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Sample records for identify reaction intermediate

  1. Identifying reaction intermediates and catalytic active sites through in situ characterization techniques

    SciTech Connect

    Foster, Andrew J.; Lobo, Raul F

    2010-01-01

    This tutorial review centers on recent advances and applications of experimental techniques that help characterize surface species and catalyst structures under in situ conditions. We start by reviewing recent applications of IR spectroscopy of working catalysis, emphasizing newer approaches such as Sum Frequency Generation and Polarization Modulation-infrared reflection absorption spectroscopy. This is followed by a section on solid-state NMR spectroscopy for the detection of surface species and reaction intermediates. These two techniques provide information mainly about the concentration and identity of the prevalent surface species. The following sections center on methods that provide structural and chemical information about the catalyst surface. The increasingly important role of high-pressure X-ray photoelectron spectroscopy in catalyst characterization is evident from the new and interesting information obtained on supported catalysts as presented in recent reports. X-Ray absorption spectroscopy (XANES and EXAFS) is used increasingly under reaction conditions to great advantage, although is inherently limited to systems where the bulk of the species in the sample are surface species. However, the ability of X-rays to penetrate the sample has been used cleverly by a number of groups to understand how changing reaction conditions change the structure and composition of surface atoms on supported catalyst.

  2. Cryogenic Trapping and Isotope Editing Identify a Protonated Water Cluster as an Intermediate in the Photosynthetic Oxygen-Evolving Reaction.

    PubMed

    Guo, Zhanjun; Barry, Bridgette A

    2016-09-01

    Internal water is known to play a catalytic role in several enzymes. In photosystem II (PSII), water is the substrate. To oxidize water, the PSII Mn4CaO5 cluster or oxygen evolving center (OEC) cycles through five oxidation states, termed Sn states. As reaction products, molecular oxygen is released, and protons are transferred through a ∼25 Å hydrogen-bonded network from the OEC to the thylakoid lumen. Previously, it was reported that a broad infrared band at 2880 cm(-1) is produced during the S1-to-S2 transition and accompanies flash-induced, S state cycling at pH 7.5. Here, we report that when the S2 state is trapped by continuous illumination under cryogenic conditions (190 K), an analogous 2740/2900 cm(-1) band is observed. The frequency depended on the sodium chloride concentration. This band is unambiguously assigned to a normal mode of water by D2(16)O and H2(18)O solvent exchange. Its large, apparent H2(18)O isotope shift, ammonia sensitivity, frequency, and intensity support assignment to a stretching vibration of a hydronium cation, H3O(+), in a small, protonated internal water cluster, nH2O(H3O(+)). Water OH stretching bands, which may be derived from the hydration shell of the hydronium ion, are also identified. Using the 2740 cm(-1) infrared marker, the results of calcium depletion and strontium reconstitution on the protonated water cluster are found to be pH dependent. This change is attributed to protonation of an amino acid side chain and a possible change in nH2O(H3O)(+) localization in the hydrogen-bonding network. These results are consistent with an internal water cluster functioning as a proton acceptor and an intermediate during the S1-to-S2 transition. Our experiments demonstrate the utility of this infrared signal as a novel functional probe in PSII. PMID:27491625

  3. Nuclear reactions at intermediate energies

    NASA Astrophysics Data System (ADS)

    Shyam, Radhey

    2016-05-01

    In the domain of Nuclear reactions at intermediate energies, the QCD coupling constant αs is large enough (~ 0.3 - 0.5) to render the perturbative calculational techniques inapplicable. In this regime the quarks are confined into colorless hadrons and it is expected that effective field theories of hadron interactions via exchange of hadrons, provide useful tools to describe such reactions. In this contribution we discuss the application of one such theory, the effective Lagrangian model, in describing the hadronic reactions at intermediate energies whose measurements are the focus of a vast international experimental program.

  4. Studying Reaction Intermediates Formed at Graphenic Surfaces

    NASA Astrophysics Data System (ADS)

    Sarkar, Depanjan; Sen Gupta, Soujit; Narayanan, Rahul; Pradeep, Thalappil

    2014-03-01

    We report in-situ production and detection of intermediates at graphenic surfaces, especially during alcohol oxidation. Alcohol oxidation to acid occurs on graphene oxide-coated paper surface, driven by an electrical potential, in a paper spray mass spectrometry experiment. As paper spray ionization is a fast process and the time scale matches with the reaction time scale, we were able to detect the intermediate, acetal. This is the first observation of acetal formed in surface oxidation. The process is not limited to alcohols and the reaction has been extended to aldehydes, amines, phosphenes, sugars, etc., where reaction products were detected instantaneously. By combining surface reactions with ambient ionization and mass spectrometry, we show that new insights into chemical reactions become feasible. We suggest that several other chemical transformations may be studied this way. This work opens up a new pathway for different industrially and energetically important reactions using different metal catalysts and modified substrate.

  5. A new intermediate in the Prins reaction.

    PubMed

    Yamabe, Shinichi; Fukuda, Takeshi; Yamazaki, Shoko

    2013-01-01

    Two Prins reactions were investigated by the use of DFT calculations. A model composed of R-CH=CH2 + H3O(+)(H2O)13 + (H2C=O)2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1). TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2) leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO-CH2-O-CH(R)-CH2-CH2-OH. This intermediate undergoes ring closure (TS4), affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. PMID:23532354

  6. A new intermediate in the Prins reaction

    PubMed Central

    Fukuda, Takeshi; Yamazaki, Shoko

    2013-01-01

    Summary Two Prins reactions were investigated by the use of DFT calculations. A model composed of R–CH=CH2 + H3O+(H2O)13 + (H2C=O)2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1). TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2) leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO–CH2–O–CH(R)–CH2–CH2–OH. This intermediate undergoes ring closure (TS4), affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. PMID:23532354

  7. Photocatalytic oxidation of paracetamol: dominant reactants, intermediates, and reaction mechanisms.

    PubMed

    Yang, Liming; Yu, Liya E; Ray, Madhumita B

    2009-01-15

    The role of primary active species (ecb(-), hvb(+), *OH, HO2*, O2*(-), and H2O2) during photocatalytic degradation of paracetamol (acetaminophen) using TiO2 catalyst was systematically investigated. Hydroxyl radicals (*OH) are responsible for the major degradation of paracetamol with a second-order rate constant (1.7 x 10(9) M(-1) s(-1)) for an *OH-paracetamol reaction. A total of 13 intermediates was identified and classified into four categories: (i) aromatic compounds, (ii) carboxylic acids, (iii) nitrogen-containing straight chain compounds, and (iv) inorganic species (ammonium and nitrate ions). Concentration profiles of identified intermediates indicate that paracetamol initially undergoes hydroxylation through *OH addition onto the aromatic ring at ortho (predominantly), meta, and para positions with respect to the -OH position of paracetamol. This initial *OH hydroxylation is followed by further oxidation generating carboxylic acids. Subsequent mineralization of smaller intermediates eventually increases ammonium and nitrate concentration in the system. PMID:19238980

  8. Radical Intermediates in Monooxygenase Reactions of Rieske Dioxygenases

    PubMed Central

    Chakrabarty, Sarmistha; Austin, Rachel N.; Deng, Dayi; Groves, John T.; Lipscomb, John D.

    2009-01-01

    Rieske dioxygenases catalyze the cis-dihydroxylation of a wide range of aromatic compounds to initiate their biodegradation. The archetypal Rieske dioxygenase naphthalene 1,2-dioxygenase (NDOS) catalyzes dioxygenation of naphthalene to form (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. NDOS is composed of three proteins: a reductase, a ferredoxin, and an α3β3 oxygenase (NDO). In each α subunit, NDO contains a Rieske Fe2S2 cluster and a mononuclear iron site where substrate dihydroxylation occurs. NDOS also catalyzes monooxygenase reactions for many substrates. The mechanism of the reaction is unknown for either the mono- or di-oxygenase reactions, but has been postulated to involve either direct reaction of a structurally characterized Fe(III)-hydroperoxy intermediate or the electronically equivalent Fe(V)-oxo-hydroxo intermediate formed by O-O bond cleavage before reaction with substrate. The reaction for the former intermediate is expected to proceed through cationic intermediates while the latter is anticipated to initially form a radical intermediate. Here the monooxygenation reactions of the diagnostic probe molecules norcarane and bicyclohexane are investigated. In each case, a significant amount of the rearrangement product derived from a radical intermediate (lifetime of 11–18 ns) is observed while little or no ring expansion product from a cationic intermediate is formed. Thus, monooxygenation of these molecules appears to proceed via the Fe(V)-oxo-hydroxo intermediate. The formation of this high-valent intermediate shows that it must also be considered as a possible participant in the dioxygenation reaction, in contrast to computational studies but in accord with previous biomimetic studies. PMID:17341076

  9. Investigation of Unexpected Reaction Intermediates in the Alkaline Hydrolysis of Methyl 3,5-Dinitrobenzoate

    ERIC Educational Resources Information Center

    Silva, Clesia C.; Silva, Ricardo O.; Navarro, Daniela M. A. F.; Navarro, Marcelo

    2009-01-01

    An experimental project aimed at identifying stable reaction intermediates is described. Initially, the studied reaction appears to involve the simple hydrolysis, by aqueous sodium hydroxide, of methyl 3,5-dinitrobenzoate dissolved in dimethyl sulfoxide. On mixing the substrates, however, the reaction mixture unexpectedly turns an intense red in…

  10. Kinetics, mechanisms and products of reactions of Criegee intermediates

    NASA Astrophysics Data System (ADS)

    Orr-Ewing, Andrew

    The atmospheric ozonolysis of alkenes such as isoprene produces Criegee intermediates which are increasingly recognized as important contributors to oxidation chemistry in the Earth's troposphere. Stabilized Criegee intermediates are conveniently produced in the laboratory by ultraviolet photolysis of diiodoalkanes in the presence of O2, and can be detected by absorption spectroscopy using their strong electronic bands in the near ultraviolet region. We have used these techniques to study a wide range of reactions of Criegee intermediates, including their self-reactions, and reactions with carboxylic acids and various other trace atmospheric constituents. In collaboration with the Sandia National Laboratory group led by Drs C.A. Taatjes and D.L. Osborn, we have used photoionization and mass spectrometry methods, combined with electronic structure calculations, to characterize the products of several of these reactions. Our laboratory studies determine rate coefficients for the Criegee intermediate reactions, many of which prove to be fast. In the case of reactions with carboxylic acids, a correlation between the dipole moments of the reactants and the reaction rate coefficients suggests a dipole-capture controlled reaction and allows us to propose a structure-activity relationship to predict the rates of related processes. The contributions of these various Criegee intermediate reactions to the chemistry of the troposphere have been assessed using the STOCHEM-CRI global atmospheric chemistry model. This work was supported by NERC grant NE/K004905/1.

  11. Ligand Intermediates in Metal-Catalyzed Reactions

    SciTech Connect

    Gladysz, John A.

    1999-07-31

    The longest-running goal of this project has been the synthesis, isolation, and physical chemical characterization of homogeneous transition metal complexes containing ligand types believed to be intermediates in the metal-catalyzed conversion of CO/H{sub 2}, CO{sub 2}, CH{sub 4}, and similar raw materials to organic fuels, feedstocks, etc. In the current project period, complexes that contain unusual new types of C{sub x}(carbide) and C{sub x}O{sub y} (carbon oxide) ligands have been emphasized. A new program in homogeneous fluorous phase catalysis has been launched as described in the final report.

  12. Computational analysis of the mechanism of chemical reactions in terms of reaction phases: hidden intermediates and hidden transition States.

    PubMed

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

    Computational approaches to understanding chemical reaction mechanisms generally begin by establishing the relative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening species via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by-step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an efficient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mechanism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase. In this Account, we examine mechanistic analysis with URVA in detail, focusing on recent theoretical insights (with a variety of reaction types) from our laboratories. Through the utilization of the concept of localized adiabatic vibrational modes that are associated with the internal coordinates, q(n)(s), of the reaction complex, the chemical character of each reaction phase can be identified via the adiabatic curvature coupling coefficients, A(n,s)(s). These quantities reveal whether a local adiabatic vibrational mode supports (A(n,s) > 0) or resists

  13. Dehydropericyclic Reactions: Symmetry-Controlled Routes to Strained Reactive Intermediates.

    PubMed

    Skraba-Joiner, Sarah L; Johnson, Richard P; Agarwal, Jay

    2015-12-01

    The conceptual dehydrogenation of pericyclic reactions yields dehydropericyclic processes, which usually lead to strained or reactive intermediates. This is a simple scheme for inventing new chemical reactions. Computational results on two novel dehydropericyclic reactions are presented here. Conjugated enynes undergo a singlet-state photoisomerization that transposes the methylene carbon. We previously suggested excited-state closure to 1,2-cyclobutadiene followed by thermal ring opening. CCSD(T)//DFT computations show two minima of similar energy corresponding to 1,2-cyclobutadiene, one chiral and closed shell and the second a planar diradical. The chiral structure has a low barrier to ring opening and may best explain results on enyne photoisomerization. The first examples of 1,3-diyne + yne cycloadditions to give o-benzynes were reported in 1997. Computations on intramolecular versions of this tridehydro (-3H2) Diels-Alder reaction support a concerted mechanism for the parent triyne (1,3,8-nonatriyne); however, a slight electronic advantage in the concerted path may be outweighed by the difference in entropy of activation for sequential vs simultaneous formation of two new ring bonds. PMID:26418846

  14. Accomplishing structural change: Identifying intermediate indicators of success

    PubMed Central

    Miller, Robin Lin; Reed, Sarah J.; Francisco, Vincent

    2012-01-01

    Coalitions are routinely employed across the United States as a method of mobilizing communities to improve local conditions that impact on citizens’ well-being. Success in achieving specific objectives for environmental or structural community change may not quickly translate into improved population outcomes in the community, posing a dilemma for coalitions that pursue changes that focus on altering community conditions. Considerable effort by communities to plan for and pursue structural change objectives, without evidence of logical and appropriate intermediate markers of success could lead to wasted effort. Yet, the current literature provides little guidance on how coalitions might select intermediate indicators of achievement to judge their progress and the utility of their effort. The current paper explores the strengths and weaknesses of various indicators of intermediate success in creating structural changes among a sample of 13 coalitions organized to prevent exposure to HIV among high-risk adolescents in their local communities. PMID:22875684

  15. Silyloxyazadienes: one intermediate and two competitive pericyclic reactions.

    PubMed

    Bongini, Alessandro; Panunzio, Mauro; Venturini, Alessandro

    2010-05-21

    The two competing mechanisms in the reaction of 3-trialkylsilyloxy-2-aza-1,3 dienes to form beta-lactams through a [2+2] electrocyclic ring closure or tetrahydrooxazinan-4-ones via a [4+2] hetero-Diels-Alder reaction were studied using Density Functional computations. Although the [2+2] and [4+2] mechanisms are typical of dienes, their competition, starting from the same diene intermediate, has not yet been observed and analyzed. This competition is governed by a delicate interplay between temperature and substituents at the diene and dienophile, respectively. Clearly, entropy tends to favor the [4+2] hetero-Diels-Alder at low temperatures and the [2+2] electrocyclic ring closure at high temperatures, but simple substituent modifications at the diene and dienophile, can make the [4+2] competitive at high temperatures and sometimes even transform the [4+2] concerted mechanism into a two-step Mukaiyama-type process. Moreover, a study of the global electrophilicity values showed that charge transfer in the hetero-Diels-Alder transition states is driven by chemical hardness rather than by chemical potential.

  16. Mechanistic insight into the hydrazine decomposition on Rh(111): effect of reaction intermediate on catalytic activity.

    PubMed

    Deng, Zhigang; Lu, Xiaoqing; Wen, Zengqiang; Wei, Shuxian; Liu, Yunjie; Fu, Dianling; Zhao, Lianming; Guo, Wenyue

    2013-10-14

    Periodic density functional theory (DFT) calculations have been performed to systematically investigate the effect of reaction intermediate on catalytic activity for hydrazine (N2H4) decomposition on Rh(111). Reaction mechanisms via intramolecular and NH2-assisted N2H4 decompositions are comparatively analyzed, including adsorption configuration, reaction energy and barrier of elementary step, and reaction network. Our results show that the most favorable N2H4 decomposition pathway starts with the initial N-N bond scission to the NH2 intermediate, followed by stepwise H stripping from adsorbed N2Hx (x = 1-4) species, and finally forms the N2 and NH3 products. Comparatively, the stepwise intramolecular dehydrogenation via N2H4→ N2H3→ N2H2→ N2H → N2, and N2H4→ NH2→ NH → N with or without NH2 promotion effect, are unfavorable due to higher energy barriers encountered. Energy barrier analysis, reaction rate constants, and electronic structures are used to identify the crucial competitive route. The promotion effect of the NH2 intermediate is structurally reflected in the weakening of the N-H bond and strengthening of the N-N bond in N2Hx in the coadsorption system; it results intrinsically from the less structural deformation of the adsorbate, and weakening of the interaction between dehydrogenated fragment and departing H in transition state. Our results highlight the crucial effect of reaction intermediate on catalytic activity and provide a theoretical approach to analyze the effect. PMID:23990024

  17. Mechanistic insight into the hydrazine decomposition on Rh(111): effect of reaction intermediate on catalytic activity.

    PubMed

    Deng, Zhigang; Lu, Xiaoqing; Wen, Zengqiang; Wei, Shuxian; Liu, Yunjie; Fu, Dianling; Zhao, Lianming; Guo, Wenyue

    2013-10-14

    Periodic density functional theory (DFT) calculations have been performed to systematically investigate the effect of reaction intermediate on catalytic activity for hydrazine (N2H4) decomposition on Rh(111). Reaction mechanisms via intramolecular and NH2-assisted N2H4 decompositions are comparatively analyzed, including adsorption configuration, reaction energy and barrier of elementary step, and reaction network. Our results show that the most favorable N2H4 decomposition pathway starts with the initial N-N bond scission to the NH2 intermediate, followed by stepwise H stripping from adsorbed N2Hx (x = 1-4) species, and finally forms the N2 and NH3 products. Comparatively, the stepwise intramolecular dehydrogenation via N2H4→ N2H3→ N2H2→ N2H → N2, and N2H4→ NH2→ NH → N with or without NH2 promotion effect, are unfavorable due to higher energy barriers encountered. Energy barrier analysis, reaction rate constants, and electronic structures are used to identify the crucial competitive route. The promotion effect of the NH2 intermediate is structurally reflected in the weakening of the N-H bond and strengthening of the N-N bond in N2Hx in the coadsorption system; it results intrinsically from the less structural deformation of the adsorbate, and weakening of the interaction between dehydrogenated fragment and departing H in transition state. Our results highlight the crucial effect of reaction intermediate on catalytic activity and provide a theoretical approach to analyze the effect.

  18. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates

    SciTech Connect

    Lin, M.C.

    1993-12-01

    Small aromatic radicals such as C{sub 6}H{sub 5}, C{sub 6}H{sub 5}O and C{sub 6}H{sub 4} are key prototype species of their homologs. C{sub 6}H{sub 5} and its oxidation product, C{sub 6}H{sub 5}O are believed to be important intermediates which play a pivotal role in hydrocarbon combustion, particularly with regard to soot formation. Despite their fundamental importance, experimental data on the reaction mechanisms and reactivities of these species are very limited. For C{sub 6}H{sub 5}, most kinetic data except its reactions with NO and NO{sub 2}, were obtained by relative rate measurements. For C{sub 6}H{sub 5}O, the authors have earlier measured its fragmentation reaction producing C{sub 5}H{sub 5} + CO in shock waves. For C{sub 6}H{sub 4}, the only rate constant measured in the gas phase is its recombination rate at room temperature. The authors have proposed to investigate systematically the kinetics and mechanisms of this important class of molecules using two parallel laser diagnostic techniques--laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the past two years, study has been focused on the development of a new multipass adsorption technique--the {open_quotes}cavity-ring-down{close_quotes} technique for kinetic applications. The preliminary results of this study appear to be quite good and the sensitivity of the technique is at least comparable to that of the laser-induced fluorescence method.

  19. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    SciTech Connect

    Heroux, A.; Bozinovski, D; Valley, M; Fitzpatrick, P; Orville, A

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

  20. Separation of chemical reaction intermediates by metal-organic frameworks.

    PubMed

    Centrone, Andrea; Santiso, Erik E; Hatton, T Alan

    2011-08-22

    HPLC columns custom-packed with metal-organic framework (MOF) materials are used for the separation of four small intermediates and byproducts found in the commercial synthesis of an important active pharmaceutical ingredient in methanol. In particular, two closely related amines can be separated in the methanol reaction medium using MOFs, but not with traditional C18 columns using an optimized aqueous mobile phase. Infrared spectroscopy, UV-vis spectroscopy, X-ray diffraction, and thermogravimetric analysis are used in combination with molecular dynamic simulations to study the separation mechanism for the best-performing MOF materials. It is found that separation with ZIF-8 is the result of an interplay between the thermodynamic driving force for solute adsorption within the framework pores and the kinetics of solute diffusion into the material pores, while the separation with Basolite F300 is achieved because of the specific interactions between the solutes and Fe(3+) sites. This work, and the exceptional ability to tailor the porous properties of MOF materials, points to prospects for using MOF materials for the continuous separation and synthesis of pharmaceutical compounds.

  1. Reaction intermediates in the catalytic Gif-type oxidation from nuclear inelastic scattering

    NASA Astrophysics Data System (ADS)

    Rajagopalan, S.; Asthalter, T.; Rabe, V.; Laschat, S.

    2016-12-01

    Nuclear inelastic scattering (NIS) of synchrotron radiation, also known as nuclear resonant vibrational spectroscopy (NRVS), has been shown to provide valuable insights into metal-centered vibrations at Mössbauer-active nuclei. We present a study of the iron-centered vibrational density of states (VDOS) during the first step of the Gif-type oxidation of cyclohexene with a novel trinuclear Fe3(μ 3-O) complex as catalyst precursor. The experiments were carried out on shock-frozen solutions for different combinations of reactants: Fe3(μ 3-O) in pyridine solution, Fe3(μ 3-O) plus Zn/acetic acid in pyridine without and with addition of either oxygen or cyclohexene, and Fe3(μ 3-O)/Zn/acetic acid/pyridine/cyclohexene (reaction mixture) for reaction times of 1 min, 5 min, and 30 min. The projected VDOS of the Fe atoms was calculated on the basis of pseudopotential density functional calculations. Two possible reaction intermediates were identified as [Fe(III)(C5H5N)2(O2CCH3)2]+ and Fe(II)(C5H5N)4(O2CCH3)2, yielding evidence that NIS (NRVS) allows to identify the presence of iron-centered intermediates also in complex reaction mixtures.

  2. Spectroscopic features of cytochrome P450 reaction intermediates

    PubMed Central

    Luthra, Abhinav; Denisov, Ilia G.; Sligar, Stephen G.

    2010-01-01

    Preface Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2-3]. Historically these enzymes received their name from ‘pigment 450’ due to the unusual position of the Soret band in UV-Vis absorption spectra of the reduced CO-saturated state [4-5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other ‘P450-like heme enzymes’ such as nitric oxide synthase and chloroperoxidase, the phenomenological term ‘cytochrome P450’ is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420 nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle. PMID:21167809

  3. Structural characterization of the reaction pathway in phosphoserine phosphatase: Crystallographic 'snapshots' of intermediate states.

    SciTech Connect

    Wang, Weiru; Cho, Ho S.; Kim, Rosalind; Jancarik, Jaru; Yokota, Hisao; Nguyen, Henry H.; Grigoriev, Igor V.; Wemmer, David E.; Kim, Sung-Hou

    2004-04-12

    Phosphoserine phosphatase (PSP) is a member of a large class of enzymes that catalyze phosphoester hydrolysis using a phosphoaspartate enzyme intermediate. PSP is a likely regulator of the steady-state-serine level in the brain, which is a critical co-agonist of the N-methyl--aspartate type of glutamate receptors. Here, we present high-resolution (1.5 1.9 Angstrom) structures of PSP from Methanococcus jannaschii, which define the open state prior to substrate binding, the complex with phosphoserine substrate bound (with a D to N mutation in the active site), and the complex with AlF3, a transition-state analog for the phospho-transfer steps in the reaction. These structures, together with those described for the BeF3- complex (mimicking the phospho-enzyme) and the enzyme with phosphate product in the active site, provide a detailed structural picture of the full reaction cycle. The structure of the apostate indicates partial unfolding of the enzyme to allow substrate binding, with refolding in the presence of substrate to provide specificity. Interdomain and active-site conformational changes are identified. The structure with the transition state analog bound indicates a ''tight'' intermediate. A striking structure homology, with significant sequence conservation, among PSP, P-type ATPases and response regulators suggests that the knowledge of the PSP reaction mechanism from the structures determined will provide insights into the reaction mechanisms of the other enzymes in this family.

  4. Oxidation Reactions Performed by Soluble Methane Monooxygenase Hydroxylase Intermediates Hperoxo and Q Proceed by Distinct Mechanisms†

    PubMed Central

    Tinberg, Christine E.; Lippard, Stephen J.

    2010-01-01

    Soluble methane monooxygenase is a bacterial enzyme that converts methane to methanol at a carboxylate-bridged diiron center with exquisite control. Because the oxidizing power required for this transformation is demanding, it is not surprising that the enzyme is also capable of hydroxylating and epoxidizing a broad range of hydrocarbon substrates in addition to methane. In this work we took advantage of this promiscuity of the enzyme to gain insight into the mechanisms of action of Hperoxo and Q, two oxidants that are generated sequentially during the reaction of reduced protein with O2. Using double-mixing stopped flow spectroscopy, we investigated the reactions of the two intermediate species with a panel of substrates of varying C–H bond strength. Three classes of substrates were identified according to the rate-determining step in the reaction. We show for the first time that an inverse trend exists between the rate constant of reaction with Hperoxo and the C–H bond strength of the hydrocarbon examined for those substrates in which C–H bond activation is rate-determining. Deuterium kinetic isotope effects revealed that reactions performed by Q, but not Hperoxo, involve extensive quantum mechanical tunneling. This difference sheds light on the observation that Hperoxo is not a potent enough oxidant to hydroxylate methane, whereas Q can perform this reaction in a facile manner. In addition, the reaction of Hperoxo with acetonitrile appears to proceed by a distinct mechanism in which a cyanomethide anionic intermediate is generated, bolstering the argument that Hperoxo is an electrophilic oxidant and operates via two-electron transfer chemistry. PMID:20681546

  5. Microwave kinetic spectroscopy of reaction intermediates: O+ethylene reaction at low pressure

    NASA Astrophysics Data System (ADS)

    Endo, Yasuki; Tsuchiya, Soji; Yamada, Chikashi; Hirota, Eizi; Koda, Seiichiro

    1986-10-01

    A microwave spectroscopic method has been developed to study elementary reactions in real time through in situ observation of rotational spectra of reaction intermediates such as free radicals with lifetime as short as 1 ms. This method was applied to the O(3P)+ethylene reaction in order to assess the roles of (a) vinoxy+H and (b) CH3+CHO channels in the initial process. The reaction was initiated by irradiating an N2O/C2H4 mixture containing a trace amount of mercury with the 253.7 nm mercury resonance line, and the time evolution of vinoxy, HCO, and H2CO was followed by measuring their microwave absorption intensities as functions of time. The branching ratio was thus determined to be 0.4±0.1 and 0.5±0.1 for (a) and (b), respectively, at the sample pressure of 30 mTorr. The present result agrees with those obtained by Hunziker et al. [J. Photochem. 17, 377 (1981)] using much higher pressures of samples, but is not compatible with the observation of Buss et al. [J. Photochem. 17, 389 (1981)] that (a) is dominant in collision-free conditions.

  6. Structural Insights into Intermediate Steps in the Sir2 Deacetylation Reaction

    SciTech Connect

    Hawse, William F.; Hoff, Kevin G.; Fatkins, David G.; Daines, Alison; Zubkova, Olga V.; Schramm, Vern L.; Zheng, Weiping; Wolberger, Cynthia

    2010-07-22

    Sirtuin enzymes comprise a unique class of NAD{sup +}-dependent protein deacetylases. Although structures of many sirtuin complexes have been determined, structural resolution of intermediate chemical steps are needed to understand the deacetylation mechanism. We report crystal structures of the bacterial sirtuin, Sir2Tm, in complex with an S-alkylamidate intermediate, analogous to the naturally occurring O-alkylamidate intermediate, and a Sir2Tm ternary complex containing a dissociated NAD{sup +} analog and acetylated peptide. The structures and biochemical studies reveal critical roles for the invariant active site histidine in positioning the reaction intermediate, and for a conserved phenylalanine residue in shielding reaction intermediates from base exchange with nicotinamide. The new structural and biochemical studies provide key mechanistic insight into intermediate steps of the Sir2 deacetylation reaction.

  7. Ozonation of benzotriazole and methylindole: Kinetic modeling, identification of intermediates and reaction mechanisms.

    PubMed

    Benitez, F Javier; Acero, Juan L; Real, Francisco J; Roldán, Gloria; Rodríguez, Elena

    2015-01-23

    The ozonation of 1H-benzotriazole (BZ) and 3-methylindole (ML), two emerging contaminants that are frequently present in aquatic environments, was investigated. The experiments were performed with the contaminants (1μM) dissolved in ultrapure water. The kinetic study led to the determination of the apparent rate constants for the ozonation reactions. In the case of 1H-benzotriazole, these rate constants varied from 20.1 ± 0.4M(-1)s(-1) at pH=3 to 2143 ± 23 M(-1)s(-1) at pH=10. Due to its acidic nature (pKa=8.2), the degree of dissociation of this pollutant was determined at every pH of work, and the specific rate constants of the un-dissociated and dissociated species were evaluated, being the values of these rate constants 20.1 ± 2.0 and 2.0 ± 0.3 × 10(3)M(-1)s(-1), respectively. On the contrary, 3-methylindole does not present acidic nature, and therefore, it can be proposed an average value for its rate constant of 4.90 ± 0.7 × 10(5)M(-1)s(-1) in the whole pH range 3-10. Further experiments were performed to identify the main degradation byproducts (10 mg L(-1) of contaminants, 0.023 gh(-1) of ozone). Up to 8 intermediates formed in the ozonation of 3-methylindole were identified by LC-TOFMS, while 6 intermediates were identified in the ozonation of 1H-benzotriazole. By considering these intermediate compounds, the reaction mechanisms were proposed and discussed. Finally, evaluated rate constants allowed to predict and modeling the oxidation of these micropollutants in general aquatic systems. PMID:24953706

  8. Ozonation of benzotriazole and methylindole: Kinetic modeling, identification of intermediates and reaction mechanisms.

    PubMed

    Benitez, F Javier; Acero, Juan L; Real, Francisco J; Roldán, Gloria; Rodríguez, Elena

    2015-01-23

    The ozonation of 1H-benzotriazole (BZ) and 3-methylindole (ML), two emerging contaminants that are frequently present in aquatic environments, was investigated. The experiments were performed with the contaminants (1μM) dissolved in ultrapure water. The kinetic study led to the determination of the apparent rate constants for the ozonation reactions. In the case of 1H-benzotriazole, these rate constants varied from 20.1 ± 0.4M(-1)s(-1) at pH=3 to 2143 ± 23 M(-1)s(-1) at pH=10. Due to its acidic nature (pKa=8.2), the degree of dissociation of this pollutant was determined at every pH of work, and the specific rate constants of the un-dissociated and dissociated species were evaluated, being the values of these rate constants 20.1 ± 2.0 and 2.0 ± 0.3 × 10(3)M(-1)s(-1), respectively. On the contrary, 3-methylindole does not present acidic nature, and therefore, it can be proposed an average value for its rate constant of 4.90 ± 0.7 × 10(5)M(-1)s(-1) in the whole pH range 3-10. Further experiments were performed to identify the main degradation byproducts (10 mg L(-1) of contaminants, 0.023 gh(-1) of ozone). Up to 8 intermediates formed in the ozonation of 3-methylindole were identified by LC-TOFMS, while 6 intermediates were identified in the ozonation of 1H-benzotriazole. By considering these intermediate compounds, the reaction mechanisms were proposed and discussed. Finally, evaluated rate constants allowed to predict and modeling the oxidation of these micropollutants in general aquatic systems.

  9. 18F-Labelled Intermediates for Radiosynthesis by Modular Build-Up Reactions: Newer Developments

    PubMed Central

    Ermert, Johannes

    2014-01-01

    This brief review gives an overview of newer developments in 18F-chemistry with the focus on small 18F-labelled molecules as intermediates for modular build-up syntheses. The short half-life (<2 h) of the radionuclide requires efficient syntheses of these intermediates considering that multistep syntheses are often time consuming and characterized by a loss of yield in each reaction step. Recent examples of improved synthesis of 18F-labelled intermediates show new possibilities for no-carrier-added ring-fluorinated arenes, novel intermediates for tri[18F]fluoromethylation reactions, and 18F-fluorovinylation methods. PMID:25343144

  10. Bimetallic oxidative addition involving radical intermediates in nickel-catalyzed alkyl-alkyl Kumada coupling reactions.

    PubMed

    Breitenfeld, Jan; Ruiz, Jesus; Wodrich, Matthew D; Hu, Xile

    2013-08-14

    Many nickel-based catalysts have been reported for cross-coupling reactions of nonactivated alkyl halides. The mechanistic understanding of these reactions is still primitive. Here we report a mechanistic study of alkyl-alkyl Kumada coupling catalyzed by a preformed nickel(II) pincer complex ([(N2N)Ni-Cl]). The coupling proceeds through a radical process, involving two nickel centers for the oxidative addition of alkyl halide. The catalysis is second-order in Grignard reagent, first-order in catalyst, and zero-order in alkyl halide. A transient species, [(N2N)Ni-alkyl(2)](alkyl(2)-MgCl), is identified as the key intermediate responsible for the activation of alkyl halide, the formation of which is the turnover-determining step of the catalysis.

  11. Bimetallic oxidative addition involving radical intermediates in nickel-catalyzed alkyl-alkyl Kumada coupling reactions.

    PubMed

    Breitenfeld, Jan; Ruiz, Jesus; Wodrich, Matthew D; Hu, Xile

    2013-08-14

    Many nickel-based catalysts have been reported for cross-coupling reactions of nonactivated alkyl halides. The mechanistic understanding of these reactions is still primitive. Here we report a mechanistic study of alkyl-alkyl Kumada coupling catalyzed by a preformed nickel(II) pincer complex ([(N2N)Ni-Cl]). The coupling proceeds through a radical process, involving two nickel centers for the oxidative addition of alkyl halide. The catalysis is second-order in Grignard reagent, first-order in catalyst, and zero-order in alkyl halide. A transient species, [(N2N)Ni-alkyl(2)](alkyl(2)-MgCl), is identified as the key intermediate responsible for the activation of alkyl halide, the formation of which is the turnover-determining step of the catalysis. PMID:23865460

  12. X-ray Crystallography of A Metalloprotein: A Reaction Intermediate of Heme Oxygenase

    NASA Astrophysics Data System (ADS)

    Unno, Masaki; Matsui, Toshitaka; Ikeda-Saito, Masao

    X-ray crystallographic analysis of a metalloprotein requires knowing the electronic state of the metal center, if one wants to elucidate the exact function and/or reaction mechanism. As an example, we show our recent structural analysis of the heme oxygenase reaction intermediate which is involved in the third step of the heme degradation reaction. The reaction intermediate was crystallized under anaerobic condition, and the obtained crystals were frozen into liquid nitrogen. The absorption spectra of the single crystal before and after X-ray irradiation were compared with that of the frozen solution in 100 K cold nitrogen stream. The determined structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. This structure combined with the QM/MM calculation supports our proposal that the biliverdin is produced via Fe-OOH verdoheme intermediate.

  13. Kinetics and intermediates of the reaction of fully reduced Escherichia coli bo₃ ubiquinol oxidase with O₂.

    PubMed

    Szundi, Istvan; Kittredge, Clive; Choi, Sylvia K; McDonald, William; Ray, Jayashree; Gennis, Robert B; Einarsdóttir, Ólöf

    2014-08-26

    Cytochrome bo₃ ubiquinol oxidase from Escherichia coli catalyzes the reduction of O₂ to water by ubiquinol. The reaction mechanism and the role of ubiquinol continue to be a subject of discussion. In this study, we report a detailed kinetic scheme of the reaction of cytochrome bo₃ with O₂ with steps specific to ubiquinol. The reaction was investigated using the CO flow-flash method, and time-resolved optical absorption difference spectra were collected from 1 μs to 20 ms after photolysis. Singular value decomposition-based global exponential fitting resolved five apparent lifetimes, 22 μs, 30 μs, 42 μs, 470 μs, and 2.0 ms. The reaction mechanism was derived by an algebraic kinetic analysis method using frequency-shifted spectra of known bovine states to identify the bo3 intermediates. It shows 42 μs O₂ binding (3.8 × 10(7) M(-1) s(-1)), producing compound A, followed by faster (22 μs) heme b oxidation, yielding a mixture of PR and F, and rapid heme b rereduction by ubiquinol (30 μs), producing the F intermediate and semiquinone. In the 470 μs step, the o₃ F state is converted into the o₃(3+) oxidized state, presumably by semiquinone/ubiquinol, without the concomitant oxidation of heme b. The final 2 ms step shows heme b reoxidation and the partial rereduction of the binuclear center and, following O₂ binding, the formation of a mixture of P and F during a second turnover cycle. The results show that ubiquinol/semiquinone plays a complex role in the mechanism of O₂ reduction by bo₃, displaying kinetic steps that have no analogy in the CuA-containing heme-copper oxidases. PMID:25076393

  14. Incomplete Combustion of Hydrogen: Trapping a Reaction Intermediate

    ERIC Educational Resources Information Center

    Mattson, Bruce; Hoette, Trisha

    2007-01-01

    The combustion of hydrogen in air is quite complex with at least 28 mechanistic steps and twelve reaction species. Most of the species involved are radicals (having unpaired electrons) in nature. Among the various species generated, a few are stable, including hydrogen peroxide. In a normal hydrogen flame, the hydrogen peroxide goes on to further…

  15. Elusive Reaction Intermediates in Solution Explored by ESI-MS: Reverse Periscope for Mechanistic Investigations.

    PubMed

    Iacobucci, Claudio; Reale, Samantha; De Angelis, Francesco

    2016-02-24

    Just as periscopes allow a submarine to visually search for objects above the surface of the sea, in a reversed periscope fashion electrospray mass spectrometry (ESI-MS) can analyze the compounds at the gas phase/liquid phase interface for chemical entities which may exist in solution. The challenge is the identification and structural characterization of key elusive reaction intermediates in chemical transformations, intermediates which are able to explain how chemical processes occur. This Minireview summarizes recent selected publications on the use of ESI-MS techniques for studying solution intermediates of homogeneous chemical reactions. PMID:26799781

  16. Elusive Reaction Intermediates in Solution Explored by ESI-MS: Reverse Periscope for Mechanistic Investigations.

    PubMed

    Iacobucci, Claudio; Reale, Samantha; De Angelis, Francesco

    2016-02-24

    Just as periscopes allow a submarine to visually search for objects above the surface of the sea, in a reversed periscope fashion electrospray mass spectrometry (ESI-MS) can analyze the compounds at the gas phase/liquid phase interface for chemical entities which may exist in solution. The challenge is the identification and structural characterization of key elusive reaction intermediates in chemical transformations, intermediates which are able to explain how chemical processes occur. This Minireview summarizes recent selected publications on the use of ESI-MS techniques for studying solution intermediates of homogeneous chemical reactions.

  17. Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

    SciTech Connect

    Yang, Xiaojing; Ren, Zhong; Kuk, Jane; Moffat, Keith

    2012-03-27

    Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C{sub 15} = C{sub 16} double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C{sub 15} methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

  18. Cycloaddition reactions of allenes with N-phenylmaleimide. A two-step, diradical-intermediate process

    SciTech Connect

    Pasto, D.J.; Heid, P.F.; Warren, S.E.

    1982-06-30

    The stereoselectivities, chemoselectivities, relative reactivities, and kinetic isotope effects have been determined in the cycloaddition reactions of substituted allenes with N-phenylmaleimide. The comparison of these results with those derived from the studies of the cycloaddition of 1,1-dichloro-2,2-difluoroethene and the radical-chain addition of benzenethiol to allenes strongly indicates that the cycloadditions with N-phenylmaleimide occur via a two-step, diradical-intermediate process. The stereochemical features controlling the formation of the stereoisomeric diradical intermediates and their ring closures are discussed. In addition to the cycloaddition processes, competitive ene reactions occur to produce intermediate dienes, which react further to produce 1:2 adducts or nonreactive alkyne-containing 1:1 adducts. These ene reactions also appear to proceed via diradical intermediates.

  19. Ketene as a Reaction Intermediate in the Carbonylation of Dimethyl Ether to Methyl Acetate over Mordenite.

    PubMed

    Rasmussen, Dominik B; Christensen, Jakob M; Temel, Burcin; Studt, Felix; Moses, Poul Georg; Rossmeisl, Jan; Riisager, Anders; Jensen, Anker D

    2015-06-15

    Unprecedented insight into the carbonylation of dimethyl ether over Mordenite is provided through the identification of ketene (CH2CO) as a reaction intermediate. The formation of ketene is predicted by detailed DFT calculations and verified experimentally by the observation of doubly deuterated acetic acid (CH2DCOOD), when D2O is introduced in the feed during the carbonylation reaction. PMID:25967363

  20. Study of intermediates from transition metal excited-state electron-transfer reactions

    SciTech Connect

    Hoffman, M.Z.

    1992-07-31

    Conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used to study the intermediates involved in transition metal excited-state electron-transfer reactions. These intermediates were excited state of Ru(II) and Cr(III) photosensitizers, their reduced forms, and species formed in reactions of redox quenchers and electron-transfer agents. Of particular concern was the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes. (DLC)

  1. Identifying the Tautomeric Form of a Deoxyguanosine-Estrogen Quinone Intermediate

    PubMed Central

    Stack, Douglas E.

    2015-01-01

    Mechanistic insights into the reaction of an estrogen o-quinone with deoxyguanosine has been further investigated using high level density functional calculations in addition to the use of 4-hyroxycatecholestrone (4-OHE1) regioselectivity labeled with deuterium at the C1-position. Calculations using the M06-2X functional with large basis sets indicate the tautomeric form of an estrogen-DNA adduct present when glycosidic bonds cleavage occurs is comprised of an aromatic A ring structure. This tautomeric form was further verified by use of deuterium labelling of the catechol precursor use to form the estrogen o-quinone. Regioselective deuterium labelling at the C1-position of the estrogen A ring allows discrimination between two tautomeric forms of a reaction intermediate either of which could be present during glycosidic bond cleavage. HPLC-MS analysis indicates a reactive intermediate with a m/z of 552.22 consistent with a tautomeric form containing no deuterium. This intermediate is consistent with a reaction mechanism that involves: (1) proton assisted Michael addition; (2) re-aromatization of the estrogen A ring; and (3) glycosidic bond cleavage to form the known estrogen-DNA adduct, 4-OHE1-1-N7Gua. PMID:26378590

  2. Population of bound excited states in intermediate-energy fragmentation reactions

    SciTech Connect

    Obertelli, A.; Gade, A.; Bazin, D.; Hansen, P.G.; Hoagland, T.; Lecouey, J.-L.; Mueller, W.F.; Yoneda, K.; Campbell, C.M.; Cook, J.M.; Davies, A.D.; Dinca, D.-C.; Glasmacher, T.; Terry, J.R.; Zwahlen, H.; Cottle, P.D.; Kemper, K.W.; Reynolds, R.R.; Roeder, B.T.; Tostevin, J.A.

    2006-04-15

    Fragmentation reactions with intermediate-energy heavy-ion beams exhibit a wide range of reaction mechanisms, ranging from direct reactions to statistical processes. We examine this transition by measuring the relative population of excited states in several sd-shell nuclei produced by fragmentation with the number of removed nucleons ranging from two to sixteen. The two-nucleon removal is consistent with a non-dissipative process, whereas the removal of more than five nucleons appears to be mainly statistical.

  3. Multidimensional least-squares resolution of Raman spectra from intermediates in sensitized photochemical reactions

    SciTech Connect

    Fister, J.C. III; Harris, J.M.

    1995-12-01

    Transient resonance Raman spectroscopy is used to elicit reaction kinetics and intermediate spectra from sensitized photochemical reactions. Nonlinear least-squares analysis of Raman spectra of a triplet-state photosensitizer (benzophenone), acquired as a function of laser intensity and/or quencher concentration allow the Raman spectra of the sensitizer excited state and intermediate photoproducts to be resolved from the spectra of the ground state and solvent. In cases where physical models describing the system kinetics cannot be found, factor analysis techniques are used to obtain the intermediate spectra. Raman spectra of triplet state benzophenone and acetophenone, obtained as a function of laser excitation kinetics, and the Raman spectra of intermediates formed by energy transfer (triplet-state biacetyl) and hydrogen abstraction (benzhydrol radical) are discussed.

  4. N-heterocyclic carbene organocatalytic reductive β,β-coupling reactions of nitroalkenes via radical intermediates.

    PubMed

    Du, Yu; Wang, Yuhuang; Li, Xin; Shao, Yaling; Li, Guohui; Webster, Richard D; Chi, Yonggui Robin

    2014-11-01

    An unprecedented N-heterocyclic carbene catalytic reductive β,β-carbon coupling of α,β-nitroalkenes, by using an organic substrate to mimic the one-electron oxidation role of the pyruvate ferredoxin oxidoreductase (PFOR) in living systems, has been developed. The reaction goes through a radical anion intermediate generated under a catalytic redox process. For the first time, the presence of radical anion intermediate in NHC organocatalysis is observed and clearly verified. PMID:25343564

  5. Recent developments in methods for identifying reaction coordinates.

    PubMed

    Li, Wenjin; Ma, Ao

    2014-01-01

    In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor.

  6. Intermediates Formed in the Reactions of Organocuprates with α,β-Unsaturated Nitriles.

    PubMed

    Putau, Aliaksei; Brand, Harald; Koszinowski, Konrad

    2016-08-26

    Conjugate additions of organocuprates are of outstanding importance for organic synthesis. To improve our mechanistic understanding of these reactions, we have used electrospray ionization mass spectrometry for the identification of the ionic intermediates formed upon the treatment of LiCuR2 ⋅LiCN (R=Me, Bu, Ph) with a series of α,β-unsaturated nitriles. Acrylonitrile, the weakest Michael acceptor included, did not afford any detectable intermediates. Fumaronitrile (FN) yielded adducts of the type Lin-1 Cun R2n (FN)n (-) , n=1-3. When subjected to fragmentation in the gas phase, these adducts were not converted into the conjugate addition products, but re-dissociated into the reactants. In contrast, the reaction with 1,1-dicyanoethylene furnished the products of the conjugate addition without any observable intermediates. Tri- and tetracyanoethylene proved to be quite reactive as well. The presence of several cyano groups in these substrates opened up reaction pathways different from simple conjugate additions, however, and led to dimerization and substitution reactions. Moreover, the gas-phase fragmentation behavior of the species formed from these substrates indicated the occurrence of single-electron transfer processes. Additional quantum-chemical calculations provided insight into the structures and stabilities of the observed intermediates and their consecutive reactions. PMID:27461093

  7. On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study

    NASA Astrophysics Data System (ADS)

    Carnevale, V.; Raugei, S.; Piana, S.; Carloni, P.

    2008-07-01

    Several mechanistic aspects of Aspartic Proteases' enzymatic reaction are currently highly controversial. There is general consensus that the first step of the reaction involves a nucleophilic attack of a water molecule to the substrate carbonyl carbon with subsequent formation of a metastable intermediate (INT). However, the exact nature of this intermediate is subject of debate. While ab initio and QM/MM calculations predict that INT is a neutral gem-diol specie, empirical valence bond calculations suggest that the protein frame can stabilize a charged oxyanion intermediate. Here the relative stability of the gem diol and oxyanion intermediate is calculated by performing density functional and post-Hartree-Fock calculations. The robustness of the results is assessed by increasing the size of the system and of the basis set and by performing QM/MM calculations that explicitly include protein/solvent electrostatic effects. Our results suggest that the neutral gem-diol intermediate is 20-30 kcal/mol more stable than the charged oxyanion. It is therefore concluded that only the neutral specie is populated during the enzymatic reaction.

  8. Pulsed electron paramagnetic resonance experiments identify the paramagnetic intermediates in the pyruvate ferredoxin oxidoreductase catalytic cycle.

    PubMed

    Astashkin, Andrei V; Seravalli, Javier; Mansoorabadi, Steven O; Reed, George H; Ragsdale, Stephen W

    2006-03-29

    Pyruvate ferredoxin oxidoreductase (PFOR) is central to the anaerobic metabolism of many bacteria and amitochondriate eukaryotes. PFOR contains thiamine pyrophosphate (TPP) and three [4Fe-4S] clusters, which link pyruvate oxidation to reduction of ferredoxin. In the PFOR reaction, TPP reacts with pyruvate to form lactyl-TPP, which undergoes decarboxylation to form a hydroxyethyl-TPP (HE-TPP) intermediate. One electron is then transferred from HE-TPP to one of the three [4Fe-4S] clusters to form an HE-TPP radical and a [4Fe-4S]1+ intermediate. Pulsed EPR methods have been used to measure the distance between the HE-TPP radical and the [4Fe-4S]1+ cluster to which it is coupled. Computational analysis including the PFOR crystal structure and the spin distribution in the HE-TPP radical and in the reduced [4Fe-4S] cluster demonstrates that the distance between the HE-TPP radical and the medial cluster B matches the experimentally determined dipolar interaction, while one of the other two clusters is too close and the other is too far away. These results clearly demonstrate that it is the medial cluster (cluster B) that is reduced. Thus, rapid electron transfer occurs through the electron-transfer chain, which leaves an oxidized proximal cluster poised to accept an electron from the HE-TPP radical in the subsequent reaction step. PMID:16551078

  9. 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.

  10. Structure of hemiaminal intermediate of the reaction of diethylamine with cyclobutanone

    NASA Astrophysics Data System (ADS)

    Yufit, Dmitry S.; Howard, Judith A. K.

    2010-12-01

    The intermediate of the reaction between cyclobutanone and diethylamine has been crystallized in situ in form of co-crystal with diethylamine and its structure has been determined by X-ray crystallography. The study made possible to have an insight in the mechanism of the reaction and reveals the potential of in situ cryo-crystallization technique as an additional tool for studying the mechanisms of chemical reactions. The related structure of co-crystal of diethylamine with adipic acid, which is a product of cyclohexanone oxidative cleavage, is also reported.

  11. Study of intermediates from transition metal excited-state electron-transfer reactions

    SciTech Connect

    Hoffman, M.Z.

    1991-12-31

    During this period, conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used for the characterization of the intermediates that are involved in transition metal excited-state electron-transfer reactions. The intermediates of interest were the excited states of Ru(II) and Cr(III) photosensitizers, their reduced forms, and the species formed in the reactions of redox quenchers and electron-transfer agents. Of particular concern has been the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes.

  12. Benchmarking of activation reaction distribution in an intermediate energy neutron field.

    PubMed

    Ogawa, Tatsuhiko; Morev, Mikhail N; Hirota, Masahiro; Abe, Takuya; Koike, Yuya; Iwai, Satoshi; Iimoto, Takeshi; Kosako, Toshiso

    2011-07-01

    Neutron-induced reaction rate depth profiles inside concrete shield irradiated by intermediate energy neutron were calculated using a Monte-Carlo code and compared with an experiment. An irradiation field of intermediate neutron produced in the forward direction from a thick (stopping length) target bombarded by 400 MeV nucleon(-1) carbon ions was arranged at the heavy ion medical accelerator in Chiba. Ordinary concrete shield of 90 cm thickness was installed 50 cm downstream the iron target. Activation detectors of aluminum, gold and gold covered with cadmium were inserted at various depths. Irradiated samples were extracted after exposure and gamma-ray spectrometry was performed for each sample. Comparison of experimental and calculated shows good agreement for both low- and high-energy neutron-induced reaction except for (27)Al(n,X)(24)Na reaction at the surface. PMID:21515619

  13. Recent developments in methods for identifying reaction coordinates

    PubMed Central

    Li, Wenjin; Ma, Ao

    2014-01-01

    In the study of rare events in complex systems with many degrees of freedom, a key element is to identify the reaction coordinates of a given process. Over recent years, a number of methods and protocols have been developed to extract the reaction coordinates based on limited information from molecular dynamics simulations. In this review, we provide a brief survey over a number of major methods developed in the past decade, some of which are discussed in greater detail, to provide an overview of the problems that are partially solved and challenges that still remain. A particular emphasis has been placed on methods for identifying reaction coordinates that are related to the committor. PMID:25197161

  14. Controlling the ambiphilic nature of σ-arylpalladium intermediates in intramolecular cyclization reactions.

    PubMed

    Solé, Daniel; Fernández, Israel

    2014-01-21

    The reactivity of main group organometallics, such as organolithium compounds (RLi) and Grignard reagents (RMgX), is quite straightforward. In these species the R group usually exhibits nucleophilic reactivity without any possibility of inducing electrophilic character. In contrast, in organopalladium complexes, researchers can switch the reactivity from electrophilic to nucleophilic relatively simply. Although σ-aryl and σ-vinylpalladium complexes are commonly used as electrophiles in C-C bond-forming reactions, recent research has demonstrated that they can also react with carbon-heteroatom multiple bonds in a nucleophilic manner. Nevertheless, researchers have completely ignored the issue of controlling the ambiphilic nature of such species. This Account describes our efforts toward selectively promoting the same starting materials toward either electrophilic α-arylation or nucleophilic addition reactions to different carbonyl groups. We could tune the properties of the σ-arylpalladium intermediates derived from amino-tethered aryl halides and carbonyl compounds to achieve chemoselective transformations. Therefore, chemists can control the ambiphilic nature of such intermediates and, consequently, the competition between the alternative reaction pathways by the adequate selection of the reaction conditions and additives (base, presence/absence of phenol, bidentate phosphines). The nature of the carbonyl group (aldehydes, ketones, esters, and amides) and the length of the tether connecting it to the aniline moiety also play an important role in the outcome of these processes. Our joint computational and experimental efforts to elucidate the reaction mechanism of these palladium-catalyzed transformations suggest that beyond the formation of the four-membered azapalladacycle, two major factors help to control the dual character of the palladium(II) intermediates derived from 2-haloanilines. First, their high nucleophilicity strongly modifies the interaction of

  15. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.

    1985-01-01

    Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

  16. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.; Phillips, D. H.

    1986-01-01

    Ab initio quantum chemical techniques have been used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types were identified. Basic sets of polarized double-zeta quality and large scale configuration interaction wave functions have been utilized. Based upon electronic energies, the covalently-bonded HOOOH species is found to be 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen-bonded HO-HO2 species is found to have an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen-bonded form is found to be planar, to possess one relatively 'normal' hydrogen bond, and to have lowest energy 3A-prime and 1A-prime states that are essentially degenerate. The 1A-double prime and 3A-double prime excited states produced by rotation of the unpaired OH electron into the molecular plane are found to be very slightly bound.

  17. Insights into the Mechanism of Type I Dehydroquinate Dehydratases from Structures of Reaction Intermediates

    SciTech Connect

    Light, Samuel H.; Minasov, George; Shuvalova, Ludmilla; Duban, Mark-Eugene; Caffrey, Michael; Anderson, Wayne F.; Lavie, Arnon

    2012-02-27

    The biosynthetic shikimate pathway consists of seven enzymes that catalyze sequential reactions to generate chorismate, a critical branch point in the synthesis of the aromatic amino acids. The third enzyme in the pathway, dehydroquinate dehydratase (DHQD), catalyzes the dehydration of 3-dehydroquinate to 3-dehydroshikimate. We present three crystal structures of the type I DHQD from the intestinal pathogens Clostridium difficile and Salmonella enterica. Structures of the enzyme with substrate and covalent pre- and post-dehydration reaction intermediates provide snapshots of successive steps along the type I DHQD-catalyzed reaction coordinate. These structures reveal that the position of the substrate within the active site does not appreciably change upon Schiff base formation. The intermediate state structures reveal a reaction state-dependent behavior of His-143 in which the residue adopts a conformation proximal to the site of catalytic dehydration only when the leaving group is present. We speculate that His-143 is likely to assume differing catalytic roles in each of its observed conformations. One conformation of His-143 positions the residue for the formation/hydrolysis of the covalent Schiff base intermediates, whereas the other conformation positions the residue for a role in the catalytic dehydration event. The fact that the shikimate pathway is absent from humans makes the enzymes of the pathway potential targets for the development of non-toxic antimicrobials. The structures and mechanistic insight presented here may inform the design of type I DHQD enzyme inhibitors.

  18. Holliday intermediates and reaction by-products in FLP protein-promoted site-specific recombination.

    PubMed Central

    Meyer-Leon, L; Huang, L C; Umlauf, S W; Cox, M M; Inman, R B

    1988-01-01

    Holliday structures are formed and resolved by FLP protein during site-specific recombination. These structures have been isolated and are visualized in both native and partially denatured states by electron microscopy. No single-strand breaks are found within the junction, indicating that the structure results from a reciprocal exchange of strands. These structures have properties consistent with being reaction intermediates. Double-strand cleavage products and "Y structures" are also detected and appear to be by-products of the reaction. The Y structures are three-armed branched molecules with a covalently closed junction located at the FLP recombination target site. Models are discussed, suggesting that both of these novel structures are made by aberrant cleavages during formation and resolution of the Holliday intermediate. Images PMID:3065624

  19. Multifragment azimuthal correlation functions: Probes for reaction dynamics in collisions of intermediate energy heavy ions

    SciTech Connect

    Lacey, R.A.; Elmaani, A.; Lauret, J.; Li, T.; Bauer, W.; Craig, D.; Cronqvist, M.; Gualtieri, E.; Hannuschke, S.; Reposeur, T.; Vander Molen, A.; Westfall, G.D.; Wilson, W.K.; Winfield, J.S.; Yee, J.; Yennello, S.; Nadasen, A.; Tickle, R.S.; Norbeck, E. National Superconducting Cyclotron Laboratory Department of Physics, Michigan State University, East Lansing, Michigan 48824-1321 Department of Physics, University of Michigan at Dearborn, Dearborn, Michigan 48128 Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1120 Department of Physics, University of Iowa, Iowa City, Iowa 52242 )

    1993-03-01

    Multifragment azimuthal correlation functions have been measured as a function of beam energy and impact parameter for the Ar+Sc system ([ital E]/[ital A]=35 to 115 MeV). The observed azimuthal correlation functions---which do not require corrections for dispersion of the reaction plane---exhibit strong asymmetries which are dependent on impact parameter and beam energy. Rotational collective motion and flow seem to dominate the correlation functions at low beam energies. It is proposed that multifragment azimuthal correlation functions can provide a useful probe for intermediate energy heavy ion reaction dynamics.

  20. Random sampling of the Green’s Functions for reversible reactions with an intermediate state

    SciTech Connect

    Plante, Ianik; Devroye, Luc; Cucinotta, Francis A.

    2013-06-01

    Exact random variate generators were developed to sample Green’s functions used in Brownian Dynamics (BD) algorithms for the simulations of chemical systems. These algorithms, which use less than a kilobyte of memory, provide a useful alternative to the table look-up method that has been used in similar work. The cases that are studied with this approach are (1) diffusion-influenced reactions; (2) reversible diffusion-influenced reactions and (3) reactions with an intermediate state such as enzymatic catalysis. The results are validated by comparison with those obtained by the Independent Reaction Times (IRT) method. This work is part of our effort in developing models to understand the role of radiation chemistry in the radiation effects on human body and may eventually be included in event-based models of space radiation risk.

  1. LC/MS/MS structure elucidation of reaction intermediates formed during the TiO2 photocatalysis of microcystin-LR

    EPA Science Inventory

    Microcystin-LR (MC-LR), a cyanotoxin and emerging drinking water contaminant, was treated with TiO(2) photocatalysts immobilized on stainless steel plates as an alternative to nanoparticles in slurry. The reaction intermediates of MC-LR were identified with mass spectrometry (MS)...

  2. Aromatic intermediate formation during oxidative degradation of Bisphenol A by homogeneous sub-stoichiometric Fenton reaction.

    PubMed

    Poerschmann, Juergen; Trommler, Ulf; Górecki, Tadeusz

    2010-05-01

    The elimination of Bisphenol A (BPA) from contaminated waters is an urgent challenge. This contribution focuses on BPA degradation by homogeneous Fenton reagent based on reactive ()OH radicals. Pronounced sub-stoichiometric amounts of H(2)O(2) oxidant were used to simulate economically viable processes and operation under not fully controlled conditions, as for example in in situ groundwater remediation. Aside from the most abundant benzenediols and the monohydroxylated BPA intermediate (which were detected as stable intermediates in earlier contributions), a wide array of aromatic products in the molecular weight range between 94 Da (phenol) and approximately 500 Da could be detected, the overwhelming majority of which have not been reported thus far. The identification was carried out by GC/MS analysis of trimethylsilyl ethers. The structural assignments were confirmed through the use of fully deuterated [(2)H(16)] BPA as the substrate, as well as using retention indices calculated on the basis of the increment system. The occurrence of aromatic intermediates larger than BPA, which typically share either a biphenyl- or a diphenylether structure, can be explained by oxidative coupling reactions of stabilized free radicals or by the addition of organoradicals (organocations) onto BPA molecules or benzenediols. The hydroxycyclohexadienyl radical of BPA was recognized to play central role in the degradation pathways. Ring opening products, including lactic, acetic and dicarboxylic acids, could be detected in addition to aromatic intermediates. Since some of those intermediates and products are recalcitrant to further oxidation under the conditions of sub-stoichiometric Fenton reaction, they should be carefully considered when designing and optimizing Fenton-driven remediation systems.

  3. Identifying Understudied Nuclear Reactions by Text-mining the EXFOR Experimental Nuclear Reaction Library

    NASA Astrophysics Data System (ADS)

    Hirdt, J. A.; Brown, D. A.

    2016-01-01

    The EXFOR library contains the largest collection of experimental nuclear reaction data available as well as the data's bibliographic information and experimental details. We text-mined the REACTION and MONITOR fields of the ENTRYs in the EXFOR library in order to identify understudied reactions and quantities. Using the results of the text-mining, we created an undirected graph from the EXFOR datasets with each graph node representing a single reaction and quantity and graph links representing the various types of connections between these reactions and quantities. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. We use various graph theoretical tools to identify important yet understudied reactions and quantities in EXFOR. Although we identified a few cross sections relevant for shielding applications and isotope production, mostly we identified charged particle fluence monitor cross sections. As a side effect of this work, we learn that our abstract graph is typical of other real-world graphs.

  4. Structural rearrangements and reaction intermediates in a di-Mn water oxidation catalyst.

    PubMed

    Vallés-Pardo, J L; de Groot, H J M; Buda, F

    2012-11-28

    By using first-principles molecular dynamics simulations combined with metadynamics to simulate rare events we analyse competing reaction coordinates for a di-Mn water oxidation catalyst ([(bis(imino)pyridine)(H(2)O)Mn(IV)(μ-O)(2)Mn(V)(O)(bis(imino)pyridine)](3+)). The catalytic water oxidation cycle of the complex is examined by addressing the thermodynamic accessibility of the hydroperoxo species that is considered a critical and rate-limiting intermediate. To achieve this, hybrid quantum-mechanics/molecular-mechanics (QM/MM) and full QM simulations have been performed for an explicit treatment of the water environment that plays an active role in the reaction processes. Starting from a likely active species for the O-O bond formation, we observe that during the water approach to the oxo ligand a facile structural rearrangement of the complex takes place, leading to the opening of one μ-O bridge and the release of a water ligand, and resulting in two pentacoordinated Mn centers. This complex appears weakly active in the water oxidation process, since a concerted reaction is required to establish a Mn-OOH hydroperoxo intermediate. The slow kinetics of a concerted reaction can allow other processes, including linear degradation of the catalyst, to take precedence over catalytic water oxidation.

  5. Structural Analysis of Substrate, Reaction Intermediate, and Product Binding in Haemophilus influenzae Biotin Carboxylase

    PubMed Central

    Broussard, Tyler C.; Pakhomova, Svetlana; Neau, David B.; Bonnot, Ross; Waldrop, Grover L.

    2015-01-01

    Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1′-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1′-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO2 from the carboxyphosphate intermediate to biotin. PMID:26020841

  6. Reactions between Criegee Intermediates and the Inorganic Acids HCl and HNO3 : Kinetics and Atmospheric Implications.

    PubMed

    Foreman, Elizabeth S; Kapnas, Kara M; Murray, Craig

    2016-08-22

    Criegee intermediates (CIs) are a class of reactive radicals that are thought to play a key role in atmospheric chemistry through reactions with trace species that can lead to aerosol particle formation. Recent work has suggested that water vapor is likely to be the dominant sink for some CIs, although reactions with trace species that are sufficiently rapid can be locally competitive. Herein, we use broadband transient absorption spectroscopy to measure rate constants for the reactions of the simplest CI, CH2 OO, with two inorganic acids, HCl and HNO3 , both of which are present in polluted urban atmospheres. Both reactions are fast; at 295 K, the reactions of CH2 OO with HCl and HNO3 have rate constants of 4.6×10(-11)  cm(3)  s(-1) and 5.4×10(-10)  cm(3)  s(-1) , respectively. Complementary quantum-chemical calculations show that these reactions form substituted hydroperoxides with no energy barrier. The results suggest that reactions of CIs with HNO3 in particular are likely to be competitive with those with water vapor in polluted urban areas under conditions of modest relative humidity.

  7. Direct observation of unstable reaction intermediates by acid-base complex formation.

    PubMed

    Ohashi, Yuji

    2013-06-01

    The structures of several unstable or metastable reaction intermediates that were photoproduced in crystals were analyzed by using X-ray techniques. The presence of enough void space around the reactive group(s) is an essential factor for the reaction to occur with retention of the single-crystal form. To expand the void space, an acid group (COOH) was substituted onto the reactant molecule and acid-base complex crystals were prepared with several amines, such as dibenzylamine and dicyclohexylamine. Following the formation of such acid-base complexes in crystals, the metastable structures of nitrenes and red species of photochromic salicylideneanilines have been successfully analyzed by using X-ray techniques. Moreover, the structure of a Pt complex anion in the excited state has been analyzed, which formed acid-base complex crystals with various alkylammonium cations. The formation of acid-base complexes will be a powerful tool for directly observing the structure of unstable or metastable reaction intermediates by using X-ray techniques.

  8. Regioselective, Transition Metal-Free C-O Coupling Reactions Involving Aryne Intermediates.

    PubMed

    Dong, Yuyang; Lipschutz, Michael I; Tilley, T Don

    2016-04-01

    A new transition-metal-free synthetic method for C-O coupling between various aryl halides and alkoxides is described. This type of transformation is typically accomplished using palladium catalysts containing a specialized phosphine ligand. The reactions reported here can be performed under mild, ambient conditions using certain potassium alkoxides and a range of aryl halides, with iodide and bromide derivatives giving the best results. A likely mechanistic pathway involves the in situ generation of an aryne intermediate, and directing groups on the aryl ring inductively control regioselectivity.

  9. Intermediate colloidal formation and the varying width of periodic precipitation bands in reaction-diffusion systems.

    PubMed

    George, Jacob; Varghese, George

    2005-02-15

    The mechanism of rhythmic pattern formation in reaction-diffusion systems is investigated theoretically by introducing a new concept. The boundary that separates the two reacting species virtually migrates as the diffusion proceeds into the gelatinous medium. Based on this boundary migration scenario, all the well-established relations on Liesegang patterns could be proved, in a rather modified way. The idea of formation of intermediate colloidal haze prior to patterning along with the moving boundary model proved to be efficient in predicting the concentration dependence of the width of the spatiotemporal patterns. The experimental observations support the width law relation developed.

  10. Photocatalytic removal of pesticide dichlorvos from indoor air: a study of reaction parameters, intermediates and mineralization.

    PubMed

    Sleiman, Mohamad; Ferronato, Corinne; Chovelon, Jean-Marc

    2008-04-15

    This paper presents for the first time the investigation of TiO2 photocatalysis for the removal of pesticides in gas phase. Dichlorvos was used as a model pesticide, and experiments were carried out using both static and dynamic reaction systems to explore the different aspects of the process. Thus, adsorption, reaction kinetics, and the influence of several operational parameters such as relative humidity (RH), inlet concentration, flow rate, and association of TiO2 with activated carbon (AC) were all examined in detail. Furthermore, a special attention was devoted to the analysis of reaction products by means of various analytical techniques such as Fourier transform infrared spectroscopy, automated thermal desorption technique coupled to gas chromatography-mass spectrometry instrument, gas chromatography equipped with a pulse discharge helium photoionization detector, and ion chromatography. The results showed an immediate and total removal of dichlorvos at ppbv levels (50-350 ppbv) along with a high mineralization extent (50-85%) into harmless final products (CO2, HCl, PO43-). Moreover, RH was found to significantly affectthe mineralization extent and the formation of reaction intermediates. On the basis of identification data, direct charge transfer and chlorine radical (Cl*) attack were shown to play a key role in the reaction mechanism at low RH, whereas at high RH, HO* radicals were the predominant active species.

  11. Fast and Sequence-Specific Palladium-Mediated Cross-Coupling Reaction Identified from Phage Display

    PubMed Central

    2015-01-01

    Fast and specific bioorthogonal reactions are highly desirable because they provide efficient tracking of biomolecules that are present in low abundance and/or involved in fast dynamic process in living systems. Toward this end, classic strategy involves the optimization of substrate structures and reaction conditions in test tubes, testing their compatibility with biological systems, devising synthetic biology schemes to introduce the modified substrates into living cells or organisms, and finally validating the superior kinetics for enhanced capacity in tracking biomolecules in vivo—a lengthy process often mired by unexpected results. Here, we report a streamlined approach in which the “microenvironment” of a bioorthogonal chemical reporter is exploited directly in biological systems via phage-assisted interrogation of reactivity (PAIR) to optimize not only reaction kinetics but also specificity. Using the PAIR strategy, we identified a short alkyne-containing peptide sequence showing fast kinetics (k2 = 13 000 ± 2000 M–1 s–1) in a palladium-mediated cross-coupling reaction. Site-directed mutagenesis studies suggested that the residues surrounding the alkyne moiety facilitate the assembly of a key palladium–alkyne intermediate along the reaction pathway. When this peptide sequence was inserted into the extracellular domain of epidermal growth factor receptor (EGFR), this reactive sequence directed the specific labeling of EGFR in live mammalian cells. PMID:25025771

  12. Fast and sequence-specific palladium-mediated cross-coupling reaction identified from phage display.

    PubMed

    Lim, Reyna K V; Li, Nan; Ramil, Carlo P; Lin, Qing

    2014-09-19

    Fast and specific bioorthogonal reactions are highly desirable because they provide efficient tracking of biomolecules that are present in low abundance and/or involved in fast dynamic process in living systems. Toward this end, classic strategy involves the optimization of substrate structures and reaction conditions in test tubes, testing their compatibility with biological systems, devising synthetic biology schemes to introduce the modified substrates into living cells or organisms, and finally validating the superior kinetics for enhanced capacity in tracking biomolecules in vivo--a lengthy process often mired by unexpected results. Here, we report a streamlined approach in which the "microenvironment" of a bioorthogonal chemical reporter is exploited directly in biological systems via phage-assisted interrogation of reactivity (PAIR) to optimize not only reaction kinetics but also specificity. Using the PAIR strategy, we identified a short alkyne-containing peptide sequence showing fast kinetics (k2=13,000±2000 M(-1) s(-1)) in a palladium-mediated cross-coupling reaction. Site-directed mutagenesis studies suggested that the residues surrounding the alkyne moiety facilitate the assembly of a key palladium-alkyne intermediate along the reaction pathway. When this peptide sequence was inserted into the extracellular domain of epidermal growth factor receptor (EGFR), this reactive sequence directed the specific labeling of EGFR in live mammalian cells. PMID:25025771

  13. Total reaction cross sections in CEM and MCNP6 at intermediate energies

    SciTech Connect

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-05-14

    Accurate total reaction cross section models are important to achieving reliable predictions from spallation and transport codes. The latest version of the Cascade Exciton Model (CEM) as incorporated in the code CEM03.03, and the Monte Carlo N-Particle transport code (MCNP6), both developed at Los Alamos National Laboratory (LANL), each use such cross sections. Having accurate total reaction cross section models in the intermediate energy region (50 MeV to 5 GeV) is very important for different applications, including analysis of space environments, use in medical physics, and accelerator design, to name just a few. The current inverse cross sections used in the preequilibrium and evaporation stages of CEM are based on the Dostrovsky et al. model, published in 1959. Better cross section models are now available. Implementing better cross section models in CEM and MCNP6 should yield improved predictions for particle spectra and total production cross sections, among other results.

  14. Gold-Catalyzed Reactions via Cyclopropyl Gold Carbene-like Intermediates

    PubMed Central

    2015-01-01

    Cycloisomerizations of 1,n-enynes catalyzed by gold(I) proceed via electrophilic species with a highly distorted cyclopropyl gold(I) carbene-like structure, which can react with different nucleophiles to form a wide variety of products by attack at the cyclopropane or the carbene carbons. Particularly important are reactions in which the gold(I) carbene reacts with alkenes to form cyclopropanes either intra- or intermolecularly. In the absence of nucleophiles, 1,n-enynes lead to a variety of cycloisomerized products including those resulting from skeletal rearrangements. Reactions proceeding through cyclopropyl gold(I) carbene-like intermediates are ideally suited for the bioinspired synthesis of terpenoid natural products by the selective activation of the alkyne in highly functionalized enynes or polyenynes. PMID:26061916

  15. Direct Observation of Intermediates Involved in the Interruption of the Bischler–Napieralski Reaction

    PubMed Central

    White, Kolby L.; Mewald, Marius; Movassaghi, Mohammad

    2015-01-01

    The first mechanistic investigation of electrophilic amide activation of α,α-disubstituted tertiary lactams and the direct observation of key intermediates by in situ FTIR, 1H, 13C, and 19F NMR in our interrupted Bischler–Napieralski based synthetic strategy to the aspidosperma alkaloids, including a complex tetracyclic diiminium ion, is discussed. The reactivity of a wide range of pyridines with trifluoromethanesulfonic anhydride was systematically examined, and characteristic IR absorption bands for the corresponding N-trifluoromethanesulfonylated pyridinium trifluoromethanesulfonates were assigned. The reversible formation of diiminium ether intermediates was studied, providing insight into divergent mechanistic pathways as a function of the steric environment of the amide substrate and stoichiometry of reagents. Importantly, when considering base additives during electrophilic amide activation, more hindered α-quaternary tertiary lactams require the use of non-nucleophilic pyridine additives in order to avoid deactivation via a competing desulfonylation reaction. The isolation and full characterization of a tetracyclic iminium trifluoromethanesulfonate provided additional correlation between in situ characterization of sensitive intermediates and isolable compounds involved in this synthetic transformation. PMID:26166404

  16. Global assessment of molecularly identified Anisakis Dujardin, 1845 (Nematoda: Anisakidae) in their teleost intermediate hosts.

    PubMed

    Kuhn, Thomas; Hailer, Frank; Palm, Harry W; Klimpel, Sven

    2013-05-01

    Here, we present the ITS ribosomal DNA (rDNA) sequence data on 330 larvae of nematodes of the genus Anisakis Dujardin, 1845 collected from 26 different bony fish species from 21 sampling locations and different climatic zones. New host records are provided for Anisakis simplex (Rudolphi, 1809) sensu stricto (s.s.) and A. pegreffli Campana-Rouget et Biocca, 1955 from Anoplopoma fimbria (Pallas) (Santa Barbara, East Pacific), A. typica (Diesing, 1860) from Caesio cuning (Bloch), Lepturacanthus savala (Cuvier) and Katsuwonus pelamis (Linnaeus) (Indonesia, West Pacific), A. simplex s.s. from Cololabis saira (Brevoort) (Hawaii, Central Pacific), A. simplex C of Nascetti et al. (1986) from Sebastolobus alascanus Bean (Santa Barbara, East Pacific) and A. physeteris Baylis, 1923 from Synaphobranchus kaupii Johnson (Namibia, East Atlantic). Comparison with host records from 60 previous molecular studies of Anisakis species reveals the teleost host range so far recorded for the genus. Perciform (57 species) and gadiform (21) fishes were the most frequently infected orders, followed by pleuronectiforms (15) and scorpaeniforms (15). Most commonly infected fish families were Scombridae (12), Gadidae (10), Carangidae (8) and Clupeidae (7), with Merluccius merluccius (Linnaeus) alone harbouring eight Anisakis species. Different intermediate host compositions implicate differing life cycles for the so far molecularly identified Anisakis sibling species. PMID:23724731

  17. Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy.

    PubMed

    Riss, Alexander; Paz, Alejandro Pérez; Wickenburg, Sebastian; Tsai, Hsin-Zon; De Oteyza, Dimas G; Bradley, Aaron J; Ugeda, Miguel M; Gorman, Patrick; Jung, Han Sae; Crommie, Michael F; Rubio, Angel; Fischer, Felix R

    2016-07-01

    Chemical transformations at the interface between solid/liquid or solid/gaseous phases of matter lie at the heart of key industrial-scale manufacturing processes. A comprehensive study of the molecular energetics and conformational dynamics that underlie these transformations is often limited to ensemble-averaging analytical techniques. Here we report the detailed investigation of a surface-catalysed cross-coupling and sequential cyclization cascade of 1,2-bis(2-ethynyl phenyl)ethyne on Ag(100). Using non-contact atomic force microscopy, we imaged the single-bond-resolved chemical structure of transient metastable intermediates. Theoretical simulations indicate that the kinetic stabilization of experimentally observable intermediates is determined not only by the potential-energy landscape, but also by selective energy dissipation to the substrate and entropic changes associated with key transformations along the reaction pathway. The microscopic insights gained here pave the way for the rational design and control of complex organic reactions at the surface of heterogeneous catalysts. PMID:27325094

  18. Multifragmentation in intermediate energy {sup 129}Xe-induced heavy-ion reactions

    SciTech Connect

    Tso, Kin

    1996-05-01

    The {sup 129}Xe-induced reactions on {sup nat}Cu, {sup 89}Y, {sup 165}Ho, and {sup 197}Au at bombarding energies of E/A = 40 & 60 MeV have been studied theoretically and experimentally in order to establish the underlying mechanism of multifragmentation at intermediate energy heavy-Ion collisions. Nuclear disks formed in central heavy-ion collisions, as simulated by means of Boltzmann-like kinetic equations, break up into several fragments due to a new kind of Rayleigh-like surface instability. A sheet of liquid, stable in the limit of non-interacting surfaces, is shown to become unstable due to surface-surface interactions. The onset of this instability is determined analytically. A thin bubble behaves like a sheet and is susceptible to the surface instability through the crispation mode. The Coulomb effects associated with the depletion of charges in the central cavity of nuclear bubbles are investigated. The onset of Coulomb instability is demonstrated for perturbations of the radial mode. Experimental intermediate-mass-fragment multiplicity distributions for the {sup 129}Xe-induced reactions are shown to be binomial at each transverse energy. From these distributions, independent of the specific target, an elementary binary decay probability p can be extracted that has a thermal dependence. Thus it is inferred that multifragmentation is reducible to a combination of nearly independent emission processes. If sequential decay is assumed, the increase of p with transverse energy implies a contraction of the emission time scale. The sensitivity of p to the lower Z threshold in the definition of intermediate-mass-fragments points to a physical Poisson simulations of the particle multiplicities show that the weak auto-correlation between the fragment multiplicity and the transverse energy does not distort a Poisson distribution into a binomial distribution. The effect of device efficiency on the experimental results has also been studied.

  19. Chemically Activated Formation of Organic Acids in Reactions of the Criegee Intermediate with Aldehydes and Ketones

    SciTech Connect

    Jalan, Amrit; Allen, Joshua W.; Green, William H.

    2013-08-08

    Reactions of the Criegee intermediate (CI, .CH2OO.) are important in atmospheric ozonolysis models. In this work, we compute the rates for reactions between .CH2OO. and HCHO, CH3CHO and CH3COCH3 leading to the formation of secondary ozonides (SOZ) and organic acids. Relative to infinitely separated reactants, the SOZ in all three cases is found to be 48–51 kcal mol-1 lower in energy, formed via 1,3- cycloaddition of .CH2OO. across the CQO bond. The lowest energy pathway found for SOZ decomposition is intramolecular disproportionation of the singlet biradical intermediate formed from cleavage of the O–O bond to form hydroxyalkyl esters. These hydroxyalkyl esters undergo concerted decomposition providing a low energy pathway from SOZ to acids. Geometries and frequencies of all stationary points were obtained using the B3LYP/MG3S DFT model chemistry, and energies were refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. RRKM calculations were used to obtain microcanonical rate coefficients (k(E)) and the reservoir state method was used to obtain temperature and pressure dependent rate coefficients (k(T, P)) and product branching ratios. At atmospheric pressure, the yield of collisionally stabilized SOZ was found to increase in the order HCHO o CH3CHO o CH3COCH3 (the highest yield being 10-4 times lower than the initial .CH2OO. concentration). At low pressures, chemically activated formation of organic acids (formic acid in the case of HCHO and CH3COCH3, formic and acetic acid in the case of CH3CHO) was found to be the major product channel in agreement with recent direct measurements. Collisional energy transfer parameters and the barrier heights for SOZ reactions were found to be the most sensitive parameters determining SOZ and organic acid yield.

  20. Identifying Multimodal Intermediate Phenotypes Between Genetic Risk Factors and Disease Status in Alzheimer's Disease.

    PubMed

    Hao, Xiaoke; Yao, Xiaohui; Yan, Jingwen; Risacher, Shannon L; Saykin, Andrew J; Zhang, Daoqiang; Shen, Li

    2016-10-01

    Neuroimaging genetics has attracted growing attention and interest, which is thought to be a powerful strategy to examine the influence of genetic variants (i.e., single nucleotide polymorphisms (SNPs)) on structures or functions of human brain. In recent studies, univariate or multivariate regression analysis methods are typically used to capture the effective associations between genetic variants and quantitative traits (QTs) such as brain imaging phenotypes. The identified imaging QTs, although associated with certain genetic markers, may not be all disease specific. A useful, but underexplored, scenario could be to discover only those QTs associated with both genetic markers and disease status for revealing the chain from genotype to phenotype to symptom. In addition, multimodal brain imaging phenotypes are extracted from different perspectives and imaging markers consistently showing up in multimodalities may provide more insights for mechanistic understanding of diseases (i.e., Alzheimer's disease (AD)). In this work, we propose a general framework to exploit multi-modal brain imaging phenotypes as intermediate traits that bridge genetic risk factors and multi-class disease status. We applied our proposed method to explore the relation between the well-known AD risk SNP APOE rs429358 and three baseline brain imaging modalities (i.e., structural magnetic resonance imaging (MRI), fluorodeoxyglucose positron emission tomography (FDG-PET) and F-18 florbetapir PET scans amyloid imaging (AV45)) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The empirical results demonstrate that our proposed method not only helps improve the performances of imaging genetic associations, but also discovers robust and consistent regions of interests (ROIs) across multi-modalities to guide the disease-induced interpretation. PMID:27277494

  1. 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.

  2. X-ray absorption spectroscopy of lithium sulfur battery reaction intermediates

    NASA Astrophysics Data System (ADS)

    Wujcik, Kevin; Pascal, Tod; Prendergast, David; Balsara, Nitash

    2015-03-01

    Lithium sulfur batteries have a theoretical energy density nearly five times greater than current lithium ion battery standards, but questions still remain regarding the reaction pathways through which soluble lithium polysulfide (Li2Sx, ``x'' ranging from 2 to 8) reaction intermediates are formed. Complicating spectroelectrochemical approaches to elucidate redox pathways is the challenge of obtaining spectral standards for individual Li2Sx species. Lithium polysulfides cannot be isolated as individual component and exist only in solution as a distribution of different Li2Sx molecules formed via disproportionation reactions (e.g. 2Li2S4 goes to Li2S3 + Li2S5). X-ray absorption spectroscopy (XAS) at the sulfur K-edge has recently been employed as a technique to study Li-S chemistry. We have recently obtained XAS standards for individual Li2Sx species via first principles DFT simulations and the excited electron and core hole approach. Here, experimental sulfur K-edge XAS of Li2Sx species dissolved in poly(ethylene oxide) are compared to spectra obtained from analogous theoretical calculations. The impact that polysulfide solution concentration and the presence of other lithium salts (e.g. LiNO3) have on X-ray spectra of Li2Sx species is explored via experiment and theory.

  3. Theoretical prediction of a perepoxide intermediate for the reaction of singlet oxygen with trans-cyclooctene contrasts with the two-step no-intermediate ene reaction for acyclic alkenes.

    PubMed

    Leach, Andrew G; Houk, K N; Foote, Christopher S

    2008-11-01

    B3LYP/6-31G* and CASMP2 calculations have been employed to study the ene reaction of singlet oxygen with trans-cyclooctene. These methods predict that the reaction involves a perepoxide intermediate, whereas alkenes such as tetramethylethylene are predicted by the same methods to occur by a two-step no-intermediate mechanism, with no perepoxide intermediate. The change in mechanism arises because the trans-cyclooctene imposes a substantial strain in the transition state for hydrogen abstraction. The perepoxide is formed through a polarized diradical intermediate that can lead to the observation of alkene isomerization. The polarized diradical also becomes a minimum because of the barrier to abstraction.

  4. Workshop on hadron structure from photo-reactions at intermediate energies: Proceedings

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M.

    1992-10-01

    This report contains papers on the following topics: The proton compton effect: Recent measurements of the electric and magnetic polorizabilities of the proton; experiments on the electric polarizability of the neutron; chiral symmetry and nucleon polarizabilities; chiral model predictions for electromagnetic polarizabilities of the nucleon, a consumer report; the polarizabilities of bound nucleons; nucleon polarizability in free space and in nuclear matter; mechanisms of photon scattering on nucleons at intermediate energies; pion polarizabilities in chiral perturbation theory; pion polarizabilities and the shielding of {sigma}(700)-meson exchange in {gamma}{gamma}{yields}{pi}{pi} processes; pion and kaon polarizabilities in the quark confinement model; radiative pion photoproduction and pion polarizabilities; pion and sigma polarizabilities and radiative transitions; the quadrupole amplitude in the {gamma}{Nu}-{Delta} transition; pion photoproduction and the {gamma}{Nu}-{Delta} amplitudes; effective- lagrangians, Watson`s theorem, and the E2/M1 mixing ratio in the excitation of the delta resonance; new measurements of the p({rvec {gamma}}, {pi}{sup o}) reaction; multipole analyses and photo-decay couplings at intermediate energies; compton scattering off the proton; connections between compton scattering and pion photoproduction in the delta region; single-pion electroproduction and the transverse one-half and scalar helicity transition form factors; relativistic effects, QCD mixing angles, and {Nu} {yields} {Nu}{gamma} and {Delta} {yields} {gamma}{Nu} transition form factors; electroproduction studies of the {Nu} {yields} {Delta} transition at bates and CEBAF.

  5. Investigation of the O+allyl addition/elimination reaction pathways from the OCH(2)CHCH(2) radical intermediate.

    PubMed

    Fitzpatrick, Benjamin L; Lau, Kai-Chung; Butler, Laurie J; Lee, Shih-Huang; Lin, Jim Jr-Min

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH(2)CHCH(2), a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH(2)CHCH(2) radicals; these undergo a facile ring opening to the OCH(2)CHCH(2) radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcalmol. To elucidate the product channels resulting from the OCH(2)CHCH(2) radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C(3)H(4)O (acrolein)+H, C(2)H(4)+HCO (formyl radical), and H(2)CO (formaldehyde)+C(2)H(3). A small signal from C(2)H(2)O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at me=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C(2)H(5)+CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to

  6. Synthesis of ultrastable copper sulfide nanoclusters via trapping the reaction intermediate: potential anticancer and antibacterial applications.

    PubMed

    Wang, Hong-Yin; Hua, Xian-Wu; Wu, Fu-Gen; Li, Bolin; Liu, Peidang; Gu, Ning; Wang, Zhifei; Chen, Zhan

    2015-04-01

    Copper-based nanomaterials have broad applications in electronics, catalysts, solar energy conversion, antibiotics, tissue imaging, and photothermal cancer therapy. However, it is challenging to prepare ultrasmall and ultrastable CuS nanoclusters (NCs) at room temperature. In this article, a simple method to synthesize water-soluble, monodispersed CuS NCs is reported based on the strategy of trapping the reaction intermediate using thiol-terminated, alkyl-containing short-chain poly(ethylene glycol)s (HS-(CH2)11-(OCH2CH2)6-OH, abbreviated as MUH). The MUH-coated CuS NCs have superior stability in solutions with varied pH values and are stable in pure water for at least 10 months. The as-prepared CuS NCs were highly toxic to A549 cancer cells at a concentration of higher than 100 μM (9.6 μg/mL), making them be potentially applicable as anticancer drugs via intravenous administration by liposomal encapsulation or by direct intratumoral injection. Besides, for the first time, CuS NCs were used for antibacterial application, and 800 μM (76.8 μg/mL) CuS NCs could completely kill the E. coli cells through damaging the cell walls. Moreover, the NCs synthesized here have strong near-infrared (NIR) absorption and can be used as a candidate reagent for photothermal therapy and photoacoustic imaging. The method of trapping the reaction intermediate for simple and controlled synthesis of nanoclusters is generally applicable and can be widely used to synthesize many metal-based (such as Pt, Pd, Au, and Ag) nanoclusters and nanocrystals.

  7. Enzymatic formation of prostamide F2alpha from anandamide involves a newly identified intermediate metabolite, prostamide H2.

    PubMed

    Yang, Wu; Ni, Jinsong; Woodward, David F; Tang-Liu, Diane D-S; Ling, Kah-Hiing John

    2005-12-01

    Prostaglandin F2alpha 1-ethanolamide (prostamide F2alpha) is a potent ocular hypotensive agent in animals and represents a new class of fatty acid amide compounds. Accumulated evidence indicated that anandamide, an endogenous bioactive ligand for cannabinoid receptors, may serve as a common substrate to produce all prostamides, including prostamide F2alpha. After incubation of anandamide with cyclooxygenase 2 (COX-2), the reaction mixture was profiled by HPLC and an intermediate metabolite was discovered and characterized as a cyclic endoperoxide ethanolamide using HPLC-tandem mass spectrometry. Formation of prostamide F2alpha was also demonstrated when the intermediate metabolite was isolated and incubated with prostaglandin F synthase (PGF synthase). These results suggest that the biosynthesis of prostamide F2alpha proceeds in two consecutive steps: oxidation of anandamide to form an endoperoxide intermediate by COX-2, and reduction of the endoperoxide intermediate to form prostamide F2alpha by PGF synthase. This endoperoxide ethanolamide intermediate has been proposed as prostamide H2. PMID:16150817

  8. Direct Determination of the Simplest Criegee Intermediate (CH2OO) Self Reaction Rate.

    PubMed

    Buras, Zachary J; Elsamra, Rehab M I; Green, William H

    2014-07-01

    The rate of self-reaction of the simplest Criegee intermediate, CH2OO, is of importance in many current laboratory experiments where CH2OO concentrations are high, such as flash photolysis and alkene ozonolysis. Using laser flash photolysis while simultaneously probing both CH2OO and I atom by direct absorption, we can accurately determine absolute CH2OO concentrations as well as the UV absorption cross section of CH2OO at our probe wavelength (λ = 375 nm), which is in agreement with a recently published value. Knowing absolute concentrations we can accurately measure kself = 6.0 ± 2.1 × 10(-11)cm(3) molecule(-1) s(-1) at 297 K. We are also able to put an upper bound on the rate coefficient for CH2OO + I of 1.0 × 10(-11) cm(3) molecule(-1) s(-1). Both of these rate coefficients are at least a factor of 5 smaller than other recent measurements of the same reactions.

  9. Total reaction cross sections in CEM and MCNP6 at intermediate energies

    DOE PAGES

    Kerby, Leslie M.; Mashnik, Stepan G.

    2015-05-14

    Accurate total reaction cross section models are important to achieving reliable predictions from spallation and transport codes. The latest version of the Cascade Exciton Model (CEM) as incorporated in the code CEM03.03, and the Monte Carlo N-Particle transport code (MCNP6), both developed at Los Alamos National Laboratory (LANL), each use such cross sections. Having accurate total reaction cross section models in the intermediate energy region (50 MeV to 5 GeV) is very important for different applications, including analysis of space environments, use in medical physics, and accelerator design, to name just a few. The current inverse cross sections used inmore » the preequilibrium and evaporation stages of CEM are based on the Dostrovsky et al. model, published in 1959. Better cross section models are now available. Implementing better cross section models in CEM and MCNP6 should yield improved predictions for particle spectra and total production cross sections, among other results.« less

  10. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    SciTech Connect

    Carraher, Jack McCaslin

    2014-01-01

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding ‘greener’ sources of commodity chemicals and fuels.

  11. Developing mononuclear copper-active-oxygen complexes relevant to reactive intermediates of biological oxidation reactions.

    PubMed

    Itoh, Shinobu

    2015-07-21

    Active-oxygen species generated on a copper complex play vital roles in several biological and chemical oxidation reactions. Recent attention has been focused on the reactive intermediates generated at the mononuclear copper active sites of copper monooxygenases such as dopamine β-monooxygenase (DβM), tyramine β-monooxygenase (TβM), peptidylglycine-α-hydroxylating monooxygenase (PHM), and polysaccharide monooxygenases (PMO). In a simple model system, reaction of O2 and a reduced copper(I) complex affords a mononuclear copper(II)-superoxide complex or a copper(III)-peroxide complex, and subsequent H(•) or e(-)/H(+) transfer, which gives a copper(II)-hydroperoxide complex. A more reactive species such as a copper(II)-oxyl radical type species could be generated via O-O bond cleavage of the peroxide complex. However, little had been explored about the chemical properties and reactivity of the mononuclear copper-active-oxygen complexes due to the lack of appropriate model compounds. Thus, a great deal of effort has recently been made to develop efficient ligands that can stabilize such reactive active-oxygen complexes in synthetic modeling studies. In this Account, I describe our recent achievements of the development of a mononuclear copper(II)-(end-on)superoxide complex using a simple tridentate ligand consisting of an eight-membered cyclic diamine with a pyridylethyl donor group. The superoxide complex exhibits a similar structure (four-coordinate tetrahedral geometry) and reactivity (aliphatic hydroxylation) to those of a proposed reactive intermediate of copper monooxygenases. Systematic studies based on the crystal structures of copper(I) and copper(II) complexes of the related tridentate supporting ligands have indicated that the rigid eight-membered cyclic diamine framework is crucial for controlling the geometry and the redox potential, which are prerequisites for the generation of such a unique mononuclear copper(II)-(end-on)superoxide complex

  12. How to identify carbonate rock reactions in concrete

    SciTech Connect

    Katayama, Tetsuya . E-mail: katayamat@kge.co.jp

    2004-11-15

    This paper summarizes the modern petrographic techniques used to diagnose carbonate rock reactions in concrete. Concrete microbar specimens of the prototype RILEM AAR-5 test, provided by the Austrian Cement Research Institute, and typical Canadian concrete that had undergone alkali-carbonate reaction (ACR) were examined. Scanning electron microscopy, element mapping and quantitative analysis using electron-probe microanalyzer with energy-dispersive spectrometry (EPMA/EDS: around x 2000, <0.1 nA) were made of polished thin sections after completing polarizing microscopy. Dedolomitization produced a myrmekitic texture, composed of spotted brucite (<3 {mu}m) and calcite within the reaction rim, along with a carbonate halo of calcite in the surrounding cement paste. However, no evidence was detected that dedolomitization had produced the expansion cracks in the cement paste, while the classical definition of alkali-carbonate reaction postulates their development. It was found that the alkali-silica reaction (ASR) due to cryptocrystalline quartz hidden in the matrix, always associated with dedolomitization in all the carbonate aggregates tested, was responsible for the expansion of both the laboratory and field concretes, even with the Canadian dolomitic limestone from Kingston, the reference material for alkali-carbonate reaction. It is suggested that the term alkali-carbonate reaction is misleading.

  13. The millisecond intermediate in the reaction of nitric oxide with oxymyoglobin is an iron(III)--nitrato complex, not a peroxynitrite.

    PubMed

    Yukl, Erik T; de Vries, Simon; Moënne-Loccoz, Pierre

    2009-06-01

    The dioxygenation of nitric oxide by oxyheme in globin proteins is a major route for NO detoxification in aerobic biological systems. In myoglobin, this reaction is thought to proceed through an iron(III)-bound peroxynitrite before homolytic cleavage of the O-O bond to form an iron(IV)-oxo and NO(2) radical followed by recombination and nitrate production. Single turnover experiments at alkaline pH have revealed the presence of a millisecond high-spin heme intermediate. It is widely presumed that this species is an iron(III)-peroxynitrite species, but detailed characterization of the intermediate is lacking. Using resonance Raman spectroscopy and rapid-freeze quench techniques, we identify the millisecond intermediate as an iron(III)-nitrato complex with a symmetric NO(2) stretch at 1282 cm(-1). Greater time resolution techniques will be required to detect the putative iron(III) peroxynitrite complex.

  14. A chemometric method to identify enzymatic reactions leading to the transition from glycolytic oscillations to waves

    NASA Astrophysics Data System (ADS)

    Zimányi, László; Khoroshyy, Petro; Mair, Thomas

    2010-06-01

    In the present work we demonstrate that FTIR-spectroscopy is a powerful tool for the time resolved and noninvasive measurement of multi-substrate/product interactions in complex metabolic networks as exemplified by the oscillating glycolysis in a yeast extract. Based on a spectral library constructed from the pure glycolytic intermediates, chemometric analysis of the complex spectra allowed us the identification of many of these intermediates. Singular value decomposition and multiple level wavelet decomposition were used to separate drifting substances from oscillating ones. This enabled us to identify slow and fast variables of glycolytic oscillations. Most importantly, we can attribute a qualitative change in the positive feedback regulation of the autocatalytic reaction to the transition from homogeneous oscillations to travelling waves. During the oscillatory phase the enzyme phosphofructokinase is mainly activated by its own product ADP, whereas the transition to waves is accompanied with a shift of the positive feedback from ADP to AMP. This indicates that the overall energetic state of the yeast extract determines the transition between spatially homogeneous oscillations and travelling waves.

  15. Reactions of spinach nitrite reductase with its substrate, nitrite, and a putative intermediate, hydroxylamine.

    PubMed

    Kuznetsova, Sofya; Knaff, David B; Hirasawa, Masakazu; Sétif, Pierre; Mattioli, Tony A

    2004-08-24

    Plant nitrite reductase (NiR) catalyzes the reduction of nitrite (NO(2)(-)) to ammonia, using reduced ferredoxin as the electron donor. NiR contains a [4Fe-4S] cluster and an Fe-siroheme, which is the nitrite binding site. In the enzyme's as-isolated form ([4Fe-4S](2+)/Fe(3+)), resonance Raman spectroscopy indicated that the siroheme is in the high-spin ferric hexacoordinated state with a weak sixth axial ligand. Kinetic and spectroscopic experiments showed that the reaction of NiR with NO(2)(-) results in an unexpectedly EPR-silent complex formed in a single step with a rate constant of 0.45 +/- 0.01 s(-)(1). This binding rate is slow compared to that expected from the NiR turnover rates reported in the literature, suggesting that binding of NO(2)(-) to the as-isolated form of NiR is not the predominant type of substrate binding during enzyme turnover. Resonance Raman spectroscopic characterization of this complex indicated that (i) the siroheme iron is low-spin hexacoordinated ferric, (ii) the ligand coordination is unusually heterogeneous, and (iii) the ligand is not nitric oxide, most likely NO(2)(-). The reaction of oxidized NiR with hydroxylamine (NH(2)OH), a putative intermediate, results in a ferrous siroheme-NO complex that is spectroscopically identical to the one observed during NiR turnover. Resonance Raman and absorption spectroscopy data show that the reaction of oxidized NiR ([4Fe-4S](2+)/Fe(3+)) with hydroxylamine is binding-limited, while the NH(2)OH conversion to nitric oxide is much faster.

  16. The thermodynamic properties of 2-aminobiphenyl (an intermediate in the carbazole/hydrogen reaction network)

    SciTech Connect

    Steele, W.V.; Chirico, R.D.; Knipmeyer, S.E.; Nguyen, A.

    1990-12-01

    Catalytic hydrodenitrogenation (HDN) is a key step in upgrading processes for conversion of heavy petroleum, shale oil, tar sands, and the products of the liquefaction of coal to economically viable products. This research program provides accurate experimental thermochemical and thermophysical properties for key organic nitrogen-containing compounds present in the range of alternative feedstocks, and applies the experimental information to thermodynamic analyses of key HDN reaction networks. This report is the first in a series that will lead to an analysis of a three-ring HDN system; the carbazole/hydrogen reaction network. 2-Aminobiphenyl is the initial intermediate in the HDN pathway for carbazole, which consumes the least hydrogen possible. Measurements leading to the calculation of the ideal-gas thermodynamic properties for 2-aminobiphenyl are reported. Experimental methods included combustion calorimetry, adiabatic heat-capacity calorimetry, comparative ebulliometry, inclined-piston gauge manometry, and differential-scanning calorimetry (d.s.c). Entropies, enthalpies, and Gibbs energies of formation were derived for the ideal gas for selected temperatures between 298.15 K and 820 K. The critical temperature and critical density were determined for 2-aminobiphenyl with the d.s.c., and the critical pressure was derived. The Gibbs energies of formation are used in thermodynamic calculations to compare the feasibility of the initial hydrogenolysis step in the carbazole/H{sub 2} network with that of its hydrocarbon and oxygen-containing analogous; i.e., fluorene/H{sub 2} and dibenzofuran/H{sub 2}. Results of the thermodynamic calculations are compared with those of batch-reaction studies reported in the literature. 57 refs., 8 figs., 18 tabs.

  17. Oligomer Formation Reactions of Criegee Intermediates in the Ozonolysis of Small Unsaturated Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Sakamoto, Y.; Inomata, S.; Hirokawa, J.

    2013-12-01

    Secondary organic aerosol (SOA) constitutes a substantial fraction of atmospheric fine particulate matters and has an effect on visibility, climate and human health. One of the major oxidizing processes leading to SOA formation is an ozonolysis of unsaturated hydrocarbons (UHCs).[1] Despite of its importance, the contribution of the ozonolysis of UHCs to the SOA formation in the troposphere is not sufficiently understood due to a lack of information on reaction pathways to produce low volatile compounds. While many studies have previously been focused on SOA formation from the ozonolysis of large UHCs, SOA formation from the ozonolysis of UHCs with less than six carbon atoms have been rarely investigated because their products are expected to be too volatile to contribute to the SOA formation. Very recently, a few studies have reported the SOA formation from the ozonolysis of such small UHCs but chemical mechanisms are still unclear. [2-4] In order to understand SOA formation from the ozonolysis of the small UHCs, this study investigated gas- and particle-phase products in laboratory experiments with a Teflon bag using a negative ion chemical ionization mass spectrometry (NI-CIMS) with chloride ion transfer for chemical ionization. This technique is suitable for analysis of compounds such as carboxylic acids and hydroperoxides expected to be produced in the ozonolysis of UHCs with less fragmentation, high selectivity, and high sensitivity. In the particle-phase analysis, SOAs collected on a PTFE filter were heated, and thermally desorbed compounds were analyzed. In the gas-phase analysis, series of peaks with an interval of a mass-to-charge ratio equal to the molecular weight of a Criegee intermediate formed in their ozonolysis were observed. These peaks were attributed to oligomeric hydroperoxides composed of Criegee intermediates as a chain unit. These oligomeric hydroperoxides were also observed in the particle-phase analysis, indicating that the oligomeric

  18. ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations.

    PubMed

    Williams, Benfeard; Convertino, Marino; Das, Jhuma; Dokholyan, Nikolay V

    2015-10-01

    The increased risk of developing Alzheimer's disease (AD) is associated with the APOE gene, which encodes for three variants of Apolipoprotein E, namely E2, E3, E4, differing only by two amino acids at positions 112 and 158. ApoE4 is known to be the strongest risk factor for AD onset, while ApoE3 and ApoE2 are considered to be the AD-neutral and AD-protective isoforms, respectively. It has been hypothesized that the ApoE isoforms may contribute to the development of AD by modifying the homeostasis of ApoE physiological partners and AD-related proteins in an isoform-specific fashion. Here we find that, despite the high sequence similarity among the three ApoE variants, only ApoE4 exhibits a misfolded intermediate state characterized by isoform-specific domain-domain interactions in molecular dynamics simulations. The existence of an ApoE4-specific intermediate state can contribute to the onset of AD by altering multiple cellular pathways involved in ApoE-dependent lipid transport efficiency or in AD-related protein aggregation and clearance. We present what we believe to be the first structural model of an ApoE4 misfolded intermediate state, which may serve to elucidate the molecular mechanism underlying the role of ApoE4 in AD pathogenesis. The knowledge of the structure for the ApoE4 folding intermediate provides a new platform for the rational design of alternative therapeutic strategies to fight AD.

  19. ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

    PubMed Central

    Williams II, Benfeard; Convertino, Marino; Das, Jhuma; Dokholyan, Nikolay V.

    2015-01-01

    The increased risk of developing Alzheimer’s disease (AD) is associated with the APOE gene, which encodes for three variants of Apolipoprotein E, namely E2, E3, E4, differing only by two amino acids at positions 112 and 158. ApoE4 is known to be the strongest risk factor for AD onset, while ApoE3 and ApoE2 are considered to be the AD-neutral and AD-protective isoforms, respectively. It has been hypothesized that the ApoE isoforms may contribute to the development of AD by modifying the homeostasis of ApoE physiological partners and AD-related proteins in an isoform-specific fashion. Here we find that, despite the high sequence similarity among the three ApoE variants, only ApoE4 exhibits a misfolded intermediate state characterized by isoform-specific domain-domain interactions in molecular dynamics simulations. The existence of an ApoE4-specific intermediate state can contribute to the onset of AD by altering multiple cellular pathways involved in ApoE-dependent lipid transport efficiency or in AD-related protein aggregation and clearance. We present what we believe to be the first structural model of an ApoE4 misfolded intermediate state, which may serve to elucidate the molecular mechanism underlying the role of ApoE4 in AD pathogenesis. The knowledge of the structure for the ApoE4 folding intermediate provides a new platform for the rational design of alternative therapeutic strategies to fight AD. PMID:26506597

  20. Electron Paramagnetic Resonance and Electron-Nuclear Double Resonance Studies of the Reactions of Cryogenerated Hydroperoxoferric–Hemoprotein Intermediates

    PubMed Central

    2015-01-01

    The fleeting ferric peroxo and hydroperoxo intermediates of dioxygen activation by hemoproteins can be readily trapped and characterized during cryoradiolytic reduction of ferrous hemoprotein–O2 complexes at 77 K. Previous cryoannealing studies suggested that the relaxation of cryogenerated hydroperoxoferric intermediates of myoglobin (Mb), hemoglobin, and horseradish peroxidase (HRP), either trapped directly at 77 K or generated by cryoannealing of a trapped peroxo-ferric state, proceeds through dissociation of bound H2O2 and formation of the ferric heme without formation of the ferryl porphyrin π-cation radical intermediate, compound I (Cpd I). Herein we have reinvestigated the mechanism of decays of the cryogenerated hydroperoxyferric intermediates of α- and β-chains of human hemoglobin, HRP, and chloroperoxidase (CPO). The latter two proteins are well-known to form spectroscopically detectable quasistable Cpds I. Peroxoferric intermediates are trapped during 77 K cryoreduction of oxy Mb, α-chains, and β-chains of human hemoglobin and CPO. They convert into hydroperoxoferric intermediates during annealing at temperatures above 160 K. The hydroperoxoferric intermediate of HRP is trapped directly at 77 K. All studied hydroperoxoferric intermediates decay with measurable rates at temperatures above 170 K with appreciable solvent kinetic isotope effects. The hydroperoxoferric intermediate of β-chains converts to the S = 3/2 Cpd I, which in turn decays to an electron paramagnetic resonance (EPR)-silent product at temperature above 220 K. For all the other hemoproteins studied, cryoannealing of the hydroperoxo intermediate directly yields an EPR-silent majority product. In each case, a second follow-up 77 K γ-irradiation of the annealed samples yields low-spin EPR signals characteristic of cryoreduced ferrylheme (compound II, Cpd II). This indicates that in general the hydroperoxoferric intermediates relax to Cpd I during cryoanealing at low temperatures, but

  1. Kinetics and mechanisms of reactions involving small aromatic reactive intermediates. Annual report

    SciTech Connect

    Lin, M.C.

    1994-04-01

    Phenyl (C{sub 6}H{sub 5}), phenoxy (C{sub 6}H{sub 5}O) and benzyne (C{sub 6}H{sub 4}) are fundamentally important prototype molecules. C{sub 6}H{sub 5} and C{sub 6}H{sub 5}O are also very important reactive intermediates in hydrocarbon combustion systems, particularly with regard to soot formation chemistry, as well as to the combustion chemistry of aromatic additives in gasoline. The authors proposed to study the kinetics and mechanisms of these three benchmark reactive intermediates using two complementary laser diagnostic techniques -- laser resonance absorption (LRA) and resonance enhanced multiphoton ionization mass spectrometry (REMPI/MS). In the first year of this contractual work, they have employed a new type of LRA, i.e. the intra-cavity resonance absorption technique, to measure the rate constants for C{sub 6}H{sub 5} reactions, extending the limit of rate constant measurement down to 10{sup {minus}18} cm{sup 3}/s. They have tested this method for the following reactions: C{sub 6}H{sub 5} + HBr, CH{sub 2}O, O{sub 2}, C{sub 2}H{sub 2} and C{sub 2}H{sub 4} at 297 K and obtained their rate constants to be 3.0 {times} 10{sup {minus}11}, 1.2 {times} 10{sup {minus}14}, 1.0 {times} 10{sup {minus}16}, 7.0 {times} 10{sup {minus}18} and 6.7 {times} 10{sup {minus}18} cm{sup 3}/s, respectively. In the second study, the REMPI spectroscopy of C{sub 6}H{sub 5} is being investigated with the two laser pump-probe surface photolysis method. The desorbed C{sub 6}H{sub 5} photofragment is ionized by (1+1) MPI in the spectral range 200--260 nm. Similarly, the NO photofragment is also detected by (1+1) MPI in the same spectral region. The detailed photofragmentation of the absorbed C{sub 6}H{sub 5}NO at 193 and 248 nm is being analyzed presently and a new experiment with acetophenone on a quartz surface is under way.

  2. Identification of a Critical Intermediate in Galvanic Exchange Reactions by Single-Nanoparticle Resolved Kinetics

    NASA Astrophysics Data System (ADS)

    Smith, Jeremy George; Jain, Prashant

    2014-06-01

    The realization of common materials transformations in nanocrystalline systems is fostering the development of novel nanostructures and allowing a deep look into the atomistic mechanisms involved. Galvanic corrosion is one such transformation. We studied galvanic replacement within individual metal nanoparticles by using plasmonic spectroscopy. This proved to be a powerful approach to studying materials transformations in the absence of ensemble averaging. Individual nanoscale units act as domains that can be interrogated optically in isolation, whereas the averaging of all such domains provides a bulk reaction trajectory. Single-nanoparticle reaction trajectories showed that a Ag nanoparticle exposed to Au3+ makes an abrupt transition into a nanocage structure. The transition is limited by a critical structural event, which we identified by electron microscopy to comprise the formation of a nanosized void, similar to the pitting process commonly observed in the corrosion of metals. Trajectories also revealed a surprisingly strong nonlinearity of the reaction kinetics, which we explain by a model involving the critical coalescence of vacancies into a growing void. The critical void size for galvanic exchange to spontaneously proceed was found to be 20 atomic vacancies. In the future we hope to extend this approach to examine a wide variety of materials transformations and chemical reactions.

  3. Thermodynamical properties of reaction intermediates during apoplastocyanin folding in time domain

    NASA Astrophysics Data System (ADS)

    Baden, N.; Hirota, S.; Takabe, T.; Funasaki, N.; Terazima, M.

    2007-11-01

    Two intermediates observed for the folding process of apoplastocyanin (apoPC) were investigated by using a photoinduced triggering system combined with the transient grating and transient lens methods. The thermodynamic quantities, enthalpy, heat capacity, partial volume, and thermal expansion volume changes during the protein folding reaction were measured in time domain for the first time. An interesting observation is the positive enthalpy changes during the folding process. This positive enthalpy change must be compensated by positive entropy changes, which could be originated from the dehydration effect of hydrophobic residues and/or the translational entropy gain of bulk water molecules. Observed negative heat capacity change was explained by the dehydration effect of hydrophilic residues and/or motional confinement of amino acid side chains and water molecules in apoPC. The signs of the volume change and thermal expansion volume were different for two processes and these changes were interpreted in terms of the different relative contributions of the hydration and the dehydration of the hydrophilic residues. These results indicated two-step hydrophobic collapses in the early stage of the apoPC folding, but the nature of the dynamics was different.

  4. Intermediates in the cation reactions in solution probed by an in situ surface enhanced Raman scattering method

    NASA Astrophysics Data System (ADS)

    Tan, Chih-Shan; Chen, Hung-Ying; Chen, Hsueh-Szu; Gwo, Shangjr; Chen, Lih-Juann

    2015-09-01

    For chemical reactions in liquid state, such as catalysis, understanding of dynamical changes is conducive to practical applications. Solvation of copper salts in aqueous solution has implications for life, the environment, and industry. In an ongoing research, the question arises that why the color of aqueous CuCl2 solution changes with solution concentration? In this work, we have developed a convenient and efficient in situ surface enhanced Raman scattering technique to probe the presence of many intermediates, some of them are responsible for color change, in crystallization of aqueous copper chloride solution. The versatility of the novel technique was confirmed in the identification of five intermediates states in the transition from CdS to MoS2 nanowires in solution. The facile in situ method is expected to be widely applicable in probing intermediate states in a variety of chemical reactions in solution.

  5. Intermediates in the cation reactions in solution probed by an in situ surface enhanced Raman scattering method.

    PubMed

    Tan, Chih-Shan; Chen, Hung-Ying; Chen, Hsueh-Szu; Gwo, Shangjr; Chen, Lih-Juann

    2015-01-01

    For chemical reactions in liquid state, such as catalysis, understanding of dynamical changes is conducive to practical applications. Solvation of copper salts in aqueous solution has implications for life, the environment, and industry. In an ongoing research, the question arises that why the color of aqueous CuCl2 solution changes with solution concentration? In this work, we have developed a convenient and efficient in situ surface enhanced Raman scattering technique to probe the presence of many intermediates, some of them are responsible for color change, in crystallization of aqueous copper chloride solution. The versatility of the novel technique was confirmed in the identification of five intermediates states in the transition from CdS to MoS2 nanowires in solution. The facile in situ method is expected to be widely applicable in probing intermediate states in a variety of chemical reactions in solution. PMID:26333518

  6. Intermediates in the cation reactions in solution probed by an in situ surface enhanced Raman scattering method

    PubMed Central

    Tan, Chih-Shan; Chen, Hung-Ying; Chen, Hsueh-Szu; Gwo, Shangjr; Chen, Lih-Juann

    2015-01-01

    For chemical reactions in liquid state, such as catalysis, understanding of dynamical changes is conducive to practical applications. Solvation of copper salts in aqueous solution has implications for life, the environment, and industry. In an ongoing research, the question arises that why the color of aqueous CuCl2 solution changes with solution concentration? In this work, we have developed a convenient and efficient in situ surface enhanced Raman scattering technique to probe the presence of many intermediates, some of them are responsible for color change, in crystallization of aqueous copper chloride solution. The versatility of the novel technique was confirmed in the identification of five intermediates states in the transition from CdS to MoS2 nanowires in solution. The facile in situ method is expected to be widely applicable in probing intermediate states in a variety of chemical reactions in solution. PMID:26333518

  7. Identification of a critical intermediate in galvanic exchange reactions by single-nanoparticle-resolved kinetics.

    PubMed

    Smith, Jeremy G; Yang, Qing; Jain, Prashant K

    2014-03-10

    The realization of common materials transformations in nanocrystalline systems is fostering the development of novel nanostructures and allowing a deep look into the atomistic mechanisms involved. Galvanic corrosion is one such transformation. We studied galvanic replacement within individual metal nanoparticles by using a combination of plasmonic spectroscopy and scanning transmission electron microscopy. Single-nanoparticle reaction trajectories showed that a Ag nanoparticle exposed to Au³⁺ makes an abrupt transition into a nanocage structure. The transition is limited by a critical structural event, which we identified by electron microscopy to comprise the formation of a nanosized void. Trajectories also revealed a surprisingly strong nonlinearity of the reaction kinetics, which we explain by a model involving the critical coalescence of vacancies into a growing void. The critical void size for galvanic exchange to spontaneously proceed was found to be 20 atomic vacancies.

  8. Exploring the intermediates of photochemical CO2 reduction: reaction of Re(dmb)(CO)3 COOH with CO2.

    PubMed

    Agarwal, Jay; Sanders, Brian C; Fujita, Etsuko; Schaefer, Henry F; Harrop, Todd C; Muckerman, James T

    2012-07-11

    We have investigated the reaction of Re(dmb)(CO)(3)COOH with CO(2) using density functional theory, and propose a mechanism for the production of CO. This mechanism supports the role of Re(dmb)(CO)(3)COOH as a key intermediate in the formation of CO. Our new experimental work supports the proposed scheme.

  9. The genome sequence of the emerging common midwife toad virus identifies an evolutionary intermediate within ranaviruses.

    PubMed

    Mavian, Carla; López-Bueno, Alberto; Balseiro, Ana; Casais, Rosa; Alcamí, Antonio; Alejo, Alí

    2012-04-01

    Worldwide amphibian population declines have been ascribed to global warming, increasing pollution levels, and other factors directly related to human activities. These factors may additionally be favoring the emergence of novel pathogens. In this report, we have determined the complete genome sequence of the emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in several amphibian species across Europe. Phylogenetic and gene content analyses of the first complete genomic sequence from a ranavirus isolated in Europe show that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome structure is novel and represents an intermediate evolutionary stage between the two previously described ALRV groups. We find that CMTV clusters with several other ranaviruses isolated from different hosts and locations which might also be included in this novel ranavirus group. This work sheds light on the phylogenetic relationships within this complex group of emerging, disease-causing viruses.

  10. The Genome Sequence of the Emerging Common Midwife Toad Virus Identifies an Evolutionary Intermediate within Ranaviruses

    PubMed Central

    Mavian, Carla; López-Bueno, Alberto; Balseiro, Ana; Casais, Rosa; Alcamí, Antonio

    2012-01-01

    Worldwide amphibian population declines have been ascribed to global warming, increasing pollution levels, and other factors directly related to human activities. These factors may additionally be favoring the emergence of novel pathogens. In this report, we have determined the complete genome sequence of the emerging common midwife toad ranavirus (CMTV), which has caused fatal disease in several amphibian species across Europe. Phylogenetic and gene content analyses of the first complete genomic sequence from a ranavirus isolated in Europe show that CMTV is an amphibian-like ranavirus (ALRV). However, the CMTV genome structure is novel and represents an intermediate evolutionary stage between the two previously described ALRV groups. We find that CMTV clusters with several other ranaviruses isolated from different hosts and locations which might also be included in this novel ranavirus group. This work sheds light on the phylogenetic relationships within this complex group of emerging, disease-causing viruses. PMID:22301140

  11. Spectroscopically identified intermediate age stars at 0.5-3 pc distance from Sagittarius A*

    NASA Astrophysics Data System (ADS)

    Nishiyama, Shogo; Schödel, Rainer; Yoshikawa, Tatsuhito; Nagata, Tetsuya; Minowa, Yosuke; Tamura, Motohide

    2016-04-01

    Context. Nuclear star clusters (NSCs) at the dynamical center of galaxies appear to have a complex star formation history. This suggests repeated star formation, even in the influence of the strong tidal field from supermassive black holes. Although the central region of our Galaxy is an ideal target for studies of the star formation history in the NSCs, most studies in the past have concentrated on a projected distance of RSgr A ∗ ~ 0.5 pc from the supermassive black hole Sgr A*. Aims: In our previous study, we detected 31 so far unknown early-type star candidates throughout the Galactic NSC (at RSgr A ∗ = 0.5-3 pc). They were found via near-infrared (NIR) imaging observations with narrow-band filters which are sensitive to CO absorption lines at ~2.3 μm, a prominent feature for old, late-type stars. The aim of this study is to confirm the spectral type for the early-type star candidates. Methods: We have carried out NIR spectroscopic observations of the early-type star candidates using Subaru/IRCS/AO188 and the laser guide star system. K-band spectra for 20 out of the 31 candidates and reference late-type stars were obtained. By determining an equivalent width, EW(CO), of the 12CO absorption feature at ≈2.294 μm, we have derived an effective temperature and a bolometric magnitude for each candidate and late-type star, and then constructed an HR diagram. Results: No young (~Myr) massive stars are included in the 20 candidates we observed; however, 13 candidates are most likely intermediate-age giants (50-500 Myr). Two other sources have ages of ~1 Gyr and the remaining five sources are old (>1 Gyr), late-type giants. Conclusions: Although none of the early-type star candidates from our previous narrow-band imaging observations can be confirmed as a young star, we find that the photometric technique can distinguish old, late-type giants from young and intermediate-age populations. From the 20 spectroscopically observed candidates, 65% of them are confirmed

  12. Quantum-chemical ab initio investigation of the two-step charge transfer process of hydrogen reaction: approach of reaction pathways via hydrogen intermediate on Cu(100)

    NASA Astrophysics Data System (ADS)

    Kuznetsov, An. M.; Lorenz, W.

    1994-08-01

    Local reaction events in the course of the electrochemical two-step hydrogen evolution reaction have been investigated by means of quantum-chemical all-electron ab initio calculations on interfacial supermolecular cluster models including a hydrated hydrogen intermediate on Cu(100). Expanding on preceding study to larger hydration clusters, an approach to relevant reaction path characteristics has been pursued for two processes: (i) the transfer of hydrated hydronium ion into a chemisorbed hydrogen intermediate: (ii) the reaction of hydronium ion with the intermediate to molecular hydrogen. Computations were carried out on RHF level, using contracted (12,8,4)/[8,6,2,] and/or 6-31G * or G ** pol-O bases for the metal and adsorbate part, respectively. Destruction of the hydronium configuration in process (i) has been confirmed. Electronic partial charge transfer dut to chemical bond conversions in both steps (i) and (ii) has been displayed along relevant cuts of adiabatic potential surfaces, proving significantly different amounts of charge transfer in both steps, λ 1 > 1, λ 2≡(2-λ 1) < 1. In advance of consideration of macroscopic double layer effects, first insight has been gained into coupled nuclear motions and into the origin of reaction barriers

  13. Identifying the Molecular Structures of Intermediates for Optimizing the Fabrication of High-Quality Perovskite Films.

    PubMed

    Cao, Jing; Jing, Xiaojing; Yan, Juanzhu; Hu, Chengyi; Chen, Ruihao; Yin, Jun; Li, Jing; Zheng, Nanfeng

    2016-08-10

    During the past two years, the introduction of DMSO has revolutionized the fabrication of high-quality pervoskite MAPbI3 (MA = CH3NH3) films for solar cell applications. In the developed DMSO process, the formation of (MA)2Pb3I8·2DMSO (shorted as Pb3I8) has well recognized as a critical factor to prepare high-quality pervoskite films and thus accomplish excellent performances in perovskite solar cells. However, Pb3I8 is an I-deficient intermediate and must further react with methylammonium iodide (MAI) to be fully converted into MAPbI3. By capturing and solving the molecular structures of several intermediates involved in the fabrication of perovskite films, we report in this work that the importance of DMSO is NOT due to the formation of Pb3I8. The use of different PbI2-DMSO ratios leads to two different structures of PbI2-DMSO precursors (PbI2·DMSO and PbI2·2DMSO), thus dramatically influencing the quality of fabricated perovskite films. However, such an influence can be minimized when the PbI2-DMSO precursor films are thermally treated to create mesoporous PbI2 films before reacting with MAI. Such a development makes the fabrication of high-quality pervoskite films highly reproducible without the need to precisely control the PbI2:DMSO ratio. Moreover, the formation of ionic compound (MA)4PbI6 is observed when excess MAI is used in the preparation of perovskite film. This I-rich phase heavily induces the hysteresis in PSCs, but is readily removed by isopropanol treatment. On the basis of all these findings, we develop a new effective protocol to fabricate high-performance PSCs. In the new protocol, high-quality perovskite films are prepared by simply treating the mesoporous PbI2 films (made from PbI2-DMSO precursors) with an isopropanol solution of MAI, followed by isopropanol washing. The best efficiency of fabricated MAPbI3 PSCs is up to 19.0%. As compared to the previously reported DMSO method, the devices fabricated by the method reported in this work

  14. Direct detection and kinetic analysis of covalent intermediate formation in the 4-amino-4-deoxychorismate synthase catalyzed reaction.

    PubMed

    He, Ze; Toney, Michael D

    2006-04-18

    Chorismate-utilizing enzymes catalyze diverse reactions, providing critical physiological functions unique to plants, bacteria, fungi, and some parasites. Their absence in animals makes them excellent targets for antimicrobials and herbicides. 4-Amino-4-deoxychorismate synthase (ADCS) catalyzes the first step in folate biosynthsis and shares a common core mechanism with isochorismate synthase (IS) and anthranilate synthase (AS), in which nucleophile addition at C2 initiates these reactions. Evidence was presented previously [He, Z., Stigers Lavoie, K. D., Bartlett, P. A., and Toney, M. D. (2004) J. Am. Chem. Soc. 126, 2378-2385] that K274 is the nucleophile in ADCS, implying formation of a covalent intermediate. Herein, we report the direct detection of this covalent intermediate formed in ADCS-catalyzed reactions by ESI-MS. Difference spectra show the covalent intermediate has an absorption maximum at 310 nm. This was used to study the pre-steady-state kinetics of covalent intermediate formation under various conditions. Additionally, E258 in ADCS was shown to be critical to formation of the covalent intermediate by acting as a general acid catalyst for loss of the C4 hydroxyl group. The E258A/D mutants both exhibit very low activity. Acetate is a poor chemical rescue agent for E258D but an excellent one for E258A, with a 20000-fold and 3000-fold rate increase for Gln-dependent and NH(4)(+)-dependent activities, respectively. Lastly, A213 in IS (structurally homologous to K274 in ADCS) was changed to lysine in an attempt to convert IS to an ADCS-like enzyme. HPLC studies support the formation of a covalent intermediate with this mutant. PMID:16605270

  15. Extremely rapid self-reaction of the simplest Criegee intermediate CH2OO and its implications in atmospheric chemistry

    NASA Astrophysics Data System (ADS)

    Su, Yu-Te; Lin, Hui-Yu; Putikam, Raghunath; Matsui, Hiroyuki; Lin, M. C.; Lee, Yuan-Pern

    2014-06-01

    Criegee intermediates, which are carbonyl oxides produced when ozone reacts with unsaturated hydrocarbons, play an important role in the formation of OH and organic acids in the atmosphere, but they have eluded direct detection until recently. Reactions that involve Criegee intermediates are not understood fully because data based on their direct observation are limited. We used transient infrared absorption spectroscopy to probe directly the decay kinetics of formaldehyde oxide (CH2OO) and found that it reacts with itself extremely rapidly. This fast self-reaction is a result of its zwitterionic character. According to our quantum-chemical calculations, a cyclic dimeric intermediate that has the terminal O atom of one CH2OO bonded to the C atom of the other CH2OO is formed with large exothermicity before further decomposition to 2H2CO + O2(1Δg). We suggest that the inclusion of this previously overlooked rapid reaction in models may affect the interpretation of previous laboratory experiments that involve Criegee intermediates.

  16. The GC-MS Observation of Intermediates in a Stepwise Grignard Addition Reaction

    ERIC Educational Resources Information Center

    Latimer, Devin

    2007-01-01

    Preparation of phenylmagnesium bromide described by Eckert, addition of three equivalents of Grignard reagent to diethyl carbonate to form triphenylmethanol and a series of GC-MS procedures that form intermediates. The analysis is consistent with a gas chromatogram and mass spectrum for each of the expected intermediates and final product of the…

  17. Uridine Diphosphate-4-Keto-Glucose, an Intermediate in the Uridine Diphosphate-Galactose-4-Epimerase Reaction

    PubMed Central

    Maitra, Utpalendu S.; Ankel, Helmut

    1971-01-01

    When UDP-galactose 4-epimerase (EC 5.1.3.2) from Escherichia coli is incubated with UDP-galactose, then reduced with NaB3H4, label is found in UDP-glucose and UDP-galactose. Enzymatic and chemical degradation demonstrates that the label is bound to carbon 4 of the glycosyl moieties. These results provide direct evidence for the existence of UDP-4-keto-glucose as an enzyme-bound intermediate in the epimerization reaction, and they exclude the formation of a 3-keto intermediate. PMID:4941982

  18. Intermediate in the O−O Bond Cleavage Reaction of an Extradiol Dioxygenase

    SciTech Connect

    Kovaleva, Elena G.; Lipscomb, John D.

    2009-02-16

    The reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and O{sub 2} in adjacent ligand positions of the active site metal [usually Fe(II)]. This intermediate and the following Fe(II)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (HPCD). Here a subsequent intermediate in which the O-O bond is broken to yield a gem diol species is structurally characterized. This new intermediate is stabilized in the crystal by using the alternative substrate, 4-sulfonylcatechol, and the Glu323Leu variant of HPCD, which alters the crystal packing.

  19. Identifying of meat species using polymerase chain reaction (PCR)

    NASA Astrophysics Data System (ADS)

    Foong, Chow Ming; Sani, Norrakiah Abdullah

    2013-11-01

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one's diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing.

  20. Identifying of meat species using polymerase chain reaction (PCR)

    SciTech Connect

    Foong, Chow Ming; Sani, Norrakiah Abdullah

    2013-11-27

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one’s diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing.

  1. The reaction of [FeII(tpa)] with H2O2 in acetonitrile and acetone--distinct intermediates and yet similar catalysis.

    PubMed

    Mairata i Payeras, Antoni; Ho, Raymond Y N; Fujita, Megumi; Que, Lawrence

    2004-10-11

    The reaction of [FeII(tpa)(OTf)2] (tpa=tris(2-pyridylmethyl)amine) and its related 5-Me3-tpa complex with hydrogen peroxide affords spectroscopically distinct iron(III)-peroxo intermediates in CH3CN and acetone. The reaction in acetonitrile at -40 degrees C results in the formation of the previously reported Fe(III)-OOH intermediate, the end-on hydroperoxo coordination mode of which is established in this paper by detailed resonance Raman isotope-labeling experiments. On the other hand, the reaction in acetone below -40 degrees C leads to the observation of a different peroxo intermediate identified by resonance Raman spectroscopy to be an FeIII-OOC (CH3)2OH species; this represents the first example of an intermediate derived from the adduct of H2O2 and acetone. The peroxoacetone intermediate decays more rapidly than the corresponding FeIII-OOH species and converts to an FeIV=O species by O-O bond homolysis. This decay process is analogous to that observed for [FeIII(tpa)(OOtBu)]2+ and in fact exhibits a comparable enthalpy of activation of 54(3) kJ mol(-1). Thus, with respect to their physical properties at low temperature, the peroxoacetone intermediate resembles [FeIII(tpa)(OOtBu)]2+ more than the corresponding FeIII-OOH species. At room temperature, however, the behavior of the Fe(tpa)/H2O2 combination in acetone in catalytic hydrocarbon oxidations differs significantly from that of the Fe(tpa)/tBuOOH combination and more closely matches that of the Fe(tpa)/H2O2 combination in CH3CN. Like the latter, the Fe(tpa)/H2O2 combination in acetone catalyzes the hydroxylation of cis-1,2-dimethylcyclohexane to its tertiary alcohol with high stereoselectivity and carries out the epoxidation and cis-dihydroxylation of olefins. These results demonstrate the subtle complexity of the Fe(tpa)/H2O2 reaction surface.

  2. An efficient graph theory based method to identify every minimal reaction set in a metabolic network

    PubMed Central

    2014-01-01

    Background Development of cells with minimal metabolic functionality is gaining importance due to their efficiency in producing chemicals and fuels. Existing computational methods to identify minimal reaction sets in metabolic networks are computationally expensive. Further, they identify only one of the several possible minimal reaction sets. Results In this paper, we propose an efficient graph theory based recursive optimization approach to identify all minimal reaction sets. Graph theoretical insights offer systematic methods to not only reduce the number of variables in math programming and increase its computational efficiency, but also provide efficient ways to find multiple optimal solutions. The efficacy of the proposed approach is demonstrated using case studies from Escherichia coli and Saccharomyces cerevisiae. In case study 1, the proposed method identified three minimal reaction sets each containing 38 reactions in Escherichia coli central metabolic network with 77 reactions. Analysis of these three minimal reaction sets revealed that one of them is more suitable for developing minimal metabolism cell compared to other two due to practically achievable internal flux distribution. In case study 2, the proposed method identified 256 minimal reaction sets from the Saccharomyces cerevisiae genome scale metabolic network with 620 reactions. The proposed method required only 4.5 hours to identify all the 256 minimal reaction sets and has shown a significant reduction (approximately 80%) in the solution time when compared to the existing methods for finding minimal reaction set. Conclusions Identification of all minimal reactions sets in metabolic networks is essential since different minimal reaction sets have different properties that effect the bioprocess development. The proposed method correctly identified all minimal reaction sets in a both the case studies. The proposed method is computationally efficient compared to other methods for finding minimal

  3. Synthesis and properties of 2-acetylthiamin pyrophosphate: an enzymatic reaction intermediate

    SciTech Connect

    Gruys, K.J.; Halkides, C.J.; Frey, P.A.

    1987-12-01

    The synthesis of 2-acetylthiamin pyrophosphate (acetyl-TPP) is described. The synthesis of this compound is accomplished at 23/sup 0/C by the oxidation of 2-(1-hydroxyethyl) thiamin pyrophosphate using aqueous chromic acid as the oxidizing agent under conditions where Cr(III) coordination to the pyrophosphoryl moiety and hydrolysis of both the pyrophosphate and acetyl moieties were prevented. Although the chemical properties exhibited by acetyl-TPP are similar to those of the 2-acetyl-3,4-dimethylthiazolium ion examined by Lienhard, significant differences exist because of the pyrimidine ring in acetyl-TPP. Characterization of acetyl-TPP by ultraviolet spectroscopy, /sup 1/H NMR, /sup 13/C NMR, and /sup 31/P NMR provided evidence that the compound in aqueous solution exists as an equilibrium mixture of keto, hydrate, and intramolecular carbinolamine forms. The equilibria for the hydration and carbinolamine formation reactions at pD 1.3 as determined by /sup 1/H NMR are strongly dependent on the temperature, showing an increase in the hydrate and carbinolamine forms at the expense of the keto form with decreasing temperature. The concentration of keto form also decreases with increasing pH. Acetyl-TPP is stable in aqueous acid but rapidly deacetylates at higher pH to form acetate and thiamin pyrophosphate. Trapping of the acetyl moiety in aqueous solution occurs efficiently with 1.0 M hydroxylamine at pH 5.5-6.5 to form acetohydroxamic acid and to a much smaller extent with 1.0 M 2-mercaptoethanol at pH 4.0 and 5.0 to form thio ester. Transfer of the acetyl group to 0.5 M dihydrolipoic acid at pH 5.0 and 1.0 M phosphate dianion at pH 7.0 is not observed to any significant extent in water. The kinetic and thermodynamic reactivity of acetyl-TPP with water and other nucleophiles is compatible with a hypothetical role for acyl-TPPs as enzymatic acyl-transfer intermediates.

  4. L-myo-inosose-1 as a probable intermediate in the reaction catalyzed by myo-inositol oxygenase

    SciTech Connect

    Naber, N.I.; Swan, J.S.; Hamilton, G.A.

    1986-11-04

    In previous investigations, it was necessary to have Fe(II) and cysteine present in order to assay the catalytic activity of purified hog kidney myo-inositol oxygenase. In the present study it was found that, if this purified nonheme iron enzyme is slowly frozen in solution with glutathione and stored at -20 degrees C, it is fully active in the absence of activators if catalase is present to remove adventitious H/sub 2/O/sub 2/. With this simpler assay system it was possible to clarify the effects of several variables on the enzymic reaction. Thus, the maximum velocity is pH-dependent with a maximum around pH 9.5, but the apparent Km for myo-inositol (air atmosphere) remains constant at 5.0 mM throughout a broad pH range. The enzyme is quite specific for its substrate myo-inositol, is very sensitive to oxidants and reductants, but is not affected by a variety of complexing agents, nucleotides, sulfhydryl reagents, etc. In other experiments it was found that L-myo-inosose-1, a potential intermediate in the enzymic reaction, is a potent competitive inhibitor (Ki = 62 microM), while other inososes and a solution thought to contain D-glucodialdehyde, another potential intermediate, are weak inhibitors. Also, both a kinetic deuterium isotope effect (kH/kD = 2.1) and a tritium isotope effect (kH/kT = 7.5) are observed for the enzymic reaction when (1-2H)- and (1-3H)-myo-inositol are used as reactants. These latter results are considered strong evidence that the oxygenase reaction proceeds by a pathway involving L-myo-inosose-1 as an intermediate rather than by an alternative pathway that would have D-glucodialdehyde as the intermediate.

  5. Modeling of catalytically active metal complex species and intermediates in reactions of organic halides electroreduction.

    PubMed

    Lytvynenko, Anton S; Kolotilov, Sergey V; Kiskin, Mikhail A; Eremenko, Igor L; Novotortsev, Vladimir M

    2015-02-28

    The results of quantum chemical modeling of organic and metal-containing intermediates that occur in electrocatalytic dehalogenation reactions of organic chlorides are presented. Modeling of processes that take place in successive steps of the electrochemical reduction of representative C1 and C2 chlorides - CHCl3 and Freon R113 (1,1,2-trifluoro-1,2,2-trichloroethane) - was carried out by density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). It was found that taking solvation into account using an implicit solvent model (conductor-like screening model, COSMO) or considering explicit solvent molecules gave similar results. In addition to modeling of simple non-catalytic dehalogenation, processes with a number of complexes and their reduced forms, some of which were catalytically active, were investigated by DFT. Complexes M(L1)2 (M = Fe, Co, Ni, Cu, Zn, L1H = Schiff base from 2-pyridinecarbaldehyde and the hydrazide of 4-pyridinecarboxylic acid), Ni(L2) (H2L2 is the Schiff base from salicylaldehyde and 1,2-ethylenediamine, known as salen) and Co(L3)2Cl2, representing a fragment of a redox-active coordination polymer [Co(L3)Cl2]n (L3 is the dithioamide of 1,3-benzenedicarboxylic acid), were considered. Gradual changes in electronic structure in a series of compounds M(L1)2 were observed, and correlations between [M(L1)2](0) spin-up and spin-down LUMO energies and the relative energies of the corresponding high-spin and low-spin reduced forms, as well as the shape of the orbitals, were proposed. These results can be helpful for determination of the nature of redox-processes in similar systems by DFT. No specific covalent interactions between [M(L1)2](-) and the R113 molecule (M = Fe, Co, Ni, Zn) were found, which indicates that M(L1)2 electrocatalysts act rather like electron transfer mediators via outer-shell electron transfer. A relaxed surface scan of the adducts {M(L1)2·R113}(-) (M = Ni or Co) versus the distance between the

  6. Reactivity of TEMPO toward 16- and 17-electron organometallic reaction intermediates: a time-resolved IR study.

    PubMed

    Lomont, Justin P; Nguyen, Son C; Harris, Charles B

    2013-07-31

    The (2,2,6,6-tetramethylpiperidin-1-yl)oxyl radical (TEMPO) has been employed for an extensive range of chemical applications, ranging from organometallic catalysis to serving as a structural probe in biological systems. As a ligand in an organometallic complex, TEMPO can exhibit several distinct coordination modes. Here we use ultrafast time-resolved infrared spectroscopy to study the reactivity of TEMPO toward coordinatively unsaturated 16- and 17-electron organometallic reaction intermediates. TEMPO coordinates to the metal centers of the 16-electron species CpCo(CO) and Fe(CO)4, and to the 17-electron species CpFe(CO)2 and Mn(CO)5, via an associative mechanism with concomitant oxidation of the metal center. In these adducts, TEMPO thus behaves as an anionic ligand, characterized by a pyramidal geometry about the nitrogen center. Density functional theory calculations are used to facilitate interpretation of the spectra and to further explore the structures of the TEMPO adducts. To our knowledge, this study represents the first direct characterization of the mechanism of the reaction of TEMPO with coordinatively unsaturated organometallic complexes, providing valuable insight into its reactions with commonly encountered reaction intermediates. The similar reactivity of TEMPO toward each of the species studied suggests that these results can be considered representative of TEMPO's reactivity toward all low-valent transition metal complexes.

  7. Reaction of serine-glyoxylate aminotransferase with the alternative substrate ketomalonate indicates rate-limiting protonation of a quinonoid intermediate.

    PubMed

    Karsten, William E; Ohshiro, Takashi; Izumi, Yoshikazu; Cook, Paul F

    2005-12-01

    Serine-glyoxylate aminotransferase (SGAT) from Hyphomicrobium methylovorum is a pyridoxal 5'-phosphate (PLP) enzyme that catalyzes the interconversion of L-serine and glyoxylate to hydroxypyruvate and glycine. The primary deuterium isotope effect using L-serine 2-D is one on (V/K)serine and V in the steady state. Pre-steady-state experiments also indicate that there is no primary deuterium isotope effect with L-serine 2-D. The results suggest there is no rate limitation by abstraction of the alpha proton of L-serine in the SGAT reaction. In the steady-state a solvent deuterium isotope effect of about 2 was measured on (V/K)L-serine and (V/K)ketomalonate and about 5.5 on V. Similar solvent isotope effects were observed in the pre-steady-state for the natural substrates and the alternative substrate ketomalonate. In the pre-steady-state, no reaction intermediates typical of PLP enzymes were observed with the substrates L-serine, glyoxylate, and hydroxypyruvate. The data suggest that breakdown and formation of the ketimine intermediate is the primary rate-limiting step with the natural substrates. In contrast, using the alternative substrate ketomalonate, pre-steady-state experiments display the transient formation of a 490 nm absorbing species typical of a quinonoid intermediate. The solvent isotope effect results also suggest that with ketomalonate as substrate protonation at C(alpha) is the slowest step in the SGAT reaction. This is the first report of a rate-limiting protonation of a quinonoid at C(alpha) of the external Schiff base in an aminotransferase reaction. PMID:16313196

  8. Novel mechanistic aspects on the reaction between low spin Fe(II) Schiff base amino acid complexes and hydrogen peroxide-spectrophotometric tracer of intraperoxo intermediate catalyzed reaction.

    PubMed

    Awad, Aida M; Shaker, Ali Mohamad; Zaki, Ahmad Borhan El-Din; Nassr, Lobna Abdel-Mohsen Ebaid

    2008-12-01

    The kinetics and mechanism of the reaction of hydrogen peroxide with some Fe(II) Schiff base complexes were investigated spectrophotometrically in aqueous solution at pH 8 and 35 degrees C under pseudo-first-order conditions. The used ligands were derived from salicylaldehyde or o-hydroxynaphthaldehyde and some amino acids (l-leucine, l-iso-leucine, l-serine, l-methionine and dl-tryptophan). It was found that the formation of the purple interaperoxo complex appears only above pH 7.5. The reaction consists of two steps. The first step involves reversible formation of the intraperoxo intermediate which renders irreversible at pH 8. The second step consists of inner-sphere electron transfer. The suggested scheme illustrated first-order kinetics at low [H(2)O(2)] and zero-order at high [H(2)O(2)]. Moreover, the activation parameters of the reaction were evaluated. PMID:18394952

  9. Synthesis of complex benzenoids via the intermediate generation of o-benzynes through the hexadehydro-Diels-Alder reaction.

    PubMed

    Baire, Beeraiah; Niu, Dawen; Willoughby, Patrick H; Woods, Brian P; Hoye, Thomas R

    2013-03-01

    The hexadehydro-Diels-Alder (HDDA) cascade enables the synthesis of complex benzenoid products with various substitution patterns through aryne intermediates. The first stage of this cascade involves the generation of a highly reactive ortho-benzyne intermediate by a net [4+2] cycloisomerization of a triyne substrate. The benzyne can be rapidly 'trapped' either intramolecularly or intermolecularly with myriad nucleophilic or π-bond-donating reactants. As a representative example of a general procedure for synthesizing highly substituted benzenoids, this protocol describes the synthesis of a typical triyne substrate and its use as the reactant in an HDDA cascade to form a phthalide. The synthetic procedure detailed herein (four chemical reactions) takes 16-20 h of active effort over a period of several days for the preparation of the triyne precursor and ∼2 h of active effort over a 3-d period for the generation and trapping of the benzyne and isolation of the phthalide product.

  10. Synthesis of complex benzenoids via the intermediate generation of o-benzynes through the hexadehydro-Diels–Alder reaction

    PubMed Central

    Baire, Beeraiah; Niu, Dawen; Willoughby, Patrick H.; Woods, Brian P.; Hoye, Thomas R.

    2014-01-01

    The hexadehydro-Diels–Alder (HDDA) cascade enables the synthesis of complex benzenoid products with various substitution patterns via aryne intermediates. The first stage of this cascade involves generation of a highly reactive ortho-benzyne intermediate by a net [4+2] cycloisomerization of a triyne substrate. The benzyne can be rapidly ‘trapped’ either intra- or intermolecularly with a myriad of nucleophilic or π-bond-donating reactants. As a representative example of a general procedure to synthesize highly substituted benzenoids, this protocol describes the synthesis of a typical triyne substrate and its use as the reactant in an HDDA cascade to form a phthalide. The synthetic procedure detailed herein (four chemical reactions) takes 16–20 h of active effort over a several day period for preparation of the triyne precursor and ~2 h of active effort over a 3-day period for generation and trapping of the benzyne and isolation of the phthalide product. PMID:23411632

  11. Active intermediates of polyhydroxyalkanoate synthase from Aeromonas caviae in polymerization reaction.

    PubMed

    Numata, Keiji; Motoda, Yoko; Watanabe, Satoru; Tochio, Naoya; Kigawa, Takanori; Doi, Yoshiharu

    2012-11-12

    Polyhydroxyalkanoate (PHA) synthase from Aeromonas caviae FA440 (PhaC(Ac), BAA21815) is one of the most valuable PHA synthase, because of its function to synthesize a practical bioplastic, poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)]. However, biochemical activity and active intermediates of PhaC(Ac) have not been clarified until now. In the present study, a gene of PhaC(Ac) was cloned and overexpressed by a cell-free protein expression system. Both the polymerization activity and oligomerization behavior of the purified PhaC(Ac) were characterized in order to clarify the active intermediates of PhaC(Ac) based on the hydrodynamic diameters and specific activities of PhaC(Ac). The influences of a substrate, (R)-3-hydroxybutyryl-CoA (3HB-CoA), on the oligomerization of PhaC(Ac) (7.5 μM) were also investigated, and then the Hill coefficient (n = 2.6 ± 0.4) and the microscopic dissociation constant (K(m) = 77 ± 5 μM) were determined. Based on the results, the active intermediate of PhaC(Ac) was concluded to be the dimeric PhaC(Ac) containing 3HB-CoA as an activator for its dimerization. This information is critical for revealing the relationships between its dimerization and function in PHA synthesis.

  12. Active intermediates of polyhydroxyalkanoate synthase from Aeromonas caviae in polymerization reaction.

    PubMed

    Numata, Keiji; Motoda, Yoko; Watanabe, Satoru; Tochio, Naoya; Kigawa, Takanori; Doi, Yoshiharu

    2012-11-12

    Polyhydroxyalkanoate (PHA) synthase from Aeromonas caviae FA440 (PhaC(Ac), BAA21815) is one of the most valuable PHA synthase, because of its function to synthesize a practical bioplastic, poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)]. However, biochemical activity and active intermediates of PhaC(Ac) have not been clarified until now. In the present study, a gene of PhaC(Ac) was cloned and overexpressed by a cell-free protein expression system. Both the polymerization activity and oligomerization behavior of the purified PhaC(Ac) were characterized in order to clarify the active intermediates of PhaC(Ac) based on the hydrodynamic diameters and specific activities of PhaC(Ac). The influences of a substrate, (R)-3-hydroxybutyryl-CoA (3HB-CoA), on the oligomerization of PhaC(Ac) (7.5 μM) were also investigated, and then the Hill coefficient (n = 2.6 ± 0.4) and the microscopic dissociation constant (K(m) = 77 ± 5 μM) were determined. Based on the results, the active intermediate of PhaC(Ac) was concluded to be the dimeric PhaC(Ac) containing 3HB-CoA as an activator for its dimerization. This information is critical for revealing the relationships between its dimerization and function in PHA synthesis. PMID:23043466

  13. Processes forming Gas, Tar, and Coke in Cellulose Gasification from Gas-Phase Reactions of Levoglucosan as Intermediate.

    PubMed

    Fukutome, Asuka; Kawamoto, Haruo; Saka, Shiro

    2015-07-01

    The gas-phase pyrolysis of levoglucosan (LG), the major intermediate species during cellulose gasification, was studied experimentally over the temperature range of 400-900 °C. Gaseous LG did not produce any dehydration products, which include coke, furans, and aromatic substances, although these are characteristic products of the pyrolysis of molten LG. Alternatively, at >500 °C, gaseous LG produced only fragmentation products, such as noncondensable gases and condensable C1 -C3 fragments, as intermediates during noncondensable gas formation. Therefore, it was determined that secondary reactions of gaseous LG can result in the clean (tar- and coke-free) gasification of cellulose. Cooling of the remaining LG in the gas phase caused coke formation by the transition of the LG to the molten state. The molecular mechanisms that govern the gas- and molten-phase reactions of LG are discussed in terms of the acid catalyst effect of intermolecular hydrogen bonding to promote the molten-phase dehydration reactions. PMID:26099988

  14. Processes forming Gas, Tar, and Coke in Cellulose Gasification from Gas-Phase Reactions of Levoglucosan as Intermediate.

    PubMed

    Fukutome, Asuka; Kawamoto, Haruo; Saka, Shiro

    2015-07-01

    The gas-phase pyrolysis of levoglucosan (LG), the major intermediate species during cellulose gasification, was studied experimentally over the temperature range of 400-900 °C. Gaseous LG did not produce any dehydration products, which include coke, furans, and aromatic substances, although these are characteristic products of the pyrolysis of molten LG. Alternatively, at >500 °C, gaseous LG produced only fragmentation products, such as noncondensable gases and condensable C1 -C3 fragments, as intermediates during noncondensable gas formation. Therefore, it was determined that secondary reactions of gaseous LG can result in the clean (tar- and coke-free) gasification of cellulose. Cooling of the remaining LG in the gas phase caused coke formation by the transition of the LG to the molten state. The molecular mechanisms that govern the gas- and molten-phase reactions of LG are discussed in terms of the acid catalyst effect of intermolecular hydrogen bonding to promote the molten-phase dehydration reactions.

  15. Liquid-phase hydrogenation of citral over Pt/SiO{sub 2} catalysts. 2. Hydrogenation of reaction intermediate compounds

    SciTech Connect

    Singh, U.K.; Sysak, M.N.; Vannice, M.A.

    2000-04-01

    Liquid-phase hydrogenation of the four principal reaction intermediates formed during citral hydrogenation, i.e., nerol, geraniol, citronellal, and citronellol, was studied at 298 and 373 K under 20 atm H{sub 2} at concentrations of 0.5 to 1.0 M in hexane. A decrease in the initial reaction rate as temperature increased from 298 to 373 K was exhibited during the hydrogenation of all four compounds, just as reported earlier for citral; however, the decrease in rate at 373 K was only one-half for citronellal whereas it was orders of magnitude greater for nerol and geraniol. Furthermore, simultaneous hydrogenation of citronellal and geraniol at 298 K resulted in a continuous decrease in the rate of citronellal disappearance in contrast to the nearly constant rate of disappearance observed during hydrogenation of citronellal alone. Competitive hydrogenation of citral with either geraniol or citronellal showed that geraniol hydrogenation to citronellol is kinetically insignificant during citral hydrogenation at 373 K. The initial activity for hydrogenation of the intermediates at 298 K follows the following trend: geraniol > nerol < citronellol < E-citral, citronellal > Z-citral. Based on the relative hydrogenation rates of the intermediate alone versus its hydrogenation in the presence of other reactants, the relative size of the adsorption equilibrium constants for the various organic compounds appears to be as follows: citral > citronellal > geraniol, nerol > citronellol > 3,7-dimethyloctanol. This study indicates that activation of the C{double_bond}O bond should be performed at higher reaction temperatures to maximize selectivity to the unsaturated alcohols.

  16. Water oxidation: Intermediate identification

    NASA Astrophysics Data System (ADS)

    Cowan, Alexander J.

    2016-08-01

    The slow kinetics of light-driven water oxidation on haematite is an important factor limiting the material's efficiency. Now, an intermediate of the water-splitting reaction has been identified offering hope that the full mechanism will soon be resolved.

  17. N,O-Nucleosides from ene reactions of nitrosocarbonyl intermediates with the 3-methyl-2-buten-1-ol.

    PubMed

    Quadrelli, Paolo; Mella, Mariella; Carosso, Serena; Bovio, Bruna

    2013-01-18

    Nitrosocarbonyl intermediates undergo ene reactions with allylic alcohols, affording regioisomeric adducts in fair yields. Nitrosocarbonyl benzene reacts with 3-methyl-2-buten-1-ol and follows a Markovnikov orientation and abstracts preferentially the twix hydrogens over the lone ones. With the more sterically demanding nitrosocarbonyl mesitylene and anthracene, the Markovnikov directing effect is relieved and lone abstraction is observed, affording the 5-hydroxy-isoxazolidines that serve as synthons for the preparation of N,O-nucleoside analogues according to the Vorbrüggen protocol.

  18. Precursors in the preparation of transition metal nitrides and transition metal carbonitrides and their reaction intermediates

    DOEpatents

    Maya, Leon

    1991-01-01

    A process for making ammonolytic precursors to nitride and carbonitride ceramics. Extreme reaction conditions are not required and the precursor is a powder-like substance that produces ceramics of improved purity and morphology upon pyrolysis.

  19. Process for preparing transition metal nitrides and transition metal carbonitrides and their reaction intermediates

    DOEpatents

    Maya, Leon

    1988-05-24

    A process for making ammonolytic precursors to nitride and carbonitride ceramics. Extreme reaction conditions are not required and the precursor is a powder-like substance that produces ceramics of improved purity and morphology upon pyrolysis.

  20. Energy-loss cross sections for inclusive charge-exchange reactions at intermediate energies

    NASA Technical Reports Server (NTRS)

    Cucinotta, Francis A.; Townsend, Lawrence W.; Dubey, Rajendra R.

    1993-01-01

    Charge-exchange reactions for scattering to the continuum are considered in a high-energy multiple scattering model. Calculations for (p,n) and (He-3,H-3) reactions are made and compared with experimental results for C-12, O-16, and Al-27 targets. Coherent effects are shown to lead to an important role for inelastic multiple scattering terms when light projectiles are considered.

  1. Can we identify patients at risk of life-threatening allergic reactions to food?

    PubMed

    Turner, P J; Baumert, J L; Beyer, K; Boyle, R J; Chan, C-H; Clark, A T; Crevel, R W R; DunnGalvin, A; Fernández-Rivas, M; Gowland, M H; Grabenhenrich, L; Hardy, S; Houben, G F; O'B Hourihane, J; Muraro, A; Poulsen, L K; Pyrz, K; Remington, B C; Schnadt, S; van Ree, R; Venter, C; Worm, M; Mills, E N C; Roberts, G; Ballmer-Weber, B K

    2016-09-01

    Anaphylaxis has been defined as a 'severe, life-threatening generalized or systemic hypersensitivity reaction'. However, data indicate that the vast majority of food-triggered anaphylactic reactions are not life-threatening. Nonetheless, severe life-threatening reactions do occur and are unpredictable. We discuss the concepts surrounding perceptions of severe, life-threatening allergic reactions to food by different stakeholders, with particular reference to the inclusion of clinical severity as a factor in allergy and allergen risk management. We review the evidence regarding factors that might be used to identify those at most risk of severe allergic reactions to food, and the consequences of misinformation in this regard. For example, a significant proportion of food-allergic children also have asthma, yet almost none will experience a fatal food-allergic reaction; asthma is not, in itself, a strong predictor for fatal anaphylaxis. The relationship between dose of allergen exposure and symptom severity is unclear. While dose appears to be a risk factor in at least a subgroup of patients, studies report that individuals with prior anaphylaxis do not have a lower eliciting dose than those reporting previous mild reactions. It is therefore important to consider severity and sensitivity as separate factors, as a highly sensitive individual will not necessarily experience severe symptoms during an allergic reaction. We identify the knowledge gaps that need to be addressed to improve our ability to better identify those most at risk of severe food-induced allergic reactions. PMID:27138061

  2. Can we identify patients at risk of life-threatening allergic reactions to food?

    PubMed

    Turner, P J; Baumert, J L; Beyer, K; Boyle, R J; Chan, C-H; Clark, A T; Crevel, R W R; DunnGalvin, A; Fernández-Rivas, M; Gowland, M H; Grabenhenrich, L; Hardy, S; Houben, G F; O'B Hourihane, J; Muraro, A; Poulsen, L K; Pyrz, K; Remington, B C; Schnadt, S; van Ree, R; Venter, C; Worm, M; Mills, E N C; Roberts, G; Ballmer-Weber, B K

    2016-09-01

    Anaphylaxis has been defined as a 'severe, life-threatening generalized or systemic hypersensitivity reaction'. However, data indicate that the vast majority of food-triggered anaphylactic reactions are not life-threatening. Nonetheless, severe life-threatening reactions do occur and are unpredictable. We discuss the concepts surrounding perceptions of severe, life-threatening allergic reactions to food by different stakeholders, with particular reference to the inclusion of clinical severity as a factor in allergy and allergen risk management. We review the evidence regarding factors that might be used to identify those at most risk of severe allergic reactions to food, and the consequences of misinformation in this regard. For example, a significant proportion of food-allergic children also have asthma, yet almost none will experience a fatal food-allergic reaction; asthma is not, in itself, a strong predictor for fatal anaphylaxis. The relationship between dose of allergen exposure and symptom severity is unclear. While dose appears to be a risk factor in at least a subgroup of patients, studies report that individuals with prior anaphylaxis do not have a lower eliciting dose than those reporting previous mild reactions. It is therefore important to consider severity and sensitivity as separate factors, as a highly sensitive individual will not necessarily experience severe symptoms during an allergic reaction. We identify the knowledge gaps that need to be addressed to improve our ability to better identify those most at risk of severe food-induced allergic reactions.

  3. Inverse Kinematics Studies of Intermediate-Energy Reactions Relevant for SEE and Medical Problems

    NASA Astrophysics Data System (ADS)

    Aichelin, J.; Bargholtz, Ch.; Blomgren, J.; Budzanowski, A.; Chubarov, M.; Czech, B.; Ekström, C.; Gerén, L.; Jakobsson, B.; Kolozhvari, A.; Lozhkin, O.; Murin, Yu.; Nomokonov, P.; Olsson, N.; Persson, H.; Pljuschev, V.; Skwirczynska, I.; Tang, H. H. K.; Tegnér, P.-E.; Westerberg, L.; Zartova, I.; Zubkov, M.; Watanabe, Y.

    2005-05-01

    The lack of systematic experimental checks on the intermediate-energy nuclear model simulations of heavily ionizing recoils from nucleon-nucleus collisions — critical inputs for the Single Event Effect analysis of microelectronics and dosimetry calculations including high-LET components in the cancer tumor radiation therapy — has been a primary motivation for a new experiment planned at the CELSIUS nuclear storage ring of The Svedberg Laboratory, Uppsala, Sweden. Details of the experiment and the first results from a feasibility study are presented here.

  4. Synthesis of Y1BaCu3O(x) superconducting powders by intermediate phase reactions

    NASA Technical Reports Server (NTRS)

    Moure, C.; Fernandez, J. F.; Tartaj, J.; Recio, P.; Duran, P.

    1991-01-01

    A procedure for synthesizing Y1Ba2Cu3O(x) by solid state reactions was developed. The method is based on the use of barium compounds, previously synthesized, as intermediate phases for the process. The reaction kinetics of this procedure were established between 860 C and 920 C. The crystal structure and the presence of second phases were studied by means of XRD. The sintering behavior and ceramic parameters were also determined. The orthorhombic type-I structure was obtained on the synthesized bodies after a cooling cycle in an air atmosphere. Superconducting transition took place at 91 K. Sintering densities higher than 95 percent D sub th were attained at temperatures below 940 C.

  5. Evidence for reversible formation of an intermediate in the spontaneous hydrolysis reaction of p-methoxystryrene oxide

    SciTech Connect

    Ukachukwu, V.C.; Blumenstein, J.J.; Whalen, D.L.

    1986-08-06

    The authors have now examined the hydrolysis reactions of p-methoxystyrene oxide (1) and a deuterium-labeled derivative and wish to report /sup 1/H NMR data that provide evidence for reversible formation of an intermediate in the spontaneous reaction that yields mainly p-methoxyphenylacetaldehyde. The rates of reaction of 1 in 0.1 M NaClO/sub 4/ solutions, at 25.0/sup 0/C over the pH range 4.7-13, were fit to the equation k/sub obsd/ = k/sub H/sup +//a/sub H/sup +// + k/sub 0/. The values of k/sub H/sup +// and k/sub 0/ were determined to be 1.1 +/- 0.2 x 10/sup 4/ M/sup -1/s/sup -1/ and 3.0 +/- 0.1 x 10/sup -3/ s/sup -1/, respectively. Product studies showed that the acid-catalyzed reaction yielded >95% of glycol product, whereas the spontaneous (k/sub 0/) reaction proceeded mainly to rearranged aldehyde. p-Methoxy-trans-..beta..-deuteriostyrene oxide (4) was also prepared, and its hydrolysis reactions were studied. The kinetic deuterium isotope effects k/sub H/sup +//(H)/k/sub H/sup +//(D) and k/sub 0/(H)/k/sub 0/(D) were determined to be 0.97 +/- 0.01 and 1.17 +/- 0.02, respectively. /sup 1/H NMR and mass spectral analyses of the aldehyde product from the k/sub 0/ reaction of 4 showed that the ratio of hydrogen migration to deuterium migration was ca. 3:1. The value of this ratio is similar to the kinetic isotope effect for migration of deuterium and suggests that both hydrogens in the methylene position of 1 migrate to similar extents.

  6. Mechanistic Studies of Reactions of Peroxodiiron(III) Intermediates in T201 Variants of Toluene/o-Xylene Monooxygenase Hydroxylase†

    PubMed Central

    Song, Woon Ju; Lippard, Stephen J.

    2011-01-01

    Site-directed mutagenesis studies of a strictly conserved T201 residue in the active site of toluene/o-xylene monooxygenase hydroxylase (ToMOH) revealed that a single mutation can facilitate kinetic isolation of two distinctive peroxodiiron(III) species, designated T201peroxo and ToMOHperoxo, during dioxygen activation. Previously we characterized both oxygenated intermediates by UV-vis and Mössbauer spectroscopy, proposed structures from DFT and QM/MM computational studies, and elucidated chemical steps involved in dioxygen activation through the kinetic studies of T201peroxo formation. In the current study, we investigated the kinetics of T201peroxo decay to explore the reaction mechanism of the oxygenated intermediates following O2 activation. The decay rates of T201peroxo were monitored in the absence and presence of external (phenol) or internal (tryptophan residue in an I100W variant) substrates under pre-steady-state conditions. Three possible reaction pathways were evaluated and the results demonstrate that T201peroxo is on the pathway of arene oxidation and appears to be in equilibrium with ToMOHperoxo. PMID:21595439

  7. Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric water and in the absence of light: Identification of intermediates and reaction pathways.

    PubMed

    Santos, Patrícia S M; Domingues, M Rosário M; Duarte, Armando C

    2016-07-01

    A previous work showed that the night period is important for the occurrence of Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric waters, which originate new chromophoric compounds apparently more complex than the precursors, although the chemical transformations involved in the process are still unknown. In this work were identified by gas chromatography-mass spectrometry (GC-MS) and by electrospray mass spectrometry (ESI-MS) the organic intermediate compounds formed during the Fenton-like oxidation of three aromatic acids from biomass burning (benzoic, 4-hydroxybenzoic and 3,5-dihydroxybenzoic acids), the same compounds evaluated in the previous study, in water and in the absence of light, which in turns allows to disclose the chemical reaction pathways involved. The oxidation intermediate compounds found for benzoic acid were 2-hydroxybenzoic, 3-hydroxybenzoic, 4-hydroxybenzoic, 2,3-dihydroxybenzoic, 2,5-dihydroxybenzoic, 2,6-dihydroxybenzoic and 3,4-dihydroxybenzoic acids. The oxidation intermediates for 4-hydroxybenzoic acid were 3,4-hydroxybenzoic acid and hydroquinone, while for 3,5-dihydroxybenzoic acid were 2,4,6-trihydroxybenzoic and 3,4,5-trihydroxybenzoic acids, and tetrahydroxybenzene. The results suggested that the hydroxylation of the three small aromatic acids is the main step of Fenton-like oxidation in atmospheric waters during the night, and that the occurrence of decarboxylation is also an important step during the oxidation of the 4-dihydroxybenzoic and 3,5-dihydroxybenzoic acids. In addition, it is important to highlight that the compounds produced are also small aromatic compounds with potential adverse effects on the environment, besides becoming available for further chemical reactions in atmospheric waters.

  8. Fear load: The psychophysiological over-expression of fear as an intermediate phenotype associated with trauma reactions.

    PubMed

    Norrholm, Seth Davin; Glover, Ebony M; Stevens, Jennifer S; Fani, Negar; Galatzer-Levy, Isaac R; Bradley, Bekh; Ressler, Kerry J; Jovanovic, Tanja

    2015-11-01

    Psychophysiological measures of fear expression provide observable intermediate phenotypes of fear-related symptoms. Research Domain Criteria (RDoC) advocate using neurobiological intermediate phenotypes that provide dimensional correlates of psychopathology. Negative Valence Systems in the RDoC matrix include the construct of acute threat, which can be measured on a physiological level using potentiation of the acoustic startle reflex assessed via electromyography recordings of the orbicularis oculi muscle. Impairments in extinction of fear-potentiated startle due to high levels of fear (termed fear load) during the early phases of extinction have been observed in posttraumatic stress disorder (PTSD). The goals of the current work were to examine dimensional associations between fear-related symptoms of PTSD and fear load variables to test their validity as an intermediate phenotype. We examined extinction of fear-potentiated startle in a cohort (n=269) of individuals with a broad range of civilian trauma exposure (range 0-13 traumatic events per person, mean=3.5). Based on previously reported findings, we hypothesized that fear load would be significantly associated with intrusion and fear memories of an index traumatic event. The results indicated that early extinction was correlated with intrusive thoughts (p=0.0007) and intense physiological reactions to trauma reminders (p=0.036). Degree of adult or childhood trauma exposure, and depression severity were not associated with fear load. After controlling for age, sex, race, income, level of prior trauma, and level of fear conditioning, fear load during extinction was still significantly predictive of intrusive thoughts (p=0.004). The significance of these findings is that they support dimensional associations with symptom severity rather than diagnostic category and, as such, fear load may emerge as a transdiagnostic intermediate phenotype expressed across fear-related disorders (e.g., specific phobia, social

  9. High Resolution Reaction Intermediates of rabbit Muscle Fructose-1,6-bisphosphate Aldolase: Substrate Cleavage and Induced Fit

    SciTech Connect

    St-Jean,M.; Lafrance-Vanasse, J.; Liotard, B.; Sygusch, J.

    2005-01-01

    Crystal structures were determined to 1.8-Angstrom resolution of the glycolytic enzyme fructose-1, 6-bis(phosphate) aldolase trapped in complex with its substrate and a competitive inhibitor, mannitol-1, 6-bis(phosphate). The enzyme substrate complex corresponded to the postulated Schiff base intermediate and has reaction geometry consistent with incipient C3-C4 bond cleavage catalyzed by Glu-187, which is adjacent to the Schiff base forming Lys-229. Atom arrangement about the cleaved bond in the reaction intermediate mimics a pericyclic transition state occurring in non-enzymatic aldol condensations. Lys-146 hydrogen bonds the substrate C4 hydroxyl and assists substrate cleavage by stabilizing the developing negative charge on the C4 hydroxyl during proton abstraction. Mannitol-1, 6-bis(phosphate) forms a non-covalent complex in the active site whose binding geometry mimics the covalent carbinolamine precursor. Glu-187 hydrogen bonds the C2 hydroxyl of the inhibitor in the enzyme complex substantiating a proton transfer role by Glu-187 in catalyzing the conversion of the carbinolamine intermediate to Schiff base. Modeling of the acyclic substrate configuration into the active site shows Glu-187, in acid form, hydrogen bonding both substrate C2 carbonyl and C4 hydroxyl, thereby aligning the substrate ketose for nucleophilic attack by Lys-229. The multi-functional role by Glu-187 epitomizes a canonical mechanistic feature conserved in Schiff base forming aldolases catalyzing carbohydrate metabolism. Trapping of tagatose-1, 6-bis(phosphate), a diastereoisomer of fructose-1, 6-bis(phosphate), displayed stereospecific discrimination and reduced ketohexose binding specificity. Each ligand induces homologous conformational changes in two adjacent a-helical regions that promote phosphate binding in the active site.

  10. New model catalysts (platinum nanoparticles) and new techniques (SFG and STM) for studies of reaction intermediates and surface restructuring at high pressures during catalytic reactions

    NASA Astrophysics Data System (ADS)

    Somorjai, G. A.

    1997-11-01

    Single-crystal surfaces have long served us well as model catalysts; however, a new type of model catalyst has been prepared using electron beam lithography. Ordered arrays of platinum nano-particles in the 2.5-50 nm size range are deposited on oxide substrates (silica, alumina, and titania) of 1 cm 2 surface area, and are used in catalyzed surface reactions at high pressures (atmospheres). Their preparation, cleaning, and reactivity is discussed. Scanning tunneling microscopy (STM) and vibrational spectroscopy by sum frequency generation (SFG) can be utilized to monitor the substrate and adsorbate structure, respectively, over a fourteen order of magnitude pressure range (10 -10-10 4 Torr). As a consequence, we can monitor the surface structure and reaction intermediates during high pressure catalytic reactions. An STM that operates at both high pressure (atmosphere) and high temperature has been constructed and utilized to monitor platinum (111) and (110) surface structure during chemisorption of H 2, O 2 and CO, and during catalytic reactions of olefin hydrogenation and hydrogenolysis. Changes of surface structure upon chemisorption and during reactions have been monitored. Catalysis by the platinum tip was also detected in the presence of H 2 or O 2 at high pressures and 300 K, leading to hydrogenation or oxidation of carbonaceous deposits with nanometer spatial resolution. Vibrational spectroscopy using SFG has been used to monitor pressure dependent changes in the chemisorption of CO and NO over Pt(111). Bonding — which is similar to that in Pt m(CO) n (where n/m > 1 ) clusters and for an incommensurate CO overlayer — is observed above 100 Torr. Reaction intermediates that form during ethylene, propylene, and isobutene hydrogenation, as well as CO oxidation, at atmospheric pressures and 300 K were monitored by SFG. The dominant reacting species that hydrogenate are the weakly π-bonded olefins, while the strongly chemisorbed alkylidyne and di-σ bonded

  11. Workshop on hadron structure from photo-reactions at intermediate energies: Proceedings

    SciTech Connect

    Nathan, A.M.; Sandorfi, A.M.

    1992-01-01

    This report contains papers on the following topics: The proton compton effect: Recent measurements of the electric and magnetic polorizabilities of the proton; experiments on the electric polarizability of the neutron; chiral symmetry and nucleon polarizabilities; chiral model predictions for electromagnetic polarizabilities of the nucleon, a consumer report; the polarizabilities of bound nucleons; nucleon polarizability in free space and in nuclear matter; mechanisms of photon scattering on nucleons at intermediate energies; pion polarizabilities in chiral perturbation theory; pion polarizabilities and the shielding of [sigma](700)-meson exchange in [gamma][gamma][yields][pi][pi] processes; pion and kaon polarizabilities in the quark confinement model; radiative pion photoproduction and pion polarizabilities; pion and sigma polarizabilities and radiative transitions; the quadrupole amplitude in the [gamma][Nu]-[Delta] transition; pion photoproduction and the [gamma][Nu]-[Delta] amplitudes; effective- lagrangians, Watson's theorem, and the E2/M1 mixing ratio in the excitation of the delta resonance; new measurements of the p([rvec [gamma

  12. Ionotropic Receptors Identified within the Tentacle of the Freshwater Snail Biomphalaria glabrata, an Intermediate Host of Schistosoma mansoni.

    PubMed

    Liang, Di; Wang, Tianfang; Rotgans, Bronwyn A; McManus, Donald P; Cummins, Scott F

    2016-01-01

    Biomphalaria glabrata (B. glabrata) is an air-breathing aquatic mollusc found in freshwater habitats across the Western Hemisphere. It is most well-known for its recognized capacity to act as a major intermediate host for Schistosoma mansoni, the human blood fluke parasite. Ionotropic receptors (IRs), a variant family of the ionotropic glutamate receptors (iGluR), have an evolutionary ancient function in detecting odors to initiate chemosensory signaling. In this study, we applied an array of methods towards the goal of identifying IR-like family members in B. glabrata, ultimately revealing two types, the iGluR and IR. Sequence alignment showed that three ligand-binding residues are conserved in most Biomphalaria iGluR sequences, while the IRs did exhibit a variable pattern, lacking some or all known glutamate-interactingresidues, supporting their distinct classification from the iGluRs. We show that B. glabrata contains 7 putative IRs, some of which are expressed within its chemosensory organs. To further investigate a role for the more ancient IR25a type in chemoreception, we tested its spatial distribution pattern within the snail cephalic tentacle by in situ hybridization. The presence of IR25a within presumptive sensory neurons supports a role for this receptor in olfactory processing, contributing to our understanding of the molecular pathways that are involved in Biomphalaria olfactory processing. PMID:27253696

  13. Ionotropic Receptors Identified within the Tentacle of the Freshwater Snail Biomphalaria glabrata, an Intermediate Host of Schistosoma mansoni

    PubMed Central

    Liang, Di; Wang, Tianfang; Rotgans, Bronwyn A.; McManus, Donald P.; Cummins, Scott F.

    2016-01-01

    Biomphalaria glabrata (B. glabrata) is an air-breathing aquatic mollusc found in freshwater habitats across the Western Hemisphere. It is most well-known for its recognized capacity to act as a major intermediate host for Schistosoma mansoni, the human blood fluke parasite. Ionotropic receptors (IRs), a variant family of the ionotropic glutamate receptors (iGluR), have an evolutionary ancient function in detecting odors to initiate chemosensory signaling. In this study, we applied an array of methods towards the goal of identifying IR-like family members in B. glabrata, ultimately revealing two types, the iGluR and IR. Sequence alignment showed that three ligand-binding residues are conserved in most Biomphalaria iGluR sequences, while the IRs did exhibit a variable pattern, lacking some or all known glutamate-interactingresidues, supporting their distinct classification from the iGluRs. We show that B. glabrata contains 7 putative IRs, some of which are expressed within its chemosensory organs. To further investigate a role for the more ancient IR25a type in chemoreception, we tested its spatial distribution pattern within the snail cephalic tentacle by in situ hybridization. The presence of IR25a within presumptive sensory neurons supports a role for this receptor in olfactory processing, contributing to our understanding of the molecular pathways that are involved in Biomphalaria olfactory processing. PMID:27253696

  14. Thioredoxin A Active-Site Mutants Form Mixed Disulfide Dimers That Resemble Enzyme–Substrate Reaction Intermediates

    PubMed Central

    Kouwen, Thijs R.H.M.; Andréll, Juni; Schrijver, Rianne; Dubois, Jean-Yves F.; Maher, Megan J.; Iwata, So; Carpenter, Elisabeth P.; van Dijl, Jan Maarten

    2008-01-01

    Thioredoxin functions in nearly all organisms as the major thiol–disulfide oxidoreductase within the cytosol. Its prime purpose is to maintain cysteine-containing proteins in the reduced state by converting intramolecular disulfide bonds into dithiols in a disulfide exchange reaction. Thioredoxin has been reported to contribute to a wide variety of physiological functions by interacting with specific sets of substrates in different cell types. To investigate the function of the essential thioredoxin A (TrxA) in the low-GC Gram-positive bacterium Bacillus subtilis, we purified wild-type TrxA and three mutant TrxA proteins that lack either one or both of the two cysteine residues in the CxxC active site. The pure proteins were used for substrate-binding studies known as “mixed disulfide fishing” in which covalent disulfide-bonded reaction intermediates can be visualized. An unprecedented finding is that both active-site cysteine residues can form mixed disulfides with substrate proteins when the other active-site cysteine is absent, but only the N-terminal active-site cysteine forms stable interactions. A second novelty is that both single-cysteine mutant TrxA proteins form stable homodimers due to thiol oxidation of the remaining active-site cysteine residue. To investigate whether these dimers resemble mixed enzyme–substrate disulfides, the structure of the most abundant dimer, C32S, was characterized by X-ray crystallography. This yielded a high-resolution (1.5Å) X-ray crystallographic structure of a thioredoxin homodimer from a low-GC Gram-positive bacterium. The C32S TrxA dimer can be regarded as a mixed disulfide reaction intermediate of thioredoxin, which reveals the diversity of thioredoxin/substrate-binding modes. PMID:18455736

  15. Solvent dependent structural perturbations of chemical reaction intermediates visualized by time-resolved x-ray diffraction

    SciTech Connect

    Vincent, Jonathan; Eklund, Mattias; Davidsson, Jan; Andersson, Magnus; Woehri, Annemarie B.; Odelius, Michael; Malmerberg, Erik; Neutze, Richard; Kong, Qingyu; Wulff, Michael

    2009-04-21

    Ultrafast time-resolved wide angle x-ray scattering from chemical reactions in solution has recently emerged as a powerful technique for determining the structural dynamics of transient photochemical species. Here we examine the structural evolution of photoexcited CH{sub 2}I{sub 2} in the nonpolar solvent cyclohexane and draw comparisons with a similar study in the polar solvent methanol. As with earlier spectroscopic studies, our data confirm a common initial reaction pathway in both solvents. After photoexcitation, CH{sub 2}I{sub 2} dissociates to form CH{sub 2}I{center_dot}+I{center_dot}. Iodine radicals remaining within the solvent cage recombine with a nascent CH{sub 2}I{center_dot} radical to form the transient isomer CH{sub 2}I-I, whereas those which escape the solvent cage ultimately combine to form I{sub 2} in cyclohexane. Moreover, the transient isomer has a lifetime approximately 30 times longer in the nonpolar solvent. Of greater chemical significance is the property of time-resolved wide angle x-ray diffraction to accurately determine the structure of the of CH{sub 2}I-I reaction intermediate. Thus we observe that the transient iodine-iodine bond is 0.07 A {+-}0.04 A shorter in cyclohexane than in methanol. A longer iodine-iodine bond length for the intermediate arises in methanol due to favorable H-bond interaction with the polar solvent. These findings establish that time-resolved x-ray diffraction has sufficient sensitivity to enable solvent dependent structural perturbations of transient chemical species to be accurately resolved.

  16. Spectral and kinetic characterization of intermediates in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase.

    PubMed

    Bruckner, Robert C; Jorns, Marilyn Schuman

    2009-06-01

    The flavoenzyme nikD, a 2-electron acceptor, catalyzes a remarkable aromatization of piperideine-2-carboxylate (P2C) to picolinate, an essential component of nikkomycin antibiotics. Steady-state kinetic data are indicative of a sequential mechanism where oxygen reacts with a reduced enzyme.dihydropicolinate (DHP) complex. The kinetics observed for complex formation with competitive inhibitors are consistent with a one-step binding mechanism. The anaerobic reaction with P2C involves three steps. The first step yields an enzyme.substrate charge transfer complex likely to contain the electron-rich P2C enamine. Calculated rates of formation and dissociation of the nikD.P2C complex are similar to those observed for the enzyme.1-cyclohexenoate complex. Formation of a reduced enzyme.DHP complex, (EH(2).DHP)(ini), occurs in a second step that exhibits a hyperbolic dependence on substrate concentration. The limiting rate of nikD reduction is at least 10-fold faster than the turnover rate observed with unlabeled or [4,4,5,5,6,6-D(6)]-P2C and exhibits a kinetic isotope effect (KIE = 6.4). The observed KIE on K(d apparent) (4.7) indicates that P2C is a sticky substrate. Formation of a final reduced species, (EH(2).DHP)(fin), occurs in a third step that is independent of P2C concentration and equal to the observed turnover rate. The observed KIE (3.3) indicates that the final step involves cleavage of at least one C-H bond. Tautomerization, followed by isomerization, of the initial DHP intermediate can produce an isomer that could be oxidized to picolinate in a reaction that satisfies known steric constraints of flavoenzyme reactions without the need to reposition a covalently tethered flavin or tightly bound intermediate.

  17. Identifying individual chemical bonds in single-molecule chemical reaction products using nc-AFM

    NASA Astrophysics Data System (ADS)

    Wickenburg, Sebastian; de Oteyza, Dimas G.; Chen, Yen-Chia; Riss, Alexander; Tsai, Hsin-Zon; Pedramrazi, Zahra; Bradley, Aaron J.; Ugeda, Miguel M.; Gorman, Patrick; Etkin, Grisha; Mowbray, Duncan J.; Perez, Alejandro; Rubio, Angel; Crommie, Michael F.; Fischer, Felix R.

    2014-03-01

    Determining reaction pathways and products is an integral part of chemical synthesis. Ensemble measurements are commonly used, but identifying products of complex reactions at surfaces presents a significant challenge. Here we present a non-contact AFM (nc-AFM) study to directly address this issue. We followed the change of the chemical structures, from reactants to products of enediyne cyclization reactions on metal surfaces. Thermal annealing of enediynes induced a series of cyclization cascades leading to radical species and the formation of dimers. Atomically resolved nc-AFM images reveal the precise chemical structure and the formation of chemical bonds between single molecular units. With the support of DFT calculations, we identified the underlying chemical pathways and barriers, demonstrating the potential of this atomically resolved AFM technique to study unknown reaction products in surface chemistry at the single-molecule level.

  18. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

    DOE PAGES

    Hashimoto, Hideharu; Pais, June E.; Dai, Nan; Corrêa, Jr., Ivan R.; Zhang, Xing; Zheng, Yu; Cheng, Xiaodong

    2015-08-31

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solvedmore » NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.« less

  19. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

    PubMed Central

    Hashimoto, Hideharu; Pais, June E.; Dai, Nan; Corrêa, Ivan R.; Zhang, Xing; Zheng, Yu; Cheng, Xiaodong

    2015-01-01

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably because the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate. PMID:26323320

  20. Study of intermediates from transition metal excited-state electron-transfer reactions. [Annual] progress report, August 1, 1989--July 31, 1992

    SciTech Connect

    Hoffman, M.Z.

    1992-07-31

    Conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used to study the intermediates involved in transition metal excited-state electron-transfer reactions. These intermediates were excited state of Ru(II) and Cr(III) photosensitizers, their reduced forms, and species formed in reactions of redox quenchers and electron-transfer agents. Of particular concern was the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes. (DLC)

  1. Adsorption and oxidation of formaldehyde on a polycrystalline Pt film electrode: An in situ IR spectroscopy search for adsorbed reaction intermediates.

    PubMed

    Jusys, Zenonas; Behm, R Jürgen

    2014-01-01

    As part of a mechanistic study of the electrooxidation of C1 molecules we have systematically investigated the dissociative adsorption/oxidation of formaldehyde on a polycrystalline Pt film electrode under experimental conditions optimizing the chance for detecting weakly adsorbed reaction intermediates. Employing in situ IR spectroscopy in an attenuated total reflection configuration (ATR-FTIRS) with p-polarized IR radiation to further improve the signal-to-noise ratio, and using low reaction temperatures (3 °C) and deuterium substitution to slow down the reaction kinetics and to stabilize weakly adsorbed reaction intermediates, we could detect an IR absorption band at 1660 cm(-1) characteristic for adsorbed formyl intermediates. This assignment is supported by an isotope shift in wave number. Effects of temperature, potential and deuterium substitution on the formation and disappearance of different adsorbed species (COad, adsorbed formate, adsorbed formyl), are monitored and quantified. Consequences on the mechanism for dissociative adsorption and oxidation of formaldehyde are discussed.

  2. Reactivity and reaction intermediates for acetic acid adsorbed on CeO2(111)

    SciTech Connect

    Calaza, Florencia C.; Chen, Tsung -Liang; Mullins, David R.; Xu, Ye; Steven H. Overbury

    2015-05-02

    Adsorption and reaction of acetic acid on a CeO2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO2 surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone and acetic acid desorb. Furthermore, DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.

  3. Reactivity and reaction intermediates for acetic acid adsorbed on CeO2(111)

    DOE PAGES

    Calaza, Florencia C.; Chen, Tsung -Liang; Mullins, David R.; Xu, Ye; Steven H. Overbury

    2015-05-02

    Adsorption and reaction of acetic acid on a CeO2(1 1 1) surface was studied by a combination of ultra-highvacuum based methods including temperature desorption spectroscopy (TPD), soft X-ray photoelectronspectroscopy (sXPS), near edge X-ray absorption spectroscopy (NEXAFS) and reflection absorption IRspectroscopy (RAIRS), together with density functional theory (DFT) calculations. TPD shows that thedesorption products are strongly dependent upon the initial oxidation state of the CeO2 surface, includingselectivity between acetone and acetaldehyde products. The combination of sXPS and NEXAFS demon-strate that acetate forms upon adsorption at low temperature and is stable to above 500 K, above whichpoint ketene, acetone and acetic acidmore » desorb. Furthermore, DFT and RAIRS show that below 500 K, bridge bondedacetate coexists with a moiety formed by adsorption of an acetate at an oxygen vacancy, formed bywater desorption.« less

  4. Detection of spirorchiid trematodes in gastropod tissues by polymerase chain reaction: preliminary identification of an intermediate host of Learedius learedi.

    PubMed

    Stacy, Brian A; Frankovich, Thomas; Greiner, Ellis; Alleman, A Rick; Herbst, Lawrence H; Klein, Paul; Bolten, Alan; McIntosh, Antoinette; Jacobson, Elliott R

    2010-08-01

    Marine spirorchiid trematodes are associated with morbidity and mortality in sea turtles worldwide. The intermediate hosts remain unknown, and discovery efforts are hindered by the large number and great diversity of potential hosts within sea turtle habitats, as well the potential for low prevalence and overdispersion. A high-throughput DNA extraction and polymerase chain reaction-based method was developed to detect the internal transcribed spacer 2 (ITS2) region of the ribosomal gene of 2 spirorchiid genera, Learedius and Hapalotrema , within pooled samples of gastropod tissues. A model system consisting of freshwater snail ( Pomacea bridgesii ) tissues and DNA extracts spiked with adult Learedius learedi and known quantities of spirorchiid DNA was used to develop and test the technique. Threshold of detection was found to be equivalent to an early prepatent infection within 1.5 g of gastropod tissue. This technique was used to screen approximately 25 species of marine gastropods at a captive facility where green turtles ( Chelonia mydas ) become infected by L. learedi . The parasite was detected in a sample of knobby keyhole limpet ( Fissurella nodosa ), thus providing the first evidence of an intermediate host for a marine spirorchiid trematode. This technique has many potential applications in trematode life cycle discovery studies.

  5. Investigation of the O+allyl addition/elimination reaction pathways from the OCH{sub 2}CHCH{sub 2} radical intermediate

    SciTech Connect

    FitzPatrick, Benjamin L.; Lau, K.-C.; Butler, Laurie J.; Lee, S.-H.; Lin, Jim Jr-Min

    2008-08-28

    These experiments study the preparation of and product channels resulting from OCH{sub 2}CHCH{sub 2}, a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH{sub 2}CHCH{sub 2} radicals; these undergo a facile ring opening to the OCH{sub 2}CHCH{sub 2} radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH{sub 2}CHCH{sub 2} radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C{sub 3}H{sub 4}O (acrolein)+H, C{sub 2}H{sub 4}+HCO (formyl radical), and H{sub 2}CO (formaldehyde)+C{sub 2}H{sub 3}. A small signal from C{sub 2}H{sub 2}O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C{sub 2}H{sub 5}+CO, does not contribute significantly to the product branching. The higher internal energy onset of the

  6. Single Turnover Kinetics of Tryptophan Hydroxylase: Evidence for a New Intermediate in the Reaction of the Aromatic Amino Acid Hydroxylases

    PubMed Central

    Pavon, Jorge Alex; Eser, Bekir; Huynh, Michaela T.; Fitzpatrick, Paul F.

    2010-01-01

    Tryptophan hydroxylase (TrpH) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. The reactions of the TrpH·Fe(II), TrpH·Fe(II)·tryptophan, TrpH·Fe(II)·6MePH4·tryptophan, and TrpH·Fe(II)·6MePH4·phenylalanine complexes with O2 were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. The second-order rate constant for the oxidation of TrpH·Fe(II) has a value of 104 M−1s−1 irrespective of the presence of tryptophan. Stopped-flow absorbance analyses of the reaction of the TrpH·Fe(II)·6MePH4·tryptophan complex with oxygen are consistent with the initial step being reversible binding of oxygen, followed by the formation with a rate constant of 65 s−1 of an intermediate I that has maximal absorbance at 420 nm. The rate constant for decay of I, 4.4 s−1, matches that for formation of the 4a-hydroxypterin product monitored at 248 nm. Chemical-quench analyses show that 5-hydroxytryptophan forms with a rate constant of 1.3 s−1, and that overall turnover is limited by a subsequent slow step, presumably product release, with a rate constant of 0.2 s−1. All of the data with tryptophan as substrate can be described by a five-step mechanism. In contrast, with phenylalanine as substrate, the reaction can be described by three steps: a second-order reaction with oxygen to form I, decay of I as tyrosine forms, and slow product release. PMID:20687613

  7. Reactions of Atmospheric Particulate Stabilized Criegee Intermediates Lead to High-Molecular-Weight Aerosol Components.

    PubMed

    Wang, MingYi; Yao, Lei; Zheng, Jun; Wang, XinKe; Chen, JianMin; Yang, Xin; Worsnop, Douglas R; Donahue, Neil M; Wang, Lin

    2016-06-01

    Aging of organic aerosol particles is one of the most poorly understood topics in atmospheric aerosol research. Here, we used an aerosol flow tube together with an iodide-adduct high-resolution time-of-flight chemical-ionization mass spectrometer equipped with a Filter Inlet for Gases and AEROsols (FIGAERO-HRToF-CIMS) to investigate heterogeneous ozonolysis of oleic acid (OL), developing a comprehensive oxidation mechanism with observed products. In addition to the well-known first-generation C9 products including nonanal, nonanoic acid, azelaic acid, and 9-oxononanoic acid, the iodide-adduct chemical ionization permitted unambiguous determination of a large number of high-molecular-weight particulate products up to 670 Da with minimum amounts of fragmentation. These high-molecular-weight products are characterized by a fairly uniform carbon oxidation state but stepwise addition of a carbon backbone moiety, and hence continuous decrease in the volatility. Our results demonstrate that heterogeneous oxidation of organic aerosols has a significant effect on the physiochemical properties of organic aerosols and that reactions of particulate SCIs from ozonolysis of an unsaturated particulate species represent a previously underappreciated mechanism that lead to formation of high-molecular-weight particulate products that are stable under typical atmospheric conditions.

  8. Two progressive substrates of the M-intermediate can be identified in glucose-embedded, wild-type bacteriorhodopsin.

    PubMed Central

    Vonck, J; Han, B G; Burkard, F; Perkins, G A; Glaeser, R M

    1994-01-01

    Glucose-embedded bacteriorhodopsin shows M-intermediates with different Amide I infrared bands when samples are illuminated at 240 or 260 K, in contrast with fully hydrated samples where a single M-intermediate is formed at all temperatures. In hydrated, but not in glucose-embedded specimens, the N intermediate is formed together with M at 260 K. Both Fourier transform infrared and electron diffraction data from glucose-embedded bacteriorhodopsin suggest that at 260 K a mixture is formed of the M-state that is trapped at 240 K, and a different M-intermediate (MN) that is also formed by mutant forms of bacteriorhodopsin that lack a carboxyl group at the 96 position, necessary for the M to N transition. The fact that an MN species is trapped in glucose-embedded, wild-type bacteriorhodopsin suggests that the glucose samples lack functionally important water molecules that are needed for the proton transfer aspartate 96 to the Schiff base (and, thus, to form the N-intermediate); thus, aspartate 96 is rendered ineffective as a proton donor. PMID:7811930

  9. Design Factors Affecting the Reaction Time for Identifying Toilet Signs: A Preliminary Study.

    PubMed

    Chen, Yi-Lang; Sie, Cai-Cin

    2016-04-01

    This study focused on the manner in which design factors affect the reaction time for identifying toilet signs. Taiwanese university students and staff members (50 men, 50 women; M age = 23.5 year, SD = 5.7) participated in the study. The 36 toilet signs were modified on three factors (six presenting styles, two figure-ground exchanges, and three colors), and the reaction time data of all participants were collected when the signs were presented in a simulation onscreen. Participants were quickest when reading Chinese text, followed by graphics and English texts. The findings also showed that men and women had different reaction times across various design combinations. These findings can serve as a reference for practically designing toilet signs, since design factors can lead to difficulties with comprehension based on reaction time measurements.

  10. Reactions of connective tissue to amalgam, intermediate restorative material, mineral trioxide aggregate, and mineral trioxide aggregate mixed with chlorhexidine.

    PubMed

    Sumer, Mahmut; Muglali, Mehtap; Bodrumlu, Emre; Guvenc, Tolga

    2006-11-01

    The aim of this study was to histopathologically examine the biocompatibility of the high-copper amalgam, intermediate restorative material (IRM), mineral trioxide aggregate (MTA), and MTA mixed with chlorhexidine (CHX). This study was conducted to observe the rat subcutaneous connective tissue reaction to the implanted tubes filled with amalgam, IRM, MTA, and MTA mixed with CHX. The animals were sacrificed 15, 30, and 60 days after the implantation procedure. The implant sites were excised and prepared for histological evaluation. Sections of 5 to 6 microm thickness were cut by a microtome and stained with hemotoxylin eosin and examined under a light microscope. The inflammatory reactions were categorized as weak (none or few inflammatory cells < or =25 cells), moderate (>25 cells), and severe (a lot of inflammatory cells not to be counted, giant cells, and granulation tissue). Thickness of fibrous capsules measured five different areas by the digital imaging and the mean values were scored. Amalgam, IRM, and MTA mixed with CHX caused a weak inflammatory response on days 15, 30, and 60. MTA provoked an initial severe inflammatory response that subsided at the 30 and 60 day study period. A clear fibrous capsule was observed beginning from the 15 days in all of the groups. Within the limits of this study, amalgam, IRM, MTA, and MTA mixed with CHX materials were surrounded by fibrous connective tissue indicated that they were well tolerated by the tissues, therefore, MTA/CHX seemed to be biocompatible.

  11. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    SciTech Connect

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-03-28

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} group by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  12. Identifying Stressors and Reactions to Stressors in Gifted and Non-Gifted Students

    ERIC Educational Resources Information Center

    Amini, Marzieh

    2005-01-01

    Using the Student Life Stress Inventory and the Coopersmith Self-Esteem Inventory, stressors and reactions to stressors were identified in gifted high school students and compared with non-gifted students. Altogether, 340 boys and girls (156 gifted and 184 non-gifted students) from four high schools in Shiraz (two high schools for gifted and two…

  13. Synthesis of Y1Ba2Cu3O(sub x) superconducting powders by intermediate phase reaction

    NASA Technical Reports Server (NTRS)

    Moore, C.; Fernandez, J. F.; Recio, P.; Duran, P.

    1990-01-01

    One of the more striking problems for the synthesis of the Y1Ba2Cu3Ox compound is the high-temperature decomposition of the BaCO3. This compound is present as raw material or as an intermediate compound in chemical processes such as amorphous citrate, coprecipitation oxalate, sol-gel process, acetate pyrolisis, etc. This fact makes difficult the total formation reaction of the Y1Ba2Cu3Ox phase and leads to the presence of undesirable phases such as the BaCuO2 phase, the 'green phase', Y2BaCuO5 and others. Here, a new procedure to overcome this difficulty is studied. The barium cation is previously combined with yttrium and/or copper to form intermediate compounds which can react between them to give Y1Ba2Cu3Ox. BaY2O4 and BaCu2O3 react according to the equation BaY2O4+3BaCu2O3 yields 2Y1Ba2Cu3Ox. BaY2O4 is a stable compound of the Y2O3-BaO system; BaCu2O3 is an intimate mixture of BaCuO2 and uncombined CuO. The reaction kinetics of these phases have been established between 860 and 920 C. The phase evolution has been determined. The crystal structure of the Y1Ba2Cu3Ox obtained powder was studied. According to the results obtained from the kinetics study the Y1Ba2Cu3Ox the synthesis was performed at temperatures of 910 to 920 C for short treatment times (1 to 2 hours). Pure Y1Ba2Cu3Ox was prepared, which develops orthorombic type I structure despite of the cooling cycle. Superconducting transition took place at 91 K. The sintering behavior and the superconducting properties of sintered samples were studied. Density, microstructure and electrical conductivity were measured. Sintering densities higher than 95 percent D(sub th) were attained at temperatures below 940 C. Relatively fine grained microstructure was observed, and little or no-liquid phase was detected.

  14. Nitrite reduction by biogenic hydroxycarbonate green rusts: evidence for hydroxy-nitrite green rust formation as an intermediate reaction product.

    PubMed

    Guerbois, Delphine; Ona-Nguema, Georges; Morin, Guillaume; Abdelmoula, Mustapha; Laverman, Anniet M; Mouchel, Jean-Marie; Barthelemy, Kevin; Maillot, Fabien; Brest, Jessica

    2014-04-15

    The present study investigates for the first time the reduction of nitrite by biogenic hydroxycarbonate green rusts, bio-GR(CO3), produced from the bioreduction of ferric oxyhydroxycarbonate (Fohc), a poorly crystalline solid phase, and of lepidocrocite, a well-crystallized Fe(III)-oxyhydroxide mineral. Results show a fast Fe(II) production from Fohc, which leads to the precipitation of bio-GR(CO3) particles that were roughly 2-fold smaller (2.3 ± 0.4 μm) than those obtained from the bioreduction of lepidocrocite (5.0 ± 0.4 μm). The study reveals that both bio-GR(CO3) are capable of reducing nitrite ions into gaseous nitrogen species such as NO, N2O, or N2 without ammonium production at neutral initial pH and that nitrite reduction proceeded to a larger extent with smaller particles than with larger ones. On the basis of the identification of intermediates and end-reaction products using X-ray diffraction and X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge, our study shows the formation of hydroxy-nitrite green rust, GR(NO2), a new type of green rust 1, and suggests that the reduction of nitrite by biogenic GR(CO3) involves both external and internal reaction sites and that such a mechanism could explain the higher reactivity of green rust with respect to nitrite, compared to other mineral substrates possessing only external reactive sites.

  15. 4'-CyanoPLP presents better prospect for the experimental detection of elusive cyclic intermediate radical in the reaction of lysine 5,6-aminomutase.

    PubMed

    Maity, Amarendra Nath; Ke, Shyue-Chu

    2015-02-01

    The results of our calculations suggest that the reaction of 4'-cyanoPLP with lysine 5,6-aminomutase offers better prospect for the experimental detection of elusive cyclic azacyclopropylcarbinyl radical (I), which is proposed to be a key intermediate in the reaction of pyridoxal-5'-phosphate dependent radical aminomutases. We have calculated the corresponding hyperfine coupling constants (HFCCs) for (14)N and (13)C of cyano group using several basis sets to help the characterization of 4'-cyanoI.

  16. Transition Metal Donor-Peptide-Acceptor Complexes: From Intramolecular Electron Transfer Reactions to the Study of Reactive Intermediates

    SciTech Connect

    Isied, Stephan S.

    2003-03-11

    The trans-polyproline (PII) oligomers (Figure 1) are unusually rigid peptide structures which have been extensively studied by our group for peptide mediated intramolecular electron transfer (ET) at long distances. We have previously studied ET across a series of metal ion donor (D) acceptor (A) oligoproline peptides with different distances, driving forces and reorganizational energies. The majority of these experiments involve generating the ET intermediate using pulse radiolysis methods, although more recently photochemical methods are also used. Results of these studies showed that ET across peptides can vary by more than twelve orders of magnitude. Using ruthenium bipyridine donors, ET reaction rate constants across several proline residues (n = 4 - 9) occurred in the millisecond (ms) to {micro}s timescale, thus limiting the proline peptide conformational motions to only minor changes (far smaller than the large changes that occur on the ms to sec timescale, such as trans to cis proline isomerization). The present report describes our large data base of experimental results for D-peptide-A complexes in terms of a model where the involvement of both superexchange and hopping (hole and electron) mechanisms account for the long range ET rate constants observed. Our data shows that the change from superexchange to hopping mechanisms occurs at different distances depending on the type of D and A and their interactions with the peptides. Our model is also consistent with generalized models for superexchange and hopping which have been put forward by a number of theoretical groups to account for long range ET phenomena.

  17. An intermediate in the phage lambda site-specific recombination reaction is revealed by phosphorothioate substitution in DNA.

    PubMed Central

    Kitts, P A; Nash, H A

    1988-01-01

    It has been proposed that phage lambda site-specific recombination proceeds via two independent strand exchanges: the first exchange forming a Holliday-structure which is then converted into complete recombinant products by the second strand exchange. If this hypothesis is correct, one should be able to trap the putative Holliday intermediate by preventing the second strand exchange. In this paper, we show that substitution of phosphorothioate for phosphate in one strand of a recombination site is an effective way to block recombination while permitting the accumulation of a novel structure. This effect is seen only when phosphorothioate is positioned at a point of potential cleavage by Int recombinase, demonstrating that the inhibition of strand exchange is highly specific. Analysis of the novel structure that accumulates in these reactions proves that it contains a Holliday joint. Holliday-structures can also be detected in unblocked recombinations but are present at very low levels. The characteristics of Holliday-structure formation that we describe substantiate the proposed recombination pathway. Images PMID:2970060

  18. Photocatalytic degradation of herbicide bentazone in aqueous suspension of TiO2: mineralization, identification of intermediates and reaction pathways.

    PubMed

    Mir, Niyaz A; Haque, M M; Khan, A; Muneer, M; Vijayalakshmi, S

    2014-01-01

    Semiconductor-mediated hydrogen peroxide-assisted photocatalytic degradation of a selected herbicide, Bentazone (1) has been investigated in aqueous suspensions of TiO2 under a variety of conditions. The degradation was studied by monitoring the depletion in total organic carbon content as a function of irradiation time. The degradation kinetics was investigated under different conditions such as type of TiO2 (Anatase/Anatase-Rutile mixture), reaction pH, catalyst dosage and hydrogen peroxide (H202) concentration. The degradation rates were found to be strongly influenced by all the above parameters. Titanium dioxide Degussa P25 was found to be more efficient as compared with other two commercially available TiO2 powders like Hombikat UV100 and PC500 from Millennium Inorganic Chemicals. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of the irradiated mixture of Bentazone (1) indicates the formation of several intermediate products which have been characterized on the basis of molecular ion/mass fragmentation pattern and also on comparison with the National Institute of Standards and Technology (NIST) library. Plausible mechanism for the formation of different products during photocatalytic treatment of Bentazone in the presence of TiO2 has been proposed. The use of H202 substantially increased the efficiency of TiO2 photocatalytic degradation.

  19. pH-jump studies at subzero temperatures on an intermediate in the reaction of xanthine oxidase with xanthine.

    PubMed Central

    Tsopanakis, A D; Tanner, S J; Bray, R C

    1978-01-01

    Xanthine oxidase is stable and active in aqueous dimethyl sulphoxide solutions of up to at least 57% (w/w). Simple techniques are described for mixing the enzyme in this solvent at--82 degrees C, with its substrate, xanthine. When working at high pH values under such conditions, no reaction occurred, as judged by the absence of e.p.r. signals. On warming to--60 degrees C, for 10 min, however, the Very Rapid molybdenum(V) e.p.r. signal was obtained. This signal did not change on decreasing the pH, while maintaining the sample in liquid nitrate reductase, caused its molybdenum(V) e.p.r. signal to change from the high-pH to the low-pH form. These findings are not compatible with the conclusions of Edmondson, Ballou, Van Heuvelen, Palmer & Massey [J. Biol. Chem. (1973) 248, 6135-6144], that the Very Rapid signal is in prototropic equilibrium with the Rapid signal, and should be important in understanding the mechanism of action of the enzyme. They emphasize the unique nature of the intermediate represented by the Very Rapid e.p.r. signal. The possible value of the pK for loss of an exchangeable proton from the Rapid signal is discussed. PMID:33666

  20. Mixed Anhydride Intermediates in the Reaction of 5(4H)-Oxazolones with Phosphate Esters and Nucleotides

    PubMed Central

    Liu, Ziwei; Rigger, Lukas; Rossi, Jean-Christophe; Sutherland, John D.; Pascal, Robert

    2016-01-01

    5(4H)-Oxazolones can be formed through the activation of acylated α-amino acids or of peptide C termini. They constitute potentially activated intermediates in the abiotic chemistry of peptides that preceded the origin of life or early stages of biology and are capable of yielding mixed carboxylic-phosphoric anhydrides upon reaction with phosphate esters and nucleotides. Here, we present the results of a study aimed at investigating the chemistry that can be built through this interaction. As a matter of fact, the formation of mixed anhydrides with mononucleotides and nucleic acid models is shown to take place at positions involving a mono-substituted phosphate group at the 3’- or 5’-terminus but not at the internal phosphodiester linkages. In addition to the formation of mixed anhydrides, the subsequent intramolecular acyl or phosphoryl transfers taking place at the 3’-terminus are considered to be particularly relevant to the common prebiotic chemistry of α-amino acids and nucleotides. PMID:27534830

  1. Photofragment imaging study of the CH{sub 2}CCH{sub 2}OH radical intermediate of the OH+allene reaction

    SciTech Connect

    Raman, Arjun S.; Justine Bell, M.; Lau, K.-C.; Butler, Laurie J.

    2007-10-21

    These velocity map imaging experiments characterize the photolytic generation of one of the two radical intermediates formed when OH reacts via an addition mechanism with allene. The CH{sub 2}CCH{sub 2}OH radical intermediate is generated photolytically from the photodissociation of 2-chloro-2-propen-1-ol at 193 nm. Detecting the Cl atoms using [2+1] resonance-enhanced multiphoton ionization evidences an isotropic angular distribution for the Cl+CH{sub 2}CCH{sub 2}OH photofragments, a spin-orbit branching ratio for Cl({sup 2}P{sub 1/2}):Cl({sup 2}P{sub 3/2}) of 0.28, and a bimodal recoil kinetic energy distribution. Conservation of momentum and energy allows us to determine from this data the internal energy distribution of the nascent CH{sub 2}CCH{sub 2}OH radical cofragment. To assess the possible subsequent decomposition pathways of this highly vibrationally excited radical intermediate, we include electronic structure calculations at the G3//B3LYP level of theory. They predict the isomerization and dissociation transition states en route from the initial CH{sub 2}CCH{sub 2}OH radical intermediate to the three most important product channels for the OH+allene reaction expected from this radical intermediate: formaldehyde+C{sub 2}H{sub 3}, H+acrolein, and ethene+CHO. We also calculate the intermediates and transition states en route from the other radical adduct, formed by addition of the OH to the center carbon of allene, to the ketene+CH{sub 3} product channel. We compare our results to a previous theoretical study of the O+allyl reaction conducted at the CBS-QB3 level of theory, as the two reactions include several common intermediates.

  2. The key intermediates that interact with the fluorophores in the peroxyoxalate chemiluminescence reaction of 2,4,6-trichlorophenyl N-aryl-N-tosyloxamates.

    PubMed

    Koike, Ryu; Motoyoshiya, Jiro; Takaguchi, Yutaka; Aoyama, Hiromu

    2003-03-21

    A kinetic study of peroxyoxalate chemiluminescence reactions employing 2,4,6-trichlorophenyl N-aryl-N-tosyloxamates supports the 1,2-dioxetanones still bearing the eliminating group as the key intermediates that interact with the fluorophores rather than 1,2-dioxetanedione. PMID:12703827

  3. Kinetic and mechanistic studies of reactive intermediates in photochemical and transition metal-assisted oxidation, decarboxylation and alkyl transfer reactions

    NASA Astrophysics Data System (ADS)

    Carraher, Jack McCaslin

    Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding 'greener' sources of commodity chemicals and fuels. High-valent Chromium from Hydroperoxido-Chromium(III). The decomposition of pentaaquahydroperoxido chromium(III) ion (hereafter Cr aqOOH2+) in acidic aqueous solutions is kinetically complex and generates mixtures of products (Craq3+, HCrO 4-, H2O2, and O2). The yield of high-valent chromium products (known carcinogens) increased from a few percent at pH 1 to 70 % at pH 5.5 (near biological pH). Yields of H 2O2 increased with acid concentration. The reproducibility of the kinetic data was poor, but became simplified in the presence of H2O2 or 2,2‧-azinobis(3-ethylbenzothiazoline-6-sulfonate) dianion (ABTS2-). Both are capable of scavenging strongly oxidizing intermediates). The observed rate constants (pH 1, [O2] ≤ 0.03 mM) in the presence of these scavengers are independent of [scavenger] and within the error are the same (k,ABTS2- = (4.9 +/- 0.2) x 10-4 s-1 and kH2O2 = (5.3 +/- 0.7) x 10-4 s-1); indicating involvement of the scavengers in post-rate determining steps. In the presence of either scavenger, decomposition of CrOOH2+ obeyed a two-term rate law, k obs / s-1 = (6.7 +/- 0.7) x 10-4 + (7.6 +/- 1.1) x 10-4 [H+]. Effect of [H+] on the kinetics and the product distribution, cleaner kinetics in the presence of scavengers, and independence of kobs on [scavenger] suggest a dual-pathway mechanism for the decay of Craq OOH2+. The H+-catalyzed path

  4. An oxyferrous heme/protein-based radical intermediate is catalytically competent in the catalase reaction of Mycobacterium tuberculosis catalase-peroxidase (KatG).

    PubMed

    Suarez, Javier; Ranguelova, Kalina; Jarzecki, Andrzej A; Manzerova, Julia; Krymov, Vladimir; Zhao, Xiangbo; Yu, Shengwei; Metlitsky, Leonid; Gerfen, Gary J; Magliozzo, Richard S

    2009-03-13

    A mechanism accounting for the robust catalase activity in catalase-peroxidases (KatG) presents a new challenge in heme protein enzymology. In Mycobacterium tuberculosis, KatG is the sole catalase and is also responsible for peroxidative activation of isoniazid, an anti-tuberculosis pro-drug. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy both at the X-band and at the D-band, and mutagenesis are used to identify catalase reaction intermediates in M. tuberculosis KatG. In the presence of millimolar H2O2 at neutral pH, oxyferrous heme is formed within milliseconds from ferric (resting) KatG, whereas at pH 8.5, low spin ferric heme is formed. Using rapid freeze-quench EPR at X-band under both of these conditions, a narrow doublet radical signal with an 11 G principal hyperfine splitting was detected within the first milliseconds of turnover. The radical and the unique heme intermediates persist in wild-type KatG only during the time course of turnover of excess H2O2 (1000-fold or more). Mutation of Met255, Tyr229, or Trp107, which have covalently linked side chains in a unique distal side adduct (MYW) in wild-type KatG, abolishes this radical and the catalase activity. The D-band EPR spectrum of the radical exhibits a rhombic g tensor with dual gx values (2.00550 and 2.00606) and unique gy (2.00344) and gz values (2.00186) similar to but not typical of native tyrosyl radicals. Density functional theory calculations based on a model of an MYW adduct radical built from x-ray coordinates predict experimentally observed hyperfine interactions and a shift in g values away from the native tyrosyl radical. A catalytic role for an MYW adduct radical in the catalase mechanism of KatG is proposed.

  5. EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates

    PubMed Central

    Welch, Joshua D.; Slevin, Michael K.; Tatomer, Deirdre C.; Duronio, Robert J.

    2015-01-01

    Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3′ ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3′ ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol that preserves the 3′ end of RNA molecules, and AppEnD, a computational method for analyzing high-throughput sequencing data. Together these allow determination of the 3′ ends of RNA molecules, including nontemplated additions. Applying EnD-Seq and AppEnD to histone mRNAs revealed that a significant fraction of cytoplasmic histone mRNAs end in one or two uridines, which have replaced the 1–2 nt at the 3′ end of mature histone mRNA maintaining the length of the histone transcripts. Histone mRNAs in fly embryos and ovaries show the same pattern, but with different tail nucleotide compositions. We increase the sensitivity of EnD-Seq by using cDNA priming to specifically enrich low-abundance tails of known sequence composition allowing identification of degradation intermediates. In addition, we show the broad applicability of our computational approach by using AppEnD to gain insight into 3′ additions from diverse types of sequencing data, including data from small capped RNA sequencing and some alternative polyadenylation protocols. PMID:26015596

  6. A Dianionic Phosphorane Intermediate and Transition States in an Associative AN+DN Mechanism for the RibonucleaseA Hydrolysis Reaction

    SciTech Connect

    Elsasser, Brigitta M; Valiev, Marat; Weare, John H

    2009-03-25

    The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an AN+DN reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH- species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2' position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.

  7. Study of intermediates from transition metal excited-state electron-transfer reactions. Progress report, August 1, 1989--December 31, 1991

    SciTech Connect

    Hoffman, M.Z.

    1991-12-31

    During this period, conventional and fast-kinetics techniques of photochemistry, photophysics, radiation chemistry, and electrochemistry were used for the characterization of the intermediates that are involved in transition metal excited-state electron-transfer reactions. The intermediates of interest were the excited states of Ru(II) and Cr(III) photosensitizers, their reduced forms, and the species formed in the reactions of redox quenchers and electron-transfer agents. Of particular concern has been the back electron-transfer reaction between the geminate pair formed in the redox quenching of the photosensitizers, and the dependence of its rate on solution medium and temperature in competition with transformation and cage escape processes.

  8. A quantum-chemical study of intermediates of the 1O2 photogeneration sensitized by buckminsterfullerene and accompanying photochemical reactions

    NASA Astrophysics Data System (ADS)

    Semenov, S. G.; Bedrina, M. E.

    2014-02-01

    The intermediates of hypothetical photochemical reactions that accompany the quenching of the 3C{60/*} triplet state by triplet oxygen are studied by the (U)PBE0 quantum-chemical method. The diradical C60-O-O formed from 3O2 and photoexcited buckminsterfullerene 3C{60/*} is characterized by a negative binding energy -1.11 eV (with respect to C60 and 3O2), the singlet-triplet splitting Δ E ST of 0.07 eV, and the dipole moment of 3.2 D at the equilibrium internuclear separations 1.522 Å (CO) and 1.294 Å (OO). Its decay produces 1O2. The formation of a dioxetane circle lowers the energy by 0.8 eV. The ground-state energy of diketone C58(C=O)2 is 2.0 eV lower than the energy of C60-O-O. The metastable centrosymmetric diradical C60-C60, formed upon ineffective light absorption by clusters (C60)N, has a single interpolyhedral C-C bond (1.657 Å). Its triplet state T 1 lies 0.16 eV higher than the S 1 singlet. The S 1 → S 0 relaxation leads to the formation of a stable C60-C60 dimer with a shorter (1.584 Å) bis-single exothermic (+0.24 eV) bond of polyhedra. The photoexcited C60-C60 dimer is able to form isomeric metastable diradicals C60-C60-O-O.

  9. Interaction of Gd-DTPA with phosphate and phosphite: toward the reaction intermediate in nephrogenic systemic fibrosis.

    PubMed

    Gao, Song; George, Simon J; Zhou, Zhao-Hui

    2016-03-28

    Direct reactions of the MRI contrast agent K2[Gd(DTPA)(H2O)]·5H2O (1) (H5DTPA = diethylenetriaminepentaacetic acid) with dipotassium hydrogen phosphate (K2HPO4) or phosphite (K2HPO3) result in the isolation of well-defined Gd-DTPA phosphite K6[Gd2(DTPA)2(HPO3)]·7H2O (2) or phosphate K6[Gd2(DTPA)2(HPO4)]·10H2O (3), respectively. Their lanthanum analogs K4[La2(DTPA)2(H2O)]·8H2O (4), K6[La2(DTPA)2(HPO3)]·7H2O (5) and K6[La2(DTPA)2(HPO4)]·10H2O (6) are used for comparison. The phosphate and phosphite groups are able to substitute the coordinated water molecules in 1 and 4 in a close physiological aqueous solution, and act as bridging ligands to link adjacent Ln(DTPA)(2-) (Ln = Gd and La) into dimeric structures. Solid state and solution (13)C NMR spectra of dimer 4 show complete dissociation into its monomeric species in solution, while no dissociation is observed for lanthanum phosphite 5 and phosphate 6 in solution, which show only one set of (13)C spectra with the largest downfield shifts at 182.0 and 182.3 ppm respectively. Comparisons of the bond distances and spectral data indicate that the interaction between DTPA and central Ln(3+) cations are weakened after the substitutions, which support phosphate substituted Gd-DTPA as an initial intermediate in nephrogenic systemic fibrosis. PMID:26906409

  10. Adsorption and oxidation of formaldehyde on a polycrystalline Pt film electrode: An in situ IR spectroscopy search for adsorbed reaction intermediates

    PubMed Central

    Behm, R Jürgen

    2014-01-01

    Summary As part of a mechanistic study of the electrooxidation of C1 molecules we have systematically investigated the dissociative adsorption/oxidation of formaldehyde on a polycrystalline Pt film electrode under experimental conditions optimizing the chance for detecting weakly adsorbed reaction intermediates. Employing in situ IR spectroscopy in an attenuated total reflection configuration (ATR-FTIRS) with p-polarized IR radiation to further improve the signal-to-noise ratio, and using low reaction temperatures (3 °C) and deuterium substitution to slow down the reaction kinetics and to stabilize weakly adsorbed reaction intermediates, we could detect an IR absorption band at 1660 cm−1 characteristic for adsorbed formyl intermediates. This assignment is supported by an isotope shift in wave number. Effects of temperature, potential and deuterium substitution on the formation and disappearance of different adsorbed species (COad, adsorbed formate, adsorbed formyl), are monitored and quantified. Consequences on the mechanism for dissociative adsorption and oxidation of formaldehyde are discussed. PMID:24991512

  11. Studies on the mechanism of the peroxyoxalate chemiluminescence reaction: part 2. Further identification of intermediates using 2D EXSY 13C nuclear magnetic resonance spectroscopy.

    PubMed

    Tonkin, Sarah A; Bos, Richard; Dyson, Gail A; Lim, Kieran F; Russell, Richard A; Watson, Simon P; Hindson, Christopher M; Barnett, Neil W

    2008-05-01

    Further consideration has been given to the reaction pathway of a model peroxyoxalate chemiluminescence system. Again utilising doubly labelled oxalyl chloride and anhydrous hydrogen peroxide, 2D EXSY (13)C nuclear magnetic resonance (NMR) spectroscopy experiments allowed for the characterisation of unknown products and key intermediate species on the dark side of the peroxyoxalate chemiluminescence reaction. Exchange spectroscopy afforded elucidation of a scheme comprised of two distinct mechanistic pathways, one of which contributes to chemiluminescence. (13)C NMR experiments carried out at varied reagent molar ratios demonstrated that excess amounts of hydrogen peroxide favoured formation of 1,2-dioxetanedione: the intermediate that, upon thermolysis, has been long thought to interact with a fluorophore to produce light. PMID:18420048

  12. Exploring the aryl esterase catalysis of paraoxonase-1 through solvent kinetic isotope effects and phosphonate-based isosteric analogues of the tetrahedral reaction intermediate.

    PubMed

    Bavec, Aljoša; Knez, Damijan; Makovec, Tomaž; Stojan, Jure; Gobec, Stanislav; Goličnik, Marko

    2014-11-01

    Although a recent study of Debord et al. in Biochimie (2014; 97:72-77) described the thermodynamics of the catalysed hydrolysis of phenyl acetate by human paraoxonase-1, the mechanistic details along the reaction route of this enzyme remain unclear. Therefore, we briefly present the solvent kinetic isotope effects on the phenyl acetate esterase activity of paraoxonase-1 and its inhibition with the phenyl methylphosphonate anion, which is a stable isosteric analogue that mimics the high-energy tetrahedral intermediate on the hydroxide-promoted hydrolysis pathway. The data show normal isotope effects, while proton inventory analysis indicates that two protons contribute to the kinetic isotope effect. Coherently, moderate competitive inhibition with the phenyl methylphosphonate anion reveals that the rate-limiting transition state suboptimally resembles the tetrahedral intermediate. The implications of these findings can be attributed to two possible reaction mechanisms that might occur during the paraoxonase-1-catalysed hydrolysis of phenyl acetate.

  13. Using EMMA and MIX analysis to assess mixing ratios and to identify hydrochemical reactions in groundwater.

    PubMed

    Tubau, Isabel; Vàzquez-Suñé, Enric; Jurado, Anna; Carrera, Jesús

    2014-02-01

    This study presents a methodology using an end-member mixing analysis (EMMA) and MIX to compute mixing ratios and to identify hydrochemical reactions in groundwater. The methodology consists of (1) identifying the potential sources of recharge, (2) characterising recharge sources and mixed water samples using hydrogeochemistry, (3) selecting chemical species to be used in the analysis and (4) calculating mixing ratios and identification of hydrochemical reactions in groundwater. This approach has been applied in the Besòs River Delta area, where we have collected 51 groundwater samples and a long data register of the hydrogeochemistry of the Besòs River created by the Catalan Water Agency is also available. The EMMA performed in the Besòs River suggests that 3 end-members are required to explain its temporal variability, accounting for the species chloride, sulphate, sodium, bicarbonate, calcium, magnesium, potassium, ammonium, total nitrogen, and electrical conductivity. One river end-member is from the wet periods (W1), and two are from dry periods (D1 and D2). These end-members have been used to compute mixing ratios in groundwater samples because the Besòs River is considered the main recharge source for the aquifer. Overall, dry season end-members dominated over the wet season end-member, in a proportion of 4:1. Moreover, when departures from the mixing line exist, geochemical processes might be identified. Redox processes, carbonate dissolution/precipitation and ion exchange processes may occur in Besòs Delta aquifer.

  14. Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes.

    PubMed

    Hernández Anzaldo, Samuel; Arroyo Abad, Uriel; León García, Armando; Ramírez Rosales, Daniel; Zamorano Ulloa, Rafael; Reyes Ortega, Yasmi

    2016-06-27

    The spectroscopic and kinetic characterization of two intermediates from the H₂O₂ oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1-3 + guaiacol + H₂O₂ → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H₂O₂, resulting in only two types of kinetics that were developed during the first 0-4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N'-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, ¹H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity.

  15. Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes.

    PubMed

    Hernández Anzaldo, Samuel; Arroyo Abad, Uriel; León García, Armando; Ramírez Rosales, Daniel; Zamorano Ulloa, Rafael; Reyes Ortega, Yasmi

    2016-01-01

    The spectroscopic and kinetic characterization of two intermediates from the H₂O₂ oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1-3 + guaiacol + H₂O₂ → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H₂O₂, resulting in only two types of kinetics that were developed during the first 0-4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N'-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, ¹H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity. PMID:27355940

  16. Heptad repeat 2-based peptides inhibit avian sarcoma and leukosis virus subgroup a infection and identify a fusion intermediate.

    PubMed

    Netter, Robert C; Amberg, Sean M; Balliet, John W; Biscone, Mark J; Vermeulen, Arwen; Earp, Laurie J; White, Judith M; Bates, Paul

    2004-12-01

    Fusion proteins of enveloped viruses categorized as class I are typified by two distinct heptad repeat domains within the transmembrane subunit. These repeats are important structural elements that assemble into the six-helix bundles characteristic of the fusion-activated envelope trimer. Peptides derived from these domains can be potent and specific inhibitors of membrane fusion and virus infection. To facilitate our understanding of retroviral entry, peptides corresponding to the two heptad repeat domains of the avian sarcoma and leukosis virus subgroup A (ASLV-A) TM subunit of the envelope protein were characterized. Two peptides corresponding to the C-terminal heptad repeat (HR2), offset from one another by three residues, were effective inhibitors of infection, while two overlapping peptides derived from the N-terminal heptad repeat (HR1) were not. Analysis of envelope mutants containing substitutions within the HR1 domain revealed that a single amino acid change, L62A, significantly reduced sensitivity to peptide inhibition. Virus bound to cells at 4 degrees C became sensitive to peptide within the first 5 min of elevating the temperature to 37 degrees C and lost sensitivity to peptide after 15 to 30 min, consistent with a transient intermediate in which the peptide binding site is exposed. In cell-cell fusion experiments, peptide inhibitor sensitivity occurred prior to a fusion-enhancing low-pH pulse. Soluble receptor for ASLV-A induces a lipophilic character in the envelope which can be measured by stable liposome binding, and this activation was found to be unaffected by inhibitory HR2 peptide. Finally, receptor-triggered conformational changes in the TM subunit were also found to be unaffected by inhibitory peptide. These changes are marked by a dramatic shift in mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, from a subunit of 37 kDa to a complex of about 80 kDa. Biotinylated HR2 peptide bound specifically to the 80-kDa complex

  17. SABER: A computational method for identifying active sites for new reactions

    PubMed Central

    Nosrati, Geoffrey R; Houk, K N

    2012-01-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  18. SABER: a computational method for identifying active sites for new reactions.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  19. Reaction mechanism of Escherichia coli cystathionine gamma-synthase: direct evidence for a pyridoxamine derivative of vinylglyoxylate as a key intermediate in pyridoxal phosphate dependent gamma-elimination and gamma-replacement reactions.

    PubMed

    Brzović, P; Holbrook, E L; Greene, R C; Dunn, M F

    1990-01-16

    Cystathionine gamma-synthase catalyzes a pyridoxal phosphate dependent synthesis of cystathionine from O-succinyl-L-homoserine (OSHS) and L-cysteine via a gamma-replacement reaction. In the absence of L-cysteine, OSHS undergoes an enzyme-catalyzed, gamma-elimination reaction to form succinate, alpha-ketobutyrate, and ammonia. Since elimination of the gamma-substituent is necessary for both reactions, it is reasonable to assume that the replacement and elimination reaction pathways diverge from a common intermediate. Previously, this partitioning intermediate has been assigned to a highly conjugated alpha-iminovinylglycine quininoid (Johnston et al., 1979a). The experiments reported herein support an alternative assignment for the partitioning intermediate. We have examined the gamma-replacement and gamma-elimination reactions of cystathionine gamma-synthase via rapid-scanning stopped-flow and single-wavelength stopped-flow UV-visible spectroscopy. The gamma-elimination reaction is characterized by a rapid decrease in the amplitude of the enzyme internal aldimine spectral band at 422 nm with a concomitant appearance of a new species which absorbs in the 300-nm region. A 485-nm species subsequently accumulates in a much slower relaxation. The gamma-replacement reaction shows a red shift of the 422-nm peak to 425 nm which occurs in the experiment dead time (approximately 3 ms). This relaxation is followed by a decrease in absorbance at 425 nm that is tightly coupled to the appearance of a species which absorbs in the 300-nm region. Reaction of the substrate analogues L-alanine and L-allylglycine with cystathionine gamma-synthase results in bleaching of the 422-nm absorbance and the appearance of a 300-nm species. In the absence of L-cysteine, L-allylglycine undergoes facile proton exchange; in the presence of L-cysteine, L-allylglycine undergoes a gamma-replacement reaction to form a new amino acid, gamma-methylcystathionine. No long-wavelength-absorbing species

  20. Branched Intermediate Formation Is the Slowest Step in the Protein Splicing Reaction of the Ala1 KlbA Intein from Methanococcus jannaschii

    PubMed Central

    2011-01-01

    We report the first detailed investigation of the kinetics of protein splicing by the Methanococcus jannaschii KlbA (Mja KlbA) intein. This intein has an N-terminal Ala in place of the nucleophilic Cys or Ser residue that normally initiates splicing but nevertheless splices efficiently in vivo [Southworth, M. W., Benner, J., and Perler, F. B. (2000) EMBO J.19, 5019–5026]. To date, the spontaneous nature of the cis splicing reaction has hindered its examination in vitro. For this reason, we constructed an Mja KlbA intein–mini-extein precursor using intein-mediated protein ligation and engineered a disulfide redox switch that permits initiation of the splicing reaction by the addition of a reducing agent such as dithiothreitol (DTT). A fluorescent tag at the C-terminus of the C-extein permits monitoring of the progress of the reaction. Kinetic analysis of the splicing reaction of the wild-type precursor (with no substitutions in known nucleophiles or assisting groups) at various DTT concentrations shows that formation of the branched intermediate from the precursor is reversible (forward rate constant of 1.5 × 10–3 s–1 and reverse rate constant of 1.7 × 10–5 s–1 at 42 °C), whereas the productive decay of this intermediate to form the ligated exteins is faster and occurs with a rate constant of 2.2 × 10–3 s–1. This finding conflicts with reports about standard inteins, for which Asn cyclization has been assigned as the rate-determining step of the splicing reaction. Despite being the slowest step of the reaction, branched intermediate formation in the Mja KlbA intein is efficient in comparison with those of other intein systems. Interestingly, it also appears that this intermediate is protected against thiolysis by DTT, in contrast to other inteins. Evidence is presented in support of a tight coupling between the N-terminal and C-terminal cleavage steps, despite the fact that the C-terminal single-cleavage reaction occurs in variant Mja Klb

  1. Kinetics and Spectroscopic Evidence that the Cu(I) − Semiquinone Intermediate Reduces Molecular Oxygen in the Oxidative Half-Reaction of Arthrobacter globiformis Amine Oxidase†

    PubMed Central

    Shepard, Eric M.; Okonski, Kristina M.; Dooley, David M.

    2009-01-01

    The role of copper during the reoxidation of substrate-reduced amine oxidases by O2 has not yet been definitively established. Both outer-sphere and inner-sphere pathways for the reduction of O2 to H2O2 have been proposed. A key step in the inner-sphere mechanism is the reaction of O2 directly with the Cu(I) center of a [Cu(I) − semiquinone] intermediate. To thoroughly examine this possibility, we have measured the spectral changes associated with single-turnover reoxidation by O2 of substrate-reduced Arthrobacter globiformis amine oxidase (AGAO) under a wide range of conditions. We have previously demonstrated that the internal electron-transfer reaction [Cu(II) − TPQAMQ → Cu(I) − TPQSQ] (where TPQAMQ is the aminoquinol form of reduced TPQ and TPQSQ is the semiquinone form) occurs at a rate that could permit the reaction of O2 with both species to be observed on the stopped-flow time scale (Shepard EM and Dooley DM (2006) JBIC 11:1039-1048). The transient absorption spectra observed for the reaction of O2 with substrate-reduced AGAO provide compelling support for the reaction of the Cu(I) − TPQSQ form. Further, global analysis of the kinetics and the transient absorption spectra are fully consistent with an inner-sphere reaction of the Cu(I)-semiquinone intermediate with O2 and are inconsistent with an outer-sphere mechanism for the reaction of the reduced enzyme with O2. PMID:19053231

  2. Interaction of CO with OH on Au(111): HCOO, CO3, and HOCO as Key Intermediates in the Water-Gas Shift Reaction

    SciTech Connect

    Senanayake, S.; Stacchiola, D; Liu, P; Mullins, C; Hrbek, J; Rodriguez, J

    2009-01-01

    We have investigated the role of formate (HCOO), carbonate (CO{sub 3}), and carboxyl (HOCO) species as possible intermediates in the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction on Au(111) using synchrotron-based core level photoemission, near-edge X-ray absorption fine structure (NEXAFS), and infrared absorption spectroscopy (IR). Adsorbed HCOO, CO{sub 3}, and OH species were prepared by adsorbing formic acid, carbon dioxide, and water on a Au(111) surface precovered with 0.2 ML of atomic oxygen, respectively. HCOOH interacts weakly with Au(111), but on O/Au(111) it dissociates its acidic H to yield adsorbed formate. The results of NEXAFS, IR, and density-functional calculations indicate that the formate adopts a bidentate configuration on Au(111). Since the HCOO groups are stable on Au(111) up to temperatures near 350 K, it is not likely that formate is a key intermediate for the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction at low temperatures. In fact, the formation of this species could lead eventually to surface poisoning. When compared to a formate species, a carbonate species formed by the reaction of CO{sub 2} with O/Au(111) has low stability, decomposing at temperatures between 100 and 125 K, and should not poison the gold surface. Neither HCOO nor CO{sub 3} was detected during the reaction of CO with OH on Au(111) at 90-120 K. The results of photoemission and IR spectroscopy point to HO {leftrightarrow} CO interactions, consistent with the formation of an unstable HOCO intermediate which has a very short lifetime on the gold surface. The possible mechanism for the low-temperature water-gas shift on gold catalysts is discussed in light of these results.

  3. Protein Vivisection Reveals Elusive Intermediates in Folding

    SciTech Connect

    Zheng, Zhongzhou; Sosnick, Tobin R.

    2010-05-25

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu {yields} Glu{sup -}) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the {beta}5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  4. Protein vivisection reveals elusive intermediates in folding.

    PubMed

    Zheng, Zhongzhou; Sosnick, Tobin R

    2010-04-01

    Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here, we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu-->Glu(-)) to destabilize and unfold a specific region of the protein. We applied this strategy to ubiquitin, reversibly trapping a folding intermediate in which the beta5-strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high-energy states.

  5. Production cross sections for heavy-ion fragmentation reactions on a liquid deuterium target at intermediate energies

    SciTech Connect

    Roeder, B. T.; Kemper, K. W.; Aoi, N.; Motobayashi, T.; Takeuchi, S.; Bazin, D.; Mueller, W. F.; Yoneda, K.; Bowen, M.; Campbell, C. M.; Cook, J. M.; Dinca, D.-C.; Gade, A.; Glasmacher, T.; Terry, J. R.; Zwahlen, H.; Iwasaki, H.; Sakurai, H.; Suzuki, H.; Kanno, S.

    2006-09-15

    The inclusive cross sections for 38 different reaction products produced in the interaction of {sup 48}Ca, {sup 40}S, and {sup 42}S beams around 100 MeV/nucleon with a liquid deuterium target are reported. The cross sections for the {sup 48}Ca +{sup 2}H products are compared to those with {sup 48}Ca incident on the commonly used fragmentation targets {sup 9}Be and {sup 181}Ta and also to global calculations for fragmentation reaction cross sections based on the EPAX parameterization. The sizes of the measured reaction cross sections for the deuterium target were comparable to those of the cross sections measured on the heavier targets, indicating that nucleon removal from a deuterium target can be carried out for single- and multiple-nucleon knockout reaction studies. It was also found that the charge exchange cross sections were large enough that it should be possible to obtain nuclear structure information from these reactions.

  6. Structural and Kinetic Evidence That Catalytic Reaction of Human UDP-glucose 6-Dehydrogenase Involves Covalent Thiohemiacetal and Thioester Enzyme Intermediates*

    PubMed Central

    Egger, Sigrid; Chaikuad, Apirat; Klimacek, Mario; Kavanagh, Kathryn L.; Oppermann, Udo; Nidetzky, Bernd

    2012-01-01

    Biosynthesis of UDP-glucuronic acid by UDP-glucose 6-dehydrogenase (UGDH) occurs through the four-electron oxidation of the UDP-glucose C6 primary alcohol in two NAD+-dependent steps. The catalytic reaction of UGDH is thought to involve a Cys nucleophile that promotes formation of a thiohemiacetal enzyme intermediate in the course of the first oxidation step. The thiohemiacetal undergoes further oxidation into a thioester, and hydrolysis of the thioester completes the catalytic cycle. Herein we present crystallographic and kinetic evidence for the human form of UGDH that clarifies participation of covalent catalysis in the enzymatic mechanism. Substitution of the putative catalytic base for water attack on the thioester (Glu161) by an incompetent analog (Gln161) gave a UGDH variant (E161Q) in which the hydrolysis step had become completely rate-limiting so that a thioester enzyme intermediate accumulated at steady state. By crystallizing E161Q in the presence of 5 mm UDP-glucose and 2 mm NAD+, we succeeded in trapping a thiohemiacetal enzyme intermediate and determined its structure at 2.3 Å resolution. Cys276 was covalently modified in the structure, establishing its role as catalytic nucleophile of the reaction. The thiohemiacetal reactive C6 was in a position suitable to become further oxidized by hydride transfer to NAD+. The proposed catalytic mechanism of human UGDH involves Lys220 as general base for UDP-glucose alcohol oxidation and for oxyanion stabilization during formation and breakdown of the thiohemiacetal and thioester enzyme intermediates. Water coordinated to Asp280 deprotonates Cys276 to function as an aldehyde trap and also provides oxyanion stabilization. Glu161 is the Brønsted base catalytically promoting the thioester hydrolysis. PMID:22123821

  7. From bis(silylene) and bis(germylene) pincer-type nickel(II) complexes to isolable intermediates of the nickel-catalyzed Sonogashira cross-coupling reaction.

    PubMed

    Gallego, Daniel; Brück, Andreas; Irran, Elisabeth; Meier, Florian; Kaupp, Martin; Driess, Matthias; Hartwig, John F

    2013-10-16

    The first [ECE]Ni(II) pincer complexes with E = Si(II) and E = Ge(II) metallylene donor arms were synthesized via C-X (X = H, Br) oxidative addition, starting from the corresponding [EC(X)E] ligands. These novel complexes were fully characterized (NMR, MS, and XRD) and used as catalyst for Ni-catalyzed Sonogashira reactions. These catalysts allowed detailed information on the elementary steps of this catalytic reaction (transmetalation → oxidative addition → reductive elimination), resulting in the isolation and characterization of an unexpected intermediate in the transmetalation step. This complex, {[ECE]Ni acetylide → CuBr} contains both nickel and copper, with the copper bound to the alkyne π-system. Consistent with these unusual structural features, DFT calculations of the {[ECE]Ni acetylide → CuBr} intermediates revealed an unusual E-Cu-Ni three-center-two-electron bonding scheme. The results reveal a general reaction mechanism for the Ni-based Sonogashira coupling and broaden the application of metallylenes as strong σ-donor ligands for catalytic transformations. PMID:24053603

  8. Identifying Enclosed Chemical Reaction and Dynamics at the Molecular Level Using Shell-Isolated Miniaturized Plasmonic Liquid Marble.

    PubMed

    Han, Xuemei; Lee, Hiang Kwee; Lee, Yih Hong; Hao, Wei; Liu, Yejing; Phang, In Yee; Li, Shuzhou; Ling, Xing Yi

    2016-04-21

    Current microscale tracking of chemical kinetics is limited to destructive ex situ methods. Here we utilize Ag nanocube-based plasmonic liquid marble (PLM) microreactor for in situ molecular-level identification of reaction dynamics. We exploit the ultrasensitive surface-enhanced Raman scattering (SERS) capability imparted by the plasmonic shell to unravel the mechanism and kinetics of aryl-diazonium surface grafting reaction in situ, using just a 2-μL reaction droplet. This reaction is a robust approach to generate covalently functionalized metallic surfaces, yet its kinetics remain unknown to date. Experiments and simulations jointly uncover a two-step sequential grafting process. An initial Langmuir chemisorption of sulfonicbenzene diazonium (dSB) salt onto Ag surfaces forms an intermediate sulfonicbenzene monolayer (Ag-SB), followed by subsequent autocatalytic multilayer growth of Ag-SB3. Kinetic rate constants reveal 19-fold faster chemisorption than multilayer growth. Our ability to precisely decipher molecular-level reaction dynamics creates opportunities to develop more efficient processes in synthetic chemistry and nanotechnology.

  9. Intermediate partitioning kinetic isotope effects for the NIH shift of 4-hydroxyphenylpyruvate dioxygenase and the hydroxylation reaction of hydroxymandelate synthase reveal mechanistic complexity.

    PubMed

    Shah, Dhara D; Conrad, John A; Moran, Graham R

    2013-09-01

    4-Hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are similar enzymes that catalyze complex dioxygenation reactions using the substrates 4-hydroxyphenylpyruvate (HPP) and dioxygen. Both enzymes decarboxylate HPP and then hydroxylate the resulting hydroxyphenylacetate (HPA). The hydroxylation reaction catalyzed by HPPD displaces the aceto substituent of HPA in a 1,2-shift to form 2,5-dihydroxyphenylacetate (homogentisate, HG), whereas the hydroxylation reaction of HMS places a hydroxyl on the benzylic carbon forming 3'-hydroxyphenylacetate (S-hydroxymandelate, HMA) without ensuing chemistry. The wild-type form of HPPD and variants of both enzymes uncouple to form both native and non-native products. We have used intermediate partitioning to probe bifurcating steps that form these products by substituting deuteriums for protiums at the benzylic position of the HPP substrate. These substitutions result in altered ratios of products that can be used to calculate kinetic isotope effects (KIE) for the formation of a specific product. For HPPD, secondary normal KIEs indicate that cleavage of the bond in the displacement reaction prior to the shift occurs by a homolytic mechanism. NMR analysis of HG derived from HPPD reacting with enantiomerically pure R-3'-deutero-HPP indicates that no rotation about the bond to the radical occurs, suggesting that collapse of the biradical intermediate is rapid. The production of HMA was observed in HMS and HPPD variant reactions. HMS hydroxylates to form exclusively S-hydroxymandelate. When HMS is reacted with R-3'-deutero-HPP, the observed kinetic isotope effect represents geometry changes in the initial transition state for the nonabstracted proton. These data show evidence of sp(3) hybridization in a HPPD variant and sp(2) hybridization in HMS variants, suggesting that HMS stabilizes a more advanced transition state in order to catalyze H-atom abstraction.

  10. Model for particle production in nuclear reactions at intermediate energies: Application to C-C collisions at 95 MeV/nucleon

    NASA Astrophysics Data System (ADS)

    Dudouet, J.; Durand, D.

    2016-07-01

    A model describing nuclear collisions at intermediate energies is presented and the results are compared with recently measured double differential cross sections in C-C reactions at 95 MeV/nucleon. Results show the key role played by geometrical effects and the memory of the entrance channel, in particular the momentum distributions of the two incoming nuclei. Special attention is paid to the description of processes occurring at midrapidity. To this end, a random particle production mechanism by means of a coalescence process in velocity space is considered in the overlap region of the two interacting nuclei.

  11. Kinetic and product studies of Criegee intermediate reactions with halogenated and non-halogenated carboxylic acids and their implications in the troposphere

    NASA Astrophysics Data System (ADS)

    Chhantyal-Pun, Rabi; Rotavera, Brandon; Eskola, Arkke; Taatjes, Craig; Percival, Carl; Shallcross, Dudley; Orr-Ewing, Andrew

    2016-04-01

    Criegee intermediates are important species formed during the ozonolysis of alkenes. Direct measurement and modelling studies have shown that reactions of stabilized Criegee intermediates with species like SO2 and NO2 may have a significant effect in tropospheric chemistry.[1, 2] Reaction rates of Criegee intermediates with simple carboxylic acids like HCOOH and CH3COOH have been shown to be near the collision limit and may be a significant sink for these otherwise stable species in the atmosphere.[3, 4] Results obtained from our time-resolved Cavity Ring-Down Spectroscopy (CRDS) apparatus[5] for reactions of the Criegee intermediates, CH2OO and (CH3)2COO with various halogenated (CF3COOH, CF3CF2COOH, CClF2COOH and CHCl2COOH) and non-halogenated (HCOOH and CH3COOH) carboxylic acids will be presented, together with Structure Activity Relationship (SAR) based on these observations. Structure characterization of the products from these reactions using the Multiplexed PhotoIonization Mass Spectrometry (MPIMS) apparatus[1,3] as well as implications for Secondary Organic Aerosol (SOA) formation, assessed using the global atmospheric model STOCHEM, will also be discussed. Bibliography 1. O. Welz, J. D. Savee, D. L. Osborn, S. S. Vasu, C. J. Percival, D. E. Shallcross and C. A. Taatjes, Science, 2012, 335, 204-207. 2. C. J. Percival, O. Welz, A. J. Eskola, J. D. Savee, D. L. Osborn, D. O. Topping, D. Lowe, S. R. Utembe, A. Bacak, G. McFiggans, M. C. Cooke, P. Xiao, A. T. Archibald, M. E. Jenkin, R. G. Derwent, I. Riipinen, D. W. K. Mok, E. P. F. Lee, J. M. Dyke, C. A. Taatjes and D. E. Shallcross, Faraday Discuss., 2013, 165, 45-73. 3. O. Welz, A. J. Eskola, L. Sheps, B. Rotavera, J. D. Savee, A. M. Scheer, D. L. Osborn, D. Lowe, A. M. Booth, P. Xiao, M. A. H. Khan, C. J. Percival, D. E. Shallcross and C. A. Taatjes, Angew. Chem. Int. Ed., 2014, 53, 4547-4550. 4. M. D. Hurley, M. P. S. Andersen, T. J. Wallington, D. A. Ellis, J. W. Martin and S. A. Mabury, J. Phys. Chem. A

  12. The oxidation of Ni(II) N-confused porphyrins (NCPs) with azo radical initiators and an unexpected intramolecular nucleophilic substitution reaction via a proposed Ni(III) NCP intermediate.

    PubMed

    Jiang, Hua-Wei; Chen, Qing-Yun; Xiao, Ji-Chang; Gu, Yu-Cheng

    2009-07-01

    The oxidation of Ni(II) N-confused porphyrins (NCPs) with azo radical initiators resulted in an unexpected intramolecular nucleophilic substitution reaction via a proposed Ni(III) NCP intermediate, which could be detected by HRMS.

  13. A Pan-Carina Young Stellar Object Catalog: Intermediate-mass Young Stellar Objects in the Carina Nebula Identified Via Mid-infrared Excess Emission

    NASA Astrophysics Data System (ADS)

    Povich, Matthew S.; Smith, Nathan; Majewski, Steven R.; Getman, Konstantin V.; Townsley, Leisa K.; Babler, Brian L.; Broos, Patrick S.; Indebetouw, Rémy; Meade, Marilyn R.; Robitaille, Thomas P.; Stassun, Keivan G.; Whitney, Barbara A.; Yonekura, Yoshinori; Fukui, Yasuo

    2011-05-01

    We present a catalog of 1439 young stellar objects (YSOs) spanning the 1.42 deg2 field surveyed by the Chandra Carina Complex Project (CCCP), which includes the major ionizing clusters and the most active sites of ongoing star formation within the Great Nebula in Carina. Candidate YSOs were identified via infrared (IR) excess emission from dusty circumstellar disks and envelopes, using data from the Spitzer Space Telescope (the Vela-Carina survey) and the Two-Micron All Sky Survey. We model the 1-24 μm IR spectral energy distributions of the YSOs to constrain physical properties. Our Pan-Carina YSO Catalog (PCYC) is dominated by intermediate-mass (2 M sun < m <~ 10 M sun) objects with disks, including Herbig Ae/Be stars and their less evolved progenitors. The PCYC provides a valuable complementary data set to the CCCP X-ray source catalogs, identifying 1029 YSOs in Carina with no X-ray detection. We also catalog 410 YSOs with X-ray counterparts, including 62 candidate protostars. Candidate protostars with X-ray detections tend to be more evolved than those without. In most cases, X-ray emission apparently originating from intermediate-mass, disk-dominated YSOs is consistent with the presence of low-mass companions, but we also find that X-ray emission correlates with cooler stellar photospheres and higher disk masses. We suggest that intermediate-mass YSOs produce X-rays during their early pre-main-sequence evolution, perhaps driven by magnetic dynamo activity during the convective atmosphere phase, but this emission dies off as the stars approach the main sequence. Extrapolating over the stellar initial mass function scaled to the PCYC population, we predict a total population of >2 × 104 YSOs and a present-day star formation rate (SFR) of >0.008 M sun yr-1. The global SFR in the Carina Nebula, averaged over the past ~5 Myr, has been approximately constant.

  14. Identifying plausible adverse drug reactions using knowledge extracted from the literature

    PubMed Central

    Shang, Ning; Xu, Hua; Rindflesch, Thomas C.; Cohen, Trevor

    2014-01-01

    Pharmacovigilance involves continually monitoring drug safety after drugs are put to market. To aid this process; algorithms for the identification of strongly correlated drug/adverse drug reaction (ADR) pairs from data sources such as adverse event reporting systems or Electronic Health Records have been developed. These methods are generally statistical in nature, and do not draw upon the large volumes of knowledge embedded in the biomedical literature. In this paper, we investigate the ability of scalable Literature Based Discovery (LBD) methods to identify side effects of pharmaceutical agents. The advantage of LBD methods is that they can provide evidence from the literature to support the plausibility of a drug/ ADR association, thereby assisting human review to validate the signal, which is an essential component of pharmacovigilance. To do so, we draw upon vast repositories of knowledge that has been extracted from the biomedical literature by two Natural Language Processing tools, MetaMap and SemRep. We evaluate two LBD methods that scale comfortably to the volume of knowledge available in these repositories. Specifically, we evaluate Reflective Random Indexing (RRI), a model based on concept-level co-occurrence, and Predication-based Semantic Indexing (PSI), a model that encodes the nature of the relationship between concepts to support reasoning analogically about drug-effect relationships. An evaluation set was constructed from the Side Effect Resource 2 (SIDER2), which contains known drug/ADR relations, and models were evaluated for their ability to “rediscover” these relations. In this paper, we demonstrate that both RRI and PSI can recover known drug-adverse event associations. However, PSI performed better overall, and has the additional advantage of being able to recover the literature underlying the reasoning pathways it used to make its predictions. PMID:25046831

  15. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions.

    PubMed

    Lambrecht, Jennifer A; Flynn, Jeffrey M; Downs, Diana M

    2012-01-27

    The YjgF/YER057c/UK114 family of proteins is conserved in all domains of life, suggesting that the role of these proteins arose early and was maintained throughout evolution. Metabolic consequences of lacking this protein in Salmonella enterica and other organisms have been described, but the biochemical function of YjgF remained unknown. This work provides the first description of a conserved biochemical activity for the YjgF protein family. Our data support the conclusion that YjgF proteins have enamine/imine deaminase activity and accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA). Results from structure-guided mutagenesis experiments suggest that YjgF lacks a catalytic residue and that it facilitates ammonia release by positioning a critical water molecule in the active site. YjgF is renamed RidA (reactive intermediate/imine deaminase A) to reflect the conserved activity of the protein family described here. This study, combined with previous physiological studies on yjgF mutants, suggests that intermediates of pyridoxal 5'-phosphate-mediated reactions may have metabolic consequences in vivo that were previously unappreciated. The conservation of the RidA/YjgF family suggests that reactive enamine/imine metabolites are of concern to all organisms.

  16. Probing the neutron-skin thickness by photon production from reactions induced by intermediate-energy protons

    NASA Astrophysics Data System (ADS)

    Wei, Gao-Feng

    2015-07-01

    The photon from neutron-proton bremsstrahlung in p +Pb reactions is examined as a potential probe of the neutron-skin thickness in different centralities and at different proton incident energies. It is shown that the best choice of reaction environment is about 140 MeV for the incident proton and the 95%-100% centrality for the reaction system since the incident proton mainly interacts with neutrons inside the skin of the target and thus leads to different photon production to a maximal extent. Moreover, considering two main uncertainties from both photon production probability and nucleon-nucleon cross section in the reaction, I propose to use the ratio of photon production from two reactions to measure the neutron-skin thickness because of its cancellation effects on these uncertainties simultaneously, but preserved about 13%-15% sensitivities on the varied neutron-skin thickness from 0.1 to 0.3 fm within the current experimental uncertainty range of the neutron-skin size in 208Pb.

  17. The roles of coenzyme A in the pyruvate:ferredoxin oxidoreductase reaction mechanism: rate enhancement of electron transfer from a radical intermediate to an iron-sulfur cluster.

    PubMed

    Furdui, Cristina; Ragsdale, Stephen W

    2002-08-01

    Pyruvate:ferredoxin oxidoreductase (PFOR) catalyzes the coenzyme A (CoA)-dependent oxidative decarboxylation of pyruvate. In many autotrophic anaerobes, PFOR links the Wood-Ljungdahl pathway to glycolysis and to cell carbon synthesis. Herein, we cloned and sequenced the M. thermoacetica PFOR, demonstrating strong structural homology with the structurally characterized D. africanus PFOR, including the presence of three [4Fe-4S] clusters per monomeric unit. The PFOR reaction includes a hydroxyethyl-thiamin pyrophosphate (HE-TPP) radical intermediate, which forms rapidly after PFOR reacts with pyruvate. This step precedes electron transfer from the HE-TPP radical intermediate to an intramolecular [4Fe-4S] cluster. We show that CoA increases the rate of this redox reaction by 10(5)-fold. Analysis by Marcus theory indicates that, in the absence of CoA, this is a true electron-transfer reaction; however, in its presence, electron transfer is gated by an adiabatic event. Analysis by the Eyring equation indicates that entropic effects dominate this rate enhancement. Our results indicate that the energy of binding CoA contributes minimally to the rate increase since the thiol group of CoA lends over 40 kJ/mol to the reaction, whereas components of CoA that afford most of the cofactor's binding energy contribute minimally. Major conformational changes also do not appear to explain the rate enhancement. We propose several ways that CoA can accomplish this rate increase, including formation of a highly reducing adduct with the HE-TPP radical to increase the driving force for electron transfer. We also consider the possibility that CoA itself forms part of the electron-transfer pathway. PMID:12146957

  18. Identifying the Structure of the Intermediate, Li2/3CoPO4, Formed during Electrochemical Cycling of LiCoPO4

    PubMed Central

    2014-01-01

    In situ synchrotron diffraction measurements and subsequent Rietveld refinements are used to show that the high energy density cathode material LiCoPO4 (space group Pnma) undergoes two distinct two-phase reactions upon charge and discharge, both occurring via an intermediate Li2/3(Co2+)2/3(Co3+)1/3PO4 phase. Two resonances are observed for Li2/3CoPO4 with intensity ratios of 2:1 and 1:1 in the 31P and 7Li NMR spectra, respectively. An ordering of Co2+/Co3+ oxidation states is proposed within a (a × 3b × c) supercell, and Li+/vacancy ordering is investigated using experimental NMR data in combination with first-principles solid-state DFT calculations. In the lowest energy configuration, both the Co3+ ions and Li vacancies are found to order along the b-axis. Two other low energy Li+/vacancy ordering schemes are found only 5 meV per formula unit higher in energy. All three configurations lie below the LiCoPO4–CoPO4 convex hull and they may be readily interconverted by Li+ hops along the b-direction. PMID:25960604

  19. An important difference between "exposed" and "photodistributed" underscores the importance of identifying common reactions.

    PubMed

    Jacob, Sharon E; Breithaupt, Andrew D

    2009-09-01

    This article presents the case of a patient with rheumatoid arthritis who was referred to dermatology for what was suspected to be a photosensitivity reaction to hydroxychloroquine, a common culprit in photodrug reactions. Despite the patient's insistence to the contrary, the cause of her eruption was an airborne allergic contact dermatitis to chemicals she was exposed to during her longtime hobby of soap-making. This case serves as an important illustration of the anatomical differences between eruptions occurring in exposed and photodistributed areas. This article also discusses the causes of dermatitis that may mimic photodrug reactions.

  20. Origin of product selectivity in a prenyl transfer reaction from the same intermediate: exploration of multiple FtmPT1-catalyzed prenyl transfer pathways.

    PubMed

    Pan, Li-Li; Yang, Yue; Merz, Kenneth M

    2014-09-30

    FtmPT1 is a fungal indole prenyltransferase that catalyzes the reaction of tryptophan derivatives with dimethylallyl pyrophosphate to form various biologically active compounds. Herein, we describe detailed studies of FtmPT1 catalysis involving dimethylallyl pyrophosphate and Brevianamide F following the native pathway (yielding Tryprostatin B) and an alternate pathway observed in the Gly115Thr mutant of FtmPT1 yielding a novel cyclized product. Importantly, these two products arise from the same intermediate state, meaning that a step other than the cleavage of the dimethylallyl pyrophosphate (DMAPP; C-O) bond is differentiating between the two product reaction channels. From detailed potential of mean force (PMF) and two-dimensional PMF analyses, we conclude that the rate-limiting step is the cleavage of the C-O bond in DMAPP, while the deprotonation/cyclization step determines the final product distribution. Hence, in the case of FtmPT1, the optimization of the necessary catalytic machinery guides the generation of the final product after formation of the intermediate carbocation.

  1. Superstructure in the Metastable Intermediate-Phase Li2/3 FePO4 Accelerating the Lithium Battery Cathode Reaction.

    PubMed

    Nishimura, Shin-ichi; Natsui, Ryuichi; Yamada, Atsuo

    2015-07-27

    LiFePO4 is an important cathode material for lithium-ion batteries. Regardless of the biphasic reaction between the insulating end members, Lix FePO4 , x≈0 and x≈1, optimization of the nanostructured architecture has substantially improved the power density of positive LiFePO4 electrode. The charge transport that occurs in the interphase region across the biphasic boundary is the primary stage of solid-state electrochemical reactions in which the Li concentrations and the valence state of Fe deviate significantly from the equilibrium end members. Complex interactions among Li ions and charges at the Fe sites have made understanding stability and transport properties of the intermediate domains difficult. Long-range ordering at metastable intermediate eutectic composition of Li2/3 FePO4 has now been discovered and its superstructure determined, which reflected predominant polaron crystallization at the Fe sites followed by Li(+) redistribution to optimize the Li-Fe interactions. PMID:26074480

  2. Reductive activation of the heme iron-nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study.

    PubMed

    Bykov, Dmytro; Neese, Frank

    2012-06-01

    Cytochrome c nitrite reductase catalyzes the six-electron, seven-proton reduction of nitrite to ammonia without release of any detectable reaction intermediate. This implies a unique flexibility of the active site combined with a finely tuned proton and electron delivery system. In the present work, we employed density functional theory to study the recharging of the active site with protons and electrons through the series of reaction intermediates based on nitrogen monoxide [Fe(II)-NO(+), Fe(II)-NO·, Fe(II)-NO(-), and Fe(II)-HNO]. The activation barriers for the various proton and electron transfer steps were estimated in the framework of Marcus theory. Using the barriers obtained, we simulated the kinetics of the reduction process. We found that the complex recharging process can be accomplished in two possible ways: either through two consecutive proton-coupled electron transfers (PCETs) or in the form of three consecutive elementary steps involving reduction, PCET, and protonation. Kinetic simulations revealed the recharging through two PCETs to be a means of overcoming the predicted deep energetic minimum that is calculated to occur at the stage of the Fe(II)-NO· intermediate. The radical transfer role for the active-site Tyr(218), as proposed in the literature, cannot be confirmed on the basis of our calculations. The role of the highly conserved calcium located in the direct proximity of the active site in proton delivery has also been studied. It was found to play an important role in the substrate conversion through the facilitation of the proton transfer steps.

  3. Studies on the inhibition of sphingosine-1-phosphate lyase by stabilized reaction intermediates and stereodefined azido phosphates.

    PubMed

    Sanllehí, Pol; Abad, José-Luís; Bujons, Jordi; Casas, Josefina; Delgado, Antonio

    2016-11-10

    Two kinds of inhibitors of the PLP-dependent enzyme sphingosine-1-phosphate lyase have been designed and tested on the bacterial (StS1PL) and the human (hS1PL) enzymes. Amino phosphates 1, 12, and 32, mimicking the intermediate aldimines of the catalytic process, were weak inhibitors on both enzyme sources. On the other hand, a series of stereodefined azido phosphates, resulting from the replacement of the amino group of the natural substrates with an azido group, afforded competitive inhibitors in the low micromolar range on both enzyme sources. This similar behavior represents an experimental evidence of the reported structural similarities for both enzymes at their active site level. Interestingly, the anti-isomers of the non-natural enantiomeric series where the most potent inhibitors on hS1PL.

  4. Kinetics and Mechanism of the Chlorite-Periodate System: Formation of a Short-Lived Key Intermediate OClOIO3 and Its Subsequent Reactions.

    PubMed

    Baranyi, Nóra; Csekő, György; Valkai, László; Xu, Li; Horváth, Attila K

    2016-03-01

    The chlorite-periodate reaction has been studied spectrophotometrically in acidic medium at 25.0 ± 0.1 °C, monitoring the absorbance at 400 nm in acetate/acetic acid buffer at constant ionic strength (I = 0.5 M). We have shown that periodate was exclusively reduced to iodate, but chlorite ion was oxidized to chlorate and chlorine dioxide via branching pathways. The stoichiometry of the reaction can be described as a linear combination of two limiting stoichiometries under our experimental conditions. Detailed initial rate studies have clearly revealed that the formal kinetic orders of hydrogen ion, chlorite ion, and periodate ion are all strictly one, establishing an empirical rate law to be d[ClO2]/dt = kobs[ClO2(-)][IO4(-)][H(+)], where the apparent rate coefficient (kobs) was found to be 70 ± 13 M(-2) s(-1). On the basis of the experiments, a simple four-step kinetic model with three fitted kinetic parameters is proposed by nonlinear parameter estimation. The reaction was found to proceed via a parallel oxygen transfer reaction leading to the exclusive formation of chlorate and iodate as well as via the formation of a short-lived key intermediate OClOIO3 followed by its further transformations by a sequence of branching pathways. PMID:26849795

  5. Kinetics and Mechanism of the Chlorite-Periodate System: Formation of a Short-Lived Key Intermediate OClOIO3 and Its Subsequent Reactions.

    PubMed

    Baranyi, Nóra; Csekő, György; Valkai, László; Xu, Li; Horváth, Attila K

    2016-03-01

    The chlorite-periodate reaction has been studied spectrophotometrically in acidic medium at 25.0 ± 0.1 °C, monitoring the absorbance at 400 nm in acetate/acetic acid buffer at constant ionic strength (I = 0.5 M). We have shown that periodate was exclusively reduced to iodate, but chlorite ion was oxidized to chlorate and chlorine dioxide via branching pathways. The stoichiometry of the reaction can be described as a linear combination of two limiting stoichiometries under our experimental conditions. Detailed initial rate studies have clearly revealed that the formal kinetic orders of hydrogen ion, chlorite ion, and periodate ion are all strictly one, establishing an empirical rate law to be d[ClO2]/dt = kobs[ClO2(-)][IO4(-)][H(+)], where the apparent rate coefficient (kobs) was found to be 70 ± 13 M(-2) s(-1). On the basis of the experiments, a simple four-step kinetic model with three fitted kinetic parameters is proposed by nonlinear parameter estimation. The reaction was found to proceed via a parallel oxygen transfer reaction leading to the exclusive formation of chlorate and iodate as well as via the formation of a short-lived key intermediate OClOIO3 followed by its further transformations by a sequence of branching pathways.

  6. Nucleon-induced reactions at intermediate energies: New data at 96 MeV and theoretical status

    NASA Astrophysics Data System (ADS)

    Blideanu, V.; Lecolley, F. R.; Lecolley, J. F.; Lefort, T.; Marie, N.; Ataç, A.; Ban, G.; Bergenwall, B.; Blomgren, J.; Dangtip, S.; Elmgren, K.; Eudes, Ph.; Foucher, Y.; Guertin, A.; Haddad, F.; Hildebrand, A.; Johansson, C.; Jonsson, O.; Kerveno, M.; Kirchner, T.; Klug, J.; Le Brun, Ch.; Lebrun, C.; Louvel, M.; Nadel-Turonski, P.; Nilsson, L.; Olsson, N.; Pomp, S.; Prokofiev, A. V.; Renberg, P.-U.; Rivière, G.; Slypen, I.; Stuttgé, L.; Tippawan, U.; Österlund, M.

    2004-07-01

    Double-differential cross sections for light charged particle production (up to A=4 ) were measured in 96 MeV neutron-induced reactions, at the TSL Laboratory Cyclotron in Uppsala (Sweden). Measurements for three targets, Fe , Pb , and U , were performed using two independent devices, SCANDAL and MEDLEY. The data were recorded with low-energy thresholds and for a wide angular range ( 20° 160° ) . The normalization procedure used to extract the cross sections is based on the np elastic scattering reaction that we measured and for which we present experimental results. A good control of the systematic uncertainties affecting the results is achieved. Calculations using the exciton model are reported. Two different theoretical approaches proposed to improve its predictive power regarding the complex particle emission are tested. The capabilities of each approach is illustrated by comparison with the 96 MeV data that we measured, and with other experimental results available in the literature.

  7. Reaction of alkynes and azides: not triazoles through copper-acetylides but oxazoles through copper-nitrene intermediates.

    PubMed

    Haldón, Estela; Besora, Maria; Cano, Israel; Cambeiro, Xacobe C; Pericàs, Miquel A; Maseras, Feliu; Nicasio, M Carmen; Pérez, Pedro J

    2014-03-17

    Well-defined copper(I) complexes of composition [Tpm*(,Br) Cu(NCMe)]BF4 (Tpm*(,Br) =tris(3,5-dimethyl-4-bromo-pyrazolyl)methane) or [Tpa(*) Cu]PF6 (Tpa(*) =tris(3,5-dimethyl-pyrazolylmethyl)amine) catalyze the formation of 2,5-disubstituted oxazoles from carbonyl azides and terminal alkynes in a direct manner. This process represents a novel procedure for the synthesis of this valuable heterocycle from readily available starting materials, leading exclusively to the 2,5-isomer, attesting to a completely regioselective transformation. Experimental evidence and computational studies have allowed the proposal of a reaction mechanism based on the initial formation of a copper-acyl nitrene species, in contrast to the well-known mechanism for the copper-catalyzed alkyne and azide cycloaddition reactions (CuAAC) that is triggered by the formation of a copper-acetylide complex.

  8. Reaction of alkynes and azides: not triazoles through copper-acetylides but oxazoles through copper-nitrene intermediates.

    PubMed

    Haldón, Estela; Besora, Maria; Cano, Israel; Cambeiro, Xacobe C; Pericàs, Miquel A; Maseras, Feliu; Nicasio, M Carmen; Pérez, Pedro J

    2014-03-17

    Well-defined copper(I) complexes of composition [Tpm*(,Br) Cu(NCMe)]BF4 (Tpm*(,Br) =tris(3,5-dimethyl-4-bromo-pyrazolyl)methane) or [Tpa(*) Cu]PF6 (Tpa(*) =tris(3,5-dimethyl-pyrazolylmethyl)amine) catalyze the formation of 2,5-disubstituted oxazoles from carbonyl azides and terminal alkynes in a direct manner. This process represents a novel procedure for the synthesis of this valuable heterocycle from readily available starting materials, leading exclusively to the 2,5-isomer, attesting to a completely regioselective transformation. Experimental evidence and computational studies have allowed the proposal of a reaction mechanism based on the initial formation of a copper-acyl nitrene species, in contrast to the well-known mechanism for the copper-catalyzed alkyne and azide cycloaddition reactions (CuAAC) that is triggered by the formation of a copper-acetylide complex. PMID:24616053

  9. Infrared Spectroscopy of OH··CH3OH: Hydrogen-Bonded Intermediate Along the Hydrogen Abstraction Reaction Path.

    PubMed

    Hernandez, Federico J; Brice, Joseph T; Leavitt, Christopher M; Pino, Gustavo A; Douberly, Gary E

    2015-07-23

    Substantial non-Arrhenius behavior has been previously observed in the low temperature reaction between the hydroxyl radical and methanol. This behavior can be rationalized assuming the stabilization of an association adduct in the entrance channel of the reaction, from which barrier penetration via quantum mechanical tunneling produces the CH3O radical and H2O. Helium nanodroplet isolation and a serial pick-up technique are used to stabilize the hydrogen bonded prereactive OH··CH3OH complex. Mass spectrometry and infrared spectroscopy are used to confirm its production and probe the OH stretch vibrations. Stark spectroscopy reveals the magnitude of the permanent electric dipole moment, which is compared to ab initio calculations that account for wide-amplitude motion in the complex. The vibrationally averaged structure has Cs symmetry with the OH moiety hydrogen bonded to the hydroxyl group of methanol. Nevertheless, the zero-point level of the complex exhibits a wave function significantly delocalized over a bending coordinate leading to the transition state of the CH3O producing reaction.

  10. Electro-Fenton degradation of the antibiotic sulfanilamide with Pt/carbon-felt and BDD/carbon-felt cells. Kinetics, reaction intermediates, and toxicity assessment.

    PubMed

    El-Ghenymy, Abdellatif; Rodríguez, Rosa María; Brillas, Enric; Oturan, Nihal; Oturan, Mehmet A

    2014-01-01

    The degradation of 230 mL of a 0.6-mM sulfanilamide solution in 0.05 M Na₂SO₄ of pH 3.0 has been studied by electro-Fenton process. The electrolytic cell contained either a Pt or boron-doped diamond (BDD) anode and a carbon-felt cathode. Under these conditions, organics are oxidized by hydroxyl radicals formed at the anode surface from water oxidation and in the bulk from Fenton's reaction between initially added (and then electrochemically regenerated) Fe(2+) and cathodically generated H₂O₂. From the decay of sulfanilamide concentration determined by reversed-phase liquid chromatography, an optimum Fe(2+) concentration of 0.20 mM in both cells was found. The drug disappeared more rapidly using BDD than Pt, and, in both cases, it was more quickly removed with raising applied current. Almost total mineralization was achieved using the BDD/carbon-felt cell, whereas the alternative use of Pt anode led to a slightly lower mineralization degree. In both cells, the degradation rate was accelerated at higher current but with the concomitant fall of mineralization current efficiency due to the greater increase in rate of the parasitic reactions of hydroxyl radicals. Reversed-phase liquid chromatography allowed the identification of catechol, resorcinol, hydroquinone, p-benzoquinone, and 1,2,4-trihydroxybenzene as aromatic intermediates, whereas ion exclusion chromatography revealed the formation of malic, maleic, fumaric, acetic, oxalic, formic, and oxamic acids. NH₄(+), NO₃(-), and SO₄(2-) ions were released during the electro-Fenton process. A plausible reaction sequence for sulfanilamide mineralization involving all detected intermediates has been proposed. The toxicity of the solution was assessed from the Vibrio fischeri bacteria luminescence inhibition. Although it acquired its maximum value at short electrolysis time, the solution was completely detoxified at the end of the electro-Fenton treatment, regardless of the anode used. PMID:24687785

  11. Cutting the Gordian Knot: Identifiability of anaplerotic reactions in Corynebacterium glutamicum by means of (13) C-metabolic flux analysis.

    PubMed

    Kappelmann, Jannick; Wiechert, Wolfgang; Noack, Stephan

    2016-03-01

    Corynebacterium glutamicum is the major workhorse for the microbial production of several amino and organic acids. As long as these derive from tricarboxylic acid cycle intermediates, the activity of anaplerotic reactions is pivotal for a high biosynthetic yield. To determine single anaplerotic activities (13) C-Metabolic Flux Analysis ((13) C-MFA) has been extensively used for C. glutamicum, however with different network topologies, inconsistent or poorly determined anaplerotic reaction rates. Therefore, in this study we set out to investigate whether a focused isotopomer model of the anaplerotic node can at all admit a unique solution for all fluxes. By analyzing different scenarios of active anaplerotic reactions, we show in full generality that for C. glutamicum only certain anaplerotic deletion mutants allow to uniquely determine the anaplerotic fluxes from (13) C-isotopomer data. We stress that the result of this analysis for different assumptions on active enzymes is directly transferable to other compartment-free organisms. Our results demonstrate that there exist biologically relevant metabolic network topologies for which the flux distribution cannot be inferred by classical (13) C-MFA. PMID:26375179

  12. Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

    PubMed

    Holme, Petter; Huss, Mikael; Lee, Sang Hoon

    2011-01-01

    The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.

  13. Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

    SciTech Connect

    Hashimoto, Hideharu; Pais, June E.; Dai, Nan; Corrêa, Jr., Ivan R.; Zhang, Xing; Zheng, Yu; Cheng, Xiaodong

    2015-08-31

    The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solved NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH2 towards the metal-ligand water molecule, where a dioxygen O2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.

  14. EPR and pulsed ENDOR study of intermediates from reactions of aromatic azides with group 13 metal trichlorides

    PubMed Central

    Bencivenni, Giorgio; Cesari, Riccardo; Nanni, Daniele; El Mkami, Hassane

    2010-01-01

    Summary The reactions of group 13 metal trichlorides with aromatic azides were examined by CW EPR and pulsed ENDOR spectroscopies. Complex EPR spectra were obtained from reactions of aluminium, gallium and indium trichlorides with phenyl azides containing a variety of substituents. Analysis of the spectra showed that 4-methoxy-, 3-methoxy- and 2-methoxyphenyl azides all gave ‘dimer’ radical cations [ArNHC6H4NH2]+• and trimers [ArNHC6H4NHC6H4NH2]+• followed by polymers. 4-Azidobenzonitrile, with its electron-withdrawing substituent, did not react. In general the aromatic azides appeared to react most rapidly with AlCl3 but this reagent tended to generate much polymer. InCl3 was the least reactive group 13 halide. DFT computations of the radical cations provided corroborating evidence and suggested that the unpaired electrons were accommodated in extensive π-delocalised orbitals. A mechanism to account for the reductive conversion of aromatic azides to the corresponding anilines and thence to the dimers and trimers is proposed. PMID:21049080

  15. Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods.

    PubMed

    Dong, Geng; Ryde, Ulf

    2016-06-01

    The [NiFe] hydrogenases catalyse the reversible conversion of H2 to protons and electrons. The active site consists of a Fe ion with one carbon monoxide, two cyanide, and two cysteine (Cys) ligands. The latter two bridge to a Ni ion, which has two additional terminal Cys ligands. It has been suggested that one of the Cys residues is protonated during the reaction mechanism. We have used combined quantum mechanical and molecular mechanics (QM/MM) geometry optimisations, large QM calculations with 817 atoms, and QM/MM free energy simulations, using the TPSS and B3LYP methods with basis sets extrapolated to the quadruple zeta level to determine which of the four Cys residues is more favourable to protonate for four putative states in the reaction mechanism, Ni-SIa, Ni-R, Ni-C, and Ni-L. The calculations show that for all states, the terminal Cys-546 residue is most easily protonated by 14-51 kJ/mol, owing to a more favourable hydrogen-bond pattern around this residue in the protein. PMID:26940957

  16. A model for the compositions of non-stoichiometric intermediate phases formed by diffusion reactions, and its application to Nb3Sn superconductors

    PubMed Central

    Xu, X.; Sumption, M. D.

    2016-01-01

    In this work we explore the compositions of non-stoichiometric intermediate phases formed by diffusion reactions: a mathematical framework is developed and tested against the specific case of Nb3Sn superconductors. In the first part, the governing equations for the bulk diffusion and inter-phase interface reactions during the growth of a compound are derived, numerical solutions to which give both the composition profile and growth rate of the compound layer. The analytic solutions are obtained with certain approximations made. In the second part, we explain an effect that the composition characteristics of compounds can be quite different depending on whether it is the bulk diffusion or grain boundary diffusion that dominates in the compounds, and that “frozen” bulk diffusion leads to unique composition characteristics that the bulk composition of a compound layer remains unchanged after its initial formation instead of varying with the diffusion reaction system; here the model is modified for the case of grain boundary diffusion. Finally, we apply this model to the Nb3Sn superconductors and propose approaches to control their compositions. PMID:26754774

  17. Analyzing powers in the dd{yields}{sup 3}Hen({sup 3}Hp) reactions at intermediate energies

    SciTech Connect

    Ladygin, V. P.; Kiselev, A. S.; Kurilkin, A. K.; Vasiliev, T. A.; Isupov, A. Yu.; Ladygina, N. B.; Malakhov, A. I.; Reznikov, S. G.; Uesaka, T.; Saito, T.; Hatano, M.; Kato, H.; Sakoda, S.; Uchigashima, N.; Yako, K.; Janek, M.; Maeda, Y.; Nishikawa, J.; Ohnishi, T.; Sakamoto, N.

    2008-04-29

    Data for the deuteron analyzing powers in the dd{yields}{sup 3}Hen({sup 3}Hp) reactions obtained at 140-270 MeV are discussed. The observed negative sign of the tensor analyzing powers A{sub yy}, A{sub xx} and A{sub xz} at small angles clearly demonstrate the sensitivity to the ratio of the D and S state components of the {sup 3}He wave function. The behavior of the tensor analyzing powers at backward angles is sensitive to the short-range spin structure of the deuteron. However, the one-nucleon exchange calculations using standard {sup 3}He and deuteron wave functions fail to reproduce the strong variation of the tensor analyzing powers as a function of angle in the cms. Sensitivity to relativistic effects is also discussed.

  18. An optimized polymerase chain reaction assay to identify avian virus vaccine contamination with Chicken anemia virus.

    PubMed

    Amer, Haitham M; Elzahed, Hanan M; Elabiare, Elham A; Badawy, Ahmed A; Yousef, Ausama A

    2011-01-01

    The use of embryonating chicken eggs in preparation of avian virus vaccines is the principle cause for contamination with Chicken anemia virus (CAV). Identification of CAV in contaminated vaccines relies on the expensive, tedious, and time-consuming practice of virus isolation in lymphoblastoid cell lines. The experience of the last 2 decades indicates that polymerase chain reaction is extending to replace most of the classic methods for detection of infectious agents. In the present report, a simple, rapid, and accurate polymerase chain reaction method for detection of CAV in poultry vaccines is described. Oligonucleotide primers homologous to highly conserved sequences of the VP1 gene were used to amplify a fragment of 676 bp. The developed assay was specific for detecting CAV from different sources, with no cross reactivity with many avian viruses. No inter- and intra-assay variations were observed. The analytical sensitivity of the test was high enough to detect 5 TCID(50) (50% tissue culture infective dose) of the virus per reaction; however, different factors related to the vaccine matrix showed considerable effects on the detection limit. In conclusion, this method may represent a suitable alternative to virus isolation for identification of CAV contamination of poultry virus vaccines.

  19. Formation of gold and gold sulfide nanoparticles and mesoscale intermediate structures in the reactions of aqueous HAuCl4 with sulfide and citrate ions.

    PubMed

    Mikhlin, Yuri; Likhatski, Maxim; Karacharov, Anton; Zaikovski, Vladimir; Krylov, Alexander

    2009-07-14

    The effects of the molar ratio of sodium sulfide to chloroauric acid in the range of 0.5 to 5 and the time factor on the formation of the nanoparticles (NPs) of metallic Au, Au(2)S or their mixtures have been studied applying in situ and ex situ techniques (UV-Vis absorption spectroscopy, potentiometry, TEM, SPM, SERS, XPS). The products and intermediates have been compared with those for the reduction of chloroaurate with citrate ions and combinations of citrate and sulfide ions. An increase in the concentration of sulfide ions accelerates the reduction of Au(iii) complexes but hinders the nucleation and growth of Au NPs, resulting in a prolonged period before the appearance of plasmon peaks. The electrochemical potential is not directly associated with the plasmon intensities, although the potential sharply decreases simultaneously with a blue shift of the near-IR peak emerging with the Na(2)S/HAuCl(4) ratios of 0.5 to 1.5. It was concluded that the peak is due to longitudinal plasmon resonance of gold nanoplates. Au(2)S NPs, the nucleation of which is effectively inhibited, and probably some structures and fragments visible in TEM and AFM, including 2-5 nm Au NPs, crystallize in part outside the solutions. The evidence of partially liquid mesoscale structures comprising intermediate gold species as precursors of nanoparticles is presented, and their origin, ex situ transformation and role in the reaction mechanisms are discussed.

  20. A study of the precursors, intermediates and reaction by-products in the synthesis of 3,4-methylenedioxymethylamphetamine and its application to forensic drug analysis.

    PubMed

    Renton, R J; Cowie, J S; Oon, M C

    1993-08-01

    3,4-Methylenedioxymethylamphetamine (MDMA) was prepared by three synthetic routes. Analytical data from thin-layer chromatography, gas chromatography and gas chromatography-mass spectrometry of the precursors (safrole and isosafrole), intermediates (isosafrole glycol, piperonylmethylketone, N-formyl-3,4-methylenedioxymethylamphetamine, N-formyl-3,4-methylenedioxyamphetamine and 1-(3,4-methylenedioxyphenyl)-2-bromopropane), reaction by-products and the product MDMA were obtained. Further analyses of MDMA using other techniques including 1H- and 13C-nuclear magnetic resonance spectroscopy, X-ray diffraction, infrared spectroscopy, ultraviolet spectroscopy and high performance liquid chromatography were also carried out. The results were then used as reference data for the identification of MDMA in case samples and also to establish the route of synthesis of illicitly prepared MDMA by the study of trace impurities.

  1. Detection of alkylperoxo and ferryl, (Fe sup IV = O) sup 2+ , intermediates during the reaction of tert-butyl hydroperoxide with iron porphyrins in toluene solution

    SciTech Connect

    Arasasingham, R.D.; Cornman, C.R.; Balch, A.L. )

    1989-11-27

    PFe{sup II} and PFe{sup III}OH (P is a porphyrin dianion) catalyze the decomposition of tert-butyl hydroperoxide in toluene solution without appreciable attack on the porphyrin ligand. {sup 1}H NMR spectroscopic studies at low temperature ({minus}70{degree}C) give evidence for the formation of a high-spin, five-coordinate intermediate, PFe{sup III}OOC(CH{sub 3}){sub 3}. Organic products formed from this reaction are tert-butyl alcohol, di-tert-butyl peroxide, benzaldehyde, acetone, and benzyl-tert-butyl peroxide, which arise largely from a radical chain process initiated by the iron porphyrin but continuing without its intervention.

  2. Heterolytic cleavage of peroxide by a diferrous compound generates metal-based intermediates identical to those observed with reactions utilizing oxygen-atom-donor molecules.

    PubMed

    Rowe, Gerard T; Rybak-Akimova, Elena V; Caradonna, John P

    2008-01-01

    Under cryogenic stopped-flow conditions, addition of 2-methyl-1-phenylprop-2-yl hydroperoxide (MPPH) to the diiron(II) compound, [Fe(2)(H(2)Hbamb)(2)(NMeIm)(2)] (1; NMeIm=N-methylimidazole; H(4)HBamb: 2,3-bis(2-hydroxybenzamido)dimethylbutane) results in heterolytic peroxide O-O bond cleavage, forming a high-valent species, 2. The UV/Vis spectrum of 2 and its kinetic behavior suggest parallel reactivity to that seen in the reaction of 1 with oxygen-atom-donor (OAD) molecules, which has been reported previously. Like the interaction with OAD molecules, the reaction of 1 with MPPH proceeds through a three step process, assigned to oxygen-atom transfer to the iron center to form a high-valent intermediate (2), ligand rearrangement of the metal complex, and, finally, decay to a diferric mu-oxo compound. Careful examination of the order of the reaction with MPPH reveals saturation behavior. This, coupled with the anomalous non-Arrhenius behavior of the first step of the reaction, indicates that there is a preequilibrium peroxide binding step prior to O-O bond cleavage. At higher temperatures, the addition of the base, proton sponge, results in a marked decrease in the rate of O-O bond cleavage to form 2; this is assigned as a peroxide deprotonation effect, indicating that the presence of protons is an important factor in the heterolytic cleavage of peroxide. This phenomenon has been observed in other iron-containing enzymes, the catalytic cycles of which include peroxide O-O bond cleavage. PMID:18680115

  3. FTIR/TDS studies of reaction paths and surface intermediates following multilayer adsorption of formamide on Ni(111)

    SciTech Connect

    Gao, Quanyin; Hemminger, J.C. ); Erley, W.; Sander, D.; Ibach, H. )

    1991-01-10

    The adsorption and reaction of HCONH{sub 2} and HCOND{sub 2} molecules on Ni(111) were studied following initial multilayer exposures with thermal desorption spectroscopy (TDS) and reflection absorption infrared spectroscopy (RAIR). At 90 K, formamide molecules (HCONH{sub 2}) adsorb on Ni(111) forming multilayers. Three molecular desorption peaks were observed at 160, 170, and 190 K, respectively. Heating this system to above 220 K leads to the decomposition of formamide molecules. Two parallel decomposition paths were observed. One path leads to the production of NH{sub 3}, H{sub 2}, and CO. The other path, which is first reported here, gives HNCO and H{sub 2}. Possible surface precursors for the two decomposition paths are discussed. The temperature-dependent RAIR spectra indicated that ammonia (NH{sub 3(a)}) was formed at about 230 K, isocyanic acid (HNCO{sub (a)}) at about 285 K, and CO at about 285 K. The observed desorption temperature from TDS are 260 K for ammonia (NH{sub 3}) 325 K for isocyanic acid (HNCO), 340 K for hydrogen (H{sub 2}), and 410 K for carbon monoxide (CO). The competing route for formamide decomposition that leads to HNCO production on Ni(111) has not been reported on other transition-metal substrates.

  4. Brominated lipids identify lipid binding sites on the surface of the reaction center from Rhodobacter sphaeroides.

    PubMed

    Roszak, Aleksander W; Gardiner, Alastair T; Isaacs, Neil W; Cogdell, Richard J

    2007-03-20

    This study describes the use of brominated phospholipids to distinguish between lipid and detergent binding sites on the surface of a typical alpha-helical membrane protein. Reaction centers isolated from Rhodobacter sphaeroides were cocrystallized with added brominated phospholipids. X-ray structural analysis of these crystals has revealed the presence of two lipid binding sites from the characteristic strong X-ray scattering from the bromine atoms. These results demonstrate the usefulness of this approach to mapping lipid binding sites at the surface of membrane proteins.

  5. Utilization of Microwave Spectroscopy to Identify and Probe Reaction Dynamics of Hsno, a Crucial Biological Signaling Molecule

    NASA Astrophysics Data System (ADS)

    Nava, Matthew; Martin-Drumel, Marie-Aline; Stanton, John F.; Cummins, Christopher; McCarthy, Michael C.

    2016-06-01

    Thionitrous acid (HSNO), a potential key intermediate in biological signaling pathways, has been proposed to link NO and H2S biochemistries. Its existence and stability in vivo, however, remain controversial. By means of Fourier-transform microwave spectroscopy, we establish that HSNO is spontaneously formed in high concentration when NO and H2S gases are simply mixed at room temperature in the presence of metallic surfaces. Our measurements reveal that HSNO is formed with high efficiency by the reaction H2S and N2O3 to produce HSNO and HNO2, where N2O3 is a product of NO disproportionation. These studies also suggest that further reaction of HSNO with H2S may form HNO and HSSH. The length of the S--N bond has been derived to high precision from isotopic studies, and is found to be unusually long, 1.84 Å -- the longest S--N bond reported to date for an SNO compound. The present structural and reactivity investigations of this elusive molecule provide a firm fundation to better understand its physiological chemistry and propensity to undergo S--N bond homolysis in vivo.

  6. Characterization of Metastable Intermediates Formed in the Reaction Between a Mn(II) Complex and Dioxygen, Including a Crystallographic Structure of a Binuclear Mn(III)-Peroxo Species

    PubMed Central

    Coggins, Michael K.; Sun, Xianru; Kwak, Yeonju; Solomon, Edward I.; Rybak-Akimova, Elena; Kovacs, Julie A.

    2013-01-01

    Transition-metal peroxos have been implicated as key intermediates in a variety of critical biological processes involving O2. Due to their highly reactive nature, very few metal-peroxos have been characterized. The dioxygen chemistry of manganese remains largely unexplored despite the proposed involvement of a binuclear Mn-peroxo, either as a precursor to O2, or derived from O2, in both photosynthetic H2O oxidation and DNA biosynthesis, arguably two of the most fundamental processes of life. Neither of these biological intermediates has been observed. Herein we describe the dioxygen chemistry of coordinatively unsaturated [MnII(SMe2N4(6-MeDPEN))] +(1), and the characterization of intermediates formed en route to a binuclear mono-oxo bridged Mn(III) product {[MnIII(SMe2N4(6-MeDPEN)]2-(μ-O)}2+ (2), the oxo atom of which is derived from 18O2. At low-temperatures, a dioxygen intermediate, [Mn(SMe2N4(6-MeDPEN))(O2)]+ (4), is observed (by stopped-flow) to rapidly and irreversibly form in this reaction (k1(−10 °C)= 3780±180M−1s−1, ΔH1‡ = 26.4±1.7 kJ mol−1, ΔS1‡ = − 75.6±6.8 J mol−1K−1), and then convert more slowly (k2(−10 °C)= 417±3.2 M−1s−1, ΔH2‡ = 47.1±1.4 kJ mol−1, ΔS2‡ = − 15.0±5.7 J mol−1K−1) to a species 3 with isotopically sensitive stretches at νo-o (Δ18O) = 819(47) cm−1, kO–O= 3.02 mdyn/Å, and νMn-O(Δ18O) = 611(25) cm−1 consistent with a peroxo. Intermediate 3 releases approximately 0.5 equiv of H2O2 per Mn ion upon protonation, and the rate of conversion of 4 to 3 is dependent on [Mn(II)] concentration, consistent with the formation of a binuclear Mn-peroxo. This was verified by X-ray crystallography, where the peroxo of {[MnIII(SMe2N4(6-Me-DPEN)]2(trans–μ–1,2–O2)}2+ (3) is shown to be bridging between two Mn(III) ions in an end-on trans-μ-1,2-fashion. This represents the first characterized example of a binuclear Mn(III)-peroxo, and a rare case in which more than one intermediate is observed

  7. Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction.

    PubMed

    Hoerndli, Frédéric J; Toigo, Marco; Schild, Andreas; Götz, Jürgen; Day, Philip J

    2004-12-01

    Transcriptomic methods are widely used as an initial approach to gain a mechanistic insight into physiological and pathological processes. Because differences in gene regulation to be assessed by RNA screening methods (e.g., SAGE, Affymetrix GeneChips) can be very subtle, these techniques require stable reference genes for accurate normalization. It is widely known that housekeeping genes, which are routinely used for normalization, can vary significantly depending on the tissue, and experimental test. In this study, we aimed at identifying stable reference genes for a fibrillar Abeta(42) peptide-treated, human tau-expressing SH-SY5Y neuroblastoma cell line derived to model aspects of Alzheimer's disease in tissue culture. We selected genes exhibiting potential normalization characteristics from public databases to create a custom-made microarray allowing the identification of reference genes for low, intermediate, and abundant mRNAs. A subset of these candidates was subjected to quantitative real-time polymerase chain reaction and was analyzed with geNorm software. By doing so, we were able to identify GAPD, M-RIP, and POLR2F as stable and usable reference genes irrespective of differentiation status and Abeta(42) treatment. PMID:15519568

  8. Students' Understanding on Newton's Third Law in Identifying the Reaction Force in Gravity Interactions

    ERIC Educational Resources Information Center

    Zhou, Shaona; Zhang, Chunbin; Xiao, Hua

    2015-01-01

    In the past three decades, previous researches showed that students had various misconceptions of Newton's Third Law. The present study focused on students' difficulties in identifying the third-law force pair in gravity interaction situations. An instrument involving contexts with gravity and non-gravity associated interactions was designed and…

  9. Intramolecular charge transfer of 4-(dimethylamino)benzonitrile probed by time-resolved fluorescence and transient absorption: No evidence for two ICT states and a pisigma( *) reaction intermediate.

    PubMed

    Zachariasse, Klaas A; Druzhinin, Sergey I; Kovalenko, Sergey A; Senyushkina, Tamara

    2009-12-14

    For the double exponential fluorescence decays of the locally excited (LE) and intramolecular charge transfer (ICT) states of 4-(dimethylamino)benzonitrile (DMABN) in acetonitrile (MeCN) the same times tau(1) and tau(2) are observed. This means that the reversible LE<==>ICT reaction, starting from the initially excited LE state, can be adequately described by a two state mechanism. The most important factor responsible for the sometimes experimentally observed differences in the nanosecond decay time, with tau(1)(LE)intermediate in the ICT reaction of DMABN are discussed. From the appearance of an excited state absorption (ESA) band in the spectral region between 700 and 800 nm in MeCN for N,N-dimethylanilines with CN, Br, F, CF(3), and C(=O)OC(2)H(2) p-substituents, it is concluded that this ESA band cannot be attributed to a pisigma( *) state, as only the C-C[Triple Bond]N group can undergo the required 120 degrees bending. PMID:20001042

  10. Physicochemical Changes and Glycation Reaction in Intermediate-Moisture Protein-Sugar Foods with and without Addition of Resveratrol during Storage.

    PubMed

    Sheng, Zhanwu; Gu, Mantun; Hao, Wangjun; Shen, Yixiao; Zhang, Weimin; Zheng, Lili; Ai, Binling; Zheng, Xiaoyan; Xu, Zhimin

    2016-06-22

    An intermediate-moisture food (IMF) model consisting of whey protein isolate and glucose and an IMF model fortified with resveratrol were used to study the effect of resveratrol on physicochemical changes and glycation of protein-sugar-rich foods during storage. The water activity (aw) of the storage was controlled at 0.75 or 0.56. The browning rate or hardness of fortified IMFs was significantly lower than that of IMFs after 45-day storage. The rate of Maillard reaction in the samples stored at aw 0.56 was higher than that of samples stored at aw 0.75. The fortified IMFs had lower levels of AGEs (advanced glycation end products), CML (N(ε)-(carboxymethyl)-l-lysine), and insoluble protein during storage. The inhibition capability of resveratrol against glycation was also confirmed by using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), liquid chromatography mass spectrometry (LC-MS), and Fourier transform infrared spectroscopy (FTIR) analysis to monitor glycated proteins and protein aggregation in the samples. The results of this study suggested that resveratrol could be used as an inhibitor to reduce the formation of undesirable AGEs and other Maillard reaction products in foods during storage. PMID:27218138

  11. Reaction pathways of 2-iodoacetic acid on Cu(100): coverage-dependent competition between C-I bond scission and COOH deprotonation and identification of surface intermediates.

    PubMed

    Lin, Yi-Shiue; Lin, Jain-Shiun; Liao, Yung-Hsuan; Yang, Che-Ming; Kuo, Che-Wei; Lin, Hong-Ping; Fan, Liang-Jen; Yang, Yaw-Wen; Lin, Jong-Liang

    2010-06-01

    The chemistry of 2-iodoacetic acid on Cu(100) has been studied by a combination of reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), temperature-programmed reaction/desorption (TPR/D), and theoretical calculations based on density functional theory for the optimized intermediate structures. In the thermal decomposition of ICH(2)COOH on Cu(100) with a coverage less than a half monolayer, three surface intermediates, CH(2)COO, CH(3)COO, and CCOH, are generated and characterized spectroscopically. Based on their different thermal stabilities, the reaction pathways of ICH(2)COOH on Cu(100) at temperatures higher than 230 K are established to be ICH(2)COOH --> CH(2)COO + H + I, CH(2)COO + H --> CH(3)COO, and CH(3)COO --> CCOH. Theoretical calculations suggest that the surface CH(2)COO has the skeletal plane, with delocalized pi electrons, approximately parallel to the surface. The calculated Mulliken charges agree with the detected binding energies for the two carbon atoms in CH(2)COO on Cu(100). The CCOH derived from CH(3)COO decomposition has a CC stretching frequency at 2025 cm(-1), reflecting its triple-bond character which is consistent with the calculated CCOH structure on Cu(100). Theoretically, CCOH at the bridge and hollow sites has a similar stability and is adsorbed with the molecular axis approximately perpendicular to the surface. The TPR/D study has shown the evolution of the products of H(2), CH(4), H(2)O, CO, CO(2), CH(2)CO, and CH(3)COOH from CH(3)COO decomposition between 500 and 600 K and the formation of H(2) and CO from CCOH between 600 and 700 K. However, at a coverage near one monolayer, the major species formed at 230 and 320 K are proposed to be ICH(2)COO and CH(3)COO. CH(3)COO becomes the only species present on the surface at 400 K. That is, there are two reaction pathways of ICH(2)COOH --> ICH(2)COO + H and ICH(2)COO + H --> CH(3)COO + I (possibly via CH(2)COO), which are different from those

  12. Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms.

    PubMed

    Boland, Mary Regina; Jacunski, Alexandra; Lorberbaum, Tal; Romano, Joseph D; Moskovitch, Robert; Tatonetti, Nicholas P

    2016-01-01

    Small molecules are indispensable to modern medical therapy. However, their use may lead to unintended, negative medical outcomes commonly referred to as adverse drug reactions (ADRs). These effects vary widely in mechanism, severity, and populations affected, making ADR prediction and identification important public health concerns. Current methods rely on clinical trials and postmarket surveillance programs to find novel ADRs; however, clinical trials are limited by small sample size, whereas postmarket surveillance methods may be biased and inherently leave patients at risk until sufficient clinical evidence has been gathered. Systems pharmacology, an emerging interdisciplinary field combining network and chemical biology, provides important tools to uncover and understand ADRs and may mitigate the drawbacks of traditional methods. In particular, network analysis allows researchers to integrate heterogeneous data sources and quantify the interactions between biological and chemical entities. Recent work in this area has combined chemical, biological, and large-scale observational health data to predict ADRs in both individual patients and global populations. In this review, we explore the rapid expansion of systems pharmacology in the study of ADRs. We enumerate the existing methods and strategies and illustrate progress in the field with a model framework that incorporates crucial data elements, such as diet and comorbidities, known to modulate ADR risk. Using this framework, we highlight avenues of research that may currently be underexplored, representing opportunities for future work.

  13. Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

    DOEpatents

    Holzrichter, John F.; Siekhaus, Wigbert J.

    1997-01-01

    A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule.

  14. Method for identifying biochemical and chemical reactions and micromechanical processes using nanomechanical and electronic signal identification

    DOEpatents

    Holzrichter, J.F.; Siekhaus, W.J.

    1997-04-15

    A scanning probe microscope, such as an atomic force microscope (AFM) or a scanning tunneling microscope (STM), is operated in a stationary mode on a site where an activity of interest occurs to measure and identify characteristic time-varying micromotions caused by biological, chemical, mechanical, electrical, optical, or physical processes. The tip and cantilever assembly of an AFM is used as a micromechanical detector of characteristic micromotions transmitted either directly by a site of interest or indirectly through the surrounding medium. Alternatively, the exponential dependence of the tunneling current on the size of the gap in the STM is used to detect micromechanical movement. The stationary mode of operation can be used to observe dynamic biological processes in real time and in a natural environment, such as polymerase processing of DNA for determining the sequence of a DNA molecule. 6 figs.

  15. Wildtype and engineered monomeric triosephosphate isomerase from Trypanosoma brucei: partitioning of reaction intermediates in D2O and activation by phosphite dianion.

    PubMed

    Malabanan, M Merced; Go, Maybelle K; Amyes, Tina L; Richard, John P

    2011-06-28

    Product yields for the reactions of (R)-glyceraldehyde 3-phosphate (GAP) in D2O at pD 7.9 catalyzed by wildtype triosephosphate isomerase from Trypanosoma brucei brucei (Tbb TIM) and a monomeric variant (monoTIM) of this wildtype enzyme were determined by (1)H NMR spectroscopy and were compared with the yields determined in earlier work for the reactions catalyzed by TIM from rabbit and chicken muscle [O'Donoghue, A. C., Amyes, T. L., and Richard, J. P. (2005), Biochemistry 44, 2610 - 2621]. Three products were observed from the reactions catalyzed by TIM: dihydroxyacetone phosphate (DHAP) from isomerization with intramolecular transfer of hydrogen, d-DHAP from isomerization with incorporation of deuterium from D2O into C-1 of DHAP, and d-GAP from incorporation of deuterium from D2O into C-2 of GAP. The yield of DHAP formed by intramolecular transfer of hydrogen decreases from 49% for the muscle enzymes to 40% for wildtype Tbb TIM to 34% for monoTIM. There is no significant difference in the ratio of the yields of d-DHAP and d-GAP for wildtype TIM from muscle sources and Trypanosoma brucei brucei, but partitioning of the enediolate intermediate of the monoTIM reaction to form d-DHAP is less favorable ((k(C1))(D)/(k(C2))(D) = 1.1) than for the wildtype enzyme ((k(C1))(D)/(k(C2))(D) = 1.7). Product yields for the wildtype Tbb TIM and monoTIM-catalyzed reactions of glycolaldehyde labeled with carbon-13 at the carbonyl carbon ([1-(13)C]-GA) at pD 7.0 in the presence of phosphite dianion and in its absence were determined by (1)H NMR spectroscopy [Go, M. K., Amyes, T. L., and Richard, J. P. (2009) Biochemistry 48, 5769-5778]. There is no detectable difference in the yields of the products of wildtype muscle and Tbb TIM-catalyzed reactions of [1-(13)C]-GA in D2O. The kinetic parameters for phosphite dianion activation of the reactions of [1-(13)C]-GA catalyzed by wildtype Tbb TIM are similar to those reported for the enzyme from rabbit muscle [Amyes, T. L. and Richard, J

  16. Toward understanding the dissociation of weak acids in water: 1. Using ir spectroscopy to identify proton-shared hydrogen-bonded ion-pair intermediates.

    PubMed

    Thomas, Vibin; Iftimie, Radu

    2009-04-01

    Cryogenic conditions favor the formation of ion-pair dissociation intermediates in amorphous mixtures of HF and H(2)O, making possible their characterization by means of infrared spectroscopy. The experimental infrared spectra show a structurally rich "continuous" absorption ranging from 1000 to 3400 cm(-1), which, in principle, contains important information regarding the microscopic structure of the aforementioned dissociation intermediates. Herein, we demonstrate that this microscopic information can be extracted by comparing and contrasting experimental spectra with those obtained by means of carefully designed first-principles molecular dynamics calculations. Very good, systematic agreement between theoretical and experimental spectra can be obtained for HF/H(2)O mixtures of various compositions, revealing the presence of proton-shared, dissociation intermediates F(delta-) * * * H * * * (delta+)OH(2). The existence of similar proton-shared, hydrogen-bonded intermediates of ionization, that are stable in solution, but not in the gas phase, has been previously suggested by other groups, using, among other techniques, low temperature NMR data and aprotic, dipolar, solvents. Our investigation reveals that similar structures are also stable in aqueous solutions of HF. We discuss some of the implications of the present findings as far as the mechanism of dissociation of weak acids is concerned.

  17. Imino-Oxy Acetic Acid Dealkylation as Evidence for an Inner-Sphere Alcohol Intermediate in the Reaction Catalyzed by Peptidylglycine α-Hydroxylating Monooxygenase (PHM)

    PubMed Central

    McIntyre, Neil R.; Lowe, Edward W.; Merkler, David J.

    2009-01-01

    Peptidylglycine α-hydroxylating monooxygenase (PHM, EC 1.14.17.3) catalyzes the stereospecific hydroxylation of a glycyl α-carbon in a reaction that requires O2 and ascorbate. Subsequent dealkylation of the α-hydroxyglycine by another enzyme, peptidylamidoglycolate lyase (PAL. EC 4.3.2.5), yields a bioactive amide and glyoxylate. PHM is a non-coupled, type II dicopper monooxygenase which activates O2 at only a single copper atom, CuM. In this study, the PHM mechanism was probed using a non-natural substrate, benzaldehyde imino-oxy acetic acid (BIAA). PHM catalyzes the O-oxidative dealkylation of BIAA to benzaldoxime and glyoxylate with no involvement of PAL. The minimal kinetic mechanism for BIAA was shown to be steady-state ordered using primary deuterium kinetic isotope effects. The D(V/K)APPARENT, BIAA decreased from 14.7 ± 1.0 as [O2] → 0 to 1.0 ± 0.2 as [O2] → ∞ suggesting the dissociation rate constant from the PHM·BIAA complex decreases as [O2] increases; thereby, reducing the steady-state concentration of [PHM]free. BIAA was further used to differentiate between potential oxidative Cu/O species using a QM/MM reaction coordinate simulation to determine which species could yield product O-dealkylation that matched our experimental data. The results of this study provided compelling evidence for the presence of a covalently linked CuII-alkoxide intermediate with a quartet spin state responsible BIAA oxidation. PMID:19569683

  18. [Intermediate phenotype of schizophrenia].

    PubMed

    Hashimoto, Ryota

    2013-04-01

    Genes are major contributors to schizophrenia. The intermediate phenotype concept represents a strategy for identifying risk genes for schizophrenia and for characterizing the neural systems affected by risk gene variants to elucidate quantitative, mechanistic aspects of brain function implicated in schizophrenia. Intermediate phenotypes are defined by being heritable, being able to measure quantitatively; being related to the disorder and its symptoms in the general population; being stable over time; showing increased expression in unaffected relatives of probands; and cosegregation with the disorder in families. Intermediate phenotypes in schizophrenia are neurocognition, neuroimaging, neurophysiology, etc. In this review, we present concept, recent work, and future perspective of intermediate phenotype.

  19. Hydride, hydrogen, proton, and electron affinities of imines and their reaction intermediates in acetonitrile and construction of thermodynamic characteristic graphs (TCGs) of imines as a "molecule ID card".

    PubMed

    Zhu, Xiao-Qing; Liu, Qiao-Yun; Chen, Qiang; Mei, Lian-Rui

    2010-02-01

    A series of 61 imines with various typical structures were synthesized, and the thermodynamic affinities (defined as enthalpy changes or redox potentials in this work) of the imines to abstract hydride anions, hydrogen atoms, and electrons, the thermodynamic affinities of the radical anions of the imines to abstract hydrogen atoms and protons, and the thermodynamic affinities of the hydrogen adducts of the imines to abstract electrons in acetonitrile were determined by using titration calorimetry and electrochemical methods. The pure heterolytic and homolytic dissociation energies of the C=N pi-bond in the imines were estimated. The polarity of the C=N double bond in the imines was examined using a linear free-energy relationship. The idea of a thermodynamic characteristic graph (TCG) of imines as an efficient "Molecule ID Card" was introduced. The TCG can be used to quantitatively diagnose and predict the characteristic chemical properties of imines and their various reaction intermediates as well as the reduction mechanism of the imines. The information disclosed in this work could not only supply a gap of thermodynamics for the chemistry of imines but also strongly promote the fast development of the applications of imines.

  20. Ab initio study of hypervalent sulfur hydrides as model intermediates in the interconversion reactions of compounds containing sulfur-sulfur bonds

    SciTech Connect

    Laitinen, R.S.; Pakkanen, T.A.; Steudel, R.

    1987-02-04

    Ab initio MO calculations involving the 4-31G* basis set have been used to predict the equilibrium geometries of the hypervalent sulfur hydrides H/sub 2/SS, (HS)/sub 2/SS, H/sub 2/S(SH)/sub 2/, H/sub 2/S(SSH)/sub 2/, and the cyclic H/sub 4/S/sub 4/. The energy changes in their formation from appropriate sulfanes H/sub 2/S/sub n/ (n = 1-4) have been studied with the 6-31G* basis set including the correction for the electron correlation by the second- and third-order Moeller-Plesset perturbation theory. The results are used to discuss the possible pathways in the interconversion reactions between various sulfur compounds containing cumulated SS bonds, for example, the formation of S/sub 7/ from S/sub 8/ for which hypervalent intermediates have been proposed recently. Comparison with experimental evidence is made whenever possible.

  1. The Validity of Claims-Based Algorithms to Identify Serious Hypersensitivity Reactions and Osteonecrosis of the Jaw.

    PubMed

    Wright, Nicole C; Curtis, Jeffrey R; Arora, Tarun; Smith, Wilson K; Kilgore, Meredith L; Saag, Kenneth G; Safford, Monika M; Delzell, Elizabeth S

    2015-01-01

    Validation of claims-based algorithms to identify serious hypersensitivity reactions and osteonecrosis of the jaw has not been performed in large osteoporosis populations. The objective of this project is to estimate the positive predictive value of the claims-based algorithms in older women with osteoporosis enrolled in Medicare. Using the 2006-2008 Medicare 5% sample data, we identified potential hypersensitivity and osteonecrosis of the jaw cases based on ICD-9 diagnosis codes. Potential hypersensitivity cases had a 995.0, 995.2, or 995.3 diagnosis code on emergency department or inpatient claims. Potential osteonecrosis of the jaw cases had ≥1 inpatient or outpatient physician claim with a 522.7, 526.4, 526.5, or 733.45 diagnosis code or ≥2 claims of any type with a 526.9 diagnosis code. All retrieved records were redacted and reviewed by experts to determine case status: confirmed, not confirmed, or insufficient information. We calculated the positive predictive value as the number of confirmed cases divided by the total number of retrieved records with sufficient information. We requested 412 potential hypersensitivity and 304 potential osteonecrosis of the jaw records and received 174 (42%) and 84 (28%) records respectively. Of 84 potential osteonecrosis of the jaw cases, 6 were confirmed, resulting in a positive predictive value (95% CI) of 7.1% (2.7, 14.9). Of 174 retrieved potential hypersensitivity records, 95 were confirmed. After exclusion of 25 records with insufficient information for case determination, the overall positive predictive value (95% CI) for hypersensitivity reactions was 76.0% (67.5, 83.2). In a random sample of Medicare data, a claim-based algorithm to identify serious hypersensitivity reactions performed well. An algorithm for osteonecrosis of the jaw did not, partly due to the inclusion of diagnosis codes that are not specific for osteoporosis of the jaw.

  2. Structure-reactivity relationships for beta-galactosidase (Escherichia coli, lac Z). 4. Mechanism for reaction of nucleophiles with the galactosyl-enzyme intermediates of E461G and E461Q beta-galactosidases.

    PubMed

    Richard, J P; Huber, R E; Heo, C; Amyes, T L; Lin, S

    1996-09-24

    Second-order rate constants for transfer of the beta-D-galactopyranosyl group from the galactosyl-enzyme intermediates of the galactosyl transfer reactions catalyzed by E461G and E461Q beta-galactosidases to anionic nucleophiles have been determined. The second-order rate constant for reaction of the galactosylated E461G enzyme with azide ion is 4900 M-1 s-1. By contrast, there is no detectable reaction of the galactosylated wild type enzyme with azide ion (Richard et al., 1995b), and the E461G mutation leads to a large decrease in the second-order rate constant kcat/Km for catalysis of cleavage of beta-D-galactopyranosyl azide, which is the microscopic reverse of the reaction of azide ion with the galactosyl-enzyme intermediate. These data show that the E461G mutation causes a more than 8000-fold increase in the equilibrium constant for transfer of the beta-D-galactopyranosyl group from beta-galactosidase to azide ion. We propose that this change represents the requirement for the coupling of galactosyl transfer from the native enzyme to the thermodynamically unfavorable protonation of the carboxylate group of Glu-461, but the expression of the full chemical affinity of azide ion for galactosyl transfer from the mutant enzyme which lacks this ionizable side chain at position 461. The reactions of acetate, butyrate and methoxyacetate ions with the galactosylated E461G enzyme and of acetate with the galactosylated E461Q enzyme give both the corresponding beta-galactopyranosyl derivatives and D-galactose, and the formation of the latter represents formal catalysis of the reaction of water with the galactosylated enzyme. However, the reaction of formate ion with the galactosylated E461G enzyme gives only D-galactose. These results suggest that carboxylate anions can take the place of the excised propionate side chain of Glu-461 to provide general base catalysis of the reaction of water with the galactosyl-enzyme intermediates. The relative reactivity of anionic

  3. Reaction of homopiperazine with endogenous formaldehyde: a carbon hydrogen addition metabolite/product identified in rat urine and blood.

    PubMed

    Martin, Scott; Lenz, Eva M; Temesi, Dave; Wild, Martin; Clench, Malcolm R

    2012-08-01

    Drug reactivity and bioactivation are of major concern to the development of potential drug candidates in the pharmaceutical industry (Chem Res Toxicol 17:3-16, 2004; Chem Res Toxicol 19:889-893, 2006). Identifying potentially problematic compounds as soon as possible in the discovery process is of great importance, so often early in vitro screening is used to speed up attrition. Identification of reactive moieties is relatively straightforward with appropriate in vitro trapping experiments; however, on occasion unexpected reactive intermediates can be found later during more detailed in vivo studies. Here, we present one such example involving a series of compounds from an early drug discovery campaign. These compounds were found to react with endogenous formaldehyde from a rat in vivo study, resulting in the formation of novel +13-Da bridged homopiperazine products (equivalent to the addition of one carbon and one hydrogen atom), which were detected in urine and blood. The identification of these +13-Da products and their origin and mechanism of formation are described in detail through analyses of a representative homopiperazine compound [N-(3-(3-fluorophenyl)-1,2,4-thiadiazol-5-yl)-4-(4-isopropyl-1,4-diaze-pane-2-carbonyl)piperazine-1-carboxamide (AZX)] by liquid chromatography-UV-mass spectrometry, (1)H NMR, and chemical tests. PMID:22550270

  4. Hydrogen storage in LiAlH4 : predictions of the crystal structures and reaction mechanisms of intermediate phases from quantum mechanics.

    SciTech Connect

    Lee, Jai Young; Muller, Richard Partain; Kang, Jeung Ku; Goddard, William A., III

    2005-06-01

    We use the density functional theory and x-ray and neutron diffraction to investigate the crystal structures and reaction mechanisms of intermediate phases likely to be involved in decomposition of the potential hydrogen storage material LiAlH{sub 4}. First, we explore the decomposition mechanism of monoclinic LiAlH4 into monoclinic Li{sub 3}AlH{sub 6} plus face-centered cubic (fcc) Al and hydrogen. We find that this reaction proceeds through a five-step mechanism with an overall activation barrier of 36.9 kcal/mol. The simulated x ray and neutron diffraction patterns from LiAlH{sub 4} and Li{sub 3}AlH{sub 6} agree well with experimental data. On the other hand, the alternative decomposition of LiAlH{sub 4} into LiAlH2 plus H2 is predicted to be unstable with respect to that through Li{sub 3}AlH{sub 6}. Next, we investigate thermal decomposition of Li{sub 3}AlH{sub 6} into fcc LiH plus Al and hydrogen, occurring through a four-step mechanism with an activation barrier of 17.4 kcal/mol for the rate-limiting step. In the first and second steps, two Li atoms accept two H atoms from AlH{sub 6} to form the stable Li-H-Li-H complex. Then, two sequential H2 desorption steps are followed, which eventually result in fcc LiH plus fcc Al and hydrogen: Li{sub 3}AlH{sub 6}(monoclinic) {yields} 3 LiH(fcc) + Al(fcc) + 3/2 H{sub 2} is endothermic by 15.8 kcal/mol. The dissociation energy of 15.8 kcal/mol per formula unit compares to experimental enthalpies in the range of 9.8-23.9 kcal/mol. Finally, we explore thermal decomposition of LiH, LiH(s) + Al(s) {yields} LiAl(s) + 1/2 H{sub 2}(g) is endothermic by 4.6 kcal/mol. The B32 phase, which we predict as the lowest energy structure for LiAl, shows covalent bond characters in the Al-Al direction. Additionally, we determine that transformation of LiH plus Al into LiAlH is unstable with respect to transformation of LiH through LiAl.

  5. Kinetics of stabilised Criegee intermediates derived from alkene ozonolysis: reactions with SO2, H2O and decomposition under boundary layer conditions.

    PubMed

    Newland, Mike J; Rickard, Andrew R; Alam, Mohammed S; Vereecken, Luc; Muñoz, Amalia; Ródenas, Milagros; Bloss, William J

    2015-02-14

    The removal of SO2 in the presence of alkene-ozone systems has been studied for ethene, cis-but-2-ene, trans-but-2-ene and 2,3-dimethyl-but-2-ene, as a function of humidity, under atmospheric boundary layer conditions. The SO2 removal displays a clear dependence on relative humidity for all four alkene-ozone systems confirming a significant reaction for stabilised Criegee intermediates (SCI) with H2O. The observed SO2 removal kinetics are consistent with relative rate constants, k(SCI + H2O)/k(SCI + SO2), of 3.3 (±1.1) × 10(-5) for CH2OO, 26 (±10) × 10(-5) for CH3CHOO derived from cis-but-2-ene, 33 (±10) × 10(-5) for CH3CHOO derived from trans-but-2-ene, and 8.7 (±2.5) × 10(-5) for (CH3)2COO derived from 2,3-dimethyl-but-2-ene. The relative rate constants for k(SCI decomposition)/k(SCI + SO2) are -2.3 (±3.5) × 10(11) cm(-3) for CH2OO, 13 (±43) × 10(11) cm(-3) for CH3CHOO derived from cis-but-2-ene, -14 (±31) × 10(11) cm(-3) for CH3CHOO derived from trans-but-2-ene and 63 (±14) × 10(11) cm(-3) for (CH3)2COO. Uncertainties are ±2σ and represent combined systematic and precision components. These values are derived following the approximation that a single SCI is present for each system; a more comprehensive interpretation, explicitly considering the differing reactivity for syn- and anti-SCI conformers, is also presented. This yields values of 3.5 (±3.1) × 10(-4) for k(SCI + H2O)/k(SCI + SO2) of anti-CH3CHOO and 1.2 (±1.1) × 10(13) for k(SCI decomposition)/k(SCI + SO2) of syn-CH3CHOO. The reaction of the water dimer with CH2OO is also considered, with a derived value for k(CH2OO + (H2O)2)/k(CH2OO + SO2) of 1.4 (±1.8) × 10(-2). The observed SO2 removal rate constants, which technically represent upper limits, are consistent with decomposition being a significant, structure dependent, sink in the atmosphere for syn-SCI.

  6. Kinetics of stabilised Criegee intermediates derived from alkene ozonolysis: reactions with SO2, H2O and decomposition under boundary layer conditions.

    PubMed

    Newland, Mike J; Rickard, Andrew R; Alam, Mohammed S; Vereecken, Luc; Muñoz, Amalia; Ródenas, Milagros; Bloss, William J

    2015-02-14

    The removal of SO2 in the presence of alkene-ozone systems has been studied for ethene, cis-but-2-ene, trans-but-2-ene and 2,3-dimethyl-but-2-ene, as a function of humidity, under atmospheric boundary layer conditions. The SO2 removal displays a clear dependence on relative humidity for all four alkene-ozone systems confirming a significant reaction for stabilised Criegee intermediates (SCI) with H2O. The observed SO2 removal kinetics are consistent with relative rate constants, k(SCI + H2O)/k(SCI + SO2), of 3.3 (±1.1) × 10(-5) for CH2OO, 26 (±10) × 10(-5) for CH3CHOO derived from cis-but-2-ene, 33 (±10) × 10(-5) for CH3CHOO derived from trans-but-2-ene, and 8.7 (±2.5) × 10(-5) for (CH3)2COO derived from 2,3-dimethyl-but-2-ene. The relative rate constants for k(SCI decomposition)/k(SCI + SO2) are -2.3 (±3.5) × 10(11) cm(-3) for CH2OO, 13 (±43) × 10(11) cm(-3) for CH3CHOO derived from cis-but-2-ene, -14 (±31) × 10(11) cm(-3) for CH3CHOO derived from trans-but-2-ene and 63 (±14) × 10(11) cm(-3) for (CH3)2COO. Uncertainties are ±2σ and represent combined systematic and precision components. These values are derived following the approximation that a single SCI is present for each system; a more comprehensive interpretation, explicitly considering the differing reactivity for syn- and anti-SCI conformers, is also presented. This yields values of 3.5 (±3.1) × 10(-4) for k(SCI + H2O)/k(SCI + SO2) of anti-CH3CHOO and 1.2 (±1.1) × 10(13) for k(SCI decomposition)/k(SCI + SO2) of syn-CH3CHOO. The reaction of the water dimer with CH2OO is also considered, with a derived value for k(CH2OO + (H2O)2)/k(CH2OO + SO2) of 1.4 (±1.8) × 10(-2). The observed SO2 removal rate constants, which technically represent upper limits, are consistent with decomposition being a significant, structure dependent, sink in the atmosphere for syn-SCI. PMID:25562069

  7. Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes generated furans appending reactive phosphorus ylides through cumulated trienoates as key intermediates: a phosphine α-addition-δ-evolvement of an anion pathway.

    PubMed

    Deng, Jie-Cheng; Chuang, Shih-Ching

    2014-11-01

    Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes have been demonstrated, providing trisubstituted furans appending reactive phosphorus ylides, through cumulated trienoates as key intermediates. The proposed trienoate intermediates, 1,5-dipolar species formed via nucleophilic α-attack of phosphines toward diynedioates (α-addition-δ-evolvement of an anion, abbreviated αAδE), undergo addition to aryl aldehydes followed by 5-endo-dig cyclization, proton transfer, and resonance to give trisubstituted furans. Furthermore, the phosphorus ylides are oxidized to α-keto ester furans and utilized as Wittig reagents.

  8. Perspective: Spectroscopy and kinetics of small gaseous Criegee intermediates

    SciTech Connect

    Lee, Yuan-Pern

    2015-07-14

    The Criegee intermediates, carbonyl oxides proposed by Criegee in 1949 as key intermediates in the ozonolysis of alkenes, play important roles in many aspects of atmospheric chemistry. Because direct detection of these gaseous intermediates was unavailable until recently, previous understanding of their reactions, derived from indirect experimental evidence, had great uncertainties. Recent laboratory detection of the simplest Criegee intermediate CH{sub 2}OO and some larger members, produced from ultraviolet irradiation of corresponding diiodoalkanes in O{sub 2}, with various methods such as photoionization, ultraviolet absorption, infrared absorption, and microwave spectroscopy opens a new door to improved understanding of the roles of these Criegee intermediates. Their structures and spectral parameters have been characterized; their significant zwitterionic nature is hence confirmed. CH{sub 2}OO, along with other products, has also been detected directly with microwave spectroscopy in gaseous ozonolysis reactions of ethene. The detailed kinetics of the source reaction, CH{sub 2}I + O{sub 2}, which is critical to laboratory studies of CH{sub 2}OO, are now understood satisfactorily. The kinetic investigations using direct detection identified some important atmospheric reactions, including reactions with NO{sub 2}, SO{sub 2}, water dimer, carboxylic acids, and carbonyl compounds. Efforts toward the characterization of larger Criegee intermediates and the investigation of related reactions are in progress. Some reactions of CH{sub 3}CHOO are found to depend on conformation. This perspective examines progress toward the direct spectral characterization of Criegee intermediates and investigations of the associated reaction kinetics, and indicates some unresolved problems and prospective challenges for this exciting field of research.

  9. Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions

    PubMed Central

    Luo, Heng; Du, Tingting; Zhou, Peng; Yang, Lun; Mei, Hu; Ng, Huiwen; Zhang, Wenqian; Shu, Mao; Tong, Weida; Shi, Leming; Mendrick, Donna L.; Hong, Huixiao

    2015-01-01

    Idiosyncratic drug reactions (IDRs) are rare, somewhat dose-independent, patient-specific and hard to predict. Human leukocyte antigens (HLAs) are the major histocompatibility complex (MHC) in humans, are highly polymorphic and are associated with specific IDRs. Therefore, it is important to identify potential drug-HLA associations so that individuals who would develop IDRs can be identified before drug exposure. We harvested the associations between drugs and class I HLAs from the literature. Molecular docking was used to explore the known associations. From the analysis of docking scores between the 17 drugs and 74 class I HLAs, it was observed that the significantly associated drug-HLA pairs had statistically lower docking scores than those not reported to be significantly associated (t-test p < 0.05). This indicates that molecular docking can be utilized for screening drug-HLA interactions and predicting potential IDRs. Examining the binding modes of drugs in the docked HLAs suggested several distinct binding sites inside class I HLAs, expanding our knowledge of the underlying interaction mechanisms between drugs and HLAs. PMID:25747444

  10. MCNP{trademark} simulations for identifying environmental contaminants using prompt gamma-rays from thermal neutron capture reactions

    SciTech Connect

    Frankle, S.C.; Conaway, J.G.

    1996-12-31

    The primary purposes of the Multispectral Neutron Logging Project, (MSN Project, funded by the U.S. Department of Energy), were to assess the effectiveness of existing neutron- induced spectral gamma-ray logging techniques for identifying environmental contaminants along boreholes, to further improve the technology, and to transfer that technology to industry. Using a pulsed neutron source with a high-resolution gamma-ray detector, spectra from thermal neutron capture reactions may be used to identify contaminants in the borehole environment. Direct borehole measurements such as this complement physical sampling and are useful in environmental restoration projects where characterization of contaminated sites is required and long-term monitoring may be needed for many years following cleanup or stabilization. In the MSN Project, a prototype logging instrument was designed which incorporated a pulsed 14-MeV neutron source and HPGe detector. Experimental measurements to determine minimum detection thresholds with the prototype instrument were conducted in the variable-contaminant test model for Cl, Cd, Sm, Gd, and Hg. We benchmarked an enhanced version of the Monte Carlo N-Particle computer code MCNP{trademark} using experimental data for Cl provide by our collaborators and experimental data from the variable-contaminant test model. MCNP was then used to estimate detection thresholds for the other contaminants used in the variable-contaminant model with the goal of validating the use of MCNP to estimate detection thresholds for many other contaminants that were not measured.

  11. Comment on “A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states” [J. Chem. Phys. 142, 124312 (2015)

    SciTech Connect

    Harding, Lawrence B.; Klippenstein, Stephen J.

    2015-10-28

    We discuss the recent report of a roaming type mechanism for the decomposition of the Criegee intermediate. We show that the predicted barrier height for this new pathway is too low by ∼30 kcal/mol owing to an inconsistent use of spin-restricted and spin-unrestricted calculations. As a result, this new pathway is not expected to compete significantly with the well-known dioxirane pathways for the decomposition of the Criegee intermediate.

  12. Comment on "A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states" [J. Chem. Phys. 142, 124312 (2015)].

    PubMed

    Harding, Lawrence B; Klippenstein, Stephen J

    2015-10-28

    We discuss the recent report of a roaming type mechanism for the decomposition of the Criegee intermediate. We show that the predicted barrier height for this new pathway is too low by ∼30 kcal/mol owing to an inconsistent use of spin-restricted and spin-unrestricted calculations. As a result, this new pathway is not expected to compete significantly with the well-known dioxirane pathways for the decomposition of the Criegee intermediate.

  13. Role of the reaction intermediates in determining PHIP (parahydrogen induced polarization) effect in the hydrogenation of acetylene dicarboxylic acid with the complex [Rh (dppb)]{sup +} (dppb: 1,4-bis(diphenylphosphino)butane)

    SciTech Connect

    Reineri, F.; Aime, S.; Gobetto, R.; Nervi, C.

    2014-03-07

    This study deals with the parahydrogenation of the symmetric substrate acetylene dicarboxylic acid catalyzed by a Rh(I) complex bearing the chelating diphosphine dppb (1,4-bis(diphenylphosphino)butane). The two magnetically equivalent protons of the product yield a hyperpolarized emission signal in the {sup 1}H-NMR spectrum. Their polarization intensity varies upon changing the reaction solvent from methanol to acetone. A detailed analysis of the hydrogenation pathway is carried out by means of density functional theory calculations to assess the structure of hydrogenation intermediates and their stability in the two solvents. The observed polarization effects have been accounted on the basis of the obtained structures. Insights into the lifetime of a short-lived reaction intermediate are also obtained.

  14. Pathways of the North Pacific Intermediate Water identified through the tangent linear and adjoint models of an ocean general circulation model

    NASA Astrophysics Data System (ADS)

    Fujii, Y.; Nakano, T.; Usui, N.; Matsumoto, S.; Tsujino, H.; Kamachi, M.

    2014-12-01

    This study develops a strategy for tracing a target water mass, and applies it to analyzing the pathway of the North Pacific Intermediate Water (NPIW) from the subarctic gyre to the northwestern part of the subtropical gyre south of Japan in a simulation of an ocean general circulation model. This strategy estimates the pathway of the water mass that travels from an origin to a destination area during a specific period using a conservation property concerning tangent linear and adjoint models. In our analysis, a large fraction of the low salinity origin water mass of NPIW initially comes from the Okhotsk or Bering Sea, flows through the southeastern side of the Kuril Islands, and is advected to the Mixed Water Region (MWR) by the Oyashio current. It then enters the Kuroshio Extension (KE) at the first KE ridge, and is advected eastward by the KE current. However, it deviates southward from the KE axis around 158°E over the Shatsky Rise, or around 170ºE on the western side of the Emperor Seamount Chain, and enters the subtropical gyre. It is finally transported westward by the recirculation flow. This pathway corresponds well to the shortcut route of NPIW from MWR to the region south of Japan inferred from analysis of the long-term freshening trend of NPIW observation.

  15. The ability of intermediate-band Strömgren photometry to correctly identify dwarf, subgiant, and giant stars and provide stellar metallicities and surface gravities

    NASA Astrophysics Data System (ADS)

    Árnadóttir, A. S.; Feltzing, S.; Lundström, I.

    2010-10-01

    .40 < (b-y)0 < 0.95 and 1.10 < (v-y)0 < 2.38. Conclusions: We recommend the calibrations of Ramírez & Meléndez (2005) in deriving metallicities from Strömgren photometry and find that intermediate band photometry, such as Strömgren photometry, more accurately than broad band photometry reproduces spectroscopically determined [Fe/H]. Strömgren photometry is also better at differentiating between dwarf and giant stars. We conclude that additional investigations of the differences between metallicities derived from ugriz photometry and intermediate-band photometry, such as Strömgren photometry, are required. Appendix A is only available in electronic form at http://www.aanda.org, Appendix B is available in electronic form at http://www.aanda.org and at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/521/A40

  16. Bacterial contamination of blood components: Norwegian strategies in identifying donors with higher risk of inducing septic transfusion reactions in recipients.

    PubMed

    Klausen, Sofie Strand; Hervig, Tor; Seghatchian, Jerard; Reikvam, Håkon

    2014-10-01

    Bacterial contamination of blood and its cellular components remains the most common microbiological cause of transfusion associated morbidity and mortality, even in developed countries. This yet unresolved complication is seen more often in platelet transfusions, as platelet concentrates are stored at room temperature, in gas permeable containers with constant agitation, which support bacterial proliferation from relatively low undetectable levels, at the beginning of storage time, to relatively high virulent bacteria titers and endotoxin generation, at the end of shelf life. Accordingly, several combined strategies are introduced and implemented to at least reduce the potential risk of bacterial contaminated products for transfusion. These embody: improved donors arms cleaning; bacterial avoidance by diversion of the first portion of collection; reducing bacterial growth through development of newer storage media for longer platelet shelf life; bacterial load reduction by leucoreduction/viral inactivation, in some countries and eliminating the use potentially contaminated units through screening, through current available testing procedures, though none are not yet fully secure. We have not seen the same reduction in bacterial associated transfusion infections as we have observed for the sharp drop in transfusion associated transmission rates of HIV and hepatitis B and C. This great viral reduction is not only caused by the introduction of newer and more sensitive and specific detection methods for different viruses, but also the identification of donor risk groups through questionnaires and personal interviews. While search for more efficient methods for identifying potential blood donors with asymptomatic bacteremia, as well as a better way for detecting bacteria in stored blood components will be continuing, it is necessary to establish more standardized guidelines for the recognition the adverse reactions in recipients of potentially contaminated units

  17. New mechanistic insight into the oxygen reduction reaction on Ruddlesden-Popper cathodes for intermediate-temperature solid oxide fuel cells.

    PubMed

    Li, Wenyuan; Guan, Bo; Zhang, Xinxin; Yan, Jianhua; Zhou, Yue; Liu, Xingbo

    2016-03-28

    Ruddlesden-Popper (R-P) phase materials have been investigated widely as cathode candidates for IT-SOFCs. However, widespread application of R-P phase cathodes demands further improvement in electrode activity whose progress is hindered by the limited information in the oxygen reduction reaction (ORR). The ORR mechanism for the R-P phase is therefore investigated in this paper using (LaSr)2NiO(4±δ) as an example. Accurate characterization of the surface oxygen exchange process is realized by developing thin and dense polycrystalline LSNO layers via a versatile spray-modified pressing method we invented before to avoid perceptible bulk diffusion contribution, surface enrichment and geometry complication. The governing factors of the ORR are identified as oxygen adsorption and incorporation based on the findings in reaction orders from electrochemical impedance spectroscopy (EIS), stoichiometry-related chemical capacitance and intrinsic anisotropic properties. The incorporation rate is proven to drastically depend on the amount of interstitial oxygen (O(i)"). Since the unfilled interstitial sites(V(i)(×)) in the R-P phase serve to accommodate the adsorbed oxygen during incorporation, like vacancies in the perovskite structure (V(O)(••)), more O(i)" would seem to suppress the kinetics of this process. In regards to this, for the first time, a physical model is proposed to reconcile the discrepancy between the experimental results and intuitive reasoning. Based on supporting evidence, this model illustrates a possibility of how O(i)" works to regulate the exchange rate, and how the contradiction between V(O)(••) and O(i)" is harmonized so that the latter in the R-P structure also positively promotes the incorporation rate in the ORR.

  18. A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

    PubMed

    Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

    2006-06-01

    The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important. PMID:16531404

  19. Electrospray ionization mass spectrometric investigations of [alpha]-dicarbonyl compounds--Probing intermediates formed in the course of the nonenzymatic browning reaction of l-ascorbic acid

    NASA Astrophysics Data System (ADS)

    Schulz, Anke; Trage, Claudia; Schwarz, Helmut; Kroh, Lothar W.

    2007-05-01

    A new method is presented which allows the simultaneous detection of various [alpha]-dicarbonyl compounds generated in the course of the nonenzymatic browning reaction initiated by thermal treatment of l-ascorbic acid, namely: glyoxal, methylglyoxal, diacetyl, 3-deoxy-l-pentosone, and l-threosoneE 3-Deoxy-l-threosone was successfully identified as a new C4-[alpha]-dicarbonyl structure for the first time in the degradation of Vitamin C by application of this non-chromatographic mass spectrometric approach. Moreover, a more detailed elucidation of the mechanistic scenario with respect to the oxidative and nonoxidative pathways is presented by using dehydro-l-ascorbic acid and 2,3-diketo-l-gulonic acid instead of l-ascorbic acid as a starting material. Furthermore, the postulated pathways are corroborated with the aid of 13C-isotopic labeling studies. The investigations were extended to baby food, and the successful detection of [alpha]-dicarbonyl compounds characteristic for Vitamin C degradation proved the matrix tolerance of the introduced method.

  20. The synthesis, testing and use of 5-fluoro-alpha-D-galactosyl fluoride to trap an intermediate on green coffee bean alpha-galactosidase and identify the catalytic nucleophile.

    PubMed

    Ly, H D; Howard, S; Shum, K; He, S; Zhu, A; Withers, S G

    2000-11-17

    5-Fluoro-alpha-D-galactopyranosyl fluoride was synthesized and its interaction with the active site of an alpha-galactosidase from green coffee bean (Coffea arabica), a retaining glycosidase, characterized kinetically and structurally. The compound behaves as an apparently tight binding (Ki = 600 nM) competitive inhibitor, achieving this high affinity through reaction as a slow substrate that accumulates a high steady-state concentration of the glycosyl-enzyme intermediate, as evidenced by ESiMS. Proteolysis of the trapped enzyme coupled with HPLC/MS analysis allowed the localization of a labeled peptide that was subsequently sequenced. Comparison of this sequence information to that of other members of the same glycosidase family revealed the active site nucleophile to be Asp145 within the sequence LKYDNCNNN. The importance of this residue to catalysis has been confirmed by mutagenesis studies.

  1. An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core.

    PubMed

    Park, S H; O'Neil, K T; Roder, H

    1997-11-25

    The folding kinetics of a 57-residue IgG binding domain of streptococcal protein G has been studied under varying solvent conditions, using stopped-flow fluorescence methods. Although GB1 has been cited as an example of a protein that obeys a two-state folding mechanism, the following kinetic observations suggest the presence of an early folding intermediate. Under stabilizing conditions (low denaturant concentrations, especially in the presence of sodium sulfate), the kinetics of folding shows evidence of a major unresolved fluorescence change during the 1.5 ms dead time of the stopped-flow experiment (burst phase). Together with some curvature in the rate profile for the single observable folding phase, this provides clear evidence of the rapid formation of compact states with native-like fluorescence for the single tryptophan at position 43. In refolding experiments at increasing denaturant concentrations, the amplitude of the sub-millisecond phase decreases sharply and the corresponding slope (m value) is only about 30% lower than that of the equilibrium unfolding curve indicative of a pre-equilibrium transition involving cooperative unfolding of an ensemble of compact intermediates. The dependence on guanidine hydrochloride concentration of both rates and amplitudes (including the equilibrium transition) is described quantitatively by a sequential three-state mechanism, U [symbol: see text] I [symbol: see text] N, where an intermediate (I) in rapid equilibrium with the unfolded state (U) precedes the rate-limiting formation of the native state (N). A 66-residue fragment of GB1 with an N-terminal extension containing five apolar side chains exhibits three-state kinetic behavior virtually identical to that of the 57-residue fragment. This is consistent with the presence of a well-shielded native-like core excluding the N-terminal tail in the early folding intermediate and argues against a mechanism involving random hydrophobic collapse, which would predict a

  2. Sterol biosynthesis: strong inhibition of maize delta 5,7-sterol delta 7-reductase by novel 6-aza-B-homosteroids and other analogs of a presumptive carbocationic intermediate of the reduction reaction.

    PubMed

    Rahier, A; Taton, M

    1996-06-01

    A series of mono- and diazasteroids have been synthesized as analogs of a predicted carbocationic intermediate of delta 5,7-sterol delta 7-reductase (delta 7-SR). 6-Aza-B-homo-5 alpha-cholest-7-en-3 beta-ol (4), a novel compound whose synthesis is described for the first time, and 6,7-diaza-5 alpha-cholest-8(14)-en-3 beta-ol (6) were shown to be very powerful inhibitors of delta 7-SR in a preparation isolated from maize (Zea mays) (K(i),app = 50-70 nM, Ki,app/Km,app = 1.0 x 10(-4) to 1.3 x 10(-4). The data are consistent with a carbonium ion mechanism for the reduction; compounds 4 and 6 probably act as reaction intermediate analogs. Compound 4, in contrast to compound 6, displayed in the same microsomal preparation more than 50-fold selectivity for inhibition of the delta 7-SR versus delta 8-delta 7-sterol isomerase, cycloeucalenol isomerase, and delta 8,14-sterol delta 14-reductase, the mechanism of these four enzymes involving presumptive cationic intermediates centered respectively at C7, C8, C9, and C14. These observations highlight the paramount importance of the location of the positively charged nitrogen atom(s) in the B-ring structure for selectivity among these enzymes involving structurally close cationic reaction intermediates. Efficient in vivo inhibition of sterol biosynthesis in bramble cell suspension cultures by a low concentration of compound 4 was demonstrated and confirmed the in vitro properties of this derivative.) PMID:8679532

  3. Predicted reaction rates of H(x)N(y)O(z) intermediates in the oxidation of hydroxylamine by aqueous nitric acid.

    PubMed

    Ashcraft, Robert W; Raman, Sumathy; Green, William H

    2008-08-21

    This work reports computed rate coefficients of 90 reactions important in the autocatalytic oxidation of hydroxylamine in aqueous nitric acid. Rate coefficients were calculated using four approaches: Smoluchowski (Stokes-Einstein) diffusion, a solution-phase incarnation of transition state theory based on quantum chemistry calculations, simple Marcus theory for electron-transfer reactions, and a variational TST approach for dissociative isomerization reactions that occur in the solvent cage. Available experimental data were used to test the accuracy of the computations. There were significant discrepancies between the computed and experimental values for some key parameters, indicating a need for improvements in computational methodology. Nonetheless, the 90-reaction mechanism showed the ability to reproduce many of the trends seen in experimental studies of this very complicated kinetic system. This work highlights reactions that may govern the system evolution and branching behavior critical to the stability of the system. We hope that this analysis will guide experimental investigations to reduce the uncertainties in the critical rate coefficients and thermochemistry, allowing an unambiguous determination of the dominant reaction pathways in the system. Advances in efficient and accurate solvation models that effectively separate entropic and enthalpic contributions will most directly benefit solution-phase modeling efforts. Methods for more accurately estimating activity coefficients, including at infinite dilution in multicomponent mixtures, are needed for modeling high ionic strength aqueous systems. A detailed derivation of the solution-phase equilibrium and transition state theory rate expressions in solution is included in the Supporting Information. PMID:18652432

  4. Caffeoylquinic acid derived free radicals identified during antioxidant reactions of bitter tea (Ilex latifolia and Ilex kudincha).

    PubMed

    Pirker, Katharina Franziska; Goodman, Bernard Albert

    2010-12-01

    In order to provide some insight into the chemical basis for the antioxidant behaviour of bitter tea, the Chinese medicinal beverage derived from leaves of Ilex kudincha or Ilex latifolia, free radicals generated during the oxidation of aqueous extracts of dried leaves have been investigated by electron paramagnetic resonance (EPR) spectroscopy. With both beverages, the major components in the EPR spectra after accelerated autoxidation under alkaline conditions or oxidation with the superoxide anion radical were comparable to those derived from reactions of caffeoylquinic acids. Thus these reaction products have sufficient stability for biological activity, and the present results suggest that such molecules contribute appreciably to the antioxidant chemistry of these beverages.

  5. Photon-induced neutron polarization from the {sup 2}H({gamma},n-vector){sup 1}H reaction within the NN-force model with an intermediate dibaryon

    SciTech Connect

    Kukulin, V. I.; Obukhovsky, I. T.; Pomerantsev, V. N.; Faessler, Amand; Grabmayr, Peter

    2008-04-15

    A model for the NN force, which is induced by the formation of an intermediate dibaryon dressed with {sigma}- and other meson fields, has been developed by the present authors in previous years. This model is applied to the deuteron photodisintegration processes with the main focus on the {gamma}-induced polarization P{sub y}{sup '} of the neutron at energies below E{sub {gamma}} < or approx. 30 MeV. The inclusion of the intermediate dibaryon leads to a model of the NN force completely different to the conventional NN potential models at short distances. Here the model is tested on the nucleonic level through comparison to rather similar predictions from the conventional NN potential model both for the total and differential cross sections and also for the spin polarization of the ejected neutrons. The predictions of the present model are at least of the same quality than those for the Nijmegen potential; the visible differences with experimental data for P{sub y}{sup '} still remain. However, in combination with the previous results a consistent description can be achieved simultaneously for many observables.

  6. PAH Intermediates: Links between the Atmosphere and Biological Systems

    PubMed Central

    SIMONICH, STACI L. MASSEY; MOTORYKIN, OLEKSII; JARIYASOPIT, NARUMOL

    2010-01-01

    China is now the world's largest emitter of polycyclic aromatic hydrocarbons (PAHs). In addition, PAHs, and their reactive intermediates, undergo trans-Pacific atmospheric transport to the Western U.S. The objectives of our research are to predict, identify and quantify novel PAH intermediates in the atmosphere and biological systems, using computational methods, as well as laboratory and field experiments. Gaussian is used to predict the thermodynamic properties of parent structure PAHs, as well as the associated nitro-, oxy-, and hydroxy- PAH intermediates. Based on these predictions, state-of-the-art analytical chemistry techniques are used to identify and quantify these potential intermediates on Asian particulate matter before and after reaction in a continuous flow photochemical reactor. These same techniques are used to identify the relative proportion of PAH intermediates in PAH source regions (such as Beijing, China) and during long-range atmospheric transport to the Western U.S. PAH personal exposure studies in China and the Confederated Tribes of the Umatilla Indian Reservation in Oregon will be used to assess the similarities and differences in the PAH intermediates in biological systems relative to the atmosphere. PMID:20849837

  7. Study of the CH2I + O2 Reaction with a Step-Scan Fourier-Transform Infrared Absorption Spectrometer: Spectra of the Criegee Intermediate CH2OO and DIOXIRANE(?)

    NASA Astrophysics Data System (ADS)

    Huang, Yu-Hsuan; Lee, Yuan-Pern

    2014-06-01

    The Criegee intermediates are carbonyl oxides that play key roles in ozonolysis of unsaturated organic compounds. This mechanism was first proposed by Criegee in 1949, but the first direct observation of the simplest Criegee intermediate CH2OO in the gaseous phase has been reported only recently using photoionization mass spectrometry. Our group has reported the low-resolution IR spectra of CH2OO, produced from the reaction of CH2I + O2, with a second-generation step-scan Fourier-transfom IR absorption spectrometer. The spectral assignments were based on comparison of observed vibrational wavenumbers and rotational contours with theoretical predictions. Here, we report the IR absorption spectra of CH2OO at a resolution of 0.32 wn, showing partially rotationally-resolved structures. The origins of the νb{3}, νb{4}, νb{6}, and νb{8} vibrational modes of CH2OO are determined to be 1434.1, 1285.7, 909.2, and 847.3 wn, respectively. With the analysis of the vibration-rotational spectra, we provide a definitive assignment of these bands to CH2OO. The observed vibrational wavenumbers indicate a zwitterionic contribution to this singlet biradical showing a strengthened C-O bond and a weakened O-O bond. This zwitterionic character results to an extremely rapid self reaction via a cyclic dimer to form 2H2CO + O2 (1Δg). Another group of weak transient IR bands centered at 1231.5, 1213.3, and 899.8 wn are also observed. These bands might be contributed from dioxirane, which was postulated to be another important intermediate that might be isomerized from the Criegee intermediate in the reaction of O3 with 1-alkenes. O. Welz, J. D. Savee, D. L. Osborn, S. S.Vasu, C. J. Percival, D. E. Shallcross, and C. A. Taatjes, Science 335, 204 (2012). Y.-T. Su, Y.-H. Huang, H. A.Witek, and Y.-P. Lee, Science 340, 174 (2013).

  8. Structure-Reactivity Relationships for β-Galactosidase (Escherichia coli, lac Z): A Second Derivative Effect on β(nuc) for Addition of Alkyl Alcohols to an Oxocarbenium Ion Reaction Intermediate.

    PubMed

    Richard, John P; Heo, Christina K; Toteva, Maria M

    2008-07-01

    Velocities for the synthesis of trifluoroethyl 2-deoxy-β-D-galactopyranoside by transfer of the 2-deoxygalactosyl group from β-galactosidase to trifluoroethanol were determined from studies of the β-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-β-D-galactopyranoside as the difference in rates of appearance of 4-nitrophenoxide anion and 2-D-deoxygalactose. These data were used to calculate a rate constant ratio of k(ROH)/k(s) = 2.3 M(-1) for partitioning of the intermediate between addition of trifluoroethanol and solvent water. Velocities for the synthesis of other alkyl 2-deoxy-β-D-galactopyranosides by transfer of the 2-deoxygalactosyl group from β-galactosidase to alkyl alcohols were determined from the effect of alkyl alcohols on the velocity of β-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-β-D-galactopyranoside in a reaction where breakdown of the intermediate is rate determining. These data were used to calculate rate constant ratios k(ROH)/k(s) for the reactions of eight alkyl alcohols. Absolute rate constants k(ROH) (M(-1) s(-1)) were calculated from k(ROH)/k(s) and k(s) = 0.002 s(-1) for the addition of water. A Brønsted coefficient of β(nuc) = -0.07 ± 0.08 was determined as the slope of a logarithmic correlation of k(ROH) against alcohol pK(a). The change from a 2-OH to a 2-H substituent at the β-D-galactopyranosyl intermediate causes a 0.12 ± 0.04 increase in the value of β(nuc) for alcohol addition. This anti-Hammond effect provides evidence that general basecatalyzed addition of alcohols to an enzyme bound β-D-galactopyranosyl oxocarbenium ion intermediate proceeds along a reaction coordinate in which there is strong coupling between carbon-oxygen bond formation and proton transfer from the alcohol to a basic residue at the enzyme.

  9. Carbon-carbon cross-coupling reactions catalyzed by a two-coordinate nickel(II)-bis(amido) complex via observable Ni(I) , Ni(II) , and Ni(III) intermediates.

    PubMed

    Lipschutz, Michael I; Tilley, T Don

    2014-07-01

    Recently, the development of more sustainable catalytic systems based on abundant first-row metals, especially nickel, for cross-coupling reactions has attracted significant interest. One of the key intermediates invoked in these reactions is a Ni(III) -alkyl species, but no such species that is part of a competent catalytic cycle has yet been isolated. Herein, we report a carbon-carbon cross-coupling system based on a two-coordinate Ni(II) -bis(amido) complex in which a Ni(III) -alkyl species can be isolated and fully characterized. This study details compelling experimental evidence of the role played by this Ni(III) -alkyl species as well as those of other key Ni(I) and Ni(II) intermediates. The catalytic cycle described herein is also one of the first examples of a two-coordinate complex that competently catalyzes an organic transformation, potentially leading to a new class of catalysts based on the unique ability of first-row transition metals to accommodate two-coordinate complexes.

  10. Identifying environmental variables explaining genotype-by-environment interaction for body weight of rainbow trout (Onchorynchus mykiss): reaction norm and factor analytic models

    PubMed Central

    2014-01-01

    Background Identifying the relevant environmental variables that cause GxE interaction is often difficult when they cannot be experimentally manipulated. Two statistical approaches can be applied to address this question. When data on candidate environmental variables are available, GxE interaction can be quantified as a function of specific environmental variables using a reaction norm model. Alternatively, a factor analytic model can be used to identify the latent common factor that explains GxE interaction. This factor can be correlated with known environmental variables to identify those that are relevant. Previously, we reported a significant GxE interaction for body weight at harvest in rainbow trout reared on three continents. Here we explore their possible causes. Methods Reaction norm and factor analytic models were used to identify which environmental variables (age at harvest, water temperature, oxygen, and photoperiod) may have caused the observed GxE interaction. Data on body weight at harvest was recorded on 8976 offspring reared in various locations: (1) a breeding environment in the USA (nucleus), (2) a recirculating aquaculture system in the Freshwater Institute in West Virginia, USA, (3) a high-altitude farm in Peru, and (4) a low-water temperature farm in Germany. Akaike and Bayesian information criteria were used to compare models. Results The combination of days to harvest multiplied with daily temperature (Day*Degree) and photoperiod were identified by the reaction norm model as the environmental variables responsible for the GxE interaction. The latent common factor that was identified by the factor analytic model showed the highest correlation with Day*Degree. Day*Degree and photoperiod were the environmental variables that differed most between Peru and other environments. Akaike and Bayesian information criteria indicated that the factor analytical model was more parsimonious than the reaction norm model. Conclusions Day*Degree and

  11. Ultrafast absorption spectroscopy of photodissociated CF2Br2: Details of the reaction mechanism and evidence for anomalously slow intramolecular vibrational redistribution within the CF2Br intermediate

    NASA Astrophysics Data System (ADS)

    Gosnell, T. R.; Taylor, A. J.; Lyman, J. L.

    1991-05-01

    Ultrafast time-resolved absorption spectroscopy in the hard ultraviolet has been used to investigate the photodissociation of gas-phase CF2Br2 photolyzed at 248 nm. The broadband spectra obtained in the 250-265 nm region have shown that absorption of a single photon activates a two-step sequential elimination of the molecule's two bromine atoms, leaving the product CF2 radical in the ground or first-excited vibrational state of its ν2 bending mode. The spectra also demonstrate the direct detection of the vibrationally hot CF2Br intermediate species itself. We interpret the ˜6 ps time scale over which the diffuse CF2Br spectrum evolves as evidence for slow intramolecular vibrational redistribution within this molecule.

  12. Shedding new light on ZnCl2-mediated addition reactions of Grignard reagents to ketones: structural authentication of key intermediates and diffusion-ordered NMR studies.

    PubMed

    Armstrong, David R; Clegg, William; García-Alvarez, Pablo; McCall, Matthew D; Nuttall, Lorraine; Kennedy, Alan R; Russo, Luca; Hevia, Eva

    2011-04-11

    Building on recent advances in synthesis showing that the addition of inorganic salts to Grignard reagents can greatly enhance their performance in alkylation reactions to ketones, this study explores the reactions of EtMgCl with benzophenone in the presence of stoichiometric or catalytic amounts of ZnCl(2) with the aim of furthering the understanding of the role and constitution of the organometallic species involved in these transformations. Investigations into the metathesis reactions of three molar equivalents of EtMgCl with ZnCl(2) led to the isolation and characterisation (X-ray crystallography and (1)H and (13)C NMR spectroscopy) of novel magnesium "zinc-rich" zincate [{(THF)(6)Mg(2)Cl(3)}(+){Zn(2)Et(5)}(-)] (1), whose complicated constitution in THF solutions was assessed by variable-temperature (1)H DOSY NMR studies. Compound 1 reacted with one equivalent of benzophenone to yield magnesium magnesiate [{(THF)(6)Mg(2)Cl(3)}(+){Mg(2)(OC(Et)Ph(2))(2)Cl(3)(THF)}(-)] (3), whose structure was determined by X-ray crystallography. (1)H NMR monitoring of this reaction showed two equivalents of ZnEt(2) formed as a co-product, which together with the "magnesium only constitution" of 3 provides experimental insights into how zinc can be efficiently recycled in these reactions, and therefore used catalytically. The chemoselectivity of this reaction can be rationalised in terms of the synergic effect of magnesium and zinc and contrasts with the results obtained when benzophenone was allowed to react with EtMgCl in the absence of ZnCl(2), where the reduction of the ketone takes place preferentially. The reduction product [{(THF)(5)Mg(3)Cl(4){OC(H)Ph(CF(3))}(2)] (4) obtained from the reaction of EtMgCl with 2,2,2-trifluoroacetophenone was established by X-ray crystallography and multinuclear ((1)H, (13)C and (19)F) NMR spectroscopy. Compounds 3 and 4 exhibit new structural motifs in magnesium chemistry having MgCl(2) integrated within their constitution, which highlights

  13. Identifying and managing an adverse food reaction in a polar bear (Ursus maritimus) by an elimination diet trial.

    PubMed

    Monson, Sara; Minter, Larry J; Krouse, Marissa; De Voe, Ryan S

    2014-06-01

    A 16-yr-old polar bear (Ursus maritimus) presented with severe diarrhea shortly following transfer to the North Carolina Zoological Park. Multiple diagnostic procedures were performed over several months and the cause of the chronic diarrhea was inconclusive. Histologically, colonic mucosal biopsies were consistent with severe chronic eosinophilic and lymphoplasmacytic colitis with no evidence of etiologic agents present. A dietary elimination trial was conducted and an adverse food reaction to the dog chow in the diet was confirmed. PMID:25000711

  14. Identifying and managing an adverse food reaction in a polar bear (Ursus maritimus) by an elimination diet trial.

    PubMed

    Monson, Sara; Minter, Larry J; Krouse, Marissa; De Voe, Ryan S

    2014-06-01

    A 16-yr-old polar bear (Ursus maritimus) presented with severe diarrhea shortly following transfer to the North Carolina Zoological Park. Multiple diagnostic procedures were performed over several months and the cause of the chronic diarrhea was inconclusive. Histologically, colonic mucosal biopsies were consistent with severe chronic eosinophilic and lymphoplasmacytic colitis with no evidence of etiologic agents present. A dietary elimination trial was conducted and an adverse food reaction to the dog chow in the diet was confirmed.

  15. Oxidative hemoglobin reactions: Applications to drug metabolism.

    PubMed

    Spolitak, Tatyana; Hollenberg, Paul F; Ballou, David P

    2016-06-15

    Hb is a protein with multiple functions, acting as an O2 transport protein, and having peroxidase and oxidase activities with xenobiotics that lead to substrate radicals. However, there is a lack of evidence for intermediates involved in these reactions of Hb with redox-active compounds, including those with xenobiotics such as drugs, chemical carcinogens, and sulfides. In particular, questions exist as to what intermediates participate in reactions of either metHb or oxyHb with sulfides. The studies presented here elaborate kinetics and intermediates involved in the reactions of Hb with oxidants (H2O2 and mCPBA), and they demonstrate the formation of high valent intermediates, providing insights into mechanistic issues of sulfur and drug oxidations. Overall, we propose generalized mechanisms that include peroxidatic reactions using H2O2 generated from the autooxidation of oxyHb, with involvement of substrate radicals in reactions of Hb with oxidizable drugs such as metyrapone or 2,4-dinitrophenylhydrazine and with sulfides. We identify ferryl intermediates (with a Soret band at 407 nm) in oxidative reactions with all of the above-mentioned reactions. These spectral properties are consistent with a protonated ferryl heme, such as Cpd II or Cpd ES-like species (Spolitak et al., JIB, 2006, 100, 2034-2044). Mechanism(s) of Hb oxidative reactions are discussed.

  16. Synthesized TiO2/ZSM-5 composites used for the photocatalytic degradation of azo dye: Intermediates, reaction pathway, mechanism and bio-toxicity

    NASA Astrophysics Data System (ADS)

    Zhou, Kefu; Hu, Xin-Yan; Chen, Bor-Yann; Hsueh, Chung-Chuan; Zhang, Qian; Wang, Jiajie; Lin, Yu-Jung; Chang, Chang-Tang

    2016-10-01

    In this study, a one-step solid dispersion method was used to synthesize titanium dioxide (TiO2)/Zeolite Socony Mobil-5 (ZSM-5) composites with substantially reduced time and energy consumption. A degradation efficiency of more than 95% was achieved within 10 min using 50% PTZ (synthesized TiO2/ZSM-5 composites with TiO2 contents of 50 wt% loaded on ZSM-5) at pH 7 and 25 °C. The possible degradation pathway of azo-dye Reactive Black 5 (RB5) was investigated using gas chromatography-mass spectrometry and ion chromatography (IC). The bonds between the N atoms and naphthalene groups are likely attacked first and cleaved by hydroxyl radicals, ultimately resulting in the decolorization and mineralization of the azo dye. A comparative assessment of the characteristics of abiotic and biotic dye decolorization was completed. In addition, the toxicity effects of the degradation intermediates of azo-dye RB5 on cellular respiratory activity were analyzed. The bio-toxicity results showed that the decay rate constants of CO2 production from the azo-dye RB5 samples at different degradation times increased initially and subsequently decreased, indicating that intermediates of higher toxicity could adhere to the catalyst surface and gradually destroyed by further photocatalytic oxidation. Additionally, EDTA (hole scavengers) and t-BuOH (radical scavengers) were used to detect the main active oxidative species in the system. The results showed that the hydroxyl radicals are the main oxidation species in the photocatalytic process.

  17. Intermediate filaments: not just for structure anymore.

    PubMed

    Liem, Ronald K H

    2013-04-22

    A recent paper has identified the tumor suppressor APC as a linker protein between intermediate filaments and microtubules. In the absence of APC, intermediate filaments collapse and the cells are no longer polarized and fail to migrate.

  18. Ni/Fe-supported over hydrotalcites precursors as catalysts for clean and selective oxidation of Basic Yellow 11: reaction intermediates determination.

    PubMed

    Ovejero, G; Rodríguez, A; Vallet, A; García, J

    2013-01-01

    In this work, Basic Yellow 11 (BY 11) was employed as model compound to study catalytic wet air oxidation as a pre-treatment step to the conventional biological oxidation. Ni and Fe catalysts supported over hydrotalcite (HT) were prepared by incipient wetness and excess impregnation to obtain catalysts with different metal loadings (from 1 to 10 wt.%). HTs were synthesized by co-precipitation and characterized with XRD, X-ray fluorescence (XRF), BET, thermogravimetric analysis and SEM. Results showed that dye conversion increased with Ni and Fe content up to 7 wt.% and that the most effective catalyst were prepared by incipient wetness impregnation. The influence of metal loading in the catalyst, and the preparation method as well as the reaction conditions was investigated. A mechanism and reaction pathways for BY 11 during catalytic liquid phase oxidation have also been proposed.

  19. Ni/Fe-supported over hydrotalcites precursors as catalysts for clean and selective oxidation of Basic Yellow 11: reaction intermediates determination.

    PubMed

    Ovejero, G; Rodríguez, A; Vallet, A; García, J

    2013-01-01

    In this work, Basic Yellow 11 (BY 11) was employed as model compound to study catalytic wet air oxidation as a pre-treatment step to the conventional biological oxidation. Ni and Fe catalysts supported over hydrotalcite (HT) were prepared by incipient wetness and excess impregnation to obtain catalysts with different metal loadings (from 1 to 10 wt.%). HTs were synthesized by co-precipitation and characterized with XRD, X-ray fluorescence (XRF), BET, thermogravimetric analysis and SEM. Results showed that dye conversion increased with Ni and Fe content up to 7 wt.% and that the most effective catalyst were prepared by incipient wetness impregnation. The influence of metal loading in the catalyst, and the preparation method as well as the reaction conditions was investigated. A mechanism and reaction pathways for BY 11 during catalytic liquid phase oxidation have also been proposed. PMID:22960061

  20. Identifying the active site in nitrogen-doped graphene for the VO2+/VO2(+) redox reaction.

    PubMed

    Jin, Jutao; Fu, Xiaogang; Liu, Qiao; Liu, Yanru; Wei, Zhiyang; Niu, Kexing; Zhang, Junyan

    2013-06-25

    Nitrogen-doped graphene sheets (NGS), synthesized by annealing graphite oxide (GO) with urea at 700-1050 °C, were studied as positive electrodes in a vanadium redox flow battery. The NGS, in particular annealed at 900 °C, exhibited excellent catalytic performance in terms of electron transfer (ET) resistance (4.74 ± 0.51 and 7.27 ± 0.42 Ω for the anodic process and cathodic process, respectively) and reversibility (ΔE = 100 mV, Ipa/Ipc = 1.38 at a scan rate of 50 mV s(-1)). Detailed research confirms that not the nitrogen doping level but the nitrogen type in the graphene sheets determines the catalytic activity. Among four types of nitrogen species doped into the graphene lattice including pyridinic-N, pyrrolic-N, quaternary nitrogen, and oxidic-N, quaternary nitrogen is verified as a catalytic active center for the [VO](2+)/[VO2](+) couple reaction. A mechanism is proposed to explain the electrocatalytic performance of NGS for the [VO](2+)/[VO2](+) couple reaction. The possible formation of a N-V transitional bonding state, which facilitates the ET between the outer electrode and reactant ions, is a key step for its high catalytic activity.

  1. A polymerase chain reaction assay for non-random X chromosome inactivation identifies monoclonal endometrial cancers and precancers.

    PubMed

    Mutter, G L; Chaponot, M L; Fletcher, J A

    1995-02-01

    We hypothesize that endometrial carcinoma and their precursors share a monoclonal growth pattern and tested this thesis with archival paraffin-embedded tissues using a polymerase chain reaction-based assay for non-random X chromosome inactivation. Of the 10 well-differentiated endometrial adenocarcinoma cases with heterozygous markers (HUMARA, X-linked androgen receptor gene), 9 had skewed X inactivation consistent with a monoclonal process, and one contained a structurally altered HUMARA gene. X inactivation skewing similar to that of the tumor was seen in matched control polyclonal tissues of 4 (of 9) cases, caused by the small number of endometrial stem cells at the time of embryonic X inactivation. When the polymerase chain reaction assay was applied to four potential endometrial precancers (atypical endometrial hyperplasia) and matched control tissues, two were inconclusive, and two were found to be monoclonal. We conclude that 1) it is essential to include polyclonal control tissues in X inactivation analyses to determine whether skewing is a specific indicator of monoclonality; and 2) endometrial adenocarcinomas and some putative precancers, atypical endometrial hyperplasia, are monoclonal.

  2. The reaction of pristane (2,6,10,14-tetramethylpentadecane) with radiolytically generated reactive oxygen intermediates results in a stable genotoxic compound as assessed by the SOS chromotest.

    PubMed

    Janz, S; Brede, O; Müller, J

    1991-07-01

    The most widely studied model of plasmacytomagenesis is the induction of plasmacytomas in BALB/c mice by i.p. injections of the isoalkane pristane (2,6,10,14-tetramethylpentadecane). Employing a simple quantitative and well-established short-term bacterial genotoxicity assay, the SOS chromotest, as a model system, we have investigated whether pristane may potentially be involved in causing or modulating the genotoxic events thought to induce plasma cell tumorigenesis. We found that incorporation of pristane into the cell membranes enhance the SOS response in Escherichia coli PQ37 and PQ300 induced by gamma-radiation under hyperoxic conditions. Moreover, the oxidation of pristane by radiolytically generated reactive oxygen intermediates yielded a stable, genotoxic product active on E. coli PQ300, a SOS tester strain designed to detect oxidative genotoxins. We discuss these findings in relation to the tumor-promoting role of the chronic i.p. inflammation that accompanies plasmacytomagenesis and conclude that, under these specific conditions, pristane may possess a previously unrecognized genotoxic activity in its tumorigenic potential. PMID:2070489

  3. Role of a Guanidinium Cation-Phosphodianion Pair in Stabilizing the Vinyl Carbanion Intermediate of Orotidine 5'-Phosphate Decarboxylase-Catalyzed Reactions.†

    PubMed Central

    Goryanova, Bogdana; Goldman, Lawrence M.; Amyes, Tina L.; Gerlt, John A; Richard, John P.

    2013-01-01

    The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae (OMPDC) catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(β-d-erythrofuranosyl)orotic acid and 1-(β-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, while the 7.2 kcal/mol side-chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex while the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation. PMID:24053466

  4. Effect of radial flow on two particle correlations with identified triggers at intermediate pT in p-Pb collisions at √{sNN} = 5.02 TeV

    NASA Astrophysics Data System (ADS)

    Sarkar, Debojit; Choudhury, Subikash; Chattopadhyay, Subhasis

    2016-09-01

    Results from two-particle correlation between identified triggers (pions (π±), protons (p / p bar)) and un-identified charged particles at intermediate transverse momentum (pT) in p-Pb collisions at √{sNN} = 5.02 TeV have been presented. The events generated from a hybrid Monte-Carlo event generator, EPOS 3.107 that implements a flux-tube initial conditions followed by event by event 3+1D viscous hydrodynamical evolution, have been analyzed to calculate two-dimensional correlation functions in Δη- Δϕ. The strength of angular correlations at small relative angles (jet-like correlations), quantified in terms of near-side jet-like per-trigger yield has been calculated as a function of the event multiplicity. The yield associated with pion triggers exhibit negligible multiplicity dependence, while the proton-triggered yield shows a gradual suppression from low to high multiplicity events. In small collision systems like p-Pb where jet modification is expected to be less dominant, the observed suppression may be associated with the hydrodynamical evolution of the bulk system that generates an outward radial flow. Analogous measurements in Au-Au collisions at RHIC energy have shown a hint of dilution in proton-triggered correlation at its highest multiplicity suggesting that the soft physics processes in p-Pb and heavy ion collisions may have qualitative similarity.

  5. Thermally-generated reactive intermediates: Trapping of the parent ferrocene-based o-quinodimethane and reactions of diradicals generated by hydrogen-atom transfers

    SciTech Connect

    Ferguson, J.M.

    1993-09-01

    Ferrocenocyclobutene is prepared by flash vacuum pyrolysis (FVP) of the N-amino-2-phenylaziridine hydrazone of 2-methylferrocenealdehyde. In the second section of this dissertation, a series of hydrocarbon rearrangements were observed. FVP of o-allyltoluene at 0.1 Torr (700--900 C) gives 2-methylindan and indene, accompanied by o-propenyltoluene. FVP of 2-methyl-2`-vinylbiphenyl gives 9-methyl-9,10-dihydrophenanthrene, which fits the proposed mechanism. However, FVP of 2-(o-methylbenzyl)styrene gives mainly anthracene and 1-methylanthracene. This cyclization reaction was also successful with o-allylphenol and o-(2-methylallyl)phenol.

  6. Initial electron donor and acceptor in isolated Photosystem II reaction centers identified with femtosecond mid-IR spectroscopy

    PubMed Central

    Groot, Marie Louise; Pawlowicz, Natalia P.; van Wilderen, Luuk J. G. W.; Breton, Jacques; van Stokkum, Ivo H. M.; van Grondelle, Rienk

    2005-01-01

    Despite the apparent similarity between the plant Photosystem II reaction center (RC) and its purple bacterial counterpart, we show in this work that the mechanism of charge separation is very different for the two photosynthetic RCs. By using femtosecond visible-pump–mid-infrared probe spectroscopy in the region of the chlorophyll ester and keto modes, between 1,775 and 1,585 cm–1, with 150-fs time resolution, we show that the reduction of pheophytin occurs on a 0.6- to 0.8-ps time scale, whereas P+, the precursor state for water oxidation, is formed after ≈6 ps. We conclude therefore that in the Photosystem II RC the primary charge separation occurs between the “accessory chlorophyll” ChlD1 and the pheophytin on the so-called active branch. PMID:16135567

  7. Intramolecular hydroarylation of aryl propargyl ethers catalyzed by indium: the mechanism of the reaction and identifying the catalytic species.

    PubMed

    Menkir, Mengistu Gemech; Lee, Shyi-Long

    2016-07-01

    The mechanism and regioselectivity of the intramolecular hydroarylation of phenyl propargyl ether catalyzed by indium in gas and solvent phases were investigated by means of the density functional theory method. The computed results revealed that the reaction proceeds through initial π-coordination of the propargyl moiety to the catalyst, which triggers the nucleophilic attack of the phenyl ring via an exo- or endo-dig pathway in a Friedel-Crafts type mechanism. Calculation results obtained employing InI2(+) as the possible catalyst show similar activation energies for the 5-exo-dig and 6-endo-dig pathways. In contrast, the neural catalyst InI3 shows a kinetic preference for 6-endo-dig versus 5-exo-dig cyclizations leading to the experimentally observed product, 2H-chromene. The calculation results suggest that InI3 could be the real catalytic species for this reaction as it shows regioselectivity in agreement with the experimental observation. Furthermore, the 6-endo-dig cyclization through deprotonation/protonation steps is kinetically more favored than the stepwise two consecutive [1,2]-H shift steps. The rate determining step of the whole catalytic cycle is the deprotonation step with an energy barrier of 18.9 kcal mol(-1) in toluene solvent. The effects of substituents on both the phenyl ring and the propargyl moiety on the selectivity and elementary steps of the hydroarylation process were investigated. A methoxy group, particularly at the meta-position, on the phenyl ring largely decreases the energy barrier of the first step for the 6-endo path, though it shows little effect on the activation energies of the second and third steps. Our calculation results are in good agreement with the experimental results. PMID:27298068

  8. Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB*

    PubMed Central

    Guo, Zhong; Hou, Xiaomin; Goody, Roger S.; Itzen, Aymelt

    2013-01-01

    Small G-proteins of the Ras superfamily control the temporal and spatial coordination of intracellular signaling networks by acting as molecular on/off switches. Guanine nucleotide exchange factors (GEFs) regulate the activation of these G-proteins through catalytic replacement of GDP by GTP. During nucleotide exchange, three distinct substrate·enzyme complexes occur: a ternary complex with GDP at the start of the reaction (G-protein·GEF·GDP), an intermediary nucleotide-free binary complex (G-protein·GEF), and a ternary GTP complex after productive G-protein activation (G-protein·GEF·GTP). Here, we show structural snapshots of the full nucleotide exchange reaction sequence together with the G-protein substrates and products using Rabin8/GRAB (GEF) and Rab8 (G-protein) as a model system. Together with a thorough enzymatic characterization, our data provide a detailed view into the mechanism of Rabin8/GRAB-mediated nucleotide exchange. PMID:24072714

  9. Impetigo-like tinea faciei around the nostrils caused by Arthroderma vanbreuseghemii identified using polymerase chain reaction-based sequencing of crusts.

    PubMed

    Kang, Daoxian; Ran, Yuping; Li, Conghui; Dai, Yaling; Lama, Jebina

    2013-01-01

    We report a case of Arthroderma vanbreuseghemii (a teleomorph of Trichophyton interdigitale) infection around the nostrils in a 3-year-old girl. The culture was negative, so the pathogenic agent was identified using polymerase chain reaction-based sequencing of the crusts taken from the lesion on the nostril. Treatment with oral itraconazole and topical 1% naftifine/0.25% ketoconazole cream after a topical wash with ketoconazole shampoo was effective. PMID:23278484

  10. Impetigo-like tinea faciei around the nostrils caused by Arthroderma vanbreuseghemii identified using polymerase chain reaction-based sequencing of crusts.

    PubMed

    Kang, Daoxian; Ran, Yuping; Li, Conghui; Dai, Yaling; Lama, Jebina

    2013-01-01

    We report a case of Arthroderma vanbreuseghemii (a teleomorph of Trichophyton interdigitale) infection around the nostrils in a 3-year-old girl. The culture was negative, so the pathogenic agent was identified using polymerase chain reaction-based sequencing of the crusts taken from the lesion on the nostril. Treatment with oral itraconazole and topical 1% naftifine/0.25% ketoconazole cream after a topical wash with ketoconazole shampoo was effective.

  11. Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP

    NASA Astrophysics Data System (ADS)

    Khrenova, Maria G.; Grigorenko, Bella L.; Nemukhin, Alexander V.

    2016-09-01

    The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted.

  12. Browning inhibition mechanisms by cysteine, ascorbic acid and citric acid, and identifying PPO-catechol-cysteine reaction products.

    PubMed

    Ali, Hussein M; El-Gizawy, Ahmed M; El-Bassiouny, Rawia E I; Saleh, Mahmoud A

    2015-06-01

    The titled compounds were examined as PPO inhibitors and antibrowning agents; their various mechanisms were investigated and discussed. All compounds reduced significantly both the browning process and PPO activity. Browning index gave strong correlation with PPO activity (r(2) = 0.96, n = 19) indicating that the browning process is mainly enzymatic. Ascorbic acid could reduce the formed quinone instantly to the original substrate (catechol) at high concentration (>1.5 %) while at lower concentrations acted as competitive inhibitor (KI = 0.256 ± 0.067 mM). Cysteine, at higher concentrations (≥1.0 %), reacted with the resulted quinone to give a colorless products while at the low concentrations, cysteine worked as competitive inhibitor (KI = 1.113 ± 0.176 mM). Citric acid acted only as PPO non-competitive inhibitor with KI = 2.074 ± 0.363 mM. The products of PPO-catechole-cysteine reaction could be separation and identification by LC-ESI-MS. Results indicated that the product of the enzymatic oxidation of catechol, quinone, undergoes two successive nucleophilic attacks by cysteine thiol group. Cysteine was condensed with the resulted mono and dithiocatechols to form peptide side chains.

  13. Improving the Production of L-Phenylalanine by Identifying Key Enzymes Through Multi-Enzyme Reaction System in Vitro.

    PubMed

    Ding, Dongqin; Liu, Yongfei; Xu, Yiran; Zheng, Ping; Li, Haixing; Zhang, Dawei; Sun, Jibin

    2016-08-25

    L-Phenylalanine (L-Phe) is an important amino acid used in both food and medicinal applications. We developed an in vitro system that allowed a direct, quantitative investigation of phenylalanine biosynthesis in E. coli. Here, the absolute concentrations of six enzymes (AroK, AroL, AroA, AroC, PheA and TyrB) involved in the shikimate (SHIK) pathway were determined by a quantitative proteomics approach and in vitro enzyme titration experiments. The reconstitution of an in vitro reaction system for these six enzymes was established and their effects on the phenylalanine production were tested. The results showed that the yield of phenylalanine increased 3.0 and 2.1 times when the concentrations of shikimate kinase (AroL) and 5-enolpyruvoyl shikimate 3-phosphate (EPSP) synthase (AroA) were increased 2.5 times. Consistent results were obtained from in vivo via the overexpression of AroA in a phenylalanine-producing strain, and the titer of phenylalanine reached 62.47 g/l after 48 h cultivation in a 5-liter jar fermentor. Our quantitative findings provide a practical method to detect the potential bottleneck in a specific metabolic pathway to determine which gene products should be targeted to improve the yield of the desired product.

  14. Improving the Production of L-Phenylalanine by Identifying Key Enzymes Through Multi-Enzyme Reaction System in Vitro.

    PubMed

    Ding, Dongqin; Liu, Yongfei; Xu, Yiran; Zheng, Ping; Li, Haixing; Zhang, Dawei; Sun, Jibin

    2016-01-01

    L-Phenylalanine (L-Phe) is an important amino acid used in both food and medicinal applications. We developed an in vitro system that allowed a direct, quantitative investigation of phenylalanine biosynthesis in E. coli. Here, the absolute concentrations of six enzymes (AroK, AroL, AroA, AroC, PheA and TyrB) involved in the shikimate (SHIK) pathway were determined by a quantitative proteomics approach and in vitro enzyme titration experiments. The reconstitution of an in vitro reaction system for these six enzymes was established and their effects on the phenylalanine production were tested. The results showed that the yield of phenylalanine increased 3.0 and 2.1 times when the concentrations of shikimate kinase (AroL) and 5-enolpyruvoyl shikimate 3-phosphate (EPSP) synthase (AroA) were increased 2.5 times. Consistent results were obtained from in vivo via the overexpression of AroA in a phenylalanine-producing strain, and the titer of phenylalanine reached 62.47 g/l after 48 h cultivation in a 5-liter jar fermentor. Our quantitative findings provide a practical method to detect the potential bottleneck in a specific metabolic pathway to determine which gene products should be targeted to improve the yield of the desired product. PMID:27558633

  15. Improving the Production of L-Phenylalanine by Identifying Key Enzymes Through Multi-Enzyme Reaction System in Vitro

    PubMed Central

    Ding, Dongqin; Liu, Yongfei; Xu, Yiran; Zheng, Ping; Li, Haixing; Zhang, Dawei; Sun, Jibin

    2016-01-01

    L-Phenylalanine (L-Phe) is an important amino acid used in both food and medicinal applications. We developed an in vitro system that allowed a direct, quantitative investigation of phenylalanine biosynthesis in E. coli. Here, the absolute concentrations of six enzymes (AroK, AroL, AroA, AroC, PheA and TyrB) involved in the shikimate (SHIK) pathway were determined by a quantitative proteomics approach and in vitro enzyme titration experiments. The reconstitution of an in vitro reaction system for these six enzymes was established and their effects on the phenylalanine production were tested. The results showed that the yield of phenylalanine increased 3.0 and 2.1 times when the concentrations of shikimate kinase (AroL) and 5-enolpyruvoyl shikimate 3-phosphate (EPSP) synthase (AroA) were increased 2.5 times. Consistent results were obtained from in vivo via the overexpression of AroA in a phenylalanine-producing strain, and the titer of phenylalanine reached 62.47 g/l after 48 h cultivation in a 5-liter jar fermentor. Our quantitative findings provide a practical method to detect the potential bottleneck in a specific metabolic pathway to determine which gene products should be targeted to improve the yield of the desired product. PMID:27558633

  16. Browning inhibition mechanisms by cysteine, ascorbic acid and citric acid, and identifying PPO-catechol-cysteine reaction products.

    PubMed

    Ali, Hussein M; El-Gizawy, Ahmed M; El-Bassiouny, Rawia E I; Saleh, Mahmoud A

    2015-06-01

    The titled compounds were examined as PPO inhibitors and antibrowning agents; their various mechanisms were investigated and discussed. All compounds reduced significantly both the browning process and PPO activity. Browning index gave strong correlation with PPO activity (r(2) = 0.96, n = 19) indicating that the browning process is mainly enzymatic. Ascorbic acid could reduce the formed quinone instantly to the original substrate (catechol) at high concentration (>1.5 %) while at lower concentrations acted as competitive inhibitor (KI = 0.256 ± 0.067 mM). Cysteine, at higher concentrations (≥1.0 %), reacted with the resulted quinone to give a colorless products while at the low concentrations, cysteine worked as competitive inhibitor (KI = 1.113 ± 0.176 mM). Citric acid acted only as PPO non-competitive inhibitor with KI = 2.074 ± 0.363 mM. The products of PPO-catechole-cysteine reaction could be separation and identification by LC-ESI-MS. Results indicated that the product of the enzymatic oxidation of catechol, quinone, undergoes two successive nucleophilic attacks by cysteine thiol group. Cysteine was condensed with the resulted mono and dithiocatechols to form peptide side chains. PMID:26028748

  17. ReacKnock: identifying reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network.

    PubMed

    Xu, Zixiang; Zheng, Ping; Sun, Jibin; Ma, Yanhe

    2013-01-01

    Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP) based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT) method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.

  18. An Artificial Enzyme Made by Covalent Grafting of an Fe(II) Complex into β-Lactoglobulin: Molecular Chemistry, Oxidation Catalysis, and Reaction-Intermediate Monitoring in a Protein.

    PubMed

    Buron, Charlotte; Sénéchal-David, Katell; Ricoux, Rémy; Le Caër, Jean-Pierre; Guérineau, Vincent; Méjanelle, Philippe; Guillot, Régis; Herrero, Christian; Mahy, Jean-Pierre; Banse, Frédéric

    2015-08-17

    An artificial metalloenzyme based on the covalent grafting of a nonheme Fe(II) polyazadentate complex into bovine β-lactoglobulin has been prepared and characterized by using various spectroscopic techniques. Attachment of the Fe(II) catalyst to the protein scaffold is shown to occur specifically at Cys121. In addition, spectrophotometric titration with cyanide ions based on the spin-state conversion of the initial high spin (S=2) Fe(II) complex into a low spin (S=0) one allows qualitative and quantitative characterization of the metal center's first coordination sphere. This biohybrid catalyst activates hydrogen peroxide to oxidize thioanisole into phenylmethylsulfoxide as the sole product with an enantiomeric excess of up to 20 %. Investigation of the reaction between the biohybrid system and H2 O2 reveals the generation of a high spin (S=5/2) Fe(III) (η(2) -O2 ) intermediate, which is proposed to be responsible for the catalytic sulfoxidation of the substrate.

  19. Degradation mechanisms of geosmin and 2-MIB during UV photolysis and UV/chlorine reactions.

    PubMed

    Kim, Tae-Kyoung; Moon, Bo-Ram; Kim, Taeyeon; Kim, Moon-Kyung; Zoh, Kyung-Duk

    2016-11-01

    We conducted chlorination, UV photolysis, and UV/chlorin reactions to investigate the intermediate formation and degradation mechanisms of geosmin and 2-methylisoborneol (2-MIB) in water. Chlorination hardly removed geosmin and 2-MIB, while the UV/chlorine reaction at 254 nm completely removed geosmin and 2-MIB within 40 min and 1 h, respectively, with lesser removals of both compounds during UV photolysis. The kinetics during both UV photolysis and UV/chlorine reactions followed a pseudo first-order reaction. Chloroform was found as a chlorinated intermediate during the UV/chlorine reaction of both geosmin and 2-MIB. The pH affected both the degradation and chloroform production during the UV/chlorine reaction. The open ring and dehydration intermediates identified during UV/chlorine reactions were 1,4-dimethyl-adamantane, and 1,3-dimethyl-adamantane from geosmin, 2-methylenebornane, and 2-methyl-2-bornene from 2-MIB, respectively. Additionally, 2-methyl-3-pentanol, 2,4-dimethyl-1-heptene, 4-methyl-2-heptanone, and 1,1-dichloro-2,4-dimethyl-1-heptane were newly identified intermediates from UV/chlorine reactions of both geosmin and 2-MIB. These intermediates were degraded as the reaction progressed. We proposed possible degradation pathways during the UV photolysis and UV/chlorine reactions of both compounds using the identified intermediates. PMID:27494316

  20. Degradation mechanisms of geosmin and 2-MIB during UV photolysis and UV/chlorine reactions.

    PubMed

    Kim, Tae-Kyoung; Moon, Bo-Ram; Kim, Taeyeon; Kim, Moon-Kyung; Zoh, Kyung-Duk

    2016-11-01

    We conducted chlorination, UV photolysis, and UV/chlorin reactions to investigate the intermediate formation and degradation mechanisms of geosmin and 2-methylisoborneol (2-MIB) in water. Chlorination hardly removed geosmin and 2-MIB, while the UV/chlorine reaction at 254 nm completely removed geosmin and 2-MIB within 40 min and 1 h, respectively, with lesser removals of both compounds during UV photolysis. The kinetics during both UV photolysis and UV/chlorine reactions followed a pseudo first-order reaction. Chloroform was found as a chlorinated intermediate during the UV/chlorine reaction of both geosmin and 2-MIB. The pH affected both the degradation and chloroform production during the UV/chlorine reaction. The open ring and dehydration intermediates identified during UV/chlorine reactions were 1,4-dimethyl-adamantane, and 1,3-dimethyl-adamantane from geosmin, 2-methylenebornane, and 2-methyl-2-bornene from 2-MIB, respectively. Additionally, 2-methyl-3-pentanol, 2,4-dimethyl-1-heptene, 4-methyl-2-heptanone, and 1,1-dichloro-2,4-dimethyl-1-heptane were newly identified intermediates from UV/chlorine reactions of both geosmin and 2-MIB. These intermediates were degraded as the reaction progressed. We proposed possible degradation pathways during the UV photolysis and UV/chlorine reactions of both compounds using the identified intermediates.

  1. Microeconomic Concepts Students Should Learn before Intermediate Macroeconomics.

    ERIC Educational Resources Information Center

    Salemi, Michael K.

    1996-01-01

    Identifies four microeconomic concepts students should learn before entering the study of intermediate macroeconomics. Included are relative prices, general versus partial equilibrium, constrained optimization, and the nature of production concepts. Recommends making intermediate microeconomics a prerequisite for intermediate macroeconomics. (MJP)

  2. Infrared Spectra and Density Functional Calculations for Singlet CH2═SiX2 and Triplet HC-SiX3 and XC-SiX3 Intermediates in Reactions of Laser-Ablated Silicon Atoms with Di-, Tri-, and Tetrahalomethanes.

    PubMed

    Cho, Han-Gook; Andrews, Lester

    2016-03-21

    Reactions of laser-ablated silicon atoms with di-, tri-, and tetrahalomethanes in excess argon were investigated, and the products were identified from the matrix infrared spectra, isotopic shifts, and density functional theory energy, bond length, and frequency calculations. Dihalomethanes produce planar singlet silenes (CH2═SiX2), and tri- and tetrahalomethanes form triplet halosilyl carbenes (HC-SiX3 and XC-SiX3). The Si-bearing molecules identified are the most stable, lowest-energy product in the reaction systems. While the C-Si bond in the silene is a true double bond, the C-Si bond in the carbene is a shortened single bond enhanced by hyperconjugation of the two unpaired electrons on C to σ*(Si-X) orbitals, which contributes stabilization through a small amount of π-bonding and reduction of the HCSi or XCSi angles. The C-Si bond lengths in these carbenes (1.782 Å for HC-SiF3) are between the single-bond length in the unobserved first insertion intermediate (1.975 Å for CHF2-SiF) and the double-bond length in the silene (1.704 Å for CHF═SiF2). The silicon s(2)p(2) and titanium s(2)d(2) electron configurations produce similar primary products, but the methylidyne with Ti has a bond to carbon stronger than that of the halosilyl carbene.

  3. Study of intermediates from transition metal excited-state electron-transfer reactions. Final report, August 4, 1986--August 31, 1997

    SciTech Connect

    Hoffman, M.Z.

    1997-12-31

    The techniques of continuous photolysis and pulsed laser flash photolysis, continuous and pulse radiolysis, fast-scan cyclic voltammetry, and time-resolved fluorimetry have been used to examine intramolecular electron transfer within the solvent quenching cage, photodynamics of quenching of the excited states of transition-metal photosensitizers, the properties of excites states and one-electron reduced forms, ground- and excited-state interactions with solutes, and photoinduced oxidations of organic solutes in aqueous solution. The following specific areas were examined: (1) the parameters that govern the yields of redox products from excited-state electron-transfer quenching reactions; (2) the mediation of the properties of excited states and one-electron reduced forms by the ligands and the solution medium; (3) the effect of the interactions between the ground state of the complex and the solution components on the behavior of the excited state; (4) the yields of singlet oxygen from excited-state energy-transfer quenching by O{sub 2}; and (5) the oxidations of solutes by singlet oxygen, excited-state electron-transfer quenching, and free radicals. This report contains the abstracts of 50 publications describing the studies.

  4. LiCuS, an intermediate phase in the electrochemical conversion reaction of CuS with Li: A potential environment-friendly battery and solar cell material

    NASA Astrophysics Data System (ADS)

    Beleanu, Andreea; Kiss, Janos; Baenitz, Michael; Majumder, Mayukh; Senyshyn, Anatoliy; Kreiner, Guido; Felser, Claudia

    2016-05-01

    The crystal structure of a ternary sulfide with the approximate composition LiCuS, which is a promising candidate for environment-friendly battery and solar cell materials is reported. The crystal structure was solved by a combination of neutron and X-ray powder diffraction data, and 7Li solid-state NMR analysis. A yellow powder, Li1.1Cu0.9S, was obtained by the reaction of CuS with a slight excess of Li metal. The compound crystallizes in the Na3AgO2 structure type in the space group Ibam. An idealized crystal structure of Li1.1Cu0.9S can be derived from the cubic Li2S structure by moving a part of the Li along the c axis so that these Li atoms become linearly coordinated by S. All the metal sites are occupied by randomly mixed Li and Cu atoms; however, there is a strong preference for linear coordination by Cu. The density functional theory calculations show that Li1.1Cu0.9S is a direct band-gap semiconductor with an energy gap of 1.95 eV in agreement with experimental data.

  5. Stochastic-convective transport with nonlinear reaction and mixing: application to intermediate-scale experiments in aerobic biodegradation in saturated porous media

    NASA Astrophysics Data System (ADS)

    Ginn, T. R.; Murphy, E. M.; Chilakapati, A.; Seeboonruang, U.

    2001-03-01

    Aerobic biodegradation of benzoate by Pseudomonas cepacia sp. in a saturated heterogeneous porous medium was simulated using the stochastic-convective reaction (SCR) approach. A laboratory flow cell was randomly packed with low permeability silt-size inclusions in a high permeability sand matrix. In the SCR upscaling approach, the characteristics of the flow field are determined by the breakthrough of a conservative tracer. Spatial information on the actual location of the heterogeneities is not used. The mass balance equations governing the nonlinear and multicomponent reactive transport are recast in terms of reactive transports in each of a finite number of discrete streamtubes. The streamtube ensemble members represent transport via a steady constant average velocity per streamtube and a conventional Fickian dispersion term, and their contributions to the observed breakthroughs are determined by flux-averaging the streamtube solute concentrations. The resulting simulations were compared to those from a high-resolution deterministic simulation of the reactive transport, and to alternative ensemble representations involving (i) effective Fickian travel time distribution function, (ii) purely convective streamtube transport, and (iii) streamtube ensemble subset simulations. The results of the SCR simulation compare favorably to that of a sophisticated high-resolution deterministic approach.

  6. LiCuS, an intermediate phase in the electrochemical conversion reaction of CuS with Li: A potential environment-friendly battery and solar cell material

    NASA Astrophysics Data System (ADS)

    Beleanu, Andreea; Kiss, Janos; Baenitz, Michael; Majumder, Mayukh; Senyshyn, Anatoliy; Kreiner, Guido; Felser, Claudia

    2016-05-01

    The crystal structure of a ternary sulfide with the approximate composition LiCuS, which is a promising candidate for environment-friendly battery and solar cell materials is reported. The crystal structure was solved by a combination of neutron and X-ray powder diffraction data, and 7Li solid-state NMR analysis. A yellow powder, Li1.1Cu0.9S, was obtained by the reaction of CuS with a slight excess of Li metal. The compound crystallizes in the Na3AgO2 structure type in the space group Ibam. An idealized crystal structure of Li1.1Cu0.9S can be derived from the cubic Li2S structure by moving a part of the Li along the c axis so that these Li atoms become linearly coordinated by S. All the metal sites are occupied by randomly mixed Li and Cu atoms; however, there is a strong preference for linear coordination by Cu. The density functional theory calculations show that Li1.1Cu0.9S is a direct band-gap semiconductor with an energy gap of 1.95 eV in agreement with experimental data.

  7. Revisiting the GroEL-GroES Reaction Cycle via the Symmetric Intermediate Implied by Novel Aspects of the GroEL(D398A) Mutant*♦

    PubMed Central

    Koike-Takeshita, Ayumi; Yoshida, Masasuke; Taguchi, Hideki

    2008-01-01

    The Escherichia coli chaperonin GroEL is a double-ring chaperone that assists in protein folding with the aid of GroES and ATP. It is believed that GroEL alternates the folding-active rings and that the substrate protein (and GroES) can bind to the open trans-ring only after ATP in the cis-ring is hydrolyzed. However, we found that a substrate protein prebound to the trans-ring remained bound during the first ATP cycle, and this substrate was assisted by GroEL-GroES when the second cycle began. Moreover, a slow ATP-hydrolyzing GroEL mutant (D398A) in the ATP-bound form bound a substrate protein and GroES to the trans-ring. The apparent discrepancy with the results from an earlier study (Rye, H. S., Roseman, A. M., Chen, S., Furtak, K., Fenton, W. A., Saibil, H. R., and Horwich, A. L. (1999) Cell 97, 325–338) can be explained by the previously unnoticed fact that the ATP-bound form of the D398A mutant exists as a symmetric 1:2 GroEL-GroES complex (the “football”-shaped complex) and that the substrate protein (and GroES) in the medium is incorporated into the complex only after the slow turnover. In light of these results, the current model of the GroEL-GroES reaction cycle via the asymmetric 1:1 GroEL-GroES complex deserves reexamination. PMID:18567584

  8. Radiolytic oxidation of 1,2,4-benzenetriol. An application of time-resolved resonance Raman spectroscopy to kinetic studies of reaction intermediates

    SciTech Connect

    Qin, L.; Tripathi, G.N.R.; Schuler, R.H.

    1987-03-26

    In acidic solution, 1,2,4-benzenetriol is rapidly oxidized by OH or N/sub 3/ to form a mixture of neutral 2,4- and 3,4-dihydroxyphenoxyl radicals. At higher pH these radicals deprotonate (pK/sub a/(1) = 4.75) to form the 2-hydroxy-p-benzosemiquinone radical anion which exhibits a prominent resonance Raman band at 1625 cm/sup -1/ attributable to the Wilson 8a ring stretching mode. In basic solutions this radical subsequently reacts with OH/sup -/ to form the radical dianion (pK/sub a/(2) = 8.85) in which the 8a band is shifted to an appreciably lower frequency (1587 cm/sup -1/). While the absorption spectra of these latter radicals are very similar and do not allow ready examination of their interconversion by absorption spectrophotometry, the difference between these 8a frequencies is sufficiently great that the Raman method can be used to examine the acid-base equilibrium between the two forms of the radical and to follow the deprotonation kinetics. It is shown that even at high pH the radical monoanion is initially formed on oxidation by N/sub 3/ and that deprotonation subsequently occurs by its reaction with base with a rate constant of (9.6 +/- 1.5) x 10/sup 9/ M/sup -1/ d/sup -1/. These studies illustrate very well the application of time-resolved resonance Raman spectroscopy as a complement to kinetic spectrophotometry in sorting out the details of secondary processes in pulse radiolysis studies.

  9. Reaction of [TpRh(C2 H4 )2 ] with Dimethyl Acetylenedicarboxylate: Identification of Intermediates of the [2+2+2] Alkyne and Alkyne-Ethylene Cyclo(co)trimerizations.

    PubMed

    Bottari, Giovanni; Santos, Laura L; Posadas, Cristina M; Campos, Jesús; Mereiter, Kurt; Paneque, Margarita

    2016-09-12

    The reaction between the bis(ethylene) complex [TpRh(C2 H4 )2 ], 1, (Tp=hydrotris(pyrazolyl)borate), and dimethyl acetylenedicarboxylate (DMAD) has been studied under different experimental conditions. A mixture of products was formed, in which TpRh(I) species were prevalent, whereas the presence of trapping agents, like water or acetonitrile, allowed for the stabilization and isolation of octahedral TpRh(III) compounds. An excess of DMAD gave rise to a small amount of the [2+2+2] cyclotrimerization product hexamethyl mellitate (6). Although no catalytic application of 1 was achieved, mechanistic insights shed light on the formation of stable rhodium species representing the resting state of the catalytic cycle of rhodium-mediated [2+2+2] cyclo(co)trimerization reactions. Metallacyclopentene intermediate species, generated from the activation of one alkyne and one ethylene molecule from 1, and metallacyclopentadiene species, formed by oxidative coupling of two alkynes to the rhodium centre, are crucial steps in the pathways leading to the final organometallic and organic products.

  10. Reaction of [TpRh(C2 H4 )2 ] with Dimethyl Acetylenedicarboxylate: Identification of Intermediates of the [2+2+2] Alkyne and Alkyne-Ethylene Cyclo(co)trimerizations.

    PubMed

    Bottari, Giovanni; Santos, Laura L; Posadas, Cristina M; Campos, Jesús; Mereiter, Kurt; Paneque, Margarita

    2016-09-12

    The reaction between the bis(ethylene) complex [TpRh(C2 H4 )2 ], 1, (Tp=hydrotris(pyrazolyl)borate), and dimethyl acetylenedicarboxylate (DMAD) has been studied under different experimental conditions. A mixture of products was formed, in which TpRh(I) species were prevalent, whereas the presence of trapping agents, like water or acetonitrile, allowed for the stabilization and isolation of octahedral TpRh(III) compounds. An excess of DMAD gave rise to a small amount of the [2+2+2] cyclotrimerization product hexamethyl mellitate (6). Although no catalytic application of 1 was achieved, mechanistic insights shed light on the formation of stable rhodium species representing the resting state of the catalytic cycle of rhodium-mediated [2+2+2] cyclo(co)trimerization reactions. Metallacyclopentene intermediate species, generated from the activation of one alkyne and one ethylene molecule from 1, and metallacyclopentadiene species, formed by oxidative coupling of two alkynes to the rhodium centre, are crucial steps in the pathways leading to the final organometallic and organic products. PMID:27535720

  11. Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K.

    PubMed

    Zhu, Chen; Warncke, Kurt

    2008-12-15

    The decay kinetics of the aminoethanol-generated Co(II)-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10(5) s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 < or = T < or = 207 K: the decay is biexponential with constant fast (0.57 +/- 0.04) and slow (0.43 +/- 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T > or = 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k(obs,m)) and the fast phase of the biexponential decay (k(obs,f)) adhere to the same linear relation on an lnk versus T(-1) (Arrhenius) plot. Thus, k(obs,m) and k(obs,f) correspond to the same apparent Arrhenius prefactor and activation energy (logA(app,f) (s(-1)) = 13.0, E(a,app,f) = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k(obs,m) and k(obs,f) represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k(obs,s)) for 190 < or = T < or = 207 K obeys a different linear Arrhenius relation (logA(app,s) (s(-1)) = 13.9, E(a,app,s) = 16.6 kcal/mol). In the transition temperature range, k(obs,s) displays a super-Arrhenius increase with increasing temperature. The change in E(a,app,s) with temperature and the narrow range over

  12. Eleven new heaviest isotopes of elements Z = 105 to Z = 117 identified among the products of 249Bk+48Ca reactions

    SciTech Connect

    Oganessian, Yuri Ts.; Abdullin, F. Sh.; Bailey, P. D.; Benker, D. E.; Bennett, M. E.; Dmitriev, S.; Ezold, Julie G.; Hamilton, J. H.; Henderson, R.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Moody, K.; Nelson, S. L.; Polyakov, A. N.; Porter, C. E.; Ramayya, A. V.; Riley, F. D.; Roberto, James B; Ryabinin, M. A.; Rykaczewski, Krzysztof Piotr; Taylor, R; Tsyganov, Yu. S.; Utyonkov, V.; Voinov, A. A.; Vostokin, G. K.; Wilk, P. A.

    2011-01-01

    The heaviest isotopes of elements Z = 117 to Z = 105, 294117, 293117, 290115, 289115, 286113, 285113, 282Rg, 281Rg, 278Mt, 274Bh, and 270Db, were identified by means of the Dubna gas-filled recoil separator among the products of the 249Bk + 48Ca reaction. The details of the observed six decay chains, indicating the production and decay of isotopes 293117 and 294117, are presented and discussed. The decay energies and resulting half-lives of these new nuclei show a strong rise of stability with increasing neutron number, validating the concept of the island of enhanced stability for superheavy nuclei.

  13. The deterioration of intermediate moisture foods

    NASA Technical Reports Server (NTRS)

    Labruza, T. P.

    1971-01-01

    Deteriorative reactions are low and food quality high if intermediate moisture content of a food is held at a water activity of 0.6 to 0.75. Information is of interest to food processing and packaging industry.

  14. The serum D-xylose test as a useful tool to identify malabsorption in rats with antigen specific gut inflammatory reaction.

    PubMed

    Antunes, Danielle Mota Fontes; da Costa, Janilda Pacheco; Campos, Sylvia Maria Nicolau; Paschoal, Patrícia Olaya; Garrido, Valéria; Siqueira, Munique; Teixeira, Gerlinde Agate Platais Brasil; Cardoso, Gilberto Perez

    2009-04-01

    The inappropriate immune response to foods, such as peanut, wheat and milk may be the basis in the pathogenesis of enteropathies like coeliac and Crohn disease, which present small intestinal malabsorption. A number of recent studies have utilized d-xylose absorption as an investigative tool to study small intestinal function in a variety of clinical settings. Thus, the aim of this experimental study was to evaluate the intestinal absorption of D-xylose in an antigen-specific gut inflammatory reaction rat model. Animals of the experimental group were inoculated with peanut protein extract before their exposure to a challenge diet containing exclusively peanut seeds to induce the gut inflammatory reaction caused by peanut allergy. Our results show that systemic inoculation with peanut protein extract renders significantly higher antibody titres (5.085 +/- 0.126 units) (P < 0.0001) than control rats (0.905 +/- 0.053 units) and that the antibody titres correlate positively to an inflammatory alteration of the gut morphology (P < 0.0001). Animals pertaining to the experimental group showed an intestinal absorption of D-xylose lower than control rats (P < 0.0001). We also observed that D-xylose absorption correlates negatively with IgG titres and positively with morphometric parameters (Pearson correlation). In conclusion, the use of serum D-xylose test was useful to identify the presence of small intestinal malabsorption in our antigen specific gut inflammatory reaction rat model.

  15. Use of duplex polymerase chain reaction (duplex-PCR) technique to identify bovine and water buffalo milk used in making mozzarella cheese.

    PubMed

    Rea, S; Chikuni, K; Branciari, R; Sangamayya, R S; Ranucci, D; Avellini, P

    2001-11-01

    Molecular biology techniques have been used for species identification in food of animal origin in relatively recent years. A polymerase chain reaction (PCR) based method, the multiplex PCR, was recently applied to species identification in meat and meat products. It allows co-amplification of separate regions of a single gene or specific fragments, each typical of a different animal species in a single PCR reaction, using different pairs of primers in the same reaction mix. In the present paper, the duplex-PCR technique is proposed to identify bovine and water buffalo DNA in a single PCR assay in milk and mozzarella cheese (a typical Italian cheese, originally made from pure water buffalo milk). Because of its lower cost, undeclared bovine milk is added to water buffalo milk for making different kinds of mozzarella cheese. The results of this experiment indicate the applicability of this method, which showed an absolute specificity for the two species and a high sensitivity even down to low DNA concentrations (1 pg). In bovine and water buffalo mixtures of both milk and mozzarella cheese, the minimum concentration tested was 1% of bovine in water buffalo milk and water buffalo in bovine milk. The importance of the somatic cell content in raw milk is also discussed with special reference to the evaluation of mixtures (milk or cheese) of the two species.

  16. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

    PubMed

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I; Wilmanns, Matthias; Vértessy, Beáta G

    2013-12-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure. PMID:23982515

  17. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling

    PubMed Central

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I.; Wilmanns, Matthias; Vértessy, Beáta G.

    2013-01-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason–Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy (31P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme–product complex structure. PMID:23982515

  18. An Artificial Enzyme Made by Covalent Grafting of an Fe(II) Complex into β-Lactoglobulin: Molecular Chemistry, Oxidation Catalysis, and Reaction-Intermediate Monitoring in a Protein.

    PubMed

    Buron, Charlotte; Sénéchal-David, Katell; Ricoux, Rémy; Le Caër, Jean-Pierre; Guérineau, Vincent; Méjanelle, Philippe; Guillot, Régis; Herrero, Christian; Mahy, Jean-Pierre; Banse, Frédéric

    2015-08-17

    An artificial metalloenzyme based on the covalent grafting of a nonheme Fe(II) polyazadentate complex into bovine β-lactoglobulin has been prepared and characterized by using various spectroscopic techniques. Attachment of the Fe(II) catalyst to the protein scaffold is shown to occur specifically at Cys121. In addition, spectrophotometric titration with cyanide ions based on the spin-state conversion of the initial high spin (S=2) Fe(II) complex into a low spin (S=0) one allows qualitative and quantitative characterization of the metal center's first coordination sphere. This biohybrid catalyst activates hydrogen peroxide to oxidize thioanisole into phenylmethylsulfoxide as the sole product with an enantiomeric excess of up to 20 %. Investigation of the reaction between the biohybrid system and H2 O2 reveals the generation of a high spin (S=5/2) Fe(III) (η(2) -O2 ) intermediate, which is proposed to be responsible for the catalytic sulfoxidation of the substrate. PMID:26178593

  19. Eleven new heaviest isotopes of elements Z=105 to Z=117 identified among the products of {sup 249}Bk+{sup 48}Ca reactions

    SciTech Connect

    Oganessian, Yu. Ts.; Abdullin, F. Sh.; Dmitriev, S. N.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Polyakov, A. N.; Sagaidak, R. N.; Shirokovsky, I. V.; Subbotin, V. G.; Sukhov, A. M.; Tsyganov, Yu. S.; Utyonkov, V. K.; Voinov, A. A.; Vostokin, G. K.; Bailey, P. D.; Benker, D. E.; Ezold, J. G.; Porter, C. E.; Riley, F. D.

    2011-05-15

    The heaviest isotopes of elements Z=117 to Z=105, {sup 294}117, {sup 293}117, {sup 290}115, {sup 289}115, {sup 286}113, {sup 285}113, {sup 282}Rg, {sup 281}Rg, {sup 278}Mt, {sup 274}Bh, and {sup 270}Db, were identified by means of the Dubna gas-filled recoil separator among the products of the {sup 249}Bk + {sup 48}Ca reaction. The details of the observed six decay chains, indicating the production and decay of isotopes {sup 293}117 and {sup 294}117, are presented and discussed. The decay energies and resulting half-lives of these new nuclei show a strong rise of stability with increasing neutron number, validating the concept of the island of enhanced stability for superheavy nuclei [Oganessian et al., Phys. Rev. Lett. 104, 142502 (2010)].

  20. Dihydrogen catalysis: a degradation mechanism for N2-fixation intermediates.

    PubMed

    Asatryan, Rubik; Bozzelli, Joseph W; Ruckenstein, Eli

    2012-11-29

    Molecular hydrogen plays multiple roles in activation of nitrogen. Among others, it inhibits the overall process of N(2)-reduction catalyzed by nitrogenase enzyme. The H(2)-assisted dehydrogenation and the H-atom transfer reactions (called dihydrogen catalysis, DHC) are suggested as possible mechanisms for the degradation and removal of potential intermediates formed during the reduction of nitrogen. Several iron-organic model reactions associated with the core stereospecific reaction (cis-N(2)H(2) + H(2) → N(2) + H(2) + H(2)) are examined using a comprehensive density functional theory and ab initio analysis of the corresponding potential energy surfaces. A variety of energetically feasible decomposition pathways are identified for the DHC-oxidation of iron-bound [N(x)H(y)]-species. A liberated diazene intermediate (HN═NH) is suggested to interact in situ with two proximal hydridic H-atoms of an activated (hydrided) Fe-catalyst to produce N(2) and H(2) with a low or even no activation barrier. The majority of identified pathways are shown to be highly sensitive to the electronic environment and spin configuration of metallocomplexes. The H(2)-assisted transport of a single H-atom from a bound [N(x)H(y)] moiety to either the proximal or distal (Fe, S or N) active centers of a catalyst provides an alternative degradation (interconversion) mechanism for the relevant intermediates. The two types of molecular hydrogen-assisted reactions highlighted above, namely, the H(2)-assisted dehydrogenation and the transport of H-atoms, suggest theoretical interpretations for the observed H(2)-inhibition of N(2) activation and HD formation (in the presence of D(2)). The DHC reactions of various [N(x)H(y)] moieties are expected to play significant roles in the industrial high-pressure hydrodenitrification and other catalytic processes involving the metabolism of molecular hydrogen. PMID:23095090

  1. Reaction of o-benzyne with tropothione involving biradical processes.

    PubMed

    Yamabe, Shinichi; Minato, Tsutomu; Ishiwata, Akihiro; Irinamihira, Osamu; Machiguchi, Takahisa

    2007-04-13

    A benzyne-tropothione reaction was studied experimentally and computationally. Three isomeric products were detected by a careful experiment using two benzyne sources. The three equimolar products were identified. The expected symmetry-allowed [4+2] or [8+2] cycloadduct was not detected. In order to explain the unexpected products, density functional calculations and complete active space self-consistent field (CASSCF) calculations were carried out. The benzyne is, first, added to the tropothione via one-center C-S bond formation. Then a singlet biradical intermediate is formed. In the biradical, an alpha hydrogen atom of the tropothione moiety is moved to the benzyne moiety. A closed-shell intermediate is generated. This allene-type intermediate is isomerized to the second intermediate. The intramolecular proton shift in the latter leads to the three products. The biradical character of the benzyne has a key role in the present reaction and was discussed in reference to other benzyne reactions.

  2. Development and evaluation of real-time polymerase chain reaction assays to identify mosquito (Diptera: Culicidae) bloodmeals originating from native Australian mammals.

    PubMed

    van den Hurk, Andrew F; Smith, Ina L; Smith, Greg A

    2007-01-01

    Real-time TaqMan polymerase chain reaction (PCR) assays were developed for the identification of mosquito (Diptera: Culicidae) bloodmeals originating from three groups of native Australian mammals. Primers and probes were designed to amplify a partial fragment of the cytochrome b gene of the agile wallaby, Macropus agilis (Gould); brushtail possum, Trichosurus vulpecula (Kerr); and the consensus sequence of the four species of Australian flying fox: Pteropus alecto Temminck, Pteropus conspicillatus Gould, Pteropus poliocephalus Temminck, and Pteropus scapulatus Peters. When tested on DNA extracted from whole tissue, each assay was shown to be specific for the vertebrate host that it was designed to identify. To evaluate the TaqMan assays, 137 field-collected blood-fed mosquitoes were analyzed, from which 128 (93.4%) were identified using one of the assays. Compared with other PCR-based techniques for bloodmeal identification, the TaqMan assays are sensitive, specific, and provide a rapid result without the need for post-PCR manipulation and visualization of products. PMID:17294925

  3. Functionalization of the corrole ring: the role of isocorrole intermediates.

    PubMed

    Tortora, Luca; Nardis, Sara; Fronczek, Frank R; Smith, Kevin M; Paolesse, Roberto

    2011-04-14

    Bromination of 3-nitro-5,10,15-triarylcorrole selectively provides two regioisomers, depending on the reaction pathway. An isocorrole species is the key intermediate to drive the reaction towards the 2-Br-17-nitro regioisomer.

  4. Propene oxidation at low and intermediate temperatures

    SciTech Connect

    Wilk, R.D.; Cernansky, N.P. . Dept. of Mechanical Engineering); Pitz, W.J.; Westbrook, C.K. )

    1989-08-01

    A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 530-740 {Kappa}, equivalence ratios of 0.8-2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species and all conditions measured experimentally in the static reactor. Overall, the calculated concentrations of carbon monoxide and acetaldehyde agreed well with those measured. The calculated concentrations of ethene are low compared to the experimental measurements, and the calculated concentrations of the formaldehyde are high. Agreement for concentrations of carbon dioxide, methane, methanol, acrolein, and propene oxide is mixed. The characteristic s-shape of the fuel concentration history is well predicted. Modeling calculations identified some of the key reaction steps at the present conditions. Addition of OH to propene and H-atom abstraction by OH from propene are important steps in determining the subsequent distributions of intermediate products, such as acetaldehyde, acrolein and formaldehyde. Allyl radicals are very abundant in propene oxidation, and the primary steps found to be responsible for their consumption are reaction with HO/sub 2/ and CH/sub 3/O/sub 2/.

  5. A Label-free Selected Reaction Monitoring Workflow Identifies a Subset of Pregnancy Specific Glycoproteins as Potential Predictive Markers of Early-onset Pre-eclampsia*

    PubMed Central

    Blankley, Richard T.; Fisher, Christal; Westwood, Melissa; North, Robyn; Baker, Philip N.; Walker, Michael J.; Williamson, Andrew; Whetton, Anthony D.; Lin, Wanchang; McCowan, Lesley; Roberts, Claire T.; Cooper, Garth J. S.; Unwin, Richard D.; Myers, Jenny E.

    2013-01-01

    Pre-eclampsia (PE) is a serious complication of pregnancy with potentially life threatening consequences for both mother and baby. Presently there is no test with the required performance to predict which healthy first-time mothers will go on to develop PE. The high specificity, sensitivity, and multiplexed nature of selected reaction monitoring holds great potential as a tool for the verification and validation of putative candidate biomarkersfor disease states. Realization of this potential involves establishing a high throughput, cost effective, reproducible sample preparation workflow. We have developed a semi-automated HPLC-based sample preparation workflow before a label-free selected reaction monitoring approach. This workflow has been applied to the search for novel predictive biomarkers for PE. To discover novel candidate biomarkers for PE, we used isobaric tagging to identify several potential biomarker proteins in plasma obtained at 15 weeks gestation from nulliparous women who later developed PE compared with pregnant women who remained healthy. Such a study generates a number of “candidate” biomarkers that require further testing in larger patient cohorts. As proof-of-principle, two of these proteins were taken forward for verification in a 100 women (58 PE, 42 controls) using label-free SRM. We obtained reproducible protein quantitation across the 100 samples and demonstrated significant changes in protein levels, even with as little as 20% change in protein concentration. The SRM data correlated with a commercial ELISA, suggesting that this is a robust workflow suitable for rapid, affordable, label-free verification of which candidate biomarkers should be taken forward for thorough investigation. A subset of pregnancy-specific glycoproteins (PSGs) had value as novel predictive markers for PE. PMID:23897580

  6. Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

    SciTech Connect

    Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Tropsha, Alexander

    2015-04-15

    Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using Random Forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers was 71–88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR Toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the Scorecard database of possible skin or sense organ toxicants as primary candidates for experimental validation. - Highlights: • It was compiled the largest publicly-available skin sensitization dataset. • Predictive QSAR models were developed for skin sensitization. • Developed models have higher prediction accuracy than OECD QSAR Toolbox. • Putative

  7. Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

    PubMed Central

    Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Andrade, Carolina H.; Tropsha, Alexander

    2015-01-01

    Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using random forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers were 71–88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the ScoreCard database of possible skin or sense organ toxicants as primary candidates for experimental validation. PMID:25560674

  8. Some Intermediate-Level Violin Concertos.

    ERIC Educational Resources Information Center

    Abramson, Michael

    1997-01-01

    Contends that many violin students attempt difficult concertos before they are technically or musically prepared. Identifies a variety of concertos at the intermediate and advanced intermediate-level for students to study and master before attempting the advanced works by Bach and Mozart. Includes concertos by Vivaldi, Leclair, Viotti, Haydn,…

  9. Multiplex polymerase chain reaction to identify and determine the toxigenicity of Corynebacterium spp with zoonotic potential and an overview of human and animal infections

    PubMed Central

    Torres, Luciene de Fátima Costa; Ribeiro, Dayana; Hirata, Raphael; Pacheco, Luis Gustavo Carvalho; Souza, Monica Cristina; dos Santos, Louisy Sanches; dos Santos, Cíntia Silva; Salah, Mohammad; da Costa, Mateus Matiuzzi; Ribeiro, Marcio Garcia; Selim, Salah A; Azevedo, Vasco Ariston de Carvalho; Mattos-Guaraldi, Ana Luiza

    2013-01-01

    Corynebacterium diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis constitute a group of potentially toxigenic microorganisms that are related to different infectious processes in animal and human hosts. Currently, there is a lack of information on the prevalence of disease caused by these pathogens, which is partially due to a reduction in the frequency of routine laboratory testing. In this study, a multiplex polymerase chain reaction (mPCR) assay that can simultaneously identify and determine the toxigenicity of these corynebacterial species with zoonotic potential was developed. This assay uses five primer pairs targeting the following genes: rpoB (Corynebacterium spp), 16S rRNA (C. ulcerans and C. pseudotuberculosis), pld (C. pseudotuberculosis), dtxR (C. diphtheriae) and tox [diphtheria toxin (DT) ]. In addition to describing this assay, we review the literature regarding the diseases caused by these pathogens. Of the 213 coryneform strains tested, the mPCR results for all toxigenic and non-toxigenic strains of C . diphtheriae, C. ulcerans and C. pseudotuberculosis were in 100% agreement with the results of standard biochemical tests and PCR-DT. As an alternative to conventional methods, due to its advantages of specificity and speed, the mPCR assay used in this study may successfully be applied for the diagnosis of human and/or animal diseases caused by potentially toxigenic corynebacterial species. PMID:23778659

  10. Multiplex polymerase chain reaction to identify and determine the toxigenicity of Corynebacterium spp with zoonotic potential and an overview of human and animal infections.

    PubMed

    Torres, Luciene de Fátima Costa; Ribeiro, Dayana; Hirata Jr, Raphael; Pacheco, Luis Gustavo Carvalho; Souza, Monica Cristina; dos Santos, Louisy Sanches; dos Santos, Cíntia Silva; Salah, Mohammad; Costa, Mateus Matiuzzi da; Ribeiro, Marcio Garcia; Selim, Salah A; Azevedo, Vasco Ariston de Carvalho; Mattos-Guaraldi, Ana Luiza

    2013-05-01

    Corynebacterium diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis constitute a group of potentially toxigenic microorganisms that are related to different infectious processes in animal and human hosts. Currently, there is a lack of information on the prevalence of disease caused by these pathogens, which is partially due to a reduction in the frequency of routine laboratory testing. In this study, a multiplex polymerase chain reaction (mPCR) assay that can simultaneously identify and determine the toxigenicity of these corynebacterial species with zoonotic potential was developed. This assay uses five primer pairs targeting the following genes: rpoB (Corynebacterium spp), 16S rRNA (C. ulcerans and C. pseudotuberculosis), pld (C. pseudotuberculosis), dtxR (C. diphtheriae) and tox [diphtheria toxin (DT) ]. In addition to describing this assay, we review the literature regarding the diseases caused by these pathogens. Of the 213 coryneform strains tested, the mPCR results for all toxigenic and non-toxigenic strains of C . diphtheriae, C. ulcerans and C. pseudotuberculosis were in 100% agreement with the results of standard biochemical tests and PCR-DT. As an alternative to conventional methods, due to its advantages of specificity and speed, the mPCR assay used in this study may successfully be applied for the diagnosis of human and/or animal diseases caused by potentially toxigenic corynebacterial species.

  11. Individual and combined diagnostic accuracy of ultrasound diagnosis, ultrasound-guided fine-needle aspiration and polymerase chain reaction in identifying tuberculous lymph nodes in the neck.

    PubMed

    Kim, Dong Wook; Jung, Soo Jin; Ha, Tae Kwun; Park, Ha Kyoung

    2013-12-01

    The aim of this study was to assess the efficacy of, both individually and in combination, ultrasound (US) diagnosis, US-guided fine-needle aspiration (US-FNA) and polymerase chain reaction (PCR) in diagnosing tuberculous lymph nodes in the neck (i.e., tuberculous cervical lymph nodes [TCLs]). Eighty-two patients who underwent US diagnosis, US-FNA and PCR for clinical suspicion of TCLs were enrolled. Of the 82 patients, 31 were confirmed as having TCLs. The sensitivity, specificity, positive and negative predictive values and accuracy of US diagnosis, US-FNA and PCR were 93.5%, 76.5%, 70.7%, 95.1% and 82.9%; 64.5%, 98.0%, 95.2%, 82.0% and 85.4%; and 100%, 96.1%, 93.9%, 100% and 97.6%, respectively. The diagnostic values of PCR alone and in combination with US-FNA were found to be higher than those of other methods. No US feature with high sensitivity and specificity was identified.

  12. Data requirements for intermediate energy nuclear applications

    SciTech Connect

    Pearlstein, S.

    1990-01-01

    Several applications that include spallation neutron sources, space radiation effects, biomedical isotope production, accelerator shielding and radiation therapy make use of intermediate energy nuclear data extending to several GeV. The overlapping data needs of these applications are discussed in terms of what projectiles, targets and reactions are of interest. Included is a discussion of what is generally known about these data and what is needed to facilitate their use in intermediate energy applications. 40 refs., 2 figs., 2 tabs.

  13. Degradation of methyl bromide and methyl chloride in soil microcosms: Use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms

    NASA Astrophysics Data System (ADS)

    Miller, Laurence G.; Warner, Karen L.; Baesman, Shaun M.; Oremland, Ronald S.; McDonald, Ian R.; Radajewski, Stefan; Murrell, J. Colin

    2004-08-01

    Bacteria in soil microcosm experiments oxidized elevated levels of methyl chloride (MeCl) and methyl bromide (MeBr), the former compound more rapidly than the latter. MeBr was also removed by chemical reactions while MeCl was not. Chemical degradation dominated the early removal of MeBr and accounted for more than half of its total loss. Fractionation of stable carbon isotopes during chemical degradation of MeBr resulted in a kinetic isotope effect (KIE) of 59 ± 7‰. Soil bacterial oxidation dominated the later removal of MeBr and MeCl and was characterized by different KIEs for each compound. The KIE for MeBr oxidation was 69 ± 9‰ and the KIE for MeCl oxidation was 49 ± 3‰. Stable isotope probing revealed that different populations of soil bacteria assimilated added 13C-labeled MeBr and MeCl. The identity of the active MeBr and MeCl degrading bacteria in soil was determined by analysis of 16S rRNA gene sequences amplified from 13C-DNA fractions, which identified a number of sequences from organisms not previously thought to be involved in methyl halide degradation. These included Burkholderia, the major clone type in the 13C-MeBr fraction, and Rhodobacter, Lysobacter and Nocardioides the major clone types in the 13C-MeCl fraction. None of the 16S rRNA gene sequences for methyl halide oxidizing bacteria currently in culture (including Aminobacter strain IMB-1 isolated from fumigated soil) were identified. Functional gene clone types closely related to Aminobacter spp. were identified in libraries containing the sequences for the cmuA gene, which codes for the enzyme known to catalyze the initial step in the oxidation of MeBr and MeCl. The cmuA gene was limited to members of the alpha-Proteobacteria whereas the greater diversity demonstrated by the 16S rRNA gene may indicate that other enzymes catalyze methyl halide oxidation in different groups of bacteria.

  14. Degradation of methyl bromide and methyl chloride in soil microcosms: Use of stable C isotope fractionation and stable isotope probing to identify reactions and the responsible microorganisms

    USGS Publications Warehouse

    Miller, L.G.; Warner, K.L.; Baesman, S.M.; Oremland, R.S.; McDonald, I.R.; Radajewski, S.; Murrell, J.C.

    2004-01-01

    Bacteria in soil microcosm experiments oxidized elevated levels of methyl chloride (MeCl) and methyl bromide (MeBr), the former compound more rapidly than the latter. MeBr was also removed by chemical reactions while MeCl was not. Chemical degradation dominated the early removal of MeBr and accounted for more than half of its total loss. Fractionation of stable carbon isotopes during chemical degradation of MeBr resulted in a kinetic isotope effect (KIE) of 59 ?? 7???. Soil bacterial oxidation dominated the later removal of MeBr and MeCl and was characterized by different KIEs for each compound. The KIE for MeBr oxidation was 69 ?? 9??? and the KIE for MeCl oxidation was 49 ?? 3???. Stable isotope probing revealed that different populations of soil bacteria assimilated added 13C-labeled MeBr and MeCl. The identity of the active MeBr and MeCl degrading bacteria in soil was determined by analysis of 16S rRNA gene sequences amplified from 13C-DNA fractions, which identified a number of sequences from organisms not previously thought to be involved in methyl halide degradation. These included Burkholderia , the major clone type in the 13C-MeBr fraction, and Rhodobacter, Lysobacter and Nocardioides the major clone types in the 13C-MeCl fraction. None of the 16S rRNA gene sequences for methyl halide oxidizing bacteria currently in culture (including Aminobacter strain IMB-1 isolated from fumigated soil) were identified. Functional gene clone types closely related to Aminobacter spp. were identified in libraries containing the sequences for the cmuA gene, which codes for the enzyme known to catalyze the initial step in the oxidation of MeBr and MeCl. The cmuA gene was limited to members of the alpha-Proteobacteria whereas the greater diversity demonstrated by the 16S rRNA gene may indicate that other enzymes catalyze methyl halide oxidation in different groups of bacteria. Copyright ?? 2004 Elsevier Ltd.

  15. Reactions of the bis(dialkylphosphino)methane complexes Pd2X2(μ-R2PCH2PR2)2 (X = halogen, R = Me or Et) with H2S, S8, COS, and CS2; detection of reaction intermediates.

    PubMed

    Pamplin, Craig B; Rettig, Steven J; Patrick, Brian O; James, Brian R

    2011-09-01

    The Pd(2)X(2)(dmpm)(2) complexes [X = Cl (1a), Br (1b), I (1c); dmpm = bis(dimethylphosphino)methane. In all the dipalladium complexes mentioned in this paper, the dmpm, depm, and dppm ligands (unless stated otherwise) are bridging, but for convenience the μ-symbol is omitted.] react with H(2)S to yield H(2) and the bridged-sulfido complexes Pd(2)X(2)(μ-S)(dmpm)(2) (2a-c), of which 2a and 2b are structurally characterized. With 1a, two rapid reversible equilibria are observed by NMR spectroscopy below -30 °C, and two reaction intermediates are detected; both are likely hydrido(mercapto) species. Reaction of 1a with 1 equiv of elemental sulfur also yields 2a. The reaction of 1a with COS results in the initial formation of Pd(2)Cl(2)(μ-COS)(dmpm)(2) (3) that undergoes decarbonylation to yield 2a and Pd(2)Cl(2)(μ-CO)(dmpm)(2) (4), which is also formed via reversible insertion of the CO into the Pd-Pd bond of 1a. The solid-state molecular structure of the previously reported complex Pd(2)Cl(2)(μ-CS(2))(dmpm)(2) (5), together with solution NMR data for 3 and 5, reveal that the bridging heterocumulene ligands coordinate in an η(2)-C,S fashion. Analogous findings were made for the corresponding Pd(2)X(2)(depm)(2) complexes [X = Cl (1a'), Br (1b'), I (1c'); depm = bis(diethylphosphino)methane], although no μ-COS species was detected. The Pd(2)X(2)(μ-S)(depm)(2) complex was structurally characterized. Differences in the chemistry of the previously studied, corresponding dppm systems (dppm = bis(diphenylphosphino)methane) are discussed.

  16. Water-Shale interactions in bench-top and high pressure/high temperature autoclave experiments: Identifying geochemical reaction controlling flow back water chemistry

    NASA Astrophysics Data System (ADS)

    Mickler, P. J.; Lu, J.; Nicot, J.

    2013-12-01

    increase in alkalinity during the experiment. Molar comparisons between Na-Cl and Ca-SO4 suggest Ca is preferentially removed from solution and Na is added to solution through interactions with clay minerals. Cation exchange and desorption during clay hydration likely has a secondary effect on the observed geochemical trend. Ca is sorbed and Na is released preferentially resulting in a Ca depletion seen on the Ca vs. SO4 plot and a Na excess seen in the Na vs. Cl plot. Although this study does not consider mixing of HF-water with formation brines, the identified water-rock reactions may provide insights into observed flow-back water chemistry.

  17. Water-Shale interactions in bench-top and high pressure/high temperature autoclave experiments: Identifying geochemical reaction controlling flow back water chemistry

    NASA Astrophysics Data System (ADS)

    Molnar, I. L.; O'Carroll, D. M.; Willson, C. S.; Gerhard, J.

    2011-12-01

    increase in alkalinity during the experiment. Molar comparisons between Na-Cl and Ca-SO4 suggest Ca is preferentially removed from solution and Na is added to solution through interactions with clay minerals. Cation exchange and desorption during clay hydration likely has a secondary effect on the observed geochemical trend. Ca is sorbed and Na is released preferentially resulting in a Ca depletion seen on the Ca vs. SO4 plot and a Na excess seen in the Na vs. Cl plot. Although this study does not consider mixing of HF-water with formation brines, the identified water-rock reactions may provide insights into observed flow-back water chemistry.

  18. Unraveling curcumin degradation: autoxidation proceeds through spiroepoxide and vinylether intermediates en route to the main bicyclopentadione.

    PubMed

    Gordon, Odaine N; Luis, Paula B; Sintim, Herman O; Schneider, Claus

    2015-02-20

    Curcumin is a dietary anti-inflammatory and chemopreventive agent consisting of two methoxyphenol rings connected by a conjugated heptadienedione chain. Curcumin is unstable at physiological pH and rapidly degrades in an autoxidation reaction to a major bicyclopentadione product in which the 7-carbon chain has undergone oxygenation and double cyclization. Early degradation products (but not the final bicyclopentadione) mediate topoisomerase poisoning and possibly many other activities of curcumin, but it is not known how many and what autoxidation products are formed, nor their mechanism of formation. Here, using [(14)C2]curcumin as a tracer, seven novel autoxidation products, including two reaction intermediates, were isolated and identified using one- and two-dimensional NMR and mass spectrometry. The unusual spiroepoxide and vinylether reaction intermediates are precursors to the final bicyclopentadione product. A mechanism for the autoxidation of curcumin is proposed that accounts for the addition and exchange of oxygen that have been determined using (18)O2 and H2(18)O. Several of the by-products are formed from an endoperoxide intermediate via reactions that are well precedented in lipid peroxidation. The electrophilic spiroepoxide intermediate formed a stable adduct with N-acetylcysteine, suggesting that oxidative transformation is required for biological effects mediated by covalent adduction to protein thiols. The spontaneous autoxidation distinguishes curcumin among natural polyphenolic compounds of therapeutic interest; the formation of chemically diverse reactive and electrophilic products provides a novel paradigm for understanding the polypharmacological effects of curcumin.

  19. Molecular response assessment by quantitative real-time polymerase chain reaction after induction therapy in NPM1-mutated patients identifies those at high risk of relapse

    PubMed Central

    Hubmann, Max; Köhnke, Thomas; Hoster, Eva; Schneider, Stephanie; Dufour, Annika; Zellmeier, Evelyn; Fiegl, Michael; Braess, Jan; Bohlander, Stefan K.; Subklewe, Marion; Sauerland, Maria-Cristina; Berdel, Wolfgang E.; Büchner, Thomas; Wörmann, Bernhard; Hiddemann, Wolfgang; Spiekermann, Karsten

    2014-01-01

    Monitoring minimal residual disease is an important way to identify patients with acute myeloid leukemia at high risk of relapse. In this study we investigated the prognostic potential of minimal residual disease monitoring by quantitative real-time polymerase chain reaction analysis of NPM1 mutations in patients treated in the AMLCG 1999, 2004 and 2008 trials. Minimal residual disease was monitored - in aplasia, after induction therapy, after consolidation therapy, and during follow-up - in 588 samples from 158 patients positive for NPM1 mutations A, B and D (with a sensitivity of 10−6). One hundred and twenty-seven patients (80.4%) achieved complete remission after induction therapy and, of these, 56 patients (44.1%) relapsed. At each checkpoint, minimal residual disease cut-offs were calculated. After induction therapy a cut-off NPM1 mutation ratio of 0.01 was associated with a high hazard ratio of 4.26 and the highest sensitivity of 76% for the prediction of relapse. This was reflected in a cumulative incidence of relapse after 2 years of 77.8% for patients with ratios above the cut-off versus 26.4% for those with ratios below the cut-off. In the favorable subgroup according to European LeukemiaNet, the cut-off after induction therapy also separated the cohort into two prognostic groups with a cumulative incidence of relapse of 76% versus 6% after 2 years. Our data demonstrate that in addition to pre-therapeutic factors, the course of minimal residual disease in an individual is an important prognostic factor and could be included in clinical trials for the guidance of post-remission therapy. The trials from which data were obtained were registered at www.clinicaltrials.gov (#NCT01382147, #NCT00266136) and at the European Leukemia Trial Registry (#LN_AMLINT2004_230). PMID:24816240

  20. A comparative study of nitrite reduction by synthetic and biogenic Fe(II-III) hydroxysalts green rusts: Evidence for hydroxyl-nitrite green rust formation as an intermediate reaction product.

    NASA Astrophysics Data System (ADS)

    Ona-Nguema, G.; Guerbois, D.; Morin, G.; Zhang, Y.; Noel, V.; Brest, J.

    2013-12-01

    -GR(Cl) led to the reduction of nitrite ions to ammonium, and that the production of ammonium depended on their Fe(II) content. XRD patterns indicated that both synthetic green rusts were fully oxidized into magnetite during the reaction with nitrite. For biogenic green rusts, the study revealed that both bio-GR(CO3)F and bio-GR(CO3)L were capable of reducing nitrite ions without ammonium production, suggesting the conversion of nitrite ions to nitrogen gas. Moreover, we provided evidence for the first time that the interactions of bio-GR(CO3)F with nitrite led to the formation of an hydroxy-nitrite green rust as a result of the incorporation of nitrite in the interlayer region of bio-GR(CO3)F; such an intercalation of nitrite ions was not observed in experiments with bio-GR(CO3)L. XRD analysis indicated that GR(NO2) was formed as an intermediate reaction product prior to the fully oxidation of GR to ferric oxyhydroxides. [1] Philips S., Laanbroek H. J. and Verstraete W. (2002). Rev. Environ. Sci. Biotechnol. 1, 115-141.

  1. Intermediate-energy nuclear chemistry workshop

    SciTech Connect

    Butler, G.W.; Giesler, G.C.; Liu, L.C.; Dropesky, B.J.; Knight, J.D.; Lucero, F.; Orth, C.J.

    1981-05-01

    This report contains the proceedings of the LAMPF Intermediate-Energy Nuclear Chemistry Workshop held in Los Alamos, New Mexico, June 23-27, 1980. The first two days of the Workshop were devoted to invited review talks highlighting current experimental and theoretical research activities in intermediate-energy nuclear chemistry and physics. Working panels representing major topic areas carried out indepth appraisals of present research and formulated recommendations for future research directions. The major topic areas were Pion-Nucleus Reactions, Nucleon-Nucleus Reactions and Nuclei Far from Stability, Mesonic Atoms, Exotic Interactions, New Theoretical Approaches, and New Experimental Techniques and New Nuclear Chemistry Facilities.

  2. [Intermediate phenotype studies in psychiatric disorder].

    PubMed

    Hashimoto, Ryota

    2016-02-01

    The concept of intermediate phenotype was proposed by Dr. Weinberger of the National Institute of Mental Health (NIMH). The risk genes for mental disorders define intermediate phenotypes, neurobiological characteristics observed in psychiatric disorders, and intermediate phenotypes increase the risk of mental disorders. The author worked at Dr. Weinberger's laboratory, and after returning home, introduced the concept to Japan, creating a term "Chukanhyogengata" to translate "intermediate phenotype". Intermediate phenotype has been proposed as a tool for the identification of risk genes for mental disorders, spreading the concept as a biomarker for the bridging between genes and behaviors. Intermediate phenotype studies later became one of the main pillars of psychiatric research. As a large number of data and samples are needed for intermediate phenotype research, we built a research resource database that combines the brain phenotype and bioresources. We performed genome-wide association analysis of cognitive decline in schizophrenia and identified the DEGS2 gene using this sample. This research resource database was developed for a multicenter study by COCORO (Cognitive Genetics Collaborative Research Organization). COCORO carried out genome-wide association analysis of the gray matter volume of the superior temporal gyrus and identified genome-wide significant loci. In this paper, we introduce the concept and history of intermediate phenotype study of mental illness and the latest trends. We hope to contribute to the future development of mental illness research through translational research. PMID:27044135

  3. [Intermediate phenotype studies in psychiatric disorder].

    PubMed

    Hashimoto, Ryota

    2016-02-01

    The concept of intermediate phenotype was proposed by Dr. Weinberger of the National Institute of Mental Health (NIMH). The risk genes for mental disorders define intermediate phenotypes, neurobiological characteristics observed in psychiatric disorders, and intermediate phenotypes increase the risk of mental disorders. The author worked at Dr. Weinberger's laboratory, and after returning home, introduced the concept to Japan, creating a term "Chukanhyogengata" to translate "intermediate phenotype". Intermediate phenotype has been proposed as a tool for the identification of risk genes for mental disorders, spreading the concept as a biomarker for the bridging between genes and behaviors. Intermediate phenotype studies later became one of the main pillars of psychiatric research. As a large number of data and samples are needed for intermediate phenotype research, we built a research resource database that combines the brain phenotype and bioresources. We performed genome-wide association analysis of cognitive decline in schizophrenia and identified the DEGS2 gene using this sample. This research resource database was developed for a multicenter study by COCORO (Cognitive Genetics Collaborative Research Organization). COCORO carried out genome-wide association analysis of the gray matter volume of the superior temporal gyrus and identified genome-wide significant loci. In this paper, we introduce the concept and history of intermediate phenotype study of mental illness and the latest trends. We hope to contribute to the future development of mental illness research through translational research.

  4. Intermediate Filament Diseases: Desminopathy

    PubMed Central

    Goldfarb, Lev G.; Olivé, Montse; Vicart, Patrick; Goebel, Hans H.

    2009-01-01

    Desminopathy is one of the most common intermediate filament human disorders associated with mutations in closely interacting proteins, desmin and alphaB-crystallin. The inheritance pattern in familial desminopathy is characterized as autosomal dominant or autosomal recessive, but many cases have no family history. At least some and likely most sporadic desminopathy cases are associated with de novo DES mutations. The age of disease onset and rate of progression may vary depending on the type of inheritance and location of the causative mutation. Typically, the illness presents with lower and later upper limb muscle weakness slowly spreading to involve truncal, neck-flexor, facial and bulbar muscles. Skeletal myopathy is often combined with cardiomyopathy manifested by conduction blocks, arrhythmias and chronic heart failure resulting in premature sudden death. Respiratory muscle weakness is a major complication in some patients. Sections of the affected skeletal and cardiac muscles show abnormal fibre areas containing chimeric aggregates consisting of desmin and other cytoskeletal proteins. Various DES gene mutations: point mutations, an insertion, small in-frame deletions and a larger exon-skipping deletion, have been identified in desminopathy patients. The majority of these mutations are located in conserved alpha-helical segments, but additional mutations have recently been identified in the tail domain. Filament and network assembly studies indicate that most but not all disease-causing mutations make desmin assembly-incompetent and able to disrupt a pre-existing filamentous network in dominant-negative fashion. AlphaB-crystallin serves as a chaperone for desmin preventing its aggregation under various forms of stress; mutant CRYAB causes cardiac and skeletal myopathies identical to those resulting from DES mutations. PMID:19181099

  5. Single cell laser dissection with molecular beacon polymerase chain reaction identifies 2A as the predominant serotonin receptor subtype in hypoglossal motoneurons.

    PubMed

    Zhan, G; Shaheen, F; Mackiewicz, M; Fenik, P; Veasey, S C

    2002-01-01

    We hypothesize that sleep state-dependent withdrawal of serotonin (5-hydroxytryptamine, 5-HT) at upper airway (UAW) dilator motoneurons contributes significantly to sleep-related suppression of dilator muscle activity in obstructive sleep apnea. Identification of 5-HT receptor subtypes involved in postsynaptic facilitation of UAW motoneuron activity may provide pharmacotherapies for this prevalent disorder. We have adapted two assays to provide semi-quantitative measurements of mRNA copy numbers for 5-HT receptor subtypes in single UAW motoneurons. Specifically, soma of 111 hypoglossal (XII) motoneurons in 10 adult male rats were captured using a laser dissection microscope, and then used individually in single round molecular beacon polymerase chain reaction (PCR) for real-time quantitation of 5-HT(2A), 5-HT(2C), 5-HT(3), 5-HT(4), 5-HT(5A), 5-HT(5B), 5-HT(6) or 5-HT(7) receptor. Receptor mRNA copy numbers from single XII motoneurons were compared to control samples from within the XII nucleus and lateral medulla. All 20 motoneuronal soma assayed for the 5-HT(2A) receptor had measurable copy numbers (7028+/-2656 copies/cell). In contrast, copy numbers for the 5-HT(2A) receptor in XII non-motoneuronal (n=17) and lateral medulla (n=15) samples were 81+/-51 copies and 83+/-35 copies, respectively, P<0.05. Seven of 13 XII motoneurons assayed had measurable 5-HT(2C) receptor copy numbers of mRNA (287+/-112 copies/cell). XII soma had minimal 5-HT(3), 5-HT(4), 5-HT(5A), 5-HT(5B), 5-HT(6) or 5-HT(7) receptor mRNA. 5-HT(2A) receptor mRNA presence within XII motoneurons was confirmed with digoxigenin-labeled in situ hybridization. In summary, combined use of laser dissection and molecular beacon PCR revealed 5-HT(2A) receptor as the predominant 5-HT receptor mRNA in XII motoneurons, and identified small quantities of 5-HT(2C) receptor. This information will allow a more complete understanding of serotonergic control of respiratory activity.

  6. Systematic interpretation of molecular beacon polymerase chain reaction for identifying rpoB mutations in Mycobacterium tuberculosis isolates with mixed resistant and susceptible bacteria.

    PubMed

    Gomez, Diana I; Fisher-Hoch, Susan P; Bordt, Andrea S; Quitugua, Teresa N; Robledo, Jaime; Alvarez, Nataly; Correa, Nidia; McCormick, Joseph B; Restrepo, Blanca I

    2010-05-01

    Detection of multidrug-resistant tuberculosis (MDR-TB), a frequent cause of treatment failure, takes 2 or more weeks to identify by culture. Rifampicin (RIF) resistance is a hallmark of MDR-TB, and detection of mutations in the rpoB gene of Mycobacterium tuberculosis using molecular beacon probes with real-time quantitative polymerase chain reaction (qPCR) is a novel approach that takes

  7. Carbon-13 nuclear magnetic resonance spectroscopic investigation of the Kiliani reaction

    SciTech Connect

    Blazer, R.M.; Whaley, T.W.

    1980-07-16

    The Kiliani reaction of D-arabinose with sodium (/sup 13/C)cyanide (or (/sup 13/C,/sup 15/N)cyanide) was studied by /sup 13/C NMR. The C-1 resonances of intermediates and products were observed as the reaction evolved. Intermediates were identified by addition of authentic samples to reaction solutions, interpretation of chemical shifts and coupling constants, and chemical experiments. Intermediates identified included cyanohydrins, amides, lactones, amidines, and an imidate. A discussion of the course of the reaction over the pH range 5.1 to 12.5 is presented. The final mannonate-to-gluconate ratio was shown to be a function of pH and not associated with the presence of certain metal ions. 2 figures, 1 table.

  8. A common intermediate for N2 formation in enzymes and zeolites: side-on Cu-nitrosyl complexes

    SciTech Connect

    Kwak, Ja Hun; Lee, Jong H.; Burton, Sarah D.; Lipton, Andrew S.; Peden, Charles HF; Szanyi, Janos

    2013-09-16

    Understanding the mechanisms of catalytic processes requires the identification of reaction centers and key intermediates, both of which are often achieved by the use of spectroscopic characterization tools. Due to the heterogeneity of active centers in heterogeneous catalysts, it is frequently difficult to identify the specific sites that are responsible for the overall activity. Furthermore, the simultaneous presence of a large number of surface species on the catalyst surface often poses a great challenge for the unambiguous determination of the relevant species in the reaction mechanism. In contrast, enzymes possess catalytically active centers with precisely defined coordination environments that are only able to accommodate intermediates relevant to the specific catalytic process. Here we show that side-on Cu+-NO+ complexes characterized by high magnetic field solid state magic angle spinning nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopies are the key intermediates in the selective catalytic reduction of NO over Cu-SSZ-13 zeolite catalysts. Analogous intermediates have been observed and characterized in nitrite reductase enzymes, and shown to be the critical intermediates in the formation of N2 for anaerobic ammonium oxidation reactions.[1] The identification of this key reaction intermediate, combined with the results of our prior kinetic studies, allows us to propose a new reaction mechanism for the selective catalytic reduction of NO with NH3 under oxygen-rich environments over Cu-SSZ-13 zeolites, a key reaction in automotive emission control. The authors acknowledge the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy/Vehicle Technologies Program for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental

  9. The aromatic ene reaction

    PubMed Central

    Niu, Dawen; Hoye, Thomas R.

    2014-01-01

    The ene reaction is a pericyclic process in which an alkene having an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed π-bond. The aromatic ene reaction, in which the alkene component is embedded in an aromatic ring, has only been reported in a few (four) instances and has proceeded in low yield (≤6%). Here we show efficient aromatic ene reactions in which a thermally generated aryne engages a pendant m-alkylarene substituent to produce a dearomatized isotoluene, itself another versatile but rare reactive intermediate. Our experiments were guided by computational studies that revealed structural features conducive to the aromatic ene process. We proceeded to identify a cascade comprising three reactions: (i) hexadehydro-Diels-Alder (for aryne generation), (ii) intramolecular aromatic ene, and (iii) bimolecular Alder ene. The power of this cascade is evident from the structural complexity of the final products, the considerable scope, and the overall efficiency of these multi-stage, reagent- and byproduct-free, single-pot transformations. PMID:24345944

  10. Efficient short step synthesis of Corey's tamiflu intermediate.

    PubMed

    Kipassa, Nsiama Tienabe; Okamura, Hiroaki; Kina, Kengo; Hamada, Toshiyuki; Iwagawa, Tetsuo

    2008-03-01

    Corey's tamiflu intermediate was synthesized from a bicyclolactam adduct obtained by base-catalyzed Diels-Alder reaction of N-nosyl-3-hydroxy-2-pyridone with ethyl acrylate. A compound that has the same array of functional groups with the Corey's intermediate was obtained in four steps from the DA adduct in 47% overall yield. The intermediate itself was also prepared efficiently by simply changing the protective group.

  11. Structure and Mechanistic Implications of a Tryptophan Synthase Quinonoid Intermediate

    SciTech Connect

    Barends,T.; Domratcheva, T.; Kulik, V.; Blumenstein, L.; Niks, D.; Dunn, M.; Schlichting, I.

    2008-01-01

    Quinonoid intermediates play a key role in the catalytic mechanism of pyridoxal 5'-phosphate (PLP)-dependent enzymes. Whereas structures of other PLP-bound reaction intermediates have been determined, a high-quality structure of a quinonoid species has not been reported. We present the crystal structure of the indoline quinonoid intermediate of tryptophan synthase (see figure) and discuss its implications for the enzymatic mechanism and allosteric regulation.

  12. The physical chemistry of Criegee intermediates in the gas phase

    SciTech Connect

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular and bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.

  13. The physical chemistry of Criegee intermediates in the gas phase

    DOE PAGES

    Osborn, David L.; Taatjes, Craig A.

    2015-07-24

    Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular andmore » bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.« less

  14. Photogenerated radical intermediates of vitamin K 1: a time-resolved resonance Raman study

    NASA Astrophysics Data System (ADS)

    Balakrishnan, G.; Umapathy, S.

    1999-01-01

    Quinones play a vital role in the process of electron transfer in bacterial photosynthetic reaction centers. It is of interest to investigate the photochemical reactions involving quinones with a view to elucidating the structure-function relationships in the biological processes. Resonance Raman spectra of radical anions and the time-resolved resonance Raman spectra of vitamin K 1 (model compound for Q A in Rhodopseudomonas viridis, a bacterial photosynthetic reception center) are presented. The photochemical intermediates of vitamin K 1, viz. radical anion, ketyl radical and o-quinone methide have been identified. The vibrational assignments of all these intermediates are made on the basis of comparison with our earlier TR3 studies on radical anions of naphthoquinone and menaquinone.

  15. A unified intermediate and mechanism for soot combustion on potassium-supported oxides

    PubMed Central

    Li, Qian; Wang, Xiao; Xin, Ying; Zhang, Zhaoliang; Zhang, Yexin; Hao, Ce; Meng, Ming; Zheng, Lirong; Zheng, Lei

    2014-01-01

    The soot combustion mechanism over potassium-supported oxides (MgO, CeO2 and ZrO2) was studied to clarify the active sites and discover unified reaction intermediates in this typical gas-solid-solid catalytic reaction. The catalytically active sites were identified as free K+ rather than K2CO3, which can activate gaseous oxygen. The active oxygen spills over to soot and forms a common intermediate, ketene, before it was further oxidized into the end product CO2. The existence of ketene species was confirmed by density functional theory (DFT) calculations. The oxygen spillover mechanism is proposed, which is explained as an electron transfer from soot to gaseous oxygen through the active K+ sites. The latter mechanism is confirmed for the first time since it was put forward in 1950, not only by ultraviolet photoelectron spectroscopy (UPS) results but also by semi-empirical theoretical calculations. PMID:24740213

  16. Intermediates in the Formation of Aromatics in Hydrocarbon Combustion

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    The formation of the first benzene ring is believed to be the rate limiting step in soot formation. Two different mechanisms have been proposed for formation of cyclic C6 species. The first involves the reaction of two acetylenes to give CH2CHCCH (vinyl acetylene), the loss of a H to give CHCHCCH (n-C41-13) or CH2CCCH (iso-C4H3), and addition of another acetylene to n-C4H3, followed by ring closure to give phenyl radical. Miller and Melius argue that only n-C4H3 leads to phenyl radical and since iso-C4H3 is more stable than n-C4H3 this mechanism is unlikely. An alternative mechanism proposed by them is formation of benzene from the dimerization of two CH2CCH (propargyl) radicals (formed by the reaction of singlet methylene with C2H2). We report reaction pathways and accurate energetics (from CASSCF/internally contracted CI calculations) for the reactions of CH(pi-2) and CH2-1 with acetylene, the reaction of vinylidene with acetylene, and the reaction of n-C4H3 and iso-C4H3 with acetylene. These calculations identify two new reactive intermediates CHCHCH ( a A"-2 ground state in Cs symmetry; spin coupling is a doublet from three singly occupied orbitals) and CHCCH (B-3 ground state in C2 symmetry) from the reaction of CH with acetylene. These species dimerize with no barrier to form benzene and para-benzyne, respectively. CHCCH is proposed as a reactive intermediate which can add to benzene to give higher polynuclear aromatic hydrocarbons or fullerenes. The addition of a C3H2 unit releases two C-C bond energies and thus the resulting addition product contains sufficient energy to break several CH bonds leading to a reduction in the H to C ratio as the cluster size increases. It is found that iso-C4H3 adds to acetylene to initially give a fulvene radical but that this species rearranges to phenyl radical. Thus, the reaction of acetylene with iso-C4H3 does lead to phenyl radical and the cyclization pathway may also contribute to formation of the initial benzene ring.

  17. The Shopping Center. Intermediate.

    ERIC Educational Resources Information Center

    Timmons, Darrell; And Others

    This teaching guide is designed to develop thinking skills of intermediate elementary school children by using the concept of a shopping center. Thinking skills defined in the guide are observing, recalling, noticing differences and similarities, ordering, grouping, concept labeling, classifying, concept testing, inferring causes and effects,…

  18. Sara Intermediate Course.

    ERIC Educational Resources Information Center

    Thayer, James E.; Maraby, Julien

    This volume consists of an intermediate course in Sara, a language of the Chad Republic of Africa. It is designed for native speakers of English and includes forty reading selections in Sara and an English translation of each selection. The readings are followed by a corresponding set of dialogues in Sara, accompanied by an English translation.…

  19. Intermediate Mathematics Study Guide.

    ERIC Educational Resources Information Center

    Stanford Univ., CA. School Mathematics Study Group.

    This SMSG study guide is intended to provide teachers who use "Intermediate Mathematics," as a textbook with references to materials which will help them to gain a better understanding of the mathematics contained in the text. For each chapter of the text a brief resume of its content is followed by a list of annotated references which are…

  20. SPACE: Intermediate Level Modules.

    ERIC Educational Resources Information Center

    Indiana State Dept. of Education, Indianapolis. Center for School Improvement and Performance.

    These modules were developed to assist teachers at the intermediate level to move away from extensive skill practice and toward more meaningful interdisciplinary learning. This packet, to be used by teachers in the summer Extended Learning Program, provides detailed thematic lesson plans matched to the Indiana Curriculum Proficiency Guide. The…

  1. Experimental and Theoretical Study on the OH-Reaction Kinetics and Photochemistry of Acetyl Fluoride (CH3C(O)F), an Atmospheric Degradation Intermediate of HFC-161 (C2H5F).

    PubMed

    Song, Xinli; Zügner, Gábor L; Farkas, Mária; Illés, Ádám; Sarzyński, Dariusz; Rozgonyi, Tamás; Wang, Baoshan; Dóbé, Sándor

    2015-07-16

    The direct reaction kinetic method of low pressure fast discharge flow (DF) with resonance fluorescence monitoring of OH (RF) has been applied to determine rate coefficients for the overall reactions OH + C2H5F (EtF) (1) and OH + CH3C(O)F (AcF) (2). Acetyl fluoride reacts slowly with the hydroxyl radical, the rate coefficient at laboratory temperature is k2(300 K) = (0.74 ± 0.05) × 10(-14) cm(3) molecule(-1) s(-1) (given with 2σ statistical uncertainty). The temperature dependence of the reaction does not obey the Arrhenius law and it is described well by the two-exponential rate expression of k2(300-410 K) = 3.60 × 10(-3) exp(-10500/T) + 1.56 × 10(-13) exp(-910/T) cm(3) molecule(-1) s(-1). The rate coefficient of k1 = (1.90 ± 0.19) × 10(-13) cm(3) molecule(-1) s(-1) has been determined for the EtF-reaction at room temperature (T = 298 K). Microscopic mechanisms for the OH + CH3C(O)F reaction have also been studied theoretically using the ab initio CBS-QB3 and G4 methods. Variational transition state theory was employed to obtain rate coefficients for the OH + CH3C(O)F reaction as a function of temperature on the basis of the ab initio data. The calculated rate coefficients are in good agreement with the experimental data. It is revealed that the reaction takes place predominantly via the indirect H-abstraction mechanism involving H-bonded prereactive complexes and forming the nascent products of H2O and the CH2CFO radical. The non-Arrhenius behavior of the rate coefficient at temperatures below 500 K is ascribed to the significant tunneling effect of the in-the-plane H-abstraction dynamic bottleneck. The production of FC(O)OH + CH3 via the addition/elimination mechanism is hardly competitive due to the significant barriers along the reaction routes. Photochemical experiments of AcF were performed at 248 nm by using exciplex lasers. The total photodissociation quantum yield for CH3C(O)F has been found significantly less than unity; among the primary

  2. Criegee intermediates in the indoor environment. New insights

    DOE PAGES

    Shallcross, D. E.; Taatjes, C. A.; Percival, C. J.

    2014-03-25

    Criegee intermediates are formed in the ozonolysis of alkenes and play an important role in indoor chemistry, notably as a source of OH radicals. Recent studies have shown that these Criegee intermediates react very quickly with NO2, SO2, and carbonyls, and in this study, steady-state calculations are used to inspect the potential impact of these data on indoor chemistry. It is shown that these reactions could accelerate NO3 formation and SO2 removal in the indoor environment significantly. In addition, reaction between Criegee intermediates and halogenated carbonyls could provide a significant loss process indoors, where currently one does not exist.

  3. New Site(s) of Methylglyoxal-Modified Human Serum Albumin, Identified by Multiple Reaction Monitoring, Alter Warfarin Binding and Prostaglandin Metabolism

    PubMed Central

    Kimzey, Michael J.; Yassine, Hussein N.; Riepel, Brent M.; Tsaprailis, George; Monks, Terrence J.; Lau, Serrine S.

    2010-01-01

    Methylglyoxal (MG) is a biologically reactive byproduct of glucose metabolism levels of which increase in diabetes. MG modification of protein generates neutral hydroimidazolone adducts on arginine residues which can alter functional active sites. We investigated the site-specificity of MG adduction to human serum albumin (HSA) using multiple reaction monitoring (MRM) of 13 MG modified tryptic peptides, each containing an internal arginine. Seven new sites for MG modification (R257 >R209 >R222 >R81 >R485 >R472 >R10) are described. Analysis of MG-treated HSA showed substantial R257 and R410 modification, with MG-modified R257 (at 100 μM MG) in drug site I causing significant inhibition of prostaglandin catalysis. The MG hydroimidazolone (MG-H1) adduct was modeled at R257, and molecular dynamics simulations and affinity docking revealed a decrease of 12.8–16.5 kcal/mol (S and R isomers, respectively) for warfarin binding in drug site I. Taken together, these results suggest that R257 is a likely site for MG modification in vivo, which may have functional consequences for prostaglandin metabolism and drug bioavailability. PMID:20934417

  4. Unveiling the crucial intermediates in androgen production

    PubMed Central

    Mak, Piotr J.; Gregory, Michael C.; Denisov, Ilia G.; Sligar, Stephen G.; Kincaid, James R.

    2015-01-01

    Ablation of androgen production through surgery is one strategy against prostate cancer, with the current focus placed on pharmaceutical intervention to restrict androgen synthesis selectively, an endeavor that could benefit from the enhanced understanding of enzymatic mechanisms that derives from characterization of key reaction intermediates. The multifunctional cytochrome P450 17A1 (CYP17A1) first catalyzes the typical hydroxylation of its primary substrate, pregnenolone (PREG) and then also orchestrates a remarkable C17–C20 bond cleavage (lyase) reaction, converting the 17-hydroxypregnenolone initial product to dehydroepiandrosterone, a process representing the first committed step in the biosynthesis of androgens. Now, we report the capture and structural characterization of intermediates produced during this lyase step: an initial peroxo-anion intermediate, poised for nucleophilic attack on the C20 position by a substrate-associated H-bond, and the crucial ferric peroxo-hemiacetal intermediate that precedes carbon–carbon (C-C) bond cleavage. These studies provide a rare glimpse at the actual structural determinants of a chemical transformation that carries profound physiological consequences. PMID:26668369

  5. The Intermediate Neutrino Program

    SciTech Connect

    Adams, C.; et al.

    2015-03-23

    The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topics on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop.

  6. Intermediate water recovery system

    NASA Technical Reports Server (NTRS)

    Deckman, G.; Anderson, A. R. (Editor)

    1973-01-01

    A water recovery system for collecting, storing, and processing urine, wash water, and humidity condensates from a crew of three aboard a spacecraft is described. The results of a 30-day test performed on a breadboard system are presented. The intermediate water recovery system produced clear, sterile, water with a 96.4 percent recovery rate from the processed urine. Recommendations for improving the system are included.

  7. Modeling DNA Replication Intermediates

    SciTech Connect

    Broyde, S.; Roy, D.; Shapiro, R.

    1997-06-01

    While there is now available a great deal of information on double stranded DNA from X-ray crystallography, high resolution NMR and computer modeling, very little is known about structures that are representative of the DNA core of replication intermediates. DNA replication occurs at a single strand/double strand junction and bulged out intermediates near the junction can lead to frameshift mutations. The single stranded domains are particularly challenging. Our interest is focused on strategies for modeling the DNA of these types of replication intermediates. Modeling such structures presents special problems in addressing the multiple minimum problem and in treating the electrostatic component of the force field. We are testing a number of search strategies for locating low energy structures of these types and we are also investigating two different distance dependent dielectric functions in the coulombic term of the force field. We are studying both unmodified DNA and DNA damaged by aromatic amines, carcinogens present in the environment in tobacco smoke, barbecued meats and automobile exhaust. The nature of the structure adopted by the carcinogen modified DNA at the replication fork plays a key role in determining whether the carcinogen will cause a mutation during replication that can initiate the carcinogenic process. In the present work results are presented for unmodified DNA.

  8. Appropriate chicken sample size for identifying the composition of broiler intestinal microbiota affected by dietary antibiotics, using the polymerase chain reaction-denaturing gradient gel electrophoresis technique.

    PubMed

    Zhou, H; Gong, J; Brisbin, J T; Yu, H; Sanei, B; Sabour, P; Sharif, S

    2007-12-01

    The bacterial microbiota in the broiler gastrointestinal tract are crucial for chicken health and growth. Their composition can vary among individual birds. To evaluate the composition of chicken microbiota in response to environmental disruption accurately, 4 different pools made up of 2, 5, 10, and 15 individuals were used to determine how many individuals in each pool were required to assess the degree of variation when using the PCR-denaturing gradient gel electrophoresis (DGGE) profiling technique. The correlation coefficients among 3 replicates within each pool group indicated that the optimal sample size for comparing PCR-DGGE bacterial profiles and downstream applications (such as identifying treatment effects) was 5 birds per pool for cecal microbiota. Subsequently, digesta from 5 birds was pooled to investigate the effects on the microbiota composition of the 2 most commonly used dietary antibiotics (virginiamycin and bacitracin methylene disalicylate) at 2 different doses by using PCR-DGGE, DNA sequencing, and quantitative PCR techniques. Thirteen DGGE DNA bands were identified, representing bacterial groups that had been affected by the antibiotics. Nine of them were validated. The effect of dietary antibiotics on the microbiota composition appeared to be dose and age dependent. These findings provide a working model for elucidating the mechanisms of antibiotic effects on the chicken intestinal microbiota and for developing alternatives to dietary antibiotics. PMID:18029800

  9. Radicals: Reactive Intermediates with Translational Potential

    PubMed Central

    2016-01-01

    This Perspective illustrates the defining characteristics of free radical chemistry, beginning with its rich and storied history. Studies from our laboratory are discussed along with recent developments emanating from others in this burgeoning area. The practicality and chemoselectivity of radical reactions enable rapid access to molecules of relevance to drug discovery, agrochemistry, material science, and other disciplines. Thus, these reactive intermediates possess inherent translational potential, as they can be widely used to expedite scientific endeavors for the betterment of humankind. PMID:27631602

  10. Statistical properties of multistep enzyme-mediated reactions

    SciTech Connect

    Nemenman, Ilya; Sinitsyn, Nikolai A; De Ronde, Wiet H; Daniels, Bryan C; Mugler, Andrew

    2008-01-01

    Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this paper, we address this problem by solving the chemical master equations for various enzymatic reactions. We devise a perturbation theory analogous to that used in quantum mechanics that allows us to determine the first () and the second (variance) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d/dt (or 'dose-response' curve) and the Fano factor F=variance/ are both realistically measurable quantities, and while the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and we explore this possibility in the context of four sample multistep enzymatic reactions. We argue that measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events.

  11. Impact of sulfur dioxide oxidation by Stabilized Criegee Intermediate on sulfate

    EPA Science Inventory

    We revise the Carbon Bond chemical mechanism to explicitly represent three Stabilized Criegee Intermediates (SCIs) and their subsequent reactions with sulfur dioxide, water monomer, and water dimer, and incorporate the reactions into the Community Multiscale Air Quality model. Th...

  12. Covalent functionalization of graphene with reactive intermediates.

    PubMed

    Park, Jaehyeung; Yan, Mingdi

    2013-01-15

    Graphene, a material made exclusively of sp(2) carbon atoms with its π electrons delocalized over the entire 2D network, is somewhat chemically inert. Covalent functionalization can enhance graphene's properties including opening its band gap, tuning conductivity, and improving solubility and stability. Covalent functionalization of pristine graphene typically requires reactive species that can form covalent adducts with the sp(2) carbon structures in graphene. In this Account, we describe graphene functionalization reactions using reactive intermediates of radicals, nitrenes, carbenes, and arynes. These reactive species covalently modify graphene through free radical addition, CH insertion, or cycloaddition reactions. Free radical additions are among the most common reaction, and these radicals can be generated from diazonium salts and benzoyl peroxide. Electron transfer from graphene to aryl diazonium ion or photoactivation of benzoyl peroxide yields aryl radicals that subsequently add to graphene to form covalent adducts. Nitrenes, electron-deficient species generated by thermal or photochemical activation of organic azides, can functionalize graphene very efficiently. Because perfluorophenyl nitrenes show enhanced bimolecular reactions compared with alkyl or phenyl nitrenes, perfluorophenyl azides are especially effective. Carbenes are used less frequently than nitrenes, but they undergo CH insertion and C═C cycloaddition reactions with graphene. In addition, arynes can serve as a dienophile in a Diels-Alder type reaction with graphene. Further study is needed to understand and exploit the chemistry of graphene. The generation of highly reactive intermediates in these reactions leads to side products that complicate the product composition and analysis. Fundamental questions remain about the reactivity and regioselectivity of graphene. The differences in the basal plane and the undercoordinated edges of graphene and the zigzag versus arm-chair configurations

  13. Synthetic mononuclear nonheme iron-oxygen intermediates.

    PubMed

    Nam, Wonwoo

    2015-08-18

    Mononuclear nonheme iron-oxygen species, such as iron-superoxo, -peroxo, -hydroperoxo, and -oxo, are key intermediates involved in dioxygen activation and oxidation reactions catalyzed by nonheme iron enzymes. Because these iron-oxygen intermediates are short-lived due to their thermal instability and high reactivity, it is challenging to investigate their structural and spectroscopic properties and reactivity in the catalytic cycles of the enzymatic reactions themselves. One way to approach such problems is to synthesize biomimetic iron-oxygen complexes and to tune their geometric and electronic structures for structural characterization and reactivity studies. Indeed, a number of biologically important iron-oxygen species, such as mononuclear nonheme iron(III)-superoxo, iron(III)-peroxo, iron(III)-hydroperoxo, iron(IV)-oxo, and iron(V)-oxo complexes, were synthesized recently, and the first X-ray crystal structures of iron(III)-superoxo, iron(III)-peroxo, and iron(IV)-oxo complexes in nonheme iron models were successfully obtained. Thus, our understanding of iron-oxygen intermediates in biological reactions has been aided greatly from the studies of the structural and spectroscopic properties and the reactivities of the synthetic biomimetic analogues. In this Account, we describe our recent results on the synthesis and characterization of mononuclear nonheme iron-oxygen complexes bearing simple macrocyclic ligands, such as N-tetramethylated cyclam ligand (TMC) and tetraamido macrocyclic ligand (TAML). In the case of iron-superoxo complexes, an iron(III)-superoxo complex, [(TAML)Fe(III)(O2)](2-), is described, including its crystal structure and reactivities in electrophilic and nucleophilic oxidative reactions, and its properties are compared with those of a chromium(III)-superoxo complex, [(TMC)Cr(III)(O2)(Cl)](+), with respect to its reactivities in hydrogen atom transfer (HAT) and oxygen atom transfer (OAT) reactions. In the case of iron-peroxo intermediates

  14. Measurements of the {sup 116}Cd(p,n) and {sup 116}Sn(n,p) reactions at 300 MeV for studying Gamow-Teller transition strengths in the intermediate nucleus of the {sup 116}Cd double-{beta} decay

    SciTech Connect

    Sasano, M.; Kuboki, H.; Sekiguchi, K.; Sakai, H.; Yako, K.; Miki, K.; Noji, S.; Wakasa, T.; Dozono, M.; Fujita, K.; Greenfield, M. B.; Hatanaka, K.; Okamura, H.; Tamii, A.; Kawabata, T.; Maeda, Y.; Sakemi, Y.; Shimizu, Y.; Uesaka, T.; Sasamoto, Y.

    2009-11-09

    The double differential cross sections for the {sup 116}Cd(p,n) and {sup 116}Sn(n,p) reactions at 300 MeV have been measured over a wide excitation-energy region including Gamow-Teller (GT) giant resonance (GTGR) for studying GT transition strengths in the intermediate nucleus of the {sup 116}Cd double-{beta} decay, namely {sup 116}In. A large amount of the strengths in the {beta}{sup +} direction has been newly found in the energy region up to 30 MeV, which may imply that the GT strengths in the GTGR region contribute to the nuclear matrix element of the two-neutrino double-{beta} decay.

  15. Infrared and EPR spectroscopic characterization of a Ni(I) species formed by photolysis of a catalytically competent Ni(I)-CO intermediate in the acetyl-CoA synthase reaction.

    PubMed

    Bender, Güneş; Stich, Troy A; Yan, Lifen; Britt, R David; Cramer, Stephen P; Ragsdale, Stephen W

    2010-09-01

    Acetyl-CoA synthase (ACS) catalyzes the synthesis of acetyl-CoA from CO, coenzyme A (CoA), and a methyl group from the CH(3)-Co(3+) site in the corrinoid iron-sulfur protein (CFeSP). These are the key steps in the Wood-Ljungdahl pathway of anaerobic CO and CO(2) fixation. The active site of ACS is the A-cluster, which is an unusual nickel-iron-sulfur cluster. There is significant evidence for the catalytic intermediacy of a CO-bound paramagnetic Ni species, with an electronic configuration of [Fe(4)S(4)](2+)-(Ni(p)(+)-CO)-(Ni(d)(2+)), where Ni(p) and Ni(d) represent the Ni centers in the A-cluster that are proximal and distal to the [Fe(4)S(4)](2+) cluster, respectively. This well-characterized Ni(p)(+)-CO intermediate is often called the NiFeC species. Photolysis of the Ni(p)(+)-CO state generates a novel Ni(p)(+) species (A(red)*) with a rhombic electron paramagnetic resonance spectrum (g values of 2.56, 2.10, and 2.01) and an extremely low (1 kJ/mol) barrier for recombination with CO. We suggest that the photolytically generated A(red)* species is (or is similar to) the Ni(p)(+) species that binds CO (to form the Ni(p)(+)-CO species) and the methyl group (to form Ni(p)-CH(3)) in the ACS catalytic mechanism. The results provide support for a binding site (an "alcove") for CO near Ni(p), indicated by X-ray crystallographic studies of the Xe-incubated enzyme. We propose that, during catalysis, a resting Ni(p)(2+) state predominates over the active Ni(p)(+) species (A(red)*) that is trapped by the coupling of a one-electron transfer step to the binding of CO, which pulls the equilibrium toward Ni(p)(+)-CO formation.

  16. Intermediates of stigmasterol metabolism in Spodoptera littoralis

    SciTech Connect

    Svoboda, J.A.; Rees, H.H.; Thompson, M.J.; Hoggard, N. )

    1989-03-01

    Stigmasterol-24,28-epoxide, 22E-stigmasta-5,22,24(28E)-trien-3 beta-ol, and 22E-cholesta-5,22,24-trien-3 beta-ol were identified as normal metabolites of (3H)stigmasterol in Spodoptera littoralis larvae. Relative concentrations of all three of these metabolites increased when a diazasterol inhibitor was fed in combination with stigmasterol in the artificial diet. Identification of these sterols as intermediates in the conversion of stigmasterol to cholesterol in this insect indicates that intermediates analogous to fucosterol and fucosterol-24,28-epoxide in the conversion of sitosterol to cholesterol are produced in the metabolism of stigmasterol. This is the first published identification of stigmasterol-24,28-epoxide and 22E-stigmasta-5,22,24(28E)-trien-3 beta-ol as intermediates in this pathway in an insect.

  17. Membrane Fission: Model for Intermediate Structures

    PubMed Central

    Kozlovsky, Yonathan; Kozlov, Michael M.

    2003-01-01

    Membrane budding-fission is a fundamental process generating intracellular carriers of proteins. Earlier works were focused only on formation of coated buds connected to the initial membrane by narrow membrane necks. We present the theoretical analysis of the whole pathway of budding-fission, including the crucial stage where the membrane neck undergoes fission and the carrier separates from the donor membrane. We consider two successive intermediates of the reaction: 1), a constricted membrane neck coming out of aperture of the assembling protein coat, and 2), hemifission intermediate resulting from self-fusion of the inner monolayer of the neck, while its outer monolayer remains continuous. Transformation of the constricted neck into the hemifission intermediate is driven by the membrane stress produced in the neck by the protein coat. Although apparently similar to hemifusion, the fission is predicted to have an opposite dependence on the monolayer spontaneous curvature. Analysis of the further stages of the process demonstrates that in all practically important cases the hemifission intermediate decays spontaneously into two separate membranes, thereby completing the fission process. We formulate the “job description” for fission proteins by calculating the energy they have to deliver and the radii of the protein coat aperture which have to be reached to drive the fission process. PMID:12829467

  18. Experiments in intermediate energy physics

    SciTech Connect

    Dehnhard, D.

    2003-02-28

    Research in experimental nuclear physics was done from 1979 to 2002 primarily at intermediate energy facilities that provide pion, proton, and kaon beams. Particularly successful has been the work at the Los Alamos Meson Physics Facility (LAMPF) on unraveling the neutron and proton contributions to nuclear ground state and transition densities. This work was done on a wide variety of nuclei and with great detail on the carbon, oxygen, and helium isotopes. Some of the investigations involved the use of polarized targets which allowed the extraction of information on the spin-dependent part of the triangle-nucleon interaction. At the Indiana University Cyclotron Facility (IUCF) we studied proton-induced charge exchange reactions with results of importance to astrophysics and the nuclear few-body problem. During the first few years, the analysis of heavy-ion nucleus scattering data that had been taken prior to 1979 was completed. During the last few years we created hypernuclei by use of a kaon beam at Brookhaven National Laboratory (BNL) and an electron beam at Jefferson Laboratory (JLab). The data taken at BNL for a study of the non-mesonic weak decay of the A particle in a nucleus are still under analysis by our collaborators. The work at JLab resulted in the best resolution hypernuclear spectra measured thus far with magnetic spectrometers.

  19. Communications: Elementary oxygen electrode reactions in the aprotic Li-air battery

    NASA Astrophysics Data System (ADS)

    Hummelshøj, J. S.; Blomqvist, J.; Datta, S.; Vegge, T.; Rossmeisl, J.; Thygesen, K. S.; Luntz, A. C.; Jacobsen, K. W.; Nørskov, J. K.

    2010-02-01

    We discuss the electrochemical reactions at the oxygen electrode of an aprotic Li-air battery. Using density functional theory to estimate the free energy of intermediates during the discharge and charge of the battery, we introduce a reaction free energy diagram and identify possible origins of the overpotential for both processes. We also address the question of electron conductivity through the Li2O2 electrode and show that in the presence of Li vacancies Li2O2 becomes a conductor.

  20. [Intermediate gastric cancer].

    PubMed

    Fontán, A N; Marzano, C A; Martínez, M M; Palau, G; Rubio, H H

    1980-01-01

    Gastric Cancer comprises two basic types: Advanced Gastric Cancer (A.G.C.) and Early Gastric Cancer (E.G.C.). A.G.C. extends beyond the proper muscle layer with a 5 to 17%, five years survival rate after surgery. E.G.C. does not extend beyond the submucosa (with or without metastasis to regional lymph nodes) and has a 80 - 95% five years survival rate. Intermediate Gastric Cancer, PM G.C. (Gastric cancer of the proper muscle layer) does not surpass the proper muscle layer and offers a five years life expectance of near 60% after adequate surgical treatment, with peculiar features in radiology, endoscopy and evolutivity. We report a case of PM G.C., "depressed" and "protruded". The proper muscle layer was invaded by the depressed lesion". Both lesions were continguous.

  1. Incoherence in the South African Labour Market for Intermediate Skills

    ERIC Educational Resources Information Center

    Kraak, Andre

    2008-01-01

    This article is concerned with the production and employment of technically skilled labour at the intermediate level in South Africa. Three differing labour market pathways to intermediate skilling are identified. These are: the traditional apprenticeship route, the new "Learnerships" pathway (similar to the "modern apprenticeship" schemes adopted…

  2. A Mechanochemical Switch to Control Radical Intermediates

    PubMed Central

    2015-01-01

    B12-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB12-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is “off”, the 5′-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch “on,” the enzyme environment becomes the driving force to impose a distinct conformation of the 5′-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions. PMID:24846280

  3. A mechanochemical switch to control radical intermediates.

    PubMed

    Brunk, Elizabeth; Kellett, Whitney F; Richards, Nigel G J; Rothlisberger, Ursula

    2014-06-17

    B₁₂-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB₁₂-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is "off", the 5'-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch "on," the enzyme environment becomes the driving force to impose a distinct conformation of the 5'-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions.

  4. Photoelectron-photoion coincidence spectroscopy for multiplexed detection of intermediate species in a flame.

    PubMed

    Krüger, Julia; Garcia, Gustavo A; Felsmann, Daniel; Moshammer, Kai; Lackner, Alexander; Brockhinke, Andreas; Nahon, Laurent; Kohse-Höinghaus, Katharina

    2014-11-01

    Complex reactive processes in the gas phase often proceed via numerous reaction steps and intermediate species that must be identified and quantified to develop an understanding of the reaction pathways and establish suitable reaction mechanisms. Here, photoelectron-photoion coincidence (PEPICO) spectroscopy has been applied to analyse combustion intermediates present in a premixed fuel-rich (ϕ = 1.7) ethene-oxygen flame diluted with 25% argon, burning at a reduced pressure of 40 mbar. For the first time, multiplexing fixed-photon-energy PEPICO measurements were demonstrated in a chemically complex reactive system such as a flame in comparison with the scanning "threshold" TPEPICO approach used in recent pioneering combustion investigations. The technique presented here is capable of detecting and identifying multiple species by their cations' vibronic fingerprints, including radicals and pairs or triplets of isomers, from a single time-efficient measurement at a selected fixed photon energy. Vibrational structures for these species have been obtained in very good agreement with scanning-mode threshold photoelectron spectra taken under the same conditions. From such spectra, the temperature in the ionisation volume was determined. Exemplary analysis of species profiles and mole fraction ratios for isomers shows favourable agreement with results obtained by more common electron ionisation and photoionisation mass spectrometry experiments. It is expected that the multiplexing fixed-photon-energy PEPICO technique can contribute effectively to the analysis of chemical reactivity and kinetics in and beyond combustion. PMID:25237782

  5. Degradation of the Intermediate Filament Family by Gigaxonin.

    PubMed

    Bomont, Pascale

    2016-01-01

    Intermediate filament turnover is a highly dynamic process required to maintain tissue integrity and is implicated in degenerative and regenerative processes. Despite these essential roles, little is known about the mechanisms that cause the degradation of intermediate filaments. Nevertheless, the last decade has seen the emergence of the ubiquitin proteasome system, in particular E3 ubiquitin ligases, as important regulators. Here, we will focus on the first identified factor controlling the degradation of the entire intermediate filament family, the gigaxonin-E3 ligase. We will present the scientific achievements and the methodologies to study gigaxonin and its crucial role in intermediate filament turnover.

  6. Deformylation Reaction by a Nonheme Manganese(III)-Peroxo Complex via Initial Hydrogen-Atom Abstraction.

    PubMed

    Barman, Prasenjit; Upadhyay, Pranav; Faponle, Abayomi S; Kumar, Jitendra; Nag, Sayanta Sekhar; Kumar, Devesh; Sastri, Chivukula V; de Visser, Sam P

    2016-09-01

    Metal-peroxo intermediates are key species in the catalytic cycles of nonheme metalloenzymes, but their chemical properties and reactivity patterns are still poorly understood. The synthesis and characterization of a manganese(III)-peroxo complex with a pentadentate bispidine ligand system and its reactivity with aldehydes was studied. Manganese(III)-peroxo can react through hydrogen-atom abstraction reactions instead of the commonly proposed nucleophilic addition reaction. Evidence of the mechanism comes from experiments which identify a primary kinetic isotope effect of 5.4 for the deformylation reaction. Computational modeling supports the established mechanism and identifies the origin of the reactivity preference of hydrogen-atom abstraction over nucleophilic addition.

  7. Formation of a stalled early intermediate of pseudouridine synthesis monitored by real-time FRET.

    PubMed

    Hengesbach, Martin; Voigts-Hoffmann, Felix; Hofmann, Benjamin; Helm, Mark

    2010-03-01

    Pseudouridine is the most abundant of more than 100 chemically distinct natural ribonucleotide modifications. Its synthesis consists of an isomerization reaction of a uridine residue in the RNA chain and is catalyzed by pseudouridine synthases. The unusual reaction mechanism has become the object of renewed research effort, frequently involving replacement of the substrate uridines with 5-fluorouracil (f(5)U). f(5)U is known to be a potent inhibitor of pseudouridine synthase activity, but the effect varies among the target pseudouridine synthases. Derivatives of f(5)U have previously been detected, which are thought to be either hydrolysis products of covalent enzyme-RNA adducts, or isomerization intermediates. Here we describe the interaction of pseudouridine synthase 1 (Pus1p) with f(5)U-containing tRNA. The interaction described is specific to Pus1p and position 27 in the tRNA anticodon stem, but the enzyme neither forms a covalent adduct nor stalls at a previously identified reaction intermediate of f(5)U. The f(5)U27 residue, as analyzed by a DNAzyme-based assay using TLC and mass spectrometry, displayed physicochemical properties unaltered by the reversible interaction with Pus1p. Thus, Pus1p binds an f(5)U-containing substrate, but, in contrast to other pseudouridine synthases, leaves the chemical structure of f(5)U unchanged. The specific, but nonproductive, interaction demonstrated here thus constitutes an intermediate of Pus turnover, stalled by the presence of f(5)U in an early state of catalysis. Observation of the interaction of Pus1p with fluorescence-labeled tRNA by a real-time readout of fluorescence anisotropy and FRET revealed significant structural distortion of f(5)U-tRNA structure in the stalled intermediate state of pseudouridine catalysis.

  8. Structure and reactivity of bis(silyl) dihydride complexes (PMe(3))(3)Ru(SiR(3))(2)(H)(2): model compounds and real intermediates in a dehydrogenative C-Si bond forming reaction.

    PubMed

    Dioumaev, Vladimir K; Yoo, Bok R; Procopio, Leo J; Carroll, Patrick J; Berry, Donald H

    2003-07-23

    A series of stable complexes, (PMe(3))(3)Ru(SiR(3))(2)(H)(2) ((SiR(3))(2) = (SiH(2)Ph)(2), 3a; (SiHPh(2))(2), 3b; (SiMe(2)CH(2)CH(2)SiMe(2)), 3c), has been synthesized by the reaction of hydridosilanes with (PMe(3))(3)Ru(SiMe(3))H(3) or (PMe(3))(4)Ru(SiMe(3))H. Compounds 3a and 3c adopt overall pentagonal bipyramidal geometries in solution and the solid state, with phosphine and silyl ligands defining trigonal bipyramids and ruthenium hydrides arranged in the equatorial plane. Compound 3a exhibits meridional phosphines, with both silyl ligands equatorial, whereas the constraints of the chelate in 3c result in both axial and equatorial silyl environments and facial phosphines. Although there is no evidence for agostic Si-H interactions in 3a and 3b, the equatorial silyl group in 3c is in close contact with one hydride (1.81(4) A) and is moderately close to the other hydride (2.15(3) A) in the solid state and solution (nu(Ru.H.Si) = 1740 cm(-)(1) and nu(RuH) = 1940 cm(-)(1)). The analogous bis(silyl) dihydride, (PMe(3))(3)Ru(SiMe(3))(2)(H)(2) (3d), is not stable at room temperature, but can be generated in situ at low temperature from the 16e(-) complex (PMe(3))(3)Ru(SiMe(3))H (1) and HSiMe(3). Complexes 3b and 3d have been characterized by multinuclear, variable temperature NMR and appear to be isostructural with 3a. All four complexes exhibit dynamic NMR spectra, but the slow exchange limit could not be observed for 3c. Treatment of 1 with HSiMe(3) at room temperature leads to formation of (PMe(3))(3)Ru(SiMe(2)CH(2)SiMe(3))H(3) (4b) via a CH functionalization process critical to catalytic dehydrocoupling of HSiMe(3) at higher temperatures. Closer inspection of this reaction between -110 and -10 degrees C by NMR reveals a plethora of silyl hydride phosphine complexes formed by ligand redistribution prior to CH activation. Above ca. 0 degrees C this mixture converts cleanly via silane dehydrogenation to the very stable tris(phosphine) trihydride carbosilyl complex 4b

  9. Investigation of the reactions of small neutral iron oxide clusters with methanol

    NASA Astrophysics Data System (ADS)

    Xie, Yan; Dong, Feng; Heinbuch, Scott; Rocca, Jorge J.; Bernstein, Elliot R.

    2009-03-01

    Reactions of neutral iron oxide clusters (FemOn, m =1-2, n =0-5) with methanol (CH3OH) in a fast flow reactor are investigated by time of flight mass spectrometry. Detection of the neutral iron oxide cluster distribution and reaction intermediates and products is accomplished through single photon ionization by a 118 nm (10.5 eV) VUV laser. Partially deuterated methanol (CD3OH) is employed to distinguish reaction products and reaction mechanisms. Three major reactions are identified experimentally: CH3OH association with FeO; methanol dehydrogenation on FeO1,2 and Fe2O2-5; and (CH2O)Fe formation. Density functional theory calculations are carried out to identify reaction products, and to explore the geometric and electronic structures of the iron oxide clusters, reaction intermediates, and transition states, and to evaluate reaction pathways. Neutral formaldehyde is calculated to be formed on FeO1,2 and Fe2O2-5 clusters. Hydrogen transfer from methanol to iron oxide clusters occurs first from the O-H moiety of methanol, and is followed by a hydrogen transfer from the C-H moiety of methanol. Computational results are in good agreement with experimental observations and reveal reaction mechanisms for neutral iron oxide clusters taking methanol to formaldehyde through various reaction intermediates. Based on the experimental results and the calculated reaction mechanisms and pathways, complete catalytic cycles are suggested for the heterogeneous reaction of CH3OH to CH2O facilitated by an iron oxide catalyst.

  10. Noncanonical reactions of flavoenzymes.

    PubMed

    Sobrado, Pablo

    2012-01-01

    Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the protein environment modulates the reactivity of the flavin to perform novel chemistries. Recent mechanistic and structural data supporting novel flavin functionalities in reactions catalyzed by chorismate synthase, type II isopentenyl diphosphate isomerase, UDP-galactopyranose mutase, and alkyl-dihydroxyacetonephosphate synthase are presented in this review. In these enzymes, the flavin plays either a direct role in acid/base reactions or as a nucleophile or electrophile. In addition, the flavin cofactor is proposed to function as a "molecular scaffold" in the formation of UDP-galactofuranose and alkyl-dihydroxyacetonephosphate by forming a covalent adduct with reaction intermediates.

  11. Isoporphyrin intermediate in heme oxygenase catalysis. Oxidation of alpha-meso-phenylheme.

    PubMed

    Evans, John P; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

    2008-07-11

    Human heme oxygenase-1 (hHO-1) catalyzes the O2- and NADPH-dependent oxidation of heme to biliverdin, CO, and free iron. The first step involves regiospecific insertion of an oxygen atom at the alpha-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin pi-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of alpha-meso-phenylheme-IX, alpha-meso-(p-methylphenyl)-mesoheme-III, and alpha-meso-(p-trifluoromethylphenyl)-mesoheme-III. In agreement with previous experiments (Wang, J., Niemevz, F., Lad, L., Huang, L., Alvarez, D. E., Buldain, G., Poulos, T. L., and Ortiz de Montellano, P. R. (2004) J. Biol. Chem. 279, 42593-42604), only the alpha-biliverdin isomer is produced with concomitant formation of the corresponding benzoic acid. The transient intermediate observed in the NADPH-P450 reductase-catalyzed reaction accumulated when the reaction was supported by H2O2 and exhibited the absorption maxima at 435 and 930 nm characteristic of an isoporphyrin. Product analysis by reversed phase high performance liquid chromatography and liquid chromatography electrospray ionization mass spectrometry of the product generated with H2O2 identified it as an isoporphyrin that, on quenching, decayed to benzoylbiliverdin. In the presence of H218O2, one labeled oxygen atom was incorporated into these products. The hHO-1-isoporphyrin complexes were found to have half-lives of 1.7 and 2.4 h for the p-trifluoromethyl- and p-methyl-substituted phenylhemes, respectively. The addition of NADPH-P450 reductase to the H2O2-generated hHO-1-isoporphyrin complex produced alpha-biliverdin, confirming its role as a reaction intermediate. Identification of an isoporphyrin intermediate in the catalytic sequence of hHO-1, the first such intermediate observed in hemoprotein catalysis, completes our understanding of the critical first step of heme oxidation.

  12. Masonry. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Thompson, Moses

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 13 terminal objectives for an intermediate masonry course. These materials, developed for a two-semester (3 hours daily) course, are designed to provide the student with the skills and knowledge necessary for entry level employment in the field…

  13. Welding. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Vincent, Kenneth

    Several intermediate performance objectives and corresponding criterion measures are listed for each of nine terminal objectives for an intermediate welding course. The materials were developed for a 36-week (3 hours daily) course designed to prepare the student for employment in the field of welding. Electric welding and specialized (TIG & MIG)…

  14. Printing. Performance Objectives. Intermediate Course.

    ERIC Educational Resources Information Center

    Seivert, Chester

    Several intermediate performance objectives and corresponding criterion measures are listed for each of 13 terminal objectives for an intermediate printing course. The materials were developed for a two-semester (3 hours daily) course with specialized classroom, shop, and practical experiences designed to enable the student to develop proficiency…

  15. Mössbauer- and EPR-Snapshots of an Enzymatic Reaction: The Cytochrome P450 Reaction Cycle

    NASA Astrophysics Data System (ADS)

    Schünemann, V.; Jung, C.; Lendzian, F.; Barra, A.-L.; Teschner, T.; Trautwein, A. X.

    2004-12-01

    In this communication we present a complimentary Mössbauer- and EPR-study of the time dependance of the reaction of substrate free P450cam with peracetic acid within a time region ranging from 8 ms up to 5 min. An Fe(IV) species as well as a tyrosyl radical residing on the amino acid residue Tyr96 have been identified as reaction intermediates. These species possibly are formed by the reduction of compound I by means of transferring an electron from Tyr 96 to the heme moiety.

  16. Intermediate filaments of the lung.

    PubMed

    Yi, Hayan; Ku, Nam-On

    2013-07-01

    Intermediate filaments (IF), a subfamily of the cytoskeletal filaments, provide structural support to cells. Human diseases related to mutations in IF proteins in which their tissue-specific expression is reflected have been found in a broad range of patients. The properties of identified IF mutants are well-studied in vitro in cultured cells and in vivo using transgenic mice expressing IF mutants. However, the association of IF proteins with diseases of the lung is not fully studied yet. Epithelial cells in normal lung express vimentin and various keratins, and the patterns of their expression are altered depending on the progression of the lung diseases. A growing number of studies performed in alveolar epithelial cells demonstrated IF involvement in disease-related aspects including their usefulness as tumor marker, in epithelial-mesenchymal transition and cell migration. However, the lung disease-associated IF functions in animal models are poorly understood, and IF mutations associated with lung diseases in humans have not been reported. In this review, we summarize recent studies that show the significance of IF proteins in lung epithelial cells. Understanding these aspects is an important prerequisite for further investigations on the role of lung IF in animal models and human lung diseases.

  17. Reaction of atomic hydrogen with formic acid.

    PubMed

    Cao, Qian; Berski, Slawomir; Latajka, Zdzislaw; Räsänen, Markku; Khriachtchev, Leonid

    2014-04-01

    We study the reaction of atomic hydrogen with formic acid and characterize the radical products using IR spectroscopy in a Kr matrix and quantum chemical calculations. The reaction first leads to the formation of an intermediate radical trans-H2COOH, which converts to the more stable radical trans-cis-HC(OH)2via hydrogen atom tunneling on a timescale of hours at 4.3 K. These open-shell species are observed for the first time as well as a reaction between atomic hydrogen and formic acid. The structural assignment is aided by extensive deuteration experiments and ab initio calculations at the UMP2 and UCCSD(T) levels of theory. The simplest geminal diol radical trans-cis-HC(OH)2 identified in the present work as the final product of the reaction should be very reactive, and further reaction channels are of particular interest. These reactions and species may constitute new channels for the initiation and propagation of more complex organic species in the interstellar clouds.

  18. Reaction of Molecular Hydrogen with Tetraaminecopper(II) Sulfate Monohydrate

    NASA Astrophysics Data System (ADS)

    Kanda, Seiichi; Kori, Toshinari; Kida, Sigeo

    1994-02-01

    The reaction of tetraammincopper(II) sulfate monohydrate in a solid state with H 2 (10 MPa) was studied. The Cu(II) ion in the complex was reduced to Cu(0). The final product was a mixture of (NH 4) 2SO 4 and colloidal black Cu(0) which showed a remarkable reactivity as follows. In thermogravimetric analysis up to 440°C under nitrogen atmosphere, the above product reacted between the components very much differently from a control sample with the same composition. The six intermediate samples, taken at successive reaction times, were examined by powder diffraction method. As one of the intermediates, the copper double salt, (NH 4) 2Cu(SO 4) 2, was identified.

  19. Surface intermediates in selective olefin oxidation and ammoxidation

    SciTech Connect

    Burrington, J.D.; Kartisek, C.T.; Grasselli, R.K.

    1983-02-01

    An investigation of the mechanism of the oxidation and ammoxidation of propylene was made. The products of the above reactions were acrylonitrile and acrolein for ammoxidation and oxidation, respectively. Also, the ammoxidation and oxidation of allyl alcohol, allyl amine, and their allylic deuterium substituted analogues was studied. It was concluded that oxidation and ammoxidation of propylene have the same rate determining step. Other conclusions about the reaction intermediates were also made.

  20. Criegee intermediates in the indoor environment. New insights

    SciTech Connect

    Shallcross, D. E.; Taatjes, C. A.; Percival, C. J.

    2014-03-25

    Criegee intermediates are formed in the ozonolysis of alkenes and play an important role in indoor chemistry, notably as a source of OH radicals. Recent studies have shown that these Criegee intermediates react very quickly with NO2, SO2, and carbonyls, and in this study, steady-state calculations are used to inspect the potential impact of these data on indoor chemistry. It is shown that these reactions could accelerate NO3 formation and SO2 removal in the indoor environment significantly. In addition, reaction between Criegee intermediates and halogenated carbonyls could provide a significant loss process indoors, where currently one does not exist.

  1. Serotype specific polymerase chain reaction identifies a higher prevalence of streptococcus mutans serotype k and e in a random group of children with dental caries from the Southern region of India

    PubMed Central

    Rao, Arun Prasad; Austin, Ravi David

    2014-01-01

    Background: The development of dental caries has been associated with the oral prevalence of Streptococcus mutans. Four serotypes of S. mutans have been reported, namely serotype c, e, f, and k that are classified based on the composition and linkages of cell wall polysaccharides, response to physiological reactions, sero-specificity and 16s rRNA homology. Although the oral prevalence of S. mutans serotype c in Indian subjects with or without caries is known, the prevalence of the other three serotypes, e, f, and k are not known. Hence in this study, we have investigated the occurrence of the e, f, and k serotypes in children with or without caries within the age group of 6-12 years. Materials and Methods: Genomic DNA isolated from whole saliva of caries active (CA) and caries free (CF) groups were first screened for the presence of S. mutans by strain specific polymerase chain reaction (PCR). Those samples that tested positive for the presence of S. mutans were further analyzed by serotype specific PCR to identify the prevalence of the serotypes. Results: Strain specific PCR indicated a higher prevalence of S. mutans in CA group (80%) relative to CF group (43%). Further analysis of the S. mutans positive samples in both groups indicated a higher prevalence of serotype k and e, followed by serotype f in CA group. Conclusion: The present data clearly establishes a novel S. mutans serotype prevalence hierarchy in children from this region, compared with those that have been reported elsewhere. Besides, the data are also clinically significant as the occurrence of serotype k has been associated with infective endocarditis. PMID:25191062

  2. Roles of microfilaments and intermediate filaments in adrenal steroidogenesis.

    PubMed

    Hall, P F; Almahbobi, G

    1997-03-15

    The problem for the steroidogenic cell if it is to accelerate steroid synthesis in response to trophic stimulation, consists in moving cholesterol from the sites of synthesis and storage to mitochondria at an accelerated rate. The most intensely studied situation is that in which the sterol is stored as ester in lipid droplets. Cholesterol ester must be de-esterified and transported to mitochondria where steroid synthesis begins. Since droplets and mitochondria are now known to be attached to intermediate filaments and since these structures are not contractile, it appears to be necessary to invoke the actions of other cytoskeletal elements. Actin microfilaments are involved in cholesterol transport so that it is tempting to propose that the contractile properties of actomyosin are used in this process. It is known that an energy-dependent contractile process involving actin is capable of disrupting intermediate filaments. Since the intermediate filaments appear to act by keeping lipid droplets and mitochondria apart, disruption of the filaments accompanied by a contractile process would be expected to allow these two structures to come together. This would open the way for the transfer of cholesterol to the steroidogenic pathway. This should be regarded as a first step. The events necessary for entry of cholesterol from droplets into the mitochondria remain to be clarified. In addition, the transport process for newly synthesized cholesterol that is not stored in droplets, is still not understood. At least four protein kinase enzymes have been identified in the cytoskeletons of adrenal cells, namely, Ca2+/calmodulin-dependent kinase, protein kinase (Ca2+ and phospholipid-dependent), myosin light chain kinase, and protein kinase A (cyclic AMP-dependent). The Ca2+/calmodulin kinase promotes transport of cholesterol to mitochondria and does so under conditions in which phosphorylation of vimentin and myosin light chain occurs. Phosphorylation of vimentin results in

  3. Moving beyond Intermediate English Proficiency

    ERIC Educational Resources Information Center

    Jewell, Mary

    2009-01-01

    Too many English learners get stuck at intermediate levels of English language proficiency. In this article, teacher Mary Jewell describes how she uses literature and scaffolds to ensure that students develop academic language.

  4. Acyl silicates and acyl aluminates as activated intermediates in peptide formation on clays

    NASA Technical Reports Server (NTRS)

    White, D. H.; Kennedy, R. M.; Macklin, J.

    1984-01-01

    Glycine reacts with heating on dried clays and other minerals to give peptides in much better yield than in the absence of mineral. This reaction was proposed to occur by way of an activated intermediate such as an acyl silicate or acyl aluminate analogous to acyl phosphates involved in several biochemical reactions including peptide bond synthesis. The proposed mechanism has been confirmed by trapping the intermediate, as well as by direct spectroscopic observation of a related intermediate. The reaction of amino acids on periodically dried mineral surfaces represents a widespead, geologically realistic setting for prebiotic peptide formation via in situ activation.

  5. Intermediate ions in the atmosphere

    NASA Astrophysics Data System (ADS)

    Tammet, Hannes; Komsaare, Kaupo; Hõrrak, Urmas

    2014-01-01

    Intermediate air ions are charged nanometer-sized aerosol particles with an electric mobility of about 0.03-0.5 cm2 V- 1 s- 1 and a diameter of about 1.5-7.5 nm. Intensive studies of new particle formation provided good knowledge about intermediate ions during burst events of atmospheric aerosol nucleation. Information about intermediate ions during quiet periods between the bursts remained poor. The new mobility analyzer SIGMA can detect air ions at concentrations of mobility fractions of about 1 cm- 3 and enables studying intermediate ions during quiet periods. It became evident that intermediate ions always exist in atmospheric air and should be considered an indicator and a mediator of aerosol nucleation. The annual average concentration of intermediate ions of one polarity in Tartu, Estonia, was about 40 cm- 3 while 5% of the measurements showed a concentration of less than 10 cm- 3. The fraction concentrations in logarithmic 1/8-decade mobility bins between 0.1 and 0.4 cm2 V- 1 s- 1 often dropped below 1 cm- 3. The bursts of intermediate ions at stations separated by around 100 km appeared to be correlated. The lifespan of intermediate ions in the atmosphere is a few minutes, and they cannot be carried by wind over long distances. Thus the observed long-range correlation of intermediate ions is explained by simultaneous changes in air composition in widely spaced stations. A certain amount of intermediate ion bursts, predominantly of negative polarity, are produced by the balloelectric effect at the splashing of water drops during rain. These bursts are usually excluded when speaking about new particle formation because the balloelectric particles are assumed not to grow to the size of the Aitken mode. The mobility distribution of balloelectric ions is uniform in shape in all measurements. The maximum is located at a mobility of about 0.2 cm2 V- 1 s- 1, which corresponds to the diameter of particles of about 2.5 nm.

  6. A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis.

    PubMed

    Song, Haigang; Dong, Chen; Qin, Mingming; Chen, Yaozong; Sun, Yueru; Liu, Jingjing; Chan, Wan; Guo, Zhihong

    2016-06-15

    Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. However, this intermediate is not found in the thiamine-dependent catalysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and was structurally determined at 1.34 Å resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring nitrogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 Å. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.

  7. A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis.

    PubMed

    Song, Haigang; Dong, Chen; Qin, Mingming; Chen, Yaozong; Sun, Yueru; Liu, Jingjing; Chan, Wan; Guo, Zhihong

    2016-06-15

    Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. However, this intermediate is not found in the thiamine-dependent catalysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and was structurally determined at 1.34 Å resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring nitrogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 Å. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry. PMID:27213829

  8. Benzoxazinone-Mediated Triazine Degradation: A Proposed Reaction Mechanism.

    PubMed

    Willett, C D; Lerch, R N; Lin, C-H; Goyne, K W; Leigh, N D; Roberts, C A

    2016-06-22

    The role of benzoxazinones (Bx, 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one) in triazine resistance in plants has been studied for over half a century. In this research, fundamental parameters of the reaction between DIBOA-Glc (2-β-d-glucopyranosyloxy-4-hydroxy-1,4-benzoxazin-3-one) and atrazine (ATR, 6-chloro-N-ethyl-N'-(1-methylethyl)-1,3,5-triazine-2,4-diamine) were examined. Through a series of experiments employing a variety of chromatographic and spectroscopic techniques, the DIBOA-Glc/ATR reaction was characterized in terms of reactant and product kinetics, stoichiometry, identification of a reaction intermediate, and reaction products formed. Results of these experiments demonstrated that the reaction mechanism proceeds via nucleophilic attack of the hydroxamic acid moiety of DIBOA-Glc at the C-2 position of the triazine ring to form hydroxyatrazine (HA, 2-hydroxy-4-ethylamino-6-isopropylamino-s-triazine), with associated degradation of DIBOA-Glc. Degradation of reactants followed first-order kinetics with a noncatalytic role of DIBOA-Glc. A reaction intermediate was identified as a DIBOA-Glc-HA conjugate, indicating a 1:1 DIBOA-Glc:ATR stoichiometry. Reaction products included HA and Cl(-), but definitive identification of DIBOA-Glc reaction product(s) was not attained. With these reaction parameters elucidated, DIBOA-Glc can be evaluated in terms of its potential for a myriad of applications, including its use to address the problem of widespread ATR contamination of soil and water resources.

  9. General Method for Functionalized Polyaryl Synthesis via Aryne Intermediates

    PubMed Central

    2015-01-01

    A method for base-promoted arylation of arenes and heterocycles by aryl halides and aryl triflates is described. Additionally, in situ electrophilic trapping of ArLi intermediates generated in the reaction of benzyne with deprotonated arenes or heterocycles has been developed, providing rapid and easy access to a wide range of highly functionalized polyaryls. Base-promoted arylation methodology complements transition-metal-catalyzed direct arylation and allows access to structures that are not easily accessible via other direct arylation methods. The reactions are highly functional-group tolerant, with alkene, ether, dimethylamino, trifluoromethyl, ester, cyano, halide, hydroxyl, and silyl functionalities compatible with reaction conditions. PMID:24893069

  10. Time-resolved heme protein intermediates

    NASA Astrophysics Data System (ADS)

    Rousseau, Denis

    2005-03-01

    To determine the enzymatic mechanisms of heme proteins, it is necessary to identify the intermediates along the catalytic pathway and measure the times of their formation and decay. Resonance Raman scattering spectra are especially powerful for obtaining such information as the electronic structure of the heme group and the nature of the ligand coordinated to the heme iron atom may be monitored. The oxygen intermediates of two physiologically important enzymes will be presented. Nitric oxide synthase (NOS) uses oxygen to convert arginine to NO and citrulline; and cytochrome c oxidase (CcO) reduces oxygen to water to support oxidative phosphorylation. The fate or the oxygen in each of these enzymes has been followed by resonance Raman scattering. In NOS the oxygen is slowly converted to an activated species that then reacts fast, whereas in CcO the oxygen is rapidly converted to a reactive species that subsequently reacts slowly. The properties of the intermediates and the origin of the differences between these enzymes will be discussed.

  11. The Photocatalyzed Aza-Henry Reaction of N-Aryltetrahydroisoquinolines: Comprehensive Mechanism, H(•)- versus H(+)-Abstraction, and Background Reactions.

    PubMed

    Bartling, Hanna; Eisenhofer, Anna; König, Burkhard; Gschwind, Ruth M

    2016-09-14

    The cross-dehydrogenative coupling (CDC) reaction of N-aryltetrahydroisoquinolines (THIQ) is one of the most exploited photocatalytic transformation and a test reaction for an exceptional variety of catalysts. However, its mechanism remained unclear concerning involved intermediates, reactive pathways of the amine radical cation and the influence of oxygen and the light source. Therefore, nuclear magnetic resonance (NMR), electron spin resonance (ESR) and synthetic methods were combined to provide a comprehensive picture of the reaction mechanism using Ru(bpy)3Cl2 as a photocatalyst under aerobic and anaerobic conditions. The reaction profiles and involved intermediates were monitored and analyzed by NMR spectroscopy. Several intermediates contributing to product formation were identified, the iminium ion, the hydroperoxide and dimer of THIQ, and a new ring opened intermediate, cleaved at the benzylic C-N bond. Mechanistic evidence is given that under anaerobic conditions preferentially the α-amino radical is formed by deprotonation, in contrast to the formation of iminium ions via H(•)-abstraction in the presence of oxygen. Further, the light-induced background reaction in the absence of the catalyst was studied in detail, revealing that the product formation rate is correlated to the intensity and wavelength of the light source and that oxygen is essential for an efficient conversion. The reaction rate and efficiency is comparable to previously reported photocatalytic systems, performed under aerobic conditions in combination with intense blue light sources. Thus, the multitude of reaction parameters investigated reveals the preference for hydrogen atom or proton abstraction in photoreactions and allows to assess the influence of experimental conditions on the mechanistic pathways.

  12. The Photocatalyzed Aza-Henry Reaction of N-Aryltetrahydroisoquinolines: Comprehensive Mechanism, H(•)- versus H(+)-Abstraction, and Background Reactions.

    PubMed

    Bartling, Hanna; Eisenhofer, Anna; König, Burkhard; Gschwind, Ruth M

    2016-09-14

    The cross-dehydrogenative coupling (CDC) reaction of N-aryltetrahydroisoquinolines (THIQ) is one of the most exploited photocatalytic transformation and a test reaction for an exceptional variety of catalysts. However, its mechanism remained unclear concerning involved intermediates, reactive pathways of the amine radical cation and the influence of oxygen and the light source. Therefore, nuclear magnetic resonance (NMR), electron spin resonance (ESR) and synthetic methods were combined to provide a comprehensive picture of the reaction mechanism using Ru(bpy)3Cl2 as a photocatalyst under aerobic and anaerobic conditions. The reaction profiles and involved intermediates were monitored and analyzed by NMR spectroscopy. Several intermediates contributing to product formation were identified, the iminium ion, the hydroperoxide and dimer of THIQ, and a new ring opened intermediate, cleaved at the benzylic C-N bond. Mechanistic evidence is given that under anaerobic conditions preferentially the α-amino radical is formed by deprotonation, in contrast to the formation of iminium ions via H(•)-abstraction in the presence of oxygen. Further, the light-induced background reaction in the absence of the catalyst was studied in detail, revealing that the product formation rate is correlated to the intensity and wavelength of the light source and that oxygen is essential for an efficient conversion. The reaction rate and efficiency is comparable to previously reported photocatalytic systems, performed under aerobic conditions in combination with intense blue light sources. Thus, the multitude of reaction parameters investigated reveals the preference for hydrogen atom or proton abstraction in photoreactions and allows to assess the influence of experimental conditions on the mechanistic pathways. PMID:27541322

  13. Intermediate Mass Fragments Emission in Peripheral Heavy-Ion Collisions

    NASA Astrophysics Data System (ADS)

    Bini, M.; Casini, G.; Maurenzig, P. R.; Olmi, A.; Pasquali, G.; Piantelli, S.; Poggi, G.; Stefanini, A. A.; Taccetti, N.

    The collision 116Sn + 93Nb at 29.5 AMeV in direct and reverse kinematics has been studied at LNS in Catania. In particular the emission pattern in the νperp - νpar plane of Intermediate Mass Fragments with Z=3-7 (IMF's) shows that for peripheral reactions most of IMF's are emitted at velocities intermediate between those of the projectile- and target-like products. From coulomb trajectory calculations one can infere that these IMF's are produced mainly in the interaction zone, in a short time interval at the end of the target-projectile interaction.

  14. Compact intermediates in RNA folding

    SciTech Connect

    Woodson, S.A.

    2011-12-14

    Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

  15. Non-enzymatic synthesis of the coenzymes, uridine diphosphate glucose and cytidine diphosphate choline, and other phosphorylated metabolic intermediates

    NASA Technical Reports Server (NTRS)

    Mar, A.; Dworkin, J.; Oro, J.

    1987-01-01

    Using urea and cyanamide, the two condensing agents considered to have been present on the primitive earth, uridine diphosphate glucose (UDPG), cytidine diphosphate choline (CDP-choline), glucose-1-phosphate (G1P), and glucose-6-phosphate (G6P) were synthesized under simulated prebiotic conditions. The reaction products were separated and identified using paper chromatography, thin layer chromatography, enzymatic analyses, and ion-pair reverse-phase high performance liquid chromatography. The possibility of nonenzymatic synthesis of metabolic intermediates on the primitive earth from simple precursors was thus demonstrated.

  16. A regioselective double Stille coupling reaction of bicyclic stannolanes.

    PubMed

    Kamimura, Akio; Tanaka, Toshiyuki; So, Masahiro; Itaya, Tomoyuki; Matsuda, Kantaro; Kawamoto, Takuji

    2016-09-14

    A regioselective double Stille coupling reaction was explored using bicyclic stannolanes that were easily prepared from the radical cascade reaction of β-amino-α-methylene esters. Various 1-bromo-2-iodoarenes underwent the double coupling reaction to afford benzoisoindole derivatives in a regioselective manner, where the carbon attached to the iodine selectively coupled with the vinylic carbon, and then the carbon attached to bromine coupled with the alkyl carbon. The combination of intra- and intermolecular coupling reactions provided hexahydroindeno[1,2-b]pyrrole derivatives in good yields. The yields were further improved in the presence of excess amounts of CsF. An attempt to identify the reaction intermediate was made wherein the decomposition of the stannolanes with aqueous HCl and HBr afforded trigonal bipyramidal (TBP) pentacoordinated tin complexes, as confirmed by microanalyses and (119)Sn NMR. Using DCl for the decomposition selectively introduced a deuterium to the E-position of the exomethylene unit. The complexes smoothly underwent the intramolecular Stille coupling reaction in the presence of both a palladium catalyst and DABCO, affording hexahydroindeno[1,2-b]pyrroles in good yields. These results suggest that the double coupling reaction progresses through a TBP tin complex, promoting the second intramolecular coupling reaction between the aryl halide and Csp(3)-tin bond. PMID:27506959

  17. A regioselective double Stille coupling reaction of bicyclic stannolanes.

    PubMed

    Kamimura, Akio; Tanaka, Toshiyuki; So, Masahiro; Itaya, Tomoyuki; Matsuda, Kantaro; Kawamoto, Takuji

    2016-09-14

    A regioselective double Stille coupling reaction was explored using bicyclic stannolanes that were easily prepared from the radical cascade reaction of β-amino-α-methylene esters. Various 1-bromo-2-iodoarenes underwent the double coupling reaction to afford benzoisoindole derivatives in a regioselective manner, where the carbon attached to the iodine selectively coupled with the vinylic carbon, and then the carbon attached to bromine coupled with the alkyl carbon. The combination of intra- and intermolecular coupling reactions provided hexahydroindeno[1,2-b]pyrrole derivatives in good yields. The yields were further improved in the presence of excess amounts of CsF. An attempt to identify the reaction intermediate was made wherein the decomposition of the stannolanes with aqueous HCl and HBr afforded trigonal bipyramidal (TBP) pentacoordinated tin complexes, as confirmed by microanalyses and (119)Sn NMR. Using DCl for the decomposition selectively introduced a deuterium to the E-position of the exomethylene unit. The complexes smoothly underwent the intramolecular Stille coupling reaction in the presence of both a palladium catalyst and DABCO, affording hexahydroindeno[1,2-b]pyrroles in good yields. These results suggest that the double coupling reaction progresses through a TBP tin complex, promoting the second intramolecular coupling reaction between the aryl halide and Csp(3)-tin bond.

  18. Widely expressed transcripts for chemokine receptor CXCR1 in identified glutamatergic, gamma-aminobutyric acidergic, and cholinergic neurons and astrocytes of the rat brain: a single-cell reverse transcription-multiplex polymerase chain reaction study.

    PubMed

    Danik, M; Puma, C; Quirion, R; Williams, S

    2003-10-15

    Increasing evidence suggests that the chemokine interleukin (IL)-8/CXCL8 plays important roles in CNS development, neuronal survival, modulation of excitability, and neuroimmune response. Recently, we have shown that CXCL8 can acutely modulate ion channel activity in septal neurons expressing receptors CXCR1 and/or CXCR2. This was a surprising finding, insofar as CXCR1 expression had not been described for the mammalian brain. Here we investigated whether CXCR1 transcripts are present in other brain regions, whether they are expressed at the single-cell level in molecularly identified neurons and astrocytes, and how they are regulated during early postnatal development. In addition, possible cellular colocalization of CXCR1 and CXCR2 transcripts was examined. Semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) revealed that CXCR1 mRNAs were expressed in the septum, striatum, hippocampus, cerebellum, and cortex (temporoparietal and entorhinal) at different levels and appeared to be regulated independently from CXCR2 during development. By using RT multiplex PCR on acutely dissociated cells from these brain regions, we show that CXCR1 transcripts were expressed in 83% of 84 sampled neurons displaying cholinergic (choline acetyltransferase mRNAs), gamma-aminobutyric acidergic (glutamic acid decarboxylases 65 and 67 mRNAs), or glutamatergic (vesicular glutamate transporters 1 and 2 mRNAs) phenotypes. CXCR1 and CXCR2 transcripts were colocalized in 45% of neurons sampled and also were present in some glial fibrillary acidic protein mRNA-expressing astrocytes. This is the first study to demonstrate the widespread expression of CXCR1 transcripts in the brain and suggests that CXCR1 may have hitherto unsuspected roles in neuromodulation and inflammation. PMID:14515358

  19. Intermediate role of α-keto acids in the formation of Strecker aldehydes.

    PubMed

    Hidalgo, Francisco J; Delgado, Rosa M; Zamora, Rosario

    2013-11-15

    The ability of α-keto acids to covert amino acids into Strecker aldehydes was investigated in an attempt to both identify new pathways for Strecker degradation, and analyse the role of α-keto acids as intermediate compounds in the formation of Strecker aldehydes by oxidised lipids. The results obtained indicated that phenylalanine was converted into phenylacetaldehyde to a significant extent by all α-keto acids assayed; glyoxylic acid being the most reactive α-keto acid for this reaction. It has been proposed that the reaction occurs by formation of an imine between the keto group of the α-keto acid, and the amino group of the amino acid. This then undergoes an electronic rearrangement with the loss of carbon dioxide to produce a new imine. This final imine is the origin of both the Strecker aldehyde and the amino acid from which the α-keto acid is derived. When glycine was incubated in the presence of 4,5-epoxy-2-decenal, the amino acid was converted into glyoxylic acid, and this α-keto acid was then able to convert phenylalanine into phenylacetaldehyde. All these results suggest that Strecker aldehydes can be produced by amino acid degradation initiated by different reactive carbonyl compounds, included those coming from amino acids and proteins. In addition, α-keto acids may act as intermediates for the Strecker degradation of amino acids by oxidised lipids.

  20. Intermediates in the Formation of the Chlorophyll Isocyclic Ring 1

    PubMed Central

    Wong, Yum-Shing; Castelfranco, Paul A.; Goff, Dane A.; Smith, Kevin M.

    1985-01-01

    Cell-free, organelle-free synthesis of Mg-2,4-divinylpheoporphyrin a5 (MgDVP) from Mg-protoporphyrin IX monomethyl ester (Mg-Proto Me) has been described (Wong and Castelfranco 1984 Plant Physiol 75: 658-661). This system consists of plastid membrane and stromal fractions and requires O2, NAD(P)H and S-adenosylmethionine (SAM). The synthetic 6-methyl-β-ketopropionate analog of Mg-Proto Me was converted to MgDVP by the same catalytic system in the presence of O2 and NADPH. SAM was not required. A compound (X) displaying the kinetic behavior of an intermediate was isolated from reaction mixtures with Mg-Proto Me as the substrate, but not with the 6-methyl-β-ketopropionate analog as the substrate. X was identified as the 6-methyl-β-hydroxypropionate analog of Mg-Proto Me by conversion to the dimethyl ester with CH2N2 and comparison with authentic 6-β-hydroxydimethyl ester. X was converted to MgDVP by the same catalytic system in the presence of O2 and NADPH. We conclude that the conversion of Mg-Proto Me to MgDVP proceeds through the 6-β-hydroxy and the 6-β-ketopropionate esters in agreement with earlier suggestions. PMID:16664481

  1. Fenton Oxidation Kinetics and Intermediates of Nonylphenol Ethoxylates

    PubMed Central

    Cui, Kai; Yi, Hao; Zhou, Zi-jian; Zhuo, Qiong-fang; Bing, Yong-xin; Guo, Qing-wei; Xu, Zhen-cheng

    2014-01-01

    Abstract Removal of nonylphenol ethoxylates (NPEOs) in aqueous solution by Fenton oxidation process was studied in a laboratory-scale batch reactor. Operating parameters, including initial pH temperature, hydrogen peroxide, and ferrous ion dosage, were thoroughly investigated. Maximum NPEOs reduction of 84% was achieved within 6 min, under an initial pH of 3.0, 25°C, an H2O2 dosage of 9.74×10−3 M, and a molar ratio of [H2O2]/[Fe2+] of 3. A modified pseudo-first-order kinetic model was found to well represent experimental results. Correlations of reaction rate constants and operational parameters were established based on experimental data. Results indicated that the Fenton oxidation rate and removal efficiency were more dependent on the dosage of H2O2 than Fe2+, and the apparent activation energy (ΔE) was 17.5 kJ/mol. High-performance liquid chromatography and gas chromatograph mass spectrometer analytical results indicated degradation of NPEOs obtained within the first 2 min stepwise occurred by ethoxyl (EO) unit shortening. Long-chain NPEOs mixture demonstrated a higher degradation rate than shorter-chain ones. Nonylphenol (NP), short-chain NPEOs, and NP carboxyethoxylates were identified as the primary intermediates, which were mostly further degraded. PMID:24868141

  2. Controlling reaction specificity in pyridoxal phosphate enzymes

    PubMed Central

    Toney, Michael D.

    2012-01-01

    Pyridoxal 5'-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly α-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at Cα of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site. PMID:21664990

  3. Cestina pro Pokrocile (Intermediate Czech).

    ERIC Educational Resources Information Center

    Kabat, Grazyna; And Others

    The textbook in intermediate Czech is designed for second-year students of the language and those who already have a basic knowledge of Czech grammar and vocabulary. It is appropriate for use in a traditional college language classroom, the business community, or a government language school. It can be covered in a year-long conventional…

  4. Material Voices: Intermediality and Autism

    ERIC Educational Resources Information Center

    Trimingham, Melissa; Shaughnessy, Nicola

    2016-01-01

    Autism continues to be regarded enigmatically; a community that is difficult to access due to perceived disruptions of interpersonal connectedness. Through detailed observations of two children participating in the Arts and Humanities Research Council funded project "Imagining Autism: Drama, Performance and Intermediality as Interventions for…

  5. Intermediate Filaments: A Historical Perspective

    PubMed Central

    Oshima, Robert G.

    2007-01-01

    Intracellular protein filaments intermediate in size between actin microfilaments and microtubules are composed of a surprising variety of tissue specific proteins commonly interconnected with other filamentous systems for mechanical stability and decorated by a variety of proteins that provide specialized functions. The sequence conservation of the coiled-coil, alpha-helical structure responsible for polymerization into individual 10 nm filaments defines the classification of intermediate filament proteins into a large gene family. Individual filaments further assemble into bundles and branched cytoskeletons visible in the light microscope. However, it is the diversity of the variable terminal domains that likely contributes most to different functions. The search for the functions of intermediate filament proteins has led to discoveries of roles in diseases of the skin, heart, muscle, liver, brain, adipose tissues and even premature aging. The diversity of uses of intermediate filaments as structural elements and scaffolds for organizing the distribution of decorating molecules contrasts with other cytoskeletal elements. This review is an attempt to provide some recollection of how such a diverse field emerged and changed over about 30 years. PMID:17493611

  6. Intermediality and the Child Performer

    ERIC Educational Resources Information Center

    Budd, Natasha

    2016-01-01

    This report details examples of praxis in the creation and presentation of "Joy Fear and Poetry": an intermedial theatre performance in which children aged 7-12 years generated aesthetic gestures using a range of new media forms. The impetus for the work's development was a desire to make an intervention into habituated patterns of…

  7. Authentic Video in Intermediate German.

    ERIC Educational Resources Information Center

    Lutcavage, Charles

    1992-01-01

    Assorted techniques are offered for introducing authentic German video into the intermediate language curriculum. Television commercials, weather forecasts, and news programs are described as tools for enhancing listening comprehension and expanding students' cultural awareness. Various preparatory activities and follow-up assignments are…

  8. Learning through Literature: Geography, Intermediate.

    ERIC Educational Resources Information Center

    Sterling, Mary Ellen

    This resource book provides specific strategies and activities for integrating the intermediate geography curriculum with related children's literature selections. The book includes the following sections: (1) "World Geography Overview"; (2) "Oceans"; (3) "Polar Regions"; (4) "Islands"; (5) "Rain Forests"; (6) "Mountains"; (7) "Forests"; (8)…

  9. Materials System for Intermediate Temperature Solid Oxide Fuel Cell

    SciTech Connect

    Uday B. Pal; Srikanth Gopalan

    2005-01-24

    AC complex impedance spectroscopy studies were conducted between 600-800 C on symmetrical cells that employed strontium-and-magnesium-doped lanthanum gallate electrolyte, La{sub 0.9}Sr{sub 0.1}Ga{sub 0.8}Mg{sub 0.2}O{sub 3} (LSGM). The objective of the study was to identify the materials system for fabrication and evaluation of intermediate temperature (600-800 C) solid oxide fuel cells (SOFCs). The slurry-coated electrode materials had fine porosity to enhance catalytic activity. Cathode materials investigated include La{sub 1-x}Sr{sub x}MnO{sub 3} (LSM), LSCF (La{sub 1-x}Sr{sub x}Co{sub y}Fe{sub 1-y}O{sub 3}), a two-phase particulate composite consisting of LSM-doped-lanthanum gallate (LSGM), and LSCF-LSGM. The anode materials were Ni-Ce{sub 0.85}Gd{sub 0.15}O{sub 2} (Ni-GDC) and Ni-Ce{sub 0.6}La{sub 0.4}O{sub 2} (Ni-LDC) composites. Experiments conducted with the anode materials investigated the effect of having a barrier layer of GDC or LDC in between the LSGM electrolyte and the Ni-composite anode to prevent adverse reaction of the Ni with lanthanum in LSGM. For proper interpretation of the beneficial effects of the barrier layer, similar measurements were performed without the barrier layer. The ohmic and the polarization resistances of the system were obtained over time as a function of temperature (600-800 C), firing temperature, thickness, and the composition of the electrodes. The study revealed important details pertaining to the ohmic and the polarization resistances of the electrode as they relate to stability and the charge-transfer reactions that occur in such electrode structures.

  10. Special Relativity and Reactions with Unstable Nuclei

    SciTech Connect

    Bertulani, C.A.

    2005-10-14

    Dynamical relativistic effects are often neglected in the description of reactions with unstable nuclear beams at intermediate energies (ELab {approx_equal} 100 MeV/nucleon). Evidently, this introduces sizable errors in experimental analysis and theoretical descriptions of these reactions. This is particularly important for the experiments held in GANIL/France, MSU/USA, RIKEN/Japan and GSI/Germany. I review a few examples where relativistic effects have been studied in nucleus-nucleus scattering at intermediate energies.

  11. Oxidation of Refractory Benzothiazoles with PMS/CuFe2O4: Kinetics and Transformation Intermediates.

    PubMed

    Zhang, Tao; Chen, Yin; Leiknes, TorOve

    2016-06-01

    Benzothiazole (BTH) and its derivatives 2-(methylthio)bezothiazole (MTBT), 2-benzothiazolsulfonate (BTSA), and 2-hydroxybenzothiazole (OHBT) are refractory pollutants ubiquitously existing in urban runoff at relatively high concentrations. Here, we report their oxidation by CuFe2O4-activated peroxomonosulfate (PMS/CuFe2O4), focusing on kinetics and transformation intermediates. These benzothiazoles can be efficiently degraded by this oxidation process, which is confirmed to generate mainly sulfate radicals (with negligible hydroxyl-radical formation) under slightly acidic to neutral pH conditions. The molar exposure ratio of sulfate radical to residual PMS (i.e., Rct) for this process is a constant that is related to the reaction condition and can be easily determined. The reaction rate constants of these benzothiazoles toward sulfate radical are (3.3 ± 0.3) × 10(9), (1.4 ± 0.3) × 10(9), (1.5 ± 0.1) × 10(9), and (4.7 ± 0.5) × 10(9) M(-1) s(-1), respectively (pH 7 and 20 °C). On the basis of Rct and these rate constants, their degradation in the presence of organic matter can be well-predicted. A number of transformation products were detected and tentatively identified using triple-quadruple/linear ion trap MS/MS and high-resolution MS. It appears that sulfate radicals attack BTH, MTBT, and BTSA on their benzo ring via electron transfer, generating multiple hydroxylated intermediates that are reactive toward common oxidants. For OHBT oxidation, the thiazole ring is preferentially broken down. Due to competitions of the transformation intermediates, a minimum PMS/pollutant molar ratio of 10-20 is required for effective degradation. The flexible PMS/CuFe2O4 could be a useful process to remove the benzothiazoles from low dissolved organic carbon waters like urban runoff or polluted groundwater. PMID:27144396

  12. Oxidation of Refractory Benzothiazoles with PMS/CuFe2O4: Kinetics and Transformation Intermediates.

    PubMed

    Zhang, Tao; Chen, Yin; Leiknes, TorOve

    2016-06-01

    Benzothiazole (BTH) and its derivatives 2-(methylthio)bezothiazole (MTBT), 2-benzothiazolsulfonate (BTSA), and 2-hydroxybenzothiazole (OHBT) are refractory pollutants ubiquitously existing in urban runoff at relatively high concentrations. Here, we report their oxidation by CuFe2O4-activated peroxomonosulfate (PMS/CuFe2O4), focusing on kinetics and transformation intermediates. These benzothiazoles can be efficiently degraded by this oxidation process, which is confirmed to generate mainly sulfate radicals (with negligible hydroxyl-radical formation) under slightly acidic to neutral pH conditions. The molar exposure ratio of sulfate radical to residual PMS (i.e., Rct) for this process is a constant that is related to the reaction condition and can be easily determined. The reaction rate constants of these benzothiazoles toward sulfate radical are (3.3 ± 0.3) × 10(9), (1.4 ± 0.3) × 10(9), (1.5 ± 0.1) × 10(9), and (4.7 ± 0.5) × 10(9) M(-1) s(-1), respectively (pH 7 and 20 °C). On the basis of Rct and these rate constants, their degradation in the presence of organic matter can be well-predicted. A number of transformation products were detected and tentatively identified using triple-quadruple/linear ion trap MS/MS and high-resolution MS. It appears that sulfate radicals attack BTH, MTBT, and BTSA on their benzo ring via electron transfer, generating multiple hydroxylated intermediates that are reactive toward common oxidants. For OHBT oxidation, the thiazole ring is preferentially broken down. Due to competitions of the transformation intermediates, a minimum PMS/pollutant molar ratio of 10-20 is required for effective degradation. The flexible PMS/CuFe2O4 could be a useful process to remove the benzothiazoles from low dissolved organic carbon waters like urban runoff or polluted groundwater.

  13. Baeyer-Villiger C-C bond cleavage reaction in gilvocarcin and jadomycin biosynthesis

    PubMed Central

    Tibrewal, Nidhi; Pahari, Pallab; Wang, Guojun; Kharel, Madan K.; Morris, Caleb; Downey, Theresa; Hou, Yanpeng; Bugni, Tim S.; Rohr, Jürgen

    2012-01-01

    GilOII has been unambiguously identified as the key enzyme performing the crucial C-C bond cleavage reaction responsible for the unique rearrangement of a benz[a]anthracene skeleton to the benzo[d]naphthopyranone backbone typical for the gilvocarcin type natural anticancer antibiotics. Further investigations of this enzyme led to the isolation of a hydroxy-oxepinone intermediate which allowed important conclusions regarding the cleavage mechanism. PMID:23102024

  14. Reactions of Pseudomonas aeruginosa pyocyanin with reduced glutathione.

    PubMed

    Cheluvappa, Rajkumar; Shimmon, Ronald; Dawson, Michael; Hilmer, Sarah N; Le Couteur, David G

    2008-01-01

    Pseudomonas aeruginosa is the most common cause of chronic and recurrent lung infections in patients with cystic fibrosis (CF) whose sputa contain copious quantities of P. aeruginosa toxin, pyocyanin. Pyocyanin triggers tissue damage mainly by its redox cycling and induction of reactive oxygen species (ROS). The reactions between reduced glutathione (GSH) and pyocyanin were observed using absorption spectra from spectrophotometry and the reaction products analysed by nuclear magnetic resonance imaging. Pyocyanin reacted with GSH non-enzymatically at 37 degrees C resulting in the production of red-brown products, spectophotometrically visible as a 480 nm maximum absorption peak after 24 h of incubation. The reaction was concentration-dependent on reduced glutathione but not on pyocyanin. Minimizing the accessibility of oxygen to the reaction decreased its rate. The anti-oxidant enzyme catalase circumvented the reaction. Proton-NMR analysis demonstrated the persistence of the original aromatic ring and the methyl-group of pyocyanin in the red-brown products. Anti-oxidant agents having thiol groups produced similar spectophotometrically visible peaks. The presence of a previously unidentified non-enzymatic GSH-dependent metabolic pathway for pyocyanin has thus been identified. The reaction between pyocyanin and GSH is concentration-, time-, and O(2)-dependent. The formation of H(2)O(2) as an intermediate and the thiol group in GSH seem to be important in this reaction. PMID:18797520

  15. Mechanics of vimentin intermediate filaments

    NASA Technical Reports Server (NTRS)

    Wang, Ning; Stamenovic, Dimitrijie

    2002-01-01

    It is increasingly evident that the cytoskeleton of living cells plays important roles in mechanical and biological functions of the cells. Here we focus on the contribution of intermediate filaments (IFs) to the mechanical behaviors of living cells. Vimentin, a major structural component of IFs in many cell types, is shown to play an important role in vital mechanical and biological functions such as cell contractility, migration, stiffness, stiffening, and proliferation.

  16. Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.

    PubMed

    Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B

    2016-05-13

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes.

  17. Intermediates revealed in the kinetic mechanism for DNA unwinding by a monomeric helicase.

    PubMed

    Eoff, Robert L; Raney, Kevin D

    2006-03-01

    Helicases unwind dsDNA during replication, repair and recombination in an ATP-dependent reaction. The mechanism for helicase activity can be studied using oligonucleotide substrates to measure formation of single-stranded (ss) DNA from double-stranded (ds) DNA. This assay provides an 'all-or-nothing' readout because partially unwound intermediates are not detected. We have determined conditions under which an intermediate in the reaction cycle of Dda helicase can be detected by trapping a partially unwound substrate. The appearance of this intermediate supports a model in which each ssDNA product interacts with the helicase after unwinding has occurred. Kinetic analysis indicates that the intermediate appears during a slow step in the reaction cycle that is flanked by faster steps for unwinding. These observations demonstrate a complex mechanism containing nonuniform steps for a monomeric helicase. The potential biological significance of such a mechanism is discussed.

  18. Chronic candida endophthalmitis as a cause of intermediate uveitis.

    PubMed

    Amin, Rowayda Mohamed; Hamdy, Islam; Osman, Ihab Mohamed

    2015-04-13

    Intermediate uveitis is a subset of intraocular inflammation where vitritis is the most consistent sign, with or without snowball opacities or snow banks over the pars plana. Some patients will have an associated underlying systemic disease such as sarcoidosis, multiple sclerosis, ocular tuberculosis, inflammatory bowel disease, possibly Behçet's disease and intraocular lymphoma, whereas some will be classified as pars planitis in case of the lack of an identifiable systemic disease association. Our patient, a 47-year-old woman, developed intermediate uveitis after cataract surgery in her right eye, was misdiagnosed as pars planitis, and received steroid monotherapy for 8 months. Her inflammation only fully resolved after vitrectomy with removal of the intraocular lens (IOL) and capsular bag. Oral fluconazole and intravitreal amphotericin B injection had failed to resolve her inflammation when Candida albicans was identified as the cause of her persistent intermediate uveitis.

  19. Intermediate Temperature Solid Oxide Fuel Cell Development

    SciTech Connect

    S. Elangovan; Scott Barnett; Sossina Haile

    2008-06-30

    Solid oxide fuel cells (SOFCs) are high efficiency energy conversion devices. Present materials set, using yttria stabilized zirconia (YSZ) electrolyte, limit the cell operating temperatures to 800 C or higher. It has become increasingly evident however that lowering the operating temperature would provide a more expeditious route to commercialization. The advantages of intermediate temperature (600 to 800 C) operation are related to both economic and materials issues. Lower operating temperature allows the use of low cost materials for the balance of plant and limits degradation arising from materials interactions. When the SOFC operating temperature is in the range of 600 to 700 C, it is also possible to partially reform hydrocarbon fuels within the stack providing additional system cost savings by reducing the air preheat heat-exchanger and blower size. The promise of Sr and Mg doped lanthanum gallate (LSGM) electrolyte materials, based on their high ionic conductivity and oxygen transference number at the intermediate temperature is well recognized. The focus of the present project was two-fold: (a) Identify a cell fabrication technique to achieve the benefits of lanthanum gallate material, and (b) Investigate alternative cathode materials that demonstrate low cathode polarization losses at the intermediate temperature. A porous matrix supported, thin film cell configuration was fabricated. The electrode material precursor was infiltrated into the porous matrix and the counter electrode was screen printed. Both anode and cathode infiltration produced high performance cells. Comparison of the two approaches showed that an infiltrated cathode cells may have advantages in high fuel utilization operations. Two new cathode materials were evaluated. Northwestern University investigated LSGM-ceria composite cathode while Caltech evaluated Ba-Sr-Co-Fe (BSCF) based pervoskite cathode. Both cathode materials showed lower polarization losses at temperatures as low as 600

  20. Monte Carlo Simulation of Heavy Nuclei Photofission at Intermediate Energies

    SciTech Connect

    Andrade-II, E.; Freitas, E.; Garcia, F.; Tavares, O. A. P.; Duarte, S. B.

    2009-06-03

    A detailed description of photofission process at intermediate energies (200 to 1000 MeV) is presented. The study of the reaction is performed by a Monte Carlo method which allows the investigation of properties of residual nuclei and fissioning nuclei. The information obtained indicate that multifragmentation is negligible at the photon energies studied here, and that the symmetrical fission is dominant. Energy and mass distributions of residual and fissioning nuclei were calculated.

  1. Mechanistic features of the copper-free Sonogashira reaction from ESI-MS.

    PubMed

    Ahmadi, Zohrab; Yunker, Lars P E; Oliver, Allen G; McIndoe, J Scott

    2015-12-21

    The mechanism of the Sonogashira reaction in methanol was studied in detail using pressurized sample infusion electrospray ionization mass spectrometry (PSI-ESI-MS). Several key intermediates were identified and their structures were assigned by MS/MS studies. Cationic and anionic charged-tagged substrates were employed to look into the mechanism of this reaction from variety of angles. A reverse kinetic isotope effect was observed in which the reaction rate is accelerated in deuterated solvents (kH/kD = 0.6). The reaction was found to be zero order with respect to the aryl iodide and first order with respect to the phenylacetylene. A Hammett parameter of ρ = 1.4 indicates that the reaction is more favorable for aryl iodides with para EWGs. No evidence of product inhibition, dimerization of palladium catalyst, or agglomeration were observed. However, catalyst decomposition was inferred from a non-zero intercept in the plot of catalyst loading versus reaction rate. Monitoring the reaction by PSI-ESI-(-)MS on neutral and negatively charged substrates at variety of concentrations and conditions did not reveal any detectable anionic palladium complexes. Likewise no evidence of carbopalladation and relevant intermediates in the absence of a base was observed.

  2. Mechanistic features of the copper-free Sonogashira reaction from ESI-MS.

    PubMed

    Ahmadi, Zohrab; Yunker, Lars P E; Oliver, Allen G; McIndoe, J Scott

    2015-12-21

    The mechanism of the Sonogashira reaction in methanol was studied in detail using pressurized sample infusion electrospray ionization mass spectrometry (PSI-ESI-MS). Several key intermediates were identified and their structures were assigned by MS/MS studies. Cationic and anionic charged-tagged substrates were employed to look into the mechanism of this reaction from variety of angles. A reverse kinetic isotope effect was observed in which the reaction rate is accelerated in deuterated solvents (kH/kD = 0.6). The reaction was found to be zero order with respect to the aryl iodide and first order with respect to the phenylacetylene. A Hammett parameter of ρ = 1.4 indicates that the reaction is more favorable for aryl iodides with para EWGs. No evidence of product inhibition, dimerization of palladium catalyst, or agglomeration were observed. However, catalyst decomposition was inferred from a non-zero intercept in the plot of catalyst loading versus reaction rate. Monitoring the reaction by PSI-ESI-(-)MS on neutral and negatively charged substrates at variety of concentrations and conditions did not reveal any detectable anionic palladium complexes. Likewise no evidence of carbopalladation and relevant intermediates in the absence of a base was observed. PMID:26469767

  3. Isomeric product detection in the heterogeneous reaction of hydroxyl radicals with aerosol composed of branched and linear unsaturated organic molecules.

    PubMed

    Nah, Theodora; Zhang, Haofei; Worton, David R; Ruehl, Christopher R; Kirk, Benjamin B; Goldstein, Allen H; Leone, Stephen R; Wilson, Kevin R

    2014-12-11

    The influence of molecular structure (branched vs linear) on product formation in the heterogeneous oxidation of unsaturated organic aerosol is investigated. Particle phase product isomers formed from the reaction of squalene (C30H50, a branched alkene with six C═C double bonds) and linolenic acid (C18H30O2, a linear carboxylic acid with three C═C double bonds) with OH radicals are identified and quantified using two-dimensional gas chromatography-mass spectrometry. The reactions are measured at low and high [O2] (∼1% vs 10% [O2]) to understand the roles of hydroxyalkyl and hydroxyperoxy radical intermediates in product formation. A key reaction step is OH addition to a C═C double bond to form a hydroxyalkyl radical. In addition, allylic alkyl radicals, formed from H atom abstraction reactions by hydroxyalkyl or OH radicals play important roles in the chemistry of product formation. Functionalization products dominate the squalene reaction at ∼1% [O2], with the total abundance of observed functionalization products being approximately equal to the fragmentation products at 10% [O2]. The large abundance of squalene fragmentation products at 10% [O2] is attributed to the formation and dissociation of tertiary hydroxyalkoxy radical intermediates. For linolenic acid aerosol, the formation of functionalization products dominates the reaction at both ∼1% and 10% [O2], suggesting that the formation and dissociation of secondary hydroxyalkoxy radicals are minor reaction channels for linear molecules. The distribution of linolenic acid functionalization products depends upon [O2], indicating that O2 controls the reaction pathways of the secondary hydroxyalkyl radical. For both reactions, alcohols are formed in favor of carbonyl functional groups, suggesting that there are some key differences between heterogeneous reactions involving allylic radical intermediates and those reactions of OH radicals with simple saturated hydrocarbons.

  4. Electrochemical incineration of 4-chlorophenol and the identification of products and intermediates by mass spectrometry

    SciTech Connect

    Johnson, S.K.; Houk, L.L.; Feng, J.; Houk, R.S.; Johnson, D.C. )

    1999-08-01

    This report summarizes results obtained as part of a larger effort to demonstrate the applicability of electrolytic procedures for the direct anodic (oxidative) degradation of toxic organic wastes. The authors refer to this process as electrochemical incineration (ECI) because the ultimate degradation products are equivalent to those achieved by thermal incineration processes. In this work, the ECI of 4-chlorophenol is achieved in an aqueous medium using a platinum anode coated with a quaternary metal oxide film containing Ti, Ru, Sn, and Sb oxides. The electrode is stable and active when used with a solid Nafion membrane without the addition of soluble supporting electrolyte. Liquid chromatography (LC), including reverse phase and ion exchange chromatography, is coupled with electrospray mass spectrometry (ES-MS) and used, along with gas chromatography-mass spectrometry (GC-MS) and measurements of pH, chemical oxygen demand (COD), and total organic carbon (TOC), to study the reaction and identify the intermediate products from the ECI of 4-chlorophenol. Twenty-six intermediate products are identified and reported. The most abundant of these products are benzoquinone, 4-chlorocatechol, maleic acid, succinic acid, malonic acid, and the inorganic anions chloride, chlorate, and perchlorate. After 24 h of ECI, a solution that initially contained 108 ppm 4-chlorophenol yields only 1 ppm TOC with 98% of the original chlorine remaining in the specified inorganic forms. LC-ES-MS and direct infusion ES-MS detection limits are between 80 ppb and 4 ppm for these intermediate products. Elemental analysis of the electrolyzed solutions by inductively coupled plasma mass spectrometry ICP-MS showed that only trace amounts of the metallic elements comprising the metal oxide film were present in the solution.

  5. Applications of Reaction Rate

    ERIC Educational Resources Information Center

    Cunningham, Kevin

    2007-01-01

    This article presents an assignment in which students are to research and report on a chemical reaction whose increased or decreased rate is of practical importance. Specifically, students are asked to represent the reaction they have chosen with an acceptable chemical equation, identify a factor that influences its rate and explain how and why it…

  6. Diphosphine is an intermediate in the photolysis of phosphine to phosphorus and hydrogen. [Jupiter atmospheric chemistry

    NASA Technical Reports Server (NTRS)

    Ferris, J. P.; Benson, R.

    1980-01-01

    The photolysis of phosphine to red phosphorus (P4) and hydrogen is investigated in light of the potential significance of the reaction in the atmospheric chemistry of Jupiter. It is reported that the photolysis of PH3 at room temperature by a 206.2-nm light source gave rise to a product identified by its UV and IR spectra and gas chromatographic retention time as P2H4, the yield of which is found to increase to a maximum and then decrease to 20% of the maximum value with illumination time. A mechanism for phosphine photolysis including diphosphine formation as an intermediate step is proposed, and it is concluded that P2H4 is a likely constituent of the atmospheres of the Jovian planets.

  7. Error Analysis in Composition of Iranian Lower Intermediate Students

    ERIC Educational Resources Information Center

    Taghavi, Mehdi

    2012-01-01

    Learners make errors during the process of learning languages. This study examines errors in writing task of twenty Iranian lower intermediate male students aged between 13 and 15. A subject was given to the participants was a composition about the seasons of a year. All of the errors were identified and classified. Corder's classification (1967)…

  8. Lexical Patterns in the Eyes of Intermediate EFL Readers

    ERIC Educational Resources Information Center

    Yamada, Kyoko

    2005-01-01

    Hoey (1991) claims that lexical patterns, which are a network of repetitious and synonymous words of a text, can be identified even by elementary foreign language readers. The present study investigates whether intermediate Japanese EFL readers can actually find elements of lexical patterns of a text Hoey uses in his book to demonstrate the…

  9. Vocabulary Learning Strategies of Iranian Upper-Intermediate EFL Learners

    ERIC Educational Resources Information Center

    Khatib, Mohammad; Hassanzadeh, Mohammad; Rezaei, Saeed

    2011-01-01

    This study examines the preferred vocabulary learning strategies of Iranian upper-intermediate EFL learners. In order to identify the aforementioned group in terms of language proficiency, a TOEFL test was administered to a population of 146 undergraduate EFL students at the university of Vali-e-Asr in Rafsanjan, Iran. Those scoring above 480 were…

  10. 40 CFR 721.983 - Sulfonyl azide intermediate (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.983 Sulfonyl azide intermediate (generic). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as sulfonyl azide...

  11. Catalytic degradation of recalcitrant pollutants by Fenton-like process using polyacrylonitrile-supported iron (II) phthalocyanine nanofibers: Intermediates and pathway.

    PubMed

    Zhu, Zhexin; Chen, Yi; Gu, Yan; Wu, Fei; Lu, Wangyang; Xu, Tiefeng; Chen, Wenxing

    2016-04-15

    Iron (II) phthalocyanine (FePc) molecules were isolated in polyacrylonitrile (PAN) nanofibers by electrospinning to prevent the formation of dimers and oligomers. Carbamazepine (CBZ) and Rhodamine B (RhB) degradation was investigated during a Fenton-like process with FePc/PAN nanofibers. Classical quenching tests with isopropanol and electron paramagnetic resonance tests with 5,5-dimethyl-pyrroline-oxide as spin-trapping agent were performed to determine the formation of active species during hydrogen peroxide (H2O2) decomposition by FePc/PAN nanofibers. After eight recycles for CBZ degradation over the FePc/PAN nanofibers/H2O2 system, the removal ratios of CBZ remained at 99%. Seven by-products of RhB and twelve intermediates of CBZ were identified using ultra-performance liquid chromatography and high-resolution mass spectrometry. Pathways of CBZ and RhB degradation were proposed based on the identified intermediates. As the reaction proceeded, all CBZ and RhB aromatic nucleus intermediates decreased and were transformed to small acids, but also to potentially toxic epoxide-containing intermediates and acridine, because of the powerful oxidation ability of •OH in the catalytic system. PMID:26949842

  12. Communications: Elementary oxygen electrode reactions in the aprotic Li-air battery.

    PubMed

    Hummelshøj, J S; Blomqvist, J; Datta, S; Vegge, T; Rossmeisl, J; Thygesen, K S; Luntz, A C; Jacobsen, K W; Nørskov, J K

    2010-02-21

    We discuss the electrochemical reactions at the oxygen electrode of an aprotic Li-air battery. Using density functional theory to estimate the free energy of intermediates during the discharge and charge of the battery, we introduce a reaction free energy diagram and identify possible origins of the overpotential for both processes. We also address the question of electron conductivity through the Li(2)O(2) electrode and show that in the presence of Li vacancies Li(2)O(2) becomes a conductor. PMID:20170208

  13. The Mechanisms of Oxygen Reduction and Evolution Reactions in Nonaqueous Lithium-Oxygen Batteries

    SciTech Connect

    Cao, Ruiguo; Walter, Eric D.; Xu, Wu; Nasybulin, Eduard N.; Bhattacharya, Priyanka; Bowden, Mark E.; Engelhard, Mark H.; Zhang, Jiguang

    2014-09-01

    The oxygen reduction/evolution reaction (ORR/OER) mechanisms in nonaqueous Li-O2 batteries have been investigated by using electron paramagnetic resonance spectroscopy in this work. We identified the superoxide radical anion (O2•-) as an intermediate in the ORR process using 5,5-dimethyl-pyrroline N-oxide as a spin trap, while no O2•- in OER was detected during the charge process. These findings provide insightful understanding on the fundamental oxygen reaction mechanisms in rechargeable nonaqueous Li-O2 batteries.

  14. Role of Intermediate Filaments in Vesicular Traffic.

    PubMed

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  15. Role of Intermediate Filaments in Vesicular Traffic

    PubMed Central

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  16. Intermediate Filaments in Caenorhabditis elegans.

    PubMed

    Zuela, Noam; Gruenbaum, Yosef

    2016-01-01

    More than 70 different genes in humans and 12 different genes in Caenorhabditis elegans encode the superfamily of intermediate filament (IF) proteins. In C. elegans, similar to humans, these proteins are expressed in a cell- and tissue-specific manner, can assemble into heteropolymers and into 5-10nm wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. At least 5 of the 11 cytoplasmic IFs, as well as the nuclear IF, lamin, are essential. In this chapter, we will include a short review of our current knowledge of both cytoplasmic and nuclear IFs in C. elegans and will describe techniques used for their analyses.

  17. Pineal parenchymal tumor of intermediate differentiation.

    PubMed

    Patil, Meena; Karandikar, Manjiri

    2015-01-01

    The 2007 World Health Organization classification of tumors of the central nervous system identified "pineal parenchymal tumor of intermediate differentiation" (PPTID) as a new pineal parenchymal neoplasm, located between pineocytoma and pineoblastoma as grade II or III. Because of the small number of reported cases, the classification of PPT is still a matter of controversy. We report a case of PPTID. A 25-year-old female patient was admitted to hospital with complaints of a headache, nausea, vomiting since 1-year. Computed tomography/magnetic resonance imaging of the brain showed well-defined, mildly enhancing lesion in the region of the pineal gland with areas of calcification. The tumor was excised. After 3 years, she presented with metastasis in thoracic and lumbosacral spinal region. This is a rare event. PMID:26549088

  18. EGRET sources at intermediate galactic latitude

    NASA Technical Reports Server (NTRS)

    Halpern, Jules P. (Principal Investigator)

    1996-01-01

    This paper presents the abstracts of four papers (using ROSAT data) that are submitted to refereed journals during the current reporting period. The papers are: (1) Extreme x-ray variability in the narrow-line QSO PHL 1092; (2) The Geminga pulsar (soft x-ray variability and an EUVE observation); (3) a broad-band x-ray study of the geminga pulsar; and (4) Classification of IRAS-selected x-ray galaxies in the ROSAT all-sky survey. The abstracts of these papers are given in the next four sections of this report, and their status is given in the Appendix. Finally, two new projects (De-identifying a non-AGN and EGRET sources at intermediate galactic latitude) for which ROSAT data were recently received are currently being studied under this grant. A summary of work in progress on these new projects is given in the last two sections of this report.

  19. Characterizing the Integral Intermediate Polar Population

    NASA Astrophysics Data System (ADS)

    Norton, Andrew

    A major surprise of the INTEGRAL mission is that, although Intermediate Polars are <10% of the population of Cataclysmic Variables, they make up >90% of the CVs detected by the IBIS survey. We propose to observe 8 probable IPs detected by INTEGRAL, plus 4 more recently identified likely IPs, for which no pointed X-ray observations exist in order to (i) search for and characterize their pulsed X-ray emission and (ii) measure their 2-20 keV spectrum. This will confirm their classification and address how/why this hard X-ray selected sample differ from the known IPs. They may have different magnetic field strengths, accretion rates or accretion flow structures, and so follow a different evolutionary path. It's even possible they represent the long sought after IPs that evolve into polars.

  20. 34 CFR 200.17 - Intermediate goals.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Intermediate goals. 200.17 Section 200.17 Education... Programs Operated by Local Educational Agencies Adequate Yearly Progress (ayp) § 200.17 Intermediate goals. Each State must establish intermediate goals that increase in equal increments over the period...

  1. Intramolecular hydrogen transfer reaction: menthon from isopulegol.

    PubMed

    Schaub, Thomas; Rüdenauer, Stefan; Weis, Martine

    2014-05-16

    The flavor menthon (isomeric mixture of (-)-menthon and (+)-isomenthon) was obtained in good yields and selectivities by a solventless ruthenium catalyzed isomerization of the homoallylic alcohol (-)-isopulegol. In contrast to most previous assumptions on such "isomerization" reactions, this reaction follows an intermolecular pathway, with menthol and pulegon being the central intermediates in this transformation. PMID:24779450

  2. Gold(I)-catalyzed enantioselective cycloaddition reactions.

    PubMed

    López, Fernando; Mascareñas, José L

    2013-10-30

    In recent years there have been extraordinary developments of gold(I)-catalyzed enantioselective processes. This includes progress in the area of cycloaddition reactions, which are of particular interest due to their potential for the rapid construction of optically active cyclic products. In this article we will summarize some of the most remarkable examples, emphasizing reaction mechanisms and key intermediates involved in the processes.

  3. Cerium doped red mud catalytic ozonation for bezafibrate degradation in wastewater: Efficiency, intermediates, and toxicity.

    PubMed

    Xu, Bingbing; Qi, Fei; Sun, Dezhi; Chen, Zhonglin; Robert, Didier

    2016-03-01

    In this study, the performance of bezafibrate (BZF) degradation and detoxification in the aqueous phase using cerium-modified red mud (RM) catalysts prepared using different cerium sources and synthesis methods were evaluated. Experimental results showed that the surface cerium modification was responsible for the development of the catalytic activity of RM and this was influenced by the cerium source and the synthesis method. Catalyst prepared from cerium (IV) by precipitation was found to show the best catalytic activity in BZF degradation and detoxification. Reactive oxygen species including peroxides, hydroxyl radicals, and super oxide ions were identified in all reactions and we proposed the corresponding catalytic reaction mechanism for each catalyst that prepared from different cerium source and method. This was supported by the intermediates profiles that were generated upon BZF degradation. The surface and the structural properties of cerium-modified RM were characterized in detail by several analytical methods. Two interesting findings were made: (1) the surface texture (specific surface area and mesoporous volume) influenced the catalytic reaction pathway; and (2) Ce(III) species and oxygen vacancies were generated on the surface of the catalyst after cerium modification. This plays an important role in the development of the catalytic activity. PMID:26706928

  4. Propene oxidation at low and intermediate temperatures: A detailed chemical kinetic study

    SciTech Connect

    Wilk, R.D.; Cernansky, N.P.; Pitz, W.J.; Westbrook, C.K.

    1987-03-24

    A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 575-715 K, equivalence ratios of 0.8 - 2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species and all conditions measured experimentally in the static reactor. Overall, the calculated concentrations of carbon monoxide, acetaldehyde, acrolein, and propane oxide agreed well with those measured. The calculated concentrations of ethane are low compared to the experimental measurements, and the calculated concentrations of formaldehyde are high. Agreement for concentrations of carbon dioxide, methane, and methanol is mixed. The characteristic s-shape of the fuel concentration history is well predicted. Modeling calculations identified some of the key reaction steps at the present conditions. Addition of OH to propene and H atom abstraction by OH from propene are important steps in determining the subsequent distributions of intermediate products, such as acetaldehyde, acrolein and formaldehyde. Allyl radicals are very abundant in propene oxidation, and the primary steps found to be responsible for their consumption are reaction with CH/sub 3/O/sub 2/ and HO/sub 2/. 37 refs., 5 figs., 1 tab.

  5. Propene oxidation at low and intermediate temperatures: A detailed chemical kinetic study

    SciTech Connect

    Wilk, R.D.; Gernansky, N.P.; Pitz, W.J.; Westbrook, C.K.

    1987-01-01

    A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 575-715 K, equivalence ratios of 0.8 - 2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species and all conditions measured experimentally in the static reactor. Overall, the calculated concentrations of carbon monoxide, acetaldehyde, acrolein, and propene oxide agreed well with those measured. The calculated concentrations of ethene are low compared to the experimental measurements, and the calculated concentrations of formaldehyde are high. Agreement for concentrations of carbon dioxide, methane, and methanol is mixed. The characteristic s-shape of the fuel concentration history is well predicted. Modeling calculations identified some of the key reaction steps at the present conditions. Addition of OH to propene and H atom abstraction by OH from propene are important steps in determining the subsequent distributions of intermediate products, such as acetaldehyde, acrolein and formaldehyde. Allyl radicals are very abundant in propene oxidation, and the primary steps found to be responsible for their consumption are reaction with CH/sub 3/O/sub 2/ and HO/sub 2/.

  6. Radiation-induced reactions in polymer films

    NASA Astrophysics Data System (ADS)

    Biscoglio, Michael Benedict

    Since the 1950's, there has been a considerable interest in the effects of ionizing radiation on the physical properties of polymer systems. Radiation induced chemical changes that were found to be helpful in producing specialty polymers, but also potentially harmful by degrading the physical performance of the material. Therefore, solute molecules, which act as excited state quenchers, and free radical scavengers, have been incorporated into the polymers in order to regulate the crosslinking, scission and desaturation reactions. This work is focused on using spectroscopic techniques to characterize the physical properties of polymeric media and the reactions occurring within them following pulsed radiolysis. This is done primarily by using arene doped polymer films which have highly absorbing excited states and radical ions that are easily monitored by transient studies. The probes are used to characterize the polymeric microenvironment, to monitor reaction rates, and to interfere in the radical reactions. Photophysical and photochemical characterization of partially crystalline polyethylene complements data previously obtained by conventional physical techniques for polymer characterization. Probe molecules are excluded from crystalline zones and distributed in a networked structure of amorphous zones. Upon high energy radiolysis, it is found that polyolefin systems efficiently donate all radical ions and excited states to the solute molecules, even when the energy is absorbed within the polymer crystalline zones. Studies of the subsequent reactions of the solute excited states and radical ions reveal information about their long term effectiveness as protectants. It is found that highly excited states formed by the recombination of solute radical ions are energetic enough to cause dissociation of halo-arenes. Also, arenes are found to become attached to the polymer chain through a polymer-aryl radical intermediate. These intermediates have been isolated and

  7. Mineral catalyzed hydrothermal reactions as precursors to extant anabolic pathways

    NASA Astrophysics Data System (ADS)

    Cody, G. D.

    Investigations into hydrothermal reactions under conditions of moderate hydrostatic pressure and in the presence of transition metal sulfides reveal reaction pathways the bear remarkable similarity with extant anabolic reactions. First, it is seen that most common transition metal sulfides are capable of promoting all of the key reactions at the core of Acetyl Co-A synthesis. These include CO reduction to methyl groups and carbonyl insertion to form transferable acetyl groups. The synthesis of alpha-keto acids are also promoted, presumably by double carbonylation. A pathway starting with CO2 and H2 has been identified leading to the synthesis of citric acid. Citric acid provides a crucial abiotic, anabolic, branch point to the prebiotic synthesis of various amino acids, as well. As the pyrimidines, orotic acid and uracil. In many cases the abiotic reaction pathways differ slightly from extant anabolic pathways by shunting past particularly reactive intermediates, e.g. oxaloacetic acid. These reactions have the capacity to provide the prebiotic world with many, but not all, of the molecular constituents to aid the emergence of an RNA world.

  8. Cofactor mobility determines reaction outcome in the IMPDH/GMPR (β/α)8 barrel enzymes

    PubMed Central

    Patton, Gregory C.; Stenmark, Pål; Gollapalli, Deviprasad R.; Sevastik, Robin; Kursula, Petri; Flodin, Susanne; Schuler, Herwig; Swales, Colin T.; Eklund, Hans; Himo, Fahmi; Nordlund, Pär; Hedstrom, Lizbeth

    2015-01-01

    IMP dehydrogenase (IMPDH) and GMP reductase (GMPR) belong to the same structural family, share a common set of catalytic residues and bind the same ligands. The structural and mechanistic features that determine reaction outcome in the IMPDH/GMPR family have not been identified. Here, we show that the GMPR reaction utilizes the same intermediate E-XMP* as IMPDH, but this intermediate reacts with ammonia instead of water. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimic a distinct step in the catalytic cycle of GMPR. The cofactor is found in two conformations, an "in" conformation poised for hydride transfer, and an "out" conformation where the cofactor is 6 Å from IMP. Mutagenesis, substrate/cofactor analog experiments demonstrate that the “out” conformation is required for the deamination of GMP. Remarkably, the cofactor is part of the catalytic machinery activating ammonia. PMID:22037469

  9. Drug Reactions

    MedlinePlus

    ... or diabetes. But medicines can also cause unwanted reactions. One problem is interactions, which may occur between ... more serious. Drug allergies are another type of reaction. They can be mild or life-threatening. Skin ...

  10. MCNP6 fragmentation of light nuclei at intermediate energies

    NASA Astrophysics Data System (ADS)

    Mashnik, Stepan G.; Kerby, Leslie M.

    2014-11-01

    Fragmentation reactions induced on light target nuclei by protons and light nuclei of energies around 1 GeV/nucleon and below are studied with the latest Los Alamos Monte Carlo transport code MCNP6 and with its cascade-exciton model (CEM) and Los Alamos version of the quark-gluon string model (LAQGSM) event generators, version 03.03, used as stand-alone codes. Such reactions are involved in different applications, like cosmic-ray-induced single event upsets (SEU's), radiation protection, and cancer therapy with proton and ion beams, among others; therefore, it is important that MCNP6 simulates them as well as possible. CEM and LAQGSM assume that intermediate-energy fragmentation reactions on light nuclei occur generally in two stages. The first stage is the intranuclear cascade (INC), followed by the second, Fermi breakup disintegration of light excited residual nuclei produced after the INC. Both CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to 4He from energetic nucleons emitted during INC. We investigate the validity and performance of MCNP6, CEM, and LAQGSM in simulating fragmentation reactions at intermediate energies and discuss possible ways of further improving these codes.

  11. Identification of free radical intermediates in oxidized wine using electron paramagnetic resonance spin trapping.

    PubMed

    Elias, Ryan J; Andersen, Mogens L; Skibsted, Leif H; Waterhouse, Andrew L

    2009-05-27

    Free radicals are thought to be key intermediates in the oxidation of wine, but their nature has not been established. Electron paramagnetic resonance spectroscopy was used to detect and identify several free radical species in wine under oxidative conditions with the aid of spin traps. The 1-hydroxylethyl radical was the sole radical species observed when α-(4-pyridyl-1-oxide)-N-tert-butylnitrone was used as a spin trap in a heated (55 °C), low-sulfite (15 mg L(-1)) red wine. This radical appears to arise from ethanol oxidation via the hydroxyl radical, and this latter species was confirmed by using a high concentration (1.5 M) of the 5,5-dimethylpyrroline-N-oxide spin trap, thus providing the first direct evidence of the Fenton reaction in wine. Hydroxyl radical formation in wine was corroborated by converting hydroxyl radicals to methyl radicals by its reaction with dimethyl sulfoxide. The novel spin trap 5-tert-butoxycarbonyl 5-methyl-1-pyrroline N-oxide was also used in this study to identify sulfite radicals in wine for the first time. This spin trap has also been shown to trap hydroperoxyl radicals, the generation of which is predicted in wine; however, no evidence of this species was observed. PMID:19358607

  12. Intermediate reboiler and condenser arrangement for binary distillation columns

    SciTech Connect

    Agrawal, R.; Herron, D.M.

    1998-06-01

    The most thermodynamically efficient configuration for adding or removing heat from an intermediate location of an ideal binary distillation column distilling pure products is derived. The optimal policy requires that preconditioning of the feed be part of the overall decision-making process. The optimal configuration can be determined through the use of two parameters, {alpha}{sub IR} and {alpha}{sub IC}, that are solely functions of feed composition. Simple and readily usable heuristics using these parameters are developed that help instantly identify the most efficient selection among (1) totally vaporizing and returning a side-draw liquid stream from an intermediate location of the distillation column, (2) partially or totally vaporizing a portion of the given saturated liquid feed, (3) partially or totally condensing a portion of the given saturated vapor feed, and (4) totally condensing and returning a side-draw vapor stream from an intermediate location of the distillation column.

  13. Demonstration of HNE-related aldehyde formation via lipoxygenase-catalyzed synthesis of a bis-allylic dihydroperoxide intermediate

    PubMed Central

    Jin, Jing; Zheng, Yuxiang; Brash, Alan R.

    2013-01-01

    One of the proposed pathways to the synthesis of 4-hydroxy-nonenal (HNE) and related aldehydes entails formation of an intermediate bis-allylic fatty acid dihydroperoxide. As a first direct demonstration of such a pathway and proof of principle, herein we show that 8R-lipoxygenase (8R-LOX) catalyzes the enzymatic production of the HNE-like product (11-oxo-8-hydroperoxy-undeca-5,9-dienoic acid) via synthesis of 8,11-dihydroperoxy-eicosa-5,9,12,14-tetraenoic acid intermediate. Incubation of arachidonic acid with 8R-LOX formed initially 8R-hydroperoxyeicosatetraenoic acid (8R-HPETE) which was further converted to a mixture of products including a prominent HPNE-like enone. A new bis-allylic dihydroperoxide was trapped when the incubation was repeated on ice. Re-incubation of this intermediate with 8R-LOX successfully demonstrated its conversion to the enone products, and this reaction was greatly accelerated by co-incubation with NDGA, a reductant of the LOX iron. These findings identify a plausible mechanism that could contribute to the production of 4-hydroxy-alkenals in vivo. PMID:23668325

  14. Top predators induce the evolutionary diversification of intermediate predator species.

    PubMed

    Zu, Jian; Yuan, Bo; Du, Jianqiang

    2015-12-21

    We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator׳s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct. PMID:26431773

  15. Top predators induce the evolutionary diversification of intermediate predator species.

    PubMed

    Zu, Jian; Yuan, Bo; Du, Jianqiang

    2015-12-21

    We analyze the evolutionary branching phenomenon of intermediate predator species in a tritrophic food chain model by using adaptive dynamics theory. Specifically, we consider the adaptive diversification of an intermediate predator species that feeds on a prey species and is fed upon by a top predator species. We assume that the intermediate predator׳s ability to forage on the prey can adaptively improve, but this comes at the cost of decreased defense ability against the top predator. First, we identify the general properties of trade-off relationships that lead to a continuously stable strategy or to evolutionary branching in the intermediate predator species. We find that if there is an accelerating cost near the singular strategy, then that strategy is continuously stable. In contrast, if there is a mildly decelerating cost near the singular strategy, then that strategy may be an evolutionary branching point. Second, we find that after branching has occurred, depending on the specific shape and strength of the trade-off relationship, the intermediate predator species may reach an evolutionarily stable dimorphism or one of the two resultant predator lineages goes extinct.

  16. Dearomatization through Halofunctionalization Reactions.

    PubMed

    Liang, Xiao-Wei; Zheng, Chao; You, Shu-Li

    2016-08-16

    Recent advances in dearomatization through halofunctionalization reactions are summarized in this Minireview. Two general categories of strategies are currently employed in this field. On one hand, the reaction can be initiated with electrophilic halogenation at an alkyne or alkene moiety. The resulting halonium ion intermediate is then captured by a pendant aromatic ring at the ipso position, affording the dearomatization product. On the other hand, electrophilic halogenation can directly take place at a substituted arene, and the final dearomatization product is furnished by deprotonation or intramolecular nucleophilic trap. Highly enantioselective variants have been realized in the latter case by organocatalysis or transition metal catalysis. By applying these methods, various valuable halogenated polycyclic molecular architectures have been obtained from readily available starting materials. PMID:27377184

  17. Kinetic Intermediates in RNA Folding

    NASA Astrophysics Data System (ADS)

    Zarrinkar, Patrick P.; Williamson, James R.

    1994-08-01

    The folding pathways of large, highly structured RNA molecules are largely unexplored. Insight into both the kinetics of folding and the presence of intermediates was provided in a study of the Mg2+-induced folding of the Tetrahymena ribozyme by hybridization of complementary oligodeoxynucleotide probes. This RNA folds via a complex mechanism involving both Mg2+-dependent and Mg2+-independent steps. A hierarchical model for the folding pathway is proposed in which formation of one helical domain (P4-P6) precedes that of a second helical domain (P3-P7). The overall rate-limiting step is formation of P3-P7, and takes place with an observed rate constant of 0.72 ± 0.14 minute-1. The folding mechanism of large RNAs appears similar to that of many multidomain proteins in that formation of independently stable substructures precedes their association into the final conformation.

  18. Intermediate Filaments in Caenorhabditis elegans.

    PubMed

    Zuela, Noam; Gruenbaum, Yosef

    2016-01-01

    More than 70 different genes in humans and 12 different genes in Caenorhabditis elegans encode the superfamily of intermediate filament (IF) proteins. In C. elegans, similar to humans, these proteins are expressed in a cell- and tissue-specific manner, can assemble into heteropolymers and into 5-10nm wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. At least 5 of the 11 cytoplasmic IFs, as well as the nuclear IF, lamin, are essential. In this chapter, we will include a short review of our current knowledge of both cytoplasmic and nuclear IFs in C. elegans and will describe techniques used for their analyses. PMID:26795488

  19. Displays for future intermediate UAV

    NASA Astrophysics Data System (ADS)

    Desjardins, Daniel; Metzler, James; Blakesley, David; Rister, Courtney; Nuhu, Abdul-Razak

    2008-04-01

    The Dedicated Autonomous Extended Duration Airborne Long-range Utility System (DAEDALUS) is a prototype Unmanned Aerial Vehicle (UAV) that won the 2007 AFRL Commander's Challenge. The purpose of the Commander's Challenge was to find an innovative solution to urgent warfighter needs by designing a UAV with increased persistence for tactical employment of sensors and communication systems. DAEDALUS was chosen as a winning prototype by AFRL, AFMC and SECAF. Follow-on units are intended to fill an intermediate role between currently fielded Tier I and Tier II UAV's. The UAV design discussed in this paper, including sensors and displays, will enter Phase II for Rapid Prototype Development with the intent of developing the design for eventual production. This paper will discuss the DAEDALUS UAV prototype system, with particular focus on its communications, to include the infrared sensor and electro-optical camera, but also displays, specifically man-portable.

  20. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface

    NASA Astrophysics Data System (ADS)

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-01

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH4) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH4 over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH4 decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C2) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface.