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Sample records for c-s bond formation

  1. Sulfide synthesis through copper-catalyzed C-S bond formation under biomolecule-compatible conditions.

    PubMed

    Zhang, Yonghong; Li, Yiming; Zhang, Xiaomei; Jiang, Xuefeng

    2015-01-18

    We report here an efficient and mild method for constructing C-S bonds. The reactions were carried out with Na2S2O3 as a sulfurating reagent, CuSO4 as a catalyst, and water as solvent without any surfactant. The products were achieved in moderate to excellent yields at room temperature under air. Notably, this reaction is compatible with various biomolecules including amino acids, oligosaccharides, nucleosides, proteins, and cell lysates.

  2. Regioselectivity of the oxidative C-S bond formation in ergothioneine and ovothiol biosyntheses.

    PubMed

    Song, Heng; Leninger, Maureen; Lee, Norman; Liu, Pinghua

    2013-09-20

    Ergothioneine (5) and ovothiol (8) are two novel thiol-containing natural products. Their C-S bonds are formed by oxidative coupling reactions catalyzed by EgtB and OvoA enzymes, respectively. In this work, it was discovered that in addition to catalyzing the oxidative coupling between histidine and cysteine (1 → 6 conversion), OvoA can also catalyze a direct oxidative coupling between hercynine (2) and cysteine (2 → 4 conversion), which can shorten the ergothioneine biosynthetic pathway by two steps.

  3. Regio-selectivity of the Oxidative C-S Bond Formation in Ergothioneine and Ovothiol Biosyntheses

    PubMed Central

    Song, Heng; Leninger, Maureen; Lee, Norman

    2014-01-01

    Ergothioneine (5) and ovothiol (8) are two novel thiol-containing natural products. Their C-S bonds are formed by oxidative coupling reactions catalyzed by EgtB and OvoA enzymes, respectively. In this work, it was discovered that besides catalyzing the oxidative coupling between histidine and cysteine (1 → 6 conversion), OvoA can also catalyze a direct oxidative coupling between hercynine (2) and cysteine (2 → 4 conversion), which can shorten the ergothioneine biosynthetic pathway by two steps. PMID:24016264

  4. Deep Eutectic Solvents as Reaction Media for the Palladium-Catalysed C-S Bond Formation: Scope and Mechanistic Studies.

    PubMed

    Marset, Xavier; Guillena, Gabriela; Ramón, Diego J

    2017-08-04

    A unique jigsaw catalytic system based on deep eutectic solvents and palladium nanoparticles where C-S bonds are formed from aryl boronic acids and sodium metabisulfite, is introduced. The functionalization step is compatible with a broad spectrum of reagents such as nucleophiles, electrophiles or radical scavengers. This versatile approach allows the formation of different types of products in an environmentally friendly medium by selecting the components of the reaction, which engage one with another as pieces in a jigsaw. This simple procedure avoids the use of toxic volatile organic solvents allowing the formation of complex molecules in a one-pot reaction under mild conditions. Despite the fact that only 1 mol % of metal loading is used, the recyclability of the catalytic system is possible. Kinetic experiments were performed and the reaction order for all reagents, catalyst and ligand was determined. The obtained results were compared to palladium nanocrystals of different known shapes in order to shed some light on the properties of the catalyst. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Copper-catalyzed double C-S bonds formation via different paths: synthesis of benzothiazoles from N-benzyl-2-iodoaniline and potassium sulfide.

    PubMed

    Zhang, Xiaoyun; Zeng, Weilan; Yang, Yuan; Huang, Hui; Liang, Yun

    2014-02-07

    A new, highly efficient procedure for the synthesis of benzothiazoles from easily available N-benzyl-2-iodoaniline and potassium sulfide has been developed. The results show copper-catalyzed double C-S bond formation via a traditional cross-coupling reaction and an oxidative cross-coupling reaction.

  6. Synthesis of 1,2,4-Triazoles via Oxidative Heterocyclization: Selective C-N Bond Over C-S Bond Formation.

    PubMed

    Gogoi, Anupal; Guin, Srimanta; Rajamanickam, Suresh; Rout, Saroj Kumar; Patel, Bhisma K

    2015-09-18

    The higher propensity of C-N over C-S bond forming ability was demonstrated, through formal C-H functionalization during the construction of 4,5-disubstituted 1,2,4-triazole-3-thiones from arylidenearylthiosemicarbazides catalyzed by Cu(II). However, steric factors imparted by the o-disubstituted substrates tend to change the reaction path giving thiodiazole as the major or an exclusive product. Upon prolonging the reaction time, the in situ generated thiones are transformed to 4,5-disubstituted 1,2,4-triazoles via a desulfurization process. Two classes of heterocycles viz. 4,5-disubstituted 1,2,4-triazole-3-thiones and 4,5-disubstituted 1,2,4-triazoles can be synthesized from arylidenearylthiosemicarbazides by simply adjusting the reaction time. Desulfurization of 1,2,4-triazole-3-thiones is assisted by thiophilic Cu to provide 1,2,4-triazoles with concomitant formation of CuS and polynuclear sulfur anions as confirmed from scanning electron microscope and energy dispersive X-ray spectroscopy measurements. A one-pot synthesis of an antimicrobial compound has been successfully achieved following this strategy.

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

    PubMed

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

    2012-08-04

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

  8. Aqueous Reaction of Alcohols, Organohalides, and Odorless Sodium Thiosulfate under Transition-Metal-Free Conditions: Synthesis of Unsymmetrical Aryl Sulfides via Dual C-S Bond Formation.

    PubMed

    Liu, Bei-Bei; Chu, Xue-Qiang; Liu, Huan; Yin, Ling; Wang, Shun-Yi; Ji, Shun-Jun

    2017-10-06

    A transition-metal-free process for the synthesis of unsymmetrical aryl sulfides via dual C-S bond formation by a one-pot three-component reaction of alcohols, organohalides, and odorless sodium thiosulfate in water has been developed. In addition, the aryl sulfides could also be prepared by the reaction of the corresponding alcohols and Bunte salts under the identical conditions. This protocol provides a green and efficient manner for the construction of various unsymmetrical aryl sulfides.

  9. 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.

  10. Microbial cleavage of organic C-S bonds

    DOEpatents

    Kilbane, II, John J.

    1994-01-01

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

  11. Kinetic and DFT studies on the mechanism of C-S bond formation by alkyne addition to the [Mo3S4(H2O)9]4+ cluster.

    PubMed

    Pino-Chamorro, Jose Ángel; Algarra, Andrés G; Fernández-Trujillo, M Jesús; Hernández-Molina, Rita; Basallote, Manuel G

    2013-12-16

    Reaction of [Mo3(μ3-S)(μ-S)3] clusters with alkynes usually leads to formation of two C-S bonds between the alkyne and two of the bridging sulfides. The resulting compounds contain a bridging alkenedithiolate ligand, and the metal centers appear to play a passive role despite reactions at those sites being well illustrated for this kind of cluster. A detailed study including kinetic measurements and DFT calculations has been carried out to understand the mechanism of reaction of the [Mo3(μ3-S)(μ-S)3(H2O)9](4+) (1) cluster with two different alkynes, 2-butyne-1,4-diol and acetylenedicarboxylic acid. Stopped-flow experiments indicate that the reaction involves the appearance in a single kinetic step of a band at 855 or 875 nm, depending on the alkyne used, a position typical of clusters with two C-S bonds. The effects of the concentrations of the reagents, the acidity, and the reaction medium on the rate of reaction have been analyzed. DFT and TD-DFT calculations provide information on the nature of the product formed, its electronic spectrum and the energy profile for the reaction. The structure of the transition state indicates that the alkyne approaches the cluster in a lateral way and both C-S bonds are formed simultaneously.

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

    PubMed Central

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

    2015-01-01

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

  13. Thiourea in the Construction of C-S Bonds as Part of an Undergraduate Organic Chemistry Laboratory Course

    ERIC Educational Resources Information Center

    Lu, Guo-ping; Chen, Fei; Cai, Chun

    2017-01-01

    The nucleophilic aromatic substitution reaction and thia-Michael addition using thiourea as an odorless, cheap, and easy-to-handle sulfur source in water are described, which can be used to teach upper-division undergraduates the role of thiourea in the formation of C-S bonds and the principles of green chemistry. The use of a cheap, nontoxic…

  14. Engineering the bonding scheme in C-S-H: The iono-covalent framework

    SciTech Connect

    Pellenq, R.J.-M.; Lequeux, N.; Damme, H. van

    2008-02-15

    On the basis of recent molecular simulation and experimental studies, we discuss two possible strategies for tuning the mechanical properties of cementitious materials by modifying the bonding scheme in the hydrates at molecular level. We focus the discussion on the calcium silicate hydrates (C-S-H). A first strategy would be based on the strengthening of the network of cohesion forces acting between the individual C-S-H lamellae or between their crystallites. Atomic scale simulations by ab initio, molecular dynamics and energy minimization techniques show that the iono-covalent forces between individual C-S-H layers or C-S-H layer stacks, separated by strongly localized calcium ions and water molecules, are orders of magnitude larger than the ionic correlation forces acting between C-S-H surfaces separated by nm- or multi-nm-thick layers of mobile water molecules and ions. The elastic properties derived from this iono-covalent bonding scheme are in good agreement with experimental values obtained by ultrasonic or statistical ('grid') nanoindentation techniques. The concept picture for C-S-H which follows is that of a crystalline semi-continuum, with dense domains ('crystallites' or 'particles') iono-covalently bonded to each other, possibly entangled also, and embedded as long as the mesoscale porosity is water-saturated in a relatively weak attractive stress field due to fluctuating electrostatic forces. Depending on the size, the aspect ratio, and the turbostratic order of the crystallites, and also the composition of the interstitial solution, the relative importance of each contribution could be modified. This provides the basis for a better control of properties such as early age or long term strength development for instance. In this respect, the microstructure-properties relationships in clay minerals provide interesting leads, pointing to the importance of bonding continuity rather than bond strength. A second strategy to tune the mechanical properties of

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

    SciTech Connect

    Gland, J.L.

    1992-12-01

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

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

    SciTech Connect

    Gland, J.L.

    1992-01-01

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

  17. Oxidative Cleavage of C=S and P=S Bonds at an Al(I) Center: Preparation of Terminally Bound Aluminum Sulfides.

    PubMed

    Chu, Terry; Vyboishchikov, Sergei F; Gabidullin, Bulat; Nikonov, Georgii I

    2016-10-10

    The treatment of cyclic thioureas with the aluminum(I) compound NacNacAl (1; NacNac=[ArNC(Me)CHC(Me)NAr](-) , Ar=2,6-Pr(i)2 C6 H3 ) resulted in oxidative cleavage of the C=S bond and the formation of 3 and 5, the first monomeric aluminum complexes with an Al=S double bond stabilized by N-heterocyclic carbenes. Compound 1 also reacted with triphenylphosphine sulfide in a similar manner, which resulted in cleavage of the P=S bond and production of the adduct [NacNacAl=S(S=PPh3 )] (8). The Al=S double bond in 3 can react with phenyl isothiocyanate to furnish the cycloaddition product 9 and zwitterion 10 as a result of coupling between the liberated carbene and PhN=C=S. All novel complexes were characterized by multinuclear NMR spectroscopy, and the structures of 5, 9, and 10 were confirmed by X-ray diffraction analysis. The nature of the Al=S bond in 5 was also probed by DFT calculations.

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

    PubMed

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

    2009-09-21

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

  19. Bond ionicities in CuBC2 chalcogenides (B=Al, Ga, In; C=S, Se, Te)

    NASA Astrophysics Data System (ADS)

    Merino, J. M.; Díaz, R.; León, M.

    2000-04-01

    The bond ionicities, fi,Cu-C and fi,BC of several CuBC2 (B=Al, Ga, In, and C=S, Se, Te) chalcopyrite compounds are estimated by means of the Phillips-Van Vechten dielectric theory for binary tetrahedral compounds and Levine's extension to multibond crystals in the same way as Neumann [Crystal Res. Technol. 18, 1299 (1983)]. The influence of Cu 3d electrons has been taken into account considering Jaffe-Zunger [Phys. Rev. B 29, 1882 (1984)] band-structure calculations in chalcopyrite compounds, and performing a simple extrapolation for Te compounds. The Cu-C bond susceptibilities have been estimated from the static dielectric constant values obtained by Márquez and Rincón [Phys. Status Solidi B 191, 115 (1995)], and a set of Cu-C bond susceptibilities is proposed. The evaluated fi,Cu-C bond ionicities were found to increase with the atomic fractional coordinate of the C atom, x[anion], indicating that the anion position is a good estimation of the Cu-C bond ionicity.

  20. Hydrodesulfurization on Transition Metal Catalysts: Elementary Steps of C-S Bond Activation and Consequences of Bifunctional Synergies

    NASA Astrophysics Data System (ADS)

    Yik, Edwin Shyn-Lo

    convergence to a single phase is expected and predictable from thermodynamics at a given temperature and sulfur chemical potential, metastability of two phases can exist. We demonstrate, through extensive characterization and kinetic evidence, such behaviors exist in Re, where structural disparities between its phases lead to kinetic hurdles that prevent interconversions between layered ReSx nanostructures and sulfur-covered Re metal clusters. Such features allowed, for the first time, direct comparisons of reaction rates at identical conditions on two disparate phases of the same transition metal identity. Rigorous assessments of kinetic and selectivity data indicated that more universal mechanistic features persist across all catalysts studied, suggesting that differences in their catalytic activity were the result of different densities of HDS sites, which appeared to correlate with their respective metal-sulfur bond energies. Kinetic responses and product distributions indicated that the consumption of thiophene proceeds by the formation of a partially-hydrogenated surface intermediate, which subsequently produces tetrahydrothiophene (THT) and butene/butane (C4) via primary routes on similar types of sites. These sites are formed from desorption of weakly-bound sulfur adatoms on sulfur-covered metal surfaces, which can occur when the heat of sulfur adsorption is sufficiently low at high sulfur coverage as a result of increased sulfur-sulfur repulsive interactions. Relative stabilities and differences in the molecularity of the respective transition states that form THT and C4 dictate product distributions. THT desulfurization to form C4 occurs via readsorption and subsequent dehydrogenation, evidenced by secondary rates that exhibited negative H2 dependences. These behaviors suggest that C-S bond activation occurs on a partially (un)saturated intermediate, analogous to behaviors observed in C-C bond scission reactions of linear and cycloalkanes on hydrogen-covered metal

  1. Platinum-mediated coupling of methane and small nucleophiles (H{sub 2}O, PH{sub 3}, H{sub 2}S, CH{sub 3}NH{sub 2}) as a model for C-N, C-O, C-P, and C-S bond formation in the gas phase

    SciTech Connect

    Broenstrup, M.; Schroeder, D.; Schwarz, H.

    1999-05-10

    The reactions of Pt{sup +} and PtCH{sub 2}{sup +} with the nucleophiles H{sub 2}O, PH{sub 3}, H{sub 2}S, HCl, CH{sub 3}NH{sub 2}, and CH{sub 3}OH are studied by Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry. In the reactions of PtCH{sub 2}{sup +}, carbon-heteroatom bond formation can be accomplished for all substrates except CH{sub 3}OH and HCl. The reaction of PtCH{sub 2}{sup +} with two molecules of water yields Pt(CO)(H{sub 2}O){sup +} and constitutes a gas-phase model for the platinum-mediated generation of water gas according to CH{sub 4} + H{sub 2}O {r_arrow} CO + 3H{sub 2}. In the reactions with PH{sub 3} and H{sub 2}S, carbon-phosphorus and carbon-sulfur bond formation to PtCPH{sup +} and PtCS{sup +} competes with demethanation and dehydrogenation of the substrates to yield PtS{sub n}{sup +} (n = 1--4) and PtP{sub n}H{sub m}{sup +} (n = 1--6; m = 0--3) compounds, respectively. For organic nucleophiles such as CH{sub 3}NH{sub 2} and CH{sub 3}OH, C-N and C-O coupling is much less efficient than platinum-mediated C-H bond activation of the substrates.

  2. Halogen-bonding-triggered supramolecular gel formation.

    PubMed

    Meazza, Lorenzo; Foster, Jonathan A; Fucke, Katharina; Metrangolo, Pierangelo; Resnati, Giuseppe; Steed, Jonathan W

    2013-01-01

    Supramolecular gels are topical soft materials involving the reversible formation of fibrous aggregates using non-covalent interactions. There is significant interest in controlling the properties of such materials by the formation of multicomponent systems, which exhibit non-additive properties emerging from interaction of the components. The use of hydrogen bonding to assemble supramolecular gels in organic solvents is well established. In contrast, the use of halogen bonding to trigger supramolecular gel formation in a two-component gel ('co-gel') is essentially unexplored, and forms the basis for this study. Here, we show that halogen bonding between a pyridyl substituent in a bis(pyridyl urea) and 1,4-diiodotetrafluorobenzene brings about gelation, even in polar media such as aqueous methanol and aqueous dimethylsulfoxide. This demonstrates that halogen bonding is sufficiently strong to interfere with competing gel-inhibitory interactions and create a 'tipping point' in gel assembly. Using this concept, we have prepared a halogen bond donor bis(urea) gelator that forms co-gels with halogen bond acceptors.

  3. Reliable aluminum contact formation by electrostatic bonding

    NASA Astrophysics Data System (ADS)

    Kárpáti, T.; Pap, A. E.; Radnóczi, Gy; Beke, B.; Bársony, I.; Fürjes, P.

    2015-07-01

    The paper presents a detailed study of a reliable method developed for aluminum fusion wafer bonding assisted by the electrostatic force evolving during the anodic bonding process. The IC-compatible procedure described allows the parallel formation of electrical and mechanical contacts, facilitating a reliable packaging of electromechanical systems with backside electrical contacts. This fusion bonding method supports the fabrication of complex microelectromechanical systems (MEMS) and micro-opto-electromechanical systems (MOEMS) structures with enhanced temperature stability, which is crucial in mechanical sensor applications such as pressure or force sensors. Due to the applied electrical potential of  -1000 V the Al metal layers are compressed by electrostatic force, and at the bonding temperature of 450 °C intermetallic diffusion causes aluminum ions to migrate between metal layers.

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

    SciTech Connect

    Gland, J.L.

    1994-12-31

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

  5. Cobalt(II) and cobalt(III) complexes of thioether-containing hexadentate pyrazine amide ligands: C-S bond cleavage and cyclometallation reaction.

    PubMed

    Singh, Akhilesh Kumar; Mukherjee, Rabindranath

    2008-01-14

    Anaerobic reaction of Co(O2CMe)2.4H2O with the thioether-containing acyclic pyrazine amide hexadentate ligand 1,4-bis[o-(pyrazine-2-carboxamidophenyl)]-1,4-dithiobutane (H2L1) (-CH2CH2- spacer between the two pyrazine amide tridentate coordination units) furnishes [CoII(L1)].MeOH (1a) having CoN2(pyrazine)N'2(amide)S2(thioether) coordination. It exhibits an eight-line EPR spectrum, attesting to a low-spin (S = 1/2) state of CoII. A similar reaction in air, however, furnishes [CoIII(L3a)(L3b)].2MeOH (2a) (S = 0), resulting from a C-S bond cleavage reaction triggered by an acetate ion as a base, having CoN2(pyrazine)N'2(amide)S(thioether)S'(thiolate) coordination. On the other hand, the reaction of Co(O2CMe)2.4H2O with 1,4-bis[o-(pyrazine-2-carboxamidophenyl)]-1,5-dithiopentane (H2) (-CH2CH2CH2- spacer between the two pyrazine amide tridentate coordination units) in air affords a cobalt(II) complex [CoII(L2)].MeOH (1b.MeOH) (S = 1/2); its structurally characterized variety has the composition 1b.C6H6. Interestingly, 1b.MeOH undergoes facile metal-centred oxidation by aerial O2-H2O2-[Fe(eta5-C5H5)2][PF6], which led to the isolation of the corresponding cobalt(iii) complex [CoIII(L2)][ClO4] (2b). When treated with methanolic KOH, 2b affords a low-spin (S = 0) organocobalt(III) complex [Co(III)((L2')] (3). Structures of all complexes, except 1a, have been authenticated by X-ray crystallography. A five-membered chelate-ring forming ligand L1(2-) effects C-S bond cleavage and a six-membered chelate-ring forming ligand L2(2-) gives rise to Co-C bond formation, in cobalt(III)-coordinated thioether functions due to alpha C-H bond activation by the base. A rationale has been provided for the observed difference in the reactivity properties. The spectroscopic properties of the complexes have also been investigated. Cyclic voltammetry experiments in MeCN-CH2Cl2 reveal facile metal-centred reversible-to-quasireversible CoIV-CoIII (or a ligand-centred redox process; 2a), Co

  6. Femtosecond quantum control of molecular bond formation.

    PubMed

    Nuernberger, Patrick; Wolpert, Daniel; Weiss, Horst; Gerber, Gustav

    2010-06-08

    Ultrafast lasers are versatile tools used in many scientific areas, from welding to eye surgery. They are also used to coherently manipulate light-matter interactions such as chemical reactions, but so far control experiments have concentrated on cleavage or rearrangement of existing molecular bonds. Here we demonstrate the synthesis of several molecular species starting from small reactant molecules in laser-induced catalytic surface reactions, and even the increase of the relative reaction efficiency by feedback-optimized laser pulses. We show that the control mechanism is nontrivial and sensitive to the relative proportion of the reactants. The control experiments open up a pathway towards photocatalysis and are relevant for research in physics, chemistry, and biology where light-induced bond formation is important.

  7. Determination of the bond dissociation energies of FeX and NiX (X = C, S, Se)

    NASA Astrophysics Data System (ADS)

    Matthew, Daniel J.; Tieu, Erick; Morse, Michael D.

    2017-04-01

    The bond dissociation energies of FeC, NiC, FeS, NiS, FeSe, and NiSe have been measured by the observation of a predissociation threshold in their resonant two-photon ionization spectra. Because the lowest separated atom limits generate a vast number of potential energy curves, it is thought that the molecules dissociate as soon as the ground separated atom limit is exceeded in energy. From the observed thresholds, dissociation energies have been measured as D0(FeC) = 3.961(19), D0(NiC) = 4.167(3), D0(FeS) = 3.240(3), D0(NiS) = 3.651(3), D0(FeSe) = 2.739(6), and D0(NiSe) = 3.218(3) eV. Through the use of thermochemical cycles, these values have been combined with other precisely known values to improve the accuracy of other quantities, providing: D0(Fe+-C) = 4.270(19) eV, D0(Ni+-C) = 3.435(3) eV, IE(FeS) = 8.06(4) eV, IE(NiS) = 8.82(4) eV, and D0 (Fe-S-) = 2.92(10) or 2.89(10) eV, depending on the reference employed for EA(FeS-). Comparisons to previous values are noted, when available. The periodic trends observed are discussed in terms of a molecular orbital diagram for these species. Finally, these results have also been used to calculate 0 K enthalpies of formation of the gaseous MX molecules.

  8. Iridium-mediated C-S bond activation and transformation: organoiridium(III) thioether, thiolato, sulfinato and thiyl radical compounds. Synthesis, mechanistic, spectral, electrochemical and theoretical aspects.

    PubMed

    Das, Ujjwal; Ghorui, Tapas; Adhikari, Basab; Roy, Sima; Pramanik, Shuvam; Pramanik, Kausikisankar

    2015-05-14

    An attractive methodology, single-electron transfer (SET) reductive cleavage of the C-S bond mediated by a metal in the presence of the external stimuli PPh3, has been applied to the kinetically inert IrCl3 in order to synthesize the thiolato complex [Ir(III)(L(S))Cl(PPh3)2] 3 from precursor thioether complexes [Ir(III)(L(SR))Cl2(PPh3)] (R = alkyl) 2. The aforesaid cleavage process in association with (arene)C-H activation furnishes a new class of organosulfur compounds of iridium(III). The thiolato chelate 3 displays a reversible oxidative wave at 0.75 V vs. Ag/AgCl signifying its remarkable nucleophilic character. The high electron density on the thiolato-S vis-à-vis superior nucleophilicity can be envisaged through the formation of a number of S-centered derivatives. This observation has been corroborated with the nature of HOMO in 3, which assumes 49% of S(3p). Notably, the facile oxidative nature of 3 makes it an apposite precursor for metal-stabilized thiyl radical species. Indeed, iridium(III)-stabilized 3˙(+) can be generated by chemical/electrochemical means. The axial EPR spectra with g ∼ 2.0 along with theoretical analysis of SOMO (S(3p) 24% + Ph(π) 43% + d(yz) 15%) and spin density (ρ(S) = +0.543, ρ(Ph) = +0.315, ρ(Ir) = +0.151) of one-electron oxidized 3˙(+) validate the iridium-stabilized thiyl radical description. This observation suggests that the CNS coordination mode in thiophenolato complex 3 is redox-active. Complex 3 is very prone to S-centered oxidation under normal aerobic conditions to yield metallosulfoxide [Ir(III)(L(SO2))Cl(PPh3)2] 4. The enhanced nucleophilicity of thiolato-S can also be manifested via the smooth S-C bond making process with alkyl halides (R'X, R' = Me and allyl; X = Br, I) and subsequent formation of thioether complexes of type [Ir(III)(L(SR'))ClX(PPh3)] 5. The organosulfur compounds of iridium(III) exhibit rich spectral properties including luminescence and the origin of these transitions is scrutinized with

  9. Incorporation of zinc into calcium silicate hydrates, Part I: formation of C-S-H(I) with C/S=2/3 and its isochemical counterpart gyrolite

    SciTech Connect

    Stumm, Andreas . E-mail: andreas.stumm@itc-wgt.fzk.de; Garbev, Krassimir; Beuchle, Guenter; Black, Leon; Stemmermann, Peter; Nueesch, Rolf

    2005-09-01

    We have investigated the incorporation of zinc into both nanocrystalline and crystalline calcium silicate hydrates with starting C/S ratios of 2/3 (0.66). Zinc was added replacing calcium in the starting mixtures [Zn/(Zn+Ca)=0-1/4; 0-10 wt.% Zn], and the resultant phases were characterised using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), differential thermal analysis-thermogravimetry (DTA-TG) and environmental scanning electron microscopy (ESEM). In both groups of samples, increasing zinc content led to gradual structural changes, until eventually a second phase was formed. Zinc was incorporated to similar limits in both sets of samples. The thermal stability of the structures increased to a certain zinc content, beyond which there was structural destabilisation. Zinc incorporation is possible up to {approx}6 wt.%. Our observations strongly indicate similar zinc incorporation mechanisms in both sample series, namely incorporation of zinc into the interlayer of C-S-H(I) and the X-sheet of gyrolite for nanocrystalline and crystalline samples, respectively.

  10. Cellular disulfide bond formation in bioactive peptides and proteins.

    PubMed

    Patil, Nitin A; Tailhades, Julien; Hughes, Richard Anthony; Separovic, Frances; Wade, John D; Hossain, Mohammed Akhter

    2015-01-14

    Bioactive peptides play important roles in metabolic regulation and modulation and many are used as therapeutics. These peptides often possess disulfide bonds, which are important for their structure, function and stability. A systematic network of enzymes--a disulfide bond generating enzyme, a disulfide bond donor enzyme and a redox cofactor--that function inside the cell dictates the formation and maintenance of disulfide bonds. The main pathways that catalyze disulfide bond formation in peptides and proteins in prokaryotes and eukaryotes are remarkably similar and share several mechanistic features. This review summarizes the formation of disulfide bonds in peptides and proteins by cellular and recombinant machinery.

  11. Cellular Disulfide Bond Formation in Bioactive Peptides and Proteins

    PubMed Central

    Patil, Nitin A.; Tailhades, Julien; Hughes, Richard Anthony; Separovic, Frances; Wade, John D.; Hossain, Mohammed Akhter

    2015-01-01

    Bioactive peptides play important roles in metabolic regulation and modulation and many are used as therapeutics. These peptides often possess disulfide bonds, which are important for their structure, function and stability. A systematic network of enzymes—a disulfide bond generating enzyme, a disulfide bond donor enzyme and a redox cofactor—that function inside the cell dictates the formation and maintenance of disulfide bonds. The main pathways that catalyze disulfide bond formation in peptides and proteins in prokaryotes and eukaryotes are remarkably similar and share several mechanistic features. This review summarizes the formation of disulfide bonds in peptides and proteins by cellular and recombinant machinery. PMID:25594871

  12. Alkyl Aryl Ether Bond Formation with PhenoFluor**

    PubMed Central

    Shen, Xiao; Neumann, Constanze N.; Kleinlein, Claudia; Claudia, Nathaniel W.; Ritter, Tobias

    2015-01-01

    An alkyl aryl ether bond formation reaction between phenols and primary and secondary alcohols with PhenoFluor has been developed. The reaction features a broad substrate scope and tolerates many functional groups, and substrates that are challenging for more conventional ether bond forming processes may be coupled. A preliminary mechanistic study indicates reactivity distinct from conventional ether bond formation. PMID:25800679

  13. Role of TBATB in nano indium oxide catalyzed C-S bond formation.

    PubMed

    Gogoi, Prasanta; Hazarika, Sukanya; Barman, Pranjit

    2015-09-29

    Nano sized indium oxide is found to be an efficient catalyst for the conversion of thiols to sulfides using Na2CO3 as base and TBATB as reagent in DMSO at 110 °C. Here in situ generation of bromo intermediate by TBATB takes place through indium surface. A variety of aryl sulfides can be synthesized in excellent yields from less reactive chlorides, boronic acids and thiols.

  14. Role of TBATB in nano indium oxide catalyzed C-S bond formation

    PubMed Central

    Gogoi, Prasanta; Hazarika, Sukanya; Barman, Pranjit

    2015-01-01

    Nano sized indium oxide is found to be an efficient catalyst for the conversion of thiols to sulfides using Na2CO3 as base and TBATB as reagent in DMSO at 110 °C. Here in situ generation of bromo intermediate by TBATB takes place through indium surface. A variety of aryl sulfides can be synthesized in excellent yields from less reactive chlorides, boronic acids and thiols. PMID:26415729

  15. Role of TBATB in nano indium oxide catalyzed C-S bond formation

    NASA Astrophysics Data System (ADS)

    Gogoi, Prasanta; Hazarika, Sukanya; Barman, Pranjit

    2015-09-01

    Nano sized indium oxide is found to be an efficient catalyst for the conversion of thiols to sulfides using Na2CO3 as base and TBATB as reagent in DMSO at 110 °C. Here in situ generation of bromo intermediate by TBATB takes place through indium surface. A variety of aryl sulfides can be synthesized in excellent yields from less reactive chlorides, boronic acids and thiols.

  16. Organometallic Modeling of the Hydrodesulfurization (HDS) Process: Rhenium Carbonyl-promoted C-S Bond Cleavage and Hydrogenation of Thiophenes and Benozothiophenes

    SciTech Connect

    Reynolds, Michael A.

    2000-09-21

    Organometallic modeling of the HDS process at single or multiple metal centers is one approach to better understanding the mechanism that govern commercial HDS. Therefore, we have currently been investigating the use of Re2(CO)10 as a potential model system for catalytic HDS with respect to S-binding, ring-opening, and hydrogenation of thiophenes andbenzothiophenes. We have also been investigating the use of UV-light as a method for activating thiophenic molecules towards C-S and C-H bond cleavage.

  17. Peptide Bond Formation Mechanism Catalyzed by Ribosome.

    PubMed

    Świderek, Katarzyna; Marti, Sergio; Tuñón, Iñaki; Moliner, Vicent; Bertran, Juan

    2015-09-23

    In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708-8719), but the reaction mechanisms are noticeably different. Our simulations reproduce the experimentally determined catalytic effect of ribosome that can be explained by the different behavior of the two environments. While the solvent reorganizes during the chemical process involving an entropic penalty, the ribosome is preorganized in the formation of the Michaelis complex and does not suffer important changes along the reaction, dampening the charge redistribution of the chemical system.

  18. Peptide Bond Formation Mechanism Catalyzed by Ribosome

    PubMed Central

    Świderek, Katarzyna; Marti, Sergio; Tuñón, Iñaki; Moliner, Vicent; Bertran, Juan

    2015-01-01

    In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favourable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708–8719) but the reaction mechanisms are noticeable different. Our simulations reproduce the experimentally determined catalytic effect of ribosome that can be explained by the different behaviour of the two environments. While the solvent reorganizes during the chemical process involving an entropic penalty, the ribosome is preorganized in the formation of the Michaelis complex and does not suffer important changes along the reaction, dampening the charge redistribution of the chemical system. PMID:26325003

  19. Symbiotic Control in Mechanical Bond Formation.

    PubMed

    Wang, Yuping; Sun, Junling; Liu, Zhichang; Nassar, Majed S; Botros, Youssry Y; Stoddart, J Fraser

    2016-09-26

    Since the advent of mechanically interlocked molecules (MIMs), many approaches to templating their formation using various different noncovalent bonding interactions have been introduced and explored. In particular, employing radical-pairing interactions between BIPY(.+) units, the radical cationic state of 4,4'-bipyridinium (BIPY(2+) ) units, in syntheses is not only a convenient but also an attractive source of templation because of the unique properties residing in the resulting catenanes and rotaxanes. Herein, we report a copper-mediated procedure that enables the generation, in the MIM-precursors, of BIPY(.+) radical cations, while the metal itself, which is oxidized to Cu(I) , catalyzes the azide-alkyne cycloaddition reactions that result in the efficient syntheses of two catenanes and one rotaxane, assisted by radical-pairing interactions between the BIPY(.+) radical cations. This procedure not only provides a fillip for making and investigating the properties of Coulombically challenged catenanes and rotaxanes, but it also opens up the possibility of synthesizing artificial molecular machines which operate away from equilibrium.

  20. Homolytic C-S bond scission in the desulfurization of aromatic and aliphatic thiols mediated by a Mo/Co/S cluster: Mechanistic aspects relevant to HDS catalysis

    SciTech Connect

    Curtis, M.D.; Druker, S.H.

    1997-02-05

    The kinetics of the reaction of a series of aromatic and aliphatic thiols with cluster 1 were determined. These reactions form cluster 2 and the arene alkane corresponding to the thiol: Cp`{sub 2}Mo{sub 2}Co{sub 2}S{sub 3}(CO){sub 4} (1) + RSH {yields} Cp`{sub 2}Mo{sub 2}Co{sub 2}S{sub 4}(CO){sub 2} (2) + RH + 2CO. These reactions are first order in thiol and first order in cluster 1 with appreciable negative entropies of activation. These data suggest that the rate determining step of the desulfurization reaction is the initial association of the thiol to the cluster. The more nucleophilic thiolate anions react with 1 at -40{degree}C to form an adduct in which the thiolate anion is bound {eta}{sup 1} to the Co atom. At -25{degree}C, the initial adduct rearranges to a fluxional {mu}{sub 2},{eta}{sup 1}-bound thiolate. The fluxional process is proposed to involve a concerted `walking` of the thiolate and a {mu}{sub 2}-bound sulfide ligand on the surface of the cluster. Near 35 {degree}C, the thiolate-cluster adduct undergoes C-S bond homolysis to give the paramagnetic anion of cluster 1 and the phenyl or alkyl radical. The radical nature of the C-S bond cleavage was confirmed by the desulfurization of the radical clock reagents, cyclopropylmethanethiol and -thiolate anion, that form the cyclopropylmethyl radical which rearranged to the butenyl radical. 42 refs., 5 figs., 3 tabs.

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

    PubMed

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

    2015-10-12

    The formation of C-C bonds embodies the core of organic chemistry because of its fundamental application in generation of molecular diversity and complexity. C-C bond-forming reactions are well-known challenges. To achieve this goal through direct functionalization of C-H bonds in both of the coupling partners represents the state-of-the-art in organic synthesis. Oxidative C-C bond formation obviates the need for prefunctionalization of both substrates. This Minireview is dedicated to the field of C-C bond-forming reactions through direct C-H bond functionalization under completely metal-free oxidative conditions. Selected important developments in this area have been summarized with representative examples and discussions on their reaction mechanisms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Preparation of phosphines through C–P bond formation

    PubMed Central

    Wauters, Iris; Debrouwer, Wouter

    2014-01-01

    Summary Phosphines are an important class of ligands in the field of metal-catalysis. This has spurred the development of new routes toward functionalized phosphines. Some of the most important C–P bond formation strategies were reviewed and organized according to the hybridization of carbon in the newly formed C–P bond. PMID:24991257

  3. Resolving the molecular mechanism of cadherin catch bond formation

    SciTech Connect

    Manibog, Kristine; Li, Hui; Rakshit, Sabyasachi; Sivasankar, Sanjeevi

    2014-06-02

    Classical cadherin Ca(2+)-dependent cell-cell adhesion proteins play key roles in embryogenesis and in maintaining tissue integrity. Cadherins mediate robust adhesion by binding in multiple conformations. One of these adhesive states, called an X-dimer, forms catch bonds that strengthen and become longer lived in the presence of mechanical force. Here we use single-molecule force-clamp spectroscopy with an atomic force microscope along with molecular dynamics and steered molecular dynamics simulations to resolve the molecular mechanisms underlying catch bond formation and the role of Ca(2+) ions in this process. Our data suggest that tensile force bends the cadherin extracellular region such that they form long-lived, force-induced hydrogen bonds that lock X-dimers into tighter contact. When Ca(2+) concentration is decreased, fewer de novo hydrogen bonds are formed and catch bond formation is eliminated

  4. Trimethyltin-mediated covalent gold-carbon bond formation.

    PubMed

    Batra, Arunabh; Kladnik, Gregor; Gorjizadeh, Narjes; Meisner, Jeffrey; Steigerwald, Michael; Nuckolls, Colin; Quek, Su Ying; Cvetko, Dean; Morgante, Alberto; Venkataraman, Latha

    2014-09-10

    We study the formation of covalent gold-carbon bonds in benzyltrimethylstannane (C10H16Sn) deposited on Au in ultra-high-vacuum conditions. Through X-ray photoemission spectroscopy and X-ray absorption measurements, we find that the molecule fragments at the Sn-benzyl bond when exposed to Au surfaces at temperatures as low as -110 °C. The resulting benzyl species is stabilized by the presence of Au(111) but only forms covalent Au-C bonds on more reactive Au surfaces like Au(110). We also present spectroscopic proof for the existence of an electronic "gateway" state localized on the Au-C bond that is responsible for its unique electronic properties. Finally, we use DFT-based nudged elastic band calculations to elucidate the crucial role played by the under-coordinated Au surface in the formation of Au-C bonds.

  5. Formation of Irreversible H-bonds in Cellulose Materials

    Treesearch

    Umesh P. Agarwal; Sally A. Ralph; Rick S. Reiner; Nicole M. Stark

    2015-01-01

    Understanding of formation of irreversible Hbonds in cellulose is important in a number of fields. For example, fields as diverse as pulp and paper and enzymatic saccharification of cellulose are affected. In the present investigation, the phenomenon of formation of irreversible H-bonds is studied in a variety of celluloses and under two different drying conditions....

  6. Cooperative Hydrogen Bonding in Amyloid Formation.

    SciTech Connect

    Tsemekhman, Kiril L.; Goldschmidt, Lukasz; Eisenberg, Dvaid; Baker, David

    2007-04-01

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Amyloid diseases, including Alzheimer's and prion diseases, are each associated with unbranched protein fibrils. Each fibril is made of a particular protein, yet they share common properties. One such property is nucleation-dependent fibril growth. Monomers of amyloid-forming proteins can remain in dissolved form for long periods, before rapidly assembly into fibrils. The lag before growth has been attributed to slow kinetics of formation of a nucleus, on which other molecules can deposit to form the fibril. We have explored the energetics of fibril formation, based on the known molecular structure of a fibril-forming peptide from the yeast prion, Sup35, using both classical and quantum (density functional theory) methods. We find that the energetics of fibril formation for the first three layers are cooperative using both methods. This cooperativity is consistent with the observation that formation of amyloid fibrils involves slow nucleation and faster growth.

  7. Aspects of glycosidic bond formation in aqueous solution: chemical bonding and the role of water.

    PubMed

    Stubbs, John M; Marx, Dominik

    2005-04-22

    A model of the specific acid-catalyzed glycosidic bond formation in liquid water at ambient conditions is studied based on constrained Car-Parrinello ab initio molecular dynamics. Specifically the reaction of alpha-D-glucopyranose and methanol is found to proceed by a D(N)A(N) mechanism. The D(N) step consists of a concerted protonation of the O(1) hydroxyl leaving group; this process results in the breaking of the C(1)-O(1) bond, and oxocarbenium ion formation involving C(1)=O(5). The second step, A(N), is the formation of the C(1)-O(m) glycosidic bond, deprotonation of the methanol hydroxyl group O(m)H(m), and re-formation of the C(1)-O(5) single bond. A focus of this study is the analysis of the electronic structure during this condensed phase reaction relying on both Boys/Wannier localized orbitals and the electron localization function ELF. This analysis allows the clear elucidation of the chemical bonding features of the intermediate bracketed by the D(N) and A(N) steps, which is a non-solvent equilibrated oxocarbenium cation. Most interestingly, it is found that the oxygen in the pyranose ring becomes "desolvated" upon double bond/oxocarbenium formation, whereas it is engaged in the hydrogen-bonded water network before and after this period. This demonstrates that hydrogen bonding and thus the aqueous solvent play an active role in this reaction implying that microsolvation studies in the gas phase, both theoretical and experimental, might lead to qualitatively different reaction mechanisms compared to solution.

  8. Disulphide bond formation in food protein aggregation and gelation.

    PubMed

    Visschers, Ronald W; de Jongh, Harmen H J

    2005-01-01

    In this short review we discuss the role of cysteine residues and cystine bridges for the functional aggregation of food proteins. We evaluate how formation and cleavage of disulphide bonds proceeds at a molecular level, and how inter- and intramolecular disulfide bonds can be detected and modified. The differences between heat-, high-pressure-, and denaturant-induced unfolding and aggregation are discussed. The effect of disulphide bonding between aggregates of proteins and protein mixtures on the functional macroscopic properties of space filling networks in protein gels is briefly presented.

  9. Disulfide Bond Formation in Prokaryotes: History, Diversity and Design

    PubMed Central

    Hatahet, Feras; Boyd, Dana; Beckwith, Jon

    2014-01-01

    The formation of structural disulfide bonds is essential for the function and stability of a great number of proteins, particularly those that are secreted. There exists a variety of dedicated cellular catalysts and pathways from Archaea to humans that ensure the formation of native disulfide bonds. In this review we describe the initial discoveries of these pathways and report progress in recent years in our understanding of the diversity of these pathways in prokaryotes, including those newly discovered in some Archaea. We will also discuss the various successful efforts to achieve laboratory-based evolution and design of synthetic disulfide bond formation machineries in the bacterium E. coli. These latter studies have also led to new more general insights into the redox environment of the cytoplasm and bacterial cell envelope. PMID:24576574

  10. Homolytic S-S bond dissociation of 11 bis(thiocarbonyl)disulfides R-C(=S)-S-S-C(=S)R and prediction of a novel rubber vulcanization accelerator.

    PubMed

    Mak, Adrian Matthew; Steudel, Ralf; Wong, Ming Wah

    2008-06-02

    The structures and energetics of eight substituted bis(thiocarbonyl)disulfides (RCS(2))(2), their associated radicals RCS(2)(*), and their coordination compounds with a lithium cation have been studied at the G3X(MP2) level of theory for R = H, Me, F, Cl, OMe, SMe, NMe(2), and PMe(2). The effects of substituents on the dissociation of (RCS(2))(2) to RCS(2)(*) were analyzed using isodesmic stabilization reactions. Electron-donating groups with an unshared pair of electrons have a pronounced stabilization effect on both (RCS(2))(2) and RCS(2)(*). The S-S bond dissociation enthalpy of tetramethylthiuram disulfide (TMTD, R = NMe(2)) is the lowest in the above series (155 kJ mol(-1)), attributed to the particular stability of the formed Me(2)NCS(2)(*) radical. Both (RCS(2))(2) and the fragmented radicals RCS(2)(*) form stable chelate complexes with a Li(+) cation. The S-S homolytic bond cleavage in (RCS(2))(2) is facilitated by the reaction [Li(RCS(2))(2)](+)+Li(+)-->2 [Li(RCS(2))](*+). Three other substituted bis(thiocarbonyl) disulfides with the unconventional substituents R = OSF(5), Gu(1), and Gu(2) have been explored to find suitable alternative rubber vulcanization accelerators. Bis(thiocarbonyl)disulfide with a guanidine-type substituent, (Gu(1)CS(2))(2), is predicted to be an effective accelerator in sulfur vulcanization of rubber. Compared to TMTD, (Gu(1)CS(2))(2) is calculated to have a lower bond dissociation enthalpy and smaller associated barrier for the S-S homolysis.

  11. Peptide Bond Formation in Water Mediated by Carbon Disulfide.

    PubMed

    Leman, Luke J; Huang, Zheng-Zheng; Ghadiri, M Reza

    2015-09-01

    Demonstrating plausible nonenzymatic polymerization mechanisms for prebiotic monomers represents a fundamental goal in prebiotic chemistry. While a great deal is now known about the potentially prebiotic synthesis of amino acids, our understanding of abiogenic polymerization processes to form polypeptides is less well developed. Here, we show that carbon disulfide (CS2), a component of volcanic emission and sulfide mineral weathering, and a widely used synthetic reagent and solvent, promotes peptide bond formation in modest yields (up to ∼20%) from α-amino acids under mild aqueous conditions. Exposure of a variety of α-amino acids to CS2 initially yields aminoacyl dithiocarbamates, which in turn generate reactive 2-thiono-5-oxazolidone intermediates, the thio analogues of N-carboxyanhydrides. Along with peptides, thiourea and thiohydantoin species are produced. Amino acid stereochemistry was preserved in the formation of peptides. Our findings reveal that CS2 could contribute to peptide bond formation, and possibly other condensation reactions, in abiogenic settings.

  12. Bivalent cation binding effect on formation of the peptide bond

    NASA Astrophysics Data System (ADS)

    Remko, Milan; Rode, Bernd Michael

    2000-01-01

    The reactions between formic acid (or glycine) and ammonia, without and with Mg 2+, Ni 2+ and Cu 2+ cations as catalysts, have been studied as model reactions for peptide bond formation using the Becke3LYP functional and 6-311+G(d,p) basis set of DFT theory. Enthalpies and free energies for the stationary points of each reaction have been calculated to determine the thermodynamics of reactions investigated. A substantial decrease in reaction enthalpies and free energies was found for formic acid-ammonia and glycine-ammonia reactions catalysed by Mg 2+, Ni 2+ and Cu 2+ ions compared with those of the uncatalysed amide bond formation. The catalytic effect of the transition metal ions Ni 2+ and Cu 2+ is of similar strength and more pronounced than that of the Mg 2+ cation.

  13. Amide and Peptide Bond Formation in Water at Room Temperature.

    PubMed

    Gabriel, Christopher M; Keener, Megan; Gallou, Fabrice; Lipshutz, Bruce H

    2015-08-21

    A general and environmentally responsible method for the formation of amide/peptide bonds in an aqueous micellar medium is described. Use of uronium salt (1-cyano-2-ethoxy-2-oxoethylidenaminooxy)dimethylaminomorpholinocarbenium hexafluorophosphate (COMU) as a coupling reagent, 2,6-lutidine, and TPGS-750-M represents mild conditions associated with these valuable types of couplings. The aqueous reaction medium is recyclable leading to low E Factors.

  14. Carbon-CArbon bond formation by Lewis superacid catalysis.

    PubMed

    Dunach, Elisabet

    2014-11-01

    Diverse intramolecular cyclizations involving the formation of CC bonds are described using catalytic methodologies based on Lewis superacids. Examples are presented on 1,6-diene cyclizations to gem-dimethylcyclohexane structures. Tandem cyclization of trienes are described to afford bicyclic structures in reactions involving rearrangements. Hydroarylation of olefins and of allenes is developed in catalytic FriedelCrafts-type coupling processes, which can give rise to tandem reactions. The olfactory evaluation of the series of prepared compounds is also presented.

  15. Late-stage formation of carbon-fluorine bonds.

    PubMed

    Campbell, Michael G; Ritter, Tobias

    2014-06-01

    In this account, we review work from our lab on the development of methods for carbon-fluorine bond formation, with an emphasis on late-stage fluorination of functionalized small molecules and synthesis of (18) F-labeled molecules for potential use as tracers in positron emission tomography (PET). We attempt to highlight reactions that we feel are of particular practical relevance, as well as areas of research where there is still significant room for advancement.

  16. Heats of Formation and Bond Energies in Group III Compounds

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Allendorf, Mark D.; Melius, Carl F.; Arnold, James O. (Technical Monitor)

    1999-01-01

    We present heats of formation and bond energies for Group-III compounds obtained from calculations of molecular ground-state I electronic energies. Data for compounds of the form MXn are presented, where M = B, Al, Ga, and In, X = He H, Cl, and CH3, and n = 1-3. Energies for the B, Al, and Ga compounds are obtained from G2 predictions, while those for the In compounds are obtained from CCSD(T)/CBS calculations; these are the most accurate calculations for indium-containing compounds published to date. In most cases, the calculated thermochemistry is in good agreement with published values derived from experiments for those species that have well-established heats of formation. Bond energies obtained from the heats of formation follow the expected trend (Cl much greater than CH3 approx. H). However, the CH3M-(CH3)2 bond energies obtained for trimethylgallium and trimethylindium are considerably stronger (greater than 15 kcal/mol) than currently accepted values.

  17. Amide-directed photoredox-catalysed C-C bond formation at unactivated sp(3) C-H bonds.

    PubMed

    Chu, John C K; Rovis, Tomislav

    2016-11-10

    Carbon-carbon (C-C) bond formation is paramount in the synthesis of biologically relevant molecules, modern synthetic materials and commodity chemicals such as fuels and lubricants. Traditionally, the presence of a functional group is required at the site of C-C bond formation. Strategies that allow C-C bond formation at inert carbon-hydrogen (C-H) bonds enable access to molecules that would otherwise be inaccessible and the development of more efficient syntheses of complex molecules. Here we report a method for the formation of C-C bonds by directed cleavage of traditionally non-reactive C-H bonds and their subsequent coupling with readily available alkenes. Our methodology allows for amide-directed selective C-C bond formation at unactivated sp(3) C-H bonds in molecules that contain many such bonds that are seemingly indistinguishable. Selectivity arises through a relayed photoredox-catalysed oxidation of a nitrogen-hydrogen bond. We anticipate that our findings will serve as a starting point for functionalization at inert C-H bonds through a strategy involving hydrogen-atom transfer.

  18. Amide-directed photoredox-catalysed C-C bond formation at unactivated sp3 C-H bonds

    NASA Astrophysics Data System (ADS)

    Chu, John C. K.; Rovis, Tomislav

    2016-11-01

    Carbon-carbon (C-C) bond formation is paramount in the synthesis of biologically relevant molecules, modern synthetic materials and commodity chemicals such as fuels and lubricants. Traditionally, the presence of a functional group is required at the site of C-C bond formation. Strategies that allow C-C bond formation at inert carbon-hydrogen (C-H) bonds enable access to molecules that would otherwise be inaccessible and the development of more efficient syntheses of complex molecules. Here we report a method for the formation of C-C bonds by directed cleavage of traditionally non-reactive C-H bonds and their subsequent coupling with readily available alkenes. Our methodology allows for amide-directed selective C-C bond formation at unactivated sp3 C-H bonds in molecules that contain many such bonds that are seemingly indistinguishable. Selectivity arises through a relayed photoredox-catalysed oxidation of a nitrogen-hydrogen bond. We anticipate that our findings will serve as a starting point for functionalization at inert C-H bonds through a strategy involving hydrogen-atom transfer.

  19. Sequence-Selective Formation of Synthetic H-Bonded Duplexes.

    PubMed

    Stross, Alexander E; Iadevaia, Giulia; Núñez-Villanueva, Diego; Hunter, Christopher A

    2017-09-13

    Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (10(2) to 10(5) M(-1)). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.

  20. Intermetallic compound formation at Cu-Al wire bond interface

    NASA Astrophysics Data System (ADS)

    Bae, In-Tae; Young Jung, Dae; Chen, William T.; Du, Yong

    2012-12-01

    Intermetallic compound (IMC) formation and evolution at Cu-Al wire bond interface were studied using focused ion beam /scanning electron microscopy, transmission electron microscopy (TEM)/energy dispersive x-ray spectroscopy (EDS), nano beam electron diffraction (NBED) and structure factor (SF) calculation. It was found that discrete IMC patches were formed at the Cu/Al interface in as-packaged state and they grew toward Al pad after high temperature storage (HTS) environment at 150 °C. TEM/EDS and NBED results combined with SF calculation revealed the evidence of metastable θ'-CuAl2 IMC phase (tetragonal, space group: I4¯m2, a = 0.404 nm, c = 0.580 nm) formed at Cu/Al interfaces in both of the as-packaged and the post-HTS samples. Two feasible mechanisms for the formation of the metastable θ'-CuAl2 phase are discussed based on (1) non-equilibrium cooling of wire bond that is attributed to highly short bonding process time and (2) the epitaxial relationships between Cu and θ'-CuAl2, which can minimize lattice mismatch for θ'-CuAl2 to grow on Cu.

  1. Peptide bond formation via glycine condensation in the gas phase.

    PubMed

    Van Dornshuld, Eric; Vergenz, Robert A; Tschumper, Gregory S

    2014-07-24

    Four unique gas phase mechanisms for peptide bond formation between two glycine molecules have been mapped out with quantum mechanical electronic structure methods. Both concerted and stepwise mechanisms, each leading to a cis and trans glycylglycine product (four mechanisms total), were examined with the B3LYP and MP2 methods and Gaussian atomic orbital basis sets as large as aug-cc-pVTZ. Electronic energies of the stationary points along the reaction pathways were also computed with explicitly correlated MP2-F12 and CCSD(T)-F12 methods. The CCSD(T)-F12 computations indicate that the electronic barriers to peptide bond formation are similar for all four mechanisms (ca. 32-39 kcal mol(-1) relative to two isolated glycine fragments). The smallest barrier (32 kcal mol(-1)) is associated with the lone transition state for the concerted mechanism leading to the formation of a trans peptide bond, whereas the largest barrier (39 kcal mol(-1)) was encountered along the concerted pathway leading to the cis configuration of the glycylglycine dipeptide. Two significant barriers are encountered for the stepwise mechanisms. For both the cis and trans pathways, the early electronic barrier is 36 kcal mol(-1) and the subsequent barrier is approximately 1 kcal mol(-1) lower. A host of intermediates and transition states lie between these two barriers, but they all have very small relative electronic energies (ca. ± 4 kcal mol(-1)). The isolated cis products (glycylglycine + H2O) are virtually isoenergetic with the isolated reactants (within -1 kcal mol(-1)), whereas the trans products are about 5 kcal mol(-1) lower in energy. In both products, however, the water can hydrogen bond to the dipeptide and lower the energy by roughly 5-9 kcal mol(-1). This study indicates that the concerted process leading to a trans configuration about the peptide bond is marginally favored both thermodynamically (exothermic by ca. 5 kcal mol(-1)) and kinetically (barrier height ≈ 32 kcal mol(-1

  2. Simultaneous bond degradation and bond formation during phenol-formaldehyde curing with wood

    Treesearch

    Daniel J. Yelle; John Ralph

    2016-01-01

    Bonding of wood using phenol–formaldehyde adhesive develops highly durable bonds. Phenol– formaldehyde is believed to form primary bonds with wood cell wall polymers (e.g., lignin). However, it is unclear how this adhesive interacts and bonds to lignin. Through wood solubilisation methodologies, earlywood and latewood bonded assemblies were characterized using two-...

  3. [Cu30I16(mtpmt)12(μ(10-S4))]: an unusual 30-membered copper(I) cluster derived from the C-S bond cleavage and its use in heterogeneous catalysis.

    PubMed

    Li, Hong-Xi; Zhao, Wei; Li, Hai-Yan; Xu, Zhong-Lin; Wang, Wen-Xia; Lang, Jian-Ping

    2013-05-14

    The Cu(I)-mediated C-S bond cleavage of 5-methyl-4-(p-tolyl)pyrimidine-2-thiol (mtpmtH) gave one 30-nuclear cluster [Cu30I16(mtpmt)12(μ10-S4)], one polymeric complex [(bmtpms)Cu-(μ-I)]n and one tetranuclear complex [(bmptmds){Cu(μ-I)}2]2; the 30-nuclear cluster displayed excellent catalytic performances in the coupling reactions of N-heterocycles and arylboronic acids and could be recycled and reused.

  4. Ala-His Mediated Peptide Bond Formation Revisited

    NASA Astrophysics Data System (ADS)

    Larkin, Deana C.; Martinis, Susan A.; Roberts, Deborah J.; Fox, George E.

    2001-12-01

    The historical origin of the translation machinery remains unresolved. Although the large 23S ribosomal RNA (rRNA) is almost certainly the catalytic component of the peptidyl transferase center in the modern ribosome, it is likely that greatly simplified systems were initially employed in the late stages of the prebiotic world. In particular, it has been suggested that small RNAs carrying amino acids were important for the genesis of protein synthesis. Consistent with this, a dipeptide, Ala-His, was previously claimed to be a prebiotically feasible catalyst mediating peptide bond formation in the presence of aminoacylated tRNA and cognate mRNA template, in the absence of other ribosomal components (Shimizu, 1996). We herein report a detailed study of putative dipeptide formation by Ala-His and RNAs carrying leucine. Based on the results presented here, it is unlikely that the dipeptide, Ala-His, catalyzes significant levels of Leu-Leu dipeptide formation in solution. A product is produced which can be readily mistaken for a dipeptide in the TLC separation systems employed in earlier work. We offer explanations for the formation of this product as well as another unexpected product. The results presented here are consistent with the notion that the translation machinery was likely based on catalytic RNA from its very inception.

  5. Diastereoselective imine-bond formation through complementary double-helix formation.

    PubMed

    Yamada, Hidekazu; Furusho, Yoshio; Yashima, Eiji

    2012-05-02

    Optically active amidine dimer strands having a variety of chiral and achiral linkers with different stereostructures are synthesized and used as templates for diastereoselective imine-bond formations between two achiral carboxylic acid monomers bearing a terminal aldehyde group and racemic 1,2-cyclohexanediamine, resulting in a preferred-handed double helix stabilized by complementary salt bridges. The diastereoselectivity of the racemic amine is significantly affected by the chirality of the amidine residues along with the rigidity and/or chirality of the linkers in the templates. NMR and kinetic studies reveal that the present imine-bond formation involves a two-step reversible reaction. The second step involves formation of a preferred-handed complementary double helix assisted by the chiral amidine templates and determines the overall reaction rate and diastereoselectivity of the amine. © 2012 American Chemical Society

  6. Copper-catalyzed oxidative carbon-heteroatom bond formation: a recent update.

    PubMed

    Zhu, Xu; Chiba, Shunsuke

    2016-08-08

    This review updates recent advances in Cu-catalyzed (anaerobic) oxidative carbon-heteroatom bond formation on sp(3)- and sp(2)-C-H bonds as well as alkenes, classified according to the types of stoichiometric oxidants.

  7. Liquid phase diffusion bonding of A1070 by using metal formate coated Zn sheet

    NASA Astrophysics Data System (ADS)

    Ozawa, K.; Koyama, S.; shohji, I.

    2017-05-01

    Aluminium alloy have high strength and easily recycle due to its low melting point. Therefore, aluminium is widely used in the manufacturing of cars and electronic devices. In recent years, the most common way for bonding aluminium alloy is brazing and friction stir welding. However, brazing requires positional accuracy and results in the formation of voids by the flax residue. Moreover, aluminium is an excellent heat radiating and electricity conducting material; therefore, it is difficult to bond together using other bonding methods. Because of these limitations, liquid phase diffusion bonding is considered to the suitable method for bonding aluminium at low temperature and low bonding pressure. In this study, the effect of metal formate coating processing of zinc surface on the bond strength of the liquid phase diffusion bonded interface of A1070 has been investigated by SEM observation of the interfacial microstructures and fractured surfaces after tensile test. Liquid phase diffusion bonding was carried out under a nitrogen gas atmosphere at a bonding temperature of 673 K and 713 K and a bonding load of 6 MPa (bonding time: 15 min). As a result of the metal formate coating processing, a joint having the ultimate tensile strength of the base aluminium was provided. It is hypothesized that this is because metallic zinc is generated as a result of thermal decomposition of formate in the bonded interface at lower bonding temperatures.

  8. Lessons from nature: biomimetic organocatalytic carbon-carbon bond formations.

    PubMed

    Enders, Dieter; Narine, Arun A

    2008-10-17

    Nature utilizes simple C2 and C3 building blocks, such as dihydroxyacetone phosphate (DHAP), phosphoenolpyruvate (PEP), and the "active aldehyde" in various enzyme-catalyzed carbon-carbon bond formations to efficiently build up complex organic molecules. In this Perspective, we describe the transition from using enantiopure chemical synthetic equivalents of these building blocks, employing our SAMP/RAMP hydrazone methodology and metalated chiral alpha-amino nitriles, to the asymmetric organocatalytic versions developed in our laboratory. Following this biomimetic strategy, the DHAP equivalent 2,2-dimethyl-1,3-dioxan-5-one (dioxanone) has been used in the proline-catalyzed synthesis of carbohydrates, aminosugars, carbasugars, polyoxamic acid, and various sphingosines. Proline-catalyzed aldol reactions involving a PEP-like equivalent have also allowed for the asymmetric synthesis of ulosonic acid precursors. By mimicking the "active aldehyde" nucleophilic acylations in Nature catalyzed by the thiamine-dependent enzyme, transketolase, enantioselective N-heterocyclic carbene-catalyzed benzoin and Stetter reactions have been developed. Finally, based on Nature's use of domino reactions to convert simple building blocks into complex and highly functionalized molecules, we report on our development of biomimetic asymmetric multicomponent domino reactions which couple enamine and iminium catalysis.

  9. Copper-catalyzed aerobic oxidative C-C bond cleavage for C-N bond formation: from ketones to amides.

    PubMed

    Tang, Conghui; Jiao, Ning

    2014-06-16

    A novel copper-catalyzed aerobic oxidative C(CO)-C(alkyl) bond cleavage reaction of aryl alkyl ketones for C-N bond formation is described. A series of acetophenone derivatives as well as more challenging aryl ketones with long-chain alkyl substituents could be selectively cleaved and converted into the corresponding amides, which are frequently found in biologically active compounds and pharmaceuticals. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Single, double, triple bonds and chains: the formation of electron-precise B-B bonds.

    PubMed

    Braunschweig, Holger; Dewhurst, Rian D

    2013-03-25

    The construction of boron-boron bonds, despite the intense synthetic interest in diboranes and the high B-B bond enthalpy, is still difficult, uncontrollable, and unpredictable. Methods for the construction of B-B multiple bonds are rarer still. These problems have witnessed some progress in recent years; this Minireview attempts to provide a background to the history of B-B bond synthesis and summarize the recent results in the area. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Ribosomal crystallography: peptide bond formation, chaperone assistance and antibiotics activity.

    PubMed

    Yonath, Ada

    2005-08-31

    The peptidyl transferase center (PTC) is located in a protein free environment, thus confirming that the ribosome is a ribozyme. This arched void has dimensions suitable for accommodating the 3' ends of the A-and the P-site tRNAs, and is situated within a universal sizable symmetry-related region that connects all ribosomal functional centers involved in amino-acid polymerization. The linkage between the elaborate PTC architecture and the A-site tRNA position revealed that the A- to P-site passage of the tRNA 3' end is performed by a rotatory motion, which leads to stereochemistry suitable for peptide bond formation and for substrate mediated catalysis, thus suggesting that the PTC evolved by gene-fusion. Adjacent to the PTC is the entrance of the protein exit tunnel, shown to play active roles in sequence-specific gating of nascent chains and in responding to cellular signals. This tunnel also provides a site that may be exploited for local co-translational folding and seems to assist in nascent chain trafficking into the hydrophobic space formed by the first bacterial chaperone, the trigger factor. Many antibiotics target ribosomes. Although the ribosome is highly conserved, subtle sequence and/or conformational variations enable drug selectivity, thus facilitating clinical usage. Comparisons of high-resolution structures of complexes of antibiotics bound to ribosomes from eubacteria resembling pathogens, to an archaeon that shares properties with eukaryotes and to its mutant that allows antibiotics binding, demonstrated the unambiguous difference between mere binding and therapeutical effectiveness. The observed variability in antibiotics inhibitory modes, accompanied by the elucidation of the structural basis to antibiotics mechanism justifies expectations for structural based improved properties of existing compounds as well as for the development of novel drugs.

  12. The formation of sp3 bonding in compressed BN

    NASA Astrophysics Data System (ADS)

    Meng, Yue; Mao, Ho-Kwang; Eng, Peter J.; Trainor, Thomas P.; Newville, Matthew; Hu, Michael Y.; Kao, Chichang; Shu, Jinfu; Hausermann, Daniel; Hemley, Russell J.

    2004-02-01

    Attributed to their specific atomic bonding, the soft, graphite-like, hexagonal boron nitride (h-BN) and its superhard, diamond-like, cubic polymorph (c-BN) are important technological materials with a wide range of applications. At high pressure and temperature, h-BN can directly transform to a hexagonal close-packed polymorph (w-BN) that can be partially quenched after releasing pressure. Previous theoretical calculations and experimental measurements (primarily on quenched samples) provided substantial information on the transition, but left unsettled questions due to the lack of in situ characterization at high pressures. Using inelastic X-ray scattering to probe the boron and nitrogen near K-edge spectroscopy, here we report the first observation of the conversion process of boron and nitrogen sp2- and p-bonding to sp3 and the directional nature of the sp3 bonding. In combination with in situ X-ray diffraction probe, we have further clarified the structure transformation mechanism. The present archetypal example opens two enormous, element-specific, research areas on high-pressure bonding evolutions of boron and nitrogen; each of the two elements and their respective compounds have displayed a wealth of intriguing pressure-induced phenomena that result from bonding changes, including metallization, superconductivity, semiconductivity, polymerization and superhardness.

  13. Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates.

    PubMed

    Ravi, Vijay Kumar; Goel, Mohit; Kotamarthi, Hema Chandra; Ainavarapu, Sri Rama Koti; Swaminathan, Rajaram

    2014-01-01

    Nonnative disulfide bonds have been observed among protein aggregates in several diseases like amyotrophic lateral sclerosis, cataract and so on. The molecular mechanism by which formation of such bonds promotes protein aggregation is poorly understood. Here in this work we employ previously well characterized aggregation of hen eggwhite lysozyme (HEWL) at alkaline pH to dissect the molecular role of nonnative disulfide bonds on growth of HEWL aggregates. We employed time-resolved fluorescence anisotropy, atomic force microscopy and single-molecule force spectroscopy to quantify the size, morphology and non-covalent interaction forces among the aggregates, respectively. These measurements were performed under conditions when disulfide bond formation was allowed (control) and alternatively when it was prevented by alkylation of free thiols using iodoacetamide. Blocking disulfide bond formation affected growth but not growth kinetics of aggregates which were ∼50% reduced in volume, flatter in vertical dimension and non-fibrillar in comparison to control. Interestingly, single-molecule force spectroscopy data revealed that preventing disulfide bond formation weakened the non-covalent interaction forces among monomers in the aggregate by at least ten fold, thereby stalling their growth and yielding smaller aggregates in comparison to control. We conclude that while constrained protein chain dynamics in correctly disulfide bonded amyloidogenic proteins may protect them from venturing into partial folded conformations that can trigger entry into aggregation pathways, aberrant disulfide bonds in non-amyloidogenic proteins (like HEWL) on the other hand, may strengthen non-covalent intermolecular forces among monomers and promote their aggregation.

  14. C-F Bond Formation for the Synthesis of Aryl Fluorides.

    PubMed

    Furuya, Takeru; Klein, Johannes E M N; Ritter, Tobias

    2010-06-01

    A selection of carbon-fluorine bond-forming reactions is presented with particular focus on transition metal-mediated fluorination. A brief summary of conventional fluorination reactions is followed by a discussion of fluorination reactions mediated by palladium and silver. Investigations into the mechanism as well as the conceptual difficulty associated with transition metal-mediated carbon-fluorine bond formation are presented.

  15. Adhesives with wood materials : bond formation and performance

    Treesearch

    Charles R. Frihart; Christopher G. Hunt

    2010-01-01

    Adhesive bonding of wood plays an increasing role in the forest products industry and is a key factor for efficiently utilizing our timber resource. The main use of adhesives is in the manufacture of building materials, including plywood, oriented strandboard, particleboard, fiberboard, structural composite lumber, doors, windows and frames, and factory-laminated wood...

  16. Mild Catalytic methods for Alkyl-Alkyl Bond Formation

    SciTech Connect

    Vicic, David A

    2009-08-10

    Overview of Research Goals and Accomplishments for the Period 07/01/06 – 06/30/07: Our overall research goal is to transform the rapidly emerging synthetic chemistry involving alkyl-alkyl cross-couplings into more of a mechanism-based field so that that new, rationally-designed catalysts can be performed under energy efficient conditions. Our specific objectives for the previous year were 1) to obtain a proper electronic description of an active catalyst for alkyl-alkyl cross-coupling reactions and 2) to determine the effect of ligand structure on the rate, scope, selectivity, and functional group compatibility of C(sp3)-C(sp3) cross-coupling catalysis. We have completed both of these initial objectives and established a firm base for further studies. The specific significant achievements of the current grant period include: 1) we have performed magnetic and computational studies on (terpyridine)NiMe, an active catalyst for alkyl-alkyl cross couplings, and have discovered that the unpaired electron resides heavily on the terpyridine ligand and that the proper electronic description of this nickel complex is a Ni(II)-methyl cation bound to a reduced terpyridine ligand; 2) we have for the first time shown that alkyl halide reduction by terpyridyl nickel catalysts is substantially ligand based; 3) we have shown by isotopic labeling studies that the active catalyst (terpyridine)NiMe is not produced via a mechanism that involves the formation of methyl radicals when (TMEDA)NiMe2 is used as the catalyst precursor; 4) we have performed an extensive ligand survey for the alkyl-alkyl cross-coupling reactions and have found that electronic factors only moderately influence reactivity in the terpyridine-based catalysis and that the most dramatic effects arise from steric and solubility factors; 5) we have found that the use of bis(dialkylphosphino)methanes as ligands for nickel does not produce active catalysts for cross-coupling but rather leads to bridging hydride

  17. Molecular and ionic hydrogen bond formation in fluorous solvents.

    PubMed

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-08

    There are only a few studies of noncovalent association in fluorous solvents and even fewer that are quantitative. A full understanding, particularly of stoichiometry and binding strength of noncovalent interactions in fluorous solvents could be very useful in improved molecular-receptor-based extractions, advancements in sensor technologies, crystal engineering, and supramolecular chemistry. This work investigates hydrogen bonding between heterocyclic bases and a perfluoropolyether with a terminal carboxylic acid group (Krytox 157FSH (1)), chiefly in FC-72 (a mixture of perfluorohexanes). In particular, we were interested in whether or not proton transfer occurs, and if so, under what conditions in H-bonded complexes. Continuous variations experiments show that in FC-72 weaker bases (pyrazine, pyrimidine, and quinazoline) form 1:1 complexes with 1, whereas stronger bases (quinoline, pyridine, and isoquinoline) form 1:3 complexes. Ultraviolet and infrared spectral signatures reveal that the 1:1 complexes are molecular (B.HA) whereas the 1:3 complexes are ionic (BH+.A-HAHA). Infrared spectra of 1:3 ionic complexes are discussed in detail. Literature and experimental data on complexes between N-heterocyclic bases and carboxylic acids in a range of solvents are compiled to compare solvent effects on proton transfer. Polar solvents support ionic hydrogen bonds at a 1:1 mol ratio. In nonpolar organic solvents, ionic hydrogen bonds are only observed in complexes with 1:2 (base/acid) stoichiometries. In fluorous solvents, a larger excess of acid, 1:3, is necessary to facilitate proton transfer in hydrogen bonds between carboxylic acids and the bases studied.

  18. Csbnd N bond formation in alicyclic and heterocyclic compounds by amine-modified nanoclay

    NASA Astrophysics Data System (ADS)

    Zarnegar, Zohre; Alizadeh, Roghayeh; Ahmadzadeh, Majid; Safari, Javad

    2017-09-01

    In the current protocol, amine functionalized montmorillonite K10 nanoclay (NH2-MMT) was applied to catalyze the formation of Csbnd N bonds in the synthesis of azines and 2-aminothiazoles at room temperature. In comparison with the current methods of Csbnd N bond formation, this approach displays specific advantages include atom economy, clean conversion, design for energy efficiency, the use of nontoxic and heterogeneous catalyst, higher purity and yields, safer solvent and reagents for this organic transformation.

  19. Ru-Catalyzed Dehydrogenative C-O Bond Formation with Anilines and Phenols.

    PubMed

    Heitz, Christophe; Jones, Alexander W; Oezkaya, Bünyamin S; Bub, Christina L; Louillat-Habermeyer, Marie-Laure; Wagner, Victoria; Patureau, Frederic W

    2016-12-12

    The Ru catalyzed cross-dehydrogenative C-O bond formation between anilines and phenols is described and discussed. The exclusive C-O versus C-N bond-formation selectivity, moreover in the absence of chelating-assisting directing groups and while leaving the N-H position untouched, is a remarkable feature of this metal-catalyzed radical cross-dehydrogenative coupling. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Insights into the spontaneity of hydrogen bond formation between formic acid and phthalimide derivatives.

    PubMed

    Júnior, Rogério V A; Moura, Gustavo L C; Lima, Nathalia B D

    2016-11-01

    We evaluated a group of phthalimide derivatives, which comprise a convenient test set for the study of the multiple factors involved in the energetics of hydrogen bond formation. Accordingly, we carried out quantum chemical calculations on the hydrogen bonded complexes formed between a sample of phthalimide derivatives with formic acid with the intent of identifying the most important electronic and structural factors related to how their strength and spontaneity vary across the series. The geometries of all species considered were fully optimized at DFT B3LYP/6-31++G(d,p), RM1, RM1-DH2, and RM1-D3H4 level, followed by frequency calculations to determine their Gibbs free energies of hydrogen bond formation using Gaussian 2009 and MOPAC 2012. Our results indicate that the phthalimide derivatives that form hydrogen bond complexes most favorably, have in their structures only one C=O group and at least one NH group. On the other hand, the phthalimide derivatives predicted to form hydrogen bonds least favorably, possess in their structures two carbonyl groups, C=O, and no NH group. The ability to donate electrons and simultaneously receive one acidic hydrogen is the most important property related to the spontaneity of hydrogen bond formation. We further chose two cyclic compounds, phthalimide and isoindolin-1-one, in which to study the main changes in molecular, structural and spectroscopic properties as related to the formation of hydrogen bonds. Thus, the greatest ability of the isoindolin-1-one compound in forming hydrogen bonds is evidenced by the larger effect on the structural, vibrational, and chemical shifts properties associated with the O-H group. In summary, the electron-donating ability of the hydrogen bond acceptor emerged as the most important property differentiating the spontaneity of hydrogen bond formation in this group of complexes.

  1. Reactivity of the zwitterionic ligand EtNHC(S)Ph2P[double bond, length as m-dash]NPPh2C(S)NEt towards [Ru3(CO)12]. Sulfur transfer and ligand fragmentation leading to the methideylamide [-N(Et)-CH(R)-] micro3-bridging moiety.

    PubMed

    Delferro, Massimiliano; Pattacini, Roberto; Cauzzi, Daniele; Graiff, Claudia; Terenghi, Mattia; Predieri, Giovanni; Tiripicchio, Antonio

    2009-01-21

    The reaction of EtNHC(S)Ph2P[double bond, length as m-dash]NP+Ph2C(S)N(-)Et (HEtSNS) with [Ru3(CO)12] has been carried out under two different experimental conditions: in the first case [Ru3(CO)12], previously turned into the labile intermediate [Ru3(CO)10(CH3CN)2], afforded, at room temperature in dichloromethane, the trinuclear clusters [Ru3(CO)11(CNEt)] (1), [Ru3(CO)9(micro-H)[(micro-S:kappa-P)Ph2PN[double bond, length as m-dash]PPh2C(S)NEt

  2. Mechanisms of hydrogen bond formation between ionic liquids and cellulose and the influence of water content.

    PubMed

    Rabideau, Brooks D; Ismail, Ahmed E

    2015-02-28

    We study the dynamics of the formation of multiple hydrogen bonds between ionic liquid anions and cellulose using molecular dynamics simulations. We examine fifteen different ionic liquids composed of 1-alkyl-3-methylimidazolium cations ([Cnmim], n = 1, 2, 3, 4, 5) paired with either chloride, acetate or dimethylphosphate. We map the transitions of anions hydrogen bonded to cellulose into different bonding states. We find that increased tail length in the ionic liquids has only a very minor effect on these transitions, tending to slow the dynamics of the transitions and increasing the hydrogen bond lifetimes. Each anion can form up to four hydrogen bonds with cellulose. We find that this hydrogen bond "redundancy" leads to multiply bonded anions having lifetimes three to four times that of singly bound anions. Such redundant hydrogen bonds account for roughly half of all anion-cellulose hydrogen bonds. Additional simulations for [C2mim]Cl, [C2mim]Ac and [C2mim]DMP were performed at different water concentrations between 70 mol% and 90 mol%. It was found that water crowds the hydrogen bond-accepting sites of the anions, preventing interactions with cellulose. The more water that is present in the system, the more crowded these sites become. Thus, if a hydrogen bond between an anion and cellulose breaks, the likelihood that it will be replaced by a nearby water molecule increases as well. We show that the formation of these "redundant" hydrogen bonding states is greatly affected by the presence of water, leading to steep drops in hydrogen bonding between the anions and cellulose.

  3. Carbon–heteroatom bond formation catalysed by organometallic complexes

    PubMed Central

    Hartwig, John F.

    2010-01-01

    At one time the synthetic chemist’s last resort, reactions catalysed by transition metals are now the preferred method for synthesizing many types of organic molecule. A recent success in this type of catalysis is the discovery of reactions that form bonds between carbon and heteroatoms (such as nitrogen, oxygen, sulphur, silicon and boron) via complexes of transition metals with amides, alkoxides, thiolates, silyl groups or boryl groups. The development of these catalytic processes has been supported by the discovery of new elementary reactions that occur at metal–heteroatom bonds and by the identification of factors that control these reactions. Together, these findings have led to new synthetic processes that are in daily use and have formed a foundation for the development of processes that are likely to be central to synthetic chemistry in the future. PMID:18800130

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

    SciTech Connect

    Colby, Denise; Bergman, Robert; Ellman, Jonathan

    2010-05-13

    seen widespread success involves the use of a proximal heteroatom that serves as a directing group for the selective functionalization of a specific C-H bond. In a survey of examples of heteroatom-directed Rh catalysis, two mechanistically distinct reaction pathways are revealed. In one case, the heteroatom acts as a chelator to bind the Rh catalyst, facilitating reactivity at a proximal site. In this case, the formation of a five-membered metallacycle provides a favorable driving force in inducing reactivity at the desired location. In the other case, the heteroatom initially coordinates the Rh catalyst and then acts to stabilize the formation of a metal-carbon bond at a proximal site. A true test of the utility of a synthetic method is in its application to the synthesis of natural products or complex molecules. Several groups have demonstrated the applicability of C-H bond functionalization reactions towards complex molecule synthesis. Target-oriented synthesis provides a platform to test the effectiveness of a method in unique chemical and steric environments. In this respect, Rh-catalyzed methods for C-H bond functionalization stand out, with several syntheses being described in the literature that utilize C-H bond functionalization in a key step. These syntheses are highlighted following the discussion of the method they employ.

  5. Radical S-adenosylmethionine enzyme catalyzed thioether bond formation in sactipeptide biosynthesis.

    PubMed

    Flühe, Leif; Marahiel, Mohamed A

    2013-08-01

    Sactipeptides represent a new emerging class of ribosomally assembled and posttranslationally modified peptides that show diverse bioactivities. Their common hallmark is an intramolecular thioether bond that crosslink the sulfur atom of a cysteine residue with the α-carbon of an acceptor amino acid. This review summarizes recent achievements concerning the biosynthesis of sactipeptides in general and with special focus on the common enzymatic radical SAM mechanism leading to the thioether linkage formation. In addition this mechanism is compared to the mechanism of thioether bond formation during lanthipeptide biosynthesis and to other radical based thioether bond forming reactions.

  6. C-O bond Formation in a Microfluidic Reactor: High Yield SNAr Substitution of Heteroaryl Chlorides.

    PubMed

    Alam, Mohammad Parvez; Jagodzinska, Barbara; Campagna, Jesus; Spilman, Patricia; John, Varghese

    2016-05-11

    This study describes our development of a novel and efficient procedure for C-O bond formation under mild conditions, for coupling heteroaryl chlorides with phenols or primary aliphatic alcohols. We utilized a continuous-flow microfluidic reactor for C-O bond formation in electron-deficient pyrimidines and pyridines in a much more facile manner with a cleaner reaction profile, high yield, quick scalability and without the need for the transition metal catalyst. This approach can be of general utility to make C-O bond containing intermediates of industrial importance in a continuous and safe manner.

  7. Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape

    PubMed Central

    Manibog, Kristine; Sankar, Kannan; Kim, Sun-Ae; Zhang, Yunxiang; Jernigan, Robert L.; Sivasankar, Sanjeevi

    2016-01-01

    Classical cadherin cell–cell adhesion proteins are essential for the formation and maintenance of tissue structures; their primary function is to physically couple neighboring cells and withstand mechanical force. Cadherins from opposing cells bind in two distinct trans conformations: strand-swap dimers and X-dimers. As cadherins convert between these conformations, they form ideal bonds (i.e., adhesive interactions that are insensitive to force). However, the biophysical mechanism for ideal bond formation is unknown. Here, we integrate single-molecule force measurements with coarse-grained and atomistic simulations to resolve the mechanistic basis for cadherin ideal bond formation. Using simulations, we predict the energy landscape for cadherin adhesion, the transition pathways for interconversion between X-dimers and strand-swap dimers, and the cadherin structures that form ideal bonds. Based on these predictions, we engineer cadherin mutants that promote or inhibit ideal bond formation and measure their force-dependent kinetics using single-molecule force-clamp measurements with an atomic force microscope. Our data establish that cadherins adopt an intermediate conformation as they shuttle between X-dimers and strand-swap dimers; pulling on this conformation induces a torsional motion perpendicular to the pulling direction that unbinds the proteins and forms force-independent ideal bonds. Torsional motion is blocked when cadherins associate laterally in a cis orientation, suggesting that ideal bonds may play a role in mechanically regulating cadherin clustering on cell surfaces. PMID:27621473

  8. Cross-dehydrogenative coupling (CDC): exploring C-C bond formations beyond functional group transformations.

    PubMed

    Li, Chao-Jun

    2009-02-17

    Synthetic chemists aspire both to develop novel chemical reactions and to improve reaction conditions to maximize resource efficiency, energy efficiency, product selectivity, operational simplicity, and environmental health and safety. Carbon-carbon bond formation is a central part of many chemical syntheses, and innovations in these types of reactions will profoundly improve overall synthetic efficiency. This Account describes our work over the past several years to form carbon-carbon bonds directly from two different C-H bonds under oxidative conditions, cross-dehydrogenative coupling (CDC). We have focused most of our efforts on carbon-carbon bonds formed via the functionalization of sp(3) C-H bonds with other C-H bonds. In the presence of simple and cheap catalysts such as copper and iron salts and oxidants such as hydrogen peroxide, dioxygen, tert-butylhydroperoxide, and 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ), we can directly functionalize various sp(3) C-H bonds by other C-H bonds without requiring preactivation. We demonstrate (1) reaction of alpha-C-H bonds of nitrogen in amines, (2) reaction of alpha-C-H bonds of oxygen in ethers, (3) reaction of allylic and benzylic C-H bonds, and (4) reaction of alkane C-H bonds. These CDC reactions can tolerate a variety of functional groups, and some can occur under aqueous conditions. Depending on the specific transformation, we propose the in situ generation of different intermediates. These methods provide an alternative to the separate steps of prefunctionalization and defunctionalization that have traditionally been part of synthetic design. As a result, these methods will increase synthetic efficiencies at the most fundamental level. On an intellectual level, the development of C-C bond formations based on the reaction of only C-H bonds (possibly in water) challenges us to rethink some of the most fundamental concepts and theories regarding chemical reactivities. A successful reaction requires the

  9. Overview of the regulation of disulfide bond formation in Peptide and protein folding.

    PubMed

    Hidaka, Yuji

    2014-04-01

    Disulfide bonds play a critical role in the maintenance of the native conformation of proteins under thermodynamic control. In general, disulfide bond formation is associated with protein folding, and this restricts the formation of folding intermediates such as misbridged disulfide isomers or kinetically trapped conformations, which provide important information related to how proteins fold into their native conformation. Therefore, numerous studies have focused on the structural analysis of folding intermediates in vitro. However, isolating or trapping folding intermediates, as well as the entire proteins, including mutant proteins, is not an easy task. Several chemical methods have recently been developed for examining peptide and protein folding and for producing, e.g., intact, post-translationally modified, or kinetically trapped proteins, or proteins with misbridged disulfide bonds. This overview introduces chemical methods for regulating the formation of disulfide bonds of peptides and proteins in the context of the thermodynamic and kinetic control of peptide and protein folding.

  10. Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.

    PubMed

    Watanabe, Kazunori; Toh, Yukimatsu; Suto, Kyoko; Shimizu, Yoshihiro; Oka, Natsuhisa; Wada, Takeshi; Tomita, Kozo

    2007-10-18

    Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.

  11. Phase formation at bonded vanadium and stainless steel interfaces

    SciTech Connect

    Summers, T.S.E.

    1992-01-01

    The interface between vanadium bonded to stainless steel was studies to determine whether a brittle phase formed during three joining operations. Inertia friction welds between V and 21-6-9 stainless steel were examined using TEM. In the as-welded condition, a continuous, polygranular intermetallic layer about 0.25 {mu}m thick was present at the interface. This layer grew to about 50 {mu}m thick during heat treatment at 1000{degrees}C for two hours. Analysis of electron diffraction patterns confirmed that this intermetallic was the {omega} phase. The interface between vanadium and type 304, SANDVIK SAF 2205, and 21-6-9 stainless steel bonded by a co-extrusion process had intermetallic particles at the interface in the as-extruded condition. Heat treatment at 1000{degrees}C for two hours caused these particles to grow into continuous layers in all three cases. Based on the appearance, composition and hardness of this interfacial intermetallic, it was also concluded to be {omega} phase. Bonding V to type 430 stainless steel by co-extrusion caused V-rich carbides to form at the interface due to the higher concentration of C in the type 430 than in the other stainless steels investigated. The carbide particles initially present grew into a continuous layer during a two-hour heat treatment at 1000{degrees}C. Co-hipping 21-6-9 stainless steel tubing with V rod resulted in slightly more concentric specimens than the co-extruded ones, but a continuous layer of the {omega} phase formed during the hipping operation. This brittle layer could initiate failure during subsequent forming operations. The vanadium near the stainless steel interface in the co-extruded and co-hipped tubing in some cases was harder than before heat treatment. It was concluded that this hardening was due to thermal straining during cooling following heat treatment and that thermal strains might present a greater problem than seen here when longer tubes are used in actual applications.

  12. Catalytic asymmetric carbon-carbon bond formation via allylic alkylations with organolithium compounds.

    PubMed

    Pérez, Manuel; Fañanás-Mastral, Martín; Bos, Pieter H; Rudolph, Alena; Harutyunyan, Syuzanna R; Feringa, Ben L

    2011-05-01

    Carbon-carbon bond formation is the basis for the biogenesis of nature's essential molecules. Consequently, it lies at the heart of the chemical sciences. Chiral catalysts have been developed for asymmetric C-C bond formation to yield single enantiomers from several organometallic reagents. Remarkably, for extremely reactive organolithium compounds, which are among the most broadly used reagents in chemical synthesis, a general catalytic methodology for enantioselective C-C formation has proven elusive, until now. Here, we report a copper-based chiral catalytic system that allows carbon-carbon bond formation via allylic alkylation with alkyllithium reagents, with extremely high enantioselectivities and able to tolerate several functional groups. We have found that both the solvent used and the structure of the active chiral catalyst are the most critical factors in achieving successful asymmetric catalysis with alkyllithium reagents. The active form of the chiral catalyst has been identified through spectroscopic studies as a diphosphine copper monoalkyl species.

  13. Relationship between chemical structure and supramolecular effective molarity for formation of intramolecular H-bonds.

    PubMed

    Sun, Hongmei; Hunter, Christopher A; Navarro, Cristina; Turega, Simon

    2013-09-04

    Effective molarity (EM) is a key parameter that determines the efficiency of a range of supramolecular phenomena from the folding of macromolecules to multivalent ligand binding. Coordination complexes formed between zinc porphyrins equipped H-bond donor sites and pyridine ligands equipped with H-bond acceptor sites have allowed systematic quantification of EM values for the formation of intramolecular H-bonds in 240 different systems. The results provide insights into the relationship of EM to supramolecular architecture, H-bond strength, and solvent. Previous studies on ligands equipped with phosphonate diester and ether H-bond acceptors were inconclusive, but the experiments described here on ligands equipped with phosphine oxide, amide, and ester H-bond acceptors resolve these ambiguities. Chemical double-mutant cycles were used to dissect the thermodynamic contributions of individual H-bond interactions to the overall stabilities of the complexes and hence determine the values of EM, which fall in the range 1-1000 mM. Solvent has little effect on EM, and the values measured in toluene and 1,1,2,2-tetrachloroethane are similar. For H-bond acceptors that have similar geometries but different H-bond strengths (amide and ester), the values of EM are very similar. For H-bond acceptors that have different geometries but similar H-bond strengths (amide and phosphonate diester), there is little correlation between the values of EM. These results imply that supramolecular EMs are independent of solvent and intrinsic H-bond strength but depend on supramolecular architecture and geometric complementarity.

  14. C–F Bond Formation for the Synthesis of Aryl Fluorides

    PubMed Central

    Furuya, Takeru; Klein, Johannes E. M. N.

    2010-01-01

    A selection of carbon–fluorine bond-forming reactions is presented with particular focus on transition metal-mediated fluorination. A brief summary of conventional fluorination reactions is followed by a discussion of fluorination reactions mediated by palladium and silver. Investigations into the mechanism as well as the conceptual difficulty associated with transition metal-mediated carbon–fluorine bond formation are presented. PMID:20953341

  15. Site and bond selective H- formation in methylated pyrimidine bases driven by potassium molecule collisions

    NASA Astrophysics Data System (ADS)

    Ferreira da Silva, F.; Almeida, D.; Martins, G.; Nunes, Y.; Garcia, G.; Limão-Vieira, P.

    2012-11-01

    In this study we present for the first time site (N1-H / N3-H) and bond (N-H / C-H) selectivity of H- formation in 1-methylthymine, 3-methyluracil and deuterated thymine (C positions) triggered by potassium molecule collisions. By comparing the H loss of these molecules with H loss in thymine and uracil and setting the energy one can predict site and bond selectivity in these set of molecules.

  16. Hydrogen bond formation in regioselectively functionalized 3-mono-O-methyl cellulose.

    PubMed

    Kondo, Tetsuo; Koschella, Andreas; Heublein, Brigitte; Klemm, Dieter; Heinze, Thomas

    2008-10-13

    The hydrogen bond systems of cellulose and its derivatives are one of the most important factors regarding their physical- and chemical properties such as solubility, crystallinity, gel formation, and resistance to enzymatic degradation. In this paper, it was attempted to clarify the intra- and intermolecular hydrogen bond formation in regioselectively functionalized 3-mono-O-methyl cellulose (3MC). First, the 3MC was synthesized and the cast film thereof was characterized in comparison to 2,3-di-O-methyl cellulose, 6-mono-O-methyl cellulose, and 2,3,6-tri-O-methyl cellulose by means of wide angle X-ray diffraction (WAXD) and (13)C cross polarization/magic angle spinning NMR spectroscopy. Second, the hydrogen bonds in the 3MC film were analyzed by means of FTIR spectroscopy in combination with a curve fitting method. After deconvolution, the resulting two main bands (Fig. 3) indicated that instead of intramolecular hydrogen bonds between position OH-3 and O-5 another intramolecular hydrogen bond between OH-2 and OH-6 may exist. The large deconvoluted band at 3340cm(-1) referred to strong interchain hydrogen bonds involving the hydroxyl groups at C-6. The crystallinity of 54% calculated from the WAXD supports also the dependency of the usually observed crystallization in cellulose of the hydroxyl groups at C-6 to engage in interchain hydrogen bonding.

  17. Proximal Pocket Hydrogen Bonds Significantly Influence the Mechanism of Chloroperoxidase Compound I Formation.

    PubMed

    Pardillo, Armando D; Morozov, Alexander N; Chatfield, David C

    2015-10-01

    The influence of backbone hydrogen bonds to the sulfur atom of the proximal thiolate (NH···S hydrogen bonds) on the formation of compound I in chloroperoxidase is investigated with DFT calculations. Reaction profiles for the transformation of the ferric resting state into compound I in the presence of a peroxide substrate are calculated for a model system incorporating the heme and key proximal and distal amino acid residues. We find that NH···S hydrogen bonds (1) reduce the barrier for the formation of compound 0 by 7.6 kcal/mol, (2) increase the stability of compound 0 by 5.2 kcal/mol, (3) reduce the stability of compound I relative to compound 0 by 6.2 kcal/mol, and (4) reduce the stability of protonated compound 0, favoring a hybrid homo-heterolytic relative to a classic heterolytic mechanism for O-O bond scission. In general, the influence of the NH···S hydrogen bonds can be traced to a reduction in the pKa of the heme-bound substrate. We find that the hydrogen bond networks on the proximal and distal sides of the heme function together to modulate the mechanism of reaction. These results confirm and extend long-standing theories that the NH···S hydrogen bonds in heme thiolate proteins influence reactivity by tuning the thiolate "push" effect.

  18. Visualizing Au-Au bond formation in solution with femtosecond X-ray scattering

    NASA Astrophysics Data System (ADS)

    Adachi, Shin-Ichi

    2015-05-01

    Bond formation is an essential process in chemical reactions, but it is challenging to keep track of detailed atomic movements associated with bond formation because of its bimolecular nature. Bond formation in solution phase has been especially elusive because it is difficult to initiate and follow such diffusion-limited bimolecular processes with ultrafast time resolution. In this regard, a Au oligomer complex, [Au(CN)]n-, offers a good model system in which to study the dynamics of bond formation in solution.Using femtosecond time-resolved X-ray scattering, we successfully visualized in real time the birth of a gold trimer complex, [Au(CN)2-]3,that occurs via photoinduced formation of Au-Au covalent bonds. The ground state of the trimer has Au atoms that are weakly bound to each other by aurophilic interaction and aligned in a bent geometry. Upon photoexcitation, the ground state rapidly converts into the first excited state where Au-Au covalent bonds are formed among Au atoms aligned in a linear geometry. Subsequently, the state transforms to a triplet state in 1.6 ps while accompanying further contraction of Au-Au bonds by 0.1 Å. Later, the triplet state of the trimer converts to a tetramer on nanosecond time scale. This work showcases the possibility of tracking detailed structural changes in solution with sub-ps temporal and sub-angstrom spatial resolutions, thanks to the advent of X-ray free electron lasers and the advance of data analysis of time-resolved solution scattering data.

  19. Does silica surface catalyse peptide bond formation? New insights from first-principles calculations.

    PubMed

    Rimola, Albert; Tosoni, Sergio; Sodupe, Mariona; Ugliengo, Piero

    2006-01-16

    The role that silica surface could have played in prebiotic chemistry as a catalyst for peptide bond formation has been addressed at the B3LYP/6-31+G(d,p) level for a model reaction involving glycine and ammonia on a silica cluster mimicking an isolated terminal silanol group present at the silica surface. Hydrogen-bond complexation between glycine and the silanol is followed by the formation of the mixed surface anhydride Si(surf)-O-C(=O)-R, which has been suggested in the literature to activate the C=O bond towards nucleophilic attack by a second glycine molecule, here simulated by the simpler NH3 molecule. However, B3LYP/6-31+G(d,p) calculations show that formation of the surface mixed anhydride Si(surf)-O-C(=O)-R is disfavoured (delta(r)G298 approximately 6 kcal mol(-1)), and that the surface bond only moderately lowers the free-energy barrier of the nucleophilic attack responsible for peptide bond formation (deltaG298(double dagger) approximately 48 kcal mol(-1)) in comparison with the uncatalysed reaction (deltaG298(double dagger) approximately 52 kcal mol(-1)). A further decrease of the free-energy barrier of peptide bond formation (deltaG298(double dagger) approximately 41 kcal mol(-1)) is achieved by a single water molecule close to the reaction centre acting as a proton-transfer helper in the activated complex. A possible role of strained silica surface defects on the formation of the surface mixed anhydride Si(surf)-O-C(=O)-R has also been addressed.

  20. Disulfide bond formation in the Escherichia coli cytoplasm: an in vivo role reversal for the thioredoxins.

    PubMed Central

    Stewart, E J; Aslund, F; Beckwith, J

    1998-01-01

    Cytoplasmic proteins do not generally contain structural disulfide bonds, although certain cytoplasmic enzymes form such bonds as part of their catalytic cycles. The disulfide bonds in these latter enzymes are reduced in Escherichia coli by two systems; the thioredoxin pathway and the glutathione/glutaredoxin pathway. However, structural disulfide bonds can form in proteins in the cytoplasm when the gene (trxB) for the enzyme thioredoxin reductase is inactivated by mutation. This disulfide bond formation can be detected by assessing the state of the normally periplasmic enzyme alkaline phosphatase (AP) when it is localized to the cytoplasm. Here we show that the formation of disulfide bonds in cytoplasmic AP in the trxB mutant is dependent on the presence of two thioredoxins in the cell, thioredoxins 1 and 2, the products of the genes trxA and trxC, respectively. Our evidence supports a model in which the oxidized forms of these thioredoxins directly catalyze disulfide bond formation in cytoplasmic AP, a reversal of their normal role. In addition, we show that the recently discovered thioredoxin 2 can perform many of the roles of thioredoxin 1 in vivo, and thus is able to reduce certain essential cytoplasmic enzymes. Our results suggest that the three most effective cytoplasmic disulfide-reducing proteins are thioredoxin 1, thioredoxin 2 and glutaredoxin 1; expression of any one of these is sufficient to support aerobic growth. Our results help to explain how the reducing environment in the cytoplasm is maintained so that disulfide bonds do not normally occur. PMID:9755155

  1. Self-Assembly Can Direct Dynamic Covalent Bond Formation toward Diversity or Specificity.

    PubMed

    Komáromy, Dávid; Stuart, Marc C A; Monreal Santiago, Guillermo; Tezcan, Meniz; Krasnikov, Victor V; Otto, Sijbren

    2017-05-03

    With the advent of reversible covalent chemistry the study of the interplay between covalent bond formation and noncovalent interactions has become increasingly relevant. Here we report that the interplay between reversible disulfide chemistry and self-assembly can give rise either to molecular diversity, i.e., the emergence of a unprecedentedly large range of macrocycles or to molecular specificity, i.e., the autocatalytic emergence of a single species. The two phenomena are the result of two different modes of self-assembly, demonstrating that control over self-assembly pathways can enable control over covalent bond formation.

  2. The Disulfide Bond Formation Pathway Is Essential for Anaerobic Growth of Escherichia coli.

    PubMed

    Meehan, Brian M; Landeta, Cristina; Boyd, Dana; Beckwith, Jonathan

    2017-08-15

    Disulfide bonds are critical to the stability and function of many bacterial proteins. In the periplasm of Escherichia coli, intramolecular disulfide bond formation is catalyzed by the two-component disulfide bond forming (DSB) system. Inactivation of the DSB pathway has been shown to lead to a number of pleotropic effects, although cells remain viable under standard laboratory conditions. However, we show here that dsb strains of E. coli reversibly filament under aerobic conditions and fail to grow anaerobically unless a strong oxidant is provided in the growth medium. These findings demonstrate that the background disulfide bond formation necessary to maintain the viability of dsb strains is oxygen dependent. LptD, a key component of the lipopolysaccharide transport system, fails to fold properly in dsb strains exposed to anaerobic conditions, suggesting that these mutants may have defects in outer membrane assembly. We also show that anaerobic growth of dsb mutants can be restored by suppressor mutations in the disulfide bond isomerization system. Overall, our results underscore the importance of proper disulfide bond formation to pathways critical to E. coli viability under conditions where oxygen is limited.IMPORTANCE While the disulfide bond formation (DSB) system of E. coli has been studied for decades and has been shown to play an important role in the proper folding of many proteins, including some associated with virulence, it was considered dispensable for growth under most laboratory conditions. This work represents the first attempt to study the effects of the DSB system under strictly anaerobic conditions, simulating the environment encountered by pathogenic E. coli strains in the human intestinal tract. By demonstrating that the DSB system is essential for growth under such conditions, this work suggests that compounds inhibiting Dsb enzymes might act not only as antivirulents but also as true antibiotics. Copyright © 2017 American Society for

  3. Reactivity-dependent PCR: direct, solution-phase in vitro selection for bond formation.

    PubMed

    Gorin, David J; Kamlet, Adam S; Liu, David R

    2009-07-08

    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.

  4. Kinetics and intracellular location of intramolecular disulfide bond formation mediated by the cytoplasmic redox system encoded by vaccinia virus

    SciTech Connect

    Bisht, Himani; Brown, Erica; Moss, Bernard

    2010-03-15

    Poxviruses encode a redox system for intramolecular disulfide bond formation in cytoplasmic domains of viral proteins. Our objectives were to determine the kinetics and intracellular location of disulfide bond formation. The vaccinia virus L1 myristoylated membrane protein, used as an example, has three intramolecular disulfide bonds. Reduced and disulfide-bonded forms of L1 were distinguished by electrophoretic mobility and reactivity with monoclonal and polyclonal antibodies. Because disulfide bonds formed during 5 min pulse labeling with radioactive amino acids, a protocol was devised in which dithiothreitol was present at this step. Disulfide bond formation was detected by 2 min after removal of reducing agent and was nearly complete in 10 min. When the penultimate glycine residue was mutated to prevent myristoylation, L1 was mistargeted to the endoplasmic reticulum and disulfide bond formation failed to occur. These data suggested that viral membrane association was required for oxidation of L1, providing specificity for the process.

  5. Minimal transition state charge stabilization of the oxyanion during peptide bond formation by the ribosome.

    PubMed

    Carrasco, Nicolas; Hiller, David A; Strobel, Scott A

    2011-12-06

    Peptide bond formation during ribosomal protein synthesis involves an aminolysis reaction between the aminoacyl α-amino group and the carbonyl ester of the growing peptide via a transition state with a developing negative charge, the oxyanion. Structural and molecular dynamic studies have suggested that the ribosome may stabilize the oxyanion in the transition state of peptide bond formation via a highly ordered water molecule. To biochemically investigate this mechanistic hypothesis, we estimated the energetic contribution to catalytic charge stabilization of the oxyanion using a series of transition state mimics that contain different charge distributions and hydrogen bond potential on the functional group mimicking the oxyanion. Inhibitors containing an oxyanion mimic that carried a neutral charge and a mimic that preserved the negative charge but could not form hydrogen bonds had less than a 3-fold effect on inhibitor binding affinity. These observations argue that the ribosome provides minimal transition state charge stabilization to the oxyanion during peptide bond formation via the water molecule. This is in contrast to the substantial level of oxyanion stabilization provided by serine proteases. This suggests that the oxyanion may be neutralized via a proton shuttle, resulting in an uncharged transition state.

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

    PubMed

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

    2016-04-01

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

  7. Static and dynamic descriptions of bond breaking/formation: A complementary view?

    NASA Astrophysics Data System (ADS)

    Joubert, Laurent; Adamo, Carlo

    2005-12-01

    Ab initio molecular-dynamic simulations using density-functional theory and the recent atom-centered density-matrix propagation (ADMP) method were used to study the bond breaking and formation for a case-study substitution nucleophilic bimolecular reaction, namely, the Walden inversion. Using the atoms-in-molecule approach, we have performed a detailed analysis to investigate intra- and intermolecular charge transfer along the ADMP trajectory. These results were compared to those obtained considering a static approach, such as the intrinsic reaction path. In particular, the topological properties computed along the dynamic trajectory well evidence a stronger electron exchange tending to spontaneously maximize the rising covalent interaction. Furthermore, their analysis suggests that the bond formation mechanism involves a reactive intermediate with a bonding interaction stronger than in the final product.

  8. Disulfide Bond Formation and Activation of Escherichia coli β-Galactosidase under Oxidizing Conditions

    PubMed Central

    Seras-Franzoso, Joaquin; Affentranger, Roman; Ferrer-Navarro, Mario; Daura, Xavier; Villaverde, Antonio

    2012-01-01

    Escherichia coli β-galactosidase is probably the most widely used reporter enzyme in molecular biology, cell biology, and biotechnology because of the easy detection of its activity. Its large size and tetrameric structure make this bacterial protein an interesting model for crystallographic studies and atomic mapping. In the present study, we investigate a version of Escherichia coli β-galactosidase produced under oxidizing conditions, in the cytoplasm of an Origami strain. Our data prove the activation of this microbial enzyme under oxidizing conditions and clearly show the occurrence of a disulfide bond in the β-galactosidase structure. Additionally, the formation of this disulfide bond is supported by the analysis of a homology model of the protein that indicates that two cysteines located in the vicinity of the catalytic center are sufficiently close for disulfide bond formation. PMID:22286993

  9. Directed evolution of cytochrome c for carbon-silicon bond formation: Bringing silicon to life.

    PubMed

    Kan, S B Jennifer; Lewis, Russell D; Chen, Kai; Arnold, Frances H

    2016-11-25

    Enzymes that catalyze carbon-silicon bond formation are unknown in nature, despite the natural abundance of both elements. Such enzymes would expand the catalytic repertoire of biology, enabling living systems to access chemical space previously only open to synthetic chemistry. We have discovered that heme proteins catalyze the formation of organosilicon compounds under physiological conditions via carbene insertion into silicon-hydrogen bonds. The reaction proceeds both in vitro and in vivo, accommodating a broad range of substrates with high chemo- and enantioselectivity. Using directed evolution, we enhanced the catalytic function of cytochrome c from Rhodothermus marinus to achieve more than 15-fold higher turnover than state-of-the-art synthetic catalysts. This carbon-silicon bond-forming biocatalyst offers an environmentally friendly and highly efficient route to producing enantiopure organosilicon molecules. Copyright © 2016, American Association for the Advancement of Science.

  10. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery.

    PubMed

    Davidovich, Chen; Belousoff, Matthew; Bashan, Anat; Yonath, Ada

    2009-09-01

    Structural analysis supported by biochemical, mutagenesis and computational evidence, revealed that the contemporary ribosome's active site is a universal symmetrical pocket made of ribosomal RNA. This pocket seems to be the remnant of the proto-ribosome, a dimeric RNA assembly evolved by gene duplication, capable of autonomously catalyzing peptide bond formation and non-coded amino acid polymerization.

  11. Synthesis of Functionalized Dihydrobenzofurans by Direct Aryl C-O Bond Formation under Mild Conditions.

    PubMed

    Alvarado, Joseph; Fournier, Jeremy; Zakarian, Armen

    2016-09-12

    A method for the synthesis of dihydrobenzofurans by a direct aryl C-O bond formation is described. A mechanistic pathway for the reaction, distinct from previously described similar transformations, allows for mild reaction conditions that are expected to be compatible with functionalized substrates.

  12. Hydrogen bonding changes of internal water molecules in rhodopsin during metarhodopsin I and metarhodopsin II formation.

    PubMed Central

    Rath, P; Delange, F; Degrip, W J; Rothschild, K J

    1998-01-01

    Rhodopsin is a 7-helix, integral membrane protein found in the rod outer segments, which serves as the light receptor in vision. Light absorption by the retinylidene chromophore of rhodopsin triggers an 11-cis-->all-trans isomerization, followed by a series of protein conformational changes, which culminate in the binding and activation of the G-protein transducin by the metarhodopsin II (Meta II) intermediate. Fourier transform IR difference spectroscopy has been used to investigate the structural changes that water, as well as other OH- and NH-containing groups, undergo during the formation of the metarhodopsin I (Meta I) and Meta II intermediates. Bands associated with the OH stretch modes of water are identified by characteristic downshifts upon substitution of H2(18)O for H2O. Compared with earlier work, several negative bands associated with water molecules in unphotolysed rhodopsin were detected, which shift to lower frequencies upon formation of the Meta I and Meta II intermediates. These data indicate that at least one water molecule undergoes an increase in hydrogen bonding upon formation of the Meta I intermediate, while at least one other increases its hydrogen bonding during Meta II formation. Amino acid residue Asp-83, which undergoes a change in its hydrogen bonding during Meta II formation, does not appear to interact with any of the structurally active water molecules. Several NH and/or OH groups, which are inaccessible to hydrogen/deuterium exchange, also undergo alterations during Meta I and Meta II formation. PMID:9445403

  13. Interaction between the antibiotic spiramycin and a ribosomal complex active in peptide bond formation.

    PubMed

    Dinos, G; Synetos, D; Coutsogeorgopoulos, C

    1993-10-12

    The inhibition of peptide bond formation by spiramycin was studied in an in vitro system derived from Escherichia coli. Peptide bonds are formed between puromycin (S) and Ac-Phe-tRNA, which is a component of complex C, i.e., of the [Ac-Phe-tRNA-70S ribosome-poly(U)] complex, according to the puromycin reaction: C+S (Ks)<==>CS (k3)==>C'+P [Synetos, D., & Coutsogeorgopoulos, C. (1987) Biochim. Biophys. Acta 923, 275-285]. It is shown that spiramycin (A) reacts with complex C and forms the spiramycin complex C*A, which is inactive toward puromycin. C*A is the tightest complex formed between complex C and any of a number of antibiotics, such as chloramphenicol, blasticidin S, lincomycin, or sparsomycin. C*A remains stable following gel chromatography on Sephadex G-200 and sucrose gradient ultracentrifugation. Detailed kinetic study suggests that C*A is formed in a variation of a two-step mechanism in which the initial encounter complex CA is kinetically insignificant and C*A is the product of a conformational change of complex CA according to the equation, C+A (kassoc)<==>(kdissoc) C*A. The rate constants of this reaction (spiramycin reaction) are kassoc = 3.0 x 10(4) M-1 s-1 and kdissoc = 5.0 x 10(-5) s-1. Such values allow the classification of spiramycin as a slow-binding, slowly reversible inhibitor; they also lead to the calculation of an apparent overall dissociation constant equal to 1.8 nM for the C*A complex. Furthermore, they render spiramycin a useful tool in the study of antibiotic action on protein synthesis in vitro. Thus, the spiramycin reaction, in conjunction with the puromycin reaction, is applied (i) to detect a strong preincubation effect exerted by chloramphenicol and lincomycin (this effect constitutes further evidence that these two antibiotics combine with complex C as slow-binding inhibitors) and (ii) to determine the rate constant for the regeneration (k7 = 2.0 x 10(-3) s-1) of complex C from the sparsomycin complex C*I [Theocharis, D. A

  14. Nonnative Disulfide Bond Formation Activates the σ32-Dependent Heat Shock Response in Escherichia coli

    PubMed Central

    Müller, Alexandra; Hoffmann, Jörg H.; Meyer, Helmut E.; Narberhaus, Franz; Jakob, Ursula

    2013-01-01

    Formation of nonnative disulfide bonds in the cytoplasm, so-called disulfide stress, is an integral component of oxidative stress. Quantification of the extent of disulfide bond formation in the cytoplasm of Escherichia coli revealed that disulfide stress is associated with oxidative stress caused by hydrogen peroxide, paraquat, and cadmium. To separate the impact of disulfide bond formation from unrelated effects of these oxidative stressors in subsequent experiments, we worked with two complementary approaches. We triggered disulfide stress either chemically by diamide treatment of cells or genetically in a mutant strain lacking the major disulfide-reducing systems TrxB and Gor. Studying the proteomic response of E. coli exposed to disulfide stress, we found that intracellular disulfide bond formation is a particularly strong inducer of the heat shock response. Real-time quantitative PCR experiments showed that disulfide stress induces the heat shock response in E. coli σ32 dependently. However, unlike heat shock treatment, which induces these genes transiently, transcripts of σ32-dependent genes accumulated over time in disulfide stress-treated cells. Analyzing the stability of σ32, we found that this constant induction can be attributed to an increase of the half-life of σ32 upon disulfide stress. This is concomitant with aggregation of E. coli proteins treated with diamide. We conclude that oxidative stress triggers the heat shock response in E. coli σ32 dependently. The component of oxidative stress responsible for the induction of heat shock genes is disulfide stress. Nonnative disulfide bond formation in the cytoplasm causes protein unfolding. This stabilizes σ32 by preventing its DnaK- and FtsH-dependent degradation. PMID:23585533

  15. Influence of substituent effects on the formation of P···Cl pnicogen bonds or halogen bonds.

    PubMed

    Del Bene, Janet E; Alkorta, Ibon; Elguero, José

    2014-03-27

    Ab initio MP2/aug'-cc-pVTZ calculations have been carried out in search of equilibrium structures with P···Cl pnicogen bonds or halogen bonds on the potential energy surfaces H2FP:ClY for Y = F, NC, Cl, CN, CCH, CH3, and H. Three different types of halogen-bonded complexes with traditional, chlorine-shared, and ion-pair bonds have been identified. Two different pnicogen-bonded complexes have also been found on these surfaces. The most electronegative substituents F and NC form only halogen-bonded complexes, while the most electropositive substituents CH3 and H form only pnicogen-bonded complexes. The halogen-bonded complexes involving the less electronegative groups Cl and CN are more stable than the corresponding pnicogen-bonded complexes, while the pnicogen-bonded complexes with CCH are more stable than the corresponding halogen-bonded complex. Traditional halogen-bonded complexes are stabilized by charge transfer from the P lone pair to the Cl-A σ* orbital, where A is the atom of Y directly bonded to Cl. Charge transfer from the Cl lone pair to the P-F σ* orbital stabilizes pnicogen-bonded complexes. As a result, the H2FP unit becomes positively charged in halogen-bonded complexes and negatively charged in pnicogen-bonded complexes. Spin-spin coupling constants (1X)J(P-Cl) for complexes with traditional halogen bonds increase with decreasing P-Cl distance, reach a maximum value for complexes with chlorine-shared halogen bonds, and then decrease and change sign when the bond is an ion-pair bond. (1p)J(P-Cl) coupling constants across pnicogen bonds tend to increase with decreasing P-Cl distance.

  16. In situ observation of peptide bond formation at the water-air interface.

    PubMed

    Griffith, Elizabeth C; Vaida, Veronica

    2012-09-25

    We report unambiguous spectroscopic evidence of peptide bond formation at the air-water interface, yielding a possible mechanism providing insight into the formation of modern ribosomal peptide bonds, and a means for the emergence of peptides on early Earth. Protein synthesis in aqueous environments, facilitated by sequential amino acid condensation forming peptides, is a ubiquitous process in modern biology, and a fundamental reaction necessary in prebiotic chemistry. Such reactions, however, are condensation reactions, requiring the elimination of a water molecule for every peptide bond formed, and are thus unfavorable in aqueous environments both from a thermodynamic and kinetic point of view. We use the hydrophobic environment of the air-water interface as a favorable venue for peptide bond synthesis, and demonstrate the occurrence of this chemistry with in situ techniques using Langmuir-trough methods and infrared reflection absorption spectroscopy. Leucine ethyl ester (a small amino acid ester) first partitions to the water surface, then coordinates with Cu(2+) ions at the interface, and subsequently undergoes a condensation reaction selectively forming peptide bonds at the air-water interface.

  17. Evidence for chemical bond formation at rubber-brass interface: Photoelectron spectroscopy study of bonding interaction between copper sulfide and model molecules of natural rubber

    NASA Astrophysics Data System (ADS)

    Ozawa, Kenichi; Mase, Kazuhiko

    2016-12-01

    Strong adhesion between rubber and brass has been considered to arise mainly from the mechanical interaction, which is characterized by dendritic interlocking at the interface. In order to examine a possible contribution of the chemical interaction, chemical state analysis was carried out for model molecules of natural rubber (2-methyl-2-butene and isoprene) adsorbed on Cu2S, a key chemical species for adhesion, by means of photoelectron spectroscopy (PES). Absence of a C 1s PES component associated with C=C bonds and the appearance of adsorption-induced components in the S 2p region indicate that the molecules interact with the Cu2S surface via the C=C bond to form C-S covalent bonds. This proves that the chemical interaction certainly plays a role in rubber-brass adhesion along with the mechanical interaction.

  18. The transition state for formation of the peptide bond in the ribosome.

    PubMed

    Gindulyte, Asta; Bashan, Anat; Agmon, Ilana; Massa, Lou; Yonath, Ada; Karle, Jerome

    2006-09-05

    Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3' end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, E(a), is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be approximately 18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2' OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments.

  19. Bonding analyses, formation energies, and vibrational properties of M-R2dtc complexes (M=Ag(I), Ni(II), Cu(II), or Zn(II)).

    PubMed

    Georgieva, I; Trendafilova, N

    2007-12-20

    the nu(CS) band: It is very high for the unidentate dtc bonding (nu(C=S)) and low for the bidentate bonding (nuas(CS)).

  20. Spontaneous intermolecular amide bond formation between side chains for irreversible peptide targeting.

    PubMed

    Zakeri, Bijan; Howarth, Mark

    2010-04-07

    Peptides and synthetic peptide-like molecules are powerful tools for analysis and control of biological function. One major limitation of peptides is the instability of their interactions with biomolecules, because of the limited accessible surface area for noncovalent interactions and the intrinsic flexibility of peptides. Peptide tags are nonetheless fundamental for protein detection and purification, because their small size minimizes the perturbation to protein function. Here we have designed a 16 amino acid peptide that spontaneously forms an amide bond to a protein partner, via reaction between lysine and asparagine side chains. This depended upon splitting a pilin subunit from a human pathogen, Streptococcus pyogenes, which usually undergoes intramolecular amide bond formation to impart mechanical and proteolytic stability to pili. Reaction of the protein partner was able to proceed to 98% conversion. The amide bond formation was independent of redox state and occurred at pH 5-8. The reaction was efficient in phosphate buffered saline and a wide range of biological buffers. Surprisingly, amide bond formation occurred at a similar rate at 4 and 37 degrees C. Both peptide and protein partners are composed of the regular 20 amino acids and reconstituted efficiently inside living E. coli. Labeling also showed high specificity on the surface of mammalian cells. Irreversible targeting of a peptide tag may have application in bioassembly, in cellular imaging, and to lock together proteins subject to high biological forces.

  1. ONIOM and ab-initio calculations on the mechanism of uncatalyzed peptide bond formation.

    PubMed

    Monajemi, Hadieh; Daud, Mohammad Noh; Mohd Zain, Sharifuddin; Wan Abdullah, Wan Ahmad Tajuddin

    2012-12-01

    Finding a proper transition structure for the peptide bond formation process can lead one to a better understanding of the role of ribosome in catalyzing this reaction. Using computer simulations, we performed the potential energy surface scan on the ester bond dissociation of P-site aminoacyl-tRNA and the peptide bond formation of P-site and A-site amino acids. The full fragments of initiator tRNA(i)(met) and elongator tRNA(phe) are attached to both cognate and non-cognate amino acids as the P-site substrate. The A-site amino acid for all four calculations is methionine. We used ONIOM calculations to reduce the computational cost. Our study illustrates the reduced rate of peptide bond formation for misacylated tRNA(i)(met) in the absence of ribosomal bases. The misacylated elongator tRNA(phe), however, did not show any difference in its PES compared with that for the phe-tRNA(phe). This demonstrates the structural specification of initiator tRNA(i)(met) for the amino acids side chain.

  2. Tribromobenzene on Cu(111): Temperature-dependent formation of halogen-bonded, organometallic, and covalent nanostructures

    SciTech Connect

    Fan, Qitang; Wang, Tao; Zhu, Junfa; Liu, Liming; Zhao, Jin; Gottfried, J. Michael

    2015-03-14

    The temperature-controlled surface-assisted synthesis of halogen bonded, organometallic, and covalent nanostructures based on 1,3,5-tribromo-benzene (TriBB) was studied with scanning tunneling microscopy and X-ray photoemission spectroscopy in ultrahigh vacuum. Vapor deposition of TriBB onto a Cu(111) surface held at 90 K leads to the formation of large domains of a honeycomb-like organic monolayer structure stabilized by triangular nodes with Br⋯Br intermolecular bonds. Upon annealing the organic monolayer to ∼140 K, a new hexagonal close-packed structure with intact TriBB molecules connected by Cu adatoms is formed. Further warming up the sample to 300 K gives rise to the scission of C–Br bonds and formation of C–Cu–C bonds between phenyl fragments such that stable dendritic organometallic networks are formed. Larger islands of organometallic networks are obtained by maintaining the temperature of Cu(111) at 420 K during deposition of TriBB. Simultaneously, large islands of Br atoms are formed around the organometallic networks. Annealing the more extended organometallic network (prepared at 420 K) to 520 K leads to the formation of a branched covalent organic framework (COF) which comprises structural elements of porous graphene and is surrounded by Br islands. These organometallic networks and COFs appear as small dendritic and branched domains, most likely due to the steric influence exerted by the Br islands.

  3. Tribromobenzene on Cu(111): Temperature-dependent formation of halogen-bonded, organometallic, and covalent nanostructures

    NASA Astrophysics Data System (ADS)

    Fan, Qitang; Wang, Tao; Liu, Liming; Zhao, Jin; Zhu, Junfa; Gottfried, J. Michael

    2015-03-01

    The temperature-controlled surface-assisted synthesis of halogen bonded, organometallic, and covalent nanostructures based on 1,3,5-tribromo-benzene (TriBB) was studied with scanning tunneling microscopy and X-ray photoemission spectroscopy in ultrahigh vacuum. Vapor deposition of TriBB onto a Cu(111) surface held at 90 K leads to the formation of large domains of a honeycomb-like organic monolayer structure stabilized by triangular nodes with Br⋯Br intermolecular bonds. Upon annealing the organic monolayer to ˜140 K, a new hexagonal close-packed structure with intact TriBB molecules connected by Cu adatoms is formed. Further warming up the sample to 300 K gives rise to the scission of C-Br bonds and formation of C-Cu-C bonds between phenyl fragments such that stable dendritic organometallic networks are formed. Larger islands of organometallic networks are obtained by maintaining the temperature of Cu(111) at 420 K during deposition of TriBB. Simultaneously, large islands of Br atoms are formed around the organometallic networks. Annealing the more extended organometallic network (prepared at 420 K) to 520 K leads to the formation of a branched covalent organic framework (COF) which comprises structural elements of porous graphene and is surrounded by Br islands. These organometallic networks and COFs appear as small dendritic and branched domains, most likely due to the steric influence exerted by the Br islands.

  4. Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure on phosphodiester bond formation

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; KAMALUDDIN

    1989-01-01

    The formation of oligomers from deoxynucleotides, catalyzed by Na(+)-montmorillonite, was investigated with special attention given to the effect of the monomer structure on the phosphodiester bond formation. It was found that adenine deoxynucleotides bind more strongly to montmorillonite than do the corresponding ribonucleotides and thymidine nucleotides. Tetramers of 2-prime-dpA were detected in the reaction of 2-prime-d-5-prime-AMP with a water-soluble carbodiimide EDAC in the presence of Na(+)-montmorillonite, illustrating the possible role of minerals in the formation of biopolymers on the primitive earth.

  5. Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure on phosphodiester bond formation

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; KAMALUDDIN

    1989-01-01

    The formation of oligomers from deoxynucleotides, catalyzed by Na(+)-montmorillonite, was investigated with special attention given to the effect of the monomer structure on the phosphodiester bond formation. It was found that adenine deoxynucleotides bind more strongly to montmorillonite than do the corresponding ribonucleotides and thymidine nucleotides. Tetramers of 2-prime-dpA were detected in the reaction of 2-prime-d-5-prime-AMP with a water-soluble carbodiimide EDAC in the presence of Na(+)-montmorillonite, illustrating the possible role of minerals in the formation of biopolymers on the primitive earth.

  6. Identification of disulfide bond formation between MitoNEET and glutamate dehydrogenase 1.

    PubMed

    Roberts, Morgan E; Crail, Jacquelyn P; Laffoon, Megan M; Fernandez, William G; Menze, Michael A; Konkle, Mary E

    2013-12-17

    MitoNEET is a protein that was identified as a drug target for diabetes, but its cellular function as well as its role in diabetes remains elusive. Protein pull-down experiments identified glutamate dehydrogenase 1 (GDH1) as a potential binding partner. GDH1 is a key metabolic enzyme with emerging roles in insulin regulation. MitoNEET forms a covalent complex with GDH1 through disulfide bond formation and acts as an activator. Proteomic analysis identified the specific cysteine residues that participate in the disulfide bond. This is the first report that effectively links mitoNEET to activation of the insulin regulator GDH1.

  7. Identification of non-heme diiron proteins that catalyze triple bond and epoxy group formation.

    PubMed

    Lee, M; Lenman, M; Banaś, A; Bafor, M; Singh, S; Schweizer, M; Nilsson, R; Liljenberg, C; Dahlqvist, A; Gummeson, P O; Sjödahl, S; Green, A; Stymne, S

    1998-05-08

    Acetylenic bonds are present in more than 600 naturally occurring compounds. Plant enzymes that catalyze the formation of the Delta12 acetylenic bond in 9-octadecen-12-ynoic acid and the Delta12 epoxy group in 12,13-epoxy-9-octadecenoic acid were characterized, and two genes, similar in sequence, were cloned. When these complementary DNAs were expressed in Arabidopsis thaliana, the content of acetylenic or epoxidated fatty acids in the seeds increased from 0 to 25 or 15 percent, respectively. Both enzymes have characteristics similar to the membrane proteins containing non-heme iron that have histidine-rich motifs.

  8. Preferential formation of the different hydrogen bonds and their effects in tetrahydrofuran and tetrahydropyran microhydrated complexes.

    PubMed

    Vallejos, Margarita M; Peruchena, Nélida M

    2012-04-26

    The role of cycloether-water (c-w) and water-water (w-w) hydrogen bonds (H-bonds) on the stability of the tetrahydrofuran THF/(H(2)O)(n) and the tetrahydropyran THP/(H(2)O)(n) complexes with n = 1-4 was investigated herein using the density functional and ab initio methods and the atoms in molecules theory. Geometry optimizations for these complexes were carried out with various possible initial guess structures. It was revealed that the major contributions of the mono and dihydrated complexes came from c-w H-bonds. A competition between c-w and w-w H-bonds contribution was observed for trihydrated complexes. For most of tetrahydrated complexes, the inter-water H-bonds provided the greatest contribution, whereas the c-w contributions were small but not negligible. It was confirmed that to produce a hydrophobic hydration of cycloethers, the C-H···O(w) H-bond should be associated with a network of H-bonds that connects both portions of the solute, through the formation of a bifunctional H-bond. A linear correlation is obtained for the sum of electron density at the bond critical points (ρ(b)) with the interaction energy (ΔE) and with the solute-solvent interaction energy (ΔE(s-w)) of the microhydrated complexes. In addition, a new way to estimate the energetic contribution as well as the preferential formation of the different H-bonds based completely on ρ(b) was found. Even more, it allows to differentiate the contribution from c-w interactions in both hydrophilic and hydrophobic contributions, it is therefore a useful tool for studying the hydration of large biomolecules. The analysis of the modifications in the atomic and group properties brought about by successive addition of H(2)O molecules allowed to pinpoint the atoms or molecular groups that undergo the greatest changes in electron population and energetic stabilization. It was identified that the remarkable stabilization of the water oxygen atoms is crucial for the stabilization of the complexes.

  9. Exploration of an imide capture/N,N-acyl shift sequence for asparagine native peptide bond formation.

    PubMed

    Mhidia, Reda; Boll, Emmanuelle; Fécourt, Fabien; Ermolenko, Mikhail; Ollivier, Nathalie; Sasaki, Kaname; Crich, David; Delpech, Bernard; Melnyk, Oleg

    2013-06-15

    Imide capture of a C-terminal peptidylazide with a side-chain thioacid derivative of an N-terminally protected aspartyl peptide leads to the formation of an imide bond bringing the two peptide ends into close proximity. Unmasking of the N(α) protecting group and intramolecular acyl migration results in the formation of a native peptide bond to asparagine.

  10. A mechanistic study supports a two-step mechanism for peptide bond formation on the ribosome.

    PubMed

    Byun, Byung Jin; Kang, Young Kee

    2013-09-28

    We report the feasible pathways of the quaternary model system for the ribosome-catalyzed PT reaction obtained by density functional calculations. Our results indicate that the step from the reactant complex to the first six-membered TS involving a proton shuttle via the 2'-OH of the P-site A76 in the stepwise pathway is the most favored rate-limiting step in solution. It is found that the C-O3' bond-breaking of A76 is not significant but the C-N bond formation with a tetrahedral intermediate occurs in the rate-limiting step and that the fast breakdown of the C-O3' bond is followed in the second transition state. These are consistent with recent kinetic experiments.

  11. 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 π-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

  12. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

    PubMed Central

    Serganov, Alexander; Keiper, Sonja; Malinina, Lucy; Tereshko, Valentina; Skripkin, Eugene; Höbartner, Claudia; Polonskaia, Anna; Phan, Anh Tuân; Wombacher, Richard; Micura, Ronald; Dauter, Zbigniew; Jäschke, Andres; Patel, Dinshaw J

    2015-01-01

    The majority of structural efforts addressing RNA’s catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions. PMID:15723077

  13. A two-step chemical mechanism for ribosome-catalysed peptide bond formation.

    PubMed

    Hiller, David A; Singh, Vipender; Zhong, Minghong; Strobel, Scott A

    2011-07-17

    The chemical step of natural protein synthesis, peptide bond formation, is catalysed by the large subunit of the ribosome. Crystal structures have shown that the active site for peptide bond formation is composed entirely of RNA. Recent work has focused on how an RNA active site is able to catalyse this fundamental biological reaction at a suitable rate for protein synthesis. On the basis of the absence of important ribosomal functional groups, lack of a dependence on pH, and the dominant contribution of entropy to catalysis, it has been suggested that the role of the ribosome is limited to bringing the substrates into close proximity. Alternatively, the importance of the 2'-hydroxyl of the peptidyl-transfer RNA and a Brønsted coefficient near zero have been taken as evidence that the ribosome coordinates a proton-transfer network. Here we report the transition state of peptide bond formation, based on analysis of the kinetic isotope effect at five positions within the reaction centre of a peptidyl-transfer RNA mimic. Our results indicate that in contrast to the uncatalysed reaction, formation of the tetrahedral intermediate and proton transfer from the nucleophilic nitrogen both occur in the rate-limiting step. Unlike in previous proposals, the reaction is not fully concerted; instead, breakdown of the tetrahedral intermediate occurs in a separate fast step. This suggests that in addition to substrate positioning, the ribosome is contributing to chemical catalysis by changing the rate-limiting transition state.

  14. Is the peptide bond formation activated by Cu(2+) interactions? Insights from density functional calculations.

    PubMed

    Rimola, A; Rodríguez-Santiago, L; Ugliengo, P; Sodupe, M

    2007-05-24

    The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.

  15. Conceptual quantum chemical analysis of bonding and noncovalent interactions in the formation of frustrated Lewis pairs.

    PubMed

    Skara, Gabriella; Pinter, Balazs; Top, Jens; Geerlings, Paul; De Proft, Frank; De Vleeschouwer, Freija

    2015-03-27

    The contributions of covalent and noncovalent interactions to the formation of classical adducts of bulky Lewis acids and bases and frustrated Lewis pairs (FLPs) were scrutinized by using various conceptual quantum chemical techniques. Significantly negative complexation energies were calculated for fourteen investigated Lewis pairs containing bases and acids with substituents of various sizes. A Ziegler-Rauk-type energy decomposition analysis confirmed that two types of Lewis pairs can be distinguished on the basis of the nature of the primary interactions between reactants; dative-bond formation and concomitant charge transfer from the Lewis base to the acid is the dominant and most stabilizing factor in the formation of Lewis acid-base adducts, whereas weak interactions are the main thermodynamic driving force (>50 %) for FLPs. Moreover, the ease and extent of structural deformation of the monomers appears to be a key component in the formation of the former type of Lewis pairs. A Natural Orbital for Chemical Valence (NOCV) analysis, which was used to visualize and quantify the charge transfer between the base and the acid, clearly showed the importance and lack of this type of interaction for adducts and FLPs, respectively. The Noncovalent Interaction (NCI) method revealed several kinds of weak interactions between the acid and base components, such as dispersion, π-π stacking, C-H⋅⋅⋅π interaction, weak hydrogen bonding, halogen bonding, and weak acid-base interactions, whereas the Quantum Theory of Atoms in Molecules (QTAIM) provided further conceptual insight into strong acid-base interactions.

  16. Enhancement of peptide bond formation by polyribonucleotides on clay surfaces in fluctuating environments

    NASA Technical Reports Server (NTRS)

    White, D. H.; Erickson, J. C.

    1981-01-01

    The selective effects of polyribonucleotides on the formation of glycine peptide bonds in glycine on clay surfaces are investigated as a model for a template mechanism for the effects of polynucleotides on peptide bond formation. Free oligoglycine yields were determined for the cycling reaction of glycine in the presence and absence of clay and polyribonucleotides or polydeoxyribonucleotides. The polyribonucleotides are observed to lead to increases of up to fourfold increases in oligoglycine formed, with greater enhancements for poly-G nucleotides than for poly-A, poly-U and poly-C, indicating a codonic bias. Polydeoxyribonucleotides are found to provide no enhancement in peptide formation rates, and yields were also greatly reduced in the absence of clay. A mechanism for peptide synthesis is proposed which involves the activation of glycine on the clay surface, followed by the formation of esters between glycine and the 2-prime OH groups of the polyribonucleotide and peptide bonds between adjacent amino acyl esters. It is pointed out that if this mechanism is correct, it may provide a basis for a direct template translation process, which would produce a singlet genetic code.

  17. Enhancement of peptide bond formation by polyribonucleotides on clay surfaces in fluctuating environments

    NASA Technical Reports Server (NTRS)

    White, D. H.; Erickson, J. C.

    1981-01-01

    The selective effects of polyribonucleotides on the formation of glycine peptide bonds in glycine on clay surfaces are investigated as a model for a template mechanism for the effects of polynucleotides on peptide bond formation. Free oligoglycine yields were determined for the cycling reaction of glycine in the presence and absence of clay and polyribonucleotides or polydeoxyribonucleotides. The polyribonucleotides are observed to lead to increases of up to fourfold increases in oligoglycine formed, with greater enhancements for poly-G nucleotides than for poly-A, poly-U and poly-C, indicating a codonic bias. Polydeoxyribonucleotides are found to provide no enhancement in peptide formation rates, and yields were also greatly reduced in the absence of clay. A mechanism for peptide synthesis is proposed which involves the activation of glycine on the clay surface, followed by the formation of esters between glycine and the 2-prime OH groups of the polyribonucleotide and peptide bonds between adjacent amino acyl esters. It is pointed out that if this mechanism is correct, it may provide a basis for a direct template translation process, which would produce a singlet genetic code.

  18. Self-assembly of nanostructured materials through irreversible covalent bond formation.

    PubMed

    Baek, Kangkyun; Hwang, Ilha; Roy, Indranil; Shetty, Dinesh; Kim, Kimoon

    2015-08-18

    Over the past decades, numerous efforts have been devoted to synthesizing nanostructured materials with specific morphology because their size and shape play an important role in determining their functions. Self-assembly using weak and reversible interactions or bonds has provided synthetic routes toward various nanostructures because it allows a "self-checking" and "self-error-correcting" process under thermodynamic control. By contrast, the use of irreversible covalent bonds, despite the potential to generate more robust structures, has been disfavored in the synthesis of well-defined nanomaterials largely due to the lack of such self-error-correcting mechanisms. To date, the use of irreversible bonds is largely limited to covalent fixation of preorganized building blocks on a template, which, though capable of producing shape-persistent and robust nanostructured materials, often requires a laborious and time-consuming multistep processes. Constructing well-defined nanostructures by self-assembly using irreversible covalent bonds without help of templates or preorganization of components remains a challenge. This Account describes our recent discoveries and progress in self-assembly of nanostructured materials through strong, practically irreversible covalent bond formation and their applications in various areas including drug delivery, anticancer therapy, and heterogeneous catalysis. The key to the success of this approach is the use of rationally designed building blocks possessing multiple in-plane reactive groups at the periphery. These blocks can then successfully grow into flat oligomeric patches through irreversible covalent bond formation without the aid of preorganization or templates. Further growth of the patches with or without curvature generation drives the system to the formation of polymer nanocapsules, two-dimensional (2D) polymer films, and toroidal nanotubular microrings. Remarkably, the final morphology can be specified by a few simple

  19. Practical carbon–carbon bond formation from olefins through nickel-catalyzed reductive olefin hydrocarbonation

    PubMed Central

    Lu, Xi; Xiao, Bin; Zhang, Zhenqi; Gong, Tianjun; Su, Wei; Yi, Jun; Fu, Yao; Liu, Lei

    2016-01-01

    New carbon–carbon bond formation reactions expand our horizon of retrosynthetic analysis for the synthesis of complex organic molecules. Although many methods are now available for the formation of C(sp2)–C(sp3) and C(sp3)–C(sp3) bonds via transition metal-catalyzed cross-coupling of alkyl organometallic reagents, direct use of readily available olefins in a formal fashion of hydrocarbonation to make C(sp2)–C(sp3) and C(sp3)–C(sp3) bonds remains to be developed. Here we report the discovery of a general process for the intermolecular reductive coupling of unactivated olefins with alkyl or aryl electrophiles under the promotion of a simple nickel catalyst system. This new reaction presents a conceptually unique and practical strategy for the construction of C(sp2)–C(sp3) and C(sp3)–C(sp3) bonds without using any organometallic reagent. The reductive olefin hydrocarbonation also exhibits excellent compatibility with varieties of synthetically important functional groups and therefore, provides a straightforward approach for modification of complex organic molecules containing olefin groups. PMID:27033405

  20. Active Site Formation, Not Bond Kinetics, Limits Adhesion Rate between Human Neutrophils and Immobilized Vascular Cell Adhesion Molecule 1

    PubMed Central

    Waugh, Richard E.; Lomakina, Elena B.

    2009-01-01

    Abstract The formation of receptor ligand bonds at the interface between different cells and between cells and substrates is a widespread phenomenon in biological systems. Physical measurements of bond formation rates between cells and substrates have been exploited to increase our understanding of the biophysical mechanisms that regulate bond formation at interfaces. Heretofore, these measurements have been interpreted in terms of simple bimolecular reaction kinetics. Discrepancies between this simple framework and the behavior of neutrophils adhering to surfaces expressing vascular cell adhesion molecule 1 (VCAM-1) motivated the development of a new kinetic framework in which the explicit formation of active bond formation sites (reaction zones) are a prerequisite for bond formation to occur. Measurements of cells interacting with surfaces having a wide range of VCAM-1 concentrations, and for different durations of contact, enabled the determination of novel kinetic rate constants for the formation of reaction zones and for the intrinsic bond kinetics. Comparison of these rates with rates determined previously for other receptor-ligand pairs points to a predominant role of extrinsic factors such as surface topography and accessibility of active molecules to regions of close contact in determining forward rates of bond formation at cell interfaces. PMID:19134479

  1. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.

    PubMed

    Simonović, Miljan; Steitz, Thomas A

    2009-01-01

    The ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mRNA into specific proteins. Its highly conserved active site, the peptidyl-transferase center (PTC), is located on the large (50S) ribosomal subunit and is comprised solely of rRNA, which makes the ribosome the only natural ribozyme with polymerase activity. The last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire ribosome. This has allowed studies on the mechanism of peptide bond formation at a level of detail that surpasses that for the classical protein enzymes. A current understanding of the mechanism of the ribosome-catalyzed peptide bond formation is the focus of this review. Implications on the mechanism of peptide release are discussed as well.

  2. Chemical methods and approaches to the regioselective formation of multiple disulfide bonds.

    PubMed

    Shimamoto, Shigeru; Katayama, Hidekazu; Okumura, Masaki; Hidaka, Yuji

    2014-04-01

    Disulfide-bond formation plays an important role in the stabilization of the native conformation of peptides and proteins. In the case of multidisulfide-containing peptides and proteins, numerous folding intermediates are produced, including molecules that contain non-native and native disulfide bonds during in vitro folding. These intermediates can frequently be trapped covalently during folding and subsequently analyzed. The structural characterization of these kinetically trapped disulfide intermediates provides a clue to understanding the oxidative folding pathway. To investigate the folding of disulfide-containing peptides and proteins, in this unit, chemical methods are described for regulating regioselective disulfide formation (1) by using a combination of several types of thiol protecting groups, (2) by incorporating unique SeCys residues into a protein or peptide molecule, and (3) by combining with post-translational modification.

  3. Formation of a covalent bond between a polyoxometalate and silica covered by SiH moieties.

    PubMed

    Grinenval, Eva; Bayard, François; Basset, Jean-Marie; Lefebvre, Frédéric

    2014-02-17

    Dehydroxylated silica was modified by grafting reaction of SiHMe2 groups. The resulting material was fully characterized by various methods including infrared and one- and two-dimensional solid-state NMR. This material can further react with dehydrated polyoxometalates (POMs), leading to the formation of a covalent POM-silica bond. In the case of H4PVMo11O40, hydrogen released during the grafting reaction reduces the POM. This leads to the formation of two surface species, which can be reoxidized in presence of oxygen. In the case of H3PW12O40, no reduction is observed. In both cases, (29)Si solid-state NMR shows that the POM-silica bond is covalent, contrary to what was observed in homogeneous conditions.

  4. Cytosolic disulfide bond formation in cells infected with large nucleocytoplasmic DNA viruses.

    PubMed

    Hakim, Motti; Fass, Deborah

    2010-10-01

    Proteins that have evolved to contain stabilizing disulfide bonds generally fold in a membrane-delimited compartment in the cell [i.e., the endoplasmic reticulum (ER) or the mitochondrial intermembrane space (IMS)]. These compartments contain sulfhydryl oxidase enzymes that catalyze the pairing and oxidation of cysteine residues. In contrast, most proteins in a healthy cytosol are maintained in reduced form through surveillance by NADPH-dependent reductases and the lack of sulfhydryl oxidases. Nevertheless, one of the core functionalities that unify the broad and diverse set of nucleocytoplasmic large DNA viruses (NCLDVs) is the ability to catalyze disulfide formation in the cytosol. The substrates of this activity are proteins that contribute to the assembly, structure, and infectivity of the virions. If the last common ancestor of NCLDVs was present during eukaryogenesis as has been proposed, it is interesting to speculate that viral disulfide bond formation pathways may have predated oxidative protein folding in intracellular organelles.

  5. Formation of activated biomolecules by condensation on mineral surfaces--a comparison of peptide bond formation and phosphate condensation.

    PubMed

    Georgelin, Thomas; Jaber, Maguy; Bazzi, Houssein; Lambert, Jean-François

    2013-10-01

    Many studies have reported condensation reactions of prebiotic molecules, such as the formation of peptide bonds between amino acids, to occur to some degree on mineral surfaces. We have studied several such reactions on the same divided silica. When drying steps are applied, the equilibria of peptide formation from glycine, and polyphosphate formation from monophosphate, are displaced to the right because these reactions are dehydrating condensations, accompanied by the emission of water. In contrast, the equilibrium of AMP dismutation is not significantly favored by drying. The silica surface plays little role (if any) in the thermochemistry of the condensation reactions, but is does play a significant kinetic role by acting as a catalyst, lowering the condensation temperatures with respect to bulk solids. Of course, the surface also catalyzes the inverse hydrolysis reactions.

  6. Novel tetranuclear copper |2 + 4| cubanes resulting from unprecedented C-O bond formation cum dearomatization.

    PubMed

    Kumar, Amit; Pandey, Rampal; Gupta, Rakesh Kumar; Dubey, Mrigendra; Pandey, Daya Shankar

    2014-09-21

    Novel tetranuclear copper |2 + 4| cubanes 1 and 2 have been synthesized from the reaction of hydrated copper salts/precursors with N,O chelating β-ketoaminato ligands. Creation of 1 and 2 occurs by in situ generation of the tridentate chelating species HL1O(2-) via copper mediated C-O bond formation and dearomatization of H3L1, while anhydrous salts afforded mononuclear complex 3.

  7. Real-time electrochemical monitoring of covalent bond formation in solution via nanoparticle-electrode collisions.

    PubMed

    Li, Da; Kong, Na; Liu, Jingquan; Wang, Hongbin; Barrow, Colin J; Zhang, Shusheng; Yang, Wenrong

    2015-11-25

    We describe an alternative electrochemical technique to monitor covalent bond formation in real-time using nanoparticle-electrode collisions. The method is based on recognising the redox current when MP-11 functionalised chemical reduced graphene oxide (rGO) nanosheets collide with Lomant's reagent modified gold microelectrode. This facile and highly sensitive monitoring method can be useful for investigating the fundamental of single-molecule reactions.

  8. Oxidation-Reduction Condensation of Diazaphosphites for Carbon-Heteroatom Bond Formation Based on Mitsunobu Mechanism.

    PubMed

    Huang, Hai; Kang, Jun Yong

    2017-02-03

    An efficient oxidation-reduction condensation reaction of diazaphosphites with various nonacidic pronucleophiles in the presence of DIAD as a weak oxidant has been developed for carbon-heteroatom bond formation. This mild process affords structurally diverse tertiary amines, secondary amines, esters, ethers, and thioethers in moderate to excellent yields. The selective synthesis of secondary amines from primary amines has been achieved. Importantly, a practical application to the synthesis of antiparkinsonian agent piribedil has been demonstrated.

  9. Nickel-catalyzed Csp2-Csp3 bond formation by carbon-fluorine activation.

    PubMed

    Sun, Alex D; Leung, Kaylyn; Restivo, Anita D; LaBerge, Nicole A; Takasaki, Harumi; Love, Jennifer A

    2014-03-10

    We report herein a general catalytic method for Csp(2)-Csp(3) bond formation through C-F activation. The process uses an inexpensive nickel complex with either diorganozinc or alkylzinc halide reagents, including those with β-hydrogen atoms. A variety of fluorine substitution patterns and functional groups can be readily incorporated. Sequential reactions involving different precatalysts and coupling partners permit the synthesis of densely functionalized fluorinated building blocks.

  10. Renewable Formate from C-H Bond Formation with CO2: Using Iron Carbonyl Clusters as Electrocatalysts.

    PubMed

    Loewen, Natalia D; Neelakantan, Taruna V; Berben, Louise A

    2017-09-19

    As a society, we are heavily dependent on nonrenewable petroleum-derived fuels and chemical feedstocks. Rapid depletion of these resources and the increasingly evident negative effects of excess atmospheric CO2 drive our efforts to discover ways of converting excess CO2 into energy dense chemical fuels through selective C-H bond formation and using renewable energy sources to supply electrons. In this way, a carbon-neutral fuel economy might be realized. To develop a molecular or heterogeneous catalyst for C-H bond formation with CO2 requires a fundamental understanding of how to generate metal hydrides that selectively donate H(-) to CO2, rather than recombining with H(+) to liberate H2. Our work with a unique series of water-soluble and -stable, low-valent iron electrocatalysts offers mechanistic and thermochemical insights into formate production from CO2. Of particular interest are the nitride- and carbide-containing clusters: [Fe4N(CO)12](-) and its derivatives and [Fe4C(CO)12](2-). In both aqueous and mixed solvent conditions, [Fe4N(CO)12](-) forms a reduced hydride intermediate, [H-Fe4N(CO)12](-), through stepwise electron and proton transfers. This hydride selectively reacts with CO2 and generates formate with >95% efficiency. The mechanism for this transformation is supported by crystallographic, cyclic voltammetry, and spectroelectrochemical (SEC) evidence. Furthermore, installation of a proton shuttle onto [Fe4N(CO)12](-) facilitates proton transfer to the active site, successfully intercepting the hydride intermediate before it reacts with CO2; only H2 is observed in this case. In contrast, isoelectronic [Fe4C(CO)12](2-) features a concerted proton-electron transfer mechanism to form [H-Fe4C(CO)12](2-), which is selective for H2 production even in the presence of CO2, in both aqueous and mixed solvent systems. Higher nuclearity clusters were also studied, and all are proton reduction electrocatalysts, but none promote C-H bond formation. Thermochemical

  11. Investigation of enzymatic C-P bond formation using multiple quantum HCP nuclear magnetic resonance spectroscopy.

    PubMed

    Hu, Kaifeng; Werner, Williard J; Allen, Kylie D; Wang, Susan C

    2015-04-01

    The biochemical mechanism for the formation of the C-P-C bond sequence found in l-phosphinothricin, a natural product with antibiotic and herbicidal activity, remains unclear. To obtain further insight into the catalytic mechanism of PhpK, the P-methyltransferase responsible for the formation of the second C-P bond in l-phosphinothricin, we utilized a combination of stable isotopes and two-dimensional nuclear magnetic resonance spectroscopy. Exploiting the newly emerged Bruker QCI probe (Bruker Corp.), we specifically designed and ran a (13) C-(31) P multiple quantum (1) H-(13) C-(31) P (HCP) experiment in (1) H-(31) P two-dimensional mode directly on a PhpK-catalyzed reaction mixture using (13) CH3 -labeled methylcobalamin as the methyl group donor. This method is particularly advantageous because minimal sample purification is needed to maximize product visualization. The observed 3:1:1:3 multiplet specifically and unequivocally illustrates direct bond formation between (13) CH3 and (31) P. Related nuclear magnetic resonance experiments based upon these principles may be designed for the study of enzymatic and/or synthetic chemical reaction mechanisms.

  12. Active site remodelling accompanies thioester bond formation in the SUMO E1.

    PubMed

    Olsen, Shaun K; Capili, Allan D; Lu, Xuequan; Tan, Derek S; Lima, Christopher D

    2010-02-18

    E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 A, respectively. These structures show that side chain contacts to ATP.Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.

  13. Active site remodelling accompanies thioester bond formation in the SUMO E1

    SciTech Connect

    Olsen, Shaun K.; Capili, Allan D.; Lu, Xuequan; Tan, Derek S.; Lima, Christopher D.

    2010-03-30

    E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 {angstrom}, respectively. These structures show that side chain contacts to ATP-Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.

  14. Computational study of peptide bond formation in the gas phase through ion-molecule reactions.

    PubMed

    Redondo, Pilar; Martínez, Henar; Cimas, Alvaro; Barrientos, Carmen; Largo, Antonio

    2013-08-21

    A computational study of peptide bond formation from gas-phase ion-molecule reactions has been carried out. We have considered the reaction between protonated glycine and neutral glycine, as well as the reaction between two neutral glycine molecules for comparison purposes. Two different mechanisms, concerted and stepwise, were studied. Both mechanisms show significant energy barriers for the neutral reaction. The energy requirements for peptide bond formation are considerably reduced upon protonation of one of the glycine molecules. For the reaction between neutral glycine and N-protonated glycine the lowest energy barrier is observed for the concerted mechanism. For the reaction between neutral glycine and protonated glycine at carbonyl oxygen, the preferred mechanism is the stepwise one, with a relatively small energy barrier (23 kJ mol(-1) at 0 K) and leading to the lowest-lying protonated glycylglycine isomer. In the case that the reaction could be initiated by protonated glycine at hydroxyl oxygen the process would be barrier-free and clearly exothermic. In that case peptide bond formation could take place even under interstellar conditions if glycine is present in space.

  15. Peptide bond formation does not involve acid-base catalysis by ribosomal residues.

    PubMed

    Bieling, Peter; Beringer, Malte; Adio, Sarah; Rodnina, Marina V

    2006-05-01

    Ribosomes catalyze the formation of peptide bonds between aminoacyl esters of transfer RNAs within a catalytic center composed of ribosomal RNA only. Here we show that the reaction of P-site formylmethionine (fMet)-tRNA(fMet) with a modified A-site tRNA substrate, Phelac-tRNA(Phe), in which the nucleophilic amino group is replaced with a hydroxyl group, does not show the pH dependence observed with small substrate analogs such as puromycin and hydroxypuromycin. This indicates that acid-base catalysis by ribosomal residues is not important in the reaction with the full-size substrate. Rather, the ribosome catalyzes peptide bond formation by positioning the tRNAs, or their 3' termini, through interactions with rRNA that induce and/or stabilize a pH-insensitive conformation of the active site and provide a preorganized environment facilitating the reaction. The rate of peptide bond formation with unmodified Phe-tRNA(Phe) is estimated to be >300 s(-1).

  16. Formation of metalsbnd F bonds during frictional sliding: Influence of water and applied load

    NASA Astrophysics Data System (ADS)

    Shen, J. T.; Pei, Y. T.; De Hosson, J. Th. M.

    2016-04-01

    Effects of water lubrication and applied load on the formation of PTFE transfer films and metalsbnd F bonds during sliding when PTFE filled composites sliding against steel and Al2O3 are investigated. In water-lubricated conditions, XPS analysis reveals that a thin layer of water molecules at the sliding interface inhibits the formation of PTFE transfer films and Alsbnd F bonds on the Al2O3 ball, leading to a detrimental effect on the tribo-performance. Under various normal loads in dry sliding condition, it is found that the smearing of PTFE onto the wear surface of the composite and the transfer of PTFE onto the surface of the steel counterpart are stimulated by a high load. During sliding, the contact pressure is found to be the driving force of the reaction between steel and PTFE. It is concluded that under various loads, the total amount of PTFE transfer films has a larger impact on the friction behavior than the formation of Fesbnd F bonds.

  17. Peptide bond formation of alanine on silica and alumina surfaces as a catalyst

    NASA Astrophysics Data System (ADS)

    Sánchez Arenillas, M.; Mateo-Martí, E.

    2012-09-01

    Polymerization of amino acids has been important for the origin of life because the peptides may have been the first self-replicating systems. The amino acid concentrations in the oceans may have been too diluted in the early phases of the Earth. The formation of the biopolymers could have been due to the catalytic action of various minerals (such as silica or alumina). Our work is based on the comparison between alumina and silica minerals with and without prior activation of their silanol groups for the formation of peptide bonds using alanina like amino acid which it is the simplest quiral amino acid.

  18. Palladium(II)-Catalyzed C-H Bond Activation/C-C and C-O Bond Formation Reaction Cascade: Direct Synthesis of Coumestans.

    PubMed

    Neog, Kashmiri; Borah, Ashwini; Gogoi, Pranjal

    2016-12-02

    A palladium catalyzed cascade reaction of 4-hydroxycoumarins and in situ generated arynes has been developed for the direct synthesis of coumestans. This cascade strategy proceeds via C-H bond activation/C-O and C-C bond formations in a single reaction vessel. This methodology affords moderate to good yields of coumestans and is tolerant of a variety of functional groups including halide. The methodology was applied to the synthesis of natural product flemichapparin C.

  19. Effects of flowable resin on bond strength and gap formation in Class I restorations.

    PubMed

    Miguez, Patricia A; Pereira, Patricia N R; Foxton, Richard M; Walter, Ricardo; Nunes, Mauro F; Swift, Edward J

    2004-11-01

    This study measured resin/dentin bond strengths and evaluated gap formation at the pulpal floor of occlusal composite restorations using a flowable resin as a liner with either bulk or incremental placement of the restorative composite. Class I occlusal preparations were made in 16 extracted molars, and were randomly divided into two groups for restoration using either One-Step adhesive (OS, BISCO) and Renew composite (RW, BISCO) or OptiBond SOLO adhesive (SOLO, Kerr) and Herculite XRV composite (XRV, Kerr). A flowable resin [AEliteFlo (AE, BISCO) or Revolution (RV, Kerr)] was applied as a liner in half of the specimens of each group. The lined and unlined groups were restored with composite cured in bulk, or cured in 1.5 mm increments. After 24 h in water, the teeth were sectioned into 0.7-mm thick slabs and were examined with an optical microscope (400 x) to determine the presence of internal resin-dentin gaps. The gap-free specimens were trimmed and were subjected to microtensile bond strength testing. Specimens that contained gaps had Knoop hardness of the restorative material measured. All incrementally filled restorations were well adapted to the pulpal floor but nearly all bulk-cured specimens had gaps between the flowable and the hybrid composites. The use of a flowable resin increased the bond strength of OS, but not SOLO. The incremental technique prevented gap formation regardless of the use of a flowable resin. In contrast, the use of a flowable composite did not guarantee gap-free restorations or improved bond strength of resin to dentin in bulk-filled restorations.

  20. Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation

    PubMed Central

    Schmidt, Brian J.; Papin, Jason A.; Lawrence, Michael B.

    2009-01-01

    The interaction of proteins at cellular interfaces is critical for many biological processes, from intercellular signaling to cell adhesion. For example, the selectin family of adhesion receptors plays a critical role in trafficking during inflammation and immunosurveillance. Quantitative measurements of binding rates between surface-constrained proteins elicit insight into how molecular structural details and post-translational modifications contribute to function. However, nano-scale transport effects can obfuscate measurements in experimental assays. We constructed a biophysical simulation of the motion of a rigid microsphere coated with biomolecular adhesion receptors in shearing flow undergoing thermal motion. The simulation enabled in silico investigation of the effects of kinetic force dependence, molecular deformation, grouping adhesion receptors into clusters, surface-constrained bond formation, and nano-scale vertical transport on outputs that directly map to observable motions. Simulations recreated the jerky, discrete stop-and-go motions observed in P-selectin/PSGL-1 microbead assays with physiologic ligand densities. Motion statistics tied detailed simulated motion data to experimentally reported quantities. New deductions about biomolecular function for P-selectin/PSGL-1 interactions were made. Distributing adhesive forces among P-selectin/PSGL-1 molecules closely grouped in clusters was necessary to achieve bond lifetimes observed in microbead assays. Initial, capturing bond formation effectively occurred across the entire molecular contour length. However, subsequent rebinding events were enhanced by the reduced separation distance following the initial capture. The result demonstrates that vertical transport can contribute to an enhancement in the apparent bond formation rate. A detailed analysis of in silico motions prompted the proposition of wobble autocorrelation as an indicator of two-dimensional function. Insight into two-dimensional bond

  1. Mechanisms of formation of chemical bonding and defect formation at the a-SiO 2 /BaTiO 3 interfaces

    SciTech Connect

    Kimmel, Anna V.; Sushko, Peter V.

    2015-10-28

    The structure and mechanisms of bonding and defect formation at the interfaces between amorphous silica (a-SiO2) and BaTiO3(0 0 1) were investigated using ab initio molecular dynamics. It was found that the nature of interfacial bonds crucially depends on the BaTiO3 surface termination. In particular, the interface between silica and TiO2-terminated BaTiO3 (BTO) slab is characterised by strong covalent Ti–O–Si bonds, while the interface between silica and BaO-terminated BTO demonstrates ionic character of interfacial bonds and exhibits bond instability. In both cases, the dynamics of oxygen species at oxide interfaces is a driving force of the formation of interfacial bonds and defects.

  2. Understanding bond formation in polar one-step reactions. Topological analyses of the reaction between nitrones and lithium ynolates.

    PubMed

    Roca-López, David; Polo, Victor; Tejero, Tomás; Merino, Pedro

    2015-04-17

    The mechanism of the reaction between nitrones and lithium ynolates has been studied using DFT methods at the M06-2X/cc-pVTZ/PCM=THF level. After the formation of a starting complex an without energy barrier, in which the lithium atom is coordinated to both nitrone and ynolate, the reaction takes place in one single kinetic step through a single transition structure. However, the formation of C-C and C-O bonds takes place sequentially through a typical two-stage, one-step process. A combined study of noncovalent interactions (NCIs) and electron localization function (ELFs) of selected points along the intrinsic reaction coordinate (IRC) of the reaction confirmed that, in the transition structure, only the C-C bond is being formed to some extent, whereas an electrostatic interaction is present between carbon and oxygen atoms previous to the formation of the C-O bond. Indeed, the formation of the second C-O bond only begins when the first C-C bond is completely formed without formation of any intermediate. Once the C-C bond is formed and before the C-O bond formation starts the RMS gradient norm dips, approaching but not reaching 0, giving rise to a hidden intermediate.

  3. Enthalpy of hydrogen bond formation in a protein-ligand binding reaction.

    PubMed Central

    Connelly, P R; Aldape, R A; Bruzzese, F J; Chambers, S P; Fitzgibbon, M J; Fleming, M A; Itoh, S; Livingston, D J; Navia, M A; Thomson, J A

    1994-01-01

    Parallel measurements of the thermodynamics (free-energy, enthalpy, entropy and heat-capacity changes) of ligand binding to FK506 binding protein (FKBP-12) in H2O and D2O have been performed in an effort to probe the energetic contributions of single protein-ligand hydrogen bonds formed in the binding reactions. Changing tyrosine-82 to phenylalanine in FKBP-12 abolishes protein-ligand hydrogen bond interactions in the FKBP-12 complexes with tacrolimus or rapamycin and leads to a large apparent enthalpic stabilization of binding in both H2O and D2O. High-resolution crystallographic analysis reveals that two water molecules bound to the tyrosine-82 hydroxyl group in unliganded FKBP-12 are displaced upon formation of the protein-ligand complexes. A thermodynamic analysis is presented that suggests that the removal of polar atoms from water contributes a highly unfavorable enthalpy change to the formation of C=O...HO hydrogen bonds as they occur in the processes of protein folding and ligand binding. Despite the less favorable enthalpy change, the entropic advantage of displacing two water molecules upon binding leads to a slightly more favorable free-energy change of binding in the reactions with wild-type FKBP-12. Images PMID:7510408

  4. Building Bridges: Biocatalytic C–C-Bond Formation toward Multifunctional Products

    PubMed Central

    2016-01-01

    Carbon–carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C–C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C–C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C–C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand. PMID:27398261

  5. Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products.

    PubMed

    Schmidt, Nina G; Eger, Elisabeth; Kroutil, Wolfgang

    2016-07-01

    Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.

  6. Enthalpy of hydrogen bond formation in a protein-ligand binding reaction.

    PubMed

    Connelly, P R; Aldape, R A; Bruzzese, F J; Chambers, S P; Fitzgibbon, M J; Fleming, M A; Itoh, S; Livingston, D J; Navia, M A; Thomson, J A

    1994-03-01

    Parallel measurements of the thermodynamics (free-energy, enthalpy, entropy and heat-capacity changes) of ligand binding to FK506 binding protein (FKBP-12) in H2O and D2O have been performed in an effort to probe the energetic contributions of single protein-ligand hydrogen bonds formed in the binding reactions. Changing tyrosine-82 to phenylalanine in FKBP-12 abolishes protein-ligand hydrogen bond interactions in the FKBP-12 complexes with tacrolimus or rapamycin and leads to a large apparent enthalpic stabilization of binding in both H2O and D2O. High-resolution crystallographic analysis reveals that two water molecules bound to the tyrosine-82 hydroxyl group in unliganded FKBP-12 are displaced upon formation of the protein-ligand complexes. A thermodynamic analysis is presented that suggests that the removal of polar atoms from water contributes a highly unfavorable enthalpy change to the formation of C=O...HO hydrogen bonds as they occur in the processes of protein folding and ligand binding. Despite the less favorable enthalpy change, the entropic advantage of displacing two water molecules upon binding leads to a slightly more favorable free-energy change of binding in the reactions with wild-type FKBP-12.

  7. B-H activation and H-H formation: two consecutive heterolytic processes on an osmium-hydrogensulfide bond.

    PubMed

    Esteruelas, Miguel A; López, Ana M; Mora, Malka; Oñate, Enrique

    2013-09-04

    Heterolytic B-H activation and H-H formation on an Os-SH bond give borylthiolate-dihydrogen derivatives. These species exchange borylthiol by borane to afford σ-borane derivatives or release H2 and undergo a hydride-boryl exchange to yield boryl-hydrogensulfide complexes depending on the boryl group bonded to the sulfur atom.

  8. Formation and stability of As-H bonds in H-implanted GaAs

    SciTech Connect

    Stein, H.J.

    1990-01-01

    The chemical bonding and isochronal annealing of H implanted into GaAs at 80 K has been investigated by infrared absorption measurements. Based upon the frequency shift when deuterium is substituted for H, and an equivalent band formation in InAs, assignment of a new band at 2029 cm{sup {minus}1} is made to As-H centers. Bonding of H at interstitial As of and As-vacancy pair which anneals between 150 and 250K is suggested as the structure for the defect. A previously-reported absorption band at 1834 cm{sup {minus}1} assigned to Ga-H centers in H-implanted GaAS increase in intensity when H is released from As-H centers. 15 refs., 5 figs.

  9. Reversible extrusion and uptake of HCl molecules by crystalline solids involving coordination bond cleavage and formation.

    PubMed

    Mínguez Espallargas, Guillermo; Brammer, Lee; van de Streek, Jacco; Shankland, Kenneth; Florence, Alastair J; Adams, Harry

    2006-08-02

    Yellow crystalline salts (3-XpyH)2[CuCl4] (3-XpyH = 3-halopyridinium, X = Cl, Br) lose HCl upon exposure to air in an open vessel, yielding quantitatively blue crystalline coordination compounds [CuCl2(3-Xpy)2]. The reaction is prevented if the vessel is sealed, but can be driven forward under such conditions by providing a trapping agent for HCl, such as an aqueous solution of AgNO3. The reaction requires cleavage of Cu-Cl and N-H bonds and formation of Cu-N bonds. The metal coordination geometry also changes from distorted tetrahedral to square planar. Remarkably, the reaction is fully reversible upon exposure of the blue coordination compound to vapor from a concentrated aqueous solution of HCl, and the initial yellow crystalline salt results. The structural changes occurring in these reactions have been followed by X-ray powder diffraction, including Rietveld refinement, of the crystal structures.

  10. Hydrogen bond formations between pyrazine and formic acid and between pyrazine and trichloroacetic acid.

    PubMed

    Osaki, Tomoe; Suzuki, Yoshio; Hirokawa, Kenichiro; Shimada, Ryoichi

    2011-12-01

    The hydrogen bond formations between pyrazine and formic acids and between pyrazine and trichloroacetic acids were studied through observation of the Raman and infrared spectra for mixture of pyrazine and formic acid and also mixture of pyrazine and trichloroacetic acid at 77 K. It was observed that the mutual exclusion principle held for the Raman and infrared spectra of both mixtures, even for the spectra of the samples whose mixing mole ratio of acids was very low. This fact clearly indicates that the hydrogen bonded molecule does not exist in the form of formic acid-pyrazine or trichloroacetic acid-pyrazine whose geometry belongs to the Cs point group, but exists in the form of formic acid-pyrazine-formic acid or trichloroacetic acid-pyrazine-trichloroacetic acid belonging to the C(i) point group. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. C–C Bond formation catalyzed by natural gelatin and collagen proteins

    PubMed Central

    Kühbeck, Dennis; Bijayi Dhar, Basab; Schön, Eva-Maria; Cativiela, Carlos; Gotor-Fernández, Vicente

    2013-01-01

    Summary The activity of gelatin and collagen proteins towards C–C bond formation via Henry (nitroaldol) reaction between aldehydes and nitroalkanes is demonstrated for the first time. Among other variables, protein source, physical state and chemical modification influence product yield and kinetics, affording the nitroaldol products in both aqueous and organic media under mild conditions. Significantly, the scale-up of the process between 4-nitrobenzaldehyde and nitromethane is successfully achieved at 1 g scale and in good yield. A comparative kinetic study with other biocatalysts shows an increase of the first-order rate constant in the order chitosan < gelatin < bovine serum albumin (BSA) < collagen. The results of this study indicate that simple edible gelatin can promote C–C bond forming reactions under physiological conditions, which may have important implications from a metabolic perspective. PMID:23843902

  12. Hydrophilicity of dentin bonding systems influences in vitro Streptococcus mutans biofilm formation.

    PubMed

    Brambilla, Eugenio; Ionescu, Andrei; Mazzoni, Annalisa; Cadenaro, Milena; Gagliani, Massimo; Ferraroni, Monica; Tay, Franklin; Pashley, David; Breschi, Lorenzo

    2014-08-01

    To evaluate in vitro Streptococcus mutans (S. mutans) biofilm formation on the surface of five light-curing experimental dental bonding systems (DBS) with increasing hydrophilicity. The null hypothesis tested was that resin chemical composition and hydrophilicity does not affect S. mutans biofilm formation. Five light-curing versions of experimental resin blends with increasing hydrophilicity were investigated (R1, R2, R3, R4 and R5). R1 and R2 contained ethoxylated BisGMA/TEGDMA or BisGMA/TEGDMA, respectively, and were very hydrophobic, were representative of pit-and-fissure bonding agents. R3 was representative of a typical two-step etch-and-rinse adhesive, while R4 and R5 were very hydrophilic resins analogous to self-etching adhesives. Twenty-eight disks were prepared for each resin blend. After a 24h-incubation at 37°C, a multilayer monospecific biofilm of S. mutans was obtained on the surface of each disk. The adherent biomass was determined using the MTT assay and evaluated morphologically with confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). R2 and R3 surfaces showed the highest biofilm formation while R1 and R4 showed a similar intermediate biofilm formation. R5 was more hydrophilic and acidic and was significantly less colonized than all the other resins. A significant quadratic relationship between biofilm formation and hydrophilicity of the resin blends was found. CLSM and SEM evaluation confirmed MTT assay results. The null hypothesis was rejected since S. mutans biofilm formation was influenced by hydrophilicity, surface acidity and chemical composition of the experimental resins. Further studies using a bioreactor are needed to confirm the results and clarify the role of the single factors. Copyright © 2014 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  13. Hydrophilicity of dentin bonding systems influences in vitro Streptococcus mutans biofilm formation

    PubMed Central

    Brambilla, Eugenio; Ionescu, Andrei; Mazzoni, Annalisa; Cadenaro, Milena; Gagliani, Massimo; Ferraroni, Monica; Tay, Franklin; Pashley, David; Breschi, Lorenzo

    2014-01-01

    Objectives To evaluate in vitro Streptococcus mutans (S. mutans) biofilm formation on the surface of five light-curing experimental dental bonding systems (DBS) with increasing hydrophilicity. The null hypothesis tested was that resin chemical composition and hydrophilicity does not affect S. mutans biofilm formation. Methods Five light-curing versions of experimental resin blends with increasing hydrophilicity were investigated (R1, R2, R3, R4 and R5). R1 and R2 contained ethoxylated BisGMA/TEGDMA or BisGMA/TEGDMA, respectively, and were very hydrophobic, were representative of pit-and-fissure bonding agents. R3 was representative of a typical two-step etch- and-rinse adhesive, while R4 and R5 were very hydrophilic resins analogous to self-etching adhesives. Twenty-eight disks were prepared for each resin blend. After a 24 h-incubation at 37 °C, a multilayer monospecific biofilm of S. mutans was obtained on the surface of each disk. The adherent biomass was determined using the MTT assay and evaluated morphologically with confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). Results R2 and R3 surfaces showed the highest biofilm formation while R1 and R4 showed a similar intermediate biofilm formation. R5 was more hydrophilic and acidic and was significantly less colonized than all the other resins. A significant quadratic relationship between biofilm formation and hydrophilicity of the resin blends was found. CLSM and SEM evaluation confirmed MTT assay results. Conclusions The null hypothesis was rejected since S. mutans biofilm formation was influenced by hydrophilicity, surface acidity and chemical composition of the experimental resins. Further studies using a bioreactor are needed to confirm the results and clarify the role of the single factors. PMID:24954666

  14. Cross-dehydrogenative coupling for the intermolecular C–O bond formation

    PubMed Central

    Krylov, Igor B; Vil’, Vera A

    2015-01-01

    Summary The present review summarizes primary publications on the cross-dehydrogenative C–O coupling, with special emphasis on the studies published after 2000. The starting compound, which donates a carbon atom for the formation of a new C–O bond, is called the CH-reagent or the C-reagent, and the compound, an oxygen atom of which is involved in the new bond, is called the OH-reagent or the O-reagent. Alcohols and carboxylic acids are most commonly used as O-reagents; hydroxylamine derivatives, hydroperoxides, and sulfonic acids are employed less often. The cross-dehydrogenative C–O coupling reactions are carried out using different C-reagents, such as compounds containing directing functional groups (amide, heteroaromatic, oxime, and so on) and compounds with activated C–H bonds (aldehydes, alcohols, ketones, ethers, amines, amides, compounds containing the benzyl, allyl, or propargyl moiety). An analysis of the published data showed that the principles at the basis of a particular cross-dehydrogenative C–O coupling reaction are dictated mainly by the nature of the C-reagent. Hence, in the present review the data are classified according to the structures of C-reagents, and, in the second place, according to the type of oxidative systems. Besides the typical cross-dehydrogenative coupling reactions of CH- and OH-reagents, closely related C–H activation processes involving intermolecular C–O bond formation are discussed: acyloxylation reactions with ArI(O2CR)2 reagents and generation of O-reagents in situ from C-reagents (methylarenes, aldehydes, etc.). PMID:25670997

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

    PubMed

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

    2016-05-17

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

  16. A Synthesis of 1H-Indazoles via a Cu(OAc)2-Catalyzed N-N Bond Formation.

    PubMed

    Chen, Cheng-yi; Tang, Guangrong; He, Fengxian; Wang, Zhaobin; Jing, Hailin; Faessler, Roger

    2016-04-01

    A facile synthesis of 1H-indazoles featuring a Cu(OAc)2-catalyzed N-N bond formation using oxygen as the terminal oxidant is described. The reaction of readily available 2-aminobenzonitriles with various organometallic reagents led to o-aminoaryl N-H ketimine species. The subsequent Cu(OAc)2-catalyzed N-N bond formation in DMSO under oxygen afforded a wide variety of 1H-indazoles in good to excellent yields.

  17. Activation of carboxyl group with cyanate: peptide bond formation from dicarboxylic acids.

    PubMed

    Danger, Grégoire; Charlot, Solenne; Boiteau, Laurent; Pascal, Robert

    2012-06-01

    The reaction of cyanate with C-terminal carboxyl groups of peptides in aqueous solution was considered as a potential pathway for the abiotic formation of peptide bonds under the condition of the primitive Earth. The catalytic effect of dicarboxylic acids on cyanate hydrolysis was definitely attributed to intramolecular nucleophilic catalysis by the observation of the 1H-NMR signal of succinic anhydride when reacting succinic acid with KOCN in aqueous solution (pH 2.2-5.5). The formation of amide bonds was noticed when adding amino acids or amino acid derivatives into the solution. The reaction of N-acyl aspartic acid derivatives was observed to proceed similarly and the scope of the cyanate-promoted reaction was analyzed from the standpoint of prebiotic peptide formation. The role of cyanate in activating peptide C-terminus constitutes a proof of principle that intramolecular reactions of adducts of peptides C-terminal carboxyl groups with activating agents represent a pathway for peptide activation in aqueous solution, the relevance of which is discussed in connexion with the issue of the emergence of homochirality.

  18. Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state

    PubMed Central

    Osterman, Ilya A.; Khabibullina, Nelli F.; Komarova, Ekaterina S.; Kasatsky, Pavel; Kartsev, Victor G.; Bogdanov, Alexey A.; Dontsova, Olga A.

    2017-01-01

    Abstract The emergence of multi-drug resistant bacteria is limiting the effectiveness of commonly used antibiotics, which spurs a renewed interest in revisiting older and poorly studied drugs. Streptogramins A is a class of protein synthesis inhibitors that target the peptidyl transferase center (PTC) on the large subunit of the ribosome. In this work, we have revealed the mode of action of the PTC inhibitor madumycin II, an alanine-containing streptogramin A antibiotic, in the context of a functional 70S ribosome containing tRNA substrates. Madumycin II inhibits the ribosome prior to the first cycle of peptide bond formation. It allows binding of the tRNAs to the ribosomal A and P sites, but prevents correct positioning of their CCA-ends into the PTC thus making peptide bond formation impossible. We also revealed a previously unseen drug-induced rearrangement of nucleotides U2506 and U2585 of the 23S rRNA resulting in the formation of the U2506•G2583 wobble pair that was attributed to a catalytically inactive state of the PTC. The structural and biochemical data reported here expand our knowledge on the fundamental mechanisms by which peptidyl transferase inhibitors modulate the catalytic activity of the ribosome. PMID:28505372

  19. Design of Modular Protein Tags for Orthogonal Covalent Bond Formation at Specific DNA Sequences.

    PubMed

    Nguyen, Thang Minh; Nakata, Eiji; Saimura, Masayuki; Dinh, Huyen; Morii, Takashi

    2017-06-28

    Simultaneous formation of specific covalent linkages at nucleotides in given DNA sequences demand distinct orthogonal reactivity of DNA modification agents. Such highly specific reactions require well-balanced reactivity and affinity of the DNA modification agents. Conjugation of a sequence-specific DNA binding zinc finger protein and a self-ligating protein tag provides a modular adaptor that expedites formation of a covalent bond between the protein tag and a substrate-modified nucleotide at a specific DNA sequence. The modular adaptor stably locates a protein of interest fused to it at the target position on DNA scaffold in its functional form. Modular adaptors with orthogonal selectivity and fast reaction kinetics to specific DNA sequences enable site-specific location of different protein molecules simultaneously. Three different modular adaptors consisting of zinc finger proteins with distinct DNA sequence specificities and self-ligating protein tags with different substrate specificities achieved orthogonal covalent bond formation at respective sequences on the same DNA scaffold with an overall coassembly yield over 90%. Application of this unique set of orthogonal modular adaptors enabled construction of a cascade reaction of three enzymes from xylose metabolic pathway on DNA scaffold.

  20. Bridging and bonding interactions in higher education: social capital and students’ academic and professional identity formation

    PubMed Central

    Jensen, Dorthe H.; Jetten, Jolanda

    2015-01-01

    It is increasingly recognized that graduates’ achievements depend in important ways on their opportunities to develop an academic and a professional identity during their studies. Previous research has shown that students’ socio-economic status (SES) and social capital prior to entering university affects their ability to obtain these identities in higher education. However, what is less well understood is whether social capital that is built during university studies shapes identity development, and if so, whether the social capital gained during university years impacts on academic and professional identity differently. In a qualitative study, we interviewed 26 Danish and 11 Australian university students about their social interaction experiences, their opportunities to develop bonding capital as well as bridging capital, and their academic and professional identity. Findings show that while bonding social capital with co-students facilitated academic identity formation, such social capital does not lead to professional identity development. We also found that the development of bridging social capital with educators facilitated students’ professional identity formation. However, bonding social capital among students stood in the way of participating in bridging interaction with educators, thereby further hindering professional identity formation. Finally, while students’ parental background did not affect the perceived difficulty of forming professional identity, there was a tendency for students from lower SES backgrounds to be more likely to make internal attributions while those from higher SES backgrounds were more likely to make external attributions for the failure to develop professional identity. Results point to the importance of creating opportunities for social interaction with educators at university because this facilitates the generation of bridging social capital, which, in turn, is essential for students’ professional identity

  1. Bridging and bonding interactions in higher education: social capital and students' academic and professional identity formation.

    PubMed

    Jensen, Dorthe H; Jetten, Jolanda

    2015-01-01

    It is increasingly recognized that graduates' achievements depend in important ways on their opportunities to develop an academic and a professional identity during their studies. Previous research has shown that students' socio-economic status (SES) and social capital prior to entering university affects their ability to obtain these identities in higher education. However, what is less well understood is whether social capital that is built during university studies shapes identity development, and if so, whether the social capital gained during university years impacts on academic and professional identity differently. In a qualitative study, we interviewed 26 Danish and 11 Australian university students about their social interaction experiences, their opportunities to develop bonding capital as well as bridging capital, and their academic and professional identity. Findings show that while bonding social capital with co-students facilitated academic identity formation, such social capital does not lead to professional identity development. We also found that the development of bridging social capital with educators facilitated students' professional identity formation. However, bonding social capital among students stood in the way of participating in bridging interaction with educators, thereby further hindering professional identity formation. Finally, while students' parental background did not affect the perceived difficulty of forming professional identity, there was a tendency for students from lower SES backgrounds to be more likely to make internal attributions while those from higher SES backgrounds were more likely to make external attributions for the failure to develop professional identity. Results point to the importance of creating opportunities for social interaction with educators at university because this facilitates the generation of bridging social capital, which, in turn, is essential for students' professional identity development.

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

    PubMed

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

    2014-07-15

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

  3. Supramolecular organic photochemistry: Control of covalent bond formation through noncovalent supramolecular interactions and magnetic effects

    PubMed Central

    Turro, Nicholas J.

    2002-01-01

    Supramolecular organic photochemistry, a field concerned with the interaction of light with supramolecular assemblies of organic molecules, has been inspired by the remarkable structural and dynamic features of guest@host chemistry, particularly as exemplified by enzymes. Exemplars of supramolecular organic photochemistry from soft-matter hosts (micelles) and hard-matter hosts (porous solids) are discussed with an emphasis on how noncovalent interactions, which are at the heart of supramolecular chemistry, can be systematically exploited to control the catalytic and magnetic effects on the formation of covalent bonds from photochemically produced pairs of radicals. PMID:11880603

  4. Properties of synthetic ferrihydrite as an amino acid adsorbent and a promoter of peptide bond formation.

    PubMed

    Matrajt, G; Blanot, D

    2004-03-01

    Ferrihydrite, an iron oxide hydroxide, is found in all kinds of environments, from hydrothermal hot springs to extraterrestrial materials. It has been shown that this material is nanoporous, and because of its high surface area, it has outstanding adsorption properties and in some cases catalysis properties. In this work we studied the adsorption properties of ferrihydrite with respect to amino acids. Samples of pure ferrihydrite were synthesised and exposed to solutions of amino acids including both proteinaceous and non-proteinaceous species. These experiments revealed important characteristics of this mineral as both an adsorbent of amino acids and a promoter of peptide bond formation.

  5. Thermal Condensation of Glycine and Alanine on Metal Ferrite Surface: Primitive Peptide Bond Formation Scenario.

    PubMed

    Iqubal, Md Asif; Sharma, Rachana; Jheeta, Sohan; Kamaluddin

    2017-03-27

    The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe₂O₄), cobalt ferrite (CoFe₂O₄), copper ferrite (CuFe₂O₄), zinc ferrite (ZnFe₂O₄), and manganese ferrite (MnFe₂O₄) nanoparticles surfaces, in the temperature range from 50-120 °C for 1-35 days, without applying any wetting/drying cycles. Among the metal ferrites tested for their catalytic activity, NiFe₂O₄ produced the highest yield of products by oligomerizing glycine to the trimer level and alanine to the dimer level, whereas MnFe₂O₄ was the least efficient catalyst, producing the lowest yield of products, as well as shorter oligomers of amino acids under the same set of experimental conditions. It produced primarily diketopiperazine (Ala) with a trace amount of alanine dimer from alanine condensation, while glycine was oligomerized to the dimer level. The trend in product formation is in accordance with the surface area of the minerals used. A temperature as low as 50 °C can even favor peptide bond formation in the present study, which is important in the sense that the condensation process is highly feasible without any sort of localized heat that may originate from volcanoes or hydrothermal vents. However, at a high temperature of 120 °C, anhydrides of glycine and alanine formation are favored, while the optimum temperature for the highest yield of product formation was found to be 90 °C.

  6. Thermal Condensation of Glycine and Alanine on Metal Ferrite Surface: Primitive Peptide Bond Formation Scenario

    PubMed Central

    Iqubal, Md. Asif; Sharma, Rachana; Jheeta, Sohan; Kamaluddin

    2017-01-01

    The amino acid condensation reaction on a heterogeneous mineral surface has been regarded as one of the important pathways for peptide bond formation. Keeping this in view, we have studied the oligomerization of the simple amino acids, glycine and alanine, on nickel ferrite (NiFe2O4), cobalt ferrite (CoFe2O4), copper ferrite (CuFe2O4), zinc ferrite (ZnFe2O4), and manganese ferrite (MnFe2O4) nanoparticles surfaces, in the temperature range from 50–120 °C for 1–35 days, without applying any wetting/drying cycles. Among the metal ferrites tested for their catalytic activity, NiFe2O4 produced the highest yield of products by oligomerizing glycine to the trimer level and alanine to the dimer level, whereas MnFe2O4 was the least efficient catalyst, producing the lowest yield of products, as well as shorter oligomers of amino acids under the same set of experimental conditions. It produced primarily diketopiperazine (Ala) with a trace amount of alanine dimer from alanine condensation, while glycine was oligomerized to the dimer level. The trend in product formation is in accordance with the surface area of the minerals used. A temperature as low as 50 °C can even favor peptide bond formation in the present study, which is important in the sense that the condensation process is highly feasible without any sort of localized heat that may originate from volcanoes or hydrothermal vents. However, at a high temperature of 120 °C, anhydrides of glycine and alanine formation are favored, while the optimum temperature for the highest yield of product formation was found to be 90 °C. PMID:28346388

  7. Efficient and directed peptide bond formation in the gas phase via ion/ion reactions.

    PubMed

    McGee, William M; McLuckey, Scott A

    2014-01-28

    Amide linkages are among the most important chemical bonds in living systems, constituting the connections between amino acids in peptides and proteins. We demonstrate the controlled formation of amide bonds between amino acids or peptides in the gas phase using ion/ion reactions in a mass spectrometer. Individual amino acids or peptides can be prepared as reagents by (i) incorporating gas phase-labile protecting groups to silence otherwise reactive functional groups, such as the N terminus; (ii) converting the carboxyl groups to the active ester of N-hydroxysuccinimide; and (iii) incorporating a charge site. Protonation renders basic sites (nucleophiles) unreactive toward the N-hydroxysuccinimide ester reagents, resulting in sites with the greatest gas phase basicities being, in large part, unreactive. The N-terminal amines of most naturally occurring amino acids have lower gas phase basicities than the side chains of the basic amino acids (i.e., those of histidine, lysine, or arginine). Therefore, reagents may be directed to the N terminus of an existing "anchor" peptide to form an amide bond by protonating the anchor peptide's basic residues, while leaving the N-terminal amine unprotonated and therefore reactive. Reaction efficiencies of greater than 30% have been observed. We propose this method as a step toward the controlled synthesis of peptides in the gas phase.

  8. Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach

    NASA Astrophysics Data System (ADS)

    Suresh, D. M.; Amalanathan, M.; Sebastian, S.; Sajan, D.; Hubert Joe, I.; Bena Jothy, V.; Nemec, Ivan

    2013-11-01

    The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.

  9. Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach.

    PubMed

    Suresh, D M; Amalanathan, M; Sebastian, S; Sajan, D; Hubert Joe, I; Bena Jothy, V; Nemec, Ivan

    2013-11-01

    The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.

  10. Dissecting the role of disulfide bonds on the amyloid formation of insulin

    SciTech Connect

    Li, Yang; Gong, Hao; Sun, Yue; Yan, Juan; Cheng, Biao; Zhang, Xin; Huang, Jing; Yu, Mengying; Guo, Yu; Zheng, Ling; Huang, Kun

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer We dissect how individual disulfide bond affects the amyloidogenicity of insulin. Black-Right-Pointing-Pointer A controlled reduction system for insulin is established in this study. Black-Right-Pointing-Pointer Disulfide breakage is associated with unfolding and increased amyloidogenicity. Black-Right-Pointing-Pointer Breakage of A6-A11 is associated with significantly increased cytotoxicity. Black-Right-Pointing-Pointer Analogs without A6-A11 have a higher potency to form high order toxic oligomers. -- Abstract: Disulfide bonds play a critical role in the stability and folding of proteins. Here, we used insulin as a model system, to investigate the role of its individual disulfide bond during the amyloid formation of insulin. Tris(2-carboxyethyl)phosphine (TCEP) was applied to reduce two of the three disulfide bonds in porcine insulin and the reduced disulfide bonds were then alkylated by iodoacetamide. Three disulfide bond-modified insulin analogs, INS-2 (lack of A6-A11), INS-3 (lack of A7-B7) and INS-6 (lack of both A6-A11 and A7-B7), were obtained. Far-UV circular dichroism (CD) spectroscopy results indicated that the secondary structure of INS-2 was the closest to insulin under neutral conditions, followed by INS-3 and INS-6, whereas in an acidic solution all analogs were essentially unfolded. To test how these modifications affect the amyloidogenicity of insulin, thioflavin-T (ThT) fluorescence and transmission electronic microscopy (TEM) were performed. Our results showed that all analogs were more prone to aggregation than insulin, with the order of aggregation rates being INS-6 > INS-3 > INS-2. Cross-linking of unmodified proteins (PICUP) assay results showed that analogs without A6-A11 (INS-2 and INS-6) have a higher potential for oligomerization than insulin and INS-3, which is accompanied with a higher cytotoxicity as the hemolytic assays of human erythrocytes suggested. The results indicated that breakage of A7

  11. Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries.

    PubMed

    Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario

    2016-08-08

    DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.

  12. Formation of III-V-on-insulator structures on Si by direct wafer bonding

    NASA Astrophysics Data System (ADS)

    Yokoyama, Masafumi; Iida, Ryo; Ikku, Yuki; Kim, Sanghyeon; Takagi, Hideki; Yasuda, Tetsuji; Yamada, Hisashi; Ichikawa, Osamu; Fukuhara, Noboru; Hata, Masahiko; Takenaka, Mitsuru; Takagi, Shinichi

    2013-09-01

    We have studied the formation of III-V-compound-semiconductors-on-insulator (III-V-OI) structures with thin buried oxide (BOX) layers on Si wafers by using developed direct wafer bonding (DWB). In order to realize III-V-OI MOSFETs with ultrathin body and extremely thin body (ETB) InGaAs-OI channel layers and ultrathin BOX layers, we have developed an electron-cyclotron resonance (ECR) O2 plasma-assisted DWB process with ECR sputtered SiO2 BOX layers and a DWB process based on atomic-layer-deposition Al2O3 (ALD-Al2O3) BOX layers. It is essential to suppress micro-void generation during wafer bonding process to achieve excellent wafer bonding. We have found that major causes of micro-void generation in DWB processes with ECR-SiO2 and ALD-Al2O3 BOX layers are desorption of Ar and H2O gas, respectively. In order to suppress micro-void generation in the ECR-SiO2 BOX layers, it is effective to introduce the outgas process before bonding wafers. On the other hand, it is a possible solution for suppressing micro-void generation in the ALD-Al2O3 BOX layers to increase the deposition temperature of the ALD-Al2O3 BOX layers. It is also another possible solution to deposit ALD-Al2O3 BOX layers on thermally oxidized SiO2 layers, which can absorb the desorption gas from ALD-Al2O3 BOX layers.

  13. Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

    PubMed Central

    Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

    2015-01-01

    Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism. PMID:25588215

  14. Evaluation of the Role of Water in the H2 Bond Formation by Ni(II)-Based Electrocatalysts.

    PubMed

    Ho, Ming-Hsun; Raugei, Simone; Rousseau, Roger; Dupuis, Michel; Bullock, R Morris

    2013-08-13

    We investigate the role of water in the H-H bond formation by a family of nickel molecular catalysts that exhibit high rates for H2 production in acetonitrile solvent. A key feature leading to the high reactivity is the Lewis acidity of the Ni(II) center and pendant amines in the diphosphine ligand that function as Lewis bases, facilitating H-H bond formation or cleavage. Significant increases in the rate of H2 production have been reported in the presence of added water. Our calculations show that molecular water can displace an acetonitrile solvent molecule in the first solvation shell of the metal. One or two water molecules can also participate in shuttling a proton that can combine with a metal hydride to form the H-H bond. However the participation of the water molecules does not lower the barrier to H-H bond formation. Thus these calculations suggest that the rate increase due to water in these electrocatalysts is not associated with the elementary step of H-H bond formation or cleavage but rather with the proton delivery steps. We attribute the higher barrier in the H-H bond formation in the presence of water to a decrease in direct interaction between the protic and hydridic hydrogen atoms forced by the water molecules.

  15. Structural analysis of SgvP involved in carbon-sulfur bond formation during griseoviridin biosynthesis.

    PubMed

    Li, Qin; Chen, Yan; Zhang, Guiqin; Zhang, Huaidong

    2017-05-01

    Griseoviridin (GV) is a broad-spectrum antibiotic with antibacterial and antifungal activity. In the GV biosynthetic pathway, SgvP catalyzes formation of the carbon-sulfur bond in GV. Herein, we report the recombinant expression and characterization of SgvP from Streptomyces griseoviridis NRRL2427. We also present the 2.6 Å crystal structure of SgvP, which is the first structure of a cytochrome P450 involved in carbon-sulfur bond formation in GV. Structural analysis indicates that Pro237 in the I-helix of SgvP may play a critical role in dioxygen binding and proton transfer during the catalytic cycle. Of the three channels we observed in SgvP, channel 3 may be essential for substrate ingress and egress from the active site, while channels 1 and 2 may be the solvent and water pathway, respectively. Coordinate and structure factor were deposited in the Protein Data Bank database under the accession number 4MM0. © 2017 Federation of European Biochemical Societies.

  16. Control of Reactivity and Regioselectivity for On-Surface Dehydrogenative Aryl-Aryl Bond Formation.

    PubMed

    Kocić, Nemanja; Liu, Xunshan; Chen, Songjie; Decurtins, Silvio; Krejčí, Ondřej; Jelínek, Pavel; Repp, Jascha; Liu, Shi-Xia

    2016-05-04

    Regioselectivity is of fundamental importance in chemical synthesis. Although many concepts for site-selective reactions are well established for solution chemistry, it is not a priori clear whether they can easily be transferred to reactions taking place on a metal surface. A metal will fix the chemical potential of the electrons and perturb the electronic states of the reactants because of hybridization. Additionally, techniques to characterize chemical reactions in solution are generally not applicable to on-surface reactions. Only recent developments in resolving chemical structures by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) paved the way for identifying individual reaction products on surfaces. Here we exploit a combined STM/AFM technique to demonstrate the on-surface formation of complex molecular architectures built up from a heteroaromatic precursor, the tetracyclic pyrazino[2,3-f][4,7]phenanthroline (pap) molecule. Selective intermolecular aryl-aryl coupling via dehydrogenative C-H activation occurs on Au(111) upon thermal annealing under ultrahigh vacuum (UHV) conditions. A full atomistic description of the different reaction products based on an unambiguous discrimination between pyrazine and pyridine moieties is presented. Our work not only elucidates that ortho-hydrogen atoms of the pyrazine rings are preferentially activated over their pyridine equivalents, but also sheds new light onto the participation of substrate atoms in metal-organic coordination bonding during covalent C-C bond formation.

  17. In vivo biofilm formation on stainless steel bonded retainers during different oral health-care regimens

    PubMed Central

    Jongsma, Marije A; van der Mei, Henny C; Atema-Smit, Jelly; Busscher, Henk J; Ren, Yijin

    2015-01-01

    Retention wires permanently bonded to the anterior teeth are used after orthodontic treatment to prevent the teeth from relapsing to pre-treatment positions. A disadvantage of bonded retainers is biofilm accumulation on the wires, which produces a higher incidence of gingival recession, increased pocket depth and bleeding on probing. This study compares in vivo biofilm formation on single-strand and multi-strand retention wires with different oral health-care regimens. Two-centimetre wires were placed in brackets that were bonded to the buccal side of the first molars and second premolars in the upper arches of 22 volunteers. Volunteers used a selected toothpaste with or without the additional use of a mouthrinse containing essential oils. Brushing was performed manually. Regimens were maintained for 1 week, after which the wires were removed and the oral biofilm was collected to quantify the number of organisms and their viability, determine the microbial composition and visualize the bacteria by electron microscopy. A 6-week washout period was employed between regimens. Biofilm formation was reduced on single-strand wires compared with multi-strand wires; bacteria were observed to adhere between the strands. The use of antibacterial toothpastes marginally reduced the amount of biofilm on both wire types, but significantly reduced the viability of the biofilm organisms. Additional use of the mouthrinse did not result in significant changes in biofilm amount or viability. However, major shifts in biofilm composition were induced by combining a stannous fluoride- or triclosan-containing toothpaste with the mouthrinse. These shifts can be tentatively attributed to small changes in bacterial cell surface hydrophobicity after the adsorption of the toothpaste components, which stimulate bacterial adhesion to the hydrophobic oil, as illustrated for a Streptococcus mutans strain. PMID:25572920

  18. Relay stations for electron hole migration in peptides: possibility for formation of three-electron bonds along peptide chains.

    PubMed

    Chen, Xiaohua; Zhang, Liang; Wang, Zhiping; Li, Jilai; Wang, Wen; Bu, Yuxiang

    2008-11-13

    Our calculations found that the O thereforeO three-electron (3e) bonds (2.16 approximately 2.27 A) can be formed not only between two neighboring peptide units in a main chain but also between two adjacent peptide units in two different main chains in proteins. This finding may address electron hole migration from one peptide unit to the next in proteins. Evidently, stability of the O thereforeO 3e bonded species is strongly dependent on the component of the oligopeptides and is reduced owing to the steric hindrance of the side chains when the big chains present in oligopeptides. Besides, formation of the O thereforeO 3e bonds competes with the formation of the other forms of three-electron bonds depending on the component of the polypeptides. Formation of the O thereforeS 3e bond is thermodynamically more favorable than that of the O thereforeO 3e bond for the oligopeptides containing sulfur atom in their side chains. Similarly, formation of the O thereforepi 3e bond between aromatic ring of the side chain and the neighboring peptide unit is more stable than that of the O thereforeO 3e bond when the aromatic amino acids present in the oligopeptides. We infer that a series of three-electron bonds may be formed during the electron hole migration along the peptide backbone in proteins and assist electron hole transport as relay stations, supporting the peptide chain as a conduction wire. The ab initio molecular dynamics simulations of the polypeptides also support this conclusion.

  19. Interfacial micromorphological differences in hybrid layer formation between water- and solvent-based dentin bonding systems.

    PubMed

    Gregoire, Geneviève L; Akon, Bernadette A; Millas, Arlette

    2002-06-01

    Many dentin bonding systems of different compositions, and in particular containing different solvents, have been introduced to the market. Their effect on the quality of the interface requires clarification by means of comparative trials. This study investigated micromorphological differences in hybrid layer formation with a variety of commercially available water- or solvent-based dentin bonding products and their recommended compomers. Five bonding systems were used on groups of 10 teeth each as follows: group I, acetone-based system used with 36% phosphoric acid; group II, a different acetone-based system containing nano-sized particles for filler loading and used with a non-rinsing conditioner containing maleic acid; group III, the acetone-based system of group II used with 36% phosphoric acid (the only difference in the treatment for groups II and III was the acid etching system); group IV, a mixed-solvent-based system (water/ethanol) used with 37% phosphoric acid; and group V, a water-based system used with 37% phosphoric acid. Each bonding system was covered with the recommended compomer. Class I occlusal preparations were made in extracted teeth and restored with one of the above systems. Five specimens of each group were studied with optical microscopy after staining. Scanning electron microscopy was used to examine the interface of the bonding system/dentin of the other 5 teeth in each group. The optical microscopy measurements were made with a 10 x 10 reticle. A micron mark with scale was used for the scanning electron microscope. All measurements were made in microm. The following criteria were used to define a good interface: absence of voids between the different parts of the interface, uniformity of the hybrid layer, good opening of the tubuli orifices, and tag adherence to the tubuli walls. Morphological differences were found at the interface depending on dentin treatment and adhesive composition. The acetone-containing systems were associated

  20. Levoglucosan formation from crystalline cellulose: importance of a hydrogen bonding network in the reaction.

    PubMed

    Hosoya, Takashi; Sakaki, Shigeyoshi

    2013-12-01

    Levoglucosan (1,6-anhydro-β-D-glucopyranose) formation by the thermal degradation of native cellulose was investigated by MP4(SDQ)//DFT(B3LYP) and DFT(M06-2X)//DFT(B3LYP) level computations. The computational results of dimer models lead to the conclusion that the degradation occurs by a concerted mechanism similar to the degradation of methyl β-D-glucoside reported in our previous study. One-chain models of glucose hexamer, in which the interchain hydrogen bonds of real cellulose crystals are absent, do not exhibit the correct reaction behavior of levoglucosan formation; for instance, the activation enthalpy (Ea =≈38 kcal mol(-1) ) is considerably underestimated compared to the experimental value (48-60 kcal mol(-1) ). This problem is solved with the use of two-chain models that contain interchain hydrogen bonds. The theoretical study of this model clearly shows that the degradation of the internal glucosyl residue leads to the formation of a levoglucosan precursor at the chain end and levoglucosan is selectively formed from this levoglucosan end. The calculated Ea (56-62 kcal mol(-1) ) agrees well with the experimental value. The computational results of three-chain models indicate that this degradation occurs selectively on the crystalline surface. All these computational results provide a comprehensive understanding of several experimental facts, the mechanisms of which have not yet been elucidated. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Maternal nicotine exposure leads to impaired disulfide bond formation and augmented endoplasmic reticulum stress in the rat placenta.

    PubMed

    Wong, Michael K; Nicholson, Catherine J; Holloway, Alison C; Hardy, Daniel B

    2015-01-01

    Maternal nicotine exposure has been associated with many adverse fetal and placental outcomes. Although underlying mechanisms remain elusive, recent studies have identified that augmented endoplasmic reticulum (ER) stress is linked to placental insufficiency. Moreover, ER function depends on proper disulfide bond formation--a partially oxygen-dependent process mediated by protein disulfide isomerase (PDI) and ER oxidoreductases. Given that nicotine compromised placental development in the rat, and placental insufficiency has been associated with poor disulfide bond formation and ER stress, we hypothesized that maternal nicotine exposure leads to both placental ER stress and impaired disulfide bond formation. To test this hypothesis, female Wistar rats received daily subcutaneous injections of either saline (vehicle) or nicotine bitartrate (1 mg/kg) for 14 days prior to mating and during pregnancy. Placentas were harvested on embryonic day 15 for analysis. Protein and mRNA expression of markers involved in ER stress (e.g., phosphorylated eIF2α, Grp78, Atf4, and CHOP), disulfide bond formation (e.g., PDI, QSOX1, VKORC1), hypoxia (Hif1α), and amino acid deprivation (GCN2) were quantified via Western blot and/or Real-time PCR. Maternal nicotine exposure led to increased expression of Grp78, phosphorylated eIF2α, Atf4, and CHOP (p<0.05) in the rat placenta, demonstrating the presence of augmented ER stress. Decreased expression of PDI and QSOX1 (p<0.05) reveal an impaired disulfide bond formation pathway, which may underlie nicotine-induced ER stress. Finally, elevated expression of Hif1α and GCN2 (p<0.05) indicate hypoxia and amino acid deprivation in nicotine-exposed placentas, respectively, which may also cause impaired disulfide bond formation and augmented ER stress. This study is the first to link maternal nicotine exposure with both placental ER stress and disulfide bond impairment in vivo, providing novel insight into the mechanisms underlying nicotine

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

    PubMed

    Schneider, Uwe; Kobayashi, Shu

    2012-08-21

    The development of innovative metal catalysis for selective bond formation is an important task in organic chemistry. The group 13 metal indium is appealing for catalysis because indium-based reagents are minimally toxic, selective, and tolerant toward various functional groups. Among elements in this group, the most stable oxidation state is typically +3, but in molecules with larger group 13 atoms, the chemistry of the +1 oxidation state is also important. The use of indium(III) compounds in organic synthesis has been well-established as Lewis acid catalysts including asymmetric versions thereof. In contrast, only sporadic examples of the use of indium(I) as a stoichiometric reagent have been reported: to the best of our knowledge, our investigations represent the first synthetic method that uses a catalytic amount of indium(I). Depending on the nature of the ligand or the counteranion to which it is coordinated, indium(I) can act as both a Lewis acid and a Lewis base because it has both vacant p orbitals and a lone pair of electrons. This potential ambiphilicity may offer unique reactivity and unusual selectivity in synthesis and may have significant implications for catalysis, particularly for dual catalytic processes. We envisioned that indium(I) could be employed as a metallic Lewis base catalyst to activate Lewis acidic boron-based pronucleophiles for selective bond formation with suitable electrophiles. Alternatively, indium(I) could serve as an ambiphilic catalyst that activates both reagents at a single center. In this Account, we describe the development of low-oxidation state indium catalysts for carbon-carbon bond formation between boron-based pronucleophiles and various electrophiles. We discovered that indium(I) iodide was an excellent catalyst for α-selective allylations of C(sp(2)) electrophiles such as ketones and hydrazones. Using a combination of this low-oxidation state indium compound and a chiral semicorrin ligand, we developed catalytic

  3. Formation of porous surface layers in reaction bonded silicon nitride during processing

    NASA Technical Reports Server (NTRS)

    Shaw, N. J.; Glasgow, T. K.

    1979-01-01

    An effort was undertaken to determine if the formation of the generally observed layer of large porosity adjacent to the as-nitride surfaces of reaction bonded silicon nitrides could be prevented during processing. Isostatically pressed test bars were prepared from wet vibratory milled Si powder. Sintering and nitriding were each done under three different conditions:(1) bars directly exposed to the furnance atmosphere; (2) bars packed in Si powder; (3) bars packed in Si3N4 powder. Packing the bars in either Si of Si3N4 powder during sintering retarded formation of the layer of large porosity. Only packing the bars in Si prevented formation of the layer during nitridation. The strongest bars (316 MPa) were those sintered in Si and nitrided in Si3N4 despite their having a layer of large surface porosity; failure initiated at very large pores and inclusions. The alpha/beta ratio was found to be directly proportional to the oxygen content; a possible explanation for this relationship is discussed.

  4. Elucidation of an Iterative Process of Carbon-Carbon Bond Formation of Prebiotic Significance

    NASA Astrophysics Data System (ADS)

    Loison, Aurélie; Dubant, Stéphane; Adam, Pierre; Albrecht, Pierre

    2010-12-01

    Laboratory experiments carried out under plausible prebiotic conditions (under conditions that might have occurred at primitive deep-sea hydrothermal vents) in water and involving constituents that occur in the vicinity of submarine hydrothermal vents (e.g., CO, H2S, NiS) have disclosed an iterative Ni-catalyzed pathway of C-C bond formation. This pathway leads from CO to various organic molecules that comprise, notably, thiols, alkylmono- and disulfides, carboxylic acids, and related thioesters containing up to four carbon atoms. Furthermore, similar experiments with organic compounds containing various functionalities, such as thiols, carboxylic acids, thioesters, and alcohols, gave clues to the mechanisms of this novel synthetic process in which reduced metal species, in particular Ni(0), appear to be the key catalysts. Moreover, the formation of aldehydes (and ketones) as labile intermediates via a hydroformylation-related process proved to be at the core of the chain elongation process. Since this process can potentially lead to organic compounds with any chain length, it could have played a significant role in the prebiotic formation of lipidic amphiphilic molecules such as fatty acids, potential precursors of membrane constituents.

  5. Anodic Oxide Formation on Ti-6A1-4V in Chromic Acid for Adhesive Bonding.

    DTIC Science & Technology

    1984-03-01

    I. LIST OF FIGURES Figure pg 1. Schematic diagram of adhesive joint strength as a function of degree of surface attachment according to the...16 3. Activation energy diagram when the rate- determining step of oxide formation is (a) at the oxide/metal interface and (b) ion...maintains that surface contact at the interface alone is not sufficient for good bonding. Also required is that the molecules of the bonding surfaces

  6. Involvement of SgvP in carbon-sulfur bond formation during Griseoviridin biosynthesis.

    PubMed

    Xie, Yunchang; Li, Qinglian; Song, Yongxiang; Ma, Junying; Ju, Jianhua

    2014-05-26

    Griseoviridin (GV) is an A-type streptogramin antibiotic displaying antimicrobial activity and acting synergistically with viridogrisein (VG). Bioinformatic analyses reveal SgvP as the sole cytochrome P450 enzyme in the GV/VG gene cluster. To explore the role of SgvP in the GV/VG pathway, we inactivated the sgvP gene. The resulting ΔsgvP mutant generated two new products: GV-1 and GV-2, both lacking the CS bridge. In trans complementation of the sgvP gene into the ΔsgvP mutant strain partially restores GV production. Feeding [1-(13) C]-labeled cysteine to the wild-type strain led to enrichment of C-7 in the GV scaffold, thus verifying that the CS bond in GV is formed through direct coupling of the free SH group provided by the side chain of cysteine. The above results highlight the significance of SgvP in CS bond formation in griseoviridin biosynthesis.

  7. Nucleophilicity and P-C Bond Formation Reactions of a Terminal Phosphanido Iridium Complex.

    PubMed

    Serrano, Ángel L; Casado, Miguel A; Ciriano, Miguel A; de Bruin, Bas; López, José A; Tejel, Cristina

    2016-01-19

    The diiridium complex [{Ir(ABPN2)(CO)}2(μ-CO)] (1; [ABPN2](-) = [(allyl)B(Pz)2(CH2PPh2)](-)) reacts with diphenylphosphane affording [Ir(ABPN2)(CO)(H) (PPh2)] (2), the product of the oxidative addition of the P-H bond to the metal. DFT studies revealed a large contribution of the terminal phosphanido lone pair to the HOMO of 2, indicating nucleophilic character of this ligand, which is evidenced by reactions of 2 with typical electrophiles such as H(+), Me(+), and O2. Products from the reaction of 2 with methyl chloroacetate were found to be either [Ir(ABPN2)(CO)(H)(PPh2CH2CO2Me)][PF6] ([6]PF6) or [Ir(ABPN2)(CO)(Cl)(H)] (7) and the free phosphane (PPh2CH2CO2Me), both involving P-C bond formation, depending on the reaction conditions. New complexes having iridacyclophosphapentenone and iridacyclophosphapentanone moieties result from reactions of 2 with dimethyl acetylenedicarboxylate and dimethyl maleate, respectively, as a consequence of a further incorporation of the carbonyl ligand. In this line, the terminal alkyne methyl propiolate gave a mixture of a similar iridacyclophosphapentanone complex and [Ir(ABPN2){CH═C(CO2Me)-CO}{PPh2-CH═CH(CO2Me)}] (10), which bears the functionalized phosphane PPh2-CH═CH(CO2Me) and an iridacyclobutenone fragment. Related model reactions aimed to confirm mechanistic proposals are also studied.

  8. A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

    NASA Astrophysics Data System (ADS)

    Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

    2016-10-01

    Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation.

  9. A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

    PubMed Central

    Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

    2016-01-01

    Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation. PMID:27731375

  10. Formation of chemical bonds and morphological studies of a-CNx : Effects of PECVD deposition pressure

    NASA Astrophysics Data System (ADS)

    Purhanudin, Noorain; Awang, Rozidawati

    2016-11-01

    We report the structural difference and film properties of amorphous carbon nitride (a-CNx) thin films as a function of PECVD deposition pressure using precursor gases of ethane (C2H6) and nitrogen (N2). The Fourier transform infra-red (FTIR) spectra reveal peaks of single C-N (1100 cm-1), double C=C (1500 cm-1), double C=N (1670 cm-1) and triple C≡N (2340 cm-1). A systematic change in the preferential peaks correspond to the C=N and C≡N triple bonds were found to increase as deposition pressure increased. Field emission scanning electron microscopy (FESEM) provides morphological structure of the film. From the samples prepare at low deposition pressure, the particles tend to agglomerate into clusters with non-homogenous grains distributed over the surface. Higher deposition pressure results in coalescence process of the film, reflecting the formation of grains evenly distributed on the film. The film morphology is increased in voids structure with increase in deposition pressure. Finally, the samples were successfully prepared by PECVD technique with deposition pressure in varied, and the effect of deposition pressure on the chemical bonding and the morphology of the films had been studied.

  11. 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

  12. Isotopic Studies of O-O Bond Formation During Water Oxidation (SISGR)

    SciTech Connect

    Roth, Justine P.

    2015-03-03

    Isotopic Studies of O-O Bond Formation During Water Oxidation (SISGR) Research during the project period focused primarily on mechanisms of water oxidation by structurally defined transition metal complexes. Competitive oxygen isotope fractionation of water, mediated by oxidized precursors or reduced catalysts together with ceric, Ce(IV), ammonium nitrate in aqueous media, afforded oxygen-18 kinetic isotope effects (O-18 KIEs). Measurement, calculation, and interpretation of O-18 KIEs, described in the accompanying report has important ramifications for the production of electricity and solar hydrogen (as fuel). The catalysis division of BES has acknowledged that understanding mechanisms of transition metal catalyzed water oxidation has major ramifications, potentially leading to transformation of the global economy and natural environment in years to come. Yet, because of program restructuring and decreased availability of funds, it was recommended that the Solar Photochemistry sub-division of BES would be a more appropriate parent program for support of continued research.

  13. Terminal phosphanido rhodium complexes mediating catalytic P-P and P-C bond formation.

    PubMed

    Geer, Ana M; Serrano, Ángel L; de Bruin, Bas; Ciriano, Miguel A; Tejel, Cristina

    2015-01-07

    Complexes with terminal phosphanido (M-PR2) functionalities are believed to be crucial intermediates in new catalytic processes involving the formation of P-P and P-C bonds. We showcase here the isolation and characterization of mononuclear phosphanide rhodium complexes ([RhTp(H)(PR2)L]) that result from the oxidative addition of secondary phosphanes, a reaction that was also explored computationally. These compounds are active catalysts for the dehydrocoupling of PHPh2 to Ph2P-PPh2. The hydrophosphination of dimethyl maleate and the unactivated olefin ethylene is also reported. Reliable evidence for the prominent role of mononuclear phosphanido rhodium species in these reactions is also provided. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Formation of porous surface layers in reaction bonded silicon nitride during processing

    NASA Technical Reports Server (NTRS)

    Shaw, N. J.; Glasgow, T. K.

    1979-01-01

    Microstructural examination of reaction bonded silicon nitride (RBSN) has shown that there is often a region adjacent to the as-nitrided surfaces that is even more porous than the interior of this already quite porous material. Because this layer of large porosity is considered detrimental to both the strength and oxidation resistance of RBSN, a study was undertaken to determine if its formation could be prevented during processing. All test bars studied were made from a single batch of Si powder which was milled for 4 hours in heptane in a vibratory mill using high density alumina cylinders as the grinding media. After air drying the powder, bars were compacted in a single acting die and hydropressed.

  15. Role of hydrogen bonds in hydrophobicity: the free energy of cavity formation in water models with and without the hydrogen bonds.

    PubMed

    Madan, B; Lee, B

    1994-08-01

    The free energies of cavity formation in water with and without hydrogen bonding potential were computed from the results of a set of Monte Carlo simulation calculations on pure liquid TIP4P water model and on the same model but with the electrostatic charges turned off (Lennard-Jones liquid). The free energies of cavity formation in the Lennard-Jones liquids are higher than or approximately equal to those in TIP4P water, depending, respectively, on whether the Lennard-Jones size parameter sigma is set equal to 3.15 A, which is the value of sigma for TIP4P water, or to 2.8 A, which is the commonly assumed value for the oxygen-oxygen distance between two hydrogen-bonded water molecules. This result indicates that changes in the hydrogen-bonded structure of water and/or in the orientational degree of freedom of water are not essential features in the production of the large free energy change upon cavity formation.

  16. Effect of Oxidation on the Bonding Formation of Plasma-Sprayed Stainless Steel Splats onto Stainless Steel Substrate

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Li, Chang-Jiu; Yang, Guan-Jun; Li, Cheng-Xin

    2017-01-01

    Stainless steel splats were deposited on 304 stainless substrates with different thicknesses of oxide layer to examine the effect of substrate oxidation on splat morphology and splat-substrate interface bonding by inert low-pressure plasma spraying. The cross sections of splats showing the splat-substrate interface were prepared by focus ion beam (FIB). The splat morphology and splat-substrate interface bonding state were characterized by scanning electron microscopy. The interface bonding was also examined by an electrolytic etching process. Results showed that with increasing oxide layer thickness and surface roughness, the morphology of splat changed from disk shape to splashed finger-like shape. The examination into the interface bonding by using FIB-prepared cross-sectional samples revealed that the splat interface bonding depended on the oxide roughness and composition. The interface bonding with a ratio of 44% was formed at the inner part of a splat on the pre-oxidized substrate when iron oxide presented on the surface, and the roughness of oxide scale was <5 nm. When the pre-oxidizing temperature exceeded 800 °C, the surface roughness increased to 14 nm and chromium oxide covered the pre-oxidized surface, resulting in no effective bonding forming at the whole interface. Thus, surface roughness and oxide composition have a significant influence on the splat interface bonding formation.

  17. Identification of an Atypical Membrane Protein Involved in the Formation of Protein Disulfide Bonds in Oxygenic Photosynthetic Organisms*S⃞

    PubMed Central

    Singh, Abhay K.; Bhattacharyya-Pakrasi, Maitrayee; Pakrasi, Himadri B.

    2008-01-01

    The evolution of oxygenic photosynthesis in cyanobacteria nearly three billion years ago provided abundant reducing power and facilitated the elaboration of numerous oxygen-dependent reactions in our biosphere. Cyanobacteria contain an internal thylakoid membrane system, the site of photosynthesis, and a typical Gram-negative envelope membrane system. Like other organisms, the extracytoplasmic space in cyanobacteria houses numerous cysteine-containing proteins. However, the existence of a biochemical system for disulfide bond formation in cyanobacteria remains to be determined. Extracytoplasmic disulfide bond formation in non-photosynthetic organisms is catalyzed by coordinated interaction between two proteins, a disulfide carrier and a disulfide generator. Here we describe a novel gene, SyndsbAB, required for disulfide bond formation in the extracytoplasmic space of cyanobacteria. The SynDsbAB orthologs are present in most cyanobacteria and chloroplasts of higher plants with fully sequenced genomes. The SynDsbAB protein contains two distinct catalytic domains that display significant similarity to proteins involved in disulfide bond formation in Escherichia coli and eukaryotes. Importantly, SyndsbAB complements E. coli strains defective in disulfide bond formation. In addition, the activity of E. coli alkaline phosphatase localized to the periplasm of Synechocystis 6803 is dependent on the function of SynDsbAB. Deletion of SyndsbAB in Synechocystis 6803 causes significant growth impairment under photoautotrophic conditions and results in hyper-sensitivity to dithiothreitol, a reductant, whereas diamide, an oxidant had no effect on the growth of the mutant strains. We conclude that SynDsbAB is a critical protein for disulfide bond formation in oxygenic photosynthetic organisms and required for their optimal photoautotrophic growth. PMID:18413314

  18. Affiliation, reward, and immune biomarkers coalesce to support social synchrony during periods of bond formation in humans.

    PubMed

    Ulmer-Yaniv, Adi; Avitsur, Ronit; Kanat-Maymon, Yaniv; Schneiderman, Inna; Zagoory-Sharon, Orna; Feldman, Ruth

    2016-08-01

    Social bonds are critical for survival and adaptation and periods of bond formation involve reorganization of neurobiological systems as mediated by social behavior. Theoretical accounts and animal studies suggest similarity between parent-infant and pair bonding, a hypothesis not yet directly tested in humans. In this study, we recruited three groups of human adults (N=189); parents who had their firstborn child in the last 4-6months, new lovers who began a romantic relationship within the past 4months, and non-attached singles. We measured plasma oxytocin (OT), beta endorphin (β-End), and interlukin-6 (IL-6), biomarkers of the affiliation, reward, and stress-response systems, and micro-coded gaze and affect synchrony between parents and infants and among new lovers during social interaction. OT significantly increased during periods of parental and romantic bonding and was highest in new lovers. In contrast, IL-6 and β-End were highest in new parents and lowest in singles. Biomarkers became more tightly coupled during periods of bond formation and inter-correlation among hormones was highest during romantic bonding. Structural equation modeling indicated that the effects of IL-6 and β-End on behavioral synchrony were mediated by their impact on OT, highlighting the integrative role of the oxytocinergic system in supporting human social affiliation. Findings suggest that periods of bond formation are accompanied by increased activity, as well as tighter cross-talk among systems underpinning affiliation, reward, and stress management and that research on the multidimensional process of bonding may shed further light on the effects of attachment on health. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.

    PubMed

    Świderek, Katarzyna; Tuñón, Iñaki; Martí, Sergio; Moliner, Vicent; Bertrán, Juan

    2013-06-12

    Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional. According to the results, the formation of adduct zwitterion species is a preliminary step required for all possible mechanisms. Then, from different conformers of this species, four different paths were found: three of them taking place through concerted mechanisms of four-, six- and eight-membered ring transition states, and a stepwise mechanism through a neutral intermediate. Comparison of the free energy profiles indicates that the concerted mechanisms would be kinetically favored, with free energy barriers in very good agreement with experimental data. Calculations of kinetic isotope effects, when including the solute interactions with the first solvation shell, show that the 8-membered ring TS renders values in better agreement with available experimental data. Quantitative discrepancies can be attributed to different employed models in experiments and calculations.

  20. Biotin synthase: insights into radical-mediated carbon-sulfur bond formation.

    PubMed

    Fugate, Corey J; Jarrett, Joseph T

    2012-11-01

    The enzyme cofactor and essential vitamin biotin is biosynthesized in bacteria, fungi, and plants through a pathway that culminates with the addition of a sulfur atom to generate the five-membered thiophane ring. The immediate precursor, dethiobiotin, has methylene and methyl groups at the C6 and C9 positions, respectively, and formation of a thioether bridging these carbon atoms requires cleavage of unactivated CH bonds. Biotin synthase is an S-adenosyl-l-methionine (SAM or AdoMet) radical enzyme that catalyzes reduction of the AdoMet sulfonium to produce 5'-deoxyadenosyl radicals, high-energy carbon radicals that can directly abstract hydrogen atoms from dethiobiotin. The available experimental and structural data suggest that a [2Fe-2S](2+) cluster bound deep within biotin synthase provides a sulfur atom that is added to dethiobiotin in a stepwise reaction, first at the C9 position to generate 9-mercaptodethiobiotin, and then at the C6 position to close the thiophane ring. The formation of sulfur-containing biomolecules through a radical reaction involving an iron-sulfur cluster is an unprecedented reaction in biochemistry; however, recent enzyme discoveries suggest that radical sulfur insertion reactions may be a distinct subgroup within the burgeoning Radical SAM superfamily. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.

  1. Thermodynamic analysis of alkali metal complex formation of polymer-bonded crown ether.

    PubMed

    Bey, Alexandra; Dreyer, Oliver; Abetz, Volker

    2017-06-21

    The complex formation of two crown ethers with colored alkali metal salts was investigated by UV/Vis spectroscopy. Complexation was accomplished with free benzo-15-crown-5 (B15C5) and 15-crown-5 bonded to a diblock copolymer (Poly15C5). The diblock copolymer was synthesized by two controlled polymerization techniques and copper(i)-catalyzed azide-alkyne cycloaddition. Depending on the inserted cation, 1 : 1- or 1 : 2-complexes are formed. A significant difference of the stability constants was determined by concentration dependence solvent extraction with sodium or potassium salt. For Poly15C5 the stability constants increase for both salts compared to the stability constants of B15C5, which suggests a more effective complexation. Evaluation of the thermodynamics (ΔH, ΔS, ΔG) of cation complexation was achieved by temperature dependence phase extraction on the basis of established thermodynamic equations. Remarkably, in all cases the entropic gain seems to be the major propulsion facilitating the complexation between alkali metal salts and crown ethers. Indeed, by using Poly15C5 a more pronounced dependency of enthalpy and entropy on the complex formation is calculated.

  2. Evaluation of the Role of Water in the H2 Bond Formation by Ni(II)-based Electrocatalysts

    SciTech Connect

    Ho, Ming-Hsun; Raugei, Simone; Rousseau, Roger J.; Dupuis, Michel; Bullock, R. Morris

    2013-07-17

    We investigate the role of water in the H-H bond formation by a family of nickel molecular catalysts that exhibit high rates for H2 production in acetonitrile solvent. A key feature leading to the high reactivity is the Lewis acidity of the Ni(II) center and pendant amines in the diphosphine ligand that function as Lewis bases, facilitating H-H bond formation or cleavage. Significant increases in the rate of H2 production have been reported in the presence of added water. Our calculations show that molecular water can displace an acetonitrile solvent molecule in the first solvation shell of the metal. One or two water molecules can also participate in shuttling a proton that can combine with a metal hydride to form the H-H bond. However the participation of the water molecules does not lower the barrier to H-H bond formation. Thus these calculations suggest that the rate increase due to water in these electrocatalysts is not associated with the elementary step of H-H bond formation or cleavage, but rather with the proton delivery steps. We attribute the higher barrier in the H-H bond formation in the presence of water to a decrease in direct interaction between the protic and hydridic hydrogen atoms forced by the water molecules. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory - Pacific Northwest National Laboratory, the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory, and the Jaguar supercomputer at Oak Ridge National Laboratory.

  3. Intermolecular charge flux as the origin of infrared intensity enhancement upon halogen-bond formation of the peptide group

    NASA Astrophysics Data System (ADS)

    Torii, Hajime

    2010-07-01

    The changes in the vibrational properties of the peptide group upon formation of O⋯X and N⋯X halogen bonds are studied theoretically. Calculations are carried out for complexes of N-methylacetamide (NMA), a well known model molecule of the peptide group, with halogen-containing molecules. For comparison, calculations are also carried out for some NMA-water hydrogen-bonding complexes. It is shown that the infrared (IR) intensity of the amide I mode of the peptide group is enhanced significantly (up to about 520 km mol-1 or 2.6 times) upon CO⋯X halogen-bond formation, in spite of rather modest magnitudes of the intermolecular electric field and of the changes in the CO bond length and in the amide I vibrational frequency as compared with the cases of the CO⋯H(D) hydrogen bonding. From the analysis of the changes in the dipole derivative and in the electronic structure, it is shown that this IR intensity enhancement arises from the intermolecular charge flux. For the N⋯X halogen bonding complexes, some characteristic changes in the vibrational properties are seen, among which the IR intensity enhancement of the ND out-of-plane wagging mode is most notable. The reason why such large IR intensity enhancements are seen for these particular vibrational modes is examined.

  4. Intermolecular charge flux as the origin of infrared intensity enhancement upon halogen-bond formation of the peptide group.

    PubMed

    Torii, Hajime

    2010-07-21

    The changes in the vibrational properties of the peptide group upon formation of O...X and N...X halogen bonds are studied theoretically. Calculations are carried out for complexes of N-methylacetamide (NMA), a well known model molecule of the peptide group, with halogen-containing molecules. For comparison, calculations are also carried out for some NMA-water hydrogen-bonding complexes. It is shown that the infrared (IR) intensity of the amide I mode of the peptide group is enhanced significantly (up to about 520 km mol(-1) or 2.6 times) upon C=O...X halogen-bond formation, in spite of rather modest magnitudes of the intermolecular electric field and of the changes in the C=O bond length and in the amide I vibrational frequency as compared with the cases of the C=O...H(D) hydrogen bonding. From the analysis of the changes in the dipole derivative and in the electronic structure, it is shown that this IR intensity enhancement arises from the intermolecular charge flux. For the N...X halogen bonding complexes, some characteristic changes in the vibrational properties are seen, among which the IR intensity enhancement of the ND out-of-plane wagging mode is most notable. The reason why such large IR intensity enhancements are seen for these particular vibrational modes is examined.

  5. Heterolytic OO bond cleavage: Functional role of Glu113 during bis-Fe(IV) formation in MauG.

    PubMed

    Geng, Jiafeng; Huo, Lu; Liu, Aimin

    2017-02-01

    The diheme enzyme MauG utilizes H2O2 to perform oxidative posttranslational modification on a protein substrate. A bis-Fe(IV) species of MauG was previously identified as a key intermediate in this reaction. Heterolytic cleavage of the OO bond of H2O2 drives the formation of the bis-Fe(IV) intermediate. In this work, we tested a hypothesis that a glutamate residue, Glu113 in the distal pocket of the pentacoordinate heme of MauG, facilitates heterolytic OO bond cleavage, thereby leading to bis-Fe(IV) formation. This hypothesis was proposed based on sequence alignment and structural comparison with other H2O2-utilizing hemoenzymes, especially those from the diheme enzyme superfamily that MauG belongs to. Electron paramagnetic resonance (EPR) characterization of the reaction between MauG and H2O2 revealed that mutation of Glu113 inhibited heterolytic OO bond cleavage, in agreement with our hypothesis. This result was further confirmed by the HPLC study in which an analog of H2O2, cumene hydroperoxide, was used to probe the pattern of OO bond cleavage. Together, our data suggest that Glu113 functions as an acid-base catalyst to assist heterolytic OO bond cleavage during the early stage of the catalytic reaction. This work advances our mechanistic understanding of the H2O2-activation process during bis-Fe(IV) formation in MauG.

  6. Molecular Orbital Study of the Formation of Intramolecular Hydrogen Bonding of a Ligand Molecule in a Protein Aromatic Hydrophobic Pocket.

    PubMed

    Koseki, Jun; Gouda, Hiroaki; Hirono, Shuichi

    2016-01-01

    The natural product argadin is a cyclopentapeptide chitinase inhibitor that binds to chitinase B (ChiB) from the pathogenic bacteria Serratia marcescens. N(ω)-Acetyl-L-arginine and L-aminoadipic acid of argadin form intramolecular ionic hydrogen bonds in the aromatic hydrophobic pocket of ChiB. We performed ab initio molecular orbital and density functional theory calculations to elucidate the role of this intramolecular hydrogen bonding on intermolecular interactions between argadin and ChiB. We found that argadin accrues large stabilization energies from the van der Waals dispersion interactions, such as CH-π, π-π, and π-lone pair interactions, in the aromatic hydrophobic pocket of ChiB, although intramolecular hydrogen bonding within argadin might result in loss of entropy. The intramolecular ionic hydrogen bonding formation canceled local molecular charges and provided good van der Waals interactions with surrounding aromatic residues.

  7. Organometallic nickel(III) complexes relevant to cross-coupling and carbon-heteroatom bond formation reactions.

    PubMed

    Zheng, Bo; Tang, Fengzhi; Luo, Jia; Schultz, Jason W; Rath, Nigam P; Mirica, Liviu M

    2014-04-30

    Nickel complexes have been widely employed as catalysts in C-C and C-heteroatom bond formation reactions. In addition to Ni(0) and Ni(II) intermediates, several Ni-catalyzed reactions are proposed to also involve odd-electron Ni(I) and Ni(III) oxidation states. We report herein the isolation, structural and spectroscopic characterization, and organometallic reactivity of Ni(III) complexes containing aryl and alkyl ligands. These Ni(III) species undergo transmetalation and/or reductive elimination reactions to form new C-C or C-heteroatom bonds and are also competent catalysts for Kumada and Negishi cross-coupling reactions. Overall, these results provide strong evidence for the direct involvement of organometallic Ni(III) species in cross-coupling reactions and oxidatively induced C-heteroatom bond formation reactions.

  8. Jargonial-Obfuscation(J-O) DISambiguation Elimination via Siegel-Baez Cognition Category-Semantics(C-S) in Siegel FUZZYICS=CATEGORYICS (Son of TRIZ)/(F=C) Tabular List-Format Dichotomy Truth-Table Matrix Analytics

    NASA Astrophysics Data System (ADS)

    Siegel, Carl Ludwig; Siegel, Edward Carl-Ludwig

    2011-03-01

    NOT "philosophy" per se but raising serious salient Arnol'd [Huygens and Barrow, Newton and Hooke(96)] questions begged is Rota empiricism Husserl VS. Frege maths-objects Dichotomy controversy: Hill-Haddock[Husserl or Frege?(00)]as manifestly-demonstrated by Hintikka[B.U.]-Critchey[Derrida Deconstruction Ethics(78)] deconstruction; Altshuler TRIZ; Siegel F=C/C-S; Siegel-Baez(UCR) Cognition C-S = "Category-theory ``+'' Cognitive-Semantics[Wierzbica-Langacker-Lakoff-Nunez[Where Maths Comes From(00)]-Fauconnier-Turner[Blending(98)]-Coulson[Semantic-Leaps (00)

  9. MICROWAVE-ASSISTED CHEMISTRY: SYNTHESIS OF AMINES AND HETEROCYCLES VIA CARBON-NITROGEN BOND FORMATION IN AQUEOUS MEDIA

    EPA Science Inventory

    Improved C-N bond formation under MW influence is demonstrated by a) solventless three-component coupling reaction to generate propargyl amines that uses only Cu (I); b) aqueous N-alkylation of amines by alkyl halides that proceeds expeditiously in the presence of NaOH to deliver...

  10. MICROWAVE-ASSISTED CHEMISTRY: SYNTHESIS OF AMINES AND HETEROCYCLES VIA CARBON-NITROGEN BOND FORMATION IN AQUEOUS MEDIA

    EPA Science Inventory

    Improved C-N bond formation under MW influence is demonstrated by a) solventless three-component coupling reaction to generate propargyl amines that uses only Cu (I); b) aqueous N-alkylation of amines by alkyl halides that proceeds expeditiously in the presence of NaOH to deliver...

  11. I2-Catalyzed C-O Bond Formation and Dehydrogenation: Facile Synthesis of Oxazolines and Oxazoles Controlled by Bases.

    PubMed

    Gao, Wen-Chao; Hu, Fei; Huo, Yu-Ming; Chang, Hong-Hong; Li, Xing; Wei, Wen-Long

    2015-08-07

    A general method for the synthesis of oxazolines and oxazoles was developed through I2-catalyzed C-O bond formation and dehydrogenation with the same oxidant, TBHP. By simply tuning reaction bases, either oxazolines or oxazoles were selectively produced from β-acylamino ketones.

  12. Emotional Experiences of Preservice Science Teachers in Online Learning: The Formation, Disruption and Maintenance of Social Bonds

    ERIC Educational Resources Information Center

    Bellocchi, Alberto; Mills, Kathy A.; Ritchie, Stephen M.

    2016-01-01

    The enactment of learning to become a science teacher in online mode is an emotionally charged experience. We attend to the formation, maintenance and disruption of social bonds experienced by online preservice science teachers as they shared their emotional online learning experiences through blogs, or e-motion diaries, in reaction to videos of…

  13. Iron-promoted C-C bond formation in the total synthesis of natural products and drugs.

    PubMed

    Legros, Julien; Figadère, Bruno

    2015-11-01

    Iron salts are inexpensive and almost innocuous; they are thus the promoters of choice, even in stoichiometric amounts, for the formation of carbon-carbon bonds in the backbone of complex molecules. This review encompasses the key role of iron complexes in the total synthesis of some natural products or pharmacologically important compounds.

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

    PubMed

    Semproni, Scott P; Chirik, Paul J

    2013-12-02

    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.

  15. Emotional Experiences of Preservice Science Teachers in Online Learning: The Formation, Disruption and Maintenance of Social Bonds

    ERIC Educational Resources Information Center

    Bellocchi, Alberto; Mills, Kathy A.; Ritchie, Stephen M.

    2016-01-01

    The enactment of learning to become a science teacher in online mode is an emotionally charged experience. We attend to the formation, maintenance and disruption of social bonds experienced by online preservice science teachers as they shared their emotional online learning experiences through blogs, or e-motion diaries, in reaction to videos of…

  16. Electrochemical Formation of Fe(V) (O) and Mechanism of Its Reaction with Water During O-O Bond Formation.

    PubMed

    Pattanayak, Santanu; Chowdhury, Debarati Roy; Garai, Bikash; Singh, Kundan K; Paul, Amit; Dhar, Basab B; Gupta, Sayam Sen

    2017-03-08

    A detailed electrochemical investigation of a series of iron complexes (biuret-modified tetraamido iron macrocycles Fe(III) -bTAML), including the first electrochemical generation of Fe(V) (O), and demonstration of their efficacy as homogeneous catalysts for electrochemical water oxidation (WO) in aqueous medium are reported. Spectroelectrochemical and mass spectral studies indicated Fe(V) (O) as the active oxidant, formed due to two redox transitions, which were assigned as Fe(IV) (O)/Fe(III) (OH2 ) and Fe(V) (O)/Fe(IV) (O). The spectral properties of both of these high-valent iron oxo species perfectly match those of their chemically synthesised versions, which were thoroughly characterised by several spectroscopic techniques. The O-O bond-formation step occurs by nucleophilic attack of H2 O on Fe(V) (O). A kinetic isotope effect of 3.2 indicates an atom-proton transfer (APT) mechanism. The reaction of chemically synthesised Fe(V) (O) in CH3 CN and water was directly probed by electrochemistry and was found to be first-order in water. The pKa value of the buffer base plays a critical role in the rate-determining step by increasing the reaction rate several-fold. The electronic effect on redox potential, WO rates, and onset overpotential was studied by employing a series of iron complexes. The catalytic activity was enhanced by the presence of electron-withdrawing groups on the bTAML framework. Changing the substituents from OMe to NO2 resulted in an eightfold increase in reaction rate, while the overpotential increased threefold.

  17. The Pediocin PA-1 Accessory Protein Ensures Correct Disulfide Bond Formation in the Antimicrobial Peptide Pediocin PA-1.

    PubMed

    Oppegård, Camilla; Fimland, Gunnar; Anonsen, Jan Haug; Nissen-Meyer, Jon

    2015-05-19

    Peptides, in contrast to proteins, are generally not large enough to form stable and well-defined three-dimensional structures. However, peptides are still able to form correct disulfide bonds. Using pediocin-like bacteriocins, we have examined how this may be achieved. Some pediocin-like bacteriocins, such as pediocin PA-1 and sakacin P[N24C+44C], have four cysteines. There are three possible ways by which the four cysteines may combine to form two disulfide bonds, and the three variants are expected to be produced in approximately equal amounts if their formation is random. Pediocin PA-1 and sakacin P[N24C+44C] with correct disulfide bonds were the main products when they were secreted by the pediocin PA-1 ABC transporter and accessory protein, but when they were secreted by the corresponding secretion machinery for sakacin A, a pediocin-like bacteriocin with one disulfide bond (two cysteines), peptides with all three possible disulfide bonds were produced in approximately equal amounts. All five cysteines in the pediocin PA-1 ABC transporter and the two cysteines (that form a CxxC motif) in the accessory protein were individually replaced with serines to examine their involvement in disulfide bond formation in pediocin PA-1. The Cys86Ser mutation in the accessory protein caused a 2-fold decrease in the amount of pediocin PA-1 with correct disulfide bonds, while the Cys83Ser mutation nearly abolished the production of pediocin PA-1 and resulted in the production of all three disufide bond variants in equal amounts. The Cys19Ser mutation in the ABC transporter completely abolished secretion of pediocin PA-1, suggesting that Cys19 is in the proteolytic active site and involved in cleaving the prebacteriocin. Replacing the other four cysteines in the ABC transporter with serines caused a slight reduction in the overall amount of secreted pediocin PA-1, but the relative amount with the correct disulfide bonds remained large. These results indicate that the pediocin

  18. Ions colliding with clusters of fullerenes--decay pathways and covalent bond formations.

    PubMed

    Seitz, F; Zettergren, H; Rousseau, P; Wang, Y; Chen, T; Gatchell, M; Alexander, J D; Stockett, M H; Rangama, J; Chesnel, J Y; Capron, M; Poully, J C; Domaracka, A; Méry, A; Maclot, S; Vizcaino, V; Schmidt, H T; Adoui, L; Alcamí, M; Tielens, A G G M; Martín, F; Huber, B A; Cederquist, H

    2013-07-21

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C60 molecules following collisions with Ar(2+), He(2+), and Xe(20+) at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C60 monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C60]n(+) → C60(+)+(n-1)C60 evaporation model. Excitation energies in the range of only ~0.7 eV per C60 molecule in a [C60]13(+) cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar(2+) and He(2+) collisions, we observe very efficient C119(+) and C118(+) formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C59(+) or C58(+) and C60 during cluster fragmentation. In the Ar(2+) case, it is possible to form even smaller C120-2m(+) molecules (m = 2-7), while no molecular fusion reactions are observed for the present Xe(20+) collisions.

  19. Ions colliding with clusters of fullerenes—Decay pathways and covalent bond formations

    NASA Astrophysics Data System (ADS)

    Seitz, F.; Zettergren, H.; Rousseau, P.; Wang, Y.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Rangama, J.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Domaracka, A.; Méry, A.; Maclot, S.; Vizcaino, V.; Schmidt, H. T.; Adoui, L.; Alcamí, M.; Tielens, A. G. G. M.; Martín, F.; Huber, B. A.; Cederquist, H.

    2013-07-01

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C60 molecules following collisions with Ar2 +, He2 +, and Xe20 + at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C60 monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C_{60}]_n^+ → C_{60}+ + (n-1)C_{60} evaporation model. Excitation energies in the range of only ˜0.7 eV per C60 molecule in a [C_{60}]_{13}^+ cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar2 + and He2 + collisions, we observe very efficient C_{119}+ and C_{118}+ formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C_{59}+ or C_{58}+ and C60 during cluster fragmentation. In the Ar2 + case, it is possible to form even smaller C_{120-2m}+ molecules (m = 2-7), while no molecular fusion reactions are observed for the present Xe20 + collisions.

  20. Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress

    PubMed Central

    2012-01-01

    Background The protein secretory pathway must process a wide assortment of native proteins for eukaryotic cells to function. As well, recombinant protein secretion is used extensively to produce many biologics and industrial enzymes. Therefore, secretory pathway dysfunction can be highly detrimental to the cell and can drastically inhibit product titers in biochemical production. Because the secretory pathway is a highly-integrated, multi-organelle system, dysfunction can happen at many levels and dissecting the root cause can be challenging. In this study, we apply a systems biology approach to analyze secretory pathway dysfunctions resulting from heterologous production of a small protein (insulin precursor) or a larger protein (α-amylase). Results HAC1-dependent and independent dysfunctions and cellular responses were apparent across multiple datasets. In particular, processes involving (a) degradation of protein/recycling amino acids, (b) overall transcription/translation repression, and (c) oxidative stress were broadly associated with secretory stress. Conclusions Apparent runaway oxidative stress due to radical production observed here and elsewhere can be explained by a futile cycle of disulfide formation and breaking that consumes reduced glutathione and produces reactive oxygen species. The futile cycle is dominating when protein folding rates are low relative to disulfide bond formation rates. While not strictly conclusive with the present data, this insight does provide a molecular interpretation to an, until now, largely empirical understanding of optimizing heterologous protein secretion. This molecular insight has direct implications on engineering a broad range of recombinant proteins for secretion and provides potential hypotheses for the root causes of several secretory-associated diseases. PMID:22380681

  1. Ions colliding with clusters of fullerenes-Decay pathways and covalent bond formations

    SciTech Connect

    Seitz, F.; Zettergren, H.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Schmidt, H. T.; Cederquist, H.; Rousseau, P.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Mery, A.; Maclot, S.; Adoui, L.; Wang, Y.; Martin, F.; Rangama, J.; Domaracka, A.; Vizcaino, V. [CIMAP, UMR 6252, CEA and others

    2013-07-21

    We report experimental results for the ionization and fragmentation of weakly bound van der Waals clusters of n C{sub 60} molecules following collisions with Ar{sup 2+}, He{sup 2+}, and Xe{sup 20+} at laboratory kinetic energies of 13 keV, 22.5 keV, and 300 keV, respectively. Intact singly charged C{sub 60} monomers are the dominant reaction products in all three cases and this is accounted for by means of Monte Carlo calculations of energy transfer processes and a simple Arrhenius-type [C{sub 60}]{sub n}{sup +}{yields}C{sub 60}{sup +}+(n-1)C{sub 60} evaporation model. Excitation energies in the range of only {approx}0.7 eV per C{sub 60} molecule in a [C{sub 60}]{sub 13}{sup +} cluster are sufficient for complete evaporation and such low energies correspond to ion trajectories far outside the clusters. Still we observe singly and even doubly charged intact cluster ions which stem from even more distant collisions. For penetrating collisions the clusters become multiply charged and some of the individual molecules may be promptly fragmented in direct knock-out processes leading to efficient formations of new covalent systems. For Ar{sup 2+} and He{sup 2+} collisions, we observe very efficient C{sub 119}{sup +} and C{sub 118}{sup +} formation and molecular dynamics simulations suggest that they are covalent dumb-bell systems due to bonding between C{sub 59}{sup +} or C{sub 58}{sup +} and C{sub 60} during cluster fragmentation. In the Ar{sup 2+} case, it is possible to form even smaller C{sub 120-2m}{sup +} molecules (m= 2-7), while no molecular fusion reactions are observed for the present Xe{sup 20+} collisions.

  2. Enhancing peptide ligand binding to vascular endothelial growth factor by covalent bond formation.

    PubMed

    Marquez, Bernadette V; Beck, Heather E; Aweda, Tolulope A; Phinney, Brett; Holsclaw, Cynthia; Jewell, William; Tran, Diana; Day, Jeffrey J; Peiris, Malalage N; Nwosu, Charles; Lebrilla, Carlito; Meares, Claude F

    2012-05-16

    Formation of a stable covalent bond between a synthetic probe molecule and a specific site on a target protein has many potential applications in biomedical science. For example, the properties of probes used as receptor-imaging ligands may be improved by increasing their residence time on the targeted receptor. Among the more interesting cases are peptide ligands, the strongest of which typically bind to receptors with micromolar dissociation constants, and which may depend on processes other than simple binding to provide images. The side chains of cysteine, histidine, or lysine are attractive for chemical attachment to improve binding to a receptor protein, and a system based on acryloyl probes attaching to engineered cysteine provides excellent positron emission tomographic images in animal models (Wei et al. (2008) J. Nucl. Med. 49, 1828-1835). In nature, lysine is a more common but less reactive residue than cysteine, making it an interesting challenge to modify. To seek practically useful cross-linking yields with naturally occurring lysine side chains, we have explored not only acryloyl but also other reactive linkers with different chemical properties. We employed a peptide-VEGF model system to discover that a 19mer peptide ligand, which carried a lysine-tagged dinitrofluorobenzene group, became attached stably and with good yield to a unique lysine residue on human vascular endothelial growth factor (VEGF), even in the presence of 70% fetal bovine serum. The same peptide carrying acryloyl and related Michael acceptors gave low yields of attachment to VEGF, as did the chloroacetyl peptide.

  3. The transition state for peptide bond formation reveals the ribosome as a water trap.

    PubMed

    Wallin, Göran; Aqvist, Johan

    2010-02-02

    Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered "double proton shuttle" mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.

  4. Quantum-mechanical study on the mechanism of peptide bond formation in the ribosome.

    PubMed

    Acosta-Silva, Carles; Bertran, Joan; Branchadell, Vicenç; Oliva, Antoni

    2012-04-04

    Ribosomes transform the genetic information encoded within genes into proteins. In recent years, there has been much progress in the study of this complex molecular machine, but the mechanism of peptide bond formation and the origin of the catalytic power of this ancient enzymatic system are still an unsolved puzzle. A quantum-mechanical study of different possible mechanisms of peptide synthesis in the ribosome has been carried out using the M06-2X density functional. The uncatalyzed processes in solution have been treated with the SMD solvation model. Concerted and two-step mechanisms have been explored. Three main points suggested in this work deserve to be deeply analyzed. First, no zwitterionic intermediates are found when the process takes place in the ribosome. Second, the proton shuttle mechanism is suggested to be efficient only through the participation of the A2451 2'-OH and two crystallographic water molecules. Finally, the mechanisms in solution and in the ribosome are very different, and this difference may help us to understand the origin of the efficient catalytic role played by the ribosome.

  5. Reaction of nitrosonium cation with resorc[4]arenes activated by supramolecular control: covalent bond formation.

    PubMed

    Ghirga, Francesca; D'Acquarica, Ilaria; Delle Monache, Giuliano; Mannina, Luisa; Molinaro, Carmela; Nevola, Laura; Sobolev, Anatoly P; Pierini, Marco; Botta, Bruno

    2013-07-19

    Resorc[4]arenes 1 and 2, which previously proved to entrap NO(+) cation within their cavities under conditions of host-to-guest excess, were treated with a 10-fold excess of NOBF4 salt in chloroform. Kinetic and spectral UV-visible analyses revealed the formation of isomeric 1:2 complexes as a direct evolution of the previously observed event. Accordingly, three-body 1-(NO(+))2 and 2-(NO(+))2 adducts were built by MM and fully optimized by DFT calculations at the B3LYP/6-31G(d) level of theory. Notably, covalent nitration products 4, 5 and 6, 7 were obtained by reaction of NOBF4 salt with host 1 and 2, respectively, involving macrocycle ring-opening and insertion of a nitro group in one of the four aromatic rings. In particular, compounds 4 and 6, both containing a trans-double bond in the place of the methine bridge, were oxidized to aldehydes 5 and 7, respectively, after addition of water to the reaction mixture. Calculation of the charge and frontier orbitals of the aromatic donor (HOMO) and the NO(+) acceptor (LUMO) clearly suggests an ipso electrophilic attack by a first NO(+) unit on the resorcinol ring, mediated by the second NO(+) unit.

  6. Bimodal supramolecular functionalization of carbon nanotubes triggered by covalent bond formation.

    PubMed

    Leret, Sofía; Pouillon, Yann; Casado, Santiago; Navío, Cristina; Rubio, Ángel; Pérez, Emilio M

    2017-03-01

    Many applications of carbon nanotubes require their chemical functionalization. Both covalent and supramolecular approaches have been extensively investigated. A less trodden path is the combination of both covalent and noncovalent chemistries, where the formation of covalent bonds triggers a particularly stable noncovalent interaction with the nanotubes. We describe a series of naphthalene diimide (NDI) bisalkene molecules that, upon mixing with single-walled carbon nanotubes (SWNTs) and Grubbs' catalyst, undergo two different reaction pathways. On one hand, they ring-close around the SWNTs to form rotaxane-like mechanically interlocked derivatives of SWNTs (MINTs). Alternatively, they oligomerize and then wrap around the SWNTs. The balance of MINTs to oligomer-wrapped SWNTs depends on the affinity of the NDI molecules for the SWNTs and the kinetics of the metathesis reactions, which can be controlled by varying the solvent. Thorough characterization of the products (TGA, TEM, AFM, Raman, UV-vis-NIR, PLE, XPS and UPS) confirms their structure and shows that each type of functionalization affects the electronic properties of the SWNTs differently.

  7. Covalent bond formation between amino acids and lignin: cross-coupling between proteins and lignin.

    PubMed

    Cong, Fang; Diehl, Brett G; Hill, Joseph Lee; Brown, Nicole R; Tien, Ming

    2013-12-01

    The present study characterized the products formed from the reaction of amino acids and in turn, proteins, with lignin resulting in cross-coupling. When added to reaction mixtures containing coniferyl alcohol, horseradish peroxidase and H2O2, three amino acids (Cys, Tyr, and Thr) are able to form adducts. The low molecular weight products were analyzed by HPLC and from each reaction mixture, one product was isolated and analyzed by LC/MS. LC/MS results are consistent with bond formation between the polar side-chain of these amino acids with Cα. These results are consistent with the cross-coupling of Cys, Tyr and Thr through a quinone methide intermediate. In addition to the free amino acids, it was found that the cross-coupling of proteins with protolignin through Cys or Tyr residues. The findings provide a mechanism by which proteins and lignin can cross-couple in the plant cell wall. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Artifactual formation of disulfide bonds during SDS-PAGE analysis of type I copper proteins

    SciTech Connect

    Kumar, M.A.; Davidson, V.L. )

    1991-03-11

    Amicyanin is a monomeric Type I blue' copper protein, which possesses a single cysteine that serves as one of the ligands to copper. Amicyanin denatured by heating in SDS in the presence of {beta}-mercaptoethanol ({beta}ME) migrated during SDS-PAGE with an M{sub r} = 15,000. When heated in SDS in the absence of {beta}ME it exhibited an M{sub r} = 30,000. If treated with {beta}ME, but not heated it exhibited an M{sub r} = 15,000. Similar data were obtained with the small blue copper protein, azurin. Ascorbate oxidase is a multicopper enzyme which is composed of two identical non-covalently bound subunits, each of which possesses a Type I copper center. When this blue' oxidase was denatured by heating in SDS with {beta}ME, or incubated with {beta}ME without heating, a single band of M{sub r} = 70,000 was observed. When heated in SDS without {beta}ME, a species twice that size was observed. Thus, exposure during denaturation of the free sulfhydryl of the Type I copper binding site can cause formation of disulfide bonds between otherwise unlinked polypeptides.

  9. Modulating weak intramolecular interactions through the formation of beryllium bonds: complexes between squaric acid and BeH2.

    PubMed

    Montero-Campillo, M Merced; Lamsabhi, Al Mokhtar; Mó, Otilia; Yáñez, Manuel

    2013-07-01

    The electronic structure of the two most stable isomers of squaric acid and their complexes with BeH2 were investigated at the B3LYP/6-311 + G(3df,2p)// B3LYP/6-31 + G(d,p) level of theory. Squaric acid forms rather strong beryllium bonds with BeH2, with binding energies of the order of 60 kJ mol(-1). The preferential sites for BeH2 attachment are the carbonyl oxygen atoms, but the global minima of the potential energy surfaces of both EZ and ZZ isomers are extra-stabilized through the formation of a BeH···HO dihydrogen bond. More importantly, analysis of the electron density of these complexes shows the existence of significant cooperative effects between the beryllium bond and the dihydrogen bond, with both becoming significantly reinforced. The charge transfer involved in the formation of the beryllium bond induces a significant electron density redistribution within the squaric acid subunit, affecting not only the carbonyl group interacting with the BeH2 moiety but significantly increasing the electron delocalization within the four membered ring. Accordingly the intrinsic properties of squaric acid become perturbed, as reflected in its ability to self-associate.

  10. Probabilistic modeling of shear-induced formation and breakage of doublets cross-linked by receptor-ligand bonds.

    PubMed

    Long, M; Goldsmith, H L; Tees, D F; Zhu, C

    1999-02-01

    A model was constructed to describe previously published experiments of shear-induced formation and breakage of doublets of red cells and of latexes cross-linked by receptor-ligand bonds (. Biophys. J. 65:1318-1334; Tees and Goldsmith. 1996. Biophys. J. 71:1102-1114;. Biophys. J. 71:1115-1122). The model, based on McQuarrie's master equations (1963. J. Phys. Chem. 38:433-436), provides unifying treatments for three distinctive time periods in the experiments of particles in a Couette flow in which a doublet undergoes 1) formation upon two-body collision between singlets; 2) evolution of bonds at low shear rate; and 3) break-up at high shear rate. Neglecting the applied force at low shear rate, the probability of forming a doublet per collision as well as the evolution of probability distribution of bonds in a preformed doublet were solved analytically and found to be in quite good agreement with measurements. At high shear rate with significant force acting to accelerate bond dissociation, the predictions for break-up of doublets were obtained numerically and compared well with data in both individual and population studies. These comparisons enabled bond kinetic parameters for three types of particles cross-linked by two receptor-ligand systems to be calculated, which agreed well with those computed from Monte Carlo simulations. This work can be extended to analyze kinetics of receptor-ligand binding in cell aggregates, such as those of neutrophils and platelets in the circulation.

  11. Protonation switching to the least-basic heteroatom of carbamate through cationic hydrogen bonding promotes the formation of isocyanate cations.

    PubMed

    Kurouchi, Hiroaki; Sumita, Akinari; Otani, Yuko; Ohwada, Tomohiko

    2014-07-07

    We found that phenethylcarbamates that bear ortho-salicylate as an ether group (carbamoyl salicylates) dramatically accelerate OC bond dissociation in strong acid to facilitate generation of isocyanate cation (N-protonated isocyanates), which undergo subsequent intramolecular aromatic electrophilic cyclization to give dihydroisoquinolones. To generate isocyanate cations from carbamates in acidic media as electrophiles for aromatic substitution, protonation at the ether oxygen, the least basic heteroatom, is essential to promote CO bond cleavage. However, the carbonyl oxygen of carbamates, the most basic site, is protonated exclusively in strong acids. We found that the protonation site can be shifted to an alternative basic atom by linking methyl salicylate to the ether oxygen of carbamate. The methyl ester oxygen ortho to the phenolic (ether) oxygen of salicylate is as basic as the carbamate carbonyl oxygen, and we found that monoprotonation at the methyl ester oxygen in strong acid resulted in the formation of an intramolecular cationic hydrogen bond (>CO(+) H⋅⋅⋅O<) with the phenolic ether oxygen. This facilitates OC bond dissociation of phenethylcarbamates, thereby promoting isocyanate cation formation. In contrast, superacid-mediated diprotonation at the methyl ester oxygen of the salicylate and the carbonyl oxygen of the carbamate afforded a rather stable dication, which did not readily undergo CO bond dissociation. This is an unprecedented and unknown case in which the monocation has greater reactivity than the dication.

  12. Intermetallic Compound Formation Mechanisms for Cu-Sn Solid-Liquid Interdiffusion Bonding

    NASA Astrophysics Data System (ADS)

    Liu, H.; Wang, K.; Aasmundtveit, K. E.; Hoivik, N.

    2012-09-01

    Cu-Sn solid-liquid interdiffusion (SLID) bonding is an evolving technique for wafer-level packaging which features robust, fine pitch and high temperature tolerance. The mechanisms of Cu-Sn SLID bonding for wafer-level bonding and three-dimensional (3-D) packaging applications have been studied by analyzing the microstructure evolution of Cu-Sn intermetallic compounds (IMCs) at elevated temperature up to 400°C. The bonding time required to achieve a single IMC phase (Cu3Sn) in the final interconnects was estimated according to the parabolic growth law with consideration of defect-induced deviation. The effect of predominantly Cu metal grain size on the Cu-Sn interdiffusion rate is discussed. The temperature versus time profile (ramp rate) is critical to control the morphology of scallops in the IMC. A low temperature ramp rate before reaching the bonding temperature is believed to be favorable in a SLID wafer-level bonding process.

  13. Photosynthesis. Electronic structure of the oxygen-evolving complex in photosystem II prior to O-O bond formation.

    PubMed

    Cox, Nicholas; Retegan, Marius; Neese, Frank; Pantazis, Dimitrios A; Boussac, Alain; Lubitz, Wolfgang

    2014-08-15

    The photosynthetic protein complex photosystem II oxidizes water to molecular oxygen at an embedded tetramanganese-calcium cluster. Resolving the geometric and electronic structure of this cluster in its highest metastable catalytic state (designated S3) is a prerequisite for understanding the mechanism of O-O bond formation. Here, multifrequency, multidimensional magnetic resonance spectroscopy reveals that all four manganese ions of the catalyst are structurally and electronically similar immediately before the final oxygen evolution step; they all exhibit a 4+ formal oxidation state and octahedral local geometry. Only one structural model derived from quantum chemical modeling is consistent with all magnetic resonance data; its formation requires the binding of an additional water molecule. O-O bond formation would then proceed by the coupling of two proximal manganese-bound oxygens in the transition state of the cofactor.

  14. The Intermetallic Compound Formation for the Wire Bond Between an Al Pad and Ag-xPd Alloy Wire

    NASA Astrophysics Data System (ADS)

    Huang, Wei-Hsiang; Lin, Kwang-Lung; Lin, Yu-Wei; Cheng, Yun-Kai

    2016-12-01

    Silver-palladium alloy wire has been shown as an economical and reliable substitute for gold wire in various applications in the electronic packaging industry. The success of wire bonding relies on the formation of an interfacial intermetallic compound (IMC). This study is aimed to investigate the formation behavior of IMCs between an Al pad and Ag-Pd alloy wire with various Pd concentrations of 1.0-6.0% for the as-bonded commercial Ag/Al joint. The interfacial IMCs were investigated with scanning electron microscopy and energy-dispersive x-ray spectroscopy. The IMCs formed are separate (Ag, Pd)2Al and (Ag, Pd)3Al2 for a Ag6Pd wire bond, while (Ag, Pd)2Al and (Ag, Pd)3Al2 are mixed for the other Ag(1-4.5)Pd alloy wire bonds. The thickness of the total IMC layer varies from 0.65 μm for Ag1Pd to 0.91 μm for Ag6Pd, yet a minimum of 0.44 μm exists for Ag3.5Pd. The compound formation behavior was found to correspond with the Ag-Al phase diagram. After pressure cooker tests, a less stable IMC (Ag, Pd)3Al formed at the AgxPd/Al interface.

  15. Topological plasticity of enzymes involved in disulfide bond formation allows catalysis in either the periplasm or the cytoplasm.

    PubMed

    Hatahet, Feras; Ruddock, Lloyd W

    2013-09-23

    The transmembrane enzymes disulfide bond forming enzyme B (DsbB) and vitamin K epoxide reductase (VKOR) are central to oxidative protein folding in the periplasm of prokaryotes. Catalyzed formation of structural disulfide bonds in proteins also occurs in the cytoplasm of some hyperthermophilic prokaryotes through currently, poorly defined mechanisms. We aimed to determine whether DsbB and VKOR can be inverted in the membrane with retention of activity. By rational design of inversion of membrane topology, we engineered DsbB mutants that catalyze disulfide bond formation in the cytoplasm of Escherichia coli. This represents the first engineered inversion of a transmembrane protein with demonstrated conservation of activity and substrate specificity. This successful designed engineering led us to identify two naturally occurring and oppositely oriented VKOR homologues from the hyperthermophile Aeropyrum pernix that promote oxidative protein folding in the periplasm or cytoplasm, respectively, and hence defines the probable route for disulfide bond formation in the cytoplasm of hyperthermophiles. Our findings demonstrate how knowledge on the determinants of membrane protein topology can be used to de novo engineer a metabolic pathway and to unravel an intriguingly simple evolutionary scenario where a new "adaptive" cellular process is constructed by means of membrane protein topology inversion.

  16. Legionella pneumophila utilizes a single-player disulfide-bond oxidoreductase system to manage disulfide bond formation and isomerization.

    PubMed

    Kpadeh, Zegbeh Z; Day, Shandra R; Mills, Brandy W; Hoffman, Paul S

    2015-03-01

    Legionella pneumophila uses a single homodimeric disulfide bond (DSB) oxidoreductase DsbA2 to catalyze extracytoplasmic protein folding and to correct DSB errors through protein-disulfide isomerase (PDI) activity. In Escherichia coli, these functions are separated to avoid futile cycling. In L. pneumophila, DsbA2 is maintained as a mixture of disulfides (S-S) and free thiols (SH), but when expressed in E. coli, only the SH form is observed. We provide evidence to suggest that structural differences in DsbB oxidases (LpDsbB1 and LpDsbB2) and DsbD reductases (LpDsbD1 and LpDsbD2) (compared with E. coli) permit bifunctional activities without creating a futile cycle. LpdsbB1 and LpdsbB2 partially complemented an EcdsbB mutant while neither LpdsbD1 nor LpdsbD2 complemented an EcdsbD mutant unless DsbA2 was also expressed. When the dsb genes of E. coli were replaced with those of L. pneumophila, motility was restored and DsbA2 was present as a mixture of redox forms. A dominant-negative approach to interfere with DsbA2 function in L. pneumophila determined that DSB oxidase activity was necessary for intracellular multiplication and assembly/function of the Dot/Icm Type IVb secretion system. Our studies show that a single-player system may escape the futile cycle trap by limiting transfer of reducing equivalents from LpDsbDs to DsbA2.

  17. μ-Opioid receptors within subregions of the striatum mediate pair bond formation through parallel yet distinct reward mechanisms.

    PubMed

    Resendez, Shanna L; Dome, Mackenzie; Gormley, Gwen; Franco, Dena; Nevárez, Natalie; Hamid, Arif A; Aragona, Brandon J

    2013-05-22

    The prairie vole is a socially monogamous rodent that is an excellent animal model for studies of the neurobiology of social attachment. Such studies have demonstrated that activation of reward circuitry during social interactions facilitates pair bond formation. Within this circuitry, μ-opioid receptors (MORs) modulate naturally rewarding behavior in an anatomically segregated manner; MORs located throughout the striatum (dorsal striatum, NAc core, and the entire NAc shell) are implicated in general motivational processes, whereas those located specifically within the dorsomedial NAc shell mediate positive hedonics (and are referred to as a "hedonic hotspot"). The purpose of the present study was to determine whether MORs within these distinct subregions differentially mediate pair bond formation. We first used receptor autoradiography to compare MOR binding densities between these regions. MOR binding was significantly higher in the NAc core and dorsomedial NAc shell compared with the ventral NAc shell. We next used partner preference testing to determine whether MORs within these subregions differentially mediate pair bonding. Blockade of MORs using 1 or 3 μg of H-d-Phe-Cys-Tyr-d-Trp-Arg-Thr-Pen-Thr-NH2 within the dorsal striatum decreased mating during the cohabitation period and inhibited partner preference formation. In contrast, blockade of MORs within dorsomedial NAc shell inhibited partner preference formation without effecting mating behavior, whereas other regions were not involved. Thus, MORs within the dorsal striatum mediate partner preference formation via impairment of mating, whereas those in the dorsomedial NAc shell appear to mediate pair bond formation through the positive hedonics associated with mating.

  18. Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

    NASA Technical Reports Server (NTRS)

    Oie, T.; Loew, G. H.; Burt, S. K.; MacElroy, R. D.

    1984-01-01

    The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

  19. Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

    NASA Technical Reports Server (NTRS)

    Oie, T.; Loew, G. H.; Burt, S. K.; MacElroy, R. D.

    1984-01-01

    The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

  20. Directional diffusion and void formation at a Si (001) bonded wafer interface

    NASA Astrophysics Data System (ADS)

    Esser, R. H.; Hobart, K. D.; Kub, F. J.

    2002-08-01

    Low-temperature hydrophobic bonding is an enabling technology allowing the fabrication of device structures. Current research into improvement of hydrophobic bonding has focused on the elimination of thermally generated voids. It has been observed that a regular grid etched into the bonding interface can eliminate the thermally generated voids. By manipulation of patterns etched into the bond interface, it was possible to ascertain that the diffusion of interfacial gasses that form the thermally generated voids is enhanced along the <110> directions. This is shown by an analysis of the void density at various locations in relation to the etched trenches at the bonded interface. Void density between trenches is shown to be 12% of the void density near trenches but nto along a <110> direction.

  1. In-situ formation and detailed analysis of imine bonds for the construction of conjugated aromatic monolayers on Au(111)

    NASA Astrophysics Data System (ADS)

    Luo, Y.; Piantek, M.; Miguel, J.; Bernien, M.; Kuch, W.; Haag, R.

    2008-08-01

    We present the synthesis of 4'-amino-4-mercaptobiphenyl (AMB) and its deposition from solution onto Au(111) substrates. The resulting organic thin films were characterized by contact angle, infrared reflection absorption spectroscopy (IRRAS), X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure (NEXAFS) measurements. It is demonstrated that the majority of AMB molecules are coupled to the gold surface via S Au covalent bonds, although only little orientational order of the AMB layer could be detected by NEXAFS. Furthermore, aromatic imine bonds between AMB and 4-hydroxybenzaldehyde (HB), 4-carboxybenzaldehyde (CB), 4-methylbenzaldehyde (MB), or 4-(trifluoromethyl) benzaldehyde (TMB) have been successfully formed. As a result of the limited order, this coupling reaction was incomplete. Nevertheless, the experimental results confirmed the formation of conjugated aromatic imine bonds.

  2. Inefficient delivery but fast peptide bond formation of unnatural L-aminoacyl-tRNAs in translation.

    PubMed

    Ieong, Ka-Weng; Pavlov, Michael Y; Kwiatkowski, Marek; Forster, Anthony C; Ehrenberg, Måns

    2012-10-31

    Translations with unnatural amino acids (AAs) are generally inefficient, and kinetic studies of their incorporations from transfer ribonucleic acids (tRNAs) are few. Here, the incorporations of small and large, non-N-alkylated, unnatural l-AAs into dipeptides were compared with those of natural AAs using quench-flow techniques. Surprisingly, all incorporations occurred in two phases: fast then slow, and the incorporations of unnatural AA-tRNAs proceeded with rates of fast and slow phases similar to those for natural Phe-tRNA(Phe). The slow phases were much more pronounced with unnatural AA-tRNAs, correlating with their known inefficient incorporations. Importantly, even for unnatural AA-tRNAs the fast phases could be made dominant by using high EF-Tu concentrations and/or lower reaction temperature, which may be generally useful for improving incorporations. Also, our observed effects of EF-Tu concentration on the fraction of the fast phase of incorporation enabled direct assay of the affinities of the AA-tRNAs for EF-Tu during translation. Our unmodified tRNA(Phe) derivative adaptor charged with a large unnatural AA, biotinyl-lysine, had a very low affinity for EF-Tu:GTP, while the small unnatural AAs on the same tRNA body had essentially the same affinities to EF-Tu:GTP as natural AAs on this tRNA, but still 2-fold less than natural Phe-tRNA(Phe). We conclude that the inefficiencies of unnatural AA-tRNA incorporations were caused by inefficient delivery to the ribosome by EF-Tu, not slow peptide bond formation on the ribosome.

  3. Slow peptide bond formation by proline and other N-alkylamino acids in translation

    PubMed Central

    Pavlov, Michael Y.; Watts, Richard E.; Tan, Zhongping; Cornish, Virginia W.; Ehrenberg, Måns; Forster, Anthony C.

    2009-01-01

    Proteins are made from 19 aa and, curiously, one N-alkylamino acid (“imino acid”), proline (Pro). Pro is thought to be incorporated by the translation apparatus at the same rate as the 19 aa, even though the alkyl group in Pro resides directly on the nitrogen nucleophile involved in peptide bond formation. Here, by combining quench-flow kinetics and charging of tRNAs with cognate and noncognate amino acids, we find that Pro incorporates in translation significantly more slowly than Phe or Ala and that other N-alkylamino acids incorporate much more slowly. Our results show that the slowest step in incorporation of N-alkylamino acids is accommodation/peptidyl transfer after GTP hydrolysis on EF-Tu. The relative incorporation rates correlate with expectations from organic chemistry, suggesting that amino acid sterics and basicities affect translation rates at the peptidyl transfer step. Cognate isoacceptor tRNAs speed Pro incorporation to rates compatible with in vivo, although still 3–6 times slower than Phe incorporation from Phe-tRNAPhe depending on the Pro codon. Results suggest that Pro is the only N-alkylamino acid in the genetic code because it has a privileged cyclic structure that is more reactive than other N-alkylamino acids. Our data on the variation of the rate of incorporation of Pro from native Pro-tRNAPro isoacceptors at 4 different Pro codons help explain codon bias not accounted for by the “tRNA abundance” hypothesis. PMID:19104062

  4. The formation of new phase and chemical bonds in N-doped diamond films induced by swift heavy ion irradiation

    NASA Astrophysics Data System (ADS)

    Wang, Z. G.; Zhao, Z. M.; Song, Y.; Liu, J.; Sun, Y. M.; Zhang, C. H.; Duan, J. L.; Jin, Y. F.

    2004-06-01

    In this paper, the formation of the new phase and chemical bonds in N-doped diamond films after swift heavy ion irradiations was studied. The original samples were diamond films grown on (1 1 1) oriented p-Si by CVD deposition. These samples were implanted with 100 keV N-ions at room temperature to 5 × 10 17, 1 × 10 18 and 5 × 10 18 N/cm 2, irradiated with 345 MeV Xe or 2.64 GeV U ions, and then analyzed by means of RBS, micro-FTIR, micro-Raman and XRD spectroscopy. The obtained results suggested that N-sp 2C and N-sp 3C bonds formed in all N-doped diamond films, CN bond exists in all 5 × 10 18 N/cm 2 doped samples but could not form in the 5 × 10 17 N/cm 2 doped samples. In the 1 × 10 18 N/cm 2 doped sample, CN bond could form only after swift heavy ion irradiation. Intense energy deposition from the incident swift heavy ions induces the increase of sp 3/sp 2 bonding ratio and thus enhances the formation of N-sp 3C bonds in the samples. Furthermore, the X-ray diffraction analysis indicated that there existed new phases, α- and β-C 3N 4 in the N-doped diamond samples after irradiation by swift heavy ions.

  5. Prediction of Bond Dissociation Energies/Heats of Formation for Diatomic Transition Metal Compounds: CCSD(T) Works.

    PubMed

    Fang, Zongtang; Vasiliu, Monica; Peterson, Kirk A; Dixon, David A

    2017-03-14

    It was recently reported ( J. Chem. Theory Comput. 2015 , 11 , 2036 - 2052 ) that the coupled cluster singles and doubles with perturbative triples method, CCSD(T), should not be used as a benchmark tool for the prediction of dissociation energies (heats of formation) for the first row transition metal diatomics based on a comparison with the experimental thermodynamic values for a set of 20 diatomics. In the present work the bond dissociation energies as well as the heats of formation for those diatomics have been calculated by the Feller-Peterson-Dixon approach at the CCSD(T)/complete basis set (CBS) level of theory including scalar relativistic corrections and correlation of the outer shell of core electrons in addition to the valence electrons. Revised experimental values for the hydrides are presented that are based on new heterolytic R-H bond dissociation energies, which are needed for analysis of the mass spectrometry experiments. The agreement between the calculated bond dissociation energies and the revised experimental values of the hydrides is good. Good agreement of the calculated bond dissociation energies/heats of formation is also found for most of the chlorides, oxides, and sulfides given the experimental error bars from experiment and those of the transition metal atoms in the gas phase. Thus, reliable results can be achieved by the CCSD(T) method at the CBS limit. The use of PW91 orbitals for the CCSD(T) calculations improves the predictions for some compounds with large T1 diagnostics at the HF-CCSD(T) level. The optimized bond distances and calculated vibrational frequencies for the diatomics also agree well with the available experimental values.

  6. Theoretical study of the formation of naphthalene from the radical/π-bond addition between single-ring aromatic hydrocarbons.

    PubMed

    Comandini, Andrea; Brezinsky, Kenneth

    2011-06-09

    The experimental investigations performed in the 1960s on the o-benzyne + benzene reaction as well as the more recent studies on reactions involving π-electrons highlight the importance of π-bonding for different combustion processes related to PAH's and soot formation. In the present investigation radical/π-bond addition reactions between single-ring aromatic compounds have been proposed and computationally investigated as possible pathways for the formation of two-ring fused compounds, such as naphthalene, which serve as precursors to soot formation. The computationally generated optimized structures for the stationary points were obtained with uB3LYP/6-311+G(d,p) calculations, while the energies of the optimized complexes were refined using the uCCSD(T) method and the cc-pVDZ basis set. The computations have addressed the relevance of a number of radical/π-bond addition reactions including the singlet benzene + o-benzyne reaction, which leads to formation of naphthalene and acetylene through fragmentation of the benzobicyclo[2,2,2]octatriene intermediate. For this reaction, the high-pressure limit rate constants for the individual elementary reactions involved in the overall process were evaluated using transition state theory analysis. Other radical/π-bond addition reactions studied were between benzene and triplet o-benzyne, between benzene and phenyl radical, and between phenyl radicals, for all of which potential energy surfaces were produced. On the basis of the results of these reaction studies, it was found necessary to propose and subsequently confirm additional, alternative pathways for the formation of the types of PAH compounds found in combustion systems. The potential energy surface for one reaction in particular, the phenyl + phenyl addition, is shown to contain a low-energy channel leading to formation of naphthalene that is energetically comparable to the other examined conventional pathways leading to formation of biphenyl compounds. This

  7. High Performance C/S Composite Cathodes with Conventional Carbonate-Based Electrolytes in Li-S Battery

    PubMed Central

    Zheng, Shiyou; Han, Pan; Han, Zhuo; Zhang, Huijuan; Tang, Zhihong; Yang, Junhe

    2014-01-01

    High stable C/S composites are fabricated by a novel high-temperature sulfur infusion into micro-mesoporous carbon method following with solvent cleaning treatment. The C/S composite cathodes show high Coulombic efficiency, long cycling stability and good rate capability in the electrolyte of 1.0 M LiPF6 + EC/DEC (1:1 v/v), for instance, the reversible capacity of the treated C/S-50 (50% S) cathode retains around 860 mAh/g even after 500 cycles and the Coulombic efficiency is close to 100%, which demonstrates the best electrochemical performance of carbon-sulfur composite cathodes using the carbonate-based electrolyte reported to date. It is believed that the chemical bond of C-S is responsible for the superior electrochemical properties in Li-S battery, that is, the strong interaction between S and carbon matrix significantly improves the conductivity of S, effectively buffers the structural strain/stress caused by the large volume change during lithiation/delithiation, completely eliminates the formation of high-order polysulfide intermediates, and substantially avoids the shuttle reaction and the side reaction between polysulfide anions and carbonate solvent, and thus enables the C/S cathode to use conventional carbonate-based electrolytes and achieve outstanding electrochemical properties in Li-S battery. The results may substantially contribute to the progress of the Li-S battery technology. PMID:24776750

  8. Influence of different light sources on microtensile bond strength and gap formation of resin cement under porcelain inlay restorations.

    PubMed

    Ozturk, A N; Usumez, A

    2004-09-01

    Clinical success with ceramic inlays/onlays has been assisted by the ability to develop a reliable bond of composite resin to dental tissues. The purpose of this study was to test the efficiency of two different light sources on microtensile bond strength and the gap formation of resin cement under class II porcelain inlay restorations. Standardized mesio-occlusal cavities were prepared in 30 freshly extracted, intact human premolar teeth. Then impressions were made and ceramic inlays were fabricated. In the cementation process, the resin cement/inlay combinations were exposed to two different photopolymerization units. The polymerizations through 15 specimens were performed with a conventional halogen light source for 60 s, and the other specimens were cured by a plasma arc light for 9 s. After the cementation process, two 1.2 x 1.2 mm wide 'I' shape sections per tooth were produced with a sectioning machine and sections were subjected to microtensile testing after 24 h or 1 week. Gap formation of specimens cured by different photopolymerization units were evaluated with scanning electron microscopy (SEM). Statistically significant differences were found between the microtensile bond strength of inlays exposed to conventional light and plasma arc curing unit (P < 0.001). Plasma arc curing units make it possible to polymerize composite in much shorter times than conventional curing unit. However, the samples polymerized with conventional halogen light produced better microtensile bond strength than the plasma arc unit.

  9. Self-Assembled Amphiphilic Water Oxidation Catalysts: Control of O-O Bond Formation Pathways by Different Aggregation Patterns.

    PubMed

    Yang, Bing; Jiang, Xin; Guo, Qing; Lei, Tao; Zhang, Li-Ping; Chen, Bin; Tung, Chen-Ho; Wu, Li-Zhu

    2016-05-17

    The oxidation of water to molecular oxygen is the key step to realize water splitting from both biological and chemical perspective. In an effort to understand how water oxidation occurs on a molecular level, a large number of molecular catalysts have been synthesized to find an easy access to higher oxidation states as well as their capacity to make O-O bond. However, most of them function in a mixture of organic solvent and water and the O-O bond formation pathway is still a subject of intense debate. Herein, we design the first amphiphilic Ru-bda (H2 bda=2,2'-bipyridine-6,6'-dicarboxylic acid) water oxidation catalysts (WOCs) of formula [Ru(II) (bda)(4-OTEG-pyridine)2 ] (1, OTEG=OCH2 CH2 OCH2 CH2 OCH3 ) and [Ru(II) (bda)(PySO3 Na)2 ] (2, PySO3 (-) =pyridine-3-sulfonate), which possess good solubility in water. Dynamic light scattering (DLS), scanning electron microscope (SEM), critical aggregation concentration (CAC) experiments and product analysis demonstrate that they enable to self-assemble in water and form the O-O bond through different routes even though they have the same bda(2-) backbone. This work illustrates for the first time that the O-O bond formation pathway can be regulated by the interaction of ancillary ligands at supramolecular level.

  10. The role of disulfide bond formation in the structural transition observed in the intermediate filaments of developing hair.

    PubMed

    Bruce Fraser, R D; Parry, David A D

    2012-10-01

    Hair keratin is a composite structure in which intermediate filaments (IF) are embedded in a protein matrix. During the early stages of development in the hair follicle the redox potential is such that the cysteine residues in the IF are maintained in a reduced form. However, at a late stage of development the redox potential changes to produce an oxidizing environment and the IF undergo a structural transition involving both molecular slippage and radial compaction. In our earlier study the changes in the molecular parameters were estimated from knowledge of the sites of artificially induced crosslinks, and it was noted that the changes in these parameters realigned many of the cysteine residues to positions more favorable to disulfide bond formation. As the energy involved in the formation of disulfide bonds is much greater than that of hydrogen bonds or van der Waals interactions the structural transition is likely to be dominated by the requirement that the bonded cysteine residues occur at closely equivalent axial positions. This criterion was used in the present study to obtain more precise values for the molecular parameters in the oxidized fiber than has hitherto been possible. A comparison of the sequences of hair keratins and epidermal keratins suggests that the slippage observed in trichocyte IF during keratinization does not occur in epidermal IF. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Activation of Water in Titanium Dioxide Photocatalysis by Formation of Surface Hydrogen Bonds: An In Situ IR Spectroscopy Study.

    PubMed

    Sheng, Hua; Zhang, Hongna; Song, Wenjing; Ji, Hongwei; Ma, Wanhong; Chen, Chuncheng; Zhao, Jincai

    2015-05-11

    The hole-driving oxidation of titanium-coordinated water molecules on the surface of TiO2 is both thermodynamically and kinetically unfavorable. By avoiding the direct coordinative adsorption of water molecules to the surface Ti sites, the water can be activated to realize its oxidation. When TiO2 surface is covered by the H-bonding acceptor F, the first-layer water adsorption mode is switched from Ti coordination to a dual H-bonding adsorption on adjacent surface F sites. Detailed in situ IR spectroscopy and isotope-labeling studies reveal that the adsorbed water molecules by dual H-bonding can be oxidized to O2 even in the absence of any electron scavengers. Combined with theoretical calculations, it is proposed that the formation of the dual H-bonding structure can not only enable the hole transfer to the water molecules thermodynamically, but also facilitate kinetically the cleavage of O-H bonds by proton-coupled electron transfer process during water oxidation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. An atom in molecules study of infrared intensity enhancements in fundamental donor stretching bands in hydrogen bond formation.

    PubMed

    Terrabuio, Luiz A; Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E; Haiduke, Roberto L A

    2014-12-07

    Vibrational modes ascribed to the stretching of X-H bonds from donor monomers (HXdonor) in complexes presenting hydrogen bonds (HF···HF, HCl···HCl, HCN···HCN, HNC···HNC, HCN···HF, HF···HCl and H2O···HF) exhibit large (4 to 7 times) infrared intensity increments during complexation according to CCSD/cc-pVQZ-mod calculations. These intensity increases are explained by the charge-charge flux-dipole flux (CCFDF) model based on multipoles from the Quantum Theory of Atoms in Molecules (QTAIM) as resulting from a reinforcing interaction between two contributions to the dipole moment derivatives with respect to the vibrational displacements: charge and charge flux. As such, variations that occur in their intensity cross terms in hydrogen bond formation correlate nicely with the intensity enhancements. These stretching modes of HXdonor bonds can be approximately modeled by sole displacement of the positively charged hydrogens towards the acceptor terminal atom with concomitant electronic charge transfers in the opposite direction that are larger than those occurring for the H atom displacements of their isolated donor molecules. This analysis indicates that the charge-charge flux interaction reinforcement on H-bond complexation is associated with variations of atomic charge fluxes in both parent molecules and small electronic charge transfers between them. The QTAIM/CCFDF model also indicates that atomic dipole flux contributions do not play a significant role in these intensity enhancements.

  13. Native Conformation and Canonical Disulfide Bond Formation Are Interlinked Properties of HIV-1 Env Glycoproteins

    PubMed Central

    Go, Eden P.; Cupo, Albert; Ringe, Rajesh; Pugach, Pavel; Moore, John P.

    2015-01-01

    ABSTRACT We investigated whether there is any association between a native-like conformation and the presence of only the canonical (i.e., native) disulfide bonds in the gp120 subunits of a soluble recombinant human immunodeficiency virus type 1 (HIV-1) envelope (Env) glycoprotein. We used a mass spectrometry (MS)-based method to map the disulfide bonds present in nonnative uncleaved gp140 proteins and native-like SOSIP.664 trimers based on the BG505 env gene. Our results show that uncleaved gp140 proteins were not homogeneous, in that substantial subpopulations (20 to 80%) contained aberrant disulfide bonds. In contrast, the gp120 subunits of the native-like SOSIP.664 trimer almost exclusively retained the canonical disulfide bond pattern. We also observed that the purification method could influence the proportion of an Env protein population that contained aberrant disulfide bonds. We infer that gp140 proteins may always contain a variable but substantial proportion of aberrant disulfide bonds but that the impact of this problem can be minimized via design and/or purification strategies that yield native-like trimers. The same factors may also be relevant to the production and purification of monomeric gp120 proteins that are free of aberrant disulfide bonds. IMPORTANCE It is widely thought that a successful HIV-1 vaccine will include a recombinant form of the Env protein, a trimer located on the virion surface. To increase yield and simplify purification, Env proteins are often made in truncated, soluble forms. A consequence, however, can be the loss of the native conformation concomitant with the virion-associated trimer. Moreover, some soluble recombinant Env proteins contain aberrant disulfide bonds that are not expected to be present in the native trimer. To assess whether these observations are linked, to determine the extent of disulfide bond scrambling, and to understand why scrambling occurs, we determined the disulfide bond profiles of two soluble Env

  14. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.

    PubMed

    Polikanov, Yury S; Steitz, Thomas A; Innis, C Axel

    2014-09-01

    During peptide-bond formation on the ribosome, the α-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-Å resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.

  15. Site- and bond-selective H- formation in methylated pyrimidine bases driven by potassium-molecule collisions

    NASA Astrophysics Data System (ADS)

    Ferreira da Silva, F.; Almeida, D.; Garcia, G.; Limão-Vieira, P.

    2012-11-01

    Electron transfer in alkali-molecule collisions to gas phase thymine and uracil yielding H- formation is selectively controlled in the energy range between 5 and 65 eV. By tuning the collision energy, electron transfer from the alkali to methylated thymine (at the N1 position), methylated uracil (at the N3 position) and partly deuterated thymine, enables H-formation. Such process proceeds not only through the breaking of the (C-H) against (N-H) bonds but also through N1 against N3 sites. Such selectivity, as far as bond and site are concerned, is here reported for the first time in collision induced dissociation experiments by alkali-molecule interactions.

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

    PubMed

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

    2010-12-07

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

  17. Accelerating Pd-Catalyzed C—F Bond Formation: Use of a Microflow Packed-Bed Reactor

    PubMed Central

    Noël, Timothy; Maimone, Thomas J.; Buchwald, Stephen L.

    2012-01-01

    A flow process for Pd-catalyzed carbon fluorine bond formation is described. A microreactor using a packed-bed design allows for easy handling of large quantities of insoluble CsF with precise control over reaction times, efficient mixing, and the ability to safely handle elevated temperatures and pressures. A variety of aryl triflates, including heteroaryl ones, were converted to their corresponding aryl fluoride in short reaction times that would be difficult to achieve in a typical batch process. PMID:21837710

  18. Spontaneous ion-pair formation in the gas phase induced by Beryllium bonds

    NASA Astrophysics Data System (ADS)

    Yáñez, Manuel; Mó, Otilia; Alkorta, Ibon; Elguero, José

    2013-12-01

    The changes in the structure and bonding of the hydrogen bonded complexes between hydrogen halides and ammonia, phosphine and water, when the hydrogen halides form beryllium bonds with BeCl2 have been investigated by CCSD(T)/aug-cc-pVTZ ab initio calculations. Although the experimental evidence showed that a spontaneous proton transfer (PT) from hydrogen halides toward ammonia does not occur, and only is observed for HI when interacting with trimethylamine, we have found that a spontaneous PT does occur when the halide forms beryllium bonds with BeCl2. The complexes so formed are the result of the interaction of Cl2BeX- with NH4+, PH4+, H3O+, respectively.

  19. Formation of Lamellar Pores for Splats via Interfacial or Sub-interfacial Delamination at Chemically Bonded Region

    NASA Astrophysics Data System (ADS)

    Chen, Lin; Yang, Guan-Jun; Li, Cheng-Xin

    2017-02-01

    To comprehensively understand the formation mechanism of lamellar pores in splats, the delamination morphologies and crack patterns of yttria-stabilized zirconia (YSZ) and lanthanum zirconia splats were examined. Results showed that both types of splats grew epitaxially on well-polished YSZ substrates, evidently confirming the formation of chemical bonding between splats and substrate. However, the interfacial or sub-interfacial delamination was observed in all kinds of splats in this study. Residual vertical cracks passing through delaminated domains (on bare substrate) were also observed, which clearly indicated that transverse delamination followed vertical cracking. Mechanical analysis about delamination was addressed, and the results were consistent with the experimental data.

  20. Functional-Group-Tolerant, Silver-Catalyzed N-N Bond Formation by Nitrene Transfer to Amines.

    PubMed

    Maestre, Lourdes; Dorel, Ruth; Pablo, Óscar; Escofet, Imma; Sameera, W M C; Álvarez, Eleuterio; Maseras, Feliu; Díaz-Requejo, M Mar; Echavarren, Antonio M; Pérez, Pedro J

    2017-02-15

    Silver(I) promotes the highly chemoselective N-amidation of tertiary amines under catalytic conditions to form aminimides by nitrene transfer from PhI═NTs. Remarkably, this transformation proceeds in a selective manner in the presence of olefins and other functional groups without formation of the commonly observed aziridines or C-H insertion products. The methodology can be applied not only to rather simple tertiary amines but also to complex natural molecules such as brucine or quinine, where the products derived from N-N bond formation were exclusively formed. Theoretical mechanistic studies have shown that this selective N-amidation reaction proceeds through triplet silver nitrenes.

  1. Formation, Reactivity, and Properties of Nondative Late Transition Metal–Oxygen and–Nitrogen Bonds

    PubMed Central

    FULTON, J. ROBIN; HOLLAND, ANDREW W.; FOX, DANIEL J.; BERGMAN*, ROBERT G.

    2005-01-01

    Complexes containing bonds between heteroatoms such as nitrogen and oxygen and “late” transition metals (i.e., those located on the right side of the transition series) have been implicated as reactive intermediates in numerous important catalytic systems. Despite this, our understanding of such M–X linkages still lags behind that of their M–H and M–C analogues. New synthetic strategies have now made possible the isolation and study of a variety of monomeric late-metal alkoxide, aryloxide, and amide complexes, including parent hydroxide and amide species. The heteroatoms in these materials form surprisingly strong bonds to their metal centers, and their bond energies do not necessarily correlate with the energies of the corresponding H–X bonds. The M–X complexes typically exhibit nucleophilic reactivity, in some cases form strong hydrogen bonds to proton donors, and even deprotonate relatively weak acids. These observations, as well as thermodynamic investigations, suggest that late metal–heteroatom bonds are strongly polarized and possess significant ionic character, properties that play an important role in their interactions with organic compounds. PMID:11790088

  2. Cooperativity between Al Sites Promotes Hydrogen Transfer and Carbon–Carbon Bond Formation upon Dimethyl Ether Activation on Alumina

    PubMed Central

    2015-01-01

    The methanol-to-olefin (MTO) process allows the conversion of methanol/dimethyl ether into olefins on acidic zeolites via the so-called hydrocarbon pool mechanism. However, the site and mechanism of formation of the first carbon–carbon bond are still a matter of debate. Here, we show that the Lewis acidic Al sites on the 110 facet of γ-Al2O3 can readily activate dimethyl ether to yield CH4, alkenes, and surface formate species according to spectroscopic studies combined with a computational approach. The carbon–carbon forming step as well as the formation of methane and surface formate involves a transient oxonium ion intermediate, generated by a hydrogen transfer between surface methoxy species and coordinated methanol on adjacent Al sites. These results indicate that extra framework Al centers in acidic zeolites, which are associated with alumina, can play a key role in the formation of the first carbon–carbon bond, the initiation step of the industrial MTO process. PMID:27162986

  3. Hydroxamate-based colorimetric assay to assess amide bond formation by adenylation domain of nonribosomal peptide synthetases.

    PubMed

    Hara, Ryotaro; Suzuki, Ryohei; Kino, Kuniki

    2015-05-15

    We demonstrated the usefulness of a hydroxamate-based colorimetric assay for predicting amide bond formation (through an aminoacyl-AMP intermediate) by the adenylation domain of nonribosomal peptide synthetases. By using a typical adenylation domain of tyrocidine synthetase (involved in tyrocidine biosynthesis), we confirmed the correlation between the absorbance at 490 nm of the l-Trp-hydroxamate-Fe(3+) complex and the formation of l-Trp-l-Pro, where l-Pro was used instead of hydroxylamine. Furthermore, this assay was adapted to the adenylation domains of surfactin synthetase (involved in surfactin biosynthesis) and bacitracin synthetase (involved in bacitracin biosynthesis). Consequently, the formation of various aminoacyl l-Pro formations was observed.

  4. Oxides formation on hydrophilic bonding interface in plasma-assisted InP/Al2O3/SOI direct wafer bonding

    NASA Astrophysics Data System (ADS)

    Gong, Kewei; Sun, Changzheng; Xiong, Bing; Han, Yanjun; Hao, Zhibiao; Wang, Jian; Wang, Lai; Li, Hongtao

    2017-01-01

    Successful direct wafer bonding between InP and silicon-on-insulator (SOI) wafers has been demonstrated by adopting a 20-nm-thick Al2O3 as the intermediate layer. A detailed investigation on the property of the bonding interface is carried out. Water contact angle test reveals an improved hydrophilicity for both the InP and the Al2O3/SOI wafers after oxygen plasma surface activation. X-ray photoelectron spectroscopy is employed to characterize the bonding interface before and after the wafer bonding process. It is found that oxides are formed on the bonding interface during bonding, which helps ensure high quality hydrophilic bonding.

  5. Exploring the Role of Substitution on the Formation of Se···O/N Noncovalent Bonds.

    PubMed

    Shukla, Rahul; Chopra, Deepak

    2015-11-25

    In this article, we have examined the effect of substitution on the formation of neutral XHSe···O/N (X = -H, -F, -CH3, -CF3, -Cl, -OH, -OCH3, -NH2, -NHCH3, -CN) noncovalent bonds with the oxygen atom from H2O molecule and the nitrogen atom from NH3 being the electron donor atoms, respectively. In addition to this, analysis has also been performed on XMeSe···O/N complexes to study the effect of the role of hydrogen bonding with the hydrogen atoms of the methyl group on Se···O/N interactions. Binding energy calculations were performed to determine the strength of these contacts. The obtained results establish the fact that the presence of a methyl group influences the strength of the observed Se···O/N interactions. Also in some cases, the O-H···Se interaction was observed to be more preferable over the Se···O interaction. The major contribution for stabilization of such Se···O/N interactions is from an interplay among the electrostatics and the exchange energy. To obtain deeper insights and understanding of such Se···O/N contacts, a topological analysis, using the QTAIM approach were also performed. This analysis showed that although the presence of a Me group modifies the Se···O/N interaction, it does not necessitate the formation of hydrogen bonds. To obtain insights into the orbital contributions, a natural bond orbital (NBO) analysis were performed which depicts that the strength of such interactions were derived via charge transfer from the oxygen/nitrogen lone pair to the σ* orbital of the Se-X bond.

  6. Computational study of glucosepane-water and hydrogen bond formation: an electron topology and orbital analysis.

    PubMed

    Nash, Anthony; Saßmannshausen, Jörg; Bozec, Laurent; Birch, Helen L; de Leeuw, Nora H

    2017-04-01

    The collagen protein provides tensile strength to the extracellular matrix in addition to localising cells, proteins and protein cofactors. Collagen is susceptible to a build up of glycation modifications as a result of an exceptionally long half-life. Glucosepane is a collagen cross-linking advanced glycation end product; the structural and mechanical effects of glucosepane are still the subjects of much debate. With the prospect of an ageing population, the management and treatment of age-related diseases is becoming a pressing concern. One area of interest is the isolation of hydrated glucosepane, which has yet to be reported at an atomistic level. This study presents a series of glucosepane-water complexes within an implicit aqueous environment. Electronic structure calculations were performed using density functional theory and a high level basis set. Hydrogen bonds between glucosepane and explicit water were identified by monitoring changes to covalent bonds, calculating levels of electron donation from Natural Bonding Orbital analysis and the detection of bond critical points. Hydrogen bond strength was calculated using second-order perturbation calculations. The combined results suggest that glucosepane is very hydrophilic, with the imidazole feature being energetically more attractive to water than either hydroxyl group, although all hydrogen bonds, regardless of bond strength, were electrostatic in nature. Our results are in growing support of an earlier hypothesis that cross-links may result in an increase in interstitial water retention, which would permit the collagen fibril to swell, thereby potentially affecting the tensile and compression properties and biological function of connective tissues.

  7. Overexpression of the rhodanese PspE, a single cysteine-containing protein, restores disulfide bond formation to an Escherichia coli strain lacking DsbA

    PubMed Central

    Chng, Shu-Sin; Dutton, Rachel J.; Denoncin, Katleen; Vertommen, Didier; Collet, Jean-Francois; Kadokura, Hiroshi; Beckwith, Jonathan

    2012-01-01

    Summary Escherichia coli uses the DsbA/DsbB system for introducing disulfide bonds into proteins in the cell envelope. Deleting either dsbA or dsbB or both reduces disulfide bond formation but does not entirely eliminate it. Whether such background disulfide bond forming activity is enzyme-catalyzed is not known. To identify possible cellular factors that might contribute to the background activity, we studied the effects of overexpressing endogenous proteins on disulfide bond formation in the periplasm. We find that overexpressing PspE, a periplasmic rhodanese, partially restores substantial disulfide bond formation to a dsbA strain. This activity depends on DsbC, the bacterial disulfide bond isomerase, but not on DsbB. We show that overexpressed PspE is oxidized to the sulfenic acid form and reacts with substrate proteins to form mixed disulfide adducts. DsbC either prevents the formation of these mixed disulfides or resolves these adducts subsequently. In the process, DsbC itself gets oxidized and proceeds to catalyze disulfide bond formation. Although this PspE/DsbC system is not responsible for the background disulfide bond forming activity, we suggest that it might be utilized in other organisms lacking the DsbA/DsbB system. PMID:22809289

  8. A theoretical study on the strength of the C-NO2 bond and ring strain upon the formation of the intermolecular H-bonding interaction between HF and nitro group in nitrocyclopropane, nitrocyclobutane, nitrocyclopentane or nitrocyclohexane.

    PubMed

    Qiu, Wei; Ren, Fu-de; Shi, Wen-jing; Wang, Yan-hong

    2015-05-01

    As a follow-up to our investigation into the influence of H-bond on the C-NO2 trigger bond, a comparison of the effect of the H-bond on the ring strain energy with the C-NO2 bond dissociation energy was carried out in the HF complex with nitrocyclopropane, nitrocyclobutane, nitrocyclopentane, and nitrocyclohexane by using the DFT-B3LYP and MP2 (full) methods with the 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. The C-NO2 bond length decreases with strengthening of trigger-bond while the ring perimeter increases companied by weakening of ring strain upon the complex formation. The H-bonding energy correlates well with the increment of ring perimeter and the change of ring bond angle. For nitrocyclopropane∙∙∙HF, the effect of H-bond on the ring strain energy is notable, while for the other complex, it is negligible. Therefore, for nitrocyclopropane∙∙∙HF, the origin of the change of explosive sensitivity might be due to the increment of the C-NO2 bond dissociation energy and decrease of the ring strain energy, while for the other complex, it might be only due to the strengthening of C-NO2 bond. The analysis of electron density shifts shows that the C-C bond in ring loses density while the C-NO2 bond gains density, leading to the weakened ring strain and strengthened C-NO2 bond, and thus the possibly reduced explosive sensitivity.

  9. Synthesis of a fluorine-substituted puromycin derivative for Brønsted studies of ribosomal-catalyzed peptide bond formation.

    PubMed

    Okuda, Kensuke; Hirota, Takashi; Kingery, David A; Nagasawa, Hideko

    2009-03-20

    The mechanism by which the ribosome catalyzes peptide bond formation remains controversial. Here we describe the synthesis of a nucleoside that can be used in Brønsted experiments to assess the transition state of ribosome catalyzed peptide bond formation. This substrate is the nucleoside 3'-amino-3'-deoxy-3'-[(3''R)-3-fluoro-l-phenyl-alanyl]-N(6),N(6)-dimethyladenosine, which was prepared from (1R,2R)-2-amino-1-phenylpropane-1,3-diol. This substrate is active in peptide bond formation on the ribosome and is a useful probe for Brønsted analysis experiments on the ribosome.

  10. Rh(III)/Cu(II)-cocatalyzed synthesis of 1H-indazoles through C-H amidation and N-N bond formation.

    PubMed

    Yu, Da-Gang; Suri, Mamta; Glorius, Frank

    2013-06-19

    Substituted 1H-indazoles can be formed from readily available arylimidates and organo azides by Rh(III)-catalyzed C-H activation/C-N bond formation and Cu-catalyzed N-N bond formation. For the first time the N-H-imidates are demonstrated to be good directing groups in C-H activation, also capable of undergoing intramolecular N-N bond formation. The process is scalable and green, with O2 as the terminal oxidant and N2 and H2O formed as byproducts. Moreover, the products could be transformed to diverse important derivatives.

  11. Disruption of disulfide bond formation alters the trafficking of prothyrotropin releasing hormone (proTRH)-derived peptides.

    PubMed

    Mulcahy, Lawrence R; Barker, Alison J; Nillni, Eduardo A

    2006-01-15

    Rat prothyrotropin releasing hormone (proTRH) is processed in the regulated secretory pathway (RSP) of neuroendocrine cells yielding five TRH peptides and several non-TRH peptides. It is not understood how these peptides are targeted to the RSP. We show here that a disulfide bond in the carboxy-terminus of proTRH plays an important role in the trafficking of this prohormone. Recombinant proTRH was observed to migrate faster on a native gel when treated with dithiothreitol (DTT) suggesting the presence of a disulfide bond. In vitro disulfide bond formation was prevented either by DTT treatment or by mutating cysteines 213 and 219 to glycines. In both cases the peptides derived from these mutants exhibited increased constitutive release and processing defects when expressed in AtT20 cells, a neuroendocrine cell line used in our prior studies on proTRH processing. Immunocytochemistry revealed that wild-type proTRH and mutant proTRH localized in a punctate pattern typical of proteins sorted to the regulated secretory pathway. These data suggest that the proposed disulfide bond of proTRH is involved in sorting of proTRH-derived peptides and in their retention within maturing secretory granules. This is the first evidence of structural motifs being important for the sorting of proTRH.

  12. Pair bond formation leads to a sustained increase in global cerebral glucose metabolism in monogamous male titi monkeys (Callicebus cupreus).

    PubMed

    Maninger, Nicole; Hinde, Katie; Mendoza, Sally P; Mason, William A; Larke, Rebecca H; Ragen, Benjamin J; Jarcho, Michael R; Cherry, Simon R; Rowland, Douglas J; Ferrer, Emilio; Bales, Karen L

    2017-04-21

    Social bonds, especially attachment relationships, are crucial to our health and happiness. However, what we know about the neural substrates of these bonds is almost exclusively limited to rodent models and correlational experiments in humans. Here, we used socially monogamous non-human primates, titi monkeys (Callicebus cupreus) to experimentally examine changes in regional and global cerebral glucose metabolism (GCGM) during the formation and maintenance of pair bonds. Baseline positron emission tomography (PET) scans were taken of thirteen unpaired male titi monkeys. Seven males were then experimentally paired with females, scanned and compared, after one week, to six age-matched control males. Five of the six control males were then also paired and scanned after one week. Scans were repeated on all males after four months of pairing. PET scans were coregistered with structural magnetic resonance imaging (MRI), and region of interest (ROI) analysis was carried out. A primary finding was that paired males showed a significant increase in [(18)F]-fluorodeoxyglucose (FDG) uptake in whole brain following one week of pairing, which is maintained out to four months. Dopaminergic, "motivational" areas and those involved in social behavior showed the greatest change in glucose uptake. In contrast, control areas changed only marginally more than GCGM. These findings confirm the large effects of social bonds on GCGM. They also suggest that more studies should examine how social manipulations affect whole-brain FDG uptake, as opposed to assuming that it does not change across condition.

  13. Synthesis of Oxygen Heterocycles via Aromatic C-O Bond Formation Using Arynes.

    PubMed

    Miyabe, Hideto

    2015-07-09

    Most of the synthetic approaches to the benzo-fused heterocycles containing an oxygen atom have involved the use of phenol derivatives as a starting material. This review highlights the new synthetic approaches involving the aromatic C-O bond-forming process using arynes. The insertion of arynes into the C=O bond gives the unstable intermediates, [2 + 2] cycloaddition-type adducts, which can be easily converted into a variety of oxygen atom-containing heterocycles in a single operation. In this review, the syntheses of oxygen heterocycles, such as coumarin, chromene, xanthene, dihydrobenzofuran and benzofuran derivatives, via the insertion of arynes into the C=O bond of aldehydes or formamides are summarized.

  14. Dynamics of Plug Formation in a Circular Cylinder Under Low Bond Number Conditions: Experiment and Simulation

    NASA Astrophysics Data System (ADS)

    Hallaby, Ghazi; Kizito, John P.

    2016-08-01

    The goal of the current study is to investigate the dynamics of two phase interface under a low Bond number condition. Silicone oil is injected into a cylinder under a Bond number of about 0.47 via a side tube forming a T-junction with the former. The time evolution of the interface of silicon oil in a cylinder is captured using a high speed camera. The volume at which the plug is formed is then determined using an image processing tool to analyze the captured images. A numerical simulation is carried out where fluid is injected into a cylinder, under a less than unity Bond number condition, via a side tube. Numerical and experimental results are then compared.

  15. Drosophila Ebony: a novel type of nonribosomal peptide synthetase related enzyme with unusually fast peptide bond formation kinetics.

    PubMed

    Hartwig, Silvia; Dovengerds, Christine; Herrmann, Christian; Hovemann, Bernhard T

    2014-11-01

    Drosophila Ebony is a β-alanyl biogenic amine synthetase with proven function in cuticle and in glia of the nervous system. It is closely related to nonribosomal peptide synthetases (NRPSs), which typically consist of at least an adenylation, a peptidyl carrier protein and a peptide bond forming condensation domain. Besides its role in cuticle formation, Ebony is in most glia of the brain thought to convert biogenic amines to β-alanyl conjugates. If the metabolization of the neurotransmitter histamine to β-alanyl histamine requires a fast reaction in visual signal transduction, Ebony must be able to fulfill this requirement. Since NRPSs are in general slowly acting multi-modular protein machineries, the enigma of how Ebony quickly facilitates this inactivation remains a key question for understanding its role in vision. To quantitatively analyze the reaction kinetics, we used phosphopantetheinylated holo-Ebony prepared from Baculovirus infected Sf9 cells. Kinetic parameters for the loading reaction, e.g. the formation of β-alanyl-Ebony thioester, complied with those of slow NRPSs. In contrast, single-turnover analysis of the last reaction step, peptide bond formation between pre-activated β-alanyl Ebony thioester and histamine, revealed a very rapid conjugation reaction. This biphasic nature of activity identifies Ebony as a novel type of NRPS related molecule that combines a slow amino acid activation phase with a very fast product formation step.

  16. Effects of strong and weak hydrogen bond formation on VCD spectra: a case study of 2-chloropropionic acid.

    PubMed

    Góbi, Sándor; Vass, Elemér; Magyarfalvi, Gábor; Tarczay, György

    2011-08-21

    The vibrational circular dichroism (VCD) spectrum of S-(-) and R-(+)-2-chloropropionic acid is thoroughly analyzed. Besides the VCD spectrum of the monomer, the dimers (stabilized by strong hydrogen bonds) and the 2-chloropropionic acid-CHCl(3) complexes (stabilized by a weak hydrogen bond) are studied both experimentally (in solution and in low-temperature Ar matrix) and by quantum chemical computations. It is shown that dimer formation drastically changes, and even weak complex formation can also substantially affect the overall shape of the VCD spectrum. The present and previous results can be generalized for the practice of absolute configuration determination of carboxylic acids by VCD spectroscopy. For these measurements, if bulky groups do not block dimer formation, comparison of the computed spectra of the dimers with the experimental spectra recorded in relatively concentrated (∼0.1 mol dm(-3)) solutions is suggested. Our study also shows that due to the stabilization of monomers and/or the formation of weak complexes, the VCD spectrum recorded in CHCl(3) is more complex and, like in the present case, can have a lower intensity than that of the spectrum recorded in CCl(4). Therefore, if solubility allows, CCl(4) is a much preferred solvent over CHCl(3).

  17. Bond formations by intermolecular and intramolecular trappings of acylketenes and their applications in natural product synthesis†

    PubMed Central

    Reber, Keith P.; Tilley, S. David

    2011-01-01

    The reactive intermediates known as acylketenes exhibit a rich chemistry and have been extensively utilized for many types of inter- and intramolecular bond-forming reactions within the field of organic synthesis. Characteristic reactions of acylketenes include cycloadditions, carbon–carbon bond-forming reactions, and nucleophilic capture with alcohols or amines to give β-keto acid derivatives. In particular, the intramolecular capture of acylketene intermediates with pendant nucleophiles represents a powerful method for forming both medium-sized rings and macrocycles, often in high yield. This tutorial review examines the history, generation, and reactivity of acylketenes with a special focus on their applications in the synthesis of natural products. PMID:19847338

  18. Alternative mechanisms for O2 release and O-O bond formation in the oxygen evolving complex of photosystem II.

    PubMed

    Li, Xichen; Siegbahn, Per E M

    2015-05-14

    In a previous detailed study of all the steps of water oxidation in photosystem II, it was surprisingly found that O2 release is as critical for the rate as O-O bond formation. A new mechanism for O2 release has now been found, which can be described as an opening followed by a closing of the interior of the oxygen evolving complex. A transition state for peroxide rotation forming a superoxide radical, missed in the previous study, and a structural change around the outside manganese are two key steps in the new mechanism. However, O2 release may still remain rate-limiting. Additionally, for the step forming the O-O bond, an alternative, experimentally suggested, mechanism was investigated. The new model calculations can rule out the precise use of that mechanism. However, a variant with a rotation of the ligands around the outer manganese by about 30° will give a low barrier, competitive with the old DFT mechanism. Both these mechanisms use an oxyl-oxo mechanism for O-O bond formation involving the same two manganese atoms and the central oxo group (O5).

  19. Do zwitterionic species exist in the non-enzymatic peptide bond formation?

    PubMed

    Świderek, Katarzyna; Tuñón, Iñaki; Martí, Sergio; Moliner, Vicent; Bertrán, Juan

    2012-11-25

    The use of proper computational methods and models has allowed answering the controversial question of whether zwitterionic species exist in the mechanism of peptide bond synthesis in aqueous solution. In fact, the different conformations of zwitterionic species open the door to different mechanistic paths.

  20. Asymmetric organocascades involving the formation of two C-heteroatom bonds from two distinct heteroatoms.

    PubMed

    Bonne, Damien; Constantieux, Thierry; Coquerel, Yoann; Rodriguez, Jean

    2012-05-28

    In the vast and expanding world of enantioselective organocascades, the ones in which two C-heteroatom bonds are created from two distinct heteroatoms are rare. These fascinating domino processes constitutes real synthetic challenges and allow very convenient syntheses of diverse optically active heterocycles and also highly functionalised acyclic derivatives.

  1. Carbon-Carbon Bond Formation in a Weak Ligand Field: Leveraging Open Shell First Row Transition Metal Catalysts.

    PubMed

    Chirik, Paul James

    2017-01-12

    Unique features of Earth abundant transition metal catalysts are reviewed in the context of catalytic carbon-carbon bond forming reactions. Aryl-substituted bis(imino)pyridine iron and cobalt dihalide compounds, when activated with alkyl aluminum reagents, form highly active catalysts for the polymerization of ethylene. Open shell iron and cobalt alkyl complexes have been synthesized that serve as single component olefin polymerization catalysts. Reduced bis(imino)pyridine iron- and cobalt dinitrogen compounds have also been discovered that promote the unique [2+2] cycloaddition of unactivated terminal alkenes. Electronic structure studies support open shell intermediates, a deviation from traditional strong field organometallic compounds that promote catalytic C-C bond formation.

  2. Peptide synthesis in aqueous environments: the role of extreme conditions on peptide bond formation and peptide hydrolysis.

    PubMed

    Schreiner, Eduard; Nair, Nisanth N; Marx, Dominik

    2009-09-30

    The mechanisms and free energetics underlying the formation of peptides from alpha-amino acids and alpha-amino acid N-carboxyanhydrides (NCAs) in bulk water at both ambient and extreme temperature and pressure conditions were investigated using accelerated ab initio molecular dynamics. In particular, peptide bond formation using an activated amino acid in form of its NCA, subsequent decarboxylation, as well as hydrolysis of the formed peptide were studied using glycine. It is shown to what extent thermodynamic conditions affect the reaction mechanisms qualitatively and the energetics quantitatively in solution. In particular, the zwitterionic intermediate in the peptidization step found in ambient water degenerates into a transient species in hot-pressurized water, whereas the hydrolysis reaction is found to follow qualitatively different pathways at ambient and extreme conditions. The work also quantifies the impact of extreme solvent conditions on both peptide bond formation and peptide hydrolysis in aqueous media. Beyond the specific case, the results provide important insights into how elevated temperatures and increased pressures affect organic reactions in aqueous solutions.

  3. A novel metal-to-metal bonding process through in-situ formation of Ag nanoparticles using Ag2O microparticles

    NASA Astrophysics Data System (ADS)

    Hirose, Akio; Tatsumi, Hiroaki; Takeda, Naoya; Akada, Yusuke; Ogura, Tomo; Ide, Eiichi; Morita, Toshiaki

    2009-05-01

    The metal-to-metal bonding has been successfully achieved via the bonding process using Ag metallo-organic nanoparticles at a bonding temperature of around 300-, which can be alternative to the current microsoldering in electronics assembly using high-temperature solders. However, further reduction of bonding temperature and/or bonding pressure is needed. In the present research, a novel bonding process through in-situ formation of Ag nanoparticles instead of the filler material of the Ag metallo-organic nanoparticles has been developed. The Ag nanoparticles can form by the reduction of Ag2O particles. In this study, the Ag2O particles were mixed with triethylene glycol as a reducing agent to form a paste for bonding. The Au coated cylindrical specimens were bonded using the paste. The Ag nanoparticles formed at around 130 to 160 through the reduction process of Ag2O particles with triethylene glycol. The Ag nanoparticles were immediately sintered each other due to a great surface energy per volume. A transmission electron microscope observation revealed that the sintered Ag metallurgically bonded to the Au substrate at around 160 and a dense Ag layer formed after further heating. The tensile strength of the joint bonded at 250 under a bonding pressure of 5MPa was around 60MPa

  4. Entropy reduction effect imposed by hydrogen bond formation on protein folding cooperativity: Evidence from a hydrophobic minimalist model

    NASA Astrophysics Data System (ADS)

    Barbosa, Marco Aurélio A.; Garcia, Leandro G.; Pereira de Araújo, Antônio F.

    2005-11-01

    Conformational restrictions imposed by hydrogen bond formation during protein folding are investigated by Monte Carlo simulations of a non-native-centric, two-dimensional, hydrophobic model in which the formation of favorable contacts is coupled to an effective reduction in lattice coordination. This scheme is intended to mimic the requirement that polar backbone groups of real proteins must form hydrogen bonds concomitantly to their burial inside the apolar protein core. In addition to the square lattice, with z=3 conformations per monomer, we use extensions in which diagonal step vectors are allowed, resulting in z=5 and z=7 . Thermodynamics are governed by the hydrophobic energy function, according to which hydrophobic monomers tend to make contacts unspecifically while the reverse is true for hydrophilic monomers, with the additional restriction that only contacts between monomers adopting one of zhbond formation. The folding transition abruptness and van’t Hoff-to-calorimetric-enthalpy ratio are found to increase dramatically by this simple and physically motivated mechanism. The observed increase in folding cooperativity is correlated to an increase in the convexity of the underlying microcanonical conformational entropy as a function of energy. Preliminary simulations in three dimensions, even though using a smaller relative reduction in lattice effective coordination zh/z=4/5 , display a slight increase in cooperativity for a hydrophobic model of 40 monomers and a more pronounced increase in cooperativity for a native-centric Go-model with the same native conformation, suggesting that this purely entropic effect is not an artifact of dimensionality and is likely to be of fundamental importance in the theoretical understanding of folding cooperativity.

  5. What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.

    PubMed

    Heuts, Dominic P H M; Scrutton, Nigel S; McIntire, William S; Fraaije, Marco W

    2009-07-01

    Many enzymes use one or more cofactors, such as biotin, heme, or flavin. These cofactors may be bound to the enzyme in a noncovalent or covalent manner. Although most flavoproteins contain a noncovalently bound flavin cofactor (FMN or FAD), a large number have these cofactors covalently linked to the polypeptide chain. Most covalent flavin-protein linkages involve a single cofactor attachment via a histidyl, tyrosyl, cysteinyl or threonyl linkage. However, some flavoproteins contain a flavin that is tethered to two amino acids. In the last decade, many studies have focused on elucidating the mechanism(s) of covalent flavin incorporation (flavinylation) and the possible role(s) of covalent protein-flavin bonds. These endeavors have revealed that covalent flavinylation is a post-translational and self-catalytic process. This review presents an overview of the known types of covalent flavin bonds and the proposed mechanisms and roles of covalent flavinylation.

  6. Characterization of covalent bond formation between PPARγ and oxo-fatty acids.

    PubMed

    Egawa, Daichi; Itoh, Toshimasa; Yamamoto, Keiko

    2015-04-15

    Covalent modification of proteins is important for normal cellular regulation. Here, we report on the covalent modification of peroxisome proliferator-activated receptor γ (PPARγ), an important drug target, by oxo-fatty acids. In this study, ESI mass spectroscopy showed that the reactivities of oxo-fatty acids with PPARγ are different from one another and that these behaviors are related to the structure of the fatty acids. X-ray crystallography showed that three oxo-fatty acids all bound to the same residue of PPARγ (Cys285), but displayed different hydrogen bonding modes. Moreover, fatty acids formed covalent bonds with both PPARγ moieties in the homodimer, one in an active conformation and the other in an alternative conformation. These two conformations may explain why covalently bound fatty acids show partial rather than full agonist activity.

  7. The central role of broken bond-bending constraints in promoting glass formation in the oxides.

    PubMed

    Zhang, M; Boolchand, P

    1994-11-25

    A glass network of N atoms with n(1) of the atoms with a coordination number of 1, and m(2) of the atoms with a coordination number of 2 about which the bond-angle constraint is broken, will in general display a stiffness threshold (rigidity percolation threshold) when the average coordination increases to a critical value (r)(c) = 2.4 - 0.4 (n(1) - m(2))/N. Silica and sodium tellurate glasses provide model examples for which this general relation predicts the observed rigidity percolation threshold; this relation predicts the percolation threshold only if one includes broken bond-bending constraints due to bridging oxygen in the former network and nonbridging oxygen in the latter network. The rigidity percolation threshold in (Na(2)O)x,(TeO(2))1-x glasses observed to occur near x approximately 0.18 in tellurium-125 Lamb-Mössbauer factor measurments.

  8. Total synthesis of feglymycin based on a linear/convergent hybrid approach using micro-flow amide bond formation

    NASA Astrophysics Data System (ADS)

    Fuse, Shinichiro; Mifune, Yuto; Nakamura, Hiroyuki; Tanaka, Hiroshi

    2016-11-01

    Feglymycin is a naturally occurring, anti-HIV and antimicrobial 13-mer peptide that includes highly racemizable 3,5-dihydroxyphenylglycines (Dpgs). Here we describe the total synthesis of feglymycin based on a linear/convergent hybrid approach. Our originally developed micro-flow amide bond formation enabled highly racemizable peptide chain elongation based on a linear approach that was previously considered impossible. Our developed approach will enable the practical preparation of biologically active oligopeptides that contain highly racemizable amino acids, which are attractive drug candidates.

  9. Concurrent Formation of Carbon–Carbon Bonds and Functionalized Graphene by Oxidative Carbon-Hydrogen Coupling Reaction

    PubMed Central

    Morioku, Kumika; Morimoto, Naoki; Takeuchi, Yasuo; Nishina, Yuta

    2016-01-01

    Oxidative C–H coupling reactions were conducted using graphene oxide (GO) as an oxidant. GO showed high selectivity compared with commonly used oxidants such as (diacetoxyiodo) benzene and 2,3-dichloro-5,6-dicyano-p-benzoquinone. A mechanistic study revealed that radical species contributed to the reaction. After the oxidative coupling reaction, GO was reduced to form a material that shows electron conductivity and high specific capacitance. Therefore, this system could concurrently achieve two important reactions: C–C bond formation via C–H transformation and production of functionalized graphene. PMID:27181191

  10. Total synthesis of feglymycin based on a linear/convergent hybrid approach using micro-flow amide bond formation

    PubMed Central

    Fuse, Shinichiro; Mifune, Yuto; Nakamura, Hiroyuki; Tanaka, Hiroshi

    2016-01-01

    Feglymycin is a naturally occurring, anti-HIV and antimicrobial 13-mer peptide that includes highly racemizable 3,5-dihydroxyphenylglycines (Dpgs). Here we describe the total synthesis of feglymycin based on a linear/convergent hybrid approach. Our originally developed micro-flow amide bond formation enabled highly racemizable peptide chain elongation based on a linear approach that was previously considered impossible. Our developed approach will enable the practical preparation of biologically active oligopeptides that contain highly racemizable amino acids, which are attractive drug candidates. PMID:27892469

  11. Visible Light Mediated Oxidative C-N Bond Formation/Aromatization Cascade: A New Photocatalytic Entry to N-Arylindoles

    PubMed Central

    Maity, Soumitra

    2012-01-01

    Indoles: A joint effort of light and air We have developed a mild aerobic oxidation protocol using visible light photocatalysis to synthesize structurally diverse N-arylindoles. The procedure employs 4 mol% [Ru(bpz)3](PF6)2, 18W LED light, and is performed open to the atmosphere. Readily prepared o-stryryl anilines are converted to a variety of indoles via a cascade sequence composed of oxidation of anilines, C-N bond formation, and aromatization. A 1,2-carbon shift can be also incorporated into this cascade event to further extend the substrate scope of the method. bpz = 2, 2′-Bipyrazine PMID:22915489

  12. Concurrent Formation of Carbon–Carbon Bonds and Functionalized Graphene by Oxidative Carbon-Hydrogen Coupling Reaction

    NASA Astrophysics Data System (ADS)

    Morioku, Kumika; Morimoto, Naoki; Takeuchi, Yasuo; Nishina, Yuta

    2016-05-01

    Oxidative C–H coupling reactions were conducted using graphene oxide (GO) as an oxidant. GO showed high selectivity compared with commonly used oxidants such as (diacetoxyiodo) benzene and 2,3-dichloro-5,6-dicyano-p-benzoquinone. A mechanistic study revealed that radical species contributed to the reaction. After the oxidative coupling reaction, GO was reduced to form a material that shows electron conductivity and high specific capacitance. Therefore, this system could concurrently achieve two important reactions: C–C bond formation via C–H transformation and production of functionalized graphene.

  13. Aryl-aryl bond formation by the fluoride-free cross-coupling of aryldisiloxanes with aryl bromides.

    PubMed

    Boehner, Christine M; Frye, Elizabeth C; O'Connell, Kieron M G; Galloway, Warren R J D; Sore, Hannah F; Dominguez, Patricia Garcia; Norton, David; Hulcoop, David G; Owen, Martin; Turner, Gillian; Crawford, Claire; Horsley, Helen; Spring, David R

    2011-11-18

    The prevalence of the biaryl structural motif in biologically interesting and synthetically important molecules has inspired considerable interest in the development of methods for aryl-aryl bond formation. Herein we describe a novel strategy for this process involving the fluoride-free, palladium-catalysed cross-coupling of readily accessible aryldisiloxanes and aryl bromides. Using a statistical-based optimisation process, preparatively useful reaction conditions were formulated to allow the cross-coupling of a wide range of different substrates. This methodology represents an attractive, cost-efficient, flexible and robust alternative to the traditional transition-metal-catalysed routes typically used to generate molecules containing the privileged biaryl scaffold.

  14. Early biofilm formation and the effects of antimicrobial agents on orthodontic bonding materials in a parallel plate flow chamber.

    PubMed

    Chin, Mervyn Y H; Busscher, Henk J; Evans, Robert; Noar, Joseph; Pratten, Jonathan

    2006-02-01

    Decalcification is a commonly recognized complication of orthodontic treatment with fixed appliances. A technology, based on a parallel plate flow chamber, was developed to investigate early biofilm formation of a strain of Streptococcus sanguis on the surface of four orthodontic bonding materials: glass ionomer cement (Ketac Cem), resin-modified glass ionomer cement (Fuji Ortho LC), chemically-cured composite resin (Concise) and light-cured composite resin (Transbond XT). S. sanguis was used as it is one of the primary colonizers of dental hard surfaces. Artificial saliva was supplied as a source of nutrients for the biofilms. The effects of two commercially available mouthrinses (i.e. a fluoride containing rinse and chlorhexidine) were evaluated. Initial colonization of the bacterium was assessed after 6 hours of growth by the percentage surface coverage (PSC) of the biofilm on the disc surfaces. There were statistically significant differences in bacterial accumulation between different bonding materials (P < 0.05), Concise being the least colonized and Transbond XT being the most colonized by S. sanguis biofilms. All materials pre-treated with 0.05 per cent sodium fluoride mouthrinse showed more than 50 per cent reduction in biofilm formation. The 0.2 per cent chlorhexidine gluconate mouthrinse caused significant reduction of biofilm formation on all materials except Ketac Cem. This in vitro study showed that the use of a chemically-cured composite resin (Concise) reduced early S. sanguis biofilm formation. Also, fluoride had a greater effect in reducing the PSC by S. sanguis biofilms than chlorhexidine. Rinsing with 0.05 per cent sodium fluoride prior to placement of orthodontic appliances is effective in reducing early biofilm formation.

  15. Carbon-Phosphorus Bond Formation on Anilines Mediated by a Hypervalent Iodine Reagent.

    PubMed

    Deruer, Elsa; Coulibali, Siomenan; Boukercha, Saad; Canesi, Sylvain

    2017-08-25

    Substituted anilines containing a sulfonyl group may be oxidized in situ in the presence of methanol and a hypervalent iodine reagent to form an active iminium species. Subsequent addition of phosphines or phosphites in the same pot produces meta-substituted anilines in good yields. This formal C-H bond functionalization is a direct and efficient means of selectively substituting the meta-position of anilines to produce aromatic phosphonium ions or phosphonates.

  16. Coordinate covalent C --> B bonding in phenylborates and latent formation of phenyl anions from phenylboronic Acid.

    PubMed

    Glaser, Rainer; Knotts, Nathan

    2006-02-02

    The results are reported of a theoretical study of the addition of small nucleophiles Nu(-) (HO(-), F(-)) to phenylboronic acid Ph-B(OH)(2) and of the stability of the resulting complexes [Ph-B(OH)(2)Nu](-) with regard to Ph-B heterolysis [Ph-B(OH)(2)Nu](-) --> Ph(-) + B(OH)(2)Nu as well as Nu(-)/Ph(-) substitution [Ph-B(OH)(2)Nu](-) + Nu(-) --> Ph(-) + [B(OH)(2)Nu(2)](-). These reactions are of fundamental importance for the Suzuki-Miyaura cross-coupling reaction and many other processes in chemistry and biology that involve phenylboronic acids. The species were characterized by potential energy surface analysis (B3LYP/6-31+G*), examined by electronic structure analysis (B3LYP/6-311++G**), and reaction energies (CCSD/6-311++G**) and solvation energies (PCM and IPCM, B3LYP/6-311++G*) were determined. It is shown that Ph-B bonding in [Ph-B(OH)(2)Nu](-) is coordinate covalent and rather weak (<50 kcal.mol(-1)). The coordinate covalent bonding is large enough to inhibit unimolecular dissociation and bimolecular nucleophile-assisted phenyl anion liberation is slowed greatly by the negative charge on the borate's periphery. The latter is the major reason for the extraordinary differences in the kinetic stabilities of diazonium ions and borates in nucleophilic substitution reactions despite their rather similar coordinate covalent bond strengths.

  17. Competition for hydrogen-bond formation in the helix-coil transition and protein folding.

    PubMed

    Badasyan, A V; Tonoyan, Sh A; Mamasakhlisov, Y Sh; Giacometti, Achille; Benight, A S; Morozov, V F

    2011-05-01

    The problem of the helix-coil transition of biopolymers in explicit solvents, such as water, with the ability for hydrogen bonding with a solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress, or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.

  18. Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate

    PubMed Central

    Song, Heng; Hu, Wen; Naowarojna, Nathchar; Her, Ampon Sae; Wang, Shu; Desai, Rushil; Qin, Li; Chen, Xiaoping; Liu, Pinghua

    2015-01-01

    Ergothioneine is a histidine thio-derivative isolated in 1909. In ergothioneine biosynthesis, the combination of a mononuclear non-heme iron enzyme catalyzed oxidative C-S bond formation reaction and a PLP-mediated C-S lyase (EgtE) reaction results in a net sulfur transfer from cysteine to histidine side-chain. This demonstrates a new sulfur transfer strategy in the biosynthesis of sulfur-containing natural products. Due to difficulties associated with the overexpression of Mycobacterium smegmatis EgtE protein, the proposed EgtE functionality remained to be verified biochemically. In this study, we have successfully overexpressed and purified M. smegmatis EgtE enzyme and evaluated its activities under different in vitro conditions: C-S lyase reaction using either thioether or sulfoxide as a substrate in the presence or absence of reductants. Results from our biochemical characterizations support the assignment of sulfoxide 4 as the native EgtE substrate and the involvement of a sulfenic acid intermediate in the ergothioneine C-S lyase reaction. PMID:26149121

  19. Characterization of Sviceucin from Streptomyces Provides Insight into Enzyme Exchangeability and Disulfide Bond Formation in Lasso Peptides.

    PubMed

    Li, Yanyan; Ducasse, Rémi; Zirah, Séverine; Blond, Alain; Goulard, Christophe; Lescop, Ewen; Giraud, Caroline; Hartke, Axel; Guittet, Eric; Pernodet, Jean-Luc; Rebuffat, Sylvie

    2015-11-20

    Lasso peptides are bacterial ribosomally synthesized and post-translationally modified peptides. They have sparked increasing interest in peptide-based drug development because of their compact, interlocked structure, which offers superior stability and protein-binding capacity. Disulfide bond-containing lasso peptides are rare and exhibit highly sought-after activities. In an effort to expand the repertoire of such molecules, we heterologously expressed, in Streptomyces coelicolor, the gene cluster encoding sviceucin, a type I lasso peptide with two disulfide bridges originating from Streptomyces sviceus, which allowed it to be fully characterized. Sviceucin and its reduced forms were characterized by mass spectrometry and peptidase digestion. The three-dimensional structure of sviceucin was determined using NMR. Sviceucin displayed antimicrobial activity selectively against Gram-positive bacteria and inhibition of fsr quorum sensing in Enterococcus faecalis. This study adds sviceucin to the type I lasso peptide family as a new representative. Moreover, new clusters encoding disulfide-bond containing lasso peptides from Actinobacteria were identified by genome mining. Genetic and functional analyses revealed that the formation of disulfide bonds in sviceucin does not require a pathway-encoded thiol-disulfide oxidoreductase. Most importantly, we demonstrated the functional exchangeability of the sviceucin and microcin J25 (a non-disulfide-bridged lasso peptide) macrolactam synthetases in vitro, highlighting the potential of hybrid lasso synthetases in lasso peptide engineering.

  20. Rhodium Complexes Promoting C-O Bond Formation in Reactions with Oxygen: The Role of Superoxo Species.

    PubMed

    Vilella-Arribas, Laia; García-Melchor, Max; Balcells, David; Lledós, Agustí; López, José A; Sancho, Sofía; Villarroya, B Eva; Del Río, M Pilar; Ciriano, Miguel A; Tejel, Cristina

    2017-01-28

    C-O bond formation in reactions of olefins with oxygen is a long standing challenge in chemistry for which the very complicated-sometimes controversial-mechanistic panorama slows down the design of catalysts for oxygenations. In this regard, the mechanistic details of the oxidation of the complex [Rh(cod)(Ph2 N3 )] (1) (cod=1,5-cyclooctadiene) with oxygen to the unique 2-rhodaoxetane compound [{Rh(OC8 H12 )(Ph2 N3 )}2 ] (2) has been investigated by DFT calculations. The results of this study provide evidences for a novel bimetallic mechanism in which two rhodium atoms redistribute the four electrons involved in the cleavage of the O=O bond. Furthermore, both oxygen atoms are used to create two new C-O bonds in a controlled fashion with 100 % atom economy. The key intermediates that we have found in this process are a mononuclear open-shell triplet superoxo compound, an open-shell singlet "μ-(peroxo)" derivative, and a closed-shell singlet "bis(μ-oxo)" complex. Some of the findings are used to predict the reactions of Rh(I) complexes with oxygen, exemplified by that of the complex [Rh(cod)(OnapyMe2 )] (3). Starting from 3, [{Rh(OC8 H12 )(OnapyMe2 )}2 ] (4) has been prepared and characterized, which represents the second example of a 2-rhodaoxetane compound coming from an oxygenation reaction with oxygen.

  1. The Human Coparental Bond Implicates Distinct Corticostriatal Pathways: Longitudinal Impact on Family Formation and Child Well-Being.

    PubMed

    Abraham, Eyal; Gilam, Gadi; Kanat-Maymon, Yaniv; Jacob, Yael; Zagoory-Sharon, Orna; Hendler, Talma; Feldman, Ruth

    2017-11-01

    Alloparental care, the cooperative care of offspring by group members other than the biological mother, has been widely practiced since early hominin evolution to increase infant survival and thriving. The coparental bond-a relationship of solidarity and commitment between two adults who join their effort to care for children-is a central contributor to children's well-being and sociality; yet, the neural basis of coparenting has not been studied in humans. Here, we followed 84 first-time co-parents (42 couples) across the first 6 years of family formation, including opposite-sex and same-sex couples, measured brain response to coparental stimuli, observed collaborative and undermining coparental behaviors in infancy and preschool, assayed oxytocin (OT) and vasopressin (AVP), and measured coparenting and child behavior problems at 6 years. Across family types, coparental stimuli activated the striatum, specifically the ventral striatum and caudate, striatal nodes implicated in motivational goal-directed social behavior. Psychophysiological interaction analysis indicated that both nodes were functionally coupled with the vmPFC in support of the human coparental bond and this connectivity was stronger as collaborative coparental behavior increased. Furthermore, caudate functional connectivity patterns differentiated distinct corticostriatal pathways associated with two stable coparental behavioral styles; stronger caudate-vmPFC connectivity was associated with more collaborative coparenting and was linked to OT, whereas a stronger caudate-dACC connectivity was associated with increase in undermining coparenting and was related to AVP. Finally, dyadic path-analysis model indicated that the parental caudate-vmPFC connectivity in infancy predicted lower child externalizing symptoms at 6 years as mediated by collaborative coparenting in preschool. Findings indicate that the coparental bond is underpinned by striatal activations and corticostriatal connectivity similar to

  2. Porous solids arising from synergistic and competing modes of assembly: combining coordination chemistry and covalent bond formation.

    PubMed

    Dutta, Ananya; Koh, Kyoungmoo; Wong-Foy, Antek G; Matzger, Adam J

    2015-03-23

    Design and synthesis of porous solids employing both reversible coordination chemistry and reversible covalent bond formation is described. The combination of two different linkage modes in a single material presents a link between two distinct classes of porous materials as exemplified by metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). This strategy, in addition to being a compelling material-discovery method, also offers a platform for developing a fundamental understanding of the factors influencing the competing modes of assembly. We also demonstrate that even temporary formation of reversible connections between components may be leveraged to make new phases thus offering design routes to polymorphic frameworks. Moreover, this approach has the striking potential of providing a rich landscape of structurally complex materials from commercially available or readily accessible feedstocks.

  3. The first chiral diene-based metal-organic frameworks for highly enantioselective carbon-carbon bond formation reactions

    SciTech Connect

    Sawano, Takahiro; Ji, Pengfei; McIsaac, Alexandra R.; Lin, Zekai; Abney, Carter W.; Lin, Wenbin

    2016-02-01

    We have designed the first chiral diene-based metal–organic framework (MOF), E₂-MOF, and postsynthetically metalated E₂-MOF with Rh(I) complexes to afford highly active and enantioselective single-site solid catalysts for C–C bond formation reactions. Treatment of E₂-MOF with [RhCl(C₂H₄)₂]₂ led to a highly enantioselective catalyst for 1,4-additions of arylboronic acids to α,β-unsaturated ketones, whereas treatment of E₂-MOF with Rh(acac)(C₂H₄)₂ afforded a highly efficient catalyst for the asymmetric 1,2-additions of arylboronic acids to aldimines. Interestingly, E₂-MOF·Rh(acac) showed higher activity and enantioselectivity than the homogeneous control catalyst, likely due to the formation of a true single-site catalyst in the MOF. E₂-MOF·Rh(acac) was also successfully recycled and reused at least seven times without loss of yield and enantioselectivity.

  4. An alternative mechanism for the catalysis of peptide bond formation by L/F transferase: substrate binding and orientation.

    PubMed

    Fung, Angela W; Ebhardt, H Alexander; Abeysundara, Heshani; Moore, Jack; Xu, Zhizhong; Fahlman, Richard P

    2011-06-17

    Eubacterial leucyl/phenylalanyl tRNA protein transferase (L/F transferase) catalyzes the transfer of a leucine or a phenylalanine from an aminoacyl-tRNA to the N-terminus of a protein substrate. This N-terminal addition of an amino acid is analogous to that of peptide synthesis by ribosomes. A previously proposed catalytic mechanism for Escherichia coli L/F transferase identified the conserved aspartate 186 (D186) and glutamine 188 (Q188) as key catalytic residues. We have reassessed the role of D186 and Q188 by investigating the enzymatic reactions and kinetics of enzymes possessing mutations to these active-site residues. Additionally three other amino acids proposed to be involved in aminoacyl-tRNA substrate binding are investigated for comparison. By quantitatively measuring product formation using a quantitative matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based assay, our results clearly demonstrate that, despite significant reduction in enzymatic activity as a result of different point mutations introduced into the active site of L/F transferase, the formation of product is still observed upon extended incubations. Our kinetic data and existing X-ray crystal structures result in a proposal that the critical roles of D186 and Q188, like the other amino acids in the active site, are for substrate binding and orientation and do not directly participate in the chemistry of peptide bond formation. Overall, we propose that L/F transferase does not directly participate in the chemistry of peptide bond formation but catalyzes the reaction by binding and orientating the substrates for reaction in an analogous mechanism that has been described for ribosomes.

  5. Access to Pyrazolidin-3,5-diones through Anodic N-N Bond Formation.

    PubMed

    Gieshoff, Tile; Schollmeyer, Dieter; Waldvogel, Siegfried R

    2016-08-01

    Pyrazolidin-3,5-diones are important motifs in heterocyclic chemistry and are of high interest for pharmaceutical applications. In classic organic synthesis, the hydrazinic moiety is installed through condensation using the corresponding hydrazine building blocks. However, most N,N'-diaryl hydrazines are toxic and require upstream preparation owing to their low commercial availability. We present an alternative and sustainable synthetic approach to pyrazolidin-3,5-diones that employs readily accessible dianilides as precursors, which are anodically converted to furnish the N-N bond. The electroconversion is conducted in a simple undivided cell under constant-current conditions.

  6. Synthesis of complex allylic esters via C-H oxidation vs C-C bond formation.

    PubMed

    Vermeulen, Nicolaas A; Delcamp, Jared H; White, M Christina

    2010-08-18

    A highly general, predictably selective C-H oxidation method for the direct, catalytic synthesis of complex allylic esters is introduced. This Pd(II)/sulfoxide-catalyzed method allows a wide range of complex aryl and alkyl carboxylic acids to couple directly with terminal olefins to furnish (E)-allylic esters in synthetically useful yields and selectivities (16 examples, E/Z >or= 10:1) and without the use of stoichiometric coupling reagents or unstable intermediates. Strategic advantages of constructing allylic esters via C-H oxidation vs C-C bond-forming methods are evaluated and discussed in four "case studies".

  7. Palladium fluoride complexes: one more step toward metal-mediated C-F bond formation.

    PubMed

    Grushin, Vladimir V

    2002-03-01

    The first molecular complexes of palladium containing a Pd-F bond, both fluorides and bifluorides, were synthesized and fully characterized in the solid state and in solution. Reactivity studies of the Pd fluoride complexes revealed their unexpected stability and unusual chemical properties, different from the hydroxo, chloro, bromo, and iodo analogues. A novel efficient method to generate "naked fluoride" was developed using [(Ph(3)P)(2)Pd(F)Ph]. The naked fluoride from the Pd source fluorinated dichloromethane, deprotonated chloroform, and catalyzed di- and trimerization of hexafluoropropene under uncommonly mild conditions.

  8. Formation of C-C bonds via ruthenium-catalyzed transfer hydrogenation().

    PubMed

    Moran, Joseph; Krische, Michael J

    2012-01-01

    Ruthenium-catalyzed transfer hydrogenation of diverse π-unsaturated reactants in the presence of aldehydes provides products of carbonyl addition. Dehydrogenation of primary alcohols in the presence of the same π-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.

  9. Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates.

    PubMed

    Siegmund, Vanessa; Piater, Birgit; Zakeri, Bijan; Eichhorn, Thomas; Fischer, Frank; Deutsch, Carl; Becker, Stefan; Toleikis, Lars; Hock, Björn; Betz, Ulrich A K; Kolmar, Harald

    2016-12-16

    Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation.

  10. Emotional experiences of preservice science teachers in online learning: the formation, disruption and maintenance of social bonds

    NASA Astrophysics Data System (ADS)

    Bellocchi, Alberto; Mills, Kathy A.; Ritchie, Stephen M.

    2016-09-01

    The enactment of learning to become a science teacher in online mode is an emotionally charged experience. We attend to the formation, maintenance and disruption of social bonds experienced by online preservice science teachers as they shared their emotional online learning experiences through blogs, or e-motion diaries, in reaction to videos of face-to-face lessons. A multi-theoretic framework drawing on microsociological perspectives of emotion informed our hermeneutic interpretations of students' first-person accounts reported through an e-motion diary. These accounts were analyzed through our own database of emotion labels constructed from the synthesis of existing literature on emotion across a range of fields of inquiry. Preservice science teachers felt included in the face-to-face group as they watched videos of classroom transactions. The strength of these feelings of social solidarity were dependent on the quality of the video recording. E-motion diaries provided a resource for interactions focused on shared emotional experiences leading to formation of social bonds and the alleviation of feelings of fear, trepidation and anxiety about becoming science teachers. We offer implications to inform practitioners who wish to improve feelings of inclusion amongst their online learners in science education.

  11. Alcohol and group formation: a multimodal investigation of the effects of alcohol on emotion and social bonding.

    PubMed

    Sayette, Michael A; Creswell, Kasey G; Dimoff, John D; Fairbairn, Catharine E; Cohn, Jeffrey F; Heckman, Bryan W; Kirchner, Thomas R; Levine, John M; Moreland, Richard L

    2012-08-01

    We integrated research on emotion and on small groups to address a fundamental and enduring question facing alcohol researchers: What are the specific mechanisms that underlie the reinforcing effects of drinking? In one of the largest alcohol-administration studies yet conducted, we employed a novel group-formation paradigm to evaluate the socioemotional effects of alcohol. Seven hundred twenty social drinkers (360 male, 360 female) were assembled into groups of 3 unacquainted persons each and given a moderate dose of an alcoholic, placebo, or control beverage, which they consumed over 36 min. These groups' social interactions were video recorded, and the duration and sequence of interaction partners' facial and speech behaviors were systematically coded (e.g., using the facial action coding system). Alcohol consumption enhanced individual- and group-level behaviors associated with positive affect, reduced individual-level behaviors associated with negative affect, and elevated self-reported bonding. Our results indicate that alcohol facilitates bonding during group formation. Assessing nonverbal responses in social contexts offers new directions for evaluating the effects of alcohol.

  12. Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome

    SciTech Connect

    Blaha, Gregor; Stanley, Robin E.; Steitz, Thomas A.; Yale

    2009-10-21

    Elongation factor P (EF-P) is an essential protein that stimulates the formation of the first peptide bond in protein synthesis. Here we report the crystal structure of EF-P bound to the Thermus thermophilus 70S ribosome along with the initiator transfer RNA N-formyl-methionyl-tRNAi (fMet-tRNA{sub i}{sup fMet}) and a short piece of messenger RNA (mRNA) at a resolution of 3.5 angstroms. EF-P binds to a site located between the binding site for the peptidyl tRNA (P site) and the exiting tRNA (E site). It spans both ribosomal subunits with its amino-terminal domain positioned adjacent to the aminoacyl acceptor stem and its carboxyl-terminal domain positioned next to the anticodon stem-loop of the P site-bound initiator tRNA. Domain II of EF-P interacts with the ribosomal protein L1, which results in the largest movement of the L1 stalk that has been observed in the absence of ratcheting of the ribosomal subunits. EF-P facilitates the proper positioning of the fMet-tRNA{sub i}{sup fMet} for the formation of the first peptide bond during translation initiation.

  13. Formation of the First Peptid Bond: the Structure of EF-P Bound to the 70S Ribosome

    SciTech Connect

    Blaha, G.; Stanley, R; Steitz, T

    2009-01-01

    Elongation factor P (EF-P) is an essential protein that stimulates the formation of the first peptide bond in protein synthesis. Here we report the crystal structure of EF-P bound to the Thermus thermophilus 70S ribosome along with the initiator transfer RNA N-formyl-methionyl-tRNAi (fMet-tRNAifMet) and a short piece of messenger RNA (mRNA) at a resolution of 3.5 angstroms. EF-P binds to a site located between the binding site for the peptidyl tRNA (P site) and the exiting tRNA (E site). It spans both ribosomal subunits with its amino-terminal domain positioned adjacent to the aminoacyl acceptor stem and its carboxyl-terminal domain positioned next to the anticodon stem-loop of the P site-bound initiator tRNA. Domain II of EF-P interacts with the ribosomal protein L1, which results in the largest movement of the L1 stalk that has been observed in the absence of ratcheting of the ribosomal subunits. EF-P facilitates the proper positioning of the fMet-tRNAifMet for the formation of the first peptide bond during translation initiation.

  14. Spontaneous Isopeptide Bond Formation as a Powerful Tool for Engineering Site-Specific Antibody-Drug Conjugates

    PubMed Central

    Siegmund, Vanessa; Piater, Birgit; Zakeri, Bijan; Eichhorn, Thomas; Fischer, Frank; Deutsch, Carl; Becker, Stefan; Toleikis, Lars; Hock, Björn; Betz, Ulrich A. K.; Kolmar, Harald

    2016-01-01

    Spontaneous isopeptide bond formation, a stabilizing posttranslational modification that can be found in gram-positive bacterial cell surface proteins, has previously been used to develop a peptide-peptide ligation technology that enables the polymerization of tagged-proteins catalyzed by SpyLigase. Here we adapted this technology to establish a novel modular antibody labeling approach which is based on isopeptide bond formation between two recognition peptides, SpyTag and KTag. Our labeling strategy allows the attachment of a reporting cargo of interest to an antibody scaffold by fusing it chemically to KTag, available via semi-automated solid-phase peptide synthesis (SPPS), while equipping the antibody with SpyTag. This strategy was successfully used to engineer site-specific antibody-drug conjugates (ADCs) that exhibit cytotoxicities in the subnanomolar range. Our approach may lead to a new class of antibody conjugates based on peptide-tags that have minimal effects on protein structure and function, thus expanding the toolbox of site-specific antibody conjugation. PMID:27982100

  15. Basic ancillary ligands promote O-O bond formation in iridium-catalyzed water oxidation: a DFT study.

    PubMed

    Vilella, Laia; Vidossich, Pietro; Balcells, David; Lledós, Agustí

    2011-11-14

    The cationic iridium complex [Ir(OH(2))(2)(phpy)(2)](+) (phpy = o-phenylpyridine) is among the most efficient mononuclear catalysts for water oxidation. The postulated active species is the oxo complex [Ir(O)(X)(phpy)(2)](n), with X = OH(2) (n = +1), OH(-) (n = 0) or O(2-) (n = -1), depending on the pH. The reactivity of these species has been studied computationally at the DFT(B3LYP) level. The three [Ir(O)(X)(phpy)(2)](n) complexes have an electrophilic Ir(v)-oxo moiety, which yields an O-O bond by undergoing a nucleophilic attack of water in the critical step of the mechanism. In this step, water transfers one proton to either the Ir(V)-oxo moiety or the ancillary X ligand. Five different reaction pathways associated with this acid/base mechanism have been characterized. The calculations show that the proton is preferably accepted by the X ligand, which plays a key role in the reaction. The higher the basicity of X, the lower the energy barrier associated with O-O bond formation. The anionic species, [Ir(O)(2)(phpy)(2)](-), which has the less electrophilic Ir(V)-oxo moiety but the most basic X ligand, promotes O-O bond formation through the lowest energy barrier, 14.5 kcal mol(-1). The other two active species, [Ir(O)(OH)(phpy)(2)] and [Ir(O)(OH(2))(phpy)(2)](+), which have more electrophilic Ir(V)-oxo moieties but less basic X ligands, involve higher energy barriers, 20.2 kcal mol(-1) and 25.9 kcal mol(-1), respectively. These results are in good agreement with experiments showing important pH effects in similar catalytic systems. The theoretical insight given by the present study can be useful in the design of more efficient water oxidation catalysts. The catalytic activity may increase by using ligand scaffolds bearing internal bases.

  16. Reactions of a Dinitrogen Complex of Molybdenum: Formation of a Carbon-Nitrogen Bond.

    ERIC Educational Resources Information Center

    Busby, David C.; And Others

    1981-01-01

    Reports a procedure for the formation of alkyldiazenido complexes of molybdenum in the absence of dioxygen, suitable for inclusion in an advanced inorganic chemistry laboratory. Includes background information and experimental procedures for two complexes. (SK)

  17. Reactions of a Dinitrogen Complex of Molybdenum: Formation of a Carbon-Nitrogen Bond.

    ERIC Educational Resources Information Center

    Busby, David C.; And Others

    1981-01-01

    Reports a procedure for the formation of alkyldiazenido complexes of molybdenum in the absence of dioxygen, suitable for inclusion in an advanced inorganic chemistry laboratory. Includes background information and experimental procedures for two complexes. (SK)

  18. Formation of Me-O-Si covalent bonds at the interface between polysilazane and stainless steel

    NASA Astrophysics Data System (ADS)

    Amouzou, Dodji; Fourdrinier, Lionel; Maseri, Fabrizio; Sporken, Robert

    2014-11-01

    In earlier works, we demonstrated the potential of polysilazane (PSZ) coatings for a use as insulating layers in Cu(In,Ga)Se2 (CIGS) solar cells prepared on steels substrates and showed a good adhesion between PSZ coatings and both AISI316 and AISI430 steels. In the present paper, spectroscopic techniques are used to elucidate the reason of such adhesion. X-ray Photoelectron Spectroscopy (XPS) was used to investigate surfaces for the two steel substrates and showed the presence of metal oxides and metal hydroxides at the top surface. XPS has been also used to probe interfaces between substrates and PSZ, and metallosiloxane (Me-O-Si) covalent bonds have been detected. These results were confirmed by Infra-Red Reflection Absorption Spectroscopy (IRRAS) analyses since vibrations related to Cr-O-Si and Fe-O-Si compounds were detected. Thus, the good adhesion between steel substrates and PSZ coatings was explained by covalent bonding through chemical reactions between PSZ precursors and hydroxide functional groups present on top surface of the two types of steel. Based on these results, an adhesion mechanism between steel substrates and PSZ coatings is proposed.

  19. Structure, bonding and formation of molecular germanium oxides, hydroxides and oxyhydroxides

    NASA Astrophysics Data System (ADS)

    Johnson, J. R. Tobias; Panas, Itai

    1999-11-01

    Molecular germanium oxides, hydroxides and oxyhydroxides were studied by means of density functional theory. The polymerization reactions of GeO and GeO 2 were found exothermic up to the tetramer, and possible product structures were characterized. Important features are the instability of larger ring structures, and how Ge 2O 2 rings become important building blocks, independently on whether the long-range order resembles clusters or chains. This unit is proposed to provide a clue to the unknown bulk structure of GeO(s). Water additions to both (GeO) n and (GeO 2) n polymers are investigated. The reactions with GeO bonds are found exothermic by 230-250 kJ/mol, while similar water additions to Ge-O-Ge bridges are exothermic only when reacting with one of the bridges in the strained Ge 2O 2 ring. Reactions with larger clusters as well as further fragmentation are found slightly endothermic. The most stable product of water addition to Ge 2O 4 is (HO) 3GeOGe(OH) 3, which has one Ge-O-Ge bridge and two intramolecular hydrogen bonds. In addition, structures and stabilities of the `odd' oxides Ge 2O, Ge 2O 3, Ge 3O 4 and GeO 3 are investigated.

  20. A new quadruple hydrogen-bonding module with a DDAA array: formation of a stable homodimer without competition from undesired hydrogen-bonded dimers.

    PubMed

    Hisamatsu, Yosuke; Shirai, Naohiro; Ikeda, Shin-ichi; Odashima, Kazunori

    2009-10-01

    A new DDAA hydrogen-bonding module (UImp-2), based on a ureidoimidazo[1,2-a]pyrimidine structure, forms a highly stable homodimer (K(dim) > 1.1 x 10(5) M(-1) in CDCl(3)) without competition from undesired hydrogen-bonded dimers.

  1. Catalysis of peptide bond formation by histidyl-histidine in a fluctuating clay environment

    NASA Technical Reports Server (NTRS)

    White, D. H.; Erickson, J. C.

    1980-01-01

    The condensation of glycine to form oligoglycines during wet-dry fluctuations on clay surfaces was enhanced up to threefold or greater by small amounts of histidyl-histidine. In addition, higher relative yields of the longer oligomers were produced. Other specific dipeptides tested gave no enhancement, and imidazole, histidine, and N-acetylhistidine gave only slight enhancements. Histidyl-histidine apparently acts as a true catalyst (in the sense of repeatedly catalyzing the reaction), since up to 52 nmol of additional glycine were incorporated into oligoglycine for each nmol of catalyst added. This is the first known instance of a peptide or similar molecule demonstrating a catalytic turnover number greater than unity in a prebiotic oligomer synthesis reaction, and suggests that histidyl-histidine is a model for a primitive prebiotic proto-enzyme. Catalysis of peptide bond synthesis by a molecule which is itself a peptide implies that related systems may be capable of exhibiting autocatalytic growth.

  2. Biosynthesis of pyranonaphthoquinone polyketides reveals diverse strategies for enzymatic carbon-carbon bond formation.

    PubMed

    Metsä-Ketelä, Mikko; Oja, Terhi; Taguchi, Takaaki; Okamoto, Susumu; Ichinose, Koji

    2013-08-01

    Pyranonaphthoquinones synthesized by Streptomyces bacteria via type II polyketide pathways are aromatic compounds build around a common three-ring structure, which is composed of pyran, quinone and benzene rings. Over the years, actinorhodin in particular has served as a model compound for studying the biosynthesis of aromatic polyketides, while some of the other metabolites such as granaticin, medermycin, frenolicin and alnumycin A have enabled comparative studies that complement our understanding how these complex biological systems function and have evolved. In addition, despite the similarity of the aglycone units, pyranonaphthoquinones in effect display remarkable diversity in tailoring reactions, which include numerous enzymatic carbon-carbon bond forming reactions. This review focuses on the current status of molecular genetic, biochemical and structural investigations on this intriguing family of natural products.

  3. Catalysis of peptide bond formation by histidyl-histidine in a fluctuating clay environment

    NASA Technical Reports Server (NTRS)

    White, D. H.; Erickson, J. C.

    1980-01-01

    The condensation of glycine to form oligoglycines during wet-dry fluctuations on clay surfaces was enhanced up to threefold or greater by small amounts of histidyl-histidine. In addition, higher relative yields of the longer oligomers were produced. Other specific dipeptides tested gave no enhancement, and imidazole, histidine, and N-acetylhistidine gave only slight enhancements. Histidyl-histidine apparently acts as a true catalyst (in the sense of repeatedly catalyzing the reaction), since up to 52 nmol of additional glycine were incorporated into oligoglycine for each nmol of catalyst added. This is the first known instance of a peptide or similar molecule demonstrating a catalytic turnover number greater than unity in a prebiotic oligomer synthesis reaction, and suggests that histidyl-histidine is a model for a primitive prebiotic proto-enzyme. Catalysis of peptide bond synthesis by a molecule which is itself a peptide implies that related systems may be capable of exhibiting autocatalytic growth.

  4. Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide.

    PubMed

    Huang, Jing; MacKerell, Alexander D

    2014-08-19

    Cooperativity is a central feature in the formation of secondary structures in proteins. However, the driving forces behind this cooperativity are poorly understood. The present work shows that the cooperativity of helix formation in the acetyl-(AAQAA)3-NH2 peptide is significantly enhanced using an empirical force field that explicitly includes the treatment of electronic polarizability. Polarizable simulations yield helical content consistent with experimental measurements and indicate that the dependence of helical content on temperature is improved over additive models, though further sampling is required to fully validate this conclusion. Cooperativity is indicated by the peptide sampling either the coiled state or long helices with relatively low populations of short helices. The cooperativity is shown to be associated with enhanced dipole moments of the peptide backbone upon helix formation. These results indicate the polarizable force field to more accurately model peptide-folding cooperativity based on its physically realistic treatment of electronic polarizability.

  5. Induction of Peptide Bond Dipoles Drives Cooperative Helix Formation in the (AAQAA)3 Peptide

    PubMed Central

    Huang, Jing; MacKerell, Alexander D.

    2014-01-01

    Cooperativity is a central feature in the formation of secondary structures in proteins. However, the driving forces behind this cooperativity are poorly understood. The present work shows that the cooperativity of helix formation in the acetyl-(AAQAA)3-NH2 peptide is significantly enhanced using an empirical force field that explicitly includes the treatment of electronic polarizability. Polarizable simulations yield helical content consistent with experimental measurements and indicate that the dependence of helical content on temperature is improved over additive models, though further sampling is required to fully validate this conclusion. Cooperativity is indicated by the peptide sampling either the coiled state or long helices with relatively low populations of short helices. The cooperativity is shown to be associated with enhanced dipole moments of the peptide backbone upon helix formation. These results indicate the polarizable force field to more accurately model peptide-folding cooperativity based on its physically realistic treatment of electronic polarizability. PMID:25140435

  6. Enthalpy of Formation and O-H Bond Dissociation Enthalpy of Phenol: Inconsistency between Theory and Experiment.

    PubMed

    Dorofeeva, Olga V; Ryzhova, Oxana N

    2016-04-21

    Gas-phase O–H homolytic bond dissociation enthalpy in phenol, DH298°(C6H5O–H), is still disputed, despite a large number of experimental and computational studies. In estimating this value, the experimental enthalpy of formation of phenol, ΔfH298°(C6H5OH, g) = −96.4 ± 0.6 kJ/mol (Cox, J. D. Pure Appl. Chem. 1961, 2, 125−128), is often used assuming high accuracy of the experimental value. In the present work a substantially less negative value of ΔfH298°(C6H5OH, g) = −91.8 ± 2.5 kJ/mol was calculated combining G4 theory with an isodesmic reaction approach. A benchmark quality of this result was achieved by using a large number of reliable reference species in isodesmic reaction calculations. Among these are the most accurate ΔfH298° values currently available from the Active Thermochemical Tables (ATcT) for 36 species (neutral molecules, radicals, and ions), anisole with recently reassessed enthalpy of formation, and 13 substituted phenols. The internal consistency of the calculated ΔfH298°(C6H5OH, g) value with the experimental enthalpies of formation of more than 50 reference species suggests that the reported experimental enthalpy of formation of phenol is in error. Taking into account that the enthalpy of formation of phenol has not been investigated experimentally since 1961, the new measurements would be extremely valuable. Using the accurate enthalpies of formation of C6H5OH and C6H5O• calculated in the present work, we obtained DH298°(C6H5O–H) = 369.6 ± 4.0 kJ/mol. This value is in satisfactory agreement with that determined from the most precise experimental measurement.

  7. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler.

    PubMed

    Shaffer, Christopher J; Andrikopoulos, Prokopis C; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

    2016-04-01

    Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific (13)C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)(+) ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H](+) ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase. Graphical Abstract ᅟ.

  8. Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

    NASA Astrophysics Data System (ADS)

    Shaffer, Christopher J.; Andrikopoulos, Prokopis C.; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

    2016-04-01

    Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific 13C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)+ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]+ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase.

  9. Strain shielding from mechanically activated covalent bond formation during nanoindentation of graphene delays the onset of failure.

    PubMed

    Kumar, Sandeep; Parks, David M

    2015-03-11

    Mechanical failure of an ideal crystal is dictated either by an elastic instability or a soft-mode instability. Previous interpretations of nanoindentation experiments on suspended graphene sheets,1,2 however, indicate an anomaly: the inferred strain in the graphene sheet directly beneath the diamond indenter at the measured failure load is anomalously large compared to the fracture strains predicted by both soft-mode and acoustic analyses. Through multiscale modeling combining the results of continuum, atomistic, and quantum calculations, and analysis of experiments, we identify a strain-shielding effect initiated by mechanochemical interactions at the graphene-indenter interface as the operative mechanism responsible for this anomaly. Transmission electron micrographs and a molecular model of the diamond indenter's tip suggest that the tip surface contains facets comprising crystallographic {111} and {100} planes. Ab initio and molecular dynamics (MD) simulations confirm that a covalent bond (weld) formation between graphene and the crystallographic {111} and {100} facets on the indenter's surface can be induced by compressive contact stresses of the order achieved in nanoindentation tests. Finite element analysis (FEA) and MD simulations of nanoindentation reveal that the shear stiction provided by the induced covalent bonding restricts relative slip of the graphene sheet at its contact with the indenter, thus initiating a local strain-shielding effect. As a result, subsequent to stress-induced bonding at the graphene-indenter interface, the spatial variation of continuing incremental strain is substantially redistributed, locally shielding the region directly beneath the indenter by limiting the buildup of strain while imparting deformation to the surrounding regions. The extent of strain shielding is governed by the strength of the shear stiction, which depends upon the level of hydrogen saturation at the indenter's surface. We show that at intermediate levels

  10. The KIM-family protein-tyrosine phosphatases use distinct reversible oxidation intermediates: Intramolecular or intermolecular disulfide bond formation.

    PubMed

    Machado, Luciana E S F; Shen, Tun-Li; Page, Rebecca; Peti, Wolfgang

    2017-05-26

    The kinase interaction motif (KIM) family of protein-tyrosine phosphatases (PTPs) includes hematopoietic protein-tyrosine phosphatase (HePTP), striatal-enriched protein-tyrosine phosphatase (STEP), and protein-tyrosine phosphatase receptor type R (PTPRR). KIM-PTPs bind and dephosphorylate mitogen-activated protein kinases (MAPKs) and thereby critically modulate cell proliferation and differentiation. PTP activity can readily be diminished by reactive oxygen species (ROS), e.g. H2O2, which oxidize the catalytically indispensable active-site cysteine. This initial oxidation generates an unstable sulfenic acid intermediate that is quickly converted into either a sulfinic/sulfonic acid (catalytically dead and irreversible inactivation) or a stable sulfenamide or disulfide bond intermediate (reversible inactivation). Critically, our understanding of ROS-mediated PTP oxidation is not yet sufficient to predict the molecular responses of PTPs to oxidative stress. However, identifying distinct responses will enable novel routes for PTP-selective drug design, important for managing diseases such as cancer and Alzheimer's disease. Therefore, we performed a detailed biochemical and molecular study of all KIM-PTP family members to determine their H2O2 oxidation profiles and identify their reversible inactivation mechanism(s). We show that despite having nearly identical 3D structures and sequences, each KIM-PTP family member has a unique oxidation profile. Furthermore, we also show that whereas STEP and PTPRR stabilize their reversibly oxidized state by forming an intramolecular disulfide bond, HePTP uses an unexpected mechanism, namely, formation of a reversible intermolecular disulfide bond. In summary, despite being closely related, KIM-PTPs significantly differ in oxidation profiles. These findings highlight that oxidation protection is critical when analyzing PTPs, for example, in drug screening. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3'-5' phosphodiester bonds

    NASA Technical Reports Server (NTRS)

    Rohatgi, R.; Bartel, D. P.; Szostak, J. W.

    1996-01-01

    We have found that nonenzymatic, template-directed ligation reactions of oligoribonucleotides display high selectivity for the formation of 3'-5' rather than 2'-5' phosphodiester bonds. Formation of the 3'-5'-linked product is favored regardless of the metal ion catalyst or the leaving group, and for several different ligation junction sequences. The degree of selectivity depends on the leaving group: the ratio of 3'-5'- to 2'-5'-linked products was 10-15:1 when the 5'-phosphate was activated as the imidazolide, and 60-80:1 when the 5'-phosphate was activated by the formation of a 5'-triphosphate. Comparison of oligonucleotide ligation reactions with previously characterized single nucleotide primer extension reactions suggests that the strong preference for 3'-5'-linkages in oligonucleotide ligation is primarily due to occurence of ligation within the context of an extended Watston-Crick duplex. The ability of RNA to correctly self-assemble by template-directed ligation is an intrinsic consequence of its chemical structure and need not be imposed by an external catalyst (i.e., an enzyme polymerase); RNA therefore provides a reasonable structural basis for a self-replicating system in a prebiological world.

  12. Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3'-5' phosphodiester bonds

    NASA Technical Reports Server (NTRS)

    Rohatgi, R.; Bartel, D. P.; Szostak, J. W.

    1996-01-01

    We have found that nonenzymatic, template-directed ligation reactions of oligoribonucleotides display high selectivity for the formation of 3'-5' rather than 2'-5' phosphodiester bonds. Formation of the 3'-5'-linked product is favored regardless of the metal ion catalyst or the leaving group, and for several different ligation junction sequences. The degree of selectivity depends on the leaving group: the ratio of 3'-5'- to 2'-5'-linked products was 10-15:1 when the 5'-phosphate was activated as the imidazolide, and 60-80:1 when the 5'-phosphate was activated by the formation of a 5'-triphosphate. Comparison of oligonucleotide ligation reactions with previously characterized single nucleotide primer extension reactions suggests that the strong preference for 3'-5'-linkages in oligonucleotide ligation is primarily due to occurence of ligation within the context of an extended Watston-Crick duplex. The ability of RNA to correctly self-assemble by template-directed ligation is an intrinsic consequence of its chemical structure and need not be imposed by an external catalyst (i.e., an enzyme polymerase); RNA therefore provides a reasonable structural basis for a self-replicating system in a prebiological world.

  13. Selective covalent bond formation in polypeptide ions via gas-phase ion/ion reaction chemistry.

    PubMed

    Han, Hongling; McLuckey, Scott A

    2009-09-16

    Primary amines present in protonated polypeptides can be covalently modified via gas-phase ion/ion reactions using bifunctional reagent ions. The use of reagent anions with a charge-bearing site that leads to strong interactions with the polypeptide, such as sulfonic acid, gives rise to the formation of a long-lived adduct. A distinct reactive functional group, an aldehyde in the present case, can then undergo reaction with the peptide. Collisional activation of the adduct ion formed from a reagent with an aldehyde group and a peptide ion with a primary amine gives rise to water loss in conjunction with imine (Schiff base) formation. The covalently bound modification is retained upon subsequent collisional activation. This work demonstrates the ability to selectively modify polypeptide ions in the gas phase within the context of a multistage mass spectrometry experiment.

  14. Elucidating the Role of Disulfide Bond on Amyloid Formation and Fibril Reversibility of Somatostatin-14

    PubMed Central

    Anoop, Arunagiri; Ranganathan, Srivastav; Dhaked, Bhagwan Das; Jha, Narendra Nath; Pratihar, Supriya; Ghosh, Saikat; Sahay, Shruti; Kumar, Santosh; Das, Subhadeep; Kombrabail, Mamata; Agarwal, Kumud; Jacob, Reeba S.; Singru, Praful; Bhaumik, Prasenjit; Padinhateeri, Ranjith; Kumar, Ashutosh; Maji, Samir K.

    2014-01-01

    The storage of protein/peptide hormones within subcellular compartments and subsequent release are crucial for their native function, and hence these processes are intricately regulated in mammalian systems. Several peptide hormones were recently suggested to be stored as amyloids within endocrine secretory granules. This leads to an apparent paradox where storage requires formation of aggregates, and their function requires a supply of non-aggregated peptides on demand. The precise mechanism behind amyloid formation by these hormones and their subsequent release remain an open question. To address this, we examined aggregation and fibril reversibility of a cyclic peptide hormone somatostatin (SST)-14 using various techniques. After proving that SST gets stored as amyloid in vivo, we investigated the role of native structure in modulating its conformational dynamics and self-association by disrupting the disulfide bridge (Cys3–Cys14) in SST. Using two-dimensional NMR, we resolved the initial structure of somatostatin-14 leading to aggregation and further probed its conformational dynamics in silico. The perturbation in native structure (S-S cleavage) led to a significant increase in conformational flexibility and resulted in rapid amyloid formation. The fibrils formed by disulfide-reduced noncyclic SST possess greater resistance to denaturing conditions with decreased monomer releasing potency. MD simulations reveal marked differences in the intermolecular interactions in SST and noncyclic SST providing plausible explanation for differential aggregation and fibril reversibility observed experimentally in these structural variants. Our findings thus emphasize that subtle changes in the native structure of peptide hormone(s) could alter its conformational dynamics and amyloid formation, which might have significant implications on their reversible storage and secretion. PMID:24782311

  15. Papain-catalyzed peptide bond formation: enzyme-specific activation with guanidinophenyl esters.

    PubMed

    de Beer, Roseri J A C; Zarzycka, Barbara; Amatdjais-Groenen, Helene I V; Jans, Sander C B; Nuijens, Timo; Quaedflieg, Peter J L M; van Delft, Floris L; Nabuurs, Sander B; Rutjes, Floris P J T

    2011-09-19

    The substrate mimetics approach is a versatile method for small-scale enzymatic peptide-bond synthesis in aqueous systems. The protease-recognized amino acid side chain is incorporated in an ester leaving group, the substrate mimetic. This shift of the specific moiety enables the acceptance of amino acids and peptide sequences that are normally not recognized by the enzyme. The guanidinophenyl group (OGp), a known substrate mimetic for the serine proteases trypsin and chymotrypsin, has now been applied for the first time in combination with papain, a cheap and commercially available cysteine protease. To provide insight in the binding mode of various Z-X(AA)-OGp esters, computational docking studies were performed. The results strongly point at enzyme-specific activation of the OGp esters in papain through a novel mode of action, rather than their functioning as mimetics. Furthermore, the scope of a model dipeptide synthesis was investigated with respect to both the amino acid donor and the nucleophile. Molecular dynamics simulations were carried out to prioritize 22 natural and unnatural amino acid donors for synthesis. Experimental results correlate well with the predicted ranking and show that nearly all amino acids are accepted by papain.

  16. Proton transfer in hydrogen-bonded network of phenol molecules: intracluster formation of water.

    PubMed

    Lengyel, Jozef; Gorejová, Radka; Herman, Zdeněk; Fárník, Michal

    2013-11-07

    Electron ionization and time-of-flight mass spectrometry was used to investigate the phenol clusters (PhOH)n of different size from single molecule to large clusters: in coexpansion with He, the dimers n = 2 are mostly generated; in Ar, large species of n ≥ 10 also occur. Besides [(PhOH)n](+•) cluster ion series, hydrated phenol cluster ions [(PhOH)n·xH2O](+•) with up to x = 3 water molecules and dehydrated phenol clusters [(PhOH)n-H2O](+•) were observed. The hydrated phenol series exhibits minima and maxima that are interpreted as evidence for proton transfer between the hydrogen bonded cluster ions of cyclic structures. The proton transfer leads to a water generation within the clusters, and subsequent elimination of the diphenyl ether molecule(s) from the cluster yields the hydrated phenol cluster ions. Alternatively, a water molecule release yields a series of dehydrated phenols, among which the diphenyl ether ion [PhOPh](+•) (n = 2) constitutes the maximum.

  17. Polymer GARD: computer simulation of covalent bond formation in reproducing molecular assemblies.

    PubMed

    Shenhav, Barak; Bar-Even, Arren; Kafri, Ran; Lancet, Doron

    2005-04-01

    The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly's composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a 'monomer world' towards polymer-based living entities. We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a 'scaffold' for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer 'take-over' - the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.

  18. Late Quaternary Normal Faulting and Hanging Wall Basin Evolution of the Southwestern Rift Margin From Gravity and Geology, B.C.S., MX and Exploring the Influence of Text-Figure Format on Introductory Geology Learning

    NASA Astrophysics Data System (ADS)

    Busch, Melanie M. D.

    2011-12-01

    should, therefore, be formatted to include a number of natural breaks so that learners can pause to inspect the figure without the risk of losing their place in the reading and to provide a chance to process the material in small chunks. Multimedia instructional materials should be designed to support the cognitive processes of the learner.

  19. Characterization of irreversible kinase inhibitors by directly detecting covalent bond formation: a tool for dissecting kinase drug resistance.

    PubMed

    Klüter, Sabine; Simard, Jeffrey R; Rode, Haridas B; Grütter, Christian; Pawar, Vijaykumar; Raaijmakers, Hans C A; Barf, Tjeerd A; Rabiller, Matthias; van Otterlo, Willem A L; Rauh, Daniel

    2010-12-10

    Targeting protein kinases in cancer therapy with irreversible small-molecule inhibitors is moving to the forefront of kinase-inhibitor research and is thought to be an effective means of overcoming mutation-associated drug resistance in epidermal growth factor receptor kinase (EGFR). We generated a detection technique that allows direct measurements of covalent bond formation without relying on kinase activity, thereby allowing the straightforward investigation of the influence of steric clashes on covalent inhibitors in different resistant kinase mutants. The obtained results are discussed together with structural biology and biochemical studies of catalytic activity in both wild-type and gatekeeper mutated kinase variants to draw conclusions about the impact of steric hindrance and increased catalytic activity in drug-resistant kinase variants.

  20. The vinyl-sulfonium bond in human myeloperoxidase: Impact on compound I formation and reduction by halides and thiocyanate

    SciTech Connect

    Zederbauer, Martina; Furtmueller, Paul Georg; Ganster, Bernadette; Moguilevsky, Nicole; Obinger, Christian . E-mail: christian.obinger@boku.ac.at

    2007-05-04

    In human myeloperoxidase (MPO) the heme is covalently attached to the protein via two ester linkages and a unique sulfonium ion linkage between the sulfur atom of Met243 and the {beta}-carbon of the vinyl ring on pyrrole ring A. Here, we have investigated the variant Met243Val produced in Chinese hamster ovary cells in order to elucidate the role of the electron withdrawing sulfonium bond in compound I formation and reduction. Disruption of this MPO-typical bond causes a blue-shifted UV-vis spectrum and an increase in the heme flexibility. This had no impact on compound I formation mediated by hydrogen peroxide (2.2 x 10{sup 7} M{sup -1} s{sup -1} at pH 7.0 and 25 {sup o}C). Compared with wild-type recombinant MPO the cyanide association rate with ferric Met243Val was significantly enhanced as were also the calculated apparent bimolecular compound I reduction rates by iodide (>10{sup 8} M{sup -1} s{sup -1}) and thiocyanate (>10{sup 8} M{sup -1} s{sup -1}). By contrast, the overall chlorination and bromination activities were decreased by 98.1% and 87.4%, respectively, compared with the wild-type protein. Compound I reduction by chloride was slower than compound I decay to a compound II-like species (0.4 s{sup -1}), whereas compound I reduction by bromide was about 10-times slower (1.3 x 10{sup 4} M{sup -1} s{sup -1}) than the wild-type rate. These findings are discussed with respect to the known crystal structure of MPO and its bromide complex as well as the known redox chemistry of its intermediates and substrates.

  1. Redox‐dependent disulfide bond formation in SAP30L corepressor protein: Implications for structure and function

    PubMed Central

    Laitaoja, Mikko; Tossavainen, Helena; Pihlajamaa, Tero; Valjakka, Jarkko; Viiri, Keijo; Lohi, Olli; Permi, Perttu

    2015-01-01

    Abstract Sin3A‐associated protein 30‐like (SAP30L) is one of the key proteins in a multi‐subunit protein complex involved in transcriptional regulation via histone deacetylation. SAP30L, together with a highly homologous SAP30 as well as other SAP proteins (i.e., SAP25, SAP45, SAP130, and SAP180), is an essential component of the Sin3A corepressor complex, although its actual role has remained elusive. SAP30L is thought to function as an important stabilizing and bridging molecule in the complex and to mediate its interactions with other corepressors. SAP30L has been previously shown to contain an N‐terminal Cys3His type zinc finger (ZnF) motif, which is responsible for the key protein–protein, protein–DNA, and protein–lipid interactions. By using high‐resolution mass spectrometry, we studied a redox‐dependent disulfide bond formation in SAP30L ZnF as a regulatory mechanism for its structure and function. We showed that upon oxidative stress SAP30L undergoes the formation of two specific disulfide bonds, a vicinal Cys29‐Cys30 and Cys38‐Cys74, with a concomitant release of the coordinated zinc ion. The oxidized protein was shown to remain folded in solution and to bind signaling phospholipids. We also determined a solution NMR structure for SAP30L ZnF that showed an overall fold similar to that of SAP30, determined earlier. The NMR titration experiments with lipids and DNA showed that the binding is mediated by the C‐terminal tail as well as both α‐helices of SAP30L ZnF. The implications of these results for the structure and function of SAP30L are discussed. PMID:26609676

  2. Synthesis of Reusable Silica Nanosphere-Supported Pt(IV) Complex for Formation of Disulfide Bonds in Peptides.

    PubMed

    Hou, Xiaonan; Zhao, Xiaowei; Zhang, Yamei; Han, Aiying; Huo, Shuying; Shen, Shigang

    2017-02-22

    Some peptide-based drugs, including oxytocin, vasopressin, ziconotide, pramlintide, nesiritide, and octreotide, contain one intramolecular disulfide bond. A novel and reusable monodispersed silica nanosphere-supported Pt(IV) complex (SiO₂@TPEA@Pt(IV)); TPEA: N-[3-(trimethoxysilyl)propyl]ethylenediamine) was synthesized via a four-step procedure and was used for the formation of intramolecular disulfide bonds in peptides. Transmission electron microscopy (TEM) and chemical mapping results for the Pt(II) intermediates and for SiO₂@TPEA@Pt(IV) show that the silica nanospheres possess a monodisperse spherical structure and contain uniformly-distributed Si, O, C, N, Cl, and Pt. The valence state of Pt on the silica nanospheres was characterized by X-ray photoelectron spectroscopy (XPS). The Pt(IV) loaded on SiO₂@TPEA@Pt(IV) was 0.15 mmol/g, as determined by UV-VIS spectrometry. The formation of intramolecular disulfides in six dithiol-containing peptides of variable lengths by the use of SiO₂@TPEA@Pt(IV) was investigated, and the relative oxidation yields were determined by high-performance liquid chromatography (HPLC). In addition, peptide 1 (Ac-CPFC-NH₂) was utilized to study the reusability of SiO₂@TPEA@Pt(IV). No significant decrease in the relative oxidation yield was observed after ten reaction cycles. Moreover, the structure of SiO₂@TPEA@Pt(IV) after being used for ten cycles was determined to be similar to its initial one, demonstrating the cycling stability of the complex.

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

    NASA Astrophysics Data System (ADS)

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

    2006-06-01

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

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

    PubMed Central

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

    2006-01-01

    Cu-catalyzed cross-dehydrogenative coupling (CDC) methodologies were developed based on the oxidative activation of sp3 C–H bonds adjacent to a nitrogen atom. Various sp, sp2, and sp3 C–H bonds of pronucleophiles were used in the Cu-catalyzed CDC reactions. Based on these results, the mechanisms of the CDC reactions also are discussed. PMID:16754869

  5. Yttrium (amidate) complexes for catalytic C-N bond formation. Rapid, room temperature amidation of aldehydes.

    PubMed

    Thomson, Jaclyn A; Schafer, Laurel L

    2012-07-14

    Yttrium (amidate) precatalysts are highly active for the mild amidation of aldehydes with amines. Reactions occur at room temperature within 5 min in up to 98% isolated yield. These rare-earth systems are effective for this transformation in the absence of supplementary heat, light, base, or oxidants. The reaction proceeds with functionalized amines and/or aldehydes. A comparison of various amidate precatalysts in combination with reaction monitoring suggests that the targeted amide products formed during the reaction promote the formation of alternative catalytically active amidate species in situ.

  6. Modulation of an active-site cysteine pKa allows PDI to act as a catalyst of both disulfide bond formation and isomerization.

    PubMed

    Karala, Anna-Riikka; Lappi, Anna-Kaisa; Ruddock, Lloyd W

    2010-03-05

    Protein disulfide isomerase (PDI) plays a central role in disulfide bond formation in the endoplasmic reticulum. It is implicated both in disulfide bond formation and in disulfide bond reduction and isomerization. To be an efficient catalyst of all three reactions requires complex mechanisms. These include mechanisms to modulate the pK(a) values of the active-site cysteines of PDI. Here, we examined the role of arginine 120 in modulating the pK(a) values of these cysteines. We find that arginine 120 plays a significant role in modulating the pK(a) of the C-terminal active-site cysteine in the a domain of PDI and plays a role in determining the reactivity of the N-terminal active-site cysteine but not via direct modulation of its pK(a). Mutation of arginine 120 and the corresponding residue, arginine 461, in the a' domain severely reduces the ability of PDI to catalyze disulfide bond formation and reduction but enhances the ability to catalyze disulfide bond isomerization due to the formation of more stable PDI-substrate mixed disulfides. These results suggest that the modulation of pK(a) of the C-terminal active cysteine by the movement of the side chain of these arginine residues into the active-site locales has evolved to allow PDI to efficiently catalyze both oxidation and isomerization reactions. (c) 2009 Elsevier Ltd. All rights reserved.

  7. Fundamental and overtone vibrational spectroscopy, enthalpy of hydrogen bond formation and equilibrium constant determination of the methanol-dimethylamine complex.

    PubMed

    Du, Lin; Mackeprang, Kasper; Kjaergaard, Henrik G

    2013-07-07

    We have measured gas phase vibrational spectra of the bimolecular complex formed between methanol (MeOH) and dimethylamine (DMA) up to about 9800 cm(-1). In addition to the strong fundamental OH-stretching transition we have also detected the weak second overtone NH-stretching transition. The spectra of the complex are obtained by spectral subtraction of the monomer spectra from spectra recorded for the mixture. For comparison, we also measured the fundamental OH-stretching transition in the bimolecular complex between MeOH and trimethylamine (TMA). The enthalpies of hydrogen bond formation (ΔH) for the MeOH-DMA and MeOH-TMA complexes have been determined by measurements of the fundamental OH-stretching transition in the temperature range from 298 to 358 K. The enthalpy of formation is found to be -35.8 ± 3.9 and -38.2 ± 3.3 kJ mol(-1) for MeOH-DMA and MeOH-TMA, respectively, in the 298 to 358 K region. The equilibrium constant (Kp) for the formation of the MeOH-DMA complex has been determined from the measured and calculated transition intensities of the OH-stretching fundamental transition and the NH-stretching second overtone transition. The transition intensities were calculated using an anharmonic oscillator local mode model with dipole moment and potential energy curves calculated using explicitly correlated coupled cluster methods. The equilibrium constant for formation of the MeOH-DMA complex was determined to be 0.2 ± 0.1 atm(-1), corresponding to a ΔG value of about 4.0 kJ mol(-1).

  8. On the formation and bonding of a surface carbonate on Ni(100)

    NASA Astrophysics Data System (ADS)

    Behm, R. J.; Brundle, C. R.

    1991-09-01

    The formation, stability, adsorption geometry and electronic structure of a surface carbonate on Ni(100) have been investigated by photoemission (XPS, UPS) and temperature-programmed reaction (TPR). The core level binding energies of 531.2 eV for 0(1s) and 289.0 eV for C(1s) are comparable to those of bulk carbonates. The He(II) spectrum of the carbonate valence levels is not well defined because of the coexisting adsorbed and oxidic oxygen. The angular dependence of the carbonate core level intensities is characteristic of the carbonate being present as an overlayer species rather than a thicker surface phase. The XPS data and isotope labelled TPR experiments indicate the oxygen atoms of the carbonate to be electronically and chemically equivalent, and on this basis we favor a structure in which the carbonate is attached to the metal via all three oxygen atoms. This is supported by comparision with the core level binding energies of HCOO ab and chemisorbed CO 2,ad, which are similarly attached to the surface. From the core level angular behavior, the close similarity of core level binding energies and available vibrational spectroscopic data, a (nearly) planar geometry of the CO 3,ad on Ni(100) is concluded, which is comparable to the planar bulk carbonate anion and the planar carbonate species on Ag(110). The activation barrier for decomposition is estimated from the observed maximum in TPR at 420 K to be 25 ± 2 kcal/mol. CO 2 does not accumulate on the clean or O ad-precovered Ni(100) surface at 130 K. The stabilized, chemisorbed CO 2,ad species often observed on other metal surfaces therefore does not play a critical role for carbonate formation on Ni(100). Also a mechanism involving the disproportionation of a CO 2… CO 2,ad- dimer anion can be ruled out from TPR data. The evidence of the experiments discussed in this paper suggests that the carbonate is predominantly formed by reaction of CO 2,ad with a less stable, defect (disordered) O ad species rather

  9. Mineral catalysis of the formation of the phosphodiester bond in aqueous solution - The possible role of montmorillonite clays

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; Ertem, Gozen; KAMALUDDIN; Agarwal, Vipin; Hua, Lu Lin

    1989-01-01

    The possible role of montmorillonite clays in the spontaneous formation on the primitive earth of the phosphodiester bond in the presence of water was investigated in experiments measuring the binding of various nucleosides and nucleotides with Na(+)-montmorillonite 22A and the reactions of these compounds with a water-soluble carbodiimide. It was found that, at neutral pH, adenine derivatives bind stronger than the corresponding uracil derivatives, consistent with the protonation of the adenine by the acidic clay surface and a cationic binding of the protonated ring to the anionic clay surface. The reaction of the 5-prime-AMP with carbodiimide resulted in the formation of 2-prime,5-prime-pApA (18.9 percent), 3-prime,5-prime-pApA (11 percent), and AppA (4.8 percent). The yields of these oligomers obtained when poly(U) was used in place of the clay were 15.5 percent, 3.7 percent, and 14.9 percent AppA, respectively.

  10. Dispersion-corrected first-principles calculation of terahertz vibration, and evidence for weak hydrogen bond formation

    NASA Astrophysics Data System (ADS)

    Takahashi, Masae; Ishikawa, Yoichi; Ito, Hiromasa

    2013-03-01

    A weak hydrogen bond (WHB) such as CH-O is very important for the structure, function, and dynamics in a chemical and biological system WHB stretching vibration is in a terahertz (THz) frequency region Very recently, the reasonable performance of dispersion-corrected first-principles to WHB has been proven. In this lecture, we report dispersion-corrected first-principles calculation of the vibrational absorption of some organic crystals, and low-temperature THz spectral measurement, in order to clarify WHB stretching vibration. The THz frequency calculation of a WHB crystal has extremely improved by dispersion correction. Moreover, the discrepancy in frequency between an experiment and calculation and is 10 1/cm or less. Dispersion correction is especially effective for intermolecular mode. The very sharp peak appearing at 4 K is assigned to the intermolecular translational mode that corresponds to WHB stretching vibration. It is difficult to detect and control the WHB formation in a crystal because the binding energy is very small. With the help of the latest intense development of experimental and theoretical technique and its careful use, we reveal solid-state WHB stretching vibration as evidence for the WHB formation that differs in respective WHB networks The research was supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan (Grant No. 22550003).

  11. Mineral catalysis of the formation of the phosphodiester bond in aqueous solution - The possible role of montmorillonite clays

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; Ertem, Gozen; KAMALUDDIN; Agarwal, Vipin; Hua, Lu Lin

    1989-01-01

    The possible role of montmorillonite clays in the spontaneous formation on the primitive earth of the phosphodiester bond in the presence of water was investigated in experiments measuring the binding of various nucleosides and nucleotides with Na(+)-montmorillonite 22A and the reactions of these compounds with a water-soluble carbodiimide. It was found that, at neutral pH, adenine derivatives bind stronger than the corresponding uracil derivatives, consistent with the protonation of the adenine by the acidic clay surface and a cationic binding of the protonated ring to the anionic clay surface. The reaction of the 5-prime-AMP with carbodiimide resulted in the formation of 2-prime,5-prime-pApA (18.9 percent), 3-prime,5-prime-pApA (11 percent), and AppA (4.8 percent). The yields of these oligomers obtained when poly(U) was used in place of the clay were 15.5 percent, 3.7 percent, and 14.9 percent AppA, respectively.

  12. An unusual cysteine VL87 affects the antibody fragment conformations without interfering with the disulfide bond formation.

    PubMed

    Attallah, Carolina; Aguilar, María Fernanda; Garay, A Sergio; Herrera, Fernando E; Etcheverrigaray, Marina; Oggero, Marcos; Rodrigues, Daniel E

    2017-10-01

    The Cys residues are almost perfectly conserved in all antibodies. They contribute significantly to the antibody fragment stability. The relevance of two natural contiguous Cys residues of an anti-recombinant human-follicle stimulation hormone (rhFSH) in a format of single-chain variable fragment (scFv) was studied. This scFv contains 5 Cys residues: VH22 and VH92 in the variable heavy chain (VH) and VL23, VL87 and VL88 in the variable light chain (VL). The influence of two unusual contiguous Cys at positions VL87 and VL88 was studied by considering the wild type fragment and mutant variants: VL-C88S, VL-C87S, VL-C87Y. The analysis was carried out using antigen-binding ability measurement by indirect specific ELISA and a detailed molecular modeling that comprises homology methods, long molecular dynamics simulations and docking. We found that VL-C87 affected the antibody fragment stability without interfering with the disulfide bond formation. The effect of mutating the VL-C87 by a usual residue at this position like Tyr caused distant structural changes at the VH region that confers a higher mobility to the VH-CDR2 and VH-CDR3 loops improving the scFv binding to the antigen. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Bond formation kinetics affects self-assembly directed by ligand-receptor interactions.

    PubMed

    Jan Bachmann, Stephan; Petitzon, Marius; Mognetti, Bortolo Matteo

    2016-11-28

    In this paper we study aggregation kinetics in systems of particles functionalised by complementary linkers. Most of the coarse-grained models currently employed to study large-scale self-assembly of these systems rely on effective potentials between particles as calculated using equilibrium statistical mechanics. In these approaches the kinetic aspects underlying the formation of inter-particle linkages are neglected. We show how the rate at which supramolecular linkages form drastically changes the self-assembly pathway. In order to do this we develop a method that combines Brownian dynamics simulations with a Gillespie algorithm accounting for the evolution of inter-particle linkages. If compared with dynamics based on effective potentials, an explicit description of inter-particle linkages results in aggregates that in the early stages of self-assembly have a lower valency. Relaxation towards equilibrium is hampered by the time required to break existing linkages within one cluster and to reorient them toward free particles. This effect is more important at low temperature and high particle diffusion constant. Our results highlight the importance of including kinetic rates into coarse-grained descriptions of ligand-receptor systems.

  14. Efficient routes to carbon-silicon bond formation for the synthesis of silicon-containing peptides and azasilaheterocycles.

    PubMed

    Min, Geanna K; Hernández, Dácil; Skrydstrup, Troels

    2013-02-19

    Silasubstitution, where silicon is substituted for carbon at specific sites of the substrate, has become a growing practice in medicinal chemistry. Introducing silicon into bioactive compounds provides slight physical and electronic alterations to the parent compound, which in certain instances could make the substrate a more viable candidate for a drug target. One application is in the field of protease inhibition. Various silane diol isosteres can act as potent inhibitors of aspartic and metalloproteases because of their ability to mimic the high-energy tetrahedral intermediate in peptide bond hydrolysis. In particular, since 1998, the Sieburth group has prepared a number of functionalized peptide silane diol isosteres. In a seminal study, they demonstrated that these molecules can bind to the active site of the enzymes. Inspired by these results, we initiated a study to develop a concise and straightforward route to access highly functionalized silicon diol based peptidomimetic analogs, which we describe in this Account. The synthesis of such analogs is challenging because the dipeptide mimics require the formation of two carbon-silicon bonds as well as two chiral carbon centers. Our first strategy was to assemble the two C-Si bonds from diphenylsilane through an initial regioselective hydrosilylation step of a terminal alkene, followed by lithiation of the formed alkyldiphenylsilane by a simple lithium metal reduction. Subsequent diastereoselective addition of this silyllithium species to a tert-butylsulfinimine provided a rapid method to assemble the dipeptide mimic with stereochemical control at the new chiral carbon center adjacent to the silicon. This strategy worked with a wide range of functional groups. However, there were some limitations with the more elaborate targets. In particular, we needed to exchange the phenyl groups of the diphenylsilane with aryl groups that were more labile under acidic conditions in order to introduce Si-O bonds in the end

  15. Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains.

    PubMed

    Nagy, Peter I; Erhardt, Paul W

    2008-05-08

    Hydrogen bonding was studied in 24 pairs of isopropyl alcohol and phenol as one partner, and water and amino-acid mimics (methanol, acetamide, neutral and protonated imidazole, protonated methylalamine, methyl-guanidium cation, and acetate anion) as the other partner. MP2/6-31+G* and MP2/aug-cc-pvtz calculations were conducted in the gas phase and in a model continuum dielectric environment with dielectric constant of 15.0. Structures were optimized in the gas phase with both basis sets, and zero-point energies were calculated at the MP2/6-31+G* level. At the MP2/aug-cc-pvtz level, the BSSE values from the Boys-Bernardi counterpoise calculations amount to 10-20 and 5-10% of the uncorrected binding energies of the neutral and ionic complexes, respectively. The geometry distortion energy upon hydrogen-bond formation is up to 2 kcal/mol, with the exception of the most strongly bound complexes. The BSSE-corrected MP2/aug-cc-pvtz binding energy of -27.56 kcal/mol for the gas-phase acetate...phenol system has been classified as a short and strong hydrogen bond (SSHB). The CH3NH3+...isopropyl alcohol complex with binding energy of -22.54 kcal/mol approaches this classification. The complete basis set limit (CBS) for the binding energy was calculated for twelve and six complexes on the basis of standard and counterpoise-corrected geometry optimizations, respectively. The X...Y distances of the X-H...Y bridges differ by up to 0.03 A as calculated by the two methods, whereas the corresponding CBS energy values differ by up to 0.03 kcal/mol. Uncorrected MP2/aug-cc-pvtz hydrogen-bonding energies are more negative by up to 0.35 kcal/mol than the MP2/CBS values, and overestimate the CCSD(T)/CBS binding energies generally by up to 5% for the eight studied complexes in the gas phase. The uncorrected MP2/aug-cc-pvtz binding energies decreased (in absolute value) by 11-18 kcal/mol for the ionic species and by up to 5 kcal/mol for the neutral complexes when the electrostatic effect

  16. Enthalpy of formation of anisole: implications for the controversy on the O-H bond dissociation enthalpy in phenol.

    PubMed

    Simões, Ricardo G; Agapito, Filipe; Diogo, Hermínio P; da Piedade, Manuel E Minas

    2014-11-20

    Significant discrepancies in the literature data for the enthalpy of formation of gaseous anisole, ΔfHmo(PhOCH3, g), have fueled an ongoing controversy regarding the most reliable enthalpy of formation of the phenoxy radical and of the gas phase O-H bond dissociation enthalpy, DHo(PhO-H), in phenol. In the present work ΔfHmo(PhOCH3, g) was reassessed using a combination of calorimetric determinations and high-level (W2-F12) ab initio calculations. Static-bomb combustion calorimetry led to the standard molar enthalpy of formation of liquid anisole at 298.15 K, ΔfHmo(PhOCH3, l) = −(117.1 ± 1.4) kJ·mol(-1). The corresponding enthalpy of vaporization was obtained as, ΔvapHmo(PhOCH3) = 46.41 ± 0.26 kJ·mol(-1), by Calvet-drop microcalorimetry. These results give ΔfHmo(PhOCH3, g) = −(70.7 ± 1.4) kJ·mol(-1), in excellent agreement with ΔfHmo(PhOCH3, g) = −(70.8 ± 3.2) kJ·mol(-1), obtained from the W2-F12 calculations. The ΔfHmo(PhOCH3, g) here recommended leads to ΔfHmo(PhO•, g) = 55.5 ± 2.4 kJ·mol(-)1 and DH°(PhO-H) = 368.1 ± 2.6 kJ·mol(-1).

  17. Cubic Siloxanes with Both Si-H and Si-OtBu Groups for Site-Selective Siloxane Bond Formation.

    PubMed

    Saito, Shohei; Yamasue, Nao; Wada, Hiroaki; Shimojima, Atsushi; Kuroda, Kazuyuki

    2016-09-19

    Cage-type siloxanes have attracted increasing attention as building blocks for silica-based nanomaterials as their corners can be modified with various functional groups. Cubic octasiloxanes incorporating both Si-H and Si-OtBu groups [(tBuO)n H8-n Si8 O12 ; n=1, 2 or 7] have been synthesized by the reaction of octa(hydridosilsesquioxane) (H8 Si8 O12 ) and tert-butyl alcohol in the presence of a Et2 NOH catalyst. The Si-H and Si-OtBu groups are useful for site-selective formation of Si-O-Si linkages without cage structure deterioration. The Si-H group can be selectively hydrolyzed to form a Si-OH group in the presence of Et2 NOH, enabling the formation of the monosilanol compound (tBuO)7 (HO)Si8 O12 . The Si-OH group can be used for either intermolecular condensation to form a dimeric cage compound or silylation to introduce new reaction sites. Additionally, the alkoxy groups of (tBuO)7 HSi8 O12 can be treated with organochlorosilanes in the presence of a BiCl3 catalyst to form Si-O-Si linkages, while the Si-H group remains intact. These results indicate that such bifunctional cage siloxanes allow for stepwise Si-O-Si bond formation to design new siloxane-based nanomaterials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Mechanism of and exquisite selectivity for O–O bond formation by the heme-dependent chlorite dismutase

    PubMed Central

    Lee, Amanda Q.; Streit, Bennett R.; Zdilla, Michael J.; Abu-Omar, Mahdi M.; DuBois, Jennifer L.

    2008-01-01

    Chlorite dismutase (Cld) is a heme b-dependent, O–O bond forming enzyme that transforms toxic chlorite (ClO2−) into innocuous chloride and molecular oxygen. The mechanism and specificity of the reaction with chlorite and alternate oxidants were investigated. Chlorite is the sole source of dioxygen as determined by oxygen-18 labeling studies. Based on ion chromatography and mass spectrometry results, Cld is highly specific for the dismutation of chlorite to chloride and dioxygen with no other side products. Cld does not use chlorite as an oxidant for oxygen atom transfer and halogenation reactions (using cosubstrates guaiacol, thioanisole, and monochlorodimedone, respectively). When peracetic acid or H2O2 was used as an alternative oxidant, oxidation and oxygen atom transfer but not halogenation reactions occurred. Monitoring the reaction of Cld with peracetic acid by rapid-mixing UV-visible spectroscopy, the formation of the high valent compound I intermediate, [(Por•+)FeIV = O], was observed [k1 = (1.28 ± 0.04) × 106 M−1 s−1]. Compound I readily decayed to form compound II in a manner that is independent of peracetic acid concentration (k2 = 170 ± 20 s−1). Both compound I and a compound II-associated tryptophanyl radical that resembles cytochrome c peroxidase (Ccp) compound I were observed by EPR under freeze-quench conditions. The data collectively suggest an O–O bond-forming mechanism involving generation of a compound I intermediate via oxygen atom transfer from chlorite, and subsequent recombination of the resulting hypochlorite and compound I. PMID:18840691

  19. From Molecules to Surfaces: Radical-Based Mechanisms of Si-S and Si-Se Bond Formation on Silicon.

    PubMed

    Buriak, Jillian M; Sikder, Md Delwar H

    2015-08-05

    The derivatization of silicon surfaces can have profound effects on the underlying electronic properties of the semiconductor. In this work, we investigate the radical surface chemistry of silicon with a range of organochalcogenide reagents (comprising S and Se) on a hydride-terminated silicon surface, to cleanly and efficiently produce surface Si-S and Si-Se bonds, at ambient temperature. Using a diazonium-based radical initiator, which induces formation of surface silicon radicals, a group of organochalcogenides were screened for reactivity at room temperature, including di-n-butyl disulfide, diphenyl disulfide, diphenyl diselenide, di-n-butyl sulfide, diphenyl selenide, diphenyl sulfide, 1-octadecanethiol, t-butyl disulfide, and t-butylthiol, which comprises the disulfide, diselenide, thiol, and thioether functionalities. The surface reactions were monitored by transmission mode Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy, and time-of-flight secondary ionization mass spectrometry. Calculation of Si-Hx consumption, a semiquantitative measure of yield of production of surface-bound Si-E bonds (E = S, Se), was carried out via FTIR spectroscopy. Control experiments, sans the BBD diazonium radical initiator, were all negative for any evident incorporation, as determined by FTIR spectroscopy. The functional groups that did react with surface silicon radicals included the dialkyl/diphenyl disulfides, diphenyl diselenide, and 1-octadecanethiol, but not t-butylthiol, diphenyl sulfide/selenide, and di-n-butyl sulfide. Through a comparison with the rich body of literature regarding molecular radicals, and in particular, silyl radicals, reaction mechanisms were proposed for each. Armed with an understanding of the reaction mechanisms, much of the known chemistry within the extensive body of radical-based reactivity has the potential to be harnessed on silicon and could be extended to a range of technologically relevant semiconductor

  20. Streptothricin biosynthesis is catalyzed by enzymes related to nonribosomal peptide bond formation.

    PubMed Central

    Fernández-Moreno, M A; Vallín, C; Malpartida, F

    1997-01-01

    In a search for strains producing biocides with a wide spectrum of activity, a new strain was isolated. This strain was taxonomically characterized as Streptomyces rochei F20, and the chemical structure of the bioactive product extracted from its fermentation broth was determined to be a mixture of streptothricins. From a genomic library of the producer strain prepared in the heterologous host Streptomyces lividans, a 7.2-kb DNA fragment which conferred resistance to the antibiotic was isolated. DNA sequencing of 5.2 kb from the cloned fragment revealed five open reading frames (ORFs) such that ORF1, -2, -3, and -4 were transcribed in the same direction while ORF5 was convergently arranged. The deduced product of ORF1 strongly resembled those of genes involved in peptide formation by a nonribosomal mechanism; the ORF2 product strongly resembled that of mphA and mphB isolated from Escherichia coli, which determines resistance to several macrolides by a macrolide 2'-phosphotransferase activity; the ORF3 product had similarities with several hydrolases; and the ORF5 product strongly resembled streptothricin acetyltransferases from different gram-positive and gram-negative bacteria. ORF5 was shown to be responsible for acetyl coenzyme A-dependent streptothricin acetylation. No similarities in the databases for the ORF4 product were found. Unlike other peptide synthases, that for streptothricin biosynthesis was arranged as a multienzymatic system rather than a multifunctional protein. Insertional inactivation of ORF1 and ORF2 (and to a lesser degree, of ORF3) abolishes antibiotic biosynthesis, suggesting their involvement in the streptothricin biosynthetic pathway. PMID:9371436

  1. Controlling the Formation of Ionic-Liquid-based Aqueous Biphasic Systems by Changing the Hydrogen-Bonding Ability of Polyethylene Glycol End Groups.

    PubMed

    Pereira, Jorge F B; Kurnia, Kiki A; Freire, Mara G; Coutinho, João A P; Rogers, Robin D

    2015-07-20

    The formation of aqueous biphasic systems (ABS) when mixing aqueous solutions of polyethylene glycol (PEG) and an ionic liquid (IL) can be controlled by modifying the hydrogen-bond-donating/-accepting ability of the polymer end groups. It is shown that the miscibility/immiscibility in these systems stems from both the solvation of the ether groups in the oxygen chain and the ability of the PEG terminal groups to preferably hydrogen bond with water or the anion of the salt. The removal of even one hydrogen bond in PEG can noticeably affect the phase behavior, especially in the region of the phase diagram in which all the ethylene oxide (EO) units of the polymeric chain are completely solvated. In this region, removing or weakening the hydrogen-bond-donating ability of PEG results in greater immiscibility, and thus, in a higher ability to form ABS, as a result of the much weaker interactions between the IL anion and the PEG end groups.

  2. Formation of an ordered phase by ceramides and diacylglycerols in a fluid phosphatidylcholine bilayer--Correlation with structure and hydrogen bonding capacity.

    PubMed

    Ekman, Peik; Maula, Terhi; Yamaguchi, Shou; Yamamoto, Tetsuya; Nyholm, Thomas K M; Katsumura, Shigeo; Slotte, J Peter

    2015-10-01

    Ceramides and diacylglycerols are lipids with a large hydrophobic part (acyl chains and long-chain base) whereas their polar function (hydroxyl group) is small. They need colipids with large head groups to coexist in bilayer membranes. In this study, we have determined how saturated and unsaturated ceramides and acyl-chain matched diacylglycerols form ordered domains in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers as a function of bilayer concentration. The formation of ordered domains was determined from lifetime analysis of trans-parinaric acid. Ceramides formed ordered domains with equal average tPA lifetime at lower bilayer concentration when compared to acyl-chain matched diacylglycerols. This was true for both saturated (16:0) and mono-unsaturated (18:1) species. This finding suggested that hydrogen bonding among ceramides contributed to their more efficient ordered phase formation, since diacylglycerols do not form similar hydrogen bonding networks. The role of hydrogen bonding in ordered domain formation was further verified by using palmitoyl ceramide analogs with 2N and 3OH methylated long-chain bases. These analogs do not form hydrogen bonds from the 2NH or the 3OH, respectively. While methylation of the 3OH did not affect ordered phase formation compared to native palmitoyl ceramide, 2NH methylation markedly attenuated ceramide ordered phase formation. We conclude that in addition to acyl chain length, saturation, molecular order, and lack of large head group, also hydrogen bonding involving the 2NH is crucial for efficient formation of ceramide-rich domains in fluid phosphatidylcholine bilayers.

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

    PubMed

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

    2016-04-21

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

  4. Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm

    USDA-ARS?s Scientific Manuscript database

    We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, HdeB and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALD...

  5. Remarkably efficient synthesis of 2H-indazole 1-oxides and 2H-indazoles via tandem carbon-carbon followed by nitrogen-nitrogen bond formation.

    PubMed

    Bouillon, Isabelle; Zajícek, Jaroslav; Pudelová, Nadĕzda; Krchnák, Viktor

    2008-11-21

    Base-catalyzed tandem carbon-carbon followed by nitrogen-nitrogen bond formations quantitatively converted N-alkyl-2-nitro-N-(2-oxo-2-aryl-ethyl)-benzenesulfonamides to 2H-indazoles 1-oxides under mild conditions. Triphenylphosphine or mesyl chloride/triethylamine-mediated deoxygenation afforded 2H-indazoles.

  6. Remarkably Efficient Synthesis of 2H-Indazole 1-oxides and 2H-Indazoles via Tandem Carbon–Carbon Followed by Nitrogen–Nitrogen Bond Formation

    PubMed Central

    Bouillon, Isabelle; Zajíček, Jaroslav; Pudelová, Naděžda; Krchňák, Viktor

    2009-01-01

    Synthesis of Indazoles Base-catalyzed tandem carbon–carbon followed by nitrogen–nitrogen bond formations quantitatively converted N-alkyl-2-nitro-N-(2-oxo-2-aryl-ethyl)-benzenesulfonamides to 2H-indazoles 1-oxides under mild conditions. Triphenylphosphine or mesyl chloride/triethylamine-mediated deoxygenation afforded 2H-indazoles. PMID:18937414

  7. Theoretical studies on N-O or N-N bond formation from aryl azide catalyzed by iron(II) bromide complex.

    PubMed

    Li, Juan; Zhang, Qi; Zhou, Lixin

    2012-03-02

    DFT calculations have been carried out to study the reaction mechanism on N-O or N-N bond formation from aryl azide catalyzed by iron(II) bromide complex. A favorable reaction pathway is proposed to account for the construction of the core structure of 2H-indazoles or 2,1-benzisoxazoles.

  8. Consecutive condensation, C-N and N-N bond formations: a copper- catalyzed one-pot three-component synthesis of 2H-indazole.

    PubMed

    Kumar, Manian Rajesh; Park, Ahbyeol; Park, Namjin; Lee, Sunwoo

    2011-07-01

    2H-Indazoles are synthesized using copper-catalyzed, one-pot, three-component reactions of 2-bromobenzaldehydes, primary amines, and sodium azide. A copper catalyst plays the key role in the formation of C-N and N-N bonds. This method has a broad substrate scope with a high tolerance for a variety of functional groups.

  9. Molecular dynamics simulation to investigate the impact of disulfide bond formation on conformational stability of chicken cystatin I66Q mutant.

    PubMed

    He, Jianwei; Xu, Linan; Zou, Zhiyuan; Ueyama, Nobuhiro; Li, Hui; Kato, Akio; Jones, Gary W; Song, Youtao

    2013-10-01

    Chicken cystatin (cC) mutant I66Q is located in the hydrophobic core of the protein and increases the propensity for amyloid formation. Here, we demonstrate that under physiological conditions, the replacement of Ile with the Gln in the I66Q mutant increases the susceptibility for the disulfide bond Cys71-Cys81 to be reduced when compared to the wild type (WT) cC. Molecular dynamics (MD) simulations under conditions favoring cC amyloid fibril formation are in agreement with the experimental results. MD simulations were also performed to investigate the impact of disrupting the Cys71-Cys81 disulfide bond on the conformational stability of cC at the atomic level, and highlighted major disruption to the cC appendant structure. Domain swapping and extensive unfolding has been proposed as one of the possible mechanisms initiating amyloid fibril formation by cystatin. Our in silico studies suggest that disulfide bond formation between residues Cys95 and Cys115 is necessary to maintain conformational stability of the I66Q mutant following breakage of the Cys71-Cys81 disulfide bridge. Subsequent breakage of disulfide bond Cys95-Cys115 resulted in large structural destabilization of the I66Q mutant, which increased the α-β interface distance and expanded the hydrophobic core. These experimental and computational studies provide molecular-level insight into the relationship between disulfide bond formation and progressive unfolding of amyloidogenic cC mutant I66Q. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:23.

  10. Total Syntheses of (−)-Kopsifoline D and (−)-Deoxoapodine: Divergent Total Synthesis via Late-Stage Key Strategic Bond Formation

    PubMed Central

    2015-01-01

    Divergent total syntheses of (−)-kopsifoline D and (−)-deoxoapodine are detailed from a common pentacyclic intermediate 15, enlisting the late-stage formation of two different key strategic bonds (C21–C3 and C21–O–C6) unique to their hexacyclic ring systems that are complementary to its prior use in the total syntheses of kopsinine (C21–C2 bond formation) and (+)-fendleridine (C21–O–C19 bond formation). The combined efforts represent the total syntheses of members of four classes of natural products from a common intermediate functionalized for late-stage formation of four different key strategic bonds uniquely embedded in each natural product core structure. Key to the first reported total synthesis of a kopsifoline that is detailed herein was the development of a transannular enamide alkylation for late-stage formation of the C21–C3 bond with direct introduction of the reactive indolenine C2 oxidation state from a penultimate C21 functionalized Aspidosperma-like pentacyclic intermediate. Central to the assemblage of the underlying Apidosperma skeleton is a powerful intramolecular [4 + 2]/[3 + 2] cycloaddition cascade of a 1,3,4-oxadiazole that provided the functionalized pentacyclic ring system 15 in a single step in which the C3 methyl ester found in the natural products served as a key 1,3,4-oxadiazole substituent, activating it for participation in the initiating Diels–Alder reaction and stabilizing the intermediate 1,3-dipole. PMID:24499015

  11. Rapid preparation of branched and degradable AIE-active fluorescent organic nanoparticles via formation of dynamic phenyl borate bond.

    PubMed

    Long, Zi; Liu, Meiying; Mao, Liucheng; Zeng, Guangjian; Wan, Qing; Xu, Dazhuang; Deng, Fengjie; Huang, Hongye; Zhang, Xiaoyong; Wei, Yen

    2017-02-01

    The fluorescent organic nanoparticles (FNPs) with aggregation-induced emission (AIE) feature have received increasing attention for their advanced optical properties. Although many efforts have been devoted to the fabrication and biomedical applications of AIE-active FNPs, the preparation of branched AIE-active FNPs with degradability through formation of dynamic bonds have rarely been reported. In this work, branched AIE-active FNPs were fabricated via dynamic linkage of hydrophobic hyperbranched and degradable Boltorn H40 (H40) with phenylboronic acid terminated AIE dye (PhB(OH)2) and mPEG (mPEG-B(OH)2), which relied on a facile one-pot strategy between phenylboronic acid and diol group of H40. The branched H40-star-mPEG-PhB(OH)2 FNPs were characterized using nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, and fluorescence spectroscopy. Benefiting from their highly branched structure and amphiphilic properties, H40-star-mPEG-PhB(OH)2 could self-assemble into micelles and emit strong orange-red fluorescence. More importantly, cell viability results demonstrated that H40-star-mPEG-PhB(OH)2 FNPs showed good biocompatibility and promising candidates for bio-imaging. Taken together, we developed a one-pot strategy for preparation of branched AIE-active FNPs through the formation of dynamic phenyl borate. The resultant H40-star-mPEG-PhB(OH)2 FNPs should be promising biomaterials for different applications for biodegradability of H40 and responsiveness of phenyl borate. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Constructing safe and durable antibacterial textile surfaces using a robust graft-to strategy via covalent bond formation

    NASA Astrophysics Data System (ADS)

    He, Liang; Li, Sha; Chung, Cordelia T. W.; Gao, Chang; Xin, John H.

    2016-11-01

    Recently zwitterionic materials have been widely applied in the biomedical and bioengineering fields due to their excellent biocompatibility. Inspired by these, this study presents a graft-to strategy via covalent bond formation to fabricate safe and durable antibacterial textile surfaces. A novel zwitterionic sulfobetaine containing triazine reactive group was specifically designed and synthesized. MTT assay showed that it had no obvious cytotoxicity to human skin HaCaT cells as verified by ca. 89.9% relative viability at a rather high concentration of 0.8 mg·mL-1. In the evaluation for its skin sensitization, the maximum score for symptoms of erythema and edema in all tests were 0 in all observation periods. The sulfobetaine had a hydrophilic nature and the hydrophilicity of the textiles was enhanced by 43.9% when it was covalently grafted onto the textiles. Moreover, the textiles grafted with the reactive sulfobetaine exhibited durable antibacterial activities, which was verified by the fact that they showed antibacterial rates of 97.4% against gram-positive S. aureus and 93.2% against gram-negative E. coli even after they were laundered for 30 times. Therefore, the titled zwitterionic sulfobetaine is safe to human for healthcare and wound dressing and shows a promising prospect on antibacterial textile application.

  13. Constructing safe and durable antibacterial textile surfaces using a robust graft-to strategy via covalent bond formation

    PubMed Central

    He, Liang; Li, Sha; Chung, Cordelia T. W.; Gao, Chang; Xin, John H.

    2016-01-01

    Recently zwitterionic materials have been widely applied in the biomedical and bioengineering fields due to their excellent biocompatibility. Inspired by these, this study presents a graft-to strategy via covalent bond formation to fabricate safe and durable antibacterial textile surfaces. A novel zwitterionic sulfobetaine containing triazine reactive group was specifically designed and synthesized. MTT assay showed that it had no obvious cytotoxicity to human skin HaCaT cells as verified by ca. 89.9% relative viability at a rather high concentration of 0.8 mg·mL−1. In the evaluation for its skin sensitization, the maximum score for symptoms of erythema and edema in all tests were 0 in all observation periods. The sulfobetaine had a hydrophilic nature and the hydrophilicity of the textiles was enhanced by 43.9% when it was covalently grafted onto the textiles. Moreover, the textiles grafted with the reactive sulfobetaine exhibited durable antibacterial activities, which was verified by the fact that they showed antibacterial rates of 97.4% against gram-positive S. aureus and 93.2% against gram-negative E. coli even after they were laundered for 30 times. Therefore, the titled zwitterionic sulfobetaine is safe to human for healthcare and wound dressing and shows a promising prospect on antibacterial textile application. PMID:27808248

  14. Chemically fixed p-n heterojunctions for polymer electronics by means of covalent B-F bond formation.

    PubMed

    Hoven, Corey V; Wang, Huiping; Elbing, Mark; Garner, Logan; Winkelhaus, Daniel; Bazan, Guillermo C

    2010-03-01

    Widely used solid-state devices fabricated with inorganic semiconductors, including light-emitting diodes and solar cells, derive much of their function from the p-n junction. Such junctions lead to diode characteristics and are attained when p-doped and n-doped materials come into contact with each other. Achieving bilayer p-n junctions with semiconducting polymers has been hindered by difficulties in the deposition of thin films with independent p-doped and n-doped layers. Here we report on how to achieve permanently fixed organic p-n heterojunctions by using a cationic conjugated polyelectrolyte with fluoride counteranions and an underlayer composed of a neutral conjugated polymer bearing anion-trapping functional groups. Application of a bias leads to charge injection and fluoride migration into the neutral layer, where irreversible covalent bond formation takes place. After the initial charging and doping, one obtains devices with no delay in the turn on of light-emitting electrochemical behaviour and excellent current rectification. Such devices highlight how mobile ions in organic media can open opportunities to realize device structures in ways that do not have analogies in the world of silicon and promise new opportunities for integrating organic materials within technologies now dominated by inorganic semiconductors.

  15. Kinetics of T3-DNA Ligase-Catalyzed Phosphodiester Bond Formation Measured Using the α-Hemolysin Nanopore.

    PubMed

    Tan, Cherie S; Riedl, Jan; Fleming, Aaron M; Burrows, Cynthia J; White, Henry S

    2016-12-27

    The latch region of the wild-type α-hemolysin (α-HL) protein channel can be used to distinguish single base modifications in double-stranded DNA (dsDNA) via ion channel measurements upon electrophoretic capture of dsDNA in the vestibule of α-HL. Herein, we investigated the use of the latch region to detect a nick in the phosphodiester DNA backbone. The presence of a nick in the phosphodiester backbone of one strand of the duplex results in a significant increase in both the blockade current and noise level relative to the intact duplex. Differentiation between the nicked and intact duplexes based on blockade current or noise, with near baseline resolution, allows real-time monitoring of the rate of T3-DNA ligase-catalyzed phosphodiester bond formation. Under low ionic strength conditions containing divalent cations and a molecular crowding agent (75 mg mL(-1) PEG), the rate of enzyme-catalyzed reaction in the bulk solution was continuously monitored by electrophoretically capturing reaction substrate or product dsDNA in the α-HL protein channel vestibule. Enzyme kinetic results obtained from the nanopore experiments match those from gel electrophoresis under the same reaction conditions, indicating the α-HL nanopore measurement provides a viable approach for monitoring enzymatic DNA repair activity.

  16. Constructing safe and durable antibacterial textile surfaces using a robust graft-to strategy via covalent bond formation.

    PubMed

    He, Liang; Li, Sha; Chung, Cordelia T W; Gao, Chang; Xin, John H

    2016-11-03

    Recently zwitterionic materials have been widely applied in the biomedical and bioengineering fields due to their excellent biocompatibility. Inspired by these, this study presents a graft-to strategy via covalent bond formation to fabricate safe and durable antibacterial textile surfaces. A novel zwitterionic sulfobetaine containing triazine reactive group was specifically designed and synthesized. MTT assay showed that it had no obvious cytotoxicity to human skin HaCaT cells as verified by ca. 89.9% relative viability at a rather high concentration of 0.8 mg·mL(-1). In the evaluation for its skin sensitization, the maximum score for symptoms of erythema and edema in all tests were 0 in all observation periods. The sulfobetaine had a hydrophilic nature and the hydrophilicity of the textiles was enhanced by 43.9% when it was covalently grafted onto the textiles. Moreover, the textiles grafted with the reactive sulfobetaine exhibited durable antibacterial activities, which was verified by the fact that they showed antibacterial rates of 97.4% against gram-positive S. aureus and 93.2% against gram-negative E. coli even after they were laundered for 30 times. Therefore, the titled zwitterionic sulfobetaine is safe to human for healthcare and wound dressing and shows a promising prospect on antibacterial textile application.

  17. Effects of the pouring temperature on the formation of the bonding zone between AZ91 and AlSi17 in the compound casting process

    NASA Astrophysics Data System (ADS)

    Mola, R.; Bucki, T.; Dziadoń, A.

    2017-02-01

    The compound casting process was used to join AZ91 magnesium alloy to AlSi17 aluminium alloy. Liquid AZ91 was poured onto a solid AlSi17 insert placed in a steel mould heated to 370 °C. The experimental results showed that the temperature of the AZ91 melt affected the formation of the bonding zone between the two alloys. A continuous bonding zone was formed by applying a pouring temperature of 650 °C. The use of higher temperatures, i.e. 680 °C and 700 °C, did not lead to the formation of a continuous metallurgical transition zone at the AZ91/AlSi17 interface. The bonding zone was analysed using an optical microscope and a scanning electron microscope equipped with an energy dispersive X-ray (EDS) detector. The structural constituents of the bonding zone near the AlSi17 alloy were: an Al3Mg2 intermetallic phase, primary Si particles surrounded by a rim of an Mg2Si intermetallic phase and fine Mg2Si particles. The area of the bonding zone that was adjacent to the AZ91 alloy had a eutectic structure composed of an Mg17Al12 intermetallic phase and a solid solution of Al and Si in Mg.

  18. Unusual nickel-mediated C-S cleavage of alkyl and aryl sulfoxides.

    PubMed

    Schaub, Thomas; Backes, Marc; Radius, Udo

    2007-05-28

    The first examples of transition metal mediated C-S cleavage of sulfoxides containing sp2- and sp3-hybridized carbon bonds attached to the sulfur atom and the first example of a structurally characterized complex featuring an oxygen-bound sulfinyl ligand are presented.

  19. Initial Carbon–Carbon Bond Formation during the Early Stages of the Methanol‐to‐Olefin Process Proven by Zeolite‐Trapped Acetate and Methyl Acetate

    PubMed Central

    Chowdhury, Abhishek Dutta; Houben, Klaartje; Whiting, Gareth T.; Mokhtar, Mohamed; Asiri, Abdullah M.; Al‐Thabaiti, Shaeel A.; Basahel, Suliman N.

    2016-01-01

    Abstract Methanol‐to‐olefin (MTO) catalysis is a very active field of research because there is a wide variety of sometimes conflicting mechanistic proposals. An example is the ongoing discussion on the initial C−C bond formation from methanol during the induction period of the MTO process. By employing a combination of solid‐state NMR spectroscopy with UV/Vis diffuse reflectance spectroscopy and mass spectrometry on an active H‐SAPO‐34 catalyst, we provide spectroscopic evidence for the formation of surface acetate and methyl acetate, as well as dimethoxymethane during the MTO process. As a consequence, new insights in the formation of the first C−C bond are provided, suggesting a direct mechanism may be operative, at least in the early stages of the MTO reaction. PMID:27805783

  20. Construction of Fused Pyrrolidines and β-Lactones by Carbene-Catalyzed C-N, C-C, and C-O Bond Formations.

    PubMed

    Wu, Xingxing; Hao, Lin; Zhang, Yuexia; Rakesh, Maiti; Reddi, Rambabu N; Yang, Song; Song, Bao-An; Chi, Yonggui Robin

    2017-03-15

    A carbene-catalyzed intermolecular C-N bond formation, which initiates a highly selective cascade reaction for the synthesis of pyrrolidine fused β-lactones, is disclosed. The nitrogen-containing bicyclic β-lactone products are obtained with good yields and excellent stereoselectivities. Synthetic transformations of the reaction products into useful functional molecules, such as amino catalysts, can be efficiently realized under mild reaction conditions. Mechanistically, this study provides insights into modulating the reactivities of heteroatoms, such as nitrogen atoms, in challenging carbene-catalyzed asymmetric carbon-heteroatom bond-forming reactions.

  1. Experimental and theoretical study on palladium-catalyzed C-P bond formation via direct coupling of triarylbismuths with P(O)-H compounds.

    PubMed

    Wang, Tao; Sang, Shuai; Liu, Liu; Qiao, Hongwei; Gao, Yuxing; Zhao, Yufen

    2014-01-17

    A novel and highly efficient Pd-catalyzed cross-coupling of triarylbismuths with a variety of P(O)-H compounds has been developed that proceeds smoothly without exclusion of moisture or air and provides a general and powerful tool for the preparation of various valuable arylphosphonates, arylphosphinates, and arylphosphine oxides, with high atom-economy, operational simplicity of the procedure, and good to high yield. The coupling reaction is the first example of transition-metal-catalyzed C-P bond construction using triarylbismuth compounds as substrates. DFT calculations reveal that C-P bond formation is the rate-determing step.

  2. First insertion of NO into a transition-metal cluster-carbon bond: regioselective formation, structure, and reactions of the first alkanenitrile oxide complexes

    SciTech Connect

    Goldhaber, A.; Vollhardt, K.P.C.; Walborsky, E.C.; Wolfgruber, M.

    1986-02-05

    The chemistry of NO in the presence of transition metals is receiving considerable current attention because of its role in air pollution, its potential in organic synthesis by carbon-nitrogen bond formation, and an increasing interest in its basic features. The nitrosyl cation has been reacted with many mono and polynuclear metal systems, leading mainly to substitution and reduction. Insertion into alkyl and aryl metal bonds in mono-metallic complexes is documented. The unprecedented title reaction and some preliminary chemistry of the products are reported here. 27 references, 1 figure.

  3. A Palladium-Catalyzed Method for the Synthesis of Carbazoles via Tandem C-H Functionalization and C-N Bond Formation

    PubMed Central

    Tsang, W. C. Peter; Munday, Rachel H.; Brasche, Gordon; Zheng, Nan; Buchwald, Stephen L.

    2009-01-01

    The development of a new method for the assembly of unsymmetrical carbazoles is reported. The strategy involves the selective intramolecular functionalization of an arene C-H bond and the formation of a new arene C-N bond. The substitution pattern of the carbazole product can be controlled by the design of the biaryl amide substrate, and the method is compatible with a variety of functional groups. The utility of the new protocol was demonstrated by the concise synthesis of three natural products from commercially available materials. PMID:18761437

  4. Formation of carbon nitride with sp{sup 3}-bonded carbon in CN{sub x}/ZrN superlattice coatings

    SciTech Connect

    Wu, M. L.; Guruz, M. U.; Dravid, V. P.; Chung, Y. W.; Anders, S.; Freire, F. L. Jr.; Mariotto, G.

    2000-05-08

    A carbon nitride phase with primarily sp{sup 3}-bonded carbon is stabilized in CN{sub x}/ZrN superlattice coatings. Rutherford backscattering spectrometry measurements give a N/C atomic ratio {approx}1.3 for the CN{sub x} layers. High-resolution transmission electron microscopy and Z-contrast imaging from the superlattice show a well-defined layer structure. Raman and near-edge x-ray absorption fine structure spectroscopy results reveal the formation of sp{sup 3}-bonded carbon atoms in short-period CN{sub x}/ZrN superlattices. (c) 2000 American Institute of Physics.

  5. Formation of As-As Interlayer Bonding in the collapsed tetragonal phase of NaFe2As2 under pressure

    PubMed Central

    Stavrou, Elissaios; Chen, Xiao-Jia; Oganov, Artem R.; Wang, A. F.; Yan, Y. J.; Luo, X. G.; Chen, X. H.; Goncharov, Alexander F.

    2015-01-01

    NaFe2As2 is investigated experimentally using powder x-ray diffraction and Raman spectroscopy at pressures up to 23 GPa at room temperature and using ab-initio calculations. The results reveal a pressure-induced structural modification at 4 GPa from the starting tetragonal to a collapsed tetragonal phase. We determined the changes in interatomic distances under pressure that allowed us to connect the structural changes and superconductivity. The transition is related to the formation of interlayer As-As bonds at the expense of weakening of Fe-As bonds in agreement with recent theoretical predictions. PMID:26014105

  6. Density functional study of hydrogen bond formation between methanol and organic molecules containing Cl, F, NH2, OH, and COOH functional groups.

    PubMed

    Kolev, Stefan K; St Petkov, Petko; Rangelov, Miroslav A; Vayssilov, Georgi N

    2011-12-08

    Various hydrogen-bonded complexes of methanol with different proton accepting and proton donating molecules containing Cl, F, NH(2), OH, OR, and COOH functional groups have been modeled using DFT with hybrid B3LYP and M05-2X functionals. The latter functional was found to provide more accurate estimates of the structural and thermodynamic parameters of the complexes of halides, amines, and alcohols. The characteristics of these complexes are influenced not only by the principle hydrogen bond of the methanol OH with the proton acceptor heteroatom, but also by additional hydrogen bonds of a C-H moiety with methanol oxygen as a proton acceptor. The contribution of the former hydrogen bond in the total binding enthalpy increases in the order chlorides < fluorides < alcohols < amines, while the contribution of the second type of hydrogen bond increases in the reverse order. A general correlation was found between the binding enthalpy of the complex and the electrostatic potential at the hydrogen center participating in the formation of the hydrogen bond. The calculated binding enthalpies of different complexes were used to clarify which functional groups can potentially form a hydrogen bond to the 2'-OH hydroxyl group in ribose, which is strong enough to block it from participation in the intramolecular catalytic activation of the peptide bond synthesis. Such blocking could result in inhibition of the protein biosynthesis in the living cell if the corresponding group is delivered as a part of a drug molecule in the vicinity of the active site in the ribosome. According to our results, such activity can be accomplished by secondary or tertiary amines, alkoxy groups, deprotonated carboxyl groups, and aliphatic fluorides, but not by the other modeled functional groups.

  7. The Kringle-like Domain Facilitates Post-endoplasmic Reticulum Changes to Premelanosome Protein (PMEL) Oligomerization and Disulfide Bond Configuration and Promotes Amyloid Formation*

    PubMed Central

    Ho, Tina; Watt, Brenda; Spruce, Lynn A.; Seeholzer, Steven H.; Marks, Michael S.

    2016-01-01

    The formation of functional amyloid must be carefully regulated to prevent the accumulation of potentially toxic products. Premelanosome protein (PMEL) forms non-toxic functional amyloid fibrils that assemble into sheets upon which melanins ultimately are deposited within the melanosomes of pigment cells. PMEL is synthesized in the endoplasmic reticulum but forms amyloid only within post-Golgi melanosome precursors; thus, PMEL must traverse the secretory pathway in a non-amyloid form. Here, we identified two pre-amyloid PMEL intermediates that likely regulate the timing of fibril formation. Analyses by non-reducing SDS-PAGE, size exclusion chromatography, and sedimentation velocity revealed two native high Mr disulfide-bonded species that contain Golgi-modified forms of PMEL. These species correspond to disulfide bond-containing dimeric and monomeric PMEL isoforms that contain no other proteins as judged by two-dimensional PAGE of metabolically labeled/immunoprecipitated PMEL and by mass spectrometry of affinity-purified complexes. Metabolic pulse-chase analyses, small molecule inhibitor treatments, and evaluation of site-directed mutants suggest that the PMEL dimer forms around the time of endoplasmic reticulum exit and is resolved by disulfide bond rearrangement into a monomeric form within the late Golgi or a post-Golgi compartment. Mutagenesis of individual cysteine residues within the non-amyloid cysteine-rich Kringle-like domain stabilizes the disulfide-bonded dimer and impairs fibril formation as determined by electron microscopy. Our data show that the Kringle-like domain facilitates the resolution of disulfide-bonded PMEL dimers and promotes PMEL functional amyloid formation, thereby suggesting that PMEL dimers must be resolved to monomers to generate functional amyloid fibrils. PMID:26694611

  8. Merging allylic C-H bond activation and C-C bond cleavage en route to the formation of a quaternary carbon stereocenter in acyclic systems.

    PubMed

    Vasseur, Alexandre; Marek, Ilan

    2017-01-01

    This protocol describes a diastereoselective approach for the synthesis of complex molecular architectures containing two stereogenic centers in a 1,4 relationship, one of which being an all-carbon quaternary stereogenic center. Such molecules could be intermediates in the synthesis of steroids, for example. Conceived as a single-flask synthetic sequence from ω-ene cyclopropanes, the protocol involves a concerted allylic C-H and C-C bond activation promoted by the Negishi reagent (Cp2Zr(η(2)-butene)). This zirconium-promenade-based procedure affords bifunctionalized products in high diastereomeric ratios after reaction of ω-ene cyclopropanes with the Negishi complex, followed by a thermal treatment and sequential addition of two different electrophiles. The method proves to be particularly efficient when carbonyl compounds are used as first electrophiles and hydrogen or elemental halides are used as second electrophiles. In addition, it offers the opportunity to create new C-C bonds via remote functionalization of a (sp(3))-C-H bond, a result of a copper or copper/palladium transmetalation step that extends the scope of the process to alkyl, acyl and aromatic halide compounds as second electrophiles. The typical described protocol allows the synthesis of the highly diastereo-enriched 2-((1R*,2S*)-2-butyl-2 propylcyclopropyl)ethanol and may provide a new entry to access complex molecular segments of natural products such as steroids or C30 botryococcene. It requires a simple reaction setup and takes ∼18.5 h to run the reaction and 2 h for isolation and purification.

  9. Formation of the Si-B bond: insertion reactions of silylenes into B-X(X = F, Cl, Br, O, and N) bonds.

    PubMed

    Geng, Bing; Xu, Chongjuan; Chen, Zhonghe

    2016-06-01

    The insertion reactions of the silylene H2Si with H2BXHn-1 (X = F, Cl, Br, O, N; n = 1, 1, 1, 2, 3) have been studied by DFT and MP2 methods. The calculations show that the insertions occur in a concerted manner, forming H2Si(BH2)(XHn-1). The essences of H2Si insertions with H2BXHn-1 are the transfers of the σ electrons on the Si atom to the positive BH2 group and the electrons of X into the empty p orbital on the Si atom in H2Si. The order of reactivity in vacuum shows the barrier heights increase for the same-family element X from up to down and the same-row element X from right to left in the periodic table. The energies relating to the B-X bond in H2BXHn-1, and the bond energies of Si-X and Si-B in H2Si(BH2)(XHn-1) may determine the preference of insertions of H2Si into B-X bonds for the same-column element X or for the same-row element X. The insertion reactions in vacuum are similar to those in solvents, acetone, ether, and THF. The barriers in vacuum are lower than those in solvents and the larger polarities of solvents make the insertions more difficult to take place. Both in vacuum and in solvents, the silylene insertions are thermodynamically exothermic. Graphical Abstract The insertion process of H2Si and H2BXHn-1(X = F, Cl, Br, O, and N; n = 1, 1 , 1, 2, 3).

  10. Silver-Catalyzed Oxidative C(sp(3) )-P Bond Formation through C-C and P-H Bond Cleavage.

    PubMed

    Li, Lili; Huang, Wenbin; Chen, Lijin; Dong, Jiaxing; Ma, Xuebing; Peng, Yungui

    2017-08-21

    The silver-catalyzed oxidative C(sp(3) )-H/P-H cross-coupling of 1,3-dicarbonyl compounds with H-phosphonates, followed by a chemo- and regioselective C(sp(3) )-C(CO) bond-cleavage step, provided heavily functionalized β-ketophosphonates. This novel method based on a readily available reaction system exhibits wide scope, high functional-group tolerance, and exclusive selectivity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. A thiophosphinidene complex as a vehicle in phosphinidene transmetalation: easy formation and cleavage of a P-S bond.

    PubMed

    Alvarez, Belén; Alvarez, M Angeles; Amor, Inmaculada; García, M Esther; Ruiz, Miguel A

    2011-11-07

    A method for the generation of transition metal-phosphorus multiple bonds has been developed using the reactions of a novel thiophosphinidene-bridged dimolybdenum complex with different metal carbonyls. The overall process could be considered as a transmetalation of the phosphinidene ligand involving the activation of P-S and P-Mo bonds. © 2011 American Chemical Society

  12. Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth.

    PubMed

    Forsythe, Jay G; Yu, Sheng-Sheng; Mamajanov, Irena; Grover, Martha A; Krishnamurthy, Ramanarayanan; Fernández, Facundo M; Hud, Nicholas V

    2015-08-17

    Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides-oligomers with a combination of ester and amide linkages-in model prebiotic reactions that are driven by wet-cool/dry-hot cycles. Through a combination of ester-amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Ester-Mediated Amide Bond Formation Driven by Wet–Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth**

    PubMed Central

    Forsythe, Jay G; Yu, Sheng-Sheng; Mamajanov, Irena; Grover, Martha A; Krishnamurthy, Ramanarayanan; Fernández, Facundo M; Hud, Nicholas V

    2015-01-01

    Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors. PMID:26201989

  14. Peptide bonds affect the formation of haloacetamides, an emerging class of N-DBPs in drinking water: free amino acids versus oligopeptides

    NASA Astrophysics Data System (ADS)

    Chu, Wenhai; Li, Xin; Gao, Naiyun; Deng, Yang; Yin, Daqiang; Li, Dongmei; Chu, Tengfei

    2015-09-01

    Haloacetamides (HAcAms), an emerging class of nitrogenous disinfection by-products (N-DBPs) of health concern, have been frequently identified in drinking waters. It has long been appreciated that free amino acids (AAs), accounting for a small fraction of the dissolved organic nitrogen (DON) pool, can form dichloroacetamide (DCAcAm) during chlorination. However, the information regarding the impacts of combined AAs, which contribute to the greatest identifiable DON portion in natural waters, is limited. In this study, we compared the formation of HAcAms from free AAs (tyrosine [Tyr] and alanine [Ala]) and combined AAs (Tyr-Ala, Ala-Tyr, Tyr-Tyr-Tyr, Ala-Ala-Ala), and found that HAcAm formation from the chlorination of AAs in combined forms (oligopeptides) significantly exhibited a different pattern with HAcAm formation from free AAs. Due to the presence of peptide bonds in tripeptides, Tyr-Tyr-Tyr and Ala-Ala-Ala produced trichloroacetamide (TCAcAm) in which free AAs was unable to form TCAcAm during chlorination. Moreover, peptide bond in tripeptides formed more tri-HAcAms than di-HAcAms in the presence of bromide. Therefore, the peptide bond may be an important indicator to predict the formation of specific N-DBPs in chlorination. The increased use of algal- and wastewater-impacted water as drinking water sources will increase health concerns over exposure to HAcAms in drinking water.

  15. Peptide bonds affect the formation of haloacetamides, an emerging class of N-DBPs in drinking water: free amino acids versus oligopeptides

    PubMed Central

    Chu, Wenhai; Li, Xin; Gao, Naiyun; Deng, Yang; Yin, Daqiang; Li, Dongmei; Chu, Tengfei

    2015-01-01

    Haloacetamides (HAcAms), an emerging class of nitrogenous disinfection by-products (N-DBPs) of health concern, have been frequently identified in drinking waters. It has long been appreciated that free amino acids (AAs), accounting for a small fraction of the dissolved organic nitrogen (DON) pool, can form dichloroacetamide (DCAcAm) during chlorination. However, the information regarding the impacts of combined AAs, which contribute to the greatest identifiable DON portion in natural waters, is limited. In this study, we compared the formation of HAcAms from free AAs (tyrosine [Tyr] and alanine [Ala]) and combined AAs (Tyr-Ala, Ala-Tyr, Tyr-Tyr-Tyr, Ala-Ala-Ala), and found that HAcAm formation from the chlorination of AAs in combined forms (oligopeptides) significantly exhibited a different pattern with HAcAm formation from free AAs. Due to the presence of peptide bonds in tripeptides, Tyr-Tyr-Tyr and Ala-Ala-Ala produced trichloroacetamide (TCAcAm) in which free AAs was unable to form TCAcAm during chlorination. Moreover, peptide bond in tripeptides formed more tri-HAcAms than di-HAcAms in the presence of bromide. Therefore, the peptide bond may be an important indicator to predict the formation of specific N-DBPs in chlorination. The increased use of algal- and wastewater-impacted water as drinking water sources will increase health concerns over exposure to HAcAms in drinking water. PMID:26394759

  16. Peptide bonds affect the formation of haloacetamides, an emerging class of N-DBPs in drinking water: free amino acids versus oligopeptides.

    PubMed

    Chu, Wenhai; Li, Xin; Gao, Naiyun; Deng, Yang; Yin, Daqiang; Li, Dongmei; Chu, Tengfei

    2015-09-23

    Haloacetamides (HAcAms), an emerging class of nitrogenous disinfection by-products (N-DBPs) of health concern, have been frequently identified in drinking waters. It has long been appreciated that free amino acids (AAs), accounting for a small fraction of the dissolved organic nitrogen (DON) pool, can form dichloroacetamide (DCAcAm) during chlorination. However, the information regarding the impacts of combined AAs, which contribute to the greatest identifiable DON portion in natural waters, is limited. In this study, we compared the formation of HAcAms from free AAs (tyrosine [Tyr] and alanine [Ala]) and combined AAs (Tyr-Ala, Ala-Tyr, Tyr-Tyr-Tyr, Ala-Ala-Ala), and found that HAcAm formation from the chlorination of AAs in combined forms (oligopeptides) significantly exhibited a different pattern with HAcAm formation from free AAs. Due to the presence of peptide bonds in tripeptides, Tyr-Tyr-Tyr and Ala-Ala-Ala produced trichloroacetamide (TCAcAm) in which free AAs was unable to form TCAcAm during chlorination. Moreover, peptide bond in tripeptides formed more tri-HAcAms than di-HAcAms in the presence of bromide. Therefore, the peptide bond may be an important indicator to predict the formation of specific N-DBPs in chlorination. The increased use of algal- and wastewater-impacted water as drinking water sources will increase health concerns over exposure to HAcAms in drinking water.

  17. Hypertriglyceridemia associated with the c.553G>T APOA5 SNP results from aberrant hetero-disulfide bond formation

    PubMed Central

    Sharma, Vineeta; Witkowski, Andrzej; Witkowska, H. Ewa; Dykstra, Andrew; Simonsen, Jens B.; Nelbach, Lisa; Beckstead, Jennifer A.; Pullinger, Clive R.; Kane, John P.; Malloy, Mary J.; Watson, Gordon; Forte, Trudy M.; Ryan, Robert O.

    2014-01-01

    Objective Apolipoprotein (apo) A-V is a low abundance plasma protein that modulates triacylglycerol (TG) homeostasis. Gene transfer studies were undertaken in apoa5 (−/−) mice to define the mechanism underlying the correlation between the single nucleotide polymorphism (SNP) c.553G>T in APOA5 and hypertriglyceridemia (HTG). Approach and Results Adeno-associated virus (AAV) 2/8 mediated gene transfer of wild type (WT) apoA-V induced a dramatic lowering of plasma TG in apoa5 (−/−) mice while AAV2/8-Gly162Cys apoA-V (corresponding to the c.553G>T SNP: rs2075291) had a modest effect. Characterization studies revealed that plasma levels of WT- and G162C apoA-V in transduced mice were similar and within the physiological range. Fractionation of plasma from mice transduced with AAV2/8-G162C apoA-V indicated that, unlike WT apoA-V, >50% of G162C apoA-V was recovered in the lipoprotein-free fraction. Non-reducing SDS-PAGE immunoblot analysis provided evidence that G162C apoA-V present in the lipoprotein-free fraction, but not that portion associated with lipoproteins, displayed altered electrophoretic mobility consistent with disulfide-linked hetero-dimer formation. Immunoprecipitation followed by liquid chromatography/mass spectrometry of human plasma from subjects homozygous for WT APOA5 and c.553G>T APOA5 revealed that G162C apoA-V forms adducts with extraneous plasma proteins including fibronectin, kininogen-1 and others. Conclusion Substitution of Cys for Gly at position 162 of mature apoA-V introduces a free cysteine that forms disulfide bonds with plasma proteins such that its lipoprotein binding and TG modulation functions are compromised. PMID:25127531

  18. Formation of Solution-derived Hydroxyapatite Coatings on Titanium Alloy in the Presence of Magnetron-sputtered Alumina Bond Coats.

    PubMed

    Zykova, Anna; Safonov, Vladimir; Yanovska, Anna; Sukhodub, Leonid; Rogovskaya, Renata; Smolik, Jerzy; Yakovin, Stas

    2015-01-01

    Hydroxyapatite Ca10(PO4)6(OH)2 (HAp) and calcium phosphate ceramic materials and coatings are widely used in medicine and dentistry because of their ability to enhance the tissue response to implant surfaces and promote bone ingrowth and osseoconduction processes. The deposition conditions have a great influence on the structure and biofunctionality of calcium phosphate coatings. Corrosion processes and poor adhesion to substrate material reduce the lifetime of implants with calcium phosphate coatings. The research has focused on the development of advanced methods to deposit double-layered ceramic oxide/calcium phosphate coatings by a hybrid technique of magnetron sputtering and thermal methods. The thermal method can promote the crystallization and the formation of HAp coatings on titanium alloy Ti6Al4V substrates at low temperature, based on the principle that the solubility of HAp in aqueous solutions decreases with increasing substrate temperature. By this method, hydroxyapatite directly coated the substrate without precipitation in the initial solution. Using a thermal substrate method, calcium phosphate coatings were prepared at substrate temperatures of 100-105 (o)C. The coated metallic implant surfaces with ceramic bond coats and calcium phosphate layers combine the excellent mechanical properties of metals with the chemical stability of ceramic materials. The corrosion test results show that the ceramic oxide (alumina) coatings and the double-layered alumina-calcium phosphate coatings improve the corrosion resistance compared with uncoated Ti6Al4V and single-layered Ti6Al4V/calcium phosphate substrates. In addition, the double-layered alumina/hydroxyapatite coatings demonstrate the best biocompatibility during in vitro tests.

  19. Isotopic studies of trans- and cis-HOCO using rotational spectroscopy: Formation, chemical bonding, and molecular structures.

    PubMed

    McCarthy, Michael C; Martinez, Oscar; McGuire, Brett A; Crabtree, Kyle N; Martin-Drumel, Marie-Aline; Stanton, John F

    2016-03-28

    HOCO is an important intermediate in combustion and atmospheric processes because the OH + CO → H + CO2 reaction represents the final step for the production of CO2 in hydrocarbon oxidation, and theoretical studies predict that this reaction proceeds via various intermediates, the most important being this radical. Isotopic investigations of trans- and cis-HOCO have been undertaken using Fourier transform microwave spectroscopy and millimeter-wave double resonance techniques in combination with a supersonic molecular beam discharge source to better understand the formation, chemical bonding, and molecular structures of this radical pair. We find that trans-HOCO can be produced almost equally well from either OH + CO or H + CO2 in our discharge source, but cis-HOCO appears to be roughly two times more abundant when starting from H + CO2. Using isotopically labelled precursors, the OH + C(18)O reaction predominately yields HOC(18)O for both isomers, but H(18)OCO is observed as well, typically at the level of 10%-20% that of HOC(18)O; the opposite propensity is found for the (18)OH + CO reaction. DO + C(18)O yields similar ratios between DOC(18)O and D(18)OCO as those found for OH + C(18)O, suggesting that some fraction of HOCO (or DOCO) may be formed from the back-reaction H + CO2, which, at the high pressure of our gas expansion, can readily occur. The large (13)C Fermi-contact term (aF) for trans- and cis-HO(13)CO implicates significant unpaired electronic density in a σ-type orbital at the carbon atom, in good agreement with theoretical predictions. By correcting the experimental rotational constants for zero-point vibration motion calculated theoretically using second-order vibrational perturbation theory, precise geometrical structures have been derived for both isomers.

  20. Reversible carbon-carbon bond formation induced by oxidation and reduction at a redox-active cobalt complex.

    PubMed

    Atienza, Crisita Carmen Hojilla; Milsmann, Carsten; Semproni, Scott P; Turner, Zoë R; Chirik, Paul J

    2013-05-06

    The electronic structure of the diamagnetic pyridine imine enamide cobalt dinitrogen complex, ((iPr)PIEA)CoN2 ((iPr)PIEA = 2-(2,6-(i)Pr2-C6H3N═CMe)-6-(2,6-(i)Pr2-C6H3NC═CH2)C5H3N), was determined and is best described as a low-spin cobalt(II) complex antiferromagnetically coupled to an imine radical anion. Addition of potential radical sources such as NO, PhSSPh, or Ph3Cl resulted in C-C coupling at the enamide positions to form bimetallic cobalt compounds. Treatment with the smaller halocarbon, PhCH2Cl, again induced C-C coupling to form a bimetallic bis(imino)pyridine cobalt chloride product but also yielded a monomeric cobalt chloride product where the benzyl group added to the enamide carbon. Similar cooperative metal-ligand addition was observed upon treatment of ((iPr)PIEA)CoN2 with CH2═CHCH2Br, which resulted in allylation of the enamide carbon. Reduction of Coupled-((iPr)PDI)CoCl (Coupled-((iPr)PDI)CoCl = [2-(2,6-(i)Pr2-C6H3N═CMe)-C5H3N-6-(2,6-(i)Pr2-C6H3N═CCH2-)CoCl]2) with NaBEt3H led to quantitative formation of ((iPr)PIEA)CoN2, demonstrating the reversibility of the C-C bond forming reactions. The electronic structures of each of the bimetallic cobalt products were also elucidated by a combination of experimental and computational methods.

  1. Formation of Solution-derived Hydroxyapatite Coatings on Titanium Alloy in the Presence of Magnetron-sputtered Alumina Bond Coats

    PubMed Central

    Zykova, Anna; Safonov, Vladimir; Yanovska, Anna; Sukhodub, Leonid; Rogovskaya, Renata; Smolik, Jerzy; Yakovin, Stas

    2015-01-01

    Hydroxyapatite Ca10(PO4)6(OH)2 (HAp) and calcium phosphate ceramic materials and coatings are widely used in medicine and dentistry because of their ability to enhance the tissue response to implant surfaces and promote bone ingrowth and osseoconduction processes. The deposition conditions have a great influence on the structure and biofunctionality of calcium phosphate coatings. Corrosion processes and poor adhesion to substrate material reduce the lifetime of implants with calcium phosphate coatings. The research has focused on the development of advanced methods to deposit double-layered ceramic oxide/calcium phosphate coatings by a hybrid technique of magnetron sputtering and thermal methods. The thermal method can promote the crystallization and the formation of HAp coatings on titanium alloy Ti6Al4V substrates at low temperature, based on the principle that the solubility of HAp in aqueous solutions decreases with increasing substrate temperature. By this method, hydroxyapatite directly coated the substrate without precipitation in the initial solution. Using a thermal substrate method, calcium phosphate coatings were prepared at substrate temperatures of 100-105 oC. The coated metallic implant surfaces with ceramic bond coats and calcium phosphate layers combine the excellent mechanical properties of metals with the chemical stability of ceramic materials. The corrosion test results show that the ceramic oxide (alumina) coatings and the double-layered alumina-calcium phosphate coatings improve the corrosion resistance compared with uncoated Ti6Al4V and single-layered Ti6Al4V/calcium phosphate substrates. In addition, the double-layered alumina/hydroxyapatite coatings demonstrate the best biocompatibility during in vitro tests. PMID:25893018

  2. Tomographic Evaluation of Reparative Dentin Formation after Direct Pulp Capping with Ca(OH)2, MTA, Biodentine, and Dentin Bonding System in Human Teeth.

    PubMed

    Nowicka, Alicja; Wilk, Grażyna; Lipski, Mariusz; Kołecki, Janusz; Buczkowska-Radlińska, Jadwiga

    2015-08-01

    New materials can increase the efficiency of pulp capping through the formation of a complete reparative dentin bridge with no toxic effects. The present study involved tomographic evaluations of reparative dentin bridge formation after direct pulp capping with calcium hydroxide, mineral trioxide aggregate (MTA), Biodentine (Septodont, Saint Maur des Fossés, France), and Single Bond Universal (3M ESPE, Seefeld, Germany) in human teeth. Forty-four caries-free, intact, human third molars scheduled for extraction were subjected to mechanical pulp exposure and assigned to 1 of 4 experimental groups depending on the pulp capping agent used: calcium hydroxide, MTA, Biodentine, or Single Bond Universal. After 6 weeks, the teeth were extracted and processed for cone-beam computed tomographic imaging and histologic examination. Tomographic data, including the density and volume of formed reparative dentin bridges, were evaluated using a scoring system. The reparative dentin formed in the calcium hydroxide, MTA, and Biodentine groups was significantly superior to that formed in the Single Bond Universal group in terms of thickness and volume. The dentin bridges in the Biodentine group showed the highest average and maximum volumes. The mean density of dentin bridges was the highest in the MTA group and the lowest in the Single Bond Universal group. The volume of reparative dentin bridges formed after direct pulp capping is dependent on the material used. Biodentine and MTA resulted in the formation of bridges with a significantly higher average volume compared with Single Bond Universal, and cone-beam computed tomographic imaging allowed for the identification of the location of dentin bridges. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  3. The bond-forming reactions of atomic dications with neutral molecules: formation of ArNH+ and ArN+ from collisions of Ar2+ with NH3.

    PubMed

    Lambert, Natalie; Kearney, Dominic; Kaltsoyannis, Nikolas; Price, Stephen D

    2004-03-24

    An experimental and computational study has been performed to investigate the bond-forming reactivity between Ar(2+) and NH(3). Experimentally, we detect two previously unobserved bond-forming reactions between Ar(2+) and NH(3) forming ArN(+) and ArNH(+). This is the first experimental observation of a triatomic product ion (ArNH(+)) following a chemical reaction of a rare gas dication with a neutral. The intensity of ArNH(+) was found to decrease with increasing collision energy, with a corresponding increase in the intensity of ArN(+), indicating that ArN(+) is formed by the dissociation of ArNH(+). Key features on the potential energy surface for the reaction were calculated quantum chemically using CASSCF and MRCI methods. The calculated reaction mechanism, which takes place on a singlet surface, involves the initial formation of an Ar-N bond to give Ar-NH(3)(2+). This complexation is followed by proton loss via a transition state, and then loss of the two remaining hydrogen atoms in two subsequent activationless steps to give the products (3)ArN(+) + H(+) + 2H. This calculated pathway supports the sequential formation of ArN(+) from ArNH(+), as suggested by the experimental data. The calculations also indicate that no bond-forming pathway exists on the ground triplet surface for this system.

  4. Carbon-carbon bond formation involving reactions of alkynes with group 9 metals (Ir, Rh, Co): preparation of conjugated olefins.

    PubMed

    Chin, Chong Shik; Won, Gyongshik; Chong, Daesung; Kim, Mieock; Lee, Hyungeui

    2002-04-01

    Stable alkynyl complexes of iridium(III) (L(n)Ir-triple bond-R) that are prepared from the reactions of terminal alkynes readily undergo the intramolecular C-C bond-forming reactions between the alkynyl and adjacent hydrocarbyl ligands to yield conjugated olefins. These reactions are initiated by electrophiles (H(+), Me(+)) that attack the beta carbon of the alkynyl ligand to increase the electrophilicity of the alpha carbon of the alkynyl ligand. The C-C bond is then formed between the alpha carbons of the alkynyl and adjacent hydrocarbyl ligands.

  5. O-O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O-O radical coupling.

    PubMed

    Shaffer, David W; Xie, Yan; Concepcion, Javier J

    2017-09-01

    In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O-O bond formation, oxidative activation of peroxide intermediates, and O2 evolution. A significant portion of the review is dedicated to the O-O bond formation step as the key step in water oxidation catalysis. The two main pathways to accomplish this step, single-site water nucleophilic attack and O-O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.

  6. A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Gao, Jun; Zhang, Dongju; Liu, Chengbu

    2015-04-01

    The ribosome is the macromolecular machine that catalyzes protein synthesis. The kinetic isotope effect analysis reported by Strobel group supports the two-step mechanism. However, the destination of the proton originating from the nucleophilic amine is uncertain. A computational simulation of different mechanisms including water molecules is carried out using the same reaction model and theoretical level. Formation the tetrahedral intermediate with proton transfer from nucleophilic nitrogen, is the rate-limiting step when two water molecules participate in peptide bond formation. The first water molecule forming hydrogen bonds with O9‧ and H15‧ in the A site can decrease the reaction barriers. Combined with results of the solvent isotope effects analysis, we conclude that the three-proton transfer mechanism in which water molecule mediate the proton shuttle between amino and carbon oxygen in rate-limiting step is the favorable mechanism. Our results will shield light on a better understand the reaction mechanism of ribosome.

  7. A novel crystallization-induced diastereomeric transformation based on a reversible carbon-sulfur bond formation. Application to the synthesis of a gamma-secretase inhibitor.

    PubMed

    Davies, Antony J; Scott, Jeremy P; Bishop, Brian C; Brands, Karel M J; Brewer, Sarah E; Dasilva, Jimmy O; Dormer, Peter G; Dolling, Ulf-H; Gibb, Andrew D; Hammond, Deborah C; Lieberman, David R; Palucki, Michael; Payack, Joseph F

    2007-06-22

    This paper describes a remarkably efficient process for the preparation of gamma-secretase inhibitor 1. The target is synthesized in only five steps with an overall yield of 58%. The key operation is a highly selective and practical, crystallization-driven transformation for the conversion of a mixture of tertiary benzylic alcohols into the desired sulfide diastereomer with 94:6 dr. This unprecedented process is based upon a reversible carbon-sulfur bond formation under acidic conditions.

  8. Paramagnetic-diamagnetic phase transition accompanied by coordination bond formation-dissociation in the dithiolate complex Na[Ni(pdt)2]·2H2O.

    PubMed

    Takaishi, Shinya; Ishihara, Nozomi; Kubo, Kazuya; Katoh, Keiichi; Breedlove, Brian K; Miyasaka, Hitoshi; Yamashita, Masahiro

    2011-07-18

    Bis(2,3-pyrazinedithiolate)nickel complex Na[Ni(pdt)(2)]·2H(2)O formed one-dimensional stacks of the Ni(pdt)(2) units and showed strong antiferromagnetic interactions along the stacking direction. A first-order phase transition between the paramagnetic and diamagnetic states, which was driven by dimerization of the Ni(pdt)(2) units, accompanied by coordination bond formation, was observed.

  9. Formation of supramolecular hetero-triads by controlling the hydrogen bonding of conjugate bases with a diprotonated porphyrin based on electrostatic interaction.

    PubMed

    Suzuki, Wataru; Kotani, Hiroaki; Ishizuka, Tomoya; Shiota, Yoshihito; Yoshizawa, Kazunari; Kojima, Takahiko

    2017-06-08

    The thermodynamic stability of diprotonated saddle-distorted dodecaphenylporphyrin (H4DPP(2+)(X(-))2) was controlled by the hydrogen-bonding strength of conjugate bases (X(-)) of strong acids (HX) or acids (R(+)-COOH) having positively charged moieties. The thermodynamic control of H4DPP(2+)(X(-))2 made it possible to achieve selective formation of supramolecular hetero-triads, H4DPP(2+)(X(-))(Cl(-)).

  10. Possible Evidence of Amide Bond Formation Between Sinapinic Acid and Lysine-Containing Bacterial Proteins by Matrix-Assisted Laser Desorption/Ionization (MALDI) at 355 nm

    NASA Astrophysics Data System (ADS)

    Fagerquist, Clifton K.; Sultan, Omar; Carter, Michelle Q.

    2012-12-01

    We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, Hde, and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALDI) time-of-flight-time-of-flight tandem mass spectrometry (TOF-TOF-MS/MS) and post-source decay (PSD). We also reported the absence of adduct formation when using α-cyano-4-hydroxycinnamic acid (CHCA) matrix. Further mass spectrometric analysis of disulfide-intact and disulfide-reduced over-expressed HdeA and HdeB proteins from lysates of gene-inserted E. coli plasmids suggests covalent attachment of SA occurs not at cysteine residues but at lysine residues. In this revised hypothesis, the attachment of SA is preceded by formation of a solid phase ammonium carboxylate salt between SA and accessible lysine residues of the protein during sample preparation under acidic conditions. Laser irradiation at 355 nm of the dried sample spot results in equilibrium retrogradation followed by nucleophilic attack by the amine group of lysine at the carbonyl group of SA and subsequent amide bond formation and loss of water. The absence of CHCA adducts suggests that the electron-withdrawing effect of the α-cyano group of this matrix may inhibit salt formation and/or amide bond formation. This revised hypothesis is supported by dissociative loss of SA (-224 Da) and the amide-bound SA (-206 Da) from SA-adducted HdeA and HdeB ions by MS/MS (PSD). It is proposed that cleavage of the amide-bound SA from the lysine side-chain occurs via rearrangement involving a pentacyclic transition state followed by hydrogen abstraction/migration and loss of 3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-ynal (-206 Da).

  11. A macroscopic reaction: direct covalent bond formation between materials using a Suzuki-Miyaura cross-coupling reaction.

    PubMed

    Sekine, Tomoko; Kakuta, Takahiro; Nakamura, Takashi; Kobayashi, Yuichiro; Takashima, Yoshinori; Harada, Akira

    2014-09-18

    Cross-coupling reactions are important to form C-C covalent bonds using metal catalysts. Although many different cross-coupling reactions have been developed and applied to synthesize complex molecules or polymers (macromolecules), if cross-coupling reactions are realized in the macroscopic real world, the scope of materials should be dramatically broadened. Here, Suzuki-Miyaura coupling reactions are realized between macroscopic objects. When acrylamide gel modified with an iodophenyl group (I-gel) reacts with a gel possessing a phenylboronic group (PB-gel) using a palladium catalyst, the gels bond to form a single object. This concept can also be adapted for bonding between soft and hard materials. I-gel or PB-gel selectively bonds to the glass substrates whose surfaces are modified with an electrophile or nucleophile, respectively.

  12. Sequential Carbon-Carbon/Carbon-Selenium Bond Formation Mediated by Iron(III) Chloride and Diorganyl Diselenides: Synthesis and Reactivity of 2-Organoselenyl-Naphthalenes.

    PubMed

    Recchi, Ana M S; Back, Davi F; Zeni, Gilson

    2017-03-03

    In this paper, we report an intramolecular cyclization of benzylic-substituted propargyl alcohols promoted by iron(III) chloride and diorganyl diselenides to give 2-organoselenyl-naphthalenes via a sequential carbon-carbon/carbon-selenium bond formation. The present reaction tolerated a wide range of substituents in both propargyl alcohols and diorganyl diselenides to give the desired 2-organoselenyl-naphthalenes in good yields with high selectivity. In addition, O-acyl protected propargyl alcohol and propargyl bromide were also subjected to this protocol giving the corresponding 2-organoselenyl-naphthalenes. We found that dichalcogenide species affected the formation of cyclized products, whereas diorganyl diselenides gave high yields, moderate yields were obtained with diorganyl disulfides, and no product formation was found with diorganyl ditellurides. The key transformations could be attributed to the carbon-carbon triple bond activation of benzylic-substituted propargyl alcohols by a seleniranium ion, antiattack of the electron cloud from the aromatic ring at the activated triple bond, and cyclization via an exclusive 6-endo-dig process. We also found that the corresponding 2-organoselenyl-naphthalenes are suitable substrates to the selenium-lithium exchange reactions followed by trapping with aldehydes affording the corresponding secondary alcohols.

  13. Enthalpy of formation of the cyclohexadienyl radical and the C-H bond enthalpy of 1,4-cyclohexadiene: an experimental and computational re-evaluation.

    PubMed

    Gao, Yide; DeYonker, Nathan J; Garrett, E Chauncey; Wilson, Angela K; Cundari, Thomas R; Marshall, Paul

    2009-06-25

    A quantitative understanding of the thermochemistry of cyclohexadienyl radical and 1,4-cyclohexadiene is beneficial for diverse areas of chemistry. Given the interest in these two species, it is surprising that more detailed thermodynamic data concerning the homolytic C-H bond enthalpies of such entities have not been forthcoming. We thus undertook an experimental and computational evaluation of (a) the enthalpy of formation of cyclohexadienyl radical (C(6)H(7)), (b) the homolytic C-H bond enthalpy of 1,4-cyclohexadiene (C(6)H(8)), and (c) the enthalpy of the addition of a hydrogen atom to benzene. Using laser photolysis experiments coupled with highly accurate ab initio quantum mechanical techniques, a newly recommended enthalpy of formation for C(6)H(7) is determined to be 208.0 +/- 3.9 kJ mol(-1), leading to a homolytic bond dissociation enthalpy of 321.7 +/- 2.9 kJ mol(-1), almost 9 kJ mol(-1) higher than previously determined enthalpies that used less certain experimental values for the C(6)H(7) enthalpy of formation.

  14. Why Is Cobalt the Best Transition Metal in Transition-Metal Hangman Corroles for O-O Bond Formation during Water Oxidation?

    PubMed

    Lai, Wenzhen; Cao, Rui; Dong, Geng; Shaik, Sason; Yao, Jiannian; Chen, Hui

    2012-09-06

    O-O bond formation catalyzed by a variety of β-octafluoro hangman corrole metal complexes was investigated using density functional theory methods. Five transition metal elements, Co, Fe, Mn, Ru, and Ir, that are known to lead to water oxidation were examined. Our calculations clearly show that the formal Co(V) catalyst has a Co(IV)-corrole(•+) character and is the most efficient water oxidant among all eight transition-metal complexes. The O-O bond formation barriers were found to change in the following order: Co(V) ≪ Fe(V) < Mn(V) < Ir(V) < Co(IV) < Ru(V) < Ir(IV) < Mn(IV). The efficiency of water oxidation is discussed by analysis of the O-O bond formation step. Thus, the global trend is determined by the ability of the ligand d-block to accept two electrons from the nascent OH(-), as well as by the OH(•) affinity of the TM(IV)═O species of the corresponding TM(V)═O·H2O complex. Exchange-enhanced reactivity (EER) is responsible for the high catalytic activity of the Co(V) species in its S = 1 state.

  15. Selective recognition of cyanide anion via formation of multipoint NH and phenyl CH hydrogen bonding with acyclic ruthenium bipyridine imidazole receptors in water.

    PubMed

    Mo, Hao-Jun; Shen, Yong; Ye, Bao-Hui

    2012-07-02

    Five imidazole-based anion receptors A-E are designed for cyanide anion recognition via hydrogen bonding interaction in water. Only receptors A [Ru(bpy)(2)(mpipH)](ClO(4))(2) (bpy is bipyridine and mpipH is 2-(4-methylphenyl)-imidazo[4,5-f]-1,10-phenanthroline) and E [Ru(2)(bpy)(4)(mbpibH(2))](ClO(4))(4) (mbpibH(2) is 1,3-bis([1,10]-phenanthroline-[5,6-d]imidazol-2-yl)benzene) selectively recognize CN(-) from OAc(-), F(-), Cl(-), Br(-), I(-), NO(3)(-), HSO(4)(-), ClO(4)(-), H(2)PO(4)(-), HCO(3)(-), N(3)(-), and SCN(-) anions in water (without organic solvent) at physiological conditions via formation of multiple hydrogen bonding interaction with binding constants of K(A(H2O)) = 345 ± 21 and K(E(H2O)) = 878 ± 41, respectively. The detection limits of A and E toward CN(-) in water are 100 and 5 μM, respectively. Receptor E has an appropriate pK(a2)* value (8.75) of N-H proton and a C-shape cavity structure with three-point hydrogen bonding, consisting of two NH and one cooperative phenyl CH hydrogen bonds. Appropriate acidity of N-H proton and multipoint hydrogen bonding are both important in enhancing the selectivity and sensitivity toward CN(-) in water. The phenyl CH···CN(-) hydrogen bonding interaction is observed by the HMBC NMR technique for the first time, which provides an efficient approach to directly probe the binding site of the receptor toward CN(-). Moreover, CN(-) induced emission lifetime change of the receptor has been exploited in water for the first time. The energy-optimized structure of E-CN adduct is also proposed on the basis of theoretical calculations.

  16. Identification and cloning of an NADPH-dependent hydroxycinnamoyl-CoA double bond reductase involved in dihydrochalcone formation in Malus×domestica Borkh.

    PubMed

    Ibdah, Mwafaq; Berim, Anna; Martens, Stefan; Valderrama, Andrea Lorena Herrera; Palmieri, Luisa; Lewinsohn, Efraim; Gang, David R

    2014-11-01

    The apple tree (Malus sp.) is an agriculturally and economically important source of food and beverages. Many of the health beneficial properties of apples are due to (poly)phenolic metabolites that they contain, including various dihydrochalcones. Although many of the genes and enzymes involved in polyphenol biosynthesis are known in many plant species, the specific reactions that lead to the biosynthesis of the dihydrochalcone precursor, p-dihydrocoumaroyl-CoA (3), are unknown. To identify genes involved in the synthesis of these metabolites, existing genome databases of the Rosaceae were screened for apple genes with significant sequence similarity to Arabidopsis alkenal double bond reductases. Herein described are the isolation and characterization of a Malus hydroxycinnamoyl-CoA double bond reductase, which catalyzed the NADPH-dependent reduction of p-coumaroyl-CoA and feruloyl-CoA to p-dihydrocoumaroyl-CoA and dihydroferuloyl-CoA, respectively. Its apparent Km values for p-coumaroyl-CoA, feruloyl-CoA and NADPH were 96.6, 92.9 and 101.3μM, respectively. The Malus double bond reductase preferred feruloyl-CoA to p-coumaroyl-CoA as a substrate by a factor of 2.1 when comparing catalytic efficiencies in vitro. Expression analysis of the hydroxycinnamoyl-CoA double bond reductase gene revealed that its transcript levels showed significant variation in tissues of different developmental stages, but was expressed when expected for involvement in dihydrochalcone formation. Thus, the hydroxycinnamoyl-CoA double bond reductase appears to be responsible for the reduction of the α,β-unsaturated double bond of p-coumaroyl-CoA, the first step of dihydrochalcone biosynthesis in apple tissues, and may be involved in the production of these compounds. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Control of two-electron four-center (2e-/4c) C-C bond formation observed for tetracyanoethenide dimerization, [TCNE]2(2-).

    PubMed

    Novoa, Juan J; Novoa, Juan N; Ribas-Ariño, Jordi; Shum, William W; Miller, Joel S

    2007-01-08

    Cu(PPh3)3(TCNE) (TCNE = tetracyanoethylene) and 14 other examples form [TCNE]22- dimers possessing a long 2.89 +/- 0.05 A two-electron four-center (2e-/4c) C-C bond in the solid state. This bond arises from the overlap of the b2g pi* singly occupied molecular orbital (SOMO) on each [TCNE]*- fragment, forming a filled bonding orbital of b2u symmetry, and the stabilizing effect of the cation...anion interactions in the crystal that exceed the anionic repulsion. In contrast, Mn(C5H5)(CO)2(TCNE) exhibits a related, but different, [TCNE]*-...TCNE]*- motif in the solid state that lacks the 2e-/4c C-C bonding. To better understand the unusual nature of 2e-/4c C-C bonding, the genesis of the differences between their respective pi-[TCNE]*-...TCNE]*- interactions was sought. The lack of 2e-/4c C-C bond formation is attributed to the weaker radical character of the [TCNE]*- ligand, which has a total spin population of only 0.5 electron, half of that required for two S = 1/2 [TCNE]*- moieties to form a [TCNE]22- dimer. Hence, the antiferromagnetic MnII-[TCNE]*- intramolecular interaction (between the formally S = 1/2 Mn-bound [TCNE]*- and the paramagnetic Mn(II)) dominates over the intermolecular pi-[TCNE]*--[TCNE]*- spin coupling (between two S = 1/2 [TCNE]*- needed to form [TCNE]22-). Therefore, by selecting specific metal ions that can interact with sigma-[TCNE]*-, dimerization forming [TCNE]22- can be favored or disfavored.

  18. C-H Bond Functionalization via Hydride Transfer: Formation of α-Arylated Piperidines and 1,2,3,4-Tetrahydroisoquinolines via Stereoselective Intramolecular Amination of Benzylic C-H Bonds

    PubMed Central

    Vadola, Paul A.; Carrera, Ignacio; Sames, Dalibor

    2012-01-01

    We here report a study of the intramolecular amination of sp3 C-H bonds via the hydride transfer cyclization of N-tosylimines (HT-amination). In this transformation, 5-aryl-aldehydes are subjected to N-toluenesulfonamide in the presence of BF3•OEt2 to effect imine formation and HT-cyclization, leading to 2-aryl-piperidines and 3-aryl-1,2,3,4-tetrahydroisoquinolines in a one-pot procedure. We examined the reactivity of a range of aldehyde substrates as a function of their conformational flexibility. Substrates of higher conformational rigidity were more reactive, giving higher yields of the desired products. However, a single substituent on the alkyl chain linking the N-tosylimine and the benzylic sp3 C-H bonds was sufficient for HT-cyclization to occur. In addition, an examination of various arenes revealed that the electronic character of the hydridic C-H bonds dramatically affects the efficiency of the reaction. We also found that this transformation is highly stereoselective; 2-substituted aldehydes yield cis-2,5-disubstituted piperidines, while 3-substituted aldehydes afford trans-2,4-disubstituted piperidines. The stereoselectivity is a consequence of thermodynamic control. The pseudo-allylic strain between the arene and tosyl group on the piperidine ring is proposed to rationalize the greater stability of the isomer with the aryl ring in the axial position. This preferential placement of the arene is proposed to affect the observed stereoselectivity. PMID:22672002

  19. Enthalpies of formation, bond dissociation energies, and molecular structures of the n-aldehydes (acetaldehyde, propanal, butanal, pentanal, hexanal, and heptanal) and their radicals.

    PubMed

    da Silva, Gabriel; Bozzelli, Joseph W

    2006-12-07

    Aldehydes are important intermediates and products in a variety of combustion and gas-phase oxidation processes, such as in low-temperature combustion, in the atmosphere, and in interstellar media. Despite their importance, the enthalpies of formation and bond dissociation energies (BDEs) for the aldehydes are not accurately known. We have determined enthalpies of formation for acetaldehyde, propanal, and butanal from thermodynamic cycles, using experimentally measured reaction and formation enthalpies. All enthalpy values used for reference molecules and reactions were first verified to be accurate to within around 1 kcal mol-1 using high-level ab initio calculations. Enthalpies of formation were found to be -39.72 +/- 0.16 kcal mol-1 for acetaldehyde, -45.18 +/- 1.1 kcal mol-1 for propanal, and -49.27 +/- 0.16 kcal mol-1 for butanal. Enthalpies of formation for these three aldehydes, as well as for pentanal, hexanal, and heptanal, were calculated using the G3, G3B3, and CBS-APNO theoretical methods, in conjunction with bond-isodesmic work reactions. On the basis of the results of our thermodynamic cycles, theoretical calculations using isodesmic work reactions, and existing experimental measurements, we suggest that the best available formation enthalpies for the aldehydes acetaldehyde, propanal, butanal, pentanal, hexanal, and heptanal are -39.72, -45.18, -50.0, -54.61, -59.37, and -64.2 kcal mol-1, respectively. Our calculations also identify that the literature enthalpy of formation of crotonaldehyde is in error by as much as 1 kcal mol-1, and we suggest a value of -25.1 kcal mol-1, which we calculate using isodesmic work reactions. Bond energies for each of the bonds in the aldehydes up to pentanal were calculated at the CBS-APNO level. Analysis of the BDEs reveals the R-CH(2)CH=O to be the weakest bond in all aldehydes larger than acetaldehyde, due to formation of the resonantly stabilized vinoxy radical (vinyloxy radical/formyl methyl radical). It is

  20. Two distinct mechanisms of alkyne insertion into the metal-sulfur bond: combined experimental and theoretical study and application in catalysis.

    PubMed

    Ananikov, Valentine P; Gayduk, Konstantin A; Orlov, Nikolay V; Beletskaya, Irina P; Khrustalev, Victor N; Antipin, Mikhail Yu

    2010-02-15

    The present study reports the evidence for the multiple carbon-carbon bond insertion into the metal-heteroatom bond via a five-coordinate metal complex. Detailed analysis of the model catalytic reaction of the carbon-sulfur (C-S) bond formation unveiled the mechanism of metal-mediated alkyne insertion: a new pathway of C-S bond formation without preliminary ligand dissociation was revealed based on experimental and theoretical investigations. According to this pathway alkyne insertion into the metal-sulfur bond led to the formation of intermediate metal complex capable of direct C-S reductive elimination. In contrast, an intermediate metal complex formed through alkyne insertion through the traditional pathway involving preliminary ligand dissociation suffered from "improper" geometry configuration, which may block the whole catalytic cycle. A new catalytic system was developed to solve the problem of stereoselective S-S bond addition to internal alkynes and a cost-efficient Ni-catalyzed synthetic procedure is reported to furnish formation of target vinyl sulfides with high yields (up to 99%) and excellent Z/E selectivity (>99:1).

  1. Hemoglobin C, S-C, and E Diseases

    MedlinePlus

    ... Hemolytic Anemia Hemoglobin C, S-C, and E Diseases Iron Deficiency Anemia Sickle Cell Disease Thalassemias Vitamin Deficiency Anemia ( ... Hemolytic Anemia Hemoglobin C, S-C, and E Diseases Iron Deficiency Anemia Sickle Cell Disease Thalassemias Vitamin Deficiency Anemia ...

  2. Mechanistic and computational studies of oxidatively-induced aryl-CF3 bond-formation at Pd: rational design of room temperature aryl trifluoromethylation.

    PubMed

    Ball, Nicholas D; Gary, J Brannon; Ye, Yingda; Sanford, Melanie S

    2011-05-18

    This article describes the rational design of first generation systems for oxidatively induced Aryl-CF(3) bond-forming reductive elimination from Pd(II). Treatment of (dtbpy)Pd(II)(Aryl)(CF(3)) (dtbpy = di-tert-butylbipyridine) with NFTPT (N-fluoro-1,3,5-trimethylpyridinium triflate) afforded the isolable Pd(IV) intermediate (dtbpy)Pd(IV)(Aryl)(CF(3))(F)(OTf). Thermolysis of this complex at 80 °C resulted in Aryl-CF(3) bond-formation. Detailed experimental and computational mechanistic studies have been conducted to gain insights into the key reductive elimination step. Reductive elimination from this Pd(IV) species proceeds via pre-equilibrium dissociation of TfO(-) followed by Aryl-CF(3) coupling. DFT calculations reveal that the transition state for Aryl-CF(3) bond formation involves the CF(3) acting as an electrophile with the Aryl ligand serving as a nucleophilic coupling partner. These mechanistic considerations along with DFT calculations have facilitated the design of a second generation system utilizing the tmeda (N,N,N',N'-tetramethylethylenediamine) ligand in place of dtbpy. The tmeda complexes undergo oxidative trifluoromethylation at room temperature.

  3. Un-catalyzed peptide bond formation between two monomers of glycine, alanine, serine, threonine, and aspartic acid in gas phase: a density functional theory study

    NASA Astrophysics Data System (ADS)

    Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K.

    2016-05-01

    In the present report, un-catalyzed peptide bond formation between two monomers of glycine (Gly), alanine (Ala), serine (Ser), threonine (Thr), and aspartic acid (Asp) has been investigated in gas phase via two steps reaction mechanism and concerted mechanism at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. The peptide bond is formed through a nucleophilic reaction via transition states, TS1 and TS2 in stepwise mechanism. The TS1 reveals formation of a new C-N bond while TS2 illustrate the formation of C=O bond. In case of concerted mechanism, C-N bond is formed by a single four-centre transition state (TS3). The energy barrier is used to explain the involvement of energy at each step of the reaction. The energy barrier (20-48 kcal/mol) is required for the transformation of reactant state R1 to TS1 state and intermediate state I1 to TS2 state. The large value of energy barrier is explained in terms of distortion and interaction energies for stepwise mechanism. The energy barrier of TS3 in concerted mechanism is very close to the energy barrier of the first transition state (TS1) of the stepwise mechanism for the formation of Gly-Gly and Ala-Ala di- peptide. However, in case of Ser-Ser, Thr-Thr and Asp-Asp di-peptide, the energy barrier of TS3 is relatively high than that of the energy barrier of TS1 calculated at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. In both the mechanisms, the value of energy barrier calculated at B3LYP/6-31G(d,p) level of theory is greater than that of the value calculated at M062X/6-31G(d,p) level of theory.

  4. N-cyanoimidazole and diimidazole imine: water-soluble condensing agents for the formation of the phosphodiester bond

    NASA Technical Reports Server (NTRS)

    Ferris, J. P.; Huang, C. H.; Hagan, W. J. Jr

    1989-01-01

    The reaction of BrCN with imidazole results in the formation of N-cyanoimidazole and diimidazole imine. These compounds were shown to be useful condensing agents for the formation of the phosphodiester bound in aqueous solution.

  5. N-cyanoimidazole and diimidazole imine: water-soluble condensing agents for the formation of the phosphodiester bond

    NASA Technical Reports Server (NTRS)

    Ferris, J. P.; Huang, C. H.; Hagan, W. J. Jr

    1989-01-01

    The reaction of BrCN with imidazole results in the formation of N-cyanoimidazole and diimidazole imine. These compounds were shown to be useful condensing agents for the formation of the phosphodiester bound in aqueous solution.

  6. Strength and formation of poor metals from insulators: bonds to bands in Al2O3 and H2

    NASA Astrophysics Data System (ADS)

    Nellis, W. J.

    2011-06-01

    HELs of Al2O3 and H2 are ~15 GPa and 0, respectively, while Al-O and H-H bond energies are both 4.5 eV and both are wide gap insulators at ambient. Al2O3 is a likely metallic glass at ~300 GPa; hydrogen is a metallic fluid at 140 GPa. How can such different materials at ambient both be disordered poor metals at 100 GPas? As McQueen pointed out, shock dissipation TS is absorbed in temperature T and entropy S (disorder). Because of strength, the split between T and S differs greatly between these two. H2s interact via weak pair interactions, which means high compressibility, high shock Ts, and dissociation (S) to monatomic metal at high pressures. Al and O atoms interact strongly via directional bonds in large 3D networks. Dissipation is first absorbed breaking bonds (S), which keeps T and thermal pressure low up to 400 GPa. Once most Al-O bonds are broken, Al2O3 is amorphous and atom densities so large that atomic wave functions probably overlap to form a metallic glass. Existing conductivity measurements to 220 GPa need to be extended to ~300 GPa to test this prediction.

  7. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation.

    PubMed

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A; Lambrecht, Marlies A; Koehler, Peter; Delcour, Jan A

    2015-07-20

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing.

  8. New chromogenic and fluorogenic reagents and sensors for neutral and ionic analytes based on covalent bond formation--a review of recent developments.

    PubMed

    Mohr, Gerhard J

    2006-11-01

    To date, hydrogen bonding and Coulomb, van der Waals and hydrophobic interactions are the major contributors to non-covalent analyte recognition using ionophores, ligands, aptamers and chemosensors. However, this article describes recent developments in the use of (reversible) covalent bond formation to detect analyte molecules, with special focus on optical signal transduction. Several new indicator dyes for analytes such as amines and diamines, amino acids, cyanide, formaldehyde, hydrogen peroxide, organophosphates, nitrogen oxide and nitrite, peptides and proteins, as well as saccharides have become available. New means of converting analyte recognition into optical signals have also been introduced, such as colour changes of chiral nematic layers. This article gives an overview of recent developments and discusses response mechanisms, selectivity and sensitivity.

  9. Formation of native disulfide bonds in endothelin-1. Structural evidence for the involvement of a highly specific salt bridge between the prosequence and the endothelin-1 sequence.

    PubMed

    Aumelas, A; Kubo, S; Chino, N; Chiche, L; Forest, E; Roumestand, C; Kobayashi, Y

    1998-04-14

    The [Lys-Arg]-endothelin-1 analogue (KR-ET-1) yields almost selectively the native disulfide pattern (96%), in contrast to endothelin-1 (ET-1) that gives at least 25% of the non-native disulfide pattern. We have previously shown that the carboxylate-state structure of KR-ET-1 is more constrained and stabilized by a salt bridge between Arg(-1) and the Asp8 or Glu10 side chain [Aumelas et al. (1995) Biochemistry 34, 4546-4561]. To identify this salt bridge and its potential involvement in the disulfide bond formation, [E10Q], [D18N], and [D8N] carboxamide analogues were studied, which led to the unambiguous identification of the Arg(-1)-Asp8 salt bridge. Furthermore, while [E10Q] and [D18N] analogues gave a high yield of the native isomer (>/=90%), the [D8N] analogue afforded a ratio of the two isomers close to that observed for ET-1 (68%) [Kubo et al. (1997) Lett. Pept. Sci. 4, 185-192]. Assuming that the formation of disulfide bonds occurs in a thermodynamically controlled step, we have hypothesized that the Arg(-1)-Asp8 salt bridge and concomitant interactions could be responsible for the increase in yield of the native isomer of KR-ET-1. In the present work, we describe the structural studies of the carboxamide analogues and of the minor non-native KR-ET-1 isomer. On the basis of 1H NMR and CD spectra as a function of pH, [E10Q] and [D18N] analogues display a conformational change similar to that of the parent peptide, whereas the structure of the [D8N] analogue is unchanged. For the non-native isomer, we measured a lower helical content than for the native isomer and observed a marked difference in the orientation of the KRCSC backbone. In addition, no salt bridge was experimentally observed. Altogether, these results allow us to hypothesize that the salt bridge between two highly conserved residues, one belonging to the prosequence [Arg(-1)] and the other to the mature sequence [Asp8], is involved in the formation of the native disulfide isomer of ET-1. The

  10. Transmembrane domain interactions and residue proline 378 are essential for proper structure, especially disulfide bond formation, in the human vitamin K-dependent gamma-glutamyl carboxylase.

    PubMed

    Tie, Jian-Ke; Zheng, Mei-Yan; Hsiao, Kuang-Ling N; Perera, Lalith; Stafford, Darrel W; Straight, David L

    2008-06-17

    We used recombinant techniques to create a two-chain form (residues 1-345 and residues 346-758) of the vitamin K-dependent gamma-glutamyl carboxylase, a glycoprotein located in the endoplasmic reticulum containing five transmembrane domains. The two-chain carboxylase had carboxylase and epoxidase activities similar to those of one-chain carboxylase. In addition, it had normal affinity for the propeptide of factor IX. We employed this molecule to investigate formation of the one disulfide bond in carboxylase, the transmembrane structure of carboxylase, and the potential interactions among the carboxylase's transmembrane domains. Our results indicate that the two peptides of the two-chain carboxylase are joined by a disulfide bond. Proline 378 is important for the structure necessary for disulfide formation. Results with the P378L carboxylase indicate that noncovalent bonds maintain the two-chain structure even when the disulfide bond is disrupted. As we had previously proposed, the fifth transmembrane domain of carboxylase is the last and only transmembrane domain in the C-terminal peptide of the two-chain carboxylase. We show that the noncovalent association between the two chains of carboxylase involves an interaction between the fifth transmembrane domain and the second transmembrane domain. Results of a homology model of transmembrane domains 2 and 5 suggest that not only do these two domains associate but that transmembrane domain 2 may interact with another transmembrane domain. This latter interaction may be mediated at least in part by a motif of glycine residues in the second transmembrane domain.

  11. Self-assembly and glass-formation in a lattice model of telechelic polymer melts: Influence of stiffness of the sticky bonds.

    PubMed

    Xu, Wen-Sheng; Freed, Karl F

    2016-06-07

    Telechelic polymers are chain macromolecules that may self-assemble through the association of their two mono-functional end groups (called "stickers"). A deep understanding of the relation between microscopic molecular details and the macroscopic physical properties of telechelic polymers is important in guiding the rational design of telechelic polymer materials with desired properties. The lattice cluster theory (LCT) for strongly interacting, self-assembling telechelic polymers provides a theoretical tool that enables establishing the connections between important microscopic molecular details of self-assembling polymers and their bulk thermodynamics. The original LCT for self-assembly of telechelic polymers considers a model of fully flexible linear chains [J. Dudowicz and K. F. Freed, J. Chem. Phys. 136, 064902 (2012)], while our recent work introduces a significant improvement to the LCT by including a description of chain semiflexibility for the bonds within each individual telechelic chain [W.-S. Xu and K. F. Freed, J. Chem. Phys. 143, 024901 (2015)], but the physically associative (or called "sticky") bonds between the ends of the telechelics are left as fully flexible. Motivated by the ubiquitous presence of steric constraints on the association of real telechelic polymers that impart an additional degree of bond stiffness (or rigidity), the present paper further extends the LCT to permit the sticky bonds to be semiflexible but to have a stiffness differing from that within each telechelic chain. An analytical expression for the Helmholtz free energy is provided for this model of linear telechelic polymer melts, and illustrative calculations demonstrate the significant influence of the stiffness of the sticky bonds on the self-assembly and thermodynamics of telechelic polymers. A brief discussion is also provided for the impact of self-assembly on glass-formation by combining the LCT description for this extended model of telechelic polymers with the

  12. Supramolecular chemistry of halogens: complementary features of inorganic (M-X) and organic (C-X') halogens applied to M-X...X'-C halogen bond formation.

    PubMed

    Zordan, Fiorenzo; Brammer, Lee; Sherwood, Paul

    2005-04-27

    Electronic differences between inorganic (M-X) and organic (C-X) halogens in conjunction with the anisotropic charge distribution associated with terminal halogens have been exploited in supramolecular synthesis based upon intermolecular M-X...X'-C halogen bonds. The synthesis and crystal structures of a family of compounds trans-[MCl(2)(NC(5)H(4)X-3)(2)] (M = Pd(II), Pt(II); X = F, Cl, Br, I; NC(5)H(4)X-3 = 3-halopyridine) are reported. With the exception of the fluoropyridine compounds, network structures propagated by M-Cl...X-C halogen bonds are adopted and involve all M-Cl and all C-X groups. M-Cl...X-C interactions show Cl...X separations shorter than van der Waals values, shorter distances being observed for heavier halogens (X). Geometries with near linear Cl...X-C angles (155-172 degrees ) and markedly bent M-Cl...X angles (92-137 degrees ) are consistently observed. DFT calculations on the model dimers {trans-[MCl(2)(NH(3))(NC(5)H(4)X-3)]}(2) show association through M-Cl...X-C (X not equal F) interactions with geometries similar to experimental values. DFT calculations of the electrostatic potential distributions for the compounds trans-[PdCl(2)(NC(5)H(4)X-3)(2)] (X = F, Cl, Br, I) demonstrate the effectiveness of the strategy to activate C-X groups toward halogen bond formation by enhancing their electrophilicity, and explain the absence of M-Cl...F-C interactions. The M-Cl...X-C halogen bonds described here can be viewed unambiguously as nucleophile-electrophile interactions that involve an attractive electrostatic contribution. This contrasts with some types of halogen-halogen interactions previously described and suggests that M-Cl...X-C halogen bonds could provide a valuable new synthon for supramolecular chemists.

  13. The Radical S-Adenosyl-l-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds*

    PubMed Central

    Nakai, Tadashi; Ito, Hiroto; Kobayashi, Kazuo; Takahashi, Yasuhiro; Hori, Hiroshi; Tsubaki, Motonari; Tanizawa, Katsuyuki; Okajima, Toshihide

    2015-01-01

    The bacterial enzyme designated QhpD belongs to the radical S-adenosyl-l-methionine (SAM) superfamily of enzymes and participates in the post-translational processing of quinohemoprotein amine dehydrogenase. QhpD is essential for the formation of intra-protein thioether bonds within the small subunit (maturated QhpC) of quinohemoprotein amine dehydrogenase. We overproduced QhpD from Paracoccus denitrificans as a stable complex with its substrate QhpC, carrying the 28-residue leader peptide that is essential for the complex formation. Absorption and electron paramagnetic resonance spectra together with the analyses of iron and sulfur contents suggested the presence of multiple (likely three) [4Fe-4S] clusters in the purified and reconstituted QhpD. In the presence of a reducing agent (sodium dithionite), QhpD catalyzed the multiple-turnover reaction of reductive cleavage of SAM into methionine and 5′-deoxyadenosine and also the single-turnover reaction of intra-protein sulfur-to-methylene carbon thioether bond formation in QhpC bound to QhpD, producing a multiknotted structure of the polypeptide chain. Homology modeling and mutagenic analysis revealed several conserved residues indispensable for both in vivo and in vitro activities of QhpD. Our findings uncover another challenging reaction catalyzed by a radical SAM enzyme acting on a ribosomally translated protein substrate. PMID:25778402

  14. Development of a dye molecule-biocatalyst hybrid system with visible-light induced carbon-carbon bond formation from CO2 as a feedstock.

    PubMed

    Amao, Yutaka; Ikeyama, Shusaku; Katagiri, Takayuki; Fujita, Kohei

    2017-03-09

    Recently, CO2 utilization technology, including artificial photosynthesis, has received much attention. In this field, CO2 is used as a feedstock for fuels, polymers and in other chemical processes. Of note are malic enzymes (MEs) which catalyze the reaction of malic acid to pyruvic acid and CO2 with the co-enzyme NADP(+), and catalyze the reverse reaction of pyruvic acid and CO2 to malic acid with the co-enzyme NADPH. Thus, MEs are also an attractive biocatalyst for carbon-carbon bond formation from CO2. Studies of the visible light-induced malic acid production from pyruvic acid and CO2 using an electron donor, a photosensitizer, an electron mediator, ferredoxin-NADP(+) reductase, NADP(+), and ME have been reported. However, modification of these systems is required, as they are very complicated. In this study, the visible light-induced carbon-carbon bond formation from pyruvic acid and CO2 with ME using the photoreduction of 1,1'-diphenyl-4,4'-bipyridinium salt derivatives as a novel electron mediator with water-soluble tetraphenylporphyrin tetrasulfonate (H2TPPS) in the presence of triethanolamine (TEOA) as an electron donor was developed. When a sample solution containing TEOA, H2TPPS, 1,1'-diphenyl-4,4'-bipyridinium salt derivative, pyruvic acid, and ME in CO2-saturated bis-tris buffer was irradiated, the major product was oxaloacetic acid. Thus, a visible light-induced photoredox system for carbon-carbon bond formation from CO2 with ME using 1,1'-diphenyl-4,4'-bipyridinium salt derivative as an electron mediator was developed.

  15. Unprecedented chemical reactivity of a paramagnetic endohedral metallofullerene La@C(s)-C82 that leads hydrogen addition in the 1,3-dipolar cycloaddition reaction.

    PubMed

    Takano, Yuta; Slanina, Zdenek; Mateos, Jaime; Tsuchiya, Takayoshi; Kurihara, Hiroki; Uhlik, Filip; Herranz, María Ángeles; Martín, Nazario; Nagase, Shigeru; Akasaka, Takeshi

    2014-12-17

    Synthesizing unprecedented diamagnetic adducts of an endohedral metallofullerene was achieved by using 1,3-dipolar cycloaddition reaction of paramagnetic La@C(s)-C82 with a simultaneous hydrogen addition. The selective formation of two main products, La@C(s)-C82HCMe2NMeCHPh (2a and 2b), was first detected by HPLC analysis and MALDI-TOF mass spectrometry. 2a and 2b-O, which was readily formed by the oxidation of 2b, were isolated by multistep HPLC separation and were fully characterized by spectroscopic methods, including 1D and 2D-NMR, UV-vis-NIR measurements and electrochemistry. The hydrogen atom was found to be connected to the fullerene cage directly in the case of 2a, and the redox behavior indicated that the C-H bond can still be readily oxidized. The reaction mechanism and the molecular structures of 2a and 2b were reasonably proposed by the interplay between experimental observations and DFT calculations. The feasible order of the reaction process would involve a 1,3-dipolar cycloaddition followed by the hydrogen addition through a radical pathway. It is concluded that the characteristic electronic properties and molecular structure of La@C(s)-C82 resulted in a site-selective reaction, which afforded a unique chemical derivative of an endohedral metallofullerene in high yields. Derivative 2a constitutes the first endohedral metallofullerene where the direct linking of a hydrogen atom has been structurally proven.

  16. The Stereoselective Formation of Bicyclic Enamines with Bridgehead Unsaturation via Tandem C-H Bond Activation/Alkenylation/Electrocyclization

    SciTech Connect

    Ellman, Jonathan A.; Yotphan, Sirilata; Bergman, Robert

    2007-12-10

    Rhodium-catalyzed intermolecular C-H activation of {alpha}, {beta}-unsaturated imines in the presence of alkynes leads to a tandem process in which coupling to the alkyne occurs at the {beta}-C-H bond of the imine, followed by electrocyclization of the resulting azatriene intermediates to give dihydropyridines (eq 1). Consideration of the intramolecular version of this overall transformation (Scheme 1) raises interesting regiochemical issues. For example in a compound such as 1, where the nitrogen and alkyne are connected by a 4-carbon tether, the presumed first-formed hydrido(vinyl)rhodium function can add to the triple bond in a 1,2-fashion, producing complex 2 with a new endocyclic double bond. Alternatively, addition might occur in a 2,1-fashion, leading to product 4 with an exocyclic double bond. We now wish to report that this intramolecular cyclization occurs smoothly at 100 C, and the exocyclic double bond route is exclusively followed. Remarkably, products such as 4 do not resist further cyclization. Even though both the transition state for this process and the resulting product are presumably strained, the overall transformation leads to good yields of unusual bridgehead doubly-bonded enamines such as 5. The unique chemistry of conjugated enamine 5 is consistent with the increased strain of this molecule as well as with inhibited conjugation between the nitrogen lone pair and the adjacent double bond (vida infra). We began our investigation into the C-H activation/cyclization of alkyne-tethered imine 1 by extensive screening of transition metal catalysts for this process. Rhodium-based catalysts were found to be the most efficient (Table 1), leading exclusively to the bridgehead dienamine; none of the catalysts that were employed in the screening led to quinolizidine 3 or to the product of intramolecular Diels-Alder reaction. The optimized reaction conditions employ the electron-rich monophosphine ligand (p-NMe{sub 2})PhPEt{sub 2} in 1:1 ratio relative

  17. Determination of the optimal position of adjacent proton-donor centers for the activation or inhibition of peptide bond formation--a computational model study.

    PubMed

    Rangelov, Miroslav A; Petrova, Galina P; Yomtova, Vihra M; Vayssilov, Georgi N

    2011-09-01

    The study reports a computational analysis of the influence of proton donor group adjacent to the reaction center during ester ammonolysis of an acylated diol as a model reaction for peptide bond formation. This analysis was performed using catalytic maps constructed after a detailed scanning of the available space around the reaction centers in different transition states, a water molecule acting as a typical proton donor. The calculations suggest that an adjacent proton donor center can reduce the activation barrier of the rate determining transition states by up to 7.2 kcal/mol, while no inhibition of the reaction can be achieved by such a group.

  18. A conserved secondary structural motif in 23S rRNA defines the site of interaction of amicetin, a universal inhibitor of peptide bond formation.

    PubMed Central

    Leviev, I G; Rodriguez-Fonseca, C; Phan, H; Garrett, R A; Heilek, G; Noller, H F; Mankin, A S

    1994-01-01

    The binding site and probable site of action have been determined for the universal antibiotic amicetin which inhibits peptide bond formation. Evidence from in vivo mutants, site-directed mutations and chemical footprinting all implicate a highly conserved motif in the secondary structure of the 23S-like rRNA close to the central circle of domain V. We infer that this motif lies at, or close to, the catalytic site in the peptidyl transfer centre. The binding site of amicetin is the first of a group of functionally related hexose-cytosine inhibitors to be localized on the ribosome. Images PMID:8157007

  19. Reactivity of damaged pyrimidines: formation of a Schiff base intermediate at the glycosidic bond of saturated dihydrouridine.

    PubMed

    Jian, Yajun; Lin, Gengjie; Chomicz, Lidia; Li, Lei

    2015-03-11

    DNA glycosylases catalyze the first step of the base excision repair (BER) pathway. The chemistry used by these enzymes for deglycosylation has been largely considered as the chemistry of the oxocarbenium ion, e.g., direct rupture of the C1'-N1 bond resulting in an oxocarbenium ion intermediate. Here we present mechanistic studies revealing the 2'-deoxyribose isomerization and subsequent deglycosylation processes in two pyrimidine lesions: 5,6-dihydro-2'-deoxyuridine (dHdU) and 5,6-dihydrothymidine (dHT), formed via ionizing radiation damage to 2'-deoxycytidine and thymidine, respectively, under anoxic conditions. Acid or heat treatment of these two lesions leads to the production of two pairs of C1' epimers containing a pyranose and a furanose, respectively, indicating that both lesions favor the rupture of the C1'-O4' bond, resulting in a Schiff base intermediate at the N-glycosidic bond. Such a Schiff base intermediate was trapped and characterized by either Pd-catalyzed hydrogenation or thiol-mediated addition reaction. In contrast, in undamaged 2'-deoxyuridine and thymidine, reactions at elevated temperatures lead to the release of nucleobases most likely via the traditional oxocarbenium ion pathway. DFT calculations further support the experimental findings, suggesting that the oxocarbenium ion intermediate is responsible for the deglycosylation process if the integrity of the pyrimidine ring is maintained, while the Schiff base intermediate is preferred if the C5═C6 bond is saturated. Currently, the oxocarbenium ion pathway is indicated to be solely responsible for the deglycosylation in BER enzymes, however our results suggest an alternative Schiff base mechanism which may be responsible for the repair of saturated pyrimidine damages.

  20. Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm.

    PubMed

    Fagerquist, Clifton K; Sultan, Omar; Carter, Michelle Q

    2012-12-01

    We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, Hde, and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALDI) time-of-flight-time-of-flight tandem mass spectrometry (TOF-TOF-MS/MS) and post-source decay (PSD). We also reported the absence of adduct formation when using α-cyano-4-hydroxycinnamic acid (CHCA) matrix. Further mass spectrometric analysis of disulfide-intact and disulfide-reduced over-expressed HdeA and HdeB proteins from lysates of gene-inserted E. coli plasmids suggests covalent attachment of SA occurs not at cysteine residues but at lysine residues. In this revised hypothesis, the attachment of SA is preceded by formation of a solid phase ammonium carboxylate salt between SA and accessible lysine residues of the protein during sample preparation under acidic conditions. Laser irradiation at 355 nm of the dried sample spot results in equilibrium retrogradation followed by nucleophilic attack by the amine group of lysine at the carbonyl group of SA and subsequent amide bond formation and loss of water. The absence of CHCA adducts suggests that the electron-withdrawing effect of the α-cyano group of this matrix may inhibit salt formation and/or amide bond formation. This revised hypothesis is supported by dissociative loss of SA (-224 Da) and the amide-bound SA (-206 Da) from SA-adducted HdeA and HdeB ions by MS/MS (PSD). It is proposed that cleavage of the amide-bound SA from the lysine side-chain occurs via rearrangement involving a pentacyclic transition state followed by hydrogen abstraction/migration and loss of 3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-ynal (-206 Da).

  1. Calmodulin Methionine Residues are Targets For One-Electron Oxidation by Hydroxyl Radicals: Formation of S therefore N three-electron bonded Radical Complexes

    SciTech Connect

    Nauser, Thomas; Jacoby, Michael E.; Koppenol, Willem H.; Squier, Thomas C.; Schoneich, Christian

    2005-02-01

    The one-electron (1e) oxidation of organic sulfides and methionine (Met) constitutes an important reaction mechanism in vivo.1,2 Evidence for a Cu(II)-catalyzed oxidation of Met35 in the Alzheimer's disease -amyloid peptide was obtained,3 and, based on theoretical studies, Met radical cations were proposed as intermediates.4 In the structure of -amyloid peptide, the formation of Met radical cations appears to be facilitated by a preexisting close sulfur-oxygen (S-O) interaction between the Met35 sulfur and the carbonyl oxygen of the peptide bond C-terminal to Ile31.5 Substitution of Ile31 with Pro31 abolishes this S-O interaction,5 significantly reducing the ability of -amyloid to reduce Cu(II), and converts the neurotoxic wild-type -amyloid into a non-toxic peptide.6 The preexisting S-O bond characterized for wild-type -amyloid suggests that electron transfer from Met35 to Cu(II) is supported through stabilization of the Met radical cation by the electron-rich carbonyl oxygen, generating an SO-bonded7 sulfide radical cation (Scheme 1, reaction 1).5

  2. Exploring large O 1s and N 1s core level shifts due to intermolecular hydrogen bond formation in organic molecules

    NASA Astrophysics Data System (ADS)

    Garcia-Gil, S.; Arnau, A.; Garcia-Lekue, A.

    2013-07-01

    Core level shifts (CLSs) induced by intermolecular hydrogen bond (H-bond) formation are studied with a recent implementation based on density functional theory using pseudopotentials and localized atomic orbitals, as applied to the SIESTA code. By calculating different CLSs for a set of representative simple systems containing O and/or N atoms as proton donors and/or acceptors, we are able to determine the role of the core hole screening, from the difference of CLS values calculated in the final and initial state approximations. Our calculations show that CLSs are dominated by electrostatic effects, and that the final magnitude of the CLSs, which are positive (higher binding energy) for the proton acceptor and negative for the proton donor, can be larger than 1 eV for strong H-bonds. We also find that core hole screening contribution to final CLS absolute values is always negative, thus being responsible for the difference in the magnitude of the CLS of the proton donor and proton acceptor.

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

    PubMed

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

    2016-04-26

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

  4. A Facile Method to Prepare Double-Layer Isoporous Hollow Fiber Membrane by In Situ Hydrogen Bond Formation in the Spinning Line.

    PubMed

    Noor, Nazia; Koll, Joachim; Radjabian, Maryam; Abetz, Clarissa; Abetz, Volker

    2016-03-01

    A double-layer hollow fiber is fabricated where an isoporous surface of polystyrene-block-poly(4-vinylpyridine) is fixed on a support layer by co-extrusion. Due to the sulfonation of the support layer material, delamination of the two layers is suppressed without increasing the number of subsequent processing steps for isoporous composite membrane formation. Electron microscope-energy-dispersive X-ray spectroscopy images unveil the existence of a high sulfur concentration in the interfacial region by which in-process H-bond formation between the layers is evidenced. For the very first time, our study reports a facile method to fabricate a sturdy isoporous double-layer hollow fiber.

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

    SciTech Connect

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

    1993-08-01

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

  6. 3D micro-CT analysis of void formations and push-out bonding strength of resin cements used for fiber post cementation.

    PubMed

    Uzun, İsmail Hakkı; Malkoç, Meral Arslan; Keleş, Ali; Öğreten, Ayşe Tuba

    2016-04-01

    To investigate the void parameters within the resin cements used for fiber post cementation by micro-CT (µCT) and regional push-out bonding strength. Twenty-one, single and round shaped roots were enlarged with a low-speed drill following by endodontic treatment. The roots were divided into three groups (n=7) and fiber posts were cemented with Maxcem Elite, Multilink N and Superbond C&B resin cements. Specimens were scanned using µCT scanner at resolution of 13.7 µm. The number, area, and volume of voids between dentin and post were evaluated. A method of analysis based on the post segmentation was used, and coronal, middle and apical thirds considered separately. After the µCT analysis, roots were embedded in epoxy resin and sectioned into 2 mm thick slices (63 sections in total). Push-out testing was performed with universal testing device at 0.5 mm/min cross-head speed. Data were analyzed with Kruskal-Wallis and Mann-Whitney U tests (α=.05). Overall, significant differences between the resin cements and the post level were observed in the void number, area, and volume (P<.05). Super-Bond C&B showed the most void formation (44.86 ± 22.71). Multilink N showed the least void surface (3.51 ± 2.24 mm(2)) and volume (0.01 ± 0.01 mm(3)). Regional push-out bond strength of the cements was not different (P>.05). µCT proved to be a powerful non-destructive 3D analysis tool for visualizing the void parameters. Multilink N had the lowest void parameters. When efficiency of all cements was evaluated, direct relationship between the post region and push-out bonding strength was not observed.

  7. 3D micro-CT analysis of void formations and push-out bonding strength of resin cements used for fiber post cementation

    PubMed Central

    2016-01-01

    PURPOSE To investigate the void parameters within the resin cements used for fiber post cementation by micro-CT (µCT) and regional push-out bonding strength. MATERIALS AND METHODS Twenty-one, single and round shaped roots were enlarged with a low-speed drill following by endodontic treatment. The roots were divided into three groups (n=7) and fiber posts were cemented with Maxcem Elite, Multilink N and Superbond C&B resin cements. Specimens were scanned using µCT scanner at resolution of 13.7 µm. The number, area, and volume of voids between dentin and post were evaluated. A method of analysis based on the post segmentation was used, and coronal, middle and apical thirds considered separately. After the µCT analysis, roots were embedded in epoxy resin and sectioned into 2 mm thick slices (63 sections in total). Push-out testing was performed with universal testing device at 0.5 mm/min cross-head speed. Data were analyzed with Kruskal–Wallis and Mann–Whitney U tests (α=.05). RESULTS Overall, significant differences between the resin cements and the post level were observed in the void number, area, and volume (P<.05). Super-Bond C&B showed the most void formation (44.86 ± 22.71). Multilink N showed the least void surface (3.51 ± 2.24 mm2) and volume (0.01 ± 0.01 mm3). Regional push-out bond strength of the cements was not different (P>.05). CONCLUSION µCT proved to be a powerful non-destructive 3D analysis tool for visualizing the void parameters. Multilink N had the lowest void parameters. When efficiency of all cements was evaluated, direct relationship between the post region and push-out bonding strength was not observed. PMID:27141253

  8. Toward Design Principles for Diffusionless Transformations: The Frustrated Formation of Co-Co Bonds in a Low-Temperature Polymorph of GdCoSi2.

    PubMed

    Vinokur, Anastasiya I; Fredrickson, Daniel C

    2016-06-20

    Diffusionless (or displacive) phase transitions allow inorganic materials to show exquisite responsiveness to external stimuli, as is illustrated vividly by the superelasticity, shape memory, and magnetocaloric effects exhibited by martensitic materials. In this Article, we present a new diffusionless transition in the compound GdCoSi2, whose origin in frustrated bonding points toward generalizable design principles for these transformations. We first describe the synthesis of GdCoSi2 and the determination of its structure using single crystal X-ray diffraction. While previous studies based on powder X-ray diffraction assigned this compound to the simple CeNi1-xSi2 structure type (space group Cmcm), our structure solution reveals a superstructure variant (space group Pbcm) in which the Co sublattice is distorted to create zigzag chains of Co atoms. DFT-calibrated Hückel calculations, coupled with a reversed approximation Molecular Orbital (raMO) analysis, trace this superstructure to the use of Co-Co isolobal bonds to complete filled 18 electron configurations on the Co atoms, in accordance with the 18-n rule. The formation of these Co-Co bonds is partially impeded, however, by a small degree of electron transfer from Si-based electronic states to those with Co-Co σ* character. The incomplete success of Co-Co bond creation suggests that these interactions are relatively weak, opening the possibility of them being overcome by thermal energy at elevated temperatures. In fact, high-temperature powder and single crystal X-ray diffraction data, as well as differential scanning calorimetry, indicate that a reversible Pbcm to Cmcm transition occurs at about 380 K. This transition is diffusionless, and the available data point toward it being first-order. We expect that similar cases of frustrated interactions could be staged in other rare earth-transition metal-main group phases, providing a potentially rich source of compounds exhibiting diffusionless transformations

  9. Bent Bonds and Multiple Bonds.

    ERIC Educational Resources Information Center

    Robinson, Edward A.; Gillespie, Ronald J.

    1980-01-01

    Considers carbon-carbon multiple bonds in terms of Pauling's bent bond model, which allows direct calculation of double and triple bonds from the length of a CC single bond. Lengths of these multiple bonds are estimated from direct measurements on "bent-bond" models constructed of plastic tubing and standard kits. (CS)

  10. Large Scale Solid Phase Synthesis of Peptide Drugs: Use of Commercial Anion Exchange Resin as Quenching Agent for Removal of Iodine during Disulphide Bond Formation.

    PubMed

    Reddy, K M Bhaskara; Kumari, Y Bharathi; Mallikharjunasarma, Dokka; Bulliraju, Kamana; Sreelatha, Vanjivaka; Ananda, Kuppanna

    2012-01-01

    The S-acetamidomethyl (Acm) or trityl (Trt) protecting groups are widely used in the chemical synthesis of peptides that contain one or more disulfide bonds. Treatment of peptides containing S-Acm protecting group with iodine results in simultaneous removal of the sulfhydryl protecting group and disulfide formation. However, the excess iodine needs to be quenched or adsorbed as quickly as possible after completion of the disulfide bond formation in order to minimize side reactions that are often associated with the iodination step. We report here a simple method for simultaneous quenching and removal of iodine and isolation of disulphide bridge peptides. The use of excess inexpensive anion exchange resin to the oxidized peptide from the aqueous acetic acid/methanol solution affords quantitative removal of iodine and other color impurities. This improves the resin life time of expensive chromatography media that is used in preparative HPLC column during the purification of peptide using preparative HPLC. Further, it is very useful for the conversion of TFA salt to acetate in situ. It was successfully applied commercially, to the large scale synthesis of various peptides including Desmopressin, Oxytocin, and Octreotide. This new approach offers significant advantages such as more simple utility, minimal side reactions, large scale synthesis of peptide drugs, and greater cost effectiveness.

  11. Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs.

    PubMed

    Beringer, Malte; Rodnina, Marina V

    2007-07-01

    The major enzymatic activity of the ribosome is the catalysis of peptide bond formation. The active site -- the peptidyl transferase center -- is composed of ribosomal RNA (rRNA), and interactions between rRNA and the reactants, peptidyl-tRNA and aminoacyl-tRNA, are crucial for the reaction to proceed rapidly and efficiently. Here, we describe the influence of rRNA interactions with cytidine residues in A-site substrate analogs (C-puromycin or CC-puromycin), mimicking C74 and C75 of tRNA on the reaction. Base-pairing of C75 with G2553 of 23S rRNA accelerates peptide bond formation, presumably by stabilizing the peptidyl transferase center in its productive conformation. When C74 is also present in the substrate analog, the reaction is slowed down considerably, indicating a slow step in substrate binding to the active site, which limits the reaction rate. The tRNA-rRNA interactions lead to a robust reaction that is insensitive to pH changes or base substitutions in 23S rRNA at the active site of the ribosome.

  12. Intramolecular Oxyl Radical Coupling Promotes O-O Bond Formation in a Homogeneous Mononuclear Mn-based Water Oxidation Catalyst: A Computational Mechanistic Investigation.

    PubMed

    Crandell, Douglas W; Xu, Song; Smith, Jeremy M; Baik, Mu-Hyun

    2017-04-04

    The mechanism of water oxidation performed by a recently discovered manganese pyridinophane catalyst [Mn(Py2N(t)Bu2)(H2O)2](2+) is studied using density functional theory methods. A complete catalytic cycle is constructed and the catalytically active species is identified to consist of a Mn(V)-bis(oxo) moiety that is generated from the resting state by a series of proton-coupled electron transfer reactions. Whereas the electronic ground state of this key intermediate is found to be a triplet, the most favorable pathway for O-O bond formation is found on the quintet potential energy surface and involves an intramolecular coupling of two oxyl radicals with opposite spins bound to the Mn-center that adopts an electronic structure most consistent formally with a high-spin Mn(III) ion. Therefore, the thermally accessible high-spin quintet state that constitutes a typical and innate property of a first-row transition metal center plays a critical role for catalysis. It enables facile electron transfer between the oxo moieties and the Mn-center and promotes O-O bond formation via a radical coupling reaction with a calculated reaction barrier of only 14.7 kcal mol(-1). This mechanism of O-O coupling is unprecedented and provides a novel possible pathway to coupling two oxygen atoms bound to a single metal site.

  13. C-Cl bond activation and catalytic hydrodechlorination of hexachlorobenzene by cobalt and nickel complexes with sodium formate as a reducing agent.

    PubMed

    Li, Junye; Li, Xiaoyan; Wang, Lin; Hu, Qingping; Sun, Hongjian

    2014-05-14

    A benzyne cobalt complex, Co(η(2)-C6Cl4)(PMe3)3 (2), was generated from the reaction of hexachlorobenzene with 2 equiv. of Co(PMe3)4 through selective activation of two C-Cl bonds of hexachlorobenzene. Meanwhile, the byproduct CoCl2(PMe3)3 was also confirmed by IR spectra. The cobalt(II) complex, CoCl(C6Cl5)(PMe3)3 (1), as an intermediate in the formation of aryne complex 2, was also isolated by the reaction of hexachlorobenzene with the stoichiometric amount of Co(PMe3)4. Complex 2 could be obtained by the reaction of 1 with Co(PMe3)4. Under similar reaction conditions, the reaction of Ni(PMe3)4 with hexachlorobenzene afforded only a mono-(C-Cl) bond activation nickel(II) complex, NiCl(C6H5)(PMe3)2 (5). The expected benzyne nickel complex was not formed. The structures of complexes 2 and 5 were determined by X-ray single crystal diffraction. Successful selective hydrodechlorinations of hexachlorobenzene were studied and in the presence of Co(PMe3)4 or Ni(PMe3)4 as catalysts and sodium formate as a reducing agent pentachlorobenzene and 1,2,4,5-tetrachlorobenzene were obtained. The catalytic hydrodechlorination mechanism is proposed and discussed.

  14. Large Scale Solid Phase Synthesis of Peptide Drugs: Use of Commercial Anion Exchange Resin as Quenching Agent for Removal of Iodine during Disulphide Bond Formation

    PubMed Central

    Reddy, K. M. Bhaskara; Kumari, Y. Bharathi; Mallikharjunasarma, Dokka; Bulliraju, Kamana; Sreelatha, Vanjivaka; Ananda, Kuppanna

    2012-01-01

    The S-acetamidomethyl (Acm) or trityl (Trt) protecting groups are widely used in the chemical synthesis of peptides that contain one or more disulfide bonds. Treatment of peptides containing S-Acm protecting group with iodine results in simultaneous removal of the sulfhydryl protecting group and disulfide formation. However, the excess iodine needs to be quenched or adsorbed as quickly as possible after completion of the disulfide bond formation in order to minimize side reactions that are often associated with the iodination step. We report here a simple method for simultaneous quenching and removal of iodine and isolation of disulphide bridge peptides. The use of excess inexpensive anion exchange resin to the oxidized peptide from the aqueous acetic acid/methanol solution affords quantitative removal of iodine and other color impurities. This improves the resin life time of expensive chromatography media that is used in preparative HPLC column during the purification of peptide using preparative HPLC. Further, it is very useful for the conversion of TFA salt to acetate in situ. It was successfully applied commercially, to the large scale synthesis of various peptides including Desmopressin, Oxytocin, and Octreotide. This new approach offers significant advantages such as more simple utility, minimal side reactions, large scale synthesis of peptide drugs, and greater cost effectiveness. PMID:23118772

  15. Bonding, moment formation, and magnetic interactions in Ca14MnBi11 and Ba14MnBi11

    NASA Astrophysics Data System (ADS)

    Sánchez-Portal, D.; Martin, Richard M.; Kauzlarich, S. M.; Pickett, W. E.

    2002-04-01

    ``14-1-11'' phase compounds, based on magnetic Mn ions and typified by Ca14MnBi11 and Ba14MnBi11, show an unusual magnetic behavior, but the large number (104) of atoms in the primitive cell has precluded any previous full electronic structure study. Using an efficient, local-orbital-based method within the local-spin-density approximation to study the electronic structure, we find a gap between a bonding valence-band complex and an antibonding conduction-band continuum. The bonding bands lack one electron per formula unit of being filled, making them low carrier density p-type metals. The hole resides in the MnBi4 tetrahedral unit, and partially compensates for the high-spin d5 Mn moment, leaving a net spin near 4μB that is consistent with experiment. These manganites are composed of two disjoint but interpenetrating ``jungle gym'' networks of spin-4/2 MnBi9-4 units with ferromagnetic interactions within the same network, and weaker couplings between the networks whose sign and magnitude is sensitive to materials parameters. Ca14MnBi11 is calculated to be ferromagnetic as observed, while for Ba14MnBi11 (which is antiferromagnetic) the ferromagnetic and antiferromagnetic states are calculated to be essentially degenerate. The band structure of the ferromagnetic states is very close to half metallic.

  16. When friendship formation goes down the toilet: design features of shared accommodation influence interpersonal bonds and well-being.

    PubMed

    Easterbrook, Matthew J; Vignoles, Vivian L

    2015-03-01

    Despite its omnipresence, the influence of the built environment on human psychology is not well understood. In a five-wave longitudinal study, we investigated whether physical design features within shared student accommodation predicted the frequency of coincidental meetings between new flatmates, and whether these meetings predicted the strength of their interpersonal bonds and psychological well-being. Multilevel latent growth modelling on responses from 462 new university residents supported our hypotheses: Respondents living in flats with design features that encouraged the use of communal areas--a shared common area and an absence of ensuite toilets--reported unintentionally meeting their flatmates more frequently within their flats. This in turn predicted the initial strength of their interpersonal bonds with their flatmates, which in turn positively predicted their well-being. These effects were maintained throughout the 10-week study. Our findings provide an empirical basis for the development of shared housing designed to foster positive relationships and well-being among residents. © 2014 The British Psychological Society.

  17. Experimental Study of the Rate of Bond Formation Betwwen Individual Receptor-Coated Spheres and Ligand-Bearing Surfaces

    NASA Astrophysics Data System (ADS)

    Pierres, Anne; Benoliel, Anne-Marie; Bongrand, Pierre

    1996-06-01

    The efficiency of cell adhesion is highly dependent on the rate of association between adhesion molecules when membranes are at bonding distances. Whereas kinetic parameters of interactions involving at least one soluble molecular species have been extensively studied, the definition and experimental determination of corresponding parameters when both receptors and ligands are bound to surfaces are much more difficult to achieve. In the present work, we explore the feasibility of measuring the rate of association between antibody-coated spheres and antigen-derivatized surfaces in presence of an hydrodynamic shear force lower than the strength of a single bond. An image analysis procedure allows continuous recording of particle position with about 0.05 μm accuracy and a time resolution of 5 milliseconds. We present an original procedure allowing direct determination of the wall shear rate by processing the images of moving spheres. Further, simultaneous determination of the Brownian fluctuations perpendicular to the bulk fluid motion and the mean translational velocity of particles allows in principle a numerical determination of the sphere-to-substrate distance within a range of about 10 to 1000 nm. It is concluded that: i) particle motion is in rough agreement with current hydrodynamic theories based on creeping flow approximation. ii) In our experimental system adhesion seems to be diffusion-limited, therefore, only a lower boundary for the kinetic constant of molecular association can be obtained. iii) Further improvement of our method will require the production of molecularly smooth receptor-coated surfaces.

  18. Light-induced hydrogen evolution from hydrogenated amorphous silicon: Hydrogen diffusion by formation of bond centered hydrogen

    NASA Astrophysics Data System (ADS)

    Tanimoto, H.; Arai, H.; Mizubayashi, H.; Yamanaka, M.; Sakata, I.

    2014-02-01

    The light-induced hydrogen evolution (LIHE) from amorphous (a-) Si:H by the order of at. % is observed during white light soaking (WLS) of 100-400 mW/cm2 at 350-500 K or ultra violet light soaking (UVLS) of 30-120 mW/cm2 at 305-320 K in a vacuum. The thermal desorption spectroscopy indicates that LIHE originated from bonded hydrogen takes place through the diffusion of light-induced mobile hydrogen (LIMH) with the activation energy of 0.5 eV. LIMH is assigned to bond centered hydrogen and the hydrogen diffusion process becomes prominent when LIMH can leave from a-Si:H such under light soaking in a vacuum above room temperature. For H2 in microvoids, the hydrogen evolution rate is governed by the surface barrier and its activation energy of 1.0 eV in dark decreases to 0.4 eV under WLS or UVLS.

  19. 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.

  20. On the Enthalpy of Formation of Hydroxyl Radical and Gas-Phase Bond Dissociation Energies of Water and Hydroxyl

    SciTech Connect

    Ruscic, Branko; Wagner, Albert F.; Harding, Lawerence B.; Asher, Robert L.; Feller, David F. ); Dixon, David A. ); Peterson, Kirk A.; Song, Yang; Qian, Ximei; Ng, C Y.; Liu, Jianbo; Wenwu, Chen

    2001-12-01

    Several photoionization experiments utilizing the positive ion cycle to derive the O-H bond energy converge to a consensus value of AE0(OH+/H2O)= 146117? 24 cm-1 (18.1162? 0.0030 eV). With the most accurate currently available ZEKE value. IE(OH)= 104989? 2 cm-1, corroborated by a number of photoelectron measurements,Error! Bookmark not defined.,Error! Bookmark not defined.,Error! Bookmark not defined.,Error! Bookmark not defined. this leads to D0(H?OH)= 41128? 24 cm-1= 117.59? 0.07 kcal/mol. This corresponds to DHf 0(OH)= 8.85? 0.07 kcal/mol, and implies D0(OH)= 35593? 24 cm-1= 101.76? 0.07 kcal/mol. The most sophisticated theoretical calculations performed so far on the HxO system, CCSD(T)/aug-cc-pVnZ, n=Q, 5, 6, and 7, extrapolated to the CBS limit and including corrections for core-valence effects, scalar relativistic effects, incomplete correlation recovery, and diagonal Born-Oppenheimer corrections reproduce the experimental results to within 0.0 - 0.2 k cal/mol. The new values of the two successive bond dissociation energies of water supersede the previously accepted values,Error! Bookmark not defined.,Error! Bookmark not defined. which were based on spectroscopic determinationsError! Bookmark not defined.,Error! Bookmark not defined. of D0(OH) using a very short Birge-Sponer extrapolation on OH/OD A1S+. An exhaustive analysis of the latter approach, combined with the application of the same procedure on a calculated potential energy curve for the state in question, demonstrates that the Birge-Sponer extrapolation underestimates the bond dissociation energy, in spite of the fact that only the last vibrational level was not observed experimentally. The new values affect a large number of other thermochemical quantities which directly or indirectly rely on or refer to D0(H-OH), D0(OH), or DHf?(OH).

  1. A theoretical investigation into the strength of N-NO2 bonds, ring strain and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX.

    PubMed

    Wang, Bao-Guo; Ren, Fu-de; Shi, Wen-Jing

    2015-11-01

    Changes in N-NO2 bond strength, ring strain energy and electrostatic potential upon formation of intermolecular H-bonds between HF and the nitro group in nitrogen heterocyclic rings C n H2n N-NO2 (n = 2-5), RDX and HMX were investigated using DFT-B3LYP and MP2(full) methods with the 6-311++G(2df,2p) and aug-cc-pVTZ basis sets. Analysis of electron density shifts was also carried out. The results indicate that H-bonding energy correlates well with the increment of ring strain energy. Upon complex formation, the strength of the N-NO2 trigger-bond is enhanced, suggesting reduced sensitivity, while judged by the increased ring strain energy, sensitivity is increased. However, some features of the molecular surface electrostatic potential, such as a local maximum above the N-NO2 bond and ring, σ + (2) and electrostatic balance parameter ν, remain essentially unchanged upon complex formation, and only a small change in the impact sensitivity h 50 is suggested. It is not sufficient to determine sensitivity solely on the basis of trigger bond or ring strain; as a global feature of a molecule, the molecular surface electrostatic potential is available to help judge the change of sensitivity in H-bonded complexes. Graphical Abstract The strengthened N-NO2 bond suggests reduced sensitivity, while it is reverse by theincreased ring strain energy upon the complex formation. However, the molecular surfaceelectrostatic potential (V S) shows the little change of h 50. The V S should be taken into accountin the analysis of explosive sensitivity in the H-bonded complex.

  2. An Infrared Spectroscopic Study on the Formation of the Hydrogen Bonded Inclusion-Structures in the Protonated Metnanol Water Clusters

    NASA Astrophysics Data System (ADS)

    Katada, Marusu; Hsu, Po-Jen; Fujii, Asuka; Kuo, Jer-Lai

    2016-06-01

    We measured IR spectra of the protonated methanol-water mixed clusters (H+(CH3OH)n(H2O)1, n =6 - 10) in the OH stretching vibrational region. Spectra of their Ar tagged clusters were also measured to explore hydrogen-bonded structure changes by the vibrational cooling. The temperature dependence of the isomer distribution was also examined by the harmonic superposition approximation (HSA) simulation. No essential change of the structures with the Ar tagging (lowering of temperature) was concluded in the size range of n = 8 - 10, indicating the remarkable stability of the inclusion structures in this size range. On the other hand, at n = 7, the large isomer distribution change with the Ar tagging is suggested. Moreover, at n = 6, the IR spectrum showed dramatic changes upon the Ar tagging. The protonated site switching from water to methanol well explained these observed changes.

  3. Formation of a Room Temperature Stable FeV(O) Complex: Reactivity Toward Unactivated C–H Bonds

    PubMed Central

    Ghosh, Munmun; Singh, Kundan K.; Panda, Chakadola; Weitz, Andrew; Hendrich, Michael P.; Collins, Terrence J.; Dhar, Basab B.; Gupta, Sayam Sen

    2016-01-01

    An FeV(O) complex has been synthesized from equimolar solutions of (Et4N)2[FeIII(Cl)(biuret-amide)] and mCPBA in CH3CN at room temperature. The FeV(O) complex has been characterized by UV–vis, EPR, Mössbauer, and HRMS and shown to be capable of oxidizing a series of alkanes having C–H bond dissociation energies ranging from 99.3 kcal mol−1 (cyclohexane) to 84.5 kcal mol−1 (cumene). Linearity in the Bell–Evans–Polayni graph and the finding of a large kinetic isotope effect suggest that hydrogen abstraction is engaged the rate-determining step. PMID:24387595

  4. Synthesis of bicyclic organo-peptide hybrids via oxime/intein-mediated macrocyclization followed by disulfide bond formation.

    PubMed

    Smith, Jessica M; Hill, Nicholas C; Krasniak, Peter J; Fasan, Rudi

    2014-02-21

    A new strategy is described to generate bicyclic peptides that incorporate non-peptidic backbone elements starting from recombinant polypeptide precursors. These compounds are produced via a one-pot, two-step sequence, in which peptide macrocyclization by means of a bifunctional oxyamine/1,3-amino-thiol synthetic precursor is followed by intramolecular disulfide formation between the synthetic precursor-borne thiol and a cysteine embedded in the peptide sequence. This approach was found to be compatible with the cysteine residue occupying different positions within 8mer and 10mer target peptide sequences and across different synthetic precursor scaffolds, thereby enabling the formation of a variety of diverse bicyclic scaffolds.

  5. Importance of multicenter bonding in the structure of Si 3C 3

    NASA Astrophysics Data System (ADS)

    Mühlhäuser, Max; Froudakis, Georgios; Zdetsis, Aristides; Peyerimhoff, Sigrid D.

    1993-03-01

    We have investigated the nature of the chemical bonding in the ground state of the Si 3C 3 cluster on the ab initio level. In this state the molecule shows a pyramid-like structure of C s geometry, which is stabilized against competing structures by the formation of the multicenter bonds. This finding is supported by two kinds of population analysis. In order to facilitate future experimental characterization, we have also calculated 1s chemical shifts, the dipole moment, harmonic vibrational frequencies and IR intersites for this system.

  6. Sulphur-radical control on petroleum formation rates

    USGS Publications Warehouse

    Lewan, M.D.

    1998-01-01

    Most petroleum is formed through the partial decomposition of kerogen (an insoluble sedimentary organic material) in response to thermal stress during subsurface burial in a sedimentary basin. Knowing the mechanisms and kinetics of this process allows the determination of the extent and timing of petroleum formation, which, in turn, are critical for evaluating the potential for petroleum occurrences within a sedimentary basin. Kinetic models of petroleum generation are derived mainly from pyrolysis experiments, in which it is usually assumed that formation rates are controlled by the strength of the bonds within the precursor compounds: this agrees with the observation that petroleum formation rates increase with increasing sulphur content of thermally immature kerogen, C-S bonds being weaker than C-C bonds. However, this explanation fails to account for the overall composition of petroleum. Here I argue, on the basis of pyrolysis experiments, that it is the presence of sulphur radicals, rather than the relative weakness of C-S bonds, that controls petroleum formation rates. My findings suggest that the rate of petroleum formation depends critically on the concentration of sulphur radicals generated during the initial stages of thermal maturation. The proposed mechanism appears to provide a realistic explanation for both the overall composition of petroleum and the observed variation in formation rates.

  7. Radical formation in the FMN-photosensitized reactions of unsaturated fatty acids bearing double bonds at different positions.

    PubMed

    Nishihama, Nao; Iwahashi, Hideo

    2016-08-15

    Although the reaction mechanisms through which flavin mononucleotide works as an endogenous photosensitizer have been investigated (Baier et al., 2006; Edwards and Silva, 2001; Pajares et al., 2001; Criado et al., 2003; Massad et al., 2008) [23-27], few studies have been performed for the reactions of flavin mononucleotide with unsaturated fatty acids. To examine the reactions of flavin mononucleotide with unsaturated fatty acids bearing a double bond at different positions, an electron spin resonance, a high performance liquid chromatography-electron spin resonance and a high performance liquid chromatography-electron spin resonance-mass spectrometry were employed. The control reaction mixtures contained 25μmolL(-1) of flavin mononucleotide, 1.0mmolL(-1) of FeSO4(NH4)2SO4, 10mmolL(-1) of cholic acid, 30mmolL(-1) of phosphate buffer (pH 7.4) and 0.1molL(-1) of α-(4-pyridyl-1-oxide)-N-tert-butylnitrone in deuterium oxide. In addition, it also contained 4.3mmolL(-1) of one of the following: (z)-11-octadecenoic acid, (z)-6-octadecenoic acid, (z)-9-octadecenoic acid or (z, z)-9, 12-octadecadienoic acid. The control reaction mixtures without FeSO4(NH4)2SO4 and α-(4-pyridyl-1-oxide)-N-tert-butylnitrone were exposed to the visible light at 436nm (7.8Jcm(-2)). After the irradiation, α-(4-pyridyl-1-oxide)-N-tert-butylnitrone was added. The reactions started from adding FeSO4(NH4)2SO4 and performed at 25°C for 1min. Electron spin resonance measurements of the control reaction mixtures showed prominent signals (α(N)=1.58mT and α(Hβ)=0.26mT). High performance liquid chromatography-electron spin resonance analyses of the control reaction mixtures showed prominent peaks at the retention times of 31.1min {(z)-6-octadecenoic acid}, 39.6min {(z)-9-octadecenoic acid}, 44.9min {(z)-11-octadecenoic acid} and 40.2min {(z, z)-9, 12-octadecadienoic acid}. High performance liquid chromatography-electron spin resonance-mass analyses of the control reaction mixtures showed that 4

  8. Identification of an oxidative refolding intermediate of recombinant consensus interferon from inclusion bodies and design of a two-stage strategy to promote correct disulfide-bond formation.

    PubMed

    Liu, Yong-Dong; Zhang, Gui-Feng; Li, Jing-Jing; Chen, Jing; Wang, Yin-Jue; Ding, Hong; Su, Zhi-Guo

    2007-12-01

    Dilution refolding of recombinant consensus IFN (interferon) from inclusion bodies suffers from low yield. A stable intermediate was found to mix with the correct product and to have an antiviral activity of less than 10% of the latter. This intermediate would form precipitates upon removal of the precipitation inhibitor arginine. Compared with the native protein, the intermediate moved more slowly on non-reducing SDS/PAGE. The CD and fluorescence spectra indicated that it had formed a native-like structure, but had only one disulfide bond: Cys(29)-Cys(139). Further evidence showed that the formation of Cys(29)-Cys(139) is specific and very likely to happen, even in the presence of a high concentration of reducing agent, whereas pairing of the other disulfide (Cys(1)-Cys(99)) needed a stronger oxidative condition. It competed with intermolecular disulfide bonding to form covalent oligomers. On the basis of this discovery, a two-stage refolding step strategy was designed that employed a modified dilution refolding step followed by a dialysis refolding step. The first stage used a high concentration of reducing agent together with the precipitation inhibitor arginine. The purpose was to hinder any reaction through Cys(1) or Cys(99) but allow the intramolecular disulfide bonding of Cys(29)-Cys(139). The second stage was a dialysis step that gradually increased the oxidative agent concentration and simultaneously decreased the arginine concentration. The refolding yield was increased from 35 to 82%, while the mass recovery was increased from 60 to 96%. Moreover, this strategy could suppress precipitation even after arginine was completely removed.

  9. Paleobotany and palynology of the Bristol Hill Coal Member (Bond Formation) and Friendsville Coal Member (Mattoon Formation) of the Illinois Basin (Upper Pennsylvanian)

    USGS Publications Warehouse

    Willard, D.A.; Phillips, T.L.

    1993-01-01

    Late Pennsylvanian coal swamps of the Illinois Basin were dominated by Psarnius tree ferns with a spatially heterogeneous distribution of medullosan pteridosperms (subdominant), calamites, sigillarian lycopsids, and cordaites. Miospore and coal-ball plant assemblages from the Missourian-age Bristol Hill Coal Member (Mattoon Formation) of southeastern Illinois were quantified to analyze vegetational patterns in Late Pennsylvanian peat swamps and to compare vegetational composition of the coals. -from Authors

  10. Peptide bond formation through gas-phase reactions in the interstellar medium: formamide and acetamide as prototypes

    SciTech Connect

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2014-09-20

    A theoretical study of the reactions of NH{sub 4}{sup +} with formaldehyde and CH{sub 5}{sup +} with formamide is carried out. The viability of these gas-phase ion-molecule reactions as possible sources of formamide and acetamide under the conditions of interstellar medium is evaluated. We report a theoretical estimation of the reaction enthalpies and an analysis of their potential energy surfaces. Formation of protonated formamide from the reaction between ammonium cation and formaldehyde is an exothermic process, but all the channels located on the potential energy surface leading to this product present net activation energies. For the reaction between methanium and formamide, different products are possible from a thermodynamic point of view. An analysis of its potential energy surface showed that formation of protonated acetamide and amino acetaldehyde takes place through barrier-free paths. Therefore, this reaction could be a feasible source of acetamide and amino acetaldehyde in space.

  11. Peptide Bond Formation through Gas-phase Reactions in the Interstellar Medium: Formamide and Acetamide as Prototypes

    NASA Astrophysics Data System (ADS)

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2014-09-01

    A theoretical study of the reactions of NH_4+ with formaldehyde and CH_5+ with formamide is carried out. The viability of these gas-phase ion-molecule reactions as possible sources of formamide and acetamide under the conditions of interstellar medium is evaluated. We report a theoretical estimation of the reaction enthalpies and an analysis of their potential energy surfaces. Formation of protonated formamide from the reaction between ammonium cation and formaldehyde is an exothermic process, but all the channels located on the potential energy surface leading to this product present net activation energies. For the reaction between methanium and formamide, different products are possible from a thermodynamic point of view. An analysis of its potential energy surface showed that formation of protonated acetamide and amino acetaldehyde takes place through barrier-free paths. Therefore, this reaction could be a feasible source of acetamide and amino acetaldehyde in space.

  12. Tetrapeptide-coumarin conjugate 3D networks based on hydrogen-bonded charge transfer complexes: gel formation and dye release.

    PubMed

    Guo, Zongxia; Gong, Ruiying; Jiang, Yi; Wan, Xiaobo

    2015-08-14

    Oligopeptide-based derivatives are important synthons for bio-based functional materials. In this article, a Gly-(L-Val)-Gly-(L-Val)-coumarin (GVGV-Cou) conjugate was synthesized, which forms 3D networks in ethanol. The gel nanostructures were characterized by UV-vis spectroscopy, FT-IR spectroscopy, X-ray diffraction (XRD), SEM and TEM. It is suggested that the formation of charge transfer (CT) complexes between the coumarin moieties is the main driving force for the gel formation. The capability of the gel to encapsulate and release dyes was explored. Both Congo Red (CR) and Methylene Blue (MB) can be trapped in the CT gel matrix and released over time. The present gel might be used as a functional soft material for guest encapsulation and release.

  13. Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure, phosphate activation and montmorillonite composition on phosphodiester bond formation

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; KAMALUDDIN; Ertem, Gozen

    1990-01-01

    The 2(prime)-d-5(prime)-GMP and 2(prime)-d-5(prime)-AMP bind 2 times more strongly to montmorillonite 22A than do 2(prime)-d-5(prime)-CMP and 5(prime)-TMP. The dinucleotide d(pG)2 forms in 9.2 percent yield and the cyclic dinucleotide c(dpG)2 in 5.4 percent yield in the reaction of 2(prime)-d-5(prime)-GMP with EDAC in the presence of montmorillonite 22A. The yield of dimers which contain the phosphodiester bond decreases as the reaction medium is changed from 0.2 M NaCl to a mixture of 0.2 M NaCl and 0.075 M MgCl2. A low yield of d(pA)2 was observed in the condensation reaction of 5(prime)-ImdpA on montmorillonite 22A. The yield of d(pA)2 obtained when EDAC is used as the condensing agent increases with increasing iron content of the Na(+)-montmorillonite used as catalyst. Evidence is presented which shows that the acidity of the Na(+)-montmorillonite is a necessary but not sufficient factor for the montmorillonite catalysis of phosphodiester bond formation.

  14. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation

    PubMed Central

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A.; Koehler, Peter; Delcour, Jan A.

    2015-01-01

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing. PMID:26193081

  15. Trimethylsilylmethyl complexes of the rare-earth metals with sterically hindered N-heterocyclic carbene ligands: adduct formation and C-H bond activation.

    PubMed

    Fegler, Waldemar; Spaniol, Thomas P; Okuda, Jun

    2010-08-07

    Tris(trimethylsilylmethyl) complexes of yttrium and lutetium [LnR(3)(THF)(2)] (R = CH(2)SiMe(3)) were treated with sterically bulky N-heterocyclic carbenes (NHC) 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr) and 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene (IMes). IPr gave labile mono-adducts [LnR(3)(NHC)], isolated as thermally robust crystals and fully characterized by NMR spectroscopy and X-ray diffraction. IMes gave a similar lutetium mono-adduct [LuR(3)(IMes)] with the lutetium alkyl [LuR(3)(THF)(2)], whereas the yttrium alkyl [YR(3)(THF)(2)] resulted in the formation of an ortho-metalated product. This compound, isolated as a crystalline bis(THF) adduct, contains a strained six-membered chelate ring that has been formed by the C-H bond activation of one of the ortho-methyl groups of the mesityl group. In contrast [LuR(3)(IMes)] only slowly underwent a similar C-H bond activation.

  16. Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure, phosphate activation and montmorillonite composition on phosphodiester bond formation

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; KAMALUDDIN; Ertem, Gozen

    1990-01-01

    The 2(prime)-d-5(prime)-GMP and 2(prime)-d-5(prime)-AMP bind 2 times more strongly to montmorillonite 22A than do 2(prime)-d-5(prime)-CMP and 5(prime)-TMP. The dinucleotide d(pG)2 forms in 9.2 percent yield and the cyclic dinucleotide c(dpG)2 in 5.4 percent yield in the reaction of 2(prime)-d-5(prime)-GMP with EDAC in the presence of montmorillonite 22A. The yield of dimers which contain the phosphodiester bond decreases as the reaction medium is changed from 0.2 M NaCl to a mixture of 0.2 M NaCl and 0.075 M MgCl2. A low yield of d(pA)2 was observed in the condensation reaction of 5(prime)-ImdpA on montmorillonite 22A. The yield of d(pA)2 obtained when EDAC is used as the condensing agent increases with increasing iron content of the Na(+)-montmorillonite used as catalyst. Evidence is presented which shows that the acidity of the Na(+)-montmorillonite is a necessary but not sufficient factor for the montmorillonite catalysis of phosphodiester bond formation.

  17. A Novel Strategy for Biomass Upgrade: Cascade Approach to the Synthesis of Useful Compounds via C-C Bond Formation Using Biomass-Derived Sugars as Carbon Nucleophiles.

    PubMed

    Yamaguchi, Sho; Baba, Toshihide

    2016-07-20

    Due to the depletion of fossil fuels, biomass-derived sugars have attracted increasing attention in recent years as an alternative carbon source. Although significant advances have been reported in the development of catalysts for the conversion of carbohydrates into key chemicals (e.g., degradation approaches based on the dehydration of hydroxyl groups or cleavage of C-C bonds via retro-aldol reactions), only a limited range of products can be obtained through such processes. Thus, the development of a novel and efficient strategy targeted towards the preparation of a range of compounds from biomass-derived sugars is required. We herein describe the highly-selective cascade syntheses of a range of useful compounds using biomass-derived sugars as carbon nucleophiles. We focus on the upgrade of C2 and C3 oxygenates generated from glucose to yield useful compounds via C-C bond formation. The establishment of this novel synthetic methodology to generate valuable chemical products from monosaccharides and their decomposed oxygenated materials renders carbohydrates a potential alternative carbon resource to fossil fuels.

  18. Formation of a Trifluorophosphane Platinum(II) Complex by P-F Bond Activation of Phosphorus Pentafluoride with a Pt(0) Complex.

    PubMed

    Arnold, Nicole; Bertermann, Rüdiger; Bickelhaupt, F Matthias; Braunschweig, Holger; Drisch, Michael; Finze, Maik; Hupp, Florian; Poater, Jordi; Sprenger, Jan A P

    2017-05-02

    The reaction of PF5 with [(Cy3 P)2 Pt] gave the PF3 complex trans-[(Cy3 P)2 PtF(PF3 )][PF6 ], which was characterized by single-crystal X-ray diffraction, multinuclear NMR spectroscopy, and elemental analysis. To the best of our knowledge, this reaction is the first example of the oxidative addition of a P-F bond to a transition metal and is a rare example of an activation of a main-group-element-fluorine bond by a metal. Relativistic DFT calculations showed that the formation of the Lewis pair [(Cy3 P)2 Pt→PF5 ], which was not observed even at low temperatures, represents the initial step of the reaction. From this key intermediate, the cation trans-[(Cy3 P)2 PtF(PF3 )](+) was furnished by a two-step mechanism involving, successively, a second and a third PF5 molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair

    NASA Astrophysics Data System (ADS)

    Kaul, Corinna; Müller, Markus; Wagner, Mirko; Schneider, Sabine; Carell, Thomas

    2011-10-01

    The universal genetic code relies on two hydrogen-bonded Watson-Crick base pairs that can form 64 triplet codons. This places a limit on the number of amino acids that can be encoded, which has motivated efforts to create synthetic base pairs that are orthogonal to the natural ones. An additional base pair would result in another 61 triplet codons. Artificial organic base pairs have been described in enzymatic incorporation studies, and inorganic T-Hg-T and C-Ag-C base pairs have been reported to form in primer extension studies. Here, we demonstrate a metal base pair that is fully orthogonal and can be replicated, and can even be amplified by polymerase chain reaction in the presence of the canonical pairs dA:dT and dG:dC. Crystal structures of a dS-Cu-dS base pair inside a polymerase show that reversible chemistry is possible directly inside the polymerase, which enables the efficient copying of the inorganic crosslink. The results open up the possibility of replicating and amplifying artificial inorganic DNA nanostructures by extending the genetic alphabet.

  20. Identification of Coevolving Residues and Coevolution Potentials Emphasizing Structure, Bond Formation and Catalytic Coordination in Protein Evolution

    PubMed Central

    Little, Daniel Y.; Chen, Lu

    2009-01-01

    The structure and function of a protein is dependent on coordinated interactions between its residues. The selective pressures associated with a mutation at one site should therefore depend on the amino acid identity of interacting sites. Mutual information has previously been applied to multiple sequence alignments as a means of detecting coevolutionary interactions. Here, we introduce a refinement of the mutual information method that: 1) removes a significant, non-coevolutionary bias and 2) accounts for heteroscedasticity. Using a large, non-overlapping database of protein alignments, we demonstrate that predicted coevolving residue-pairs tend to lie in close physical proximity. We introduce coevolution potentials as a novel measure of the propensity for the 20 amino acids to pair amongst predicted coevolutionary interactions. Ionic, hydrogen, and disulfide bond-forming pairs exhibited the highest potentials. Finally, we demonstrate that pairs of catalytic residues have a significantly increased likelihood to be identified as coevolving. These correlations to distinct protein features verify the accuracy of our algorithm and are consistent with a model of coevolution in which selective pressures towards preserving residue interactions act to shape the mutational landscape of a protein by restricting the set of admissible neutral mutations. PMID:19274093