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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. 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

  6. 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

  7. 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

  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. 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.

  1. 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.

  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. 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

  1. 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.

  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. 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

  5. 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

  6. 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

  7. 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

  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. 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

  13. 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

  14. 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.

  15. 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

  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. 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

  1. 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

  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 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

  6. 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

  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. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  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. 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

  19. 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

  20. 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

  1. 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

  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. 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.

  6. 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.

  7. 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

  8. 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

  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. 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.

  11. 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

  12. 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

  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. 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

  6. 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.

  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. 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

  10. 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

  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. 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

  14. 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

  15. 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

  16. 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

  17. 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)

  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. 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

  2. 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

  3. 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

  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. 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

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  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. 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

  18. 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

  19. 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

  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. 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

  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. 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

  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. 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

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  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. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  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. 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)

  14. 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

  15. 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

  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

    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.

  1. 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

  2. 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

  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. 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).

  17. 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.

  18. 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

  19. 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

  20. 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.

  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