Sample records for c-c bond cleavage

  1. Mechanistic insight into the cleavage of an aromatic C-C bond by tungsten.

    PubMed

    Li, Jun; Yoshizawa, Kazunari

    2012-01-16

    The pathway for the cleavage of an aromatic C-C bond in quinoxaline by a tungsten(II) complex [W(PMe(3))(4)(?(2)-CH(2)PMe(2))H] is explored by performing detailed DFT calculations. The real active complex was found to be [W(PMe(3))(2)(?(2)-CH(2)PMe(2))H] rather than [W(PMe(3))(4)]. The key step in the whole reaction is the reductive elimination of two hydrides that are located originally on quinoxaline (see scheme). PMID:22170350

  2. Extended reaction scope of thiamine diphosphate dependent cyclohexane-1,2-dione hydrolase: from C-C bond cleavage to C-C bond ligation.

    PubMed

    Loschonsky, Sabrina; Wacker, Tobias; Waltzer, Simon; Giovannini, Pier Paolo; McLeish, Michael J; Andrade, Susana L A; Müller, Michael

    2014-12-22

    ThDP-dependent cyclohexane-1,2-dione hydrolase (CDH) catalyzes the C?C bond cleavage of cyclohexane-1,2-dione to 6-oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH-H28A is much less able to catalyze the C?C bond formation, while the ability for C?C bond cleavage is still intact. The double variant CDH-H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane-1,2-dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54-94?% enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane-2,3-dione are alternative donor substrates for C?C bond formation. Thus, the very rare aldehyde-ketone cross-benzoin reaction has been solved by design of an enzyme variant. PMID:25382418

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

    PubMed

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

    2015-01-01

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

  4. 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 C–C bond cleavage in methylcyclohexane were studied over supported Ir catalysts. The rate of endocyclic C–C 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 C–C bond cleavage decreased monotonically with increasing H2 pressure and decreasing Ir particle size. The distinct dependencies of endocyclic and exocyclic C–C 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.

  5. FeCl2-promoted cleavage of the unactivated C-C bond of alkylarenes and polystyrene: direct synthesis of arylamines.

    PubMed

    Qin, Chong; Shen, Tao; Tang, Conghui; Jiao, Ning

    2012-07-01

    Ironing it out: an efficient and convenient nitrogenation strategy involving C-C bond cleavage for the straightforward synthesis of versatile arylamines is presented. Various alkyl azides and alkylarenes, including the common industrial by-product cumene, react using this protocol. Moreover, this method provides a potential strategy for the degradation of polystyrene. PMID:22689538

  6. Transition-metal-free tandem oxidative removal of benzylic methylene group by C-C and C-N bond cleavage followed by intramolecular new aryl C-N bond formation under radical conditions.

    PubMed

    Laha, Joydev K; Tummalapalli, K S Satyanarayana; Gupta, Ankur

    2014-09-01

    A novel tandem oxidative conversion of 10,11-dihydro-5H-dibenzo[b,e][1,4]diazepines to phenazines has been achieved under transition-metal-free, mild conditions using K2S2O8 or DDQ as the oxidizing agent. The transformation proceeds through oxidative removal of a benzylic methylene group by C-C and C-N bond cleavage followed by a new aryl C-N bond formation under radical conditions. PMID:25119523

  7. 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

  8. Iridium-catalyzed reductive carbon-carbon bond cleavage reaction on a curved pyridylcorannulene skeleton.

    PubMed

    Tashiro, Shohei; Yamada, Mihoko; Shionoya, Mitsuhiko

    2015-04-27

    The cleavage of C?C bonds in ?-conjugated systems is an important method for controlling their shape and coplanarity. An efficient way for the cleavage of an aromatic C?C bond in a typical buckybowl corannulene skeleton is reported. The reaction of 2-pyridylcorannulene with a catalytic amount of IrCl3 ?n?H2 O in ethylene glycol at 250?°C resulted in a structural transformation from the curved corannulene skeleton to a strain-free flat benzo[ghi]fluoranthene skeleton through a site-selective C?C cleavage reaction. This cleavage reaction was found to be driven by both the coordination of the 2-pyridyl substituent to iridium and the relief of strain in the curved corannulene skeleton. This finding should facilitate the design of carbon nanomaterials based on C?C bond cleavage reactions. PMID:25756834

  9. 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

  10. Dissecting alkynes: full cleavage of polarized C?C moiety via sequential bis-Michael addition/retro-Mannich cascade.

    PubMed

    Roy, Saumya; Davydova, Maria P; Pal, Runa; Gilmore, Kerry; Tolstikov, Genrikh A; Vasilevsky, Sergei F; Alabugin, Igor V

    2011-09-16

    The reaction of diaryl ketoalkynes with 1,2-diamino ethane leads to the full scission of the triple bond with the formation of acetophenone and imidazoline fragments. In this transformation, one of the alkyne carbons undergoes formal reduction with the formation of three C-H bonds, whereas the other carbon undergoes formal oxidation via the formation of three C-N bonds (one ? and two ?). Computational analysis confirmed that the key fragmentation step proceeds via a six-membered TS in a concerted manner. Both amines are involved in the fragmentation: the N-H moiety of one amine transfers a proton to the developing negative charge at the enolate oxygen, while the other amine provides direct stereoelectronic assistance to the C-C bond cleavage via a hyperconjugative n(N) ? ?*(C-C) interaction. PMID:21806030

  11. Selective cleavage of the C(?)-C(?) linkage in lignin model compounds via Baeyer-Villiger oxidation.

    PubMed

    Patil, Nikhil D; Yao, Soledad G; Meier, Mark S; Mobley, Justin K; Crocker, Mark

    2015-03-21

    Lignin is an amorphous aromatic polymer derived from plants and is a potential source of fuels and bulk chemicals. Herein, we present a survey of reagents for selective stepwise oxidation of lignin model compounds. Specifically, we have targeted the oxidative cleavage of C?-C? bonds as a means to depolymerize lignin and obtain useful aromatic compounds. In this work, we prepared several lignin model compounds that possess structures, characteristic reactivity, and linkages closely related to the parent lignin polymer. We observed that selective oxidation of benzylic hydroxyl groups, followed by Baeyer-Villiger oxidation of the resulting ketones, successfully cleaves the C?-C? linkage in these model compounds. PMID:25641654

  12. 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.

  13. 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…

  14. 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

  15. 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.

  16. 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.

  17. Extending the chemistry of carbones: P-N bond cleavage via an SN2'-like mechanism.

    PubMed

    Gurnani, Chitra; ?or?evi?, Nemanja; Muthaiah, Senthilkumar; Dimi?, Dušan; Ganguly, Rakesh; Petkovi?, Milena; Vidovi?, Dragoslav

    2015-07-01

    The reactivity of nucleophilic carbodiphosphorane (C(PPh3)2, 1) and carbodicarbene (C(C(NMe)2C6H4)2, 2) towards various dichlorophosphines has been explored. In most cases the expected carbone-for-chloride ligand exchange was observed. However, the use of MeN(PCl2)2 resulted in a unique P-N bond cleavage that, according to computational studies, occurred via an SN2'-like mechanism. PMID:26051013

  18. 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.

  19. Direct Conversion of Glycerol into Formic Acid via Water Stable Pd(II) Catalyzed Oxidative Carbon-Carbon Bond Cleavage

    PubMed Central

    Pullanikat, Prasanna; Lee, Joo Ho; Yoo, Kyung Soo; Jung, Kyung Woon

    2013-01-01

    Using our tridentate NHC-amidate-alkoxide Pd(II) complex, we developed a catalytic method for oxidative C-C bond cleavage of glycerol. The glycerol was degraded exclusively to formic acid and CO2. Two possible degradation pathways were proposed through 13C labeled studies. PMID:23997315

  20. 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

  1. Direct Annulation of Hydrazides to 1,3,4-Oxadiazoles via Oxidative C(CO)-C(Methyl) Bond Cleavage of Methyl Ketones.

    PubMed

    Gao, Qinghe; Liu, Shan; Wu, Xia; Zhang, Jingjing; Wu, Anxin

    2015-06-19

    A new strategy for the synthesis of 1,3,4-oxadiazoles was established through direct annulation of hydrazides with methyl ketones. It was found that the use of K2CO3 as a base achieves an unexpected and highly efficient C-C bond cleavage. This reaction is proposed to go through oxidative cleavage of Csp(3)-H bonds, followed by cyclization and deacylation. PMID:26035338

  2. Rh-catalyzed C-C cleavage of benzyl/allylic alcohols to produce benzyl/allylic amines or other alcohols by nucleophilic addition of intermediate rhodacycles to aldehydes and imines.

    PubMed

    Zhang, Xi-Sha; Li, Yang; Li, Hu; Chen, Kang; Lei, Zhi-Quan; Shi, Zhang-Jie

    2012-12-01

    We report three transformations: 1)?direct transformation from biarylmethanols into biarylmethylamines; 2)?direct transformation from one biarylmethanol into another biarylmethanol; 3)?direct transformation from allylic alcohols into allylic amines. These transformations are based on pyridyl-directed Rh-catalyzed C-C bond cleavage of secondary alcohols and subsequent addition to C=X (X = N or O) double bonds. The reaction conditions are simple and no additive is required. The driving force of C-C bond cleavage is the formation of the stable rhodacycle intermediate. Other directing groups, such as the pyrazolyl group, can also be used although it is not as efficient as the pyridyl group. We carried out in-depth investigations for transformation 1 and found that: 1)?the substrate scope was broad and electron-rich alcohols and electron-deficient imines are more efficient; 2)?as the leaving group, aldehyde had no significant impact on either the C-C bond cleavage or the whole transformation; 3)?mechanistic studies (intermediate isolation, in situ NMR spectroscopic studies, competing reactions, isotopic labeling experiments) implied that: i)?The C-C cleavage was very efficient under these conditions; ii)?there is an equilibrium between the rhodacycle intermediate and the protonated byproduct phenylpyridine; iii)?the addition step of the rhodacycle intermediate to imines was slower than the C-C cleavage and the equilibrium between the rhodacycle and phenylpyridine; iv)?the whole transformation was a combination of two sequences of C-C cleavage/nucleophilic addition and C-C cleavage/protonation/C-H activation/nucleophilic addition, with the latter being perhaps the main pathway. We also demonstrated the first example of cleavage of an C(alkenyl)-C(benzyl) bond. These transformations showed the exchange (or substitution) of the alcohol group with either an amine or another alcohol group. Like the "group transplant", this method offers a new concept that can be used to directly synthesize the desired products from other chemicals through reorganization of carbon skeletons. PMID:23080063

  3. 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

  4. Carbon-Fluorine Bond Cleavage by Zirconium Metal Hydride Complexes

    E-print Network

    Jones, William D.

    Carbon-Fluorine Bond Cleavage by Zirconium Metal Hydride Complexes Brian L. Edelbach, A. K. Fazlur, Rochester, New York 14627 Received April 8, 1999 The zirconium hydride dimer [Cp2ZrH2]2 reacts with C6F6. [Cp2ZrH2]2 reacts with C6F5H to give Cp2Zr(p-C6F4H)F, Cp2ZrF2, C6F4H2, and H2. The zirconium hydride

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

    SciTech Connect

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

    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}).

  6. Csp(3)-csp(3) bond cleavage in the palladium-catalyzed aminohydroxylation of allylic hydrazones using atmospheric oxygen as the sole oxidant.

    PubMed

    Chen, Yu-Chen; Zhu, Ming-Kui; Loh, Teck-Peng

    2015-06-01

    A C-C bond cleavage was observed in the palladium-catalyzed aminohydroxylation of allylic hydrazones, using atmospheric oxygen as the sole oxidant. This reaction could also proceed in a one-pot manner, starting from keto-alkene compounds and phenylhydrazine. PMID:25973749

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

    PubMed Central

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

    2010-01-01

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

  8. Recent advances in the gold-catalyzed additions to C–C multiple bonds

    PubMed Central

    Huang, He; Zhou, Yu

    2011-01-01

    Summary C–O, C–N and C–C bonds are the most widespread types of bonds in nature, and are the cornerstone of most organic compounds, ranging from pharmaceuticals and agrochemicals to advanced materials and polymers. Cationic gold acts as a soft and carbophilic Lewis acid and is considered one of the most powerful activators of C–C multiple bonds. Consequently, gold-catalysis plays an important role in the development of new strategies to form these bonds in more convenient ways. In this review, we highlight recent advances in the gold-catalyzed chemistry of addition of X–H (X = O, N, C) bonds to C–C multiple bonds, tandem reactions, and asymmetric additions. This review covers gold-catalyzed organic reactions published from 2008 to the present. PMID:21804887

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2014-03-13

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

  11. Stereoselective C-C bond formation catalysed by engineered carboxymethylproline synthases

    NASA Astrophysics Data System (ADS)

    Hamed, Refaat B.; Gomez-Castellanos, J. Ruben; Thalhammer, Armin; Harding, Daniel; Ducho, Christian; Claridge, Timothy D. W.; Schofield, Christopher J.

    2011-05-01

    The reaction of enol(ate)s with electrophiles is used extensively in organic synthesis for stereoselective C-C bond formation. Protein-based catalysts have had comparatively limited application for the stereoselective formation of C-C bonds of choice via enolate chemistry. We describe protein engineering studies on 5-carboxymethylproline synthases, members of the crotonase superfamily, aimed at enabling stereoselective C-C bond formation leading to N-heterocycles via control of trisubstituted enolate intermediates. Active site substitutions, including at the oxyanion binding site, enable the production of substituted N-heterocycles in high diastereomeric excesses via stereocontrolled enolate formation and reaction. The results reveal the potential of the ubiquitous crotonase superfamily as adaptable catalysts for the control of enolate chemistry.

  12. Mass spectrometric and theoretical studies on dissociation of the Csbnd S bond in the benzenesulfonic acid and benzenesulfinic acid anion series: Homolytic cleavage vs heterolytic cleavage

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang

    2012-11-01

    The dissociation of the Csbnd S bond in a variety of para-substituted benzenesulfonic acid and benzenesulfinic acid anions has been investigated through the tandem mass spectrometry and density functional theory (DFT). For the Csbnd S bond in the para-substituted benzenesulfonic acid anions, only the homolytic cleavage occurs. DFT calculations indicate that the homolytic cleavage is 14.1 kcal/mol at least less than the heterolytic cleavage in the dissociation enthalpy. On the other hand, for the Csbnd S bond in the para-substituted benzenesulfinic acid anions, both homolytic cleavage and heterolytic cleavage take place. Calculations show that the enthalpy difference between these two cleavage modes is 9.5 kcal/mol at most. It is obvious that DFT calculations are well consistent with the MS/MS experiments.

  13. Reversible Cleavage of Carbon-Carbon Bonds in Benzonitrile Using Nickel(0)

    E-print Network

    Jones, William D.

    Reversible Cleavage of Carbon-Carbon Bonds in Benzonitrile Using Nickel(0) Juventino J. Garcia 3, 2000 Summary: The nickel(0) fragment [(dippe)Ni] has been found to -coordinate to the CN bond efficient and reversible. The nickel dimer [(dippe)NiH]2 has been reported to be capable of cleaving the C

  14. 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

  15. Aerobic dehydrogenative ?-diarylation of benzyl ketones with aromatics through carbon-carbon bond cleavage.

    PubMed

    More, Nagnath Yadav; Jeganmohan, Masilamani

    2014-02-01

    Substituted benzyl ketones reacted with aromatics in the presence of K2S2O8 in CF3COOH at room temperature, yielding ?-diaryl benzyl ketones through a carbon-carbon bond cleavage. In the reaction, two new carbon-carbon bonds were formed and one carbon-carbon bond was cleaved. It is very interesting that two different nucleophiles such as benzyl ketones and aromatics were coupled together without metal, which is unusual in organic synthesis. PMID:24479373

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

    PubMed Central

    Bower, John F.; Krische, Michael J.

    2011-01-01

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

  17. Formation of C-C Bonds via Iridium-Catalyzed Hydrogenation and Transfer Hydrogenation

    NASA Astrophysics Data System (ADS)

    Bower, John F.; Krische, Michael J.

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

  18. Bronsted-Evans-Polanyi 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, Rajeev S.; Broadbelt, Linda J; Curtiss, Larry A

    2011-04-27

    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 Brønsted-Evans-Polanyi (BEP) relationships such as that proposed here have found broad application in heterogeneous catalysis, their extension to enzymatic catalysis is limited. We report here on density functional theory (DFT) studies for C–C bond formation and C–C bond cleavage associated with the decarboxylation of six 2-keto acids by a thiamine-containing enzyme (EC 1.2.7.1) and demonstrate a linear relationship between the free energy of reaction and the activation barrier. We then applied this relationship to predict the activation barriers of 17 chemically similar novel reactions. These calculations reveal that there is a clear correlation between the free energy of formation of the transition state and the free energy of the reaction, suggesting that this method can be further extended to predict the kinetics of novel reactions through our computational framework for discovery of novel biochemical transformations.

  19. 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. (Center for Nanoscale Materials); ( MSD); (Northwestern Univ.)

    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.

  20. Nickel-Catalyzed C?O/C?H Cross-Coupling Reactions for C?C Bond Formation.

    PubMed

    Chen, Tieqiao; Han, Li-Biao

    2015-07-20

    Halides not required: Nickel-catalyzed C?O/C?H cross-couplings for the construction of C?C bonds have recently been disclosed. By carefully optimizing the nickel catalyst, new C?C bond-forming reactions were developed, and even quaternary stereogenic centers are now accessible in high yields from readily available phenoxide derivatives and hydrocarbons. PMID:26073575

  1. 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.

  2. Plasma induced oxidative cleavage of disulfide bonds in polypeptides during nanoelectrospray ionization.

    PubMed

    Xia, Yu; Cooks, R Graham

    2010-04-01

    Cleavage of the disulfide bond within a polypeptide was observed when the nanoelectrospray (nanoESI) plume of a peptide solution interacted with a low-temperature helium plasma in air. Online mass spectrometric analysis revealed that chain separation accompanied by a mass increase of 1 or 16 Da for each chain was common to peptides having an interchain disulfide bond, while for peptides having intrachain disulfide bonds, the reaction products typically showed mass increases of 17 Da. Experimental results suggested that hydroxyl radicals initiated from the plasma were likely to be responsible via dissociative addition to the disulfide bond (RSSR'), giving rise to RSH and R'SO*. When the hydroxyl radical addition product ions ([M + nH + OH](n*+), n is the charge state) generated from peptides having intrachain peptides were subjected to collision-induced dissociation (CID) in an ion trap, a-, b-, and y-type sequence ions within the cyclic structure defined by the disulfide bond were observed in addition to the exocyclic cleavages typically seen from CID of [M + nH](n+) peptide ions. Rich structural information could thus be obtained. These findings were demonstrated in 14 peptides containing disulfide bonds and further by bovine insulin, which has three disulfide bonds. Collisional activation of the [M + 5H + OH](5*+) insulin ions provided 76% of the possible backbone cleavages as compared to 26% acquired from CID of the [M + 5H](5+) ions. PMID:20196567

  3. Room temperature ring expansion of N-heterocyclic carbenes and b?b bond cleavage of diboron(4) compounds.

    PubMed

    Pietsch, Sabrina; Paul, Ursula; Cade, Ian A; Ingleson, Michael J; Radius, Udo; Marder, Todd B

    2015-06-15

    We report the isolation and detailed structural characterization, by solid-state and solution NMR spectroscopy, of the neutral mono- and bis-NHC adducts of bis(catecholato)diboron (B2 cat2 ). The bis-NHC adduct undergoes thermally induced rearrangement, forming a six-membered -B?C?N?C?C-N-heterocyclic ring via C?N bond cleavage and ring expansion of the NHC, whereas the mono-NHC adduct is stable. Bis(neopentylglycolato)diboron (B2 neop2 ) is much more reactive than B2 cat2 giving a ring expanded product at room temperature, demonstrating that ring expansion of NHCs can be a very facile process with significant implications for their use in catalysis. PMID:25960171

  4. Single C-C bond in (C{sub 60}){sub 2}{sup 2{minus}}

    SciTech Connect

    Oszlanyi, G.; Bortel, G.; Faigel, G.; Granasy, L. [Research Institute for Solid State Physics, H-1525 Budapest, POB. 49. (Hungary); Bendele, G.M.; Stephens, P.W. [Department of Physics, State University of New York, Stony Brook, New York 11794-3800 (United States); Forro, L. [Laboratoire de Physique des Solides Semicristallins, Institut de Genie Atomique, Departement de Physique, Ecole Polytechnique Federale de Lausanne, 1015-Lausanne (Switzerland)

    1996-11-01

    The structure of the dimer phases of RbC{sub 60} and KC{sub 60} were investigated by x-ray powder diffraction. We have established that the dimer molecule forms through a single C-C interfullerene bond in contrast to the four-membered rings of C{sub 60} polymers. Molecular orientation and space group symmetry were also determined. {copyright} {ital 1996 The American Physical Society.}

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

    PubMed

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

    2011-06-28

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

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

    PubMed

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

    2014-12-01

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

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

    E-print Network

    Jones, William D.

    Cleavage of Carbon-Carbon Bonds in Alkyl Cyanides Using Nickel(0) Juventino J. Garci´a,*, Alma Are of alkyl cyanides afforded nickel(0) compounds of the type [(dippe)Ni(2 -RCN)], where R ) Me, Et, Pr, i Pr cyanides using [(dippe)NiH]2, leading to the formation of an 2- nitrile complex of nickel(0), which

  8. Carbon-Carbon Bond Cleavage Reaction: Synthesis of Multisubstituted Pyrazolo[1,5-a]pyrimidines.

    PubMed

    Saikia, Pallabi; Gogoi, Sanjib; Boruah, Romesh C

    2015-07-01

    A new carbon-carbon bond cleavage reaction was developed for the efficient synthesis of multisubstituted pyrazolo[1,5-a]pyrimidines. This base induced reaction of 1,3,5-trisubstituted pentane-1,5-diones and substituted pyrazoles afforded good yields of the pyrazolo[1,5-a]pyrimidines. PMID:26083788

  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. Borane B-C Bond Cleavage by a Low-Coordinate Iron Hydride Complex and N-N Bond Cleavage by the Hydridoborate Product

    PubMed Central

    Yu, Ying; Brennessel, William W.; Holland, Patrick L.

    2008-01-01

    The iron(II) hydride dimers [LRFe(?-H)2FeLR] (LMe = 2,4-bis(2,6-diisopropylphenylimino) pent-3-yl; LtBu = 2,2,6,6-tetramethyl-3,5-bis(2,6-diisopropylphenylimino)hept-4-yl) abstract hydrocarbyl groups from BR?3 (R? = Et, Ph) to give LRFeR? and LRFe(?-H)2BR?2. Mechanistic studies with R = R? = Me are consistent with a process in which the hyride dimer opens one Fe-H bond, and subsequent B-H bond formation is concerted with dissociation of an Fe-H unit. Cleavage of boron-carbon bonds is likely to proceed at least in part from transient quaternary borate anions. In a separate bond-breaking reaction, LMeFe(?-H)2BEt2 reacts with N2H4 to eject H2 from the bridging hydrides and cleave the N-N bond in the diaminoborate complex LMeFe(?-NH2)2BEt2. These novel bond-breaking reactions are facilitated by the low coordination number at the iron(II) center. PMID:18725998

  11. 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.

  12. 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.

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

    PubMed Central

    Moran, Joseph; Krische, Michael J.

    2013-01-01

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

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

    PubMed

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

    2014-06-01

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

  15. Bimetallic cleavage of aromatic C-H bonds by rare-earth-metal complexes.

    PubMed

    Huang, Wenliang; Dulong, Florian; Khan, Saeed I; Cantat, Thibault; Diaconescu, Paula L

    2014-12-17

    A new type of C-H bond activation mediated by rare-earth metals under reducing conditions is reported. The synergy between reductants and rare-earth-metal complexes allows the cleavage of unactivated aromatic C-H bonds. The reaction between rare-earth-metal iodides supported by a 1,1'-ferrocenediamide ligand and potassium graphite in benzene leads to the formation of a 1:1 metal molar ratio of the corresponding metal hydride and metal phenyl complex. A proposed mechanism involving an inverse sandwich arene bimetallic intermediate is supported by experimental and computational studies. PMID:25431837

  16. Anti-Arrhenius cleavage of covalent bonds in bottlebrush macromolecules on substrate

    PubMed Central

    Lebedeva, Natalia V.; Nese, Alper; Sun, Frank C.; Matyjaszewski, Krzysztof; Sheiko, Sergei S.

    2012-01-01

    Spontaneous degradation of bottlebrush macromolecules on aqueous substrates was monitored by atomic force microscopy. Scission of C?C covalent bonds in the brush backbone occurred due to steric repulsion between the adsorbed side chains, which generated bond tension on the order of several nano-Newtons. Unlike conventional chemical reactions, the rate of bond scission was shown to decrease with temperature. This apparent anti-Arrhenius behavior was caused by a decrease in the surface energy of the underlying substrate upon heating, which results in a corresponding decrease of bond tension in the adsorbed macromolecules. Even though the tension dropped minimally from 2.16 to 1.89 nN, this was sufficient to overpower the increase in the thermal energy (kBT) in the Arrhenius equation. The rate constant of the bond-scission reaction was measured as a function of temperature and surface energy. Fitting the experimental data by a perturbed Morse potential V = V0(1 - e-?x)2 - fx, we determined the depth and width of the potential to be V0 = 141 ± 19 kJ/mol and ?-1 = 0.18 ± 0.03 ?, respectively. Whereas the V0 value is in reasonable agreement with the activation energy Ea = 80–220 kJ/mol of mechanical and thermal degradation of organic polymers, it is significantly lower than the dissociation energy of a C?C bond De = 350 kJ/mol. Moreover, the force constant Kx = 2?2V0 = 1.45 ± 0.36 kN/m of a strained bottlebrush along its backbone is markedly larger than the force constant of a C?C bond Kl = 0.44 kN/m, which is attributed to additional stiffness due to deformation of the side chains. PMID:22645366

  17. Identification of bacterial carotenoid cleavage dioxygenase homologs that cleave the interphenyl ?,? double bond of stilbene derivatives via a monooxygenase reaction

    PubMed Central

    Marasco, Erin K.; Schmidt-Dannert, Claudia

    2013-01-01

    Carotenoid cleavage oxygenases (CCOs, also referred to as carotenoid cleavage dioxygenases (CCDs) in the literature) are a new class of non-heme iron-type enzymes that oxidatively cleave double bonds in the conjugated carbon chain of carotenoids. The oxidative cleavage mechanism of these enzymes is not clear and both monooxygenase and dioxygenase mechanisms have been proposed for different carotenoid cleavage enzymes. CCOs have been described from plants, animals, fungi and cyanobacteria but little is known about their distribution and activities in bacteria other than cyanobacteria. We surveyed bacterial genome sequences for CCO homologs and report the characterization of CCO homologs identified in Novosphingobium aromaticivorans DSM 12444 (NOV1 and NOV2) and in Bradyrhizobium sp. (BRA-J and BRA-S). In vitro and in vivo assays with carotenoid and stilbene compounds were used to investigate cleavage activities of the recombinant enzymes. The NOV enzymes cleaved the interphenyl ?-? double bond of stilbenes with an oxygen functional group at the 4’ carbon (e.g. resveratrol, piceatannol, and rhaponticin) to the corresponding aldehyde products. Carotenoids and apocarotenoids were not substrates for these enzymes. The two homologous enzymes from Bradyrhizobium sp. did not possess carotenoid or stilbene cleavage oxygenase activities, but showed activity with farnesol. To investigate whether oxidative cleavage of stilbenes proceeds via a monooxygenase or dioxygenase reaction, oxygen labeling studies were conducted with NOV2. Our labeling studies show that double-bond cleavage of stilbenes occurs via a monooxygenase reaction mechanism. PMID:18478524

  18. 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

  19. 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

  20. Concise Synthesis of the Bryostatin A-Ring via Consecutive C-C Bond Forming Transfer Hydrogenations

    PubMed Central

    Lu, Yu; Krische, Michael J.

    2009-01-01

    Under the conditions of C-C bond forming transfer hydrogenation, 1,3-propanediol 1 engages in double asymmetric carbonyl allylation to furnish the C2-symmetric diol 2. Double ozonolysis of 2 followed by TBS protection delivers aldehyde 3, which is subject to catalyst directed carbonyl prenylation via transfer hydrogenation to deliver neopentyl alcohol 4 and, ultimately, the bryostatin A-ring 7. Through use of two consecutive C-C bond forming transfer hydrogenations, the Evans’ bryostatin A-ring 7 is prepared in less than half the manipulations previously reported. PMID:19586066

  1. Concise synthesis of the bryostatin A-ring via consecutive C-C bond forming transfer hydrogenations.

    PubMed

    Lu, Yu; Krische, Michael J

    2009-07-16

    Under the conditions of C-C bond forming transfer hydrogenation, 1,3-propanediol 1 engages in double asymmetric carbonyl allylation to furnish the C(2)-symmetric diol 2. Double ozonolysis of 2 followed by TBS protection delivers aldehyde 3, which is subject to catalyst directed carbonyl reverse prenylation via transfer hydrogenation to deliver neopentyl alcohol 4 and, ultimately, the bryostatin A-ring 7. Through use of two consecutive C-C bond forming transfer hydrogenations, the Evans' bryostatin A-ring 7 is prepared in less than half the manipulations previously reported. PMID:19586066

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

    PubMed

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

    2014-02-01

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

  3. 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.

  4. 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.

  5. Monitoring protein cleavage and concurrent disulfide bond assignment using thermospray LC/MS.

    PubMed

    Stachowiak, K; Otlewski, J; Polanowski, A; Dyckes, D F

    1990-01-01

    The arrangement of the disulfide bridges of Cucurbita maxima trypsin inhibitor, CMTI I, has been confirmed by enzymatic and chemical cleavages of the native protein and analysis of the resulting disulfide-bridged fragments using thermospray liquid chromatography/mass spectrometry. Although the disulfide bridges of CMTI I have recently been assigned from the x-ray crystallographic structure, direct chemical analysis of the S-S bonds using classical techniques proved difficult. The CMTI I molecule is extremely resistant to enzymatic digestion, and only one site of the peptide chain (Met-8) can be used efficiently for chemical cleavage. A series of degradative conditions were employed in the studies reported here. The progress of protein modification was monitored directly by high-performance liquid chromatography/thermospray mass spectrometry. The disulfide pairings could be deduced directly from the mass spectra of the peptides produced by the fragmentation processes and resolved by high-performance liquid chromatography. In two instances, fragments involving a disulfide bond were isolated and further analyzed, and these confirmed the mass spectral assignments. The disulfide bridges identified, 3-20, 10-22 and 16-28, correspond to those of the x-ray structure and are consistent with those assigned for two other closely related trypsin inhibitors. PMID:2134058

  6. Total Synthesis of Bryostatin 7 via C-C Bond Forming Hydrogenation: Merged Redox-Construction Events for Synthetic Efficiency

    PubMed Central

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

    2011-01-01

    The marine macrolide bryostatin 7 is prepared in 20 steps (longest linear sequence) and 36 total steps. A total of 5 C-C bonds are formed using hydrogenative methods. The present approach represents the most concise synthesis of any bryostatin reported, to date, setting the stage for practical syntheses of simplified functional analogues. PMID:21780806

  7. 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.

  8. Computational study of the effects of steric hindrance on amide bond cleavage.

    PubMed

    Matsubara, Toshiaki; Ueta, Chikako

    2014-09-25

    The reaction mechanism of amide bond cleavages of the 2,2,6,6-tetramethylpiperidine derivatives, which proceeds in methanol solvent under mild conditions, is examined by the density functional method (B3LYP) using a model substrate. We performed the calculations to clarify the reason why the amide bond is readily broken in the present system, on the basis of an experimentally proposed "proton switching pathway" that is different from the generally known mechanisms. As a result, it was found that the stepwise decomposition of the amide bond by the "proton switching pathway" significantly lowers the energy barrier. The delocalization of the ? electron in the -C(?O)-N< part is hindered by the steric effect of the four Me groups of the piperidine so that the acetyl group can easily rotate around the C-N axis and then the ?-H migrates to the amide N. The subsequent amide bond dissociation, which is thought to be a rate-determining step in the experiment, was very facile. The reaction is completed by the addition of methanol to the formed ketene. Both the energy barriers of the ?-H migration to the amide N and the methanol addition to ketene are largely decreased by the mediation of methanol solvent molecules. The rate-determining step of the entire reaction was found to be the ?-H migration. PMID:25209437

  9. 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.

  10. RhI-Catalyzed Decarbonylative Spirocyclization via C–C Cleavage of Benzocyclobutenones: An Efficient Approach to Access Functionalized Spirocycles

    PubMed Central

    Xu, Tao; Savage, Nikolas A.; Dong, Guangbin

    2014-01-01

    We describe a rhodium-catalyzed all-carbon spirocenter formation through a decarbonylative coupling of trisubstituted cyclic olefins and benzocyclobutenones via C–C activation. A [Rh(CO)2Cl]2/P(C6F5)3 metal-ligand combination was found to catalyze this transformation most efficiently. A range of diverse spirocyclic rings were synthesized in good to excellent yields and many sensitive functional groups were tolerated. Mechanistic study supports the hydrogen-transfer process that occurs via a ?-H elimination/decarbonylation pathway. PMID:24446067

  11. 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

  12. Catalytic C-O Bond Cleavage of 2-Aryloxy-1-arylethanols and Its Application to the Depolymerization of Lignin Related Polymers

    PubMed Central

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

    2010-01-01

    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

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

    PubMed

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

    2014-07-01

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

  14. Silver-catalyzed amidation of benzoylformic acids with tertiary amines via selective carbon-nitrogen bond cleavage.

    PubMed

    Zhang, Xiaobin; Yang, Wenchao; Wang, Lei

    2013-06-14

    A novel approach towards the synthesis of ?-ketoamides using tertiary amines as nitrogen group sources via C-N bond cleavage has been developed. In the presence of Ag2CO3 and K2S2O8, ?-keto acids reacted with tertiary amines to afford the corresponding ?-ketoamides in good yields. PMID:23598925

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

    SciTech Connect

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

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

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

    PubMed

    Domingo, Luis R; Pérez, Patricia

    2014-07-21

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

  18. 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.; (UIUC)

    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.

  19. An Unusual Carbon-Carbon Bond Cleavage Reaction During Phosphinothricin Biosynthesis

    PubMed Central

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

    2010-01-01

    Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture1. One such compound, phosphinothricin tripeptide (PTT), contains the unusual amino acid phosphinothricin (PT) attached to two alanine residues (Fig. 1). Synthetic PT (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 PTT biosynthesis 2-hydroxyethylphosphonate (HEP) is converted to hydroxymethylphosphonate (HMP) (Fig. 1)2. Reported here are the in vitro reconstitution of this unprecedented C(sp3)-C(sp3) bond cleavage reaction and X-ray crystal structures of the enzyme. The protein is a mononuclear non-heme 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 catalyzed by the 2-His-1-carboxylate mononuclear non-heme iron family of enzymes. PMID:19516340

  20. 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 Limão-Vieira and Malgorzata Smialek-Telega.

  1. Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from C-D quadrupolar splittings.

    PubMed Central

    Douliez, J P; Léonard, A; Dufourc, E J

    1995-01-01

    An expression for the C-C bond order parameter, SCC, of membrane hydrocarbon chains has been derived from the observed C-D bond order parameters. It allows calculation of the probability of each of the C-C bond rotamers and, consequently, the number of gauche defects per chain as well as their projected average length onto the bilayer normal, thus affording the calculation of accurate hydrophobic bilayer thicknesses. The effect of temperature has been studied on dilauroyl-, dimyristoyl-, and dipalmitoylphosphatidylcholine (DLPC, DMPC, DPPC) membranes, as has the effect of cholesterol on DMPC. The salient results are as follows: 1) an odd-even effect is observed for the SCC versus carbon position, k, whose amplitude increases with temperature; 2) calculation of SCC, from nonequivalent deuterons on the sn-2 chain of lipids, SCC2, leads to negative values, indicating the tendency for the C1-C2 bond to be oriented parallel to the bilayer surface; this bond becomes more parallel to the surface as the temperature increases or when cholesterol is added; 3) calculation on the sn-2 chain length can be performed from C1 to Cn, where n is the number of carbon atoms in the chain, and leads to 10.4, 12.2, and 13.8 A for DLPC, DMPC, and DPPC close to the transition temperature, TC, of each of the systems and to 9.4, 10.9, and 12.6 for T-TC = 30-40 degrees C, respectively; 4) separation of intra- and intermolecular motions allows quantitation of the number of gauche defects per chain, which is equal to 1.9, 2.7, and 3.5 for DLPC, DMPC, and DPPC near TC and to 2.7, 3.5, and 4.4 at T-TC = 30-40 degrees C, respectively. Finally, the validity of our model is discussed and compared with previously published models. PMID:7612816

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

    PubMed Central

    Hassan, Abbas; Krische, Michael J.

    2011-01-01

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

  3. Presolvated Low Energy Electron Attachment to Peptide Methyl esters in Aqueous Solution: C-O Bond Cleavage at 77K

    PubMed Central

    Kheir, Jeanette; Chomicz, Lidia; Engle, Alyson; Rak, Janusz; Sevilla, Michael D.

    2013-01-01

    In this study, the reactions of presolvated electrons with glycine methyl ester and N-acetylalanylalanine methyl ester (N-aAAMe) are investigated by electron spin resonance (ESR) spectroscopy and DFT calculations. Electrons were produced by gamma irradiation in neutral 7.5 M LiCl-D2O aqueous glasses at low temperatures. For glycine methyl ester electron addition at 77K results in both N-terminal deamination to form a glycyl radical and C-O ester bond cleavage to form methyl radicals. For samples of N-acetylalanylalanine methyl ester electrons are found to add to the peptide bonds at 77K and cleave the carboxyl ester groups to produce methyl radicals. On annealing to 160K electron adducts at the peptide links undergo chain scission to produce alanyl radicals and further annealing to 170K ?-carbon peptide backbone radicals are produced by hydrogen abstraction. DFT calculations for electron addition to the methyl ester portion of N-aAAMe show the cleavage reaction is highly favorable (free energy equals to ?30.7 kcal/mol) with the kinetic barrier of only 9.9 kcal/mol. A substantial electron affinity of the ester link (38.0 kcal/mol) provides more than sufficient energy to overcome this small barrier. Protonated peptide bond electron adducts, also show favorable N-C chain cleavage reactions of ?12.7 to ?15.5 kcal/mol with a barrier from 7.4 to 10.0 kcal/mol. The substantial adiabatic electron affinity (AEA) of the peptide bond and ester groups provides sufficient energy for the bond dissociation. PMID:23406302

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

    PubMed Central

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

    2010-01-01

    Prostacyclin is a potent mediator of vasodilation and anti-platelet aggregation. It is synthesized from prostaglandin H2 by prostacyclin synthase (PGIS), a member of Family 8 in the cytochrome P450 superfamily. Unlike most P450s, which require exogenous reducing equivalents and an oxygen molecule for mono-oxygenation, PGIS catalyzes an isomerization with an initial step of endoperoxide bond cleavage of prostaglandin H2 (PGH2). The low abundance of PGIS in natural tissues necessitates heterologous expression for studies of structure/function relationships and reaction mechanism. We report here a high-yield prokaryotic system for expression of enzymatically active human PGIS. The PGIS cDNA is modified by replacing the hydrophobic amino-terminal sequence with the more hydrophilic amino-terminal sequence from P450 2C5 and by adding a four-histidine tag at the carboxyl terminus. The resulting recombinant PGIS associates with host cell membranes and was purified to electrophoretic homogeneity by nickel affinity, hydroxyapatite and CM Sepharose column chromatography. The recombinant PGIS, with a heme:protein ratio of 0.9:1, catalyzes prostacyclin formation at a Km of 13.3 µM PGH2 and a Vmax of 980 per min. The dithionite-reduced PGIS binds CO with an on-rate of 5.6 × 105 M?1 s?1 and an off-rate of 15 s?1. The ferrous–CO complex of PGIS is very short-lived and decays at a rate of 0.7 s?1. Spectral binding assays showed that imidazole binds weakly to PGIS (Kd ~0.5 mM,) but clotrimazole, a bulky and rigid imidazole derivative, binds strongly (Kd ~1 µM). The transient nature of the CO complex and the weak imidazole binding seem to support an earlier proposal that PGIS active site has a limited space, but the tight binding of clotrimazole argues against this view. It appears that the heme distal pocket of PGIS is fairly adaptable to ligands of various structures. UV-visible absorption, magnetic circular dichroism and electron paramagnetic resonance spectra indicate that PGIS has a typical low-spin heme with a hydrophobic active site. PGIS catalyzes homolytic scission of the peroxide bond of a test substrate, 10-hydroperoxyoctadeca-8,12-dienoic acid, accompanied by formation of a heme intermediate with a Compound II-like optical spectrum. PMID:16406803

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  7. TRANSITION METAL ACTIVATION AND FUNCTIONALIZATION OF CARBON-HYDROGEN BONDS

    E-print Network

    Jones, William D.

    TRANSITION METAL ACTIVATION AND FUNCTIONALIZATION OF CARBON-HYDROGEN BONDS William D. Jones-H and C-C bond functionalization, and (4) carbon-fluorine bond activation. We have made progress in each in our proposal where we have had success. These include: (1) carbon-carbon bond cleavage reactions, (2

  8. A novel approach for C-C, C-N, and C-O bond formation reactions: a facile synthesis of benzophenazine, quinoxaline, and phenoxazine derivatives via ring opening of benzoxepines.

    PubMed

    Raju, Bhimapaka China; Prasad, Kasagani Veera; Saidachary, Gannerla; Sridhar, Balasubramanian

    2014-01-17

    A new one-pot protocol has been developed for the synthesis of benzophenazine, quinoxaline, and phenoxazine derivatives by the reaction of benzoxepine-4-carboxylates with benzene-1,2-diamines, ethane-1,2-diamine, and 2-aminophenols in the presence of Bi(OTf)3 (5 mol %) under mild conditions in very good yields. The present protocol opens a new way for C-C, C-N, and C-O bond-formation reactions in a single-step process. The structural assignment was confirmed by X-ray analysis. PMID:24328679

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

    SciTech Connect

    Bausch, M.

    1992-08-01

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

  10. C-H Bond Cleavage by Bioinspired Nonheme Oxoiron(IV) Complexes, Including Hydroxylation of n-Butane.

    PubMed

    Kleespies, Scott T; Oloo, Williamson N; Mukherjee, Anusree; Que, Lawrence

    2015-06-01

    The development of efficient and selective hydrocarbon oxidation processes with low environmental impact remains a major challenge of the 21st century because of the strong and apolar nature of the C-H bond. Naturally occurring iron-containing metalloenzymes can, however, selectively functionalize strong C-H bonds on substrates under mild and environmentally benign conditions. The key oxidant in a number of these transformations is postulated to possess an S = 2 Fe(IV)?O unit in a nonheme ligand environment. This oxidant has been trapped and spectroscopically characterized and its reactivity toward C-H bonds demonstrated for several nonheme iron enzyme classes. In order to obtain insight into the structure-activity relationships of these reactive intermediates, over 60 synthetic nonheme Fe(IV)(O) complexes have been prepared in various laboratories and their reactivities investigated. This Forum Article summarizes the current status of efforts in the characterization of the C-H bond cleavage reactivity of synthetic Fe(IV)(O) complexes and provides a snapshot of the current understanding of factors that control this reactivity, such as the properties of the supporting ligands and the spin state of the iron center. In addition, new results on the oxidation of strong C-H bonds such as those of cyclohexane and n-butane by a putative S = 2 synthetic Fe(IV)(O) species that is generated in situ using dioxygen at ambient conditions are presented. PMID:25751610

  11. Purification and characterization of carbon-phosphorus bond-cleavage enzyme from glyphosate degrading Pseudomonas putida T5.

    PubMed

    Selvi, A Arul; Manonmani, H K

    2015-01-01

    An inducible, carbon-phosphorus bond-cleavage enzyme was purified from cells of Pseudomonas putida T5 grown on N-phosphonomethyl glycine. The native enzyme had a molecular mass of approximately 70 kD and upon sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), yielded a homogeneous protein band with an apparent molecular mass of about 70 kD. Activity of purified enzyme was increased by 627-fold compared to the crude extract and showed pH and temperature optima of approximately 7 and 30°C, respectively. The purified enzyme had an apparent Km and Vmax of 3.7 mM and 6.8 mM/min, respectively, for its sole substrate N-phosphonomethyl glycine. The enzyme was inhibited by phenylmethylsulfonyl fluoride (PMSF), indicating the presence of serine at the active site. The enzyme was not inhibited by SDS, suggesting the absence of disulfide linkage in the enzyme. The enzyme was found to be inhibited by most of the metals studied except Mg(2+). Detergents studied also inhibited glyphosate acting as a carbon-phosphorus bond-cleavage enzyme. Thus initial characterization of the purified enzyme suggested that it could be used as a potential candidate for glyphosate bioremediation. PMID:24840030

  12. Use of a novel fluorinated organosulfur compound to isolate bacteria capable of carbon-sulfur bond cleavage.

    PubMed

    Van Hamme, Jonathan D; Fedorak, Phillip M; Foght, Julia M; Gray, Murray R; Dettman, Heather D

    2004-03-01

    The vacuum residue fraction of heavy crudes contributes to the viscosity of these oils. Specific microbial cleavage of C-S bonds in alkylsulfide bridges that form linkages in this fraction may result in dramatic viscosity reduction. To date, no bacterial strains have been shown conclusively to cleave C-S bonds within alkyl chains. Screening for microbes that can perform this activity was greatly facilitated by the use of a newly synthesized compound, bis-(3-pentafluorophenylpropyl)-sulfide (PFPS), as a novel sulfur source. The terminal pentafluorinated aromatic rings of PFPS preclude growth of aromatic ring-degrading bacteria but allow for selective enrichment of strains capable of cleaving C-S bonds. A unique bacterial strain, Rhodococcus sp. strain JVH1, that used PFPS as a sole sulfur source was isolated from an oil-contaminated environment. Gas chromatography-mass spectrometry analysis revealed that JVH1 oxidized PFPS to a sulfoxide and then a sulfone prior to cleaving the C-S bond to form an alcohol and, presumably, a sulfinate from which sulfur could be extracted for growth. Four known dibenzothiophene-desulfurizing strains, including Rhodococcus sp. strain IGTS8, were all unable to cleave the C-S bond in PFPS but could oxidize PFPS to the sulfone via the sulfoxide. Conversely, JVH1 was unable to oxidize dibenzothiophene but was able to use a variety of alkyl sulfides, in addition to PFPS, as sole sulfur sources. Overall, PFPS is an excellent tool for isolating bacteria capable of cleaving subterminal C-S bonds within alkyl chains. The type of desulfurization displayed by JVH1 differs significantly from previously described reaction results. PMID:15006770

  13. Use of a Novel Fluorinated Organosulfur Compound To Isolate Bacteria Capable of Carbon-Sulfur Bond Cleavage

    PubMed Central

    Van Hamme, Jonathan D.; Fedorak, Phillip M.; Foght, Julia M.; Gray, Murray R.; Dettman, Heather D.

    2004-01-01

    The vacuum residue fraction of heavy crudes contributes to the viscosity of these oils. Specific microbial cleavage of C—S bonds in alkylsulfide bridges that form linkages in this fraction may result in dramatic viscosity reduction. To date, no bacterial strains have been shown conclusively to cleave C—S bonds within alkyl chains. Screening for microbes that can perform this activity was greatly facilitated by the use of a newly synthesized compound, bis-(3-pentafluorophenylpropyl)-sulfide (PFPS), as a novel sulfur source. The terminal pentafluorinated aromatic rings of PFPS preclude growth of aromatic ring-degrading bacteria but allow for selective enrichment of strains capable of cleaving C—S bonds. A unique bacterial strain, Rhodococcus sp. strain JVH1, that used PFPS as a sole sulfur source was isolated from an oil-contaminated environment. Gas chromatography-mass spectrometry analysis revealed that JVH1 oxidized PFPS to a sulfoxide and then a sulfone prior to cleaving the C—S bond to form an alcohol and, presumably, a sulfinate from which sulfur could be extracted for growth. Four known dibenzothiophene-desulfurizing strains, including Rhodococcus sp. strain IGTS8, were all unable to cleave the C—S bond in PFPS but could oxidize PFPS to the sulfone via the sulfoxide. Conversely, JVH1 was unable to oxidize dibenzothiophene but was able to use a variety of alkyl sulfides, in addition to PFPS, as sole sulfur sources. Overall, PFPS is an excellent tool for isolating bacteria capable of cleaving subterminal C—S bonds within alkyl chains. The type of desulfurization displayed by JVH1 differs significantly from previously described reaction results. PMID:15006770

  14. Mild and Robust Redox-Neutral Pd/C-Catalyzed Lignol ?-O-4' Bond Cleavage Through a Low-Energy-Barrier Pathway.

    PubMed

    Galkin, Maxim V; Dahlstrand, Christian; Samec, Joseph S M

    2015-07-01

    A Pd/C catalyzed redox neutral C?O bond cleavage of 2-aryloxy-1-arylethanols has been developed. The reactions are carried out at 80?°C, in air, using a green solvent system to yield the aryl ketones in near quantitative yields. Addition of catalytic amounts of a hydrogen source to the reaction mixture activates the catalyst to proceed through a low energy barrier pathway. Initial studies support a transfer hydrogenolysis reaction mechanism that proceeds through an initial dehydrogenation followed by an enol adsorption to Pd/C and a reductive C?O bond cleavage. PMID:25925736

  15. Cleavage of thymine N3H bonds by low-energy electrons attached Magali Theodore 1

    E-print Network

    Simons, Jack

    ´odore 1 , Monika Sobczyk, Jack Simons * Chemistry Department and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT 84112, USA Received 9 April 2006; accepted 8 May 2006 or to phosphate P@O p* orbitals to cleave sugar­phosphate C­O bonds or base­sugar N1­C bonds. We also studied

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

    PubMed Central

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

    2013-01-01

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

  17. 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.

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

    SciTech Connect

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

    1993-12-31

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

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

    PubMed

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

    2014-02-27

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

  20. Million-fold activation of the [Fe2(?-O)2] diamond core for C-H bond cleavage

    PubMed Central

    Xue, Genqiang; De Hont, Raymond; Münck, Eckard; Que, Lawrence

    2010-01-01

    In biological systems, the cleavage of strong C–H bonds is often carried out by iron centers – such as the methane monooxygenase in methane hydroxylation – through dioxygen activation mechanisms. High valent species with [Fe2(?-O)2] diamond cores are thought to act as the oxidizing moieties, but the synthesis of complexes that cleave strong C–H bonds efficiently has remained a challenge. We report here the conversion of a synthetic complex with a valence-delocalized [Fe3.5(?-O)2Fe3.5]3+ diamond core (1) into a complex with a valence-localized [HO-FeIII-O-FeIV=O]2+ open core (4), which cleaves C–H bonds over million-fold faster. This activity enhancement results from three factors: the formation of a terminal oxoiron(IV) moiety, the conversion of the low-spin (S = 1) FeIV=O center to a high-spin (S = 2) center, and the concentration of the oxidizing capability to the active terminal oxoiron(IV) moiety. This suggests that similar isomerization strategies might be employed by nonheme diiron enzymes. PMID:20414242

  1. 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

  2. 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

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

    PubMed

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

    2014-11-21

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

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

    SciTech Connect

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

    1995-05-25

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

  5. 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.

  6. Vibrational state controlled bond cleavage in the photodissociation of isocyanic acid (HNCO)

    NASA Astrophysics Data System (ADS)

    Brown, Steven S.; Berghout, H. Laine; Crim, F. Fleming

    1995-06-01

    We report the bond selected photodissociation of isocyanic acid (HNCO). This molecule dissociates from its first excited singlet state, breaking either the N-H bond to form H+NCO (X 2?) or the C-N bond to form NH (a 1?)+CO (1?+). The threshold for production of NH lies about 3900 cm-1 above that of NCO, and we detect both of these channels by laser induced fluorescence on either the NH or the NCO fragment. Dissociating the molecule out of a vibrationally excited state on its ground electronic surface containing four quanta of N-H stretch (4?1) enhances the efficiency of the NCO channel over the NH channel by a factor of at least 20. We reach this conclusion by comparing the results of such a vibrationally mediated photodissociation experiment to those from a conventional single photon dissociation at the same total energy (about 1000 cm-1 above the threshold for the NH channel). Our estimate of the branching ratio in the one photon dissociation at this energy is roughly ?NCO/?NH?20, and it grows to ?NCO/?NH?400 in the vibrationally mediated photodissociation.

  7. Transition-metal-free oxidative carboazidation of acrylamides via cascade C-N and C-C bond-forming reactions.

    PubMed

    Qiu, Jun; Zhang, Ronghua

    2014-07-01

    A novel transition-metal-free oxidative carboazidation of acrylamides using inexpensive NaN3 and K2S2O8 was achieved, which not only provided an efficient method to prepare various N3-substituted oxindoles, but also represented a novel strategy for C-N and C-C bond formation via a free-radical cascade process. This transformation exhibits excellent functional group tolerance, affording the desired oxindoles in good to excellent yields. PMID:24854242

  8. Silver-mediated radical cyclization of alkynoates and ?-keto acids leading to coumarins via cascade double C-C bond formation.

    PubMed

    Yan, Kelu; Yang, Daoshan; Wei, Wei; Wang, Fen; Shuai, Yuanyuan; Li, Qiannan; Wang, Hua

    2015-02-01

    A novel and convenient silver-mediated radical cyclization method for the synthesis of coumarin derivatives via the direct difunctionalization of alkynoates with ?-keto acids through double C-C bond formation under mild conditions has been developed. This new method is highly efficient and practical, and the starting materials are readily prepared. The present method should provide a useful strategy for the construction of coumarin motifs. PMID:25562802

  9. C-H vs C-C Bond Activation of Acetonitrile and Benzonitrile via Oxidative Addition: Rhodium vs Nickel and Cp* vs Tp

    E-print Network

    Jones, William D.

    C-H vs C-C Bond Activation of Acetonitrile and Benzonitrile via Oxidative Addition: Rhodium vs@chem.rochester.edu Abstract: The photochemical reaction of (C5Me5)Rh(PMe3)H2 (1) in neat acetonitrile leads to formation of the C-H activation product, (C5Me5)Rh(PMe3)(CH2CN)H (2). Thermolysis of this product in acetonitrile

  10. 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 kJ·mol(-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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

    Xue, Genqiang; Pokutsa, Alexander; Que, Lawrence

    2011-01-01

    An [FeIV2(?-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(?-O)2] cores. We report here that water or alcohol substrates can activate synthetic [FeIIIFeIV(?-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(?-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(?-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(?-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

  13. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis

    SciTech Connect

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

    1982-05-25

    The objective of this project is to determine the proportions of the various kinds of connecting links in coal and how they can best be broken - in other words, to determine the structure of bituminous coal, with emphasis on the cross-links and breakable single bonds. An extraction of Illinois No. 6 coal, some swelling experiments on Illinois No. 6 coal products, and some extractions of other recently acquired coal samples are described. The results show that on long heating at a high solvent-to-coal ratio ethanolamine does not extract as much material from whole coal as either BnNH/sub 2/ or EDA, yet the swelling ratio of the extracted coal is greater than with the other amines. BnNH/sub 2/ swells both EDA/DMSO- and pyridine-extracted coals better than other amine solvents tested, including ethanolamine. The EDA/DMSO-extracted coal is swollen more by all the solvents tested than pyridine-extracted coal. Preliminary results show that solvents swell EDA/DMSO-extracted coal more when either t-BuOK or tetraalkylammonium hydroxides are added to the solvents than when the pure solvents are used but are not conclusive. Results from pyridine extractions of several coals of varying ranks show that less coal is extracted by pyridine as the coal rank increases. A series of oxidations with nitric acid and sodium hypochlorite are described. Model compounds are being oxidized to determine the best way to distinguish between single and multiple methylene groups. Results from ESR measurements on a pyridine extraction of Illinois No. 6 coal are reported. Most of the free spins remain in the insoluble fractions and 38 +- 7% of the spins are lost during the extraction.

  14. Metal-Free Reductive Cleavage of C–N and S–N Bonds by Photoactivated Electron Transfer from a Neutral Organic Donor**

    PubMed Central

    O'Sullivan, Steven; Doni, Eswararao; Tuttle, Tell; Murphy, John A

    2014-01-01

    A photoactivated neutral organic super electron donor cleaves challenging arenesulfonamides derived from dialkylamines at room temperature. It also cleaves a) ArC–NR and b) ArN–C bonds. This study also highlights the assistance given to these cleavage reactions by the groups attached to N in (a) and to C in (b), by lowering LUMO energies and by stabilizing the products of fragmentation. PMID:24311295

  15. Indium(III) chloride-catalyzed oxidative cleavage of carbon–carbon multiple bonds by tert-butyl hydroperoxide in water—a safer alternative to ozonolysis

    Microsoft Academic Search

    Brindaban C. Ranu; Sukalyan Bhadra; Laksmikanta Adak

    2008-01-01

    An efficient and general method for the oxidative cleavage of alkenes and alkynes using tert-butyl hydroperoxide and indium(III) chloride as catalyst in water to give the corresponding carboxylic acids or ketones has been achieved. The reaction conditions are compatible with sensitive moieties such as peptide bonds, tert-butyl carboxylic esters and N-Boc-protected tryptophan. The catalyst could be recycled.

  16. Reaction of SO2 with pure and metal-doped MgO: Basic principles for the cleavage of S-O bonds

    NASA Astrophysics Data System (ADS)

    Rodriguez, J. A.; Jirsak, T.; González, L.; Evans, J.; Pérez, M.; Maiti, A.

    2001-12-01

    Synchrotron-based high-resolution photoemission, x-ray absorption near-edge spectroscopy, and first-principles density-functional calculations are used to examine the interaction of SO2 with pure and modified surfaces of magnesium oxide. On a MgO(100) single crystal, SO2 reacts with O centers to form SO3 and SO4 species. The bonding interactions with the Mg cations are weak and do not lead to cleavage of S-O bonds. An identical result is found after adsorbing SO2 on pure stoichiometric powders of MgO and other oxides (TiO2, Cr2O3, Fe2O3, NiO, CuO, ZnO, V2O5, CeO2, BaO). In these systems, the occupied cations bands are too stable for effective bonding interactions with the LUMO of SO2. To activate an oxide for S-O bond cleavage, one has to create occupied metal states above the valence band of the oxide. DF calculations predict that in the presence of these "extra" electronic states the adsorption energy of SO2 should increase, and there should be a significant oxide?SO2(LUMO) charge transfer that facilitates the cleavage of the S-O bonds. In this article, we explore three different approaches (formation of O vacancies, promotion with alkali metals, and doping with transition metals) that lead to the activation of SO2 and S-O bond breaking on MgO and oxides in general. Basic principles for a rational design of catalysts with a high efficiency for the destruction of SO2 are presented.

  17. 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

  18. Carbon–carbon 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 carbon–carbon (C–C) bonds is an effective strategy in building functional molecules. The C–C 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 C–C bond activation. Here we describe an organocatalytic activation of C–C bonds through the addition of an NHC to a ketone moiety that initiates a C–C 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 C–C bond activation process. Structurally diverse and multicyclic compounds could be obtained with high optical purities via an atom and redox economic process. PMID:25652912

  19. Stability of the C-C covalent bonds in fullerenes in the solid body-vapor structure during the thermodynamic action by a quasi-pulsed electron beam

    NASA Astrophysics Data System (ADS)

    Semenov, A. P.; Semenova, I. A.; Churilov, G. N.

    2015-04-01

    The explosive evaporation of a fullerene mixture in a vacuum of ˜10-2 Pa during the contraction of a 1-kW hollow electron beam into a spot on a substrate in a time of 0.1-1 s is considered. A comparative analysis of the Raman spectra and the absorption electron spectra of a starting fullerene mixture powder and the vapor condensates shows that the evaporation of C60 and C70 fullerenes proceeds without breaking C-C covalent bonds.

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

    PubMed

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

    2014-04-01

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

  1. Electroreduction of a series of alkylcobalamins: mechanism of stepwise reductive cleavage of the Co-C bond.

    PubMed

    Birke, Ronald L; Huang, Qingdong; Spataru, Tudor; Gosser, David K

    2006-02-15

    The electrochemical (EC) reduction mechanism of methylcobalamin (Me-Cbl) in a mixed DMF/MeOH solvent in 0.2 M tetrabutylammonium fluoroborate electrolyte was studied as a function of temperature and solvent ratio vs a nonaqueous Ag/AgCl/Cl(-) reference electrode. Double-potential-step chronoamperometry allowed the rate constant of the subsequent homogeneous reaction to be measured over the temperature range from 0 to -80 degrees C in 40:60 and 50:50 DMF:MeOH ratios. Activation enthalpies are 5.8 +/- 0.5 and 7.6 +/- 0.3 kcal/mol in the 40:60 and 50:50 mixtures of DMF/MeOH, respectively. Digital simulation and curve-fitting for an EC mechanism using a predetermined homogeneous rate constant of 5.5 x 10(3) s(-1) give E degrees' = -1.466 V, k degrees = 0.016 cm/s, and alpha = 0.77 at 20 degrees C for a quasi-reversible electrode process. Digital simulation of the results of Lexa and Savéant (J. Am. Chem. Soc. 1978, 100, 3220-3222) shows that the mechanism is a series of stepwise homogeneous equilibrium processes with an irreversible step following the initial electron transfer (ET) and allows estimation of the equilibrium and rate constants of these reactions. An electron coupling matrix element of H(kA) = (4.7 +/- 1.1) x 10(-4) eV ( approximately 46 J/mol) is calculated for the nonadiabatic ET step for reduction to the radical anion. A reversible bond dissociation enthalpy for homolytic cleavage of Me-Cbl is calculated as 31 +/- 2 kcal/mol. The voltammetry of the ethyl-, n-propyl-, n-butyl-, isobutyl-, and adenosyl-substituted cobalamin was studied, and estimated reversible redox potentials were correlated with Co-C bond distances as determined by DFT (B3LYP/ LANL2DZ) calculations. PMID:16464094

  2. 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, E-mail: msarma@iitg.ernet.in [Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781 039 (India)

    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 ?{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 ?{sup *} orbital of the base to the ?{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.

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

    SciTech Connect

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

    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.``

  4. Assessment of the Intermediacy of Arylpalladium Carboxylate Complexes in the Direct Arylation of Benzene: Evidence for C-H Bond Cleavage by "Ligandless" Species

    PubMed Central

    Tan, Yichen; Hartwig, John F.

    2011-01-01

    Palladium-catalyzed direct arylations of benzene have been proposed to occur by the generation of a phosphine-ligated arylpalladium pivalate complex LPd(Ar)(OPiv) and reaction of this complex with benzene. We have isolated an example of the proposed intermediate and evaluated whether this complex reacts with benzene to form the biaryl products of the catalytic process. In contrast to the proposed mechanism, no biaryl product was formed from cleavage of the benzene C-H bond by LPd(Ar)(OPiv). However, reactions of LPd(Ar)OPiv with benzene and additives that displace or consume the phosphine ligand formed the arylated products in good yield, suggesting that a “ligandless” arylpalladium(II) carboxylate complexes undergoes the C-H cleavage step. Consistent with this conclusion, we found that reactions catalyzed by Pd(OAc)2 without ligand occur faster than, and with comparable selectivities to, reactions catalyzed by Pd(OAc)2 and phosphine ligand. PMID:21314146

  5. 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

  6. Identification and cleavage of breakable single bonds by selective oxidation, reduction, and hydrolysis. Quarterly report No. 13, October 1-December 31, 1981

    SciTech Connect

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

    1982-02-26

    Bituminous coal is assumed to consist mostly of aggregates of condensed aromatic and aliphatic rings which are connected and made soluble by crosslinks containing single bonds. The objective of this project is to determine the structure of bituminous coal with emphasis on the crosslinks and breakable single bonds. During this past quarter the following studies were conducted on Illinois No. 6 coal: extraction with benzylamine (BnH/sub 2/), ethanolamine, ethylenediamine (EDA), pyridine; saponification of some toluene-insoluble, pyridine-soluble (TIPS) fraction; cleavages by amines; oxidation with aqueous NaOCl of butylated and methylated pyridine-extracted coal; decarboxylation on black acids. The investigations dealt with two kinds of connecting links in coal, which are designated as ester and ether groups. The ester groups are cleaved by strongly basic amines (to give amides) at 25/sup 0/C and by alcoholic KOH at 100/sup 0/C (to give salts and alcohols or phenols). Both esters and ethers are cleaved by HI or ZnCL/sub 2/ in pyridine at or below 50/sup 0/C. The ethers are also cleaved by BnNH/sub 2/, EDA, and EDA/DMSO to nearly the same extent on several days heating at 100/sup 0/C. Although a cleavage of model ethers by amines were not established, the parallel easy reactions of HI and ZnCl/sub 2/ and the slow 100/sup 0/C reactions of amines on coal lead the authors to designate the non-ester cleavages as ether cleavages. (ATT)

  7. Heterolytic cleavage of hydrogen by an iron hydrogenase model: an Fe-H???H-N dihydrogen bond characterized by neutron diffraction.

    PubMed

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

    2014-05-19

    Hydrogenase enzymes in nature use hydrogen as a fuel, but the heterolytic cleavage of H-H bonds cannot be readily observed in enzymes. Here we show that an iron complex with pendant amines in the diphosphine ligand cleaves hydrogen heterolytically. The product has a strong Fe-H???H-N dihydrogen bond. The structure was determined by single-crystal neutron diffraction, and has a remarkably short H???H distance of 1.489(10)?Å between the protic N-H(?+) and hydridic Fe-H(?-) part. The structural data for [Cp(C5F4N)FeH(P(tBu)2N(tBu)2H)](+) provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes. These results now provide a full picture for the first time, illustrating structures and reactivity of the dihydrogen complex and the product of the heterolytic cleavage of H2 in a functional model of the active site of the [FeFe] hydrogenase enzyme. PMID:24757087

  8. Iron carbonyl complexes from 2-[2,3-diaza-4-(2-thienyl)buta-1,3-dienyl]thiophene: N?N bond cleavage and cyclometalation

    Microsoft Academic Search

    Chi-Jeh Lin; Wen-Shu Hwang; Michael Y Chiang

    2001-01-01

    When thienyl Schiff base 1, derived from 2-formylthiophene and hydrazine, reacted with Fe2(CO)9 in n-hexane, three major complexes were obtained: (1) a diironhexacarbonyl complex with two 2-thienylmethylideneamido bridging ligands 2, which resulted from the ?N?N? bond cleavage of ligand 1; (2) a doubly cyclometalated di-?-di-(?1:?2-thienyl; ?1:?1(N))bis(hexacarbonyldiiron) complex (3); and (3) a cyclometalated (?-?1:?2-thienyl; ?1:?1(N))hexacarbonyldiiron complex (4). Molecular structures of compounds

  9. Electron-pair distributions in the C=C double bond. Effects of a push-pull substitution

    SciTech Connect

    Marcos, E.S.; Sanz, J.F. (Univ. of Sevilla (Spain)); Karafiloglou, P. (Aristotelian Univ. of Thessaloniki (Greece))

    1990-04-05

    By application of a recently developed method, the populations of ionic and spin-alternant electron-pair distributions are calculated in ethylene, aminoethylene, nitroethylene, and 2-nitroethenamine, one of the simplest push-pull ethylenes. Occupation numbers, giving a measure of the existence of an ionic electron pair in one carbon atom and of a spin-alternant electron pair in the two carbon atoms of the ethylenic double bond, are investigated from ab initio MO wave functions. The effects of either an electron-donating or an electron-withdrawing group and the cooperative push-pull substitution are discussed.

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

    NASA Astrophysics Data System (ADS)

    Hörvin Billsten, Helena; Zigmantas, Donatas; Sundström, Villy; Polívka, Tomáš

    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.

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

    PubMed

    Biswas, Abhijit; Banerjee, Arindam

    2014-12-01

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

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

    PubMed

    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

  13. 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

  14. 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.

  15. On-line cleavage of disulfide bonds by soluble and immobilized tris-(2-carboxyethyl)phosphine using sequential injection analysis

    Microsoft Academic Search

    Paraskevas D. Tzanavaras; Constantina Mitani; Aristidis Anthemidis; Demetrius G. Themelis

    Reduction of disulfide bonds is – in many cases – a critical pretreatment step for the determination of thiols in real samples. This study reports the first systematic investigation of the potentials of the on-line reduction of disulfide bonds under flow conditions in a sequential injection setup. One of the most promising reducing agents, tris-(2-carboxyethyl)phosphine (TCEP) was selected for this

  16. 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.

  17. Iron-oxidation-state-dependent O-O bond cleavage of meta-chloroperbenzoic acid to form an iron(IV)-oxo complex

    PubMed Central

    Ray, Kallol; Lee, Sang Mok; Que, Lawrence

    2008-01-01

    The mechanism of formation of [FeIV(O)(N4Py)]2+ (2, N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine) from the reaction of [FeII(N4Py)(CH3CN)]2+ (1) with m-chloroperbenzoic acid (mCPBA) in CH2Cl2 at ?30 °C has been studied on the basis of the visible spectral changes observed and the reaction stoichiometry. It is shown that the conversion of 1 to 2 in 90% yield requires 1.5 equiv peracid and takes place in two successive one-electron steps via an [FeIII(N4Py)OH]2+(3) intermediate. The first oxidation step uses 0.5 equiv peracid and produces 0.5 equiv 3-chlorobenzoic acid, while the second step uses 1 equiv peracid and affords byproducts derived from chlorophenyl radical. We conclude that the FeII(N4Py) center promotes O-O bond heterolysis, while the FeIII(N4Py) center favors O-O bond homolysis, so the nature of O-O bond cleavage is dependent on the iron oxidation state. PMID:18443654

  18. 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

  19. Transition state for intramolecular C–H bond cleavage in [(LCu)2(?-O)2]2+ (L?=?1,4,7-tribenzyl-1,4,7-triazacyclononane)

    Microsoft Academic Search

    Christopher J. Cramer; Youngshang Pak

    2001-01-01

    .   Hybrid quantum mechanical\\/molecular mechanical electronic structure calculations reveal the transition state for C–H bond\\u000a cleavage in [(LCu)2 (?-O)2]2+ (L=1,4,7-tribenzyl-1,4,7-triazacyclononane) to be consistent with a hydrogen-atom-transfer mechanism from carbon to oxygen.\\u000a At the MPW1K\\/double-zeta effective core potential(+)|univeral force field level, 0?K activation enthalpies for the parent,\\u000a p-CF3, and p-OH substituted benzyl systems are predicted to be 8.8, 9.5, and 7.8?kcal\\/mol.

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

    PubMed

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

    2010-11-21

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

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

    PubMed

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

    2015-07-01

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

  2. Silylations of Arenes with Hydrosilanes: From Transition-Metal-Catalyzed C?X Bond Cleavage to Environmentally Benign Transition-Metal-Free C?H 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 C?H 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

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

    PubMed

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

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

    SciTech Connect

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

    2013-11-21

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

  5. 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. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Wang, Xiaoping [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Hoffmann, Christina [Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); DuBois, Daniel L. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Bullock, R. Morris [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

    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-H?+ and hydridic Fe-H?-. 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.

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

    PubMed Central

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

    2012-01-01

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

  7. Glycosidic Bond Cleavage is Not Required for Phytosteryl Glycoside-Induced Reduction of Cholesterol Absorption in Mice

    PubMed Central

    Lin, Xiaobo; Ma, Lina; Moreau, Robert A.

    2012-01-01

    Phytosteryl glycosides occur in natural foods but little is known about their metabolism and bioactivity. Purified acylated steryl glycosides (ASG) were compared with phytosteryl esters (PSE) in mice. Animals on a phytosterol-free diet received ASG or PSE by gavage in purified soybean oil along with tracers cholesterol-d7 and sitostanol-d4. In a three-day fecal recovery study, ASG reduced cholesterol absorption efficiency by 45 ± 6% compared with 40 ± 6% observed with PSE. Four hours after gavage, plasma and liver cholesterol-d7 levels were reduced 86% or more when ASG was present. Liver total phytosterols were unchanged after ASG administration but were significantly increased after PSE. After ASG treatment both ASG and deacylated steryl glycosides (SG) were found in the gut mucosa and lumen. ASG was quantitatively recovered from stool samples as SG. These results demonstrate that ASG reduces cholesterol absorption in mice as efficiently as PSE while having little systemic absorption itself. Cleavage of the glycosidic linkage is not required for biological activity of ASG. Phytosteryl glycosides should be included in measurements of bioactive phytosterols. PMID:21538209

  8. Mechanistic elucidation of the stepwise formation of a tetranuclear manganese pinned butterfly cluster via N-N bond cleavage, hydrogen atom transfer, and cluster rearrangement.

    PubMed

    Hamilton, Clifton R; Gau, Michael R; Baglia, Regina A; McWilliams, Sean F; Zdilla, Michael J

    2014-12-31

    A mechanistic pathway for the formation of the structurally characterized manganese-amide-hydrazide pinned butterfly complex, Mn4(?3-PhN-NPh-?(3)N,N')2(?-PhN-NPh-?(2)-N,N')(?-NHPh)2L4 (L = THF, py), is proposed and supported by the use of labeling studies, kinetic measurements, kinetic competition experiments, kinetic isotope effects, and hydrogen atom transfer reagent substitution, and via the isolation and characterization of intermediates using X-ray diffraction and electron paramagnetic resonance spectroscopy. The data support a formation mechanism whereby bis[bis(trimethylsilyl)amido]manganese(II) (Mn(NR2)2, where R = SiMe3) reacts with N,N'-diphenylhydrazine (PhNHNHPh) via initial proton transfer, followed by reductive N-N bond cleavage to form a long-lived Mn(IV) imido multinuclear complex. Coordinating solvents activate this cluster for abstraction of hydrogen atoms from an additional equivalent of PhNHNHPh resulting in a Mn(II)phenylamido dimer, Mn2(?-NHPh)2(NR2)2L2. This dimeric complex further assembles in fast steps with two additional equivalents of PhNHNHPh replacing the terminal silylamido ligands with ?(1)-hydrazine ligands to give a dimeric Mn2(?-NHPh)2(PhN-NHPh)2L4 intermediate, and finally, the addition of two additional equivalents of Mn(NR2)2 and PhNHNHPh gives the pinned butterfly cluster. PMID:25424971

  9. Direct evidence for preferential {beta} C-H bond cleavage resulting from 248 nm photolysis of the n-propyl radical using selectively-deuterated 1-bromopropane precursors

    SciTech Connect

    Wang, Z.; Mathews, M.G.; Koplitz, B. [Tulane Univ., New Orleans, LA (United States)

    1995-05-04

    A series of selectively deuterated 1-bromopropane precursors have been used to study site-specific photolysis in the n-propyl radical. A two-color photolysis approach (222 nm followed by 248 nm radiation) is used to create an intermediate photofragment and produce an H or a D atom, which is detected by 1 + 1 resonance ionization through Lyman-{alpha}. Target precursors are BrCH{sub 2}CD{sub 2}CD{sub 3}, BrCD{sub 2}CH{sub 2}CD{sub 3}, and BrCD{sub 2}CD{sub 2}CH{sub 3} as well as BrCD{sub 2}CH{sub 2}CH{sub 3}, BrCH{sub 2}CD{sub 2}CH{sub 3}, and BrCH{sub 2}CH{sub 2}CD{sub 3}. The `enhanced` H (or D) atom signals clearly demonstrate that C-H (or C-D) bond cleavage at the {beta} position is strongly favored. The net enhancement process undoubtedly involves photolysis of an intermediate, almost certainly the n-propyl radical. A comparison with systems involving ethyl and isopropyl radical photolysis is also presented. 14 refs., 4 figs.

  10. Direct, Redox Neutral Prenylation and Geranylation of Secondary Carbinol C-H Bonds: C4 Regioselectivity in Ruthenium Catalyzed C-C Couplings of Dienes to ?-Hydroxy Esters

    PubMed Central

    Leung, Joyce C.; Geary, Laina M.; Chen, Te-Yu; Zbieg, Jason R.

    2012-01-01

    The ruthenium catalyst generated in situ from Ru3(CO)12 and tricyclohexylphosphine, PCy3, promotes the redox-neutral C-C coupling of aryl substituted ?-hydroxy esters to isoprene and myrcene at the diene C4-position, resulting in direct carbinol C-H prenylation and geranylation, respectively. This process enables direct conversion of secondary to tertiary alcohols in the absence of stoichiometric byproducts or premetallated reagents, and is the first example of C4-regioselectivity in catalytic C-C couplings of 2-substituted dienes to carbonyl partners. Mechanistic studies corroborate a catalytic cycle involving diene-carbonyl oxidative coupling. PMID:22985393

  11. Sequence-Specific Ultrasonic Cleavage of DNA

    PubMed Central

    Grokhovsky, Sergei L.; Il'icheva, Irina A.; Nechipurenko, Dmitry Yu.; Golovkin, Michail V.; Panchenko, Larisa A.; Polozov, Robert V.; Nechipurenko, Yury D.

    2011-01-01

    We investigated the phenomenon of ultrasonic cleavage of DNA by analyzing a large set of cleavage patterns of DNA restriction fragments using polyacrylamide gel electrophoresis. The cleavage intensity of individual phosphodiester bonds was found to depend on the nucleotide sequence and the position of the bond with respect to the ends of the fragment. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined by multivariate statistical analysis. We observed a remarkable enhancement of the mean values of the relative intensities of cleavage (cleavage rates) in phosphodiester bonds following deoxycytidine, which diminished in the row of dinucleotides: d(CpG) > d(CpA) > d(CpT) >> d(CpC). The cleavage rates for all pairs of complementary dinucleotides were significantly different from each other. The effect of flanking nucleotides in tetranucleotides on cleavage rates of all 16 types of central dinucleotides was also statistically significant. The sequence-dependent ultrasonic cleavage rates of dinucleotides are consistent with reported data on the intensity of the conformational motion of their 5?-deoxyribose. As a measure of local conformational dynamics, cleavage rates may be useful for characterizing functional regions of the genome. PMID:21190663

  12. Chords: Em 022000 Em Em Em Em C C C C

    E-print Network

    Reiners, Peter W.

    Verse 1 Chorus Verse 2 Chorus Verse 3 Chords: Em 022000 C 035553 G 320002 F 133211 Intro: Em Em Em Em C C C C Em Em Em Em C C C C Em Em Em Em C C C C Em Em Em Em C C C C Verse: Em Em Em Em C C C C G G G G G G G G Em Em Em Em C C C C G G G G G G G G Em Em Em Em C C C C G G G G G G G G Em Em Em Em C C

  13. 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 ?-{3-(pyridin-2-yl)-pyrazolato} and 3-(pyridin-2-yl)-1H-pyrazole ligands attached to each of the Cu(II) centre atom. The copper(II) ion assisted the cleavage of the CbenzoylN bond afforded a 3-(pyridin-2-yl)-1H-pyrazole molecule. Deprotonation of the 3-(pyridin-2-yl)-1H-pyrazole gave a 3-(pyridin-2-yl)-pyrazolato, which subsequently reacted with the Cu(II) ion to give the {3-(pyridin-2-yl)-pyrazolato}{3-(pyridin-2-yl)-1H-pyrazole}Cu(II) product moiety. The structure of the dinuclear complex was confirmed by x-ray crystallography. The complex crystallized in a monoclinic crystal system with P2(1)/n space group and cell dimensions of a = 12.2029(8) Å, b = 11.4010(7) Å, c = 14.4052(9) Å and ? = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (? = 116 dm3 mol-1 cm-1) supports the presence of Cu(II) centres.

  14. 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. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia); Kassim, Mohammad B. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor, Malaysia and Fuel Cell Institute, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia)

    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 ?-(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 ? = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (? = 116 dm{sup 3} mol{sup ?1} cm{sup ?1}) supports the presence of Cu(II) centres.

  15. C?C and C?H bond activation of 1,2-propanedioxy by atomic oxygen on Ag(110): Effects of CO-adsorbed oxygen on reaction mechanism

    NASA Astrophysics Data System (ADS)

    Ayre, Caroline R.; Madix, Robert J.

    1994-02-01

    The stability of adsorbed 1,2-propanedioxy OCH(CH 3)CH 2O, generated via O?H bond activation of 1,2-propanediol by oxygen adatoms on Ag(110), has been shown to be sensitive to the relative concentrations of 1,2-propanedioxy and O (a). When the concentration of O (a) is sufficiently large, OCH(CH 3)CH 2O (a) is formed via O?H bond activation upon the adsorption of 1,2-propanediol at 175 K. C?H bond activation, nucleophilic attack by O (a) and C?C bond scission subsequently occur to yield formaldehyde, water, formate and acetate by 275 K. Acetol CH 3C(?O)CH 2OH evolves at 335 K, driven from the surface either by the onset of the conversion of CH 3COO (a) to HCOO (a) and CO 2(g) or by through-surface interactions. CO 2(g), H 2O (g), acetol, lactaldehyde CH 3CH(OH)CH??O and 1,2-propanediol evolve at 360 K. Production of pyruvaldehyde CH 3C(?O)CH?O, acetol, and lactaldehyde occurs at 415 K and is accompanied by the evolution of additional CO 2(g) and H 2)O (g) due to formate decomposition in the presence of O (a)(OH (a)). No H 2(g) evolves. Residual acetate decomposes to yield CO 2(g), CH 3COOH (g), and CH 2?C?O (g) in the absence of O (a) near 580-620 K. The evolution of H 2CO (g) and H 2)O (g) at 275 K and the production of acetol at 335 K suggest that initial C?H bond activation occurs preferentially at the central carbon of 1,2-propanedioxy. The production of lactaldehyde at both 360 and 415 K and pyruvaldehyde at 415 K indicates that with heating subsequent C?H bond activation occurs at carbon-1. Furthermore, these results demonstrate that O?H and C?H bond activation and C?C bond scission are characteristic oxidation mechanisms for diols on oxygen-activated Ag(110).

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

    PubMed

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

    2002-11-13

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

  17. Bonding

    MedlinePLUS

    ... is a procedure that uses a tooth-colored composite resin (plastic) to repair a tooth. Bonding can ... cleaned regularly by a dental hygienist. Risks The composite resin used in bonding isn't nearly as ...

  18. 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

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

    SciTech Connect

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

    2010-08-26

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

  20. Exclusive selectivity in the one-pot formation of C-C and C-Se bonds involving Ni-catalyzed alkyne hydroselenation: optimization of the synthetic procedure and a mechanistic study.

    PubMed

    Orlov, Nikolay V; Chistyakov, Igor V; Khemchyan, Levon L; Ananikov, Valentine P; Beletskaya, Irina P; Starikova, Zoya A

    2014-12-19

    A unique Ni-catalyzed transformation is reported for the one-pot highly selective synthesis of previously unknown monoseleno-substituted 1,3-dienes starting from easily available terminal alkynes and benzeneselenol. The combination of a readily available catalyst precursor, Ni(acac)2, and an appropriately tuned phosphine ligand, PPh2Cy, resulted in the exclusive assembly of the s-gauche diene skeleton via the selective formation of C-C and C-Se bonds. The unusual diene products were stable under regular experimental conditions, and the products maintained the s-gauche geometry both in the solid state and in solution, as confirmed by X-ray analysis and NMR spectroscopy. Thorough mechanistic studies using ESI-MS revealed the key Ni-containing species involved in the reaction. PMID:25288369

  1. A dominant homolytic O-Cl bond cleavage with low-spin triplet-state Fe(IV)=O formed is revealed in the mechanism of heme-dependent chlorite dismutase.

    PubMed

    Sun, Shuo; Li, Ze-Sheng; Chen, Shi-Lu

    2014-01-21

    Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO? radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO? radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry. PMID:24162174

  2. 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 PKC? (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 PKC?, 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

  3. Palladium(0)-mediated C-H bond activation of N-(naphthyl)salicylaldimine and related ligands: utilization of the resulting organopalladium complexes in catalytic C-C and C-N coupling reactions.

    PubMed

    Dutta, Jayita; Richmond, Michael G; Bhattacharya, Samaresh

    2015-07-21

    N-(Naphthyl)-4-R-salicylaldimines (R = OCH3, H and Cl; H2L(1)-H2L(3)) and 2-hydroxy-N-(naphthyl)naphthaldimine (H2L(4)) readily undergo, upon reaction with Na2[PdCl4] in the presence of triphenylphosphine, cyclopalladation via C-H bond activation at the peri-position to afford complexes of type [Pd(L)(PPh3)] (L = L(1)-L(4)). The C-H bond activation has been found to be mediated by palladium(0) formed in situ. A similar reaction of H2L(1) with Na2[PdCl4] in the presence of 1,2-bis(diphenylphosphino)ethane (dppe), in a 2?:?2?:?1 mole ratio, yields a dinuclear complex of type [{Pd(L(1))}2(dppe)]. Reaction of H2L(1) with Na2[PdCl4] in the presence of 4-picoline (pic) yields [Pd(L(1))(pic)]. The molecular structures of the six complexes have been determined by X-ray crystallography. The aldiminate ligand in each compound is coordinated to the metal center as a di-anionic tridentate ONC-donor, with the fourth coordination site occupied by a phosphine or picoline ligand. The new complexes show intense absorptions in the visible and ultraviolet regions, and the nature of the optical transitions has been analyzed by TDDFT calculations. The palladium complexes display notable efficiency in catalyzing C-C and C-N bond coupling reactions. The thermodynamics for the formation of the cyclometalated catalyst precursor [Pd(L(2))(PPh3)] has been evaluated by DFT calculations. PMID:26146368

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

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

  6. 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. [Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637 (United States); Lee, Shih-Huang [National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China); Lin, Jim Jr-Min [Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan 10617 (China)

    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.

  7. Rhodium-catalyzed borylation of aryl 2-pyridyl ethers through cleavage of the carbon-oxygen bond: borylative removal of the directing group.

    PubMed

    Kinuta, Hirotaka; Tobisu, Mamoru; Chatani, Naoto

    2015-02-01

    The rhodium-catalyzed reaction of aryl 2-pyridyl ethers with a diboron reagent results in the formation of arylboronic acid derivatives via activation of the C(aryl)-O bonds. The straightforward synthesis of 1,2-disubstituted arenes was enabled through catalytic ortho C-H bond functionalization directed by the 2-pyridyloxy group followed by substitution of this group with a boryl group. Several control experiments revealed that the presence of a sp(2) nitrogen atom at the 2-position of the substrate and the use of a boron-based reagent were crucial for the activation of the relatively inert C(aryl)-O bond of aryl 2-pyridyl ethers. PMID:25565225

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

    PubMed Central

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

    2014-01-01

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

  9. Mild and Robust Redox-Neutral Pd/C-Catalyzed Lignol ?-O-4' Bond Cleavage Through a Low-Energy-Barrier Pathway.

    PubMed

    Galkin, Maxim V; Dahlstrand, Christian; Samec, Joseph S M

    2015-07-01

    Invited for this month's cover is the group of Joseph Samec at Uppsala University. The image shows that native lignin ?-O-4' bond model compounds react at very mild and accurately tuned redox-neutral conditions while other models have higher hydrogen and temperature demands. The Communication itself is available at 10.1002/cssc.201500117. PMID:26118361

  10. Cleavage of Disulfide Bonds Leads to Inactivation and Degradation of the Type IIa, But not Type IIb Sodium Phosphate Cotransporter Expressed in Xenopus laevis Oocytes

    Microsoft Academic Search

    G. Lambert; M. Traebert; J. Biber; H. Murer

    2000-01-01

    Tris(2-carboxyethyl)phosphine (TCEP) reduces (cleaves) disulfide bonds of the renal proximal tubule type IIa Na\\/Pi- cotransporter (rat NaPi IIa) and thereby inhibits its function. We tested the effect of TCEP on the murine type IIa Na\\/Pi-cotransporter and the corresponding IIb intestinal isoform both expressed in Xenopus laevis oocytes. After incubation with TCEP the function of NaPi IIa was inhibited and protein

  11. Cleavage of Disulfide Bonds Leads to Inactivation and Degradation of the Type IIa, But not Type IIb Sodium Phosphate Cotransporter Expressed in Xenopus laevis Oocytes

    Microsoft Academic Search

    G. Lambert; M. Traebert; J. Biber; H. Murer

    2000-01-01

    .   Tris(2-carboxyethyl)phosphine (TCEP) reduces (cleaves) disulfide bonds of the renal proximal tubule type IIa Na\\/Pi- cotransporter\\u000a (rat NaPi IIa) and thereby inhibits its function. We tested the effect of TCEP on the murine type IIa Na\\/P\\u000a \\u000a i\\u000a \\u000a -cotransporter and the corresponding IIb intestinal isoform both expressed in Xenopus laevis oocytes. After incubation with TCEP the function of NaPi IIa was

  12. Bipodal surface organometallic complexes with surface N-donor ligands and application to the catalytic cleavage of C-H and C-C bonds in n-butane.

    PubMed

    Bendjeriou-Sedjerari, Anissa; Azzi, Joachim M; Abou-Hamad, Edy; Anjum, Dalaver H; Pasha, Fahran A; Huang, Kuo-Wei; Emsley, Lyndon; Basset, Jean-Marie

    2013-11-27

    We present a new generation of "true vicinal" functions well-distributed on the inner surface of SBA15: [(?Si-NH2)(?Si-OH)] (1) and [(?Si-NH2)2] (2). From these amine-modified SBA15s, two new well-defined surface organometallic species [(?Si-NH-)(?Si-O-)]Zr(CH2tBu)2 (3) and [(?Si-NH-)2]Zr(CH2tBu)2 (4) have been obtained by reaction with Zr(CH2tBu)4. The surfaces were characterized with 2D multiple-quantum (1)H-(1)H NMR and infrared spectroscopies. Energy-filtered transmission electron microscopy (EFTEM), mass balance, and elemental analysis unambiguously proved that Zr(CH2tBu)4 reacts with these vicinal amine-modified surfaces to give mainly bipodal bis(neopentyl)zirconium complexes (3) and (4), uniformly distributed in the channels of SBA15. (3) and (4) react with hydrogen to give the homologous hydrides (5) and (6). Hydrogenolysis of n-butane catalyzed by these hydrides was carried out at low temperature (100 °C) and low pressure (1 atm). While (6) exhibits a bis(silylamido)zirconium bishydride, [(?Si-NH-)2]Zr(H)2 (6a) (60%), and a bis(silylamido)silyloxozirconium monohydride, [(?Si-NH-)2(?Si-O-)]ZrH (6b) (40%), (5) displays a new surface organometallic complex characterized by an (1)H NMR signal at 14.46 ppm. The latter is assigned to a (silylimido)(silyloxo)zirconium monohydride, [(?Si-N?)(?Si-O-)]ZrH (5b) (30%), coexistent with a (silylamido)(silyloxo)zirconium bishydride, [(?Si-NH-)(?Si-O-)]Zr(H)2 (5a) (45%), and a silylamidobis(silyloxo)zirconium monohydride, [(?Si-NH-)(?Si-O-)2]ZrH (5c) (25%). Surprisingly, nitrogen surface ligands possess catalytic properties already encountered with silicon oxide surfaces, but interestingly, catalyst (5) with chelating [N,O] shows better activity than (6) with chelating [N,N]. PMID:24195760

  13. Structural insights into the role of iron–histidine 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 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

  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.

    PubMed

    Carrasco, Javier; López-Durán, David; Liu, Zongyuan; Ducho?, Tomáš; Evans, Jaime; Senanayake, Sanjaya D; Crumlin, Ethan J; Matolín, Vladimir; Rodríguez, José A; Ganduglia-Pirovano, M Verónica

    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

  15. 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

    DOE PAGESBeta

    Carrasco, Javier [Inst. de Catalisis y Petroleoquimica, CSIC, Madrid (Spain); CIC Energigune, Minana, Alava (Spain); Rodriguez, Jose A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Stony Brook Univ., NY (United States); Lopez-Duran, David [Inst. de Catalisis y Petroleoquimica, CSIC, Madrid (Spain); CIC Energigune, Minana, Alava (Spain); Liu, Zongyuan [Brookhaven National Lab. (BNL), Upton, NY (United States); Stony Brook Univ., NY (United States); Duchon, Tomas [Charles Univ., Praha (Czech Republic); Evans, Jaime [Univ. Central de Venezuela, Caracas (Venezuela); Senanayake, Sanjaya D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Crumlin, Ethan J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Matolin, Vladimir [Charles Univ., Praha (Czech Republic); Ganduglia-Pirovano, M. Veronica [Inst. de Catalisis y Petroleoquimica, CSIC, Madrid (Spain)

    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 Ni²? 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.

  16. New in situ cleavage of both S-S and S-C(sp2) bonds and rearrangement reactions toward the construction of copper(I) cluster-based coordination networks.

    PubMed

    Wang, Jing; Zheng, Shao-Liang; Hu, Sheng; Zhang, Yue-Hua; Tong, Ming-Liang

    2007-02-01

    Solvothermal reaction of 4,4'-dithiodipyridine (dtdp) with CuI at 120 or 160 degrees C results in the formation of three new coordination networks formulated with [Cu4I4(tdp)2] (1; tdp = 4,4'-thiodipyridine), [Cu5I5(ptp)2] (2), and [Cu6I6(ptp)2] [3; ptp = 1-(4-pyridyl)-4-thiopyridine]. The starting dtdp reagent was unprecedentedly converted into two tdp and ptp ligands via new in situ cleavage of both S-S and S-C(sp2) bonds and temperature-dependent in situ ligand rearrangement of dtdp. 1 is a two-dimensional (2D) Cu4I4 cubane-like coordination network of 2-fold interpenetration. While in 2, the Cu8I8 and Cu2I2 cluster units are alternately connected by the mu2-sulfur bridges into one-dimensional inorganic chains along the a axis, which are further joined by the ptp spacers into a three-dimensional (3D) coordination network of 2-fold interpenetration. 3 is a 3D non-interpenetrating coordination network constructed with 2D inorganic (Cu2I2)n layers and the ptp spacers. 1 displays an intense orange-red emission light with a maximum at ca. 563 nm. While luminescence quenching occurs in 2 and 3 by electron transfer of a photoelectron to the electronegative acceptor molecule of ptp. PMID:17257022

  17. 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

    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 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 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/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.« less

  18. Iridium porphyrins in CD3OD: reduction of Ir(III), CD3-OD bond cleavage, Ir-D acid dissociation and alkene reactions.

    PubMed

    Bhagan, Salome; Imler, Gregory H; Wayland, Bradford B

    2013-04-15

    Methanol solutions of iridium(III) tetra(p-sulfonatophenyl)porphyrin [(TSPP)Ir(III)] form an equilibrium distribution of methanol and methoxide complexes ([(TSPP)Ir(III)(CD3OD)(2-n)(OCD3)n]((3+n)-)). Reaction of [(TSPP)Ir(III) with dihydrogen (D2) in methanol produces an iridium hydride [(TSPP)Ir(III)-D(CD3OD)](4-) in equilibrium with an iridium(I) complex ([(TSPP)Ir(I)(CD3OD)](5-)). The acid dissociation constant of the iridium hydride (Ir-D) in methanol at 298 K is 3.5 × 10(-12). The iridium(I) complex ([(TSPP)Ir(I)(CD3OD)](5-)) catalyzes reaction of [(TSPP)Ir(III)-D(CD3OD)](4-) with CD3-OD to produce an iridium methyl complex [(TSPP)Ir(III)-CD3(CD3OD)](4-) and D2O. Reactions of the iridium hydride with ethene and propene produce iridium alkyl complexes, but the Ir-D complex fails to give observable addition with acetaldehyde and carbon monoxide in methanol. Reaction of the iridium hydride with propene forms both the isopropyl and propyl complexes with free energy changes (?G° 298 K) of -1.3 and -0.4 kcal mol(-1) respectively. Equilibrium thermodynamics and reactivity studies are used in discussing relative Ir-D, Ir-OCD3 and Ir-CD2- bond energetics in methanol. PMID:23540797

  19. 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., E-mail: qasimm@ipfw.edu [Department of Chemistry, Indiana University Purdue University Fort Wayne, 2101 E. Coliseum Blvd., Fort Wayne, IN 46805 (United States); Song, Jikui; Markley, John L. [Department of Biochemistry, University of Wisconsin-Madison, WI 53706 (United States)] [Department of Biochemistry, University of Wisconsin-Madison, WI 53706 (United States); Laskowski, Michael [Department of Chemistry, Purdue University, West Lafayette, IN 47907 (United States)] [Department of Chemistry, Purdue University, West Lafayette, IN 47907 (United States)

    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.

  20. Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.

    PubMed

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

    2002-01-01

    The three-dimensional structures of the native cytochrome c(2) from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 A and in the reduced state at 1.95 A resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c(2) with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 3(10)-helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c(2) with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles phi and psi of approximately -140 and -130 degrees, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 A resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c(2) of the rare six-residue insertion in the helix 3(10) conformation that increases Met loop flexibility. PMID:11742117

  1. Ligand substitution behavior of Ru6(mu6-C)(CO)17 with unsaturated diphosphines: facile capping of a polyhedral face and photochemically promoted P C bond cleavage in the cluster Ru6(mu6-C)(CO)14(mu3-bpcd)

    SciTech Connect

    Kandala, Srikanth [University of North Texas; Hammons, Casey [University of North Texas; Watson, William H. [Texas Christian University; Wang, Xiaoping [ORNL; Richmond, Michael G. [University of North Texas

    2010-01-01

    The ligand substitution chemistry of the hexaruthenium cluster Ru-6(mu(6)-C)(CO)(17) (1) with several unsaturated diphosphine ligands has been investigated. Thermolysis of 1 with (Z)-Ph2PCH=CHPPh2 (dppen) furnishes the new cluster compounds Ru-5(mu(5)-C)(CO)(12)(mu(3)-dppen) (2), Ru-6(mu(6)-C)(CO)(14)(mu(3)-dppen) (3), and Ru-6(mu(6)-C)(CO)(12)(mu(3)-dppen)(mu-dppen) (4). Clusters 2 and 3 are also obtained when a mixture of 1 and dppen is treated with the oxidative-decarbonylation reagent Me3NO. Thermolysis or Me3NO activation of 1 in the presence of 4,5-bis(diphenylphosphino)-4-cyclopenten- 1,3-dione (bpcd) yields Ru-6(mu(6)-C)(CO)(14)(mu(3)-bpcd) (4) as the sole observable product. Near-UV irradiation of 4 leads to P-C bond cleavage and the formation of phosphido-bridged cluster Ru-6(mu(6)-C)(CO)(13)[mu(3)-C=C(PPh2)C(O)CH2C(O)](mu-PPh2) (6) in essentially quantitative yield. The reaction between 1 and the ligand 3,4-bis(diphenylphosphino)-5-methoxy-2(5H)-furanone (bmf) leads to the formation of Ru-6(mu(6)-C)(CO)(14)(mu(3)-bmf) (7), which exists as a single diastereomer in solution as shown by H-1 and P-31 NMR spectroscopy. The molecular structures and the binding mode of the ancillary diphosphine ligand(s) in 2-7 have all been established by X-ray diffraction analyses. The solid-state structure of 7 reveals that the chiral bmf ligand caps one of the metallic faces stereospecifically with the 5-methoxy moiety oriented distal or trans relative to the Ru-6 polyhedral core. The new substitution products are discussed relative to the products obtained from 1 and the related diphosphine ligands dppm, dppe, dppf, and dppbz.

  2. Efficient C–H bond activations via O2 cleavage by a dianionic cobalt(ii) complex† †Electronic supplementary information (ESI) available: Experimental procedures, spectroscopic and electrochemical figures. CCDC 980872–980875. 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 C–H 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 C–H bond cleavage greatly depends on the pK a of the C–H bond, rather than on the C–H bond dissociation energy. Kinetic isotope experiments reveal a moderate KIE value of ca. 3.5 using either O2 or PhIO. The possible involvement of a cobalt(iv) oxo species in this chemistry is discussed. PMID:25071930

  3. Cleavage in zinc

    Microsoft Academic Search

    M. H. Kamdar

    1971-01-01

    It is known that cleavage cracks initiate and propagate in the same (0001) plane in zinc crystals. This suggested that if\\u000a conditions are ideal for brittle fracture then ?I, the energy to iniate a cleavage crack in the (0001) plane in zinc should be the same as ?p that to propagate the crack in the same plane. If fracture is

  4. 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 ?*-anti-bonding orbital of the adduct bond and electron withdrawal from the ?-bonding orbital are found to be responsible for this bond elongation. PMID:24339005

  5. Brønsted acid-promoted C-H bond cleavage via electron transfer from toluene derivatives to a protonated nonheme iron(IV)-oxo complex with no kinetic isotope effect.

    PubMed

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

    2013-04-01

    The reactivity of a nonheme iron(IV)-oxo complex, [(N4Py)Fe(IV)(O)](2+) (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine), was markedly enhanced by perchloric acid (70% HClO4) in the oxidation of toluene derivatives. Toluene, which has a high one-electron oxidation potential (Eox = 2.20 V vs SCE), was oxidized by [(N4Py)Fe(IV)(O)](2+) in the presence of HClO4 in acetonitrile (MeCN) to yield a stoichiometric amount of benzyl alcohol, in which [(N4Py)Fe(IV)(O)](2+) was reduced to [(N4Py)Fe(III)(OH2)](3+). The second-order rate constant (kobs) of the oxidation of toluene derivatives by [(N4Py)Fe(IV)(O)](2+) increased with increasing concentration of HClO4, showing the first-order dependence on [HClO4]. A significant kinetic isotope effect (KIE) was observed when mesitylene was replaced by mesitylene-d12 in the oxidation with [(N4Py)Fe(IV)(O)](2+) in the absence of HClO4 in MeCN at 298 K. The KIE value drastically decreased from KIE = 31 in the absence of HClO4 to KIE = 1.0 with increasing concentration of HClO4, accompanied by the large acceleration of the oxidation rate. The absence of KIE suggests that electron transfer from a toluene derivative to the protonated iron(IV)-oxo complex ([(N4Py)Fe(IV)(OH)](3+)) is the rate-determining step in the acid-promoted oxidation reaction. The detailed kinetic analysis in light of the Marcus theory of electron transfer has revealed that the acid-promoted C-H bond cleavage proceeds via the rate-determining electron transfer from toluene derivatives to [(N4Py)Fe(IV)(OH)](3+) through formation of strong precursor complexes between toluene derivatives and [(N4Py)Fe(IV)(OH)](3+). PMID:23528016

  6. 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.

  7. 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.

  8. 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.

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

    SciTech Connect

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

    1993-09-01

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

  10. Coordination-Resolved C?C Bond Length and the C 1s Binding Energy of Carbon Allotropes and the Effective Atomic Coordination of the Few-Layer Graphene

    Microsoft Academic Search

    Chang Q. Sun; Yi Sun; Y. G. Nie; Yan Wang; J. S. Pan; G. Ouyang; L. K. Pan; Zhuo Sun

    2009-01-01

    Binding energy variation due to the change of atomic coordination has formed the key to the different fascinating properties of carbon allotropes such as graphene nanoribbons, carbon nanotubes, graphite, and diamond. However, determination of the binding energies of these allotropes with a consistent understanding of the effect of bond order variation on the binding energy change has long been a

  11. Transition metal catalyzed manipulation of non-polar carbon-hydrogen bonds for synthetic purpose.

    PubMed

    Murai, Shinji

    2011-01-01

    The direct addition of ortho C-H 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 C-C bond is the rate-determining step, while the C-H bond cleavage step is not. (Communicated by Ryoji NoyorI, M.J.A.). PMID:21558759

  12. Electronic effect in C-H and C-C bond activation: state-specific reactions of Fe/sup +/(/sup 6/D, /sup 4/F) with methane, ethane, and propane

    SciTech Connect

    Schultz, R.H.; Elkind, J.L.; Armentrout, P.B.

    1988-01-20

    Reactions of atomic iron ions with methane, ethane, and propane are studied with guided ion beam mass spectrometry. By using different ion sources different electronic states of the ion can be prepared and studied in detail. The first excited state, Fe/sup +/(/sup 4/F), is more reactive than the ground state, Fe/sup +/(/sup 6/D), for all endothermic reactions in all three systems. This result is similar to recent observations of the reactions of these states with H/sub 2/. The different reactivities are explained by using simple molecular orbital arguments. In contrast, Fe/sup +/(/sup 4/F) reacts less efficiently than Fe/sup +/(/sup 6/D) in the exothermic reactions of ethane and propane below 0.5 eV but more efficiently at higher energies. This behavior is explained by a potential energy surface crossing that is avoided at low kinetic energies due to spin-orbit interactions and is permitted at higher energies. Finally, analysis of the threshold behavior of the endothermic reactions provides the bond dissociation energies, D/sup 0/(Fe/sup +/-CH/sub 3/) = 2.51 +/- 0.10 eV (57.9 +/- 2.4 kcal/mol) and D/sup 0/(FeH) = 1.98 +/- 0.13 eV (45.7 +/- 3.0 kcal/mol).

  13. Mechanisms of Catalytic Cleavage of Benzyl Phenyl Ether in Aqueous and Apolar Phases

    SciTech Connect

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

    2014-03-03

    Catalytic pathways for the cleavage of the ether bonds in benzyl phenyl ether (BPE) in the condensed liquid phases using Ni and zeolite based catalysts are explored. In absence of catalysts, the C?O bond is selectively cleaved in water by hydrolysis forming phenol and benzyl alcohol as intermediates, followed by C?C bond alkylation. The hydronium ions catalyzing the reactions are provided by the dissociation of water at the high temperature (523 K). Upon addition of a solid acid (HZSM-5), rates of hydrolysis and alkylation are markedly increased in proportion to the acid concentrations. In the presence of a metal (Ni/SiO2), the selective hydrogenolysis dominates for cleaving the Caliphatic?O bond. Catalyzed by the dual-functional Ni/HZSM-5, hydrogenolysis occurs as the major route rather than hydrolysis (minor). In the apolar undecane, the non-catalytic thermal pyrolysis route dominates. Hydrogenolysis of BPE appears to be the major reaction pathway in undecane in presence of Ni/SiO2 or Ni/HZSM-5, almost suppressing the radical reactions completely. The density functional theory (DFT) calculations perfectly support the proposed C?O bond cleavage mechanisms on BPE in the aqueous and apolar phases. DFT calculations show that BPE is initially protonated and subsequently hydrolyzed in the aqueous phase. The radical reaction plays a significant role for generating primary benzyl and phenoxy radicals in undecane evidenced by DFT calculation, which leads to heavier condensation products without the aid of metals for providing dissociated hydrogen radicals. J.H., L.L., and C.Z. gratefully acknowledge support from the graduate school (Faculty Graduate Center of Chemistry) of the Technische Universität München and the Elitenetzwerk Bayern (graduate school NanoCat). D.M. and J.A.L. thank 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.

  14. 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.

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

    E-print Network

    Huang, Xiaohua, 1973-

    2003-01-01

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

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

    PubMed

    Wu, Wen-Bin; Huang, Jing-Mei

    2014-11-01

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

  17. Aliphatic C-H to C-C Conversion: Synthesis of (?)-Cameroonan-7?-ol

    PubMed Central

    Taber, Douglass F.; Nelson, Christopher G.

    2011-01-01

    In the course of a synthesis of the tricyclic sesquiterpene (?)-cameroonan-7?-ol from the acyclic (+)-citronellal, seven aliphatic C-H bonds were converted to C-C bonds, and three rings and four new stereogenic centers were established. PMID:21344897

  18. Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments. V. Study of single-strand cleavages.

    PubMed Central

    Yolov, A A; Gromova, E S; Kubareva, E A; Potapov, V K; Shabarova, Z A

    1985-01-01

    Concatemer DNA duplexes which contain at the EcoRII restriction endonuclease cleavage sites (formula; see text) phosphodiester, phosphoamide or pyrophosphate internucleotide bonds have been synthesized. It has been shown that this enzyme did not cleave the substrate at phosphoamide bond. EcoRII endonuclease catalyzes single-strand cleavages both in dA- and dT-containing strands of the recognition site if the cleavage of the other strand has been blocked by modification of scissile bond or if the other strand has been cleaved. This enzyme interacts with both strands of the DNA recognition site, each of them being cleaved independently on the cleavage of another one. Nucleotide sequences flanking the EcoRII site on both sides are necessary for effective cleavage of the substrate. Images PMID:3001655

  19. 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

  20. Mechanism for Intein C-Terminal Cleavage: A Proposal from Quantum Mechanical Calculations

    PubMed Central

    Shemella, Philip; Pereira, Brian; Zhang, Yiming; Van Roey, Patrick; Belfort, Georges; Garde, Shekhar; Nayak, Saroj K.

    2007-01-01

    Inteins are autocatalytic protein cleavage and splicing elements. A cysteine to alanine mutation at the N-terminal of inteins inhibits splicing and isolates the C-terminal cleavage reaction. Experiments indicate an enhanced C-terminal cleavage reaction rate upon decreasing the solution pH for the cleavage mutant, which cannot be explained by the existing mechanistic framework. We use intein crystal structure data and the information about conserved amino acids to perform semiempirical PM3 calculations followed by high-level density functional theory calculations in both gas phase and implicit solvent environments. Based on these calculations, we propose a detailed “low pH” mechanism for intein C-terminal cleavage. Water plays an important role in the proposed reaction mechanism, acting as an acid as well as a base. The protonation of the scissile peptide bond nitrogen by a hydronium ion is an important first step in the reaction. That step is followed by the attack of the C-terminal asparagine side chain on its carbonyl carbon, causing succinimide formation and simultaneous peptide bond cleavage. The computed reaction energy barrier in the gas phase is ?33 kcal/mol and reduces to ?25 kcal/mol in solution, close to the 21 kcal/mol experimentally observed at pH 6.0. This mechanism is consistent with the observed increase in C-terminal cleavage activity at low pH for the cleavage mutant of the Mycobacterium tuberculosis RecA mini-intein. PMID:17085503

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. In vivo and in vitro studies on the carotenoid cleavage oxygenases from Sphingopyxis alaskensis RB2256 and Plesiocystis pacifica SIR-1 revealed their substrate specificities and non-retinal-forming cleavage activities.

    PubMed

    Hoffmann, Jana; Bóna-Lovász, Judit; Beuttler, Holger; Altenbuchner, Josef

    2012-10-01

    Carotenoid cleavage oxygenases are nonheme iron enzymes that specifically cleave carbon-carbon double bonds of carotenoids. Their apocarotenoid cleavage products serve as important signaling molecules that are involved in various biological processes. A database search revealed the presence of putative carotenoid cleavage oxygenase genes in the genomes of Sphingopyxis alaskensis RB2256 and Plesiocystis pacifica SIR-1. The four genes sala_1698, sala_1008, ppsir1_15490 and ppsir1_17230 were cloned and heterologously expressed in carotenoid-producing Escherichia coli JM109 strains. Two of the four encoded proteins exhibited carotenoid cleavage activity. S. alaskensis RB2256 carotenoid cleavage oxygenase (SaCCO), which is encoded by sala_1698, was shown to cleave acyclic and monocyclic substrates. Coexpression of sala_1698 in carotenoid-producing E. coli JM109 strains revealed cleavage activity for lycopene, hydroxylycopene, and dihydroxylycopene. The monocyclic substrate apo-8'-carotenal was cleaved in vitro by purified SaCCO at the 9'/10' and 11'/12' double bonds. The second enzyme, P. pacifica SIR-1 carotenoid cleavage oxygenase (PpCCO), is encoded by ppsir1_15490. PpCCO-mediated carotenoid cleavage requires the presence of either hydroxy or keto groups. PpCCO cleaved zeaxanthin, hydroxylycopene, and dihydroxylycopene, and also the C(50) carotenoids decaprenoxanthin, sarprenoxanthin and sarcinaxanthin, in carotenoid-producing E. coli JM109 strains. Whole cells of E. coli JM109 overexpressing ppsir1_15490mut, a mutant of ppsir1_15490 with enhanced gene expression, were applied for the conversion of carotenoids. Analysis of the carotenoid cleavage products revealed a single cleavage site at the 13'/14' double bond for astaxanthin, and two cleavage sites at the 11'/12' or 13'/14' double bond for zeaxanthin, nostoxanthin, and canthaxanthin. PMID:22901074

  6. Ligand substitution behavior of Ru(6)(mu(6)-C)(CO)(17) with unsaturated diphosphines: facile capping of a polyhedral face and photochemically promoted P-C bond cleavage in the cluster Ru(6)(mu(6)-C)(CO)(14)(mu(3)-bpcd).

    PubMed

    Kandala, Srikanth; Hammons, Casey; Watson, William H; Wang, Xiaoping; Richmond, Michael G

    2010-02-14

    The ligand substitution chemistry of the hexaruthenium cluster Ru(6)(mu(6)-C)(CO)(17) () with several unsaturated diphosphine ligands has been investigated. Thermolysis of with (Z)-Ph(2)PCH[double bond, length as m-dash]CHPPh(2) (dppen) furnishes the new cluster compounds Ru(5)(mu(5)-C)(CO)(12)(mu(3)-dppen) (), Ru(6)(mu(6)-C)(CO)(14)(mu(3)-dppen) (), and Ru(6)(mu(6)-C)(CO)(12)(mu(3)-dppen)(mu-dppen) (). Clusters and are also obtained when a mixture of and dppen is treated with the oxidative-decarbonylation reagent Me(3)NO. Thermolysis or Me(3)NO activation of in the presence of 4,5-bis(diphenylphosphino)-4-cyclopenten-1,3-dione (bpcd) yields Ru(6)(mu(6)-C)(CO)(14)(mu(3)-bpcd) () as the sole observable product. Near-UV irradiation of leads to P-C bond cleavage and the formation of phosphido-bridged cluster Ru(6)(mu(6)-C)(CO)(13)[mu(3)-C[double bond, length as m-dash]C(PPh(2))C(O)CH(2)C(O)](mu-PPh(2)) () in essentially quantitative yield. The reaction between and the ligand 3,4-bis(diphenylphosphino)-5-methoxy-2(5H)-furanone (bmf) leads to the formation of Ru(6)(mu(6)-C)(CO)(14)(mu(3)-bmf) (), which exists as a single diastereomer in solution as shown by (1)H and (31)P NMR spectroscopy. The molecular structures and the binding mode of the ancillary diphosphine ligand(s) in have all been established by X-ray diffraction analyses. The solid-state structure of reveals that the chiral bmf ligand caps one of the metallic faces stereospecifically with the 5-methoxy moiety oriented distal or trans relative to the Ru(6) polyhedral core. The new substitution products are discussed relative to the products obtained from and the related diphosphine ligands dppm, dppe, dppf, and dppbz. PMID:20104326

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

    PubMed Central

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

    2013-01-01

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

  8. Anti-metastatic semi-synthetic sulfated maltotriose C-C linked dimers. Synthesis and characterisation.

    PubMed

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

    2012-01-01

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

  9. ?-Cleavage of cellular prion protein

    PubMed Central

    Liang, Jingjing; Kong, Qingzhong

    2012-01-01

    The cellular prion protein (PrPC) is subjected to various processing under physiological and pathological conditions, of which the ?-cleavage within the central hydrophobic domain not only disrupts a region critical for both PrP toxicity and PrPC to PrPSc conversion but also produces the N1 fragment that is neuroprotective and the C1 fragment that enhances the pro-apoptotic effect of staurosporine in one report and inhibits prion in another. The proteases responsible for the ?-cleavage of PrPC are controversial. The effect of ADAM10, ADAM17, and ADAM9 on N1 secretion clearly indicates their involvement in the ?-cleavage of PrPC, but there has been no report of direct PrPC ?-cleavage activity with any of the three ADAMs in a purified protein form. We demonstrated that, in muscle cells, ADAM8 is the primary protease for the ?-cleavage of PrPC, but another unidentified protease(s) must also play a minor role. We also found that PrPC regulates ADAM8 expression, suggesting that a close examination on the relationships between PrPC and its processing enzymes may reveal novel roles and underlying mechanisms for PrPC in non-prion diseases such as asthma and cancer. PMID:23052041

  10. Identification of the cleavage site and determinants required for poliovirus 3CPro-catalyzed cleavage of human TATA-binding transcription factor TBP.

    PubMed Central

    Das, S; Dasgupta, A

    1993-01-01

    Host cell RNA polymerase II-mediated transcription is inhibited by poliovirus infection. We have shown previously that the human TATA-binding protein (TBP), a general transcription factor required for transcription of all RNA polymerase II genes, is directly cleaved both in vitro and in vivo by the virus-coded protease 3CPro. 3CPro specifically cleaves glutamine-glycine bonds in the viral polyprotein. Cellular transcription factor TBP contains three glutamine-glycine sites, at amino acids 12, 18, and 108. By using site-directed mutagenesis, we determined that the glutamine-glycine bond at amino acid 18, but not that at amino acid 12 or 108, is cleaved by the viral protease. Both the glutamine and the glycine appear to be important for the cleavage. Further mutations around the glutamine-glycine site at position 18 suggest that determinants other than the glutamine-glycine bond in TBP are also required for 3CPro-induced cleavage. An alanine at position P4 and a proline at position P2, proximal to the scissile glutamine-glycine pair, appear to be important for 3CPro-mediated cleavage of TBP. Our results suggest that the cleavage specificity of 3CPro for a cellular transcription factor is very similar to its mode of cleavage of viral polyproteins. Images PMID:8388502

  11. Localization of double bonds in triacylglycerols using high-performance liquid chromatography/atmospheric pressure chemical ionization ion-trap mass spectrometry.

    PubMed

    Háková, Eva; Vrkoslav, Vladimír; Míková, Radka; Schwarzová-Pecková, Karolina; Bosáková, Zuzana; Cva?ka, Josef

    2015-07-01

    A method for localizing double bonds in triacylglycerols using high-performance liquid chromatography-tandem mass spectrometry with atmospheric pressure chemical ionization (APCI) was developed. The technique was based on collision-induced dissociation or pulsed Q collision-induced dissociation of the C3H5N(+•) adducts ([M + 55](+•)) formed in the presence of acetonitrile in the APCI source. The spectra were investigated using a large series of standards obtained from commercial sources and prepared by randomization. The fragmentation spectra made it possible to determine (i) the total number of carbons and double bonds in the molecule, (ii) the number of carbons and double bonds in acyls, (iii) the acyl in the sn-2 position on the glycerol backbone, and (iv) the double-bond positions in acyls. The double-bond positions were determined based on two types of fragments (alpha and omega ions) formed by cleavages of C-C bonds vinylic to the original double bond. The composition of the acyls and their positions on glycerol were established from the masses and intensities of the ions formed by the elimination of fatty acids from the [M + 55](+•) precursor. The method was applied for the analysis of triacylglycerols in olive oil and vernix caseosa. Graphical Abstract The diagnostic fragments in the APCI PQD MS(2) spectrum of the [M + 55](+•) adduct of triolein. PMID:25701424

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

    PubMed

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

    2013-07-01

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

  13. Vibrational overtone spectroscopy, energy levels, and intensities of (CH3)3C-C?C-H.

    PubMed

    Perez-Delgado, Yasnahir; Barroso, Jenny Z; Garofalo, Lauren A; Manzanares, Carlos E

    2012-03-01

    The vibrational overtone spectra of the acetylenic (?? = 4, 5) and methyl (?? = 5, 6) C-H stretch transitions of tert-butyl acetylene [(CH(3))(3)C-C?C-H] were obtained using the phase shift cavity ring down (PS-CRD) technique at 295 K. The C-H stretch fundamental and overtone absorptions of the acetylenic (?? = 2 and 3) and methyl (?? = 2-4) C-H bonds have been obtained using a Fourier transform infrared and near-infrared spectrophotometer. Harmonic frequency ?(?(1)) and anharmonicities x(?(1)) and x(?(1), ?(24)) are reported for the acetylenic C-H bond. Molecular orbital calculations of geometry and vibrational frequencies were performed. A harmonically coupled anharmonic oscillator (HCAO) model was used to determine the overtone energy levels and assign the absorption bands to vibrational transitions of methyl C-H bonds. Band strength values were obtained experimentally and compared with intensities calculated in terms of the HCAO model where only the C-H modes are considered. No adjustable parameters were used to get order of magnitude agreement with experimental intensities for all pure local mode C-H transitions. PMID:22263573

  14. Mechanistic Analysis of Oxidative C–H 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 carbon–hydrogen 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 carbon–hydrogen bond cleavage is rate determining and that a radical cation is most likely a key intermediate in the reaction mechanism. PMID:20640173

  15. Mineral Cleavage: a practical experiment

    NSDL National Science Digital Library

    Sharon Browning

    In this geology activity, students investigate the physical property of mineral cleavage by physically trying to break down a block of halite and describing the results. This lab addresses many misunderstandings non-majors have about the physical properties of minerals and includes a brief write up of their conclusions.

  16. 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.

  17. Copper-catalyzed, C-C coupling-based one-pot tandem reactions for the synthesis of benzofurans using o-iodophenols, acyl chlorides, and phosphorus ylides.

    PubMed

    Liu, Yunyun; Wang, Hang; Wan, Jie-Ping

    2014-11-01

    One-pot reactions involving acyl chlorides, phosphorus ylides, and o-iodophenols with copper catalysis have been established for the rapid synthesis of functionalized benzofurans. With all of these easily available and stable reactants, the construction of the target products has been accomplished via tandem transformations involving a key C-C coupling, leading to the formation of one C(sp(2))-C bond, one C(sp(2))-O bond, and one C ? C bond. PMID:25279735

  18. Unequal cleavage in the early Tubifex embryo.

    PubMed

    Shimizu, T; Ishii, R; Takahashi, H

    1998-06-01

    Unequal cleavage that produces two blastomeres of different size is a cleavage pattern that many animals in a variety of phyla, particularly in Spiralia, adopt during early development. This cleavage pattern is apparently instrumental for asymmetric segregation of developmental potential, but it is also indispensable for normal embryogenesis in many animals. Mechanically, unequal cleavage is achieved by either simple unequal cytokinesis or by forming a polar lobe at the egg's vegetal pole. In the present paper, the mechanisms for unequal cytokinesis involved in the first three cleavages in the oligochaete annelid Tubifex are reviewed. The three unequal cleavages are all brought about by an asymmetrically organized mitotic apparatus (MA). The MA of the first cleavage is monastral in that an aster is present at one pole of a bipolar spindle but not at the other. This monastra form, which arises as a result of the involvement of a single centrosome in the MA assembly, is both necessary and sufficient for unequal first cleavage. The egg cortex during the first mitosis is devoid of the ability to remodel spindle poles. In contrast to the non-cortical mechanisms for the first cleavage, asymmetry in the MA organization at the second and third cleavages depends solely on specialized properties of the cell cortex, to which one spindle pole is physically connected. A cortical attachment site for the second cleavage spindle is generated de novo at the cleavage membrane resulting from the first cleavage; it is an actin-based, cell contact-dependent structure. The cortical microtubule attachment site for the third cleavage, which functions independently of contact with other cells, is not generated at the cleavage membrane resulting from the second cleavage, but is located at the animal pole; it may originate from the second polar body formation and become functional at the 4-cell stage. PMID:9639353

  19. Exotic c c-bar Mesons

    E-print Network

    Eric Braaten

    2008-08-21

    A surprising number of new c c-bar mesons with masses above the D D-bar threshold have been discovered at the B factories. Some of them are ordinary charmonium states, but others are definitely exotic mesons. The current theoretical status of the new c c-bar mesons is summarized.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. Selectivity in ROS-induced peptide backbone bond cleavage.

    PubMed

    Stringfellow, Hannah M; Jones, Michael R; Green, Mandy C; Wilson, Angela K; Francisco, Joseph S

    2014-12-01

    Post-translational mechanisms of protein oxidation as a result of reactive oxygen species (ROS) can occur under physiological conditions to yield selective side-chain and backbone modifications including abstractions, donations, additions, substitutions, and fragmentation. In order to characterize the selectivity of radical-mediated fragmentation, quantum mechanical investigations using ab initio and density functional methods were employed to evaluate site, conformation, and pathway trends of small trialanine peptides resembling a ?-strand and a ?-turn. Comparisons of reaction enthalpies show that the diamide pathway is more energetically favorable than the ?-amidation pathway and that both pathways are site and conformationally selective. These findings readily contribute to the understanding of oxidative stress in biochemical processes. PMID:25369550

  6. 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.; Kühn, 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.; Savrié, 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.

    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.

  7. Failure mechanisms in wood joints bonded with urea-formaldehyde adhesives

    Microsoft Academic Search

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

    1994-01-01

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

  8. Interactive LDAP in C\\/C++ Interpreter

    Microsoft Academic Search

    Joshua Liu; Harry H. Cheng

    This article describes how to use the Lightweight Directory Access Protocol (LDAP) interactively with a C\\/C++ interpreter through the Ch LDAP package. Ch is an embeddable C\\/C++ interpreter that provides a superset of C. Ch LDAP is an open source binding to the open source OpenLDAP C API, and can be used to build client LDAP programs to add, delete,

  9. 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.

  10. Tuning of the Copper–Thioether Bond in Tetradentate N3S(thioether) Ligands; O–O 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 Cu–S 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 Cu–S 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

  11. Backbone and side-chain cleavages in electron detachment dissociation (EDD).

    PubMed

    Anusiewicz, Iwona; Jasionowski, Marek; Skurski, Piotr; Simons, Jack

    2005-12-15

    Ab-initio electronic structure methods are used to explore potential energy profiles pertinent to the fragmentations of gas-phase radicals thought to be formed in the new negative-ion mode EDD mass spectroscopic studies of peptides. Barriers to fragmentation as well as the associated overall energy differences are computed for the observed Calpha-C backbone bond cleavage as well as for side-chain loss for a variety of side chains (valine, arginine, glutamic acid, and tyrosine). It is found that Calpha-C bond cleavage is favored over side-chain loss, although loss of a tyrosine side chain may compete with Calpha-C cleavage because the tyrosine radical formed can delocalize its unpaired electron over its aromatic ring. In addition, it is found that fragmentation of the nitrogen-centered radicals formed in EDD results in cleavage to produce so-called a*/x fragments rather than a/x* fragments both because producing the former involves a significantly smaller barrier and is nearly thermoneutral, while cleavage to yield a/x* is significantly endothermic. PMID:16331920

  12. Exploring the structural constraints at cleavage site of mucin 1 isoform through molecular dynamics simulation.

    PubMed

    Kumari, J Lesitha Jeeva; Sudandiradoss, C

    2015-07-01

    In silico alanine scanning mutagenesis on the cleavable isoform of mucin 1 revealed isoleucine 67 as one of the key factors contributing to the strain at the autoproteolytic cleavage site. In this study, we demonstrate the structural basis of isoleucine-induced rigidity towards the strain-driven autoproteolysis at G(-1)S(+1) cleavage site of mucin 1. We further evaluated the gain in flexibility upon isoleucine 67 mutation through molecular dynamics and essential dynamics studies. The results show that the mutant exhibits stability in its secondary structural elements while the native displays a less-bonded network, however the cleavage site of native remains constrained. Essential dynamics revealed that large motions of the mutant were confined to the loop although the internal domain of the structure remains unaffected. Also, the mutation exerted a larger effect on the intraprotein interactions and consequently resulted in a stabilized motif at the cleavage. Analyses on MD trajectory conformations illustrate a completely disrupted motif in native as an effect of the peptide strain. The study also revealed that in mutant, the cleavage competent catalytic groups C=O and OG were in geometrical aspects unfavorable for a nucleophilic attack. The results support the earlier speculation that the presence of bulky isoleucine proximal G(-1)S(+1) cleavage site limits the conformational sampling of residues and therefore maintains the residues in a torsionally restrained conformation. PMID:25861899

  13. Autoactivation of mouse trypsinogens is regulated by chymotrypsin C via cleavage of the autolysis loop.

    PubMed

    Németh, Balázs Csaba; Wartmann, Thomas; Halangk, Walter; Sahin-Tóth, Miklós

    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

  14. Autoactivation of Mouse Trypsinogens Is Regulated by Chymotrypsin C via Cleavage of the Autolysis Loop*

    PubMed Central

    Németh, Balázs Csaba; Wartmann, Thomas; Halangk, Walter; Sahin-Tóth, Miklós

    2013-01-01

    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

  15. 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.

  16. 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

  17. 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

  18. 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

  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. [Cleavage of DNA fragments induced by UV nanosecond laser excitation at 193 nm].

    PubMed

    Vtiurina, N N; Grokhovski?, S L; Filimonov, I V; Medvedkov, O I; Nechipurenko, D Iu; Vasil'ev, S A; Nechipurenko, Iu D

    2011-01-01

    The cleavage of dsDNA fragments in aqueous solution after irradiation with UV laser pulses at 193 nm has been studied. Samples were investigated using polyacrylamide gel electrophoresis. The intensity of damage of particular phosphodiester bond after hot alkali treatment was shown to depend on the base pair sequence. It was established that the probability of cleavage is twice higher for sites of DNA containing two or more successively running guanine residues. A possible mechanism of damage to the DNA molecule connected with the migration of holes along the helix is discussed. PMID:21786693

  1. 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.

  2. (669)revision:2011-11-07modified:2011-11-08 NON COHEN ORACLE C.C.C

    E-print Network

    Shelah, Saharon

    (669)revision:2011-11-07modified:2011-11-08 NON COHEN ORACLE C.C.C SH669 SAHARON SHELAH Abstract. The oracle c.c.c. is closely related to Cohen forcing. During an iteration we can "omit a type"; i the parallel of the oracle c.c.c. and end with a criterion for extracting a subforcing (not a complete

  3. C/C++ Causal Cycles Confound Compositionality

    E-print Network

    Gotsman, Alexey

    , mainstream languages have begun to offer primi- tives for concurrent programming. To avoid the cost of inter-core cycles are known to be problematic: the Java standard tried to rule them out, but inadvertently forbade out cycles which avoids Java's problems. This remains a difficult open problem. BODY C/C++ permit

  4. CUDA C/C++ BASICS NVIDIA Corporation

    E-print Network

    Crawford, T. Daniel

    in this session? ! Start from "Hello World!" ! Write and launch CUDA C/C++ kernels ! Manage GPU memory() Asynchronous operation Handling errors Managing devices CONCEPTS #12;HELLO WORLD! Heterogeneous Computing results from GPU memory to CPU memory PCI Bus #12;Hello World! int main(void) { printf("Hello World

  5. The Extended Cleavage Specificity of Human Thrombin

    PubMed Central

    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

  6. MECHANISTIC STUDIES OF ARYL-OXYGEN BOND ACTIVATION IN A NICKEL(0) DIPHOSPHINE-ETHER COMPLEX

    E-print Network

    Winfree, Erik

    6 CHAPTER 2 MECHANISTIC STUDIES OF ARYL-OXYGEN BOND ACTIVATION IN A NICKEL(0) DIPHOSPHINE-ETHER of the reductive cleavage of aryl ethers by nickel, the reactivity of terphenyl diphosphine aryl alkyl ethers adjacent to a methyl aryl ether bond were isolated. Heating these systems led to aryl-oxygen bond

  7. ?c ? ??c* transition in lattice QCD

    NASA Astrophysics Data System (ADS)

    Bahtiyar, H.; Can, K. U.; Erkol, G.; Oka, M.

    2015-07-01

    We study the electromagnetic ?c ? ??c* transition in 2 + 1 flavor lattice QCD, which gives access to the dominant decay mode of ?c* baryon. The magnetic dipole and the electric quadrupole transition form factors are computed. The magnetic dipole form factor is found to be mainly determined by the strange quark and the electric quadrupole form factor to be negligibly small, in consistency with the quark model. We also evaluate the helicity amplitudes and the decay rate.

  8. Antisense oligonucleotide containing an internal, non-nucleotide-based linker promote site-specific cleavage of RNA.

    PubMed Central

    Reynolds, M A; Beck, T A; Say, P B; Schwartz, D A; Dwyer, B P; Daily, W J; Vaghefi, M M; Metzler, M D; Klem, R E; Arnold, L J

    1996-01-01

    We have designed and synthesized a series of novel antisense methylphosphonate oligonucleotide (MPO) cleaving agents that promote site-specific cleavage on a complementary RNA target. These MPOs contain a non- nucleotide-based linking moiety near the middle of the sequence in place of one of the nucleotide bases. The region surrounding the unpaired base on the RNA strand (i.e. the one directly opposite the non-nucleotide-linker) is sensitive to hydrolytic cleavage catalyzed by ethylenediamine hydrochloride. Furthermore, the regions of the RNA comprising hydrogen bonded domains are resistant to cleavage compared with single-stranded RNA alone. Several catalytic moieties capable of supporting acid/base hydrolysis were coupled to the non-nucleotide-based linker via simple aqueous coupling chemistries. When tethered to the MPO in this manner these moieties are shown to catalyze site-specific cleavage on the RNA target without any additional catalyst. PMID:8604321

  9. An unusal case of facile non-degenerate P-C bond making and breaking.

    PubMed

    Nesterov, Vitaly; Özbolat-Schön, Aysel; Schnakenburg, Gregor; Shi, Lili; Cangönül, Asli; van Gastel, Maurice; Neese, Frank; Streubel, Rainer

    2012-06-01

    Oxidation of Li/X phosphinidenoid complex 2, obtained via selective deprotonation from the P-H precursor 1, with [Ph(3)C]BF(4) led to the formation of two P-F substituted diorganophosphane complexes 6,7; the latter tautomer 7 formed via H-shift from 6. In contrast, oxidation of 2 with [(p-Tol)(3)C]BF(4) led to three major and one minor intermediates at low temperature, which we tentatively assign to two pairs of P-C atropisomers 10?a,a' and 10?c,c' and which differ by the relative orientations of their CH(SiMe(3))(2) and W(CO)(5) groups. Conversion of all isomers led finally to complex 11 having a ligand with a long P-C bond to the central trityl* carbon atom, firmly established by single-crystal X-ray analysis. DFT calculations at the B3LYP/def2-TZVPP//BP86/def2-TZVP level of theory on real molecular entities revealed the structures of the in situ formed combined singlet diradicals (4+5 and 5+9) and the nature of intermediates on the way to the final product, complex 11. Remarkable is that all isomers of 11 possess relative energies in the narrow energy regime of about 20?kcal ?mol(-1). A preliminary study revealed that complex 11 undergoes selective P-C bond cleavage at 75?°C in toluene solution. PMID:22488865

  10. Chemical Bonds

    NSDL National Science Digital Library

    The Concord Consortium

    2011-12-11

    Electrons are key to forming the two broad categories of chemical bonds: covalent and ionic. Atoms, which have a nucleus surrounded by electrons, are represented in several different ways. In the Chemical Bonds activity, students explore the different kinds of chemical bonds that can form, ranging from non-polar covalent to ionic. In the model depicted above students adjust the electronegativity of two atoms and see the effect it has on electron distribution and bond type.

  11. A New Paradigm for Enzymatic Control of ?-Cleavage and ?-Cleavage of the Prion Protein*

    PubMed Central

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

    2014-01-01

    The cellular form of the prion protein (PrPC) is found in both full-length and several different cleaved forms in vivo. Although the precise functions of the PrPC proteolytic products are not known, cleavage between the unstructured N-terminal domain and the structured C-terminal domain at Lys-109?His-110 (mouse sequence), termed ?-cleavage, has been shown to produce the anti-apoptotic N1 and the scrapie-resistant C1 peptide fragments. ?-Cleavage, residing adjacent to the octarepeat domain and N-terminal to the ?-cleavage site, is thought to arise from the action of reactive oxygen species produced from redox cycling of coordinated copper. We sought to elucidate the role of key members of the ADAM (a disintegrin and metalloproteinase) enzyme family, as well as Cu2+ redox cycling, in recombinant mouse PrP (MoPrP) cleavage through LC/MS analysis. Our findings show that although Cu2+ redox-generated reactive oxygen species do produce fragmentation corresponding to ?-cleavage, ADAM8 also cleaves MoPrP in the octarepeat domain in a Cu2+- and Zn2+-dependent manner. Additional cleavage by ADAM8 was observed at the previously proposed location of ?-cleavage, Lys-109?His-110 (MoPrP sequencing); however, upon addition of Cu2+, the location of ?-cleavage shifted by several amino acids toward the C terminus. ADAM10 and ADAM17 have also been implicated in ?-cleavage at Lys-109?His-110; however, we observed that they instead cleaved MoPrP at a novel location, Ala-119?Val-120, with additional cleavage by ADAM10 at Gly-227?Arg-228 near the C terminus. Together, our results show that MoPrP cleavage is far more complex than previously thought and suggest a mechanism by which PrPC fragmentation responds to Cu2+ and Zn2+. PMID:24247244

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

    PubMed

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

    2013-08-29

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

  13. Local Approach to Strength MisMatch Effect on Cleavage Fracture of Notched Material

    Microsoft Academic Search

    M. Ohata; F. Minami; M. Toyoda

    1996-01-01

    This paper discusses the strength mis-match effect on cleavage fracture of notched materials based on the local approach. The aim of the study is to verify the independence of the critical Weibull stress at fracture on the strength mis-match condition. Diffusion bonded joints were made with two materials S and H different in strength level. Two types of 3-point bend

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

    E-print Network

    Devoto, Stephen H.

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

  15. Does Cleavage Work at Work? Men, but Not Women, Falsely Believe Cleavage Sells a Weak Product

    ERIC Educational Resources Information Center

    Glick, Peter; Chrislock, Karyna; Petersik, Korinne; Vijay, Madhuri; Turek, Aleksandra

    2008-01-01

    We examined whether men, but not women, would be distracted by a female sales representative's exposed cleavage, leading to greater perceived efficacy for a weak, but not for a strong product. A community sample of 88 men and 97 women viewed a video of a female pharmaceutical sales representative who (a) had exposed cleavage or dressed modestly…

  16. 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 1.06×108 ?(3686) events collected with the BESIII detector, we present the first observation of the decays of ?(3686)???¯+?-+c.c. and ?(3686)???¯-?++c.c. The branching fractions are measured to be B(?(3686)???¯+?-+c.c.)=(1.40±0.03±0.13)×10-4 and B(?(3686)???¯-?++c.c.)=(1.54±0.04±0.13)×10-4, where the first errors are statistical and the second ones systematic.

  17. 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. (Purdue); (UBC)

    2014-10-02

    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.

  18. Computational prediction of cleavage using proteasomal in vitro digestion and MHC I ligand data*

    PubMed Central

    Lu, Yu-feng; Sheng, Hao; Zhang, Yi; Li, Zhi-yang

    2013-01-01

    Proteasomes are responsible for the production of the majority of cytotoxic T lymphocyte (CTL) epitopes. Hence, it is important to identify correctly which peptides will be generated by proteasomes from an unknown protein. However, the pool of proteasome cleavage data used in the prediction algorithms, whether from major histocompatibility complex (MHC) I ligand or in vitro digestion data, is not identical to in vivo proteasomal digestion products. Therefore, the accuracy and reliability of these models still need to be improved. In this paper, three types of proteasomal cleavage data, constitutive proteasome (cCP), immunoproteasome (iCP) in vitro cleavage, and MHC I ligand data, were used for training cleave-site predictive methods based on the kernel-function stabilized matrix method (KSMM). The predictive accuracies of the KSMM+pair coefficients were 75.0%, 72.3%, and 83.1% for cCP, iCP, and MHC I ligand data, respectively, which were comparable to the results from support vector machine (SVM). The three proteasomal cleavage methods were combined in turn with MHC I-peptide binding predictions to model MHC I-peptide processing and the presentation pathway. These integrations markedly improved MHC I peptide identification, increasing area under the receiver operator characteristics (ROC) curve (AUC) values from 0.82 to 0.91. The results suggested that both MHC I ligand and proteasomal in vitro degradation data can give an exact simulation of in vivo processed digestion. The information extracted from cCP and iCP in vitro cleavage data demonstrated that both cCP and iCP are selective in their usage of peptide bonds for cleavage. PMID:24009202

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  20. 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…

  1. Measurements of $?(3686) \\to K^{-} ?\\bar?^{+} +c.c.$ and $?(3686) \\to ?K^{-} ?\\bar?^{+} +c.c$

    E-print Network

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

    2015-04-08

    Using a sample of $1.06\\times10^8\\ \\psip$ events produced in $e^+e^-$ collisions at $\\sqrt{s}$ = 3.686 GeV and collected with the BESIII detector at the BEPCII collider, we present studies of the decays $\\klx+c.c.$ and $\\gklx+c.c.$. We observe two hyperons, $\\Xi(1690)^-$ and $\\Xi(1820)^-$, in the $K^-\\Lambda$ invariant mass distribution in the decay $\\klx+c.c.$ with significances of $4.9 \\sigma$ and $6.2 \\sigma$, respectively. The branching fractions of $\\klx+c.c.$, $\\ksx+c.c.$, $\\psip\\to\\gamma \\chi_{cJ}\\to \\gamma K^- \\Lambda \\bar{\\Xi}^+ +c.c.$ $(J=0,\\ 1,\\ 2)$, and $\\psip\\to \\Xi(1690/1820)^{-} \\bar{\\Xi}^++c.c$ with subsequent decay $\\Xi(1690/1820)^-\\to K^-\\Lambda$ are measured for the first time.

  2. 562 Organometallics 1983, 2, 562-563 atom to form a double bond to carbon. Thus the first-row

    E-print Network

    Jones, William D.

    suggest that the initial effect of the iron carbonyl is to causea ring openingby cleavage of the S(Se)-N bond, thus forming the diazoketo form of the ligand possibly stabilizedby a metal carbonyl fragment

  3. Aneuploidy in the Human Cleavage Stage Embryo

    Microsoft Academic Search

    A. Mantzouratou; J. D. A. Delhanty

    2011-01-01

    The cleavage stage embryo (days 1–3) stands out due to the high level of chromosomal anomalies, especially mosaicism that arises prior to global embryonic genome activation. Molecular cytogenetic studies show that an average of 60% of in vitro derived embryos have at least one aneuploid cell by the time they are 3 days old. However, comprehensive studies of the chromosome

  4. EDDIE fusion proteins: Triggering autoproteolytic cleavage

    Microsoft Academic Search

    Rene Ueberbacher; Astrid Dürauer; Karin Ahrer; Sabrina Mayer; Wolfgang Sprinzl; Alois Jungbauer; Rainer Hahn

    2009-01-01

    Heterologous proteins are often poorly expressed in Escherichia coli and especially small peptides are prone to degradation. Npro autoprotease fusion proteins, deposited as inclusion bodies in E. coli, are a versatile tool for peptide and protein overexpression and generate an authentic N terminus at the target molecule. Autoproteolytic cleavage and subsequent release of the fusion partner are initiated upon refolding.

  5. Bond Dissociation Free Energies (BDFEs) of the Acidic H-A Bonds in HA(*)(-) Radical Anions by Three Different Pathways.

    PubMed

    Zhao, Yongyu; Bordwell, Frederick G.

    1996-09-20

    Cleavage of radical anions, HA(*)(-), have been considered to give either H(*) + A(-) (path a) or H(-) + A(*) (path b), and factors determining the preferred mode of cleavage have been discussed. It is conceivable that cleavage to give a proton and a radical dianion, HA(*)(-) right harpoon over left harpoon H(+) + A(*)(2)(-) (path c), might also be feasible. A method, based on a thermodynamic cycle, to estimate the bond dissociation free energy (BDFE) by path c has been devised. Comparison of the BDFEs for cleavage of the radical anions derived from 24 nitroaromatic OH, SH, NH, and CH acids by paths a, b, c has shown that path c is favored thermodynamically. PMID:11667531

  6. 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.

  7. Strong Bond Activation with Late Transition-Metal Pincer Complexes as a Foundation for Potential Catalysis 

    E-print Network

    Zhu, Yanjun

    2012-07-16

    cleavage of B-H and B-B bonds across the N-Pd bond in a cationic (PNP)Pd fragment, the C-H oxidative addition to a (PNP)Ir center and the recent results on the C-H and C-O oxidative addition in reactions of aryl carboxylates with the (PNP)Rh fragment...

  8. Strong Bond Activation with Late Transition-Metal Pincer Complexes as a Foundation for Potential Catalysis

    E-print Network

    Zhu, Yanjun

    2012-07-16

    cleavage of B-H and B-B bonds across the N-Pd bond in a cationic (PNP)Pd fragment, the C-H oxidative addition to a (PNP)Ir center and the recent results on the C-H and C-O oxidative addition in reactions of aryl carboxylates with the (PNP)Rh fragment...

  9. Copper.Lys-Gly-His-Lys mediated cleavage of tRNA(Phe): studies of reaction mechanism and cleavage specificity.

    PubMed

    Bradford, Seth; Kawarasaki, Yuta; Cowan, J A

    2009-06-01

    The reactivity of [Cu2+.Lys-Gly-His-Lys-NH2]2+ and [Cu2+.Lys-Gly-His-Lys]+ toward tRNA(Phe) has been evaluated. The amidated and carboxylate forms of the copper peptides display complex binding behavior with strong and weak sites evident (K(D1)(app) approximately 71 microM, K(D2)(app) approximately 211 microM for the amide form; and K(D1)(app) approximately 34 microM, K(D2)(app) approximately 240 microM for the carboxylate form), while Cu2+(aq) yielded K(D1)(app) approximately 81 microM and K(D2)(app) approximately 136 microM. The time-dependence of the reaction of [Cu2+.Lys-Gly-His-Lys]+ and [Cu2+.Lys-Gly-His-Lys-NH2]2+ with tRNA(Phe) yielded k(obs) approximately 0.075 h(-1) for both complexes. HPLC analysis of the reaction products demonstrated guanine as the sole base product. Mass spectrometric data shows a limited number of cleavage fragments with product peak masses consistent with chemistry occurring at a discrete site defined by the structurally contiguous D and TPsiC loops, and in a domain where high affinity magnesium centers have previously been observed to promote hydrolysis of the tRNA(Phe) backbone. This cleavage pattern is more selective than that previously observed by Long and coworkers for nickel complexes of a series of C-terminally amidated peptides (Gly-Gly-His, Lys-Gly-His, and Arg-Gly-His), and may reflect variations in structural recognition and a distinct reaction path by the nickel derivatives. The data emphasizes the optimal positioning of the metal-associated reactive oxygen species, relative to scissile bonds, as a major criterion for development of efficient catalytic nucleases or therapeutics. PMID:19386364

  10. Insights into Avian Influenza Virus Pathogenicity: the Hemagglutinin Precursor HA0 of Subtype H16 Has an Alpha-Helix Structure in Its Cleavage Site with Inefficient HA1/HA2 Cleavage

    PubMed Central

    Lu, Xishan; Shi, Yi; Gao, Feng; Xiao, Haixia; Wang, Ming; Qi, Jianxun

    2012-01-01

    With a new serotype (H17) of hemagglutinin (HA) recently being discovered, there are now 17 serotypes (H1 to H17) of influenza A viruses in total. It is believed that HA is initially expressed as a precursor of HA0 and then cleaved into HA1 and HA2, forming a disulfide bond-linked complex, for its full function. Structural data show that a loop structure exists in the cleavage site between HA1 and HA2, and this flexible loop is crucial for the efficient cleavage of HA0. Here, the crystal structures of H16 (a low-pathogenicity avian influenza virus) in their HA0 form (H16HA0) have been solved at 1.7-? and 2.0-? resolutions. To our surprise, an ?-helix element in the cleavage site which inserts into the negatively charged cavity with the key residue R329 hidden behind the helix was observed. In vitro trypsin cleavage experiments demonstrated inefficient cleavage of H16HA0 under both neutral and low-pH conditions. The results provide new insights into influenza A virus pathogenicity; both the relatively stable ?-helix structure in the flexible cleavage loop and inaccessibility of the cleavage site likely contribute to the low pathogenicity of avian influenza A virus. Furthermore, compared to all of the HAs whose structures have been solved, H16 is a good reference for assigning the HA subtypes into two groups on the basis of the three-dimensional structure, which is consistent with the phylogenetic grouping. We conclude that in light of the current H16HA0 structure, the natural ?-helix element might provide a new opportunity for influenza virus inhibitor design. PMID:22993148

  11. Insights into avian influenza virus pathogenicity: the hemagglutinin precursor HA0 of subtype H16 has an alpha-helix structure in its cleavage site with inefficient HA1/HA2 cleavage.

    PubMed

    Lu, Xishan; Shi, Yi; Gao, Feng; Xiao, Haixia; Wang, Ming; Qi, Jianxun; Gao, George F

    2012-12-01

    With a new serotype (H17) of hemagglutinin (HA) recently being discovered, there are now 17 serotypes (H1 to H17) of influenza A viruses in total. It is believed that HA is initially expressed as a precursor of HA0 and then cleaved into HA1 and HA2, forming a disulfide bond-linked complex, for its full function. Structural data show that a loop structure exists in the cleavage site between HA1 and HA2, and this flexible loop is crucial for the efficient cleavage of HA0. Here, the crystal structures of H16 (a low-pathogenicity avian influenza virus) in their HA0 form (H16HA0) have been solved at 1.7-? and 2.0-? resolutions. To our surprise, an ?-helix element in the cleavage site which inserts into the negatively charged cavity with the key residue R329 hidden behind the helix was observed. In vitro trypsin cleavage experiments demonstrated inefficient cleavage of H16HA0 under both neutral and low-pH conditions. The results provide new insights into influenza A virus pathogenicity; both the relatively stable ?-helix structure in the flexible cleavage loop and inaccessibility of the cleavage site likely contribute to the low pathogenicity of avian influenza A virus. Furthermore, compared to all of the HAs whose structures have been solved, H16 is a good reference for assigning the HA subtypes into two groups on the basis of the three-dimensional structure, which is consistent with the phylogenetic grouping. We conclude that in light of the current H16HA0 structure, the natural ?-helix element might provide a new opportunity for influenza virus inhibitor design. PMID:22993148

  12. Deprotonation of coordinated phosphanes in a rhenium complex: C-C coupling with diimine coligands.

    PubMed

    Arévalo, Rebeca; Pérez, Julio; Riera, Lucía

    2015-02-23

    The reaction of fac-[Re(bipy)(CO)3(PMe3)][OTf] (bipy = 2,2'-bipyridine) with KN(SiMe3)2 affords two neutral products: cis,trans-[Re(bipy)(CO)2(CN)(PMe3)], and a thermally unstable compound, which features a new C-C bond between a P-bonded methylene group (from methyl group deprotonation) and the C6 position of bipy. The solid-state structures of more stable 1,2-bis[(2,6-diisopropylphenyl)imino]acenaphthene analogs, resulting from the deprotonation of PMe3, PPhMe2, and PPh2Me ligands, are determined by X-ray diffraction. PMID:25604138

  13. Small molecule activators of pre-mRNA 3? cleavage

    PubMed Central

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

    2009-01-01

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

  14. Mechanochemistry: One Bond at a Time

    PubMed Central

    Liang, Jian; Fernández, Julio M.

    2009-01-01

    Single-molecule force clamp spectroscopy offers a novel platform for mechanically denaturing proteins by applying a constant force to a polyprotein. A powerful emerging application of the technique is that, by introducing a disulfide bond in each protein module, the chemical kinetics of disulfide bond cleavage under different stretching forces can be probed at the single-bond level. Even at forces much lower than that can rupture the chemical bond, the breaking of the S-S bond at the presence of various chemical reducing agents is significantly accelerated. Our previous work demonstrated that the rate of thiol/disulfide exchange reaction is force-dependent, and well described by an Arrhenius term of the form: r = A(exp((F?xr-Ea)/kBT)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate we measured the bond elongation parameter, ?xr, along the reaction coordinate to the transition state of the SN2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the ?xr value can help depicting the energy landscapes and elucidating the mechanisms of the reactions at the single-molecule level. Small nucleophiles, such as 1, 4-DL-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP) and L-cysteine, react with the S-S bond with monotonically increasing rates under the applied force; while thioredoxin enzymes exhibit both stretching-favored and —resistant reaction-rate regimes. These measurements demonstrate the power of single-molecule force clamp spectroscopy approach in providing unprecedented access to chemical reactions. PMID:19572737

  15. Reductive cleavage of demeton-S-methyl by Corynebacterium glutamicum in cometabolism on more readily metabolizable substrates.

    PubMed

    Girbal, L; Hilaire, D; Leduc, S; Delery, L; Rols, J L; Lindley, N D

    2000-03-01

    Corynebacterium glutamicum is able to biotransform demeton-S-methyl, an organophosphorus compound, during cometabolism with more readily metabolizable substrates. Among the cosubstrates used, fructose is the growth substrate that is most favorable for demeton-S-methyl biotransformation. The reaction mechanism of demeton-S-methyl biotransformation involves reductive cleavage of an S-C bond, which leads to accumulation of dimethyl thiophosphate in the culture medium. PMID:10698792

  16. Reductive Cleavage of Demeton-S-Methyl by Corynebacterium glutamicum in Cometabolism on More Readily Metabolizable Substrates

    PubMed Central

    Girbal, Laurence; Hilaire, Didier; Leduc, Sébastien; Delery, Laure; Rols, Jean-Luc; Lindley, Nicholas D.

    2000-01-01

    Corynebacterium glutamicum is able to biotransform demeton-S-methyl, an organophosphorus compound, during cometabolism with more readily metabolizable substrates. Among the cosubstrates used, fructose is the growth substrate that is most favorable for demeton-S-methyl biotransformation. The reaction mechanism of demeton-S-methyl biotransformation involves reductive cleavage of an S-C bond, which leads to accumulation of dimethyl thiophosphate in the culture medium. PMID:10698792

  17. Oxidative cleavage of cellulose by fungal copper-dependent polysaccharide monooxygenases.

    PubMed

    Beeson, William T; Phillips, Christopher M; Cate, Jamie H D; Marletta, Michael A

    2012-01-18

    Fungal-derived, copper-dependent polysaccharide monooxygenases (PMOs), formerly known as GH61 proteins, have recently been shown to catalyze the O(2)-dependent oxidative cleavage of recalcitrant polysaccharides. Different PMOs isolated from Neurospora crassa were found to generate oxidized cellodextrins modified at the reducing or nonreducing ends upon incubation with cellulose and cellobiose dehydrogenase. Here we show that the nonreducing end product formed by an N. crassa PMO is a 4-ketoaldose. Together with isotope labeling experiments, further support is provided for a mechanism involving oxygen insertion and subsequent elimination to break glycosidic bonds in crystalline cellulose. PMID:22188218

  18. 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

  19. 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.

  20. Photophysical properties of cyclometalated Pt(II) complexes attached with pyrene by C C single bond

    Microsoft Academic Search

    Qian Wang; Fei Xiong; Fabrice Morlet-Savary; Shayu Li; Yi Li; Jean-Pierre Fouassier; Guoqiang Yang

    2008-01-01

    Luminescent complexes, [(C^N^N)Pt(C?CR)](HC^N^N=4-(1-phenyl)-6-phenyl-2,2?-bipyridine, R=Ph (1, PPPt); HC^N^N=4-(1-pyrene)-6-phenyl-2, 2?-bipyridine; R=Ph (2, PyPPt), p-Et-Ph (3, PyEPPt)), were synthesized and their photophysical properties were investigated in acetonitrile liquid solution and butyronitrile glasses at 77K. These complexes display steady state dual emissions at room temperature and 77K. The emission lifetime and transient absorption of these complexes illustrated that the 3IL triplet state of the

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

    PubMed Central

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

    2013-01-01

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

  2. C-C Activation in Biphenylene. Synthesis, Structure, and Reactivity of (C5Me5)2M2(2,2-biphenyl) (M ) Rh, Co)

    E-print Network

    Jones, William D.

    in which unstrained C-C bonds are cleaved, but these typically rely upon formation of an 5-C5R5 or 6-C6R6. Chem. Ber. 1976, 109, 1429. Crabtree, R. H.; Dion, R. P.; Gibboni, D. J.; McGrath, D. V.; Holt, E. M. J

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

    PubMed

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

    2010-01-21

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

  4. Prediction of Missed Proteolytic Cleavages for the Selection of Surrogate Peptides for Quantitative Proteomics

    PubMed Central

    Lawless, Craig

    2012-01-01

    Abstract Quantitative proteomics experiments are usually performed using proteolytic peptides as surrogates for their parent proteins, inferring protein amounts from peptide-level quantitation. This process is frequently dependent on complete digestion of the parent protein to its limit peptides so that their signal is truly representative. Unfortunately, proteolysis is often incomplete, and missed cleavage peptides are frequently produced that are unlikely to be optimal surrogates for quantitation, particularly for label-mediated approaches seeking to derive absolute values. We have generated a predictive computational tool that is able to predict which candidate proteolytic peptide bonds are likely to be missed by the standard enzyme trypsin. Our cross-validated prediction tool uses support vector machines and achieves high accuracy in excess of 0.94 precision (PPV), with attendant high sensitivity of 0.79, across multiple proteomes. We believe this is a useful tool for selecting candidate quantotypic peptides, seeking to minimize likely loss owing to missed cleavage, which will be a boon for quantitative proteomic pipelines as well as other areas of proteomics. Our results are discussed in the context of recent results examining the kinetics of missed cleavages in proteomic digestion protocols, and show agreement with observed experimental trends. The software has been made available at http://king.smith.man.ac.uk/mcpred. PMID:22804685

  5. Unequal cleavage and the differentiation of echinoid primary mesenchyme.

    PubMed

    Langelan, R E; Whiteley, A H

    1985-06-01

    The role of unequal cleavage in echinoid micromere determination was investigated by equalizing the fourth and fifth cleavages with brief surfactant treatment. The surfactant sodium dodecyl sulfate was found to be effective in equalizing fourth cleavage when generally applied to 4-cell stage embryos of all species tested. Embryos of the sand dollar Dendraster excentricus developed normally when equalized at the fourth and fifth cleavages by surfactant treatment, as did untreated equally cleaving embryos of the sea urchin Strongylocentrotus droebachiensis. Embryos of the sea urchins Lytechinus pictus and S. purpuratus were animalized by the treatment but were capable of forming spicules after treatments which equalized the fourth cleavage. In addition, orientation of the fourth division spindles was found to have no effect on differentiation of the primary mesenchyme in D. excentricus. The results confirm that micromere determination in echinoids does not depend upon a strict cleavage pattern at the 16-cell stage. PMID:3996759

  6. Autocatalytic cleavage within classical swine fever virus NS3 leads to a functional separation of protease and helicase.

    PubMed

    Lamp, Benjamin; Riedel, Christiane; Wentz, Eveline; Tortorici, Maria-Alejandra; Rümenapf, Till

    2013-11-01

    Classical swine fever virus (CSFV) is a positive-stranded RNA virus belonging to the genus Pestivirus within the Flaviviridae family. Pivotal for processing of a large portion of the viral polyprotein is a serine protease activity within nonstructural protein 3 (NS3) that also harbors helicase and NTPase activities essential for RNA replication. In CSFV-infected cells, NS3 appears as two forms, a fully processed NS3 of 80 kDa and the precursor molecule NS2-3 of 120 kDa. Here we report the identification and mapping of additional autocatalytic intramolecular cleavages. One cleavable peptide bond occurs between Leu1781 and Met1782, giving rise to a helicase subunit of 55 kDa and, depending on the substrate, a NS2-3 fragment of 78 kDa (NS2-3p) or a NS3 protease subunit of 26 kDa (NS3p). In trans-cleavage assays using NS4-5 as a substrate, NS3p acts as a fully functional protease that is able to process the polyprotein. NS3p comprises the minimal essential protease, as deletion of Leu1781 results in inactivation. A second intramolecular cleavage was mapped to the Leu1748/Lys1749 peptide bond that yields a proteolytically inactive NS3 fragment. Deletion of either of the cleavage site residues resulted in a loss of RNA infectivity, indicating the functional importance of amino acid identity at the respective positions. Our data suggest that internal cleavage within the NS3 moiety is a common process that further extends the functional repertoires of the multifunctional NS2-3 or NS3 and represents another level of the complex polyprotein processing of Flaviviridae. PMID:23986594

  7. 7. Historic American Buildings Survey, C. C. Adams, Photographer August ...

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

    7. Historic American Buildings Survey, C. C. Adams, Photographer August 1931, SEED PACKING ROOM, Gift of New York State Department of Education. - Shaker North Family Washhouse (first), Shaker Road, New Lebanon, Columbia County, NY

  8. 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-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.

  9. 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)

  10. The N-terminal nucleophile serine of cephalosporin acylase executes the second autoproteolytic cleavage and acylpeptide hydrolysis.

    PubMed

    Yin, Jun; Deng, Zixin; Zhao, Guoping; Huang, Xi

    2011-07-01

    Cephalosporin acylase (CA) precursor is translated as a single polypeptide chain and folds into a self-activating pre-protein. Activation requires two peptide bond cleavages that excise an internal spacer to form the mature ?? heterodimer. Using Q-TOF LC-MS, we located the second cleavage site between Glu(159) and Gly(160), and detected the corresponding 10-aa spacer (160)GDPPDLADQG(169) of CA mutants. The site of the second cleavage depended on Glu(159): moving Glu into the spacer or removing 5-10 residues from the spacer sequence resulted in shorter spacers with the cleavage at the carboxylic side of Glu. The mutant E159D was cleaved more slowly than the wild-type, as were mutants G160A and G160L. This allowed kinetic measurements showing that the second cleavage reaction was a first-order, intra-molecular process. Glutaryl-7-aminocephalosporanic acid is the classic substrate of CA, in which the N-terminal Ser(170) of the ?-subunit, is the nucleophile. Glu and Asp resemble glutaryl, suggesting that CA might also remove N-terminal Glu or Asp from peptides. This was indeed the case, suggesting that the N-terminal nucleophile also performed the second proteolytic cleavage. We also found that CA is an acylpeptide hydrolase rather than a previously expected acylamino acid acylase. It only exhibited exopeptidase activity for the hydrolysis of an externally added peptide, supporting the intra-molecular interaction. We propose that the final CA activation is an intra-molecular process performed by an N-terminal nucleophile, during which large conformational changes in the ?-subunit C-terminal region are required to bridge the gap between Glu(159) and Ser(170). PMID:21576250

  11. 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

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

    PubMed Central

    Rodrigo, María J.; Alquézar, Berta; Al-Babili, Salim

    2013-01-01

    Citrus is the first tree crop in terms of fruit production. The colour of Citrus fruit is one of the main quality attributes, caused by the accumulation of carotenoids and their derivative C30 apocarotenoids, mainly ?-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

  13. 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.

  14. A dense and strong bonding collagen film for carbon/carbon composites

    NASA Astrophysics Data System (ADS)

    Cao, Sheng; Li, Hejun; Li, Kezhi; Lu, Jinhua; Zhang, Leilei

    2015-08-01

    A strong bonding collagen film was successfully prepared on carbon/carbon (C/C) composites. The surface conditions of the modified C/C composites were detected by contact angle measurements, scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS) and Raman spectra. The roughness, optical morphology, bonding strength and biocompatibility of collagen films at different pH values were detected by confocal laser scanning microscope (CLSM), universal test machine and cytology tests in vitro. After a 4-h modification in 30% H2O2 solution at 100 °C, the contact angle on the surface of C/C composites was decreased from 92.3° to 65.3°. Large quantities of hydroxyl, carboxyl and carbonyl functional groups were formed on the surface of the modified C/C composites. Then a dense and continuous collagen film was prepared on the modified C/C substrate. Bonding strength between collagen film and C/C substrate was reached to 8 MPa level when the pH value of this collagen film was 2.5 after the preparing process. With 2-day dehydrathermal treatment (DHT) crosslinking at 105 °C, the bonding strength was increased to 12 MPa level. At last, the results of in vitro cytological test showed that this collagen film made a great improvement on the biocompatibility on C/C composites.

  15. Analysis of the recognition mechanism involved in the EcoRV catalyzed cleavage of DNA using modified oligodeoxynucleotides.

    PubMed Central

    Fliess, A; Wolfes, H; Seela, F; Pingoud, A

    1988-01-01

    We have prepared a series of undecadeoxynucleotides that contain changes in the functional group pattern present within the EcoRV recognition site - GATATC-. Oligonucleotides were synthesized on solid phase using normal and modified beta-cyanoethylphosphoramidites and analyzed in steady state cleavage experiments with the EcoRV restriction endonuclease. The following groups appear to interact strongly with the enzyme, since their modification or substitution renders the oligonucleotides refractory to cleavage: the exocyclic NH2-groups of both A residues, the N7 of the first A residue, the exocyclic NH2-group of the C residue and the CH3-groups of both T residues. The exocyclic NH-group of the G residue supports effective recognition, since its absence lowers the kcat of the cleavage reaction. The N7 of the second A residue and the C5 position of the C residue apparently are not recognized by EcoRV; their substitution by -CH- or modification with -Br or -CH3, resp., does not considerably change the rate of cleavage. All oligonucleotides investigated compete with the unmodified substrate for binding to the enzyme. We conclude that EcoRV recognizes its substrate presumably through hydrogen bonds to the exocyclic NH2-group and the N7 of the first A residue, the exocyclic NH2-groups of the second A and the C residue, as well as through hydrophobic interactions with both T residues. PMID:3062581

  16. Vicariance patterns in the Mediterranean Sea: eastwest cleavage and low

    E-print Network

    Teixeira, Sara

    ORIGINAL ARTICLE Vicariance patterns in the Mediterranean Sea: east­west cleavage and low dispersal oceanica is a clonal angiosperm endemic to the Mediterranean Sea. Previous studies have suggested of the Mediterranean Sea as a whole, a strong east­west cleavage was detected (amova). These results are in line

  17. Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by

    E-print Network

    Sali, Andrej

    Resource Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling this method to study apoptosis, we have sequenced 333 caspase-like cleavage sites distributed among 292 to elicit apoptosis. INTRODUCTION Apoptosis is a noninflammatory form of cell death that regulates tissue

  18. Specific oxidative cleavage of carotenoids by VP14 of maize

    Microsoft Academic Search

    S. H. Schwartz; J. A. D. Zeevaart; D. A. Gage; Bao Cai Tan

    1997-01-01

    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

  19. Resistance curve behavior of polycrystalline niobium failing via cleavage

    Microsoft Academic Search

    D Padhi; J. J Lewandowski

    2004-01-01

    The present work illustrates the crack growth resistance behavior of polycrystalline niobium failing via transgranular cleavage fracture. Bend tests were conducted on fatigue-precracked Charpy specimens at ?125 and ?75°C under different loading rates. Crack growth was monitored in situ during the tests in order to compute the fracture initiation toughness and develop crack growth resistance curves. The cleavage fracture initiation

  20. Highly Selective Dissociation of a Peptide Bond Following Excitation of Core Electrons.

    PubMed

    Lin, Yi-Shiue; Tsai, Cheng-Cheng; Lin, Huei-Ru; Hsieh, Tsung-Lin; Chen, Jien-Lian; Hu, Wei-Ping; Ni, Chi-Kung; Liu, Chen-Lin

    2015-06-18

    The controlled breaking of a specific chemical bond with photons in complex molecules remains a major challenge in chemistry. In principle, using the K-edge absorption of a particular atomic element, one might excite selectively a specific atomic entity in a molecule. We report here highly selective dissociation of the peptide bonds in N-methylformamide and N-methylacetamide on tuning the X-ray wavelength to the K-edge absorption of the atoms connected to (or near) the peptide bond. The high selectivity (56-71%) of this cleavage arises from the large energy shift of X-ray absorption, a large overlap of the 1s orbital and the valence ?* orbital that is highly localized on a peptide bond with antibonding character, and the relatively low bond energy of the peptide bonds. These characteristics indicate that the high selectivity on bond dissociation following core excitation could be a general feature for molecules containing peptide bonds. PMID:25988354

  1. c/c: UAB, SRH Universidade de Braslia

    E-print Network

    Maier, Rudolf Richard

    -UnB). Brasília, 22 de janeiro de 2010. Prof ª Márcia Abrahão Moura Decana de Ensino de Graduação #12;c/c: UAB Márcia Abrahão Moura Decana de Ensino de Graduação #12;c/c: UAB, SRH Universidade de Brasília Decanato de Brasil (UAB-UnB). Brasília, 22 de janeiro de 2010. Prof ª Márcia Abrahão Moura Decana de Ensino de

  2. Quantification of C?C and C?O Surface Carbons in Detonation Nanodiamond by NMR

    SciTech Connect

    Cui, J -F; Fang, X -W; Schmidt-Rohr, K

    2014-05-08

    The ability of solid-state 13C NMR to detect and quantify small amounts of sp2-hybridized carbon on the surface of ?5 nm diameter nanodiamond particles is demonstrated. The C?C carbon fraction is only 1.1 ± 0.4% in pristine purified detonation nanodiamond, while a full single-layer graphitic or “bucky diamond” shell would contain ca. 25% of all C in a 5 nm diameter particle. Instead of large aromatic patches repeatedly proposed in the recent literature, sp3-hybridized CH and COH carbons cover most of the nanodiamond particle surface, accounting for ?5% each. C?O and COO groups also seen in X-ray absorption near-edge structure spectroscopy (XANES) but not detected in previous NMR studies make up ca. 1.5% of all C. They are removed by heat treatment at 800 °C, which increases the aromatic fraction. 13C{1H} NMR demonstrates that the various sp2-hybridized carbons are mostly not protonated, but cross-polarization shows that they are separated from 1H by only a few bond lengths, which proves that they are near the protonated surface. Together, the observed C–H, C–OH, C?O, and C?C groups account for 12–14% of all C, which matches the surface fraction expected for bulk-terminated 5 nm diameter diamond particles.

  3. Facile scission of isonitrile carbon–nitrogen triple bond using a diborane(4) reagent

    PubMed Central

    Asakawa, Hiroki; Lee, Ka-Ho; Lin, Zhenyang; Yamashita, Makoto

    2014-01-01

    Transition metal reagents and catalysts are generally effective to cleave all three bonds (one ? and two ?) in a triple bond despite its high bonding energy. Recently, chemistry of single-bond cleavage by using main-group element compounds is rapidly being developed in the absence of transition metals. However, the cleavage of a triple bond using non-transition-metal compounds is less explored. Here we report that an unsymmetrical diborane(4) compound could react with carbon monoxide and tert-butyl isonitrile at room temperature. In the latter case, the carbon–nitrogen triple bond was completely cleaved in the absence of transition metal as confirmed by X-ray crystallographic analysis, 13C NMR spectroscopy with 13C labelling and DFT calculations. The DFT calculations also revealed the detailed reaction mechanism and indicated that the key for the carbon–nitrogen triple-bond cleavage could be attributed to the presence of nucleophilic nitrogen atom in one of the intermediates. PMID:24967910

  4. Rubber Oxygenase and Latex Clearing Protein Cleave Rubber to Different Products and Use Different Cleavage Mechanisms

    PubMed Central

    Birke, Jakob

    2014-01-01

    Two types of enzyme for oxidative cleavage of poly(cis-1,4-isoprene) are known. One is rubber oxygenase (RoxA) that is secreted by Xanthomonas sp. strain 35Y and a few other Gram-negative rubber-degrading bacteria during growth on polyisoprene. RoxA was studied in the past, and the recently solved structure showed a structural relationship to bacterial cytochrome c peroxidases (J. Seidel et al., Proc. Natl. Acad. Sci. U. S. A. 110:13833–13838, 2013, http://dx.doi.org/10.1073/pnas.1305560110). The other enzyme is latex-clearing protein (Lcp) that is secreted by rubber-degrading actinomycetes, but Lcp has not yet been purified. Here, we expressed Lcp of Streptomyces sp. strain K30 in a ?roxA background of Xanthomonas sp. strain 35Y and purified native (untagged) Lcp. The specific activities of Lcp and RoxA were 0.70 and 0.48 U/mg, respectively. Lcp differed from RoxA in the absence of heme groups and other characteristics. Notably, Lcp degraded polyisoprene via endo-type cleavage to tetra-C20 and higher oligo-isoprenoids with aldehyde and keto end groups, whereas RoxA used an exo-type cleavage mechanism to give the main end product 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD). RoxA was able to cleave isolated Lcp-derived oligo-isoprenoid molecules to ODTD. Inhibitor studies, spectroscopic investigations and metal analysis gave no indication for the presence of iron, other metals, or cofactors in Lcp. Our results suggest that Lcp could be a member of the growing group of cofactor-independent oxygenases and differs in the cleavage mechanism from heme-dependent RoxA. In conclusion, RoxA and Lcp represent two different answers to the same biochemical problem, the cleavage of polyisoprene, a polymer that has carbon-carbon double bonds as the only functional groups for enzymatic attack. PMID:24907333

  5. [On the classification of the cleavage patterns in amphibian embryos].

    PubMed

    Desnitski?, 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

  6. 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.

  7. Topological properties of hydrogen bonds and covalent bonds from charge densities obtained by the maximum entropy method (MEM)

    PubMed Central

    Netzel, Jeanette; van Smaalen, Sander

    2009-01-01

    Charge densities have been determined by the Maximum Entropy Method (MEM) from the high-resolution, low-temperature (T ? 20?K) X-ray diffraction data of six different crystals of amino acids and peptides. A comparison of dynamic deformation densities of the MEM with static and dynamic deformation densities of multipole models shows that the MEM may lead to a better description of the electron density in hydrogen bonds in cases where the multipole model has been restricted to isotropic displacement parameters and low-order multipoles (l max = 1) for the H atoms. Topological properties at bond critical points (BCPs) are found to depend systematically on the bond length, but with different functions for covalent C—C, C—N and C—O bonds, and for hydrogen bonds together with covalent C—H and N—H bonds. Similar dependencies are known for AIM properties derived from static multipole densities. The ratio of potential and kinetic energy densities |V(BCP)|/G(BCP) is successfully used for a classification of hydrogen bonds according to their distance d(H?O) between the H atom and the acceptor atom. The classification based on MEM densities coincides with the usual classification of hydrogen bonds as strong, intermediate and weak [Jeffrey (1997) ?. An Introduction to Hydrogen Bonding. Oxford University Press]. MEM and procrystal densities lead to similar values of the densities at the BCPs of hydrogen bonds, but differences are shown to prevail, such that it is found that only the true charge density, represented by MEM densities, the multipole model or some other method can lead to the correct characterization of chemical bonding. Our results do not confirm suggestions in the literature that the promolecule density might be sufficient for a characterization of hydrogen bonds. PMID:19767685

  8. C.C. Berndt: Professional 1 Following your Passion while

    E-print Network

    Alpay, S. Pamir

    Applications · Neck Rings · Plungers · Bottom Plates · Moulds · Preform Blanks · Guide Rings · I.D. Fan Blades and Compressor Rods ·Plungers ·Valves, Thermowells ·Pump Impellors · Brick and Tile · Cement Mixers · Conveyers · Saw Blades #2 5 #12;C.C. Berndt: Professional Biomedical: Dental & Orthopedic Applications

  9. Photonics Integration for THz Generation , C.C. Renaud

    E-print Network

    Haddadi, Hamed

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

  10. Submitted to: c C. Colombo and G. J. Pace

    E-print Network

    Pace, Gordon J.

    Submitted to: FESCA 2014 c C. Colombo and G. J. Pace This work is licensed under the Creative Commons Attribution License. Comprehensive Monitor-Oriented Compensation Programming Christian Colombo Gordon J. Pace Department of Computer Science University of Malta {christian.colombo | gordon

  11. CARBON ISOTOPE EFFECTS (C\\/C) IN BIOLOGICAL SYSTEMS

    Microsoft Academic Search

    Alexander A. Ivlev

    2001-01-01

    Carbon isotope (C\\/C) fractionation (CIF) occurring in cells of organisms of different types is considered. Three metabolic points are shown to have an exceptional significance for the observed carbon isotope distribution in a living matter: 1) ribulose bisphosphate carboxylation in CO2 photoassimilation; 2) glycine decarboxylation in photorespiration; and 3) pyruvate decarboxylation in respiration metabolism. Carbon isotope effects (CIE) in ribulose

  12. C\\/C++ Conditional Compilation Analysis using Symbolic Execution

    Microsoft Academic Search

    Ying Hu; Ettore Merlo; Michel Dagenaisl; Bruno Laguë

    2000-01-01

    Conditional compilation is one of the most powerful parts of a C\\/C++ environment available for building software for different platforms with different feature sets. Although conditional compilation is powerful, it can be difficult to understand and is error-prone. In large software systems, file inclusion, conditional compilation and macro substitution are closely related and are often largely interleaved. Without adequate tools,

  13. SUBJECT NAME 30033 1 Evolutionary Computation C C R

    E-print Network

    Autonoma de Madrid, Universidad

    SUBJECT NAME 30033 1 Evolutionary Computation C C R 30034 1 Model Driven Formal Software Design C 30041 1 Connectivity Models C 30042 1 Computational Neuroscience I: Theoretical Models and Applications in Neuronal Computing C 30044 1 New Technologies for Communications C 30046 1 Information Recovery and Storage

  14. Google's C/C++ toolchain for smart handheld devices

    E-print Network

    Tomkins, Andrew

    of Android R 1 Open Source Project [1] version 4.0.1 written in C, C++ and assembly lan- guages alone toolchain for generating code on different platforms and for conducting compiler research and development productivity of a programmer by reducing the length of the edit/compile/debug cycle [26]. 1Android and Chrome

  15. 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.

  16. Specific oxidative cleavage of carotenoids by VP14 of maize

    SciTech Connect

    Schwartz, S.H.; Zeevaart, J.A.D.; Gage, D.A. [Michigan State Univ., East Lansing, MI (United States)] [Michigan State Univ., East Lansing, MI (United States); Tan, Bao Cai [Univ. of Florida, Gainesville, FL (United States)] [and others] [Univ. of Florida, Gainesville, FL (United States); and others

    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.

  17. Signals for pre-mRNA cleavage and polyadenylation

    PubMed Central

    Tian, Bin; Graber, Joel H.

    2015-01-01

    Pre-mRNA cleavage and polyadenylation is an essential step for 3? end formation of almost all protein-coding transcripts in eukaryotes. The reaction, involving cleavage of nascent mRNA followed by addition of a polyadenylate or poly(A) tail, is controlled by cis-acting elements in the pre-mRNA surrounding the cleavage site. Experimental and bioinformatic studies in the past three decades have elucidated conserved and divergent elements across eukaryotes, from yeast to human. Here we review histories and current models of these elements in a broad range of species. PMID:22012871

  18. Lessons from Nature: Unraveling Biological C—H Bond Activation

    PubMed Central

    Stone, Kari L.; Borovik, A. S.

    2009-01-01

    The cleavage of unactivated C—H bonds is one of the most challenging reactions in chemical biology. Metalloenzymes have evolved that efficiently perform these transformations with exquisite control of selectivity; however, a proposed requirement is the generation of highly reactive intermediates that could be lethal. A thermodynamic argument involving the putative reactive species is outlined, whereby the interplay between two tunable parameters, redox potential and pKa, may be the key to sustainable function. In addition, factors that control these parameters are also described, including hydrogen-bonding networks found within protein active sites. Synthetic examples are used to corroborate these ideas. PMID:19297238

  19. Chemical Bonds II

    ERIC Educational Resources Information Center

    Sanderson, R. T.

    1972-01-01

    The continuation of a paper discussing chemical bonding from a bond energy viewpoint, with a number of examples of single and multiple bonds. (Part I appeared in volume 1 number 3, pages 16-23, February 1972.) (AL)

  20. Bonding with Grandparents

    MedlinePLUS

    ... Sports: Keeping Kids Safe Concussions: What to Know Bonding With Grandparents KidsHealth > Parents > School & Family Life > Family ... encouraging a close relationship can benefit everyone involved. Bonding Benefits Establishing a bond with grandparents can benefit ...

  1. Bonding with Your Baby

    MedlinePLUS

    ... the child's social and cognitive development. Why Is Bonding Important? Bonding is essential for a baby. Studies ... as biological parents and their children. Back Continue Bonding With Daddy Men these days spend more time ...

  2. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...

  3. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...

  4. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...

  5. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...

  6. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...bonds, separate bonds and additional bonding. 2580.412-20 Section 2580...DEPARTMENT OF LABOR TEMPORARY BONDING RULES UNDER THE EMPLOYEE RETIREMENT INCOME SECURITY ACT OF 1974 TEMPORARY BONDING RULES General Bond Rules §...

  7. Endonucleolytic RNA cleavage by a eukaryotic exosome.

    PubMed

    Lebreton, Alice; Tomecki, Rafal; Dziembowski, Andrzej; Séraphin, 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

  8. Stable alkanes containing very long carbon-carbon bonds.

    PubMed

    Fokin, Andrey A; Chernish, Lesya V; Gunchenko, Pavel A; Tikhonchuk, Evgeniya Yu; Hausmann, Heike; Serafin, Michael; Dahl, Jeremy E P; Carlson, Robert M K; Schreiner, Peter R

    2012-08-22

    The metal-induced coupling of tertiary diamondoid bromides gave highly sterically congested hydrocarbon (hetero)dimers with exceptionally long central C-C bonds of up to 1.71 Å in 2-(1-diamantyl)[121]tetramantane. Yet, these dimers are thermally very stable even at temperatures above 200 °C, which is not in line with common C-C bond length versus bond strengths correlations. We suggest that the extraordinary stabilization arises from numerous intramolecular van der Waals attractions between the neighboring H-terminated diamond-like surfaces. The C-C bond rotational dynamics of 1-(1-adamantyl)diamantane, 1-(1-diamantyl)diamantane, 2-(1-adamantyl)triamantane, 2-(1-diamantyl)triamantane, and 2-(1-diamantyl)[121]tetramantane were studied through variable-temperature (1)H- and (13)C NMR spectroscopies. The shapes of the inward (endo) CH surfaces determine the dynamic behavior, changing the central C-C bond rotation barriers from 7 to 33 kcal mol(-1). We probe the ability of popular density functional theory (DFT) approaches (including BLYP, B3LYP, B98, B3LYP-Dn, B97D, B3PW91, BHandHLYP, B3P86, PBE1PBE, wB97XD, and M06-2X) with 6-31G(d,p) and cc-pVDZ basis sets to describe such an unusual bonding situation. Only functionals accounting for dispersion are able to reproduce the experimental geometries, while most DFT functionals are able to reproduce the experimental rotational barriers due to error cancellations. Computations on larger diamondoids reveal that the interplay between the shapes and the sizes of the CH surfaces may even allow the preparation of open-shell alkyl radical dimers (and possibly polymers) that are strongly held together exclusively by dispersion forces. PMID:22835264

  9. Detection of nucleic acids by multiple sequential invasive cleavages 02

    DOEpatents

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (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. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  10. Detection of nucleic acids by multiple sequential invasive cleavages

    DOEpatents

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (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. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  11. Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage

    PubMed Central

    2014-01-01

    Background Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg2+ ions in efficient self-cleavage are of crucial interest. Results We report the first Raman characterization of the structure and activity of ASBVd, for plus and minus viroid strands. Both strands exhibit a typical A-type RNA conformation with an ordered double-helical content and a C3?-endo/anti sugar pucker configuration, although small but specific differences are found in the sugar puckering and base-stacking regions. The ASBVd(-) is shown to self-cleave 3.5 times more actively than ASBVd(+). Deuteration and temperature increase perturb differently the double-helical content and the phosphodiester conformation, as revealed by corresponding characteristic Raman spectral changes. Our data suggest that the structure rigidity and stability are higher and the D2O accessibility to H-bonding network is lower for ASBVd(+) than for ASBVd(-). Remarkably, the Mg2+-activated self-cleavage of the viroid does not induce any significant alterations of the secondary viroid structure, as evidenced from the absence of intensity changes of Raman marker bands that, however exhibit small but noticeable frequency downshifts suggesting several minor changes in phosphodioxy, internal loops and hairpins of the cleaved viroids. Conclusions Our results demonstrate the sensitivity of Raman spectroscopy in monitoring structural and conformational changes of the viroid and constitute the basis for further studies of its interactions with therapeutic agents and cell membranes. PMID:24655924

  12. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

    PubMed Central

    Frusciante, Sarah; Diretto, Gianfranco; Bruno, Mark; Ferrante, Paola; Pietrella, Marco; Prado-Cabrero, Alfonso; Rubio-Moraga, Angela; Beyer, Peter; Gomez-Gomez, Lourdes; Al-Babili, Salim; Giuliano, Giovanni

    2014-01-01

    Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7?,8? double bonds adjacent to a 3-OH-?-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-?-apo-8?-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-?-apo-8?-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the ?-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope. PMID:25097262

  13. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis.

    PubMed

    Frusciante, Sarah; Diretto, Gianfranco; Bruno, Mark; Ferrante, Paola; Pietrella, Marco; Prado-Cabrero, Alfonso; Rubio-Moraga, Angela; Beyer, Peter; Gomez-Gomez, Lourdes; Al-Babili, Salim; Giuliano, Giovanni

    2014-08-19

    Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7',8' double bonds adjacent to a 3-OH-?-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-?-apo-8'-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-?-apo-8'-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the ?-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope. PMID:25097262

  14. Cleavage Luminescence and Crack Progression in Some Semiconductors

    Microsoft Academic Search

    Dong-Guang Li

    1993-01-01

    The aim of this work was to obtain information about the structure and properties of cleaved surfaces of Si, Ge_{x}Si_{1 -x}, Ge, GaAs, and InP. Measurements of luminescence produced by cleavage in vacua and ambients, have provided novel information about the nature of the surfaces and crack progression. The principle is that cleavage promotes some electrons into the bulk and

  15. Cell numbers during cleavage of the zebra fish egg

    Microsoft Academic Search

    A. W. MARRABLE

    1965-01-01

    THI S paper reports a study of the timing of early cleavage divisions in the zebra fish and of the changes that occur during cleavage in cell size and number. MATERIAL The eggs of the zebra fish Brachydanio rerio (Hamilton-Buchanan) were used in these studies. Roosen-Runge (1936, 1938, 1939), Marrable (1959,1962a) and others have described various aspects of the biology

  16. Molecular Basis of Catalytic Chamber-assisted Unfolding and Cleavage of Human Insulin by Human Insulin-degrading Enzyme

    SciTech Connect

    Manolopoulou, Marika; Guo, Qing; Malito, Enrico; Schilling, Alexander B.; Tang, Wei-Jen; (UC); (UIC)

    2009-06-02

    Insulin is a hormone vital for glucose homeostasis, and insulin-degrading enzyme (IDE) plays a key role in its clearance. IDE exhibits a remarkable specificity to degrade insulin without breaking the disulfide bonds that hold the insulin A and B chains together. Using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry to obtain high mass accuracy, and electron capture dissociation (ECD) to selectively break the disulfide bonds in gas phase fragmentation, we determined the cleavage sites and composition of human insulin fragments generated by human IDE. Our time-dependent analysis of IDE-digested insulin fragments reveals that IDE is highly processive in its initial cleavage at the middle of both the insulin A and B chains. This ensures that IDE effectively splits insulin into inactive N- and C-terminal halves without breaking the disulfide bonds. To understand the molecular basis of the recognition and unfolding of insulin by IDE, we determined a 2.6-A resolution insulin-bound IDE structure. Our structure reveals that IDE forms an enclosed catalytic chamber that completely engulfs and intimately interacts with a partially unfolded insulin molecule. This structure also highlights how the unique size, shape, charge distribution, and exosite of the IDE catalytic chamber contribute to its high affinity ( approximately 100 nm) for insulin. In addition, this structure shows how IDE utilizes the interaction of its exosite with the N terminus of the insulin A chain as well as other properties of the catalytic chamber to guide the unfolding of insulin and allowing for the processive cleavages.

  17. Anaerobic and aerobic cleavage of the steroid core ring structure by Steroidobacter denitrificans[S

    PubMed Central

    Wang, Po-Hsiang; Leu, Yann-Lii; Ismail, Wael; Tang, Sen-Lin; Tsai, Ching-Yen; Chen, Hsing-Ju; Kao, Ann-Tee; Chiang, Yin-Ru

    2013-01-01

    The aerobic degradation of steroids by bacteria has been studied in some detail. In contrast, only little is known about the anaerobic steroid catabolism. Steroidobacter denitrificans can utilize testosterone under both oxic and anoxic conditions. By conducting metabolomic investigations, we demonstrated that S. denitrificans adopts the 9,10-seco-pathway to degrade testosterone under oxic conditions. This pathway depends on the use of oxygenases for oxygenolytic ring fission. Conversely, the detected degradation intermediates under anoxic conditions suggest a novel, oxygenase-independent testosterone catabolic pathway, the 2,3-seco-pathway, which differs significantly from the aerobic route. In this anaerobic pathway, testosterone is first transformed to 1-dehydrotestosterone, which is then reduced to produce 1-testosterone followed by water addition to the C-1/C-2 double bond of 1-testosterone. Subsequently, the C-1 hydroxyl group is oxidized to produce 17-hydroxy-androstan-1,3-dione. The A-ring of this compound is cleaved by hydrolysis as evidenced by H218O-incorporation experiments. Regardless of the growth conditions, testosterone is initially transformed to 1-dehydrotestosterone. This intermediate is a divergence point at which the downstream degradation pathway is governed by oxygen availability. Our results shed light into the previously unknown cleavage of the sterane ring structure without oxygen. We show that, under anoxic conditions, the microbial cleavage of steroidal core ring system begins at the A-ring. PMID:23458847

  18. Copper- and Vanadium-Catalyzed Oxidative Cleavage of Lignin using Dioxygen.

    PubMed

    Mottweiler, Jakob; Puche, Marta; Räuber, Christoph; Schmidt, Thomas; Concepción, Patricia; Corma, Avelino; Bolm, Carsten

    2015-06-22

    Transition-metal-containing hydrotalcites (HTc) and V(acac)3 /Cu(NO3 )2 ?3?H2 O (acac=acetylacetonate) mixtures were tested for their catalytic activity in the cleavage of the lignin model compound erythro-1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-l,3-propanediol (1) with molecular oxygen as oxidant. Both catalytic systems displayed high activity and good selectivity and afforded veratric acid as the main product. The catalyst behavior was studied by EPR spectroscopy, XRD, and Raman spectroscopy. After the catalysts were established for the model system, lignin depolymerization studies were performed with various organsolv and kraft lignin sources. The oxidative depolymerization and lignin bond cleavage were monitored by gel permeation chromatography (GPC), MALDI MS, and 2D-NMR (HSQC). Irrespective of the lignin pretreatment, both HTc-Cu-V and V(acac)3 /Cu(NO3 )2 ?3?H2 O were able to cleave the ?-O-4 linkages and the resinol structures to form dimeric and trimeric products. PMID:26013592

  19. Identification and expression pattern of a new carotenoid cleavage dioxygenase gene member from Bixa orellana

    PubMed Central

    Rodríguez-Ávila, N. L.; Narváez-Zapata, J. A.; Ramírez-Benítez, J. E.; Aguilar-Espinosa, M. L.; Rivera-Madrid, R.

    2011-01-01

    Carotenoid cleavage dioxygenases (CCDs) are a class of enzymes involved in the biosynthesis of a broad diversity of secondary metabolites known as apocarotenoids. In plants, CCDs are part of a genetic family with members which cleave specific double bonds of carotenoid molecules. CCDs are involved in the production of diverse and important metabolites such as vitamin A and abscisic acid (ABA). Bixa orellana L. is the main source of the natural pigment annatto or bixin, an apocarotenoid accumulated in large quantities in its seeds. Bixin biosynthesis has been studied and the involvement of a CCD has been confirmed in vitro. However, the CCD genes involved in the biosynthesis of the wide variety of apocarotenoids found in this plant have not been well documented. In this study, a new CCD1 gene member (BoCCD1) was identified and its expression was charaterized in different plant tissues of B. orellana plantlets and adult plants. The BoCCD1 sequence showed high homology with plant CCD1s involved mainly in the cleavage of carotenoids in several sites to generate multiple apocarotenoid products. Here, the expression profiles of the BoCCD1 gene were analysed and discussed in relation to total carotenoids and other important apocarotenoids such as bixin. PMID:21813796

  20. Naturally Occurring Eccentric Cleavage Products of Provitamin A ?-Carotene Function as Antagonists of Retinoic Acid Receptors*

    PubMed Central

    Eroglu, Abdulkerim; Hruszkewycz, Damian P.; dela Sena, Carlo; Narayanasamy, Sureshbabu; Riedl, Ken M.; Kopec, Rachel E.; Schwartz, Steven J.; Curley, Robert W.; Harrison, Earl H.

    2012-01-01

    ?-Carotene is the major dietary source of provitamin A. Central cleavage of ?-carotene catalyzed by ?-carotene oxygenase 1 yields two molecules of retinaldehyde. Subsequent oxidation produces all-trans-retinoic acid (ATRA), which functions as a ligand for a family of nuclear transcription factors, the retinoic acid receptors (RARs). Eccentric cleavage of ?-carotene at non-central double bonds is catalyzed by other enzymes and can also occur non-enzymatically. The products of these reactions are ?-apocarotenals and ?-apocarotenones, whose biological functions in mammals are unknown. We used reporter gene assays to show that none of the ?-apocarotenoids significantly activated RARs. Importantly, however, ?-apo-14?-carotenal, ?-apo-14?-carotenoic acid, and ?-apo-13-carotenone antagonized ATRA-induced transactivation of RARs. Competitive radioligand binding assays demonstrated that these putative RAR antagonists compete directly with retinoic acid for high affinity binding to purified receptors. Molecular modeling studies confirmed that ?-apo-13-carotenone can interact directly with the ligand binding site of the retinoid receptors. ?-Apo-13-carotenone and the ?-apo-14?-carotenoids inhibited ATRA-induced expression of retinoid responsive genes in Hep G2 cells. Finally, we developed an LC/MS method and found 3–5 nm ?-apo-13-carotenone was present in human plasma. These findings suggest that ?-apocarotenoids function as naturally occurring retinoid antagonists. The antagonism of retinoid signaling by these metabolites may have implications for the activities of dietary ?-carotene as a provitamin A and as a modulator of risk for cardiovascular disease and cancer. PMID:22418437

  1. Cleavage of T4 species I ribonucleic acid by Escherichia coli ribonuclease III.

    PubMed Central

    Paddock, G V; Fukada, K; Abelson, J; Robertson, H D

    1976-01-01

    T4 Species I RNA, a molecule 140 nucleotides in length with some structural features very much like a tRNA, is specifically cleaved by an enzymatic activity in Escherichia coli extracts to give three segments with 19, 48 and 73 nucleotides. We report the purification and characterization of the E. coli RNase which cleaves two 3' phosphodiester bonds of T4 Species I RNA. This reaction has many properties in common with those catalyzed by E. coli RNase III, although the optimal salt conditions for T4 Species I RNA cleavage differ significantly from those for other RNase III-catalyzed reactions. The reaction is not catalyzed by extracts from an E. coli strain lacking RNase III activity. Furthermore, T4 Species I RNA is cleaved by highly purified E. coli RNase III to yield the same three specific fragments. We conclude that this specific cleavage is due to the action of RNase III, and that the requirement for lower ionic strength may reveal further important properties about this RNA processing enzyme. Images PMID:781626

  2. I2-Catalyzed Aerobic Oxidative C(sp(3))-H Amination/C-N Cleavage of Tertiary Amine: Synthesis of Quinazolines and Quinazolinones.

    PubMed

    Yan, Yizhe; Xu, Ying; Niu, Bin; Xie, Huifang; Liu, Yanqi

    2015-06-01

    An iodine-catalyzed oxidative C(sp(3))-H amination/C-N cleavage of tertiary amines couducted under an oxygen atmosphere has been developed and affords a route to quinazolines and quinazolinones in good to excellent yields via a domino ring annulation. The method is metal-free, peroxide-free, and operationally simple to implement with a wide scope of substrates and represents a new avenue for multiple C-N bond formations. PMID:25942678

  3. Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation

    Microsoft Academic Search

    Eric Ennifar; Joachim E. W. Meyer; Frank Buchholz; A. Francis Stewart; Dietrich Suck

    2003-01-01

    Escherichia coli phage P1 Cre recombinase cata- lyzes the site-specific recombination of DNA con- taining loxP sites. We report here two crystal structures of a wild-type Cre recombinase-loxP syn- aptic complex corresponding to two distinct reac- tion states: an initial pre-cleavage complex, trapped using a phosphorothioate modification at the cleav- able scissile bond that prevents the recombination reaction, and a

  4. Bypassing a highly unstable frustrated Lewis pair: dihydrogen cleavage by a thermally robust silylium-phosphine adduct.

    PubMed

    Herrington, Thomas J; Ward, Bryan J; Doyle, Laurence R; McDermott, Joe; White, Andrew J P; Hunt, Patricia A; Ashley, Andrew E

    2014-10-28

    The thermally robust silylium complex [iPr3Si-PtBu3](+)[B(C6F5)4](-) (1) activates H2/D2 at 90 °C (PhCl); no evidence for dissociation into the separated Lewis pair is found. DFT calculations show H2 cleavage proceeds via Si-P bond elongation to form an encounter complex directly from the adduct, thus avoiding the non-isolable iPr3Si(+)-PtBu3 FLP. PMID:25204297

  5. Solar System planetary tests of \\dot c/c

    E-print Network

    Lorenzo Iorio

    2009-05-15

    Analytical and numerical calculations show that a putative temporal variation of the speed of light c, with the meaning of space-time structure constant c_ST, assumed to be linear over timescales of about one century, would induce a secular precession of the longitude of the pericenter \\varpi of a test particle orbiting a spherically symmetric body. By comparing such a predicted effect to the corrections \\Delta\\dot\\varpi to the usual Newtonian/Einsteinian perihelion precessions of the inner planets of the Solar System, recently estimated by E.V. Pitjeva by fitting about one century of modern astronomical observations with the standard dynamical force models of the EPM epehemerides, we obtained \\dot c/c =(0.5 +/- 2)\\times 10^-7 yr^-1. Moreover, the possibility that \\dot c/c\

  6. Hepatitis C Virus-Encoded NS2-3 Protease: Cleavage-Site Mutagenesis and Requirements for Bimolecular Cleavage

    Microsoft Academic Search

    KAREN E. REED; ARASH GRAKOUI; ANDCHARLES M. RICE

    1995-01-01

    Cleavage at the 2\\/3 site of hepatitis C virus (HCV) is thought to be mediated by a virus-encoded protease composed of the region of the polyprotein encoding NS2 and the N-terminal one-third of NS3. This protease is distinct from the NS3 serine protease, which is responsible for downstream cleavages in the nonstructural region. Site-directed mutagenesis of residues surrounding the 2\\/3

  7. Dislocation dissociation in some f.c.c. metals

    NASA Technical Reports Server (NTRS)

    Esterling, D. M.

    1980-01-01

    The dissociation of a perfect screw dislocation into a stacking fault in an f.c.c. lattice is modeled by the modified lattice statics. The interatomic potentials are obtained from the work of Esterling and Swaroop and differ substantially from those empirical potentials usually employed in defect simulations. The calculated stacking fault widths for aluminum, copper, and silver are in good agreement with weak beam microscopy results.

  8. Measurements of $\\psi(3686) \\to K^{-} \\Lambda \\bar{\\Xi}^{+} +c.c.$ and $\\psi(3686) \\to \\gamma K^{-} \\Lambda \\bar{\\Xi}^{+} +c.c$

    E-print Network

    Ablikim, M; 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; Cibinetto, G; Cronin-Hennessy, D; Dai, H L; Dai, J P; Dbeyssi, A; Dedovich, D; Deng, Z Y; Denig, A; Denysenko, I; Destefanis, M; DeMori, 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; Kühn, 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, 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 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, 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; 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; Savrié, 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, 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

    2015-01-01

    Using a sample of $1.06\\times10^8\\ \\psip$ events produced in $e^+e^-$ collisions at $\\sqrt{s}$ = 3.686 GeV and collected with the BESIII detector at the BEPCII collider, we present studies of the decays $\\klx+c.c.$ and $\\gklx+c.c.$. We observe two hyperons, $\\Xi(1690)^-$ and $\\Xi(1820)^-$, in the $K^-\\Lambda$ invariant mass distribution in the decay $\\klx+c.c.$ with significances of $4.9 \\sigma$ and $6.2 \\sigma$, respectively. The branching fractions of $\\klx+c.c.$, $\\ksx+c.c.$, $\\psip\\to\\gamma \\chi_{cJ}\\to \\gamma K^- \\Lambda \\bar{\\Xi}^+ +c.c.$ $(J=0,\\ 1,\\ 2)$, and $\\psip\\to \\Xi(1690/1820)^{-} \\bar{\\Xi}^++c.c$ with subsequent decay $\\Xi(1690/1820)^-\\to K^-\\Lambda$ are measured for the first time.

  9. X-ray analysis of Co-C bond cleavage in the crystalline state.

    PubMed

    Ohashi, Y; Sasada, Y

    1977-05-12

    During serial structure analysis of cobaloxime derivatives, aimed at interpreting the catalytic capability of the asymmetric hydrogenation, we have found that the crystal of R-alpha-cyanoethyl (S-alpha-methylbenzylamine)-cobaloxime changes its unit cell dimensions by X-ray exposure without degradation of a single crystal form. The rate of the change was so slow that it was possible to collect the intensity data for several intermediate stages. We have proved, by calculating electron density in each stage, that the change reflects the racemisation of the cyanoethyl group. PMID:16073420

  10. Bond cleavage reactions in oxygen and nitrogen heterocycles by a rhodium phosphine complex

    SciTech Connect

    Jones, W.D.; Dong, L.; Myers, A.W. (Univ. of Rochester, NY (United States))

    1995-02-01

    The reactions of (C[sub 5]Me[sub 5])Rh(PMe[sub 3])PhH with furan, 2,5-dimethylfuran, 2,3-dihydrofuran, dibenzofuran, pyrrole, 1-methylpyrrole, 2,5-dimethylpyrrole, 1,2,5-trimethylpyrrole, carbazole, 9-methylcarbazole, pyrrolidine, pyridine, 3,5-lutidine, 2,4,6-collidine, pyrazole, 3-methylpyrazole, and piperidine have been investigated. While the oxygen heterocycles give only C-H activation, the nitrogen heterocycles yield C-H and N-H insertion products. The chloro derivative (C[sub 5]Me[sub 5])Rh(PMe[sub 3])[2-(1-methylpyrrole)]Cl was found to crystallize in the monoclinic space group C2/c with a = 13.753 (6) A, b = 9.665 (5) A, c = 30.14 (2) A, [beta] = 99.77 (5)-[degree], Z = 8, and V = 3949 (4.1) A[sup 3] while (C[sub 5]Me[sub 5])Rh(PMe[sub 5])[2-(3,5-lutidine)]Cl was found to crystallize in the monoclinic space group P2[sub 1]/c with a = 14.976 (8) A, b = 8.613 (5) A, c = 17.12 (2) A, [beta] = 101.90 (6)[degree], Z = 4, and V = 2160 (5.2) A[sup 3]. 30 refs., 2 figs., 3 tabs.

  11. Nitrogen dioxide reaction with proteins: Evidence for peptide bond cleavage at lysine residues

    SciTech Connect

    Hood, D.B.

    1991-01-01

    Nitrogen dioxide (NO{sub 2}), an air pollutant produced by burning fossil fuels and a component of cigarette smoke, is thought to contribute to the pathogenesis of pulmonary diseases, such as emphysema. To gain information on the mechanism by which NO{sub 2} damages the lung, in vitro exposures of {alpha}{sub 1}-proteinase inhibitor ({alpha}{sub 1}-PI), elastin, bovine serum albumin (BSA), human serum albumin (HSA) and synthetic poly-L-lysine were performed. A genetic deficiency of {alpha}{sup 1}-PI predisposes humans to emphysema and NO{sub 2} has been hypothesized to damage {alpha}{sub 1}-PI, which would leave proteases such as human neutrophil elastase, (HNE) free to attack lung structural proteins. The ability of {alpha}{sub 1}-PI to inhibit HNE declined with exposure to 50% of the control value at molar ratios of NO{sub 2}:{alpha}{sub 1}-PI of 400:1 and greater. Exposure of {alpha}{sub 1}-PI to NO{sub 2} resulted in a 50% lose of immunoreactivity with either monoclonal or polyclonal antibodies in an enzyme-linked immunosorbent assay at molar ratios of NO{sub 2}:{alpha}{sub 1}-PI of essentially 100:1 and greater. The mechanisms of these effects were investigated via ultraviolet-visible spectroscopy and amino acid analysis. The remaining target molecules were labeled by reductive methylation of amino groups with {sup 3}H-HCHO prior to treatment with NO{sub 2} in aqueous solutions at physiological pH. Time course exposure of 5 mg {sup 3}H-insoluble bovine ligamentum nuchae elastin suspensions with up to 120 {mu}moles of NO{sub 2} resulted in 90% solubilization of the label. Amino acid analysis of the soluble and insoluble fractions from these exposures confirmed that 80% of the {sup 3}H-dimethyllysine residues were in the soluble fraction.

  12. Separation of long DNA molecules through cleavage of hydrogen bonds under a stretching force

    E-print Network

    Wu, Jianzhong

    . Here, they demonstrate efficient separation of lambda DNA 48 502 base pairs from human genomic DNA 100 separation by length is the foundation for DNA sequencing, manipulation, analysis, and cloning in molecular DNA 48 502 bp from human genomic ds-DNA 90% of the sample is greater than 100 kbp in size based

  13. Investing in Bonds.com

    NSDL National Science Digital Library

    Investing in Bonds was created by the Bond Market Association to educate investors about the benefits of bonds investing. The Investor's Guide to Bond Basics educates investors about the types of bonds available, criteria for evaluating a bond, a guide to buying bonds, bond investment strategies and a glossary of bond market terms. The Bond Market section provides an overview of the U.S. bond market while the Investor's Checklist section takes the investor step-by-step through the bond investment decision process. Investors will also find sections with information on municipal bonds, corporate bonds, mortgage securities and U.S. Inflation-Indexed Securities.

  14. LET'S BOND! A Chemical Bonding Webquest

    NSDL National Science Digital Library

    Mrs. Hicken

    2009-04-08

    Today we are going to use the internet to explore chemical bonding! Even though there are just a few questions for each website, you need to read the entire content. Don't worry about understanding all of it, but make sure that you are familiar with it! Stay on task and have fun! Let's start with some basics. Click on the link below and answer the questions on your worksheet under "Bonding Basics". Bonding Basics Good job! Lets move on and talk about ions. Ions are a big part of bonding, so make sure you get this section down pat! Click on the ...

  15. Analysis of RNA cleavage by MALDI-TOF mass spectrometry.

    PubMed

    Joyner, Jeff C; Keuper, Kevin D; Cowan, J A

    2013-01-01

    A method of analysis is presented that utilizes matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to monitor the kinetics and products of RNA cleavage, by use of a program designed to mass-match observed MS peaks with predicted RNA cleavage products. The method is illustrated through application to the study of targeted oxidation of RNA stem loops from HIV-1 Rev Response Element mRNA (RRE RNA) and ribosomal 16S A-site RNA (16S RNA) by metallonucleases. Following incubation of each RNA with catalysts and/or redox co-reactants, reaction mixtures were desalted, and MALDI-TOF MS was used to monitor both time-resolved formation of cleavage products and disappearance of full-length RNA. For each RNA, a unique list was generated that contained the predicted masses of both the full-length, and all of the possible RNA cleavage fragments that resulted from the combination of all possible cleavage sites and each of the six expected overhangs formed at nascent termini adjacent to the cleavage sites. The overhangs corresponded to 2',3'-cyclic phosphate, 3'-phosphate, 3'-phosphoglycolate, 5'- hydroxyl and 5'- phosphate, which corresponded to differing oxidative, hydrolytic, and/or 2'-OH-mediated-endonucleolytic modes of scission. Each mass spectrum was compared with a corresponding list of predicted masses, and peaks were rapidly assigned by use of a Perl script, with a mass-matching tolerance of 200 ppm. Both time-dependent cleavage mediated by metallonucleases and MALDI-TOF-induced fragmentation were observed, and these were distinguished by time-dependent experiments. The resulting data allowed a semi-quantitative assessment of the rate of formation of each overhang at each nucleotide position. Limitations included artifactual skewing of quantification by mass bias, a limited mass range for quantification, and a lack of detection of secondary cleavage products. Nevertheless, the method presented herein provides a rapid, accurate, highly-detailed and semi-quantitative analysis of RNA cleavage that should be widely applicable. PMID:22941655

  16. Analysis of RNA cleavage by MALDI-TOF mass spectrometry

    PubMed Central

    Joyner, Jeff C.; Keuper, Kevin D.; Cowan, J. A.

    2013-01-01

    A method of analysis is presented that utilizes matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to monitor the kinetics and products of RNA cleavage, by use of a program designed to mass-match observed MS peaks with predicted RNA cleavage products. The method is illustrated through application to the study of targeted oxidation of RNA stem loops from HIV-1 Rev Response Element mRNA (RRE RNA) and ribosomal 16S A-site RNA (16S RNA) by metallonucleases. Following incubation of each RNA with catalysts and/or redox co-reactants, reaction mixtures were desalted, and MALDI-TOF MS was used to monitor both time-resolved formation of cleavage products and disappearance of full-length RNA. For each RNA, a unique list was generated that contained the predicted masses of both the full-length, and all of the possible RNA cleavage fragments that resulted from the combination of all possible cleavage sites and each of the six expected overhangs formed at nascent termini adjacent to the cleavage sites. The overhangs corresponded to 2?,3?-cyclic phosphate, 3?-phosphate, 3?-phosphoglycolate, 5?- hydroxyl and 5?- phosphate, which corresponded to differing oxidative, hydrolytic, and/or 2?-OH-mediated-endonucleolytic modes of scission. Each mass spectrum was compared with a corresponding list of predicted masses, and peaks were rapidly assigned by use of a Perl script, with a mass-matching tolerance of 200 ppm. Both time-dependent cleavage mediated by metallonucleases and MALDI-TOF-induced fragmentation were observed, and these were distinguished by time-dependent experiments. The resulting data allowed a semi-quantitative assessment of the rate of formation of each overhang at each nucleotide position. Limitations included artifactual skewing of quantification by mass bias, a limited mass range for quantification, and a lack of detection of secondary cleavage products. Nevertheless, the method presented herein provides a rapid, accurate, highly-detailed and semi-quantitative analysis of RNA cleavage that should be widely applicable. PMID:22941655

  17. The cleavage pattern in the leech Theromyzon tessulatum (Hirudinea, Glossiphoniidae).

    PubMed

    Sandig, M; Dohle, W

    1988-05-01

    In order to evaluate the differences in the cleavage patterns of the glossiphoniid leeches Glossiphonia complanata and Theromyzon tessulatum, previously studied by Müller ('32) and Schmidt ('17, '41), the cleavage of Theromyzon tessulatum was reexamined. For the period of the first 29 hours of development embryos were observed, photographed, and serially sectioned for light microscopy at each developmental stage. The exact cell lineage until completion of teloblast formation is reported. Besides some other not previously reported features, we show that the mesoteloblast precursor cell in the glossiphoniid leeches, as probably in most Annelida, is not the cell 3D, but cell 4d formed by an additional division of cell 3D. The results further indicate that all glossiphoniid leeches likely share a common cleavage pattern, and that major differences between Glossiphonia complanata and Theromyzon tessulatum do not exist. A comparison between the cleavage patterns of some Oligochaeta and Hirudinea is made, and plesiomorphic characters in the cleavage of a clitellate ancestor species and their deviations in present day species are discussed. PMID:3385778

  18. Morphological aspects of in vivo cleavage in Myocastor coypus (coypu).

    PubMed

    Felipe, A E; Teruel, M T; Cabodevila, J A; Callejas, S S

    2004-04-01

    The objective of the present work was to characterize the in vivo cleavage stage of Myocastor coypus embryos. For this purpose a colpocytological follow-up and controlled mating of 18 females were performed. Specimens from the beginning of the first cleavage to the acquisition of a morula appearance were considered to be in cleavage stage. Embryos in cleavage were collected between days 3 and 6 post-coitus. Of the collected embryos, 80% presented an even number of blastomeres and the remaining 20% an odd number. Embryos from 3 to 7 cells were blastomere associations in a spherical disposition within the zona pellucida. Blastomeres were spherical or ovoid, presenting slight flattening in areas contacting with other blastomeres. Embryos of 8 and 9 cells were as a group of blastomeres slightly elongated, surrounded by a spherical zona pellucida. The percentage of peri-vitelline space occupied by the embryonic mass ranged from 74.1 to 95.8% for all the substages. The cleavage pattern, developed in the oviduct, was of a rotational holoblastic type and asynchronic. PMID:15027947

  19. Binding and cleavage of nucleic acids by the "hairpin" ribozyme.

    PubMed

    Chowrira, B M; Burke, J M

    1991-09-01

    The "hairpin" ribozyme derived from the minus strand of tobacco ringspot virus satellite RNA [(-)sTRSV] efficiently catalyzes sequence-specific RNA hydrolysis in trans (Feldstein et al., 1989; Hampel & Triz, 1989; Haseloff & Gerlach, 1989). The ribozyme does not cleave DNA. An RNA substrate analogue containing a single deoxyribonucleotide residue 5' to the cleavage site (A-1) binds to the ribozyme efficiently but cannot be cleaved. A DNA substrate analogue with a ribonucleotide at A-1 is cleaved; thus A-1 provides the only 2'-OH required for cleavage. These results support cleavage via a transphosphorylation mechanism initiated by attack of the 2'-OH of A-1 on the scissile phosphodiester. The ribozyme discriminates between DNA and RNA in both binding and cleavage. Results indicate that the 2'-OH of A-1 functions in complex stabilization as well as cleavage. The ribozyme efficiently cleaves a phosphorothioate diester linkage, suggesting that the pro-Rp oxygen at the scissile phosphodiester does not coordinate Mg2+. PMID:1909564

  20. Functionalized olefin cross-coupling to construct carbon–carbon bonds

    NASA Astrophysics Data System (ADS)

    Lo, Julian C.; Gui, Jinghan; Yabe, Yuki; Pan, Chung-Mao; Baran, Phil S.

    2014-12-01

    Carbon-carbon (C-C) bonds form the backbone of many important molecules, including polymers, dyes and pharmaceutical agents. The development of new methods to create these essential connections in a rapid and practical fashion has been the focus of numerous organic chemists. This endeavour relies heavily on the ability to form C-C bonds in the presence of sensitive functional groups and congested structural environments. Here we report a chemical transformation that allows the facile construction of highly substituted and uniquely functionalized C-C bonds. Using a simple iron catalyst, an inexpensive silane and a benign solvent under ambient atmosphere, heteroatom-substituted olefins are easily reacted with electron-deficient olefins to create molecular architectures that were previously difficult or impossible to access. More than 60 examples are presented with a wide array of substrates, demonstrating the chemoselectivity and mildness of this simple reaction.

  1. Functionalized olefin cross-coupling to construct carbon–carbon bonds

    PubMed Central

    Lo, Julian C.; Gui, Jinghan; Yabe, Yuki; Pan, Chung-Mao; Baran, Phil S.

    2014-01-01

    Carbon–carbon (C–C) bonds form the backbone of many important molecules, including polymers, dyes, and pharmaceutical agents. The development of new methods to create these essential connections in a rapid and practical fashion has been the focus of numerous organic chemists. This endeavor heavily relies on the ability to form C–C bonds in the presence of sensitive functional groups and congested structural environments. Here we report a fundamentally new chemical transformation that allows for the facile construction of highly substituted and uniquely functionalized C–C bonds. Using a simple iron catalyst, an inexpensive silane, and a benign solvent under an ambient atmosphere, heteroatom-substituted olefins are easily merged with electron-deficient olefins to create molecular architectures that were previously difficult or impossible to access. More than sixty examples are presented with a wide array of substrates, demonstrating the unique chemoselectivity and mildness of this simple reaction. PMID:25519131

  2. Facile electrochemical detection of botulinum neurotoxin type E using a two-step proteolytic cleavage.

    PubMed

    Park, Seonhwa; Shin, Yu Mi; Song, Ji-Joon; Yang, Haesik

    2015-10-15

    Facile electrochemical methods for measuring protease concentration or protease activity are essential for point-of-care testing of toxic proteases. However, electrochemical detection of proteases, such as botulinum neurotoxin type E (BoNT/E), that cleave a peptide bond between two specific amino acid residues is challenging. This study reports a facile and sensitive electrochemical method for BoNT/E detection. The method is based on a two-step proteolytic cleavage using a target BoNT/E light chain (BoNT/E-LC) and an externally supplemented exopeptidase, l-leucine-aminopeptidase (LAP). BoNT/E-LC cleaves a peptide bond between arginine and isoleucine in IDTQNRQIDRI-4-amino-1-naphthol (oligopeptide-AN) to generate isoleucine-AN. Subsequently, LAP cleaves a bond between isoleucine and AN to liberate a free electroactive AN species. The liberated AN participates in electrochemical-chemical-chemical (ECC) redox cycling involving Ru(NH3)6(3+), AN, and a reducing agent, which allows a high signal amplification. Electrochemical detection is carried out without surface modification of indium-tin oxide electrodes. We show that dithiothreitol is beneficial for enhancing the enzymatic activity of BoNT/E-LC and also for achieving a fast ECC redox cycling. An incubation temperature of 37°C and the use of phosphate buffered saline (PBS) buffer resulted in optimal signal-to-background ratios for efficient BoNT/E detection. BoNT/E-LC could be detected at concentrations of approximately 2.0pg/mL, 0.2, and 3ng/mL after 4h, 2h, and 15min incubation in PBS buffer, respectively, and approximately 0.3ng/mL after 2-h incubation in bottled water. The method developed could be applied in fast, sensitive, and selective detection of any protease that cleaves a peptide bond between two specific amino acid residues. PMID:25982730

  3. Channel Bonding Notes 03/25/2004 Channel Bonding Notes

    E-print Network

    Jain, Amit

    Channel Bonding Notes 03/25/2004 Channel Bonding Notes Luke Hindman Department of Computer Science by attempting to use the Linux kernel bonding driver (bonding.o) to implement channel bonding on the master node. However, each time I would bring up the bonded interface (bond0) I would loose communication

  4. Modular functionalized polyphosphines for supported materials: previously unobserved (31)P-NMR «through-space» ABCD spin systems and heterogeneous palladium-catalysed C-C and C-H arylation.

    PubMed

    Beaupérin, Matthieu; Smaliy, Radomyr; Cattey, Hélène; Meunier, Philippe; Ou, Jun; Toy, Patrick H; Hierso, Jean-Cyrille

    2014-08-28

    The modular design of polyphosphines, diversely functionalized for facile immobilization on virtually any kind of support, is reported. Previously unobserved ABCD (31)P NMR spin-spin systems evidence the control exercised on the polyphosphines conformation. We illustrate the catalytic performance at low Pd loading of the recyclable immobilized polyphosphines in C-C bond formation reactions. PMID:25008866

  5. Redox-Triggered C-C Coupling of Alcohols and Vinyl Epoxides: Diastereo- and Enantioselective Formation of All-Carbon Quaternary Centers via tert-(Hydroxy)-Prenylation

    PubMed Central

    Feng, Jiajie; Garza, Victoria J.; Krische, Michael J.

    2014-01-01

    Iridium catalyzed primary alcohol oxidation triggers reductive C-O bond cleavage of isoprene oxide to form aldehyde-allyliridium pairs that combine to form products of tert-(hydroxy)-prenylation, a motif found in >2000 terpenoid natural products. Curtin-Hammett effects are exploited to enforce high levels of anti-diastereo- and enantioselectivity in the formation of an all-carbon quaternary center. The present redox-triggered carbonyl additions occur in the absence of stoichiometric byproducts, premetallated reagents and discrete alcohol-to-aldehyde redox manipulations. PMID:24915473

  6. Evolution of development in the sea star genus Patiriella: clade-specific alterations in cleavage.

    PubMed

    Cerra, Anna; Byrne, Maria

    2004-01-01

    Examination of early development in five species of the Patiriella sea star species complex indicates that the ancestral-type radial holoblastic cleavage (Type I) is characteristic of P. regularis and P. exigua, whereas cleavage in species from the calcar clade followed multiple alternatives (Types II-IV) from holoblastic to meroblastic. Considering that invariant radial cleavage is thought to play a role in embryonic axis formation in echinoderms, we documented the details of blastomere formation in Patiriella sp. and followed development of the embryos. In Type II cleavage, the first and second cleavage planes appeared simultaneously at one pole of the embryo, dividing it directly into four equally sized blastomeres. In Type III cleavage, the first and second cleavage planes appeared simultaneously, followed promptly by the third cleavage plane, dividing the embryo directly into eight equally sized blastomeres. In Type IV cleavage, numerous furrows appeared simultaneously at one end of the embryo, dividing it into 32-40 equally sized blastomeres. Confocal sections revealed that embryos with cleavage Types II-IV were initially syncytial. The timing of karyokinesis in embryos with Types II and III cleavage was similar to that seen in clutch mates with Type I cleavage. Karyokinesis in embryos with Type IV cleavage, however, differed in timing compared with Type I clutch mates. Alteration in cleavage was not associated with polarized distribution of maternally provided nutrients. For each cleavage type, development was normal to the competent larval stage. Although variable blastomere configuration in the calcar clade may be linked to possession of a lecithotrophic development, other Patiriella species with this mode of development have typical cleavage. The presence of variable cleavage in all calcar clade species indicates that phylogenetic history has played a role in the distribution of this embryonic trait in Patiriella. The plasticity in early cleavage in these sea stars indicates that this aspect of early development is not constrained against change and that there are many ways to achieve multicellularity. PMID:15009123

  7. Structure and electronic spectra of the C C6- anion

    NASA Astrophysics Data System (ADS)

    Hammoutene, D.; Hochlaf, M.; Senent, M. L.

    2012-08-01

    Ab initio calculations are employed for determining structures, spectroscopic parameters and transitions to the excited electronic states of the astrophysical relevant C C6- anion, which is a potential intermediate of chemical processes involving carbon chains and polycyclic aromatic hydrocarbons. Calculations confirm the prominent stability of linear carbon chain anions which guarantees their formation. The lowest doublet potential energy surface of C? displays six isomers, whereas in the lowest quartet potential energy surface, a unique minimum energy geometry is found. The most stable form is the linear anion l-C? (X2?u) followed by the c-C?(X2A1')at 9291 cm-1 above in energy, which presents a distorted D3h structure. The other isomers are also located at more than 9000 cm-1 above l-C? (X2?u). For each isomer, a set of spectroscopic parameters including their equilibrium structures, rotational constants at equilibrium, harmonic wavenumbers, dipole moments and electron affinities are predicted. For linear C?, eight electronic states lying below the electron detachment threshold, are computed. Four doublet electronic states, which play important roles in the C? reactivity, lie below 2 eV. Spin-orbit constants for the upper electronic states of l-C? are predicted.

  8. Essays on corporate bonds

    E-print Network

    Bao, Jack (Jack C.)

    2009-01-01

    This thesis consists of three empirical essays on corporate bonds, examining the role of both credit risk and liquidity. In the first chapter, I test the ability of structural models of default to price corporate bonds in ...

  9. Rhodium-catalyzed enantioselective silylation of arene C-h bonds: desymmetrization of diarylmethanols.

    PubMed

    Lee, Taegyo; Wilson, Tyler W; Berg, Robert; Ryberg, Per; Hartwig, John F

    2015-06-01

    We report a Rh-catalyzed, enantioselective silylation of arene C-H bonds directed by a (hydrido)silyl group. (Hydrido)silyl ethers that are formed in situ by hydrosilylation of benzophenone or its derivatives undergo asymmetric C-H silylation in high yield with excellent enantioselectivity in the presence of [Rh(cod)Cl]2 and a chiral bisphosphine ligand. The stereoselectivity of this process also allows enantioenriched diarylmethanols to react with site selectivity at one aryl group over the other. Enantioenriched benzoxasiloles from the silylation process undergo a range of transformations to form C-C, C-O, C-I, or C-Br bonds. PMID:25948056

  10. Diffusion bonding aeroengine components

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, G. A.; Broughton, T.

    1988-10-01

    The use of diffusion bonding processes at Rolls-Royce for the manufacture of titanium-alloy aircraft engine components and structures is described. A liquid-phase diffusion bonding process called activated diffusion bonding has been developed for the manufacture of the hollow titanium wide chord fan blade. In addition, solid-state diffusion bonding is being used in the manufacture of hollow vane/blade airfoil constructions mainly in conjunction with superplastic forming and hot forming techniques.

  11. Bonding silicones with epoxies

    SciTech Connect

    Tira, J.S.

    1980-01-01

    It is shown that silicones, both room temperature vulcanizing (RTV) and millable rubber (press cured) can be successfully bonded to other materials using plasma treatment and epoxy adhesives. The plasma treatment using dry air atmosphere increases the surface energy of the silicone and thus provides a lower water contact angle. This phenomenon allows the epoxy adhesive to wet the silicone surface and ultimately bond. Bond strengths are sufficiently high to result in failures in the silicone materials rather than the adhesive bond.

  12. Allosteric Disulfide Bonds

    Microsoft Academic Search

    Jason W. H. Wong; Philip J. Hogg

    \\u000a Protein disulfide bonds link cysteine residues in the polypeptide chain. The bonds contribute, sometimes crucially, to protein\\u000a stability and function and are strongly conserved through the evolution of species. By analyzing the conservation of all structurally\\u000a validated disulfide bonds across 29 completely sequenced eukaryotic genomes, we found that disulfide-bonded cysteines are\\u000a even more conserved than tryptophan – the most conserved

  13. Analysis of carotenoid isomerase activity in a prototypical carotenoid cleavage enzyme, apocarotenoid oxygenase (ACO).

    PubMed

    Sui, Xuewu; Kiser, Philip D; Che, Tao; Carey, Paul R; Golczak, Marcin; Shi, Wuxian; von Lintig, Johannes; Palczewski, Krzysztof

    2014-05-01

    Carotenoid cleavage enzymes (CCEs) constitute a group of evolutionarily related proteins that metabolize a variety of carotenoid and non-carotenoid substrates. Typically, these enzymes utilize a non-heme iron center to oxidatively cleave a carbon-carbon double bond of a carotenoid substrate. Some members also isomerize specific double bonds in their substrates to yield cis-apocarotenoid products. The apocarotenoid oxygenase from Synechocystis has been hypothesized to represent one such member of this latter category of CCEs. Here, we developed a novel expression and purification protocol that enabled production of soluble, native ACO in quantities sufficient for high resolution structural and spectroscopic investigation of its catalytic mechanism. High performance liquid chromatography and Raman spectroscopy revealed that ACO exclusively formed all-trans products. We also found that linear polyoxyethylene detergents previously used for ACO crystallization strongly inhibited the apocarotenoid oxygenase activity of the enzyme. We crystallized the native enzyme in the absence of apocarotenoid substrate and found electron density in the active site that was similar in appearance to the density previously attributed to a di-cis-apocarotenoid intermediate. Our results clearly demonstrated that ACO is in fact a non-isomerizing member of the CCE family. These results indicate that careful selection of detergent is critical for the success of structural studies aimed at elucidating structures of CCE-carotenoid/retinoid complexes. PMID:24648526

  14. Cleavage strongly influences whether soluble HIV-1 envelope glycoprotein trimers adopt a native-like conformation

    PubMed Central

    Ringe, Rajesh P.; Sanders, Rogier W.; Yasmeen, Anila; Kim, Helen J.; Lee, Jeong Hyun; Cupo, Albert; Korzun, Jacob; Derking, Ronald; van Montfort, Thijs; Julien, Jean-Philippe; Wilson, Ian A.; Klasse, Per Johan; Ward, Andrew B.; Moore, John P.

    2013-01-01

    We compare the antigenicity and conformation of soluble, cleaved vs. uncleaved envelope glycoprotein (Env gp)140 trimers from the subtype A HIV type 1 (HIV-1) strain BG505. The impact of gp120–gp41 cleavage on trimer structure, in the presence or absence of trimer-stabilizing modifications (i.e., a gp120–gp41 disulfide bond and an I559P gp41 change, together designated SOSIP), was assessed. Without SOSIP changes, cleaved trimers disintegrate into their gp120 and gp41-ectodomain (gp41ECTO) components; when only the disulfide bond is present, they dissociate into gp140 monomers. Uncleaved gp140s remain trimeric whether SOSIP substitutions are present or not. However, negative-stain electron microscopy reveals that only cleaved trimers form homogeneous structures resembling native Env spikes on virus particles. In contrast, uncleaved trimers are highly heterogeneous, adopting a variety of irregular shapes, many of which appear to be gp120 subunits dangling from a central core that is presumably a trimeric form of gp41ECTO. Antigenicity studies with neutralizing and nonneutralizing antibodies are consistent with the EM images; cleaved, SOSIP-stabilized trimers express quaternary structure-dependent epitopes, whereas uncleaved trimers expose nonneutralizing gp120 and gp41ECTO epitopes that are occluded on cleaved trimers. These findings have adverse implications for using soluble, uncleaved trimers for structural studies, and the rationale for testing uncleaved trimers as vaccine candidates also needs to be reevaluated. PMID:24145402

  15. Overcoming lability of extremely long alkane carbon-carbon bonds through dispersion forces.

    PubMed

    Schreiner, Peter R; Chernish, Lesya V; Gunchenko, Pavel A; Tikhonchuk, Evgeniya Yu; Hausmann, Heike; Serafin, Michael; Schlecht, Sabine; Dahl, Jeremy E P; Carlson, Robert M K; Fokin, Andrey A

    2011-09-15

    Steric effects in chemistry are a consequence of the space required to accommodate the atoms and groups within a molecule, and are often thought to be dominated by repulsive forces arising from overlapping electron densities (Pauli repulsion). An appreciation of attractive interactions such as van der Waals forces (which include London dispersion forces) is necessary to understand chemical bonding and reactivity fully. This is evident from, for example, the strongly debated origin of the higher stability of branched alkanes relative to linear alkanes and the possibility of constructing hydrocarbons with extraordinarily long C-C single bonds through steric crowding. Although empirical bond distance/bond strength relationships have been established for C-C bonds (longer C-C bonds have smaller bond dissociation energies), these have no present theoretical basis. Nevertheless, these empirical considerations are fundamental to structural and energetic evaluations in chemistry, as summarized by Pauling as early as 1960 and confirmed more recently. Here we report the preparation of hydrocarbons with extremely long C-C bonds (up to 1.704?Å), the longest such bonds observed so far in alkanes. The prepared compounds are unexpectedly stable--noticeable decomposition occurs only above 200?°C. We prepared the alkanes by coupling nanometre-sized, diamond-like, highly rigid structures known as diamondoids. The extraordinary stability of the coupling products is due to overall attractive dispersion interactions between the intramolecular H•••H contact surfaces, as is evident from density functional theory computations with and without inclusion of dispersion corrections. PMID:21921913

  16. Making and Breaking Bonds

    NSDL National Science Digital Library

    The Concord Consortium

    2011-12-11

    Atoms collide and, under certain circumstances, react to form bonds with one another. The process of association is the bonding of atoms into a molecule while dissociation is the process by which a molecule breaks apart into simpler groups of atoms, individual atoms, or ions. Students interact with a molecular dynamics model to explore the making and breaking of bonds.

  17. Rapid adhesive bonding concepts

    NASA Technical Reports Server (NTRS)

    Stein, B. A.; Tyeryar, J. R.; Hodges, W. T.

    1984-01-01

    Adhesive bonding in the aerospace industry typically utilizes autoclaves or presses which have considerable thermal mass. As a consequence, the rates of heatup and cooldown of the bonded parts are limited and the total time and cost of the bonding process is often relatively high. Many of the adhesives themselves do not inherently require long processing times. Bonding could be performed rapidly if the heat was concentrated in the bond lines or at least in the adherends. Rapid adhesive bonding concepts were developed to utilize induction heating techniques to provide heat directly to the bond line and/or adherends without heating the entire structure, supports, and fixtures of a bonding assembly. Bonding times for specimens are cut by a factor of 10 to 100 compared to standard press bonding. The development of rapid adhesive bonding for lap shear specimens (per ASTM D1003 and D3163), for aerospace panel bonding, and for field repair needs of metallic and advanced fiber reinforced polymeric matrix composite structures are reviewed.

  18. Rhodium-Catalyzed Alkylation of C-H Bonds in Aromatic Amides with Styrenes via Bidentate-Chelation Assistance.

    PubMed

    Shibata, Kaname; Yamaguchi, Takuma; Chatani, Naoto

    2015-07-17

    Rhodium-catalyzed alkylation reactions of aromatic C-H bonds in aromatic amides with styrene derivatives have been developed by using an 8-aminoquinoline as a bidentate directing group. C-C bond formation selectively occurred between the ortho C-H bonds in aromatic amides and the terminal carbon of the styrene derivatives. The presence of an 8-aminoquinoline moiety is essential for the success of the reaction. PMID:26125539

  19. Folding and particle assembly are disrupted by single-point mutations near the autocatalytic cleavage site of Nudaurelia capensis ? virus capsid protein

    PubMed Central

    Taylor, Derek J.; Johnson, John E.

    2005-01-01

    Protein subunits of several RNA viruses are known to undergo post-assembly, autocatalytic cleavage that is required for infectivity. Nudaurelia capensis ? virus (N? V) is one of the simplest viruses to undergo an autocatalytic cleavage, making it an excellent model to understand both assembly and the mechanism of autoproteolysis. Heterologous expression of the coat protein gene of N? V in a baculovirus system results in the spontaneous assembly of virus-like particles (VLPs) that remain uncleaved when purified at neutral pH. After acidification to pH 5.0, the VLPs autocatalytically cleave at residue 570, providing an in vitro control of the cleavage. The crystal structure of N? V displays three residues near the scissile bond that were candidates for participation in the reaction. These were changed by site-directed mutagenesis to conservative and nonconservative residues and the products analyzed. Even conservative changes at the three residues dramatically reduced cleavage when the subunits assembled properly. Unexpectedly, we discovered that these residues are not only critical to the kinetics of N? V autoproteolysis, but are also necessary for proper folding of subunits and, ultimately, assembly of N? V VLPs. PMID:15659373

  20. Increasing Fragmentation of Disulfide-Bonded Proteins for Top-Down Mass Spectrometry by Supercharging

    PubMed Central

    Zhang, Jiang; Ogorzalek Loo, Rachel R.; Loo, Joseph A.

    2015-01-01

    The disulfide bond is an important post-translational modification to form and maintain the native structure and biological functions of proteins. Characterization of disulfide bond linkages is therefore of essential interest in the structural elucidation of proteins. Top-down mass spectrometry (MS) of disulfide-bonded proteins has been hindered by relatively low sequence coverage due to disulfide cross-linking. In this study, we employed top-down ESI-MS with Fourier-transform ion cyclotron resonance (FT-ICR) MS with electron capture dissociation (ECD) and collisionally activated dissociation (CAD) to study the fragmentation of supercharged proteins with multiple intramolecular disulfide bonds. With charge enhancement upon the addition of sulfolane to the analyte solution, improved protein fragmentation and disulfide bond cleavage efficiency was observed for proteins including bovine ?-lactoglobulin, soybean trypsin inhibitor, human proinsulin, and chicken lysozyme. Both the number and relative abundances of product ions representing disulfide cleavage increase with increasing charge states for the proteins studied. Our studies suggest supercharging ESI-MS is a promising tool to aid in the top-down MS analysis of disulfide-bonded proteins, providing potentially useful information for the determination of disulfide bond linkages. PMID:26028988

  1. Computational Study of Bond Dissociation Enthalpies for Lignin Model Compounds. Substituent Effects in Phenethyl Phenyl Ethers

    SciTech Connect

    Beste, Ariana [ORNL; Buchanan III, A C [ORNL

    2009-01-01

    Lignin is an abundant natural resource that is a potential source of valuable chemicals. Improved understanding of the pyrolysis of lignin occurs through the study of model compounds for which phenethyl phenyl ether (PhCH2CH2OPh, PPE) is the simplest example representing the dominant -O-4 ether linkage. The initial step in the thermal decomposition of PPE is the homolytic cleavage of the oxygen-carbon bond. The rate of this key step will depend on the bond dissociation enthalpy, which in turn will depend on the nature and location of relevant substituents. We used modern density functional methods to calculate the oxygen-carbon bond dissociation enthalpies for PPE and several oxygen substituted derivatives. Since carbon-carbon bond cleavage in PPE could be a competitive initial reaction under high temperature pyrolysis conditions, we also calculated substituent effects on these bond dissociation enthalpies. We found that the oxygen-carbon bond dissociation enthalpy is substantially lowered by oxygen substituents situated at the phenyl ring adjacent to the ether oxygen. On the other hand, the carbon-carbon bond dissociation enthalpy shows little variation with different substitution patterns on either phenyl ring.

  2. Analysis of the Microwave Spectrum of Tricarbon Oxide Sulfide, 0 = C = C = C = S, in Highly Excited Bending States

    NASA Astrophysics Data System (ADS)

    Winnewisser, M.; Peau, E. W.; Yamada, K.; Christiansen, J. J.

    1981-08-01

    In The microwave spectrum of tricarbon oxide sulphide (3-thioxo-l,2-propadiene-l-one), 0=C= C=C=S, has been measured in the frequency range from 8 to 40 GHz and includes vibrational satellite lines arising from the vibrational manifold of the lowest-lying doubly-degenerate bending mode i>7. The method of analysis followed the theory of rotation-vibrational interaction as devel-oped by Nielsen and Amat. The spectroscopic constants B v and D v as well as several vibration-rotational constants for each vibrational state vy = 0 to 7, = 1 and vq = 1 were determined with the aid of a newly written least squares program. The program structure relies on the cor-relation of the symmetry classification of energy levels in linear and bent molecules, and follows closely the analysis of asymmetric rotor spectra. From the «»vibrational spectrum of C3OS in excited states of vy up to t'7 — 7 and 1 — 6 the sign and magnitude of the effective vibrational anharmonicity constant xi t i t were determined. The interpretation of these results yields the infor-mation that in C3OS the potential function describing the two-dimensional oscillator of the vj bending mode is very harmonic and does not contain a perturbing hump. The dynamic behaviour of C3OS, a classical example of a linear molecule, is thus in sharp contrast to the quasilinear be-haviour of C3O2 •

  3. Bonding thermoplastic polymers

    DOEpatents

    Wallow, Thomas I. (Fremont, CA); Hunter, Marion C. (Livermore, CA); Krafcik, Karen Lee (Livermore, CA); Morales, Alfredo M. (Livermore, CA); Simmons, Blake A. (San Francisco, CA); Domeier, Linda A. (Danville, CA)

    2008-06-24

    We demonstrate a new method for joining patterned thermoplastic parts into layered structures. The method takes advantage of case-II permeant diffusion to generate dimensionally controlled, activated bonding layers at the surfaces being joined. It is capable of producing bonds characterized by cohesive failure while preserving the fidelity of patterned features in the bonding surfaces. This approach is uniquely suited to production of microfluidic multilayer structures, as it allows the bond-forming interface between plastic parts to be precisely manipulated at micrometer length scales. The bond enhancing procedure is easily integrated in standard process flows and requires no specialized equipment.

  4. Prospective bonding applications

    NASA Astrophysics Data System (ADS)

    Ancenay, H.; Benazet, D.

    1981-07-01

    Adhesive bonding in industry and in the laboratory is surveyed and prospects for its wider utilization are assessed. The economic impact of bonding technology on industry is discussed. Research is reviewed, centering on the development of nondestructive testing and inspection techniques. Traditional (wood) as well as new materials susceptible to bonding are considered. Applications in construction and civil engineering, in aeronautics, and in the automobile industry are covered. The use of glues in mechanical constructions, in assembling cylindrical parts, and in metal-metal bonding are examined. Hybrid assembling and bonding of composite materials are included.

  5. High temperature reactions of bibenzyl with elemental sulfur and hydrogen sulfide in the presence and absence of hydrogen and carbon monoxide

    Microsoft Academic Search

    Hei

    1985-01-01

    High temperature reactions were done with bibenzyl and related compounds to study C-C bond cleavage under coal liquefaction conditions. Reactions were run in 12-ml stainless steel, 3.7-ml glass and 8.0-ml aluminum autoclaves. The range of temperatures studied was 250-515°C and that of pressure was 0-1800 psi (initial). Mechanisms for the cleavage of the aromatic-aliphatic C-C bonds (..cap alpha..-cleavage) and the

  6. Modeling Radial Holoblastic Cleavage: A Laboratory Activity for Developmental Biology.

    ERIC Educational Resources Information Center

    Ellis, Linda K.

    2000-01-01

    Introduces a laboratory activity designed for an undergraduate developmental biology course. Uses Play-Doh (plastic modeling clay) to build a multicellular embryo in order to provide a 3-D demonstration of cleavage. Includes notes for the instructor and student directions. (YDS)

  7. Growth phase dependency of chromatin cleavage and degradation by bleomycin.

    PubMed Central

    Moore, C W; Jones, C S; Wall, L A

    1989-01-01

    Preferential cleavage of Saccharomyces cerevisiae chromosomes in internucleosomal (linker) regions and nonspecific degradation of chromatin by an anticancer antibiotic which degrades DNA were investigated and found to increase in consecutive stages of growth. Cleavage of DNA in internucleosomal regions and intensities and multiplicities of nucleosomal bands were dependent on drug concentration, growth phase of the cells, and length of incubation. Cellular DNA was least degraded during logarithmic phase. After cells progressed only one generation in logarithmic phase, low concentrations (6.7 x 10(-7) to 3.4 x 10(-6) M) of bleomycin produced approximately three to seven times more DNA breaks. Internucleosomal cleavage was highest, and the most extended oligonucleosomal series and extensive chromatin degradation were observed during stationary phase. It is concluded that the growth phase of cells is critical in determining amounts of the highly preferential cleavage in internucleosomal regions and overall breakage and degradation of DNA. Mononucleosomal bands were most intense, indicating the greatest accumulation of DNA of this size. Mean mononucleosomal lengths were 165.9 +/- 3.9 base pairs, in agreement with yeast mononucleosomal lengths. As high-molecular-weight chromatin was digested by bleomycin, oligonucleosomes and, eventually, mononucleosomes became digested. Therefore, it is also concluded that bleomycin degradation of oligonucleosomes and trimming of DNA linker regions proceed to degradation of the monosomes (core plus linker DNA). Images PMID:2479336

  8. A review of statistical methods for prediction of proteolytic cleavage.

    PubMed

    duVerle, David A; Mamitsuka, Hiroshi

    2012-05-01

    A fundamental component of systems biology, proteolytic cleavage is involved in nearly all aspects of cellular activities: from gene regulation to cell lifecycle regulation. Current sequencing technologies have made it possible to compile large amount of cleavage data and brought greater understanding of the underlying protein interactions. However, the practical impossibility to exhaustively retrieve substrate sequences through experimentation alone has long highlighted the need for efficient computational prediction methods. Such methods must be able to quickly mark substrate candidates and putative cleavage sites for further analysis. Available methods and expected reliability depend heavily on the type and complexity of proteolytic action, as well as the availability of well-labelled experimental data sets: factors varying greatly across enzyme families. For this review, we chose to give a quick overview of the general issues and challenges in cleavage prediction methods followed by a more in-depth presentation of major techniques and implementations, with a focus on two particular families of cysteine proteases: caspases and calpains. Through their respective differences in proteolytic specificity (high for caspases, broader for calpains) and data availability (much lower for calpains), we aimed to illustrate the strengths and limitations of techniques ranging from position-based matrices and decision trees to more flexible machine-learning methods such as hidden Markov models and Support Vector Machines. In addition to a technical overview for each family of algorithms, we tried to provide elements of evaluation and performance comparison across methods. PMID:22138323

  9. N-cadherin prodomain cleavage regulates synapse formation in vivo

    Microsoft Academic Search

    Nazlie S. Latefi; Liliana Pedraza; Anne Schohl; Ziwei Li; Edward S. Ruthazer

    2009-01-01

    Cadherins are initially synthesized bearing a prodomain that is thought to limit adhesion during early stages of biosynthesis. Functional cadherins lack this prodomain, raising the intriguing possibility that cells may utilize prodomain cleavage as a means to tempo- rally or spatially regulate adhesion after delivery of cad- herin to the cell surface. In support of this idea, immuno- staining for

  10. Mitochondria Localize to the Cleavage Furrow in Mammalian Cytokinesis

    PubMed Central

    Lawrence, Elizabeth J.; Mandato, Craig A.

    2013-01-01

    Mitochondria are dynamic organelles with multiple cellular functions, including ATP production, calcium buffering, and lipid biosynthesis. Several studies have shown that mitochondrial positioning is regulated by the cytoskeleton during cell division in several eukaryotic systems. However, the distribution of mitochondria during mammalian cytokinesis and whether the distribution is regulated by the cytoskeleton has not been examined. Using live spinning disk confocal microscopy and quantitative analysis of mitochondrial fluorescence intensity, we demonstrate that mitochondria are recruited to the cleavage furrow during cytokinesis in HeLa cells. After anaphase onset, the mitochondria are recruited towards the site of cleavage furrow formation, where they remain enriched as the furrow ingresses and until cytokinesis completion. Furthermore, we show that recruitment of mitochondria to the furrow occurs in multiple mammalian cells lines as well as in monopolar, bipolar, and multipolar divisions, suggesting that the mechanism of recruitment is conserved and robust. Using inhibitors of cytoskeleton dynamics, we show that the microtubule cytoskeleton, but not actin, is required to transport mitochondria to the cleavage furrow. Thus, mitochondria are specifically recruited to the cleavage furrow in a microtubule-dependent manner during mammalian cytokinesis. Two possible reasons for this could be to localize mitochondrial function to the furrow to facilitate cytokinesis and / or ensure accurate mitochondrial inheritance. PMID:23991162

  11. Drosophila Nicastrin Is Essential for the Intramembranous Cleavage of Notch

    Microsoft Academic Search

    Hernán López-Schier; Daniel St Johnston

    2002-01-01

    The catalytic subunit of ?-secretase is thought to be Presenilin, which is required for both the cleavage of APP and in the processing of Notch. Presenilin is found in a multisubunit complex that also contains Nicastrin. Nicastrin has been implicated in APP processing, but its role in Notch signaling remains unclear. Here we show that Drosophila Nicastrin is required for

  12. Synthesis of a base-free hafnium nitride from N2 cleavage: a versatile platform for dinitrogen functionalization.

    PubMed

    Semproni, Scott P; Chirik, Paul J

    2013-07-31

    The synthesis and characterization of a metastable, base-free isocyanato dihafnocene ?-nitrido complex from CO-induced dinitrogen cleavage is described. The open coordination site at hafnium suggested the possibility of functionalization of the nitrogen atom by cycloaddition and insertion chemistry. Addition of the strained, activated alkyne, cyclooctyne, resulted in N-C bond formation by cycloaddition. The alkyne product is kinetically unstable engaging the terminal hafnocene isocyanate and promoting deoxygenation and additional N-C bond formation resulting in a substituted cyanamide ligand. Group transfer between hafnium centers was observed upon treatment with Me3SiCl resulting in bridging carbodiimidyl ligands. Amidinato-type ligands, [NC(R)N](3-) were prepared by addition of either cyclohexyl or isobutyronitrile to the base free dihafnocene ?-nitrido complex, which also engages in additional N-C bond formation with the terminal isocyanate to form bridging ureate-type ligands. Heterocummulenes also proved reactive as exposure of the nitride complex to CO2 resulted in deoxygenation and N-C bond formation to form isocyanate ligands. With substituted isocyanates, cycloaddition to the dihafnocene ?-nitrido was observed forming ureate ligands, which upon thermolysis isomerize to bridging carbodiimides. Taken together, these results establish the base free dihafnocene ?-nitrido as a versatile platform to synthesize organic molecules from N2 and carbon monoxide. PMID:23829435

  13. Cinematographic observation of “surface contraction waves” (SCW) during the early cleavage of axolotl eggs

    Microsoft Academic Search

    K. Hara

    1971-01-01

    Prior to the appearance of the cleavage furrows circular or semicircular zones suggesting surface contraction originate at the future initiation point of the cleavage furrow. They expand and travel in animal-vegetative direction.

  14. Activation of dinitrogen-derived hafnium nitrides for nucleophilic N-C bond formation with a terminal isocyanate.

    PubMed

    Semproni, Scott P; Chirik, Paul J

    2013-12-01

    Better by Hf: Anion coordination to a bridging hafnocene nitride complex, prepared from CO-induced N2 cleavage, increases the nucleophilicity of the nitrogen atom, thus promoting additional N?C bond formation with a typically inert terminal isocyanate ligand. This cascade sequence allows synthesis of otherwise challenging mono-substituted ureas using N2 , CO, and an appropriate electrophile. PMID:24123920

  15. Defect structures in deformed F.C.C. metals

    SciTech Connect

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

    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.

  16. DEFORMATION-DEPENDENT ENZYME MECHANOKINETIC CLEAVAGE OF TYPE I COLLAGEN

    PubMed Central

    Wyatt, Karla E-K.; Bourne, Jonathan W.; Torzilli, Peter A.

    2009-01-01

    Collagen is a key structural protein in the extracellular matrix of many tissues. It provides biological tissues with tensile mechanical strength and is enzymatically cleaved by a class of matrix metalloproteinases (MMPs) known as collagenases. Collagen enzymatic kinetics has been well characterized in solubilized, gel and reconstituted forms. However limited information exists on enzyme degradation of structurally intact collagen fibers and, more important, on the effect of mechanical deformation on collagen cleavage. We studied the degradation of native rat tail tendon fibers by collagenase after the fibers were mechanically elongated to strains of ? = 1-10%. After the fibers were elongated and the stress allowed to relax, the fiber was immersed in Clostridium histolyticum collagenase and the decrease in stress (?) monitored as a means of calculating the rate of enzyme cleavage of the fiber. An enzyme mechanokinetic (EMK) relaxation function TE(?) in sec-1 was calculated from the linear stress-time response during fiber cleavage, where TE(?) corresponds to the zero-order Michaelis-Menten enzyme-substrate kinetic response. The EMK relaxation function TE(?) was found to decrease with applied strain at a rate of ~9% per percent strain, with complete inhibition of collagen cleavage predicted to occur at a strain of ~11%. However, comparison of the EMK response (TE vs ?) to collagen’s stress-strain response (? vs ?) suggested the possibility of three different EMK responses; (1) constant TE(?) within the toe region (?<3%), (2) a rapid decrease (~50%) at the transition of the toe-to-heel region (??3%) followed by (3) a constant value throughout the heel (?=3 to 5%) and linear (?=5 to 10%) regions. This observation suggests that the mechanism for the strain-dependent inhibition of enzyme cleavage of the collagen triple helix may be by a conformational change in the triple helix since the decrease in TE(?) appeared concomitant with stretching of the collagen molecule. PMID:19388774

  17. A pathway sensor for genome-wide screens of intracellular proteolytic cleavage

    PubMed Central

    Ketteler, Robin; Sun, Zairen; Kovacs, Karl F; He, Wei-Wu; Seed, Brian

    2008-01-01

    Protein cleavage is a central event in many regulated biological processes. We describe a system for detecting intracellular proteolysis based on non-conventional secretion of Gaussia luciferase (GLUC). GLUC exits the cell without benefit of a secretory leader peptide, but can be anchored in the cell by fusion to ?-actin. By including protease cleavage sites between GLUC and ?-actin, proteolytic cleavage can be detected. Using this assay, we have identified regulators of autophagy, apoptosis and ?-actin cleavage. PMID:18387192

  18. Proteolytic cleavage of Ser52Pro variant transthyretin triggers its amyloid fibrillogenesis

    PubMed Central

    Mangione, P. Patrizia; Porcari, Riccardo; Gillmore, Julian D.; Pucci, Piero; Monti, Maria; Porcari, Mattia; Giorgetti, Sofia; Marchese, Loredana; Raimondi, Sara; Serpell, Louise C.; Chen, Wenjie; Relini, Annalisa; Marcoux, Julien; Clatworthy, Innes R.; Taylor, Graham W.; Tennent, Glenys A.; Robinson, Carol V.; Hawkins, Philip N.; Stoppini, Monica; Wood, Stephen P.; Pepys, Mark B.; Bellotti, Vittorio

    2014-01-01

    The Ser52Pro variant of transthyretin (TTR) produces aggressive, highly penetrant, autosomal-dominant systemic amyloidosis in persons heterozygous for the causative mutation. Together with a minor quantity of full-length wild-type and variant TTR, the main component of the ex vivo fibrils was the residue 49-127 fragment of the TTR variant, the portion of the TTR sequence that previously has been reported to be the principal constituent of type A, cardiac amyloid fibrils formed from wild-type TTR and other TTR variants [Bergstrom J, et al. (2005) J Pathol 206(2):224–232]. This specific truncation of Ser52Pro TTR was generated readily in vitro by limited proteolysis. In physiological conditions and under agitation the residue 49-127 proteolytic fragment rapidly and completely self-aggregates into typical amyloid fibrils. The remarkable susceptibility to such cleavage is likely caused by localized destabilization of the ?-turn linking strands C and D caused by loss of the wild-type hydrogen-bonding network between the side chains of residues Ser52, Glu54, Ser50, and a water molecule, as revealed by the high-resolution crystallographic structure of Ser52Pro TTR. We thus provide a structural basis for the recently hypothesized, crucial pathogenic role of proteolytic cleavage in TTR amyloid fibrillogenesis. Binding of the natural ligands thyroxine or retinol-binding protein (RBP) by Ser52Pro variant TTR stabilizes the native tetrameric assembly, but neither protected the variant from proteolysis. However, binding of RBP, but not thyroxine, inhibited subsequent fibrillogenesis. PMID:24474780

  19. Analysis of Carotenoid Isomerase Activity in a Prototypical Carotenoid Cleavage Enzyme, Apocarotenoid Oxygenase

    E-print Network

    Palczewski, Krzysztof

    Analysis of Carotenoid Isomerase Activity in a Prototypical Carotenoid Cleavage Enzyme non-isomerizing member of the carotenoid cleavage enzyme family. Carotenoid cleavage enzymes (CCEs) constitute a group of evolutionarily related proteins that metabolize a variety of carotenoid and non-carotenoid

  20. The Decreased apical dominance1/Petunia hybrida CAROTENOID CLEAVAGE DIOXYGENASE8 Gene Affects

    E-print Network

    Klee, Harry J.

    The Decreased apical dominance1/Petunia hybrida CAROTENOID CLEAVAGE DIOXYGENASE8 Gene Affects, Gainesville, Florida 32611-0670 Carotenoids and carotenoid cleavage products play an important and integral hybrida) encodes a hypothetical carotenoid cleavage dioxygenase (CCD) and ortholog of the MORE AXILLARY

  1. FUSION OF CONDITIONAL RANDOM FIELD AND SIGNALP FOR PROTEIN CLEAVAGE SITE PREDICTION

    E-print Network

    Mak, Man-Wai

    FUSION OF CONDITIONAL RANDOM FIELD AND SIGNALP FOR PROTEIN CLEAVAGE SITE PREDICTION Man-Wai Mak-Hsing University, ROC ABSTRACT Prediction of protein cleavage sites is an important step in drug design. Recent-- Conditional random fields, discriminative models, signal peptides, cleavage sites, protein sequences. Web

  2. Transfers of fresh blastocysts and blastocysts cultured from thawed cleavage embryos are associated with fewer miscarriages

    Microsoft Academic Search

    Yueping Alex Wang; Michael Costello; Michael Chapman; Deborah Black; Elizabeth Anne Sullivan

    The literature shows an inconsistent relationship between miscarriage and assisted reproduction treatment factors. This study assessed the association between miscarriage and transfer of fresh or thawed embryos at cleavage\\/blastocyst stages. A population study included 52,874 pregnancies following autologous cycles. The miscarriage rate was compared by groups of transferred embryos (fresh cleavage embryo, fresh blastocyst, thawed cleavage embryo, blastocyst from thawed

  3. Molecular-dynamics simulation of crystalline 18-crown-6: thermal shortening of covalent bonds

    Microsoft Academic Search

    J. van Eerden; S. Harkema; D. Feil

    1990-01-01

    Molecular-dynamics simulations of crystalline 18-crown-6 have been performed in a study of the apparent thermal shortening of covalent bonds observed in crystal structures. At 100 K, a shortening of 0.006 _+ 0.001 A for C----C and C----O bonds was obtained. This result was found to be independent of details of the force field and the simulation. There was agreement between

  4. Atomic diffraction study of the interaction of helium atoms with the surface of an organic single crystal: The (001) cleavage planes of guanidinium methanesulfonate

    NASA Astrophysics Data System (ADS)

    Bracco, Gianangelo; Ward, Michael D.; Scoles, Giacinto

    2003-05-01

    The guanidinium methanesulfonate is a layered self-assembled organic crystal which presents a bilayer structure and two different (001) planes can be exposed upon cleavage. In a previous paper we have shown that the analysis of the rate of decay in the thermal attenuation of the diffraction intensities in the scattering from the (001) surface of single crystal guanidinium methanesulfonate allows for distinguishing between the two possible (001) cleavage planes. However, since a more detailed knowledge of the He-surface interaction was lacking, in this paper we complete the investigation by studying the attractive part of the interaction potential between He and the surface terminated by methyl groups projecting outward from the hydrogen bonded sulfonate and guanidinium sheets. Four bound state levels have been determined and a well depth D=(6.7±0.2) meV has been estimated.

  5. Alkene oxidation catalyzed by a ruthenium-substituted heteropolyanion, SiRu(L)W sub 11 O sub 39 : The mechanism of the periodate mediated oxidative cleavage

    SciTech Connect

    Neumann, R.; Abu-Gnim, C. (Hebrew Univ. of Jerusalem (Israel))

    1990-08-01

    A ruthenium-substituted heteropolyanion SiRu(H{sub 2}O)W{sub 11}O{sub 39}{sup 5{minus}} was synthesized and characterized. The hydrophobic quaternary ammonium salt of the heteropolyanion ((C{sub 6}H{sub 13}){sub 4}N){sub 5}SiRu{sup III}(H{sub 2}O)W{sub 11}O{sub 39} was used as a catalyst for the oxidation of alkenes with tert-butyl hydroperoxide, potassium persulfate, iodosobenzene, and sodium periodate as primary oxidants. Reactivity and selectivity were found to be dependent on the oxidant used; several different types of oxidation processes could be identified including allylic oxidation, epoxidation, and oxidative cleavage. Use of sodium periodate as oxidant enabled selective bond cleavage with aldehydes as the exclusive product.

  6. Mpe1, a Zinc Knuckle Protein, Is an Essential Component of Yeast Cleavage and Polyadenylation Factor Required for the Cleavage and Polyadenylation of mRNA

    Microsoft Academic Search

    L. T. A. Vo; MICHELE MINET; JEAN-MARIE SCHMITTER; FRANCOIS LACROUTE; F. Wyers

    2001-01-01

    In Saccharomyces cerevisiae, in vitro mRNA cleavage and polyadenylation require the poly(A) binding protein, Pab1p, and two multiprotein complexes: CFI (cleavage factor I) and CPF (cleavage and polyadenylation factor). We characterized a novel essential gene, MPE1 (YKL059c), which interacts genetically with the PCF11 gene encoding a subunit of CFI. Mpe1p is an evolutionarily conserved protein, a homolog of which is

  7. Bonded semiconductor substrate

    DOEpatents

    Atwater, Jr.; Harry A. (South Pasadena, CA), Zahler; James M. (Pasadena, CA)

    2010-07-13

    Ge/Si and other nonsilicon film heterostructures are formed by hydrogen-induced exfoliation of the Ge film which is wafer bonded to a cheaper substrate, such as Si. A thin, single-crystal layer of Ge is transferred to Si substrate. The bond at the interface of the Ge/Si heterostructures is covalent to ensure good thermal contact, mechanical strength, and to enable the formation of an ohmic contact between the Si substrate and Ge layers. To accomplish this type of bond, hydrophobic wafer bonding is used, because as the invention demonstrates the hydrogen-surface-terminating species that facilitate van der Waals bonding evolves at temperatures above 600.degree. C. into covalent bonding in hydrophobically bound Ge/Si layer transferred systems.

  8. Pd loaded amphiphilic COF as catalyst for multi-fold Heck reactions, C-C couplings and CO oxidation.

    PubMed

    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 Pd(0) nanoparticles into it. An 18-20% nano-Pd loading gives highly active composite working in open air at low concentrations (Conc. Pd(0) <0.05?mol%, average TON 1500) catalyzing simultaneous multiple site Heck couplings and C-C couplings using 'non-boronic acid' substrates, and exhibits good recyclability with no sign of catalyst leaching. As an oxidation catalyst, it shows 100% conversion of CO to CO2 at 150?°C with no loss of activity with time and between cycles. Both vapor sorptions and contact angle measurements confirm the amphiphilic character of the COF. DFT-TB studies showed the presence of Pd-triazine and Pd-Schiff bond interactions as being favorable. PMID:26057044

  9. Self-cleavage of the Pseudomonas aeruginosa Cell-surface Signaling Anti-sigma Factor FoxR Occurs through an N-O Acyl Rearrangement.

    PubMed

    Bastiaansen, Karlijn C; van Ulsen, Peter; Wijtmans, Maikel; Bitter, Wilbert; Llamas, María A

    2015-05-01

    The Fox system of Pseudomonas aeruginosa is a cell-surface signaling (CSS) pathway employed by the bacterium to sense and respond to the presence of the heterologous siderophore ferrioxamine in the environment. This regulatory pathway controls the transcription of the foxA ferrioxamine receptor gene through the extracytoplasmic function sigma factor ?(FoxI). In the absence of ferrioxamine, the activity of ?(FoxI) is inhibited by the transmembrane anti-sigma factor FoxR. Upon binding of ferrioxamine by the FoxA receptor, FoxR is processed by a complex proteolytic cascade leading to the release and activation of ?(FoxI). Interestingly, we have recently shown that FoxR undergoes self-cleavage between the periplasmic Gly-191 and Thr-192 residues independent of the perception of ferrioxamine. This autoproteolytic event, which is widespread among CSS anti-sigma factors, produces two distinct domains that interact and function together to transduce the presence of the signal. In this work, we provide evidence that the self-cleavage of FoxR is not an enzyme-dependent process but is induced by an N-O acyl rearrangement. Mutation analysis showed that the nucleophilic side chain of the Thr-192 residue at +1 of the cleavage site is required for an attack on the preceding Gly-191, after which the resulting ester bond is likely hydrolyzed. Because the cleavage site is well preserved and the hydrolysis of periplasmic CSS anti-sigma factors is widely observed, we hypothesize that cleavage via an N-O acyl rearrangement is a conserved feature of these proteins. PMID:25809487

  10. Semiconductor Wafer Bonding

    Microsoft Academic Search

    U. Gosele; Q.-Y. Tong

    1998-01-01

    When mirror-polished, flat, and clean wafers of almost any material are brought into contact at room temperature, they are locally attracted to each other by van der Waals forces and adhere or bond. This phenomenon is referred to as wafer bonding. The most prominent applications of wafer bonding are silicon-on-insulator (SOI) devices, silicon-based sensors and actuators, as well as optical

  11. Energy pulse bonding

    NASA Technical Reports Server (NTRS)

    Smith, G. C.

    1972-01-01

    To eliminate many of the present termination problems a technique called energy pulse bonding (EPB) was developed. The process demonstrated the capability of: (1) joining conductors without prior removal of insulations, (2) joining conductors without danger of brittle intermetallics, (3) increased joint temperature capability, (4) simultaneous formation of several bonds, (5) capability of higher joint density, and (6) a production oriented process. The following metals were successfully bonded in the solid state: copper, beryllium copper, phosphor bronze, aluminum, brass, and Kovar.

  12. Chemical bonding technology

    NASA Technical Reports Server (NTRS)

    Plueddemann, E.

    1986-01-01

    Primers employed in bonding together the various material interfaces in a photovoltaic module are being developed. The approach develops interfacial adhesion by generating actual chemical bonds between the various materials bonded together. The current status of the program is described along with the progress toward developing two general purpose primers for ethylene vinyl acetate (EVA), one for glass and metals, and another for plastic films.

  13. Reactivity-Dependent PCR: Direct, Solution-Phase in Vitro Selection for Bond Formation

    PubMed Central

    2009-01-01

    In vitro selection is a key component of efforts to discover functional nucleic acids and small molecules from libraries of DNA, RNA, and DNA-encoded small molecules. Such selections have been widely used to evolve RNA and DNA catalysts and, more recently, to discover new reactions from DNA-encoded libraries of potential substrates. While effective, current strategies for selections of bond-forming and bond-cleaving reactivity are generally indirect, require the synthesis of biotin-linked substrates, and involve multiple solution-phase and solid-phase manipulations. In this work we report the successful development and validation of reactivity-dependent PCR (RDPCR), a new method that more directly links bond formation or bond cleavage with the amplification of desired sequences and that obviates the need for solid-phase capture, washing, and elution steps. We show that RDPCR can be used to select for bond formation in the context of reaction discovery and for bond cleavage in the context of protease activity profiling. PMID:19522494

  14. One Bond Strategy

    NSDL National Science Digital Library

    2001-01-01

    Provided by SmartMoney.com (see the May 20, 1999 Scout Report for Business & Economics), this quick and easy yet thorough guide takes readers through the process of developing a bond portfolio. At the site, users will find help on deciding how much to invest in bonds, how to divide their portfolio, and tips on investing for both income and profit. First, however, visitors might want to wet their feet in the bond primer section, which covers all the basics, explains the yield curve, offers a calculator and glossary, and throws in "ten things your broker won't tell you about bonds" for good measure.

  15. Hydrogen bonding and anaesthesia

    NASA Astrophysics Data System (ADS)

    Sándorfy, C.

    2004-12-01

    General anaesthetics act by perturbing intermolecular associations without breaking or forming covalent bonds. These associations might be due to a variety of van der Waals interactions or hydrogen bonding. Neurotransmitters all contain OH or NH groups, which are prone to form hydrogen bonds with those of the neurotransmitter receptors. These could be perturbed by anaesthetics. Aromatic rings in amino acids can act as weak hydrogen bond acceptors. On the other hand the acidic hydrogen in halothane type anaesthetics are weak proton donors. These two facts together lead to a probable mechanism of action for all general anaesthetics.

  16. (N-heterocyclic-carbene)Copper(I)-catalyzed carbon-carbon bond formation using carbon dioxide

    E-print Network

    Sirokman, Gergely

    2007-01-01

    This thesis presents work towards the development of a new catalytic C-C bond forming reaction. Alkynes and olefins insert into [(IPr)CuH]2 (IPr = N,N-bis-(2,6-diisopropylphenyl)-1,3-imidazol-2-ylidene) to give copper vinyl ...

  17. Use of specific endonuclease cleavage in RNA sequencing.

    PubMed Central

    Gupta, R C; Randerath, K

    1977-01-01

    Nonradioactive RNA fragments may be sequenced by incorporation of (3H)-label into 3'-terminal positions, controlled digestion with specific ribonucleases, and separation according to size of the digestion products on polyethyleneimine- (PEI-) cellulose thin layers. This combination of techniques allows one to measure accurately distances of specific cleavage sites from the labeled terminal positions. The cleavage specificities of RNases T1, U2, and A are utilized to identify the positions of G, A, and pyrimidine residues respectively. C and U may be distinguished by mobility differences on PEI-cellulose thin layers at ph 2.6. The procedure is simple, rapid, and highly sensitive; as little as 0.5 - 1 microgram of a RNA of the size of tRNA will be needed to sequence all fragments in a complete RNase digest. Images PMID:331267

  18. Enhancement of Neurospora VS ribozyme cleavage by tuberactinomycin antibiotics.

    PubMed Central

    Olive, J E; De Abreu, D M; Rastogi, T; Andersen, A A; Mittermaier, A K; Beattie, T L; Collins, R A

    1995-01-01

    Several examples of inhibition of the function of a ribozyme or RNA-protein complex have shown that certain antibiotics can interact specifically with RNA. There are, however, few examples of antibiotics that have a positive, rather than a negative, effect on the function of an RNA. We have found that micromolar concentrations of viomycin, a basic, cyclic peptide antibiotic of the tuberactinomycin group, enhance the cleavage of a ribozyme derived from Neurospora VS RNA. Viomycin decreases by an order of magnitude the concentration of magnesium required for cleavage. It also stimulates an otherwise insignificant transcleavage reaction by enhancing interactions between RNA molecules. The ability of viomycin to enhance some RNA-mediated reactions but inhibit others, including translation and Group I intron splicing, demonstrates the potential for natural selection by small molecules during evolution in the 'RNA world' and may have broader implications with respect to ribozyme expression and activity in contemporary cells. Images PMID:7621836

  19. Sequence specific inhibition of DNA restriction enzyme cleavage by PNA.

    PubMed Central

    Nielsen, P E; Egholm, M; Berg, R H; Buchardt, O

    1993-01-01

    Plasmids containing double-stranded 10-mer PNA (peptide nucleic acid chimera) targets proximally flanked by two restriction enzyme sites were challenged with the complementary PNA or PNAs having one or two mismatches, and the effect on the restriction enzyme cleavage of the flanking sites was assayed. The following PNAs were used: T10-LysNH2, T5CT4-LysNH2 and T2CT2CT4-LysNH2 and the corresponding targets cloned into pUC 19 were flanked by BamH1, Sal1 or Pstl sites, respectively. In all cases it was found that complete inhibition of restriction enzyme cleavage was obtained with the complementary PNA, a significantly reduced effect was seen with a PNA having one mismatch, and no effect was seen with a PNA having two mismatches. These results show that PNA can be used as sequence specific blockers of DNA recognizing proteins. Images PMID:8382793

  20. Drosha Regulates Gene Expression Independently of RNA Cleavage Function

    PubMed Central

    Gromak, Natalia; Dienstbier, Martin; Macias, Sara; Plass, Mireya; Eyras, Eduardo; Cáceres, Javier F.; Proudfoot, Nicholas J.

    2013-01-01

    Summary Drosha is the main RNase III-like enzyme involved in the process of microRNA (miRNA) biogenesis in the nucleus. Using whole-genome ChIP-on-chip analysis, we demonstrate that, in addition to miRNA sequences, Drosha specifically binds promoter-proximal regions of many human genes in a transcription-dependent manner. This binding is not associated with miRNA production or RNA cleavage. Drosha knockdown in HeLa cells downregulated nascent gene transcription, resulting in a reduction of polyadenylated mRNA produced from these gene regions. Furthermore, we show that this function of Drosha is dependent on its N-terminal protein-interaction domain, which associates with the RNA-binding protein CBP80 and RNA Polymerase II. Consequently, we uncover a previously unsuspected RNA cleavage-independent function of Drosha in the regulation of human gene expression. PMID:24360955

  1. Total Synthesis of (+)-Trienomycins A and F via C-C Bond-Forming Hydrogenation and Transfer Hydrogenation

    PubMed Central

    Del Valle, David J.; Krische, Michael J.

    2013-01-01

    The triene-containing C17-benzene ansamycins trienomycins A and F are prepared in 16 steps (longest linear sequence, LLS) and 28 total steps. The C11-C13 stereotriad is prepared via enantioselective ruthenium catalyzed alcohol CH-syn-crotylation followed by chelation-controlled carbonyl dienylation. Enantioselective rhodium catalyzed acetylene-aldehyde reductive coupling mediated by gaseous hydrogen forms a diene that ultimately is subjected to diene-diene ring closing metathesis to form the macrocycle. The present approach is 14 steps shorter (LLS) than the prior syntheses of trienomycins A and F, and 8 steps shorter (LLS) than any prior synthesis of a triene-containing C17-benzene ansamycin. PMID:23862627

  2. Reversible Sigma C-C Bond Formation Between Phenanthroline Ligands Activated by (C5Me5)2Yb

    SciTech Connect

    Nocton, Gr& #233; 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.

  3. Cyanide-catalyzed C-C bond formation: synthesis of novel compounds, materials and ligands for homogeneous catalysis 

    E-print Network

    Reich, Blair Jesse Ellyn

    2007-04-25

    Cyanide-catalyzed aldimine coupling was employed to synthesize compounds with 1,2-ene-diamine and �±-imine-amine structural motifs: 1,2,N,N'- tetraphenyletheylene-1,2-diamine (13) and (+/-)-2,3-di-(2-hydroxyphenyl)-1,2 ...

  4. Nickel N-heterocyclic carbene catalyzed c?c bond formation: a new route to aryl ketones.

    PubMed

    Gu, Li-Jun; Jin, Cheng; Zhang, Hong-Tao

    2015-06-01

    A novel nickel N-heterocyclic carbene catalyzed cross-coupling reaction of aryl aldehydes with boronic esters for the synthesis of aryl ketones was developed. This reaction provides a mild, practical method toward aryl ketones, which are versatile intermediates and building blocks in organic synthesis. PMID:25925163

  5. An efficient and general route to reduced polypropionates via Zr-catalyzed asymmetric C—C bond formation

    PubMed Central

    Negishi, Ei-ichi; Tan, Ze; Liang, Bo; Novak, Tibor

    2004-01-01

    An efficient and general method for the synthesis of reduced polypropionates has been developed through the application of asymmetric carboalumination of alkenes catalyzed by dichlorobis(1-neomenthylindenyl)zirconium [(NMI)2ZrCl2]. In this investigation, attention has been focused on those reduced polypropionates that are ?-monoheterofunctional and either ?-ethyl or ?-n-propyl. The reaction of 3-buten-1-ol with triethylaluminum (Et3Al) or tripropylaluminum (nPr3Al) in the presence of (NMI)2ZrCl2 and isobutylaluminoxane gave, after protonolysis, (R)-3-methyl-1-pentanol as well as (R)- and (S)-3-methyl-1-hexanols in 88–92% yield in 90–92% enantiomeric excess in one step. These 3-monomethyl-1-alkanols were then converted to two stereoisomers each of 2,4-dimethyl-1-hexanols and 2,4-dimethyl-1-heptanols via methylalumination catalyzed by (NMI)2ZrCl2 and methylaluminoxane followed by oxidation with O2. The four-step (or three-isolation-step) protocol provided syn-2,4-dimethyl-1-alkanols of ?98% stereoisomeric purity in ?50% overall yields, whereas (2S,4R)-2,4-dimethyl-1-hexanol of comparable purity was obtained in 40% overall yield. Commercial availability of (S)-2-methyl-1-butanol as a relatively inexpensive material suggested its use in the synthesis of (2S,4S)- and (2R,4S)-2,4-dimethyl-1-hexanols via a three-step protocol consisting of (i) iodination, (ii) zincation followed by Pd-catalyzed vinylation, and (iii) Zr-catalyzed methylalumination followed by oxidation with O2. This three-step protocol is iterative and applicable to the synthesis of reduced polypropionates containing three or more branching methyl groups, rendering this method for the synthesis of reduced polypropionates generally applicable. Its synthetic utility has been demonstrated by preparing the side chain of zaragozic acid A and the C11–C20 fragment of antibiotics TMC-151 A–F. PMID:15073327

  6. Expanding the substrate scope in palladium-catalyzed C-N and C-C bond-forming reactions

    E-print Network

    Anderson, Kevin William

    2006-01-01

    Chapter 1. The first detailed study of the palladium-catalyzed amination of aryl nonaflates is reported. Use of bulky electron-rich monophosphinobiaryl ligands or BINAP allow for the catalytic amination of electron-rich ...

  7. Thermal degradation of polyisobutylene: effect of rotational motion around C?C· bond on the ? scission leading to monomer formation

    Microsoft Academic Search

    T. Sawaguchi; M. Seno

    1996-01-01

    The formation of isobutylene monomer and volatile oligomers by the thermal degradation of polyisobutylene at 300 °C is simulated by using assigned values of the rate constants (ktd and kpd) of the depolymerization of primary and tertiary terminal macroradicals (Rp· and Rt·), based on a radical chain reaction model including diffusion-controlled termination reactions. With increasing reaction time, the composition of

  8. Probing o-diphenylphosphanyl benzoate (o-DPPB)-directed C-C bond formation: total synthesis of dictyostatin.

    PubMed

    Wünsch, Sebastian; Breit, Bernhard

    2015-02-01

    Herein, we report a robust total synthesis of dictyostatin. This polyketide natural product has attracted much attention because of its impressive antiproliferative activity against several human cancer-cell lines. We accomplished its synthesis in a highly convergent manner from three fragments of equal complexity, which were prepared on multigram scale. The southern and northwestern subunits were constructed through application of our o-DPPB-directed hydroformylation and allylic substitution methodology, respectively. These methods generated the C6 and C14 stereocenters of dictyostatin with good diastereoselectivities and simultaneously allowed further elaboration of the fragments by Wittig olefination and Sharpless asymmetric epoxidation, respectively. The compelling performance of the hydroformylation and allylic substitution with regard to practicability, selectivity, and scale underline their value for the construction of propionate motifs. PMID:25524890

  9. Single-Molecule Analysis of the Target Cleavage Reaction by the Drosophila RNAi Enzyme Complex.

    PubMed

    Yao, Chunyan; Sasaki, Hiroshi M; Ueda, Takuya; Tomari, Yukihide; Tadakuma, Hisashi

    2015-07-01

    Small interfering RNAs (siRNAs) direct cleavage of complementary target RNAs via an RNA-induced silencing complex (RISC) that contains Argonatute2 protein at its core. However, what happens after target cleavage remains unclear. Here we analyzed the cleavage reaction by Drosophila Argonaute2-RISC using single-molecule imaging and revealed a series of intermediate states in target recognition, cleavage, and product release. Our data suggest that, after cleavage, RISC generally releases the 5' cleavage fragment from the guide 3' supplementary region first and then the 3' fragment from the seed region, highlighting the reinforcement of the seed pairing in RISC. However, this order can be reversed by extreme stabilization of the 3' supplementary region or mismatches in the seed region. Therefore, the release order of the two cleavage fragments is influenced by the stability in each region, in contrast to the unidirectional base pairing propagation from the seed to the 3' supplementary region upon target recognition. PMID:26140368

  10. Chemical Bonding, again ionic bonding (in salts): transfer of e-

    E-print Network

    Zakarian, Armen

    Chemical Bonding, again · ionic bonding (in salts): transfer of e- · covalent bonding (organic molecules, non-metals): sharing e- · metallic bonding: electron pooling (delocalization) Lewis electron 3A 4A 5A 6A 7A 8A 2 3 (exceptions) #12;Ionic Bonding Model See sample problem 9.1 4Na + O2 ! 2Na2O

  11. Restriction endonuclease cleavage map of mitochondrial DNA from Aspergillus nidulans.

    PubMed Central

    Stepie?, P P; Bernard, U; Cooke, H J; Küntzel, H

    1978-01-01

    Mitochondrial DNA of the ascomycete fungus Aspergillus nidulans, a circular molecule of 31 500 base pairs, is cleaved by restriction endonucleases Eco R I, Hind II, Hind III and Bgl II into 3, 7, 9 and 5 fragments, respectively. The relative positions of the cleavage sites could be mapped by analysis of fragments obtained by double enzyme digestions of whole DNA and by complete and partial redigestion of isolated restriction fragments. Images PMID:345242

  12. Features of controlled laser thermal cleavage of crystal quartz

    NASA Astrophysics Data System (ADS)

    Serdyukov, A. N.; Shershnev, E. B.; Nikityuk, Yu. V.; Sholokh, V. F.; Sokolov, S. I.

    2012-11-01

    Controlled laser thermal cleavage of crystalline quartz has been simulated. The thermoelastic fields formed in a square single-crystal quartz plate as a result of successive laser heating and exposure to coolant have been calculated for five different versions specified by the crystal cut orientation and direction of laser beam displacement. The results have been verified experimentally using a CO2 laser. The simulation results can be used in the electronics industry to optimize laser cutting of quartz crystals.

  13. Demethylation and cleavage of dimethylsulfoniopropionate in marine intertidal sediments

    USGS Publications Warehouse

    Visscher, P.T.; Kiene, R.P.; Taylor, B.F.

    1994-01-01

    Demethylation and cleavage of dimethylsulfoniopropionate (DMSP) was measured in three different types of,intertidal marine sediments: a cyanobacterial mat, a diatom-covered tidal flat and a carbonate sediment. Consumption rates of added DMSP were highest in cyanobacterial mat slurries (59 ?? mol DMSP l-1 slurry h-1) and lower in slurries from a diatom mat and a carbonate tidal sediment (24 and 9 ??mol DMSP l-1 h-1, respectively). Dimethyl sulfide (DMS) and 3-mercaptopropionate (MPA) were produced simultaneously during DMSP consumption, indicating that cleavage and demethylation occurred at the same time. Viable counts of DMSP-utilizing bacteria revealed a population of 2 x 107 cells cm-3 sediment (90% of these cleaved DMSP to DMS, 10% demethylated DMSP to MPA) in the cyanobacterial mat, 7 x 105 cells cm-3 in the diatom mat (23% cleavers, 77% demethylators), and 9 x 104 cells cm-3 (20% cleavers and 80% demethylators) in the carbonate sediment. In slurries of the diatom mat, the rate of MPA production from added 3-methiolpropionate (MMPA) was 50% of the rate of MPA formation from DMSP. The presence of a large population of demethylating bacteria and the production of MPA from DMSP suggest that the demethylation pathway, in addition to cleavage, contributes significantly to DMSP consumption in coastal sediments.

  14. Telomere lengths in human oocytes, cleavage stage embryos and blastocysts

    PubMed Central

    Turner, S.; Wong, H.P.; Rai, J.; Hartshorne, G.M.

    2010-01-01

    Telomeres are repeated sequences that protect the ends of chromosomes and harbour DNA repair proteins. Telomeres shorten during each cell division in the absence of telomerase. When telomere length becomes critically short, cell senescence occurs. Telomere length therefore reflects both cellular ageing and capacity for division. We have measured telomere length in human germinal vesicle (GV) oocytes and preimplantation embryos, by quantitative fluorescence in situ hybridization (Q-FISH), providing baseline data towards our hypothesis that telomere length is a marker of embryo quality. The numbers of fluorescent foci suggest that extensive clustering of telomeres occurs in mature GV stage oocytes, and in preimplantation embryos. When calculating average telomere length by assuming that each signal presents one telomere, the calculated telomere length decreased from the oocyte to the cleavage stages, and increased between the cleavage stages and the blastocyst (11.12 versus 8.43 versus 12.22 kb, respectively, P < 0.001). Other methods of calculation, based upon expected maximum and minimum numbers of telomeres, confirm that telomere length in blastocysts is significantly longer than cleavage stages. Individual blastomeres within an embryo showed substantial variation in calculated average telomere length. This study implies that telomere length changes according to the stage of preimplantation embryo development. PMID:20573647

  15. Programmable RNA recognition and cleavage by CRISPR/Cas9

    PubMed Central

    O’Connell, Mitchell R.; Oakes, Benjamin L.; Sternberg, Samuel H.; East-Seletsky, Alexandra; Kaplan, Matias; Doudna, Jennifer A.

    2014-01-01

    The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA:DNA complementarity to identify target sites for sequence-specific doublestranded DNA (dsDNA) cleavage1-5. In its native context, Cas9 acts on DNA substrates exclusively because both binding and catalysis require recognition of a short DNA sequence, the protospacer adjacent motif (PAM), next to and on the strand opposite the 20-nucleotide target site in dsDNA4-7. Cas9 has proven to be a versatile tool for genome engineering and gene regulation in many cell types and organisms8, but it has been thought to be incapable of targeting RNA5. Here we show that Cas9 binds with high affinity to single-stranded RNA (ssRNA) targets matching the Cas9-associated guide RNA sequence when the PAM is presented in trans as a separate DNA oligonucleotide. Furthermore, PAM-presenting oligonucleotides (PAMmers) stimulate site-specific endonucleolytic cleavage of ssRNA targets, similar to PAM-mediated stimulation of Cas9-catalyzed DNA cleavage7. Using specially designed PAMmers, Cas9 can be specifically directed to bind or cut RNA targets while avoiding corresponding DNA sequences, and we demonstrate that this strategy enables the isolation of a specific endogenous mRNA from cells. These results reveal a fundamental connection between PAM binding and substrate selection by Cas9, and highlight the utility of Cas9 for programmable and tagless transcript recognition. PMID:25274302

  16. Gleevec inhibits ?-amyloid production but not Notch cleavage

    PubMed Central

    Netzer, William J.; Dou, Fei; Cai, Dongming; Veach, Darren; Jean, Stephanie; Li, Yueming; Bornmann, William G.; Clarkson, Bayard; Xu, Huaxi; Greengard, Paul

    2003-01-01

    Amyloid-? (A?) peptides, consisting mainly of 40 and 42 aa (A?40 and A?42, respectively), are metabolites of the amyloid precursor protein and are believed to be major pathological determinants of Alzheimer's disease. The proteolytic cleavages that form the A? N and C termini are catalyzed by ?-secretase and ?-secretase, respectively. Here we demonstrate that ?-secretase generation of A? in an N2a cell-free system is ATP dependent. In addition, the Abl kinase inhibitor imatinib mesylate (Gleevec, or STI571), which targets the ATP-binding site of Abl and several other tyrosine kinases, potently reduces A? production in the N2a cell-free system and in intact N2a cells. Both STI571 and a related compound, inhibitor 2, also reduce A? production in rat primary neuronal cultures and in vivo in guinea pig brain. STI571 does not inhibit the ?-secretase-catalyzed S3 cleavage of Notch-1. Furthermore, production of A? and its inhibition by STI571 were demonstrated to occur to similar extents in both Abl-/- and WT mouse fibroblasts, indicating that the effect of STI571 on A? production does not involve Abl kinase. The efficacy of STI571 in reducing A? without affecting Notch-1 cleavage may prove useful as a basis for developing novel therapies for Alzheimer's disease. PMID:14523244

  17. N-cadherin prodomain cleavage regulates synapse formation in vivo.

    PubMed

    Latefi, Nazlie S; Pedraza, Liliana; Schohl, Anne; Li, Ziwei; Ruthazer, Edward S

    2009-07-01

    Cadherins are initially synthesized bearing a prodomain that is thought to limit adhesion during early stages of biosynthesis. Functional cadherins lack this prodomain, raising the intriguing possibility that cells may utilize prodomain cleavage as a means to temporally or spatially regulate adhesion after delivery of cadherin to the cell surface. In support of this idea, immunostaining for the prodomain of zebrafish N-cadherin revealed enriched labeling at neuronal surfaces at the soma and along axonal processes. To determine whether post-translational cleavage of the prodomain affects synapse formation, we imaged Rohon-Beard cells in zebrafish embryos expressing GFP-tagged wild-type N-cadherin (NCAD-GFP) or a GFP-tagged N-cadherin mutant expressing an uncleavable prodomain (PRON-GFP) rendering it nonadhesive. NCAD-GFP accumulated at synaptic microdomains in a developmentally regulated manner, and its overexpression transiently accelerated synapse formation. PRON-GFP was much more diffusely distributed along the axon and its overexpression delayed synapse formation. Our results support the notion that N-cadherin serves to stabilize pre- to postsynaptic contacts early in synapse development and suggests that regulated cleavage of the N-cadherin prodomain may be a mechanism by which the kinetics of synaptogenesis are regulated. PMID:19365814

  18. N-CADHERIN PRODOMAIN CLEAVAGE REGULATES SYNAPSE FORMATION IN VIVO

    PubMed Central

    Latefi, Nazlie S.; Pedraza, Liliana; Schohl, Anne; Li, Ziwei; Ruthazer, Edward S.

    2009-01-01

    Cadherins are initially synthesized bearing a prodomain that is thought to limit adhesion during early stages of biosynthesis. Functional cadherins lack this prodomain, raising the intriguing possibility that cells may utilize prodomain cleavage as a means to temporally or spatially regulate adhesion after delivery of cadherin to the cell surface. In support of this idea, immunostaining for the prodomain of zebrafish N-cadherin revealed enriched labeling at neuronal surfaces at the soma and along axonal processes. To determine whether post-translational cleavage of the prodomain affects synapse formation, we imaged Rohon-Beard cells in zebrafish embryos expressing GFP-tagged wild-type N-cadherin (NCAD-GFP) or a GFP-tagged N-cadherin mutant expressing an uncleavable prodomain (PRON-GFP) rendering it non-adhesive. NCAD-GFP accumulated at synaptic microdomains in a developmentally regulated manner, and its overexpression transiently accelerated synapse formation. PRON-GFP was much more diffusely distributed along the axon and its overexpression delayed synapse formation. Our results support the notion that N-cadherin serves to stabilize pre- to postsynaptic contacts early in synapse development and suggests that regulated cleavage of the N-cadherin prodomain may be a mechanism by which the kinetics of synaptogenesis are regulated. PMID:19365814

  19. Carotenoid-cleavage activities of crude enzymes from Pandanous amryllifolius.

    PubMed

    Ningrum, Andriati; Schreiner, Matthias

    2014-11-01

    Carotenoid degradation products, known as norisoprenoids, are aroma-impact compounds in several plants. Pandan wangi is a common name of the shrub Pandanus amaryllifolius. The genus name 'Pandanus' is derived from the Indonesian name of the tree, pandan. In Indonesia, the leaves from the plant are used for several purposes, e.g., as natural colorants and flavor, and as traditional treatments. The aim of this study was to determine the cleavage of ?-carotene and ?-apo-8'-carotenal by carotenoid-cleavage enzymes isolated from pandan leaves, to investigate dependencies of the enzymatic activities on temperature and pH, to determine the enzymatic reaction products by using Headspace Solid Phase Microextraction Gas Chromatography/Mass Spectrophotometry (HS-SPME GC/MS), and to investigate the influence of heat treatment and addition of crude enzyme on formation of norisoprenoids. Crude enzymes from pandan leaves showed higher activity against ?-carotene than ?-apo-8'-carotenal. The optimum temperature of crude enzymes was 70°, while the optimum pH value was 6. We identified ?-ionone as the major volatile reaction product from the incubations of two different carotenoid substrates, ?-carotene and ?-apo-8'-carotenal. Several treatments, e.g., heat treatment and addition of crude enzymes in pandan leaves contributed to the norisoprenoid content. Our findings revealed that the crude enzymes from pandan leaves with carotenoid-cleavage activity might provide a potential application, especially for biocatalysis, in natural-flavor industry. PMID:25408328

  20. Numerical modeling of ductile tearing effects on cleavage fracture toughness

    SciTech Connect

    Dodds, R.H. Jr.; Tang, M. [Univ. of Illinois, Urbana (United States); Anderson, T.L. [Texas A& M Univ., College Station, TX (United States)

    1994-05-01

    Experimental studies demonstrate a significant effect of specimen size, a/W ratio and prior ductile tearing on cleavage fracture toughness values (J{sub c}) measured in the ductile-to-brittle transition region of ferritic materials. In the lower-transition region, cleavage fracture often occurs under conditions of large-scale yielding but without prior ductile crack extension. The increased toughness develops when plastic zones formed at the crack tip interact with nearby specimen surfaces which relaxes crack-tip constraint (stress triaxiality). In the mid-to-upper transition region, small amounts of ductile crack extension (often < 1-2 mm) routinely precede termination of the J-{Delta}a curve by brittle fracture. Large-scale yielding, coupled with small amounts of ductile tearing, magnifies the impact of small variations in microscale material properties on the macroscopic fracture toughness which contributes to the large amount scatter observed in measured J{sub c}-values. Previous work by the authors described a micromechanics fracture model to correct measured J{sub c}-values for the mechanistic effects of large-scale yielding. This new work extends the model to also include the influence of ductile crack extension prior to cleavage. The paper explores development of the new model, provides necessary graphs and procedures for its application and demonstrates the effects of the model on fracture data sets for two pressure vessel steels (A533B and A515).

  1. Time-resolved EPR and laser photolysis investigations of photoinduced ?-bond dissociation in an aromatic carbonyl compound having triplet ?,?* character

    NASA Astrophysics Data System (ADS)

    Yamaji, Minoru; Inomata, Susumu; Nakajima, Satoru; Akiyama, Kimio; Tero-Kubota, Shozo; Tobita, Seiji; Marciniak, Bronislaw

    2006-01-01

    Photochemical properties of photoinduced ?-bond dissociation in p-phenylbenzoylbenzyl phenyl sulfide (PPS) having the lowest triplet state (T 1) of ?,?* character in solution were investigated by time-resolved EPR and laser flash photolysis techniques. PPS was found to undergo photoinduced ?-bond cleavage in the excited lowest singlet state (S 1(n,?*)) with a quantum yield ( ?rad) of 0.15 for the radical formation, which was independent of excitation wavelengths. Based on the facts of the observation of the absorption spectrum of triplet PPS upon triplet sensitization of xanthone, and absence of CIDEP signal, ?-cleavage was shown to be absent in the T 1(?,?*) state of PPS. Considering the electronic character of the excited and dissociative states of PPS, a schematic energy diagram for the ?-bond dissociation of PPS was shown.

  2. Chemical Bonds I

    ERIC Educational Resources Information Center

    Sanderson, R. T.

    1972-01-01

    Chemical bonding is discussed from a bond energy, rather than a wave mechanics, viewpoint. This approach is considered to be more suitable for the average student. (The second part of the article will appear in a later issue of the journal.) (AL)

  3. The Sibling Bond.

    ERIC Educational Resources Information Center

    Bank, Stephen P.; Kahn, Michael D.

    The relationships among brothers and sisters are infinitely varied, but whatever their characteristics, these bonds last throughout life. This book examines the sibling relationship as a distinctive emotional, passionate, painful, and solacing power. Chapter 1, "Unraveling the Sibling Bond," addresses research on siblings and development of the…

  4. Convertible Bonds as \\

    Microsoft Academic Search

    Jeremy C. Stein

    1992-01-01

    This paper argues that corporations may use convertible bonds as an indirect (albeit possibly risky) method for getting equity into their capital structures in situations where adverse selection problems make a conventional stock issue unattractive. Unlike other theories of convertible bond issuance, the model of this paper highlights: 1) the importance of call provisions on convertibles; and 2) the significance

  5. PBGA wire bonding development

    Microsoft Academic Search

    W. K. Shu

    1996-01-01

    In a PBGA package, the existence of a glass transition temperature of 170~215°C for PCB substrate puts an upper ceiling to the usable wire bond temperature. The low thermal conductivity of PCB substrate and the need for a thicker material make fine pad pitch wire bonding even more difficult to do. To compensate for the limitation in thermal energy, high

  6. Ultrasonically bonded value assembly

    NASA Technical Reports Server (NTRS)

    Salvinski, R. J. (inventor)

    1975-01-01

    A valve apparatus capable of maintaining a fluid-tight seal over a relatively long period of time by releasably bonding a valve member to its seat is described. The valve member is bonded or welded to the seat and then released by the application of the same energy to the bond joint. The valve member is held in place during the bonding by a clamping device. An appropriate force device can activate the opening and closing of the valve member. Various combinations of material for the valve member and valve seat can be utilized to provide an adequate sealing bond. Aluminum oxide, stainless steel, inconel, tungsten carbide as hard materials and copper, aluminum, titanium, silver, and gold as soft materials are suggested.

  7. Antimicrobial Activities of Amphiphilic Peptides Covalently Bonded to a Water-Insoluble Resin

    Microsoft Academic Search

    SHARON L. HAYNIE; GRACE A. CRUM; ANDBRUCE A. DOELE

    1995-01-01

    A series of polymer-bound antimicrobial peptides was prepared, and the peptides were tested for their antimicrobial activities. The immobilized peptides were prepared by a strategy that used solid-phase peptide synthesis that linked the carboxy-terminal amino acid with an ethylenediamine-modified polyamide resin (PepsynK). The acid-stable, permanent amide bond between the support and the nascent peptide renders the peptide resistant to cleavage

  8. Cleavage of diblock copolymer brushes in a selective solvent and fusion of vesicles self-assembled by pinned micelles.

    PubMed

    Sun, Lichao; Zhao, Hanying

    2015-02-17

    Lipid membrane fusion is a fundamental process in nature. In the fusion process two distinct bilayers merge the hydrophobic layers, and an interconnected structure is produced. In this research, the fusion of polymer membrane self-assembled by cleaved pinned micelles is investigated. Disulfide-tethered poly(tert-butyl acrylate-block-styrene) diblock copolymer brushes on the surfaces of silica particles were prepared by the "grafting to" or "grafting from" method. In acetone, the diblock copolymer brushes self-assemble into pinned micelles. Upon cleavage from the surfaces of the silica particles with n-tributylphosphine, the pinned micelles self-assemble into vesicles. In the meanwhile, thiol groups at the ends of the block copolymer brushes were produced in the cleavage reaction. Because of the oxidation of the thiol groups and the formation of the disulfide bonds, the vesicle structures are fused into bigger hollow structures and fiber-like structures. The further fusion of the fiber-like structures results in precipitation of the polymer from the solution. PMID:25625528

  9. Application of C/C composites to the combustion chamber of rocket engines. Part 1: Heating tests of C/C composites with high temperature combustion gases

    NASA Astrophysics Data System (ADS)

    Tadano, Makoto; Sato, Masahiro; Kuroda, Yukio; Kusaka, Kazuo; Ueda, Shuichi; Suemitsu, Takeshi; Hasegawa, Satoshi; Kude, Yukinori

    1995-04-01

    Carbon fiber reinforced carbon composite (C/C composite) has various superior properties, such as high specific strength, specific modulus, and fracture strength at high temperatures of more than 1800 K. Therefore, C/C composite is expected to be useful for many structural applications, such as combustion chambers of rocket engines and nose-cones of space-planes, but C/C composite lacks oxidation resistivity in high temperature environments. To meet the lifespan requirement for thermal barrier coatings, a ceramic coating has been employed in the hot-gas side wall. However, the main drawback to the use of C/C composite is the tendency for delamination to occur between the coating layer on the hot-gas side and the base materials on the cooling side during repeated thermal heating loads. To improve the thermal properties of the thermal barrier coating, five different types of 30-mm diameter C/C composite specimens constructed with functionally gradient materials (FGM's) and a modified matrix coating layer were fabricated. In this test, these specimens were exposed to the combustion gases of the rocket engine using nitrogen tetroxide (NTO) / monomethyl hydrazine (MMH) to evaluate the properties of thermal and erosive resistance on the thermal barrier coating after the heating test. It was observed that modified matrix and coating with FGM's are effective in improving the thermal properties of C/C composite.

  10. Structure-Function Analysis of Staphylococcus aureus Amidase Reveals the Determinants of Peptidoglycan Recognition and Cleavage*

    PubMed Central

    Büttner, Felix Michael; Zoll, Sebastian; Nega, Mulugeta; Götz, Friedrich; Stehle, Thilo

    2014-01-01

    The bifunctional major autolysin AtlA of Staphylococcus aureus cleaves the bacterium's peptidoglycan network (PGN) at two distinct sites during cell division. Deletion of the enzyme results in large cell clusters with disordered division patterns, indicating that AtlA could be a promising target for the development of new antibiotics. One of the two functions of AtlA is performed by the N-acetylmuramyl-l-alanine amidase AmiA, which cleaves the bond between the carbohydrate and the peptide moieties of PGN. To establish the structural requirements of PGN recognition and the enzymatic mechanism of cleavage, we solved the crystal structure of the catalytic domain of AmiA (AmiA-cat) in complex with a peptidoglycan-derived ligand at 1.55 ? resolution. The peptide stem is clearly visible in the structure, forming extensive contacts with protein residues by docking into an elongated groove. Less well defined electron density and the analysis of surface features indicate likely positions of the carbohydrate backbone and the pentaglycine bridge. Substrate specificity analysis supports the importance of the pentaglycine bridge for fitting into the binding cleft of AmiA-cat. PGN of S. aureus with l-lysine tethered with d-alanine via a pentaglycine bridge is completely hydrolyzed, whereas PGN of Bacillus subtilis with meso-diaminopimelic acid directly tethered with d-alanine is not hydrolyzed. An active site mutant, H370A, of AmiA-cat was completely inactive, providing further support for the proposed catalytic mechanism of AmiA. The structure reported here is not only the first of any bacterial amidase in which both the PGN component and the water molecule that carries out the nucleophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidoglycan amidase complex structure of an important human pathogen. PMID:24599952

  11. Kissing bonds A kissing bond is adhesively bonded but holds little of the strength usually

    E-print Network

    Sóbester, András

    Kissing bonds · A kissing bond is adhesively bonded but holds little of the strength usually weight saving and excellent stress transfer. · The ability to reliably assess defects in adhesive bonds · To develop a non destructive method to assess the integrity of adhesive bonds using pulsed phase thermography

  12. The Mechanism of E-H (E = N, O) Bond Activation by a Germanium Corrole Complex: A Combined Experimental and Computational Study.

    PubMed

    Fang, Huayi; Jing, Huize; Ge, Haonan; Brothers, Penelope J; Fu, Xuefeng; Ye, Shengfa

    2015-06-10

    (TPFC)Ge(TEMPO) (1, TPFC = tris(pentafluorophenyl)corrole, TEMPO(•) = (2,2,6,6-tetramethylpiperidin-1-yl)oxyl) shows high reactivity toward E-H (E = N, O) bond cleavage in R1R2NH (R1R2 = HH, (n)PrH, (i)Pr2, Et2, PhH) and ROH (R = H, CH3) under visible light irradiation. Electron paramagnetic resonance (EPR) analyses together with the density functional theory (DFT) calculations reveal the E-H bond activation by [(TPFC)Ge](0)(2)/TEMPO(•) radical pair, generated by photocleavage of the labile Ge-O bond in compound 1, involving two sequential steps: (i) coordination of substrates to [(TPFC)Ge](0) and (ii) E-H bond cleavage induced by TEMPO(•) through proton coupled electron transfer (PCET). PMID:25985282

  13. Reversed Electron Apportionment in Mesolytic Cleavage: The Reduction of Benzyl Halides by SmI2.

    PubMed

    Yitzhaki, Offir; Hoz, Shmaryahu

    2015-06-15

    The paradigm that the cleavage of the radical anion of benzyl halides occurs in such a way that the negative charge ends up on the departing halide leaving behind a benzyl radical is well rooted in chemistry. By studying the kinetics of the reaction of substituted benzylbromides and chlorides with SmI2 in THF it was found that substrates para-substituted with electron-withdrawing groups (CN and CO2 Me), which are capable of forming hydrogen bonds with a proton donor and coordinating to samarium cation, react in a reversed electron apportionment mode. Namely, the halide departs as a radical. This conclusion is based on the found convex Hammett plots, element effects, proton donor effects, and the effect of tosylate (OTs) as a leaving group. The latter does not tend to tolerate radical character on the oxygen atom. In the presence of a proton donor, the tolyl derivatives were the sole product, whereas in its absence, the coupling dimer was obtained by a SN 2 reaction of the benzyl anion on the neutral substrate. The data also suggest that for the para-CN and CO2 Me derivatives in the presence of a proton donor, the first electron transfer is coupled with the proton transfer. PMID:25965697

  14. Wafer-Level Thermocompression Bonds

    E-print Network

    Tsau, Christine H.

    Thermocompression bonding of gold is a promising technique for achieving low temperature, wafer-level bonding without the application of an electric field or complicated pre-bond cleaning procedure. The presence of a ductile ...

  15. Theoretical study of the bond dissociation energies of propyne (C3H4)

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

    The C-C and C-H bond dissociation energies (BDEs) of propyne have been computed using the modified coupled-pair functional method. Due to hyperconjugation, the C-C and methyl C-H single bonds are stronger and weaker, respectively than those in ethane. The acetylenic C-H and C triple bond C BDEs are larger and smaller, respectively, than in acetylene, also as a result of the hyperconjugation. Our best estimate of 92.5 +/- 2 kcal/mol for the methyl C-H BDE in propyne is slightly larger than the experimental value. For the acetylenic C-H BDE in propyne we predict 135.9 +/- 2 kcal/mol.

  16. E\\/R Schema for the Datrix C\\/C++\\/Java Exchange Format

    Microsoft Academic Search

    Richard C. Holt; Ahmed E. Hassan; Bruno Laguë; Sébastien Lapierre; Charles Leduc

    2000-01-01

    A SEF (software exchange format), such as GXL (6), TA (4) or RSF (7), is used to exchange data between tools that analyze software. Researchers at Bell Canada have specified the Datrix (3) SEF in TA (and soon to be, GXL) for C, C++ and Java. It is designed so that a parser for the language, C, C++ or Java,

  17. Operadores positivos em dimens\\~ao finita: uma caracteriza\\c{c}\\~ao

    E-print Network

    Fassarella, L

    2011-01-01

    A characterization of positive operators in finite dimensional complex vector spaces based on the Routh-Hurwitz Criterion. ----- Uma caracteriza\\c{c}\\~ao dos operadores positivos em espa\\c{c}os vetoriais complexos de dimens\\~ao finita a partir do Crit\\'erio de Routh-Hurwitz.

  18. Cleavage of dT8 and dT8 phosphorothioyl analogues by Escherichia coli DNA topoisomerase I: product and rate analysis.

    PubMed

    Domanico, P L; Tse-Dinh, Y C

    1988-08-23

    Escherichia coli DNA topoisomerase I catalyzes the cleavage of short, single-stranded oligodeoxynucleotides with dT8 as the shortest cleavable oligo(thymidylic acid). The 5'-32P-labeled products formed from the cleavage of [5'-32P]dT8 are dT5, dT4, and dT3 with over 70% of the substrate cleaved to dT4. Mg(II) ions affect this product distribution by increasing the percentage of dT4 formed. The substitution of a sulfur atom for a nonbridging oxygen atom in a phosphodiester linkage yields oligodeoxynucleotide phosphorothioyl (PS) analogues. The epimers of the analogues were separated, and the position and stereochemistry of the phosphorothiodiester bond were determined. Topoisomerase I is stereospecific in its reactivity toward these analogues. With the oligodeoxynucleotide PS analogue substrates, the rate of cleavage, the stereospecificity, and the product distribution depend upon the position and the stereochemistry of the phosphorothiodiester linkage. PMID:2851323

  19. Gold Thermocompression Wafer Bonding

    E-print Network

    Spearing, S. Mark

    Thermocompression bonding of gold is a promising technique for the fabrication and packaging microelectronic and MEMS devices. The use of a gold interlayer and moderate temperatures and pressures results in a hermetic, ...

  20. Characterization of anodic bonding

    E-print Network

    Tudryn, Carissa Debra, 1978-

    2004-01-01

    Anodic bonding is a common process used in MicroElectroMechanical Systems (MEMS) device fabrication and packaging. Polycrystalline chemical vapor deposited (CVD) silicon carbide (SiC) is emerging as a new MEMS device and ...

  1. Hydrogen bonds animation

    NSDL National Science Digital Library

    Northland Community and Technical College Biology Department

    2007-12-12

    This color animation of water molecules interacting and forming hydrogen bonds is a hybrid between a PowerPoint slide show an an animation. Students can replay portions or click next if they do not need to replay a segment.

  2. Junk-Bond Colleges.

    ERIC Educational Resources Information Center

    Van Der Werf, Martin

    2003-01-01

    Describes how a long-predicted decline in the fortunes of small private colleges is beginning to show up in the bond market, as the number of colleges now rated in the junk category has nearly doubled. (EV)

  3. Bonding aerogels with polyurethanes

    SciTech Connect

    Matthews, F.M.; Hoffman, D.M.

    1989-11-01

    Aerogels, porous silica glasses with ultra-fine cell size (30nm), are made by a solution gelation (sol-gel) process. The resulting gel is critical point dried to densities from 0.15--0.60 g/cc. This material is machinable, homogeneous, transparent, coatable and bondable. To bond aerogel an adhesive should have long cure time, no attack on the aerogel structure, and high strength. Several epoxies and urethanes were examined to determine if they satisfied these conditions. Bond strengths above 13 psi were found with double bubble and DP-110 epoxies and XI-208/ODA-1000 and Castall U-2630 urethanes. Hardman Kalex Tough Stuff'' A-85 hardness urethane gave 18 psi bond strength. Hardman A-85, Tuff-Stuff'' was selected for further evaluation because it produced bond strengths comparable to the adherend cohesive strength. 5 refs., 2 figs.

  4. Roof bolt bond tester

    SciTech Connect

    Not Available

    1982-01-01

    An intrinsically safe, electronic instrument has been developed that determines the holding quality of a fully grouted roof bolt by testing the integrity of the resin bond to both the bolt and to the surrounding rock.

  5. Validation of doubled haploid plants by enzymatic mismatch cleavage

    PubMed Central

    2013-01-01

    Background Doubled haploidy is a fundamental tool in plant breeding as it provides the fastest way to generate populations of meiotic recombinants in a genetically fixed state. A wide range of methods has been developed to produce doubled haploid (DH) plants and recent advances promise efficient DH production in otherwise recalcitrant species. Since the cellular origin of the plants produced is not always certain, rapid screening techniques are needed to validate that the produced individuals are indeed homozygous and genetically distinct from each other. Ideal methods are easily implemented across species and in crops where whole genome sequence and marker resources are limited. Results We have adapted enzymatic mismatch cleavage techniques commonly used for TILLING (Targeting Induced Local Lesions IN Genomes) for the evaluation of heterozygosity in parental, F1 and putative DH plants. We used barley as a model crop and tested 26 amplicons previously developed for TILLING. Experiments were performed using self-extracted single-strand-specific nuclease and standard native agarose gels. Eleven of the twenty-six tested primers allowed unambiguous assignment of heterozygosity in material from F1 crosses and loss of heterozygosity in the DH plants. Through parallel testing of previously developed Simple Sequence Repeat (SSR) markers, we show that 3/32 SSR markers were suitable for screening. This suggests that enzymatic mismatch cleavage approaches can be more efficient than SSR based screening, even in species with well-developed markers. Conclusions Enzymatic mismatch cleavage has been applied for mutation discovery in many plant species, including those with little or no available genomic DNA sequence information. Here, we show that the same methods provide an efficient system to screen for the production of DH material without the need of specialized equipment. This gene target based approach further allows discovery of novel nucleotide polymorphisms in candidate genes in the parental lines. PMID:24220637

  6. Cnidarian microRNAs frequently regulate targets by cleavage

    PubMed Central

    Moran, Yehu; Fredman, David; Praher, Daniela; Li, Xin Z.; Wee, Liang Meng; Rentzsch, Fabian; Zamore, Phillip D.; Technau, Ulrich; Seitz, Hervé

    2014-01-01

    In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA “seed”) to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state. PMID:24642861

  7. All about Chemical Bonding

    NSDL National Science Digital Library

    Lower, Stephen

    Stephen Lower, a retired professor at Simon Fraser University, created this expansive and instructive website as a supplement to formal chemistry education for undergraduate students. Visitors will find in-depth descriptions along with several diagrams dealing with chemical bonding issues including their properties, shared-electron covalent bonds, hybrid orbitals, coordination complexes, and metals and semiconductors. General chemistry students looking for assistance should visit this well-developed educational site.

  8. Features of Controlled Laser Thermal Cleavage of Crystalline Silicon

    SciTech Connect

    Serdyukov, A. N., E-mail: shalupaev@gsu.by; Shalupaev, S. V.; Nikityuk, Yu. V. [Gomel State University (Belarus)

    2010-11-15

    Controlled laser thermal cleavage of crystalline silicon has been numerically simulated. A 3D analysis of the thermoelastic fields formed in a single-crystal silicon wafer as a result of successive laser heating and exposure to a coolant was performed for three different versions of anisotropy. The simulation was performed for laser irradiation with different wavelengths: 1.06 and 0.808 {mu}m. The calculation results have been experimentally verified using a YAG laser. The results can be used in the electronics industry to optimize the precise separation of silicon wafers into crystals.

  9. Cholesterol Side-Chain Cleavage Enzyme (SCC) Deficiency

    PubMed Central

    Katsumata, Noriyuki

    2007-01-01

    Cholesterol side-chain cleavage enzyme (SCC) catalyzes the conversion of cholesterol to pregnenolone, the first step in the biosynthesis of all steroid hormones. It was once postulated that SCC deficiency would be lethal, but recent studies have established that SCC deficiency is an autosomal recessive disorder caused by inactivating mutations in the CYP11A1 gene. Clinical manifestations include adrenal insufficiency and 46,XY sex reversal due to disrupted steroidogenesis, which are similar to StAR deficiency. Further accumulation of patients with SCC deficiency should clarify the similarities and differences between SCC deficiency and StAR deficiency. PMID:24790347

  10. Water's Hydrogen Bond Strength

    E-print Network

    Martin Chaplin

    2007-06-10

    Water is necessary both for the evolution of life and its continuance. It possesses particular properties that cannot be found in other materials and that are required for life-giving processes. These properties are brought about by the hydrogen bonded environment particularly evident in liquid water. Each liquid water molecule is involved in about four hydrogen bonds with strengths considerably less than covalent bonds but considerably greater than the natural thermal energy. These hydrogen bonds are roughly tetrahedrally arranged such that when strongly formed the local clustering expands, decreasing the density. Such low density structuring naturally occurs at low and supercooled temperatures and gives rise to many physical and chemical properties that evidence the particular uniqueness of liquid water. If aqueous hydrogen bonds were actually somewhat stronger then water would behave similar to a glass, whereas if they were weaker then water would be a gas and only exist as a liquid at sub-zero temperatures. The overall conclusion of this investigation is that water's hydrogen bond strength is poised centrally within a narrow window of its suitability for life.

  11. Active Metal Brazing and Characterization of Brazed Joints in C-C and C-SiC Composites to Copper-Clad-Molybdenum System

    NASA Technical Reports Server (NTRS)

    Singh, M.; Asthana, R.

    2008-01-01

    Carbon/carbon composites with CVI and resin-derived matrices, and C/SiC composites reinforced with T-300 carbon fibers in a CVI SiC matrix were joined to Cu-clad Mo using two Ag-Cu braze alloys, Cusil-ABA (1.75% Ti) and Ticusil (4.5% Ti). The brazed joints revealed good interfacial bonding, preferential precipitation of Ti at the composite/braze interface, and a tendency toward delamination in resin-derived C/C composite. Extensive braze penetration of the inter-fiber channels in the CVI C/C composites was observed. The Knoop microhardness (HK) distribution across the C/C joints indicated sharp gradients at the interface, and a higher hardness in Ticusil than in Cusil-ABA. For the C/SiC composite to Cu-clad-Mo joints, the effect of composite surface preparation revealed that ground samples did not crack whereas unground samples cracked. Calculated strain energy in brazed joints in both systems is comparable to the strain energy in a number of other ceramic/metal systems. Theoretical predictions of the effective thermal resistance suggest that such joined systems may be promising for thermal management applications.

  12. 30 CFR 581.33 - Bonds and bonding requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...Resources 2 2013-07-01 2013-07-01 false Bonds and bonding requirements. 581.33 Section 581.33 Mineral Resources...CONTINENTAL SHELF Financial Considerations § 581.33 Bonds and bonding requirements. (a) When the leasing notice...

  13. Fair Scheduling on Parallel Bonded Channels with Intersecting Bonding Groups

    E-print Network

    Martin, Jim

    Fair Scheduling on Parallel Bonded Channels with Intersecting Bonding Groups Gongbing Hong, James for providing weighted sharing of aggregate capacity in networks having parallel bonded channels in which a single channel may simultaneously be a member of multiple bonding groups. Our work is motivated

  14. 30 CFR 281.33 - Bonds and bonding requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...Resources 2 2011-07-01 2011-07-01 false Bonds and bonding requirements. 281.33 Section 281.33 Mineral Resources...CONTINENTAL SHELF Financial Considerations § 281.33 Bonds and bonding requirements. (a) When the leasing notice...

  15. 30 CFR 581.33 - Bonds and bonding requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...Resources 2 2014-07-01 2014-07-01 false Bonds and bonding requirements. 581.33 Section 581.33 Mineral Resources...CONTINENTAL SHELF Financial Considerations § 581.33 Bonds and bonding requirements. (a) When the leasing notice...

  16. 30 CFR 581.33 - Bonds and bonding requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...Resources 2 2012-07-01 2012-07-01 false Bonds and bonding requirements. 581.33 Section 581.33 Mineral Resources...CONTINENTAL SHELF Financial Considerations § 581.33 Bonds and bonding requirements. (a) When the leasing notice...

  17. Infrared spectroscopic investigation of photoionization-induced acidic C-h bonds in cyclic ethers.

    PubMed

    Xie, Min; Matsuda, Yoshiyuki; Fujii, Asuka

    2015-06-01

    Infrared (IR) predissociation spectroscopy based on vacuum-ultraviolet photoionization detection is performed for the neutral and cationic tetrahydrofuran (THF) and tetrahydropyran (THP). The CH bonds in neutral THF and THP are regarded as aprotic, even though the CH bonds are weakened by the negative hyperconjugation. After 118 nm photoionization, however, the negative hyperconjugation changes to the positive hyperconjugation and their CH bond acidities remarkably increase. In the IR spectrum of the THF cation, an intense band is observed at ca. 2700 cm(-1). This band is assigned to the antisymmetric stretch vibration of the two C?H bonds next to the oxygen atom. The high intensity and low frequency of this band are due to the delocalization of the ? electrons of the two C?H bonds to the singly occupied molecular orbital (SOMO) through the hyperconjugation. In the IR spectrum of the THP cation, on the other hand, the stretch bands of the C?H bonds do not show obvious low-frequency shift and intensity enhancement, while the stretch band of the equatorial C?H bond, at the para-position to the oxygen atom, appears at 2855 cm(-1) with high intensity. This acidity enhancement of the equatorial C?H bond is attributed to the mutiple hyperconjugation among the C?H bond, two C?C? bonds, and SOMO of the oxygen atom. These results suggest that the difference of the hyperconjugation mechanism between the THF and THP cations arises from their preferable conformations. PMID:25978525

  18. Impaired Autoproteolytic Cleavage of mCLCA6, a Murine Integral Membrane Protein Expressed in Enterocytes, Leads to Cleavage at the Plasma Membrane Instead of the Endoplasmic Reticulum

    PubMed Central

    Bothe, Melanie K.; Mundhenk, Lars; Beck, Carol L.; Kaup, Matthias; Gruber, Achim D.

    2012-01-01

    CLCA proteins (calcium-activated chloride channel regulators) have been linked to diseases involving secretory disorders, including cystic fibrosis (CF) and asthma. They have been shown to modulate endogenous chloride conductance, possibly by acting as metalloproteases. Based on the differential processing of the subunits after post-translational cleavage, two subgroups of CLCA proteins can be distinguished. In one subgroup, both subunits are secreted, in the other group, the carboxy-terminal subunit possesses a transmembrane segment, resulting in shedding of only the amino-terminal subunit. Recent data on the post-translational cleavage and proteolytic activity of CLCA are limited to secreted CLCA. In this study, we characterized the cleavage of mCLCA6, a murine CLCA possessing a transmembrane segment. As for secreted CLCA, the cleavage in the endoplasmic reticulum was not observed for a protein with the E157Q mutation in the HEXXH motif of mCLCA6, suggesting that this mutant protein and secreted CLCA family members share a similar autoproteolytic cleavage mechanism. In contrast to secreted CLCA proteins with the E157Q mutation, the uncleaved precursor of the mCLCA6E157Q mutant reached the plasma membrane, where it was cleaved and the amino-terminal subunit was shed into the supernatant. Using crude membrane fractions, we showed that cleavage of the mCLCA6E157Q protein is zinc-dependent and sensitive to metalloprotease inhibitors, suggesting secondary cleavage by a metalloprotease. Interestingly, anchorage of mCLCA6E157Q to the plasma membrane is not essential for its secondary cleavage, because the mCLCA6?™E157Q mutant still underwent cleavage. Our data suggest that the processing of CLCA proteins is more complex than previously recognized. PMID:22350745

  19. Effects of neighboring sequence environment in predicting cleavage sites of signal peptides.

    PubMed

    Li, Yizhou; Wen, Zhining; Zhou, Cuisong; Tan, Fuyuan; Li, Menglong

    2008-09-01

    Signal peptide has a pivotal role in the translocation of secretory protein. Some models have been designed to predict its cleavage site. It is reported that the cleavage site has relationship with the neighboring sequence environment, i.e., hydrophobic core h-region, and the specific patterns in c-region. In some studies, this finding does facilitate the prediction of cleavage site. However, in these models, sequence environment information is merely taken account of as model inputs and no detailed investigation into its effect on the prediction of cleavage site has been made. In this work, we analyze the constraint on cleave site placed by the hydrophobic core of signal peptide and then use it to improve the performance of the signal peptide cleavage site prediction. Our model is designed as follows: firstly, a sliding window is used to scan sample and artificial neural network (ANN) is employed to give cleavage site/non-cleavage site scores. Then, based on an estimated hydrophobic h-region a correcting function is proposed to improve the prediction result, in which the sequence environment is taken into account. A trend of cleavage site is indicated by our analysis for each position, which is consistent with experimental findings. Through this correcting step, the improvement of prediction accuracy is over 7%. It therefore demonstrates the neighboring sequence environment is helpful for determination of cleavage site. Program written in Matlab can be downloaded from http://www.scucic.cn/combined model/source code.html. PMID:18635288

  20. Silicon Wafer Bonding by Modified Surface Activated Bonding Methods

    Microsoft Academic Search

    Chenxi Wang; E. Higurashi; T. Suga

    2007-01-01

    8-inch Si-Si wafer bonding at room temperature is performed by means of two modified surface activated bonding (SAB) methods respectively, namely the SAB with nano-adhesion layer and sequential plasma activated bonding (SPAB). And post-annealing processes in atmospheric air utilized do not aim to improve the bonding strength, but to investigate void formation if the bonded wafers heated in subsequent heated

  1. Quantitative analysis of PMLA nanoconjugate components after backbone cleavage.

    PubMed

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L; Ljubimova, Julia Y; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

  2. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis.

    PubMed

    Goh, Wee Siong Sho; Falciatori, Ilaria; Tam, Oliver H; Burgess, Ralph; Meikar, Oliver; Kotaja, Noora; Hammell, Molly; Hannon, Gregory J

    2015-05-15

    MIWI catalytic activity is required for spermatogenesis, indicating that piRNA-guided cleavage is critical for germ cell development. To identify meiotic piRNA targets, we augmented the mouse piRNA repertoire by introducing a human meiotic piRNA cluster. This triggered a spermatogenesis defect by inappropriately targeting the piRNA machinery to mouse mRNAs essential for germ cell development. Analysis of such de novo targets revealed a signature for pachytene piRNA target recognition. This enabled identification of both transposable elements and meiotically expressed protein-coding genes as targets of native piRNAs. Cleavage of genic targets began at the pachytene stage and resulted in progressive repression through meiosis, driven at least in part via the ping-pong cycle. Our data support the idea that meiotic piRNA populations must be strongly selected to enable successful spermatogenesis, both driving the response away from essential genes and directing the pathway toward mRNA targets that are regulated by small RNAs in meiotic cells. PMID:25995188

  3. Stress-induced cleavage of Myc promotes cancer cell survival

    PubMed Central

    Conacci-Sorrell, Maralice; Ngouenet, Celine; Anderson, Sarah; Brabletz, Thomas; Eisenman, Robert N.

    2014-01-01

    Evasion of apoptosis is critical in Myc-induced tumor progression. Here we report that cancer cells evade death under stress by activating calpain-mediated proteolysis of Myc. This generates Myc-nick, a cytoplasmic, transcriptionally inactive cleavage product of Myc. We found conversion of Myc into Myc-nick in cell lines and tissues derived from multiple cancers. In colon cancer, the production of Myc-nick is enhanced under stress conditions such as hypoxia and nutrient deprivation. Under these conditions, ectopic expression of Myc-nick promotes anchorage-independent growth and cell survival at least in part by promoting autophagy. Myc-nick also delays colon cancer cell death after treatment with chemotherapeutic drugs such as etoposide, cisplatin, and imatinib. Furthermore, colon cancer cells expressing a cleavage-resistant form of Myc undergo extensive apoptosis but are rescued by overexpression of Myc-nick. We also found that ectopic expression of Myc-nick results in the induction of the actin-bundling protein fascin, formation of filopodia, and increased cell motility—all mediators of tumor metastasis. Myc-nick-induced survival, autophagy, and motility require Myc box II (MBII), a region of Myc-nick that recruits acetyltransferases that in turn modify cytoplasmic proteins, including ?-tubulin and ATG3. Our results suggest that Myc-nick-induced survival and motility contribute to colon cancer progression and metastasis. PMID:24696454

  4. Quantitative Analysis of PMLA Nanoconjugate Components after Backbone Cleavage

    PubMed Central

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L.; Ljubimova, Julia Y.; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

  5. Surveillance and Cleavage of Eukaryotic tRNAs

    PubMed Central

    Megel, Cyrille; Morelle, Geoffrey; Lalande, Stéphanie; Duchêne, Anne-Marie; Small, Ian; Maréchal-Drouard, Laurence

    2015-01-01

    Beyond their central role in protein synthesis, transfer RNAs (tRNAs) have many other crucial functions. This includes various roles in the regulation of gene expression, stress responses, metabolic processes and priming reverse transcription. In the RNA world, tRNAs are, with ribosomal RNAs, among the most stable molecules. Nevertheless, they are not eternal. As key elements of cell function, tRNAs need to be continuously quality-controlled. Two tRNA surveillance pathways have been identified. They act on hypo-modified or mis-processed pre-tRNAs and on mature tRNAs lacking modifications. A short overview of these two pathways will be presented here. Furthermore, while the exoribonucleases acting in these pathways ultimately lead to complete tRNA degradation, numerous tRNA-derived fragments (tRFs) are present within a cell. These cleavage products of tRNAs now potentially emerge as a new class of small non-coding RNAs (sncRNAs) and are suspected to have important regulatory functions. The tRFs are evolutionarily widespread and created by cleavage at different positions by various endonucleases. Here, we review our present knowledge on the biogenesis and function of tRFs in various organisms. PMID:25599528

  6. RNA recognition and cleavage by the SARS coronavirus endoribonuclease.

    PubMed

    Bhardwaj, Kanchan; Sun, Jingchuan; Holzenburg, Andreas; Guarino, Linda A; Kao, C Cheng

    2006-08-11

    The emerging disease SARS is caused by a novel coronavirus that encodes several unusual RNA-processing enzymes, including non-structural protein 15 (Nsp15), a hexameric endoribonuclease that preferentially cleaves at uridine residues. How Nsp15 recognizes and cleaves RNA is not well understood and is the subject of this study. Based on the analysis of RNA products separated by denaturing gel electrophoresis, Nsp15 has been reported to cleave both 5' and 3' of the uridine. We used several RNAs, including some with nucleotide analogs, and mass spectrometry to determine that Nsp15 cleaves only 3' of the recognition uridylate, with some cleavage 3' of cytidylate. A highly conserved RNA structure in the 3' non-translated region of the SARS virus was cleaved preferentially at one of the unpaired uridylate bases, demonstrating that both RNA structure and base-pairing can affect cleavage by Nsp15. Several modified RNAs that are not cleaved by Nsp15 can bind Nsp15 as competitive inhibitors. The RNA binding affinity of Nsp15 increased with the content of uridylate in substrate RNA and the co-factor Mn(2+). The hexameric form of Nsp15 was found to bind RNA in solution. A two-dimensional crystal of Nsp15 in complex with RNA showed that at least two RNA molecules could be bound per hexamer. Furthermore, an 8.3 A structure of Nsp15 was developed using cyroelectron microscopy, allowing us to generate a model of the Nsp15-RNA complex. PMID:16828802

  7. Advanced copper wire bonding technology

    Microsoft Academic Search

    Hong Meng Ho

    2010-01-01

    Wire bonding is the most dominant form of first-level chip interconnects in microelectronics with gold wire bonding taking the lead for the past few decades. Today, it is evident that the shift from gold to copper wire bonding is genuinely picking up, due to both a surge in gold prices and recent developments in copper wire bonding technology. The course

  8. Wire bonds over active circuits

    Microsoft Academic Search

    Gail Heinen; Roger J. Stierman; Darvin Edwards; L. Nye

    1994-01-01

    A reliable process-for wire bonding over active integrated circuits, which are subsequently assembled in plastic packages, has been developed. This technology accommodates reducing the silicon die area required for bond pads and for on-chip bussing. Further, it supports area array wire bonding by allowing larger bond pads with relaxed pitch without sacrificing silicon area. This is accomplished by processing an

  9. Merging allylic carbon-hydrogen and selective carbon-carbon bond activation

    NASA Astrophysics Data System (ADS)

    Masarwa, Ahmad; Didier, Dorian; Zabrodski, Tamar; Schinkel, Marvin; Ackermann, Lutz; Marek, Ilan

    2014-01-01

    Since the nineteenth century, many synthetic organic chemists have focused on developing new strategies to regio-, diastereo- and enantioselectively build carbon-carbon and carbon-heteroatom bonds in a predictable and efficient manner. Ideal syntheses should use the least number of synthetic steps, with few or no functional group transformations and by-products, and maximum atom efficiency. One potentially attractive method for the synthesis of molecular skeletons that are difficult to prepare would be through the selective activation of C-H and C-C bonds, instead of the conventional construction of new C-C bonds. Here we present an approach that exploits the multifold reactivity of easily accessible substrates with a single organometallic species to furnish complex molecular scaffolds through the merging of otherwise difficult transformations: allylic C-H and selective C-C bond activations. The resulting bifunctional nucleophilic species, all of which have an all-carbon quaternary stereogenic centre, can then be selectively derivatized by the addition of two different electrophiles to obtain more complex molecular architecture from these easily available starting materials.

  10. Insulation bonding test system

    NASA Technical Reports Server (NTRS)

    Beggs, J. M.; Johnston, G. D.; Coleman, A. D.; Portwood, J. N.; Saunders, J. M.; Redmon, J. W.; Porter, A. C. (inventors)

    1984-01-01

    A method and a system for testing the bonding of foam insulation attached to metal is described. The system involves the use of an impacter which has a calibrated load cell mounted on a plunger and a hammer head mounted on the end of the plunger. When the impacter strikes the insulation at a point to be tested, the load cell measures the force of the impact and the precise time interval during which the hammer head is in contact with the insulation. This information is transmitted as an electrical signal to a load cell amplifier where the signal is conditioned and then transmitted to a fast Fourier transform (FFT) analyzer. The FFT analyzer produces energy spectral density curves which are displayed on a video screen. The termination frequency of the energy spectral density curve may be compared with a predetermined empirical scale to determine whether a igh quality bond, good bond, or debond is present at the point of impact.

  11. Adhesive bond degradation sensor

    NASA Astrophysics Data System (ADS)

    Wilson, Alan R.; Olsson-Jacques, Christina; Muscat, Richard F.

    2002-11-01

    Early detection of adhesive bond degradation using sensing elements embedded within the 100um bond-line of aluminium epoxy adhesive joints has been demonstrated. Sensing elements of varying heights were fabricated at the ends of narrow conductors on a flexi-circuit carrier. This construction simulates the active sensing region on a patented silicon adhesive bond degradation sensor and has been used to characterize the sensing elements without the expense and time associated with fabricating the complete integrated silicon sensor. The highest elements on the flexi-circuit serve both as electrical pickup studs, providing a circuit from the flexi-circuit to the top aluminium plate, and as spacers to ensure that the shorter sensing elements do not contact the aluminium plate. The non-contacting sensing elements are thus arranged to be close to the metal/adhesive interface and are sensitive to any change in conductivity in this region due to release of ions as the interface is degraded by the environment. Accelerated aging tests were performed on flexi-circuit sensors embedded in the bond-line of double cantilever beam specimens. The specimens were immersed in 50° C water and pre-loaded to just initiate a crack. Load on the specimen was then maintained by applying a constant load point displacement with a very low velocity to ensure that the environment would degrade the bond-line in advance of the crack front. The change of load and the conductivity measured by the sensing elements were then logged with time. The onset of bond degradation was detected approximately 10-20 mm ahead of the crack tip.

  12. Analysis of CO hydrogenation pathways using the bond-order-conservation method

    SciTech Connect

    Shustorovich, E. (Eastman Kodak Co., Rochester, NY (USA)); Bell, A.T. (Univ. of California, Berkeley (USA))

    1988-10-01

    The bond-order-conservation (BOC) method has been used to identify the energetics associated with the hydrogenation of CO over (111) surfaces of Ni, Pd, and Pt. In the formation of CH{sub 4}, the C-O bond of CO is cleaved. BOC calculations for Ni indicate that cleavage of the C-O bond occurs primarily by direct dissociation of molecularly adsorbed CO. The activation energy for direct dissociation of CO on Pd and Pt is significantly greater than that for hydrogen assisted dissociation, and hence the latter process is more significant. The BOC calculations indicate that for these metals the species from which C-O bond cleavage occurs is CH{sub 3}O{sub 5}. Because the activation barriers for CH{sub 3}O{sub 5} dissociation and hydrogenation to form CH{sub 3}OH are close for Pd and Pt, these metals are effective catalysts for both CH{sub 4} and CH{sub 3}OH synthesis. By contrast, the BOC method predicts that CH{sub 4} should be the principal product formed over Ni. 36 refs.

  13. General Education Coursework: Credits General Education Coursework: Credits ENGL 110C (C or better) 3 ENGL 211C, 221C or 231C ( C or better) 3

    E-print Network

    General Education Coursework: Credits General Education Coursework: Credits ENGL 110C (C or better: Credits General Education Coursework: Credits Information Literacy and Research 3 Human Creativity 3 BIOL SEMESTER (17 credits) SPRING SEMESTER (18 Major Coursework: Major Coursework: Major Coursework: Credits

  14. REVIEW OF THE ELECTRONIC SPECIFIC HEAT OF B. C. C. AND F. C. C. SOLID SOLUTIONS OF FIRST LONG PERIOD TRANSITION ELEMENTS

    E-print Network

    Boyer, Edmond

    with f. c. c. solid solutions in the Mn-Fe, Mn-Ni, Fe-Ni, V-Ni systems gave coefficients for the specific coefficient V independent of composition. It was found that the CsCl-type ordered alloys in the ternary Ti Fe

  15. Comparative and phylogenetic perspectives of the cleavage process in tailed amphibians.

    PubMed

    Desnitskiy, Alexey G; Litvinchuk, Spartak N

    2014-09-01

    Summary The order Caudata includes about 660 species and displays a variety of important developmental traits such as cleavage pattern and egg size. However, the cleavage process of tailed amphibians has never been analyzed within a phylogenetic framework. We use published data on the embryos of 36 species concerning the character of the third cleavage furrow (latitudinal, longitudinal or variable) and the magnitude of synchronous cleavage period (up to 3-4 synchronous cell divisions in the animal hemisphere or a considerably longer series of synchronous divisions followed by midblastula transition). Several species from basal caudate families Cryptobranchidae (Andrias davidianus and Cryptobranchus alleganiensis) and Hynobiidae (Onychodactylus japonicus) as well as several representatives from derived families Plethodontidae (Desmognathus fuscus and Ensatina eschscholtzii) and Proteidae (Necturus maculosus) are characterized by longitudinal furrows of the third cleavage and the loss of synchrony as early as the 8-cell stage. By contrast, many representatives of derived families Ambystomatidae and Salamandridae have latitudinal furrows of the third cleavage and extensive period of synchronous divisions. Our analysis of these ontogenetic characters mapped onto a phylogenetic tree shows that the cleavage pattern of large, yolky eggs with short series of synchronous divisions is an ancestral trait for the tailed amphibians, while the data on the orientation of third cleavage furrows seem to be ambiguous with respect to phylogeny. Nevertheless, the midblastula transition, which is characteristic of the model species Ambystoma mexicanum (Caudata) and Xenopus laevis (Anura), might have evolved convergently in these two amphibian orders. PMID:25180466

  16. Cleavage and gastrulation of the dendrobranchiate shrimp Penaeus monodon (Crustacea, Malacostraca, Decapoda)

    E-print Network

    Alwes, Frederike

    Cleavage and gastrulation of the dendrobranchiate shrimp Penaeus monodon (Crustacea, Malacostraca of the black tiger shrimp Penaeus monodon was analyzed from the first division until gastrulation. Observations for stereotypic develop- ment is the cleavage pattern in dendrobranchiate shrimps among the Decapoda. Starting

  17. Cleavage and gastrulation in the shrimp Penaeus (Litopenaeus) vannamei (Malacostraca, Decapoda, Dendrobranchiata)

    E-print Network

    Hertzler, Philip L.

    Cleavage and gastrulation in the shrimp Penaeus (Litopenaeus) vannamei (Malacostraca, Decapoda, and Dendrobranchiata (Decapoda) cleavage is complete. Euphausiaceans and dendrobranchiate shrimp share a similar early in the Dendrobranchiata, embryos of the Pacific white shrimp Penaeus (Litopenaeus) vannamei were stained with Sytox Green

  18. Cohesin Cleavage by Separase Required for Anaphase and Cytokinesis in Human Cells

    Microsoft Academic Search

    Silke Hauf; Irene C. Waizenegger; Jan-Michael Peters

    2001-01-01

    Cell division depends on the separation of sister chromatids in anaphase. In yeast, sister separation is initiated by cleavage of cohesin by the protease separase. In vertebrates, most cohesin is removed from chromosome arms by a cleavage-independent mechanism. Only residual amounts of cohesin are cleaved at the onset of anaphase, coinciding with its disappearance from centromeres. We have identified two

  19. Evolutionary dissociation between cleavage, cell lineage and embryonic axes in sea urchin embryos.

    PubMed

    Henry, J J; Klueg, K M; Raff, R A

    1992-04-01

    Using vital dye staining and the microinjection of fluorescent cell lineage-autonomous tracers, the relationship between the first cleavage plane and the prospective larval dorsoventral axis was examined in several sea urchin species, including: Strongylocentrotus purpuratus, S. droebachiensis, Lytechinus pictus, Clypeaster rosaceus, Heliocidaris tuberculata and H. erythrogramma. The results indicate that there is no single relationship between the early cleavage pattern and the dorsoventral axis for all sea urchins; however, specific relationships exist for individual species. In S. purpuratus the first cleavage plane occurs at an angle 45 degrees clockwise with respect to the prospective dorsoventral axis in most cases, as viewed from the animal pole. On the other hand, in S. droebachiensis, L. pictus and H. tuberculata, the first cleavage plane generally corresponds with the plane of bilateral symmetry. There does not appear to be a predominant relationship between the first cleavage plane and the dorsoventral axis in C. rosaceus. In the direct-developing sea urchin H. erythrogramma the first cleavage plane bisects the dorsoventral axis through the frontal plane. Clearly, evolutionary differences have arisen in the relationship between cleavage pattern and developmental axes. Therefore, the mechanism of cell determination is not necessarily tied to any particular pattern of cell cleavage, but to an underlying framework of axial systems resident within sea urchin eggs and embryos. PMID:1618154

  20. Lysineenediyne conjugates as photochemically triggered DNA double-strand cleavage agents{

    E-print Network

    Alabugin, Igor

    reported in the literature shows ds DNA cleavage at mM concentrations (1026 ­1025 M)2a and it still remains of the ability of positively charged amino acids to bind to DNA,5 we designed hybrid molecular systems 1, 3Lysine­enediyne conjugates as photochemically triggered DNA double- strand cleavage agents{ Serguei