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1

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

2

Temperature-sensitive reaction intermediate of F1-ATPase  

PubMed Central

F1-ATPase is a rotary molecular motor that makes 120° stepping rotations, with each step being driven by a single-ATP hydrolysis. In this study, a new reaction intermediate of F1-ATPase was discovered at a temperature below 4°C, which makes a pause at the same angle in its rotation as when ATP binds. The rate constant of the intermediate reaction was strongly dependent on temperature with a Q10 factor of 19, implying that the intermediate reaction accompanies a large conformational change. Kinetic analyses showed that the intermediate state does not correspond to ATP binding or hydrolysis. The addition of ADP to the reaction mixture did not alter the angular position of the intermediate state, but specifically lengthened the time constant of this state. Conversely, the addition of inorganic phosphate caused a pause at an angle of +80° from that of the intermediate state. These observations strongly suggest that the newly found reaction intermediate is an ADP-releasing step. PMID:18064048

Watanabe, Rikiya; Iino, Ryota; Shimabukuro, Katsuya; Yoshida, Masasuke; Noji, Hiroyuki

2008-01-01

3

Temperature-sensitive reaction intermediate of F1ATPase  

Microsoft Academic Search

F1-ATPase is a rotary molecular motor that makes 120° stepping rotations, with each step being driven by a single-ATP hydrolysis. In this study, a new reaction intermediate of F1-ATPase was discovered at a temperature below 4°C, which makes a pause at the same angle in its rotation as when ATP binds. The rate constant of the intermediate reaction was strongly

Rikiya Watanabe; Ryota Iino; Katsuya Shimabukuro; Masasuke Yoshida; Hiroyuki Noji

2007-01-01

4

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. PMID:5941332

Zwaig, N.; Milstein, C.

1966-01-01

5

Spectroscopic predictions for alkali-atom-alkali-halide reaction intermediates  

NASA Astrophysics Data System (ADS)

The semi-empirical Roach-Child model is used to predict ionisation potentials, rotational constants, vibrational frequencies and the first three electronic absorption bands for the reaction intermediates Na 2Cl, K 2Cl and NaKCl, which are known to be isolatable by supersonic beam techniques.

Thompson, J. W.; Child, M. S.

1989-05-01

6

Imidazolidinone intermediates in prolinamide-catalyzed aldol reactions.  

PubMed

The reaction between acetone and 4-nitrobenzaldehyde catalyzed by aniline prolinamide 1 was studied in depth. Working in different solvents with equimolar amounts of reagents and monitoring the reaction by 1H NMR, we detected and identified several imidazolidinones, such as those of the acetone 4, the aldol products 5a and 5b, and aldehydes 10a and 10b. According to our results, these compounds could influence the reaction rate and diminish product enantioselectivity. Furthermore, acetone imidazolidinone 4 was seen to react with 4-nitrobenzaldehyde to furnish the aldol product 3. This reaction can be catalyzed by different nucleophiles and acids. In fact, strong acids such as camphorsulfonic or trifluoroacetic acid, convert imidazolidinones into iminium salts and afford more enantioselective aldol reactions when different aromatic prolinamides are used. Enantiomeric excesses of ca. 82% are reached. PMID:20461270

Fuentes de Arriba, Angel L; Simón, Luis; Raposo, César; Alcázar, Victoria; Sanz, Francisca; Muñiz, Francisco M; Morán, Joaquín R

2010-06-28

7

Kinetics and mechanisms of reactions involving small aromatic reactive intermediates  

SciTech Connect

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

Lin, M.C. [Emory Univ., Atlanta, GA (United States)

1993-12-01

8

Novel association of APC with intermediate filaments identified using a new versatile APC antibody  

E-print Network

identified 42 proteins in complex with APC, including ?-catenin and intermediate filament (IF) proteins lamin B1 and keratin 81. Association of lamin B1 with APC in cultured cells and human colonic tissue was verified by co...

Wang, Yang; Azuma, Yoshiaki; Friedman, David B.; Coffey, Robert J.; Neufeld, Kristi L.

2009-10-21

9

Spectroscopic identification and stability of the intermediate in the OH + HONO2 reaction  

PubMed Central

The reaction of nitric acid with the hydroxyl radical influences the residence time of HONO2 in the lower atmosphere. Prior studies [Brown SS, Burkholder JB, Talukdar RK, Ravishankara AR (2001) J Phys Chem A 105:1605–1614] have revealed unusual kinetic behavior for this reaction, including a negative temperature dependence, a complex pressure dependence, and an overall reaction rate strongly affected by isotopic substitution. This behavior suggested that the reaction occurs through an intermediate, theoretically predicted to be a hydrogen-bonded OH–HONO2 complex in a six-membered ring-like configuration. In this study, the intermediate is generated directly by the association of photolytically generated OH radicals with HONO2 and stabilized in a pulsed supersonic expansion. Infrared action spectroscopy is used to identify the intermediate by the OH radical stretch (?1) and OH stretch of nitric acid (?2) in the OH–HONO2 complex. Two vibrational features are attributed to OH–HONO2: a rotationally structured ?1 band at 3516.8 cm?1 and an extensively broadened ?2 feature at 3260 cm?1, both shifted from their respective monomers. These same transitions are identified for OD–DONO2. Assignments of the features are based on their vibrational frequencies, analysis of rotational band structure, and comparison with complementary high level ab initio calculations. In addition, the OH (v = 0) product state distributions resulting from ?1 and ?2 excitation are used to determine the binding energy of OH–HONO2, D0 ? 5.3 kcal·mol?1, which is in good accord with ab initio predictions. PMID:18678905

O'Donnell, Bridget A.; Li, Eunice X. J.; Lester, Marsha I.; Francisco, Joseph S.

2008-01-01

10

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

PubMed Central

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

Tinberg, Christine E.; Lippard, Stephen J.

2010-01-01

11

Solving the structure of reaction intermediates by time-resolved synchrotron x-ray absorption spectroscopy  

E-print Network

Solving the structure of reaction intermediates by time-resolved synchrotron x-ray absorption present a robust data analysis method of time-resolved x-ray absorption spectroscopy experiments suitable for chemical speciation and structure determination of reaction intermediates. Chemical speciation is done

Frenkel, Anatoly

12

In vivo identification of intermediate stages of the DNA inversion reaction catalyzed by the Salmonella Hin recombinase.  

PubMed Central

The Hin recombinase catalyzes a site-specific recombination reaction that results in the reversible inversion of a 1-kbp segment of the Salmonella chromosome. The DNA inversion reaction catalyzed by the Salmonella Hin recombinase is a dynamic process proceeding through many intermediate stages, requiring multiple DNA sites and the Fis accessory protein. Biochemical analysis of this reaction has identified intermediate steps in the inversion reaction but has not yet revealed the process by which transition from one step to another occurs. Because transition from one reaction step to another proceeds through interactions between specific amino acids, and between amino acids and DNA bases, it is possible to study these transitions through mutational analysis of the proteins involved. We isolated a large number of mutants in the Hin recombinase that failed to carry out the DNA exchange reaction. We generated genetic tools that allowed the assignment of these mutants to specific transition steps in the recombination reaction. This genetic analysis, combined with further biochemical analysis, allowed us to define contributions by specific amino acids to individual steps in the DNA inversion reaction. Evidence is also presented in support of a model that Fis protein enhances the binding of Hin to the hixR recombination site. These studies identified regions within the Hin recombinase involved in specific transition steps of the reaction and provided new insights into the molecular details of the reaction mechanism. PMID:9691026

Nanassy, O Z; Hughes, K T

1998-01-01

13

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

PubMed

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

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

2015-01-23

14

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

PubMed Central

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

Ermert, Johannes

2014-01-01

15

Kinetics and intermediates of the reaction of fully reduced Escherichia coli bo? ubiquinol oxidase with O?.  

PubMed

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

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

2014-08-26

16

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...

17

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

18

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 successfully 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.

G. Tagliente; R. Ghetti; N. Colonna; E. De Filippo

1999-12-31

19

Direct kinetic measurement of the reaction of the simplest Criegee intermediate with water vapor.  

PubMed

Carbonyl oxides, or Criegee intermediates, are important transient species formed in the reactions of unsaturated hydrocarbons with ozone. Although direct detection of Criegee intermediates has recently been realized, the main atmospheric sink of Criegee intermediates remains unclear. We report ultraviolet absorption spectroscopic measurements of the lifetime of the simplest Criegee intermediate, CH2OO, at various relative humidity levels up to 85% at 298 kelvin. An extremely fast decay rate of CH2OO was observed at high humidity. The observed quadratic dependence of the decay rate on water concentration implied a predominant reaction with water dimer. On the basis of the water dimer equilibrium constant, the effective rate coefficient of the CH2OO + (H2O)2 reaction was determined to be 6.5 (±0.8) × 10(-12) cubic centimeters per second. This work would help modelers to better constrain the atmospheric concentrations of CH2OO. PMID:25569112

Chao, Wen; Hsieh, Jun-Ting; Chang, Chun-Hung; Lin, Jim Jr-Min

2015-02-13

20

Recent developments in methods for identifying reaction coordinates  

PubMed Central

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

Li, Wenjin; Ma, Ao

2014-01-01

21

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

22

Investigation of the intermediate-energy deuteron breakup reaction  

SciTech Connect

The Udagawa-Tamura formalism is employed to calculate the proton singles both in the bound and unbound regions. Both the Elastic-Breakup (EB) and the Breakup-Fusion (BF) processes are considered to calculate the doubly-differential cross section for light and intermediate mass nuclei. The calculated spectra for 25 and 56 MeV deuterons reproduce the experimental spectra very well except for the spectra at large angle and at low energies, of the outgoing particle. Contributions due to precompound and evaporation processes are estimated to supplement the spectral results based on the Elastic-Breakup and Breakup-Fusion mechanisms. An extension of the model calculations to higher deuteron energies is being made to test the (EB + BF) model limitations. 5 refs., 1 fig.

Divadeenam, M.; Ward, T.E.; Mustafa, M.G.; Udagawa, T.; Tamura, T.

1989-01-01

23

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

24

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. PMID:22002602

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

2012-01-01

25

Glutathione peroxidase's reaction intermediate selenenic acid is stabilized by the protein microenvironment.  

PubMed

Selenenic acids are highly reactive intermediates of selenoproteins' enzymatic reactions. Knowledge of how the protein environment protects and stabilizes them is fundamental not only to descriptions of selenoproteins' reactivity but also potentially for proteomics and therapeutics. However, selenenic acids are considered particularly short-lived and are not yet identified in wild-type selenoproteins. Here, we report trapping the selenenic acid in glutathione peroxidase, an antioxidant enzyme that efficiently eliminates hydroperoxides. It has long been thought that selenium-containing glutathione peroxidases form a selenenic acid intermediate. However, this putative species has eluded detection. Here, we report its identification. The selenenic acid in bovine glutathione peroxidase 1 was chemically trapped using dimedone, an alkylating agent specific to sulfenic and selenenic acids. The alkylation of the catalytic selenocysteine was verified by electrospray ionization mass spectrometry. In the presence of glutathione, the selenocysteine was not alkylated because the selenenic acid condenses faster with glutathione than the alkylation reaction. In the absence of thiols, the selenenic acid was surprisingly long-lived with 95% of the protein still able to react with dimedone 10 min after hydrogen peroxide was removed, indicating that the protein environment stabilizes the selenenic acid by shielding it from reactive groups in the protein. After 30 min, the selenocysteine was no longer modified but became accessible once the protein was exposed to reducing agents. This suggests that the selenenic acid reacted with a protein's amide or amine to form a selenylamide bond. Such a modification may play a role in protecting glutathione peroxidase?' reactivity. PMID:25124921

Li, Fei; Liu, Jun; Rozovsky, Sharon

2014-11-01

26

A specific polymerase chain reaction method to identify Stenotrophomonas maltophilia  

PubMed Central

Stenotrophomonas maltophilia is a multidrug-resistant nosocomial pathogen that is difficult to identify unequivocally using current methods. Accordingly, because the presence of this microorganism in a patient may directly determine the antimicrobial treatment, conventional polymerase chain reaction (PCR) and real-time PCR assays targeting 23S rRNA were developed for the specific identification of S. maltophilia. The PCR protocol showed high specificity when tested against other species of Stenotrophomonas, non-fermentative Gram-negative bacilli and 100 clinical isolates of S. maltophilia previously identified using the Vitek system. PMID:23778655

Gallo, Stephanie Wagner; Ramos, Patrícia Locosque; Ferreira, Carlos Alexandre Sanchez; de Oliveira, Sílvia Dias

2013-01-01

27

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. PMID:22908224

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

2012-01-01

28

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. 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

2014-01-01

29

The first chemoselective tandem acylation of the Blaise reaction intermediate: a novel method for the synthesis of alpha-acyl-beta-enamino esters, key intermediate for pyrazoles.  

PubMed

The Blaise reaction intermediate, a zinc bromide complex of beta-enamino ester, could be activated in situ by addition of a stoichiometric or catalytic amount of n-BuLi to allow chemoselective tandem C2-acylation providing alpha-acyl-beta-enamino esters, which are valuable intermediates for the syntheses of tri- and tetrasubstituted pyrazoles. PMID:18956034

Chun, Yu Sung; Lee, Ki Kon; Ko, Young Ok; Shin, Hyunik; Lee, Sang-gi

2008-11-01

30

DOI: 10.1002/cphc.201000294 Identification of Hydroperoxy Species as Reaction Intermediates in the  

E-print Network

the first spectroscopic identification of sur- face-bound OOH as intermediates of oxygen evolution reaction and facilitate their spec- troscopic detection. A confocal Raman microscope coupled with a high numeri- cal in Figure 1. At 1.0 V, the Au sur- face is reduced, as can be seen from its relatively featureless SER

Bell, Alexis

31

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

32

Electron nuclear double resonance determined structures of enzyme reaction intermediates: structural evidence for substrate destabilization  

NASA Astrophysics Data System (ADS)

Angle selective ENDOR of nitroxyl spin-labels is briefly reviewed to illustrate the methodology of structure analysis developed in our laboratory for characterizing catalytically competent intermediates of enzyme catalyzed reactions. ENDOR structure determination of a reaction intermediate of ?-chymotrypsin formed with a kinetically specific spin-labeled substrate and of an enzyme-inhibitor complex formed with a spin-labeled transition-state inhibitor analog is briefly described. Both spin-labeled molecules bound in the active site of the enzyme are found in torsionally distorted conformations. It is suggested that this torsionally distorted state in which the bound ligand is of higher potential energy than in the ground state conformation reflects substrate destabilization in the course of the enzyme catalyzed reaction.

Makinen, Marvin W.

1998-12-01

33

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)...

34

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

PubMed

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, F(0), F(0)/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. PMID:23902001

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

2013-07-28

35

A kinetic study of the CH2OO Criegee intermediate self-reaction, reaction with SO2 and unimolecular reaction using cavity ring-down spectroscopy.  

PubMed

Criegee intermediates are important species formed during the ozonolysis of alkenes. Reaction of stabilized Criegee intermediates with various species like SO2 and NO2 may contribute significantly to tropospheric chemistry. In the laboratory, self-reaction can be an important loss pathway for Criegee intermediates and thus needs to be characterized to obtain accurate bimolecular reaction rate coefficients. Cavity ring-down spectroscopy was used to perform kinetic measurements for various reactions of CH2OO at 293 K and under low pressure (7 to 30 Torr) conditions. For the reaction CH2OO + CH2OO (8), a rate coefficient k8 = (7.35 ± 0.63) × 10(-11) cm(3) molecule(-1) s(-1) was derived from the measured CH2OO decay rates, using an absorption cross section value reported previously. A rate coefficient of k4 = (3.80 ± 0.04) × 10(-11) cm(3) molecule(-1) s(-1) was obtained for the CH2OO + SO2 (4) reaction. An upper limit for the unimolecular CH2OO loss rate coefficient of 11.6 ± 8.0 s(-1) was deduced from studies of reaction (4). SO2 catalysed CH2OO isomerization or intersystem crossing is proposed to occur with a rate coefficient of (3.53 ± 0.32) × 10(-11) cm(3) molecule(-1) s(-1). PMID:25553776

Chhantyal-Pun, Rabi; Davey, Anthony; Shallcross, Dudley E; Percival, Carl J; Orr-Ewing, Andrew J

2015-02-01

36

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

37

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

38

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

39

Kinetics, mechanism and intermediates of some radiation-induced reactions in aqueous solutions  

NASA Astrophysics Data System (ADS)

The results of pulse radiolysis studies of the kinetics and mechanism of fast one-electron redox reactions of halide ions, metal ions, actinides and other compounds with hydrated electrons, hydroxyl and other radicals and hydrogen atoms and the properties of intermediates formed in these reactions are analysed. The oxidation of a mixture of chloride and bromide ions yields mixed radical anions ClBr-·. Data on the formation of metal atoms and ions in unusual and unstable oxidation states by the reduction of metal ions in aqueous solutions and on the reactions involving such ions are presented. It is shown that the reduction of compounds in aqueous solutions with organic radicals takes place through outer- or inner-sphere electron transfer.

Ershov, Boris G.

2004-01-01

40

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. PMID:23538785

Vora, Harit U.; Wheeler, Philip

2013-01-01

41

A mass spectrometry-based probe of equilibrium intermediates in protein-folding reactions.  

PubMed

Described here is a mass spectrometry- and H/D exchange-based approach for the detection of equilibrium intermediate state(s) in protein-folding reactions. The approach utilizes the stability of unpurified proteins from rates of H/D exchange (SUPREX) technique to measure the m value (i.e., delta DeltaG/delta [denaturant] value) associated with the folding reaction of a protein. Such SUPREX m-value analyses can be made over a wide range of denaturant concentrations. Thus, the described approach is well-suited for the detection of high-energy intermediates that might be populated at low denaturant concentrations and hard to detect in conventional chemical denaturation experiments using spectroscopic probes. The approach is demonstrated on four known non-two-state folding proteins, including alpha-lactalbumin, cytochrome c, intestinal fatty acid binding protein (IFABP), and myoglobin. The non-two-state folding behavior of each model protein system was detected by the described method. The cytochrome c, myoglobin, and IFABP systems each had high-energy intermediate states that were undetected in conventional optical spectroscopy-based studies and previously required other more specialized biophysical approaches (e.g., nuclear magnetic resonance spectroscopy-based methods and protease protection assays) for their detection. The SUPREX-based approach outlined here offers an attractive alternative to these other approaches, because it has the advantage of speed and the ability to analyze both purified and unpurified protein samples in either concentrated or dilute solution. PMID:17042507

Dai, Susie Y; Fitzgerald, Michael C

2006-10-24

42

Criegee intermediate reaction with CO: mechanism, barriers, conformer-dependence, and implications for ozonolysis chemistry.  

PubMed

Density functional theory and transition state theory rate constant calculations have been performed to gain insight into the bimolecular reaction of the Criegee intermediate (CI) with carbon monoxide (CO) that is proposed to be important in both atmospheric and industrial chemistry. A new mechanism is suggested in which the CI acts as an oxidant by transferring an oxygen atom to the CO, resulting in the formation of a carbonyl compound (aldehyde or ketone depending upon the CI) and carbon dioxide. Fourteen different CIs, including ones resulting from biogenic ozonolysis, are considered. Consistent with previous reports for other CI bimolecular reactions, the anti conformers are found to react faster than the syn conformers. However, this can be attributed to steric effects and not hyperconjugation as generally invoked. The oxidation reaction is slow, with barrier heights between 6.3 and 14.7 kcal/mol and estimated reaction rate constants 6-12 orders-of-magnitude smaller than previously reported literature estimates. The reaction is thus expected to be unimportant in the context of tropospheric oxidation chemistry. However, the reaction mechanism suggests that CO could be exploited in ozonolysis to selectively obtain industrially important carbonyl compounds. PMID:24527836

Kumar, Manoj; Busch, Daryle H; Subramaniam, Bala; Thompson, Ward H

2014-03-13

43

New insights into the nature of observable reaction intermediates in cytochrome P450 NO reductase by using a combination of spectroscopy and quantum mechanics/molecular mechanics calculations.  

PubMed

Cytochrome P450 NO reductase is an unusual member of the cytochrome P450 superfamily. It catalyzes the reduction of nitric oxide to nitrous oxide. The reaction intermediates were studied in detail by a combination of experimental and computational methods. They have been characterized experimentally by UV/Vis, EPR, Mössbauer, and MCD spectroscopy. In conjunction with quantum mechanics/molecular mechanics (QM/MM) calculations, we sought to characterize the resting state and the two detectable intermediates in detail and to elucidate the nature of the key intermediate I of the reaction. Six possible candidates were taken into account for the unknown key intermediate in the computational study, differing in protonation state and electronic structure. Two out of the six candidates could be identified as putative intermediates I with the help of the spectroscopic data: singlet diradicals Fe(III)-NHO(·)(-) and Fe(III)-NHOH(.). In a companion publication (C. Riplinger, F. Neese, ChemPhysChem- 2011, 12, 3192) we have used QM/MM models based on these structures and performed a kinetic simulation. The combination of these two studies shows the nature of the key intermediate to be the singlet diradical, Fe(III)-NHOH(·). PMID:24453075

Riplinger, Christoph; Bill, Eckhard; Daiber, Andreas; Ullrich, Volker; Shoun, Hirofumi; Neese, Frank

2014-02-01

44

How to identify carbonate rock reactions in concrete  

SciTech Connect

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

Katayama, Tetsuya [Department of Concrete Maintenance, Kawasaki Geological Engineering Co. Ltd., 2-11-15 Mita, Minato-ku, Tokyo 108-8337 (Japan)]. E-mail: katayamat@kge.co.jp

2004-11-15

45

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

PubMed

This paper presents for the first time the investigation of TiO2 photocatalysis for the removal of pesticides in gas phase. Dichlorvos was used as a model pesticide, and experiments were carried out using both static and dynamic reaction systems to explore the different aspects of the process. Thus, adsorption, reaction kinetics, and the influence of several operational parameters such as relative humidity (RH), inlet concentration, flow rate, and association of TiO2 with activated carbon (AC) were all examined in detail. Furthermore, a special attention was devoted to the analysis of reaction products by means of various analytical techniques such as Fourier transform infrared spectroscopy, automated thermal desorption technique coupled to gas chromatography-mass spectrometry instrument, gas chromatography equipped with a pulse discharge helium photoionization detector, and ion chromatography. The results showed an immediate and total removal of dichlorvos at ppbv levels (50-350 ppbv) along with a high mineralization extent (50-85%) into harmless final products (CO2, HCl, PO43-). Moreover, RH was found to significantly affectthe mineralization extent and the formation of reaction intermediates. On the basis of identification data, direct charge transfer and chlorine radical (Cl*) attack were shown to play a key role in the reaction mechanism at low RH, whereas at high RH, HO* radicals were the predominant active species. PMID:18497160

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

2008-04-15

46

The CRISP package for intermediate- and high-energy photonuclear reactions  

NASA Astrophysics Data System (ADS)

The two-step process that characterizes the intermediate- and high-energy photonuclear reactions (between 40 MeV and 4 GeV) has been successfully described by Monte Carlo calculations. Recently, a new class of codes capable to perform those calculations according to a more realistic method has been developed, improving the possibilities for simulating the reactions in more details. In this work we present the CRISP package (standing for Rio-São Paulo Collaboration), which is a coupling of the multi collisional Monte Carlo (MCMC) and the Monte Carlo for evaporation-fission (MCEF) codes. The first one describes the intranuclear cascade process, while the second one is dedicated to the evaporation/fission competition step. Both codes have already shown to be useful for calculating several features of different nuclear reactions. The CRISP code, coupling these two software, represents a good tool to describe the complex characteristics of the nuclear reactions, and opens the opportunity for applications in quite different fields, such as studies of hadron physics inside the nucleus, specific nuclear reactions, spallation and/or fission processes initiated by different probes and many others.

Deppman, A.; Duarte, S. B.; Silva, G.; Tavares, O. A. P.; Anéfalos, S.; Arruda-Neto, J. D. T.; Rodrigues, T. E.

2004-12-01

47

Biomphalaria havanensis Identified as a Potential Intermediate Host for the Digenetic Trematode Bolbophorus damnificus  

Microsoft Academic Search

The digenetic trematode Bolbophorus damnificus has been associated with mortalities in commercial channel catfish Ictalurus punctatus in the Mississippi Delta. In the life cycle of B. damnificus, the only confirmed first intermediate host is the ram's horn snail Planorbella trivolvis. Recently, the exotic snail Biomphalaria havanensis has been isolated in several channel catfish ponds in the Mississippi Delta. The aim

Marlena C. Yost; Linda M. Pote; David J. Wise; Brian S. Dorr; Terry D. Richardson

2009-01-01

48

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

49

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

Microsoft Academic Search

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

A. Banu; L. Trache; F. Carstoiu; N. A. Orr; N. L. Achouri; A. Bonaccorso; W. N. Catford; M. Chartier; B. Fernandez-Dominguez; M. Freer; L. Gaudefroy; M. Horoi; M. Labiche; B. Laurent; R. C. Lemmon; F. Negoita; S. Paschalis; N. Patterson; B. Pietras; B. Roeder; F. Rotaru; P. Roussel-Chomaz; E. Simmons; J. S. Thomas; R. E. Tribble

2010-01-01

50

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

SciTech Connect

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

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

2013-08-08

51

Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor  

PubMed Central

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 stereocontrol in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral ?-hydroxyketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2?-phosphonomandelylThDP) of the covalent ThDP-substrate adduct C2?-mandelylThDP. 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 Å. 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. PMID:19320438

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

2009-01-01

52

Radical intermediates in photoinduced reactions on TiO2 (an EPR spin trapping study).  

PubMed

The radical intermediates formed upon UVA irradiation of titanium dioxide suspensions in aqueous and non-aqueous environments were investigated applying the EPR spin trapping technique. The results showed that the generation of reactive species and their consecutive reactions are influenced by the solvent properties (e.g., polarity, solubility of molecular oxygen, rate constant for the reaction of hydroxyl radicals with the solvent). The formation of hydroxyl radicals, evidenced as the corresponding spin-adducts, dominated in the irradiated TiO2 aqueous suspensions. The addition of 17O-enriched water caused changes in the EPR spectra reflecting the interaction of an unpaired electron with the 17O nucleus. The photoexcitation of TiO2 in non-aqueous solvents (dimethylsulfoxide, acetonitrile, methanol and ethanol) in the presence of 5,5-dimethyl-1-pyrroline N-oxide spin trap displayed a stabilization of the superoxide radical anions generated via electron transfer reaction to molecular oxygen, and various oxygen- and carbon-centered radicals from the solvents were generated. The character and origin of the carbon-centered spin-adducts was confirmed using nitroso spin trapping agents. PMID:25353381

Dvoranová, Dana; Barbieriková, Zuzana; Brezová, Vlasta

2014-01-01

53

[Spectroscopic measurement of intermediate free radicals of n-heptane in the combustion reaction].  

PubMed

Using an intensified spectroscopic detector CCD and a chemical shock tube, transient emission spectra of n-heptane during the reaction process of combustion were measured, with exposure time of 6 micros and a spectral range of 200 - 850 nm Experiments were conducted at an ignition temperature of 1 408 K and pressure of 2.0 atmos, with an initial fuel mole fraction of 1.0% and an equivalence ratio of 1.0. Measured emission bands were determined to be produced by OH, CH and C2 free radicals, which reveals that small OH, CH and C2 radicals are important intermediate products in the combustion process of n-heptane. Time-resolved spectra indicate that radical concentrations of OH, CH and C2 reached their peaks sharply; however, CH and C2 reduced and disappeared rapidly while the duration of OH was much longer in the reaction. This work provides experimental data for understanding the microscopic process and validating the mechanism of n-heptane combustion reaction. PMID:22715748

Ye, Bin; Li, Ping; Zhang, Chang-hua; Wang, Li-dong; Tang, Hong-chang; Li, Xiang-yuan

2012-04-01

54

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

NSDL National Science Digital Library

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.

2005-10-11

55

Direct observation of intermediates in a thermodynamically controlled solid-state dynamic covalent reaction.  

PubMed

We present the first polymorph interconversion study that uses solid-state dynamic covalent chemistry (DCC). This system exhibits unexpected and rich behavior, including the observation that under appropriate conditions the polymorph interconversion of a heterodimer proceeds through reversible covalent chemistry intermediates, and this route is facilitated by one of the two disulfide homodimers involved in the reaction. Furthermore, we demonstrate experimentally that in all cases a dynamic equilibrium is reached, meaning that changing the milling conditions affects the free energy difference between the two polymorphs and thus their relative stability. We suggest that this effect is due to the surface solvation energy combined with the high surface to volume ratio of the nanocrystalline powder. PMID:25314624

Belenguer, Ana M; Lampronti, Giulio I; Wales, David J; Sanders, Jeremy K M

2014-11-19

56

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

PubMed Central

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

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

2012-01-01

57

Dehydration reactions and intermediate depth earthquakes: Is gypsum the right analog material for an experimental investigation?  

NASA Astrophysics Data System (ADS)

In addition to melting or runaway creep along shear zones, plastic instabilities and solid-solid phase transitions, the mechanical effect of dehydration reactions has been suggested as a process responsible for the occurrence of intermediate depth earthquakes: If the porosity and permeability of the source region are low and the overall molar volume change of the reaction is positive the effective pressure acting on the rock is significantly reduced. Rocks initially deforming in their ductile field could then embrittle and fail. Experimental investigations have previously been performed on both dehydrating gypsum as an analog material and natural rock samples like serpentinite (antigorite). Dehydration in nature occurs syntectonically and the occurrence of earthquakes always requires at least a partial release of stored elastic energy associated with a drop in stress. Therefore only those deformation experiments are significant that are performed in parallel with the progressing reaction. In addition, at constant strain rate, the measured stress-strain curve must show a significant and rapid stress drop which is symptomatic for brittle failure. If this feature is not observed for a specific analog material, it is not suitable for the investigation of the above process in the context of earthquakes. For this reaction induced embrittlement to be expected the hydrous material should show brittle failure at low confining pressures. Nominally dry cylindrical samples of finegrained natural gypsum were strained up to 15% in a gas-medium apparatus at 0.1 to 50 MPa confining pressure, 20 to 110^oC and a strain rate of 1.5 \\cdot 10-6 to 1.5 \\cdot 10-5 1/s. The samples showed nearly ideally ductile behavior suggesting cataclastic flow. The flow stress was independent of strain rate, decreased with decreasing confining pressure and increasing temperature and had a maximum of 80 MPa. Only at room temperature and ambient pressure did the samples show slow strain weakening indicating ductile stress relaxation. The maximum flow stress in this case was only 30 MPa. This raises the question if for the case of gypsum a reaction induced reduction in effective pressure can initiate embrittlement. Results on clarifying deformation experiments under reaction conditions will be presented in addition to the results summarized above.

Milsch, H.; Scholz, C.

2003-04-01

58

Electron paramagnetic resonance and electron-nuclear double resonance studies of the reactions of cryogenerated hydroperoxoferric-hemoprotein intermediates.  

PubMed

The fleeting ferric peroxo and hydroperoxo intermediates of dioxygen activation by hemoproteins can be readily trapped and characterized during cryoradiolytic reduction of ferrous hemoprotein-O2 complexes at 77 K. Previous cryoannealing studies suggested that the relaxation of cryogenerated hydroperoxoferric intermediates of myoglobin (Mb), hemoglobin, and horseradish peroxidase (HRP), either trapped directly at 77 K or generated by cryoannealing of a trapped peroxo-ferric state, proceeds through dissociation of bound H2O2 and formation of the ferric heme without formation of the ferryl porphyrin ?-cation radical intermediate, compound I (Cpd I). Herein we have reinvestigated the mechanism of decays of the cryogenerated hydroperoxyferric intermediates of ?- and ?-chains of human hemoglobin, HRP, and chloroperoxidase (CPO). The latter two proteins are well-known to form spectroscopically detectable quasistable Cpds I. Peroxoferric intermediates are trapped during 77 K cryoreduction of oxy Mb, ?-chains, and ?-chains of human hemoglobin and CPO. They convert into hydroperoxoferric intermediates during annealing at temperatures above 160 K. The hydroperoxoferric intermediate of HRP is trapped directly at 77 K. All studied hydroperoxoferric intermediates decay with measurable rates at temperatures above 170 K with appreciable solvent kinetic isotope effects. The hydroperoxoferric intermediate of ?-chains converts to the S = 3/2 Cpd I, which in turn decays to an electron paramagnetic resonance (EPR)-silent product at temperature above 220 K. For all the other hemoproteins studied, cryoannealing of the hydroperoxo intermediate directly yields an EPR-silent majority product. In each case, a second follow-up 77 K ?-irradiation of the annealed samples yields low-spin EPR signals characteristic of cryoreduced ferrylheme (compound II, Cpd II). This indicates that in general the hydroperoxoferric intermediates relax to Cpd I during cryoanealing at low temperatures, but when this state is not captured by reaction with a bound substrate, it is reduced to Cpd II by redox-active products of radiolysis. PMID:25046203

Davydov, Roman; Laryukhin, Mikhail; Ledbetter-Rogers, Amy; Sono, Masanori; Dawson, John H; Hoffman, Brian M

2014-08-01

59

X-ray absorption spectroscopy of reaction intermediates of lithium-sulfur batteries dissolved in polymer electrolytes  

NASA Astrophysics Data System (ADS)

Lithium polysulfide reaction intermediates formed during the charge and discharge reactions of a lithium-sulfur battery are known to diffuse out of the cathode during cycling, thus lowering battery capacity and lifetime. While numerous techniques have been developed to confine intermediates to the battery cathode, little is known about the complex reaction mechanism responsible for their formation. Work to understand the reaction mechanism requires an experimental technique capable of distinguishing the various lithium polysulfide intermediates formed during the charge/discharge reactions. We report on the use of x-ray absorption spectroscopy (XAS) to distinguish lithium polysulfide molecules in polymer electrolytes. Polysulfide intermediates dissolved in poly(ethylene oxide) and a block copolymer of polystyrene-poly(ethylene oxide) were probed at the oxygen, carbon, and sulfur K-edges. Simulated x-ray spectra based on ab-initio molecular dynamics were used to interpret experimental x-ray spectra. Theories regarding the physical and chemical nature of the polysulfide--polymer electrolyte interaction were developed.

Wujcik, Kevin; Balsara, Nitash

2013-03-01

60

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

61

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

SciTech Connect

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

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

1990-12-01

62

Identification of transient intermediates in the bisphosphatase reaction of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase by 31P-NMR spectroscopy.  

PubMed Central

31P-NMR spectroscopy was used to identify reaction intermediates during catalytic turn-over of the fructose-2,6-bisphosphatase domain (Fru-2,6-P2ase) of the bifunctional enzyme, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. When fructose-2,6-bisphosphate (Fru-2,6-P2) was added to the enzyme, the 31P-NMR spectrum showed three resonances in addition to those of free substrate: the phosphohistidine (His-P) intermediate, the C-6 phosphoryl group of fructose-6-phosphate bound to the phosphoenzyme, and phosphate generated by the hydrolysis of substrate. Direct analysis of the alkali-denatured phospho-enzyme intermediate by 1H-31P heteronuclear multiple quantum-filtered coherence spectroscopy confirmed the formation of 3-N-phosphohistidine. Binding of fructose 6-phosphate to the bisphosphatase was detected by a down-field shift and broadening of the C-6 phosphoryl resonance. The down-field shift was greater in the presence of the phosphoenzyme intermediate. Inhibition of Fru-2,6-P2 hydrolysis by fructose 6-phosphate and Fru-2,6-P2 was shown to involve binding of the sugar phosphates to the phosphoenzyme. This study provides new experimental evidence in support of the reaction mechanism of Fru-2,6-P2ase and suggests that the steady-state His-P intermediate exists primarily in the E-P.fructose 6-phosphate complex. These results lay a solid foundation for the use of 31P-NMR magnetization transfer studies to provide an in-depth analysis of the bisphosphatase reaction mechanism. PMID:7755565

Okar, D A; Kakalis, L T; Narula, S S; Armitage, I M; Pilkis, S J

1995-01-01

63

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

64

Radicals in the Reaction between Peroxynitrite and Uric Acid Identified by Electron Spin Resonance Spectroscopy and Liquid Chromatography Mass Spectrometry  

PubMed Central

Peroxynitrite is a reactive oxidant produced in vivo in response to oxidative and other stress by the diffusion-limited reaction of nitric oxide and superoxide. This contribution is focused on the identification of free radical intermediates of uric acid formed during its reaction with peroxynitrite. The experimental approach included the ESR spin trapping of the radical generated from the reaction between uric acid and peroxynitrite at pH 7.4 and mass spectrometry studies of the trapped radicals. Using PBN (N-tert-butyl-?-phenylnitrone) as the spin trapping agent, a six-line ESR spectrum was obtained and its hyperfine coupling constants, a(N) = 15.6 G; and a(H) = 4.4 G, revealed the presence of carbon-based radicals. Further structural identification of the PBN-radical adducts was carried out using liquid chromatography-mass spectrometry. After comparison with the control reactions, two species were identified corresponding to the protonated molecules (M+1) at m/z 352 and 223, respectively. The ions of m/z 352 were characterized as the PBN-triuretcarbonyl radical adduct and the m/z 223 ion was identified as the PBN-aminocarbonyl radical adduct. Their mechanism of formation is discussed. PMID:20406679

Imaram, Witcha; Gersch, Christine; Kim, Kyung Mee; Johnson, Richard J.; Henderson, George N.; Angerhofer, Alexander

2010-01-01

65

Water-sensitive low-frequency vibrations of reaction intermediates during S-state cycling in photosynthetic water oxidation.  

PubMed

In photosynthetic water oxidation, two water molecules are converted to an oxygen molecule through five reaction intermediates, designated S(n) (n = 0-4), at the catalytic Mn cluster of photosystem II. To understand the mechanism of water oxidation, changes in the chemical nature of the substrate water as well as the Mn cluster need to be defined during S-state cycling. Here, we report for the first time a complete set of Fourier transform infrared difference spectra during S-state cycling in the low-frequency (670-350 cm(-1)) region, in which interactions between the Mn cluster and its ligands can be detected directly, in PS II core particles from Thermosynechococcus elongatus. Furthermore, vibrations from oxygen and/or hydrogen derived from the substrate water and changes in them during S-state cycling were identified using multiplex isotope-labeled water, including H2(18)O, D2(16)O, and D2(18)O. Each water isotope affected the low-frequency S-state cycling spectra, characteristically. The bands sensitive only to (16)O/(18)O exchange were assigned to the modes from structures involving Mn and oxygen having no interactions with hydrogen, while the bands sensitive only to H/D exchange were assigned to modes from amino acid side chains and/or polypeptide backbones that associate with water hydrogen. The bands sensitive to both (16)O/(18)O and H/D exchanges were attributed to the structure involving Mn and oxygen structurally coupled with hydrogen in a direct or an indirect manner through hydrogen bonds. These bands include the changes of intermediate species derived from substrate water during the process of photosynthetic water oxidation. PMID:15909976

Kimura, Yukihiro; Ishii, Asako; Yamanari, Toshihiro; Ono, Taka-aki

2005-05-31

66

Aberrant S(RN)1 Reaction of 4-Aminophenol with alpha,p-Dinitrocumene: EPR Observation of Intermediates.  

PubMed

The tert-butoxide-induced substitution of alpha,p-dinitrocumene by 4-aminophenol unexpectedly afforded the N-coupled product, 2-(4-hydroxyanilino)-2-(4-nitrophenyl)propane. EPR observations revealed arylaminyl radical intermediates as well as coupled anion radicals, hence the normal S(RN)1 process may compete with an alternative nonchain reaction pathway. PMID:10814434

Scamehorn; Mahnke; Krause; Frey; Hendriksen; Jahn; Kultgen; Walton

2000-03-23

67

The use of the magnetic field effect for studying a chemiluminescent chemical reaction in aqueous solution. Reaction rate constants and lifetimes of intermediate molecules  

NASA Astrophysics Data System (ADS)

The phase shift magnetic field effect technique is applied for investigation of the chemiluminescent (ChL) reaction of luminol oxidation by potassium ferricyanide in aqueous alkali solution. The external modulated magnetic field changed the rate constant of recombination of luminol radicals. Rate constants of intermediate stages of the reaction are obtained: 10 8 M -1 s -1 for diazaquinone reaction with hydrogen peroxide, 2 X 10 6 M -1 s -1 for diazaquinone hydrolysis and 2 X 10 5 s -1 for the decomposition of hydroperoxide, which is a precursor of the light emitter.

Triebel, Michael M.; Totrov, Maxim M.; Zorinyants, George E.; Frankevich, Eugene L.

1993-11-01

68

Unstable reaction intermediates and hysteresis during the catalytic cycle of 5-aminolevulinate synthase: implications from using pseudo and alternate substrates and a promiscuous enzyme variant.  

PubMed

5-Aminolevulinate (ALA), an essential metabolite in all heme-synthesizing organisms, results from the pyridoxal 5'-phosphate (PLP)-dependent enzymatic condensation of glycine with succinyl-CoA in non-plant eukaryotes and ?-proteobacteria. The predicted chemical mechanism of this ALA synthase (ALAS)-catalyzed reaction includes a short-lived glycine quinonoid intermediate and an unstable 2-amino-3-ketoadipate intermediate. Using liquid chromatography coupled with tandem mass spectrometry to analyze the products from the reaction of murine erythroid ALAS (mALAS2) with O-methylglycine and succinyl-CoA, we directly identified the chemical nature of the inherently unstable 2-amino-3-ketoadipate intermediate, which predicates the glycine quinonoid species as its precursor. With stopped-flow absorption spectroscopy, we detected and confirmed the formation of the quinonoid intermediate upon reacting glycine with ALAS. Significantly, in the absence of the succinyl-CoA substrate, the external aldimine predominates over the glycine quinonoid intermediate. When instead of glycine, L-serine was reacted with ALAS, a lag phase was observed in the progress curve for the L-serine external aldimine formation, indicating a hysteretic behavior in ALAS. Hysteresis was not detected in the T148A-catalyzed L-serine external aldimine formation. These results with T148A, a mALAS2 variant, which, in contrast to wild-type mALAS2, is active with L-serine, suggest that active site Thr-148 modulates ALAS strict amino acid substrate specificity. The rate of ALA release is also controlled by a hysteretic kinetic mechanism (observed as a lag in the ALA external aldimine formation progress curve), consistent with conformational changes governing the dissociation of ALA from ALAS. PMID:24920668

Stojanovski, Bosko M; Hunter, Gregory A; Jahn, Martina; Jahn, Dieter; Ferreira, Gloria C

2014-08-15

69

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

70

Initial electron donor and acceptor in isolated Photosystem II reaction centers identified  

E-print Network

Initial electron donor and acceptor in isolated Photosystem II reaction centers identified similarity between the plant Photosystem II reaction center (RC) and its purple bacterial counterpart, we oxidation, is formed after 6 ps. We conclude therefore that in the Photosystem II RC the primary charge

van Stokkum, Ivo

71

Detection of intermediates for the Eschweiler-Clarke reaction by liquid-phase reactive desorption electrospray ionization mass spectrometry.  

PubMed

Desorption electrospray ionization mass spectrometry (DESI-MS) has been developed dramatically as a powerful tool for the rapid analysis of samples in their native environment. Here a novel application of DESI-MS was demonstrated for direct probing of the reactive intermediates in the liquid-phase Eschweiler-Clarke reaction, a reductive amination reaction whereby a primary (or secondary) amine is successively N-methylated using excess formaldehyde and formic acid. The intermediates ion species of sodiated amino alcohol ([I + Na](+)) and iminium ([II](+)), along with the corresponding protonated molecules of amine reactant ([M + H](+)) and end product ([III + H](+)), were simultaneously and unambiguously characterized by the positive ion DESI-MS in the native liquid-phase reactive condition. The operating variables were optimized for better analytical performance including the spray solvent composition (such as formic acid concentration, proportion of methanol-water), voltage applied, spray spatial distance and incident angle. The feasibility of the reactive DESI-MS detection of acid-formaldehyde methylations was further validated using amines of a large variety of chemical types (2 primary and 3 secondary amines). Thus, the liquid-phase reactive DESI-MS technique allows the direct analysis of reaction intermediates occurring in complex liquid solutions without sample preparation to provide a valuable insight into chemical reaction mechanisms. PMID:21491029

Xu, Guangming; Chen, Bo; Guo, Bin; He, Dongxiu; Yao, Shouzhuo

2011-06-01

72

Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate  

PubMed Central

Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential ?-elimination steps. However, Nei differs significantly from Fpg in substrate specificity. We determined the structure of Nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 ? resolution. The crosslink is derived from a Schiff base intermediate that precedes ?-elimination and is stabilized by reduction with NaBH4. Nei consists of two domains connected by a hinge region, creating a DNA binding cleft between domains. DNA in the complex is sharply kinked, the deoxyribitol moiety is bound covalently to Pro1 and everted from the duplex into the active site. Amino acids involved in substrate binding and catalysis are identified. Molecular modeling and analysis of amino acid conservation suggest a site for recognition of the damaged base. Based on structural features of the complex and site-directed mutagenesis studies, we propose a catalytic mechanism for Nei. PMID:11847126

Zharkov, Dmitry O.; Golan, Gali; Gilboa, Rotem; Fernandes, Andrea S.; Gerchman, Sue Ellen; Kycia, Jadwiga H.; Rieger, Robert A.; Grollman, Arthur P.; Shoham, Gil

2002-01-01

73

(/sup 14/C)Acrylonitrile: preparation via a stable tosylate intermediate and quantitative reaction with amine residues in collagen  

SciTech Connect

A simple, convenient synthetic procedure for (/sup 14/C)acrylonitrile is described. Na/sup 14/CN is used as the radioactive starting material. Small (milligram) amounts are converted to 3-(/sup 14/C)Hydroxypropionitrile by a substitution reaction with 2-chloroethanol. 3-(/sup 14/C)Hydroxypropionitrile is then tosylated, and the specific activity of this intermediate product is easily determined using its uv extinction coefficient and scintillation counting. (/sup 14/C)Acrylonitrile is obtained rapidly on distillation by heating the tosylate in the presence of a high boiling tertiary amine base catalyst. The tosylate intermediate can be stored, in contrast to radioactive acrylonitrile, which is unstable. The reaction of acrylonitrile with lysine, hydroxylysine, and histidine residues in human Achilles tendon collagen, as well as chromatographic separation and identification of the carboxyethyl derivatives of these amino acids, is also described.

Graham, L.; Mechanic, G.L.

1986-03-01

74

Light Charged Particles and Intermediate Mass Fragments from the Reactions 486, 550, 640, and 730 Mev KRYPTON86 + COPPER63  

Microsoft Academic Search

A detailed study has been made of the reaction ^{86}Kr + ^ {63}Cu at incident energies of 486, 550, 640, and 730 MeV. Measurements include cross sections, angular distributions, and energy spectra for light charged particles (^{1,2,3}H and ^4He), intermediate mass fragments (IMF) (4 <= Z = 18). Coincidences between light charged particles and between particles and fragments have also

John Thomas Boger

1992-01-01

75

NO3 radical production from the reaction between the Criegee intermediate CH2OO and NO2.  

PubMed

Formation of the NO3 radical was observed following photolysis of the CH2I2 + O2 system at 248 nm under ambient atmospheric boundary layer conditions (~760 Torr and 297 K) in the presence of NO2. The Criegee intermediate (CI) CH2OO is believed to be responsible for the NO3 production. The potential of such reactions to enhance the rate of NO3 production in the atmosphere is discussed. PMID:24030640

Ouyang, Bin; McLeod, Matthew W; Jones, Roderic L; Bloss, William J

2013-10-28

76

Mechanism of the EPSP synthase catalyzed reaction: evidence for the lack of a covalent carboxyvinyl intermediate in catalysis  

SciTech Connect

In order to detect covalent reaction intermediates in the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase reaction, we have investigated the interaction of EPSP synthase with the reaction product EPSP. An exchange of EPSP-methylene protons could be demonstrated by incubating EPSPS with EPSP in D/sub 2/O. Since trace amounts of contaminating Pi would lead to reversal of EPSPS reaction and hence methylene proton exchange, we added pyruvate kinase, ADP, Mg++ and K+. Under these conditions, any contaminating Pi that is converted to PEP is trapped as ATP. No exchange of EPSP protons with those of the solvent could be detected in the presence of this trap system, suggesting that enzyme-bound EPSP is unable to form a covalent tetrahedral complex. Incorporation of (/sup 14/C) from (/sup 14/C)-S3P and (/sup 14/C)-PEP into EPSP could be detected, but only in the absence of a PEP (or Pi) trap system. This indicates that for the exchange reaction, Pi is required, and also indicates the absence of a covalent intermediate, unless the carboxyvinyl-enzyme-bound S3P is completely restricted from exchange.

Wibbenmeyer, J.; Brundage, L.; Padgette, S.R.; Likos, J.J.; Kishore, G.M.

1988-06-16

77

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

78

Production of Neutron-Unbound States in Intermediate - Fragments from Nitrogen + Silver Reactions at E/a = 35 Mev  

NASA Astrophysics Data System (ADS)

The populations of neutron-unbound states and of bound states in intermediate-mass fragments have been measured at 15^circ, 31 ^circ, and 64^circ from the ^{14}N + Ag reaction at E/A = 35 MeV. The data are identified in terms of the reaction mechanism producing them, which is either a deep-inelastic mechanism or a quasielastic mechanism. In order to test the assumption that the deep -inelastic data are produced from a thermal source, the unbound-state/bound-state population ratios of deep-inelastic fragments are compared to the predictions of a thermal sequential decay model. Most, but not all, of the deep -inelastic population ratios are fitted with model calculations that assume a source temperature between 2.5 and 3.4 MeV. Three or more populations from the same isotope were measured for ^{13}C, ^ {12}B, and ^{10} Be. The deep-inelastic populations from ^{13}C and ^{10 }Be were fitted with a single temperature, while the deep-inelastic populations from ^ {12}B were not fitted. There is enough of the deep-inelastic data that is not fitted with the predictions of a thermal model that the assumption of a thermal source for the production of deep-inelastic fragments may be incorrect, or there may be other effects present which alter the thermal properties of the data. The dependence of the unbound-state/bound-state population ratio on the fragment kinetic energy shows a difference between the quasielastic and deep-inelastic data. For quasielastic fragments whose mass is near the mass of the beam, the ratio decreases towards zero as the fragment velocity approaches the beam velocity. In contrast, the ratio for half-beam mass quasielastic fragments is constant or only slightly decreasing as the kinetic energy increases. The ratio for deep-inelastic fragments is approximately constant as a function of kinetic energy, independent of fragment mass. The amount of feeding from several neutron-unbound channels into bound states is measured and compared to the sequential decay model. The effect of feeding on both spectral temperatures and on population temperatures is investigated. The effect of feeding on both temperatures, as determined by model calculations, cannot account for the discrepancy in the values between the two.

Heilbronn, Lawrence Harvey

79

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

PubMed

The results of quantum chemical modeling of organic and metal-containing intermediates that occur in electrocatalytic dehalogenation reactions of organic chlorides are presented. Modeling of processes that take place in successive steps of the electrochemical reduction of representative C1 and C2 chlorides - CHCl3 and Freon R113 (1,1,2-trifluoro-1,2,2-trichloroethane) - was carried out by density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2). It was found that taking solvation into account using an implicit solvent model (conductor-like screening model, COSMO) or considering explicit solvent molecules gave similar results. In addition to modeling of simple non-catalytic dehalogenation, processes with a number of complexes and their reduced forms, some of which were catalytically active, were investigated by DFT. Complexes M(L1)2 (M = Fe, Co, Ni, Cu, Zn, L1H = Schiff base from 2-pyridinecarbaldehyde and the hydrazide of 4-pyridinecarboxylic acid), Ni(L2) (H2L2 is the Schiff base from salicylaldehyde and 1,2-ethylenediamine, known as salen) and Co(L3)2Cl2, representing a fragment of a redox-active coordination polymer [Co(L3)Cl2]n (L3 is the dithioamide of 1,3-benzenedicarboxylic acid), were considered. Gradual changes in electronic structure in a series of compounds M(L1)2 were observed, and correlations between [M(L1)2](0) spin-up and spin-down LUMO energies and the relative energies of the corresponding high-spin and low-spin reduced forms, as well as the shape of the orbitals, were proposed. These results can be helpful for determination of the nature of redox-processes in similar systems by DFT. No specific covalent interactions between [M(L1)2](-) and the R113 molecule (M = Fe, Co, Ni, Zn) were found, which indicates that M(L1)2 electrocatalysts act rather like electron transfer mediators via outer-shell electron transfer. A relaxed surface scan of the adducts {M(L1)2·R113}(-) (M = Ni or Co) versus the distance between the chlorine atom leaving during reduction and the corresponding carbon atom showed an energy barrier to electron transfer (the first stage of R113 catalytic reduction), while DFT optimization of the {Ni(L2)·R113}(-) adduct showed barrier-free decomposition. The difference between the stabilities of the {Ni(L1)2·R113}(-) and {Ni(L2)·R113}(-) adducts correlates with the difference between the catalytic activities of Ni(L1)2 and Ni(L2) in the electrochemical reduction of R113. PMID:25623515

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

2015-02-10

80

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. PMID:23411632

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

2014-01-01

81

Application of Galactose Oxidase in Chemoenzymatic One-Pot Cascade Reactions Without Intermediate Recovery Steps  

Microsoft Academic Search

Various cascade routes starting from D-galactose derivatives—via 6-CH2OH oxidation catalyzed by galactose oxidase—are reported as one-pot procedures. The approach consists of combined bio- and chemocatalytic reactions as well as “spontaneous” chemical conversions. Workup is avoided by using compatible aqueous reaction conditions for all the consecutive reactions involved. A great benefit of this method is that D-galactose containing di-, tri- and

Rob Schoevaart; Tom Kieboom

2004-01-01

82

Identifying Neutrinos and Antineutrinos in Neutral-Current Scattering Reactions N. Jachowicz,1,* ,1  

E-print Network

Identifying Neutrinos and Antineutrinos in Neutral-Current Scattering Reactions N. Jachowicz,1,* ,1 August 2004) We study neutrino-induced nucleon knockout from nuclei. Expressions for the induced-wave approximation. Large dissimilarities in the nucleon polarization asymmetries are observed between neutrino

Gent, Universiteit

83

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

SciTech Connect

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

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

2000-04-01

84

Direct observation of reaction intermediates for a well defined heterogeneous alkene metathesis catalyst  

PubMed Central

Grafting of [W(?NAr)(=CHtBu)(2,5-Me2NC4H2)2] on a silica partially dehydroxylated at 700°C (SiO2- (700)) generates the corresponding monosiloxy complex [(?SiO)W(?NAr)(=CHtBu)(2,5-Me2NC4H2)] as the major species (?90%) along with [(?SiO)W(?NAr)(CH2tBu)(2,5-Me2NC4H2)2], according to mass balance analysis, IR, and NMR studies. This heterogeneous catalyst displays good activity and stability in the metathesis of propene. Very importantly, solid state NMR spectroscopy allows observation of the propagating alkylidene as well as stable metallacyclobutane intermediates. These species have the same reactivity as the initial surface complex [(?SiO)W(?NAr)(=CHtBu)(2,5-Me2NC4H2)], which shows that they are the key intermediates of alkene metathesis. PMID:18723685

Blanc, Frédéric; Berthoud, Romain; Copéret, Christophe; Lesage, Anne; Emsley, Lyndon; Singh, Rojendra; Kreickmann, Thorsten; Schrock, Richard R.

2008-01-01

85

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

PubMed

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

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

2012-11-12

86

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

87

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

88

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

89

Probing elastic and inelastic breakup contributions to intermediate-energy two-proton removal reactions  

E-print Network

The two-proton removal reaction from 28Mg projectiles has been studied at 93 MeV/u at the NSCL. First coincidence measurements of the heavy 26Ne projectile residues, the removed protons and other light charged particles enabled the relative cross sections from each of the three possible elastic and inelastic proton removal mechanisms to be determined. These more final-state-exclusive measurements are key for further interrogation of these reaction mechanisms and use of the reaction channel for quantitative spectroscopy of very neutron-rich nuclei. The relative and absolute yields of the three contributing mechanisms are compared to reaction model expectations - based on the use of eikonal dynamics and sd-shell-model structure amplitudes.

K. Wimmer; D. Bazin; A. Gade; J. A. Tostevin; T. Baugher; Z. Chajecki; D. Coupland; M. A. Famiano; T. K. Ghosh; G. F. Grinyer; R. Hodges; M. E. Howard; M. Kilburn; W. G. Lynch; B. Manning; K. Meierbachtol; P. Quarterman; A. Ratkiewicz; A. Sanetullaev; S. R. Stroberg; M. B. Tsang; D. Weisshaar; J. Winkelbauer; R. Winkler M. Youngs

2012-05-09

90

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

91

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

92

Kinetics and Mechanism of Oxidation Reactions of Porphyrin-Iron(IV)-Oxo Intermediates  

PubMed Central

The kinetics of reactions of three porphyrin-iron(IV)-oxo derivatives with alkenes and benzylic alcohols were measured. The iron-oxo systems studied were 5,10,15,20-tetrakis(2,6-dichlorophenyl)porphyrin-iron(IV)-oxo (2a), 5,10,15,20-tetrakis(2,6-difluorophenyl)porphyrin-iron(IV)-oxo (2b), and 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin-iron(IV)-oxo (2c). Species 2 were stable for hours at room temperature as dilute solutions in acetonitrile and reacted hundreds to thousands of times faster in the presence of high concentrations of substrates. Typical second-order rate constants determined from pseudo-first-order kinetic studies are 1–2 × 10?2 M?1 s?1 for reactions with styrene and 3 × 10?2 M?1 s?1 for reactions with benzyl alcohol. The reactivity order for the iron-oxo species was 2a > 2b > 2c, which is inverted from that expected on the basis of the electron demand of the porphyrin macrocycles, and the oxidation reaction was suppressed when excess porphyrin-iron(III) complex was added to reaction mixtures. These observations indicate that the reactions involve disproportionation of the iron(IV)-oxo species 2 to give an iron(III) species and a more highly oxidized iron species, presumed to be iron(IV)-oxo porphyrin radical cation, that is the true oxidant in the reactions. Analyses of the kinetics of oxidations of a series of para-substituted benzylic alcohols with Hammett ?+ substituent constants and with a dual parameter method developed by Jiang (Jiang, X. K. Acc. Chem. Res. 1997, 30, 283) indicated that considerable positive charge developed on the benzylic carbons in the oxidation reactions, as expected for electrophilic oxidants, and also that substantial radical character developed on the benzyl carbon in the transition states. PMID:17630728

Pan, Zhengzheng; Newcomb, Martin

2010-01-01

93

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

94

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

95

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. PMID:21595439

Song, Woon Ju; Lippard, Stephen J.

2011-01-01

96

Identifying genomic and developmental causes of adverse drug reactions in children  

PubMed Central

Adverse drug reactions are a concern for all clinicians who utilize medications to treat adults and children; however, the frequency of adult and pediatric adverse drug reactions is likely to be under-reported. In this age of genomics and personalized medicine, identifying genetic variation that results in differences in drug biotransformation and response has contributed to significant advances in the utilization of several commonly used medications in adults. In order to better understand the variability of drug response in children however, we must not only consider differences in genotype, but also variation in gene expression during growth and development, namely ontogeny. In this article, recommendations for systematically approaching pharmacogenomic studies in children are discussed, and several examples of studies that investigate the genomic and developmental contribution to adverse drug reactions in children are reviewed. PMID:21121777

Becker, Mara L; Leeder, J Steven

2011-01-01

97

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

98

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

99

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

100

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. PMID:24991512

Behm, R Jürgen

2014-01-01

101

Formula for proton-nucleus reaction cross section at intermediate energies and its application  

E-print Network

We construct a formula for proton-nucleus total reaction cross section as a function of the mass and neutron excess of the target nucleus and the proton incident energy. We deduce the dependence of the cross section on the mass number and the proton incident energy from a simple argument involving the proton optical depth within the framework of a black sphere approximation of nuclei, while we describe the neutron excess dependence by introducing the density derivative of the symmetry energy, L, on the basis of a radius formula constructed from macroscopic nuclear models. We find that the cross section formula can reproduce the energy dependence of the cross section measured for stable nuclei without introducing any adjustable energy dependent parameter. We finally discuss whether or not the reaction cross section is affected by an extremely low density tail of the neutron distribution for halo nuclei.

Kei Iida; Akihisa Kohama; Kazuhiro Oyamatsu

2006-02-03

102

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

SciTech Connect

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

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

2009-03-25

103

Choice reaction times for identifying the direction of first-order motion and different varieties of second-order motion  

E-print Network

Choice reaction times for identifying the direction of first-order motion and different varieties of the human visual system by measuring forced-choice reaction times for dis- criminating the drift direction of stimulus modulation depths. In general, reaction times for all types of second-order motion were slower

Nottingham, University of

104

Tandem processes identified from reaction screening: nucleophilic addition to aryl N-phosphinylimines employing La(III)-TFAA activation.  

PubMed

Reaction screening of nucleophilic reaction partners for addition to N-diphenylphosphinylimines employing lanthanum(III) triflate as a catalyst and trifluoroacetic anhydride (TFAA) as an activator is reported. A number of tandem processes leading to novel chemotypes including aza-Prins/intramolecular Friedel-Crafts annulations have been identified, and both reaction scope and mechanism further investigated. PMID:20394364

Kinoshita, Hidenori; Ingham, Oscar J; Ong, Winnie W; Beeler, Aaron B; Porco, John A

2010-05-12

105

A study of stopping power in nuclear reactions at intermediate energies  

E-print Network

We show a systematic experimental study based on INDRA data of the stopping power in central symmetric nuclear reactions. Total mass of the systems goes from 80 to 400 nucleons while the incident energy range is from 12 AMeV to 100 AMeV. The role of isospin diffusion at 32 and 45 MeV/nucleon with 124,136Xe projectiles on 112,124Sn targets performed at GANIL is also discussed. Results suggest a strong memory of the entrance channel above 20 AMeV/A (nuclear transparency) and, as such, constitute valuable tests of the microscopic transport models.

G. Lehaut; D. Durand; O. Lopez

2010-01-25

106

Models for reactions of acetylene on platinum(111): the vinylidene intermediate  

SciTech Connect

One of the most studied surface reactions is that of acetylene on platinum(111). A ..mu../sub 3/-eta/sup 2/-acetylene complex is formed at low temperature but this rearranges on warming to a ..mu../sub 3/-eta/sup 2/-vinylidene, Pt/sub 3/(..mu../sub 3/-eta/sup 2/-C=CH/sub 2/), which then reacts with surface-bound hydrogen to give a ..mu../sub 3/-ethylidyne, Pt/sub 3/(..mu../sub 3/-CMe). Since the cluster (Pt/sub 3/(..mu../sub 3/-H)(..mu..-dppm)/sub 3/)/sup +/ (dppm = Ph/sub 2/PCH/sub 2/PPh/sub 2/) acts as a useful model for the triply bridging sites on a Pt(111) surface, a study of its reaction with acetylene was initiated with the aim of isolating complexes having the above functional groups, none of which appears to be known. This article reports the formation of a stable ..mu../sub 3/-eta/sup 2/-C=CH/sub 2/ complex.

Rashidi, M.; Puddephatt, R.J.

1986-10-29

107

A quantum chemical investigation of possible intermediates in the reaction of the amidogen and hydroperoxyl radicals  

NASA Astrophysics Data System (ADS)

The reaction NH2+HO2?products, a reaction of atmospheric interest, has been studied using ab initio molecular orbital calculations with extended basis sets [6-311++G** and 6-311++G(2df,2pd)], and a variety of methods accounting for electron correlation such as second order Møller-Plesset perturbation theory (MP2) with all electrons, quadratic configuration interaction singles and doubles with triples correction [QCISD(T)], complete active space [CAS(8,8)], and multireference double excitation configuration interaction (MRDCI). Also, the performance of density functional (DFT) calculations has been investigated. In the present study, all stationary points on various potential energy surfaces giving rise to different products, HNO+H2O, NH2O+OH, NH3+O2, H2O2+NH, and HNOO+H2, have been optimized and characterized by their Hessian matrix. Amine oxide and dihydroxyamine have been found to be the precursors for HNO formation. In addition, the paper attempts to explain the experimental finding, nonobservation of OH? during photolysis of ammonia, and it demands new experiments with spectroscopic identification of OH radicals.

Sumathi, R.; Engels, Bernd; Peyerimhoff, S. D.

1996-11-01

108

Direct detection of the oxygen rebound intermediates, ferryl Mb and NO2, in the reaction of metmyoglobin with peroxynitrite.  

PubMed

Oxygenated hemoproteins are known to react rapidly with nitric oxide (NO) to produce peroxynitrite (PN) at the heme site. This process could lead either to attenuation of the effects of NO or to nitrosative protein damage. Peroxynitrite is a powerful nitrating and oxidizing agent that has been implicated in a variety of cell injuries. Accordingly, it is important to delineate the nature and variety of reaction mechanisms of PN reactions with heme proteins. Here, we present direct evidence that ferrylMb and NO(2) are both produced during the reaction of PN and metmyoglobin (metMb). Kinetic evidence indicates that these products evolve from initial formation of a caged radical intermediate [Fe(IV)=O *NO(2)]. This caged pair reacts mainly via internal return with a rate constant k(r) to form metMb and nitrate in an oxygen rebound scenario. Detectable amounts of ferrylMb are observed by stopped-flow spectrophotometry, appearing at a rate consistent with the rate, k(obs), of heme-mediated PN decomposition. Freely diffusing NO(2), which is liberated concomitantly from the radical pair (k(e)), preferentially nitrates Tyr103 in horse heart myoglobin. The ratio of the rates of in-cage rebound and cage escape, k(r)/k(e), was found to be approximately 10 by examining the nitration yields of fluorescein, an external NO(2) trap. This rebound/escape model for the metMb/PN interaction is analogous to the behavior of alkyl hyponitrites and the well-studied geminate recombination processes of deoxymyoglobin with O(2), CO, and NO. The scenario is also similar to the stepwise events of substrate hydroxylation by cytochrome P450 and other oxygenases. It is likely, therefore, that the reaction of metMb with ONOO(-) and that of oxyMb with NO proceed through the same [Fe(IV)=O *NO(2)] caged radical intermediate and lead to similar outcomes. The results indicate that while oxyMb may reduce the concentration of intracellular NO, it would not eliminate the formation of NO(2) as a decomposition product of peroxynitrite. PMID:19705829

Su, Jia; Groves, John T

2009-09-16

109

Two-proton and two-neutron correlation functions for intermediate-energy heavy-ion reactions  

NASA Astrophysics Data System (ADS)

Two-particle intensity interferometry is used to study the space-time characteristics of the reaction zone formed in intermediate-energy heavy ion reactions. The results are compared to appropriate models. Because of the recently reported discrepancies between BUU calculations and measured two-proton correlation functions at beam energies E/A > 100 MeV, a two-proton correlation function has been measured for the reaction 16O + 197Au at E/A = 200 MeV. The measured total correlation function agrees with the BUU predictions, but the dependence of the correlation function on the total momentum predicted by the BUU model is larger than the data show. In the evaporative regime, questions arise in interpreting charged particle correlations because of the Coulomb field of the heavy residue. Therefore, in this energy region two-neutron correlation functions were measured. Two-neutron correlation functions for the reaction 40Ar + 165Ho at E/A = 25 MeV are presented and comparisons made to models. Corrections and event selection are made for the coincident neutrons to eliminate the effects of crosstalk and background scattering. These corrections are compared to two independent simulations. The experimental results show a strong correlation at q = 0, which is comparable to emission from the surface of a sphere with a radius of 7 fm and an exponential lifetime of 700 fm/c. An evaporative model with and without preequilibrium corrections was compared to the data. The measured lifetime is within a factor of two of the lifetime the evaporative model predicts. This comparison provides a useful test of the statistical models used for fission lifetime measurements.

Gaff, Sally Janine

110

Phenylpyruvate tautomerase activity of trans-3-chloroacrylic acid dehalogenase: evidence for an enol intermediate in the dehalogenase reaction?  

PubMed

The enzymatic conversion of cis- or trans-3-chloroacrylic acid to malonate semialdehyde is a key step in the bacterial degradation of the nematocide 1,3-dichloropropene. Two mechanisms have been proposed for the isomer-specific hydrolytic dehalogenases, cis- and trans-3-chloroacrylic acid dehalogenase (cis-CaaD and CaaD, respectively), responsible for this step. In one mechanism, the enol isomer of malonate semialdehyde is produced by the alpha,beta-elimination of HCl from an initial halohydrin species. Phenylenolpyruvate has now been found to be a substrate for CaaD with a kcat/Km value that approaches the one determined for the CaaD reaction using trans-3-chloroacrylate. Moreover, the reaction is stereoselective, generating the 3S isomer of [3-2H]phenylpyruvate in a 1.8:1 ratio in 2H2O. These two observations and a kinetic analysis of active site mutants of CaaD suggest that the active site of CaaD is responsible for the phenylpyruvate tautomerase (PPT) activity. The activity is a striking example of catalytic promiscuity and could reflect the presence of an enol intermediate in CaaD-mediated dehalogenation of trans-3-chloroacrylate. CaaD and cis-CaaD represent different families in the tautomerase superfamily, a group of structurally homologous proteins characterized by a core beta-alpha-beta building block and a catalytic Pro-1. The eukaryotic immunoregulatory protein known as macrophage migration inhibitory factor (MIF), also a tautomerase superfamily member, exhibits a PPT activity, but the biological relevance is unknown. In addition to the mechanistic implications, these results establish a functional link between CaaD and the superfamily tautomerases, highlight the catalytic and binding promiscuity of the beta-alpha-beta scaffold, and suggest that the PPT activity of MIF could reflect a partial reaction in an unknown MIF-catalyzed reaction. PMID:17661448

Poelarends, Gerrit J; Johnson, William H; Serrano, Hector; Whitman, Christian P

2007-08-21

111

Preverbal infants identify emotional reactions that are incongruent with goal outcomes  

PubMed Central

Identifying the goal of another agent’s action allows an observer to make inferences not only about the outcomes the agent will pursue in the future and the means to be deployed in a given context, but also about the emotional consequences of goal-related outcomes. While numerous studies have characterized the former abilities in infancy, expectations about emotions have gone relatively unexplored. Using a violation of expectation paradigm, we present infants with an agent who attains or fails to attain a demonstrated goal, and reacts with positive or negative affect. Across several studies, we find that infants’ attention to a given emotional display differs depending on whether that reaction is congruent with the preceding goal outcome. Specifically, infants look longer at a negative emotional display when it follows a completed goal compared to when it follows a failed goal. The present results suggest that infants’ goal representations support expectations not only about future actions but also about emotional reactions, and that infants in the first year of life can relate different emotional reactions to conditions that elicit them. PMID:24321623

Skerry, Amy E.; Spelke, Elizabeth S.

2014-01-01

112

Intramolecular and intermolecular kinetic isotope effects (KIE) in the nitrosoarene ene reaction: experimental evidence for reversible intermediate formation.  

PubMed

The intramolecular and intermolecular kinetic isotope effects (KIE) have been determined for the nitrosoarene ene reaction with deuterium-stereolabeled 2,3-dimethyl-2-butenes (TME). trans-TME-d(6) (k(H)/k(D) = 3.0) and gem-TME-d(6) (k(H)/k(D) = 4.0) show large intramolecular primary isotope effects. In contrast, the intramolecular competition in cis-TME-d(6) (k(H)/k(D) = 1.5) and the intermolecular competition for the TME-d(0)/TME-d(12) pair (k(H)/k(D) = 1.98) show considerably smaller, but mechanistically significant kinetic isotope effects. The latter fact is rationalized in terms of reversible formation of a three-membered-ring intermediate, namely the aziridine N-oxide, or a similar unsymmetrical, polarized diradical in the first step of the reaction. Such reversibility has also been implied earlier for triazolinedione (TAD) and singlet oxygen ((1)O(2)) with deuterium-stereolabeled 2-butenes, but of the three enophiles, ArNO is the most sensitive toward reversibility, which is due to its moderate reactivity and its high steric demand. PMID:12636411

Adam, Waldemar; Krebs, Oliver; Orfanopoulos, Michael; Stratakis, Manolis; Vougioukalakis, Georgios C

2003-03-21

113

Identifiability for the pointwise source detection in Fisher’s reaction-diffusion equation  

NASA Astrophysics Data System (ADS)

We are interested in the detection of a pointwise source in a class of semi-linear advection-diffusion-reaction equations of Fisher type. The source is determined by its location, which may be steady or unsteady, and its time-dependent intensity. Observations recorded at a couple of points are the available data. One observing station is located upstream of the source and the other downstream. This is a severely ill-posed nonlinear inverse problem. In this paper, we pursue an identifiability result. The process we follow has been developed earlier for the linear model and may be sharpened to operate for the semi-linear equation. It is based on the uniqueness for a parabolic (semi-linear) sideways problem, which is obtained by a suitable unique continuation theorem. We state a maximum principle that turns out to be necessary for our proof. The identifiability is finally obtained for a stationary or a moving source. Many applications may be found in biology, chemical physiology or environmental science. The problem we deal with is the detection of pointwise organic pollution sources in rivers and channels. The basic equation to consider is the one-dimensional biochemical oxygen demand equation, with a nonlinear power growth inhibitor and/or the Michaelis-Menten reaction coefficient.

Ben Belgacem, Faker

2012-06-01

114

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

115

Intramolecular Schmidt reaction of acyl chlorides with alkyl azides: preparation of pyrrolizine by intramolecular capture of intermediates with alkenes or alkynes.  

PubMed

The preparation of substituted pyrrolizines through the Schmidt reaction of acyl chlorides with alkyl azides has been realized. Intramolecular capture of the isocyanate ion and N-acyliminium ion intermediates from the Schmidt process with alkene or alkyne units was achieved, and the efficiency of the conversion with respect to ring construction and bond formation was demonstrated. PMID:25558477

Wang, Bao-Juan; Xue, Ping; Gu, Peiming

2015-01-27

116

Models for reactions of acetylene on platinum(111): a vinyl(acetylene)triplatinum complex and evidence for an ethylidyne intermediate  

SciTech Connect

Reaction of (Pt/sub 3/(..mu../sub 3/-H)(..mu..-dppm)/sub 3/)/sup +/ (1) with excess acetylene gives (Pt/sub 3/(CH=CH/sub 2/)(..mu../sub 3/-eta/sup 2/(parallel)-HCCH)(..mu..-dppm)/sub 3/)/sup +/, where dppm = Ph/sub 2/PCH/sub 2/PPh/sub 2/. Deuterium-labeling studies indicate that H-D scrambling occurs within the vinyl group but not in the acetylene ligand. For example, (Pt/sub 3/(..mu../sub 3/-D)(..mu..-dppm)/sub 3/)/sup +/ with HCCH gave (Pt/sub 3/(CH==CH/sub 7/-d/sub 1/)(..mu../sub 3/-eta/sup 2/(parallel)-HCCH)(..mu..-dppm)/sub 3/)/sup +/, in which the deuterium label was distributed randomly in all three possible positions in the vinyl group. It is possible that this scrambling occurs by way of a short-lived ethylidyne intermediate. The complex is fluxional, due to rotation of the acetylene ligand, at room temperature. Similar reaction of 1 with excess propyne gives (Pt/sub 3/(CH=CHMe)(..mu../sub 3/-eta/sup 2/(**)-MeCCH)(..mu..-dppm)/sub 3/)/sup +/, but this complex is not fluxional at room temperature and is formed selectively by cis insertion of propyne into the Pt-H groups. There is a strong resemblance to the chemistry resulting from chemisorption of acetylene on a Pt(111) surface, thus providing a clear example of the value of coordinatively unsaturated clusters as mimics of metal surfaces.

Rashidi, M.; Puddephatt, R.J.

1988-07-01

117

Spectral studies of intermediate species formed in one-electron reactions of bovine liver catalase at room and low temperatures. A comparison with peroxidase reactions.  

PubMed

The reactions of native bovine catalase with superoxide and solvated electrons have been investigated using three different methods for generation of these reducing substrates: gamma-radiolysis of oxygenated or deaerated buffer solutions in the presence of an OH radical scavenger; either xanthine or acetaldehyde with xanthine oxidase; and low-temperature (77 K) gamma-radiolysis of buffered ethylene glycol/water solutions with subsequent annealing of samples at 183 K. The first spectral evidence for catalase compound II formation from native catalase via reaction with superoxide was obtained. The results are compared with results for peroxidase compound II or III formation observed under the same experimental conditions. A scheme is proposed to explain these observations involving intermediate formation of catalase compounds I and III and the ferrous enzyme. The one-electron reduction of catalase and peroxidase by radiolytically-generated solvated electrons was compared. In the present study the first absorption spectrum of a high-spin ferrous catalase which has peaks at 561 and 594 nm is reported, in comparison with a hemochromogen low-spin ferrous peroxidase observed under the same experimental conditions (peaks at 527 and 556 nm). Both spectra were recorded at 77 K. Data presented in this work also provide the first spectral evidence indicating the low temperature (183 K) conversion of high-spin ferrous catalase into compound III (oxycatalase) in the presence of dioxygen. Under the same experimental conditions low-spin ferrous peroxidase was converted into the high-spin ferrous form without oxyperoxidase formation. PMID:1361511

Metodiewa, D; Dunford, H B

1992-11-01

118

Agreement between footswitch and ground reaction force techniques for identifying gait events: Intersession repeatability and the effect of walking speed  

Microsoft Academic Search

This study assessed the inter-session repeatability of agreement between foot–ground contact events (foot contact and foot off) identified from ground reaction force and footswitch-based techniques over a range of gait speeds. No inter-session differences in agreement between the ground reaction force and footswitch-based techniques were identified and while agreement between foot–ground contact events defined by the two techniques was found

Peter M. Mills; Rod S. Barrett; Steven Morrison

2007-01-01

119

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

NASA Astrophysics Data System (ADS)

Reactive species like high-valent metal-oxo complexes and carbon and oxygen centered radicals are important intermediates in enzymatic systems, atmospheric chemistry, and industrial processes. Understanding the pathways by which these intermediates form, their relative reactivity, and their fate after reactions is of the utmost importance. Herein are described the mechanistic detail for the generation of several reactive intermediates, synthesis of precursors, characterization of precursors, and methods to direct the chemistry to more desirable outcomes yielding 'greener' sources of commodity chemicals and fuels. High-valent Chromium from Hydroperoxido-Chromium(III). The decomposition of pentaaquahydroperoxido chromium(III) ion (hereafter Cr aqOOH2+) in acidic aqueous solutions is kinetically complex and generates mixtures of products (Craq3+, HCrO 4-, H2O2, and O2). The yield of high-valent chromium products (known carcinogens) increased from a few percent at pH 1 to 70 % at pH 5.5 (near biological pH). Yields of H 2O2 increased with acid concentration. The reproducibility of the kinetic data was poor, but became simplified in the presence of H2O2 or 2,2?-azinobis(3-ethylbenzothiazoline-6-sulfonate) dianion (ABTS2-). Both are capable of scavenging strongly oxidizing intermediates). The observed rate constants (pH 1, [O2] ? 0.03 mM) in the presence of these scavengers are independent of [scavenger] and within the error are the same (k,ABTS2- = (4.9 +/- 0.2) x 10-4 s-1 and kH2O2 = (5.3 +/- 0.7) x 10-4 s-1); indicating involvement of the scavengers in post-rate determining steps. In the presence of either scavenger, decomposition of CrOOH2+ obeyed a two-term rate law, k obs / s-1 = (6.7 +/- 0.7) x 10-4 + (7.6 +/- 1.1) x 10-4 [H+]. Effect of [H+] on the kinetics and the product distribution, cleaner kinetics in the presence of scavengers, and independence of kobs on [scavenger] suggest a dual-pathway mechanism for the decay of Craq OOH2+. The H+-catalyzed path leads to the dissociation of H2O2 from Cr(III), while in the H+-independent reaction, CraqOOH2+ is transformed to Cr(V). Both scavengers rapidly remove Cr(V) and simplify both the kinetics and products by impeding formation of Cr(IV, V, VI). Syntheses, Reactivity, and Thermodynamic Considerations LRhR2+. Macrocyclic rhodium(II) complexes LRh(H 2O)2+ (L = L1= cyclam and L2 = meso-Me6-cyclam) react with alkyl hydroperoxides R(CH3)2COOH to generate the corresponding rhodium(III) alkyls LRh(H2O)R2+ (R = CH3, C2 H5, PhCH2). Methyl and benzyl complexes can also be prepared by bimolecular group transfer from alkyl cobaloximes (dmgX) 2(H2O)CoR (where R = CH3, CH2Ph and dmgX is either dimethylglyoxime or a BF2-capped derivative of dmg) to LRh(H2O)2+. When R = C2H5, C3H7 or C4H9, the mechanism changes from group transfer to hydrogen atom abstraction from the coordinated alkyl and produces LRh(H2O)H2+ and an a-olefin. The new LRh(H2O)R2+ complexes were characterized by solution NMR and by crystal structure analysis. They exhibit great stability in aqueous solution at room temperature, but undergo efficient Rh-C bond cleavage upon photolysis. 'Green' Model for Decarboxylation of Biomass Derived Acids via Photolysis of in situ formed Metal-Carboxylate Complexes. Photolysis of aqueous solutions containing propionic acid and Fe 3+ aq in the absence of oxygen generates a mixture of hydrocarbons (ethane, ethylene and butane), carbon dioxide, and Fe2+. Photolysis in the presence of O2 yields catalytic amounts of hydrocarbon products. When halide ions are present during photolysis; nearly quantitative yields of ethyl halides are produced via extraction of a halide atom from FeX2+ by ethyl radical. The rate constants for ethyl radical reactions with FeCl2+ (k = 4.0 (+/- 0.5) x 106 M-1s-1) and with FeBr 2+ (k = 3.0 (+/- 0.5) x 107 M-1s -1) were determined via competition reactions. Irradiation of solutions containing aqueous Cu2+ salts and linear carboxylic acids yield alpha-olefins selectively. This process is made catalytic by the introduction of O2. Photochemical decarboxylation of

Carraher, Jack McCaslin

120

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

SciTech Connect

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

Isied, Stephan S.

2003-03-11

121

P-Cadherin Linking Breast Cancer Stem Cells and Invasion: A Promising Marker to Identify an “Intermediate/Metastable” EMT State  

PubMed Central

Epithelial–mesenchymal transition (also known as EMT) is a fundamental mechanism occurring during embryonic development and tissue differentiation, being also crucial for cancer progression. Actually, the EMT program contributes to the dissemination of cancer cells from solid tumors and to the formation of micro-metastasis that subsequently develop into clinically detectable metastases. Besides being a process that is defined by the progressive loss of epithelial cell characteristics and the acquisition of mesenchymal features, EMT has also been implicated in therapy resistance, immune escape, and maintenance of cancer stem cell properties, such as self-renewal capacity. However, the majority of the studies usually neglect the progressive alterations occurring during intermediate EMT states, which imply a range of phenotypic cellular heterogeneity that can potentially generate more metastable and plastic tumor cells. In fact, few studies have tried to identify these transitory states, partly due to the current lack of a detailed understanding of EMT, as well as of reliable readouts for its progression. Herein, a brief review of evidences is presented, showing that P-cadherin expression, which has been already identified as a breast cancer stem cell marker and invasive promoter, is probably able to identify an intermediate EMT state associated with a metastable phenotype. This hypothesis is based on our own work, as well as on the results described by others, which suggest the use of P-cadherin as a promising EMT marker, clearly functioning as an important clinical prognostic factor and putative therapeutic target in breast carcinogenesis. PMID:25601904

Ribeiro, Ana Sofia; Paredes, Joana

2014-01-01

122

Novel apocarotenoid intermediates in Neurospora crassa mutants imply a new biosynthetic reaction sequence leading to neurosporaxanthin formation.  

PubMed

Neurosporaxanthin, beta-apo-4'-carotenoic acid (C35), represents the end-product of the carotenoid pathway in Neurospora crassa. It is supposed to be synthesized in three steps catalyzed by sequential AL-2, CAO-2 and YLO-1 activities: (i) cyclization of 3,4-didehydrolycopene (C40); (ii) cleavage of torulene into beta-apo-4'-carotenal (C35); and finally (iii) oxidation of beta-apo-4'-carotenal. However, analyses of the ylo-1 mutant revealed the accumulation of intermediates other than beta-apo-4'-carotenal. Here, we generated a 3,4-didehydrolycopene accumulating Escherichia coli strain and showed that CAO-2 cleaves this acyclic carotene in vivo and in vitro yielding apo-4'-lycopenal. The apocarotenoids accumulated in the ylo-1 mutant were then identified as apo-4'-lycopenal and apo-4'-lycopenol, pointing to the former as the YLO-1 substrate and indicating that cyclization is the last step in neurosporaxanthin biosynthesis. This was further substantiated by analyses of a cyclase-deficient al-2 mutant, revealing the accumulation of apo-4'-lycopenoic acid. The three acyclic apocarotenoids presented here have not been found naturally before. PMID:18812228

Estrada, Alejandro F; Maier, Dominic; Scherzinger, Daniel; Avalos, Javier; Al-Babili, Salim

2008-11-01

123

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 13.1wt.% hydrogen, was calculated to have an activation barrier of 2.33eV per formula unit and was endothermic by 1.28eV per formula unit, while the second step was endothermic by 0.23eV 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 1.50eV. 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 13.1wt.% 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 6.5wt.% 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

124

Turning regioselectivity into stereoselectivity: efficient dual resolution of P-stereogenic phosphine oxides through bifurcation of the reaction pathway of a common intermediate.  

PubMed

Synthetic routes that provide facile access to either enantiomeric form of a target compound are particularly valuable. The crystallization-free dual resolution of phosphine oxides that gives highly enantioenriched materials (up to 94?% ee) in excellent yields is reported. Both enantiomeric oxides have been prepared from a single intermediate, (RP )-alkoxyphosphonium chloride, which is formed in the course of a selective dynamic kinetic resolution using a single enantiomer of menthol as the chiral auxiliary. The origin of the dual stereoselectivity lies in bifurcation of the reaction pathway of this intermediate, which works as a stereochemical railroad switch. Under controlled conditions, Arbuzov-type collapse of this intermediate proceeds through C?O bond fission with retention of the configuration at the phosphorus center. Conversely, alkaline hydrolysis of the P?O bond leads to the opposite SP ?enantiomer. PMID:24474623

Nikitin, Kirill; Rajendran, Kamalraj V; Müller-Bunz, Helge; Gilheany, Declan G

2014-02-10

125

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

PubMed

Although a recent study of Debord et al. in Biochimie (2014; 97:72-77) described the thermodynamics of the catalysed hydrolysis of phenyl acetate by human paraoxonase-1, the mechanistic details along the reaction route of this enzyme remain unclear. Therefore, we briefly present the solvent kinetic isotope effects on the phenyl acetate esterase activity of paraoxonase-1 and its inhibition with the phenyl methylphosphonate anion, which is a stable isosteric analogue that mimics the high-energy tetrahedral intermediate on the hydroxide-promoted hydrolysis pathway. The data show normal isotope effects, while proton inventory analysis indicates that two protons contribute to the kinetic isotope effect. Coherently, moderate competitive inhibition with the phenyl methylphosphonate anion reveals that the rate-limiting transition state suboptimally resembles the tetrahedral intermediate. The implications of these findings can be attributed to two possible reaction mechanisms that might occur during the paraoxonase-1-catalysed hydrolysis of phenyl acetate. PMID:25180809

Bavec, Aljoša; Knez, Damijan; Makovec, Tomaž; Stojan, Jure; Gobec, Stanislav; Goli?nik, Marko

2014-11-01

126

Protein Vivisection Reveals Elusive Intermediates in Folding  

SciTech Connect

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

Zheng, Zhongzhou; Sosnick, Tobin R. (UC)

2010-05-25

127

Density functional theory calculation of cyclic carboxylic phosphorus mixed anhydrides as possible intermediates in biochemical reactions: implications for the Pro-Tide approach.  

PubMed

Cyclic acyl phosphoramidates (CAPAs) are important components in several fundamental biological reactions such as protein synthesis and phosphorylation. These structures are particularly interesting in the nucleotide pro-drug approach, Pro-Tide, since they are putative intermediates in one of the hydrolysis steps required for activation. The central role played by the amino acid carboxylate function suggests first the formation of a cyclic mixed phosphorus anhydride, rapidly followed by water attack. To investigate such speculations, we performed quantum mechanical calculations using the B3LYP/6-311+G** level of theory for the plausible mechanisms of action considered. In the five-membered ring case, transition state theory demonstrated how the overall, gas-phase, mechanism of action could be split into two in-line addition-elimination (A-E) steps separated by a penta-coordinate phosphorane intermediate. The difference between five-membered and six-membered ring first A-E was also explored, revealing a single step, unimolecular reaction for the six-membered ring A-E profile. Implicit solvent contribution further confirmed the importance of CAPAs as reactive intermediates in such kind of reactions. Lastly, the second A-E pathway was analyzed to understand the complete pathway of the reaction. This analysis is the first attempt to clarify the putative mechanism of action involved in the activation of Pro-Tides and casts light also on the possible mechanism of action involved in primordial protein syntheses, strengthening the hypothesis of a common cyclic mixed phosphorus anhydride species as a common intermediate. PMID:22318882

Ricci, Antonio; Brancale, Andrea

2012-04-15

128

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

PubMed

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

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

2014-12-01

129

2'Carboxy3-Keto-D-Arabinitol 1,5-Bisphosphate, the Six-Carbon Intermediate of the Ribulose Bisphosphate Carboxylase Reaction  

Microsoft Academic Search

The six-carbon intermediate of the ribulose 1,5-bisphosphate (RuBP) carboxylase reaction, 2'-carboxy-3-keto-D-arabinitol 1,5-bisphosphate (CKABP), was prepared enzymatically by quenching the reaction with acid after a short time (ca 12 ms). Over a wide pH range (4-11), CKABP undergoes a slow (t{_1\\/2} = 1 h), pH-independent decarboxylation. No detectable decomposition of CKABP occurs over a six-week period at -80^circC. The decarboxylation of

G. H. Lorimer; T. J. Andrews; J. Pierce; J. V. Schloss

1986-01-01

130

Structural Identifiability of the Yield Coefficients in Bioprocess Models When the Reaction Rates  

E-print Network

submodels. The first submodel depends only on the reaction structure and is independent of the kinetics are known, the second submodel can be used for modeling the kinetic structure. This submodel is in a form

Bastin, Georges

131

Inverse-kinematics one-proton pickup with intermediate-energy beams: The Be9 (Ne20,21Na+?)X reaction  

NASA Astrophysics Data System (ADS)

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 Be9(Ne20,Na21)X proton pickup reaction measured using a Ne20 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 Na21 residue spectroscopy prediction by the sd-shell model. The measured cross sections are broadly consistent with these expectations.

Gade, A.; Adrich, P.; Bazin, D.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; Hosier, K.; McDaniel, S.; McGlinchery, D.; Obertelli, A.; Riley, L. A.; Siwek, K.; Tostevin, J. A.; Weisshaar, D.

2007-12-01

132

A two-hybrid screen identifies an unconventional role for the intermediate filament peripherin in regulating the subcellular distribution of the SNAP25-interacting protein, SIP30.  

PubMed

Peripherin is a type III intermediate filament protein, the expression of which is associated with the acquisition and maintenance of a terminally differentiated neuronal phenotype. Peripherin up-regulation occurs during acute neuronal injury and in degenerating motor neurons of amyotrophic lateral sclerosis. The functional role(s) of peripherin during normal, injurious, and disease conditions remains unknown, but may be related to differential expression of spliced isoforms. To better understand peripherin function, we performed a yeast two-hybrid screen on a mouse brain cDNA library using an assembly incompetent peripherin isoform, Per-61, as bait. We identified new peripherin interactors with roles in vesicular trafficking, signal transduction, DNA/RNA processing, protein folding, and mitochondrial metabolism. We focused on the interaction of Per-61 and the constitutive isoform, Per-58, with SNAP25 interacting protein 30 (SIP30), a neuronal protein involved in SNAP receptor-dependent exocytosis. We found that peripherin and SIP30 interacted through coiled-coil domains and colocalized in cytoplasmic aggregates in SW13vim(-) cells. Interestingly, Per-61 and Per-58 differentially altered the subcellular distribution of SIP30 and SNAP25 in primary motor neurons. Our findings suggest a novel role of peripherin in vesicle trafficking. PMID:25113441

Gentil, Benoit J; McLean, Jesse R; Xiao, Shangxi; Zhao, Beibei; Durham, Heather D; Robertson, Janice

2014-12-01

133

Complete and incomplete fusion competition in 11B-induced fission reaction on medium mass targets at intermediate energies  

E-print Network

The cross sections for the binary fission of 197Au, 181Ta and 209Bi targets induced by 11B ions were measured at intermediate energies. The fission products cross sections were studied by means of activation analysis in off-line regime observed gamma-ray spectra. The fission cross section is reconstructed on the basis of charge and mass distribution of the fission products.

N. A. Demekhina; G. S. Karapetyan; A. R. Balabekyan

2014-12-22

134

Novel apocarotenoid intermediates in Neurospora crassa mutants imply a new biosynthetic reaction sequence leading to neurosporaxanthin formation  

Microsoft Academic Search

Neurosporaxanthin, ?-apo-4?-carotenoic acid (C35), represents the end-product of the carotenoid pathway in Neurospora crassa. It is supposed to be synthesized in three steps catalyzed by sequential AL-2, CAO-2 and YLO-1 activities: (i) cyclization of 3,4-didehydrolycopene (C40); (ii) cleavage of torulene into ?-apo-4?-carotenal (C35); and finally (iii) oxidation of ?-apo-4?-carotenal. However, analyses of the ylo-1 mutant revealed the accumulation of intermediates

Alejandro F. Estrada; Dominic Maier; Daniel Scherzinger; Javier Avalos; Salim Al-Babili

2008-01-01

135

arXiv:nuclth/0406078 Identifying neutrinos and antineutrinos in neutral-current scattering reactions  

E-print Network

arXiv:nucl­th/0406078 v1 26 Jun 2004 Identifying neutrinos and antineutrinos in neutral study neutrino-induced nucleon knockout from nuclei. Expressions for the induced polarization approximation. Large dissimilarities in the nucleon polarization asymmetries are observed between neutrino

Gent, Universiteit

136

Reaction pathways in the electrochemical degradation of thiocarbamate herbicides in NaCl solution  

Microsoft Academic Search

We have identified the intermediates and end products which are formed during the electrolytic degradation of thiocarbamate pesticides in aqueous NaCl solutions and investigated how the intermediate and end product volumes and ratios depend on reaction conditions. Further, we have defined both the reaction pathways leading to intermediate and end product formation and the methods affecting this process. The degradation

FERENC MOGYORÓDY

2006-01-01

137

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

PubMed

FtmPT1 is a fungal indole prenyltransferase that catalyzes the reaction of tryptophan derivatives with dimethylallyl pyrophosphate to form various biologically active compounds. Herein, we describe detailed studies of FtmPT1 catalysis involving dimethylallyl pyrophosphate and Brevianamide F following the native pathway (yielding Tryprostatin B) and an alternate pathway observed in the Gly115Thr mutant of FtmPT1 yielding a novel cyclized product. Importantly, these two products arise from the same intermediate state, meaning that a step other than the cleavage of the dimethylallyl pyrophosphate (DMAPP; C-O) bond is differentiating between the two product reaction channels. From detailed potential of mean force (PMF) and two-dimensional PMF analyses, we conclude that the rate-limiting step is the cleavage of the C-O bond in DMAPP, while the deprotonation/cyclization step determines the final product distribution. Hence, in the case of FtmPT1, the optimization of the necessary catalytic machinery guides the generation of the final product after formation of the intermediate carbocation. PMID:25188320

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

2014-09-30

138

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. PMID:17971785

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

139

Mechanistic Studies on the Reaction of Nitrocobalamin with Glutathione: Kinetic evidence for formation of an aquacobalamin intermediate  

PubMed Central

The essential but also toxic gaseous signaling molecule nitric oxide is scavenged by the reduced vitamin B12 complex cob(II)alamin. The resulting complex, nitroxylcobalamin (NO?-Cbl(III)), is rapidly oxidized to nitrocobalamin (NO2Cbl) in the presence of oxygen; however it is unlikely that nitrocobalamin is itself stable in biological systems. Kinetic studies on the reaction between NO2Cbl and the important intracellular antioxidant, glutathione (GSH), are reported. In this study, a reaction pathway is proposed in which the ?-axial ligand of NO2Cbl is first substituted by water to give aquacobalamin (H2OCbl+), which then reacts further with GSH to form glutathionylcobalamin (GSCbl). Independent measurements of the four associated rate constants k1, k?1, k2, and k?2 support the proposed mechanism. These findings provide insight into the fundamental mechanism of ligand substitution reactions of cob(III)alamins with inorganic ligands at the ?-axial site. PMID:24415907

Walker, David T.; Dassanayake, Rohan S.; Garcia, Kamille A.; Mukherjee, Riya; Brasch, Nicola E.

2013-01-01

140

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

141

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 Na?SO? 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 H?O?. 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. NH?(+), NO?(-), and SO?(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

142

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.

Holzrichter, John F. (Berkeley, CA); Siekhaus, Wigbert J. (Berkeley, CA)

1997-01-01

143

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

144

Synthesis of anionic hypervalent cyclic selenenate esters: relevance to the hypervalent intermediates in nucleophilic substitution reactions at the selenium(II) center.  

PubMed

The synthesis of a diaryl diselenide that contains 2,6-dicarboxylic acid groups, 2,2'-diselanediylbis(5-tert-butylisophthalic acid) (10), is described. Diselenide 10 undergoes intramolecular cyclization in methanol to form a cyclic selenenate ester, 5-tert-butyl-3-oxo-3H-benzo[c][1,2]oxaselenole-7-carboxylic acid (11). The cyclization reaction proceeds more rapidly in the presence of organic bases, such as pyridine, adenine, and 4,4'-bipyridine, to form pyridinium 5-tert-butyl-3-oxo-3H-benzo[c][1,2]oxaselenole-7-carboxylate (14), adeninium 5-tert-butyl-3-oxo-3H-benzo[c][1,2]oxaselenole-7-carboxylate (15), and 4,4'-bipyridiniumbis(5-tert-butyl-3-oxo-3H-benzo[c][1,2]oxaselenole-7-carboxylate) (16), respectively. However, 2,2'-diselanediyldibenzoic acid (22) does not undergo cyclization under similar conditions. Structural studies on cyclic selenenate esters 14-16 revealed that the Se···O (COO(-)) secondary distances (2.170, 2.075, and 2.176 Å) were significantly shorter than the corresponding Se···O distances (2.465, 2.472, and 2.435 Å) observed for the selenenate esters stabilized by the neutral donors (CHO, COOH, and COOEt). (1)H, (13)C, and (77)Se NMR spectroscopy of compounds 11 and 14-16 reveal that the aryl protons of compound 11 and the organic cations of compounds 14-16 exchange between the two carboxylate groups via a hypercoordinate intermediate. The corresponding hypercoordinate intermediate (14b, pyridinium selenuranide) for compound 14 was detected at low temperatures using (77)Se NMR spectroscopy. The presumed hypercoordinate intermediates in the carboxylate-exchange reactions at the selenium(II) center for a set of model reactions were optimized using DFT-B3LYP/6-311+g(d) calculations and their structural features compared with the X-ray structure of anionic selenenate esters 14-16. PMID:22190290

Selvakumar, Karuthapandi; Singh, Harkesh B; Goel, Nidhi; Singh, Udai P; Butcher, Ray J

2012-01-27

145

Photodegradation of imidacloprid insecticide by ag-deposited titanate nanotubes: a study of intermediates and their reaction pathways.  

PubMed

The present work demonstrates the influence of Ag-loading (0.2-1.0 wt %) onto sodium titanate nanotubes (TNT) for complete photomineralization of the neurotoxic imidacloprid (IMI) insecticide under UV light illumination. It has been observed that degradation of IMI follows pseudo-first-order kinetics, where 0.5 wt % Ag-loaded TNT exhibited highest apparent rate constant (2.2 × 10(-2) min(-1)) and corresponding least half-life (t1/2) of 31 min for IMI relative to bare P25-TiO2 (3.4 × 10(-3) min(-1), t1/2 = 230 min). The mineralization of IMI intermediates to CO2 during its photooxidation has been described by time course GC-MS and GC analysis and has been correlated with the kinetic analysis. The investigation for the role and quantitative estimation of the fate of heteroatoms (N, O, and Cl) present in IMI revealed an increase in the amount of nitrate, nitrite, and chloride ions with time during its photooxidation. On the basis of these results a mechanistic pathway for photomineralization of IMI is proposed. PMID:25458204

Grover, Inderpreet Singh; Singh, Satnam; Pal, Bonamali

2014-12-31

146

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

PubMed

Cryogenic conditions favor the formation of ion-pair dissociation intermediates in amorphous mixtures of HF and H(2)O, making possible their characterization by means of infrared spectroscopy. The experimental infrared spectra show a structurally rich "continuous" absorption ranging from 1000 to 3400 cm(-1), which, in principle, contains important information regarding the microscopic structure of the aforementioned dissociation intermediates. Herein, we demonstrate that this microscopic information can be extracted by comparing and contrasting experimental spectra with those obtained by means of carefully designed first-principles molecular dynamics calculations. Very good, systematic agreement between theoretical and experimental spectra can be obtained for HF/H(2)O mixtures of various compositions, revealing the presence of proton-shared, dissociation intermediates F(delta-) * * * H * * * (delta+)OH(2). The existence of similar proton-shared, hydrogen-bonded intermediates of ionization, that are stable in solution, but not in the gas phase, has been previously suggested by other groups, using, among other techniques, low temperature NMR data and aprotic, dipolar, solvents. Our investigation reveals that similar structures are also stable in aqueous solutions of HF. We discuss some of the implications of the present findings as far as the mechanism of dissociation of weak acids is concerned. PMID:19425221

Thomas, Vibin; Iftimie, Radu

2009-04-01

147

endo/exo stereoselectivity in Diels-Alder reactions of ?,?-dialkylated conjugated enals to cyclic 1,3-dienes: intermediates in the synthesis of (-)-?-santalol and its analogs.  

PubMed

Highly exo-selective [4+2] cycloadditions of cyclopenta-1,3-diene 2a to ?,?-dialkyl conjugated enals 5 are compared with the analogous endo-favored Diels-Alder reaction of cyclohexa-1,3-diene 7. The exo-stereoselectivity is lower in the homologous case of methylcyclopenta-1,3-diene 9. This diastereoselectivity is discussed either in terms of a retro-homo-Diels-Alder reaction, associated with thermodynamic control, or with respect to either a competing hetero-Diels-Alder/Claisen or Cope domino pathway, or retro-Claisen/retro-hetero-Diels-Alder of the endo-homo-cycloadducts. These hypothetical mechanisms have been examined by DFT calculations at the MPW1K(CH2 Cl2 )/6-31+G** level of theory for the AlCl3 -mediated cycloadditions of 5d to 2a and 7. Application of Corey's methodology to the ?-halogeno-?-methyl-substituted dienophiles 5a and 5b allowed an enantioselective preparation of known and useful intermediates for the synthesis of either the naturally occurring (-)-?-santalol or its potentially olfactive structural analogs. PMID:25329781

Chapuis, Christian; Skuy, David; de Saint Laumer, Jean-Yves; Brauchli, Robert

2014-10-01

148

Combining real-time polymerase chain reaction using SYBR Green I detection and sequencing to identify vertebrate bloodmeals in fleas.  

PubMed

Programs that aim to control vector-borne zoonotic diseases require information on zoonotic hosts and on the feeding behavior of bridging vectors that are capable of transmitting pathogens from those hosts to humans. Here we describe an assay developed to identify bloodmeals in field-collected cat fleas (Ctenocephalides felis Bouché) to assess this species' potential role as a Yersinia pestis bridging vector in a plague-endemic region of Uganda. Our assay uses a single primer set and SYBR Green I-based real-time polymerase chain reaction to amplify a segment of the 12S mitochondrial ribosomal RNA gene for identification by sequencing. The assay capitalizes on the sensitivity of real-time polymerase chain reaction and the specificity of sequencing and can be used to differentiate vertebrate bloodmeals to the genus or species level without a priori knowledge of the host community. Because real-time assays that detect vertebrate DNA are highly sensitive to human DNA contamination, we analyzed detection in artificially fed and unfed fleas to establish a Ct cutoff that optimized specificity without completely sacrificing sensitivity. Using the established cutoff, our assay detected human, rat, and goat DNA in artificially fed C. felis up to 72 h postfeeding. PMID:23270174

Graham, Christine B; Black, William C; Boegler, Karen A; Montenieri, John A; Holmes, Jennifer L; Gage, Kenneth L; Eisen, Rebecca J

2012-11-01

149

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

150

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

151

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

PubMed

Bacterial contamination of blood and its cellular components remains the most common microbiological cause of transfusion associated morbidity and mortality, even in developed countries. This yet unresolved complication is seen more often in platelet transfusions, as platelet concentrates are stored at room temperature, in gas permeable containers with constant agitation, which support bacterial proliferation from relatively low undetectable levels, at the beginning of storage time, to relatively high virulent bacteria titers and endotoxin generation, at the end of shelf life. Accordingly, several combined strategies are introduced and implemented to at least reduce the potential risk of bacterial contaminated products for transfusion. These embody: improved donors arms cleaning; bacterial avoidance by diversion of the first portion of collection; reducing bacterial growth through development of newer storage media for longer platelet shelf life; bacterial load reduction by leucoreduction/viral inactivation, in some countries and eliminating the use potentially contaminated units through screening, through current available testing procedures, though none are not yet fully secure. We have not seen the same reduction in bacterial associated transfusion infections as we have observed for the sharp drop in transfusion associated transmission rates of HIV and hepatitis B and C. This great viral reduction is not only caused by the introduction of newer and more sensitive and specific detection methods for different viruses, but also the identification of donor risk groups through questionnaires and personal interviews. While search for more efficient methods for identifying potential blood donors with asymptomatic bacteremia, as well as a better way for detecting bacteria in stored blood components will be continuing, it is necessary to establish more standardized guidelines for the recognition the adverse reactions in recipients of potentially contaminated units. Efforts also should be also directed to identify blood donors with significant risk of bacteremia, at the time of donation in the first place as a high priority. The goal of this review is to highlights strategies for identifying both the sources of bacterial contamination of blood components in Norway and identifying donors with a higher risk of bacteremia at the time of donation. The key to achieving this goal is initiating continual revising and upgrading the Norwegian transfusion guidelines, based on the transfusion legislation and by introducing a relevant specialized donor bacterial questionnaire. PMID:25242310

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

2014-10-01

152

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

153

A simple polymerase chain reaction/restriction fragment length polymorphism assay capable of identifying medically relevant filamentous fungi.  

PubMed

Because of the accumulating evidence that suggests that numerous unhealthy conditions in the indoor environment are the result of abnormal growth of the filamentous fungi (mold) in and on building surfaces, it is necessary to accurately reflect the organisms responsible for these maladies and to identify them in precise and timely manner. To this end, we have developed a method that is cost effective, easy to perform, and accurate. We performed a simple polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) analysis on multiple members of species known to negatively influence the indoor environment. The genera analyzed were Stachybotrys, Penicillium, Aspergillus, and Cladosporium. Each organism underwent PCR with universal primers that amplified ribosomal sequences generating products from 550 to 600 bp followed by enzymatic digestion with EcoRI, HaeIII, MspI, and HinfI. Our results show that using this combination of restriction enzymes enables the identification of these fungal organisms at the species level. PMID:16118412

Dean, Timothy R; Kohan, Michael; Betancourt, Doris; Menetrez, Marc Y

2005-09-01

154

Neutrons in Coincidence with Intermediate Mass Fragments at Large Angles from NITROGEN-14 + Silver Reactions at 20 and 35 Mev/nucleon.  

NASA Astrophysics Data System (ADS)

The spectral shape and multiplicity of neutrons from the reaction of ^{14}N + Ag at E/A = 20 and 35 MeV have been measured for neutrons in coincidence with intermediate mass nuclei emitted at 50, 70 and 90^circ. The spectral shape clearly suggests two moving sources. The slower source velocity is about 65% of the center of mass velocity for E/A = 35 MeV and 80% of the center of mass velocity for E/A = 20 MeV (7% and 9% of the beam velocity, respectively). The faster source velocity is slightly less than half of the beam velocity for each case. Knowledge of the neutron multiplicity is necessary for models which attempts to explain the low effective temperature which has been determined from recent measurements of excited state populations. The data are also compared to the Harp-Miller-Bern exciton model. In addition, the neutron decay of excited states of ^ 7Li, ^ 8Li, ^{10}Be, ^ {11}Be, and ^ {12 }B has been investigated in the same reactions. The production of these excited states is compared to that of the ground state and other states of lower excitation energy for each isotope investigated. Under the assumption of a Boltzmann distribution of excited state populations, each of these comparisons imply a nuclear temperature. Furthermore, the feeding of the ^ 7Li ground state from the neutron decay of the 2.255 MeV unbound state in ^ 8Li (one of those measured) is another process that could lead to low temperature observations in previous experiments. The degree of feeding is compared to predictions made by a quantum statistical model to determine the total feeding from all possible channels. The net effect of this feeding is applied to these and other recent nuclear temperature measurements to determine if the data are consistent with a single nuclear emission temperature characterizing the energies of these reactions. In general, temperatures in the 2-3 MeV range are obtained.

Bloch, Charles Dennis

1987-09-01

155

Metabolism-dependent mutagenicity of a compound containing a piperazinyl indazole motif: Role of a novel p450-mediated metabolic reaction involving a putative oxaziridine intermediate.  

PubMed

Compound 1a (6-chloro-5-{3-[4-(1H-indazol-3-yl)-piperazin-1-yl]-propyl}-3,3-dimethyl-1,3-dihydro-indol-2-one) was mutagenic to Salmonella typhimurium TA98 in the presence of rat liver S9 subcellular fraction. The metabolism of 1a in rat liver S9 or microsomes demonstrated that it underwent a P450-mediated N-deindazolation (loss of indazole ring) as a predominant metabolic pathway. To investigate a possible link between metabolism and mutagenicity, a structural analogue 1b (6-chloro-5-{3-[4-(1H-indazol-3-yl)-piperidin-1-yl]-propyl}-3,3-dimethyl-1,3-dihydro-indol-2-one), the cleaved product 2a (6-chloro-3,3-dimethyl-5-(3-piperazin-1-yl-propyl)-1,3-dihydro-indol-2-one), and the core motif 3a (3-piperazinyl indazole) were evaluated in the Ames assay. It was found that 1b was not mutagenic to Salmonella typhimurium TA98 in the absence or presence of a metabolic activating system. In contrast to 1a, 1b did not undergo the metabolic cleavage (loss of indazole ring). Marginal mutagenicity of 2a to TA98 was observed with rat liver S9, whereas 3a was shown to be a promutagen. It was further demonstrated that 1a inactivated P450 3A, the principle enzyme catalyzing the N-deindazolation reaction, in an NADPH-, time-, and concentration-dependent manner. The kinetics of inactivation was characterized by a K(I) of 8.1 microM and k(inact) of 0.114 min(-1). The differences in mutagenicity between 1a and 1b suggest that a chemical bond extending from the 3-position of the indazole to a heteroatom (as part of another cyclic ring) is a prerequisite for the toxicity. The metabolic process leading to the elimination of the indazole from the rest of the molecule apparently plays a key role in causing mutagenicity. It is postulated that the N-deindazolation of 1a proceeds via an oxaziridine intermediate, the formation of which is indirectly inferred from the presence of benzoic acid in microsomal incubations. Benzoic acid is thought to be derived from the hydrolysis of 3-indazolone, an unstable product generated from the oxaziridine. Evidence suggests that the electrophilic oxaziridine intermediate may be responsible for the mutagenicity and inactivation of P450 3A. PMID:17040103

Chen, Hao; Murray, Joel; Kornberg, Brian; Dethloff, Lloyd; Rock, David; Nikam, Sham; Mutlib, Abdul E

2006-10-01

156

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

SciTech Connect

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

Lee, Jai Young (KAIST, Republic of Korea); Muller, Richard Partain; Kang, Jeung Ku (KAIST, Republic of Korea); Goddard, William A., III (California Institute of Technology, Pasadena, CA)

2005-06-01

157

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

PubMed

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

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

2015-01-28

158

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

SciTech Connect

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

Reineri, F.; Aime, S. [Department of Molecular Biotechnologies and Health Sciences, University of Torino, Via Nizza 52, 10123 Torino (Italy)] [Department of Molecular Biotechnologies and Health Sciences, University of Torino, Via Nizza 52, 10123 Torino (Italy); Gobetto, R.; Nervi, C. [Department of Chemistry, University of Torino, via P. Giuria 7, 10125 Torino (Italy)] [Department of Chemistry, University of Torino, via P. Giuria 7, 10125 Torino (Italy)

2014-03-07

159

Breakup of proton-rich nuclei ^24Si and ^23Al at intermediate energies for reaction rates in explosive H-burning in novae and X-ray bursts  

Microsoft Academic Search

We present the use of one-proton-removal reactions of loosely bound nuclei at intermediate energies as an indirect method in nuclear astrophysics, with particular reference to the results of a GANIL experiment with a cocktail beam around ^23Al at 50 MeV\\/nucleon. Momentum distributions of the core fragments, inclusive and in coincidence with gamma rays, from which we determine configuration mixing in

A. Banu; L. Trache; R. E. Tribble; B. Roeder; E. Simmons; N. Orr; M. Chartier; R. Lemmon; W. Catford; M. Freer; F. Carstoiu; M. Horoi; A. Bonaccorso

2009-01-01

160

Choice reaction times for identifying the direction of first-order motion and different varieties of second-order motion  

Microsoft Academic Search

This study sought to quantify the temporal properties of the human visual system by measuring forced-choice reaction times for discriminating the drift direction of first-order motion (luminance-modulated noise) and a variety of second-order motion patterns (modulations of either the contrast, polarity, orientation or spatial length of a noise carrier) over a range of stimulus modulation depths. In general, reaction times

Tim Ledgeway; Claire V. Hutchinson

2008-01-01

161

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

162

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

PubMed

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

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

2006-06-01

163

A General Method for Identifying Recessive Diploid-Specific Mutations in Saccharomyces Cerevisiae, Its Application to the Isolation of Mutants Blocked at Intermediate Stages of Meiotic Prophase and Characterization of a New Gene Sae2  

PubMed Central

We describe a general new approach for identifying recessive mutations that affect diploid strains of yeast Saccharomyces cerevisiae and the application of this method to the identification of mutations that confer an intermediate block in meiotic prophase chromosome metabolism. The method uses a temperature-sensitive conjugation mutation ste7-1 in combination with homothallism. The mutations of interest confer a defect in spore formation that is dependent upon a gene required for initiation of meiotic recombination and development of meiosis-specific chromosome structure (SPO11). Identified in this screen were null mutations of the DMC1 gene, nonnull mutations of RAD50 (rad50S), and mutations in three new genes designated SAE1, SAE2 and SAE3 (Sporulation in the Absence of Spo Eleven). Molecular characterization of the SAE2 gene and characterization of meiotic and mitotic phenotypes of sae2 mutants are also presented. The phenotypes conferred by a sae2 null mutation are virtually indistinguishable from those conferred by the previously identified nonnull mutations of RAD50 (rad50S). Most notably, both mutations confer only weak sensitivity to the radiomimetic agent methyl methane sulfonate (MMS) but completely block resection and turnover of meiosis-specific double-strand breaks. These observations provide further evidence that this constellation of phenotypes identifies a specific molecular function. PMID:9215888

McKee, AHZ.; Kleckner, N.

1997-01-01

164

An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis  

PubMed Central

The biosynthesis of many vitamins and coenzymes has often proved difficult to elucidate due to a combination of low abundance and kinetic lability of the pathway intermediates. Through a serial reconstruction of the cobalamin (vitamin B12) pathway in E. coli, and by His-tagging the terminal enzyme in the reaction sequence, we have observed that many unstable intermediates can be isolated as tightly-bound enzyme-product complexes. Together, these approaches have been used to extract intermediates between precorrin-4 and hydrogenobyrinic acid in their free acid form and permitted the delineation of the overall reaction catalysed by CobL, including the formal elucidation of precorrin-7 as a metabolite. Furthermore, a substrate-carrier protein, CobE, has been identified, which can also be used to stabilize some of the transient metabolic intermediates and enhance their onward transformation. The tight association of pathway intermediates with enzymes provides evidence for a form of metabolite channeling. PMID:23042036

Deery, Evelyne; Schroeder, Susanne; Lawrence, Andrew D.; Taylor, Samantha L.; Seyedarabi, Arefeh; Waterman, Jitka; Wilson, Keith S.; Brown, David; Geeves, Michael A.; Howard, Mark J.; Pickersgill, Richard W.; Warren, Martin J.

2012-01-01

165

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

PubMed

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

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

2014-06-01

166

Impetigo-like tinea faciei around the nostrils caused by Arthroderma vanbreuseghemii identified using polymerase chain reaction-based sequencing of crusts.  

PubMed

We report a case of Arthroderma vanbreuseghemii (a teleomorph of Trichophyton interdigitale) infection around the nostrils in a 3-year-old girl. The culture was negative, so the pathogenic agent was identified using polymerase chain reaction-based sequencing of the crusts taken from the lesion on the nostril. Treatment with oral itraconazole and topical 1% naftifine/0.25% ketoconazole cream after a topical wash with ketoconazole shampoo was effective. PMID:23278484

Kang, Daoxian; Ran, Yuping; Li, Conghui; Dai, Yaling; Lama, Jebina

2013-01-01

167

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

PubMed

Nitrogen-doped graphene sheets (NGS), synthesized by annealing graphite oxide (GO) with urea at 700-1050 °C, were studied as positive electrodes in a vanadium redox flow battery. The NGS, in particular annealed at 900 °C, exhibited excellent catalytic performance in terms of electron transfer (ET) resistance (4.74 ± 0.51 and 7.27 ± 0.42 ? for the anodic process and cathodic process, respectively) and reversibility (?E = 100 mV, Ipa/Ipc = 1.38 at a scan rate of 50 mV s(-1)). Detailed research confirms that not the nitrogen doping level but the nitrogen type in the graphene sheets determines the catalytic activity. Among four types of nitrogen species doped into the graphene lattice including pyridinic-N, pyrrolic-N, quaternary nitrogen, and oxidic-N, quaternary nitrogen is verified as a catalytic active center for the [VO](2+)/[VO2](+) couple reaction. A mechanism is proposed to explain the electrocatalytic performance of NGS for the [VO](2+)/[VO2](+) couple reaction. The possible formation of a N-V transitional bonding state, which facilitates the ET between the outer electrode and reactant ions, is a key step for its high catalytic activity. PMID:23647240

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

2013-06-25

168

Using Random Sequence Primers in the Polymerase Chain Reaction to identify Gender-Specific Genetic Markers in House Wrens  

Microsoft Academic Search

In order to fully understand the biology of asexually reproducing organism, it is essential that one is able to distinguish the males from the females. In determining the gender of monomorphic birds, standard techniques including visual identification, surgery, and karyotyping are impossible or impractical for large-scale studies. A reliable gender identification method that uses genetic markers identified within the DNA

Jeremy J. Kirchman

1994-01-01

169

Vocational and Psychosocial Mentoring Functions: Identifying Mentors Who Serve Both [and] Invited Reaction: Challenging Research in Mentoring.  

ERIC Educational Resources Information Center

Mullen's survey of 160 mentors and 140 proteges showed that mentors who initiated relationships, who felt valued by the organization, who were older, or who perceived proteges as competent were most likely to perform both career-related and psychosocial mentoring functions. Chao's response identifies problems in the research. (SK)

Mullen, Ellen J.; Chao, Georgia T.

1998-01-01

170

Basal Serum Thyroglobulin Measured by a Second-Generation Assay Is Equivalent to Stimulated Thyroglobulin in Identifying Metastases in Patients with Differentiated Thyroid Cancer with Low or Intermediate Risk of Recurrence  

PubMed Central

Background Guidelines for the follow-up of differentiated thyroid cancer (DTC) recommend the measurement of TSH-stimulated thyroglobulin (s-Tg) instead of basal Tg on T4 therapy (b-Tg). However, these guidelines were established using first-generation Tg assays with a functional sensitivity (FS) of 0.5-1.0 ng/ml. Current more sensitive second-generation Tg assays (Tg2G; FS 0.05-0.10 ng/ml) have shown that low-risk DTC patients with undetectable b-Tg rarely have recurrences. Objectives This study was undertaken to compare b-Tg using a chemiluminescent Tg2G assay (Tg2GICMA; FS 0.1 ng/ml) with s-Tg in DTC patients with an intermediate risk of recurrence. Methods We evaluated 168 DTC patients with a low (n = 101) and intermediate (n = 67) risk of recurrence treated by total thyroidectomy (147 also treated with radioiodine), with a mean follow-up of 5 years. Results b-Tg was undetectable with the Tg2GICMA in 142 of 168 patients. s-Tg was <2 ng/ml in 138 of these 142 patients, and only 3 of these 138 (2%) presented metastases on cervical ultrasound (US). Of the 4 of 142 patients with s-Tg >2 ng/ml, 1 had cervical metastases seen after radioiodine. Furthermore, 26 of 168 patients presented detectable b-Tg with the Tg2GICMA; 17 of these 26 patients also presented s-Tg >2 ng/ml. In 10 of these 17 patients, metastases were detected. Cervical US or b-Tg were positive in 14 of 15 patients with recurrent disease. Globally, the sensitivity and negative predictive value of the Tg2GICMA plus US were 93 and 99%, respectively. Conclusion b-Tg measured with a Tg2GICMA and cervical US, used together, are equivalent to s-Tg in identifying metastases in patients with DTC with a low or intermediate risk of recurrence. PMID:24847465

Nakabashi, Cláudia C.D.; Kasamatsu, Teresa S.; Crispim, Felipe; Yamazaki, Claudia A.; Camacho, Cléber P.; Andreoni, Danielle M.; Padovani, Rosalia P.; Ikejiri, Elza S.; Mamone, Maria C.O.M.; Aldighieri, Flávia C.; Wagner, Jairo; Hidal, Jairo T.; Vieira, José G.H.; Biscolla, Rosa P.M.; Maciel, Rui M.B.

2014-01-01

171

A simple polymerase chain reaction-sequencing analysis capable of identifying multiple medically relevant filamentous fungal species  

Microsoft Academic Search

Due to the accumulating evidence that suggests that numerous unhealthy conditions in the indoor environment are the result\\u000a of abnormal growth of the filamentous fungi (mold) in and on building surfaces it is necessary to accurately determine the\\u000a organisms responsible for these maladies and to identify them in an accurate and timely manner. Historically, identification\\u000a of filamentous fungal (mold) species

Timothy R. Dean; Michael Kohan; Doris Betancourt; Marc Y. Menetrez

2006-01-01

172

A simple polymerase chain reaction\\/restriction fragment length polymorphism assay capable of identifying medically relevant filamentous fungi  

Microsoft Academic Search

Because of the accumulating evidence that suggests that numerous unhealthy conditions in the indoor environment are the result\\u000a of abnormal growth of the filamentous fungi (mold) in and on building surfaces, it is necessary to accurately reflect the\\u000a organisms responsible for these maladies and to identify them in precise and timely manner. To this end, we have developed\\u000a a method

Timothy R. Dean; Michael Kohan; Doris Betancourt; Marc Y. Menetrez

2005-01-01

173

A simple polymerase chain reaction-sequencing analysis capable of identifying multiple medically relevant filamentous fungal species.  

PubMed

Due to the accumulating evidence that suggests that numerous unhealthy conditions in the indoor environment are the result of abnormal growth of the filamentous fungi (mold) in and on building surfaces it is necessary to accurately determine the organisms responsible for these maladies and to identify them in an accurate and timely manner. Historically, identification of filamentous fungal (mold) species has been based on morphological characteristics, both macroscopic and microscopic. These methods may often be time consuming and inaccurate, necessitating the development of identification protocols that are rapid, sensitive, and precise. To this end, we have devised a simple PAN-PCR approach which when coupled to cloning and sequencing of the clones allows for the unambiguous identification of multiple fungal organisms. Universal primers are used to amplify ribosomal DNA sequences which are then cloned and transformed into Escherichia coli. Individual clones are then sequenced and individual sequences analyzed and organisms identified. Using this method we were capable of identifying Stachybotrys chartarum, Penicillium purpurogenum, Aspergillus sydowii, and Cladosporium cladosporioides from a mixed culture. This method was found to be rapid, highly specific, easy to perform, and cost effective. PMID:17039272

Dean, Timothy R; Kohan, Michael; Betancourt, Doris; Menetrez, Marc Y

2006-10-01

174

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

175

Detection and identification of intermediates in the reaction of L-serine with Escherichia coli tryptophan synthase via rapid-scanning ultraviolet-visible spectroscopy  

Microsoft Academic Search

Rapid-scanning stopped-flow (RSSF) UV-visible spectroscopy has been used to investigate the UV-visible absorption changes (300-550 nm) that occur in the spectrum of enzyme-bound pyridoxal 5'-phosphate during the reaction of L-serine with the alpha 2 beta 2 and beta 2 forms of Escherichia coli tryptophan synthase. In agreement with previous kinetic studies the reaction with alpha 2 beta 2 was found

William Frederick Drewe; Michael F. Dunn

1985-01-01

176

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. PMID:22629174

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

2012-01-01

177

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

178

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

179

The Children's Interaction Matrix: Intermediate Form, Primary Form. Preliminary Manual. Research Edition 1975.  

ERIC Educational Resources Information Center

The Children's Interaction Matrix, Intermediate and Primary Forms, are designed to identify the preferred work and content styles of children in group situations. These factors aid the researcher, teacher, and counselor in understanding the individual's preferred mode of behavior in groups as well as indicating the students' reaction to group…

Drummond, Robert J.; And Others

180

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

E-print Network

Hydrogen storage in LiAlH4 : Predictions of the crystal structures and reaction mechanisms in decomposition of the potential hydrogen storage material LiAlH4 . First, we explore the decomposition mechanism of monoclinic LiAlH4 into monoclinic Li3AlH6 plus face-centered cubic fcc Al and hydrogen. We find

Goddard III, William A.

181

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

182

On-line electrospray mass analysis of photoallylation reactions of dicyanobenzenes by allylic silanes via photoinduced electron transfer  

NASA Astrophysics Data System (ADS)

Photoinduced electron transfer reaction of 1,4-dicyanobenzene with allyltrimethylsilane in acetonitrile was analyzed by on-line electrospray mass spectrometry. A reductive allylation product of 1,4-dicyanobenzene was detected for the first time as a key intermediate in the photoinduced electron transfer reaction. The electrospray technique, combined with a flowing photoreaction cell, was shown to be a useful tool for detecting and identifying unstable intermediates or primary products in organic photochemical reactions.

Arakawa, Ryuichi; Lu, Jian; Mizuno, Kazuhiko; Inoue, Hiroo; Doe, Hidekazu; Matsuo, Takekiyo

1997-01-01

183

Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB*  

PubMed Central

Small G-proteins of the Ras superfamily control the temporal and spatial coordination of intracellular signaling networks by acting as molecular on/off switches. Guanine nucleotide exchange factors (GEFs) regulate the activation of these G-proteins through catalytic replacement of GDP by GTP. During nucleotide exchange, three distinct substrate·enzyme complexes occur: a ternary complex with GDP at the start of the reaction (G-protein·GEF·GDP), an intermediary nucleotide-free binary complex (G-protein·GEF), and a ternary GTP complex after productive G-protein activation (G-protein·GEF·GTP). Here, we show structural snapshots of the full nucleotide exchange reaction sequence together with the G-protein substrates and products using Rabin8/GRAB (GEF) and Rab8 (G-protein) as a model system. Together with a thorough enzymatic characterization, our data provide a detailed view into the mechanism of Rabin8/GRAB-mediated nucleotide exchange. PMID:24072714

Guo, Zhong; Hou, Xiaomin; Goody, Roger S.; Itzen, Aymelt

2013-01-01

184

Reaction Plane Determination at Intermediate Rapidity in ?s_NN = 200 GeV Au-Au Collisions in PHENIX at RHIC-BNL  

NASA Astrophysics Data System (ADS)

In mid-central heavy ion collisions, the nuclear overlap region is almond shaped. This spatial anisotropy leads to a momentum space anisotropy, which has symmetry about the plane defined by the beam axis and the impact parameter. This reaction plane (or event plane) can be determined in experiment using the final particle azimuthal distribution. The reaction plane resolution depends on particle multiplicity, azimuthal angle resolution, azimuthal hermeticity, and the amount of actual asymmetry that exists in the collision. We will present the effect of these factors on the resolution of the reaction plane for Au-Au collisions in general and more specifically for the pad planes of the PHENIX Multiplicity Vertex Detector (MVD). These pad planes are in the pseudorapidity range 1.8<|?|<2.6 on either side of the vertex region for which PHOBOS data (nucl-ex/0403025) suggest a v2 of about 4 percent for mid-central Au-Au collisions at ?s_NN = 200 GeV.

Norman, B.

2004-10-01

185

A new view of the mechanisms of UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate-3-phosphate synthase (AroA) derived from X-ray structures of their tetrahedral reaction intermediate states.  

PubMed

UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and 5-enolpyruvylshikimate-3-phosphate synthase (AroA) constitute the small enzyme family of enolpyruvyl transferases, which catalyze the chemically unusual reaction of enolpyruvyl transfer. MurA catalyzes the first step in the biosynthesis of the bacterial cell wall; AroA is the sixth enzyme of the shikimate pathway leading to the synthesis of aromatic compounds in numerous microorganisms and plants. Because both metabolic pathways are absent from mammals but essential for the growth of microorganisms, MurA and AroA are attractive targets for the development of novel antimicrobial drugs. We have determined the x-ray structures of the D305A mutant of Enterobacter cloacae MurA and the D313A mutant of Escherichia coli AroA, both of which crystallized in the presence of their substrates. The structures depict the tetrahedral reaction intermediate states of the enzymes and prove that, without the aspartate side chain, the overall addition-elimination reaction in both enzymes is halted after the addition step. The presented structures lead to a new view of the catalytic mechanism and, moreover, provide an ideal starting point for the rational design of potent inhibitors of MurA and AroA. PMID:13129913

Eschenburg, Susanne; Kabsch, Wolfgang; Healy, Martha L; Schonbrunn, Ernst

2003-12-01

186

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

PubMed

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

Janz, S; Brede, O; Müller, J

1991-07-01

187

Extensional flow convecting a reactant undergoing a first order homogeneous reaction and diffusional mass transfer from a sphere at low to intermediate Peclet and Damkohler numbers  

NASA Technical Reports Server (NTRS)

Forced convective diffusion-reaction is considered for viscous axisymmetric extensional convecting velocity in the neighborhood of a sphere. For Peclet numbers in the range 0.1 less than or equal to Pe less than or equal to 500 and for Damkohler numbers increasing with increasing Pe but in the overall range 0.02 less than or equal to Da less than or equal to 10, average and local Sherwood numbers have been computed. By introducing the eigenfunction expansion c(r, Theta) = Sum of c(n)(r)P(n)(cos Theta) into the forced convective diffusion equation for the concentration of a chemical species undergoing a first order homogeneous reaction and by using properties of the Legendre functions Pn(cos Theta), the variable coefficient PDE can be reduced to a system of N + 1 second order ODEs for the radial functions c(sub n)(r), n = 0, 1, 2,..., N. The adaptive grid algorithm of Pereyra and Lentini can be used to solve the corresponding 2(N + 1) first order differential equations as a two-point boundary value problem on 1 less than or equal to r less than or equal to r(sub infinity). Convergence of the expansion for a specific value of N can thus be established and provides 'spectral' behavior as well as the full concentration field c(r, Theta).

Shah, N. Y.; Reed, X. B., Jr.

1995-01-01

188

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

189

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

190

Heterogeneous Reactions of Epoxides in Acidic Media  

E-print Network

Committee: Dr. Renyi Zhang Epoxides have been recently identified as one of the intermediate species in the gas phase oxidation of alkenes. This study investigates the reaction of isoprene oxide and ?-pinene oxide with sulfuric acid to identify... who have always inspired me and motivated me to aim high. vi ACKNOWLEDGEMENTS I would like to thank my committee chair, Dr. Zhang, and my committee members, Dr. Brooks, Dr. Collins and Dr. Ying, for their guidance and support throughout...

Lal, Vinita

2012-02-14

191

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

192

Revisiting the GroEL-GroES Reaction Cycle via the Symmetric Intermediate Implied by Novel Aspects of the GroEL(D398A) Mutant*?  

PubMed Central

The Escherichia coli chaperonin GroEL is a double-ring chaperone that assists in protein folding with the aid of GroES and ATP. It is believed that GroEL alternates the folding-active rings and that the substrate protein (and GroES) can bind to the open trans-ring only after ATP in the cis-ring is hydrolyzed. However, we found that a substrate protein prebound to the trans-ring remained bound during the first ATP cycle, and this substrate was assisted by GroEL-GroES when the second cycle began. Moreover, a slow ATP-hydrolyzing GroEL mutant (D398A) in the ATP-bound form bound a substrate protein and GroES to the trans-ring. The apparent discrepancy with the results from an earlier study (Rye, H. S., Roseman, A. M., Chen, S., Furtak, K., Fenton, W. A., Saibil, H. R., and Horwich, A. L. (1999) Cell 97, 325–338) can be explained by the previously unnoticed fact that the ATP-bound form of the D398A mutant exists as a symmetric 1:2 GroEL-GroES complex (the “football”-shaped complex) and that the substrate protein (and GroES) in the medium is incorporated into the complex only after the slow turnover. In light of these results, the current model of the GroEL-GroES reaction cycle via the asymmetric 1:1 GroEL-GroES complex deserves reexamination. PMID:18567584

Koike-Takeshita, Ayumi; Yoshida, Masasuke; Taguchi, Hideki

2008-01-01

193

A Label-free Selected Reaction Monitoring Workflow Identifies a Subset of Pregnancy Specific Glycoproteins as Potential Predictive Markers of Early-onset Pre-eclampsia*  

PubMed Central

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.

2013-01-01

194

Trimeric binding of the 70-kD uncoating ATPase to the vertices of clathrin triskelia: a candidate intermediate in the vesicle uncoating reaction  

PubMed Central

Clathrin-coated vesicles were uncoated with the 70-kD "uncoating ATPase" from bovine brain, and the molecular products were visualized by freeze-etch electron microscopy. This yielded images of released clathrin triskelia with up to three 70-kD uncoating ATPase molecules bound to their vertices. Likewise, incubation of soluble clathrin triskelia with purified uncoating ATPase also led to trimeric binding of the ATPase to the vertices of clathrin triskelia. However, this occurred only when either EDTA or nonhydrolyzable analogues of ATP were present, in which case the ATPase also appeared to self-associate. When ATP was present instead, no 70-kD ATPases could be found on clathrin triskelia and all ATPases remained monomeric. These observations support the notion that ATP controls an allosteric conversion of the 70- kD uncoating ATPase between two different molecular conformations, an ATP-charged state in which the molecule has relatively low affinity for itself as well as low affinity for clathrin, and an ATP-discharged state in which both of these affinities are high. We presume that in vivo, the latter condition is brought about by ATP hydrolysis and product release, at which point the ATPase will bind tightly to clathrin and/or self-associate. We further propose that these reactions, when occurring in concert within a clathrin lattice, will tend to destabilize it by a mechanism we call "protein polymer competition". We stress the analogies between such a mechanism of uncoating and the ATP-driven events in muscle contraction. Finally, we show that under experimental conditions in which the uncoating ATPase fully removes the coats from brain coated vesicles, identical aliquots of the enzyme do not affect plasmalemmal coated pits in situ. This remarkable selectivity, the mechanism of which remains a complete mystery, is at least consistent with the idea that the 70-kD ATPase indeed plays a role in uncoating coated vesicles after they have formed in vivo. PMID:2571614

1989-01-01

195

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

Corynebacterium diphtheriae, Corynebacterium ulcerans and Corynebacterium pseudotuberculosis constitute a group of potentially toxigenic microorganisms that are related to different infectious processes in animal and human hosts. Currently, there is a lack of information on the prevalence of disease caused by these pathogens, which is partially due to a reduction in the frequency of routine laboratory testing. In this study, a multiplex polymerase chain reaction (mPCR) assay that can simultaneously identify and determine the toxigenicity of these corynebacterial species with zoonotic potential was developed. This assay uses five primer pairs targeting the following genes: rpoB (Corynebacterium spp), 16S rRNA (C. ulcerans and C. pseudotuberculosis), pld (C. pseudotuberculosis), dtxR (C. diphtheriae) and tox [diphtheria toxin (DT) ]. In addition to describing this assay, we review the literature regarding the diseases caused by these pathogens. Of the 213 coryneform strains tested, the mPCR results for all toxigenic and non-toxigenic strains of C . diphtheriae, C. ulcerans and C. pseudotuberculosis were in 100% agreement with the results of standard biochemical tests and PCR-DT. As an alternative to conventional methods, due to its advantages of specificity and speed, the mPCR assay used in this study may successfully be applied for the diagnosis of human and/or animal diseases caused by potentially toxigenic corynebacterial species. PMID:23778659

Torres, Luciene de Fátima Costa; Ribeiro, Dayana; Hirata Jr, Raphael; Pacheco, Luis Gustavo Carvalho; Souza, Monica Cristina; dos Santos, Louisy Sanches; dos Santos, Cíntia Silva; Salah, Mohammad; Costa, Mateus Matiuzzi da; Ribeiro, Marcio Garcia; Selim, Salah A; Azevedo, Vasco Ariston de Carvalho; Mattos-Guaraldi, Ana Luiza

2013-05-01

196

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. PMID:23778659

Torres, Luciene de Fátima Costa; Ribeiro, Dayana; Hirata, Raphael; Pacheco, Luis Gustavo Carvalho; Souza, Monica Cristina; dos Santos, Louisy Sanches; dos Santos, Cíntia Silva; Salah, Mohammad; da Costa, Mateus Matiuzzi; Ribeiro, Marcio Garcia; Selim, Salah A; Azevedo, Vasco Ariston de Carvalho; Mattos-Guaraldi, Ana Luiza

2013-01-01

197

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

198

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

199

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

200

Closer insight into the reactivity of TMP-dialkyl zincates in directed ortho-zincation of anisole: experimental evidence of amido basicity and structural elucidation of key reaction intermediates.  

PubMed

The new dialkyl(aryl) lithium zincates [(THF)(2)Li(C(6)H(4)-OMe)MeZnMe] (4), [(TMEDA)Li(C(6)H(4)-OMe)MeZnMe] (6), [(THF)(3)Li(C(6)H(4)-OMe)(t)BuZn(t)Bu] (7), and [(PMDETA)Li(C(6)H(4)-OMe)(t)BuZn(t)Bu] (8) have been prepared by co-complexation reactions of lithiated anisole with the relevant dialkylzinc compound and the relevant Lewis base. These new heterobimetallic compounds have been characterized in solution using (1)H, (13)C{H}, and (7)Li NMR spectroscopy, and the molecular structures of 6 and 8 have been elucidated by X-ray crystallography. In 6 the distinct metals are connected through the anisole ligand which binds in an ambidentate fashion (through carbon-zinc and oxygen-lithium contacts) and also through one of the methyl groups, to close a [LiOCCZnC] six-membered ring; whereas 8 displays an open structure where anisole connects the two metals (in the same mode as in 6) but with the tert-butyl groups exclusively bonded terminally to zinc. Reactivity studies of zincates 4 and 7 with the amine TMP(H) supply experimental evidence that these heterobimetallic compounds are intermediates in the two-step deprotonation reaction of anisole by TMP-dialkyl zincates and show the relevance of the alkyl groups in the efficiency of TMP-dialkyl zincate bases. In addition, important solvent effects have also been evaluated. When hexane is added to THF solutions of compounds 4 or 7, the homoleptic tetraorganozincate [(THF)(2)Li(2)Zn(C(6)H(4)-OMe)(4)] (5) is obtained as the result of a disproportionation process. This lithium-rich zincate has also been spectroscopically and crystallographically characterized. PMID:19199628

Clegg, William; Conway, Ben; Hevia, Eva; McCall, Matthew D; Russo, Luca; Mulvey, Robert E

2009-02-18

201

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

202

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 BaFeO(3-?).  

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 BaFeO(3-?) (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

203

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. PMID:7663345

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

1995-01-01

204

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

205

Data requirements for intermediate energy nuclear applications  

NASA Astrophysics Data System (ADS)

Several applications that include spallation neutron sources, space radiation effects, biomedical isotope production, accelerator shielding and radiation therapy make use of intermediate energy nuclear data extending to several GeV. The overlapping data needs of these applications are discussed in terms of what projectiles, targets and reactions are of interest. Included is a discussion of what is generally known about these data and what is needed to facilitate their use in intermediate energy applications.

Pearlstein, Sol

206

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

207

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

208

The aromatic ene reaction  

PubMed Central

The ene reaction is a pericyclic process in which an alkene having an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed ?-bond. The aromatic ene reaction, in which the alkene component is embedded in an aromatic ring, has only been reported in a few (four) instances and has proceeded in low yield (?6%). Here we show efficient aromatic ene reactions in which a thermally generated aryne engages a pendant m-alkylarene substituent to produce a dearomatized isotoluene, itself another versatile but rare reactive intermediate. Our experiments were guided by computational studies that revealed structural features conducive to the aromatic ene process. We proceeded to identify a cascade comprising three reactions: (i) hexadehydro-Diels-Alder (for aryne generation), (ii) intramolecular aromatic ene, and (iii) bimolecular Alder ene. The power of this cascade is evident from the structural complexity of the final products, the considerable scope, and the overall efficiency of these multi-stage, reagent- and byproduct-free, single-pot transformations. PMID:24345944

Niu, Dawen; Hoye, Thomas R.

2014-01-01

209

Peroxo-type intermediates in class I ribonucleotide reductase and related binuclear non-heme iron enzymes.  

PubMed

We have performed a systematic study of chemically possible peroxo-type intermediates occurring in the non-heme di-iron enzyme class Ia ribonucleotide reductase, using spectroscopically calibrated computational chemistry. Density functional computations of equilibrium structures, Fe-O and O-O stretch frequencies, Mossbauer isomer shifts, absorption spectra, J-coupling constants, electron affinities, and free energies of O(2) and proton or water binding are presented for a series of possible intermediates. The results enable structure-property correlations and a new rationale for the changes in carboxylate conformations occurring during the O(2) reaction of this class of non-heme iron enzymes. Our procedure identifies and characterizes various possible candidates for peroxo intermediates experimentally observed along the ribonucleotide reductase dioxygen activation reaction. The study explores how water or a proton can bind to the di-iron site of ribonucleotide reductase and facilitate changes that affect the electronic structure of the iron sites and activate the site for further reaction. Two potential reaction pathways are presented: one where water adds to Fe1 of the cis-mu-1,2 peroxo intermediate P causing opening of a bridging carboxylate to form intermediate P' that has an increased electron affinity and is activated for proton-coupled electron transfer to form the Fe(III)Fe(IV) intermediate X; and one that is more energetically favorable where the P to P' conversion involves addition of a proton to a terminal carboxylate ligand in the site which increases the electron affinity and triggers electron transfer to form X. Both pathways provide a mechanism for the activation of peroxy intermediates in binuclear non-heme iron enzymes for reactivity. The studies further show that water coordination can induce the conformational changes observed in crystal structures of the met state. PMID:19663382

Jensen, Kasper P; Bell, Caleb B; Clay, Michael D; Solomon, Edward I

2009-09-01

210

A comparative study of nitrite reduction by synthetic and biogenic Fe(II-III) hydroxysalts green rusts: Evidence for hydroxyl-nitrite green rust formation as an intermediate reaction product.  

NASA Astrophysics Data System (ADS)

The occurrence of high nitrite concentrations as a result of anthropogenic activities is an important water quality concern as it is highly toxic to human and fauna, and it is used as a nitrogen source for the assimilation process. The toxicity of nitrite is related to its transformation into carcinogenic N-nitroso compounds, which are suspected to be responsible for some gastric cancers, and to its ability to convert the hemoglobin to methaemoglobin what is then unable to fix oxygen and to transport it to the tissues, involving hypoxia and the blue-baby syndrome [1]. To reduce the adverse effect of nitrite on human health and on macroalgal blooms, any process enhancing the transformation of nitrite ions to nitrogen gas is of interest for the remediation of natural environments. To achieve this purpose the use of processes involving Fe(II)-containing minerals could be considered as one of the best options. Green-rusts are mixed Fe(II-III) layered double hydroxides commonly found in anoxic zones of natural environments such as sediments and hydromorphic soils. In such anoxic environments, green rust minerals play an important role in the biogeochemical redox cycling of iron and nitrogen, and can affect the speciation and mobility of many organic and inorganic contaminants. The present study investigates the reduction of nitrite by two synthetic and two biogenic green rusts. On the one hand, Fe(II-III) hydroxychloride and Fe(II-III) hydroxycarbonate green rusts were used as synthetic interlayer forms of GR, which are referred to as ';syn-GR(CO3)' and ';syn-GR(Cl)', respectively. On the other hand, the study was performed with biogenic Fe(II-III) hydroxycarbonate green rusts obtained from the bioreduction of two ferric precursors, either Fe(III)-oxyhydroxycarbonate or lepidocrocite; these biogenic green rusts are referred to as ';bio-GR(CO3)F' and ';bio-GR(CO3)L', respectively. For synthetic green rusts, results showed that the oxidation of both syn-GR(CO3) and syn-GR(Cl) led to the reduction of nitrite ions to ammonium, and that the production of ammonium depended on their Fe(II) content. XRD patterns indicated that both synthetic green rusts were fully oxidized into magnetite during the reaction with nitrite. For biogenic green rusts, the study revealed that both bio-GR(CO3)F and bio-GR(CO3)L were capable of reducing nitrite ions without ammonium production, suggesting the conversion of nitrite ions to nitrogen gas. Moreover, we provided evidence for the first time that the interactions of bio-GR(CO3)F with nitrite led to the formation of an hydroxy-nitrite green rust as a result of the incorporation of nitrite in the interlayer region of bio-GR(CO3)F; such an intercalation of nitrite ions was not observed in experiments with bio-GR(CO3)L. XRD analysis indicated that GR(NO2) was formed as an intermediate reaction product prior to the fully oxidation of GR to ferric oxyhydroxides. [1] Philips S., Laanbroek H. J. and Verstraete W. (2002). Rev. Environ. Sci. Biotechnol. 1, 115-141.

Ona-Nguema, G.; Guerbois, D.; Morin, G.; Zhang, Y.; Noel, V.; Brest, J.

2013-12-01

211

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. PMID:24740213

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

2014-01-01

212

Photogenerated radical intermediates of vitamin K 1: a time-resolved resonance Raman study  

NASA Astrophysics Data System (ADS)

Quinones play a vital role in the process of electron transfer in bacterial photosynthetic reaction centers. It is of interest to investigate the photochemical reactions involving quinones with a view to elucidating the structure-function relationships in the biological processes. Resonance Raman spectra of radical anions and the time-resolved resonance Raman spectra of vitamin K 1 (model compound for Q A in Rhodopseudomonas viridis, a bacterial photosynthetic reception center) are presented. The photochemical intermediates of vitamin K 1, viz. radical anion, ketyl radical and o-quinone methide have been identified. The vibrational assignments of all these intermediates are made on the basis of comparison with our earlier TR3 studies on radical anions of naphthoquinone and menaquinone.

Balakrishnan, G.; Umapathy, S.

1999-01-01

213

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.

214

Pathways for methanol steam reforming involving adsorbed formaldehyde and hydroxyl intermediates on Cu(111): density functional theory studies.  

PubMed

Plane-wave density functional theory calculations have been carried out to explore possible pathways in methanol steam reforming (MSR) on Cu(111). We focus on reactions involving the adsorbed formaldehyde intermediate (CH(2)O) produced by methanol decomposition and the surface hydroxyl (OH) species generated by dissociative adsorption of H(2)O. Several possible pathways leading to the H(2) + CO(2) products have been identified. The two most likely pathways involve the formate (CHOO), rather than the carboxyl (COOH), intermediate, and they possess barriers lower than that of the rate-limiting step of MSR, namely the dehydrogenation of adsorbed methoxyl (CH(3)O) species. PMID:21487630

Lin, Sen; Johnson, Ryan S; Smith, Gregory K; Xie, Daiqian; Guo, Hua

2011-05-28

215

Endometriosis-Specific Genes Identified by Real-Time Reverse Transcription-Polymerase Chain Reaction Expression Profiling of Endometriosis Versus Autologous Uterine Endometrium  

Microsoft Academic Search

Context: The etiology and molecular pathogenesis of endometriosis, a prevalent estrogen-dependent gynecologic disease, are poorly understood. Objective: The objective of the study was to identify the differentially expressed genes between autologous ectopic and eutopic endometrium. Design: Subtractive hybridization was used for a genome-wide search for differentially expressed genes between autologous ectopic and eutopic endometrium. Real-time RT-PCR was used for gene

Wei-Ping Hu; Sun Kuie Tay; Yi Zhao

216

Identifying the major bacteria causing intramammary infections in individual milk samples of sheep and goats using traditional bacteria culturing and real-time polymerase chain reaction.  

PubMed

Use of DNA-based methods, such as real-time PCR, has increased the sensitivity and shortened the time for bacterial identification, compared with traditional bacteriology; however, results should be interpreted carefully because a positive PCR result does not necessarily mean that an infection exists. One hundred eight lactating dairy ewes (56 Manchega and 52 Lacaune) and 24 Murciano-Granadina dairy goats were used for identifying the main bacteria causing intramammary infections (IMI) using traditional bacterial culturing and real-time PCR and their effects on milk performance. Udder-half milk samples were taken for bacterial culturing and somatic cell count (SCC) 3 times throughout lactation. Intramammary infections were assessed based on bacteria isolated in ?2 samplings accompanied by increased SCC. Prevalence of subclinical IMI was 42.9% in Manchega and 50.0% in Lacaune ewes and 41.7% in goats, with the estimated milk yield loss being 13.1, 17.9, and 18.0%, respectively. According to bacteriology results, 87% of the identified single bacteria species (with more than 3 colonies/plate) or culture-negative growth were identical throughout samplings, which agreed 98.9% with the PCR results. Nevertheless, the study emphasized that 1 sampling may not be sufficient to determine IMI and, therefore, other inflammatory responses such as increased SCC should be monitored to identify true infections. Moreover, when PCR methodology is used, aseptic and precise milk sampling procedures are key for avoiding false-positive amplifications. In conclusion, both PCR and bacterial culture methods proved to have similar accuracy for identifying infective bacteria in sheep and goats. The final choice will depend on their response time and cost analysis, according to the requirements and farm management strategy. PMID:24996276

Rovai, M; Caja, G; Salama, A A K; Jubert, A; Lázaro, B; Lázaro, M; Leitner, G

2014-09-01

217

Structure-property relationship of bifunctional MnO2 nanostructures: highly efficient, ultra-stable electrochemical water oxidation and oxygen reduction reaction catalysts identified in alkaline media.  

PubMed

Manganese oxides of various structures (?-, ?-, and ?-MnO2 and amorphous) were synthesized by facile methods. The electrocatalytic properties of these materials were systematically investigated for catalyzing both oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) in alkaline media. Extensive characterization was correlated with the activity study by investigating the crystal structures (XRD, HRTEM), morphologies (SEM), porosities (BET), surfaces (XPS, O2-TPD/MS), and electrochemical properties (Tafel analysis, Koutechy-Levich plots, and constant-current electrolysis). These combined results show that the electrocatalytic activities are strongly dependent on the crystallographic structures, and follow an order of ?-MnO2 > AMO > ?-MnO2 > ?-MnO2. Both OER studies and ORR studies reveal similar structure-determined activity trends in alkaline media. In the OER studies, ?-MnO2 displays an overpotential of 490 mV compared to 380 mV shown by an Ir/C catalyst in reaching 10 mA cm(-2). Meanwhile, ?-MnO2 also exhibits stability for 3 h when supplying a constant current density of 5 mA cm(-2). This was further improved by adding Ni(2+) dopants (ca. 8 h). The superior OER activity was attributed to several factors, including abundant di-?-oxo bridges existing in ?-MnO2 as the protonation sites, analogous to the OEC in PS-II of the natural water oxidation system; the mixed valencies (AOS = 3.7); and the lowest charge transfer resistances (91.8 ?, ? = 430 mV) as revealed from in situ electrochemical impedance spectroscopy (EIS). In the ORR studies, when reaching 3 mA cm(-2), ?-MnO2 shows 760 mV close to 860 mV for the best ORR catalyst (20% Pt/C). The outstanding ORR activity was due to the strongest O2 adsorption capability of ?-MnO2 suggested by temperature-programmed desorption. As a result, this discovery of the structure-related electrocatalytic activities could provide guidance in the further development of easily prepared, scalable, and low-cost catalysts based on metal oxides and their derivatives. PMID:25058174

Meng, Yongtao; Song, Wenqiao; Huang, Hui; Ren, Zheng; Chen, Sheng-Yu; Suib, Steven L

2014-08-13

218

The utilization of bridgehead intermediates in organic synthesis.  

E-print Network

??Bridgehead intermediates have only recently been employed in organic synthesis. This study was undertaken to further explore and broaden their usefulness. Reaction of 9-oxabicyclo(3.3.1) octane… (more)

Hansen, Jeffrey Alan

1991-01-01

219

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

220

Teaching about "Intermediate Forms."  

ERIC Educational Resources Information Center

Argues that the common assumption about the lack of intermediate forms in evolutionary history is inaccurate and misleading. Points out that there are many transitional forms, although special creationists refuse to recognize them as such. (DDR)

Hazard, Evan B.

1998-01-01

221

Methods For Determining Reactive Intermediates By FT-IR Spectroscopy  

NASA Astrophysics Data System (ADS)

The ability to actually examine a reaction mechanism is limited by the various intermediates along a reaction coordinate. Detailed information concerning a mechanism is critical for the thorough understanding of the chemistry and physics involved. Matrix isolation affords the opportunity to slow down or freeze out molecular or atomic species which would be unobservable at or near room temperature. In combination with FT-IR, matrix isolation techniques can be used to obtain high quality spectral data of various intermediates.

Rosenthal, R. J.; Walder, F. T.

1985-12-01

222

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

223

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

224

IsoTagger: Identification of isomeric nuclear states produced in fragmentation reactions with radioactive beams  

NASA Astrophysics Data System (ADS)

A new method has been developed to detect and identify isomeric states produced in intermediate beam-energy reactions with secondary radioactive beams. Event-by-event identification of the reaction products allows for an unambiguous assignment of isomeric states to certain nuclei produced in fragmentation reactions. This versatile device allows for the identification of isomeric states with lifetimes between 100 ns and several ms. Combined prompt and delayed ?-ray spectroscopy give detailed information on the level schemes of exotic nuclei. This is particularly important in measurements of exclusive reaction cross-sections to several final states in the residue nucleus.

Wimmer, K.; Barofsky, D.; Bazin, D.; Fraile, L. M.; Lloyd, J.; Tompkins, J. R.; Williams, S. J.

2015-01-01

225

[Therapy of intermediate uveitis].  

PubMed

Intermediate uveitis is a form of intraocular inflammation in which the vitreous body is the major site of inflammation. Intermediate uveitis is primarily treated medicinally and systemic corticosteroids are the mainstay of therapy. When recurrence of uveitis or side effects occur during corticosteroid therapy an immunosuppressive treatment is required. Cyclosporine A is the only immunosuppressive agent that is approved for therapy of uveitis in Germany; however, other immunosuppressive drugs have also been shown to be effective and well-tolerated in patients with intermediate uveitis. In severe therapy-refractory cases when conventional immunosuppressive therapy has failed, biologics can be used. In patients with unilateral uveitis or when the systemic therapy is contraindicated because of side effects, an intravitreal steroid treatment can be carried out. In certain cases a vitrectomy may be used. PMID:25448321

Doycheva, D; Deuter, C; Zierhut, M

2014-12-01

226

Substrate Activation by Iron Superoxo Intermediates  

PubMed Central

A growing number of non-heme-iron oxygenases and oxidases catalyze reactions for which the well-established mechanistic paradigm involving a single C-H-bond cleaving intermediate of the Fe(IV)-oxo (ferryl) type [1] is insufficient to explain the chemistry. It is becoming clear that, in several of these cases, Fe(III)-superoxide complexes formed by simple addition of O2 to the reduced [Fe(II)] cofactor initiate substrate oxidation by abstracting hydrogen [2]. This substrate-oxidizing entry route into high-valent-iron intermediates makes possible an array of complex and elegant oxidation reactions without consumption of valuable reducing equivalents. Examples of this novel mechanistic strategy are discussed with the goal of bringing forth unifying principles. PMID:20951572

van der Donk, Wilfred A.; Krebs, Carsten; Bollinger, J. Martin

2010-01-01

227

Impact of sulfur dioxide oxidation by Stabilized Criegee Intermediate on sulfate  

EPA Science Inventory

We revise the Carbon Bond chemical mechanism to explicitly represent three Stabilized Criegee Intermediates (SCIs) and their subsequent reactions with sulfur dioxide, water monomer, and water dimer, and incorporate the reactions into the Community Multiscale Air Quality model. Th...

228

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

229

Stereochemical course of enzymatic enolpyruvyl transfer and catalytic conformation of the active site revealed by the crystal structure of the fluorinated analogue of the reaction tetrahedral intermediate bound to the active site of the C115A mutant of MurA.  

PubMed

MurA (UDP-GlcNAc enolpyruvyl transferase), the first enzyme in bacterial peptidoglycan biosynthesis, catalyzes the enolpyruvyl transfer from phosphoenolpyruvate (PEP) to the 3'-OH of UDP-GlcNAc by an addition-elimination mechanism that proceeds through a tetrahedral ketal intermediate. The crystal structure of the Cys115-to-Ala (C115A) mutant of Escherichia coli MurA complexed with a fluoro analogue of the tetrahedral intermediate revealed the absolute configuration of the adduct and the stereochemical course of the reaction. The fluorinated adduct was generated in a preincubation of wild-type MurA with (Z)-3-fluorophosphoenolpyruvate (FPEP) and UDP-GlcNAc and purified after enzyme denaturation. The fluorine substituent stabilizes the tetrahedral intermediate toward decomposition by a factor of 10(4)-10(6), facilitating manipulation of the adduct. The C115A mutant of MurA was utilized to avoid the microheterogeneity that arises in the wild-type MurA from the attack of Cys115 on C-2 of FPEP in competition with the formation of the fluorinated adduct. The crystal structure of the complex was determined to 2.8 A resolution, and the absolute configuration at C-2 of the adduct was found to be 2R. Thus, addition of the 3'-OH of UDP-GlcNAc is to the 2-si face of FPEP, corresponding to the 2-re face of PEP. Given the previous observation that, in D2O, the addition of D+ to C-3 of PEP proceeds from the 2-si face [Kim, D. H., Lees, W. J., and Walsh, C. T. (1995) J. Am. Chem. Soc. 117, 6380-6381], the addition across the double bond of PEP is anti. Also, because the overall stereochemical course has been shown to be either anti/syn or syn/anti [Lees, W. J., and Walsh, C. T. (1995) J. Am. Chem. Soc. 117, 7329-7337], it now follows that the stereochemistry of elimination of H+ from C-3 and Pi from C-2 of the tetrahedral intermediate of the reaction is syn. PMID:9485407

Skarzynski, T; Kim, D H; Lees, W J; Walsh, C T; Duncan, K

1998-02-24

230

Incoherence in the South African Labour Market for Intermediate Skills  

ERIC Educational Resources Information Center

This article is concerned with the production and employment of technically skilled labour at the intermediate level in South Africa. Three differing labour market pathways to intermediate skilling are identified. These are: the traditional apprenticeship route, the new "Learnerships" pathway (similar to the "modern apprenticeship" schemes adopted…

Kraak, Andre

2008-01-01

231

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

232

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

233

Intermediate inflation from rainbow gravity  

E-print Network

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

2013-01-01

234

Characterization of the Replication Rate and Intermediates Produced Following Hydroxyurea treatment in Escherichia coli  

E-print Network

1 Characterization of the Replication Rate and Intermediates Produced Following Hydroxyurea how other impediments to replication are processed. Hydroxyurea is thought to stall replication responds to treatment with hydroxyurea and identify the replication intermediates that arise in Escherichia

Courcelle, Justin

235

Trapping of Hepatitis B Virus capsid assembly intermediates by phenylpropenamide assembly accelerators  

PubMed Central

Understanding the biological self-assembly process of virus capsids is key to understanding the viral life cycle, as well as serving as a platform for the design of assembly-based antiviral drugs. Here we identify and characterize the phenylpropenamide family of small molecules, known to have antiviral activity in vivo, as assembly effectors of the Hepatitis B Virus (HBV) capsid. We have found two representative phenylpropenamides to be assembly accelerators, increasing the rate of assembly with only modest increases in the stability of the HBV capsids; these data provide a physical-chemical basis for their antiviral activity. Unlike previously described HBV assembly effectors, the phenylpropenamides do not misdirect assembly; rather, the accelerated reactions proceed on-path to produce morphologically normal capsids. However, capsid assembly in the presence of phenylpropenamides is characterized by kinetic trapping of assembly intermediates. These traps resolve under conditions close to physiological, but under conditions which favor phenylpropenamide binding and strong core protein-protein interactions, we found that trapped intermediates persist. The phenylpropenamides serve as chemical probes of the HBV capsid assembly pathway by trapping on-path assembly intermediates, illustrating the governing influence of reaction kinetics on capsid assembly. PMID:20845949

Katen, Sarah P.; Chirapu, Srinivas Reddy; Finn, M.G.; Zlotnick, Adam

2010-01-01

236

Intermediate/borderline disseminated cutaneous leishmaniasis.  

PubMed

Leishmaniasis is a diverse group of vector-borne diseases caused by a subset of predominantly intracellular protozoal species of the genus Leishmania. Cutaneous disease may be subdivided into localized, intermediate, and diffuse forms. Intermediate cutaneous leishmaniasis is distributed widely in Latin America and is characterized by cutaneous lesions, which may be accompanied by mucosal disease and demonstrate a tendency toward chronicity and relapse as well as resistance to standard treatment regimens. Leishmania parasites of the subgenus Viannia have been identified as the major etiologic agent of this subset of infections. The present review provides a brief perspective on leishmaniasis followed by a review of classification, transmission, clinical presentation, and evolution of disease, immunology, and current treatment approaches for the intermediate/borderline disseminated subset of cutaneous leishmaniasis. PMID:23231577

Paniz Mondolfi, Alberto E; Duffey, Gabrielle Baker; Horton, Lucy E; Tirado, Mariantonieta; Reyes Jaimes, Oscar; Perez-Alvarez, Alexandra; Zerpa, Olga

2013-04-01

237

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

238

A mechanochemical switch to control radical intermediates.  

PubMed

B??-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB??-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is "off", the 5'-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch "on," the enzyme environment becomes the driving force to impose a distinct conformation of the 5'-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions. PMID:24846280

Brunk, Elizabeth; Kellett, Whitney F; Richards, Nigel G J; Rothlisberger, Ursula

2014-06-17

239

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

240

Membrane fission: model for intermediate structures.  

PubMed

Membrane budding-fission is a fundamental process generating intracellular carriers of proteins. Earlier works were focused only on formation of coated buds connected to the initial membrane by narrow membrane necks. We present the theoretical analysis of the whole pathway of budding-fission, including the crucial stage where the membrane neck undergoes fission and the carrier separates from the donor membrane. We consider two successive intermediates of the reaction: 1), a constricted membrane neck coming out of aperture of the assembling protein coat, and 2), hemifission intermediate resulting from self-fusion of the inner monolayer of the neck, while its outer monolayer remains continuous. Transformation of the constricted neck into the hemifission intermediate is driven by the membrane stress produced in the neck by the protein coat. Although apparently similar to hemifusion, the fission is predicted to have an opposite dependence on the monolayer spontaneous curvature. Analysis of the further stages of the process demonstrates that in all practically important cases the hemifission intermediate decays spontaneously into two separate membranes, thereby completing the fission process. We formulate the "job description" for fission proteins by calculating the energy they have to deliver and the radii of the protein coat aperture which have to be reached to drive the fission process. PMID:12829467

Kozlovsky, Yonathan; Kozlov, Michael M

2003-07-01

241

Advances in studying bioinorganic reaction mechanisms: isotopic probes of activated oxygen  

E-print Network

Advances in studying bioinorganic reaction mechanisms: isotopic probes of activated oxygen intermediates in metalloenzymes Justine P Roth Metalloenzymes catalyze reactions of molecular oxygen and its reduced forms through the controlled formation of metal- bound, activated oxygen intermediates

Roth, Justine P.

242

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

243

Isospin of intermediate mass fragments produced in peripheral, midperipheral, and central collisions from the 58Ni+12C,24Mg reactions at 34.5A MeV  

NASA Astrophysics Data System (ADS)

Isotopic yields of IMF's produced in the 58Ni+12C,24Mg reactions at 34.5A MeV are investigated. Analysis of experimental data from the CRL-Laval 4? multidetector array focuses on events where at least 75% (60%) of the charge and momentum were detected for the 58Ni+12C (58Ni+24Mg) system. Averaged isospin ratios (N/Z) for IMF's with Z=3 and 4 are plotted as a function of emission angle and parallel velocity in the center-of-mass frame. Results from simulations with the statistical codes SMM and GEMINI, assuming an equilibrated source, are compared to the experimental ratios. The ratios seem to indicate the presence of a midrapidity necklike structure that would produce IMF's richer in neutrons than the two main emitters, even for very central collisions.

Larochelle, Y.; Gingras, L.; Ball, G. C.; Beaulieu, L.; Gagné, P.; Hagberg, E.; He, Z. Y.; Horn, D.; Laforest, R.; Roy, R.; St-Pierre, C.

2000-11-01

244

Coke formation and minimisation during steam reforming reactions  

Microsoft Academic Search

The formation of coke during the steam reforming of light hydrocarbons results mainly from catalytic reactions. It is believed that the process is endemic to steam reforming in that the same intermediates are involved in the main reaction as are involved in coking. As a result, control of coking depends on the control of the kinetics of intermediate reactions. On

D. L. Trimm

1997-01-01

245

Synthesis and characterization of La0.9Sr0.1Ga0.8Mg0.2O3-? intermediate-temperature electrolyte using conventional solid state reaction  

NASA Astrophysics Data System (ADS)

The perovskite-type La0.9Sr0.1Ga0.8Mg0.2O3-?(LSGM9182) with high oxygen-ionic conductivity is successfully synthesized using conventional solid-state reaction. The phase composition, grain size distribution, relative density, and oxygen-ionic conductivity of the samples are studied. The XRD result shows that the main perovskite LaGaO3 phase can be produced at 1,250 °C, with trace amount of second phase LaSrGaO4. When the temperature increases to 1,400 °C, the pure phase LSGM can be obtained. The relative density of LSGM pellets sintered at 1,400 °C reaches 98.08%. The average grain size of final powders is ?0.12 ?m, which is appropriate for the deposition of LSGM electrolyte film. The ideal oxygen-ionic conductivities of 0.04, 0.06, and 0.08 S cm-1 can be obtained at 700 °C, 750 °C, and 800 °C, respectively. Porous anode supported single cells with LSGM electrolyte film are fabricated using the as-prepared LSGM powders and the cells provide an open-circuit voltage of above 1.0 V, revealing that the LSGM film is gas-tight and crack-free.

Li, Minxia; Zhang, Yaohui; An, Maozhong; Lü, Zhe; Huang, Xiqiang; Xiao, Juncheng; Wei, Bo; Zhu, Xingbao; Su, Wenhui

2012-11-01

246

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.

2011-11-01

247

Reaction coordinates for electron transfer reactions  

SciTech Connect

The polarization fluctuation and energy gap formulations of the reaction coordinate for outer sphere electron transfer are linearly related to the constant energy constraint Lagrangian multiplier m in Marcus' theory of electron transfer. The quadratic dependence of the free energies of the reactant and product intermediates on m and m+1, respectively, leads to similar dependence of the free energies on the reaction coordinates and to the same dependence of the activation energy on the reorganization energy and the standard reaction free energy. Within the approximations of a continuum model of the solvent and linear response of the longitudinal polarization to the electric field in Marcus' theory, both formulations of the reaction coordinate are expected to lead to the same results.

Rasaiah, Jayendran C. [Department of Chemistry, University of Maine, Orono, Maine 04469 (United States); Zhu Jianjun [Department of Chemistry, State University of New York, Stonybrook, New York 11790 (United States) and Department of Chemistry, Henan Normal University, Xinxiang, Henan (China)

2008-12-07

248

Structure and Electronic Configurations of the Intermediates of Water Oxidation in Blue Ruthenium Dimer Catalysis  

SciTech Connect

Catalytic O{sub 2} evolution with cis,cis-[(bpy){sub 2}(H{sub 2}O)Ru{sup III}ORu{sup III}(OH{sub 2})(bpy){sub 2}]{sup 4+} (bpy is 2,2-bipyridine), the so-called blue dimer, the first designed water oxidation catalyst, was monitored by UV-vis, EPR, and X-ray absorption spectroscopy (XAS) with ms time resolution. Two processes were identified, one of which occurs on a time scale of 100 ms to a few seconds and results in oxidation of the catalyst with the formation of an intermediate, here termed [3,4]'. A slower process occurring on the time scale of minutes results in the decay of this intermediate and O{sub 2} evolution. Spectroscopic data suggest that within the fast process there is a short-lived transient intermediate, which is a precursor of [3,4]'. When excess oxidant was used, a highly oxidized form of the blue dimer [4,5] was spectroscopically resolved within the time frame of the fast process. Its structure and electronic state were confirmed by EPR and XAS. As reported earlier, the [3,4]' intermediate likely results from reaction of [4,5] with water. While it is generated under strongly oxidizing conditions, it does not display oxidation of the Ru centers past [3,4] according to EPR and XAS. EXAFS analysis demonstrates a considerably modified ligand environment in [3,4]'. Raman measurements confirmed the presence of the O-O fragment by detecting a new vibration band in [3,4]' that undergoes a 46 cm{sup -1} shift to lower energy upon {sup 16}O/{sup 18}O exchange. Under the conditions of the experiment at pH 1, the [3,4]' intermediate is the catalytic steady state form of the blue dimer catalyst, suggesting that its oxidation is the rate-limiting step.

Moonshiram, Dooshaye; Jurss, Jonah W.; Concepcion, Javier J.; Zakharova, Taisiya; Alperovich, Igor; Meyer, Thomas J.; Pushkar, Yulia (Purdue); (UNC)

2013-04-08

249

Nucleosynthesis in intermediate mass AGB stars  

E-print Network

We present a summary of the main sites for nucleosynthesis in intermediate mass Asymptotic Giant Branch (AGB) stars. We then discuss some detailed evolutionary models and how these have been used to create a synthetic evolution code which calculates the nucleosynthesis very rapidly, enabling us to investigate changes in some uncertain parameters in AGB evolution, such as mass-loss and dredge-up. We then present results for C, C/O, Mg and Al. We also discuss the changes due to the recent NACRE compilation of reaction rates.

John Lattanzio; Corinne Charbonnel; Manuel Forestini

1999-12-15

250

Carbenium ion intermediates in catalytic cracking  

E-print Network

ion two times in 1 M NH4NO3 to remove any remaining sodium in the zeolite and any exchangeable cationic forms of aluminum. A Si/Al ratio of 4. 5 was determined by X-ray diffraction using PbNO3 as an internal reference (42). The latter... intermediates in a number of catalytic reactions on acidic zeolites, such as the conversion of methanol to gasoline-range hydrocarbons and aromatics, olefin polymerization and isomerization. The intent of this study was to determine whether...

Zardkoohi, Minoo

1987-01-01

251

Specific substrate recognition and thioester intermediate determinations in ubiquitin and SUMO conjugation cascades revealed by a high-sensitive FRET assay.  

PubMed

Ubiquitin and ubiquitin-like proteins (Ubls), such as SUMO, are covalently conjugated to their targets by related, but distinct enzymatic conjugation reactions that involve the dynamic E1-E2-E3 enzyme cascade. E1s activate Ubls by catalyzing Ubl C-terminal adenylation, with the help of ATP, to form a covalent thioester bond. Subsequently, Ubls are transferred to E2 to generate a thioester-linked product. In previous studies, we showed the dynamic processes and thioester intermediates of SUMO with its E1 and E2 conjugating enzymes. Studies of the enzyme specificity of the Ubl conjugation cascade are normally carried out by tedious biochemical processes, and the reaction intermediates are often difficult to capture because they are unstable and have short half-lives. Here, using our recently developed robust quantitative FRET-based technology, we describe systematic investigations of enzymatic specificity and thioester intermediate determination of ubiquitin with its E1-E2 ligases in conjugation with SUMO and its ligases. Our technology easily determined the strong specificity of enzyme-substrate interactions and thioester intermediates in ubiquitination and SUMOylation cascades. The traditional FRET pair ECFP/EYFP lacked adequate signals for these assays. However, in contrast, the highly sensitive FRET pair CyPet/YPet was easily harnessed to define the reaction specificities and intermediates. In addition, the thioester intermediates can be readily monitored by a newly defined FRET index parameter. These results provide an example of a systems biology approach to determine Ubl conjugation specificity and demonstrate that a robust FRET technology can be used to identify enzymes and substrates in other Ubl pathways. PMID:24452848

Jiang, Ling; Saavedra, Amanda N; Way, George; Alanis, Jose; Kung, Raphael; Li, Jun; Xiang, Wensheng; Liao, Jiayu

2014-04-01

252

Masonry. 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 masonry course. These materials, developed for a two-semester (3 hours daily) course, are designed to provide the student with the skills and knowledge necessary for entry level employment in the field…

Thompson, Moses

253

Welding. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of nine terminal objectives for an intermediate welding course. The materials were developed for a 36-week (3 hours daily) course designed to prepare the student for employment in the field of welding. Electric welding and specialized (TIG & MIG)…

Vincent, Kenneth

254

Higgs bosons: Intermediate mass range at e+e- colliders  

Microsoft Academic Search

We elaborate on the production of the standard model Higgs particle at high-energy e+e- colliders through the reaction e+e--->ZH. Particular emphasis is put on the intermediate mass range. In addition to the signal we discuss in detail the background processes. Angular distributions which are sensitive to the spin and parity of the Higgs particle are analyzed.

V. Barger; K. Cheung; A. Djouadi; B. A. Kniehl; P. M. Zerwas

1994-01-01

255

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.

256

Identification of thioether intermediates in the reductive transformation of gonyautoxins into saxitoxins by thiols  

Microsoft Academic Search

O-Sulfate group of gonyautoxin I and IV is transformed into methylene to form neosaxitoxin by thiols such as glutathione, a common cellular scavenger, in mild conditions. We isolated the intermediate of this conversion and propose that this reaction proceeds through formation of thiohemiketal, 1,2 shift to form stable thioether intermediate, and then redox exchange at sulfur atom to form the

Shigeru Sato; Ryuichi Sakai; Masaaki Kodama

2000-01-01

257

Intercepting the Breslow Intermediate via Claisen Rearrangement: Synthesis of Complex 3° Alcohols without Organometallic Reagents  

PubMed Central

A novel Claisen rearrangement in which the Breslow intermediate is engaged as a hydroxy-substituted N,S-ketene acetal to provide complex 3° alcohols without the use of organometallic reagents is reported. The reaction constitutes an unprecedented reactivity mode for the Breslow intermediate. PMID:23214715

Alwarsh, Sefat; Ayinuola, Kolawole; Dormi, Silvana S.; McIntosh, Matthias C.

2013-01-01

258

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. PMID:20814582

Hoenger, Andrea; Buehler, Markus J.; Kreplak, Laurent

2010-01-01

259

Intermediates in the Formation of the Chlorophyll Isocyclic Ring 1  

PubMed Central

Cell-free, organelle-free synthesis of Mg-2,4-divinylpheoporphyrin a5 (MgDVP) from Mg-protoporphyrin IX monomethyl ester (Mg-Proto Me) has been described (Wong and Castelfranco 1984 Plant Physiol 75: 658-661). This system consists of plastid membrane and stromal fractions and requires O2, NAD(P)H and S-adenosylmethionine (SAM). The synthetic 6-methyl-?-ketopropionate analog of Mg-Proto Me was converted to MgDVP by the same catalytic system in the presence of O2 and NADPH. SAM was not required. A compound (X) displaying the kinetic behavior of an intermediate was isolated from reaction mixtures with Mg-Proto Me as the substrate, but not with the 6-methyl-?-ketopropionate analog as the substrate. X was identified as the 6-methyl-?-hydroxypropionate analog of Mg-Proto Me by conversion to the dimethyl ester with CH2N2 and comparison with authentic 6-?-hydroxydimethyl ester. X was converted to MgDVP by the same catalytic system in the presence of O2 and NADPH. We conclude that the conversion of Mg-Proto Me to MgDVP proceeds through the 6-?-hydroxy and the 6-?-ketopropionate esters in agreement with earlier suggestions. PMID:16664481

Wong, Yum-Shing; Castelfranco, Paul A.; Goff, Dane A.; Smith, Kevin M.

1985-01-01

260

Gas Producing Micro-Reaction  

NSDL National Science Digital Library

In this chemistry activity, learners use common chemicals and metals to examine reactions that produce gaseous substances. Learners will identify the gases produced and write a balanced equation for each reaction. Use this activity to also introduce learners to single displacement and double displacement reactions, two types of chemical reactions.

2014-01-28

261

Tachyon field in intermediate inflation  

SciTech Connect

The tachyonic inflationary universe model in the context of intermediate inflation is studied. General conditions for this model to be realizable are discussed. In the slow-roll approximation, we describe in great detail the characteristics of this model.

Campo, Sergio del; Herrera, Ramon; Toloza, Adolfo [Instituto de Fisica, Pontificia Universidad Catolica de Valparaiso, Casilla 4059, Valparaiso (Chile)

2009-04-15

262

Plasticity of Intermediate Filament Subunits  

E-print Network

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 ...

Kirmse, Robert

263

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

264

THE REACTION OF ALUMINIUM CHLORIDE WITH LITHIUM BOROHYDRIDE  

Microsoft Academic Search

The synthesis of aluminum borohydride by the reaction between lithium ; borohydride and aluminum chloride seems to occur, ai least in pant, through the ; decomposition of very unstable, volatile intermediates. Attempts to isolate ; these intermediates in pure state were unsuccessful but by trapping intermediate ; fractions at low temperatures and destroying them with excess hydrogen chloride, ; it

W. M. Olson; R. T. Sanderson

1958-01-01

265

Drug Reactions  

MedlinePLUS

... version Drug Reactions Drug Reactions What is an adverse drug reaction? Medicines can treat or prevent illness and ... medicines can cause problems. These problems are called adverse drug reactions. You should know what to do if ...

266

Controlling reaction specificity in pyridoxal phosphate enzymes  

PubMed Central

Pyridoxal 5'-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly ?-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at C? of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site. PMID:21664990

Toney, Michael D.

2012-01-01

267

Correlations in intermediate energy two-proton removal reactions.  

PubMed

We report final-state-exclusive measurements of the light charged fragments in coincidence with (26)Ne residual nuclei following the direct two-proton removal from a neutron-rich (28)Mg secondary beam. A Dalitz-plot analysis and comparisons with simulations show that a majority of the triple-coincidence events with two protons display phase-space correlations consistent with the (two-body) kinematics of a spatially correlated pair-removal mechanism. The fraction of such correlated events, 56(12)%, is consistent with the fraction of the calculated cross section, 64%, arising from spin S=0 two-proton configurations in the entrance-channel (shell-model) (28)Mg ground state wave function. This result promises access to an additional and more specific probe of the spin and spatial correlations of valence nucleon pairs in exotic nuclei produced as fast secondary beams. PMID:23215478

Wimmer, K; Bazin, D; Gade, A; Tostevin, J A; Baugher, T; Chajecki, Z; Coupland, D; Famiano, M A; Ghosh, T K; Grinyer, G F; Hodges, R; Howard, M E; Kilburn, M; Lynch, W G; Manning, B; Meierbachtol, K; Quarterman, P; Ratkiewicz, A; Sanetullaev, A; Simpson, E C; Stroberg, S R; Tsang, M B; Weisshaar, D; Winkelbauer, J; Winkler, R; Youngs, M

2012-11-16

268

Structural Insight into RNA Hairpin Folding Intermediates  

PubMed Central

Hairpins are a ubiquitous secondary structure motif in RNA molecules. Despite their simple structure, there is some debate over whether they fold in a two-state or multi-state manner. We have studied the folding of a small tetraloop hairpin using a serial version of replica exchange molecular dynamics on a distributed computing environment. On the basis of these simulations, we have identified a number of intermediates that are consistent with experimental results. We also find that folding is not simply the reverse of high-temperature unfolding and suggest that this may be a general feature of biomolecular folding. PMID:18593120

2008-01-01

269

The critical iron-oxygen intermediate in human aromatase.  

PubMed

Aromatase (CYP19) is the target of several therapeutics used for breast cancer treatment and catalyzes the three-step conversion of androgens to estrogens, with an unusual C-C cleavage reaction in the third step. To better understand the CYP19 reaction, the oxy-ferrous complex of CYP19 with androstenedione substrate was cryotrapped, characterized by UV-vis spectroscopy, and cryoreduced to generate the next reaction cycle intermediate. EPR analysis revealed that the initial intermediate observed following cryoreduction is the unprotonated g(1)=2.254 peroxo-ferric intermediate, which is stable up to 180K. Upon gradual cryoannealing, the low-spin (g(1)=2.39) product complex is formed, with no evidence for accumulation of the g(1)=2.30 hydroperoxo-ferric intermediate. The relative stabilization of the peroxo-ferric heme and the lack of observed hydroperoxo-ferric heme distinguish CYP19 from other P450s, suggesting that the proton delivery pathway is more hindered in CYP19 than in most other P450s. PMID:19591804

Gantt, Stephanie L; Denisov, Ilia G; Grinkova, Yelena V; Sligar, Stephen G

2009-09-11

270

The critical iron-oxygen intermediate in human aromatase  

SciTech Connect

Aromatase (CYP19) is the target of several therapeutics used for breast cancer treatment and catalyzes the three-step conversion of androgens to estrogens, with an unusual C-C cleavage reaction in the third step. To better understand the CYP19 reaction, the oxy-ferrous complex of CYP19 with androstenedione substrate was cryotrapped, characterized by UV-vis spectroscopy, and cryoreduced to generate the next reaction cycle intermediate. EPR analysis revealed that the initial intermediate observed following cryoreduction is the unprotonated g{sub 1} = 2.254 peroxo-ferric intermediate, which is stable up to 180 K. Upon gradual cryoannealing, the low-spin (g{sub 1} = 2.39) product complex is formed, with no evidence for accumulation of the g{sub 1} = 2.30 hydroperoxo-ferric intermediate. The relative stabilization of the peroxo-ferric heme and the lack of observed hydroperoxo-ferric heme distinguish CYP19 from other P450s, suggesting that the proton delivery pathway is more hindered in CYP19 than in most other P450s.

Gantt, Stephanie L.; Denisov, Ilia G.; Grinkova, Yelena V. [Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)] [Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Sligar, Stephen G., E-mail: s-sligar@uiuc.edu [Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States); Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 (United States)

2009-09-11

271

Reactions of aminomalononitrile with electrophiles. [simulating prebiotic conditions  

NASA Technical Reports Server (NTRS)

Aminomalononitrile (HCN trimer) reacts with electrophiles such as aldehydes and acrylonitrile under very mild conditions of temperature and pH to produce intermediates which, after acid hydrolysis, yield amino acids. The following amino acids have been identified and quantitated: glycine, D,L-erythro- and D,L-threo-beta-hydroxyaspartic acids, D,L glutamic acid, and D,L-threonine and allo-threonine. The mechanism of their formation and the possible significance of these reactions in prebiotic syntheses are discussed.

Thanassi, J. W.

1975-01-01

272

34 CFR 200.17 - Intermediate goals.  

Code of Federal Regulations, 2012 CFR

...2012-07-01 false Intermediate goals. 200.17 Section 200...Programs Operated by Local Educational Agencies Adequate Yearly...200.17 Intermediate goals. Each State must establish intermediate goals that increase in equal...

2012-07-01

273

34 CFR 200.17 - Intermediate goals.  

Code of Federal Regulations, 2014 CFR

...2014-07-01 false Intermediate goals. 200.17 Section 200...Programs Operated by Local Educational Agencies Adequate Yearly...200.17 Intermediate goals. Each State must establish intermediate goals that increase in equal...

2014-07-01

274

34 CFR 200.17 - Intermediate goals.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 false Intermediate goals. 200.17 Section 200...Programs Operated by Local Educational Agencies Adequate Yearly...200.17 Intermediate goals. Each State must establish intermediate goals that increase in equal...

2013-07-01

275

34 CFR 200.17 - Intermediate goals.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Intermediate goals. 200.17 Section 200...Programs Operated by Local Educational Agencies Adequate Yearly...200.17 Intermediate goals. Each State must establish intermediate goals that increase in equal...

2010-07-01

276

34 CFR 200.17 - Intermediate goals.  

Code of Federal Regulations, 2011 CFR

...2011-07-01 false Intermediate goals. 200.17 Section 200...Programs Operated by Local Educational Agencies Adequate Yearly...200.17 Intermediate goals. Each State must establish intermediate goals that increase in equal...

2011-07-01

277

The Mechanisms of Oxygen Reduction and Evolution Reactions in Nonaqueous Lithium-Oxygen Batteries  

SciTech Connect

The oxygen reduction/evolution reaction (ORR/OER) mechanisms in nonaqueous Li-O2 batteries have been investigated by using electron paramagnetic resonance spectroscopy in this work. We identified the superoxide radical anion (O2•-) as an intermediate in the ORR process using 5,5-dimethyl-pyrroline N-oxide as a spin trap, while no O2•- in OER was detected during the charge process. These findings provide insightful understanding on the fundamental oxygen reaction mechanisms in rechargeable nonaqueous Li-O2 batteries.

Cao, Ruiguo; Walter, Eric D.; Xu, Wu; Nasybulin, Eduard N.; Bhattacharya, Priyanka; Bowden, Mark E.; Engelhard, Mark H.; Zhang, Jiguang

2014-09-30

278

Cyclohexane isomerization. Unimolecular dynamics of the twist-boat intermediate.  

PubMed

Direct dynamics simulations were performed at the HF/6-31G level of theory to investigate the intramolecular and unimolecuar dynamics of the twist-boat (TB) intermediate on the cyclohexane potential energy surface (PES). Additional calculations were performed at the MP2/aug-cc-pVDZ level of theory to further characterize the PES's stationary points. The trajectories were initiated at the C(1) and C(2) half-chair transition states (TSs) connecting a chair conformer with a TB intermediate, via an intrinsic reaction coordinate (IRC). Energy was added in accord with a microcanonical ensemble at the average energy for experiments at 263 K. Important nontransition state theory (TST), non-IRC, and non-RRKM dynamics were observed in the simulations. Trajectories initially directed toward the chair conformer had a high probability of recrossing the TS, with approximately 30% forming a TB intermediate instead of accessing the potential energy well for the conformer. The TB intermediate initially formed was not necessarily the one connected to the TS via the IRC. Of the trajectories initiated at the C(2) half-chair TS and initially directed toward the chair conformer, 35% formed a TB intermediate instead of the chair conformer. Also, of the trajectories forming a TB intermediate, only 16% formed the TB intermediate connected with the C(2) TS via the IRC. Up to eight consecutive TB --> TB isomerizations were followed, and non-RRKM behavior was observed in their dynamics. A TB can isomerize to two different TBs, one by a clockwise rotation of C-C-C-C dihedral angles and the other by a counterclockwise rotation. In contrast to RRKM theory, which predicts equivalent probabilities for these rotations, the trajectory dynamics show they are not equivalent and depend on whether the C(1) or C(2) half-chair TS is initially excited. Non-RRKM dynamics is also observed in the isomerization of the TB intermediates to the chair conformers. RRKM theory assumes equivalent probabilities for isomerizing to the two chair conformers. In contrast, for the first and following TB intermediate formed, there is a preference to isomerize to the chair conformer connected to the TS at which the trajectories were initiated. For the first TB intermediate formed, approximately 30% of the isomerization is to a chair conformer, but this fraction decreases for the later formed TB intermediates and becomes approximately 10% for the eighth consecutive TB intermediate formed. PMID:19290605

Kakhiani, Khatuna; Lourderaj, Upakarasamy; Hu, Wenfang; Birney, David; Hase, William L

2009-04-23

279

ChemTeacher: Combination Reactions  

NSDL National Science Digital Library

ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Combination Reactions page includes resources for teaching students about identifying and predicting combination reactions.

2011-01-01

280

ChemTeacher: Decomposition Reactions  

NSDL National Science Digital Library

ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Decomposition Reactions page includes resources for teaching students about identifying and predicting decomposition reactions.

2011-01-01

281

The adsorption and reaction of halogenated volatile organic compounds (VOC's) on metal oxides. 1998 annual progress report  

SciTech Connect

'The goal of the research is to elucidate the properties of the materials responsible for the activation of halocarbons and the nature of the intermediates formed in the dissociative adsorption of this class of compounds. This information is essential for interpreting and predicting stoichiometric and catalytic pathways for the safe destruction of halocarbon pollutants. The specific objectives are: (1) to study the adsorption and reactivity of chloromethanes and chloroethanes on metal oxides; (2) to identify the reaction intermediates using spectroscopic methods; and (3) to develop kinetic models for the reaction of these halocarbons with oxide surfaces. This report summarizes work after 20 months of a 36-month project. Emphasis has been placed understanding the surfaces phases, as well as the bulk phases that are present during the reactions of chlorinated hydrocarbons with strongly basic metal oxides. Most of the research has been carried out with carbon tetrachloride.'

Lunsford, J.; Goodman, D.W.; Haw, J.F.

1998-06-01

282

In Situ Ultrafast 2D NMR Spectroelectrochemistry for Real-Time Monitoring of Redox Reactions.  

PubMed

The in situ implementation of an electrochemical cell (EC) inside a nuclear magnetic resonance (NMR) spectrometer is extremely powerful to study redox reactions in real time and identify unstable reaction intermediates. Unfortunately, the implementation of an electrochemical device near the sensitive volume of an NMR probe significantly affects the quality of the NMR signal, inducing significant line broadening resulting in peak overlap and partial loss of the multiplet structures. Two-dimensional (2D) NMR spectroscopy allows one to bypass signal overlapping by spreading the peaks along two orthogonal dimensions, while providing precious information in terms of structural elucidation. Nevertheless, the acquisition of 2D NMR data suffers from long acquisition durations which are incompatible with fast redox processes taking place in solution. Here, we present a new approach to deal with this issue, consisting of coupling EC-NMR with ultrafast 2D spectroscopy, capable of recording 2D spectra much faster than conventional 2D NMR. This approach is applied to the real-time monitoring of a model reaction. Fast correlation spectroscopy (COSY) spectra are recorded every 3 min in the course of the 80 min reaction, leading to the unambiguous identification of one reaction intermediate and two reaction products. The evolution of 2D NMR peak volumes in the course of time provides further insight into the mechanism of this reaction involving an unstable intermediate. This study demonstrates the feasibility and the relevance of coupling in situ spectroelectrochemistry with ultrafast 2D spectroscopy to monitor real-time electrochemical reactions in the NMR tube. PMID:25506791

Boisseau, Renaud; Bussy, Ugo; Giraudeau, Patrick; Boujtita, Mohammed

2015-01-01

283

Ozonation and peroxone oxidation of benzophenone-3 in water: effect of operational parameters and identification of intermediate products.  

PubMed

The goal of this study was to bring forward new data and insights with respect to the effect of operational variables and reaction pathways during ozonation and peroxone oxidation of the UV filter compound benzophenone-3 (BP3) in water. A systematic parameter study, investigating the effect of the ozone inlet concentration, temperature, pH, H(2)O(2) and t-butanol addition in a lab-scale bubble reactor, showed the promising potential of ozonation towards BP3 degradation. pH showed to be a major process parameter, with half-life times (5.1-15.0 min) being more than two times shorter at pH10 compared to neutral and acid conditions. This indicates the important role of hydroxyl radicals as supported by the addition of H(2)O(2) and t-butanol as HO promoter and scavenger, respectively. Ozonation intermediate products were identified by liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry (HPLC-QqTOF-MS/MS). Demethylation and non-selective HO attack proved to be the major reaction mechanisms. Where available, identified intermediates were confirmed using analytical standards, and concentration profiles along the ozonation process were determined through selective targeted MS/MS analysis. Benzophenone-1 (BP1), also being a UV-filter compound, and 2,2'-dihydroxy-4-methoxybenzophenone (DHMB) revealed to be the major BP3 degradation products, showing a maximum concentration at about the half-life time of BP3. PMID:23186632

Gago-Ferrero, Pablo; Demeestere, Kristof; Silvia Díaz-Cruz, M; Barceló, Damià

2013-01-15

284

Diphosphine is an intermediate in the photolysis of phosphine to phosphorus and hydrogen. [Jupiter atmospheric chemistry  

NASA Technical Reports Server (NTRS)

The photolysis of phosphine to red phosphorus (P4) and hydrogen is investigated in light of the potential significance of the reaction in the atmospheric chemistry of Jupiter. It is reported that the photolysis of PH3 at room temperature by a 206.2-nm light source gave rise to a product identified by its UV and IR spectra and gas chromatographic retention time as P2H4, the yield of which is found to increase to a maximum and then decrease to 20% of the maximum value with illumination time. A mechanism for phosphine photolysis including diphosphine formation as an intermediate step is proposed, and it is concluded that P2H4 is a likely constituent of the atmospheres of the Jovian planets.

Ferris, J. P.; Benson, R.

1980-01-01

285

Integrated One-Flow Synthesis of Heterocyclic Thioquinazolinones through Serial Microreactions with Two Organolithium Intermediates.  

PubMed

The synthesis of pharmaceutical compounds via short-lived intermediates in a microreactor is attractive, because of the fast flow and high throughput. Additionally, intermediates can be utilized sequentially to efficiently build up a library in a short time. Here we present an integrated microfluidic synthesis of biologically active thioquinazolinone libraries. Generation of o-lithiophenyl isothiocyanate and subsequent reaction with aryl isocyanate is optimized by controlling the residence time in the microreactor to 16?ms at room temperature. Various S-benzylic thioquinazolinone derivatives are synthesized within 10?s in high yields (75-98?%) at room temperature. These three-step reactions involve two organolithium intermediates, an isothiocyanate-functionalized aryllithium intermediate, and a subsequent lithium thiolate intermediate. We also demonstrate the gram-scale synthesis of a multifunctionalized thioquinazolinone in the microfluidic device with a high yield (91?%) and productivity (1.25?g in 5?min). PMID:25521442

Kim, Heejin; Lee, Hyune-Jea; Kim, Dong-Pyo

2015-02-01

286

Experimental studies on intermediate compound of LiBH4  

NASA Astrophysics Data System (ADS)

The formation condition of an intermediate compound of LiBH4 during the partial dehydriding reaction and its local atomistic structure have been experimentally investigated. LiBH4 changes into an intermediate compound accompanying the release of approximately 11mass% of hydrogen at 700-730K. The Raman spectra indicate that the B-H bending and stretching modes of the compound appear at lower and higher frequencies, respectively, as compared to those of LiBH4. These features are consistent with the theoretical calculation on the monoclinic Li2B12H12, consisting of Li + and [B12H12]2- ions, as a possible intermediate compound of LiBH4.

Orimo, Shin-Ichi; Nakamori, Yuko; Ohba, Nobuko; Miwa, Kazutoshi; Aoki, Masakazu; Towata, Shin-ichi; Züttel, Andreas

2006-07-01

287

A Putative Fe2+-bound Persulfenate Intermediate in Cysteine Dioxygenase  

PubMed Central

The common reactions of dioxygen, superoxide and hydroperoxides with thiolates are thought to proceed via persulfenate intermediates, yet these have never been visualized. Here we report a 1.4 Å resolution crystal structure of the Fe2+-dependent enzyme cysteine dioxygenase (CDO) containing this putative intermediate trapped in its active site pocket. The complex raises the possibility that, distinct from known dioxygenases and proposed CDO mechanisms, the Fe-proximal oxygen atom may be involved in the primary oxidation event to yield a unique three-membered Fe-S-O cyclic intermediate. A non-polar environment of the distal oxygen would facilitate isomerization of the persulfenate to the sulfinate product. PMID:18847220

Simmons, Chad R.; Krishnamoorthy, Kalyanaraman; Granett, Spencer L.; Schuller, David J.; Dominy, John E.; Begley, Tadhg P.; Stipanuk, Martha H.; Karplus, P. Andrew

2008-01-01

288

Compact intermediates in RNA folding  

SciTech Connect

Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains, depends on RNA sequence and counterions. It determines the specificity of the folding pathways and the magnitude of the free energy barriers to the ensuing search for the native conformation. By coupling helix assembly with nascent tertiary interactions, compact folding intermediates in RNA also play a crucial role in ligand binding and RNA-protein recognition.

Woodson, S.A. (JHU)

2011-12-14

289

Elucidation of intermediates and mechanisms in heterogeneous catalysis using infrared spectroscopy.  

PubMed

Infrared spectroscopy has a long history as a tool for the identification of chemical compounds. More recently, various implementations of infrared spectroscopy have been successfully applied to studies of heterogeneous catalytic reactions with the objective of identifying intermediates and determining catalytic reaction mechanisms. We discuss selective applications of these techniques with a focus on several heterogeneous catalytic reactions, including hydrogenation, deNOx, water-gas shift, and reverse-water-gas shift. The utility of using isotopic substitutions and other techniques in tandem with infrared spectroscopy is discussed. We comment on the modes of implementation and the advantages and disadvantages of the various infrared techniques. We also note future trends and the role of computational calculations in such studies. The infrared techniques considered are transmission Fourier transform infrared spectroscopy, infrared reflection-absorption spectroscopy, polarization-modulation infrared reflection-absorption spectroscopy, sum-frequency generation, diffuse reflectance infrared Fourier transform spectroscopy, attenuated total reflectance, infrared emission spectroscopy, photoacoustic infrared spectroscopy, and surface-enhanced infrared absorption spectroscopy. PMID:24689797

Savara, Aditya; Weitz, Eric

2014-01-01

290

Elucidation of Intermediates and Mechanisms in Heterogeneous Catalysis Using Infrared Spectroscopy  

NASA Astrophysics Data System (ADS)

Infrared spectroscopy has a long history as a tool for the identification of chemical compounds. More recently, various implementations of infrared spectroscopy have been successfully applied to studies of heterogeneous catalytic reactions with the objective of identifying intermediates and determining catalytic reaction mechanisms. We discuss selective applications of these techniques with a focus on several heterogeneous catalytic reactions, including hydrogenation, deNOx, water-gas shift, and reverse-water-gas shift. The utility of using isotopic substitutions and other techniques in tandem with infrared spectroscopy is discussed. We comment on the modes of implementation and the advantages and disadvantages of the various infrared techniques. We also note future trends and the role of computational calculations in such studies. The infrared techniques considered are transmission Fourier transform infrared spectroscopy, infrared reflection-absorption spectroscopy, polarization-modulation infrared reflection-absorption spectroscopy, sum-frequency generation, diffuse reflectance infrared Fourier transform spectroscopy, attenuated total reflectance, infrared emission spectroscopy, photoacoustic infrared spectroscopy, and surface-enhanced infrared absorption spectroscopy.

Savara, Aditya; Weitz, Eric

2014-04-01

291

Intermediate filaments: a historical perspective.  

PubMed

Intracellular protein filaments intermediate in size between actin microfilaments and microtubules are composed of a surprising variety of tissue specific proteins commonly interconnected with other filamentous systems for mechanical stability and decorated by a variety of proteins that provide specialized functions. The sequence conservation of the coiled-coil, alpha-helical structure responsible for polymerization into individual 10 nm filaments defines the classification of intermediate filament proteins into a large gene family. Individual filaments further assemble into bundles and branched cytoskeletons visible in the light microscope. However, it is the diversity of the variable terminal domains that likely contributes most to different functions. The search for the functions of intermediate filament proteins has led to discoveries of roles in diseases of the skin, heart, muscle, liver, brain, adipose tissues and even premature aging. The diversity of uses of intermediate filaments as structural elements and scaffolds for organizing the distribution of decorating molecules contrasts with other cytoskeletal elements. This review is an attempt to provide some recollection of how such a diverse field emerged and changed over about 30 years. PMID:17493611

Oshima, Robert G

2007-06-10

292

Learning through Literature: Geography, Intermediate.  

ERIC Educational Resources Information Center

This resource book provides specific strategies and activities for integrating the intermediate geography curriculum with related children's literature selections. The book includes the following sections: (1) "World Geography Overview"; (2) "Oceans"; (3) "Polar Regions"; (4) "Islands"; (5) "Rain Forests"; (6) "Mountains"; (7) "Forests"; (8)…

Sterling, Mary Ellen

293

Portraits of Intermediate Science Classes.  

ERIC Educational Resources Information Center

Designed to examine the key factors that characterize effective science instruction, this particular volume of the Intermediate Life Science Study portrays the ways in which 11 teachers taught two topics in seventh grade life science. The participating teachers were volunteers from schools in the greater San Francisco Bay area and from the greater…

Lash, Andrea A.

294

Intermediate Mechanics Tutorials: The Lagrangian  

NSDL National Science Digital Library

This set of tutorial materials focuses on explaining the use of the Lagrangian in classical mechanics. In the tutorial, students describe a basic physics problem using a Newtonian notation, then using the Lagrangian, and then compare the two. This material includes a tutorial and example homework. This is part of a large collection of similar tutorial materials in intermediate classical mechanics.

Wittmann, Michael C.; Ambrose, Bradley S.

2009-07-26

295

Intermediates in fatty acid oxidation  

PubMed Central

1. Aqueous extracts of acetone-dried liver and kidney mitochondria, supplemented with NAD+, CoA and phenazine methosulphate, efficiently convert fatty-acyl-CoA compounds into acetyl-CoA; the process was followed with an O2 electrode. 2. Label from [1-14C]octanoyl-CoA appears in acetyl-CoA more rapidly than that from [8-14C]octanoyl-CoA. 3. Oxidation of [8-14C]octanoyl-CoA was terminated by addition of neutral ethanolic hydroxylamine and the resulting hydroxamates were separated chromatographically. Hydroxamate derivatives of 3-hydroxyoctanoyl-, hexanoyl-, butyryl- and acetyl-CoA were obtained. 4. These and other observations suggest that oxidation of octanoyl-CoA by extracts involves participation of free intermediates rather than uninterrupted complete degradation of individual molecules to acetyl-CoA by a multienzyme complex. 5. Intact liver mitochondria studied by the hydroxamate technique were also shown to form intermediates during oxidation of labelled octanoates. In addition to octanoylhydroxamate, [8-14C]octanoate gave rise to small amounts of hexanoyl-, butyryl- and 3-hydroxyoctanoyl-hydroxamate. In contrast with extracts, however, where the quantity of intermediates found was a significant fraction of the precursors, mitochondria oxidizing octanoate contained much larger quantities of octanoyl-CoA than of any other intermediate. PMID:4722901

Stewart, H. B.; Tubbs, P. K.; Stanley, K. K.

1973-01-01

296

Eikonal reaction theory for two-neutron removal reactions  

NASA Astrophysics Data System (ADS)

The eikonal reaction theory (ERT) proposed lately is a method of calculating one-neutron removal reactions at intermediate incident energies in which Coulomb breakup is treated accurately with the continuum discretized coupled-channels method. ERT is extended to two-neutron removal reactions. ERT reproduces measured one- and two-neutron removal cross sections for He6 scattering on C12 and Pb208 targets at 240 MeV/nucleon and also on a Si28 target at 52 MeV/nucleon. For the heavier target in which Coulomb breakup is important, ERT yields much better agreement with the measured cross sections than the Glauber model.

Minomo, K.; Matsumoto, T.; Egashira, K.; Ogata, K.; Yahiro, M.

2014-08-01

297

Intermediate Temperature Solid Oxide Fuel Cell Development  

SciTech Connect

Solid oxide fuel cells (SOFCs) are high efficiency energy conversion devices. Present materials set, using yttria stabilized zirconia (YSZ) electrolyte, limit the cell operating temperatures to 800 C or higher. It has become increasingly evident however that lowering the operating temperature would provide a more expeditious route to commercialization. The advantages of intermediate temperature (600 to 800 C) operation are related to both economic and materials issues. Lower operating temperature allows the use of low cost materials for the balance of plant and limits degradation arising from materials interactions. When the SOFC operating temperature is in the range of 600 to 700 C, it is also possible to partially reform hydrocarbon fuels within the stack providing additional system cost savings by reducing the air preheat heat-exchanger and blower size. The promise of Sr and Mg doped lanthanum gallate (LSGM) electrolyte materials, based on their high ionic conductivity and oxygen transference number at the intermediate temperature is well recognized. The focus of the present project was two-fold: (a) Identify a cell fabrication technique to achieve the benefits of lanthanum gallate material, and (b) Investigate alternative cathode materials that demonstrate low cathode polarization losses at the intermediate temperature. A porous matrix supported, thin film cell configuration was fabricated. The electrode material precursor was infiltrated into the porous matrix and the counter electrode was screen printed. Both anode and cathode infiltration produced high performance cells. Comparison of the two approaches showed that an infiltrated cathode cells may have advantages in high fuel utilization operations. Two new cathode materials were evaluated. Northwestern University investigated LSGM-ceria composite cathode while Caltech evaluated Ba-Sr-Co-Fe (BSCF) based pervoskite cathode. Both cathode materials showed lower polarization losses at temperatures as low as 600 C than conventional manganite or cobaltite cathodes.

S. Elangovan; Scott Barnett; Sossina Haile

2008-06-30

298

Reactivity of 1-deoxy-D-erythro-hexo-2,3-diulose: a key intermediate in the maillard chemistry of hexoses.  

PubMed

Degradation of 1-deoxyhexo-2,3-diulose, a key intermediate in Maillard chemistry, in the presence of l-alanine under moderate conditions (37 and 50 degrees C) was investigated. Different analytical strategies were accomplished to cover the broad range of products formed and their differing chemical properties. These involved GC-MS analysis of trimethylsilyl and O-benzyloxime trimethylsilyl derivatives (after reaction with O-benzylhydroxylamine and N,O-bis(trimethylsilyl)acetamide), GC-FID analysis of the decyl ester of acetic acid (after reaction with decyl chloroformate), and HPLC-UV analysis of quinoxaline derivatives (after reaction with o-phenylenediamine). Among the compounds identified were carboxylic acids (glyceric acid and acetic acid) that can be seen as stable Maillard end-products. However, the formation of dicarbonyls (3,4-dihydroxy-2-oxobutanal, 1-hydroxybutane-2,3-dione, and 4-hydroxy-2-oxobutanal) and of hydroxycarbonyls (acetol) was verified presenting unstable, reactive Maillard intermediates. Results confirmed that beta-dicarbonyl cleavage is a very important pathway within the degradation of 1-deoxyhexo-2,3-diulose. Other reactions taking place include enolization, water elimination, and oxidation. PMID:19422225

Voigt, Michael; Glomb, Marcus A

2009-06-10

299

Aerobic biodegradation of odorous dimethyl disulfide in aqueous medium by isolated Bacillus cereus GIGAN2 and identification of transformation intermediates.  

PubMed

A novel, flagellated, rod-shape, Gram-positive facultative aerobe, was isolated and identified as Bacillus cereus GIGAN2. It can effectively remove model odorous organics dimethyl disulfide (DMDS) in aqueous solution under aerobic conditions. Initial concentration, pH value and temperature played important role in DMDS biodegradation, and up to 100% of 10mgL(-1) of DMDS could be removed within 96h under the optimum conditions (30°C, pH 7.0 and 200rpm) with a maximum biodegradation rate constant of 0.0330h(-1) and minimum half-life of 21.0h, respectively. Three main intermediates were identified using gas chromatography-mass spectrometry during this biodegradation process. Further, a reaction scheme is also proposed to explain the possible DMDS biodegradation mechanism by GIGAN2 based on the above-identified intermediates. Overall, this is the first report to demonstrate a newly isolated strain using high concentrated DMDS as the sole carbon and energy source with high efficiency. PMID:25459868

Liang, Zhishu; An, Taicheng; Li, Guiying; Zhang, Zhengyong

2014-11-01

300

Theoretical study of the ammonia-hypochlorous acid reaction mechanism.  

PubMed

A mechanism for the oxidation of ammonia by hypochlorous acid to form nitrogen gas has been developed at the B3LYP/6-31G(d,p) level of theory using the Gaussian 03 software package. The formation of NH(2)Cl, NHCl(2), and NCl(3) was studied in the gas phase, with explicit water molecules included to examine the transition state energy in aqueous solution. The inclusion of explicit water molecules in the transition state dramatically reduced the reaction barrier in reactions involving transfer of a hydrogen atom between molecules, effects that were not taken into account through use of a solvation model alone. Three mechanisms were identified for the decomposition of chloramine species to form N(2), involving the combination of two chloramine species to form hydrazine, dichlorohydrazine and tetrachlorohydrazine intermediates. The highest barrier in each pathway was found to be the formation of the hydrazine derivative. PMID:20112901

Rayson, Mark S; Altarawneh, Mohammednoor; Mackie, John C; Kennedy, Eric M; Dlugogorski, Bogdan Z

2010-02-25

301

Reaction times  

Microsoft Academic Search

Reviews 11 studies dealing with reaction times (1910-1911). Reaction time has been utilized to study a variety of problems. The studies indicate that accurate results can not be obtained without careful attention to the technique of the method of reaction time. The topics covered include effect of intensity of stimulus on reaction time, rapidity of perception of sound and light

Herbert Woodrow

1911-01-01

302

Intermediate conformations during viral fusion glycoprotein structural transition.  

PubMed

Entry of enveloped viruses into cells requires the fusion of viral and cellular membranes, driven by conformational changes in viral glycoproteins. Three different classes of viral fusion proteins have been hitherto identified based on common structural elements. Crystal structures have provided static pictures of pre-fusion and post-fusion conformations of these proteins and have revealed the dramatic reorganization of the molecules, but the transition pathway remains elusive. In this review, we will focus on recent data aiming to characterize intermediate structures during the conformational change. All these data support the existence of a pre-hairpin intermediate, but its oligomeric status is still a matter of debate. PMID:23562213

Baquero, Eduard; Albertini, Aurélie A; Vachette, Patrice; Lepault, Jean; Bressanelli, Stéphane; Gaudin, Yves

2013-04-01

303

A Caged, Destabilized Free Radical Intermediate in the Q Cycle  

PubMed Central

The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase sites (Qo), in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models are proposed. In previous work we trapped a Q-cycle semiquinone anion intermediate, termed SQo, in bacterial cyt bc1 by rapid freeze-quenching. In this work, we apply pulsed EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and may even be destabilized with respect to solution. It is trapped in the Qo at a site, which is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analysis show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves “stripping” of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL, while minimizing certain Q-cycle bypass reactions including oxidation of pre-reduced cytochrome b and reduction of O2. PMID:24009094

Vennam, Preethi R.; Fisher, Nicholas; Krzyaniak, Matthew D.; Kramer, David M.

2013-01-01

304

Fundamentals of flight, intermediate text  

NSDL National Science Digital Library

This website is an intermediate on-line textbook on the fundamentals of flight. Initially, this resource examines different kinds of flight. Specifically gliding and true flight are explored. Further topics in the principles of flight will cover aeronautics, the movement of fluids, water and liquids, movement of air, measurements, properties of flight, air moving objects, and forces in flight. This resource also provides fundamentals of flight references. Copyright 2005 International Technology Education Association

Aerospace, Cislunar

1996-01-01

305

The Intermediate State of Supraconductors  

Microsoft Academic Search

IN a previous paper1, I have shown that a body in the so-called `intermediate' state consists of alternating layers of the supraconducting and normal phases. It can be shown, however, that the plane-parallel form of these layers discussed in this paper does not correspond to a minimum of the free energy*. A detailed investigation leads to the result that the

L. Landau

1938-01-01

306

EGRET sources at intermediate galactic latitude  

NASA Technical Reports Server (NTRS)

This paper presents the abstracts of four papers (using ROSAT data) that are submitted to refereed journals during the current reporting period. The papers are: (1) Extreme x-ray variability in the narrow-line QSO PHL 1092; (2) The Geminga pulsar (soft x-ray variability and an EUVE observation); (3) a broad-band x-ray study of the geminga pulsar; and (4) Classification of IRAS-selected x-ray galaxies in the ROSAT all-sky survey. The abstracts of these papers are given in the next four sections of this report, and their status is given in the Appendix. Finally, two new projects (De-identifying a non-AGN and EGRET sources at intermediate galactic latitude) for which ROSAT data were recently received are currently being studied under this grant. A summary of work in progress on these new projects is given in the last two sections of this report.

Halpern, Jules P. (Principal Investigator)

1996-01-01

307

Alkene hydroboration: hot intermediates that react while they are cooling.  

PubMed

Non-TST behavior has recently attracted a great deal of attention. If such behavior is general, then the standard way in which synthetic chemists rationalize and predict reactivity and selectivity would be at least partially invalid. The work in this article was inspired by recent results which highlighted a departure from the predictions of TST for rationalization of the regiochemical outcome of the hydroboration reaction mechanism, suggesting that the isomeric product ratios arise because of nonstatistical dynamical effects (J. Am. Chem. Soc. 2009, 131, 3130-3131). We suggest, based on new calculations using a weak collision RRKM-Master Equation (ME) model, an alternative interpretation of the experimental results which preserves a statistical reaction model. While it is a common assumption that all intermediates and transition states along the reaction path are in thermal equilibrium with solvent, our ME results show that hot intermediates may react while they are undergoing stepwise relaxation through weak collisions, even in solution. To our knowledge, this work represents the first application of master equation methodology to a solution phase thermal reaction in organic chemistry that cannot be otherwise explained using conventional TST. Explicit modeling of solvent and solute dynamics is often prohibitively expensive; however, the master equation offers a computationally tractable model with considerable predictive power that may be utilized to investigate whether stepwise collisional relaxation is prevalent in other polyatomic systems. PMID:20831167

Glowacki, David R; Liang, C H; Marsden, Stephen P; Harvey, Jeremy N; Pilling, Michael J

2010-10-01

308

MCNP6 fragmentation of light nuclei at intermediate energies  

NASA Astrophysics Data System (ADS)

Fragmentation reactions induced on light target nuclei by protons and light nuclei of energies around 1 GeV/nucleon and below are studied with the latest Los Alamos Monte Carlo transport code MCNP6 and with its cascade-exciton model (CEM) and Los Alamos version of the quark-gluon string model (LAQGSM) event generators, version 03.03, used as stand-alone codes. Such reactions are involved in different applications, like cosmic-ray-induced single event upsets (SEU's), radiation protection, and cancer therapy with proton and ion beams, among others; therefore, it is important that MCNP6 simulates them as well as possible. CEM and LAQGSM assume that intermediate-energy fragmentation reactions on light nuclei occur generally in two stages. The first stage is the intranuclear cascade (INC), followed by the second, Fermi breakup disintegration of light excited residual nuclei produced after the INC. Both CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to 4He from energetic nucleons emitted during INC. We investigate the validity and performance of MCNP6, CEM, and LAQGSM in simulating fragmentation reactions at intermediate energies and discuss possible ways of further improving these codes.

Mashnik, Stepan G.; Kerby, Leslie M.

2014-11-01

309

MCNP6 fragmentation of light nuclei at intermediate energies  

E-print Network

Fragmentation reactions induced on light target nuclei by protons and light nuclei of energies around 1 GeV/nucleon and below are studied with the latest Los Alamos Monte Carlo transport code MCNP6 and with its cascade-exciton model (CEM) and Los Alamos version of the quark-gluon string model (LAQGSM) event generators, version 03.03, used as stand-alone codes. Such reactions are involved in different applications, like cosmic-ray-induced single event upsets (SEU's), radiation protection, and cancer therapy with proton and ion beams, among others; therefore, it is important that MCNP6 simulates them as well as possible. CEM and LAQGSM assume that intermediate-energy fragmentation reactions on light nuclei occur generally in two stages. The first stage is the intranuclear cascade (INC), followed by the second, Fermi breakup disintegration of light excited residual nuclei produced after INC. Both CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to He4 from energetic nucleons emitted during INC. We investigate the validity and performance of MCNP6, CEM, and LAQGSM in simulating fragmentation reactions at intermediate energies and discuss possible ways of further improving these codes.

Stepan G. Mashnik; Leslie M. Kerby

2014-04-30

310

Improved evidence for the existence of an intermediate phase during hydration of tricalcium silicate  

SciTech Connect

Tricalcium silicate (Ca{sub 3}SiO{sub 5}) with a very small particle size of approximately 50 nm has been prepared and hydrated for a very short time (5 min) by two different modes in a paste experiment, using a water/solid-ratio of 1.20, and by hydration as a suspension employing a water/solid-ratio of 4000. A phase containing uncondensed silicate monomers close to hydrogen atoms (either hydroxyl groups or water molecules) was formed in both experiments. This phase is distinct from anhydrous tricalcium silicate and from the calcium-silicate-hydrate (C-S-H) phase, commonly identified as the hydration product of tricalcium silicate. In the paste experiment, approximately 79% of silicon atoms were present in the hydrated phase containing silicate monomers as determined from {sup 29}Sileft brace{sup 1}Hright brace CP/MAS NMR. This result is used to show that the hydrated silicate monomers are part of a separate phase and that they cannot be attributed to a hydroxylated surface of tricalcium silicate after contact with water. The phase containing hydrated silicate monomers is metastable with respect to the C-S-H phase since it transforms into the latter in a half saturated calcium hydroxide solution. These data is used to emphasize that the hydration of tricalcium silicate proceeds in two consecutive steps. In the first reaction, an intermediate phase containing hydrated silicate monomers is formed which is subsequently transformed into C-S-H as the final hydration product in the second step. The introduction of an intermediate phase in calculations of the early hydration of tricalcium silicate can explain the presence of the induction period. It is shown that heterogeneous nucleation on appropriate crystal surfaces is able to reduce the length of the induction period and thus to accelerate the reaction of tricalcium silicate with water.

Bellmann, Frank, E-mail: frank.bellmann@uni-weimar.d [Institute for Building Materials Science, Bauhaus University Weimar, 99423 Weimar (Germany); Damidot, Denis [Ecole des Mines de Douai, Civil and Environmental Engineering Department, 941 rue Charles Bourseul, BP 10838, 59508 Doua cedexi (France); Moeser, Bernd [Institute for Building Materials Science, Bauhaus University Weimar, 99423 Weimar (Germany); Skibsted, Jorgen [Instrument Center for Solid-State NMR Spectroscopy and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University DK-8000 Aarhus C (Denmark)

2010-06-15

311

Microfabricated electrochemiluminescence cell for chemical reaction detection  

DOEpatents

A detector cell for a silicon-based or non-silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The detector cell is an electrochemiluminescence cell constructed of layers of silicon with a cover layer of glass, with spaced electrodes located intermediate various layers forming the cell. The cell includes a cavity formed therein and fluid inlets for directing reaction fluid therein. The reaction chamber and detector cell may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The ECL cell may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

Northrup, M. Allen (Berkeley, CA); Hsueh, Yun-Tai (Davis, CA); Smith, Rosemary L. (Davis, CA)

2003-01-01

312

Thio FCMA intermediates as strong acyl donors: a general solution to the formation of complex amide bonds.  

PubMed

Novel methodology for the formation of amide bonds under neutral conditions is described. Evidence is presented that the active acyl donors are thio FCMA intermediates, generated from the reactions of thioacids with isonitriles. PMID:19697932

Rao, Yu; Li, Xuechen; Danishefsky, Samuel J

2009-09-16

313

Thio FCMA Intermediates as Strong Acyl Donors: A General Solution to the Formation of Complex Amide Bonds  

PubMed Central

Novel methodology for the formation of amide bonds under neutral conditions is described. Evidence is presented that the active acyl donors are thio FCMA intermediates, generated from the reactions of thioacids with isonitriles. PMID:19697932

Rao, Yu; Li, Xuechen; Danishefsky, Samuel J.

2009-01-01

314

Study of the reactions in preparing ultrafine KTN powders by sol—gel method  

Microsoft Academic Search

This paper reported the ractions in preparing ultrafine KTN powders by Sol—Gel method, and discovered that. In the heat treatment process, Gel not only occured the carbonized, oxidized reactions of ethyoxy and the carbonates formation reactions, but also occured the two intermediate phases formation reactions, the formation reaction of KTN phase in one step, and the reaction that the two

Shimin Wang; Jianhong Zhao; Caojing Lu; Dinhua Bao; Haoshuang Gu; Guiyu Huang; Anxiang Kuang

1994-01-01

315

Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.  

PubMed

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe(3+) to activate O2 and catecholic substrates for reaction. The inability of Fe(3+) to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe(3+) species, and the anhydride-Fe(3+) intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe(2+)-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe(2+) intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage. PMID:25548185

Knoot, Cory J; Purpero, Vincent M; Lipscomb, John D

2015-01-13

316

Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis  

PubMed Central

Despite the importance of tryptophan (Trp) radicals in biology, very few radicals have been trapped and characterized in a physiologically meaningful context. Here we demonstrate that the diheme enzyme MauG uses Trp radical chemistry to catalyze formation of a Trp-derived tryptophan tryptophylquinone cofactor on its substrate protein, premethylamine dehydrogenase. The unusual six-electron oxidation that results in tryptophan tryptophylquinone formation occurs in three discrete two-electron catalytic steps. Here the exact order of these oxidation steps in the processive six-electron biosynthetic reaction is determined, and reaction intermediates are structurally characterized. The intermediates observed in crystal structures are also verified in solution using mass spectrometry. Furthermore, an unprecedented Trp-derived diradical species on premethylamine dehydrogenase, which is an intermediate in the first two-electron step, is characterized using high-frequency and -field electron paramagnetic resonance spectroscopy and UV-visible absorbance spectroscopy. This work defines a unique mechanism for radical-mediated catalysis of a protein substrate, and has broad implications in the areas of applied biocatalysis and understanding of oxidative protein modification during oxidative stress. PMID:23487750

Yukl, Erik T.; Liu, Fange; Krzystek, J.; Shin, Sooim; Jensen, Lyndal M. R.; Davidson, Victor L.; Wilmot, Carrie M.; Liu, Aimin

2013-01-01

317

Reversible Reactions  

NSDL National Science Digital Library

Watch a reaction proceed over time. How does total energy affect a reaction rate? Vary temperature, barrier height, and potential energies. Record concentrations and time in order to extract rate coefficients. Do temperature dependent studies to extract Arrhenius parameters. This simulation is best used with teacher guidance because it presents an analogy of chemical reactions.

Simulations, Phet I.; Barbera, Jack; Koch, Linda; Lemaster, Ron; Adams, Wendy

2005-09-01

318

Enzyme Reactions  

NSDL National Science Digital Library

This video shows an enzyme reaction lab. The teacher demonstrates how the enzyme, catalase, reacts with hydrogen peroxide (a substrate found in cells). The teacher first demonstrates a normal enzyme reaction. He or she then goes on to show how manipulating temperature and pH will affect the reaction of an enzyme.

School, Minerva D.

2011-10-03

319

Chemical Reactions  

NSDL National Science Digital Library

We don't often stop to think about it, but underlying many of our everyday activities are chemical reactions. From the cooking of an egg to the growth of a child, chemical reactions make things happen. Although many of the reactions that support our lives

National Science Teachers Association (NSTA)

2009-05-01

320

?-Ionone reactions with ozone and OH radical: Rate constants and gas-phase products  

NASA Astrophysics Data System (ADS)

The bimolecular rate constants, kOH rad + ?-ionone (118±30)×10 -12 cm 3 molecule -1 s -1 and k+?-ionone, (0.19±0.05)×10 -16 cm 3 molecule -1 s -1, were measured using the relative rate technique for the reaction of the hydroxyl radical (OH) and ozone (O 3) with 4-(2,6,6-trimethyl-1-cyclohexen-1-yl)-3-buten-2-one ( ?-ionone) at 297±3 K and 1 atm total pressure. To more clearly define part of ?-ionone's indoor environment degradation mechanism, the products of the ?-ionone+OH rad and ?-ionone+O 3 reactions were also investigated. The identified ?-ionone+OH rad reaction products were: glyoxal (ethanedial, HC(=O)C(=O)H), and methylglyoxal (2-oxopropanal, CH 3C(=O)C(=O)H) and the identified ?-ionone+O 3 reaction product was 2-oxopropanal. The derivatizing agents O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) and N, O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) were used to propose 2,6,6-trimethylcyclohex-1-ene-1-carbaldehyde as the other major ?-ionone+OH rad and ?-ionone+O 3 reaction product. The elucidation of this other reaction product was facilitated by mass spectrometry of the derivatized reaction products coupled with plausible ?-ionone+OH rad and ?-ionone+O 3 reaction mechanisms based on previously published volatile organic compound+OH rad and volatile organic compound+O 3 gas-phase reaction mechanisms. The additional gas-phase products observed from the ?-ionone+OH rad reaction are proposed to be the result of cyclization through a radical intermediate.

Forester, Crystal D.; Ham, Jason E.; Wells, J. Raymond

321

Degradation of toluene-2,4-diamine by persulfate: kinetics, intermediates and degradation pathway.  

PubMed

Abstract In this study, the degradation of toluene-2,4-diamine (TDA) by persulfate (PS) in an aqueous solution at near-neutral pH was examined. The result showed that degradation rate of TDA increased with increasing PS concentrations. The optimal dosage of PS in the reaction system was determined by efficiency indicator (I) coupling in the consumption of PS and decay half-life of TDA. Calculation showed that 0.74?mM of PS was the most effective dosage for TDA degradation, at that level the maximum I of 24.51 was obtained. PS can oxidize TDA for an extended reaction time period. Under neutral condition without activation, four degradation intermediates, 2,4-diamino-3-hydroxy-5-sulfonicacidtoluene, 2,4-diaminobenzaldehyde, 2,4-bis (vinylamino) benzaldehyde, and 3,5-diamino-4-hydroxy-2-pentene were identified by high-performance liquid chromatography-mass spectrometry. The tentative degradation pathway of TDA was proposed as well. It was found that hydroxyl radical played an important role in degradation of TDA with activation of Fe(2+), whereas PS anion and sulfate radicals were responsible for the degradation without activation of Fe(2+). PMID:25442404

Jiang, Yong-Hai; Zhang, Jin-Bao; Xi, Bei-Dou; An, Da; Yang, Yu; Li, Ming-Xiao

2014-12-01

322

Intermediate P* from soluble methane monooxygenase contains a diferrous cluster.  

PubMed

During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the Fe(II)Fe(II) state (H(red)). O? binds rapidly at a site away from the cluster to form the Fe(II)Fe(II) intermediate O, which converts to an Fe(III)Fe(III)-peroxo intermediate P and finally to the Fe(IV)Fe(IV) intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of H(red) and O is lost. This was interpreted as signaling oxidation of the cluster, but a low level of accumulation of P* prevented further characterization. In this study, three methods for directly detecting and trapping P* are applied together to allow its spectroscopic and kinetic characterization. First, the MMOB mutant His33Ala is used to specifically slow the decay of P* without affecting its formation rate, leading to its nearly quantitative accumulation. Second, spectra-kinetic data collection is used to provide a sensitive measure of the formation and decay rate constants of intermediates as well as their optical spectra. Finally, the substrate furan is included to react with Q and quench its strong chromophore. The optical spectrum of P* closely mimics those of H(red) and O, but it is distinctly different from that of P. The reaction cycle rate constants allowed prediction of the times for maximal accumulation of the intermediates. Mössbauer spectra of rapid freeze-quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mössbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the Fe(II)Fe(II) state. Thus, the loss of the g = 16 EPR signal results from a change in the electronic structure of the Fe(II)Fe(II) center rather than oxidation. The similarity of the optical and Mössbauer spectra of H(red), O, and P* suggests that only subtle changes occur in the electronic and physical structure of the diiron cluster as P* forms. Nevertheless, the changes that do occur are necessary for O? to be activated for hydrocarbon oxidation. PMID:23718184

Banerjee, Rahul; Meier, Katlyn K; Münck, Eckard; Lipscomb, John D

2013-06-25

323

Characterization of protein folding intermediates  

SciTech Connect

The three-dimensional structure of a protein is encoded in its linear sequence of amino acids. Studies of protein folding are aimed at understanding the nature of this code which translates one-dimensional information to three-dimensions. It is now well-established that protein folding intermediates exist and can be populated significantly under some conditions. A method to characterize kinetic folding intermediates is described. The method takes advantage of the decrease in exchange rates between amide protons (i.e., peptide backbone NH) and solvent water protons, when the amide proton is involved in structure. The feasibility of using amide proton exchange to pulse-label proteins during folding has been demonstrated using (/sup 3/H)-H/sub 2/O. The results with ribonuclease A (RNase A) support a framework model for folding, in which the secondary structure of a protein is formed before tertiary structure changes are complete. Extension of these studies using NMR should permit characterization of early secondary structure folding frameworks.

Kim, P.S.

1986-01-01

324

Physics with Identified Particles at STAR  

E-print Network

New physics results with identified particles at STAR are presented. Measurements at low $p_T$ address bulk properties of the collision, while those at high $p_T$ address jet energy loss in the bulk matter produced. Between these extremes, measurements at intermediate $p_T$ address the interplay between jets and the bulk. We highlight: measurements of $v_2$ fluctuations as a new, sensitive probe of the initial conditions and the equation of state; correlations involving multi-strange particles, along with ratios of identified particles to test coalescence as a mechanism of particle production at intermediate $p_T$; three particle azimuthal correlation to search for conical emission; and the energy and particle-type dependence of hadron production at high $p_T$ to study quark and gluon jet energy loss.

Lijuan Ruan

2007-01-29

325

Storage Stability and Improvement of Intermediate Moisture Foods, Phase 3  

NASA Technical Reports Server (NTRS)

Methods were determined for the improvement of shelf-life stability of intermediate moisture foods (IMF). Microbial challenge studies showed that protection against molds and Staphylococcus aureus could be achieved by a combination of antimicrobial agents, humectants and food acids. Potassium sorbate and propylene glycol gave the best results. It was also confirmed that the maximum in heat resistance shown by vegetative pathogens at intermediate water activities also occurred in a solid food. Glycols and sorbitol both achieve browning inhibition because of their action as a medium for reaction and effect on viscosity of the adsorbed phase. Chemical availability results showed rapid lysine loss before visual discoloration occurred. This is being confirmed with a biological test using Tetrahymena pyriformis W. Accelerated temperature tests show that effectiveness of food antioxidants against rancidity development can be predicted; however, the protection factor changes with temperature. BHA was found to be the best antioxidant for iron catalyzed oxidation.

Labuza, T. P.

1975-01-01

326

INTERMEDIATE FILAMENTS IN SMOOTH MUSCLE  

PubMed Central

The intermediate filament (IF) network is one of the three cytoskeletal systems in smooth muscle. The type III IF proteins vimentin and desmin are major constituents of the network in smooth muscle cells and tissues. Lack of vimentin or desmin impairs contractile ability of various smooth muscle preparations, implying their important role for smooth muscle force development. The IF framework has long been viewed as a fixed cytostructure that solely provides mechanical integrity for the cell. However, recent studies suggest that the IF cytoskeleton is dynamic in mammalian cells in response to various external stimulation. In this review, the structure and biological properties of IF proteins in smooth muscle are summarized. The role of IF proteins in the modulation of smooth muscle force development and redistribution/translocation of signaling partners (such as p130 Crk-associated substrate, CAS) is depicted. This review also summarizes our latest understanding on how the IF network may be regulated in smooth muscle. PMID:18256275

Tang, Dale D.

2008-01-01

327

DXRD studies of sodium nickel ferrocyanide reactions with equimolar nitrate/nitrite salts  

SciTech Connect

Dynamic X-ray diffraction (DXRD) has been used to identify and quantify the solid-state reactions that take place between sodium nickel ferrocyanide, Na[sub 2]NiFe(CN)[sub 6], and equimolar concentrations of sodium nitrate/nitrite, reactions of interest to the continued environmental safety of certain waste storage tanks at the Hanford site in eastern Washington. The results are supportive of previous work that indicated that endothermic dehydration and melting of the nitrates take place prior to the occurrence of exothermic reactions, which begin about 300[degree]C. The DXRD results show that a major reaction set at these temperatures is the occurrence of a series reaction which produces sodium cyanate, NaCNO, as an intermediate in a mildly exothermic first step. In the presence of gaseous oxygen, NaCNO subsequently reacts exothermally and at a faster rate to form metal oxides. Measurements of the rate of this reaction are used to estimate the heat release, and comparisons of this with heat-transfer rates from a hypothetical [open quotes]hot spot[close quotes] show that, even in a worse case scenario, the heat-transfer rates are approximately eight times higher than the rate of energy release from the exothermic reactions. 20 refs., 7 figs., 3 tabs.

Dodds, J.N.; Thomson, W.J. (Washington State Univ., Pullman, WA (United States))

1994-05-01

328

Intramolecular anodic olefin coupling reactions: using competition studies to probe the mechanism of oxidative cyclization reactions.  

PubMed

A competition experiment was designed so that the relative rates of anodic cyclization reactions under various electrolysis conditions can be determined. Reactions with ketene dithioacetal and enol ether-based substrates that use lithium methoxide as a base were shown to proceed through radical cation intermediates that were trapped by a sulfonamide anion. Results for the oxidative coupling of a vinyl sulfide with a sulfonamide anion using the same conditions were consistent with the reaction proceeding through a nitrogen-radical. PMID:20302359

Xu, Hai-Chao; Moeller, Kevin D

2010-04-16

329

Intramolecular Anodic Olefin Coupling Reactions: Using Competition Studies to Probe the Mechanism of Oxidative Cyclization Reactions  

PubMed Central

A competition experiment was designed so that the relative rates of anodic cyclization reactions under various electrolysis conditions can be determined. Reactions with ketene dithioacetal and enol ether-based substrates that use lithium methoxide as a base were shown to proceed through radical cation intermediates that were trapped by a sulfonamide anion. Results for the oxidative coupling of a vinyl sulfide with a sulfonamide anion using the same conditions were consistent with the reaction proceeding through a nitrogen-radical. PMID:20302359

Xu, Hai-Chao; Moeller, Kevin D.

2014-01-01

330

General properties of astrophysical reaction rates in explosive nucleosynthesis  

E-print Network

Fundamental differences in the prediction of reaction rates with intermediate and heavy target nuclei compared to the ones with light nuclei are discussed, with special emphasis on stellar modifications of the rates. Ground and excited state contributions to the stellar rates are quantified, deriving a linear weighting of excited state contributions despite of a Boltzmann population of the nuclear states. A Coulomb suppression effect of the excited state contributions is identified, acting against the usual Q-value rule in some reactions. The proper inclusion of experimental data in revised stellar rates is shown, containing revised uncertainties. An application to the s-process shows that the actual uncertainties in the neutron capture rates are larger than would be expected from the experimental errors alone. Sensitivities of reaction rates and cross sections are defined and their application in reaction studies is discussed. The conclusion provides a guide to experiment as well as theory on how to best improve the rates used in astrophysical simulations and how to assess their uncertainties.

T. Rauscher

2012-09-25

331

An investigation of a Friedel-Crafts alkylation reaction in homogeneous supercritical CO 2 and under subcritical and splitphase reaction conditions  

Microsoft Academic Search

This study investigates the Friedel-Crafts alkylation reaction of triphenylmethanol with methoxybenzene (anisole) in supercritical and subcritical carbon dioxide, and under two-phase (gas\\/liquid) reaction conditions at moderate pressures and temperatures. The reaction was initiated using trifluoroacetic acid to produce triphenylmethlycarbocation as the reaction intermediate. Isolated product yields of the Friedel-Crafts product, p-methoxytetraphenylmethane, are reported.

John E. Chateauneuf; Kan Nie

2000-01-01

332

Reaction mechanisms of aqueous monoethanolamine with carbon dioxide: a combined quantum chemical and molecular dynamics study.  

PubMed

Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines. PMID:25382097

Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya

2015-01-14

333

Reaction paths for production of singlet oxygen from hydrogen peroxide and hypochlorite  

NASA Astrophysics Data System (ADS)

The mechanism for production of singlet oxygen from hydrogen peroxide and hypochlorite in aqueous solution is studied computationally. Geometries of various complexes and transition states are found by quantum mechanical geometry optimizations of the species in gas phase. The activation energies pertaining to the mechanism in aqueous solution are estimated using the isodensity polarized continuum method at various levels of theory up to CCSD//B3LYP/6-311+G(d,p). Three reaction paths have been identified: two with a single transition state and one involving two transition states and a H 2O 3 intermediate. The latter path has the smallest activation energy.

Maetzke, Alice; Knak Jensen, Svend J.

2006-07-01

334

Overexpression of the Coq8 Kinase in Saccharomyces cerevisiae coq Null Mutants Allows for Accumulation of Diagnostic Intermediates of the Coenzyme Q6 Biosynthetic Pathway*  

PubMed Central

Most of the Coq proteins involved in coenzyme Q (ubiquinone or Q) biosynthesis are interdependent within a multiprotein complex in the yeast Saccharomyces cerevisiae. Lack of only one Coq polypeptide, as in ?coq strains, results in the degradation of several Coq proteins. Consequently, ?coq strains accumulate the same early intermediate of the Q6 biosynthetic pathway; this intermediate is therefore not informative about the deficient biosynthetic step in a particular ?coq strain. In this work, we report that the overexpression of the protein Coq8 in ?coq strains restores steady state levels of the unstable Coq proteins. Coq8 has been proposed to be a kinase, and we provide evidence that the kinase activity is essential for the stabilizing effect of Coq8 in the ?coq strains. This stabilization results in the accumulation of several novel Q6 biosynthetic intermediates. These Q intermediates identify chemical steps impaired in cells lacking Coq4 and Coq9 polypeptides, for which no function has been established to date. Several of the new intermediates contain a C4-amine and provide information on the deamination reaction that takes place when para-aminobenzoic acid is used as a ring precursor of Q6. Finally, we used synthetic analogues of 4-hydroxybenzoic acid to bypass deficient biosynthetic steps, and we show here that 2,4-dihydroxybenzoic acid is able to restore Q6 biosynthesis and respiratory growth in a ?coq7 strain overexpressing Coq8. The overexpression of Coq8 and the use of 4-hydroxybenzoic acid analogues represent innovative tools to elucidate the Q biosynthetic pathway. PMID:22593570

Xie, Letian X.; Ozeir, Mohammad; Tang, Jeniffer Y.; Chen, Jia Y.; Jaquinod, Sylvie-Kieffer; Fontecave, Marc; Clarke, Catherine F.; Pierrel, Fabien

2012-01-01

335

Subbarrier fusion of spherical nuclei of intermediate atomic number  

SciTech Connect

A two-humped model was proposed for explaining the suppression of the cross sections for the deep-subbarrier fusion of spherical nuclei that have intermediate atomic numbers. It was shown that the suppression of these cross sections was due to the interference between the incident and reflected fluxes between the two barriers. The results of fitting the cross sections calculated within the two-humped model revealed the invariability of the distance between the vertices of the two barriers. As the charges of colliding nuclei increase, the inner barrier becomes higher than the outer one, and this determines the competition with cross sections for deep-inelastic-transfer reactions.

Shilov, V. M. [Joint Institute for Nuclear Research, Bogolyubov Laboratory of Theoretical Physics (Russian Federation)

2012-04-15

336

Three-nucleon force studies at intermediate energies  

SciTech Connect

High-precision data in three-nucleon scattering processes and state-of-the-art few-body calculations have contributed significantly to our present understanding of three-nucleon forces at intermediate energies. This paper discusses in more detail the pd{yields}3He{gamma} reaction as a probe for electromagnetic currents in the three-nucleon system. Experimental data are reviewed and interpreted by a comparison with Faddeev and coupled-channel calculations from the Bochum-Cracow and Hanover theory groups, respectively.

Messchendorp, J.G. [Kernfysisch Versneller Instituut (KVI), Zernikelaan 25, 9747 AA Groningen (Netherlands)

2005-05-06

337

Radical trapping by gold chlorides forming organogold intermediates.  

PubMed

Organogold compounds arising from the trapping of carbon-centered radicals by gold chlorides (AuCl, AuCl3, and HAuCl4) and colloidal gold have been characterized by different spectroscopic techniques. Laser flash photolysis has provided kinetic evidence of the occurrence of radical trapping in the microsecond time scale, while theoretical calculations give the energetics of the elementary steps. The trapping of carbon radicals by gold species observed here may explain why the presence of radical initiators enhance dramatically the activity of gold catalysts for some reactions occurring through radical intermediates. PMID:16802790

Aprile, Carmela; Boronat, Mercedes; Ferrer, Belén; Corma, Avelino; García, Hermenegildo

2006-07-01

338

The M intermediate of Pharaonis phoborhodopsin is photoactive.  

PubMed Central

The retinal protein phoborhodopsin (pR) (also called sensory rhodopsin II) is a specialized photoreceptor pigment used for negative phototaxis in halobacteria. Upon absorption of light, the pigment is transformed into a short-wavelength intermediate, M, that most likely is the signaling state (or its precursor) that triggers the motility response of the cell. The M intermediate thermally decays into the initial pigment, completing the cycle of transformations. In this study we attempted to determine whether M can be converted into the initial state by light. The M intermediate was trapped by the illumination of a water glycerol suspension of phoborhodopsin from Natronobacterium pharaonis called pharaonis phoborhodopsin (ppR) with yellow light (>450 nm) at -50 degrees C. The M intermediate absorbing at 390 nm is stable in the dark at this temperature. We found, however, that M is converted into the initial (or spectrally similar) state with an absorption maximum at 501 nm upon illumination with 380-nm light at -60 degrees C. The reversible transformations ppR if M are accompanied by the perturbation of tryptophan(s) and probably tyrosine(s) residues, as reflected by changes in the UV absorption band. Illumination at lower temperature (-160 degrees C) reveals two intermediates in the photoconversion of M, which we termed M' (or M'(404)) and ppR' (or ppR'(496)). A third photoproduct, ppR'(504), is formed at -110 degrees C during thermal transformations of M'(404) and ppR'(496). The absorption spectrum of M'(404) (maximum at 404 nm) consists of distinct vibronic bands at 362, 382, 404, and 420 nm that are different from the vibronic bands of M at 348, 368, 390, and 415 nm. ppR'(496) has an absorption band that is shifted to shorter wavelengths by 5 nm compared to the initial ppR, whereas ppR'(504) is redshifted by at least 3 nm. As in bacteriorhodopsin, photoexcitation of the M intermediate of ppR and, presumably, photoisomerization of the chromophore during the M --> M' transition result in a dramatic increase in the proton affinity of the Schiff base, followed by its reprotonation during the M' --> ppR' transition. Because the latter reaction occurs at very low temperature, the proton is most likely taken from the counterion (Asp(75)) rather than from the bulk. The phototransformation of M reveals a certain heterogeneity of the pigment, which probably reflects different populations of M or its photoproduct M'. Photoconversion of the M intermediate provides a possible pathway for photoreception in halobacteria and a useful tool for studying the mechanisms of signal transduction by phoborhodopsin (sensory rhodopsin II). PMID:10827991

Balashov, S P; Sumi, M; Kamo, N

2000-01-01

339

ChemTeacher: Single Replacement Reactions  

NSDL National Science Digital Library

ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Single Replacement Reactions page includes resources for teaching students about identifying and predicting single replacement reactions.

2012-07-23

340

ChemTeacher: Double Replacement Reactions  

NSDL National Science Digital Library

ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Double Replacement Reactions page includes resources for teaching students about identifying and predicting double replacement reactions.

2011-01-01

341

Reaction Time  

NSDL National Science Digital Library

In this activity, learners explore reaction time and challenge themselves to improve their coordination. Do you want to move faster? Catch that ball that you never seem to see in time? Use a simple test to help you improve your reaction (or response) time.

Science, New Y.

1999-01-01

342

Scattering and reaction cross-sections measured at SPES I Results compiled by  

E-print Network

for low energy nuclear physics measurements i.e. : diffe- rential cross-section (a = deT/dQ) versus This article gives all the differential cross-sections for two body reactions at intermediate energy measured (Saclay) in 1971 in order to investigate intermediate energy two body reactions. This magne- tic

Boyer, Edmond

343

Crystal structure of the covalent intermediate of amylosucrase from Neisseria polysaccharea.  

PubMed

The alpha-retaining amylosucrase from the glycoside hydrolase family 13 performs a transfer reaction of a glucosyl moiety from sucrose to an acceptor molecule. Amylosucrase has previously been shown to be able to use alpha-D-glucopyranosyl fluoride as a substrate, which suggested that it could also be used for trapping the reaction intermediate for crystallographic studies. In this paper, the crystal structure of the acid/base catalyst mutant, E328Q, with a covalently bound glucopyranosyl moiety is presented. Sucrose cocrystallized crystals were soaked with alpha-D-glucopyranosyl fluoride, which resulted in the trapping of a covalent intermediate in the active site of the enzyme. The structure is refined to a resolution of 2.2 A and showed that binding of the covalent intermediate resulted in a backbone movement of 1 A around the location of the nucleophile, Asp286. This structure reveals the first covalent intermediate of an alpha-retaining glycoside hydrolase where the glucosyl moiety is identical to the expected biologically relevant entity. Comparison to other enzymes with anticipated glucosylic covalent intermediates suggests that this structure is a representative model for such intermediates. Analysis of the active site shows how oligosaccharide binding disrupts the putative nucleophilic water binding site found in the hydrolases of the GH family 13. This reveals important parts of the structural background for the shift in function from hydrolase to transglycosidase seen in amylosucrase. PMID:15023061

Jensen, Malene H; Mirza, Osman; Albenne, Cecile; Remaud-Simeon, Magali; Monsan, Pierre; Gajhede, Michael; Skov, Lars K

2004-03-23

344

Copper-Catalyzed Oxidative Heck Reactions between Alkyltrifluoroborates and Vinylarenes  

PubMed Central

We report herein that potassium alkyltrifluoroborates can be utilized in oxidative Heck-type reactions with vinyl arenes. The reaction is catalyzed by a Cu(OTf)2/1,10-phenanthroline with MnO2 as the stoichiometric oxidant. In addition to the alkyl Heck, amination, esterification and dimerization reactions of alkyltrifluoroborates are demonstrated under analogous reaction conditions. Evidence for an alkyl radical intermediate is presented. PMID:23734764

Liwosz, Timothy W.; Chemler, Sherry R.

2013-01-01

345

Understanding side reactions in K-O2 batteries for improved cycle life.  

PubMed

Superoxide based metal-air (or metal-oxygen) batteries, including potassium and sodium-oxygen batteries, have emerged as promising alternative chemistries in the metal-air battery family because of much improved round-trip efficiencies (>90%). In order to improve the cycle life of these batteries, it is crucial to understand and control the side reactions between the electrodes and the electrolyte. For potassium-oxygen batteries using ether-based electrolytes, the side reactions on the potassium anode have been identified as the main cause of battery failure. The composition of the side products formed on the anode, including some reaction intermediates, have been identified and quantified. Combined experimental studies and density functional theory (DFT) calculations show the side reactions are likely driven by the interaction of potassium with ether molecules and the crossover of oxygen from the cathode. To inhibit these side reactions, the incorporation of a polymeric potassium ion selective membrane (Nafion-K(+)) as a battery separator is demonstrated that significantly improves the battery cycle life. The K-O2 battery with the Nafion-K(+) separator can be discharged and charged for more than 40 cycles without increases in charging overpotential. PMID:25295518

Ren, Xiaodi; Lau, Kah Chun; Yu, Mingzhe; Bi, Xuanxuan; Kreidler, Eric; Curtiss, Larry A; Wu, Yiying

2014-11-12

346

Intermediate care: the role of medicines management.  

PubMed

Healthcare systems worldwide are facing an unprecedented demographic change as globally, the number of older people will triple to 2 billion by the year 2050. The resulting pressures on acute services have been instrumental in the development of intermediate care (IC) as a new healthcare model, which has its origins in the National Health Service in the UK. IC is an umbrella term for patient services that do not require the resources of a general hospital but are beyond the scope of a traditional primary care team. IC aims to promote timely discharge from hospital, prevent unnecessary hospital admissions and reduce the need for long-term residential care by optimizing functional independence. Various healthcare providers around the world have adopted similar models of care to manage changing healthcare needs. Polypharmacy, along with age-related changes, places older people at an increased risk of adverse drug events, including inappropriate prescribing, which has been shown to be prevalent in this population in other healthcare settings. Medicines management (the practice of maximizing health through optimal use of medicines) of older people has been discussed in the literature in a variety of settings; however, its place within IC is largely unknown. Despite IC being a multidisciplinary healthcare model, there is a lack of evidence to suggest that enhanced pharmaceutical involvement is core to the service provided within IC. This review article highlights the gap in the literature surrounding medicines management within IC and identifies potential solutions aimed at improving patient outcomes in this setting. PMID:24197610

Millar, Anna N; Hughes, Carmel M; Passmore, A Peter; Ryan, Cristín

2014-01-01

347

Groups of Galaxies at Intermediate Redshift  

E-print Network

Galaxy groups are key tracers of galaxy evolution, cluster evolution, and structure formation, yet they are difficult to study at even moderate redshift. We have undertaken a project to observe a flux-limited sample of intermediate-redshift (0.1 < z < 0.5) group candidates identified by the XBootes Chandra survey. When complete, this project will nearly triple the current number of groups with measured temperatures in this redshift range. Here we present deep Suzaku/XIS and Chandra/ACIS follow-up observations of the first 10 targets in this project; all are confirmed sources of diffuse, thermal emission with derived temperatures and luminosities indicative of rich groups/poor clusters. By exploiting the multi-wavelength coverage of the XBootes/NOAO Deep Wide Field Survey (NDWFS) field, we aim to (1) constrain non-gravitational effects that alter the energetics of the intragroup medium, and (2) understand the physical connection between the X-ray and optical properties of groups. We discuss the propertie...

Miller, Eric D; Grant, Catherine; Hickox, Ryan; Brodwin, Mark; Murray, Stephen; Jones, Christine; Forman, William; Vikhlinin, Alexey

2009-01-01

348

Clustered arrangement of keratin intermediate filament genes.  

PubMed Central

We report here that component members of the keratin intermediate filament (IF) type I and type II gene families of sheep are closely linked but apparently the two families are not. Nine genes, accounting for up to half of the keratin IF gene repertoire, were mapped in four cosmid clones and the linkage between the genes ranged from several kilobases to 20 kilobases. In one cosmid, three tandem type I genes had the same transcriptional arrangement and were regularly spaced. In another cosmid, tandem genes encoding type II keratins were identified and, surprisingly, a solitary exon was discovered in the intergene region between the two type II genes. In a normal gene this exon encodes one of the most conserved amino acid regions of IF proteins, the C-terminal end of the alpha-helical core. Homologous C-terminal protein subdomains were encoded by two wool keratin type II genes and we suggest that this arrangement may also exist in the other wool keratin type II genes. Images PMID:2425360

Powell, B C; Cam, G R; Fietz, M J; Rogers, G E

1986-01-01

349

Stochastic operator-splitting method for reaction-diffusion systems  

NASA Astrophysics Data System (ADS)

Many biochemical processes at the sub-cellular level involve a small number of molecules. The local numbers of these molecules vary in space and time, and exhibit random fluctuations that can only be captured with stochastic simulations. We present a novel stochastic operator-splitting algorithm to model such reaction-diffusion phenomena. The reaction and diffusion steps employ stochastic simulation algorithms and Brownian dynamics, respectively. Through theoretical analysis, we have developed an algorithm to identify if the system is reaction-controlled, diffusion-controlled or is in an intermediate regime. The time-step size is chosen accordingly at each step of the simulation. We have used three examples to demonstrate the accuracy and robustness of the proposed algorithm. The first example deals with diffusion of two chemical species undergoing an irreversible bimolecular reaction. It is used to validate our algorithm by comparing its results with the solution obtained from a corresponding deterministic partial differential equation at low and high number of molecules. In this example, we also compare the results from our method to those obtained using a Gillespie multi-particle (GMP) method. The second example, which models simplified RNA synthesis, is used to study the performance of our algorithm in reaction- and diffusion-controlled regimes and to investigate the effects of local inhomogeneity. The third example models reaction-diffusion of CheY molecules through the cytoplasm of Escherichia coli during chemotaxis. It is used to compare the algorithm's performance against the GMP method. Our analysis demonstrates that the proposed algorithm enables accurate simulation of the kinetics of complex and spatially heterogeneous systems. It is also computationally more efficient than commonly used alternatives, such as the GMP method.

Choi, TaiJung; Maurya, Mano Ram; Tartakovsky, Daniel M.; Subramaniam, Shankar

2012-11-01

350

Intermediates and the folding of proteins L and G  

SciTech Connect

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.

Brown, Scott; Head-Gordon, Teresa

2003-07-01

351

Cutaneous allergic reactions to tattoo ink.  

PubMed

Tattoo artists use many compounds to create tattoo pigment and several allergic reactions can occur as a result of these additives. The compositions of many inks have been identified; however, as new mixtures are created it becomes difficult to identify the specific ingredients in a particular ink. Allergic reactions to a particular pigment can manifest in several ways including allergic contact dermatitis and photoallergic dermatitis. Subsequently, tattoo ink or pigment allergy reactions can be classified as acute inflammatory reactions, allergic hypersensitivities, and granulomatous, lichenoid, and pseudolymphomatous types of reactions. This paper will review the clinical manifestations and the most common compounds associated with cutaneous reactions to tattoo ink. PMID:19958434

Kaur, Ravneet Ruby; Kirby, William; Maibach, Howard

2009-12-01

352

Study of Compound Nuclei Produced in Low Energy Nuclear Reactions in Solids  

Microsoft Academic Search

The array of reaction products from experimental studies of Low Energy Nuclear Reactions (LENRs) suggest that such reactions occur through the formation of the intermediate heavy compound nucleus which can then fission or decay into the reaction products. These experiments used an electrolytic technique to obtain a very high loading of protons in thin (2000-8000 Å) metallic films of palladium,

G. H. Miley; H. Hora

2003-01-01

353

Reaction studies of hot silicon and germanium radicals. Progress report, September 1, 1979-August 31, 1980  

SciTech Connect

The experimental approach to attaining the goals of this research program is briefly outlined and the progress made in the last year is reviewed in sections entitled: (a) primary steps in the reaction of recoiling silicon and germanium atoms and the identification of reactive intermediates in the recoil reactions; (b) thermally induced silylene and germylene reactions; (c) ion-molecule reaction studies.

Gaspar, P.P.

1980-08-31

354

Marine Engine Mechanics. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are presented for each of ten terminal objectives for a two-semester course (3 hours daily). This 540-hour intermediate course includes advanced troubleshooting techniques on outboard marine engines, inboard-outboard marine engines, inboard marine engines, boat…

Jones, Marion

355

Geography 115C Intermediate Remote Sensing Techniques  

E-print Network

patterns from space and land (TRMM, NexRAD, GRACE) 12. May 14 (W) Introduction to remote sensing and GIS1 Geography 115C ­ Intermediate Remote Sensing Techniques Spring 2014 Instructor: Bodo Bookhagen (bodo@eri.ucsb.edu) Geog115C, Intermediate Remote Sensing, M, W 11:00-12:15 pm, EH3621 Lab: W 5-7:50pm

Bookhagen, Bodo

356

Uninterrupted power supply with intermediate HF circuit  

Microsoft Academic Search

Contents This work presents an uninterrupted monophase power supply with IGBT transistors and HF intermediate circuit. Two three-phase UPS circuits with intermediate HF circuit are also presented, based on the suggested control method. All the suggested versions are characterized by small dimensions and a high fundamental content (0,995) of the alternating output voltages.

D. Alexa; M. Florea

1992-01-01

357

Magnetic properties of intermediate-mass stars  

E-print Network

Magnetic fields play an important role in producing and modifying the photospheric chemical peculiarities of intermediate-mass main sequence stars. This article discusses the basic theory and methods of measurement used to detect and characterise stellar magnetic fields, and reviews our current knowledge of selected characteristics of magnetic fields in intermediate-mass stars.

G. A. Wade

2006-01-30

358

Automotive Body Repair. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of 10 terminal objectives for an intermediate automotive body repair and refinishing course. The materials were developed for a two-semester (3 hours daily) course for specialized classrooms, shop, and practical experiences designed to enable the…

Lang, Thomas

359

Air Conditioning. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of seven terminal objectives for an intermediate air conditioning course. The titles of the seven terminal objectives are Refrigeration Cycle, Job Requirement Skills, Air Conditioning, Trouble Shooting, Performance Test, Shop Management, and S.I.E.…

Long, William

360

Business Machine Maintenance. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of 28 terminal objectives presented in this guide for an intermediate business machine maintenance course at the secondary level. (For the basic course guide see CE 010 949.) Titles of the 28 terminal objective sections are Career Opportunities,…

McMinn, Robert

361

Understanding intermediate-band solar cells  

Microsoft Academic Search

The intermediate-band solar cell is designed to provide a large photogenerated current while maintaining a high output voltage. To make this possible, these cells incorporate an energy band that is partially filled with electrons within the forbidden bandgap of a semiconductor. Photons with insufficient energy to pump electrons from the valence band to the conduction band can use this intermediate

Antonio Martí; Colin Stanley; Antonio Luque

2012-01-01

362

ART F301 F71 INTERMEDIATE CERAMICS  

E-print Network

ART F301 F71 INTERMEDIATE CERAMICS Summer 2014 3credits Meeting times: M-Th 2-5pm Fine Arts Bldg@alaska.edu COURSE DESCRIPTION: Intermediate Ceramics provides an overview of the medium of ceramics and it of various ceramic forming techniques and an understanding of visual elements and principles of design. You

Sikes, Derek S.

363

Diesel Mechanics. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of six terminal objectives for an intermediate diesel mechanics course (two semesters, 3 hours daily) designed for high school students who upon completion would be ready for an on-the-job training experience in diesel service and repair. Through…

Tidwell, Joseph

364

Gasoline Engine Mechanics. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of six terminal objectives presented in this curriculum guide for an intermediate gasoline engine mechanics course at the secondary level. (For the beginning course guide see CE 010 947.) The materials were developed for a two-semester (2 hour…

Jones, Marion

365

Appliance Services. Intermediate Course. Career Education.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of 16 terminal objectives for an intermediate appliance repair course. The materials were developed for a 36-week course (3 hours daily) covering the areas of refrigeration, maintenance, repair, and troubleshooting of refrigerators and air…

Killough, Joseph

366

Substrate-induced activation of a trapped IMC-mediated protein folding intermediate.  

PubMed

While several unfolded proteins acquire native structures through distinct folding intermediates, the physiological relevance and importance of such states in the folding kinetics remain controversial. The intramolecular chaperone (IMC) of subtilisin was used to trap a partially folded, stable crosslinked intermediate conformer (CLIC) through a disulfide bond between mutated IMC and subtilisin. The trapped CLIC contains non-native interactions. Here we show that CLIC can be induced into a catalytically active form by incubating it with small peptide substrates. The structure and catalytic properties of the activated crosslinked intermediate conformer (A-CLIC) differ from those of the fully folded enzyme in that A-CLIC lacks any endopeptidase activity toward a large protein substrate. Our results show that a disulfide-linked partially folded protein can be induced to acquire catalytic activity with a substrate specificity that is different from completely folded subtilisin. These results also suggest that protein folding intermediates may also participate in catalytic reactions. PMID:11276251

Inouye, M; Fu, X; Shinde, U

2001-04-01

367

Intermediate System to Intermediate System (ISIS) Extensions for Traffic Engineering (TE)  

Microsoft Academic Search

This document describes extensions to the Intermediate System to Intermediate System (IS-IS) protocol to support Traffic Engineering (TE). This document extends the IS-IS protocol by specifying new information that an Intermediate System (router) can place in Link State Protocol (LSP) Data Units. This information describes additional details regarding the state of the network that are useful for traffic engineering computations.

H. Smit; T. Li

2004-01-01

368

Improving Intermediate Grade Geography Skills.  

ERIC Educational Resources Information Center

This report describes a program for improving student geographical skill components identified as place and orientation, cultural geography, economic geography, physical geography, and plants and animals. Middle school students in a middle class community in the midwest participated in the study. Three major categories of interventions were…

Neihengen, Thomas; Silva, Martha; Zimmer, Marilynn

369

Base-Mediated Intermolecular sp2 C-H Bond Arylation via Benzyne Intermediates  

PubMed Central

A transition-metal-free method for arylation of heterocycle and arene carbon-hydrogen bonds by aryl chlorides and fluorides has been developed. The reactions proceed via aryne intermediates and are highly regioselective with respect to the C-H bond coupling component. PMID:21384889

Truong, Thanh; Daugulis, Olafs

2011-01-01

370

Unveiling New Degradation Intermediates/Pathways from the Photocatalytic Degradation of Microcystin-LR  

EPA Science Inventory

This study focuses on the identification of reaction intermediates formed during the photocatalytic degradation of the cyanotoxin microcystin-LR with immobilized TiO2 Tphotocatalysts at neutral pH. To differentiate between impurities already existing in the MC-LR stand...

371

Synthesis of an Advanced Intermediate of the Jatrophane Diterpene Pl-4: A Dibromide Coupling Approach  

PubMed Central

The preparation of an advanced intermediate toward the synthesis of the jatrophane diterpene Pl-4 is described. The key step is a regioselective chelation-controlled lithiation of the (Z)-configured bromide in the corresponding vinyl dibromide precursor. The method outlined within this Article is suitable for the facile access of sterically hindered internal vinyl halides for further coupling reactions. PMID:23895274

2013-01-01

372

C3-C4 Intermediate Species in Alternanthera (Amaranthaceae) 1  

PubMed Central

Two naturally occurring species of the genus Alternanthera, namely A. ficoides and A. tenella, were identified as C3-C4 intermediates based on leaf anatomy, photosynthetic CO2 compensation point (?), O2 response of ?, light intensity response of ?, and the activities of key enzymes of photosynthesis. A. ficoides and A. tenella exhibited a less distinct Kranz-like leaf anatomy with substantial accumulation of starch both in mesophyll and bundle sheath cells. Photosynthetic CO2 compensation points of these two intermediate species at 29°C were much lower than in C3 plants and ranged from 18 to 22 microliters per liter. Although A. ficoides and A. tenella exhibited similar intermediacy in ?, the apparent photorespiratory component of O2 inhibition in A. ficoides is lower than in A. tenella. The ? progressively decreases from 35 microliters per liter at lowest light intensity to 18 microliters per liter at highest light intensity in A. tenella. It was, however, constant in A. ficoides at 20 to 25 microliters per liter between light intensities measured. The rates of net photosynthesis at 21% O2 and 29°C by A. ficoides and A. tenella were 25 to 28 milligrams CO2 per square decimeter per hour which are intermediate between values obtained for Tridax procumbens and A. pungens, C3 and C4 species, respectively. The activities of key enzymes of C4 photosynthesis, phosphoenolpyruvate carboxylase, pyruvate Pi dikinase, NAD malic enzyme, NADP malic enzyme and phosphoenolpyruvate carboxykinase in the two intermediates, A. ficoides and A. tenella are very low or insignificant. Results indicated that the relatively low apparent photorespiratory component in these two species is presumably the basis for the C3-C4 intermediate photosynthesis. Images Fig. 2 PMID:16664634

Rajendrudu, Gedupudi; Prasad, Jasty S. R.; Das, V. S. Rama

1986-01-01

373

Nuclear structure at intermediate energies  

SciTech Connect

The theme that unites the sometimes seemingly disparate experiments undertaken by the Bonner Lab Medium Energy Group is a determination to understand in detail the many facets and manifestations of the strong interaction, that which is now referred to as nonperturbative QCD. Whether we are investigating the question of just what does carry the spin of baryons, or the extent of the validity of the SU(6) wavefunctions for the excited hyperons (as will be measured in their radiative decays in our CEBAF experiment), or questions associated with the formation of a new state of matter predicted by QCD (the subject of our BNL experiments E810, E854, as well as our approved experiment at RHIC), -- all these projects share this common goal. Our other experiments represent different approaches to the same broad undertaking. LAMPF E1097 will provide definitive answers to the question of the spin dependence of the inelastic channel of pion production in the n-p interaction. FNAL E683 may well open a new field of investigation in nuclear physics: that of just how quarks and gluons interact with nuclear matter as they transverse nuclei of different sizes. In most all of the experiments mentioned above, the Bonner Lab Group is playing major leadership roles as well as doing a big fraction of the hard work that such experiments require. We use many of the facilities that are unavailable to the intermediate energy physics community and we use our expertise to design and fabricate the detectors and instrumentation that are required to perform the measurements which we decide to do.

Bonner, B.E.; Mutchler, G.S.

1991-09-30

374

Phase Behavior of Diblock Copolymers in the Intermediate Segregation Regime.  

NASA Astrophysics Data System (ADS)

The phase behavior of several poly(ethylene) - poly(ethyl ethylene) diblock copolymers with volume fractions ranging from 0.35 to 0.51 have been studied in the intermediate segregation regime (\\chi N = 45). Samples with compositions located in the hexagonal cylinder phase or the lamellar phase, far from phase boundaries, show well-ordered structures as observed with TEM. However, samples with compositions near the HEX/LAM boundary do not have long-range orientation, but instead contain a large number of defects which appear to stabilize regions of non-equilibrium morphologies. The HEX/LAM transition is where complex phases, such as the gyroid and hexagonal perforated layers (HPL) phases, have been identified in the weak segregation limit. This work shows the importance of microstructure lattice defects on the phase behavior of diblock copolymers near phase boundaries in the intermediate segregation regime.

Lipic, Paul M.; Bates, Frank S.; Majumdar, Biswaroop

1996-03-01

375

Drug Reactions  

MedlinePLUS

Most of the time, medicines make our lives better. They reduce aches and pains, fight infections, and control problems such as high blood pressure or diabetes. But medicines can also cause unwanted reactions. One problem is ...

376

ESI-MS, DFT and Synthetic Studies on the H2-Mediated Coupling of Acetylene: Insertion of C=X Bonds into Rhodacyclopentadienes and Brønsted Acid Cocatalyzed Hydrogenolysis of Organorhodium Intermediates  

PubMed Central

The catalytic mechanism of the hydrogen-mediated coupling of acetylene to carbonyl compounds and imines has been examined using three techniques: (a) ESI-MS and ESI-CAD-MS analyses, (b) computational modeling, and (c) experiments wherein putative reactive intermediates are diverted to alternative reaction products. ESI-MS analysis of reaction mixtures from the hydrogen-mediated reductive coupling of acetylene to ?-ketoesters or N-benzenesulfonyl aldimines corroborate a catalytic mechanism involving C=X (X = O, NSO2Ph) insertion into a cationic rhodacyclopentadiene obtained by way of acetylene oxidative dimerization with subsequent Brønsted acid cocatalyzed hydrogenolysis of the resulting oxa- or azarhodacycloheptadiene. Hydrogenation of 1,6-diynes in the presence of ?-ketoesters provides analogous coupling products. ESI mass spectrometric analysis again corroborates a catalytic mechanism involving carbonyl insertion into a cationic rhodacyclopentadiene. For all ESI-MS experiments, the structural assignments of ions are supported by multi-stage collisional activated dissociation (CAD) ESI-MS analyses. Further support for the proposed catalytic mechanism derives from experiments aimed at the interception of putative reactive intermediates and their diversion to alternate reaction products. For example, rhodium catalyzed coupling of acetylene to aldehyde in the absence of hydrogen or Brønsted acid cocatalyst provides the corresponding (Z)-butadienyl ketone, which arises from ?-hydride elimination of the proposed oxarhodacycloheptadiene intermediate, as corroborated by isotopic labeling. Additionally, the putative rhodacyclopentadiene intermediate obtained from the oxidative coupling of acetylene is diverted to the product of reductive [2+2+2] cycloaddition when N-p-toluenesulfonyl-dehydroalanine ethyl ester is used as the coupling partner. The mechanism of this transformation also is corroborated by isotopic labeling. Computer model studies based on density functional theory (DFT) support the proposed mechanism and identify Brønsted acid cocatalyst assisted hydrogenolysis to be the most difficult step. The collective studies provide new insight into the reactivity of cationic rhodacyclopentadienes, which should facilitate the design of related rhodium catalyzed C-C couplings. PMID:19845357

Williams, Vanessa M.; Kong, Jong Rock; Ko, Byoung Joon; Mantri, Yogita; Brodbelt, Jennifer S.; Baik, Mu-Hyun; Krische, Michael J.

2009-01-01

377

Enzyme Reactions  

NSDL National Science Digital Library

The enzyme reaction rate activity allows students to simulate the effects of variables such as temperature and pH on the reaction rate of the enzyme catalase. This computer simulation is best used after the students have done a wet lab experiment. The value of the simulation is that it requires the students to interpret and analyze the graphical representation of data and it enables the running of mutiple experiments in a short amount of time.

Maryland Virtual High School

378

First intermediate host of the digenean trematode Proctoeces lintoni (Fellodistomidae) in Chile.  

PubMed

The digenetic trematode, Proctoeces lintoni, is a parasite of the rocky intertidal ecosystems of the Chilean Pacific coastline. Although this species is relatively well known, the first intermediate host has not yet been described. In the present study, we used experimental protocols and field studies to identify the host that harbors the sporocysts and cercariae stages of the parasite. The first intermediate host was shown to be the dominant mussel of the mid-littoral zone, Perumytilus purpuratus. PMID:19545188

Aldana, Marcela; González, Karen; Loot, Geraldine; Pulgar, José; Marquet, Pablo A

2009-12-01

379

Reactions of cyclopropane over zeolite catalysts  

SciTech Connect

The reaction of cyclopropane on NaY, CaNaY, and NaHY zeolites yielded isobutane, 2-methylbutene, propane, isobutene, 2-methylbutane, 2-methylpentane, and heptanes among the minor products, probably as a result of complex oligomerization, isomerization, and cracking processes of a propylene intermediate.

Kiricsi, I.; Hannus, I.; Varca, K.; Fejes, P.

1980-06-01

380

Absorption-Fluctuation Theorem for Nuclear Reactions: Brink-Axel, Incomplete Fusion and All That  

E-print Network

We discuss the connection between absorption, averages and fluctuations in nuclear reactions. The fluctuations in the entrance channel result in the compound nucleus, Hauser-Feshbach, cross section, the fluctuations in the intermediate channels, result in modifications of multistep reaction cross sections, while the fluctuations in the final channel result in hybrid cross sections that can be used to describe incomplete fusion reactions. We discuss the latter in details and comment on the validity of the assumptions used in the develpoment of the Surrogate method. We also discuss the theory of multistep reactions with regards to intermediate state fluctuations and the energy dependence and non-locality of the intermediate channels optical potentials.

M. S. Hussein

2007-12-18

381

Reversible and Irreversible Intermediates during Photoinhibition of Photosystem II: Stable Reduced Q_A Species Promote Chlorophyll Triplet Formation  

Microsoft Academic Search

Photoinhibition of photosynthesis was studied in isolated photosystem II membranes by using chlorophyll fluorescence and electron paramagnetic resonance (EPR) spectroscopy combined with protein analysis. Under anaerobic conditions four sequentially intermediate steps in the photoinhibitory process were identified and characterized. These intermediates show high dark chlorophyll fluorescence (Foi) with typical decay kinetics (fast, semistable, stable, and nondecaying). The fast-decaying state has

Imre Vass; Stenbjorn Styring; Torill Hundal; Antti Koivuniemi; Eva-Mari Aro; Bertil Andersson

1992-01-01

382

Thermochemistry and reaction paths in the oxidation reaction of benzoyl radical: C6H5C•(?O).  

PubMed

Alkyl substituted aromatics are present in fuels and in the environment because they are major intermediates in the oxidation or combustion of gasoline, jet, and other engine fuels. The major reaction pathways for oxidation of this class of molecules is through loss of a benzyl hydrogen atom on the alkyl group via abstraction reactions. One of the major intermediates in the combustion and atmospheric oxidation of the benzyl radicals is benzaldehyde, which rapidly loses the weakly bound aldehydic hydrogen to form a resonance stabilized benzoyl radical (C6H5C(•)?O). A detailed study of the thermochemistry of intermediates and the oxidation reaction paths of the benzoyl radical with dioxygen is presented in this study. Structures and enthalpies of formation for important stable species, intermediate radicals, and transition state structures resulting from the benzoyl radical +O2 association reaction are reported along with reaction paths and barriers. Enthalpies, ?fH298(0), are calculated using ab initio (G3MP2B3) and density functional (DFT at B3LYP/6-311G(d,p)) calculations, group additivity (GA), and literature data. Bond energies on the benzoyl and benzoyl-peroxy systems are also reported and compared to hydrocarbon systems. The reaction of benzoyl with O2 has a number of low energy reaction channels that are not currently considered in either atmospheric chemistry or combustion models. The reaction paths include exothermic, chain branching reactions to a number of unsaturated oxygenated hydrocarbon intermediates along with formation of CO2. The initial reaction of the C6H5C(•)?O radical with O2 forms a chemically activated benzoyl peroxy radical with 37 kcal mol(-1) internal energy; this is significantly more energy than the 21 kcal mol(-1) involved in the benzyl or allyl + O2 systems. This deeper well results in a number of chemical activation reaction paths, leading to highly exothermic reactions to phenoxy radical + CO2 products. PMID:21942384

Sebbar, Nadia; Bozzelli, Joseph W; Bockhorn, Henning

2011-10-27

383

L-serine analogues form Schiff base and quinonoidal intermediates with Escherichia coli tryptophan synthase.  

PubMed

Substrate analogues of L-serine have been found that react with the alpha 2 beta 2 complex of Escherichia coli tryptophan synthase. Upon reaction with alpha 2 beta 2, the analogues glycine, L-histidine, L-alanine, and D-histidine form chemical intermediates derived from reaction with enzyme-bound pyridoxal 5'-phosphate with characteristic UV-visible spectral bands. The spectra of the products of the glycine, L-histidine, and L-alanine reactions with alpha 2 beta 2 contain contributions from the external aldimine, the quinonoid species, and other intermediates along the catalytic pathway. Just as previously reported for the reaction of L-serine with beta 2 [Goldberg, M. E., York, S., & Stryer, L. (1968) Biochemistry 7, 3662-3667], the reactions of glycine, L-histidine, and L-alanine with the beta 2 form of tryptophan synthase yield spectra with no contributions from catalytic intermediates beyond the external aldimine. The kinetics of intermediate formation and comparisons of the time courses for the exchange of alpha-1H for solvent 2H catalyzed by alpha 2 beta 2 or beta 2 were found to be consistent with these assignments. Intermediates further along the tryptophan synthase catalytic pathway are stabilized to a greater degree in the alpha 2 beta 2 complex than in the beta 2 species alone. This observation strongly suggests that the association of alpha and beta subunits to form the native alpha 2 beta 2 species lowers the activation energies for the interconversion of the external aldimine with chemical species further along the catalytic path.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2504276

Houben, K F; Kadima, W; Roy, M; Dunn, M F

1989-05-16

384

N-Oxidation of 4-chloroaniline by prostaglandin synthase. Redox cycling of radical intermediate(s).  

PubMed

4-Chloroaniline undergoes N-oxidation in ram seminal-vesicle microsomal preparations supplemented with arachidonic acid to yield N-(4-chlorophenyl)-hydroxylamine and 1-chloro-4-nitrosobenzene. H2O2 also supports metabolism of the amine substrate to the same organic-solvent-extractable products, suggesting that the hydroperoxidase activity of prostaglandin synthase is responsible for the co-oxidation. Analysis of the reaction mixtures by e.s.r. spectrometry reveals the formation of a radical intermediate bearing the characteristics of a strongly immobilized nitroxide. Arylamine-stimulated O2.- release can be observed when the arachidonic acid-containing incubation media are supplemented with NADPH. Redox cycling of the nitroxide/hydroxylamine couple is presumed to represent the major source of O2.-, but additional mechanisms, such as redox changes of nitro anion radicals resulting from potential further metabolism of 1-chloro-4-nitrosobenzene, cannot be excluded. The concerted action of carrier-bound nitroxides and O2.- in initiating damage of cellular macromolecules is discussed. PMID:2985047

Golly, I; Hlavica, P

1985-03-15

385

N-Oxidation of 4-chloroaniline by prostaglandin synthase. Redox cycling of radical intermediate(s).  

PubMed Central

4-Chloroaniline undergoes N-oxidation in ram seminal-vesicle microsomal preparations supplemented with arachidonic acid to yield N-(4-chlorophenyl)-hydroxylamine and 1-chloro-4-nitrosobenzene. H2O2 also supports metabolism of the amine substrate to the same organic-solvent-extractable products, suggesting that the hydroperoxidase activity of prostaglandin synthase is responsible for the co-oxidation. Analysis of the reaction mixtures by e.s.r. spectrometry reveals the formation of a radical intermediate bearing the characteristics of a strongly immobilized nitroxide. Arylamine-stimulated O2.- release can be observed when the arachidonic acid-containing incubation media are supplemented with NADPH. Redox cycling of the nitroxide/hydroxylamine couple is presumed to represent the major source of O2.-, but additional mechanisms, such as redox changes of nitro anion radicals resulting from potential further metabolism of 1-chloro-4-nitrosobenzene, cannot be excluded. The concerted action of carrier-bound nitroxides and O2.- in initiating damage of cellular macromolecules is discussed. PMID:2985047

Golly, I; Hlavica, P

1985-01-01

386

Pharmacogenomics of adverse drug reactions  

PubMed Central

Considerable progress has been made in identifying genetic risk factors for idiosyncratic adverse drug reactions in the past 30 years. These reactions can affect various tissues and organs, including liver, skin, muscle and heart, in a drug-dependent manner. Using both candidate gene and genome-wide association studies, various genes that make contributions of varying extents to each of these forms of reactions have been identified. Many of the associations identified for reactions affecting the liver and skin involve human leukocyte antigen (HLA) genes and for reactions relating to the drugs abacavir and carbamazepine, HLA genotyping is now in routine use prior to drug prescription. Other HLA associations are not sufficiently specific for translation but are still of interest in relation to underlying mechanisms for the reactions. Progress on non-HLA genes affecting adverse drug reactions has been less, but some important associations, such as those of SLCO1B1 and statin myopathy, KCNE1 and drug-induced QT prolongation and NAT2 and isoniazid-induced liver injury, are considered. Future prospects for identification of additional genetic risk factors for the various adverse drug reactions are discussed. PMID:23360680

2013-01-01

387

[Skin reactions to tattoo ink].  

PubMed

Ritual and artistic tattoos rely on the use of numerous pigments which are not all entirely inert once placed in the dermis. The compositions of some tattoo inks are identified. However, new but less well identified compounds appear on the market. Allergic reactions can be present under different aspects. They may correspond to allergic contact dermatitis or to photodermatitis. Other reactions include allergic hypersensitivity reactions as well as lichenoid, granulomatous or pseudolymphoma reactions. Pulsed light and laser are typically used for regular tattoo removal. These procedures are not indicated in inflamed tattoos. Indeed, the pigment dispersed during photolysis may perpetuate the reaction. Pseudotattoos due to the stratum corneum staining are frequently responsible for photoeczema. PMID:21942077

Piérard-Franchimont, C; Hermanns, J-F; Piérard, G E

2011-01-01

388

List of HIPAA Identifiers  

Cancer.gov

List of HIPAA Identifiers ER-0001-F1 VER. 1.0.0 Effective Date: 9/14/2011 Page 1 of 1 The following is a list of the HIPAA Identifiers referenced in the federal regulations: Names; All geographical subdivisions smaller than a state, including

389

Identifying and Classifying Rocks  

NSDL National Science Digital Library

How do we identify and classify rocks? In this lesson, we are going to learn about different ways that we classify and identify rocks! There are three types of rocks. Sedimentary Metamorphic Igneous As we are learning about the three types of rocks, print out this chart and use it to write down what you learn about each type of ...

Owen, Elisabeth

2010-11-03

390

Modulation of proton-coupled electron-transfer reactions in azurin : : quantum yield and pKa analyses.  

E-print Network

??Long-range electron transfer (ET) reactions are central to many biochemical processes. To accomplish these long-range reactions, biomolecules often utilize multi-step ET processes via redox-active intermediates… (more)

Larson, Bethany Corrine

2013-01-01

391

Taxol reactions.  

PubMed

Paclitaxel (Taxol) a taxane antineoplastic agent causing irreversible microtubule aggregation with activity against breast, ovarian, lung, head and neck, bladder, testicular, esophageal, endometrial and other less common tumors was derived from the bark of the Pacific yew (Taxus brevifolia). Phase I trials conducted in the late 1980s were almost halted because of the high frequency of hypersensitivity-like reactions. Respiratory distress (dyspnea and/or bronchospasm), hypotension, and angioedema were the major manifestations, but flushing, urticaria, chest, abdomen, and extremity pains were described also. Reactions occurred on first exposure in the majority of cases raising etiologic questions. The vehicle for paclitaxel Cremophor EL (polyoxyethylated castor oil in 50% ethanol) was strongly suspect as a direct (non-immunoglobulin E dependent) histamine releaser. Premedication regimens and longer infusion times lowered the incidence of reactivity allowing phase II and III trials to progress through the early 1990s. The mechanism(s) underlying paclitaxel hypersensitivity-like reactions is still unknown, and clinical data on probable complement and mast cell activation are lacking. The original clinical trial protocols for paclitaxel required discontinuation of therapy for patients who experienced hypersensitivity-like reactions. Here, we review the current etiologic knowledge of these reactions and describe our clinical approach to allow completion of chemotherapy with this powerful plant-derived agent. PMID:12125509

Price, Kursteen S; Castells, Mariana C

2002-01-01

392

Using Chemical Change to Identify an Unknown  

NSDL National Science Digital Library

In this activity, learners will develop a method to test five similar-looking powders (baking soda, baking powder, cream of tartar, detergent, and cornstarch) with four test liquids (water, vinegar, iodine solution, red cabbage solution). They will use the characteristic set of reactions for each powder to identify an unknown powder, which is one of the five powders they have tested.

Kessler, James H.; Galvan, Patricia M.

2007-01-01

393

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations  

Microsoft Academic Search

BACKGROUND: Genetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321

Naama M Kopelman; Lewi Stone; Chaolong Wang; Dov Gefel; Marcus W Feldman; Jossi Hillel; Noah A Rosenberg

2009-01-01

394

QM/MM studies of mono-zinc ?-lactamase CphA suggest that the crystal structure of an enzyme-intermediate complex represents a minor pathway  

PubMed Central

QM/MM studies of the hydrolysis of a ?-lactam antibiotic molecule (biapenem) catalyzed by a mono-zinc ?-lactamase (CphA) reveal the complete reaction mechanism and show that an experimentally determined enzyme-intermediate complex is a stable intermediate or product in a minor pathway. PMID:21138257

Wu, Shanshan; Xu, Dingguo; Guo, Hua

2010-01-01

395

Cue usage in volleyball: a time course comparison of elite, intermediate and novice female players.  

PubMed

This study compared visual search strategies in adult female volleyball players of three levels. Video clips of the attack of the opponent team were presented on a large screen and participants reacted to the final pass before the spike. Reaction time, response accuracy and eye movement patterns were measured. Elite players had the highest response accuracy (97.50 ± 3.5%) compared to the intermediate (91.50 ± 4.7%) and novice players (83.50 ± 17.6%; p<0.05). Novices had a remarkably high range of reaction time but no significant differences were found in comparison to the reaction time of elite and intermediate players. In general, the three groups showed similar gaze behaviour with the apparent use of visual pivots at moments of reception and final pass. This confirms the holistic model of image perception for volleyball and suggests that expert players extract more information from parafoveal regions. PMID:25609887

Vansteenkiste, P; Vaeyens, R; Zeuwts, L; Philippaerts, R; Lenoir, M

2014-12-01

396

CUE USAGE IN VOLLEYBALL: A TIME COURSE COMPARISON OF ELITE, INTERMEDIATE AND NOVICE FEMALE PLAYERS  

PubMed Central

This study compared visual search strategies in adult female volleyball players of three levels. Video clips of the attack of the opponent team were presented on a large screen and participants reacted to the final pass before the spike. Reaction time, response accuracy and eye movement patterns were measured. Elite players had the highest response accuracy (97.50 ± 3.5%) compared to the intermediate (91.50 ± 4.7%) and novice players (83.50 ± 17.6%; p<0.05). Novices had a remarkably high range of reaction time but no significant differences were found in comparison to the reaction time of elite and intermediate players. In general, the three groups showed similar gaze behaviour with the apparent use of visual pivots at moments of reception and final pass. This confirms the holistic model of image perception for volleyball and suggests that expert players extract more information from parafoveal regions. PMID:25609887

Vaeyens, R; Zeuwts, L; Philippaerts, R; Lenoir, M

2014-01-01

397

MICROWAVE-FACILITATED MULTICOMPONENT REACTIONS UNDER SOLVENT-FREE CONDITIONS  

EPA Science Inventory

The application of microwave-expedited solvent-free synthetic protocols in multi-component (MCC) reactions will be exemplified by several condensation and cyclization reactions including the rapid one-pot assembly of heterocyclic compounds from in situ generated intermediates. R...

398

Ferrocyanide Safety Project Dynamic X-Ray Diffraction studies of sodium nickel ferrocyanide reactions with equimolar nitrate/nitrite salts  

SciTech Connect

Dynamic X-ray Diffraction (DXRD) has been to used to identify and quantify the solid state reactions that take place between sodium nickel ferrocyanide, Na{sub 2}NiFe(CN){sub 6}, and equimolar concentrations of sodium nitrate/nitrite, reactions of interest to the continued environmental safety of several large underground waste storage tanks at the Hanford site in eastern Washington. The results are supportive of previous work, which indicated that endothermic dehydration and melting of the nitrates take place before the occurrence of exothermic reactions that being about 300{degrees}C. The DXRD results show that a major reaction set at these temperatures is the occurrence of a series reaction that produces sodium cyanate, NaCNO, as an intermediate in a mildly exothermic first step. In the presence of gaseous oxygen, NaCNO subsequently reacts exothermally and at a faster rate to form metal oxides. Measurements of the rate of this reaction are used to estimate the heat release. Comparisons of this estimated heat release rate with heat transfer rates from a hypothetical ``hot spot`` show that, even in a worst-case scenario, the heat transfer rates are approximately eight times higher than the rate of energy release from the exothermic reactions.

Dodds, J.N. [Washington State Univ., Pullman, WA (United States). Dept. of Chemical Engineering]|[UNOCAL, Brea, CA (United States). Hartley Research Center

1994-07-01

399

Trans-SNARE pairing can precede a hemifusion intermediate in intracellular membrane fusion.  

PubMed

The question concerning whether all membranes fuse according to the same mechanism has yet to be answered satisfactorily. During fusion of model membranes or viruses, membranes dock, the outer membrane leaflets mix (termed hemifusion), and finally the fusion pore opens and the contents mix. Viral fusion proteins consist of a membrane-disturbing 'fusion peptide' and a helical bundle that pin the membranes together. Although SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complexes form helical bundles with similar topology, it is unknown whether SNARE-dependent fusion events on intracellular membranes proceed through a hemifusion state. Here we identify the first hemifusion state for SNARE-dependent fusion of native membranes, and place it into a sequence of molecular events: formation of helical bundles by SNAREs precedes hemifusion; further progression to pore opening requires additional peptides. Thus, SNARE-dependent fusion may proceed along the same pathway as viral fusion: both use a docking mechanism via helical bundles and additional peptides to destabilize the membrane and efficiently induce lipid mixing. Our results suggest that a common lipidic intermediate may underlie all fusion reactions of lipid bilayers. PMID:15924133

Reese, Christoph; Heise, Felix; Mayer, Andreas

2005-07-21

400

A portable and inexpensive method for quantifying ambient intermediate volatility organic compounds  

NASA Astrophysics Data System (ADS)

Volatile organic compounds (VOCs) and intermediate volatility VOCs (IVOCs) are gas-phase organic compounds which may participate in chemical reactions affecting air quality and climate. The development of an inexpensive, field-portable quantification method for higher molecular weight VOCs and IVOCs utilizing commercially available components could be used as a tool to survey aerosol precursors or identify and monitor air quality in various communities. We characterized the performance characteristics for the HayeSep-Q adsorbent with a representative selection of anthropogenic and biogenic VOC standards and optimized experimental conditions and procedures for field collections followed by laboratory analysis. All VOCs were analyzed using gas chromatography coupled with mass spectrometry. Precision (average 22%) and accuracy were reasonable and the limit of detection ranged from 10 to 80 pmol/mol (ppt) for the studied compounds. The method was employed at the Los Angeles site during the CalNex campaign in summer 2010 and ambient mixing ratios agreed well (slope 0.69-1.06, R2 0.67-0.71) with measurements made using an in-situ GC-MS - a distinctly different sampling and quantification method. This new technique can be applied to quantify ambient biogenic and anthropogenic C8-C15 VOCs and IVOCs.

Bouvier-Brown, Nicole C.; Carrasco, Erica; Karz, James; Chang, Kylee; Nguyen, Theodore; Ruiz, Daniel; Okonta, Vivian; Gilman, Jessica B.; Kuster, William C.; de Gouw, Joost A.

2014-09-01

401

Polar reactions of acyclic conjugated bisallenes  

PubMed Central

Summary The chemical behaviour of various alkyl-substituted, acyclic conjugated bisallenes in reactions involving polar intermediates and/or transition states has been investigated on a broad scale for the first time. The reactions studied include lithiation, reaction of the thus formed organolithium salts with various electrophiles (among others, allyl bromide, DMF and acetone), oxidation to cyclopentenones and epoxides, hydrohalogenation (HCl, HBr addition), halogenation (Br2 and I2 addition), and [2 + 2] cycloaddition with chlorosulfonyl isocyanate. The resulting adducts were fully characterized by spectroscopic and analytical methods; they constitute interesting substrates for further organic transformations. PMID:23400309

Stamm, Reiner

2013-01-01

402

Bragg fibres with an intermediate layer  

SciTech Connect

This paper examines the effect of an intermediate layer between the core and periodic cladding of a Bragg fibre on its optical properties. It is shown that any TE{sub 0{kappa}} mode of a standard Bragg fibre can be transformed into the fundamental mode of a Bragg fibre with an intermediate layer by adjusting the thickness of the first cladding layer. Varying the thickness of the intermediate layer, one can tune the mode composition of the transmitted light in a periodic manner. The periodic variation of the optical loss with the thickness of the intermediate layer is due to resonances and antiresonances in this layer. The resonances correspond to two-mode light propagation through the fibre, whereas the antiresonances, to single-mode light propagation.

Kulchin, Yurii N; Zinin, Yu A; Nagornyi, I G

2012-03-31

403

Types and Intermediate Representations Michael Hicks  

E-print Network

al. 1992], and the BEAM (Bogdans's Erlang Abstract Machine) [Hausman 1994]. For SML, I look, highlighting the use types and intermedi­ ate representation(s), and to what advantages and disadvantages. I

Hicks, Michael

404

Intermediate Level Mechanisms Supporting Face Perception.  

E-print Network

??I propose that the intermediate neural mechanisms involved in face processing may be better understood by studying concentric form-from-structure integration. This dissertation involves behavioral adaptation… (more)

Feczko, Eric J.

2013-01-01

405

Intermediate/Advanced Research Design and Statistics  

NASA Technical Reports Server (NTRS)

The purpose of this module is To provide Institutional Researchers (IRs) with an understanding of the principles of advanced research design and the intermediate/advanced statistical procedures consistent with such designs

Ploutz-Snyder, Robert

2009-01-01

406

Davidson Scholars Seminar Intermediate KenKen  

E-print Network

Davidson Scholars Seminar Intermediate KenKen 1 Introduction Welcome to a week of puzzling. I hope to http://math.uncc.edu/~hbreiter/DavidsonInstitute/KenKen.htm You'll also enjoy two websites with lots

Reiter, Harold

407

Intermediate-Frequency-to-Video-Band Converter  

NASA Technical Reports Server (NTRS)

Analog and digital circuits combined to frequency-convert from intermediate frequencies directly to video-band frequencies to meet stringent requirements. IF-to-video-band converter operates on principle of signal-band cancellation in phase-quadrature circuits. Downconverts intermediate frequencies directly to video-band frequencies to near-zero frequency with good image-band rejection and low phase variation within passband.

Ham, N. C.; Chavez, V. M.; Chen, V. S.; Sato, T.

1986-01-01

408

Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids  

PubMed Central

Isoprenoids constitute the largest class of natural products with greater than 55,000 identified members. They play essential roles in maintaining proper cellular function leading to maintenance of human health, plant defense mechanisms against predators, and are often exploited for their beneficial properties in the pharmaceutical and nutraceutical industries. Most impressively, all known isoprenoids are derived from one of two C5-precursors, isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). In order to study the enzyme transformations leading to the extensive structural diversity found within this class of compounds there must be access to the substrates. Sometimes, intermediates within a biological pathway can be isolated and used directly to study enzyme/pathway function. However, the primary route to most of the isoprenoid intermediates is through chemical catalysis. As such, this review provides the first exhaustive examination of synthetic routes to isoprenoid and isoprenoid precursors with particular emphasis on the syntheses of intermediates found as part of the 2C-methylerythritol 4-phosphate (MEP) pathway. In addition, representative syntheses are presented for the monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes (C30) and tetraterpenes (C40). Finally, in some instances, the synthetic routes to substrate analogs found both within the MEP pathway and downstream isoprenoids are examined. PMID:25009443

Jarchow-Choy, Sarah K; Koppisch, Andrew T; Fox, David T

2014-01-01

409

Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids.  

PubMed

Isoprenoids constitute the largest class of natural products with greater than 55,000 identified members. They play essential roles in maintaining proper cellular function leading to maintenance of human health, plant defense mechanisms against predators, and are often exploited for their beneficial properties in the pharmaceutical and nutraceutical industries. Most impressively, all known isoprenoids are derived from one of two C5-precursors, isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). In order to study the enzyme transformations leading to the extensive structural diversity found within this class of compounds there must be access to the substrates. Sometimes, intermediates within a biological pathway can be isolated and used directly to study enzyme/pathway function. However, the primary route to most of the isoprenoid intermediates is through chemical catalysis. As such, this review provides the first exhaustive examination of synthetic routes to isoprenoid and isoprenoid precursors with particular emphasis on the syntheses of intermediates found as part of the 2C-methylerythritol 4-phosphate (MEP) pathway. In addition, representative syntheses are presented for the monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes (C30) and tetraterpenes (C40). Finally, in some instances, the synthetic routes to substrate analogs found both within the MEP pathway and downstream isoprenoids are examined. PMID:25009443

Jarchow-Choy, Sarah K; Koppisch, Andrew T; Fox, David T

2014-04-01

410

A reaction path study of the catalysis and inhibition of the Bacillus anthracis CapD ?-glutamyl transpeptidase.  

PubMed

The CapD enzyme of Bacillus anthracis is a ?-glutamyl transpeptidase from the N-terminal nucleophile hydrolase superfamily that covalently anchors the poly-?-D-glutamic acid (pDGA) capsule to the peptidoglycan. The capsule hinders phagocytosis of B. anthracis by host cells and is essential for virulence. The role CapD plays in capsule anchoring and remodeling makes the enzyme a promising target for anthrax medical countermeasures. Although the structure of CapD is known, and a covalent inhibitor, capsidin, has been identified, the mechanisms of CapD catalysis and inhibition are poorly understood. Here, we used a computational approach to map out the reaction steps involved in CapD catalysis and inhibition. We found that the rate-limiting step of either CapD catalysis or inhibition was a concerted asynchronous formation of the tetrahedral intermediate with a barrier of 22-23 kcal/mol. However, the mechanisms of these reactions differed for the two amides. The formation of the tetrahedral intermediate with pDGA was substrate-assisted with two proton transfers. In contrast, capsidin formed the tetrahedral intermediate in a conventional way with one proton transfer. Interestingly, capsidin coupled a conformational change in the catalytic residue of the tetrahedral intermediate to stretching of the scissile amide bond. Furthermore, capsidin took advantage of iminol-amide tautomerism of its diacetamide moiety to convert the tetrahedral intermediate to the acetylated CapD. As evidence of the promiscuous nature of CapD, the enzyme cleaved the amide bond of capsidin by attacking it on the opposite side compared to pDGA. PMID:25334088

Khavrutskii, Ilja V; Legler, Patricia M; Friedlander, Arthur M; Wallqvist, Anders

2014-11-11

411

Novel Approaches for the Accumulation of Oxygenated Intermediates to Multi-Millimolar Concentrations  

PubMed Central

Metalloenzymes that utilize molecular oxygen as a co-substrate catalyze a wide variety of chemically difficult oxidation reactions. Significant insight into the reaction mechanisms of these enzymes can be obtained by the application of a combination of rapid kinetic and spectroscopic methods to the direct structural characterization of intermediate states. A key limitation of this approach is the low aqueous solubility (< 2 mM) of the co-substrate, O2, which undergoes further dilution (typically by one-third or one-half) upon initiation of reactions by rapid-mixing. This situation imposes a practical upper limit on [O2] (and therefore on the concentration of reactive intermediate(s) that can be rapidly accumulated) of ?1-1.3 mM in such experiments as they are routinely carried out. However, many spectroscopic methods benefit from or require significantly greater concentrations of the species to be studied. To overcome this problem, we have recently developed two new approaches for the preparation of samples of oxygenated intermediates: (1) direct oxygenation of reduced metalloenzymes using gaseous O2 and (2) the in situ generation of O2 from chlorite catalyzed by the enzyme chlorite dismutase (Cld). Whereas the former method is applicable only to intermediates with half lives of several minutes, owing to the sluggishness of transport of O2 across the gas-liquid interface, the latter approach has been successfully applied to trap several intermediates at high concentration and purity by the freeze-quench method. The in situ approach permits generation of a pulse of at least 5 mM O2 within ? 1 ms and accumulation of O2 to effective concentrations of up to ? 11 mM (i.e. ? 10-fold greater than by the conventional approach). The use of these new techniques for studies of oxygenases and oxidases is discussed. PMID:24368870

Krebs, Carsten; Dassama, Laura M. K.; Matthews, Megan L.; Jiang, Wei; Price, John C.; Korboukh, Victoria; Li, Ning; Bollinger, J. Martin

2012-01-01

412

Identifying Extreme Exposure Values  

Cancer.gov

There are various perspectives on whether to exclude potentially unlikely exposure values. If the researcher chooses to do so, several approaches exist for identifying extreme values. We examined the plausibility of the reported frequencies for each food item in the NHANES 2009-10 DSQ and chose to exclude extreme values using a method that identifies them based on the actual distribution of the sample, but also minimizes the number of values excluded.

413

Identifying Conserved Discriminative Motifs  

Microsoft Academic Search

The identification of regulatory motifs underlying gene expression is a challenging problem, particularly in eukaryotes. An\\u000a algorithm to identify statistically significant discriminative motifs that distinguish between gene expression clusters is\\u000a presented. The predictive power of the identified motifs is assessed with a supervised Naïve Bayes classifier. An information-theoretic\\u000a feature selection criterion helps find the most informative motifs. Results on benchmark

Jyotsna Kasturi; Raj Acharya; Ross Hardison

2008-01-01

414

Reaction Time  

NSDL National Science Digital Library

In this activity, learners conduct an experiment to test how fast they can react. Learners try to catch a piece of paper with a ruler printed on it (or a ruler) as quickly as they can. Learners collect data and compare the reaction times of friends and family.

Boston, Wgbh

2003-01-01

415

Reaction Time  

NSDL National Science Digital Library

This lab is not an inquiry activity. There are some students whose reaction times will not allow them to catch a 12 inch ruler. They may use a dowel, stick, strip of cardboard, etc. Although the students are led to believe that the point of the lab is to

Horton, Michael

2009-05-30

416

Mapping the ? Integrase bridges in the nucleoprotein Holliday junction intermediates of viral integrative and excisive recombination.  

PubMed

The site-specific recombinase encoded by bacteriophage ? [? Integrase (Int)] is responsible for integrating and excising the viral chromosome into and out of the chromosome of its Escherichia coli host. In contrast to the other well-studied and highly exploited tyrosine recombinase family members, such as Cre and Flp, Int carries out a reaction that is highly directional, tightly regulated, and depends on an ensemble of accessory DNA bending proteins acting on 240 bp of DNA encoding 16 protein binding sites. This additional complexity enables two pathways, integrative and excisive recombination, whose opposite, and effectively irreversible, directions are dictated by different physiological and environmental signals. Int recombinase is a heterobivalent DNA binding protein that binds via its small amino-terminal domain to high affinity arm-type DNA sites and via its large, compound carboxyl-terminal domain to core-type DNA sites, where DNA cleavage and ligation are executed. Each of the four Int protomers, within a multiprotein 400-kDa recombinogenic complex, is thought to bind and, with the aid of DNA bending proteins, bridge one arm- and one core-type DNA site. Despite a wealth of genetic, biochemical, and functional information generated by many laboratories over the last 50 y, it has not been possible to decipher the patterns of Int bridges, an essential step in understanding the architectures responsible for regulated directionality of recombination. We used site-directed chemical cross-linking of Int in trapped Holliday junction recombination intermediates and recombination reactions with chimeric recombinases, to identify the unique and monogamous patterns of Int bridges for integrative and excisive recombination. PMID:25114247

Tong, Wenjun; Warren, David; Seah, Nicole E; Laxmikanthan, Gurunathan; Van Duyne, Gregory D; Landy, Arthur

2014-08-26

417

42 CFR 438.702 - Types of intermediate sanctions.  

Code of Federal Regulations, 2010 CFR

...2010-10-01 false Types of intermediate sanctions. 438.702 Section 438.702 Public...MEDICAL ASSISTANCE PROGRAMS MANAGED CARE Sanctions § 438.702 Types of intermediate sanctions. (a) The types of intermediate...

2010-10-01

418

Roaming dynamics in radical addition-elimination reactions  

NASA Astrophysics Data System (ADS)

Radical addition-elimination reactions are a major pathway for transformation of unsaturated hydrocarbons. In the gas phase, these reactions involve formation of a transient strongly bound intermediate. However, the detailed mechanism and dynamics for these reactions remain unclear. Here we show, for reaction of chlorine atoms with butenes, that the Cl addition-HCl elimination pathway occurs from an abstraction-like Cl-H-C geometry rather than a conventional three-centre or four-centre transition state. Furthermore, access to this geometry is attained by roaming excursions of the Cl atom from the initially formed adduct. In effect, the alkene ? cloud serves to capture the Cl atom and hold it, allowing many subsequent opportunities for the energized intermediate to find a suitable approach to the abstraction geometry. These bimolecular roaming reactions are closely related to the roaming radical dynamics recently discovered to play an important role in unimolecular reactions.

Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G.; Mebel, Alexander M.

2014-06-01

419

Roaming dynamics in radical addition-elimination reactions.  

PubMed

Radical addition-elimination reactions are a major pathway for transformation of unsaturated hydrocarbons. In the gas phase, these reactions involve formation of a transient strongly bound intermediate. However, the detailed mechanism and dynamics for these reactions remain unclear. Here we show, for reaction of chlorine atoms with butenes, that the Cl addition-HCl elimination pathway occurs from an abstraction-like Cl-H-C geometry rather than a conventional three-centre or four-centre transition state. Furthermore, access to this geometry is attained by roaming excursions of the Cl atom from the initially formed adduct. In effect, the alkene ? cloud serves to capture the Cl atom and hold it, allowing many subsequent opportunities for the energized intermediate to find a suitable approach to the abstraction geometry. These bimolecular roaming reactions are closely related to the roaming radical dynamics recently discovered to play an important role in unimolecular reactions. PMID:24905903

Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G; Mebel, Alexander M

2014-01-01

420

Biotin synthase from Escherichia coli: isolation of an enzyme-generated intermediate and stoichiometry of S-adenosylmethionine use.  

PubMed

A cell-free extract from Escherichia coli containing an E. coli biotin synthase that was expressed to approx. 1% of soluble cell protein by cloning the E. coli bioB gene was used to investigate the biotin synthase reaction. The pH optimum was between 8 and 8.5, and the reaction velocity was dependent on the concentrations of dethiobiotin, cysteine, S-adenosylmethionine and asparagine. The catalytic-centre activity of the enzyme in vitro was estimated to be 0.95 h-1, and each molecule of enzyme turned over less than one molecule of dethiobiotin, i.e. the enzyme was not acting catalytically. HPLC analysis of reaction mixtures revealed the presence of a compound with the characteristics of an intermediate: (1) it was labelled with 14C, and therefore derived from the [14C]dethiobiotin substrate; (2) it was present only in reaction mixtures containing biotin synthase; (3) it was not derived from [14C]biotin; (4) 35S from [35S]cystine was incorporated into the intermediate during the reaction; (5) its synthesis was dependent on the presence of S-adenosylmethionine, and was decreased when free cysteine was omitted from the reaction; (6) it could be isolated from the reaction mixture by chromatography and then re-introduced into an assay as the substrate, whereupon it was converted to biotin; (7) this conversion to biotin was S-adenosylmethionine-dependent. During the reaction S-adenosylmethionine was cleaved to methionine and presumably 5'-deoxyadenosine. Observation of the intermediate allowed us to perform experiments to determine the stoichiometry of S-adenosylmethionine use. We propose that two molecules of S-adenosylmethionine are used to synthesize one molecule of biotin, i.e. one from dethiobiotin to the intermediate, and a second from the intermediate to biotin. PMID:9494071

Shaw, N M; Birch, O M; Tinschert, A; Venetz, V; Dietrich, R; Savoy, L A

1998-03-15

421

Biotin synthase from Escherichia coli: isolation of an enzyme-generated intermediate and stoichiometry of S-adenosylmethionine use.  

PubMed Central

A cell-free extract from Escherichia coli containing an E. coli biotin synthase that was expressed to approx. 1% of soluble cell protein by cloning the E. coli bioB gene was used to investigate the biotin synthase reaction. The pH optimum was between 8 and 8.5, and the reaction velocity was dependent on the concentrations of dethiobiotin, cysteine, S-adenosylmethionine and asparagine. The catalytic-centre activity of the enzyme in vitro was estimated to be 0.95 h-1, and each molecule of enzyme turned over less than one molecule of dethiobiotin, i.e. the enzyme was not acting catalytically. HPLC analysis of reaction mixtures revealed the presence of a compound with the characteristics of an intermediate: (1) it was labelled with 14C, and therefore derived from the [14C]dethiobiotin substrate; (2) it was present only in reaction mixtures containing biotin synthase; (3) it was not derived from [14C]biotin; (4) 35S from [35S]cystine was incorporated into the intermediate during the reaction; (5) its synthesis was dependent on the presence of S-adenosylmethionine, and was decreased when free cysteine was omitted from the reaction; (6) it could be isolated from the reaction mixture by chromatography and then re-introduced into an assay as the substrate, whereupon it was converted to biotin; (7) this conversion to biotin was S-adenosylmethionine-dependent. During the reaction S-adenosylmethionine was cleaved to methionine and presumably 5'-deoxyadenosine. Observation of the intermediate allowed us to perform experiments to determine the stoichiometry of S-adenosylmethionine use. We propose that two molecules of S-adenosylmethionine are used to synthesize one molecule of biotin, i.e. one from dethiobiotin to the intermediate, and a second from the intermediate to biotin. PMID:9494071

Shaw, N M; Birch, O M; Tinschert, A; Venetz, V; Dietrich, R; Savoy, L A

1998-01-01

422

Cutaneous allergic reactions to tattoo ink  

Microsoft Academic Search

Summary Tattoo artists use many compounds to create tattoo pigment and several allergic reactions can occur as a result of these additives. The compositions of many inks have been identified; however, as new mixtures are created it becomes difficult to identify the specific ingredients in a particular ink. Allergic reactions to a particular pigment can manifest in several ways including

Ravneet Ruby Kaur; William Kirby; Howard Maibach

2009-01-01

423

Arenium ions are not obligatory intermediates in electrophilic aromatic substitution  

PubMed Central

Our computational and experimental investigation of the reaction of anisole with Cl2 in nonpolar CCl4 solution challenges two fundamental tenets of the traditional SEAr (arenium ion) mechanism of aromatic electrophilic substitution. Instead of this direct substitution process, the alternative addition–elimination (AE) pathway is favored energetically. This AE mechanism rationalizes the preferred ortho and para substitution orientation of anisole easily. Moreover, neither the SEAr nor the AE mechanisms involve the formation of a ?-complex (Wheland-type) intermediate in the rate-controlling stage. Contrary to the conventional interpretations, the substitution (SEAr) mechanism proceeds concertedly via a single transition state. Experimental NMR investigations of the anisole chlorination reaction course at various temperatures reveal the formation of tetrachloro addition by-products and thus support the computed addition–elimination mechanism of anisole chlorination in nonpolar media. The important autocatalytic effect of the HCl reaction product was confirmed by spectroscopic (UV-visible) investigations and by HCl-augmented computational modeling. PMID:24972792

Galabov, Boris; Koleva, Gergana; Simova, Svetlana; Hadjieva, Boriana; Schaefer, Henry F.; Schleyer, Paul von Ragué

2014-01-01

424

MCNP6 fragmentation of light nuclei at intermediate energies  

E-print Network

Fragmentation reactions induced on light target nuclei by protons and light nuclei of energies around 1 GeV/nucleon and below are studied with the latest Los Alamos Monte Carlo transport code MCNP6 and with its cascade-exciton model (CEM) and Los Alamos version of the quark-gluon string model (LAQGSM) event generators, version 03.03, used as stand-alone codes. Such reactions are involved in different applications, like cosmic-ray-induced single event upsets (SEU's), radiation protection, and cancer therapy with proton and ion beams, among others; therefore, it is important that MCNP6 simulates them as well as possible. CEM and LAQGSM assume that intermediate-energy fragmentation reactions on light nuclei occur generally in two stages. The first stage is the intranuclear cascade (INC), followed by the second, Fermi breakup disintegration of light excited residual nuclei produced after INC. Both CEM and LAQGSM account also for coalescence of light fragments (complex particles) up to He4 from energetic nucleons ...

Mashnik, Stepan G

2014-01-01

425

X-ray structure and reactivity of (Ru(bpy)/sub 2/(CO)H)PF/sub 6/ x 1/2 C/sub 3/H/sub 6/O (bpy = 2,2'-bipyridyl), a possible intermediate in the water-gas shift reaction catalyzed by ruthenium polypyridyl complexes  

SciTech Connect

The structure of (Ru(C/sub 10/H/sub 8/N/sub 2/)/sub 2/(CO)H)PF/sub 6/ x 1/2 C/sub 3/H/sub 6/O is reported. The compound crystallizes in the monoclinic C2/c space group with unit cell parameters a = 26.680 (4) A, b = 7.005 (3) A, c = 25.936 (2) A, and ..beta.. = 93.96 (2)/sup 0/ (V = 4836.04 A/sup 3/, Z = 8). The cationic species has a cis geometry for CO and H. The ruthenium-hydride and ruthenium-carbon distances are 1.68 (4) and 1.804 (6) A, respectively. The average ruthenium-nitrogen distance is 2.109 A. In acidic solution the title compound acts as a hydride donor to produce dihydrogen gas in a pseudo-first-order reaction; the second-order rate constant for this reaction is 0.105 -/+ 0.01 dm/sup 3/ mol/sup -1/ s/sup -1/ at 303 K with an activation energy 56 -/+ 2 kJ mol/sup -1/. A value of -100 -/+ 8 J mol/sup -1/ deg/sup -1/ has been obtained for the entropy of activation. The consequences of these results for the possible reaction mechanism of the homogeneous water-gas shift reaction catalyzed by (Ru(bpy)/sub 2/(CO)Cl)/sup +/ are discussed. 15 references, 4 figures, 6 tables.

Haasnoot, J.G.; Hinrichs, W.; Weir, O.; Vos, J.G.

1986-11-05

426

Global reaction route mapping of isomerization pathways of exotic C{sub 6}H molecular species  

SciTech Connect

C{sub 6}H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C{sub 6}H is explored to search isomers of C{sub 6}H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C{sub 6}H. The reaction route search is performed through global reaction route mapping method, which utilizes an uphill walking technique based on an anharmonic downward distortion following approach to search intermediates and transition states. The computations performed at the CASSCF/aug-cc-pVTZ, CCSD(T)/6-311++G(d,p)//DFT/B3LYP/6-311++G(d,p), and DFT/B3LYP/aug-cc-pVTZ levels of the theory identified 14 isomers (including 8 new isomeric forms of C{sub 6}H) and 28 transition states. Most of the identified isomers are found to have significant multireference character. The kinetic stability and natural bond orbital analysis of the identified isomers is also investigated. The isomeric forms are further characterized using spectral analysis involving rotational constants, vibrational frequencies, and Raman scattering activities as well as analyzing the effect of isotopic substitution of hydrogen on the spectral features. This study proposes that the linear-C{sub 6}H can readily isomerize to a six-member ring isomer.

Vikas,, E-mail: qlabspu@pu.ac.in, E-mail: qlabspu@yahoo.com; Kaur, Gurpreet [Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160 014 (India)] [Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh 160 014 (India)

2013-12-14

427

Hydrothermal reaction of Ca(OH){sub 2} with quartz in connection with coal demineralization  

SciTech Connect

The hydrothermal reaction of Ca(OH){sub 2} with reagent quartz at temperatures between 175 and 340 C has been studied to obtain fundamental information on coal demineralization with Ca-(OH){sub 2}. X-ray diffraction analysis was used to measure the conversion of quartz and to identify reaction products. The reaction sequence strongly depended on Ca/Si atomic ratio and on autoclaving conditions. At a Ca/Si atomic ratio of about 1, quartz was first converted to Ca{sub 2}-Si{sub 7}O{sub 4}{center_dot}H{sub 2}O, which then reacted with residual quartz or residual Ca(OH){sub 2}, forming a silica-rich phase or a calcium-rich phase, and finally all these intermediate compounds were transformed to xonotlite upon a prolonged high-temperature treatment. At higher Ca/Si ratios, a fraction of quartz remained unreacted even after severe treatments, and the final products were jaffeite (Ca/Si = 3) and tobermorite-like compounds (Ca/Si = {approximately}1) instead of xonotlite. On the basis of the above investigations on model reaction, demineralization reactions to remove quartz from coal through Ca(OH){sub 2}/HCl leaching were interpreted and a suitable acid-washing method was proposed.

Wang, J.; Tomita, Akira [Tohoku Univ., Sendai (Japan). Inst. for Chemical Reaction Science] [Tohoku Univ., Sendai (Japan). Inst. for Chemical Reaction Science

1997-05-01

428

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach  

PubMed Central

Motivation: Metabolic pathway analysis is crucial not only in metabolic engineering but also in rational drug design. However, the biosynthetic/biodegradation pathways are known only for a small portion of metabolites, and a vast amount of pathways remain uncharacterized. Therefore, an important challenge in metabolomics is the de novo reconstruction of potential reaction networks on a metabolome-scale. Results: In this article, we develop a novel method to predict the multistep reaction sequences for de novo reconstruction of metabolic pathways in the reaction-filling framework. We propose a supervised approach to learn what we refer to as ‘multistep reaction sequence likeness’, i.e. whether a compound–compound pair is possibly converted to each other by a sequence of enzymatic reactions. In the algorithm, we propose a recursive procedure of using step-specific classifiers to predict the intermediate compounds in the multistep reaction sequences, based on chemical substructure fingerprints/descriptors of compounds. We further demonstrate the usefulness of our proposed method on the prediction of enzymatic reaction networks from a metabolome-scale compound set and discuss characteristic features of the extracted chemical substructure transformation patterns in multistep reaction sequences. Our comprehensively predicted reaction networks help to fill the metabolic gap and to infer new reaction sequences in metabolic pathways. Availability and implementation: Materials are available for free at http://web.kuicr.kyoto-u.ac.jp/supp/kot/ismb2014/ Contact: goto@kuicr.kyoto-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931980

Kotera, Masaaki; Tabei, Yasuo; Yamanishi, Yoshihiro; Muto, Ai; Moriya, Yuki; Tokimatsu, Toshiaki; Goto, Susumu

2014-01-01

429

Mechanism of cis-prenyltransferase reaction probed by substrate analogues  

SciTech Connect

Research highlights: {yields} The extremely slow trans-OPPS reaction using 2-Fluoro-FPP supports the sequential mechanism with the carbocation intermediate. {yields} The similar UPPS reaction rate under single turnover supports the concerted mechanism, without the carbocation intermediate. {yields} The secondary kinetic isotope effect also supports associate transition state for UPPS reaction, without the carbocation intermediate. -- Abstract: Undecaprenyl pyrophosphate synthase (UPPS) is a cis-type prenyltransferases which catalyzes condensation reactions of farnesyl diphosphate (FPP) with eight isopentenyl pyrophosphate (IPP) units to generate C{sub 55} product. In this study, we used two analogues of FPP, 2-fluoro-FPP and [1,1-{sup 2}H{sub 2}]FPP, to probe the reaction mechanism of Escherichia coli UPPS. The reaction rate of 2-fluoro-FPP with IPP under single-turnover condition is similar to that of FPP, consistent with the mechanism without forming a farnesyl carbocation intermediate. Moreover, the deuterium secondary KIE of 0.985 {+-} 0.022 measured for UPPS reaction using [1,1-{sup 2}H{sub 2}]FPP supports the associative transition state. Unlike the sequential mechanism used by trans-prenyltransferases, our data demonstrate E. coli UPPS utilizes the concerted mechanism.

Lu, Yen-Pin; Liu, Hon-Ge [Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan, ROC (China)] [Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan, ROC (China); Teng, Kuo-Hsun [Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, ROC (China)] [Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, ROC (China); Liang, Po-Huang, E-mail: phliang@gate.sinica.edu.tw [Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan, ROC (China) [Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan, ROC (China); Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, ROC (China)

2010-10-01

430

Dynamic flexibility in the light reactions of photosynthesis governed by both electron and proton transfer reactions  

Microsoft Academic Search

Plant photosynthesis performs the remarkable feat of converting light energy into usable chemical forms, which involves taming highly reactive intermediates without harming plant cells. This requires an apparatus that is not only efficient and robust but also flexible in its responses to changing environmental conditions. It also requires that the output of the energy-storing reactions be matched with the demands

David M. Kramer; Thomas J. Avenson; Gerald E. Edwards

2004-01-01

431

Metal alloy identifier  

DOEpatents

To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

Riley, William D. (Avondale, MD); Brown, Jr., Robert D. (Avondale, MD)

1987-01-01