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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 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

  6. 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

  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

    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

  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.

    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

  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. 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

  2. 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).

  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

    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.

  9. 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

  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. 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.

  12. 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

  13. 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

  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. 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.

  2. 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

  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. 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.

  6. 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

  7. 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.

  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. 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.

  16. 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

  17. 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

  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

    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

  20. 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

  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. 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

  14. 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.

  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. 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.

  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.

    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

  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 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

  3. 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].

  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. 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

  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. 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

  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. 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.

  14. 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

  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. 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.

  17. 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.

  18. 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.

  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. 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

  4. 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

  5. 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

  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.