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Sample records for c-s bond formation

  1. Manganese-catalyzed regiospecific sp(3) C-S bond formation through C-C bond cleavage of cyclobutanols.

    PubMed

    Ren, Rongguo; Wu, Zhen; Zhu, Chen

    2016-06-21

    A manganese-catalyzed regioselective sp(3) C-S bond formation through C-C bond cleavage of cyclobutanols is described. A variety of primary and secondary alkyl thioethers are efficiently prepared under mild reaction conditions. The mechanistic pathways involving radical-mediated tandem C-C bond cleavage and C-S bond formation are proposed. PMID:27279018

  2. 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. PMID:25435202

  3. Copper-Catalyzed Domino Synthesis of 2-Arylthiochromanones through Concomitant C-S Bond Formations Using Xanthate as Sulfur Source.

    PubMed

    Sangeetha, Subramani; Muthupandi, Pandi; Sekar, Govindasamy

    2015-12-18

    An efficient domino process for the synthesis of thioflavanones has been described using a copper catalyst without addition of any external ligand. A variety of thioflavanones have been synthesized from easily accessible 2'-iodochalcones or 2'-bromochalcones in excellent yield through in situ incorporation of sulfur using xanthate as an odorless sulfur source. This domino process proceeds through Cu-catalyzed C(aryl)-S bond formation by the coupling reaction of xanthate with 2'-halochalcones followed by C-S bond cleavage of thioester then S-C bond formation by intramolecular Michael addition. PMID:26642368

  4. Catalytic C-N, C-O, and C-S Bond Formation Promoted by Organoactinide Complexes

    NASA Astrophysics Data System (ADS)

    Eisen, Moris S.

    Throughout this last decade, we have witnessed impressively how the chemistry of electrophilic d0/fn actinides has been prospering either in their new synthetic approaches reaching very interesting compounds or in their use in stoichiometric and catalytic reactions leading to high levels of complexity. The unique rich and complex features of organoactinides prompted the development of this field toward catalysis in demanding chemical transformations. In this review, we present a brief and selective survey of the recent developments in homogenous catalysis of organoactinide complexes, especially toward the formation of new C-N, C-O, and C-S bonds. We start by presenting the synthesis and characterization of the corresponding organoactinide complexes, followed by the homogeneous catalytic chemical transformations that include the hydroamination of terminal alkynes, the polymerization of ɛ-caprolactone and L-lactide, the reduction of azides and hydrazines by high-valent organouranium complexes, the hydrothiolation of terminal alkynes, and the catalytic Tishchenko reaction. For each reaction, the scope and the thermodynamic, kinetic, and mechanistic aspects are presented.

  5. Application of Thio-Ugi Adducts for the Preparation of Benzo[b]thiophene and S-Heterocycle Library via Copper Catalyzed Intramolecular C-S Bond Formation.

    PubMed

    Kim, Yong-Sang; Kwak, Se Hun; Gong, Young-Dae

    2015-06-01

    Fused heterocycles, such as benzo[b]thiophene, thiochroman, benzo[b][1,4]thiazine, and 1,4-benzothiazepine were generated from thio-Ugi adducts containing a thioamide group through copper-catalyzed intramolecular C-S bond formation under microwave irradiation. PMID:25961783

  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. PMID:26332253

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

    PubMed

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

    2012-08-01

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

  8. Cu(II)-mediated C-S/N-S bond formation via C-H activation: access to benzoisothiazolones using elemental sulfur.

    PubMed

    Chen, Fa-Jie; Liao, Gang; Li, Xin; Wu, Jun; Shi, Bing-Feng

    2014-11-01

    A copper-mediated C-S/N-S bond-forming reaction via C-H activation that uses elemental sulfur has been developed. The addition of TBAI was found to be crucial for the success of this transformation. The method is scalable, shows excellent functional group tolerance, and is compatible with heterocycle substrates, providing efficient and practical access to benzoisothiazolones. The direct diversification of the benzoisothiazolone products into a variety of sulfur-containing compounds is also demonstrated. PMID:25325568

  9. 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.

  10. 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.

  11. Bond activation with an apparently benign ethynyl dithiocarbamate Ar-C≡C-S-C(S)NR2.

    PubMed

    Ung, Gaël; Frey, Guido D; Schoeller, Wolfgang W; Bertrand, Guy

    2011-10-10

    The hedgehog molecule: A simple ethynyl dithiocarbamate [Ar-C≡C-S-C(S)NR(2)] is able to cleave a broad range of enthalpically strong σ bonds and to activate carbon dioxide and elemental sulfur. Depending on the substrate, the bond activation process involves either the existence of an equilibrium with the nonobservable mesoionic carbene isomer or the cooperation of the nucleophilic carbon-carbon triple bond and the electrophilic CS carbon atom. PMID:23210141

  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. Sulfur in coal: Model studies of the role of ArS radicals in C-C and C-S bond formation and structural evolution in coal liquefaction

    SciTech Connect

    Alnajjar, M.S.; Franz, J.A.

    1987-06-01

    Experiments in this paper show the importance of thiyl radicals in sulfur containing coals during coal liquefaction processes. The presence of arylthiyl radicals enhances the cleavage of C-C, C=C, and C=C bonds in these otherwise refactory systems. Abstraction reactions, 1,2-phenyl migration from sulfur to carbon and displacement reactions at sulfur may be important mechanisms of structural evolution during liquefaction. In addition to cleavage of arylalkyl structures, the results also show that undesirable retrograde formation of inert diaryl- and triarylmethanes may be a consequence of the presence of sulfur and the attending aryl thiol structures. Thus, while a reaction medium including sulfur and hydrogen has been demonstrated to lead to the enhance cleavage of the bibenzyl model structure the present results suggest that retrograde reactions may be significant undesired pathways in coal liquefaction in the presence of sulfur. 17 refs.

  14. Rhodium-Catalyzed ipso-Borylation of Alkylthioarenes via C-S Bond Cleavage.

    PubMed

    Uetake, Yuta; Niwa, Takashi; Hosoya, Takamitsu

    2016-06-01

    Rhodium-catalyzed transformation of alkyl aryl sulfides into arylboronic acid pinacol esters via C-S bond cleavage is reported. In combination with transition-metal-catalyzed sulfanyl group-guided regioselective C-H borylation reactions of alkylthioarenes, this method allows the synthesis of a diverse range of multisubstituted arenes. PMID:27210907

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. Protein folding guides disulfide bond formation

    PubMed Central

    Qin, Meng; Wang, Wei; Thirumalai, D.

    2015-01-01

    The Anfinsen principle that the protein sequence uniquely determines its structure is based on experiments on oxidative refolding of a protein with disulfide bonds. The problem of how protein folding drives disulfide bond formation is poorly understood. Here, we have solved this long-standing problem by creating a general method for implementing the chemistry of disulfide bond formation and rupture in coarse-grained molecular simulations. As a case study, we investigate the oxidative folding of bovine pancreatic trypsin inhibitor (BPTI). After confirming the experimental findings that the multiple routes to the folded state contain a network of states dominated by native disulfides, we show that the entropically unfavorable native single disulfide [14–38] between Cys14 and Cys38 forms only after polypeptide chain collapse and complete structuring of the central core of the protein containing an antiparallel β-sheet. Subsequent assembly, resulting in native two-disulfide bonds and the folded state, involves substantial unfolding of the protein and transient population of nonnative structures. The rate of [14–38] formation increases as the β-sheet stability increases. The flux to the native state, through a network of kinetically connected native-like intermediates, changes dramatically by altering the redox conditions. Disulfide bond formation between Cys residues not present in the native state are relevant only on the time scale of collapse of BPTI. The finding that formation of specific collapsed native-like structures guides efficient folding is applicable to a broad class of single-domain proteins, including enzyme-catalyzed disulfide proteins. PMID:26297249

  1. [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.

  2. Femtosecond quantum control of molecular bond formation

    PubMed Central

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

    2010-01-01

    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. PMID:20505117

  3. 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

  4. 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.

  5. 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

  6. Protein Nanopatterns by Oxime Bond Formation

    PubMed Central

    Christman, Karen L.; Broyer, Rebecca M.; Schopf, Eric; Kolodziej, Christopher M.; Chen, Yong; Maynard, Heather D.

    2011-01-01

    Patterning proteins at the nanoscale is important for applications in biology and medicine. As feature sizes are reduced, it is critical that immobilization strategies provide site-specific attachment of the biomolecules. In this study, oxime chemistry was exploited to conjugate proteins onto nanometer-sized features. Poly(Boc-aminooxy tetra(ethylene glycol) methacrylate) was synthesized by free radical polymerization. The polymer was patterned onto silicon wafers using an electron beam writer. Trifluoroacetic acid removal of the Boc groups provided the desired aminooxy functionality. In this manner, patterns of concentric squares and contiguous bowtie shapes were fabricated with 150–170 nm wide features. Ubiquitin modified at the N-terminus with an α-ketoamide group and Nε-levulinyl lysine modified bovine serum albumin were subsequently conjugated to the polymer nanopatterns. Protein immobilization was confirmed by fluorescence microscopy. Control studies on protected surfaces and using proteins presaturated with O-methoxyamine indicated that attachment occurred via oxime bond formation. PMID:21192671

  7. Protein nanopatterns by oxime bond formation.

    PubMed

    Christman, Karen L; Broyer, Rebecca M; Schopf, Eric; Kolodziej, Christopher M; Chen, Yong; Maynard, Heather D

    2011-02-15

    Patterning proteins on the nanoscale is important for applications in biology and medicine. As feature sizes are reduced, it is critical that immobilization strategies provide site-specific attachment of the biomolecules. In this study, oxime chemistry was exploited to conjugate proteins onto nanometer-sized features. Poly(Boc-aminooxy tetra(ethylene glycol) methacrylate) was synthesized by free radical polymerization. The polymer was patterned onto silicon wafers using an electron beam writer. Trifluoroacetic acid removal of the Boc groups provided the desired aminooxy functionality. In this manner, patterns of concentric squares and contiguous bowtie shapes were fabricated with 150-170-nm wide features. Ubiquitin modified at the N-terminus with an α-ketoamide group and N(ε)-levulinyl lysine-modified bovine serum albumin were subsequently conjugated to the polymer nanopatterns. Protein immobilization was confirmed by fluorescence microscopy. Control studies on protected surfaces and using proteins presaturated with O-methoxyamine indicated that attachment occurred via oxime bond formation. PMID:21192671

  8. Novel carbon–carbon bond formations for biocatalysis

    PubMed Central

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

    2011-01-01

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

  9. 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

  10. Resolving the molecular mechanism of cadherin catch bond formation

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    Classical cadherin Ca2+-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 Ca2+ 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 Ca2+ concentration is decreased, fewer de novo hydrogen bonds are formed and catch bond formation is eliminated.

  11. 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.

  12. 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

  13. Creating σ-holes through the formation of beryllium bonds.

    PubMed

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

    2015-09-01

    Through the use of ab initio theoretical models based on MP2/aug-cc-pVDZ-optimized geometries and CCSD(T)/aug-cc-pVTZ and CCSD(T)/aug-c-pVDZ total energies, it has been shown that the significant electron density rearrangements that follow the formation of a beryllium bond may lead to the appearance of a σ-hole in systems that previously do not exhibit this feature, such as CH3 OF, NO2 F, NO3 F, and other fluorine-containing systems. The creation of the σ-hole is another manifestation of the bond activation-reinforcement (BAR) rule. The appearance of a σ-hole on the F atoms of CH3 OF is due to the enhancement of the electronegativity of the O atom that participates in the beryllium bond. This atom recovers part of the charge transferred to Be by polarizing the valence density of the F into the bonding region. An analysis of the electron density shows that indeed this bond becomes reinforced, but the F atom becomes more electron deficient with the appearance of the σ-hole. Importantly, similar effects are also observed even when the atom participating in the beryllium bond is not directly attached to the F atom, as in NO2 F, NO3 F, or NCF. Hence, whereas the isolated CH3 OF, NO2 F, and NO3 F are unable to yield F⋅⋅⋅Base halogen bonds, their complexes with BeX2 derivatives are able to yield such bonds. Significant cooperative effects between the new halogen bond and the beryllium bond reinforce the strength of both noncovalent interactions. PMID:26212472

  14. Diacetoxyiodobenzene assisted C-O bond formation via sequential acylation and deacylation process: synthesis of benzoxazole amides and their mechanistic study by DFT.

    PubMed

    Nahakpam, Lokendrajit; Chipem, Francis A S; Chingakham, Brajakishor S; Laitonjam, Warjeet S

    2016-08-10

    An efficient method for the transformation of N-substituted-N'-benzoylthioureas to substituted N-benzoxazol-2-yl-amides using diacetoxyiodobenzene (DIB) is described in this work. The transformation follows the C-O bond formation leading to the benzoxazole derivative, due to oxidative dehydrogenation by DIB, instead of the expected C-S bond formation of the benzothiazole moiety. The C-O bond formation leading to benzoxazole is due to consecutive acylation and deacylation in conjunction with the reduction of two moles of DIB. A plausible mechanism was proposed for the reaction and density functional calculations were also performed to study the reaction mechanism. PMID:27461562

  15. Electrochemical controlling and monitoring of halogen bond formation in solution.

    PubMed

    Groni, Sihem; Maby-Raud, Tanguy; Fave, Claire; Branca, Mathieu; Schöllhorn, Bernd

    2014-12-01

    Cyclic voltammetry has been used for the first time to probe and to control the formation of non-covalent halogen bonding (XB) via redox switching. These results strongly encourage the use of electrochemistry as an economical and precisely controllable tool for the investigation of XB in solution. PMID:25313384

  16. 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. PMID:26308392

  17. 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

    2008-06-01

    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. PMID:18418826

  18. Ribosomal crystallography: peptide bond formation and its inhibition.

    PubMed

    Bashan, Anat; Zarivach, Raz; Schluenzen, Frank; Agmon, Ilana; Harms, Joerg; Auerbach, Tamar; Baram, David; Berisio, Rita; Bartels, Heike; Hansen, Harly A S; Fucini, Paola; Wilson, Daniel; Peretz, Moshe; Kessler, Maggie; Yonath, Ada

    2003-09-01

    Ribosomes, the universal cellular organelles catalyzing the translation of genetic code into proteins, are protein/RNA assemblies, of a molecular weight 2.5 mega Daltons or higher. They are built of two subunits that associate for performing protein biosynthesis. The large subunit creates the peptide bond and provides the path for emerging proteins. The small has key roles in initiating the process and controlling its fidelity. Crystallographic studies on complexes of the small and the large eubacterial ribosomal subunits with substrate analogs, antibiotics, and inhibitors confirmed that the ribosomal RNA governs most of its activities, and indicated that the main catalytic contribution of the ribosome is the precise positioning and alignment of its substrates, the tRNA molecules. A symmetry-related region of a significant size, containing about two hundred nucleotides, was revealed in all known structures of the large ribosomal subunit, despite the asymmetric nature of the ribosome. The symmetry rotation axis, identified in the middle of the peptide-bond formation site, coincides with the bond connecting the tRNA double-helical features with its single-stranded 3' end, which is the moiety carrying the amino acids. This thus implies sovereign movements of tRNA features and suggests that tRNA translocation involves a rotatory motion within the ribosomal active site. This motion is guided and anchored by ribosomal nucleotides belonging to the active site walls, and results in geometry suitable for peptide-bond formation with no significant rearrangements. The sole geometrical requirement for this proposed mechanism is that the initial P-site tRNA adopts the flipped orientation. The rotatory motion is the major component of unified machinery for peptide-bond formation, translocation, and nascent protein progression, since its spiral nature ensures the entrance of the nascent peptide into the ribosomal exit tunnel. This tunnel, assumed to be a passive path for the

  19. 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. PMID:26251952

  20. Hydrophobic interactions and hydrogen bonds in β-sheet formation

    NASA Astrophysics Data System (ADS)

    Narayanan, Chitra; Dias, Cristiano L.

    2013-09-01

    In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for β-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimers adopt β-sheet conformations at short interpeptide distances (ξ ˜ 0.5 nm) and at intermediate distances (˜0.8 nm), valine and leucine homodimers assume cross-β-like conformations with side chains interpenetrating each other. These two states are identified as minima in the potential of mean force. While the number of interpeptide hydrogen bonds increases with decreasing interpeptide distance, the total hydrogen bond number in the system does not change significantly, suggesting that formation of β-sheet structures from extended conformations is not driven by hydrogen bonds. This is supported by an increase in electrostatic energy at short interpeptide distances. A remarkable correlation between the volume of the system and the total electrostatic energy is observed, further reinforcing the idea that excluding water in proteins comes with an enthalpic penalty. We also discuss microscopic mechanisms accounting for β-sheet formation based on computed enthalpy and entropy and we show that they are different for peptides with small and large side chains.

  1. 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.

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

    SciTech Connect

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

    2012-12-15

    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 Degree-Sign C. TEM/EDS and NBED results combined with SF calculation revealed the evidence of metastable {theta} Prime -CuAl{sub 2} IMC phase (tetragonal, space group: I4m2, 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 {theta} Prime -CuAl{sub 2} 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 {theta} Prime -CuAl{sub 2}, which can minimize lattice mismatch for {theta} Prime -CuAl{sub 2} to grow on Cu.

  3. Signatures of bond formation and bond scission dynamics in dissociative electron attachment to methane.

    PubMed

    Douguet, N; Slaughter, D S; Adaniya, H; Belkacem, A; Orel, A E; Rescigno, T N

    2015-10-14

    We present a combined experimental and theoretical investigation of the dynamics and angular dependence of dissociative electron attachment to methane. We show that a triply degenerate (T2) Feshbach resonance is responsible for the broad 10 eV dissociation peak in methane. This resonance alone is shown to correlate asymptotically to the various dissociation channels observed experimentally. The molecular-frame entrance amplitude for electron attachment is calculated for each component of the threefold degenerate resonance. By investigating the topology of the anion potential energy surfaces, we deduce the main pathways to two- and three-body breakup channels involving both bond scission and bond formation. The computed fragment angular distributions reproduce the main trends of the experimental measurements. PMID:26371546

  4. Bond formation in ultrasonically welded aluminum sheet metal

    NASA Astrophysics Data System (ADS)

    Wilkosz, Daniel Edward

    Ultrasonic welding (USW), a solid state joining technology, has been used to bond aluminum alloys commonly used in the automotive industry. Bonding occurs due to USW's high frequency (˜20 kHz) in-plane vibration of sample interfaces while being held under moderate clamp pressure normal to the plane of vibration. Vibration and clamp pressure are transmitted into bond formation via contact with a weld-tip. To better understand how weld-tip geometry affected bond formation, experiments were conducted to quantify how tip geometry influenced plastic deformation characteristics between fully welded coupons of 0.9mm thick AA6111-T4 aluminum alloy. Weld-interface microstructure features were documented by optical microscopy and features quantified in a 19 point matrix. Correlation between microstructure features, such as rolling-wakes, and resulting weld bond strengths of more than 3.0kN is made. Weld zone microstructure features appear to result from deformation at and severe migration of the original weld interface during USW. To confirm this hypothesis, intrinsic and extrinsic markers were employed to monitor weld interface deformation characteristics. Various physical and analytical techniques were used in conjunction with these markers to show that joining of "like" and "dislike" aluminum samples is achieved through mechanical mixing of mating interfaces and not by elemental diffusion. It is also hypothesized that severe deformation of the original interface would result in areas of high residual strain within a formed weld zone. To investigate this and the influence that tip geometry may have on residual strain, fully welded samples were annealed at 500°C for a controlled period of time and recovery, recrystallization and grain growth characteristics were monitored. In all welds, initial recrystallization and grain growth occurred at the outer ends of weld zones and along weld interfaces where the most turbulent mixing and grain size reduction was observed

  5. Comparison of the kinetics and thermodynamics for methyl radical addition to C=C, C=O, and C=S double bonds.

    PubMed

    Henry, David J; Coote, Michelle L; Gómez-Balderas, Rodolfo; Radom, Leo

    2004-02-18

    The barriers, enthalpies, and rate constants for the addition of methyl radical to the double bonds of a selection of alkene, carbonyl, and thiocarbonyl species (CH(2)=Z, CH(3)CH=Z, and (CH(3))(2)C=Z, where Z = CH(2), O, or S) and for the reverse beta-scission reactions have been investigated using high-level ab inito calculations. The results are rationalized with the aid of the curve-crossing model. The addition reactions proceed via early transition structures in all cases. The barriers for addition of methyl radical to C=C bonds are largely determined by the reaction exothermicities. Addition to the unsubstituted carbon center of C=C double bonds is favored over addition to the substituted carbon center, both kinetically (lower barriers) and thermodynamically (greater exothermicities). The barriers for addition to C=O bonds are influenced by both the reaction exothermicity and the singlet-triplet gap of the substrate. Addition to the carbon center is favored over addition to the oxygen, also both thermodynamically and kinetically. For the thiocarbonyl systems, addition to the carbon center is thermodynamically favored over addition to sulfur. However, in this case, the reaction is contrathermodynamic, addition to the sulfur center having a lower barrier due to spin density considerations. Entropic differences among corresponding addition and beta-scission reactions are relatively minor, and the differences in reaction rates are thus dominated by differences in the respective reaction barriers. PMID:14871104

  6. Recognition of a novel type X═N-Hal···Hal (X = C, S, P; Hal = F, Cl, Br, I) halogen bonding.

    PubMed

    Gushchin, Pavel V; Kuznetsov, Maxim L; Haukka, Matti; Kukushkin, Vadim Yu

    2013-04-01

    The chlorination of the eight-membered platinum(II) chelates [PtCl2{NH═C(NR2)N(Ph)C(═NH)N(Ph)C(NR2)═NH}] (R = Me (1); R2 = (CH2)5 (2)) with uncomplexed imino group with Cl2 gives complexes bearing the ═N-Cl moiety [PtCl4{NH═C(NR2)N(Ph)C(═NCl)N(Ph)C(NR2)═NH}] (R = Me (3); R2 = (CH2)5 (4)). X-ray study for 3 revealed a novel type intermolecular halogen bonding ═N-Cl···Cl(-), formed between the Cl atom of the chlorinated imine and the chloride bound to the platinum(IV) center. The processing relevant structural data retrieved from the Cambridge Structural Database (CSDB) shows that this type of halogen bonding is realized in 18 more molecular species having X═N-Hal moieties (X = C, P, S, V, W; Hal = Cl, Br, I), but this weak ═N-Hal···Hal(-) bonding was totally neglected in the previous works. The presence of the halogen bonding in 3 was confirmed by theoretical calculations at the density functional theory (DFT, M06-2X) level, and its nature was analyzed. PMID:23469756

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

    PubMed

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

    2015-11-01

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

  8. Hydrogen Bond Formation between the Carotenoid Canthaxanthin and the Silanol Group on MCM-41 Surface.

    PubMed

    Gao, Yunlong; Xu, Dayong; Kispert, Lowell D

    2015-08-20

    The formation of one or two hydrogen bonds (H-bonds) between canthaxanthin (CAN), a dye, and the silanol group(s) on the MCM-41 surface has been studied by density functional theory (DFT) calculations and calorimetric experiments. It was found that the formation of the H-bond(s) stabilized the CAN molecule more than its radical cation (CAN(•+)). The charge distribution, bond lengths, and the HOMO and LUMO energies of CAN are also affected. The formation of the H-bond(s) explains the lower photoinduced electron transfer efficiency of CAN imbedded in Cu-MCM-41 versus that for β-carotene (CAR) imbedded in Cu-MCM-41 where complex formation with Cu(2+) dominates. These calculations show that to achieve high electron transfer efficiency for a dye-sensitized solar cell, H-bonding between the dye and the host should be avoided. PMID:26230844

  9. Formation of disulfide bonds in insect prophenoloxidase enhances immunity through improving enzyme activity and stability.

    PubMed

    Lu, Anrui; Peng, Qin; Ling, Erjun

    2014-06-01

    Type 3 copper proteins, including insect prophenoloxidase (PPO), contain two copper atoms in the active site pocket and can oxidize phenols. Insect PPO plays an important role in immunity. Insects and other invertebrates show limited recovery from pathogen invasion and wounds if phenoloxidase (PO) activity is low. In most insect PPOs, two disulfide bonds are present near the C-terminus. However, in Pimpla hypochondriaca (a parasitoid wasp), each PPO contains one disulfide bond. We thus questioned whether the formation of two sulfide bonds in insect PPOs improved protein stability and/or increased insect innate immunity over time. Using Drosophila melanogaster PPO1 as a model, one or two disulfide bonds were deleted to evaluate the importance of disulfide bonds in insect immunity. rPPO1 and mutants lacking disulfide bonds could be expressed and showed PO activity. However, the PO activities of mutants lacking one or two disulfide bonds significantly decreased. Deletion of disulfide bonds also reduced PPO thermostability. Furthermore, antibacterial activities against Escherichia coli and Bacillus subtilis significantly decreased when disulfide bonds were deleted. Therefore, the formation of two disulfide bond(s) in insect PPO enhances antibacterial activity by increasing PO activity and stability. PMID:24480295

  10. Enhancement of L-selectin, but not P-selectin, bond formation frequency by convective flow.

    PubMed

    Paschall, Christopher D; Guilford, William H; Lawrence, Michael B

    2008-02-01

    L-selectin-mediated leukocyte rolling has been proposed to require a high rate of bond formation compared to that of P-selectin to compensate for its much higher off-rate. To test this hypothesis, a microbead system was utilized to measure relative L-selectin and P-selectin bond formation rates on their common ligand P-selectin glycoprotein ligand-1 (PSGL-1) under shear flow. Using video microscopy, we tracked selectin-coated microbeads to detect the formation frequency of adhesive tether bonds. From velocity distributions of noninteracting and interacting microbeads, we observed that tether bond formation rates for P-selectin on PSGL-1 decreased with increasing wall shear stress, from 0.14 +/- 0.04 bonds/microm at 0.2 dyn/cm(2) to 0.014 +/- 0.003 bonds/microm at 1.0 dyn/cm(2). In contrast, L-selectin tether bond formation increased from 0.017 +/- 0.005 bonds/microm at 0.2 dyn/cm(2) to 0.031 +/- 0.005 bonds/microm at 1.0 dyn/cm(2). L-selectin tether bond formation rates appeared to be enhanced by convective transport, whereas P-selectin rates were inhibited. The transition force for the L-selectin catch-slip transition of 44 pN/bond agreed well with theoretical models (Pereverzev et al. 2005. Biophys. J. 89:1446-1454). Despite catch bond behavior, hydrodymanic shear thresholding was not detected with L-selectin beads rolling on PSGL-1. We speculate that shear flow generated compressive forces may enhance L-selectin bond formation relative to that of P-selectin and that L-selectin bonds with PSGL-1 may be tuned for the compressive forces characteristic of leukocyte-leukocyte collisions during secondary capture on the blood vessel wall. This is the first report, to our knowledge, comparing L-selectin and P-selectin bond formation frequencies in shear flow. PMID:17890384

  11. Formation of Silicon-Gold Eutectic Bond Using Localized Heating Method

    NASA Astrophysics Data System (ADS)

    Lin, Liwei; Cheng, Yu-Ting; Najafi, Khalil

    1998-11-01

    A new bonding technique is proposed by using localized heating to supplythe bonding energy.Heating is achieved by applying a dc current through micromachined heaters made of gold which serves as both the heating and bonding material.At the interface of silicon and gold, the formation of eutectic bond takes place in about 5 minutes.Assembly of two substrates in microfabrication processescan be achieved by using this method.In this paper the following important results are obtained:1) Gold diffuses into silicon to form a strong eutectic bond by means of localized heating.2) The bonding strength reaches the fracture toughness of the bulk silicon.3) This bonding technique greatly simplifies device fabrication andassembly processes.

  12. 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

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

    PubMed

    O'Neal, Kristi L; Weber, Stephen G

    2009-01-01

    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. PMID:19195102

  14. 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

  15. 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.

  16. 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. PMID:23891473

  17. "Pnicogen bonds" or "chalcogen bonds": exploiting the effect of substitution on the formation of PSe noncovalent bonds.

    PubMed

    Shukla, Rahul; Chopra, Deepak

    2016-05-18

    In this article, we have analyzed the nature and characteristics of PSe noncovalent interactions by studying the effect of substitution on XH2PSeH2, H3PSeHX and XH2PSeHX (X= -H, -F, -CH3, -CF3, -Cl, -OH, -OCH3, -NH2, -NHCH3, and -CN) as our systems of interest at MP2/aug-cc-pVDZ level of theory. Binding energy calculations depict that binding energy increases in the order XH2PSeH2 < H3PSeHX < XH2PSeHX with the nature of the substituent having a direct effect on the strength of the interactions. PSe contacts as short as 2.52 Å were observed and analyzed in our study. The energy values for PSe contacts were found to exist in the range of -1.20 kcal mol(-1) to -7.89 kcal mol(-1). The topological analysis confirms the presence of PSe contacts in all the complexes with characteristics similar to hydrogen bonds. NBO analysis helped in categorizing these interactions into pnicogen and chalcogen bonds, depending on the strength of P(lp) to σ*(Se-X) orbitals or Se(lp) to σ*(P-X) orbitals. PMID:27145973

  18. Formation of Halogen Bond-Based 2D Supramolecular Assemblies by Electric Manipulation.

    PubMed

    Zheng, Qing-Na; Liu, Xuan-He; Chen, Ting; Yan, Hui-Juan; Cook, Timothy; Wang, Dong; Stang, Peter J; Wan, Li-Jun

    2015-05-20

    Halogen bonding has attracted much attention recently as an important driving force for supramolecular assembly and crystal engineering. Herein, we demonstrate for the first time the formation of a halogen bond-based open porous network on a graphite surface using ethynylpyridine and aryl-halide based building blocks. We found that the electrical stimuli of a scanning tunneling microscopy (STM) tip can induce the formation of a binary supramolecular structure on the basis of halogen bond formation between terminal pyridyl groups and perfluoro-iodobenzene. This electrical manipulation method can be applied to engineer a series of linear or porous structures by selecting halogen bond donor and acceptor fragments with different symmetries, as the directional interactions ultimately determine the structural outcome. PMID:25948133

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

    NASA Astrophysics Data System (ADS)

    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.

  20. Mechanistic studies of carbonate macrocyclization: Rates of carbonate bond formation

    SciTech Connect

    Aquino, E.; Brittain, W.J.; Brunelle, D.J.

    1993-12-31

    High yields of cyclic oligomeric carbonates can be prepared using an amine-catalyzed reaction of bisphenol A-bischloroformate. The authors have studied the kinetics of this carbonate macrocyclization by the isolated study of key chemical events. Using stopped-flow FT-IR spectroscopy, it was found that the rate of carbonate formation between the intermediate acyl ammonium salt (1) and 4-isopropylphenol (4-IPP) is the same for tributylamine, triethylamine and diethylmethylamine. Previously, it was found that conversion of 1 to urethane was also insensitive to amine structure while the formation of 1 is profoundly dependent on amine structure.

  1. Direct observation of bond formation in solution with femtosecond X-ray scattering

    NASA Astrophysics Data System (ADS)

    Kim, Kyung Hwan; Kim, Jong Goo; Nozawa, Shunsuke; Sato, Tokushi; Oang, Key Young; Kim, Tae Wu; Ki, Hosung; Jo, Junbeom; Park, Sungjun; Song, Changyong; Sato, Takahiro; Ogawa, Kanade; Togashi, Tadashi; Tono, Kensuke; Yabashi, Makina; Ishikawa, Tetsuya; Kim, Joonghan; Ryoo, Ryong; Kim, Jeongho; Ihee, Hyotcherl; Adachi, Shin-Ichi

    2015-02-01

    The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2-]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of ~500 femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-ångström spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.

  2. Formation of RNA phosphodiester bond by histidine-containing dipeptides.

    PubMed

    Wieczorek, Rafał; Dörr, Mark; Chotera, Agata; Luisi, Pier Luigi; Monnard, Pierre-Alain

    2013-01-21

    A new scenario for prebiotic formation of nucleic acid oligomers is presented. Peptide catalysis is applied to achieve condensation of activated RNA monomers into short RNA chains. As catalysts, L-dipeptides containing a histidine residue, primarily Ser-His, were used. Reactions were carried out in self-organised environment, a water-ice eutectic phase, with low concentrations of reactants. Incubation periods up to 30 days resulted in the formation of short oligomers of RNA. During the oligomerisation, an active intermediate (dipeptide-mononucleotide) is produced, which is the reactive species. Details of the mechanism and kinetics, which were elucidated with a set of control experiments, further establish that the imidazole side chain of a histidine at the carboxyl end of the dipeptide plays a crucial role in the catalysis. These results suggest that this oligomerisation catalysis occurs by a transamination mechanism. Because peptides are much more likely products of spontaneous condensation than nucleotide chains, their potential as catalysts for the formation of RNA is interesting from the origin-of-life perspective. Finally, the formation of the dipeptide-mononucleotide intermediate and its significance for catalysis might also be viewed as the tell-tale signs of a new example of organocatalysis. PMID:23255284

  3. Shear band formation in plastic bonded explosive (PBX)

    SciTech Connect

    Dey, T.N.; Johnson, J.N.

    1997-07-01

    Adiabatic shear bands can be a source of ignition and lead to detonation. At low to moderate deformation rates, 10-1000/s , two other mechanisms can also give rise to shear bands. These mechanisms are: 1) softening caused by microcracking and 2) a constitutive response with a non-associated flow rule as is observed in granular material such as soil. Brittle behavior at small strains and the granular nature of HMX suggest that PBX-9501 constitutive behavior may be similar to sand. A constitutive model for the first of these mechanisms is studied in a series of calculations. This viscoelastic constitutive model for PBX-9501 softens via a statistical crack model. A sand model is used to provide a non-associated flow rule and detailed results will be reported elsewhere. Both models generate shear band formation at 1-2% strain at nominal strain rates at and below 1000/s. Shear band formation is suppressed at higher strain rates. Both mechanisms may accelerate the formation of adiabatic shear bands.

  4. Cuprous Oxide Catalyzed Oxidative C-C Bond Cleavage for C-N Bond Formation: Synthesis of Cyclic Imides from Ketones and Amines.

    PubMed

    Wang, Min; Lu, Jianmin; Ma, Jiping; Zhang, Zhe; Wang, Feng

    2015-11-16

    Selective oxidative cleavage of a C-C bond offers a straightforward method to functionalize organic skeletons. Reported herein is the oxidative C-C bond cleavage of ketone for C-N bond formation over a cuprous oxide catalyst with molecular oxygen as the oxidant. A wide range of ketones and amines are converted into cyclic imides with moderate to excellent yields. In-depth studies show that both α-C-H and β-C-H bonds adjacent to the carbonyl groups are indispensable for the C-C bond cleavage. DFT calculations indicate the reaction is initiated with the oxidation of the α-C-H bond. Amines lower the activation energy of the C-C bond cleavage, and thus promote the reaction. New insight into the C-C bond cleavage mechanism is presented. PMID:26494312

  5. Modern Transition-Metal-Catalyzed Carbon-Halogen Bond Formation.

    PubMed

    Petrone, David A; Ye, Juntao; Lautens, Mark

    2016-07-27

    The high utility of halogenated organic compounds has prompted the development of a vast number of transformations which install the carbon-halogen motif. Traditional routes to these building blocks have commonly involved multiple steps, harsh reaction conditions, and the use of stoichiometric and/or toxic reagents. In this regard, using transition metals to catalyze the synthesis of organohalides has become a mature field in itself, and applying these technologies has allowed for a decrease in the production of waste, higher levels of regio- and stereoselectivity, and the ability to produce enantioenriched target compounds. Furthermore, transition metals offer the distinct advantage of possessing a diverse spectrum of mechanistic possibilities which translate to the capability to apply new substrate classes and afford novel and difficult-to-access structures. This Review provides comprehensive coverage of modern transition metal-catalyzed syntheses of organohalides via a diverse array of mechanisms. Attention is given to the seminal stoichiometric organometallic studies which led to the corresponding catalytic processes being realized. By breaking this field down into the synthesis of aryl, vinyl, and alkyl halides, it becomes clear which methods have surfaced as most favored for each individual class. In general, a pronounced shift toward the use of C-H bonds as key functional groups, in addition to methods which proceed by catalytic, radical-based mechanisms has occurred. Although always evolving, this field appears to be heading in the direction of using starting materials with a significantly lower degree of prefunctionalization in addition to less expensive and abundant metal catalysts. PMID:27341176

  6. Monitoring Backbone Hydrogen-Bond Formation in β-Barrel Membrane Protein Folding.

    PubMed

    Raschle, Thomas; Rios Flores, Perla; Opitz, Christian; Müller, Daniel J; Hiller, Sebastian

    2016-05-10

    β-barrel membrane proteins are key components of the outer membrane of bacteria, mitochondria and chloroplasts. Their three-dimensional structure is defined by a network of backbone hydrogen bonds between adjacent β-strands. Here, we employ hydrogen-deuterium (H/D) exchange in combination with NMR spectroscopy and mass spectrometry to monitor backbone hydrogen bond formation during folding of the outer membrane protein X (OmpX) from E. coli in detergent micelles. Residue-specific kinetics of interstrand hydrogen-bond formation were found to be uniform in the entire β-barrel and synchronized to formation of the tertiary structure. OmpX folding thus propagates via a long-lived conformational ensemble state in which all backbone amide protons exchange with the solvent and engage in hydrogen bonds only transiently. Stable formation of the entire OmpX hydrogen bond network occurs downhill of the rate-limiting transition state and thus appears cooperative on the overall folding time scale. PMID:27062600

  7. Disulfide Bond Formation in the Bacterial Periplasm: Major Achievements and Challenges Ahead

    PubMed Central

    Denoncin, Katleen

    2013-01-01

    Abstract Significance: The discovery of the oxidoreductase disulfide bond protein A (DsbA) in 1991 opened the way to the unraveling of the pathways of disulfide bond formation in the periplasm of Escherichia coli and other Gram-negative bacteria. Correct oxidative protein folding in the E. coli envelope depends on both the DsbA/DsbB pathway, which catalyzes disulfide bond formation, and the DsbC/DsbD pathway, which catalyzes disulfide bond isomerization. Recent Advances: Recent data have revealed an unsuspected link between the oxidative protein-folding pathways and the defense mechanisms against oxidative stress. Moreover, bacterial disulfide-bond-forming systems that differ from those at play in E. coli have been discovered. Critical Issues: In this review, we discuss fundamental questions that remain unsolved, such as what is the mechanism employed by DsbD to catalyze the transfer of reducing equivalents across the membrane and how do the oxidative protein-folding catalysts DsbA and DsbC cooperate with the periplasmic chaperones in the folding of secreted proteins. Future Directions: Understanding the mechanism of DsbD will require solving the structure of the membranous domain of this protein. Another challenge of the coming years will be to put the knowledge of the disulfide formation machineries into the global cellular context to unravel the interplay between protein-folding catalysts and chaperones. Also, a thorough characterization of the disulfide bond formation machineries at work in pathogenic bacteria is necessary to design antimicrobial drugs targeting the folding pathway of virulence factors stabilized by disulfide bonds. Antioxid. Redox Signal. 19, 63–71. PMID:22901060

  8. 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.

  9. Formation of an unusually short hydrogen bond in photoactive yellow protein.

    PubMed

    Saito, Keisuke; Ishikita, Hiroshi

    2013-03-01

    The photoactive chromophore of photoactive yellow protein (PYP) is p-coumaric acid (pCA). In the ground state, the pCA chromophore exists as a phenolate anion, which is H-bonded by protonated Glu46 (O(Glu46)-O(pCA)=~2.6Å) and protonated Tyr42. On the other hand, the O(Glu46)-O(pCA) H-bond was unusually short (O(Glu46)-O(pCA)=2.47Å) in the intermediate pR(CW) state observed in time-resolved Laue diffraction studies. To understand how the existence of the unusually short H-bond is energetically possible, we analyzed the H-bond energetics adopting a quantum mechanical/molecular mechanical (QM/MM) approach based on the atomic coordinates of the PYP crystal structures. In QM/MM calculations, the O(Glu46)-O(pCA) bond is 2.60Å in the ground state, where Tyr42 donates an H-bond to pCA. In contrast, when the hydroxyl group of Tyr42 is flipped away from pCA, the H-bond was significantly shortened to 2.49Å in the ground state. The same H-bond pattern reproduced the unusually short H-bond in the pR(CW) structure (O(Glu46)-O(pCA)=2.49Å). Intriguingly, the potential-energy profile resembles that of a single-well H-bond, suggesting that the pK(a) values of the donor (Glu46) and acceptor (pCA) moieties are nearly equal. The present results indicate that the "equal pK(a)" requirement for formation of single-well or low-barrier H-bond (LBHB) is satisfied only when Tyr42 does not donate an H-bond to pCA, and argue against the possibility that the O(Glu46)-O(pCA) bond is an LBHB in the ground state, where Tyr42 donates an H-bond to pCA. PMID:23201477

  10. Oxidant regulated inter-subunit disulfide bond formation between ASIC1a subunits

    PubMed Central

    Zha, Xiang-ming; Wang, Runping; Collier, Dan M.; Snyder, Peter M.; Wemmie, John A.; Welsh, Michael J.

    2009-01-01

    The acid-sensing ion channel-1a (ASIC1a) is composed of 3 subunits and is activated by a decrease in extracellular pH. It plays an important role in diseases associated with a reduced pH and production of oxidants. Previous work showed that oxidants reduce ASIC1a currents. However, the effects on channel structure and composition are unknown. We found that ASIC1a formed inter-subunit disulfide bonds and the oxidant H2O2 increased this link between subunits. Cys-495 in the ASIC1a C terminus was particularly important for inter-subunit disulfide bond formation, although other C-terminal cysteines contributed. Inter-subunit disulfide bonds also produced some ASIC1a complexes larger than trimers. Inter-subunit disulfide bond formation reduced the proportion of ASIC1a located on the cell surface and contributed to the H2O2-induced decrease in H+-gated current. These results indicate that channel function is controlled by disulfide bond formation between intracellular residues on distinct ASIC1a subunits. They also suggest a mechanism by which the redox state can dynamically regulate membrane protein activity by forming intracellular bridges. PMID:19218436

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  12. Toxin-induced pore formation is hindered by intermolecular hydrogen bonding in sphingomyelin bilayers.

    PubMed

    García-Linares, Sara; Palacios-Ortega, Juan; Yasuda, Tomokazu; Åstrand, Mia; Gavilanes, José G; Martínez-del-Pozo, Álvaro; Slotte, J Peter

    2016-06-01

    Sticholysin I and II (StnI and StnII) are pore-forming toxins that use sphingomyelin (SM) for membrane binding. We examined how hydrogen bonding among membrane SMs affected the StnI- and StnII-induced pore formation process, resulting in bilayer permeabilization. We compared toxin-induced permeabilization in bilayers containing either SM or dihydro-SM (lacking the trans Δ(4) double bond of the long-chain base), since their hydrogen-bonding properties are known to differ greatly. We observed that whereas both StnI and StnII formed pores in unilamellar vesicles containing palmitoyl-SM or oleoyl-SM, the toxins failed to similarly form pores in vesicles prepared from dihydro-PSM or dihydro-OSM. In supported bilayers containing OSM, StnII bound efficiently, as determined by surface plasmon resonance. However, StnII binding to supported bilayers prepared from dihydro-OSM was very low under similar experimental conditions. The association of the positively charged StnII (at pH7.0) with unilamellar vesicles prepared from OSM led to a concentration-dependent increase in vesicle charge, as determined from zeta-potential measurements. With dihydro-OSM vesicles, a similar response was not observed. Benzyl alcohol, which is a small hydrogen-bonding compound with affinity to lipid bilayer interfaces, strongly facilitated StnII-induced pore formation in dihydro-OSM bilayers, suggesting that hydrogen bonding in the interfacial region originally prevented StnII from membrane binding and pore formation. We conclude that interfacial hydrogen bonding was able to affect the membrane association of StnI- and StnII, and hence their pore forming capacity. Our results suggest that other types of protein interactions in bilayers may also be affected by hydrogen-bonding origination from SMs. PMID:26975250

  13. The CXXC motif: imperatives for the formation of native disulfide bonds in the cell.

    PubMed Central

    Chivers, P T; Laboissière, M C; Raines, R T

    1996-01-01

    The rapid formation of native disulfide bonds in cellular proteins is necessary for the efficient use of cellular resources. This process is catalyzed in vitro by protein disulfide isomerase (PDI), with the PDI1 gene being essential for the viability of Saccharomyces cerevisiae. PDI is a member of the thioredoxin (Trx) family of proteins, which have the active-site motif CXXC. PDI contains two Trx domains as well as two domains unrelated to the Trx family. We find that the gene encoding Escherichia coli Trx is unable to complement PDI1 null mutants of S.cerevisiae. Yet, Trx can replace PDI if it is mutated to have a CXXC motif with a disulfide bond of high reduction potential and a thiol group of low pKa. Thus, an enzymic thiolate is both necessary and sufficient for the formation of native disulfide bonds in the cell. Images PMID:8654363

  14. Synthesis of Spirocyclic Pyrazolones by Oxidative C-N Bond Formation.

    PubMed

    Agejas, Javier; Ortega, Laura

    2015-06-19

    The two-step synthesis of spirocyclic pyrazolone derivatives from simple and commercially available reagents is described. The unusual reaction of 1,3-dicarbonyls with hydrazines and an iodine-mediated oxidative carbon-nitrogen bond formation, joined in a two-step, one-pot reaction, allows the straightforward synthesis of these spirocycles. PMID:26018762

  15. 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

  16. Resummed thermodynamic perturbation theory for bond cooperativity in associating fluids with small bond angles: Effects of steric hindrance and ring formation

    SciTech Connect

    Marshall, Bennett D. Haghmoradi, Amin; Chapman, Walter G.

    2014-04-28

    In this paper we develop a thermodynamic perturbation theory for two site associating fluids which exhibit bond cooperativity (system energy is non-pairwise additive). We include both steric hindrance and ring formation such that the equation of state is bond angle dependent. Here, the bond angle is the angle separating the centers of the two association sites. As a test, new Monte Carlo simulations are performed, and the theory is found to accurately predict the internal energy as well as the distribution of associated clusters as a function of bond angle.

  17. 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.

  18. 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.

  19. 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.

  20. Bond formation of surface-tethered receptor-ligand pairs in relative separation

    NASA Astrophysics Data System (ADS)

    Qian, Jin; Lin, Yuan; Jiang, Hongyuan; Yao, Haimin

    2013-11-01

    We theoretically and numerically investigate the interplay between diffusion of a surface-bound receptor and its reaction with an opposing ligand. Special attention has been paid to the mechanical regulation of bond association by varying the initial gap distance and relative separation speed between the protein-bearing surfaces. Such diffusion-reaction coupling effects can cause the apparent on-rate or reciprocal of the average waiting time for bond formation, to be not constant, but instead a function sensitive to the system parameters that affect the transport of proteins. The results provide a quantitative understanding of how significantly the transport mechanism can affect overall binding behavior of molecular interactions and call for a paradigm shift in modeling receptor-ligand bond association when the protein-bearing surfaces are in relative separation.

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    Bower, John F.; Krische, Michael J.

    The formation of C-C bonds via catalytic hydrogenation and transfer hydrogenation enables carbonyl and imine addition in the absence of stoichiometric organometallic reagents. In this review, iridium-catalyzed C-C bond-forming hydrogenations and transfer hydrogenations are surveyed. These processes encompass selective, atom-economic methods for the vinylation and allylation of carbonyl compounds and imines. Notably, under transfer hydrogenation conditions, alcohol dehydrogenation drives reductive generation of organoiridium nucleophiles, enabling carbonyl addition from the aldehyde or alcohol oxidation level. In the latter case, hydrogen exchange between alcohols and 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.

  3. 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.

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

    PubMed

    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(sp(2))-C(sp(3)) and C(sp(3))-C(sp(3)) 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(sp(2))-C(sp(3)) and C(sp(3))-C(sp(3)) 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(sp(2))-C(sp(3)) and C(sp(3))-C(sp(3)) 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

  5. 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

  6. Drinking alcohol has sex-dependent effects on pair bond formation in prairie voles.

    PubMed

    Anacker, Allison M J; Ahern, Todd H; Hostetler, Caroline M; Dufour, Brett D; Smith, Monique L; Cocking, Davelle L; Li, Ju; Young, Larry J; Loftis, Jennifer M; Ryabinin, Andrey E

    2014-04-22

    Alcohol use and abuse profoundly influences a variety of behaviors, including social interactions. In some cases, it erodes social relationships; in others, it facilitates sociality. Here, we show that voluntary alcohol consumption can inhibit male partner preference (PP) formation (a laboratory proxy for pair bonding) in socially monogamous prairie voles (Microtus ochrogaster). Conversely, female PP is not inhibited, and may be facilitated by alcohol. Behavior and neurochemical analysis suggests that the effects of alcohol on social bonding are mediated by neural mechanisms regulating pair bond formation and not alcohol's effects on mating, locomotor, or aggressive behaviors. Several neuropeptide systems involved in the regulation of social behavior (especially neuropeptide Y and corticotropin-releasing factor) are modulated by alcohol drinking during cohabitation. These findings provide the first evidence to our knowledge that alcohol has a direct impact on the neural systems involved in social bonding in a sex-specific manner, providing an opportunity to explore the mechanisms by which alcohol affects social relationships. PMID:24711424

  7. Drinking alcohol has sex-dependent effects on pair bond formation in prairie voles

    PubMed Central

    Anacker, Allison M. J.; Ahern, Todd H.; Hostetler, Caroline M.; Dufour, Brett D.; Smith, Monique L.; Cocking, Davelle L.; Li, Ju; Young, Larry J.; Loftis, Jennifer M.; Ryabinin, Andrey E.

    2014-01-01

    Alcohol use and abuse profoundly influences a variety of behaviors, including social interactions. In some cases, it erodes social relationships; in others, it facilitates sociality. Here, we show that voluntary alcohol consumption can inhibit male partner preference (PP) formation (a laboratory proxy for pair bonding) in socially monogamous prairie voles (Microtus ochrogaster). Conversely, female PP is not inhibited, and may be facilitated by alcohol. Behavior and neurochemical analysis suggests that the effects of alcohol on social bonding are mediated by neural mechanisms regulating pair bond formation and not alcohol’s effects on mating, locomotor, or aggressive behaviors. Several neuropeptide systems involved in the regulation of social behavior (especially neuropeptide Y and corticotropin-releasing factor) are modulated by alcohol drinking during cohabitation. These findings provide the first evidence to our knowledge that alcohol has a direct impact on the neural systems involved in social bonding in a sex-specific manner, providing an opportunity to explore the mechanisms by which alcohol affects social relationships. PMID:24711424

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

    PubMed Central

    Simonović, Miljan; Steitz, Thomas A.

    2009-01-01

    The ribosome is a large ribonucleoprotein particle that translates zgenetic 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. PMID:19595805

  9. Regulation of the activity of Escherichia coli quinolinate synthase by reversible disulfide-bond formation.

    PubMed

    Saunders, Allison H; Booker, Squire J

    2008-08-19

    Quinolinate synthase (NadA) catalyzes a unique condensation reaction between dihydroxyacetone phosphate and iminoaspartate, yielding inorganic phosphate, 2 mol of water, and quinolinic acid, a central intermediate in the biosynthesis of nicotinamide adenine dinucleotide and its derivatives. The enzyme from Escherichia coli contains a C (291)XXC (294)XXC (297) motif in its primary structure. Bioinformatics analysis indicates that only Cys297 serves as a ligand to a [4Fe-4S] cluster that is required for turnover. In this report, we show that the two remaining cysteines, Cys291 and Cys294, undergo reversible disulfide-bond formation, which regulates the activity of the enzyme. This mode of redox regulation of NadA appears physiologically relevant, since disulfide-bond formation and reduction are effected by oxidized and reduced forms of E. coli thioredoxin. A midpoint potential of -264 +/- 1.77 mV is approximated for the redox couple. PMID:18651751

  10. 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. PMID:24522982

  11. Extraction of pyridines into fluorous solvents based on hydrogen bond complex formation with carboxylic acid receptors.

    PubMed

    O'Neal, Kristi L; Geib, Steven; Weber, Stephen G

    2007-04-15

    A molecular receptor embedded in a 'poor-solvent' receiving phase, such as a fluorous phase, should offer the ideal medium for selective extraction and sensing. The limited solubility of most solutes in fluorous phases enhances selectivity by reducing the extraction of unwanted matrix components. Thus, receptor-doped fluorous phases may be ideal extraction media. Unfortunately, sufficient data do not exist to judge the capability of this approach. The solubilities of very few nonfluorous solutes are known. As far as we are aware, such important quantities as the strength of a hydrogen bond in a fluorous environment are not known. Thus, it is currently impossible to predict whether a particular receptor/solute complex based on a particular set of noncovalent interactions will provide enough thermodynamic stabilization to extract the solute into the fluorous phase. In this work, fluorous carboxylic acids (a carboxylic acid-terminated perfluoropolypropylene oxide called Krytox and perfluorodecanoic acid (PFDA)) were used as receptors and substituted pyridines as solutes to show that the fluorous receptor dramatically enhances the liquid-liquid extraction of the polar substrates from chloroform into perfluorohexanes. The method of continuous variations was used to determine the receptor-pyridine complex stoichiometry of 3:1. The free energies of formation of the 3:1 complexes from one pyridine and 3/2 H-bonded cyclic dimers of the fluorous carboxylic acid are -30.4 (Krytox) and -37.3 kJ mol-1 (PFDA). The free energy required to dissociate the dimer in perfluorohexanes is +16.5 kJ mol-1 (Krytox). The crystal structure of the complex showed a 1:1 stoichiometry with a mixed strong-weak hydrogen-bonded motif. Based on the stoichiometry, crystal structure, and UV and IR spectroscopic shifts, we propose that the 3:1 complex has four hydrogen bonds and the carboxylic acid transfers a proton to pyridine. The resulting pyridinium carboxylate N+H-O- hydrogen bond is accompanied

  12. 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. PMID:25594737

  13. Possible involvement of Escherichia coli 23S ribosomal RNA in peptide bond formation.

    PubMed Central

    Nitta, I; Ueda, T; Watanabe, K

    1998-01-01

    Experimental results are presented suggesting that 23S rRNA is directly involved in the peptide bond formation usually performed on the ribosome. Although several reports have indicated that the eubacterial peptidyltransferase reaction does not necessarily require all the ribosomal proteins, the reconstitution of peptidyltransferase activity by a naked 23S rRNA without the help of any of the ribosomal proteins has not been reported previously. It is demonstrated that an E. coli 23S rRNA transcript synthesized by T7 RNA polymerase in vitro was able to promote peptide bond formation in the presence of 0.5% SDS. The reaction was inhibited by the peptidyltransferase-specific antibiotics chloramphenicol and carbomycin, and by digestion with RNases A and T1. Site-directed mutageneses at two highly conserved regions close to the peptidyltransferase center ring, G2252 to U2252 and C2507G2581 to U2507A2581, also suppressed peptide bond formation. These findings strongly suggest that 23S rRNA is the peptidyltransferase itself. PMID:9510328

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

    PubMed Central

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

    2015-01-01

    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 13C-31P multiple quantum 1H-13C-31P (HCP) experiment in 1H-31P two-dimensional mode directly on a PhpK-catalyzed reaction mixture using 13CH3-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 13CH3 and 31P. Related nuclear magnetic resonance experiments based upon these principles may be designed for the study of enzymatic and/or synthetic chemical reaction mechanisms. PMID:25594737

  15. 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.

  16. Slow-to-fast transition of hydrogen bond dynamics in acetamide hydration shell formation.

    PubMed

    D'Amico, Francesco; Rossi, Barbara; Camisasca, Gaia; Bencivenga, Filippo; Gessini, Alessandro; Principi, Emiliano; Cucini, Riccardo; Masciovecchio, Claudio

    2015-04-28

    The formation of a hydration shell in acetamide aqueous solution has been investigated by means of UV Raman spectroscopy. The experimental results reveal the existence of two distinct regimes of water dynamics. At high acetamide concentration water molecules show a structural and dynamical behavior consistent with the so-called iceberg model. Upon increasing the amount of water we observe the formation of a hydration shell marked by fastening of hydrogen-bond dynamics. Such a behavior may help to shed light on the scientific debate on how water rearranges around the hydrophobic portions of solute molecules (iceberg vs. non-iceberg models). PMID:25824617

  17. Formation and characterization of two interconvertible side-on and end-on bonded beryllium ozonide complexes.

    PubMed

    Zhou, Zijian; Li, Yuzhen; Zhuang, Jia; Wang, Guanjun; Chen, Mohua; Zhao, Yanying; Zheng, Xuming; Zhou, Mingfei

    2011-09-01

    The reactions of beryllium atoms with dioxygen were reinvestigated by matrix isolation infrared absorption spectroscopy. Besides the previously reported linear OBeO and cyclic Be(2)O(2) molecules, two interconvertible beryllium ozonide complexes were prepared and characterized. The BeOBe(η(2)-O(3)) complex was formed on annealing, which is characterized to be a side-on bonded ozonide complex with a planar C(2v) structure. The BeOBe(η(2)-O(3)) complex isomerized to the BeOBe(η(1)-O(3)) isomer under visible light excitation, which is an end-on bonded ozonide complex with planar C(s) symmetry. These two isomers are interconvertible; that is, visible light induces the conversion of the side-on bonded complex to the end-on bonded isomer, and vice versa on annealing. In addition, evidence is also presented for the linear BeOBeOBe cluster. PMID:21806010

  18. 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. PMID:25803829

  19. 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

  20. Tuning the Formation and Rupture of Single Ligand-Receptor Bonds by Hyaluronan-Induced Repulsion

    PubMed Central

    Robert, Philippe; Sengupta, Kheya; Puech, Pierre-Henri; Bongrand, Pierre; Limozin, Laurent

    2008-01-01

    We used a combination of laminar flow chamber and reflection interference microscopy to study the formation and rupture of single bonds formed between Fc-ICAM-1 attached to a substrate and anti-ICAM-1 carried by micrometric beads in the presence of a repulsive hyaluronan (HA) layer adsorbed onto the substrate. The absolute distance between the colloids and the surface was measured under flow with an accuracy of a few nanometers. We could verify the long-term prediction of classical lubrication theory for the movement of a sphere near a wall in a shear flow. The HA polymer layer exerted long-range repulsive steric force on the beads and the hydrodynamics at the boundary remained more or less unchanged. By incubating HA at various concentrations, the thickness of the layer, as estimated by beads most probable height, was tuned in the range 20–200 nm. Frequency of bond formation was decreased by more than one order of magnitude by increasing the thickness of the repulsive layer, while the lifetime of individual bonds was not affected. This study opens the way for further quantitative studies of the effect of molecular environment and separation distance on ligand-receptor association and dissociation. PMID:18599637

  1. Key amino acids of arabidopsis VKOR in the activity of phylloquinone reduction and disulfide bond formation.

    PubMed

    Yang, Xiao-Jian; Cui, Hao-Ran; Yu, Zhi-Bo; Du, Jia-Jia; Xu, Jia-Ning; Wang, Xiao-Yun

    2015-01-01

    Many proteins in chloroplast are regulated through the disulfide bond/thiol transformation to realize their activities. A homologue of VKOR (Vitamin K epoxide reductase) in Arabidopsis chloroplast is found to catalyze the disulfide bond formation in vivo and to mediate the specific phylloquinone reduction in vitro. It is also called LTO1 (Lumen Thiol Oxidoreductase 1). Investigations about functions and essential amino acid residues of AtVKOR have important theoretical significance to clarify the chloroplast redox regulation mechanism. In this study, several amino acids in the VKOR domain of AtVKOR were identified to be involved in binding of phylloquinone. Site-directed mutagenesis was used to study the function of these positions. The results suggested that residues Ser77, Leu87, Phe137 and Leu141 were quite important in the binding and catalyzing the reduction of phylloquinone. These residues were also involved in the electron transferring and disulfide bond formation of substrate proteins by motility assays in vivo, suggesting that the binding of phylloquinone not only affected the delivery of electrons to phylloquinone but also affected the whole electron transfer process. The conserved cysteines in the AtVKOR domain also played critical roles in phylloquinone reduction. When each of the four conserved cysteines was mutated to alanine, the mutants lost reduction activity entirely, suggesting that the four conserved cysteines played crucial roles in the electron transfer process. PMID:25267254

  2. TIMING OF HAMSTER SPERM NUCLEAR DECONDENSATION AND MALE PRONUCLEUS FORMATION IS RELATED TO SPERM NUCLEAR DISULFIDE BOND CONTENT

    EPA Science Inventory

    The relationship between the timing of both sperm nuclear decondensation and male pronucleus formation in the oocyte and the relative level of disulfide bonds within the sperm nucleus was evaluated. Four types of hamster sperm nuclei, in which the extent of S-S bonding differed, ...

  3. Thioether bond formation by SPASM domain radical SAM enzymes: Cα H-atom abstraction in subtilosin A biosynthesis.

    PubMed

    Benjdia, Alhosna; Guillot, Alain; Lefranc, Benjamin; Vaudry, Hubert; Leprince, Jérôme; Berteau, Olivier

    2016-05-01

    AlbA is a radical SAM enzyme catalyzing the formation of three unusual thioether bonds in the antibiotic subtilosin A. We demonstrate here that AlbA catalyzes direct Cα H-atom abstraction and likely contains three essential [4Fe-4S] centers. This leads us to propose novel mechanistic perspectives for thioether bond catalysis by radical SAM enzymes. PMID:27087315

  4. 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

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

    PubMed

    Krylov, Igor B; Vil', Vera A; Terent'ev, Alexander O

    2015-01-01

    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

  6. 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

  7. 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

  8. 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. PMID:24243863

  9. 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

  10. A free-standing condensation enzyme catalyzing ester bond formation in C-1027 biosynthesis.

    PubMed

    Lin, Shuangjun; Van Lanen, Steven G; Shen, Ben

    2009-03-17

    Nonribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of many biologically active peptides and typically are modular, with each extension module minimally consisting of a condensation, an adenylation, and a peptidyl carrier protein domain responsible for incorporation of an amino acid into the growing peptide chain. C-1027 is a chromoprotein antitumor antibiotic whose enediyne chromophore consists of an enediyne core, a deoxy aminosugar, a benzoxazolinate, and a beta-amino acid moiety. Bioinformatics analysis suggested that the activation and incorporation of the beta-amino acid moiety into C-1027 follows an NRPS mechanism whereby biosynthetic intermediates are tethered to the peptidyl carrier protein SgcC2. Here, we report the biochemical characterization of SgcC5, an NRPS condensation enzyme that catalyzes ester bond formation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and (R)-1-phenyl-1,2-ethanediol, a mimic of the enediyne core. SgcC5 uses (S)-3-chloro-5-hydroxy-beta-tyrosyl-SgcC2 as the donor substrate and exhibits regiospecificity for the C-2 hydroxyl group of the enediyne core mimic as the acceptor substrate. Remarkably, SgcC5 is also capable of catalyzing amide bond formation, albeit with significantly reduced efficiency, between (S)-3-chloro-5-hydroxy-beta-tyrosyl-(S)-SgcC2 and (R)-2-amino-1-phenyl-1-ethanol, an alternative enediyne core mimic bearing an amine at its C-2 position. Thus, SgcC5 is capable of catalyzing both ester and amide bond formation, providing an evolutionary link between amide- and ester-forming condensation enzymes. PMID:19246381

  11. Regioselective Synthesis of N-Heteroaromatic Trifluoromethoxy Compounds by Direct O-CF3 Bond Formation.

    PubMed

    Liang, Apeng; Han, Shuaijun; Liu, Zhenwei; Wang, Liang; Li, Jingya; Zou, Dapeng; Wu, Yangjie; Wu, Yusheng

    2016-04-01

    The first one-step method for the synthesis of ortho-N-heteroaromatic trifluoromethoxy derivatives by site-specific O-CF3 bond formation using hydroxylated N-heterocycles and Togni's reagent is described. The approach enables the unprecedented syntheses of a wide range of six or five-membered N-heteroaromatic trifluoromethoxy compounds containing one or two heteroatoms from most commonly used hydroxylated N-heterocycles. Notable advantages of this method include its simplicity and mild conditions, avoidance of the need for metals or toxic reagents, and compatibility with a variety of functional groups. Furthermore, this method is especially suitable for the larger scale application. PMID:26791812

  12. Controlling Disulfide Bond Formation and Crystal Growth from 2-Mercaptobenzoic Acid

    SciTech Connect

    Rowland, Clare E.; Cantos, P. M.; Toby, B. H.; Frisch, M.; Deschamps, J. R.; Cahill, Christopher L.

    2011-03-02

    We report disulfide bond formation from 2-mercaptobenzoic acid (2-MBA) under hydrothermal conditions as a function of pH. Under acidic conditions, 2-MBA remains unchanged. Upon increasing pH, however, we observe 50% oxidation to 2,2'-disulfanediyldibenzoic acid (2,2'-DSBA), which is isolated as a cocrystal of both the thiol and disulfide molecules. At neutral pH, we observe complete oxidation and concurrent crystal growth. The pH sensitivity of this system allows targeting crystals of specific composition from simple building units through a straightforward pH manipulation.

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

    PubMed

    Van de Vyver, Stijn; Román-Leshkov, Yuriy

    2015-10-19

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

  14. Ceramic Nano-particle/Substrate Interface Bonding Formation Derived from Dynamic Mechanical Force at Room Temperature: HRTEM Examination

    NASA Astrophysics Data System (ADS)

    Yao, Hai-Long; Yang, Guan-Jun; Fan, Sheng-Qiang; Li, Cheng-Xin; Li, Chang-Jiu

    2015-04-01

    The bonding of TiO2 nano-particle/substrate is a critical factor influencing the performance of dye-sensitized solar cells. In order to reveal the bonding properties at TiO2 nano-particle/substrate interface, high-resolution transmission electron microscopy (HRTEM) analysis was adopted to TiO2 coatings prepared by three different approaches. In the HRTEM analysis, the effective bonding mode is allowed to distinguish from the false image overlapping. Results show that large areas of effective bonding between nano-TiO2 particles and the substrate surface formed in the room temperature cold sprayed coating and mechanically pressed coating, while only limited interface areas with the effective bonding were observed in the coating deposited by non-pressed method. These results confirm that both high impact pressure during the room temperature cold spraying and mechanical pressure contribute to the bonding formation at the particle/substrate interface.

  15. 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

  16. Accelerated C-N Bond Formation in Dropcast Thin Films on Ambient Surfaces

    NASA Astrophysics Data System (ADS)

    Badu-Tawiah, Abraham K.; Campbell, Dahlia I.; Cooks, R. Graham

    2012-09-01

    The aza-Michael addition and the Mannich condensation occur in thin films deposited on ambient surfaces. The reagents for both C-N bond formation reactions were transferred onto the surface by drop-casting using a micropipette. The surface reactions were found to be much more efficient than the corresponding bulk solution-phase reactions performed on the same scale in the same acetonitrile solvent. The increase in rate of product formation in the thin film is attributed to solvent evaporation in the open air which results in reagent concentration and produces rate acceleration similar to that seen in evaporating droplets in desorption electrospray ionization. This thin film procedure has potential for the rapid synthesis of reaction products on a small scale, as well as allowing rapid derivatization of analytes to produce forms that are easily ionized by electrospray ionization. Analysis of the derivatized sample directly from the reaction surface through the use of desorption electrospray ionization is also demonstrated.

  17. 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

  18. On the formation of equilibrium gels via a macroscopic bond limitation.

    PubMed

    Lindquist, B A; Jadrich, R B; Milliron, D J; Truskett, T M

    2016-08-21

    Restricting the number of attractive physical "bonds" that can form between particles in a fluid suppresses the usual demixing phase transition to very low particle concentrations, allowing for the formation of open, percolated, and homogeneous states, aptly called equilibrium or "empty" gels. Most demonstrations of this concept have directly limited the microscopic particle valence via anisotropic (patchy) attractions; however, an alternative macroscopic valence limitation would be desirable for greater experimental tunability and responsiveness. One possibility, explored in this paper, is to employ primary particles with attractions mediated via a secondary species of linking particles. In such a system, the linker-to-primary particle ratio serves as a macroscopic control parameter for the average microscopic valence. We show that the phase behavior of such a system predicted by Wertheim's first order perturbation theory is consistent with equilibrium gel formation: the primary particle concentrations corresponding to the two-phase demixing transition are significantly suppressed at both low and high linker-to-primary particle ratios. Extensive molecular dynamics simulations validate these theoretical predictions but also reveal the presence of loops of bonded particles, which are neglected in the theory. Such loops cause densification and inhibit percolation, and hence the range of viable empty gel state conditions is somewhat reduced relative to the Wertheim theory predictions. PMID:27544125

  19. 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

    2016-05-01

    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. PMID:27059121

  20. 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

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

    PubMed

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

    2015-03-01

    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

  2. Structural control of nonadiabatic bond formation: the photochemical formation and stability of substituted 4a,4b-dihydrotriphenylenes.

    PubMed

    Snyder, Joshua A; Bragg, Arthur E

    2015-04-30

    Nonadiabatic photocyclization makes bonds and is the first step in the photoinduced cyclodehydrogenation of ortho-arenes to yield polycyclic aromatic hydrocarbons. How molecular structure alters potential-energy landscapes, excited-state dynamics, and stabilities of reactants and intermediates underlies the feasibility of desirable photochemistry. In order to gain insight into these structure-dynamics relationships, we have used femtosecond transient absorption spectroscopy (TAS) to examine photoinduced dynamics of 1,2,3-triphenylbenzene (TPB) and ortho-quaterphenyl (OQTP), phenyl-subsituted analogues of ortho-terphenyl (OTP). Dynamics of TPB and OTP are quite similar: TPB exhibits fast (7.4 ps) excited-state decay with concomitant formation and vibrational relaxation of 9-phenyl-dihydrotriphenylene (9-phenyl DHT). In contrast, photoexcited OQTP exhibits multistate kinetics leading to formation of 1-phenyl DHT. Excited-state calculations reveal the existence of two distinct minima on the OQTP S1 surface and, together with photophysical data, support a mechanism involving both direct cyclization by way of an asymmetric structure and indirect cyclization by way of a symmetric quinoid-like minimum. Temperature-dependent nanosecond TAS was utilized to assess the relative stabilities of intermediates, substantiating the observed trend in photochemical reactivity OTP > OQTP > TPB. In total, this work demonstrates how specific structural variations alter the course of the excited-state dynamics and photoproduct stability that underlies desired photochemistry. PMID:25849258

  3. 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

  4. Control of stability of polypeptide multilayer nanofilms by quantitative control of disulfide bond formation

    NASA Astrophysics Data System (ADS)

    Zhong, Yang; Li, Bingyun; Haynie, Donald T.

    2006-12-01

    The crosslinking of polymers in a polymeric material will alter the mechanical properties of the material. Control over the mechanical properties of polyelectrolyte multilayer films (PEMs) could be useful for applications of the technology in medicine and other areas. Disulfide bonds are 'natural' polypeptide crosslinks found widely in wild-type proteins. Here, we have designed and synthesized three pairs of oppositely charged 32mer polypeptide to have 0, 4, or 8 cysteine (Cys) residues per molecule, and we have characterized physical properties of the peptides in a PEM context. The average linear density of free thiol in the designed peptides was 0, 0.125, or 0.25 per amino acid residue. The peptides were used to make 10-bilayer PEMs by electrostatic layer-by-layer self-assembly (LBL). Cys was included in the peptides to study specific effects of disulfide bond formation on PEM properties. Features of film assembly have been found to depend on the amino acid sequence, as in protein folding. Following polypeptide self-assembly into multilayer films, Cys residues were disulfide-crosslinked under mild oxidizing conditions. The stability of the crosslinked films at acidic pH has been found to depend on the number of Cys residues per peptide for a given crosslinking procedure. Crosslinked and non-crosslinked films have been analysed by ultraviolet spectroscopy (UVS), ellipsometry, and atomic force microscopy (AFM) to characterize film assembly, surface morphology, and disassembly. A selective etching model of the disassembly process at acidic pH is proposed on the basis of the experimental data. In this model, regions of film in which the disulfide bond density is low are etched at a higher rate than regions where the density is high.

  5. 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.

  6. 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.

  7. Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

    PubMed Central

    Sheng, Jia; Zhang, Wen; Hassan, Abdalla E. A.; Gan, Jianhua; Soares, Alexei S.; Geng, Song; Ren, Yi; Huang, Zhen

    2012-01-01

    Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation. PMID:22641848

  8. Calcium phosphate formation on the phosphorylated dental bonding agent in electrolyte solution.

    PubMed

    Hayakawa, T; Yoshinari, M; Sakae, T; Nemoto, K

    2004-01-01

    The aim of the present study was to study the mineral formation on a phosphorylated dental bonding agent using a mineralization inductive solution. Clearfil Photobond, which contained phosphate monomer, was cured by photo-irradiation and heat treated, and was then immersed in Hanks' balanced salt solution (HBSS) with pH = 7.4 for 1, 3, 5, 7, 14, and 28 days at 37 degrees C. The white substances were deposited on the phosphorylated polymer, i.e. cured Photobond disk, after the immersion in HBSS. The white substances become visible after 3 days immersion. After 7 days immersion, surface of the phosphorylated polymer disk was almost covered with white substance layers. The measurement of white substances by means of X-ray diffraction, Fourier-transform infrared and electron probe microanalysis revealed that their main component was carbonate-containing hydroxyapatite. Scanning electron microscopy pictures showed that a large number of globules of hydroxyapatite were fused together, and that each globule was composed of a group of numerous thin-film form flakes uniting and/or clustering together. The results obtained in this study concluded that the presence of phosphonic acid and phosphate group of phosphorylated dental bonding agent enhanced the nucleation and growth of hydroxyapatite crystals on its surface. PMID:15125600

  9. 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.

  10. 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

  11. 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.

  12. The effect of smectite composition on the catalysis of peptide bond formation.

    PubMed

    Bujdák, J; Rode, B M

    1996-10-01

    Clay-catalyzed glycine and diglycine oligomerizations were performed as drying/wetting cycles at 80 degrees C. Two trioctahedral smectites (hectorite and saponite), three pure montmorillonites, a ferruginous smectite, an Fe(II)-rich smectite, and three smectites containing goethite admixture were used as catalysts. Highest peptide bond formation was found with trioctahedral smectites. About 7% of glycine was converted to diglycine and diketopiperazine on hectorite after 7 days. In the case of dioctahedral smectites, highest yields were achieved using clays with a negative-layer charge localized in the octahedral sheets (up to 2% of converted glycine after 7 days). The presence of Fe(II) in clay is reflected in a higher efficiency in catalyzing amino acid dimerization (about 3.5% of converted glycine after 7 days). The possible significance of the results for prebiotic chemistry is discussed. PMID:8798338

  13. Maternal Nicotine Exposure Leads to Impaired Disulfide Bond Formation and Augmented Endoplasmic Reticulum Stress in the Rat Placenta

    PubMed Central

    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

  14. 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

  15. 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. PMID:26902915

  16. Estimation of Abraham solvation equation coefficients for hydrogen bond formation from Abraham solvation parameters for solute acidity and basicity.

    PubMed

    van Noort, Paul

    2013-01-01

    Abraham solvation equations find widespread use in environmental chemistry and pharmaco-chemistry. The coefficients in these equations, which are solvent (system) descriptors, are usually determined by fitting experimental data. To simplify the determination of these coefficients in Abraham solvation equations, this study derives equations, based on Abraham solvation parameters for hydrogen acidity and basicity of the solvents involved, to estimate the value of the coefficients for hydrogen bond formation. These equations were applied to calculate Abraham solvation parameters for hydrogen acidity and basicity for polyoxymethylene, polyacrylate, sodium dodecylsulfate, some ionic liquids, alkanoyl phosphatidyl cholines, and lipids for which fitted values for Abraham coefficients for hydrogen bond formation were available. PMID:22892357

  17. 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.

  18. 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.

  19. 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. PMID:26695592

  20. Bond formation effects on the metal-insulator transition in the half-filled kagome Hubbard model

    NASA Astrophysics Data System (ADS)

    Higa, Ryota; Asano, Kenichi

    2016-06-01

    We study the metal-insulator transition in the half-filled Hubbard model on a Kagome lattice using the variational cluster approximation. The strong coupling limit of the model corresponds to the S =1 /2 Kagome Heisenberg antiferromagnet, which is known to have a singlet ground state, although its detail is still debated. As the results of the cluster methods generally depend much on the choice of the unit cluster, we have chosen the clusters that are compatible with these singlet ground states in the strong coupling case found so far, which basically consist of even number of sites. It is found that the correlated electrons on the Kagome lattice have a strong tendency to form valence-bond structures, which are the resonation of electrons on a single bond or several bonds forming loops. The zero-temperature metal-insulator transition at some interaction strength is possibly driven by the formation of such short range valence bonds and shows a second order character, which is distinctive from the Brinkman-Rice scenario. The electrons on these valence bonds further localizes onto each site as the interaction increases, and the valence bonds of electrons finally turn into magnetic singlet bonds between localized S =1 /2 spins, which are consistent with the ground states of the Kagome antiferromagnet.

  1. 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. PMID:27373666

  2. Formation Mechanism of the First Carbon-Carbon Bond and the First Olefin in the Methanol Conversion into Hydrocarbons.

    PubMed

    Liu, Yue; Müller, Sebastian; Berger, Daniel; Jelic, Jelena; Reuter, Karsten; Tonigold, Markus; Sanchez-Sanchez, Maricruz; Lercher, Johannes A

    2016-05-01

    The elementary reactions leading to the formation of the first carbon-carbon bond during early stages of the zeolite-catalyzed methanol conversion into hydrocarbons were identified by combining kinetics, spectroscopy, and DFT calculations. The first intermediates containing a C-C bond are acetic acid and methyl acetate, which are formed through carbonylation of methanol or dimethyl ether even in presence of water. A series of acid-catalyzed reactions including acetylation, decarboxylation, aldol condensation, and cracking convert those intermediates into a mixture of surface bounded hydrocarbons, the hydrocarbon pool, as well as into the first olefin leaving the catalyst. This carbonylation based mechanism has an energy barrier of 80 kJ mol(-1) for the formation of the first C-C bond, in line with a broad range of experiments, and significantly lower than the barriers associated with earlier proposed mechanisms. PMID:27037603

  3. 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...

  4. Descent of low-Bond-number liquid-metal diapirs with trailing conduits during core formation

    NASA Astrophysics Data System (ADS)

    Rains, C.; Weeraratne, D. S.

    2012-12-01

    Formation of the early Earth involved violent impacts and meteorite bombardment which partially or fully melted surface materials, facilitating separation of iron metal from silicates. Geochemical constraints on core formation times indicate that this liquid metal must have been transported to the center of the Earth within 30 Ma. Among the mechanisms that have been proposed, metal-silicate plumes resulting from Rayleigh-Taylor instabilities of a liquid-metal pond at the bottom of a magma ocean provide the fastest rates of delivery to the core. Recent studies have shown that these rapidly descending plumes develop trailing conduits that fill with the overlying melted silicate material. However, while large plumes descend quickly, they do not provide enough time or surface area for metal-silicate equilibration to be achieved throughout the mantle. Instead, small metal drops descending in the wake of larger diapirs or in conduits of their own making may have been crucial in the equilibration process that resulted in the excess siderophile mantle abundance. We investigate the instability and descent of liquid-metal drops through a highly viscous layer using three-component laboratory fluid experiments representing the Earth's proto-mantle (layer 2) covered by a magma ocean (layer 1), and a liquid iron pond (layer 3) initially resting at their interface. Silicate materials are represented by dehydrated (layer 2), or diluted (layer 1) glucose and salt solutions. Liquid gallium represents the iron metal phase. We scale our experiments to the Earth's mantle through the use of Bond numbers to characterize drops and diapirs, and a non-dimensional length scale λ, which we define as the ratio of radius to height, to characterize conduits. Previous laboratory work using liquid gallium has investigated high-Bond-number diapirs (B = 13 - 66) and conduits of λ ~ 0.2, analogous to large plumes in the Earth. Here, we focus on low Bond numbers (B ~ 4), and small λ ~ .05 to

  5. 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.

  6. 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

  7. Pressure-induced bonding and compound formation in xenon-hydrogen solids

    SciTech Connect

    Somayazulu, Maddury; Dera, Przemyslaw; Goncharov, Alexander F; Gramsch, Stephen A; Liermann, Peter; Yang, Wenge; Liu, Zhenxian; Mao, Ho-kwang; Hemley, Russell J

    2010-11-03

    Closed electron shell systems, such as hydrogen, nitrogen or group 18 elements, can form weakly bound stoichiometric compounds at high pressures. An understanding of the stability of these van der Waals compounds is lacking, as is information on the nature of their interatomic interactions. We describe the formation of a stable compound in the Xe-H{sub 2} binary system, revealed by a suite of X-ray diffraction and optical spectroscopy measurements. At 4.8 GPa, a unique hydrogen-rich structure forms that can be viewed as a tripled solid hydrogen lattice modulated by layers of xenon, consisting of xenon dimers. Varying the applied pressure tunes the Xe-Xe distances in the solid over a broad range from that of an expanded xenon lattice to the distances observed in metallic xenon at megabar pressures. Infrared and Raman spectra indicate a weakening of the intramolecular covalent bond as well as persistence of semiconducting behaviour in the compound to at least 255 GPa.

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

    PubMed

    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-tRNA(Phe) 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-tRNA(Pro) isoacceptors at 4 different Pro codons help explain codon bias not accounted for by the "tRNA abundance" hypothesis. PMID:19104062

  9. Modulation of reactivity in the cavity of liposomes promotes the formation of peptide bonds.

    PubMed

    Grochmal, Anna; Prout, Luba; Makin-Taylor, Robert; Prohens, Rafel; Tomas, Salvador

    2015-09-30

    In living cells, reactions take place in membrane-bound compartments, often in response to changes in the environment. Learning how the reactions are influenced by this compartmentalization will help us gain an optimal understanding of living organisms at the molecular level and, at the same time, will offer vital clues on the behavior of simple compartmentalized systems, such as prebiotic precursors of cells and cell-inspired artificial systems. In this work we show that a reactive building block (an activated amino acid derivative) trapped in the cavity of a liposome is protected against hydrolysis and reacts nearly quantitatively with another building block, which is membrane-permeable and free in solution, to form the dipeptide. By contrast, when the activated amino acid is found outside the liposome, hydrolysis is the prevalent reaction, showing that the cavity of the liposomes promotes the formation of peptide bonds. We attribute this result to the large lipid concentration in small compartments from the point of view of a membrane-impermeable molecule. Based on this result, we show how the outcome of the reaction can be predicted as a function of the size of the compartment. The implications of these results on the behavior of biomolecules in cell compartments, abiogenesis, and the design of artificial cell-inspired systems are considered. PMID:26356087

  10. Balancing oxidative protein folding: the influences of reducing pathways on disulfide bond formation.

    PubMed

    Kojer, Kerstin; Riemer, Jan

    2014-08-01

    Oxidative protein folding is confined to few compartments, including the endoplasmic reticulum, the mitochondrial intermembrane space and the bacterial periplasm. Conversely, in compartments in which proteins are translated such as the cytosol, the mitochondrial matrix and the chloroplast stroma proteins are kept reduced by the thioredoxin and glutaredoxin systems that functionally overlap. The highly reducing NADPH pool thereby serves as electron donor that enables glutathione reductase and thioredoxin reductase to keep glutathione pools and thioredoxins in their reduced redox state, respectively. Notably, also compartments containing oxidizing machineries are linked to these reducing pathways. Reducing pathways aid in proofreading of disulfide bond formation by isomerization or they provide reducing equivalents for the reduction of disulfides prior to degradation. In addition, they contribute to the thiol-dependent regulation of protein activities, and they help to counteract oxidative stress. The existence of oxidizing and reducing pathways in the same compartment poses a potential problem as the cell has to avoid futile cycles of oxidation and subsequent reduction reactions. Thus, compartments that contain oxidizing machineries have developed sophisticated ways to spatiotemporally balance and regulate oxidation and reduction. In this review, we discuss oxidizing and reducing pathways in the endoplasmic reticulum, the periplasm and the mitochondrial intermembrane space and highlight the role of glutathione especially in the endoplasmic reticulum and the intermembrane space. This article is part of a Special Issue entitled: Thiol-Based Redox Processes. PMID:24534645

  11. 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.

  12. Dentin bonding performance using Weibull statistics and evaluation of acid-base resistant zone formation of recently introduced adhesives.

    PubMed

    Guan, Rui; Takagaki, Tomohiro; Matsui, Naoko; Sato, Takaaki; Burrow, Michael F; Palamara, Joseph; Nikaido, Toru; Tagami, Junji

    2016-07-30

    Dentin bonding durability of recently introduced dental adhesives: Clearfil SE Bond 2 (SE2), Optibond XTR (XTR), and Scotchbond Universal (SBU) was investigated using Weibull analysis as well as analysis of the micromorphological features of the acid-base resistant zone (ABRZ) created for the adhesives. The bonding procedures of SBU were divided into three subgroups: self-etch (SBS), phosphoric acid (PA) etching on moist (SBM) or dry dentin (SBD). All groups were thermocycled for 0, 5,000 and 10,000 cycles followed by microtensile bond strength testing. Acid-base challenge was undertaken before SEM and TEM observations of the adhesive interface. The etch-and-rinse method with SBU (SBM and SBD) created inferior interfaces on the dentin surface which resulted in reduced bond durability. ABRZ formation was detected with the self-etch adhesive systems; SE2, XTR and SBS. In the PA etching protocols of SBM and SBD, a thick hybrid layer but no ABRZ was detected, which might affect dentin bond durability. PMID:27335136

  13. 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)

  14. 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. PMID:25124437

  15. Legionella pneumophila utilizes a Single Player Disulfide-Bond Oxidoreductase System to Manage Disulfide Bond Formation and Isomerization

    PubMed Central

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

    2015-01-01

    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 to 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. PMID:25534767

  16. Coherent anti-Stokes Raman scattering microspectroscopic kinetic study of fast hydrogen bond formation in microfluidic devices.

    PubMed

    Oshovsky, Gennady V; Rago, Gianluca; Day, James P R; Soudijn, Maarten L; Rock, William; Parekh, Sapun H; Ciancaleoni, Gianluca; Reek, Joost N H; Bonn, Mischa

    2013-10-01

    The kinetics of a key noncovalent, hydrogen bonding interaction was studied in situ using coherent anti-stokes Raman scattering (CARS) microspectroscopy in a microfluidic device. The association of model compounds, pyridine and hexafluoroisopropanol, was quantitatively monitored with submicrometer resolution. Lower limits for the very high formation and dissociation rate constants of the model 1:1 pyridine-hexafluoroisopropanol hydrogen bonded complex in dichloromethane-d2 were determined to be k1 > 10(5) M(-1)s(-1) and k-1 > 333.3 s(-1), respectively. PMID:23987583

  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. PMID:23699524

  18. C-H Bond activation and C-C bond formation in the reaction of 2,5-dimethylthiophene with TpMe2Ir compounds.

    PubMed

    Paneque, Margarita; Poveda, Manuel L; Carmona, Ernesto; Salazar, Verónica

    2005-04-21

    The bulky 2,5-dimethylthiophene (2,5-Me2T) reacts at 60 degrees C with TpMe2Ir(C2H4)2 to give a mixture of two TpMe2Ir(III) hydride products, 3 and 4, that contain in addition a thienyl (3) or a thienyl-derived ligand (4). For the generation of 3 only sp2 C-H activation is needed, but the formation of 4 requires also the activation of an sp3 C-H bond and the formation of a new C-C bond (between vinyl and thienyl fragments). In the presence of 2,5-Me2T, compound 4 reacts further to produce a complex thiophenic structure (5, characterized by X-ray methods) that derives formally from two molecules of 2,5-Me2T and a vinyl fragment. Compounds 3-5 can be readily protonated by [H(OEt2)2][BAr'4](Ar'= 3,5-C6H3(CF3)2), with initial generation of carbene ligands (in the case of 3 and 5) as a consequence of H+ attack at the beta-carbon of the Ir-thienyl unit. Free, substituted thiophenes, derived from the original 2,5-Me2T, may be isolated in this way. PMID:15824780

  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. Chemoselective Radical Dehalogenation and C-C Bond Formation on Aryl Halide Substrates Using Organic Photoredox Catalysts.

    PubMed

    Poelma, Saemi O; Burnett, G Leslie; Discekici, Emre H; Mattson, Kaila M; Treat, Nicolas J; Luo, Yingdong; Hudson, Zachary M; Shankel, Shelby L; Clark, Paul G; Kramer, John W; Hawker, Craig J; Read de Alaniz, Javier

    2016-08-19

    Despite the number of methods available for dehalogenation and carbon-carbon bond formation using aryl halides, strategies that provide chemoselectivity for systems bearing multiple carbon-halogen bonds are still needed. Herein, we report the ability to tune the reduction potential of metal-free phenothiazine-based photoredox catalysts and demonstrate the application of these catalysts for chemoselective carbon-halogen bond activation to achieve C-C cross-coupling reactions as well as reductive dehalogenations. This procedure works both for conjugated polyhalides as well as unconjugated substrates. We further illustrate the usefulness of this protocol by intramolecular cyclization of a pyrrole substrate, an advanced building block for a family of natural products known to exhibit biological activity. PMID:27276418

  1. Enhancing Peptide Ligand Binding to Vascular Endothelial Growth Factor by Covalent Bond Formation

    PubMed Central

    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.

    2012-01-01

    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. PMID:22537066

  2. Oxidatively Triggered Carbon-Carbon Bond Formation in Ene-amide Complexes.

    PubMed

    Jacobs, Brian P; Wolczanski, Peter T; Lobkovsky, Emil B

    2016-05-01

    Ene-amides have been explored as ligands and substrates for oxidative coupling. Treatment of CrCl2, Cl2Fe(PMe3)2, and Cl2Copy4 with 2 equiv of {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}Li afforded pseudosquare planar {η(3)-C,C,N-(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}2Cr (1-Cr, 78%), trigonal {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}2Fe(PMe3) (2-Fe, 80%), and tetrahedral {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}2Co(py)2 (3-Co, 91%) in very good yields. The addition of CrCl3 to 1-Cr, and FeCl3 to 2-Fe, afforded oxidatively triggered C-C bond formation as rac-2,2'-di(2,6-(i)Pr2C6H3N═)2dicyclohexane (EA2) was produced in modest yields. Various lithium ene-amides were similarly coupled, and the mechanism was assessed via stoichiometric reactions. Some ferrous compounds (e.g., 2-Fe, FeCl2) were shown to catalyze C-arylation of {(2,6-(i)Pr2C6H3)(1-(c)Hexenyl)N}Li with PhBr, but the reaction was variable. Structural characterizations of 1-Cr, 2-Fe, and 3-Co are reported. PMID:27064509

  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. 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. PMID:27071858

  5. Detection and formation mechanism of micro-defects in ultrafine pitch Cu—Cu direct bonding

    NASA Astrophysics Data System (ADS)

    Zi-Yu, Liu; Jian, Cai; Qian, Wang; Yu, Chen

    2016-01-01

    In this paper, Cu-Cu interconnects with ultrafine pad pitches of 6 μm, 8 μm, and 15 μm are implemented on the 12 inch wafers by a direct bonding process. Defects are not found by traditional non-destructive (NDT) c-mode scanning acoustic microscopy (c-SAM). However, cross sectional observation of bonding interfaces reveals that micro-defects such as micro seams are located at SiO2 bonding interfaces. In order to examine the micro-defects in the ultra-fine pitch direct bonding process by the NDT technology, a novel “defect-enlarged approach” is proposed. The bonded dies are first annealed in an N2 oven at 300 °C for a few hours and then cooled quickly in air. The c-SAM scanning images show large defects at the place where nothing can be detected by c-SAM before this treatment. Cross sectional observation of the bonding interfaces indicates that these defects consist of large size micro seams at the SiO2 bonding interface, especially near Cu pads with an ultrafine pitch of 6 μm. However, these large defects disappear after several hours at room temperature, observed by c-SAM. It is inferred that the disappearance of these defects inspected by the “defect-enlarged approach” results from the combination of intrinsic micro seams and “weak” bonds in the silicon oxide layer. Then the underlying physical mechanism of these micro-defects is proposed, which is influenced by Cu pad surface topology and bonding models. Project supported by the National Natural Science Foundation of China (Grant No. 61274111) and the National Basic Research Program of China (Grant No. 2015CB057205).

  6. Modification of the Catalytic Function of Human Hydroxysteroid Sulfotransferase hSULT2A1 by Formation of Disulfide Bonds

    PubMed Central

    Qin, Xiaoyan; Teesch, Lynn M.

    2013-01-01

    The human cytosolic sulfotransferase hSULT2A1 catalyzes the sulfation of a broad range of xenobiotics, as well as endogenous hydroxysteroids and bile acids. Reversible modulation of the catalytic activity of this enzyme could play important roles in its physiologic functions. Whereas other mammalian sulfotransferases are known to be reversibly altered by changes in their redox environment, this has not been previously shown for hSULT2A1. We have examined the hypothesis that the formation of disulfide bonds in hSULT2A1 can reversibly regulate the catalytic function of the enzyme. Three thiol oxidants were used as model compounds to investigate their effects on homogeneous preparations of hSULT2A1: glutathione disulfide, 5,5′-dithiobis(2-nitrobenzoic acid), and 1,1’-azobis(N,N-dimethylformamide) (diamide). Examination of the effects of disulfide bond formation with these agents indicated that the activity of the enzyme is reversibly altered. Studies on the kinetics of the hSULT2A1-catalyzed sulfation of dehydroepiandrosterone (DHEA) showed the effects of disulfide bond formation on the substrate inhibition characteristics of the enzyme. The effects of these agents on the binding of substrates and products, liquid chromatography-mass spectrometry identification of the disulfides formed, and structural modeling of the modified enzyme were examined. Our results indicate that conformational changes at cysteines near the nucleotide binding site affect the binding of both the nucleotide and DHEA to the enzyme, with the specific effects dependent on the structure of the resulting disulfide. Thus, the formation of disulfide bonds in hSULT2A1 is a potentially important reversible mechanism for alterations in the rates of sulfation of both endogenous and xenobiotic substrates. PMID:23444386

  7. How Alcohol Chain-Length and Concentration Modulate Hydrogen Bond Formation in a Lipid Bilayer

    PubMed Central

    Dickey, Allison N.; Faller, Roland

    2007-01-01

    Molecular dynamics simulations are used to measure the change in properties of a hydrated dipalmitoylphosphatidylcholine bilayer when solvated with ethanol, propanol, and butanol solutions. There are eight oxygen atoms in dipalmitoylphosphatidylcholine that serve as hydrogen bond acceptors, and two of the oxygen atoms participate in hydrogen bonds that exist for significantly longer time spans than the hydrogen bonds at the other six oxygen atoms for the ethanol and propanol simulations. We conclude that this is caused by the lipid head group conformation, where the two favored hydrogen-bonding sites are partially protected between the head group choline and the sn-2 carbonyl oxygen. We find that the concentration of the alcohol in the ethanol and propanol simulations does not have a significant influence on the locations of the alcohol/lipid hydrogen bonds, whereas the concentration does impact the locations of the butanol/lipid hydrogen bonds. The concentration is important for all three alcohol types when the lipid chain order is examined, where, with the exception of the high-concentration butanol simulation, the alcohol molecules having the longest hydrogen-bonding relaxation times at the favored carbonyl oxygen acceptor sites also have the largest order in the upper chain region. The lipid behavior in the high-concentration butanol simulation differs significantly from that of the other alcohol concentrations in the order parameter, head group rotational relaxation time, and alcohol/lipid hydrogen-bonding location and relaxation time. This appears to be the result of the system being very near to a phase transition, and one occurrence of lipid flip-flop is seen at this concentration. PMID:17218462

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

    PubMed

    Domingo, Luis R; Pérez, Patricia

    2014-07-21

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

  9. 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

  10. 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

  11. High performance C/S composite cathodes with conventional carbonate-based electrolytes in Li-S battery.

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    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.

  13. 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

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

    PubMed

    Comas-Vives, Aleix; Valla, Maxence; Copéret, Christophe; Sautet, Philippe

    2015-09-23

    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

  15. The lengthening of the HF bond on formation of heterodimers B. . .HF - Determination and dependence on the strength of the hydrogen bond

    NASA Astrophysics Data System (ADS)

    Legon, A. C.; Millen, D. J.

    1986-03-01

    A procedure that allows the lengthening (dr) of the H-A bond that accompanies dimer formation in B-HA complexes is described. In this procedure, dr is determined indirectly from the hyperfine coupling constants which are available from the rotational spectra of B-HF and B-DF, namely the H,F nuclear spin-nuclear spin coupling constant and the D nuclear quadrupole coupling constant. It is shown that the two constants taken together with the known electric charge distribution of B lead to dr and that it is now possible to evaluate dr using this method for the series in which B is, successively, Ar, Kr, Xe, N2, CO, H2S, HCN, CH3CN, and H2O. It is found that dr increases smoothly from zero for Ar to 0.016 A for CH3CN when plotted against the intermolecular stretching force constant. It is also shown that dr increases monotonically with the strength of the hydrogen bond.

  16. 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

  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. Dynamic effects in friction and adhesion through cooperative rupture and formation of supramolecular bonds

    NASA Astrophysics Data System (ADS)

    Blass, Johanna; Albrecht, Marcel; Bozna, Bianca L.; Wenz, Gerhard; Bennewitz, Roland

    2015-04-01

    We introduce a molecular toolkit for studying the dynamics in friction and adhesion from the single molecule level to effects of multivalency. As experimental model system we use supramolecular bonds established by the inclusion of ditopic adamantane connector molecules into two surface-bound cyclodextrin molecules, attached to a tip of an atomic force microscope (AFM) and to a flat silicon surface. The rupture force of a single bond does not depend on the pulling rate, indicating that the fast complexation kinetics of adamantane and cyclodextrin are probed in thermal equilibrium. In contrast, the pull-off force for a group of supramolecular bonds depends on the unloading rate revealing a non-equilibrium situation, an effect discussed as the combined action of multivalency and cantilever inertia effects. Friction forces exhibit a stick-slip characteristic which is explained by the cooperative rupture of groups of host-guest bonds and their rebinding. No dependence of friction on the sliding velocity has been observed in the accessible range of velocities due to fast rebinding and the negligible delay of cantilever response in AFM lateral force measurements.We introduce a molecular toolkit for studying the dynamics in friction and adhesion from the single molecule level to effects of multivalency. As experimental model system we use supramolecular bonds established by the inclusion of ditopic adamantane connector molecules into two surface-bound cyclodextrin molecules, attached to a tip of an atomic force microscope (AFM) and to a flat silicon surface. The rupture force of a single bond does not depend on the pulling rate, indicating that the fast complexation kinetics of adamantane and cyclodextrin are probed in thermal equilibrium. In contrast, the pull-off force for a group of supramolecular bonds depends on the unloading rate revealing a non-equilibrium situation, an effect discussed as the combined action of multivalency and cantilever inertia effects. Friction

  19. Facile synthesis of disubstituted isoxazoles from homopropargylic alcohol via C═N bond formation.

    PubMed

    Gao, Pin; Li, Hong-Xia; Hao, Xin-Hua; Jin, Dong-Po; Chen, Dao-Qian; Yan, Xiao-Biao; Wu, Xin-Xing; Song, Xian-Rong; Liu, Xue-Yuan; Liang, Yong-Min

    2014-12-19

    A novel iron-catalyzed aerobic oxidative reaction to synthesize disubstituted isoxazoles from homopropargylic alcohol, t-BuONO, and H2O is developed. The method provides mild conditions to afford a variety of useful substituted heterocycles in an efficient and regioselective manner. The mechanism has been studied and proposed, which indicates that the transformation can be realized through construction of a C═N bond and C═O bond, C-H oxidation, and then cyclization. Moreover, this method can be enlarged to gram scale. PMID:25423918

  20. Characterization of the Amicetin Biosynthesis Gene Cluster from Streptomyces vinaceusdrappus NRRL 2363 Implicates Two Alternative Strategies for Amide Bond Formation

    PubMed Central

    Zhang, Gaiyun; Zhang, Haibo; Li, Sumei; Xiao, Ji; Zhang, Guangtao; Zhu, Yiguang; Niu, Siwen; Ju, Jianhua

    2012-01-01

    Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis. PMID:22267658

  1. Disulfide bond formation is a determinant of glycosylation site usage in the hemagglutinin-neuraminidase glycoprotein of Newcastle disease virus.

    PubMed Central

    McGinnes, L W; Morrison, T G

    1997-01-01

    Determinants of glycosylation site usage were explored by using the hemagglutinin-neuraminidase (HN) glycoprotein of the paramyxovirus Newcastle disease virus. The amino acid sequence of the HN protein, a type II glycoprotein, has six N-linked glycosylation addition sites, G1 to G6, two of which, G5 and G6, are not used for the addition of carbohydrate (L. McGinnes and T. Morrison, Virology 212:398-410, 1995). The sequence of this protein also has 13 cysteine residues in the ectodomain (C2 to C14). Mutation of either cysteine 13 or cysteine 14 resulted in the addition of another oligosaccharide chain to the protein. These cysteine residues flank the normally unused G6 glycosylation addition site, and mutation of the G6 site eliminated the extra glycosylation found in the cysteine mutants. These results suggested that failure to form an intramolecular disulfide bond resulted in the usage of a normally unused glycosylation site. This conclusion was confirmed by preventing cotranslational disulfide bond formation in cells by using dithiothreitol. Under these conditions, the wild-type protein acquired extra glycosylation, which was eliminated by mutation of the G6 site. These results suggest that localized folding events on the nascent chain, such as disulfide bond formation, which block access to the oligosaccharyl transferase are a determinant of glycosylation site usage. PMID:9060670

  2. Dynamic effects in friction and adhesion through cooperative rupture and formation of supramolecular bonds.

    PubMed

    Blass, Johanna; Albrecht, Marcel; Bozna, Bianca L; Wenz, Gerhard; Bennewitz, Roland

    2015-05-01

    We introduce a molecular toolkit for studying the dynamics in friction and adhesion from the single molecule level to effects of multivalency. As experimental model system we use supramolecular bonds established by the inclusion of ditopic adamantane connector molecules into two surface-bound cyclodextrin molecules, attached to a tip of an atomic force microscope (AFM) and to a flat silicon surface. The rupture force of a single bond does not depend on the pulling rate, indicating that the fast complexation kinetics of adamantane and cyclodextrin are probed in thermal equilibrium. In contrast, the pull-off force for a group of supramolecular bonds depends on the unloading rate revealing a non-equilibrium situation, an effect discussed as the combined action of multivalency and cantilever inertia effects. Friction forces exhibit a stick-slip characteristic which is explained by the cooperative rupture of groups of host-guest bonds and their rebinding. No dependence of friction on the sliding velocity has been observed in the accessible range of velocities due to fast rebinding and the negligible delay of cantilever response in AFM lateral force measurements. PMID:25833225

  3. Nickel-Catalyzed Intramolecular C-O Bond Formation: Synthesis of Cyclic Enol Ethers.

    PubMed

    Han, Seo-Jung; Doi, Ryohei; Stoltz, Brian M

    2016-06-20

    An efficient and exceptionally mild intramolecular nickel-catalyzed carbon-oxygen bond-forming reaction between vinyl halides and primary, secondary, and tertiary alcohols has been achieved. Zinc powder was found to be an essential additive for obtaining high catalyst turnover and yields. This operationally simple method allows direct access to cyclic vinyl ethers in high yields in a single step. PMID:27159831

  4. Clients' Representations of Childhood Emotional Bonds with Parents, Social Support, and Formation of the Working Alliance.

    ERIC Educational Resources Information Center

    Mallinckrodt, Brent

    1991-01-01

    Collected survey data from 102 client-counselor dyads with regard to client and counselor third-session working alliance ratings, quality of clients' current social relationships, and clients' representations of care and overprotection in memories of childhood emotional bonds with parents. Social support was significant predictor of client-rated…

  5. Alternative pathways of disulfide bond formation yield secretion-competent, stable and functional immunoglobulins

    PubMed Central

    Elkabetz, Yechiel; Ofir, Ayala; Argon, Yair; Bar-Nun, Shoshana

    2009-01-01

    Disulfide bonds within and between proteins are responsible for stabilizing folding and covalent assembly. They are thought to form by an obligatory pathway that leads to a single native structure compatible with secretion. We have previously demonstrated that the intradomain disulfide in the CH1 domain of the Ig γ2b heavy chains was dispensable for secretion (Elkabetz et al., 2005). Here we show that the heavy chain-light chain interchain disulfide is also dispensable. γ2b with mutated Cys128, which normally disulfide bonds with the light chain, still assembled with λI light chain into a secretion-competent, tetrameric IgG2b. This assembly comprised of a covalent homo-dimer of mutant heavy chains (C128S2) accompanied non-covalently by a covalent homo-dimer of light chains (λ2). The λ2 homo-dimer formed only upon association with C128S2, through disulfide bonding of the two “orphan” heavy chain-interacting Cys214 in λI. The unique Ig tetramer was secreted efficiently as a functional antibody whose antigen binding capacity resembled that of normal IgG2b. Therefore, disulfide bonding of Ig manifests considerable plasticity and can generate more than one functional structure that is considered native by the cellular quality control system. PMID:18692901

  6. Ruthenium-Catalyzed Transfer Hydrogenation for C-C Bond Formation: Hydrohydroxyalkylation and Hydroaminoalkylation via Reactant Redox Pairs.

    PubMed

    Perez, Felix; Oda, Susumu; Geary, Laina M; Krische, Michael J

    2016-06-01

    Merging the chemistry of transfer hydrogenation and carbonyl or imine addition, a broad new family of redox-neutral or reductive hydrohydroxyalkylations and hydroaminomethylations have been developed. In these processes, hydrogen redistribution between alcohols and π-unsaturated reactants is accompanied by C-C bond formation, enabling direct conversion of lower alcohols to higher alcohols. Similarly, hydrogen redistribution between amines to π-unsaturated reactants results in direct conversion of lower amines to higher amines. Alternatively, equivalent products of hydrohydroxyalkylation and hydroaminomethylation may be generated through the reaction of carbonyl compounds or imines with π-unsaturated reactants under the conditions of 2-propanol-mediated reductive coupling. Finally, using vicinally dioxygenated reactants, that is, diol, ketols, or diones, successive transfer hydrogenative coupling occurs to generate 2 C-C bonds, resulting in products of formal [4+2] cycloaddition. PMID:27573275

  7. Syntheses of [1,2,4]triazolo[1,5-a]benzazoles enabled by the transition-metal-free oxidative N-N bond formation.

    PubMed

    Shang, Erchang; Zhang, Junzhi; Bai, Jinyi; Wang, Zhan; Li, Xiang; Zhu, Bing; Lei, Xiaoguang

    2016-05-19

    A transition-metal-free oxidative N-N bond formation strategy was developed to generate various structurally interesting [1,2,4]triazolo[1,5-a]benzazoles efficiently. The mechanism of the key oxidative N-N bond formation was investigated by using an intramolecular competition reaction. Notably, the first single crystal structure was also obtained to confirm the structure of 2-aryl[1,2,4]triazolo[1,5-a]benzimidazole. PMID:27161847

  8. Regularities in the formation of dislocation networks on the boundary of bonded Si(001) wafers

    SciTech Connect

    Vdovin, V. I. Ubyivovk, E. V.; Vyvenko, O. F.

    2013-02-15

    The dislocation networks in structures with hydrophilically bonded Si (001) wafers are investigated by transmission electron microscopy. Networks with differing geometry and type of dominant dislocations are observed. One type of networks, which is typical of bonded structures, is formed on the basis of a square network of screw dislocations and contains a system of unidirectional 60 Degree-Sign zigzag-shaped dislocations. It is established that such dislocation networks are flat in structures with an azimuthal misorientation of wafers exceeding 2 Degree-Sign , whereas they are three-dimensional at smaller misorientation angles. A unique network of another type is formed only by 60 Degree-Sign dislocations, the majority of which are extended along one direction, which does not coincide with the Left-Pointing-Angle-Bracket 110 Right-Pointing-Angle-Bracket directions in the boundary plane and has a number of specific features, the explanation of which is impossible within the framework of conventional representations.

  9. Facile amine formation by intermolecular catalytic amidation of carbon-hydrogen bonds.

    PubMed

    Fructos, Manuel R; Trofimenko, Swiatoslaw; Díaz-Requejo, M Mar; Pérez, Pedro J

    2006-09-13

    A simple copper-based catalytic system has been developed for the carbon-hydrogen amidation reaction. The copper-homoscorpionate complex Tp(Br3)Cu(NCMe) catalyzes the transfer of the nitrene unit NTs (Ts = p-toluenesulfonyl) and its subsequent insertion into the sp(3) C-H bonds of alkyl aromatic and cyclic ethers or the sp(2) C-H bonds of benzene using PhI=NTs as the nitrene source, affording the corresponding trisubstitued NR(1)HTs amines in moderate to high yields. The use of the environmentally friendly chloramine-T has also proven effective, with the advantage that sodium chloride is formed as the only byproduct. A tandem, one-pot consecutive nitrene-carbene insertion system has been developed to yield amino acid derivatives. PMID:16953617

  10. Amide bond formation through iron-catalyzed oxidative amidation of tertiary amines with anhydrides.

    PubMed

    Li, Yuanming; Ma, Lina; Jia, Fan; Li, Zhiping

    2013-06-01

    A general and efficient method for amide bond synthesis has been developed. The method allows for synthesis of tertiary amides from readily available tertiary amines and anhydrides in the presence of FeCl2 as catalyst and tert-butyl hydroperoxide in water (T-Hydro) as oxidant. Mechanistic studies indicated that the in situ-generated α-amino peroxide of tertiary amine and iminium ion act as key intermediates in this oxidative transformation. PMID:23668222

  11. 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. PMID:16373451

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

    PubMed

    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

  13. Interactions of Isonitriles with Metal-Boron Bonds: Insertions, Coupling, Ring Formation, and Liberation of Monovalent Boron.

    PubMed

    Braunschweig, Holger; Celik, Mehmet Ali; Dewhurst, Rian D; Ferkinghoff, Katharina; Hermann, Alexander; Jimenez-Halla, J Oscar C; Kramer, Thomas; Radacki, Krzysztof; Shang, Rong; Siedler, Eva; Weißenberger, Felix; Werner, Christine

    2016-08-01

    Boryl, borylene, and base-stabilized borylene complexes of manganese and iron undergo a range of different reactions when treated with isonitriles including single, double, and partial isonitrile insertions into metal-boron bonds, ring formation, isonitrile coupling, and the liberation of new monovalent boron species. Two of the resulting cyclic species have also been found to react selectively with anhydrous HCl to form ring-opened products. The diverse isonitrile-promoted reactivity of transition-metal-boron compounds has been explored computationally. PMID:27388206

  14. 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.

  15. 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

  16. Pair Bond Formation is Impaired by VPAC Receptor Antagonism in the Socially Monogamous Zebra Finch

    PubMed Central

    Kingsbury, Marcy A.; Goodson, James L.

    2014-01-01

    A variety of recent data demonstrate that vasoactive intestinal polypeptide (VIP) and VPAC receptors (which bind VIP, and to a lesser extent, pituitary adenylatecyclase activating peptide) are important for numerous social behaviors in songbirds, including grouping and aggression, although VIP relates to these behaviors in a site-specific manner. In order to determine the global effects of central VPAC receptor activation on social behavior, we here infused a VPAC receptor antagonist or vehicle twice daily into the lateral ventricle of colony-housed male and female zebra finches and quantified a wide range of behaviors. Aggressive behaviors were not altered by ventricular infusions, consistent with known opposing, site-specific relationships of VIP innervation to aggression. Courtship and self-maintenance behaviors were likewise not altered. However, VPAC antagonism produced significant deficits in pair bonding. Antagonist subjects took longer to form a pair bond and were paired for significantly fewer observation sessions relative to control subjects (median 1.5 of 6 observation sessions for antagonist subjects versus 4 for control subjects). Antagonist subjects were also significantly less likely to be paired in the final observation session. Based on the known distribution of VPAC receptors in finches and other vertebrates, we propose that VPAC receptors may mediate pair bonding via a variety of brain areas that are known to be important for the establishment of partner preferences in voles, including the lateral septum, ventral tegmental area, nucleus accumbens and ventral pallidum. PMID:25014003

  17. High-pressure synthesis of new materials via formation of new bonding patterns and unusual stoichiometries

    NASA Astrophysics Data System (ADS)

    Goncharov, Alexander

    2013-06-01

    The search for new materials synthesized under extreme conditions of high pressure and high pressure is currently actively pursued. There are multiple theoretical predictions for superior material properties, such as ultra-hardness, superior transport properties such as electrical and thermal conductivity, high energy-density, high-temperature superconductivity, ability to storage hydrogen, etc. Synthesis of new materials at high pressures is based on changes in the equilibrium chemical bonding. Moreover, materials with ``unusual'' stoichiometries have been predicted to become thermodynamically stable at high pressures. Implications of this novel extreme chemistry for synthesis of new materials for practical applications remain challenging because high-pressure bonding patterns are often thermodynamically unstable at ambient pressure. Search for a recovery mechanisms or attempts of synthesis in nominally metastable conditions require detailed knowledge of the energy landscape; extensive collaborative efforts of experiment and theory are needed for its determination. Here, I emphasize the importance for this task of in situ fast diagnostic methods. I will present new results on synthesis of materials with new bonding patterns and unusual stoichiometries containing hydrogen, nitrogen, carbon, and halogens. This work has been performed in collaboration with M. Somayazulu, V. V. Struzhkin, V. Prakapenka, E. Stavrou, T. Muramatsu,A. Oganov, W. Zhang, Q. Zhu, S. E. Boulfelfel, A. O. Lyakhov, Z. Konopkova, H.-P. Liermann, D.-Y. Kim. I acknowledge the support of NSF, EFRee (DOE), DARPA, Army Research Office, Deep Carbon Observatory.

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

    PubMed

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

    2015-09-21

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

  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. PMID:26343290

  20. Theoretical enthalpies of formation and O H bond dissociation enthalpy of an α-tocopherol model and its free radical

    NASA Astrophysics Data System (ADS)

    Espinosa-García, J.

    2004-04-01

    Using DFT computations (B3LYP and BHandHLYP functionals) with isodesmic reactions as working chemical reactions, and extended basis sets with diffuse functions, the standard enthalpies of formation of an α-tocopherol model (where the aliphatic chain and the neighbour methyl group have been changed to hydrogen atoms) and its free radical α-tocopheroxy were theoretically estimated for the first time: -79.4 ± 2.0, and -54.9 ± 2.0 kcal mol -1, respectively. These enthalpies of formation correspond to the O-H bond dissociation enthalpy of BDE(O-H)=76.6 ± 2.0 kcal mol -1, in excellent agreement with the gas-phase experimental value for natural α-tocopherol, which lends confidence to the method and model used.

  1. 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. PMID:25678276

  2. Bile salt–induced intermolecular disulfide bond formation activates Vibrio cholerae virulence

    PubMed Central

    Yang, Menghua; Liu, Zhi; Hughes, Chambers; Stern, Andrew M.; Wang, Hui; Zhong, Zengtao; Kan, Biao; Fenical, William; Zhu, Jun

    2013-01-01

    To be successful pathogens, bacteria must often restrict the expression of virulence genes to host environments. This requires a physical or chemical marker of the host environment as well as a cognate bacterial system for sensing the presence of a host to appropriately time the activation of virulence. However, there have been remarkably few such signal–sensor pairs identified, and the molecular mechanisms for host-sensing are virtually unknown. By directly applying a reporter strain of Vibrio cholerae, the causative agent of cholera, to a thin layer chromatography (TLC) plate containing mouse intestinal extracts, we found two host signals that activate virulence gene transcription. One of these was revealed to be the bile salt taurocholate. We then show that a set of bile salts cause dimerization of the transmembrane transcription factor TcpP by inducing intermolecular disulfide bonds between cysteine (C)-207 residues in its periplasmic domain. Various genetic and biochemical analyses led us to propose a model in which the other cysteine in the periplasmic domain, C218, forms an inhibitory intramolecular disulfide bond with C207 that must be isomerized to form the active C207–C207 intermolecular bond. We then found bile salt–dependent effects of these cysteine mutations on survival in vivo, correlating to our in vitro model. Our results are a demonstration of a mechanism for direct activation of the V. cholerae virulence cascade by a host signal molecule. They further provide a paradigm for recognition of the host environment in pathogenic bacteria through periplasmic cysteine oxidation. PMID:23341592

  3. Gold-catalyzed homogeneous oxidative C-O bond formation: efficient synthesis of 1-benzoxyvinyl ketones.

    PubMed

    Peng, Yu; Cui, Li; Zhang, Guozhu; Zhang, Liming

    2009-04-15

    A novel Au-catalyzed homogeneous oxidative C-O bond-forming reaction involving a Au(I)/Au(III) catalytic cycle is developed. Mechanistic studies reveal the involvement of a unique intramolecular carboxy migration. From readily available propargylic benzoates, this chemistry allows efficient access to captodative alkenes and dienones, demonstrating the synthetic potential of incorporating Au(I)/Au(III) catalytic cycles into contemporary Au chemistry. The unique reactivity and the mechanistic insights would help open a new research area in gold catalysis. PMID:19301899

  4. 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. PMID:23430602

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

    PubMed Central

    Moran, Joseph; Krische, Michael J.

    2013-01-01

    Ruthenium-catalyzed transfer hydrogenation of diverse 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. PMID:23430602

  6. 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. PMID:27392318

  7. Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate.

    PubMed

    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

  8. 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

  9. 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.

    2015-08-01

    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.

  10. 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.

  11. 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.

  12. Small molecule inhibitors of disulfide bond formation by the bacterial DsbA-DsbB dual enzyme system.

    PubMed

    Halili, Maria A; Bachu, Prabhakar; Lindahl, Fredrik; Bechara, Chérine; Mohanty, Biswaranjan; Reid, Robert C; Scanlon, Martin J; Robinson, Carol V; Fairlie, David P; Martin, Jennifer L

    2015-04-17

    The DsbA:DsbB redox machinery catalyzes disulfide bond formation in secreted proteins and is required for bacterial virulence factor assembly. Both enzymes have been identified as targets for antivirulence drugs. Here, we report synthetic analogues of ubiquinone (dimedone derivatives) that inhibit disulfide bond formation (IC50∼1 μM) catalyzed by E. coli DsbA:DsbB. The mechanism involves covalent modification of a single free cysteine leaving other cysteines unmodified. A vinylogous anhydride in each inhibitor is cleaved by the thiol, which becomes covalently modified to a thioester by a propionyl substituent. Cysteines and lysines on DsbA and DsbB and a nonredox enzyme were modified in a manner that implies some specificity. Moreover, human thioredoxin was not inhibited under the same conditions that inhibited EcDsbA. This proof of concept work uses small molecules that target specific cysteines to validate the DsbA and DsbB dual enzyme system as a viable and potentially druggable antivirulence target. PMID:25603425

  13. 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. PMID:22760882

  14. Enzyme mediated silicon-oxygen bond formation; the use of Rhizopus oryzae lipase, lysozyme and phytase under mild conditions.

    PubMed

    Abbate, Vincenzo; Bassindale, Alan R; Brandstadt, Kurt F; Lawson, Rachel; Taylor, Peter G

    2010-10-21

    The potential for expanding the variety of enzymic methods for siloxane bond formation is explored. Three enzymes, Rhizopus oryzae lipase (ROL), lysozyme and phytase are reported to catalyse the condensation of the model compound, trimethylsilanol, formed in situ from trimethylethoxysilane, to produce hexamethyldisiloxane in aqueous media at 25 °C and pH 7. Thermal denaturation and reactant inhibition experiments were conducted to better understand the catalytic role of these enzyme candidates. It was found that enzyme activities were significantly reduced following thermal treatment, suggesting a potential key-role of the enzyme active sites in the catalysis. Similarly, residue-specific modification of the key-amino acids believed to participate in the ROL catalysis also had a significant effect on the silicon bio-catalysis, indicating that the catalytic triad of the lipase may be involved during the enzyme-mediated formation of the silicon-oxygen bond. E. coli phytase was found to be particularly effective at catalysing the condensation of trimethylsilanol in a predominantly organic medium consisting of 95% acetonitrile and 5% water. Whereas the use of enzymes in silicon chemistry is still very much a developing and frontier activity, the results presented herein give some grounds for optimism that the variety of enzyme mediated reactions will continue to increase and may one day become a routine element in the portfolio of the synthetic silicon chemist. PMID:20683529

  15. 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)

  16. Oxo-group-14-element bond formation in binuclear uranium(V) Pacman complexes.

    PubMed

    Jones, Guy M; Arnold, Polly L; Love, Jason B

    2013-07-29

    Simple and versatile routes to the functionalization of uranyl-derived U(V)-oxo groups are presented. The oxo-lithiated, binuclear uranium(V)-oxo complexes [{(py)3LiOUO}2(L)] and [{(py)3LiOUO}(OUOSiMe3)(L)] were prepared by the direct combination of the uranyl(VI) silylamide "ate" complex [Li(py)2][(OUO)(N")3] (N" = N(SiMe3)2) with the polypyrrolic macrocycle H4L or the mononuclear uranyl (VI) Pacman complex [UO2(py)(H2L)], respectively. These oxo-metalated complexes display distinct U-O single and multiple bonding patterns and an axial/equatorial arrangement of oxo ligands. Their ready availability allows the direct functionalization of the uranyl oxo group leading to the binuclear uranium(V) oxo-stannylated complexes [{(R3Sn)OUO}2(L)] (R = nBu, Ph), which represent rare examples of mixed uranium/tin complexes. Also, uranium-oxo-group exchange occurred in reactions with [TiCl(OiPr)3] to form U-O-C bonds [{(py)3LiOUO}(OUOiPr)(L)] and [(iPrOUO)2(L)]. Overall, these represent the first family of uranium(V) complexes that are oxo-functionalised by Group 14 elements. PMID:23794441

  17. 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.

  18. 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.

  19. Formation of hydrogen-bonded chains through inter- and intra-molecular hydrogen bonds by a strong base of guanidine-like character and 2,2'-biphenols

    NASA Astrophysics Data System (ADS)

    Brzezinski, B.; Wojciechowski, G.; Bartl, F.; Zundel, G.

    2000-11-01

    2,2'-Biphenol mixtures with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) were studied by FTIR spectroscopy. In chloroform, a proton transfer from 2,2'-biphenol to MTBD occurs. In this solution the protonated MTBD molecules are hydrogen-bonded to the 2,2'-biphenol-2,2'-biphenolate chains. In acetonitrile, after the proton transfer, the complexes dissociate and hence protonated MTBD molecules and hydrogen-bonded 2,2'-biphenol-2,2'-biphenolate chains are present. The hydrogen bonds and the hydrogen-bonded chains show large proton polarizability. In the systems intra- as well as inter-molecular hydrogen bonds are formed.

  20. 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. PMID:26817657

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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. PMID:16010993

  6. Polymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies

    NASA Astrophysics Data System (ADS)

    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.

  7. Reusable ionic liquid-catalyzed oxidative coupling of azoles and benzylic compounds via sp(3) C-N bond formation under metal-free conditions.

    PubMed

    Liu, Wenbo; Liu, Chenjiang; Zhang, Yonghong; Sun, Yadong; Abdukadera, Ablimit; Wang, Bin; Li, He; Ma, Xuecheng; Zhang, Zengpeng

    2015-07-14

    The heterocyclic ionic liquid-catalyzed direct oxidative amination of benzylic sp(3) C-H bonds via intermolecular sp(3) C-N bond formation for the synthesis of N-alkylated azoles under metal-free conditions is reported for the first time. The catalyst 1-butylpyridinium iodide can be recycled and reused with similar efficacies for at least eight cycles. PMID:26060993

  8. C-N Bond Formation from a Masked High-Valent Copper Complex Stabilized by Redox Non-Innocent Ligands.

    PubMed

    Jacquet, Jérémy; Chaumont, Pauline; Gontard, Geoffrey; Orio, Maylis; Vezin, Hervé; Blanchard, Sébastien; Desage-El Murr, Marine; Fensterbank, Louis

    2016-08-26

    The reactivity of a stable copper(II) complex bearing fully oxidized iminobenzoquinone redox ligands towards nucleophiles is described. In sharp contrast with its genuine low-valent counterpart bearing reduced ligands, this complex performs high-yielding C-N bond formations. Mechanistic studies suggest that this behavior could stem from a mechanism akin to reductive elimination occurring at the metal center but facilitated by the ligand: it is proposed that a masked high oxidation state of the metal can be stabilized as a lower copper(II) oxidation state by the redox ligands without forfeiting its ability to behave as a high-valent copper(III) center. These observations are substantiated by a combination of advanced EPR spectroscopy techniques with DFT studies. This work sheds light on the potential of redox ligands as promoters of unusual reactivities at metal centers and illustrates the concept of masked high-valent metallic species. PMID:27504607

  9. 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. PMID:21080395

  10. The HNCO heat of formation and the N{endash}H and C{endash}N bond enthalpies from initial state selected photodissociation

    SciTech Connect

    Brown, S.S.; Berghout, H.L.; Crim, F.F.

    1996-11-01

    We measure upper limits for the bond enthalpies of the N{endash}H and C{endash}N bonds in HNCO by observation of photodissociation appearance thresholds for the NCO ({ital X}{sup 2}{Pi}) and NH ({ital a}{sup 1}{Delta}) fragments from initially selected HNCO vibrational states. The upper limit of the dissociation energy of the H{endash}N bond is {ital D}{sub 0}(H{endash}NCO){le}109.6{plus_minus}0.4 kcal/mol and that of the N{endash}C bond is {ital D}{sub 0} (HN{endash}CO){le}122.1{plus_minus}0.3 kcal/mol. Observation of unrelaxed fragment quantum state distributions at fixed energies supports the bond enthalpy measurement. The two appearance thresholds, together with known heats of formation of NH, NCO, H, and CO, provide two independent methods of calculating the HNCO heat of formation. Both methods give a value of {Delta}H{sub {ital f}{sub 0}}{sup 0} (HNCO){ge}{minus}27.7{plus_minus}1.1 kcal/mol. The consistency of the two methods for calculating {Delta}H{sub {ital f}{sub 0}}{sup 0} (HNCO) suggests that the actual bond enthalpies for the N{endash}H and C{endash}N bonds are close to the upper limits from the measurement. {copyright} {ital 1996 American Institute of Physics.}

  11. 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.

  12. 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

  13. Rotational and hinge dynamics of discoidal high density lipoproteins probed by interchain disulfide bond formation

    PubMed Central

    Li, Ling; Li, Songlin; Jones, Martin K.; Segrest, Jere P.

    2013-01-01

    To develop a detailed double belt model for discoidal HDL, we previously scored inter-helical salt bridges between all possible registries of two stacked antiparallel amphipathic helical rings of apolipoprotein (apo) A-I. The top score was the antiparallel apposition of helix 5 with 5 followed closely by appositions of helix 5 with 4 and helix 5 with 6. The rationale for the current study is that, for each of the optimal scores, a pair of identical residues can be identified in juxtaposition directly on the contact edge between the two antiparallel helical belts of apoA-I. Further, these residues are always in the ‘9th position’ in one of the eighteen 11-mer repeats that make up the lipid-associating domain of apoA-I. To illustrate our terminology, 129j (LL5/5) refers to the juxtaposition of the Ca atoms of G129 (in a ‘9th position’) in the pairwise helix 5 domains. We reasoned that if identical residues in the double belt juxtapositions were mutated to a cysteine and kept under reducing conditions during disc formation, we would have a precise method for determining registration in discoidal HDL by formation of a disulfide-linked apoA-I homodimer. Using this approach, we conclude that 129j (LL5/5) is the major rotamer orientation for double belt HDL and propose that the small ubiquitous gap between the pairwise helix 5 portions of the double belt in larger HDL discoidal particles is significantly dynamic to hinge off the disc edge under certain conditions, e.g., in smaller particles or perhaps following binding of the enzyme LCAT. PMID:22063273

  14. Directing Group in Decarboxylative Cross-Coupling: Copper-Catalyzed Site-Selective C-N Bond Formation from Nonactivated Aliphatic Carboxylic Acids.

    PubMed

    Liu, Zhao-Jing; Lu, Xi; Wang, Guan; Li, Lei; Jiang, Wei-Tao; Wang, Yu-Dong; Xiao, Bin; Fu, Yao

    2016-08-01

    Copper-catalyzed directed decarboxylative amination of nonactivated aliphatic carboxylic acids is described. This intramolecular C-N bond formation reaction provides efficient access to the synthesis of pyrrolidine and piperidine derivatives as well as the modification of complex natural products. Moreover, this reaction presents excellent site-selectivity in the C-N bond formation step through the use of directing group. Our work can be considered as a big step toward controllable radical decarboxylative carbon-heteroatom cross-coupling. PMID:27439145

  15. Succinimidyl residue formation in hen egg-white lysozyme favors the formation of intermolecular covalent bonds without affecting its tertiary structure.

    PubMed

    Desfougères, Yann; Jardin, Julien; Lechevalier, Valérie; Pezennec, Stéphane; Nau, Françoise

    2011-01-10

    Protein chemical degradations occur naturally into living cells as soon as proteins have been synthesized. Among these modifications, deamidation of asparagine or glutamine residues has been extensively studied, whereas the intermediate state, a succinimide derivative, was poorly investigated because of the difficulty of isolating those transient species. We used an indirect method, a limited thermal treatment in the dry state at acidic pH, to produce stable cyclic imide residues in hen lysozyme molecules, enabling us to examine the structural and functional properties of so modified proteins. Five cyclic imide rings have been located at sites directly accessible to solvent and did not lead to any changes in secondary or tertiary structures. However, they altered the catalytic properties of lysozyme and significantly decreased the intrinsic stability of the molecules. Moreover, dimerization occurred during the treatment, and this phenomenon was proportional to the extent of chemical degradation. We propose that succinimide formation could be responsible for covalent bond formation under specific physicochemical conditions that could be found in vivo. PMID:21166442

  16. 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.

  17. 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).

  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. Formation of C-C bonds by mandelonitrile lyase in organic solvents.

    PubMed

    Wehtje, E; Adlercreutz, P; Mattiasson, B

    1990-06-01

    Mandelonitrile lyase (EC 4.1.2.10) catalyzes the formation of D-mandelonitrile from HCN and benzaldehyde. Mandelonitrile lyase was immobilized by adsorption to support materials, for example, Celite. The enzyme preparations were used in diisopropyl ether for production of D-mandelonitrile. In order to obtain optically pure D-mandelonitrile it was necessary to use reaction conditions which favor the enzymatic reaction and suppress the competing spontaneous reaction, which yields a racemic mixture of D, L-mandelonitrile. The effects of substrate concentrations, water content, and support materials on both the spontaneous and enzymatic reactions were studied. The enzymatic reaction was carried out under conditions where the importance of the spontaneous reaction was negligible and high enantiomeric purity of D-mandelonitrile was achieved (at least 98% enantiomeric excess). The operational stability of the enzyme preparations was studied in batch as well as in continuous systems. It was vital to control the water content in the system to maintain an active preparation. In a packed bed reactor the enzyme preparations were shown to be active and stable. The reactors were run for 50 h with only a small decrease in product yield. PMID:18592607

  20. Structural Control of Nonadiabatic Photochemical Bond Formation: Photocyclization in Structurally Modified ortho-Terphenyls.

    PubMed

    Molloy, Molly S; Snyder, Joshua A; DeFrancisco, Justin R; Bragg, Arthur E

    2016-06-16

    Understanding how molecular structure impacts the shapes of potential energy surfaces and prospects for nonadiabatic photochemical dynamics is critical for predicting and controlling the chemistry of molecular excited states. Ultrafast transient absorption spectroscopy was used to interrogate photoinduced, nonadiabatic 6π cyclization of a collection of ortho-terphenyls (OTP) modified with alkyl substituents of different sizes and electron-donating/withdrawing character positioned on its central and pendant phenyl rings. OTP alkylated at the 4,4″ and 4',5' positions of the pendant and central rings, respectively, exhibiting biphasic excited-state relaxation; this is qualitatively similar to relaxation of OTP itself, including a fast decrease in excited-state absorption (τ1 = 1-4 ps) followed by formation of metastable cyclized photoproducts (τ2 = 3-47 ps) that share common characteristic spectroscopic features for all substitutions despite variations in chemical nature of the substituents. By contrast, anomalous excited-state dynamics are observed for 3',6'dimethyl-OTP, in which the methyl substituents crowd the pendant rings sterically; time-resolved spectral dynamics and low photochemical reactivity with iodine reveal that methylation proximal to the pendant rings impedes nonadiabatic cyclization. Results from transient measurements and quantum-chemical calculations are used to decipher the nature of excited state relaxation mechanisms in these systems and how they are perturbed by mechanical, electronic, and steric interactions induced by substituents. PMID:27171560

  1. 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

  2. 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

  3. 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

    2015-08-01

    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

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

    PubMed

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

    2016-04-21

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

  5. Formation of C(sp(3))-C(sp(3)) Bonds by Palladium Catalyzed Cross-Coupling of α-Diazoketones and Allylboronic Acids.

    PubMed

    Belhomme, Marie-Charlotte; Wang, Dong; Szabó, Kálmán J

    2016-05-20

    Palladium catalyzed cross-coupling of allylboronic acids with α-diazoketones was studied. The reaction selectively affords the linear allylic product. The reaction proceeds with formation of a new C(sp(3))-C(sp(3)) bond. The reaction was performed without an external oxidant, likely without the Pd-catalyst undergoing redox reactions. PMID:27166509

  6. Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. Transition Metal Free Intermolecular Direct Oxidative C-N Bond Formation to Polysubstituted Pyrimidines Using Molecular Oxygen as the Sole Oxidant.

    PubMed

    Guo, Wei; Li, Chunsheng; Liao, Jianhua; Ji, Fanghua; Liu, Dongqing; Wu, Wanqing; Jiang, Huanfeng

    2016-07-01

    Various polysubstituted pyrimidines are smoothly formed via a base-promoted intermolecular oxidation C-N bond formation of allylic C(sp(3))-H and vinylic C(sp(2))-H of allyllic compounds with amidines using O2 as the sole oxidant. This protocol features protecting group free nitrogen sources, good functional group tolerance, high atom economy, and environmental advantages. PMID:27275869

  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. PMID:21644532

  9. Bond formation and slow heterogeneous dynamics in adhesive spheres with long-ranged repulsion: quantitative test of mode coupling theory.

    PubMed

    Henrich, O; Puertas, A M; Sperl, M; Baschnagel, J; Fuchs, M

    2007-09-01

    A colloidal system of spheres interacting with both a deep and narrow attractive potential and a shallow long-ranged barrier exhibits a prepeak in the static structure factor. This peak can be related to an additional mesoscopic length scale of clusters and/or voids in the system. Simulation studies of this system have revealed that it vitrifies upon increasing the attraction into a gel-like solid at intermediate densities. The dynamics at the mesoscopic length scale corresponding to the prepeak represents the slowest mode in the system. Using mode coupling theory with all input directly taken from simulations, we reveal the mechanism for glassy arrest in the system at 40% packing fraction. The effects of the low-q peak and of polydispersity are considered in detail. We demonstrate that the local formation of physical bonds is the process whose slowing down causes arrest. It remains largely unaffected by the large-scale heterogeneities, and sets the clock for the slow cluster mode. Results from mode-coupling theory without adjustable parameters agree semiquantitatively with the local density correlators but overestimate the lifetime of the mesoscopic structure (voids). PMID:17930244

  10. On-Surface Synthesis of Two-Dimensional Covalent Organic Structures versus Halogen-Bonded Self-Assembly: Competing Formation of Organic Nanoarchitectures.

    PubMed

    Peyrot, David; Silly, Fabien

    2016-05-24

    The competition between the on-surface synthesis of covalent nanoarchitectures and the self-assembly of star-shaped 1,3,5-Tris(4-iodophenyl)benzene molecules on Au(111) in vacuum is investigated using scanning tunneling microscopy above room temperature. The molecules form covalent polygonal nanoachitectures at the gold surface step edges and at the elbows of the gold reconstruction at low coverage. With coverage increasing two-dimensional halogen-bonded structures appear and grow on the surface terraces. Two different halogen-bonded nanoarchitectures are coexisting on the surface and hybrid covalent-halogen bonded structures are locally observed. At high coverage covalent nanoarchitectures are squeezed at the domain boundary of the halogen-bonded structures. The competitive growth between the covalent and halogen-bonded nanoarchitectures leads to formation of a two-layer film above one monolayer deposition. For this coverage, the covalent nanoarchitectures are propelled on top of the halogen-bonded first layer. These observations open up new opportunities for decoupling covalent nanoarchitectures from catalytically active and metal surfaces in vacuum. PMID:27158901

  11. 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). PMID:27184004

  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. PMID:26201989

  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.

    PubMed

    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

  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. Isotopic studies of trans- and cis-HOCO using rotational spectroscopy: Formation, chemical bonding, and molecular structures

    NASA Astrophysics Data System (ADS)

    McCarthy, Michael C.; Martinez, Oscar; McGuire, Brett A.; Crabtree, Kyle N.; Martin-Drumel, Marie-Aline; Stanton, John F.

    2016-03-01

    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 + C18O reaction predominately yields HOC18O for both isomers, but H18OCO is observed as well, typically at the level of 10%-20% that of HOC18O; the opposite propensity is found for the 18OH + CO reaction. DO + C18O yields similar ratios between DOC18O and D18OCO as those found for OH + C18O, 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 13C Fermi-contact term (aF) for trans- and cis-HO13CO 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.

  17. 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

  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. PMID:25893018

  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. PMID:27036445

  20. Temperature evolution of structure and bonding of formic acid and formate on fully oxidized and highly reduced CeO2(111)

    SciTech Connect

    Gordon, Wesley O; Xu, Ye; Mullins, David R; Overbury, Steven {Steve} H

    2009-01-01

    Adsorption of formate on oxide surfaces plays a role in water-gas shift (WGS) and other reactions related to H2 production and CO2 utilization. CeO2 is of particular interest because its reducibility affects the redox of organic molecules. In this work, the adsorption and thermal evolution of formic acid and formate on highly ordered films of fully oxidized CeO2(111) and highly reduced CeOx(111) surfaces have been studied using reflection absorption infrared spectroscopy (RAIRS) under ultra-high vacuum conditions, and the experimental results are combined with density functional theory (DFT) calculations to probe the identity, symmetry, and bonding of the surface intermediates. Disordered ice, ordered a-polymorph and molecular formic acid bonded through the carbonyl are observed at low temperatures. By 250 K, desorption and deprotonation lead to formate coexisting with hydroxyl on CeO2(111), identified to be a bridging bidentate formate species that is coordinated to Ce cations in nearly C2v symmetry and interacting strongly with neighboring H. Changes in the spectra at higher temperatures are consistent with additional tilting of the formate, resulting in Cs(2) or lower symmetry. This change in bonding is caused primarily by interaction with oxygen vacancies introduced by water desorption at 300 K. On reduced CeOx, multiple low-symmetry formate states exist likewise due to interactions with oxygen vacancies. Isotopic studies demonstrate that the formyl hydrogen does not contribute to H incorporated in hydroxyl on the surface, and that both formate oxygen atoms may exchange with lattice oxygen at 400 K. The combined experimental and theoretical results thus provide important insights on the surface reaction pathways of formic acid on ceria.

  1. Femtosecond X-ray solution scattering reveals that bond formation mechanism of a gold trimer complex is independent of excitation wavelength

    PubMed Central

    Kim, Kyung Hwan; Kim, Jong Goo; Oang, Key Young; Kim, Tae Wu; Ki, Hosung; Jo, Junbeom; Kim, Jeongho; Sato, Tokushi; Nozawa, Shunsuke; Adachi, Shin-ichi; Ihee, Hyotcherl

    2016-01-01

    The [Au(CN)2−]3 trimer in water experiences a strong van der Waals interaction between the d10 gold atoms due to large relativistic effect and can serve as an excellent model system to study the bond formation process in real time. The trimer in the ground state (S0) exists as a bent structure without the covalent bond between the gold atoms, and upon the laser excitation, one electron in the antibonding orbital goes to the bonding orbital, thereby inducing the formation of a covalent bond between gold atoms. This process has been studied by various time-resolved techniques, and most of the interpretation on the structure and dynamics converge except that the structure of the first intermediate (S1) has been debated due to different interpretations between femtosecond optical spectroscopy and femtosecond X-ray solution scattering. Recently, the excitation wavelength of 267 nm employed in our previous scattering experiment was suggested as the culprit for misinterpretation. Here, we revisited this issue by performing femtosecond X-ray solution scattering with 310 nm excitation and compared the results with our previous study employing 267 nm excitation. The data show that a linear S1 structure is formed within 500 fs regardless of excitation wavelength and the structural dynamics observed at both excitation wavelengths are identical to each other within experimental errors. PMID:27191012

  2. Femtosecond X-ray solution scattering reveals that bond formation mechanism of a gold trimer complex is independent of excitation wavelength.

    PubMed

    Kim, Kyung Hwan; Kim, Jong Goo; Oang, Key Young; Kim, Tae Wu; Ki, Hosung; Jo, Junbeom; Kim, Jeongho; Sato, Tokushi; Nozawa, Shunsuke; Adachi, Shin-Ichi; Ihee, Hyotcherl

    2016-07-01

    The [Au(CN)2 (-)]3 trimer in water experiences a strong van der Waals interaction between the d(10) gold atoms due to large relativistic effect and can serve as an excellent model system to study the bond formation process in real time. The trimer in the ground state (S0) exists as a bent structure without the covalent bond between the gold atoms, and upon the laser excitation, one electron in the antibonding orbital goes to the bonding orbital, thereby inducing the formation of a covalent bond between gold atoms. This process has been studied by various time-resolved techniques, and most of the interpretation on the structure and dynamics converge except that the structure of the first intermediate (S1) has been debated due to different interpretations between femtosecond optical spectroscopy and femtosecond X-ray solution scattering. Recently, the excitation wavelength of 267 nm employed in our previous scattering experiment was suggested as the culprit for misinterpretation. Here, we revisited this issue by performing femtosecond X-ray solution scattering with 310 nm excitation and compared the results with our previous study employing 267 nm excitation. The data show that a linear S1 structure is formed within 500 fs regardless of excitation wavelength and the structural dynamics observed at both excitation wavelengths are identical to each other within experimental errors. PMID:27191012

  3. Titanium oxide complexes with dinitrogen. Formation and characterization of the side-on and end-on bonded titanium oxide-dinitrogen complexes in solid neon.

    PubMed

    Zhou, Mingfei; Zhuang, Jia; Zhou, Zijian; Li, Zhen Hua; Zhao, Yanying; Zheng, Xuming; Fan, Kangnian

    2011-06-23

    The reactions of titanium oxide molecules with dinitrogen have been studied by matrix isolation infrared spectroscopy. The titanium monoxide molecule reacts with dinitrogen to form the TiO(N(2))(x) (x = 1-4) complexes spontaneously on annealing in solid neon. The TiO(η(1)-NN) complex is end-on bonded and was predicted to have a (3)A'' ground state arising from the (3)Δ ground state of TiO. Argon doping experiments indicate that TiO(η(1)-NN) is able to form complexes with one or more argon atoms. Argon atom coordination induces a large red-shift of the N-N stretching frequency. The TiO(η(2)-N(2))(2) complex was characterized to have C(2v) symmetry, in which both the N(2) ligands are side-on bonded to the titanium metal center. The tridinitrogen complex TiO(η(1)-NN)(3) most likely has C(3v) symmetry with three end-on bonded N(2) ligands. The TiO(η(1)-NN)(4) complex was determined to have a C(4v) structure with four equivalent end-on bonded N(2) ligands. In addition, evidence is also presented for the formation of the TiO(2)(η(1)-NN)(x) (x = 1-4) complexes, which were predicted to be end-on bonded. PMID:21604730

  4. Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: the interplay between hydrophobic interactions and formation of intermolecular disulfide bonds.

    PubMed

    Xie, Jinbing; Qin, Meng; Cao, Yi; Wang, Wei

    2011-08-01

    Recently, it was reported that ultraviolet (UV) illumination could trigger the unfolding of proteins by disrupting the buried disulfide bonds. However, the consequence of such unfolding has not been adequately evaluated. Here, we report that unfolded chicken egg white lysozyme (CEWL) triggered by UV illumination can form uniform globular aggregates as confirmed by dynamic light scattering, atomic force microscopy, and transmission electron microscopy. The assembling process of such aggregates was also monitored by several other methods, such as circular dichroism, fluorescence spectroscopy, mass spectrometry based on chymotrypsin digestion, ANS-binding assay, Ellman essay, and SDS-PAGE. Our finding is that due to the dissociation of the native disulfide bonds by UV illumination, CEWL undergoes drastic conformational changes resulting in the exposure of some hydrophobic residues and free thiols. Subsequently, these partially unfolded molecules self-assemble into small granules driven by intermolecular hydrophobic interaction. With longer UV illumination or longer incubation time, these granules can further self-assemble into larger globular aggregates. The combined effects from both the hydrophobic interaction and the formation of intermolecular disulfide bonds dominate this process. Additionally, similar aggregation behavior can also be found in other three typical disulfide-bonded proteins, that is, α-lactalbumin, RNase A, and bovine serum albumin. Thus, we propose that such aggregation behavior might be a general mechanism for some disulfide-bonded proteins under UV irradiation. PMID:21661057

  5. An approach to benzophosphole oxides through silver- or manganese-mediated dehydrogenative annulation involving C-C and C-P bond formation.

    PubMed

    Unoh, Yuto; Hirano, Koji; Satoh, Tetsuya; Miura, Masahiro

    2013-12-01

    Benzophosphole construction was achieved through the Ag(I) -mediated dehydrogenative annulation of phenylphosphine oxides with internal alkynes in a process involving CC and CP bond formation. A wide range of asymmetrical phenylacetylenes could be employed and the reactions proceeded with perfect regioselectivity. Moreover, the annulation could be conducted even at room temperature when a Mn(III) promoter was used in place of Ag(I) . PMID:24127410

  6. 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).

  7. A Macroscopic Reaction: Direct Covalent Bond Formation between Materials Using a Suzuki-Miyaura Cross-Coupling Reaction

    NASA Astrophysics Data System (ADS)

    Sekine, Tomoko; Kakuta, Takahiro; Nakamura, Takashi; Kobayashi, Yuichiro; Takashima, Yoshinori; Harada, Akira

    2014-09-01

    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.

  8. A Macroscopic Reaction: Direct Covalent Bond Formation between Materials Using a Suzuki-Miyaura Cross-Coupling Reaction

    PubMed Central

    Sekine, Tomoko; Kakuta, Takahiro; Nakamura, Takashi; Kobayashi, Yuichiro; Takashima, Yoshinori; Harada, Akira

    2014-01-01

    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. PMID:25231557

  9. Cp*Rh(III)-Catalyzed Cross-Coupling of Alkyltrifluoroborate with α-Diazomalonates for C(sp(3))-C(sp(3)) Bond Formation.

    PubMed

    Lu, Yin-Suo; Yu, Wing-Yiu

    2016-03-18

    A Cp*Rh(III)-catalyzed cross-coupling of alkyltrifluoroborate with α-diazomalonates was developed; the C(sp(3))-C(sp(3)) bond coupled products were formed in up to 97% yields. The reaction tolerates some useful functional groups, including ketone, ester, amide, ether, sulfonyl, and thiophene. Electrospray ionization mass spectrometry (ESI-MS) analysis revealed the formation of a distinct molecular species corresponding to σ-alkylrhodium(III) complexes. The successful diazo coupling reaction may be attributed to coordination of the amide group that promotes stability of the alkylrhodium(III) complex through the formation of a five-membered metallacycle. PMID:26926387

  10. Carbon monoxide-induced dinitrogen cleavage with group 4 metallocenes: reaction scope and coupling to N-H bond formation and CO deoxygenation.

    PubMed

    Knobloch, Donald J; Lobkovsky, Emil; Chirik, Paul J

    2010-08-01

    The scope of CO-induced N(2) cleavage in a series of zirconocene and hafnocene complexes containing activated, side-on bound dinitrogen ligands has been studied. In each case, bridging oxamidide ligands, [N(2)C(2)O(2)](4-), were formed from N-N bond cleavage coupled to N-C and C-C bond assembly. For the zirconium examples, [(eta(5)-C(5)Me(4)H)(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) and [Me(2)Si(eta(5)-C(5)Me(4))(eta(5)-C(5)H(3)-3-(t)Bu)Zr](2)(mu(2),eta(2),eta(2)-N(2)), dinitrogen loss became competitive with N(2) carbonylation, and significant quantities of the zirconocene dicarbonyl accompanied oxamidide formation. In contrast, the hafnocene complex [(eta(5)-C(5)Me(4)H)(2)Hf](2)(mu(2),eta(2),eta(2)-N(2)) underwent clean carbonylative dinitrogen cleavage with no evidence of N(2) loss. CO-induced N(2) cleavage was also coupled to N-H bond formation by hydrogenation and C-H bond activation, as carbonylation of the zirconocene and hafnocene dinitrogen complexes in the presence of H(2) or phenylacetylene furnished isocyanato metallocene complexes with bridging imido (mu-NH) ligands. In the case of the ansa-hafnocene dinitrogen complex, replacing the dihydrogen atmosphere with various primary silanes yielded an isocyanato hafnocene mu-oxo hydride resulting from cleavage of N(2) and CO, the diatomics with the two strongest bonds in chemistry. PMID:20662528

  11. Cytoglobin ligand binding regulated by changing haem-co-ordination in response to intramolecular disulfide bond formation and lipid interaction.

    PubMed

    Beckerson, Penny; Wilson, Michael T; Svistunenko, Dimitri A; Reeder, Brandon J

    2015-01-01

    Cytoglobin (Cygb) is a hexa-co-ordinate haem protein from the globin superfamily with a physiological function that is unclear. We have previously reported that the haem co-ordination is changed in the presence of lipids, potentially transforming the redox properties of the protein and hence the function of Cygb in vivo. Recent research suggests that the protein can exist in a number of states depending on the integrity and position of disulfide bonds. In the present study, we show that the monomeric protein with an internal disulfide bond between the two cysteine residues Cys38 and Cys83, interacts with lipids to induce a change in haem co-ordination. The dimeric protein with intermolecular disulfide bonds and monomeric protein without an intramolecular disulfide bond does not exhibit these changes in haem co-ordination. Furthermore, monomeric Cygb with an intramolecular disulfide bond has significantly different properties, oxidizing lipid membranes and binding ligands more rapidly as compared with the other forms of the protein. The redox state of these cysteine residues in vivo is therefore highly significant and may be a mechanism to modulate the biochemical properties of the haem under conditions of stress. PMID:25327890

  12. Silicon-Carbon Bond Formation via Nickel-Catalyzed Cross-Coupling of Silicon Nucleophiles with Unactivated Secondary and Tertiary Alkyl Electrophiles.

    PubMed

    Chu, Crystal K; Liang, Yufan; Fu, Gregory C

    2016-05-25

    A wide array of cross-coupling methods for the formation of C-C bonds from unactivated alkyl electrophiles have been described in recent years. In contrast, progress in the development of methods for the construction of C-heteroatom bonds has lagged; for example, there have been no reports of metal-catalyzed cross-couplings of unactivated secondary or tertiary alkyl halides with silicon nucleophiles to form C-Si bonds. In this study, we address this challenge, establishing that a simple, commercially available nickel catalyst (NiBr2·diglyme) can achieve couplings of alkyl bromides with nucleophilic silicon reagents under unusually mild conditions (e.g., -20 °C); especially noteworthy is our ability to employ unactivated tertiary alkyl halides as electrophilic coupling partners, which is still relatively uncommon in the field of cross-coupling chemistry. Stereochemical, relative reactivity, and radical-trap studies are consistent with a homolytic pathway for C-X bond cleavage. PMID:27187869

  13. Origin of the synchronicity in bond formation in polar Diels-Alder reactions: an ELF analysis of the reaction between cyclopentadiene and tetracyanoethylene.

    PubMed

    Domingo, Luis R; Pérez, Patricia; Sáez, Jose A

    2012-05-21

    The origin of the synchronicity in C-C bond formation in polar Diels-Alder (P-DA) reactions involving symmetrically substituted electrophilic ethylenes has been studied by an ELF analysis of the electron reorganization along the P-DA reaction of cyclopentadiene (Cp) with tetracyanoethylene (TCE) at the B3LYP/6-31G* level. The present study makes it possible to establish that the synchronicity in C-C bond formation in P-DA reactions is controlled by the symmetric distribution of the electron-density excess reached in the electrophile through the charge transfer process, which can be anticipated by an analysis of the spin electron-density at the corresponding radical anion. The ELF comparative analysis of bonding along the DA reactions of Cp with ethylene and with TCE asserts that these DA reactions, which have a symmetric electron reorganization, do not have a cyclic electron reorganization as the pericyclic mechanism states. Due to the very limited number of cases of symmetrically substituted ethylenes, we can conclude that the synchronous mechanism is an exception of DA reactions. PMID:22527420

  14. Identification and characterization of the Escherichia coli gene dsbB, whose product is involved in the formation of disulfide bonds in vivo.

    PubMed Central

    Missiakas, D; Georgopoulos, C; Raina, S

    1993-01-01

    We have identified and characterized the Escherichia coli gene dsbB, whose product is required for disulfide bond formation of periplasmic proteins, by using two different approaches: (i) screening of a multicopy plasmid library for clones which protect E. coli from the lethal effects of dithiothreitol (DTT), and (ii) screening of insertion libraries of E. coli for DTT-sensitive mutants. Mapping and characterization of mutations conferring a DTT-sensitive phenotype also identified the dsbA, trxA, and trxB genes, whose products are involved in different oxidation-reduction pathways. Null mutations in dsbB conferred pleiotropic phenotypes such as sensitivity to benzylpenicillin and inability to support plaque formation of filamentous phages, and they were shown to severely affect disulfide bond oxidation of secreted proteins such as OmpA and beta-lactamase. These phenotypes resemble the phenotype of bacteria carrying either a null mutation in the dsbA gene or the double mutation dsbA dsbB. Sequencing and expression of the dsbB gene revealed that it encodes a 20-kDa protein predicted to possess an "exchangeable" disulfide bond in -Cys-Val-Leu-Cys-. The dsbB gene maps at 26.5 min on the genetic map of the E. coli chromosome, and its transcription is directed from two promoters, neither of which resembles the canonical E sigma 70-recognized promoter. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:7688471

  15. 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.

  16. 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.

  17. Substrate Controlled Synthesis of Benzisoxazole and Benzisothiazole Derivatives via PhI(OAc)2-Mediated Oxidation Followed by Intramolecular Oxidative O-N/S-N Bond Formation.

    PubMed

    Anand, Devireddy; Patel, Om P S; Maurya, Rahul K; Kant, Ruchir; Yadav, Prem P

    2015-12-18

    A phenyliodine(III) diacetate (PIDA)-mediated, highly efficient and tandem approach for the synthesis of aryldiazenylisoxazolo(isothiazolo)arenes from simple 2-amino-N'-arylbenzohydrazides has been developed. The reaction proceeds via formation of (E)-(2-aminoaryl)(aryldiazenyl)methanone as the key intermediate, followed by intramolecular oxidative O-N/S-N bond formation in one pot at room temperature. The quiet different reactivity of the substrate is due to the formation of a diazo intermediate which encounters a nucleophilic attack by carbonyl oxygen on the electrophilic amine to produce isoxazole products, as compared to the previous reportsa,b,4 in which an N-acylnitrenium ion intermediate is intramolecularly trapped by an amine group. PMID:26565748

  18. Stereoelectronic control in peptide bond formation. Ab initio calculations and speculations on the mechanism of action of serine proteases.

    PubMed Central

    Gorenstein, D G; Taira, K

    1984-01-01

    Ab initio molecular orbital calculations have been performed on the reaction profile for the addition/elimination reaction between ammonia and formic acid, proceeding via a tetrahedral intermediate: NH3 + HCO2H----H2NCH(OH)2----NH2CHO + H2O. Calculated transition state energies for the first addition step of the reaction revealed that a lone pair on the oxygen of the OH group, which is antiperiplanar to the attacking nitrogen, stabilized the transition state by 3.9 kcal/mol, thus supporting the hypothesis of stereoelectronic control for this reaction. In addition, a secondary, counterbalancing stereoelectronic effect stabilizes the second step, water elimination, transition state by 3.1 kcal/mol if the lone pair on the leaving water oxygen is not antiperiplanar to the C-N bond. The best conformation for the transition states was thus one with a lone pair antiperiplanar to the adjacent scissile bond and also one without a lone-pair orbital on the scissile bond oxygen or nitrogen antiperiplanar to the adjacent polar bond. The significance of these stereoelectronic effects for the mechanism of action of serine proteases is discussed. PMID:6394065

  19. Coherent vibration and ultrafast dynamics upon bond formation in excited dimers of an Au(i) complex.

    PubMed

    Iwamura, Munetaka; Wakabayashi, Ryo; Maeba, Junichi; Nozaki, Koichi; Takeuchi, Satoshi; Tahara, Tahei

    2016-02-10

    Au-Au bond strengthening in photoexcited dimers of an Au(i) complex is captured in solution as oscillations of femtosecond absorption signals. The subsequent dynamics, when compared to the trimer's data, confirm that the bent-to-linear structural change of the trimer occurs in the first few picoseconds. PMID:26821585

  20. 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

    2015-01-01

    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

  1. 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. PMID:17039383

  2. Transmembrane Domain Interactions and Residue Proline 378 Are Essential for Proper Structure, Especially Disulfide Bond Formation, in the Human Vitamin K-Dependent γ-Glutamyl Carboxylase†

    PubMed Central

    Tie, Jian-Ke; Zheng, Mei-Yan; Hsiao, Kuang-Ling N.; Perera, Lalith; Stafford, Darrel W.; Straight, David L.

    2009-01-01

    We used recombinant techniques to create a two-chain form (residues 1–345 and residues 346–758) of the vitamin K-dependent γ-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. PMID:18498174

  3. 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

    2016-06-01

    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

  4. The Radical S-Adenosyl-L-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds.

    PubMed

    Nakai, Tadashi; Ito, Hiroto; Kobayashi, Kazuo; Takahashi, Yasuhiro; Hori, Hiroshi; Tsubaki, Motonari; Tanizawa, Katsuyuki; Okajima, Toshihide

    2015-04-24

    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

  5. 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

  6. Evidence that the pathway of disulfide bond formation in Escherichia coli involves interactions between the cysteines of DsbB and DsbA.

    PubMed Central

    Guilhot, C; Jander, G; Martin, N L; Beckwith, J

    1995-01-01

    Disulfide bond formation is catalyzed in the periplasm of Escherichia coli. This process involves at least two proteins: DsbA and DsbB. Recent evidence suggests that DsbA, a soluble periplasmic protein directly catalyzes disulfide bond formation in proteins, whereas DsbB, an inner membrane protein, is involved in the reoxidation of DsbA. Here we present direct evidence of an interaction between DsbA and DsbB. (Kishigami et al. [Kishigami, S., Kanaya, E., Kikuchi, M. & Ito, K. (1995) J. Biol. Chem. 270, 17072-17074] have described similar findings.) We isolated a dominant negative mutant of dsbA, dsbAd, where Cys-33 of the DsbA active site is changed to tyrosine. Both DsbAd and DsbA are able to form a mixed disulfide with DsbB, which may be an intermediate in the reoxidation of DsbA. This complex is more stable with DsbAd. The dominance can be suppressed by increasing the production of DsbB. By using mutants of DsbB in which one or two cysteines have been changed to alanine, we show that only Cys-104 is important for complex formation. Therefore, we suggest that in vivo, reduced DsbA forms a complex with DsbB in which Cys-30 of DsbA is disulfide-bonded to Cys-104 of DsbB. Cys-104 is rapidly replaced by Cys-33 of DsbA to generate the oxidized form of this protein. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:7568240

  7. 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

  8. Rhodium-catalysed C(sp(2))-C(sp(2)) bond formation via C-H/C-F activation.

    PubMed

    Tian, Panpan; Feng, Chao; Loh, Teck-Peng

    2015-01-01

    Fluoroalkenes represent a class of privileged structural motifs, which found widespread use in medicinal chemistry. However, the synthetic access to fluoroalkenes was much underdeveloped with previous reported methods suffering from either low step economy or harsh reaction conditions. Here we present a Rh(III)-catalysed tandem C-H/C-F activation for the synthesis of (hetero)arylated monofluoroalkenes. The use of readily available gem-difluoroalkenes as electrophiles provides a highly efficient and operationally simple method for the introduction of α-fluoroalkenyl motifs onto (hetero)arenes under oxidant-free conditions. Furthermore, the employment of alcoholic solvent and the in-situ generated hydrogen fluoride are found to be beneficial in this transformation, indicating the possibility of the involvement of hydrogen bond activation mode with regards to the C-F bond cleavage step. PMID:26081837

  9. 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. PMID:25671389

  10. Copper-Catalyzed Phosphonation-Annulation Approaches to the Synthesis of β-Phosphonotetrahydrofurans Involving C-P and C-O Bonds Formation.

    PubMed

    Gao, Yuzhen; Li, Xueqin; Chen, Weizhu; Tang, Guo; Zhao, Yufen

    2015-11-20

    Substituted tetrahydrofuran derivatives play important roles as biological activities. A versatile method for the synthesis of β-phosphonotetrahydrofurans has been developed based on Cu-catalyzed difunctionalization of alkenes. This transformation would provide a new pathway for the formation of Csp(3)-P and Csp(3)-O bonds in one step. Furthermore, this copper catalyst system can be used in the synthesis of β-phosphonotetrahydropyrans and phosphono-γ-butyrolactones. These reactions were also performed well by using 3 equiv of Mn(OAc)3·2H2O as the oxidant without copper catalyst. PMID:26523923

  11. 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

  12. C-C Bond Formation: Synthesis of C5 Substituted Pyrimidine and C8 Substituted Purine Nucleosides Using Water Soluble Pd-imidate Complex.

    PubMed

    Gayakhe, Vijay; Ardhapure, Ajaykumar V; Kapdi, Anant R; Sanghvi, Yogesh S; Serrano, Jose Luis; Schulzke, Carola

    2016-01-01

    The synthesis of a highly efficient, water soluble [Pd(Sacc)2 (TPA)2 ] complex for C-C bond formation is described. Additionally, application of the [Pd(Sacc)2 (TPA)2 ] complex for Suzuki-Miyaura arylation of all four nucleosides (5-iodo-2'-deoxyuridine [5-IdU], 5-iodo-2'-deoxycytidine [5-IdC], 8-bromo-2'-deoxyadenosine, and 8-bromo-2'-deoxyguanosine) with various aryl/heteroaryl boronic acids in plain water under milder conditions is demonstrated. © 2016 by John Wiley & Sons, Inc. PMID:27248782

  13. B-N, B-O, and B-CN Bond Formation via Palladium-Catalyzed Cross-Coupling of B-Bromo-Carboranes.

    PubMed

    Dziedzic, Rafal M; Saleh, Liban M A; Axtell, Jonathan C; Martin, Joshua L; Stevens, Simone L; Royappa, A Timothy; Rheingold, Arnold L; Spokoyny, Alexander M

    2016-07-27

    Carboranes are boron-rich molecules that can be functionalized through metal-catalyzed cross-coupling. Here, for the first time, we report the use of bromo-carboranes in palladium-catalyzed cross-coupling for efficient B-N, B-O, and unprecedented B-CN bond formation. In many cases bromo-carboranes outperform the traditionally utilized iodo-carborane species. This marked difference in reactivity is leveraged to circumvent multistep functionalization by directly coupling small nucleophiles (-OH, -NH2, and -CN) and multiple functional groups onto the boron-rich clusters. PMID:27384544

  14. Formation of the Δ18,19 Double Bond and Bis(spiroacetal) in Salinomycin Is Atypically Catalyzed by SlnM, a Methyltransferase‐like Enzyme†

    PubMed Central

    Jiang, Chunyan; Qi, Zhen; Kang, Qianjin; Liu, Jing; Jiang, Ming

    2015-01-01

    Abstract Salinomycin is a widely used polyether coccidiostat and was recently found to have antitumor activities. However, the mechanism of its biosynthesis remained largely speculative until now. Reported herein is the identification of an unprecedented function of SlnM, homologous to O‐methyltransferases, by correlating its activity with the formation of the Δ18,19 double bond and bis(spiroacetal). Detailed in vivo and in vitro investigations revealed that SlnM, using positively charged S‐adenosylmethionine (SAM) or sinefungin as the cofactor, catalyzed the spirocyclization‐coupled dehydration of C19 in a highly atypical fashion to yield salinomycin. PMID:26096919

  15. Intramolecular electron density redistribution upon hydrogen bond formation in the anion methyl orange at the water/1,2-dichloroethane interface probed by phase interference second harmonic generation

    PubMed

    Rinuy; Piron; Brevet; Blanchard-Desce; Girault

    2000-09-15

    Surface second harmonic generation (SSHG) studies of the azobenzene derivative p-dimethylaminoazobenzene sulfonate, often referred as Methyl Orange (MO), at the neat water/1,2-dichloroethane (DCE) interface is reported. The two forms of the anionic MO dye, which are usually observed in bulk solution, with one form being hydrogen bonded to a water molecule through the azo nitrogens (MO/H2O) and the other form not being hydrogen bonded (MO) have also been observed at the water/DCE interface. Their equilibrium constant has been compared with the corresponding bulk solution and found to be identical. The adsorption equilibrium of the two forms has been determined and the Gibbs energy of adsorption measured to be -30 kJmol(-1) for both forms. From a light polarisation analysis of the SH signal, the angle of orientation of the MO transition dipole moment was found to be 34 +/- 2 degrees for MO and 43 +/- 2 degrees for MO/H2O under the assumption of a Dirac delta function for the angle distribution, a difference explained by the different solvation properties of the two forms. Furthermore, the wavelength dependence analysis of these data revealed an interference pattern resulting from the electronic density redistribution within the hydrated anionic form occurring upon the formation of the hydrogen bond with a water molecule. This interference pattern was clearly evidenced with the use of another dye at the interface in order to define a phase reference to both forms of Methyl Orange. PMID:11039537

  16. Two [4Fe-4S] clusters containing radical SAM enzyme SkfB catalyze thioether bond formation during the maturation of the sporulation killing factor.

    PubMed

    Flühe, Leif; Burghaus, Olaf; Wieckowski, Beata M; Giessen, Tobias W; Linne, Uwe; Marahiel, Mohamed A

    2013-01-23

    The sporulation killing factor (SKF) is a 26-residue ribosomally assembled and posttranslationally modified sactipeptide. It is produced by Bacillus subtilis 168 and plays a key role in its sporulation. Like all sactipeptides, SKF contains a thioether bond, which links the cysteine residue Cys4 with the α-carbon of the methionine residue Met12. In this study we demonstrate that this bond is generated by the two [4Fe-4S] clusters containing radical SAM enzyme SkfB, which is encoded in the skf operon. By mutational analysis of both cluster-binding sites, we were able to postulate a mechanism for thioether generation which is in agreement with that of AlbA. Furthermore, we were able to show that thioether bond formation is specific toward hydrophobic amino acids at the acceptor site. Additionally we demonstrate that generation of the thioether linkage is leader-peptide-dependent, suggesting that this reaction is the first step in SKF maturation. PMID:23282011

  17. 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

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

    PubMed

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

    2016-04-26

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

  19. 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

  20. 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. PMID:26685710

  1. 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)

  2. Controlling pore assembly of staphylococcal gamma-haemolysin by low temperature and by disulphide bond formation in double-cysteine LukF mutants.

    PubMed

    Nguyen, Vananh T; Higuchi, Hideo; Kamio, Yoshiyuki

    2002-09-01

    Staphylococcal LukF and Hlg2 are water-soluble monomers of gamma-haemolysin that assemble into oligomeric pores on the erythrocyte membranes. Here, we have created double-cysteine LukF mutants, in which single disulphide bonds connect either the prestem domain and the cap domain (V12C-T136C, Cap-Stem), or two beta-strands within the prestem domain (T117C-T136C, Stem-Stem) to control pore assembly of gamma-haemolysin at intermediate stages. The disulphide-trapped mutants were inactive in erythrocyte lysis, but gained full haemolytic activity if the disulphide bonds were reduced. The disulphide bonds blocked neither the membrane binding ability nor the intermediate prepore oligomerization, but efficiently inhibited the transition from prepores to pores. The prepores of Cap-Stem were dissociated into monomers in 1% SDS. In contrast, the prepores of Stem-Stem were stable in SDS and had ring-shaped structures similar to those of wild-type LukF, as observed by transmission electron microscopy. The transition of both mutants from prepores to pores could even be achieved by reducing disulphide bonds at low temperature (2 degrees C), whereas prepore oligomerization was effectively inhibited by low temperature. Finally, real-time transition of Stem-Stem from prepores to pores on ghost cells, visualized using a Ca2+-sensitive fluorescent indicator (Rhod2), was shown by the sequential appearance of fluorescence spots, indicating pore-opening events. Taken together, these data indicate that the prepores are legitimate intermediates during gamma-haemolysin pore assembly, and that conformational changes around residues 117 and 136 of the prestem domain are essential for pore formation, but not for membrane binding or prepore oligomerization. We propose a mechanism for gamma-haemolysin pore assembly based on the demonstrated intermediates. PMID:12354220

  3. 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

  4. Interaction of 1,2,5-chalcogenadiazole derivatives with thiophenolate: hypercoordination with formation of interchalcogen bond versus reduction to radical anion.

    PubMed

    Suturina, Elizaveta A; Semenov, Nikolay A; Lonchakov, Anton V; Bagryanskaya, Irina Yu; Gatilov, Yuri V; Irtegova, Irina G; Vasilieva, Nadezhda V; Lork, Enno; Mews, Rüdiger; Gritsan, Nina P; Zibarev, Andrey V

    2011-05-12

    According to the DFT calculations, [1,2,5]thiadiazolo[3,4-c][1,2,5]thiadiazole (4), [1,2,5]selenadiazolo[3,4-c][1,2,5]thiadiazole (5), 3,4-dicyano-1,2,5-thiadiazole (6), and 3,4-dicyano-1,2,5-selenadiazole (7) have nearly the same positive electron affinity (EA). Under the CV conditions they readily produce long-lived π-delocalized radical anions (π-RAs) characterized by EPR. Whereas 4 and 5 were chemically reduced into the π-RAs with thiophenolate (PhS(-)), 6 did not react and 7 formed a product of hypercoordination at the Se center (9) isolated in the form of the thermally stable salt [K(18-crown-6)][9] (10). The latter type of reactivity has never been observed previously for any 1,2,5-chalcogenadiazole derivatives. The X-ray structure of salt 10 revealed that the Se-S distance in the anion 9 (2.722 Å) is ca. 0.5 Å longer than the sum of the covalent radii of these atoms but ca. 1 Å shorter than the sum of their van der Waals radii. According to the QTAIM and NBO analysis, the Se-S bond in 9 can be considered a donor-acceptor bond whose formation leads to transfer of ca. 40% of negative charge from PhS(-) onto the heterocycle. For various PhS(-)/1,2,5-chalcogenadiazole reaction systems, thermodynamics and kinetics were theoretically studied to rationalize the interchalcogen hypercoordination vs reduction to π-RA dichotomy. It is predicted that interaction between PhS(-) and 3,4-dicyano-1,2,5-telluradiazole (12), whose EA slightly exceeds that of 6 and 7, will lead to hypercoordinate anion (17) with the interchalcogen Te-S bond being stronger than the Se-S bond observed in anion 9. PMID:21500829

  5. Identification of protein disulfide isomerase 1 as a key isomerase for disulfide bond formation in apolipoprotein B100.

    PubMed

    Wang, Shiyu; Park, Shuin; Kodali, Vamsi K; Han, Jaeseok; Yip, Theresa; Chen, Zhouji; Davidson, Nicholas O; Kaufman, Randal J

    2015-02-15

    Apolipoprotein (apo) B is an obligatory component of very low density lipoprotein (VLDL), and its cotranslational and posttranslational modifications are important in VLDL synthesis, secretion, and hepatic lipid homeostasis. ApoB100 contains 25 cysteine residues and eight disulfide bonds. Although these disulfide bonds were suggested to be important in maintaining apoB100 function, neither the specific oxidoreductase involved nor the direct role of these disulfide bonds in apoB100-lipidation is known. Here we used RNA knockdown to evaluate both MTP-dependent and -independent roles of PDI1 in apoB100 synthesis and lipidation in McA-RH7777 cells. Pdi1 knockdown did not elicit any discernible detrimental effect under normal, unstressed conditions. However, it decreased apoB100 synthesis with attenuated MTP activity, delayed apoB100 oxidative folding, and reduced apoB100 lipidation, leading to defective VLDL secretion. The oxidative folding-impaired apoB100 was secreted mainly associated with LDL instead of VLDL particles from PDI1-deficient cells, a phenotype that was fully rescued by overexpression of wild-type but not a catalytically inactive PDI1 that fully restored MTP activity. Further, we demonstrate that PDI1 directly interacts with apoB100 via its redox-active CXXC motifs and assists in the oxidative folding of apoB100. Taken together, these findings reveal an unsuspected, yet key role for PDI1 in oxidative folding of apoB100 and VLDL assembly. PMID:25518935

  6. Formation of C(sp(3) )-C(sp(3) ) Bonds through Nickel-Catalyzed Decarboxylative Olefin Hydroalkylation Reactions.

    PubMed

    Lu, Xi; Xiao, Bin; Liu, Lei; Fu, Yao

    2016-08-01

    Olefins and carboxylic acids are among the most important feedstock compounds. They are commonly found in natural products and drug molecules. We report a new reaction of nickel-catalyzed decarboxylative olefin hydroalkylation, which provides a novel practical strategy for the construction of C(sp(3) )-C(sp(3) ) bonds. This reaction can tolerate a variety of synthetically relevant functional groups and shows good chemo- and regioselectivity. It enables cross-coupling of complex organic molecules containing olefin groups and carboxylic acid groups in a convergent fashion. PMID:27245257

  7. Imaging ion-molecule reactions: Charge transfer and C-N bond formation in the C{sup +}+ NH{sub 3} system

    SciTech Connect

    Pei, Linsen; Farrar, James M.

    2012-05-28

    The velocity mapping ion imaging method is applied to the ion-molecule reactions occurring between C{sup +} and NH{sub 3}. The velocity space images are collected over the relative collision energy range from 1.5 to 3.3 eV, allowing both product kinetic energy distributions and angular distributions to be obtained from the data. The charge transfer process appears to be direct, dominated by long-range electron transfer that results in minimal deflection of the products. The product kinetic energy distributions are consistent with a process dominated by energy resonance. The kinetic energy distributions for C-N bond formation appear to scale with the total available energy, providing strong evidence that energy in the [CNH{sub 3}]{sup +} precursor to products is distributed statistically. The angular distributions for C-N bond formation show pronounced forward-backward symmetry, as expected for a complex that resembles a prolate symmetric top decaying along its symmetry axis.

  8. 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

  9. Correlating Extent of Pt–Ni Bond Formation with Low-temperature Hydrogenation of Benzene and 1,3-butadiene over Supported Pt/Ni Bimetallic Catalysts

    SciTech Connect

    Lonergan, W.; Vlachos, D; Chen, J

    2010-01-01

    Low-temperature hydrogenation of benzene and 1,3-butadiene on supported Pt/Ni catalysts have been used as probe reactions to correlate hydrogenation activity with the extent of Pt-Ni bimetallic bond formation. Pt/Ni bimetallic and Pt and Ni monometallic catalysts were supported on {gamma}-Al{sub 2}O{sub 3} using incipient wetness impregnation. Two sets of bimetallic catalysts were synthesized: one set to study the effect of metal atomic ratio and the other to study the effect of impregnation sequence. Fourier transform infrared spectroscopy (FTIR) CO adsorption studies were performed to characterize the surface composition of the bimetallic nanoparticles, and transmission electron microscopy (TEM) was utilized to characterize the particle size distribution. Batch reactor studies with FTIR demonstrated that all bimetallic catalysts outperformed monometallic catalysts for both benzene and 1,3-butadiene hydrogenation. Within the two sets of bimetallic catalysts, it was found that catalysts with a smaller Pt:Ni ratio possessed higher hydrogenation activity and that catalysts synthesized using co-impregnation had greater activity than sequentially impregnated catalysts. Extended X-ray absorption fine structure (EXAFS) measurements were performed in order to verify the extent of Pt-Ni bimetallic bond formation, which was found to correlate with the hydrogenation activity.

  10. The high yielding synthesis of pillar[5]arenes under Friedel-Crafts conditions explained by dynamic covalent bond formation.

    PubMed

    Holler, Michel; Allenbach, Nicolas; Sonet, Jordan; Nierengarten, Jean-François

    2012-03-01

    Systematic investigations of the cyclooligomerization of 1,4-disubstituted hydroquinone derivatives under Friedel-Crafts conditions have been carried out to demonstrate that the formation of pillar[5]arenes occurs under thermodynamic control. PMID:22159430

  11. A nanosensor for in vivo selenol imaging based on the formation of AuSe bonds.

    PubMed

    Hu, Bo; Cheng, Ranran; Liu, Xiaojun; Pan, Xiaohong; Kong, Fanpeng; Gao, Wen; Xu, Kehua; Tang, Bo

    2016-06-01

    Selenol is a key metabolite of Na2SeO3 and plays an important role in many physiological and pathological processes. The real-time monitoring of selenol is of scientific interest for understanding the anti-cancer mechanism of Na2SeO3. Based on selenol's ability to specifically break AuS bonds and form more stable AuSe bonds on the surfaces of gold nanoparticles (AuNPs), we developed a novel near-infrared fluorescent nanosensor (Cy5.5-peptide-AuNPs) for detecting selenol. The nanosensor exhibited rapid response to selenol with high selectivity and sensitivity, and it was successfully used to image changes in the selenol level in HepG2 cells during Na2SeO3-induced apoptosis. Moreover, in vivo fluorescence imaging of selenol was obtained from H22 tumor-bearing mice injected with both the nanosensor and sodium selenite. The results showed that the tumor cell apoptosis induced by Na2SeO3 is correlated with high-level of selenol under hypoxic conditions. We believe that this nanosensor could serve as a powerful tool for monitoring selenol and exploring the physiological function of selenol in a variety of physiological and pathological contexts and that the probe-designed strategy will provide a new platform for research on relevant selenium chemistry. PMID:27043769

  12. 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.

  13. 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).

  14. The Shono-type electroorganic oxidation of unfunctionalised amides. Carbon–carbon bond formation via electrogenerated N-acyliminium ions

    PubMed Central

    2014-01-01

    Summary N-acyliminium ions are useful reactive synthetic intermediates in a variety of important carbon–carbon bond forming and cyclisation strategies in organic chemistry. The advent of an electrochemical anodic oxidation of unfunctionalised amides, more commonly known as the Shono oxidation, has provided a complementary route to the C–H activation of low reactivity intermediates. In this article, containing over 100 references, we highlight the development of the Shono-type oxidations from the original direct electrolysis methods, to the use of electroauxiliaries before arriving at indirect electrolysis methodologies. We also highlight new technologies and techniques applied to this area of electrosynthesis. We conclude with the use of this electrosynthetic approach to challenging syntheses of natural products and other complex structures for biological evaluation discussing recent technological developments in electroorganic techniques and future directions. PMID:25670975

  15. The Shono-type electroorganic oxidation of unfunctionalised amides. Carbon-carbon bond formation via electrogenerated N-acyliminium ions.

    PubMed

    Jones, Alan M; Banks, Craig E

    2014-01-01

    N-acyliminium ions are useful reactive synthetic intermediates in a variety of important carbon-carbon bond forming and cyclisation strategies in organic chemistry. The advent of an electrochemical anodic oxidation of unfunctionalised amides, more commonly known as the Shono oxidation, has provided a complementary route to the C-H activation of low reactivity intermediates. In this article, containing over 100 references, we highlight the development of the Shono-type oxidations from the original direct electrolysis methods, to the use of electroauxiliaries before arriving at indirect electrolysis methodologies. We also highlight new technologies and techniques applied to this area of electrosynthesis. We conclude with the use of this electrosynthetic approach to challenging syntheses of natural products and other complex structures for biological evaluation discussing recent technological developments in electroorganic techniques and future directions. PMID:25670975

  16. Theoretical study on the transition-metal oxoboryl complex: M-BO bonding nature, mechanism of the formation reaction, and prediction of a new oxoboryl complex.

    PubMed

    Zeng, Guixiang; Sakaki, Shigeyoshi

    2012-04-16

    The Pt-BO bonding nature and the formation reaction of the experimentally reported platinum(II) oxoboryl complex, simplified to PtBr(BO)(PMe(3))(2), were theoretically investigated with the density functional theory method. The BO(-) ligand was quantitatively demonstrated to have extremely strong σ-donation but very weak d(π)-electron-accepting abilities. Therefore, it exhibits a strong trans influence. The formation reaction occurs through a four-center transition state, in which the B(δ+)-Br(δ-) polarization and the Br → Si and O p(π) → B p(π) charge-transfer interactions play key roles. The Gibbs activation energy (ΔG°(++)) and Gibbs reaction energy (ΔG°) of the formation reaction are 32.2 and -6.1 kcal/mol, respectively. The electron-donating bulky phosphine ligand is found to be favorable for lowering both ΔG°(++) and ΔG°. In addition, the metal effect is examined with the nickel and palladium analogues and MBrCl[BBr(OSiMe(3))](CO)(PR(3))(2) (M = Ir and Rh). By a comparison of the ΔG°(++) and ΔG° values, the M-BO (M = Ni, Pd, Ir, and Rh) bonding nature, and the interaction energy between [MBrCl(CO)(PR(3))(2)](+) and BO(-) with those of the platinum system, MBrCl(BO)(CO)(PR(3))(2) (M = Ir and Rh) is predicted to be a good candidate for a stable oxoboryl complex. PMID:22458310

  17. 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

  18. C-H activation and C=C double bond formation reactions in iridium ortho-methyl arylphosphane complexes.

    PubMed

    Baratta, Walter; Ballico, Maurizio; Del Zotto, Alessandro; Zangrando, Ennio; Rigo, Pierluigi

    2007-01-01

    The Vaska-type iridium(I) complex [IrCl(CO){PPh(2)(2-MeC(6)H(4))}(2)] (1), characterized by an X-ray diffraction study, was obtained from iridium(III) chloride hydrate and PPh(2)(2,6-MeRC(6)H(3)) with R=H in DMF, whereas for R=Me, activation of two ortho-methyl groups resulted in the biscyclometalated iridium(III) compound [IrCl(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}(2)] (2). Conversely, for R=Me the iridium(I) compound [IrCl(CO){PPh(2)(2,6-Me(2)C(6)H(3))}(2)] (3) can be obtained by treatment of [IrCl(COE)(2)](2) (COE=cyclooctene) with carbon monoxide and the phosphane in acetonitrile. Compound 3 in CH(2)Cl(2) undergoes intramolecular C-H oxidative addition, affording the cyclometalated hydride iridium(III) species [IrHCl(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}{PPh(2)(2,6-Me(2)C(6)H(3))}] (4). Treatment of 2 with Na[BAr(f) (4)] (Ar(f)=3,5-C(6)H(3)(CF(3))(2)) gives the fluxional cationic 16-electron complex [Ir(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}(2)][BAr(f) (4)] (5), which reversibly reacts with dihydrogen to afford the delta-agostic complex [IrH(CO){PPh(2)(2,6-CH(2)MeC(6)H(3))}{PPh(2)(2,6-Me(2)C(6)H(3))}][BAr(f)(4)] (6), through cleavage of an Ir-C bond. This species can also be formed by treatment of 4 with Na[BAr(f)(4)] or of 2 with Na[BAr(f)(4)] through C-H oxidative addition of one ortho-methyl group, via a transient 14-electron iridium(I) complex. Heating of the coordinatively unsaturated biscyclometalated species 5 in toluene gives the trans-dihydride iridium(III) complex [IrH(2)(CO){PPh(2)(2,6-MeC(6)H(3)CH=CHC(6)H(3)Me-2,6)PPh(2)}][BAr(f) (4)] (7), containing a trans-stilbene-type terdentate ligand, as result of a dehydrogenative carbon-carbon double bond coupling reaction, possibly through an iridium carbene species. PMID:17535000

  19. Simple Bond Cleavage

    SciTech Connect

    Gary S. Groenewold

    2005-08-01

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

  20. 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

  1. 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.

  2. 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. PMID:26138931

  3. Formation of stable phosphorus-carbon bond for enhanced performance in black phosphorus nanoparticle-graphite composite battery anodes.

    PubMed

    Sun, Jie; Zheng, Guangyuan; Lee, Hyun-Wook; Liu, Nian; Wang, Haotian; Yao, Hongbin; Yang, Wensheng; Cui, Yi

    2014-08-13

    High specific capacity battery electrode materials have attracted great research attention. Phosphorus as a low-cost abundant material has a high theoretical specific capacity of 2596 mAh/g with most of its capacity at the discharge potential range of 0.4-1.2 V, suitable as anodes. Although numerous research progress have shown other high capacity anodes such as Si, Ge, Sn, and SnO2, there are only a few studies on phosphorus anodes despite its high theoretical capacity. Successful applications of phosphorus anodes have been impeded by rapid capacity fading, mainly caused by large volume change (around 300%) upon lithiation and thus loss of electrical contact. Using the conducting allotrope of phosphorus, "black phosphorus" as starting materials, here we fabricated composites of black phosphorus nanoparticle-graphite by mechanochemical reaction in a high energy mechanical milling process. This process produces phosphorus-carbon bonds, which are stable during lithium insertion/extraction, maintaining excellent electrical connection between phosphorus and carbon. We demonstrated high initial discharge capacity of 2786 mAh·g(-1) at 0.2 C and an excellent cycle life of 100 cycles with 80% capacity retention. High specific discharge capacities are maintained at fast C rates (2270, 1750, 1500, and 1240 mAh·g(-1) at C/5, 1, 2, and 4.5 C, respectively). PMID:25019417

  4. How covalent heme to protein bonds influence the formation and reactivity of redox intermediates of a bacterial peroxidase.

    PubMed

    Auer, Markus; Nicolussi, Andrea; Schütz, Georg; Furtmüller, Paul G; Obinger, Christian

    2014-11-01

    The most striking feature of mammalian peroxidases, including myeloperoxidase and lactoperoxidase (LPO) is the existence of covalent bonds between the prosthetic group and the protein, which has a strong impact on their (electronic) structure and biophysical and chemical properties. Recently, a novel bacterial heme peroxidase with high structural and functional similarities to LPO was described. Being released from Escherichia coli, it contains mainly heme b, which can be autocatalytically modified and covalently bound to the protein by incubation with hydrogen peroxide. In the present study, we investigated the reactivity of these two forms in their ferric, compound I and compound II state in a multi-mixing stopped-flow study. Upon heme modification, the reactions between the ferric proteins with cyanide or H2O2 were accelerated. Moreover, apparent bimolecular rate constants of the reaction of compound I with iodide, thiocyanate, bromide, and tyrosine increased significantly and became similar to LPO. Kinetic data are discussed and compared with known structure-function relationships of the mammalian peroxidases LPO and myeloperoxidase. PMID:25246525

  5. Efficient Amide Bond Formation through a Rapid and Strong Activation of Carboxylic Acids in a Microflow Reactor**

    PubMed Central

    Fuse, Shinichiro; Mifune, Yuto; Takahashi, Takashi

    2014-01-01

    The development of highly efficient amide bond forming methods which are devoid of side reactions, including epimerization, is important, and such a method is described herein and is based on the concept of rapid and strong activation of carboxylic acids. Various carboxylic acids are rapidly (0.5 s) converted into highly active species, derived from the inexpensive and less-toxic solid triphosgene, and then rapidly (4.3 s) reacted with various amines to afford the desired peptides in high yields (74 %–quant.) without significant epimerization (≤3 %). Our process can be carried out at ambient temperature, and only CO2 and HCl salts of diisopropylethyl amine are generated. In the long history of peptide synthesis, a significant number of active coupling reagents have been abandoned because the highly active electrophilic species generated are usually susceptible to side reactions such as epimerization. The concept presented herein should renew interest in the use of these reagents. PMID:24402801

  6. How Covalent Heme to Protein Bonds Influence the Formation and Reactivity of Redox Intermediates of a Bacterial Peroxidase*

    PubMed Central

    Auer, Markus; Nicolussi, Andrea; Schütz, Georg; Furtmüller, Paul G.; Obinger, Christian

    2014-01-01

    The most striking feature of mammalian peroxidases, including myeloperoxidase and lactoperoxidase (LPO) is the existence of covalent bonds between the prosthetic group and the protein, which has a strong impact on their (electronic) structure and biophysical and chemical properties. Recently, a novel bacterial heme peroxidase with high structural and functional similarities to LPO was described. Being released from Escherichia coli, it contains mainly heme b, which can be autocatalytically modified and covalently bound to the protein by incubation with hydrogen peroxide. In the present study, we investigated the reactivity of these two forms in their ferric, compound I and compound II state in a multi-mixing stopped-flow study. Upon heme modification, the reactions between the ferric proteins with cyanide or H2O2 were accelerated. Moreover, apparent bimolecular rate constants of the reaction of compound I with iodide, thiocyanate, bromide, and tyrosine increased significantly and became similar to LPO. Kinetic data are discussed and compared with known structure-function relationships of the mammalian peroxidases LPO and myeloperoxidase. PMID:25246525

  7. 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.

  8. 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

  9. Roles of a conserved arginine residue of DsbB in linking protein disulfide-bond-formation pathway to the respiratory chain of Escherichia coli

    PubMed Central

    Kadokura, Hiroshi; Bader, Martin; Tian, Hongping; Bardwell, James C. A.; Beckwith, Jon

    2000-01-01

    The active-site cysteines of DsbA, the periplasmic disulfide-bond-forming enzyme of Escherichia coli, are kept oxidized by the cytoplasmic membrane protein DsbB. DsbB, in turn, is oxidized by two kinds of quinones (ubiquinone for aerobic and menaquinone for anaerobic growth) in the electron-transport chain. We describe the isolation of dsbB missense mutations that change a highly conserved arginine residue at position 48 to histidine or cysteine. In these mutants, DsbB functions reasonably well aerobically but poorly anaerobically. Consistent with this conditional phenotype, purified R48H exhibits very low activity with menaquinone and an apparent Michaelis constant (Km) for ubiquinone seven times greater than that of the wild-type DsbB, while keeping an apparent Km for DsbA similar to that of wild-type enzyme. From these results, we propose that this highly conserved arginine residue of DsbB plays an important role in the catalysis of disulfide bond formation through its role in the interaction of DsbB with quinones. PMID:11005861

  10. 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

    2016-01-01

    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. PMID:27447603

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

    PubMed

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

    2016-05-23

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

  12. The PqqD homologous domain of the radical SAM enzyme ThnB is required for thioether bond formation during thurincin H maturation.

    PubMed

    Wieckowski, Beata M; Hegemann, Julian D; Mielcarek, Andreas; Boss, Linda; Burghaus, Olaf; Marahiel, Mohamed A

    2015-07-01

    Thurincin H is a 31-residue, ribosomally synthesized bacteriocin originating from the thn operon of Bacillus thuringiensis SF361. It is the only known sactipeptide carrying four thioether bridges between four cysteines and the α-carbons of a serine, an asparagine and two threonine residues. By analysis of the thn operon and use of in vitro studies we now reveal that ThnB is a radical S-adenosylmethionine (SAM) enzyme containing two [4Fe-4S] clusters. Furthermore, we confirm the involvement of ThnB in the formation of the thioether bonds present within the structure of thurincin H. Finally, we show that the PqqD homologous N-terminal domain of ThnB is essential for maturation of the thurincin H precursor peptide, but not for the SAM cleavage activity of ThnB. PMID:26026269

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

    PubMed

    Biswas, Abhijit; Banerjee, Arindam

    2014-12-01

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

  14. Palladium-catalyzed C–N and C–O bond formation of N-substituted 4-bromo-7-azaindoles with amides, amines, amino acid esters and phenols

    PubMed Central

    Surasani, Rajendra; Rao, A V Dhanunjaya; Chandrasekhar, K B

    2012-01-01

    Summary Simple and efficient procedures for palladium-catalyzed cross-coupling reactions of N-substituted 4-bromo-7-azaindole (1H-pyrrole[2,3-b]pyridine), with amides, amines, amino acid esters and phenols through C–N and C–O bond formation have been developed. The C–N cross-coupling reaction of amides, amines and amino acid esters takes place rapidly by using the combination of Xantphos, Cs2CO3, dioxane and palladium catalyst precursors Pd(OAc)2/Pd2(dba)3. The combination of Pd(OAc)2, Xantphos, K2CO3 and dioxane was found to be crucial for the C–O cross-coupling reaction. This is the first report on coupling of amides, amino acid esters and phenols with N-protected 4-bromo-7-azaindole derivatives. PMID:23209536

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

    PubMed Central

    2015-01-01

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

  16. On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul.

    PubMed

    Agmon, Ilana; Auerbach, Tamar; Baram, David; Bartels, Heike; Bashan, Anat; Berisio, Rita; Fucini, Paola; Hansen, Harly A S; Harms, Joerg; Kessler, Maggie; Peretz, Moshe; Schluenzen, Frank; Yonath, Ada; Zarivach, Raz

    2003-06-01

    High-resolution crystal structures of large ribosomal subunits from Deinococcus radiodurans complexed with tRNA-mimics indicate that precise substrate positioning, mandatory for efficient protein biosynthesis with no further conformational rearrangements, is governed by remote interactions of the tRNA helical features. Based on the peptidyl transferase center (PTC) architecture, on the placement of tRNA mimics, and on the existence of a two-fold related region consisting of about 180 nucleotides of the 23S RNA, we proposed a unified mechanism integrating peptide bond formation, A-to-P site translocation, and the entrance of the nascent protein into its exit tunnel. This mechanism implies sovereign, albeit correlated, motions of the tRNA termini and includes a spiral rotation of the A-site tRNA-3' end around a local two-fold rotation axis, identified within the PTC. PTC features, ensuring the precise orientation required for the A-site nucleophilic attack on the P-site carbonyl-carbon, guide these motions. Solvent mediated hydrogen transfer appears to facilitate peptide bond formation in conjunction with the spiral rotation. The detection of similar two-fold symmetry-related regions in all known structures of the large ribosomal subunit, indicate the universality of this mechanism, and emphasizes the significance of the ribosomal template for the precise alignment of the substrates as well as for accurate and efficient translocation. The symmetry-related region may also be involved in regulatory tasks, such as signal transmission between the ribosomal features facilitating the entrance and the release of the tRNA molecules. The protein exit tunnel is an additional feature that has a role in cellular regulation. We showed by crystallographic methods that this tunnel is capable of undergoing conformational oscillations and correlated the tunnel mobility with sequence discrimination, gating and intracellular regulation. PMID:12787020

  17. 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

  18. Synthesis of the proteinase inhibitor LEKTI domain 6 by the fragment condensation method and regioselective disulfide bond formation.

    PubMed

    Vasileiou, Zoe; Barlos, Kostas K; Gatos, Dimitrios; Adermann, Knut; Deraison, Celine; Barlos, Kleomenis

    2010-01-01

    Proteinase inhibitors are of high pharmaceutical interest and are drug candidates for a variety of indications. Specific kallikrein inhibitors are important for their antitumor activity and their potential application to the treatment of skin diseases. In this study we describe the synthesis of domain 6 of the kallikrein inhibitor Lympho-Epithilial Kazal-Type Inhibitor (LEKTI) by the fragment condensation method and site-directed cystine bridge formation. To obtain the linear LEKTI precursor, the condensation was best performed in solution, coupling the protected fragment 1-22 to 23-68. This method yielded LEKTI domain 6 of high purity and equipotent to the recombinantly produced peptide. PMID:20069636

  19. Velocity Map Imaging Study of Ion-Radical Chemistry: Charge Transfer and Carbon-Carbon Bond Formation in the Reactions of Allyl Radicals with C(.).

    PubMed

    Pei, Linsen; Farrar, James M

    2016-08-11

    We present an experimental and computational study of the dynamics of collisions of ground state carbon cations with allyl radicals, C3H5, at a collision energy of 2.2 eV. Charge transfer to produce the allyl cation, C3H5(+), is exoergic by 3.08 eV and proceeds via energy resonance such that the electron transfer occurs without a significant change in nuclear velocities. The products have sufficient energy to undergo the dissociation process C3H5(+) → C3H4(+) + H. Approximately 80% of the reaction products are ascribed to charge transfer, with ∼40% of those products decaying via loss of a hydrogen atom. We also observe products arising from the formation of new carbon-carbon bonds. The experimental velocity space flux distributions for the four-carbon products are symmetric about the centroid of the reactants, providing direct evidence that the products are mediated by formation of a C4H5(+) complex living at least a few rotational periods. The primary four-carbon reaction products are formed by elimination of molecular hydrogen from the C4H5(+) complex. More than 75% of the nascent C4H3(+) products decay by C-H bond cleavage to yield a C4H2(+) species. Quantum chemical calculations at the MP2/6-311+g(d,p) level of theory support the formation of a nonplanar cyclic C4H5(+) adduct that is produced when the p-orbital containing the unpaired electron on C(+) overlaps with the unpaired spin density on the terminal carbon atoms in allyl. Product formation then occurs by 1,2-elimination of molecular hydrogen from the cyclic intermediate to form a planar cyclic C4H3(+) product. The large rearrangement in geometry as the C4H3(+) products are formed is consistent with high vibrational excitation in that product and supports the observation that the majority of those products decay to form the C4H2(+) species. PMID:27434380

  20. A DFT study on the NHC catalysed Michael addition of enols to α,β-unsaturated acyl-azoliums. A base catalysed C-C bond-formation step.

    PubMed

    Domingo, Luis R; Sáez, José A; Arnó, Manuel

    2014-02-14

    The NHC catalysed nucleophilic additions of enols to α,β-unsaturated acyl-azolium intermediates have been investigated using DFT methods at the MPWB1K/6-31G** computational level. In the direct and the conjugate additions, formation of a hydrogen bond (HB) with the carboxyl oxygen is not sufficient to favour the C-C bond formation as a consequence of the low nucleophilic character of enols. Interestingly, when enols form a HB with the chloride counterion, the activation energies associated with the conjugate addition decrease as a consequence of the increased nucleophilic character of enols and the increased electrophilic character of the 'acyl-azolium + Cl' ion pair. Analysis of the DFT reactivity indices allows establishing a base catalysed C-C bond-formation step promoted by the chloride counterion. PMID:24343422

  1. Bonded semiconductor substrate

    DOEpatents

    Atwater, Jr.; Harry A. , Zahler; James M.

    2010-07-13

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

  2. Real-time Monitoring of Intermediates Reveals the Reaction Pathway in the Thiol-Disulfide Exchange between Disulfide Bond Formation Protein A (DsbA) and B (DsbB) on a Membrane-immobilized Quartz Crystal Microbalance (QCM) System*

    PubMed Central

    Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

    2013-01-01

    Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

  3. Real-time monitoring of intermediates reveals the reaction pathway in the thiol-disulfide exchange between disulfide bond formation protein A (DsbA) and B (DsbB) on a membrane-immobilized quartz crystal microbalance (QCM) system.

    PubMed

    Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

    2013-12-13

    Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

  4. Tetrakis- and tris(1-Methyluracil) complexes of Pt(II): formation and properties of a carbon-bonded nucleobase species as well as of heternonuclear derivatives.

    PubMed

    Holland, Lars; Shen, Wei-Zheng; Micklitz, Wolfgang; Lippert, Bernhard

    2007-12-24

    The reaction of K2PtCl4 with an excess of 1-methyluracilate (1-MeU) in water at 60 degrees C leads to the formation of two major products, K2[Pt(1-MeU-N3)4].10H2O (1) and trans-K[Pt(1-MeU-N3)2(1-MeU-C5)(H2O)].3H2O (2). Addition of CuCl2 to an aqueous solution of 2 yields the mixed-metal complex trans-[PtCl(1-MeU-N3,O4)2(1-MeU-C5,O4)Cu(H2O)].H2O (4). Single-crystal X-ray analysis was carried out for 1 and 4. In both compounds, the heterometals (K+ in 1 and Cu2+ in 4) are bonded to exocyclic oxygens atoms of the 1-MeU ligands, giving rise to intermetallic distances of 3.386(2) and 3.528(2) A in 1 and 2.458(1) A in 4. The shortness of the Pt-Cu separation in 4 is consistent with a dative bond between PtII and CuII. The aqua ligand in 2 is readily substituted by a series of other ligands (e.g., 1-MeC, 9-MeGH, and CN-), as demonstrated by 1H NMR spectroscopy, with 3J(195Pt-1H(6)) coupling constants being sensitive indicators. Acid-base equilibria of 1 and 2 have been studied in detail and reveal some unexpected features: 1 has a relatively high basicity, with protonation starting below pH 5, and first and second pKa values being ca. 3.4 and 0.4, respectively. These pKa values are markedly higher than those of related neutral 2:1 or cationic 1:1 complexes and are attributed to both charge effects (-2 charge of 1) and a favorable stabilization of oxygen-protonated species by the arrangement of four exocyclic oxygen groups of 1-MeU ligands at either sides of the platinum coordination planes. Whereas in 2, H+ affinities of the three uracil ligands are in the normal range, there is a surprisingly low acidity of N(3)H of the C5-bonded uracil with a pKa of approximately 12.2, which compares with 9.75 for free 1-methyluracil. This implies that the C5-bonded PtII does not induce the typical acidifying effect of a PtII metal entity when bonded to a ring nitrogen atom of a neutral nucleobase. Rather, the effect is qualitatively similar to that of a metal ion bonded to N3 of an

  5. Polymerization of ionized acetylene clusters into covalent bonded ions: evidence for the formation of benzene radical cation.

    PubMed

    Momoh, Paul O; Abrash, Samuel A; Mabrouki, Ridha; El-Shall, M Samy

    2006-09-27

    Since the discovery of acetylene and benzene in protoplanetary nebulae under powerful ultraviolet ionizing radiation, efforts have been made to investigate the polymerization of ionized acetylene. Here we report the efficient formation of benzene ions within gas-phase ionized acetylene clusters (C2H2)n+ with n = 3-60. The results from experiments, which use mass-selected ion mobility techniques, indicate that the (C2H2)3+ ion has unusual stability similar to that of the benzene cation; its primary fragment ions are similar to those reported from the benzene cation, and it has a collision cross section of 47.4 A2 in helium at 300 K, similar to the value of 47.9 A2 reported for the benzene cation. In other words, (C2H2)3+ structurally looks like benzene, it has stability similar to that of benzene, it fragments such as benzene, therefore, it must be benzene! PMID:16984178

  6. Effect of aluminum chloride on formation of a polyconjugated bond system in the initial stage of polyvinyl alcohol thermal decomposition

    NASA Astrophysics Data System (ADS)

    Kulak, A. I.; Bondareva, G. V.; Shchurevich, O. A.

    2013-03-01

    Fine-structure bands have been located in electronic absorption spectra of polyvinyl alcohol (PVA) films decomposed thermally in air at 80-150°C. Doping of the PVA film with aluminum chloride (thermolysis catalyst) was found both to enhance the degree of thermal decomposition and to reduce the starting temperature for formation of poly-π-conjugated chains although it had no effect on the spectral positions of the polyene-unit absorption bands. Values of the band gap of heat-treated PVA films were determined to be in the range 1.65-1.78 eV based on an analysis of the electronic spectra long-wavelength edge.

  7. Suppression of Boride Formation in Transient Liquid Phase Bonding of Pairings of Parent Superalloy Materials with Different Compositions and Grain Structures and Resulting Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Steuer, Susanne; Singer, Robert F.

    2014-07-01

    Two Ni-based superalloys, columnar grained Alloy 247 and single-crystal PWA1483, are joined by transient liquid phase bonding using an amorphous brazing foil containing boron as a melting point depressant. At lower brazing temperatures, two different morphologies of borides develop in both base materials: plate-like and globular ones. Their ratio to each other is temperature dependent. With very high brazing temperatures, the deleterious boride formation in Alloy 247 can be totally avoided, probably because the three-phase-field moves to higher alloying element contents. For the superalloy PWA1483, the formation of borides cannot be completely avoided at high brazing temperatures as incipient melting occurs. During subsequent solidification of these areas, Chinese-script-like borides precipitate. The mechanical properties (tensile tests at room and elevated temperatures and short-term creep rupture tests at elevated temperatures) for brazed samples without boride precipitation are very promising. Tensile strengths and creep times to 1 pct strain are comparable, respectively, higher than the ones of the weaker parent material for all tested temperatures and creep conditions (from 90 to 100 pct rsp. 175 to 250 pct).

  8. Hydrogen implantation in silicates: The role of solar wind in SiOH bond formation on the surfaces of airless bodies in space

    NASA Astrophysics Data System (ADS)

    Schaible, Micah J.; Baragiola, Raúl A.

    2014-09-01

    Hydroxyl on the lunar surface revealed by remote measurements has been thought to originate from solar wind hydrogen implantation in the regolith. The hypothesis is tested here through experimental studies of the rate and mechanisms of OH bond formation due to H+ implantation of amorphous SiO2 and olivine in ultrahigh vacuum. The samples were implanted with 2-10 keV H+, in the range of solar wind energies, and the OH absorption band at ~2.8 µm measured by transmission Fourier transform infrared spectroscopy. For 2 keV protons in SiO2, the OH band depth saturated at fluences F ~5 × 1016 H+/cm2 to a maximum 0.0032 absorption band depth, corresponding to a column density ηs = 1.1 × 1016 OH/cm2. The corresponding values for 5 keV protons in olivine are >2 × 1017/cm2, 0.0067, and 4.0 × 1016 OH/cm2. The initial conversion rate of implanted H+ into hydroxyl species was found to be ~90% and decreased exponentially with fluence. There was no evidence for molecular water formation due to proton irradiation. Translating the laboratory measurements in thin plate samples to the granular lunar regolith, it is estimated that the measurements can account for a maximum of 17% relative OH absorption in reflectance spectroscopy of mature soils, consistent with spacecraft observations in the infrared of the Moon.

  9. Application of copper(I) iodide/diorganoyl dichalcogenides to the synthesis of 4-organochalcogen isoquinolines by regioselective C-N and C-chalcogen bond formation.

    PubMed

    Stein, André L; Bilheri, Filipe N; da Rocha, Juliana T; Back, Davi F; Zeni, Gilson

    2012-08-20

    A copper-catalyzed cyclization of (ortho-alkynyl)benzaldimines with diorganoyl dichalcogenides allowed the synthesis of 4-organochalcogen isoquinolines, whereas the presence of base in the reaction medium inhibited the product formation producing the undesirable isoquinoline without the organochalcogen atom at the 4-position. The cyclization reaction was carried out by using CuI (20 %) as a catalyst with diorganoyl dichalcogenides (1.5 equiv) in the presence of DMF at 100 °C. Furthermore, the reaction did not require an argon atmosphere and was carried out in an open flask. The cyclization reaction tolerated a variety of functional groups both in ortho-alkynylbenzaldimines and diorganoyl dichalcogenides, such as trifluoromethyl, chloro, fluorine, and methoxyl, to give the six-membered heterocyclic ring exclusively through a 6-endo-dig cyclization process. The organochalcogen group present at the 4-position of the isoquinoline ring was further subjected to a selective chalcogen-lithium exchange reaction followed by the addition of aldehydes to afford the desired secondary alcohols in good yields. The obtained isoquinolines also proved to be suitable substrates for the Suzuki and Sonogashira coupling conditions affording the corresponding products through C-C bond formation. PMID:22807116

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  11. Silico-ferrite of Calcium and Aluminum (SFCA) Iron Ore Sinter Bonding Phases: New Insights into Their Formation During Heating and Cooling

    NASA Astrophysics Data System (ADS)

    Webster, Nathan A. S.; Pownceby, Mark I.; Madsen, Ian C.; Kimpton, Justin A.

    2012-12-01

    The formation of silico-ferrite of calcium and aluminum (SFCA) and SFCA-I iron ore sinter phases during heating and cooling of synthetic iron ore sinter mixtures in the range 298 K to 1623 K (25 °C to 1350 °C) and at oxygen partial pressure of 5 × 10-3 atm has been characterized using in situ synchrotron X-ray diffraction. SFCA and SFCA-I are the key bonding phases in iron ore sinter, and an improved understanding of their formation mechanisms may lead to improved efficiency of industrial sintering processes. During heating, SFCA-I formation at 1327 K to 1392 K (1054 °C to 1119 °C) (depending on composition) was associated with the reaction of Fe2O3, 2CaO·Fe2O3, and SiO2. SFCA formation (1380 K to 1437 K [1107 °C to 1164 °C]) was associated with the reaction of CaO·Fe2O3, SiO2, and a phase with average composition 49.60, 9.09, 0.14, 7.93, and 32.15 wt pct Fe, Ca, Si, Al, and O, respectively. Increasing Al2O3 concentration in the starting sinter mixture increased the temperature range over which SFCA-I was stable before the formation of SFCA, and it stabilized SFCA to a higher temperature before it melted to form a Fe3O4 + melt phase assemblage (1486 K to 1581 K [1213 °C to 1308 °C]). During cooling, the first phase to crystallize from the melt (1452 K to 1561 K [1179 °C to 1288 °C]) was an Fe-rich phase, similar in composition to SFCA-I, and it had an average composition 58.88, 6.89, 0.82, 3.00, and 31.68 wt pct Fe, Ca, Si, Al, and O, respectively. At lower temperatures (1418 K to 1543 K [1145 °C to 1270 °C]), this phase reacted with melt to form SFCA. Increasing Al2O3 increased the temperature at which crystallization of the Fe-rich phase occurred, increased the temperature at which crystallization of SFCA occurred, and suppressed the formation of Fe2O3 (1358 K to 1418 K [1085 °C to 1145 °C]) to lower temperatures.

  12. 2-Benzoylpyridine thiosemicarbazone as a novel reagent for the single pot synthesis of dinuclear Cu(I)-Cu(II) complexes: formation of stable copper(II)-iodide bonds.

    PubMed

    Lobana, Tarlok S; Khanna, Sonia; Butcher, Ray J

    2012-04-28

    2-Benzoylpyridine thiosemicarbazone {R(1)R(2)C(2)=N(2)·N(3)H-C(1)(=S)-N(4)H(2), R(1) = py-N(1), R(2) = Ph; Hbpytsc} with copper(I) iodide in acetonitrile-dichloromethane mixture has formed stable Cu(II)-I bonds in a dark green Cu(II) iodo-bridged dimer, [Cu(2)(II)(μ-I)(2)(η(3)-N(1),N(2),S-bpytsc)(2)] 1. Copper(I) bromide also formed similar Cu(II)-Br bonds in a dark green Cu(II) bromo-bridged dimer, [Cu(2)(II)(μ-Br)(2)(η(3)-N(1),N(2),S-bpytsc)(2)] 3. The formation of dimers 1 and 3 appears to be due to a proton coupled electron transfer (PCET) process wherein copper(I) loses an electron to form copper(II), and this is accompanied by a loss of -N(3)H proton of Hbpytsc ligand resulting in the formation of anionic bpytsc(-). When copper(I) iodide was reacted with triphenylphosphine (PPh(3)) in acetonitrile followed by the addition of 2-benzoylpyridine thiosemicarbazone in dichloromethane (Cu : PPh(3) : Hbpytsc in the molar ratio 1:1:1), both Cu(II) dimer 1 and an orange Cu(I) sulfur-bridged dimer, [Cu(2)(I)I(2)(μ-S-Hbpytsc)(2)(PPh(3))(2)] 2 were formed. Copper(I) bromide with PPh(3) and Hbpytsc also formed Cu(II) dimer 3 and an orange Cu(I) sulfur-bridged dimer, [Cu(2)(I)Br(2)(μ-S-Hbpytsc)(2)(PPh(3))(2)] 4. While complexes 2 and 4 exist as sulfur-bridged Cu(I) dimers, 1 and 3 are halogen-bridged. The central Cu(2)S(2) cores of 2 and 4 as well as Cu(2)X(2) of 1 (X = I) and 3 (X = Br) are parallelograms. One set of Cu(II)-I and Cu(II)-Br bonds are short, while the second set is very long {1, Cu-I, 2.565(1), 3.313(1) Å; 3, Cu-Br, 2.391(1), 3.111(1) Å}. The Cu···Cu separations are long in all four complexes {1, 4.126(1); 2, 3.857(1); 3, 3.227(1); 4, 3.285(1) Å}, more than twice the van der Waals radius of a Cu atom, 2.80 Å. The pyridyl group appears to be necessary for stabilizing the Cu(II)-I bond, as this group can accept π-electrons from the metal. PMID:22395858

  13. On the Relationship between the Enthalpy of Formation of Carbenes upon Cleavage of the Double Bond in Fluoroolefins and the Electron Density on the pi Bond: An Ab Initio Study

    SciTech Connect

    Borisov, Yurii A.; Garrett, Bruce C.; Kobanovskii, Y. A.; Bilera, I. V.; Buravtsev, N. N.

    2003-08-07

    In this study, we established a correlation between the enthalpy of cleavage of the C=C bond in fluorine-substituted olefins giving rise to two carbenes in the electronic ground state and the distribution of the electron density on this bond.

  14. Preferential formation of 13C- 18O bonds in carbonate minerals, estimated using first-principles lattice dynamics

    NASA Astrophysics Data System (ADS)

    Schauble, Edwin A.; Ghosh, Prosenjit; Eiler, John M.

    2006-05-01

    Equilibrium constants for internal isotopic exchange reactions of the type: Ca12C18O16O2+Ca13C16O3↔Ca13C18O16O2+Ca12C16O3 for individual CO 32- groups in the carbonate minerals calcite (CaCO 3), aragonite (CaCO 3), dolomite (CaMg(CO 3) 2), magnesite (MgCO 3), witherite (BaCO 3), and nahcolite (NaHCO 3) are calculated using first-principles lattice dynamics. Calculations rely on density functional perturbation theory (DFPT) with norm-conserving planewave pseudopotentials to determine the vibrational frequencies of isotopically substituted crystals. Our results predict an ˜0.4‰ excess of 13C18O16O22- groups in all studied carbonate minerals at room-temperature equilibrium, relative to what would be expected in a stochastic mixture of carbonate isotopologues with the same bulk 13C/ 12C, 18O/ 16O, and 17O/ 16O ratios. The amount of excess 13C18O16O22- decreases with increasing temperature of equilibration, from 0.5‰ at 0 °C to <0.1‰ at 300 °C, suggesting that measurements of multiply substituted isotopologues of carbonate could be used to infer temperatures of ancient carbonate mineral precipitation and alteration events, even where the δ 18O of coexisting fluids is uncertain. The predicted temperature sensitivity of the equilibrium constant is ˜0.003‰/°C at 25 °C. Estimated equilibrium constants for the formation of 13C18O16O22- are remarkably uniform for the variety of minerals studied, suggesting that temperature calibrations will also be applicable to carbonate minerals not studied here without greatly compromising accuracy. A related equilibrium constant for the reaction: Ca12C18O16O2+Ca12C17O16O2↔Ca12C18O17O16O+Ca12C16O3 in calcite indicates formation of 0.1‰ excess 12C 18O 17O 16O 2- at 25 °C. In a conventional phosphoric acid reaction of carbonate to form CO 2 for mass-spectrometric analysis, molecules derived from 13C18O16O22- dominate (˜96%) the mass 47 signal, and 12C 18O 17O 16O 2- contributes most of the remainder (3%). This suggests

  15. Slow rate of phosphodiester bond formation accounts for the strong bias that Taq DNA polymerase shows against 2',3'-dideoxynucleotide terminators.

    PubMed

    Brandis, J W; Edwards, S G; Johnson, K A

    1996-02-20

    Taq and T7 DNA polymerases have become basic molecular biology "tools" for DNA sequence analysis. However, Taq, unlike T7 DNA polymerase, is strongly biased against the incorporation of 2',3'-dideoxynucleotide triphosphates (ddNTPs) indicating very different substrate selectivities. Equilibrium binding and rate constants were measured for 2',3'-ddNTPs as well as for several other 3'-substituted terminators and compared to 2'-deoxynucleotide substrates (dNTPs). In steady-state experiments, Taq Pol I was strongly biased in favor of dATP1 over ddATP incorporation by about 700 to 1, in contrast to T7 DNA polymerase which showed a preference of only about 4 to 1. Manganese reduced but did not eliminate selectivity against 2',3'-ddNTPs. Transient kinetic traces indicated different rate-limiting steps for substrate and terminator incorporation. Further mechanistic studies showed that the binding constants for substrates and terminators were equivalent. However, the rate constants for phosphodiester bond formation for 2',3'-ddNTPs were 200-3000-fold lower than for dNTPs. Alternative terminators showed only slight improvements. The data were consistent with a model in which both substrates and terminators undergo ground-state binding followed by formation of a tight-binding Enz.DNA.Nucleotide complex. Immediately after complex formation, substrates undergo a rapid nucleoside phosphoryl transfer reaction. However, the reaction rates for terminators were slower presumably due to misalignment of reactive groups in the active site. Thus, the strong bias that Taq DNA polymerase shows against terminators is due to a very slow "chemistry" step. Such a strong bias has several kinetic consequences for DNA sequence patterns. These consequences are discussed in the text. PMID:8652560

  16. Hydrogen Implantation in Silicates: The role of solar wind in OH bond formation on the lunar surface

    NASA Astrophysics Data System (ADS)

    Schaible, Micah J; Baragiola, Raul

    2014-06-01

    Airless bodies in space such as the Moon, asteroids and interplanetary dust particles are subject to bombardment from energetic electrons and ions, ultraviolet photons, micrometeorites and cosmic rays. These bombarding particles modify optical, chemical and physical characteristics of the ices and minerals that make up these bodies in a process known as space weathering. In particular, solar wind protons implanted in silicate materials can participate in hydroxylation reactions with the oxygen to form OH. This mechanism has been suggested to explain a reported 3-14% absorption signal identified as OH on the surface of lunar soil grains and present in decreasing magnitude from polar to equatorial latitudes. With the goal of determining a precise OH formation rate due to H+ implantation in silicates, a series of experiments were carried out on terrestrial minerals as analogs to lunar and interstellar material.Experiments were carried out under UHV pressures (<10-9 Torr) and irradiation was performed using a mass analyzed ion accelerator. The samples were first outgassed to ~200 °C for 12 hrs then directly transferred to the analysis position without exposure to laboratory air. In-situ transmission FTIR spectroscopy was used to determine the content of OH in thermally grown silicon oxide and San Carlos olivine, before and after irradiated with 1 - 5 keV H+ ions. The increase in Si-OH content due to irradiation was determined by subtracting the unirradiated spectra from the irradiated spectra. The implanted protons induced OH stretch absorptions in the mid-infrared peaked at 3673 cm-1 for SiO2 and 3570 cm-1 for olivine. The initial yield (OH formed per incident ion) was ~90% and the OH absorption band was found to saturate at implantation fluences of ~2x1017 H/cm2. Irradiation also modified the Si-O stretch band at ~1090 cm-1 (9.2 μm) causing an exponential decrease in the peak height with increasing fluence and the appearance of a silanol structure peaking at ~1030

  17. Direct construction of 2-alkylbenzo-1,3-azoles via C-H activation of alkanes for C-C and C-X (X = O, S) bond formation.

    PubMed

    Yadav, Arvind K; Yadav, Lal Dhar S

    2015-03-01

    Copper catalyzed straightforward synthesis of 2-alkylbenzoxa(thia)azoles from aryl isocyanates/isothiocyanates and simple alkanes is reported. The protocol utilizes ditertiary butyl peroxide (DTBP) as a radical initiator and involves sequential formation of C-C and C-X (X = O, S) bonds followed by aromatization in a one-pot procedure. PMID:25578954

  18. Cu(OAc)2-Mediated Cascade Annulation of Diarylalkyne Sulfonamides through Dual C-N Bond Formation: Synthesis of 5,10-Dihydroindolo[3,2-b]indoles.

    PubMed

    Yu, Junchao; Zhang-Negrerie, Daisy; Du, Yunfei

    2016-07-15

    An unusual cascade reaction featuring annulation of diarylalkyne sulfonamides to form 5,10-dihydroindolo[3,2-b]indoles has been realized with Cu(OAc)2 as the sole oxidant. This unprecedented process encompasses two sequential C-N bond formations, allowing for an efficient synthesis of the biologically important indoloindole derivatives. PMID:27366912

  19. Bond Issues.

    ERIC Educational Resources Information Center

    Pollack, Rachel H.

    2000-01-01

    Notes trends toward increased borrowing by colleges and universities and offers guidelines for institutions that are considering issuing bonds to raise money for capital projects. Discussion covers advantages of using bond financing, how use of bonds impacts on traditional fund raising, other cautions and concerns, and some troubling aspects of…

  20. Formation of C-C and C-O bonds and oxygen removal in reactions of alkanediols, alkanols, and alkanals on copper catalysts.

    PubMed

    Sad, María E; Neurock, Matthew; Iglesia, Enrique

    2011-12-21

    This study reports evidence for catalytic deoxygenation of alkanols, alkanals, and alkanediols on dispersed Cu clusters with minimal use of external H(2) and with the concurrent formation of new C-C and C-O bonds. These catalysts selectively remove O-atoms from these oxygenates as CO or CO(2) through decarbonylation or decarboxylation routes, respectively, that use C-atoms present within reactants or as H(2)O using H(2) added or formed in situ from CO/H(2)O mixtures via water-gas shift. Cu catalysts fully convert 1,3-propanediol to equilibrated propanol-propanal intermediates that subsequently form larger oxygenates via aldol-type condensation and esterification routes without detectable involvement of the oxide supports. Propanal-propanol-H(2) equilibration is mediated by their chemisorption and interconversion at surfaces via C-H and O-H activation and propoxide intermediates. The kinetic effects of H(2), propanal, and propanol pressures on turnover rates, taken together with measured selectivities and the established chemical events for base-catalyzed condensation and esterification reactions, indicate that both reactions involve kinetically relevant bimolecular steps in which propoxide species, acting as the base, abstract the α-hydrogen in adsorbed propanal (condensation) or attack the electrophilic C-atom at its carbonyl group (esterification). These weakly held basic alkoxides render Cu surfaces able to mediate C-C and C-O formation reactions typically catalyzed by basic sites inherent in the catalyst, instead of provided by coadsorbed organic moieties. Turnover rates for condensation and esterification reactions decrease with increasing Cu dispersion, because low-coordination corner and edge atoms prevalent on small clusters stabilize adsorbed intermediates and increase the activation barriers for the bimolecular kinetically relevant steps required for both reactions. PMID:22023723

  1. {tau} phase formation in a TiC + TiB{sub 2} composite bonded with a nickel based binder alloy

    SciTech Connect

    Ogwu, A.A.; Davies, T.J.

    1999-05-21

    Densification and ductility has been achieved in a TiC + TiB{sub 2} cermet prepared by pressureless sintering using a nickel based binder with an additive, based on their proposed empirical model. In the context of bonding in the binary, Holleck et al have suggested that the structures of TiC and TiB{sub 2} allows coherence to be established between their most densely packed lattice planes. This favorable interfacial match in the TiC + TiB{sub 2} composite is assumed to encourage a high mobility of atoms across the interface, leading to densification during sintering. The fracture toughness of a TiC + TiB{sub 2} composite would also be expected to improve when good interfacial coherence exists between TiC and TiB{sub 2}. In the case of their preferred nickel-based binder, one of the reasons for selecting the additive is to prevent the formation o deleterious grain boundary phases like the {tau} phase which often forms in Ni-TiB{sub 2} systems, with the expectation that if new phases do form they would be soluble in a TiC + TiB{sub 2} matrix. Previous attempts to find suitable sintering additives for TiB{sub 2} revealed that Fe, Co and Ni binders reacted with the TiB{sub 2} at the sintering temperatures forming secondary borides of the type M{sub 2}B. The formation of these undesirable (secondary) borides has been identified to be linked to either the presence of contaminants like oxygen, carbon and nitrogen which react with Ti, leaving behind free boron for reaction with the selected metallic binder, or, a direct reaction between the metal binder and TiB{sub 2}.

  2. Phylogeny of the Vitamin K 2,3-Epoxide Reductase (VKOR) Family and Evolutionary Relationship to the Disulfide Bond Formation Protein B (DsbB) Family

    PubMed Central

    Bevans, Carville G.; Krettler, Christoph; Reinhart, Christoph; Watzka, Matthias; Oldenburg, Johannes

    2015-01-01

    In humans and other vertebrate animals, vitamin K 2,3-epoxide reductase (VKOR) family enzymes are the gatekeepers between nutritionally acquired K vitamins and the vitamin K cycle responsible for posttranslational modifications that confer biological activity upon vitamin K-dependent proteins with crucial roles in hemostasis, bone development and homeostasis, hormonal carbohydrate regulation and fertility. We report a phylogenetic analysis of the VKOR family that identifies five major clades. Combined phylogenetic and site-specific conservation analyses point to clade-specific similarities and differences in structure and function. We discovered a single-site determinant uniquely identifying VKOR homologs belonging to human pathogenic, obligate intracellular prokaryotes and protists. Building on previous work by Sevier et al. (Protein Science 14:1630), we analyzed structural data from both VKOR and prokaryotic disulfide bond formation protein B (DsbB) families and hypothesize an ancient evolutionary relationship between the two families where one family arose from the other through a gene duplication/deletion event. This has resulted in circular permutation of primary sequence threading through the four-helical bundle protein folds of both families. This is the first report of circular permutation relating distant α-helical membrane protein sequences and folds. In conclusion, we suggest a chronology for the evolution of the five extant VKOR clades. PMID:26230708

  3. Photoinduced, Copper-Catalyzed Carbon-Carbon Bond Formation with Alkyl Electrophiles: Cyanation of Unactivated Secondary Alkyl Chlorides at Room Temperature.

    PubMed

    Ratani, Tanvi S; Bachman, Shoshana; Fu, Gregory C; Peters, Jonas C

    2015-11-01

    We have recently reported that, in the presence of light and a copper catalyst, nitrogen nucleophiles such as carbazoles and primary amides undergo C-N coupling with alkyl halides under mild conditions. In the present study, we establish that photoinduced, copper-catalyzed alkylation can also be applied to C-C bond formation, specifically, that the cyanation of unactivated secondary alkyl chlorides can be achieved at room temperature to afford nitriles, an important class of target molecules. Thus, in the presence of an inexpensive copper catalyst (CuI; no ligand coadditive) and a readily available light source (UVC compact fluorescent light bulb), a wide array of alkyl halides undergo cyanation in good yield. Our initial mechanistic studies are consistent with the hypothesis that an excited state of [Cu(CN)2](-) may play a role, via single electron transfer, in this process. This investigation provides a rare example of a transition metal-catalyzed cyanation of an alkyl halide, as well as the first illustrations of photoinduced, copper-catalyzed alkylation with either a carbon nucleophile or a secondary alkyl chloride. PMID:26491957

  4. New insights into water bonding during early tricalcium silicate hydration with quasielastic neutron scattering

    SciTech Connect

    Gutberlet, T.; Hilbig, H.; Beddoe, R.E.; Lohstroh, W.

    2013-09-15

    New information on the water bonding during the first 36 h of hydration of tricalcium silicate was obtained using the high neutron flux at the sample position of the time-of-flight spectrometer (TOFTOF), FRM II in Garching, Germany, together with {sup 29}Si NMR and X-ray diffraction measurements. A rapid increase in the amount of constrained water was observed at the beginning of the induction period. This is attributed to the formation of an early C-S-H with a large specific surface area (around 800 m{sup 2}/g). During subsequent hydration, the amount of constrained water, as given by the total surface area of the hydration products, is controlled by (a) the formation of new metastable early C-S-H which increases total surface area and (b) polymerisation processes which reduce total surface area. The relative contribution of these processes varies during hydration.

  5. Palladium(ii)-catalyzed C-C and C-O bond formation for the synthesis of C1-benzoyl isoquinolines from isoquinoline N-oxides and nitroalkenes.

    PubMed

    Li, Jiu-Ling; Li, Wei-Ze; Wang, Ying-Chun; Ren, Qiu; Wang, Heng-Shan; Pan, Ying-Ming

    2016-08-01

    C1-Benzoyl isoquinolines can be generated via a palladium(ii)-catalyzed C-C and C-O coupling of isoquinoline N-oxides with aromatic nitroalkenes. The reaction proceeds through remote C-H bond activation and subsequent intramolecular oxygen atom transfer (OAT). In this reaction, the N-O bond was designed as a directing group in the C-H bond activation as well as the source of an oxygen atom. PMID:27443150

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

    SciTech Connect

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

    2014-09-03

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

  7. Formation of hydrogen-bonded chains through inter- and intra-molecular hydrogen bonds by a strong base of guanidine-like character and 5,5'-dibromo-2,2'-biphenols

    NASA Astrophysics Data System (ADS)

    Wojciechowski, G.; Brzezinski, B.

    2002-04-01

    5,5'-dibromo-2,2'-biphenol mixtures with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) were studied by FTIR as well as 1H NMR spectroscopy. In chloroform, a proton transfer from DBBPh to MTBD occurs and the protonated MTBD molecule is hydrogen-bonded to the chain formed between 5,5'-dibromo-2,2'-biphenol and 5,5'-dibromo-2,2'-biphenolate molecule. In acetonitrile, the complex dissociates and hence protonated MTBD molecules and hydrogen-bonded chains formed between 5,5'-dibromo-2,2'-biphenol and 5,5'-dibromo-2,2'-biphenolate are present. The hydrogen bonds of these chains show large proton polarizability.

  8. Formation of hydrogen-bonded chains through inter- and intra-molecular hydrogen bonds by 5,5'-dinitro-2,2'-biphenol with a strong base of guanidine-like character and triethylamine

    NASA Astrophysics Data System (ADS)

    Wojciechowski, Grzegorz; Brzezinski, Bogumil

    2002-04-01

    The complexes of 5,5'-dinitro-2,2'-biphenol (DNBPh) with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) and triethylamine (TEA) were studied by FTIR and 1H NMR spectroscopy. In chloroform and in acetonitrile a proton transfer from DNBPh to N-bases (MTBD, TEA) occurs. In chloroform solution the protonated N-base molecules are hydrogen-bonded to the deprotonated DNBPh molecules whereas in acetonitrile the complexes dissociate and hence protonated N-base molecules and hydrogen-bonded chains formed between DNBPh and 5,5'-dinitro-2,2'-biphenolate are present. The intra- as well as inter-molecular hydrogen bonds within the chains show large proton polarizability.

  9. Reduction of N-allylamides by LiAlH4: unexpected attack of the double bond with mechanistic studies of product and byproduct formation.

    PubMed

    Thiedemann, Birk; Schmitz, Christin M L; Staubitz, Anne

    2014-11-01

    The reduction of secondary allyl amides with LiAlH4 can lead to a concomitant reduction of the double bond. Previously, an excess of LiAlH4 in hazardous solvents was used for the reduction. This work discusses optimized reaction conditions in tBuOMe as a safe solvent, with only a 1.5-fold excess of LiAlH4, without reduction of the double bond in most cases. (1)H and (2)D NMR spectroscopic studies give evidence for the mechanism of the reduction of the amide as well as the double bond: Amide reduction generally precedes double bond reduction. Sterically hindered allylamides are an exception. They are reduced considerably more slowly at higher temperatures, and double bond reduction is observed before amide reduction has gone to completion. PMID:25347383

  10. C. S. Peirce's Dialogical Conception of Sign Processes

    ERIC Educational Resources Information Center

    Bergman, Mats

    2005-01-01

    This article examines the contention that the central concepts of C. S. Peirce's semeiotic are inherently communicational. It is argued that the Peircean approach avoids the pitfalls of objectivism and constructivism, rendering the sign-user neither a passive recipient nor an omnipotent creator of meaning. Consequently, semeiotic may serve as a…

  11. The Use of C. S. Lewis's "Poems" for Oral Interpretation.

    ERIC Educational Resources Information Center

    Keefe, Carolyn

    Suggestions are offered in this paper for adapting C. S. Lewis's poems for oral interpretation. A discussion of Lewis's lifelong correspondence with his friend Arthur Greeves provides insights into Lewis's perceptions of his own writing. Eighty poems selected from Lewis's "Poems" as appropriate for oral interpretation are classified according to…

  12. S-OO bond dissociation energies and enthalpies of formation of the thiomethyl peroxyl radicals CH{sub 3}S(O){sub n}OO (n=0,1,2)

    SciTech Connect

    Salta, Zoi; Kosmas, Agnie Mylona; Lesar, Antonija

    2014-10-06

    Optimized geometries, S-OO bond dissociation energies and enthalpies of formation for a series of thiomethyl peroxyl radicals are investigated using high level ab initio and density functional theory methods. The results show that the S-OO bond dissociation energy is largest in the methylsulfonyl peroxyl radical, CH{sub 3}S(O){sub 2}OO, which contains two sulfonic type oxygen atoms followed by the methylthiyl peroxyl radical, CH{sub 3}SOO. The methylsulfinyl peroxyl radical, CH{sub 3}S(O)OO, which contains only one sulfonic type oxygen shows the least stability with regard to dissociation to CH{sub 3}S(O)+O{sub 2}. This stabilization trend is nicely reflected in the variations of the S-OO bond distance which is found to be shortest in CH{sub 3}S(O){sub 2}OO and longest in CH{sub 3}S(O)OO.

  13. Erythromycin, roxithromycin, and clarithromycin: use of slow-binding kinetics to compare their in vitro interaction with a bacterial ribosomal complex active in peptide bond formation.

    PubMed

    Dinos, George P; Connell, Sean R; Nierhaus, Knud H; Kalpaxis, Dimitrios L

    2003-03-01

    In a cell-free system derived from Escherichia coli, it is shown that clarithromycin and roxithromycin, like their parent compound erythromycin, do not inhibit the puromycin reaction (i.e., the peptide bond formation between puromycin and AcPhe-tRNA bound at the P-site of 70S ribosomes programmed with heteropolymeric mRNA). Nevertheless, all three antibiotics compete for binding on the ribosome with tylosin, a 16-membered ring macrolide that behaves as a slow-binding, slowly reversible inhibitor of peptidyltransferase. The mutually exclusive binding of these macrolides to ribosomes is also corroborated by the fact that they protect overlapping sites in domain V of 23S rRNA from chemical modification by dimethyl sulfate. From this competition effect, detailed kinetic analysis revealed that roxithromycin or clarithromycin (A), like erythromycin, reacts rapidly with AcPhe-tRNA.MF-mRNA x 70S ribosomal complex (C) to form the encounter complex CA which is then slowly isomerized to a more tight complex, termed C*A. The value of the overall dissociation constant, K, encompassing both steps of macrolide interaction with complex C, is 36 nM for erythromycin, 20 nM for roxithromycin, and 8 nM for clarithromycin. Because the off-rate constant of C*A complex does not significantly differ among the three macrolides, the superiority of clarithromycin as an inhibitor of translation in E. coli cells and many Gram-positive bacteria may be correlated with its greater rate of association with ribosomes. PMID:12606769

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

    PubMed

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

    2016-02-11

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

  15. Institutional Bonding.

    ERIC Educational Resources Information Center

    Allard, M. June

    Institutional bonding was examined at a public, urban commuter college with exceptionally high attrition and visibly low morale. Changes in bonding and attrition were measured 6 years after a 2-year effort to develop school identity and student feelings of membership. It was found that a simple index of campus morale is provided by level of…

  16. Raman spectroscopy study on the ν1-2ν2 Fermi resonance of liquid carbon disulfide in binary solutions: Effect of the weak hydrogen bond formation on the Fermi resonance

    NASA Astrophysics Data System (ADS)

    Li, DongFei; Sun, Shang; Sun, ChengLin; Jiang, XiuLan; Gao, ShuQin; Li, ZuoWei

    2012-10-01

    We have measured the Raman spectra of liquid CS2 at different volume concentrations in CHCl3 and CH2Cl2 solutions. With decreasing the volume concentration of CS2, a noticeable growth in the 2ν2 band frequency was observed, while the ν1 band location remained practically unchanged. This asymmetric wavenumber shift phenomenon of the Fermi doublet ν1 and 2ν2 of CS2 has been ascribed to weak, non-conventional hydrogen bonds formed between the CS2 and the solvent molecules. These weak hydrogen bonds were also responsible for significant decreases in the C-H bond symmetric stretching vibration band frequencies of CHCl3 and CH2Cl2. The values of the ν1-2ν2 FR parameters of CS2 in CH2Cl2 and CHCl3 at different volume concentrations were calculated according to the FR theory. The magnitude of the FR coupling coefficient W of CS2 increases upon dilution with CH2Cl2 and CHCl3, indicating that the vibrational anharmonicity is relatively sensitive to variations in the weak hydrogen bonding. Compared with the changing tendencies of Fermi coupling coefficient W of CS2 in CH2Cl2 and CHCl3 at different volume concentrations, we discussed the effect of the weak hydrogen bond formation on the FR and the asymmetric wavenumber shift phenomenon of the Fermi doublet ν1 and 2ν2 of CS2.

  17. Synthesis of 2-amino-1,3,4-oxadiazoles and 2-amino-1,3,4-thiadiazoles via sequential condensation and I2-mediated oxidative C–O/C–S bond formation.

    PubMed

    Niu, Pengfei; Kang, Jinfeng; Tian, Xianhai; Song, Lina; Liu, Hongxu; Wu, Jie; Yu, Wenquan; Chang, Junbiao

    2015-01-16

    2-Amino-substituted 1,3,4-oxadiazoles and 1,3,4-thiadiazoles were synthesized via condensation of semicarbazide/thiosemicarbazide and the corresponding aldehydes followed by I2-mediated oxidative C–O/C–S bond formation. This transition-metal-free sequential synthesis process is compatible with aromatic, aliphatic, and cinnamic aldehydes, providing facile access to a variety of diazole derivatives bearing a 2-amino substituent in an efficient and scalable fashion. PMID:25506709

  18. Polynuclear platinum phosphanido/phosphinito complexes: formation of P-O and P-O-P bonds through reductive coupling processes.

    PubMed

    Ara, Irene; Forniés, Juan; Ibáñez, Susana; Mastrorilli, Piero; Todisco, Stefano; Gallo, Vito

    2016-02-01

    A mixture of the asymmetric complexes of formula [(RF)2Pt(μ-Ph2PO)(μ-PPh2)Pt(μ-PPh2)2Pt(solv)(solv')] [(1-(solv)(solv')] (solv, solv' = acetone, H2O, CH3CN) has been prepared by reaction of [(RF)2Pt(II)(μ-PPh2)2Pt(II)(μ-PPh2)2Pt(II)(NCCH3)2] with AgClO4 in CH3CN/acetone. The lability of the Pt-solvent bonds allows the displacement of the coordinated solvent molecules by dppm or Cl(-) and the isolation of the tri- or hexanuclear phosphanido/phosphinito Pt(ii) complexes [(C6F5)2Pt(μ-PPh2)(μ-PPh2O)Pt(μ-PPh2)2Pt(dppm)] (2) or [NBu4]2[(C6F5)2Pt(μ-PPh2)(μ-PPh2O)Pt(μ-PPh2)2Pt(μ-Cl)2Pt(μ-PPh2)2Pt(μ-PPh2)(μ-PPh2O)Pt(C6F5)2] (as a mixture of the two possible isomers 4a and 4b). Complex 2 reacts with AgClO4 to form the tetranuclear derivative [(C6F5)2Pt(μ-PPh2)(μ-PPh2O)Pt(μ-PPh2)2Pt(dppm)Ag(OClO3)] (3), which displays two Pt-Ag donor-acceptor bonds. The mixture of the hexanuclear isomers 4a-4b reacts with Tl(acac) producing the acetylacetonato complex [NBu4][(C6F5)2Pt(μ-PPh2)(μ-PPh2O)Pt(μ-PPh2)2Pt(acac)] (5) which, upon reaction with HCl, yields back the mixture of 4a-4b. The reaction of 4a-4b with PPh3 produces [NBu4][(C6F5)2Pt(μ-PPh2)(μ-PPh2O)Pt(μ-PPh2)2Pt(Cl)(PPh3)] (6) as a mixture of isomers with the chloro ligand located syn (6a) or anti (6b) to the PPh2O(-) group. Either the reaction of 6 with AgClO4 or the treatment of 5 with HPPh3ClO4 results in the formation of the species [(C6F5)2Pt(II)(μ-PPh2)2Pt(I)(μ-PPh2OPPh2)Pt(I)(PPh3)] (7) (44 VEC), which can be explained as the consequence of a PPh2O/PPh2 reductive coupling and a rearrangement of ligands in the molecule generating a Pt(ii),Pt(i),Pt(i) compound. All complexes were characterised in the solid state by XRD (only one of the isomers, in the cases of 4 and 6) and in solution by NMR spectroscopy. PMID:26555928

  19. Possible interstellar formation of glycine through a concerted mechanism: a computational study on the reaction of CH2[double bond, length as m-dash]NH, CO2 and H2.

    PubMed

    Nhlabatsi, Zanele P; Bhasi, Priya; Sitha, Sanyasi

    2016-07-27

    Glycine being the simplest amino acid and also having significant astrobiological implications, has meant that intensive investigations have been carried out in the past, starting from its detection in the interstellar medium (ISM) to analysis of meteorites and cometary samples and laboratory synthesis, as well as computational studies on the possible reaction paths. In this present work quantum chemical calculations have been performed to investigate the possible interstellar formation of glycine via two different paths; (1) in a two-step process via a dihydroxy carbene intermediate and (2) through a one-step concerted mechanism, starting from reactants like CH2[double bond, length as m-dash]NH, CO, CO2, H2O and H2. For the two reactions representing the carbene route, it was observed that the formation of dihydroxy carbene from either CO + H2O or CO2 + H2 is highly endothermic with large barrier heights, whereas the subsequent step of interaction of this carbene with CH2[double bond, length as m-dash]NH to give glycine is exothermic and the barrier is below the reactants. Based on this observation it is suggested that the formation of glycine via the carbene route is a least favourable or even unfavourable path. On the other hand, the two reactions CH2[double bond, length as m-dash]NH + CO + H2O and CH2[double bond, length as m-dash]NH + CO2 + H2 representing the concerted paths were found to be favourable in leading to the formation of glycine. After an extensive study on the first concerted reaction in our previous work (Phys. Chem. Chem. Phys., 2016, 18, 375-381), in this work a detailed investigation has been carried out for the second concerted reaction, CH2[double bond, length as m-dash]NH + CO2 + H2, which can possibly lead to the interstellar formation of glycine. It was observed that this reaction proceeds through a large barrier and at the same time the transition state shows prominent hydrogen dynamics, indicating a tunnelling possibility for this

  20. In Vivo Formation of the Protein Disulfide Bond That Enhances the Thermostability of Diphosphomevalonate Decarboxylase, an Intracellular Enzyme from the Hyperthermophilic Archaeon Sulfolobus solfataricus

    PubMed Central

    Hattori, Ai; Unno, Hideaki; Goda, Shuichiro; Motoyama, Kento; Yoshimura, Tohru

    2015-01-01

    ABSTRACT In the present study, the crystal structure of recombinant diphosphomevalonate decarboxylase from the hyperthermophilic archaeon Sulfolobus solfataricus was solved as the first example of an archaeal and thermophile-derived diphosphomevalonate decarboxylase. The enzyme forms a homodimer, as expected for most eukaryotic and bacterial orthologs. Interestingly, the subunits of the homodimer are connected via an intersubunit disulfide bond, which presumably formed during the purification process of the recombinant enzyme expressed in Escherichia coli. When mutagenesis replaced the disulfide-forming cysteine residue with serine, however, the thermostability of the enzyme was significantly lowered. In the presence of β-mercaptoethanol at a concentration where the disulfide bond was completely reduced, the wild-type enzyme was less stable to heat. Moreover, Western blot analysis combined with nonreducing SDS-PAGE of the whole cells of S. solfataricus proved that the disulfide bond was predominantly formed in the cells. These results suggest that the disulfide bond is required for the cytosolic enzyme to acquire further thermostability and to exert activity at the growth temperature of S. solfataricus. IMPORTANCE This study is the first report to describe the crystal structures of archaeal diphosphomevalonate decarboxylase, an enzyme involved in the classical mevalonate pathway. A stability-conferring intersubunit disulfide bond is a remarkable feature that is not found in eukaryotic and bacterial orthologs. The evidence that the disulfide bond also is formed in S. solfataricus cells suggests its physiological importance. PMID:26303832

  1. Formation of hydrogen-bonded complexes of 3,3',5,5'-tetrabromo-2,2'-biphenol with MTBD and triethylamine

    NASA Astrophysics Data System (ADS)

    Wojciechowski, Grzegorz; Brzezinski, Bogumil

    2002-10-01

    The complexes of 3,3',5,5'-tetrabromo-2,2'-biphenol (TBBPh) with 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene (MTBD) and triethylamine (TEA) were studied by FTIR spectroscopy. In chloroform and in acetonitrile a proton transfer from TBBPh to N-bases (MTBD, TEA) occurs. In chloroform solution the protonated N-base molecules are hydrogen-bonded to the deprotonated TBBPh molecules, whereas in acetonitrile the complexes dissociate. The intra- as well as intermolecular hydrogen bonds within the chains show large proton polarizability.

  2. Site-Selective Tertiary Alkyl-Fluorine Bond Formation from α-Bromoamides Using a Copper/CsF Catalyst System.

    PubMed

    Nishikata, Takashi; Ishida, Syo; Fujimoto, Ryo

    2016-08-16

    A copper-catalyzed site-selective fluorination of α-bromoamides possessing multiple reaction sites, such as primary and secondary alkyl-Br bonds, using inexpensive CsF is reported. Tertiary alkyl-F bonds, which are very difficult to synthesize, can be formed by this fluorination reaction with the aid of an amide group. Control experiments revealed that in situ generated CuF2 is a key fluorinating reagent that reacts with the tertiary alkyl radicals generated by the reaction between an α-bromocarbonyl compound and a copper(I) salt. PMID:27282558

  3. Social bonding: regulation by neuropeptides

    PubMed Central

    Lieberwirth, Claudia; Wang, Zuoxin

    2014-01-01

    Affiliative social relationships (e.g., among spouses, family members, and friends) play an essential role in human society. These relationships affect psychological, physiological, and behavioral functions. As positive and enduring bonds are critical for the overall well-being of humans, it is not surprising that considerable effort has been made to study the neurobiological mechanisms that underlie social bonding behaviors. The present review details the involvement of the nonapeptides, oxytocin (OT), and arginine vasopressin (AVP), in the regulation of social bonding in mammals including humans. In particular, we will discuss the role of OT and AVP in the formation of social bonds between partners of a mating pair as well as between parents and their offspring. Furthermore, the role of OT and AVP in the formation of interpersonal bonding involving trust is also discussed. PMID:25009457

  4. Distinguishing Bonds.

    PubMed

    Rahm, Martin; Hoffmann, Roald

    2016-03-23

    The energy change per electron in a chemical or physical transformation, ΔE/n, may be expressed as Δχ̅ + Δ(VNN + ω)/n, where Δχ̅ is the average electron binding energy, a generalized electronegativity, ΔVNN is the change in nuclear repulsions, and Δω is the change in multielectron interactions in the process considered. The last term can be obtained by the difference from experimental or theoretical estimates of the first terms. Previously obtained consequences of this energy partitioning are extended here to a different analysis of bonding in a great variety of diatomics, including more or less polar ones. Arguments are presented for associating the average change in electron binding energy with covalence, and the change in multielectron interactions with electron transfer, either to, out, or within a molecule. A new descriptor Q, essentially the scaled difference between the Δχ̅ and Δ(VNN + ω)/n terms, when plotted versus the bond energy, separates nicely a wide variety of bonding types, covalent, covalent but more correlated, polar and increasingly ionic, metallogenic, electrostatic, charge-shift bonds, and dispersion interactions. Also, Q itself shows a set of interesting relations with the correlation energy of a bond. PMID:26910496

  5. Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

    NASA Astrophysics Data System (ADS)

    Wittmaack, Klaus

    2013-03-01

    implantation can be evaluated as a function of Cs coverage.The summarised results imply that secondary ions are commonly not formed by charge transfer between an escaping atom and the electronic system of the sample but are already emitted as ions. The probability of ion formation appears to be controlled by the local ionic character of the alkali-target atom bonds, i.e., by the difference in electronegativity between the involved elements as well as by the electron affinity and the ionisation potential of the departing atom. This idea is supported by the finding that Si- yields exhibit the same very strong dependence on Cs coverage as Si+ and O- yields on the oxygen fraction in oxygen loaded Si. Most challenging to theoreticians is the finding that the ionisation probability is independent of the emission velocity of sputtered ions. This phenomenon cannot be rationalised along established routes of thinking. Different concepts need to be explored. An old, somewhat exotic idea takes account of the heavy perturbation created for a very short period of time at the site of ion emission (dynamic randomisation). Molecular dynamics simulations are desirable to clarify the issue. Ultimately it may be possible to describe all phenomena of enhanced or suppressed secondary ion formation, produced either by surface loading with alkali atoms or by enforced surface oxidation, on the basis of a single universal model. There is plenty of room for exciting new studies.

  6. Unravelling the secrets of Cs controlled secondary ion formation: Evidence of the dominance of site specific surface chemistry, alloying and ionic bonding

    NASA Astrophysics Data System (ADS)

    Wittmaack, Klaus

    2013-03-01

    implantation can be evaluated as a function of Cs coverage. The summarised results imply that secondary ions are commonly not formed by charge transfer between an escaping atom and the electronic system of the sample but are already emitted as ions. The probability of ion formation appears to be controlled by the local ionic character of the alkali-target atom bonds, i.e., by the difference in electronegativity between the involved elements as well as by the electron affinity and the ionisation potential of the departing atom. This idea is supported by the finding that Si- yields exhibit the same very strong dependence on Cs coverage as Si+ and O- yields on the oxygen fraction in oxygen loaded Si. Most challenging to theoreticians is the finding that the ionisation probability is independent of the emission velocity of sputtered ions. This phenomenon cannot be rationalised along established routes of thinking. Different concepts need to be explored. An old, somewhat exotic idea takes account of the heavy perturbation created for a very short period of time at the site of ion emission (dynamic randomisation). Molecular dynamics simulations are desirable to clarify the issue. Ultimately it may be possible to describe all phenomena of enhanced or suppressed secondary ion formation, produced either by surface loading with alkali atoms or by enforced surface oxidation, on the basis of a single universal model. There is plenty of room for exciting new studies.

  7. Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus

    SciTech Connect

    Hendrickx, Antoni P.A.; Poor, Catherine B.; Jureller, Justin E.; Budzik, Jonathan M.; He, Chuan; Schneewind, Olaf

    2012-09-05

    Bacillus cereus strains elaborate pili on their surface using a mechanism of sortase-mediated cross-linking of major and minor pilus components. Here we used a combination of electron microscopy and atomic force microscopy to visualize these structures. Pili occur as single, double or higher order assemblies of filaments formed from monomers of the major pilin, BcpA, capped by the minor pilin, BcpB. Previous studies demonstrated that within assembled pili, four domains of BcpA -- CNA{sub 1}, CNA{sub 2}, XNA and CNA{sub 3} -- each acquire intramolecular lysine-asparagine isopeptide bonds formed via catalytic glutamic acid or aspartic acid residues. Here we showed that mutants unable to form the intramolecular isopeptide bonds in the CNA2 or CNA3 domains retain the ability to form pilus bundles. A mutant lacking the CNA{sub 1} isopeptide bond assembled deformed pilin subunits that failed to associate as bundles. X-ray crystallography revealed that the BcpA variant Asp{sup 312}Ala, lacking an aspartyl catalyst, did not generate the isopeptide bond within the jelly-roll structure of XNA. The Asp{sup 312}Ala mutant was also unable to form bundles and promoted the assembly of deformed pili. Thus, structural integrity of the CNA{sub 1} and XNA domains are determinants for the association of pili into higher order bundle structures and determine native pilus structure.

  8. Discovery of molluscicidal and cercaricidal activities of 3-substituted quinazolinone derivatives by a scaffold hopping approach using a pseudo-ring based on the intramolecular hydrogen bond formation.

    PubMed

    Guo, Wei; Zheng, Lv-Yin; Li, Yong-Dong; Wu, Ren-Miao; Chen, Qiang; Yang, Ding-Qiao; Fan, Xiao-Lin

    2016-06-10

    Discovery of novel topological agents against Oncomelania hupensis snails and cercariae remains a significant challenge in current Schistosomiasis control. A pseudo-ring formed from salicylanilide by an intramolecular hydrogen bond led to the discovery of 3-substituted quinazolinone derivatives which showed a potent molluscicidal and cercaricidal activities. PMID:27017555

  9. A Model for the Chemical Bond

    ERIC Educational Resources Information Center

    Magnasco, Valerio

    2004-01-01

    Bond stereochemistry in polyatomic hydrides is explained in terms of the principle of bond energies maximization, which yields X-H straight bonds and suggests the formation of appropriate sp hybrids on the central atom. An introduction to the electron charge distribution in molecules is given, and atomic, overlap, gross and formal charges are…

  10. [Bond selective chemistry beyond the adiabatic approximation

    SciTech Connect

    Butler, L.J.

    1993-02-28

    The adiabatic Born-Oppenheimer potential energy surface approximation is not valid for reaction of a wide variety of energetic materials and organic fuels; coupling between electronic states of reacting species plays a key role in determining the selectivity of the chemical reactions induced. This research program initially studies this coupling in (1) selective C-Br bond fission in 1,3- bromoiodopropane, (2) C-S:S-H bond fission branching in CH[sub 3]SH, and (3) competition between bond fission channels and H[sub 2] elimination in CH[sub 3]NH[sub 2].

  11. The thermodynamics and kinetics of phosphoester bond formation, use, and dissociation in biology, with the example of polyphosphate in platelet activation, trasience, and mineralization.

    NASA Astrophysics Data System (ADS)

    Omelon, S. J.

    2014-12-01

    Mitochondria condense orthophosphates (Pi), forming phosphoester bonds for ATP production that is important to life. This represents an exchange of energy from dissociated carbohydrate bonds to phosophoester bonds. These bonds are available to phosphorylate organic compounds or hydrolyze to Pi, driving many biochemical processes. The benthic bacteria T. namibiensis 1 and Beggiatoa 2 condense Pi into phosphate polymers in oxygenated environments. These polyphosphates (polyPs) are stored until the environment becomes anoxic, when these bacteria retrieve the energy from polyP dissociation into Pi3. Dissociated Pi is released outside of the bacteria, where it precipitates as apatite.The Gibbs free energy of polyP phosphoester bond hydrolysis is negative, however, the kinetics are slow4. Diatoms contain a polyP pool that is stable until after death, after which the polyPs hydrolyze and form apatite5. The roles of polyP in eukaryotic organism biochemistry continue to be discovered. PolyPs have a range of biochemical roles, such as bioavailable P-storage, stress adaptation, and blood clotting6. PolyP-containing granules are released from anuclear platelets to activate factor V7 and factor XII in the blood clotting process due to their polyanionic charge8. Platelets have a lifespan of approximately 8 days, after which they undergo apoptosis9. Data will be presented that demonstrate the bioactive, thermodynamically unstable polyP pool within older platelets in vitro can spontaneously hydrolyze and form phosphate minerals. This process is likely avoided by platelet digestion in the spleen and liver, possibly recycling platelet polyPs with their phosphoester bond energy for other biochemical roles. 1 Schulz HN et al. Science (2005) 307: 416-4182 Brüchert V et al. Geochim Cosmochim Acta (2003) 67: 4505-45183 Goldhammer T et al. Nat Geosci (2010) 3: 557-5614 de Jager H-J et al. J Phys Chem A (1988) 102: 2838-28415 Diaz, J et al. Science (2008) 320: 652-6556 Mason KD et al

  12. Yankee bonds

    SciTech Connect

    Delaney, P. )

    1993-10-01

    Yankee and Euromarket bonds may soon find their way into the financing of power projects in Latin America. For developers seeking long-term commitments under build, own, operate, and transfer (BOOT) power projects in Latin America, the benefits are substantial.

  13. Rhodium-catalysed C(sp2)–C(sp2) bond formation via C–H/C–F activation

    PubMed Central

    Tian, Panpan; Feng, Chao; Loh, Teck-Peng

    2015-01-01

    Fluoroalkenes represent a class of privileged structural motifs, which found widespread use in medicinal chemistry. However, the synthetic access to fluoroalkenes was much underdeveloped with previous reported methods suffering from either low step economy or harsh reaction conditions. Here we present a RhIII-catalysed tandem C–H/C–F activation for the synthesis of (hetero)arylated monofluoroalkenes. The use of readily available gem-difluoroalkenes as electrophiles provides a highly efficient and operationally simple method for the introduction of α-fluoroalkenyl motifs onto (hetero)arenes under oxidant-free conditions. Furthermore, the employment of alcoholic solvent and the in-situ generated hydrogen fluoride are found to be beneficial in this transformation, indicating the possibility of the involvement of hydrogen bond activation mode with regards to the C–F bond cleavage step. PMID:26081837

  14. Comparison of the kinetics of S-S bond, secondary structure, and active site formation during refolding of reduced denatured hen egg white lysozyme.

    PubMed Central

    Roux, P.; Ruoppolo, M.; Chaffotte, A. F.; Goldberg, M. E.

    1999-01-01

    To investigate the role of some tertiary interactions, the disulfide bonds, in the early stages of refolding of hen lysozyme, we report the kinetics of reoxidation of denatured and reduced lysozyme under the same refolding conditions as those previously used to investigate the kinetics of regain of its circular dichroism (CD), fluorescence, and activity. At different stages of the refolding, the oxidation of the protein was blocked by alkylation of the free cysteines with iodoacetamide and the various oxidation states present in the samples were identified by electrospray-mass spectrometry. Thus, it was possible to monitor the appearance and/or disappearance of the species with 0 to 4 disulfide bonds. Using a simulation program, these kinetics were compared with those of regain of far-UV CD, fluorescence, and enzymatic activity and were discussed in terms of a refined model for the refolding of reduced hen egg white lysozyme. PMID:10631992

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

    PubMed

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

    2014-10-01

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

  16. Theoretical investigation of the role of clay edges in prebiotic peptide bond formation. II - Structures and thermodynamics of the activated complex species

    NASA Technical Reports Server (NTRS)

    Collins, Jack R.; Loew, Gilda H.; Luke, Brian T.; White, David H.

    1988-01-01

    Molecular orbital calculations are used to study amino acid activation by anhydride formation in neutral phosphates and in tetrahedral silicate and aluminate sites on clay edges. The results agree with previous ab initio studies of Luke et al. (1984) on the reactant species. Relative heats of formation of the anhydrides indicate the extent of anhydride formation to be the greatest for Al and the least for phosphate, which is the same order as the stability of hydrolysis.

  17. Recent developments in alkene hydro-functionalisation promoted by homogeneous catalysts based on earth abundant elements: formation of C-N, C-O and C-P bond.

    PubMed

    Rodriguez-Ruiz, Violeta; Carlino, Romain; Bezzenine-Lafollée, Sophie; Gil, Richard; Prim, Damien; Schulz, Emmanuelle; Hannedouche, Jérôme

    2015-07-21

    This Perspective article provides an overview of the recent advancements in the field of intra- and inter-molecular C-N, C-O and C-P bond formation by hydroamination, hydroalkoxylation, hydrophosphination, hydrophosphonylation or hydrophosphinylation of unactivated alkenes, including allenes, 1,3-dienes and strained alkenes, promoted by (chiral) homogeneous catalysts based on earth abundant elements of the s and p blocks, the first row transition metals and the rare-earth metals. The relevant literature from 2009 until late 2014 has been covered. PMID:25803322

  18. Diffusion bonding

    DOEpatents

    Anderson, Robert C.

    1976-06-22

    1. A method for joining beryllium to beryllium by diffusion bonding, comprising the steps of coating at least one surface portion of at least two beryllium pieces with nickel, positioning a coated surface portion in a contiguous relationship with an other surface portion, subjecting the contiguously disposed surface portions to an environment having an atmosphere at a pressure lower than ambient pressure, applying a force upon the beryllium pieces for causing the contiguous surface portions to abut against each other, heating the contiguous surface portions to a maximum temperature less than the melting temperature of the beryllium, substantially uniformly decreasing the applied force while increasing the temperature after attaining a temperature substantially above room temperature, and maintaining a portion of the applied force at a temperature corresponding to about maximum temperature for a duration sufficient to effect the diffusion bond between the contiguous surface portions.

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

    PubMed Central

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

    2012-01-01

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

  20. The cystic fibrosis V232D mutation inhibits CFTR maturation by disrupting a hydrophobic pocket rather than formation of aberrant interhelical hydrogen bonds.

    PubMed

    Loo, Tip W; Clarke, David M

    2014-03-01

    Processing mutations that inhibit folding and trafficking of CFTR are the main cause of cystic fibrosis. Repair of CFTR mutants requires an understanding of the mechanisms of misfolding caused by processing mutations. Previous studies on helix-loop-helix fragments of the V232D processing mutation suggested that its mechanism was to lock transmembrane (TM) segments 3 and 4 together by a non-native hydrogen bond (Asp232(TM4)/Gln207(TM3)). Here, we performed mutational analysis to test for Asp232/Gln207 interactions in full-length CFTR. The rationale was that a V232N mutation should mimic V232D and a V232D/Q207A mutant should mature if the processing defect was caused by hydrogen bonds. We report that only Val232 mutations to charged amino acids severely blocked CFTR maturation. The V232N mutation did not mimic V232D as V232N showed 40% maturation compared to 2% for V232D. Mutation of Val232 to large nonpolar residues (Leu, Phe) had little effect. The Q207L mutation did not rescue V232D because Q207L showed about 50% maturation in the presence of corrector VX-809 while V232D/Q207A could no longer be rescued. These results suggest that V232D inhibits maturation by disrupting a hydrophobic pocket between TM segments rather than forming a non-native hydrogen bond. Disulfide cross-linking analysis of cysteines W356C(TM6) and W1145C(TM12) suggest that the V232D mutation inhibits maturation by trapping CFTR as a partially folded intermediate. Since correctors can efficiently rescue V232D CFTR, the results suggest that hydrophilic processing mutations facing a hydrophobic pocket are good candidates for rescue with pharmacological chaperones. PMID:24412276

  1. Accumulation of β-Conglycinin in Soybean Cotyledon through the Formation of Disulfide Bonds between α′- and α-Subunits1[W][OA

    PubMed Central

    Wadahama, Hiroyuki; Iwasaki, Kensuke; Matsusaki, Motonori; Nishizawa, Keito; Ishimoto, Masao; Arisaka, Fumio; Takagi, Kyoko; Urade, Reiko

    2012-01-01

    β-Conglycinin, one of the major soybean (Glycine max) seed storage proteins, is folded and assembled into trimers in the endoplasmic reticulum and accumulated into protein storage vacuoles. Prior experiments have used soybean β-conglycinin extracted using a reducing buffer containing a sulfhydryl reductant such as 2-mercaptoethanol, which reduces both intermolecular and intramolecular disulfide bonds within the proteins. In this study, soybean proteins were extracted from the cotyledons of immature seeds or dry beans under nonreducing conditions to prevent the oxidation of thiol groups and the reduction or exchange of disulfide bonds. We found that approximately half of the α′- and α-subunits of β-conglycinin were disulfide linked, together or with P34, prior to amino-terminal propeptide processing. Sedimentation velocity experiments, size-exclusion chromatography, and two-dimensional polyacrylamide gel electrophoresis (PAGE) analysis, with blue native PAGE followed by sodium dodecyl sulfate-PAGE, indicated that the β-conglycinin complexes containing the disulfide-linked α′/α-subunits were complexes of more than 720 kD. The α′- and α-subunits, when disulfide linked with P34, were mostly present in approximately 480-kD complexes (hexamers) at low ionic strength. Our results suggest that disulfide bonds are formed between α′/α-subunits residing in different β-conglycinin hexamers, but the binding of P34 to α′- and α-subunits reduces the linkage between β-conglycinin hexamers. Finally, a subset of glycinin was shown to exist as noncovalently associated complexes larger than hexamers when β-conglycinin was expressed under nonreducing conditions. PMID:22218927

  2. General and facile method for exo-methlyene synthesis via regioselective C-C double-bond formation using a copper-amine catalyst system.

    PubMed

    Nishikata, Takashi; Nakamura, Kimiaki; Itonaga, Kohei; Ishikawa, Shingo

    2014-11-01

    In this study, for distal-selective β-hydride elimination to produce exomethylene compounds with a newly formed Csp(3)-Csp(3) bond between tertiary alkyl halides and α-alkylated styrenes, a combination of a Cu(I) salt and a pyridine-based amine ligand (TPMA) is found to be a very efficient catalyst system. The yields and regioselectivities were high, and the regioselectivity was found to be dependent on the structure of the alkyl halide, with bulky alkyl halides showing the highest distal selectivities. PMID:25315319

  3. Isolation of a Diborane(6) Dication: Formation and Cleavage of an Electron-Precise B(sp(3))-B(sp(3)) Bond.

    PubMed

    Kong, Lingbing; Lu, Wei; Li, Yongxin; Ganguly, Rakesh; Kinjo, Rei

    2016-07-13

    One-electron oxidation of organoboron L2PhB: 1 (L = oxazol-2-ylidene) afforded a dicationic diborane(6) species [L2PhB-BPhL2]·2X (X = OTf, BF4, AlCl4) 3, representing a new strategy to construct a B(sp(3))-B(sp(3)) covalent bond. Each boron atom in 3 is in the formal oxidation state +II, and tetracoordinate with a Ph group and two oxazol-2-ylidenes. The cyclic voltammetry of 3 shows irreversible reduction and oxidation. Indeed, two-electron reduction of 3 with potassium graphite (KC8) afforded 1, making a fully reversible 1 ↔ 3 redox system, whereas two-electron oxidation with AuCl produced a boronium [L2PhBCl]OTf 4. Moreover, the reactions of 3 with isonitrile derivatives RNC: under heating conditions gave a cyano-substituted boronium [L2PhBCN]BF4 5 and a 2-boranyl-indole derivative 6, depending on the substituent R. The proposed reaction mechanism involves a borinylium radical 1(•+) which is generated via a homolytic cleavage of the B-B bond of 3. PMID:27309118

  4. Pi Bond Orders and Bond Lengths

    ERIC Educational Resources Information Center

    Herndon, William C.; Parkanyi, Cyril

    1976-01-01

    Discusses three methods of correlating bond orders and bond lengths in unsaturated hydrocarbons: the Pauling theory, the Huckel molecular orbital technique, and self-consistent-field techniques. (MLH)

  5. Formation of a Metal-to-Nitrogen Bond of Normal Length by a Neutral Sufonamide Group within a Tridentate Ligand. A New Approach to Radiopharmaceutical Bioconjugation

    PubMed Central

    Perera, Theshini; Abhayawardhana, Pramuditha; Marzilli, Patricia A.; Fronczek, Frank R.

    2014-01-01

    We demonstrate that a tertiary sulfonamide group, N(SO2R)R′2, can re-hybridize to form a M–N bond of normal length even when the group is in a linear tridentate ligand, such as in the new tridentate N(SO2R)dpa ligands derived from di-(2-picolyl)amine (N(H)dpa). N(SO2R)dpa ligands were used to prepare fac-[Re(CO)3(N(SO2R)dpa)](PF6 or BF4) complexes. Structural characterization of the new complexes established that the tertiary sulfonamide nitrogen atom binds to Re with concomitant sp2-to-sp3 re-hybridization, facilitating facial coordination. The new fac-[Re(CO)3(N(SO2R)dpa)]X structures provide the only examples for any metal with the sulfonamide as part of a noncyclic linear tridentate ligand and with a normal metal-to-nitrogen(tertiary sulfonamide) bond length. Rare previous examples of such normal M–N bonds have been found only in more constrained situations, such as with tripodal tetradentate ligands. Our long-term objectives for the new tridentate N(SO2R)dpa ligands are to develop the fundamental chemistry relevant to the eventual use of the fac-[MI(CO)3]+ core (M = 99mTc, 186/188Re) in imaging and therapy. The sulfonamide group uniquely contributes to two of our goals: expanding ways to conjugate the fac-[MI(CO)3]+ core to biological molecules and also developing new symmetrical tridentate ligands that can coordinate facially to this core. Tests of our conjugation method, conducted by linking the fac-[ReI(CO)3]+ core to a new tetraarylporphyrin (T(N(SO2C6H4)dpa)P) as well as to a dansyl (5-(dimethylamino)naphthalene-1-sulfonyl) group, demonstrate that large molecular fragments can be tethered via a coordinated tertiary sulfonamide linkage to this core. PMID:23421481

  6. Special catalyst improves c-s compounds conversion

    SciTech Connect

    Pearson, M.J.

    1981-04-01

    Carbon-sulfur compounds normally formed in the Claus furnace can be almost totally decomposed when a promoted catalyst is used rather than a standard unpromoted catalyst. Compound formation and decomposition chemistries are described. The use of a promoted active alumina is shown to yield better results compared with a standard active alumina catalyst.

  7. Formation of three new bonds and two stereocenters in acyclic systems by zinc-mediated enantioselective alkynylation of acylsilanes, Brook rearrangement, and ene-allene carbocyclization reactions.

    PubMed

    Smirnov, Polina; Katan, Einat; Mathew, Jomon; Kostenko, Arseni; Karni, Miriam; Nijs, Anne; Bolm, Carsten; Apeloig, Yitzhak; Marek, Ilan

    2014-12-19

    Diastereoisomerically pure (dr > 99:1) and enantiomerically enriched (er up to 98:2) substituted propargyl diols possessing a tertiary hydroxyl group were synthesized in a single-pot operation from simple acylsilanes through a combined catalytic enantioselective alkynylation of acylsilanes, followed by an allenyl-Zn-Brook rearrangement and Zn-ene-allene (or Zn-yne-allene) cyclization reaction. Two remarkable features of these reactions are the near complete transfer of chirality in the allenyl-Zn-Brook rearrangement and the highly organized six-membered transition state of the Zn-ene-allene carbocyclization found by DFT calculations. In this process, three new bonds and two new stereogenic centers are created in a single-pot operation in excellent diastereo- and enantiomeric ratios. DFT calculations show that the allenyl-Zn-Brook rearrangement occurs in preference to the classic [1,2]-Zn-Brook rearrangement owing to its significantly lower activation barrier. PMID:25271364

  8. A new approach to carbon-carbon bond formation: Development of aerobic Pd-catalyzed reductive coupling reactions of organometallic reagents and styrenes

    PubMed Central

    Gligorich, Keith M.; Iwai, Yasumasa; Cummings, Sarah A.; Sigman, Matthew S.

    2009-01-01

    Alkenes are attractive starting materials for organic synthesis and the development of new selective functionalization reactions are desired. Previously, our laboratory discovered a unique Pd-catalyzed hydroalkoxylation reaction of styrenes containing a phenol. Based upon deuterium labeling experiments, a mechanism involving an aerobic alcohol oxidation coupled to alkene functionalization was proposed. These results inspired the development of a new Pd-catalyzed reductive coupling reaction of alkenes and organometallic reagents that generates a new carbon-carbon bond. Optimization of the conditions for the coupling of both organostannanes and organoboronic esters is described and the initial scope of the transformation is presented. Additionally, several mechanistic experiments are outlined and support the rationale for the development of the reaction based upon coupling alcohol oxidation to alkene functionalization. PMID:20161306

  9. Access to novel fluorovinylidene ligands via exploitation of outer-sphere electrophilic fluorination: new insights into C-F bond formation and activation.

    PubMed

    Milner, Lucy M; Hall, Lewis M; Pridmore, Natalie E; Skeats, Matthew K; Whitwood, Adrian C; Lynam, Jason M; Slattery, John M

    2016-01-28

    Metal vinylidene complexes are widely encountered, or postulated, as intermediates in a range of important metal-mediated transformations of alkynes. However, fluorovinylidene complexes have rarely been described and their reactivity is largely unexplored. By making use of the novel outer-sphere electrophilic fluorination (OSEF) strategy we have developed a rapid, robust and convenient method for the preparation of fluorovinylidene and trifluoromethylvinylidene ruthenium complexes from non-fluorinated alkynes. Spectroscopic investigations (NMR and UV/Vis), coupled with TD-DFT studies, show that fluorine incorporation results in significant changes to the electronic structure of the vinylidene ligand. The reactivity of fluorovinylidene complexes shows many similarities to non-fluorinated analogues, but also some interesting differences, including a propensity to undergo unexpected C-F bond cleavage reactions. Heating fluorovinylidene complex [Ru(η(5)-C5H5)(PPh3)2(C[double bond, length as m-dash]C{F}R)][BF4] led to C-H activation of a PPh3 ligand to form an orthometallated fluorovinylphosphonium ligand. Reaction with pyridine led to nucleophilic attack at the metal-bound carbon atom of the vinylidene to form a vinyl pyridinium species, which undergoes both C-H and C-F activation to give a novel pyridylidene complex. Addition of water, in the presence of chloride, leads to anti-Markovnikov hydration of a fluorovinylidene complex to form an α-fluoroaldehyde, which slowly rearranges to its acyl fluoride isomer. Therefore, fluorovinylidenes ligands may be viewed as synthetic equivalents of 1-fluoroalkynes providing access to reactivity not possible by other routes. PMID:26701305

  10. Bonded Lubricants

    NASA Technical Reports Server (NTRS)

    1977-01-01

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

  11. Diffusion bonding of mismatch dental alloys.

    PubMed

    Liu, Honghua; Ni, Jiahua; Wu, Luhai; He, Guo

    2010-04-01

    The diffusion bonding of Ti-6Al-4V and Co-Cr-Mo dental alloys has been investigated in terms of the atoms diffusion, the microstructure evolution, and the bonding strength. The bonding performance reveals asymmetry diffusion profiles for both the Co and Cr in Ti-6Al-4V and the Ti in Co-Cr-Mo alloy. Their diffusion coefficients (Arrhenius relations) have been established based on the experiments. Co and Cr diffusion into Ti-6Al-4V leads to alpha --> beta transformation and the intermetallics-formation. Maximum bonding strength occurs at about 840 degrees C. The bonding joint fails under the shear stress in the Ti-6Al-4V side near the bonding interface in brittle manner. The intermetallics in the diffusion layer together with the unbonded areas and other flaws in the bonding interface are responsible for the shear brittle fracture, which also weaken the bonding strength. PMID:19957358

  12. Basics of Fidelity Bonding.

    ERIC Educational Resources Information Center

    Kahn, Steven P.

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

  13. Specific collapse followed by slow hydrogen-bond formation of beta-sheet in the folding of single-chain monellin.

    PubMed

    Kimura, Tetsunari; Uzawa, Takanori; Ishimori, Koichiro; Morishima, Isao; Takahashi, Satoshi; Konno, Takashi; Akiyama, Shuji; Fujisawa, Tetsuro

    2005-02-22

    Characterization of the conformational landscapes for proteins with different secondary structures is important in elucidating the mechanism of protein folding. The folding trajectory of single-chain monellin composed of a five-stranded beta-sheet and a helix was investigated by using a pH-jump from the alkaline unfolded to native state. The kinetic changes in the secondary structures and in the overall size and shape were measured by circular dichroism spectroscopy and small-angle x-ray scattering, respectively. The formation of the tertiary structure was monitored by intrinsic and extrinsic fluorescence. A significant collapse was observed within 300 micros after the pH-jump, leading to the intermediate with a small amount of secondary and tertiary structures but with an overall oblate shape. Subsequently, the stepwise formation of secondary and tertiary structures was detected. The current observation was consistent with the theoretical prediction that a more significant collapse precedes the formation of secondary structures in the folding of beta-sheet proteins than that of helical proteins [Shea, J. E., Onuchic, J. N. & Brooks, C. L., III (2002) Proc. Natl. Acad. Sci. USA 99, 16064-16068]. Furthermore, it was implied that the initial collapse was promoted by the formation of some specific structural elements, such as tight turns, to form the oblate shape. PMID:15710881

  14. Specific collapse followed by slow hydrogen-bond formation of β-sheet in the folding of single-chain monellin

    PubMed Central

    Kimura, Tetsunari; Uzawa, Takanori; Ishimori, Koichiro; Morishima, Isao; Takahashi, Satoshi; Konno, Takashi; Akiyama, Shuji; Fujisawa, Tetsuro

    2005-01-01

    Characterization of the conformational landscapes for proteins with different secondary structures is important in elucidating the mechanism of protein folding. The folding trajectory of single-chain monellin composed of a five-stranded β-sheet and a helix was investigated by using a pH-jump from the alkaline unfolded to native state. The kinetic changes in the secondary structures and in the overall size and shape were measured by circular dichroism spectroscopy and small-angle x-ray scattering, respectively. The formation of the tertiary structure was monitored by intrinsic and extrinsic fluorescence. A significant collapse was observed within 300 μs after the pH-jump, leading to the intermediate with a small amount of secondary and tertiary structures but with an overall oblate shape. Subsequently, the stepwise formation of secondary and tertiary structures was detected. The current observation was consistent with the theoretical prediction that a more significant collapse precedes the formation of secondary structures in the folding of β-sheet proteins than that of helical proteins [Shea, J. E., Onuchic, J. N. & Brooks, C. L., III (2002) Proc. Natl. Acad. Sci. USA 99, 16064–16068]. Furthermore, it was implied that the initial collapse was promoted by the formation of some specific structural elements, such as tight turns, to form the oblate shape. PMID:15710881

  15. Surface carbonation of synthetic C-S-H samples: A comparison between fresh and aged C-S-H using X-ray photoelectron spectroscopy

    SciTech Connect

    Black, Leon Garbev, Krassimir; Gee, Ian

    2008-06-15

    This paper presents a continuation of studies into silicate anion structure using X-ray photoelectron spectroscopy (XPS). A series of C-S-H samples have been prepared mechanochemically, and then stored under ambient conditions for six months. Storage led to surface carbonation, the extent of which was dependent upon the calcium/silicon ratio of the fresh sample. Carbonation arose through decalcification of the C-S-H, leading to increased silicate polymerisation. The surfaces of the most calcium-rich phases (C/S = 1.33 and 1.50) underwent complete decalcification to yield silica (possibly containing some silanol groups) and calcium carbonate. Carbonation, and hence changes in silicate anion structure, was minimal for the C-S-H phases with C/S = 0.67 and 0.75.

  16. Low-temperature full wafer adhesive bonding

    NASA Astrophysics Data System (ADS)

    Niklaus, Frank; Enoksson, Peter; Kälvesten, Edvard; Stemme, Göran

    2001-03-01

    We have systematically investigated the influence of different bonding parameters on void formation in a low-temperature adhesive bonding process. As a result of these studies we present guidelines for void free adhesive bonding of 10 cm diameter wafers. We have focused on polymer coatings with layer thicknesses between 1 µm and 18 µm. The tested polymer materials were benzocyclobutene (BCB) from Dow Chemical, a negative photoresist (ULTRA-i 300) and a positive photoresist (S1818) from Shipley, a polyimide (HTR3) from Arch Chemical and two different polyimides (PI2555 and PI2610) from DuPont. The polymer material, the bonding pressure and the pre-curing time and temperature for the polymer significantly influence void formation at the bond interface. High bonding pressure and optimum pre-curing times/temperatures counteract void formation. We present the process parameters to achieve void-free bonding with the BCB coating and with the ULTRA-i 300 photoresist coating as adhesive materials. Excellent void-free and strong bonds have been achieved by using BCB as the bonding material which requires a minimum bonding temperature of 180 °C.

  17. Direct carbon-carbon bond formation via reductive soft enolization: a syn-selective Mannich addition of α-iodo thioesters.

    PubMed

    Truong, Ngoc; Sauer, Scott J; Seraphin-Hatcher, Cyndie; Coltart, Don M

    2016-08-16

    The β-amino carboxylic acid moiety is a key feature of numerous important biologically active compounds. We describe a syn-selective direct Mannich addition reaction that uses α-iodo thioesters and sulfonyl imines and produces β-amino thioesters. Enolate formation is achieved by reductive soft enolization. The products of the reaction provide straightforward access to biologically important β-lactams through a variety of known reactions. PMID:27492274

  18. Dihydrogen catalysis of the reversible formation and cleavage of C-H and N-H bonds of aminopyridinate ligands bound to (η(5) -C5 Me5 )Ir(III.).

    PubMed

    Zamorano, Ana; Rendón, Nuria; López-Serrano, Joaquín; Valpuesta, José E V; Álvarez, Eleuterio; Carmona, Ernesto

    2015-02-01

    This study focuses on a series of cationic complexes of iridium that contain aminopyridinate (Ap) ligands bound to an (η(5) -C5 Me5 )Ir(III) fragment. The new complexes have the chemical composition [Ir(Ap)(η(5) -C5 Me5 )](+) , exist in the form of two isomers (1(+) and 2(+) ) and were isolated as salts of the BArF (-) anion (BArF =B[3,5-(CF3 )2 C6 H3 ]4 ). Four Ap ligands that differ in the nature of their bulky aryl substituents at the amido nitrogen atom and pyridinic ring were employed. In the presence of H2 , the electrophilicity of the Ir(III) centre of these complexes allows for a reversible prototropic rearrangement that changes the nature and coordination mode of the aminopyridinate ligand between the well-known κ(2) -N,N'-bidentate binding in 1(+) and the unprecedented κ-N,η(3) -pseudo-allyl-coordination mode in isomers 2(+) through activation of a benzylic C-H bond and formal proton transfer to the amido nitrogen atom. Experimental and computational studies evidence that the overall rearrangement, which entails reversible formation and cleavage of H-H, C-H and N-H bonds, is catalysed by dihydrogen under homogeneous conditions. PMID:25504864

  19. Formation and High Reactivity of the anti-Dioxo Form of High-Spin μ-Oxodioxodiiron(IV) as the Active Species That Cleaves Strong C-H Bonds.

    PubMed

    Kodera, Masahito; Ishiga, Shin; Tsuji, Tomokazu; Sakurai, Katsutoshi; Hitomi, Yutaka; Shiota, Yoshihito; Sajith, P K; Yoshizawa, Kazunari; Mieda, Kaoru; Ogura, Takashi

    2016-04-18

    Recently, it was shown that μ-oxo-μ-peroxodiiron(III) is converted to high-spin μ-oxodioxodiiron(IV) through O-O bond scission. Herein, the formation and high reactivity of the anti-dioxo form of high-spin μ-oxodioxodiiron(IV) as the active oxidant are demonstrated on the basis of resonance Raman and electronic-absorption spectral changes, detailed kinetic studies, DFT calculations, activation parameters, kinetic isotope effects (KIE), and catalytic oxidation of alkanes. Decay of μ-oxodioxodiiron(IV) was greatly accelerated on addition of substrate. The reactivity order of substrates is toluenebond cleavage of ethylbenzene than the most reactive diiron system reported so far. The KIE for the reaction with toluene/[D8 ]toluene is 95 at -30 °C, which the largest in diiron systems reported so far. The present diiron complex efficiently catalyzes the oxidation of various alkanes with H2 O2 . PMID:26970337

  20. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

    PubMed

    Lee, Woonghee; Stark, Jaime L; Markley, John L

    2014-11-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days. PMID:25190042

  1. Template Catalysis by Metal-Ligand Cooperation. C-C Bond Formation via Conjugate Addition of Non-activated Nitriles under Mild, Base-free Conditions Catalyzed by a Manganese Pincer Complex.

    PubMed

    Nerush, Alexander; Vogt, Matthias; Gellrich, Urs; Leitus, Gregory; Ben-David, Yehoshoa; Milstein, David

    2016-06-01

    The first example of a catalytic Michael addition reaction of non-activated aliphatic nitriles to α,β-unsaturated carbonyl compounds under mild, neutral conditions is reported. A new de-aromatized pyridine-based PNP pincer complex of the Earth-abundant, first-row transition metal manganese serves as the catalyst. The reaction tolerates a variety of nitriles and Michael acceptors with different steric features and acceptor strengths. Mechanistic investigations including temperature-dependent NMR spectroscopy and DFT calculations reveal that the cooperative activation of alkyl nitriles, which leads to the generation of metalated nitrile nucleophile species (α-cyano carbanion analogues), is a key step of the mechanism. The metal center is not directly involved in the catalytic bond formation but rather serves, cooperatively with the ligand, as a template for the substrate activation. This approach of "template catalysis" expands the scope of potential donors for conjugate addition reactions. PMID:27164437

  2. Formation of Self-Templated 2,6-Bis(1,2,3-triazol-4-yl)pyridine [2]Catenanes by Triazolyl Hydrogen Bonding: Selective Anion Hosts for Phosphate.

    PubMed

    Byrne, Joseph P; Blasco, Salvador; Aletti, Anna B; Hessman, Gary; Gunnlaugsson, Thorfinnur

    2016-07-25

    We report the remarkable ability of 2,6-bis(1,2,3-triazol-4-yl)pyridine (btp) compounds 2 with appended olefin amide arms to self-template the formation of interlocked [2]catenane structures 3 in up to 50 % yield when subjected to olefin ring-closing metathesis in CH2 Cl2 . X-ray diffraction crystallography enabled the structural characterization of both the [2]catenane 3 a and the non-interlocked macrocycle 4 a. These [2]catenanes showed selective triazolyl hydrogen-bonding interactions with the tetrahedral phosphate anion when screened against a range of ions; 3 a,b are the first examples of selective [2]catenane hosts for phosphate. PMID:27295556

  3. DsbA2 (27 kDa Com1-like protein) of Legionella pneumophila catalyses extracytoplasmic disulphide-bond formation in proteins including the Dot/Icm type IV secretion system.

    PubMed

    Jameson-Lee, Max; Garduño, Rafael A; Hoffman, Paul S

    2011-05-01

    In Gram-negative bacteria, thiol oxidoreductases catalyse the formation of disulphide bonds (DSB) in extracytoplasmic proteins. In this study, we sought to identify DSB-forming proteins required for assembly of macromolecular structures in Legionella pneumophila. Here we describe two DSB-forming proteins, one annotated as dsbA1 and the other annotated as a 27 kDa outer membrane protein similar to Com1 of Coxiella burnetii, which we designate as dsbA2. Both proteins are predicted to be periplasmic, and while dsbA1 mutants were readily isolated and without phenotype, dsbA2 mutants were not obtained. To advance studies of DsbA2, a cis-proline residue at position 198 was replaced with threonine that enables formation of stable disulphide-bond complexes with substrate proteins. Expression of DsbA2 P198T mutant protein from an inducible promoter produced dominant-negative effects on DsbA2 function that resulted in loss of infectivity for amoeba and HeLa cells and loss of Dot/Icm T4SS-mediated contact haemolysis of erythrocytes. Analysis of captured DsbA2 P198T-substrate complexes from L. pneumophila by mass spectrometry identified periplasmic and outer membrane proteins that included components of the Dot/Icm T4SS. More broadly, our studies establish a DSB oxidoreductase function for the Com1 lineage of DsbA2-like proteins which appear to be conserved among those bacteria also expressing T4SS. PMID:21375592

  4. DsbA2 (27-kDa Com1-Like Protein) of Legionella pneumophila Catalyses Extracytoplasmic Disulfide-Bond Formation in Proteins Including the Dot/Icm Type IV Secretion System

    PubMed Central

    Jameson-Lee, Max; Garduno, Rafael A.; Hoffman, Paul S.

    2011-01-01

    Summary In Gram negative bacteria, thiol oxidoreductases catalyze the formation of disulfide bonds (DSB) in extracytoplasmic proteins. In this study, we sought to identify DSB-forming proteins required for assembly of macromolecular structures in Legionella pneumophila. Here we describe two DSB forming proteins, one annotated as dsbA1 and the other annotated as a 27-kDa outer membrane protein similar to Com1 of Coxiella burnetii, which we designate as dsbA2. Both proteins are predicted to be periplasmic, and while dsbA1 mutants were readily isolated and without phenotype, dsbA2 mutants were not obtained. To advance studies of DsbA2, a cis-proline residue at position 198 was replaced with threonine that enables formation of stable disulfide-bond complexes with substrate proteins. Expression of DsbA2 P198T-mutant protein from an inducible promoter produced dominant-negative effects on DsbA2 function that resulted in loss of infectivity for amoeba and HeLa cells and loss of Dot/Icm T4SS-mediated contact hemolysis of erythrocytes. Analysis of captured DsbA2 P198T-substrate complexes from L. pneumophila by mass spectrometry identified periplasmic and outer membrane proteins that included components of the Dot/Icm T4SS. More broadly, our studies establish a DSB oxidoreductase function for the Com1 lineage of DsbA2-like proteins which appear to be conserved among those bacteria also expressing T4SS. PMID:21375592

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

    SciTech Connect

    Gland, J. L.

    2004-07-29

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

  6. Paint-Bonding Improvement for 2219 Aluminum Alloy

    NASA Technical Reports Server (NTRS)

    Daech, Alfred F.; Cibula, Audrey Y.

    1987-01-01

    Bonding of adhesives and primers to 2219 aluminum alloy improved by delaying rinse step in surface-treatment process. Delaying rinse allows formation of rougher surface for stronger bonding and greater oxide buildup.

  7. IMPROVED BONDING METHOD

    DOEpatents

    Padgett, E.V. Jr.; Warf, D.H.

    1964-04-28

    An improved process of bonding aluminum to aluminum without fusion by ultrasonic vibrations plus pressure is described. The surfaces to be bonded are coated with an aqueous solution of alkali metal stearate prior to assembling for bonding. (AEC) O H19504 Present information is reviewed on steady state proliferation, differentiation, and maturation of blood cells in mammals. Data are cited from metabolic tracer studies, autoradiographic studies, cytologic studies, studies of hematopoietic response to radiation injuries, and computer analyses of blood cell production. A 3-step model for erythropoiesis and a model for granulocyte kinetics are presented. New approaches to the study of lymphocytopoiesis described include extracorporeal blood irradiation to deplete lymphocytic tissue without direct injury to the formative tissues as a means to study the stressed system, function control, and rates of proliferation. It is pointed out that present knowledge indicates that lymphocytes comprise a mixed family, with diverse life spans, functions, and migration patterns with apparent aimless recycling from modes to lymph to blood to nodes that has not yet been quantitated. Areas of future research are postulated. (70 references.) (C.H.)

  8. Self-organized formation of hierarchically-ordered structures in laser-activated plasma CVD of sp3-bonded BN films

    NASA Astrophysics Data System (ADS)

    Komatsu, Shojiro; Shiratani, Masaharu

    2014-01-01

    The hierarchical pattern formation with three stages, that is, (1) film-thickness topography, (2) fractal or concentric-ring pattern, and (3) cone morphology at micron or sub-micrometer order, was found here for the first time in the BN films prepared by plasma CVD assisted with pulsed excimer laser irradiation at 193 nm. The detailed topography consisting of unevenness in the film-thickness was obtained owing to the two-dimensional X-ray diffraction (2D-XRD) mapping method using a collimated X-ray of 0.1 mm in the diameter, where very high sensitivity was realized by selecting the X-ray from the substrate material, that was exponentially attenuated through the absorption from the film material according to Beer’s law. The important roles of the etching reactions in this process were experimentally verified here for the first time due to the 2D-mapping method. The formation mechanism of the hierarchical patterns was discussed.

  9. Sensor/ROIC Integration using Oxide Bonding

    SciTech Connect

    Ye, Zhenyu; /Fermilab

    2009-02-01

    We explore the Ziptronix Direct Bond Interconnect (DBI) technology [2] for the integration of sensors and readout integrated circuits (ROICs) for high energy physics. The technology utilizes an oxide bond to form a robust mechanical connection between layers which serves to assist with the formation of metallic interlayer connections. We report on testing results of sample sensors bonded to ROICs and thinned to 100 {micro}m.

  10. Formation, Characterization, and O-O Bond Activation of a Peroxomanganese(III) Complex Supported by a Cross-Clamped Cyclam Ligand.

    PubMed

    Colmer, Hannah E; Howcroft, Anthony W; Jackson, Timothy A

    2016-03-01

    Although there have been reports describing the nucleophilic reactivity of peroxomanganese(III) intermediates, as well as their conversion to high-valent oxo-bridged dimers, it remains a challenge to activate peroxomanganese(III) species for conversion to high-valent, mononuclear manganese complexes. Herein, we report the generation, characterization, and activation of a peroxomanganese(III) adduct supported by the cross-clamped, macrocyclic Me2EBC ligand (4,11-dimethyl-1,4,8,11-tetraazabicyclo[6.6.2]hexadecane). This ligand is known to support high-valent, mononuclear Mn(IV) species with well-defined spectroscopic properties, which provides an opportunity to identify mononuclear Mn(IV) products from O-O bond activation of the corresponding Mn(III)-peroxo adduct. The peroxomanganese(III) intermediate, [Mn(III)(O2)(Me2EBC)](+), was prepared at low-temperature by the addition of KO2 to [Mn(II)(Cl)2(Me2EBC)] in CH2Cl2, and this complex was characterized by electronic absorption, electron paramagnetic resonance (EPR), and Mn K-edge X-ray absorption (XAS) spectroscopies. The electronic structure of the [Mn(III)(O2)(Me2EBC)](+) intermediate was examined by density functional theory (DFT) and time-dependent (TD) DFT calculations. Detailed spectroscopic investigations of the decay products of [Mn(III)(O2)(Me2EBC)](+) revealed the presence of mononuclear Mn(III)-hydroxo species or a mixture of mononuclear Mn(IV) and Mn(III)-hydroxo species. The nature of the observed decay products depended on the amount of KO2 used to generate [Mn(III)(O2)(Me2EBC)](+). The Mn(III)-hydroxo product was characterized by Mn K-edge XAS, and shifts in the pre-edge transition energies and intensities relative to [Mn(III)(O2)(Me2EBC)](+) provide a marker for differences in covalency between peroxo and nonperoxo ligands. To the best of our knowledge, this work represents the first observation of a mononuclear Mn(IV) center upon decay of a nonporphyrinoid Mn(III)-peroxo center. PMID:26908013

  11. Spectroscopy study of Zn, Cd, Pb and Cr ions immobilization on C-S-H phase

    NASA Astrophysics Data System (ADS)

    Żak, Renata; Deja, Jan

    2015-01-01

    Calcium silicate hydrates (C-S-H) have a large number of structural sites available for cations and anions to bind. The C-S-H phases are materials which have ability to toxic ions immobilization. Immobilization mechanisms for C-S-H include sorption, phase mixing, substitution and precipitation of insoluble compounds. This study presents the C-S-H (prepared with C/S ratios 1.0) phase as absorbent for immobilization of Zn, Cd, Pb and Cr ions. The C-S-H spectra before and after incorporation of heavy metals ions into the C-S-H structure were obtained. The effect of added heavy metals ions on the hydration phenomena was studied by means of X-ray diffractions analysis. FTIR spectra was measured. The microstructure and phase composition of C-S-H indicate that they can play an essential role in the immobilization of heavy metals. The properties of C-S-H in the presence of Zn, Cd, Pb and Cr cations were studied. The leaching ML test was used to evaluate the level of immobilization of heavy metals in C-S-H. The leached solutions are diluted and analyzed using atomic absorption spectrometry (AAS) and the activated solid particles are separated, washed, desiccated and analyzed by Fourier transform infrared (FTIR) spectroscopy. It was found that the degree of Cd, Zn, Pb and Cr cations immobilization was very high (exceeding 99.96%).

  12. Spectroscopy study of Zn, Cd, Pb and Cr ions immobilization on C-S-H phase.

    PubMed

    Żak, Renata; Deja, Jan

    2015-01-01

    Calcium silicate hydrates (C-S-H) have a large number of structural sites available for cations and anions to bind. The C-S-H phases are materials which have ability to toxic ions immobilization. Immobilization mechanisms for C-S-H include sorption, phase mixing, substitution and precipitation of insoluble compounds. This study presents the C-S-H (prepared with C/S ratios 1.0) phase as absorbent for immobilization of Zn, Cd, Pb and Cr ions. The C-S-H spectra before and after incorporation of heavy metals ions into the C-S-H structure were obtained. The effect of added heavy metals ions on the hydration phenomena was studied by means of X-ray diffractions analysis. FTIR spectra was measured. The microstructure and phase composition of C-S-H indicate that they can play an essential role in the immobilization of heavy metals. The properties of C-S-H in the presence of Zn, Cd, Pb and Cr cations were studied. The leaching ML test was used to evaluate the level of immobilization of heavy metals in C-S-H. The leached solutions are diluted and analyzed using atomic absorption spectrometry (AAS) and the activated solid particles are separated, washed, desiccated and analyzed by Fourier transform infrared (FTIR) spectroscopy. It was found that the degree of Cd, Zn, Pb and Cr cations immobilization was very high (exceeding 99.96%). PMID:25106815

  13. Formation versus Hydrolysis of the Peptide Bond from a Quantum-mechanical Viewpoint: The Role of Mineral Surfaces and Implications for the Origin of Life

    PubMed Central

    Rimola, Albert; Ugliengo, Piero; Sodupe, Mariona

    2009-01-01

    The condensation (polymerization by water elimination) of molecular building blocks to yield the first active biopolymers (e.g. of amino acids to form peptides) during primitive Earth is an intriguing question that nowadays still remains open since these processes are thermodynamically disfavoured in highly dilute water solutions. In the present contribution, formation and hydrolysis of glycine oligopeptides occurring on a cluster model of sanidine feldspar (001) surface have been simulated by quantum mechanical methods. Results indicate that the catalytic interplay between Lewis and Brønsted sites both present at the sanidine surface, in cooperation with the London forces acting between the biomolecules and the inorganic surface, plays a crucial role to: i) favour the condensation of glycine to yield oligopeptides as reaction products; ii) inhibit the hydrolysis of the newly formed oligopeptides. Both facts suggest that mineral surfaces may have helped in catalyzing, stabilizing and protecting from hydration the oligopeptides formed in the prebiotic era. PMID:19399219

  14. Comprehensive analysis of individual pulp fiber bonds quantifies the mechanisms of fiber bonding in paper.

    PubMed

    Hirn, Ulrich; Schennach, Robert

    2015-01-01

    The process of papermaking requires substantial amounts of energy and wood consumption, which contributes to larger environmental costs. In order to optimize the production of papermaking to suit its many applications in material science and engineering, a quantitative understanding of bonding forces between the individual pulp fibers is of importance. Here we show the first approach to quantify the bonding energies contributed by the individual bonding mechanisms. We calculated the impact of the following mechanisms necessary for paper formation: mechanical interlocking, interdiffusion, capillary bridges, hydrogen bonding, Van der Waals forces, and Coulomb forces on the bonding energy. Experimental results quantify the area in molecular contact necessary for bonding. Atomic force microscopy experiments derive the impact of mechanical interlocking. Capillary bridges also contribute to the bond. A model based on the crystal structure of cellulose leads to values for the chemical bonds. In contrast to general believe which favors hydrogen bonding Van der Waals bonds play the most important role according to our model. Comparison with experimentally derived bond energies support the presented model. This study characterizes bond formation between pulp fibers leading to insight that could be potentially used to optimize the papermaking process, while reducing energy and wood consumption. PMID:26000898

  15. Comprehensive analysis of individual pulp fiber bonds quantifies the mechanisms of fiber bonding in paper

    NASA Astrophysics Data System (ADS)

    Hirn, Ulrich; Schennach, Robert

    2015-05-01

    The process of papermaking requires substantial amounts of energy and wood consumption, which contributes to larger environmental costs. In order to optimize the production of papermaking to suit its many applications in material science and engineering, a quantitative understanding of bonding forces between the individual pulp fibers is of importance. Here we show the first approach to quantify the bonding energies contributed by the individual bonding mechanisms. We calculated the impact of the following mechanisms necessary for paper formation: mechanical interlocking, interdiffusion, capillary bridges, hydrogen bonding, Van der Waals forces, and Coulomb forces on the bonding energy. Experimental results quantify the area in molecular contact necessary for bonding. Atomic force microscopy experiments derive the impact of mechanical interlocking. Capillary bridges also contribute to the bond. A model based on the crystal structure of cellulose leads to values for the chemical bonds. In contrast to general believe which favors hydrogen bonding Van der Waals bonds play the most important role according to our model. Comparison with experimentally derived bond energies support the presented model. This study characterizes bond formation between pulp fibers leading to insight that could be potentially used to optimize the papermaking process, while reducing energy and wood consumption.

  16. Chemical Bonds II

    ERIC Educational Resources Information Center

    Sanderson, R. T.

    1972-01-01

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

  17. What Determines Bond Costs. Municipal Bonds Series.

    ERIC Educational Resources Information Center

    Young, Douglas; And Others

    Public officials in small towns who participate infrequently in the bond market need information about bond financing. This publication, one in a series of booklets published by the Western Rural Development Center using research gathered between 1967-77, discusses factors influencing the marketability and cost of bond financing for towns and…

  18. Explosion bonding: aluminum-magnesium alloys bonded to austenitic stainless steel

    SciTech Connect

    Patterson, R.A.

    1982-01-01

    The explosion bonding of 5000 series aluminum alloys to 300 series stainless steel alloys is summarized. The process technique involves a parallel gap arrangement with copper or aluminum bonding aids. Successful bonds have been achieved using either a single shot process for joining the trilayer clad or a sequential shot technique for each metal component. Bond success is monitored through a combined metallographic and tensile strength evaluation. Tensile properties are shown to be strongly dependent upon process parameters and the amount of intermetallic formation at the aluminum bond interface. Empirical data has been compared with experimental and destructive test results to determine the optimum procedures.

  19. Frameshift Deletion by Sulfolobus solfataricus P2 DNA Polymerase Dpo4 T239W Is Selective for Purines and Involves Normal Conformational Change Followed by Slow Phosphodiester Bond Formation*

    PubMed Central

    Zhang, Huidong; Beckman, Jeff W.; Guengerich, F. Peter

    2009-01-01

    The human DNA polymerase κ homolog Sulfolobus solfataricus DNA polymerase IV (Dpo4) produces “−1” frameshift deletions while copying unmodified DNA and, more frequently, when bypassing DNA adducts. As judged by steady-state kinetics and mass spectrometry, bypass of purine template bases to produce these deletions occurred rarely but with 10-fold higher frequency than with pyrimidines. The DNA adduct 1,N2-etheno-2′-deoxyguanosine, with a larger stacking surface than canonical purines, showed the highest frequency of formation of −1 frameshift deletions. Dpo4 T239W, a mutant we had previously shown to produce fluorescence changes attributed to conformational change following dNTP binding opposite cognate bases (Beckman, J. W., Wang, Q., and Guengerich, F. P. (2008) J. Biol. Chem. 283, 36711–36723), reported similar conformational changes when the incoming dNTP complemented the base following a templating purine base or bulky adduct (i.e. the “+1” base). However, in all mispairing cases, phosphodiester bond formation was inefficient. The frequency of −1 frameshift events and the associated conformational changes were not dependent on the context of the remainder of the sequence. Collectively, our results support a mechanism for −1 frameshift deletions by Dpo4 that involves formation of active complexes via a favorable conformational change that skips the templating base, without causing slippage or flipping out of the base, to incorporate a complementary residue opposite the +1 base, in a mechanism previously termed “dNTP-stabilized incorporation.” The driving force is attributed to be the stacking potential between the templating base and the incoming dNTP base. PMID:19837980

  20. Frameshift deletion by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W is selective for purines and involves normal conformational change followed by slow phosphodiester bond formation.

    PubMed

    Zhang, Huidong; Beckman, Jeff W; Guengerich, F Peter

    2009-12-11

    The human DNA polymerase kappa homolog Sulfolobus solfataricus DNA polymerase IV (Dpo4) produces "-1" frameshift deletions while copying unmodified DNA and, more frequently, when bypassing DNA adducts. As judged by steady-state kinetics and mass spectrometry, bypass of purine template bases to produce these deletions occurred rarely but with 10-fold higher frequency than with pyrimidines. The DNA adduct 1,N(2)-etheno-2'-deoxyguanosine, with a larger stacking surface than canonical purines, showed the highest frequency of formation of -1 frameshift deletions. Dpo4 T239W, a mutant we had previously shown to produce fluorescence changes attributed to conformational change following dNTP binding opposite cognate bases (Beckman, J. W., Wang, Q., and Guengerich, F. P. (2008) J. Biol. Chem. 283, 36711-36723), reported similar conformational changes when the incoming dNTP complemented the base following a templating purine base or bulky adduct (i.e. the "+1" base). However, in all mispairing cases, phosphodiester bond formation was inefficient. The frequency of -1 frameshift events and the associated conformational changes were not dependent on the context of the remainder of the sequence. Collectively, our results support a mechanism for -1 frameshift deletions by Dpo4 that involves formation of active complexes via a favorable conformational change that skips the templating base, without causing slippage or flipping out of the base, to incorporate a complementary residue opposite the +1 base, in a mechanism previously termed "dNTP-stabilized incorporation." The driving force is attributed to be the stacking potential between the templating base and the incoming dNTP base. PMID:19837980

  1. Orthogonal halogen and hydrogen bonds involving a peptide bond model† †Electronic supplementary information (ESI) available: Experimental part, DSC, IR spectroscopic and crystallographic data. CCDC 899779–899785. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4ce01514b Click here for additional data file. Click here for additional data file.

    PubMed Central

    Vasylyeva, Vera; Nayak, Susanta K.; Cavallo, Gabriella; Resnati, Giuseppe

    2014-01-01

    The peptide bond model N-methylacetamide self-assembles with a range of dihalotetrafluorobenzenes forming co-crystals that all show the occurrence of orthogonal hydrogen and halogen bonds. PMID:25663816

  2. Quantum theory of atoms in molecules/charge-charge flux-dipole flux models for fundamental vibrational intensity changes on H-bond formation of water and hydrogen fluoride

    SciTech Connect

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

    2014-02-28

    The Quantum Theory of Atoms In Molecules/Charge-Charge Flux-Dipole Flux (QTAIM/CCFDF) model has been used to investigate the electronic structure variations associated with intensity changes on dimerization for the vibrations of the water and hydrogen fluoride dimers as well as in the water-hydrogen fluoride complex. QCISD/cc-pVTZ wave functions applied in the QTAIM/CCFDF model accurately provide the fundamental band intensities of water and its dimer predicting symmetric and antisymmetric stretching intensity increases for the donor unit of 159 and 47 km mol{sup −1} on H-bond formation compared with the experimental values of 141 and 53 km mol{sup −1}. The symmetric stretching of the proton donor water in the dimer has intensity contributions parallel and perpendicular to its C{sub 2v} axis. The largest calculated increase of 107 km mol{sup −1} is perpendicular to this axis and owes to equilibrium atomic charge displacements on vibration. Charge flux decreases occurring parallel and perpendicular to this axis result in 42 and 40 km mol{sup −1} total intensity increases for the symmetric and antisymmetric stretches, respectively. These decreases in charge flux result in intensity enhancements because of the interaction contributions to the intensities between charge flux and the other quantities. Even though dipole flux contributions are much smaller than the charge and charge flux ones in both monomer and dimer water they are important for calculating the total intensity values for their stretching vibrations since the charge-charge flux interaction term cancels the charge and charge flux contributions. The QTAIM/CCFDF hydrogen-bonded stretching intensity strengthening of 321 km mol{sup −1} on HF dimerization and 592 km mol{sup −1} on HF:H{sub 2}O complexation can essentially be explained by charge, charge flux and their interaction cross term. Atomic contributions to the intensities are also calculated. The bridge hydrogen atomic contributions alone

  3. A cooperative hydrogen bonding system with a Csbnd H⋯O hydrogen bond in ofloxacin

    NASA Astrophysics Data System (ADS)

    Gao, Xiuxiang; Liu, Yufeng; Li, Huizhen; Bian, Jiang; Zhao, Ying; Cao, Ye; Mao, Yuezhi; Li, Xin; Xu, Yizhuang; Ozaki, Yukihiro; Wu, Jinguang

    2013-05-01

    We have investigated a cooperative hydrogen bonding system with a Csbnd H⋯O hydrogen bond in ofloxacin by using NMR, UV-Vis spectra together with quantum chemistry calculation. Both pH-dependent NMR experiments and DFT calculation indicate that the intra-molecular Csbnd H⋯O hydrogen bond between an aromatic proton and an oxygen atom from the carboxyl group is formed. Notably, the Csbnd H⋯O hydrogen bond forms a cooperative hydrogen bonding system with a neighboring Osbnd H⋯O hydrogen bond between the carboxyl group and the keto oxygen. The cooperative hydrogen bonding system makes the formation and disruption of the Osbnd H⋯O and Csbnd H⋯O hydrogen bonds in a synergistic manner. Comparison on the pKa value of the carboxylic group in different fluoroquinolones compounds indicates that the Csbnd H⋯O hydrogen bond plays a significant role in stabilizing the Osbnd H⋯O hydrogen bond. In addition, the formation and disruption of the cooperative hydrogen bonding system could regulate the conformation of the carboxyl group, which affects the size of the conjugated system and spectral behavior of π-π transition of ofloxacin.

  4. Anodic bonding of gallium arsenide to glass

    NASA Astrophysics Data System (ADS)

    Hök, Bertil; Dubon, Chantal; Ovrén, Christer

    1983-08-01

    We describe a modified anodic bonding technique for hermetic sealing between GaAs and glass, the modification being called for by the formation of a nonadherent oxide layer during the bonding process. We show that this can be avoided by prebaking the glass and performing the bonding operation in a reducing atmosphere. With this technique, strong, hermetic seals can be produced. Parameter dependence has been studied theoretically by solving the continuity equation for a one-dimensional model of the experimental situation. Experimentally, the bonds were evaluated with a number of methods, giving support for a model consisting of a high-field, sodium-depleted zone in the interface region during bond formation. The described technique is of particular interest for optoelectronic devices requiring transparent and hermetic seals.

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

    SciTech Connect

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

    2013-02-14

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

  6. Using Multiple Bonding Strategies.

    PubMed

    Larson, Thomas D

    2015-01-01

    There are many ways to bond to tooth structure, some micro-mechanical some chemical, some a combination. Different dentin bonding materials have different bonding strengths to differently prepared surfaces, and because of differences in their nature, different areas of tooth structure present peculiar bonding challenges. This paper will review a variety of material types, elucidating their particular bonding strengths and commenting on improved bonding strategies to increase durability, strength, and favorable pulpal response. In this discussion, resin dentin bonding systems, glass ionomers, Gluma, resin cements, and newer combined products will br reviewed. PMID:26485903

  7. Mild and General Access to Diverse 1H-Benzotriazoles via Diboron-Mediated N–OH Deoxygenation and Palladium-Catalyzed C–C and C–N Bond Formation

    PubMed Central

    Gurram, Venkateshwarlu; Akula, Hari K.; Garlapati, Ramesh; Pottabathini, Narender; Lakshman, Mahesh K.

    2015-01-01

    Benzotriazoles are a highly important class of compounds with broad-ranging applications in such diverse areas as medicinal chemistry, as auxiliaries in organic synthesis, in metallurgical applications, in aircraft deicing and brake fluids, and as antifog agents in photography. Although there are numerous approaches to N-substituted benzotriazoles, the essentially one general method to N-unsubstituted benzotriazoles is via diazotization of o-phenylenediamines, which can be limited by the availability of suitable precursors. Other methods to N-unsubstitued benzotriazoles are quite specialized. Although reduction of 1-hydroxy-1H-benzotriazoles is known the reactions are not particularly convenient or broadly applicable. This presents a limitation for easy access to and availability of diverse benzotriazoles. Herein, we demonstrate a new, broadly applicable method to diverse 1H-benzotriazoles via a mild diboron-reagent mediated deoxygenation of 1-hydroxy-1H-benzotriazoles. We have also evaluated sequential deoxygenation and Pd-mediated C–C and C–N bond formation as a one-pot process for further diversification of the benzotriazole moiety. However, results indicated that purification of the deoxygenation product prior to the Pd-mediated reaction is critical to the success of such reactions. The overall chemistry allows for facile access to a variety of new benzotriazoles. Along with the several examples presented, a discussion of the advantages of the approaches is described, as also a possible mechanism for the deoxygenation process. PMID:25729343

  8. Platinum-Containing Polyoxometalates: syn- and anti-[Pt(II) 2 (α-PW11 O39 )2 ](10-) and Formation of the Metal-Metal-Bonded di-Pt(III) Derivatives.

    PubMed

    Lin, Zhengguo; Izarova, Natalya V; Kondinski, Aleksandar; Xing, Xiaolin; Haider, Ali; Fan, Linyuan; Vankova, Nina; Heine, Thomas; Keita, Bineta; Cao, Jie; Hu, Changwen; Kortz, Ulrich

    2016-04-11

    The first examples of dimeric, di-Pt(II) -containing heteropolytungstates are reported. The two isomeric di-platinum(II)-containing 22-tungsto-2-phosphates [anti-Pt(II) 2 (α-PW11 O39 )2 ](10-) (1 a) and [syn-Pt(II) 2 (α-PW11 O39 )2 ](10-) (2 a) were synthesized in aqueous pH 3.5 medium using one-pot procedures. Polyanions 1 a and 2 a contain a core comprising two face-on PtO4 units, with a Pt⋅⋅⋅Pt distance of 2.9-3 Å. Both polyanions were investigated by single-crystal XRD, IR, TGA, UV/Vis, (31) P NMR, ESI-MS, CID-MS/MS, electrochemistry, and DFT. On the basis of DFT and electrochemistry, we demonstrated that the {Pt2 (II) } moiety in 1 a and 2 a can undergo fully reversible two-electron oxidation to {Pt2 (III) }, accompanied by formation of a single Pt-Pt bond. Hence we have discovered the novel subclass of Pt(III) -containing heteropolytungstates. PMID:26938929

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

    SciTech Connect

    Bausch, M.

    1991-01-01

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

  10. IMPACT OF PHYSICAL AND CHEMICAL MUD CONTAMINATION ON WELLBORE CEMENT- FORMATION SHEAR BOND STRENGTH Authors: Arome Oyibo1 and Mileva Radonjic1 * 1. Craft and Hawkins Department of Petroleum Engineering, 2131 Patrick F. Taylor Hall, Louisiana State University, Baton Rouge, LA 70803, aoyibo1@tigers.lsu.edu, mileva@lsu.edu

    NASA Astrophysics Data System (ADS)

    Oyibo, A. E.

    2013-12-01

    Wellbore cement has been used to provide well integrity through zonal isolation in oil & gas wells and geothermal wells. Cementing is also used to provide mechanical support for the casing and protect the casing from corrosive fluids. Failure of cement could be caused by several factors ranging from poor cementing, failure to completely displace the drilling fluids to failure on the path of the casing. A failed cement job could result in creation of cracks and micro annulus through which produced fluids could migrate to the surface which could lead to sustained casing pressure, contamination of fresh water aquifer and blow out in some cases. In addition, cement failures could risk the release of chemicals substances from hydraulic fracturing into fresh water aquifer during the injection process. To achieve proper cementing, the drilling fluid should be completely displaced by the cement slurry. However, this is hard to achieve in practice, some mud is usually left on the wellbore which ends up contaminating the cement afterwards. The purpose of this experimental study is to investigate the impact of both physical and chemical mud contaminations on cement-formation bond strength for different types of formations. Physical contamination occurs when drilling fluids (mud) dries on the surface of the formation forming a mud cake. Chemical contamination on the other hand occurs when the drilling fluids which is still in the liquid form interacts chemically with the cement during a cementing job. We investigated the impact of the contamination on the shear bond strength and the changes in the mineralogy of the cement at the cement-formation interface to ascertain the impact of the contamination on the cement-formation bond strength. Berea sandstone and clay rich shale cores were bonded with cement cores with the cement-formation contaminated either physically or chemically. For the physically contaminated composite cores, we have 3 different sample designs: clean

  11. 29 CFR 2580.412-20 - Use of existing bonds, separate bonds and additional bonding.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Use of existing bonds, separate bonds and additional..., separate bonds and additional bonding. (a) Additional bonding. Section 13 neither prevents additional... or separate bond. (b) Use of existing bonds. Insofar as a bond currently in use is adequate to...

  12. Bonded boojum-colloids in nematic liquid crystals.

    PubMed

    Eskandari, Zahra; Silvestre, Nuno M; Telo da Gama, Margarida M

    2013-08-20

    We investigate bonded boojum-colloids in nematic liquid crystals, configurations where two colloids with planar degenerate anchoring are double-bonded through line defects connecting their surfaces. This bonded structure promotes the formation of linear chains aligned with the nematic director. We show that the bonded configuration is the global minimum in systems that favor twist deformations. In addition, we investigate the influence of confinement on the stability of bonded boojum-colloids. Although the unbonded colloid configuration, where the colloids bundle at oblique angles, is favored by confinement, the bonded configuration is again the global minimum for liquid crystals with sufficiently small twist elastic constants. PMID:23859624

  13. Hydroxide-catalyzed bonding

    NASA Technical Reports Server (NTRS)

    Gwo, Dz-Hung (Inventor)

    2003-01-01

    A method of bonding substrates by hydroxide-catalyzed hydration/dehydration involves applying a bonding material to at least one surface to be bonded, and placing the at least one surface sufficiently close to another surface such that a bonding interface is formed between them. A bonding material of the invention comprises a source of hydroxide ions, and may optionally include a silicate component, a particulate filling material, and a property-modifying component. Bonding methods of the invention reliably and reproducibly provide bonds which are strong and precise, and which may be tailored according to a wide range of possible applications. Possible applications for bonding materials of the invention include: forming composite materials, coating substrates, forming laminate structures, assembly of precision optical components, and preparing objects of defined geometry and composition. Bonding materials and methods of preparing the same are also disclosed.

  14. Neural mechanisms of mother-infant bonding and pair bonding: Similarities, differences, and broader implications.

    PubMed

    Numan, Michael; Young, Larry J

    2016-01-01

    This article is part of a Special Issue "Parental Care". Mother-infant bonding is a characteristic of virtually all mammals. The maternal neural system may have provided the scaffold upon which other types of social bonds in mammals have been built. For example, most mammals exhibit a polygamous mating system, but monogamy and pair bonding between mating partners occur in ~5% of mammalian species. In mammals, it is plausible that the neural mechanisms that promote mother-infant bonding have been modified by natural selection to establish the capacity to develop a selective bond with a mate during the evolution of monogamous mating strategies. Here we compare the details of the neural mechanisms that promote mother-infant bonding in rats and other mammals with those that underpin pair bond formation in the monogamous prairie vole. Although details remain to be resolved, remarkable similarities and a few differences between the mechanisms underlying these two types of bond formation are revealed. For example, amygdala and nucleus accumbens-ventral pallidum (NA-VP) circuits are involved in both types of bond formation, and dopamine and oxytocin actions within NA appear to promote the synaptic plasticity that allows either infant or mating partner stimuli to persistently activate NA-VP attraction circuits, leading to an enduring social attraction and bonding. Further, although the medial preoptic area is essential for maternal behavior, its role in pair bonding remains to be determined. Our review concludes by examining the broader implications of this comparative analysis, and evidence is provided that the maternal care system may have also provided the basic neural foundation for other types of strong social relationships, beyond pair bonding, in mammals, including humans. PMID:26062432

  15. A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

    SciTech Connect

    Legesse, Merid; Nolan, Michael Fagas, Giorgos

    2014-05-28

    In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.

  16. Diffusion bonding aeroengine components

    NASA Astrophysics Data System (ADS)

    Fitzpatrick, G. A.; Broughton, T.

    1988-10-01

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

  17. Compression effects on electrons for chemical bonding

    NASA Astrophysics Data System (ADS)

    Hu, Anguang; Zhang, Fan

    2014-03-01

    How electrons move under compression as chemical bonds between atoms are broken and formed is central to a number of challenges on the performance of materials in extreme conditions. This is not only associated with the fundamental knowledge of material response to compressive loading but also would advance many aspects of material science towards future energy technologies. First-principles simulations of enthalpy minimization, in various target pressures on chemical transformation bonding pathways, reveal that high pressure can push electrons away from their denser regimes where the kinetic energy rises steeply on compression, causing a destabilization of intramolecular bonds. The high-pressure pushing of electrons from one regime to another thus leads to chemical bond destruction and formation with a cell volume collapse accompanied by a drop in stress components. Determination of such electron pathways following bonding conformations of molecular precursors would then result in a number of chemical transformations for novel materials, including high energy density materials.

  18. Rapid adhesive bonding concepts

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  19. Does fluorine participate in halogen bonding?

    PubMed

    Eskandari, Kiamars; Lesani, Mina

    2015-03-16

    When R is sufficiently electron withdrawing, the fluorine in the R-F molecules could interact with electron donors (e.g., ammonia) and form a noncovalent bond (F⋅⋅⋅N). Although these interactions are usually categorized as halogen bonding, our studies show that there are fundamental differences between these interactions and halogen bonds. Although the anisotropic distribution of electronic charge around a halogen is responsible for halogen bond formations, the electronic charge around the fluorine in these molecules is spherical. According to source function analysis, F is the sink of electron density at the F⋅⋅⋅N BCP, whereas other halogens are the source. In contrast to halogen bonds, the F⋅⋅⋅N interactions cannot be regarded as lump-hole interactions; there is no hole in the valence shell charge concentration (VSCC) of fluorine. Although the quadruple moment of Cl and Br is mainly responsible for the existence of σ-holes, it is negligibly small in the fluorine. Here, the atomic dipole moment of F plays a stabilizing role in the formation of F⋅⋅⋅N bonds. Interacting quantum atoms (IQA) analysis indicates that the interaction between halogen and nitrogen in the halogen bonds is attractive, whereas it is repulsive in the F⋅⋅⋅N interactions. Virial-based atomic energies show that the fluorine, in contrast to Cl and Br, stabilize upon complex formation. According to these differences, it seems that the F⋅⋅⋅N interactions should be referred to as "fluorine bond" instead of halogen bond. PMID:25652256

  20. Crystal structure of the 1,3,6,8-tetra­aza­tri­cyclo[4.3.1.13,8]undecane (TATU)–4-nitro­phenol (1/2) adduct: the role of anomeric effect in the formation of a second hydrogen-bond inter­action

    PubMed Central

    Rivera, Augusto; Osorio, Héctor Jairo; Uribe, Juan Manuel; Ríos-Motta, Jaime; Bolte, Michael

    2015-01-01

    In the title ternary co-crystalline adduct, C7H14N4·2C6H5NO3, mol­ecules are linked by two inter­molecular O—H⋯N hydrogen bonds, forming a tricomponent aggregates in the asymmetric unit. The hydrogen-bond formation to one of the N atoms is enough to induce structural stereoelectronic effects in the normal donor→acceptor direction. In the title adduct, the two independent nitro­phenol mol­ecules are essentially planar, with maximum deviations of 0.0157 (13) and 0.0039 (13) Å. The dihedral angles between the planes of the nitro group and the attached benzene rings are 4.04 (17) and 5.79 (17)°. In the crystal, aggregates are connected by C—H⋯O hydrogen bonds, forming a supra­molecular dimer enclosing an R 6 6(32) ring motif. Additional C—H⋯O inter­molecular hydrogen-bonding inter­actions form a second supra­molecular inversion dimer with an R 2 2(10) motif. These units are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming a three-dimensional network. PMID:26594510

  1. Crystal structure of the 1,3,6,8-tetra-aza-tri-cyclo[4.3.1.1(3,8)]undecane (TATU)-4-nitro-phenol (1/2) adduct: the role of anomeric effect in the formation of a second hydrogen-bond inter-action.

    PubMed

    Rivera, Augusto; Osorio, Héctor Jairo; Uribe, Juan Manuel; Ríos-Motta, Jaime; Bolte, Michael

    2015-11-01

    In the title ternary co-crystalline adduct, C7H14N4·2C6H5NO3, mol-ecules are linked by two inter-molecular O-H⋯N hydrogen bonds, forming a tricomponent aggregates in the asymmetric unit. The hydrogen-bond formation to one of the N atoms is enough to induce structural stereoelectronic effects in the normal donor→acceptor direction. In the title adduct, the two independent nitro-phenol mol-ecules are essentially planar, with maximum deviations of 0.0157 (13) and 0.0039 (13) Å. The dihedral angles between the planes of the nitro group and the attached benzene rings are 4.04 (17) and 5.79 (17)°. In the crystal, aggregates are connected by C-H⋯O hydrogen bonds, forming a supra-molecular dimer enclosing an R 6 (6)(32) ring motif. Additional C-H⋯O inter-molecular hydrogen-bonding inter-actions form a second supra-molecular inversion dimer with an R 2 (2)(10) motif. These units are linked via C-H⋯O and C-H⋯N hydrogen bonds, forming a three-dimensional network. PMID:26594510

  2. Bonding thermoplastic polymers

    DOEpatents

    Wallow, Thomas I.; Hunter, Marion C.; Krafcik, Karen Lee; Morales, Alfredo M.; Simmons, Blake A.; Domeier, Linda A.

    2008-06-24

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

  3. Prospective bonding applications

    NASA Astrophysics Data System (ADS)

    Ancenay, H.; Benazet, D.

    1981-07-01

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

  4. Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond.

    PubMed

    Arunan, Elangannan; Mani, Devendra

    2015-01-01

    In this discussion, we show that a static definition of a 'bond' is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan, Phys. Chem. Chem. Phys. 2009, 11, 8974) which showed a practical way to differentiate 'hydrogen bonding' from 'van der Waals interaction'. We report results from ab initio and atoms in molecules theoretical calculations for a series of Rg∙∙∙HX complexes (Rg=He/Ne/Ar and X=F/Cl/Br) and ethane-1,2-diol. Results for the Rg∙∙∙HX/DX complexes show that Rg∙∙∙DX could have a 'deuterium bond' even when Rg∙∙∙HX is not 'hydrogen bonded', according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an 'intra-molecular hydrogen bond' can appear during a normal mode vibration which is dominated by the OO stretching, though a 'bond' is not found in the equilibrium structure. This dynamical 'bond' formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration 'breaks' an existing bond and in the later case, a vibration leads to 'bond' formation. In both cases, the molecule/complex stays bound irrespective of what happens to this 'hydrogen bond'. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunan et al. Pure. Appl. Chem. 2011, 83 1637) and justify the inclusive nature of the definition. PMID:25627627

  5. Fluxless flip chip bonding processes and aerial fluxless bonding technology

    NASA Astrophysics Data System (ADS)

    Kim, Dongwook

    New fluxless flip chip processes of Sn-rich non-eutectic Au-Sn solder bumps were developed using vacuum deposition and electroplating technique. It is believed that this is the first report that non-eutectic Au-Sn flip chip solder bonding is achieved without the use of flux. In order to make 200mum diameter and 10mum thick Au-Sn solder bump 0.03mum of Cr, 10mum of Sn and 0.3mum of Au were vacuum deposited on the Si wafer through the high carbon steal stencil mask. Nearly void-free solder bumps with small grains of AuSn4 intermetallic compound were achieved. The re-melting temperature of solder bumps was measured to be 220°C. In the second part, first, the fluxless bonding process was performed in hydrogen environment with electroplated 4 mm x 4mm Au-Sn multi-layer chips if electroplating technique is compatible with our process. High quality and nearly void free solder joint was successfully achieved with this new process. After proving compatibility of the process, tall electroplated Sn/Au bumps (50 mum) were produced by photolithography method using Su-8 photoresist. The bumps in the chip were flip chip bonded to the borosilicate glass wafer coated with Cr (0.03 mum) and Au (0.05 mum) pads without using any flux. Fluxless and lead-free bonding technology in air ambient based on non eutectic 5 at. % Au-95 at. % Sn and eutectic 57 at. %Sn-43 at. % Bi with Au capping layer have been developed and studied. To understand the fluxless bonding principles in air ambient, phase formation mechanism of Au-Sn intermetallics embedded in Bi matrix has been postulated. The Au-Sn intermetallic-capping layer covers most outer surface of the samples and inhibits formation of oxide layer due to the minimizing exposure of (beta-Sn) phase to the air. In conclusion, new-lead free and fluxless bonding processes for flip chip packages were developed. In this work, Sn-rich Au-Sn flip chip solder bumps using vacuum deposition and electroplating process were successfully produced. It is

  6. Body of Knowledge (BOK) for Copper Wire Bonds

    NASA Technical Reports Server (NTRS)

    Rutkowski, E.; Sampson, M. J.

    2015-01-01

    Copper wire bonds have replaced gold wire bonds in the majority of commercial semiconductor devices for the latest technology nodes. Although economics has been the driving mechanism to lower semiconductor packaging costs for a savings of about 20% by replacing gold wire bonds with copper, copper also has materials property advantages over gold. When compared to gold, copper has approximately: 25% lower electrical resistivity, 30% higher thermal conductivity, 75% higher tensile strength and 45% higher modulus of elasticity. Copper wire bonds on aluminum bond pads are also more mechanically robust over time and elevated temperature due to the slower intermetallic formation rate - approximately 1/100th that of the gold to aluminum intermetallic formation rate. However, there are significant tradeoffs with copper wire bonding - copper has twice the hardness of gold which results in a narrower bonding manufacturing process window and requires that the semiconductor companies design more mechanically rigid bonding pads to prevent cratering to both the bond pad and underlying chip structure. Furthermore, copper is significantly more prone to corrosion issues. The semiconductor packaging industry has responded to this corrosion concern by creating a palladium coated copper bonding wire, which is more corrosion resistant than pure copper bonding wire. Also, the selection of the device molding compound is critical because use of environmentally friendly green compounds can result in internal CTE (Coefficient of Thermal Expansion) mismatches with the copper wire bonds that can eventually lead to device failures during thermal cycling. Despite the difficult problems associated with the changeover to copper bonding wire, there are billions of copper wire bonded devices delivered annually to customers. It is noteworthy that Texas Instruments announced in October of 2014 that they are shipping microcircuits containing copper wire bonds for safety critical automotive applications

  7. High-level ab initio predictions for the ionization energy, bond dissociation energies, and heats of formation of cobalt carbide (CoC) and its cation (CoC+)

    NASA Astrophysics Data System (ADS)

    Lau, Kai-Chung; Pan, Yi; Lam, Chow-Shing; Huang, Huang; Chang, Yih-Chung; Luo, Zhihong; Shi, Xiaoyu; Ng, C. Y.

    2013-03-01

    The ionization energy (IE) of CoC and the 0 K bond dissociation energies (D0) and the heats of formation at 0 K (ΔH°f0) and 298 K (ΔH°f298) for CoC and CoC+ are predicted by the wavefunction based coupled-cluster theory with single, double, triple and quadruple excitations (CCSDTQ) and complete basis set (CBS) approach. The CCSDTQ/CBS calculations presented here involve the approximation to the CBS limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy, high-order correlation, core-valence (CV) electronic, spin-orbit coupling, and scalar relativistic effect corrections. The present calculations provide the correct symmetry, 1Σ+, for the ground state of CoC+. The CCSDTQ/CBS IE(CoC) = 7.740 eV is found in good agreement with the experimental IE value of 7.73467 ± 0.00007 eV, determined in a two-color laser photoion and pulsed field ionization-photoelectron study. This work together with the previous experimental and theoretical investigations support the conclusion that the CCSDTQ/CBS method is capable of providing reliable IE predictions for 3d-transition metal carbides, such as FeC, CoC, and NiC. Among the single-reference based coupled-cluster methods and multi-reference configuration interaction (MRCI) approach, the CCSDTQ and MRCI methods give the best predictions to the harmonic frequencies ωe (ωe+) = 956 (992) and 976 (1004) cm-1 and the bond lengths re (re+) = 1.560 (1.528) and 1.550 (1.522) Å, respectively, for CoC (CoC+) in comparison with the experimental values. The CCSDTQ/CBS calculations give the prediction of D0(Co+-C) - D0(Co-C) = 0.175 eV, which is also consistent with the experimental determination of 0.14630 ± 0.00014 eV. The theoretical results show that the CV and valence-valence electronic correlations beyond CCSD(T) wavefunction and the relativistic effect make significant contributions to the calculated thermochemical properties of CoC/CoC+. For the experimental D0 and ΔHof0

  8. High-level ab initio predictions for the ionization energy, bond dissociation energies, and heats of formation of cobalt carbide (CoC) and its cation (CoC+).

    PubMed

    Lau, Kai-Chung; Pan, Yi; Lam, Chow-Shing; Huang, Huang; Chang, Yih-Chung; Luo, Zhihong; Shi, Xiaoyu; Ng, C Y

    2013-03-01

    The ionization energy (IE) of CoC and the 0 K bond dissociation energies (D0) and the heats of formation at 0 K (ΔH°f0) and 298 K (ΔH°f298) for CoC and CoC(+) are predicted by the wavefunction based coupled-cluster theory with single, double, triple and quadruple excitations (CCSDTQ) and complete basis set (CBS) approach. The CCSDTQ∕CBS calculations presented here involve the approximation to the CBS limit at the coupled cluster level up to full quadruple excitations along with the zero-point vibrational energy, high-order correlation, core-valence (CV) electronic, spin-orbit coupling, and scalar relativistic effect corrections. The present calculations provide the correct symmetry, (1)Σ(+), for the ground state of CoC(+). The CCSDTQ∕CBS IE(CoC) = 7.740 eV is found in good agreement with the experimental IE value of 7.73467 ± 0.00007 eV, determined in a two-color laser photoion and pulsed field ionization-photoelectron study. This work together with the previous experimental and theoretical investigations support the conclusion that the CCSDTQ∕CBS method is capable of providing reliable IE predictions for 3d-transition metal carbides, such as FeC, CoC, and NiC. Among the single-reference based coupled-cluster methods and multi-reference configuration interaction (MRCI) approach, the CCSDTQ and MRCI methods give the best predictions to the harmonic frequencies ωe (ωe (+)) = 956 (992) and 976 (1004) cm(-1) and the bond lengths re (re (+)) = 1.560 (1.528) and 1.550 (1.522) Å, respectively, for CoC (CoC(+)) in comparison with the experimental values. The CCSDTQ∕CBS calculations give the prediction of D0(Co(+)-C) - D0(Co-C) = 0.175 eV, which is also consistent with the experimental determination of 0.14630 ± 0.00014 eV. The theoretical results show that the CV and valence-valence electronic correlations beyond CCSD(T) wavefunction and the relativistic effect make significant contributions to the calculated thermochemical properties of Co

  9. Effect of temperature on the microstructure of calcium silicate hydrate (C-S-H)

    SciTech Connect

    Gallucci, E. Zhang, X.; Scrivener, K.L.

    2013-11-15

    Temperature affects the properties of concrete through its effect on the hydration of cement and its associated microstructural development. This paper focuses on the modifications to C-S-H induced by isothermal curing between 5 and 60 °C. The results show that as the temperature increases (within the range studied) the C/S ratio of C-S-H changes only slightly, with a higher degree of polymerisation of silicate chains, but there is a significant decrease in its bound water content and an increase of apparent density of 25%. This increase seems to come from a different packing of C-S-H at the nanoscale. As a consequence of these changes, the microstructure of the cement paste is much coarser and porous, which explains the lower final strengths obtained by curing at elevated temperatures. -- Highlights: •C-S-H structure studied at the atomic level •Multiple analytical techniques used •Studies conducted at temperatures above and below normal temperatures.

  10. Weak bond screening system

    NASA Astrophysics Data System (ADS)

    Chuang, S. Y.; Chang, F. H.; Bell, J. R.

    Consideration is given to the development of a weak bond screening system which is based on the utilization of a high power ultrasonic (HPU) technique. The instrumentation of the prototype bond strength screening system is described, and the adhesively bonded specimens used in the system developmental effort are detailed. Test results obtained from these specimens are presented in terms of bond strength and level of high power ultrasound irradiation. The following observations were made: (1) for Al/Al specimens, 2.6 sec of HPU irradiation will screen weak bond conditions due to improper preparation of bonding surfaces; (2) for composite/composite specimens, 2.0 sec of HPU irradiation will disrupt weak bonds due to under-cured conditions; (3) for Al honeycomb core with composite skin structure, 3.5 sec of HPU irradiation will disrupt weak bonds due to bad adhesive or oils contamination of bonding surfaces; and (4) for Nomex honeycomb with Al skin structure, 1.3 sec of HPU irradiation will disrupt weak bonds due to bad adhesive.

  11. Changes in the elastic moduli of C-S-H due to presence of interlaminar cations

    NASA Astrophysics Data System (ADS)

    Mejia, Shirley; Hoyos, Bibian

    2016-03-01

    A set of models of calcium silicate hydrate (C-S-H) with alkali cations in the interlaminar layer, various calcium/silicon ratios, and each with a density of 2.4 g cm-3 is presented. Using molecular simulation techniques, the objective was to study how the Young’s, bulk, and shear modulus, as well as the Poisson’s ratio changed due to the presence of monovalent ions. The effect of density on the elastic moduli was neglected, thus the NVT ensemble was used. Comparing the different simulation cells, it was found that models with sodium and potassium ions in the structure and an alkali/silicon ratio of 0.18 showed negative effects on the elastic moduli of C-S-H. This could be mainly ascribed to the shielding effect of the alkali on the interlaminar interactions that contribute to the cohesion between the layers of C-S-H.

  12. C-S barrier and vibrational analyses of (halocarbonyl)sulfenyl halides XCO-SX (X = F, Cl, and Br).

    PubMed

    Badawi, Hassan M

    2004-09-01

    The structural stability of (halocarbonyl)sulfenyl halides XCO-SX (X is F, Cl, and Br) was investigated by DFT-B3LYP and ab initio MP2 calculations using 6-311 + G(**) basis set. From the calculations the molecules were found to exist predominantly in the trans conformation (two halogen atoms are trans to each other). Full energy optimizations were carried out for the minima and the transition states (TS) at the two levels, from which the rotational barriers about C-S bond in the three molecules were calculated to be about 12-13 kcal mol(-1). The vibrational frequencies of (fluorocarbonyl)sulfenyl fluoride (FCO-SF), (chlorocarbonyl)-sulfenyl chloride (ClCO-SCl), and (bromocarbonyl)-sulfenyl bromide (BrCO-SBr) were computed at the DFT-B3LYP level and the vibrational assignments for the normal modes of the stable forms of the compounds were made on the basis of normal coordinate calculations and experimental data of the chloride. PMID:15294247

  13. A Coupled Thermal-Mechanical Analysis of Ultrasonic Bonding Mechanism

    NASA Astrophysics Data System (ADS)

    Zhang, Chunbo (Sam); Li, Leijun

    2009-04-01

    A three-dimensional (3-D) finite element model has been developed to simulate the coupled thermal-mechanical fields in ultrasonic welding of aluminum foils. Transient distributions and evolution of the in-process variables, including normal stress, shear stress, slide distance, heat generation, temperature, and plastic deformation on the contact interface, and their interactions have been studied in detail. The von Mises plastic strain from the simulation has been correlated with the measured bonded area of ultrasonic joints. A possible mechanism for ultrasonic bond formation is proposed. The severe, localized, plastic deformation at the bond region is believed to be the major phenomenon causing bond formation in ultrasonic welding.

  14. Low-temperature titanium-based wafer bonding

    NASA Astrophysics Data System (ADS)

    Yu, Jian

    This thesis presents novel methods of metal-based wafer bonding at back-end-of-the-line (BEOL) compatible conditions (≤450°C). For the first time to our knowledge, 200 mm diameter oxidized Si wafers are bonded with prime Si wafers using 10-300 nm thick Ti as bonding intermediate at 300-450°C. Nearly void-free bonding with strong mechanical integrity has been confirmed. Moreover, microcavity formation has been demonstrated by bonding of patterned wafers. Both Rutherford backscattering spectroscopy (RBS) and Auger electron spectroscopy (AES) show clear evidence of Si and Ti interdiffusion, whereas high-resolution transmission electron microscopy (HRTEM) reveals an approximately 8 nm thick amorphous layer at the bonding interface. Those results indicate that the strong adhesion at the Ti/Si bonding interface is attributed to a solid-state amorphization (SSA) assisted by interdiffusion. A key effort is devoted to fundamental investigation of low-temperature transition metal(TM)/Si-based wafer bonding. With the extensive work on Ti/Si system, additional experiments are performed with six other TM/Si systems, namely Ni/Si, Co/Si, Pd/Si, Hf/Si, Au/Si and Ta/Si. The results indicate there are two principal requirements for TM/Si-based wafer bonding: (1) intimate contact (able to break through kinetic barriers), and (2) adequate chemical bonding. Three kinetic barriers addressed in this thesis are: (1) enclosed microvoids due to surface roughness, (2) gas molecules at the bonding interface, and (3) interfacial oxides. Presence of these barriers can prevent formation of intimate contact, consequently retarding or even blocking interfacial interactions for chemical bonding. The unique properties of Group IVA metals (e.g., Ti and Hf) to reduce native SiO2 on Si surfaces and their exceptionally large solid solubility for O2 and N2, help overcome those issues. Once kinetic barriers are surmounted, the key for strong metal/Si-based wafer bonding is formation of chemical bonds

  15. BONDING ALUMINUM METALS

    DOEpatents

    Noland, R.A.; Walker, D.E.

    1961-06-13

    A process is given for bonding aluminum to aluminum. Silicon powder is applied to at least one of the two surfaces of the two elements to be bonded, the two elements are assembled and rubbed against each other at room temperature whereby any oxide film is ruptured by the silicon crystals in the interface; thereafter heat and pressure are applied whereby an aluminum-silicon alloy is formed, squeezed out from the interface together with any oxide film, and the elements are bonded.

  16. Chemical bonding technology

    NASA Technical Reports Server (NTRS)

    Plueddemann, E.

    1986-01-01

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

  17. Complexes between hypohalous acids and phosphine derivatives. Pnicogen bond versus halogen bond versus hydrogen bond

    NASA Astrophysics Data System (ADS)

    Li, Qingzhong; Zhu, Hongjie; Zhuo, Hongying; Yang, Xin; Li, Wenzuo; Cheng, Jianbo

    2014-11-01

    The complexes of HOBr:PH2Y (Y = H, F, Cl, Br, CH3, NH2, OH, and NO2), HOCl:PH2F, and HOI:PH2F have been investigated with ab initio calculations at the MP2/aug-cc-pVTZ level. Four types of structures (1, 2, 3a, and 3b) were observed for these complexes. 1 is stabilized by an O⋯P pnicogen bond, 2 by a P⋯X halogen bond, 3a by a H⋯P hydrogen bond and a P⋯X pnicogen bond, and 3b by H⋯P and H⋯Br hydrogen bonds. Their relative stability is related to the halogen X of HOX and the substituent Y of PH2Y. These structures can compete with interaction energy of -10.22 ∼ -29.40 kJ/mol. The Hsbnd O stretch vibration shows a small red shift in 1, a small irregular shift in 2, but a prominent red shift in 3a and 3b. The Xsbnd O stretch vibration exhibits a smaller red shift in 1, a larger red shift in 2, but an insignificant blue shift in 3a and 3b. The Psbnd Y stretch vibration displays a red shift in 1 but a blue shift in 2, 3a, and 3b. The formation mechanism, stability, and properties of these structures have been analyzed with molecular electrostatic potentials, orbital interactions, and non-covalent interaction index.

  18. T47D Cells Expressing Myeloperoxidase Are Able to Process, Traffic and Store the Mature Protein in Lysosomes: Studies in T47D Cells Reveal a Role for Cys319 in MPO Biosynthesis that Precedes Its Known Role in Inter-Molecular Disulfide Bond Formation

    PubMed Central

    Laura, Richard P.; Dong, David; Reynolds, Wanda F.; Maki, Richard A.

    2016-01-01

    Among the human heme-peroxidase family, myeloperoxidase (MPO) has a unique disulfide-linked oligomeric structure resulting from multi-step processing of the pro-protein monomer (proMPO) after it exits the endoplasmic reticulum (ER). Related family members undergo some, but not all, of the processing steps involved with formation of mature MPO. Lactoperoxidase has its pro-domain proteolytically removed and is a monomer in its mature form. Eosinophil peroxidase undergoes proteolytic removal of its pro-domain followed by proteolytic separation into heavy and light chains and is a heterodimer. However, only MPO undergoes both these proteolytic modifications and then is further oligomerized into a heterotetramer by a single inter-molecular disulfide bond. The details of how and where the post-ER processing steps of MPO occur are incompletely understood. We report here that T47D breast cancer cells stably transfected with an MPO expression plasmid are able to efficiently replicate all of the processing steps that lead to formation of the mature MPO heterotetramer. MPO also traffics to the lysosome granules of T47D cells where it accumulates, allowing in-depth immunofluorescent microscopy studies of MPO trafficking and storage for the first time. Using this novel cell model we show that formation of MPO’s single inter-molecular disulfide bond can occur normally in the absence of the proteolytic events that lead to separation of the MPO heavy and light chains. We further demonstrate that Cys319, which forms MPO’s unique inter-molecular disulfide bond, is important for events that precede this step. Mutation of this residue alters the glycosylation and catalytic activity of MPO and blocks its entry into the endocytic pathway where proteolytic processing and disulfide bonding occur. Finally, using the endocytic trafficking of lysosomal hydrolases as a guide, we investigate the role of candidate receptors in the endocytic trafficking of MPO. PMID:26890638

  19. T47D Cells Expressing Myeloperoxidase Are Able to Process, Traffic and Store the Mature Protein in Lysosomes: Studies in T47D Cells Reveal a Role for Cys319 in MPO Biosynthesis that Precedes Its Known Role in Inter-Molecular Disulfide Bond Formation.

    PubMed

    Laura, Richard P; Dong, David; Reynolds, Wanda F; Maki, Richard A

    2016-01-01

    Among the human heme-peroxidase family, myeloperoxidase (MPO) has a unique disulfide-linked oligomeric structure resulting from multi-step processing of the pro-protein monomer (proMPO) after it exits the endoplasmic reticulum (ER). Related family members undergo some, but not all, of the processing steps involved with formation of mature MPO. Lactoperoxidase has its pro-domain proteolytically removed and is a monomer in its mature form. Eosinophil peroxidase undergoes proteolytic removal of its pro-domain followed by proteolytic separation into heavy and light chains and is a heterodimer. However, only MPO undergoes both these proteolytic modifications and then is further oligomerized into a heterotetramer by a single inter-molecular disulfide bond. The details of how and where the post-ER processing steps of MPO occur are incompletely understood. We report here that T47D breast cancer cells stably transfected with an MPO expression plasmid are able to efficiently replicate all of the processing steps that lead to formation of the mature MPO heterotetramer. MPO also traffics to the lysosome granules of T47D cells where it accumulates, allowing in-depth immunofluorescent microscopy studies of MPO trafficking and storage for the first time. Using this novel cell model we show that formation of MPO's single inter-molecular disulfide bond can occur normally in the absence of the proteolytic events that lead to separation of the MPO heavy and light chains. We further demonstrate that Cys319, which forms MPO's unique inter-molecular disulfide bond, is important for events that precede this step. Mutation of this residue alters the glycosylation and catalytic activity of MPO and blocks its entry into the endocytic pathway where proteolytic processing and disulfide bonding occur. Finally, using the endocytic trafficking of lysosomal hydrolases as a guide, we investigate the role of candidate receptors in the endocytic trafficking of MPO. PMID:26890638

  20. Valence bond entanglement entropy.

    PubMed

    Alet, Fabien; Capponi, Sylvain; Laflorencie, Nicolas; Mambrini, Matthieu

    2007-09-14

    We introduce for SU(2) quantum spin systems the valence bond entanglement entropy as a counting of valence bond spin singlets shared by two subsystems. For a large class of antiferromagnetic systems, it can be calculated in all dimensions with quantum Monte Carlo simulations in the valence bond basis. We show numerically that this quantity displays all features of the von Neumann entanglement entropy for several one-dimensional systems. For two-dimensional Heisenberg models, we find a strict area law for a valence bond solid state and multiplicative logarithmic corrections for the Néel phase. PMID:17930468

  1. Biotic and abiotic carbon to sulfur bond cleavage

    SciTech Connect

    Frost, J.W.

    1991-01-01

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

  2. Hydrogen bonding part 64. IR study of hydrogen bonding in tri- i-pentylammonium halides and their hydrates, formation of a molecular ( i-C 5H 11) 3NHF species, and NMR study of conformation of tri- i-pentylammonium ion in solution

    NASA Astrophysics Data System (ADS)

    Harmon, Kenneth M.; Bulgarella, Jennifer A.

    1996-03-01

    Tri- i-pentylammonium chloride and bromide form monohydrates which contain planar (H 2O·X) 2 clusters; these clusters are sandwiched between ammonium cations with NH hydrogen bonds to each cluster X -. The iodide fails to form any lower hydrate. "Tri- i-pentylammonium fluoride" is not a salt; rather the 1:1 adduct of HF and tri- i-pentylamine is a liquid molecular complex with a three-center covalent NHF bond. This adduct is somewhat hygroscopic, but does not form a crystalline monohydrate. Fourier transform NMR spectra and molecular modeling demonstrate that rotation is restricted about the α-CH 2 to β-CH 2 σ-bonds of the cation in solution, with the R 3N + group and i-propyl group in a trans arrangement about each bond. Modeling and consideration of J values and splitting patterns suggest free rotation occurs about the β-CH 2 to γ-CH σ-bond, and that the δ-CH 3 groups also rotate freely.

  3. P.H.Y.S.I.C.S. Can Be Done!

    ERIC Educational Resources Information Center

    Spangler, Lois

    2004-01-01

    P.H.Y.S.I.C.S. (Physics Headstart Yearlong Science Inquiry at Central School) is a series of inquiry investigations and science activities designed to motivate students and teachers and develop a love of physics in our rural agricultural community. The program?s approach infuses physics into the science curriculum while capitalizing on our…

  4. 363. A.C.S., Delineator March 1934 STATE OF CALIFORNIA; DEPARTMENT OF ...

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

    363. A.C.S., Delineator March 1934 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CONTRACT NO. 6A; SUPERSTRUCTURE - WEST BAY CROSSING; SAN FRANCISCO ANCHORAGE; AMERICAN BRIDGE CO.; AMBRIDGE PLANT; ORDER NO. G4866; SHEET NO E3 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  5. 378. A.C.S., Delineator March 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

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

    378. A.C.S., Delineator March 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CONTRACT NO. 6A; SUPERSTRUCTURE - WEST BAY CROSSING; YERBA BUENA ANCHORAGE & CABLE BENT. AMERICAN BRIDGE CO.; AMBRIDGE PLANT; ORDER NO. G 4866; SHEET NO. E4 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  6. An Integrated Perspective of Humanism and Supernaturalism for Education: C. S. Lewis's Version of Education

    ERIC Educational Resources Information Center

    Lee, Seung Chun

    2013-01-01

    This paper explores some theoretical reflections on the connection between C. S. Lewis's thoughts on the purpose and process of education and his understanding of supernatural human nature which has been relatively little explored. An introduction about Lewis's career as a college teacher blends into the background of this paper. It is followed by…

  7. Oral Interpretation of C.S. Lewis'"Narnia Tales": A Refracting of "Pictures."

    ERIC Educational Resources Information Center

    Keefe, Carolyn

    "The Chronicles of Narnia" are a series of seven fairy tales written by C.S. Lewis that have become popular with both children and adults. Lewis points to five aspects of the fairy tale form that made the form suitable for expressing the images he saw. The aspects are: (1) no love interest; (2) no close psychology; (3) severe restraints on…

  8. Dorothy L. Sayers and C. S. Lewis: Christian Postmodernism beyond Boundaries

    ERIC Educational Resources Information Center

    Yuasa, Kyoko

    2012-01-01

    Modern critics do not consider science fiction and mystery novels to be "serious reading", but Dorothy L. Sayers and C. S. Lewis questioned the boundaries between "popular" and "serious" literature. Both Christian writers critically discuss the spiritual crisis of the modern world in each fiction genre. This paper will discuss Sayers and Lewis…

  9. Mathematics, Art, Research, Collaboration, and Storytelling: The High M.A.R.C.S. Project

    ERIC Educational Resources Information Center

    Reilly, Edel M.; Pagnucci, Gian S.

    2007-01-01

    This article describes a curriculum integration project designed to help students better contextualize their learning: The High M.A.R.C.S. Project linked mathematics, art, research, collaboration, and storytelling. The article explains the project in detail, discusses sample student work from the project, and describes how the project work was…

  10. Paradise Lost and Found: Obedience, Disobedience, and Storytelling in C.S. Lewis and Philip Pullman.

    ERIC Educational Resources Information Center

    Wood, Naomi

    2001-01-01

    Considers how in the fantasy series "The Chronicles of Narnia" and "His Dark Materials," by C.S. Lewis and Philip Pullman respectively, the authors use symbols and themes from "Paradise Lost." Notes that each author's narrative choice uses his view of cosmic order to persuade readers that obedience should be understood as central to coming of age.…

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

    SciTech Connect

    Bausch, M.

    1991-12-31

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

  12. Hydrogen bonding nature during ADP crystallization

    NASA Astrophysics Data System (ADS)

    Sun, Congting; Xue, Dongfeng

    2014-02-01

    The hydrogen bonding nature during ADP crystallization is studied on the basis of anisotropic chemical bonding conditions in ADP crystal combined with in situ IR observation. The variations of hydrogen bonding nature of NH4+ and HPO4- groups dominate the transformation from the free hydrated ionic state to crystalline state during ADP crystallization. Anisotropic ADP crystal morphology depends on the anisotropic chemical bonding conditions along [1 0 0] and [1 0 1] directions. ADP crystal morphologies with different HPO4-n (n = 1-8) clusters can be calculated on the basis of hydrogen bonding conditions and HPO4-n cluster structures at the growth interface. Experimentally, in situ IR spectrum can record the breaking of P-O⋯H-O-H and H-N⋯H-O-H, and the formation of P-O⋯H-O-P and H-N⋯H-O-P hydrogen bonding during ADP crystallization. The present work provides a promising strategy to identify the chemical bonding nature during crystallization processes of molecular crystals from aqueous solution.

  13. The United States Congress Can Tax Interest on State Bonds: "South Carolina v. Baker".

    ERIC Educational Resources Information Center

    Wyatt, Terrence M.; Sparkman, William E.

    1988-01-01

    The United States Supreme Court has made it clear that Congress can tax state bonds. All public purpose bonds issued by school districts must be issued in a registered format in order to continue their tax-exempt status. (MLF)

  14. Hydrogen bonding at C=Se acceptors in selenoureas, selenoamides and selones.

    PubMed

    Bibelayi, Dikima; Lundemba, Albert S; Allen, Frank H; Galek, Peter T A; Pradon, Juliette; Reilly, Anthony M; Groom, Colin R; Yav, Zéphyrin G

    2016-06-01

    In recent years there has been considerable interest in chalcogen and hydrogen bonding involving Se atoms, but a general understanding of their nature and behaviour has yet to emerge. In the present work, the hydrogen-bonding ability and nature of Se atoms in selenourea derivatives, selenoamides and selones has been explored using analysis of the Cambridge Structural Database and ab initio calculations. In the CSD there are 70 C=Se structures forming hydrogen bonds, all of them selenourea derivatives or selenoamides. Analysis of intramolecular geometries and ab initio partial charges show that this bonding stems from resonance-induced C(δ+)=Se(δ-) dipoles, much like hydrogen bonding to C=S acceptors. C=Se acceptors are in many respects similar to C=S acceptors, with similar vdW-normalized hydrogen-bond lengths and calculated interaction strengths. The similarity between the C=S and C=Se acceptors for hydrogen bonding should inform and guide the use of C=Se in crystal engineering. PMID:27240763

  15. Cerium Oxyhydroxide Clusters: Formation, Structure and Reactivity

    SciTech Connect

    Aubriet, F.; Gaumet, Jean-Jacques; De Jong, Wibe A.; Groenewold, G. S.; Gianotto, Anita K.; McIIwain, Michael E.; Van Stipdonk, Michael J.; Leavitt, Christopher M.

    2009-05-11

    Cerium oxyhydroxide cluster anions were produced by irradiating ceric oxide particles using 355 nm laser pulses that were synchronized with pulses of nitrogen gas admitted to the irradiation chamber. The gas pulse stabilized the nascent clusters that are largely anhydrous [CexOy] ions and neutrals. These initially-formed species react with water, principally forming closed-shell (c-s) oxohydroxy species that are described by the general formula [CexOy(OH)z]-. In general, the extent of hydroxylation varies from a value of 3 OH per Ce atom when x = 1 to a value slightly greater than 1 for x > 8. The Ce3 and Ce6 species deviate significantly from this trend: the x = 3 cluster accommodates more hydroxyl moieties compared to neighboring congeners at x = 2 and x = 4. Conversely, the x = 6 cluster is significantly less hydroxylated. Density functional theory (DFT) modeling of the cluster structures show that the hydrated clusters are hydrolyzed, and contain one-to-multiple hydroxide moieties, but not datively bound water. DFT also predicts an energetic preference for formation of highly symmetric structures as the size of the clusters increases. The calculated structures indicate that the ability of the Ce3 oxyhydroxide to accommodate more extensive hydroxylation is due to a more open, hexagonal structure in which the Ce atoms can participate in multiple hydrolysis reactions. Conversely the Ce6 oxyhydroxide has an octahedral structure that is not conducive to hydrolysis. In addition to the c-s clusters, open-shell (o-s) oxyhydroxides and superoxides are also formed, and they become more prominent as the size of the clusters increases, suggesting that the larger ceria clusters have an increased ability to stabilize a non-bonding electron. The overall intensity of the clusters tends to monotonically decrease as the cluster size increases, however this trend is interrupted at Ce13, which is significantly more stable compared to neighboring congeners, suggesting formation of

  16. Cerium Oxyhydroxide Clusters: Formation, Structure and Reactivity

    SciTech Connect

    Frederic Aubriet; Jean-Jacques Gaumet; Wibe A de Jong; Groenewold, Gary S; Gianotto, Anita K; McIlwain, Michael E; Michael J. Van Stipdonk; Christopher M. Leavitt

    2009-06-01

    Cerium oxyhydroxide cluster anions were produced by irradiating ceric oxide particles using 355 nm laser pulses that were synchronized with pulses of nitrogen gas admitted to the irradiation chamber. The gas pulse stabilized the nascent clusters that are largely anhydrous [CexOy] ions and neutrals. These initially-formed species react with water, principally forming closed-shell (c-s) oxohydroxy species that are described by the general formula [CexOy(OH)z]-. In general, the extent of hydroxylation varies from a value of 3 OH per Ce atom when x = 1 to a value slightly greater than 1 for x > 8. The Ce3 and Ce6 species deviate significantly from this trend: the x = 3 cluster accommodates more hydroxyl moieties compared to neighboring congeners at x = 2 and x = 4. Conversely, the x = 6 cluster is significantly less hydroxylated. Density functional theory (DFT) modeling of the cluster structures show that the hydrated clusters are hydrolyzed, and contain one-to-multiple hydroxide moieties, but not datively bound water. DFT also predicts an energetic preference for formation of highly symmetric structures as the size of the clusters increases. The calculated structures indicate that the ability of the Ce3 oxyhydroxide to accommodate more extensive hydroxylation is due to a more open, hexagonal structure in which the Ce atoms can participate in multiple hydrolysis reactions. Conversely the Ce6 oxyhydroxide has an octahedral structure that is not conducive to hydrolysis. In addition to the c-s clusters, open-shell (o-s) oxyhydroxides and superoxides are also formed, and they become more prominent as the size of the clusters increases, suggesting that the larger ceria clusters have an increased ability to stabilize a non-bonding electron. The overall intensity of the clusters tends to monotonically decrease as the cluster size increases, however this trend is interrupted at Ce13, which is significantly more stable compared to neighboring congeners, suggesting formation of

  17. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds.

    PubMed

    Ge, Chuanqi; Shen, Yuneng; Deng, Gang-Hua; Tian, Yuhuan; Yu, Dongqi; Yang, Xueming; Yuan, Kaijun; Zheng, Junrong

    2016-03-31

    Isotopic effects on the formation and dissociation kinetics of hydrogen bonds are studied in real time with ultrafast chemical exchange spectroscopy. The dissociation time of hydrogen bond between phenol-OH and p-xylene (or mesitylene) is found to be identical to that between phenol-OD and p-xylene (or mesitylene) in the same solvents. The experimental results demonstrate that the isotope substitution (D for H) has negligible effects on the hydrogen bond kinetics. DFT calculations show that the isotope substitution does not significantly change the frequencies of vibrational modes that may be along the hydrogen bond formation and dissociation coordinate. The zero point energy differences of these modes between hydrogen bonds with OH and OD are too small to affect the activation energy of the hydrogen bond dissociation in a detectible way at room temperature. PMID:26967376

  18. Diffusion Bonding of Silicon Carbide Ceramics using Titanium Interlayers

    NASA Technical Reports Server (NTRS)

    Halbig, Michael C.; Singh, Mrityunjay; Shpargel, Tarah P.; Kiser, James D.

    2006-01-01

    Robust joining approaches for silicon carbide ceramics are critically needed to fabricate leak free joints with high temperature mechanical capability. In this study, titanium foils and physical vapor deposited (PVD) titanium coatings were used to form diffusion bonds between SiC ceramics using hot pressing. Silicon carbide substrate materials used for bonding include sintered SiC and two types of CVD SiC. Microscopy results show the formation of well adhered diffusion bonds. The bond strengths as determined from pull tests are on the order of several ksi, which is much higher than required for a proposed application. Microprobe results show the distribution of silicon, carbon, titanium, and other minor elements across the diffusion bond. Compositions of several phases formed in the joint region were identified. Potential issues of material compatibility and optimal bond formation will also be discussed.

  19. Interfacial bonding stability

    NASA Technical Reports Server (NTRS)

    Boerio, J.

    1984-01-01

    Interfacial bonding stability by in situ ellipsometry was investigated. It is found that: (1) gamma MPS is an effective primer for bonding ethylene vinyl acetate (EVA) to aluminum; (2) ellipsometry is an effective in situ technique for monitoring the stability of polymer/metal interfaces; (3) the aluminized back surface of silicon wafers contain significant amounts of silicon and may have glass like properties.

  20. The dissociative bond.

    PubMed

    Gordon, Nirit

    2013-01-01

    Dissociation leaves a psychic void and a lingering sense of psychic absence. How do 2 people bond while they are both suffering from dissociation? The author explores the notion of a dissociative bond that occurs in the aftermath of trauma--a bond that holds at its core an understanding and shared detachment from the self. Such a bond is confined to unspoken terms that are established in the relational unconscious. The author proposes understanding the dissociative bond as a transitional space that may not lead to full integration of dissociated knowledge yet offers some healing. This is exemplified by R. Prince's (2009) clinical case study. A relational perspective is adopted, focusing on the intersubjective aspects of a dyadic relationship. In the dissociative bond, recognition of the need to experience mutual dissociation can accommodate a psychic state that yearns for relationship when the psyche cannot fully confront past wounds. Such a bond speaks to the need to reestablish a sense of human relatedness and connection when both parties in the relationship suffer from disconnection. This bond is bound to a silence that becomes both a means of protection against the horror of traumatic memory and a way to convey unspoken gestures toward the other. PMID:23282044