms 1:1 complexes with isocyanides where the 2,6-dimethylphenyl isocyanide derivative persists at equilibrium, but alkyl isocyanides undergo CN- alkyl bond cleavage to form alkyl, (OEP)Rh-R and cyanide, (OEP)Rh(CN)(CNR), complexes. No evidence was obtained for bridging isocyanide species analogous to the dimetal ketone RhC(O)Rh and dimetal diketone RhC(O)C(O)Rh complexes observed in reactions of [(OEP)Rh][sub 2] with CO. Carbamoyl complexes, (OEP)Rh-C(O)NHR, are formed in reactions of [(OEP)Rh][sub 2] with CNR and H[sub 2]O or CO and RNH[sub 2]. 24 refs., 7 figs., 3 tabs.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. AgNO2-mediated cleavage of the N-N bond of sulfonylhydrazones and oxygen transfer: access to fulleroisoxazolines via radical cyclization with [60]fullerene.

    PubMed

    Liu, Tong-Xin; Ma, Jinliang; Chao, Di; Zhang, Pengling; Liu, Qingfeng; Shi, Lei; Zhang, Zhiguo; Zhang, Guisheng

    2015-08-18

    An unprecedented AgNO2-mediated novel transformation of sulfonylhydrazones with [60]fullerene to various fulleroisoxazolines has been developed. The new chemistry of sulfonylhydrazones involving the cleavage of the N-N bond in synthetic application is first disclosed. Silver nitrite acts as the reaction initiator and the oxygen source in this unique transformation. This reaction is easy to perform, and exhibits a remarkably wide substrate scope under mild conditions. PMID:26165985

  7. Copper-catalyzed aerobic oxidation and cleavage/formation of C-S bond: a novel synthesis of aryl methyl sulfones from aryl halides and DMSO.

    PubMed

    Yuan, Gaoqing; Zheng, Junhua; Gao, Xiaofang; Li, Xianwei; Huang, Liangbin; Chen, Huoji; Jiang, Huanfeng

    2012-08-01

    With atmospheric oxygen as the oxidant, a novel copper(I)-catalyzed synthesis of aryl methyl sulfones from aryl halides and widely available DMSO is described. The procedure tolerates aryl halides with various functional groups (such as methoxy, acetyl, chloro, fluoro and nitro groups), which could afford aryl methyl sulfones in moderate to high yields. The copper-catalyzed aerobic oxidation and the cleavage/formation of C-S bond are the key steps for this transformation. PMID:22728918

  8. 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

  9. 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

  10. Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations.

    PubMed

    Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra

    2015-09-24

    Base excision of mismatched or damaged nucleotides catalyzed by glycosylase enzymes is the first step of the base excision repair system, a machinery preserving the integrity of DNA. Thymine DNA glycosylase recognizes and removes mismatched thymine by cleaving the C1'-N1 bond between the base and the sugar ring. Our quantum mechanical/molecular mechanical calculations of this reaction in human thymine DNA glycosylase reveal a requirement for a positive charge in the active site to facilitate C1'-N1 bond scission: protonation of His151 significantly lowers the free energy barrier for C1'-N1 bond dissociation compared to the situation with neutral His151. Shuttling a proton from His151 to the thymine base further reduces the activation free energy for glycosidic bond cleavage. Classical molecular dynamics simulations of the H151A mutant suggest that the mutation to the smaller, neutral, residue increases the water accessibility of the thymine base, rendering direct proton transfer from the bulk feasible. Quantum mechanical/molecular mechanical calculations of the glycosidic bond cleavage reaction in the H151A mutant show that the activation free energy is slightly lower than in the wild-type enzyme, explaining the experimentally observed higher reaction rates in this mutant. PMID:26320595

  11. 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.

  12. 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 ?* shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the ?* orbital of the base to the ?* orbital of the glycosidic N-C bond. In addition, the metastable state formed after impinging LEE (0-1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N-C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of 35-55 fs. Comparison of salient features of the two dissociation events, i.e., 3' C-O single strand break and glycosidic N-C bond cleavage in 3'-dCMPH molecule are also provided.

  13. Metabolism of aloesin and related compounds by human intestinal bacteria: a bacterial cleavage of the C-glucosyl bond and the subsequent reduction of the acetonyl side chain.

    PubMed

    Che, Q M; Akao, T; Hattori, M; Kobashi, K; Namba, T

    1991-03-01

    By anaerobic incubation with a bacterial mixture from human feces, aloesin (aloeresin B; 1) was converted to 2-acetonyl-7-hydroxy-5-methylchromone (aloesone; 3) and dl-7-hydroxy-2-(2'-hydroxypropyl)-5-methylchromone (aloesol; 4a + 4b) through a cleavage of the C-glucosyl bond, followed by reduction of the acetonyl side chain. An analogous compound, aloeresin A (2), was converted to p-coumaric acid and aloesin (1), the latter being subsequently transformed to aloesone (3) and dl-aloesol (4a + 4b). On the other hand, 7-O-methylated derivatives (7, 5a and 5b) of aloesin and of 8-C-glucosylaloesol were not cleaved to the corresponding aglycones, suggesting the importance of a free hydroxy group adjacent to the C-glucosyl group in the molecule for the bacterial cleavage of aloesin derivatives. This is the first report on the cleavage of the C-glycosyl bond of chromone C-glucosides by intestinal bacteria. PMID:2070451

  14. 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.``

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Interaction of a pseudo-? C-C bond with cuprous and argentous chlorides: Cyclopropane?CuCl and cyclopropane?AgCl investigated by rotational spectroscopy and ab initio calculations.

    PubMed

    Zaleski, Daniel P; Mullaney, John C; Bittner, Dror M; Tew, David P; Walker, Nicholas R; Legon, Anthony C

    2015-10-28

    Strongly bound complexes (CH2)3?MCl (M = Cu or Ag), formed by non-covalent interaction of cyclopropane and either cuprous chloride or argentous chloride, have been generated in the gas phase by means of the laser ablation of either copper or silver metal in the presence of supersonically expanded pulses of a gas mixture containing small amounts of cyclopropane and carbon tetrachloride in a large excess of argon. The rotational spectra of the complexes so formed were detected with a chirped-pulse, Fourier transform microwave spectrometer and analysed to give rotational constants and Cu and Cl nuclear quadrupole coupling constants for eight isotopologues of each of (CH2)3?CuCl and (CH2)3?AgCl. The geometry of each of these complexes was established unambiguously to have C2v symmetry, with the three C atoms coplanar, and with the MCl molecule lying along a median of the cyclopropane C3 triangle. This median coincides with the principal inertia axis a in each of the two complexes (CH2)3?MCl. The M atom interacts with the pseudo-? bond linking the pair of equivalent carbon atoms (F)C (F = front) nearest to it, so that M forms a non-covalent bond to one C-C edge of the cyclopropane molecule. The (CH2)3?MCl complexes have similar angular geometries to those of the hydrogen- and halogen-bonded analogues (CH2)3?HCl and (CH2)3?ClF, respectively. Quantitative details of the geometries were determined by interpretation of the observed rotational constants and gave results in good agreement with those from ab initio calculations carried out at the CCSD(T)(F12*)/aug-cc-pVTZ-F12 level of theory. Interesting geometrical features are the lengthening of the (F)C-(F)C bond and the shrinkage of the two equivalent (B)C-(F)C (B = back) bonds relative to the C-C bond in cyclopropane itself. The expansions of the (F)C-(F)C bond are 0.1024(9) and 0.0727(17) in (CH2)3?CuCl and (CH2)3?AgCl, respectively, according to the determined r0 geometries. The C-C bond lengthening is in each case about four times that observed by similar methods in the corresponding complexes of MCl with ethyne and ethene, even though the cyclopropane complexes are more weakly bound than their ethyne and ethene analogues. Reasons for the larger increase in r(CC) in the pseudo-? complexes are discussed. PMID:26520520

  20. Interaction of a pseudo-? CC bond with cuprous and argentous chlorides: Cyclopropane⋯CuCl and cyclopropane⋯AgCl investigated by rotational spectroscopy and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Zaleski, Daniel P.; Mullaney, John C.; Bittner, Dror M.; Tew, David P.; Walker, Nicholas R.; Legon, Anthony C.

    2015-10-01

    Strongly bound complexes (CH2)3⋯MCl (M = Cu or Ag), formed by non-covalent interaction of cyclopropane and either cuprous chloride or argentous chloride, have been generated in the gas phase by means of the laser ablation of either copper or silver metal in the presence of supersonically expanded pulses of a gas mixture containing small amounts of cyclopropane and carbon tetrachloride in a large excess of argon. The rotational spectra of the complexes so formed were detected with a chirped-pulse, Fourier transform microwave spectrometer and analysed to give rotational constants and Cu and Cl nuclear quadrupole coupling constants for eight isotopologues of each of (CH2)3⋯CuCl and (CH2)3⋯AgCl. The geometry of each of these complexes was established unambiguously to have C2v symmetry, with the three C atoms coplanar, and with the MCl molecule lying along a median of the cyclopropane C3 triangle. This median coincides with the principal inertia axis a in each of the two complexes (CH2)3⋯MCl. The M atom interacts with the pseudo-? bond linking the pair of equivalent carbon atoms FC (F = front) nearest to it, so that M forms a non-covalent bond to one CC edge of the cyclopropane molecule. The (CH2)3⋯MCl complexes have similar angular geometries to those of the hydrogen- and halogen-bonded analogues (CH2)3⋯HCl and (CH2)3⋯ClF, respectively. Quantitative details of the geometries were determined by interpretation of the observed rotational constants and gave results in good agreement with those from ab initio calculations carried out at the CCSD(T)(F12*)/aug-cc-pVTZ-F12 level of theory. Interesting geometrical features are the lengthening of the FCFC bond and the shrinkage of the two equivalent BCFC (B = back) bonds relative to the CC bond in cyclopropane itself. The expansions of the FCFC bond are 0.1024(9) and 0.0727(17) in (CH2)3⋯CuCl and (CH2)3⋯AgCl, respectively, according to the determined r0 geometries. The CC bond lengthening is in each case about four times that observed by similar methods in the corresponding complexes of MCl with ethyne and ethene, even though the cyclopropane complexes are more weakly bound than their ethyne and ethene analogues. Reasons for the larger increase in r(CC) in the pseudo-? complexes are discussed.

  1. Desorption electrospray ionisation mass spectrometry reveals in situ modification of a hindered amine light stabiliser resulting from direct N-OR bond cleavage.

    PubMed

    Paine, Martin R L; Barker, Philip J; Blanksby, Stephen J

    2011-03-01

    Detection and characterisation of structural modifications of a hindered amine light stabiliser (HALS) directly from a polyester-based coil coating have been achieved by desorption electrospray ionisation mass spectrometry (DESI-MS) for the first time. In situ detection is made possible by exposing the coating to an acetone vapour atmosphere prior to analysis. This is a gentle and non-destructive treatment that allows diffusion of analyte to the surface without promoting lateral migration. Using this approach a major structural modification of the HALS TINUVIN123 (bis(1-octyloxy-2,2,6,6-tetramethyl-4-piperidyl) sebacate) was discovered where one N-ether piperidine moiety (N-OC(8)H(17)) is converted to a secondary piperidine (N-H). With the use of 2-dimensional DESI-MS imaging the modification was observed to arise during high curing temperatures (ca. 260 C) and under simulated physiological conditions (80 C, full solar spectrum). It is proposed that the secondary piperidine derivative is a result of a highly reactive aminyl radical intermediate produced by N-O homolytic bond cleavage. The nature of the bond cleavage is also suggested by ESR spin-trapping experiments employing ?-phenyl-N-tert-butyl nitrone (PBN) in toluene at 80 C. The presence of a secondary piperidine derivative in situ and the implication of N-OR competing with NO-R bond cleavage suggest an alternative pathway for generation of the nitroxyl radical-an essential requirement in anti-oxidant activity that has not previously been described for the N-ether sub-class of HALS. PMID:21152630

  2. Carboncarbon bond activation of cyclobutenones enabled by the addition of chiral organocatalyst to ketone

    PubMed Central

    Li, Bao-Sheng; Wang, Yuhuang; Jin, Zhichao; Zheng, Pengcheng; Ganguly, Rakesh; Chi, Yonggui Robin

    2015-01-01

    The activation of carboncarbon (CC) bonds is an effective strategy in building functional molecules. The CC bond activation is typically accomplished via metal catalysis, with which high levels of enantioselectivity are difficult to achieve due to high reactivity of metal catalysts and the metal-bound intermediates. It remains largely unexplored to use organocatalysis for CC bond activation. Here we describe an organocatalytic activation of CC bonds through the addition of an NHC to a ketone moiety that initiates a CC single bond cleavage as a key step to generate an NHC-bound intermediate for chemo- and stereo-selective reactions. This reaction constitutes an asymmetric functionalization of cyclobutenones using organocatalysts via a CC bond activation process. Structurally diverse and multicyclic compounds could be obtained with high optical purities via an atom and redox economic process. PMID:25652912

  3. 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

  4. Ruthenium(0) Catalyzed Endiyne-?-Ketol [4 + 2] Cycloaddition: Convergent Assembly of Type II Polyketide Substructures via C-C Bond Forming Transfer Hydrogenation.

    PubMed

    Saxena, Aakarsh; Perez, Felix; Krische, Michael J

    2015-05-13

    Upon exposure of 3,4-benzannulated 1,5-diynes (benzo-endiynes) to ?-ketols (?-hydroxyketones) in the presence of Ru(0) catalysts derived from Ru3(CO)12 and RuPhos or CyJohnPhos, successive redox-triggered C-C coupling occurs to generate products of [4 + 2] cycloaddition. The proposed catalytic mechanism involves consecutive alkyne-carbonyl oxidative couplings to form transient oxaruthanacycles that suffer ?-ketol mediated transfer hydrogenolysis. This process provides a new, convergent means of assembling Type II polyketide substructures. PMID:25938947

  5. Transition-metal catalysed C-N bond activation.

    PubMed

    Wang, Quanjun; Su, Yijin; Li, Lixin; Huang, Hanmin

    2016-02-29

    Transition-metal catalysed C-N bond activation has attracted much attention and become one of the most promising bond disconnection and formation strategies that encompass a broad spectrum of applications in many reactions. In this tutorial review, efficient strategies for catalytic cleavage of C(sp)-N, C(sp(2))-N and C(sp(3))-N bonds and their applications in new C-C and C-N bond formation reactions are summarized. PMID:26764537

  6. 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

  7. Rhodium(III)-Catalyzed Directed ortho-C-H Bond Functionalization of Aromatic Ketazines via C-S and C-C Coupling.

    PubMed

    Wen, Jing; Wu, An; Wang, Mingyang; Zhu, Jin

    2015-11-01

    Described herein is a convenient and efficient method for sulfuration and olefination of aromatic ketazines via rhodium-catalyzed oxidative C-H bond activation. A range of substituted substrates are supported, and a possible mechanism is proposed according to experimental results of kinetic isotopic effect, reversibility studies, and catalysis of rhodacycle intermediate c1. PMID:26417874

  8. All-carbon quaternary stereogenic centers in acyclic systems through the creation of several C-C bonds per chemical step.

    PubMed

    Marek, Ilan; Minko, Yury; Pasco, Morgane; Mejuch, Tom; Gilboa, Noga; Chechik, Helena; Das, Jaya P

    2014-02-19

    In the past few decades, it has become clear that asymmetric catalysis is one of the most powerful methods for the construction of carbon-carbon as well as carbon-heteroatom bonds in a stereoselective manner. However, when structural complexity increases (i.e., all-carbon quaternary stereogenic center), the difficulty in reaching the desired adducts through asymmetric catalytic reactions leads to a single carbon-carbon bond-forming event per chemical step between two components. Issues of efficiency and convergence should therefore be addressed to avoid extraneous chemical steps. In this Perspective, we present approaches that tackle the stimulating problem of efficiency while answering interesting synthetic challenges. Ideally, if one could create all-carbon quaternary stereogenic centers via the creation of several new carbon-carbon bonds in an acyclic system and in a single-pot operation from simple precursors, it would certainly open new horizons toward solving the synthetic problems. Even more important for any further design, the presence of polyreactive intermediates in synthesis (bismetalated, carbenoid, and oxenoids species) becomes now an indispensable tool, as it creates consecutively the same number of carbon-carbon bonds as in a multi-step process, but in a single-pot operation. PMID:24512113

  9. 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

  10. Cleavage of the glycosidic C-O-C bond on size-selected subnanometer cobalt catalysts and on ALD-cobalt coated nanoporous membranes.

    SciTech Connect

    Deng, W.; Lee, S.; Libera, J. A.; Elam, J. W.; Vajda, S.; Marshall, C. L.

    2011-02-15

    The cleavage of the C-O-C bond was studied under oxidizing conditions on nanostructured membrane supported cobalt-based catalysts using a cellulose model surrogate, 1-methoxy-2-methyl-2-propanol. The cobalt catalysts were found to break the C-O-C bond, producing alcohols and/or ketones by further oxidation. The size-selected sub-nanometer size cobalt clusters exhibited a per metal activity of up to 5 orders of magnitude higher than the with atomic layer deposition uniformly coated membranes. The large difference in activity is attributed to the high fraction of the surface atoms of the subnanometer clusters. The positioning of the clusters at the entrance vs. exit of the catalytic membrane allows for a control of the contact time and consequently of the selectivity of the catalyst.

  11. Cleavage of the C-O-C bond on size-selected subnanometer cobalt catalysts and on ALD-cobalt coated nanoporous membranes.

    SciTech Connect

    Deng, W.; Lee, S.; Libera, J. A.; Elam, J. W.; Vajda, S.; Marshall, C. L.; Yale Univ.

    2011-02-15

    The cleavage of the C-O-C bond was studied under oxidizing conditions on nanostructured membrane supported cobalt-based catalysts using a cellulose model surrogate, 1-methoxy-2-methyl-2-propanol. The cobalt catalysts were found to break the C-O-C bond, producing alcohols and/or ketones by further oxidation. The size-selected sub-nanometer size cobalt clusters exhibited a per metal activity of up to 5 orders of magnitude higher than the with atomic layer deposition uniformly coated membranes. The large difference in activity is attributed to the high fraction of the surface atoms of the subnanometer clusters. The positioning of the clusters at the entrance vs. exit of the catalytic membrane allows for a control of the contact time and consequently of the selectivity of the catalyst.

  12. 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.

  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. CeCl37H2O catalyzed C-C and C-N bond-forming cascade cyclization with subsequent side-chain functionalization and rearrangement: a domino approach to pentasubstituted pyrrole analogues.

    PubMed

    Dhara, Dipankar; Gayen, Krishnanka S; Khamarui, Saikat; Pandit, Palash; Ghosh, Sukla; Maiti, Dilip K

    2012-11-16

    CeCl(3)7H(2)O is found as an efficient catalyst for new intermolecular domino reactions of three-, four- and seven-component assemblies of common precursors under benign reaction conditions. Generation of enaminioesters from ?-keto esters and primary amines, activation of their allylic sp(3) C-H, vinylic sp(2) C-H and N-H bonds, multi C-C and C-N bond-forming cascade cyclization with 1,2-diketones and subsequent side-chain alkylation have been developed to construct functionalized pentasubstituted pyrroles and their chiral analogues. The scope of the domino reaction is successfully explored toward synthesis of highly aryl-substituted pyrroles, pentasubstituted pyrroles bearing C2-olefinic side-chain and spiro-2-pyrrolinones and their chiral analogues via unusual side-chain amination, elimination and ring contraction. The new domino reaction is operationally simple, robust, substrate specific, selective and high yielding. PMID:23113545

  15. 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 ?(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

  16. Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH2BrI

    NASA Astrophysics Data System (ADS)

    Anderson, Christopher P.; Spears, Kenneth G.; Wilson, Kaitlynn R.; Sension, Roseanne J.

    2013-11-01

    It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (nX) to a carbon-halogen antibonding orbital (?*C-X). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH2BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH2BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH2Br + I radical pairs, iso-CH2Br-I, and iso-CH2I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH2Br-I. Both iso-CH2Br-I and iso-CH2I-Br are observed in cyclohexane with a ratio of 2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH2I-Br photoproduct as well as iso-CH2Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH2Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and 1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH2BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes.

  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. 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

  19. 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.

  20. 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/?1 ? 500 s?1) transforms HOPDA (?max = 434 nm) to a species with electronic absorption maxima at 473 and 492 nm. The absorbance of this enzyme-bound species (E:S) decayed in a biphasic manner (1/?2 = 54 s?1, 1/?3 = 6 s?1 ? kcat) with simultaneous biphasic appearance (48 and 8 s?1) of an absorbance band at 270 nm characteristic of one of the products, 2-hydroxypenta-2,4-dienoic acid (HPD). Increasing solution viscosity with glycerol slowed 1/?1 and 1/?2, but affected neither 1/?3 nor kcat, suggesting that 1/?2 may reflect diffusive HPD dissociation, while 1/?3 represents an intramolecular event. Product inhibition studies suggested that the other product, benzoate, is released after HPD. Contrary to studies in a related hydrolase, we found no evidence that ketonized HOPDA is partially released prior to hydrolysis, and therefore postulate that the biphasic kinetics reflect one of two mechanisms, pending assignment of E:S (?max = 492 nm). Crystal structures of wild type, the S112C variant, and S112C incubated with HOPDA were each determined to 1.6 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

  1. 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

  2. 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 ?-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]+.

  3. 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

  4. 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

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

    PubMed

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

    2014-07-21

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

  6. {{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.

  7. 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.

  8. 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.

  9. Silylations of Arenes with Hydrosilanes: From Transition-Metal-Catalyzed CX Bond Cleavage to Environmentally Benign Transition-Metal-Free CH Bond Activation.

    PubMed

    Xu, Zheng; Xu, Li-Wen

    2015-07-01

    The construction of carbon-silicon bonds is highlighted as an exciting achievement in the field of organosilicon chemistry and green chemistry. Recent developments in this area will enable the sustainable chemical conversion of silicon resources into synthetically useful compounds. Especially, the catalytic silylation through CH bond activation without directing groups and hydrogen acceptors is one of the most challenging topics in organic chemistry and green chemistry. These remarkable findings on catalytic silylation can pave the way to a more environmentally benign utilization of earth-abundant silicon-based resources in synthetic chemistry. PMID:26073645

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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 ? 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

  15. 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)

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

    PubMed

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

    2014-09-18

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

  17. Synthesis of Polyheteroaromatic Compounds via Rhodium-Catalyzed Multiple C-H Bond Activation and Oxidative Annulation.

    PubMed

    Peng, Shiyong; Liu, Suna; Zhang, Sai; Cao, Shengyu; Sun, Jiangtao

    2015-10-16

    Polyheteroaromatic compounds are potential optoelectronic conjugated materials due to their electro- and photochemical properties. Transition-metal-catalyzed multiple C-H activation and sequential oxidative annulation allows rapidly assembling of those compounds from readily available starting materials. A rhodium-catalyzed cascade oxidative annulation of ?-enamino esters or 4-aminocoumarins with internal alkynes is described to access those compounds, featuring multiple C-H/N-H bond cleavages and sequential C-C/C-N bond formations in one pot. PMID:26439472

  18. 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).

  19. 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

  20. 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

  1. Analysis of positional isotope exchange in ATP by cleavage of the beta P-O gamma P bond. Demonstration of negligible positional isotope exchange by myosin.

    PubMed

    Dale, M P; Hackney, D D

    1987-12-15

    A method for analysis of positional isotope exchange (PIX) during ATP in equilibrium with HOH oxygen exchange is presented that uses a two-step degradation of ATP resulting in cleavage of the beta P-O gamma P bond. This cleavage yields Pi derived from the gamma-phosphoryl of ATP that contains all four of the gamma oxygens. Both PIX between the beta,gamma-bridge and beta-nonbridge positions and washout of the gamma-nonbridge oxygens can be simultaneously followed by using ATP labeled with 17O at the beta-nonbridge positions and 18O at the beta,gamma-bridge and gamma-nonbridge positions. Application of this method to ATP in equilibrium with HOH exchange during single turnovers of myosin indicates that the bulk of the ATP undergoes rapid washout of gamma-nonbridge oxygens in the virtual absence of PIX. At 25 degrees C with subfragment 1 the scrambling rate is at the limit of detectability of approximately 0.001 s-1, which is 50-fold slower than the steady-state rate. This corresponds to a probability of scrambling for the beta-oxygens of bound ADP of 1 in 10,000 for each cycle of reversible hydrolysis of bound ATP. A fraction of the ATP, however, does not undergo rapid washout. With myosin and stoichiometric ATP at 0 degrees C, this fraction corresponds to 10% of the ATP remaining at 36 s, or 2% of the initial ATP, and an equivalent level of ATP is found that does not bind irreversibly to myosin in a cold chase experiment. A significant level of apparent PIX is observed with subfragment 1 in the fraction that resists washout, and this apparent PIX is shown to be due to contaminant adenylate kinase activity. This apparent PIX due to adenylate kinase provides a possible explanation for the PIX observed by Geeves et al. [Geeves, M. A., Webb, M. R., Midelfort, C. F., & Trentham, D. R. (1980) Biochemistry 19, 4748-4754] with subfragment 1. PMID:3442661

  2. Carbon monoxide-induced N-N bond cleavage of nitrous oxide that is competitive with oxygen atom transfer to carbon monoxide as mediated by a Mo(II)/Mo(IV) catalytic cycle.

    PubMed

    Reeds, Jonathan P; Yonke, Brendan L; Zavalij, Peter Y; Sita, Lawrence R

    2011-11-23

    In the presence of CO, facile N-N bond cleavage of N(2)O occurs at the formal Mo(II) center within coordinatively unsaturated mononuclear species derived from Cp*Mo[N((i)Pr)C(Me)N((i)Pr)](CO)(2) (Cp* = ?(5)-C(5)Me(5)) (1) and {Cp*Mo[N((i)Pr)C(Me)N((i)Pr)]}(2)(?-?(1):?(1)-N(2)) (9) under photolytic and dark conditions, respectively, to produce the nitrosyl, isocyanate complex Cp*Mo[N((i)Pr)C(Me)N((i)Pr)](?-N-NO)(?-N-NCO) (7). Competitive N-O bond cleavage of N(2)O proceeds under the same conditions to yield the Mo(IV) terminal metal oxo complex Cp*Mo[N((i)Pr)C(Me)N((i)Pr)](O) (3), which can be recycled to produce more 7 through oxygen-atom-transfer oxidation of CO to produce CO(2). PMID:22026748

  3. Transition-Metal-Free Deacylative Cleavage of Unstrained C(sp(3))-C(sp(2)) Bonds: Cyanide-Free Access to Aryl and Aliphatic Nitriles from Ketones and Aldehydes.

    PubMed

    Ge, Jing-Jie; Yao, Chuan-Zhi; Wang, Mei-Mei; Zheng, Hong-Xing; Kang, Yan-Biao; Li, Yadong

    2016-01-15

    A transition-metal-free deacylative C(sp(3))-C(sp(2)) bond cleavage for the synthetically practical oxidative amination of ketones and aldehydes to nitriles is first described, using cheap and commercially abundant NaNO2 as the oxidant and the nitrogen source. Various nitriles bearing aryl, heteroaryl, alkyl, and alkenyl groups could be smoothly obtained from ketones and aldehydes in high yields, avoiding highly toxic cyanides or transition metals. PMID:26704699

  4. 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

  5. Reactions of heteronuclear dimetalated olefin complexes. Reactions of CpFe-(CO){sub 2}[{mu}-(Z)-(MeO{sub 2}C)C=C(CO{sub 2}Me)]Re -(CO){sub 4} with CO and p-tolyl isothiocyanate

    SciTech Connect

    Adams, R.D.; Huang, M.

    1995-10-01

    Addition of CO to the dimetalated olefin complex CpFe(CO){sub 2} [{mu}-(Z)-(MeO{sub 2}C)C=C(CO{sub 2}Me)]-Re(CO){sub 4}, 1, at 25{degree}C/700 psi of CO resulted in the formation of the adduct CpFe(CO){sub 2}[{mu}-(E)-(MeO{sub 2}C)C=C(CO{sub 2}Me)]-Re(CO){sub 5} , 2, in 52% yield by cleavage of the Re-O bond to the coordinated carboxylate group. In contrast the reaction of 1 with CO at 70{degree}C/ 900 psi of CO provided the new compound CpFe(CO){sub 2} [{mu}-(Z)-C=O(MeO{sub 2}C)C=C(CO{sub 2}Me)]-Re(CO){sub 4}, 3, in 77% yield. Compounds 2 and 3 were characterized by single-crystal X-ray diffraction analyses. Compound 2 is a Z-dimetalated olefin formed by addition of CO to the Re(CO){sub 4} group in 1, C-C = 1. 35(1) Hi. Compound 3 is an isomer of 2 in which a CO was added to 1 and inserted into the iron-carbon bond to the alkyne. Compound 1 reacts with EtNH{sub 2} or H{sub 2}O to yield the new compound CpFe(CO){sub 2}[(MeO{sub 2}C)C=C(CO{sub 2}Me)(H)], 6, by the cleavage of the rhenium grouping from the molecule. The reaction with H{sub 2}O is catalyzed by silica gel. 22 refs., 3 figs., 6 tabs.

  6. 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.

  7. 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.

  8. 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.

  9. Carbon-nitrogen bond cleavage in an {eta}{sup 2}(N,C)-pyridine complex induced by intramolecular metal-to-ligand alkyl migration: Models for hydrodenitrogenation catalysis

    SciTech Connect

    Gray, S.D.; Weller, K.J.; Bruck, M.A.; Briggs, P.M.; Wigley, D.E.

    1995-11-01

    The reaction of the {eta}{sup 2}(N,C)-pyridine complex with LiBEt{sub 3}H affords the C-N bond scission product (2). The reactions of (1) with carbon nucleophiles RLi or RMgX provide the alkyl derivatives [R = Me (3), Et (4), {sup n}Pr (5), {sup n}Bu (6), and CH{sub 2}SiMe{sub 3} (7)]. Kinetic and mechanistic studies of the 3 {yields} 8 rearrangement reveal that methyl migration is strictly intramolecular. The reactions of this model system delineate one process by which heterocyclic C-N bonds are cleaved and offer new insight as to how nitrogen heterocycles may be further degraded after C-N bond cleavage in hydrodenitrogenation catalysis. 74 refs., 7 figs., 5 tabs.

  10. 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

  11. 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

  12. Cleavage of a P-N Bond in a Urea-Containing (Ph2 P(R)PPh2 )-Bridged Dinuclear Gold(I) Thiolate Complex by Fluoride and a Mechanistic Insight.

    PubMed

    He, Xiaoming; Lam, Wai Han; Cheng, Eddie Chung-Chin; Yam, Vivian Wing-Wah

    2015-06-01

    A urea-containing, (Ph2 P(R)PPh2 )-bridged, dinuclear, gold(I) thiolate complex, [Au2 {Ph2 PN(C6 H4 OMe-4)PPh2 }(SC6 H4 NHCONHC6 H5 )2 ] (1) was designed and synthesized and its photophysical and anion recognition properties studied. The results show that 1 has a high selectivity toward F(-) . Upon addition of F(-) , the yellow solution was decolorized, and drastic changes of emission and (1) H and (31) P{(1) H}?NMR signals were observed. Interestingly, these changes are attributed to fluoride-assisted P-N bond hydrolysis, instead of the expected hydrogen-bonding interactions with the urea receptor. Similar changes were observed for two other basic anions, AcO(-) and H2 PO4 (-) , but to a much lesser extent; and these anions were found to bind to the urea receptor at the same time. On the other hand, Cl(-) was found to only bind to the urea moiety through hydrogen-bonding interactions. Further studies with the control complex [Au2 {Ph2 PN(C6 H4 OMe-4)PPh2 }Cl2 ] (2) indicate that F(-) assists the hydrolysis process via cleavage of the P-N bond. DFT calculations were performed to study the reaction mechanism for the fluoride-assisted P-N bond hydrolysis of 2; these provide a better insight into the role of fluoride in the hydrolysis. PMID:25924954

  13. Theoretical study of the mechanism for the sequential N-O and N-N bond cleavage within N2O adducts of N-heterocyclic carbenes by a vanadium(iii) complex.

    PubMed

    Robinson, Robert; Shaw, Miranda F; Stranger, Robert; Yates, Brian F

    2016-01-01

    A theoretical study into the reactions of the N2O adducts of N-heterocyclic carbenes (NHCs) and a V((III)) complex was carried out using DFT calculations. Unlike most transition metal reactions with N2O that simply release N2 following O-atom transfer onto the metal centre, this NHC-based system traps the entire N2O molecule and then cleaves both the N-O and N-N bond in two consecutive reactions. The NHC presence increases the reactivity of N2O by altering the distribution of electron density away from the O-atom towards the two N-atoms. This electronic redistribution enables V-N binding interactions to form a reactive N,O-donor intermediate species. Our results show that bond breaking with concomitant ligand migration occurs via a concerted process for both the N-O and N-N cleavage reactions. PMID:26649949

  14. 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

  15. 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.

  16. Investigations of iridium-mediated reversible C-H bond cleavage: characterization of a 16-electron iridium(III) methyl hydride complex.

    PubMed

    Bernskoetter, Wesley H; Hanson, Susan Kloek; Buzak, Sara K; Davis, Zoe; White, Peter S; Swartz, Rodney; Goldberg, Karen I; Brookhart, Maurice

    2009-06-24

    New iridium complexes of a tridentate pincer ligand, 2,6-bis(di-tert-butylphosphinito)pyridine (PONOP), have been prepared and used in the study of hydrocarbon C-H bond activation. Intermolecular oxidative addition of a benzene C-H bond was directly observed with [(PONOP)Ir(I)(cyclooctene)][PF(6)] at ambient temperature, resulting in a cationic five-coordinate iridium(III) phenyl hydride product. Protonation of the (PONOP)Ir(I) methyl complex yielded the corresponding iridium(III) methyl hydride cation, a rare five-coordinate, 16-valence electron transition metal alkyl hydride species which was characterized by X-ray diffraction. Kinetic studies of C-H bond coupling and reductive elimination reactions from the five-coordinate complexes have been carried out. Exchange NMR spectroscopy measurements established a barrier of 17.8(4) kcal/mol (22 degrees C) for H-C(aryl) bond coupling in the iridium(III) phenyl hydride cation and of 9.3(4) kcal/mol (-105 degrees C) for the analogous H-C(alkyl) coupling in the iridium(III) methyl hydride cation. The origin of the higher barrier of H-C(aryl) relative to H-C(alkyl) bond coupling is proposed to be influenced by a hindered rotation about the Ir-C(aryl) bond, a result of the sterically demanding PONOP ligand. PMID:19489584

  17. 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

  18. Reactivity studies of a pseudo three-coordinate vanadium(II) complex: Synthesis of terminal oxo and sulfido complexes of vanadium(IV) and S?S and Se?Se reductive bond cleavage reactions

    SciTech Connect

    Tran, Ba L.; Chen, Chun-Hsing; Mindiola, Daniel J.

    2012-02-07

    Terminal oxo and sulfido complexes in the form of (nacnac)V=E(Ntol{sub 2}) (nacnac = [ArNC(CH{sub 3})]{sub 2}CH{sup -}, Ar = 2,6-(CHMe{sub 2}){sub 2}C{sub 6}H{sub 3}, Ntol{sub 2} = {sup -}N(C{sub 6}H{sub 4}-4-Me), E = O (1), S (2)) were isolated from treatment of the masked three-coordinate vanadium(II) complex, (nacnac)V(Ntol{sub 2}), with C{sub 5}H{sub 5}NO and S{sub 8}, respectively. Both vanadium(IV) species, 1 and 2, have been characterized by room temperature X-band EPR spectroscopic studies, and in the case of complex 1, a single crystal molecular structure confirmed the presence of a terminal oxo moiety. Moreover, reaction of (nacnac)V(Ntol{sub 2}) with diphenyl-disulfide and diphenyl-diselenide results in the reductive cleavage of these compounds to produce the vanadium(III) complexes (nacnac)V(XPh)(Ntol{sub 2}) (X = S, (3), Se (4)). A molecular structure of the phenylsulfide complex, 3, confirmed formation of the d{sup 2} complex resulting from reductive cleavage of the S-S bond.

  19. 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 ?CO vibration is downshifted whereas the ?CN mode is upshifted in the presence of the divalent ion. As the trivalent ion is added to the solvent, upshifts of both ?CO and ?CN 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

  20. 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

  1. Development of an Intein-Inspired Amide Cleavage Chemical Device.

    PubMed

    Komiya, Chiaki; Aihara, Keisuke; Morishita, Ko; Ding, Hao; Inokuma, Tsubasa; Shigenaga, Akira; Otaka, Akira

    2016-01-15

    A photoresponsive amide cleavage device was developed based on the asparagine imidation-mediated cleavage of peptide bonds during intein-mediated protein splicing. The chemical environment of the protein splicing process was mimicked by the incorporation of geminal dimethyl groups and a secondary amine unit in asparagine scaffold. Furthermore, the resulting photoresponsive device could induce the phototriggered cleavage of an amide bond by the protection of the secondary amine unit with an o-nitrobenzyloxycarbonyl group. PMID:26646813

  2. Applications of Bis(1-R-imidazol-2-yl)disulfides and Diselenides as Ligands for Main Group and Transition Metals: ?2-[N,N] Coordination, S-S Bond Cleavage and S-S/E-E (E = S, Se) Bond Metathesis Reactions

    PubMed Central

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

    2008-01-01

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

  3. SiliconCarbon bond cleavage reactions of Ansa tungstenocene compounds: The [Me2Si] bridge as a site for metallocene functionalization

    PubMed Central

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

    2008-01-01

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

  4. 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

  5. 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

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

    PubMed Central

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

    2014-01-01

    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 hemehistidine 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 ironhistidine 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

  7. Cleavage of ether, ester, and tosylate C(sp3)-O bonds by an iridium complex, initiated by oxidative addition of C-H bonds. Experimental and computational studies.

    PubMed

    Kundu, Sabuj; Choi, Jongwook; Wang, David Y; Choliy, Yuriy; Emge, Thomas J; Krogh-Jespersen, Karsten; Goldman, Alan S

    2013-04-01

    A pincer-ligated iridium complex, (PCP)Ir (PCP = ?(3)-C6H3-2,6-[CH2P(t-Bu)2]2), is found to undergo oxidative addition of C(sp(3))-O bonds of methyl esters (CH3-O2CR'), methyl tosylate (CH3-OTs), and certain electron-poor methyl aryl ethers (CH3-OAr). DFT calculations and mechanistic studies indicate that the reactions proceed via oxidative addition of C-H bonds followed by oxygenate migration, rather than by direct C-O addition. Thus, methyl aryl ethers react via addition of the methoxy C-H bond, followed by ?-aryloxide migration to give cis-(PCP)Ir(H)(CH2)(OAr), followed by iridium-to-methylidene hydride migration to give (PCP)Ir(CH3)(OAr). Methyl acetate undergoes C-H bond addition at the carbomethoxy group to give (PCP)Ir(H)[?(2)-CH2OC(O)Me] which then affords (PCP-CH2)Ir(H)(?(2)-O2CMe) (6-Me) in which the methoxy C-O bond has been cleaved, and the methylene derived from the methoxy group has migrated into the PCP Cipso-Ir bond. Thermolysis of 6-Me ultimately gives (PCP)Ir(CH3)(?(2)-O2CR), the net product of methoxy group C-O oxidative addition. Reaction of (PCP)Ir with species of the type ROAr, RO2CMe or ROTs, where R possesses ?-C-H bonds (e.g., R = ethyl or isopropyl), results in formation of (PCP)Ir(H)(OAr), (PCP)Ir(H)(O2CMe), or (PCP)Ir(H)(OTs), respectively, along with the corresponding olefin or (PCP)Ir(olefin) complex. Like the C-O bond oxidative additions, these reactions also proceed via initial activation of a C-H bond; in this case, C-H addition at the ?-position is followed by ?-migration of the aryloxide, carboxylate, or tosylate group. Calculations indicate that the ?-migration of the carboxylate group proceeds via an unusual six-membered cyclic transition state in which the alkoxy C-O bond is cleaved with no direct participation by the iridium center. PMID:23469859

  8. Dehydrogenative Carbon-Carbon Bond Formation Using Alkynyloxy Moieties as Hydrogen-Accepting Directing Groups.

    PubMed

    Minami, Yasunori; Kodama, Tatsuro; Hiyama, Tamejiro

    2015-09-28

    In the presence of a catalyst system consisting of Pd(OAc)2 , PCy3 , and Zn(OAc)2 , the reaction of alkynyl aryl ethers with bicycloalkenes, ?,-unsaturated esters, or heteroarenes results in the site-selective cleavage of two C-H bonds followed by the formation of C-C bonds. In all cases, the alkynyloxy group acts as a directing group for the activation of an ortho C-H bond and as a hydrogen acceptor, thus rendering the use of additives such as an oxidant or base unnecessary. PMID:26278113

  9. Transition metal catalyzed manipulation of non-polar carbonhydrogen bonds for synthetic purpose

    PubMed Central

    MURAI, Shinji

    2011-01-01

    The direct addition of ortho CH bonds in various aromatic compounds such as ketones, esters, imines, imidates, nitriles, and aldehydes to olefins and acetylenes can be achieved with the aid of transition metal catalysts. The ruthenium catalyzed reaction is usually highly efficient and useful as a general synthetic method. The coordination to the metal center by a heteroatom in a directing group such as carbonyl and imino groups in aromatic compounds is the key step in this process. Mechanistically, the reductive elimination to form a CC bond is the rate-determining step, while the CH bond cleavage step is not. PMID:21558759

  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. 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

  12. 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.

  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

    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

  14. 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.

  15. Direct-dynamics VTST study of hydrogen or deuterium abstraction and C-C bond formation or dissociation in the reactions of CH3 + CH4, CH3 + CD4, CH3D + CD3, CH3CH3 + H, and CH3CD3 + D

    NASA Astrophysics Data System (ADS)

    Ramazani, Shapour

    2013-05-01

    Direct-dynamics variational transition-state theory calculations are studied at the MPWB1K/6-311++G(d,p) level for the four parts of reactions. The first part is hydrogen or deuterium abstraction in the reactions of CH3 + CH4, CH3 + CD4, and CH3D + CH3. The second part involves C-C bond formation in these reactions. The third one is the reactions of CH3CH3 + H and CH3CD3 + D to form of H2, HD, and D2. The last one is the dissociation of C-C bonds in the last group of reactions. The ground-state vibrational adiabatic potential is plotted for all channels. We have carried out direct-dynamics calculations of the rate constants, including multidimensional tunneling in the temperature range T = 200-2200 K. The results of CVT/?OMT rate constants were in good agreement with the experimental data which were available for some reactions. Small-curvature tunneling and Large-curvature tunneling with the LCG4 version were used to include the quantum effects in calculation of the rate constants. To try to find the region of formation and dissociation of bounds we have also reported the variations of harmonic vibrational frequencies along the reaction path. The thermally averaged transmission probability (P(E)exp (-?E/RT)) and representative tunneling energy at 298 K are reported for the reactions in which tunneling is important. We have calculated kinetic isotope effect which shows tunneling and vibrational contributions are noticeable to determine the rate constant. Nonlinear least-squares fitting is used to calculate rate constant expressions in the temperature range 200-2200 K. These expressions revealed that pre-exponential factor includes two parts; the first part is a constant number which is important at low temperatures while the second part is temperature dependent which is significant at high temperatures.

  16. Direct-dynamics VTST study of hydrogen or deuterium abstraction and C-C bond formation or dissociation in the reactions of CH3 + CH4, CH3 + CD4, CH3D + CD3, CH3CH3 + H, and CH3CD3 + D.

    PubMed

    Ramazani, Shapour

    2013-05-21

    Direct-dynamics variational transition-state theory calculations are studied at the MPWB1K?6-311++G(d,p) level for the four parts of reactions. The first part is hydrogen or deuterium abstraction in the reactions of CH3 + CH4, CH3 + CD4, and CH3D + CH3. The second part involves C-C bond formation in these reactions. The third one is the reactions of CH3CH3 + H and CH3CD3 + D to form of H2, HD, and D2. The last one is the dissociation of C-C bonds in the last group of reactions. The ground-state vibrational adiabatic potential is plotted for all channels. We have carried out direct-dynamics calculations of the rate constants, including multidimensional tunneling in the temperature range T = 200-2200 K. The results of CVT??OMT rate constants were in good agreement with the experimental data which were available for some reactions. Small-curvature tunneling and Large-curvature tunneling with the LCG4 version were used to include the quantum effects in calculation of the rate constants. To try to find the region of formation and dissociation of bounds we have also reported the variations of harmonic vibrational frequencies along the reaction path. The thermally averaged transmission probability (P(E)exp (-?E?RT)) and representative tunneling energy at 298 K are reported for the reactions in which tunneling is important. We have calculated kinetic isotope effect which shows tunneling and vibrational contributions are noticeable to determine the rate constant. Nonlinear least-squares fitting is used to calculate rate constant expressions in the temperature range 200-2200 K. These expressions revealed that pre-exponential factor includes two parts; the first part is a constant number which is important at low temperatures while the second part is temperature dependent which is significant at high temperatures. PMID:23697416

  17. Human Cytochrome P450 21A2, the Major Steroid 21-Hydroxylase: STRUCTURE OF THE ENZYMEPROGESTERONE SUBSTRATE COMPLEX AND RATE-LIMITING C-H BOND CLEAVAGE.

    PubMed

    Pallan, Pradeep S; Wang, Chunxue; Lei, Li; Yoshimoto, Francis K; Auchus, Richard J; Waterman, Michael R; Guengerich, F Peter; Egli, Martin

    2015-05-22

    Cytochrome P450 (P450) 21A2 is the major steroid 21-hydroxylase, and deficiency of this enzyme is involved in ?95% of cases of human congenital adrenal hyperplasia, a disorder of adrenal steroidogenesis. A structure of the bovine enzyme that we published previously (Zhao, B., Lei, L., Kagawa, N., Sundaramoorthy, M., Banerjee, S., Nagy, L. D., Guengerich, F. P., and Waterman, M. R. (2012) Three-dimensional structure of steroid 21-hydroxylase (cytochrome P450 21A2) with two substrates reveals locations of disease-associated variants. J. Biol. Chem. 287, 10613-10622), containing two molecules of the substrate 17?-hydroxyprogesterone, has been used as a template for understanding genetic deficiencies. We have now obtained a crystal structure of human P450 21A2 in complex with progesterone, a substrate in adrenal 21-hydroxylation. Substrate binding and release were fast for human P450 21A2 with both substrates, and pre-steady-state kinetics showed a partial burst but only with progesterone as substrate and not 17?-hydroxyprogesterone. High intermolecular non-competitive kinetic deuterium isotope effects on both kcat and kcat/Km, from 5 to 11, were observed with both substrates, indicative of rate-limiting C-H bond cleavage and suggesting that the juxtaposition of the C21 carbon in the active site is critical for efficient oxidation. The estimated rate of binding of the substrate progesterone (kon 2.4 10(7) M(-1) s(-1)) is only ?2-fold greater than the catalytic efficiency (kcat/Km = 1.3 10(7) M(-1) s(-1)) with this substrate, suggesting that the rate of substrate binding may also be partially rate-limiting. The structure of the human P450 21A2-substrate complex provides direct insight into mechanistic effects of genetic variants. PMID:25855791

  18. 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.

  19. Selective cleavage of pepsin by molybdenum metallopeptidase.

    PubMed

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

    2012-03-01

    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 ?23, ?19 and ?16 kDa when the mixture of the protein and ammonium heptamolybdate tetrahydrate ((NH(4))(6)Mo(7)O(24)4H(2)O) was incubated at 37C for 24h. No self cleavage of pepsin occurs at 37 C, 24h 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(4))(6)Mo(7)O(24)4H(2)O) only for 2h. 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. PMID:22330807

  20. Cleavage of nucleic acids

    DOEpatents

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Waunakee, WI); Lyamichev, Victor I. (Madison, WI); Brow; Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    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.

  1. Cleavage of nucleic acids

    DOEpatents

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

    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.

  2. Cleavage of nucleic acids

    DOEpatents

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

    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.

  3. The Oxygenase CAO-1 of Neurospora crassa Is a Resveratrol Cleavage Enzyme

    PubMed Central

    Daz-Snchez, Violeta; F. Estrada, Alejandro; Limn, M. Carmen; Al-Babili, Salim

    2013-01-01

    The genome of the ascomycete Neurospora crassa encodes CAO-1 and CAO-2, two members of the carotenoid cleavage oxygenase family that target double bonds in different substrates. Previous studies demonstrated the role of CAO-2 in cleaving the C40 carotene torulene, a key step in the synthesis of the C35 apocarotenoid pigment neurosporaxanthin. In this work, we investigated the activity of CAO-1, assuming that it may provide retinal, the chromophore of the NOP-1 rhodopsin, by cleaving ?-carotene. For this purpose, we tested CAO-1 activity with carotenoid substrates that were, however, not converted. In contrast and consistent with its sequence similarity to family members that act on stilbenes, CAO-1 cleaved the interphenyl C?-C? double bond of resveratrol and its derivative piceatannol. CAO-1 did not convert five other similar stilbenes, indicating a requirement for a minimal number of unmodified hydroxyl groups in the stilbene background. Confirming its biological function in converting stilbenes, adding resveratrol led to a pronounced increase in cao-1 mRNA levels, while light, a key regulator of carotenoid metabolism, did not alter them. Targeted ?cao-1 mutants were not impaired by the presence of resveratrol, a phytoalexin active against different fungi, which did not significantly affect the growth and development of wild-type Neurospora. However, under partial sorbose toxicity, the ?cao-1 colonies exhibited faster radial growth than control strains in the presence of resveratrol, suggesting a moderate toxic effect of resveratrol cleavage products. PMID:23893079

  4. Efficient CH bond activations via O2 cleavage by a dianionic cobalt(ii) complex Electronic supplementary information (ESI) available: Experimental procedures, spectroscopic and electrochemical figures. CCDC 980872980875. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc00108g Click here for additional data file. Click here for additional data file.

    PubMed Central

    Nguyen, Andy I.; Hadt, Ryan G.; Solomon, Edward I.

    2014-01-01

    A dianionic, square planar cobalt(ii) complex reacts with O2 in the presence of acetonitrile to give a cyanomethylcobalt(iii) complex formed by CH bond cleavage. Interestingly, PhIO and p-tolyl azide react similarly to give the same cyanomethylcobalt(iii) complex. Competition studies with various hydrocarbon substrates indicate that the rate of CH bond cleavage greatly depends on the pK a of the CH bond, rather than on the CH 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

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

    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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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 3000? discovery of the German submarine U-166 in 5000 feet of water in the Gulf of Mexico. Adacemic disciplines required to support these technical challenges will be characterized and job opportunities in this emerging field will be addressed.

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

    NASA Astrophysics Data System (ADS)

    Lu, Shao-Yu; Lin, Jyh-Shing

    2014-01-01

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

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

    PubMed

    Lu, Shao-Yu; Lin, Jyh-Shing

    2014-01-14

    Density functional theory (DFT)-based molecular dynamics (DFTMD) simulations in combination with a Fourier transform of dipole moment autocorrelation function are performed to investigate the adsorption dynamics and the reaction mechanisms of self-coupling reactions of both acetylide (H3C-C(?)?C(?) (ads)) and ethyl (H3C(?)-C(?)H2(ads)) with I(ads) coadsorbed on the Ag(111) surface at various temperatures. In addition, the calculated infrared spectra of H3C-C(?)?C(?)(ads) and I coadsorbed on the Ag(111) surface indicate that the active peaks of -C(?)?C(?)- stretching are gradually merged into one peak as a result of the dominant motion of the stand-up -C-C(?)?C(?)- axis as the temperature increases from 200 K to 400 K. However, the calculated infrared spectra of H3C(?)-C(?)H2(ads) and I coadsorbed on the Ag(111) surface indicate that all the active peaks are not altered as the temperature increases from 100 K to 150 K because only one orientation of H3C(?)-C(?)H2(ads) adsorbed on the Ag(111) surface has been observed. These calculated IR spectra are in a good agreement with experimental reflection absorption infrared spectroscopy results. Furthermore, the dynamics behaviors of H3C-C(?)?C(?)(ads) and I coadsorbed on the Ag(111) surface point out the less diffusive ability of H3C-C(?)?C(?)(ads) due to the increasing s-character of C? leading to the stronger Ag-C? bond in comparison with that of H3C(?)-C(?)H2(ads) and I coadsorbed on the same surface. Finally, these DFTMD simulation results allow us to predict the energetically more favourable reaction pathways for self-coupling of both H3C-C(?)?C(?)(ads) and H3C(?)-C(?)H2(ads) adsorbed on the Ag(111) surface to form 2,4-hexadiyne (H3C-C?C-C?C-CH3(g)) and butane (CH3-CH2-CH2-CH3(g)), respectively. The calculated reaction energy barriers for both H3C-C?C-C?C-CH3(g) (1.34 eV) and CH3-CH2-CH2-CH3(g) (0.60 eV) are further employed with the Redhead analysis to estimate the desorption temperatures approximately at 510 K and 230 K, respectively, which are in a good agreement with the experimental low-coverage temperature programmed reaction spectroscopy measurements. PMID:24437901

  17. Different C-C coupling reactions of permethyltitanocene and permethylzirconocene with disubstituted 1,3-butadiynes

    PubMed

    Pellny; Kirchbauer; Burlakov; Baumann; Spannenberg; Rosenthal

    2000-01-01

    Herein we describe different C-C coupling reactions of permethyltitanocene and -zirconocene with disubstituted 1,3-butadiynes. The outcomes of these reactions vary depending on the metals and the diyne substituents. The reduction of [Cp2*MCl2] (Cp* = C5Me5; M = Ti, Zr) with Mg in the presence of disubstituted butadiynes RC triple bond C-C triple bond CR' is suitable for the synthesis of different C-C coupling products of the diyne and the permethylmetallocenes, and provides a new method for the generation of functionalized pentamethyl-cyclopentadienyl derivatives. For M = Zr and R = R' = tBu, the reaction gives, by a twofold activation of one pentamethylcyclopentadienyl ligand, the complex [Cp*Zr[-C(=C=CHtBu)-CHtBu-CH2-eta5-C5Me3-CH2-

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  19. 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

  20. 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

  1. 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

  2. 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

  3. Addition, cycloaddition, and metathesis reactions of the cationic carbyne complexes [Cp(CO)[sub 2]Mn[triple bond]CCH[sub 2]R][sup +] and neutral vinylidene complexes Cp(CO)[sub 2]M=C=C(H)R (M = Mn, Re)

    SciTech Connect

    Terry, M.R.; Mercando, L.A.; Kelley, C.; Geoffroy, G.L. ); Nombel, P.; Lugan, N.; Mathieu, R. ); Ostrander, R.L.; Owens-Waltermire, B.E.; Rheingold, A.L. )

    1994-03-01

    The cationic alkylidyne complexes [Cp(CO)[sub 2]M=VCCH[sub 2]R][sup +] (M = Re, R = H; M = Mn, R = H, Me, Ph) undergo facile deprotonation to give the corresponding neutral vinylidene complexes Cp(CO)[sub 2]M=C=C(H)R. For [Cp(CO)[sub 2]Re=VCCH[sub 3

  4. 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.

  5. Hypervalent Activation as a Key Step for Dehydrogenative ortho C?C Coupling of Iodoarenes.

    PubMed

    Wu, Yichen; Arenas, Ismael; Broomfield, Lewis Marc; Martin, Eddy; Shafir, Alexandr

    2015-12-14

    Building on earlier results, a direct metal-free ?- arylation of substituted cyclic 1,3-diones using ArI(O2 CCF3 )2 reagents has been developed; unlike other arylative approaches, the arylated products retain the iodine substituent ortho to the newly formed C?C bond. The mechanism is explored by using DFT calculations, which show a vanishingly small activation barrier for the C?C bond-forming step. In fact, taking advantage of an efficient in situ hypervalent activation, the iodoarenes are shown to undergo a cross- dehydrogenative C?C coupling at the C?H ortho to the iodine. When Oxone is used as terminal oxidant, the process is found to benefit from a rapid initial formation of the hypervalent ArI(OR)2 species and the sulfate-accelerated final coupling with a ketone. This method complements the ipso selectivity obtained in the metal-catalyzed ?-arylation of carbonyl compounds. PMID:26559651

  6. Lead-catalysed specific cleavage of ribosomal RNAs.

    PubMed Central

    Winter, D; Polacek, N; Halama, I; Streicher, B; Barta, A

    1997-01-01

    Ribosomes have long been known to require divalent metal ions for their functional integrity. Pb2+-induced cleavage of the sugar-phosphate backbone has now been used to probe for metal binding sites in rRNA. Only three prominent Pb2+cleavages have been detected, with cleavage sites 5' of G240 in 16S rRNA and two sites 5' of A505 and C2347 in 23S rRNA. All cleavages occur in non-paired regions of the secondary structure models of the rRNAs and can be competed for by high concentrations of Mg2+, Mn2+, Ca2+ and Zn2+ ions, suggesting that lead is bound to general metal binding sites. Although Pb2+ cleavage is very efficient, ribosomes with fragmented RNAs are still functional in binding tRNA and in peptidyl transferase activity, indicating that the scissions do not significantly alter ribosomal structure. One of the lead cleavage sites (C2347 in 23S RNA) occurs in the vicinity of a region which is implicated in tRNA binding and peptidyl transferase activity. These results are discussed in the light of a recent model which proposes that peptide bond formation might be a metal-catalysed process. PMID:9108166

  7. 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

  8. Pd-catalyzed intramolecular C-N bond cleavage, 1,4-migration, sp3 C-H activation, and Heck reaction: four controllable diverse pathways depending on the judicious choice of the base and ligand.

    PubMed

    Wang, Min; Zhang, Xiang; Zhuang, Yu-Xuan; Xu, Yun-He; Loh, Teck-Peng

    2015-01-28

    Diverse and controllable pathways induced by palladium-catalyzed intramolecular Heck reaction of N-vinylacetamides for the synthesis of nitrogen-containing products in reasonable to high yields via tuning the phosphine ligands and bases are reported. Domino reactions including unique ?-N-Pd elimination, 1,4-Pd migration, or direct acyl C-H bond functionalization were found to be involved forming different products, respectively. Given the ability of using the same starting material to generate diverse products via completely different chemoselective processes, these current methodologies offer straightforward access to valuable nitrogen-containing products under mild reaction conditions as well as inspire the discovery of novel reactions. PMID:25545361

  9. 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

  10. Invasive cleavage of nucleic acids

    DOEpatents

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

    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.

  11. Invasive cleavage of nucleic acids

    SciTech Connect

    Prudent, J.R.; Hall, J.G.; Lyamichev, V.I.; Brow, M.A.D.; Dahlberg, J.E.

    1999-11-16

    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.

  12. Invasive cleavage of nucleic acids

    DOEpatents

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

    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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  15. 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

  16. 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 basedmoreon 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

  17. 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

  18. Observation of the decay ?(3686)?????+c.c.

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    Using a sample of 1.06108 ?(3686) events collected with the BESIII detector, we present the first observation of the decays of ?(3686)???+?-+c.c. and ?(3686)???-?++c.c. The branching fractions are measured to be B(?(3686)???+?-+c.c.)=(1.400.030.13)10-4 and B(?(3686)???-?++c.c.)=(1.540.040.13)10-4, where the first errors are statistical and the second ones systematic.

  19. 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

    Acea, Jos 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 NiNH and NiO bonds providing a basis for a chiral switch model. PMID:23209532

  20. 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

  1. 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

  2. Linear ketenimines. Variable structures of C,C-dicyanoketenimines and C,C-bis-sulfonylketenimines.

    PubMed

    Finnerty, Justin; Mitschke, Ullrich; Wentrup, Curt

    2002-02-22

    C,C-dicyanoketenimines 10a-c were generated by flash vacuum thermolysis of ketene N,S-acetals 9a-c or by thermal or photochemical decomposition of alpha-azido-beta-cyanocinnamonitrile 11. In the latter reaction, 3,3-dicyano-2-phenyl-1-azirine 12 is also formed. IR spectroscopy of the keteniminines isolated in Ar matrixes or as neat films, NMR spectroscopy of 10c, and theoretical calculations (B3LYP/6-31G) demonstrate that these ketenimines have variable geometry, being essentially linear along the CCN-R framework in polar media (neat films and solution), but in the gas phase or Ar matrix they are bent, as is usual for ketenimines. Experiments and calculations agree that a single CN substituent as in 13 is not enough to enforce linearity, and sulfonyl groups are less effective that cyano groups in causing linearity. C,C-bis(methylsulfonyl)ketenimines 4-5 and a C-cyano-C-(methylsulfonyl)ketenimine 15 are not linear. The compound p-O2NC6H4N=C=C(COOMe)2 previously reported in the literature is probably somewhat linearized along the CCNR moiety. A computational survey (B3LYP/6-31G) of the inversion barrier at nitrogen indicates that electronegative C-substituents dramatically lower the barrier; this is also true of N-acyl substituents. Increasing polarity causes lower barriers. Although N-alkylbis(methylsulfonyl)ketenimines are not calculated to be linear, the barriers are so low that crystal lattice forces can induce planarity in N-methylbis(methylsulfonyl)ketenimine 3. PMID:11846648

  3. 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

  4. Thermal and electrochemically assisted Pd-Cl bond cleavage in the d9-d9 Pd2dppm2Cl2 complex by Pd3 dppm3COn+ clusters (n = 2, 1, 0).

    TOXLINE Toxicology Bibliographic Information

    Cugnet C; Mugnier Y; Dal Molin S; Brevet D; Lucas D; Harvey PD

    2007-04-16

    A new aspect of reactivity of the cluster [Pd3(dppm)3(micro3-CO)]n+, ([Pd3]n+, n = 2, 1, 0) with the low-valent metal-metal-bonded Pd2(dppm)2Cl2 dimer (Pd2Cl2) was observed using electrochemical techniques. The direct reaction between [Pd3]2+ and Pd2Cl2 in THF at room temperature leads to the known [Pd3(dppm)3(micro3-CO)(Cl)]+ ([Pd3(Cl)]+) adduct and the monocationic species Pd2(dppm)2Cl+ (very likely as Pd2(dppm)2(Cl)(THF)+, [Pd2Cl]+) as unambiguously demonstrated by UV-vis and 31P NMR spectroscopy. In this case, [Pd3]2+ acts as a strong Lewis acid toward the labile Cl- ion, which weakly dissociates from Pd2Cl2 (i.e., dissociative mechanism). Host-guest interactions between [Pd3]2+ and Pd2Cl2 seem unlikely on the basis of computer modeling because of the strong screening of the Pd-Cl fragment by the Ph-dppm groups in Pd2Cl2. The electrogenerated clusters [Pd3]+ and [Pd3]0 also react with Pd2Cl2 to unexpectedly form the same oxidized adduct, [Pd3(Cl)]+, despite the known very low affinity of [Pd3]+ and [Pd3]0 toward Cl- ions. The reduced biproduct in this case is the highly reactive zerovalent species "Pd2(dppm)2" or "Pd(dppm)" as demonstrated by quenching with CDCl3 (forming the well-known complex Pd(dppm)Cl2) or in presence of dppm (forming the known Pd2(dppm)3 d10-d10 dimer). To bring these halide-electron exchange reactions to completion for [Pd3]+ and [Pd3]0, 0.5 and 1.0 equiv of Pd2Cl2 are necessary, respectively, accounting perfectly for the number of exchanged electrons. The presence of a partial dissociation of Pd2Cl2 into the Cl- ion and the monocation [Pd2Cl]+, which is easier to reduce than Pd2Cl2, is suggested to explain the overall electrochemical results. It is possible to regulate the nature of the species formed from Pd2Cl2 by changing the state of charge of the title cluster.

  5. Thermal and electrochemically assisted Pd-Cl bond cleavage in the d9-d9 Pd2dppm2Cl2 complex by Pd3 dppm3COn+ clusters (n = 2, 1, 0).

    PubMed

    Cugnet, Cyril; Mugnier, Yves; Dal Molin, Sophie; Brevet, David; Lucas, Dominique; Harvey, Pierre D

    2007-04-16

    A new aspect of reactivity of the cluster [Pd3(dppm)3(micro3-CO)]n+, ([Pd3]n+, n = 2, 1, 0) with the low-valent metal-metal-bonded Pd2(dppm)2Cl2 dimer (Pd2Cl2) was observed using electrochemical techniques. The direct reaction between [Pd3]2+ and Pd2Cl2 in THF at room temperature leads to the known [Pd3(dppm)3(micro3-CO)(Cl)]+ ([Pd3(Cl)]+) adduct and the monocationic species Pd2(dppm)2Cl+ (very likely as Pd2(dppm)2(Cl)(THF)+, [Pd2Cl]+) as unambiguously demonstrated by UV-vis and 31P NMR spectroscopy. In this case, [Pd3]2+ acts as a strong Lewis acid toward the labile Cl- ion, which weakly dissociates from Pd2Cl2 (i.e., dissociative mechanism). Host-guest interactions between [Pd3]2+ and Pd2Cl2 seem unlikely on the basis of computer modeling because of the strong screening of the Pd-Cl fragment by the Ph-dppm groups in Pd2Cl2. The electrogenerated clusters [Pd3]+ and [Pd3]0 also react with Pd2Cl2 to unexpectedly form the same oxidized adduct, [Pd3(Cl)]+, despite the known very low affinity of [Pd3]+ and [Pd3]0 toward Cl- ions. The reduced biproduct in this case is the highly reactive zerovalent species "Pd2(dppm)2" or "Pd(dppm)" as demonstrated by quenching with CDCl3 (forming the well-known complex Pd(dppm)Cl2) or in presence of dppm (forming the known Pd2(dppm)3 d10-d10 dimer). To bring these halide-electron exchange reactions to completion for [Pd3]+ and [Pd3]0, 0.5 and 1.0 equiv of Pd2Cl2 are necessary, respectively, accounting perfectly for the number of exchanged electrons. The presence of a partial dissociation of Pd2Cl2 into the Cl- ion and the monocation [Pd2Cl]+, which is easier to reduce than Pd2Cl2, is suggested to explain the overall electrochemical results. It is possible to regulate the nature of the species formed from Pd2Cl2 by changing the state of charge of the title cluster. PMID:17371010

  6. 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}.

  7. 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

  8. 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.

  9. 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

  10. 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

  11. Facile homolytic C?S bond breaking: the reaction of 2-propene-1-thiol on Mo(110)

    NASA Astrophysics Data System (ADS)

    Wiegand, B. C.; Friend, C. M.; Uvdal, P.; Napier, M. E.

    1996-06-01

    Investigations of 2-propene-1-thiol on Mo(110) show that the facility for thiol desulfurization correlates with the homolytic C?S bond strength of the thiol. A substantial amount of C?S bond scission occurs upon adsorption of 2-propene-1-thiol on Mo(110) at 120 K based on X-ray photoelectron data. 2-Propene-1-thiol has an extremely weak C?S bond because of the resonance stabilization of the allyl radical. Propene, the product of 2-propene-1-thiol hydrogenolysis, evolves into the gas phase in the range 160-250 K; the propene evolution being controlled by the rate of desorption. Vibrational (electron energy loss) spectra are consistent with formation of 2-propene-1-thiolate via S?H bond cleavage, as well as hydrocarbon fragments at low temperature. A large fraction of the thiolate desulfurizes at 120 K to afford propene. A second hydrocarbon species is formed in the range 160-200 K, characterized by a low-frequency C?H stretch mode at 2770 cm -1, which reacts further below 250 K. The C?C bond in the thiol and in the propene product leads to a greater degree of non-selective reaction than is anticipated from a comparison of saturated thiols. Only in the order of 50% of the thiol reacts to afford propene, despite the facility for C?S bond scission.

  12. Dinitrogen cleavage and hydrogenation by a trinuclear titanium polyhydride complex.

    PubMed

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

    2013-06-28

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

  13. 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.

  14. Investigating CN- cleavage by three-coordinate M[N(R)Ar]3 complexes.

    PubMed

    Christian, Gemma; Stranger, Robert; Yates, Brian F; Cummins, Christopher C

    2008-01-21

    Three-coordinate Mo[N((t)Bu)Ar]3 binds cyanide to form the intermediate [Ar((t)Bu)N]3Mo-CN-Mo[N((t)Bu)Ar]3 but, unlike its N2 analogue which spontaneously cleaves dinitrogen, the C-N bond remains intact. DFT calculations on the model [NH2]3Mo/CN- system show that while the overall reaction is significantly exothermic, the final cleavage step is endothermic by at least 90 kJ mol(-1), accounting for why C-N bond cleavage is not observed experimentally. The situation is improved for the [H2N]3W/CN- system where the intermediate and products are closer in energy but not enough for CN- cleavage to be facile at room temperature. Additional calculations were undertaken on the mixed-metal [H2N]3Re+/CN- /W[NH2]3 and [H2N]3Re+/CN-/Ta[NH2]3 systems in which the metals ions were chosen to maximise the stability of the products on the basis of an earlier bond energy study. Although the reaction energetics for the [H2N]3Re+/CN /W[NH2]3 system are more favourable than those for the [H2N]3W/CN- system, the final C-N cleavage step is still endothermic by 32 kJ mol(-1) when symmetry constraints are relaxed. The resistance of these systems to C-N cleavage was examined by a bond decomposition analysis of [H2N]M-L1[triple bond]L2-M[NH2]3 intermediates for L1[triple bond]L2 = N2, CO and CN which showed that backbonding from the metal into the L1[triple bond]L2 pi* orbitals is significantly less for CN than for N2 or CO due to the negative charge on CN- which results in a large energy gap between the metal d(pi), and the pi* orbitals of CN-. This, combined with the very strong M-CN- interaction which stabilises the CN intermediate, makes C-N bond cleavage in these systems unfavourable even though the C[triple bond]N triple bond is not as strong as the bond in N2 or CO. PMID:18411843

  15. Tuning of the CopperThioether Bond in Tetradentate N3S(thioether) Ligands; OO Bond Reductive Cleavage via a [CuII2(?-1,2-peroxo)]2+/[CuIII2(?-oxo)2]2+ Equilibrium

    PubMed Central

    2015-01-01

    Current interest in copper/dioxygen reactivity includes the influence of thioether sulfur ligation, as it concerns the formation, structures, and properties of derived copper-dioxygen complexes. Here, we report on the chemistry of {L-CuI}2-(O2) species L = DMMESE, DMMESP, and DMMESDP, which are N3S(thioether)-based ligands varied in the nature of a substituent on the S atom, along with a related N3O(ether) (EOE) ligand. CuI and CuII complexes have been synthesized and crystallographically characterized. Copper(I) complexes are dimeric in the solid state, [{L-CuI}2](B(C6F5)4)2, however are shown by diffusion-ordered NMR spectroscopy to be mononuclear in solution. Copper(II) complexes with a general formulation [L-CuII(X)]n+ {X = ClO4, n = 1, or X = H2O, n = 2} exhibit distorted square pyramidal coordination geometries and progressively weaker axial thioether ligation across the series. Oxygenation (?130 C) of {(DMMESE)CuI}+ results in the formation of a trans-?-1,2-peroxodicopper(II) species [{(DMMESE)CuII}2(?-1,2-O22)]2+ (1P). Weakening the CuS bond via a change to the thioether donor found in DMMESP leads to the initial formation of [{(DMMESP)CuII}2(?-1,2-O22)]2+ (2P) that subsequently isomerizes to a bis-?-oxodicopper(III) complex, [{(DMMESP)CuIII}2(?-O2)2]2+ (2O), with 2P and 2O in equilibrium (Keq = [2O]/[2P] = 2.6 at ?130 C). Formulations for these Cu/O2 adducts were confirmed by resonance Raman (rR) spectroscopy. This solution mixture is sensitive to the addition of methylsulfonate, which shifts the equilibrium toward the bis-?-oxo isomer. Further weakening of the CuS bond in DMMESDP or substitution with an ether donor in DMMEOE leads to only a bis-?-oxo species (3O and 4O, respectively). Reactivity studies indicate that the bis-?-oxodicopper(III) species (2O, 3O) and not the trans-peroxo isomers (1P and 2P) are responsible for the observed ligand sulfoxidation. Our findings concerning the existence of the 2P/2O equilibrium contrast with previously established ligand-CuI/O2 reactivity and possible implications are discussed. PMID:24854766

  16. Deoxygenative C-C Bond-Forming Processes via a Net Four-Electron Reductive Coupling.

    PubMed

    Todd, David P; Thompson, Benjamin B; Nett, Alex J; Montgomery, John

    2015-10-14

    The nickel-catalyzed coupling of enones or enals with alkynes in the presence of silane and titanium alkoxide reductants provides direct access to skipped diene products. The process involves a net four-electron reductive coupling and proceeds with deoxygenation of the starting enone or enal. A new class of well-defined nickel(0) precatalysts bearing an unhindered N-heterocyclic carbene ligand, which was developed in optimization of the process, is essential for the efficiency of the transformation. The strategy allows the high reactivity of ?,?-unsaturated carbonyl substrates to be utilized in couplings with simultaneous extrusion of the oxygen atom, thus enabling a traceless strategy for alkene installation. PMID:26436636

  17. Photochemically-induced C-C bond formation between tertiary amines and nitrones.

    PubMed

    Itoh, Kennosuke; Kato, Ryo; Kinugawa, Daito; Kamiya, Hideaki; Kudo, Ryuki; Hasegawa, Masayuki; Fujii, Hideaki; Suga, Hiroyuki

    2015-09-01

    Photoexcited nitrones serve as excellent electron acceptors as well as radical acceptors in the presence of tertiary amines to give ?-amino hydroxylamines via photochemically-induced direct sp(3) C-H functionalization of the tertiary amines. The combined use of an organophotosensitizer and photoirradiation was highly effective in accelerating addition reactions. Several nitrones and tertiary amines were successfully utilized to give ?-amino hydroxylamines in good yield. Highly regioselective generation of primary ?-aminoalkyl radicals based on Lewis's stereoelectronic rule and diastereoselective addition reactions of primary ?-aminoalkyl radicals with nitrones were successfully achieved. Furthermore, a highly diastereoselective reaction of an ?-aminoalkyl radical with a chiral (E)-geometry-fixed ?-alkoxycarbonylnitrone was performed. PMID:26205235

  18. 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.

  19. 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 NC? 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

  20. 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.

  1. Novel carboncarbon bond formations for biocatalysis

    PubMed Central

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

    2011-01-01

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

  2. 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.

  3. 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)

  4. 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.

  5. Microstructure and cleavage in lath martensitic steels

    NASA Astrophysics Data System (ADS)

    Morris, John W., Jr.; Kinney, Chris; Pytlewski, Ken; Adachi, Y.

    2013-02-01

    In this paper we discuss the microstructure of lath martensitic steels and the mechanisms by which it controls cleavage fracture. The specific experimental example is a 9Ni (9 wt% Ni) steel annealed to have a large prior austenite grain size, then examined and tested in the as-quenched condition to produce a relatively coarse lath martensite. The microstructure is shown to approximate the recently identified classic lath martensite structure: prior austenite grains are divided into packets, packets are subdivided into blocks, and blocks contain interleaved laths whose variants are the two Kurjumov-Sachs relations that share the same Bain axis of the transformation. When the steel is fractured in brittle cleavage, the laths in the block share {100} cleavage planes and cleave as a unit. However, cleavage cracks deflect or blunt at the boundaries between blocks with different Bain axes. It follows that, as predicted, the block size governs the effective grain size for cleavage.

  6. 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

  7. The extended cleavage specificity of human thrombin.

    PubMed

    Gallwitz, Maike; Enoksson, Mattias; Thorpe, Michael; Hellman, Lars

    2012-01-01

    Thrombin is one of the most extensively studied of all proteases. Its central role in the coagulation cascade as well as several other areas has been thoroughly documented. Despite this, its consensus cleavage site has never been determined in detail. Here we have determined its extended substrate recognition profile using phage-display technology. The consensus recognition sequence was identified as, P2-Pro, P1-Arg, P1'-Ser/Ala/Gly/Thr, P2'-not acidic and P3'-Arg. Our analysis also identifies an important role for a P3'-arginine in thrombin substrates lacking a P2-proline. In order to study kinetics of this cooperative or additive effect we developed a system for insertion of various pre-selected cleavable sequences in a linker region between two thioredoxin molecules. Using this system we show that mutations of P2-Pro and P3'-Arg lead to an approximate 20-fold and 14-fold reduction, respectively in the rate of cleavage. Mutating both Pro and Arg results in a drop in cleavage of 200-400 times, which highlights the importance of these two positions for maximal substrate cleavage. Interestingly, no natural substrates display the obtained consensus sequence but represent sequences that show only 1-30% of the optimal cleavage rate for thrombin. This clearly indicates that maximal cleavage, excluding the help of exosite interactions, is not always desired, which may instead cause problems with dysregulated coagulation. It is likely exosite cooperativity has a central role in determining the specificity and rate of cleavage of many of these in vivo substrates. Major effects on cleavage efficiency were also observed for residues as far away as 4 amino acids from the cleavage site. Insertion of an aspartic acid in position P4 resulted in a drop in cleavage by a factor of almost 20 times. PMID:22384068

  8. Copper-catalyzed, hypervalent iodine mediated C[double bond, length as m-dash]C bond activation of enaminones for the synthesis of ?-keto amides.

    PubMed

    Wan, Jie-Ping; Lin, Yunfang; Cao, Xiaoji; Liu, Yunyun; Wei, Li

    2016-01-01

    An unprecedented C[double bond, length as m-dash]C bond cleavage of enaminones has been realized by means of copper catalysis in the presence of hypervalent iodine (PhI(OAc)2). The cascade transformation based on this bond cleavage leads to the synthesis of various ?-keto amides. Isotope labeling experiments suggest that water has acted as a source of oxygen atoms during the generation of the new carbonyl group. PMID:26612528

  9. 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

  10. 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

  11. [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

  12. 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

  13. On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

    PubMed Central

    Riml, Christian; Glasner, Heidelinde; Rodgers, M. T.; Micura, Ronald; Breuker, Kathrin

    2015-01-01

    Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in top-down strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)n+ and (M?nH)n? ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage. PMID:25904631

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

    PubMed

    Rawlings, Neil D

    2009-01-01

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

  15. Experiments on schistosity and slaty cleavage

    USGS Publications Warehouse

    Becker, George Ferdinand

    1904-01-01

    Schistosity as a structure is important, and it is a part of the business of geologists to explain its origin. Slaty cleavage has further and greater importance as a possible tectonic feature. Scarcely a great mountain range exists, or has existed, along the course of which belts of slaty rock are not found, the dip of the cleavage usually approaching verticality. Are these slate belts equivalent to minutely distributed step faults of great total throw, or do they indicate compression perpendicular to the cleavage without attendant relative dislocation? Evidently the answer to this question is of first importance in the interpretation of orogenic phenomena.

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  17. 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 CH, COH, C?O, and C?C groups account for 1214% of all C, which matches the surface fraction expected for bulk-terminated 5 nm diameter diamond particles.

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. Gas-phase structures of perfluorotetrahydrothiophene, c-C 4F 8S, tetrahydrothiophene-1-oxide, c-C 4F 8SO, and tetrahydrothiophene-1,1-dioxide, c-C 4F 8SO 2

    NASA Astrophysics Data System (ADS)

    Mack, Hans-Georg; Oberhammer, Heinz; Shreeve, Jean'ne M.; Xia, X.-B.

    1989-05-01

    The geometric structures of the three title compounds have been determined by gas-phase electron diffraction. In all cases the five-membered rings are strongly puckered and possess half chair conformations with the following geometric parameters ( ra values with 3? error limits). c-C 4F 8S: (C?C) mean=1.548(4), S?C=1.822(4) , CSC=94.5(3), SCC=107.4(3), CCC=106.4(4) and puckering amplitude q=0.411(8) . c-C 4F 8SO: (C?C) mean=1.553(5), S?C=1.903(4) , CSC=89.4(4), SCC=110.2(4), CCC=106.5(6), q=0.403(8) . c-C 4F 8SO 2: (C?C) mean=1.556(6), S?C=1.882(7) , CSC=93.2(10), SCC=107.7(10), CCC=107.9(12), q=0.382(10) . Comparison with the analogous protonated rings reveals that upon fluorination the degree of puckering decreases slightly in c-C 4F 8S and c-C 4F 8SO, whereas it increases strongly in c-C 4F 8SO 2.

  7. MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.

    PubMed

    Lee, Jae Young; Chang, Judy; Joseph, Nimesh; Ghirlando, Rodolfo; Rao, Desirazu N; Yang, Wei

    2005-10-01

    MutH initiates mismatch repair by nicking the transiently unmethylated daughter strand 5' to a GATC sequence. Here, we report crystal structures of MutH complexed with hemimethylated and unmethylated GATC substrates. Both structures contain two Ca2+ ions jointly coordinated by a conserved aspartate and the scissile phosphate, as observed in the restriction endonucleases BamHI and BglI. In the hemimethylated complexes, the active site is more compact and DNA cleavage is more efficient. The Lys residue in the conserved DEK motif coordinates the nucleophilic water in conjunction with the phosphate 3' to the scissile bond; the same Lys is also hydrogen bonded with a carbonyl oxygen in the DNA binding module. We propose that this Lys, which is conserved in many restriction endonucleases and is replaced by Glu or Gln in BamHI and BglII, is a sensor for DNA binding and the linchpin that couples base recognition and DNA cleavage. PMID:16209953

  8. 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)

  9. 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

  10. [([superscript t]Bu[subscript 2]PCH[subscript 2]SiMe[subscript 2])[subscript 2]N]Rh[superscript I]? Rapidly Reversible H-C(sp[superscript 3]) and H?C(sp[superscript 2]) Bond Cleavage by Rhodium(I)

    SciTech Connect

    Verat, Alexander Y.; Pink, Maren; Fan, Hongjun; Tomaszewski, John; Caulton, Kenneth G.

    2008-10-03

    The product of the reaction of (tBu{sub 2}PCH{sub 2}SiMe{sub 2}){sub 2}N{sup -} (MgCl{sup +} salt) with [RhCl(cyclooctene){sub 2}]{sub 2} is a Rh{sup III} complex where one {sup t}Bu methyl C-H bond has oxidatively added to Rh: (PNP*)RhH. This is in rapid exchange among all 9 x 4 C-H bonds of the four {sup t}Bu groups. (PNP*)RhH undergoes oxidative addition equilibrium with the C-H bonds of benzene at {approx}10{sup 3} s{sup -1} at 25 C and oxidatively adds the ring C-H of other arenes. (PNP*)RhH forms {eta}{sup 2}-olefin complexes with several olefins and dehydrogenates allylic C-H bonds to form (PNP)Rh(H){sub 2}.

  11. Theoretical studies of pentene cracking on zeolites: C-C beta-scission processes

    SciTech Connect

    Hay, P.J.; Redondo, A.; Guo, Y.

    1997-04-01

    The nature of the molecular species involved in the cracking of hydrocarbons into smaller fragments over zeolite catalysts has been studied extensively, as the advent of zeolites such as faujasite to carry out these transformations more selectively has revolutionized the petroleum refining technology. While the nature of the acid-catalyzed process involving proposed carbocationic species has been proposed for nearly fifty years, there have been extensive studies involving heterogeneous processes and analogs with solution superacid chemistry to elucidate these mechanisms more clearly and to attempt to detect the intermediates involved in these reactions. Also in recent years there have been an increasing number of theoretical studies on the nature of the acid sites in zeolites, the interactions of these acid sites with adsorbates including hydrocarbons, and on simple reactions of hydrocarbon species using model systems to represent the zeolite. In this study the authors report the results of ab initio and density functional studies on one aspect--the beta-scission C-C bond-breaking step--that arises in the cracking process of alkanes and alkenes. The authors focus on the species arising from pentene adsorption on an acid site and the subsequent cracking of this C{sub 5} species as an illustration of the carbon-carbon bond-breaking step. In these studies they employ a simple three-T-site to represent the immediate vicinity of the acid site in faujasite comprised of the Si-O-Al-OH-O-Si skeleton with the unsatisfied bonds terminated by hydrogens. They study the reaction of the 2-pentyl cation undergoing beta-scission in the gas phase to form propene and the ethyl cation and the corresponding reaction on the zeolite cluster. The structures of the reactants, products and transition states are determined using ab initio electronic structure techniques.

  12. 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

  13. 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.

  14. The potato carotenoid cleavage dioxygenase 4 catalyzes a single cleavage of ?-ionone ring-containing carotenes and non-epoxidated xanthophylls.

    PubMed

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

    2015-04-15

    Down-regulation of the potato carotenoid cleavage dioxygenase 4 (StCCD4) transcript level led to tubers with altered morphology and sprouting activity, which also accumulated higher levels of violaxanthin and lutein leading to elevated carotenoid amounts. This phenotype indicates a role of this enzyme in tuber development, which may be exerted by a cleavage product. In this work, we investigated the enzymatic activity of StCCD4, by expressing the corresponding cDNA in carotenoid accumulating Escherichia coli strains and by performing in vitro assays with heterologously expressed enzyme. StCCD4 catalyzed the cleavage of all-trans-?-carotene at the C9'-C10' double bond, leading to ?-ionone and all-trans-?-apo-10'-carotenal, both in vivo and in vitro. The enzyme also cleaved ?,?-cryptoxanthin, zeaxanthin and lutein either at the C9'-C10' or the C9-C10 double bond in vitro. In contrast, we did not observe any conversion of violaxanthin and only traces of activity with 9-cis-?-carotene, which led to 9-cis-?-apo-10'-carotenal. Our data indicate that all-trans-?-carotene is the likely substrate of StCCD4 in planta, and that this carotene may be precursor of an unknown compound involved in tuber development. PMID:25703194

  15. Kinetic analysis of delta ribozyme cleavage.

    PubMed

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

    1998-12-01

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

  16. 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...

  17. 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.

  18. 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

  19. Transition-Metal-Mediated Cleavage of Fluoro-Silanes under Mild Conditions.

    PubMed

    Kameo, Hajime; Kawamoto, Tatsuya; Sakaki, Shigeyoshi; Bourissou, Didier; Nakazawa, Hiroshi

    2016-02-01

    Si-F bond cleavage of fluoro-silanes was achieved by transition-metal complexes under mild and neutral conditions. The Iridium-hydride complex [Ir(H)(CO)(PPh3 )3 ] was found to readily break the Si-F bond of the diphosphine- difluorosilane {(o-Ph2 P)C6 H4 }2 Si(F)2 to afford a silyl complex [{[o-(iPh2 P)C6 H4 ]2 (F)Si}Ir(CO)(PPh3 )] and HF. Density functional theory calculations disclose a reaction mechanism in which a hypervalent silicon species with a dative Ir?Si interaction plays a crucial role. The Ir?Si interaction changes the character of the H on the Ir from hydridic to protic, and makes the F on Si more anionic, leading to the formation of H(?+) ???F(?-) interaction. Then the Si-F and Ir-H bonds are readily broken to afford the silyl complex and HF through ?-bond metathesis. Furthermore, the analogous rhodium complex [Rh(H)(CO)(PPh3 )3 ] was found to promote the cleavage of the Si-F bond of the triphosphine-monofluorosilane {(o-Ph2 P)C6 H4 }3 Si(F) even at ambient temperature. PMID:26836576

  20. On deformation twinning in b. c. c. metals

    SciTech Connect

    Lagerloef, K.P.D. . Dept. of Materials Science and Engineering)

    1993-07-01

    A new model of deformation twinning in b.c.c. metals based on the dissociation of an a/2(111) screw dislocations into three co-linear a/6(111) partials on three adjacent (11[bar 2]) planes is proposed. A short screw segment of this zonal dislocation bows out under an applied stress in a fashion similar to a Frank-Read source, where each of the three partials glides on its individuals (11[bar 2]) plane. The correlated motion of the three partials on three adjacent (11[bar 2]) planes forms a three layered micro-twin. After one Frank-Read zonal dislocation loop forms, the screw segment undergoes cross-slip in a similar fashion as the model proposed by Pirouz for twinning in Si because the formation of a second Frank-Reid zonal dislocation loop would produce a stacking sequence of (11[bar 2]) planes associated with a high energy stacking fault. However, after cross-slip the screw-segment may again bow out on a new set of parallel (11[bar 2]) planes to form another three layered micro-twin bound by the zonal dislocation loop. The repeated cross-slip and bowing out of such zonal dislocation loops results in both lateral growth and thickening of the deformation twin.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Kinetics and Relative Importance of Phosphorolytic and Hydrolytic Cleavage of Cellodextrins and Cellobiose in Cell Extracts of Clostridium thermocellum

    PubMed Central

    Zhang, Yi-Heng Percival; Lynd, Lee R.

    2004-01-01

    Rates of phosphorolytic cleavage of ?-glucan substrates were determined for cell extracts from Clostridium thermocellum ATCC 27405 and were compared to rates of hydrolytic cleavage. Reactions with cellopentaose and cellobiose were evaluated for both cellulose (Avicel)- and cellobiose-grown cultures, with more limited data also obtained for cellotetraose. To measure the reaction rate in the chain-shortening direction at elevated temperatures, an assay protocol was developed featuring discrete sampling at 60C followed by subsequent analysis of reaction products (glucose and glucose-1-phosphate) at 35C. Calculated rates of phosphorolytic cleavage for cell extract from Avicel-grown cells exceeded rates of hydrolytic cleavage by ?20-fold for both cellobiose and cellopentaose over a 10-fold range of ?-glucan concentrations (0.5 to 5 mM) and for cellotetraose at a single concentration (2 mM). Rates of phosphorolytic cleavage of ?-glucosidic bonds measured in cell extracts were similar to rates observed in growing cultures. Comparisons of Vmax values indicated that cellobiose- and cellodextrin-phosphorylating activities are synthesized during growth on both cellobiose and Avicel but are subject to some degree of metabolic control. The apparent Km for phosphorolytic cleavage was lower for cellopentaose (mean value for Avicel- and cellobiose-grown cells, 0.61 mM) than for cellobiose (mean value, 3.3 mM). PMID:15006779

  6. 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.

  7. 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 IrCNHC distances are 2.043(5)2.056(5) . 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 (??=?340530?nm (????103?dm3 mol?1 cm?1)) originate from a d?(IrIII)????*(N^N) metal-to-ligand charge transfer transition, where the d?(IrIII) level contain significant contribution from the C^C^C ligands. All these complexes are emissive in the yellow-spectral region (553604?nm in CH3CN and CH2Cl2) upon photo-excitation with quantum yields of 10?310?1.

  8. 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

  9. Luminescent Iridium(III) Complexes Supported by N-Heterocyclic Carbene-based C^C^C-Pincer Ligands and Aromatic Diimines.

    PubMed

    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 (C(1)^C^C(1)) or 1,3-bis(3-butylbenzimidazolin-2-ylidene)phenyl anion (C(2)^C^C(2)) 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) . The hydride chemical shifts for complexes bearing C(1)^C^C(1) (-20.6 to -20.3?ppm) are more upfield than those with C(2)^C^C(2) (-19.5 and -19.2?ppm), revealing that C(1)^C^C(1) is a better electron donor than C(2)^C^C(2). Spectroscopic comparisons and time-dependent density functional theory (TD-DFT) calculations suggest that the lowest-energy electronic transition associated with these complexes (??=?340-530?nm (????10(3)?dm(3) mol(-1) cm(-1))) originate from a d?(Ir(III))????*(N^N) metal-to-ligand charge transfer transition, where the d?(Ir(III)) 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

  10. 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

  11. Short RNA duplexes guide sequence-dependent cleavage by human Dicer

    PubMed Central

    Bergeron, Lucien Junior; Perreault, Jean-Pierre; Elela, Sherif Abou

    2010-01-01

    Dicer is a member of the double-stranded (ds) RNA-specific ribonuclease III (RNase III) family that is required for RNA processing and degradation. Like most members of the RNase III family, Dicer possesses a dsRNA binding domain and cleaves long RNA duplexes in vitro. In this study, Dicer substrate selectivity was examined using bipartite substrates. These experiments revealed that an RNA helix possessing a 2-nucleotide (nt) 3?-overhang may bind and direct sequence-specific Dicer-mediated cleavage in trans at a fixed distance from the 3?-end overhang. Chemical modifications of the substrate indicate that the presence of the ribose 2?-hydroxyl group is not required for Dicer binding, but some located near the scissile bonds are needed for RNA cleavage. This suggests a flexible mechanism for substrate selectivity that recognizes the overall shape of an RNA helix. Examination of the structure of natural pre-microRNAs (pre-miRNAs) suggests that they may form bipartite substrates with complementary mRNA sequences, and thus induce seed-independent Dicer cleavage. Indeed, in vitro, natural pre-miRNA directed sequence-specific Dicer-mediated cleavage in trans by supporting the formation of a substrate mimic. PMID:20974746

  12. 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

  13. Unexpected Trypsin Cleavage at Ubiquitinated Lysines

    PubMed Central

    2015-01-01

    Unexpected tryptic cleavage has been characterized at modified K48 residues in polyubiquitins. In particular, the tryptic products of all seven of the lysine-linked dimers of ubiquitin and of three trimerslinear Ub48Ub48Ub, linear Ub63Ub63Ub, and the branched trimer [Ub]26,48Ubhave been analyzed. In addition to the peptide products expected under commonly used tryptic conditions, we observe that peptides are formed with an unexpected ?-glycinylglycinyl-Lys carboxyl terminus when the site of linkage is Lys48. Trypsin from three different commercial sources exhibited this aberration. Initial cleavage at R74 is proposed in a distal ubiquitin to produce a glycinylglycinyl-lysine residue which is bound by trypsin. PMID:26182167

  14. Cleavage-based signal amplification of RNA.

    PubMed

    Zhao, Yongyun; Zhou, Li; Tang, Zhuo

    2013-01-01

    RNA detection has become an integral part of current biomedical research. Up to now, the reverse transcription-PCR has been the most practical method to detect mRNA targets. However, RNA detection by reverse transcription-PCR requires sophisticated equipment and it is highly sensitive to contamination with genomic DNA. Here we report a new isothermal reaction to simultaneously amplify and detect RNA, based on cleavage by DNAzyme and signal amplification. Cleavage-based signal amplification of RNA cannot be contaminated by genomic DNA and is suitable for the detection of both mRNA and microRNA targets, with high specificity and sensitivity. Moreover, the detection results can be reported in a colorimetric or real-time fluorometric way for different detection purposes. PMID:23422661

  15. 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.

  16. KLEAT: CLEAVAGE SITE ANALYSIS OF TRANSCRIPTOMES*

    PubMed Central

    Birol, Inan; Raymond, Anthony; Chiu, Readman; Nip, Ka Ming; Jackman, Shaun D; Kreitzman, Maayan; Docking, T Roderick; Ennis, Catherine A; Robertson, A Gordon; Karsan, Aly

    2015-01-01

    In eukaryotic cells, alternative cleavage of 3 untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as well as for clinical sequencing applications, it is desirable to characterize such events using RNA-seq data, as the latter are already widely applied to identify other relevant information, such as mutations, alternative splicing and chimeric transcripts. Here we describe KLEAT, an analysis tool that uses de novo assembly of RNA-seq data to characterize cleavage sites on 3 UTRs. We demonstrate the performance of KLEAT on three cell line RNA-seq libraries constructed and sequenced by the ENCODE project, and assembled using Trans-ABySS. Validating the KLEAT predictions with matched ENCODE RNA-seq and RNA-PET libraries, we show that the tool has over 90% positive predictive value when there are at least three RNA-seq reads supporting a poly(A) tail and requiring at least three RNA-PET reads mapping within 100 nucleotides as validation. We also compare the performance of KLEAT with other popular RNA-seq analysis pipelines that reconstruct 3 UTR ends, and show that it performs favourably, based on an ROC-like curve. PMID:25592595

  17. 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.

  18. Cleavage duplexes in the Marcellus Shale of the Appalachian foreland

    NASA Astrophysics Data System (ADS)

    Nickelsen, Richard P.

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

  19. 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.

  20. 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

  1. 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 ??-?? 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

  2. 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.

  3. 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…

  4. 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

  5. Cleavage in conical sand dollar eggs.

    PubMed

    Rappaport, R; Rappaport, B N

    1994-07-01

    Previous experiments have shown that the mitotic apparatus and the surface can interact and produce functional furrows in various unusual geometrical circumstances. The consistent development of the furrow in the plane equidistant from the aster centers has led to conjecture about the need for a special structural configuration of the subsurface in the future cleavage plane. In most experiments involving altered cell geometry, the relation between each aster and nearby surface was symmetrical, and the effect of that symmetry upon the position and orientation of the cleavage mechanism in the cortex has not been systematically analyzed. The normal symmetry of sand dollar eggs can be changed by reshaping them into cones. When the cone and mitotic axes are parallel, the aster center closer to the vertex is also closer to the nearby surface, and the cleavage plane develops on the vertex side of the midpoint between the asters. A mitotic apparatus oriented perpendicular to the cone axis produces in the base of the cone a normal unilateral furrow that advances toward the vertex, and a second contractile band that isolates the vertex region. This event only occurs when the surface is conical and the mitotic apparatus is perpendicular to the cone axis. Furrow formation is not restricted to the plane of the metaphase plate or the midpoint between the aster centers. The orientation of mitotic apparatus-produced contractile bands is not limited to the circumstances in normal cytokinesis, but may vary according to surface contour. These results confirm predictions of the Harris and Gewalt model of contractile ring induction. PMID:8026628

  6. 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

  7. 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.

  8. 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.

  9. In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme

    PubMed Central

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

    2015-01-01

    Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9- crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modeled 2?-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5? bond. Both an invariant guanosine and a Mg2+ are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently-reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site. PMID:25410397

  10. 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.

  11. 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

  12. 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 ?-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 ?-arylation with carbon or heteroatom-based electrophiles, or by performing an ?,?-heterodiarylation to install aryl groups at this position. The ?-arylation of nitrile and ester enolates gives access to 3-amino and 3-hydroxyisoquinolines and the ?-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

  13. 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

  14. Hapalindole/Ambiguine Biogenesis Is Mediated by a Cope Rearrangement, C-C Bond-Forming Cascade.

    PubMed

    Li, Shasha; Lowell, Andrew N; Yu, Fengan; Raveh, Avi; Newmister, Sean A; Bair, Nathan; Schaub, Jeffrey M; Williams, Robert M; Sherman, David H

    2015-12-16

    Hapalindoles are bioactive indole alkaloids with fascinating polycyclic ring systems whose biosynthetic assembly mechanism has remained unknown since their initial discovery in the 1980s. In this study, we describe the fam gene cluster from the cyanobacterium Fischerella ambigua UTEX 1903 encoding hapalindole and ambiguine biosynthesis along with the characterization of two aromatic prenyltransferases, FamD1 and FamD2, and a previously undescribed cyclase, FamC1. These studies demonstrate that FamD2 and FamC1 act in concert to form the tetracyclic core ring system of the hapalindoles from cis-indole isonitrile and geranyl pyrophosphate through a presumed biosynthetic Cope rearrangement and subsequent 6-exo-trig cyclization/electrophilic aromatic substitution reaction. PMID:26629885

  15. 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

  16. 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

  17. 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

  18. Chirality transfer based on reversible C-C bond formation/breaking in nickel(II) complexes.

    PubMed

    Kawamoto, Tatsuya; Suzuki, Narumi; Ono, Takeshi; Gong, Dafei; Konno, Takumi

    2013-01-25

    The reaction of (1R)-(-)-myrtenal-derived benzothiazoline with nickel(II) acetate in ethanol exclusively gave a Schiff base-type nickel(II) complex having M helical configurational myrtenyl arms, which is reversibly converted to a non-innocent-type complex having additional S,S configurational asymmetric carbon centres. PMID:23090291

  19. Cleavage initiation in Ti microalloyed steels

    SciTech Connect

    Fairchild, D.P.; Howden, D.G.; Clark, W.A.T.

    1995-12-31

    The toughness of two microalloyed, thermomechanical control process steels were investigated (steels A and B). Steel A was microalloyed with 0.076V, 0.028Nb, and 0.011 Ti, while steel B contained 0.048Ti. Coarse grain heat affected zone (CGHAZ) specimens were produced by Gleeble simulation. Toughness was measured using instrumented precracked Charpy, Charpy-V-notch, and double crack, 4-point bend tests. Optical and scanning electron microscopy were used for microstructural and fractographic analysis. In all cases, steel A showed better cleavage resistance than steel B. SEM fractography revealed no distinct features at the initiation sites of steel A. At the initiation sites of steel B, however, TiN inclusions were consistently found; their existence verified by EDS. Without exception, when a TiN related initiation site was located, a piece of TiN was found in each mating fracture surface. Evidence of matching river patterns within the inclusion halves, frequent sidecracks within the inclusions, and the absence of microvoiding established the cleavage initiation mechanism in steel B as the fracturing of brittle TiN particles. By quantitative microscopy it was estimated that about 0.0016wt% of steel B`s Ti (less than 3.5% of the total) was tied up in the TiN inclusions. This indicates that, depending on casting schedule, TiN related toughness degradation could potentially occur in steels with modest Ti content.

  20. 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

  1. DNA-dependent cohesin cleavage by separase.

    PubMed

    Kucej, Martin; Zou, Hui

    2010-01-01

    Eukaryotic genomes are organized into chromosomes. In order to maintain genomic stability during cell proliferation, a series of elaborate processes is employed to ensure that chromosomes are duplicated and segregated equally into daughter cells. Sister chromatid cohesion, a tight association of duplicated sister chromatids, allows their attachment to the opposite centrosomes. Sister chromatid cohesion depends on the cohesin complex, a proteinaceous ring that entraps the chromatids together. At the metaphase-to-anaphase transition, a protease called separase is activated and completely dissolves the cohesion by cleaving SCC1, a subunit of the cohesin complex. As one of the key executors of anaphase, separase is regulated temporally and spatially by often redundant mechanisms. A recent study revealed that chromosomal DNA is required as a cofactor for the cleavage of cohesin to occur. This DNA dependence is the underlying biochemical mechanism that allows separase to selectively cleave only the chromosome-associated cohesin. We propose that the chromosomal DNA dependent cohesin cleavage by separase is a component of a regulatory pathway that cells utilize to protect the bulk of cohesin. This intact cohesin becomes immediately available in G(1) to resume its other function-regulation of gene transcription by means of chromatin insulation. PMID:21327097

  2. Activity dependent CAM cleavage and neurotransmission.

    PubMed

    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

  3. Formation of tri- and tetranuclear titanacycles through decamethyltitanocene-mediated intermolecular C-C coupling of dinitriles.

    PubMed

    Becker, Lisanne; Arndt, Perdita; Spannenberg, Anke; Jiao, Haijun; Rosenthal, Uwe

    2015-04-27

    The reactions of [Cp*2 Ti(?(2) -Me3 SiC2 SiMe3 )] (Cp*=?(5) -pentamethylcyclopentadienyl) with various dicyano compounds were investigated. Nitrile-nitrile C?C couplings result in multinuclear complexes owing to the bifunctionality of the substrates. Applying 1,3- or 1,4-dicyanobenzene led to tri- and tetranuclear complexes of the rare 1-metalla-2,5-diaza-cyclopenta-2,4-dienes. These are potential catalysts and were tested in the ring-opening polymerization of ?-caprolactone. The reaction with adiponitrile as alkyl dinitrile afforded a trinuclear 1-metalla-2,5-diaza-cyclopent-3-ene through additional protonation of the nitrogen atoms. The structure and bonding of the products were investigated by X-ray crystallography and DFT analysis to understand the molecular organization in the macrocycles. PMID:25833142

  4. 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 1820% 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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

  7. 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

  8. 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.

  9. Early cleavage in Phoronis muelleri (Phoronida) displays spiral features.

    PubMed

    Pennerstorfer, Markus; Scholtz, Gerhard

    2012-01-01

    The view that early cleavage in Phoronida follows a radial pattern is widely accepted. However, data supporting this characterization are ambiguous. Studies have been repeatedly reporting variation between individual embryos, and the occurrence of embryos exhibiting oblique divisions or nonradial cell arrangements. Such embryos were often considered to represent variation within radial cleavage, or artificial appearances. Cleavage in Phoronis muelleri was previously characterized as "derived radial," but also oblique spindles and cell elongations, and shifted cell arrangements were observed. We studied the early cleavage in P. muelleri applying 4D microscopy, fluorescent staining, and confocal laser scanning microscopy. To deal with the problem of variation we provide statistical evaluations of our data. These show that oblique divisions do not represent variational abnormalities. In fact, they reveal that most cells divide obliquely from the third cleavage onwards. What is more, in almost all cells the axis of the third cleavage is inclined dextrally. The fourth cleavage is even stronger sinistrally pronounced. Subsequently, the pattern of alternating cleavage orientation is largely restricted to animal and vegetal blastomeres. As a result of the obliqueness of divisions, four cells encircle the poles in most embryos. Cross furrows are occasionally present. We found no indications for radial cleavage in P. muelleri. In contrast, the observed cleavage displays several characters consistent with the pattern of spiral cleavage. A close relation of phoronid and spiralian cleavage is also suggested by molecular phylogenies, allying both groups in the Lophotrochozoa. We suggest our findings to represent morphological support for this lophotrochozoan/spiralian affinity of Phoronida. PMID:23134207

  10. 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.

  11. 77 FR 10004 - C$ cMoney, Inc.; Order of Suspension of Trading

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-21

    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE 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...

  12. 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

  13. Investigation of a self-sustained volume discharge in c-C4F8

    NASA Astrophysics Data System (ADS)

    Belevtsev, A. A.; Firsov, K. N.; Kazantsev, S. Yu; Kononov, I. G.; Podlesnykh, S. V.

    2015-11-01

    This paper reports the first experimental study of a self-sustained volume discharge (SSVD) in c-C4F8. The discharge voltage and current oscillograms are taken over a wide range of gas pressures. For the first time an SSVD in c-C4F8 preheated by CO2-laser radiation has been investigated. Some special features and temperature-dependent characteristics of this discharge are revealed. There is discussion on the peculiarities of an SSVD in a preirradiated c-C4F8. To refine the static limiting field in c-C4F8 the static dielectric strength of c-C4F8 is measured on changing the gas pressure by nearly two orders of magnitude.

  14. Visible-Light Photoredox Catalysis: Direct Synthesis of Sulfonated Oxindoles from N-Arylacrylamides and Arylsulfinic Acids by Means of a Cascade C-S/C-C Formation Process.

    PubMed

    Xia, Dong; Miao, Tao; Li, Pinhua; Wang, Lei

    2015-09-01

    A novel photocatalytic synthesis of sulfonated oxindoles from N-arylacrylamides and arylsulfinic acids was developed by means of a cascade C-S/C-C bond-formation process. This method provides mild, efficient, and atom-economical access to various sulfonated oxindoles in water. PMID:26097076

  15. 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

  16. 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.

  17. 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

  18. Brittle to ductile transition in cleavage fracture

    SciTech Connect

    Argon, A.S.; Berg, Q.

    1992-09-30

    The problem of interpretation of fracture transition from brittle to ductile or vice versa is the subject of study. An instrumented tapered double cantilever beam (TDCB) has been developed as a definitive tool in the study of the intrinsic mechanism in single crystalline samples. In this experiment, the crack velocity is directly proportional to actuator velocity. In experiments performed on TDCB shaped Si single crystals, oriented for cleavage on either [l brace]111[r brace] or [l brace]110[r brace] planes, a number of troubling features of jerky carck extension were encountered. Evidence suggests that nucleation of dislocation loops from crack tip is easier than moving these dislocations away from crack tip. 14 refs, 1 fig.

  19. 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.

  20. 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, 0.370.01?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, 0.390.02?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

    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, 0.370.01?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, 0.390.02?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. 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.

  3. 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

  4. 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

  5. Trypanosome U-deletional RNA editing involves guide RNA-directed endonuclease cleavage, terminal U exonuclease, and RNA ligase activities.

    PubMed

    Cruz-Reyes, J; Sollner-Webb, B

    1996-08-20

    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. PMID:8799125

  6. 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.

  7. Control of the mitotic cleavage plane by local epithelial topology

    PubMed Central

    Gibson, William T.; Veldhuis, James H.; Rubinstein, Boris; Cartwright, Heather N.; Perrimon, Norbert; Brodland, G. Wayne; Nagpal, Radhika; Gibson, Matthew C.

    2012-01-01

    SUMMARY For nearly 150 years, it has been recognized that cell shape strongly influences the orientation of the mitotic cleavage plane (e.g. Hofmeister, 1863). However, we still understand little about the complex interplay between cell shape and cleavage plane orientation in epithelia, where polygonal cell geometries emerge from multiple factors, including cell packing, cell growth, and cell division itself. Here, using mechanical simulations, we show that the polygonal shapes of individual cells can systematically bias the long axis orientations of their adjacent mitotic neighbors. Strikingly, analysis of both animal epithelia and plant epidermis confirm a robust and nearly identical correlation between local cell topology and cleavage plane orientation in vivo. Using simple mathematics, we show that this effect derives from fundamental packing constraints. Our results suggest that local epithelial topology is a key determinant of cleavage plane orientation, and that cleavage plane bias may be a widespread property of polygonal cell sheets in plants and animals. PMID:21295702

  8. 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.

  9. 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

  10. Human IgG1 Hinge Fragmentation as the Result of H2O2-mediated Radical Cleavage

    PubMed Central

    Yan, Boxu; Yates, Zac; Balland, Alain; Kleemann, Gerd R.

    2009-01-01

    Hinge cleavage of a recombinant human IgG1 antibody, generated during production in a Chinese hamster ovary cell culture, was observed in the purified material. The cleavage products could be reproduced by incubation of the antibody with H2O2 and featured complementary ladders of the C- and N-terminal residues (Asp226Lys227Thr228His229Thr230) in the heavy chain of the Fab domain and the upper hinge of one of the Fc domains, respectively. Two adducts of +45 and +71 Da were also observed at the N-terminal residues of some Fc fragments and were identified as isocyanate and ?-ketoacyl derivatives generated by radical cleavage at the ?-carbon position through the diamide and ?-amidation pathways. We determined that the hinge cleavage was initiated by radical-induced breakage of the disulfide bond between the two hinge cysteines at position 231 (Cys231-Pro-Pro-Cys-Pro), followed by the formation of a thiyl radical (Cys231-S) on one cysteine and sulfenic acid (Cys231-SOH) on the other. The location of the initial radical attack and the critical role of Cys231 were demonstrated by the observation that 5,5-dimethyl-1-pyrroline N-oxide only reacted with the Cys231 radical and completely blocked hinge cleavage, suggesting the necessity of an electron/radical transfer from the Cys231 radical to the hinge residues where cleavage was observed. As a precursor of hydroxyl radicals, H2O2 is widely produced in healthy cells and tissues and therefore could be the source for the radical-induced fragmentation of human IgG1 antibodies in vivo. PMID:19850927

  11. 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

  12. 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

  13. 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

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

    PubMed Central

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

  15. 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)

  16. 21. Historic American Buildings Survey Copyright C.C. Pierce Original: ...

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

    21. Historic American Buildings Survey Copyright - C.C. Pierce Original: About 1902 Re-photo: April 1940 QUANDRANGLE (view from north) - Mission Nuestra Senora de la Soledad, Soledad, Monterey County, CA

  17. 5. Historic American Buildings Survey C.C. Woodburn, Photographer. January 12, ...

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

    5. Historic American Buildings Survey C.C. Woodburn, Photographer. January 12, 1934 DETAIL OF ENTRANCE (WEST ELEVATION) - Ferdinand Daniel Pulver House, County Road F-70 Vicinity, Vandalia, Jasper County, IA

  18. Combustion Gas Heating Tests of C/C Composites Coated with SiC Layer

    NASA Astrophysics Data System (ADS)

    Sato, Masaki; Moriya, Shin-ichi; Sato, Masahiro; Tadano, Makoto; Kusaka, Kazuo; Hasegawa, Keiichi; Kumakawa, Akinaga; Yoshida, Makoto

    2008-02-01

    In order to examine the applicability of carbon fiber/carbon matrix composites coated with a silicon carbide layer (C/C-SiCs) to an advanced nozzle for the future reusable rocket engines, two series of combustion gas heating tests were conducted using a small rocket combustor. In the first series of heating tests, five different kinds of C/C-SiCs were tested with specimens in the shape of a square plate for material screening. In the second series of heating tests, two selected C/C-SiCs were tested with specimens in the shape of a small nozzle. The effectiveness of an interlayer between a C/C composite and a SiC layer, which was introduced to improve the durability based on the concept of functionally graded materials (FGMs), can be observed. The typical damage mode was also pointed out in the results of heating test using the small nozzle specimens.

  19. Brazing of C/C composites and Ni-based alloy using interlayer

    NASA Astrophysics Data System (ADS)

    Ikeshoji, Toshi-Taka; Tokunaga, Tatsuya; Suzumura, Akio; Yamazaki, Takahisa

    2014-08-01

    The brazing of C/C composites and Inconel-600 Ni-based heat resistant alloy was conducted using Fe-Ni-Cr-P-Si brazing filler alloy with inserting various thickness of Nb foil as stress relief interlayer. SEM observation of cross section of brazing interface revealed that Nb foil was resolved into the brazing filler layer on C/C composites side. Nb diffused to the surface of C/C composites and acted as the active metal element to enhance the wettability of molten metal on graphite matrix of C/C composites during the brazing process. The variation in shear strength values of the brazed joint with Nb layer thickness suggested that the Nb layer should be remained at least 100 ?m.

  20. Search for the weak decays J /? ?Ds(*)-e+?e+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.; Ferroli, R. Baldini; 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.; Chu, Y. P.; Cibinetto, G.; Cronin-Hennessy, D.; Dai, H. L.; Dai, J. P.; 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.; Fu, C. D.; Gao, Q.; Gao, Y.; Garzia, I.; Goetzen, K.; Gong, W. X.; Gradl, W.; Greco, M.; Gu, M. H.; Gu, Y. T.; Guan, Y. H.; Guo, A. Q.; Guo, L. B.; Guo, T.; Guo, Y.; Guo, Y. P.; Haddadi, Z.; Hafner, A.; Han, S.; Han, Y. L.; 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.; Kuehn, W.; Kupsc, A.; Lai, W.; Lange, J. S.; Lara, M.; Larin, P.; 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, 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. L.; 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, 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.; Moeini, H.; Morales, C. Morales; 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.; 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.; Shepherd, M. R.; Song, W. M.; Song, X. Y.; Sosio, S.; Spataro, S.; Spruck, B.; Sun, G. X.; Sun, J. F.; Sun, S. S.; Sun, Y. J.; Sun, Y. Z.; Sun, Z. J.; Sun, Z. T.; Tang, C. J.; Tang, X.; Tapan, I.; Thorndike, E. H.; 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.; 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. J.; Zhang, X. Y.; Zhang, Y.; Zhang, Y. H.; Zhang, Z. H.; Zhang, Z. P.; Zhang, Z. Y.; Zhao, G.; 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.

    2014-12-01

    Using a sample of 2.25 1 08 J /? events collected with the BESIII detector at the BEPCII collider, we search for the J /? semileptonic weak decay J /? ?Ds-e+?e+c .c . with a much higher sensitivity than previous searches. We also perform the first search for J /? ?Ds*-e+?e+c .c . No significant excess of a signal above background is observed in either channel. At the 90% confidence level, the upper limits are determined to be B (J /? ?Ds-e+?e+c .c .)<1.3 1 0-6 and B (J /? ?Ds* -e+?e+c .c .)<1.8 1 0-6 , respectively. Both are consistent with Standard Model predictions.

  1. 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.

  2. Selective and nonselective cleavages in positive and negative CID of the fragments generated from in-source decay of intact proteins in MALDI-MS.

    PubMed

    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-C? 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 ?-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 ?-helical domains suggest that acidic residues in helix-free regions tend to degrade more than those in helical regions. PMID:24135807

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. Monozygotic cleavage polyembryogenesis and conifer tree improvement.

    PubMed

    Durzan, Don J

    2008-01-01

    The mass cloning of elite genotypes of commercially important conifers has led to the establishment of an industrial forest of two of the most important softwood species in the USA. Embryonal-suspensor masses, produced by monozygotic cleavage polyembryony (MCP), are rescued from controlled-pollinated seeds in tree breeding orchards. MCP is scaled up as cell suspensions and grown into mature somatic embryos. The embryos serve as a source for the production of various artificial and manufactured seeds used in replicated field trials to test genotype x environmental interactions. For the capture of genetic gains, early selections are based on correlations with known traits. This reduces the costs of years of tree improvement. Mass cloning and genotype cryopreservation enables field testing under a wider range of sites. Process-controlled bioreactors are proposed as artificial ovules to impose nutritional variables from the mother tree, and to simulate environmental factors that are known to affect the performance of the new generation. Comparisons among extant and modern conifer genotypes would provide new insights regarding their latent potentials for apomixis, the alternation of generations, and adaptive plasticity. PMID:18822861

  10. Endonucleolytic RNA cleavage by a eukaryotic exosome.

    PubMed

    Lebreton, Alice; Tomecki, Rafal; Dziembowski, Andrzej; Sraphin, Bertrand

    2008-12-18

    The exosome is a major eukaryotic nuclease located in both the nucleus and the cytoplasm that contributes to the processing, quality control and/or turnover of a large number of cellular RNAs. This large macromolecular assembly has been described as a 3'-->5' exonuclease and shown to contain a nine-subunit ring structure evolutionarily related to archaeal exosome-like complexes and bacterial polynucleotide phosphorylases. Recent results have shown that, unlike its prokaryotic counterparts, the yeast and human ring structures are catalytically inactive. In contrast, the exonucleolytic activity of the yeast exosome core was shown to be mediated by the RNB domain of the eukaryote-specific Dis3 subunit. Here we show, using in vitro assays, that yeast Dis3 has an additional endoribonuclease activity mediated by the PIN domain located at the amino terminus of this multidomain protein. Simultaneous inactivation of the endonucleolytic and exonucleolytic activities of the exosome core generates a synthetic growth phenotype in vivo, supporting a physiological function for the PIN domain. This activity is responsible for the cleavage of some natural exosome substrates, independently of exonucleolytic degradation. In contrast with current models, our results show that eukaryotic exosome cores have both endonucleolytic and exonucleolytic activities, mediated by two distinct domains of the Dis3 subunit. The mode of action of eukaryotic exosome cores in RNA processing and degradation should be reconsidered, taking into account the cooperation between its multiple ribonucleolytic activities. PMID:19060886

  11. 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

  12. [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

  13. Quantification of DNA cleavage specificity in Hi-C experiments.

    PubMed

    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

  14. 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

  15. 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.

  16. Familial Alzheimers mutations within APPTM increase A?42 production by enhancing accessibility of ?-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 A?42/A?40 production ratio is a hallmark of familial Alzheimers disease, which can be caused by mutations in the amyloid precursor protein (APP). The C-terminus of A? is generated by ?-secretase cleavage within the transmembrane domain of APP (APPTM), a process that is primed by an initial ?-cleavage at either T48 or L49, resulting in subsequent production of A?42 or A?40, 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 ?-secretase for the initial ?-cleavage, and consequently shift cleavage preference towards A?42.

  17. 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

  18. Detection of nucleic acid sequences by invader-directed cleavage

    DOEpatents

    Brow, Mary Ann D. (Madison, WI); Hall, Jeff Steven Grotelueschen (Madison, WI); Lyamichev, Victor (Madison, WI); Olive, David Michael (Madison, WI); Prudent, James Robert (Madison, WI)

    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.

  19. 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.

  20. Iridium-catalyzed borylation of secondary C-H bonds in cyclic ethers.

    PubMed

    Liskey, Carl W; Hartwig, John F

    2012-08-01

    The borylation of secondary C-H bonds, specifically secondary C-H bonds of cyclic ethers, with a catalyst generated from tetramethylphenanthroline and an iridium precursor is reported. This borylation occurs with unique selectivity for the C-H bonds located ? to the oxygen atoms over the weaker C-H bonds located ? to oxygen atoms. Mechanistic studies imply that the C-H bond cleavage occurs directly at the ? position rather than at the ? position followed by isomerization of a reaction intermediate. PMID:22804581