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1

Identifying Reactive Intermediates in the Ullmann Coupling Reaction by Scanning Tunneling Microscopy and Spectroscopy  

NASA Astrophysics Data System (ADS)

We present an atomic-scale study of substituent effects in the Ullmann coupling reaction on Cu{111} using low-temperature scanning tunneling microscopy and spectroscopy. We have observed fluorophenyl intermediates and phenyl intermediates as well as biphenyl products on Cu{111} after exposure to 4-fluoro-1-bromobenzene (p-FC6H4Br) and bromobenzene (C6H5Br), respectively. When p-FC6H4Br dissociatively chemisorbs at 298 K on Cu{111}, the relatively weakly bound Br dissociates, and fluorophenyl intermediates are formed. These intermediates couple to form 4,4'-difluorobiphenyl and desorb at temperatures below 370 K. However, by cooling the substrate to low temperature (4 K), we have observed unreacted fluorophenyl intermediates distributed randomly on terraces and at step edges of the Cu{111} surface. Alternatively, at similar coverages of C6H5Br, we have observed biphenyl distributed on terraces and step edges. In each case, Br adatoms were randomly distributed on the surface. Chemical identification of fluorophenyl and phenyl intermediates and biphenyl products was achieved by vibrational spectroscopy via inelastic tunneling spectroscopy. The strongest vibrational mode in the phenyl species disappears when the tilted intermediates couple to form biphenyl products. We infer that the surface normal component of the dipole moment is important in determining the transition strength in inelastic electron tunneling spectroscopy.

Blake, Meaghan M.; Nanayakkara, Sanjini U.; Claridge, Shelley A.; Fernández-Torres, Luis C.; Sykes, E. Charles H.; Weiss, Paul S.

2009-08-01

2

A pentacyclic reaction intermediate of riboflavin synthase  

PubMed Central

The S41A mutant of riboflavin synthase from Escherichia coli catalyzes the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine at a very low rate. Quenching of presteady-state reaction mixtures with trifluoroacetic acid afforded a compound with an absorption maximum at 412 nm (pH 1.0) that can be converted to a mixture of riboflavin and 6,7-dimethyl-8-ribityllumazine by treatment with wild-type riboflavin synthase. The compound was shown to qualify as a kinetically competent intermediate of the riboflavin synthase-catalyzed reaction. Multinuclear NMR spectroscopy, using various 13C- and 15N-labeled samples, revealed a pentacyclic structure arising by dimerization of 6,7-dimethyl-8-ribityllumazine. Enzyme-catalyzed fragmentation of this compound under formation of riboflavin can occur easily by a sequence of two elimination reactions.

Illarionov, Boris; Eisenreich, Wolfgang; Bacher, Adelbert

2001-01-01

3

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

ERIC Educational Resources Information Center

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…

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

2009-01-01

4

Radical Intermediates in Monooxygenase Reactions of Rieske Dioxygenases  

PubMed Central

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 ?3?3 oxygenase (NDO). In each ? 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.

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

2009-01-01

5

Ligand Intermediates in Metal-Catalyzed Reactions  

SciTech Connect

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.

Gladysz, John A.

1999-07-31

6

Photonuclear reaction mechanisms at intermediate energies  

NASA Astrophysics Data System (ADS)

The goal of the present experiment was to study the reaction mechanisms involved in the absorption of photons by nuclei in the tagged photon energy range E/sb/gamma = 60 to 140 MeV. For the photon energy of 64 MeV the 16O(/gamma, p)15Ng.s. reaction was measured. A description of the process in terms of a direct knockout formalism was inadequate to explain the magnitude of the measured cross section. The inclusion of two-body meson-exchange-currents in the calculation was found to give a much better fit to the data. Of particular interest for this experiment was to study the absorption of a photon on a correlated proton-neutron pair for the photon energy range E/sb/gamma = 100 to 140 MeV. The two nucleon absorption mechanism is dominant in this photon energy range. The reaction studied was 16O(/gamma, pn)14N0,1,2/... Having sufficient experimental energy resolution to determine the population to discrete states in the residual 14N nucleus provided information on the quantum numbers involved in the two nucleon absorption mechanism. Also the large continuum yield at excitation energies larger than 20 MeV compared to the yield below 20 MeV is seen as evidence that short range nucleon-nucleon correlations play a significant role for the two body reaction mechanism in the photon energy region studied.

Garrow, Kenneth Roy

1998-12-01

7

Fission decay in intermediate heavy ion reactions  

SciTech Connect

Results are presented on cross sections, parallel and perpendicular momentum transfers, charge loss and velocity systematics for fission following reactions of Fe and Nb projectiles at 50--100 MeV/A on targets of Ta, Au, and Th. The results at 100 MeV/A are compared to a detailed multistage deexcitation model. The initial collision is modeled with an intranuclear cascade. The resultant excited target residues then undergo a fast preequilibrium decay stage followed by a statistical decay involving nucleon evaporation and fission. Results from this modeling are in reasonable agreement with experimental data. 14 refs., 11 figs.

Britt, H.C.

1990-10-03

8

The phosphorylated intermediate in the phosphoglyceromutase reaction  

PubMed Central

1. High-voltage paper-electrophoresis methods have been used for the separation of 32P-labelled phosphoesters. 2. Evidence is presented which indicates that 32P-labelled phosphopeptides, obtained after acid hydrolysis of phosphoglyceromutase incubated with impure 2,3-di[32P]phosphoglycerate, are derived from phosphoglucomutase contamination. 3. The hydrolysis of 2,3-di[32P]phosphoglycerate by phosphoglyceromutase has been studied. After an apparent instantaneous hydrolysis of 1 mole of coenzyme/mole of enzyme the reaction proceeds at a very low rate. 4. This hydrolysis seems to be due to the destruction of an enzyme–coenzyme complex. The proportions of the decomposition products of the complex vary according to further handling (pH of ionophoresis). 5. The inorganic [32P]phosphate produced by the hydrolysis of the complex and the inorganic [32P]phosphate produced by the slow phosphatase activity can be differentiated by the ability of the former to be incorporated into non-radioactive substrate before enzyme denaturation. 6. The effect of enzyme concentration on the stoicheiometry of the slow phosphatase hydrolysis of the diphosphoglycerate is described and this suggests that it may occur via two independent reactions, one of them being the decomposition of the enzyme–coenzyme complex on standing.

Zwaig, N.; Milstein, C.

1966-01-01

9

Quantum mechanical investigations on the role of neutral and negatively charged enamine intermediates in organocatalyzed reactions  

NASA Astrophysics Data System (ADS)

The proline-catalyzed aldol reaction is the seminal example of asymmetric organocatalysis. Previous theoretical and experimental studies aimed at identifying its mechanism in order to rationalize the outcome of this reaction. Here, we focus on key steps with modern first principle methods, i.e. the M06-2X hybrid exchange-correlation functional combined to the solvation density model to account for environmental effects. In particular, different pathways leading to the formation of neutral and negatively charged enamine intermediates are investigated, and their reactivity towards two electrophiles, i.e. an aldehyde and a benzhydrylium cation, are compared. Regarding the self-aldol reaction, our calculations confirm that the neutral enamine intermediate is more reactive than the negatively charged one. For the reaction with benzhydrylium cations however, the negatively charged enamine intermediate is more reactive.

Hubin, Pierre O.; Jacquemin, Denis; Leherte, Laurence; Vercauteren, Daniel P.

2014-04-01

10

Accomplishing structural change: Identifying intermediate indicators of success  

PubMed Central

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.

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

2012-01-01

11

Accomplishing structural change: identifying intermediate indicators of success.  

PubMed

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

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

2013-03-01

12

Ligandless, anionic, arylpalladium halide intermediates in the Heck reaction.  

PubMed

We report the isolation and reactivity of a series of "ligandless," anionic arylpalladium complexes of the general structure [Pd(Ar)Br(2)](2)(2-) by the reaction of ((t)Bu(3)P)Pd(Ar)(Br) and bromide. These anionic complexes insert olefins at room temperature, and these fast insertions indicate that the anionic complexes are kinetically competent to be intermediates in Heck-Mizoroki reactions conducted under "ligandless" conditions (lacking added dative ligand). Kinetic studies showed that the anionic complexes insert olefins much faster than the corresponding neutral, P(t-Bu)(3)-ligated complexes. Addition of halide to the reaction of the neutral complex ((t)Bu(3)P)Pd(Ar)(Br) and styrene led to a significant rate acceleration, suggesting that the anionic complex forms rapidly and reversibly in situ from the neutral species prior to migratory insertion. These data, along with studies on the regioselectivity for reaction of aryl halides with butyl vinyl ether in the presence of the different starting catalysts, are consistent with the intermediacy of the same anionic, arylpalladium intermediates in Heck reactions catalyzed by palladium complexes containing bulky trialkylphosphine ligands as in reactions conducted under ligandless conditions. PMID:20014842

Carrow, Brad P; Hartwig, John F

2010-01-13

13

Ligandless, Anionic, Arylpalladium Halide Intermediates in the Heck Reaction  

PubMed Central

We report the isolation and reactivity of a series of “ligandless,” anionic arylpalladium complexes of the general structure [Pd(Ar)Br2]22- by the reaction of (tBu3P)Pd(Ar)(Br) and bromide. These anionic complexes insert olefins at room temperature, and these fast insertions indicate that the anionic complexes are kinetically competent as intermediates in Heck-Mizoroki reactions conducted under “ligandless” conditions (lacking added dative ligand). Kinetic studies showed that the anionic complexes insert olefins much faster than the corresponding neutral, P(t-Bu)3-ligated complexes. Addition of halide to the reaction of the neutral complex (tBu3P)Pd(Ar)(Br) and styrene led to a significant rate acceleration, suggesting that the anionic complex forms rapidly and reversibly in situ from the neutral species prior to migratory insertion. These data, along with studies on the regioselectivity for reaction of aryl halides with butyl vinyl ether in the presence of the different starting catalysts, are consistent with the intermediacy of the same anionic, arylpalladium intermediates in Heck reactions catalyzed by palladium complexes containing bulky trialkylphosphine ligands as in reactions conducted under ligandless conditions.

Carrow, Brad P.

2010-01-01

14

The Identification of Stable Reaction Intermediates on Aluminum Oxide Surfaces with Inelastic Electron Tunneling Spectroscopy  

Microsoft Academic Search

The stable surface intermediates that were formed in several heterogeneous reactions on aluminum oxide films were identified with inelastic electron tunneling spectroscopy. The alumina films were synthesized by the plasma oxidation of aluminum metal films. The temperature and exposure dependent interaction of cyclopropane carboxylic acid with alumina films was studied. Cyclopropane carboxylate and n-butane carboxylate were the only adsorbed species

Michael Karpovich Templeton

1984-01-01

15

Intermediate resonance excitation in the ?p?p?? reaction  

NASA Astrophysics Data System (ADS)

The helicity dependence of the total cross section for the ??p??p?? reaction has been measured for the first time at incident photon energies from 400 to 800 MeV. The measurement, performed at the tagged photon beam facility of the MAMI accelerator in Mainz, used the large acceptance detector DAPHNE and a longitudinally polarized frozen-spin target. This channel is found to be excited predominantly when the photon and proton have a parallel spin orientation, most likely due to the intermediate production of the D(1520) resonance. However, the contribution of the antiparallel spin configuration, arising from other reaction mechanisms, is also not negligible. This result gives important new information to resolve the existing model discrepancies in the identification of the nucleon resonances contributing to this channel.

Gdh Collaboration; Ahrens, J.; Altieri, S.; Annand, J. R. M.; Anton, G.; Arends, H.-J.; Aulenbacher, K.; Beck, R.; Bradtke, C.; Braghieri, A.; Degrande, N.; D'Hose, N.; Dutz, H.; Goertz, S.; Grabmayr, P.; Hansen, K.; Harmsen, J.; von Harrach, D.; Hasegawa, S.; Hasegawa, T.; Heid, E.; Helbing, K.; Holvoet, H.; van Hoorebeke, L.; Horikawa, N.; Iwata, T.; Jahn, O.; Jennewein, P.; Kageya, T.; Kiel, B.; Klein, F.; Kondratiev, R.; Kossert, K.; Krimmer, J.; Lang, M.; Lannoy, B.; Leukel, R.; Lisin, V.; Matsuda, T.; McGeorge, J. C.; Meier, A.; Menze, D.; Meyer, W.; Michel, T.; Naumann, J.; Panzeri, A.; Pedroni, P.; Pinelli, T.; Preobrajenski, I.; Radtke, E.; Reichert, E.; Reicherz, G.; Rohlof, Ch.; Rosner, G.; Rostomyan, T.; Ryckbosch, D.; Sauer, M.; Schoch, B.; Schumacher, M.; Seitz, B.; Speckner, T.; Takabayashi, N.; Tamas, G.; Thomas, A.; van de Vyver, R.; Wakai, A.; Weihofen, W.; Wissmann, F.; Zapadtka, F.; Zeitler, G.

2005-09-01

16

Intermediate resonance excitation in the ?p?p?? reaction  

NASA Astrophysics Data System (ADS)

The helicity dependence of the total cross section for the ??p??p?? reaction has been measured for the first time at incident photon energies from 400 to 800 MeV. The measurement, performed at the tagged photon beam facility of the MAMI accelerator in Mainz, used the large acceptance detector DAPHNE and a longitudinally polarized frozen-spin target. This channel is found to be excited predominantly when the photon and proton have a parallel spin orientation, most likely due to the intermediate production of the D(1520) resonance. However, the contribution of the antiparallel spin configuration, arising from other reaction mechanisms, is also not negligible. This result gives important new information to resolve the existing model discrepancies in the identification of the nucleon resonances contributing to this channel.

Ahrens, J.; Altieri, S.; Annand, J. R. M.; Anton, G.; Arends, H.-J.; Aulenbacher, K.; Beck, R.; Bradtke, C.; Braghieri, A.; Degrande, N.; d'Hose, N.; Dutz, H.; Goertz, S.; Grabmayr, P.; Hansen, K.; Harmsen, J.; von Harrach, D.; Hasegawa, S.; Hasegawa, T.; Heid, E.; Helbing, K.; Holvoet, H.; Van Hoorebeke, L.; Horikawa, N.; Iwata, T.; Jahn, O.; Jennewein, P.; Kageya, T.; Kiel, B.; Klein, F.; Kondratiev, R.; Kossert, K.; Krimmer, J.; Lang, M.; Lannoy, B.; Leukel, R.; Lisin, V.; Matsuda, T.; McGeorge, J. C.; Meier, A.; Menze, D.; Meyer, W.; Michel, T.; Naumann, J.; Panzeri, A.; Pedroni, P.; Pinelli, T.; Preobrajenski, I.; Radtke, E.; Reichert, E.; Reicherz, G.; Rohlof, Ch.; Rosner, G.; Rostomyan, T.; Ryckbosch, D.; Sauer, M.; Schoch, B.; Schumacher, M.; Seitz, B.; Speckner, T.; Takabayashi, N.; Tamas, G.; Thomas, A.; van de Vyver, R.; Wakai, A.; Weihofen, W.; Wissmann, F.; Zapadtka, F.; Zeitler, G.; GDH Collaboration; A2 Collaboration

17

Photodegradation of clopyralid in TiO2 suspensions: identification of intermediates and reaction pathways.  

PubMed

The work is concerned with the kinetics, identification of intermediates and reaction pathways of the photocatalytic degradation of the herbicide clopyralid (3,6-dichloropyridine-2-carboxylic acid) in UV illuminated aqueous suspensions of TiO(2) (Degussa P25). In the investigated concentration range (0.5-3.0 mM) the photocatalytic degradation kinetics of clopyralid in the first stage of the reaction follows approximately a pseudo-first kinetic order. The highest reaction rate was observed at 4 mg mL(-1)of catalyst concentration, the apparent activation energy of the reaction being 7.74 kJ mol(-1). The effect of the presence of hydrogen peroxide, potassium bromate, and ammonium persulfate, acting as electron acceptors along with molecular oxygen, were also studied. By studying the effect of ethanol as a hydroxyl radical scavenger it was shown that the heterogeneous catalysis takes place mainly via hydroxyl radicals. The reaction intermediates (3,6-dichloropyridin-2-ol, 3,6-dichloro hydroxypyridine-2-carboxylic acid, and 3,3',6,6'-tetrachloro-2,4'-bipyridine-2'-carboxylic acid) were identified and the kinetics of their appearance/disappearance was followed by LC-MS/MS (ESI+). Tentative photodegradation pathways were proposed and discussed. PMID:19264403

Soji?, Daniela V; Anderluh, Vesna B; Orci?, Dejan Z; Abramovi?, Biljana F

2009-08-30

18

Separation of chemical reaction intermediates by metal-organic frameworks.  

PubMed

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. PMID:21626684

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

2011-08-22

19

Capturing fleeting intermediates in a catalytic C-H amination reaction cycle  

PubMed Central

We have applied an ambient ionization technique, desorption electrospray ionization MS, to identify transient reactive species of an archetypal C–H amination reaction catalyzed by a dirhodium tetracarboxylate complex. Using this analytical method, we have detected previously proposed short-lived reaction intermediates, including two nitrenoid complexes that differ in oxidation state. Our findings suggest that an Rh-nitrene oxidant can react with hydrocarbon substrates through a hydrogen atom abstraction pathway and raise the intriguing possibility that two catalytic C–H amination pathways may be operative in a typical bulk solution reaction. As highlighted by these results, desorption electrospray ionization MS should have broad applicability for the mechanistic study of catalytic processes.

Perry, Richard H.; Cahill, Thomas J.; Roizen, Jennifer L.; Du Bois, Justin; Zare, Richard N.

2012-01-01

20

Functional intermediates in reaction of cytochrome oxidase with oxygen.  

PubMed Central

The development of a low temperature kinetic method for the flash photolysis of the compounds of membrane-bound cytochrome a3 with carbon monoxide in the presence of oxygen affords evidence for three categories of functional intermediate compounds of cytochrome a3 and oxygen. The three classes are identified as follows: Compounds of Type A are considered to be "oxy" compounds of the ferrous heme. They have the composition a3-2+. O2. Compounds of Type B are considered to be peroxide compounds (CU-2+A3-3+ O-2= or CU-2+A3-3+ O2H2) or the equivalent heme Fe-Cu peroxide bridge structures. Compounds of Type C are formed from the ferricyanide pretreated oxidase and may involve higher oxidation states of the heme iron such as quadrivalent iron, and peroxide. Kinetic and equilibrium studies show these compounds to be functional in oxygen reduction in the sequence A yields B yield cytochromes a, c, c1, etc.

Chance, B; Saronio, C; Leigh, J S

1975-01-01

21

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

SciTech Connect

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.

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

22

The lability of an intermediate of the ribulose bisphosphate carboxylase reaction.  

PubMed

Interruption of the catalytic cycle of ribulose-bisphosphate carboxylase by acid denaturation liberated an intermediate with a labile phosphate ester. Addition of fresh, buffered carboxylase enzyme to the acidified carboxylase reaction after 5 s inhibited phosphate release from the intermediate. Therefore, the species with a labile phosphate ester was stable for 5 s in acid and was apparently a substrate for the enzymatic reaction, since the labile intermediate was converted to a stable form by the protein. After acid denaturation, the carboxylated intermediate could be stabilized by reduction after 5 s in acid, but after 1 h no carboxylated intermediate remained. The stoichiometries of phosphate released to enzyme active sites and the carboxylated intermediate trapped to enzyme active sites were approximately 0.04. It was concluded that the labile phosphate species is probably the carboxylated intermediate rather than the enediol(ate) intermediate. The carboxylase and oxygenase reactions were probed for intermediates by the ability of the enzymatic reaction to reduce hexacyanoferrate(III), dichlorophenolindophenol, or nitroblue tetrazolium. Reduction of these reagents and hexacyanoferrate(III)-dependent paracatalytic inactivation were not observed. The copper chelate of lysine, a superoxide dismutase active species, did not selectively inhibit ribulose-bisphosphate oxygenase. PMID:6625602

Mulligan, R M; Tolbert, N E

1983-09-01

23

Metamorphic dehydration reactions control the location of intermediate-depth seismicity  

NASA Astrophysics Data System (ADS)

The cause of intermediate-depth seismicity in subduction zones is not well understood. The viability of proposed mechanisms, that include dehydration embrittlement, shear instablities, and the presence of fluids in general, depends significantly on local conditions, including pressure, temperature, and composition. A number of high resolution seismic studies have improved the location of earthquakes within the slab in Japan, Alaska and Cascadia. Intriguingly, the warm subduction zones of Nankai and Cascadia show that intermediate depth seismicity is located below the oceanic crust. In contrast, the colder subduction zones Alaska, Tohoku and Hokkaido have the upper plane of seismicity confined to the subducting crust, with a systematic deepening of the seismic belt with respect to the top of the slab with depth. We use high resolution thermal-petrological models to determine the metamorphic facies in the downgoing slab and to identify the main phase changes that cause dehydration. In Alaska and Northern Japan, the seismicity occurs at, or at shallower depths than, the blueschist-out boundary. In Nankai and Cascadia the seismicity disappears above the antigorite-out boundary. Seismicity in the lower plane of the double seismic zone in Northern Japan also occurs at pressures and temperatures below the antigorite-out boundary. These observations strongly suggest that intermediate-depth seismicity is limited by the first major dehydration reaction in the crust and mantle and that fluids liberated by this phase change are primarily responsible for causing the earthquakes.

van Keken, Peter E.; Kita, Saeko; Nakajima, Junichi; Abers, Geoff; Hacker, Brad

2013-04-01

24

Study of Projectile Fragmentation Reactions at Intermediate Energies  

Microsoft Academic Search

The experimental measurements of the present work represent a first attempt towards obtaining systematic data of projectile fragment distributions near 0 degrees produced by intermediate-energy beams delivered by the K1200 cyclotron at the NSCL. The measurements were performed with two different devices operated as 0-degree spectrometers: the K1200 interim beamline and the A1200 mass separator. Momentum distributions and limited angular

George A. Souliotis

1992-01-01

25

CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION  

EPA Science Inventory

Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

26

Intermediate Energy Nucleon-Nucleus Total Reaction Cross Section in the Dirac Phenomenology.  

National Technical Information Service (NTIS)

The total reaction cross section for intermediate energy nucleon-nucleus scattering systems is calculated within the Dirac-eikonal formalism. Comparison with data indicates that the recently proposed impulse-approximation Dirac optical potential for nucle...

B. V. Carlson M. P. Isidro Filho M. S. Hussein

1984-01-01

27

Role of compound nuclei in intermediate-energy heavy-ion reactions  

SciTech Connect

Hot compound nuclei are frequently produced in intermediate-energy reactions through a variety of processes. Their decay is shown to be an important and at times dominant source of complex fragments, high energy-gamma rays, and even pions.

Moretto, L.G.; Wozniak, G.J.

1988-05-01

28

Two-neutron interferometry in low- and intermediate-energy heavy-ion reactions  

SciTech Connect

Two-nucleon interferometry can be used in low- and intermediate-energy heavy ion reactions to probe the space-time evolution of hot and possibly compressed nuclear systems. At low energy, angle-gated correlation functions have allowed to succesfully extract the lifetime of moderately excited compound nuclei. At intermediate energy, two-neutron interferometry has been used to obtain information on the contribution of different mechanisms to the reaction dynamics.

Tagliente, G.; Colonna, N. [INFN and Dip. Fisica, V. Amendola 173, 70126 Bari (Italy); Ghetti, R. [Department of Physics, Lund Univ., Box 118, SE-221 00 Lund (Sweden); De Filippo, E. [INFN and Dip. Fisica, C.so Italia 57, 95129 Catania (Italy)

1999-11-16

29

Reaction of Stabilized Criegee Intermediates from Ozonolysis of Limonene with Water: Ab Initio and DFT Study  

PubMed Central

The mechanism of the chemical reaction of H2O with three stabilized Criegee intermediates (stabCI-OO, stabCI-CH3-OO and stabCIx-OO) produced via the limonene ozonolysis reaction has been investigated using ab initio and DFT (Density Functional Theory) methods. It has been shown that the formation of the hydrogen-bonded complexes is followed by two different reaction pathways, leading to the formation of either OH radicals via water-catalyzed H migration or of ?-hydroxy hydroperoxide. Both pathways were found to be essential sources of atmospheric OH radical and H2O2 making a significant contribution to the formation of secondary aerosols in the Earth’s atmosphere. The activation energies at the CCSD(T)/6-31G(d) + CF level of theory were found to be in the range of 14.70–21.98 kcal mol?1. The formation of ?-hydroxy hydroperoxide for the reaction of stabCIx-OO and H2O with the activation energy of 14.70 kcal mol?1 is identified as the most favorable pathway.

Jiang, Lei; Lan, Ru; Xu, Yi-Sheng; Zhang, Wen-Jie; Yang, Wen

2013-01-01

30

The platinum hydrido-methyl complex: A frozen reaction intermediate?  

SciTech Connect

Methane activation by transition metals has been a topic of growing interest during the past decade, due to economic interest in methane conversion and chemistry. Reactions of platinum-argon complexes Pt{sup +}Ar{sub m}, m = 1--6, with methane (CH{sub 4}) and methane-d{sub 4} (CD{sub 4}) were investigated by means of FT-ICR mass spectrometry and DFT calculations. Ligand exchange reactions are observed for Pt{sup +}Ar{sub m}, m = 2--6, in which up to four argon ligands are replaced by methane. In contrast, the bare platinum ion and platinum solvated with one argon ligand lead to the formation of a platinum-carbene complex. Gibbs free enthalpies from ligand exchange reactions of Pt{sup +}CH{sub 4} with CD{sub 4} and H{sub 2}O provide evidence for the inserted hydrido-methyl complex HPt{sup +}CH{sub 4} with CD{sub 4} (and the reverse reaction). This is attributed to the inability of the platinum cation to form more than three covalent bonds.

Achatz, U.; Beyer, M.; Joos, S.; Fox, B.S.; Niedner-Schatteburg, G.; Bondybey, V.E.

1999-10-14

31

Temperature-Scan Cryocrystallography Reveals Reaction Intermediates in Bacteriophytochrome  

PubMed Central

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 bacteria1. 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 responses2. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states3-7. 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 employed cryo-trapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeds. Light-induced conformational changes in PaBphP originate in ring D of the bilin chromophore, and E to Z isomerization about the C15=C16 double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C15 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 suggest 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.

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

2012-01-01

32

Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome  

SciTech Connect

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.

Yang, Xiaojing; Ren, Zhong; Kuk, Jane; Moffat, Keith (UC)

2012-03-27

33

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

SciTech Connect

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)

Hoffman, M.Z.

1992-07-31

34

Computational study on the carboligation reaction of acetohidroxyacid synthase: new approach on the role of the HEThDP- intermediate.  

PubMed

Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate dependent enzyme that catalyses the decarboxylation of pyruvate to yield the hydroxyethyl-thiamin diphosphate (ThDP) anion/enamine intermediate (HEThDP(-)). This intermediate reacts with a second ketoacid to form acetolactate or acetohydroxybutyrate as products. Whereas the mechanism involved in the formation of HEThDP(-) from pyruvate is well understood, the role of the enzyme in controlling the carboligation reaction of HEThDP(-) has not been determined yet. In this work, molecular dynamics (MD) simulations were employed to identify the aminoacids involved in the carboligation stage. These MD studies were carried out over the catalytic subunit of yeast AHAS containing the reaction intermediate (HEThDP(-)) and a second pyruvate molecule. Our results suggest that additional acid-base ionizable groups are not required to promote the catalytic cycle, in contrast with earlier proposals. This finding leads us to postulate that the formation of acetolactate relies on the acid-base properties of the HEThDP(-) intermediate itself. PM3 semiempirical calculations were employed to obtain the energy profile of the proposed mechanism on a reduced model of the active site. These calculations confirm the role of HEThDP(-) intermediate as the ionizable group that promotes the carboligation and product formation steps of the catalytic cycle. PMID:20225259

Jaña, Gonzalo; Jiménez, Verónica; Villà-Freixa, Jordi; Prat-Resina, Xavier; Delgado, Eduardo; Alderete, Joel

2010-05-15

35

The isolation and characterization of a rhodacycle intermediate implicated in metal-catalyzed reactions of alkylidenecyclopropanes.  

PubMed

The isolation and characterization of a rhodacycle intermediate implicated in rhodium-catalyzed reactions of alkylidenecyclopropanes (ACPs) is described. The structure of the metallacycle was unambiguously determined by X-ray crystallography and is catalytically competent in the rhodium-catalyzed carbocyclization and ene-cycloisomerization reactions of ACPs. This work represents a rare example of the isolation of a metallacycle in a metal-catalyzed higher-order carbocyclization reaction and thereby provides important insight into the ligand requirements for the insertion of ?-components. Furthermore, it serves as a convenient synthon for the development of challenging higher-order carbocyclization reactions, as exemplified by the reaction with an activated allene. PMID:24616050

Inglesby, Phillip A; Bacsa, John; Negru, Daniela E; Evans, P Andrew

2014-04-01

36

Exome sequencing identifies CTSK mutations in patients originally diagnosed as intermediate osteopetrosis.  

PubMed

Autosomal Recessive Osteopetrosis is a genetic disorder characterized by increased bone density due to lack of resorption by the osteoclasts. Genetic studies have widely unraveled the molecular basis of the most severe forms, while cases of intermediate severity are more difficult to characterize, probably because of a large heterogeneity. Here, we describe the use of exome sequencing in the molecular diagnosis of 2 siblings initially thought to be affected by "intermediate osteopetrosis", which identified a homozygous mutation in the CTSK gene. Prompted by this finding, we tested by Sanger sequencing 25 additional patients addressed to us for recessive osteopetrosis and found CTSK mutations in 4 of them. In retrospect, their clinical and radiographic features were found to be compatible with, but not typical for, Pycnodysostosis. We sought to identify modifier genes that might have played a role in the clinical manifestation of the disease in these patients, but our results were not informative. In conclusion, we underline the difficulties of differential diagnosis in some patients whose clinical appearance does not fit the classical malignant or benign picture and recommend that CTSK gene be included in the molecular diagnosis of high bone density conditions. PMID:24269275

Pangrazio, Alessandra; Puddu, Alessandro; Oppo, Manuela; Valentini, Maria; Zammataro, Luca; Vellodi, Ashok; Gener, Blanca; Llano-Rivas, Isabel; Raza, Jamal; Atta, Irum; Vezzoni, Paolo; Superti-Furga, Andrea; Villa, Anna; Sobacchi, Cristina

2014-02-01

37

Exome sequencing identifies CTSK mutations in patients originally diagnosed as intermediate osteopetrosis?  

PubMed Central

Autosomal Recessive Osteopetrosis is a genetic disorder characterized by increased bone density due to lack of resorption by the osteoclasts. Genetic studies have widely unraveled the molecular basis of the most severe forms, while cases of intermediate severity are more difficult to characterize, probably because of a large heterogeneity. Here, we describe the use of exome sequencing in the molecular diagnosis of 2 siblings initially thought to be affected by “intermediate osteopetrosis”, which identified a homozygous mutation in the CTSK gene. Prompted by this finding, we tested by Sanger sequencing 25 additional patients addressed to us for recessive osteopetrosis and found CTSK mutations in 4 of them. In retrospect, their clinical and radiographic features were found to be compatible with, but not typical for, Pycnodysostosis. We sought to identify modifier genes that might have played a role in the clinical manifestation of the disease in these patients, but our results were not informative. In conclusion, we underline the difficulties of differential diagnosis in some patients whose clinical appearance does not fit the classical malignant or benign picture and recommend that CTSK gene be included in the molecular diagnosis of high bone density conditions.

Pangrazio, Alessandra; Puddu, Alessandro; Oppo, Manuela; Valentini, Maria; Zammataro, Luca; Vellodi, Ashok; Gener, Blanca; Llano-Rivas, Isabel; Raza, Jamal; Atta, Irum; Vezzoni, Paolo; Superti-Furga, Andrea; Villa, Anna; Sobacchi, Cristina

2014-01-01

38

Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase  

PubMed Central

Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8–2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3–C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg70 assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg70 stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate.

Coincon, Mathieu; Wang, Weijun; Sygusch, Jurgen; Seah, Stephen Y. K.

2012-01-01

39

Nucleon radiative capture and the inverse reaction at intermediate energies  

SciTech Connect

The processes which can lead to the radiative capture of fast nucleons include direct transitions in the nuclear potential, transitions in which coherent multipole resonances are excited, transitions by nucleons which are excited in early intranuclear collisions, bremsstrahlung from nucleon-nucleon collisions and photon evaporation'' from a thermally equilibrated nucleus. Corresponding processes occur when an energetic photon ejects fast nucleons from a nucleus. As experimental information from capture and photoreactions has become more detailed, inconsistencies and uncertainties have appeared which reflect difficulties in identifying and separating the responsible processes. This has led to more sophisticated and more complicated theoretical treatments which in turn have promoted new and more demanding experiments. 38 refs. 10 figs.

Halpern, I.

1991-01-01

40

Organotrichlorogermane synthesis by the reaction of elemental germanium, tetrachlorogermane and organic chloride via dichlorogermylene intermediate.  

PubMed

Organotrichlorogermanes were synthesized by the reaction of elemental germanium, tetrachlorogermane and organic chlorides, methyl, propyl, isopropyl and allyl chlorides. Dichlorogermylene formed by the reaction of elemental germanium with tetrachlorogermane was the reaction intermediate, which was inserted into the carbon-chlorine bond of the organic chloride to give organotrichlorogermane. When isopropyl or allyl chloride was used as an organic chloride, organotrichlorogermane was formed also in the absence of tetrachlorogermane. These chlorides were converted to hydrogen chloride, which subsequently reacted with elemental germanium to give the dichlorogermylene intermediate. The reaction of elemental germanium, tetrachlorogermane and organic chlorides provides a simple and easy method for synthesizing organotrichlorogermanes, and all the raw materials are easily available. PMID:15278133

Okamoto, Masaki; Asano, Takuya; Suzuki, Eiichi

2004-08-01

41

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

SciTech Connect

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.

Kohler, Mark C. [Bucknell University; Grimes, Thomas V. [University of North Texas; Wang, Xiaoping [ORNL; Cundari, Thomas R. [University of North Texas; Stockland, Robert A. Jr. [Bucknell University

2009-01-01

42

Structure of hemiaminal intermediate of the reaction of diethylamine with cyclobutanone  

NASA Astrophysics Data System (ADS)

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.

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

2010-12-01

43

Spectral detection of an intermediate preceding the excited state in the bacterial luciferase reaction.  

PubMed

The bioluminescent reaction of luciferase isolated from Vibrio harveyi, strain M17, was initiated by mixing the luciferase-bound flavin 4a-hydroperoxide intermediate, purified in advance, with a long-chain aldehyde (dodecanal or octanal) at -4 degree C. Measurements of absorbance changes from 300 to 600 nm during the course of the reaction revealed the existence of three sets of isosbestic points and three kinetic phases, the second of which parallels kinetically the decay of bioluminescence, measured concurrently. The absorbance changes in this second step and the decay of light emission exhibited similar deuterium isotope effects; this is postulated to be the step giving rise to the excited state and the enzyme-bound flavin 4a-hydroxide. The first step of the reaction, however, did not show an isotope effect; the intermediate thereby formed, observed here for the first time, is postulated to correspond to the luciferase-bound flavin 4a-peroxyhemiacetal. PMID:8260504

Macheroux, P; Ghisla, S; Hastings, J W

1993-12-28

44

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

SciTech Connect

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.

Hoffman, M.Z.

1991-12-31

45

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

PubMed

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 ?-aryl and ?-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 ?-arylation or nucleophilic addition reactions to different carbonyl groups. We could tune the properties of the ?-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 the metal center with the carbonyl group. Second, the additive phenol exchanges the iodide ligand to give an arylpalladium(II) phenoxide complex, which has a beneficial effect on the arylation. The formation of this transient intermediate not only stabilizes the arylpalladium moiety, thus preventing the nucleophilic attack at the carbonyl group, but also assists the enolization reaction, which takes place in a more favorable intramolecular manner. The azapalladacycle intermediate is, in the words of J. R. R. Tolkien, "the one ring to bring them all and in the darkness to bind them." With this intermediate, we can easily achieve the synthesis of a variety of heterocyclic systems by selectively promoting electrophilic ?-arylation or nucleophilic addition reactions from the same precursors. PMID:23957464

Solé, Daniel; Fernández, Israel

2014-01-21

46

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

NASA Technical Reports Server (NTRS)

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.

Jackels, C. F.

1985-01-01

47

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

NASA Technical Reports Server (NTRS)

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.

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

1986-01-01

48

Methanol synthesis on ZnO(0001). II. Structure, energetics, and vibrational signature of reaction intermediates  

NASA Astrophysics Data System (ADS)

A rigorous characterization of a wealth of molecular species adsorbed at oxygen defects on ZnO(0001) is given. These defects represent the putative active sites in methanol synthesis from CO and H2. The oxidation state of the ZnO catalyst and thus the preferred charge state and the reactivity of the oxygen vacancies depend on the gas phase temperature and pressure conditions. Considering charge states of oxygen vacancies relevant at the reducing conditions of the industrial process, i.e., F++/H2, F0, F0/H2, and F--, as well as the F++ center which is abundant at UHV conditions and therefore important to allow for comparison with surface science experiments, we have investigated the structure, energetics, and vibrational frequencies of an exhaustive catalog of reaction intermediates using electronic structure calculations. After having identified the characteristic adsorption modes of CO, formate, formic acid, hydroxymethylene, formyl, formaldehyde, dioxomethylene, hydroxymethyl, hydroxymethoxide, methoxide, as well as methanol itself, the thermodynamic stability of all species with respect to the charge state of the oxygen vacancy and their electronic stabilization is discussed in detail and summarized in an energy level diagram.

Kiss, Janos; Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2013-07-01

49

The Identification of Stable Reaction Intermediates on Aluminum Oxide Surfaces with Inelastic Electron Tunneling Spectroscopy  

NASA Astrophysics Data System (ADS)

The stable surface intermediates that were formed in several heterogeneous reactions on aluminum oxide films were identified with inelastic electron tunneling spectroscopy. The alumina films were synthesized by the plasma oxidation of aluminum metal films. The temperature and exposure dependent interaction of cyclopropane carboxylic acid with alumina films was studied. Cyclopropane carboxylate and n-butane carboxylate were the only adsorbed species formed. The n-butane carboxylate results from hydrogenolysis of the cyclopropyl ring of the adsorbed cyclopropane carboxylate with hydrogen supplied by surface hydroxyl groups. The relative populations of the two surface species are strongly dependent upon coverage and temperature. The adsorption of gaseous dimethyl methyl phosphonate (DMMP) on alumina films was investigated. Surface temperatures ranged between 200 K and 673 K, and exposures ranged between 3 x 10('-4) and 10 Torr-s. Tunneling spectra of deuterium labeled DMMP, perdeutero methyl alcohol, methyl methyl phosphonic acid, methyl phosphonic acid and trimethyl phosphine oxide, all adsorbed on aluminum oxide surfaces, were used to clarify the structures of the species resulting from the adsorption and decomposition of DMMP. At 200 K, DMMP is adsorbed molecularly with high surface coverages. At surface temperatures above 295 K, DMMP is adsorbed dissociatively in low coverages. Surface temperatures above 473 K lead to the dealkylation of the dissociatively adsorbed adspecies, which results in the formation of adsorbed methyl phosphonate. The adsorption and reaction of three phosphonate esters on alumina films was comparatively examined. The phosphonate esters were diisopropyl methyl phosphonate (DIMP), dimethyl methyl phosphonate (DMMP) and diphenyl methyl phosphonate (DPMP). The adsorption temperatures ranged from 200 to 673 K. At 373 K, DIMP was found to adsorb dissociatively in low coverages as isopropyl methyl phosphonate. Above 373 K the isopropyl methyl phosphonate decomposed to the metastable hydroxy methyl phosphonate, which, in turn, decomposed completely to the methyl phosphonate above 573 K. Adsorbed DMMP decomposed similarly through the hydroxy methyl phosphonate to form the methyl phosphonate. However, in this case the hydroxy methyl phosphonate was a short -lived intermediate. DPMP was found to adsorb dissociatively at 295 K, and the adsorbed species formed is stable through 673 K. Consistent with these observations, mechanisms for the adsorption and decomposition of phosphonate esters on aluminum oxide are proposed that involve P-O bond cleavage upon adsorption but O-C bond cleavage upon decomposition of the adspecies.

Templeton, Michael Karpovich

50

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

PubMed

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

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

2013-05-01

51

Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase.  

PubMed

Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. It has recently been shown that FDTS catalysis does not rely on an enzymatic nucleophile and that the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and it has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist efforts directed toward the rational design of inhibitors as leads for future antibiotics. PMID:22295882

Mishanina, Tatiana V; Koehn, Eric M; Conrad, John A; Palfey, Bruce A; Lesley, Scott A; Kohen, Amnon

2012-03-01

52

Trapping of an intermediate in the reaction catalyzed by flavin-dependent thymidylate synthase (FDTS)  

PubMed Central

Thymidylate is a DNA nucleotide that is essential to all organisms and is synthesized by the enzyme thymidylate synthase (TSase). Several human pathogens rely on an alternative flavin-dependent thymidylate synthase (FDTS), which differs from the human TSase both in structure and molecular mechanism. Recently it has been shown that FDTS catalysis does not rely on an enzymatic nucleophile and the proposed reaction intermediates are not covalently bound to the enzyme during catalysis, an important distinction from the human TSase. Here we report the chemical trapping, isolation, and identification of a derivative of such an intermediate in the FDTS-catalyzed reaction. The chemically modified reaction intermediate is consistent with currently proposed FDTS mechanisms that do not involve an enzymatic nucleophile, and has never been observed during any other TSase reaction. These findings establish the timing of the methylene transfer during FDTS catalysis. The presented methodology provides an important experimental tool for further studies of FDTS, which may assist the efforts to rationally design inhibitors as leads for future antibiotics.

Mishanina, Tatiana V.; Koehn, Eric M.; Conrad, John A.; Palfey, Bruce A.; Lesley, Scott A.

2012-01-01

53

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

SciTech Connect

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.

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

2012-02-27

54

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)...

55

A new approach to 'megaprimer' polymerase chain reaction mutagenesis without an intermediate gel purification step  

Microsoft Academic Search

BACKGROUND: Site-directed mutagenesis is an efficient method to alter the structure and function of genes. Here we report a rapid and efficient megaprimer-based polymerase chain reaction (PCR) mutagenesis strategy that by-passes any intermediate purification of DNA between two rounds of PCR. RESULTS: The strategy relies on the use of a limiting concentration of one of the flanking primers (reverse or

Rajiv Tyagi; Richard Lai; Ronald G Duggleby

2004-01-01

56

Reactions of the peroxo intermediate of soluble methane monooxygenase hydroxylase with ethers.  

PubMed

Soluble methane monooxygenase (sMMO) isolated from Methylococcus capsulatus (Bath) utilizes a carboxylate-bridged diiron center and dioxygen to catalyze the conversion of methane to methanol. Previous studies revealed that a di(mu-oxo)diiron(IV) intermediate termed Q is responsible for the catalytic activity with hydrocarbons. In addition, the peroxodiiron(III) intermediate (H(peroxo)) that precedes Q formation in the catalytic cycle has been demonstrated to react with propylene, but its reactivity has not been extensively investigated. Given the burgeoning interest in the existence of multiple oxidants in metalloenzymes, a more exhaustive study of the reactivity of H(peroxo) was undertaken. The kinetics of single turnover reactions of the two intermediates with ethyl vinyl ether and diethyl ether were monitored by single- and double-mixing stopped-flow optical spectroscopy. For both substrates, the rate constants for reaction with H(peroxo) are greater than those for Q. An analytical model for explaining the transient kinetics is described and used successfully to fit the observed data. Activation parameters were determined through temperature-dependent studies, and the kinetic isotope effects for the reactions with diethyl ether were measured. The rate constants indicate that H(peroxo) is a more electrophilic oxidant than Q. We propose that H(peroxo) reacts via two-electron transfer mechanisms, and that Q reacts by single-electron transfer steps. PMID:15898785

Beauvais, Laurance G; Lippard, Stephen J

2005-05-25

57

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

SciTech Connect

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.

Plante, Ianik, E-mail: ianik.plante-1@nasa.gov [Division of Space Life Sciences, Universities Space Research Association, 3600 Bay Area Boulevard, Houston, TX 77058 (United States)] [Division of Space Life Sciences, Universities Space Research Association, 3600 Bay Area Boulevard, Houston, TX 77058 (United States); Devroye, Luc, E-mail: lucdevroye@gmail.com [School of Computer Science, McGill University, 3480 University Street, Montreal, Canada H3A 0E9 (Canada)] [School of Computer Science, McGill University, 3480 University Street, Montreal, Canada H3A 0E9 (Canada); Cucinotta, Francis A., E-mail: Francis.A.Cucinotta@nasa.gov [NASA Johnson Space Center, Bldg 37, Mail Code SK, 2101 NASA Parkway, Houston, TX 77058 (United States)

2013-06-01

58

Netrin Signaling Breaks the Equivalence between Two Identified Zebrafish Motoneurons Revealing a New Role of Intermediate Targets  

PubMed Central

Background We previously showed that equivalence between two identified zebrafish motoneurons is broken by interactions with identified muscle fibers that act as an intermediate target for the axons of these motoneurons. Here we investigate the molecular basis of the signaling interaction between the intermediate target and the motoneurons. Principal Findings We provide evidence that Netrin 1a is an intermediate target-derived signal that causes two equivalent motoneurons to adopt distinct fates. We show that although these two motoneurons express the same Netrin receptors, their axons respond differently to Netrin 1a encountered at the intermediate target. Furthermore, we demonstrate that when Netrin 1a is knocked down, more distal intermediate targets that express other Netrins can also function to break equivalence between these motoneurons. Significance Our results suggest a new role for intermediate targets in breaking neuronal equivalence. The data we present reveal that signals encountered during axon pathfinding can cause equivalent neurons to adopt distinct fates. Such signals may be key in diversifying a neuronal population and leading to correct circuit formation.

Hale, Laura A.; Fowler, Daniel K.; Eisen, Judith S.

2011-01-01

59

Intermediate velocity source of intermediate-mass fragments in the 40Ca+40Ca reaction at Elab=35 MeV\\/nucleon  

Microsoft Academic Search

Events with 3-5 intermediate mass fragments [(IMF's), Z>2] have been studied for peripheral and more central collisions in the 40Ca+40Ca reaction at Elab=35 MeV\\/nucleon. For a significant portion of events, in coincidence with projectilelike and with targetlike fragments, we observe IMF's, with velocities close to zero in the center-of-mass reference frame. Properties of this ``intermediate velocity'' source suggest a stochastic

P. Pawlowski; J. Brzychczyk; A. J. Cole; P. Désesquelles; W. Gawlikowicz; K. Grotowski; P. Hachaj; S. Micek; R. Planeta; Z. Sosin; A. Wieloch; D. Benchekroun; E. Bisquer; A. Chabane; A. Demeyer; M. Charvet; B. Cheynis; E. Gerlic; A. Giorni; D. Guinet; D. Heuer; P. Lautesse; L. Lebreton; A. Lléres; M. Stern; L. Vagneron; J. B. Viano

1998-01-01

60

Folylpolyglutamate synthetase: direct evidence for an acyl phosphate intermediate in the enzyme-catalyzed reaction  

SciTech Connect

The nature of the intermediate in the reaction catalyzed by folylpoly-..gamma..-glutamate synthetase (FPGS) has been investigated. Incubation of ..cap alpha..,..gamma..-(/sup 18/O)methotrexate with ATP, glutamate, and FPGS resulted in the formation of (/sup 18/O)phosphate, thus providing strong evidence for the formation of a ..gamma..-glutamyl phosphate during catalysis. The inorganic phosphate formed in the enzyme-catalyzed reaction was separated from other products and substrates by chromatography on DEAE-cellulose, then converted to the trimethyl ester, and analyzed by mass spectroscopy. Stoichiometric formation of (/sup 18/O)phosphate was observed in the case of the E. coli enzyme, isolated from a transformant containing the cloned FPGS-dihydrofolate synthetase (folC) gene. In addition, /sup 31/P-NMR analysis of the phosphate isolated from the reaction using E. coli FPGS showed the expected /sup 18/O-isotopic perturbations due to both singly bonded and doubly bonded P-/sup 18/O species. Similar experiments were carried out with FPGS isolated from hog liver. In this case, the small amounts of pure enzyme available precluded use of the NMR technique. However, mass spectral analysis of the derivatized phosphate product revealed the presence of (/sup 18/O)-trimethyl phosphate, thus indicating that the reaction catalyzed by the mammalian enzyme also proceeds via an acyl phosphate intermediate.

Banerjee, R.; McGuire, J.J.; Shane, B.; Coward, J.K.

1986-05-01

61

Exploiting Acyl and Enol Azolium Intermediates via NHeterocyclic Carbene Catalyzed Reactions of Alpha-Reducible Aldehydes  

PubMed Central

N-heterocyclic carbenes are well known for their role in catalyzing benzoin and Stetter reactions: the generation of acyl anion equivalents from simple aldehydes to react with a variety of electrophiles. However, when an aldehyde bearing a leaving group or unsaturation adjacent to the acyl anion equivalent is subjected to an NHC, a new avenue of reactivity is unlocked, leading to a number of novel transformations which can generate highly complex products from simple starting materials, many of which are assembled through unconventional bond disconnections. The field of these new reactions - those utilizing ?-reducible aldehydes to access previously unexplored catalytic intermediates – has expanded rapidly in the past eight years. This review aims to provide the reader with a historical perspective on the underlying discoveries that led to the current state of the art, a mechanistic description of these reactions, and a summary of the recent advances in this area.

Vora, Harit U.; Wheeler, Philip

2013-01-01

62

Progress in applyiong the FKK multistep reaction theory to intermediate-energy data evaluation  

SciTech Connect

Recent developments to the physics modeling in the FKK-GNASH code system are reviewed. We describe modifications to include a linking of multistep direct and multistep compound processes, which are important when the incident energy is less than about 30 MeV. A model for multiple preequilibrium emission is given, and compared with experimental measurements of proton reactions on {sup 90}Zr at 160 MeV. We also give some preliminary observations concerning FKK calculations which use both normal and non-normal DWBA matrix elements. We describe the application of the FKK-GNASH code to a range of nuclear data applications, including intermediate energy reactions of importance in the accelerator transmutation of waste, and fast neutron and proton cancer radiation treatment. We outline areas where further work is needed for the accurate modeling of nuclear reactions using the FKK theory.

Chadwick, M.B. [Lawrence Livermore National Lab., CA (United States); Young, P.G. [Los Alamos National Lab., NM (United States)

1994-07-01

63

Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb(3).  

PubMed

The proton-pumping cbb(3)-type cytochrome c oxidases catalyze cell respiration in many pathogenic bacteria. For reasons not yet understood, the apparent dioxygen (O(2)) affinity in these enzymes is very high relative to other members of the heme-copper oxidase (HCO) superfamily. Based on density functional theory (DFT) calculations on intermediates of the oxygen scission reaction in active-site models of cbb(3)- and aa(3)-type oxidases, we find that a transient peroxy intermediate (I(P), Fe[III]-OOH(-)) is ~6kcal/mol more stable in the former case, resulting in more efficient kinetic trapping of dioxygen and hence in a higher apparent oxygen affinity. The major molecular basis for this stabilization is a glutamate residue, polarizing the proximal histidine ligand of heme b(3) in the active site. PMID:21315685

Sharma, Vivek; Wikström, Mårten; Kaila, Ville R I

2011-07-01

64

Near-threshold absolute photoionization cross-sections of some reaction intermediates in combustion  

NASA Astrophysics Data System (ADS)

The use of photoionization mass spectrometry for the development of quantitative kinetic models for the complex combustion chemistry of both conventional hydrocarbon fuels and oxygenated biofuels requires near-threshold measurements of absolute photoionization cross-sections for numerous reaction intermediates. Near-threshold absolute cross-sections for molecular and dissociative photoionization for 20 stable reaction intermediates (methane, ethane, propane, n-butane, cyclopropane, methylcyclopentane, 1-butene, cis-2-butene, isobutene, 1-pentene, cyclohexene, 3,3-dimethyl-1-butene, 1,3-hexadiene, 1,3-cyclohexadiene, methyl acetate, ethyl acetate, tetrahydrofuran, propanal, 1-butyne, 2-butyne) are presented. Previously measured total photoionization cross-sections for 9 of these molecules are in good agreement with the present results. The measurements are performed with photoionization mass spectrometry (PIMS) using a monochromated VUV synchrotron light source with an energy resolution of 40 meV (fwhm) comparable to that used for flame-sampling molecular beam PIMS studies of flame chemistry and reaction kinetics.

Wang, Juan; Yang, Bin; Cool, Terrill A.; Hansen, Nils; Kasper, Tina

2008-02-01

65

Direct kinetic measurements of reactions between the simplest Criegee intermediate CH2OO and alkenes.  

PubMed

The simplest Criegee Intermediate (CH2OO), a well-known biradical formed in alkene ozonolysis, is known to add across double bonds. Here we report direct experimental rate measurements of the simplest Criegee Intermediate reacting with C2–C4 alkenes obtained using the laser flash photolysis technique probing the recently measured B(1)A? ? X(1)A? transition in CH2OO. The measured activation energy (298–494 K) for CH2OO + alkenes is Ea ? 3500 ± 1000 J mol(–1) for all alkyl substituted alkenes and Ea = 7000 ± 900 J mol(–1) for ethene. The measured Arrhenius pre-exponential factors (A) vary between (2 ± 1) × 10(–15) and (11 ± 3) × 10(–15) cm(3) molecule(–1) s(–1). Quantum chemical calculations of the corresponding rate coefficients reproduce qualitative reactivity trends but overestimate the absolute rate coefficients. Despite the small Ea's, the CH2OO + alkene rate coefficients are almost 2 orders of magnitude smaller than those of similar reactions between CH2OO and carbonyl compounds. Using the rate constants measured here, we estimate that, under typical atmospheric conditions, reaction with alkenes does not represent a significant sink of CH2OO. In environments rich in C?C double bonds, however, such as ozone-exposed rubber or emission plumes, these reactions can play a significant role. PMID:24559303

Buras, Zachary J; Elsamra, Rehab M I; Jalan, Amrit; Middaugh, Joshua E; Green, William H

2014-03-20

66

Intramolecular Schmidt Reaction of Acyl Chlorides with Alkyl Azides: Capture of N-Acyliminium Ion Intermediates with Aromatic rings.  

PubMed

Intramolecular Schmidt reaction of acyl chlorides with alkyl azides through N-acyliminium ion intermediates is designed and realized. The intramolecular capture of the intermediates with aromatic rings affords several nitrogen-containing tricyclic skeletons. The important feature of the domino process is the efficiency in bond reorganization and ring formation. PMID:24820453

Li, Xiao-Jing; Qiao, Jin-Bao; Sun, Jian; Li, Xue-Qiang; Gu, Peiming

2014-06-01

67

Synthesis, crystal structure and herbicidal activity of mimics of intermediates of the KARI reaction.  

PubMed

Two mimics of the intermediate in the reaction catalyzed by ketol-acid reductoisomerase (KARI) were synthesized. Their structures were established on the basis of elemental analyses, IR, 1H NMR and GC/mass detector. The crystal structure of compound 2 was found to be a substituted dioxane, formed by the condensation of two molecules. The two compounds showed some herbicidal activity on the basis of tests using rape root and barnyard grass growth inhibition. However, the herbicidal effect was weaker in greenhouse tests. PMID:15751008

Wang, Bao-Lei; Duggleby, Ronald G; Li, Zheng-Ming; Wang, Jian-Guo; Li, Yong-Hong; Wang, Su-Hua; Song, Hai-Bin

2005-04-01

68

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

NASA Astrophysics Data System (ADS)

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.

Zimányi, László; Khoroshyy, Petro; Mair, Thomas

2010-06-01

69

An ENDOR and HYSCORE investigation of a reaction intermediate in IspG (GcpE) catalysis.  

PubMed

IspG is a 4Fe-4S protein that carries out an essential reduction step in isoprenoid biosynthesis. Using electron-nuclear double resonance (ENDOR) and hyperfine sublevel correlation (HYSCORE) spectroscopies on labeled samples, we have specifically assigned the hyperfine interactions in a reaction intermediate. These results help clarify the nature of the reaction intermediate, supporting a direct interaction between the unique fourth Fe in the cluster and C2 and O3 of the ligand. PMID:21574560

Wang, Weixue; Wang, Ke; Li, Jikun; Nellutla, Saritha; Smirnova, Tatyana I; Oldfield, Eric

2011-06-01

70

An ENDOR and HYSCORE Investigation of a Reaction Intermediate in IspG (GcpE) Catalysis  

PubMed Central

IspG is a 4Fe-4S protein that carries out an essential reduction step in isoprenoid biosynthesis. Using electron-nuclear double resonance (ENDOR) and hyperfine sublevel correlation (HYSCORE) spectroscopies on labeled samples, we specifically assign the hyperfine interactions in a reaction intermediate. These results help clarify the nature of the reaction intermediate, supporting a direct interaction between the unique 4th Fe in the cluster and the C2 and O3 of the ligand.

Wang, Weixue; Wang, Ke; Li, Jikun; Nellutla, Saritha; Smirnova, Tatyana I.; Oldfield, Eric

2011-01-01

71

Picosecond detection of an intermediate in the photochemical reaction of bacterial photosynthesis.  

PubMed

Preparations of photosynthetic reaction centers from Rhodopseudomonas sphaeroides were excited with flashes lasting approximately 8 psec. Immediately after the excitation, there appeared a transient state which was characterized by new absorption bands near 500 and 680 nm, by a bleaching of bands near 540, 600, 760, and 870 nm, and by a blue shift of a band near 800 nm. The transient state decayed with an exponential decay time,t, of 246 plus or minus 16 psec after the flash. As the transient state decayed, the radical cation of the reaction center bacteriochlorophyll complex appeared. This indicates that the transient state is an intermediate in the photooxidation of the bacteriochlorophyll. The absorpiton spectrum of the transient state shows the state to be identical with a state (P-F) which has been detected previously in reaction centers that are prevented from completing the photooxidation, because of chemical reduction of the electron acceptor. Analysis of the spectrum suggests that the formation of P-F involves electron transfer from one bacteriochlorophyll molecule to another within the reaction center, or possibly from bacteriochlorophyll to the bacteriopheophytin of the complex. The initial absorbance changes after flash excitation also include a bleaching of an absorption band at 800 nm. The bleaching decays with tau approximately equal to 30 pse. The bleaching appers not to be a secondary effect, but rather to revael another early step in the primary photochemical reaction. PMID:1079602

Rockley, M G; Windsor, M W; Cogdell, R J; Parson, W W

1975-06-01

72

The Allyl Intermediate in Regioselective and Enantioselective Iridium-Catalyzed Asymmetric Allylic Substitution Reactions  

PubMed Central

The isolation and structural characterization of metallacyclic allyl (2a) and crotyl (2b) iridium complexes are reported. Complexes 2a and 2b are rare examples of iriduim allyl complexes that undergo nucleophilic attack at terminal position, rather than the central position, of the allyl unit. Structures of 2a and 2b were obtained by X-ray diffraction. Nucleophilic attack was observed at the carbon that is bound to iridium trans to phosphorus through a longer Ir-C bond. However, the effect of the trans phosphine ligand on the Ir-C bond lengths was smaller than the effect of the substituent on the allyl group in 2b. The competence of complexes 2a and 2b to be intermediates in the catalytic asymmetric allylic substitutions was evaluated by studying their reactivity towards stabilized carbon and heteroatom nucleophiles and comparing the rates and selectivities to those of the catalytic reactions. The stereoselectivity and regioselectivity of stoichiometric reactions of 2b were similar to those of reactions catalyzed by the previously reported iridium catalysts, supporting their intermediacy in the catalytic reactions. Based on the structural data, a model is proposed for the origin of stereoselectivity in iridium-catalyzed asymmetric allylic substitution reactions.

Madrahimov, Sherzod T.; Markovic, Dean; Hartwig., John F.

2010-01-01

73

Photonuclear reactions of actinide and pre-actinide nuclei at intermediate energies  

SciTech Connect

Photonuclear reaction is described with an approach based on the quasideuteron nuclear photoabsorption model followed by the process of competition between light particle evaporation and fission for the excited nucleus. Thus fission process is considered as a decay mode. The evaporation-fission process of the compound nucleus is simulated in a Monte Carlo framework. Photofission reaction cross sections are analysed in a systematic manner in the energy range {approx}50-70 MeV for the actinides {sup 232}Th, {sup 233}U, {sup 235}U, {sup 238}U, and {sup 237}Np and the pre-actinide nuclei {sup 208}Pb and {sup 209}Bi. The study reproduces satisfactorily well the available experimental data of photofission cross sections at energies {approx}50-70 MeV and the increasing trend of nuclear fissility with the fissility parameter Z{sup 2}/A for the actinides and pre-actinides at intermediate energies ({approx}20-140 MeV)

Mukhopadhyay, Tapan; Basu, D. N. [Variable Energy Cyclotron Centre, 1/AF Bidhan Nagar, Kolkata 700 064 (India)

2007-12-15

74

Hyperthermal O-atom exchange reaction O2 + CO2 through a CO4 intermediate.  

PubMed

O(2) and CO(2) do not react under ordinary conditions because of the thermodynamic stability of CO(2) and the large activation energy required for multiple double-bond cleavage. We present evidence for a gas-phase O-atom exchange reaction between neutral O(2) and CO(2) at elevated collision energies (approximately 160 kcal mol(-1)) from crossed-molecular-beam experiments. CCSD(T)/aug-cc-pVTZ calculations demonstrate that isotope exchange can occur on the ground triplet potential energy surface through a short-lived CO(4) intermediate that isomerizes via a symmetric CO(4) transition state containing a bridging oxygen atom. We propose a plausible adiabatic mechanism for this reaction supported by additional spin-density calculations. PMID:19743846

Yeung, Laurence Y; Okumura, Mitchio; Paci, Jeffrey T; Schatz, George C; Zhang, Jianming; Minton, Timothy K

2009-10-01

75

Study of the removal of dichlorvos and dimethoate in a titanium dioxide mediated photocatalytic process through the examination of intermediates and the reaction mechanism.  

PubMed

The photocatalytic oxidation of two selected organophosphorous insecticides (dichlorvos and dimethoate) has been investigated. The aim of the study was the identification of the intermediates that are formed during photocatalytic treatment. Intermediate products from the slurry system were identified by means of solid-phase extraction (SPE) coupled to gas chromatography-mass spectroscopy techniques (GC-MS). Nine possible by-products were identified for dimethoate and three for dichlorvos. A proposed degradation pathway for each insecticide is presented, involving mainly oxidation and dealkylation reactions. The results demonstrated that some of the transient intermediates formed (oxon derivatives, disulfide, chlorinated fragments), were more toxic compared to parent compounds whereas most of them are less toxic than the parent compounds. PMID:16647205

Evgenidou, E; Konstantinou, I; Fytianos, K; Albanis, T

2006-09-21

76

Investigating student understanding in intermediate mechanics: Identifying the need for a tutorial approach to instruction  

NASA Astrophysics Data System (ADS)

The conceptual understanding and reasoning skills of advanced undergraduates as they make the transition from a traditional sequence in introductory calculus-based physics to their first course in upper-level mechanics are probed. The results thus far are consistent with findings from other investigations in upper-division courses, which indicate that persistent difficulties with fundamental concepts can hinder meaningful learning of advanced topics. To address this problem, the tutorial approach developed at the University of Washington has been adapted and incorporated into the intermediate mechanics course at Grand Valley State University. This modification has produced promising results.

Ambrose, Bradley S.

2004-04-01

77

Characterization of endoperoxide and hydroperoxide intermediates in the reaction of pyridoxine with singlet oxygen.  

PubMed

The photosensitized oxidation of vitamin B6, pyridoxine, is investigated by product and kinetic analysis. Singlet oxygen quenching rates, measured by time-resolved laser flash generation of singlet oxygen followed by monitoring singlet oxygen phosphorescence decay, confirm previous observations that pyridoxine is a moderate quencher. The quenching rate for 3-methoxypyridine is 100 times slower than that for 3-hydroxypyridine, indicating the hydroxy moiety is required for efficient quenching. The chemical quenching rate constant, kr, was estimated by comparison with a known singlet oxygen reaction. Results indicate that the chemical quenching rate of pyridoxine dominates the total quenching. The major reaction product in methanol was isolated and characterized by NMR and MS. The data are consistent with a solvent adduct of the substituted 2,5-pyridinedione. At low temperature, two semistable intermediates were characterized by NMR. The data are consistent with a hydroperoxide and endoperoxide. These intermediates suggest initial attack of singlet oxygen para to the hydroxy group followed by either proton transfer to form the hydroperoxide or addition of the peroxide to the imine to form the endoperoxide. In the presence of protic solvents, the solvent adducts to the imine and elimination of water yield the observed 2,5-pyridinedione product. PMID:12371824

Ohta, Brian K; Foote, Christopher S

2002-10-16

78

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

SciTech Connect

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.

Tso, Kin

1996-05-01

79

Chemically activated formation of organic acids in reactions of the Criegee intermediate with aldehydes and ketones.  

PubMed

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 C=O 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 < CH3CHO < 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. PMID:23958859

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

2013-10-21

80

Two Lysine Residues in the Bacterial Luciferase Mobile Loop Stabilize Reaction Intermediates  

PubMed Central

Bacterial luciferase catalyzes the reaction of FMNH2, O2, and a long chain aliphatic aldehyde, yielding FMN, carboxylic acid, and blue-green light. The most conserved contiguous region of the primary sequence corresponds to a crystallographically disordered loop adjacent to the active center (Fisher, A. J., Raushel, F. M., Baldwin, T. O., and Rayment, I. (1995) Biochemistry 34, 6581–6586; Fisher, A. J., Thompson, T. B., Thoden, J. B., Baldwin, T. O., and Rayment, I. (1996) J. Biol. Chem. 271, 21956–21968). Deletion of the mobile loop does not alter the chemistry of the reaction but decreases the total quantum yield of bioluminescence by 2 orders of magnitude (Sparks, J. M., and Baldwin, T. O. (2001) Biochemistry 40, 15436–15443). In this study, we attempt to localize the loss of activity observed in the loop deletion mutant to individual residues in the mobile loop. Using alanine mutagenesis, the effects of substitution at 15 of the 29 mobile loop residues were examined. Nine of the point mutants had reduced activity in vivo. Two mutations, K283A and K286A, resulted in a loss in quantum yield comparable with that of the loop deletion mutant. The bioluminescence emission spectrum of both mutants was normal, and both yielded the carboxylic acid chemical product at the same efficiency as the wild-type enzyme. Substitution of Lys283 with alanine resulted in destabilization of intermediate II, whereas mutation of Lys286 had an increase in exposure of reaction intermediates to a dynamic quencher. Based on a model of the enzyme-reduced flavin complex, the two critical lysine residues are adjacent to the quininoidal edge of the isoalloxazine.

Campbell, Zachary T.; Baldwin, Thomas O.

2009-01-01

81

Evaluation of thermal rates for reactions with intermediate wells: Removal of bound state contributions to quantum flux correlation functions  

Microsoft Academic Search

We consider the calculation of rates of chemical reactions that have bound intermediate states (i.e., wells along the reaction path) using flux correlation function methods. When time-dependent wave packets are used to evaluate the propagator matrix elements, and the dividing surface is located at a point where bound states have nonzero probability density, the standard expression for the flux correlation

Mark Thachuk; Howard R. Mayne; George C. Schatz

1993-01-01

82

Experimental Determination of the Effective Nucleon-Nucleon Interaction for p-Nucleus Reactions at Intermediate Energies.  

National Technical Information Service (NTIS)

A complete measurement of the polarization transfer observables has been made for the first time in the (p,p') reaction at intermediate energies. Measurements are reported for the exp 12 C(p,p') exp 12 C reaction to the 1 exp + , T = 0(12.71 MeV) and 1 ex...

J. B. McClelland B. Aas A. Azizi

1982-01-01

83

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

PubMed

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 each of these product channels calculated at the CCSD(T)/aug-cc-pVQZ level of theory, although a clean determination of the barrier energy to H+acrolein is precluded by the substantial partitioning into rotational energy during the photolytic production of the nascent radicals. We compare the measured branching fraction to the H+acrolein product channel with a statistical prediction based on the calculated transition states. PMID:19044817

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

2008-08-28

84

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

SciTech Connect

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.

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; (Michigan); (Rutgers); (Brandeis)

2009-04-22

85

Reactions of the diiron(IV) intermediate Q in soluble methane monooxygenase with fluoromethanes  

SciTech Connect

Soluble methane monooxygenases utilize a carboxylate-bridged diiron center and dioxygen to convert methane to methanol. A diiron(IV) oxo intermediate Q is the active species for this process. Alternative substrates and theoretical studies can help elucidate the mechanism. Experimental results for reactions with derivatized methanes were previously modeled by a combination of quantum mechanical/molecular mechanical techniques and the model was extended to predict the relative reactivity of fluoromethane. We therefore studied reactions of Q with CF {sub n}H{sub 4-n} (n = 1-3) to test the prediction. The kinetics of single-turnover reactions of Q with these substrates were monitored by double-mixing stopped-flow optical spectroscopy. For fluoro- and difluoromethane, conversion to the alcohols occurred with second-order rate constants less than that of methane, the values being 28,700 (CH{sub 4}) > 25,000 (CFH{sub 3}) > 9300 (CF{sub 2}H{sub 2}) M{sup -1} s{sup -1}. KIE values for C-H versus C-D activation above the classical limit were observed, requiring modification of the theoretical predictions.

Beauvais, Laurance G. [Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Lippard, Stephen J. [Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)]. E-mail: lippard@mit.edu

2005-12-09

86

A Novel Intermediate in the Reaction of Seleno CYP119 with m-Chloroperbenzoic Acid†  

PubMed Central

Cytochrome P450 mediated monooxygenation generally proceeds via a reactive ferryl intermediate coupled to a ligand radical [Fe(IV)=O]+. referred to as Compound I (Cpd I). The proximal cysteine thiolate ligand is a critical determinant of the spectral and catalytic properties of P450 enzymes. To explore the effect of increased electron donation by the proximal ligand in the P450 catalytic cycle, we recently reported successful incorporation of SeCys into the active site of CYP119, a thermophilic cytochrome P450. Here we report relevant physical properties of SeCYP119 and a detailed analysis of the reaction of SeCYP119 with m-chloroperbenzoic acid. Our results indicate that the selenolate anion reduces rather than stabilizes Cpd I and also protects the heme from oxidative destruction, leading to the generation of a new stable species with an absorbance maximum at 406 nm. This stable intermediate can be returned to the normal ferric state by reducing agents and thiols, in agreement with oxidative modification of the selenolate ligand itself. Thus, in the seleno protein, the oxidative damage shifts from the heme to the proximal ligand, presumably because (a) increased electron donation more efficiently quenches reactive species such as Cpd I, and (b) the protection of the thiolate ligand provided by the protein active site structure is insufficient to shield the more oxidizable selenolate ligand.

Sivaramakrishnan, Santhosh; Ouellet, Hugues; Du, Jing; McLean, Kirsty J.; Medzihradszky, Katalin F.; Dawson, John H.; Munro, Andrew W.; Ortiz de Montellano, Paul R.

2011-01-01

87

A novel intermediate in the reaction of seleno CYP119 with m-chloroperbenzoic acid.  

PubMed

Cytochrome P450-mediated monooxygenation generally proceeds via a reactive ferryl intermediate coupled to a ligand radical [Fe(IV)?O]+• termed Compound I (Cpd I). The proximal cysteine thiolate ligand is a critical determinant of the spectral and catalytic properties of P450 enzymes. To explore the effect of an increased level of donation of electrons by the proximal ligand in the P450 catalytic cycle, we recently reported successful incorporation of SeCys into the active site of CYP119, a thermophilic cytochrome P450. Here we report relevant physical properties of SeCYP119 and a detailed analysis of the reaction of SeCYP119 with m-chloroperbenzoic acid. Our results indicate that the selenolate anion reduces rather than stabilizes Cpd I and also protects the heme from oxidative destruction, leading to the generation of a new stable species with an absorbance maximum at 406 nm. This stable intermediate can be returned to the normal ferric state by reducing agents and thiols, in agreement with oxidative modification of the selenolate ligand itself. Thus, in the seleno protein, the oxidative damage shifts from the heme to the proximal ligand, presumably because (a) an increased level of donation of electrons more efficiently quenches reactive species such as Cpd I and (b) the protection of the thiolate ligand provided by the protein active site structure is insufficient to shield the more oxidizable selenolate ligand. PMID:21381758

Sivaramakrishnan, Santhosh; Ouellet, Hugues; Du, Jing; McLean, Kirsty J; Medzihradszky, Katalin F; Dawson, John H; Munro, Andrew W; Ortiz de Montellano, Paul R

2011-04-12

88

Crystallographic studies of heme oxygenase complexed with an unstable reaction intermediate, verdoheme.  

PubMed

This article discusses the accuracy of X-ray structural studies of heme oxygenase (HO) in complex with an unstable intermediate, verdoheme. Heme degradation by HO proceeds through three successive steps of O(2) activation. The mechanism of the third step, the ring opening of verdoheme, has been the least understood. Recent structural studies of the verdoheme-HO complex provide detailed information concerning this mechanism. Due to X-ray-induced photoreduction and the instability of verdoheme, it has been difficult to obtain an accurate structure for the ferrous verdoheme-HO complex. Therefore, accurate structural studies, including analysis of the electronic state of the verdoheme-HO complex, are needed to elucidate the proper reaction mechanism. PMID:22673156

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

2012-08-01

89

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

PubMed

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. PMID:19469573

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

2009-06-01

90

The Millisecond Intermediate in the Reaction of Nitric Oxide with Oxymyoglobin is an iron(III)-Nitrato Complex, not a Peroxynitrite  

PubMed Central

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 NO2 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 NO2 stretch at 1282 cm?1. Greater time resolution techniques will be required to detect the putative iron(III) peroxynitrite complex.

Yukl, Erik T.; de Vries, Simon; Moenne-Loccoz, Pierre

2009-01-01

91

Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate.  

PubMed

Plant ALDH10 family members are aminoaldehyde dehydrogenases (AMADHs), which oxidize ?-aminoaldehydes to the corresponding acids. They have been linked to polyamine catabolism, osmoprotection, secondary metabolism (fragrance), and carnitine biosynthesis. Plants commonly contain two AMADH isoenzymes. We previously studied the substrate specificity of two AMADH isoforms from peas (PsAMADHs). Here, two isoenzymes from tomato (Solanum lycopersicum), SlAMADHs, and three AMADHs from maize (Zea mays), ZmAMADHs, were kinetically investigated to obtain further clues to the catalytic mechanism and the substrate specificity. We also solved the high resolution crystal structures of SlAMADH1 and ZmAMADH1a because these enzymes stand out from the others regarding their activity. From the structural and kinetic analysis, we can state that five residues at positions 163, 288, 289, 444, and 454 (PsAMADHs numbering) can, directly or not, significantly modulate AMADH substrate specificity. In the SlAMADH1 structure, a PEG aldehyde derived from the precipitant forms a thiohemiacetal intermediate, never observed so far. Its absence in the SlAMADH1-E260A structure suggests that Glu-260 can activate the catalytic cysteine as a nucleophile. We show that the five AMADHs studied here are capable of oxidizing 3-dimethylsulfoniopropionaldehyde to the cryo- and osmoprotectant 3-dimethylsulfoniopropionate. For the first time, we also show that 3-acetamidopropionaldehyde, the third aminoaldehyde besides 3-aminopropionaldehyde and 4-aminobutyraldehyde, is generally oxidized by AMADHs, meaning that these enzymes are unique in metabolizing and detoxifying aldehyde products of polyamine degradation to nontoxic amino acids. Finally, gene expression profiles in maize indicate that AMADHs might be important for controlling ?-aminoaldehyde levels during early stages of the seed development. PMID:23408433

Kope?ny, David; Kon?itíková, Radka; Tylichová, Martina; Vigouroux, Armelle; Moskalíková, Hana; Soural, Miroslav; Šebela, Marek; Moréra, Solange

2013-03-29

92

Identifying of meat species using polymerase chain reaction (PCR)  

NASA Astrophysics Data System (ADS)

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.

Foong, Chow Ming; Sani, Norrakiah Abdullah

2013-11-01

93

Reaction of ferric cytochrome P450cam with peracids: kinetic characterization of intermediates on the reaction pathway.  

PubMed

Reactions of substrate-free ferric cytochrome P450cam with peracids to generate Fe=O intermediates have previously been investigated with contradictory results. Using stopped-flow spectrophotometry, the reaction with m-chloroperoxybenzoic acid demonstrated an Fe(IV)=O + porphyrin pi-cation radical (Cpd I) (Egawa, T., Shimada, H., and Ishimura, Y. (1994) Biochem. Biophys. Res. Commun. 201, 1464-1469). By contrast, with peracetic acid, Fe(IV)=O plus a tyrosyl radical were observed by freeze-quench Mossbauer and EPR spectroscopy (Schunemann, V., Jung, C., Trautwein, A. X., Mandon, D., and Weiss, R. (2000) FEBS Lett. 479, 149-154). Our detailed kinetic studies have resolved these contradictory results. At pH >7, a significant fraction of Cpd I is formed transiently, whereas at low pH only a species with a Soret band at 406 nm, presumably Fe(IV)=O + tyrosyl radical, is observed. Evidence for formation of an acylperoxo complex en route to Cpd I was obtained. Because of rapid heme destruction, steps subsequent to formation of the highly oxidized forms could not be fully characterized. Heme destruction was avoided by including peroxidase substrates (e.g. guaiacol), which were oxidized to characteristic peroxidase products as the Fe(III)-P450 was regenerated. Addition of ascorbate to either of the high valent species also reforms the Fe(III) state with only a small loss of heme absorbance. These results indicate that typical peroxidase chemistry occurs with P450cam and offer an explanation for the contrasting results reported earlier. The delineation of improved conditions (pH, temperature, choice of peracid) for generating highly oxidized species with P450cam should be valuable for their further characterization. PMID:15781454

Spolitak, Tatyana; Dawson, John H; Ballou, David P

2005-05-27

94

Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies  

PubMed Central

M.EcoRI, a bacterial sequence-specific S-adenosyl-l-methionine-dependent DNA methyltransferase, relies on a complex conformational mechanism to achieve its remarkable specificity, including DNA bending, base flipping and intercalation into the DNA. Using transient fluorescence and fluorescence lifetime studies with cognate and noncognate DNA, we have characterized several reaction intermediates involving the WT enzyme. Similar studies with a bending-impaired, enhanced-specificity M.EcoRI mutant show minimal differences with the cognate DNA, but significant differences with noncognate DNA. These results provide a plausible explanation of the way in which destabilization of reaction intermediates can lead to changes in substrate specificity.

Youngblood, Ben; Bonnist, Eleanor; Dryden, David T.F.; Jones, Anita C.; Reich, Norbert O.

2008-01-01

95

Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies.  

PubMed

M.EcoRI, a bacterial sequence-specific S-adenosyl-L-methionine-dependent DNA methyltransferase, relies on a complex conformational mechanism to achieve its remarkable specificity, including DNA bending, base flipping and intercalation into the DNA. Using transient fluorescence and fluorescence lifetime studies with cognate and noncognate DNA, we have characterized several reaction intermediates involving the WT enzyme. Similar studies with a bending-impaired, enhanced-specificity M.EcoRI mutant show minimal differences with the cognate DNA, but significant differences with noncognate DNA. These results provide a plausible explanation of the way in which destabilization of reaction intermediates can lead to changes in substrate specificity. PMID:18385156

Youngblood, Ben; Bonnist, Eleanor; Dryden, David T F; Jones, Anita C; Reich, Norbert O

2008-05-01

96

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

PubMed Central

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 reaction sets and useful to employ with genome-scale metabolic networks.

2014-01-01

97

Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes  

PubMed Central

Background Neuroblastoma patients show heterogeneous clinical courses ranging from life-threatening progression to spontaneous regression. Recently, gene expression profiles of neuroblastoma tumours were associated with clinically different phenotypes. However, such data is still rare for important patient subgroups, such as patients with MYCN non-amplified advanced stage disease. Prediction of the individual course of disease and optimal therapy selection in this cohort is challenging. Additional research effort is needed to describe the patterns of gene expression in this cohort and to identify reliable prognostic markers for this subset of patients. Methods We combined gene expression data from two studies in a meta-analysis in order to investigate differences in gene expression of advanced stage (3 or 4) tumours without MYCN amplification that show contrasting outcomes (alive or dead) at five years after initial diagnosis. In addition, a predictive model for outcome was generated. Gene expression profiles from 66 patients were included from two studies using different microarray platforms. Results In the combined data set, 72 genes were identified as differentially expressed by meta-analysis at a false discovery rate (FDR) of 8.33%. Meta-analysis detected 34 differentially expressed genes that were not found as significant in either single study. Outcome prediction based on data of both studies resulted in a predictive accuracy of 77%. Moreover, the genes that were differentially expressed in subgroups of advanced stage patients without MYCN amplification accurately separated MYCN amplified tumours from low stage tumours without MYCN amplification. Conclusion Our findings support the hypothesis that neuroblastoma consists of two biologically distinct subgroups that differ by characteristic gene expression patterns, which are associated with divergent clinical outcome.

Warnat, Patrick; Oberthuer, Andre; Fischer, Matthias; Westermann, Frank; Eils, Roland; Brors, Benedikt

2007-01-01

98

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

NASA Astrophysics Data System (ADS)

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 hydroperoxides of low volatility formed in the gas phase are partitioned into the particle phase to contribute to the SOA formation. Here, we propose a new oligomer formation mechanism including sequential addition of Criegee intermediates to hydroperoxides. REFERENCE: (1)Kroll, J. H.; Seinfeld, J. H. Chemistry of Secondary Organic Aerosol: Formation and Evolution of Low-Volatility Organics in the Atmosphere. Atmos. Environ. 2008, 42, 3593-3624. (2)Sadezky, A.; Chaimbault, P.; Mellouki, A.; Roempp, A.; Winterhalter, R.; Le Bras, G.; Moortgat, G. K. Formation of Secondary Organic Aerosol and Oligomers from the Ozonolysis of Enol Ethers. Atmos. Chem. Phys. 2006, 6, 5009-5024. (3)Sadezky, A.; Winterhalter, R.; Kanawati, B.; Roempp, A.; Spengler, B.; Mellouki, A.; Le Bras, G.; Chaimbault, P.; Moortgat, G. K. Oligomer Formation during Gas-Phase Ozonolysis of Small Alkenes and Enol Ethers: New Evidence for the Central Role of the Criegee Intermediate as Oligomer Chain Unit. Atmos. Chem. Phys. 2008, 8, 2667-2699. (4)Klotz, B.; Barnes, I.; Imamura, T. Product Study of the Gas-Phase Reactions of O3, OH and NO3 Radicals with Methyl Vinyl Ether. Phys. Chem. Chem. Phys. 2004, 6, 1725-1734.

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

2013-12-01

99

Structure of the biliverdin radical intermediate in phycocyanobilin:ferredoxin oxidoreductase identified by high-field EPR and DFT.  

PubMed

The cyanobacterial enzyme phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the two-step four-electron reduction of biliverdin IXalpha to phycocyanobilin, the precursor of biliprotein chromophores found in phycobilisomes. It is known that catalysis proceeds via paramagnetic radical intermediates, but the structure of these intermediates and the transfer pathways for the four protons involved are not known. In this study, high-field electron paramagnetic resonance (EPR) spectroscopy of frozen solutions and single crystals of the one-electron reduced protein-substrate complex of two PcyA mutants D105N from the cyanobacteria Synechocystis sp. PCC6803 and Nostoc sp. PCC7120 are examined. Detailed analysis of Synechocystis D105N mutant spectra at 130 and 406 GHz reveals a biliverdin radical with a very narrow g tensor with principal values 2.00359(5), 2.00341(5), and 2.00218(5). Using density-functional theory (DFT) computations to explore the possible protonation states of the biliverdin radical, it is shown that this g tensor is consistent with a biliverdin radical where the carbonyl oxygen atoms on both the A and the D pyrrole rings are protonated. This experimentally confirms the reaction mechanism recently proposed (Tu, et al. Biochemistry 2007, 46, 1484). PMID:19159240

Stoll, Stefan; Gunn, Alexander; Brynda, Marcin; Sughrue, Wesley; Kohler, Amanda C; Ozarowski, Andrew; Fisher, Andrew J; Lagarias, J Clark; Britt, R David

2009-02-11

100

Spectroscopic and kinetic properties of the transient intermediate acceptor in reaction centers of Rhodopseudomonas sphaeroides.  

PubMed

The photoreductive trapping of the transient, intermediate acceptor, I-, in purified reaction centers of Rhodopseudomonas sphaeroides R-26 was investigated for different external conditions. The optical spectrum of I- was found to be similar to that reported for other systems by Shuvalov and Klimov ((1976) Biochim. Biophys. Acta 400, 587--599) and Tiede et al. (P.M. Tiede, R.C. Prince, G.H. Reed and P.L. Dutton (1976) FEBS Lett. 65, 301--304). The optical changes of I- showed characteristics of both bacteriopheophytin (e.g. bleaching at 762, 542 nm and red shift at 400 nm) and bacteriochlorophyll (bleaching at 802 and 590 nm). Two types of EPR signals of I- were observed: one was a narrow singlet at g = 2.0035, deltaH = 13.5 G, the other a doublet with a splitting of 60 G centered around g = 2.00, which was only seen after short illumination times in reaction centers reconstituted with menaquinone. The optical and EPR kinetics of I- on illumination in the presence of reduced cytochrome c and dithionite strongly support the following three-step scheme in which the doublet EPR signal is due to the unstable state DI-Q-Fe2+ and the singlet EPR signal is due to DI-Q2-Fe2+. : formula: (see text), where D is the primary donor (BChl)2+. The above model was supported by the following observations: (1) During the first illumination, sigmoidal kinetics of the formation of I- was observed. This is a direct consequence of the three-sequential reactions. (2) During the second and subsequent illuminations first-order (exponential) kinetics were observed for the formation of I-. This is due to the dark decay, k4, to the state DIQ2-Fe2+ formed after the first illumination. (3) Removal of the quinone resulted in first-order kinetics. In this case, only the first step, k1, is operative. (4) The observation of the doublet signal in reaction centers containing menaquinone but not ubiquinone is explained by the longer lifetime of the doublet species I-(Q-Fe2%) in reaction centers containing menaquinone. The value of tau2 was determined from kinetic measurements to be 0.01 s for ubiquinone and 4 s for menaquinone (T = 20 degrees C). The temperature and pH dependence of the dark electron transfer reaction I-(Q-Fe2+) yields I(Q2-Fe2+) was studied in detail. The activation energy for this process was found to be 0.42 eV for reaction centers containing ubiquinone and 0.67 eV for reaction centers with menaquinone. The activation energy and the doublet splitting were used to calculate the rate of electron transfer from I- to MQ-Fe2+ using Hopfield's theory for thermally activated electron tunneling. The calculated rate agrees well with the experimentally determined rate which provides support for electron tunneling as the mechanism for electron transfer in this reaction. Using the EPR doublet splitting and the activation energy for electron transfer, the tunneling matrix element was calculated to be 10(-3) eV. From this value the distance between I- and MQ- was estimated to be 7.5--10 A. PMID:36906

Okamura, M Y; Isaacson, R A; Feher, G

1979-06-01

101

A pivotal heme-transfer reaction intermediate in cytochrome c biogenesis.  

PubMed

c-Type cytochromes are widespread proteins, fundamental for respiration or photosynthesis in most cells. They contain heme covalently bound to protein in a highly conserved, highly stereospecific post-translational modification. In many bacteria, mitochondria, and archaea this heme attachment is catalyzed by the cytochrome c maturation (Ccm) proteins. Here we identify and characterize a covalent, ternary complex between the heme chaperone CcmE, heme, and cytochrome c. Formation of the complex from holo-CcmE occurs in vivo and in vitro and involves the specific heme-binding residues of both CcmE and apocytochrome c. The enhancement and attenuation of the amounts of this complex correlates completely with known consequences of mutations in genes for other Ccm proteins. We propose the complex is a trapped catalytic intermediate in the cytochrome c biogenesis process, at the point of heme transfer from CcmE to the cytochrome, the key step in the maturation pathway. PMID:22121193

Mavridou, Despoina A I; Stevens, Julie M; Mönkemeyer, Leonie; Daltrop, Oliver; di Gleria, Katalin; Kessler, Benedikt M; Ferguson, Stuart J; Allen, James W A

2012-01-20

102

Aryl-phenyl scrambling in intermediate organopalladium complexes: a gas-phase study of the mizoroki-heck reaction.  

PubMed

The intramolecular aryl-phenyl scrambling reaction within palladium-DPPP-aryl complex (DPPP=1,3-bis(diphenylphosphino)propane) ions was analyzed by state-of-the-art tandem MS, including gas-phase ion/molecule reactions. The Mizoroki-Heck cross-coupling reaction was performed in the gas phase, and the intrinsic reactivity of important intermediates could be examined. Moreover, linear free-energy correlations were applied, and a mechanism for the scrambling reaction proceeding via phosphonium cations was assumed. PMID:24633762

Fiebig, Lukas; Schlörer, Nils; Schmalz, Hans-Günther; Schäfer, Mathias

2014-04-22

103

Infrared matrix isolation and theoretical study of the initial intermediates in the reaction of ozone with cycloheptene  

NASA Astrophysics Data System (ADS)

Matrix isolation combined with infrared spectroscopy resulted in the observation of early intermediates in the reaction of two conformers of cycloheptene and ozone, marking the first observation of these intermediates for a cyclic alkene with conformational isomerism. Spectral evidence supports the presence of the primary ozonide of the chair and boat conformers of cis-cycloheptene, which represents the first time two primary ozonide isomers have been observed for any alkene. In addition, at least one conformer of the Criegee intermediate formed through ring-opening of the cyclic primary ozonide, as well as stable end products. Both the Criegee intermediate and primary ozonide were observed in the spectra of the initial deposition in twin jet experiments. After the matrix was annealed to 36 K, peaks of the primary ozonide increased by ˜250% while the peak of the Criegee intermediate increased by ˜150%. Supporting data was obtained from 18O-labeled ozone experiments. In addition to experimental evidence, further justification was provided by theoretical calculations at the B3LYP/6-311++G(d,2p) level. The photochemical reactions of the trapped species were also studied. After irradiation of the secondary ozonide and stable products of the ozonolysis reaction, 1-hexanal and carbon dioxide were observed. Late, stable oxidation products of cycloheptene were observed in merged jet experiments.

Pinelo, Laura; Ault, Bruce S.

2012-10-01

104

Structural evidence for a common intermediate in small G protein-GEF reactions.  

PubMed

Rho of plants (Rop) proteins belong to the superfamily of small GTP-binding (G) proteins and are vital regulators of signal transduction in plants. In order to become activated, Rop proteins need to exchange GDP for GTP, an intrinsically slow process catalyzed by guanine nucleotide exchange factors (GEFs). RopGEFs show no homology to animal RhoGEFs, and the catalytic mechanism remains elusive. GEF-catalysed nucleotide exchange proceeds via transient ternary and stable binary complexes. While a number of structural studies have analyzed binary nucleotide-free G protein-GEF complexes, very little is known about the ternary complexes. Here we report the X-ray structure of the catalytic PRONE domain of RopGEF8 from Arabidopsis thaliana, both alone and in a ternary complex with Rop4 and GDP. The features of the latter complex, a transient intermediate of the exchange reaction never directly observed before, suggest a common mechanism of catalyzed nucleotide exchange applicable to small G proteins in general. PMID:17218277

Thomas, Christoph; Fricke, Inka; Scrima, Andrea; Berken, Antje; Wittinghofer, Alfred

2007-01-12

105

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

NASA Astrophysics Data System (ADS)

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(1?g). 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.

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

2014-06-01

106

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

PubMed

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((1)?g). 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. PMID:24848232

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

2014-06-01

107

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

ERIC Educational Resources Information Center

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…

Latimer, Devin

2007-01-01

108

Thermodynamic and kinetic characteristics of intermediates of electrode reactions: Determination by direct and combined electrochemical methods  

Microsoft Academic Search

The potentialities of electrochemical and combined methods for the determination of thermodynamic characteristics and kinetic parameters of intermediates are analyzed. The electrochemical methods include polarography, versions of voltammetry, and chronopotentiometry. The combined methods combine nonelectrochemical (or indirect) generation of intermediates with electrochemical methods of their subsequent investigation: photomodulation voltammetry, method of polarography of pulsed-radiolysis products, method of indirect electrolysis, electrochemiluminescence,

A. G. Krivenko; A. S. Kotkin; V. A. Kurmaz

2005-01-01

109

Aryl transfer between Pd(II) centers or Pd(IV) intermediates in Pd-catalyzed domino reactions.  

PubMed

A computational study has been performed to determine the mechanism of the key steps of Pd-catalyzed domino reactions in which C(sp2)-C(sp2) are formed from aryl and alkenyl halides. DFT calculations were done on model complexes of the proposed intermediates, with PH3 and H2O as ancillary ligands, to explore two possible mechanisms: the oxidative addition of aryl or alkenyl halides to palladacycles to give Pd(IV) intermediates, and the transmetalation-type reaction of aryl or alkenyl ligands between two Pd(II) centers, a palladacycle, and a Pd(II) complex formed by oxidative addition of aryl or alkenyl halides to Pd0. We have shown that oxidative addition of iodoethylene to Pd0 precursors is more favorable than oxidative addition to Pd(II) palladacycles, whereas transmetalation-type reactions between Pd(II) complexes are facile. Similar results were obtained with iodobenzene instead of iodoethylene and formamide as the ancillary ligand. These results suggest that Pd(IV) intermediates are not involved in these reactions. PMID:16608337

Cárdenas, Diego J; Martín-Matute, Belén; Echavarren, Antonio M

2006-04-19

110

X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase.  

PubMed

The X-ray structure of yeast 5-aminolaevulinic acid dehydratase, in which the catalytic site of the enzyme is complexed with a putative cyclic intermediate composed of both substrate moieties, has been solved at 0.16 nm (1.6 A) resolution. The cyclic intermediate is bound covalently to Lys(263) with the amino group of the aminomethyl side chain ligated to the active-site zinc ion in a position normally occupied by a catalytic hydroxide ion. The cyclic intermediate is catalytically competent, as shown by its turnover in the presence of added substrate to form porphobilinogen. The findings, combined with those of previous studies, are consistent with a catalytic mechanism in which the C-C bond linking both substrates in the intermediate is formed before the C-N bond. PMID:12777167

Erskine, Peter T; Coates, Leighton; Butler, Danica; Youell, James H; Brindley, Amanda A; Wood, Steve P; Warren, Martin J; Shoolingin-Jordan, Peter M; Cooper, Jonathan B

2003-08-01

111

X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase.  

PubMed Central

The X-ray structure of yeast 5-aminolaevulinic acid dehydratase, in which the catalytic site of the enzyme is complexed with a putative cyclic intermediate composed of both substrate moieties, has been solved at 0.16 nm (1.6 A) resolution. The cyclic intermediate is bound covalently to Lys(263) with the amino group of the aminomethyl side chain ligated to the active-site zinc ion in a position normally occupied by a catalytic hydroxide ion. The cyclic intermediate is catalytically competent, as shown by its turnover in the presence of added substrate to form porphobilinogen. The findings, combined with those of previous studies, are consistent with a catalytic mechanism in which the C-C bond linking both substrates in the intermediate is formed before the C-N bond.

Erskine, Peter T; Coates, Leighton; Butler, Danica; Youell, James H; Brindley, Amanda A; Wood, Steve P; Warren, Martin J; Shoolingin-Jordan, Peter M; Cooper, Jonathan B

2003-01-01

112

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

SciTech Connect

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.

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

1986-11-04

113

Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs.  

PubMed

Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we report three X-ray crystal structures of the Rhizobium etli PC CT domain with the bound inhibitors oxalate, 3-hydroxypyruvate, and 3-bromopyruvate. Oxalate, a stereoelectronic mimic of the enolpyruvate intermediate, does not interact directly with the metal ion. Instead, oxalate is buried in a pocket formed by several positively charged amino acid residues and the metal ion. Furthermore, both 3-hydroxypyruvate and 3-bromopyruvate, analogs of the reaction product oxaloacetate, bind in an identical manner to oxalate suggesting that the substrate maintains its orientation in the active site throughout catalysis. Together, these structures indicate that the substrates, products and intermediates in the PC-catalyzed reaction are not oriented in the active site as previously assumed. The absence of a bidentate interaction with the active site metal appears to be a unique mechanistic feature among the small group of biotin-dependent enzymes that act on ?-keto acid substrates. PMID:24157795

Lietzan, Adam D; St Maurice, Martin

2013-11-15

114

The reaction mechanism for CD38. A single intermediate is responsible for cyclization, hydrolysis, and base-exchange chemistries.  

PubMed

Human recombinant CD38 catalyzes the formation of both cyclic ADP-ribose and ADP-ribose products from NAD+ and hydrolyzes cyclic ADP-ribose to ADP-ribose. The corresponding GDP products are formed from NGD+. The enzyme was characterized by substrate and inhibition kinetics, exchange studies, rapid-quench reactions, and stopped-flow-fluorescence spectroscopy to establish the reaction mechanism and energetics for individual steps. Noncyclizable substrates NMN+ and nicotinamide-7-deaza-hypoxanthine dinucleotide (7-deaza NHD+) were rapidly hydrolyzed by the enzyme. The kcat for NMN+ was 5-fold higher than that of NAD+ and has the greatest reported kcat of any substrate for CD38. 7-deaza-NHD+ was hydrolyzed at approximately one-third the rate of NHD+ but does not form a cyclic product. These results establish that a cyclic intermediate is not required for substrate hydrolysis. The ratio of methanolysis to hydrolysis for cADPR and NAD+ catalyzed by CD38 increases linearly with MeOH concentration. Both reactions produce predominantly the beta-methoxy riboside compound, with a relative nucleophilicity of MeOH to H2O of 11. These results indicate the existence of a stabilized cationic intermediate for all observed chemistries in the active site of CD38. The partitioning of this intermediate between cyclization, hydrolysis, and nicotinamide-exchange unites the mechanisms of CD38 chemistries. Steady-state and pre-steady-state parameters for the partition and exchange mechanisms allowed full characterization of the reaction coordinate. Stopped-flow methods indicate a burst of cGDPR formation followed by the steady-state reaction rate. A lag phase, which was NGD+ concentration dependent, was also observed. The burst size indicates that the dimeric enzyme has a single catalytic site formed by two subunits. Pre-steady-state quench experiments did not detect covalent intermediates. Nicotinamide hydrolysis of NGD+ precedes cyclization and the chemical quench decomposes the enzyme-bound species to a mixture of cyclic and hydrolysis products. The time dependence of this ratio indicated that nicotinamide bond-breakage occurs 4 times faster than the conversion of the intermediate to products. Product release is the overall rate-limiting step for enzyme reaction with NGD+. PMID:9748331

Sauve, A A; Munshi, C; Lee, H C; Schramm, V L

1998-09-22

115

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

SciTech Connect

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.

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

1987-12-01

116

Electrophilic addition reaction of ethene with hydrogen chloride on cold molecular films: evidence of ethyl cationic intermediate.  

PubMed

We studied the initial-stage mechanism of the electrophilic addition reaction of ethene with HCl by examining the interactions between ethene and HCl on water-ice and frozen molecular films at temperatures of 80-140?K. Cs(+) reactive ion scattering (RIS) and low-energy sputtering (LES) techniques were used to probe the reaction intermediates that were kinetically trapped on the surface, in conjunction with temperature-programmed desorption (TPD) mass spectrometry to monitor the desorbing species. The reaction initially produced the ??complex of HCl and ethene at temperatures below about 93?K and an "ethyl cationic species" at temperatures below about 100?K. The ethyl cationic species was formed via direct proton transfer from the HCl molecule to ethene with the assistance of water solvation, rather than via the interaction of hydronium ions and ethene. At high temperatures, this species dissociated into ethene and hydronium and chloride ions. The reaction did not, however, complete the final transition state on the ice surface to produce ethyl chloride. The observation gives evidence that the electrophilic addition reaction of ethene occurs through an ethyl-like intermediate with an ionic character. PMID:21108286

Lee, Poong-Ryul; Lee, Chang-Woo; Kim, Joon-Ki; Moon, Eui-Seong; Kang, Heon

2011-03-01

117

Subcellular fractionation of TGF-beta1-stimulated lung epithelial cells: a novel proteomic approach for identifying signaling intermediates.  

PubMed

Members of the transforming growth factor (TGF)-beta superfamily are key regulators of lung development and homeostasis, in particular by controlling alveolar/bronchial epithelial cell function. TGF-beta signaling involves ligand-dependent activation of receptor serine/threonine kinases, activation and subsequent nuclear translocation of pathway-specific transcription factors (Smads), and ultimately, modulation of gene expression. While Smad-dependent responses represent the primary signaling components activated by TGF-beta receptors, their function is controlled by a variety of cofactors. In addition, alternative signaling systems mediating TGF-beta-induced effects have recently been described such as MAP kinase pathways. To uncover novel proteins that participate in TGF-beta signaling via nuclear/cytoplasmic shuttling in lung epithelial cells, we have analyzed A549 human lung epithelial cells, using subcellular fractionation combined with 2-D PAGE, tryptic digestion, and MS. We identified a rapid increase in the cytosolic localization of KH-type splicing regulatory protein (KHSRP), far upstream element-binding protein (FUBP1), hnRNP-L, and hnRNP-H1, concomitant with a decrease in their nuclear localization in response to TGF-beta1. Proteomic data were confirmed by immunofluorescence and immunoblot analyses. In summary, we represent a powerful novel technology for the identification of previously unknown signaling intermediates. PMID:19253281

Milosevic, Jadranka; Bulau, Patrick; Mortz, Ejvind; Eickelberg, Oliver

2009-03-01

118

Intermediate-energy inverse-kinematics one-proton pickup reactions on neutron-deficient fp-shell nuclei  

NASA Astrophysics Data System (ADS)

Background: Thick-target-induced nucleon-adding transfer reactions onto energetic rare-isotope beams are an emerging spectroscopic tool. Their sensitivity to single-particle structure complements one-nucleon removal reaction capabilities in the quest to reveal the evolution of nuclear shell structure in very exotic nuclei. Purpose: Our purpose is to add intermediate-energy, carbon-target-induced one-proton pickup reactions to the arsenal of ?-ray-tagged direct reactions applicable in the regime of low beam intensities and to apply these for the first time to fp-shell nuclei. Methods: Inclusive and partial cross sections were measured for the 12C(48Cr,49Mn+?)X and 12C(50Fe,51Co+?)X proton pickup reactions at 56.7 and 61.2 MeV/nucleon, respectively, using coincident particle-? spectroscopy at the National Superconducting Cyclotron Laboratory. The results are compared to reaction theory calculations using fp-shell-model nuclear structure input. For comparison with our previous work, the same reactions were measured on 9Be targets. Results: The measured partial cross sections confirm the specific population pattern predicted by theory, with pickup into high-? orbitals being strongly favored, driven by linear and angular momentum matching. Conclusion: Carbon-target-induced pickup reactions are well suited, in the regime of modest beam intensity, to study the evolution of nuclear structure, with specific sensitivities that are well described by theory.

McDaniel, S.; Gade, A.; Tostevin, J. A.; Baugher, T.; Bazin, D.; Brown, B. A.; Cook, J. M.; Glasmacher, T.; Grinyer, G. F.; Ratkiewicz, A.; Weisshaar, D.

2012-01-01

119

Direct detection of key reaction intermediates in photochemical CO2 reduction sensitized by a rhenium bipyridine complex.  

PubMed

Photochemical CO2 reduction sensitized by rhenium-bipyridyl complexes has been studied through multiple approaches during the past several decades. However, a key reaction intermediate, the CO2-coordinated Re-bipyridyl complex, which should govern the activity of CO2 reduction in the photocatalytic cycle, has never been detected in a direct way. In this study on photoreduction of CO2 catalyzed by the 4,4'-dimethyl-2,2'-bipyridine (dmbpy) complex, [Re(dmbpy)(CO)3Cl] (1), we successfully detect the solvent-coordinated Re complex [Re(dmbpy)(CO)3DMF] (2) as the light-absorbing species to drive photoreduction of CO2. The key intermediate, the CO2-coordinated Re-bipyridyl complex, [Re(dmbpy)(CO)3(COOH)], is also successfully detected for the first time by means of cold-spray ionization spectrometry (CSI-MS). Mass spectra for a reaction mixture with isotopically labeled (13)CO2 provide clear evidence for the incorporation of CO2 into the Re-bipyridyl complex. It is revealed that the starting chloride complex 1 was rapidly transformed into the DMF-coordinated Re complex 2 through the initial cycle of photoreduction of CO2. The observed induction period in the time profile of the CSI-MS signals can well explain the subsequent formation of the CO2-coordinated intermediate from the solvent-coordinated Re-bipyridyl complex. An FTIR study of the reaction mixture in dimethyl sulfoxide clearly shows the appearance of a signal at 1682 cm(-1), which shifts to 1647 cm(-1) for the (13)CO2-labeled counterpart; this is assigned as the CO2-coordinated intermediate, Re(II)-COOH. Thus, a detailed understanding has now been obtained for the mechanism of the archetypical photochemical CO2 reduction sensitized by a Re-bipyridyl complex. PMID:24689747

Kou, Youki; Nabetani, Yu; Masui, Dai; Shimada, Tetsuya; Takagi, Shinsuke; Tachibana, Hiroshi; Inoue, Haruo

2014-04-23

120

DNA strand transfer reactions catalyzed by vaccinia topoisomerase: hydrolysis and glycerololysis of the covalent protein-DNA intermediate.  

PubMed Central

Vaccinia topoisomerase forms a covalent protein-DNA intermediate at sites containing the sequence 5'-CCCTT. The T nucleotide is linked via a 3'-phosphodiester bond to Tyr-274 of the enzyme. Here, we report that the enzyme catalyzes hydrolysis of the covalent intermediate, resulting in formation of a 3'-phosphate-terminated DNA cleavage product. The hydrolysis reaction is pH-dependent (optimum pH = 9.5) and is slower, by a factor of 10(-5), than the rate of topoisomerase-catalyzed strand transfer to a 5'-OH terminated DNA acceptor strand. Mutants of vaccinia topoisomerase containing serine or threonine in lieu of the active site Tyr-274 form no detectable covalent intermediate and catalyze no detectable DNA hydrolysis. This suggests that hydrolysis occurs subsequent to formation of the covalent protein-DNA adduct and not via direct attack by water on DNA. Vaccinia topoisomerase also catalyzes glycerololysis of the covalent intermediate. The rate of glycerololysis is proportional to glycerol concentration and is optimal at pH 9.5.

Petersen, B O; Shuman, S

1997-01-01

121

Photocatalytic degradation of methylene blue on nanocrystalline TiO2: Surface mass spectrometry of reaction intermediates  

NASA Astrophysics Data System (ADS)

Photocatalytic degradation reactions of methylene blue on nanocrystalline TiO2 (nc-TiO2) films were studied in situ by surface mass spectrometric techniques including secondary ion mass spectrometry, laser desorption direct ion mass spectrometry, and laser desorption/laser photoion mass spectrometry. The parent ion of methylene blue and/or its reduced form leucomethylene blue was observed with little fragmentation by all methods prior to ultraviolet exposure. The surface composition changed upon ultraviolet (UV) irradiation in air, an observation ascribed to photocatalytic reactions induced by UV photons: the parent molecule signal diminished and intermediate reaction products such as sulfoxides and sulfones were detected from the TiO2 surface. After prolonged UV irradiation these species also vanished and the methylene blue appeared to be almost completely mineralized.

Gnaser, Hubert; Savina, Michael R.; Calaway, Wallis F.; Tripa, C. Emil; Veryovkin, Igor V.; Pellin, Michael J.

2005-08-01

122

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

PubMed Central

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 ?-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.

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

2014-01-01

123

The role of long-lived reactive oxygen intermediates in the reaction of ozone with aerosol particles  

NASA Astrophysics Data System (ADS)

The heterogeneous reactions of O3 with aerosol particles are of central importance to air quality. They are studied extensively, but the molecular mechanisms and kinetics remain unresolved. Based on new experimental data and calculations, we show that long-lived reactive oxygen intermediates (ROIs) are formed. The chemical lifetime of these intermediates exceeds 100 seconds, which is much longer than the surface residence time of molecular O3 (~10-9 s). The ROIs explain and resolve apparent discrepancies between earlier quantum mechanical calculations and kinetic experiments. They play a key role in the chemical transformation and adverse health effects of toxic and allergenic air-particulate matter, such as soot, polycyclic aromatic hydrocarbons and proteins. ROIs may also be involved in the decomposition of O3 on mineral dust and in the formation and growth of secondary organic aerosols. Moreover, ROIs may contribute to the coupling of atmospheric and biospheric multiphase processes.

Shiraiwa, Manabu; Sosedova, Yulia; Rouvière, Aurélie; Yang, Hong; Zhang, Yingyi; Abbatt, Jonathan P. D.; Ammann, Markus; Pöschl, Ulrich

2011-04-01

124

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

Microsoft Academic Search

5-Fluoro-?-d-galactopyranosyl fluoride was synthesized and its interaction with the active site of an ?-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

Hoa D Ly; Steven Howard; Kelly Shum; Shouming He; Alex Zhu; Stephen G Withers

2000-01-01

125

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

DOEpatents

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.

Maya, Leon (Oak Ridge, TN)

1988-05-24

126

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

DOEpatents

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.

Maya, Leon (Oak Ridge, TN)

1991-01-01

127

Nuclear symmetry energy and proton-rich reactions at intermediate energies  

SciTech Connect

Based on an isospin-dependent Boltzmann-Uehling-Uhlenbeck transport model, effects of high-density behavior of nuclear symmetry energy in the proton-rich reaction {sup 22}Si+{sup 22}Si at a beam energy of 400 MeV/nucleon are studied. It is found that the symmetry energy affects {pi}{sup +} production more than {pi}{sup -}. More interestingly, compared to neutron-rich reactions, for {pi}{sup -}/{pi}{sup +} and dense matter's N/Z ratios, effects of symmetry energy in the proton-rich reaction show contrary behaviors. The practical experiment by using the proton-rich reaction {sup 22}Si+{sup 40}Ca to study nuclear symmetry energy is also provided.

Yong Gaochan [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

2011-07-15

128

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

NASA Technical Reports Server (NTRS)

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.

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

1993-01-01

129

Development of drug intermediates by using direct organocatalytic multi-component reactions.  

PubMed

Novel, economic and environmentally friendly one-pot three-component Knoevenagel/hydrogenation (K/H) and four-component Knoevenagel/hydrogenation/alkylation (K/H/A) reactions of ketones, CH-acids, dihydropyridines and alkyl halides using proline and proline/metal carbonate catalysis, respectively, have been developed. Many of the products of these K/H and K/H/A reactions have direct applications in pharmaceutical chemistry. PMID:16633553

Ramachary, Dhevalapally B; Kishor, M; Reddy, G Babul

2006-05-01

130

Local structure of reaction intermediates probed by time-resolved x-ray absorption near edge structure spectroscopy  

SciTech Connect

A method for the analysis of time-resolved x-ray absorption near edge structure (XANES) spectra is proposed. It combines principal component analysis of the series of experimental spectra, multidimensional interpolation of theoretical XANES as a function of structural parameters, and ab initio XANES calculations. It allows to determine the values of structural parameters for intermediates of chemical reactions and the concentrations of different states as a function of time. This approach is tested using numerically generated data and its possibilities and limitations are discussed. The application of this method to a reaction with methylrhenium trioxide catalyst in solution, for which experimental data were measured using stopped-flow energy-dispersive x-ray absorption spectroscopy technique, is demonstrated. Possibilities and limitations of this experimental technique are also discussed.

Smolentsev, G.; Soldatov, A. V. [Center for Nanoscale Structure of Matter and Faculty of Physics, Southern Federal University, Rostov-on-Don 344090 (Russian Federation); Guilera, G. [ALBA Synchrotron, Barcelona 08193 (Spain); Tromp, M. [University of Southampton, Southampton SO17 1BJ (United Kingdom); Pascarelli, S. [European Synchrotron Radiation Facility, Grenoble 38000 (France)

2009-05-07

131

Experimental determination of the effective nucleon-nucleon interaction for p-nucleus reactions at intermediate energies  

SciTech Connect

A complete measurement of the polarization transfer observables has been made for the first time in the (p,p') reaction at intermediate energies. Measurements are reported for the /sup 12/C(p,p') /sup 12/C reaction to the 1/sup +/, T = 0(12.71 MeV) and 1/sup +/, T = 1(15.11 MeV) states at 500 MeV at laboratory scattering angles of 3.5/sup 0/, 5.5/sup 0/, 7.5/sup 0/, and 12.0/sup 0/. Linear combinations of these observables are shown to exhibit a very selective dependence on the isoscalar and isovector spin-dependent components of the nucleon-nucleon interaction. To the extent of the validity of the single collision approximation, these amplitudes are compared directly to the free nucleon-nucleon amplitudes at small momentum transfers ( < 1 fm/sup -1/).

McClelland, J.B.; Aas, B.; Azizi, A.

1982-01-01

132

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

NASA Technical Reports Server (NTRS)

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.

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

1991-01-01

133

Characterization of the Peroxidase Mechanism upon Reaction of Prostacyclin Synthase with Peracetic Acid. Identification of a Tyrosyl Radical Intermediate  

PubMed Central

Prostacyclin synthase (PGIS) is a membrane-bound class III cytochrome P450 that catalyzes an isomerization of prostaglandin H2, an endoperoxide, to prostacyclin. We report here the characterization of the PGIS intermediates in reactions with other peroxides, peracetic acid (PA), and iodosylbenzene. Rapid-scan stopped-flow experiments revealed an intermediate with an absorption spectrum similar to that of compound ES (Cpd ES), which is an oxo–ferryl (Fe(IV)=O) plus a protein-derived radical. Cpd ES, formed upon reaction with PA, has an X-band (9 GHz) EPR signal of g = 2.0047 and a half-saturation power, P1/2, of 0.73 mW. High-field (130 GHz) EPR reveals the presence of two species of tyrosyl radicals in Cpd ES with their g-tensor components (gx, gy, gz) of 2.00970, 2.00433, 2.00211 and 2.00700, 2.00433, 2.00211 at a 1:2 ratio, indicating that one is involved in hydrogen bonding and the other is not. The line width of the g = 2 signal becomes narrower, while its P1/2 value becomes smaller as the reaction proceeds, indicating migration of the unpaired electron to an alternative site. The rate of electron migration (~0.2 s?1) is similar to that of heme bleaching, suggesting the migration is associated with the enzymatic inactivation. Moreover, a g = 6 signal that is presumably a high-spin ferric species emerges after the appearance of the amino acid radical and subsequently decays at a rate comparable to that of enzymatic inactivation. This loss of the g = 6 species thus likely indicates another pathway leading to enzymatic inactivation. The inactivation, however, was prevented by the exogenous reductant guaiacol. The studies of PGIS with PA described herein provide a mechanistic model of a peroxidase reaction catalyzed by the class III cytochromes P450.

Yeh, Hui-Chun; Gerfen, Gary J.; Wang, Jinn-Shyan; Tsai, Ah-Lim; Wang, Lee-Ho

2010-01-01

134

Photocatalytic decomposition of crotamiton over aqueous TiO(2) suspensions: determination of intermediates and the reaction pathway.  

PubMed

The photocatalytic degradation of crotamiton in aqueous solution using TiO(2) was investigated. To investigate the effect of initial pH, the photodegradation behaviors of three types of pharmaceuticals were compared (crotamiton, clofibric acid, sulfamethoxazole). The degradation rates of crotamiton in the pH range 3-9 were nearly equal, but those of clofibric acid and sulfamethoxazole were affected by pH. At pH>6.5, TiO(2) particles, clofibric acid and sulfamethoxazole had negative charge, therefore, the repulsive force between TiO(2) particles and anionic pharmaceuticals occurred and a low reaction rate at high pH was observed. The effect of UV intensity and TiO(2) concentration on photodegradation efficiency was also investigated. Linear and logarithmical relationships between UV intensity, TiO(2) concentration and the reaction rate constant were confirmed. Furthermore, the structures of photodegradation intermediates formed concomitantly with the disappearance of crotamiton were estimated. Seven intermediates were characterized by LC/MS/MS analyses, and it was assumed that the photocatalytic degradation of crotamiton was initiated by the attack of electrophilic hydroxyl radicals on aromatic rings and alkyl chains. PMID:22578794

Fukahori, Shuji; Fujiwara, Taku; Ito, Ryusei; Funamizu, Naoyuki

2012-09-01

135

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

PubMed Central

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.

Song, Woon Ju; Lippard, Stephen J.

2011-01-01

136

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

SciTech Connect

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.

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

2005-01-01

137

Electron shuttling effect of the intermediate quinones in phenol oxidation by Fenton reaction  

SciTech Connect

Fenton-type reactions have been developed for destruction of organic contaminants in water. This advanced oxidation process (AOP) shows promise for onsite destruction of hazardous organic compounds in water without generating secondary pollutants commonly associated with conventional treatment processes. Fenton-type reactions generate hydroxyl radical by iron(II) decomposition of hydrogen peroxide. Hydroxyl radical reacts rapidly and non-selectively with most organic compounds, so deep, even complete degradation may be achieved. The overall oxidation of organic compounds by Fenton-type reactions is, however, complex and may involve a series of steps. Understanding the oxidation mechanism, therefore, is prerequisite to proper engineering of Fenton based remediation technologies. We present here the results of a kinetic investigation on iron catalyzed oxidation of phenol by hydrogen peroxide in water in the dark.

Chen, Ruzhong; Pignatello, J.J. [Connecticut Agricultural Experimental Station, New Haven, CT (United States)

1996-12-31

138

Astrophysically Important Reaction Rates For Novae And X-ray Bursts From Proton Breakup At Intermediate Energies  

SciTech Connect

We discuss the use of one-nucleon removal reactions of loosely bound nuclei at intermediate energies as an indirect method in nuclear astrophysics. The breakup reactions are proved to be good spectroscopic tools and can be used to study a large number of loosely bound proton- or neutron-rich nuclei over a wide range of beam energies. As peripheral processes, they can be used to extract asymptotic normalization coefficients (ANCs) from which non-resonant capture reaction rates of astrophysical interest can be calculated parameter free. In this talk, we present results of a proton-breakup experiment carried out at GANIL (France) with a cocktail beam centered around {sup 23}Al at 50 MeV/nucleon. Momentum distributions of the breakup fragments, inclusive and in coincidence with gamma rays detected by EXOGAM Germanium clover array, were measured in the focal plan of SPEG energy-loss spectrometer. We present in particular the investigations of reaction rates for {sup 22}Mg(p,{gamma}){sup 23}Al and {sup 23}Al(p,{gamma}){sup 24}Si important for novae and X-ray bursts, respectively.

Banu, A.; Trache, L. [Cyclotron Institute, Texas A and M University, College Station, Texas 77843-3366 (United States); National Institute of Physics and Nuclear Engineering, 'Horia Hulubei' (IFIN-HH), R-077125 Magurele-Bucharest (Romania); Carstoiu, F.; Negoita, F.; Rotaru, F. [National Institute of Physics and Nuclear Engineering, 'Horia Hulubei' (IFIN-HH), R-077125 Magurele-Bucharest (Romania); Orr, N. A.; Achouri, N. L.; Laurent, B. [Laboratoire de Physique Corpusculaire, IN2P3-CNRS, ISMRA et Universite, F-14050 Caen (France); Bonaccorso, A. [Instituto Nazionale di Fisica Nucleare, Sez. Di Pisa, I-56127 Pisa (Italy); Catford, W. N.; Patterson, N.; Thomas, J. S. [Department of Physics, University of Surrey, Guildford GU2 5XH (United Kingdom); Chartier, M.; Fernandez-Dominguez, B.; Paschalis, S.; Pietras, B. [Oliver Lodge Laboratory, University of Liverpool, Liverpool L69 7ZE (United Kingdom); Freer, M. [School of Physics and Astronomy, University of Birmingham, Birmingham B15 2TT (United Kingdom); Gaudefroy, L.; Roussel-Chomaz, P. [Grand Accelerateur d'Ions Lourds, BP 55027, 14076 Caen Cedex 5 (France); Horoi, M. [Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859 (United States)

2010-11-24

139

Characterization of the low-temperature intermediates of the reaction of fully reduced soluble cytochrome oxidase with oxygen by electron-paramagnetic-resonance and optical spectroscopy.  

PubMed Central

The reaction of fully reduced soluble bovine heart cytochrome oxidase with O2 at 173K was investigated by low-temperature optical and e.p.r. spectroscopy, and the kinetics of the reaction were analysed by non-linear optimization techniques. The only e.p.r. signals seen during the course of the reaction are those attributable to low-spin cytochrome a3+ and CuA2+. Quantitative analysis of e.p.r. signals shows that, at the end point of the reaction at 173K, nearly 100% of CuA is in the cupric state but only about 40% of cytochrome a is in the ferric low-spin state. The optical spectra recorded at this stage of the reaction show incomplete oxidation of haem and the absence of a 655 nm absorption band. The only reaction scheme that accounts for both the e.p.r. and optical data is a four-intermediate mechanism involving a branching pathway. The reaction is initiated when fully reduced cytochrome oxidase reacts with O2 to form intermediate I. This is then converted into either intermediate IIA or intermediate IIB. Of these, intermediate IIB is a stable end product at 173 K, but intermediate IIA is converted into intermediate III, which is the stable state at 173 K in this branch of the mechanism. The kinetic analysis of the e.p.r. data allows the unambiguous assignments of the valence states of cytochrome a and CuA in the intermediates. Intermediate I contains cytochrome a2+ and CuA+, intermediate IIA contains low-spin cytochroma a3+ and CuA+, intermediate IIB contains cytochrome a2+ and CuA2+, and intermediate III contains low-spin cytochrome a3+ and CuA2+. The electronic state of the O2-binding CuBa3 couple during the reoxidation of cytochrome oxidase is discussed in terms of an integrated structure containing CuB, cytochrome a3 and O2.

Clore, G M; Andreasson, L E; Karlsson, B; Aasa, R; Malmstrom, B G

1980-01-01

140

Excitation and decay of giant multipole resonances in intermediate energy heavy ion reactions  

SciTech Connect

The role of intermediate energy heavy ions in the study of giant multipole resonances is explored, with emphasis on gamma decay coincidence experiments. Experiments on /sup 208/Pb bombarded by 84 MeV/nucleon /sup 17/O are discussed and compared with earlier work at 22 MeV/nucleon. The role of Coulomb excitation in the 84 MeV/nucleon data is emphasized and some consequences for study of isovector resonance strength are explored. A comparison of the excitation and decay of the isovector giant dipole resonance in /sup 208/Pb and /sup 209/Bi excited with 84 MeV/nucleon /sup 17/O scattering is presented. 35 refs., 16 figs., 1 tab.

Beene, J.R.; Bertrand, F.E.

1989-01-01

141

CO2 activation and carbonate intermediates: an operando AP-XPS study of CO2 electrolysis reactions on solid oxide electrochemical cells.  

PubMed

Through the use of ambient pressure X-ray photoelectron spectroscopy and specially designed ceria-based solid oxide electrochemical cells, carbon dioxide (CO2) electrolysis reactions (CO2 + 2e(-)? CO + O(2-)) and carbon monoxide (CO) electro-oxidation reactions (CO + O(2-)? CO2 + 2e(-)) over cerium oxide electrodes have been investigated in the presence of 0.5 Torr CO-CO2 gas mixtures at ?600 °C. Carbonate species (CO3(2-)) are identified on the ceria surface as reaction intermediates. When CO2 electrolysis is promoted on ceria electrodes at +2.0 V applied bias, we observe a higher concentration of CO3(2-) over a 400 ?m-wide active region on the ceria surface, accompanied by Ce(3+)/Ce(4+) redox changes. This increase in the CO3(2-) steady-state concentration suggests that the process of pre-coordination of CO2 to the ceria surface to form a CO3(2-) intermediate (CO2(g) + O(2-)(surface)? CO3(2-)(surface)) precedes a rate-limiting electron transfer process involving CO3(2-) reduction to give CO and oxide ions (CO3(2-)(surface) + 2Ce(3+)? CO(g) + 2O(2-)(surface) + 2Ce(4+)). When the applied bias is switched to -1.5 V to promote CO electro-oxidation on ceria, the surface CO3(2-) concentration slightly decreases from the equilibrium value, suggesting that the electron transfer process is also a rate-limiting process in the reverse direction. PMID:24806971

Yu, Yi; Mao, Baohua; Geller, Aaron; Chang, Rui; Gaskell, Karen; Liu, Zhi; Eichhorn, Bryan W

2014-06-21

142

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

SciTech Connect

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.

Vincent, Jonathan; Eklund, Mattias; Davidsson, Jan [Department of Photochemistry and Molecular Science, Uppsala University, P.O. Box 523, S-751 20 Uppsala (Sweden); Andersson, Magnus; Woehri, Annemarie B. [Department of Chemical and Biological Engineering, Chalmers University of Technology, P.O. Box 462, S-405 30 Gothenburg (Sweden); Odelius, Michael [FYSIKUM, Stockholm University, Albanova, S-106 91 Stockholm (Sweden); Malmerberg, Erik; Neutze, Richard [Department of Chemistry, Biochemistry and Biophysics, Gothenburg University, P.O. Box 462, S-405 30 Gothenburg (Sweden); Kong, Qingyu; Wulff, Michael [European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble (France)

2009-04-21

143

a Study of the DEUTERON(PROTON,2PROTON)NEUTRON Reaction at Intermediate Energy  

Microsoft Academic Search

Exclusive cross sections for the ('2)H(p,2p)n reaction at beam energies of 507 and 508 MeV have been measured at various kinematics. The results are compared with the predictions of the impulse approximation and of a calculation of the 6 lowest order terms of a multiple scattering expansion of the (tau)-matrix. At small internal momenta larger than 200 MeV\\/c a drastic

Vina Alkesh Punjabi

1986-01-01

144

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

SciTech Connect

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)

Hoffman, M.Z.

1992-07-31

145

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

PubMed Central

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.

Behm, R Jurgen

2014-01-01

146

Cobalt catalysis in the gas phase: experimental characterization of cobalt(I) complexes as intermediates in regioselective Diels-Alder reactions.  

PubMed

In situ-formed cobalt(I) complexes are proposed to act as efficient catalysts in regioselective Diels-Alder reactions of unactivated substrates such as 1,3-dienes and alkynes. We report the first experimental evidence for the in situ reduction of CoBr2(dppe) [dppe = 1,2-bis(diphenylphosphino)ethane] by Zn/ZnI2 to [Co(I)(dppe)](+) by means of electrospray MS(n) experiments. Additionally, the reactivities of Co(II) and Co(I) dppe complexes toward the Diels-Alder substrates isoprene and phenylacetylene were probed in gas-phase ion/molecule reactions (IMRs). Isoprene and phenylacetylene were introduced into the mass spectrometer via the buffer gas flow of a linear ion trap. The IMR experiments revealed a significantly higher substrate affinity of [Co(I)(dppe)](+) compared with [Co(II)Br(dppe)](+). Furthermore, the central intermediate of the solution-phase cobalt-catalyzed Diels-Alder reaction, [Co(I)(dppe)(isoprene)(phenylacetylene)](+), could be generated via IMR and examined in the gas phase. Collision activation of this complex ion delivered evidence for the gas-phase reaction of isoprene with phenylacetylene in the coordination sphere of the cobalt ion. The experimental findings are consistent with the results of quantum-chemical calculations on all of the observed Co(I) dppe complex ions. The results constitute strong analytical evidence for the formation and importance of different cobalt(I) species in regioselective Diels-Alder reactions of unactivated substrates and identify [Co(I)(dppe)](+) as the active Diels-Alder catalyst. PMID:24044877

Fiebig, Lukas; Kuttner, Julian; Hilt, Gerhard; Schwarzer, Martin C; Frenking, Gernot; Schmalz, Hans-Günther; Schäfer, Mathias

2013-10-18

147

Study of the /sup 2/H(p,2p)n reaction at intermediate energy  

SciTech Connect

Exclusive cross sections for the /sup 2/H(p,2p)n reaction at beam energies of 507 and 508 MeV have been measured at various kinematics. The results are compared with the predictions of the impulse approximation and of a calculation of the 6 lowest order terms of a multiple scattering expansion of the tau-matrix. At small internal momenta larger than 200 MeV/c a drastic deviation from theory is confirmed. Possible causes for these results are discussed.

Punjabi, V.A.

1986-01-01

148

Chemistry of low-valent molybdenum phosphite complexes: Models of seven-coordinate reaction intermediates  

PubMed Central

A simple synthesis of the zerovalent complex Mo[P(OCH3)3]6 has been devised from a potassium reduction of MoCl4(tetrahydrofuran)2 followed by reaction with trimethyl phosphite at 70°. Protonation of this octahedral complex gave only low yields of the expected seven-coordinate hydride, HMo[P(OCH3)3]6+. The major product was an octahedral nonhydridic cation, Mo[P(OCH3)3]5P(OCH3)2+, derived from proton cleavage of the P—O phosphite ester bond. This octahedral cation was stereochemically nonrigid, apparently through facile methoxy group migration. Close packing by methoxy groups in this fluxional cation was established through an x-ray crystallographic study of Mo[P(OCH3)3]5P(OCH3)2+-PF6-. Extended reaction of trifluoroactic acid with Mo[P(OCH3)3]6 yielded the seven-coordinate hydride, HMo[P(OCH3)3]4(O2CCF3), which was near pentagonal bipyramidal and was stereochemically nonrigid.

Muetterties, E. L.; Kirner, J. F.; Evans, W. J.; Watson, P. L.; Abdel-Meguid, S.; Tavanaiepour, I.; Day, V. W.

1978-01-01

149

Directly measuring reaction kinetics of ?QOOH--a crucial but elusive intermediate in hydrocarbon autoignition.  

PubMed

Hydrocarbon autoignition has long been an area of intense fundamental chemical interest, and is a key technological process for emerging clean and efficient combustion strategies. Carbon-centered radicals containing an -OOH group, commonly denoted ?QOOH radicals, are produced by isomerization of the alkylperoxy radicals that are formed in the first stages of oxidation. These ?QOOH radicals are among the most critical species for modeling autoignition, as their reactions with O2 are responsible for chain branching below 1000 K. Despite their importance, no ?QOOH radicals have ever been observed by any means, and only computational and indirect experimental evidence has been available on their reactivity. Here, we directly produce a ?QOOH radical, 2-hydroperoxy-2-methylprop-1-yl, and experimentally determine rate coefficients for its unimolecular decomposition and its association reaction with O2. The results are supported by high-level theoretical kinetics calculations. Our experimental strategy opens up a new avenue to study the chemistry of ?QOOH radicals in isolation. PMID:23689671

Zádor, Judit; Huang, Haifeng; Welz, Oliver; Zetterberg, Johan; Osborn, David L; Taatjes, Craig A

2013-07-14

150

Modeling stopped-flow data for nucleic acid duplex formation reactions: the importance of off-path intermediates.  

PubMed

Evidence for unexpected off-path intermediates to DNA duplex formation is presented. These off-path intermediates are shown to involve unimolecular and, in one case, bimolecular structure in one of the single strands of complementary DNA. Three models are developed to account for the observed single-stranded structures that are formed in parallel with duplex formation. These models are applied to the analysis of stopped-flow data for eight different nonself-complementary duplex formation reactions in order to extract the elementary rate constant for formation of the duplex from the complementary random coil single-stranded DNA. The free energy of activation (at 25 °C) for the denaturation of each duplex is calculated from these data and is shown to have a linear correlation to the overall standard free energy for duplex formation (also at 25 °C). Duplexes that contain mismatches obey a parallel linear free-energy (LFE) relationship with a y-intercept that is greater than that of duplexes without mismatches. Slopes near unity for the LFE relationships indicate that all duplexes go through an early, unstructured transition state. PMID:23902467

Sikora, Jacqueline R; Rauzan, Brittany; Stegemann, Rachel; Deckert, Alice

2013-08-01

151

Reaction of iminopropadienones with amines: mechanistic explanations of zwitterionic intermediate, ketene and ketenimine formation.  

PubMed

The complex reaction of thermally generated iminopropadienones with amines in the gas phase and upon matrix deposition and its varying product composition is investigated using density functional theory. In the high energy gas phase addition a single amine molecule reacts readily with iminopropadienone with the decisive step being a 1,3-hydrogen shift and activation barriers of at least 100 kJ/mol. In accordance with the experiment, the formation of ketenes is favored. In the condensed phase of an amine matrix, the utilization of amine dimers both as reagents and as explicit solvents lowers the activation energy required to a feasible 20-30 kJ/mol and predicts ketenimines as the main products, as observed experimentally. PMID:18759423

Koch, Rainer; Finnerty, Justin J; Bruhn, Torsten; Borget, Fabien; Wentrup, Curt

2008-09-25

152

Direct-semidirect and multistep processes in radiative proton capture reactions at intermediate energies  

SciTech Connect

The energy dependence of the 60/sup 0/ proton capture differential cross sections for /sup 11/B and /sup 27/Al targets in the proton bombarding energy range of 20 to 100 MeV were measured. The angular distributions and analyzing powers at proton bombarding energies 28.3, 49.2 MeV (/sup 11/B target) and 20.8 MeV (/sup 27/Al target) were measured. A direct-semidirect model using a global optical model parameters was used to compare with experimental data. The calculations with an energy-dependent set of OMP produce reasonable fits to the experimental data from the region of the GDR up to approximately 40 MeV. However, at energies above approx.40 MeV, the DSD differential cross sections overestimate the experimental value. The calculations with a fixed set of OMP fit the experimental data for the entire energy region. The DSD model predicts angular distributions and analyzing powers reasonably well. The second excited state of the /sup 7/Be from the reaction /sup 6/Li(p,..gamma..) was investigated to explore whether multistep processes are important in radiative capture reactions. The energy dependence, angular distributions, and analyzing powers for the 7/2/sup -/ state were obtained. It was found that this state cannot be explained by a DSD model. A theoretical model was developed and a computer program was made to calculate multistep processes. It was found that the results from the theoretical calculation failed to match the experimental data.

Kim, W.

1986-01-01

153

Anionic ligand effect on the nature of epoxidizing intermediates in iron porphyrin complex-catalyzed epoxidation reactions.  

PubMed

We have studied an anionic ligand effect in iron porphyrin complex-catalyzed competitive epoxidations of cis- and trans-stilbenes by various terminal oxidants and found that the ratios of cis- to trans-stilbene oxide products formed in competitive epoxidations were markedly dependent on the ligating nature of the anionic ligands. The ratios of cis- to trans-stilbene oxides obtained in the reactions of Fe(TPP)X (TPP = meso-tetraphenylporphinato dianion and X(-) = anionic ligand) and iodosylbenzene (PhIO) were 14 and 0.9 when the X(-) of Fe(TPP)X was Cl(-) and CF(3)SO(3)(-), respectively. An anionic ligand effect was also observed in the reactions of an electron-deficient iron(III) porphyrin complex containing a number of different anionic ligands, Fe(TPFPP)X [TPFPP = meso-tetrakis(pentafluorophenyl)porphinato dianion and X(-) = anionic ligand], and various terminal oxidants such as PhIO, m-chloroperoxybenzoic acid (m-CPBA), tetrabutylammonium oxone (TBAO), and H(2)O(2). While high ratios of cis- to trans-stilbene oxides were obtained in the reactions of iron porphyrin catalysts containing ligating anionic ligands such as Cl(-) and OAc(-), the ratios of cis- to trans-stilbene oxide were low in the reactions of iron porphyrin complexes containing nonligating or weakly ligating anionic ligands such as SbF(6)(-), CF(3)SO(3)(-), and ClO(4)(-). When the anionic ligand was NO(3)(-), the product ratios were found to depend on terminal oxidants and olefin concentrations. We suggest that the dependence of the product ratios on the anionic ligands of iron(III) porphyrin catalysts is due to the involvement of different reactive species in olefin epoxidation reactions. That is, high-valent iron(IV) oxo porphyrin cation radicals are generated as a reactive species in the reactions of iron porphyrin catalysts containing nonligating or weakly ligating anionic ligands such as SbF(6)(-), CF(3)SO(3)(-), and ClO(4)(-), whereas oxidant-iron(III) porphyrin complexes are the reactive intermediates in the reactions of iron porphyrin catalysts containing ligating anionic ligands such as Cl(-) and OAc(-). PMID:12099867

Nam, Wonwoo; Jin, Sook Won; Lim, Mi Hee; Ryu, Ju Yeon; Kim, Cheal

2002-07-15

154

Quantification of Diesel Fuel Intermediate-Volatile Organic Compounds by Proton Transfer Reaction Mass Spectrometer  

NASA Astrophysics Data System (ADS)

To understand secondary organic aerosol formation it is important to observe the precursors. The large hydrocarbon species found in diesel exhaust is thought to be a major contributor to SOA formation in urban environments. A new method was developed utilizing a proton transfer reaction mass spectrometer (PTR-MS) to measure long chain alkanes (C12 and above). There are two issues involved in directly measuring these alkanes. Diesel exhaust is present in relatively low concentrations, which often close or below the limits of detection. A preconcentration system was built to collect a large sample to increase our signal to noise. Lab tests show that all the alkanes fragment to a common set of m/z values. Interferences from other species occur at these m/z values. To overcome this obstacle, the preconcentration system was operated to discriminate between VOCs and IVOCs. This will allow for minimal interference and better quantification of the alkanes. The PTR-MS was outfitted with a new sample system that contains two inlets to allow for the measurement of VOCs while the IVOCs are being collected, which means a wide range of SOA precursors can be measured. Results from the Carbonaceous Aerosol and Radiative Effects Study in Sacramento, CA will be presented.

Erickson, M. H.; Jobson, B. T.

2010-12-01

155

Observation of organometallic and radical intermediates formed during the reaction of methyl-coenzyme M reductase with bromoethanesulfonate.  

PubMed

Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the final step of methane formation, in which methyl-coenzyme M (2-methylthioethanesulfonate, methyl-SCoM) is reduced with coenzyme B (N-(7-mercaptoheptanoyl)threonine phosphate, CoBSH) to form methane and the heterodisulfide CoBS-SCoM. The active dimeric form of MCR contains two Ni(I)-F(430) prosthetic groups, one in each monomer. This report describes studies of the reaction of the active Ni(I) state of MCR (MCR(red1)) with BES (2-bromoethanesulfonate) and CoBSH or its analogue, CoB(6)SH (N-(6-mercaptohexanoyl)threonine phosphate), by transient kinetic measurements using EPR and UV-visible spectroscopy and by global fits of the data. This reaction is shown to lead to the formation of three intermediates, the first of which is assigned as an alkyl-Ni(III) species that forms as the active Ni(I)-MCR(red1) state of the enzyme decays. Subsequently, a radical (MCR(BES) radical) is formed that was characterized by multifrequency electron paramagnetic resonance (EPR) studies at X- ( approximately 9 GHz), Q- ( approximately 35 GHz), and D- ( approximately 130 GHz) bands and by electron-nuclear double resonance (ENDOR) spectroscopy. The MCR(BES) radical is characterized by g-values at 2.00340 and 1.99832 and includes a strongly coupled nonexchangeable proton with a hyperfine coupling constant of 50 MHz. Based on transient kinetic measurements, the formation and decay of the radical coincide with a species that exhibits absorption peaks at 426 and 575 nm. Isotopic substitution, multifrequency EPR, and ENDOR spectroscopic experiments rule out the possibility that MCR(BES) is a tyrosyl radical and indicate that if a tyrosyl radical is formed during the reaction, it does not accumulate to detectable levels. The results provide support for a hybrid mechanism of methanogenesis by MCR that includes both alkyl-Ni and radical intermediates. PMID:20597483

Li, Xianghui; Telser, Joshua; Kunz, Ryan C; Hoffman, Brian M; Gerfen, Gary; Ragsdale, Stephen W

2010-08-17

156

Chromophoric spin-labeled ?-lactam antibiotics for ENDOR structural characterization of reaction intermediates of class A and class C ?-lactamases  

NASA Astrophysics Data System (ADS)

The chromophoric spin-label substrate 6- N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M -1 cm -1 at 275 nm compared to 670 M -1 cm -1 at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/ KM, determined under initial velocity conditions, were 637±36 s -1 and 13.8±1.4×10 6 M -1 s -1, respectively, for hydrolysis catalyzed by TEM-1 ?-lactamase of E. coli, and 0.5±0.04 s -1 and 3.9±0.4×10 4 M -1 s -1 for hydrolysis catalyzed by the ?-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 ?-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H 2O (30:70, v:v) cryosolvent mixtures buffered to pH ? 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 °C was ?3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 ?-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme.

Mustafi, Devkumar; Hofer, Jennifer E.; Huang, Wanzhi; Palzkill, Timothy; Makinen, Marvin W.

2004-05-01

157

Reaction Intermediates of Quinol Oxidation in a Photoactivatable System that Mimics Electron Transfer in the Cytochrome bc1 Complex  

SciTech Connect

Current competing models for the two-electron oxidation of quinol (QH{sub 2}) at the cytochrome bc{sub 1} complex and related complexes have different requirements for the reaction intermediate. At present, the intermediate species of the enzymatic oxidation process have not been observed or characterized, probably due to their transient nature. Here, we use a biomimetic oxidant, Ru(bpy){sub 2}(pbim)(PF6)2 (bpy = 2,2'-dipyridyl, pbim = 2-(2-benzimidazolate)pyridine) in an aprotic medium to probe the oxidation of the ubiquinol analogue, 2,3-dimethoxy-5-methyl-1,4-benzoquinol (UQH{sub 2}-0), an the plastoquinol analogue, trimethyl-1,4-benzoquinol (TMQH{sub 2}-0), using time-resolved and steady state spectroscopic techniques. This system qualitatively reproduces key features observed during ubiquinol oxidation by the mitochondrial cytochrome bc1 complex. Comparison of isotope dependent activation properties in the native and synthetic systems, as well as, analysis of the time-resolved direct-detection electron para magnetic resonance signals in the synthetic system allows us to conclude that: (1) the initial and rate-limiting step in quinol oxidation, both in the biological and biomimetic systems, involves electron and proton transfer, probably via a proton coupled electron transfer mechanism; (2) a neutral semiquinone intermediate is formed in the biomimetic system; and (3) oxidation of the QH*/QH{sub 2} couple for UQH{sub 2}-0, but not TMQH{sub 2}-0, exhibits a non-classical primary deuterium kinetic isotope effect on its Arrhenius activation energy ({Delta}G{sup TS}), where {Delta}G{sup TS} for the protiated form is larger than for the deuterated form. The same behavior is observed during steady state turnover of the cyt bc{sub 1} complex using ubiquinol, but not plastoquinol, as a substrate, leading to the conclusion that similar chemical pathways are involved in both systems. The synthetic system is an unambiguous n=1 electron acceptor and it is thus inferred that sequential oxidation of ubiquinol (by two sequential n=1 processes) is more rapid than a truly concerted (n=2) oxidation in the cyt bc{sub 1} complex.

Cape, Jonathan L.; Bowman, Michael K.; Kramer, David M.

2005-03-30

158

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

NASA Technical Reports Server (NTRS)

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.

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

1990-01-01

159

Roles of different intermediate active species in the mineralization reactions of phenolic pollutants under a UVA\\/C photo-Fenton process  

Microsoft Academic Search

The roles of different intermediate oxidative species, such as singlet oxygen, triplet oxygen, superoxide radical anions and hydroperoxy or hydroxyl radicals, were studied in the mineralization reactions of solutions containing a mixture of three phenolic compounds (namely gallic, p-coumaric and protocatechuic acids). The degradation process that was developed was a ferrioxalate-induced artificial ultraviolet (UV)-A\\/C photo-Fenton system. Reactions were carried out

J. M. Monteagudo; A. Durán; I. San Martin; A. Carnicer

2011-01-01

160

ACC-Oxidase like activity of a copper (II)-ACC complex in the presence of hydrogen peroxide. Detection of a reaction intermediate at low temperature.  

PubMed

A Cu(II)-ACC complex [(Bpy)Cu(ACC)(H2O)]ClO4 (1) was prepared and its treatment with hydrogen peroxide gave rise to ethylene production in an ACC-Oxidase like activity. A brown species that could be a key intermediate in the reaction was detected at low temperature. PMID:16491198

Ghattas, Wadih; Gaudin, Christian; Giorgi, Michel; Rockenbauer, Antal; Simaan, A Jalila; Réglier, Marius

2006-03-01

161

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

PubMed

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. PMID:24600881

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

2014-01-01

162

Cationic intermediates in oxidative addition reactions of Cl2 to [PtCl2(cis-1,4-DACH)].  

PubMed

Oxidative addition and reductive elimination are fundamental processes in transition-metal chemistry. New interest in this field has been generated by the exploitation of platinum(IV) complexes as antitumor drugs. The two extra ligands can be used to render these species more resistant to attack by biological nucleophiles compared to their platinum(II) counterparts, to anchor additional pharmacologically active moieties, or, finally, to target the drug to specific sites by conferring responsiveness to some type of chemotaxis. On the other hand, platinum(IV) species are considered to be prodrugs and to require reduction to Pt(II) to become active. Thus, reductive elimination promoted by biological reducing agents becomes an important issue and it too could be exploited for targeting purposes. In this paper, we investigated the oxidation step in more detail and shown that, independent of the solvent used, a solvent molecule assists the reaction by entering in a trans position with respect to the attacking oxidant. In the case of bifunctional solvent molecules, such as dimethylsulfoxide, both S- and O-coordinated species are formed, the latter being thermodynamically favored. The substitution of the axially coordinated solvent molecule by a free chloride ion is found to be quite slow in organic solvents, as well as in water. It is also shown that the intermediate solvato-species can be exploited for binding just one molecule of another substrate in the axial position. PMID:22064914

Margiotta, Nicola; Ranaldo, Rosa; Intini, Francesco P; Natile, Giovanni

2011-12-28

163

A novel microfluidic rapid freeze-quench device for trapping reactions intermediates for high field EPR analysis  

NASA Astrophysics Data System (ADS)

Rapid freeze quench electron paramagnetic resonance (RFQ)-EPR is a method for trapping short lived intermediates in chemical reactions and subjecting them to EPR spectroscopy investigation for their characterization. Two (or more) reacting components are mixed at room temperature and after some delay the mixture is sprayed into a cold trap and transferred into the EPR tube. A major caveat in using commercial RFQ-EPR for high field EPR applications is the relatively large amount of sample needed for each time point, a major part of which is wasted as the dead volume of the instrument. The small sample volume (˜2 ?l) needed for high field EPR spectrometers, such as W-band (˜3.5 T, 95 GHz), that use cavities calls for the development of a microfluidic based RFQ-EPR apparatus. This is particularly important for biological applications because of the difficulties often encountered in producing large amounts of intrinsically paramagnetic proteins and spin labeled nucleic acid and proteins. Here we describe a dedicated microfluidic based RFQ-EPR apparatus suitable for small volume samples in the range of a few ?l. The device is based on a previously published microfluidic mixer and features a new ejection mechanism and a novel cold trap that allows collection of a series of different time points in one continuous experiment. The reduction of a nitroxide radical with dithionite, employing the signal of Mn2+ as an internal standard was used to demonstrate the performance of the microfluidic RFQ apparatus.

Kaufmann, Royi; Yadid, Itamar; Goldfarb, Daniella

2013-05-01

164

Chlorinations catalyzed by chloroperoxidase occur via diffusible intermediate(s) and the reaction components play multiple roles in the overall process.  

PubMed

The chlorination mechanism of the fungal enzyme chloroperoxidase (CPO) has been debated for (1) active site chlorination and (2) diffusible species mediated chlorination. Based upon the conversion of approximately 35 different substrates belonging to different reactive groups, it was found that substrate dimensions and topography had no pronounced effect on rates of CPO chlorination reaction. Epoxidation of indene was dependent on its concentration where as chlorination was not. Also, effective conversion was seen in the chlorination mixture for substrates that could not be epoxidized or sulfoxidized. Some insoluble substrates and certain molecules that exceeded the active site dimensions were chlorinated at rates comparable to the rates required for CPO's more natural substrate, monochlorodimedone. By terminating the enzymatic reaction with an active site ligand (azide), the amount of diffusible species was correlated to CPO in the reaction mixture. The preferential utilization of a substrate, earlier attributed to the active site, is found to be due to the specificity afforded by the reaction environment. It was found that the reaction medium components of peroxide, chloride and hydronium ions affected the reaction rates through varying roles in the enzymatic and non-enzymatic process. Besides these experimental evidences, key mechanistic and kinetic arguments are presented to infer that the final chlorine transfer occurs outside the active site via a diffusible species. PMID:16870515

Murali Manoj, Kelath

2006-08-01

165

Prescription surveillance and polymerase chain reaction testing to identify pathogens during outbreaks of infection.  

PubMed

Syndromic surveillance, including prescription surveillance, offers a rapid method for the early detection of agents of bioterrorism and emerging infectious diseases. However, it has the disadvantage of not considering definitive diagnoses. Here, we attempted to definitively diagnose pathogens using polymerase chain reaction (PCR) immediately after the prescription surveillance system detected an outbreak. Specimens were collected from 50 patients with respiratory infections. PCR was used to identify the pathogens, which included 14 types of common respiratory viruses and Mycoplasma pneumoniae. Infectious agents including M. pneumoniae, respiratory syncytial virus (RSV), rhinovirus, enterovirus, and parainfluenza virus were detected in 54% of patients. For the rapid RSV diagnosis kit, sensitivity was 80% and specificity was 85%. For the rapid adenovirus diagnosis kit, no positive results were obtained; therefore, sensitivity could not be calculated and specificity was 100%. Many patients were found to be treated for upper respiratory tract infections without the diagnosis of a specific pathogen. In Japan, an outbreak of M. pneumoniae infection began in 2011, and our results suggested that this outbreak may have included false-positive cases. By combining syndromic surveillance and PCR, we were able to rapidly and accurately identify causative pathogens during a recent respiratory infection outbreak. PMID:23509772

Sugiura, Hiroaki; Fujimoto, Tsuguto; Sugawara, Tamie; Hanaoka, Nozomu; Konagaya, Masami; Kikuchi, Kiyoshi; Hanada, Eisuke; Okabe, Nobuhiko; Ohkusa, Yasushi

2013-01-01

166

Prescription Surveillance and Polymerase Chain Reaction Testing to Identify Pathogens during Outbreaks of Infection  

PubMed Central

Syndromic surveillance, including prescription surveillance, offers a rapid method for the early detection of agents of bioterrorism and emerging infectious diseases. However, it has the disadvantage of not considering definitive diagnoses. Here, we attempted to definitively diagnose pathogens using polymerase chain reaction (PCR) immediately after the prescription surveillance system detected an outbreak. Specimens were collected from 50 patients with respiratory infections. PCR was used to identify the pathogens, which included 14 types of common respiratory viruses and Mycoplasma pneumoniae. Infectious agents including M. pneumoniae, respiratory syncytial virus (RSV), rhinovirus, enterovirus, and parainfluenza virus were detected in 54% of patients. For the rapid RSV diagnosis kit, sensitivity was 80% and specificity was 85%. For the rapid adenovirus diagnosis kit, no positive results were obtained; therefore, sensitivity could not be calculated and specificity was 100%. Many patients were found to be treated for upper respiratory tract infections without the diagnosis of a specific pathogen. In Japan, an outbreak of M. pneumoniae infection began in 2011, and our results suggested that this outbreak may have included false-positive cases. By combining syndromic surveillance and PCR, we were able to rapidly and accurately identify causative pathogens during a recent respiratory infection outbreak.

Sugiura, Hiroaki; Fujimoto, Tsuguto; Sugawara, Tamie; Hanaoka, Nozomu; Konagaya, Masami; Kikuchi, Kiyoshi; Hanada, Eisuke; Okabe, Nobuhiko; Ohkusa, Yasushi

2013-01-01

167

The carbon module labeling (CAMOLA) technique: a useful tool for identifying transient intermediates in the formation of maillard-type target molecules.  

PubMed

Although the Maillard reaction is a well-known source of aroma and taste compounds in processed foods, a systematic correlation of the concentrations of most of the reaction products identified so far with human perception has scarcely been performed. Furthermore, the influence of process parameters on yields and formation mechanisms of key flavor compounds has not been systematically studied. In this short state-of-the-art review, concepts to characterize flavor-active food constituents are briefly discussed, and approaches to elucidate formation mechanisms from labeling experiments and isotopomeric quantitation are highlighted on the basis of results obtained in the author's laboratory. PMID:16037244

Schieberle, Peter

2005-06-01

168

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

SciTech Connect

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.

Hoffman, M.Z.

1991-12-31

169

A Topologically Based Procedure to Identify Invariant Reactions for Isobaric Multicomponent Phase Diagrams  

NASA Astrophysics Data System (ADS)

Invariant reactions are a common occurrence in multicomponent phase diagrams, and their underlying topological basis can be correlated with the numbers of reactant and product phases involved. Understanding and manipulating invariant reactions demand in-depth knowledge in phase diagram topologies. Based on simple equilibrium calculations, a topologically based procedure is proposed to establish invariant reactions for isobaric multicomponent phase diagrams.

Liu, Yajun; Kang, Zhitao

2014-06-01

170

A Topologically Based Procedure to Identify Invariant Reactions for Isobaric Multicomponent Phase Diagrams  

NASA Astrophysics Data System (ADS)

Invariant reactions are a common occurrence in multicomponent phase diagrams, and their underlying topological basis can be correlated with the numbers of reactant and product phases involved. Understanding and manipulating invariant reactions demand in-depth knowledge in phase diagram topologies. Based on simple equilibrium calculations, a topologically based procedure is proposed to establish invariant reactions for isobaric multicomponent phase diagrams.

Liu, Yajun; Kang, Zhitao

2013-11-01

171

A candidate LiBH4 for hydrogen storage: Crystal structures and reaction mechanisms of intermediate phases  

NASA Astrophysics Data System (ADS)

First-principles calculation and x-ray diffraction simulation methods have been used to explore crystal structures and reaction mechanisms of the intermediate phases involved in dehydriding of LiBH4. LiBH4 was found to dehydride via two sequential steps: first dehydriding through LiBH, followed by the dehydriding of LiBH through LiB. The first step, which releases 13.1 wt. % hydrogen, was calculated to have an activation barrier of 2.33 eV per formula unit and was endothermic by 1.28 eV per formula unit, while the second step was endothermic by 0.23 eV per formula unit. On the other hand, if LiBH4 and LiBH each donated one electron, possibly to the catalyst doped on their surfaces, it was found that the barrier for the first step was reduced to 1.50 eV. This implies that the development of the catalyst to induce charge migration from the bulk to the surface is essential to make LiBH4 usable as a hydrogen storage material in a moderate temperature range, which is also important to stabilize the low-temperature structure of Pnma (no. 62) LiBH on dehydrogenation. Consequently, the high 13.1 wt. % hydrogen available from the dehydriding of LiBH4 and LiBH and their phase stability on Pnma when specific catalysts were used suggest that LiBH4 has good potential to be developed as the hydrogen storage medium capable of releasing the Department of Energy target of 6.5 wt. % for a hydrogen fuel cell car in a moderate temperature range.

Kang, Jeung Ku; Kim, Se Yun; Han, Young Soo; Muller, Richard P.; Goddard, William A.

2005-09-01

172

Spectroscopic investigations of intermediates in the reaction of cytochrome P450(BM3)-F87G with surrogate oxygen atom donors.  

PubMed

Rapid mixing of substrate-free ferric cytochrome P450(BM3)-F87G with m-chloroperoxybenzoic acid (mCPBA) resulted in the sequential formation of two high-valent intermediates. The first was spectrally similar to compound I species reported previously for P450(CAM) and CYP 119 using mCPBA as an oxidant, and it featured a low intensity Soret absorption band characterized by shoulder at 370nm. This is the first direct observation of a P450 compound I intermediate in a type II P450 enzyme. The second intermediate, which was much more stable at pH values below 7.0, was characterized by an intense Soret absorption peak at 406nm, similar to that seen with P450(CAM) [T. Spolitak, J.H. Dawson, D.P. Ballou, J. Biol. Chem. 280 (2005) 20300-20309]. Double mixing experiments in which NADPH was added to the transient 406nm-absorbing intermediate resulted in rapid regeneration of the resting ferric state, with the flavins of the flavoprotein domain in their reduced state. EPR results were consistent with this stable intermediate species being a cytochrome c peroxidase compound ES-like species containing a protein-based radical, likely localized on a nearby Trp or Tyr residue in the active site. Iodosobenzene, peracetic acid, and sodium m-periodate also generated the intermediate at 406nm, but not the 370nm intermediate, indicating a probable kinetic barrier to accumulating compound I in reactions with these oxidants. The P450 ES intermediate has not been previously reported using iodosobenzene or m-periodate as the oxygen donor. PMID:17083977

Raner, Gregory M; Thompson, Jonathan I; Haddy, Alice; Tangham, Valary; Bynum, Nicole; Ramachandra Reddy, G; Ballou, David P; Dawson, John H

2006-12-01

173

A quantitative reverse transcriptase-polymerase chain reaction assay to identify metastatic carcinoma tissue of origin.  

PubMed

Identifying the primary site in patients with metastatic carcinoma of unknown primary origin can enable more specific therapeutic regimens and may prolong survival. Twenty-three putative tissue-specific markers for lung, colon, pancreatic, breast, prostate, and ovarian carcinomas were nominated by querying a gene expression profile database and by performing a literature search. Ten of these marker candidates were then selected based on validation by reverse transcriptase-polymerase chain reaction (RT-PCR) on 205 formalin-fixed, paraffin-embedded metastatic carcinoma specimens originating from these six and from other cancer types. Next, we optimized the RNA isolation and quantitative RT-PCR methods for these 10 markers and applied the quantitative RT-PCR assay to a set of 260 metastatic tumors. We then built a gene-based algorithm that predicted the tissue of origin of metastatic carcinomas with an overall leave-one-out cross-validation accuracy of 78%. Lastly, our assay demonstrated an accuracy of 76% when tested on an independent set of 48 metastatic samples, 37 of which were either a known primary or initially presented as carcinoma of unknown primary but were subsequently resolved. PMID:16825504

Talantov, Dimitri; Baden, Jonathan; Jatkoe, Tim; Hahn, Kristina; Yu, Jack; Rajpurohit, Yashoda; Jiang, Yiqiu; Choi, Chang; Ross, Jeffrey S; Atkins, David; Wang, Yixin; Mazumder, Abhijit

2006-07-01

174

A Quantitative Reverse Transcriptase-Polymerase Chain Reaction Assay to Identify Metastatic Carcinoma Tissue of Origin  

PubMed Central

Identifying the primary site in patients with metastatic carcinoma of unknown primary origin can enable more specific therapeutic regimens and may prolong survival. Twenty-three putative tissue-specific markers for lung, colon, pancreatic, breast, prostate, and ovarian carcinomas were nominated by querying a gene expression profile database and by performing a literature search. Ten of these marker candidates were then selected based on validation by reverse transcriptase-polymerase chain reaction (RT-PCR) on 205 formalin-fixed, paraffin-embedded metastatic carcinoma specimens originating from these six and from other cancer types. Next, we optimized the RNA isolation and quantitative RT-PCR methods for these 10 markers and applied the quantitative RT-PCR assay to a set of 260 metastatic tumors. We then built a gene-based algorithm that predicted the tissue of origin of metastatic carcinomas with an overall leave-one-out cross-validation accuracy of 78%. Lastly, our assay demonstrated an accuracy of 76% when tested on an independent set of 48 metastatic samples, 37 of which were either a known primary or initially presented as carcinoma of unknown primary but were subsequently resolved.

Talantov, Dimitri; Baden, Jonathan; Jatkoe, Tim; Hahn, Kristina; Yu, Jack; Rajpurohit, Yashoda; Jiang, Yiqiu; Choi, Chang; Ross, Jeffrey S.; Atkins, David; Wang, Yixin; Mazumder, Abhijit

2006-01-01

175

A PAN-CARINA YOUNG STELLAR OBJECT CATALOG: INTERMEDIATE-MASS YOUNG STELLAR OBJECTS IN THE CARINA NEBULA IDENTIFIED VIA MID-INFRARED EXCESS EMISSION  

SciTech Connect

We present a catalog of 1439 young stellar objects (YSOs) spanning the 1.42 deg{sup 2} 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 {mu}m IR spectral energy distributions of the YSOs to constrain physical properties. Our Pan-Carina YSO Catalog (PCYC) is dominated by intermediate-mass (2 M{sub sun} < m {approx}< 10 M{sub 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 x 10{sup 4} YSOs and a present-day star formation rate (SFR) of >0.008 M{sub sun} yr{sup -1}. The global SFR in the Carina Nebula, averaged over the past {approx}5 Myr, has been approximately constant.

Povich, Matthew S.; Getman, Konstantin V.; Townsley, Leisa K.; Broos, Patrick S. [Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States); Smith, Nathan [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Majewski, Steven R.; Indebetouw, Remy [Department of Astronomy, University of Virginia, P.O. Box 400325, Charlottesville, VA 22904-4325 (United States); Babler, Brian L.; Meade, Marilyn R.; Whitney, Barbara A. [Department of Astronomy, University of Wisconsin, 475 N. Charter Street, Madison, WI 53706 (United States); Robitaille, Thomas P. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Stassun, Keivan G. [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Yonekura, Yoshinori [Department of Physical Science, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531 (Japan); Fukui, Yasuo, E-mail: povich@astro.psu.edu [Department of Astrophysics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

2011-05-01

176

Studies of intermediate-mass fragment emission in the 3He+natAg, 197Au reactions between 0.48 and 3.6 GeV  

Microsoft Academic Search

Intermediate-mass fragments formed in reactions of 3He ions with natAg and 197Au targets have been studied at five energies between 0.48 and 3.6 GeV. Inclusive measurements show that as the bombarding energy increases, there is a strong enhancement in fragment cross sections and a trend toward isotropic angular distributions. Between 0.90 and 1.8 GeV, a change in the emission mechanism

S. J. Yennello; K. Kwiatkowski; E. C. Pollacco; C. Volant; Y. Cassagnou; R. Dayras; D. E. Fields; S. Harar; E. Hourani; R. Legrain; E. Norbeck; R. Planeta; J. L. Wile; N. R. Yoder; V. E. Viola

1993-01-01

177

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

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 accumulate during either of these reactions. These results establish that the partitioning intermediate is an alpha-imino beta,gamma-unsaturated pyridoxamine derivative with lambda max congruent to 300 nm and that the 485-nm species which accumulates in the elimination reaction is not on the replacement pathway. PMID:2405904

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

1990-01-16

178

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

PubMed Central

Velocities for the synthesis of trifluoroethyl 2-deoxy-?-D-galactopyranoside by transfer of the 2-deoxygalactosyl group from ?-galactosidase to trifluoroethanol were determined from studies of the ?-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-?-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 kROH/ks = 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-?-D-galactopyranosides by transfer of the 2-deoxygalactosyl group from ?-galactosidase to alkyl alcohols were determined from the effect of alkyl alcohols on the velocity of ?-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-?-D-galactopyranoside in a reaction where breakdown of the intermediate is rate determining. These data were used to calculate rate constant ratios kROH/ks for the reactions of eight alkyl alcohols. Absolute rate constants kROH (M?1 s?1) were calculated from kROH/ks and ks = 0.002 s?1 for the addition of water. A Brønsted coefficient of ?nuc = ?0.07 ± 0.08 was determined as the slope of a logarithmic correlation of kROH against alcohol pKa. The change from a 2-OH to a 2-H substituent at the ?-D-galactopyranosyl intermediate causes a 0.12 ± 0.04 increase in the value of ?nuc for alcohol addition. This anti-Hammond effect provides evidence that general basecatalyzed addition of alcohols to an enzyme bound ?-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.

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

2009-01-01

179

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

PubMed

Velocities for the synthesis of trifluoroethyl 2-deoxy-?-D-galactopyranoside by transfer of the 2-deoxygalactosyl group from ?-galactosidase to trifluoroethanol were determined from studies of the ?-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-?-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-?-D-galactopyranosides by transfer of the 2-deoxygalactosyl group from ?-galactosidase to alkyl alcohols were determined from the effect of alkyl alcohols on the velocity of ?-galactosidase-catalyzed cleavage of 4-nitrophenyl-2-deoxy-?-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 ?(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 ?-D-galactopyranosyl intermediate causes a 0.12 ± 0.04 increase in the value of ?(nuc) for alcohol addition. This anti-Hammond effect provides evidence that general basecatalyzed addition of alcohols to an enzyme bound ?-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. PMID:19684875

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

2008-07-01

180

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

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.

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

2009-01-01

181

Bromide ion promoted. beta. -elimination in. cap alpha. -bromo ester substrates. Evidence for an intermediate in the E2C reaction  

SciTech Connect

The TDKIE (temperature dependence of the kinetic isotope effect) criteria of transition state geometry in H-transfer reactions have been applied in the title reactions; a bent transition state consistent with the geometry of the E2C reaction has been verified by the results of intramolecular and intermolecular competition modes of determining k/sub H/k/sub D/ as a function of temperature. The extraordinary magnitude measured for the ..cap alpha.. secondary deuterium isotope effect in the E2C mechanism is reconciled with a very loose transition state and an acute angle of H-abstraction in the course of rearward approach to C/sub ..cap alpha../ by the promoter base. The virtual identity of the inter- and intramolecular isotope effects can be correlated by the assumption of a reaction intermediate of trigonal-bipyramid structure surrounding C/sub ..cap alpha../ and in which the extractable H and D atoms are equally available to the action of the promoter base. The properties of this intermediate, by way of contrast with the transition state of an S/sub N/2 process, are discussed in detail. 7 tables, 2 figures.

Kwart, H.; Gaffney, A.

1983-12-02

182

Kinetic reaction modeling framework for identifying and quantifying reductant reactivity in heterogeneous aquifer sediments.  

PubMed

Water-sediment interactions triggered by the injection of oxidized aqueous solutions into anoxic groundwater systems usually modify both the aquifer matrix and control the final aqueous composition. The identification and quantification of these reactions in complex heterogeneous systems remains a challenge for the analysis and prediction of water quality changes. Driven by the proposed injection of large quantities of oxic water into a deep anoxic heterogeneous pyritic aquifer; this study was undertaken to quantify the reactivity of aquifer sediments with respect to oxidant consumption and to characterize the variability of the reaction rates across different lithological units. A total of 53 samples were incubated for periods of 14, 37, and 50 days, during which the gas-phase was continuously monitored and the aqueous composition analyzed. A geochemical modeling framework was developed that incorporated a mixed set of equilibrium and kinetic reactions and supported the interpretation and quantification of the geochemical controls. The good agreement between simulated and experimental results of O2 consumption, CO2 production, pH, major ions, and trace metals suggests that the framework was able to successfully quantify reaction rates of competing redox and buffering reactions for the different lithological aquifer material. PMID:20695491

Descourvieres, Carlos; Prommer, Henning; Oldham, Carolyn; Greskowiak, Janek; Hartog, Niels

2010-09-01

183

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

SciTech Connect

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.

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

2009-01-01

184

Spectral Identification of Intermediates Generated during the Reaction of Dioxygen with the Wild-Type and EQ(I-286) Mutant of Rhodobacter sphaeroides Cytochrome c Oxidase  

PubMed Central

Cytochrome c oxidase from Rhodobacter sphaeroides (Rs) is frequently used to model the more complex mitochondrial enzyme. The O2 reduction in both enzymes is generally described by a unidirectional mechanism involving the sequential formation of the ferrous-oxy complex (compound A), the PR state, the oxyferryl F form, and the oxidized state. In this study we investigated the reaction of dioxygen with the wild-type reduced Rs cytochrome oxidase and the EQ(I-286) mutant using the CO flow-flash technique. Singular value decomposition and multi-exponential fitting of the time-resolved optical absorption difference spectra showed that three apparent lifetimes, 18 ?s, 53 ?s, and 1.3 ms, are sufficient to fit the kinetics of the O2 reaction of the wild-type enzyme. A comparison of the experimental intermediate spectra with the corresponding intermediate spectra of the bovine enzyme revealed that PR is not present in the reaction mechanism of the wild-type Rs aa3. Transient absorbance changes at 440 and 610 nm support this conclusion. For the EQ(I-286) mutant, in which a key glutamic residue in the D proton pathway is replaced by glutamine, two lifetimes, 16 and 108 ?s, were observed. A spectral analysis of the intermediates shows that the O2 reaction in the EQ(I-286) mutant terminates at the PR state, with 70% of heme a becoming oxidized. These results indicate significant differences in the kinetics of O2 reduction between the bovine and wild-type Rs aa3 oxidases, which may arise from differences in the relative rates of internal electron and proton movements in the two enzymes.

Szundi, Istvan; Funatogawa, Chie; Cassano, Jennifer; McDonald, William; Ray, Jayashree; Hiser, Carrie; Ferguson-Miller, Shelagh; Gennis, Robert B.; Einarsdottir, Olof

2012-01-01

185

Spectral identification of intermediates generated during the reaction of dioxygen with the wild-type and EQ(I-286) mutant of Rhodobacter sphaeroides cytochrome c oxidase.  

PubMed

Cytochrome c oxidase from Rhodobacter sphaeroides is frequently used to model the more complex mitochondrial enzyme. The O(2) reduction in both enzymes is generally described by a unidirectional mechanism involving the sequential formation of the ferrous-oxy complex (compound A), the P(R) state, the oxyferryl F form, and the oxidized state. In this study we investigated the reaction of dioxygen with the wild-type reduced R. sphaeroides cytochrome oxidase and the EQ(I-286) mutant using the CO flow-flash technique. Singular value decomposition and multiexponential fitting of the time-resolved optical absorption difference spectra showed that three apparent lifetimes, 18 ?s, 53 ?s, and 1.3 ms, are sufficient to fit the kinetics of the O(2) reaction of the wild-type enzyme. A comparison of the experimental intermediate spectra with the corresponding intermediate spectra of the bovine enzyme revealed that P(R) is not present in the reaction mechanism of the wild-type R. sphaeroides aa(3). Transient absorbance changes at 440 and 610 nm support this conclusion. For the EQ(I-286) mutant, in which a key glutamic residue in the D proton pathway is replaced by glutamine, two lifetimes, 16 and 108 ?s, were observed. A spectral analysis of the intermediates shows that the O(2) reaction in the EQ(I-286) mutant terminates at the P(R) state, with 70% of heme a becoming oxidized. These results indicate significant differences in the kinetics of O(2) reduction between the bovine and wild-type R. sphaeroides aa(3) oxidases, which may arise from differences in the relative rates of internal electron and proton movements in the two enzymes. PMID:23057757

Szundi, Istvan; Funatogawa, Chie; Cassano, Jennifer; McDonald, William; Ray, Jayashree; Hiser, Carrie; Ferguson-Miller, Shelagh; Gennis, Robert B; Einarsdóttir, Ólöf

2012-11-20

186

Inverse-kinematics one-proton pickup with intermediate-energy beams: The {sup 9}Be ({sup 20}Ne,{sup 21}Na+{gamma})X reaction  

SciTech Connect

The possibility of studying particle-like states near the Fermi surfaces of exotic nuclei by using measurements of heavy-ion-induced single-nucleon pickup reactions with in-flight separated rare-isotope beams is discussed. The analysis of an exploratory data set for the intermediate-energy {sup 9}Be({sup 20}Ne,{sup 21}Na)X proton pickup reaction measured using a {sup 20}Ne beam at 63 MeV per nucleon is reported. The data are compared with expectations based on model calculations of the transfer reaction cross sections and the {sup 21}Na residue spectroscopy prediction by the sd-shell model. The measured cross sections are broadly consistent with these expectations.

Gade, A.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Siwek, K. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824 (United States); Adrich, P.; Bazin, D.; Obertelli, A.; Weisshaar, D. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, Michigan 48824 (United States); Hosier, K.; McGlinchery, D.; Riley, L. A. [Department of Physics and Astronomy, Ursinus College, Collegeville, Pennsylvania 19426 (United States); Tostevin, J. A. [Department of Physics, Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom)

2007-12-15

187

Identifying genetic risk factors for serious adverse drug reactions: current progress and challenges  

Microsoft Academic Search

Serious adverse drug reactions (SADRs) are a major cause of morbidity and mortality worldwide. Some SADRs may be predictable, based upon a drug's pharmacodynamic and pharmacokinetic properties. Many, however, appear to be idiosyncratic. Genetic factors may underlie susceptibility to SADRs and the identification of predisposing genotypes may improve patient management through the prospective selection of appropriate candidates. Here we discuss

Russell A. Wilke; Debbie W. Lin; Dan M. Roden; Paul B. Watkins; David Flockhart; Issam Zineh; Kathleen M. Giacomini; Ronald M. Krauss

2007-01-01

188

Identifi cation of a 27 kDa Protein in Patients With Anaphylactic Reactions to Mango  

Microsoft Academic Search

? Abstract Mango fruit has become increasingly popular in recent years. We report on 2 patients who developed anaphylactic reactions after the ingestion of fresh mango. Allergy to mango was confi rmed by a positive skin prick test result and positive cellular allergen stimulation test results. Neither of the patients had detectable mango-specifi c immunoglobulin (Ig) E levels. Results were

R Renner; C Hipler; R Treudler; W Harth; JC Simon

189

Tracking reactive intermediates by FTIR monitoring of reactions in low-temperature sublimed solids: nitric oxide disproportionation mediated by ruthenium(II) carbonyl porphyrin Ru(TPP)(CO).  

PubMed

Interaction of NO ((15)NO) with amorphous layers of Ru(II) carbonyl porphyrin (Ru(TPP)(CO), TPP(2-) = meso-tetraphenylporphyrinato dianion) was monitored by FTIR spectroscopy from 80 K to room temperature. An intermediate spectrally characterized at very low temperatures (110 K) with ?(CO) at 2001 cm(-1) and ?(NO) at 1810 cm(-1) (1777 cm(-1) for (15)NO isotopomer) was readily assigned to the mixed carbonyl-nitrosyl complex Ru(TPP)(CO)(NO), which is the logical precursor to CO labilization. Remarkably, Ru(TPP)-mediated disproportionation of NO is seen even at 110 K, an indication of how facile this reaction is. By varying the quantity of supplied NO, it was also demonstrated that the key intermediate responsible for NO disproportionation is the dinitrosyl complex Ru(TPP)(NO)2, supporting the conclusion previously made from solution experiments. PMID:23573997

Azizyan, Arsen S; Kurtikyan, Tigran S; Martirosyan, Garik G; Ford, Peter C

2013-05-01

190

Development of an NMR interface microchip "MICCS" for direct detection of reaction products and intermediates of micro-syntheses using a "MICCS-NMR".  

PubMed

The development of an NMR interface microchip and its applications to the real-time monitoring of chemical reactions are described. The microchip device was named "MICCS" (MIcro Channeled Cell for Synthesis monitoring), and the method using it was named "MICCS-NMR". MICCS was inserted into a 5 mm Phi NMR sample tube. Thus standard solution NMR probes without any modifications can be used in MICCS-NMR measurements. A gap between MICCS and the sample tube was filled with a deuterated solvent for an NMR lock. The reaction temperature and reaction time in MICCS can be easily changed by adjusting the temperature of the NMR probe and changing the flow rates, respectively. The effectiveness of the MICCS-NMR was verified in the real-time monitoring of the Wittig reaction. Preliminary data on the direct detection of intermediates of the Grignard reaction is also reported. Besides real-time monitoring of chemical reactions, MICCS-NMR would be useful as a qualitative detection method for microchip-based synthesis. PMID:17420541

Takahashi, Yutaka; Nakakoshi, Masamichi; Sakurai, Satoshi; Akiyama, Yoshitake; Suematsu, Hiroto; Utsumi, Hiroaki; Kitamori, Takehiko

2007-04-01

191

Reaction of chromium(VI) with glutathione or with hydrogen peroxide: identification of reactive intermediates and their role in chromium(VI)-induced DNA damage.  

PubMed Central

The types of reactive intermediates generated upon reduction of chromium(VI) by glutathione or hydrogen peroxide and the resulting DNA damage have been determined. In vitro, reaction of chromium(VI) with glutathione led to formation of two chromium(V) complexes and the glutathione thiyl radical. When chromium(VI) was reacted with DNA in the presence of glutathione, chromium-DNA adducts were obtained, with no DNA strand breakage. The level of chromium-DNA adduct formation correlated with chromium(V) formation. Reaction of chromium(VI) with hydrogen peroxide led to formation of hydroxyl radical. No chromium(V) was detectable at 24 degrees C (297 K); however, low levels of the tetraperoxochromium(V) complex were detected at 77 K. Reaction of chromium(VI) with DNA in the presence of hydrogen peroxide produced significant DNA strand breakage and the 8-hydroxydeoxyguanosine adduct, whose formation correlated with hydroxyl radical production. No significant chromium-DNA adduct formation was detected. Thus, the nature of chromium(VI)-induced DNA damage appears to be dependent on the reactive intermediates, i.e. chromium(V) or hydroxyl radical, produced during the reduction of chromium(VI).

Aiyar, J; Berkovits, H J; Floyd, R A; Wetterhahn, K E

1991-01-01

192

Appearance of the. nu. (Fe sup IV double bond O) vibration from a ferryl-oxo intermediate in the cytochrome oxidase/dioxygen reaction  

SciTech Connect

Time-resolved resonance Raman spectra have been recorded during the reaction of fully reduced (a{sup 2+}a{sub 3}{sup 2+}) cytochrome oxidase with dioxygen at room temperature. In the spectrum recorded at 800 {mu}s subsequent to carbon monoxide photolysis, a mode is observed at 790 cm{sup {minus}1} that shifts to 755 cm{sup {minus}1} when the experiment is repeated with {sup 18}O{sub 2}. The frequency of this vibration and the magnitude of the {sup 18}O{sub 2} isotopic frequency shift lead the authors to assign the 790-cm{sup {minus}1} mode to the Fe{sup IV}{double bond}O stretching vibration of a ferryl-oxo cytochrome a{sub 3} intermediate that occurs in the reaction of fully reduced cytochrome oxidase with dioxygen. The appearance and vibrational frequency of this mode were not affected when D{sub 2}O was used as a solvent. This result suggests that the ferryl-oxo intermediate is not hydrogen bonded. They have also recorded Raman spectra in the high-frequency region during the oxidase/O{sub 2} reaction that show that the oxidation of cytochrome a{sup 2+} is biphasic. These results on the kinetics of the redox activity of cytochrome a are consistent with the branched pathway discussed by Hill et al. for the oxidation of reduced cytochrome oxidase by O{sub 2} at room temperature.

Varotsis, C.; Babcock, G.T. (Michigan State Univ., East Lansing (USA))

1990-08-14

193

Master equation analysis of thermal activation reactions: Energy-transfer constraints on falloff behavior in the decomposition of reactive intermediates with low thresholds  

SciTech Connect

This paper deals with the high-temperature decomposition of reactive intermediates with low reaction thresholds. If these intermediates are created in situ, for example, through radical chain processes, their initial molecular distribution functions may be characteristic of the bath temperature and, under certain circumstances, peak at energies above the reaction threshold. Such an ordering of reaction thresholds and distribution functions has some similarities to that found during chemical activation. This leads to consequences that are essentially the inverse (larger rate constants than those deduced from steady-state distributions) of the situation for stable compounds under shock-heated conditions and hence reduces falloff effects. To study this behavior, rate constants for the unimolecular decomposition of ally, ethyl, n-propyl, and n-hexyl radicals have been determined on the basis of the solution of the time-dependent master equation with specific rate constants from RRKM calculations. The time required for the molecules to attain steady-state distribution functions has been determined as a function of the energy-transfer parameter (the step size down) molecular size (heat capacity), high-pressure rate parameters, temperature, and pressure. At 101 kPa (1atm) pressure, unimolecular rate constants near 10{sup 7} s{sup -1} represent a lower boundary, above which steady-state assumptions become increasingly questionable. 21 refs., 7 figs., 1 tab.

Tsang, W.; Bedanov, V.; Zachariah, M.R. [National Inst. of Standards and Technology, Gaithersburg, MD (United States)] [National Inst. of Standards and Technology, Gaithersburg, MD (United States)

1996-03-07

194

Conversion of the aminocrotonate intermediate limits the rate of gamma-elimination reaction catalyzed by L-cystathionine gamma-lyase of the yeast Saccharomyces cerevisiae.  

PubMed

L-Cystathionine gamma-lyase [EC 4.4.1.1] of Saccharomyces cerevisiae was shown to bind cofactor pyridoxal 5'-phosphate, up to 2 molecules/subunit. The association constants of the enzyme for the cofactor were estimated to be 3.67 x 10(5) M(-1) and 9.05 x 10(3) M(-1). However, the latter value was too small for the binding to play a catalytic role. Changes in the absorption spectra of the enzyme in gamma-elimination reaction mixtures with various amino acids as substrates were observed at 10 degrees C to elucidate the reaction mechanism of the enzyme. The enzyme formed a chromophore exhibiting absorption at approximately 480 nm, which is characteristic of an aminocrotonate intermediate with O-succinyl-L-homoserine, L-cystathionine, L-homoserine, or O-acetyl-L-homoserine, at rates in this order. The intermediate was consumed at much lower rates than those of formation. The order of the rates of consumption was the same as the order of the formation rates and the order of the gamma-elimination activity of the enzyme with the above-mentioned substrates. These results strongly suggested that the intermediate was essential for gamma-elimination and that the reaction was rate-limited by its conversion into the product alpha-ketobutyrate. L-Cysteine sensitively inhibited the alpha, gamma-elimination activity of the enzyme, and also retarded the formation of the chromophore when it was provided to the enzyme together with a substrate. The reason for these phenomena is discussed. PMID:14607989

Yamagata, Shuzo; Yasugahira, Tomoko; Okuda, Yuriko; Iwama, Tomonori

2003-10-01

195

Characterisation of Criegee intermediates in the gas phase by stabilisation with a spin trap and analysis by proton transfer reaction mass spectrometry (PTR-MS)  

NASA Astrophysics Data System (ADS)

Biogenic and anthropogenic volatile organic compounds (VOCs) can react with oxidants present in the atmosphere to form less volatile compounds which could partition in the condensed phase and contribute to organic aerosol mass. One of the most important and efficient reaction for the formation of secondary organic aerosol (SOA) is the ozonolysis of alkenes. This process occurs with a generally accepted mechanism, proposed for the first time by Rudolf Criegee (Criegee, 1975). According to the Criegee mechanism, ozone coordinates to the double bond of alkenes forming a primary ozonide, which promptly decomposes to form biradical intermediates called Criegee intermediates (CIs). CIs further react quickly to form first generation oxidation products. The analysis of Criegee intermediates represent an analytical challenge due to their characteristic high reactivity and low concentrations. Their role in the formation of SOA remains highly uncertain because of uncertainty in the kinetic of their reaction with different atmospheric compounds. Up to date, only a few studies have been able to detect the CIs directly (Welz et al., 2012) or indirectly (Mauldin et al., 2012). The aim of this study is the development of a method for the on-line measurement of CIs by stabilization with a spin trap (5,5-dimethyl-pyrroline N-oxide, DMPO) and detection via proton transfer reaction mass spectrometry (PTR-MS). The novel method is used to study the ozonolysis of ?-pinene in a flow tube, one of the most important precursors in the formation of SOA, often used as a proxy in global aerosol models to study the effects of biogenic organic aerosols on climate change. Criegee R., 1975. Angewandte Chemie 14, 745-752. Welz O., et al., 2012. Science 335, 204 207. Mauldin R. L., et al., 2012. Nature 488, 193-196.

Giorio, Chiara; Tapparo, Andrea; Barbon, Antonio; Toffoletti, Antonio; Kalberer, Markus

2014-05-01

196

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

PubMed

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. PMID:23941465

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

2013-09-01

197

Ion beam studies of organometallic chemistry. High energy sampling of reaction intermediates involved in carbon-carbon bond cleavage by transition metals  

SciTech Connect

Chemical transformation often involves reactive intermediates which correspond to local minima on a complex potential energy surface. In this study of the reactions of cobalt ions with alkanes, the intermediate is provided more energy than needed for reaction. The quantitative assessment of the fragmentation of reaction intermediates provided thermodynamic data. These investigations involved organo transition metal reactions using ion beam technqiues. Results for the reaction of Co/sup +/ with 2-methylpropane and 2,2-dimethylpropane are included. The observation that the cross section for production of CoCH/sub 3//sup +/ is always greater than that of C/sub 3/H/sub 7/+ implies that IP(C/sub 0/CH/sub 3/) < IP(iso-C/sub 3/H/sub 7/) = 7.36 eV. A similar analysis of the 2,2-dimethylpropane system establishes IP(CoCH/sub 3/) > IP(tert-C/sub 4/H/sub 9/) = 6.70 eV. Measurement of the thresholds for the endothermic processes observed at high energies provides band energies of the products. Preliminary data for the endothermic reactions of Co/sup +/ with hydrogen and ethane indicate that D/sup 0/(Co/sup +/-H) = 52 +- 4 and D/sup 0/(Co -- CH/sub 3/) = 61 +- 4 kcal/mol. Combined with the ionization potentials, IP(CoH) = 7.3 +- 0.1 and IP(CoCH/sub 3/) = 7.0 +- 0.3 EV; we find the neutral band dissociation energies, D/sup 0/(CoH) = 39 +- 6 and D/sup 0/(CoCH/sub 3/) = 41 +- 10 kcal/mol. The results provide substantial evidence for the viability of a mechanism for carbon-carbon bond cleavage of alkanes which involves direct insertion of a metal into the carbon-carbon band as a first step. Thermochemical data indicating strong metal-carbon bonds corroborate this hypothesis. 2 figures. (DP)

Armentrout, P.B.; Beauchamp, J.L.

1980-02-27

198

Arbitrary primer polymerase chain reaction, a powerful method to identify Bacillus thuringiensis serovars and strains.  

PubMed Central

Arbitrary primer polymerase chain reaction technology has been applied to the identification of commercial strains of Bacillus thuringiensis by using total DNAs extracted from single bacterial colonies as templates. Characteristic DNA banding patterns can be readily and reproducibly obtained by agarose gel electrophoresis. This method has been used to distinguish commercial products containing B. thuringiensis serovar kurstaki (3a3b). When a single primer was used this method was capable of producing discriminating DNA fingerprints for 33 known serovars. Differentiation from the closely related species Bacillus cereus is also readily achieved. This technique should prove to be a powerful tool for identification and discrimination of individual B. thuringiensis strains. Images

Brousseau, R; Saint-Onge, A; Prefontaine, G; Masson, L; Cabana, J

1993-01-01

199

Reaction cross sections of intermediate energy 3He-particles on targets from 9Be to 208Pb  

Microsoft Academic Search

Reaction cross sections for 3He-particles have been measured for 9Be, 12C, 16O, 28Si, 40Ca, 58,60Ni, 112,116,118,120,124Sn, and 208Pb at 96, 138 and 167 MeV. The results are compared with predictions from optical model calculations using phenomenological and global optical potentials. The behaviour of the wavefunctions and of the contributions to the reaction cross sections from different regions in the nucleus is

A. Ingemarsson; G. J. Arendse; A. Auce; R. F. Carlson; A. A. Cowley; A. J. Cox; S. V. Förtsch; R. Johansson; B. R. Karlson; M. Lantz; J. Peavy; J. A. Stander; G. F. Steyn; G. Tibell

2001-01-01

200

Anionic Pd(0) and Pd(II) Intermediates in Palladium-Catalyzed Heck and Cross-Coupling Reactions  

Microsoft Academic Search

The anions of PdCl2L2 and Pd(OAc)2, precursors of palladium(0) used in cross-coupling and Heck reactions, play a crucial role in these reactions. Tricoordinated anionic complexes Pd 0 L2Cl - and Pd0L2(OAc)- are the effective catalysts instead of the usually postulated Pd 0 L2 complex. The anion ligated to the palladium(0) affects the kinetics of the oxidative addition to ArI as

Christian Amatore; Anny Jutand

2000-01-01

201

Assembly of the mitochondrial Tim9-Tim10 complex: a multi-step reaction with novel intermediates.  

PubMed

Protein assembly is a crucial process in biology, because most proteins must assemble into complexes to perform their function in the cell. The mitochondrial Tim9-Tim10 translocase complex, located in the mitochondrial intermembrane space, plays an essential chaperone-like role during the import of mitochondrial membrane proteins. The complex consists of three molecules of each subunit arranged alternately in a ring-shaped structure. While structural and functional studies have indicated a dynamic nature of the complex, little is known about the assembly process and the mechanism of its function. Here we investigated the assembly process of yeast Tim9-Tim10 complex in real time, using stopped-flow fluorescence coupled with Trp mutagenesis, and stopped-flow light scattering techniques. We show that different parts of the proteins are assembled at different rates; also assembly intermediates consisting four subunits arise transiently before formation of the final hexameric Tim9-Tim10 complex. Interestingly, the assembly intermediate has more organised N-terminal helices that form an inner layer of the complex, but not the C-terminal helices, which form the outer layer of the complex. In addition, using analytical ultracentrifugation techniques, we show that Tim9 forms a homo-dimer while Tim10 is a monomer. A four-step assembly pathway of Tim9-Tim10 complex, involving formation of hetero-dimer and tetramer assembly intermediates, is proposed. This study provides the first description of the assembly pathway of this translocase complex, and insight into the mechanism of its function. PMID:18022191

Ivanova, Ekaterina; Jowitt, Thomas A; Lu, Hui

2008-01-01

202

Identifying genetic risk factors for serious adverse drug reactions: current progress and challenges  

PubMed Central

Serious adverse drug reactions (SADRs) are a major cause of morbidity and mortality worldwide. Some SADRs may be predictable, based upon a drug's pharmacodynamic and pharmacokinetic properties. Many, however, appear to be idiosyncratic. Genetic factors may underlie susceptibility to SADRs and the identification of predisposing genotypes may improve patient management through the prospective selection of appropriate candidates. Here we discuss three specific SADRs with an emphasis on genetic risk factors. These SADRs, selected based on wide-sweeping clinical interest, are drug-induced liver injury, statin-induced myotoxicity and drug-induced long QT and torsades de pointes. Key challenges for the discovery of predictive risk alleles for these SADRs are also considered.

Wilke, Russell A.; Lin, Debbie W.; Roden, Dan M.; Watkins, Paul B.; Flockhart, David; Zineh, Issam; Giacomini, Kathleen M.; Krauss, Ronald M.

2009-01-01

203

Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism  

PubMed Central

Background Enzymes belonging to mechanistically diverse superfamilies often display similar catalytic mechanisms. We previously observed such an association in the case of the cyclic amidohydrolase superfamily whose members play a role in related steps of purine and pyrimidine metabolic pathways. To establish a possible link between enzyme homology and chemical similarity, we investigated further the neighbouring steps in the respective pathways. Results We identified that successive reactions of the purine and pyrimidine pathways display similar chemistry. These mechanistically-related reactions are often catalyzed by homologous enzymes. Detection of series of similar catalysis made by succeeding enzyme families suggested some modularity in the architecture of the central metabolism. Accordingly, we introduce the concept of a reaction module to define at least two successive steps catalyzed by homologous enzymes in pathways alignable by similar chemical reactions. Applying such a concept allowed us to propose new function for misannotated paralogues. In particular, we discovered a putative ureidoglycine carbamoyltransferase (UGTCase) activity. Finally, we present experimental data supporting the conclusion that this UGTCase is likely to be involved in a new route in purine catabolism. Conclusions Using the reaction module concept should be of great value. It will help us to trace how the primordial promiscuous enzymes were assembled progressively in functional modules, as the present pathways diverged from ancestral pathways to give birth to the present-day mechanistically diversified superfamilies. In addition, the concept allows the determination of the actual function of misannotated proteins.

2013-01-01

204

A novel fault-tree approach for identifying potential causes of satellite reaction wheel failure  

Microsoft Academic Search

Due to unforeseen circumstances and naturally occurring faults, it is desired that an on-board fault-diagnosis system of a space vehicle be capable of detecting, isolating, identifying or classifying faults in the system. In this paper, a novel approach is proposed which strengthens existing efficient fault-detection mechanisms with an additional ability to classify different types of faults to effectively determine potential

A. Barua; P. Sinha; K. Khorasani; S. Tafazoli

2005-01-01

205

The possible role of intermediate NH species in oscillations of the NO+H 2 reaction on noble metal surfaces  

NASA Astrophysics Data System (ADS)

A comparative study of the thermodynamic properties of adsorbed NH n species ( n = 0, 1, 2, 3) on transition metal surfaces is performed by using the semi-empirical method of interacting bonds. The principal difference between single crystal surfaces exhibiting oscillatory behavior in the NO+H 2 reaction, and those surfaces which do not show such a behavior is that the combination reaction of NH species can easily proceed in the former case, whereas it is substantially endothermic on the latter surfaces. A trigger-like route for the oscillatory behavior is considered where the combination reaction of NH species operates as a temporary reaction pathway. This pathway practically does not contribute to the N 2 formation until the nitrogen coverage reaches some critical value, which ensures a sufficiently close distance between adjacent NH particles. The trigger pathway starts upon reaching that stage initiating the surface wave propagation, and stops immediately when the wave propagation is completed. The surface becomes then nearly clean and ready for the next oscillatory cycle. In this way, the feedback mechanism and the critical point of the regular wave initiation can be understood without any further assumptions. An alternative key reaction is also considered.

Cholach, A. R.; Bulgakov, N. N.; Nieuwenhuys, B. E.

2004-12-01

206

Delayed hemolytic transfusion reaction with multiple alloantibody (Anti S, N, K) and a monospecific autoanti-JKb in intermediate ?-thalassemia patient in Tabriz  

PubMed Central

It appears that delayed hemolytic transfusion reactions may occur several days after the administration of donor red cells is true even though they have been shown to be compatible in cross match tests by the antiglobulin technique. A specific case was observed in our center, which confirms the fact. The patient was a 37-year-old male suffering from intermediate ?-thalassemia. He had a history of two previous transfusions, with unknown transfusion reaction. In the last transfusion, laboratory data showed: Hb 7.8 g/dL and Hematocrit (Hct) 24.2%. The patient received two units of cross matched, compatible concentrated red blood cells (RBCs). After eight days a severe reaction was observed with clinical evidence of tachycardia, fatigue, fever, back pain, chest discomfort, jaundice, nausea and anorexia. Accordingly delayed hemolytic transfusion reaction was suspected, and anti-RBC antibodies were tested. Laboratory tests revealed the presence of three alloantibodies: Anti-N, anti-S, anti-K, and a monospecific autoanti-JKb.

Dolatkhah, Roya; Esfahani, Ali; Torabi, Seyed Esmaeil; Kermani, Iraj Asvadi; Sanaat, Zohreh; Ziaei, Jamal Eivazei; Nikanfar, Alireza; Chavoshi, Seyed Hadi; Ghoreishi, Zohreh; Kermani, Atabak Asvadi

2013-01-01

207

Delayed hemolytic transfusion reaction with multiple alloantibody (Anti S, N, K) and a monospecific autoanti-JK(b) in intermediate ?-thalassemia patient in Tabriz.  

PubMed

It appears that delayed hemolytic transfusion reactions may occur several days after the administration of donor red cells is true even though they have been shown to be compatible in cross match tests by the antiglobulin technique. A specific case was observed in our center, which confirms the fact. The patient was a 37-year-old male suffering from intermediate ?-thalassemia. He had a history of two previous transfusions, with unknown transfusion reaction. In the last transfusion, laboratory data showed: Hb 7.8 g/dL and Hematocrit (Hct) 24.2%. The patient received two units of cross matched, compatible concentrated red blood cells (RBCs). After eight days a severe reaction was observed with clinical evidence of tachycardia, fatigue, fever, back pain, chest discomfort, jaundice, nausea and anorexia. Accordingly delayed hemolytic transfusion reaction was suspected, and anti-RBC antibodies were tested. Laboratory tests revealed the presence of three alloantibodies: Anti-N, anti-S, anti-K, and a monospecific autoanti-JK(b). PMID:24014947

Dolatkhah, Roya; Esfahani, Ali; Torabi, Seyed Esmaeil; Kermani, Iraj Asvadi; Sanaat, Zohreh; Ziaei, Jamal Eivazei; Nikanfar, Alireza; Chavoshi, Seyed Hadi; Ghoreishi, Zohreh; Kermani, Atabak Asvadi

2013-07-01

208

H2SO4 formation from the gas-phase reaction of stabilized Criegee Intermediates with SO2: Influence of water vapour content and temperature  

NASA Astrophysics Data System (ADS)

The importance of gas-phase products from alkene ozonolysis other than OH radicals, most likely stabilized Criegee Intermediates (sCI), for the process of atmospheric SO2 oxidation to H2SO4 has been recently discovered. Subjects of this work are investigations on H2SO4 formation as a function of water vapour content (RH = 2-65%) and temperature (278-343 K) starting from the ozonolysis of trans-2-butene and 2,3-dimethyl-2-butene (TME). H2SO4 production other than via the OH radical reaction was attributed to the reaction of SO2 with sCI, i.e. acetaldehyde oxide arising from trans-2-butene ozonolysis and acetone oxide from TME. Measurements have been conducted in an atmospheric pressure flow tube using NO3--CI-APi-TOF mass spectrometry for H2SO4 detection. The sCI yields derived from H2SO4 measurements at 293 K were 0.49 ± 0.22 for acetaldehyde oxide and 0.45 ± 0.20 for acetone oxide. Our findings indicate a H2SO4 yield from sCI + SO2 of unity or close to unity. The deduced rate coefficient ratio for the reaction of sCI with H2O and SO2, k(sCI + H2O)/k(sCI + SO2), was found to be strongly dependent on the structure of the Criegee Intermediate, for acetaldehyde oxide at 293 K: (8.8 ± 0.4)·10-5 (syn- and anti-conformer in total) and for acetone oxide: <4·10-6. H2SO4 formation from sCI was pushed back with rising temperature in both reaction systems most probably due to an enhancement of sCI decomposition. The ratio k(dec)/k(sCI + SO2) increased by a factor of 34 (acetone oxide) increasing the temperature from 278 to 343 K. In the case of acetaldehyde oxide the temperature effect is less pronounced. The relevance of atmospheric H2SO4 formation via sCI + SO2 is discussed in view of its dependence on the structure of the Criegee Intermediate.

Berndt, Torsten; Jokinen, Tuija; Sipilä, Mikko; Mauldin, Roy L.; Herrmann, Hartmut; Stratmann, Frank; Junninen, Heikki; Kulmala, Markku

2014-06-01

209

Measuring Rate Constants for Reactions of the Simplest Criegee Intermediate (CH2OO) by Monitoring the OH Radical  

NASA Astrophysics Data System (ADS)

While generating the CH2OO molecule by reacting CH2I with O2, significant amounts of the OH radical were observed by laser induced fluorescence (LIF). At least two different processes formed OH; a fast process was probably due to a reaction of vibrationally hot CH2I radicals. The second process appeared to be associated with the decay of the CH2OO molecule. The addition of molecules known to react with CH2OO increased the observed decay rates of the OH signal. Using the OH signals as a proxy for the CH2OO concentration, the rate constant for the reaction of hexafluoroacetone with CH2OO was determined to be (3.33 × 0.27) x 10-11 cm3 molecule-1 s-1, in good agreement with the value measured by Taatjes et al.1 The rate constant for the reaction of SO2 with CH2OO, (3.53 × 0.29) x 10-11 cm3 molecule-1 s-1, showed no pressure dependence over the range of 50 to 200 Torr and was in agreement with the value at 4 Torr reported by Welz et al.2 This lack of a pressure dependence shows that SO2 + CH2OO is almost certainly a two-body reaction forming SO3 + CH2O and not a three-body stabilization.

liu, Y.; Bayes, K. D.; Sander, S. P.

2013-12-01

210

A Fenton mechanism and an oxochromium(IV) intermediate in reactions of the hydroperoxochromium(III) ion  

SciTech Connect

The covalently bound hydroperoxo complex (H[sub 2]O)[sub 5]CrOOH[sup 2+] is reduced by Fe[sup 2+] in aqueous solution by a Fenton mechanism. The reaction is second-order, with k[sub 298] = 48.4 L mol[sup [minus]1] s[sup [minus

Weidong Wang; Bakac, A.; Espenson, J.H. (Iowa State Univ., Ames (United States))

1993-05-12

211

Crystal structures of ?-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate  

PubMed Central

?-Glutamyltranspeptidase (GGT) is a heterodimic enzyme that is generated from the precursor protein through posttranslational processing and catalyzes the hydrolysis of ?-glutamyl bonds in ?-glutamyl compounds such as glutathione and/or the transfer of the ?-glutamyl group to other amino acids and peptides. We have determined the crystal structure of GGT from Escherichia coli K-12 at 1.95 Å resolution. GGT has a stacked ???? fold comprising the large and small subunits, similar to the folds seen in members of the N-terminal nucleophile hydrolase superfamily. The active site Thr-391, the N-terminal residue of the small subunit, is located in the groove, from which the pocket for ?-glutamyl moiety binding follows. We have further determined the structure of the ?-glutamyl-enzyme intermediate trapped by flash cooling the GGT crystal soaked in glutathione solution and the structure of GGT in complex with l-glutamate. These structures revealed how the ?-glutamyl moiety and l-glutamate are recognized by the enzyme. A water molecule was seen on the carbonyl carbon of the ?-glutamyl-Thr-391 O? bond in the intermediate that is to be hydrolyzed. Notably the residues essential for GGT activity (Arg-114, Asp-433, Ser-462, and Ser-463 in E. coli GGT) shown by site-directed mutagenesis of human GGT are all involved in the binding of the ?-glutamyl moiety. The structure of E. coli GGT presented here, together with sequence alignment of GGTs, may be applicable to interpret the biochemical and genetic data of other GGTs.

Okada, Toshihiro; Suzuki, Hideyuki; Wada, Kei; Kumagai, Hidehiko; Fukuyama, Keiichi

2006-01-01

212

Nucleophilic reaction by carbonic anhydrase model zinc compound: characterization of intermediates for CO2 hydration and phosphoester hydrolysis.  

PubMed

The partially hydrophilic and hydrophobic tripodal ligands, tris(hydroxy-2-benzimidazolylmethyl)amine L1h and tris(2-benzimidazolyl)amine L1 were used for the preparation of biomimetic complex of carbonic anhydrase. The CO(2) hydration using [L1hZn(OH)]ClO(4).1.5H(2)O provided the zinc-bound and free HCO(3)(-)s, which were formed by nucleophilic attack of Zn-OH toward CO(2) in dimethyl sulfoxide (DMSO). The phenolic OH in L1h can recognize water molecules through hydrogen bonds to facilitate the collection of the water molecules around a biomimetic zinc compound; the molecular structure of [L1hZn(OH)](+) was revealed. The packing diagram has demonstrated the all the water molecules are hydrogen bonded to each phenolic OH. The nucleophilic attack of zinc-bound OH(-) to substrate is used to catalyze the CO(2) hydration and phosphoester hydrolysis. The carbonic anhydrase model compound [L1Zn(OH(2))](2+) was applied for the hydrolysis of phosphoesters, parathion and bis(p-nitrophenyl)phosphate (BNPP(-)). The low reactivity of [L1Zn(OH)](+) for parathion hydrolysis is attributed to the stability of the intermediate [L1Zn(OP(S)(OEt)(2))](+). Since the structures of the intermediates [L1Zn(OH(2))](BNPP)(2) (1) and [L1Zn(OP(S)(OEt)(2))]ClO(4) (2) formed on the way of hydrolysis are too stable to realize the catalytic cycle and are not active for hydrolysis, carbonic anhydrase model compound [L1Zn(OH(2))](2+) was not suitable for phosphoester hydrolysis; the zinc model compound surrounded by three benzimidazolyl groups is used to have the steric hindrance for bulky substrate, such as parathion and BNPP(-). PMID:15271511

Echizen, Tsuneo; Ibrahim, M M; Nakata, Kou; Izumi, Mitsunori; Ichikawa, Kazuhiko; Shiro, Motoo

2004-08-01

213

Chiral propargylic cations as intermediates in SN1-type reactions: substitution pattern, nuclear magnetic resonance studies, and origin of the diastereoselectivity.  

PubMed

Nine propargylic acetates, bearing a stereogenic center (-C*HXR(2)) adjacent to the electrophilic carbon atom, were prepared and subjected to SN1-type substitution reactions with various silyl nucleophiles employing bismuth trifluoromethanesulfonate [Bi(OTf)3] as the Lewis acid. The diastereoselectivity of the reactions was high when the alkyl group R(2) was tertiary (tert-butyl), irrespective of the substituent X. Products were formed consistently with a diastereomeric ratio larger than 95:5 in favor of the anti-diastereoisomer. If the alkyl substitutent R(2) was secondary, the diastereoselectivity decreased to 80:20. The reaction was shown to proceed stereoconvergently, and the relative product configuration was elucidated. The reaction outcome is explained by invoking a chiral propargylic cation as an intermediate, which is preferentially attacked by the nucleophile from one of its two diastereotopic faces. Density functional theory (DFT) calculations suggest a preferred conformation in which the group R(2) is almost perpendicular to the plane defined by the three substituents at the cationic center, with the nucleophile approaching the electrophilic center opposite to R(2). Transition states calculated for the reaction of allyltrimethylsilane with two representative cations support this hypothesis. Tertiary propargylic cations with a stereogenic center (-C*HXR(2)) in the ? position were generated by ionization of the respective alcohol precursors with FSO3H in SO2ClF at -80 °C. Nuclear magnetic resonance (NMR) spectra were obtained for five cations, and the chemical shifts could be unambiguously assigned. The preferred conformation of the cations as extracted from nuclear Overhauser experiments is in line with the preferred conformation responsible for the reaction of the secondary propargylic cations. PMID:24494822

Nitsch, Dominik; Huber, Stefan M; Pöthig, Alexander; Narayanan, Arjun; Olah, George A; Prakash, G K Surya; Bach, Thorsten

2014-02-19

214

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

DOEpatents

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.

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

1997-04-15

215

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

PubMed

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

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

2014-07-01

216

Preparation of sigma- and pi-allylcopper(III) intermediates in SN2 and SN2' reactions of organocuprate(I) reagents with allylic substrates.  

PubMed

The first pi-allyl complexes of CuIII have been prepared and characterized by using rapid injection nuclear magnetic resonance spectroscopy (RI-NMR). The prototype, (eta3-allyl)dimethylcopper(III), was prepared by injection of allyl chloride into a THF-d8 solution of iodo-Gilman reagent, Me2CuLi.LiI (A), spinning in the probe of an NMR spectrometer at -100 degreesC. A sigma-allyl ate complex, lithium (eta1-allyl)trimethylcuprate(III), was prepared in high yield by including 1 equiv of tributylphosphine in the reaction mixture or by using allyl acetate as the substrate. Cyano ate complex, lithium cis-(eta1-allyl)cyanodimethylcuprate(III) was obtained in high yield by injecting allyl chloride or allyl acetate into the cyano-Gilman reagent, Me2CuLi.LiCN (B), in THF-d8 at -100 degrees C. Reactions of A with allylic substrates show a definite dependence on leaving group (chloride vs acetate), whereas those of B do not. Moreover, these reagents have different regioselectivities, which in the case of A vary with temperature. Finally, the exclusive formation of cis-cyano sigma-allyl CuIII intermediates in both the 1,4-addition of B to alpha-enones and its SN2alpha reaction with allylic substrates now makes sense in terms of pi-allyl intermediates in both cases, thus unifying the mechanisms of these two kinds of conjugate addition. PMID:18671398

Bartholomew, Erika R; Bertz, Steven H; Cope, Stephen; Murphy, Michael; Ogle, Craig A

2008-08-27

217

Time-Resolved X-Ray Absorption Spectroscopy Data for the Study of Chemical Reaction Intermediate States  

SciTech Connect

Energy-dispersive X-ray absorption Spectroscopy is an increasingly powerful tool for the investigation of kinetic processes in chemical systems as an element-specific local structure and electronic-state probe. In this paper we present a study of the structural evolution of the inner-sphere electron transfer reaction between [IrCl6]2- and [Co(CN)5]3-. The experimental requirements necessary for the extraction of maximal structural and electronic information are discussed.

Diaz Moreno, Sofia [Diamond Light Source, Chilton, Didcot, OX11 ODE (United Kingdom); Bowron, Daniel T. [ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX (United Kingdom); Evans, John [School of Chemistry, University of Southampton, Southampton S017 1BJ (United Kingdom)

2007-02-02

218

Rate coefficients of c1 and c2 criegee intermediate reactions with formic and acetic Acid near the collision limit: direct kinetics measurements and atmospheric implications.  

PubMed

Rate coefficients are directly determined for the reactions of the Criegee intermediates (CI) CH2 OO and CH3 CHOO with the two simplest carboxylic acids, formic acid (HCOOH) and acetic acid (CH3 COOH), employing two complementary techniques: multiplexed photoionization mass spectrometry and cavity-enhanced broadband ultraviolet absorption spectroscopy. The measured rate coefficients are in excess of 1×10(-10) ?cm(3) ?s(-1) , several orders of magnitude larger than those suggested from many previous alkene ozonolysis experiments and assumed in atmospheric modeling studies. These results suggest that the reaction with carboxylic acids is a substantially more important loss process for CIs than is presently assumed. Implementing these rate coefficients in global atmospheric models shows that reactions between CI and organic acids make a substantial contribution to removal of these acids in terrestrial equatorial areas and in other regions where high CI concentrations occur such as high northern latitudes, and implies that sources of acids in these areas are larger than previously recognized. PMID:24668781

Welz, Oliver; Eskola, Arkke J; Sheps, Leonid; Rotavera, Brandon; Savee, John D; Scheer, Adam M; Osborn, David L; Lowe, Douglas; Murray Booth, A; Xiao, Ping; Anwar H Khan, M; Percival, Carl J; Shallcross, Dudley E; Taatjes, Craig A

2014-04-25

219

A new strategy to identify rare blood donors: single polymerase chain reaction multiplex SNaPshot reaction for detection of 16 blood group alleles  

PubMed Central

Background As an alternative to phenotyping, large-scale DNA-based assays, which are feasible for high-throughput donor red blood cell typing, were developed for determination of blood group polymorphisms. However, high-throughput genotyping platforms based on these technologies are still expensive and the inclusion of single nucleotide polymorphisms and analysis of the alleles depend on the manufacturer’s determination. To overcome this limitation and in order to develop an assay to enable the screening of rare donors, we developed a SNaPshot assay for analysis of nine single nucleotide polymorphisms related to antigens that are difficult to assess using conventional serology. Materials and methods The single polymerase chain reaction multiplex SNaPshot reaction was optimized to identify nine single nucleotide polymorphisms determining 16 alleles: KEL*3/KEL*4, KEL*6/KEL*7, DI*1/DI*2, DI*3/DI*4, YT*1/YT*2, CO*1/CO*2, DO*1/DO*2, DO*4, DO*5. We designed a single multiplex PCR with primers encompassing the blood group single nucleotide polymorphisms and performed an internal reaction with probe primers able to discriminate the alleles after fragment analysis. The SNaPshot assay was validated with 140 known alleles previously determined by PCR restriction fragment length polymorphism. Results We were able to simultaneous detect nine single nucleotide polymorphisms defining 16 blood group alleles on an assay based on a multiplex PCR combined with a single base extension using genomic DNA. Discussion This study demonstrates a robust genotyping strategy for conducting rare donor screening which can be applied in blood centers and could be an important tool for identifying antigen-negative donors and, therefore, for providing rare blood.

Latini, Flavia Roche Moreira; Gazito, Diana; Arnoni, Carine Prisco; Muniz, Janaina Guilhem; de Medeiros Person, Rosangela; Carvalho, Fabricio Oliveira; Baleotti, Wilson; Castilho, Lilian; Barreto, Jose Augusto

2014-01-01

220

Determination of elementary rate constants by fitting detailed reaction mechanisms: Application to intermediate-temperature hydrocarbon kinetics  

NASA Astrophysics Data System (ADS)

Experimental elementary rate constant determinations are vital for the construction of reaction mechanisms and the verification of theoretical rate predictions. It is often difficult to obtain direct rate measurements, however, and the best determinations often come from fitting a detailed reaction mechanism to experimental data. In this work, techniques for assessing the mechanistic dependence of rate constants determined in this manner were developed. The techniques were used to design and evaluate flow reactor experiments for the determination of rate constants important in hydrocarbon combustion. First, local, first-order sensitivity coefficients were developed for rate constants determined by a least-squares fit to flow reactor data. These coefficients give the sensitivity of the determined rate constants to the remaining model parameters and experimental data. With uncertainty estimates for the model rate constants and experimental data the uncertainty in the proposed rate constant determinations could be estimated. Such estimates were used for experimental design, where these uncertainties were minimized through adjustment of the experimental conditions in a series of simulated flow reactor experiments. The local, first-order technique could also be used for error estimates once the experiments were completed. However, given the large parameter uncertainties and strong couplings typical of kinetic mechanisms, a globally valid technique was desirable. An importance-sampled Monte Carlo technique was developed to determine global probability distributions and regressions for the fit results. Flow reactor experiments were designed to determine rate constants for the reactions of methyl radicals with HO2 and O2 and of formaldehyde with HO2. These experiments were performed in a variable pressure flow reactor and new rate constant values were determined. The local technique was used to examine the mechanistic dependence of the results. Rigorous error bounds were developed and the limitations of the local technique were examined using the Monte Carlo technique. The new determinations gave a considerable reduction in uncertainty over the previous literature values. In addition, a system for in situ far-UV absorption spectrometry was developed to measure additional species and aid in rate measurements. This system was used in initial work toward rate constant determinations for the reaction of vinyl radicals with O2.

Scire, James J., Jr.

221

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

PubMed Central

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 ?-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.

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

2010-01-01

222

Elucidation of the order of oxidations and identification of an intermediate in the multistep clavaminate synthase reaction  

SciTech Connect

The enzyme clavaminate synthase (CS) catalyzes the formation of the first bicyclic intermediate in the biosynthetic pathway to the potent {beta}-lactamase inhibitor clavulanic acid. Previous work has led to the proposal that the cyclization/desaturation of the substrate proclavaminate proceeds in two oxidative steps, each coupled to a decarboxylation of {alpha}-ketoglutarate and a reduction of dioxygen to water. The authors have now employed kinetic isotope effect studies to determine the order of oxidations for CS purified from Streptomyces clavuligerus. Using (4{prime}RS)-(4{prime}-{sup 3}H,1-{sup 14}C)-rac-proclavaminate, a primary {sup T}(V/K) = 8.3 {plus minus} 0.2 was measured from ({sup 3}H)water release data, while an {alpha}-secondary {sup T}(V/K) = 1.06 {plus minus} 0.01 was determined from the changing {sup 3}H/{sup 14}C ratio of the product clavaminate. Values for the primary and {alpha}-secondary effects of 11.9 {plus minus} 1.7 and 1.12 {plus minus} 0.07, respectively, were obtained from the changing {sup 3}H/{sup 14}C ratio of the residual proclavaminate by using new equations derived for a racemic substrate bearing isotopic label at both primary and {alpha}-secondary positions. On the basis of the body of information available and the similarities to {alpha}-ketoglutarate-dependent dioxygenases, a comprehensive mechanistic scheme for CS is proposed to account for this unusual enzymatic transformation.

Salowe, S.P.; Krol, W.J.; Iwata-Reuyl, D.; Townsend, C.A. (Johns Hopkins Univ., Baltimore, MD (United States))

1991-02-26

223

Synthesis of ?-lactams by transition metal promoted Staudinger reactions: alternative synthetic approaches from transition metal enhanced organocatalysis to in situ, highly reactive intermediate synthesis and catalytic tandem reactions.  

PubMed

The development of new types of ?-lactam antibiotics is a relevant field of contemporary pharmaceutical research. Although many types of antibiotics are available on the market and widely used, ?-lactam antibiotics are considered to be one of the best choice as they are highly effective while having reasonable safety profiles. The wide application however has led to the appearance of resistant bacteria suppressing their efficacy. In the last decade fewer and fewer new antibiotics have been launched into the market, however more and more multiresistant germs have appeared posing significant threats especially to patients who are suffering from chronic diseases and have weakened immune systems. The development of new, highly efficient antibiotics is now direly needed. One of the options to accelerate ?-lactam antibiotic research is the development of alternative robust, convenient, versatile and cheap synthetic procedures in which the ?-lactam molecules can be easily synthesized with the desired diastereoselectivity. The most general way to introduce diastereoselectivity in the chemical reactions is the application of chiral catalyst systems. While there are several systems for the synthesis of ?-lactams the transition metal assisted Staudinger reaction--[2 + 2] cycloaddition between a ketene and an imine--remained the most simple and most versatile methodology. The motivation behind this brief review is to draw the chemical community's attention to the relevance and applicability of transition metal promoted Staudinger reactions in ?-lactam based antibiotic development. This article summarizes the most relevant pioneer works completed on this field in order to open new ideas for the forthcoming organometallic systems based bioactive material development. PMID:23925443

Tuba, Robert

2013-09-28

224

Preparation and characterization of bonded silica hydride intermediate from triethoxysilane and dimethylmethoxysilane using supercritical carbon dioxide and dioxane as reaction medium.  

PubMed

This research examines bonding methodology, surface coverage and silanol conversion efficiencies on the preparation of silica hydride (SiH) intermediate from triethoxysilane (TES) and dimethylmethoxysilane (DMMS) using sc-CO(2) and dioxane as reaction solvent. Under sc-CO(2) reaction conditions (at temperature and pressure of 100 °C, 414 bar, respectively and 3h reaction time), the surface coverages of SiH (evaluated from %C obtained from elemental analysis) prepared with DMMS (3.39 ?mol/m(2)) and TES (4.46 ?mol/m(2)) increased by 2- and 4-folds respectively, when compared to reaction performed in dioxane (2.66 ?mol/m(2), SiH, DMMS and 0.69 ?mol/m(2), SiH, TES). The relatively higher surface coverage of SiH from TES over DMMS generated in sc-CO(2) is due to the inherent trialkoxy moiety of the TES that favours siloxane crosslinkage, forming polymeric surface attachments to yield a higher ligand density than the monomeric DMMS ligand. A conversion efficiency of ?84.4% of SiH prepared from TES in sc-CO(2) estimated from (29)Si CP/MAS NMR analysis is comparable to TES silanization in dioxane or toluene. Moreover, silica hydride (SiH) conversion efficiency of ca. 42.4% achieved for the hydride intermediate prepared from DMMS in sc-CO(2) is more superior to 33.3% efficiency obtained in dioxane. The differences in conversion efficiencies is attributed to the ability of sc-CO(2) being able to access silica pores that are inaccessible in organic solvents. Bonded silica hydride from TES, DMMS prepared in sc-CO(2) were characterized using elemental analysis, thermogravimetric analysis (TGA), BET surface area, Fourier transform infrared (FI-IR) and solid state NMR spectroscopy. Silica hydride technology/chemical functionalization of silica in sc-CO(2) avoid extended purification steps (i.e. filtration and washing), generation of waste organic solvent and the need of costly or energy consuming drying processing with improved modification efficiency. PMID:22446079

Ashu-Arrah, Benjamin A; Glennon, Jeremy D; Albert, Klaus

2012-05-01

225

Analyzing powers and isotope ratios for the @Ag( rvec p , intermediate-mass fragment) reaction at 200 MeV  

SciTech Connect

Analyzing powers and isotope ratios have been measured for ejectiles with {ital Z}{le}7 emitted at forward angles in the 200-MeV {ital {rvec p}}+{sup nat}Ag reaction. The observed analyzing powers are consistent with zero, and thus do not provide evidence for a significant contribution from cluster knockout, or similar direct formation mechanisms. Fragment kinetic-energy spectra above the Coulomb peak are compared with a coalescence calculation. The isotopic composition of the elemental kinetic-energy spectra is found to favor {ital N}/{ital Z}{ge}1 nuclei for fragment energies near the exit-channel Coulomb energy, whereas species with {ital N}/{ital Z}{le}1 are more abundant in the high-energy spectral tails. This behavior is consistent with the predictions of an accreting source calculation.

Renshaw, E.; Yennello, S.J.; Kwiatkowski, K.; Planeta, R.; Woo, L.W.; Viola, V.E. (Department of Chemistry and Indiana University Cyclotron Facility, Indiana University, Bloomington, Indiana 47405 (United States))

1991-12-01

226

The carboligation reaction of acetohydroxyacid synthase II: Steady-state intermediate distributions in wild type and mutants by NMR  

PubMed Central

The thiamin diphosphate (ThDP)-dependent enzyme acetohydroxyacid synthase (AHAS) catalyzes the first common step in branched-chain amino acid biosynthesis. By specific ligation of pyruvate with the alternative acceptor substrates 2-ketobutyrate and pyruvate, AHAS controls the flux through this branch point and determines the relative rates of synthesis of isoleucine, valine, and leucine, respectively. We used detailed NMR analysis to determine microscopic rate constants for elementary steps in the reactions of AHAS II and mutants altered at conserved residues Arg-276, Trp-464, and Met-250. In Arg276Lys, both the condensation of the enzyme-bound hydroxyethyl-ThDP carbanion/enamine (HEThDP) with the acceptor substrates and acetohydroxyacid release are slowed several orders of magnitude relative to the wild-type enzyme. We propose that the interaction of the guanidinium moiety of Arg-264 with the carboxylate of the acceptor ketoacid provides an optimal alignment of substrate and HEThDP orbitals in the reaction trajectory for acceptor ligation, whereas its interaction with the carboxylate of the covalent HEThDP-acceptor adduct plays a similar role in product release. Both Trp-464 and Met-250 affect the acceptor specificity. The high preference for ketobutyrate in the wild-type enzyme is lost in Trp464Leu as a consequence of similar forward rate constants of carboligation and product release for the alternative acceptors. In Met250Ala, the turnover rate is determined by the condensation of HEThDP with pyruvate and release of the acetolactate product, whereas the parallel steps with 2-ketobutyrate are considerably faster. We speculate that the specificity of carboligation and product liberation may be cumulative if the former is not completely committed.

Tittmann, Kai; Vyazmensky, Maria; Hubner, Gerhard; Barak, Ze'ev; Chipman, David M.

2005-01-01

227

Ultrastructural characteristics of novel epithelial cell types identified in human pathologic liver specimens with chronic ductular reaction.  

PubMed Central

Previous immunohistochemical studies on human liver biopsies with chronic ductular reaction revealed the presence of "small cells" with bile-duct type cytokeratin profile in the periportal area. This study identified similar cells by electron microscopy. The authors studied 13 human liver specimens with various liver diseases, but all characterized by chronic ductular reaction. In all specimens, variable numbers of "small cells" with common epithelial characteristics were identified in the periportal area. They could be classified into three types. Type I cells showed an oval cell shape and oval nucleus, early or established formation of junctional complexes with adjacent cells, a full assortment of cytoplasmic organelles, and bundles of tonofilaments. Type II cells showed features of bile-duct cell differentiation, including lateral interdigitations, apical microvilli, basal pinocytotic vacuoles, and basement membrane formation. In contrast, type III cells displayed additional features indicating hepatocellular differentiation, such as a more prominent nucleus, formation of a hemicanaliculus, and glycogen rosettes. It is concluded that these small cells of epithelial nature display variable differentiation characteristics of either bile-duct type cells or hepatocytes. These findings support the existence of bipotential progenitor epithelial cells in human liver. They may have implications for liver regeneration and carcinogenesis. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9

De Vos, R.; Desmet, V.

1992-01-01

228

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

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-(?-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, ?H1‡ = 26.4±1.7 kJ mol?1, ?S1‡ = ? 75.6±6.8 J mol?1K?1), and then convert more slowly (k2(?10 °C)= 417±3.2 M?1s?1, ?H2‡ = 47.1±1.4 kJ mol?1, ?S2‡ = ? 15.0±5.7 J mol?1K?1) to a species 3 with isotopically sensitive stretches at ?o-o (?18O) = 819(47) cm?1, kO–O= 3.02 mdyn/Å, and ?Mn-O(?18O) = 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–?–1,2–O2)}2+ (3) is shown to be bridging between two Mn(III) ions in an end-on trans-?-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 en route to a binuclear ?–oxo bridged product derived from O2. Vibrational and metrical parameters for binuclear Mn-peroxo 3 are compared with those of related binuclear Fe- and Cu-peroxo compounds.

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

2013-01-01

229

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

Transition-metal peroxos have been implicated as key intermediates in a variety of critical biological processes involving O2. Because of 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 Mn-peroxo, either as a precursor to, or derived from, O2, in both photosynthetic H2O oxidation and DNA biosynthesis. These are 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 [Mn(II)(S(Me2)N4(6-Me-DPEN))] (+) (1), and the characterization of intermediates formed en route to a binuclear mono-oxo-bridged Mn(III) product {[Mn(III)(S(Me2)N4(6-Me-DPEN)]2(?-O)}(2+) (2), the oxo atom of which is derived from (18)O2. At low-temperatures, a dioxygen intermediate, [Mn(S(Me2)N4(6-Me-DPEN))(O2)](+) (4), is observed (by stopped-flow) to rapidly and irreversibly form in this reaction (k1(-10 °C) = 3780 ± 180 M(-1) s(-1), ?H1(++) = 26.4 ± 1.7 kJ mol(-1), ?S1(++) = -75.6 ± 6.8 J mol(-1) K(-1)) and then convert more slowly (k2(-10 °C) = 417 ± 3.2 M(-1) s(-1), ?H2(++) = 47.1 ± 1.4 kJ mol(-1), ?S2(++) = -15.0 ± 5.7 J mol(-1) K(-1)) to a species 3 with isotopically sensitive stretches at ?O-O(?(18)O) = 819(47) cm(-1), kO-O = 3.02 mdyn/Å, and ?Mn-O(?(18)O) = 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 a binuclear Mn(O2(2-)) Mn peroxo. This was verified by X-ray crystallography, where the peroxo of {[Mn(III)(S(Me2)N4(6-Me-DPEN)]2(trans-?-1,2-O2)}(2+) (3) is shown to be bridging between two Mn(III) ions in an end-on trans-?-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 en route to a binuclear ?-oxo-bridged product derived from O2. Vibrational and metrical parameters for binuclear Mn-peroxo 3 are compared with those of related binuclear Fe- and Cu-peroxo compounds. PMID:23470101

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

2013-04-17

230

Do rhodium bis(?-amine-borane) complexes play a role as intermediates in dehydrocoupling reactions of amine-boranes?  

PubMed

The recently synthesized rhodium complex [Rh{P(C(5)H(9))(2)(?(2)-C(5)H(7))}(Me(2)HNBH(3))(2)]BAr(F)(4) (2), which incorporates two amine-boranes coordinated to the rhodium center with two different binding modes, namely ?(1) and ?(2), has been used to probe whether bis(?-amine-borane) motifs are important in determining the general course of amine-boranes dehydrocoupling reactions. DFT calculations have been carried out to explore mechanistic alternatives that ultimately lead to the formation of the amine-borane cyclic dimer [BH(2)NMe(2)](2) (A) by hydrogen elimination. Sequential concerted, on- or off-metal, intramolecular dehydrogenations provide two coordinated amine-borane molecules. Subsequent dimerization is likely to occur off the metal in solution. In spite of the computationally confirmed presence of a BH???NH hydrogen bond between amine-borane ligands, neither a simple intermolecular route for dehydrocoupling of complex 2 is operating, nor seems [Rh{P(C(5)H(9))(2)(?(2)-C(5)H(7))}B](+) to be important for the whole dehydrocoupling process. PMID:22106049

Butera, Valeria; Russo, Nino; Sicilia, Emilia

2011-12-16

231

Reactions of substituted arenediazonium chlorides with methylamine-formaldehyde premix revisited: reactivity and transformations of methylolamine intermediates and their biological significance.  

PubMed

Modulation of the N-azo coupling between ring-substituted arenediazonium chlorides and premixed methylamine-formaldehyde leads not only to 1-aryl-3-hydroxymethyl-3-methyltriazenes and their dimers, but also to unexpected cyclic and complex products. The syntheses comprise reactions with arenediazonium chlorides bearing both -M and +M substituents at para and ortho/para positions of the phenyl ring. One of the major constituents isolated from a mixture of products is the O-acetate of 3-hydroxymethyl-3-methyl-1-(2,4,6-trichlorophenyl)triazene. This product was obtained from the reaction of 2,4,6-trichlorobenzenediazonium chloride and methylamine-formaldehyde mixture which was then stabilized by acetylation. The structures of the isolated products could be derived from reactive methylolamines and electrophilic intermediates that possible occur in vivo and thereby offer a plausible mechanistic explanation for the carcinogenic and tumour-inhibitory activity associated with the open-chain triazene compounds in the living cell. PMID:2953132

Kolar, G F; Schendzielorz, M

1987-01-01

232

A kinetic and theoretical study of the borate catalysed reactions of hydrogen peroxide: the role of dioxaborirane as the catalytic intermediate for a wide range of substrates.  

PubMed

Our recent work has provided new insights into the equilibria and species that exist in aqueous solution at different pHs for the boric acid - hydrogen peroxide system, and the role of these species in oxidation reactions. Most recently, (M. C. Durrant, D. M. Davies and M. E. Deary, Org. Biomol. Chem., 2011, 9, 7249-7254), we have produced strong theoretical and experimental evidence for the existence of a previously unreported monocyclic three membered peroxide species, dioxaborirane, that is the likely catalytic species in borate mediated electrophilic reactions of hydrogen peroxide in alkaline solution. In the present paper, we extend our study of the borate-peroxide system to look at a wide range of substrates that include substituted dimethyl anilines, methyl-p-tolyl sulfoxide, halides, hydrogen sulfide anion, thiosulfate, thiocyanate, and hydrazine. The unusual selectivity-reactivity pattern of borate catalysed reactions compared with hydrogen peroxide and inorganic or organic peracids previously observed for the organic sulfides (D. M. Davies, M. E. Deary, K. Quill and R. A. Smith, Chem.-Eur. J., 2005, 11, 3552-3558) is also seen with substituted dimethyl aniline nucleophiles. This provides evidence that the pattern is not due to any latent electrophilic tendency of the organic sulfides and further supports dioxaborirane being the likely reactive intermediate, thus broadening the applicability of this catalytic system. Moreover, density functional theory calculations on our proposed mechanism involving dioxaborirane are consistent with the experimental results for these substrates. Results obtained at high concentrations of both borate and hydrogen peroxide require the inclusion the diperoxodiborate dianion in the kinetic analysis. A scheme detailing our current understanding of the borate-peroxide system is presented. PMID:23188177

Deary, Michael E; Durrant, Marcus C; Davies, D Martin

2013-01-14

233

A novel tool for studying auxin-metabolism: the inhibition of grapevine indole-3-acetic acid-amido synthetases by a reaction intermediate analogue.  

PubMed

An important process for the regulation of auxin levels in plants is the inactivation of indole-3-acetic acid (IAA) by conjugation to amino acids. The conjugation reaction is catalysed by IAA-amido synthetases belonging to the family of GH3 proteins. Genetic approaches to study the biological significance of these enzymes have been hampered by large gene numbers and a high degree of functional redundancy. To overcome these difficulties a chemical approach based on the reaction mechanism of GH3 proteins was employed to design a small molecule inhibitor of IAA-amido synthetase activity. Adenosine-5'-[2-(1H-indol-3-yl)ethyl]phosphate (AIEP) mimics the adenylated intermediate of the IAA-conjugation reaction and was therefore proposed to compete with the binding of MgATP and IAA in the initial stages of catalysis. Two grapevine IAA-amido synthetases with different catalytic properties were chosen to test the inhibitory effects of AIEP in vitro. GH3-1 has previously been implicated in the grape berry ripening process and is restricted to two amino acid substrates, whereas GH3-6 conjugated IAA to 13 amino acids. AIEP is the most potent inhibitor of GH3 enzymes so far described and was shown to be competitive against MgATP and IAA binding to both enzymes with K(i)-values 17-68-fold lower than the respective K(m)-values. AIEP also exhibited in vivo activity in an ex planta test system using young grape berries. Exposure to 5-20 µM of the inhibitor led to decreased levels of the common conjugate IAA-Asp and reduced the accumulation of the corresponding Asp-conjugate upon treatment with a synthetic auxin. AIEP therefore represents a novel chemical probe with which to study IAA-amido synthetase function. PMID:22649546

Böttcher, Christine; Dennis, Eric G; Booker, Grant W; Polyak, Steven W; Boss, Paul K; Davies, Christopher

2012-01-01

234

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

SciTech Connect

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.

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

1996-12-31

235

Thermolabile folding intermediates: inclusion body precursors and chaperonin substrates  

PubMed Central

An unexpected aspect of the expression of cloned genes is the frequent failure of newly synthesized polypeptide chains to reach their native state, accumulating instead as insoluble inclusion bodies. Amyloid deposits represent a related state associated with a variety of human diseases. The critical folding intermediates at the juncture of productive folding and the off-pathway aggregation reaction have been identified for the phage P22 tailspike and coat proteins. Though the parallel ? coil tailspike is thermostable, an early intracellular folding intermediate is thermolabile. As the temperature of intracellular folding is increased, this species partitions to inclusion bodies, a kinetic trap within the cell. The earliest intermediates along the in vitro aggregation pathway, sequential multimers of the thermolabile folding intermediates, have been directly identified by native gel electrophoresis. Temperature-sensitive folding (tsf) mutations identify sites in the ? coil domain, which direct the junctional intermediate down the productive pathway. Global suppressors of tsf mutants inhibit the pathway to inclusion bodies, rescuing the mutant chains. These mutants identify sites important for avoiding aggregation. Coat folding intermediates also partition to inclusion bodies as temperature is increased. Coat tsf mutants are suppressed by overexpression of the GroE chaperonin, indicating that the thermolabile intermediate is a physiological substrate for GroE. We suggest that many proteins are likely to have thermolabile intermediates in their intracellular folding pathways, which will be precursors to inclusion body formation at elevated temperatures and therefore substrates for heat shock chaperonins.

KING, JONATHAN; HAASE-PETTINGELL, CAMERON; ROBINSON, ANNE SKAJA; SPEED, MARGARET; MITRAKI, ANNA

2007-01-01

236

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)

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 170°E 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. Copyright 2013 John Wiley & Sons, Ltd.

Fujii, Yosuke; Nakano, Toshiya; Usui, Norihisa; Matsumoto, Satoshi; Tsujino, Hiroyuki; Kamachi, Masafumi

2013-04-01

237

A new experimental approach to investigate intermediate-energy proton elastic scattering and breakup reactions on exotic nuclei in inverse kinematics  

NASA Astrophysics Data System (ADS)

We report on a new experimental setup for the investigation of proton induced reactions on exotic nuclei in inverse kinematics. It was installed and successfully used in the scattering study of intermediate-energy protons ( ˜700 MeV/u) on neutron-rich nuclei 6,8He produced with the FRagment Separator (FRS) at the GSI facility, Darmstadt. A new pure liquid-hydrogen target was successfully adapted allowing to obtain low-background data as compared to commonly used (CH 2) n targets. Absolute differential cross-sections for elastic (p, 6,8He) scattering were obtained at angles corresponding to 0.05?|t|?0.125 (GeV/ c) 2 of the four-momentum transfer squared (- t) leading to the first diffraction minimum and spanning more than two orders of magnitude. They complement an earlier measurement at smaller angles 0.0025?|t|?0.05 (GeV/ c) 2 performed at the same energy with an active target. Both data sets agree well in the overlap region t?0.05 (GeV/ c) 2 and enable a refined and comparative study of the radial distribution of the nuclear matter density.

Kiselev, O. A.; Aksouh, F.; Bleile, A.; Bochkarev, O. V.; Chulkov, L. V.; Cortina-Gil, D.; Dobrovolsky, A. V.; Egelhof, P.; Geissel, H.; Hellström, M.; Isaev, N. B.; Komkov, B. G.; Matoš, M.; Moroz, F. V.; Münzenberg, G.; Mutterer, M.; Mylnikov, V. A.; Neumaier, S. R.; Pribora, V. N.; Seliverstov, D. M.; Sergueev, L. O.; Shrivastava, A.; Sümmerer, K.; Weick, H.; Winkler, M.; Yatsoura, V. I.

2011-06-01

238

A new modular phosphite-pyridine ligand library for asymmetric Pd-catalyzed allylic substitution reactions: a study of the key Pd-?-allyl intermediates.  

PubMed

A library of phosphite-pyridine ligands L1-L12?a-g has been successfully applied for the first time in the Pd-catalyzed allylic substitution reactions of several di- and trisubstituted substrates by using a wide range of C, N and O nucleophiles, among which are the little studied ?-substituted malonates, ?-diketones, and alkyl alcohols. The highly modular nature of this ligand library enables the substituents/configuration at the ligand backbone, and the substituents/configurations at the biaryl phosphite moiety to be easily and systematically varied. We found that the introduction of an enantiopure biaryl phosphite moiety played an essential role in increasing the versatility of the Pd-catalytic systems. Enantioselectivities were therefore high for several hindered and unhindered di- and trisubstituted substrates by using a wide range of C, N and O nucleophiles. Of particular note were the high enantioselectivities (up to>99%?ee) and high activities obtained for the trisubstituted substrates S6 and S7, which compare favorably with the best that have been reported in the literature. We have also extended the use of these new catalytic systems in alternative environmentally friendly solvents such as propylene carbonate and ionic liquids. Studies on the Pd-?-allyl intermediates provide a deeper understanding of the effect of ligand parameters on the origin of enantioselectivity. PMID:23297053

Mazuela, Javier; Pàmies, Oscar; Diéguez, Montserrat

2013-02-11

239

The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis  

PubMed Central

The crystal structures of pyruvate oxidase from Aerococcus viridans (AvPOX) complexed with flavin adenine dinucleotide (FAD), with FAD and thiamine diphosphate (ThDP) and with FAD and the 2-acetyl-ThDP intermediate (AcThDP) have been determined at 1.6, 1.8 and 1.9?Å resolution, respectively. Each subunit of the homotetrameric AvPOX enzyme consists of three domains, as observed in other ThDP-dependent enzymes. FAD is bound within one subunit in the elongated conformation and with the flavin moiety being planar in the oxidized form, while ThDP is bound in a conserved V-conformation at the subunit–subunit interface. The structures reveal flexible regions in the active-site tunnel which may undergo conformational changes to allow the entrance of the substrates and the exit of the reaction products. Of particular interest is the role of Lys478, the side chain of which may be bent or extended depending on the stage of catalysis. The structures also provide insight into the routes for electron transfer to FAD and the involvement of active-site residues in the catalysis of pyruvate to its products.

Juan, Ella Czarina Magat; Hoque, Md Mominul; Hossain, Md Tofazzal; Yamamoto, Tamotsu; Imamura, Shigeyuki; Suzuki, Kaoru; Sekiguchi, Takeshi; Takenaka, Akio

2007-01-01

240

Chromophoric spin-labeled beta-lactam antibiotics for ENDOR structural characterization of reaction intermediates of class A and class C beta-lactamases.  

PubMed

The chromophoric spin-label substrate 6-N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M(-1) cm(-1) at 275 nm compared to 670 M(-1) cm(-1) at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/KM, determined under initial velocity conditions, were 637 +/- 36 s(-1) and 13.8 +/- 1.4 x 10(6) M(-1) s(-1), respectively, for hydrolysis catalyzed by TEM-1 beta-lactamase of E. coli, and 0.5 +/- 0.04 s(-1) and 3.9 +/- 0.4 x 10(4) M(-1) s(-1) for hydrolysis catalyzed by the beta-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 beta-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H2O (30:70, v:v) cryosolvent mixtures buffered to pH* 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 degrees C was > or = 3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 beta-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme. PMID:15134725

Mustafi, Devkumar; Hofer, Jennifer E; Huang, Wanzhi; Palzkill, Timothy; Makinen, Marvin W

2004-05-01

241

Lithium Cell Reactions.  

National Technical Information Service (NTIS)

The objectives of Part 1 of this program were to (i) investigate reactions occurring in the Li/SOCl2 cell for a range of specified test conditions and (ii) to perform analyses to identify reactants, intermediates and products generated by the chemical and...

W. Clark F. Dampier R. McDonald A. Lombardi D. Batson

1985-01-01

242

Isoporphyrin Intermediate in Heme Oxygenase Catalysis  

PubMed Central

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 ?-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin ?-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of ?-meso-phenylheme-IX, ?-meso-(p-methylphenyl)-mesoheme-III, and ?-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 ?-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 ?-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.

Evans, John P.; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

2008-01-01

243

Interactions of plant acetohydroxy acid isomeroreductase with reaction intermediate analogues: correlation of the slow, competitive, inhibition kinetics of enzyme activity and herbicidal effects.  

PubMed Central

N-Hydroxy-N-isopropyloxamate (IpOHA) is known to inhibit extremely tightly (Ki of 22 pM) the bacterial acetohydroxy acid isomeroreductase (EC 1.1.1.86) [Aulabaugh and Schloss (1990) Biochemistry 29, 2824-2830], the second enzyme of the branched-chain-amino-acid-biosynthetic pathway. Yet, although the same pathway exists in plant cells, this compound presents only very poor herbicidal action. Towards the goal of gaining a better understanding of this behaviour, we have studied the mechanism of interaction of this compound with a highly purified acetohydroxy acid isomeroreductase of plant origin, i.e. the spinach (Spinacia oleracea) chloroplast enzyme. IpOHA behaved as a nearly irreversible inhibitor of the enzyme. Encounter complex formation was very slow (association rate constant 1.9 x 10(3) M-1.s-1) and involved a single bimolecular step. Since inhibition was competitive with respect to acetohydroxy acid substrates, the time needed to achieve substantial (90%) inhibition in vitro of enzyme activity in the simultaneous presence of substrates and inhibitors was extremely long (for example of the order of hours at 1 microM IpOHA and 100 microM acetohydroxy acid substrates). Thus, under in vivo conditions, binding of the inhibitor may be so slow that it may delay considerably the time required for inhibition of the target enzyme. Simialr kinetic behaviour was observed with another reaction intermediate analogue described by Schulz, Spönemann, Köcher and Wengenmayer [(1988) FEBS Lett. 238, 375-378], 2-dimethyl-phosphinoyl-2-hydroxyacetic acid (Hoe 704), which displays a higher herbicide activity than IpOHA. The herbicidal potency of these two compounds appeared to be correlated with their rates of association with the plant acetohydroxy acid isomeroreductase, since the bimolecular rate constant for Hoe 704 (2.2 x 10(4) M-1.s-1) was higher than that for IpOHA.

Dumas, R; Cornillon-Bertrand, C; Guigue-Talet, P; Genix, P; Douce, R; Job, D

1994-01-01

244

Kinetic competence of the cADP-ribose-CD38 complex as an intermediate in the CD38/NAD+ glycohydrolase-catalysed reactions: implication for CD38 signalling.  

PubMed Central

CD38/NAD(+) glycohydrolase is a type II transmembrane glycoprotein widely used to study T- and B-cell activation and differentiation. CD38 is endowed with two different activities: it is a signal transduction molecule and an ectoenzyme that converts NAD(+) into ADP-ribose (NAD(+) glycohydrolase activity) and small proportions of cADP-ribose (cADPR; ADP-ribosyl cyclase activity), a calcium-mobilizing metabolite, which, ultimately, can also be hydrolysed (cADPR hydrolase activity). The relationship between these two properties, and strikingly the requirement for signalling in the formation of free or enzyme-complexed cADPR, is still ill-defined. In the present study we wanted to test whether the CD38-cADPR complex is kinetically competent in the conversion of NAD(+) into the reaction product ADP-ribose. In principle, such a complex could be invoked for cross-talk, via conformational changes, with neighbouring partner(s) of CD38 thus triggering the signalling phenomena. Analysis of the kinetic parameters measured for the CD38/NAD(+) glycohydrolase-catalysed hydrolysis of 2'-deoxy-2'-aminoribo-NAD(+) and ADP-cyclo[N1,C1']-2'-deoxy-2'-aminoribose (slowly hydrolysable analogues of NAD(+) and cADPR respectively) ruled out that the CD38-cADPR complex can accumulate under steady-state conditions. This was borne out by simulation of the prevalent kinetic mechanism of CD38, which involve the partitioning of a common E.ADP-ribosyl intermediate in the formation of the enzyme-catalysed reaction products. Using this mechanism, microscopic rate conditions were found which transform a NAD(+) glycohydrolase into an ADP-ribosyl cyclase. Altogether, the present work shows that if the cross-talk with a partner depends on a conformational change of CD38, this is most probably not attributable to the formation of the CD38-cADPR complex. In line with recent results on the conformational change triggered by CD38 ligands [Berthelier, Laboureau, Boulla, Schuber and Deterre (2000) Eur. J. Biochem. 267, 3056-3064], we believe that the Michaelis CD38-NAD(+) complex could play such a role instead.

Cakir-Kiefer, C; Muller-Steffner, H; Oppenheimer, N; Schuber, F

2001-01-01

245

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

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. PMID:11128583

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

2000-11-17

246

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

PubMed

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 (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. PMID:24606361

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

2014-03-01

247

ENDOR/HYSCORE studies of the common intermediate trapped during nitrogenase reduction of N2H2, CH3N2H, and N2H4 support an alternating reaction pathway for N2 reduction.  

PubMed

Enzymatic N(2) reduction proceeds along a reaction pathway composed of a sequence of intermediate states generated as a dinitrogen bound to the active-site iron-molybdenum cofactor (FeMo-co) of the nitrogenase MoFe protein undergoes six steps of hydrogenation (e(-)/H(+) delivery). There are two competing proposals for the reaction pathway, and they invoke different intermediates. In the 'Distal' (D) pathway, a single N of N(2) is hydrogenated in three steps until the first NH(3) is liberated, and then the remaining nitrido-N is hydrogenated three more times to yield the second NH(3). In the 'Alternating' (A) pathway, the two N's instead are hydrogenated alternately, with a hydrazine-bound intermediate formed after four steps of hydrogenation and the first NH(3) liberated only during the fifth step. A recent combination of X/Q-band EPR and (15)N, (1,2)H ENDOR measurements suggested that states trapped during turnover of the ?-70(Ala)/?-195(Gln) MoFe protein with diazene or hydrazine as substrate correspond to a common intermediate (here denoted I) in which FeMo-co binds a substrate-derived [N(x)H(y)] moiety, and measurements reported here show that turnover with methyldiazene generates the same intermediate. In the present report we describe X/Q-band EPR and (14/15)N, (1,2)H ENDOR/HYSCORE/ESEEM measurements that characterize the N-atom(s) and proton(s) associated with this moiety. The experiments establish that turnover with N(2)H(2), CH(3)N(2)H, and N(2)H(4) in fact generates a common intermediate, I, and show that the N-N bond of substrate has been cleaved in I. Analysis of this finding leads us to conclude that nitrogenase reduces N(2)H(2), CH(3)N(2)H, and N(2)H(4) via a common A reaction pathway, and that the same is true for N(2) itself, with Fe ion(s) providing the site of reaction. PMID:21744838

Lukoyanov, Dmitriy; Dikanov, Sergei A; Yang, Zhi-Yong; Barney, Brett M; Samoilova, Rimma I; Narasimhulu, Kuppala V; Dean, Dennis R; Seefeldt, Lance C; Hoffman, Brian M

2011-08-01

248

ENDOR/HYSCORE Studies of the Common Intermediate Trapped During Nitrogenase Reduction of N2H2, CH3N2H, and N2H4 Support an Alternating Reaction Pathway for N2 Reduction  

PubMed Central

Enzymatic N2 reduction proceeds along a reaction pathway comprised of a sequence of intermediate states generated as a dinitrogen bound to the active-site iron-molybdenum cofactor (FeMo-co) of the nitrogenase MoFe protein undergoes six steps of hydrogenation (e?/H+ delivery). There are two competing proposals for the reaction pathway, and they invoke different intermediates. In the ‘Distal’ (D) pathway, a single N of N2 is hydrogenated in three steps until the first NH3 is liberated, then the remaining nitrido-N is hydrogenated three more times to yield the second NH3. In the ‘Alternating’ (A) pathway, the two N’s instead are hydrogenated alternately, with a hydrazine-bound intermediate formed after four steps of hydrogenation and the first NH3 liberated only during the fifth step. A recent combination of X/Q-band EPR and 15N, 1,2H ENDOR measurements suggested that states trapped during turnover of the ?-70Ala/?-195Gln MoFe protein with diazene or hydrazine as substrate correspond to a common intermediate (here denoted I) in which FeMo-co binds a substrate-derived [NxHy] moiety, and measurements reported here show that turnover with methyldiazene generates the same intermediate. In the present report we describe X/Q-band EPR and 14/15N, 1,2H ENDOR/-HYSCORE/ESEEM measurements that characterize the N-atom(s) and proton(s) associated with this moiety. The experiments establish that turnover with N2H2, CH3N2H, and N2H4 in fact generates a common intermediate, I, and show that the N-N bond of substrate has been cleaved in I. Analysis of this finding leads us to conclude that nitrogenase reduces N2H2, CH3N2H, and N2H4 via a common A reaction pathway, and that the same is true for N2 itself, with Fe ion(s) providing the site of reaction.

Lukoyanov, Dmitriy; Dikanov, Sergei A.; Yang, Zhi-Yong; Barney, Brett M.; Samoilova, Rimma I.; Narasimhulu, Kuppala V.; Dean, Dennis R.; Seefeldt, Lance C.; Hoffman, Brian M.

2011-01-01

249

Computational study of the reaction of C6F6 with [IrMe(PEt3)3]: identification of a phosphine-assisted C-F activation pathway via a metallophosphorane intermediate.  

PubMed

Density functional theory calculations have been used to model the reaction of C6F6 with [IrMe(PEt3)3], which proceeds with both C-F and P-C bond activation to yield trans-[Ir(C6F5)(PEt3)2(PEt2F)], C2H4, and CH4 (Blum, O.; Frolow, F.; Milstein, D. J. Chem. Soc., Chem. Commun. 1991, 258). Using a model species, trans-[IrMe(PH3)2(PH2Et)], a low-energy mechanism involving nucleophilic attack of the electron-rich Ir metal center at C6F6 with displacement of fluoride has been identified. A novel feature of this process is the capture of fluoride by a phosphine ligand to generate a metallophosphorane intermediate [Ir(C6F5)(Me)(PH3)2(PH2EtF)]. These events occur in a single step via a 4-centered transition state, in a process that we have termed "phosphine-assisted C-F activation". Alternative mechanisms based on C-F activation via concerted oxidative addition or electron-transfer processes proved less favorable. From the metallophosphorane intermediate the formation of the final products can be accounted for by facile ethyl group transfer from phosphorus to iridium followed by beta-H elimination of ethene and reductive elimination of methane. The interpretation of phosphine-assisted C-F activation in terms of nucleophilic attack is supported by the reduced activation barriers computed with the more electron-rich model reactant trans-[IrMe(PMe3)2(PMe2Et)] and the higher barriers found with lesser fluorinated arenes. Reactivity patterns for a range of fluoroarenes indicate the dominance of the presence of ortho-F substituents in promoting phosphine-assisted C-F activation, and an analysis of the charge distribution and transition state geometries indicates that this process is controlled by the strength of the Ir-aryl bond that is being formed. PMID:18950169

Erhardt, Stefan; Macgregor, Stuart A

2008-11-19

250

Enzyme-catalysed peptide amidation. Isolation of a stable intermediate formed by reaction of the amidating enzyme with an imino acid.  

PubMed

A series of hydrazones and semicarbazones of glyoxylic acid were shown to have a potent inhibitory effect on the enzyme-catalysed conversion of D-Tyr-Val-Gly to D-Tyr-Val-NH2. Among the derivatives tested, the inhibitory activity was increased by the presence of hydrophobic substituents and decreased by polar substituents. The inhibition produced by glyoxylic acid phenylhydrazone was shown to be competitive. No inhibition was obtained with pyruvic acid phenylhydrazone, which possesses a methyl group in place of the alpha-H of glyoxylic acid phenylhydrazone. The inhibitory potencies of these non-peptide substances are in accord with the specificity exhibited by the amidating enzyme in its reaction with peptide substrates. The inhibition produced by the glyoxylic acid derivatives was shown to be due to their ability to act as substrates for the peptide-amidating enzyme. The product formed from [14C]glyoxylic acid phenylhydrazone was identified as oxalic acid phenylhydrazide by co-chromatography in three chromatographic systems. The results demonstrate that the enzyme-catalysed oxidation of glyoxylic acid phenylhydrazone takes place by a mechanism involving hydroxylation. It is implicit that peptide amidation catalysed by the same enzyme proceeds by a similar mechanism. PMID:3691506

Bradbury, A F; Smyth, D G

1987-12-15

251

Unique stepwise substitution reaction of a mono(guanidinate)tetraplatinum complex with amidines, giving mono(amidinate)tetraplatinum complexes through mixed-ligand intermediate complexes.  

PubMed

A mono(guanidinate)tetraplatinum complex [Pt4(?-OCOCH3)7(?-(TolN)2CN(i)Pr2)] (5: Tol = C6H4Me-4) was prepared by treating [Pt4(?-OCOCH3)8] (1) with excess amounts of N,N?-bis(p-tolyl)-N??-diisopropylguanidine (4a). A substitution reaction of the guanidinate moiety of 5 with N,N?-bis(aryl)formamidine (10: aryl = C6H4Me-4, C6H4COMe-4, and C6H4OMe-4) via mixed-ligand intermediates, trans-[Pt4(?-OCOCH3)6(?-(TolN)2CN(i)Pr2)(?-ArNCHNAr)] (11: Tol = C6H4Me-4; Ar = C6H4Me-4, C6H4COMe-4, and C6H4OMe-4), as a stepwise substitution mechanism, afforded the corresponding mono(amidinate)tetraplatinum complexes [Pt4(?-OCOCH3)7(?-ArNCHNAr)] (2a: Ar = C6H4Me-4; 2b: Ar = C6H4COMe-4; 2c: Ar = C6H4OMe-4) along with trans-bis(amidinate)tetraplatinum complexes trans-[Pt4(?-OCOCH3)6(?-ArNCHNAr)2] (3a: Ar = C6H4Me-4; 3b: Ar = C6H4COMe-4; 3c: Ar = C6H4OMe-4) as minor products. A Pt4 dimer complex [Pt4(?-OCOCH3)7]2-{?-(ArN)2C(C6H4)2C(NAr)2} (13: Ar = C6H4(t)Bu-4) was selectively obtained upon treatment of 5 with a bis(amidine) linker ligand, N4,N4,N4?,N4?-tetrakis(p-(tert-butyl)phenyl)-[1,1?-biphenyl]-4,4?-dicarboxamidine (12). All in-plane acetates of the two Pt4 cores in 13 were fully substituted by 2,6-dimethylbenzoic acid, 2,4,6-triisopropylbenzoic acid, and ferrocenecarboxylic acid while maintaining its dimer structure to give the corresponding derivatives [Pt4(?-OCOCH3)4(?-OCOC6H3Me2-2,6)3]2-{?-(ArN)2C(C6H4)2C(NAr)2} (14: Ar = C6H4(t)Bu-4), [Pt4(?-OCOCH3)4(?-OCOC6H2(i)Pr3-2,4,6)3]2-{?-(ArN)2C(C6H4)2C(NAr)2} (15: Ar = C6H4(t)Bu-4), and [Pt4(?-OCOCH3)4(?-OCOC5H4FeCp)3]2-{?-(ArN)2C(C6H4)2C(NAr)2} (16: Ar = C6H4(t)Bu-4). The electrochemistry of the four Pt4 dimer complexes 13–16 displayed a one-electron process attributed to Pt4(9+)/Pt4(8+), and another one-electron process due to Fe3+/Fe2+ was observed for the hexaferrocenyl derivative 16. PMID:23254781

Tanaka, Shinji; Mashima, Kazushi

2013-02-28

252

Genes that encode botulism neurotoxins A, B, E and F in neotropical bee honey identified with the polymerase chain reaction.  

PubMed

Honey can be used for the treatment of wounds, sores and skin bums, but it might be contaminated with Clostridium botulinum spores. In order to evaluate Costa Rican raw honey samples, the detection of neurotoxin gene sequences (corresponding to the bacterium) C. botulinum A, B, E and F was done with the polymerase chain reaction. A total of 64 raw honey samples, coming from different Costa Rican sites were analyzed. Reference C. botulinum strains type A (ATCC 19397), type B (ATCC 7949), type E (ATCC 17786) and type F (ATCC 25764) were used as templates for testing the effectivity of the method. The process consisted in culturing the honey samples in prereduced triptose-peptone-glucose-yeast extract media (TGPY) for 5 days. After this, the bacteria lysate obtained was used for PCR. The amplicons, product of the reaction, were visualized using agarose gel 2%. From the 64 honey samples analyzed, none produced positive results in the PCR, since no amplicons were obtained. Even though, all the reference C. botulinum strains used as controls were visualized and showed the effectivity of the extraction method and of the PCR used. The results obtained show promising therapeutic uses for honey from Costa Rica, but further evaluations shall be done in order to be sure of the safety of the product. PMID:18457171

Fournier, Ana Teresa; Gamboa, María del Mar; Arias, María Laura

2006-03-01

253

Measurements of activation reaction rates in transverse shielding concrete exposed to the secondary particle field produced by intermediate energy heavy ions on an iron target  

NASA Astrophysics Data System (ADS)

Reaction rate distributions were measured inside a 60-cm thick concrete pile placed at the lateral position of a thick (stopping length) iron target that was bombarded with heavy ions, 400 MeV/u C and 800 MeV/u Si. Foils of aluminum and gold, as well as gold, tungsten and manganese covered with cadmium were inserted at various locations in the concrete pile to serve as activation detectors. Features of reaction rate distribution, such as the shape of the reaction rate profile, contribution of the neutrons from intra-nuclear cascade and that from evaporation to the activation reactions are determined by the analysis of measured reaction rates. The measured reaction rates were compared with those calculated with radiation transport simulation codes, FLUKA and PHITS, to verify their capability to predict induced activity. The simulated reaction rates agree with the experimental results within a factor of three in general. However, systematic discrepancies between simulated reaction rates and measured reaction rates attributed to the neutron source terms are observed.

Ogawa, T.; Morev, M. N.; Iimoto, T.; Kosako, T.

2012-01-01

254

Unexpected NO transfer reaction between trans-[Ru(II)(NO+)(NH3)4(L)]3+ and Fe(III) species: observation of a heterobimetallic NO-bridged intermediate.  

PubMed

The reaction between trans-[Ru(II)(NO(+))(NH3)4(L)](3+), L = ImN, IsN, Nic, P(OMe)3, P(OEt)3, and P(OH)(OEt)2, and the Fe(III) species [Fe(III)(TPPS)], metmyoglobin, and hemoglobin was monitored by UV-vis, EPR, and electrochemical techniques (DPV, CV). No reaction was observed when L = ImN, IsN, Nic, and P(OH)(OEt)2. However, when L = P(OMe)3 and P(OEt)3, the reaction was quantitative and the products were trans-[Ru(III)(H2O)(NH3)4(P(OR)3)](3+) and [Fe(II)(NO(+))] species. Reaction kinetics data and DFT calculations suggest a two-step reaction mechanism with the initial formation of a bridged [Ru-(?NO)-Fe] intermediate, which was confirmed through electrochemical techniques (E(0)' = -0.47 V vs NHE). The calculated specific rate constant values for the reaction were in the ranges k1 = 1.1 to 7.7 L mol(-1) s(-1) and k2 = 2.4 × 10(-3) to 11.4 × 10(-3) s(-1) for L = P(OMe)3 and P(OEt)3. The oxidation of the ruthenium center (Ru(II) to Ru(III)) containing the nitrosonium ligand suggests that NO can act as an electron transfer bridge between the two metal centers. PMID:24738470

Metzker, Gustavo; Lopes, Pietro P; da Silva, Augusto C H; da Silva, Sebastiao C; Franco, Douglas W

2014-05-01

255

Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling  

Microsoft Academic Search

We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp128beta in a reaction dominated by

Laura Masgrau; Anna Roujeinikova; Linus O. Johannissen; Parvinder Hothi; Jaswir Basran; Kara E. Ranaghan; Adrian J. Mulholland; Michael J. Sutcliffe; Nigel S. Scrutton; David Leys

2006-01-01

256

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

PubMed Central

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.

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

257

Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily.  

PubMed

3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and orotidine 5'-phosphate decarboxylase (OMPDC) are members of an enzyme suprafamily, the OMPDC suprafamily, because they are homologous enzymes that catalyze mechanistically distinct reactions using different substrates. KGPDC catalyzes the Mg(2+) ion-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to yield L-xylulose 5-phosphate and CO(2); OMPDC catalyzes the metal ion-independent decarboxylation of OMP to UMP and CO(2). Structural studies have shown that KGPDC and OMPDC share several strictly conserved active site residues that are used differently by each enzyme to catalyze their mechanistically distinct reactions. Although the mechanism of the KGPDC-catalyzed reaction has yet to be elucidated, it is thought to proceed via a Mg(2+) ion-stabilized 1,2-enediolate intermediate. Here we report the crystal structures of KGPDC complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product, L-xylulose 5-phosphate, at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively. These structures support a mechanism that involves the formation of a cis-1,2-enediolate intermediate. Contrary to expectations, the geometry of the intermediate does not involve bidentate coordination of both enediolate oxygen atoms to the Mg(2+) ion but rather involves only the coordination of the oxygen on C2 to the Mg(2+) ion. The oxygen atom on C1 instead forms hydrogen bonds to both Lys64 and Asp67, two strictly conserved active site residues. Lys64 also interacts with the oxygen on C2 and may serve to stabilize a cis conformation of the 1,2-enediolate. These structures also implicate His136 to be the general acid that protonates the 1,2-enediolate intermediate. This study further demonstrates that multiple unrelated enzyme functions can evolve from a single active site architecture without regard for substrate binding affinity or mechanism. PMID:14567674

Wise, Eric L; Yew, Wen Shan; Gerlt, John A; Rayment, Ivan

2003-10-28

258

The Chemoselective Reduction of Isoxazoline ?-Lactams Through Iminium Aza-Diels-Alder Reactions: A Short-Cut Synthesis of Aminols as Valuable Intermediates towards Nucleoside Derivatives  

PubMed Central

Isoxazoline ?-lactams are prepared starting from the regioisomeric cycloadducts of benzonitrile oxide to the N-alkyl 2-azanorbornenes taking advantage of the efficient catalytic oxidation by RuO4. The reduction of the amide groups is easily conducted in the presence of LiAlH4 under mild conditions, which allowed for the chemoselective reduction of the amide moiety followed by ring opening to afford the desired conformationally locked isoxazoline-carbocyclic aminols, as valuable intermediates for nucleoside synthesis.

Memeo, Misal Giuseppe; Mella, Mariella; Quadrelli, Paolo

2012-01-01

259

Spectroscopic investigations of intermediates in the reaction of cytochrome P450 BM3–F87G with surrogate oxygen atom donors  

Microsoft Academic Search

Rapid mixing of substrate-free ferric cytochrome P450BM3–F87G with m-chloroperoxybenzoic acid (mCPBA) resulted in the sequential formation of two high-valent intermediates. The first was spectrally similar to compound I species reported previously for P450CAM and CYP 119 using mCPBA as an oxidant, and it featured a low intensity Soret absorption band characterized by shoulder at 370nm. This is the first direct

Gregory M. Raner; Jonathan I. Thompson; Alice Haddy; Valary Tangham; Nicole Bynum; G. Ramachandra Reddy; David P. Ballou; John H. Dawson

2006-01-01

260

Linking Chemical Electron-Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron-Copper Dinuclear Complex.  

PubMed

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3-CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185-190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment. PMID:24960612

Noodleman, Louis; Han Du, Wen-Ge; Fee, James A; Götz, Andreas W; Walker, Ross C

2014-07-01

261

Probing the sensitivity of the total nucleus-nucleus reaction cross section at intermediate energies to medium effects and isospin asymmetries  

SciTech Connect

This paper presents reaction cross-section predictions. These predictions are the result of a continuous pipeline that originates from a microscopic nuclear interaction. Density parameters and effective nucleon-nucleon cross sections (both involved in the reaction calculations) are by-products of the same equation of state. First, we perform tests of sensitivity to medium effects using reactions involving {sup 208}Pb, a stable but weakly isospin-asymmetric nucleus. We also show predictions for collisions of some neutron-rich isotopes of calcium and argon. We observe significant sensitivity of the reaction cross section to medium effects but very weak sensitivity to inclusion of isospin asymmetry in the effective nucleon-nucleon cross sections.

Sammarruca, Francesca; White, Larz [Physics Department, University of Idaho, Moscow, Idaho 83844-0903 (United States)

2011-06-15

262

Interface Reactions in Metal-Matrix Composites: An intermediate layer between fiber and matrix determines the mechanical properties of the composite.  

National Technical Information Service (NTIS)

This citation summarizes a one-page announcement of technology available for utilization. A report describes a study of the interface reactions between fiber and matrix materials in graphite/aluminum- and alumina/magnesium-composite systems. The study, wh...

1984-01-01

263

A Computational Study of a Recreated G Protein-GEF Reaction Intermediate Competent for Nucleotide Exchange: Fate of the Mg Ion  

Microsoft Academic Search

Small G-proteins of the superfamily Ras function as a molecular switches, interacting with different cellular partners according to their activation state. G-protein activation involves the dissociation of bound GDP and its replacement by GTP, in an exchange reaction that is accelerated and regulated in the cell by guanine-nucleotide exchange factors (GEFs). Large conformational changes accompany the exchange reaction, and our

Mériam Ben Hamida-Rebaï; Charles H. Robert

2010-01-01

264

Multiple Reaction Monitoring to Identify Site-Specific Troponin I Phosphorylated Residues in the Failing Human Heart  

PubMed Central

Background Human cardiac troponin I is known to be phosphorylated at multiple amino acid residues by several kinases. Advances in mass spectrometry allow sensitive detection of known and novel phosphorylation sites and measurement of the level of phosphorylation simultaneously at each site in myocardial samples. Methods and Results On the basis of in silico prediction and liquid chromatography/mass spectrometry data, 14 phosphorylation sites on cardiac troponin I, including 6 novel residues (S4, S5, Y25, T50, T180, S198), were assessed in explanted hearts from end-stage heart failure transplantation patients with ischemic heart disease or idiopathic dilated cardiomyopathy and compared with samples obtained from nonfailing donor hearts (n=10 per group). Thirty mass spectrometry–based multiple reaction monitoring quantitative tryptic peptide assays were developed for each phosphorylatable and corresponding nonphosphorylated site. The results show that in heart failure there is a decrease in the extent of phosphorylation of the known protein kinase A sites (S22, S23) and other newly discovered phosphorylation sites located in the N-terminal extension of cardiac troponin I (S4, S5, Y25), an increase in phosphorylation of the protein kinase C sites (S41, S43, T142), and an increase in phosphorylation of the IT-arm domain residues (S76, T77) and C-terminal domain novel phosphorylation sites of cardiac troponin I (S165, T180, S198). In a canine dyssynchronous heart failure model, enhanced phosphorylation at 3 novel sites was found to decline toward control after resynchronization therapy. Conclusions Selective, functionally significant phosphorylation alterations occurred on individual residues of cardiac troponin I in heart failure, likely reflecting an imbalance in kinase/phosphatase activity. Such changes can be reversed by cardiac resynchronization.

Zhang, Pingbo; Kirk, Jonathan A.; Ji, Weihua; dos Remedios, Cristobal G.; Kass, David A.; Van Eyk, Jennifer E.; Murphy, Anne M.

2013-01-01

265

Observation of Covalent Intermediates in an Enzyme Mechanism at Atomic Resolution  

Microsoft Academic Search

In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant D-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and

Andreas Heine; Grace DeSantis; John G. Luz; Michael Mitchell; Chi-Huey Wong; Ian A. Wilson

2001-01-01

266

Identifying, by first-principles simulations, Cu[amyloid-?] species making Fenton-type reactions in Alzheimer's disease.  

PubMed

According to the amyloid cascade hypothesis, amyloid-? peptides (A?) play a causative role in Alzheimer's disease (AD), of which oligomeric forms are proposed to be the most neurotoxic by provoking oxidative stress. Copper ions seem to play an important role as they are bound to A? in amyloid plaques, a hallmark of AD. Moreover, Cu-A? complexes are able to catalyze the production of hydrogen peroxide and hydroxyl radicals, and oligomeric Cu-A? was reported to be more reactive. The flexibility of the unstructured A? peptide leads to the formation of a multitude of different forms of both Cu(I) and Cu(II) complexes. This raised the question of the structure-function relationship. We address this question for the biologically relevant Fenton-type reaction. Computational models for the Cu-A? complex in monomeric and dimeric forms were built, and their redox behavior was analyzed together with their reactivity with peroxide. A set of 16 configurations of Cu-A? was studied and the configurations were classified into 3 groups: (A) configurations that evolve into a linearly bound and nonreactive Cu(I) coordination; (B) reactive configurations without large reorganization between the two Cu redox states; and (C) reactive configurations with an open structure in the Cu(I)-A? coordination, which have high water accessibility to Cu. All the structures that showed high reactivity with H2O2 (to form HO(•)) fall into class C. This means that within all the possible configurations, only some pools are able to produce efficiently the deleterious HO(•), while the other pools are more inert. The characteristics of highly reactive configurations consist of a N-Cu(I)-N coordination with an angle far from 180° and high water crowding at the open side. This allows the side-on entrance of H2O2 and its cleavage to form a hydroxyl radical. Interestingly, the reactive Cu(I)-A? states originated mostly from the dimeric starting models, in agreement with the higher reactivity of oligomers. Our study gives a rationale for the Fenton-type reactivity of Cu-A? and how dimeric Cu-A? could lead to a higher reactivity. This opens a new therapeutic angle of attack against Cu-A?-based reactive oxygen species production. PMID:24313818

La Penna, Giovanni; Hureau, Christelle; Andreussi, Oliviero; Faller, Peter

2013-12-27

267

A Closer Look at the Spectroscopic Properties of Possible Reaction Intermediates in WT and Mutant (E)-4-hydroxy-3-methyl-but-2-enyl Diphosphate Reductase (IspH/LytB)†  

PubMed Central

(E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate reductase (IspH or LytB) catalyzes the terminal step of the MEP/DOXP pathway where it converts (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) into the two products isopentenyl diphosphate and dimethylallyl diphosphate. The reaction involves the reductive elimination of the C4 hydroxyl group, using a total of two electrons. Here we show that the active form of IspH contains a [4Fe-4S] cluster and not the [3Fe-4S] form. Our studies show that the cluster is not only the direct electron source for the reaction but that a reaction intermediate is bound directly to the cluster. This active form, has been trapped in a state, dubbed FeSA, that was detected in EPR spectroscopy when one-electron-reduced IspH was incubated with HMBPP. In addition, three mutants of IspH protein have been prepared and studied, His42, His124 and Glu126 (Aquifex aeolicus numbering), with particular attention to the effects on the cluster properties and possible reaction intermediates. None of the mutants affected the properties of the [4Fe-4S]+ cluster significantly, but different effects were observed when one-electron-reduced forms were incubated with HMBPP. Replacing the His42 led to an increased Km value and much lower catalytic efficiency, confirming the role of this residue in substrate binding. Replacing the His124 also resulted in lower catalytic efficiency. In this case, however, enzyme showed the loss of the [4Fe-4S]+ EPR signal upon addition of HMBPP without the subsequent formation of the FeSA signal. Instead, a radical-type signal was observed in some of the samples indicating that this residue plays a role in the correct positioning of the substrate. The incorrect orientation in the mutant leads to the formation of substrate-based radicals instead of the cluster-bound-intermediate complex FeSA. Replacing the Glu126 also resulted in lower catalytic efficiency, with yet a third type of EPR signal being detected upon incubation with HMBPP. 31P- and 2H-ENDOR measurements on the FeSA species incubated with regular and 2H-C4-labeled HMBPP reveal that the substrate binds to the enzyme in close proximity of the active-site cluster with the C4 adjacent to the site of linkage between the FeS cluster and HMBPP. Comparison of the spectroscopic properties of this intermediate to those of intermediates detected in (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase and ferredoxin:thioredoxin reductase suggest that HMBPP binds to the FeS cluster via its hydroxyl group instead of a side-on binding as previously proposed for the species detected in the inactive Glu126 variant. Consequences for the IspH reaction mechanism are discussed.

Xu, Weiya; Lees, Nicholas S.; Hall, Dominique; Welideniya, Dhanushi; Hoffman, Brian M.; Duin, Evert C.

2012-01-01

268

Ambiphilic molecules for trapping reactive intermediates: interrupted Nazarov reaction of allenyl vinyl ketones with Me2PCH2AlMe2.  

PubMed

The addition of the ambiphilic molecule Me(2)AlCH(2)PMe(2) (1) to the allenyl vinyl ketone 2 gave a trapped Nazarov reaction product. Under kinetic control, the addition of the phosphine was on the methylated carbon, contrary to expected steric and electronic considerations. Computational data pointed to hydrogen bonding between the phosphine and the methyl group guiding the regiochemistry of this reaction. This product rearranged to provide the expected, regioisomeric Nazarov product. With additional 1 this compound yielded a Michael-addition product via a retro-Nazarov process. PMID:23070293

Boudreau, Josée; Courtemanche, Marc-André; Marx, Vanessa M; Jean Burnell, D; Fontaine, Frédéric-Georges

2012-11-25

269

Radical intermediates generated in the reactions of L-arginine with hydroxyl radical and sulfate radical anion: A pulse radiolysis study  

NASA Astrophysics Data System (ADS)

Reactions of L-arginine (Arg) with hydroxyl radical ( rad OH) and sulfate radical anion (SO 4- rad ) were kinetically investigated by the pulse radiolysis technique. Hydrogen abstraction from Arg by rad OH afforded redox chemically oxidizing, neutral, and reducing carbon-centered Arg radicals. Kinetic properties of the radicals indicated that the reducing species might include the ?-C-centered Arg radical and CO 2 radical anion. Similar transient spectra were observed in the SO 4- rad reaction with Arg, suggesting direct oxidation at the guanidino group is less likely.

Ito, Takeo; Morimoto, Shota; Fujita, Shin-ichi; Nishimoto, Sei-ichi

2009-04-01

270

Intermediate inputs and economic productivity.  

PubMed

Many models of economic growth exclude materials, energy and other intermediate inputs from the production function. Growing environmental pressures and resource prices suggest that this may be increasingly inappropriate. This paper explores the relationship between intermediate input intensity, productivity and national accounts using a panel dataset of manufacturing subsectors in the USA over 47 years. The first contribution is to identify sectoral production functions that incorporate intermediate inputs, while allowing for heterogeneity in both technology and productivity. The second contribution is that the paper finds a negative correlation between intermediate input intensity and total factor productivity (TFP)--sectors that are less intensive in their use of intermediate inputs have higher productivity. This finding is replicated at the firm level. We propose tentative hypotheses to explain this association, but testing and further disaggregation of intermediate inputs is left for further work. Further work could also explore more directly the relationship between material inputs and economic growth--given the high proportion of materials in intermediate inputs, the results in this paper are suggestive of further work on material efficiency. Depending upon the nature of the mechanism linking a reduction in intermediate input intensity to an increase in TFP, the implications could be significant. A third contribution is to suggest that an empirical bias in productivity, as measured in national accounts, may arise due to the exclusion of intermediate inputs. Current conventions of measuring productivity in national accounts may overstate the productivity of resource-intensive sectors relative to other sectors. PMID:23359736

Baptist, Simon; Hepburn, Cameron

2013-03-13

271

Eleven new heaviest isotopes of elements Z = 105 to Z = 117 identified among the products of 249Bk+48Ca reactions  

SciTech Connect

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.

Oganessian, Yuri Ts. [FLNR-JINR, Russia; Abdullin, F. Sh. [Joint Institute for Nuclear Research, Dubna, Russia; Bailey, P. D. [Oak Ridge National Laboratory (ORNL); Benker, D. E. [Oak Ridge National Laboratory (ORNL); Bennett, M. E. [University of Nevada, Las Vegas; Dmitriev, S. [FLNR-JINR, Russia; Ezold, Julie G. [Oak Ridge National Laboratory (ORNL); Hamilton, J. H. [Vanderbilt University; Henderson, R. [Lawrence Livermore National Laboratory (LLNL); Itkis, M. G. [FLNR-JINR, Russia; Lobanov, Yu. V. [Joint Institute for Nuclear Research, Dubna, Russia; Mezentsev, A. N. [Joint Institute for Nuclear Research, Dubna, Russia; Moody, K. [Lawrence Livermore National Laboratory (LLNL); Nelson, S. L. [Lawrence Livermore National Laboratory (LLNL); Polyakov, A. N. [Joint Institute for Nuclear Research, Dubna, Russia; Porter, C. E. [Oak Ridge National Laboratory (ORNL); Ramayya, A. V. [Vanderbilt University; Riley, F. D. [Oak Ridge National Laboratory (ORNL); Roberto, James B [ORNL; Ryabinin, M. A. [Research Institute of Atomic Reactors, Dimitrovgrad, Russia; Rykaczewski, Krzysztof Piotr [ORNL; Taylor, R [Oak Ridge National Laboratory (ORNL); Tsyganov, Yu. S. [Joint Institute for Nuclear Research, Dubna, Russia; Utyonkov, V. [FLNR-JINR, Russia; Voinov, A. A. [Joint Institute for Nuclear Research, Dubna, Russia; Vostokin, G. K. [Joint Institute for Nuclear Research, Dubna, Russia; Wilk, P. A. [Lawrence Livermore National Laboratory (LLNL)

2011-01-01

272

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

PubMed

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 the new role of this inorganic salt in providing structural support for the newly generated alkoxide ligand. PMID:21365695

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

2011-04-11

273

The serum D-xylose test as a useful tool to identify malabsorption in rats with antigen specific gut inflammatory reaction  

PubMed Central

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.

Antunes, Danielle Mota Fontes; da Costa, Janilda Pacheco; Campos, Sylvia Maria Nicolau; Paschoal, Patricia Olaya; Garrido, Valeria; Siqueira, Munique; Teixeira, Gerlinde Agate Platais Brasil; Cardoso, Gilberto Perez

2009-01-01

274

Reactions of Peroxynitrite with Uric Acid: Formation of Reactive Intermediates, Alkylated Products and Triuret, and In Vivo Production of Triuret Under Conditions of Oxidative Stress  

Microsoft Academic Search

Hyperuricemia is associated with hypertension, metabolic syndrome, preeclampsia, cardio-vascular disease and renal disease, all conditions associated with oxidative stress. We hypothesized that uric acid, a known antioxidant, might become prooxidative following its reaction with oxidants; and, thereby contribute to the pathogenesis of these diseases. Uric acid and 1,3-N2-uric acid were reacted with peroxynitrite in different buffers and in the presence

Christine Gersch; Sergiu P. Palii; Witcha Imaram; Kyung Mee Kim; S. Ananth Karumanchi; Alexander Angerhofer; Richard J. Johnson; George N. Henderson

2009-01-01

275

Analysis of sensitivity of the reaction cross section and the forward scattering amplitude to the structure of the nuclear optical potential for intermediate-energy nucleons and antinucleons  

SciTech Connect

Within the framework of the optical model with phenomenological optical potentials describing elastic scattering we calculate the total cross section, the reaction cross section, and the real part of the forward scattering amplitude for nucleons and antinucleons in the energy range 50--200 MeV for a broad range of nuclei. It is shown that with a significantly different spatial dependence of the real part of the optical potential (the Woods-Saxon form and the ''wine-bottle bottom'' form) the real parts of the proton forward scattering amplitude differ from each other by several times, while the difference in the total cross sections and reaction cross sections is not larger than tens of per cent. The calculations are performed in first-order perturbation theory in deviation of the wave function of the incident particle from the eikonal approximation. Comparison of the results of the approximate and exact calculations shows that the error of the approximate approach in the energy range considered is not larger than 10%. We compare our results with the results of calculations of the reaction cross section for antiprotons in light nuclei in the Glauber theory.

Zavarzina, V.P.; Stepanov, A.V.

1986-04-01

276

On the Configurational Stability of Chiral Heteroatom-Substituted [D1]Methylpalladium Complexes as Intermediates of Stille and Suzuki-Miyaura Cross-Coupling Reactions  

PubMed Central

Enantiomerically pure (S)-tributylstannyl[D1]methanol and (R)- and (S)-tributylstannyl[D1]methyl benzoates were Stille-coupled with bromobenzene and benzoyl chloride in 1,4-dioxane and toluene using [(Ph3P)4Pd] or [(Ph3P)2PdCl2] either alone or in combination with CuCN as cocatalyst at temperatures up to 80 °C. The products were found to be enantiomerically pure. (R)- and (S)-N-(tributylstannyl[D1]methyl)phthalimides gave enantiomerically pure products with benzoyl chloride, but with bromobenzene protected phenyl[D1]methylamines gave products of only 52–69?% ee depending on the solvent used. Tributyl(thio[D1]methyl)stannanes could not be Stille-coupled with benzoyl chloride or with bromobenzene. Similarly, dimethyl phenyl[D1]methylboronate underwent a Suzuki–Miyaura coupling with bromobenzene to give phenyl[D1]methylsilane with 99?% ee. All couplings followed a retentive course and, except in one case, the intermediate [XCHDPdLn] complexes were found to be microscopically configurationally stable.

Malova Krizkova, Petra; Hammerschmidt, Friedrich

2013-01-01

277

Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions.  

PubMed

The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate (OMP) decarboxylase (OMPDC) from Saccharomyces cerevisiae 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-(?-d-erythrofuranosyl)orotic acid and 1-(?-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, whereas 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, whereas 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 that for FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation. PMID:24053466

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

2013-10-22

278

Eleven new heaviest isotopes of elements Z=105 to Z=117 identified among the products of Bk249+Ca48 reactions  

NASA Astrophysics Data System (ADS)

The heaviest isotopes of elements Z=117 to Z=105, 294117, 293117, 290115, 289115, 286113, 285113, Rg282, Rg281, Mt278, Bh274, and Db270, were identified by means of the Dubna gas-filled recoil separator among the products of the Bk249 + Ca48 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 [Oganessian , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.104.142502 104, 142502 (2010)].

Oganessian, Yu. Ts.; Abdullin, F. Sh.; Bailey, P. D.; Benker, D. E.; Bennett, M. E.; Dmitriev, S. N.; Ezold, J. G.; Hamilton, J. H.; Henderson, R. A.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Moody, K. J.; Nelson, S. L.; Polyakov, A. N.; Porter, C. E.; Ramayya, A. V.; Riley, F. D.; Roberto, J. B.; Ryabinin, M. A.; Rykaczewski, K. P.; Sagaidak, R. N.; Shaughnessy, D. A.; Shirokovsky, I. V.; Stoyer, M. A.; Subbotin, V. G.; Sudowe, R.; Sukhov, A. M.; Taylor, R.; Tsyganov, Yu. S.; Utyonkov, V. K.; Voinov, A. A.; Vostokin, G. K.; Wilk, P. A.

2011-05-01

279

The reaction with oxygen of cytochrome oxidase (cytochrome d) in Escherichia coli K12: optical studies of intermediate species and cytochrome b oxidation at sub-zero temperatures.  

PubMed

Optical changes in d- and b-type cytochromes, following initiation of the reaction of cytochrome oxidase d with O2, have been studied in cells and derived membrane particles from oxygen-limited cultures of Escherichia coli K12. At successively higher temperatures between -132 and -88 degrees C, the first scan after photolysis of the Co-liganded, reduced oxidase in the presence of O2 and a slow increase in absorbance at 675 to 680 nm due to an unidentified chromophore. A similar sequence occurs when a single sample is scanned repetitively at -91 degrees C. At higher temperatures, oxidation of at least two spectrally distinct cytochromes b occurs. Selective photolysis of the cytochrome d-CO complex with a He-Ne laser shows that neither of these cytochromes is the CO-binding cytochrome o436. In all oxidation states examined, no absorbance in the 720 to 860 nm region was observed; it is concluded that both cytochromes d and o436 lack redox-active copper that has an environment similar to the copper(s) in mitochondrial cytochrome c oxidase. The amount of cytochrome d650 (but not the amount of reduced cytochrome o436) formed after photolysis is directly proportional to the oxygen concentration in the sample at the time of freeze trapping. The results are discussed in relation to the composition and mechanism of action of cytochrome d. PMID:6311942

Poole, R K; Salmon, I; Chance, B

1983-05-01

280

Recoil studies of photonuclear reactions on natCu, natAg, natTa, and 197Au at intermediate energies  

NASA Astrophysics Data System (ADS)

The recoil properties of nuclides produced in the photonuclear reactions on natCu, natAg, natTa, and 197Au induced by bremsstrahlung of end-point energies (E o) of 250 to 1000 MeV have been investigated using the thick-target thick-catcher method. The obtained mean ranges of produced nuclides smoothly increase with an increase of the mass difference (?A) between products and target, and show E 0-independence at E 0?600 MeV, reflecting the limiting behavior above (3, 3) resonance region. The mean kinetic energies, T, deduced from the mean ranges show the following two components; (1) (?, xn) products by giant-resonance and/or quasi-deuteron resonance absorption, (2) (?, xnyp) products by mainly (3, 3) resonance absorption. Slightly rapid increase of T was found around ?A=15, 18, 24, and 25 for natCu, natAg, natTa and 197Au, respectively, reflecting a change in mechanism. Kinematic properties of the product nuclei were calculated by using the PICA (Photon-Induced Intranuclear Cascade Analysis) code. The T calculated by the PICA code at E 0=400 MeV well reproduced the experimental results of natCu, but the same calculation for natAg, natTa, and 197Au gave lower mean kinetic energies than the experimental results.

Fujiwara, I.; Haba, H.; Matsumura, H.; Sakamoto, K.; Miyamoto, Y.; Oura, Y.; Shibata, S.; Furukawa, M.

1999-01-01

281

Recoil studies of photonuclear reactions on natCu, natAg, natTa, and 197Au at intermediate energies  

NASA Astrophysics Data System (ADS)

The recoil properties of nuclides produced in the photonuclear reactions on natCu, natAg, natTa, and 197Au induced by bremsstrahlung of end-point energies ( E o) of 250 to 1000 MeV have been investigated using the thick-target thick-catcher method. The obtained mean ranges of produced nuclides smoothly increase with an increase of the mass difference (?A) between products and target, and show E 0-independence at E 0?600 MeV, reflecting the limiting behavior above (3, 3) resonance region. The mean kinetic energies, T, deduced from the mean ranges show the following two components; (1) (?, xn) products by giant-resonance and/or quasi-deuteron resonance absorption, (2) (?, xnyp) products by mainly (3, 3) resonance absorption. Slightly rapid increase of T was found around ?A=15, 18, 24, and 25 for natCu, natAg, natTa and 197Au, respectively, reflecting a change in mechanism. Kinematic properties of the product nuclei were calculated by using the PICA (Photon-Induced Intranuclear Cascade Analysis) code. The T calculated by the PICA code at E 0=400 MeV well reproduced the experimental results of natCu, but the same calculation for natAg, natTa, and 197Au gave lower mean kinetic energies than the experimental results.

Fujiwara, I.; Haba, H.; Matsumura, H.; Sakamoto, K.; Miyamoto, Y.; Oura, Y.; Shibata, S.; Furukawa, M.

1999-01-01

282

Atmospheric chemistry: Intermediates just want to react  

NASA Astrophysics Data System (ADS)

Many of the rate parameters used in models of tropospheric chemistry are obtained through laboratory ozonolysis experiments. Now, results on the self-reaction of an important, but long-elusive, intermediate could alter many of those inferences.

Taatjes, Craig A.; Shallcross, Dudley E.; Percival, Carl J.

2014-06-01

283

The deterioration of intermediate moisture foods  

NASA Technical Reports Server (NTRS)

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.

Labruza, T. P.

1971-01-01

284

Intramolecular charge transfer of 4-(dimethylamino)benzonitrile probed by time-resolved fluorescence and transient absorption: No evidence for two ICT states and a {pi}{sigma}{sup *} reaction intermediate  

SciTech Connect

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}{sub 1} and {tau}{sub 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}{sub 1}(LE)<{tau}{sub 1}(ICT), is photoproduct formation. By employing a global analysis of the LE and ICT fluorescence response functions with a time resolution of 0.5 ps/channel in 1200 channels reliable kinetic and thermodynamic data can be obtained. The arguments presented in the literature in favor of a {pi}{sigma}* state with a bent CN group as an 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{sub 3}, and C(=O)OC{sub 2}H{sub 2} p-substituents, it is concluded that this ESA band cannot be attributed to a {pi}{sigma}{sup *} state, as only the C-C{identical_to}N group can undergo the required 120 deg. bending.

Zachariasse, Klaas A.; Druzhinin, Sergey I.; Senyushkina, Tamara [Max-Planck-Institut fuer biophysikalische Chemie, Spektroskopie und Photochemische Kinetik, 37070 Goettingen (Germany); Kovalenko, Sergey A. [Institut fuer Chemie, Humboldt Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin (Germany)

2009-12-14

285

NMR-spectroscopic evidence of intermediate-dependent pathways for acetic acid formation from methane and carbon monoxide over a ZnZSM-5 zeolite catalyst.  

PubMed

Two ways: a Zn-modified ZSM-5 zeolite catalyst was developed for the reaction of methane with carbon monoxide to directly produce acetic acid under mild conditions (573-623 K), and two different intermediate-dependent reaction pathways were unambiguously identified for acetic acid formation by in situ solid-state NMR spectroscopy. PMID:22389151

Wang, Xiumei; Qi, Guodong; Xu, Jun; Li, Bojie; Wang, Chao; Deng, Feng

2012-04-16

286

Transient Ru-methyl formate intermediates generated with bifunctional transfer hydrogenation catalysts  

PubMed Central

Desorption electrospray ionization (DESI) coupled to high-resolution Orbitrap mass spectrometry (MS) was used to study the reactivity of a (?-amino alcohol)(arene)RuCl transfer hydrogenation catalytic precursor in methanol (CH3OH). By placing [(p-cymene)RuCl2]2 on a surface and spraying a solution of ?-amino alcohol in methanol, two unique transient intermediates having lifetimes in the submillisecond to millisecond range were detected. These intermediates were identified as Ru (II) and Ru (IV) complexes incorporating methyl formate (HCOOCH3). The Ru (IV) intermediate is not observed when the DESI spray solution is sparged with Ar gas, indicating that O2 dissolved in the solvent is necessary for oxidizing Ru (II) to Ru (IV). These proposed intermediates are supported by high-resolution and high mass accuracy measurements and by comparing experimental to calculated isotope profiles. Additionally, analyzing the bulk reaction mixture using gas chromatography-MS and nuclear magnetic resonance spectroscopy confirms the formation of HCOOCH3. These results represent an example that species generated from the (?-amino alcohol)(arene)RuCl (II) catalytic precursor can selectively oxidize CH3OH to HCOOCH3. This observation leads us to propose a pathway that can compete with the hydrogen transfer catalytic cycle. Although bifunctional hydrogen transfer with Ru catalysts has been well-studied, the ability of DESI to intercept intermediates formed in the first few milliseconds of a chemical reaction allowed identification of previously unrecognized intermediates and reaction pathways in this catalytic system.

Perry, Richard H.; Brownell, Kristen R.; Chingin, Konstantin; Cahill, Thomas J.; Waymouth, Robert M.; Zare, Richard N.

2012-01-01

287

A label-free selected reaction monitoring workflow identifies a subset of pregnancy specific glycoproteins as potential predictive markers of early-onset pre-eclampsia.  

PubMed

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

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

2013-11-01

288

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

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.

Torres, Luciene de Fatima Costa; Ribeiro, Dayana; Hirata, Raphael; Pacheco, Luis Gustavo Carvalho; Souza, Monica Cristina; dos Santos, Louisy Sanches; dos Santos, Cintia 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

289

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)

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.

Miller, Laurence G.; Warner, Karen L.; Baesman, Shaun M.; Oremland, Ronald S.; McDonald, Ian R.; Radajewski, Stefan; Murrell, J. Colin

2004-08-01

290

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

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.

Miller, L. G.; Warner, K. L.; Baesman, S. M.; Oremland, R. S.; McDonald, I. R.; Radajewski, S.; Murrell, J. C.

2004-01-01

291

Catalytic mechanism of ?-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling  

PubMed Central

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 ?-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 ?,?-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.

Barabas, Orsolya; Nemeth, Veronika; Bodor, Andrea; Perczel, Andras; Rosta, Edina; Kele, Zoltan; Zagyva, Imre; Szabadka, Zoltan; Grolmusz, Vince I.; Wilmanns, Matthias; Vertessy, Beata G.

2013-01-01

292

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)

An important side effect of hydraulic fracturing (HF) in shale gas wells is the production of saline flow-back water. This water often contains total dissolved soil (TDS) concentrations greater than 100,000 ppm which requires expensive treatment and disposal of the produced water. Possible origins of the high TDS content include: 1. Mixing of fresh HF-fluids with highly saline pore fluids in the targeted shale. 2. Migration and mixing of saline brines by newly-formed fractures into the HF-water from neighboring formations. 3. Water rock interactions between the targeted shale and HF-water that include mineral dissolution, pyrite oxidation buffered by carbonate dissolution and cation exchange in newly hydrated clay minerals.. These possibilities are not mutually exclusive and all may be operating to alter flow-back water chemistry. This study will examine geochemical reactions between a productive Gulf Coast shale and manufactured HF-waters using sealed bench top experiments and high temperature/high pressure autoclave experiments. The samples of the shale were collected from core material housed at The Bureau of Economic Geology collected from two wells. The manufactured HF-waters were produced by mixing NaCl, KCl and CaCl2 salts with De-ionized water at approximately 0, 2000 and 20,000 ppm. During experiments, elements that show large increases in aqueous concentrations are Na, Cl, Ca and SO4. Simultaneous increases in Na and Cl, coupled with high Cl/Br ratios, suggest halite dissolution rather than pore space brine is responsible for Na and Cl concentrations. Simultaneous increase in Ca and SO4 suggest anhydrite dissolution. (SEM imaging shows that anhydrite crystals are usually embedded with the framework mineral grains, rather than precipitated in pores during sample drying, which suggests mineral source of Ca and SO4, possibly for Na and Cl as well). Pyrite oxidation and calcium carbonate dissolution were not significant due to no decrease in pH and no 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.

Molnar, I. L.; O'Carroll, D. M.; Willson, C. S.; Gerhard, J.

2011-12-01

293

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)

An important side effect of hydraulic fracturing (HF) in shale gas wells is the production of saline flow-back water. This water often contains total dissolved soil (TDS) concentrations greater than 100,000 ppm which requires expensive treatment and disposal of the produced water. Possible origins of the high TDS content include: 1. Mixing of fresh HF-fluids with highly saline pore fluids in the targeted shale. 2. Migration and mixing of saline brines by newly-formed fractures into the HF-water from neighboring formations. 3. Water rock interactions between the targeted shale and HF-water that include mineral dissolution, pyrite oxidation buffered by carbonate dissolution and cation exchange in newly hydrated clay minerals.. These possibilities are not mutually exclusive and all may be operating to alter flow-back water chemistry. This study will examine geochemical reactions between a productive Gulf Coast shale and manufactured HF-waters using sealed bench top experiments and high temperature/high pressure autoclave experiments. The samples of the shale were collected from core material housed at The Bureau of Economic Geology collected from two wells. The manufactured HF-waters were produced by mixing NaCl, KCl and CaCl2 salts with De-ionized water at approximately 0, 2000 and 20,000 ppm. During experiments, elements that show large increases in aqueous concentrations are Na, Cl, Ca and SO4. Simultaneous increases in Na and Cl, coupled with high Cl/Br ratios, suggest halite dissolution rather than pore space brine is responsible for Na and Cl concentrations. Simultaneous increase in Ca and SO4 suggest anhydrite dissolution. (SEM imaging shows that anhydrite crystals are usually embedded with the framework mineral grains, rather than precipitated in pores during sample drying, which suggests mineral source of Ca and SO4, possibly for Na and Cl as well). Pyrite oxidation and calcium carbonate dissolution were not significant due to no decrease in pH and no 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.

Mickler, P. J.; Lu, J.; Nicot, J.

2013-12-01

294

Studies of intermediate-mass fragment emission in the [sup 3]He+[sup nat]Ag, [sup 197]Au reactions between 0. 48 and 3. 6 GeV  

SciTech Connect

Intermediate-mass fragments formed in reactions of [sup 3]He ions with [sup nat]Ag and [sup 197]Au targets have been studied at five energies between 0.48 and 3.6 GeV. Inclusive measurements show that as the bombarding energy increases, there is a strong enhancement in fragment cross sections and a trend toward isotropic angular distributions. Between 0.90 and 1.8 GeV, a change in the emission mechanism is suggested by (1) kinetic energy spectra with high-energy tails that become distinctly flatter, (2) a broadening of the spectral Coulomb peaks toward lower energies, and (3) charge distributions that become constant, exhibiting a power-law exponent [tau][approx]2.0. Exclusive studies of the [sup 3]He+[sup nat]Ag system at 0.90 and 3.6 GeV detected multifragment events with multiplicities up to four. The probability for high-multiplicity events increases about 40-fold between 0.90 and 3.6 GeV. At both energies, the kinetic energy spectra depend on multiplicity, especially when triggering on backward-emitted fragments. For multiplicity three events, a rapidity analysis of the data at 3.6 GeV is consistent with a single, relatively low source velocity, [ital v][sub [ital S

Yennello, S.J.; Kwiatkowski, K.; Pollacco, E.C.; Volant, C.; Cassagnou, Y.; Dayras, R.; Fields, D.E.; Harar, S.; Hourani, E.; Legrain, R.; Norbeck, E.; Planeta, R.; Wile, J.L.; Yoder, N.R.; Viola, V.E. (Indiana University, Bloomington, Indiana 47405 (United States) DAPNIA/Service de Physique Nucleaire, Centre d'Etudes Nucleaires de Saclay, F-91191, Gif-sur-Yvette (France) Grand Accelerateur National d'Ions Lourds (GANIL), Boite Postale No. 5027, boulevard Henri Becquerel, 14021 Caen Cedex (France) Institut de Physique Nucleaire Orsay, Boite Postale F-91406, Orsay (France) Iowa University, Iowa City, Iowa 52242 (United States) Jagellonian University, Krakow (Poland))

1993-09-01

295

Surprisingly High Activity for Oxygen Reduction Reaction of Selected Oxides Lacking Long Oxygen-Ion Diffusion Paths at Intermediate Temperatures: A Case Study of Cobalt-Free BaFeO3-?.  

PubMed

The widespread application of solid oxide fuel cell technology requires the development of innovative electrodes with high activity for oxygen reduction reaction (ORR) at intermediate temperatures. Here, we demonstrate that a cobalt-free parent oxide BaFeO3-? (BF), which lacks long-range oxygen-ion diffusion paths, has surprisingly high electrocatalytic activity for ORR. Both in situ high-temperature X-ray diffraction analysis on room-temperature powder and transmission electron microscopy on quenched powder are applied to investigate the crystal structure of BF. Despite the lack of long oxygen-ion diffusion paths, the easy redox of iron cations as demonstrated by thermal gravimetric analysis (TGA) and oxygen temperature-programmed desorption and the high oxygen vacancy concentration as supported by iodometric titration and TGA benefit the reduction of oxygen to oxygen ions. Moreover, the electrical conductivity relaxation technique in conjunction with a transient thermogravimetric study reveals very high surface exchange kinetics of BF oxide. At 700 °C, the area specific resistance of BF cathode, as expressed by a symmetrical cell configuration, is only ?0.021 ? cm(2), and the derived single fuel cell achieves high power output with a peak power density of 870 mW cm(-2). It suggests that an undoped BF parent oxide can be used as a high-efficiency catalyst for ORR. PMID:24978102

Dong, Feifei; Chen, Yubo; Chen, Dengjie; Shao, Zongping

2014-07-23

296

Effect of Bonding Time on Interfacial Reaction and Mechanical Properties of Diffusion-Bonded Joint Between Ti-6Al-4V and 304 Stainless Steel Using Nickel as an Intermediate Material  

NASA Astrophysics Data System (ADS)

In the current study, solid-state diffusion bonding between Ti-6Al-4V (TiA) and 304 stainless steel (SS) using pure nickel (Ni) of 200- ?m thickness as an intermediate material was carried out in vacuum. Uniaxial compressive pressure and temperature were kept at 4 MPa and 1023 K (750 °C), respectively, and the bonding time was varied from 30 to 120 minutes in steps of 15 minutes. Scanning electron microscopy images, in backscattered electron mode, revealed the layerwise Ti-Ni-based intermetallics like either Ni3Ti or both Ni3Ti and NiTi at titanium alloy-nickel (TiA/Ni) interface, whereas nickel-stainless steel (Ni/SS) interface was free from intermetallic phases for all the joints. Chemical composition of the reaction layers was determined by energy dispersive spectroscopy (SEM-EDS) and confirmed by X-ray diffraction study. Maximum tensile strength of ~382 MPa along with ~3.7 pct ductility was observed for the joints processed for 60 minutes. It was found that the extent of diffusion zone at Ni/SS interface was greater than that of TiA/Ni interface. From the microhardness profile, fractured surfaces, and fracture path, it was demonstrated that the failure of the joints was initiated and propagated apparently at TiA/Ni interface near Ni3Ti intermetallic for bonding time less than 90 minutes, and through Ni for bonding time 90 minutes and greater.

Thirunavukarasu, Gopinath; Kundu, Sukumar; Mishra, Brajendra; Chatterjee, Subrata

2014-04-01

297

The aromatic ene reaction  

NASA Astrophysics Data System (ADS)

The ene reaction is a pericyclic process in which an alkene with an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed ?-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 intermediate 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: (1) hexadehydro-Diels-Alder (for aryne generation), (2) intramolecular aromatic ene and (3) 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 multistage, reagent- and by-product-free, single-pot transformations.

Niu, Dawen; Hoye, Thomas R.

2014-01-01

298

Functionalization of the corrole ring: the role of isocorrole intermediates  

PubMed Central

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.

Tortora, Luca; Nardis, Sara; Fronczek, Frank R.; Smith, Kevin M.; Paolesse, Roberto

2011-01-01

299

On MHD intermediate shocks  

Microsoft Academic Search

The numerical solution of resistive MHD equations, in order to show that some intermediate shocks are admissible, is described. A coplanar case with v(z) = Bz = 0, and a full MHD case with v(z) and Bz not equal to zero are studied. In the first cast no intermediate wave existed, but based on the solution of the equations intermediate

C. C. Wu

1987-01-01

300

Some Intermediate-Level Violin Concertos.  

ERIC Educational Resources Information Center

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,…

Abramson, Michael

1997-01-01

301

Multimeric intermediates in the pathway to the aggregated inclusion body state for P22 tailspike polypeptide chains.  

PubMed Central

The failure of newly synthesized polypeptide chains to reach the native conformation due to their accumulation as inclusion bodies is a serious problem in biotechnology. The critical intermediate at the junction between the productive folding and the inclusion body pathway has been previously identified for the P22 tailspike endorhamnosidase. We have been able to trap subsequent intermediates in the in vitro pathway to the aggregated inclusion body state. Nondenaturing gel electrophoresis identified a sequential series of multimeric intermediates in the aggregation pathway. These represent discrete species formed from noncovalent association of partially folded intermediates rather than aggregation of native-like trimeric species. Monomer, dimer, trimer, tetramer, pentamer, and hexamer states of the partially folded species were populated in the initial stages of the aggregation reaction. This methodology of isolating early multimers along the aggregation pathway was applicable to other proteins, such as the P22 coat protein and carbonic anhydrase II.

Speed, M. A.; Wang, D. I.; King, J.

1995-01-01

302

Effect of Bonding Temperature on Interfacial Reaction and Mechanical Properties of Diffusion-Bonded Joint Between Ti-6Al-4V and 304 Stainless Steel Using Nickel as an Intermediate Material  

NASA Astrophysics Data System (ADS)

An investigation was carried out on the solid-state diffusion bonding between Ti-6Al-4V (TiA) and 304 stainless steel (SS) using pure nickel (Ni) of 200- ?m thickness as an intermediate material prepared in vacuum in the temperature range from 973 K to 1073 K (700 °C to 800 °C) in steps of 298 K (25 °C) using uniaxial compressive pressure of 3 MPa and 60 minutes as bonding time. Scanning electron microscopy images, in backscattered electron mode, had revealed existence of layerwise Ti-Ni-based intermetallics such as either Ni3Ti or both Ni3Ti and NiTi at titanium alloy-nickel (TiA/Ni) interface, whereas nickel-stainless steel (Ni/SS) diffusion zone was free from intermetallic phases for all joints processed. Chemical composition of the reaction layers was determined in atomic percentage by energy dispersive spectroscopy and confirmed by X-ray diffraction study. Room-temperature properties of the bonded joints were characterized using microhardness evaluation and tensile testing. The maximum hardness value of ~800 HV was observed at TiA/Ni interface for the bond processed at 1073 K (800 °C). The hardness value at Ni/SS interface for all the bonds was found to be ~330 HV. Maximum tensile strength of ~206 MPa along with ~2.9 pct ductility was obtained for the joint processed at 1023 K (750 °C). It was observed from the activation study that the diffusion rate at TiA/Ni interface is lesser than that at the Ni/SS interface. From microhardness profile, fractured surfaces and fracture path, it was demonstrated that failure of the joints was initiated and propagated apparently at the TiA/Ni interface near Ni3Ti intermetallic phase.

Thirunavukarasu, Gopinath; Kundu, Sukumar; Mishra, Brajendra; Chatterjee, Subrata

2014-04-01

303

Cluster analysis of time-dependent crystallographic data: Direct identification of time-independent structural intermediates.  

PubMed

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

Kostov, Konstantin S; Moffat, Keith

2011-01-19

304

Using metal-catalyzed oxidation reactions and mass spectrometry to identify amino acid residues within 10 Å of the metal in Cu-binding proteins  

Microsoft Academic Search

Metal-catalyzed oxidation (MCO) reactions and mass spectrometry (MS) can be used together to determine the amino acids bound\\u000a to Cu in a metalloprotein. Selective oxidation of only amino acids bound to Cu during the MCO\\/MS approach relies on proper\\u000a choice of the types and concentrations of the reducing and oxidizing agents. We show here that if these MCO reagent concentrations

Juma D. Bridgewater; Jihyeon Lim; Richard W. Vachet

2006-01-01

305

Identification of intra- and interspecific Leishmania genetic polymorphisms by arbitrary primed polymerase chain reactions and use of polymorphic DNA to identify differentially regulated genes  

Microsoft Academic Search

Arbitrary primed polymerase chain reactions (AP-PCR) were used to amplify different polymorphic genomic DNA fragments from various Old WorldLeishmania species. Using four 10-mer AP primers, geographic isolates ofL. donovani and various Old World species ofLeishmania could be readily distinguished from one another by the pattern of amplified DNA products. Our studies confirmed two important characteristics of AP-PCR: its abilities to

Gregory P. Pogue; Sharat Koul; Nancy S. Lee; Dennis M. Dwyer; Hira L. Nakhasi

1995-01-01

306

Trinuclear Pd?O? intermediate in aerobic oxidation catalysis.  

PubMed

The activation of O2 is a key step in selective catalytic aerobic oxidation reactions mediated by transition metals. The bridging trinuclear palladium species, [(LPd(II))3(?(3)-O)2](2+) (L=2,9-dimethylphenanthroline), was identified during the [LPd(OAc)]2(OTf)2-catalyzed aerobic oxidation of 1,2-propanediol. Independent synthesis, structural characterization, and catalytic studies of the trinuclear compound show that it is a product of oxygen activation by reduced palladium species and is a competent intermediate in the catalytic aerobic oxidation of alcohols. The formation and catalytic activity of the trinuclear Pd3O2 species illuminates a multinuclear pathway for aerobic oxidation reactions catalyzed by Pd complexes. PMID:24711099

Ingram, Andrew J; Solis-Ibarra, Diego; Zare, Richard N; Waymouth, Robert M

2014-05-26

307

Interception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds.  

PubMed

In the search for new efficacious antibiotics, biosynthetic engineering offers attractive opportunities to introduce minor alterations to antibiotic structures that may overcome resistance. Dbv29, a flavin-containing oxidase, catalyzes the four-electron oxidation of a vancomycin-like glycopeptide to yield A40926. Structural and biochemical examination of Dbv29 now provides insights into residues that govern flavinylation and activity, protein conformation and reaction mechanism. In particular, the serendipitous discovery of a reaction intermediate in the crystal structure led us to identify an unexpected opportunity to intercept the normal enzyme mechanism at two different points to create new teicoplanin analogs. Using this method, we synthesized families of antibiotic analogs with amidated and aminated lipid chains, some of which showed marked potency and efficacy against multidrug resistant pathogens. This method offers a new strategy for the development of chemical diversity to combat antibacterial resistance. PMID:21478878

Liu, Yu-Chen; Li, Yi-Shan; Lyu, Syue-Yi; Hsu, Li-Jen; Chen, Yu-Hou; Huang, Yu-Ting; Chan, Hsiu-Chien; Huang, Chuen-Jiuan; Chen, Gan-Hong; Chou, Chia-Cheng; Tsai, Ming-Daw; Li, Tsung-Lin

2011-05-01

308

Carbon-13 nuclear magnetic resonance spectroscopic investigation of the Kiliani reaction  

SciTech Connect

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.

Blazer, R.M.; Whaley, T.W.

1980-07-16

309

40 CFR 721.983 - Sulfonyl azide intermediate (generic).  

Code of Federal Regulations, 2010 CFR

...2009-07-01 2009-07-01 false Sulfonyl azide intermediate (generic). 721.983...Chemical Substances § 721.983 Sulfonyl azide intermediate (generic). (a) Chemical...substance identified generically as sulfonyl azide intermediate (PMN P-99-1202)...

2009-07-01

310

40 CFR 721.983 - Sulfonyl azide intermediate (generic).  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false Sulfonyl azide intermediate (generic). 721.983...Chemical Substances § 721.983 Sulfonyl azide intermediate (generic). (a) Chemical...substance identified generically as sulfonyl azide intermediate (PMN P-99-1202)...

2013-07-01

311

40 CFR 721.983 - Sulfonyl azide intermediate (generic).  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false Sulfonyl azide intermediate (generic). 721.983...Chemical Substances § 721.983 Sulfonyl azide intermediate (generic). (a) Chemical...substance identified generically as sulfonyl azide intermediate (PMN P-99-1202)...

2010-07-01

312

A common intermediate for N2 formation in enzymes and zeolites: side-on Cu-nitrosyl complexes  

SciTech Connect

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 Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle Memorial Institute.

Kwak, Ja Hun; Lee, Jong H.; Burton, Sarah D.; Lipton, Andrew S.; Peden, Charles HF; Szanyi, Janos

2013-09-16

313

MHD intermediate shock discontinuities. I - Rankine-Hugoniot conditions  

NASA Technical Reports Server (NTRS)

Recent numerical investigations have focused attention once more on the role of intermediate shocks in MHD. Four types of intermediate shock are identified using a graphical representation of the MHD Rankine-Hugoniot conditions. This same representation can be used to exhibit the close relationship of intermediate shocks to switch-on shocks and rotational discontinuities. The conditions under which intermediate discontinuities can be found are elucidated. The variations in velocity, pressure, entropy and magnetic-field jumps with upstream parameters in intermediate shocks are exhibited graphically. The evolutionary arguments traditionally advanced against intermediate shocks may fail because the equations of classical MHD are not strictly hyperbolic.

Kennel, C. F.; Blandford, R. D.; Coppi, P.

1989-01-01

314

Membrane Fusion Intermediates via Directional and Full Assembly of the SNARE Complex  

PubMed Central

Cellular membrane fusion is thought to proceed through intermediates including docking of apposed lipid bilayers, merging of proximal leaflets to form a hemifusion diaphragm, and fusion pore opening. A membrane-bridging four-helix complex of soluble N-ethylmaleimide–sensitive factor attachment protein receptors (SNAREs) mediates fusion. However, how assembly of the SNARE complex generates docking and other fusion intermediates is unknown. Using a cell-free reaction we identified intermediates visually and then arrested the SNARE fusion machinery when fusion was about to begin. Partial and directional assembly of SNAREs tightly docked bilayers, but efficient fusion and an extended form of hemifusion required assembly beyond the core complex to the membrane-connecting linkers. We propose that straining of lipids at the edges of an extended docking zone initiates fusion.

Hernandez, Javier M.; Stein, Alexander; Behrmann, Elmar; Riedel, Dietmar; Cypionka, Anna; Farsi, Zohreh; Walla, Peter J.; Raunser, Stefan; Jahn, Reinhard

2013-01-01

315

Kinetics : IntermediateInMech (15 Variations)  

NSDL National Science Digital Library

Suppose that for the reaction of nitrogen dioxide and carbon monoxide NO 2 + CO NO + CO 2 the following mechanism has been proposed at high temperatures: (1) NO 2 + CO O-N-O-C-O (slow) (2) O-N-O-C-O NO + CO 2 (fast) Check the box for each species that is an intermediate in this mechanism.

316

Properties of Swift`s intermediate bursts  

NASA Astrophysics Data System (ADS)

Based on their prompt, high-energy emission, gamma-ray bursts are usually classified into short-duration and long-duration classes. A third intermediate group has been identified on statistical grounds but its individual properties have not yet been studied in detail. Using the large sample of follow-up observations of GRBs produced during the Swift era we analyze the individual characteristics of this group. We find that intermediate bursts are significantly different from short GRBs but share many properties with long bursts, probably pointing to a common progenitor type. However, we find that intermediate bursts are significantly dimmer and have on average lower redshifts.

Veres, P.; de Ugarte Postigo, A.; Horvath, I.; Bagoly, Z.; Kann, D. A.; Thöne, C. C.; Balazs, L. G.; D'Avanzo, P.; Aloy, M. A.; Foley, S.; Campana, S.; Mao, J.; Jakobsson, P.; Covino, S.; Fynbo, J. P. U.; Gorosabel, J.; Castro-Tirado, A. J.; Nardini, M.; Amati, L.

2011-08-01

317

High-Energy Intermediates in Protein Unfolding Characterized by Thiol Labeling under Nativelike Conditions.  

PubMed

A protein unfolding reaction usually appears to be so dominated by a large free energy barrier that identifying and characterizing high-energy intermediates and, hence, dissecting the unfolding reaction into multiple structural transitions have proven to be a challenge. In particular, it has been difficult to identify any detected high-energy intermediate with the dry (DMG) and wet (WMG) molten globules that have been implicated in the unfolding reactions of at least some proteins. In this study, a native-state thiol labeling methodology was used to identify high-energy intermediates, as well as to delineate the barriers to the disruption of side chain packing interactions and to site-specific solvent exposure in different regions of the small protein, single-chain monellin (MNEI). Labeling studies of four single-cysteine-containing variants of MNEI have identified three high-energy intermediates, populated to very low extents under nativelike conditions. A significant dispersion in the opening rates of the cysteine side chains has allowed multiple steps, leading to the loss of side chain packing, to be resolved temporally. A detailed structural analysis of the positions of the four cysteine residue positions, which are buried to different depths within the protein, has suggested a direct correlation with the structure of a DMG, detected in previous studies. It is observed that side chain packing within the core of the protein is maintained, while that at the surface is disrupted, in the DMG. The core of the protein becomes solvent-exposed only in a WMG populated after the rate-limiting step of unfolding at high denaturant concentrations. PMID:24832528

Malhotra, Pooja; Udgaonkar, Jayant B

2014-06-10

318

Formation of Compound I and Compound II Ferryl Species in the Reaction of Hemoglobin I from Lucina pectinata with Hydrogen Peroxide  

Microsoft Academic Search

The formation of ferryl heme (Fe(IV) = O) species, i.e., compound I and compound II, has been identified as the main intermediates in heme protein peroxidative reactions. We report stopped-flow kinetic measurements which illustrate that the reaction of hemoglobin I (HbI) from Lucina pectinata with hydrogen peroxide produce ferryl intermediates compound I and compound II. Compound I appears relatively stable

Walleska De Jesús-Bonilla; José E. Cortés-Figueroa; Fernando A. Souto-Bachiller; Lolita Rodr??guez; Juan López-Garriga

2001-01-01

319

A unified intermediate and mechanism for soot combustion on potassium-supported oxides  

NASA Astrophysics Data System (ADS)

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.

Li, Qian; Wang, Xiao; Xin, Ying; Zhang, Zhaoliang; Zhang, Yexin; Hao, Ce; Meng, Ming; Zheng, Lirong; Zheng, Lei

2014-04-01

320

A unified intermediate and mechanism for soot combustion on potassium-supported oxides  

PubMed Central

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.

Li, Qian; Wang, Xiao; Xin, Ying; Zhang, Zhaoliang; Zhang, Yexin; Hao, Ce; Meng, Ming; Zheng, Lirong; Zheng, Lei

2014-01-01

321

Epidemiology of imported cutaneous leishmaniasis at the Hospital for Tropical Diseases, London, United Kingdom: use of polymerase chain reaction to identify the species.  

PubMed

This study reviewed all patients diagnosed with imported cutaneous leishmaniasis (CL) at the Hospital for Tropical Diseases in London, United Kingdom, over an 11-year period. Diagnostic and epidemiologic information was collected prospectively for all patients with imported CL to this hospital during 1998-2009. A total of 223 patients were given a diagnosis of CL. Ninety patients were diagnosed with Old World CL, which was caused most commonly by Leishmania donovani complex (n = 20). A total of 71% were tourists to the Mediterranean region, 36% were migrants or visiting friends and relatives, and 17% were soldiers. One hundred thirty-three patients were given a diagnosis of New World CL. The Leishmania subgenus Viannia caused 97 of these cases; 44% of these were in backpackers and 29% were in soldiers. Polymerase chain reaction was more sensitive and faster for detecting Leishmania DNA (86% for Old World CL and 96% for New World CL) than culture. This is the largest study of imported leishmaniasis, and demonstrates that tourists to the Mediterranean and backpackers in Central and South America are at risk for this disease. PMID:22232460

Wall, Emma C; Watson, Julie; Armstrong, Margaret; Chiodini, Peter L; Lockwood, Diana N

2012-01-01

322

Epidemiology of Imported Cutaneous Leishmaniasis at the Hospital for Tropical Diseases, London, United Kingdom: Use of Polymerase Chain Reaction to Identify the Species  

PubMed Central

This study reviewed all patients diagnosed with imported cutaneous leishmaniasis (CL) at the Hospital for Tropical Diseases in London, United Kingdom, over an 11-year period. Diagnostic and epidemiologic information was collected prospectively for all patients with imported CL to this hospital during 1998–2009. A total of 223 patients were given a diagnosis of CL. Ninety patients were diagnosed with Old World CL, which was caused most commonly by Leishmania donovani complex (n = 20). A total of 71% were tourists to the Mediterranean region, 36% were migrants or visiting friends and relatives, and 17% were soldiers. One hundred thirty-three patients were given a diagnosis of New World CL. The Leishmania subgenus Viannia caused 97 of these cases; 44% of these were in backpackers and 29% were in soldiers. Polymerase chain reaction was more sensitive and faster for detecting Leishmania DNA (86% for Old World CL and 96% for New World CL) than culture. This is the largest study of imported leishmaniasis, and demonstrates that tourists to the Mediterranean and backpackers in Central and South America are at risk for this disease.

Wall, Emma C.; Watson, Julie; Armstrong, Margaret; Chiodini, Peter L.; Lockwood, Diana N.

2012-01-01

323

[The application of monoclonal peroxidase conjugates to identify comma bacillus of serum groups 01 and 0139 in the reaction of dot-immune analysis].  

PubMed

The source of monoclonal antibodies was chosen the cultural fluid of hybridoma-producers deposited in the specialized collection of cell cultures of vertebrates (St. Petersburg) with numbers RKKK(P) 386D and RKKK(P) 674D. The specific immunoglobulin (Ig) from cultural fluid was concentrated by precipitation with saturated solution of ammonium sulfate. The scheme of obtaining monoclonal antibodies included activation of peroxidase, conjugation of activated peroxidase with Ig, removal of unbounded proteins, storage and control. The preservation of activity of conjugates was supported with BSA (10%) or glycerin (50%). The last on is preferable to be applied for this purpose. The test of monoclonal antibody-01 and monoclonal antibody-0139 of peroxidase conjugates with kit of strains of comma bacillus 01 and 0139 demonstrated their strict specificity because they interacted only with corresponding serum groups under absence of crossed reactions with representatives of geterologic microorganisms. The direct dot-immune analysis is carried out during 1.5 hour and its sensitivity is within the limits 105-106. The application of diagnostic monoclonal peroxidase conjugates 01, 0139 in laboratory practice can promote the increase of specificity of serologic analysis of cholera and saving time-frame of its application. PMID:23808022

Alekseeva, L P; Kozlova, G A; Markina, O V; Kretenchuk, O F; Iagovkin, M E; Bursha, O S

2013-03-01

324

Evaluation of repetitive extragenic palindromic-polymerase chain reaction and denatured gradient gel electrophoresis in identifying Salmonella serotypes isolated from processed turkeys.  

PubMed

The current study was conducted to determine the usefulness of 2 molecular techniques, automated repetitive extragenic palindromic-PCR (REP-PCR) and denaturing gradient gel electrophoresis (DGGE), to identify Salmonella serotypes of poultry origin. Salmonella continues to be a foodborne pathogen of principal concern in the United States. The interspersed conserved repetitive sequence of the bacterial genome and the 16-23S rDNA intergenic spacer region were amplified for REP-PCR and DGGE, respectively. Fifty-four Salmonella isolates from 2 turkey processing plants (A and B) were used for this comparison. Serotypes consisted of Brandenburg, Derby, Hadar, and Typhimurium, with n=6, 21, 12, and 15, respectively. The REP-PCR was fully automated, whereas DGGE was run on an acrylamide gel and the image was captured digitally. Both dendrograms were created using the unweighted pair group method with arithmetic average. There were more variations in percentage similarity in DGGE when compared with REP-PCR. The banding patterns were more distinct and uniform in the REP-PCR group than with DGGE. The results from the REP-PCR were generated within 1 h, whereas the DGGE required approximately 1 d to run. These data suggest that DGGE and REP-PCR are useful tools for identifying Salmonella serotypes isolated from poultry production or processing environments. In addition, REP-PCR is more rapid, may have a higher discriminatory power, but may be less cost-effective than DGGE. However, more research may be needed to validate this argument. Both DGGE and REP-PCR displayed high sensitivity in discriminating among Salmonella serotypes and either method could be considered as an alternative to more expensive and time-consuming conventional antibody-based serotyping methodologies. PMID:20460676

Anderson, P N; Hume, M E; Byrd, J A; Hernandez, C; Stevens, S M; Stringfellow, K; Caldwell, D J

2010-06-01

325

Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR.  

PubMed

Many biochemical processes proceed through the formation of functionally significant intermediates. Although the identification and characterization of such species can provide vital clues about the mechanisms of the reactions involved, it is challenging to obtain information of this type in cases where the intermediates are transient or present only at low population. One important example of such a situation involves the folding behaviour of small proteins that represents a model for the acquisition of functional structure in biology. Here we use relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy to identify, for two mutational variants of one such protein, the SH3 domain from Fyn tyrosine kinase, a low-population folding intermediate in equilibrium with its unfolded and fully folded states. By performing the NMR experiments at different temperatures, this approach has enabled characterization of the kinetics and energetics of the folding process as well as providing structures of the intermediates. A general strategy emerges for an experimental determination of the energy landscape of a protein by applying this methodology to a series of mutants whose intermediates have differing degrees of native-like structure. PMID:15282609

Korzhnev, Dmitry M; Salvatella, Xavier; Vendruscolo, Michele; Di Nardo, Ariel A; Davidson, Alan R; Dobson, Christopher M; Kay, Lewis E

2004-07-29

326

INTERMEDIATE READINGS IN TAGALOG.  

ERIC Educational Resources Information Center

THE SECOND IN A SERIES OF TEXTS DESIGNED TO HELP THE STUDENT ACHIEVE AN UNDERSTANDING OF FILIPINO CULTURE AND ACQUIRE ENOUGH PROFICIENCY IN TAGALOG TO COMMUNICATE EASILY AND MEANINGFULLY, THESE INTERMEDIATE READINGS ARE COORDINATED WITH THE EDITOR'S "BEGINNING TAGALOG" (ED 014 696). INCLUDED IN PART I ARE READINGS WRITTEN ESPECIALLY FOR THIS TEXT…

BOWEN, J. DONALD, ED.

327

Intermediate Pashto. Textbook.  

ERIC Educational Resources Information Center

The textbook for intermediate level Pashto instruction consists of 14 units (15-28) on a variety of cultural topics and linguistic structures. Cultural topics include engagement and marriage, children's education, agriculture and related subjects, the family, Pashtun history, genealogies of major Pashtun tribes, the Pashtun code of behavior,…

Tegey, Habibullah; Robson, Barbara

328

Intermediate Pashto. Workbook.  

ERIC Educational Resources Information Center

The workbook accompanies the "Intermediate Pashto" textbook (FL 019 797), and provides additional explanations, in English, of Pashtun culture and Pashto grammar. It also contains additional exercises, with answer keys. The units and sections correspond to those of the textbook. Unit overviews are intended to be read, with parallel textbook…

Tegey, Habibullah; Robson, Barbara

329

Intermediate Pashto. Teachers' Manual.  

ERIC Educational Resources Information Center

The teachers' guide to the "Intermediate Pashto" textbook (FL 019 797) contains notes for the teacher on each of the fourteen units and sub-sections of the textbook. Unit and section headings are in English and Pashto; virtually all text is in Pashto. (MSE)

Tegey, Habibullah; Robson, Barbara

330

SPACE: Intermediate Level Modules.  

ERIC Educational Resources Information Center

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…

Indiana State Dept. of Education, Indianapolis. Center for School Improvement and Performance.

331

THE EVOLVING INTERMEDIATE UNIT.  

ERIC Educational Resources Information Center

THE TRADITIONAL CONCEPT OF THE INTERMEDIATE ADMINISTRATIVE SCHOOL UNIT IS THAT OF THE COUNTY SUPERINTENDENT OF SCHOOLS OPERATING AS AN ARM OF THE STATE, WITH REGULATORY POWERS AND RECORD KEEPING DUTIES AS WELL AS EDUCATIONAL LEADERSHIP FUNCTIONS. THE NEW TYPE OF UNIT THAT IS EVOLVING IS LARGELY SERVICE ORIENTED (I.E., SPECIAL EDUCATION, DATA…

ISENBERG, ROBERT M.

332

Intermediate Cambodian Reader.  

ERIC Educational Resources Information Center

This book is a sequel to the "Cambodian System of Writing and Beginning Reader." It is intended to serve as an intermediate reader to develop the student's ability to the point of reading Cambodian texts with the aid of a dictionary. Part One of the book consists of 37 readings, graded in length and difficulty, and selected to provide a wide range…

Huffman, Franklin E., Ed.; Proum, Im, Ed.

333

MATERIALS FOR INTERMEDIATE TELUGU.  

ERIC Educational Resources Information Center

ONE OF THE FOUR DRAVIDIAN LANGUAGES RECOGNIZED BY THE INDIAN CONSTITUTION OF 1950 AS OFFICIAL LANGUAGES OF THE COUNTRY, TELUGU IS SPOKEN BY 42 MILLION PEOPLE IN ANDHRA PRADESH. THESE INSTRUCTIONAL MATERIALS ARE DESIGNED FOR THE INTERMEDIATE STUDENT OF TELUGU AND ARE DIVIDED INTO NEWSPAPER READINGS AND DIALOGUES OF EVERYDAY CONVERSATION. SUBJECTS…

KELLEY, GERALD B.

334

Hispanic American Heritage, Intermediate.  

ERIC Educational Resources Information Center

This resource book features the cultural heritage of Hispanics living within the United States and includes ideas, materials, and activities to be used with students in the intermediate grades and middle school. This book explores the definition of the term "Hispanic Americans" and suggests a multilayered population with a variety of cultural…

Shepherd, Mike

335

Lens Intermediate Filaments  

PubMed Central

The ocular lens assembles two separate Intermediate Filament systems sequentially with differentiation. Canonical 8–11 nm IFs composed of Vimentin are assembled in lens epithelial cells and younger fiber cells, while the fiber cell-specific Beaded Filaments are switched on as fiber cell elongation initiates. Some of the key features of both filament systems are reviewed.

2009-01-01

336

Intermediate Mechanics Tutorials  

NSDL National Science Digital Library

This web site provides small-group learning materials for teaching intermediate mechanics. The physics is Newtonian with very little Lagrangian formalism. Materials are a mix of conceptual, mathematical, and problem solving University of Washington-style tutorials, as well as related research results, examination questions, and suggested course outlines.

Ambrose, Bradley S.; Wittmann, Michael C.

2007-07-20

337

Multiple reaction pathways operating in the mechanism of vinylogous mannich-type reaction activated by a water molecule.  

PubMed

A systematic search for reaction pathways for the vinylogous Mannich-type reaction was performed by the artificial force induced reaction method. This reaction affords ?-amino-?-butenolide in one pot by mixing 2-trimethylsiloxyfuran, imine, and water under solvent-free conditions. Surprisingly, the search identified as many as five working pathways. Among them, two concertedly produce anti and syn isomers of the product. Another two give an intermediate, which is a regioisomer of the main product. This intermediate can undergo a retro-Mannich reaction to give a pair of intermediates: an imine and 2-furanol. The remaining pathway directly generates this intermediate pair. The imine and 2-furanol easily react with each other to afford the product. Thus, all of these stepwise pathways finally converge to give the main product. The rate-determining step of all five (two concerted and three stepwise) pathways have a common mechanism: concerted Si-O bond formation through the nucleophilic attack of a water molecule on the silicon atom followed by proton transfer from the water molecule to the imine. Therefore, these five pathways have comparable barriers and compete with each other. PMID:24115536

Uematsu, Ryohei; Maeda, Satoshi; Taketsugu, Tetsuya

2014-01-01

338

Epoxyoxoene fatty esters: key intermediates for the synthesis of long-chain pyrrole and furan fatty esters  

Microsoft Academic Search

The reaction of epoxyoxoene fatty esters, methyl (Z)-9,10-epoxy-13-oxo-(E)-11-octadecenoate (1) and methyl (Z)-12,13-epoxy-9-oxo-(E)-10-octadecenoate (2), with glycine methyl ester in the presence of a basic resin was studied to establish if these compounds might be useful intermediates in the preparation of long-chain pyrrole fatty esters. Production of C18 pyrrole fatty esters and fragmentation products with the pyrrole ring were isolated and identified

Francisco J. Hidalgo; Rosario Zamora

1995-01-01

339

Efficient oxidative cycloreversion reaction of photochromic dithiazolythiazole.  

PubMed

Electrochemical response of photochromic tearylenes was surveyed by means of cyclic voltammetry, DFT calculations, and spectroelectrochemistry. 4,5-Bis(2-phenyl-5-methylthiazolyl)-2-phenylthiazole was found to show electrochemical oxidative ring-cycloreversion reaction. The net current efficiency of the cycloreversion reaction under constant potential electrolysis was as high as 900%, which is ascribed to an electrochemical local-cell mechanism and a chain reaction mechanism. Electron transfer stopped-flow study using a chemical oxidant successfully identified radical cation intermediates of both closed- and open-ring isomers, involved in the oxidative cycloreversion process. The significantly long-lived radical cation of open-ring isomer with the lifetime of 33 s takes part in the indirect electron transfer process from the neutral closed-ring isomer to the radical cation of open-ring isomer in the chain reaction manner. PMID:23163734

Nakashima, Takuya; Kajiki, Yoshiyuki; Fukumoto, Sayo; Taguchi, Maki; Nagao, Satoshi; Hirota, Shun; Kawai, Tsuyoshi

2012-12-01

340

Carbon monosulfide: a useful synthetic intermediate  

SciTech Connect

The physical properties of carbon monosulfide, CS, are well documented. The molecule has been observed in interstellar space and is found to be a common intermediate in the thermal decomposition of carbon disulfide and other sulfur compounds. Interestingly enough, the chemistry of carbon monosulfide, a molecule that is isovalent with carbon monoxide, has received little attention. The explosive nature of the carbon monosulfide monomer, which hindered previous workers, was overcome by the development of special handling techniques. The ability to produce carbon monosulfide in gram quantities had lead to synthesis of novel compounds and to a more direct synthetic route for certain known compounds. Specifically, the following general reaction demonstrates the capabilities of carbon monosulfide on the synthetic scale. CS + RXY ..-->.. RXC(S)Y;(X = N,S), (Y = H, Cl). Note: The initial product formed in the reaction can be an unstable intermediate.

Kramer, M.P.

1986-01-01

341

Mössbauer- and EPR-Snapshots of an Enzymatic Reaction: The Cytochrome P450 Reaction Cycle  

NASA Astrophysics Data System (ADS)

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.

Schünemann, V.; Jung, C.; Lendzian, F.; Barra, A.-L.; Teschner, T.; Trautwein, A. X.

2004-12-01

342

GFP's Mechanical Intermediate States  

PubMed Central

Green fluorescent protein (GFP) mutants have become the most widely used fluorescence markers in the life sciences, and although they are becoming increasingly popular as mechanical force or strain probes, there is little direct information on how their fluorescence changes when mechanically stretched. Here we derive high-resolution structural models of the mechanical intermediate states of stretched GFP using steered molecular dynamics (SMD) simulations. These structures were used to produce mutants of EGFP and EYFP that mimic GFP's different mechanical intermediates. A spectroscopic analysis revealed that a population of EGFP molecules with a missing N-terminal ?-helix was significantly dimmed, while the fluorescence lifetime characteristic of the anionic chromophore state remained unaffected. This suggests a mechanism how N-terminal deletions can switch the protonation state of the chromophore, and how the fluorescence of GFP molecules in response to mechanical disturbance might be turned off.

Saeger, John; Hytonen, Vesa P.; Klotzsch, Enrico; Vogel, Viola

2012-01-01

343

Intermediate water recovery system  

NASA Technical Reports Server (NTRS)

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.

Deckman, G.; Anderson, A. R. (editor)

1973-01-01

344

Mesoscopic statistical properties of multistep enzyme-mediated reactions.  

PubMed

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 study, the authors address this problem by solving the chemical master equations for various enzymatic reactions. A perturbation theory analogous to that used in quantum mechanics allows the determination of the first (n) and the second (?2) 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(n)/dt (or 'dose-response' curve) and the Fano factor F= ?2/(n) are both realistically measurable quantities, and whereas 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 the authors explore this possibility in the context of four sample multistep enzymatic reactions. 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. PMID:21028932

de Ronde, W H; Daniels, B C; Mugler, A; Sinitsyn, N A; Nemenman, I

2009-09-01

345

Statistical properties of multistep enzyme-mediated reactions  

SciTech Connect

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.

Nemenman, Ilya [Los Alamos National Laboratory; Sinitsyn, Nikolai A [Los Alamos National Laboratory; De Ronde, Wiet H [AMOLF; Daniels, Bryan C [CORNELL; Mugler, Andrew [COLUMBIA

2008-01-01

346

Intermediate inflation from rainbow gravity  

NASA Astrophysics Data System (ADS)

It is possible to dualize theories based on deformed dispersion relations and Einstein gravity so as to map them into theories with trivial dispersion relations and rainbow gravity. This often leads to “dual inflation” without the usual breaking of the strong energy condition. We identify the dispersion relations in the original frame which map into “intermediate” inflationary models. These turn out to be particularly simple: power-laws modulated by powers of a logarithm. The fluctuations predicted by these scenarios are near, but not exactly scale-invariant, with a red running spectral index. These dispersion relations deserve further study within the context of quantum gravity and the phenomenon of dimensional reduction in the ultraviolet.

Barrow, John D.; Magueijo, João

2013-11-01

347

Polymer Intermediates from Limonene.  

National Technical Information Service (NTIS)

The replacement of petrochemically manufactured isophorone diamine or isophorone diisocyanate by limonene diamine obtained from limonene, a renewable raw metarial, is studied. Limonene was transformed to a bisformamide in a double Ritter reaction with hyd...

G. Klein

1983-01-01

348

Identify Symmetry  

NSDL National Science Digital Library

This unit will teach you how to identify symmetry in everyday objects and mathematical shapes in lines and rotational symmetry. What is line symmetry? Click on the link to find out: Line Symmetry Here is a line activity to see if you understand it: Line Symmetry Class Zone See if you understand the concepts by doing the following quiz: Line Symmetry Work Now for rotational symmetry: Rotational Symmetry See if you understand rotational symmetry by taking this quiz: Rotational Symmetry Work ...

Neubert, Mrs.

2011-03-03

349

Identifying Erosion  

NSDL National Science Digital Library

In this environmental science activity (page 3 of the PDF), leaners will identify and explain the causes of erosion. They will observe the effects of erosion on the surrounding area and further explore examples of erosion online. An extension activity allows learners to make a hands-on model of soil erosion. Though this was created as a pre-visit activity for a workshop about water flow and erosion, it makes a great stand-alone activity as well!

Cosi

2009-01-01

350

Exemplary Dissemination Programs for Intermediate Units Serving Rural Schools.  

ERIC Educational Resources Information Center

Utilizing information derived from documents, site visits, correspondence, and personal interviews re: 6 intermediate education units serving rural schools which were initially identified via a mail survey, this report describes intermediate education units with exemplary information dissemination programs. Varying considerably, each program is…

Edington, Everett; Hays, Leonard

351

BLUF Domain Function Does Not Require a Metastable Radical Intermediate State  

PubMed Central

BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto–enol tautomerization induced by electronic excitation of the flavin ring are considered.

2014-01-01

352

First-order phase transition through an intermediate state  

NASA Astrophysics Data System (ADS)

The theory of first-order phase transitions in systems where the direct formation of nuclei of a new phase is inhibited for any reason, for example, because of the extremely high elastic energy, has been constructed using the example of the silicon-silicon carbide phase transition due to the chemical reaction with carbon monoxide. It has been shown that, in this case, the phase transition occurs through an intermediate state, which significantly promotes the formation of new-phase nuclei. For the silicon-silicon carbide phase transition, such an intermediate state is the "pre-carbide" state of silicon saturated with dilatation dipoles, i.e., pairs formed by a carbon atom and a silicon vacancy that are strongly attracted to each other. The model dependence of the potential energy of systems with an intermediate phase on the reaction coordinates has been investigated. The kinetics of transformation of the intermediate state into a new phase has been described.

Kukushkin, S. A.; Osipov, A. V.

2014-04-01

353

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 Central

Acetyl-CoA synthase (ACS) catalyzes the synthesis of acetyl-CoA from CO, coenzyme A (CoA), and a methyl-group from the CH3-Co3+ site in the corrinoid iron-sulfur protein (CFeSP). These are the key steps in the Wood-Ljungdahl pathway of anaerobic CO and CO2 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 [Fe4S4]2+-(Nip1+–CO)-(Nid2+), where Nip and Nid represent the Ni centers in the A-cluster that are proximal and distal to the [Fe4S4]2+ cluster. This well-characterized Nip1+–CO intermediate is often called NiFeC species. Photolysis of the Nip1+–CO state generates a novel Nip1+ species (Ared*) with a rhombic electron paramagnetic resonance spectrum (g-values of 2.56, 2.10, 2.01) and an extremely low (1 kJ/mol) barrier for recombination with CO. We suggest that the photolytically generated Ared* species is (or is similar to) the Nip1+ species that binds CO (to form the Nip1+–CO species) and the methyl group (to form Nip-CH3) in the ACS catalytic mechanism. The results provide support for a binding site (an “alcove”) for CO near Nip, indicated by X-ray crystallographic studies of the Xe-incubated enzyme. We propose that, during catalysis, a resting Nip2+ state predominates over the active Nip1+ species (Ared*) that is trapped by the coupling of a one-electron transfer step to the binding of CO, which pulls the equilibrium toward Nip1+-CO formation.

Bender, Gunes; Stich, Troy A.; Yan, Lifen; Britt, R. David; Cramer, Stephen P.; Ragsdale, Stephen W.

2010-01-01

354

Inclusive Tritium Stripping Reaction Theory  

NASA Astrophysics Data System (ADS)

The angular and energy distributions and the integrated cross-section of the inclusive two-nucleon transfer reaction with the participation of three-nucleon nucleus were calculated at intermediate energies.

Akhiezer, A. I.; Soznik, A. P.; Berezhnoy, Yu. A.

355

Non-Heme Fe(IV)-Oxo Intermediates  

PubMed Central

High-valent non-heme iron-oxo intermediates have been proposed for decades as the key intermediates in numerous biological oxidation reactions. In the last three years, the first direct characterization of such intermediates has been provided by studies of several ?KG-dependent oxygenases that catalyze either hydroxylation or halogenation of their substrates. In each case, the Fe(IV)-oxo intermediate is implicated in cleavage of the aliphatic C-H bond to initiate hydroxylation or halogenation. The observation of non-heme Fe(IV)-oxo intermediates and Fe(II)-containing product(s) complexes with almost identical spectroscopic parameters in the reactions of two distantly related ?KG-dependent hydroxylases suggests that members of this sub-family follow a conserved mechanism for substrate hydroxylation. In contrast, for the ?KG-dependent non-heme-iron halogenase, CytC3, two distinct Fe(IV) complexes form and decay together, suggesting that they are in rapid equilibrium. The existence of two distinct conformers of the Fe site may be the key factor accounting for the divergence of the halogenase reaction from the more usual hydroxylation pathway after C-H cleavage. Distinct transformations catalyzed by other mononuclear non-heme enzymes are likely also to involve initial C-H-cleavage by Fe(IV)-oxo complexes, followed by diverging reactivities of the resulting Fe(III)-hydroxo/substrate radical intermediates.

Krebs, Carsten; Galonic-Fujimori, Danica P.; Walsh, Christopher T.; Bollinger, J. Martin

2012-01-01

356

Investigation of the reactions of small neutral iron oxide clusters with methanol  

NASA Astrophysics Data System (ADS)

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.

Xie, Yan; Dong, Feng; Heinbuch, Scott; Rocca, Jorge J.; Bernstein, Elliot R.

2009-03-01

357

Sentinel lymphadenectomy for staging patients with intermediate-level melanoma.  

PubMed

Sentinel lymph node dissection (SLND) as originally described by D.L. Morton et al. (Surg Oncol Clin North Am 1992;1:247-59), is currently being used at most tertiary institutions for staging patients with intermediate-level melanomas. Identification and subsequent surgical resection of occult metastasis before the development of clinical disease may improve survival in these patients. This study is a retrospective review of patients with intermediate melanomas treated by the senior author (P.S.D.). Isosulfan blue dye and a radioactive technetium-labeled dye were used to identify the sentinel node. Sentinel nodes were evaluated by routine hematoxylin and eosin staining, immunohistochemical staining for S-100 and HMB-45, and later in the study with multipanel reverse transcriptase-polymerase chain reaction analysis. All patients were followed closely. Fifty-seven patients with primary melanoma were evaluated between December 1995 and June 1998. Thirty-two patients underwent SLND; two patients underwent SLND on two separate drainage basins, for a total of 34 procedures. The median age was 49 years (range, 19-77). There were 11 females and 21 males. The locations of the primary melanoma were: head and neck, seven; extremity, 8; and trunk, 18; 1 patient had a dual primary melanoma at presentation. Clark's levels of invasion among the patients were level III, 5; and level IV, 27; median Breslow thickness was 1.4 mm (range, 0.45-3.8 mm). A sentinel node was not identified in four procedures (11.1%). Twenty-two nodes (73%) were negative by all methods, and eight (27%) were positive by at least one method. All positive patients underwent complete lymphadenectomy, and routine hematoxylin and eosin stains identified no additional positive nodes. Median follow-up was 21 months (6-36 months). Two patients developed recurrent disease. The other 30 patients remain disease free at last follow-up. SLND is a low-morbidity technique that accurately stages patients with intermediate-level melanoma. Early intervention with complete therapeutic lymphadenectomy and possible interferon therapy may improve the survival of patients with stage III melanoma. A complete discussion of the technique for SLND and an update of this data is presented. PMID:10759200

Smart, K R; Cahoon, B W; Dale, P S

2000-03-01

358

Isoporphyrin intermediate in heme oxygenase catalysis. Oxidation of alpha-meso-phenylheme.  

PubMed

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. PMID:18487208

Evans, John P; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

2008-07-11

359

Organocuprate conjugate addition: structural features of diastereomeric and supramolecular pi-intermediates.  

PubMed

In the reaction pathway of conjugate additions with organocuprate reagents, Cu(I) pi-complexes and Cu(III) sigma-complexes have been identified as central, NMR-detectable intermediate species. However, no experimental evidence for the structures of pi-intermediates with extensive chiral enones or the principal aggregation level and aggregate structure of pi-complexes in diethyl ether has been available so far. Furthermore, the structural characteristics of pi-complexes which are essential for their high reactivities and diastereoselectivities have not yet been rationalized experimentally. Therefore, the pi-intermediates of 4,4a,5,6,7,8-hexahydro-4a-methyl-naphthalen-2(3H)-one and Me2CuLi or Me2CuLi x LiX (X = I, CN) in diethyl ether are investigated in detail. For the first time, the formation of two intermediate cuprate enone pi-complexes on both sides of the double bond is observed. In addition, the conformation of the enone adopted in the major beta-face pi-complex rationalizes the exclusive syn addition observed in the synthetic product. For the investigation of the aggregation level and structure, a NMR screening of pi-complexes with Me2CuLi x LiX (X = I, CN) and three achiral enones is performed, which simplifies the spectra by the generation of enantiotopic pi-complexes. Thus, NMR diffusion experiments on cuprate intermediates and the detection of scalar couplings across copper without isotope labeling are possible for the first time. Extensive NMR studies, including those of cyclohexanone complexes, show that, in principle, salt-free dimethylcuprate is able to complex the carbonyl group. However, in the presence of salt, the carbonyl-complexing aggregates are composed of salt and cuprate moieties. These mixed aggregates cause the formation of large supramolecular pi-intermediate structures which control their reactivity. The pi-complexing cuprate units show a bent geometry as a general structural feature that is unaffected by the presence or kind of salt and the type of enone. Thus, the high diastereoselectivity and the reactivity of organocuprate 1,4-addition reactions are for the first time rationalized on the basis of structural characteristics of selected pi-intermediates. PMID:18808118

Henze, Wolfram; Gärtner, Tobias; Gschwind, Ruth M

2008-10-15

360

Conformational dynamics through an intermediate  

NASA Astrophysics Data System (ADS)

The self-assembly of biological and synthetic nanostructures commonly proceeds via intermediate states. In living systems in particular, the intermediates have the capacity to tilt the balance between functional and potentially fatal behavior. This work develops a statistical mechanical treatment of conformational dynamics through an intermediate under a variable force. An analytical solution is derived for the key experimentally measurable quantity—the distribution of forces at which a conformational transition occurs. The solution reveals rich kinetics over a broad range of parameters and enables one to locate the intermediate and extract the activation barriers and rate constants.

Garai, Ashok; Zhang, Yaojun; Dudko, Olga K.

2014-04-01

361

A Fluorogenic Aromatic Nucleophilic Substitution Reaction for Demonstrating Normal-Phase Chromatography and Isolation of Nitrobenzoxadiazole Chromophores  

ERIC Educational Resources Information Center

Normal-phase chromatography is an essential technique for monitoring chemical reactions, identifying the presence of specific components, as well as the purification of organic compounds. An experiment to facilitate the instruction and understanding of the concepts behind normal-phase chromatography at the introductory and intermediate

Key, Jessie A.; Li, Matthew D.; Cairo, Christopher W.

2011-01-01

362

Microsurgical intermediate subinguinal varicocelectomy.  

PubMed

Abstract This study was conducted to introduce a simple modification that can facilitate microsurgical subinguinal varicocelectomy (MSV) especially for surgeons inexperienced in microsurgical technique. A single surgeon performed microsurgical intermediate subinguinal varicocelectomy (MISV) on 52 patients with 61 cases between September 2010 and August 2012. Patient age, varicocele grade, operation time, intraoperative findings, postoperative complications, and 3-month follow-up results were analyzed. Patient mean age was 28 years (range, 15-69 years), and there were 9 bilateral cases. The mean operative time was 51 minutes (range, 34-109 minutes). We compared the first 31 cases to the second 30 cases, to assess investigator experience on operating times. The mean number of ligated veins was 5 (range, 3-10) in internal spermatic vein, 1 (range, 0-4) in external spermatic vein, and 1 (range, 0-3) in gubernacular vein. In 28 patients, the average postoperative sperm concentration at the 3-month follow-up was significantly higher than the preoperative sperm concentration (28.5 ± 18.2 × 10(6)/mL versus 10.5 ± 23.0 × 10(6)/mL; P = 0.003). Mean motility improved after MSIV (65.7% ± 18.2% versus 47.2% ± 21.7%; P = 0.004). In conclusion, MISV appears comparable with MSV in terms of the high success rate, low complication rate, and low postoperative pain; and it can be easily accomplished by inexperienced surgeons. PMID:25058772

Lee, Joo Yong; Yu, Ho Song; Ham, Won Sik; Kang, Dong Hyuk; Kim, Kyu Hyun; Chung, Doo Yong; Cho, Kang Su

2014-01-01

363

Stabilisation of reactive intermediates in molecular sieves  

Microsoft Academic Search

This paper presents studies on paramagnetic intermediates, free atoms and radicals produced in ?-irradiated molecular sieves and their reactions with adsorbate molecules or exchangeable cations. Four different systems\\u000a have been investigated using EPR spectroscopy, Na-A\\/CH4, AgNa-A\\/CH3OH, Ag-SAPO-11\\/C2H4 and AgCs-rho\\/NH3. It was found that methyl radicals are formed in two different sites in Na-A\\/CH4 and in one of them they are

Jacek Michalik; Marek Danilczuk; Janusz Turek; Jaroslaw Sadlo

2007-01-01

364

New quaternary compounds resulting from the reaction of copper and f-block metals in molten polychalcogenide salts at intermediate temperatures. Valence fluctuations in the layered CsCuCeS{sub 3}  

SciTech Connect

From the reaction of elemental copper and either lanthanides or actinides in molten alkali metal/polychalcogenide salts, several new quaternary phases have been discovered. Specifically, these phases are ACuM{sub 2}Q{sub 6}(where A = K, M = La, Q =S: A = Cs, M = Ce, Q = S; or A = K, M = Ce, Q = Se) and ACuMQ{sub 3} (where A = Cs, M = Ce, Q = S; or A = K, M = U, Q = Se). The CsCuCe{sub 2}S{sub 6} crystallizes in the orthorhombic space group Immm with a = 5.500-(1) {Angstrom}, b = 22.45(1) {Angstrom}, c = 4.205(4) {Angstrom}. The KCuCe{sub 2}Se{sub 6} is isostructural. The CsCuCeS{sub 3} crystallizes in the orthorhombic space group Cmcm with a = 4.024(2) {Angstrom}, b = 15.154(2) {Angstrom}, c = 10.353(3) {Angstrom}. The KCuUSe{sub 3} is isostructural. In ACuM{sub 2}Q{sub 6}, the lanthanides bond to a mixture of mono- and disulfides in a bicapped trigonal prismatic geometry; these polyhedra subsequently connect in two dimensions, forming layers equivalent to those seen in the ZrSe{sub 3} structure type with Cu{sup +} atoms residing in tetrahedral sites within the layers and alkali cations in the interlayer gallery. The compounds of the formula ACuMQ{sub 3} also possess a layered structure. Here the [MQ{sub 6}] octahedral units form corrugated, two-dimensional sheets via edge-sharing in the first dimension and corner-sharing in the second. Copper cations are coordinated to tetrahedral sites in the folds of the corrugations, and alkali cations are again in the intergallery region. Detailed of the synthesis, structure, and properties of these compounds are discussed. 42 refs., 14 figs., 8 tabs.

Sutorik, A.C.; Kanatzidis, M.G. [Michigan State Univ., East Lansing, MI (United States)] [Michigan State Univ., East Lansing, MI (United States); Albritton-Thomas, J.; Hogan, T.; Kannewurf, C.R. [Northwestern Univ., Evanston, IL (United States)] [Northwestern Univ., Evanston, IL (United States)

1996-03-01

365

Photocatalytic degradation of metoprolol tartrate in suspensions of two TiO2-based photocatalysts with different surface area. Identification of intermediates and proposal of degradation pathways.  

PubMed

This study investigates the efficiency of the photocatalytic degradation of metoprolol tartrate (MET), a widely used ?(1)-blocker, in TiO(2) suspensions of Wackherr's "Oxyde de titane standard" and Degussa P25. The study encompasses transformation kinetics and efficiency, identification of intermediates and reaction pathways. In the investigated range of initial concentrations (0.01-0.1 mM), the photocatalytic degradation of MET in the first stage of the reaction followed approximately a pseudo-first order kinetics. The TiO(2) Wackherr induced a significantly faster MET degradation compared to TiO(2) Degussa P25 when relatively high substrate concentrations were used. By examining the effect of ethanol as a scavenger of hydroxyl radicals (OH), it was shown that the reaction with OH played the main role in the photocatalytic degradation of MET. After 240 min of irradiation the reaction intermediates were almost completely mineralized to CO(2) and H(2)O, while the nitrogen was predominantly present as NH(4)(+). Reaction intermediates were studied in detail and a number of them were identified using LC-MS/MS (ESI+), which allowed the proposal of a tentative pathway for the photocatalytic transformation of MET as a function of the TiO(2) specimen. PMID:22035693

Abramovi?, Biljana; Kler, Sanja; Soji?, Daniela; Lauševi?, Mila; Radovi?, Tanja; Vione, Davide

2011-12-30

366

Printing. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

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…

Seivert, Chester

367

Bank and Nonbank Financial Intermediation  

Microsoft Academic Search

Conglomerates, trade credit arrangements, and banks are all instances of financial intermediation. However, these institutions differ significantly in the extent to which the projects financed absorb aggregate intermediary risk, in whether or not intermediation is carried out by a financial specialist, in the type of projects they fund and in the type of claims they issue to investors. The paper

PHILIP BOND

2004-01-01

368

Financial Intermediation and Endogenous Growth  

Microsoft Academic Search

An endogenous growth model with multiple assets is developed. Agents who face random future liquidity needs accumulate capital and a liquid, but unproductive, asset. The effects of introducing financial intermediation into this environment are considered. Conditions are provided under which the introduction of intermediaries shifts the composition of savings toward capital, causing intermediation to be growth promoting. In addition, intermediaries

Valerie R Bencivenga; Bruce D Smith

1991-01-01

369

Efficient catalyst-free four-component synthesis of novel ?-aminoethers mediated by a Mannich type reaction.  

PubMed

Herein, it is provided an efficient and one-pot procedure for the synthesis of novel and diversely substituted ?-aminoethers in good yields through a four-component process by treatment of benzylamines with polyformaldehyde and activated alkenes in aliphatic alcohols acting both as solvent and as etherificant agents. Reactions proceeded via a Mannich-type reaction, where the formation of iminium ions and aminals was identified as the key intermediates to obtain the target products. PMID:23167924

Abonia, Rodrigo; Castillo, Juan; Insuasty, Braulio; Quiroga, Jairo; Nogueras, Manuel; Cobo, Justo

2013-01-14

370

Kinetics, intermediates and acute toxicity of arsanilic acid photolysis.  

PubMed

Arsanilic acid (4-amino phenyl arsenic acid, ASA) is widely used in poultry production as feed additives, while most of ASA in the feed is excreted in the animal manure and released into the environment. However, the environmental behaviors of ASA were not well understood. In the present study, the photolysis behaviors of ASA and the toxicity of its metabolites to luminescent bacterium were studied. The results showed that ASA could be photodegraded and this process was strongly affected by solution pH, humic acid and dissolved oxygen. Upon UV irradiation for 360min, ASA could be completely eliminated, but the reduction of total organic carbon (TOC) was not significant. In addition, NH4(+) ions and inorganic arsenic including arsenite and arsenate were identified as the predominant end-products. The conversion of ASA included both direct and indirect photolysis involving radicals, and its possible photolysis pathways were proposed on the basis of the identified intermediates. Unfortunately, higher adverse effects of the conversion products of ASA on bacteria were observed during the photolysis reaction. The results of present study might be helpful for assessing the environmental persistence and risks of ASA. PMID:24405966

Zhu, Xiang-Dong; Wang, Yu-Jun; Liu, Cun; Qin, Wen-Xiu; Zhou, Dong-Mei

2014-07-01

371

Kinetics and product studies of the reaction ClO + BrO using discharge-flow mass spectrometry  

NASA Technical Reports Server (NTRS)

The kinetics and product branching ratios of the reaction between ClO and BrO were studied at 1 torr pressure over the temperature range 220-400 K, using the method of discharge-flow mass spectrometry. Three product channels were identified and quantified: Br + ClOO, Br + OClO, and BrCl + O2, indicating that the reaction mechanism of ClO + BrO involves metastable intermediates. The overall reaction rate coefficient and the rate coefficients for the three channel reactions are given.

Friedl, Randall R.; Sander, Stanley P.

1989-01-01

372

The MHD intermediate shock interaction with an intermediate wave - Are intermediate shocks physical?  

Microsoft Academic Search

Contrary to the usual belief that MHD intermediate shocks are extraneous, it has recently been shown by numerical solutions of dissipative MHD equations (Wu, 1987) that intermediate shocks are admissible and can be formed through nonlinear steepening from a continuous wave. In this paper, the differences between the conventional view and the results of Wu are clarified by studying the

C. C. Wu

1988-01-01

373

Time sequence and time scale of intermediate mass fragment emission  

Microsoft Academic Search

Semiperipheral collisions in the 124Sn+64Ni reaction at 35 MeV\\/nucleon were studied using the forward part of the Charged Heavy Ion Mass and Energy Resolving Array. Nearly completely determined ternary events involving projectilelike fragments (PLF), targetlike fragments (TLF), and intermediate mass fragments (IMF) were selected. A new method of studying the reaction mechanism, focusing on the analysis of the correlations between

E. de Filippo; A. Pagano; J. Wilczynski; F. Amorini; A. Anzalone; L. Auditore; V. Baran; I. Berceanu; J. Blicharska; J. Brzychczyk; A. Bonasera; B. Borderie; R. Bougault; M. Bruno; G. Cardella; S. Cavallaro; M. B. Chatterjee; A. Chbihi; J. Cibor; M. Colonna; M. D'Agostino; R. Dayras; M. di Toro; J. Frankland; E. Galichet; W. Gawlikowicz; E. Geraci; F. Giustolisi; A. Grzeszczuk; P. Guazzoni; D. Guinet; M. Iacono-Manno; S. Kowalski; E. La Guidara; G. Lanzanò; G. Lanzalone; N. Le Neindre; S. Li; C. Maiolino; Z. Majka; M. Papa; M. Petrovici; E. Piasecki; S. Pirrone; R. Planeta; G. Politi; A. Pop; F. Porto; M. F. Rivet; E. Rosato; F. Rizzo; S. Russo; P. Russotto; M. Sassi; K. Schmidt; K. Siwek-Wilczynska; I. Skwira; M. L. Sperduto; L. Swiderski; A. Trifirò; M. Trimarchi; G. Vannini; M. Vigilante; J. P. Wieleczko; H. Wu; Z. Xiao; L. Zetta; W. Zipper

2005-01-01

374

Reaction of atomic hydrogen with formic acid.  

PubMed

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. PMID:24549472

Cao, Qian; Berski, Slawomir; Latajka, Zdzislaw; Räsänen, Markku; Khriachtchev, Leonid

2014-04-01

375

Modeling the Reaction of Fe Atoms with CCl4  

SciTech Connect

The reaction of zero-valent iron with carbon tetrachloride (CCl4) in gas phase was studied using density functional theory. Temperature programmed desorption experiments over a range of Fe and CCl4 coverages on a FeO(111) surface, demonstrate a rich surface chemistry with several reaction products (C2Cl4, C2Cl6, OCCl2, CO, FeCl2, FeCl3) observed. The reactivity of Fe and CCl4 was studied under three stoichiometries, one Fe with one CCl4, one Fe with two CCl4 molecules and two Fe with one CCl4, modeling the environment of the experimental work. The electronic structure calculations give insight into the reactions leading to the experimentally observed products and suggest that novel Fe-C-Cl containing species are important intermediates in these reactions. The intermediate complexes are formed in highly exothermic reactions, in agreement with the experimentally observed reactivity with the surface at low temperature (30 K). This initial survey of the reactivity of Fe with CCl4 identifies some potential reaction pathways that are important in the effort to use Fe nano-particles to differentiate harmful pathways that lead to the formation of contaminants like chloroform (CHCl3) from harmless pathways that lead to products such as formate (HCO2-) or carbon oxides in water and soil. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

Camaioni, Donald M.; Ginovska, Bojana; Dupuis, Michel

2009-01-05

376

Noncanonical Reactions of Flavoenzymes  

PubMed Central

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.

Sobrado, Pablo

2012-01-01

377

Site Seeing: Intermediate  

NSDL National Science Digital Library

This field activity introduces students to the concept of a system. Students identify the components, inputs and outputs of the local system at a range of biometry study sites, as well as the boundaries of their investigations at these sites in terms of space and time. Collected data from the different sites are analyzed and compared. The activity includes a student worksheet and data charts. Equipment needed to do this activity includes a compass and camera. This is a learning activity associated with the GLOBE Land Cover/Biology investigations and is supported by the GLOBE Teacher's Guide, Land Cover/Biology.

378

New Cathode Materials for Intermediate Temperature Solid Oxide Fuel Cells  

Microsoft Academic Search

Operation of SOFCs at intermediate temperatures (500-800 C) requires new combinations of electrolyte and electrode materials that will provide both rapid ion transport across the electrolyte and electrode--electrolyte interfaces and efficient electrocatalysis of the oxygen reduction and fuel oxidation reactions. This project concentrates on materials and issues associated with cathode performance that are known to become limiting factors as the

Allan J. Jacobson

2005-01-01

379

Nurturing Writing Attitudes through Collaboration across the Intermediate Grades.  

ERIC Educational Resources Information Center

An 8-month practicum addressed the adverse feelings for writing (shown in responses to a writing survey) of 30 intermediate-level students. Ten students from each grade level (third, fourth, and fifth) with the lowest scores completed the practicum activities. Students viewed a film for the first strategy. The students' reactions to the film…

McKenzie, Flora I.

380

Photoreactions of cyclic sulfite esters: Evidence for diradical intermediates  

PubMed Central

Summary The photochemistry of a phenyl and 1,2-diphenyl substituted sulfite ester is reported. The performance of photoreactions under relatively mild reaction conditions enables the detection of products that have not been observed in previous studies. It is concluded that, complementary to the initially proposed carbene intermediates, diradicals may also be considered.

Arney, Benny E; Ihmels, Heiko

2012-01-01

381

Novel Reagents for Multi-Component Reactions  

NASA Astrophysics Data System (ADS)

Ketenimines are a class of versatile and highly reactive intermediates that can participate in a variety of organic reactions, such as nucleophilic additions, radical additions, [2 + 2] and [2 + 4] cycloadditions, and sigmatropic rearrangements. In this presentation, we report on a series of multi-component reactions that involve a ketenimine intermediate. These reactions could furnish diverse heterocyclic compounds, including functionalized iminocoumarin, iminodihydroqunolines, iminothiochromens, pyrrolines, isoquinolines, pyridines, ?-lactams, imino-1,2-dihydrocoumarins, and benzimidazoles.

Wang, Yanguang; Basso, Andrea; Nenajdenko, Valentine G.; Gulevich, Anton V.; Krasavin, Mikhail; Bushkova, Ekaterina; Parchinsky, Vladislav; Banfi, Luca; Basso, Andrea; Cerulli, Valentina; Guanti, Giuseppe; Riva, Renata; Rozentsveig, Igor B.; Rozentsveig, Gulnur N.; Popov, Aleksandr V.; Serykh, Valeriy J.; Levkovskaya, Galina G.; Cao, Song; Shen, Li; Liu, Nianjin; Wu, Jingjing; Li, Lina; Qian, Xuhong; Chen, Xiaopeng; Wang, Hongbo; Feng, Jinwu; Wang, Yanguang; Lu, Ping; Heravi, Majid M.; Sadjadi, Samaheh; Kazemizadeh, Ali Reza; Ramazani, Ali; Kudyakova, Yulia S.; Goryaeva, Marina V.; Burgart, Yanina V.; Saloutin, Victor I.; Mossetti, Riccardo; Pirali, Tracey; Tron, Gian Cesare; Rozhkova, Yulia S.; Mayorova, Olga A.; Shklyaev, Yuriy V.; Zhdanko, Alexander G.; Nenajdenko, Valentine G.; Stryapunina, Olga G.; Plekhanova, Irina V.; Glushkov, Vladimir A.; Shklyaev, Yurii V.

382

BB Seminar: Prediction of Survival Incorporating Intermediate Event Info  

Cancer.gov

In recent years, an increasing number of predictive markers have been identified as useful for risk prediction. When interest lies in predicting long term survival, it has often been argued that intermediate event information may be very helpful in improving the prediction. Most existing methods for incorporating potentially censored intermediate event information in predicting long term survival focus on modeling the disease process and are derived under restrictive parametric models in a multi-state survival setting.

383

One-pot Synthesis of Lactams Using Domino Reactions: Combination of Schmidt Reaction with Sakurai and Aldol Reactions  

PubMed Central

A series of domino reactions in which the intramolecular Schmidt reaction is combined with either a Sakurai reaction, an aldol reaction, or both is reported. The Sakurai reaction of an allylsilane with an azido-containing enone under Lewis acidic conditions followed by protonation of the resulting titanium enolate species allowed for a subsequent intramolecular Schmidt reaction. Alternatively, the intermediate titanium enolate could undergo an aldol reaction, followed by the intramolecular Schmidt reaction to form lactam products with multiple stereogenic centers. The stereochemical features of the titanium enolate aldol reaction with several 3-azidoaldehyde substrates during this domino process is discussed.

Huh, Chan Woo; Somal, Gagandeep K.; Katz, Christopher E.; Pei, Huaxing; Zeng, Yibin; Douglas, Justin T.; Aube, Jeffrey

2009-01-01

384

Intermediate Volume Personal Sampler (IVPS).  

National Technical Information Service (NTIS)

The historical development of the Intermediate Volume Personal Sampler, or IVPS, is described, and information is given on testing and calibration, and manufacturing considerations. Detailed instructions are given for the use of the IVPS for sampling resp...

1973-01-01

385

HETEROGENOUS DEGRADATION OF OXYGENATED INTERMEDIATES  

EPA Science Inventory

Issues surrounding the importance of including heterogeneous processes when determining the fate of oxygenated intermediates in the troposphere are discussed. esults of recent investigations are reviewed and preliminary data from a laboratory study are presented. n the laboratory...

386

Moving beyond Intermediate English Proficiency  

ERIC Educational Resources Information Center

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.

Jewell, Mary

2009-01-01

387

Metal Reactions  

NSDL National Science Digital Library

This is written as a static display, but can easily be adapted to a hands-on experiment for learners to conduct. Sodium phosphate, a clear colorless solution, is combined with six different metal ion solutions. Each metal (copper, nickel, iron, silver, cobalt, and barium) forms a different color and texture precipitate. Learners discover that a chemical reaction can be identified by a color change, and formation of a precipitate. They also learn that metals can be identified by their precipitates. For safety reasons, this activity should be conducted as a demonstration for younger audiences.

Industry, Oregon M.

1997-01-01

388

Plasticity of Intermediate Filament Subunits  

PubMed Central

Intermediate filaments (IFs) assembled in vitro from recombinantly expressed proteins have a diameter of 8–12 nm and can reach several micrometers in length. IFs assemble from a soluble pool of subunits, tetramers in the case of vimentin. Upon salt addition, the subunits form first unit length filaments (ULFs) within seconds and then assembly proceeds further by end-to-end fusion of ULFs and short filaments. So far, IF subunits have mainly been observed by electron microscopy of glycerol sprayed and rotary metal shadowed specimens. Due to the shear forces during spraying the IF subunits appear generally as straight thin rods. In this study, we used atomic force microscopy (AFM), cryo-electron microscopy (cryo-EM) combined with molecular modeling to investigate the conformation of the subunits of vimentin, desmin and keratin K5/K14 IFs in various conditions. Due to their anisotropic shape the subunits are difficult to image at high resolution by cryo-EM. In order to enhance contrast we used a cryo-negative staining approach. The subunits were clearly identified as thin, slightly curved rods. However the staining agent also forced the subunits to aggregate into two-dimensional networks of dot-like structures. To test this conformational change further, we imaged dried unfixed subunits on mica by AFM revealing a mixture of extended and dot-like conformations. The use of divalent ions such as calcium and magnesium, as well as glutaraldehyde exposure favored compact conformations over elongated ones. These experimental results as well as coarse-grained molecular dynamics simulations of a vimentin tetramer highlight the plasticity of IF subunits.

Hoenger, Andrea; Buehler, Markus J.; Kreplak, Laurent

2010-01-01

389

Hydroxo-bridged dicopper(II,III) and -(III,III) complexes: models for putative intermediates in oxidation catalysis.  

PubMed

A macrocyclic ligand (L(4-)) comprising two pyridine(dicarboxamide) donors was used to target reactive copper species relevant to proposed intermediates in catalytic hydrocarbon oxidations by particulate methane monooxygenase and heterogeneous zeolite systems. Treatment of LH4 with base and Cu(OAc)2·H2O yielded (Me4N)2[L2Cu4(?4-O)] (1) or