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Sample records for complex formation reactions

  1. Formation of Complex Molecules via radiative association reactions

    NASA Astrophysics Data System (ADS)

    Acharyya, Kinsuk; Herbst, Eric

    2016-07-01

    The detection of increasing numbers of complex organic molecules in the various phases of star formation plays a key role since they follow the same chemical rules of carbon-based chemistry that are observed in our planet Earth. Many of these molecules are believed to be formed on the surfaces of grains, and can then be released to the gas phase when these grains are heated. This is evident when we observe a rich chemistry in hot core regions. However, recently complex organic molecules have also been observed in cold clouds. Therefore, it is necessary to re-examine various pathways for the formation of these molecules in the gas phase. In this presentation, I will discuss role of radiative association reactions in the formation of complex molecules in the gas phase and at low temperature. We will compare abundance of assorted molecules with and without new radiative association reactions and will show that the abundance of a few complex molecules such as HCOOCH3, CH3OCH3 etc. can go up due to introduction of these reactions, which can help to explain their observed abundances.

  2. Redox reactions and complex formation of transplutonium elements in solutions

    SciTech Connect

    Krot, N.N.; Myasoedov, B.F.

    1986-01-01

    This paper gives a brief analysis of the kinetics and mechanism of a number of redox processes and the complex formation of transplutonium elements in unusual oxidation states. The composition and strength of complexes of TPE with various addends have been determined. The new experimental data on the oxidation potentials of americium and berkelium ions in solutions are cited in abbreviated form. It follows from the data that in phosphoric acid solutions, when the H/sub 3/PO/sub 4/ concentration is increased from 10 to 15 M, the oxidation potential of the couple Am(IV)-Am(III) decreases. The oxidation potentials of the couples Am(VI)-Am(V), Cm(V)-Cm(IV), and Bk(IV)Bk(III) are also presented.

  3. Formation of complex organic molecules in cold objects: the role of gas-phase reactions

    NASA Astrophysics Data System (ADS)

    Balucani, Nadia; Ceccarelli, Cecilia; Taquet, Vianney

    2015-04-01

    While astrochemical models are successful in reproducing many of the observed interstellar species, they have been struggling to explain the observed abundances of complex organic molecules. Current models tend to privilege grain surface over gas-phase chemistry in their formation. One key assumption of those models is that radicals trapped in the grain mantles gain mobility and react on lukewarm ( ≳ 30 K) dust grains. Thus, the recent detections of methyl formate (MF) and dimethyl ether (DME) in cold objects represent a challenge and may clarify the respective role of grain-surface and gas-phase chemistry. We propose here a new model to form DME and MF with gas-phase reactions in cold environments, where DME is the precursor of MF via an efficient reaction overlooked by previous models. Furthermore, methoxy, a precursor of DME, is also synthesized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairly well the observations towards L1544. It also explains, in a natural way, the observed correlation between DME and MF. We conclude that gas-phase reactions are major actors in the formation of MF, DME and methoxy in cold gas. This challenges the exclusive role of grain-surface chemistry and favours a combined grain-gas chemistry.

  4. 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

  5. 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)

  6. Formation of Complex Organics by Gas Phase and Intracluster Ion-Molecule Reactions Involving Acetylene and Hydrogen Cyanide

    NASA Astrophysics Data System (ADS)

    El-Shall, S.; Hamed, A.; Soliman, A. R.; Momoh, P. O.

    2011-05-01

    Many complex organics including polycyclic aromatic hydrocarbons are present in flames and combustion processes as well as in interstellar clouds and solar nebulae. Here, we present evidence for the formation of complex covalent organics by gas phase and intracluster reactions of the benzene, phenylium, pyridine, pyrimidine, phenylacetylene and benzonitrile cations with acetylene and hydrogen cyanide molecules. These reactions are studied using mass-selected ion mobility, chemical reactivity, collisional dissociation, and ab initio calculations. Measurements of collision cross sections in helium provide structural information on the adducts and allow probing structural changes at different temperatures (isomerization). We observed multiple additions of five acetylene molecules on the pyridine cation at room temperature. This is a remarkable result considering that only two acetylene molecules were added to the phenyl cation and no addition was observed on the benzene cation at room temperature. The experimental results are in full agreement with the ab initio calculations which predict that the first and second acetylenes add to the pyridine ion in barrierless, highly exothermic reactions. Similar reactions have been observed for the pyrimidine radical cation although the extent of the addition reactions is limited to only two acetylene molecules at room temperature. The results provide the first evidence for the incorporation of nitrogen in the formation cyclic hydrocarbons via the gas phase reactions of pyridine and pyrimidine ions with acetylene molecules. In addition, the formation of covalent adducts in the ionized acetylene/HCN system will be reported for the first time. Sequential reactions leading to the formation of pyridine and pyrimidine radical cations and higher adducts are observed over a wide range of temperature and pressure. The formation of these covalent adducts may represent a general class of addition reactions that can form complex

  7. Mass-dependent and -independent fractionation of isotopes in Ni and Pb chelate complex formation reactions

    NASA Astrophysics Data System (ADS)

    Nomura, Masao; Kudo, Takashi; Adachi, Atsuhiko; Aida, Masao; Fujii, Yasuhiko

    2013-11-01

    Mass independent fractionation (MIF) has been a very interesting topic in the field of inorganic isotope chemistry, in particular, geo- and cosmo- chemistry. In the present work, we studied the isotope fractionation of Ni(II) and Pb(II) ions in complex formation with chelating reagent EDTA. To obtain clear results on the mass dependence of the isotope fractionation, we have conducted long-distance ion exchange chromatography of Ni(II) and Pb(II), using chelate complex reagent EDTA. The results apparently show that the isotope fractionation in Ni complex formation system is governed by the mass dependent rule. On the other hand the isotope fractionation in the Pb complex system is governed by the mass independent rule or the nuclear volume effect.

  8. Mass-dependent and -independent fractionation of isotopes in Ni and Pb chelate complex formation reactions

    SciTech Connect

    Nomura, Masao; Kudo, Takashi; Adachi, Atsuhiko; Aida, Masao; Fujii, Yasuhiko

    2013-11-13

    Mass independent fractionation (MIF) has been a very interesting topic in the field of inorganic isotope chemistry, in particular, geo- and cosmo- chemistry. In the present work, we studied the isotope fractionation of Ni(II) and Pb(II) ions in complex formation with chelating reagent EDTA. To obtain clear results on the mass dependence of the isotope fractionation, we have conducted long-distance ion exchange chromatography of Ni(II) and Pb(II), using chelate complex reagent EDTA. The results apparently show that the isotope fractionation in Ni complex formation system is governed by the mass dependent rule. On the other hand the isotope fractionation in the Pb complex system is governed by the mass independent rule or the nuclear volume effect.

  9. A complex cortical reaction leads to formation of the fertilization envelope in the lobster, Homarus.

    PubMed

    Talbot, P; Goudeau, M

    1988-01-01

    We have examined the formation of the fertilization envelope in the lobsters Homarus americanus and H gammarus. Oocytes were fixed for electron microscopy either in the ovary or following extrusion from the gonopore. Mature ovarian oocytes are surrounded by a coat (envelope 1), which is comprised of small electron-dense granules and structures resembling "bottlebrushes." At least part of this coat is synthesized by the follicle cells of the ovary. The cortex of ovarian oocytes contains four types of vesicles that we refer to as high-density vesicles (HDV), low-density vesicles (LDV), moderately dense vesicles (MDV), and ring vesicles (RV). Oocytes that were electrically extruded from the gonopore and fixed immediately had an envelope identical to that of ovarian oocytes. The cortex of gonopore oocytes contained the four types of vesicles found in ovarian oocytes. When unfertilized gonopore oocytes were allowed to incubate in sea water, the oocyte cortex appeared unaltered, but envelope 1 swelled and the bottlebrushes dispersed. When recently fertilized oocytes were fixed during natural spawning or following in-vitro fertilization, each type of vesicle was released in sequence from the cortex of the oocyte. The contents of the HDV and LDV appeared first in the perivitelline space, but their fate could not be determined at later times. The ring-shaped elements of the RV and the moderately electron-dense material of the MDV were released exocytotically somewhat later; these materials coalesced in the perivitelline space to form a new coat (envelope 2). Envelope 1 subsequently condensed to its original thickness and appeared firmly attached to envelope 2. Our results show that the fertilized lobster egg is surrounded by two discrete coats. The outer coat, which is formed in the ovary, undergoes a swelling/condensation cycle at spawning. The inner coat originates from a complex cortical reaction. Together these coats comprise the fertilization envelope of the lobster

  10. Formation of water soluble complexes of ?: solid-state reaction between tertiary amines and ?

    NASA Astrophysics Data System (ADS)

    Mohan, H.; Priyadarsini, K. I.; Tyagi, A. K.; Mittal, J. P.

    1996-11-01

    Water soluble complexes of 0953-4075/29/21/015/img3 have been prepared on solid-state mechano-chemical reaction between 0953-4075/29/21/015/img3 and tertiary amines (hexamine, DABCO) at room temperature 0953-4075/29/21/015/img5. The product is characterized by x-ray diffraction and FTIR methods. It is presumably due to the charge transfer interactions between electron affinic 0953-4075/29/21/015/img3 and electron rich tertiary amines.

  11. The Formation Of Glycerol Monodecanoate By A Dehydration Condensation Reaction: Increasing The Chemical Complexity Of Amphiphiles On The Early Earth

    NASA Astrophysics Data System (ADS)

    Apel, Charles L.; Deamer, David W.

    2005-08-01

    Dehydration/condensation reactions between organic molecules in the prebiotic environment increased the inventory and complexity of organic compounds available for self-assembly into primitive cellular organisms. As a model of such reactions and to demonstrate this principle, we have investigated the esterification reaction between glycerol and decanoic acid that forms glycerol monodecanoate (GMD). This amphiphile enhances robustness of self-assembled membranous structures of carboxylic acids to the potentially disruptive effects of pH, divalent cation binding and osmotic stress. Experimental variables included temperature, water activity and hydrolysis of the resulting ester product, providing insights into the environmental conditions that would favor the formation and stability of this more evolved amphiphile. At temperatures exceeding 50 ∘C, the ester product formed even in the presence of bulk water, suggesting that the reaction occurs at the liquid interface of the two reactants and that the products segregate in the two immiscible layers, thereby reducing hydrolytic back reactions. This implies that esterification reactions were likely to be common in the prebiotic environment as reactants underwent cycles of wetting and drying on rare early landmasses at elevated temperatures

  12. Kinetics of actinide complexation reactions

    SciTech Connect

    Nash, K.L.; Sullivan, J.C.

    1997-09-01

    Though the literature records extensive compilations of the thermodynamics of actinide complexation reactions, the kinetics of complex formation and dissociation reactions of actinide ions in aqueous solutions have not been extensively investigated. In light of the central role played by such reactions in actinide process and environmental chemistry, this situation is somewhat surprising. The authors report herein a summary of what is known about actinide complexation kinetics. The systems include actinide ions in the four principal oxidation states (III, IV, V, and VI) and complex formation and dissociation rates with both simple and complex ligands. Most of the work reported was conducted in acidic media, but a few address reactions in neutral and alkaline solutions. Complex formation reactions tend in general to be rapid, accessible only to rapid-scan and equilibrium perturbation techniques. Complex dissociation reactions exhibit a wider range of rates and are generally more accessible using standard analytical methods. Literature results are described and correlated with the known properties of the individual ions.

  13. Reactions of dioxygen complexes. Oxidative dehydrogenation of 1,6-bis(2-pyridyl)-2,5-diazahexane through cobalt dioxygen complex formation

    SciTech Connect

    Basak, A.K.; Martell, A.E.

    1988-06-01

    The formation constants and oxygenation constants of the cobalt(II) complexes of 1,6-bis(2-pyridyl)-2,5-diazahexane (PYEN) have been determined by potentiometric equilibrium measurements under nitrogen and oxygen. The kinetics of the oxidative degradation of the coordinated ligand in the cobalt dioxygen complex have been measured spectrophotometrically, and the rate constants of two parallel degradation reactions have been determined. Both reactions were found to be second order, first order with respect to the concentration of the dioxygen complex and first order with respect to the hydroxide ion concentration. Kinetics and product analysis reveal that one of the terminal aminomethyl residues of the ligand PYEN undergoes two-electron oxidation to form the corresponding imine, which under the reaction conditions employed is converted to pyridine-2-carboxyaldehyde, identified semiquantitatively as the (2,6-dinitrophenyl)hydrazone. Comparisons of these results with those of systems investigated previously, and the large kinetic deuterium isotope effect for the dehydrogenation reaction, are employed as the basis of a proposed reaction mechanism, which involves deprotonation of an aliphatic amino group in a preequilibrium step. Reaction mechanisms are suggested. 30 references, 10 figures, 3 tables.

  14. Reactions of a chromium(III)-superoxo complex and nitric oxide that lead to the formation of chromium(IV)-oxo and chromium(III)-nitrito complexes.

    PubMed

    Yokoyama, Atsutoshi; Cho, Kyung-Bin; Karlin, Kenneth D; Nam, Wonwoo

    2013-10-01

    The reaction of an end-on Cr(III)-superoxo complex bearing a 14-membered tetraazamacrocyclic TMC ligand, [Cr(III)(14-TMC)(O2)(Cl)](+), with nitric oxide (NO) resulted in the generation of a stable Cr(IV)-oxo species, [Cr(IV)(14-TMC)(O)(Cl)](+), via the formation of a Cr(III)-peroxynitrite intermediate and homolytic O-O bond cleavage of the peroxynitrite ligand. Evidence for the latter comes from electron paramagnetic resonance spectroscopy, computational chemistry and the observation of phenol nitration chemistry. The Cr(IV)-oxo complex does not react with nitrogen dioxide (NO2), but reacts with NO to afford a Cr(III)-nitrito complex, [Cr(III)(14-TMC)(NO2)(Cl)](+). The Cr(IV)-oxo and Cr(III)-nitrito complexes were also characterized spectroscopically and/or structurally. PMID:24066924

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

    PubMed

    Zeng, Guixiang; Sakaki, Shigeyoshi

    2012-04-16

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

  16. Synthetic studies toward halichlorine: complex azaspirocycle formation with use of an NBS-promoted semipinacol reaction.

    PubMed

    Hurley, Paul B; Dake, Gregory R

    2008-06-01

    The investigations of a synthetic route incorporating a NBS-promoted semipinacol rearrangement to the 6-azaspiro[4.5]decane fragment within halichlorine ( 1) are presented. A convergent approach was pursued, utilizing two chiral, enantiomerically enriched building blocks, 2-trimethylstannyl piperidene 10 and substituted cyclobutanone 19. Noteworthy synthetic operations in this study include the following: (a) a highly diastereoselective NBS-promoted semipinacol reaction that established four stereogenic centers in ketone 25 and (b) the use of a N- p-toluenesulfonyl-2-iodo-2-piperidene as a precursor to a basic organometallic reagent, which was critical to the success of the coupling of fragments 10 and 19. PMID:18444680

  17. Dinitrosyl iron complexes with cysteine. Kinetics studies of the formation and reactions of DNICs in aqueous solution.

    PubMed

    Pereira, José Clayston Melo; Iretskii, Alexei V; Han, Rui-Min; Ford, Peter C

    2015-01-14

    Kinetics studies provide mechanistic insight regarding the formation of dinitrosyl iron complexes (DNICs) now viewed as playing important roles in the mammalian chemical biology of the ubiquitous bioregulator nitric oxide (NO). Reactions in deaerated aqueous solutions containing FeSO4, cysteine (CysSH), and NO demonstrate that both the rates and the outcomes are markedly pH dependent. The dinuclear DNIC Fe2(μ-CysS)2(NO)4, a Roussin's red salt ester (Cys-RSE), is formed at pH 5.0 as well as at lower concentrations of cysteine in neutral pH solutions. The mononuclear DNIC Fe(NO)2(CysS)2(-) (Cys-DNIC) is produced from the same three components at pH 10.0 and at higher cysteine concentrations at neutral pH. The kinetics studies suggest that both Cys-RSE and Cys-DNIC are formed via a common intermediate Fe(NO)(CysS)2(-). Cys-DNIC and Cys-RSE interconvert, and the rates of this process depend on the cysteine concentration and on the pH. Flash photolysis of the Cys-RSE formed from Fe(II)/NO/cysteine mixtures in anaerobic pH 5.0 solution led to reversible NO dissociation and a rapid, second-order back reaction with a rate constant kNO = 6.9 × 10(7) M(-1) s(-1). In contrast, photolysis of the mononuclear-DNIC species Cys-DNIC formed from Fe(II)/NO/cysteine mixtures in anaerobic pH 10.0 solution did not labilize NO but instead apparently led to release of the CysS(•) radical. These studies illustrate the complicated reaction dynamics interconnecting the DNIC species and offer a mechanistic model for the key steps leading to these non-heme iron nitrosyl complexes. PMID:25479566

  18. A STUDY OF FUNDAMENTAL REACTION PATHWAYS FOR TRANSITION METAL ALKYL COMPLEXES. I. THE REACTION OF A NICKEL METHYL COMPLEX WITH ALKYNES. II. THE MECHANISM OF ALDEHYDE FORMATION IN THE REACTION OF A MOLYBDENUM HYDRIDE WITH MOLYBDENUM ALKYLS

    SciTech Connect

    Huggins, John Mitchell

    1980-06-01

    I. This study reports the rapid reaction under mild conditions of internal or terminal alkynes with methyl (acetyl~ acetonato) (triphenylphosphine) nickel (1) in either aromatic or ether solvents. In all cases vinylnickel products 2 are formed by insertion of the alkyne into the nickel=methyl bond. These complexes may be converted into a variety of organic products (e.g. alkenes, esters, vinyl halides) by treatment with appropriate reagents. Unsymmetrical alkynes give selectively the one regioisomer with the sterically largest substituent next to the nickel atom. In order to investigate the stereochemistry of the initial insertion, a x-ray diffraction study of the reaction of 1 with diphenylacetylene was carried out. This showed that the vinylnickel complex formed by overall trans insertion was the product of the reaction. Furthermore, subsequent slow isomerization of this complex, to a mixture of it and the corresponding cis isomer, demonstrated that this trans addition product is the kinetic product of the reaction. In studies with other alkynes, the product of trans addition was not always exclusively (or even predominantly) formed, but the ratio of the stereoisomers formed kinetically was substantially different from the thermodynamic ratio. Isotope labeling, added phosphine, and other experiments have allowed us to conclude that the mechanism of this reaction does involve initial cis addition. However, a coordinatively unsaturated vinylnickel complex is initially formed which can undergo rapid, phosphine-catalyzed cis-trans isomerization in competition with its conversion to the isolable phosphine-substituted kinetic reaction products. II. The reaction of CpMo(CO){sub 3}H (1a) with CpMo(CO){sub 3}R (2, R= CH{sub 3}, C{sub 2}H{sub 5}) at 50{degrees} C in THF gives the aldehyde RCHO and the dimers [CpMo(CO){sub 3}]{sub 2} (3a) and [CpMo(CO){sub 2}]{sub 2} (4a). Labeling one of the reactants with a methylcyclopentadienyl ligand it was possible to show that the

  19. Pressure dependent low temperature kinetics for CN + CH3CN: competition between chemical reaction and van der Waals complex formation.

    PubMed

    Sleiman, Chantal; González, Sergio; Klippenstein, Stephen J; Talbi, Dahbia; El Dib, Gisèle; Canosa, André

    2016-06-01

    The gas phase reaction between the CN radical and acetonitrile CH3CN was investigated experimentally, at low temperatures, with the CRESU apparatus and a slow flow reactor to explore the temperature dependence of its rate coefficient from 354 K down to 23 K. Whereas a standard Arrhenius behavior was found at T > 200 K, indicating the presence of an activation barrier, a dramatic increase in the rate coefficient by a factor of 130 was observed when the temperature was decreased from 168 to 123 K. The reaction was found to be pressure independent at 297 K unlike the experiments carried out at 52 and 132 K. The work was complemented by ab initio transition state theory based master equation calculations using reaction pathways investigated with highly accurate thermochemical protocols. The role of collisional stabilization of a CNCH3CN van der Waals complex and of tunneling induced H atom abstractions were also considered. The experimental pressure dependence at 52 and 132 K is well reproduced by the theoretical calculations provided that an anharmonic state density is considered for the van der Waals complex CH3CNCN and its Lennard-Jones radius is adjusted. Furthermore, these calculations indicate that the experimental observations correspond to the fall-off regime and that tunneling remains small in the low-pressure regime. Hence, the studied reaction is essentially an association process at very low temperature. Implications for the chemistry of interstellar clouds and Titan are discussed. PMID:27199083

  20. Statistical Factors in Complexation Reactions.

    ERIC Educational Resources Information Center

    Chung, Chung-Sun

    1985-01-01

    Four cases which illustrate statistical factors in complexation reactions (where two of the reactants are monodentate ligands) are presented. Included are tables showing statistical factors for the reactions of: (1) square-planar complexes; (2) tetrahedral complexes; and (3) octahedral complexes. (JN)

  1. Bacterial formate hydrogenlyase complex

    PubMed Central

    McDowall, Jennifer S.; Murphy, Bonnie J.; Haumann, Michael; Palmer, Tracy; Armstrong, Fraser A.; Sargent, Frank

    2014-01-01

    Under anaerobic conditions, Escherichia coli can carry out a mixed-acid fermentation that ultimately produces molecular hydrogen. The enzyme directly responsible for hydrogen production is the membrane-bound formate hydrogenlyase (FHL) complex, which links formate oxidation to proton reduction and has evolutionary links to Complex I, the NADH:quinone oxidoreductase. Although the genetics, maturation, and some biochemistry of FHL are understood, the protein complex has never been isolated in an intact form to allow biochemical analysis. In this work, genetic tools are reported that allow the facile isolation of FHL in a single chromatographic step. The core complex is shown to comprise HycE (a [NiFe] hydrogenase component termed Hyd-3), FdhF (the molybdenum-dependent formate dehydrogenase-H), and three iron-sulfur proteins: HycB, HycF, and HycG. A proportion of this core complex remains associated with HycC and HycD, which are polytopic integral membrane proteins believed to anchor the core complex to the cytoplasmic side of the membrane. As isolated, the FHL complex retains formate hydrogenlyase activity in vitro. Protein film electrochemistry experiments on Hyd-3 demonstrate that it has a unique ability among [NiFe] hydrogenases to catalyze production of H2 even at high partial pressures of H2. Understanding and harnessing the activity of the FHL complex is critical to advancing future biohydrogen research efforts. PMID:25157147

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

    PubMed

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

    2007-01-01

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

  3. H-atom addition and abstraction reactions in mixed CO, H2CO and CH3OH ices - an extended view on complex organic molecule formation

    NASA Astrophysics Data System (ADS)

    Chuang, K.-J.; Fedoseev, G.; Ioppolo, S.; van Dishoeck, E. F.; Linnartz, H.

    2016-01-01

    Complex organic molecules (COMs) have been observed not only in the hot cores surrounding low- and high-mass protostars, but also in cold dark clouds. Therefore, it is interesting to understand how such species can be formed without the presence of embedded energy sources. We present new laboratory experiments on the low-temperature solid state formation of three complex molecules - methyl formate (HC(O)OCH3), glycolaldehyde (HC(O)CH2OH) and ethylene glycol (H2C(OH)CH2OH) - through recombination of free radicals formed via H-atom addition and abstraction reactions at different stages in the CO→H2CO→CH3OH hydrogenation network at 15 K. The experiments extend previous CO hydrogenation studies and aim at resembling the physical-chemical conditions typical of the CO freeze-out stage in dark molecular clouds, when H2CO and CH3OH form by recombination of accreting CO molecules and H-atoms on ice grains. We confirm that H2CO, once formed through CO hydrogenation, not only yields CH3OH through ongoing H-atom addition reactions, but is also subject to H-atom-induced abstraction reactions, yielding CO again. In a similar way, H2CO is also formed in abstraction reactions involving CH3OH. The dominant methanol H-atom abstraction product is expected to be CH2OH, while H-atom additions to H2CO should at least partially proceed through CH3O intermediate radicals. The occurrence of H-atom abstraction reactions in ice mantles leads to more reactive intermediates (HCO, CH3O and CH2OH) than previously thought, when assuming sequential H-atom addition reactions only. This enhances the probability to form COMs through radical-radical recombination without the need of UV photolysis or cosmic rays as external triggers.

  4. The formation of glycerol monodecanoate by a dehydration/condensation reaction: increasing the chemical complexity of amphiphiles on the early earth

    NASA Astrophysics Data System (ADS)

    Apel, C. L.; Deamer, D. W.

    Dehydration/condensation reactions between organic molecules in the prebiotic environment increased the inventory and complexity of organic compounds available for self-assembly into protocellular structures. As a model of such reactions, we have investigated the esterification reaction between glycerol and decanoic acid that forms glycerol monodecanoate. This amphiphile enhances robustness of self-assembled membranous structures of carboxylic acids to the potentially disruptive effects of pH, divalent cation binding and osmotic stress. Experimental variables included temperature, water activity and hydrolysis of the resulting ester product, providing insights into the environmental conditions that would favour the formation and stability of this more evolved amphiphile. At temperatures exceeding 500 C, the ester product formed even in the presence of bulk water, suggesting that the reaction occurs at the liquid interface of the two reactants and that the products segregate in the two immiscible layers, thereby reducing the rate of the hydrolytic back reaction. This suggests that esterification reactions were likely to commonly occur in the prebiotic environment as available reactants underwent cycles of wetting and drying on early landmasses at elevated temperatures.

  5. Characterising Complex Enzyme Reaction Data.

    PubMed

    Dönertaş, Handan Melike; Martínez Cuesta, Sergio; Rahman, Syed Asad; Thornton, Janet M

    2016-01-01

    The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution. PMID:26840640

  6. Characterising Complex Enzyme Reaction Data

    PubMed Central

    Rahman, Syed Asad; Thornton, Janet M.

    2016-01-01

    The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution. PMID:26840640

  7. Energetics and excited state dynamics of the radical pair formation in isolated CP47-reaction center complex of photosystem II at various temperatures

    SciTech Connect

    Groot, Marie-Louise; Paa lsson, Lars-Olof; Pribic, Radmila; Stokkum, Ivo H. van; Dekker, Jan P.; Grondelle, Rienk van

    1996-04-01

    The isolated CP47-reaction center complex of spinach photosystem II has been studied with time resolved picosecond fluorescence spectroscopy between 77 K and 270 K. It was observed that these particles exhibit multi-exponential fluorescence decays of the excited state at all temperatures. The major observations are an energy transfer/trapping time of {approx}40 picoseconds and a long-lived {approx}23 nanosecond component attributed to the recombination of the radical pair. These experimentally obtained parameters were used to estimate the free energy difference for the radical pair formation.

  8. Determination of boron at sub-ppm levels in uranium oxide and aluminum by hyphenated system of complex formation reaction and high-performance liquid chromatography (HPLC).

    PubMed

    Rao, Radhika M; Aggarwal, Suresh K

    2008-04-15

    Boron, at sub-ppm levels, in U3O8 powder and aluminum metal, was determined using complex formation and dynamically modified reversed-phase high-performance liquid chromatography (RP-HPLC). Curcumin was used for complexing boron extracted with 2-ethyl-1,3-hexane diol (EHD). Separation of complex from excess reagent and thereafter its determination using the online diode array detector (DAD) was carried out by HPLC. Calibration curve was found to be linear for boron amounts in the sample ranging from 0.02 microg to 0.5 microg. Precision of about 10% was achieved for B determination in samples containing less than 1 ppmw of boron. The values obtained by HPLC were in good agreement with the data available from other analytical techniques. The precision in the data obtained by HPLC was much better compared to that reported by other techniques. The present hyphenated methodology of HPLC and complex formation reaction is interesting because of cost performance, simplicity, versatility and availability when compared to other spectroscopic techniques like ICP-MS and ICP-AES. PMID:18371924

  9. Co-formation of hydroperoxides and ultra-fine particles during the reactions of ozone with a complex VOC mixture under simulated indoor conditions

    NASA Astrophysics Data System (ADS)

    Fan, Zhihua; Weschler, Charles J.; Han, In-Kyu; Zhang, Junfeng (Jim)

    In this study we examined the co-formation of hydrogen peroxide and other hydroperoxides (collectively presented as H 2O 2*) as well as submicron particles, including ultra-fine particles (UFP), resulting from the reactions of ozone (O 3) with a complex mixture of volatile organic compounds (VOCs) under simulated indoor conditions. The VOC mixture contained 23 compounds, including two terpenes ( d-limonene and α-pinene), two unsaturated alkenes (1-decene and 1-octene), and 19 other saturated organic compounds. These compounds are commonly found in indoor air but their concentrations were higher than typical indoor levels. When O 3 was added to a 25-m 3 controlled environmental facility (CEF) containing the 23 VOC mixture, both H 2O 2* and submicron particles were formed. The 2-h average concentration of H 2O 2* was 1.89±0.30 ppb, and the average total particle number concentration was 46,000±12,000 particles cm -3. A small increase of UFP (0.02-0.1 μm) occurred 5 min after the O 3 addition (17 min after the VOC addition) and a sharp increase of UFP occurred 13 min after the O 3 addition, suggesting homogeneous nucleation. The delayed onset of this event might reflect the time required to achieve saturated concentrations of the condensable organics. When the 2 terpenes were removed from the O 3/23 VOCs mixture, no H 2O 2* or particles were formed, indicating that the reactions of O 3 with the two terpenes were the key processes contributing to the formation of H 2O 2* and submicron particles in the O 3/23 VOCs system. The present study confirmed the findings of a previous study carried out in a real-world office and generated new findings regarding co-formation of UFP. Through a comparative analysis of H 2O 2* yields under different reaction conditions, this study demonstrates that VOCs co-present with the terpenes and O 3 may play a role in producing H 2O 2*.

  10. Formation, structure, and reactivity of palladium superoxo complexes

    SciTech Connect

    Talsi, E.P.; Babenko, V.P.; Shubin, A.A.; Chinakov, V.D.; Nekipelov, V.M.; Zamaraev, K.I.

    1987-11-18

    The mechanism of formation of palladium superoxo complexes, their structure, and their reactivity are discussed. The formation of the palladium superoxo complexes in the reaction of palladium(II) acetate, propionate, trifluororacetate, and bis(acetylacetonate) and palladium(0) tetrakis(triphenylphosphine) with hydrogen peroxide and potassium superoxide has been detected in solution by electron proton resonance. The oxidation of olefins and carbon monoxide by these complexes is considered. Reaction mechanisms and reaction kinetics for these oxidations are reported using the palladium superoxo complexes. 44 references, 8 figures, 2 tables.

  11. The reactions of nitrosyl complexes with cysteine.

    PubMed

    Roncaroli, Federico; Olabe, José A

    2005-06-27

    The reaction kinetics of a set of ruthenium nitrosyl complexes, {(X)5MNO}n, containing different coligands X (polypyridines, NH3, EDTA, pz, and py) with cysteine (excess conditions), were studied by UV-vis spectrophotometry, using stopped-flow techniques, at an appropriate pH, in the range 3-10, and T = 25 degrees C. The selection of coligands afforded a redox-potential range from -0.3 to +0.5 V (vs Ag/AgCl) for the NO+/NO bound couples. Two intermediates were detected. The first one, I1, appears in the range 410-470 nm for the different complexes and is proposed to be a 1:1 adduct, with the S atom of the cysteinate nucleophile bound to the N atom of nitrosyl. The adduct formation step of I1 is an equilibrium, and the kinetic rate constants for the formation and dissociation of the corresponding adducts were determined by studying the cysteine-concentration dependence of the formation rates. The second intermediate, I2, was detected through the decay of I1, with a maximum absorbance at ca. 380 nm. From similar kinetic results and analyses, we propose that a second cysteinate adds to I1 to form I2. By plotting ln k1(RS-) and ln k2(RS-) for the first and second adduct formation steps, respectively, against the redox potentials of the NO+/NO couples, linear free energy plots are obtained, as previously observed with OH- as a nucleophile. The addition rates for both processes increase with the nitrosyl redox potentials, and this reflects a more positive charge at the electrophilic N atom. In a third step, the I2 adducts decay to form the corresponding Ru-aqua complexes, with the release of N2O and formation of cystine, implying a two-electron process for the overall nitrosyl reduction. This is in contrast with the behavior of nitroprusside ([Fe(CN)5NO]2-; NP), which always yields the one-electron reduction product, [Fe(CN)5NO]3-, either under substoichiometric or in excess-cysteine conditions. PMID:15962980

  12. In-Situ Formation of Cobalt-Phosphate Oxygen-Evolving Complex-Anchored Reduced Graphene Oxide Nanosheets for Oxygen Reduction Reaction

    PubMed Central

    Zhao, Zhi-Gang; Zhang, Jing; Yuan, Yinyin; Lv, Hong; Tian, Yuyu; Wu, Dan; Li, Qing-Wen

    2013-01-01

    Oxygen conversion process between O2 and H2O by means of electrochemistry or photochemistry has lately received a great deal of attention. Cobalt-phosphate (Co-Pi) catalyst is a new type of cost-effective artificial oxygen-evolving complex (OEC) with amorphous features during photosynthesis. However, can such Co-Pi OEC also act as oxygen reduction reaction (ORR) catalyst in electrochemical processes? The question remains unanswered. Here for the first time we demonstrate that Co-Pi OEC does be rather active for the ORR. Particularly, Co-Pi OEC anchoring on reduced graphite oxide (rGO) nanosheet is shown to possess dramatically improved electrocatalytic activities. Differing from the generally accepted role of rGO as an “electron reservoir”, we suggest that rGO serves as “peroxide cleaner” in enhancing the electrocatalytic behaviors. The present study may bridge the gap between photochemistry and electrochemistry towards oxygen conversion. PMID:23877331

  13. In-Situ Formation of Cobalt-Phosphate Oxygen-Evolving Complex-Anchored Reduced Graphene Oxide Nanosheets for Oxygen Reduction Reaction

    NASA Astrophysics Data System (ADS)

    Zhao, Zhi-Gang; Zhang, Jing; Yuan, Yinyin; Lv, Hong; Tian, Yuyu; Wu, Dan; Li, Qing-Wen

    2013-07-01

    Oxygen conversion process between O2 and H2O by means of electrochemistry or photochemistry has lately received a great deal of attention. Cobalt-phosphate (Co-Pi) catalyst is a new type of cost-effective artificial oxygen-evolving complex (OEC) with amorphous features during photosynthesis. However, can such Co-Pi OEC also act as oxygen reduction reaction (ORR) catalyst in electrochemical processes? The question remains unanswered. Here for the first time we demonstrate that Co-Pi OEC does be rather active for the ORR. Particularly, Co-Pi OEC anchoring on reduced graphite oxide (rGO) nanosheet is shown to possess dramatically improved electrocatalytic activities. Differing from the generally accepted role of rGO as an ``electron reservoir'', we suggest that rGO serves as ``peroxide cleaner'' in enhancing the electrocatalytic behaviors. The present study may bridge the gap between photochemistry and electrochemistry towards oxygen conversion.

  14. In-situ formation of cobalt-phosphate oxygen-evolving complex-anchored reduced graphene oxide nanosheets for oxygen reduction reaction.

    PubMed

    Zhao, Zhi-Gang; Zhang, Jing; Yuan, Yinyin; Lv, Hong; Tian, Yuyu; Wu, Dan; Li, Qing-Wen

    2013-01-01

    Oxygen conversion process between O₂ and H₂O by means of electrochemistry or photochemistry has lately received a great deal of attention. Cobalt-phosphate (Co-Pi) catalyst is a new type of cost-effective artificial oxygen-evolving complex (OEC) with amorphous features during photosynthesis. However, can such Co-Pi OEC also act as oxygen reduction reaction (ORR) catalyst in electrochemical processes? The question remains unanswered. Here for the first time we demonstrate that Co-Pi OEC does be rather active for the ORR. Particularly, Co-Pi OEC anchoring on reduced graphite oxide (rGO) nanosheet is shown to possess dramatically improved electrocatalytic activities. Differing from the generally accepted role of rGO as an "electron reservoir", we suggest that rGO serves as "peroxide cleaner" in enhancing the electrocatalytic behaviors. The present study may bridge the gap between photochemistry and electrochemistry towards oxygen conversion. PMID:23877331

  15. Differential reaction kinetics, cleavage complex formation, and nonamer binding domain dependence dictate the structure-specific and sequence-specific nuclease activity of RAGs.

    PubMed

    Naik, Abani Kanta; Raghavan, Sathees C

    2012-01-20

    During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the "nonamer binding region," which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. PMID:22119487

  16. Reactions of a tungsten-germylyne complex with α,β-unsaturated ketones: complete cleavage of the W≡Ge bond and formation of two types of η3-germoxyallyl tungsten complexes.

    PubMed

    Fukuda, Tetsuya; Hashimoto, Hisako; Tobita, Hiromi

    2014-01-01

    Germylyne complex Cp*(CO)2W≡Ge{C(SiMe3)3} (1) reacted with two molecules of RC(O)CH═CH2 (R = Me, Et) to give η(3)-allyl complexes, in which an oxagermacyclopentene framework was bound to an η(3)-allyl ligand through an oxygen atom. In the reaction with α-Me-substituted MeC(O)C(Me)═CH2, 1 reacted with only one molecule of the substrate to give another type of η(3)-allyl complex, in which a five-membered oxagermacyclopentenyl ring was coordinated to the W center in an η(3) fashion. Both reactions resulted in unprecedented complete cleavage of a W≡Ge triple bond. PMID:24328309

  17. Audience Reactions to Two Visual Formats.

    ERIC Educational Resources Information Center

    Ramsey, Richard David

    One hundred undergraduate business students completed a questionnaire designed to determine their reactions to a traditional and a "flashier" textbook format. Before completing the questionnaire, subjects spent several minutes examining two business textbooks--one an older textbook with black ink on white paper, narrow margins, and few…

  18. Reaction front formation in contaminant plumes

    NASA Astrophysics Data System (ADS)

    Cribbin, Laura B.; Winstanley, Henry F.; Mitchell, Sarah L.; Fowler, Andrew C.; Sander, Graham C.

    2014-12-01

    The formation of successive fronts in contaminated groundwater plumes by subsoil bacterial action is a commonly accepted feature of their propagation, but it is not obviously clear from a mathematical standpoint quite how such fronts are formed or propagate. In this paper we show that these can be explained by combining classical reaction-diffusion theory involving just two reactants (oxidant and reductant), and a secondary reaction in which a reactant on one side of such a front is (re-)formed on the other side of the front via diffusion of its product across the front. We give approximate asymptotic solutions for the reactant profiles, and the propagation rate of the front.

  19. Reactions of Ph3Sb═S with copper(I) complexes supported by N-donor ligands: formation of stable adducts and S-transfer reactivity.

    PubMed

    Yang, Lei; Tehranchi, Jacqui; Tolman, William B

    2011-03-21

    In the exploration of sulfur-delivery reagents useful for synthesizing models of the tetracopper-sulfide cluster of nitrous oxide reductase, reactions of Ph(3)Sb═S with Cu(I) complexes of N,N,N',N'-tetramethyl-2R,3R-cyclohexanediamine (TMCHD) and 1,4,7-trialkyltriazacyclononanes (R(3)tacn; R = Me, Et, iPr) were studied. Treatment of [(R(3)tacn)Cu(NCCH(3))]SbF(6) (R = Me, Et, or iPr) with 1 equiv of S═SbPh(3) in CH(2)Cl(2) yielded adducts [(R(3)tacn)Cu(S═SbPh(3))]SbF(6) (1-3), which were fully characterized, including by X-ray crystallography. The adducts slowly decayed to [(R(3)tacn)(2)Cu(2)(μ-η(2):η(2)-S(2))](2+) species (4-6) and SbPh(3), or more quickly in the presence of additional [(R(3)tacn)Cu(NCCH(3))]SbF(6) to 4-6 and [(R(3)tacn)Cu(SbPh(3))]SbF(6) (7-9). The results of mechanistic studies of the latter process were consistent with rapid intermolecular exchange of S═SbPh(3) between 1-3 and added [(R(3)tacn)Cu(NCCH(3))]SbF(6), followed by conversion to product via a dicopper intermediate formed in a rapid pre-equilibrium step. Key evidence supporting this step came from the observation of saturation behavior in a plot of the initial rate of loss of 1 versus the initial concentration of [(Me(3)tacn)Cu(NCCH(3))]SbF(6). Also, treatment of [(TMCHD)Cu(CH(3)CN)]PF(6) with S═SbPh(3) led to the known tricopper cluster [(TMCHD)(3)Cu(3)(μ(3)-S)(2)](PF(6))(3) in good yield (79%), a synthetic procedure superior to that previously reported (Brown, E. C.; York, J. T.; Antholine, W. E.; Ruiz, E.; Alvarez, S.; Tolman, W. B. J. Am. Chem. Soc. 2005, 127, 13752-13753). PMID:21338053

  20. Simulation of biomolecular diffusion and complex formation.

    PubMed Central

    Allison, S A; Northrup, S H; McCammon, J A

    1986-01-01

    Diffusion is a phenomenon of very widespread importance in molecular biophysics. Diffusion can determine the rates and character of the assembly of multisubunit structures, the binding of ligands to receptors, and the internal motions of molecules and assemblies that involve solvent surface displacements. Current computer simulation techniques provide much more detailed descriptions of diffusional processes than have been available in the past. Models can be constructed to include such realistic features as structural subunits at the submolecular level (domains, monomers, or atoms); detailed electrostatic charge distributions and corresponding solvent-screened inter- and intramolecular interactions; and hydrodynamic interactions. The trajectories can be analyzed either to provide direct information on biomolecular function (e.g., the bimolecular rate constant for formation of an electron-transfer complex between two proteins), or to provide or test models for the interpretation of experimental data (e.g., the time dependence of fluorescence depolarization for segments of DNA). Here, we first review the theory of diffusional simulations, with special emphasis on new techniques such as those for obtaining transport properties of flexible assemblies and rate constants of diffusion-controlled reactions. Then we survey a variety of recent applications, including studies of large-scale motion in DNA segments and substrate "steering" in enzyme-substrate binding. We conclude with a discussion of current work (e.g., formation of protein complexes) and possible areas for future work. PMID:3955168

  1. Reaction front formation in contaminant plumes.

    PubMed

    Cribbin, Laura B; Winstanley, Henry F; Mitchell, Sarah L; Fowler, Andrew C; Sander, Graham C

    2014-12-15

    The formation of successive fronts in contaminated groundwater plumes by subsoil bacterial action is a commonly accepted feature of their propagation, but it is not obviously clear from a mathematical standpoint quite how such fronts are formed or propagate. In this paper we show that these can be explained by combining classical reaction-diffusion theory involving just two reactants (oxidant and reductant), and a secondary reaction in which a reactant on one side of such a front is (re-)formed on the other side of the front via diffusion of its product across the front. We give approximate asymptotic solutions for the reactant profiles, and the propagation rate of the front. PMID:25461883

  2. Photosynthetic reaction center complexes from heliobacteria

    NASA Technical Reports Server (NTRS)

    Trost, J. T.; Vermaas, W. F. J.; Blankenship, R. E.

    1991-01-01

    Photosynthetic reaction centers are pigment-protein complexes that are responsible for the transduction of light energy into chemical energy. Considerable evidence indicates that photosynthetic organisms were present very early in the evolution of life on Earth. The goal of this project is to understand the early evolutionary development of photosynthesis by examining the properties of reaction centers isolated from certain contemporary organisms that appear to contain the simplest photosynthetic reaction centers. The major focus is on the family of newly discovered strictly anaerobic photosynthetic organisms that are grouped with the gram-positive phylum of bacteria. The properties of these reactions centers suggest that they may be the descendants of an ancestor that also gave rise to Photosystem 1 found in oxygen-evolving photosynthetic organisms. Photoactive reaction center-core antenna complexes were isolated from the photosynthetic bacteria, Heliobacillus mobilis and Heliobacterium gestii, by extraction of membranes with Deriphat 160C followed by differential centrifugation and sucrose density gradient centrifugation. Other aspects of this investigation are briefly discussed.

  3. Synthesis, DNA binding and complex formation reactions of 3-amino-5,6-dimethyl-1,2,4-triazine with Pd(II) and some selected biorelevant ligands.

    PubMed

    Shoukry, Azza A; Alghanmi, Reem M

    2015-03-01

    With the purpose of studying the binding behavior of Pd(II) complexes with DNA as the main biological target, and their ability to penetrate reasonably into tumour cells and destroy their replication ability, Pd(ADT)Cl2 complex was synthesized and characterized, where ADT is 3-amino-5,6-dimethyl-1,2,4-triazine. Stoichiometry and stability constants of the complexes formed between various biologically relevant ligands (amino acids, amides, DNA constituents, and dicarboxylic acids) and [Pd(ADT)(H2O)2](2+) were investigated at 25°C and at constant 0.1moldm(-3) ionic strength. The concentration distribution diagrams of the various species formed are evaluated. Further investigation of the binding properties of the diaqua complex [Pd(ADT)(H2O)2](2+) with calf thymus DNA (CT-DNA) was investigated by UV-vis spectroscopy. The intrinsic binding constants (Kb) calculated from UV-vis absorption studies was calculated to be 2.00×10(3)moldm(-3). The calculated (Kb) value was found to be of lower magnitude than that of the classical intercalator EB (Ethidium bromide) (Kb=1.23(±0.07)×10(5)moldm(-3)) suggesting an electrostatic and/or groove binding mode for the interaction with CT-DNA. Thermal denaturation has been systematically studied by spectrophotometric method and the calculated ΔTm was nearly 5°C, supporting the electrostatic and/or groove binding mode for the interaction between the complex and CT-DNA. PMID:25459605

  4. Synthesis, DNA binding and complex formation reactions of 3-amino-5,6-dimethyl-1,2,4-triazine with Pd(II) and some selected biorelevant ligands

    NASA Astrophysics Data System (ADS)

    Shoukry, Azza A.; Alghanmi, Reem M.

    2015-03-01

    With the purpose of studying the binding behavior of Pd(II) complexes with DNA as the main biological target, and their ability to penetrate reasonably into tumour cells and destroy their replication ability, Pd(ADT)Cl2 complex was synthesized and characterized, where ADT is 3-amino-5,6-dimethyl-1,2,4-triazine. Stoichiometry and stability constants of the complexes formed between various biologically relevant ligands (amino acids, amides, DNA constituents, and dicarboxylic acids) and [Pd(ADT)(H2O)2]2+ were investigated at 25 °C and at constant 0.1 mol dm-3 ionic strength. The concentration distribution diagrams of the various species formed are evaluated. Further investigation of the binding properties of the diaqua complex [Pd(ADT)(H2O)2]2+ with calf thymus DNA (CT-DNA) was investigated by UV-vis spectroscopy. The intrinsic binding constants (Kb) calculated from UV-vis absorption studies was calculated to be 2.00 × 103 mol dm-3. The calculated (Kb) value was found to be of lower magnitude than that of the classical intercalator EB (Ethidium bromide) (Kb = 1.23(±0.07) × 105 mol dm-3) suggesting an electrostatic and/or groove binding mode for the interaction with CT-DNA. Thermal denaturation has been systematically studied by spectrophotometric method and the calculated ΔTm was nearly 5 °C, supporting the electrostatic and/or groove binding mode for the interaction between the complex and CT-DNA

  5. Unraveling reaction pathways and specifying reaction kinetics for complex systems.

    PubMed

    Vinu, R; Broadbelt, Linda J

    2012-01-01

    Many natural and industrial processes involve a complex set of competing reactions that include several different species. Detailed kinetic modeling of such systems can shed light on the important pathways involved in various transformations and therefore can be used to optimize the process conditions for the desired product composition and properties. This review focuses on elucidating the various components involved in modeling the kinetics of pyrolysis and oxidation of polymers. The elementary free radical steps that constitute the chain reaction mechanism of gas-phase/nonpolar liquid-phase processes are outlined. Specification of the rate coefficients of the various reaction families, which is central to the theme of kinetics, is described. Construction of the reaction network on the basis of the types of end groups and reactive moieties in a polymer chain is discussed. Modeling frameworks based on the method of moments and kinetic Monte Carlo are evaluated using illustrations. Finally, the prospects and challenges in modeling biomass conversion are addressed. PMID:22468596

  6. Kinetic analysis of complex reactions using FEMLAB

    SciTech Connect

    Cao, Chunshe; Wang, Yong

    2005-06-07

    A finite element method software FEMALB has been implemented to the kinetic analysis of complex reaction systems. The established protocol provides fast solutions to the coupled differential-algebraic equations. It shows significant advantages over the conventional coding process with the standard implicit Runge-Kutta (IRK) method. The accuracy and high efficiency have been demonstrated in the simulation of the reaction processes such as glucose/fructose hydrogenation and catalytic cracking of gasoil. As model validation, the numerical results showed satisfactory agreement with the exact solutions. With the powerful capability of solving large matrixes of differential equations (both ODE and PDE) with nonlinear algebraic constrains, such an algorithm has greatly reduced the coding labor in reaction mechanistic studies and provided a unique tool in reactor design and optimization.

  7. New Pathways for the Formation of Complex Organics and Prebiotic Synthesis in the Gas Phase

    NASA Astrophysics Data System (ADS)

    El-Shall, M. S.

    2010-04-01

    We study the formation mechanisms of complex organics that are present in interstellar clouds. The reaction of acetylene ion with water produces vinyl alcohol while the reaction of benzene ion with acetylene produces naphthalene-type ion.

  8. Chemical reactions of As complexation by glutathione: an XAFS study

    NASA Astrophysics Data System (ADS)

    Franco, M. W.; Vasconcelos, I. F.; Modolo, L. V.; Barbosa, F. A. R.

    2016-05-01

    In this study, the chemical reactions between As(III) and As(V) with glutathione, which is a target compound in As biochemistry due to its primordial role in As immobilization and intracellular reduction, in various molar ratios were investigated using As K-edge XAFS spectroscopy. Results showed a gradual substitution of As-O bonds in the coordination of aqueous As(III) and As(V) for three As-S bonds in the As+GSH complex. Moreover, the data showed reduction of As(V) to As(III) prior or concomitant to the As+GSH complex formation.

  9. Knockout driven reactions in complex molecules and their clusters

    NASA Astrophysics Data System (ADS)

    Gatchell, Michael; Zettergren, Henning

    2016-08-01

    Energetic ions lose some of their kinetic energy when interacting with electrons or nuclei in matter. Here, we discuss combined experimental and theoretical studies on such impulse driven reactions in polycyclic aromatic hydrocarbons (PAHs), fullerenes, and pure or mixed clusters of these molecules. These studies show that the nature of excitation is important for how complex molecular systems respond to ion/atom impact. Rutherford-like nuclear scattering processes may lead to prompt atom knockout and formation of highly reactive fragments, while heating of the molecular electron clouds in general lead to formation of more stable and less reactive fragments. In this topical review, we focus on recent studies of knockout driven reactions, and present new calculations of the angular dependent threshold (displacement) energies for such processes in PAHs. The so-formed fragments may efficiently form covalent bonds with neighboring molecules in clusters. These unique molecular growth processes may be important in astrophysical environments such as low velocity shock waves.

  10. Disulfirm-ethanol reaction: a complex mechanism

    SciTech Connect

    Yourick, J.J.; Faiman, M.D.

    1986-03-01

    Hypothermia has previously been shown to be a component of the disulfiram-ethanol reaction (DER). In rats, hypothermia correlated with the hypotension and tachycardia observed when ethanol was administered 8 hours after disfulfiram treatment. These studies have now been extended, and in addition, the role of diethyldithiocarbamate (DDTC) and diethyldithiocarbamate-methyl ester (DDTC-MF) in the DER have been examined. In rats challenged with ethanol (1g/kg, i.p.) 4 and 24 hours after disulfiram (75 mg/kg, i.p.) no hypothermia was observed, but was found when ethanol was given 8, 12 and 16 hours after disulfiram. Hypotension and tachycardia were found at all time periods studied. Low Km ALDH also was inhibited at the 4, 8, 16 and 24 hour time periods. Although pretreatment with DDTC and DDTC-ME failed to produce hypothermia, hypotension and tachycardia were observed in rats challenged with ethanol. As with disulfiram administration, hypothermia did not correlate with ALDH inhibition in the DDTC and DDTC-ME studies. These studies support the known myriad of effects produced during the DER, and provide additional evidence that difference mechanisms contribute to the complexity of the disulfiram-ethanol reaction.

  11. Studies on chemical kinetics of positronium complex formation

    NASA Astrophysics Data System (ADS)

    Du, Youming; Zhang, Tianbao; Cao, Chun; Chen, Yun-Ti; Liang, Jiachang

    1993-09-01

    The complex formation between ortho-positronium and N-( p-substituted-phenyl) glycine ( p-RPhG, G=NHCH 2COOH; R=NO 2, Cl, H, CH 3, CH 3O) or N-( m-substituted-phenyl) glycine ( m-RPhG, R=NO 2, Cl) in solutions of 30% (v/v) ethanol—water and 20% (v/v) dioxane—water is discussed. The application of a BaF 2 scintillation counter to a positron annihilation lifetime spectrometer is described. By means of this new type of spectrometer, the complex formation reaction rate constants of ortho-positronium with the glycine derivatives in solutions are determined. The results indicate that the rate constants mainly depend on the conjugation effect at the benzene ring, the induction effects of the substitutes on the phenyl and solvents. There exists a linear free-energy relationship between rate constants and the basicities of N-substituted phenyl glycines in ortho-positronium—glycine complex formation. It means that the transient complex formation of ortho-positronium with molecules is like a general chemical reaction and obeys classical rules.

  12. Quantum chemical mechanism in parasitic reaction of AlGaN alloys formation

    NASA Astrophysics Data System (ADS)

    Makino, Osamu; Nakamura, Koichi; Tachibana, Akitomo; Tokunaga, Hiroki; Akutsu, Nakao; Matsumoto, Koh

    2000-06-01

    The mechanism of parasitic reactions among trimethylaluminum (TMA), trimethylgallium (TMG), and NH 3 in atmospheric pressure (AP) MOVPE for growth of AlGaN is theoretically studied using the quantum chemical method. The calculations show that metal-nitrogen chain growth reaction easily proceeds through the successive reactions of 'complex formation with NH 3' and 'CH 4 elimination by the bimolecular mechanism'. Additionally, a parasitic reaction in APMOVPE using other raw material is also investigated. The calculated result shows that small change of raw material raises activation energy of parasitic reaction, and, thus, the parasitic reaction is suppressed. This result suggests a way to improve APMOVPE by a suitable choice of substituent.

  13. Complex organic molecules and star formation

    NASA Astrophysics Data System (ADS)

    Bacmann, A.; Faure, A.

    2014-12-01

    Star forming regions are characterised by the presence of a wealth of chemical species. For the past two to three decades, ever more complex organic species have been detected in the hot cores of protostars. The evolution of these molecules in the course of the star forming process is still uncertain, but it is likely that they are partially incorporated into protoplanetary disks and then into planetesimals and the small bodies of planetary systems. The complex organic molecules seen in star forming regions are particularly interesting since they probably make up building blocks for prebiotic chemistry. Recently we showed that these species were also present in the cold gas in prestellar cores, which represent the very first stages of star formation. These detections question the models which were until now accepted to account for the presence of complex organic molecules in star forming regions. In this article, we shortly review our current understanding of complex organic molecule formation in the early stages of star formation, in hot and cold cores alike and present new results on the formation of their likely precursor radicals.

  14. Surface-Guided Formation of an Organocobalt Complex.

    PubMed

    Weber, Peter B; Hellwig, Raphael; Paintner, Tobias; Lattelais, Marie; Paszkiewicz, Mateusz; Casado Aguilar, Pablo; Deimel, Peter S; Guo, Yuanyuan; Zhang, Yi-Qi; Allegretti, Francesco; Papageorgiou, Anthoula C; Reichert, Joachim; Klyatskaya, Svetlana; Ruben, Mario; Barth, Johannes V; Bocquet, Marie-Laure; Klappenberger, Florian

    2016-05-01

    Organocobalt complexes represent a versatile tool in organic synthesis as they are important intermediates in Pauson-Khand, Friedel-Crafts, and Nicholas reactions. Herein, a single-molecule-level investigation addressing the formation of an organocobalt complex at a solid-vacuum interface is reported. Deposition of 4,4'-(ethyne-1,2-diyl)dibenzonitrile and Co atoms on the Ag(111) surface followed by annealing resulted in genuine complexes in which single Co atoms laterally coordinated to two carbonitrile groups undergo organometallic bonding with the internal alkyne moiety of adjacent molecules. Alternative complexation scenarios involving fragmentation of the precursor were ruled out by complementary X-ray photoelectron spectroscopy. According to density functional theory analysis, the complexation with the alkyne moiety follows the Dewar-Chatt-Duncanson model for a two-electron-donor ligand where an alkyne-to-Co donation occurs together with a strong metal-to-alkyne back-donation. PMID:27059261

  15. Reactions and mass spectra of complex particles using Aerosol CIMS

    NASA Astrophysics Data System (ADS)

    Hearn, John D.; Smith, Geoffrey D.

    2006-12-01

    Aerosol chemical ionization mass spectrometry (CIMS) is used both on- and off-line for the analysis of complex laboratory-generated and ambient particles. One of the primary advantages of Aerosol CIMS is the low degree of ion fragmentation, making this technique well suited for investigating the reactivity of complex particles. To demonstrate the usefulness of this "soft" ionization, particles generated from meat cooking were reacted with ozone and the composition was monitored as a function of reaction time. Two distinct kinetic regimes were observed with most of the oleic acid in these particles reacting quickly but with 30% appearing to be trapped in the complex mixture. Additionally, detection limits are measured to be sufficiently low (100-200 ng/m3) to detect some of the more abundant constituents in ambient particles, including sulfate, which is measured in real-time at 1.2 [mu]g/m3. To better characterize complex aerosols from a variety of sources, a novel off-line collection method was also developed in which non-volatile and semi-volatile organics are desorbed from particles and concentrated in a cold U-tube. Desorption from the U-tube followed by analysis with Aerosol CIMS revealed significant amounts of nicotine in cigarette smoke and levoglucosan in oak and pine smoke, suggesting that this may be a useful technique for monitoring particle tracer species. Additionally, secondary organic aerosol formed from the reaction of ozone with R-limonene and volatile organics from orange peel were analyzed off-line showing large molecular weight products (m/z > 300 amu) that may indicate the formation of oligomers. Finally, mass spectra of ambient aerosol collected offline reveal a complex mixture of what appears to be highly processed organics, some of which may contain nitrogen.

  16. [Formations and reactions of aromatic furazan compounds].

    PubMed

    Hasegawa, M; Takabatake, T; Miyazawa, T

    2001-06-01

    A reaction from various kinds of nitroquinoline with hydroxylamine in potassium hydroxide alkalinity produced a novel product, furazanoquinoline, besides the known amino derivatives. The products obtained were furazano [3,4-f] quinoline (5) from 5-nitroquinoline (1) and 6-nitroquinoline (6), and furazano [3,4-h] quinoline (10) from 7-nitroquinoline (8) and 8-nitroquinoline (11). The reaction mechanism was believed to be as shown in Figs. 2 and 3. The photoreaction of benzofuroxan (19) in acetonitrile containing a little water, under a high pressure mercury lamp, produced 1H-azepine-2,7-dione (20), while under irradiation using a low pressure lamp, 6H-furazano [4,5-c] carbazole-3-oxide (21) and compound 20 were obtained. Then the photoproduct 20 produced photodimer 22 by irradiation in acetonitrile: water (9:1, v/v) using a high or low pressure mercury lamp, while photolysis with alkali proceeded as in the photoreaction of N-alkylimide to give 7-hydroxy-1H-azepine-2-one (23). When pyrido [2,3-c] furoxan (24) was irradiated in acetonitrile containing a little water with a low pressure mercury lamp, 3-nitro-2-pyridone (25) was obtained. When compound 24 was irradiated in the presence of morpholine with a low pressure mercury lamp in an argon atmosphere, 6-morpholinopyridine 2,3-dioxime (26) was produced. Quinoxaline 1,4-dioxide derivatives (31, 33), phenazine 5,10-dioxide derivatives (36, 37) and pyrido [2,3-b] pyrazine derivatives (38, 39) were synthesized from the corresponding furoxan catalyzed by silica gel or molecular sieves, and their antibacterial properties were evaluated. The results of antibacterial screening tests in vitro, revealed strong activity against Bacteroides fragilis. PMID:11433773

  17. 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

  18. MICROCALORIMETRIC STUDIES ON THE FORMATION OF MAGNESIUM COMPLEXES OF ADENINE NUCLEOTIDES

    PubMed Central

    Belaich, J. P.; Sari, J. C.

    1969-01-01

    Values for the thermodynamic quantities (ΔF, ΔH, ΔS) in reactions in which complexes of adenine nucleotides with magnesium ion (ATPMg--, ADPMg-, AMPMg) are formed have been obtained by a microcalorimetric technique by using an isothermic Calvet's apparatus. Experimental values measured at ionic strength μ = 0.2 indicate that complex formation reactions are driven by the entropic factor and that stability of complexes increases with length of the phosphate chain. PMID:5261047

  19. Synthesis and decarbonylation reactions of the triiron phosphinidene complex [Fe3Cp3(μ-H)(μ3-PPh)(CO)4]: easy cleavage and formation of P-H and Fe-Fe bonds.

    PubMed

    Alvarez, Celedonio M; Alvarez, M Angeles; García, M Esther; González, Rocío; Ramos, Alberto; Ruiz, Miguel A

    2011-11-01

    The binuclear phosphine complex [Fe(2)Cp(2)(μ-CO)(2)(CO)(PH(2)Ph)] (Cp = η(5)-C(5)H(5)) reacted with the acetonitrile adduct [Fe(2)Cp(2)(μ-CO)(2)(CO)(NCMe)] in dichloromethane at 293 K to give the trinuclear hydride-phosphinidene derivative [Fe(3)Cp(3)(μ-H)(μ(3)-PPh)(CO)(4)] as a mixture of cis,anti and trans isomers (Fe-Fe = 2.7217(6) Å for the cis,anti isomer). In contrast, photochemical treatment of the phosphine complex with [Fe(2)Cp(2)(CO)(4)] gave the phosphide-bridged complex trans-[Fe(3)Cp(3)(μ-PHPh)(μ-CO)(2)(CO)(3)] as the major product, along with small amounts of the binuclear hydride-phosphide complexes [Fe(2)Cp(2)(μ-H)(μ-PHPh)(CO)(2)] (cis and trans isomers), which are more selectively prepared from [Fe(2)Cp(2)(CO)(4)] and PH(2)Ph at 388 K. The photochemical decarbonylation of either of the mentioned triiron compounds led reversibly to three different products depending on the reaction conditions: (a) the 48-electron phosphinidene cluster [Fe(3)Cp(3)(μ-H)(μ(3)-PPh)(μ-CO)(2)] (Fe-Fe = 2.592(2)-2.718(2) Å); (b) the 50-electron complex [Fe(3)Cp(3)(μ-H)(μ(3)-PPh)(μ-CO)(CO)(2)], also having carbonyl- and hydride-bridged metal-metal bonds (Fe-Fe = 2.6177(3) and 2.7611(4) Å, respectively); and (c) the 48-electron phosphide cluster [Fe(3)Cp(3)(μ-PHPh)(μ(3)-CO)(μ-CO)(2)], an isomer of the latter phosphinidene complex now having three intermetallic bonds (Fe-Fe = 2.5332(8)-2.6158(8) Å). PMID:21981036

  20. Formation of a Bridging Phosphinidene Thorium Complex.

    PubMed

    Behrle, Andrew C; Castro, Ludovic; Maron, Laurent; Walensky, Justin R

    2015-12-01

    The synthesis and structural determination of the first thorium phosphinidene complex are reported. The reaction of 2 equiv of (C5Me5)2Th(CH3)2 with H2P(2,4,6-(i)Pr3C6H2) at 95 °C produces [(C5Me5)2Th]2(μ2-P[(2,6-CH2CHCH3)2-4-(i)PrC6H2] as well as 4 equiv of methane, 2 equiv from deprotonation of the phosphine and 2 equiv from C-H bond activation of one methyl group of each of the isopropyl groups at the 2- and 6-positions. Transition state calculations indicate that the steps in the mechanism are P-H, C-H, C-H, and then P-H bond activation to form the phosphinidene. PMID:26575219

  1. Vortex formation in a complex plasma

    NASA Astrophysics Data System (ADS)

    Ishihara, Osamu

    Complex plasma experiments in ground-based laboratories as well as in microgravity conditions have shown the formation of vortex structures in various conditions (e.g., 1,2,3,4). The vortex structures formed in a complex plasma are visible by naked eyes with the help of irradiating laser and the individual dust particles in the structure give us the opportunity to study detailed physics of the commonly observed natural phenomena known such as tornadoes, typhoons, hurricanes and dust devils. Based on the Navier-Stokes equation with proper complex plasma conditions we analyze as much as possible in a universal way the vortex structure and clarifies the role of the controlling parameters like flow velocity and external magnetic field. 1. G. E. Morfill,H. M. Thomas, U. Konopka,H. Rothermel, M. Zuzic, A. Ivlev, and J. Goree, Phys,. Rev. Lett. 83, 1598 (1999). 2. E. Nebbat and R. Annou, Phys. Plasmas 17, 093702 (2010). 3. Y. Saitou and O. Ishihara, Phys. Rev. Lett. 111, 185003 (2013). 4. V. N. Tsytovich and N. G. Gusein-zade, Plasma Phys. Rep. 39, 515 (2013).

  2. The catalytic role of uranyl in formation of polycatechol complexes

    PubMed Central

    2011-01-01

    To better understand the association of contaminant uranium with natural organic matter (NOM) and the fate of uranium in ground water, spectroscopic studies of uranium complexation with catechol were conducted. Catechol provides a model for ubiquitous functional groups present in NOM. Liquid samples were analyzed using Raman, FTIR, and UV-Vis spectroscopy. Catechol was found to polymerize in presence of uranyl ions. Polymerization in presence of uranyl was compared to reactions in the presence of molybdate, another oxyion, and self polymerization of catechol at high pH. The effect of time and dissolved oxygen were also studied. It was found that oxygen was required for self-polymerization at elevated pH. The potential formation of phenoxy radicals as well as quinones was monitored. The benzene ring was found to be intact after polymerization. No evidence for formation of ether bonds was found, suggesting polymerization was due to formation of C-C bonds between catechol ligands. Uranyl was found to form outer sphere complexes with catechol at initial stages but over time (six months) polycatechol complexes were formed and precipitated from solution (forming humic-like material) while uranyl ions remained in solution. Our studies show that uranyl acts as a catalyst in catechol-polymerization. PMID:21396112

  3. Classic reaction kinetics can explain complex patterns of antibiotic action

    PubMed Central

    zur Wiesch, P. Abel; Abel, S.; Gkotzis, S.; Ocampo, P.; Engelstädter, J.; Hinkley, T.; Magnus, C.; Waldor, M. K.; Udekwu, K.; Cohen, T.

    2015-01-01

    Finding optimal dosing strategies for treating bacterial infections is extremely difficult, and improving therapy requires costly and time-intensive experiments. To date, an incomplete mechanistic understanding of drug effects has limited our ability to make accurate quantitative predictions of drug-mediated bacterial killing and impeded the rational design of antibiotic treatment strategies. Three poorly understood phenomena complicate predictions of antibiotic activity: post-antibiotic growth suppression, density-dependent antibiotic effects, and persister cell formation. Here, we show that chemical binding kinetics alone are sufficient to explain these three phenomena, using single cell data and time-kill curves of Escherichia coli and Vibrio cholerae exposed to a variety of antibiotics in combination with a theoretical model that links chemical reaction kinetics to bacterial population biology. Our model reproduces existing observations, has a high predictive power across different experimental setups (R2= 0.86), and makes several testable predictions, which we verified in new experiments and by analysing published data from a clinical trial on tuberculosis therapy. While a variety of biological mechanisms have previously been invoked to explain post-antibiotic growth suppression, density-dependent antibiotic effects, and especially persister cell formation, our findings reveal that a simple model which considers only binding kinetics provides a parsimonious and unifying explanation for these three complex, phenotypically distinct behaviours. Current antibiotic and other chemotherapeutic regimens are often based on trial-and-error or expert opinion. Our ‘chemical reaction kinetics’-based approach may inform new strategies, that are based on rational design. PMID:25972005

  4. Classic reaction kinetics can explain complex patterns of antibiotic action.

    PubMed

    Abel Zur Wiesch, Pia; Abel, Sören; Gkotzis, Spyridon; Ocampo, Paolo; Engelstädter, Jan; Hinkley, Trevor; Magnus, Carsten; Waldor, Matthew K; Udekwu, Klas; Cohen, Ted

    2015-05-13

    Finding optimal dosing strategies for treating bacterial infections is extremely difficult, and improving therapy requires costly and time-intensive experiments. To date, an incomplete mechanistic understanding of drug effects has limited our ability to make accurate quantitative predictions of drug-mediated bacterial killing and impeded the rational design of antibiotic treatment strategies. Three poorly understood phenomena complicate predictions of antibiotic activity: post-antibiotic growth suppression, density-dependent antibiotic effects, and persister cell formation. We show that chemical binding kinetics alone are sufficient to explain these three phenomena, using single-cell data and time-kill curves of Escherichia coli and Vibrio cholerae exposed to a variety of antibiotics in combination with a theoretical model that links chemical reaction kinetics to bacterial population biology. Our model reproduces existing observations, has a high predictive power across different experimental setups (R(2) = 0.86), and makes several testable predictions, which we verified in new experiments and by analyzing published data from a clinical trial on tuberculosis therapy. Although a variety of biological mechanisms have previously been invoked to explain post-antibiotic growth suppression, density-dependent antibiotic effects, and especially persister cell formation, our findings reveal that a simple model that considers only binding kinetics provides a parsimonious and unifying explanation for these three complex, phenotypically distinct behaviours. Current antibiotic and other chemotherapeutic regimens are often based on trial and error or expert opinion. Our "chemical reaction kinetics"-based approach may inform new strategies, which are based on rational design. PMID:25972005

  5. Formation of mesic nuclei by (γ,p) reactions

    NASA Astrophysics Data System (ADS)

    Nagahiro, H.; Jido, D.; Hirenzaki, S.

    2005-10-01

    We present a theoretical study on formation rates of η and ω meson-nucleus systems induced by (γ,p) reactions on nuclear targets at ideal recoilless condition. We find that the smaller distortion effect in the (γ,p) reaction enables us to investigate properties of the mesons created deeply inside nucleus more clearly. We also consider excitation of scalar-isoscalar (σ) mode in nucleus in order to investigate spectral enhancement around two-pion threshold caused by partial restoration of chiral symmetry. We conclude that valuable information of meson-nucleus interactions can be extracted from global structure of the missing mass spectra in the (γ,p) reaction.

  6. EXFOR SYSTEMS MANUAL NUCLEAR REACTION DATA EXCHANGE FORMAT.

    SciTech Connect

    MCLANE,V.; NUCLEAR DATA CENTER NETWORK

    2000-05-19

    EXFOR is an exchange format designed to allow transmission of nuclear reaction data between the members of the Nuclear Data Centers Network. This document has been written for use by the members of the Network and includes matters of procedure and protocol, as well as detailed rules for the compilation of data. Users may prefer to consult EXFOR Basics' for a brief description of the format.

  7. The reactions of pyridinyl thioesters with triiron dodecacarbonyl: their novel diiron carbonyl complexes and mechanistic investigations.

    PubMed

    Long, Li; Xiao, Zhiyin; Zampella, Giuseppe; Wei, Zhenhong; De Gioia, Luca; Liu, Xiaoming

    2012-08-21

    Reaction of Fe(3)(CO)(12) with pyridinyl thioester ligand PyCH(2)SCOCH(3) (L(1), Py = pyridin-2-yl) produced complex, [Fe(2)(κ-COCH(3))(μ-SCH(2)Py)(CO)(5)] (1) (PyCH(2)S = pyridin-2-ylmethanethiolate). When complex 1 reacted with PPh(3), a monosubstituted complex, [Fe(2)(κ-COCH(3))(μ-SCH(2)Py)(CO)(4)PPh(3)] (2), was derived. Reaction of the same precursor with analogous thioester ligand PyCH(2)SCOPy (L(2)) generated three novel diiron complexes, [Fe(2)(κ-Py)(μ-SCH(2)Py)(CO)(5)] (3), [Fe(2)(κ-Py)'(μ-SCH(2)Py)(CO)(5)] (4), and [Fe(2)(κ-Py)(μ-SCH(2)Py)(CO)(6)] (5). Complexes 3 and 4 are structural isomers. Complex 5 could be converted into complex 4 but the conversion from complex 5 to the isomer 3 was not observed. All the five complexes were fully characterised using FTIR, NMR, and other techniques. Their structures were determined using X-ray single crystal diffraction analysis. The oxidative formation of complexes 1, 3, 4, and 5 involved C-S and/or C-C bonds cleavages. To probe possible mechanisms for these cleavages, DFT calculations were performed. From the calculations, viable reaction pathways leading to the formation of all the isolated products were delineated. The results of the theoretic calculations also allowed rationalisation of the experimental observations. PMID:22751866

  8. Multiantenna artificial photosynthetic reaction center complex.

    PubMed

    Terazono, Yuichi; Kodis, Gerdenis; Liddell, Paul A; Garg, Vikas; Moore, Thomas A; Moore, Ana L; Gust, Devens

    2009-05-21

    In order to ensure efficient utilization of the solar spectrum, photosynthetic organisms use a variety of antenna chromophores to absorb light and transfer excitation to a reaction center, where photoinduced charge separation occurs. Reported here is a synthetic molecular heptad that features two bis(phenylethynyl)anthracene and two borondipyrromethene antennas linked to a hexaphenylbenzene core that also bears two zinc porphyrins. A fullerene electron acceptor self-assembles to both porhyrins via dative bonds. Excitation energy is transferred very efficiently from all four antennas to the porphyrins. Singlet-singlet energy transfer occurs both directly and by a stepwise funnel-like pathway wherein excitation moves down a thermodynamic gradient. The porphyrin excited states donate an electron to the fullerene with a time constant of 3 ps to generate a charge-separated state with a lifetime of 230 ps. The overall quantum yield is close to unity. In the absence of the fullerene, the porphyrin excited singlet state donates an electron to a borondipyrromethene on a slower time scale. This molecule demonstrates that by incorporating antennas, it is possible for a molecular system to harvest efficiently light throughout the visible from ultraviolet wavelengths out to approximately 650 nm. PMID:19438278

  9. Reaction of (mu-oxo)diiron(III) core with CO2 in N-methylimidazole: formation of mono(mu-carboxylato)(mu-oxo)diiron(III) complexes with N-methylimidazole as ligands.

    PubMed

    Marlin, Dana S; Olmstead, Marilyn M; Mascharak, Pradip K

    2003-03-10

    Several iron(III) complexes with N-methylimidazole (N-MeIm) as the ligand have been synthesized by using N-MeIm as the solvent. Under anaerobic conditions, [Fe(N-MeIm)(6)](ClO(4))(3) (1) reacts with stoichiometric amounts of water in N-MeIm to afford the (mu-oxo)diiron(III) complex, [Fe(2)(mu-O)(N-MeIm)(10)](ClO(4))(4) (3). Exposure of a solution of 3 in N-MeIm to stoichiometric and excess CO(2) gives rise to the (mu-oxo)(mu-carboxylato)diiron(III) species [Fe(2)(mu-O)(mu-HCO(2))(N-MeIm)(8)](ClO(4))(3) (4) and the methyl carbonate complex [Fe(2)(mu-O)(mu-CH(3)OCO(2))(N-MeIm)(8)](ClO(4))(3) (5), respectively. Formation of the formato-bridged complex 4 upon fixation of CO(2) by 3 in N-MeIm is unprecedentated. Methyl transfer from N-MeIm to a bicarbonato-bridged (mu-oxo)diiron(III) intermediate appears to give rise to 5. Complex 3 is a good starting material for the synthesis of (mu-oxo)mono(mu-carboxylato)diiron(III) species [Fe(2)(mu-O)(mu-RCO(2))(N-MeIm)(8)](ClO(4))(3) (where R = H (4), CH(3) (6), or C(6)H(5) (7)); addition of the respective carboxylate ligand in stoichiometric amount to a solution of 3 in N-MeIm affords these complexes in high yields. Attempts to add a third bridge to complexes 4, 6, and 7 to form the (mu-oxo)bis(mu-carboxylato)diiron(III) species result in the isolation of the previously known triiron(III) mu-eta(3)-oxo clusters [[Fe(mu-RCO(2))(2)(N-MeIm)](3)O](ClO(4)) (8). The structures of 3, 4, 6, and 7 allow one, for the first time, to inspect the various features of the [Fe(2)(mu-O)(mu-RCO(2))](3+) moiety with no strain from the ligand framework. PMID:12611539

  10. Effect of inclusion complex on nitrous acid reaction with flavonoids

    NASA Astrophysics Data System (ADS)

    Khalafi, Lida; Rafiee, Mohammad; Sedaghat, Sajjad

    2011-10-01

    The kinetic of the nitrous acid reactions with quercetin and catechin has been studied using spectrophotometric method in aqueous solution. The results show that these antioxidants participate in oxidation reactions with nitrous acid which is derived from protonation of nitrite ion in mild acidic conditions. Corresponding o-quinones as relatively stable products were detected by spectrophotometric techniques. pH dependence of the reactions has been examined and the rate constants of reactions were obtained by non-linear fitting of kinetic profiles. The effect of β-cyclodextrin on the oxidation pathway was another object of this study. It is shown that β-cyclodextrin has an inhibitory effect on the oxidation reaction. The rate constants of oxidation reactions for complexed forms and their stability constants were obtained based on changes in the reaction rates as a function of β-cyclodextrin concentration.

  11. A complex reaction time study (Sternberg) in space flight

    NASA Technical Reports Server (NTRS)

    Thornton, W.; Uri, John; Moore, Tom

    1993-01-01

    Simple and complex (Sternberg) reaction time studies were flown on three and seven day Shuttle flights in 1985. Three subjects did selftesting with an onboard handheld calculator without difficulty. There was little change in simple reaction time. One subject demonstrated a decrease in the processing rate during space motion sickness while a second exhibited an increase in complex reaction time without a change in processing rate during a period of high work load. The population was too small to demonstrate significant changes. This study demonstrates the ease and practicality of such measurements and indicates the potential value of such studies in space.

  12. Fluid pressure and reaction zone formation at a lithological interface

    NASA Astrophysics Data System (ADS)

    Malvoisin, Benjamin; Podladchikov, Yuri

    2014-05-01

    Chemical composition variations in reaction zones between two distinct lithologies are generally interpreted in terms of chemical potential gradients and diffusion process. Concentration profiles can then be used to quantify the species diffusion coefficients or the time scale of geological events. However, chemical potential gradients are also functions of temperature and pressure and local variations of these parameters can thus potentially modify the diffusion process. In northern Corsica, a centimeter scale reaction zone formed under blueschist conditions at a serpentinite - marble contact of sedimentary origin. Three sub-zones having chemical compositions evolving from one rock end-member to another divide the reaction zone along sharp interfaces. At the reaction zone - marble interface, marble decarbonation occurs to form wollastonite and carbonaceous matter. Thermodynamic calculations for this reaction and the respective increase in density of 25 % and 7 % in the bulk rock and in the garnet minerals are interpreted as records of a pressure gradient during reaction zone formation. Moreover, the formation of a volatile-free sub-zone in the reaction zone from reaction between the H2O-bearing serpentinite and the CO2-bearing marble released fluids at the contact. The impact of such a release on the fluid pressure was modelled by considering the effects of both the rock compaction and the transport of fluid by hydraulic diffusion. Modelling results indicates that > 0.5 GPa fluid overpressure can be generated at the contact if devolatilization rates are of the order of the one experimentally measured (> 10-5 kg of fluid/m3 of rock/s). The resulting pressure gradient is of the order of magnitude of the one necessary to counter-balance the effect on chemical potential of the chemical composition variations across the contact. Finally, after the reaction has run to completion, the model predicts that fluid rapidly diffuses away from the interface which thus stops

  13. Formation of superheavy nuclei in cold fusion reactions

    SciTech Connect

    Feng Zhaoqing; Jin Genming; Li Junqing; Scheid, Werner

    2007-10-15

    Within the concept of the dinuclear system (DNS), a dynamical model is proposed for describing the formation of superheavy nuclei in complete fusion reactions by incorporating the coupling of the relative motion to the nucleon transfer process. The capture of two heavy colliding nuclei, the formation of the compound nucleus, and the de-excitation process are calculated by using an empirical coupled channel model, solving a master equation numerically and applying statistical theory, respectively. Evaporation residue excitation functions in cold fusion reactions are investigated systematically and compared with available experimental data. Maximal production cross sections of superheavy nuclei in cold fusion reactions with stable neutron-rich projectiles are obtained. Isotopic trends in the production of the superheavy elements Z=110, 112, 114, 116, 118, and 120 are analyzed systematically. Optimal combinations and the corresponding excitation energies are proposed.

  14. Cadmium(II) complex formation with glutathione.

    PubMed

    Mah, Vicky; Jalilehvand, Farideh

    2010-03-01

    Complex formation between heavy metal ions and glutathione (GSH) is considered as the initial step in many detoxification processes in living organisms. In this study the structure and coordination between the cadmium(II) ion and GSH were investigated in aqueous solutions (pH 7.5 and 11.0) and in the solid state, using a combination of spectroscopic techniques. The similarity of the Cd K-edge and L(3)-edge X-ray absorption spectra of the solid compound [Cd(GS)(GSH)]ClO(4).3H(2)O, precipitating at pH 3.0, with the previously studied cysteine compound {Cd(HCys)(2).H(2)O}(2).H(3)O(+).ClO(4) (-) corresponds to Cd(S-GS)(3)O (dominating) and Cd(S-GS)(4) four-coordination within oligomeric complexes with mean bond distances of 2.51 +/- 0.02 A for Cd-S and 2.24 +/- 0.04 A for Cd-O. For cadmium(II) solutions (C (Cd(II)) approximately 0.05 M) at pH 7.5 with moderate excess of GSH (C (GSH)/C (Cd(II)) = 3.0-5.0), a mix of Cd(S-GS)(3)O (dominating) and Cd(S-GS)(4) species is consistent with the broad (113)Cd NMR resonances in the range 632-658 ppm. In alkaline solutions (pH 11.0 and C (GSH)/C (Cd(II)) = 2.0 or 3.0), two distinct peaks at 322 and 674 ppm are obtained. The first peak indicates six-coordinated mononuclear and dinuclear complexes with CdS(2)N(2)(N/O)(2) and CdSN(3)O(2) coordination in fast exchange, whereas the second corresponds to Cd(S-GS)(4) sites. At high ligand excess the tetrathiolate complex, Cd(S-GS)(4), characterized by a sharp delta((113)Cd) NMR signal at 677 ppm, predominates. The average Cd-S distance, obtained from the X-ray absorption spectra, varied within a narrow range, 2.49-2.53 A, for all solutions (pH 7.5 and 11.0) regardless of the coordination geometry. PMID:20035360

  15. Structure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Serine acetyltransferase (SAT) catalyzes the limiting reaction in plant and microbial biosynthesis of cysteine. In addition to its enzymatic function, SAT forms a macromolecular complex with O-acetylserine sulfhydrylase (OASS). Formation of the cysteine regulatory complex (CRC) is a critical biochem...

  16. Reactions of the simple nitroalkanes with hydroxide ion in water. Evidence for a complex mechanism.

    PubMed

    Li, Zhao; Cheng, Jin-Pei; Parker, Vernon D

    2011-06-21

    Conventional kinetic analysis of the reactions of nitromethane (NM), nitroethane (NE) and 2-nitropropane (2-NP) with hydroxide ion in water revealed that the reactions are complex and involve kinetically significant intermediates. Kinetic experiments at the isosbestic points where changes in reactant and product absorbance cancel indicate the evolution and decay of absorbance characteristic of the formation of reactive intermediates. The deviations from 1st-order kinetics were observed to increase with increasing extent of reaction and in the reactant order: NM < NE < 2-NP. The apparent deuterium kinetic isotope effects for proton/deuteron transfer approach unity near zero time and increased with time toward plateau values as the reaction kinetics reach steady state. It is proposed that the initially formed preassociation complexes are transformed to more intimate reactant complexes which can give products by two possible pathways. PMID:21519607

  17. Deduction of compound nucleus formation probability from the fragment angular distributions in heavy-ion reactions

    NASA Astrophysics Data System (ADS)

    Yadav, C.; Thomas, R. G.; Mohanty, A. K.; Kapoor, S. S.

    2015-07-01

    The presence of various fissionlike reactions in heavy-ion induced reactions is a major hurdle in the path to laboratory synthesis of heavy and super-heavy nuclei. It is known that the cross section of forming a heavy evaporation residue in fusion reactions depends on the three factors—the capture cross section, probability of compound nucleus formation PCN, and the survival probability of the compound nucleus against fission. As the probability of compound nucleus formation, PCN is difficult to theoretically estimate because of its complex dependence on several parameters; attempts have been made in the past to deduce it from the fission fragment anisotropy data. In the present work, the fragment anisotropy data for a number of heavy-ion reactions are analyzed and it is found that deduction of PCN from the anisotropy data also requires the knowledge of the ratio of relaxation time of the K degree of freedom to pre-equilibrium fission time.

  18. Coupling and Reactions of 5-Hydroxyconiferyl Alcohol in Lignin Formation.

    PubMed

    Elder, Thomas; Berstis, Laura; Beckham, Gregg T; Crowley, Michael F

    2016-06-15

    The catechol alcohols, caffeyl and 5-hydroxyconiferyl alcohol, may be incorporated into lignin either naturally or through genetic manipulation. Due to the presence of o-OH groups, these compounds form benzodioxanes, a departure from the interunit connections found in lignins derived from the cinnamyl alcohols. In nature, lignins composed of caffeyl and 5-hydroxyconiferyl alcohol are linear homopolymers and, as such, may have properties that make them amenable for use in value-added products, such as lignin-based carbon fibers. In the current work, results from density functional theory calculations for the reactions of 5-hydroxyconiferyl alcohol, taking stereochemistry into account, are reported. Dehydrogenation and quinone methide formation are found to be thermodynamically favored for 5-hydroxyconiferyl alcohol, over coniferyl alcohol. The comparative energetics of the rearomatization reactions suggest that the formation of the benzodioxane linkage is under kinetic control. Ring-opening reactions of the benzodioxane groups show that the bond dissociation enthalpy of the α-O cleavage reaction is lower than that of the β-O reaction. The catechol lignins represent a novel form of the polymer that may offer new opportunities for bioproducts and genetic targets. PMID:27236926

  19. A new metalation complex for organic synthesis and polymerization reactions

    NASA Technical Reports Server (NTRS)

    Hirshfield, S. M.

    1971-01-01

    Organometallic complex of N,N,N',N' tetramethyl ethylene diamine /TMEDA/ and lithium acts as metalation intermediate for controlled systhesis of aromatic organic compounds and polymer formation. Complex of TMEDA and lithium aids in preparation of various organic lithium compounds.

  20. Diffusion impregnation of alloys under conditions of complex formation

    SciTech Connect

    Pavlina, V.S.; Matychak, Y.S.

    1985-05-01

    In most cases, diffusion impregnation of alloys with elements for the purpose of improving their service properties occurs with chemical interaction with the constituents of the base. Such processes are described within the limits of the model of reaction diffusion, assuming the formation and growth of new continuous layers by the Fick equation. At the same time, instantaneous reaction of the elements is assumed, as the result of which the rate of the whole process is limited by diffusion. Together with this, diffusion processes and chemical transformations occur simultaneously, as the result of which continuous phases are not formed (internal oxidation, nitriding, etc.). The purpose of this work was an analytical investigation of diffusion impregnation by element A from a constant source of a flat specimen initially uniformly alloyed with a mobile impurity B. The model presented makes it possible to investigate the initial stage of homogeneous formation of complexes and to reveal their influence on the kinetics of redistribution of the diffusing elements.

  1. f 1 (1285) formation in photon-photon fusion reactions

    NASA Astrophysics Data System (ADS)

    Aihara, H.; Alston-Garnjost, M.; Avery, R. E.; Barbaro-Galtieri, A.; Barker, A. R.; Barnett, B. A.; Bauer, D. A.; Bay, A.; Bengtsson, H.-U.; Bobbink, G. J.; Buchanan, C. D.; Buijs, A.; Caldwell, D. O.; Chao, H.-Y.; Chun, S.-B.; Clark, A. R.; Cowan, G. D.; Crane, D. A.; Dahl, O. I.; Daoudi, M.; Derby, K. A.; Eastman, J. J.; Eberhard, P. H.; Edberg, T. K.; Eisner, A. M.; Enomoto, R.; Erné, F. C.; Fairfield, K. H.; Hauptman, J. M.; Hofmann, W.; Hylen, J.; Kamae, T.; Kaye, H. S.; Kenney, R. W.; Khacheryan, S.; Kofler, R. R.; Langeveld, W. G. J.; Layter, J. G.; Lin, W. T.; Linde, F. L.; Loken, S. C.; Lu, A.; Lynch, G. R.; Madaras, R. J.; Magnuson, B. D.; Masek, G. E.; Mathis, L. G.; Matthews, J. A. J.; Maxfield, S. J.; Miller, E. S.; Moses, W.; Nygren, D. R.; Oddone, P. J.; Paar, H. P.; Park, S. K.; Pellett, D. E.; Pripstein, M.; Ronan, M. T.; Ross, R. R.; Rouse, F. R.; Schwitkis, K. A.; Sens, J. C.; Shapiro, G.; Shen, B. C.; Slater, W. E.; Smith, J. R.; Steinman, J. S.; Stephens, R. W.; Stevenson, M. L.; Stork, D. H.; Strauss, M. G.; Sullivan, M. K.; Takahashi, T.; Toutounchi, S.; Van Tyen, R.; Van Dalen, G. J.; Vernon, W.; Wagner, W.; Wang, E. M.; Wang, Y.-X.; Wenzel, W. A.; Wolf, Z. R.; Yamamoto, H.; Yellin, S. J.; Zeitlin, C.; TPC/Two-Gamma Collaboration

    1988-07-01

    We have observed formation of the f 1 (1285) in the reaction e +e -→e +e -π+π-η( η→ γγ). Its γγ ∗ width is determined in several Q2 bins. The γγ coupling parameter for the f 1 (1285) is found to be 2.4±0.5±0.5 keV. This value is compared to that for the X (1420), another J=1 state formed in γγ fusion reactions, which may belong to the same meson nonet.

  2. Direct computer simulation of ferredoxin and FNR complex formation in solution

    NASA Astrophysics Data System (ADS)

    Kovalenko, I. B.; Diakonova, A. N.; Abaturova, A. M.; Riznichenko, G. Yu; Rubin, A. B.

    2010-06-01

    Ferredoxin reduced by Photosystem I in light serves as an electron donor for the reduction of NADP+ to NADPH, and this reaction is catalyzed by enzyme ferredoxin:NADP+-reductase (FNR). Kinetics and mechanisms of this reaction have been extensively studied experimentally by site-specific mutagenesis, laser flash photolysis and stopped-flow methods. We have applied a method of multiparticle computer simulation to study the effects of electrostatic interactions upon the reaction rate of Fd-FNR complex formation. Using the model we calculated rate constants of Fd-FNR complex formation for the wild-type proteins and some mutant forms of FNR at different values of ionic strength. Simulation revealed that electrostatic interactions play an important role in Fd-FNR complex formation and define its specificity.

  3. Direct computer simulation of ferredoxin and FNR complex formation in solution.

    PubMed

    Kovalenko, I B; Diakonova, A N; Abaturova, A M; Riznichenko, G Yu; Rubin, A B

    2010-01-01

    Ferredoxin reduced by Photosystem I in light serves as an electron donor for the reduction of NADP(+) to NADPH, and this reaction is catalyzed by enzyme ferredoxin:NADP(+)-reductase (FNR). Kinetics and mechanisms of this reaction have been extensively studied experimentally by site-specific mutagenesis, laser flash photolysis and stopped-flow methods. We have applied a method of multiparticle computer simulation to study the effects of electrostatic interactions upon the reaction rate of Fd-FNR complex formation. Using the model we calculated rate constants of Fd-FNR complex formation for the wild-type proteins and some mutant forms of FNR at different values of ionic strength. Simulation revealed that electrostatic interactions play an important role in Fd-FNR complex formation and define its specificity. PMID:20453296

  4. Reaction of an Iron(IV) Nitrido Complex with Cyclohexadienes: Cycloaddition and Hydrogen-Atom Abstraction

    PubMed Central

    2015-01-01

    The iron(IV) nitrido complex PhB(MesIm)3Fe≡N reacts with 1,3-cyclohexadiene to yield the iron(II) pyrrolide complex PhB(MesIm)3Fe(η5-C4H4N) in high yield. The mechanism of product formation is proposed to involve sequential [4 + 1] cycloaddition and retro Diels–Alder reactions. Surprisingly, reaction with 1,4-cyclohexadiene yields the same iron-containing product, albeit in substantially lower yield. The proposed reaction mechanism, supported by electronic structure calculations, involves hydrogen-atom abstraction from 1,4-cyclohexadiene to provide the cyclohexadienyl radical. This radical is an intermediate in substrate isomerization to 1,3-cyclohexadiene, leading to formation of the pyrrolide product. PMID:25068927

  5. Light induced electron transfer reactions of metal complexes

    SciTech Connect

    Sutin, N.; Creutz, C.

    1980-01-01

    Properties of the excited states of tris(2,2'-bipyridine) and tris(1,10-phenanthroline) complexes of chromium(III), iron(II), ruthenium(II), osmium(II), rhodium(III), and iridium(III) are described. The electron transfer reactions of the ground and excited states are discussed and interpreted in terms of the driving force for the reaction and the distortions of the excited states relative to the corresponding ground states. General considerations relevant to the conversion of light into chemical energy are presented and progress in the use of polypyridine complexes to effect the light decomposition of water into hydrogen and oxygen is reviewed.

  6. Efficient stochastic simulations of complex reaction networks on surfaces.

    PubMed

    Barzel, Baruch; Biham, Ofer

    2007-10-14

    Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are negligible and the reaction rates can be evaluated using rate equations, which are based on the mean-field approximation. However, in case that the surface is partitioned into a large number of disconnected microscopic domains, the number of reactants in each domain becomes small and it strongly fluctuates. This is, in fact, the situation in the interstellar medium, where some crucial reactions take place on the surfaces of microscopic dust grains. In this case rate equations fail and the simulation of surface reactions requires stochastic methods such as the master equation. However, in the case of complex reaction networks, the master equation becomes infeasible because the number of equations proliferates exponentially. To solve this problem, we introduce a stochastic method based on moment equations. In this method the number of equations is dramatically reduced to just one equation for each reactive species and one equation for each reaction. Moreover, the equations can be easily constructed using a diagrammatic approach. We demonstrate the method for a set of astrophysically relevant networks of increasing complexity. It is expected to be applicable in many other contexts in which problems that exhibit analogous structure appear, such as surface catalysis in nanoscale systems, aerosol chemistry in stratospheric clouds, and genetic networks in cells. PMID:17935419

  7. Microkinetics of oxygenate formation in the Fischer-Tropsch reaction.

    PubMed

    van Santen, Rutger A; Ghouri, Minhaj; Hensen, Emiel M J

    2014-06-01

    Microkinetics simulations are presented on the intrinsic activity and selectivity of the Fischer-Tropsch reaction with respect to the formation of long chain oxygenated hydrocarbons. Two different chain growth mechanisms are compared: the carbide chain growth mechanism and the CO insertion chain growth mechanism. The microkinetics simulations are based on quantum-chemical data on reaction rate parameters of the elementary reaction steps of the Fischer-Tropsch reaction available in the literature. Because the overall rate constant of chain growth remains too low the CO insertion chain growth mechanism is not found to produce higher hydrocarbons, except for ethylene and acetaldehyde or the corresponding hydrogenated products. According to the carbide mechanism available quantum-chemical data are consistent with high selectivity to long chain oxygenated hydrocarbon production at low temperature. The anomalous initial increase with temperature of the chain growth parameter observed under such conditions is reproduced. It arises from the competition between the apparent rate of C-O bond activation to produce "CHx" monomers to be inserted into the growing hydrocarbon chain and the rate of chain growth termination. The microkinetics simulations data enable analysis of selectivity changes as a function of critical elementary reaction rates such as the rate of activation of the C-O bond of CO, the insertion rate of CO into the growing hydrocarbon chain or the rate constant of methane formation. Simulations show that changes in catalyst site reactivity affect elementary reaction steps differently. This has opposing consequences for oxygenate production selectivity, so an optimizing compromise has to be found. The simulation results are found to be consistent with most experimental data available today. It is concluded that Fischer-Tropsch type catalysis has limited scope to produce long chain oxygenates with high yield, but there is an opportunity to improve the yield of C2

  8. Effect of reaction time on the formation of disinfection byproducts

    USGS Publications Warehouse

    Rathbun, R.E.

    1997-01-01

    The effect of reaction time on the trihalomethane and nonpurgeable total organic-halide formation potentials was determined by chlorinating water samples from the Mississippi, Missouri, and Ohio Rivers. Samples were collected for three seasons at 12 locations on the Mississippi from Minneapolis, Minnesota, to New Orleans, Louisiana, and on the Missouri and Ohio 1.6 kilometers above their confluences with the Mississippi. Both types of compounds formed rapidly during the initial stages of the reaction-time period, with formation rates decreasing with time. The ratio of the nonpurgeable total organic-halide and trihalomethane concentrations decreased with time, with the nonpurgeable total organic-halide compounds forming faster during the first stages of the time period and the trihalomethane compounds forming faster during the latter stages of the time period. Variation with distance along the Mississippi River of the formation rates approximately paralleled the variation of the dissolved organic carbon concentration, indicating that the rates of formation, as well as the concentrations of the compounds formed, depended on the dissolved organic carbon concentration.

  9. Acid-catalyzed Heterogeneous Reactions in SOA Formation

    NASA Astrophysics Data System (ADS)

    Ng, N.; Keywood, M.; Varutbangkul, V.; Gao, S.; Loewer, E.; Surratt, J.; Richard, F. C.; John, S. H.

    2003-12-01

    The importance of heterogeneous reactions in secondary organic aerosol (SOA) formation has recently excited a great deal of interest in the aerosol community. Jang and Kamens (2001) showed enhanced aerosol yield from aldehydes, which can be produced by atmospheric photochemical reactions, in the presence of acidic seed. They suggest that the carbonyl functional groups of the aldehydes further react in the aerosol phase via hydration, polymerization, and hemiacetal/acetal formation with alcohols at an accelerated rate in the presence of acid. Jang et al. (2003) demonstrated similar results using a flow reactor and Czoschke et al. (in press) qualitatively showed increased yields for isoprene and alpha-pinene ozonolysis in the presence of acidic seed. While these findings are intriguing and important, the conditions under which the experiments were carried out were atmospherically unrealistic. A series of SOA formation experiments have been carried out in the Caltech Indoor Chamber Facility, which is comprised of dual 28 m3 FEP Teflon chambers, with the flexibility to carry out both dark ozonolysis and photochemical OH oxidation reactions. Cycloheptene and alpha-pinene were oxidized in the presence of neutral seed under dry (<10% RH) and humid (50% RH) conditions and in the presence of acidic seed under humid (50% RH) conditions. The SOA yields for these experiments will be presented, and the extent of the influence of acid-catalyzed reactions on SOA yield will be discussed. Reference List 1. Cocker, D. R. III. and R. C. Flagan and J. H. Seinfeld, State-of-the-art chamber facility for studying atmospheric aerosol chemistry, Environmental Science and Technology, 35, 2594-2601, 2001. 2. Czoschke, N. M., M. Jang, and R. M. Kamens, Effect of acid seed on biogenic sceondary organic aerosol growth, Atmospheric Environment, In press. 3. Jang, M., S. Lee, and R. M. Kamens, Organic aerosol growth by acid-catalyzed heterogeneous reactions of octanal in a flow reactor

  10. A quantitative approach to understanding amphibole reaction rims: Texture, mineralogy, and processes of formation

    NASA Astrophysics Data System (ADS)

    De Angelis, S. H.; Larsen, J. F.; Coombs, M. L.; Dunn, A.

    2012-12-01

    Amphibole is an important mineral present in many calc-alkaline volcanic deposits. A hydrous phase, volcanic amphibole is only stable at pressures greater than 100 MPa (approx. 4 km) and in melts containing at least 4 wt % H2O. When removed from their thermal and barometric stability field, amphiboles decompose to form aggregate rims of anhydrous minerals. Reaction rim thicknesses have been used to estimate timescales and rates of magma ascent, important parameters in determining eruptive style. However, the textures and mineralogy of reaction rims are complex; multiple forcing factors, such as heating and decompression, are responsible for their formation. Few studies have performed in-depth, systematic, and quantitative investigations of reaction rim textures and mineralogy: as a result, amphibole reaction rims are poorly understood. Based on natural reaction rims from Augustine Volcano Alaska, we have developed a new crystallization kinetics model for reaction rim formation in which the differences in reaction rim textures represent different degrees of forcing away from equilibrium. We present the results of an experimental study used to test this model. We performed experiments using a sintered high-silica andesite glass from the 2006 eruption of Augustine volcano. The starting powder was seeded with unrimmed amphibole phenocrysts. After at least 24 hours of equilibration at Augustine storage conditions (140 MPa/ 860oC), experiments were heated or decompressed. The experimental series experiments took samples to differing degrees of thermal of barometric instability, over different time scales, ranging from 3 hours to several days. The resulting reaction rims were analyzed using a variety of analytical imaging and X-ray mapping techniques. Reaction rims thickened and became more texturally and mineralogically complex as a result of 1) greater time spent outside of stability and; 2) the magnitude of instability experienced.

  11. The Influence of Kinetics on the Formation of Complexes Between Mercury and Dissolved Organic Matter

    NASA Astrophysics Data System (ADS)

    Miller, C. L.; Gu, B.; Brooks, S.; Southworth, G.

    2008-12-01

    Strong complexes between mercury (Hg) and dissolved organic matter (DOM) dominate the speciation of Hg(II) in most oxygenated aquatic systems but the rate of formation of these complexes has not be thoroughly investigated. Kinetic experiments were used to measure the formation rate of strong Hg(II)-DOM complexes in water collected from the Upper East Fork Poplar Creek (UEFPC) in Oak Ridge, TN and in solution prepared using various DOM isolates. The loss of reactive mercury (HgR), defined as the amount of Hg reducible by stannous chloride (SnCl2), was used to examine the formation rates of strong Hg-DOM complexes which are nonreactive with SnCl2. We found that the formation of nonreactive Hg complexes followed first-order reaction kinetics, and the rate constant for the formation these complexes is similar both in creek water and solutions containing unfractionated DOM isolates ( ~4.8 day-1 ). C-18 Solid phase extractions were also used to examine the association of Hg(II) with different fractions of DOM as the mercury transformed from reactive, inorganic complexes to strong Hg-DOM complexes. In both the UEFPC and in laboratory solutions containing Hg and an unfractionated DOM isolate, the complexation of Hg shifted from hydrophilic to hydrophobic complexes as the strong Hg-DOM complexes were formed. This study concludes that, while equilibrium models suggest that strong Hg-DOM complexes dominate the speciation of Hg under equilibrium conditions, the formation of these complexes is kinetically limited. The slow formation of strong Hg-DOM complexes may have important implications in understanding the cycling, transport and bioavailability of Hg in systems such as the UEFPC with varying input sources of organic and inorganic Hg complexes.

  12. An autocatalytic radical chain pathway in formation of an iron(IV)-oxo complex by oxidation of an iron(II) complex with dioxygen and isopropanol.

    PubMed

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

    2013-03-28

    Evidence of an autocatalytic radical chain pathway has been reported in formation of a non-heme iron(IV)-oxo complex by oxidation of an iron(II) complex with dioxygen and isopropanol in acetonitrile at 298 K. The radical chain reaction is initiated by hydrogen abstraction from isopropanol by the iron(IV)-oxo complex. PMID:23423328

  13. Kinetics of enol formation from reaction of OH with propene.

    PubMed

    Huynh, Lam K; Zhang, Hongzhi R; Zhang, Shaowen; Eddings, Eric; Sarofim, Adel; Law, Matthew E; Westmoreland, Phillip R; Truong, Thanh N

    2009-04-01

    Kinetics of enol generation from propene has been predicted in an effort to understand the presence of enols in flames. A potential energy surface for reaction of OH with propene was computed by CCSD(T)/cc-pVDZ//B3LYP/cc-pVTZ calculations. Rate constants of different product channels and branching ratios were then calculated using the Master Equation formulation (J. Phys. Chem. A 2006, 110, 10528). Of the two enol products, ethenol is dominant over propenol, and its pathway is also the dominant pathway for the OH + propene addition reactions to form bimolecular products. In the temperature range considered, hydrogen abstraction dominated propene + OH consumption by a branching ratio of more than 90%. Calculated rate constants of enol formation were included in the Utah Surrogate Mechanism to model the enol profile in a cyclohexane premixed flame. The extended model shows consistency with experimental data and gives 5% contribution of ethenol formation from OH + propene reaction, the rest coming from ethene + OH. PMID:19271758

  14. Compound nucleus formation in reactions between massive nuclei: Fusion barrier

    SciTech Connect

    Antonenko, N.V.; Cherepanov, E.A.; Nasirov, A.K.; Permjakov, V.P.; Volkov, V.V.

    1995-05-01

    The evaporation residue cross sections {sigma}{sub ER} in reactions between massive nuclei have been analyzed within different models of complete fusion. The calculations in the framework of the optical model, the surface friction model, and the macroscopic dynamic model can give the results which are by few orders of magnitude different from experimental data. This takes place due to neglect of the competition between complete fusion and quasifission. A possible mechanism of compound nucleus formation in heavy-ion-induced reactions has been suggested. The analysis of the complete fusion of nuclei on the basis of dinuclear system approach has allowed one to reveal an important feature of the fusion process of massive nuclei, that is, the appearance of the fusion barrier during dinuclear system evolution to a compound nucleus. As a result, the competition between complete fusion and quasifission arises and strongly reduces the cross section of the compound nucleus formation. A model is proposed for calculation of this competition in a massive symmetric dinuclear system. This model is applied for collision energies above the Coulomb barrier. The {sigma}{sub ER} values calculated in the framework of dinuclear system approach seem to be close to the experimental data. For illustration the reactions {sup 100}Mo+{sup 100}Mo, {sup 110}Pd+{sup 110}Pd, and {sup 124}Sn+{sup 96}Zr have been considered.

  15. Chemical reaction and dust formation studies in laboratory hydrocarbon plasmas.

    NASA Astrophysics Data System (ADS)

    Hippler, Rainer; Majumdar, Abhijit; Thejaswini, H. C.

    Plasma chemical reaction studies with relevance to, e.g., Titan's atmosphere have been per-formed in various laboratory plasmas [1,2]. Chemical reactions in a dielectric barrier discharge at medium pressure of 250-300 mbar have been studied in CH4 /N2 and CH4 /Ar gas mixtures by means of mass spectrometry. The main reaction scheme is production of H2 by fragmenta-tion of CH4 , but also production of larger hydrocarbons like Cn Hm with n up to 10 including formation of different functional CN groups is observed. [1] A. Majumdar and R. Hippler, Development of dielectric barrier discharge plasma processing apparatus for mass spectrometry and thin film deposition, Rev. Sci. Instrum. 78, 075103 (2007) [2] H.T. Do, G. Thieme, M. Frühlich, H. Kersten, and R. Hippler, Ion Molecule and Dust Particle Formation in Ar/CH4 , Ar/C2 H2 and Ar/C3 H6 Radio-frequency Plasmas, Contrib. Plasma Phys. 45, No. 5-6, 378-384 (2005)

  16. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zahn, Dirk

    2004-05-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C⋯O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate.

  17. Arylpalladium Phosphonate Complexes as Reactive Intermediates in Phosphorus-Carbon Bond Forming Reactions

    SciTech Connect

    Kohler, Mark C.; Grimes, Thomas V.; Wang, Xiaoping; Cundari, Thomas R.; Stockland, Robert A. Jr.

    2009-01-01

    Phosphorus-carbon bond formation from discrete transition metal complexes have been investigated through a combination of synthetic, spectroscopic, crystallographic, and computational methods. Reactive intermediates of the type (diphosphine)Pd(aryl)(P(O)(OEt)(2)) have been prepared, characterized, and studied as possible intermediates in metal-mediated coupling reactions. Several of the reactive intermediates were characterized crystallographicaliy, and a discussion of the solid state structures is presented. In contrast to other carbon-heteroelement bond forming reactions, palladium complexes containing electron-donating substituents on the aromatic fragment exhibited faster rates of reductive elimination. Large bite angle diphosphine ligands induced rapid rates of elimination, while bipyridine and small bite angle diphosphine ligands resulted in much slower rates of elimination. An investigation of the effect of typical impurities on the elimination reaction was carried out. While excess diphosphine, pyridine, and acetonitrile had little effect on the observed rate, the addition of water slowed the phosphorus-carbon bond forming reaction. Coordination of water to the complex was observed spectroscopically and crystallographically. Computational studies were utilized to probe the reaction pathways for P-C bond formation via Pd catalysis.

  18. Formation of superheavy elements in cold fusion reactions

    NASA Astrophysics Data System (ADS)

    Smolańczuk, Robert

    2001-04-01

    We calculate the formation cross sections of transactinides (superheavy elements), as well as heavy actinides (No and Lr), which have been or might be obtained in fusion reactions with the evaporation of only one neutron. We use both more realistic fusion barrier and survival probability of the compound nucleus in comparison with the original phenomenological model [Phys. Rev. C 59, 2634 (1999)] that prompted the Berkeley experiment on the synthesis of a new superheavy element 118 [Phys. Rev. Lett. 83, 1104 (1999)]. Calculations are performed for asymmetric and symmetric target-projectile combinations and for reactions with stable and radioactive-ion beams. The formation cross sections measured at GSI-Darmstadt for transactinides and heavy actinides, as well as that for superheavy element 118 reported by the LBNL-Berkeley group, are reproduced within a factor of 2.4, on average. Based on the obtained relatively large cross sections, we predict that optimal reactions with stable beams for the synthesis of so far unobserved superheavy elements 119, 120, and 121 are 209Bi(86Kr, 1n)294119, 208Pb(88Sr, 1n)295120, and 209Bi(88Sr, 1n)296121, respectively. This is because of the magic of both the target and the projectile that leads to larger Q value and, consequently, lower effective fusion barrier with larger transmission probability. The same effect is responsible for relatively large cross sections predicted for the symmetric reactions 136Xe(124Sn, 1n)259Rf, 136Xe(136Xe, 1n)271Hs,138Ba(136Xe, 1n)273110, and 140Ce(136Xe, 1n)275112. Although shell effects in the magic nuclei 124Sn, 136Xe, 138Ba, and 140Ce are not as strong as in 208Pb and 209Bi, they act on both the target and the projectile and lead to the prediction of measurable cross sections.

  19. First stage of CoSi{sub 2} formation during a solid-state reaction

    SciTech Connect

    Delattre, R.; Thomas, O.; Perrin-Pellegrino, C.; Rivero, C.; Simola, R.

    2014-12-28

    The kinetics of CoSi{sub 2} formation via a solid-state reaction between CoSi and single crystal Si has been the object of many studies in the past. Because of the importance of nucleation, complex kinetics has been reported. In this work, we investigate CoSi{sub 2} formation kinetics with in-situ diffraction during isothermal annealing of CoSi films on Si (100). In-situ measurements allow capturing the initial stage of CoSi{sub 2} formation. An initial t{sup 3/2} time-dependent evolution is observed and attributed to 3D growth of individual nuclei. This first regime is followed after the coalescence of the nuclei by a classical parabolic t{sup 1/2} one-dimensional film growth. We evidence a marked influence of the initial Co thickness (50 nm vs 10 nm) on the growth kinetics. A significant slowdown of the CoSi{sub 2} formation kinetics is observed for the thinnest film, whereas the activation energy remains the same. These results shine a new light on the complex formation kinetics of CoSi{sub 2} during solid-state reaction between CoSi and single crystal silicon and bring new knowledge about what occurs in the ultra-thin film regime, which is important for nanotechnologies.

  20. Formation of β-cyclodextrin complexes in an anhydrous environment.

    PubMed

    Sifaoui, Hocine; Modarressi, Ali; Magri, Pierre; Stachowicz-Kuśnierz, Anna; Korchowiec, Jacek; Rogalski, Marek

    2016-09-01

    The formation of inclusion complexes of β-cyclodextrin was studied at the melting temperature of guest compounds by differential scanning calorimetry. The complexes of long-chain n-alkanes, polyaromatics, and organic acids were investigated by calorimetry and IR spectroscopy. The complexation ratio of β-cyclodextrin was compared with results obtained in an aqueous environment. The stability and structure of inclusion complexes with various stoichiometries were estimated by quantum chemistry and molecular dynamics calculations. Comparison of experimental and theoretical results confirmed the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds. This finding gives new insight into the mechanism of formation of host-guest complexes and shows that hydrophobic interactions play a secondary role in this case. Graphical abstract The formation of complexes of β-cyclodextrin with selected n-alkanes, polyaromatics, and organic acids in an anhydrous environment is studied by differential scanning calorimetry, IR spectroscopy, and molecular modeling. The results obtained confirm the possible formation of multiple inclusion complexes with guest molecules capable of forming hydrogen bonds and give a new perspective on the mechanism of formation of host-guest complexes. PMID:27518085

  1. Reactivity of Gold Complexes towards Elementary Organometallic Reactions.

    PubMed

    Joost, Maximilian; Amgoune, Abderrahmane; Bourissou, Didier

    2015-12-01

    For a while, the reactivity of gold complexes was largely dominated by their Lewis acid behavior. In contrast to the other transition metals, the elementary steps of organometallic chemistry-oxidative addition, reductive elimination, transmetallation, migratory insertion-have scarcely been studied in the case of gold or even remained unprecedented until recently. However, within the last few years, the ability of gold complexes to undergo these fundamental reactions has been unambiguously demonstrated, and the reactivity of gold complexes was shown to extend well beyond π-activation. In this Review, the main achievements described in this area are presented in a historical context. Particular emphasis is set on mechanistic studies and structure determination of key intermediates. The electronic and structural parameters delineating the reactivity of gold complexes are discussed, as well as the remaining challenges. PMID:26768342

  2. Controlling energy transfer in ytterbium complexes: oxygen dependent lanthanide luminescence and singlet oxygen formation.

    PubMed

    Watkis, Andrew; Hueting, Rebekka; Sørensen, Thomas Just; Tropiano, Manuel; Faulkner, Stephen

    2015-11-01

    Pyrene-appended ytterbium complexes have been prepared using Ugi reactions to vary the chromophore-lanthanide separation. Formation of the ytterbium(iii) excited state is sensitised via both the singlet and triplet excited states of the chromophore. Energy transfer from the latter is relatively slow, and gives rise to oxygen-dependent luminescence. PMID:26346499

  3. N-Heterocyclic Carbene Complexes in Oxidation Reactions

    NASA Astrophysics Data System (ADS)

    Jurčík, Václav; Cazin, Catherine S. J.

    This chapter describes applications of N-heterocyclic carbenes (NHCs) in oxidation chemistry. The strong σ-donation capabilities of the NHCs allow an efficient stabilisation of metal centres in high oxidation states, while high metal-NHC bond dissociation energies suppress their oxidative decomposition. These properties make NHCs ideal ligands for oxidation processes. The first part of this chapter is dedicated to the reactivity of NHC-metal complexes towards molecular oxygen whilst the second half highlights all oxidation reactions catalysed by such complexes. These include oxidation of alcohols and olefins, oxidative cyclisations, hydrations of alkynes and nitriles, oxidative cleavage of alkenes and the oxidation of methane.

  4. Exploring complex chemical reactions by ab-initio simulation

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    1998-03-01

    Recent progress in the ab-initio molecular dynamics method and the power of parallel computing, allow the detailed study of complex chemical reaction of great industrial relevance. We illustrate this unprecedented capability by investigating the second generation Ziegler-Natta catalytic process. In this inhomogeneous catalyst, a polymerization reaction is induced by TiCl4 molecules deposited on an MgCl2 solid support. A density functional based ab-initio molecular dynamics calculation conducted with a minimum of initial assumption allows to understand the nature of the catalytic center and to determine the reaction path with the associated free energy barrier. Furthermore our calculation can explain in a nontrivial way the stereo-selectivity of the process.

  5. Theoretical aspects of product formation from the NCO + NO reaction

    SciTech Connect

    Lin, M.C.; He, Y. ); Melius, C.F. )

    1993-09-09

    The reaction of NCO with NO, an important elementary process involved in the reduction of NO[sub x] by HNCO, has been studied theoretically using the BAC-MP4 technique in conjunction with RRKM calculations. The computed molecular structures and thermochemical data for various intermediates and transition states suggest that the reaction takes place primarily via the singlet, ground electronic state OCNNO molecule according to the following mechanism; (step a) NCO + NO [leftrightarrow] [sup 1]OCNNO [yields] N[sub 2]O + CO; (step b) NCO + NO [leftrightarrow] [sup 1]OCNNO [yields] c-OCNNO[minus] N[sub 2] + CO[sub 2]. The formation of N[sub 2]O + CO occurs by the fragmentation of the singlet OCNNO intermediate step (a), whereas the production of N[sub 2] + CO[sub 2] by cyclization-fragmentation occurs via step b. The tight transition states leading to the formation of these products, coupled with the loose entrance channel, give rise to the experimentally observed strong negative temperature dependence which can be quantitatively accounted for by the results of RRKM calculations based on the BAC-MP4 data. The experimentally measured product branching ratio for channels a and b could be accounted for theoretically by lowering the calculated energy barrier for step a by 3.6 kcal/mol, corresponding to about 15% of the barrier height. 22 refs., 3 figs., 5 tabs.

  6. Formation of molecular oxygen in ultracold O + OH reaction

    SciTech Connect

    Kendrick, Brian Kent; Quemener, Goulven; Balakrishman, Naduvalath

    2008-01-01

    We discuss the formation of molecular oxygen in ultracold collisions between hydroxyl radicals and atomic oxygen. A time-independent quantum formalism based on hyperspherical coordinates is employed for the calculations. Elastic, inelastic and reactive cross sections as well as the vibrational and rotational populations of the product O{sub 2} molecules are reported. A J-shifting approximation is used to compute the rate coefficients. At temperatures T = 10--100 mK for which the OH molecules have been cooled and trapped experimentally, the elastic and reactive rate coefficients are of comparable magnitude, while at colder temperatures, T < 1 mK, the formation of molecular oxygen becomes the dominant pathway. The validity of a classical capture model to describe cold collisions of OH and O is also discussed. While very good agreement is found between classical and quantum results at T = 0.3 K, at higher temperatures, the quantum calculations predict a higher rate coefficient than the classical model, in agreement with experimental data for the O + OH reaction. The zero-temperature limiting value of the rate coefficient is predicted to be about 6 x 10{sup -12} cm{sup 3} s{sup 01}, a value comparable to that of barrierless alkali metal atom-dimer systems and about a factor of five larger than that of the tunneling dominated F + H{sub 2} reaction.

  7. Formation of ATP by the adenosine triphosphatase complex from spinach chloroplasts reconstituted together with bacteriorhodopsin.

    PubMed

    Winget, G D; Kanner, N; Racker, E

    1977-06-01

    The energy-linked ATPase complex has been isolated from spinach chloroplasts. This protein complex contained all the subunits of the chloroplast coupling factor (CF1) as well as several hydrophobic compoenents. When the activated complex was reconstituted with added soybean phospholipids, it catalyzed the exchange of radioactive inorganic phosphate with ATP. Sonication of the complex into proteoliposomes together with bacteriorhodopsin yield vesicles that catalyzed light-dependent ATP formation. Both the 32Pi-ATP exchange reactions and ATP formation were sensitive to uncouplers such as 3-tert-butyl-5,2'-dichloro-4'-nitrosalicylanilide, bis-(hexafluoroacetonyl)acetone and carbonyl cyanide-p-trifluoromethoxyphenyl-hydrazone, that act to dissipate a proton gradient. The energy transfer inhibitors dicyclohexylcarbodiimide, triphenyltin chloride and 2-beta-D-glucopyranosyl-4,6'-dihydroxydihydrochalcone were also effective inhibitors of both reactions. PMID:141938

  8. Bow shock formation in a complex plasma.

    PubMed

    Saitou, Y; Nakamura, Y; Kamimura, T; Ishihara, O

    2012-02-10

    A bow shock is observed in a two-dimensional supersonic flow of charged microparticles in a complex plasma. A thin conducting needle is used to make a potential barrier as an obstacle for the particle flow in the complex plasma. The flow is generated and the flow velocity is controlled by changing a tilt angle of the device under the gravitational force. A void, microparticle-free region, is formed around the potential barrier surrounding the obstacle. The flow is bent around the leading edge of the void and forms an arcuate structure when the flow is supersonic. The structure is characterized by the bow shock as confirmed by a polytropic hydrodynamic theory as well as numerical simulation. PMID:22401079

  9. Evolution of heliobacteria: implications for photosynthetic reaction center complexes

    NASA Technical Reports Server (NTRS)

    Vermaas, W. F.; Blankenship, R. E. (Principal Investigator)

    1994-01-01

    The evolutionary position of the heliobacteria, a group of green photosynthetic bacteria with a photosynthetic apparatus functionally resembling Photosystem I of plants and cyanobacteria, has been investigated with respect to the evolutionary relationship to Gram-positive bacteria and cyanobacteria. On the basis of 16S rRNA sequence analysis, the heliobacteria appear to be most closely related to Gram-positive bacteria, but also an evolutionary link to cyanobacteria is evident. Interestingly, a 46-residue domain including the putative sixth membrane-spanning region of the heliobacterial reaction center protein show rather strong similarity (33% identity and 72% similarity) to a region including the sixth membrane-spanning region of the CP47 protein, a chlorophyll-binding core antenna polypeptide of Photosystem II. The N-terminal half of the heliobacterial reaction center polypeptide shows a moderate sequence similarity (22% identity over 232 residues) with the CP47 protein, which is significantly more than the similarity with the Photosystem I core polypeptides in this region. An evolutionary model for photosynthetic reaction center complexes is discussed, in which an ancestral homodimeric reaction center protein (possibly resembling the heliobacterial reaction center protein) with 11 membrane-spanning regions per polypeptide has diverged to give rise to the core of Photosystem I, Photosystem II, and of the photosynthetic apparatus in green, purple, and heliobacteria.

  10. Complex formation of alkaline-earth cations with crown ethers and cryptands in methanol solutions

    SciTech Connect

    Buschman, H.J.

    1986-06-01

    The complexation of alkaline-earth cations by different crown ethers, azacrown ethers, and cryptands has been studied in methanol solutions by means of calorimetric and potentiometric titrations. The smallest monocyclic ligands examined from 2:1 complexes (ratio of ligand to cation) with cations which are too large to fit into the ligand cavity. With the smallest cryptand, only Sr/sup 2 +/ and Ba/sup 2 +/ ions are able to form exclusive complexes. In the case of the reaction of cryptand (211) with Ca/sup 2 +/, a separate estimation of stability constants for the formation of exclusive and inclusive complexes was possible for the first time. Higher values for stability constants are found for the reaction of alkaline-earth cations with cryptands compared to the reaction with alkali ions. This increase is only caused by favorable entropic contributions.

  11. Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

    DOE PAGESBeta

    Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

    2009-01-01

    Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

  12. Lead(II) complex formation with glutathione.

    PubMed

    Mah, Vicky; Jalilehvand, Farideh

    2012-06-01

    A structural investigation of complexes formed between the Pb(2+) ion and glutathione (GSH, denoted AH(3) in its triprotonated form), the most abundant nonprotein thiol in biological systems, was carried out for a series of aqueous solutions at pH 8.5 and C(Pb(2+)) = 10 mM and in the solid state. The Pb L(III)-edge extended X-ray absorption fine structure (EXAFS) oscillation for a solid compound with the empirical formula [Pb(AH(2))]ClO(4) was modeled with one Pb-S and two short Pb-O bond distances at 2.64 ± 0.04 and 2.28 ± 0.04 Å, respectively. In addition, Pb···Pb interactions at 4.15 ± 0.05 Å indicate dimeric species in a network where the thiolate group forms an asymmetrical bridge between two Pb(2+) ions. In aqueous solution at the mole ratio GSH/Pb(II) = 2.0 (C(Pb(2+)) = 10 mM, pH 8.5), lead(II) complexes with two thiolate ligands form, characterized by a ligand-to-metal charge-transfer band (LMCT) S(-) → Pb(2+) at 317 nm in the UV-vis spectrum and mean Pb-S and Pb-(N/O) bond distances of 2.65 ± 0.04 and 2.51 ± 0.04 Å, respectively, from a Pb L(III)-edge EXAFS spectrum. For solutions with higher mole ratios, GSH/Pb(II) ≥ 3.0, electrospray ionization mass spectroscopy spectra identified a triglutathionyllead(II) complex, for which Pb L(III)-edge EXAFS spectroscopy shows a mean Pb-S distance of 2.65 ± 0.04 Å in PbS(3) coordination, (207)Pb NMR spectroscopy displays a chemical shift of 2793 ppm, and in the UV-vis spectrum, an S(-) → Pb(2+) LMCT band appears at 335 nm. The complex persists at high excess of GSH and also at ∼25 K in frozen glycerol (33%)/water glasses for GSH/Pb(II) mole ratios from 4.0 to 10 (C(Pb(2+)) = 10 mM) measured by Pb L(III)-edge EXAFS spectroscopy. PMID:22594853

  13. [Riboflavin-radical formation by mechanochemical solid-state reaction using stainless steel vessel].

    PubMed

    Kondo, Shin-ichi; Furuta, Youji; Okita, Shintarou; Sasai, Yasushi; Aramaki, Hideki; Kuzuya, Masayuki

    2004-03-01

    The mechanochemical reaction of free riboflavin (FR) due to vibratory ball milling was carried out in a stainless steel vessel at room temperature under anaerobic conditions. The ESR of the fractured sample showed a broad single-line spectrum. It is suggested that the solid-state single-electron transfer (SSET) reaction from the surface of the stainless steel vessel to FR proceeded during the vibratory milling, resulting in the formation of the corresponding anion radicals. When the mechanochemical reaction of FR in the presence of calcium pantothenate (PC) was carried out, the radical concentration increased with the increasing PC content. It was shown that the anion radical in the metal complex was stable for a lengthy period of time even in highly humid air. PMID:15049132

  14. Studies of complex fragment emission in heavy ion reactions

    SciTech Connect

    Charity, R.J.; Sobotka, L.G.

    1992-01-01

    Our work involves the study of intermediate energy heavy-ion nuclear reactions. This work has two foci. On the one hand, we desire to learn about the properties of nuclear matter under abnormal conditions, in this energy domain, predominately low densities. This purpose runs abreast of the second, which is the study of the relevant reaction mechanisms. The two objectives are inexorably linked because our experimental laboratory for studying nuclear matter properties is a dynamic one. We are forced to ask how nuclear matter properties, such as phase transitions, are reflected in the dynamics of the reactions. It may be that irrefutable information about nuclear matter will not be extracted from the reaction work. Nevertheless, we are compelled to undertake this effort not only because it is the only game in town and as yet we do not know that information cannot be extracted, but also because of our second objective. The process leads to an understanding of the reaction mechanism themselves and therefore to the response characteristics of finite, perhaps non-equilibrium, strongly interacting systems. Our program has been: To study energy, mass, and angular momentum deposition by studying incomplete fusion reactions. To gain confidence that we understand how highly excited systems decompose by studying all emissions from the highly excited systems. To push these kinds of studies into the intermediate energy domain, with excitation function studies. And attempt to learn about the dynamics of the decays using particle-particle correlations. In the last effort, we have decided to focus on simple systems, where we believe, definitive statements are possible. These avenues of research share a common theme, large complex fragment production.

  15. Direct electronic probing of biological complexes formation

    NASA Astrophysics Data System (ADS)

    Macchia, Eleonora; Magliulo, Maria; Manoli, Kyriaki; Giordano, Francesco; Palazzo, Gerardo; Torsi, Luisa

    2014-10-01

    Functional bio-interlayer organic field - effect transistors (FBI-OFET), embedding streptavidin, avidin and neutravidin as bio-recognition element, have been studied to probe the electronic properties of protein complexes. The threshold voltage control has been achieved modifying the SiO2 gate diaelectric surface by means of the deposition of an interlayer of bio-recognition elements. A threshold voltage shift with respect to the unmodified dielectric surface toward more negative potential values has been found for the three different proteins, in agreement with their isoelectric points. The relative responses in terms of source - drain current, mobility and threshold voltage upon exposure to biotin of the FBI-OFET devices have been compared for the three bio-recognition elements.

  16. Linear free energy relationship rate constants and basicities of N-substituted phenyl glycines in positronium-glycine complex formation

    NASA Astrophysics Data System (ADS)

    Chen, Rongti; Liang, Jiachang; Du, Youming; Cao, Chun; Yin, Dinzhen; Wang, Shuying; Zhang, Tianbao

    1987-06-01

    Complex formation between positronium and glycine derivatives in solution is discussed and the complex reaction rate constants obtained by means of a positron annihilation lifetime spectrometer with BaF 2 detectors. Rate constants mainly depend on the conjugation effect at the benzene ring and the induction effect of the substituents at the phenyl. There is a linear free energy relationship between rate constants and basicities of N-substituted phenyl glycines in orthopositronium-glycine complex formation.

  17. Time scales for molecule formation by ion-molecule reactions

    NASA Technical Reports Server (NTRS)

    Langer, W. D.; Glassgold, A. E.

    1976-01-01

    Analytical solutions are obtained for nonlinear differential equations governing the time-dependence of molecular abundances in interstellar clouds. Three gas-phase reaction schemes are considered separately for the regions where each dominates. The particular case of CO, and closely related members of the Oh and CH families of molecules, is studied for given values of temperature, density, and the radiation field. Nonlinear effects and couplings with particular ions are found to be important. The time scales for CO formation range from 100,000 to a few million years, depending on the chemistry and regime. The time required for essentially complete conversion of C(+) to CO in the region where the H3(+) chemistry dominates is several million years. Because this time is longer than or comparable to dynamical time scales for dense interstellar clouds, steady-state abundances may not be observed in such clouds.

  18. Secondary organic aerosol formation from ozone reactions with single terpenoids and terpenoid mixtures

    NASA Astrophysics Data System (ADS)

    Waring, Michael S.; Wells, J. Raymond; Siegel, Jeffrey A.

    2011-08-01

    Ozone reacts with indoor-emitted terpenoids to form secondary organic aerosol (SOA). Most SOA research has focused on ozone reactions with single terpenoids or with consumer products, and this paper reports the results from an investigation of SOA formation from ozone reactions with both single terpenoids and mixtures of D-limonene, α-pinene, and α-terpineol. Transient experiments were conducted at low (25 ppb) and high (100 ppb) initial concentrations of ozone. The three terpenoids were tested singly and in combinations in a manner that controlled for their different reaction rates with ozone. The SOA formation was assessed by examining the evolution in time of the resulting number size-distributions and estimates of the mass concentrations. The results suggest that at higher ozone and terpenoid concentrations, SOA number formation follows a linear trend as a function of the initial rate of reaction. This finding was valid for both single terpenoids and mixtures. Generally speaking, higher ozone and terpenoid concentrations also led to larger geometric mean diameters and smaller geometric standard deviations of fitted lognormal distributions of the formed SOA. By assuming a density, mass concentrations were also assessed and did not follow as consistent of a trend. At low ozone concentration conditions, reactions with only D-limonene yielded the largest number concentrations of any experiment, even more than experiments with mixtures containing D-limonene and much higher overall terpenoid concentrations. This finding was not seen for high ozone concentrations. These experiments demonstrate quantifiable trends for SOA forming reactions of ozone and mixtures, and this work provides a framework for expanding these results to more complex mixtures and consumer products.

  19. Dynamics of Lane Formation in Driven Binary Complex Plasmas

    SciTech Connect

    Suetterlin, K. R.; Ivlev, A. V.; Raeth, C.; Thomas, H. M.; Rubin-Zuzic, M.; Morfill, G. E.; Wysocki, A.; Loewen, H.; Goedheer, W. J.; Fortov, V. E.; Lipaev, A. M.; Molotkov, V. I.; Petrov, O. F.

    2009-02-27

    The dynamical onset of lane formation is studied in experiments with binary complex plasmas under microgravity conditions. Small microparticles are driven and penetrate into a cloud of big particles, revealing a strong tendency towards lane formation. The observed time-resolved lane-formation process is in good agreement with computer simulations of a binary Yukawa model with Langevin dynamics. The laning is quantified in terms of the anisotropic scaling index, leading to a universal order parameter for driven systems.

  20. Ethanol oxidation by imidorhenium(V) complexes: formation of amidorhenium(III) complexes.

    PubMed

    Suing, A L; Dewan, C R; White, P S; Thorp, H H

    2000-12-25

    The reaction of Re(NC6H4R)Cl3(PPh3)2 (R = H, 4-Cl, 4-OMe) with 1,2-bis(diphenylphosphino)ethane (dppe) is investigated in refluxing ethanol. The reaction produces two major products, Re(NC6H4R)Cl(dppe)(2)2+ (R = H, 1-H; R = Cl, 1-Cl; R = OMe, 1-OMe) and the rhenium(III) species Re(NHC6H4R)Cl(dppe)2+ (R = H, 2-H; R = Cl, 2-Cl). Complexes 1-H (orthorhombic, Pcab, a = 22.3075(10) A, b = 23.1271(10) A, c = 23.3584(10) A, Z = 8), 1-Cl (triclinic, P1, a = 11.9403(6) A, b = 14.6673(8) A, c = 17.2664(9) A, alpha = 92.019(1) degrees, beta = 97.379(1) degrees, gamma = 90.134(1) degrees, Z = 2), and 1-OMe (triclinic, P1, a = 11.340(3) A, b = 13.134(4) A, c = 13.3796(25) A, alpha = 102.370(20) degrees, beta = 107.688(17) degrees, gamma = 114.408(20) degrees, Z = 1) are crystallographically characterized and show an average Re-N bond length (1.71 A) typical of imidorhenium(V) complexes. There is a small systematic decrease in the Re-N bond length on going from Cl to H to OMe. Complex 2-Cl (monoclinic, Cc, a = 24.2381(11) A, b = 13.4504(6) A, c = 17.466(8) A, beta = 97.06900(0) degrees, Z = 4) is also crystallographically characterized and shows a Re-N bond length (1.98 A) suggestive of amidorhenium(III). The rhenium(III) complexes exhibit unusual proton NMR spectra where all of the resonances are found at expected locations except those for the amido protons, which are at 37.8 ppm for 2-Cl and 37.3 ppm for 1-H. The phosphorus resonances are also unremarkable, but the 13C spectrum of 2-Cl shows a significantly shifted resonance at 177.3 ppm, which is assigned to the ipso carbon of the phenylamido ligand. The extraordinary shifts of the amido hydrogen and ipso carbon are attributed to second-order magnetism that is strongly focused along the axially compressed amido axis. The reducing equivalents for the formation of the Re(III) product are provided by oxidation of the ethanol solvent, which produces acetal and acetaldehyde in amounts as much as 30 equiv based on the quantity of

  1. Stochastic analysis of complex reaction networks using binomial moment equations.

    PubMed

    Barzel, Baruch; Biham, Ofer

    2012-09-01

    The stochastic analysis of complex reaction networks is a difficult problem because the number of microscopic states in such systems increases exponentially with the number of reactive species. Direct integration of the master equation is thus infeasible and is most often replaced by Monte Carlo simulations. While Monte Carlo simulations are a highly effective tool, equation-based formulations are more amenable to analytical treatment and may provide deeper insight into the dynamics of the network. Here, we present a highly efficient equation-based method for the analysis of stochastic reaction networks. The method is based on the recently introduced binomial moment equations [Barzel and Biham, Phys. Rev. Lett. 106, 150602 (2011)]. The binomial moments are linear combinations of the ordinary moments of the probability distribution function of the population sizes of the interacting species. They capture the essential combinatorics of the reaction processes reflecting their stoichiometric structure. This leads to a simple and transparent form of the equations, and allows a highly efficient and surprisingly simple truncation scheme. Unlike ordinary moment equations, in which the inclusion of high order moments is prohibitively complicated, the binomial moment equations can be easily constructed up to any desired order. The result is a set of equations that enables the stochastic analysis of complex reaction networks under a broad range of conditions. The number of equations is dramatically reduced from the exponential proliferation of the master equation to a polynomial (and often quadratic) dependence on the number of reactive species in the binomial moment equations. The aim of this paper is twofold: to present a complete derivation of the binomial moment equations; to demonstrate the applicability of the moment equations for a representative set of example networks, in which stochastic effects play an important role. PMID:23030885

  2. Formation of Formaldehyde and Glyoxal From The Toluene + Oh Reaction

    NASA Astrophysics Data System (ADS)

    Volkamer, R.; Wirtz, K.; Platt, U.

    Aromatic hydrocarbons are emitted into the urban atmosphere mostly as part of au- tomobile exhaust. Toluene thereby is the single most abundant aromatic compound emitted into the atmosphere. Despite the importance of aromatic hydrocarbon oxi- dation for the formation of photooxidants from urban plumes the oxidation mech- anism of aromatic hydrocarbons is far from being understood.Considerable progress has been made in recent years concerning our understanding of the ring-retaining path- ways, while major uncertainties remain to be linked with the operative ring-cleavage mechanisms. The representation of the aromatic oxidation in presently used chemical transport models (CTM) is estimated a major uncertainty for these models. This work presents data on formaldehyde (HCHO) and glyoxal, which are two impor- tant ring-cleavage products from the the toluene + OH reaction. While glyoxal was observed to form as a high yield primary product (Volkamer et al., JPC A, 2001, 105, 7865-7874) the formation of HCHO is observed delayed, i.e. as a secondary prod- uct. The temporal behaviour of glyoxal and HCHO concentrations allowed to con- clude that short lived stable intermediate compounds must form upon ring-cleavage of toluene. With an approximate lifetime of the order of ten minutes, these highly reac- tive intermediate compounds are likely to be a significant radical source. Atmospheric implications of the results are adressed.

  3. The formation of Kuiper-belt binaries through exchange reactions.

    PubMed

    Funato, Yoko; Makino, Junichiro; Hut, Piet; Kokubo, Eiichiro; Kinoshita, Daisuke

    2004-02-01

    Recent observations have revealed that an unexpectedly high fraction--a few per cent--of the trans-Neptunian objects (TNOs) that inhabit the Kuiper belt are binaries. The components have roughly equal masses, with very eccentric orbits that are wider than a hundred times the radius of the primary. Standard theories of binary asteroid formation tend to produce close binaries with circular orbits, so two models have been proposed to explain the unique characteristics of the TNOs. Both models, however, require extreme assumptions regarding the size distribution of the TNOs. Here we report a mechanism that is capable of producing binary TNOs with the observed properties during the early stages of their formation and growth. The only required assumption is that the TNOs were initially formed through gravitational instabilities in the protoplanetary dust disk. The basis of the mechanism is an exchange reaction in which a binary whose primary component is much more massive than the secondary interacts with a third body, whose mass is comparable to that of the primary. The low-mass secondary component is ejected and replaced by the third body in a wide but eccentric orbit. PMID:14765188

  4. Roles of acetone and diacetone alcohol in coordination and dissociation reactions of uranyl complexes.

    PubMed

    Rios, Daniel; Schoendorff, George; Van Stipdonk, Michael J; Gordon, Mark S; Windus, Theresa L; Gibson, John K; de Jong, Wibe A

    2012-12-01

    Combined collision-induced dissociation mass spectrometry experiments with DFT and MP2 calculations were employed to elucidate the molecular structures and energetics of dissociation reactions of uranyl species containing acetone and diacetone alcohol ligands. It is shown that solutions containing diacetone alcohol ligands can produce species with more than five oxygen atoms available for coordination. Calculations confirm that complexes with up to four diacetone alcohol ligands can be energetically stable but that the effective number of atoms coordinating with uranium in the equatorial plane does not exceed five. Water elimination reactions of diacetone alcohol ligands are shown to have two coordination-dependent reaction channels, through formation of mesityl oxide ligands or formation of alkoxide and protonated mesityl oxide species. The present results provide an explanation for the implausible observation of "[UO(2)(ACO)(6,7,8)](2+)" in and observed water-elimination reactions from purportedly uranyl-acetone complexes (Rios, D.; Rutkowski, P. X.; Van Stipdonk, M. J.; Gibson, J. K. Inorg. Chem. 2011, 50, 4781). PMID:23146003

  5. Studies of reductive elimination reactions to form carbon-oxygen bonds from Pt(IV) complexes.

    PubMed

    Williams, B S; Goldberg, K I

    2001-03-21

    The platinum(IV) complexes fac-L(2)PtMe(3)(OR) (L(2) = bis(diphenylphosphino)ethane, o-bis(diphenylphosphino)benzene, R = carboxyl, aryl; L = PMe(3), R = aryl) undergo reductive elimination reactions to form carbon-oxygen bonds and/or carbon-carbon bonds. The carbon-oxygen reductive elimination reaction produces either methyl esters or methyl aryl ethers (anisoles) and L(2)PtMe(2), while the carbon-carbon reductive elimination reaction affords ethane and L(2)PtMe(OR). Choice of reaction conditions allows the selection of either type of coupling over the other. A detailed mechanistic study of the reductive elimination reactions supports dissociation of the OR(-) ligand as the initial step for the C-O bond formation reaction. This is followed by a nucleophilic attack of OR(-) upon a methyl group bound to the Pt(IV) cation to produce the products MeOR and L(2)PtMe(2). C-C reductive elimination proceeds from L(2)PtMe(3)(OR) by initial L (L = PMe(3)) or OR(-) (L(2) = dppe, dppbz) dissociation, followed by C-C coupling from the resulting five-coordinate intermediate. Our studies demonstrate that both C-C and C-O reductive elimination reactions from Pt(IV) are more facile in polar solvents, in the presence of Lewis acids, and for OR(-) groups that contain electron withdrawing substituents. PMID:11456927

  6. Turing instability in reaction-diffusion models on complex networks

    NASA Astrophysics Data System (ADS)

    Ide, Yusuke; Izuhara, Hirofumi; Machida, Takuya

    2016-09-01

    In this paper, the Turing instability in reaction-diffusion models defined on complex networks is studied. Here, we focus on three types of models which generate complex networks, i.e. the Erdős-Rényi, the Watts-Strogatz, and the threshold network models. From analysis of the Laplacian matrices of graphs generated by these models, we numerically reveal that stable and unstable regions of a homogeneous steady state on the parameter space of two diffusion coefficients completely differ, depending on the network architecture. In addition, we theoretically discuss the stable and unstable regions in the cases of regular enhanced ring lattices which include regular circles, and networks generated by the threshold network model when the number of vertices is large enough.

  7. Surface complexation reaction for phase transfer of hydrophobic quantum dot from nonpolar to polar medium.

    PubMed

    Bhandari, Satyapriya; Roy, Shilaj; Pramanik, Sabyasachi; Chattopadhyay, Arun

    2014-09-01

    Chemical reaction between oleate-capped Zn(x)Cd(1-x)S quantum dots (Qdots) and 8-hydroxyquinoline (HQ) led to formation of a surface complex, which was accompanied by transfer of hydrophobic Qdots from nonpolar (hexane) to polar (water) medium with high efficiency. The stability of the complex on the surface was achieved via involvement of dangling sulfide bonds. Moreover, the transferred hydrophilic Qdots--herein called as quantum dot complex (QDC)--exhibited new and superior optical properties in comparison to bare inorganic complexes with retention of the dimension and core structure of the Qdots. Finally, the new and superior optical properties of water-soluble QDC make them potentially useful for biological--in addition to light emitting device (LED)--applications. PMID:25133937

  8. Complex molecule formation around massive young stellar objects.

    PubMed

    Oberg, Karin I; Fayolle, Edith C; Reiter, John B; Cyganowski, Claudia

    2014-01-01

    Interstellar complex organic molecules were first identified in the hot inner regions of massive young stellar objects (MYSOs), but have more recently been found in many colder sources, indicating that complex molecules can form at a range of temperatures. However, individually these observations provide limited constraints on how complex molecules form, and whether the same formation pathways dominate in cold, warm and hot environments. To address these questions, we use spatially resolved observations from the Submillimeter Array of three MYSOs together with mostly unresolved literature data to explore how molecular ratios depend on environmental parameters, especially temperature. Towards the three MYSOs, we find multiple complex organic emission peaks characterized by different molecular compositions and temperatures. In particular, CH3CCH and CH3CN seem to always trace a lukewarm (T = 60 K) and a hot (T > 100 K) complex chemistry, respectively. These spatial trends are consistent with abundance-temperature correlations of four representative complex organics--CH3CCH, CH3CN, CH3OCH3 and CH3CHO--in a large sample of complex molecule hosts mined from the literature. Together, these results indicate a general chemical evolution with temperature, i.e. that new complex molecule formation pathways are activated as a MYSO heats up. This is qualitatively consistent with model predictions. Furthermore, these results suggest that ratios of complex molecules may be developed into a powerful probe of the evolutionary stage of a MYSO, and may provide information about its formation history. PMID:25302375

  9. Complex molecule formation around massive young stellar objects

    NASA Astrophysics Data System (ADS)

    Öberg, Karin I.; Fayolle, Edith C.; Reiter, John B.; Cyganowski, Claudia

    2014-02-01

    Interstellar complex organic molecules were first identified in the hot inner regions of massive young stellar objects (MYSOs), but have more recently been found in many colder sources, indicating that complex molecules can form at a range of temperatures. However, individually these observations provide limited constraints on how complex molecules form, and whether the same formation pathways dominate in cold, warm and hot environments. To address these questions, we use spatially resolved observations from the Submillimeter Array of three MYSOs together with mostly unresolved literature data to explore how molecular ratios depend on environmental parameters, especially temperature. Towards the three MYSOs, we find multiple complex organic emission peaks characterized by different molecular compositions and temperatures. In particular, CH3CCH and CH3CN seem to always trace a lukewarm (T ≈ 60 K) and a hot (T > 100 K) complex chemistry, respectively. These spatial trends are consistent with abundance-temperature correlations of four representative complex organics - CH3CCH, CH3CN, CH3OCH3 and CH3CHO - in a large sample of complex molecule hosts mined from the literature. Together, these results indicate a general chemical evolution with temperature, i.e. that new complex molecule formation pathways are activated as a MYSO heats up. This is qualitatively consistent with model predictions. Furthermore, these results suggest that ratios of complex molecules may be developed into a powerful probe of the evolutionary stage of a MYSO, and may provide information about its formation history.

  10. Complexes of sulfur-containing ligands. I. Factors influencing complex formation between D-penicillamine and copper (II) ion.

    PubMed

    Gergely, A; Sóvágó, I

    1978-07-01

    Complex formation and redox reactions between copper (II) ion and D-penicillamine were studied in detail as functions of the metal/-ligand ratio and the concentration of halide ions. It was established that a copper (I)- D-penicillamine polymeric complex of amphoteric character is formed when excess D-penicillamine is present. When the D-penicillamine/copper (II) ratio = 1.45 in the starting reaction mixture, a mixed valence complex with an intense red-violet color is formed. The formation of this compound, which contains 44% copper (II) ion, is greatly influenced by the experimental conditions, primarily by the concentration of halide ions. The main chemical and physical characteristics of the mixed valence complex were determined via magnetic and spectroscopic measurements. It was further established that a very intense blue complex is formed when the D-penicillamine/copper (II) ratio = 2 and halide ions are present. On the basis of the nature of the products formed under various conditions it was concluded that the copper (II)-D-penicillamine system may serve as a good model for studying the binding sites of copper-containing proteins. PMID:210846

  11. Complex reaction networks in high temperature hydrocarbon chemistry.

    PubMed

    Mutlay, İbrahim; Restrepo, Albeiro

    2015-03-28

    Complex chemical reaction mechanisms of high temperature hydrocarbon decomposition are represented as networks and their underlying graph topologies are analyzed as a dynamic system. As model reactants, 1,3-butadiene, acetylene, benzene, ethane, ethylene, methane, methyl isobutyl ketone (MIBK) and toluene are chosen in view of their importance for the global environment, energy technologies as well as their quantum chemical properties. Accurate kinetic mechanisms are computationally simulated and converted to bipartite graphs for the incremental conversion steps of the main reactant. Topological analysis of the resulting temporal networks reveals novel features unknown to classical chemical kinetics theory. The time-dependent percolation behavior of the chemical reaction networks shows infinite order phase transition and a unique correlation between the percolation thresholds and electron distribution of the reactants. These observations are expected to yield important applications in the development of a new theoretical perspective to chemical reactions and technological processes e.g. inhibition of greenhouse gases, efficient utilization of fossil fuels, and large scale carbon nanomaterial production. PMID:25720589

  12. Validated spectrophotometric methods for determination of sodium valproate based on charge transfer complexation reactions

    NASA Astrophysics Data System (ADS)

    Belal, Tarek S.; El-Kafrawy, Dina S.; Mahrous, Mohamed S.; Abdel-Khalek, Magdi M.; Abo-Gharam, Amira H.

    2016-02-01

    This work presents the development, validation and application of four simple and direct spectrophotometric methods for determination of sodium valproate (VP) through charge transfer complexation reactions. The first method is based on the reaction of the drug with p-chloranilic acid (p-CA) in acetone to give a purple colored product with maximum absorbance at 524 nm. The second method depends on the reaction of VP with dichlone (DC) in dimethylformamide forming a reddish orange product measured at 490 nm. The third method is based upon the interaction of VP and picric acid (PA) in chloroform resulting in the formation of a yellow complex measured at 415 nm. The fourth method involves the formation of a yellow complex peaking at 361 nm upon the reaction of the drug with iodine in chloroform. Experimental conditions affecting the color development were studied and optimized. Stoichiometry of the reactions was determined. The proposed spectrophotometric procedures were effectively validated with respect to linearity, ranges, precision, accuracy, specificity, robustness, detection and quantification limits. Calibration curves of the formed color products with p-CA, DC, PA and iodine showed good linear relationships over the concentration ranges 24-144, 40-200, 2-20 and 1-8 μg/mL respectively. The proposed methods were successfully applied to the assay of sodium valproate in tablets and oral solution dosage forms with good accuracy and precision. Assay results were statistically compared to a reference pharmacopoeial HPLC method where no significant differences were observed between the proposed methods and reference method.

  13. Validated spectrophotometric methods for determination of sodium valproate based on charge transfer complexation reactions.

    PubMed

    Belal, Tarek S; El-Kafrawy, Dina S; Mahrous, Mohamed S; Abdel-Khalek, Magdi M; Abo-Gharam, Amira H

    2016-02-15

    This work presents the development, validation and application of four simple and direct spectrophotometric methods for determination of sodium valproate (VP) through charge transfer complexation reactions. The first method is based on the reaction of the drug with p-chloranilic acid (p-CA) in acetone to give a purple colored product with maximum absorbance at 524nm. The second method depends on the reaction of VP with dichlone (DC) in dimethylformamide forming a reddish orange product measured at 490nm. The third method is based upon the interaction of VP and picric acid (PA) in chloroform resulting in the formation of a yellow complex measured at 415nm. The fourth method involves the formation of a yellow complex peaking at 361nm upon the reaction of the drug with iodine in chloroform. Experimental conditions affecting the color development were studied and optimized. Stoichiometry of the reactions was determined. The proposed spectrophotometric procedures were effectively validated with respect to linearity, ranges, precision, accuracy, specificity, robustness, detection and quantification limits. Calibration curves of the formed color products with p-CA, DC, PA and iodine showed good linear relationships over the concentration ranges 24-144, 40-200, 2-20 and 1-8μg/mL respectively. The proposed methods were successfully applied to the assay of sodium valproate in tablets and oral solution dosage forms with good accuracy and precision. Assay results were statistically compared to a reference pharmacopoeial HPLC method where no significant differences were observed between the proposed methods and reference method. PMID:26574649

  14. TAR RNA decoys inhibit tat-activated HIV-1 transcription after preinitiation complex formation.

    PubMed Central

    Bohjanen, P R; Liu, Y; Garcia-Blanco, M A

    1997-01-01

    The ability of the HIV-1 Tat protein to trans -activate HIV-1 transcription in vitro is specifically inhibited by a circular TAR RNA decoy. This inhibition is not overcome by adding an excess of Tat to the reaction but is partially overcome by adding Tat in combination with nuclear extract, suggesting that TAR RNA might function by interacting with a complex containing Tat and cellular factor(s). A cell-free transcription system involving immobilized DNA templates was used to further define the factor(s) that interact with TAR RNA. Preinitiation complexes formed in the presence or absence of Tat were purified on immobilized templates containing the HIV-1 promoter. After washing, nucleotides and radiolabelled UTP were added and transcription was measured. The presence of Tat during preinitiation complex formation resulted in an increase in the level of full-length HIV-1 transcripts. This Tat-activated increase in HIV-1 transcription was not inhibited by circular TAR decoys added during preinitiation complex formation but was inhibited by circular TAR decoys subsequently added during the transcription reaction. These results suggest that TAR decoys inhibit Tat-activated HIV-1 transcription after preinitiation complex formation, perhaps by interacting with components of transcription complexes. PMID:9358155

  15. Thermodynamics of the formation of copper(II) complexes with L-histidine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Gorboletova, G. G.; Metlin, A. A.

    2015-02-01

    The heat effects from the reaction between L-histidine solutions and Cu(NO3)2 solutions at 298.15 K in the 0.2 to 1.0 (KNO3) range of ionic strength are measured by means of direct calorimetry. The experimental data is treated with allowance for the simultaneous proceeding of several processes. The heat effects of the formation of complexes Cu(His)+, Cu(His)2, CuHHis2+, CuH(His){2/+} and CuH2(His){2/2+} are calculated from calorimetric measurements. The standard enthalpies of formation for complexes of L-histidine with Cu2+ ions are obtained via extrapolation to zero ionic strength. The relationship between the thermodynamic characteristics of the formation of complexes of copper(II) with L-histidine and their structure is determined.

  16. Snapshot of a Reaction Intermediate: Analysis of Benzoylformate Decarboxylase in Complex with a Benzoylphosphonate Inhibitor

    SciTech Connect

    Brandt, Gabriel S.; Kneen, Malea M.; Chakraborty, Sumit; Baykal, Ahmet T.; Nemeria, Natalia; Yep, Alejandra; Ruby, David I.; Petsko, Gregory A.; Kenyon, George L.; McLeish, Michael J.; Jordan, Frank; Ringe, Dagmar

    2009-04-22

    Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2{alpha}-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2{alpha}-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 {angstrom} (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.

  17. Reactions of a Ruthenium Complex with Substituted N-Propargyl Pyrroles.

    PubMed

    Chia, Pi-Yeh; Huang, Shou-Ling; Liu, Yi-Hong; Lin, Ying-Chih

    2016-04-01

    In an investigation into the chemical reactions of N-propargyl pyrroles 1 a-c, containing aldehyde, keto, and ester groups on the pyrrole ring, with [Ru]-Cl ([Ru]=Cp(PPh3 )2 Ru; Cp=C5 H5 ), an aldehyde group in the pyrrole ring is found to play a crucial role in stimulating the cyclization reaction. The reaction of 1 a, containing an aldehyde group, with [Ru]-Cl in the presence of NH4 PF6 yields the vinylidene complex 2 a, which further reacts with allyl amine to give the carbene complex 6 a with a pyrrolizine group. However, if 1 a is first reacted with allyl amine to yield the iminenyne 8 a, then the reaction of 8 a with [Ru]-Cl in the presence of NH4 PF6 yields the ruthenium complex 9 a, containing a cationic pyrrolopyrazinium group, which has been fully characterized by XRD analysis. These results can be adequately explained by coordination of the triple bond of the propargyl group to the ruthenium metal center first, followed by two processes, that is, formation of a vinylidene intermediate or direct nucleophilic attack. Additionally, the deprotonation of 2 a by R4 NOH yields the neutral acetylide complex 3 a. In the presence of NH4 PF6 , the attempted alkylation of 3 a resulted in the formation the Fischer-type amino-carbene complex 5 a as a result of the presence of NH3 , which served as a nucleophile. With KPF6 , the alkylation of 3 a with ethyl and benzyl bromoacetates afforded the disubstituted vinylidene complexes 10 a and 11 a, containing ester groups, which underwent deprotonation reactions to give the furyl complexes 12 a and 13 a, respectively. For 13 a, containing an O-benzyl group, subsequent 1,3-migration of the benzyl group was observed to yield product 14 a with a lactone unit. Similar reactivity was not observed for the corresponding N-propargyl pyrroles 1 b and 1 c, which contained keto and ester groups, respectively, on the pyrrole ring. PMID:26865008

  18. The significance of surface complexation reactions in hydrologic systems: a geochemist's perspective

    NASA Astrophysics Data System (ADS)

    Koretsky, C.

    2000-05-01

    Complexation reactions at the mineral-water interface affect the transport and transformation of metals and organic contaminants, nutrient availability in soils, formation of ore deposits, acidification of watersheds and the global cycling of elements. Such reactions can be understood by quantifying speciation reactions in homogeneous aqueous solutions, characterizing reactive sites at mineral surfaces and developing models of the interactions between aqueous species at solid surfaces. In this paper, the application of thermodynamic principles to quantify aqueous complexation reactions is described. This is followed by a brief overview of a few of the methods that have been used to characterize reactive sites on mineral surfaces. Next, the application of empirical and semi-empirical models of adsorption at the mineral-water interface, including distribution coefficients, simple ion exchange models, and Langmuir and Freundlich isotherms is discussed. Emphasis is placed on the limitations of such models in providing an adequate representation of adsorption in hydrological systems. These limitations arise because isotherms do not account for the structure of adsorbed species, nor do they account for the development of surface charge with adsorption. This is contrasted with more sophisticated models of adsorption, termed 'surface complexation models', which include the constant capacitance model, the diffuse layer model, the triple layer model and the MUSIC model. In these models, speciation reactions between surface functional groups and dissolved species control the variable surface charge build-up and the specific adsorption properties of minerals in aqueous solutions. Next, the influence of mineral surface speciation on the reactivity of adsorbed species and on far from equilibrium dissolution rates of minerals is discussed. Finally, the applicability of microscopic models of surface complexation to field-scale systems is explored and the need to integrate

  19. 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.

  20. 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

  1. Molecular Epoxidation Reactions Catalyzed by Rhenium, Molybdenum, and Iron Complexes.

    PubMed

    Kück, Jens W; Reich, Robert M; Kühn, Fritz E

    2016-02-01

    Epoxidations are of high relevance in many organic syntheses, both in industry and academia. In this personal account, the development of rhenium, molybdenum, and iron complexes in molecular epoxidation catalysis is presented. Methyltrioxorhenium (MTO) is the benchmark catalyst for these reactions, with a thoroughly investigated mechanism and reactivity profile. More recently, highly active molecular molybdenum and iron catalysts have emerged, challenging the extraordinary role of MTO in epoxidation catalysis with high turnover frequencies (TOFs). This development is highlighted in its use of cheaper, more readily available metals, and the challenges of using base metals in catalysis are discussed. These results show the promise that relatively cheap and abundant metals, such as molybdenum and iron, hold for the future of epoxidation catalysis. PMID:26776087

  2. Electron transfer reactions of osmium(II) complexes with phenols and phenolic acids

    NASA Astrophysics Data System (ADS)

    Rajeswari, Angusamy; Ramdass, Arumugam; Muthu Mareeswaran, Paulpandian; Velayudham, Murugesan; Rajagopal, Seenivasan

    2016-07-01

    Three [Os(NN)3]2+ complexes (NN = polypyridine) with ligands of varying hydrophobicity were synthesized and characterized by NMR spectral techniques. The geometry of the molecules are optimized by DFT calculations. The interaction between [Os(NN)3]2+ complexes and phenolate ion in ground state is confirmed by absorption spectral study and the binding constant values are in the range of 3-740 M-1. The photoinduced electron transfer reaction of these [Os(NN)3]2+ complexes with phenols and phenolic acids at pH 12.5 leads to the formation of phenoxyl radical confirmed through transient absorption spectral study. Binding constants and electron transfer rate constants within the [Os(NN)3]2+-phenolate ion adduct account for the change for the overall quenching constant with the change of structure of reactants.

  3. DNA strand exchange stimulated by spontaneous complex formation with cationic comb-type copolymer.

    PubMed

    Kim, Won Jong; Akaike, Toshihiro; Maruyama, Atsushi

    2002-10-30

    Cationic comb-type copolymers (CCCs) composed of a polycation backbone and water-soluble side chains accelerate by 4-5 orders the DNA strand exchange reaction (SER) between double helical DNA and its homologous single-strand DNA. The accelerating effect is considered due to alleviation of counterion association during transitional intermediate formation in sequential displacement pathway. CCCs stabilize not only matured hybrids but also the nucleation complex to accelerate hybridization. PMID:12392411

  4. Carbon Dioxide Influence on the Thermal Formation of Complex Organic Molecules in Interstellar Ice Analogs

    NASA Astrophysics Data System (ADS)

    Vinogradoff, V.; Duvernay, F.; Fray, N.; Bouilloud, M.; Chiavassa, T.; Cottin, H.

    2015-08-01

    Interstellar ices are submitted to energetic processes (thermal, UV, and cosmic-ray radiations) producing complex organic molecules. Laboratory experiments aim to reproduce the evolution of interstellar ices to better understand the chemical changes leading to the reaction, formation, and desorption of molecules. In this context, the thermal evolution of an interstellar ice analogue composed of water, carbon dioxide, ammonia, and formaldehyde is investigated. The ice evolution during the warming has been monitored by IR spectroscopy. The formation of hexamethylenetetramine (HMT) and polymethylenimine (PMI) are observed in the organic refractory residue left after ice sublimation. A better understanding of this result is realized with the study of another ice mixture containing methylenimine (a precursor of HMT) with carbon dioxide and ammonia. It appears that carbamic acid, a reaction product of carbon dioxide and ammonia, plays the role of catalyst, allowing the reactions toward HMT and PMI formation. This is the first time that such complex organic molecules (HMT, PMI) are produced from the warming (without VUV photolysis or irradiation with energetic particles) of abundant molecules observed in interstellar ices (H2O, NH3, CO2, H2CO). This result strengthens the importance of thermal reactions in the ices’ evolution. HMT and PMI, likely components of interstellar ices, should be searched for in the pristine objects of our solar system, such as comets and carbonaceous chondrites.

  5. Geology of the Biwabik Iron Formation and Duluth Complex.

    PubMed

    Jirsa, Mark A; Miller, James D; Morey, G B

    2008-10-01

    The Biwabik Iron Formation is a approximately 1.9 billion year-old sequence of iron-rich sedimentary rocks that was metamorphosed at its eastern-most extent by approximately 1.1 billion year-old intrusions of the Duluth Complex. The metamorphic recrystallization of iron-formation locally produced iron-rich amphiboles and other fibrous iron-silicate minerals. The presence of these minerals in iron-formation along the eastern part of what is known as the Mesabi Iron Range, and their potential liberation by iron mining has raised environmental health concerns. We describe here the geologic setting and mineralogic composition of the Biwabik Iron Formation in and adjacent to the contact metamorphic aureole of the Duluth Complex. The effects of metamorphism are most pronounced within a few kilometers of the contact, and decrease progressively away from it. The contact aureole has been divided into four metamorphic zones-each characterized by the composition and crystal structure of the metamorphic minerals it contains. The recrystallization of iron-formation to iron-rich amphibole minerals (grunerite and cummingtonite) and iron-pyroxene minerals (hedenbergite and ferrohypersthene) is best developed in zones that are most proximal to the Duluth Complex contact. PMID:17997209

  6. Geology of the Biwabik Iron Formation and Duluth Complex

    USGS Publications Warehouse

    Jirsa, M.A.; Miller, J.D., Jr.; Morey, G.B.

    2008-01-01

    The Biwabik Iron Formation is a ???1.9 billion year-old sequence of iron-rich sedimentary rocks that was metamorphosed at its eastern-most extent by ???1.1 billion year-old intrusions of the Duluth Complex. The metamorphic recrystallization of iron-formation locally produced iron-rich amphiboles and other fibrous iron-silicate minerals. The presence of these minerals in iron-formation along the eastern part of what is known as the Mesabi Iron Range, and their potential liberation by iron mining has raised environmental health concerns. We describe here the geologic setting and mineralogic composition of the Biwabik Iron Formation in and adjacent to the contact metamorphic aureole of the Duluth Complex. The effects of metamorphism are most pronounced within a few kilometers of the contact, and decrease progressively away from it. The contact aureole has been divided into four metamorphic zones-each characterized by the composition and crystal structure of the metamorphic minerals it contains. The recrystallization of iron-formation to iron-rich amphibole minerals (grunerite and cummingtonite) and iron-pyroxene minerals (hedenbergite and ferrohypersthene) is best developed in zones that are most proximal to the Duluth Complex contact. ?? 2007 Elsevier Inc. All rights reserved.

  7. Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction

    SciTech Connect

    Soorkia, Satchin; Taatjes, Craig A.; Osborn, David L.; Selby, Talitha M.; Trevitt, Adam J.; Wilson, Kevin R.; Leone, Stephen R.

    2010-03-16

    The reaction of the ground state methylidyne radical CH (X2Pi) with pyrrole (C4H5N) has been studied in a slow flow tube reactor using Multiplexed Photoionization Mass Spectrometry coupled to quasi-continuous tunable VUV synchrotron radiation at room temperature (295 K) and 90 oC (363 K), at 4 Torr (533 Pa). Laser photolysis of bromoform (CHBr3) at 248 nm (KrF excimer laser) is used to produce CH radicals that are free to react with pyrrole molecules in the gaseous mixture. A signal at m/z = 79 (C5H5N) is identified as the product of the reaction and resolved from 79Br atoms, and the result is consistent with CH addition to pyrrole followed by Helimination. The Photoionization Efficiency curve unambiguously identifies m/z = 79 as pyridine. With deuterated methylidyne radicals (CD), the product mass peak is shifted by +1 mass unit, consistent with the formation of C5H4DN and identified as deuterated pyridine (dpyridine). Within detection limits, there is no evidence that the addition intermediate complex undergoes hydrogen scrambling. The results are consistent with a reaction mechanism that proceeds via the direct CH (CD) cycloaddition or insertion into the five-member pyrrole ring, giving rise to ring expansion, followed by H atom elimination from the nitrogen atom in the intermediate to form the resonance stabilized pyridine (d-pyridine) molecule. Implications to interstellar chemistry and planetary atmospheres, in particular Titan, as well as in gas-phase combustion processes, are discussed.

  8. Electron Transfer Reactions in Colloidal Quantum Dot-Ligand Complexes

    NASA Astrophysics Data System (ADS)

    Morris-Cohen, Adam Joshua

    This thesis describes a quantitative analysis of the chemical composition of colloidal II-VI quantum dot (QD)-ligand complexes and transient absorption experiments analyzing the rates of electron transfer reactions in these complexes functionalized with redox active ligands. Chemical analysis reveals that phosphonate impurities in the surfactants used to synthesize CdSe QDs are the dominant ligands on the surface of the QDs, and these phosphonate impurities cause size-dependent Cd-enrichment of the QD surface. A study of the adsorption equilibrium of solution-phase CdS quantum dots and acid-derivatized viologen ligands (V2+) reveals that the structure of the surfaces of the QDs depends on the concentration of the QDs. A new model based on the Langmuir isotherm that treats both the number of adsorbed ligands per QD and the number of available binding sites per QD as binomially-distributed quantities is described. Transient absorption spectroscopy of solution-phase mixtures of colloidal CdS QDs and V2+ indicates electron transfer occurs from the conduction band of the QD to the LUMO of V2+. The rate constant for photoinduced electron transfer (PET) is independent of the number of methylene groups in the alkyl chain on the acid-derivatized viologen. The insensitivity of the electron transfer rate constant to the length of the functional groups on the viologen suggests a van der Waals (vdW) pathway for PET, where the electron bypasses the alkylcarboxylate and tunnels through the orbitals of the QD and of the bipyridinium core. The rate of PET from colloidal CdSe quantum dots (QDs) to oxo-centered triruthenium clusters (Ru 3O) depends on the structure of the chemical headgroup by which the Ru3O clusters adsorb to the QDs. Complexes comprising QDs and Ru 3O clusters adsorbed through a pyridine-4-carboxylic acid ligand have a PET rate constant of (4.9 ± 0.9)×109 s -1 whereas complexes comprising QDs and Ru3O clusters adsorbed through a 4-mercaptopyridine ligand have an

  9. Formation of complex bacterial colonies via self-generated vortices

    NASA Astrophysics Data System (ADS)

    Czirók, András; Ben-Jacob, Eshel; Cohen, Inon; Vicsek, Tamás

    1996-08-01

    Depending on the environmental conditions bacterial colonies growing on agar surfaces can exhibit complex colony formation and various types of collective motion. Experimental results are presented concerning the hydrodynamics (vortices, migration of bacteria in clusters) and colony formation of a morphotype of Bacillus subtilis. Some of these features are not specific to this morphotype but also have been observed in several other bacterial strains, suggesting the presence of universal effects. A simple model of self-propelled particles is proposed, which is capable of describing the hydrodynamics on the intermediate level, including the experimentally observed rotating disks of bacteria. The colony formation is captured by a complex generic model taking into account nutrient diffusion, reproduction, and sporulation of bacteria, extracellular slime deposition, chemoregulation, and inhomogeneous population. Our model also sheds light on some possible biological benefits of this ``multicellular behavior.''

  10. Mössbauer study of peroxynitrito complex formation with FeIII-chelates

    NASA Astrophysics Data System (ADS)

    Homonnay, Zoltan; Buszlai, Peter; Nádor, Judit; Sharma, Virender K.; Kuzmann, Erno; Vértes, Attila

    2012-03-01

    The reaction of the μ-oxo-diiron(III)-L complex (L = EDTA, ethylene diamine tetraacetate, HEDTA, hydroxyethyl ethylene diamine triacetate, and CyDTA, cyclohexane diamine tetraacetate) with peroxynitrite in alkaline solution was studied by Mössbauer spectroscopy using rapid-freezing technique. These complexes yield an (L)FeIII( η 2-O2)^{3-} complex ion when they react with hydrogen peroxide and the formation of the peroxide adduct results in a deep purple coloration of the solution. The same color appears when the reaction occurs with peroxinitrite. Although spectrophotometry indicated some difference between the molar extinction coefficients of the peroxo and the peroxinitrito adducts, the Mössbauer parameters proved to be the same within experimental error. It is concluded that the peroxynitrite ion decomposes when reacting with FeIII(L) and the peroxo adduct forms.

  11. Multiscale Informatics for Low-Temperature Propane Oxidation: Further Complexities in Studies of Complex Reactions.

    PubMed

    Burke, Michael P; Goldsmith, C Franklin; Klippenstein, Stephen J; Welz, Oliver; Huang, Haifeng; Antonov, Ivan O; Savee, John D; Osborn, David L; Zádor, Judit; Taatjes, Craig A; Sheps, Leonid

    2015-07-16

    The present paper describes further development of the multiscale informatics approach to kinetic model formulation of Burke et al. (Burke, M. P.; Klippenstein, S. J.; Harding, L. B. Proc. Combust. Inst. 2013, 34, 547-555) that directly incorporates elementary kinetic theories as a means to provide reliable, physics-based extrapolation of kinetic models to unexplored conditions. Here, we extend and generalize the multiscale informatics strategy to treat systems of considerable complexity-involving multiwell reactions, potentially missing reactions, nonstatistical product branching ratios, and non-Boltzmann (i.e., nonthermal) reactant distributions. The methodology is demonstrated here for a subsystem of low-temperature propane oxidation, as a representative system for low-temperature fuel oxidation. A multiscale model is assembled and informed by a wide variety of targets that include ab initio calculations of molecular properties, rate constant measurements of isolated reactions, and complex systems measurements. Active model parameters are chosen to accommodate both "parametric" and "structural" uncertainties. Theoretical parameters (e.g., barrier heights) are included as active model parameters to account for parametric uncertainties in the theoretical treatment; experimental parameters (e.g., initial temperatures) are included to account for parametric uncertainties in the physical models of the experiments. RMG software is used to assess potential structural uncertainties due to missing reactions. Additionally, branching ratios among product channels are included as active model parameters to account for structural uncertainties related to difficulties in modeling sequences of multiple chemically activated steps. The approach is demonstrated here for interpreting time-resolved measurements of OH, HO2, n-propyl, i-propyl, propene, oxetane, and methyloxirane from photolysis-initiated low-temperature oxidation of propane at pressures from 4 to 60 Torr and

  12. Photochemical Reactions of Fluorinated Pyridines at Half-Sandwich Rhodium Complexes: Competing Pathways of Reaction

    PubMed Central

    2013-01-01

    Irradiation of CpRh(PMe3)(C2H4) (1; Cp = η5-C5H5) in the presence of pentafluoropyridine in hexane solution at low temperature yields an isolable η2-C,C-coordinated pentafluoropyridine complex, CpRh(PMe3)(η2-C,C-C5NF4) (2). The molecular structure of 2 was determined by single-crystal X-ray diffraction, showing coordination by C3–C4, unlike previous structures of pentafluoropyridine complexes that show N-coordination. Corresponding experiments with 2,3,5,6-tetrafluoropyridine yield the C–H oxidative addition product CpRh(PMe3)(C5NF4)H (3). In contrast, UV irradiation of 1 in hexane, in the presence of 4-substituted tetrafluoropyridines C5NF4X, where X = NMe2, OMe, results in elimination of C2H4 and HF to form the metallacycles CpRh(PMe3)(κ2-C,C-CH2N(CH3)C5NF3) (4) and CpRh(PMe3)(κ2-C,C-CH2OC5NF3) (5), respectively. The X-ray structure of 4 shows a planar RhCCNC-five-membered ring. Complexes 2–5 may also be formed by thermal reaction of CpRh(PMe3)(Ph)H with the respective pyridines at 50 °C. PMID:24563575

  13. Photochemical reactions of metal nitrosyl complexes. Mechanisms of NO reactions with biologically relevant metal centers

    DOE PAGESBeta

    Ford, Peter C.

    2001-01-01

    Tmore » he discoveries that nitric oxide (a.k.a. nitrogen monoxide) serves important roles in mammalian bioregulation and immunology have stimulated intense interest in the chemistry and biochemistry of NO and derivatives such as metal nitrosyl complexes. Also of interest are strategies to deliver NO to biological targets on demand. One such strategy would be to employ a precursor which displays relatively low thermal reactivity but is photochemically active to release NO.his proposition led us to investigate laser flash and continuous photolysis kinetics of nitrosyl complexes such as the Roussin's iron-sulfur-nitrosyl cluster anions Fe 2 S 2 ( NO ) 4 2 − and Fe 4 S 3 ( NO ) 7 − and several ruthenium salen and porphyrin nitrosyls.hese include studies using metal-nitrosyl photochemistry as a vehicle for delivering NO to hypoxic cell cultures in order to sensitize γ -radiation damage. Also studied were the rates and mechanisms of NO “on” reactions with model water soluble heme compounds, the ferriheme protein met-myoglobin and various ruthenium complexes using ns laser flash photolysis techniques. An overview of these studies is presented.« less

  14. Ubisemiquinone is the electron donor for superoxide formation by complex III of heart mitochondria.

    PubMed

    Turrens, J F; Alexandre, A; Lehninger, A L

    1985-03-01

    Much evidence indicates that superoxide is generated from O2 in a cyanide-sensitive reaction involving a reduced component of complex III of the mitochondrial respiratory chain, particularly when antimycin A is present. Although it is generally believed that ubisemiquinone is the electron donor to O2, little experimental evidence supporting this view has been reported. Experiments with succinate as electron donor in the presence of antimycin A in intact rat heart mitochondria, which contain much superoxide dismutase but little catalase, showed that myxothiazol, which inhibits reduction of the Rieske iron-sulfur center, prevented formation of hydrogen peroxide, determined spectrophotometrically as the H2O2-peroxidase complex. Similarly, depletion of the mitochondria of their cytochrome c also inhibited formation of H2O2, which was restored by addition of cytochrome c. These observations indicate that factors preventing the formation of ubisemiquinone also prevent H2O2 formation. They also exclude ubiquinol, which remains reduced under these conditions, as the reductant of O2. Since cytochrome b also remains fully reduced when myxothiazol is added to succinate- and antimycin A-supplemented mitochondria, reduced cytochrome b may also be excluded as the reductant of O2. These observations, which are consistent with the Q-cycle reactions, by exclusion of other possibilities leave ubisemiquinone as the only reduced electron carrier in complex III capable of reducing O2 to O2-. PMID:2983613

  15. a Model Study of Complex Behavior in the Belousov - Reaction.

    NASA Astrophysics Data System (ADS)

    Lindberg, David Mark

    1988-12-01

    We have studied the complex oscillatory behavior in a model of the Belousov-Zhabotinskii (BZ) reaction in a continuously-fed stirred tank reactor (CSTR). The model consisted of a set of nonlinear ordinary differential equations derived from a reduced mechanism of the chemical system. These equations were integrated numerically on a computer, which yielded the concentrations of the constituent chemicals as functions of time. In addition, solutions were tracked as functions of a single parameter, the stability of the solutions was determined, and bifurcations of the solutions were located and studied. The intent of this study was to use this BZ model to explore further a region of complex oscillatory behavior found in experimental investigations, the most thorough of which revealed an alternating periodic-chaotic (P-C) sequence of states. A P-C sequence was discovered in the model which showed the same qualitative features as the experimental sequence. In order to better understand the P-C sequence, a detailed study was conducted in the vicinity of the P-C sequence, with two experimentally accessible parameters as control variables. This study mapped out the bifurcation sets, and included examination of the dynamics of the stable periodic, unstable periodic, and chaotic oscillatory motion. Observations made from the model results revealed a rough symmetry which suggests a new way of looking at the P-C sequence. Other nonlinear phenomena uncovered in the model were boundary and interior crises, several codimension-two bifurcations, and similarities in the shapes of areas of stability for periodic orbits in two-parameter space. Each earlier model study of this complex region involved only a limited one-parameter scan and had limited success in producing agreement with experiments. In contrast, for those regions of complex behavior that have been studied experimentally, the observations agree qualitatively with our model results. Several new predictions of the model

  16. Standard thermodynamic functions of complex formation between Cu2+ and glycine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Gorboletova, G. G.; Metlin, A. A.

    2013-05-01

    Heat effects of the interaction of copper(II) solutions with aminoacetic acid (glycine) are measured by the direct calorimetry at 298.15 K and ionic strengths of 0.5, 1.0, and 1.5 against a background of potassium nitrate. Standard enthalpy values for reactions of the formation of aminoacetic acid copper complexes in aqueous solutions are obtained using an equation with a single individual parameter by extrapolating it to zero ionic strength. The standard thermodynamic characteristics of complex formation in the Cu2+-glycine system are calculated. It is shown that glycine-like coordination is most likely in Cu(II) complexes with L-asparagine, L-glutamine, and L-valine.

  17. Insights into the Halogen Oxidative Addition Reaction to Dinuclear Gold(I) Di(NHC) Complexes.

    PubMed

    Baron, Marco; Tubaro, Cristina; Basato, Marino; Isse, Abdirisak Ahmed; Gennaro, Armando; Cavallo, Luigi; Graiff, Claudia; Dolmella, Alessandro; Falivene, Laura; Caporaso, Lucia

    2016-07-11

    Gold(I) dicarbene complexes [Au2 (MeIm-Y-ImMe)2 ](PF6 )2 (Y=CH2 (1), (CH2 )2 (2), (CH2 )4 (4), MeIm=1-methylimidazol-2-ylidene) react with iodine to give the mixed-valence complex [Au(MeIm-CH2 -ImMe)2 AuI2 ](PF6 )2 (1 a(I) ) and the gold(III) complexes [Au2 I4 (MeIm-Y-ImMe)2 ](PF6 )2 (2 c(I) and 4 c(I) ). Reaction of complexes 1 and 2 with an excess of ICl allows the isolation of the tetrachloro gold(III) complexes [Au2 Cl4 (MeIm-CH2 -ImMe)2 ](PF6 )2 (1 c(Cl) ) and [Au2 Cl4 (MeIm-(CH2 )2 -ImMe)2 ](Cl)2 (2 c(Cl) -Cl) (as main product); remarkably in the case of complex 2, the X-ray molecular structure of the crystals also shows the presence of I-Au-Cl mixed-sphere coordination. The same type of coordination has been observed in the main product of the reaction of complexes 3 or 4 with ICl. The study of the reactivity towards the oxidative addition of halogens to a large series of dinuclear bis(dicarbene) gold(I) complexes has been extended and reviewed. The complexes react with Cl2 , Br2 and I2 to give the successive formation of the mixed-valence gold(I)/gold(III) n a(X) and gold(III) n c(X) (excluding compound 1 c(I) ) complexes. However, complex 3 affords with Cl2 and Br2 the gold(II) complex 3 b(X) [Au2 X2 (MeIm-(CH2 )3 -ImMe)2 ](PF6 )2 (X=Cl, Br), which is the predominant species over compound 3 c(X) even in the presence of free halogen. The observed different relative stabilities of the oxidised complexes of compounds 1 and 3 have also been confirmed by DFT calculations. PMID:27297191

  18. Reactivity of thiosemicarbazides with redox active metal ions: controlled formation of coordination complexes versus heterocyclic compounds.

    PubMed

    López-Torres, Elena; Dilworth, Jonathan R

    2009-01-01

    The reactions of 1,1-dimethyl-4-phenylthiosemicarbazide (LH) with Cu(II) and Sn(IV) have been investigated. If THF or methanol is used as solvent with Cu(II), oxidative cyclisation and coupling are observed, yielding a 1,2,4-thiadiazole or a 1,3,4-thiadiazolium salt. SnI(4) is also able to induce oxidative coupling of two thiosemicarbazide ligands, yielding 1,2,4-thiadiazolium or 1,2,4-triazolium salts, with I(3)(-) as the counterion, depending on the reaction conditions. By contrast, reaction of LH with SnI(4) in acetone yields a 1,3-thiazolium salt, with I(-) as counterion. Reaction with Cu(II) salts or SnI(4) in basic media leads to the formation of metal complexes containing two deprotonated thiosemicarbazide ligands. In the reaction of CuCl(2) in water in the presence of acid a complex containing two neutral ligands is obtained. Reactions with SnCl(4) are not able to induce ligand cyclisation, although a coordination compound with two neutral ligands was isolated from methanol. PMID:19180593

  19. Reversible Dissociation and Ligand-Glutathione Exchange Reaction in Binuclear Cationic Tetranitrosyl Iron Complex with Penicillamine

    PubMed Central

    Syrtsova, Lidia; Sanina, Natalia; Lyssenko, Konstantin; Kabachkov, Evgeniy; Psikha, Boris; Shkondina, Natal'ja; Pokidova, Olesia; Kotelnikov, Alexander; Aldoshin, Sergey

    2014-01-01

    This paper describes a comparative study of the decomposition of two nitrosyl iron complexes (NICs) with penicillamine thiolic ligands [Fe2(SC5H11NO2)2(NO)4]SO4·5H2O (I) and glutathione- (GSH-) ligands [Fe2(SC10H17N3O6)2(NO)4]SO4·2H2O (II), which spontaneously evolve to NO in aqueous medium. NO formation was measured by a sensor electrode and by spectrophotometric methods by measuring the formation of a hemoglobin- (Hb-) NO complex. The NO evolution reaction rate from (I)  k1 = (4.6 ± 0.1)·10−3 s−1 and the elimination rate constant of the penicillamine ligand k2 = (1.8 ± 0.2)·10−3 s−1 at 25°C in 0.05 M phosphate buffer,  pH 7.0, was calculated using kinetic modeling based on the experimental data. Both reactions are reversible. Spectrophotometry and mass-spectrometry methods have firmly shown that the penicillamine ligand is exchanged for GS− during decomposition of 1.5·10−4 M (I) in the presence of 10−3 M GSH, with 76% yield in 24 h. As has been established, such behaviour is caused by the resistance of (II) to decomposition due to the higher affinity of iron to GSH in the complex. The discovered reaction may impede S-glutathionylation of the essential enzyme systems in the presence of (I) and is important for metabolism of NIC, connected with its antitumor activity. PMID:24790592

  20. Reversible dissociation and ligand-glutathione exchange reaction in binuclear cationic tetranitrosyl iron complex with penicillamine.

    PubMed

    Syrtsova, Lidia; Sanina, Natalia; Lyssenko, Konstantin; Kabachkov, Evgeniy; Psikha, Boris; Shkondina, Natal'ja; Pokidova, Olesia; Kotelnikov, Alexander; Aldoshin, Sergey

    2014-01-01

    This paper describes a comparative study of the decomposition of two nitrosyl iron complexes (NICs) with penicillamine thiolic ligands [Fe2(SC5H11NO2)2(NO)4]SO4 ·5H2O (I) and glutathione- (GSH-) ligands [Fe2(SC10H17N3O6)2(NO)4]SO4 ·2H2O (II), which spontaneously evolve to NO in aqueous medium. NO formation was measured by a sensor electrode and by spectrophotometric methods by measuring the formation of a hemoglobin- (Hb-) NO complex. The NO evolution reaction rate from (I)  k 1 = (4.6 ± 0.1)·10(-3) s(-1) and the elimination rate constant of the penicillamine ligand k 2 = (1.8 ± 0.2)·10(-3) s(-1) at 25°C in 0.05 M phosphate buffer,  pH 7.0, was calculated using kinetic modeling based on the experimental data. Both reactions are reversible. Spectrophotometry and mass-spectrometry methods have firmly shown that the penicillamine ligand is exchanged for GS(-) during decomposition of 1.5·10(-4) M (I) in the presence of 10(-3) M GSH, with 76% yield in 24 h. As has been established, such behaviour is caused by the resistance of (II) to decomposition due to the higher affinity of iron to GSH in the complex. The discovered reaction may impede S-glutathionylation of the essential enzyme systems in the presence of (I) and is important for metabolism of NIC, connected with its antitumor activity. PMID:24790592

  1. Positronium formation studies in crystalline molecular complexes: Triphenylphosphine oxide - Acetanilide

    NASA Astrophysics Data System (ADS)

    Oliveira, F. C.; Denadai, A. M. L.; Guerra, L. D. L.; Fulgêncio, F. H.; Windmöller, D.; Santos, G. C.; Fernandes, N. G.; Yoshida, M. I.; Donnici, C. L.; Magalhães, W. F.; Machado, J. C.

    2013-04-01

    Hydrogen bond formation in the triphenylphosphine oxide (TPPO), acetanilide (ACN) supramolecular heterosynton system, named [TPPO0.5·ACN0.5], has been studied by Positron Annihilation Lifetime Spectroscopy (PALS) and supported by several analytical techniques. In toluene solution, Isothermal Titration Calorimetry (ITC) presented a 1:1 stoichiometry and indicated that the complexation process is driven by entropy, with low enthalpy contribution. X-ray structure determination showed the existence of a three-dimensional network of hydrogen bonds, allowing also the confirmation of the existence of a 1:1 crystalline molecular complex in solid state. The results of thermal analysis (TGA, DTA and DSC) and FTIR spectroscopy showed that the interactions in the complex are relatively weaker than those found in pure precursors, leading to a higher positronium formation probability at [TPPO0.5·ACN0.5]. These weak interactions in the complex enhance the possibility of the n- and π-electrons to interact with positrons and consequently, the probability of positronium formation is higher. Through the present work is shown that PALS is a sensible powerful tool to investigate intermolecular interactions in solid heterosynton supramolecular systems.

  2. Accelerating procelain formation by incorporating a complex additive

    SciTech Connect

    Maslennikova, G.N.; Dubovitskii, S.A.; Moroz, I.K.

    1986-05-01

    The authors studied the influence of a complex additive consisting of oxides of calcium, zinc, and magnesium on the formaton of porcelain. In order to achieve a more uniform distribution of the complex additive in the porcelain body it was incorporated in the form of water soluble salts-nitrates, which ensured comparability of results and excluded the effect of the different types of anions. The study of the main parameters of sintering (porosity, shrinkage, and mechanical strength) for the test bodies showed that they sinter at lower temperatures and attain zero porosity, maximum shrinkage, and mechanical strength. The most typical bodies indentified in this way were investigated by methods of complex differential thermal analysis and x-ray diffraction. Thus, the introduction of complex additives consisting of calcium, zinc, and magnesium oxides contributes to the earlier formation of porcelain. With the reduction of firing temperatures by 100/sup 0/C the authors observe an improvement in the basic properties of porcelain.

  3. Thermodynamics and Complexation Reactions of Anionic Silicate Species

    SciTech Connect

    Choppin, Gregory R.; Felmy, Andrew R.

    2001-06-01

    Highly basic tank wastes contain several important radionuclides, including {sup 90}Sr, {sup 99}Tc, and {sup 60}Co as well as actinide elements (isotopes of U, Pu and Am). A fraction of these wastes are known to have leaked into the vadose zone at the Hanford Site. Upon entering the sediments in the vadose zone, such highly basic solutions dissolve concentrations of silica from the silica and aluminosilicate minerals present in subsurface. These dissolution reactions alter the chemical composition of the leaking solutions, transforming them from highly basic (as high as 2 M NaOH) solution into a pore solution with dissolved silica and significantly reduced pH. This moderately basic (pH 9 to 10), high-silica solution has the potential to complex radionuclides and promote migration through the subsurface. This path of radionuclide migration currently is not a recognized transport mode in the factors that are modeled for radionuclide transport through the vadose zone beneath leaking tanks. The goal of this project is to ascertain the free monosilicic acid concentration, and the degree of polymerization as a function of pH and total concentration of silicate ions, and to use this data to measure the interaction of radionuclides of Co(II), Sr(II), Nd(III), Eu(III), Am(III), U(VI) and Th(IV) with the ionic silicate.

  4. Reactions of Co(III)-nitrosyl complexes with superoxide and their mechanistic insights.

    PubMed

    Kumar, Pankaj; Lee, Yong-Min; Park, Young Jun; Siegler, Maxime A; Karlin, Kenneth D; Nam, Wonwoo

    2015-04-01

    New Co(III)-nitrosyl complexes bearing N-tetramethylated cyclam (TMC) ligands, [(12-TMC)Co(III)(NO)](2+) (1) and [(13-TMC)Co(III)(NO)](2+) (2), were synthesized via [(TMC)Co(II)(CH3CN)](2+) + NO(g) reactions. Spectroscopic and structural characterization showed that these compounds bind the nitrosyl moiety in a bent end-on fashion. Complexes 1 and 2 reacted with KO2/2.2.2-cryptand to produce [(12-TMC)Co(II)(NO2)](+) (3) and [(13-TMC)Co(II)(NO2)](+) (4), respectively; these possess O,O'-chelated nitrito ligands. Mechanistic studies using (18)O-labeled superoxide ((18)O2(•-)) showed that one O atom in the nitrito ligand is derived from superoxide and the O2 produced comes from the other superoxide O atom. Evidence supporting the formation of a Co-peroxynitrite intermediate is also presented. PMID:25793706

  5. Complexation Key to a pH Locked Redox Reaction

    ERIC Educational Resources Information Center

    Rizvi, Masood Ahmad; Dangat, Yuvraj; Shams, Tahir; Khan, Khaliquz Zaman

    2016-01-01

    An unfavorable pH can block a feasible electron transfer for a pH dependent redox reaction. In this experiment, a series of potentiometric titrations demonstrate the sequential loss in feasibility of iron(II) dichromate redox reaction over a pH range of 0-4. The pH at which this reaction failed to occur was termed as a pH locked reaction. The…

  6. Star Formation in Giant Complexes: the Cat's Paw Nebula

    NASA Astrophysics Data System (ADS)

    Ascenso, Joana; Wolk, Scott; Lombardi, Marco; Alves, João; Rathborne, Jill; Forbrich, Jan; Leibundgut, Bruno; Hilker, Michael

    2013-07-01

    NGC 6334, the Cat's Paw Nebula, is a 106 M⊙ molecular cloud, one of the most massive known clouds in the Galaxy. It hosts the youngest massive cluster complex within 2 kpc of the Sun, and is therefore an ideal laboratory to investigate the onset and early evolution of star formation in an environment comparable to that of massive, extra-galactic complexes. Using multi-wavelength data, we are conducting the most sensitive and most complete characterization of this unique region to date.

  7. Dienamine-Catalyzed Nitrone Formation via Redox Reaction.

    PubMed

    Fraboni, Americo J; Brenner-Moyer, Stacey E

    2016-05-01

    The first catalytic method to directly introduce nitrone functionality onto aldehyde substrates is described. This reaction proceeds by an unprecedented organocatalytic redox mechanism in which an enal is oxidized to the γ-nitrone via dienamine catalysis, thereby reducing an equivalent of nitrosobenzene. This reaction is a unique example of divergent reactivity of an enal, which represents a novel strategy for rapidly accessing small libraries of N,O-heterocycles. Alternatively, divergent reactivity can be suppressed simply by changing solvents. PMID:27070296

  8. Formation mechanisms of 3,4-dinitrofuroxan via nitration reaction of furoxan

    NASA Astrophysics Data System (ADS)

    Peng, Yajing; Ye, Yuqing; Liu, Jianyong; Lai, Weipeng

    2016-03-01

    A systematic investigations on the nitration of furoxan by two typical nitration reagents nitronium tetrafluoroborate (BF4NO2) and dilute nitric acid (HNO3) in chloroform (CHCl3) solvent using density functional theory (DFT) method to reveal the formation mechanism of 3,4-dinitrofuroxan (DNFO) and explore new synthesis routes. The geometry optimizations of the minima and transition states involved in the two nitration reactions are performed at the B3LYP/6-311++G** basis set level. The CCSD single-point energy corrections at the same level are carried out on top of the optimized geometries to obtain the accurate energy. Calculated results demonstrate that the electrophilic substitutions of nitronium ions from the nitration reagents and the abstractions of protons in the complex intermediates are the main formation mechanism of DNFO. BF4- is shown to be a better proton abstracter than HNO3 and H2O due to its no barrier combination with H+. The abstraction of proton by HNO3 is predicted to be more feasible than H2O because it can supply the nitration attacker (NO2+) and release more heat. Chloroform is a feasible solvent and heating properly is necessary for the two reactions due to the relatively high barrier of 37 kcal/mol. These conclusions provide some significant indications on the new experimental synthesis of DNFO.

  9. The Copper-nicotinamide complex: sustainable applications in coupling and cycloaddition reactions

    EPA Science Inventory

    Crystalline copper (II)-nicotinamide complex, synthesized via simple mixing of copper chloride and nicotinamide solution at room temperature, catalyzes the C-S, C-N bond forming and cycloaddition reactions under a variety of sustainable reaction conditions.

  10. Computational Analyses of Complex Flows with Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Bae, Kang-Sik

    missiles. The comprehensive skeletal mechanism consists of 58 species and 315 reactions including in CPD, Benzene formation process by the theory for polycyclic aromatic hydrocarbons (PAH) and soot formation process on the constant volume combustor, premixed flame characteristics.

  11. Three-Coordinate Terminal Imidoiron(III) Complexes: Structure, Spectroscopy, and Mechanism of Formation

    PubMed Central

    Cowley, Ryan E.; DeYonker, Nathan J.; Eckert, Nathan A.; Cundari, Thomas R.; DeBeer, Serena; Bill, Eckhard; Ottenwaelder, Xavier; Flaschenriem, Christine; Holland, Patrick L.

    2010-01-01

    Reaction of 1-adamantyl azide with iron(I) diketiminate precursors gives metastable but isolable imidoiron(III) complexes LFe=NAd (L = bulky β-diketiminate ligand; Ad = 1-adamantyl). This paper addresses: (1) the spectroscopic and structural characterization of the Fe=N multiple bond in these interesting three-coordinate iron imido complexes, and (2) the mechanism through which the imido complexes form. The iron(III) imido complexes have been examined by 1H NMR and EPR spectroscopies and temperature-dependent magnetic susceptibility (SQUID), and structurally characterized by crystallography and/or X-ray absorption (EXAFS) measurements. These data show that the imido complexes have quartet ground states and short (1.68 ± 0.01 Å) iron-nitrogen bonds. The formation of the imido complexes proceeds through unobserved iron–RN3 intermediates, which are indicated by QM/MM computations to be best described as iron(II) with an RN3 radical anion. The radical character on the organoazide bends its NNN linkage to enable easy N2 loss and imido complex formation. The product distribution between imidoiron(III) products and hexazene-bridged diiron(II) products is solvent-dependent, and the solvent dependence can be explained by coordination of certain solvents to the iron(I) precursor prior to interaction with the organoazide. PMID:20524625

  12. Pattern Formation and Reaction Textures during Dunite Carbonation

    NASA Astrophysics Data System (ADS)

    Lisabeth, H. P.; Zhu, W.

    2015-12-01

    Alteration of olivine-bearing rocks by fluids is one of the most pervasive geochemical processes on the surface of the Earth. Serpentinized and/or carbonated ultramafic rocks often exhibit characteristic textures on many scales, from polygonal mesh textures on the grain-scale to onion-skin or kernel patterns on the outcrop scale. Strong disequilibrium between pristine ultramafic rocks and common geological fluids such as water and carbon dioxide leads to rapid reactions and coupled mechanical and chemical feedbacks that manifest as characteristic textures. Textural evolution during metasomatic reactions can control effective reaction rates by modulating dynamic porosity and therefore reactant supply and reactive surface area. We run hydrostatic experiments on thermally cracked dunites saturated with carbon dioxide bearing brine at 15 MPa confining pressure and 150°C to explore the evolution of physical properties and reaction textures as carbon mineralization takes place in the sample. Compaction and permeability reduction are observed throughout experiments. Rates of porosity and permeability changes are sensitive to pore fluid chemistry. After reaction, samples are imaged in 3-dimension (3D) using a dual-beam FIB-SEM. Analysis of the high resolution 3D microstructure shows that permeable, highly porous domains are created by olivine dissolution at a characteristic distance from pre-existing crack surfaces while precipitation of secondary minerals such as serpentine and magnesite is limited largely to the primary void space. The porous dissolution channels provide an avenue for fluid ingress, allow reactions to continue and could lead to progressive hierarchical fracturing. Initial modeling of the system indicates that this texture is the result of coupling between dissolution-precipitation reactions and the local stress state of the sample.

  13. Demixing-stimulated lane formation in binary complex plasma

    SciTech Connect

    Du, C.-R.; Jiang, K.; Suetterlin, K. R.; Ivlev, A. V.; Morfill, G. E.

    2011-11-29

    Recently lane formation and phase separation have been reported for experiments with binary complex plasmas in the PK3-Plus laboratory onboard the International Space Station (ISS). Positive non-additivity of particle interactions is known to stimulate phase separation (demixing), but its effect on lane formation is unknown. In this work, we used Langevin dynamics (LD) simulation to probe the role of non-additivity interactions on lane formation. The competition between laning and demixing leads to thicker lanes. Analysis based on anisotropic scaling indices reveals a crossover from normal laning mode to a demixing-stimulated laning mode. Extensive numerical simulations enabled us to identify a critical value of the non-additivity parameter {Delta} for the crossover.

  14. The Dynamics of Coalition Formation on Complex Networks

    NASA Astrophysics Data System (ADS)

    Auer, S.; Heitzig, J.; Kornek, U.; Schöll, E.; Kurths, J.

    2015-08-01

    Complex networks describe the structure of many socio-economic systems. However, in studies of decision-making processes the evolution of the underlying social relations are disregarded. In this report, we aim to understand the formation of self-organizing domains of cooperation (“coalitions”) on an acquaintance network. We include both the network’s influence on the formation of coalitions and vice versa how the network adapts to the current coalition structure, thus forming a social feedback loop. We increase complexity from simple opinion adaptation processes studied in earlier research to more complex decision-making determined by costs and benefits, and from bilateral to multilateral cooperation. We show how phase transitions emerge from such coevolutionary dynamics, which can be interpreted as processes of great transformations. If the network adaptation rate is high, the social dynamics prevent the formation of a grand coalition and therefore full cooperation. We find some empirical support for our main results: Our model develops a bimodal coalition size distribution over time similar to those found in social structures. Our detection and distinguishing of phase transitions may be exemplary for other models of socio-economic systems with low agent numbers and therefore strong finite-size effects.

  15. The Dynamics of Coalition Formation on Complex Networks

    PubMed Central

    Auer, S.; Heitzig, J.; Kornek, U.; Schöll, E.; Kurths, J.

    2015-01-01

    Complex networks describe the structure of many socio-economic systems. However, in studies of decision-making processes the evolution of the underlying social relations are disregarded. In this report, we aim to understand the formation of self-organizing domains of cooperation (“coalitions”) on an acquaintance network. We include both the network’s influence on the formation of coalitions and vice versa how the network adapts to the current coalition structure, thus forming a social feedback loop. We increase complexity from simple opinion adaptation processes studied in earlier research to more complex decision-making determined by costs and benefits, and from bilateral to multilateral cooperation. We show how phase transitions emerge from such coevolutionary dynamics, which can be interpreted as processes of great transformations. If the network adaptation rate is high, the social dynamics prevent the formation of a grand coalition and therefore full cooperation. We find some empirical support for our main results: Our model develops a bimodal coalition size distribution over time similar to those found in social structures. Our detection and distinguishing of phase transitions may be exemplary for other models of socio-economic systems with low agent numbers and therefore strong finite-size effects. PMID:26303622

  16. The Dynamics of Coalition Formation on Complex Networks.

    PubMed

    Auer, S; Heitzig, J; Kornek, U; Schöll, E; Kurths, J

    2015-01-01

    Complex networks describe the structure of many socio-economic systems. However, in studies of decision-making processes the evolution of the underlying social relations are disregarded. In this report, we aim to understand the formation of self-organizing domains of cooperation ("coalitions") on an acquaintance network. We include both the network's influence on the formation of coalitions and vice versa how the network adapts to the current coalition structure, thus forming a social feedback loop. We increase complexity from simple opinion adaptation processes studied in earlier research to more complex decision-making determined by costs and benefits, and from bilateral to multilateral cooperation. We show how phase transitions emerge from such coevolutionary dynamics, which can be interpreted as processes of great transformations. If the network adaptation rate is high, the social dynamics prevent the formation of a grand coalition and therefore full cooperation. We find some empirical support for our main results: Our model develops a bimodal coalition size distribution over time similar to those found in social structures. Our detection and distinguishing of phase transitions may be exemplary for other models of socio-economic systems with low agent numbers and therefore strong finite-size effects. PMID:26303622

  17. Correlations between Community Structure and Link Formation in Complex Networks

    PubMed Central

    Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

    2013-01-01

    Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

  18. Ab initio reaction kinetics of hydrogen abstraction from methyl formate by hydrogen, methyl, oxygen, hydroxyl, and hydroperoxy radicals.

    PubMed

    Tan, Ting; Pavone, Michele; Krisiloff, David B; Carter, Emily A

    2012-08-23

    Combustion of renewable biofuels, including energy-dense biodiesel, is expected to contribute significantly toward meeting future energy demands in the transportation sector. Elucidating detailed reaction mechanisms will be crucial to understanding biodiesel combustion, and hydrogen abstraction reactions are expected to dominate biodiesel combustion during ignition. In this work, we investigate hydrogen abstraction by the radicals H·, CH(3)·, O·, HO(2)·, and OH· from methyl formate, the simplest surrogate for complex biodiesels. We evaluate the H abstraction barrier heights and reaction enthalpies, using multireference correlated wave function methods including size-extensivity corrections and extrapolation to the complete basis set limit. The barrier heights predicted for abstraction by H·, CH(3)·, and O· are in excellent agreement with derived experimental values, with errors ≤1 kcal/mol. We also predict the reaction energetics for forming reactant complexes, transition states, and product complexes for reactions involving HO(2)· and OH·. High-pressure-limit rate constants are computed using transition state theory within the separable-hindered-rotor approximation for torsions and the harmonic oscillator approximation for other vibrational modes. The predicted rate constants differ significantly from those appearing in the latest combustion kinetics models of these reactions. PMID:22830521

  19. ESI formation of a Meisenheimer complex from tetryl and its unusual dissociation.

    PubMed

    Hubert, Cécile; Dossmann, Héloïse; Machuron-Mandard, Xavier; Tabet, Jean-Claude

    2013-03-01

    The reactivity of the explosive tetryl (N-methyl-N,2,4,6-tetranitroaniline; Mw = 287 u) was studied using electrospray ionization in negative mode. The main species detected in the spectrum corresponds to the ion observed at m/z 318 (previously assumed to be the odd-electron ion [tetryl + HNO](-•), C7H6O9N6). In this study, we show using D-labeling combined with high-resolution mass spectrometry that this species corresponds to an even-electron anion (i.e. C8H8O9N5), resulting from the formation of a Meisenheimer complex between tetryl and the methanol used as the solvent. Fragmentation of this complex under CID conditions revealed an unexpected fragment: the formation of a 2,4,6-trinitrophenoxide anion at m/z 228. (18)O-labeling combined with quantum chemical calculations helped us better understand the reaction pathways and mechanisms involved in the formation of this product ion. This occurs via a transition state leading to a SN2-type reaction, consequently evolving toward an ion-dipole complex. The latter finally dissociates into deprotonated picric acid. PMID:23494785

  20. New fluorescence reactions in DNA cytochemistry. 2. Microscopic and spectroscopic studies on fluorescent aluminum complexes

    SciTech Connect

    Del Castillo, P.; Llorente, A.R.; Gomez, A.; Gosalvez, J.; Goyanes, V.J.; Stockert, J.C. )

    1990-02-01

    Metal-dye complexes are widely applied in light microscopic techniques for chromatin staining (e.g., hematoxylin and carmine), but fluorescent complexes between phosphate-binding cations and suitable ligands have been little used. Preformed and postformed Al complexes with different anionic dyes induced strong and selective fluorescence reactions in nuclei from chicken blood smears, frozen sections, paraffin-embedded sections and Epon-embedded sections of mouse and rat tissues, mitotic chromosomes, meiotic chromosomes and kinetoplasts of Trypanosoma cruzi epimastigotes. The DNA-dependent fluorescence of these structures showed a very low fading rate. The emission colors were related to the ligand. The most suitable compounds for forming fluorescent Al chelates were 8-hydroxyquinoline, morin, nuclear fast red and purpurin. Staining with diluted carmine solutions and InCl3 mordanting, followed by 8-hydroxyquinoline, also induced chromatin fluorescence. After treating isolated mouse chromosomes with the preformed complex Al-nuclear fast red, x-ray microanalysis indicated a P:Al:dye binding ratio of about 40:15:1. The selectivity, stability and easy formation of these fluorescent Al complexes are obvious advantages for their use as new cytochemical probes in cytologic studies.

  1. Synthesis and Hydride Transfer Reactions of Cobalt and Nickel Hydride Complexes to BX3 Compounds

    SciTech Connect

    Mock, Michael T.; Potter, Robert G.; O'Hagan, Molly J.; Camaioni, Donald M.; Dougherty, William G.; Kassel, W. S.; DuBois, Daniel L.

    2011-12-05

    Hydrides of numerous transition metal complexes can be generated by the heterolytic cleavage of H{sub 2} gas such that they offer alternatives to using main group hydrides in the regeneration of ammonia borane, a compound that has been intensely studied for hydrogen storage applications. Previously, we reported that HRh(dmpe){sub 2}, dmpe = 1,2-bis(dimethylphosphinoethane) was capable of reducing a variety of BX{sub 3} compounds having hydride affinity (HA) greater than or equal to HA of BEt{sub 3}. This study examines the reactivity of less expensive cobalt and nickel hydride complexes, (HCo(dmpe){sub 2} and [HNi(dmpe){sub 2}]{sup +}), to form B-H bonds. The hydride donor abilities ({Delta}G{sub H{sup -}}{sup o}) of HCo(dmpe){sub 2} and [HNi(dmpe){sub 2}]{sup +} were positioned on a previously established scale in acetonitrile that is cross-referenced with calculated HAs of BX{sub 3} compounds. The collective data guided our selection of BX{sub 3} compounds to investigate and aided our analysis of factors that determine favorability of hydride transfer. HCo(dmpe){sub 2} was observed to transfer H{sup -} to BX{sub 3} compounds with X = H, OC{sub 6}F{sub 5} and SPh. The reaction with B(SPh){sub 3} is accompanied by formation of (BH{sub 3}){sub 2}-dmpe and (BH{sub 2}SPh){sub 2}-dmpe products that follow from reduction of multiple BSPh bonds and loss of a dmpe ligand from Co. Reactions between HCo(dmpe){sub 2} and B(SPh){sub 3} in the presence of triethylamine result in formation of Et{sub 3}N-BH{sub 2}SPh and Et{sub 3}N-BH{sub 3} with no loss of dmpe ligand. Reactions of the cationic complex [HNi(dmpe){sub 2}]{sup +} with B(SPh){sub 3} under analogous conditions give Et{sub 3}N-BH{sub 2}SPh as the final product along with the nickel-thiolate complex [Ni(dmpe){sub 2}(SPh)]{sup +}. The synthesis and characterization of HCo(dedpe){sub 2} (dedpe = diethyldiphenyl(phosphino)ethane) from H{sub 2} and a base is also discussed; including the formation of an uncommon trans

  2. Synthesis and Hydride Transfer Reactions of Cobalt and Nickel Hydride Complexes to BX₃ Compounds

    SciTech Connect

    Mock, Michael T.; Potter, Robert G.; O'Hagan, Molly; Camaioni, Donald M.; Dougherty, William G.; Kassel, W. Scott; DuBois, Daniel L.

    2011-10-31

    Hydrides of numerous transition metal complexes can be generated by the heterolytic cleavage of H₂ gas such that they offer alternatives to using main group hydrides in the regeneration of ammonia borane, a compound that has been intensely studied for hydrogen storage applications. Previously, we reported that HRh(dmpe)₂ (dmpe = 1,2-bis(dimethylphosphinoethane)) was capable of reducing a variety of BX₃ compounds having a hydride affinity (HA) greater than or equal to the HA of BEt₃. This study examines the reactivity of less expensive cobalt and nickel hydride complexes, HCo(dmpe)₂ and [HNi(dmpe)₂]+, to form B–H bonds. The hydride donor abilities (ΔGH °) of HCo(dmpe)₂ and [HNi(dmpe)₂]+ were positioned on a previously established scale in acetonitrile that is cross-referenced with calculated HAs of BX₃ compounds. The collective data guided our selection of BX₃ compounds to investigate and aided our analysis of factors that determine favorability of hydride transfer. HCo(dmpe)₂ was observed to transfer H to BX₃ compounds with X = H, OC₆F₅, and SPh. The reaction with B(SPh)₃ is accompanied by the formation of dmpe-(BH₃)₂ and dmpe-(BH₂(SPh))₂ products that follow from a reduction of multiple B–SPh bonds and a loss of dmpe ligands from cobalt. Reactions between HCo(dmpe)₂ and B(SPh)₃ in the presence of triethylamine result in the formation of Et₃N–BH₂SPh and Et₃N–BH₃ with no loss of a dmpe ligand. Reactions of the cationic complex [HNi(dmpe)₂]+ with B(SPh)₃ under analogous conditions give Et₃N–BH₂SPh as the final product along with the nickel–thiolate complex [Ni(dmpe)₂(SPh)]+. The synthesis and characterization of HCo(dedpe)₂ (dedpe = Et₂PCH₂CH₂PPh₂) from H₂ and a base is also discussed, including the formation of an uncommon trans dihydride species, trans-[(H)₂Co(dedpe)₂][BF₄].

  3. Synthesis and hydride transfer reactions of cobalt and nickel hydride complexes to BX3 compounds.

    PubMed

    Mock, Michael T; Potter, Robert G; O'Hagan, Molly J; Camaioni, Donald M; Dougherty, William G; Kassel, W Scott; DuBois, Daniel L

    2011-12-01

    Hydrides of numerous transition metal complexes can be generated by the heterolytic cleavage of H(2) gas such that they offer alternatives to using main group hydrides in the regeneration of ammonia borane, a compound that has been intensely studied for hydrogen storage applications. Previously, we reported that HRh(dmpe)(2) (dmpe = 1,2-bis(dimethylphosphinoethane)) was capable of reducing a variety of BX(3) compounds having a hydride affinity (HA) greater than or equal to the HA of BEt(3). This study examines the reactivity of less expensive cobalt and nickel hydride complexes, HCo(dmpe)(2) and [HNi(dmpe)(2)](+), to form B-H bonds. The hydride donor abilities (ΔG(H(-))°) of HCo(dmpe)(2) and [HNi(dmpe)(2)](+) were positioned on a previously established scale in acetonitrile that is cross-referenced with calculated HAs of BX(3) compounds. The collective data guided our selection of BX(3) compounds to investigate and aided our analysis of factors that determine favorability of hydride transfer. HCo(dmpe)(2) was observed to transfer H(-) to BX(3) compounds with X = H, OC(6)F(5), and SPh. The reaction with B(SPh)(3) is accompanied by the formation of dmpe-(BH(3))(2) and dmpe-(BH(2)(SPh))(2) products that follow from a reduction of multiple B-SPh bonds and a loss of dmpe ligands from cobalt. Reactions between HCo(dmpe)(2) and B(SPh)(3) in the presence of triethylamine result in the formation of Et(3)N-BH(2)SPh and Et(3)N-BH(3) with no loss of a dmpe ligand. Reactions of the cationic complex [HNi(dmpe)(2)](+) with B(SPh)(3) under analogous conditions give Et(3)N-BH(2)SPh as the final product along with the nickel-thiolate complex [Ni(dmpe)(2)(SPh)](+). The synthesis and characterization of HCo(dedpe)(2) (dedpe = Et(2)PCH(2)CH(2)PPh(2)) from H(2) and a base is also discussed, including the formation of an uncommon trans dihydride species, trans-[(H)(2)Co(dedpe)(2)][BF(4)]. PMID:22040085

  4. Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe–S Assembly Complex

    PubMed Central

    Fox, Nicholas G.; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A.; Barondeau, David P.

    2015-01-01

    Iron–sulfur (Fe–S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe–S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe–S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe–S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe–S assembly complex. Here the kinetics of Fe–S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe–S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe–S assembly complex. PMID:26016518

  5. Complex formation between polyelectrolytes and oppositely charged oligoelectrolytes.

    PubMed

    Zhou, Jiajia; Barz, Matthias; Schmid, Friederike

    2016-04-28

    We study the complex formation between one long polyanion chain and many short oligocation chains by computer simulations. We employ a coarse-grained bead-spring model for the polyelectrolyte chains and model explicitly the small salt ions. We systematically vary the concentration and the length of the oligocation and examine how the oligocations affects the chain conformation, the static structure factor, the radial and axial distribution of various charged species, and the number of bound ions in the complex. At low oligocation concentration, the polyanion has an extended structure. Upon increasing the oligocation concentration, the polyanion chain collapses and forms a compact globule, but the complex still carries a net negative charge. Once the total charge of the oligocations is equal to that of the polyanion, the collapse stops and is replaced by a slow expansion. In this regime, the net charge on the complexes is positive or neutral, depending on the microion concentration in solution. The expansion can be explained by the reduction of the oligocation bridging. We find that the behavior and the structure of the complex are largely independent of the length of oligocations, and very similar to that observed when replacing the oligocations by multivalent salt cations, and conclude that the main driving force keeping the complex together is the release of monovalent counterions and coions. We speculate on the implications of this finding for the problem of controlled oligolyte release and oligolyte substitution. PMID:27131564

  6. Complex formation between polyelectrolytes and oppositely charged oligoelectrolytes

    NASA Astrophysics Data System (ADS)

    Zhou, Jiajia; Barz, Matthias; Schmid, Friederike

    2016-04-01

    We study the complex formation between one long polyanion chain and many short oligocation chains by computer simulations. We employ a coarse-grained bead-spring model for the polyelectrolyte chains and model explicitly the small salt ions. We systematically vary the concentration and the length of the oligocation and examine how the oligocations affects the chain conformation, the static structure factor, the radial and axial distribution of various charged species, and the number of bound ions in the complex. At low oligocation concentration, the polyanion has an extended structure. Upon increasing the oligocation concentration, the polyanion chain collapses and forms a compact globule, but the complex still carries a net negative charge. Once the total charge of the oligocations is equal to that of the polyanion, the collapse stops and is replaced by a slow expansion. In this regime, the net charge on the complexes is positive or neutral, depending on the microion concentration in solution. The expansion can be explained by the reduction of the oligocation bridging. We find that the behavior and the structure of the complex are largely independent of the length of oligocations, and very similar to that observed when replacing the oligocations by multivalent salt cations, and conclude that the main driving force keeping the complex together is the release of monovalent counterions and coions. We speculate on the implications of this finding for the problem of controlled oligolyte release and oligolyte substitution.

  7. A DFT computational study of the bis-silylation reaction of acetylene catalyzed by palladium complexes.

    PubMed

    Bottoni, Andrea; Higueruelo, Alicia Perez; Miscione, Gian Pietro

    2002-05-15

    In this paper we have investigated at the DFT(B3LYP) level the catalytic cycle for the bis-silylation reaction of alkynes promoted by palladium complexes. A model-system formed by an acetylene molecule, a disilane molecule, and the Pd(PH(3))(2) complex has been used. The most relevant features of this catalytic cycle can be summarized as follows: (i) The first step of the cycle is an oxidative addition involving H(3)Si-SiH(3) and Pd(PH(3))(2). It occurs easily and leads to the cis (SiH(3))(2)Pd(PH(3))(2) complex that is 5.39 kcal mol(-1) lower in energy than reactants. (ii) The transfer of the two silyl groups to the C-C triple bond does not occur in a concerted way, but involves many steps. (iii) The cis (SiH(3))(2)Pd(PH(3))(2) complex, obtained from the oxidative addition, is involved in the formation of the first C-Si bond (activation barrier of 18.34 kcal mol(-1)). The two intermediates that form in this step cannot lead directly to the formation of the final bis(silyl)ethene product. However, they can isomerize rather easily (the two possible isomerizations have a barrier of 16.79 and 7.17 kcal mol(-1)) to new more stable species. In both these new intermediates the second silyl group is adjacent to the acetylene moiety and the formation of the second C-Si bond can occur rapidly leading to the (Z)-bis(silyl)ethene, as experimentally observed. (iv) The whole catalytic process is exothermic by 41.54 kcal mol(-1), in quite good agreement with the experimental estimate of this quantity (about 40 kcal mol(-1)). PMID:11996593

  8. Long-lived excited states of zwitterionic copper(I) complexes for photoinduced cross-dehydrogenative coupling reactions.

    PubMed

    Wang, Bin; Shelar, Deepak Prakash; Han, Xian-Zhu; Li, Ting-Ting; Guan, Xiangguo; Lu, Wei; Liu, Kun; Chen, Yong; Fu, Wen-Fu; Che, Chi-Ming

    2015-01-12

    Four heteroleptic copper(I) complexes containing phenanthroline and monoanionic nido-carborane-diphosphine ligands have been prepared and structurally characterized by various spectroscopic techniques and X-ray diffraction. These complexes exhibit intense absorptions in the visible range and excited-state lifetimes on the microsecond scale. Their application in visible-light-induced cross-dehydrogenative coupling reactions was investigated. Preliminary studies showed that one of the four copper(I) complexes is an efficient catalyst for photoinduced oxidative C-H functionalization using oxygen as oxidant. Furthermore, α-functionalized tertiary amines were obtained in good-to-excellent yields by light irradiation (λ>420 nm) of a mixture of our Cu(I) complex, tertiary amines, and a variety of nucleophiles (nitroalkane, acetone, or indoles) under aerobic conditions. Electron paramagnetic resonance measurements provided evidence for the formation of superoxide radical anions (O2(-⋅)) rather than singlet oxygen ((1)O2) during these photocatalytic reactions. PMID:25413572

  9. An Investigation of Model Catalyzed Hydrocarbon Formation Reactions

    SciTech Connect

    Tysoe, W. T.

    2001-05-02

    Work was focused on two areas aimed at understanding the chemistry of realistic catalytic systems: (1) The synthesis and characterization of model supported olefin metathesis catalysts. (2) Understanding the role of the carbonaceous layer present on Pd(111) single crystal model catalysts during reaction.

  10. EXFOR BASICS A SHORT GUIDE TO THE NEUTRON REACTION DATA EXCHANGE FORMAT.

    SciTech Connect

    MCLANE,V.; NUCLEAR DATA CENTER NETWORK

    2000-05-19

    This manual is intended as a guide to users of nuclear reaction data compiled in the EXFOR format, and is not intended as a complete guide to the EXFOR System. EXFOR is the exchange format designed to allow transmission of nuclear reaction data between the Nuclear Reaction Data Centers. In addition to storing the data and its' bibliographic information, experimental information is also compiled. The status (e.g., the source of the data) and history (e.g., date of last update) of the data set is also included. EXFOR is designed for flexibility in order to meet the diverse needs of the nuclear reaction data centers. It was originally conceived for the exchange of neutron data and was developed through discussions among personnel from centers situated in Saclay, Vienna, Livermore and Brookhaven. It was accepted as the official exchange format of the neutron data centers at Saclay, Vienna, Brookhaven and Obninsk, at a meeting held in November 1969. As a result of two meetings held in 1975 and 1976 and attended by several charged-particle data centers, the format was further developed and adapted to cover all nuclear reaction data. The exchange format should not be confused with a center-to-user format. Although users may obtain data from the centers in the EXFOR format, other center-to-user formats have been developed to meet the needs of the users within each center's own sphere of responsibility. The EXFOR format, as outlined, allows a large variety of numerical data tables with explanatory and bibliographic information to be transmitted in a format: that is machine-readable (for checking and indicating possible errors); that can be read by personnel (for passing judgment on and correcting errors). The data presently included in the EXFOR exchange file include: a complete compilation of experimental neutron-induced reaction data, a selected compilation of charged-particle-induced reaction data, a selected compilation of photon-induced reaction data.

  11. EXFOR BASICS A SHORT GUIDE TO THE NEUTRON REACTION DATA EXCHANGE FORMAT.

    SciTech Connect

    MCLANE,V.; NUCLEAR DATA CENTER NETWORK

    2000-05-19

    This manual is intended as a guide to users of nuclear reaction data compiled in the EXFOR format, and is not intended as a complete guide to the EXFOR System. EXFOR is the exchange format designed to allow transmission of nuclear reaction data between the Nuclear Reaction Data Centers. In addition to storing the data and its' bibliographic information, experimental information is also compiled. The status (e.g., the source of the data) and history (e.g., date of last update) of the data set is also included. EXFOR is designed for flexibility in order to meet the diverse needs of the nuclear reaction data centers. It was originally conceived for the exchange of neutron data and was developed through discussions among personnel from centers situated in Saclay, Vienna, Livermore and Brookhaven. It was accepted as the official exchange format of the neutron data centers at Saclay, Vienna, Brookhaven and Obninsk, at a meeting held in November 1969.3 As a result of two meetings held in 1975 and 1976 and attended by several charged-particle data centers, the format was further developed and adapted to cover all nuclear reaction data. The exchange format should not be confused with a center-to-user format. Although users may obtain data from the centers in the EXFOR format, other center-to-user formats have been developed to meet the needs of the users within each center's own sphere of responsibility. The EXFOR format, as outlined, allows a large variety of numerical data tables with explanatory and bibliographic information to be transmitted in a format: l that is machine-readable (for checking and indicating possible errors); l that can be read by personnel (for passing judgment on and correcting errors). The data presently included in the EXFOR exchange file include: a complete compilation of experimental neutron-induced reaction data, a selected compilation of charged-particle-induced reaction data, a selected compilation of photon-induced reaction data.

  12. Unified reaction pathways for the prebiotic formation of RNA and DNA nucleobases.

    PubMed

    Jeilani, Yassin Aweis; Williams, Phoenix N; Walton, Sofia; Nguyen, Minh Tho

    2016-07-27

    The reaction pathways for the prebiotic formation of nucleobases are complex and lead to the formation of a mixture of products. In the past 50 years, there has been a concerted effort for identifying a unified mechanism for the abiotic origin of the biomolecules but with little success. In the present theoretical study, we identified two prominent precursors for the building up of RNA and DNA nucleobases under prebiotic conditions: (a) 1,2-diaminomaleonitrile (DAMN), which is a tetramer of hydrogen cyanide (HCN), and (b) formamide, a hydrolysis product of HCN; it is important to emphasize that HCN is the source of both precursors. We find that free radical pathways are potentially appropriate to account for the origin of nucleobases from HCN. The current study unites the formamide pathways with the DAMN pathways. The mechanisms for the formation of the RNA and DNA nucleobases (uracil, adenine, purine, cytosine) were studied by quantum chemical computations using density functional theory at the B3LYP/6-311G(d,p) level. All the routes involved proceed with relatively low energy barriers (within the error margin of DFT methods). We showed that the radical mechanisms for the formation of nucleobases could be unified through common precursors. The results demonstrated that 4-aminoimidazole-5-carbonitrile (AICN), which is a known precursor for nucleobases, is a product of DAMN. The overall mechanisms are internally consistent with the abiotic formation of the nucleobases, namely (a) under a meteoritic impact scenario on the early Earth's surface that generated high internal energy, and/or (b) in the (gas phase) interstellar regions without the presence of catalysts. PMID:27220279

  13. Complex formation with nucleic acids and aptamers alters the antigenic properties of platelet factor 4

    PubMed Central

    Jaax, Miriam E.; Krauel, Krystin; Marschall, Thomas; Brandt, Sven; Gansler, Julia; Fürll, Birgitt; Appel, Bettina; Fischer, Silvia; Block, Stephan; Helm, Christiane A.; Müller, Sabine; Preissner, Klaus T.

    2013-01-01

    The tight electrostatic binding of the chemokine platelet factor 4 (PF4) to polyanions induces heparin-induced thrombocytopenia, a prothrombotic adverse drug reaction caused by immunoglobulin G directed against PF4/polyanion complexes. This study demonstrates that nucleic acids, including aptamers, also bind to PF4 and enhance PF4 binding to platelets. Systematic assessment of RNA and DNA constructs, as well as 4 aptamers of different lengths and secondary structures, revealed that increasing length and double-stranded segments of nucleic acids augment complex formation with PF4, while single nucleotides or single-stranded polyA or polyC constructs do not. Aptamers were shown by circular dichroism spectroscopy to induce structural changes in PF4 that resemble those induced by heparin. Moreover, heparin-induced anti-human–PF4/heparin antibodies cross-reacted with human PF4/nucleic acid and PF4/aptamer complexes, as shown by an enzyme immunoassay and a functional platelet activation assay. Finally, administration of PF4/44mer–DNA protein C aptamer complexes in mice induced anti–PF4/aptamer antibodies, which cross-reacted with murine PF4/heparin complexes. These data indicate that the formation of anti-PF4/heparin antibodies in postoperative patients may be augmented by PF4/nucleic acid complexes. Moreover, administration of therapeutic aptamers has the potential to induce anti-PF4/polyanion antibodies and a prothrombotic diathesis. PMID:23673861

  14. Apparent anti-Woodward-Hoffmann addition to a nickel bis(dithiolene) complex: the reaction mechanism involves reduced, dimetallic intermediates.

    PubMed

    Dang, Li; Shibl, Mohamed F; Yang, Xinzheng; Harrison, Daniel J; Alak, Aiman; Lough, Alan J; Fekl, Ulrich; Brothers, Edward N; Hall, Michael B

    2013-04-01

    Nickel dithiolene complexes have been proposed as electrocatalysts for alkene purification. Recent studies of the ligand-based reactions of Ni(tfd)2 (tfd = S2C2(CF3)2) and its anion [Ni(tfd)2](-) with alkenes (ethylene and 1-hexene) showed that in the absence of the anion, the reaction proceeds most rapidly to form the intraligand adduct, which decomposes by releasing a substituted dihydrodithiin. However, the presence of the anion increases the rate of formation of the stable cis-interligand adduct, and decreases the rate of dihydrodithiin formation and decomposition. In spite of both computational and experimental studies, the mechanism, especially the role of the anion, remained somewhat elusive. We are now providing a combined experimental and computational study that addresses the mechanism and explains the role of the anion. A kinetic study (global analysis) for the reaction of 1-hexene is reported, which supports the following mechanism: (1) reversible intraligand addition, (2) oxidation of the intraligand addition product prior to decomposition, and (3) interligand adduct formation catalyzed by Ni(tfd)2(-). Density functional theory (DFT) calculations were performed on the Ni(tfd)2/Ni(tfd)2(-)/ethylene system to shed light on the selectivity of adduct formation in the absence of anion and on the mechanism in which Ni(tfd)2(-) shifts the reaction from intraligand addition to interligand addition. Computational results show that in the neutral system the free energy of activation for intraligand addition is lower than that for interligand addition, in agreement with the experimental results. The computations predict that the anion enhances the rate of the cis-interligand adduct formation by forming a dimetallic complex with the neutral complex. The [(Ni(tfd)2)2](-) dimetallic complex then coordinates ethylene and isomerizes to form a Ni,S-bound ethylene complex, which then rapidly isomerizes to the stable interligand adduct but not to the intraligand adduct

  15. Noble reactions for the actinides: safe gold-based access to organouranium and azide complexes

    SciTech Connect

    Thomson, Robert K; Graves, Christopher R; Scott, Brian L; Kiplinger, Jaqueline L

    2008-01-01

    Gold has had a profound impact on organic chemistry; its compounds are spectacular catalysts for many organic transformations involving the formation of C-C, C-O, C-N and CoS bonds, and have enabled unprecedented pathways for the functionalization of C-H and C-C bonds. In general, gold complexes have not been exploited as reagents in organometallic or inorganic chemistry, although a few gold(l) aryl and alkynyl compounds have been reported to undergo transmetalation with transition metal complexes. We have been developing methods for functionalizing uranium complexes and have shown that Cu(l)-X reagents effect the oxidation of uranium with formation of U-X bonds, providing easy chemical control over uranium in oxidation states ranging from U{sup III}{yields}U{sup VI}. Although a logical approach for the direct generation of U-carbon and U-azide bonds, this Cu-based platform is limited in scope as it only works for pure and isolable copper compounds. This is problematic given the instability of organocuprates and copper azides, which can detonate violently as isolated solids. As such, this route has been confined to the synthesis of select uranium phenylacetylide complexes. Over the past few years, a variety of stable gold(l) alkyl, alkenyl, aryl, alkynyl, and azide complexes have been reported, propelling us to investigate their potential as reagents within the oxidative functionalization platform. Unlike the related CU{sup I} systems, Au{sup I} reagents are easily derivatized, and are safe to handle and isolate. Herein, we report that gold(l)-phosphine compounds can undergo a new class of reaction, and are excellent reagents for the oxidative functionalization of uranium with azide and carbon anions.

  16. Titanium complex formation of organic ligands in titania gels.

    PubMed

    Nishikiori, Hiromasa; Todoroki, Kenta; Setiawan, Rudi Agus; Teshima, Katsuya; Fujii, Tsuneo; Satozono, Hiroshi

    2015-01-27

    Thin films of organic ligand-dispersing titania gels were prepared from titanium alkoxide sols containing ligand molecules by steam treatment without heating. The formation of the ligand-titanium complex and the photoinduced electron transfer process in the systems were investigated by photoelectrochemical measurements. The complex was formed between the 8-hydroxyquinoline (HQ) and titanium species, such as the titanium ion, on the titania nanoparticle surface through the oxygen and nitrogen atoms of the quinolate. A photocurrent was observed in the electrodes containing the complex due to the electron injection from the LUMO of the complex into the titania conduction band. A bidentate ligand, 2,3-dihydroxynaphthalene (DHN), formed the complex on the titania surface through dehydration between its two hydroxyl groups of DHN and two TiOH groups of the titania. The electron injection from the HOMO of DHN to the titania conduction band was observed during light irradiation. This direct electron injection was more effective than the two-step electron injection. PMID:25535798

  17. Formation of a Ternary Complex for Selenocysteine Biosynthesis in Bacteria.

    PubMed

    Silva, Ivan R; Serrão, Vitor H B; Manzine, Livia R; Faim, Lívia M; da Silva, Marco T A; Makki, Raphaela; Saidemberg, Daniel M; Cornélio, Marinônio L; Palma, Mário S; Thiemann, Otavio H

    2015-12-01

    The synthesis of selenocysteine-containing proteins (selenoproteins) involves the interaction of selenocysteine synthase (SelA), tRNA (tRNA(Sec)), selenophosphate synthetase (SelD, SPS), a specific elongation factor (SelB), and a specific mRNA sequence known as selenocysteine insertion sequence (SECIS). Because selenium compounds are highly toxic in the cellular environment, the association of selenium with proteins throughout its metabolism is essential for cell survival. In this study, we demonstrate the interaction of SPS with the SelA-tRNA(Sec) complex, resulting in a 1.3-MDa ternary complex of 27.0 ± 0.5 nm in diameter and 4.02 ± 0.05 nm in height. To assemble the ternary complex, SPS undergoes a conformational change. We demonstrated that the glycine-rich N-terminal region of SPS is crucial for the SelA-tRNA(Sec)-SPS interaction and selenoprotein biosynthesis, as revealed by functional complementation experiments. Taken together, our results provide new insights into selenoprotein biosynthesis, demonstrating for the first time the formation of the functional ternary SelA-tRNA(Sec)-SPS complex. We propose that this complex is necessary for proper selenocysteine synthesis and may be involved in avoiding the cellular toxicity of selenium compounds. PMID:26378233

  18. Bio-Photoelectrochemical Solar Cells Incorporating Reaction Center and Reaction Center Plus Light Harvesting Complexes

    NASA Astrophysics Data System (ADS)

    Yaghoubi, Houman

    Harvesting solar energy can potentially be a promising solution to the energy crisis now and in the future. However, material and processing costs continue to be the most important limitations for the commercial devices. A key solution to these problems might lie within the development of bio-hybrid solar cells that seeks to mimic photosynthesis to harvest solar energy and to take advantage of the low material costs, negative carbon footprint, and material abundance. The bio-photoelectrochemical cell technologies exploit biomimetic means of energy conversion by utilizing plant-derived photosystems which can be inexpensive and ultimately the most sustainable alternative. Plants and photosynthetic bacteria harvest light, through special proteins called reaction centers (RCs), with high efficiency and convert it into electrochemical energy. In theory, photosynthetic RCs can be used in a device to harvest solar energy and generate 1.1 V open circuit voltage and ~1 mA cm-2 short circuit photocurrent. Considering the nearly perfect quantum yield of photo-induced charge separation, efficiency of a protein-based solar cell might exceed 20%. In practice, the efficiency of fabricated devices has been limited mainly due to the challenges in the electron transfer between the protein complex and the device electrodes as well as limited light absorption. The overarching goal of this work is to increase the power conversion efficiency in protein-based solar cells by addressing those issues (i.e. electron transfer and light absorption). This work presents several approaches to increase the charge transfer rate between the photosynthetic RC and underlying electrode as well as increasing the light absorption to eventually enhance the external quantum efficiency (EQE) of bio-hybrid solar cells. The first approach is to decrease the electron transfer distance between one of the redox active sites in the RC and the underlying electrode by direct attachment of the of protein complex

  19. Formation and Recondensation of Complex Organic Molecules during Protostellar Luminosity Outbursts

    NASA Astrophysics Data System (ADS)

    Taquet, Vianney; Wirström, Eva S.; Charnley, Steven B.

    2016-04-01

    During the formation of stars, the accretion of surrounding material toward the central object is thought to undergo strong luminosity outbursts followed by long periods of relative quiescence, even at the early stages of star formation when the protostar is still embedded in a large envelope. We investigated the gas-phase formation and recondensation of the complex organic molecules (COMs) di-methyl ether and methyl formate, induced by sudden ice evaporation processes occurring during luminosity outbursts of different amplitudes in protostellar envelopes. For this purpose, we updated a gas-phase chemical network forming COMs in which ammonia plays a key role. The model calculations presented here demonstrate that ion–molecule reactions alone could account for the observed presence of di-methyl ether and methyl formate in a large fraction of protostellar cores without recourse to grain-surface chemistry, although they depend on uncertain ice abundances and gas-phase reaction branching ratios. In spite of the short outburst timescales of about 100 years, abundance ratios of the considered species higher than 10% with respect to methanol are predicted during outbursts due to their low binding energies relative to water and methanol which delay their recondensation during cooling. Although the current luminosity of most embedded protostars would be too low to produce complex organics in the hot-core regions that are observable with current sub-millimetric interferometers, previous luminosity outburst events would induce the formation of COMs in extended regions of protostellar envelopes with sizes increasing by up to one order of magnitude.

  20. Accurately Predicting Complex Reaction Kinetics from First Principles

    NASA Astrophysics Data System (ADS)

    Green, William

    Many important systems contain a multitude of reactive chemical species, some of which react on a timescale faster than collisional thermalization, i.e. they never achieve a Boltzmann energy distribution. Usually it is impossible to fully elucidate the processes by experiments alone. Here we report recent progress toward predicting the time-evolving composition of these systems a priori: how unexpected reactions can be discovered on the computer, how reaction rates are computed from first principles, and how the many individual reactions are efficiently combined into a predictive simulation for the whole system. Some experimental tests of the a priori predictions are also presented.

  1. GABAergic complex basket formations in the human neocortex.

    PubMed

    Blazquez-Llorca, Lidia; García-Marín, Virginia; DeFelipe, Javier

    2010-12-15

    Certain GABAergic interneurons in the cerebral cortex, basket cells, establish multiple connections with cell bodies that typically outline the somata and proximal dendrites of pyramidal cells. During studies into the distribution of the vesicular GABA transporter (VGAT) in the human cerebral cortex, we were struck by the presence of a very dense, pericellular arrangement of multiple VGAT-immunoreactive (-ir) terminals in certain cortical areas. We called these terminals "Complex basket formations" (Cbk-formations) to distinguish them from the simpler and more typical pericellular GABAergic innervations of most cortical neurons. Here we examined the distribution of these VGAT-ir Cbk-formations in various cortical areas, including the somatosensory (area 3b), visual (areas 17 and 18), motor (area 4), associative frontal (dorsolateral areas 9, 10, 45, 46, and orbital areas 11, 12, 13, 14, 47), associative temporal (areas 20, 21, 22, and 38), and limbic cingulate areas (areas 24, 32). Furthermore, we used dual or triple staining techniques to study the chemical nature of the innervated cells. We found that VGAT-ir Cbk-formations were most frequently found in area 4 followed by areas 3b, 13, and 18. In addition, they were mostly observed in layer III, except in area 17, where they were most dense in layer IV. We also found that 70% of the innervated neurons were pyramidal cells, while the remaining 30% were multipolar cells. Most of these multipolar cells expressed the calcium-binding protein parvalbumin and the lectin Vicia villosa agglutinin. PMID:21031559

  2. The ribosome-associated complex antagonizes prion formation in yeast

    PubMed Central

    Amor, Alvaro J; Castanzo, Dominic T; Delany, Sean P; Selechnik, Daniel M; van Ooy, Alex; Cameron, Dale M

    2015-01-01

    Abstract The number of known fungal proteins capable of switching between alternative stable conformations is steadily increasing, suggesting that a prion-like mechanism may be broadly utilized as a means to propagate altered cellular states. To gain insight into the mechanisms by which cells regulate prion formation and toxicity we examined the role of the yeast ribosome-associated complex (RAC) in modulating both the formation of the [PSI+] prion – an alternative conformer of Sup35 protein – and the toxicity of aggregation-prone polypeptides. The Hsp40 RAC chaperone Zuo1 anchors the RAC to ribosomes and stimulates the ATPase activity of the Hsp70 chaperone Ssb. We found that cells lacking Zuo1 are sensitive to over-expression of some aggregation-prone proteins, including the Sup35 prion domain, suggesting that co-translational protein misfolding increases in Δzuo1 strains. Consistent with this finding, Δzuo1 cells exhibit higher frequencies of spontaneous and induced prion formation. Cells expressing mutant forms of Zuo1 lacking either a C-terminal charged region required for ribosome association, or the J-domain responsible for Ssb ATPase stimulation, exhibit similarly high frequencies of prion formation. Our findings are consistent with a role for the RAC in chaperoning nascent Sup35 to regulate folding of the N-terminal prion domain as it emerges from the ribosome. PMID:25739058

  3. Formation and Redox Interconversion of Niobium Methylidene and Methylidyne Complexes.

    PubMed

    Searles, Keith; Smith, Kyle T; Kurogi, Takashi; Chen, Chun-Hsing; Carroll, Patrick J; Mindiola, Daniel J

    2016-06-01

    The niobium methylidene [{(Ar'O)2 Nb}2 (μ2 -Cl)2 (μ2 -CH2 )] (2) can be cleanly prepared via thermolysis or photolysis of [(Ar'O)2 Nb(CH3 )2 Cl] (1) (OAr'=2,6-bis(diphenylmethyl)-4-tert-butylphenoxide). Reduction of 2 with two equivalents of KC8 results in formation of the first niobium methylidyne [K][{(Ar'O)2 Nb}2 (μ2 -CH)(μ2 -H)(μ2 -Cl)] (3) via a binuclear α-hydrogen elimination. Oxidation of 3 with two equiv of ClCPh3 reforms 2. In addition to solid state X-ray analysis, all these complexes were elucidated via multinuclear NMR experiments and isotopic labelling studies, including a crossover experiment, support the notion for a radical mechanism as well as a binuclear α-hydrogen abstraction pathway being operative in the formation of 2 from 1. PMID:27110689

  4. Formation of glutathionyl dinitrosyl iron complexes protects against iron genotoxicity.

    PubMed

    Lewandowska, Hanna; Sadło, Jarosław; Męczyńska, Sylwia; Stępkowski, Tomasz M; Wójciuk, Grzegorz; Kruszewski, Marcin

    2015-07-28

    Dinitrosyl iron(i) complexes (DNICs), intracellular NO donors, are important factors in nitric oxide-dependent regulation of cellular metabolism and signal transduction. It has been shown that NO diminishes the toxicity of iron ions and vice versa. To gain insight into the possible role of DNIC in this phenomenon, we examined the effect of GS-DNIC formation on the ability of iron ions to mediate DNA damage, by treatment of the pUC19 plasmid with physiologically relevant concentrations of GS-DNIC. It was shown that GS-DNIC formation protects against the genotoxic effect of iron ions alone and iron ions in the presence of a naturally abundant antioxidant, GSH. This sheds new light on the iron-related protective effect of NO under the circumstances of oxidative stress. PMID:26079708

  5. Characterization of the reaction of decoupling ubiquinone with bovine mitochondrial respiratory complex I.

    PubMed

    Masuya, Takahiro; Okuda, Kenji; Murai, Masatoshi; Miyoshi, Hideto

    2016-08-01

    We previously produced the unique ubiquinone QT ("decoupling" quinone), the catalytic reduction of which in NADH-quinone oxidoreduction with bovine heart mitochondrial NADH-ubiquinone oxidoreductase (complex I) is completely decoupled from proton translocation across the membrane domain. This feature is markedly distinct from those of typical short-chain quinones such as ubiquinone-1. To further characterize the features of the QT reaction with complex I, we herein synthesized three QT analogs, QT2-QT4, and characterized their electron transfer reactions. We found that all aspects of electron transfer (e.g. electron-accepting activity and membrane potential formation) vary significantly among these analogs. The features of QT2 as decoupling quinone were slightly superior to those of original QT. Based on these results, we conclude that the bound positions of QTs within the quinone binding cavity susceptibly change depending on their side-chain structures, and the positions, in turn, govern the behavior of QTs as electron acceptors. PMID:27140857

  6. Synthesis and reactions of U(III) complexes with tripodal nitrogen and oxygen donor ligands

    NASA Astrophysics Data System (ADS)

    McDonald, Robert; Sun, Yimin; Takats, Josef; Day, Victor W.; Eberspracher, Todd A.

    1994-10-01

    Reaction of UI3(THF)4 (where THF is tetrahydrofuran) with sodium or potassium hydrotris(3,5-dimethylpyrazolyl)borate ligand ((HBpz 3*)(-) in 1:1 and 1:2 ratios gives the corresponding U(HBpz 3*)I2(THF)2(1) and U(HBpz 3*)2I(2) complexes in excellent yields. Iodide abstraction from (2) with TlBPh4 results in the formation of the cationic complex (U(HBpz 3*)2(THF)) BPh4(3). The solid state structures of 1, 2 and 3 have been determined. Similar reactions with the anionic tripodal oxygen donor ligand ((eta (sub 5) - (5H5) Co(P(O)(OC2H5)2)3)(-) (L(sub OEt)) proceeded via oxidation of U(3+) to U(4+) and fragmentation of the ligand. The structures of some key compounds were established by X-ray crystallography. U(HBpz 3*)I2(THF)2 readily reacts with two equivalents of KH2Bpz (pz equivalent to pyrazolyl) to give U(HBpz3*)(H2Bpz2)2, but attempted substitution with other ligands led to mixtures or, in one case, displacement of the (HBpz 3*)(-) ligand.

  7. Formation of gold mineralization in ultramafic alkalic magmatic complexes

    NASA Astrophysics Data System (ADS)

    Ryabchikov, I. D.; Kogarko, L. N.; Sazonov, A. M.; Kononkova, N. N.

    2016-06-01

    Study of mineral inclusions within alluvial gold particles of the Guli Complex (East Siberia) and findings of lode gold in rocks of the same intrusion have demonstrated that gold mineralization occurs in interstitions of both early high-magnesium rocks (dunite) and later alkalic and carbonatite rocks. In dunite the native gold occurs in association with Fe-Ni sulfides (monosulfide solid solution, pentlandite, and heazlewoodite). Formation of the gold-bearing alloys took place under a low oxygen potential over a broad range of temperatures: from those close to 600°C down to below 400°C.

  8. Complex formation between uranyl and various thiosemicarbazide derivatives

    SciTech Connect

    Chuguryan, D.G.; Dzyubenko, V.I.

    1987-01-01

    Complex formation between hexavalent uranium and salicylaldehyde thiosemicarbazone (H/sub 2/L), salicylaldehyde S-methyl-isothiosemicarbazone (H/sub 2/Q), S-methyl-N/sub 1/,N/sub 4/-bis(salicylidene)isothiosemicarbazide(H/sub 2/Z), and thiosemicarbazidodiacetic acid (H/sub 2/R) has been studied spectrophotometrically in solution. Stability constants for complexes having the composition UO/sub 2/A have been calculated. Solid uranyl derivatives having the composition UO/sub 2/L x 2H/sub 2/O, UO/sub 2/Q x 2H/sub 2/O, UO/sub 2/Z x 2H/sub 2/O, and UO/sub 2/R x 2H/sub 2/O have been obtained. These derivatives were isolated and their IR spectroscopic behavior and thermal properties were investigated.

  9. Immune complex reaction after successful treatment of meningococcal disease: an excellent response to IVIG.

    PubMed

    Dass, Rashna; Barman, Himesh; Duwarah, Saurabh Gohain; Deka, Nayan Mani; Jain, Pankaj; Choudhury, Vivek

    2013-01-01

    The convalescence phase of severe meningococcal sepsis is complicated by immune complex reactions with arthritis being the commonest. No standard guidelines exist for management of such complications, but non-steroidal anti-inflammatory drugs and steroids have been used with varying success. We report excellent response to intravenous immunoglobulin in a child with immune complex reaction following meningococcal sepsis. PMID:20658236

  10. Characterization of Hydrogen Complex Formation in III-V Semiconductors

    SciTech Connect

    Williams, Michael D

    2006-09-28

    Atomic hydrogen has been found to react with some impurity species in semiconductors. Hydrogenation is a methodology for the introduction of atomic hydrogen into the semiconductor for the express purpose of forming complexes within the material. Efforts to develop hydrogenation as an isolation technique for AlGaAs and Si based devices failed to demonstrate its commercial viability. This was due in large measure to the low activation energies of the formed complexes. Recent studies of dopant passivation in long wavelength (0.98 - 1.55m) materials suggested that for the appropriate choice of dopants much higher activation energies can be obtained. This effort studied the formation of these complexes in InP, This material is extensively used in optoelectronics, i.e., lasers, modulators and detectors. The experimental techniques were general to the extent that the results can be applied to other areas such as sensor technology, photovoltaics and to other material systems. The activation energies for the complexes have been determined and are reported in the scientific literature. The hydrogenation process has been shown by us to have a profound effect on the electronic structure of the materials and was thoroughly investigated. The information obtained will be useful in assessing the long term reliability of device structures fabricated using this phenomenon and in determining new device functionalities.

  11. Clay surface catalysis of formation of humic substances: potential role of maillard reactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mechanisms of the formation of humic substances are poorly understood, especially the condensation of amino acids and reducing sugars products (Maillard reaction) in soil environments. Clay minerals behave as Lewis and Brönsted acids and catalyze several reactions and likely to catalyze the Mai...

  12. Interference-mediated synaptonemal complex formation with embedded crossover designation

    PubMed Central

    Zhang, Liangran; Espagne, Eric; de Muyt, Arnaud; Zickler, Denise; Kleckner, Nancy E.

    2014-01-01

    Biological systems exhibit complex patterns at length scales ranging from the molecular to the organismic. Along chromosomes, events often occur stochastically at different positions in different nuclei but nonetheless tend to be relatively evenly spaced. Examples include replication origin firings, formation of chromatin loops along chromosome axes and, during meiosis, localization of crossover recombination sites (“crossover interference”). We present evidence in the fungus Sordaria macrospora that crossover interference is part of a broader pattern that includes synaptonemal complex (SC) nucleation. This pattern comprises relatively evenly spaced SC nucleation sites, among which a subset are crossover sites that show a classical interference distribution. This pattern ensures that SC forms regularly along the entire length of the chromosome as required for the maintenance of homolog pairing while concomitantly having crossover interactions locally embedded within the SC structure as required for both DNA recombination and structural events of chiasma formation. This pattern can be explained by a threshold-based designation and spreading interference process. This model can be generalized to give diverse types of related and/or partially overlapping patterns, in two or more dimensions, for any type of object. PMID:25380597

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    Cross-coupling reactions are important to form C-C covalent bonds using metal catalysts. Although many different cross-coupling reactions have been developed and applied to synthesize complex molecules or polymers (macromolecules), if cross-coupling reactions are realized in the macroscopic real world, the scope of materials should be dramatically broadened. Here, Suzuki-Miyaura coupling reactions are realized between macroscopic objects. When acrylamide gel modified with an iodophenyl group (I-gel) reacts with a gel possessing a phenylboronic group (PB-gel) using a palladium catalyst, the gels bond to form a single object. This concept can also be adapted for bonding between soft and hard materials. I-gel or PB-gel selectively bonds to the glass substrates whose surfaces are modified with an electrophile or nucleophile, respectively.

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

    PubMed Central

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

    2014-01-01

    Cross-coupling reactions are important to form C–C covalent bonds using metal catalysts. Although many different cross-coupling reactions have been developed and applied to synthesize complex molecules or polymers (macromolecules), if cross-coupling reactions are realized in the macroscopic real world, the scope of materials should be dramatically broadened. Here, Suzuki-Miyaura coupling reactions are realized between macroscopic objects. When acrylamide gel modified with an iodophenyl group (I-gel) reacts with a gel possessing a phenylboronic group (PB-gel) using a palladium catalyst, the gels bond to form a single object. This concept can also be adapted for bonding between soft and hard materials. I-gel or PB-gel selectively bonds to the glass substrates whose surfaces are modified with an electrophile or nucleophile, respectively. PMID:25231557

  15. Proton exchange in acid-base complexes induced by reaction coordinates with heavy atom motions

    NASA Astrophysics Data System (ADS)

    Alavi, Saman; Taghikhani, Mahdi

    2012-06-01

    We extend previous work on nitric acid-ammonia and nitric acid-alkylamine complexes to illustrate that proton exchange reaction coordinates involve the rocking motion of the base moiety in many double hydrogen-bonded gas phase strong acid-strong base complexes. The complexes studied involve the biologically and atmospherically relevant glycine, formic, acetic, propionic, and sulfuric acids with ammonia/alkylamine bases. In these complexes, the magnitude of the imaginary frequencies associated with the proton exchange transition states are <400 cm-1. This contrasts with widely studied proton exchange reactions between symmetric carboxylic acid dimers or asymmetric DNA base pair and their analogs where the reaction coordinate is localized in proton motions and the magnitude of the imaginary frequencies for the transition states are >1100 cm-1. Calculations on complexes of these acids with water are performed for comparison. Variations of normal vibration modes along the reaction coordinate in the complexes are described.

  16. Complex behavior of self-propagating reaction waves in heterogeneous media

    PubMed Central

    Varma, Arvind; Rogachev, Alexander S.; Mukasyan, Alexander S.; Hwang, Stephen

    1998-01-01

    Self-propagating high temperature reaction waves, leading to the synthesis of advanced materials, are investigated in a variety of heterogeneous reaction systems by using a digital high-speed microscopic video recording technique. It is shown that, although on the macroscopic length and time scales, the reaction appears to move in a steady mode, on the microscopic level it has a complex character that is related to the reaction mechanism. PMID:9736688

  17. Incipient species formation in salamanders of the Ensatina complex

    PubMed Central

    Wake, David B.

    1997-01-01

    The Ensatina eschscholtzii complex of plethodontid salamanders, a well-known “ring species,” is thought to illustrate stages in the speciation process. Early research, based on morphology and coloration, has been extended by the incorporation of studies of protein variation and mitochondrial DNA sequences. The new data show that the complex includes a number of geographically and genetically distinct components that are at or near the species level. The complex is old and apparently has undergone instances of range contraction, isolation, differentiation, and then expansion and secondary contact. While the hypothesis that speciation is retarded by gene flow around the ring is not supported by molecular data, the general biogeographical hypothesis is supported. There is evidence of a north to south range expansion along two axes, with secondary contact and completion of the ring in southern California. Current research targets regions once thought to show primary intergradation, but which molecular markers reveal to be zones of secondary contact. Here emphasis is on the subspecies E. e. xanthoptica, which is involved in four distinct secondary contacts in central California. There is evidence of renewed genetic interactions upon recontact, with greater genetic differentiation within xanthoptica than between it and some of the interacting populations. The complex presents a full array of intermediate conditions between well-marked species and geographically variable populations. Geographically differentiated segments represent a diversity of depths of time of isolation and admixture, reflecting the complicated geomorphological history of California. Ensatina illustrates the continuing difficulty in making taxonomic assignments in complexes studied during species formation. PMID:9223261

  18. Fluoridonitrosyl complexes of technetium(I) and technetium(II). Synthesis, characterization, reactions, and DFT calculations.

    PubMed

    Balasekaran, Samundeeswari Mariappan; Spandl, Johann; Hagenbach, Adelheid; Köhler, Klaus; Drees, Markus; Abram, Ulrich

    2014-05-19

    A mixture of [Tc(NO)F5](2-) and [Tc(NO)(NH3)4F](+) is formed during the reaction of pertechnetate with acetohydroxamic acid (Haha) in aqueous HF. The blue pentafluoridonitrosyltechnetate(II) has been isolated in crystalline form as potassium and rubidium salts, while the orange-red ammine complex crystallizes as bifluoride or PF6(-) salts. Reactions of [Tc(NO)F5](2-) salts with HCl give the corresponding [Tc(NO)Cl4/5](-/2-) complexes, while reflux in neat pyridine (py) results in the formation of the technetium(I) cation [Tc(NO)(py)4F](+), which can be crystallized as hexafluoridophosphate. The same compound can be synthesized directly from pertechnetate, Haha, HF, and py or by a ligand-exchange procedure starting from [Tc(NO)(NH3)4F](HF2). The technetium(I) cation [Tc(NO)(NH3)4F](+) can be oxidized electrochemically or by the reaction with Ce(SO4)2 to give the corresponding Tc(II) compound [Tc(NO)(NH3)4F](2+). The fluorido ligand in [Tc(NO)(NH3)4F](+) can be replaced by CF3COO(-), leaving the "[Tc(NO)(NH3)4](2+) core" untouched. The experimental results are confirmed by density functional theory calculations on [Tc(NO)F5](2-), [Tc(NO)(py)4F](+), [Tc(NO)(NH3)4F](+), and [Tc(NO)(NH3)4F](2+). PMID:24797021

  19. Generalization of the Activated Complex Theory of Reaction Rates. I. Quantum Mechanical Treatment

    DOE R&D Accomplishments Database

    Marcus, R. A.

    1964-01-01

    In its usual form activated complex theory assumes a quasi-equilibrium between reactants and activated complex, a separable reaction coordinate, a Cartesian reaction coordinate, and an absence of interaction of rotation with internal motion in the complex. In the present paper a rate expression is derived without introducing the Cartesian assumption. The expression bears a formal resemblance to the usual one and reduces to it when the added assumptions of the latter are introduced.

  20. Evidence of reaction rate influencing cubic and hexagonal phase formation process in CdS nanocrystals

    NASA Astrophysics Data System (ADS)

    Deka, Kuldeep; Kalita, M. P. C.

    2016-05-01

    CdS nanocrystals are synthesized by co-precipitation method using 2-mercaptoethanol (ME) as capping agent. Cubic, hexagonal and their mixture are obtained by varying the ME concentration. Lower (higher) ME concentration results in cubic (hexagonal) phase. The crystallite sizes are in the range 3-7 nm. Increase in ME concentration lead to lower reaction rate between Cd2+ and S2- of the precursors, and slower reaction rate is found to favor hexagonal phase formation over the cubic one in CdS nanocrystals. Role of reaction rate in the phase formation process provides a way to synthesize CdS nanocrystals in desired crystal phase.

  1. Paramagnetic intermediates in reactions of the components of catalytic systems of the Ziegler type. Reactions of azo and azomethine complexes of Ni(II) with diethylaluminum chloride

    SciTech Connect

    Abbasov, Ya.A.; Ismailov, E.G.; Medzhidov, A.A.

    1988-04-01

    The intermediate paramagnetic particles, i.e., radical particles, complexes of Ni(I), and Ni/sub n/(O) aggregates, formed as a result of the reaction of azo and azomethine complexes of Ni(II) with Et/sub 2/AlCl in solvent media (toluene, THF, heptane) have been identified with the aid of ESR. The possibility of the stabilization of reactive intermediate complexes of Ni(I) by organophosphorus ligands (DPPE and TPP) has been demonstrated, and the magnetic-resonance parameters of their adducts have been determined. It has been postulated that the formation of radical particles occurs as a result of the coordination of the nitrogen atoms of the azo or azomethine ligands by the organoaluminum compound followed by splitting of the -N=N or -CH=N bonds.

  2. The C(3P) + NH3 Reaction in Interstellar Chemistry. I. Investigation of the Product Formation Channels

    NASA Astrophysics Data System (ADS)

    Bourgalais, Jérémy; Capron, Michael; Abhinavam Kailasanathan, Ranjith Kumar; Osborn, David L.; Hickson, Kevin M.; Loison, Jean-Christophe; Wakelam, Valentine; Goulay, Fabien; Le Picard, Sébastien D.

    2015-10-01

    The product formation channels of ground state carbon atoms, C(3P), reacting with ammonia, NH3, have been investigated using two complementary experiments and electronic structure calculations. Reaction products are detected in a gas flow tube experiment (330 K, 4 Torr) using tunable vacuum-ultraviolet (VUV) photoionization coupled with time of flight mass spectrometry. Temporal profiles of the species formed and photoionization spectra are used to identify primary products of the C + NH3 reaction. In addition, H-atom formation is monitored by VUV laser induced fluorescence (LIF) from room temperature to 50 K in a supersonic gas flow generated by the Laval nozzle technique. Electronic structure calculations are performed to derive intermediates, transition states, and complexes formed along the reaction coordinate. The combination of photoionization and LIF experiments supported by theoretical calculations indicate that in the temperature and pressure range investigated, the H + H2CN production channel represents 100% of the product yield for this reaction. Kinetics measurements of the title reaction down to 50 K and the effect of the new rate constants on interstellar nitrogen hydride abundances using a model of dense interstellar clouds are reported in Paper II.

  3. The formation of illite from nontronite by mesophilic and thermophilic bacterial reaction

    USGS Publications Warehouse

    Jaisi, D.P.; Eberl, D.D.; Dong, H.; Kim, J.

    2011-01-01

    The formation of illite through the smectite-to-illite (S-I) reaction is considered to be one of the most important mineral reactions occurring during diagenesis. In biologically catalyzed systems, however, this transformation has been suggested to be rapid and to bypass the high temperature and long time requirements. To understand the factors that promote the S-I reaction, the present study focused on the effects of pH, temperature, solution chemistry, and aging on the S-I reaction in microbially mediated systems. Fe(III)-reduction experiments were performed in both growth and non-growth media with two types of bacteria: mesophilic (Shewanella putrefaciens CN32) and thermophilic (Thermus scotoductus SA-01). Reductive dissolution of NAu-2 was observed and the formation of illite in treatment with thermophilic SA-01 was indicated by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). A basic pH (8.4) and high temperature (65??C) were the most favorable conditions forthe formation of illite. A long incubation time was also found to enhance the formation of illite. K-nontronite (non-permanent fixation of K) was also detected and differentiated from the discrete illite in the XRD profiles. These results collectively suggested that the formation of illite associated with the biologically catalyzed smectite-to-illite reaction pathway may bypass the prolonged time and high temperature required for the S-I reaction in the absence of microbial activity.

  4. Polycyclic aromatic hydrocarbon (PAH) formation from benzyl radicals: a reaction kinetics study.

    PubMed

    Sinha, Sourab; Raj, Abhijeet

    2016-03-01

    The role of resonantly stabilized radicals such as propargyl, cyclopentadienyl and benzyl in the formation of aromatic hydrocarbons such as benzene and naphthalene in the high temperature environments has been long known. In this work, the possibility of benzyl recombination to form three-ring aromatics, phenanthrene and anthracene, is explored. A reaction mechanism for it is developed, where reaction energetics are calculated using density functional theory (B3LYP functional with 6-311++G(d,p) basis set) and CBS-QB3, while temperature-dependent reaction kinetics are evaluated using transition state theory. The mechanism begins with barrierless formation of bibenzyl from two benzyl radicals with the release of 283.2 kJ mol(-1) of reaction energy. The further reactions involve H-abstraction by a H atom, H-desorption, H-migration, and ring closure to gain aromaticity. Through mechanism and rate of production analyses, the important reactions leading to phenanthrene and anthracene formation are determined. Phenanthrene is found to be the major product at high temperatures. Premixed laminar flame simulations are carried out by including the proposed reactions for phenanthrene formation from benzyl radicals and compared to experimentally observed species profiles to understand their effects on species concentrations. PMID:26923612

  5. Cadmium(II) Complex Formation with Cysteine and Penicillamine

    PubMed Central

    Jalilehvand, Farideh; Leung, Bonnie O.; Mah, Vicky

    2009-01-01

    The complex formation between cadmium(II) and the ligands cysteine (H2Cys) or penicillamine (H2Pen = 3, 3′-dimethylcysteine) in aqueous solutions, containing CCd(II) ∼ 0.1 mol dm-3 and CH2L = 0.2 – 2 mol dm-3, was studied at pH = 7.5 and 11.0 by means of 113Cd-NMR and Cd K- and L3-edge X-ray absorption spectroscopy. For all cadmium(II)-cysteine mole ratios the mean Cd-S and Cd-(N/O) bond distances were found in the ranges 2.52 – 2.54 Å and 2.27 – 2.35 Å, respectively. The corresponding cadmium(II)-penicillamine complexes showed slightly shorter Cd-S bonds, 2.50 – 2.53 Å, but with the Cd-(N/O) bond distances in a similar wide range, 2.28 – 2.33 Å. For the mole ratio CH2L / CCd(II) = 2, the 113Cd chemical shifts, in the range 509 – 527 ppm at both pH values, indicated complexes with distorted tetrahedral CdS2N(N/O) coordination geometry. With a large excess of cysteine (mole ratios CH2Cys / CCd(II) ≥ 10) complexes with CdS4 coordination geometry dominate, consistent with the 113Cd NMR chemical shifts, δ ∼ 680 ppm at pH 7.5 and 636 - 658 ppm at pH 11.0, and their mean Cd-S distances of 2.53 ± 0.02 Å. At pH 7.5, the complexes are almost exclusively sulfur-coordinated as [Cd(S-cysteinate)4]n-, while at higher pH the deprotonation of the amine groups promotes chelate formation, and at pH 11.0 a minor amount of the [Cd(Cys)3]4- complex with CdS3N coordination is formed. For the corresponding penicillamine solutions with mole ratios CH2Pen / CCd(II) ≥ 10, the 113Cd-NMR chemical shifts, δ ∼ 600 ppm at pH 7.5 and 578 ppm at pH 11.0, together with the average bond distances Cd-S 2.53 ± 0.02 Å and Cd-O 2.30 – 2.33 Å, indicate that [Cd(penicillaminate)3]n- complexes with chelating CdS3(N/O) coordination dominate already at pH 7.5, and become mixed with CdS2N(N/O) complexes at pH 11.0. The present study reveals differences between cysteine and penicillamine as ligands to the cadmium(II) ion that can explain why cysteine-rich metallothionines

  6. Cadmium(II) complex formation with cysteine and penicillamine.

    PubMed

    Jalilehvand, Farideh; Leung, Bonnie O; Mah, Vicky

    2009-07-01

    The complex formation between cadmium(II) and the ligands cysteine (H(2)Cys) and penicillamine (H(2)Pen = 3,3'-dimethylcysteine) in aqueous solutions, having C(Cd(II)) approximately 0.1 mol dm(-3) and C(H(2)L) = 0.2-2 mol dm(-3), was studied at pH = 7.5 and 11.0 by means of (113)Cd NMR and Cd K- and L(3)-edge X-ray absorption spectroscopy. For all cadmium(II)-cysteine molar ratios, the mean Cd-S and Cd-(N/O) bond distances were found in the ranges 2.52-2.54 and 2.27-2.35 A, respectively. The corresponding cadmium(II)-penicillamine complexes showed slightly shorter Cd-S bonds, 2.50-2.53 A, but with the Cd-(N/O) bond distances in a similar wide range, 2.28-2.33 A. For the molar ratio C(H(2)L)/C(Cd(II)) = 2, the (113)Cd chemical shifts, in the range 509-527 ppm at both pH values, indicated complexes with distorted tetrahedral CdS(2)N(N/O) coordination geometry. With a large excess of cysteine (molar ratios C(H(2)Cys)/C(Cd(II)) >or= 10), complexes with CdS(4) coordination geometry dominate, consistent with the (113)Cd NMR chemical shifts, delta approximately 680 ppm at pH 7.5 and 636-658 ppm at pH 11.0, and their mean Cd-S distances were 2.53 +/- 0.02 A. At pH 7.5, the complexes are almost exclusively sulfur-coordinated as [Cd(S-cysteinate)(4)](n-), while at higher pH, the deprotonation of the amine groups promotes chelate formation. At pH 11.0, a minor amount of the [Cd(Cys)(3)](4-) complex with CdS(3)N coordination is formed. For the corresponding penicillamine solutions with molar ratios C(H(2)Pen)/C(Cd(II)) >or= 10, the (113)Cd NMR chemical shifts, delta approximately 600 ppm at pH 7.5 and 578 ppm at pH 11.0, together with the average bond distances, Cd-S 2.53 +/- 0.02 A and Cd-(N/O) 2.30-2.33 A, indicate that [Cd(penicillaminate)(3)](n-) complexes with chelating CdS(3)(N/O) coordination dominate already at pH 7.5 and become mixed with CdS(2)N(N/O) complexes at pH 11.0. The present study reveals differences between cysteine and penicillamine as ligands to the

  7. Formation of polycyclic aromatic hydrocarbons from bimolecular reactions of phenyl radicals at high temperatures.

    PubMed

    Constantinidis, P; Schmitt, H-C; Fischer, I; Yan, B; Rijs, A M

    2015-11-21

    The self-reaction of the phenyl radical is one of the key reactions in combustion chemistry. Here we study this reaction in a high-temperature flow reactor by IR/UV ion dip spectroscopy, using free electron laser radiation as mid-infrared source. We identified several major reaction products based on their infrared spectra, among them indene, 1,2-dihydronaphthalene, naphthalene, biphenyl and para-terphenyl. Due to the structural sensitivity of the method, the reaction products were identified isomer-selectively. The work shows that the formation of indene and naphthalene, which was previously considered to be evidence for the HACA (hydrogen abstraction C2H2 addition) mechanism in the formation of polycyclic aromatic hydrocarbons and soot can also be understood in a phenyl addition model. PMID:26457393

  8. Stereodivergent catalytic doubly diastereoselective nitroaldol reactions using heterobimetallic complexes.

    PubMed

    Sohtome, Yoshihiro; Kato, Yuko; Handa, Shinya; Aoyama, Naohiro; Nagawa, Keita; Matsunaga, Shigeki; Shibasaki, Masakatsu

    2008-06-01

    Stereodivergent construction of three contiguous stereocenters in catalytic doubly diastereoselective nitroaldol reactions of alpha-chiral aldehydes with nitroacetaldehyde dimethyl acetal using two types of heterobimetallic catalysts is described. A La-Li-BINOL (LLB) catalyst afforded anti,syn-nitroaldol products in >20:1-14:1 selectivity, and a Pd/La/Schiff base catalyst afforded complimentary syn,syn-nitroaldol products in 10:1-5:1 selectivity. PMID:18465868

  9. What Is the Overall Stoichiometry of a Complex Reaction?

    NASA Astrophysics Data System (ADS)

    Toby, Sidney; Tobias, Irwin

    2003-05-01

    The overall stoichiometry of a reaction having a multistep mechanism can be derived using methods based on either of the following two approaches: elemental-balance or extent of reaction. The extent of reaction method (ξ method) has been used for many years. We have recently shown (J.Chem. Educ. 2000, 77, 188) that integration of rate equations (the kinetic method) offers an alternative to the ξ method using methods that may be more familiar to many chemists. The two methods are, however, equivalent and give the same results, as pointed out in the Appendix. The elemental-balance method is the simplest of the three methods but, as we shall show, it does not always give as much information about the system being analyzed as do the other two methods. In this paper both elemental-balance and kinetic methods will be used to derive stoichiometric relationships and the results will be compared. We show that each method has its advantages and conclude that both methods are useful in different contexts.

  10. Biological pattern formation: from basic mechanisms to complex structures

    SciTech Connect

    Koch, A.J.; Meinhardt, H. )

    1994-10-01

    The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of [ital Drosophila] and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

  11. Module Based Complexity Formation: Periodic Patterning in Feathers and Hairs

    PubMed Central

    Chuong, Cheng-Ming; Yeh, Chao-Yuan; Jiang, Ting-Xin; Widelitz, Randall

    2012-01-01

    Patterns describe order which emerges from homogeneity. Complex patterns on the integument are striking because of their visibility throughout an organism's lifespan. Periodic patterning is an effective design because the ensemble of hair or feather follicles (modules) allows the generation of complexity, including regional variations and cyclic regeneration, giving the skin appendages a new lease on life. Spatial patterns include the arrangements of feathers and hairs in specified number, size, and spacing. We explore how a field of equivalent progenitor cells can generate periodically arranged modules based on genetic information, physical-chemical rules and developmental timing. Reconstitution experiments suggest a competitive equilibrium regulated by activators / inhibitors involving Turing reaction-diffusion. Temporal patterns result from oscillating stem cell activities within each module (micro-environment regulation), reflected as growth (anagen) and resting (telogen) phases during the cycling of feather and hair follicles. Stimulating modules with activators initiates the spread of regenerative hair waves, while global inhibitors outside each module (macro-environment) prevent this. Different wave patterns can be simulated by Cellular Automata principles. Hormonal status and seasonal changes can modulate appendage phenotypes, leading to “organ metamorphosis”, with multiple ectodermal organ phenotypes generated from the same precursors. We discuss potential evolutionary novel steps using this module based complexity in several amniote integument organs, exemplified by the spectacular peacock feather pattern. We thus explore the application of the acquired knowledge of patterning in tissue engineering. New hair follicles can be generated after wounding. Hairs and feathers can be reconstituted through self-organization of dissociated progenitor cells. PMID:23539312

  12. Reaction mechanism of Ru(II) piano-stool complexes: umbrella sampling QM/MM MD study.

    PubMed

    Futera, Zdeněk; Burda, Jaroslav V

    2014-07-15

    Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied in this article by hybrid quantum mechanics-molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases: (i) hydration of the [Ru(II) (η(6) -benzene)(en)Cl](+) complex, (ii) monoadduct formation between the resulting aqua-Ru(II) complex and N7 position of one of the guanines in the ds-DNA oligomer, and (iii) formation of the intrastrand Ru(II) bridge (cross-link) between two adjacent guanines. Free energy profiles of all the reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex and two guanines represent a quantum core, which is described by density functional theory methods. The combined QM/MM scheme is realized by our own software, which was developed to couple several quantum chemical programs (in this study Gaussian 09) and Amber 11 package. Calculated free energy barriers of the both ruthenium hydration and Ru(II)-N7(G) DNA binding process are in good agreement with experimentally measured rate constants. Then, this method was used to study the possibility of cross-link formation. One feasible pathway leading to Ru(II) guanine-guanine cross-link with synchronous releasing of the benzene ligand is predicted. The cross-linking is an exergonic process with the energy barrier lower than for the monoadduct reaction of Ru(II) complex with ds-DNA. PMID:24865949

  13. Simulations of Pore Formation in Lipid Membranes: Reaction Coordinates, Convergence, Hysteresis, and Finite-Size Effects.

    PubMed

    Awasthi, Neha; Hub, Jochen S

    2016-07-12

    Transmembrane pores play an important role in various biophysical processes such as membrane permeation, membrane fusion, and antimicrobial peptide activity. In principal, all-atom molecular dynamics (MD) simulations provide an accurate model of pore formation in lipid membranes. However, the free energy landscape of transmembrane pore formation remains poorly understood, partly because potential of mean force (PMF) calculations of pore formation strongly depend on the choice of the reaction coordinate. In this study, we used umbrella sampling to compute PMFs for pore formation using three different reaction coordinates, namely, (i) a coordinate that steers the lipids in the lateral direction away from the pore center, (ii) the distance of a single lipid phosphate group from the membrane center, and (iii) the average water density inside a membrane-spanning cylinder. Our results show that while the three reaction coordinates efficiently form pores in membranes, they suffer from strong hysteresis between pore-opening and pore-closing simulations, suggesting that they do not restrain the systems close to the transition state for pore formation. The two reaction coordinates that act via restraining the lipids lead to more pronounced hysteresis compared with the coordinate acting on the water molecules. By comparing PMFs computed from membranes with different numbers of lipids, we observed significant artifacts from the periodic boundary conditions in small simulation systems. Further analysis suggests that the formation and disruption of a continuous hydrogen-bonding network across the membrane corresponds to the transition state for pore formation. Our study provides molecular insights into the critical steps of transmembrane pore formation, and it may guide the development of efficient reaction coordinates for pore formation. PMID:27254744

  14. EXFOR basics: A short guide to the nuclear reaction data exchange format

    SciTech Connect

    McLane, V.

    1996-07-01

    This manual is intended as a guide to users of nuclear reaction data compiled in the EXFOR format, and is not intended as a complete guide to the EXFOR System. EXFOR is the exchange format designed to allow transmission of nuclear data between the Nuclear Reaction Data Centers. In addition to storing the data and its` bibliographic information, experimental information, including source of uncertainties, is also compiled. The status and history of the data set is also included, e.g., the source of the data, any updates which have been made, and correlations to other data sets. EXFOR is designed for flexibility in order to meet the diverse needs of the nuclear data compilation centers. This format should not be confused with a center-to-user format. Although users may obtain data from the centers in the EXFOR format, other center-to-user formats have been developed to meet the needs of the users within each center`s own sphere of responsibility. The exchange format, as outlined, allows a large variety of numerical data tables with explanatory and bibliographic information to be transmitted in an easily machine-readable format (for checking and indicating possible errors) and a format that can be read by personnel (for passing judgment on and correcting any errors indicated by the machine). The data presently included in the EXFOR exchange include: a complete compilation of experimental neutron-induced reaction data, a selected compilation of charged-particle induced reaction data, a selected compilation of photon-induced reaction data.

  15. Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction.

    PubMed

    Schenk, Gerhard; Mitić, Nataša; Gahan, Lawrence R; Ollis, David L; McGeary, Ross P; Guddat, Luke W

    2012-09-18

    Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear

  16. Reaction layer formation at the graphite/copper-chromium alloy interface

    NASA Technical Reports Server (NTRS)

    Devincent, Sandra M.; Michal, Gary M.

    1993-01-01

    Sessile drop tests were used to obtain information about copper chromium alloys that suitably wet graphite. Characterization of graphite/copper-chromium alloy interfaces subjected to elevated temperatures were conducted using scanning electron micrography, energy dispersive spectroscopy, Auger electron spectroscopy, and X-ray diffraction analyses. These analyses indicate that during sessile drop tests conducted at 1130 C for one hour, copper alloys containing greater than 0.98 percent chromium form continuous reaction layers of approximately 10 micron thickness. The reaction layers adhere to the graphite surface. The copper wets the reaction layer to form a contact angle of 60 degrees or less. X-ray diffraction results indicate that the reaction layer is chromium carbide. The kinetics of reaction layer formation were modelled in terms of bulk diffusion mechanisms. Reaction layer thickness is controlled initially by the diffusion of Cr out of Cu alloy and later by the diffusion of C through chromium carbide.

  17. Reaction layer formation at the graphite/copper-chromium alloy interface

    NASA Technical Reports Server (NTRS)

    Devincent, Sandra M.; Michal, Gary M.

    1992-01-01

    Sessile drop tests were used to obtain information about copper chromium alloys that suitably wet graphite. Characterization of graphite/copper-chromium alloy interfaces subjected to elevated temperatures were conducted using scanning electron micrography, energy dispersive spectroscopy, auger electron spectroscopy, and x ray diffraction analyses. These analyses indicate that during sessile drop tests conducted at 1130 C for one hour, copper alloys containing greater than 0.98 percent chromium form continuous reaction layers of approximately 10 micron thickness. The reaction layers adhere to the graphite surface. The copper wets the reaction layer to form a contact angle of 60 degrees or less. X ray diffraction results indicate that the reaction layer is chromium carbide. The kinetics of reaction layer formation were modelled in terms of bulk diffusion mechanisms. Reaction layer thickness is controlled initially by the diffusion of Cr out of Cu alloy and later by the diffusion of C through chromium carbide.

  18. Formation of HCN+ in Heterogeneous Reactions of N2+ and N+ with Surface Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Harnisch, Martina; Keim, Alan; Scheier, Paul; Herman, Zdenek

    2013-10-01

    A significant increase of the ion yield at m/z 27 in collisions of low-energy ions of N2+ and N+ with hydrocarbon-covered room-temperature or heated surfaces of tungsten, carbon-fiber composite, and beryllium, not observed in analogous collisions of Ar+, is ascribed to the formation of HCN+ in heterogeneous reactions between N2+ or N+ and surface hydrocarbons. The formation of HCN+ in the reaction with N+ indicated an exothermic reaction with no activation barrier, likely to occur even at very low collision energies. In the reaction with N2+, the formation of HCN+ was observed to a different degree on these room-temperature and heated (150 and 300 °C) surfaces at incident energies above about 50 eV. This finding suggested an activation barrier or reaction endothermicity of the heterogeneous reaction of about 3-3.5 eV. The main process in N2+ or N+ interaction with the surfaces is ion neutralization; the probability of forming the reaction product HCN+ was very roughly estimated for both N2+ and N+ ions to about one in 104 collisions with the surfaces.

  19. Image formation in the eye: very specified complexity

    NASA Astrophysics Data System (ADS)

    Stoltzmann, David E.

    2005-08-01

    The formation of an image, and its correct interpretation by sighted living creatures, is a unique example of specified complexity unlike anything else in nature. While many of the functional aspects of living organisms are extremely complex, only an image requires a unique mapping process by the eye-brain system to be useful to the organism. The transfer of light from an object scene to a visual detection system (eye + brain) conveys an enormous amount of information. But unless that information is correctly organized into a useful image, the exchange of information is degraded and of questionable use. This paper examines the "connections" necessary for images to be interpreted correctly, as well as addressing the additional complexity requirement of dual-image mapping for stereovision capabilities. Statistics are presented for "simple eyes" consisting of a few pixels to illustrate the daunting task that random chance has to produce any form of a functional eye. For example, a 12-pixel eye (or camera) has 12! (479,001,600) possible pixel-to-brain (computer) wiring combinations, which can then be compared to the 126 million rods/cones of the actual human eye. If one tries to "connect the wires" (correctly interpret the information contained) in a 12-pixel image by random processes, by the time 6 pixels become correctly connected, over 99.9% of all the trials are incorrect, producing "noise" rather than a recognizable image. Higher numbers of pixels quickly make the problem astronomically worse for achieving any kind of useful image. This paper concludes that random-chance purposeless undirected processes cannot account for how images are perceived by living organisms.

  20. Theory of diffusion-influenced reactions in complex geometries.

    PubMed

    Galanti, Marta; Fanelli, Duccio; Traytak, Sergey D; Piazza, Francesco

    2016-06-21

    Chemical transformations involving the diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced reactions" (DIR). Virtually all biochemical processes in living media can be counted among them, together with those occurring in an ever-growing number of emerging nano-technologies. The role of the environment's geometry (obstacles, compartmentalization) and distributed reactivity (competitive reactants, traps) is key in modulating the rate constants of DIRs, and is therefore a prime design parameter. Yet, it is a formidable challenge to build a comprehensive theory that is able to describe the environment's "reactive geometry". Here we show that such a theory can be built by unfolding this many-body problem through addition theorems for special functions. Our method is powerful and general and allows one to study a given DIR reaction occurring in arbitrary "reactive landscapes", made of multiple spherical boundaries of given size and reactivity. Importantly, ready-to-use analytical formulas can be derived easily in most cases. PMID:27241805

  1. Cyclodextrins in pharmaceutical formulations I: structure and physicochemical properties, formation of complexes, and types of complex.

    PubMed

    Jambhekar, Sunil S; Breen, Philip

    2016-02-01

    Cyclodextrins are cyclic oligosaccharides that have been recognized as pharmaceutical adjuvants for the past 20 years. The molecular structure of these glucose derivatives, which approximates a truncated cone, bucket, or torus, generates a hydrophilic exterior surface and a nonpolar interior cavity. Cyclodextrins can interact with appropriately sized drug molecules to yield an inclusion complex. These noncovalent inclusion complexes offer a variety of advantages over the noncomplexed form of a drug. Cyclodextrins are primarily used to enhance the aqueous solubility, physical chemical stability, and bioavailability of drugs. Their other applications include preventing drug-drug interactions, converting liquid drugs into microcrystalline powders, minimizing gastrointestinal and ocular irritation, and reducing or eliminating unpleasant taste and smell. Here, we discuss the physical chemical properties of various cyclodextrins, including the effects of substitutions on these properties. Additionally, we report on the regulatory status of their use, commercial products containing cyclodextrins, toxicological considerations, and the forces involved in complex formation. We also highlight the types of complex formed and discuss the methods used to determine the types of complex present. PMID:26686054

  2. Calibration of Complex Subsurface Reaction Models Using a Surrogate-Model Approach

    EPA Science Inventory

    Application of model assessment techniques to complex subsurface reaction models involves numerous difficulties, including non-trivial model selection, parameter non-uniqueness, and excessive computational burden. To overcome these difficulties, this study introduces SAMM (Simult...

  3. Neutral and Cationic Alkyl Tantalum Imido Complexes: Synthesis and Migratory Insertion Reactions

    PubMed Central

    Anderson, Laura L.; Schmidt, Joseph A. R.; Arnold, John; Bergman, Robert G.

    2008-01-01

    The synthesis and reactivity of dibenzyl cationic tantalum imido complexes is described. The trialkyl tantalum imido compounds Bn3Ta=NCMe3 (1) and Np3Ta=NCMe3 (2) were synthesized as starting materials for the study of dialkyl cationic tantalum imido complexes. Compound 1 undergoes insertion reactions with diisopropylcarbodiimide and 2,6-dimethylphenylisocyanide to give (bisamidinate)imido complex 5 and (bisimino-acyl)imido complex 6, respectively. Treatment of compound 1 with B(C6F5)3 gives the zwitterionic tantalum complex [Bn2Ta=NCMe3][BnB(C6F5)3] (7) which is stabilized by η6-coordination of the benzyl triaryl borate anion. Coordination of the aryl anion can be displaced by three equivalents of pyridine to give the Lewis base complex 8. Treatment of compound 1 with [Ph3C][B(C6F5)4] gives the cationic tantalum imido complex [Bn2Ta=NCMe3][B(C6F5)4] (3). This salt forms insoluble aggregates unless trapped by THF coordination or an insertion reaction with an alkyne or an alkene. Cation 3 undergoes migratory insertion reactions with diphenylacetylene, phenylacetylene, norbornene, and cis-cyclooctene to give the corresponding alkenyl or modified alkyl imido complexes. The characterization of these products and the significance of these insertion reactions with respect to Ziegler-Natta polymerizations and hydroamination reactions are described. PMID:19079787

  4. Reactions of cationic transition metal acetonitrile complexes [M(CH3CN)n]m+ with GaCp*: novel gallium complexes of iron, cobalt, copper and silver.

    PubMed

    Bollermann, Timo; Puls, Arik; Gemel, Christian; Cadenbach, Thomas; Fischer, Roland A

    2009-02-28

    The reactions of the cationic transition metal acetonitrile complexes [M(CH3CN)n]m+ (m = 2: M = Fe, Co and m = 1: M = Cu, Ag) with GaCp* were investigated. The reaction of [Fe(CH3CN)6][BArF]2 (BAr(F) = [B{C6H3(CF3)2}4) with GaCp* leads to [Cp*Fe(GaCp*)3][BAr(F)] (1) via a redox neutral Cp* transfer and [Ga2Cp*][BAr(F)] as a by-product while the formation of [Cp*Co(GaCp*)3][BAr(F)]2 (2) from [Co(CH3CN)6][BAr(F)]2 is accompanied by oxidation of Co(II) to Co(III) with GaCp* as the oxidant. The reactions of [Cu(CH3CN)4][BAr(F)] and Ag[BPh4] with GaCp* lead to the formation of the homoleptic compounds [Cu(GaCp*)4][BAr(F)] (4) and [Ag(GaCp*)4][BPh4] (5), while treatment of Ag[CF3SO3] with GaCp* leads to the dimeric complex [Ag2(GaCp*)3(micro-GaCp*)2][CF3SO3]2 (6). All compounds were characterized by NMR spectroscopy, single crystal X-ray diffraction and elemental analysis. PMID:19462658

  5. The colorants, antioxidants, and toxicants from nonenzymatic browning reactions and the impacts of dietary polyphenols on their thermal formation.

    PubMed

    Zhang, Xinchen; Tao, Ningping; Wang, Xichang; Chen, Feng; Wang, Mingfu

    2015-02-01

    Nonenzymatic browning reactions proceed with the starting reactants of sugar and/or protein during thermal processing and storage of food. In addition to food color formation, the process also contributes to the loss of essential nutrients, generation of beneficial antioxidants, and production of toxicants, including 5-hydroxymethylfurfural (5-HMF), reactive carbonyl species, advanced glycation end products (AGEs), and heterocyclic amines (HAs). Recent research has demonstrated that dietary polyphenols can actively participate in nonenzymatic browning reactions, contributing to the generation of new colorants and antioxidants. More importantly, polyphenol addition has been found to be an effective approach to mitigate heat-induced formation of toxicants, mainly through inhibiting oxidative pathways and trapping reactive intermediates. In the matrix of polyphenol-fortified foods, a complex array of chemical interactions happen among polyphenols, traditional nutritional components, and neo-formed compounds they are thermally converted to. These reactions play a significant role in the colorants, antioxidants as well as toxicants production. Our findings support the potential of dietary polyphenols for increasing the antioxidant content and for reducing the level of toxicants when they participate in nonenzymatic browning reactions in fortified food products. PMID:25468403

  6. Analysis of the Pressure and Temperature Dependence of the Complex-Forming Bimolecular Reaction CH3OCH3 + Fe(.).

    PubMed

    Ard, Shaun G; Johnson, Ryan S; Martinez, Oscar; Shuman, Nicholas S; Guo, Hua; Troe, Jürgen; Viggiano, Albert

    2016-07-14

    The kinetics of the reaction CH3OCH3 + Fe(+) has been studied between 250 and 600 K in the buffer gas He at pressures between 0.4 and 1.6 Torr. Total rate constants and branching ratios for the formation of Fe(+)O(CH3)2 adducts and of Fe(+)OCH2 + CH4 products were determined. Quantum-chemical calculations provided the parameters required for an analysis in terms of statistical unimolecular rate theory. The analysis employed a recently developed simplified representation of the rates of complex-forming bimolecular reactions, separating association and chemical activation contributions. Satisfactory agreement between experimental results and kinetic modeling was obtained that allows for an extrapolation of the data over wide ranges of conditions. Possible reaction pathways with or without spin-inversion are discussed in relation to the kinetic modeling results. PMID:27228310

  7. Anion Effects in Oxidative Aliphatic Carbon-Carbon Bond Cleavage Reactions of Cu(II) Chlorodiketonate Complexes.

    PubMed

    Saraf, Sushma L; Miłaczewska, Anna; Borowski, Tomasz; James, Christopher D; Tierney, David L; Popova, Marina; Arif, Atta M; Berreau, Lisa M

    2016-07-18

    Aliphatic oxidative carbon-carbon bond cleavage reactions involving Cu(II) catalysts and O2 as the terminal oxidant are of significant current interest. However, little is currently known regarding how the nature of the Cu(II) catalyst, including the anions present, influence the reaction with O2. In previous work, we found that exposure of the Cu(II) chlorodiketonate complex [(6-Ph2TPA)Cu(PhC(O)CClC(O)Ph)]ClO4 (1) to O2 results in oxidative aliphatic carbon-carbon bond cleavage within the diketonate unit, leading to the formation of benzoic acid, benzoic anhydride, benzil, and 1,3-diphenylpropanedione as organic products. Kinetic studies of this reaction revealed a slow induction phase followed by a rapid decay of the absorption features of 1. Notably, the induction phase is not present when the reaction is performed in the presence of a catalytic amount of chloride anion. In the studies presented herein, a combination of spectroscopic (UV-vis, EPR) and density functional theory (DFT) methods have been used to examine the chloride and benzoate ion binding properties of 1 under anaerobic conditions. These studies provide evidence that each anion coordinates in an axial position of the Cu(II) center. DFT studies reveal that the presence of the anion in the Cu(II) coordination sphere decreases the barrier for O2 activation and the formation of a Cu(II)-peroxo species. Notably, the chloride anion more effectively lowers the barrier associated with O-O bond cleavage. Thus, the nature of the anion plays an important role in determining the rate of reaction of the diketonate complex with O2. The same type of anion effects were observed in the O2 reactivity of the simple Cu(II)-bipyridine complex [(bpy)Cu(PhC(O)C(Cl)C(O)Ph)ClO4] (3). PMID:27377103

  8. Molecular Complexity via C–H Activation: A Dehydrogenative Diels-Alder Reaction

    PubMed Central

    Stang, Erik M.; White, M. Christina

    2011-01-01

    Traditionally, C–H oxidation reactions install oxidized functionality onto a preformed molecular skeleton, resulting in a local molecular change. The use of C–H activation chemistry to construct complex molecular scaffolds is a new area with tremendous potential in synthesis. We report a Pd(II)/bis-sulfoxide catalyzed dehydrogenative Diels-Alder reaction that converts simple terminal olefins into complex cycloadducts in a single operation. PMID:21842902

  9. Zebra reaction or the recipe for the synthesis of heterodimeric zinc complexes.

    PubMed

    Jędrzkiewicz, D; Ejfler, J; John, Ł; Szafert, S

    2016-02-21

    A series of asymmetric heterodimeric zinc complexes have been synthesized in a direct reaction between conformationally flexible chiral/achiral homodimers. The cooperative activity of steric factors and coordination codes resulted in an intriguing chiral self-sorting process. Herein, we are reporting our recent exploration of the first example of such a type of reaction. PMID:26658768

  10. Numerical study on the impacts of heterogeneous reactions on ozone formation in the Beijing urban area

    NASA Astrophysics Data System (ADS)

    Xu, Jun; Zhang, Yuanhang; Wang, Wei

    2006-12-01

    The air quality model CMAQ-MADRID (Community Multiscale Air Quality-Model of Aerosol Dynamics, Reaction, Ionization and Dissolution) was employed to simulate summer O3 formation in Beijing China, in order to explore the impacts of four heterogeneous reactions on O3 formation in an urban area. The results showed that the impacts were obvious and exhibited the characteristics of a typical response of a VOC-limited regime in the urban area. For the four heterogeneous reactions considered, the NO2 and HO2 heterogeneous reactions have the most severe impacts on O3 formation. During the O3 formation period, the NO2 heterogeneous reaction increased new radical creation by 30%, raising the atmospheric activity as more NO→NO2 conversion occurred, thus causing the O3 to rise. The increase of O3 peak concentration reached a maximum value of 67 ppb in the urban area. In the morning hours, high NO titration reduced the effect of the photolysis of HONO, which was produced heterogeneously at night in the surface layer. The NO2 heterogeneous reaction in the daytime is likely one of the major reasons causing the O3 increase in the Beijing urban area. The HO2 heterogeneous reaction accelerated radical termination, resulting in a decrease of the radical concentration by 44% at the most. O3 peak concentration decreased by a maximum amount of 24 ppb in the urban area. The simulation results were improved when the heterogeneous reactions were included, with the O3 and HONO model results close to the observations.

  11. [THE THROMBUS FORMATION IN THE PROSTHESIS AS A REACTION OF ORGANISM ON ITS MATERIAL].

    PubMed

    Alekseyeva, T A; Gupalo, Yu M; Kolomoets, A M; Lazarenko, O N; Lazarenko, G O; Litvin, P M; Lohs, I V; Smorzhevskiy, V J; Stepkin, V I

    2016-04-01

    Abstract Vascular prostheses, excised because of their functional properties loss, were studied. Using different methods there was established, that this complication is caused by the thrombus formation as a reaction of organism on the prosthesis material. The testing procedure on compatibility was proposed, using atomic-power microscope. Components of a patient immunity may identify the prosthesis material and start the rejection mechanisms in case of negative reaction. PMID:27434951

  12. Formation spectra of light kaonic nuclei by in-flight (K¯,N) reactions with a chiral unitary amplitude

    NASA Astrophysics Data System (ADS)

    Yamagata-Sekihara, J.; Jido, D.; Nagahiro, H.; Hirenzaki, S.

    2009-10-01

    We study theoretically the in-flight (K-,N) reactions for the formation of light kaonic nuclear systems to get deeper physical insights on the spectra and to investigate the formation spectra of the reaction that will be observed at new facilities like the Japan Proton Accelerator Research Complex (J-PARC). We show the expected spectra for the formation of the K-pp, K-pn, K-nn, and K--B11 systems that are accessible by the (K-,N) experiments. By considering the conversion part of the Green’s function, we show the missing mass spectra of the (K-,N) reactions in coincident with the particle emissions due to K¯ absorption. To calculate the cross sections, we use the so-called Tρ approximation to evaluate the optical potential. As for the amplitude T, we adopt the chiral unitary amplitude of K¯N channel in vacuum for simplicity. The effects of the p-wave optical potential of Σ(1385) channel and the contributions from K¯0 mixing in He3(K-,n) reaction are also evaluated numerically. We also study the behavior of the poles of kaon Green’s function in nuclear matter. We conclude that He3(K-,n) and He3(K-,p) reaction spectra in coincident with the πΣ emission may show the structure in the kaon bound region indicating the existence of the unstable kaonic nuclear states. As for the C12(K-,p) spectra with the πΣ emission, we may also observe the structure in the bound region, however, we need to evaluate the medium effects carefully for larger nuclei.

  13. Formation of degradation compounds from lignocellulosic biomass in the biorefinery: sugar reaction mechanisms.

    PubMed

    Rasmussen, Helena; Sørensen, Hanne R; Meyer, Anne S

    2014-02-19

    The degradation compounds formed during pretreatment when lignocellulosic biomass is processed to ethanol or other biorefinery products include furans, phenolics, organic acids, as well as mono- and oligomeric pentoses and hexoses. Depending on the reaction conditions glucose can be converted to 5-(hydroxymethyl)-2-furaldehyde (HMF) and/or levulinic acid, formic acid and different phenolics at elevated temperatures. Correspondingly, xylose can follow different reaction mechanisms resulting in the formation of furan-2-carbaldehyde (furfural) and/or various C-1 and C-4 compounds. At least four routes for the formation of HMF from glucose and three routes for furfural formation from xylose are possible. In addition, new findings show that biomass monosaccharides themselves can react further to form pseudo-lignin and humins as well as a wide array of other compounds when exposed to high temperatures. Hence, several aldehydes and ketones and many different organic acids and aromatic compounds may be generated during hydrothermal treatment of lignocellulosic biomass. The reaction mechanisms are of interest because the very same compounds that are possible inhibitors for biomass processing enzymes and microorganisms may be valuable biobased chemicals. Hence a new potential for industrial scale synthesis of chemicals has emerged. A better understanding of the reaction mechanisms and the impact of the reaction conditions on the product formation is thus a prerequisite for designing better biomass processing strategies and forms an important basis for the development of new biorefinery products from lignocellulosic biomass as well. PMID:24412507

  14. Secondary organic aerosol formation from ozone-initiated reactions with nicotine and secondhand tobacco smoke

    NASA Astrophysics Data System (ADS)

    Sleiman, Mohamad; Destaillats, Hugo; Smith, Jared D.; Liu, Chen-Lin; Ahmed, Musahid; Wilson, Kevin R.; Gundel, Lara A.

    2010-11-01

    We used controlled laboratory experiments to evaluate the aerosol-forming potential of ozone reactions with nicotine and secondhand smoke. Special attention was devoted to real-time monitoring of the particle size distribution and chemical composition of SOA as they are believed to be key factors determining the toxicity of SOA. The experimental approach was based on using a vacuum ultraviolet photon ionization time-of-flight aerosol mass spectrometer (VUV-AMS), a scanning mobility particle sizer (SMPS) and off-line thermal desorption coupled to mass spectrometry (TD-GC-MS) for gas-phase byproducts analysis. Results showed that exposure of SHS to ozone induced the formation of ultrafine particles (<100 nm) that contained high molecular weight nitrogenated species ( m/ z 400-500), which can be due to accretion/acid-base reactions and formation of oligomers. In addition, nicotine was found to contribute significantly (with yields 4-9%) to the formation of secondary organic aerosol through reaction with ozone. The main constituents of the resulting SOA were tentatively identified and a reaction mechanism was proposed to elucidate their formation. These findings identify a new component of thirdhand smoke that is associated with the formation of ultrafine particles (UFP) through oxidative aging of secondhand smoke. The significance of this chemistry for indoor exposure and health effects is highlighted.

  15. How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

    PubMed Central

    Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

    2016-01-01

    In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy. PMID:26903405

  16. How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles.

    PubMed

    Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

    2016-01-01

    In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy. PMID:26903405

  17. Reaction Rates for the Formation of Deuterium Tritide from Deuterium and Tritium

    SciTech Connect

    McConville, G. T.; Menke, D. A.; Ellefson, R. E.

    1985-04-01

    The rates of formation of DT in a mixture of D2 and T2 have been measured as a function of initial T2 concentration, pressure, temperature,and methane concentration in a stainless steel reaction container which had been treated to inhibit protium ingrowth. An attempt has been made to explain the experimental resuts on the basis of ion-molecule chain reactions. Some of the observations are consistent with a gas-phase ion, ground-state molecule reaction, but some of the more interesting observations require more complicated models. The addition of excited state molecules or heterogeneous catalytic effects are possibilities that will need further experiments for confirmation.

  18. Substrate decomposition in galvanic displacement reaction: Contrast between gold and silver nanoparticle formation

    SciTech Connect

    Ghosh, Tapas; Satpati, Biswarup

    2015-06-24

    We have investigated substrate decomposition during formation of silver and gold nanoparticles in galvanic displacement reaction on germanium surfaces. Silver and gold nanoparticles were synthesized by electroless deposition on sputter coated germanium thin film (∼ 200 nm) grown initially on silicon substrate. The nanoparticles formation and the substrate corrosion were studied using scanning transmission electron microscopy (STEM) and the energy dispersive X-ray (EDX) spectroscopy.

  19. Substrate decomposition in galvanic displacement reaction: Contrast between gold and silver nanoparticle formation

    NASA Astrophysics Data System (ADS)

    Ghosh, Tapas; Kabiraj, D.; Satpati, Biswarup

    2015-06-01

    We have investigated substrate decomposition during formation of silver and gold nanoparticles in galvanic displacement reaction on germanium surfaces. Silver and gold nanoparticles were synthesized by electroless deposition on sputter coated germanium thin film (˜ 200 nm) grown initially on silicon substrate. The naoparticles formation and the substrate corrosion were studied using scanning transmission electron microscopy (STEM) and the energy dispersive X-ray (EDX) spectroscopy.

  20. Selenium-ligated palladium(II) complexes as highly active catalysts for carbon-carbon coupling reactions: the Heck reaction.

    PubMed

    Yao, Qingwei; Kinney, Elizabeth P; Zheng, Chong

    2004-08-19

    Three selenium-ligated Pd(II) complexes were readily synthesized and shown to be extremely active catalysts for the Heck reaction of various aryl bromides, including deactivated and heterocyclic ones. The catalytic activity of the selenide-based Pd(II) complexes not only rivals but vastly outperforms that of the corresponding phosphorus and sulfur analogues. Practical advantages of the selenium-based catalysts include their straightforward synthesis and high activity in the absence of any additives as well as the enhanced stability of the selenide ligands toward air oxidation. PMID:15330667

  1. Reactions of Complex Phenols on Aerosols with Gaseous Ozone

    NASA Astrophysics Data System (ADS)

    Hoffmann, M. R.; Enami, S.; Colussi, A. J.

    2009-12-01

    We report that α-tocopherol (α-TOH/α-TO-), as a model of substituted phenols in atmosphere, reacts with closed shell O3(g) on the surface of inert solvent microdroplets within 1 ms to produce persistent (n = 1 - 4) adducts detectable by online electrospray ionization mass spectrometry. The prototype phenolate PhO- undergoes electron transfer under identical conditions. These reactions occur at the gas/liquid interface since their rates: (1) depend on pH, (2) are several orders of magnitude faster than those in the bulk of O33-saturated microdroplets, and (3) approach O3(g) mass accommodation rates. Furthermore, they fail to incorporate solvent into the products: the same species are formed on acetonitrile or nucleophilic methanol microdroplets. Signals initially evolve with the concentration of ozone as expected from first-generation species. However, α-TO- reacts further with ozone via a collision-induced dissociation into a C19H40 fragment (vs. C19H38 from α-TO-, carrying the phytyl side-chain, whereas the higher homologues (α-TO-On ≥ 2-) are not reactive with O3(g). On this basis, α-TO- is assigned to a chroman-6-ol (4a, 8a)-ene oxide (an epoxide), α-TO-O2- to an endoperoxide, and α-TO-O3- to a secondary ozonide. These products are previous unreported. The atmospheric degradation of the substituted phenols detected in forest fires and combustion emissions is therefore expected to produce related oxidants on aerosol particles.

  2. Structural basis of complement membrane attack complex formation.

    PubMed

    Serna, Marina; Giles, Joanna L; Morgan, B Paul; Bubeck, Doryen

    2016-01-01

    In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a 'multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a 'split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration. PMID:26841837

  3. Integrin activation and focal complex formation in cardiac hypertrophy

    NASA Technical Reports Server (NTRS)

    Laser, M.; Willey, C. D.; Jiang, W.; Cooper, G. 4th; Menick, D. R.; Zile, M. R.; Kuppuswamy, D.

    2000-01-01

    Cardiac hypertrophy is characterized by both remodeling of the extracellular matrix (ECM) and hypertrophic growth of the cardiocytes. Here we show increased expression and cytoskeletal association of the ECM proteins fibronectin and vitronectin in pressure-overloaded feline myocardium. These changes are accompanied by cytoskeletal binding and phosphorylation of focal adhesion kinase (FAK) at Tyr-397 and Tyr-925, c-Src at Tyr-416, recruitment of the adapter proteins p130(Cas), Shc, and Nck, and activation of the extracellular-regulated kinases ERK1/2. A synthetic peptide containing the Arg-Gly-Asp (RGD) motif of fibronectin and vitronectin was used to stimulate adult feline cardiomyocytes cultured on laminin or within a type-I collagen matrix. Whereas cardiocytes under both conditions showed RGD-stimulated ERK1/2 activation, only collagen-embedded cells exhibited cytoskeletal assembly of FAK, c-Src, Nck, and Shc. In RGD-stimulated collagen-embedded cells, FAK was phosphorylated only at Tyr-397 and c-Src association occurred without Tyr-416 phosphorylation and p130(Cas) association. Therefore, c-Src activation is not required for its cytoskeletal binding but may be important for additional phosphorylation of FAK. Overall, our study suggests that multiple signaling pathways originate in pressure-overloaded heart following integrin engagement with ECM proteins, including focal complex formation and ERK1/2 activation, and many of these pathways can be activated in cardiomyocytes via RGD-stimulated integrin activation.

  4. Lipogenic Enzymes Complexes and Cytoplasmic Lipid Droplet Formation During Adipogenesis.

    PubMed

    Padilla-Benavides, Teresita; Velez-delValle, Cristina; Marsch-Moreno, Meytha; Castro-Muñozledo, Federico; Kuri-Harcuch, Walid

    2016-10-01

    Lipid droplets are dynamic organelles that store triglycerides and participate in their mobilization in adipose cells. These organelles require the reorganization of some structural components, the cytoskeleton, and the activation of lipogenic enzymes. Using confocal microscopy, we analyzed the participation of cytoskeletal components and two lipogenic enzymes, fatty acid synthase and glycerophosphate dehydrogenase, during lipid droplet biogenesis in differentiating 3T3-F442A cells into adipocytes. We show that subcortical actin microfilaments are extended at the basal side of the cells in parallel arrangement to the culture dish substrate, and that the microtubule network traverses the cytoplasm as a scaffold that supports the round shape of the mature adipocyte. By immunoprecipitation, we show that vimentin and perilipin1a associate during the early stages of the differentiation process for lipid droplet formation. We also report that the antibody against perilipin1 detected a band that might correspond to a modified form of the molecule. Finally, the cytosolic distribution and punctate organization of lipogenic enzymes and their co-localization in the proximity of lipid droplets suggest the existence of dynamic protein complexes involved in synthesis and storage of triglycerides. J. Cell. Biochem. 117: 2315-2326, 2016. © 2016 Wiley Periodicals, Inc. PMID:26928794

  5. Adhesion and formation of microbial biofilms in complex microfluidic devices

    SciTech Connect

    Kumar, Aloke; Karig, David K; Neethirajan, Suresh; Suresh, Anil K; Srijanto, Bernadeta R; Mukherjee, Partha P; Retterer, Scott T; Doktycz, Mitchel John

    2012-01-01

    Shewanella oneidensis is a metal reducing bacterium, which is of interest for bioremediation and clean energy applications. S. oneidensis biofilms play a critical role in several situations such as in microbial energy harvesting devices. Here, we use a microfluidic device to quantify the effects of hydrodynamics on the biofilm morphology of S. oneidensis. For different rates of fluid flow through a complex microfluidic device, we studied the spatiotemporal dynamics of biofilms, and we quantified several morphological features such as spatial distribution, cluster formation and surface coverage. We found that hydrodynamics resulted in significant differences in biofilm dynamics. The baffles in the device created regions of low and high flow in the same device. At higher flow rates, a nonuniform biofilm develops, due to unequal advection in different regions of the microchannel. However, at lower flow rates, a more uniform biofilm evolved. This depicts competition between adhesion events, growth and fluid advection. Atomic force microscopy (AFM) revealed that higher production of extra-cellular polymeric substances (EPS) occurred at higher flow velocities.

  6. Structural basis of complement membrane attack complex formation

    NASA Astrophysics Data System (ADS)

    Serna, Marina; Giles, Joanna L.; Morgan, B. Paul; Bubeck, Doryen

    2016-02-01

    In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a `multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a `split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration.

  7. Structural basis of complement membrane attack complex formation

    PubMed Central

    Serna, Marina; Giles, Joanna L.; Morgan, B. Paul; Bubeck, Doryen

    2016-01-01

    In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a ‘multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a ‘split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration. PMID:26841837

  8. Asymmetric ligand-exchange reaction of biphenol derivatives and chiral bis(oxazolinyl)phenyl-rhodium complex.

    PubMed

    Inoue, Hiroko; Ito, Jun-ichi; Kikuchi, Makoto; Nishiyama, Hisao

    2008-09-01

    Chiral bis(oxazolinyl)phenyl-rhodium acetate complex can enantioselectively capture 1,1'-binaphthol derivatives by ligand-exchange reaction. The structure of the bis(oxazolinyl)phenyl-rhodium biphenol and binaphthol complexes were confirmed by X-ray analysis. PMID:18496824

  9. Protic acid-fluorine interactions and reactions with acids of transition metal perfluoroalkyl and perfluoroolefin complexes

    SciTech Connect

    Barmore, R.M.; Richmond, T.G.

    1993-12-31

    The authors are interested in devising new methods of C-F and C-X bond activation which could be applied to destruction of environmentally significant molecules. Dihalocarbene complexes are thought to be intermediates in a variety of reactions of metal haloalkyl complexes which could be applied to this problem. This paper reports observations indicating initial interactions of protic acids and fluorocarbon complexes which can be applied toward the hydrolysis of C-F bonds. Reactions of long chain halocarbons and halolefins will also be discussed.

  10. 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.

  11. Formation of Secondary Particulate Matter by Reactions of Gas Phase Hexanal with Sulfate Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Zhang, J.

    2003-12-01

    The formation of secondary particulate matter from the atmospheric oxidation of organic compounds can significantly contribute to the particulate burden, but the formation of organic secondary particulate matter is poorly understood. One way of producing organic secondary particulate matter is the oxidation of hydrocarbons with seven or more carbon atoms to get products with low vapor pressure. However, several recent reports suggest that relatively low molecular weight carbonyls can enter the particle phase by undergoing heterogeneous reactions. This may be a very important mechanism for the formation of organic secondary particulate matter. Atmospheric aldehydes are important carbonyls in the gas phase, which form via the oxidation of hydrocarbons emitted from anthropogenic and biogenic sources. In this poster, we report the results on particle growth by the heterogeneous reactions of hexanal. A 5 L Continuous Stirred Tank Reactor (CSTR) is set up to conduct the reactions in the presence of seed aerosol particles of deliquesced ammonia bisulfate. Hexanal is added into CSTR by syringe pump, meanwhile the concentrations of hexanal are monitored with High Pressure Liquid Chromatograph (HPLC 1050). A differential Mobility Analyzer (TSI 3071) set to an appropriate voltage is employed to obtain monodisperse aerosols, and another DMA associated with a Condensation Nuclear Counter (TSI 7610) is used to measure the secondary particle size distribution by the reaction in CSTR. This permits the sensitive determination of particle growth due to the heterogeneous reaction, very little growth occurs when hexanal added alone. Results for the simultaneous addition of hexanal and alcohols will also be presented.

  12. IN VIVO FORMATION OF HALOGENATED REACTION PRODUCTS FOLLOWING PERORAL SODIUM HYPOCHLORITE

    EPA Science Inventory

    To date the principal concern of the disinfection of potable water has centered on the formation of halogenated organic reaction products and the adverse health effects that these products may have. However, an additional area for concern relating to water disinfection is the pot...

  13. THE OZONE REACTION WITH BUTADIENE: FORMATION OF TOXIC PRODUCTS. (R826236)

    EPA Science Inventory

    Abstract

    The formation yields of acrolein, 1,2-epoxy-3-butene and OH radicals have been measured from reaction of ozone with 1,3-butadiene at room temperature and atmosphere pressure. 1,3,5-Trimethyl benzene was added to scavenge OH radicals in measurements of product ...

  14. Joint catalytic activation of CO/sub 2/ and NH/sub 3/ in reaction with butadiene under the action of palladium complexes

    SciTech Connect

    Dzhemilev, U.M.; Kunakova, R.V.; Sidorova, V.V.

    1987-08-20

    In a continuation of the study of catalytic reactions in which small molecules participate they have examined the reaction of butadiene simultaneously with CO/sub 2/ and NH/sub 3/ in the presence of homogeneous Pd-containing catalyst complexes with the object of developing a single-step method for the synthesis of unsaturated higher formamides. The possibility of joint catalytic activation of small molecules (CO/sub 2/ and NH/sub 3/) has been demonstrated in their reaction with butadiene with the participation of palladium complexes, the products being mono- and bis-(2,7-octadienyl)formamides. It has been found that 2-pyrrolidone can take part in a telomerization reaction with butadiene in solutions containing palladium complexes, ammonia and carbon dioxide with the formation of N-2,7-octadienylpyrrolidone.

  15. A spectroscopic study on the formation of Cm(III) acetate complexes at elevated temperatures.

    PubMed

    Fröhlich, Daniel R; Skerencak-Frech, Andrej; Panak, Petra J

    2014-03-14

    The complexation of Cm(III) with acetate is studied by time resolved laser fluorescence spectroscopy (TRLFS) as a function of ionic strength, ligand concentration, temperature and background electrolyte (NaClO4, NaCl and CaCl2 solution). The speciation of Cm(III) is determined by peak deconvolution of the emission spectra. To obtain the thermodynamic stability constants (log K) for the formation of [Cm(Ac)n](3-n) (n = 1-3), the experimental data are extrapolated to zero ionic strength according to the specific ion interaction theory (SIT). The results show a continuous increase of the stability constants with increasing temperature (20-90 °C). The standard reaction enthalpies and entropies (ΔrH, ΔrS) of the respective reactions are derived from the integrated Van't Hoff equation. The results show that all complexation steps are endothermic and thus entropy driven (ΔrH and ΔrS > 0). PMID:24448229

  16. Bound Na(+) is a Negative Effecter for Thrombin-Substrate Stereospecific Complex Formation.

    PubMed

    Kurisaki, Ikuo; Takayanagi, Masayoshi; Nagaoka, Masataka

    2016-05-26

    Thrombin has been studied as a paradigmatic protein of Na(+)-activated allosteric enzymes. Earlier structural studies suggest that Na(+)-binding promotes the thrombin-substrate association reaction. However, it is still elusive because (1) the structural change, driven by Na(+)-binding, is as small as the thermal fluctuation, and (2) the bound Na(+) is close to Asp189 in the primary substrate binding pocket (S1-pocket), possibly preventing substrate access via repulsive interaction. It still remains a matter of debate whether Na(+)-binding actually promotes the reaction. To solve this problem, we examined the effect of Na(+) on the reaction by employing molecular dynamics (MD) simulations. By executing independent 210 MD simulations of apo and holo systems, we obtained 80 and 26 trajectories undergoing substrate access to S1-pocket, respectively. Interestingly, Na(+)-binding results in a 3-fold reduction of the substrate access. Furthermore, we examined works for the substrate access and release, and found that Na(+)-binding is disadvantageous for the presence of the substrate in the S1-pocket. These observations provide the insight that the bound Na(+) is essentially a negative effecter in thrombin-substrate stereospecific complex formation. The insight rationalizes an enigmatic feature of thrombin, relatively low Na(+)-binding affinity. This is essential to reduce the disadvantage of Na(+)-binding in the substrate-binding. PMID:27164318

  17. Secondary organic aerosol formation initiated from reactions between ozone and surface-sorbed squalene

    NASA Astrophysics Data System (ADS)

    Wang, Chunyi; Waring, Michael S.

    2014-02-01

    Previous research has shown that ozone reactions on surface-sorbed D-limonene can promote gas phase secondary organic aerosol (SOA) formation indoors. In this work, we conducted 13 steady state chamber experiments to measure the SOA formation entirely initiated by ozone reactions with squalene sorbed to glass, at chamber ozone of 57-500 ppb for two relative humidity (RH) conditions of 21% and 51%, in the absence of seed particles. Squalene is a nonvolatile compound that is a component of human skin oil and prevalent on indoor surfaces and in settled dust due to desquamation. The size distributions, mass and number secondary emission rates (SER), aerosol mass fractions (AMF), and aerosol number fractions (ANF) of formed SOA were quantified. The surface AMF and ANF are defined as the change in SOA mass or number formed, respectively, per ozone mass consumed by ozone-squalene reactions. All experiments but one exhibited nucleation and mass formation. Mass formation was relatively small in magnitude and increased with ozone, most notably for the RH = 51% experiments. The surface AMF was a function of the chamber aerosol concentration, and a multi-product model was fit using the 'volatility basis set' framework. Number formation was relatively strong at low ozone and low RH conditions. Though we cannot extrapolate our results because experiments were conducted at high air exchange rates, we speculate that this process may enhance particle number more than mass concentrations indoors.

  18. Aza-crown ether complex cation ionic liquids: preparation and applications in organic reactions.

    PubMed

    Song, Yingying; Cheng, Chen; Jing, Huanwang

    2014-09-26

    Aza-crown ether complex cation ionic liquids (aCECILs) were devised, fabricated, and characterized by using NMR spectroscopy, MS, thermogravimetric differential thermal analysis (TG-DTA), elemental analysis and physical properties. These new and room-temperature ILs were utilized as catalysts in various organic reactions, such as the cycloaddition reaction of CO2 to epoxides, esterification of acetic acid and alcohols, the condensation reaction of aniline and propylene carbonate, and Friedel-Crafts alkylation of indole with aldehydes were investigated carefully. In these reactions, the ionic liquid exhibited cooperative catalytic activity between the anion and cation. In addition, the aza-[18-C-6HK][HSO4]2 was the best acidic catalyst in the reactions of esterification and Friedel-Crafts alkylation under mild reaction conditions. PMID:25154312

  19. Complexity of lectin-mediated reactions in bacteria-induced histamine release.

    PubMed

    Jensen, C; Stahl Skov, P; Norn, S; Espersen, F; Bøg-Hansen, T C; Lihme, A

    1984-08-01

    We have earlier suggested that bacteria-induced histamine release is caused by different mechanisms, including allergic and non-immunological mechanisms, and that the latter probably depends on lectin-mediated reactions. Two possibilities of lectin-mediated reactions were examined in this study, bacterial surface lectins bind to sugars on the basophil cell membrane leading to histamine release, and the reverse reaction where bacterial aminosugars react with lectins on the basophil cell surface. In the bacterial histamine release caused by the Staph. aureus strain Wood 46 it was possible to demonstrate a reverse reaction, but not a bacterial lectin-mediated reaction. The reaction seems to be complex, as lower concentrations of sugars might potentiate the release of histamine by binding to the target cell or bacteria, while the release is inhibited by higher concentrations. PMID:6208803

  20. Formation of impeller-like helical DNA–silica complexes by polyamines induced chiral packing

    PubMed Central

    Liu, Ben; Han, Lu; Che, Shunai

    2012-01-01

    The helicity of DNA and its long-range chiral packing are widespread phenomena; however, the packing mechanism remains poorly understood both in vivo and in vitro. Here, we report the extraordinary DNA chiral self-assembly by silica mineralization, together with circular dichroism measurements and electron microscopy studies on the structure and morphology of the products. Mg2+ ion and diethylenetriamine were found to induce right- and left-handed chiral DNA packing with two-dimensional-square p4mm mesostructures, respectively, to give corresponding enantiomeric impeller-like helical DNA–silica complexes. Moreover, formation of macroscopic impeller-like helical architectures depends on the types of polyamines and co-structure-directing agents and pH values of reaction solution. It has been suggested that interaction strength between negatively charged DNA phosphate strands and positively charged counterions may be the key factor for the induction of DNA packing handedness. PMID:24098845

  1. Redox-Active-Ligand-Mediated Formation of an Acyclic Trinuclear Ruthenium Complex with Bridging Nitrido Ligands.

    PubMed

    Bagh, Bidraha; Broere, Daniël L J; Siegler, Maxime A; van der Vlugt, Jarl Ivar

    2016-07-11

    Coordination of a redox-active pyridine aminophenol ligand to Ru(II) followed by aerobic oxidation generates two diamagnetic Ru(III) species [1 a (cis) and 1 b (trans)] with ligand-centered radicals. The reaction of 1 a/1 b with excess NaN3 under inert atmosphere resulted in the formation of a rare bis(nitrido)-bridged trinuclear ruthenium complex with two nonlinear asymmetrical Ru-N-Ru fragments. The spontaneous reduction of the ligand centered radical in the parent 1 a/1 b supports the oxidation of a nitride (N(3-) ) to half an equivalent of N2 . The trinuclear omplex is reactive toward TEMPO-H, tin hydrides, thiols, and dihydrogen. PMID:27321547

  2. Attaching high charge density metal ions to surfaces and biomolecules. Reaction chemistry of hypodentate cobalt diamine complexes.

    PubMed

    Funk, Aaron R; Goldberg, Efram; Chang, Eddie L; Trammell, Scott A; Knight, D Andrew

    2013-11-28

    Hypodentate diamine cobalt(III) pentammine complexes [Co(NH3)5(NH2(CH2)(n)NH3)](ClO4)4 (8: a: n = 3; b: n = 4; c: n = 6; d: n = 8) have been synthesized via the reaction of [Co(NH3)5(OTf)](OTf)2 (TfOH = CF3SO3H) with the corresponding diamines. The analogous t-boc protected diamine complexes [Co(NH3)5(NH2(CH2)(n)NHt-boc)](ClO4)3 (7a-d) were prepared in 4-26% yield. Low yields for the formation of 7a-d are due to competing side reactions which also gave [Co(NH3)6](3+). Complexes 7a-d were deprotected using trifluoroacetic acid to give the corresponding hypodentate diamine complexes [Co(NH3)5(NH2(CH2)(n)NH3)](CF3CO2)0.5(ClO4)3.5 (9a-d). HBTU coupling of 8c with N-(t-boc)-L-phenylalanine gave an amino acid functionalized cobalt pentammine complex [Co(NH3)5(NH2(CH2)6NHt-boc)-L-phenylalanine)](ClO4)3 (10). All new complexes were characterized using UV-vis and (1)H NMR spectroscopy, and elemental analysis. Grafting of 8c onto 2.4 mm poly(ethylene-co-acrylic acid) (PEAA) beads was achieved via amide coupling. Complex 8c was coupled to thioctic acid via amide coupling and the resulting cobalt disulfide complex [Co(NH3)5(N-(6-aminohexyl)-5-(1,2-dithiolan-3-yl)pentanamide)](ClO4)3 (11) was attached to 10 nm Au nanoparticles. The amount of cobalt loading onto PEAA beads and Au nanoparticles was determined using ICP-MS and EDX. PMID:24037460

  3. Kinetics of exciplex formation/dissipation in reaction following Weller Scheme II

    SciTech Connect

    Fedorenko, S. G.; Burshtein, A. I.

    2014-09-21

    Creation of exciplexes from the charged products of photoionization is considered by means of Integral Encounter Theory. The general kinetic equations of such a reaction following the Weller scheme II are developed. The special attention is given to the particular case of irreversible remote ionization of primary excited electron donor. Kinetics of exciplex formation is considered at fast biexponential geminate transformation of exciplexes in cage that gives way to subsequent bulk reaction of equilibrated reaction products controlled by power law recombination of ions. It is shown that the initial geminate stage of exciplex kinetics is observed only in diffusion controlled regime of the reaction and disappears with increasing mobility of ions in passing to kinetic regime. The quantum yield of exciplexes is studied along with their kinetics.

  4. The thermodynamic characteristics of complex formation between calcium ions and L-leucine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Kurochkin, V. Yu.; Chernikov, V. V.; Orlova, T. D.

    2011-04-01

    Complex formation of L-leucine with calcium ions in aqueous solution was studied by potentiometric titration at 298.15 K and ionic strength values I = 0.5, 1.0, and 1.5 (KNO3). The formation of the CaL+ and CaHL2+ complex particles was established and their stability constants were determined. The enthalpies of protolytic equilibria of leucine and formation of calcium ion complexes with leucine were determined calorimetrically at 298.15 K and I = 0.5 (KNO3). The thermodynamic characteristics of complex formation between calcium ions and L-leucine were calculated.

  5. Complex Cure Kinetics of the Hydroxyl-Epoxide Reaction in DGEBA Epoxy Hardened with Diethanolamine

    NASA Astrophysics Data System (ADS)

    Ancipink, Windy; McCoy, John; Kropka, Jamie; Celina, Mathias

    The curing of a diglycidyl ether of bisphenol-A Epoxy (Epon 828) with diethanolamine (DEA) involves a fast amine-epoxide reaction followed by a slower hydroxyl-epoxide reaction. At curing temperatures below 100°C, the time scales of these two reactions are well separated, and the hydroxyl addition can be studied as an ''isolated'' reaction. The hydroxyl-epoxide reaction is of great interest due to the complex kinetics involved, which are brought about by competing reactions. The reaction kinetics are believed to be tertiary amine catalyzed and are well fit to a modified form of the Kamal-type equation. Here we study the complex long term reaction kinetics at various temperatures, by using isothermal modulated differential scanning calorimetry, micro calorimetry, and infrared spectroscopy. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  6. In Situ Catalyst Modification in Atom Transfer Radical Reactions with Ruthenium Benzylidene Complexes.

    PubMed

    Lee, Juneyoung; Grandner, Jessica M; Engle, Keary M; Houk, K N; Grubbs, Robert H

    2016-06-01

    Ruthenium benzylidene complexes are well-known as olefin metathesis catalysts. Several reports have demonstrated the ability of these catalysts to also facilitate atom transfer radical (ATR) reactions, such as atom transfer radical addition (ATRA) and atom transfer radical polymerization (ATRP). However, while the mechanism of olefin metathesis with ruthenium benzylidenes has been well-studied, the mechanism by which ruthenium benzylidenes promote ATR reactions remains unknown. To probe this question, we have analyzed seven different ruthenium benzylidene complexes for ATR reactivity. Kinetic studies by (1)H NMR revealed that ruthenium benzylidene complexes are rapidly converted into new ATRA-active, metathesis-inactive species under typical ATRA conditions. When ruthenium benzylidene complexes were activated prior to substrate addition, the resulting activated species exhibited enhanced kinetic reactivity in ATRA with no significant difference in overall product yield compared to the original complexes. Even at low temperature, where the original intact complexes did not catalyze the reaction, preactivated catalysts successfully reacted. Only the ruthenium benzylidene complexes that could be rapidly transformed into ATRA-active species could successfully catalyze ATRP, whereas other complexes preferred redox-initiated free radical polymerization. Kinetic measurements along with additional mechanistic and computational studies show that a metathesis-inactive ruthenium species, generated in situ from the ruthenium benzylidene complexes, is the active catalyst in ATR reactions. Based on data from (1) H, (13)C, and (31)P NMR spectroscopy and X-ray crystallography, we suspect that this ATRA-active species is a RuxCly(PCy3)z complex. PMID:27186790

  7. Kinetico-Mechanistic Studies of Nucleoside and Nucleotide Substitution Reactions of Co(III) Complexes of Fully Alkylated Cyclen.

    PubMed

    Martínez, Manuel; Vázquez, Marta

    2015-05-18

    The solution chemistry of complex [Co{(Me)2(μ-ET)cyclen}(H2O)2](3+) containing a fully substituted tetraammine ligand designed for the avoidance of base-conjugated substitution mechanisms in the 6-8 pH range has been studied. The study should shed some light on the possible involvement of such Co(III) skeleton in inert interactions with biomolecules. The reactivity and speciation of the complex has been found similar to that of the parent cyclen derivative with the presence of mono- and bis-hydroxo-bridged species; at pH < 7.1, all reactivity has been found to be related to the aqua/hydroxo monomeric complexes. Under these pH conditions, the substitution reactions of the aqua/hydroxo ligands by chloride, inorganic phosphate, thymidine, cytidine 5'-monophosphate (5'-CMP), and thymidine-5'-monophosphate (5'-TMP) have been studied at varying conditions; ionic strength has been kept at 1.0 NaClO4 due to the high concentration of 2-(N-morpholino)ethanesulfonic acid (MES) or N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) used to ensure buffering. Except for chloride, the process occurs neatly in a one or two step process, showing dissociatively activated substitution mechanisms, having in general large ΔH(⧧), positive ΔS(⧧), and values of ΔV(⧧) close to those corresponding to the liberation of an aqua ligand to the reaction medium. The actuation of noticeable encounter-complex formation equilibrium constants has been found to be the determinant for the reactions with nucleosides and nucleotides, a clear indication of the relevance of hydrogen-bonding interactions in the reactivity of these molecules, even in this highly ionic strength medium. For the substitution of the active aqua/hydroxo ligands with 5'-TMP, the first substitution reaction produces an Nthymine-bound 5'-TMP complex that evolves to a bis-5'-TMP with an Nthymine,Ophosphate-bonding structure. The formation of outer-sphere complexes between the dangling phosphate group of the Nthymine

  8. Charge-transfer complexes formed in the reaction of 1,4,7,10-tetraazacyclododecane with π-electron acceptors

    NASA Astrophysics Data System (ADS)

    AlQaradawi, Siham Y.; Mostafa, Adel; Bazzi, Hassan S.

    2013-04-01

    The reactions of the electron donor 1,4,7,10-tetraazacyclododecane (TACDD) with the π-electron acceptors 7,7,8,8-tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ), 2,3,5,6-tetrachloro-1,4-benzoquinone (CHL) and 2,4,4,6-tetrabromo-2,5-cyclohexadienone (TBCHD) were studied spectrophotometrically in chloroform at room temperature. The electronic and infrared spectra of the formed molecular charge-transfer (CT) complexes were recorded. The obtained results showed that the stoichiometries of the reactions are fixed and depend on the nature of both the donor and the acceptor. Based on the obtained data, the formed charge-transfer complexes were formulated as [(Donor)(Acceptor)2] for the donor (TACDD) and the acceptors TCNQ, TCNE, DDQ, CHL and TBCHD. These CT-complexes were isolated as solids and have been characterized through electronic and infrared spectra as well as elemental and thermal analysis measurements. The formation constants (KCT), charge transfer energy (ECT), molar extinction coefficients (ɛCT), free energy change ΔG0, ionization potential Ip and oscillator strength ƒ of the formed CT-complexes were obtained.

  9. Multicomponent One-pot Reactions Towards the Synthesis of Stereoisomers of Dipicolylamine Complexes.

    PubMed

    Raje, Sakthi; Gurusamy, Sureshbabu; Koner, Abhishek; Mehrotra, Sonam; Jennifer, Samson Jegan; Vasudev, Prema G; Butcher, Ray J; Angamuthu, Raja

    2016-01-01

    Reported are multi-component one-pot syntheses of chiral complexes [M(L(R) OR')Cl2 ] or [M(L(R) SR')Cl2 ] from the mixture of an N-substituted ethylenediamine, pyridine-2-carboxaldehyde, a primary alcohol or thiol and MCl2 utilizing in-situ formed cyclized Schiff bases where a C-O bond, two stereocenters, and three C-N bonds are formed (M=Zn, Cu, Ni, Cd; R=Et, Ph; R'=Me, Et, nPr, nBu). Tridentate ligands L(R) OR' and L(R) SR' comprise two chiral centers and a hemiaminal ether or hemiaminal thioether moiety on the dipicolylamine skeleton. Syn-[Zn(L(Ph) OMe)Cl2 ] precipitates out readily from the reaction mixture as a major product whereas anti-[Zn(L(Ph) OMe)Cl2 ] stays in solution as minor product. Both syn-[Zn(L(Ph) OMe)Cl2 ] and anti-[Zn(L(Ph) OMe)Cl2 ] were characterized using NMR spectroscopy and mass spectrometry. Solid-state structures revealed that syn-[Zn(L(Ph) OMe)Cl2 ] adopted a square pyramidal geometry while anti-[Zn(L(Ph) OMe)Cl2 ] possesses a trigonal bipyramidal geometry around the Zn centers. The scope of this method was shown to be wide by varying the components of the dynamic coordination assembly, and the structures of the complexes isolated were confirmed by NMR spectroscopy, mass spectrometry, and X-ray crystallography. Syn complexes were isolated as major products with Zn(II) and Cu(II) , and anti complexes were found to be major products with Ni(II) and Cd(II) . Hemiaminals and hemiaminal ethers are known to be unstable and are seldom observed as part of cyclic organic compounds or as coordinated ligands assembled around metals. It is now shown, with the support of experimental results, that linear hemiaminal ethers or thioethers can be assembled without the assistance of Lewis acidic metals in the multi-component assembly, and a possible pathway of the formation of hemiaminal ethers has been proposed. PMID:26415522

  10. Effect of gel network on pattern formation in the ferrocyanide-iodate-sulfite reaction.

    PubMed

    Ueno, Tomonaga; Yoshida, Ryo

    2011-06-01

    Stationary patterns have been researched experimentally since the discovery of the Turing pattern in the chlorite-iodide-malonic acid (CIMA) reaction and the self-replicating spot pattern in the ferrocyanide-iodate-sulfite (FIS) reaction. In this study, we reproduced the pattern formation in the FIS reaction by using poly(acrylamide) gels. Gels with different swelling ratios were prepared to use as a medium. The effect of the swelling ratio was compared with the effect of thickness. It was found that the swelling ratio greatly influenced pattern formation. Oscillating spot patterns appeared at high swelling ratios, and lamellar patterns appeared at a low swelling ratio. Self-replicating spot patterns appeared in between the two areas. The front velocities, which were observed in the initial stage of pattern formation, depended on the swelling ratio. Furthermore, this dependence obeys the free volume theory of diffusion. These results provide evidence that the change in front velocities is caused by a change in diffusion. Pattern formation can be controlled not only by thickness but also by swelling ratio, which may be useful for creating novel pattern templates. PMID:21557556

  11. Pattern formation on networks with reactions: A continuous-time random-walk approach

    NASA Astrophysics Data System (ADS)

    Angstmann, C. N.; Donnelly, I. C.; Henry, B. I.

    2013-03-01

    We derive the generalized master equation for reaction-diffusion on networks from an underlying stochastic process, the continuous time random walk (CTRW). The nontrivial incorporation of the reaction process into the CTRW is achieved by splitting the derivation into two stages. The reactions are treated as birth-death processes and the first stage of the derivation is at the single particle level, taking into account the death process, while the second stage considers an ensemble of these particles including the birth process. Using this model we have investigated different types of pattern formation across the vertices on a range of networks. Importantly, the CTRW defines the Laplacian operator on the network in a non-ad hoc manner and the pattern formation depends on the structure of this Laplacian. Here we focus attention on CTRWs with exponential waiting times for two cases: one in which the rate parameter is constant for all vertices and the other where the rate parameter is proportional to the vertex degree. This results in nonsymmetric and symmetric CTRW Laplacians, respectively. In the case of symmetric Laplacians, pattern formation follows from the Turing instability. However in nonsymmetric Laplacians, pattern formation may be possible with or without a Turing instability.

  12. Chemistry of polycyclic aromatic hydrocarbons formation from phenyl radical pyrolysis and reaction of phenyl and acetylene.

    PubMed

    Comandini, A; Malewicki, T; Brezinsky, K

    2012-03-15

    An experimental investigation of phenyl radical pyrolysis and the phenyl radical + acetylene reaction has been performed to clarify the role of different reaction mechanisms involved in the formation and growth of polycyclic aromatic hydrocarbons (PAHs) serving as precursors for soot formation. Experiments were conducted using GC/GC-MS diagnostics coupled to the high-pressure single-pulse shock tube present at the University of Illinois at Chicago. For the first time, comprehensive speciation of the major stable products, including small hydrocarbons and large PAH intermediates, was obtained over a wide range of pressures (25-60 atm) and temperatures (900-1800 K) which encompass the typical conditions in modern combustion devices. The experimental results were used to validate a comprehensive chemical kinetic model which provides relevant information on the chemistry associated with the formation of PAH compounds. In particular, the modeling results indicate that the o-benzyne chemistry is a key factor in the formation of multi-ring intermediates in phenyl radical pyrolysis. On the other hand, the PAHs from the phenyl + acetylene reaction are formed mainly through recombination between single-ring aromatics and through the hydrogen abstraction/acetylene addition mechanism. Polymerization is the common dominant process at high temperature conditions. PMID:22339468

  13. N-Heterocyclic Carbene Complexes of Rh: Reaction With Dioxygen Without Oxidation

    SciTech Connect

    Praetorius, J.M.; Allen, D.P.; Wang, R.; Webb, J.D.; Grein, F.; Kennepohl, P.; Crudden, C.M.

    2009-05-21

    The reaction of oxygen with rhodium complexes containing N-heterocyclic carbenes was found to give dioxygen complexes with rare square planar geometries and unusually short O-O bond lengths. Analysis of the bonding in these complexes by Rh L-edge X-ray absorption spectroscopy (XAS), Raman spectroscopy, and DFT calculations provides evidence for a bonding model in which singlet oxygen is bound to a Rh(I) d{sup 8} metal complex, rather than the more common Rh(III) d{sup 6} peroxo species with octahedral geometry and O-O bond lengths in the 1.4-1.5 {angstrom} range.

  14. Quantifying the ionic reaction channels in the Secondary Organic Aerosol formation from glyoxal

    NASA Astrophysics Data System (ADS)

    Maxut, Aurelia; Nozière, Barbara; Rossignol, Stéphanie; George, Christian; Waxman, Eleanor Marie; Laskin, Alexander; Slowik, Jay; Dommen, Josef; Prévôt, André; Baltensperger, Urs; Volkamer, Rainer

    2014-05-01

    Glyoxal, a common organic gas in the atmosphere, has been identified in recent years as an important Secondary Organic Aerosol (SOA) precursor (Volkamer et al., 2007). But, unlike with other precursors, the SOA is largely produced by particle-phase reactions (Volkamer et al., 2009) and equilibria (Kampf et al. 2013) that are still not entirely characterized. Since 2009 series of smog chamber experiments have been performed within the Eurochamp program at the Paul Scherrer Institute, Switzerland, to investigate SOA formation from glyoxal. In these experiments, glyoxal was produced by the gas-phase oxidation of acetylene in the presence of seeds, the seed composition and other conditions being varied. The 2011 campaign resulted in the identification of salting processes controlling the glyoxal partitioning in the seeds (Kampf et al. 2013). This presentation will report results of the 2013 campaign focusing on the identification of the various reactions (ionic or photo-induced) contributing to the SOA mass. In particular, the contribution of the ionic reactions, i.e. mediated by NH4+, were investigated by quantifying the formation of imidazoles (imidazole, imidazole-2-carboxaldehyde, 2,2'-biimidazole) from the small condensation channel of glyoxal with ammonia. For this, the SOA produced were collected on quartz filters and analyzed by Orbitrap LC/MS (Q-Exactive Thermo Fisher). The formation of other products such as organic acids was also investigated to determine potential competing reactions. Time-resolved MOUDI sampling coupled with nano-DESY/ESI-MS/MS analysis was also used to identify nitrogen- and sulphur-containing products from all the reactions. The results obtained for a range of conditions will be presented and compared with recent mechanistic information on the ionic reaction channels (Nozière et al., in preparation, 2013). The implementation of all this new information into a glyoxal-SOA model will be discussed.

  15. Photoinduced Vesicle Formation via the Copper-Catalyzed Azide-Alkyne Cycloaddition Reaction.

    PubMed

    Konetski, Danielle; Gong, Tao; Bowman, Christopher N

    2016-08-16

    Synthetic vesicles have a wide range of applications from drug and cosmetic delivery to artificial cell and membrane studies, making simple and controlled formation of vesicles a large focus of the field today. Here, we report the use of the photoinitiated copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction using visible light to introduce spatiotemporal control into the formation of vesicles. Upon the establishment of the spatiotemporal control over vesicle formation, it became possible to adjust initiation conditions to modulate vesicle sizes resulting in the formation of controllably small or large vesicles based on light intensity or giant vesicles when the formation was initiated in flow-free conditions. Additionally, this photoinitiated method enables vesicle formation at a density 400-fold higher than initiation using sodium ascorbate as the catalyst. Together, these advances enable the formation of high-density, controlled size vesicles using low-energy wavelengths while producing enhanced control over the formation characteristics of the vesicle. PMID:27443396

  16. Bioorganic modelling stereoselective reactions with chiral neutral ligand complexes as model systems for enzyme catalysis.

    PubMed

    Kellogg, R M

    1982-01-01

    amateurs. A better understanding of non-covalent interactions may also provide the key to achieving also the twin goals of both speed and selectivity in bioorganic modelling. As far as enantioselectivity is concerned it is clear that this can be achieved fairly effectively by the use of relatively small, but appropriately placed, groups that force the substrate to complex in an enantioselective step with the ligand. In other words, the problem of enantioselectivity can be solved at the stage of complex forming, which is kinetically rapid. The p]roblem of rate enhancement lies in the mentarity with the transition state of the reaction being catalyzed. Again the achievement of this goal lies in ingenuity of design. Potential areas of applications of chiral crown ether (or cryptate) ligand systems in bioorganic modelling lie in, for example, the formation of carbon-carbon bonds, development of oxidative processes (i.e... PMID:7036410

  17. Diffusion and reaction of pollutants in stratus clouds: application to nocturnal acid formation in plumes

    SciTech Connect

    Seigneur, C.; Saxena, P.; Mirabella, V.A.

    1985-09-01

    A mathematical model is presented that describes the transport, turbulent diffusion, and chemical reactions of air pollutants in stratus clouds. The chemical kinetic mechanism treats 97 gaseous, heterogeneous, and aqueous reactions between 54 species. The dispersion and night-time chemistry of a power plant plume in a stratus cloud is simulated. The contributions of various chemical pathways to the formation of sulfate and nitrate, the differences between plume and background concentrations, and the effect of reduced primary emissions on secondary pollutants are discussed. Calculated sulfate and nitrate concentrations are commensurate with measured atmospheric concentrations.

  18. Formation of Somitogenesis-like Pattern in a Reaction-Diffusion System

    NASA Astrophysics Data System (ADS)

    Sakamoto, Fumitaka; Miyakawa, Kenji

    2008-08-01

    The Belousov-Zhabotinsky reaction system showing stationary patterns is realized on the basis of water-in-oil microemulsions with the surfactant sodium bis(2-ethylhexyl)sulfosuccinate. We experimentally demonstrate the formation of somitogenesis-like pattern in which chemical waves arising from spontaneous bulk oscillations are successively arrested and then stacked. The experimental results are qualitatively reproduced by numerical simulations using the two-variable oregonator model. These show that a somitogenesis can be accounted for by the genuine reaction-diffusion model.

  19. Formations of Bacteria-like Textures by dynamic reactions in Meteorite and Syntheses

    NASA Astrophysics Data System (ADS)

    Miura, Y.

    2009-05-01

    1. Introduction Spherule texture can be formed in dynamic reaction during meteoritic impact in air. However, there are no reports on nano-bacteria-like (i.e. spherule-chained) textures with iron (and Nickel) oxides (with chlorine) in composition and micro-texture with 100nm order [1] in meteorite and synthetic experiment. The purpose of the present study is to elucidate spherule-chained texture with micro-texture of 100nm in order found in the Kuga iron meteorite, Iwakuni, Yamaguchi, Japan, and its first artificial synthesis in laboratory. 2. Two textures in the Kuga meteorite: The Kuga iron meteorite found in Kuga, Iwakuni, Yamaguchi, Japan reveals spherule-chained texture with Fe, Ni-rich composition with 10μm in size, where each spherule contained "long micro-texture in 100nm in size"[1,2]. The complex texture of flow and chained shapes can be found only in the fusion crust of the meteorite formed by quenched and random processes with vapor-melting process in air of the Earth. The FE-ASEM with EDX analyses by an in-situ observation indicate that the matrix of the spherule-chained texture with Fe, Ni, O-rich (with minor Cl) composition is carbon-rich composition formed by impact reactions in air. 3. Comparison with Martian meteorite Remnant of life in ocean can be found by mineralized fossil, which can be found in the Martian meteorite ALH84001 as bacteria-like chained texture of magnetite in composition (in 100nm order) around carbonate spherules [3]. Similarity of bacteria-like texture of the ALH84001 compared with the Kuga meteorites in this study are composition of Fe-rich, C-bearing, and chained texture of small size replaced by Fe and O-rich composition in air. Major difference of these textures is no carbonates minerals in the Kuga meteorite at dynamic reaction in air [1, 2, 3]. 4. First synthesis of bacteria- like akaganeite: A bacteria-like texture with Fe oxides (with minor chlorine as akaganeite-like compositions) is synthesized by chlorine and water

  20. Lattice based Kinetic Monte Carlo Simulations of a complex chemical reaction network

    NASA Astrophysics Data System (ADS)

    Danielson, Thomas; Savara, Aditya; Hin, Celine

    Lattice Kinetic Monte Carlo (KMC) simulations offer a powerful alternative to using ordinary differential equations for the simulation of complex chemical reaction networks. Lattice KMC provides the ability to account for local spatial configurations of species in the reaction network, resulting in a more detailed description of the reaction pathway. In KMC simulations with a large number of reactions, the range of transition probabilities can span many orders of magnitude, creating subsets of processes that occur more frequently or more rarely. Consequently, processes that have a high probability of occurring may be selected repeatedly without actually progressing the system (i.e. the forward and reverse process for the same reaction). In order to avoid the repeated occurrence of fast frivolous processes, it is necessary to throttle the transition probabilities in such a way that avoids altering the overall selectivity. Likewise, as the reaction progresses, new frequently occurring species and reactions may be introduced, making a dynamic throttling algorithm a necessity. We present a dynamic steady-state detection scheme with the goal of accurately throttling rate constants in order to optimize the KMC run time without compromising the selectivity of the reaction network. The algorithm has been applied to a large catalytic chemical reaction network, specifically that of methanol oxidative dehydrogenation, as well as additional pathways on CeO2(111) resulting in formaldehyde, CO, methanol, CO2, H2 and H2O as gas products.

  1. 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.

  2. Mechanisms of the Water-Gas Shift Reaction Catalyzed by Ruthenium Carbonyl Complexes.

    PubMed

    Liu, Naying; Guo, Ling; Cao, Zhaoru; Li, Wenli; Zheng, Xiaoli; Shi, Yayin; Guo, Juan; Xi, Yaru

    2016-04-21

    Density functional theory (DFT) is employed to study the water-gas shift (WGS) reaction in the gas phase for two complexes, Ru3(CO)12 and Ru(CO)5. Here we report four mechanisms of ruthenium carbonyl complexes catalyzed for WGS reaction. The energetic span model is applied to evaluate efficiency of the four catalytic pathways. Our results indicate that mechanism C and D show a good catalytic behavior, which is in agreement with results from the literature. The mechanism C and D not only include the important intermediate Ru3(CO)11H(-) but also exclude the energy-demanding OH(-) desorption and revise an unfavorable factor of the previous mechanism. Two complexes along mechanisms B have the highest turnover frequency (TOF) values. The trinuclear carbonyl complexes-Ru3(CO)12 is preferred over mononuclear carbonyl Ru(CO)5 by comparing TOF due to the fact that metal-metal cooperativity can enhance activity to the WGS reaction. In this work, the nature of interaction between transition states and intermediates is also analyzed by the detailed electronic densities of states, and we further clarify high catalytic activity of ruthenium carbonyl complexes as well. Our conclusions provide a guide to design catalysts for the WGS reaction. PMID:27064302

  3. Brown carbon formation by aqueous-phase carbonyl compound reactions with amines and ammonium sulfate.

    PubMed

    Powelson, Michelle H; Espelien, Brenna M; Hawkins, Lelia N; Galloway, Melissa M; De Haan, David O

    2014-01-21

    Reactions between small water-soluble carbonyl compounds, ammonium sulfate (AS), and/or amines were evaluated for their ability to form light-absorbing species in aqueous aerosol. Aerosol chemistry was simulated with bulk phase reactions at pH 4, 275 K, initial concentrations of 0.05 to 0.25 M, and UV-vis and fluorescence spectroscopy monitoring. Glycolaldehyde-glycine mixtures produced the most intense absorbance. In carbonyl compound reactions with AS, methylamine, or AS/glycine mixtures, product absorbance followed the order methylglyoxal > glyoxal > glycolaldehyde > hydroxyacetone. Absorbance extended into the visible, with a wavelength dependence fit by absorption Ångstrom coefficients (Å(abs)) of 2 to 11, overlapping the Å(abs) range of atmospheric, water-soluble brown carbon. Many reaction products absorbing between 300 and 400 nm were strongly fluorescent. On a per mole basis, amines are much more effective than AS at producing brown carbon. In addition, methylglyoxal and glyoxal produced more light-absorbing products in reactions with a 5:1 AS-glycine mixture than with AS or glycine alone, illustrating the importance of both organic and inorganic nitrogen in brown carbon formation. Through comparison to biomass burning aerosol, we place an upper limit on the contribution of these aqueous carbonyl-AS-amine reactions of ≤ 10% of global light absorption by brown carbon. PMID:24351110

  4. Double layer formation at the interface of complex plasmas

    SciTech Connect

    Yaroshenko, V. V.; Thoma, M. H.; Thomas, H. M.; Morfill, G. E.

    2008-08-15

    Necessary conditions are formulated for the generation of a double layer at the interface of a complex plasma and a particle-free electron-ion plasma in a weakly collisional discharge. Examples are calculated for realistic observed complex plasmas, and it is shown that situations of both ''smooth'' transitions and 'sharp' transitions can exist. The model can explain the abrupt boundaries observed.

  5. Synthesis of sp(3)-rich scaffolds for molecular libraries through complexity-generating cascade reactions.

    PubMed

    Flagstad, T; Min, G; Bonnet, K; Morgentin, R; Roche, D; Clausen, M H; Nielsen, T E

    2016-06-01

    An efficient strategy for the synthesis of complex small molecules from simple building blocks is presented. Key steps of the strategy include tandem Petasis and Diels-Alder reactions, and divergent complexity-generating cyclization cascades from a key dialdehyde intermediate. The methodology is validated through the synthesis of a representative compound set, which has been used in the production of 1617 molecules for the European Lead Factory. PMID:27171614

  6. Some new reaction pathways for the formation of cytosine in interstellar space - A quantum chemical study

    NASA Astrophysics Data System (ADS)

    Gupta, V. P.; Tandon, Poonam; Mishra, Priti

    2013-03-01

    The detection of nucleic acid bases in carbonaceous meteorites suggests that their formation and survival is possible outside of the Earth. Small N-heterocycles, including pyrimidine, purines and nucleobases, have been extensively sought in the interstellar medium. It has been suggested theoretically that reactions between some interstellar molecules may lead to the formation of cytosine, uracil and thymine though these processes involve significantly high potential barriers. We attempted therefore to use quantum chemical techniques to explore if cytosine can possibly form in the interstellar space by radical-radical and radical-molecule interaction schemes, both in the gas phase and in the grains, through barrier-less or low barrier pathways. Results of DFT calculations for the formation of cytosine starting from some of the simple molecules and radicals detected in the interstellar space are being reported. Global and local descriptors such as molecular hardness, softness and electrophilicity, and condensed Fukui functions and local philicity indices were used to understand the mechanistic aspects of chemical reaction. The presence and nature of weak bonds in the molecules and transition states formed during the reaction process have been ascertained using Bader's quantum theory of atoms in molecules (QTAIMs). Two exothermic reaction pathways starting from propynylidyne (CCCH) and cyanoacetylene (HCCCN), respectively, have been identified. While the first reaction path is found to be totally exothermic, it involves a barrier of 12.5 kcal/mol in the gas phase against the lowest value of about 32 kcal/mol reported in the literature. The second path is both exothermic and barrier-less. The later has, therefore, a greater probability of occurrence in the cold interstellar clouds (10-50 K).

  7. Reaction of furan-based o-quinodimethanes with triplet oxygen. Formation of cyclic peroxides

    SciTech Connect

    Chou, Chin-Hsing; Trahanovsky, W.S.

    1995-08-25

    Formation of cyclic peroxides 2a,2b, and 2c from the reactions of 2,3-dimethylene-2,3-dihydrofuran (1a) and the 5-methyl (1b) and 5-tert-butyl (1c) derivatives with triplet oxygen is reported. Thermolysis of cyclic peroxide 2c gives dialdehyde 5, hydroxy aldehydes 6 and 7, and diol 8 as products. 1 fig.

  8. Formation of O3/+/ by the reaction of metastable O2/+/ ions with O2

    NASA Technical Reports Server (NTRS)

    Ajello, J. M.; Pang, K. D.; Monahan, K. M.

    1974-01-01

    The high resolution of the photoionization mass spectrophotometer was utilized to resolve some doubts about the participating species in the reaction of metastable oxygen molecular ions with oxygen molecules to yield ozone ions and oxygen radicals. It is found from inspection of the appearance potential of the ozone ion that an a4 Pi-excited state is responsible for the formation of ozone near the appearance potential of these lines.

  9. Thermochemistry and Reaction Barriers for the Formation of Levoglucosenone from Cellobiose

    SciTech Connect

    Assary, Rajeev S.; Curtiss, Larry A.

    2011-10-19

    Cellobiose jumps the barrier: High-level quantum mechanical studies show that the ether bond cleavage in cellobiose occurs through internal hydrogen transfer in the gas phase and that the activation energy required is similar to that required for activating cellulose. The reaction barriers are computed for various pathways for the formation of levoglucosenone from levoglucosan, and the most likely pathway requires a relatively low activation barrier compared to that for the activation of cellobiose.

  10. Thermochemistry and Reaction Barriers for the Formation of Levoglucosenone from Cellobiose

    SciTech Connect

    Assary, Rajeev S.; Curtiss, Larry A.

    2012-02-06

    Cellobiose jumps the barrier: High-level quantum mechanical studies show that the ether bond cleavage in cellobiose occurs through internal hydrogen transfer in the gas phase and that the activation energy required is similar to that required for activating cellulose. The reaction barriers are computed for various pathways for the formation of levoglucosenone from levoglucosan, and the most likely pathway requires a relatively low activation barrier compared to that for the activation of cellobiose.

  11. Thermochemistry and reaction barriers for the formation of levoglucosenone from cellobiose.

    SciTech Connect

    Assary, R. S.; Curtiss, L. A.

    2012-02-06

    Cellobiose jumps the barrier: High-level quantum mechanical studies show that the ether bond cleavage in cellobiose occurs through internal hydrogen transfer in the gas phase and that the activation energy required is similar to that required for activating cellulose. The reaction barriers are computed for various pathways for the formation of levoglucosenone from levoglucosan, and the most likely pathway requires a relatively low activation barrier compared to that for the activation of cellobiose.

  12. Interaction of 2-aminopyrimidine with σ- and π-acceptors involving chemical reactions via initial charge transfer complexation

    NASA Astrophysics Data System (ADS)

    Rabie, U. M.; Abou-El-Wafa, M. H.; Mohamed, R. A.

    2007-12-01

    Interaction of 2-aminopyrimidine (AP) with iodine as a typical σ-type acceptor and with a typical π-type acceptor, 2,3,5,6-tetrachloro-1,4-benzoquinone, p-chloranil (CHL) have been studied spectrophotometrically. Electronic absorption spectra of the system AP-I 2 in several organic solvents of different polarities have performed clear charge transfer (CT) band(s). Formation constants ( KCT) and molar absorption coefficients ( ɛCT) and thermodynamic properties, Δ H, Δ S, and Δ G, of this system in various organic solvents were determined and discussed. Interaction of AP with the π-acceptor has shown unique behaviors. Chemical reaction has occurred via prior or initial formation of the outer-sphere CT complex followed by formation of the corresponding anion radicals, CHL rad - , as intermediates. UV-vis, 1H NMR, Mass, and FT-IR spectra in addition to the elemental analysis were used to confirm the proposed occurrence of the chemical reaction and to investigate the synthesized solid products.

  13. Infrared spectroscopic studies on reaction induced conformational changes in the NADH ubiquinone oxidoreductase (complex I).

    PubMed

    Hellwig, Petra; Kriegel, Sébastien; Friedrich, Thorsten

    2016-07-01

    Redox-dependent conformational changes are currently discussed to be a crucial part of the reaction mechanism of the respiratory complex I. Specialized difference Fourier transform infrared techniques allow the detection of side-chain movements and minute secondary structure changes. For complex I, (1)H/(2)H exchange kinetics of the amide modes revealed a better accessibility of the backbone in the presence of NADH and quinone. Interestingly, the presence of phospholipids, that is crucial for the catalytic activity of the isolated enzyme complex, changes the overall conformation. When comparing complex I samples from different species, very similar electrochemically induced FTIR difference spectra and very similar rearrangements are reported. Finally, the information obtained with variants and from Zn(2+) inhibited samples for the conformational reorganization of complex I upon electron transfer are discussed in this review. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt. PMID:26702948

  14. Hair dye-incorporated poly-γ-glutamic acid/glycol chitosan nanoparticles based on ion-complex formation

    PubMed Central

    Lee, Hye-Young; Jeong, Young-IL; Choi, Ki-Choon

    2011-01-01

    Background p-Phenylenediamine (PDA) or its related chemicals are used more extensively than oxidative hair dyes. However, permanent hair dyes such as PDA are known to have potent contact allergy reactions in humans, and severe allergic reactions are problematic. Methods PDA-incorporated nanoparticles were prepared based on ion-complex formation between the cationic groups of PDA and the anionic groups of poly(γ-glutamic acid) (PGA). To reinforce PDA/PGA ion complexes, glycol chitosan (GC) was added. PDA-incorporated nanoparticles were characterized using field-emission scanning electron microscopy, Fourier- transform infrared (FT-IR) spectroscopy, dynamic light scattering, and powder X-ray diffractometry (XRD). Results Nanoparticles were formed by ion-complex formation between the amine groups of PDA and the carboxyl groups of PGA. PDA-incorporated nanoparticles are small in size (<100 nm), and morphological observations showed spherical shapes. FT-IR spectra results showed that the carboxylic acid peak of PGA decreased with increasing PDA content, indicating that the ion complexes were formed between the carboxyl groups of PGA and the amine groups of PDA. Furthermore, the intrinsic peak of the carboxyl groups of PGA was also decreased by the addition of GC. Intrinsic crystalline peaks of PDA were observed by XRD. This crystalline peak of PDA was completely nonexistent when nanoparticles were formed by ion complex between PDA, PGA, and GC, indicating that PDA was complexed with PGA and no free drug existed in the formulation. During the drug-release experiment, an initial burst release of PDA was observed, and then PDA was continuously released over 1 week. Cytotoxicity testing against HaCaT human skin keratinocyte cells showed PDA-incorporated nanoparticles had lower toxicity than PDA itself. Furthermore, PDA-incorporated nanoparticles showed reduced apoptosis and necrosis reaction at HaCaT cells. Conclusion The authors suggest that these microparticles are ideal

  15. Proton Mobility in b₂ Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides.

    PubMed

    Nelson, Carissa R; Abutokaikah, Maha T; Harrison, Alex G; Bythell, Benjamin J

    2016-03-01

    A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting. PMID:26602904

  16. Proton Mobility in b2 Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides

    NASA Astrophysics Data System (ADS)

    Nelson, Carissa R.; Abutokaikah, Maha T.; Harrison, Alex G.; Bythell, Benjamin J.

    2016-03-01

    A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.

  17. Synthesis, Characterization, and Reactions of Isolable (β-Diketiminato)Nb(III) Imido Complexes.

    PubMed

    Tomson, Neil C; Arnold, John; Bergman, Robert G

    2010-11-01

    for the reduction of organic π-systems. The reduction of mesityl azide by (BDI)Nb(N(t)Bu)(py) and diphenylsulfoxide by (BDI)Nb(N(t)Bu)(CO)(2) led to the monomeric bis(imido) and dimeric oxo complexes (BDI)Nb(N(t)Bu)(NMes)(py) and [(BDI)Nb(N(t)Bu)](2)(μ2-O)(2), respectively. MeLi addition to (BDI)Nb(N(t)Bu)(CO)(2)(py) resulted in the formation of a Nb-acylate via methide addition to one of the carbonyl carbons. The acylate product was revealed to have a short Nb-C(acylate) bond distance (2.059(4) Å), consistent with multiple Nb-C bond character resulting from Nb(III) back-bonding into the acylate carbon. The interaction of (BDI)Nb(N(t)Bu)(CO)(2) with two equivalents of 4,4'-dichlorobenzophenone resulted in the clean, quantitative formation of the corresponding pinacol coupling product, but introduction of the ketone in 1: 1 molar ratios resulted in mixtures of the pinacol product and the starting material, suggesting that ketone coordination to the Nb(III) complex may be reversible. Relatedly, addition of 1-phenyl-1-propyne to (BDI)Nb(N(t)Bu)(CO)(2) formed a thermally unstable 1: 1 Nb/alkyne complex, as characterized by NMR and IR spectroscopies; reaction of this species with HCl/MeOH yielded a 2: 1 mixture of 1-phenyl-1-propene and the free alkyne, suggesting a high degree of covalency in the Nb-C bonds. PMID:21116450

  18. Synthesis, Characterization, and Reactions of Isolable (β-Diketiminato)Nb(III) Imido Complexes*

    PubMed Central

    Tomson, Neil C.; Arnold, John; Bergman, Robert G.

    2010-01-01

    mesityl azide by (BDI)Nb(NtBu)(py) and diphenylsulfoxide by (BDI)Nb(NtBu)(CO)2 led to the monomeric bis(imido) and dimeric oxo complexes (BDI)Nb(NtBu)(NMes)(py) and [(BDI)Nb(NtBu)]2(μ2-O)2, respectively. MeLi addition to (BDI)Nb(NtBu)(CO)2(py) resulted in the formation of a Nb-acylate via methide addition to one of the carbonyl carbons. The acylate product was revealed to have a short Nb–Cacylate bond distance (2.059(4) Å), consistent with multiple Nb–C bond character resulting from Nb(III) back-bonding into the acylate carbon. The interaction of (BDI)Nb(NtBu)(CO)2 with two equivalents of 4,4′-dichlorobenzophenone resulted in the clean, quantitative formation of the corresponding pinacol coupling product, but introduction of the ketone in 1: 1 molar ratios resulted in mixtures of the pinacol product and the starting material, suggesting that ketone coordination to the Nb(III) complex may be reversible. Relatedly, addition of 1-phenyl-1-propyne to (BDI)Nb(NtBu)(CO)2 formed a thermally unstable 1: 1 Nb/alkyne complex, as characterized by NMR and IR spectroscopies; reaction of this species with HCl/MeOH yielded a 2: 1 mixture of 1-phenyl-1-propene and the free alkyne, suggesting a high degree of covalency in the Nb–C bonds. PMID:21116450

  19. Interplay of Experiment and Theory in Elucidating Mechanisms of Oxidation Reactions by a Nonheme Ru(IV)O Complex.

    PubMed

    Dhuri, Sunder N; Cho, Kyung-Bin; Lee, Yong-Min; Shin, Sun Young; Kim, Jin Hwa; Mandal, Debasish; Shaik, Sason; Nam, Wonwoo

    2015-07-01

    A comprehensive experimental and theoretical study of the reactivity patterns and reaction mechanisms in alkane hydroxylation, olefin epoxidation, cyclohexene oxidation, and sulfoxidation reactions by a mononuclear nonheme ruthenium(IV)-oxo complex, [Ru(IV)(O)(terpy)(bpm)](2+) (1), has been conducted. In alkane hydroxylation (i.e., oxygen rebound vs oxygen non-rebound mechanisms), both the experimental and theoretical results show that the substrate radical formed via a rate-determining H atom abstraction of alkanes by 1 prefers dissociation over oxygen rebound and desaturation processes. In the oxidation of olefins by 1, the observations of a kinetic isotope effect (KIE) value of 1 and styrene oxide formation lead us to conclude that an epoxidation reaction via oxygen atom transfer (OAT) from the Ru(IV)O complex to the C═C double bond is the dominant pathway. Density functional theory (DFT) calculations show that the epoxidation reaction is a two-step, two-spin-state process. In contrast, the oxidation of cyclohexene by 1 affords products derived from allylic C-H bond oxidation, with a high KIE value of 38(3). The preference for H atom abstraction over C═C double bond epoxidation in the oxidation of cyclohexene by 1 is elucidated by DFT calculations, which show that the energy barrier for C-H activation is 4.5 kcal mol(-1) lower than the energy barrier for epoxidation. In the oxidation of sulfides, sulfoxidation by the electrophilic Ru-oxo group of 1 occurs via a direct OAT mechanism, and DFT calculations show that this is a two-spin-state reaction in which the transition state is the lowest in the S = 0 state. PMID:26075466

  20. Modeling Fluid Flow and Microbial Reactions in the Peru Accretionary Complex

    NASA Astrophysics Data System (ADS)

    Bekins, B. A.; Matmon, D.

    2002-12-01

    Accretionary complexes are sites where sediment compaction and deeper reactions drive large-scale flow systems that can affect global solute budgets. Extensive modeling and drilling studies have elucidated the origin of the fluids, pore pressures, duration of flow, and major flow paths in these settings. An important research goal is to quantify the effect of these flow systems on global chemical budgets of reactive solutes such as carbon. The Peru margin represents an end member setting that can serve as a basis to extend the results to other margins. The sediments are relatively high in organic carbon with an average value of 2.6%. The subduction rate at ~9 cm/yr and taper angle at 14-17° are among the largest in the world. Recent microbial studies on Ocean Drilling Program Leg 201 at the Peru accretionary margin provide many key elements needed to quantify the processes affecting organic carbon in an accretionary complex. Pore water chemistry data from Site 1230 located in the Peru accretionary prism indicate that sulfate reduction is important in the top 8 mbsf. Below this depth, methanogenesis is the dominant process and methane concentrations are among the highest measured at any site on Leg 201. The presence of high methane concentrations at shallow depths suggests that methane is transported upward in the prism by fluid flow. Measurements of in-situ pore pressures and temperatures also support the presence of upward fluid flow. A single in-situ pressure measurement at ~100 mbsf indicated an overpressure of 0.14 MPa. For a reasonable formation permeability of ~ 10-16 m2, the measured overpressure is adequate to produce flow at a rate of ~5 mm/yr. This rate is comparable to previous model estimates for flow rates in the Peru accretionary prism. In addition, curvature in the downhole temperature profile can best be explained by upward fluid flow of 1-10 mm/yr. These data are used to constrain a two-dimensional coupled fluid flow and reactive transport model

  1. Enantioconvergent Nucleophilic Substitution Reaction of Racemic Alkyne-Dicobalt Complex (Nicholas Reaction) Catalyzed by Chiral Brønsted Acid.

    PubMed

    Terada, Masahiro; Ota, Yusuke; Li, Feng; Toda, Yasunori; Kondoh, Azusa

    2016-08-31

    Catalytic enantioselective syntheses enable a practical approach to enantioenriched molecules. While most of these syntheses have been accomplished by reaction at the prochiral sp(2)-hybridized carbon atom, little attention has been paid to enantioselective nucleophilic substitution at the sp(3)-hybridized carbon atom. In particular, substitution at the chiral sp(3)-hybridized carbon atom of racemic electrophiles has been rarely exploited. To establish an unprecedented enantioselective substitution reaction of racemic electrophiles, enantioconvergent Nicholas reaction of an alkyne-dicobalt complex derived from racemic propargylic alcohol was developed using a chiral phosphoric acid catalyst. In the present enantioconvergent process, both enantiomers of the racemic alcohol were transformed efficiently to a variety of thioethers with high enantioselectivity. The key to achieving success is dynamic kinetic asymmetric transformation (DYKAT) of enantiomeric cationic intermediates generated via dehydroxylation of the starting racemic alcohol under the influence of the chiral phosphoric acid catalyst. The present fascinating DYKAT involves the efficient racemization of these enantiomeric intermediates and effective resolution of these enantiomers through utilization of the chiral conjugate base of the phosphoric acid. PMID:27490239

  2. Reaction pathways towards the formation of dolomite-analogues at ambient conditions

    NASA Astrophysics Data System (ADS)

    Pimentel, Carlos; Pina, Carlos M.

    2016-04-01

    In this paper we present results of a study of the crystallisation behaviour of the dolomite-analogues norsethite and PbMg(CO3)2 at room temperature and atmospheric pressure. Whereas precipitation of norsethite was previously obtained by mixing solutions (Hood et al., 1974; Pimentel and Pina, 2014a,b), we report, for the first time, the synthesis of PbMg(CO3)2 by using the same method. The formation of both phases was promoted by ageing slurries for periods of time ranging from a few days (norsethite) up to 6 months (PbMg(CO3)2). The crystallisation of both norsethite and PbMg(CO3)2 occurs by sequences of dissolution-precipitation reactions involving several amorphous and crystalline precursor phases, which were identified and characterised by X-ray diffraction and scanning electron microscopy. Depending on the initial composition and Ba:Mg and Pb:Mg ratios in the slurries, different precursors and reaction kinetics were observed. This demonstrates the existence of different reaction pathways towards the formation of the investigated dolomite-analogues. Our experimental results provide new insights into the possible mechanisms of formation of dolomite and other double carbonates in nature.

  3. Pattern formation in the iodate-sulfite-thiosulfate reaction-diffusion system.

    PubMed

    Liu, Haimiao; Pojman, John A; Zhao, Yuemin; Pan, Changwei; Zheng, Juhua; Yuan, Ling; Horváth, Attila K; Gao, Qingyu

    2012-01-01

    Sodium polyacrylate-induced pH pattern formation and starch-induced iodine pattern formation were investigated in the iodate-sulfite-thiosulfate (IST) reaction in a one-side fed disc gel reactor (OSFR). As binding agents of the autocatalyst of hydrogen ions or iodide ions, different content of sodium polyacrylate or starch has induced various types of pattern formation. We observed pH pulses, striped patterns, mixed spots and stripes, and hexagonal spots upon increasing the content of sodium polyacrylate and observed iodine pulses, branched patterns, and labyrinthine patterns upon increasing the starch content in the system. Coexistence of a pH front and an iodine front was also studied in a batch IST reaction-diffusion system. Both pH and iodine front instabilities were observed in the presence of sodium polyacrylate, i.e., cellular fronts and transient Turing structures resulting from the decrease in diffusion coefficients of activators. The mechanism of multiple feedback may explain the different patterns in the IST reaction-diffusion system. PMID:22068976

  4. Molybdenum Hydride and Dihydride Complexes Bearing Diphosphine Ligands with a Pendant Amine: Formation of Complexes With Bound Amines

    SciTech Connect

    Zhang, Shaoguang; Bullock, R. Morris

    2015-07-06

    CpMo(CO)(PNP)H complexes (PNP = (R2PCH2)2NMe, R = Et or Ph) were synthesized by displacement of two CO ligands of CpMo(CO)3H by the PNP ligand; these complexes were characterized by IR and variable temperature 1H and 31P NMR spectroscopy. CpMo(CO)(PNP)H complexes are formed as mixture of cis and trans-isomers. Both cis-CpMo(CO)(PEtNMePEt)H and trans-CpMo(CO)(PPhNMePPh)H were analyzed by single crystal X-ray diffraction. Electrochemical oxidation of CpMo(CO)(PEtNMePEt)H and CpMo(CO)(PPhNMePPh)H in CH3CN are both irreversible at slow scan rates and quasi-reversible at higher scan rates, with E1/2 = -0.36 V (vs. Cp2Fe+/0) for CpMo(CO)(PEtNMePEt)H and E1/2 = -0.18 V for CpMo(CO)(PPhNMePPh)H. Hydride abstraction from CpMo(CO)(PNP)H with [Ph3C]+[A]- (A = B(C6F5)4 or BArF4; [ArF = 3,5-bis(trifluoromethyl)phenyl]) afforded “tuck-in” [CpMo(CO)(κ3-PNP)]+ complexes that feature the amine bound to the metal. Displacement of the κ3 Mo-N bond by CD3CN gives [CpMo(CO)(PNP)(CD3CN)]+. The kinetics of this reaction were studied by NMR spectroscopy, providing the activation parameters ΔH‡ = 22.1 kcal/mol, ΔS‡ = 1.89 cal/(mol·K), Ea = 22.7 kcal/mol. Protonation of CpMo(CO)(PEtNMePEt)H affords [CpMo(CO)(κ2-PEtNMePEt)(H)2]+ as a Mo dihydride complex, which loses H2 to generate [CpMo(CO)(κ3-PEtNMePEt)]+ at room temperature. CpMo(CO)(dppp)H (dppp = 1,2-bis(diphenylphosphino)propane) was studied as a Mo diphosphine analogue without a pendant amine, and the product of protonation of this complex gives [CpMo(CO)(dppp)(H)2]+. Our results show that the pendant amine has a strong driving force to form stable “tuck-in” [CpMo(CO)(κ3-PNP)]+ complexes, and also promotes hydrogen elimination from [CpMo(CO)(PNP)(H)2]+ complexes by formation of Mo-N dative bond. We thank the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences for support. Pacific Northwest National Laboratory is operated by

  5. Products and Mechanisms of Aerosol Formation from Reactions of OH Radicals with Linear and Branched Alkenes in the Presence of NOx (Invited)

    NASA Astrophysics Data System (ADS)

    Ziemann, P. J.; Matsunaga, A.

    2009-12-01

    The chemical and physical processes involved in the formation of secondary organic aerosol (SOA) are complex and can include reactions of volatile organic compounds with a number of atmospheric oxidants (the major ones are O3, and OH and NO3 radicals), as well as surface and condensed-phase reactions, homogeneous nucleation, and gas-particle partitioning. It should come as no surprise that understanding and accurately modeling these processes is a major challenge that has not yet been fully addressed. Alkenes emitted from vegetation are the largest source of non-methane hydrocarbons to the global atmosphere and consist mostly of isoprene (C5H8), monoterpenes (C10H16), and sesquiterpenes (C15H24), compounds with a large range of sizes and molecular structures. Their atmospheric oxidation is initiated primarily by reactions with hydroxyl radicals and can lead to a variety of products, some of which can form SOA. Because of the complexity of terpene reactions and the large numbers of products that are formed, there are advantages to studying the chemistry of simpler alkenes in order to gain insights that can be applied to more complex reaction systems. This is the approach we have taken, and in this talk I will report results of studies of the products, SOA yields, and mechanisms of SOA formation from reactions of a variety of linear and branched alkenes with hydroxyl radicals in the presence of nitrogen oxides. Products consist of a large array of multifunctional compounds, including oligomers, containing carbonyl, hydroxy, carboxyl, and nitrate groups. I will demonstrate some of the ways in which changes in molecular structure can alter both gas and SOA products, including those formed through condensed-phase reactions, and also SOA yields, and suggest explanations for these effects based on current understanding of chemical reaction mechanisms.

  6. Nickel-catalyzed [3+1+1] cycloaddition reactions of alkenyl Fischer carbene complexes with methylenecyclopropanes.

    PubMed

    Kamikawa, Ken; Shimizu, Yasunori; Takemoto, Shin; Matsuzaka, Hiroyuki

    2006-08-31

    Methylenecyclopentanones were synthesized by the nickel-catalyzed [3+1+1] cycloaddition reactions of alkenyl Fischer carbene complexes with methylenecyclopropanes. The methylenecyclopropane was transformed into the C(2)-symmetric bis-cyclopentapyridazine derivative by reacting with p-toluenesulfonyl hydrazine. PMID:16928061

  7. Generalization of the Activated Complex Theory of Reaction Rates. II. Classical Mechanical Treatment

    DOE R&D Accomplishments Database

    Marcus, R. A.

    1964-01-01

    In its usual classical form activated complex theory assumes a particular expression for the kinetic energy of the reacting system -- one associated with a rectilinear motion along the reaction coordinate. The derivation of the rate expression given in the present paper is based on the general kinetic energy expression.

  8. Insight into the Reaction of a Dinuclear Phosphinidene Complex with Nitriles.

    PubMed

    Seidl, Michael; Weinzierl, Rudolf; Timoshkin, Alexey Y; Scheer, Manfred

    2016-04-11

    The phosphinidene complex [Cp*P{W(CO)5 }2 ] (1; Cp*=C5 Me5 ) reacted with malononitrile to give the 1,2-dihydro-1,3,2-diazaphosphinine derivative 2. The reaction of 1 with 1,4-benzodinitrile gave [1,4-{{W(CO)5 }2 P-N=C(Cp*)}2 (C6 H4 )] (3), the first example of a cumulene-like aminophosphinidene complex. The reaction of 1 with aniline gave the aminophosphinidene complex [(Ph)N(H)P{W(CO)5 }2 ] (4). To compare the reactivity of benzonitrile and aniline with 1, the phosphinidene complex 1 was reacted with three different isomers of aminobenzonitrile (2-, 3-, and 4-aminobenzonitrile). These reactions gave an insight into the reaction pathway of 1 with benzonitrile derivatives. Compounds 5, 6 a, 6 b, and 7, which are derivatives of 1,2-dihydro-1,3,2-diazaphosphinine or benzo-2H-1,2-azaphospholes, were, as well as all other products, characterized by mass spectrometry, NMR and IR spectroscopy, and X-ray structure analysis. PMID:26887793

  9. Placebo Effect upon Complex Reaction Time When Hypnotic Suggestibility is Controlled.

    ERIC Educational Resources Information Center

    Eskridge, Veronica L.

    This study was designed to investigate the effect of a placebo (sugar pill) accompanied by suggestions that the pill would either (1) improve performance as a stimulant or (2) cause a deterioration in performance as a depressant when the performance in question was the subjects' complex reaction time to a light stimulus. The Harvard Group Scale of…

  10. Chiral holmium complex-catalyzed Diels-Alder reaction of silyloxyvinylindoles: stereoselective synthesis of hydrocarbazoles.

    PubMed

    Harada, Shinji; Morikawa, Takahiro; Nishida, Atsushi

    2013-10-18

    The catalytic and asymmetric cycloaddition between 3-[1-(silyloxy)vinyl]indoles and electron-deficient olefins gave substituted hydrocarbazoles in up to 99% yield and 94% ee. This reaction was catalyzed by a novel chiral holmium(III) complex. Alkylation of the cycloadduct gave a tricyclic compound with four continuous chiral centers, one of which was a quaternary carbon. PMID:24079531

  11. Coexistence facilitates interspecific biofilm formation in complex microbial communities.

    PubMed

    Madsen, Jonas S; Røder, Henriette L; Russel, Jakob; Sørensen, Helle; Burmølle, Mette; Sørensen, Søren J

    2016-09-01

    Social interactions in which bacteria respond to one another by modifying their phenotype are central determinants of microbial communities. It is known that interspecific interactions influence the biofilm phenotype of bacteria; a phenotype that is central to the fitness of bacteria. However, the underlying role of fundamental ecological factors, specifically coexistence and phylogenetic history, in biofilm formation remains unclear. This study examines how social interactions affect biofilm formation in multi-species co-cultures from five diverse environments. We found prevalence of increased biofilm formation among co-cultured bacteria that have coexisted in their original environment. Conversely, when randomly co-culturing bacteria across these five consortia, we found less biofilm induction and a prevalence of biofilm reduction. Reduction in biofilm formation was even more predominant when co-culturing bacteria from environments where long-term coexistence was unlikely to have occurred. Phylogenetic diversity was not found to be a strong underlying factor but a relation between biofilm induction and phylogenetic history was found. The data indicates that biofilm reduction is typically correlated with an increase in planktonic cell numbers, thus implying a behavioral response rather than mere growth competition. Our findings suggest that an increase in biofilm formation is a common adaptive response to long-term coexistence. PMID:27119650

  12. Formation of Chlorotriophenoxy Radicals from Complete Series Reactions of Chlorotriophenols with H and OH Radicals.

    PubMed

    Xu, Fei; Shi, Xiangli; Zhang, Qingzhu; Wang, Wenxing

    2015-01-01

    The chlorothiophenoxy radicals (CTPRs) are key intermediate species in the formation of polychlorinated dibenzothiophenes/thianthrenes (PCDT/TAs). In this work, the formation of CTPRs from the complete series reactions of 19 chlorothiophenol (CTP) congeners with H and OH radicals were investigated theoretically by using the density functional theory (DFT) method. The profiles of the potential energy surface were constructed at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants were evaluated by the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) contribution at 600-1200 K. The present study indicates that the structural parameters, thermal data, and rate constants as well as the formation potential of CTPRs from CTPs are strongly dominated by the chlorine substitution at the ortho-position of CTPs. Comparison with the study of formation of chlorophenoxy radicals (CPRs) from chlorophenols (CPs) clearly shows that the thiophenoxyl-hydrogen abstraction from CTPs by H is more efficient than the phenoxyl-hydrogen abstraction from CPs by H, whereas the thiophenoxyl-hydrogen abstraction from CTPs by OH is less impactful than the phenoxyl-hydrogen abstraction from CPs by OH. Reactions of CTPs with H can occur more readily than that of CTPs with OH, which is opposite to the reactivity comparison of CPs with H and OH. PMID:26270566

  13. Formation of Chlorotriophenoxy Radicals from Complete Series Reactions of Chlorotriophenols with H and OH Radicals

    PubMed Central

    Xu, Fei; Shi, Xiangli; Zhang, Qingzhu; Wang, Wenxing

    2015-01-01

    The chlorothiophenoxy radicals (CTPRs) are key intermediate species in the formation of polychlorinated dibenzothiophenes/thianthrenes (PCDT/TAs). In this work, the formation of CTPRs from the complete series reactions of 19 chlorothiophenol (CTP) congeners with H and OH radicals were investigated theoretically by using the density functional theory (DFT) method. The profiles of the potential energy surface were constructed at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants were evaluated by the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) contribution at 600–1200 K. The present study indicates that the structural parameters, thermal data, and rate constants as well as the formation potential of CTPRs from CTPs are strongly dominated by the chlorine substitution at the ortho-position of CTPs. Comparison with the study of formation of chlorophenoxy radicals (CPRs) from chlorophenols (CPs) clearly shows that the thiophenoxyl-hydrogen abstraction from CTPs by H is more efficient than the phenoxyl-hydrogen abstraction from CPs by H, whereas the thiophenoxyl-hydrogen abstraction from CTPs by OH is less impactful than the phenoxyl-hydrogen abstraction from CPs by OH. Reactions of CTPs with H can occur more readily than that of CTPs with OH, which is opposite to the reactivity comparison of CPs with H and OH. PMID:26270566

  14. Zwitterion formation in titan ice analogs: reaction between HC3N and NH3.

    PubMed

    Couturier-Tamburelli, Isabelle; Sessouma, Bintou; Chiavassa, Thierry; Piétri, Nathalie

    2012-11-01

    A zwitterion is formed in the laboratory at low temperatures in the solid phase from the thermal reaction of HC(3)N and NH(3). We report for the first time its infrared spectrum. We study its reaction using Fourier transform infrared spectroscopy. Its reaction rate is estimated to be k(T) = 2.9 × 10(5) exp(-2.3 ± 0.1 (kJ mol(-1))/RT). Calculations using density functional theory (B3LYP/6-31g**) are used to characterize all the species (complexes, zwitterions, and transition states) and are in good agreement with the infrared spectra. The structure of the zwitterion is determined planar and it is characterized by a N-C bond around 1.5 Å. PMID:23075265

  15. Bifunctional mechanism of catalysis in reactions leading to formation of /alpha/-amino ketones

    SciTech Connect

    Popov, A.F.; Anikeev, A.V.

    1988-10-20

    The kinetics of the reaction of /alpha/-bromoacetophenone and benzyl bromide with aniline and pyridine in the presence of additions of acetic acid and phenol in benzene at 30/degree/C were investigated. The catalytic effects due to the activity of the uncombined forms of the catalyst, their dimers, and their 1:1 complexes with the amines were separated quantitatively. The change in the catalytic activity of the respective particles in the solutions with variation in the structure of the reagents is examined, and possible mechanisms for the catalytic reactions are discussed on this basis. It is concluded that there is a bifunctional mechanism of catalysis by acetic acid in the reaction of /alpha/-bromoacetophenone with aniline.

  16. Role of weakly bound complexes in temperature-dependence and relative rates of MxOy- + H2O (M = Mo, W) reactions

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Ray, Manisha; Raghavachari, Krishnan; Jarrold, Caroline Chick

    2016-02-01

    Results of a systematic comparison of the MoxOy- + H2O and WxOy- + H2O reaction rate coefficients are reported and compared to previous experimental and computational studies on these reactions. WxOy- clusters undergo more direct oxidation by water to yield WxOy+1- + H2, while for MoxOy- clusters, production of MoxOyH2- (trapped intermediates in the oxidation reaction) is comparatively more prevalent. However, MoxOy- clusters generally have higher rate coefficients than analogous WxOy- clusters if MoxOy+1H2- formation is included. Results of calculations on the M2Oy- + H2O (M = Mo, W; y = 4, 5) reaction entrance channel are reported. They include charge-dipole complexes formed from long-range interactions, and the requisite conversion to a Lewis acid-base complex that leads to MxOy+1H2- formation. The results predict that the Lewis acid-base complex is more strongly bound for MoxOy- clusters than for WxOy- clusters. The calculated free energies along this portion of the reaction path are also consistent with the modest anti-Arrhenius temperature dependence measured for most MoxOy- + H2O reactions, and the WxOy- + H2O reaction rate coefficients generally being constant over the temperature range sampled in this study. For clusters that exhibit evidence of both water addition and oxidation reactions, increasing the temperature increases the branching ratio toward oxidation for both species. A more direct reaction path to H2 production may therefore become accessible at modest temperatures for certain cluster stoichiometries and structures.

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

    PubMed

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

    2011-06-23

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

  18. Intimations of neck formation in heavy-ion subbarrier fusion reactions

    SciTech Connect

    Stelson, P.H.

    1990-07-01

    Since the observed fusion cross sections for collisions between heavy ions at subbarrier energies are orders of magnitude larger than would be expected for barrier tunnelling, one is faced with the task of identifying the basic force which is strong enough to overcome the strong Coulomb force and bring about fusion. The two possibilities seem to be excursions of the nuclear surface (and strong nuclear force) due to collective motions of the colliding nuclei and formation of a neck of nuclear matter. The first possibility has received the most attention. However, the systematics of fusion cross sections suggest neck formation is playing an important role. Neck formation can also result in a reseparation of the composite system and we review the experimental information on these reactions at barrier and subbarrier energies. 15 refs., 18 figs.

  19. Thermodynamic characteristics of the formation of Cd2+ ion-L-serine complexes in aqueous KNO3 solutions at 288-308 K

    NASA Astrophysics Data System (ADS)

    Kochergina, L. A.; Khokhlova, E. A.; Drobilova, O. M.

    2014-06-01

    The heats of formation of complexes of L-serine and doubly charged cadmium ions are determined by calorimetry. The heat effects of the reaction between an amino acid solution and a cadmium(II) solution and the respective heats of dilution of cadmium nitrate solution are measured at temperatures of 288.15, 298.15, and 308.15 K and ionic strengths of 0.25, 0.50, and 0.75 against the background of KNO3. The standard thermodynamic characteristics of complexation are calculated. Standard enthalpies of formation of mono-, bis-, and tris-coordinated complexes of cadmium(II) in an aqueous solution are found.

  20. Unexpected formation of π-expanded isoquinoline from anthracene possessing four electron-donating groups via the Duff reaction.

    PubMed

    Węcławski, Marek K; Deperasińska, Irena; Leniak, Arkadiusz; Banasiewicz, Marzena; Kozankiewicz, Bolesław; Gryko, Daniel T

    2016-08-01

    New synthetic methods leading towards π-expanded heterocycles are sought after mainly due to their promising opto-electronic properties. Subjecting 1,5,9,10-tetramethoxyanthracene to the modern Duff reaction conditions led to the formation of a compound possessing the 2-azabenzoanthrone (dibenzo[de,h]isoquinolin-7-on) skeleton instead of the expected dialdehyde. This non-typical course of reaction can be rationalized by the double electrophilic aromatic substitution at two neighboring electron-rich positions of anthracene followed by oxidation of the resulting intermediate to form a pyridine ring. Optical studies supported by the quantum chemistry calculations indicated the lack of excited-state intramolecular proton transfer (ESIPT); for energy reasons, only one tautomeric form, with a hydrogen atom bonded to one of the two nearby oxygen atoms, was populated in the electronic ground S0 and in the excited S1 states. Nonradiative depopulation of the S1 state proceeded via internal conversion stimulated by the presence of the low frequency vibrational modes. Our serendipitous discovery represents the most complex case of rearrangement of aromatic compounds under Duff reaction conditions and could help to design analogous processes. At the same time this is the simplest method for the synthesis of derivatives of 2-azabenzoanthrone. PMID:27367169

  1. Reaction of benzophenone UV filters in the presence of aqueous chlorine: kinetics and chloroform formation.

    PubMed

    Duirk, Stephen E; Bridenstine, David R; Leslie, Daniel C

    2013-02-01

    The transformation of two benzophenone UV filters (Oxybenzone and Dioxybenzone) was examined over the pH range 6-11 in the presence of excess aqueous chlorine. Under these conditions, both UV filters were rapidly transformed by aqueous chlorine just above circumneutral pH while transformation rates were significantly lower near the extremes of the pH range investigated. Observed first-order rate coefficients (k(obs)) were obtained at each pH for aqueous chlorine concentrations ranging from 10 to 75 μM. The k(obs) were used to determine the apparent second-order rate coefficient (k(app)) at each pH investigated as well as determine the reaction order of aqueous chlorine with each UV filter. The reaction of aqueous chlorine with either UV filter was found to be an overall second-order reaction, first-order with respect to each reactant. Assuming elemental stoichiometry described the reaction between aqueous chlorine and each UV filter, models were developed to determine intrinsic rate coefficients (k(int)) from the k(app) as a function of pH for both UV filters. The rate coefficients for the reaction of HOCl with 3-methoxyphenol moieties of oxybenzone (OXY) and dioxybenzone (DiOXY) were k(1,OxY) = 306 ± 81 M⁻¹s⁻¹ and k(1,DiOxY) = 154 ± 76 M⁻¹s⁻¹, respectively. The k(int) for the reaction of aqueous chlorine with the 3-methoxyphenolate forms were orders of magnitude greater than the un-ionized species, k(2,OxY) = 1.03(±0.52) × 10⁶ M⁻¹s⁻¹ and k(2_1,DiOxY) = 4.14(±0.68) × 10⁵ M⁻¹s⁻¹. Also, k(int) for the reaction of aqueous chlorine with the DiOXY ortho-substituted phenolate moiety was k(2_2,DiOxY) = 2.17(±0.30) × 10³ M⁻¹s⁻¹. Finally, chloroform formation potential for OXY and DiOXY was assessed over the pH range 6-10. While chloroform formation decreased as pH increased for OXY, chloroform formation increased as pH increased from 6 to 10 for DiOXY. Ultimate molar yields of chloroform per mole of UV filter were pH dependent

  2. Developing mononuclear copper-active-oxygen complexes relevant to reactive intermediates of biological oxidation reactions.

    PubMed

    Itoh, Shinobu

    2015-07-21

    Active-oxygen species generated on a copper complex play vital roles in several biological and chemical oxidation reactions. Recent attention has been focused on the reactive intermediates generated at the mononuclear copper active sites of copper monooxygenases such as dopamine β-monooxygenase (DβM), tyramine β-monooxygenase (TβM), peptidylglycine-α-hydroxylating monooxygenase (PHM), and polysaccharide monooxygenases (PMO). In a simple model system, reaction of O2 and a reduced copper(I) complex affords a mononuclear copper(II)-superoxide complex or a copper(III)-peroxide complex, and subsequent H(•) or e(-)/H(+) transfer, which gives a copper(II)-hydroperoxide complex. A more reactive species such as a copper(II)-oxyl radical type species could be generated via O-O bond cleavage of the peroxide complex. However, little had been explored about the chemical properties and reactivity of the mononuclear copper-active-oxygen complexes due to the lack of appropriate model compounds. Thus, a great deal of effort has recently been made to develop efficient ligands that can stabilize such reactive active-oxygen complexes in synthetic modeling studies. In this Account, I describe our recent achievements of the development of a mononuclear copper(II)-(end-on)superoxide complex using a simple tridentate ligand consisting of an eight-membered cyclic diamine with a pyridylethyl donor group. The superoxide complex exhibits a similar structure (four-coordinate tetrahedral geometry) and reactivity (aliphatic hydroxylation) to those of a proposed reactive intermediate of copper monooxygenases. Systematic studies based on the crystal structures of copper(I) and copper(II) complexes of the related tridentate supporting ligands have indicated that the rigid eight-membered cyclic diamine framework is crucial for controlling the geometry and the redox potential, which are prerequisites for the generation of such a unique mononuclear copper(II)-(end-on)superoxide complex

  3. Reactions of titanocene bis(trimethylsilyl)acetylene complexes with carbodiimides: an experimental and theoretical study of complexation versus C-N bond activation.

    PubMed

    Haehnel, Martin; Ruhmann, Martin; Theilmann, Oliver; Roy, Subhendu; Beweries, Torsten; Arndt, Perdita; Spannenberg, Anke; Villinger, Alexander; Jemmis, Eluvathingal D; Schulz, Axel; Rosenthal, Uwe

    2012-09-26

    The reaction of the low valent metallocene(II) sources Cp'(2)Ti(η(2)-Me(3)SiC(2)SiMe(3)) (Cp' = η(5)-cyclopentadienyl, 1a or η(5)-pentamethylcyclopentadienyl, 1b) with different carbodiimide substrates RN═C═NR' 2-R-R' (R = t-Bu; R' = Et; R = R' = i-Pr; t-Bu; SiMe(3); 2,4,6-Me-C(6)H(2) and 2,6-i-Pr-C(6)H(3)) was investigated to explore the frontiers of ring strained, unusual four-membered heterometallacycles 5-R. The product complexes show dismantlement, isomerization, or C-C coupling of the applied carbodiimide substrates, respectively, to form unusual mono-, di-, and tetranuclear titanium(III) complexes. A detailed theoretical study revealed that the formation of the unusual complexes can be attributed to the biradicaloid nature of the unusual four-membered heterometallacycles 5-R, which presents an intriguing situation of M-C bonding. The combined experimental and theoretical study highlights the delicate interplay of electronic and steric effects in the stabilization of strained four-membered heterometallacycles, accounting for the isolation of the obtained complexes. PMID:22891968

  4. Complex Type 2 Reactions in Three Patients with Hansen's Disease from a Southern United States Clinic.

    PubMed

    Leon, Kristoffer E; Salinas, Jorge L; McDonald, Robert W; Sheth, Anandi N; Fairley, Jessica K

    2015-11-01

    In non-endemic countries, leprosy, or Hansen's disease (HD), remains rare and is often underrecognized. Consequently, the literature is currently lacking in clinical descriptions of leprosy complications in the United States. Immune-mediated inflammatory states known as reactions are common complications of HD. Type 1 reactions are typical of borderline cases and occur in 30% of patients and present as swelling and inflammation of existing skin lesions, neuritis, and nerve dysfunction. Type 2 reactions are systemic events that occur at the lepromatous end of the disease spectrum, and typical symptoms include fever, arthralgias, neuritis, and classic painful erythematous skin nodules known as erythema nodosum leprosum. We report three patients with lepromatous leprosy seen at a U.S. HD clinic with complicated type 2 reactions. The differences in presentations and clinical courses highlight the complexity of the disease and the need for increased awareness of unique manifestations of lepromatous leprosy in non-endemic areas. PMID:26304919

  5. Front waves and complex spatiotemporal patterns in a reaction-diffusion-convection system with thermokinetic autocatalysis.

    PubMed

    Trávnícková, Tereza; Kohout, Martin; Schreiber, Igor; Kubícek, Milan

    2009-12-01

    We analyze dynamics of stationary nonuniform patterns, traveling waves, and spatiotemporal chaos in a simple model of a tubular cross-flow reactor. The reactant is supplied continuously via convective flow and/or by diffusion through permeable walls of the reactor. First order exothermic reaction kinetics is assumed and the system is described by mass and energy balances forming coupled reaction-diffusion-convection equations. Dynamical regimes of the reaction-diffusion subsystem range from pulses and fronts to periodic waves and complex chaotic behavior. Two distinct types of chaotic patterns are identified and characterized by Lyapunov dimension. Next we examine the effects of convection on various types of the reaction-diffusion regimes. Remarkable zigzag fronts and steady state patterns are found despite the absence of differential flow. We employ continuation techniques to elucidate the existence and form of these patterns. PMID:20059221

  6. Front waves and complex spatiotemporal patterns in a reaction-diffusion-convection system with thermokinetic autocatalysis

    NASA Astrophysics Data System (ADS)

    Trávníčková, Tereza; Kohout, Martin; Schreiber, Igor; Kubíček, Milan

    2009-12-01

    We analyze dynamics of stationary nonuniform patterns, traveling waves, and spatiotemporal chaos in a simple model of a tubular cross-flow reactor. The reactant is supplied continuously via convective flow and/or by diffusion through permeable walls of the reactor. First order exothermic reaction kinetics is assumed and the system is described by mass and energy balances forming coupled reaction-diffusion-convection equations. Dynamical regimes of the reaction-diffusion subsystem range from pulses and fronts to periodic waves and complex chaotic behavior. Two distinct types of chaotic patterns are identified and characterized by Lyapunov dimension. Next we examine the effects of convection on various types of the reaction-diffusion regimes. Remarkable zigzag fronts and steady state patterns are found despite the absence of differential flow. We employ continuation techniques to elucidate the existence and form of these patterns.

  7. Functionalized organotin-chalcogenide complexes that exhibit defect heterocubane scaffolds: formation, synthesis, and characterization.

    PubMed

    Eußner, Jens P; Barth, Beatrix E K; Leusmann, Eliza; You, Zhiliang; Rinn, Niklas; Dehnen, Stefanie

    2013-10-01

    The synthesis of new functionalized organotin-chalcogenide complexes was achieved by systematic optimization of the reaction conditions. The structures of compounds [(R(1, 2) Sn)3 S4 Cl] (1, 2), [((R(2) Sn)2 SnS4 )2 (μ-S)2 ] (3), [(R(1, 2) Sn)3 Se4 ][SnCl3 ] (4, 5), and [Li(thf)n ][(R(3) Sn)(HR(3) Sn)2 Se4 Cl] (6), in which R(1) =CMe2 CH2 C(O)Me, R(2) =CMe2 CH2 C(NNH2 )Me, and R(3) =CH2 CH2 COO, are based on defect heterocubane scaffolds, as shown by X-ray diffraction, (119) Sn NMR spectroscopy, and ESI mass spectrometry analyses. Compounds 4, 5, and 6 constitute the first examples of defect heterocubane-type metal-chalcogenide complexes that are comprised of selenide ligands. Comprehensive DFT calculations prompted us to search for the formal intermediates [(R(1) SnCl2 )2 (μ-S)] (7) and [(R(1) SnCl)2 (μ-S)2 ] (8), which were isolated and helped to understand the stepwise formation of compounds 1-6. PMID:23963989

  8. A calorimetric study of the hydrolysis and peroxide complex formation of the uranyl(VI) ion.

    PubMed

    Zanonato, Pier Luigi; Di Bernardo, Plinio; Grenthe, Ingmar

    2014-02-14

    The enthalpies of reaction for the formation of uranyl(vi) hydroxide {[(UO2)2(OH)2](2+), [(UO2)3(OH)4](2+), [(UO2)3(OH)5](+), [(UO2)3(OH)6](aq), [(UO2)3(OH)7](-), [(UO2)3(OH)8](2-), [(UO2)(OH)3](-), [(UO2)(OH)4](2-)} and peroxide complexes {[UO2(O2)(OH)](-) and [(UO2)2(O2)2(OH)](-)} have been determined from calorimetric titrations at 25 °C in a 0.100 M tetramethyl ammonium nitrate ionic medium. The hydroxide data have been used to test the consistency of the extensive thermodynamic database published by the Nuclear Energy Agency (I. Grenthe, J. Fuger, R. J. M. Konings, R. J. Lemire, A. B. Mueller, C. Nguyen-Trung and H. Wanner, Chemical Thermodynamics of Uranium, North-Holland, Amsterdam, 1992 and R. Guillaumont, T. Fanghänel, J. Fuger, I. Grenthe, V. Neck, D. J. Palmer and M. R. Rand, Update on the Chemical Thermodynamics of Uranium, Neptunium, Plutonium, Americium and Technetium, Elsevier, Amsterdam, 2003). A brief discussion is given about a possible structural relationship between the trinuclear complexes [(UO2)3(OH)n](6-n), n = 4-8. PMID:24301256

  9. Structure of tetracarbonylethyleneosmium: ethylene structure changes upon complex formation.

    PubMed

    Karunatilaka, Chandana; Tackett, Brandon S; Washington, John; Kukolich, Stephen G

    2007-08-29

    Rotational spectra of seven isotopomers of tetracarbonylethyleneosmium, Os(CO)4(eta2-C2H4), were measured in the 4-12 GHz range using a Flygare-Balle-type pulsed-beam Fourier transform microwave spectrometer system. Olefin-transition metal complexes of this type occur extensively in recent organic syntheses and serve as important models for transition states in the metal-mediated transformations of alkenes. Three osmium ((192)Os, (190)Os, and (188)Os) and three unique 13C isotopomers (13C in ethylene, axial, and equatorial positions) were observed in natural abundance. Additional spectra were measured for a perdeuterated sample, Os(CO)4(eta2-C2D4). The measured rotational constants for the main osmium isotopomer ((192)Os) are A = 929.3256(6), B = 755.1707(3), and C = 752.7446(3) MHz, indicating a near-prolate asymmetric top molecule. The approximately 140 assigned b-type transitions were fit using a Watson S-reduced Hamiltonian including A, B, C, and five centrifugal distortion constants. A near-complete r0 gas-phase structure has been determined from a least-squares structural fit using eight adjustable structural parameters to fit the 21 measured rotational constants. Changes in the structure of ethylene on coordination to Os(CO)4 are large and well-determined. For the complex, the experimental ethylene C-C bond length is 1.432(5) A, which falls between the free ethylene value of 1.3391(13) A and the ethane value of 1.534(2) A. The angle between the plane of the CH2 group and the extended ethylene C-C bond ( angleout-of-plane) is 26.0(3) degrees , indicating that this complex is better described as a metallacyclopropane than as a pi-bonded olefin-metal complex. The Os-C-C-H dihedral angle is 106.7(2) degrees , indicating that the ethylene carbon atoms have near sp3 character in the complex. Kraitchman analysis of the available rotational constants gave principal axis coordinates for the carbon and hydrogen atoms in excellent agreement with the least-squares fit

  10. Dearomatization Reactions of N-Heterocycles Mediated by Group 3 Complexes

    SciTech Connect

    Miller, Kevin L; Williams, Bryan N; Benitez, Diego; Carver, Colin T; Ogilby, Kevin R; Tkatchouk, Ekaterina; Goddard, William A; Diaconescu, Paula L

    2010-01-13

    Group 3 (Sc, Y, Lu, La) benzyl complexes supported by a ferrocene diamide ligand are reactive toward aromatic N-heterocycles by mediating their coupling and, in a few cases, the cleavage of their C-N bonds. When these complexes reacted with 2,2'-bipyridine or isoquinoline, they facilitated the alkyl migration of the benzyl ligand onto the pyridine ring, a process accompanied by the dearomatization of the N-heterocycle. The products of the alkyl-transfer reactions act as hydrogen donors in the presence of aromatic N-heterocycles, ketones, and azobenzene. Experimental and computational studies suggest that the hydrogen transfer takes place through a concerted mechanism. An interesting disproportionation reaction of the dearomatized, alkyl-substituted isoquinoline complexes is also reported.

  11. Complement activation in leprosy: a retrospective study shows elevated circulating terminal complement complex in reactional leprosy.

    PubMed

    Bahia El Idrissi, N; Hakobyan, S; Ramaglia, V; Geluk, A; Morgan, B Paul; Das, P Kumar; Baas, F

    2016-06-01

    Mycobacterium leprae infection gives rise to the immunologically and histopathologically classified spectrum of leprosy. At present, several tools for the stratification of patients are based on acquired immunity markers. However, the role of innate immunity, particularly the complement system, is largely unexplored. The present retrospective study was undertaken to explore whether the systemic levels of complement activation components and regulators can stratify leprosy patients, particularly in reference to the reactional state of the disease. Serum samples from two cohorts were analysed. The cohort from Bangladesh included multi-bacillary (MB) patients with (n = 12) or without (n = 46) reaction (R) at intake and endemic controls (n = 20). The cohort from Ethiopia included pauci-bacillary (PB) (n = 7) and MB (n = 23) patients without reaction and MB (n = 15) patients with reaction. The results showed that the activation products terminal complement complex (TCC) (P ≤ 0·01), C4d (P ≤ 0·05) and iC3b (P ≤ 0·05) were specifically elevated in Bangladeshi patients with reaction at intake compared to endemic controls. In addition, levels of the regulator clusterin (P ≤ 0·001 without R; P < 0·05 with R) were also elevated in MB patients, irrespective of a reaction. Similar analysis of the Ethiopian cohort confirmed that, irrespective of a reaction, serum TCC levels were increased significantly in patients with reactions compared to patients without reactions (P ≤ 0·05). Our findings suggests that serum TCC levels may prove to be a valuable tool in diagnosing patients at risk of developing reactions. PMID:26749503

  12. Imaging Proton Transfer and Dihalide Formation Pathways in Reactions of F– + CH3I

    PubMed Central

    2016-01-01

    Ion–molecule reactions of the type X– + CH3Y are commonly assumed to produce Y– through bimolecular nucleophilic substitution (SN2). Beyond this reaction, additional reaction products have been observed throughout the last decades and have been ascribed to different entrance channel geometries differing from the commonly assumed collinear approach. We have performed a crossed beam velocity map imaging experiment on the F– + CH3I reaction at different relative collision energies between 0.4 and 2.9 eV. We find three additional channels competing with nucleophilic substitution at high energies. Experimental branching ratios and angle- and energy differential cross sections are presented for each product channel. The proton transfer product CH2I– is the main reaction channel, which competes with nucleophilic substitution up to 2.9 eV relative collision energy. At this level, the second additional channel, the formation of IF– via halogen abstraction, becomes more efficient. In addition, we present the first evidence for an [FHI]− product ion. This [FHI]− product ion is present only for a narrow range of collision energies, indicating possible dissociation at high energies. All three products show a similar trend with respect to their velocity- and scattering angle distributions, with isotropic scattering and forward scattering of the product ions occurring at low and high energies, respectively. Reactions leading to all three reaction channels present a considerable amount of energy partitioning in product internal excitation. The internally excited fraction shows a collision energy dependence only for CH2I–. A similar trend is observed for the isoelectronic OH– + CH3I system. The comparison of our experimental data at 1.55 eV collision energy with a recent theoretical calculation for the same system shows a slightly higher fraction of internal excitation than predicted, which is, however, compatible within the experimental accuracy. PMID:26799548

  13. Imaging Proton Transfer and Dihalide Formation Pathways in Reactions of F(-) + CH3I.

    PubMed

    Carrascosa, Eduardo; Michaelsen, Tim; Stei, Martin; Bastian, Björn; Meyer, Jennifer; Mikosch, Jochen; Wester, Roland

    2016-07-14

    Ion-molecule reactions of the type X(-) + CH3Y are commonly assumed to produce Y(-) through bimolecular nucleophilic substitution (SN2). Beyond this reaction, additional reaction products have been observed throughout the last decades and have been ascribed to different entrance channel geometries differing from the commonly assumed collinear approach. We have performed a crossed beam velocity map imaging experiment on the F(-) + CH3I reaction at different relative collision energies between 0.4 and 2.9 eV. We find three additional channels competing with nucleophilic substitution at high energies. Experimental branching ratios and angle- and energy differential cross sections are presented for each product channel. The proton transfer product CH2I(-) is the main reaction channel, which competes with nucleophilic substitution up to 2.9 eV relative collision energy. At this level, the second additional channel, the formation of IF(-) via halogen abstraction, becomes more efficient. In addition, we present the first evidence for an [FHI](-) product ion. This [FHI](-) product ion is present only for a narrow range of collision energies, indicating possible dissociation at high energies. All three products show a similar trend with respect to their velocity- and scattering angle distributions, with isotropic scattering and forward scattering of the product ions occurring at low and high energies, respectively. Reactions leading to all three reaction channels present a considerable amount of energy partitioning in product internal excitation. The internally excited fraction shows a collision energy dependence only for CH2I(-). A similar trend is observed for the isoelectronic OH(-) + CH3I system. The comparison of our experimental data at 1.55 eV collision energy with a recent theoretical calculation for the same system shows a slightly higher fraction of internal excitation than predicted, which is, however, compatible within the experimental accuracy. PMID:26799548

  14. Crystal structures of complexes of NAD{sup +}-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    SciTech Connect

    Filippova, E. V. Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-07-15

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI{sub 2} with the coupled reduction of nicotinamide adenine dinucleotide (NAD{sup +}). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD{sup +}-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 A resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.

  15. The Effect of Complex Formation upon the Redox Potentials of Metallic Ions. Cyclic Voltammetry Experiments.

    ERIC Educational Resources Information Center

    Ibanez, Jorge G.; And Others

    1988-01-01

    Describes experiments in which students prepare in situ soluble complexes of metal ions with different ligands and observe and estimate the change in formal potential that the ion undergoes upon complexation. Discusses student formation and analysis of soluble complexes of two different metal ions with the same ligand. (CW)

  16. REACTIVE DESORPTION AND RADIATIVE ASSOCIATION AS POSSIBLE DRIVERS OF COMPLEX MOLECULE FORMATION IN THE COLD INTERSTELLAR MEDIUM

    SciTech Connect

    Vasyunin, A. I.; Herbst, Eric E-mail: eh2ef@virginia.edu

    2013-05-20

    The recent discovery of terrestrial-type organic species such as methyl formate and dimethyl ether in the cold interstellar gas has proved that the formation of organic matter in the Galaxy begins at a much earlier stage of star formation than was previously thought. This discovery represents a challenge for astrochemical modelers. The abundances of these molecules cannot be explained by the previously developed ''warm-up'' scenario, in which organic molecules are formed via diffusive chemistry on surfaces of interstellar grains starting at 30 K, and then released to the gas at higher temperatures during later stages of star formation. In this article, we investigate an alternative scenario in which complex organic species are formed via a sequence of gas-phase reactions between precursor species formed on grain surfaces and then ejected into the gas via efficient reactive desorption, a process in which non-thermal desorption occurs as a result of conversion of the exothermicity of chemical reactions into the ejection of products from the surface. The proposed scenario leads to reasonable if somewhat mixed results at temperatures as low as 10 K and may be considered as a step toward the explanation of abundances of terrestrial-like organic species observed during the earliest stages of star formation.

  17. Structural investigation of trifuoromethyl substituted bis(β-diketonato)-dichlorotitanium(IV) complexes displaying a mono-dinuclear equilibrium hydrolysis reaction

    NASA Astrophysics Data System (ADS)

    Kuhn, Annemarie; Conradie, Jeanet

    2015-10-01

    Mononuclear Ti(β-diketonato)2Cl2 complexes with CF3-containing β-diketonato ligands, exhibit a monomer-hydrolysed dinuclear complex equilibrium when dissolved in CDCl3 containing trace amounts of water. This result is in contrast to the more electron rich derivatives with non CF3-containing β-diketonato ligands, for example, Ti(acac)2Cl2, which exsists only as the monomer in CDCl3 solution. The X-ray structure of the μ-oxo bridged hydrolysed dinuclear complex {Ti(CF3COCHCOCH3)2Cl}2(μ-O) reveals that the two mononuclear Ti units forming the dinuclear structure, both adopt a cis-trans-cis configuration with the CF3 groups of the trifluoroacetylacetonate ligands in trans positions. In solution both mononuclear Ti(β-diketonato)2Cl2 and hydrolysed dinuclear {Ti(β-diketonato)2Cl}2(μ-O) complexes exist as equilibrium mixtures of isomers. DFT calculations, used to determine the stability of the isomers, showed that for monomeric bis(β-diketonato)-titanium(IV) complexes, there is agreement with experimental solid state structures, in that the most stable DFT calculated isomer, of a specific complex, formed in the solid state. However for the dinuclear {Ti(CF3COCHCOCH3)2Cl}2(μ-O) complex, DFT calculations revealed that although most of the 10 isomers are experimentally possible due to the small energy difference obtained between the isomers, an isomer of higher energy formed in the solid state, suggesting that the equilibrium reaction between the monomer and hydrolysed dinuclear complex may contribute to the formation of the less stable dinuclear isomer {Ti(CF3COCHCOCH3)2Cl}2(μ-O) (1111).

  18. Aqueous-Phase Reactions of Isoprene with Sulfoxy Radical Anions as a way of Wet Aerosol Formation in the Atmosphere

    NASA Astrophysics Data System (ADS)

    Kuznietsova, I.; Rudzinski, K. J.; Szmigielski, R.; Laboratory of the Environmental Chemistry

    2011-12-01

    Atmospheric aerosols exhibit an important role in the environment. They have implications on human health and life, and - in the larger scale - on climate, the Earth's radiative balance and the cloud's formation. Organic matter makes up a significant fraction of atmospheric aerosols (~35% to ~90%) and may originate from direct emissions (primary organic aerosol, POA) or result from complex physico-chemical processes of volatile organic compounds (secondary organic aerosol, SOA). Isoprene (2-methyl-buta-1,3-diene) is one of the relevant volatile precursor of ambient SOA in the atmosphere. It is the most abundant non-methane hydrocarbon emitted to the atmosphere as a result of living vegetation. According to the recent data, the isoprene emission rate is estimated to be at the level of 500 TgC per year. While heterogeneous transformations of isoprene have been well documented, aqueous-phase reactions of this hydrocarbon with radical species that lead to the production of new class of wet SOA components such as polyols and their sulfate esters (organosulfates), are still poorly recognized. The chain reactions of isoprene with sulfoxy radical-anions (SRA) are one of the recently researched route leading to the formation of organosulfates in the aqueous phase. The letter radical species originate from the auto-oxidation of sulfur dioxide in the aqueous phase and are behind the phenomenon of atmospheric acid rain formation. This is a complicated chain reaction that is catalyzed by transition metal ions, such as manganese(II), iron(III) and propagated by sulfoxy radical anions . The presented work addresses the chemical interaction of isoprene with sulfoxy radical-anions in the water solution in the presence of nitrite ions and nitrous acid, which are important trace components of the atmosphere. We showed that nitrite ions and nitrous acid significantly altered the kinetics of the auto-oxidation of SO2 in the presence of isoprene at different solution acidity from 2 to 8

  19. A novel samarium(ii) complex bearing a dianionic bis(phenolate) cyclam ligand: synthesis, structure and electron-transfer reactions.

    PubMed

    Maria, Leonor; Soares, Marina; Santos, Isabel C; Sousa, Vânia R; Mora, Elsa; Marçalo, Joaquim; Luzyanin, Konstantin V

    2016-03-01

    The reaction of the hexadentate dianionic 1,4,8,11-tetraazacyclotetradecane-based bis(phenolate) ligand, (tBu2ArO)2Me2-cyclam(2-), with [SmI2(thf )2] in thf resulted in the formation of the divalent samarium complex [Sm(κ(6)-{(tBu2ArO)2Me2-cyclam})] (1). X-ray diffraction studies revealed that after recrystallization from n-hexane/thf complex 1 has a monomeric structure and does not contain thf molecules coordinated to the Sm(II) center. However, UV-vis and (1)H NMR spectroscopy of 1 evidenced the formation of thf-solvated complexes in neat thf. Reductive studies show that complex 1 can act as a single electrontransfer reagent and form well-defined Sm(III) species. The reaction of 1 with several substrates, namely, TlBPh4, pyridine N-oxide, OPPh3, SPPh3 and bipyridines, are reported. Spectroscopy studies, including NMR, and single crystal X-ray diffraction data are in agreement with the formation of cationic Sm(III) species, monochalcogenide bridged Sm(III) complexes and Sm(III) complexes with bipyridine radical ligand, respectively. PMID:26818107

  20. Economy of operon formation: cotranscription minimizes shortfall in protein complexes.

    PubMed

    Sneppen, Kim; Pedersen, Steen; Krishna, Sandeep; Dodd, Ian; Semsey, Szabolcs

    2010-01-01

    Genes of prokaryotes and Archaea are often organized in cotranscribed groups, or operons. In contrast, eukaryotic genes are generally transcribed independently. Here we show that there is a substantial economic gain for the cell to cotranscribe genes encoding protein complexes because it synchronizes the fluctuations, or noise, in the levels of the different components. This correlation substantially reduces the shortfall in production of the complex. This benefit is relatively large in small cells such as bacterial cells, in which there are few mRNAs and proteins per cell, and is diminished in larger cells such as eukaryotic cells. PMID:20877578

  1. Spectrophotometric Determination of 6-Propyl-2-Thiouracil in Pharmaceutical Formulations Based on Prussian Blue Complex Formation: An Undergraduate Instrumental Analysis Laboratory Experiment

    ERIC Educational Resources Information Center

    Zakrzewski, Robert; Skowron, Monika; Ciesielski, Witold; Rembisz, Zaneta

    2016-01-01

    The laboratory experiment challenges students to determine 6-propyl-2-thiouracil (PTU) based on Prussian blue complex formation. Prussian blue is formed by ferricyanide and Fe(II) ions which are generated in situ from Fe(III) ions reduced by PTU. The absorbance of this product was measured at a wavelength of 840 nm, after a reaction time of 30…

  2. Synthesis of complex pyridine bases in the reaction of. cap alpha. ,omega-nitrileacetylenes with acetylene, catalyzed by cobalt complexes

    SciTech Connect

    Dzhemilev, U.M.; Selimov, F.A.; Khafizov, V.R.

    1987-01-20

    It has been shown that ..cap alpha..,omega-nitrileacetylenes under the action of homogeneous cobalt-containing catalysts undergo transformations into pyridine derivatives. In order to expand the scope of this method for synthesis of complex pyridine bases, for investigation of the reactivity of nitrileacetylenes of various structure in the reaction of cooligomerization with acetylene, as well as for the introduction to these reactions of new types of ..cap alpha..,omega-nitrileacetylenes, containing in their molecules an oxygen atom, they studied the homo- and codimerization of ..cap alpha..,omega-nitrileacetylenes with acetylene under the action of a Co(2-ethyl hexanoate)/sub 2/-AIR/sub 3/ catalyst in a toluene solution. Cyclodimerization of acetylene with ..cap alpha..,omega-nitrileacetylenes, catalyzed by a Co(2-ethyl hexanoate)/sub 2/-AlEt/sub 3/ system gives new types of mono- and bicyclic pyridines.

  3. Asymmetric 1,3-Dipolar Cycloaddition Reactions Catalyzed by Heterocycle-Based Metal Complexes

    NASA Astrophysics Data System (ADS)

    Suga, Hiroyuki

    Highly enantioselective 1,3-dipolar cycloaddition reactions of several 1,3-dipoles, such as nitrones, nitrile oxides, nitrile imines, diazoalkanes, azomethine imines and carbonyl ylides, catalyzed by heterocyclic supramolecular type of metal complexes consisting of chiral heterocyclic compounds and metal salts were described in terms of their ability of asymmetric induction and enantioface differentiation. The scope and limitations of each cycloaddition reactions were also briefly described. Of the chiral hererocycle-based ligands, chiral bisoxazoline, 2,6-bis(oxazolinyl)pyridine, and related oxazoline ligands are shown to be quite effective in obtaining high levels of asymmtric induction. The combination of the bisoxazoline ligand derived from (1S,2R)-cis-1-amino-2-indanol and metal salts was especially efficient for asymmetric cycloaddition reactions of a number of 1,3-dipoles, such as nitrones, nitrile oxide, nitrile imines, diazoacetates and azomethine imines. The metals utilized for the heterocycle-based complexes show a crucial role for degree of asymmetric induction depending upon the 1,3-dipole used. High levels of enantioselectivity were achieved in 1,3-dipolar cycloaddition reactions of unstable carbonyl ylides with benzyloxyacetaldehyde derivatives, α-keto esters, 3-(2-alkenoyl)-2-oxazolidinones, and even vinyl ethers, which were catalyzed by Pybox-lanthanoid metal complexes.

  4. The formation of glycine and other complex organic molecules in exploding ice mantles.

    PubMed

    Rawlings, J M C; Williams, D A; Viti, S; Cecchi-Pestellini, C; Duley, W W

    2014-01-01

    Complex Organic Molecules (COMs), such as propylene (CH3CHCH2) and the isomers of C2H4O2 are detected in cold molecular clouds (such as TMC-1) with high fractional abundances (Marcelino et al., Astrophys. J., 2007, 665, L127). The formation mechanism for these species is the subject of intense speculation, as is the possibility of the formation of simple amino acids such as glycine (NH2CH2COOH). At typical dark cloud densities, normal interstellar gas-phase chemistries are inefficient, whilst surface chemistry is at best ill defined and does not easily reproduce the abundance ratios observed in the gas phase. Whatever mechanism(s) is/are operating, it/they must be both efficient at converting a significant fraction of the available carbon budget into COMs, and capable of efficiently returning the COMs to the gas phase. In our previous studies we proposed a complementary, alternative mechanism, in which medium- and large-sized molecules are formed by three-body gas kinetic reactions in the warm high density gas phase. This environment exists, for a very short period of time, after the total sublimation of grain ice mantles in transient co-desorption events. In order to drive the process, rapid and efficient mantle sublimation is required and we have proposed that ice mantle 'explosions' can be driven by the catastrophic recombination of trapped hydrogen atoms, and other radicals, in the ice. Repeated cycles of freeze-out and explosion can thus lead to a cumulative molecular enrichment of the interstellar medium. Using existing studies we based our chemical network on simple radical addition, subject to enthalpy and valency restrictions. In this work we have extended the chemistry to include the formation pathways of glycine and other large molecular species that are detected in molecular clouds. We find that the mechanism is capable of explaining the observed molecular abundances and complexity in these sources. We find that the proposed mechanism is easily capable

  5. Reaction-path calculations of groundwater chemistry and mineral formation at Rainier Mesa, Nevada

    SciTech Connect

    Kerrisk, J F

    1983-12-01

    Reaction-patch calculations of groundwater chemistry and mineral formation at Rainier Mesa, Nevada, have been done using a model of volcanic-glass dissolution by water that is initially saturated with CO{sub 2}. In the reaction-path calculation, rate processes control the availability of species through dissolution of volcanic glass, and equilibrium processes distribute the species between the aqueous phase and mineral phases in equilibrium at each step in the reaction path. The EQ3/6 chemical-equilibrium programs were used for the calculation. Formation constants were estimated for three zeolites (clinoptilolite, mordenite, and heulandite), so they could be considered as possible mineral precipitates. The first stage of mineral evolution, from volcanic glass to a cristobalite, smectite clay, and zeolite mixture, was modeled quite well. Predicted aqueous-phase compositions and precipitates agree with observations at Rainier Mesa and other Nevada Test Site areas. Further mineral evolution, to quartz, clay, analcime, and albite mixtures, was also modeled. Decreasing aqueous silica activity from the first stage, where cristobalite precipitates, to later stages, where quartz is present, was the controlling variable in the mineral evolution. 30 references, 20 figures, 4 tables.

  6. Reactions Between Water Soluble Organic Acids and Nitrates in Atmospheric Aerosols: Recycling of Nitric Acid and Formation of Organic Salts

    SciTech Connect

    Wang, Bingbing; Laskin, Alexander

    2014-03-25

    Atmospheric particles often include a complex mixture of nitrate and secondary organic materials accumulated within the same individual particles. Nitrate as an important inorganic component can be chemically formed in the atmosphere. For instance, formation of sodium nitrate (NaNO3) and calcium nitrate Ca(NO3)2 when nitrogen oxide and nitric acid (HNO3) species react with sea salt and calcite, respectively. Organic acids contribute a significant fraction of photochemically formed secondary organics that can condense on the preexisting nitrate-containing particles. Here, we present a systematic microanalysis study on chemical composition of laboratory generated particles composed of water soluble organic acids and nitrates (i.e. NaNO3 and Ca(NO3)2) investigated using computer controlled scanning electron microscopy with energy dispersive analysis of X-rays (CCSEM/EDX) and Fourier transform infrared micro-spectroscopy (micro-FTIR). The results show that water-soluble organic acids can react with nitrates releasing gaseous HNO3 during dehydration process. These reactions are attributed to acid displacement of nitrate with weak organic acids driven by the evaporation of HNO3 into gas phase due to its relatively high volatility. The reactions result in significant nitrate depletion and formation of organic salts in mixed organic acids/nitrate particles that in turn may affect their physical and chemical properties relevant to atmospheric environment and climate. Airborne nitrate concentrations are estimated by thermodynamic calculations corresponding to various nitrate depletions in selected organic acids of atmospheric relevance. The results indicate a potential mechanism of HNO3 recycling, which may further affect concentrations of gas- and aerosol-phase species in the atmosphere and the heterogeneous reaction chemistry between them.

  7. Ligand substitution reactions of a phenolic quinolyl hydrazone; oxidovanadium (IV) complexes

    PubMed Central

    2011-01-01

    Background Quinoline ring has therapeutic and biological activities. Quinolyl hydrazones constitute a class of excellent chelating agents. Recently, the physiological and biological activities of quinolyl hydrazones arise from their tendency to form metal chelates with transition metal ions. In this context, we have aimed to study the competency effect of a phenolic quinolyl hydrazone (H2L; primary ligand) with some auxiliary ligands (Tmen, Phen or Oxine; secondary ligands) towards oxidovanadium (IV) ions. Results Mono- and binuclear oxidovanadium (IV) - complexes were obtained from the reaction of a phenolic quinolyl hydrazone with oxidovanadium (IV)- ion in absence and presence of N,N,N',N'- tetramethylethylenediamine (Tmen), 1,10-phenanthroline (Phen) or 8-hydroxyquinoline (Oxine). The phenolic quinolyl hydrazone ligand behaves as monobasic bidentate (NO- donor with O- bridging). All the obtained complexes have the preferable octahedral geometry except the oxinato complex (2) which has a square pyramid geometry with no axial interaction; the only homoleptic complex in this study. Conclusion The ligand exchange (substitution/replacement) reactions reflect the strong competency power of the auxiliary aromatic ligands (Phen/Oxine) compared to the phenolic quinolyl hydrazone (H2L) towards oxidovanadium (IV) ion; (complexes 2 and 3). By contrast, in case of the more flexible aliphatic competitor (Tmen), an adduct was obtained (4). The obtained complexes reflect the strength of the ligand field towards the oxidovanadium (IV)- ion; Oxine or Phen >> phenolic hydrazone (H2L) > Tmen. PMID:21846387

  8. The reaction of an iridium PNP complex with parahydrogen facilitates polarisation transfer without chemical change† †Electronic supplementary information (ESI) available: Sample preparation, signal enhancements and raw data. CCDC 1026865. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4dt03088e Click here for additional data file. Click here for additional data file.

    PubMed Central

    Holmes, Arthur J.; Rayner, Peter J.; Cowley, Michael J.; Green, Gary G. R.; Whitwood, Adrian C.

    2015-01-01

    The short lived pincer complex [(C5H3N(CH2P(tBu)2)2)Ir(H)2(py)]BF4 is shown to be active for signal amplification by reversible exchange. This catalyst formulation enables the efficient transfer of polarization from parahydrogen to be placed into just a single molecule of the hyperpolarisation target, pyridine. When the catalysts 1H nuclei are replaced by 2H, increased levels of substrate hyperpolarization result and when the reverse situation is examined the catalyst itself is clearly visible through hyperpolarised signals. The ligand exchange pathways of [(C5H3N(CH2P(tBu)2)2)Ir(H)2(py)]BF4 that are associated with this process are shown to involve the formation of 16-electron [(C5H3N(CH2P(tBu)2)2)Ir(H)2]BF4 and the 18-electron H2 addition product [(C5H3N(CH2P(tBu)2)2)Ir(H)2(H2)]BF4. PMID:25410259

  9. Monitoring benzene formation from benzoate in model systems by proton transfer reaction-mass spectrometry

    NASA Astrophysics Data System (ADS)

    Aprea, Eugenio; Biasioli, Franco; Carlin, Silvia; Märk, Tilmann D.; Gasperi, Flavia

    2008-08-01

    The presence of benzene in food and in particular in soft drinks has been reported in several studies and should be considered in fundamental investigations about formation of this carcinogen compound as well as in quality control. Proton transfer reaction-mass spectrometry (PTR-MS) has been used here for rapid, direct quantification of benzene and to monitor its formation in model systems related to the use of benzoate, a common preservative, in presence of ascorbic acid: a widespread situation that yields benzene in, e.g., soft drinks and fruit juices. Firstly, we demonstrate here that PTR-MS allows a rapid determination of benzene that is in quantitative agreement with independent solid phase micro-extraction/gas chromatography (SPME/GC) analysis. Secondly, as a case study, the effect of different sugars (sucrose, fructose and glucose) on benzene formation is investigated indicating that they inhibit its formation and that this effect is enhanced for reducing sugars. The sugar-induced inhibition of benzene formation depends on several parameters (type and concentration of sugar, temperature, time) but can be more than 80% in situations that can be expected in the storage of commercial soft drinks. This is consistent with the reported observations of higher benzene concentrations in sugar-free soft drinks.

  10. 'Super Silyl' Group for Diastereoselective Sequential Reactions: Access to Complex Chiral Architecture in One Pot

    SciTech Connect

    Boxer, Matthew B.; Yamamoto, Hisashi

    2008-04-02

    We have shown that the tris(trimethylsilyl)silyl (TTMSS) silyl enol ether of acetaldehyde undergoes aldehyde cross-aldol reactions with high selectivity and the extremely low catalyst loading (0.05 mol % of HNTf{sub 2}) allows for one-pot sequential reactions where acidic or basic nucleophiles can be subsequently added. Various ketone-derived silyl enol ethers, Grignard reagents, and dienes succeeded, generating relatively complex molecular architectures in a single step. This represents the first case where, in a single pot, highly acidic conditions followed by very basic conditions were tolerated to give products with high diastereoselectivities and good yields.

  11. Secondary organic aerosol formation by self-reactions of methylglyoxal and glyoxal in evaporating droplets.

    PubMed

    De Haan, David O; Corrigan, Ashley L; Tolbert, Margaret A; Jimenez, Jose L; Wood, Stephanie E; Turley, Jacob J

    2009-11-01

    Glyoxal and methylglyoxal are scavenged by clouds, where a fraction of these compounds are oxidized during the lifetime of the droplet. As a cloud droplet evaporates, the remaining glyoxal and methylglyoxal must either form low-volatility compounds such as oligomers and remain in the aerosol phase, or transfer back to the gas phase. A series of experiments on evaporating aqueous aerosol droplets indicates that over the atmospherically relevant concentration range for clouds and fog (4-1000 microM), 33 +/- 11% of glyoxal and 19 +/- 13% of methylglyoxal remains in the aerosol phase while the remainder evaporates. Measurements of aerosol density and time-dependent AMS signal changes are consistent with the formation of oligomers by each compound during the drying process. Unlike glyoxal, which forms acetal oligomers, exact mass AMS data indicates that the majority of methylglyoxal oligomers are formed by aldol condensation reactions, likely catalyzed by pyruvic acid, formed from methylglyoxal disproportionation. Our measurements of evaporation fractions can be used to estimate the global aerosol formation potential of glyoxal and methylglyoxal via self-reactions at 1 and 1.6 Tg C yr(-1), respectively. This is a factor of 4 less than the SOA formed by these compounds if their uptake is assumed to be irreversible. However, these estimates are likely lower limits for their total aerosol formation potential because oxidants and amines will also react with glyoxal and methylglyoxal to form additional low-volatility products. PMID:19924942

  12. The formation and decay of superheavy nuclei produced in 48Ca-induced reactions

    NASA Astrophysics Data System (ADS)

    Kumar, Sushil; Balasubramaniam, M.; Gupta, Raj K.; Münzenberg, G.; Scheid, W.

    2003-04-01

    The formation of superheavy nuclei in 48Ca+232Th, 238U, 242,244Pu and 248Cm reactions and their subsequent decay are studied within the quantum mechanical fragmentation theory (QMFT) and the QMFT-based preformed cluster decay model (PCM) of Gupta and collaborators. According to QMFT, all these 48Ca-induced reactions are cold fusion reactions with relative excitation energies larger than those for the Pb-induced cold fusion reactions and smaller than those for the lighter beam, i.e. Mg, Si or S-induced hot fusion reactions. The same reactions were first suggested by Gupta et al in 1977 on the basis of QMFT, and this study re-establishes the same result. In fact, for such heavy isotopes of Z = 110 to 116, 50Ca is shown to be a better beam for cold fusion, but 50Ca is a radioactive nucleus. The alpha-decay half-lives of these nuclei after 3n and/or 4n evaporations, i.e. of the evaporation residues of these compound systems, calculated on PCM compare reasonably well with the experiments published by the Dubna group and another recent calculation. As expected for such rare decays, PCM calculations show that the alpha-preformation factors are small, ~10-8 to 10-10. The possible competition of alpha-decays with heavy cluster emissions from these superheavy nuclei is also probed from the point of view of searching for new nuclear structure information and possible future experiments with such exotic nuclei. The decay half-lives for some clusters are in fact shown to be lower than the limits of experiments for nuclei with enough available atoms.

  13. Complex networks: Patterns of complexity

    NASA Astrophysics Data System (ADS)

    Pastor-Satorras, Romualdo; Vespignani, Alessandro

    2010-07-01

    The Turing mechanism provides a paradigm for the spontaneous generation of patterns in reaction-diffusion systems. A framework that describes Turing-pattern formation in the context of complex networks should provide a new basis for studying the phenomenon.

  14. Fission and quasifission modes in heavy-ion-induced reactions leading to the formation of Hs{sup *}

    SciTech Connect

    Itkis, I. M.; Kozulin, E. M.; Itkis, M. G.; Knyazheva, G. N.; Bogachev, A. A.; Chernysheva, E. V.; Krupa, L.; Oganessian, Yu. Ts.; Zagrebaev, V. I.; Rusanov, A. Ya.; Goennenwein, F.; Dorvaux, O.; Stuttge, L.; Hanappe, F.; Vardaci, E.; Goes Brennand, E. de

    2011-06-15

    Mass and energy distributions of binary reaction products obtained in the reactions {sup 22}Ne+{sup 249}Cf,{sup 26}Mg+{sup 248}Cm, {sup 36}S+{sup 238}U, and {sup 58}Fe+{sup 208}Pb have been measured. All reactions lead to Hs isotopes. At energies below the Coulomb barrier the bimodal fission of Hs{sup *}, formed in the reaction {sup 26}Mg+{sup 248}Cm, is observed. In the reaction {sup 36}S+{sup 238}U, leading to the formation of a similar compound nucleus, the main part of the symmetric fragments arises from the quasifission process. At energies above the Coulomb barrier fusion-fission is the main process leading to the formation of symmetric fragments for both reactions with Mg and S ions. In the case of the {sup 58}Fe+{sup 208}Pb reaction the quasifission process dominates at all measured energies.

  15. Structural Basis of Clostridium perfringens Toxin Complex Formation

    SciTech Connect

    Adams,J.; Gregg, K.; Bayer, E.; Boraston, A.; Smith, S.

    2008-01-01

    The virulent properties of the common human and livestock pathogen Clostridium perfringens are attributable to a formidable battery of toxins. Among these are a number of large and highly modular carbohydrate-active enzymes, including the {mu}-toxin and sialidases, whose catalytic properties are consistent with degradation of the mucosal layer of the human gut, glycosaminoglycans, and other cellular glycans found throughout the body. The conservation of noncatalytic ancillary modules among these enzymes suggests they make significant contributions to the overall functionality of the toxins. Here, we describe the structural basis of an ultra-tight interaction (Ka = 1.44 x 1011 M-1) between the X82 and dockerin modules, which are found throughout numerous C. perfringens carbohydrate-active enzymes. Extensive hydrogen-bonding and van der Waals contacts between the X82 and dockerin modules give rise to the observed high affinity. The {mu}-toxin dockerin module in this complex is positioned {approx}180 relative to the orientation of the dockerin modules on the cohesin module surface within cellulolytic complexes. These observations represent a unique property of these clostridial toxins whereby they can associate into large, noncovalent multitoxin complexes that allow potentiation of the activities of the individual toxins by combining complementary toxin specificities.

  16. DNA and buffers: the hidden danger of complex formation.

    PubMed

    Stellwagen, N C; Gelfi, C; Righetti, P G

    2000-08-01

    The free solution electrophoretic mobility of DNA differs significantly in different buffers, suggesting that DNA-buffer interactions are present in certain buffer systems. Here, capillary and gel electrophoresis data are combined to show that the Tris ions in Tris-acetate-EDTA (TAE) buffers are associated with the DNA helix to approximately the same extent as sodium ions. The borate ions in Tris-borate-EDTA (TBE) buffers interact with DNA to form highly charged DNA-borate complexes, which are stable both in free solution and in polyacrylamide gels. DNA-borate complexes are not observed in agarose gels, because of the competition of the agarose gel fibers for the borate residues. The resulting agarose-borate complexes increase the negative charge of the agarose gel fibers, leading to an increased electroendosmotic flow of the solvent in agarose-TBE gels. The combined results indicate that the buffers in which DNA is studied cannot automatically be assumed to be innocuous. PMID:10861374

  17. Evaluation of Multi-tRNA Synthetase Complex by Multiple Reaction Monitoring Mass Spectrometry Coupled with Size Exclusion Chromatography

    PubMed Central

    Kim, Jun Seok; Lee, Cheolju

    2015-01-01

    Eight aminoacyl-tRNA synthetases (M, K, Q, D, R, I, EP and LARS) and three auxiliary proteins (AIMP1, 2 and 3) are known to form a multi-tRNA synthetase complex (MSC) in mammalian cells. We combined size exclusion chromatography (SEC) with reversed-phase liquid chromatography multiple reaction monitoring mass spectrometry (RPLC-MRM-MS) to characterize MSC components and free ARS proteins in human embryonic kidney (HEK 293T) cells. Crude cell extract and affinity-purified proteins were fractionated by SEC in non-denaturing state and ARSs were monitored in each fraction by MRM-MS. The eleven MSC components appeared mostly in earlier SEC fractions demonstrating their participation in complex formation. TARSL2 and AIMP2-DX2, despite their low abundance, were co-purified with KARS and detected in the SEC fractions, where MSC appeared. Moreover, other large complex-forming ARS proteins, such as VARS and FARS, were detected in earlier fractions. The MRM-MS results were further confirmed by western blot analysis. Our study demonstrates usefulness of combined SEC-MRM analysis for the characterization of protein complexes and in understanding the behavior of minor isoforms or variant proteins. PMID:26544075

  18. Amide Coupling Reaction for the Synthesis of Bispyridine-based Ligands and Their Complexation to Platinum as Dinuclear Anticancer Agents

    PubMed Central

    Apps, Michael G.; Johnson, Ben W.; Sutcliffe, Oliver B.; Brown, Sarah D.; Wheate, Nial J.

    2014-01-01

    Amide coupling reactions can be used to synthesize bispyridine-based ligands for use as bridging linkers in multinuclear platinum anticancer drugs. Isonicotinic acid, or its derivatives, are coupled to variable length diaminoalkane chains under an inert atmosphere in anhydrous DMF or DMSO with the use of a weak base, triethylamine, and a coupling agent, 1-propylphosphonic anhydride. The products precipitate from solution upon formation or can be precipitated by the addition of water. If desired, the ligands can be further purified by recrystallization from hot water. Dinuclear platinum complex synthesis using the bispyridine ligands is done in hot water using transplatin. The most informative of the chemical characterization techniques to determine the structure and gross purity of both the bispyridine ligands and the final platinum complexes is 1H NMR with particular analysis of the aromatic region of the spectra (7-9 ppm). The platinum complexes have potential application as anticancer agents and the synthesis method can be modified to produce trinuclear and other multinuclear complexes with different hydrogen bonding functionality in the bridging ligand. PMID:24893964

  19. Charge-transfer complexes formed in the reaction of 2-amino-4-ethylpyridine with π-electron acceptors

    NASA Astrophysics Data System (ADS)

    AlQaradawi, Siham Y.; Mostafa, Adel; Bengali, A. A.

    2016-02-01

    Molecular charge-transfer complexes (CT) of electron donor 2-amino-4-ethylpyridine (2A4EPy) with π-acceptors tetracyanoethylene (TCNE), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) and 2,4,4,6-tetrabromo-2,5-cyclohexadienone (TBCHD) have been studied spectrophotometrically in chloroform at 25 °C. These were investigated through electronic, infrared, mass spectra and thermal measurements as well as elemental analysis. All formed complexes exhibit well resolved charge-transfer bands in the regions where neither donor nor acceptors have any absorption. The obtained results show that the formed solid CT-complexes have the structures [(2A4EPy)(TCNE)2], [(2A4EPy)2(DDQ)] and [(2A4EPy)2(TBCHD)] for 2-amino-4-ethylpyridine in full agreement with the known reaction stoichiometries in solution as well as the elemental measurements. The formation constant KCT, molar extinction coefficient εC.T, free energy change ΔG0, CT energy ECT, ionization potential Ip and oscillator strength ƒ have been calculated for these three CT-complexes.

  20. Dichotomous-noise-induced pattern formation in a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Das, Debojyoti; Ray, Deb Shankar

    2013-06-01

    We consider a generic reaction-diffusion system in which one of the parameters is subjected to dichotomous noise by controlling the flow of one of the reacting species in a continuous-flow-stirred-tank reactor (CSTR) -membrane reactor. The linear stability analysis in an extended phase space is carried out by invoking Furutzu-Novikov procedure for exponentially correlated multiplicative noise to derive the instability condition in the plane of the noise parameters (correlation time and strength of the noise). We demonstrate that depending on the correlation time an optimal strength of noise governs the self-organization. Our theoretical analysis is corroborated by numerical simulations on pattern formation in a chlorine-dioxide-iodine-malonic acid reaction-diffusion system.

  1. Phase formation during Mn thin film reaction with Ge: Self-aligned germanide process for spintronics

    NASA Astrophysics Data System (ADS)

    Abbes, O.; Portavoce, A.; Le Thanh, V.; Girardeaux, C.; Michez, L.

    2013-10-01

    Interesting results have been reported concerning the magnetic properties of the Mn5Ge3 compound, opening the road to possibly create spin injectors in Ge. However, a process compatible with the Complementary Metal Oxide Semiconductor technology, allowing to produce a Mn5Ge3 layer on the active regions of Ge-based transistors has not been well established yet. Here, we report on the solid state reaction between a 50 nm-thick Mn film and amorphous Ge, aiming to investigate a similar process than the one (Salicide) used for contact production in the standard Si technology. In situ X-ray diffraction combined with ex situ structural and magnetic characterizations were used to identify and study phase formation during the Mn/Ge reaction.

  2. Redirection of the Reaction Specificity of a Thermophilic Acetolactate Synthase toward Acetaldehyde Formation

    PubMed Central

    Cheng, Maria; Yoshiyasu, Hayato; Okano, Kenji; Ohtake, Hisao; Honda, Kohsuke

    2016-01-01

    Acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. Although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. In this study, the reaction specificity of acetolactate synthase from Thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxylase. Error-prone PCR and mutant library screening led to the identification of a quadruple mutant with 3.1-fold higher acetaldehyde-forming activity than the wild-type. Site-directed mutagenesis experiments revealed that the increased activity of the mutant was due to H474R amino acid substitution, which likely generated two new hydrogen bonds near the thiamine pyrophosphate-binding site. These hydrogen bonds might result in the better accessibility of H+ to the substrate-cofactor-enzyme intermediate and a shift in the reaction specificity of the enzyme. PMID:26731734

  3. Spatiotemporal Pattern Formation and Chaos in the Belousov-Zhabotinsky Reaction in a Reverse Microemulsion

    NASA Astrophysics Data System (ADS)

    Epstein, Irving R.; Vanag, Vladimir K.

    2003-08-01

    We study the spatiotemporal behavior of the oscillatory Belousov-Zhabotinsky (BZ) reaction in a reverse microemulsion consisting of water, octane and the surfactant sodium bis(2-ethylhexyl)sulfosuccinate (AOT). By varying the microemulsion composition, we can "tune" its structure, specifically the size and spacing between the nanometer-sized water droplets in which the polar BZ reactants reside. We find a remarkable array of pattern formation as the microemulsion structure and BZ chemistry are varied. Behaviors observed include stationary Turing patterns, traveling and standing waves, spirals, targets, antispirals and antitargets (which travel into rather than out from their center), and spatiotemporal chaos. A simple reaction-diffusion model, which accounts for the BZ chemistry and the differential diffusion of species within water droplets and in the bulk oil phase, is able to reproduce nearly all of the observed behavior.

  4. Charge recombination reactions in photoexcited C[sub 60]-amine complexes studied by picosecond pump probe spectroscopy

    SciTech Connect

    Ghosh, H.N.; Pal, H.; Sapre, A.V.; Mittal, J.P. )

    1993-12-15

    Photoexcitation of complexes between fullerence C[sub 60] and organic amines in benzene solutions is known to result in charge separation (CS) and subsequent charge recombination (CR) reactions, which lead to varying yields of fullerence triplet formation. Picosecond flash photolysis studies are carried out on C[sub 60]-diphenylamine (DPA), C[sub 60]-triethylamine (TEA), C[sub 60]-diazabicyclooctane (DABCO), and C[sub 60]-triphenylamine (TPA) systems to find out mechanistic details of the triplet formation on CR by inducing heavy atom and polarity effects by using suitable solvents. It is found that in the case of C[sub 60]-DPA, C[sub 60]-TEA, and C[sub 60]-DABCO systems proton transfer from the amine cation to the C[sub 60] anion in the ion pair state dominates, leading to poor triplet yields, which improve in heavy atom containing solvents. In TPA, proton transfer is not possible and hence fullerene triplet yields are high. Increase of solvent polarity for this system results in decreased C[sub 60] triplet yields with a consequent increase in the ion dissociation yield. A suitable reaction scheme is proposed to explain the results obtained. 34 refs., 5 figs., 2 tabs.

  5. Peculiarities in the formation of complex organic compounds in a nitrogen-methane atmosphere during hypervelocity impacts

    NASA Astrophysics Data System (ADS)

    Zaitsev, M. A.; Gerasimov, M. V.; Safonova, E. N.; Vasiljeva, A. S.

    2016-03-01

    Results of the experiments on model impact vaporization of peridotite, a mineral analogue of stony asteroids, in a nitrogen-methane atmosphere are presented. Nd-glass laser (γ = 1.06 µm) was used for simulation. Pulse energy was ~600-700 J, pulse duration ~10-3 s, vaporization tempereature ~4000-5000 K. The gaseous medium (96% vol. of N2 and 4% vol. of CH4, P = 1 atm) was a possible analogue of early atmospheres of terrestrial planets and corresponded to the present-day atmosphere composition of Titan, a satellite of Saturn. By means of pyrolytic gas chromatography/mass spectrometry, it is shown that solid condensates obtained in laser experiments contain relatively complex lowand high-molecular weight (kerogen-like) organic compounds. The main products of condensate pyrolysis were benzene and alkyl benzenes (including long-chain ones), unbranched aliphatic hydrocarbons, and various nitrogen-containing compounds (aliphatic and aromatic nitriles and pyrrol). It is shown that the nitrogen-methane atmosphere favors the formation of complex organic compounds upon hypervelocity impacts with the participation of stony bodies even with a small methane content in it. In this process, falling bodies may not contain carbon, hydrogen, and other chemical elements necessary for the formation of the organic matter. In such conditions, a noticeable contribution to the impact-induced synthesis of complex organic substances is probably made by heterogeneous catalytic reactions, in particular, Fischer-Tropsch type reactions.

  6. Characterization of self-propagating formation reactions in Ni/Zr multilayered foils using reaction heats, velocities, and temperature-time profiles

    DOE PAGESBeta

    Barron, S. C.; Knepper, R.; Walker, N.; Weihs, T. P.

    2011-01-11

    We report on intermetallic formation reactions in vapor-deposited multilayered foils of Ni/Zr with 70 nm bilayers and overall atomic ratios of Ni:Zr, 2 Ni:Zr, and 7 Ni:2 Zr. The sequence of alloy phase formation and the stored energy is evaluated at slow heating rates (~1 K/s) using differential scanning calorimetry (DSC) traces to 725ºC. All three chemistries initially form a Ni-Zr amorphous phase which crystallizes first to the intermetallic NiZr. The heat of reaction to the final phase is 34-36 kJ/mol atom for all chemistries. Intermetallic formation reactions are also studied at rapid heating rates (greater than 105 K/s) inmore » high temperature, self-propagating reactions which can be ignited in these foils by an electric spark. We find that reaction velocities and maximum reaction temperatures (Tmax) are largely independent of foil chemistry at 0.6 ± 0.1 m/s and 1220 ± 50 K, respectively, and that the measured Tmax is more than 200 K lower than predicted adiabatic temperatures (Tad). The difference between Tmax and Tad is explained by the prediction that transformation to the final intermetallic phases occurs after Tmax and results in the release of 20-30 % of the total heat of reaction and a delay in rapid cooling.« less

  7. Characterization of self-propagating formation reactions in Ni/Zr multilayered foils using reaction heats, velocities, and temperature-time profiles

    SciTech Connect

    Barron, S. C.; Knepper, R.; Walker, N.; Weihs, T. P.

    2011-01-01

    We report on intermetallic formation reactions in vapor-deposited multilayered foils of Ni/Zr with 70 nm bilayers and overall atomic ratios of Ni:Zr, 2 Ni:Zr, and 7 Ni:2 Zr. The sequence of alloy phase formation and the stored energy is evaluated at slow heating rates ({approx}1 K/s) using differential scanning calorimetry traces to 725 deg. C. All three chemistries initially form a Ni-Zr amorphous phase which crystallizes first to the intermetallic NiZr. The heat of reaction to the final phase is 34-36 kJ/mol atom for all chemistries. Intermetallic formation reactions are also studied at rapid heating rates (greater than 10{sup 5} K/s) in high temperature, self-propagating reactions which can be ignited in these foils by an electric spark. We find that reaction velocities and maximum reaction temperatures (T{sub max}) are largely independent of foil chemistry at 0.6{+-}0.1 m/s and 1220{+-}50 K, respectively, and that the measured T{sub max} is more than 200 K lower than predicted adiabatic temperatures (T{sub ad}). The difference between T{sub max} and T{sub ad} is explained by the prediction that transformation to the final intermetallic phases occurs after T{sub max} and results in the release of 20%-30% of the total heat of reaction and a delay in rapid cooling.

  8. Role of the reaction of stabilized Criegee intermediates with peroxy radicals in particle formation and growth in air.

    PubMed

    Zhao, Yue; Wingen, Lisa M; Perraud, Véronique; Greaves, John; Finlayson-Pitts, Barbara J

    2015-05-21

    Ozonolysis of alkenes is an important source of secondary organic aerosol (SOA) in the atmosphere. However, the mechanisms by which stabilized Criegee intermediates (SCI) react to form and grow the particles, and in particular the contributions from oligomers, are not well understood. In this study, ozonolysis of trans-3-hexene (C6H12), as a proxy for small alkenes, was investigated with an emphasis on the mechanisms of particle formation and growth. Ozonolysis experiments were carried out both in static Teflon chambers (18-20 min reaction times) and in a glass flow reactor (24 s reaction time) in the absence and presence of OH or SCI scavengers, and under different relative humidity (RH) conditions. The chemical composition of polydisperse and size-selected SOA particles was probed using different mass spectrometric techniques and infrared spectroscopy. Oligomers having SCI as the chain unit are found to be the dominant components of such SOA particles. The formation mechanism for these oligomers suggested by our results follows the sequential addition of SCI to organic peroxy (RO2) radicals, in agreement with previous studies by Moortgat and coworkers. Smaller particles are shown to have a relatively greater contribution from longer oligomers. Higher O/C ratios are observed in smaller particles and are similar to those of oligomers resulting from RO2 + nSCI, supporting a significant role for longer oligomers in particle nucleation and early growth. Under atmospherically relevant RH of 30-80%, water vapor suppresses oligomer formation through scavenging SCI, but also enhances particle nucleation. Under humid conditions, or in the presence of formic or hydrochloric acid as SCI scavengers, peroxyhemiacetals are formed by the acid-catalyzed particle phase reaction between oligomers from RO2 + nSCI and a trans-3-hexene derived carbonyl product. In contrast to the ozonolysis of trans-3-hexene, oligomerization involving RO2 + nSCI does not appear to be prevalent in the

  9. Scale-Dependent Rates of Uranyl Surface Complexation Reaction in Sediments

    SciTech Connect

    Liu, Chongxuan; Shang, Jianying; Kerisit, Sebastien N.; Zachara, John M.; Zhu, Weihuang

    2013-03-15

    Scale-dependency of uranyl[U(VI)] surface complexation rates was investigated in stirred flow-cell and column systems using a U(VI)-contaminated sediment from the US Department of Energy, Hanford site, WA. The experimental results were used to estimate the apparent rate of U(VI) surface complexation at the grain-scale and in porous media. Numerical simulations using molecular, pore-scale, and continuum models were performed to provide insights into and to estimate the rate constants of U(VI) surface complexation at the different scales. The results showed that the grain-scale rate constant of U(VI) surface complexation was over 3 to 10 orders of magnitude smaller, dependent on the temporal scale, than the rate constant calculated using the molecular simulations. The grain-scale rate was faster initially and slower with time, showing the temporal scale-dependency. The largest rate constant at the grain-scale decreased additional 2 orders of magnitude when the rate was scaled to the porous media in the column. The scaling effect from the grain-scale to the porous media became less important for the slower sorption sites. Pore-scale simulations revealed the importance of coupled mass transport and reactions in both intragranular and inter-granular domains, which caused both spatial and temporal dependence of U(VI) surface complexation rates in the sediment. Pore-scale simulations also revealed a new rate-limiting mechanism in the intragranular porous domains that the rate of coupled diffusion and surface complexation reaction was slower than either process alone. The results provided important implications for developing models to scale geochemical/biogeochemical reactions.

  10. Formation of the light-harvesting complex I (B870) of anoxygenic phototrophic purple bacteria.

    PubMed

    Drews, G

    1996-09-01

    The light-harvesting (LH) complex I (B870) of anoxygenic photosynthetic purple bacteria is the oligomeric form of its subunit B820 consisting of the low-molecular-weight polypeptides alpha, beta, bacteriochlorophyll (BChl), and carotenoids in the stoichiometric ratio [alpha1 beta1 (BChl2) Crt1-2]n. LHI surrounds the photochemical reaction center (RC). The major absorption band of the LHI complex is species-specific and is found at 870-890 nm; those of the subunit and the monomeric BChl a (dissolved in methanol) absorb at 820 and 770 nm, respectively. The isolated LHI complex can be reversibly dissociated to the B820 subunit or to the polypeptides and pigments by addition of detergents. Reconstitution of the B820 or the functional B870 complex is still possible after partial truncation of the N- or C-terminal regions of the alpha- or beta-polypeptide or of the beta-polypeptide only. The minimal structural requirements for reconstitution of a spectrally wild-type form after truncation of the polypeptides and/or modifications of the BChl molecule are described. The insertion of the LHIalpha- and LHIbeta-polypeptides into the membrane and the in vivo assembly of LHI, studied in a cell-free system and in whole cells of Rhodobacter capsulatus, depend on the primary structures of both polypeptides, BChl, the chaperones DnaK and GroEL, membrane-bound proteins, and energized membranes. Exchanges, deletions, or insertions of amino acyl residues, especially in the conserved region of the N-terminus of the LHIalpha-polypeptide, prevent or reduce the efficiency and stability of the LHI assembly. Therefore, reconstitution of LHI in a detergent micelle does not exactly reproduce the formation of the LHI complex in the photosynthetic membrane in vivo. The N-terminal domains play a crucial role in the formation of the oligomeric protein scaffold and of the pigment array. Facultatively phototrophic bacteria such as Rhodospirillum (Rsp.) rubrum or Rhodobacter (Rba.) capsulatus can

  11. The sol gel synthesis of perovskites by an EDTA/citrate complexing method involves nanoscale solid state reactions

    NASA Astrophysics Data System (ADS)

    Feldhoff, A.; Arnold, M.; Martynczuk, J.; Gesing, Th. M.; Wang, H.

    2008-06-01

    Nowadays, sol-gel procedures are well established in the synthesis of complex oxides as they allow to obtain phase pure products and to control precisely their stoichiometry. This quality makes them a tool of choice for the preparation of perovskite-type oxides. To optimize the functional properties of these materials, it is essential to set accurately their possible complex stoichiometries. However, details of the formation of the perovskite crystal remain obscure. Different stages of an ethylene-diamine-tetraacetic acid (EDTA)/citrate-gel based synthesis process for mixed conducting (Ba 0.5Sr 0.5)(Fe 0.8Zn 0.2)O 3- δ of cubic perovskite structure are elucidated. The combination of analytical transmission electron microscopy with X-ray diffraction reveals that the perovskite-type oxide is formed already at moderate temperatures at around 700 °C via nanoscale solid state reactions between finely-dispersed crystalline intermediates identified as a spinel and a carbonate. The reaction scheme, however, is intricate and includes stuffed tridymite structures as transient phases. The ultrafine intermixing of extremely small reactants makes EDTA/citrate-gel based procedures superior to classical solid state routes with respect to applications that demand phase purity and stoichiometry control.

  12. The formation and study of titanium, zirconium, and hafnium complexes

    NASA Technical Reports Server (NTRS)

    Wilson, Bobby; Sarin, Sam; Smith, Laverne; Wilson, Melanie

    1989-01-01

    Research involves the preparation and characterization of a series of Ti, Zr, Hf, TiO, and HfO complexes using the poly(pyrazole) borates as ligands. The study will provide increased understanding of the decomposition of these coordination compounds which may lead to the production of molecular oxygen on the Moon from lunar materials such as ilmenite and rutile. The model compounds are investigated under reducing conditions of molecular hydrogen by use of a high temperature/pressure stainless steel autoclave reactor and by thermogravimetric analysis.

  13. Ganymede and Callisto - Complex crater formation and planetary crusts

    NASA Technical Reports Server (NTRS)

    Schenk, Paul M.

    1991-01-01

    Results are presented on measurements of crater depths and other morphological parameters (such as central peak and terrace frequency) of fresh craters on Ganymede and Callisto, two geophysically very similar but geologically divergent large icy satellites of Jupiter. These data were used to investigate the crater mechanics on icy satellites and the intersatellite crater scaling and crustal properties. The morphological transition diameters of and complex crater depths on Ganymede and Callisto were found to be similar, indicating that the crusts of both satellites are dominated by water ice with only a minor rocky component.

  14. Synthesis and structures of ruthenium–NHC complexes and their catalysis in hydrogen transfer reaction

    PubMed Central

    Chen, Chao; Lu, Chunxin; Zheng, Qing; Zhang, Min

    2015-01-01

    Summary Ruthenium complexes [Ru(L1)2(CH3CN)2](PF6)2 (1), [RuL1(CH3CN)4](PF6)2 (2) and [RuL2(CH3CN)3](PF6)2 (3) (L1= 3-methyl-1-(pyrimidine-2-yl)imidazolylidene, L2 = 1,3-bis(pyridin-2-ylmethyl)benzimidazolylidene) were obtained through a transmetallation reaction of the corresponding nickel–NHC complexes with [Ru(p-cymene)2Cl2]2 in refluxing acetonitrile solution. The crystal structures of three complexes determined by X-ray analyses show that the central Ru(II) atoms are coordinated by pyrimidine- or pyridine-functionalized N-heterocyclic carbene and acetonitrile ligands displaying the typical octahedral geometry. The reaction of [RuL1(CH3CN)4](PF6)2 with triphenylphosphine and 1,10-phenanthroline resulted in the substitution of one and two coordinated acetonitrile ligands and afforded [RuL1(PPh3)(CH3CN)3](PF6)2 (4) and [RuL1(phen)(CH3CN)2](PF6)2 (5), respectively. The molecular structures of the complexes 4 and 5 were also studied by X-ray diffraction analysis. These ruthenium complexes have proven to be efficient catalysts for transfer hydrogenation of various ketones. PMID:26664598

  15. Roles of Acetone and Diacetone Alcohol in Coordination and Dissociation Reactions of Uranyl Complexes

    SciTech Connect

    Rios, Daniel; Schoendorff, George E.; Van Stipdonk, Michael J.; Gordon, Mark S.; Windus, Theresa L.; Gibson, John K.; De Jong, Wibe A.

    2012-12-03

    Combined collision-induced dissociation mass-spectrometry experiments and DFT calculations were employed to elucidate the molecular structure of "hypercoordinated" species and the energetics of water-elimination reactions of uranyl acetone complexes observed in earlier work (Rios, D.; Rutkowski, P. X.; Van Stipdonk, M. J.; Gibson, J. K. Inorg. Chem. 2011, 50, 4781). It is shown that the "hypercoordinated" species contain diacetone alcohol ligands bonded in either bidentate or monodentate fashion, which are indistinguishable from (acetone)2 in mass spectrometry. Calculations confirm that four diacetone ligands can form stable complexes, but that the effective number of atoms coordinating with uranium in the equatorial plane does not exceed five. Diacetone alcohol ligands are shown to form mesityl oxide ligands and alkoxide species through the elimination of water, providing an explanation for the observed water-elimination reactions.

  16. Synthetic and Mechanistic Studies of Strained Heterocycle Opening Reactions Mediated by Zirconium(IV) Imido Complexes

    PubMed Central

    Blum, Suzanne A.; Rivera, Vicki A.; Ruck, Rebecca T.; Michael, Forrest E.; Bergman, Robert G.

    2005-01-01

    The reactions of the bis(cyclopentadienyl)(tert-butylimido)zirconium complex (Cp2Zr=N-t-Bu)(THF) (1) with epoxides, aziridines, and episulfides were investigated. Heterocycles without accessible β-hydrogens undergo insertion/protonation of the C–X bond to produce 1,2-amino alcohols (X = O) and 1,2-diamines (X = NR), whereas heterocycles with accessible β-hydrogens undergo elimination/protonation to produce allylic alcohols (X = O) and allylic sulfides (X = S). Mechanistic investigations support a stepwise pathway with zwitterionic intermediates for the first reaction class and a concerted pathway for the second reaction class. Additionally, the feasibility of chirality transfer from the planar-chiral ebthi (ebthi = ethylenebis(tetrahydroindenyl)) ligand was demonstrated with a chiral analogue, (ebthi)-Zr=NAr(THF) (Ar = 2,6-dimethylphenyl), 2, through the diastereoselective ring opening of meso epoxides. PMID:16508693

  17. Oligomer Formation Reactions of Criegee Intermediates in the Ozonolysis of Small Unsaturated Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Sakamoto, Y.; Inomata, S.; Hirokawa, J.

    2013-12-01

    Secondary organic aerosol (SOA) constitutes a substantial fraction of atmospheric fine particulate matters and has an effect on visibility, climate and human health. One of the major oxidizing processes leading to SOA formation is an ozonolysis of unsaturated hydrocarbons (UHCs).[1] Despite of its importance, the contribution of the ozonolysis of UHCs to the SOA formation in the troposphere is not sufficiently understood due to a lack of information on reaction pathways to produce low volatile compounds. While many studies have previously been focused on SOA formation from the ozonolysis of large UHCs, SOA formation from the ozonolysis of UHCs with less than six carbon atoms have been rarely investigated because their products are expected to be too volatile to contribute to the SOA formation. Very recently, a few studies have reported the SOA formation from the ozonolysis of such small UHCs but chemical mechanisms are still unclear. [2-4] In order to understand SOA formation from the ozonolysis of the small UHCs, this study investigated gas- and particle-phase products in laboratory experiments with a Teflon bag using a negative ion chemical ionization mass spectrometry (NI-CIMS) with chloride ion transfer for chemical ionization. This technique is suitable for analysis of compounds such as carboxylic acids and hydroperoxides expected to be produced in the ozonolysis of UHCs with less fragmentation, high selectivity, and high sensitivity. In the particle-phase analysis, SOAs collected on a PTFE filter were heated, and thermally desorbed compounds were analyzed. In the gas-phase analysis, series of peaks with an interval of a mass-to-charge ratio equal to the molecular weight of a Criegee intermediate formed in their ozonolysis were observed. These peaks were attributed to oligomeric hydroperoxides composed of Criegee intermediates as a chain unit. These oligomeric hydroperoxides were also observed in the particle-phase analysis, indicating that the oligomeric

  18. Search for reaction conditions and catalyst for selective prebiotic formation of Aldopentoses from Glycolaldehyde and Formaldehyde

    NASA Astrophysics Data System (ADS)

    Delidovich, Irina; Taran, Oxana; Parmon, Valentin; Gromov, Nikolay

    2012-07-01

    Formation of organic compounds from simple precursors appears to have been one of the first steps from geochemistry towards modern biochemistry. The Earth lagoons, hydrothermal springs, cosmic dust, meteorites, protoplanetary disk, etc. has been considered as the possible ``reactors'' in which the prebiotic synthesis could have taken place. The finding of reactions and reaction conditions which allow to produce the high yields of the biologically relevant substances from simple compounds could help us to verify different hypothesis of plausible prebotic conditions. In this work we have studied the formation of vitally important sugars, namely aldopentoses (ribose, xylose, lyxose and arabinose), from glycolaldehyde and formaldehyde over catalysts. Aldopentoses nowadays play the important roles as the components of polysaccharides, glycosides, nucleic acids and ATP. Glycolaldehyde is the simplest monosaccharide, which was found in the interstellar space [1], where it could be generated as a result of several processes, for instance, condensation of formaldehyde under UV-radiation [2]. In this work the peculiarities of interaction between glycolaldehyde and formaldehyde in the presence of soluble (phosphate and borate buffers) and solid (minerals apatite and montmorillonites) catalysts were studied. The dependences of composition of the reaction products on the catalyst nature, molar ratio of substrates, pH value of reaction mixture were revealed. The yields of aldopentoses amount to ca. 60-65% in the presence of borate catalyst under optimized reaction conditions. Borate acts not only as a catalyst, but also as the stabilizer of active intermediates and aldopentoses from side reactions [3]. Borates are present in some mineral and clays (serpentine, montmorillonite etc.) and in water of Cityhot springs (Geyser valley, placeKamchatka) in rather high concentrations. Therefore catalysis by borates could be considered as plausible prebotic condition. Acknowledgements. We

  19. The complex interplay between semantics and grammar in impression formation.

    PubMed

    Shreves, Wyley B; Hart, William; Adams, John M; Guadagno, Rosanna E; Eno, Cassie A

    2014-09-01

    We sought to bridge findings showing that (a) describing a person's behavior with the perfective verb aspect (did), compared to the imperfective aspect (was doing), increases processing of semantic knowledge unrelated to the target's action such as stereotypes and (b) an increased recognition of stereotypical thoughts often promotes a judgment correction for the stereotypes. We hypothesized an interplay between grammar (verb conjugation) and semantic information (gender) in impression-formation. Participants read a resume, attributed to a male or female, for a traditionally masculine job. When the resume was written in the imperfective, people rated a male (vs. female) more positively. When the resume was in the perfective, this pattern reversed. Only these latter effects of gender were influenced by cognitive load. Further, people more quickly indicated the applicant's gender in the perfective condition, suggesting an enhanced focus on gender during processing. PMID:24950389

  20. Simplicity in complexity: the photosynthetic reaction center performs as a simple 0.2 V battery.

    PubMed

    van Rotterdam, Bart J; Crielaard, Wim; van Stokkum, Ivo H M; Hellingwerf, Klaas J; Westerhoff, Hans V

    2002-01-01

    The photosynthetic reaction center is one of the most complicated molecular complexes. Transducing photon energy to a transmembrane electrochemical potential difference for protons, it is the direct or indirect energy source for virtually all life. We show here that it operates in a simple, battery-like manner, with a maximum potential of 0.20 V. Intriguingly this is only one fifth of the energy of the absorbed photon. PMID:11755540

  1. An Iridium(I) N-Heterocyclic Carbene Complex Catalyzes Asymmetric Intramolecular Allylic Amination Reactions.

    PubMed

    Ye, Ke-Yin; Cheng, Qiang; Zhuo, Chun-Xiang; Dai, Li-Xin; You, Shu-Li

    2016-07-01

    A chiral iridium(I) N-heterocyclic carbene complex was reported for the first time as the catalyst in the highly enantioselective intramolecular allylic amination reaction. The current method provides facile access to biologically important enantioenriched indolopiperazinones and piperazinones in good yields (74-91 %) and excellent enantioselectivities (92-99 % ee). Preliminary mechanistic investigations reveal that the C-H activation occurs at the position ortho to the N-aryl group of the ligand. PMID:27162135

  2. Heterogeneous reactions of glyoxal on mineral particles: A new avenue for oligomers and organosulfate formation

    NASA Astrophysics Data System (ADS)

    Shen, Xiaoli; Wu, Huihui; Zhao, Yue; Huang, Dao; Huang, Liubin; Chen, Zhongming

    2016-04-01

    Glyoxal (GL) plays a crucial role in the formation of secondary organic aerosols (SOA), because it is highly water soluble and capable of oligomerization. This is the first study to describe irreversible heterogeneous reactions of GL on clean and acidic gas-aged SiO2, α-Al2O3, and CaCO3 particles, as models of real mineral particles, at various relative humidity and without irradiation and gas phase oxidants. A series of products, including oligomers, organosulfates, and organic acids, which contribute to SOA formation, were produced. GL uptake on SO2-aged α-Al2O3 enabled the oxidation of surface S(IV) to S(VI). The presence of adsorbed water on particles favored GL uptake and the formation of oligomers and organosulfate, but it suppressed organic acid formation. In addition, the aging process enhanced the positive effect of adsorbed water on GL uptake. These findings will further our understanding of the GL sink and SOA sources in the atmosphere.

  3. EXPERIMENTAL STUDY OF CO{sub 2} FORMATION BY SURFACE REACTIONS OF NON-ENERGETIC OH RADICALS WITH CO MOLECULES

    SciTech Connect

    Oba, Yasuhiro; Watanabe, Naoki; Kouchi, Akira; Hama, Tetsuya; Pirronello, Valerio

    2010-04-01

    Surface reactions between carbon monoxide and non-energetic hydroxyl radicals were carried out at 10 K and 20 K in order to investigate possible reaction pathways to yield carbon dioxide in dense molecular clouds. Hydroxyl radicals, produced by dissociating water molecules in microwave-induced plasma, were cooled down to 100 K prior to the introduction of CO. The abundances of species were monitored in situ using a Fourier transform infrared spectrometer. Formation of CO{sub 2} was clearly observed, even at 10 K, suggesting that reactions of CO with OH proceed with little or no activation barrier. The present results indicate that CO{sub 2} formation, due to reactions between CO and OH, occurs in tandem with H{sub 2}O formation, and this may lead to the formation of CO{sub 2} ice in polar environments, as typically observed in molecular clouds.

  4. FORMATION OF POLYCYCLIC AROMATIC HYDROCARBONS AND THEIR GROWTH TO SOOT -A REVIEW OF CHEMICAL REACTION PATHWAYS. (R824970)

    EPA Science Inventory

    The generation by combustion processes of airborne species of current health concern such as polycyclic aromatic hydrocarbons (PAH) and soot particles necessitates a detailed understanding of chemical reaction pathways responsible for their formation. The present review discus...

  5. Subcellular location for the formation of the retinol/retinol-binding protein complex in rat liver

    SciTech Connect

    Crumbaugh, L.M.; Green, E.L.; Smith, J.E.

    1986-03-01

    Retinol complexes with retinol-binding protein (RBP) within the hepatocyte, however the subcellular location where complex formation occurs has not previously been identified. A model similar to that of lipoproteins formation has been hypothesized. The authors have identified the initial site of retinol/RBP complex formation. Furthermore, the authors have elucidated the progression of the complex through the subcellular organelles. Intravenous injections of /sup 3/H-retinol suspended in Tween 40 were administered to vitamin A depleted rats. After intervals of 2, 3, 4, 5, 10, 15, 20, and 30 minutes the rat livers were removed and fractions enriched in rough and smooth microsomes and Golgi apparatus were prepared. Extracts of these subcellular fractions were chromatographed on Sephadex G-100. Simultaneous elution of /sup 3/H-retinol and immunoreactive RBP indicated the presence of the complex. The retinol/RBP complex was observed in rough microsomes 2 minute after the injection of /sup 3/H-retinal. The complex appeared subsequently in smooth microsomes and Golgi apparatus. The complex was first detected serum around 10 minutes after injection. Based on the data, they believe that the retinol/RBP complex formation occurs in rough microsomes.

  6. Organosulfate Formation through the Heterogeneous Reaction of Sulfur Dioxide with Unsaturated Fatty Acids and Long-Chain Alkenes.

    PubMed

    Passananti, Monica; Kong, Lingdong; Shang, Jing; Dupart, Yoan; Perrier, Sébastien; Chen, Jianmin; Donaldson, D James; George, Christian

    2016-08-22

    The heterogeneous reaction between SO2 and unsaturated compounds results in the efficient production of organosulfates for several fatty acids and long-chain alkenes. The presence of an acid group, the physical state of the reactants (solid or liquid), the nature of the double bond (cis, trans, terminal), and the use of light irradiation all have an impact on the reaction rate. The reaction was investigated using different set-ups (coated flow tube, aerosol flow tube, and diffuse reflectance infrared Fourier transform cell). The reaction products were identified by high-resolution mass spectrometry and the impact of this reaction on organosulfate formation in the atmosphere is discussed. PMID:27458109

  7. Enhancing the Reduction Potential of Quinones via Complex Formation.

    PubMed

    Nepal, Binod; Scheiner, Steve

    2016-05-20

    Quantum calculations are used to study the manner in which quinones interact with proton-donating molecules. For neutral donors, a stacked geometry is favored over a H-bond structure. The former is stabilized by charge transfers from the N or O lone pairs to the quinone's π* orbitals. Following the addition of an electron to the quinone, the radical anion forms strong H-bonded complexes with the various donors. The presence of the donor enhances the electron affinity of the quinone. This enhancement is on the order of 15 kcal/mol for neutral donors, but up to as much as 85 kcal/mol for a cationic donor. The increase in electron affinity is larger for electron-rich quinones than for their electron-deficient counterparts, containing halogen substituents. Similar trends are in evidence when the systems are immersed in aqueous solvent. PMID:27135719

  8. Corticospinal excitability is reduced in a simple reaction time task requiring complex timing.

    PubMed

    Kennefick, Michael; Maslovat, Dana; Chua, Romeo; Carlsen, Anthony N

    2016-07-01

    Increasing the complexity of a movement has been shown to result in longer simple reaction time (RT), which has been attributed to sequencing or timing requirements following the go-signal. However, RT differences may also be due to differences in corticospinal excitability (CE) as previous studies have found an enhanced excitatory state of corticospinal neurons in complex tasks. Transcranial magnetic stimulation (TMS) was used in the present study to probe the excitability of the motor pathway during the simple RT interval for single (simple) versus multiple (complex) key press responses. Premotor RT data indicated that participants responded significantly (p<.001) faster in the simple task compared to the complex task, confirming response complexity was manipulated appropriately. Analysis of the CE data indicated that motor evoked potential (MEP) amplitudes increased with time following the go-signal in both conditions and that MEP amplitudes in the simple task were significantly larger than those in the complex task when evoked within 75ms of movement onset (p=.009). These findings suggest that the rate of increase for initiation-related neural activation is reduced for complex as compared to simple movements, which may partially explain differences in RT. PMID:27064075

  9. Formation, Migration, and Reactivity of Au CO Complexes on Gold Surfaces

    DOE PAGESBeta

    Wang, Jun; McEntee, Monica; Tang, Wenjie; Neurock, Matthew; Baddorf, Arthur P.; Maksymovych, Petro; Yates, Jr, John T.

    2016-01-12

    Here, we report experimental as well as theoretical evidence that suggests Au CO complex formation upon the exposure of CO to active sites (step edges and threading dislocations) on a Au(111) surface. Room-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, transmission infrared spectroscopy, and density functional theory calculations point to Au CO complex formation and migration. Room-temperature STM of the Au(111) surface at CO pressures in the range from 10^ 8 to 10^ 4 Torr (dosage up to 10^6 langmuir) indicates Au atom extraction from dislocation sites of the herringbone reconstruction, mobile Au CO complex formation and diffusion, and Aumore » adatom cluster formation on both elbows and step edges on the Au surface. The formation and mobility of the Au CO complex result from the reduced Au Au bonding at elbows and step edges leading to stronger Au CO bonding and to the formation of a more positively charged CO (CO +) on Au. These studies indicate that the mobile Au CO complex is involved in the Au nanoparticle formation and reactivity, and that the positive charge on CO increases due to the stronger adsorption of CO at Au sites with lower coordination numbers.« less

  10. Formation, Migration, and Reactivity of Au-CO Complexes on Gold Surfaces.

    PubMed

    Wang, Jun; McEntee, Monica; Tang, Wenjie; Neurock, Matthew; Baddorf, Arthur P; Maksymovych, Petro; Yates, John T

    2016-02-10

    We report experimental as well as theoretical evidence that suggests Au-CO complex formation upon the exposure of CO to active sites (step edges and threading dislocations) on a Au(111) surface. Room-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, transmission infrared spectroscopy, and density functional theory calculations point to Au-CO complex formation and migration. Room-temperature STM of the Au(111) surface at CO pressures in the range from 10(-8) to 10(-4) Torr (dosage up to 10(6) langmuir) indicates Au atom extraction from dislocation sites of the herringbone reconstruction, mobile Au-CO complex formation and diffusion, and Au adatom cluster formation on both elbows and step edges on the Au surface. The formation and mobility of the Au-CO complex result from the reduced Au-Au bonding at elbows and step edges leading to stronger Au-CO bonding and to the formation of a more positively charged CO (CO(δ+)) on Au. Our studies indicate that the mobile Au-CO complex is involved in the Au nanoparticle formation and reactivity, and that the positive charge on CO increases due to the stronger adsorption of CO at Au sites with lower coordination numbers. PMID:26754257

  11. Tandem buildup of complexity of aromatic molecules through multiple successive electrophile generation in one pot, controlled by varying the reaction temperature.

    PubMed

    Sumita, Akinari; Otani, Yuko; Ohwada, Tomohiko

    2016-02-01

    While some sequential electrophilic aromatic substitution reactions, known as tandem/domino/cascade reactions, have been reported for the construction of aromatic single skeletons, one of the most interesting and challenging possibilities remains the one-pot build-up of a complex aromatic molecule from multiple starting components, i.e., ultimately multi-component electrophilic aromatic substitution reactions. In this work, we show how tuning of the leaving group ability of phenolate derivatives from carbamates and esters provides a way to successively generate multiple unmasked electrophiles in a controlled manner in one pot, simply by varying the temperature. Here, we demonstrate the autonomous formation of up to three bonds in one pot and formation of two bonds arising from a three-component electrophilic aromatic substitution reaction. This result provides a proof-of-concept of our strategy applicable for the self-directed construction of complex aromatic structures from multiple simple molecules, which can be a potential avenue to realize multi-component electrophilic aromatic substitution reactions. PMID:26699842

  12. Metal-mediated reaction modeled on nature: the activation of isothiocyanates initiated by zinc thiolate complexes.

    PubMed

    Eger, Wilhelm A; Presselt, Martin; Jahn, Burkhard O; Schmitt, Michael; Popp, Jürgen; Anders, Ernst

    2011-04-18

    On the basis of detailed theoretical studies of the mode of action of carbonic anhydrase (CA) and models resembling only its reactive core, a complete computational pathway analysis of the reaction between several isothiocyanates and methyl mercaptan activated by a thiolate-bearing model complex [Zn(NH(3))(3)SMe](+) was performed at a high level of density functional theory (DFT). Furthermore, model reactions have been studied in the experiment using relatively stable zinc complexes and have been investigated by gas chromatography/mass spectrometry and Raman spectroscopy. The model complexes used in the experiment are based upon the well-known azamacrocyclic ligand family ([12]aneN(4), [14]aneN(4), i-[14]aneN(4), and [15]aneN(4)) and are commonly formulated as ([Zn([X]aneN(4))(SBn)]ClO(4). As predicted by our DFT calculations, all of these complexes are capable of insertion into the heterocumulene system. Raman spectroscopic investigations indicate that aryl-substituted isothiocyanates predominantly add to the C═N bond and that the size of the ring-shaped ligands of the zinc complex also has a very significant influence on the selectivity and on the reactivity as well. Unfortunately, the activated isothiocyanate is not able to add to the thiolate-corresponding mercaptan to invoke a CA analogous catalytic cycle. However, more reactive compounds such as methyl iodide can be incorporated. This work gives new insight into the mode of action and reaction path variants derived from the CA principles. Further, aspects of the reliability of DFT calculations concerning the prediction of the selectivity and reactivity are discussed. In addition, the presented synthetic pathways can offer a completely new access to a variety of dithiocarbamates. PMID:21405064

  13. Peptide bond formation through gas-phase reactions in the interstellar medium: formamide and acetamide as prototypes

    SciTech Connect

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio

    2014-09-20

    A theoretical study of the reactions of NH{sub 4}{sup +} with formaldehyde and CH{sub 5}{sup +} with formamide is carried out. The viability of these gas-phase ion-molecule reactions as possible sources of formamide and acetamide under the conditions of interstellar medium is evaluated. We report a theoretical estimation of the reaction enthalpies and an analysis of their potential energy surfaces. Formation of protonated formamide from the reaction between ammonium cation and formaldehyde is an exothermic process, but all the channels located on the potential energy surface leading to this product present net activation energies. For the reaction between methanium and formamide, different products are possible from a thermodynamic point of view. An analysis of its potential energy surface showed that formation of protonated acetamide and amino acetaldehyde takes place through barrier-free paths. Therefore, this reaction could be a feasible source of acetamide and amino acetaldehyde in space.

  14. Complex Formation History of Highly Evolved Basaltic Shergottite, Zagami

    NASA Technical Reports Server (NTRS)

    Niihara, T.; Misawa, K.; Mikouchi, T.; Nyquist, L. E.; Park, J.; Hirata, D.

    2012-01-01

    Zagami, a basaltic shergottite, contains several kinds of lithologies such as Normal Zagami consisting of Fine-grained (FG) and Coarse-grained (CG), Dark Mottled lithology (DML), and Olivine-rich late-stage melt pocket (DN). Treiman and Sutton concluded that Zagami (Normal Zagami) is a fractional crystallization product from a single magma. It has been suggested that there were two igneous stages (deep magma chamber and shallow magma chamber or surface lava flow) on the basis of chemical zoning features of pyroxenes which have homogeneous Mg-rich cores and FeO, CaO zoning at the rims. Nyquist et al. reported that FG has a different initial Sr isotopic ratio than CG and DML, and suggested the possibility of magma mixing on Mars. Here we report new results of petrology and mineralogy for DML and the Olivine-rich lithology (we do not use DN here), the most evolved lithology in this rock, to understand the relationship among lithologies and reveal Zagami s formation history

  15. Formation of Lactic Acid from Cellulosic Biomass by Alkaline Hydrothermal Reaction

    NASA Astrophysics Data System (ADS)

    Yan, X.; Jini, F.; Kishita, A.; Enomoto, H.; Tohji, K.

    2008-02-01

    Glucose, as a model compound of cellulosic biomass, was used as a test material. Ca(OH)2 and NaOH were selected as alkali. Results showed that both NaOH and Ca(OH)2, can promote the formation of lactic acid in a hydrothermal reaction of glucose. In the case of the addition of NaOH, lactic acid was obtained with a good yield of 27% based on a carbon base at 300 °C for 60 s with a NaOH concentration of 2.5 M. In the case of the addition of Ca(OH)2, the highest yield of lactic acid is 20%, which occurred at 300 °C for 60 s with a Ca(OH)2 concentration of 0.32 M. The formation mechanisms of lactic acid from glucose were also discussed according to intermediate products identified. Lactic acid may be generated via formaldehyde, glycolaldehyde besides via the aldose having three carbon atoms in hydrothermal reaction which all formed by the reverse aldol condensation of hexoses.

  16. Substrate Binding Promotes Formation of the Skp1-Cul1-Fbxl3 (SCFFbxl3) Protein Complex*

    PubMed Central

    Yumimoto, Kanae; Muneoka, Tetsuya; Tsuboi, Tomohiro; Nakayama, Keiichi I.

    2013-01-01

    The Skp1–Cul1–F-box protein (SCF) complex is one of the most well characterized types of ubiquitin ligase (E3), with the E3 activity of the complex being regulated in part at the level of complex formation. Fbxl3 is an F-box protein that is responsible for the ubiquitylation and consequent degradation of cryptochromes (Crys) and thus regulates oscillation of the circadian clock. Here we show that formation of the SCFFbxl3 complex is regulated by substrate binding in vivo. Fbxl3 did not associate with Skp1 and Cul1 to a substantial extent in transfected mammalian cells. Unexpectedly, however, formation of the SCFFbxl3 complex was markedly promoted by forced expression of its substrate Cry1 in these cells. A mutant form of Fbxl3 that does not bind to Cry1 was unable to form an SCF complex, suggesting that interaction of Cry1 with Fbxl3 is essential for formation of SCFFbxl3. In contrast, recombinant Fbxl3 associated with recombinant Skp1 and Cul1 in vitro even in the absence of recombinant Cry1. Domain-swap analysis revealed that the COOH-terminal leucine-rich repeat domain of Fbxl3 attenuates the interaction of Skp1, suggesting that a yet unknown protein associated with the COOH-terminal domain of Fbxl3 and inhibited SCF complex formation. Our results thus provide important insight into the regulation of both SCF ubiquitin ligase activity and circadian rhythmicity. PMID:24085301

  17. Asymmetric catalytic cascade reactions for constructing diverse scaffolds and complex molecules.

    PubMed

    Wang, Yao; Lu, Hong; Xu, Peng-Fei

    2015-07-21

    With the increasing concerns about chemical pollution and sustainability of resources, among the significant challenges facing synthetic chemists are the development and application of elegant and efficient methods that enable the concise synthesis of natural products, drugs, and related compounds in a step-, atom- and redox-economic manner. One of the most effective ways to reach this goal is to implement reaction cascades that allow multiple bond-forming events to occur in a single vessel. This Account documents our progress on the rational design and strategic application of asymmetric catalytic cascade reactions in constructing diverse scaffolds and synthesizing complex chiral molecules. Our research is aimed at developing robust cascade reactions for the systematic synthesis of a range of interesting molecules that contain structural motifs prevalent in natural products, pharmaceuticals, and biological probes. The strategies employed to achieve this goal can be classified into three categories: bifunctional base/Brønsted acid catalysis, covalent aminocatalysis/N-heterocyclic carbene catalysis, and asymmetric organocatalytic relay cascades. By the use of rationally designed substrates with properly reactive sites, chiral oxindole, chroman, tetrahydroquinoline, tetrahydrothiophene, and cyclohexane scaffolds were successfully assembled under bifunctional base/Brønsted acid catalysis from simple and readily available substances such as imines and nitroolefins. We found that some of these reactions are highly efficient since catalyst loadings as low as 1 mol % can promote the multistep sequences affording complex architectures with high stereoselectivities and yields. Furthermore, one of the bifunctional base/Brønsted acid-catalyzed cascade reactions for the synthesis of chiral cyclohexanes has been used as a key step in the construction of the tetracyclic core of lycorine-type alkaloids and the formal synthesis of α-lycorane. Guided by the principles of

  18. The imidazole role in strontium beta-diketonate complexes formation.

    PubMed

    Marchetti, Fabio; Pettinari, Claudio; Pettinari, Riccardo; Cingolani, Augusto; Gobetto, Roberto; Chierotti, Michele R; Drozdov, Andrei; Troyanov, Sergey I

    2006-04-01

    A selection of new strontium beta-diketonate derivatives (imH2)2[Sr2(beta-dike)6] [where imH = imidazole and beta-dike = tfac (tfacH = 1,1,1-trifluoro-2,4-pentanedione), tfbz (tfbzH = 1,1,1-trifluoro-4-phenyl-2,4-butanedione), or hfac (hfacH = 1,1,1,5,5,5-hexafluoro-2,4-pentanedione)], [Sr2(tfac)4(Meim)2(H2O)2], (MeimH)2[Sr(beta-dike)4] (where Meim = 1-methylimidazole and beta-dike = tfbz or hfac), [Sr2(thd)4(imH)2(EtOH)], and [Sr2(thd)4(Meim)2(EtOH)] (where thdH = 2,2,6,6-tetramethyl-3,5-heptanedione) have been synthesized and fully characterized. (imH2)2[Sr2(beta-dike)6] and (MeimH)2[Sr(beta-dike)4] are di- and mononuclear Sr anionic complexes, respectively, while [Sr2(tfac)4(Meim)2(H2O)2], [Sr2(thd)4(imH)2(EtOH)], and [Sr2(thd)4(Meim)2(EtOH)] are neutral dinuclear molecular derivatives. The derivative (imH2)2[Sr2(hfac)6] slowly decomposes in solution under aerobic conditions, giving (imH2)2[Sr(H2O)2(tfa)3](tfa) (tfaH = trifluoroacetic acid), which is an ionic compound containing polynuclear anionic chains composed of Sr(H2O)2(tfa)3 units. When a deficiency of imH is employed, the thdH proligand forms not only the dinuclear derivative [Sr2(thd)4(imH)2(EtOH)] but also an additional product with the formula [Sr(thd)2(H2O)2(EtOH)], in which the Sr atom is seven-coordinated. A complete solid-state characterization has been accomplished by comparing X-ray and solid-state 13C NMR data. Elucidation of the H-bond interaction between the heterocyclic rings and metal complexes by cross-polarization magic-angle-spinning 15N NMR is also reported. PMID:16562964

  19. A cyclo‐P6 Ligand Complex for the Formation of Planar 2D Layers

    PubMed Central

    Heindl, Claudia; Peresypkina, Eugenia V.; Lüdeker, David; Brunklaus, Gunther; Virovets, Alexander V.

    2016-01-01

    Abstract The all‐phosphorus analogue of benzene, stabilized as middle deck in triple‐decker complexes, is a promising building block for the formation of graphene‐like sheet structures. The reaction of [(CpMo)2(μ,η6:η6‐P6)] (1) with CuX (X=Br, I) leads to self‐assembly into unprecedented 2D networks of [{(CpMo)2P6}(CuBr)4]n (2) and [{(CpMo)2P6}(CuI)2]n (3). X‐ray structural analyses show a unique deformation of the previously planar cyclo‐P6 ligand. This includes bending of one P atom in an envelope conformation as well as a bisallylic distortion. Despite this, 2 and 3 form planar layers. Both polymers were furthermore analyzed by 31P{1H} magic angle spinning (MAS) NMR spectroscopy, revealing signals corresponding to six non‐equivalent phosphorus sites. A peak assignment is achieved by 2D correlation spectra as well as by DFT chemical shift computations. PMID:26711699

  20. A cyclo-P6 Ligand Complex for the Formation of Planar 2D Layers.

    PubMed

    Heindl, Claudia; Peresypkina, Eugenia V; Lüdeker, David; Brunklaus, Gunther; Virovets, Alexander V; Scheer, Manfred

    2016-02-01

    The all-phosphorus analogue of benzene, stabilized as middle deck in triple-decker complexes, is a promising building block for the formation of graphene-like sheet structures. The reaction of [(CpMo)2 (μ,η(6) :η(6) -P6 )] (1) with CuX (X=Br, I) leads to self-assembly into unprecedented 2D networks of [{(CpMo)2 P6 }(CuBr)4 ]n (2) and [{(CpMo)2 P6 }(CuI)2 ]n (3). X-ray structural analyses show a unique deformation of the previously planar cyclo-P6 ligand. This includes bending of one P atom in an envelope conformation as well as a bisallylic distortion. Despite this, 2 and 3 form planar layers. Both polymers were furthermore analyzed by (31) P{(1) H} magic angle spinning (MAS) NMR spectroscopy, revealing signals corresponding to six non-equivalent phosphorus sites. A peak assignment is achieved by 2D correlation spectra as well as by DFT chemical shift computations. PMID:26711699

  1. Carbon Isotopic Fractionation During Formation of Macromolecular Organic Grain Coatings via FTT Reactions

    NASA Technical Reports Server (NTRS)

    Nuth, J. A.; Johnson, N. M.; Elsila-Cook, J.; Kopstein, M.

    2011-01-01

    Observations of carbon isotopic fractionation of various organic compounds found in meteorites may provide useful diagnostic information concerning the environments and mechanisms that were responsible for their formation. Unfortunately, carbon has only two stable isotopes, making interpretation of such observations quite problematic. Chemical reactions can increase or decrease the C-13/C-12 ratio by various amounts, but the final ratio will depend on the total reaction pathway followed from the source carbon to the final product, a path not readily discernable after 4.5 billion years. In 1970 Libby showed that the C-13/C-12 ratios of terrestrial and meteoritic carbon were similar by comparing carbon from the Murchison meteorite to that of terrestrial sediments. More recent studies have shown that the C-13/C-12 ratio of the Earth and meteorites may be considerably enriched in C-13 compared to the ratio observed in the solar wind [2], possibly suggesting that carbon produced via ion-molecule reactions in cold dark clouds could be an important source of terrestrial and meteoritic carbon. However, meteoritic carbon has been subjected to parent body processing that could have resulted in significant changes to the C-13/C-12 ratio originally present while significant variation has been observed in the C-13/C-12 ratio of the same molecule extracted from different terrestrial sources. Again we must conclude that understanding the ratio found in meteorites may be difficult.

  2. Impacts of diffusive transport on carbonate mineral formation from magnesium silicate-CO2-water reactions.

    PubMed

    Giammar, Daniel E; Wang, Fei; Guo, Bin; Surface, J Andrew; Peters, Catherine A; Conradi, Mark S; Hayes, Sophia E

    2014-12-16

    Reactions of CO2 with magnesium silicate minerals to precipitate magnesium carbonates can result in stable carbon sequestration. This process can be employed in ex situ reactors or during geologic carbon sequestration in magnesium-rich formations. The reaction of aqueous CO2 with the magnesium silicate mineral forsterite was studied in systems with transport controlled by diffusion. The approach integrated bench-scale experiments, an in situ spectroscopic technique, and reactive transport modeling. Experiments were performed using a tube packed with forsterite and open at one end to a CO2-rich solution. The location and amounts of carbonate minerals that formed were determined by postexperiment characterization of the solids. Complementing this ex situ characterization, (13)C NMR spectroscopy tracked the inorganic carbon transport and speciation in situ. The data were compared with the output of reactive transport simulations that accounted for diffusive transport processes, aqueous speciation, and the forsterite dissolution rate. All three approaches found that the onset of magnesium carbonate precipitation was spatially localized about 1 cm from the opening of the forsterite bed. Magnesite was the dominant reaction product. Geochemical gradients that developed in the diffusion-limited zones led to locally supersaturated conditions at specific locations even while the volume-averaged properties of the system remained undersaturated. PMID:25420634

  3. An illustration of the complexity of continent formation

    NASA Technical Reports Server (NTRS)

    Burke, Kevin

    1988-01-01

    It was pointed out that a consensus may be emerging in crustal growth models, considering the clustering of most growth curves and their uncertainties. Curves most distant from this clustering represent models involving extensive recycling of continental material back into the mantle, but the author wondered if geochemical signatures for this would be recognizable considering the lack of evidence from seismic tomography for discrete mantle reservoirs, and the likelihood of core-mantle interaction based on recent high pressure experiments. Unreactivated Archean rocks represent only 2 percent of present continental area, and the author was uncomfortable about basing inferences on what the early Earth was like on such a small amount of information. He feels that the hypothesis of continental assembly that needs testing is that of banging together of island arcs, such as in Indonesia today. As an example of how complex this process can be, the author described the geology of the Caribbean arc system, which shows evidence for reversals of subduction polarity, numerous collisional events, and substantial strike-slip movements. It seemed unlikely to the author that Archean examples would have been less complicated.

  4. Interferogram formation in the presence of complex and large deformation

    USGS Publications Warehouse

    Yun, S.-H.; Zebker, H.; Segall, P.; Hooper, A.; Poland, M.

    2007-01-01

    Sierra Negra volcano in Isabela island, Gala??pagos, erupted from October 22 to October 30 in 2005. During the 8 days of eruption, the center of Sierra Negra's caldera subsided about 5.4 meters. Three hours prior to the onset of the eruption, an earthquake (Mw 5.4) occurred, near the caldera. Because of the large and complex phase gradient due to the huge subsidence and the earthquake, it is difficult to form an interferogram inside the caldera that spans the eruption. The deformation is so large and spatially variable that the approximations used in existing InSAR software (ROI, ROI_PAC, DORIS, GAMMA) cannot properly coregister SAR image pairs spanning the eruption. We have developed here a two-step algorithm that can form intra-caldera interferograms from these data. The first step involves a "rubber-sheeting" SAR image coregistration. In the second step we use range offset estimates to mitigate the steep phase gradient. Using this new algorithm, we retrieve an interferogram with the best coverage to date inside the caldera of Sierra Negra. Copyright 2007 by the American Geophysical Union.

  5. Oxidative peptide /and amide/ formation from Schiff base complexes

    NASA Technical Reports Server (NTRS)

    Strehler, B. L.; Li, M. P.; Martin, K.; Fliss, H.; Schmid, P.

    1982-01-01

    One hypothesis of the origin of pre-modern forms of life is that the original replicating molecules were specific polypeptides which acted as templates for the assembly of poly-Schiff bases complementary to the template, and that these polymers were then oxidized to peptide linkages, probably by photo-produced oxidants. A double cycle of such anti-parallel complementary replication would yield the original peptide polymer. If this model were valid, the Schiff base between an N-acyl alpha mino aldehyde and an amino acid should yield a dipeptide in aqueous solution in the presence of an appropriate oxidant. In the present study it is shown that the substituted dipeptide, N-acetyl-tyrosyl-tyrosine, is produced in high yield in aqueous solution at pH 9 through the action of H2O2 on the Schiff-base complex between N-acetyl-tyrosinal and tyrosine and that a great variety of N-acyl amino acids are formed from amino acids and aliphatic aldehydes under similar conditions.

  6. Interferogram formation in the presence of complex and large deformation

    NASA Astrophysics Data System (ADS)

    Yun, Sang-Ho; Zebker, Howard; Segall, Paul; Hooper, Andrew; Poland, Michael

    2007-06-01

    Sierra Negra volcano in Isabela island, Galápagos, erupted from October 22 to October 30 in 2005. During the 8 days of eruption, the center of Sierra Negra's caldera subsided about 5.4 meters. Three hours prior to the onset of the eruption, an earthquake (Mw 5.4) occurred, near the caldera. Because of the large and complex phase gradient due to the huge subsidence and the earthquake, it is difficult to form an interferogram inside the caldera that spans the eruption. The deformation is so large and spatially variable that the approximations used in existing InSAR software (ROI, ROI_PAC, DORIS, GAMMA) cannot properly coregister SAR image pairs spanning the eruption. We have developed here a two-step algorithm that can form intra-caldera interferograms from these data. The first step involves a ``rubber-sheeting'' SAR image coregistration. In the second step we use range offset estimates to mitigate the steep phase gradient. Using this new algorithm, we retrieve an interferogram with the best coverage to date inside the caldera of Sierra Negra.

  7. The adenylate cyclase receptor complex and aqueous humor formation.

    PubMed Central

    Caprioli, J.; Sears, M.

    1984-01-01

    The secretory tissue of the eye, the ciliary processes, contains an enzyme receptor complex, composed of membrane proteins, the catalytic moiety of the enzyme adenylate cyclase, a guanyl nucleotide regulatory protein (or N protein), and other features. The enzyme can be activated by well-known neurohumoral or humoral agents, catecholamines, glycoprotein hormones produced by the hypothalamic pituitary axis, and other related compounds, including placental gonadotropin, organic fluorides, and forskolin, a diterpene. These compounds cause the ciliary epithelia to produce cyclic AMP at an accelerated rate. Cyclic AMP, as a second messenger, causes, either directly or indirectly, a decrease in the net rate of aqueous humor inflow that may be modulated by cofactors. Clinical syndromes fit the experimental data so that an integrated explanation can be given for the reduced intraocular pressure witnessed under certain central nervous system and adrenergic influences. The molecular biology of this concept provides important leads for future investigations that bear directly both upon the regulation of intraocular pressure and upon glaucoma. Images FIG. 11 PMID:6093393

  8. Photo-induced hydrogen exchange reaction between methanol and glyoxal: formation of hydroxyketene.

    PubMed

    Mielke, Zofia; Mucha, Małgorzata; Bil, Andrzej; Golec, Barbara; Coussan, Stephane; Roubin, Pascale

    2008-08-25

    We study the structure and photochemistry of the glyoxal-methanol system (G-MeOH) by means of FTIR matrix isolation spectroscopy and ab initio calculations. The FTIR spectra show that the non-hydrogen-bonded complex, G-MeOH-1, is present in an inert environment of solid argon. MP2/aug-cc-pVDZ calculations indicate that G-MeOH-1 is the most stable complex among the five optimized structures. The interaction energy partitioned according to the symmetry-adapted perturbation theory (SAPT) scheme demonstrates that the dispersion energy gives a larger contribution to the stabilization of a non-hydrogen-bonded G-MeOH-1 complex than compared to the hydrogen-bonded ones. The irradiation of G-MeOH-1 with the filtered output of a mercury lamp (lambda>370 nm) leads to its photo-conversion into the hydroxyketene-methanol complex HK-MeOH-1. The identity of HK-MeOH-1 is confirmed by both FTIR spectroscopy and MP2/aug-cc-pVDZ calculations. An experiment with deuterated methanol (CH(3)OD) evidences that hydroxyketene is formed in a photo-induced hydrogen exchange reaction between glyoxal and methanol. The pathway for the photo-conversion of G-MeOH-1 to HK-MeOH-1 is studied by a coupled-cluster method [CR-CC(2,3)]. The calculations confirm our experimental findings that the reaction proceeds via hydrogen atom exchange between the OH group of methanol and CH group of glyoxal. PMID:18613199

  9. Effect of heterogeneous aqueous reactions on the secondary formation of inorganic aerosols during haze events

    SciTech Connect

    Quan, Jiannong; Liu, Yangang; Liu, Quan; Li, Xia; Gao, Yang; Jia, Xingcan; Sheng, Jiujiang

    2015-09-30

    In this study, the effect of heterogeneous aqueous reactions on the secondary formation of inorganic aerosols during haze events was investigated by analysis of comprehensive measurements of aerosol composition and concentrations [e.g., particular matters (PM2.5), nitrate (NO3), sulfate (SO4), ammonium (NH4)], gas-phase precursors [e.g., nitrogen oxides (NOx), sulfur dioxide (SO2), and ozone (O3)], and relevant meteorological parameters [e.g., visibility and relative humidity (RH)]. The measurements were conducted in Beijing, China from Sep. 07, 2012 to Jan. 16, 2013. The results show that the conversion ratios of N from NOx to nitrate (Nratio) and S from SO2 to sulfate (Sratio) both significantly increased in haze events, suggesting enhanced conversions from NOx and SO2 to their corresponding particle phases in the late haze period. Further analysis shows that Nratio and Sratio increased with increasing RH, with Nratio and Sratio being only 0.04 and 0.03, respectively, when RH < 40%, and increasing up to 0.16 and 0.12 when RH reached 60–80%, respectively. The enhanced conversion ratios of N and S in the late haze period is likely due to heterogeneous aqueous reactions, because solar radiation and thus the photochemical capacity are reduced by the increases in aerosols and RH. This point was further affirmed by the relationships of Nratio and Sratio to O3: the conversion ratios increase with decreasing O3 concentration when O3 concentration is lower than <15 ppb but increased with increasing O3 when O3 concentration is higher than 15 ppb. The results suggest that heterogeneous aqueous reactions likely changed aerosols and their precursors during the haze events: in the beginning of haze events, the precursor gases accumulated quickly

  10. Effect of heterogeneous aqueous reactions on the secondary formation of inorganic aerosols during haze events

    DOE PAGESBeta

    Quan, Jiannong; Liu, Yangang; Liu, Quan; Li, Xia; Gao, Yang; Jia, Xingcan; Sheng, Jiujiang

    2015-09-30

    In this study, the effect of heterogeneous aqueous reactions on the secondary formation of inorganic aerosols during haze events was investigated by analysis of comprehensive measurements of aerosol composition and concentrations [e.g., particular matters (PM2.5), nitrate (NO3), sulfate (SO4), ammonium (NH4)], gas-phase precursors [e.g., nitrogen oxides (NOx), sulfur dioxide (SO2), and ozone (O3)], and relevant meteorological parameters [e.g., visibility and relative humidity (RH)]. The measurements were conducted in Beijing, China from Sep. 07, 2012 to Jan. 16, 2013. The results show that the conversion ratios of N from NOx to nitrate (Nratio) and S from SO2 to sulfate (Sratio) bothmore » significantly increased in haze events, suggesting enhanced conversions from NOx and SO2 to their corresponding particle phases in the late haze period. Further analysis shows that Nratio and Sratio increased with increasing RH, with Nratio and Sratio being only 0.04 and 0.03, respectively, when RH < 40%, and increasing up to 0.16 and 0.12 when RH reached 60–80%, respectively. The enhanced conversion ratios of N and S in the late haze period is likely due to heterogeneous aqueous reactions, because solar radiation and thus the photochemical capacity are reduced by the increases in aerosols and RH. This point was further affirmed by the relationships of Nratio and Sratio to O3: the conversion ratios increase with decreasing O3 concentration when O3 concentration is lower than <15 ppb but increased with increasing O3 when O3 concentration is higher than 15 ppb. The results suggest that heterogeneous aqueous reactions likely changed aerosols and their precursors during the haze events: in the beginning of haze events, the precursor gases accumulated quickly due to high emission and low reaction rate; the occurrence of heterogeneous aqueous reactions in the late haze period, together with the accumulated high concentrations of precursor gases such as SO2 and NOx, accelerated the

  11. Photo-induced reactions in the ion-molecule complex Mg+-OCNC2H5

    NASA Astrophysics Data System (ADS)

    Sun, Ju-Long; Liu, Haichuan; Han, Ke-Li; Yang, Shihe

    2003-06-01

    Ion-molecule complexes of magnesium cation with ethyl isocyanate were produced in a laser-ablation supersonic expansion nozzle source. Photo-induced reactions in the 1:1 complexes have been studied in the spectral range of 230-410 nm. Photodissociation mass spectrometry revealed the persistent product Mg+ from nonreactive quenching throughout the entire wavelength range. As for the reactive channels, the photoproducts, Mg+OCN and C2H5+, were produced only in the blue absorption band of the complex with low yields. The action spectrum of Mg+(OCNC2H5) consists of two pronounced peaks on the red and blue sides of the Mg+ 32P←32S atomic transition. The ground state geometry of Mg+-OCNC2H5 was fully optimized at B3LYP/6-31+G** level by using GAUSSIAN 98 package. The calculated absorption spectrum of the complex using the optimized structure of its ground state agrees well with the observed action spectrum. Photofragment branching fractions of the products are almost independent of the photolysis photon energy for the 3Px,y,z excitations. The very low branching ratio of reactive products to nonreactive fragment suggests that evaporation is the main relaxation pathway in the photo-induced reactions of Mg+(OCNC2H5).

  12. Chemically Activated Formation of Organic Acids in Reactions of the Criegee Intermediate with Aldehydes and Ketones

    SciTech Connect

    Jalan, Amrit; Allen, Joshua W.; Green, William H.

    2013-08-08

    Reactions of the Criegee intermediate (CI, .CH2OO.) are important in atmospheric ozonolysis models. In this work, we compute the rates for reactions between .CH2OO. and HCHO, CH3CHO and CH3COCH3 leading to the formation of secondary ozonides (SOZ) and organic acids. Relative to infinitely separated reactants, the SOZ in all three cases is found to be 48–51 kcal mol-1 lower in energy, formed via 1,3- cycloaddition of .CH2OO. across the CQO bond. The lowest energy pathway found for SOZ decomposition is intramolecular disproportionation of the singlet biradical intermediate formed from cleavage of the O–O bond to form hydroxyalkyl esters. These hydroxyalkyl esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO o CH3CHO o CH3COCH3 (the highest yield being 10-4 times lower than the initial .CH2OO. concentration). At low pressures, chemically activated formation of organic acids (formic acid in the case of HCHO and CH3COCH3, formic and acetic acid in the case of CH3CHO) was found to be the major product channel in agreement with recent direct measurements. Collisional energy transfer parameters and the barrier heights for SOZ reactions were found to be the most sensitive parameters determining SOZ and organic acid yield.

  13. Formation rates of complex organics in UV irradiated CH_3OH-rich ices. I. Experiments

    NASA Astrophysics Data System (ADS)

    Öberg, K. I.; Garrod, R. T.; van Dishoeck, E. F.; Linnartz, H.

    2009-09-01

    Context: Gas-phase complex organic molecules are commonly detected in the warm inner regions of protostellar envelopes, so-called hot cores. Recent models show that photochemistry in ices followed by desorption may explain the observed abundances. There is, however, a general lack of quantitative data on UV-induced complex chemistry in ices. Aims: This study aims to experimentally quantify the UV-induced production rates of complex organics in CH3OH-rich ices under a variety of astrophysically relevant conditions. Methods: The ices are irradiated with a broad-band UV hydrogen microwave-discharge lamp under ultra-high vacuum conditions, at 20-70 K, and then heated to 200 K. The reaction products are identified by reflection-absorption infrared spectroscopy (RAIRS) and temperature programmed desorption (TPD), through comparison with RAIRS and TPD curves of pure complex species, and through the observed effects of isotopic substitution and enhancement of specific functional groups, such as CH3, in the ice. Results: Complex organics are readily formed in all experiments, both during irradiation and during the slow warm-up of the ices after the UV lamp is turned off. The relative abundances of photoproducts depend on the UV fluence, the ice temperature, and whether pure CH3OH ice or CH3OH:CH4/CO ice mixtures are used. C2H6, CH3CHO, CH3CH2OH, CH3OCH3, HCOOCH3, HOCH2CHO and (CH2OH)2 are all detected in at least one experiment. Varying the ice thickness and the UV flux does not affect the chemistry. The derived product-formation yields and their dependences on different experimental parameters, such as the initial ice composition, are used to estimate the CH3OH photodissociation branching ratios in ice and the relative diffusion barriers of the formed radicals. At 20 K, the pure CH3OH photodesorption yield is 2.1(±1.0)×10-3 per incident UV photon, the photo-destruction cross section 2.6(±0.9)×10-18 cm^2. Conclusions: Photochemistry in CH3OH ices is efficient enough to

  14. Phosphorylation-dependent formation of a quaternary complex at the c-fos SRE.

    PubMed Central

    Gille, H; Kortenjann, M; Strahl, T; Shaw, P E

    1996-01-01

    The rapid and transient induction of the human proto-oncogene c-fos in response to a variety of stimuli depends on the serum responses element (SRE). In vivo footprinting experiments show that this promoter element is bound by a multicomponent complex including the serum response factor (SRF) and a ternary complex factor such as Elk-1. SRF is thought to recruit a ternary complex factor monomer into an asymmetric complex. In this report, we describe a quaternary complex over the SRE which, in addition to an SRF dimer, contains two Elk-1 molecules. Its formation at the SRE is strictly dependent on phosphorylation of S-383 in the Elk-1 regulatory domain and appears to involve a weak intermolecular association between the two Elk-1 molecules. The influence of mutations in Elk-1 on quaternary complex formation in vitro correlates with their effect on the induction of c-fos reporter expression in response to mitogenic stimuli in vivo. PMID:8622654

  15. DHA- Rich Fish Oil Improves Complex Reaction Time in Female Elite Soccer Players

    PubMed Central

    Guzmán, José F.; Esteve, Hector; Pablos, Carlos; Pablos, Ana; Blasco, Cristina; Villegas, José A.

    2011-01-01

    Omega-3 fatty acids (n-3) has shown to improve neuromotor function. This study examined the effects of docosahexaenoic acid (DHA) on complex reaction time, precision and efficiency, in female elite soccer players. 24 players from two Spanish female soccer Super League teams were randomly selected and assigned to two experimental groups, then administered, in a double-blind manner, 3.5 g·day-1 of either DHA-rich fish oil (FO =12) or olive oil (OO = 12) over 4 weeks of training. Two measurements (pre- and post-treatment) of complex reaction time and precision were taken. Participants had to press different buttons and pedals with left and right hands and feet, or stop responding, according to visual and auditory stimuli. Multivariate analysis of variance displayed an interaction between supplement administration (pre/post) and experimental group (FO/OO) on complex reaction time (FO pre = 0.713 ± 0.142 ms, FO post = 0.623 ± 0.109 ms, OO pre = 0.682 ± 1.132 ms, OO post = 0.715 ± 0.159 ms; p = 0.004) and efficiency (FO pre = 40.88 ± 17.41, FO post = 57.12 ± 11.05, OO pre = 49.52 ± 14.63, OO post = 49. 50 ± 11.01; p = 0.003). It was concluded that after 4 weeks of supplementation with FO, there was a significant improvement in the neuromotor function of female elite soccer players. Key points The results obtained from the study suggest that supplementation with DHA produced perceptual-motor benefits in female elite athletes. DHA could be a beneficial supplement in sports where decision making and reaction time efficiency are of importance. PMID:24149875

  16. Ligand Exchange Reaction of Au(I) R-N-Heterocyclic Carbene Complexes with Cysteine.

    PubMed

    Dos Santos, H F; Vieira, M A; Sánchez Delgado, G Y; Paschoal, D

    2016-04-14

    The chemotherapy with gold complexes has been attempted since the 90s after the clinical success of auranofin, a gold(I) coordination complex. Currently, the organometallics compounds have shown promise in cancer therapy, mainly in those complexes containing N-heterocylic carbenes (NHC) as a ligand. The present study shows a kinetic analysis of the reaction of six alkyl-substituted NHC with cysteine (Cys), which is taken as an important bionucleophile representative. The first and second ligand exchange processes were analyzed with the complete description of the mechanism and energy profiles. For the first reaction step, which is the rate-limiting step of the whole substitution reaction, the activation enthalpy follows the order 1/Me2 < 2/Me,Et < 4/n-Bu2 < 3/i-Pr2 < 6/Cy2 < 5/t-Bu2, which is fully explained by steric and electronic features. From a steric point of view, the previous reactivity order is correlated with the r(Au-S) calculated for the transition state structures where S is the sulfur ligand from the Cys entering group. This means that longer r(Au-S) leads to higher activation enthalpy and is consistent with the effectiveness of gold shielding from nucleophile attack by bulkier alkyl-substituted NHC ligand. When electronic effect was addressed we found that higher activation barrier was predicted for strongly electron-donating NHC ligand, represented by the eigenvalue of σ-HOMO orbital of the free ligands. The molecular interpretation of the electronic effects is that strong donating NHC forms strong metal-ligand bond. For the second reaction step, similar structure-reactivity relationships were obtained, however the activation energies are less sensitive to the structure. PMID:27010796

  17. Formation and Self-assembly of Gold Nanoplates through an Interfacial Reaction for Surface-Enhanced Raman Scattering.

    PubMed

    Ma, Ying; Yung, Lin-Yue Lanry

    2016-06-22

    3D hierarchical architectures assembled from individual particles have attracted great interest because they displayed novel properties from the individual building blocks as well as their complex structures. Here we present a new strategy to form 3D hierarchical gold (Au) nanostructures via an interfacial reduction reaction. An aniline (ANI) derivative, N-(3-amidino)-aniline (NAAN), and HAuCl4 were separately dissolved in toluene and water to form an organic/water interface. Au nanoplates formed at the interface and subsequently moved to the aqueous phase. As a capping agent for the nanoplate formation, the oxidized NAAN, i.e., poly(N-(3-amidino)-aniline) (PNAAN), also facilitated the self-assembly of Au nanoplates into 3D hierarchical Au nanoflowers (AuNFs) through π-π stacking. The individual AuNF exhibited good surface-enhanced Raman scattering (SERS) response both in enhancement factor and reproducibility because it integrates the SERS enhancement effects of individual Au nanoplates and their hierarchical structures. This is the first report depicting the one-pot formation and self-assembly of Au nanoplates into 3D organized hierarchical nanostructures through the molecular interaction of conducting polymer. PMID:27276116

  18. Aerobic oxidation reactions catalyzed by vanadium complexes of bis(phenolate) ligands.

    PubMed

    Zhang, Guoqi; Scott, Brian L; Wu, Ruilian; Silks, L A Pete; Hanson, Susan K

    2012-07-01

    Vanadium(V) complexes of the tridentate bis(phenolate)pyridine ligand H(2)BPP (H(2)BPP = 2,6-(HOC(6)H(2)-2,4-(t)Bu(2))(2)NC(5)H(3)) and the bis(phenolate)amine ligand H(2)BPA (H(2)BPA = N,N-bis(2-hydroxy-4,5-dimethylbenzyl)propylamine) have been synthesized and characterized. The ability of the complexes to mediate the oxidative C-C bond cleavage of pinacol was tested. Reaction of the complex (BPP)V(V)(O)(O(i)Pr) (4) with pinacol afforded the monomeric vanadium(IV) product (BPP)V(IV)(O)(HO(i)Pr) (6) and acetone. Vanadium(IV) complex 6 was oxidized rapidly by air at room temperature in the presence of NEt(3), yielding the vanadium(V) cis-dioxo complex [(BPP)V(V)(O)(2)]HNEt(3). Complex (BPA)V(V)(O)(O(i)Pr) (5) reacted with pinacol at room temperature, to afford acetone and the vanadium(IV) dimer [(BPA)V(IV)(O)(HO(i)Pr)](2). Complexes 4 and 5 were evaluated as catalysts for the aerobic oxidation of 4-methoxybenzyl alcohol and arylglycerol β-aryl ether lignin model compounds. Although both 4 and 5 catalyzed the aerobic oxidation of 4-methoxybenzyl alcohol, complex 4 was found to be a more active and robust catalyst for oxidation of the lignin model compounds. The catalytic activities and selectivities of the bis(phenolate) complexes are compared to previously reported catalysts. PMID:22708725

  19. Native Mass Spectrometry Characterizes the Photosynthetic Reaction Center Complex from the Purple Bacterium Rhodobacter sphaeroides

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Harrington, Lucas B.; Lu, Yue; Prado, Mindy; Saer, Rafael; Rempel, Don; Blankenship, Robert E.; Gross, Michael L.

    2016-08-01

    Native mass spectrometry (MS) is an emerging approach to study protein complexes in their near-native states and to elucidate their stoichiometry and topology. Here, we report a native MS study of the membrane-embedded reaction center (RC) protein complex from the purple photosynthetic bacterium Rhodobacter sphaeroides. The membrane-embedded RC protein complex is stabilized by detergent micelles in aqueous solution, directly introduced into a mass spectrometer by nano-electrospray (nESI), and freed of detergents and dissociated in the gas phase by collisional activation. As the collision energy is increased, the chlorophyll pigments are gradually released from the RC complex, suggesting that native MS introduces a near-native structure that continues to bind pigments. Two bacteriochlorophyll a pigments remain tightly bound to the RC protein at the highest collision energy. The order of pigment release and their resistance to release by gas-phase activation indicates the strength of pigment interaction in the RC complex. This investigation sets the stage for future native MS studies of membrane-embedded photosynthetic pigment-protein and related complexes.

  20. Copper complexes as catalyst precursors in the electrochemical hydrogen evolution reaction.

    PubMed

    Kügler, Merle; Scholz, Julius; Kronz, Andreas; Siewert, Inke

    2016-04-28

    Herein, we report the synthesis and species distribution of copper(ii) complexes based on two different ligand scaffolds and the application of the two complexes in the electrochemical proton reduction catalysis. The ligands bind to one or two copper(II) ions and the pH-dependent mono/dinuclear equilibrium depends on the steric bulk of the ligands. The two water soluble copper(II) complexes were investigated for their activities in the electrochemical hydrogen evolution reaction (HER). In both complexes the copper(ii) ions have a N4-coordination environment composed of N-heterocycles, although in different coordination geometries (SPY-5 and TBPY-5). The solutions of the complexes were highly active catalysts in water at acidic pH but the complexes decompose under catalytic conditions. They act as precursors for highly active copper(0) and Cu2O deposits at the electrode surface, which are in turn the active catalysts. The absence or presence of the ligands has neither an influence on the catalytic activity of the solutions nor an influence on the activity of the deposit formed during controlled potential electrolysis. Finally, we can draw some conclusions on the stability of copper catalysts in the aqueous electrochemical HER. PMID:26986849

  1. O2 reduction reaction by biologically relevant anionic ligand bound iron porphyrin complexes.

    PubMed

    Samanta, Subhra; Das, Pradip Kumar; Chatterjee, Sudipta; Sengupta, Kushal; Mondal, Biswajit; Dey, Abhishek

    2013-11-18

    Iron porphyrin complex with a covalently attached thiolate ligand and another with a covalently attached phenolate ligand has been synthesized. The thiolate bound complex shows spectroscopic features characteristic of P450, including the hallmark absorption spectrum of the CO adduct. Electrocatalytic O2 reduction by this complex, which bears a terminal alkyne group, is investigated by both physiabsorbing on graphite surfaces (fast electron transfer rates) and covalent attachment to azide terminated self-assembled monolayer (physiologically relevant electron transfer rates) using the terminal alkyne group. Analysis of the steady state electrochemical kinetics reveals that this catalyst can selectively reduce O2 to H2O with a second-order k(cat.) ~10(7) M(-1 )s(-1) at pH 7. The analogous phenolate bound iron porphyrin complex reduces O2 with a second-order rate constant of 10(5) M(-1) s(-1) under the same conditions. The anionic ligand bound iron porphyrin complexes catalyze oxygen reduction reactions faster than any known synthetic heme porphyrin analogues. The kinetic parameters of O2 reduction of the synthetic thiolate bound complex, which is devoid of any second sphere effects present in protein active sites, provide fundamental insight into the role of the protein environment in tuning the reactivity of thiolate bound iron porphyrin containing metalloenzymes. PMID:24171513

  2. ESI-MS and theoretical study on the coordination structures and reaction modes of the diperoxovanadate complexes containing histidine-like ligands

    NASA Astrophysics Data System (ADS)

    Yu, Xian-Yong; Xu, Xin; Chen, Zhong

    2008-01-01

    In order to study the coordination structures and the reaction modes of diperoxovanadate complexes in the gas phase, the interaction between K3[OV(O2)2(C2O4)]·H2O and a series of histidine-like ligands has been investigated by the combination of the electrospray ionization-mass spectrometry (ESI-MS) and the density functional theory (DFT) calculations. The experimental results proved the formation of both [OV(O2)2L]- (L = all histidine-like ligands) and [OV(O2)2L'2]- (L' = histidine and carnosine only) species. DFT calculations at the level of B3LYP/6-31+G* showed that [OV(O2)2L'2]- is a hexa-coordinated complex, instead of a hepta-coordinated complex as proposed before. The unique coordination mode in the gas phase is for one ligand to bind to the oxygen atoms via hydrogen binding, rather than both ligands to the metal center. The L'2 dimer formation and the maintenance of the hydrogen bonding within the dimer during the complex formation are two important factors that enhance the abundance of the [OV(O2)2L'2]- species. The calculated bonding enthalpy and free energy changes provided an explanation on the reaction modes of the interaction systems, in agreement with the observations of the ESI-MS experiments.

  3. Evidence of iron(III)-oxalato complex formation in aqueous solution from x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Magini, Mauro

    1981-02-01

    An aqueous solution of ferric ammonium oxalate has been examined to provide direct experimental evidence of complex formation between iron(III) and a typical organic complexing ligand. The radial distribution function as well as analysis of the structure function lead to the conclusion that the dominant species present in solution is the trioxalato-iron(III) complex in which each oxalate ion occupies two corners of a distorted octahedron around the Fe 3+ ions.

  4. Kinetics and Thermochemistry of ClCO Formation from the Cl + CO Association Reaction

    NASA Technical Reports Server (NTRS)

    Nicovich, J. M.; Kreutter, K. D.; Wine, P. H.

    1997-01-01

    Laser flash photolysis of Cl2/CO/M mixtures (M = N2, CO, Ar, CO2) has been employed in conjunction with Cl((sup 2)P(sub J)) detection by time-resolved resonance fluorescence spectroscopy to investigate equilibration kinetics in the reactions Cl((sup 2)P(sub J)) + CO ClCO as a function of temperature (185-260 K) and pressure (14-200 Torr). The association and dissociation reactions are found to be in the low-pressure limit over the range of experimental conditions investigated. In N2 and/or CO buffer gases, the temperature dependences of the ClCO formation and dissociation reaction rate constants are described by the Arrhenius expressions k(sub 1) = (1.05 +/- 0.36) x 10(exp -34) exp[(810 +/- 70)/T] cm(exp 6)/molecules(exp 2).s and k(sub -1) = (4.1 +/- 3.1) x 10(exp -10) exp[(-2960 +/- 60)/T]cu cm/(molecule.s) (errors are 2 sigma). Second- and third-law analyses of the temperature dependence of the equilbrium constant (k/k-1) lead to the following thermodynamic parameters for the association reaction: Delta-H(sub 298) = -7.7 +/- 0.6 kcal/mol, Delta-H(sub 0) = -6.9 +/- 0.7 kcal/mol, Delta-S(sub 298) = -23.8 +/- 2.0 cal/mole.K, Delta-H(sub f,298)(ClCO) = 5.2 +/- 0.6 kcal/mol (errors are 2 sigma). The results repported in this study significantly reduce the uncertainties in all reported kinetic and thermodynamic parameters.

  5. Photoinduced electron-transfer reactions of poly(pyridine)ruthenium(II) complexes with europium(III/II) cryptates

    SciTech Connect

    Sabbatini, N.; Dellonte, S.; Bonazzi, A.; Ciano, M.; Balzani, V.

    1986-05-21

    Rate constants for electron-transfer reactions between poly(pyridine)ruthenium(II) (RuL/sub 3//sup 2 +/) excited states and the europium cryptates (Eu contains 2.2.1)/sup 3 +/ and (Eu contains 2.2.1)/sup 2 +/ have been measured in aqueous solution by luminescence quenching techniques. The rate constants for a few electron-transfer back-reactions between the photogenerated RuL/sub 3//sup 3 +/ and (Eu contains 2.2.1)/sup 2 +/ or RuL/sub 3//sup +/ and (Eu contains 2.2.1)/sup 3 +/ species have also been measured by flash photolysis experiments. The results obtained have been elaborated and discussed on the basis of current electron-transfer theories. Comparison of the results obtained with those previously available for the Eu/sub aq//sup 3 +/ and Eu/sub aq//sup 2 +/ ions shows that cryptation decreases the intrinsic barrier and/or increases the adiabaticity coefficient of the electron-transfer reaction. A plot of the rate constants vs. the free energy changes of the electron-transfer processes shows that the data concerning (Eu contains 2.2.1)/sup 3 +/ reduction do not correlate with those concerning (Eu contains 2.2.1)/sup 2 +/ oxidation. Possible reasons for this asymmetric behavior include (i) different shapes of the potential energy wells for (Eu contains 2.2.1)/sup 3 +/ and (Eu contains 2.2.1)/sup 2 +/, (ii) different work terms for the formation of the precursor complex, and (iii) different distances of closest approach of (Eu contains 2.2.1)/sup 3 +/ and (Eu contains 2.2.1)/sup 2 +/ with the hydrophobic RuL/sub 3//sup n+/ reaction partners.

  6. Cellular consequences of copper complexes used to catalyze bioorthogonal click reactions.

    PubMed

    Kennedy, David C; McKay, Craig S; Legault, Marc C B; Danielson, Dana C; Blake, Jessie A; Pegoraro, Adrian F; Stolow, Albert; Mester, Zoltan; Pezacki, John Paul

    2011-11-01

    Copper toxicity is a critical issue in the development of copper-based catalysts for copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions for applications in living systems. The effects and related toxicity of copper on mammalian cells are dependent on the ligand environment. Copper complexes can be highly toxic, can induce changes in cellular metabolism, and can be rapidly taken up by cells, all of which can affect their ability to function as catalysts for CuAAC in living systems. Herein, we have evaluated the effects of a number of copper complexes that are typically used to catalyze CuAAC reactions on four human cell lines by measuring mitochondrial activity based on the metabolism of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to study toxicity, inductively coupled plasma mass spectrometry to study cellular uptake, and coherent anti-Stokes Raman scattering (CARS) microscopy to study effects on lipid metabolism. We find that ligand environment around copper influences all three parameters. Interestingly, for the Cu(II)-bis-L-histidine complex (Cu(his)(2)), cellular uptake and metabolic changes are observed with no toxicity after 72 h at micromolar concentrations. Furthermore, we show that under conditions where other copper complexes kill human hepatoma cells, Cu(I)-L-histidine is an effective catalyst for CuAAC labeling of live cells following metabolic incorporation of an alkyne-labeled sugar (Ac(4)ManNAl) into glycosylated proteins expressed on the cell surface. This result suggests that Cu(his)(2) or derivatives thereof have potential for in vivo applications where toxicity as well as catalytic activity are critical factors for successful bioconjugation reactions. PMID:21970470

  7. 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.

  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. Positronium formation studies in solid molecular complexes: Triphenylphosphine oxide-triphenylmethanol

    NASA Astrophysics Data System (ADS)

    Oliveira, F. C.; Denadai, A. M. L.; Fulgêncio, F. H.; Magalhães, W. F.; Alcântara, A. F. C.; Windmöller, D.; Machado, J. C.

    2012-06-01

    Positronium formation in triphenylphosphine oxide (TPPO), triphenylmethanol (TPM), and systems [TPPO(1-X)ṡTPMX] has been studied. The low probability of positronium formation in complex [TPPO0.5ṡTPM0.5] was attributed to strong hydrogen bond and sixfold phenyl embrace interactions. These strong interactions in complex reduce the possibility of the n- and π-electrons to interact with positrons on the spur and consequently, the probability of positronium formation is lower. The τ3 parameter and free volume (correlated to τ3) were also sensitive to the formation of hydrogen bonds and sixfold phenyl embrace interactions within the complex. For physical mixture the positron annihilation parameters remained unchanged throughout the composition range.

  10. Complex dynamic behavior in the bromate-oxalic acid-acetone-Mn(II) oscillating reaction in a continuous stirred tank reactor (CSTR)

    NASA Astrophysics Data System (ADS)

    Silva, Lucyane C.; Faria, Roberto B.

    2007-05-01

    The oscillating reaction bromate-oxalic acid-acetone-Mn(II)-sulfuric acid was observed for the first time in a CSTR at 20 °C. Depending on the bromate concentrations and flow rate, the system showed large amplitude oscillations, two kinds of mixed mode oscillations, quasiperiodicity and bursts of large amplitude oscillations, all mapped in a phase diagram. More complex behavior was favored at low bromate concentrations. The system without acetone was discovered to oscillate too, but the more complex patterns were not seen, indicating that acetone is implied in their formation.

  11. Reactions between vanadium ions and biogenic reductants of tunicates: Spectroscopic probing for complexation and redox products in vitro

    SciTech Connect

    Ryan, D.E.; Grant, K.B.; Nakanishi, K.

    1996-07-02

    Several species of marine tunicates store oxygen-sensitive V{sup III} in blood cells. A sensitive colorimetric V{sup III} assay was used t survey the leading candidates for the native reducing agent of vanadate in tunicates (i.e., An-type tunichromes, glutathione, NADPH, and H{sub 2}S) in reactions with V{sup V} or V{sup IV} ions under anaerobic, aqueous conditions at acidic or neutral pH. Except for the case of An-1 and V{sup V} ions in pH 7 buffer, the assay results for the biogenic reducing agents clearly showed that appreciable quantities of V{sup III} products were not generated under the conditions tested. Therefore, the assay results place new limits on hypothetical mechanisms of V{sup III} formation in vivo. For reactions between An-1 and V{sup V} ions in pH 7 buffer, low levels of V{sup III} products could not be ruled out because of an interfering peak in the colorimetric assays. For similar reactions between V{sup V} ions and An-1, or an An-1,2 mixture, in mildly to moderately basic media, the product mixtures precipitated as greenish black solids. Analyses of the precipitated V/An mixtures using vanadium K-edge X-ray absorption spectroscopy (XAS) showed that the major products were tris(catecholate)-type V{sup IV} complexes (65 {plus_minus} 6%) and bis(catecholate)-type V{sup IV}O complexes (20 {plus_minus} 4%). XAS analysis of the V/An-1 product mixture also provided evidence of a minor V{sup III} component (9 {plus_minus} 5% of total V), notable for possible relevance to tunicate biochemistry. The combined results of XAS studies, spectrophotometric studies, and EPR studies consistently establish that reactions between tunichromes (Mm-1 or An-1) and V{sup V} ions generate predominantly V{sup IV}-tunichrome complexes in neutral to moderately basic aqueous media. 53 refs., 4 figs., 3 tabs.

  12. The chitosan-gelatin (bio)polyelectrolyte complexes formation in an acidic medium.

    PubMed

    Voron'ko, Nicolay G; Derkach, Svetlana R; Kuchina, Yuliya A; Sokolan, Nina I

    2016-03-15

    The interaction of cationic polysaccharide chitosan and gelatin accompanied by the stoichiometric (bio)polyelectrolyte complexes formation has been studied by the methods of capillary viscometry, UV and FTIR spectroscopy and dispersion of light scattering. Complexes were formed in the aqueous phase, with pH being less than the isoelectric point of gelatin (pIgel). The particle size of the disperse phase increases along with the growth of the relative viscosity in comparison with sols of the individual components-polysaccharide and gelatin. Possible models and mechanism of (bio)polyelectrolyte complexes formation have been discussed. It was shown that the complex formation takes place not only due to the hydrogen bonds, but also due to the electrostatic interactions between the positively charged amino-groups of chitosan and negatively charged amino acid residues (glutamic Glu and aspartic Asp acids) of gelatin. PMID:26794762

  13. Density functional computational studies on the glucose and glycine Maillard reaction: Formation of the Amadori rearrangement products

    NASA Astrophysics Data System (ADS)

    Jalbout, Abraham F.; Roy, Amlan K.; Shipar, Abul Haider; Ahmed, M. Samsuddin

    Theoretical energy changes of various intermediates leading to the formation of the Amadori rearrangement products (ARPs) under different mechanistic assumptions have been calculated, by using open chain glucose (O-Glu)/closed chain glucose (A-Glu and B-Glu) and glycine (Gly) as a model for the Maillard reaction. Density functional theory (DFT) computations have been applied on the proposed mechanisms under different pH conditions. Thus, the possibility of the formation of different compounds and electronic energy changes for different steps in the proposed mechanisms has been evaluated. B-Glu has been found to be more efficient than A-Glu, and A-Glu has been found more efficient than O-Glu in the reaction. The reaction under basic condition is the most favorable for the formation of ARPs. Other reaction pathways have been computed and discussed in this work.0

  14. Complexity of Central Processing in Simple and Choice Multilimb Reaction-Time Tasks

    PubMed Central

    Boisgontier, Matthieu P.; Wittenberg, George F.; Fujiyama, Hakuei; Levin, Oron; Swinnen, Stephan P.

    2014-01-01

    The default mode of the motor system is a coupling between limbs. However, in some movements, a decoupling is required and thus calls for selection and facilitation/inhibition processes. Here, we investigate the relative contribution of recruitment versus selection processes to the overall processing complexity. To this aim we proposed a new multilimb reaction-time task (MUL-RT). Simple, choice and normalized (choice minus simple) RT were analysed together with error rates in thirty-six young adults for 15 coordination modes including all possible configuration of limb recruitment. Simple and normalized RTs were respectively assumed to be indicative of the recruitment and selection processes. Results supported a model of coupling/decoupling interactions respectively reporting weak, intermediate and strong interaction for selecting diagonal, ipsilateral and homologous limbs. Movement laterality (left vs. right) had no effect on selection complexity, whereas selecting upper limbs was less challenging than selecting lower limbs. Results in the different coordination modes suggested that recruitment complexity decreased as follows: 3 limbs = 4 limbs>2 limbs (homologous, ipsilateral and diagonal)>1 limb, and selection complexity as follows: 2 diagonal limbs>3 limbs>2 ipsilateral limbs>1 limb = 2 homologous limbs>4 limbs. Based on these ordinal scales of recruitment and selection complexity, we extrapolated the overall processing complexity of the simple and choice MUL-RT. This method was efficient in reproducing the absolute results we obtained on a ratio scale (ms) and demonstrated that processing complexity in simple RT was mainly governed by the ‘recruitment principle’ (the more limbs recruited the lower the performance), whereas contributions of recruitment and ‘selection principle’ (nature of the coordination determines performance) to overall processing complexity were similar in choice RT. PMID:24587371

  15. Novel access to azaphosphiridine complexes and first applications using Brønsted acid-induced ring expansion reactions.

    PubMed

    Fankel, Stefan; Helten, Holger; von Frantzius, Gerd; Schnakenburg, Gregor; Daniels, Jörg; Chu, Victoria; Müller, Christina; Streubel, Rainer

    2010-04-14

    Synthesis of azaphosphiridine complexes 3a-e was achieved via thermal group transfer reaction using 2H-azaphosphirene complex 1 and N-methyl C-aryl imines 2a-e (i) or via reaction of transient Li/Cl phosphinidenoid complex 5 (prepared from dichloro(organo)phosphane complex 4) using 2a-c (ii), respectively. Reaction of complexes 3a,d and trifluoromethane sulfonic acid in the presence of dimethyl cyanamide led to a highly bond- and regioselective ring expansion yielding 1,3,4sigma3lambda3-diazaphosphol-2-ene complexes 8a,d after deprotonation with NEt3. 31P NMR reaction monitoring revealed that protonation of complex 3a yields the azaphosphiridinium complex 6a, unambiguously identified by NMR spectroscopy at low temperature. All isolated products were characterized by multinuclear NMR spectroscopy, IR and UV/Vis (for 3a,d, 6a, 8a,d), MS and single-crystal X-ray crystallography in the cases of complexes 3b-d, 8a and 8d. DFT studies on the reaction mechanism and compliance constants of the model complex of 6a are presented. PMID:20379537

  16. Cationic cluster formation versus disproportionation of low-valent indium and gallium complexes of 2,2'-bipyridine

    PubMed Central

    Lichtenthaler, Martin R.; Stahl, Florian; Kratzert, Daniel; Heidinger, Lorenz; Schleicher, Erik; Hamann, Julian; Himmel, Daniel; Weber, Stefan; Krossing, Ingo

    2015-01-01

    Group 13 MI compounds often disproportionate into M0 and MIII. Here, however, we show that the reaction of the MI salt of the weakly coordinating alkoxyaluminate [GaI(C6H5F)2]+[Al(ORF)4]− (RF=C(CF3)3) with 2,2'-bipyridine (bipy) yields the paramagnetic and distorted octahedral [Ga(bipy)3]2+•{[Al(ORF)4]−}2 complex salt. While the latter appears to be a GaII compound, both, EPR and DFT investigations assign a ligand-centred [GaIII{(bipy)3}•]2+ radical dication. Surprisingly, the application of the heavier homologue [InI(C6H5F)2]+[Al(ORF)4]− leads to aggregation and formation of the homonuclear cationic triangular and rhombic [In3(bipy)6]3+, [In3(bipy)5]3+ and [In4(bipy)6]4+ metal atom clusters. Typically, such clusters are formed under strongly reductive conditions. Analysing the unexpected redox-neutral cationic cluster formation, DFT studies suggest a stepwise formation of the clusters, possibly via their triplet state and further investigations attribute the overall driving force of the reactions to the strong In−In bonds and the high lattice enthalpies of the resultant ligand stabilized [M3]3+{[Al(ORF)4]−}3 and [M4]4+{[Al(ORF)4]−}4 salts. PMID:26478464

  17. Short relaxation times but long transient times in both simple and complex reaction networks.

    PubMed

    Henry, Adrien; Martin, Olivier C

    2016-07-01

    When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time τ, i.e. the inverse of the decay rate, is the longest characteristic time in the system. However, that need not be true, other times such as the lifetime of an infinitesimal perturbation can be much longer. In the present work, we demonstrate that this paradoxical property can arise even in quite simple systems such as a linear chain of reactions obeying mass action (MA) kinetics. By mathematical analysis of simple reaction networks, we pin-point the reason why the standard relaxation time does not provide relevant information on the potentially long transient times of typical infinitesimal perturbations. Overall, we consider four characteristic times and study their behaviour in both simple linear chains and in more complex reaction networks taken from the publicly available database 'Biomodels'. In all these systems, whether involving MA rates, Michaelis-Menten reversible kinetics, or phenomenological laws for reaction rates, we find that the characteristic times corresponding to lifetimes of tracers and of concentration perturbations can be significantly longer than τ. PMID:27411726

  18. Short relaxation times but long transient times in both simple and complex reaction networks

    PubMed Central

    Henry, Adrien; Martin, Olivier C.

    2016-01-01

    When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time τ, i.e. the inverse of the decay rate, is the longest characteristic time in the system. However, that need not be true, other times such as the lifetime of an infinitesimal perturbation can be much longer. In the present work, we demonstrate that this paradoxical property can arise even in quite simple systems such as a linear chain of reactions obeying mass action (MA) kinetics. By mathematical analysis of simple reaction networks, we pin-point the reason why the standard relaxation time does not provide relevant information on the potentially long transient times of typical infinitesimal perturbations. Overall, we consider four characteristic times and study their behaviour in both simple linear chains and in more complex reaction networks taken from the publicly available database ‘Biomodels’. In all these systems, whether involving MA rates, Michaelis–Menten reversible kinetics, or phenomenological laws for reaction rates, we find that the characteristic times corresponding to lifetimes of tracers and of concentration perturbations can be significantly longer than τ. PMID:27411726

  19. Accelerating the Computation of Detailed Chemical Reaction Kinetics for Simulating Combustion of Complex Fuels

    SciTech Connect

    Sankaran, R.; Grout, R.

    2012-01-01

    Combustion of hydrocarbon fuels has been a very challenging scientific and engineering problem due to the complexity of turbulent flows and hydrocarbon reaction kinetics. There is an urgent need to develop an efficient modeling capability to accurately predict the combustion of complex fuels. Detailed chemical kinetic models for the surrogates of fuels such as gasoline, diesel and JP-8 consist of thousands of chemical species and Arrhenius reaction steps. Oxygenated fuels such as bio-fuels and heavier hydrocarbons, such as from newer fossil fuel sources, are expected to have a much more complex chemistry requiring increasingly larger chemical kinetic models. Such models are beyond current computational capability, except for homogeneous or partially stirred reactor type calculations. The advent of highly parallel multi-core processors and graphical processing units (GPUs) promises a steep increase in computational performance in the coming years. This paper will present a software framework that translates the detailed chemical kinetic models to high-performance code targeted for GPU accelerators.

  20. Insertion Reactions of Neutral Phosphidozirconocene Complexes as a Convenient Entry into Frustrated Lewis Pair Territory.

    PubMed

    Normand, Adrien T; Daniliuc, Constantin G; Wibbeling, Birgit; Kehr, Gerald; Le Gendre, Pierre; Erker, Gerhard

    2016-03-14

    Neutral phosphidozirconocene complexes [Cp2Zr(PR2)Me] (Cp=cyclopentadienyl; 1a: R=cyclohexyl (Cy); 1b: R=mesityl (Mes); 1c: R=tBu) undergo insertion into the Zr-P bond by non-enolisable carbonyl building blocks (O=CR'R''), such as benzophenone, aldehydes, paraformaldehyde or CO2, to give [Cp2Zr(OCR'R''PR2)Me] (3-7). Depending on the steric bulk around P, complexes 3-7 react with B(C6F5)3 to give O-bridged cationic zirconocene dimers that display typical frustrated Lewis pair (FLP)/ambiphilic ligand behaviour. Thus, the reaction of {[Cp2Zr(μ-OCHPhPCy2)][MeB(C6F5)3]}2 (10a) with chalcone results in 1,4 addition of the Zr(+)/P FLP, whereas the reaction of {[Cp2Zr(μ-OCHFcPCy2)][MeB(C6F5)3]}2 (11a; Fc=(C5H4)CpFe) with [Pd(η(3)C3H5)Cl]2 yields the unique Zr-Fe-Pd trimetallic complex 13a, which has been characterised by XRD analysis. PMID:26864796

  1. Accelerating the Computation of Detailed Chemical Reaction Kinetics for Simulating Combustion of Complex Fuels

    SciTech Connect

    Grout, Ray W

    2012-01-01

    Combustion of hydrocarbon fuels has been a very challenging scientific and engineering problem due to the complexity of turbulent flows and hydrocarbon reaction kinetics. There is an urgent need to develop an efficient modeling capability to accurately predict the combustion of complex fuels. Detailed chemical kinetic models for the surrogates of fuels such as gasoline, diesel and JP-8 consist of thousands of chemical species and Arrhenius reaction steps. Oxygenated fuels such as bio-fuels and heavier hydrocarbons, such as from newer fossil fuel sources, are expected to have a much more complex chemistry requiring increasingly larger chemical kinetic models. Such models are beyond current computational capability, except for homogeneous or partially stirred reactor type calculations. The advent of highly parallel multi-core processors and graphical processing units (GPUs) promises a steep increase in computational performance in the coming years. This paper will present a software framework that translates the detailed chemical kinetic models to high- performance code targeted for GPU accelerators.

  2. Secondary Organic Aerosol Formation in Aerosol Water by Photochemical Reactions of Gaseous Mixture of Monoterpene and Hydrogen Peroxide

    NASA Astrophysics Data System (ADS)

    Lim, H.; Yi, S.; Park, J.; Cho, H.; Jung, K.

    2011-12-01

    There exist large uncertainties in model predictions for climate change and regional air quality. It could be caused by incomplete integration of secondary organic aerosol (SOA) formation in atmospheric chemical models. Recent laboratory studies have found SOA formation through chemical reactions on aerosol surface and in aerosol water. Water soluble organics formed by photochemical degradation of biogenic organics including isoprene and anthropogenic aromatics are predicted to form substantial amount of SOA through the newly found pathways. Although SOA formation in bulk aqueous solution was reported for laboratory experiments of various precursors (e.g., water soluble carbonyls and phenols), little is known for SOA formation in real aerosol water. In this study, photochemical reactions of the gaseous mixture of monoterpene and hydrogen peroxide were examined to investigate SOA formation through reactions in real aerosol phase water. SOA formation was conducted using a flow tube reactor (ID 30 cm x L 150 cm, FEP) and a smog chamber using FEP film in the presence of dry and wet seed particles. Acidity and chemical composition of seed aerosol were also controlled as important parameters influencing SOA formation. Particle size distribution and aerosol composition were analyzed to account for differences in SOA formation mechanisms and yields for dry and wet particles. The differences might be mainly associated with SOA formation in aerosol phase water. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (No. 2011-0000221).

  3. Time-dependent insulin oligomer reaction pathway prior to fibril formation: Cooling and seeding

    PubMed Central

    Sorci, Mirco; Grassucci, Robert A.; Hahn, Ingrid; Frank, Joachim; Belfort, Georges

    2009-01-01

    The difficulty in identifying the toxic agents in all amyloid-related diseases is likely due to the complicated kinetics and thermodynamics of the nucleation process and subsequent fibril formation. The slow progression of these diseases suggests that the formation, incorporation and/or action of toxic agents is possibly rate limiting. Candidate toxic agents include precursors (some at very low concentrations), also called oligomers and protofibrils, and the fibrils. Here, we investigate the kinetic and thermodynamic behavior of human insulin oligomers (imaged by cryo-EM) under fibril forming conditions (pH 1.6 and 65°C) by probing the reaction pathway to insulin fibril formation using two different types of experiments – cooling and seeding – and confirm the validity of the nucleation model and its effect on fibril growth. The results from both the cooling and seeding studies confirm the existence of a time-changing oligomer reaction process prior to fibril formation that likely involves a rate-limiting nucleation process followed by structural rearrangements of intermediates (into β-sheet rich entities) to form oligomers that then form fibrils. The latter structural rearrangement step occurs even in the absence of nuclei (i.e. with added heterologous seeds). Nuclei are formed at the fibrillation conditions (pH 1.6 and 65°C) but are also continuously formed during cooling at pH 1.6 and 25°C. Within the time-scale of the experiments, only after increasing the temperature to 65°C are the trapped insulin nuclei and resultant structures able to induce the structural rearrangement step and overcome the energy barrier to form fibrils. This delay in fibrillation and accumulation of nuclei at low temperature (25°C), result in a decrease in the mean length of the fibers when placed at 65°C. Fits of an empirical model to the data provide quantitative measures of the delay in the lag-time during the nucleation process and subsequent reduction in fibril growth rate

  4. 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

  5. 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.

  6. 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

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

    PubMed

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

    2012-05-21

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

  8. Reactions of heteroatom and carbon nucleophiles with the cationic bridging methylidyne complex

    SciTech Connect

    Casey, C.P.; Crocker, M.; Vosejpka, P.C.; Fagan, P.J.; Marder, S.R.; Gohdes, M.A.

    1988-03-01

    The reaction of the ..mu..-methylidyne complex /((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CO)(..mu..-CH)//sup +/PF/sub 6//sup -/ (1) with NMe/sub 3/ and (C/sub 6/H/sub 5/)/sub 2/C=NH gave the cationic 1:1 adducts /((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CO)(..mu..-CHNMe/sub 3/)//sup +/PF/sub 6//sup -/ (3) and /((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CHNH=C(C/sub 6/H/sub 5/)/sub 2/)//sup +/PF/sub 6//sup -/ (9), respectively, arising from attack of nitrogen on the methylidyne carbon. The reaction of 1 with KOC(CH/sub 3/)/sub 3/ gave the neutral ..mu..-carbene complex ((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CO)(..mu..-CHOC(CH/sub 3/)P/sub 3/) (4). Reaction of 1 with water afforded a 1:1 mixture of ..mu..methylene complex ((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CO)(..mu..-CH/sub 2/) (2) and ((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CO)/sub 2/; these products are proposed to arise from disproportionation of an initially formed hydroxy carbene species. Reaction of 1 with Et/sub 4/N/sup +/Br/sup -/ gave the unstable /sup +/-carbene complex ((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CO)(..mu..-CHBr) (6). Reaction of 1 with the carbon nucleophiles CH/sub 3/Li and Li(C/sub 6/H/sub 5/CuCN) gave the ..mu..-carbene complexes ((C/sub 5/H/sub 5/)(CO)Fe/sub 2/(..mu..-CO)(..mu..-CHCH/sub 3/) (11) and ((C/sub 5/H/sub 5/)(CO)Fe)/sub 2/(..mu..-CO)(..mu..-CHC/sub 6/H/sub 5/ (12), while reaction of 1 with HFe(CO)/sub 4//sup -/ afforded 2. 1 reacted with acetone via nucleophilic addition of the enol affording the neutral ..mu..-carbene complex (C/sub 5/H/sub 5/)-(CO)Fe)/sub 2/(..mu..-CO)(..mu..-CHCH/sub 2/COCH/sub 3/)) (13). 1 also reacted with cyclohexanone, 2-butanone, 4-methyl-2-pentanone, 2,4-pentanedione, 5,5-dimethyl-1,3-cyclohexanedione, ethyl acetoacetate, and the sodium salt of diethyl malonate to give similar ..mu..-carbene products.

  9. Formation of Complex Organic molecules from Formaldehyde Chemistry in Cometary Ice Analogues

    NASA Astrophysics Data System (ADS)

    Duvernay, fabrice; Vinogradoff, Vassilissa; Danger, Grégoire; Theulé, Patrice; Chiavassa, Thierry

    2015-04-01

    There is convincing evidence that the formation of complex organic molecules occurred in a variety of astrophysical environments. Among them, precursors of biomolecules are of particular significance due to their exobiological implications. Hexamethylenetetramine (HMT, C6H12N4) and the polyoxymethylene (POM, -(CH2-O)n-) are of prime interest since they are supposed to be present in cometary environments. They are also ones of the main components of the organic residue formed from the warming of photolysed interstellar/cometary ice analogs. In this work, we study the warming of water-dominated cometary ice analogs containing formaldehyde (H2CO). Based on infrared and mass spectrometry measurements, and complemented by quantum chemical calculations, we report that NH2CH2OH, HOCH2OH, and POM are the only reaction products when the ice also contains NH3. The branching ratio between the three products strongly depends on the initial H2CO/NH3 concentration ratio. Moreover, the influence of the initial ice composition on the formation of POM oligomers (HO-(CH2O)n-H, n<5) as well as their thermal instability between 200 and 320 K are investigated. Finally, the implications of these results with respect to cometary nucleus chemistry and their impact on POM detection by the Rosetta mission are discussed. In addition, the mechanism for HMT formation in interstellar or cometary ice analogs containing H2CO, NH3, and HCOOH has been determined by combining laboratory experiments and DFT calculations. We show that HMT is thermally formed from H2CO and NH3 activated by HCOOH. Two intermediates has been unambiguously detected: NH2CH2OH and the trimer of CH2NH (1,3,5-triazinane, TMT). Unlike to what it was previously thought, HMT is not an indicator of ice photochemistry, but an indicator of thermal processing of ice. These results strengthen the hypothesis that HMT and its intermediates should be present in comets, where they may be detected with the COSAC or COSIMA instrument of

  10. Chemical pattern formation driven by a neutralization reaction. I. Mechanism and basic features

    NASA Astrophysics Data System (ADS)

    Eckert, Kerstin; Acker, Margret; Shi, Ying

    2004-02-01

    We study the chemohydrodynamic pattern formation during interfacial mass transfer accompanied by a neutralization reaction. The system, which is placed in a Hele-Shaw cell, is a configuration of two immiscible liquid phases in contact along a plane interface. In the upper, organic layer a carboxylic acid is dissolved, the concentration of which is far beyond the equilibrium partition ratio. Interfacial acid transfer initiates the neutralization with an organic base dissolved in the lower, aqueous layer. Focus is on the exploration of a novel instability consisting of a regular cellular structure penetrating into the aqueous bulk solution. By several complementary experimental methods, including shadowgraph visualization with different magnifications, particle image velocimetry, differential interferometry, and detailed measurements of relevant material properties, the driving mechanism of the instability is identified. Synthesis of the experimental results suggests that lateral differences in buoyancy are responsible for the convection.

  11. 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.

  12. Uranyl triazolate formation via an in situ Huisgen 1,3-dipolar cycloaddition reaction

    SciTech Connect

    Knope, Karah E.; Cahill, Christopher L.

    2010-08-27

    A two dimensional UO22+ coordination polymer, (UO2)3(C10H5N3O4)2(OH)2(H2O)2, has been synthesized under solvothermal conditions. The triazolate ligand, 1-(4-carboxyphenyl)-1H-1,2,3-triazole-4-carboxylic acid (CPTAZ) has been generated via a 1,3-dipolar cycloaddition of 4-azidobenzoic acid and propiolic acid. Reactions of the UO22+ cation with both the in situ generated triazolate ligand and the presynthesized ligand have been explored. The structure, fluorescent and thermal behaviour of this material are presented, as is a discussion of the utility of in situ ligand formation versus direct assembly.

  13. SEPALLATA3: the 'glue' for MADS box transcription factor complex formation

    PubMed Central

    Immink, Richard GH; Tonaco, Isabella AN; de Folter, Stefan; Shchennikova, Anna; van Dijk, Aalt DJ; Busscher-Lange, Jacqueline; Borst, Jan W; Angenent, Gerco C

    2009-01-01

    Background Plant MADS box proteins play important roles in a plethora of developmental processes. In order to regulate specific sets of target genes, MADS box proteins dimerize and are thought to assemble into multimeric complexes. In this study a large-scale yeast three-hybrid screen is utilized to provide insight into the higher-order complex formation capacity of the Arabidopsis MADS box family. SEPALLATA3 (SEP3) has been shown to mediate complex formation and, therefore, special attention is paid to this factor in this study. Results In total, 106 multimeric complexes were identified; in more than half of these at least one SEP protein was present. Besides the known complexes involved in determining floral organ identity, various complexes consisting of combinations of proteins known to play a role in floral organ identity specification, and flowering time determination were discovered. The capacity to form this latter type of complex suggests that homeotic factors play essential roles in down-regulation of the MADS box genes involved in floral timing in the flower via negative auto-regulatory loops. Furthermore, various novel complexes were identified that may be important for the direct regulation of the floral transition process. A subsequent detailed analysis of the APETALA3, PISTILLATA, and SEP3 proteins in living plant cells suggests the formation of a multimeric complex in vivo. Conclusions Overall, these results provide strong indications that higher-order complex formation is a general and essential molecular mechanism for plant MADS box protein functioning and attribute a pivotal role to the SEP3 'glue' protein in mediating multimerization. PMID:19243611

  14. Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme.

    PubMed

    Khrenova, Maria G; Grigorenko, Bella L; Kolomeisky, Anatoly B; Nemukhin, Alexander V

    2015-10-01

    Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras·GAP protein complex are fully investigated by using modern modeling tools. The previously hypothesized stages of the cleavage of the phosphorus-oxygen bond in GTP and the formation of the imide form of catalytic Gln61 from Ras upon creation of Pi are confirmed by using the higher-level quantum-based calculations. The steps of the enzyme regeneration are modeled for the first time, providing a comprehensive description of the catalytic cycle. It is found that for the reaction Ras·GAP·GTP·H2O → Ras·GAP·GDP·Pi, the highest barriers correspond to the process of regeneration of the active site but not to the process of substrate cleavage. The specific shape of the energy profile is responsible for an interesting kinetic mechanism of the GTP hydrolysis. The analysis of the process using the first-passage approach and consideration of kinetic equations suggest that the overall reaction rate is a result of the balance between relatively fast transitions and low probability of states from which these transitions are taking place. Our theoretical predictions are in excellent agreement with available experimental observations on GTP hydrolysis rates. PMID:26374425

  15. URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries

    PubMed Central

    2012-01-01

    Background Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. Results We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic

  16. Formation of photosystem II reaction centers that work as energy sinks in lichen symbiotic Trebouxiophyceae microalgae.

    PubMed

    Guéra, Alfredo; Gasulla, Francisco; Barreno, Eva

    2016-04-01

    Lichens are poikilohydric symbiotic organisms that can survive in the absence of water. Photosynthesis must be highly regulated in these organisms, which live under continuous desiccation-rehydration cycles, to avoid photooxidative damage. Analysis of chlorophyll a fluorescence induction curves in the lichen microalgae of the Trebouxiophyceae Asterochloris erici and in Trebouxia jamesii (TR1) and Trebouxia sp. (TR9) phycobionts, isolated from the lichen Ramalina farinacea, shows differences with higher plants. In the presence of the photosynthetic electron transport inhibitor DCMU, the kinetics of Q(A) reduction is related to variable fluorescence by a sigmoidal function that approaches a horizontal asymptote. An excellent fit to these curves was obtained by applying a model based on the following assumptions: (1) after closure, the reaction centers (RCs) can be converted into "energy sink" centers (sRCs); (2) the probability of energy leaving the sRCs is very low or zero and (3) energy is not transferred from the antenna of PSII units with sRCs to other PSII units. The formation of sRCs units is also induced by repetitive light saturating pulses or at the transition from dark to light and probably requires the accumulation of reduced Q(A), as well as structural changes in the reaction centers of PSII. This type of energy sink would provide a very efficient way to protect symbiotic microalgae against abrupt changes in light intensity. PMID:26482588

  17. Formation of cysteine-S-conjugates in the Maillard reaction of cysteine and xylose.

    PubMed

    Cerny, Christoph; Guntz-Dubini, Renée

    2013-11-15

    Cysteine-S-conjugates (CS-conjugates) occur in foods derived from plant sources like grape, passion fruit, onion, garlic, bell pepper and hops. During eating CS-conjugates are degraded into aroma-active thiols by β-lyases that originate from oral microflora. The present study provides evidence for the formation of the CS-conjugates S-furfuryl-l-cysteine (FFT-S-Cys) and S-(2-methyl-3-furyl)-l-cysteine (MFT-S-Cys) in the Maillard reaction of xylose with cysteine at 100°C for 2h. The CS-conjugates were isolated using cationic exchange and reversed-phase chromatography and identified by (1)H NMR, (13)C NMR and LC-MS(2). Spectra and LC retention times matched those of authentic standards. To the best of our knowledge, this is the first time that CS-conjugates are described as Maillard reaction products. Furfuryl alcohol (FFA) is proposed as an intermediate which undergoes a nucleophilic substitution with cysteine. Both FFT-S-Cys and MFT-S-Cys are odourless but produce strong aroma when tasted in aqueous solutions, supposedly induced by β -lyases from the oral microflora. The perceived aromas resemble those of the corresponding aroma-active thiols 2-furfurylthiol (FFT) and 2-methyl-3-furanthiol (MFT) which smell coffee-like and meaty, respectively. PMID:23790889

  18. Understanding the Mechanism of the Divergent Reactivity of Non-Heteroatom-Stabilized Chromium Carbene Complexes with Furfural Imines: Formation of Benzofurans and Azetines.

    PubMed

    Funes-Ardoiz, Ignacio; González, Jairo; Santamaría, Javier; Sampedro, Diego

    2016-02-19

    The mechanisms of the reaction between non-heteroatom-stabilized alkynyl chromium carbene complexes prepared in situ and furfural imines to yield benzofurans and/or azetines have been explored by means of density functional theory method calculations. The reaction proceeds through a complex cascade of steps triggered by a nucleophilic addition of the imine nitrogen atom. The formation of two benzofuran regioisomers has been explained in terms of competitive nucleophilic attacks to different positions of the carbene complex. Each of these regioisomers can be obtained as the major product depending on the starting materials. The overall sequence could be controlled to yield benzofurans or azetines by adjusting the substituents present in the initial carbene complex. This mechanistic information allowed for the preparation of new benzofurans and azetinylcarbenes in good yields. PMID:26799934

  19. Spectrophotometric study of complex formation between oxovanadium (IV) and antiamebic drugs.

    PubMed

    Abu-Eittah, R; El-Nasr, M S

    1976-09-01

    Complex formation between oxovanadium(IV) and the antiamebic drugs 5, 7-dibromo-8-quinolinol and 5, 7-dichloro-8-quinolinol was studied in the pH 1.5-2.0 range, using ethanol, dioxane-water, and dimethylformamide as solvents. The composition of the formed complexes was determined by more than one procedure. In ethanol and dioxane-water, the 1:1 and 1:2 complexes were formed; in dimethylformamide, the 1:1, 1:2 and 1:3 complexes were formed. The stability constants were computed using two procedures: the molar ratio method and the extrapolation method. The reproducibility or results in satisfactory. PMID:966156

  20. Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine.

    PubMed

    Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

    2014-10-20

    The N≡N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. PMID:25214300

  1. Nearside-farside, local angular momentum and resummation theories: Useful tools for understanding the dynamics of complex-mode reactions

    NASA Astrophysics Data System (ADS)

    Hankel, Marlies; Connor, J. N. L.

    2015-07-01

    A valuable tool for understanding the dynamics of direct reactions is Nearside-Farside (NF) scattering theory. It makes a decomposition of the (resummed) partial wave series for the scattering amplitude, both for the differential cross section (DCS) and the Local Angular Momentum (LAM). This paper makes the first combined application of these techniques to complex-mode reactions. We ask if NF theory is a useful tool for their identification, in particular, can it distinguish complex-mode from direct-mode reactions? We also ask whether NF theory can identify NF interference oscillations in the full DCSs of complex-mode reactions. Our investigation exploits the fact that accurate quantum scattering matrix elements have recently become available for complex-mode reactions. We first apply NF theory to two simple models for the scattering amplitude of a complex-mode reaction: One involves a single Legendre polynomial; the other involves a single Legendre function of the first kind, whose form is suggested by complex angular momentum theory. We then study, at fixed translational energies, four state-to-state complex-mode reactions. They are: S(1D) + HD → SH + D, S(1D) + DH → SD + H, N(2D) +H2 → NH + H, and H+ + D2 → HD + D+. We compare the NF results for the DCSs and LAMs with those for a state-to-state direct reaction, namely, F + H2 → FH + H. We demonstrate that NF theory is a valuable tool for identifying and analyzing the dynamics of complex-mode reactions.

  2. Nearside-farside, local angular momentum and resummation theories: Useful tools for understanding the dynamics of complex-mode reactions

    SciTech Connect

    Hankel, Marlies E-mail: j.n.l.connor@manchester.ac.uk; Connor, J. N. L. E-mail: j.n.l.connor@manchester.ac.uk

    2015-07-15

    A valuable tool for understanding the dynamics of direct reactions is Nearside-Farside (NF) scattering theory. It makes a decomposition of the (resummed) partial wave series for the scattering amplitude, both for the differential cross section (DCS) and the Local Angular Momentum (LAM). This paper makes the first combined application of these techniques to complex-mode reactions. We ask if NF theory is a useful tool for their identification, in particular, can it distinguish complex-mode from direct-mode reactions? We also ask whether NF theory can identify NF interference oscillations in the full DCSs of complex-mode reactions. Our investigation exploits the fact that accurate quantum scattering matrix elements have recently become available for complex-mode reactions. We first apply NF theory to two simple models for the scattering amplitude of a complex-mode reaction: One involves a single Legendre polynomial; the other involves a single Legendre function of the first kind, whose form is suggested by complex angular momentum theory. We then study, at fixed translational energies, four state-to-state complex-mode reactions. They are: S({sup 1}D) + HD → SH + D, S({sup 1}D) + DH → SD + H, N({sup 2}D) +H{sub 2} → NH + H, and H{sup +} + D{sub 2} → HD + D{sup +}. We compare the NF results for the DCSs and LAMs with those for a state-to-state direct reaction, namely, F + H{sub 2} → FH + H. We demonstrate that NF theory is a valuable tool for identifying and analyzing the dynamics of complex-mode reactions.

  3. The kinetics of complex formation in the trithiadiazoletri[3,4-di(4- tert-butylphenyl)-pyrrole] macrocycle-copper(II) acetate-DMFA-H2O system

    NASA Astrophysics Data System (ADS)

    Lomova, T. N.; Mozhzhukhina, E. G.; Danilova, E. A.; Islyaikin, M. K.

    2009-10-01

    The paper presents the results of a study of the kinetics of coordination of a macroheterocyclic compound with an increased coordination cavity of the (3 + 3) McH3 composition consisting of sequentially alternating 1,3,4-thiadiazole and 3,4-bis(4- tert-butylphenyl)pyrrole fragments to dehydrated Cu(OAc)2 in dimethylformamide with and without H2O admixtures. The reaction could be controlled spectrophotometrically over the salt and ligand concentration ranges (0.175-0.55) × 10-4 and (0.16-0.64) × 10-5 mol/l, respectively, at temperatures of 288-303 K. A kinetic equation of an unusual form with a negative order with respect to the salt was for the first time obtained experimentally for a macrocyclic ligand by the method of excess concentrations. The kinetics of the complex formation reaction was given a theoretical interpretation. Quantitative characteristics were obtained, and the role played by water in the kinetics of complex formation was studied. These data were of importance for practical applications, for the development of optimum conditions increasing the yield of complexes when they were synthesized in complex formation reactions.

  4. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

    PubMed Central

    Szczelkun, Mark D.; Tikhomirova, Maria S.; Sinkunas, Tomas; Gasiunas, Giedrius; Karvelis, Tautvydas; Pschera, Patrizia; Siksnys, Virginijus; Seidel, Ralf

    2014-01-01

    Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems protect bacteria and archaea from infection by viruses and plasmids. Central to this defense is a ribonucleoprotein complex that produces RNA-guided cleavage of foreign nucleic acids. In DNA-targeting CRISPR-Cas systems, the RNA component of the complex encodes target recognition by forming a site-specific hybrid (R-loop) with its complement (protospacer) on an invading DNA while displacing the noncomplementary strand. Subsequently, the R-loop structure triggers DNA degradation. Although these reactions have been reconstituted, the exact mechanism of R-loop formation has not been fully resolved. Here, we use single-molecule DNA supercoiling to directly observe and quantify the dynamics of torque-dependent R-loop formation and dissociation for both Cascade- and Cas9-based CRISPR-Cas systems. We find that the protospacer adjacent motif (PAM) affects primarily the R-loop association rates, whereas protospacer elements distal to the PAM affect primarily R-loop stability. Furthermore, Cascade has higher torque stability than Cas9 by using a conformational locking step. Our data provide direct evidence for directional R-loop formation, starting from PAM recognition and expanding toward the distal protospacer end. Moreover, we introduce DNA supercoiling as a quantitative tool to explore the sequence requirements and promiscuities of orthogonal CRISPR-Cas systems in rapidly emerging gene-targeting applications. PMID:24912165

  5. Complex Formation of Human Proelastases with Procarboxypeptidases A1 and A2.

    PubMed

    Szabó, András; Pilsak, Claudia; Bence, Melinda; Witt, Heiko; Sahin-Tóth, Miklós

    2016-08-19

    The pancreas secretes digestive proenzymes typically in their monomeric form. A notable exception is the ternary complex formed by proproteinase E, chymotrypsinogen C, and procarboxypeptidase A (proCPA) in cattle and other ruminants. In the human and pig pancreas binary complexes of proCPA with proelastases were found. To characterize complex formation among human pancreatic protease zymogens in a systematic manner, we performed binding experiments using recombinant proelastases CELA2A, CELA3A, and CELA3B; chymotrypsinogens CTRB1, CTRB2, CTRC, and CTRL1; and procarboxypeptidases CPA1, CPA2, and CPB1. We found that proCELA3B bound not only to proCPA1 (KD 43 nm) but even more tightly to proCPA2 (KD 18 nm), whereas proCELA2A bound weakly to proCPA1 only (KD 152 nm). Surprisingly, proCELA3A, which shares 92% identity with proCELA3B, did not form stable complexes due to the evolutionary replacement of Ala(241) with Gly. The polymorphic nature of position 241 in both CELA3A (∼4% Ala(241) alleles) and CELA3B (∼2% Gly(241) alleles) points to individual variations in complex formation. The functional effect of complex formation was delayed procarboxypeptidase activation due to increased affinity of the inhibitory activation peptide, whereas proelastase activation was unchanged. We conclude that complex formation among human pancreatic protease zymogens is limited to a subset of proelastases and procarboxypeptidases. Complex formation stabilizes the inhibitory activation peptide of procarboxypeptidases and thereby increases zymogen stability and controls activation. PMID:27358403

  6. Complex formation of cadmium with sugar residues, nucleobases, phosphates, nucleotides, and nucleic acids.

    PubMed

    Sigel, Roland K O; Skilandat, Miriam; Sigel, Astrid; Operschall, Bert P; Sigel, Helmut

    2013-01-01

    Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromatic-nitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono- to the di- and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono- or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand

  7. Oxidation Reactions with Bioinspired Mononuclear Non-Heme Metal-Oxo Complexes.

    PubMed

    Engelmann, Xenia; Monte-Pérez, Inés; Ray, Kallol

    2016-06-27

    The selective functionalization of strong C-H bonds and the oxidation of water by cheap and nontoxic metals are some of the key targets of chemical research today. It has been proposed that high-valent iron-, manganese-, and copper-oxo cores are involved as reactive intermediates in important oxidation reactions performed by biological systems, thus making them attractive targets for biomimetic synthetic studies. The generation and characterization of metal-oxo model complexes of iron, manganese, and copper together with detailed reactivity studies can help in understanding how the steric and electronic properties of the metal centers modulate the reactivity of the metalloenzymes. This Review provides a focused overview of the advances in the chemistry of biomimetic high-valent metal-oxo complexes from the last 5-10 years that can be related to our understanding of biological systems. PMID:27311082

  8. CuAAC click reactions for the design of multifunctional luminescent ruthenium complexes.

    PubMed

    Zabarska, Natalia; Stumper, Anne; Rau, Sven

    2016-02-01

    CuAAC (Cu(i) catalyzed azide-alkyne cycloaddition) click chemistry has emerged as a versatile tool in the development of photoactive ruthenium complexes with multilateral potential applicability. In this contribution we discuss possible synthetic approaches towards CuAAC reactions with ruthenium(ii) polypyridine complexes and their differences with respect to possible applications. We focus on two main application possibilities of the click-coupled ruthenium assemblies. New results within the development of ruthenium based photosensitizers for the field of renewable energy supply, i.e. DSSCs (dye-sensitized solar cells) and artificial photocatalysis for the production of hydrogen, or for anticancer photodynamic therapeutic applications are reviewed. PMID:26758682

  9. Complex dynamics and enhanced photosensitivity in a modified Belousov-Zhabotinsky reaction

    SciTech Connect

    Li Nan; Zhao Jinpei; Wang Jichang

    2008-06-28

    This study presents an experimental investigation of nonlinear dynamics in a modified Belousov-Zhabotinsky (BZ) reaction, in which the addition of 1,4-benzoquinone induced various complex behaviors such as mixed-mode oscillations and consecutive period-adding bifurcations. In addition, the presence of 1,4-benzoquinone significantly enhanced the photosensitivity of the ferroin-catalyzed BZ system, in which light-induced transitions between simple and complex oscillations have been achieved. Mechanistic study suggests that the influence of benzoquinone may arise from its interactions with the metal catalyst ferroin/ferriin, where cyclic voltammograms illustrate that the presence of benzoquinone causes an increase in the redox potential of ferroin/ferriin couple, which may consequently alternate the oxidation and reduction paths of the catalyst.

  10. (Phenoxyimidazolyl-salicylaldimine)iron complexes: synthesis, properties and iron catalysed ethylene reactions.

    PubMed

    Yankey, Margaret; Obuah, Collins; Guzei, Ilia A; Osei-Twum, Emmanuel; Hearne, Giovanni; Darkwa, James

    2014-10-01

    The reaction of 2-{[2-(1H-imidazol-4-yl)-ethylimino]-methyl}-phenol (L1), 2,4-di-tert-butyl-6-{[2-(1H-imidazol-4-yl)-ethylimino]-methyl}-phenol (L2) or 4-tert-butyl-2-{[2-(1H-imidazol-4-yl)-ethylimino]-methyl}-phenol (L3) with iron(ii) precursors produced either iron(ii) or iron(iii) complexes, depending on the nature of the anions in the iron(ii) precursor and the ligand. When the anion is chloride and the ligand L1, the product is [(L1)2Fe][FeCl4] (1), but when the anion is triflate (OTf(-)) and the ligand is L2, the product is [(L2)2Fe][OTf]2 (2). With iron(ii) halides and tert-butyl groups on the phenoxy ligands L2 and L3, the iron(iii) complexes [(L2)FeX2] {where X = Cl (3), Br (4) and I = (5)} and [(L3)FeCl2] (6) were formed. Complexes 1-6 were characterised by a combination of elemental analyses, IR spectroscopy and mass spectrometry; and in selected cases (3 and 4) by single crystal X-ray crystallography. The crystal structures of 3 and 4 indicated that the iron(ii) precursors oxidised to iron(iii) in forming complexes 3-6; an observation that was corroborated by the magnetic properties and the (57)Fe Mössbauer spectra of 3 and 4. The iron(iii) complexes 3-6 were used as pre-catalysts for the oligomerisation and polymerisation of ethylene. Products of these ethylene reactions depended on the solvent used. In toluene ethylene oligomerised mainly to 1-butene and was followed by the 1-butene alkylating the solvent to form butyl-toluenes via a Friedel-Crafts alkylation reaction. In chlorobenzene, ethylene oligomerised mainly to a mixture of C4-C12 alkenes. Interestingly small amounts of butyl-chlorobenzenes and hexyl-chlorobenzenes were also formed via a Friedel-Crafts alkylation with butenes and hexenes from the oligomerisation of ethylene. PMID:25111396

  11. Kinetics and mechanism of the reaction of [RuIII(edta)(H2O)]- with HOBr to form an intermediate RuV=O complex in aqueous solution.

    PubMed

    Chatterjee, Debabrata; Mitra, Anannya; van Eldik, Rudi

    2006-10-21

    The interaction of [Ru(III)(edta)(H(2)O)](-) (1) (edta = ethylenediaminetetraacetate) with the oxygen transfer agent HOBr, was studied kinetically as a function of [HOBr] and temperature (5-35 degrees C) at a fixed pH of 6.2. Spectroscopic evidence is reported for the formation of a high valent intermediate (edta)Ru(V)=O complex. Water soluble 2,2'-azobis(3-ethylbenzithiazoline-6-sulfonate) (ABTS) was employed as a trap for this intermediate in order to gain further mechanistic information. Reactions were carried out under pseudo-first conditions for [ABTS] > [HOBr] > [1], and were monitored as a function of time for the formation of the one-electron oxidation product ABTS(*+). The reported kinetic data are interpreted in terms of a suggested reaction mechanism and discussed in reference to data reported before. PMID:17028677

  12. Phosphine and thiophene cyclopalladated complexes: hydrolysis reactions in strong acidic media.

    PubMed

    García, Begoña; Hoyuelos, Francisco J; Ibeas, Saturnino; Muñoz, María S; Navarro, Ana M; Peñacoba, Indalecio A; Leal, José M

    2010-12-01

    The mechanisms for the hydrolysis of organopalladium complexes [Pd(CNN)R]BF(4) (R=P(OPh)(3), PPh(3), and SC(4)H(8)) were investigated at 25 °C by using UV/Vis absorbance measurements in 10 % v/v ethanol/water mixtures containing different sulphuric acid concentrations in the 1.3-11.7 M range. In all cases, a biphasic behavior was observed with rate constants k(1obs), which corresponds to the initial step of the hydrolysis reaction, and k(2obs), where k(1obs)>k(2obs). The plots of k(1obs) and k(2obs) versus sulfuric acid concentration suggest a change in the reaction mechanism. The change with respect to the k(1obs) value corresponds to 35 %, 2 %, and 99 % of the protonated complexes for R=PPh(3), P(OPh)(3), and SC(4)H(8), respectively. Regarding k(2obs), the change occurred in all cases at about 6.5 M H(2)SO(4) and matched up with the results reported for the hydrolysis of the 2-acetylpyridinephenylhydrazone (CNN) ligand. By using the excess acidity method, the mechanisms were elucidated by carefully looking at the variation of k(i),(obs) (i=1,2) versus cH+. The rate-determining constants, k(0,A-1), k(0,A-2), and k(0,A-SE2) were evaluated in all cases. The R=P(OPh)(3) complex was most reactive due to its π-acid character, which favors the rupture of the trans nitrogen-palladium bond in the A-2 mechanism and also that of the pyridine nitrogen-palladium bond in the A-1 mechanism. The organometallic bond exerts no effect on the relative basicity of the complexes, which are strongly reliant on the substituent. PMID:21125574

  13. Condensation Reactions and Formation of Amides, Esters, and Nitriles Under Hydrothermal Conditions

    NASA Astrophysics Data System (ADS)

    Rushdi, Ahmed I.; Simoneit, Bernd R. T.

    2004-06-01

    Hydrothermal pyrolysis experiments were performed to assess condensation (dehydration) reactions to amide, ester, and nitrile functionalities from lipid precursors. Beside product formation, organic compound alteration and stability were also evaluated. Mixtures of nonadecanoic acid, hexadecanedioic acid, or hexadecanamide with water, ammonium bicarbonate, and oxalic acid were heated at 300°C for 72 h. In addition, mixtures of ammonium bicarbonate and oxalic acid solutions were used to test the abiotic formation of organic nitrogen compounds at the same temperature. The resulting products were condensation compounds such as amides, nitriles, and minor quantities of N-methylalkyl amides, alkanols, and esters. Mixtures of alkyl amide in water or oxalic acid yielded mainly hydrolysis and dehydration products, and with ammonium bicarbonate and oxalic acid the yield of condensation products was enhanced. The synthesis experiments with oxalic acid and ammonium bicarbonate solutions yielded homologous series of alkyl amides, alkyl amines, alkanes, and alkanoic acids, all with no carbon number predominances. These organic nitrogen compounds are stable and survive under the elevated temperatures of hydrothermal fluids.

  14. Formation of carriers in Ti-oxide thin films by substitution reactions

    SciTech Connect

    Liu, Y. S.; Lin, Y. H.; Wei, Y. S.; Liu, C. Y.

    2012-02-15

    Conductive Ti-oxide thin films are produced using a reactive sputtering and post-annealing process. The lowest resistivity of Ti-oxide thin films (2.30 x 10{sup -2}{Omega}-cm) can be achieved after annealing for 1 h at 400 deg. C in ambient O{sub 2}. Additionally, the Hall measurement results indicate that the carrier concentration increases during the initial 1-h annealing process before decreasing during subsequent annealing. By curve fitting the O{sub ls} core-level peaks in the x ray photoelectron spectroscopy (XPS) spectrum of the annealed Ti-oxide thin films, we found that the oxygen (O) vacancy concentration monotonically increases with annealing time, which differs from the behavior of the carrier concentration regarding annealing time. This means that the O-vacancy mechanism alone cannot explain the formation of carriers in Ti-oxide thin films. By curve-fitting core-level Ti peaks in the XPS spectrum of annealed Ti-oxide thin films, a Ti{sup 3+}-to-Ti{sup 4+} substitution reaction in the TiO{sub 2} phase of the Ti-oxide thin film after annealing plays the dominant role in the formation of conduction carriers. Instead of the O-vacancy mechanism, the Ti{sup 3+}-to-Ti{sup 4+} substitution mechanism can explain the concentration of carriers in Ti-oxide thin films following annealing.

  15. Intramolecular condensation reactions of {alpha}, {omega}- bis(triethoxy-silyl)alkanes. Formation of cyclic disilsesquioxanes

    SciTech Connect

    Loy, D.A.; Carpenter, J.P.; Myers, S.A.; Assink, R.A.; Small, J.H.; Greaves, J.; Shea, K.J.

    1996-08-01

    Under acidic sol-gel polymerization conditions, 1,3-bis(triethoxysilyl)-propane (1) and 1,4-bis(triethoxysilyl)butane (2) were shown to preferentially form cyclic disilsesquioxanes 3 and 4 rather than the expected 1,3-propylene- and 1,4-butylene-bridged polysilsesquioxane gels. Formation of 3 and 4 is driven by a combination of an intramolecular cyclization to six and seven membered rings, and a pronounced reduction in reactivity under acidic conditions as a function of increasing degree of condensation. The ease with which these relatively unreactive cyclic monomers and dimers are formed (under acidic conditions) helps to explain the difficulties in forming gels from 1 and 2. The stability of cyclic disilsesquioxanes was confirmed withe the synthesis of 3 and 4 in gram quantities; the cyclic disilsesquioxanes react slowly to give tricyclic dimers containing a thermodynamically stable eight membered siloxane ring. Continued reactions were shown to perserve the cyclic structure, opening up the possibility of utilizing cyclic disilsesquioxanes as sol-gel monomers. Preliminary polymerization studies with these new, carbohydrate-like monomers revealed the formation of network poly(cyclic disilsesquioxanes) under acidic conditions and polymerization with ring-opening under basic conditions.

  16. Effect of chelate dynamics on water exchange reactions of paramagnetic aminopolycarboxylate complexes.

    PubMed

    Maigut, Joachim; Meier, Roland; Zahl, Achim; van Eldik, Rudi

    2008-07-01

    Because of our interest in evaluating a possible relationship between complex dynamics and water exchange reactivity, we performed (1)H NMR studies on the paramagnetic aminopolycarboxylate complexes Fe (II)-TMDTA and Fe (II)-CyDTA and their diamagnetic analogues Zn (II)-TMDTA and Zn (II)-CyDTA. Whereas a fast Delta-Lambda isomerization was observed for the TMDTA species, no acetate scrambling between in-plane and out-of-plane positions is accessible for any of the CyDTA complexes because the rigid ligand backbone prevents any configurational changes in the chelate system. In variable-temperature (1)H NMR studies, no evidence of spectral coalescence due to nitrogen inversion was found for any of the complexes in the available temperature range. The TMDTA complexes exhibit the known solution behavior of EDTA, whereas the CyDTA complexes adopt static solution structures. Comparing the exchange kinetics of flexible EDTA-type complexes and static CyDTA complexes appears to be a suitable method for evaluating the effect of ligand dynamics on the overall reactivity. In order to assess information concerning the rates and mechanism of water exchange, we performed variable-temperature and -pressure (17)O NMR studies of Ni (II)-CyDTA, Fe (II)-CyDTA, and Mn (II)-CyDTA. For Ni (II)-CyDTA, no significant effects on line widths or chemical shifts were apparent, indicating either the absence of any chemical exchange or the existence of a very small amount of the water-coordinated complex in solution. For [Fe (II)(CyDTA)(H 2O)] (2-) and [Mn (II)(CyDTA)(H 2O)] (2-), exchange rate constant values of (1.1 +/- 0.3) x 10 (6) and (1.4 +/- 0.2) x 10 (8) s (-1), respectively, at 298 K were determined from fits to resonance-shift and line-broadening data. A relationship between chelate dynamics and reactivity seems to be operative, since the CyDTA complexes exhibited significantly slower reactions than their EDTA counterparts. The variable-pressure (17)O NMR measurements for [Mn (II

  17. Effects of chemical and enzymatic modifications on starch-oleic acid complex formation.

    PubMed

    Arijaje, Emily Oluwaseun; Wang, Ya-Jane

    2015-04-29

    The solubility of starch-inclusion complexes affects the digestibility and bioavailability of the included molecules. Acetylation with two degrees of substitution, 0.041 (low) and 0.091 (high), combined without or with a β-amylase treatment was employed to improve the yield and solubility of the inclusion complex between debranched potato starch and oleic acid. Both soluble and insoluble complexes were recovered and analyzed for their degree of acetylation, complexation yields, molecular size distributions, X-ray diffraction patterns, and thermal properties. Acetylation significantly increased the amount of recovered soluble complexes as well as the complexed oleic acid in both soluble and insoluble complexes. High-acetylated debranched-only starch complexed the highest amount of oleic acid (38.0 mg/g) in the soluble complexes; low-acetylated starch with or without the β-amylase treatment resulted in the highest complexed oleic acid in the insoluble complexes (37.6-42.9 mg/g). All acetylated starches displayed the V-type X-ray pattern, and the melting temperature generally decreased with acetylation. The results indicate that starch acetylation with or without the β-amylase treatment can improve the formation and solubility of the starch-oleic acid complex. PMID:25877005

  18. High density of REC8 constrains sister chromatid axes and prevents illegitimate synaptonemal complex formation.

    PubMed

    Agostinho, Ana; Manneberg, Otto; van Schendel, Robin; Hernández-Hernández, Abrahan; Kouznetsova, Anna; Blom, Hans; Brismar, Hjalmar; Höög, Christer

    2016-06-01

    During meiosis, cohesin complexes mediate sister chromatid cohesion (SCC), synaptonemal complex (SC) assembly and synapsis. Here, using super-resolution microscopy, we imaged sister chromatid axes in mouse meiocytes that have normal or reduced levels of cohesin complexes, assessing the relationship between localization of cohesin complexes, SCC and SC formation. We show that REC8 foci are separated from each other by a distance smaller than 15% of the total chromosome axis length in wild-type meiocytes. Reduced levels of cohesin complexes result in a local separation of sister chromatid axial elements (LSAEs), as well as illegitimate SC formation at these sites. REC8 but not RAD21 or RAD21L cohesin complexes flank sites of LSAEs, whereas RAD21 and RAD21L appear predominantly along the separated sister-chromatid axes. Based on these observations and a quantitative distribution analysis of REC8 along sister chromatid axes, we propose that the high density of randomly distributed REC8 cohesin complexes promotes SCC and prevents illegitimate SC formation. PMID:27170622

  19. Severe inflammatory reaction induced by peritoneal trauma is the key driving mechanism of postoperative adhesion formation

    PubMed Central

    2011-01-01

    Background Many factors have been put forward as a driving mechanism of surgery-triggered adhesion formation (AF). In this study, we underline the key role of specific surgical trauma related with open surgery (OS) and laparoscopic (LS) conditions in postoperative AF and we aimed to study peritoneal tissue inflammatory reaction (TIR), remodelling specific complications of open surgery (OS) versus LS and subsequently evaluating AF induced by these conditions. Methods A prospective randomized study was done in 80 anaesthetised female Wistar rats divided equally into 2 groups. Specific traumatic OS conditions were induced by midline incision line (MIL) extension and tissue drying and specific LS conditions were remodelled by intraperitoneal CO2 insufflation at the 10 cm of water. TIR was evaluated at the 24th, 72nd, 120th and 168th hour by scoring scale. Statistical analysis was performed by the non-parametric t test and two-way ANOVA using Bonferroni post-tests. Results More pronounced residual TIR was registered after OS than after LS. There were no significant TIR interactions though highly significant differences were observed between the OS and LS groups (p < 0.0001) with regard to surgical and time factors. The TIR change differences between the OS and LS groups were pronounced with postoperative time p < 0.05 at the 24th and 72nd; p < 0.01 - 120th and p < 0.001 - 168th hrs. Adhesion free wounds were observed in 20.0 and 31.0% of cases after creation of OS and LS conditions respectively; with no significant differences between these values (p > 0.05). However larger adhesion size (41.67 ± 33.63) was observed after OS in comparison with LS (20.31 ± 16.38). The upper-lower 95% confidential limits ranged from 60.29 to 23.04 and from 29.04 to 11.59 respectively after OS and LS groups with significant differences (p = 0.03). Analogous changes were observed in adhesion severity values. Subsequently, severe TIR parameters were followed by larger sizes of severe

  20. The Aqueous Thermodynamics and Complexation Reactions of Anionic Silica and Uranium Species to High Concentration

    SciTech Connect

    Felmy, Andrew R.

    2004-06-01

    Highly basic tank wastes contain several important radionuclides, including 90Sr, 99Tc, and 60Co, as well as actinide elements (i.e., isotopes of U, Pu, and Am). These highly basic tank wastes are known to have leaked into the vadose zone at the Hanford Site. Upon entering the sediments in the vadose zone, the highly basic solutions dissolve large concentrations of silica from the silica and aluminosilicate minerals present in the subsurface. These dissolution reactions alter the chemical composition of the leaking solutions, transforming them from a highly basic (as high 2M NaOH) solution into a pore solution with a very high concentration of dissolved silica and a significantly reduced pH. This moderately basic (pH 9 to 11), high-silica solution has the potential to complex radionuclides and move through the subsurface. Such strong radionuclide complexation is a currently unconsidered transport vector that has the potential to expedite radionuclide transport through the vad ose zone. These strong complexation effects have the ability to significantly alter current conceptual models of contaminant migration beneath leaking tanks. In this project, we are determining the aqueous thermodynamics and speciation of dissolved silica and silica-radionuclide complexes to high silica concentration. We are also initiating studies of U(VI) speciation under strongly basic conditions.