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Sample records for additional reaction pathways

  1. The Aldol Addition and Condensation: The Effect of Conditions on Reaction Pathway

    ERIC Educational Resources Information Center

    Crouch, R. David; Richardson, Amie; Howard, Jessica L.; Harker, Rebecca L.; Barker, Kathryn H.

    2007-01-01

    The reaction of a ketone and an aldehyde in aqueous Na[subscript 2]CO[subscript 2] is described. This experiment is performed in the absence of strong bases or organic solvents and offers the opportunity for students to observe the critical role that reaction temperature and base strength have in determining the product of the base-mediated…

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

    PubMed

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

    2008-08-28

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

  3. Combustion kinetics and reaction pathways

    SciTech Connect

    Klemm, R.B.; Sutherland, J.W.

    1993-12-01

    This project is focused on the fundamental chemistry of combustion. The overall objectives are to determine rate constants for elementary reactions and to elucidate the pathways of multichannel reactions. A multitechnique approach that features three independent experiments provides unique capabilities in performing reliable kinetic measurements over an exceptionally wide range in temperature, 300 to 2500 K. Recent kinetic work has focused on experimental studies and theoretical calculations of the methane dissociation system (CH{sub 4} + Ar {yields} CH{sub 3} + H + Ar and H + CH{sub 4} {yields} CH{sub 3} + H{sub 2}). Additionally, a discharge flow-photoionization mass spectrometer (DF-PIMS) experiment is used to determine branching fractions for multichannel reactions and to measure ionization thresholds of free radicals. Thus, these photoionization experiments generate data that are relevant to both reaction pathways studies (reaction dynamics) and fundamental thermochemical research. Two distinct advantages of performing PIMS with high intensity, tunable vacuum ultraviolet light at the National Synchrotron Light Source are high detection sensitivity and exceptional selectivity in monitoring radical species.

  4. Pressure-Dependent Competition among Reaction Pathways from First- and Second-O2 Additions in the Low-Temperature Oxidation of Tetrahydrofuran.

    PubMed

    Antonov, Ivan O; Zádor, Judit; Rotavera, Brandon; Papajak, Ewa; Osborn, David L; Taatjes, Craig A; Sheps, Leonid

    2016-08-25

    We report a combined experimental and quantum chemistry study of the initial reactions in low-temperature oxidation of tetrahydrofuran (THF). Using synchrotron-based time-resolved VUV photoionization mass spectrometry, we probe numerous transient intermediates and products at P = 10-2000 Torr and T = 400-700 K. A key reaction sequence, revealed by our experiments, is the conversion of THF-yl peroxy to hydroperoxy-THF-yl radicals (QOOH), followed by a second O2 addition and subsequent decomposition to dihydrofuranyl hydroperoxide + HO2 or to γ-butyrolactone hydroperoxide + OH. The competition between these two pathways affects the degree of radical chain-branching and is likely of central importance in modeling the autoignition of THF. We interpret our data with the aid of quantum chemical calculations of the THF-yl + O2 and QOOH + O2 potential energy surfaces. On the basis of our results, we propose a simplified THF oxidation mechanism below 700 K, which involves the competition among unimolecular decomposition and oxidation pathways of QOOH. PMID:27441526

  5. Adverse reactions to food additives.

    PubMed

    Simon, R A

    1986-01-01

    There are thousands of agents that are intentionally added to the food that we consume. These include preservatives, stabilizers, conditioners, thickeners, colorings, flavorings, sweeteners, antioxidants, etc. etc. Yet only a surprisingly small number have been associated with hypersensitivity reactions. Amongst all the additives, FD&C dyes have been most frequently associated with adverse reactions. Tartrazine is the most notorious of them all; however, critical review of the medical literature and current Scripps Clinic studies would indicate that tartrazine has been confirmed to be at best only occasionally associated with flares of urticaria or asthma. There is no convincing evidence in the literature of reactivity to the other azo or nonazo dyes. This can also be said of BHA/BHT, nitrites/nitrates and sorbates. Parabens have been shown to elicit IgE mediated hypersensitivity reactions when used as pharmaceutical preservatives; however, as with the other additives noted above, ingested parabens have only occasionally been associated with adverse reactions. MSG, the cause of the 'Chinese restaurant syndrome' has only been linked to asthma in one report. Sulfiting agents used primarily as food fresheners and to control microbial growth in fermented beverages have been established as the cause of any where from mild to severe and even fatal reactions in at least 5% of the asthmatic population. Other reactions reported to follow sulfite ingestion include anaphylaxis, gastro intestinal complaints and dermatological eruptions. The prevalence of these non asthmatic reactions is unknown. The mechanism of sulfite sensitive asthma is also unknown but most likely involves hyperreactivity to inhale SO2 in the great majority of cases; however, there are reports of IgE mediated reactions and other sulfite sensitive asthmatics have been found with low levels of sulfite oxidase; necessary to oxidize endogenous sulfite to sulfate. PMID:3302664

  6. Fundamental reaction pathways during coprocessing

    SciTech Connect

    Stock, L.M.; Gatsis, J.G.

    1992-12-01

    The objective of this research was to investigate the fundamental reaction pathways in coal petroleum residuum coprocessing. Once the reaction pathways are defined, further efforts can be directed at improving those aspects of the chemistry of coprocessing that are responsible for the desired results such as high oil yields, low dihydrogen consumption, and mild reaction conditions. We decided to carry out this investigation by looking at four basic aspects of coprocessing: (1) the effect of fossil fuel materials on promoting reactions essential to coprocessing such as hydrogen atom transfer, carbon-carbon bond scission, and hydrodemethylation; (2) the effect of varied mild conditions on the coprocessing reactions; (3) determination of dihydrogen uptake and utilization under severe conditions as a function of the coal or petroleum residuum employed; and (4) the effect of varied dihydrogen pressure, temperature, and residence time on the uptake and utilization of dihydrogen and on the distribution of the coprocessed products. Accomplishments are described.

  7. Reaction pathways of propene pyrolysis.

    PubMed

    Qu, Yena; Su, Kehe; Wang, Xin; Liu, Yan; Zeng, Qingfeng; Cheng, Laifei; Zhang, Litong

    2010-05-01

    The gas-phase reaction pathways in preparing pyrolytic carbon with propene pyrolysis have been investigated in detail with a total number of 110 transition states and 50 intermediates. The structure of the species was determined with density functional theory at B3PW91/6-311G(d,p) level. The transition states and their linked intermediates were confirmed with frequency and the intrinsic reaction coordinates analyses. The elementary reactions were explored in the pathways of both direct and the radical attacking decompositions. The energy barriers and the reaction energies were determined with accurate model chemistry method at G3(MP2) level after an examination of the nondynamic electronic correlations. The heat capacities and entropies were obtained with statistical thermodynamics. The Gibbs free energies at 298.15 K for all the reaction steps were reported. Those at any temperature can be developed with classical thermodynamics by using the fitted (as a function of temperature) heat capacities. It was found that the most favorable paths are mainly in the radical attacking chain reactions. The chain was proposed with 26 reaction steps including two steps of the initialization of the chain to produce H and CH(3) radicals. For a typical temperature (1200 K) adopted in the experiments, the highest energy barriers were found in the production of C(3) to be 203.4 and 193.7 kJ/mol. The highest energy barriers for the production of C(2) and C were found 174.1 and 181.4 kJ/mol, respectively. These results are comparable with the most recent experimental observation of the apparent activation energy 201.9 +/- 0.6 or 137 +/- 25 kJ/mol. PMID:20082392

  8. Reaction pathway for alkane dehydrocyclization

    SciTech Connect

    Shi, Buchang; Davis, B.H.

    1996-08-01

    Naphtha reforming to produce high octane gasoline is an important process. Many reaction mechanisms are involved in this process. For example, the study of the fundamentals of this process led to the concept of bi- or poly-functional catalysis. The results of this study provide additional mechanistic information about the dehydrocyclization of an n-alkane to produce aromatics. The reaction coordinate diagram advanced to account for the observation of irreversible adsorption should be modified to account for the present results. 32 refs., 1 fig.

  9. Multistage reaction pathways in detonating high explosives

    SciTech Connect

    Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya

    2014-11-17

    Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N{sub 2} and H{sub 2}O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N{sub 2} and H{sub 2}O productions.

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

    SciTech Connect

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

    2008-08-28

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

  11. Roaming dynamics in radical addition-elimination reactions

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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 π 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.

  12. Asthma and anaphylactoid reactions to food additives.

    PubMed Central

    Tarlo, S. M.; Sussman, G. L.

    1993-01-01

    Presumed allergic reactions to hidden food additives are both controversial and important. Clinical manifestations include asthma, urticaria, angioedema, and anaphylactic-anaphylactoid events. Most adverse reactions are caused by just a few additives, such as sulfites and monosodium glutamate. Diagnosis is suspected from the history and confirmed by specific challenge. The treatment is specific avoidance. PMID:8499792

  13. Multistage reaction pathways in detonating high explosives

    NASA Astrophysics Data System (ADS)

    Li, Ying; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; CACS Collaboration; ALCF Team

    2015-06-01

    Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N2 and H2O within 10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct uni-molecular and intermolecular reaction pathways, respectively, for the rapid N2 and H2O productions. This work was supported by the Office of Naval Research Grant No. N000014-12-1-0555 and the Basic Research Program of Defense Threat Reduction Agency (DTRA) Grant No. HDTRA1-08-1-0036. All the simulations were performed at USC and Argonne LCF.

  14. Adverse reactions to the sulphite additives

    PubMed Central

    Misso, Neil LA

    2012-01-01

    Sulphites are widely used as preservative and antioxidant additives in the food and pharmaceutical industries. Exposure to sulphites has been reported to induce a range of adverse clinical effects in sensitive individuals, ranging from dermatitis, urticaria, flushing, hypotension, abdominal pain and diarrhoea to life-threatening anaphylactic and asthmatic reactions. Exposure to the sulphites arises mainly from the consumption of foods and drinks that contain these additives; however exposure may also occur through the use of pharmaceutical products, as well as in occupational settings. Most studies report a prevalence of sulphite sensitivity of 3 to 10% among asthmatic subjects who ingest these additives. However, the severity of these reactions varies, and steroid-dependent asthmatics, those with marked airway hyperresponsiveness, and children with chronic asthma, appear to be at greater risk. Although a number of potential mechanisms have been proposed, the precise mechanisms underlying sulphite sensitivity remain unclear. PMID:24834193

  15. Conjugate addition-enantioselective protonation reactions.

    PubMed

    Phelan, James P; Ellman, Jonathan A

    2016-01-01

    The addition of nucleophiles to electron-deficient alkenes represents one of the more general and commonly used strategies for the convergent assembly of more complex structures from simple precursors. In this review the addition of diverse protic and organometallic nucleophiles to electron-deficient alkenes followed by enantioselective protonation is summarized. Reactions are first categorized by the type of electron-deficient alkene and then are further classified according to whether catalysis is achieved with chiral Lewis acids, organocatalysts, or transition metals. PMID:27559372

  16. Serpentinization reaction pathways: implications for modeling approach

    SciTech Connect

    Janecky, D.R.

    1986-01-01

    Experimental seawater-peridotite reaction pathways to form serpentinites at 300/sup 0/C, 500 bars, can be accurately modeled using the EQ3/6 codes in conjunction with thermodynamic and kinetic data from the literature and unpublished compilations. These models provide both confirmation of experimental interpretations and more detailed insight into hydrothermal reaction processes within the oceanic crust. The accuracy of these models depends on careful evaluation of the aqueous speciation model, use of mineral compositions that closely reproduce compositions in the experiments, and definition of realistic reactive components in terms of composition, thermodynamic data, and reaction rates.

  17. Minimum Energy Pathways for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Walch, S. P.; Langhoff, S. R. (Technical Monitor)

    1995-01-01

    Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives useful results for a number of chemically important systems. The talk will focus on a number of applications to reactions leading to NOx and soot formation in hydrocarbon combustion.

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

    PubMed

    Vinu, R; Broadbelt, Linda J

    2012-01-01

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

  19. Method for promoting Michael addition reactions

    DOEpatents

    Shah, Pankaj V.; Vietti, David E.; Whitman, David William

    2010-09-21

    Homogeneously dispersed solid reaction promoters having an average particle size from 0.01 .mu.m to 500 .mu.m are disclosed for preparing curable mixtures of at least one Michael donor and at least one Michael acceptor. The resulting curable mixtures are useful as coatings, adhesives, sealants and elastomers.

  20. Classification of the Electrophilic Addition Reactions of Olefins and Acetylenes

    ERIC Educational Resources Information Center

    Wilson, Michael A.

    1975-01-01

    Divides addition reactions into molecular, stepwise, or termolecular, depending on whether the reaction is synchronous or multistep; and further into nucleophilic, electrophilic, or concerted, depending on how the electrons are transferred in the initiation step. (MLH)

  1. Pathways of the Maillard reaction under physiological conditions.

    PubMed

    Henning, Christian; Glomb, Marcus A

    2016-08-01

    Initially investigated as a color formation process in thermally treated foods, nowadays, the relevance of the Maillard reaction in vivo is generally accepted. Many chronic and age-related diseases such as diabetes, uremia, atherosclerosis, cataractogenesis and Alzheimer's disease are associated with Maillard derived advanced glycation endproducts (AGEs) and α-dicarbonyl compounds as their most important precursors in terms of reactivity and abundance. However, the situation in vivo is very challenging, because Maillard chemistry is paralleled by enzymatic reactions which can lead to both, increases and decreases in certain AGEs. In addition, mechanistic findings established under the harsh conditions of food processing might not be valid under physiological conditions. The present review critically discusses the relevant α-dicarbonyl compounds as central intermediates of AGE formation in vivo with a special focus on fragmentation pathways leading to formation of amide-AGEs. PMID:27291759

  2. Addition reaction of methyl cinnamate with 2-amino-4- nitrophenol

    NASA Astrophysics Data System (ADS)

    Suryanti, Venty; Rakhman Wibowo, Fajar; Pranoto; Robingatun Isnaeni, Siti; Ratna Kumala Sari, Meiyanti; Handayani, Sekar

    2016-02-01

    A novel compound which have one N-H fragment and nitrophenyl group has been designed and synthesized from cinnamaldehyde. The reaction was conducted in 3 step reactions to give the final product. Firstly, cinnamaldehyde was converted into cinnamic acid, which was then esterified with methyl alcohol to obtained methyl cinnamate. The last step was the addition reaction between methyl cinnamate and 2-amino-4-nitrophenol to give a cinnamaldehyde derivative, namely methyl-3-(2-hidroksi-5-nitrophenyl amino)-3- phenylpropanoate.

  3. Deuterium separation by infrared-induced addition reaction

    DOEpatents

    Marling, John B.

    1977-01-01

    A method for deuterium enrichment by the infrared-induced addition reaction of a deuterium halide with an unsaturated aliphatic compound. A gaseous mixture of a hydrogen halide feedstock and an unsaturated aliphatic compound, particularly an olefin, is irradiated to selectively vibrationally excite the deuterium halide contained therein. The excited deuterium halide preferentially reacts with the unsaturated aliphatic compound to produce a deuterated addition product which is removed from the reaction mixture.

  4. Copper-Catalyzed Divergent Addition Reactions of Enoldiazoacetamides with Nitrones.

    PubMed

    Cheng, Qing-Qing; Yedoyan, Julietta; Arman, Hadi; Doyle, Michael P

    2016-01-13

    Catalyst-controlled divergent addition reactions of enoldiazoacetamides with nitrones have been developed. By using copper(I) tetrafluoroborate/bisoxazoline complex as the catalyst, a [3+3]-cycloaddition reaction was achieved with excellent yield and enantioselectivity under exceptionally mild conditions, which represents the first highly enantioselective base-metal-catalyzed vinylcarbene transformation. When the catalyst was changed to copper(I) triflate, Mannich addition products were formed in high yields with near exclusivity under otherwise identical conditions. PMID:26699516

  5. Continuous In Vitro Evolution of a Ribozyme that Catalyzes Three Successive Nucleotidyl Addition Reactions

    NASA Technical Reports Server (NTRS)

    McGinness, Kathleen E.; Wright, Martin C.; Joyce, Gerald F.

    2002-01-01

    Variants of the class I ligase ribozyme, which catalyzes joining of the 3' end of a template bound oligonucleotide to its own 5' end, have been made to evolve in a continuous manner by a simple serial transfer procedure that can be carried out indefinitely. This process was expanded to allow the evolution of ribozymes that catalyze three successive nucleotidyl addition reactions, two template-directed mononucleotide additions followed by RNA ligation. During the development of this behavior, a population of ribozymes was maintained against an overall dilution of more than 10(exp 406). The resulting ribozymes were capable of catalyzing the three-step reaction pathway, with nucleotide addition occurring in either a 5' yieldig 3' or a 3' yielding 5' direction. This purely chemical system provides a functional model of a multi-step reaction pathway that is undergoing Darwinian evolution.

  6. From formamide to purine: an energetically viable mechanistic reaction pathway.

    PubMed

    Wang, Jing; Gu, Jiande; Nguyen, Minh Tho; Springsteen, Greg; Leszczynski, Jerzy

    2013-02-28

    A step-by-step mechanistic pathway following the transformation of formamide to purine through a five-membered ring intermediate has been explored by density functional theory computations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest reaction pathway. All necessary reactants are generated from a single starting compound, formamide, through energetically viable reactions. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-membered ring-closure, and deamination. On the basis of the study of noncatalytic pathways, catalytic water has been found to provide energetically viable step-by-step mechanistic pathways. Among these reaction steps, five-member ring-closure is the rate-determining step. The energy barrier (ca. 42 kcal/mol) of this rate-control step is somewhat lower than the rate-determining step (ca. 44 kcal/mol) for a pyrimidine-based pathway reported previously. The mechanistic pathway reported herein is less energetically demanding than for previously proposed routes to adenine. PMID:23347082

  7. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    SciTech Connect

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  8. Hydrogen addition reactions of aliphatic hydrocarbons in comets

    NASA Astrophysics Data System (ADS)

    Kobayashi, Hitomi; Watanabe, N.; Watanabe, Y.; Fukushima, T.; Kawakita, H.

    2013-10-01

    Comets are thought as remnants of early solar nebula. Their chemical compositions are precious clue to chemical and physical evolution of the proto-planetary disk. Some hydrocarbons such as C2H6, C2H2 and CH4 in comets have been observed by using near-infrared spectroscopy. Although the compositions of C2H6 were about 1% relative to the water in normal comets, there are few reports on the detection of C2H6 in ISM. Some formation mechanisms of C2H6 in ISM have been proposed, and there are two leading hypotheses; one is the dimerizations of CH3 and another is the hydrogen addition reactions of C2H2 on cold icy grains. To evaluate these formation mechanisms for cometary C2H6 quantitatively, it is important to search the C2H4 in comets, which is the intermediate product of the hydrogen addition reactions toward C2H6. However, it is very difficult to detect the C2H4 in comets in NIR (3 microns) regions because of observing circumstances. The hydrogen addition reactions of C2H2 at low temperature conditions are not well characterized both theoretically and experimentally. For example, there are no reports on the reaction rate coefficients of those reaction system. To determine the production rates of those hydrogen addition reactions, we performed the laboratory experiments of the hydrogenation of C2H2 and C2H4. We used four types of the initial composition of the ices: pure C2H4, pure C2H2, C2H2 on amorphous solid water (ASW) and C2H4 on ASW at three different temperatures of 10, 20, and 30K. We found 1) reactions are more efficient when there are ASW in the initial compositions of the ice; 2) hydrogenation of C2H4 occur more rapid than that of C2H2.

  9. Thermochemical Kinetics for Multireference Systems: Addition Reactions of Ozone

    SciTech Connect

    Zhao, Yan; Tishchenko, Oksana; Gour, Jeffrey R.; Li, Wei; Lutz, Jesse; Piecuch, Piotr; Truhlar, Donald G.

    2009-05-14

    The 1,3-dipolar cycloadditions of ozone to ethyne and ethene provide extreme examples of multireference singlet-state chemistry, and they are examined here to test the applicability of several approaches to thermochemical kinetics of systems with large static correlation. Four different multireference diagnostics are applied to measure the multireference characters of the reactants, products, and transition states; all diagnostics indicate significant multireference character in the reactant portion of the potential energy surfaces. We make a more complete estimation of the effect of quadruple excitations than was previously available, and we use this with CCSDT/CBS estimation of Wheeler et al. (Wheeler, S. E.; Ess, D. H.; Houk, K. N. J. Phys. Chem. A 2008, 112, 1798.) to make new best estimates of the van der Waals association energy, the barrier height, and the reaction energy to form the cycloadduct for both reactions. Comparing with these best estimates, we present comprehensive mean unsigned errors for a variety of coupled cluster, multilevel, and density functional methods. Several computational aspects of multireference reactions are considered: (i) the applicability of multilevel theory, (ii) the convergence of coupled cluster theory for reaction barrier heights, (iii) the applicability of completely renormalized coupled cluster methods to multireference systems, (iv) the treatment by density functional theory, (v) the multireference perturbation theory for multireference reactions, and (vi) the relative accuracy of scaling-type multilevel methods as compared with additive ones. It is found that scaling-type multilevel methods do not perform better than the additive-type multilevel methods. Among the 48 tested density functionals, only M05 reproduces the best estimates within their uncertainty. Multireference perturbation theory based on the complete-active-space reference wave functions constructed using a small number of reaction-specific active orbitals

  10. Reactome: a database of reactions, pathways and biological processes.

    PubMed

    Croft, David; O'Kelly, Gavin; Wu, Guanming; Haw, Robin; Gillespie, Marc; Matthews, Lisa; Caudy, Michael; Garapati, Phani; Gopinath, Gopal; Jassal, Bijay; Jupe, Steven; Kalatskaya, Irina; Mahajan, Shahana; May, Bruce; Ndegwa, Nelson; Schmidt, Esther; Shamovsky, Veronica; Yung, Christina; Birney, Ewan; Hermjakob, Henning; D'Eustachio, Peter; Stein, Lincoln

    2011-01-01

    Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice. PMID:21067998

  11. Reaction pathways of the diketonitrile degradate of isoxaflutole with hypochlorite in water.

    PubMed

    Lerch, R N; Lin, C H; Leigh, N D

    2007-03-01

    Isoxaflutole (IXF; Balance) belongs to a new class of isoxazole herbicides. Isoxaflutole has a very short half-life in soil and rapidly degrades to a stable and phytotoxic degradate, diketonitrile (DKN). DKN was previously discovered to rapidly react with hypochlorite (OCl-) in tap water, yielding the benzoic acid (BA) degradate as a major product, but the complete reaction pathway and mechanism have not been elucidated. Thus, the objectives of this work were to (1) determine the stoichiometry of the reaction between DKN and OCl-; (2) identify products in addition to BA; and (3) propose a complete pathway and reaction mechanism for oxidation of DKN by OCl-. Stoichiometry of the reaction showed a molar ratio of OCl-/DKN of 2. In addition, two previously uncharacterized chlorinated intermediates were identified under conditions in which OCl- was the limiting reactant. The proposed chemical structure of a chlorinated benzoyl intermediate was inferred from a series of HPLC/MS and HPLC/MS/MS experiments and the use of mass spectral simulation software. A chlorinated ketone intermediate was also identified using ion trap GC/MS. Two additional end products were also identified: cyclopropanecarboxylic acid (CPCA) and dichloroacetonitrile (DCAN). On the basis of the reaction stoichiometry, the structure of the chlorinated intermediates, and the identification of the products, two reaction pathways are proposed. Both pathways involve a two-step nucleophilic attack and oxidation of the diketone structure of DKN, leading to formation of BA, DCAN, and CPCA. PMID:17284050

  12. A chain reaction approach to modelling gene pathways.

    PubMed

    Cheng, Gary C; Chen, Dung-Tsa; Chen, James J; Soong, Seng-Jaw; Lamartiniere, Coral; Barnes, Stephen

    2012-08-01

    BACKGROUND: Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. RESULTS: In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By

  13. A chain reaction approach to modelling gene pathways

    PubMed Central

    Cheng, Gary C.; Chen, Dung-Tsa; Chen, James J.; Soong, Seng-jaw; Lamartiniere, Coral; Barnes, Stephen

    2012-01-01

    Background Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. Results In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By

  14. A multi-pathway model for photosynthetic reaction center.

    PubMed

    Qin, M; Shen, H Z; Yi, X X

    2016-03-28

    Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments. PMID:27036480

  15. A multi-pathway model for photosynthetic reaction center

    NASA Astrophysics Data System (ADS)

    Qin, M.; Shen, H. Z.; Yi, X. X.

    2016-03-01

    Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments.

  16. Branching ratios between the abstraction and addition channels in the reactions of OH radicals with monoterpenes

    NASA Astrophysics Data System (ADS)

    Rio, C.; Loison, J. C.; Caralp, F.; Flaud, P. M.; Villenave, E.

    2009-04-01

    Secondary Organic Aerosol (SOA) formation in the atmosphere is described as a mass transfer of volatile organic compound oxidation products with low vapour pressures in particular phases. Among the different aerosol components, the SOA represent an important fraction, but, the fundamental processes governing their physics and chemistry in the atmosphere are poorly understood. So it is important to characterize and understand the mechanisms of their formation. It is well-known that atmospheric oxidation of monoterpenes is an important process in tropospheric SOA formation. Consequently, the identification and quantification of reaction products from the oxidation of monoterpenes in the gas phase have been receiving great attention over the past years. However, the atmospheric degradation leads to the formation of a plethora of reaction products and proceeds through a very complex mechanism that is still not fully characterised. In our study, we have focused on SOA formation from OH + monoterpene reactions and more precisely on the primary oxidation steps of γ-terpinene and d-limonene by OH radicals. Indeed, the primary reaction of monoterpenes with hydroxyl radicals can in principle occur by two reaction pathways: OH-addition and H-abstraction. In this work, we have determined branching ratios of these reactions. Although there seems to be a consensus in the literature that OH-monoterpene reactions proceed almost exclusively by addition, several measurements have shown that in some case H-abstraction can represent up to 30% of the total reaction rate constant. Therefore it is necessary to determine this branching ratio in order to know, in particular, the main peroxy radicals formed and propose a mechanism for the gas phase oxidation of terpene by hydroxyl radicals. (γ-terpinene + OH) and (d-limonene + OH) reactions have been studied i) at atmospheric pressure, using laser photolysis coupled with UV absorption radical detection, and ii) at low pressure, using

  17. Reaction pathways for the thermal decomposition of methyl butanoate.

    PubMed

    Akbar Ali, Mohamad; Violi, Angela

    2013-06-21

    In recent years, biodiesel fuels, consisting of long-chain alkyl (methyl, ethyl, propyl) esters, have emerged as viable alternatives to petroleum-based fuels. From a combustion chemistry standpoint, there is great interest in developing accurate reaction models for these new molecules that can be used to predict their behaviors in various regimes. In this paper, we report a detailed study of the unimolecular decomposition pathways of methyl butanoate (MB), a short-chain ester that contains the basic chemical structure of biodiesel fuels. Using ab initio/DFT methods, we identified five homolytic fissions of C-C and C-O bonds and five hydrogen transfer reactions. Rate constants were determined using the G3B3 theory coupled with both variational transition state theory and Rice-Ramsperger-Kassel-Marcus/master equation simulations with hindered rotation corrections. Branching ratios in the temperature range 1500-2200 K indicate that the main pathway for thermal decomposition of MB is the reaction CH3CH2CH2C(═O)OCH3 → C2H5 + CH2C(═O)OCH3. The results, in terms of reaction pathways and rate constants, can be used for future development of mechanisms for long alkyl-chain esters. PMID:23679139

  18. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    DOE PAGESBeta

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; Popolan-Vaida, Denisia M.; Shankar, Vijai Shankar Bhavani; Lucassen, Arnas; Hemken, Christian; Taatjes, Craig A.; Leone, Stephen R.; Kohse-Hoinghaus, Katharina; et al

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS).more » Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have implications on atmospheric gas-phase chemistry and the oxidative stability of organic substances.« less

  19. Human Argonaute 2 Has Diverse Reaction Pathways on Target RNAs.

    PubMed

    Jo, Myung Hyun; Shin, Soochul; Jung, Seung-Ryoung; Kim, Eunji; Song, Ji-Joon; Hohng, Sungchul

    2015-07-01

    Argonaute is a key enzyme of various RNA silencing pathways. We use single-molecule fluorescence measurements to characterize the reaction mechanisms of the core-RISC (RNA-induced silencing complex) composed of human Argonaute 2 and a small RNA. We found that target binding of core-RISC starts at the seed region, resulting in four distinct reaction pathways: target cleavage, transient binding, stable binding, and Argonaute unloading. The target cleavage requires extensive sequence complementarity and dramatically accelerates core-RISC recycling. The stable binding of core-RISC is efficiently established with the seed match only, providing a potential explanation for the seed-match rule of miRNA (microRNA) target selection. Target cleavage on perfect-match targets sensitively depends on RNA sequences, providing an insight into designing more efficient siRNAs (small interfering RNAs). PMID:26140367

  20. Biothiol Xenon MRI Sensor Based on Thiol-Addition Reaction.

    PubMed

    Yang, Shengjun; Jiang, Weiping; Ren, Lili; Yuan, Yaping; Zhang, Bin; Luo, Qing; Guo, Qianni; Bouchard, Louis-S; Liu, Maili; Zhou, Xin

    2016-06-01

    Biothiols such as cysteine (Cys), homocysteine (Hcy), and glutathione (GSH) play an important role in regulating the vital functions of living organisms. Knowledge of their biodistribution in real-time could help diagnose a variety of conditions. However, existing methods of biothiol detection are invasive and require assays. Herein we report a molecular biosensor for biothiol detection using the nuclear spin resonance of (129)Xe. The (129)Xe biosensor consists of a cryptophane cage encapsulating a xenon atom and an acrylate group. The latter serves as a reactive site to covalently bond biothiols through a thiol-addition reaction. The biosensor enables discrimination of Cys from Hcy and GSH through the chemical shift and average reaction rate. This biosensor can be detected at a concentration of 10 μM in a single scan and it has been applied to detect biothiols in bovine serum solution. Our results indicate that this biosensor is a promising tool for the real-time imaging of biothiol distributions. PMID:27128102

  1. Chemical and mathematical modeling of asphaltene reaction pathways

    SciTech Connect

    Salvage, P.E.

    1986-01-01

    Precipitated asphaltene was subjected to pyrolysis and hydropyrolysis, both neat and in solvents, and catalytic hydroprocessing. A solvent extraction procedure defined gas, maltene, asphaltene, and coke product fractions. The apparent first order rate constant for asphaltene conversion at 400/sup 0/C was relatively insensitive to the particular reaction scheme. The yield of gases likewise showed little variation and was always less than 10%. On the other hand, the maltene and coke yields were about 20% and 60%, respectively, from neat pyrolysis, and about 60% and less than 5%, respectively, from catalytic reactions. The temporal variations of the product fractions allowed discernment of asphaltene reaction pathways. The primary reaction of asphaltene was to residual asphaltene, maltenes, and gases. The residual asphaltene reacted thermally to coke and catalytically to maltenes at the expense of coke. Secondary degradation of these primary products led to lighter compounds. Reaction mechanism for pyrolysis of asphaltene model compounds and alkylaromstics were determined. The model compound kinetics results were combined with a stochastic description of asphaltene structure in a mathematical model of asphaltene pyrolysis. Individual molecular product were assigned to either the gas, maltene, asphaltene, or coke product fractions, and summation of the weights of each constituted the model's predictions. The temporal variation of the product fractions from simulated asphaltene pyrolysis compared favorably with experimental results.

  2. Phosphite radicals and their reactions. Examples of redox, substitution, and addition reactions. [Gamma rays and electrons

    SciTech Connect

    Schaefer, K.; Asmus, K.D.

    1980-08-21

    Phosphite radicals HPO/sub 3/- and PO/sub 3//sup 2/-, which exist in an acid-base equilibrium with pK = 5.75, are shown to take part in various types of reactions. In the absence of scavengers, they disappear mainly by second-order disproportionation and combination; a first-order contribution to the decay is also indicated. HPO/sub 3/- and PO/sub 3//sup 2/- are good reductants toward electron acceptors such as tetranitromethane. In this reaction phosphate and C(NO/sub 2/)/sub 3/- are formed. Phosphite radicals can, however, also act as good oxidants, e.g., toward thiols and thiolate ions. These reactions lead to the formation of RS. radicals which were identified either directly, as in the case of penicillamine, through the optical absorption of PenS. or more indirectly through equilibration of RS. with RS- to the optically absorbing RSSR-. disulfide radical anion. A homolytic substitution reaction (S/sub H/2) occurs in the reaction of the phosphite radicals with aliphatic disulfides, yielding RS. radicals and phosphate thioester RSPO/sub 3//sup 2/-. Lipoic acid, as an example of a cyclic disulfide, is reduced to the corresponding RSSR-. radical anion and also undergoes the S/sub H/2 reaction with about equal probability. An addition reaction is observed between phosphite radicals and molecular oxygen. The resulting peroxo phosphate radicals establish an acid-base equilibrium HPO/sub 5//sup -/. reversible PO/sub 5//sup 2 -/. + H+ with a pK = 3.4. Absolute rate constants were determined for all reactions discussed.

  3. Membrane Fission Reactions of the Mammalian ESCRT Pathway

    PubMed Central

    McCullough, John; Colf, Leremy A.; Sundquist, Wesley I.

    2014-01-01

    The endosomal sorting complexes required for transport (ESCRT) pathway was initially defined in yeast genetic screens that identified the factors necessary to sort membrane proteins into intraluminal endosomal vesicles. Subsequent studies have revealed that the mammalian ESCRT pathway also functions in a series of other key cellular processes, including formation of extracellular microvesicles, enveloped virus budding, and the abscission stage of cytokinesis. The core ESCRT machinery comprises Bro1 family proteins and ESCRT-I, ESCRT-II, ESCRT-III, and VPS4. Site-specific adaptors recruit these soluble factors to assemble on different cellular membranes, where they carry out membrane fission reactions. ESCRT-III proteins form filaments that draw membranes together from the cytoplasmic face, and mechanistic models have been advanced to explain how ESCRT-III filaments and the VPS4 ATPase can work together to catalyze membrane fission. PMID:23527693

  4. Diels-Alder reactions: The effects of catalyst on the addition reaction

    NASA Astrophysics Data System (ADS)

    Yilmaz, Özgür; Kus, Nermin Simsek; Tunç, Tuncay; Sahin, Ertan

    2015-10-01

    The reaction between 2,3-dimethyl-1,3-butadiene and dimethyl 7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate is efficiently achieved with small amounts of catalyst, i.e. phenol, AcOH, nafion, and β-cyclodextrin. Exo-diastereoselective cycloaddition reactions were observed both without catalyst and different catalysts for 48 days. As a result, different products (tricyclicmolecule 5, retro-Diels-Alder product 6, and oxidation product 7) were obtained with different catalysts. In addition, we synthesized Diels-Alders product 8 and tricyclocyclitol 10 via Diels-Alder reaction. The structures of these products were characterized by 1H NMR, 13C NMR, MS and IR spectroscopy.

  5. Theoretical investigation of the methane cracking reaction pathways on Ni (1 1 1) surface

    NASA Astrophysics Data System (ADS)

    Li, Jingde; Croiset, Eric; Ricardez-Sandoval, Luis

    2015-10-01

    A comprehensive methane cracking reaction pathway was investigated by performing density functional theory (DFT) calculations. In addition to the sequential dissociation reaction, i.e. CH4 → CHx + (4 - x)H → C + 2H2, a more sophisticated surface reaction network was studied, i.e. CHx + C → CHx - 1 + CH. The results show that CHx dehydrogenation is promoted with a low energy barrier through bimolecular reaction and provide an alternative kinetic favorable route for methane cracking. This study also demonstrates that the production of gas phase C2 hydrocarbon species, e.g. C2H2 and C2H4, in methane cracking reaction is unlikely due to the high barrier energy of C2H3 formation and their strong adsorption energy on Ni (1 1 1).

  6. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    SciTech Connect

    Wang, Zhandong; Zhang, Lidong; Moshammer, Kai; Popolan-Vaida, Denisia M.; Shankar, Vijai Shankar Bhavani; Lucassen, Arnas; Hemken, Christian; Taatjes, Craig A.; Leone, Stephen R.; Kohse-Hoinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Sarathy, S. Mani

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS). Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth's troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. Furthermore, the results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have

  7. 78 FR 41703 - Regulation of Fuels and Fuel Additives: Additional Qualifying Renewable Fuel Pathways Under the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-11

    ... renewable fuels they produce through approved fuel pathways. See 75 FR 14670 (March 26, 2010); 75 FR 26026 (May 10, 2010); 75 FR 37733 (June 30, 2010); 75 FR 59622 (September 28, 2010); 75 FR 76790 (December 9, 2010); 75 FR 79964 (December 21, 2010); 77 FR 1320 (January 9, 2012); 77 FR 74592 (December 17,...

  8. Roaming dynamics in ion-molecule reactions: Phase space reaction pathways and geometrical interpretation

    NASA Astrophysics Data System (ADS)

    Mauguière, Frédéric A. L.; Collins, Peter; Ezra, Gregory S.; Farantos, Stavros C.; Wiggins, Stephen

    2014-04-01

    A model Hamiltonian for the reaction CH_4^+ rArr CH_3^+ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose transition states and conventional/roaming reaction pathways are identified in terms of time-invariant objects in phase space. These are dividing surfaces associated with normally hyperbolic invariant manifolds (NHIMs). For systems with two degrees of freedom NHIMS are unstable periodic orbits which, in conjunction with their stable and unstable manifolds, unambiguously define the (locally) non-recrossing dividing surfaces assumed in statistical theories of reaction rates. By constructing periodic orbit continuation/bifurcation diagrams for two values of the potential function parameter corresponding to late and early transition states, respectively, and using the total energy as another parameter, we dynamically assign different regions of phase space to reactants and products as well as to conventional and roaming reaction pathways. The classical dynamics of the system are investigated by uniformly sampling trajectory initial conditions on the dividing surfaces. Trajectories are classified into four different categories: direct reactive and non-reactive trajectories, which lead to the formation of molecular and radical products respectively, and roaming reactive and non-reactive orbiting trajectories, which represent alternative pathways to form molecular and radical products. By analysing gap time distributions at several energies, we demonstrate that the phase space structure of the roaming region, which is strongly influenced by nonlinear resonances between the two degrees of freedom, results in nonexponential (nonstatistical) decay.

  9. Theoretical studies on the reaction pathways of electronically excited DAAF

    SciTech Connect

    Quenneville, Jason M; Moore, David S

    2009-01-01

    The use of temporally and spectrally shaped ultrafast laser pulses to initiate, as well as detect, high explosives is being explored at Los Alamos. High level ab initio calculations, presented here, are employed to help guide and interpret the experiments. The ground and first excited electronic states of 3,3{prime}-diamino-4,4{prime}-azoxyfurazan (DAAF) are investigated using complete active space self-consistent field (CASSCF) and time-dependent density functional theory (TD-DFT). The geometrical and energetic character of the excited state minima, conical intersections and reaction pathways of DAAF are described. Two radiative and two non-radiative excited state population quenching mechanisms are outlined, and possible pathways for photochemical and spectroscopic control are discussed. The use of laser light to control chemical reactions has many applications. The initiation and the detection of explosives are two such applications currently under development at Los Alamos. Though inherently experimental, the project can be aided by theory through both prediction and interpretation. When the laser light is in the UV/visible region of the electromagnetic spectrum, the absorbing molecule is excited electronically and excitation decay may occur either radiatively (fluorescence or phosphorescence) or non-radiatively (through internal conversion). In many cases decay of the excitation occurs through a mixture of processes, and maximizing the desired result requires sophisticated laser pulses whose amplitude has been optimally modulated in time and/or frequency space. Control of cis-stilbene photochemistry was recently demonstrated in our group, and we aim to extend this work to high explosive compounds. Maximizing radiative decay leads to increased fluorescence quantum yields and enhances the possibility of spectral detection of the absorbing molecule. Maximizing non-radiative decay can lead to chemistry, heating of the sample and possibly detonation initiation in

  10. Eco-friendly polyethylene glycol promoted Michael addition reactions of α,β-unsaturated carbonyl compounds

    EPA Science Inventory

    Abstract- Intra- and inter-nucleophilic addition reactions of different unsaturated compounds were found to be highly effective without any additives in PEG-400 as a recyclable reaction medium under neutral conditions.

  11. Solvent-Dependent Reaction Pathways Operating in Copper(II) Tetrafluoroborate Promoted Oxidative Ring-Opening Reactions of Cyclopropyl Silyl Ethers.

    PubMed

    Hasegawa, Eietsu; Nemoto, Kazuki; Nagumo, Ryosuke; Tayama, Eiji; Iwamoto, Hajime

    2016-04-01

    Oxidative ring-opening reactions of benzene-fused bicyclic cyclopropyl silyl ethers, promoted by copper(II) tetrafluoroborate, were investigated. The regioselectivity of cyclopropane ring-opening as well as product distributions were found to be highly dependent on the nature of the solvent. In alcohols, dimeric substances arising from external bond cleavage are major products. Radical rearrangement products are also formed in solvents such as ether and ethyl acetate. On the contrary, nucleophile addition to carbocation intermediates, generated by internal bond cleavage, occurs mainly in reactions taking place in acetonitrile. It is proposed that the observed solvent effects that govern the reaction pathways followed are a consequence of varying solvation of copper intermediates, which governs their reactivity and redox properties. In addition, the influence of counteranions of the copper salts, organonitriles, cyclic dienes, and substrate structures on the pathways followed in these reactions was also examined. PMID:26799089

  12. Heterogeneous Chemistry of Lipopolysaccharides with Gas-Phase Nitric Acid: Reactive Sites and Reaction Pathways.

    PubMed

    Trueblood, Jonathan V; Estillore, Armando D; Lee, Christopher; Dowling, Jacqueline A; Prather, Kimberly A; Grassian, Vicki H

    2016-08-18

    Recent studies have shown that sea spray aerosol (SSA) has a size-dependent, complex composition consisting of biomolecules and biologically derived organic compounds in addition to salts. This additional chemical complexity most likely influences the heterogeneous reactivity of SSA, as these other components will have different reactive sites and reaction pathways. In this study, we focus on the reactivity of a class of particles derived from some of the biological components of sea spray aerosol including lipopolysaccharides (LPS) that undergo heterogeneous chemistry within the reactive sites of the biological molecule. Examples of these reactions and the relevant reactive sites are proposed as follows: R-COONa(s) + HNO3(g) → NaNO3 + R-COOH and R-HPO4Na(s) + HNO3(g) → NaNO3 + R-H2PO4. These reactions may be a heterogeneous pathway not only for sea spray aerosol but also for a variety of other types of atmospheric aerosol as well. PMID:27445084

  13. Theoretical investigation of the addition reaction of the aluminum chlorosilylenoid H2SiAlCl3 with ethylene.

    PubMed

    Zhang, Mingxia; Li, Wenzuo; Liu, Zhenbo; Li, Qingzhong; Cheng, Jianbo

    2016-07-01

    The addition reaction of the aluminum chlorosilylenoid H2SiAlCl3 with ethylene was investigated using the M06-2X and QCISD methods for the first time. The calculated results demonstrate that the addition reaction proceeds via two pathways: path I involves just one transition state, while path II involves two transition states. Path I is more feasible dynamically, as it has a lower barrier height than path II. The effect of the solvent CH2Cl2 was taken into consideration using the PCM model. The results indicated that the addition reaction is less likely to occur in CH2Cl2 solvent than in vacuum. This work has therefore highlighted a new pathway for the synthesis of silicon heterocyclic compounds. Graphical Abstract Relative energies (in kJ·mol(-1)) of the stationary points along the potential energy surfaces of the addition reaction of H2SiAlCl3 with C2H4 (values in parentheses were calculated in CH2Cl2 solvent). PMID:27271163

  14. Diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams

    PubMed Central

    2015-01-01

    Summary The conjugate addition reaction has been a useful tool in the formation of carbon–carbon bonds. The utility of this reaction has been demonstrated in the synthesis of many natural products, materials, and pharmacological agents. In the last three decades, there has been a significant increase in the development of asymmetric variants of this reaction. Unfortunately, conjugate addition reactions using α,β-unsaturated amides and lactams remain underdeveloped due to their inherently low reactivity. This review highlights the work that has been done on both diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams. PMID:25977728

  15. The reaction pathways of the oxygen plasma pulse in the hafnium oxide atomic layer deposition process

    SciTech Connect

    Jeon, Hyeongtag; Won, Youngdo

    2008-09-22

    The plasma enhanced atomic layer deposition process for the HfO{sub 2} thin film is modeled as simple reactions between Hf(OH){sub 3}NH{sub 2} and reactive oxygen species. The density functional theory calculation was performed for plausible reaction pathways to construct the reaction profile. While the triplet molecular oxygen is unlikely to form a reactive complex, the singlet molecular oxygen forms the stable adduct that goes through the transition state and completes the reaction pathway to the products. Either two singlet or two triplet oxygen atoms make the singlet adduct complex, which follows the same pathway to the product as the singlet molecular oxygen reacts.

  16. WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways.

    PubMed

    Sekiguchi, Tatsuya; Okamoto, Masahiro

    2006-06-01

    We have implemented an efficient, user-friendly biochemical reaction simulator called Web-based BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing large-scale nonlinear networks such as metabolic pathways. Users can easily design and analyze an arbitrary reaction scheme through the Internet and an efficient graphical user interface without considering the mathematical equations. The reaction scheme can include several reaction types, which are represented by both the mass action law (mass balance) and approximated velocity functions of enzyme kinetics at steady state, such as Michaelis-Menten, Hill cooperative, Competitive inhibition. However, since all modules in Web-based BEST-KIT have been developed in Java applet style, users cannot optionally make use of original mathematical equations in addition to the prepared equations. In the present study, we have developed a new version of BEST-KIT (for Microsoft Windows called WinBEST-KIT) to allow users to define original mathematical equations and to customize these equations very easily as user-defined reaction symbols. The following powerful system-analytical methods are prepared for system analysis: time-course calculation, parameter scanning, estimation of the values of unknown kinetic parameters based on experimentally observed time-course data of reactants, dynamic response of reactants against virtual external perturbations, and real-time simulation (Virtual Dry Lab). PMID:16960966

  17. Redox Controls and Reaction Pathways during Serpentinization of Abyssal Peridotite

    NASA Astrophysics Data System (ADS)

    Klein, Frieder; Bach, Wolfgang; Kahl, Wolf-Achim; Humphris, Susan

    2013-04-01

    The aqueous alteration of ultramafic rocks liberates substantial amounts of hydrogen via the oxidation of ferrous iron in primary minerals to ferric iron in secondary minerals; however, the underlying mechanisms of this process remain poorly understood. We examined partly to completely serpentinized peridotites from continental rifted margins, mid-ocean ridges, and fore-arc settings of subduction zones recovered during DSDP/ODP Legs 82, 107, 125, 147, 149, 153, 173, 195, 209, 210, and 304/305 using a variety of microscopic and spectroscopic methods. We merged petrographic observations and chemical analyses with thermodynamic reaction path models and hydrothermal experiments to establish basic conceptual mechanisms of peridotite-seawater interactions. In principle, the complex variations in temperature, host-rock composition, water-to-rock ratio, and reaction kinetics are recorded by the secondary mineralogy. Our results suggest that high temperature (>250°C) serpentinization of olivine at low water-to-rock ratios leads to the formation of magnetite and serpentine together with relatively Fe-poor brucite in mesh texture, and thus to strongly reducing conditions (e.g., at Leg 153). If serpentinization of peridotite proceeds at low temperatures, production of magnetite is limited and brucite generally Fe-richer (e.g., Leg 173), which results in somewhat less reducing conditions. Serpentinization of orthopyroxene-rich lithologies does not generate significant amounts of magnetite (unless it undergoes post-serpentinization oxidation), while serpentine in bastite texture is Fe-rich. In addition to protolith composition, the relative dissolution kinetics of olivine and orthopyroxene can influence the silica activity during serpentinization of peridotite and thus control whether the assemblage brucite-serpentine-clinopyroxene-magnetite or serpentine-talc-tremolite-chlorite is stable. The former assemblage is associated with strongly reducing, high pH, silica poor and Ca

  18. On the deduction of chemical reaction pathways from measurements of time series of concentrations

    NASA Astrophysics Data System (ADS)

    Samoilov, Michael; Arkin, Adam; Ross, John

    2001-03-01

    We discuss the deduction of reaction pathways in complex chemical systems from measurements of time series of chemical concentrations of reacting species. First we review a technique called correlation metric construction (CMC) and show the construction of a reaction pathway from measurements on a part of glycolysis. Then we present two new improved methods for the analysis of time series of concentrations, entropy metric construction (EMC), and entropy reduction method (ERM), and illustrate (EMC) with calculations on a model reaction system.

  19. General low-temperature reaction pathway from precursors to monomers before nucleation of compound semiconductor nanocrystals.

    PubMed

    Yu, Kui; Liu, Xiangyang; Qi, Ting; Yang, Huaqing; Whitfield, Dennis M; Y Chen, Queena; Huisman, Erik J C; Hu, Changwei

    2016-01-01

    Little is known about the molecular pathway to monomers of semiconductor nanocrystals. Here we report a general reaction pathway, which is based on hydrogen-mediated ligand loss for the precursor conversion to 'monomers' at low temperature before nucleation. We apply (31)P nuclear magnetic resonance spectroscopy to monitor the key phosphorous-containing products that evolve from MXn+E=PPh2H+HY mixtures, where MXn, E=PPh2H, and HY are metal precursors, chalcogenide precursors, and additives, respectively. Surprisingly, the phosphorous-containing products detected can be categorized into two groups, Ph2P-Y and Ph2P(E)-Y. On the basis of our experimental and theoretical results, we propose two competing pathways to the formation of M2En monomers, each of which is accompanied by one of the two products. Our study unravels the pathway of precursor evolution into M2En monomers, the stoichiometry of which directly correlates with the atomic composition of the final compound nanocrystals. PMID:27531507

  20. General low-temperature reaction pathway from precursors to monomers before nucleation of compound semiconductor nanocrystals

    PubMed Central

    Yu, Kui; Liu, Xiangyang; Qi, Ting; Yang, Huaqing; Whitfield, Dennis M.; Y. Chen, Queena; Huisman, Erik J. C.; Hu, Changwei

    2016-01-01

    Little is known about the molecular pathway to monomers of semiconductor nanocrystals. Here we report a general reaction pathway, which is based on hydrogen-mediated ligand loss for the precursor conversion to ‘monomers' at low temperature before nucleation. We apply 31P nuclear magnetic resonance spectroscopy to monitor the key phosphorous-containing products that evolve from MXn+E=PPh2H+HY mixtures, where MXn, E=PPh2H, and HY are metal precursors, chalcogenide precursors, and additives, respectively. Surprisingly, the phosphorous-containing products detected can be categorized into two groups, Ph2P–Y and Ph2P(E)–Y. On the basis of our experimental and theoretical results, we propose two competing pathways to the formation of M2En monomers, each of which is accompanied by one of the two products. Our study unravels the pathway of precursor evolution into M2En monomers, the stoichiometry of which directly correlates with the atomic composition of the final compound nanocrystals. PMID:27531507

  1. A mechanistic study of the addition of alcohol to a five-membered ring silene via a photochemical reaction.

    PubMed

    Su, Ming-Der

    2016-03-21

    The mechanism for the photochemical rearrangement of a cyclic divinyldisilane (1-Si) in its first excited state ((1)π → (1)π*) is determined using the CAS/6-311G(d) and MP2-CAS/6-311++G(3df,3pd) levels of theory. The photoproduct, a cyclic silene, reacts with various alcohols to yield a mixture of cis- and trans- adducts. The two reaction pathways are denoted as the cis- addition path (path A) and the trans-addition path (path B). These model studies demonstrate that conical intersections play a crucial role in the photo-rearrangements of cyclic divinyldisilanes. The theoretical evidence also demonstrates that the addition of alcohol to a cyclic divinyldisilane follows the reaction path: cyclic divinyldisilane → Franck-Condon region → conical intersection → photoproduct (cyclic silene) → local intermediate (with alcohol) → transition state → cis- or trans-adduct. The theoretical studies demonstrate that the steric effects as well as the concentrations of CH3OH must have a dominant role in determining the yields of the final adducts by stereochemistry. The same mechanism for the carbon derivative (1-C) is also considered in this work. However, the theoretical results indicate that 1-C does not undergo a methanol addition reaction via the photochemical reaction pathway, since its energy of conical intersection (S1/S0-CI-C) is more than that of its FC (FC-C). The reason for these phenomena could be that the atomic radius of carbon is much smaller than that of silicon (77 and 117 pm, respectively). As a result, the conformation for 1-C is more sterically congested than that for 1-Si, along the 1,3-silyl-migration pathway. PMID:26928893

  2. [Risk hidden in the small print? : Some food additives may trigger pseudoallergic reactions].

    PubMed

    Zuberbier, Torsten; Hengstenberg, Claudine

    2016-06-01

    Some food additives may trigger pseudoallergenic reactions. However, the prevalence of such an overreaction is - despite the increasing number of food additives - rather low in the general population. The most common triggers of pseudoallergic reactions to food are naturally occurring ingredients. However, symptoms in patients with chronic urticaria should improve significantly on a pseudoallergen-free diet. In addition, some studies indicate that certain food additives may also have an impact on the symptoms of patients with neurodermatitis and asthma. PMID:27173908

  3. Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of “hunger hormone” ghrelin

    PubMed Central

    Yao, Jianzhuang; Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

    2016-01-01

    Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway. PMID:26922910

  4. Flash Vacuum Pyrolysis of Lignin Model Compounds: Reaction Pathways of Aromatic Methoxy Groups

    SciTech Connect

    Britt, P.F.; Buchanan, A.C., III; Martineau, D.R.

    1999-03-21

    Currently, there is interest in utilizing lignin, a major constituent of biomass, as a renewable source of chemicals and fuels. High yields of liquid products can be obtained from the flash or fast pyrolysis of biomass, but the reaction pathways that lead to product formation are not understood. To provide insight into the primary reaction pathways under process relevant conditions, we are investigating the flash vacuum pyrolysis (FVP) of lignin model compounds at 500 C. This presentation will focus on the FVP of {beta}-ether linkages containing aromatic methoxy groups and the reaction pathways of methoxy-substituted phenoxy radicals.

  5. Reaction Pathway and Free Energy Barrier for Reactivation of Dimethylphosphoryl-inhibited Human Acetylcholinesterase

    PubMed Central

    Liu, Junjun; Zhang, Yingkai; Zhan, Chang-Guo

    2009-01-01

    The dephosphorylation/reactivation mechanism and the corresponding free energy profile of dimethylphosphoryl-inhibited conjugate of human acetylcholinesterase (AChE) has been studied by performing first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations. Based on the QM/MM-FE results, for the favorable reaction pathway, the entire dephosphorylation/reactivation process consists of three reaction steps, including the nucleophilic water attack on the P atom, the spatial reorganization of the dimethylphosphoryl group, and the dissociation between the dimethylphosphoryl group and Ser203 of AChE. The overall free energy barrier for the entire dephosphorylation/reactivation reaction is found to be the free energy change from the initial reactant to the transition state associated with the spatial reorganization step, and the calculated overall free energy barrier (20.1 to 23.5 kcal/mol) is reasonably close to the experimentally-derived activation free energy of 22.3 kcal/mol. In addition, key amino acid residues and their specific roles in the reaction process have been identified. PMID:19924840

  6. Chemical pathways in ultracold reactions of SrF molecules

    SciTech Connect

    Meyer, Edmund R.; Bohn, John L.

    2011-03-15

    We present a theoretical investigation of the chemical reaction SrF + SrF {yields} products, focusing on reactions at ultralow temperatures. We find that bond swapping SrF + SrF {yields} Sr{sub 2} + F{sub 2} is energetically forbidden at these temperatures. Rather, the only energetically allowed reaction is SrF + SrF {yields} SrF{sub 2} + Sr, and even then only singlet states of the SrF{sub 2} trimer can form. A calculation along a reduced reaction path demonstrates that this abstraction reaction is barrierless and proceeds by one SrF molecule ''handing off'' a fluorine atom to the other molecule.

  7. Formation pathways of DMSO(2) in the addition channel of the OH-initiated DMS oxidation: A theoretical study.

    PubMed

    Ramírez-Anguita, Juan M; González-Lafont, Angels; Lluch, José M

    2009-07-15

    The production of dimethyl sulfoxide (DMSO) and dimethyl sulfone (DMSO(2)) in the dimethyl sulfide (DMS) degradation scheme initiated by the hydroxyl (OH) radical has been shown to be very sensitive to nitrogen oxides (NO(x)) levels. In the present work we have explored the potential energy surfaces corresponding to several reaction pathways which yield DMSO(2) from the CH(3)S(O)(OH)CH(3) adduct [including the formation of CH(3)S(O)(OH)CH(3) from the reaction of DMSO with OH] and the reaction channels that yield DMSO or/and DMSO(2) from the CH(3)S(O(2))(OH)CH(3) adduct are also studied. The formation of the CH(3)S(O(2))(OH)CH(3) adduct from CH(3)S(OH)CH(3) (DMS-OH) and O(2) was analyzed in our previous work. All these pathways due to the presence of NO(x) (NO and NO(2)) and also due to the reactions with O(2), OH and HO(2) are compared with the objective of inferring their kinetic relevance in the laboratory experiments that measure DMSO(2) (and DMSO) formation yields. In particular, our theoretical results clearly show the existence of NO(x)-dependent pathways leading to the formation of DMSO(2), which could explain some of these experimental results in comparison with experimental measurements carried out in NO(x)-free conditions. Our results indicate that the relative importance of the addition channel in the DMS oxidation process can be dependent on the NO(x) content of chamber experiments and of atmospheric conditions. PMID:19072765

  8. Reaction pathway and oxidation mechanisms of dibutyl phthalate by persulfate activated with zero-valent iron.

    PubMed

    Li, Huanxuan; Wan, Jinquan; Ma, Yongwen; Wang, Yan

    2016-08-15

    This study investigated reaction pathway and oxidation mechanisms of dibutyl phthalate (DBP) by persulfate (PS) activated with zero-valent iron (ZVI). The DBP degradation was studied at three pH values (acidic, neutral and basic) in the presence of different organic scavengers. Using a chemical probe method, both sulfate radical (SO4(-)) and hydroxyl radical (·OH) were found to be primary oxidants at pH3.0 and pH7.0, respectively while ·OH was the major specie to oxidize DBP at pH11.0. A similar result was found in an experiment of Electron Spin Resonance spin-trapping where in addition to OH, superoxide radical (O2(-)) was detected at pH11.0. The transformation of degradation products including dimethyl phthalate (DMP), diethyl phthalate (DEP), phthalic anhydride, and acetophenone exhibited diverse variation during the reaction processes. The phthalic anhydride concentration appeared to be maximum at all pHs. Another eleven intermediate products were also found at pH3.0 by GC-MS and HPLC analysis, and their degradation mechanisms and pathways were proposed. It was suggested that dealkylation, hydroxylation, decarboxylation and hydrogen extraction were the dominant degradation mechanisms of DBP at pH3.0. PMID:27125682

  9. The pathways for the removal of acrylamide in model systems using glycine based on the identification of reaction products.

    PubMed

    Liu, Jie; Chen, Fang; Man, Yong; Dong, Jing; Hu, Xiaosong

    2011-09-15

    The reaction between acrylamide and glycine was studied in the aqueous model system heated at 150°C. The main reaction products were identified as C5H10N2O3, C8H15N3O4, C7H12N2O5 and C10H17N3O6 using HPLC-MS/MS, IT-TOF and NMR. Both of the critical intermediates were identified as glyoxylic acid and iminodiacetic acid. The pathways for the removal of acrylamide by glycine were proposed as the Michael addition between acrylamide and glycine with or without the initial oxidation of glycine. The changes in the contents of reactants and products provided quantitative evidence for the above pathways. The addition products between acrylamide and other 14 amino acids were identified by HPLC-MS/MS also. PMID:25212154

  10. Laccase-catalyzed removal of the antimicrobials chlorophene and dichlorophen from water: Reaction kinetics, pathway and toxicity evaluation.

    PubMed

    Shi, Huanhuan; Peng, Jianbiao; Li, Jianhua; Mao, Liang; Wang, Zunyao; Gao, Shixiang

    2016-11-01

    As active agents in cleaning and disinfecting products, antimicrobials have been widely spread in the environment and have drawn extensive attention as potential threats to the ecological system and human health. In this study, the laccase-catalyzed removal of two emerging antimicrobials, chlorophene (CP) and dichlorophen (DCP), was investigated under simulated environmental conditions. Intrinsic reaction kinetics showed that the removal of CP and DCP followed second-order reaction kinetics, first-order with respect to both the enzyme and the substrate concentration. It was also found that fulvic acid could suppress the transformation of CP and DCP by reversing the oxidation reactions through its action as a scavenger of the free radical intermediates produced from reactions between laccase and the substrates. Several reaction products were identified by a quadrupole time-of-flight mass spectrometer, and detailed reaction pathways were proposed. For both CP and DCP, direct polymerization was the principal pathway, and the coupling patterns were further corroborated based on molecular modeling. The nucleophilic substitution of chlorine by the hydroxyl group was observed, and further oxidation products capable of coupling with each other were also found. Additionally, toxicity evaluation tests using Scenedesmus obliquus confirmed that the toxicity of CP and DCP was effectively eliminated during the reaction processes. PMID:27262275

  11. Effect of bromide ion on the reaction pathway between hydroxyl radical and glycine.

    PubMed

    Ying, Liwen; Dong, Wenbo; Yuan, Haixia; Liu, Yan; Ma, Luming

    2015-06-01

    Br(-) and nitrogen-containing organic pollutants, such as amino acids, protein, etc., were often detected in water and wastewater treatment plants using advanced oxidation technologies. All these technologies have one common characteristic, that is, the removal processes involve ·OH. Therefore, it is necessary to study the different reaction pathways among ·OH, Br(-), and amino acids. In this research, glycine was chosen as the representative of amino acids and H2O2 was selected as ·OH precursor. Results showed that Br(-) had a shielding effect on [Formula: see text] of α-carbon in glycine, when it was abstracted by ·OH. The main reaction pathway in the system containing Br(-) was the abstraction of H from amino group in glycine by ·OH, contributing 85 % of total abstracted H. This system had a prominent phenomenon of decarboxylation and performed as alkali production dominating. However, in the system not containing Br(-), the main reaction pathway was the abstraction of H from α-carbon in glycine by ·OH, contributing 97 % of total abstracted H. This system performed as acid production dominating. By laser flash photolysis, the second-order rate constants of abstraction of H from both α-carbon and amino group in glycine by ·OH were obtained as (3.3 ± 0.5) × 10(7) M(-1)·s(-1) and (8.2 ± 0.8) × 10(8) M(-1)·s(-1), respectively. The second-order rate constants of the reaction between [Formula: see text], HṄCH2COO(-) and H2O2 were (1.5 ± 1.1) × 10(7) M(-1)·s(-1) and (4.4 ± 0.3) × 10(7) M(-1)·s(-1), respectively. In addition, Br(-) was found to play a catalytic role in the decomposition of H2O2 under UV radiation. The results mentioned above were significant for the application of advanced oxidation technologies for water containing both amino acids and Br(-) in water and wastewater treatment plants. PMID:25548016

  12. Total Synthesis of Clavosolide A via Tandem Allylic Oxidation/Oxa-Conjugate Addition Reaction

    PubMed Central

    Baker, Joseph B.; Kim, Hyoungsu; Hong, Jiyong

    2015-01-01

    The tandem allylic oxidation/oxa-conjugate addition reaction promoted by the gem-disubstituent effect in conjunction with the NHC-mediated oxidative esterification was explored for the facile synthesis of clavosolide A. PMID:26236051

  13. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

    PubMed Central

    Wu, Dongsheng; Fajer, Mikolai I.; Cao, Liaoran; Cheng, Xiaolin; Yang, Wei

    2016-01-01

    Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this mini presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634

  14. Reaction Pathways for Oxygen Evolution Promoted by Cobalt Catalyst

    PubMed Central

    Mattioli, Giuseppe; Giannozzi, Paolo; Bonapasta, Aldo Amore; Guidoni, Leonardo

    2014-01-01

    The in-depth understanding of the molecular mechanisms regulating the water oxidation catalysis is of key relevance for the rationalization and the design of efficient oxygen evolution catalysts based on earth-abundant transition metals. Performing ab initio DFT+U molecular dynamics calculations of cluster models in explicit water solution, we provide insight into the pathways for oxygen evolution of a cobalt-based catalyst (CoCat). The fast motion of protons at the CoCat/water interface and the occurrence of cubane-like Co-oxo units at the catalyst boundaries are the keys to unlock the fast formation of O–O bonds. Along the resulting pathways, we identified the formation of Co(IV)-oxyl species as the driving ingredient for the activation of the catalytic mechanism, followed by their geminal coupling with O atoms coordinated by the same Co. Concurrent nucleophilic attack of water molecules coming directly from the water solution is discouraged by high activation barriers. The achieved results suggest also interesting similarities between the CoCat and the Mn4Ca-oxo oxygen evolving complex of photosystem II. PMID:24044778

  15. Olefin Metathesis Reaction in Water and in Air Improved by Supramolecular Additives.

    PubMed

    Tomasek, Jasmine; Seßler, Miriam; Gröger, Harald; Schatz, Jürgen

    2015-01-01

    A range of water-immiscible commercially available Grubbs-type precatalysts can be used in ring-closing olefin metathesis reaction in high yields. The synthetic transformation is possible in pure water under ambient conditions. Sulfocalixarenes can help to boost the reactivity of the metathesis reaction by catalyst activation, improved mass transfer, and solubility of reactants in the aqueous reaction media. Additionally, the use of supramolecular additives allows lower catalyst loadings, but still high activity in pure water under aerobic conditions. PMID:26506329

  16. A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

    PubMed Central

    Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

    2013-01-01

    Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

  17. Electron transfer pathways in photosystem I reaction centers

    NASA Astrophysics Data System (ADS)

    Ivashin, Nikolaj; Larsson, Sven

    2003-07-01

    Electron transfer following charge separation in the photosystem I (PSI) reaction center of Synechococcus elongatus is studied using theoretical methods. The difference in rate between two almost symmetrical A- and B-branches is caused by a difference in a single residue (Trp B673 versus Gly A693), close to the F X iron-sulfur cluster. Partly due to its polar environment, Trp B673 acts as an electron acceptor in its π-system. The rate increases on the B-side due to shortened distances for electron transfer.

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

    PubMed Central

    2013-01-01

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

  19. Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment.

    PubMed

    Qu, Ruijuan; Feng, Mingbao; Wang, Xinghao; Huang, Qingguo; Lu, Junhe; Wang, Liansheng; Wang, Zunyao

    2015-01-01

    Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters. PMID:26430733

  20. Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment

    PubMed Central

    Wang, Xinghao; Huang, Qingguo; Lu, Junhe; Wang, Liansheng; Wang, Zunyao

    2015-01-01

    Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters. PMID:26430733

  1. Density Functional Theory Calculations and Analysis of Reaction Pathways for Reduction of Nitric Oxide by Hydrogen on Pt(111)

    SciTech Connect

    Farberow, Carrie A.; Dumesic, James A.; Mavrikakis, Manos

    2014-10-03

    Reaction pathways are explored for low temperature (e.g., 400 K) reduction of nitric oxide by hydrogen on Pt(111). First-principles electronic structure calculations based on periodic, self-consistent density functional theory(DFT-GGA, PW91) are employed to obtain thermodynamic and kinetic parameters for proposed reaction schemes on Pt(111). The surface of Pt(111) during NO reduction by H₂ at low temperatures is predicted to operate at a high NO coverage, and this environment is explicitly taken into account in the DFT calculations. Maximum rate analyses are performed to assess the most likely reaction mechanisms leading to formation of N₂O, the major product observed experimentally at low temperatures. The results of these analyses suggest that the reaction most likely proceeds via the addition of at least two H atoms to adsorbed NO, followed by cleavage of the N-O bond.

  2. Markovnikov free radical addition reactions, a sleeping beauty kissed to life.

    PubMed

    Hoffmann, Reinhard W

    2016-02-01

    This review covers free radical additions, which are initiated by the formal addition of a hydrogen atom to a C[double bond, length as m-dash]C double bond. These reactions originated in the realms of inorganic chemistry, polymer chemistry, and organic chemistry, whereby barriers between these disciplines impeded the rapid implementation of the findings. PMID:26753913

  3. O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

    NASA Technical Reports Server (NTRS)

    Slanger, T. G.; Black, G.

    1978-01-01

    The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

  4. On the reaction pathways and determination of transition-state structures for retaining alpha-galactosyltransferases.

    PubMed

    André, Isabelle; Tvaroska, Igor; Carver, Jeremy P

    2003-04-22

    The catalytic mechanism of retaining glycosyltransferases is not yet completely understood, but one possible mechanism, by analogy with retaining glycosidases, is a double-displacement mechanism via a covalent glycosyl-enzyme intermediate (CGE). We have investigated various reaction pathways for this mechanism using non-empirical quantum mechanical methods. Because a double-displacement mechanism presumes a reaction happening in two steps, we have used predefined reaction coordinates to calculate the potential energy surface describing each step of the mechanism. By investigating several potential candidates to act as a catalytic base, this study attempts to shed some light on the unclear mechanism of the second step of the reaction. All intermediates and transition states on the reaction pathways were characterized using basis sets up to the DFT/B3LYP/6-311++G**//DFT/B3LYP/6-31G* level. Reaction pathways and structural changes were compared with the results previously obtained for inverting glycosyltransferases. The outcome of this study indicates, that among the reaction models investigated, the energetically favorable one is also the most plausible given the existing experimental data. This model requires the presence of only one catalytic acid in the active site with the UDP functioning as a general base in the second step of the reaction. This mechanism is in agreement with both kinetic data in the literature and the description of X-ray structures of retaining glycosyltransferases solved up to today. PMID:12681911

  5. A Computational Approach to Design and Evaluate Enzymatic Reaction Pathways: Application to 1-Butanol Production from Pyruvate

    SciTech Connect

    Wu, Di; Wang, Qin; Assary, Rajeev S.; Broadbelt, Linda J.; Krilov, Goran

    2011-07-25

    We present a new computational strategy for the design and evaluation of novel enzymatic pathways for the biosynthesis of fuels and chemicals. The approach combines the use of the Biochemical Network Integrated Computational Explorer (BNICE) framework and a structure-based screening method for rapid generation and evaluation of novel enzymatic reactions and pathways. The strategy is applied to a case study of 1-butanol production from pyruvate, which yielded nine novel biosynthetic pathways. Using screening criteria based on pathway length, thermodynamic feasibility, and metabolic flux analysis, all nine novel pathways were deemed to be attractive candidates. To further assess their feasibility of implementation, we introduced a new screening criterion based on structural complementarity using molecular docking methods. We show that this approach correctly reproduces the native binding poses for a wide range of enzymes in key classes related to 1-butanol production and provides qualitative agreement with experimental measures of catalytic activity for different substrates. In addition, we show that the structure-based methods can be used to select specific proteins that may be promising candidates to catalyze novel reactions.

  6. A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate.

    SciTech Connect

    Wu, D.; Wang, Q.; Assary, R. S.; Broadbelt, L. J.; Krilov, G.

    2011-01-01

    We present a new computational strategy for the design and evaluation of novel enzymatic pathways for the biosynthesis of fuels and chemicals. The approach combines the use of the Biochemical Network Integrated Computational Explorer (BNICE) framework and a structure-based screening method for rapid generation and evaluation of novel enzymatic reactions and pathways. The strategy is applied to a case study of 1-butanol production from pyruvate, which yielded nine novel biosynthetic pathways. Using screening criteria based on pathway length, thermodynamic feasibility, and metabolic flux analysis, all nine novel pathways were deemed to be attractive candidates. To further assess their feasibility of implementation, we introduced a new screening criterion based on structural complementarity using molecular docking methods. We show that this approach correctly reproduces the native binding poses for a wide range of enzymes in key classes related to 1-butanol production and provides qualitative agreement with experimental measures of catalytic activity for different substrates. In addition, we show that the structure-based methods can be used to select specific proteins that may be promising candidates to catalyze novel reactions.

  7. On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis

    PubMed Central

    Li, Bing; Chun, Hyonho; Zhao, Hongyu

    2014-01-01

    We introduce a nonparametric method for estimating non-gaussian graphical models based on a new statistical relation called additive conditional independence, which is a three-way relation among random vectors that resembles the logical structure of conditional independence. Additive conditional independence allows us to use one-dimensional kernel regardless of the dimension of the graph, which not only avoids the curse of dimensionality but also simplifies computation. It also gives rise to a parallel structure to the gaussian graphical model that replaces the precision matrix by an additive precision operator. The estimators derived from additive conditional independence cover the recently introduced nonparanormal graphical model as a special case, but outperform it when the gaussian copula assumption is violated. We compare the new method with existing ones by simulations and in genetic pathway analysis. PMID:26401064

  8. Systematic Analysis of the Associations between Adverse Drug Reactions and Pathways

    PubMed Central

    Chen, Xiaowen; Wang, Yanqiu; Wang, Pingping; Lian, Baofeng; Li, Chunquan; Wang, Jing; Li, Xia; Jiang, Wei

    2015-01-01

    Adverse drug reactions (ADRs) are responsible for drug candidate failure during clinical trials. It is crucial to investigate biological pathways contributing to ADRs. Here, we applied a large-scale analysis to identify overrepresented ADR-pathway combinations through merging clinical phenotypic data, biological pathway data, and drug-target relations. Evaluation was performed by scientific literature review and defining a pathway-based ADR-ADR similarity measure. The results showed that our method is efficient for finding the associations between ADRs and pathways. To more systematically understand the mechanisms of ADRs, we constructed an ADR-pathway network and an ADR-ADR network. Through network analysis on biology and pharmacology, it was found that frequent ADRs were associated with more pathways than infrequent and rare ADRs. Moreover, environmental information processing pathways contributed most to the observed ADRs. Integrating the system organ class of ADRs, we found that most classes tended to interact with other classes instead of themselves. ADR classes were distributed promiscuously in all the ADR cliques. These results reflected that drug perturbation to a certain pathway can cause changes in multiple organs, rather than in one specific organ. Our work not only provides a global view of the associations between ADRs and pathways, but also is helpful to understand the mechanisms of ADRs. PMID:26495310

  9. Origin of fatty acid synthesis - Thermodynamics and kinetics of reaction pathways

    NASA Technical Reports Server (NTRS)

    Weber, Arthur L.

    1991-01-01

    The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, an alternative pathway of primitive fatty acid synthesis is proposed that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy. Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.

  10. Covalent binding of aniline to humic substances. 2. 15N NMR studies of nucleophilic addition reactions

    USGS Publications Warehouse

    Thorn, K.A.; Pettigrew, P.J.; Goldenberg, W.S.; Weber, E.J.

    1996-01-01

    Aromatic amines are known to undergo covalent binding with humic substances in the environment. Although previous studies have examined reaction conditions and proposed mechanisms, there has been no direct spectroscopic evidence for the covalent binding of the amines to the functional groups in humic substances. In order to further elucidate the reaction mechanisms, the Suwannee River and IHSS soil fulvic and humic acids were reacted with 15N-labeled aniline at pH 6 and analyzed using 15N NMR spectrometry. Aniline underwent nucleophilic addition reactions with the quinone and other carbonyl groups in the samples and became incorporated in the form of anilinohydroquinone, anilinoquinone, anilide, imine, and heterocyclic nitrogen, the latter comprising 50% or more of the bound amine. The anilide and anilinohydroquinone nitrogens were determined to be susceptible to chemical exchange by ammonia. In the case of Suwannee River fulvic acid, reaction under anoxic conditions and pretreatment with sodium borohydride or hydroxylamine prior to reaction under oxic conditions resulted in a decrease in the proportion of anilinohydroquinone nitrogen incorporated. The relative decrease in the incorporation of anilinohydroquinone nitrogen with respect to anilinoquinone nitrogen under anoxic conditions suggested that inter- or intramolecular redox reactions accompanied the nucleophilic addition reactions.

  11. New Direction in Hydrogeochemical Transport Modeling: Incorporating Multiple Kinetic and Equilibrium Reaction Pathways

    SciTech Connect

    Steefel, C.I.

    2000-02-02

    At least two distinct kinds of hydrogeochemical models have evolved historically for use in analyzing contaminant transport, but each has important limitations. One kind, focusing on organic contaminants, treats biodegradation reactions as parts of relatively simple kinetic reaction networks with no or limited coupling to aqueous and surface complexation and mineral dissolution/precipitation reactions. A second kind, evolving out of the speciation and reaction path codes, is capable of handling a comprehensive suite of multicomponent complexation (aqueous and surface) and mineral precipitation and dissolution reactions, but has not been able to treat reaction networks characterized by partial redox disequilibrium and multiple kinetic pathways. More recently, various investigators have begun to consider biodegradation reactions in the context of comprehensive equilibrium and kinetic reaction networks (e.g. Hunter et al. 1998, Mayer 1999). Here we explore two examples of multiple equilibrium and kinetic reaction pathways using the reactive transport code GIMRT98 (Steefel, in prep.): (1) a computational example involving the generation of acid mine drainage due to oxidation of pyrite, and (2) a computational/field example where the rates of chlorinated VOC degradation are linked to the rates of major redox processes occurring in organic-rich wetland sediments overlying a contaminated aerobic aquifer.

  12. Fundamental reaction pathway and free energy profile for proteasome inhibition by syringolin A (SylA)

    PubMed Central

    Wei, Donghui; Tang, Mingsheng; Zhan, Chang-Guo

    2015-01-01

    In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-Oγ directly by Thr1-Nz to form a zwitterionic intermediate. The next step is nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-Oγ atom. The last step is a proton transfer from Thr1-Nz to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal/mol, which is reasonably close to the activation free energy (∼22.4 – 23.0 kcal/mol) derived from available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome. PMID:26018983

  13. Reaction Mechanisms of a Photo-Induced [1,3] Sigmatropic Rearrangement via a Nonadiabatic Pathway

    NASA Astrophysics Data System (ADS)

    Wu, Weiqiang; Liu, Kunhui; Yang, Chunfan; Zhao, Hongmei; Wang, Huan; Yu, Youqing; Su, Hongmei

    2009-11-01

    Time-resolved Fourier transform infrared absorption spectroscopy measurements and B3LYP/cc-pVDZ calculations have been conducted to characterize the reaction dynamics of a remarkable photoinduced 1,3-Cl sigmatropic rearrangement reaction upon 193 or 266 nm excitation of the model systems acryloyl chloride (CH2CHCOCl) and crotonyl chloride (CH3CHCHCOCl) in solution. The reaction is elucidated to follow nonadiabatic pathways via two rapid ISC processes, S1 → T1 and T1 → S0, and the S1/T1 and T1/S0 surface intersections are found to play significant roles leading to the nonadiabatic pathways. The S1 → T1 → S0 reaction pathway involving the key participation of the T1 state is the most favorable, corresponding to the lowest energy path. It is also suggested that the photoinduced 1,3-Cl migration reaction of RCHCHCOCl (R = H, CH3) proceeds through a stepwise mechanism involving radical dissociation-recombination, which is quite different from the generally assumed one-step concerted process for pericyclic reactions.

  14. Formation Of Cometary Hydrocarbons By Hydrogen Addition Reactions On Cold Grains

    NASA Astrophysics Data System (ADS)

    Kobayashi, Hitomi; Watanabe, N.; Kawakita, H.; Fukushima, T.

    2012-10-01

    Hydrogen addition reactions on cold grains are considered to play an important role to form many kinds of volatiles in low temperature conditions like molecular clouds or early solar nebula. We can investigate the physical conditions (e.g., temperature, gas density, and etc.) of the early solar nebula via chemical properties of the pristine bodies like comets. The hydrocarbons like C2H2 and C2H6 have been studied so far and C2H6 might be a product of successive hydrogen addition of C2H2 on the cold grain. To evaluate the efficiency of hydrogen addition reactions from C2H2 to C2H6 quantitatively, we conducted laboratory measurements of those reactions under multiple conditions of the samples (on H2O ice) at different temperatures (10, 20, 30 K) with the LASSIE apparatus at Hokkaido University. Our results provide more detailed information about those reactions than previous quantitative studies. We discuss about the reaction rates with different samples and conditions.

  15. Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

    PubMed Central

    Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

    2015-01-01

    As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. PMID:25867482

  16. Chemical conversion pathways and kinetic modeling for the OH-initiated reaction of triclosan in gas-phase.

    PubMed

    Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

    2015-01-01

    As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. PMID:25867482

  17. Reaction pathways of biomass-derived oxygenates on noble metal surfaces

    NASA Astrophysics Data System (ADS)

    McManus, Jesse R.

    As the global demand for energy continues to rise, the environmental concerns associated with increased fossil fuel consumption have motivated the use of biomass as an alternative, carbon-renewable energy feedstock. Controlling reactive chemistry of the sugars that comprise biomass through the use of catalysis becomes essential in effectively producing green fuels and value-added chemicals. Recent work on biomass conversion catalysts have demonstrated the efficacy of noble metal catalyst systems for the reforming of biomass to hydrogen fuel, and the hydrodeoxygenation of biomass-derived compounds to value-added chemicals. In particular, Pt and Pd surfaces have shown considerable promise as reforming catalysts in preliminary aqueous phase reforming studies. It becomes important to understand the mechanisms by which these molecules react on the catalyst surfaces in order to determine structure-activity relationships and bond scission energetics as to provide a framework for engineering more active and selective catalysts. Fundamental surface science techniques provide the tools to do this; however, work in this field has been so far limited to simple model molecules like ethanol and ethylene glycol. Herein, temperature programmed desorption and high resolution electron energy loss spectroscopy are utilized in an ultra-high vacuum surface science study of the biomass-derived sugar glucose on Pt and Pd single crystal catalysts. Overall, it was determined that the aldehyde function of a ring-open glucose molecule plays an integral part in the initial bonding and reforming reaction pathway, pointing to the use of aldoses glycolaldehyde and glyceraldehyde as the most appropriate model compounds for future studies. Furthermore, the addition of adatom Zn to a Pt(111) surface was found to significantly decrease the C-H and C-C bond scission activity in aldehyde containing compounds, resulting in a preferred deoxygenation pathway in opposition to the decarbonylation pathway

  18. Effects of Ga Addition on Interfacial Reactions Between Sn-Based Solders and Ni

    NASA Astrophysics Data System (ADS)

    Wang, Chao-Hong; Li, Kuan-Ting

    2016-07-01

    The use of Ga as a micro-alloying element in Sn-based solders can change the microstructure of solder joints to improve the mechanical properties, and even suppress the interfacial intermetallic compound (IMC) growth. This research investigated the effects of Ga addition (0.2-1 wt.%Ga) on the IMC formation and morphological evolution in the Sn-based solder joints with Ni substrate. In the soldering reaction at 250°C and with less than 0.2 wt.%Ga addition, the formed phase was Ni3Sn4. When the Ga addition increased to 0.5 wt.%, it changed to a thin Ni2Ga3 layer of ˜1 μm thick, which stably existed at the interface in the initial 1-h reaction. Subsequently, the whole Ni2Ga3 layer detached from the Ni substrate and drifted into the molten solder. The Ni3Sn4 phase became dominant in the later stage. Notably, the Ga addition significantly reduced the grain size of Ni3Sn4, resulting in the massive spalling of Ni3Sn4 grains. With 1 wt.%Ga addition, the Ni2Ga3 layer remained very thin with no significant growth, and it stably existed at the interface for more than 10 h. In addition, the solid-state reactions were examined at temperatures of 160°C to 200°C. With addition of 0.5 wt.%Ga, the Ni3Sn4 phase dominated the whole reaction. By contrast, with increasing to 1 wt.%Ga, only a thin Ni2Ga3 layer was found even after aging at 160°C for more than 1200 h. The 1 wt.%Ga addition in solder can effectively inhibit the Ni3Sn4 formation in soldering and the long-term aging process.

  19. Development of new palladium(0)-catalyzed reactions based on novel oxidative addition mode.

    PubMed

    Tsukamoto, Hirokazu

    2008-09-01

    We have developed palladium(0)/monophosphine-catalyzed trans-selective arylative, alkenylative, alkylative, and alkynylative cyclization reactions of alkyne-aldehydes and -ketones with organoboron reagents. These reactions afford six-membered allylic alcohols with endo tri- or tetra-substituted olefin groups and/or five-membered counterparts with exo olefin groups. The ratios of these products are dramatically affected by alkyne substituents as well as the phosphine ligand. The remarkable trans selectivity of the process results from the novel reaction mechanism involving 'anti-Wacker'-type oxidative addition. Although the cyclization reactions are influenced by the length of the tether between the alkyne and carbonyl group, they can be applied to a multi-component synthesis of biologically important indenes bearing three substituent groups at 1, 2, 3-positions from available o-ethynylbenzaldehyde derivatives. A two-component coupling reaction in methanol provides 1H-indenols, while a three-component reaction involving secondary aliphatic amines as the third component in DMF affords 1H-indenamines. This method allows combinatorial preparation of unsymmetrically substituted 1H-indenes that cannot be prepared via previous synthetic routes. The same catalytic system can also transform allene-carbonyl compounds into 3-cyclohexenols and -cyclopentenols with alkyl, aryl, alkenyl, alkynyl, and boryl groups at C-3. Microwave irradiation efficiently increases not only the reaction rate but also the product yield by suppressing formation of hydroarylation byproducts. Cyclization of optically active 1,3-disubstituted allene-aldehyde reveals that the reaction proceeds through not carbopalladation but 'anti-Wacker'-type oxidative addition. PMID:18758139

  20. Reaction of arynes with vinylogous amides: nucleophilic addition to the ortho-quinodimethide intermediate.

    PubMed

    Li, Ran; Wang, Xuemei; Wei, Zhibin; Wu, Chunrui; Shi, Feng

    2013-09-01

    The reaction of arynes with vinylogous amides containing no free N-H bonds proceeds in a [2 + 2] cycloaddition fashion at ambient temperature. The electronic properties of the vinylogous amides allow for the cycloadducts undergoing a facile ring-opening process, leading to electronically biased ortho-quinodimethide intermediates. Subsequent nucleophilic addition with alcohols affords 2-substituted benzaldehydes or ketones. PMID:23957502

  1. The role of grain boundaries and transient porosity in rocks as fluid pathways for reaction front propagation

    NASA Astrophysics Data System (ADS)

    Jonas, Laura; John, Timm; King, Helen E.; Geisler, Thorsten; Putnis, Andrew

    2014-01-01

    The pseudomorphic replacement of Carrara marble by calcium phosphates was used as a model system in order to study the influence of different fluid pathways for reaction front propagation induced by fluid-rock interaction. In this model, grain boundaries present in the rock as well as the transient porosity structures developing throughout the replacement reaction enable the reaction front to progress further into the rock as well as to the center of each single grain until transformation is complete. Hydrothermal treatment of the marble using phosphate bearing solutions led to the formation of hydroxylapatite and β-TCP; the formation of the latter phase was probably promoted by the presence of ∼0.6 wt.% Mg in the parent carbonate phase. Completely transformed single grains show a distinctive zoning, both in composition and texture. Whereas areas next to the grain boundary consist of nearly pure hydroxylapatite and show a coarse porosity, areas close to the center of the single grains show a high amount of β-TCP and a very fine porous microstructure. If fluorine was added as an additional solution component, up to 3 wt.% of F were incorporated into the product apatite and the formation of β-TCP was avoided. The use of the isotope 18O as a chronometer for the replacement reaction makes it possible to reconstruct the chronological development of the calcium phosphate reaction front. Raman analysis revealed that the incorporation of 18O in the PO4 tetrahedron of hydroxylapatite results in the development of distinct profiles in the calcium phosphate reaction front perpendicular to the grain boundaries of the marble. Through the use of the 18O chronometer, it is possible to estimate and compare the time effectiveness of the different fluid pathways in this model system. The results demonstrate that the grain boundaries are an effective pathway enabling the fluid to penetrate the rock more than one order of magnitude faster compared to the newly developing channel

  2. Reaction Pathway and Free Energy Barrier for Urea Elimination in Aqueous Solution

    PubMed Central

    Yao, Min; Chen, Xi; Zhan, Chang-Guo

    2015-01-01

    To accurately predict the free energy barrier for urea elimination in aqueous solution, we examined the reaction coordinates for the direct and water-assisted elimination pathways, and evaluated the corresponding free energy barriers by using the surface and volume polarization for electrostatics (SVPE) model-based first-principles electronic-structure calculations. Based on the computational results, the water-assisted elimination pathway is dominant for urea elimination in aqueous solution, and the corresponding free energy barrier is 25.3 kcal/mol. The free energy barrier of 25.3 kcal/mol predicted for the dominant reaction pathway of urea elimination in aqueous solution is in good agreement with available experimental kinetic data. PMID:25821238

  3. High Throughput Engineering to Revitalize a Vestigial Electron Transfer Pathway in Bacterial Photosynthetic Reaction Centers*

    PubMed Central

    Faries, Kaitlyn M.; Kressel, Lucas L.; Wander, Marc J.; Holten, Dewey; Laible, Philip D.; Kirmaier, Christine; Hanson, Deborah K.

    2012-01-01

    Photosynthetic reaction centers convert light energy into chemical energy in a series of transmembrane electron transfer reactions, each with near 100% yield. The structures of reaction centers reveal two symmetry-related branches of cofactors (denoted A and B) that are functionally asymmetric; purple bacterial reaction centers use the A pathway exclusively. Previously, site-specific mutagenesis has yielded reaction centers capable of transmembrane charge separation solely via the B branch cofactors, but the best overall electron transfer yields are still low. In an attempt to better realize the architectural and energetic factors that underlie the directionality and yields of electron transfer, sites within the protein-cofactor complex were targeted in a directed molecular evolution strategy that implements streamlined mutagenesis and high throughput spectroscopic screening. The polycistronic approach enables efficient construction and expression of a large number of variants of a heteroligomeric complex that has two intimately regulated subunits with high sequence similarity, common features of many prokaryotic and eukaryotic transmembrane protein assemblies. The strategy has succeeded in the discovery of several mutant reaction centers with increased efficiency of the B pathway; they carry multiple substitutions that have not been explored or linked using traditional approaches. This work expands our understanding of the structure-function relationships that dictate the efficiency of biological energy-conversion reactions, concepts that will aid the design of bio-inspired assemblies capable of both efficient charge separation and charge stabilization. PMID:22247556

  4. Role of Carbon-Addition and Hydrogen-Migration Reactions in Soot Surface Growth.

    PubMed

    Zhang, Hong-Bo; Hou, Dingyu; Law, Chung K; You, Xiaoqing

    2016-02-11

    Using density functional theory and master equation modeling, we have studied the kinetics of small unsaturated aliphatic molecules reacting with polycyclic aromatic hydrocarbon (PAH) molecules having a diradical character. We have found that these reactions follow the mechanism of carbon addition and hydrogen migration (CAHM) on both spin-triplet and open-shell singlet potential energy surfaces at a rate that is about ten times those of the hydrogen-abstraction-carbon-addition (HACA) reactions at 1500 K in the fuel-rich postflame region. The results also show that the most active reaction sites are in the center of the zigzag edges of the PAHs. Furthermore, the reaction products are more likely to form straight rather than branched aliphatic side chains in the case of reacting with diacetylene. The computed rate constants are also found to be independent of pressure at conditions of interest in soot formation, and the activation barriers of the CAHM reactions are linearly correlated with the diradical characters. PMID:26799641

  5. Reaction products of amido-amine and epoxide useful as fuel additives

    SciTech Connect

    Efner, H.F.

    1988-04-12

    A method for reducing engine deposits in an internal combustion engine is described comprising the addition of a detergent fuel additive package to a hydrocarbon fuel for the engine. The fuel detergent is added in an amount effective to reduce deposits and the hydrocarbon fuel is used with detergent additive as fuel in an internal combustion engine. The detergent fuel additive package comprises: (1) a fuel detergent additive that is the reaction product prepared by reacting (a) vegetable oil or (b) higher carboxylic acid chosen from (i) aliphatic fatty acids having 10-25 carbon atoms and (ii) aralkyl acids having 12-42 carbon atoms with (c) multiamine to obtain a fist product mixture with the first product mixture reacted with alklylene oxide to produce a second product mixture and (2) a fuel detergent additive solvent compatible with the fuels.

  6. Reaction pathways and free energy profiles for spontaneous hydrolysis of urea and tetramethylurea: Unexpected substituent effects

    PubMed Central

    Yao, Min; Tu, Wenlong; Chen, Xi; Zhan, Chang-Guo

    2013-01-01

    It has been difficult to directly measure the spontaneous hydrolysis rate of urea and, thus, 1,1,3,3-tetramethylurea (Me4U) was used as a model to determine the “experimental” rate constant for urea hydrolysis. The use of Me4U was based on an assumption that the rate of urea hydrolysis should be 2.8 times that of Me4U hydrolysis because the rate of acetamide hydrolysis is 2.8 times that of N,N-dimethyl-acetamide hydrolysis. The present first-principles electronic-structure calculations on the competing non-enzymatic hydrolysis pathways have demonstrated that the dominant pathway is the neutral hydrolysis via the CN addition for both urea (when pH<~11.6) and Me4U (regardless of pH), unlike the non-enzymatic hydrolysis of amides where alkaline hydrolysis is dominant. Based on the computational data, the substituent shift of free energy barrier calculated for the neutral hydrolysis is remarkably different from that for the alkaline hydrolysis, and the rate constant for the urea hydrolysis should be ~1.3×109-fold lower than that (4.2×10−12 s−1) measured for the Me4U hydrolysis. As a result, the rate enhancement and catalytic proficiency of urease should be 1.2×1025 and 3×1027 M−1, respectively, suggesting that urease surpasses proteases and all other enzymes in its power to enhance the rate of reaction. All of the computational results are consistent with available experimental data for Me4U, suggesting that the computational prediction for urea is reliable. PMID:24097048

  7. Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

  8. Fluorescent probes for tracking the transfer of iron-sulfur cluster and other metal cofactors in biosynthetic reaction pathways.

    PubMed

    Vranish, James N; Russell, William K; Yu, Lusa E; Cox, Rachael M; Russell, David H; Barondeau, David P

    2015-01-14

    Iron-sulfur (Fe-S) clusters are protein cofactors that are constructed and delivered to target proteins by elaborate biosynthetic machinery. Mechanistic insights into these processes have been limited by the lack of sensitive probes for tracking Fe-S cluster synthesis and transfer reactions. Here we present fusion protein- and intein-based fluorescent labeling strategies that can probe Fe-S cluster binding. The fluorescence is sensitive to different cluster types ([2Fe-2S] and [4Fe-4S] clusters), ligand environments ([2Fe-2S] clusters on Rieske, ferredoxin (Fdx), and glutaredoxin), and cluster oxidation states. The power of this approach is highlighted with an extreme example in which the kinetics of Fe-S cluster transfer reactions are monitored between two Fdx molecules that have identical Fe-S spectroscopic properties. This exchange reaction between labeled and unlabeled Fdx is catalyzed by dithiothreitol (DTT), a result that was confirmed by mass spectrometry. DTT likely functions in a ligand substitution reaction that generates a [2Fe-2S]-DTT species, which can transfer the cluster to either labeled or unlabeled Fdx. The ability to monitor this challenging cluster exchange reaction indicates that real-time Fe-S cluster incorporation can be tracked for a specific labeled protein in multicomponent assays that include several unlabeled Fe-S binding proteins or other chromophores. Such advanced kinetic experiments are required to untangle the intricate networks of transfer pathways and the factors affecting flux through branch points. High sensitivity and suitability with high-throughput methodology are additional benefits of this approach. We anticipate that this cluster detection methodology will transform the study of Fe-S cluster pathways and potentially other metal cofactor biosynthetic pathways. PMID:25478817

  9. Matrix isolation study of the ozonolysis of 1,3- and 1,4-cyclohexadiene: identification of novel reaction pathways.

    PubMed

    Pinelo, Laura; Gudmundsdottir, Anna D; Ault, Bruce S

    2013-05-23

    The ozonolysis reactions of 1,3- and 1,4-cyclohexadiene have been studied using a combination of matrix isolation, infrared spectroscopy, and theoretical calculations. Experimental and theoretical results demonstrate that these reactions predominantly do not follow the long-accepted Criegee mechanism. Rather, the reaction of O3 with 1,4-cyclohexadiene leads to the essentially barrierless formation of benzene, C6H6, and H2O3. These two species are then trapped in the same argon matrix cage and weakly interact to form a molecular complex. There is also evidence for the formation of a small amount of the primary ozonide as a minor product, formed through a transition state that is slightly higher in energy. The reaction of O3 with 1,3-cyclohexadiene follows two pathways, one of which is the Criegee mechanism through a low energy transition state leading to formation of the primary ozonide. In addition, with a similar barrier, ozone abstracts a single hydrogen from C5 while adding to C1, forming a hydroperoxy intermediate. This study presents two of the rare cases in which the Criegee mechanism is not the dominant pathway for the ozonolysis of an alkene as well as the first evidence for dehydrogenation of an alkene by ozone. PMID:23638640

  10. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

    PubMed

    Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

    2016-09-19

    Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions. PMID:27573794

  11. Oxidation of LDL by myeloperoxidase and reactive nitrogen species: reaction pathways and antioxidant protection.

    PubMed

    Carr, A C; McCall, M R; Frei, B

    2000-07-01

    Oxidative modification of low density lipoprotein (LDL) appears to play an important role in atherogenesis. Although the precise mechanisms of LDL oxidation in vivo are unknown, several lines of evidence implicate myeloperoxidase and reactive nitrogen species, in addition to ceruloplasmin and 15-lipoxygenase. Myeloperoxidase generates a number of reactive species, including hypochlorous acid, chloramines, tyrosyl radicals, and nitrogen dioxide. These reactive species oxidize the protein, lipid, and antioxidant components of LDL. Modification of apolipoprotein B results in enhanced uptake of LDL by macrophages with subsequent formation of lipid-laden foam cells. Nitric oxide synthases produce nitric oxide and, under certain conditions, superoxide radicals. Numerous other sources of superoxide radicals have been identified in the arterial wall, including NAD(P)H oxidases and xanthine oxidase. Nitric oxide and superoxide readily combine to form peroxynitrite, a reactive nitrogen species capable of modifying LDL. In this review, we examine the reaction pathways involved in LDL oxidation by myeloperoxidase and reactive nitrogen species and the potential protective effects of the antioxidant vitamins C and E. PMID:10894808

  12. 4-Trifluoromethyl-p-quinols as dielectrophiles: three-component, double nucleophilic addition/aromatization reactions

    NASA Astrophysics Data System (ADS)

    Dong, Jinhuan; Shi, Lou; Pan, Ling; Xu, Xianxiu; Liu, Qun

    2016-06-01

    In recent years, numerous methods have emerged for the synthesis of trifluoromethylated arenes based on the late-stage introduction of a trifluoromethyl group onto an aryl ring. In sharp comparison, the synthesis of trifluoromethylated arenes based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon has rarely been addressed. It has been found that 4-trifluoromethyl-p-quinol silyl ethers, the readily available and relatively stable compounds, can act as dielectrophiles to be applied to multi-component reactions for the synthesis of various trifluoromethylated arenes. Catalyzed by In(OTf)3, 4-trifluoromethyl-p-quinol silyl ethers react with C-, N-, and S-nucleophiles, respectively, in a regiospecific 1,2-addition manner to generate the corresponding highly reactive electrophilic intermediates. Further reaction of the in-situ generated electrophiles with a C-nucleophile followed by spontaneous aromatization enables the construction of functionalized trifluoromethyl arenes. This three-component, double nucleophilic addition/aromatization reaction based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon provides a divergent strategy for the synthesis of trifluoromethylated arenes under mild reaction conditions in a single operation.

  13. Dynamic effect of sodium-water reaction in fast flux test facility power addition sodium pipes

    SciTech Connect

    Huang, S.N.; Anderson, M.J.

    1990-03-01

    The Fast Flux Facility (FFTF) is a demonstration and test facility of the sodium-cooled fast breeder reactor. A power addition'' to the facility is being considered to convert some of the dumped, unused heat into electricity generation. Components and piping systems to be added are sodium-water steam generators, sodium loop extensions from existing dump heat exchangers to sodium-water steam generators, and conventional water/steam loops. The sodium loops can be subjected to the dynamic loadings of pressure pulses that are caused by postulated sodium leaks and subsequent sodium-water reaction in the steam generator. The existing FFTF secondary pipes and the new power addition sodium loops were evaluated for exposure to the dynamic effect of the sodium-water reaction. Elastic and simplified inelastic dynamic analyses were used in this feasibility study. The results indicate that both the maximum strain and strain range are within the allowable limits. Several cycles of the sodium-water reaction can be sustained by the sodium pipes that are supported by ordinary pipe supports and seismic restraints. Expensive axial pipe restraints to withstand the sodium-water reaction loads are not needed, because the pressure-pulse-induced alternating bending stresses act as secondary stresses and the pressure pulse dynamic effect is a deformation-controlled quantity and is self-limiting. 14 refs., 7 figs., 3 tabs.

  14. 4-Trifluoromethyl-p-quinols as dielectrophiles: three-component, double nucleophilic addition/aromatization reactions

    PubMed Central

    Dong, Jinhuan; Shi, Lou; Pan, Ling; Xu, Xianxiu; Liu, Qun

    2016-01-01

    In recent years, numerous methods have emerged for the synthesis of trifluoromethylated arenes based on the late-stage introduction of a trifluoromethyl group onto an aryl ring. In sharp comparison, the synthesis of trifluoromethylated arenes based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon has rarely been addressed. It has been found that 4-trifluoromethyl-p-quinol silyl ethers, the readily available and relatively stable compounds, can act as dielectrophiles to be applied to multi-component reactions for the synthesis of various trifluoromethylated arenes. Catalyzed by In(OTf)3, 4-trifluoromethyl-p-quinol silyl ethers react with C-, N-, and S-nucleophiles, respectively, in a regiospecific 1,2-addition manner to generate the corresponding highly reactive electrophilic intermediates. Further reaction of the in-situ generated electrophiles with a C-nucleophile followed by spontaneous aromatization enables the construction of functionalized trifluoromethyl arenes. This three-component, double nucleophilic addition/aromatization reaction based on the pre-introduction of a trifluoromethyl group onto an “aromatic to be” carbon provides a divergent strategy for the synthesis of trifluoromethylated arenes under mild reaction conditions in a single operation. PMID:27246540

  15. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  16. Additive Anti-Tumor Effects of Lovastatin and Everolimus In Vitro through Simultaneous Inhibition of Signaling Pathways

    PubMed Central

    Nölting, Svenja; Maurer, Julian; Spöttl, Gerald; Aristizabal Prada, Elke Tatjana; Reuther, Clemens; Young, Karen; Korbonits, Márta; Göke, Burkhard; Grossman, Ashley; Auernhammer, Christoph J.

    2015-01-01

    Background The mTORC1-inhibitor everolimus shows limited efficacy in treating patients with gastro-entero-pancreatic or pulmonary neuroendocrine tumors (NETs), and poor outcome in patients with malignant pheochromocytoma or hepatic carcinoma. We speculated that any effect may be enhanced by antogonising other signaling pathways. Methods Therefore, we tested the effect of lovastatin—known to inhibit both ERK and AKT signaling—and everolimus, separately and in combination, on cell viability and signaling pathways in human midgut (GOT), pancreatic (BON1), and pulmonary (H727) NET, hepatocellular carcinoma (HepG2, Huh7), and mouse pheochromocytoma (MPC, MTT) cell lines. Results Lovastatin and everolimus separately significantly reduced cell viability in H727, HepG2, Huh7, MPC and MTT cells at clinically relevant doses (P ≤ 0.05). However, high doses of lovastatin were necessary to affect GOT or BON1 cell viability. Clinically relevant doses of both drugs showed additive anti-tumor effects in H727, HepG2, Huh7, MPC and MTT cells (P ≤ 0.05), but not in BON1 or GOT cells. In all cell lines investigated, lovastatin inhibited EGFR and AKT signaling. Subsequently, combination treatment more strongly inhibited EGFR and AKT signaling than everolimus alone, or at least attenuated everolimus-induced EGFR or AKT activation. Vice versa, everolimus constantly decreased pp70S6K and combination treatment more strongly decreased pp70S6K than lovastatin alone, or attenuated lovastatin-induced p70S6K activation: in BON1 cells lovastatin-induced EGFR inhibition was least pronounced, possibly explaining the low efficacy and consequent absent additive effect. Conclusion In summary, clinically relevant doses of lovastatin and everolimus were effective separately and showed additive effects in 5 out of 7 cell lines. Our findings emphasize the importance of targeting several interacting signaling pathways simultaneously when attempting to attenuate tumor growth. However, the variable

  17. Metal-Catalyzed β-Functionalization of Michael Acceptors through Reductive Radical Addition Reactions.

    PubMed

    Streuff, Jan; Gansäuer, Andreas

    2015-11-23

    Transition-metal-catalyzed radical reactions are becoming increasingly important in modern organic chemistry. They offer fascinating and unconventional ways for connecting molecular fragments that are often complementary to traditional methods. In particular, reductive radical additions to α,β-unsaturated compounds have recently gained substantial attention as a result of their broad applicability in organic synthesis. This Minireview critically discusses the recent landmark achievements in this field in context with earlier reports that laid the foundation for today's developments. PMID:26471460

  18. Dissociation Pathways of the CH2CH2ONO Radical: NO2 + Ethene, NO + Oxirane, and a Non-Intrinsic Reaction Coordinate HNO + Vinoxy Pathway.

    PubMed

    Scrape, Preston G; Roberts, Trevor D; Lee, Shih-Huang; Butler, Laurie J

    2016-07-14

    We first characterize the dissociation pathways of BrCH2CH2ONO, a substituted alkyl nitrite, upon photoexcitation at 193 nm under collision-free conditions, in a crossed laser-molecular beam scattering apparatus using vacuum ultraviolet photoionization detection. Three primary photodissociation pathways occur: photoelimination of HNO, leading to the products HNO + BrCH2CHO; C-Br bond photofission, leading to Br + CH2CH2ONO; and O-NO bond photofission, leading to NO + BrCH2CH2O. The data show that alkyl nitrites can eliminate HNO via a unimolecular mechanism in addition to the commonly accepted bulk disproportionation mechanism. Some of the products from the primary photodissociation pathways are highly vibrationally excited, so we then probe the product branching from the unimolecular dissociation of these unstable intermediates. Notably, the vibrationally excited CH2CH2ONO radicals undergo two channels predicted by statistical transition-state theory, and an additional non-intrinsic reaction coordinate channel, HNO elimination. CH2CH2ONO is formed with high rotational energy; by employing rotational models based on conservation of angular momentum, we predict, and verify experimentally, the kinetic energies of stable CH2CH2ONO radicals and the angular distribution of dissociation products. The major dissociation pathway of CH2CH2ONO is NO2 + ethene, and some of the NO2 is formed with sufficient internal energy to undergo further photodissociation. Nascent BrCH2CHO and CH2Br are also photodissociated upon absorption of a second 193 nm photon; we derive the kinetic energy release of these dissociations based on our data, noting similarities to the analogous photodissociation of ClCH2CHO and CH2Cl. PMID:27124098

  19. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface

    NASA Astrophysics Data System (ADS)

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-01

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH4) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH4 over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH4 decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C2) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface.

  20. Lewis base activation of Lewis acids: catalytic, enantioselective vinylogous aldol addition reactions.

    PubMed

    Denmark, Scott E; Heemstra, John R

    2007-07-20

    The generality of Lewis base catalyzed, Lewis acid mediated, enantioselective vinylogous aldol addition reactions has been investigated. The combination of silicon tetrachloride and chiral phosphoramides is a competent catalyst for highly selective additions of a variety of alpha,beta-unsaturated ketone-, 1,3-diketone-, and alpha,beta-unsaturated amide-derived dienolates to aldehydes. These reactions provided high levels of gamma-site selectivity for a variety of substitution patterns on the dienyl unit. Both ketone- and morpholine amide-derived dienol ethers afforded high enantio- and diastereoselectivity in the addition to conjugated aldehydes. Although alpha,beta-unsaturated ketone-derived dienolate did not react with aliphatic aldehydes, alpha,beta-unsaturated amide-derived dienolates underwent addition at reasonable rates affording high yields of vinylogous aldol product. The enantioselectivities achieved with the morpholine derived-dienolate in the addition to aliphatic aldehydes was the highest afforded to date with the silicon tetrachloride-chiral phosphoramide system. Furthermore, the ability to cleanly convert the morpholine amide to a methyl ketone was demonstrated. PMID:17583959

  1. Reaction pathways and free energy profiles for cholinesterase-catalyzed hydrolysis of 6-monoacetylmorphine.

    PubMed

    Qiao, Yan; Han, Keli; Zhan, Chang-Guo

    2014-04-14

    As the most active metabolite of heroin, 6-monoacetylmorphine (6-MAM) can penetrate into the brain for the rapid onset of heroin effects. The primary enzymes responsible for the metabolism of 6-MAM to the less potent morphine in humans are acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). The detailed reaction pathways for AChE- and BChE-catalyzed hydrolysis of 6-MAM to morphine have been explored, for the first time, in the present study by performing first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the two enzymatic reaction processes follow similar catalytic reaction mechanisms, and the whole catalytic reaction pathway for each enzyme consists of four reaction steps. According to the calculated results, the second reaction step associated with the transition state TS2(a)/TS2(b) should be rate-determining for the AChE/BChE-catalyzed hydrolysis, and the free energy barrier calculated for the AChE-catalyzed hydrolysis (18.3 kcal mol(-1)) is 2.5 kcal mol(-1) lower than that for the BChE-catalyzed hydrolysis (20.8 kcal mol(-1)). The free energy barriers calculated for the AChE- and BChE-catalyzed reactions are in good agreement with the experimentally derived activation free energies (17.5 and 20.7 kcal mol(-1) for the AChE- and BChE-catalyzed reactions, respectively). Further structural analysis reveals that the aromatic residues Phe295 and Phe297 in the acyl pocket of AChE (corresponding to Leu286 and Val288 in BChE) contribute to the lower energy of TS2(a) relative to TS2(b). The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse. PMID:24595354

  2. Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

  3. Parameterization of phosphine ligands reveals mechanistic pathways and predicts reaction outcomes

    NASA Astrophysics Data System (ADS)

    Niemeyer, Zachary L.; Milo, Anat; Hickey, David P.; Sigman, Matthew S.

    2016-06-01

    The mechanistic foundation behind the identity of a phosphine ligand that best promotes a desired reaction outcome is often non-intuitive, and thus has been addressed in numerous experimental and theoretical studies. In this work, multivariate correlations of reaction outcomes using 38 different phosphine ligands were combined with classic potentiometric analyses to study a Suzuki reaction, for which the site selectivity of oxidative addition is highly dependent on the nature of the phosphine. These studies shed light on the generality of hypotheses regarding the structural influence of different classes of phosphine ligands on the reaction mechanism(s), and deliver a methodology that should prove useful in future studies of phosphine ligands.

  4. Reaction pathways of model compounds of biomass-derived oxygenates on Fe/Ni bimetallic surfaces

    NASA Astrophysics Data System (ADS)

    Yu, Weiting; Chen, Jingguang G.

    2015-10-01

    Controlling the activity and selectivity of converting biomass-derivatives to fuels and valuable chemicals is critical for the utilization of biomass feedstocks. There are primarily three classes of non-food competing biomass, cellulose, hemicellulose and lignin. In the current work, glycolaldehyde, furfural and acetaldehyde are studied as model compounds of the three classes of biomass-derivatives. Monometallic Ni(111) and monolayer (ML) Fe/Ni(111) bimetallic surfaces are studied for the reaction pathways of the three biomass surrogates. The ML Fe/Ni(111) surface is identified as an efficient surface for the conversion of biomass-derivatives from the combined results of density functional theory (DFT) calculations and temperature programmed desorption (TPD) experiments. A correlation is also established between the optimized adsorption geometry and experimental reaction pathways. These results should provide helpful insights in catalyst design for the upgrading and conversion of biomass.

  5. Coupling of Fast and Slow Modes in the Reaction Pathway of the Minimal Hammerhead Ribozyme Cleavage

    PubMed Central

    Radhakrishnan, Ravi

    2007-01-01

    By employing classical molecular dynamics, correlation analysis of coupling between slow and fast dynamical modes, and free energy (umbrella) sampling using classical as well as mixed quantum mechanics molecular mechanics force fields, we uncover a possible pathway for phosphoryl transfer in the self-cleaving reaction of the minimal hammerhead ribozyme. The significance of this pathway is that it initiates from the minimal hammerhead crystal structure and describes the reaction landscape as a conformational rearrangement followed by a covalent transformation. The delineated mechanism is catalyzed by two metal (Mg2+) ions, proceeds via an in-line-attack by CYT 17 O2′ on the scissile phosphorous (ADE 1.1 P), and is therefore consistent with the experimentally observed inversion configuration. According to the delineated mechanism, the coupling between slow modes involving the hammerhead backbone with fast modes in the cleavage site appears to be crucial for setting up the in-line nucleophilic attack. PMID:17545240

  6. Chimerogenesis in estimation of specificity and pathway directions for cytochrome p45017alpha catalyzed reactions.

    PubMed

    Gilep, A A; Estabrook, R W; Usanov, S A

    2004-04-01

    Cytochrome P45017alpha is a key enzyme in steroid hormone biosynthesis. It catalyzes the reaction of 17alpha-hydroxylation of progesterone (P4) and pregnenolone (P5) and the 17,20-lyase reaction resulting in side chain cleavage of C21 steroids to form C19 steroids. Depending on the activity of cytochrome P45017alpha, steroid hormone biosynthesis pathways are directed either for biosynthesis of mineralocorticoids and glucocorticoids or sex hormones. The formation of sex hormones starts from biosynthesis of androstenedione. Androstenedione formation is a result of two reactions: 17,20-lyase reaction of 17alpha-hydroxyprogesterone (Delta4-pathway) and 3beta-hydroxysteroid dehydrogenase/Delta4,Delta5-isomerase reaction using dehydroepiandrosterone as substrate (Delta5-pathway). In case of exclusive direction of the 17,20-lyase reaction either through the Delta4- or the Delta5-pathway, the formation of sex hormones depends more on specificity and activity of 3beta-hydroxysteroid-dehydrogenase/Delta4,Delta5-isomerase. Depending on species, the cytochromes P45017alpha can utilize as a substrate for 17,20-lyase activity Delta4-steroids, Delta5-steroids, or both types of steroids. To identify the structural elements of cytochrome P45017alpha responsible for substrate recognition, in the present work we used exchange of homologous fragments of cytochrome P45017alpha having different types of activities. We engineered more than 10 different types of chimeric cytochrome P45017alpha. Chimeric cytochromes P45017alpha have been expressed in E. coli and purified. The expression of chimeric cytochrome P45017alpha with the point of exchange between exons III and IV results in inability of the recombinant hemeprotein to properly bind heme. The determination of activity of chimeric cytochromes P45017alpha shows that the structural element responsible for switching activity between Delta4- or Delta5-pathway is located in the region of polypeptide chain coded by exons II-V of CYP17 gene

  7. Influence of the heterogeneous reaction HCL + HOCl on an ozone hole model with hydrocarbon additions

    SciTech Connect

    Elliott, S.; Cicerone, R.J.; Turco, R.P.

    1994-02-20

    Injection of ethane or propane has been suggested as a means for reducing ozone loss within the Antarctic vortex because alkanes can convert active chlorine radicals into hydrochloric acid. In kinetic models of vortex chemistry including as heterogeneous processes only the hydrolysis and HCl reactions of ClONO{sub 2} and N{sub 2}O{sub 5}, parts per billion by volume levels of the light alkanes counteract ozone depletion by sequestering chlorine atoms. Introduction of the surface reaction of HCl with HOCl causes ethane to deepen baseline ozone holes and generally works to impede any mitigation by hydrocarbons. The increased depletion occurs because HCl + HOCl can be driven by HO{sub x} radicals released during organic oxidation. Following initial hydrogen abstraction by chlorine, alkane breakdown leads to a net hydrochloric acid activation as the remaining hydrogen atoms enter the photochemical system. Lowering the rate constant for reactions of organic peroxy radicals with ClO to 10{sup {minus}13} cm{sup 3} molecule{sup {minus}1} s{sup {minus}1} does not alter results, and the major conclusions are insensitive to the timing of the ethane additions. Ignoring the organic peroxy radical plus ClO reactions entirely restores remediation capabilities by allowing HO{sub x} removal independent of HCl. Remediation also returns if early evaporation of polar stratospheric clouds leaves hydrogen atoms trapped in aldehyde intermediates, but real ozone losses are small in such cases. 95 refs., 4 figs., 7 tabs.

  8. A Simple and Inexpensive Device for Slow, Controlled Addition of a Solution to a Reaction Mixture

    NASA Astrophysics Data System (ADS)

    Osvath, Peter

    1995-07-01

    A number of reactions require the slow and controlled addition of a solution containing one reagent to another. Attempting to control the flow rate over a number of hours using a conventional constant pressure addition funnel is a frustrating exercise; commercially available constant volume addition funnels are expensive and must be adjusted by trial and error each time a reaction is carried out. The use of an (expensive) peristaltic pump or syringe pump overcomes these problems but can introduce other complications. We have recently had occasion to carry out the synthesis of thioether macrocycles and cages requiring the slow and controlled addition of DMF solutions of (offensively odoriferous) thiols or (air-sensitive) thiolates to a reactant solution under nitrogen(1), Although the use of a syringe pump was called for, there are obvious difficulties associated with purging the solution and assembling such an apparatus under nitrogen, and we report a simple and inexpensive solution. A Male Luer Lock tip (recovered from a broken syringe) was sweated onto the flattened tip of a pressure-equalizing addition funnel and a syringe needle was attached. Judicious selection of needle length, bore size, and reactant volume can be used to control the addition time simply and reproducibly. With a 250-mL funnel, the flow rate changes by <25% from the beginning to the end of the addition. (In fact, a reduction in the rate of addition may even be advantageous as the reaction proceeds, the reagent in the receiving flask is consumed, its concentration drops, and the rate of reaction will decrease). A piece of fine Teflon tubing of appropriate length attached to the needle can be used to reduce the flow rate even further, but this is only necessary for very slow rates of addition. For example, the time of addition of 200 mL, of an ethanolic solution could be varied from approximately 5 minutes (150mm/17 gauge) to approximately 5 h (200mm/22 gauge), and once the addition time for a

  9. Multiple Pathways Suppress Telomere Addition to DNA Breaks in the Drosophila Germline

    PubMed Central

    Beaucher, Michelle; Zheng, Xiao-Feng; Amariei, Flavia; Rong, Yikang S.

    2012-01-01

    Telomeres protect chromosome ends from being repaired as double-strand breaks (DSBs). Just as DSB repair is suppressed at telomeres, de novo telomere addition is suppressed at the site of DSBs. To identify factors responsible for this suppression, we developed an assay to monitor de novo telomere formation in Drosophila, an organism in which telomeres can be established on chromosome ends with essentially any sequence. Germline expression of the I-SceI endonuclease resulted in precise telomere formation at its cut site with high efficiency. Using this assay, we quantified the frequency of telomere formation in different genetic backgrounds with known or possible defects in DNA damage repair. We showed that disruption of DSB repair factors (Rad51 or DNA ligase IV) or DSB sensing factors (ATRIP or MDC1) resulted in more efficient telomere formation. Interestingly, partial disruption of factors that normally regulate telomere protection (ATM or NBS) also led to higher frequencies of telomere formation, suggesting that these proteins have opposing roles in telomere maintenance vs. establishment. In the ku70 mutant background, telomere establishment was preceded by excessive degradation of DSB ends, which were stabilized upon telomere formation. Most strikingly, the removal of ATRIP caused a dramatic increase in telomeric retrotransposon attachment to broken ends. Our study identifies several pathways thatsuppress telomere addition at DSBs, paving the way for future mechanistic studies. PMID:22446318

  10. S3S63 Terminal Ynamides: Synthesis, Coupling Reactions and Additions to Common Electrophiles

    PubMed Central

    Cook, Andrea M.

    2015-01-01

    Ynamides consist of a polarized triple bond that is directly attached to a nitrogen atom carrying a sulfonyl, an alkoxycarbonyl, an acyl or another electron withdrawing group. The triple bond polarization renders ynamides broadly useful building blocks with synthetic opportunities that go far beyond traditional alkyne chemistry. The versatile reactivity of ynamides in cycloadditions, cycloisomerizations, regioselective additions with various nucleophiles or electrophiles, ring-closing metathesis, and many other reactions has been investigated in detail during the past decades. A common feature of these methods is that the triple bond is consumed and either cleaved or transformed to a new functionality. The wealth of reports on these ynamide reactions is in stark contrast to the dearth of carbon-carbon bond formations that leave the triple bond of terminal ynamides intact. The recent introduction of effective synthetic methods for the preparation of terminal ynamides has set the stage to fully explore the synthetic potential of this intriguing class of compounds. This digest letter summarizes the most effective routes to terminal ynamides and the current state of selective nucleophilic addition, substitution and coupling reactions, including the first examples of asymmetric synthesis. PMID:26085692

  11. Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways.

    PubMed

    Jin, Biao; Rolle, Massimo

    2016-03-01

    The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. To demonstrate specific features of the modeling approach, we simulated the degradation of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model accurately reproduces the multi-element isotope data observed in previous experimental studies. Furthermore, it precisely captures the dual element isotope trends characteristic of different reaction pathways as well as their range of variation consistent with observed bulk isotope fractionation. It was also possible to directly validate the model capability to predict the evolution of position-specific isotope ratios with available experimental data. Therefore, the approach is useful both for a mechanism-based evaluation of experimental results and as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. PMID:26708763

  12. Glucose and fructose decomposition in subcritical and supercritical water: Detailed reaction pathway, mechanisms, and kinetics

    SciTech Connect

    Kabyemela, B.M.; Adschiri, T.; Malaluan, R.M.; Arai, K.

    1999-08-01

    The authors are developing a new catalyst-free process of cellulose decomposition in supercritical water. In their initial study on the cellulose decomposition in supercritical water, the main products of cellulose decomposition were found to be oligomers of glucose (cellobiose, cellotriose, etc.) and glucose at short residence times (400 C, 25 MPa, 0.05 s). The kinetics of glucose at these conditions can be useful in understanding the reaction pathways of cellulose. Experiments were performed on the products of glucose decomposition at short residence times to elucidate the reaction pathways and evaluate kinetics of glucose and fructose decomposition in sub- and supercritical water. The conditions were a temperature of 300--400 C and pressure of 25--40 MPa for extremely short residence times between 0.02 and 2 s. The products of glucose decomposition were fructose, a product of isomerization, 1,6-anhydroglucose, a product of dehydration, and erythrose and glyceraldehyde, products of C-C bond cleavage. Fructose underwent reactions similar to glucose except that it did not form 1,6-anhydroglucose and isomerization to glucose is negligible. The mechanism for the products formed from C-C bond cleavage could be explained by reverse aldol condensation and the double-bond rule of the respective enediols formed during the Lobry de Bruyn Alberda van Ekenstein transformation. The differential equations resulting from the proposed pathways were fit to experimental results to obtain the kinetic rate constants.

  13. Reaction pathway of the degradation of the p-hydroxybenzoic acid by sulfate radical generated by ionizing radiations

    NASA Astrophysics Data System (ADS)

    Criquet, Justine; Leitner, Nathalie Karpel Vel

    2015-01-01

    The degradation of p-hydroxybenzoic acid (HBA) in aqueous solutions by ionizing radiation was studied. The phenolic pollutant was easily removed by the electron beam irradiation, as more than 80% of the initial 100 μM introduced was degraded for a dose of 600 Gy. It was shown that the addition of persulfate, producing the sulfate radical as additional reactive species, induced a change in the reaction pathway. LC-MS analyses were performed in order to identify the different by-products formed. In the absence of persulfate, the main by-product formed was 3,4-dihydroxybenzoic acid, while in presence of persulfate, 1,4-benzoquinone was detected and the hydroxylated by-products were not present. A reaction pathway of HBA degradation by hydroxyl and sulfate radicals was proposed from the identification of the chemical structure of the different by-products detected. The influences of pH and dissolved oxygen were also studied. A high decline of HBA degradation was observed at pH 11 compared to pH 4.5, this decrease was minimized in the presence of persulfate. The dissolved oxygen concentration was found to be a limiting parameter of HBA degradation, however an excess of dissolved oxygen in solution did not improve the degradation to a large extent.

  14. High-resolution mineralogical characterization and biogeochemical modeling of uranium reaction pathways at the FRC

    SciTech Connect

    Chen Zhu

    2006-06-15

    High-Resolution Mineralogical Characterization and Biogeochemical Modeling of Uranium Reduction Pathways at the Oak Ridge Field-Research Center (FRC) Chen Zhu, Indiana University, David R. Veblen, Johns Hopkins University We have successfully completed a proof-of-concept, one-year grant on a three-year proposal from the former NABIR program, and here we seek additional two-year funding to complete and publish the research. Using a state-of-the-art 300-kV, atomic resolution, Field Emission Gun Transmission Electron Microscope (TEM), we have successfully identified three categories of mineral hosts for uranium in contaminated soils: (1) iron oxides; (2) mixed manganese-iron oxides; and (3) uranium phosphates. Method development using parallel electron energy loss spectroscopy (EELS) associated with the TEM shows great promise for characterizing the valence states of immobilized U during bioremediation. We have also collected 27 groundwater samples from two push-pull field biostimulation tests, which form two time series from zero to approximately 600 hours. The temporal evolution in major cations, anions, trace elements, and the stable isotopes 34S, 18O in sulfate, 15N in nitrate, and 13C in dissolved inorganic carbon (DIC) clearly show that biostimulation resulted in reduction of nitrate, Mn(IV), Fe(III), U(VI), sulfate, and Tc(VII), and these reduction reactions were intimately coupled with a complex network of inorganic reactions evident from alkalinity, pH, Na, K, Mg, and Ca concentrations. From these temporal trends, apparent zero order rates were regressed. However, our extensive suite of chemical and isotopic data sets, perhaps the first and only comprehensive data set available at the FRC, show that the derived rates from these field biostimulation experiments are composite and lump-sum rates. There were several reactions that were occurring at the same time but were masked by these pseudo-zero order rates. A reaction-path model comprising a total of nine

  15. Oxidative degradation of decabromodiphenyl ether (BDE 209) by potassium permanganate: reaction pathways, kinetics, and mechanisms assisted by density functional theory calculations.

    PubMed

    Shi, Jiaqi; Qu, Ruijuan; Feng, Mingbao; Wang, Xinghao; Wang, Liansheng; Yang, Shaogui; Wang, Zunyao

    2015-04-01

    This study found that decabromodiphenyl ether (BDE 209) could be oxidized effectively by potassium permanganate (KMnO4) in sulfuric acid medium. A total of 15 intermediate oxidative products were detected. The reaction pathways were proposed, which primarily included cleavage of the ether bond to form pentabromophenol. Direct oxidation on the benzene ring also played an important role because hydroxylated polybrominated diphenyl ethers (PBDEs) were produced during the oxidation process. The degradation occurred dramatically in the first few minutes and fitted pseudo-first-order kinetics. Increasing the water content decelerated the reaction rate, whereas increasing the temperature facilitated the reaction. In addition, density functional theory (DFT) was employed to determine the frontier molecular orbital (FMO) and frontier electron density (FED) of BDE 209 and the oxidative products. The theoretical calculation results confirmed the proposed reaction pathways. PMID:25751737

  16. Phospha-Michael Addition as a New Click Reaction for Protein Functionalization.

    PubMed

    Lee, Yan-Jiun; Kurra, Yadagiri; Liu, Wenshe R

    2016-03-15

    A new type of click reaction between an alkyl phosphine and acrylamide was developed and applied for site-specific protein labeling in vitro and in live cells. Acrylamide is a small electrophilic olefin that readily undergoes phospha-Michael addition with an alkyl phosphine. Our kinetic study indicated a second-order rate constant of 0.07 m(-1)  s(-1) for the reaction between tris(2-carboxyethyl)phosphine and acrylamide at pH 7.4. To demonstrate its application in protein functionalization, we used a dansyl-phosphine conjugate to successfully label proteins that were site-specifically installed with N(ɛ) -acryloyl-l-lysine and employed a biotin-phosphine conjugate to selectively probe human proteins that were metabolically labeled with N-acryloyl-galactosamine. PMID:26756316

  17. Hydrogen generation from alcohols catalyzed by ruthenium-triphenylphosphine complexes: multiple reaction pathways.

    PubMed

    Sieffert, Nicolas; Bühl, Michael

    2010-06-16

    We report a comprehensive density functional theory (DFT) study of the mechanism of the methanol dehydrogenation reaction catalyzed by [RuH(2)(H(2))(PPh(3))(3)]. Using the B97-D dispersion-corrected functional, four pathways have been fully characterized, which differ in the way the critical beta-hydrogen transfer step is brought about (e.g., by prior dissociation of one PPh(3) ligand). All these pathways are found to be competitive (DeltaG(++) = 27.0-32.1 kcal/mol at 150 degrees C) and strongly interlocked. The reaction can thus follow multiple reaction channels, a feature which is expected to be at the origin of the good kinetics of this system. Our results also point to the active role of PPh(3) ligands, which undergo significant conformational changes as the reaction occurs, and provide insights into the role of the base, which acts as a "co-catalyst" by facilitating proton transfers within active species. Activation barriers decrease on going from methanol to ethanol and 2-propanol substrates, in accord with experiment. PMID:20481632

  18. Evaluating reaction pathways of hydrothermal abiotic organic synthesis at elevated temperatures and pressures using carbon isotopes

    NASA Astrophysics Data System (ADS)

    Fu, Qi; Socki, Richard A.; Niles, Paul B.

    2015-04-01

    Experiments were performed to better understand the role of environmental factors on reaction pathways and corresponding carbon isotope fractionations during abiotic hydrothermal synthesis of organic compounds using piston cylinder apparatus at 750 °C and 5.5 kbars. Chemical compositions of experimental products and corresponding carbon isotopic values were obtained by a Pyrolysis-GC-MS-IRMS system. Alkanes (methane and ethane), straight-chain saturated alcohols (ethanol and n-butanol) and monocarboxylic acids (formic and acetic acids) were generated with ethanol being the only organic compound with higher δ13C than CO2. CO was not detected in experimental products owing to the favorable water-gas shift reaction under high water pressure conditions. The pattern of δ13C values of CO2, carboxylic acids and alkanes are consistent with their equilibrium isotope relationships: CO2 > carboxylic acids > alkanes, but the magnitude of the fractionation among them is higher than predicted isotope equilibrium values. In particular, the isotopic fractionation between CO2 and CH4 remained constant at ∼31‰, indicating a kinetic effect during CO2 reduction processes. No "isotope reversal" of δ13C values for alkanes or carboxylic acids was observed, which indicates a different reaction pathway than what is typically observed during Fischer-Tropsch synthesis under gas phase conditions. Under constraints imposed in experiments, the anomalous 13C isotope enrichment in ethanol suggests that hydroxymethylene is the organic intermediate, and that the generation of other organic compounds enriched in 12C were facilitated by subsequent Rayleigh fractionation of hydroxymethylene reacting with H2 and/or H2O. Carbon isotope fractionation data obtained in this study are instrumental in assessing the controlling factors on abiotic formation of organic compounds in hydrothermal systems. Knowledge on how environmental conditions affect reaction pathways of abiotic synthesis of organic

  19. Precipitation Reactions in Age-Hardenable Alloys During Laser Additive Manufacturing

    NASA Astrophysics Data System (ADS)

    Jägle, Eric A.; Sheng, Zhendong; Wu, Liang; Lu, Lin; Risse, Jeroen; Weisheit, Andreas; Raabe, Dierk

    2016-03-01

    We describe and study the thermal profiles experienced by various age-hardenable alloys during laser additive manufacturing (LAM), employing two different manufacturing techniques: selective laser melting and laser metal deposition. Using scanning electron microscopy and atom probe tomography, we reveal at which stages during the manufacturing process desired and undesired precipitation reactions can occur in age-hardenable alloys. Using examples from a maraging steel, a nickel-base superalloy and a scandium-containing aluminium alloy, we demonstrate that precipitation can already occur during the production of the powders used as starting material, during the deposition of material (i.e. during solidification and subsequent cooling), during the intrinsic heat treatment effected by LAM (i.e. in the heat affected zones) and, naturally, during an ageing post-heat treatment. These examples demonstrate the importance of understanding and controlling the thermal profile during the entire additive manufacturing cycle of age-hardenable materials including powder synthesis.

  20. Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane

    SciTech Connect

    Rotavera, Brandon; Zádor, Judit; Welz, Oliver; Sheps, Leonid; Scheer, Adam M.; Savee, John D.; Akbar Ali, Mohamad; Lee, Taek Soon; Simmons, Blake A.; Osborn, David L.; Violi, Angela; Taatjes, Craig A.

    2014-09-19

    The product formation from R + O2 reactions relevant to low-temperature autoignition chemistry was studied for 2,5-dimethylhexane, a symmetrically branched octane isomer, at 550 and 650 K using Cl-atom initiated oxidation and multiplexed photoionization mass spectrometry (MPIMS). The interpretation of time- and photon-energy-resolved mass spectra led to three specific results important to characterizing the initial oxidation steps: (1) quantified isomer-resolved branching ratios for HO2 + alkene channels; (2) 2,2,5,5-tetramethyltetrahydrofuran is formed in substantial yield from addition of O2 to tertiary 2,5-dimethylhex-2-yl followed by isomerization of the resulting ROO adduct to tertiary hydroperoxyalkyl (QOOH) and exhibits a positive dependence on temperature over the range covered leading to a higher flux relative to aggregate cyclic ether yield. The higher relative flux is explained by a 1,5-hydrogen atom shift reaction that converts the initial primary alkyl radical (2,5-dimethylhex-1-yl) to the tertiary alkyl radical 2,5-dimethylhex-2-yl, providing an additional source of tertiary alkyl radicals. Furthermore, quantum-chemical and master-equation calculations of the unimolecular decomposition of the primary alkyl radical reveal that isomerization to the tertiary alkyl radical is the most favorable pathway, and is favored over O2-addition at 650 K under the conditions herein. The isomerization pathway to tertiary alkyl radicals therefore contributes an additional mechanism to 2,2,5,5-tetramethyltetrahydrofuran formation; (3) carbonyl species (acetone, propanal, and methylpropanal) consistent with β-scission of QOOH radicals were formed in significant yield, indicating unimolecular QOOH decomposition into carbonyl + alkene + OH.

  1. Photoionization mass spectrometric measurements of initial reaction pathways in low-temperature oxidation of 2,5-dimethylhexane

    DOE PAGESBeta

    Rotavera, Brandon; Zádor, Judit; Welz, Oliver; Sheps, Leonid; Scheer, Adam M.; Savee, John D.; Akbar Ali, Mohamad; Lee, Taek Soon; Simmons, Blake A.; Osborn, David L.; et al

    2014-09-19

    The product formation from R + O2 reactions relevant to low-temperature autoignition chemistry was studied for 2,5-dimethylhexane, a symmetrically branched octane isomer, at 550 and 650 K using Cl-atom initiated oxidation and multiplexed photoionization mass spectrometry (MPIMS). The interpretation of time- and photon-energy-resolved mass spectra led to three specific results important to characterizing the initial oxidation steps: (1) quantified isomer-resolved branching ratios for HO2 + alkene channels; (2) 2,2,5,5-tetramethyltetrahydrofuran is formed in substantial yield from addition of O2 to tertiary 2,5-dimethylhex-2-yl followed by isomerization of the resulting ROO adduct to tertiary hydroperoxyalkyl (QOOH) and exhibits a positive dependence on temperaturemore » over the range covered leading to a higher flux relative to aggregate cyclic ether yield. The higher relative flux is explained by a 1,5-hydrogen atom shift reaction that converts the initial primary alkyl radical (2,5-dimethylhex-1-yl) to the tertiary alkyl radical 2,5-dimethylhex-2-yl, providing an additional source of tertiary alkyl radicals. Furthermore, quantum-chemical and master-equation calculations of the unimolecular decomposition of the primary alkyl radical reveal that isomerization to the tertiary alkyl radical is the most favorable pathway, and is favored over O2-addition at 650 K under the conditions herein. The isomerization pathway to tertiary alkyl radicals therefore contributes an additional mechanism to 2,2,5,5-tetramethyltetrahydrofuran formation; (3) carbonyl species (acetone, propanal, and methylpropanal) consistent with β-scission of QOOH radicals were formed in significant yield, indicating unimolecular QOOH decomposition into carbonyl + alkene + OH.« less

  2. Reaction Pathways and Energetics of Etheric C–O Bond Cleavage Catalyzed by Lanthanide Triflates

    SciTech Connect

    Assary, Rajeev S.; Atesin, Abdurrahman C.; Li, Zhi; Curtiss, Larry A.; Marks, Tobin J.

    2013-09-06

    Efficient and selective cleavage of etheric C-O bonds is crucial for converting biomass into platform chemicals and liquid transportation fuels. In this contribution, computational methods at the DFT B3LYP level of theory are employed to understand the efficacy of lanthanide triflate catalysts (Ln(OTf)3, Ln = La, Ce, Sm, Gd, Yb, and Lu) in cleaving etheric C-O bonds. In agreement with experiment, the calculations indicate that the reaction pathway for C-O cleavage occurs via a C-H → O-H proton transfer in concert with weakening of the C-O bond of the coordinated ether substrate to ultimately yield a coordinated alkenol. The activation energy for this process falls as the lanthanide ionic radius decreases, reflecting enhanced metal ion electrophilicity. Details of the reaction mechanism for Yb(OTf)3-catalyzed ring opening are explored in depth, and for 1-methyl-d3-butyl phenyl ether, the computed primary kinetic isotope effect of 2.4 is in excellent agreement with experiment (2.7), confirming that etheric ring-opening pathway involves proton transfer from the methyl group alpha to the etheric oxygen atom, which is activated by the electrophilic lanthanide ion. Calculations of the catalytic pathway using eight different ether substrates indicate that the more rapid cleavage of acyclic versus cyclic ethers is largely due to entropic effects, with the former C-O bond scission processes increasing the degrees of freedom/particles as the transition state is approached.

  3. Detection of additional genes of the patulin biosynthetic pathway in Penicillium griseofulvum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genes in the patulin biosynthetic pathway are likely to be arranged in a cluster as has been found for biosynthetic pathways of other mycotoxins. The mycotoxin patulin, common in apples and apple juice, is most often associated with Penicillium expansum. However, of 15 fungal species capable of sy...

  4. Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

    PubMed Central

    2011-01-01

    Background With the advent of high-throughput targeted metabolic profiling techniques, the question of how to interpret and analyze the resulting vast amount of data becomes more and more important. In this work we address the reconstruction of metabolic reactions from cross-sectional metabolomics data, that is without the requirement for time-resolved measurements or specific system perturbations. Previous studies in this area mainly focused on Pearson correlation coefficients, which however are generally incapable of distinguishing between direct and indirect metabolic interactions. Results In our new approach we propose the application of a Gaussian graphical model (GGM), an undirected probabilistic graphical model estimating the conditional dependence between variables. GGMs are based on partial correlation coefficients, that is pairwise Pearson correlation coefficients conditioned against the correlation with all other metabolites. We first demonstrate the general validity of the method and its advantages over regular correlation networks with computer-simulated reaction systems. Then we estimate a GGM on data from a large human population cohort, covering 1020 fasting blood serum samples with 151 quantified metabolites. The GGM is much sparser than the correlation network, shows a modular structure with respect to metabolite classes, and is stable to the choice of samples in the data set. On the example of human fatty acid metabolism, we demonstrate for the first time that high partial correlation coefficients generally correspond to known metabolic reactions. This feature is evaluated both manually by investigating specific pairs of high-scoring metabolites, and then systematically on a literature-curated model of fatty acid synthesis and degradation. Our method detects many known reactions along with possibly novel pathway interactions, representing candidates for further experimental examination. Conclusions In summary, we demonstrate strong signatures of

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  6. Degradation of ibuprofen by hydrodynamic cavitation: Reaction pathways and effect of operational parameters.

    PubMed

    Musmarra, Dino; Prisciandaro, Marina; Capocelli, Mauro; Karatza, Despina; Iovino, Pasquale; Canzano, Silvana; Lancia, Amedeo

    2016-03-01

    Ibuprofen (IBP) is an anti-inflammatory drug whose residues can be found worldwide in natural water bodies resulting in harmful effects to aquatic species even at low concentrations. This paper deals with the degradation of IBP in water by hydrodynamic cavitation in a convergent-divergent nozzle. Over 60% of ibuprofen was degraded in 60 min with an electrical energy per order (EEO) of 10.77 kWh m(-3) at an initial concentration of 200 μg L(-1) and a relative inlet pressure pin=0.35 MPa. Five intermediates generated from different hydroxylation reactions were identified; the potential mechanisms of degradation were sketched and discussed. The reaction pathways recognized are in line with the relevant literature, both experimental and theoretical. By varying the pressure upstream the constriction, different degradation rates were observed. This effect was discussed according to a numerical simulation of the hydroxyl radical production identifying a clear correspondence between the maximum kinetic constant kOH and the maximum calculated OH production. Furthermore, in the investigated experimental conditions, the pH parameter was found not to affect the extent of degradation; this peculiar feature agrees with a recently published kinetic insight and has been explained in the light of the intermediates of the different reaction pathways. PMID:26584987

  7. Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetics, and Rate Rule Optimizations for 2-Methylhexane.

    PubMed

    Mohamed, Samah Y; Cai, Liming; Khaled, Fethi; Banyon, Colin; Wang, Zhandong; Al Rashidi, Mariam J; Pitsch, Heinz; Curran, Henry J; Farooq, Aamir; Sarathy, S Mani

    2016-04-14

    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model's performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model. PMID:26998618

  8. Ring Walking/Oxidative Addition Reactions for the Controlled Synthesis of Conjugated Polymers

    SciTech Connect

    Bazan, Guillermo C

    2012-04-03

    Power conversion efficiencies of plastic solar cells depend strongly on the molecular weight characteristics of the semiconducting polymers used for their fabrication. The synthesis of these materials typically relies on transition metal mediated catalytic reactions. In many instances, the ideal structures cannot be attained because of deficiencies in these reactions, particularly when it comes to being able to achieve high number average molecular weights and narrow molecular weight distributions. Another important conjugated polymer structure of interest is one in which a single functional group is attached at the end group of the chain. Such systems would be ideal for modifying surface properties at interfaces and for labeling biomolecular probes used in fluorescent biosensors. To respond to the challenges above, our efforts have centered on the design of homogenous transition metal complexes that are easy to prepare and effective in carrying out living, or quasi-living, condensative chain polymerization reactions. The key mechanistic challenge for the success of this reaction is to force the insertion of one monomer unit at a time via a process that involves migration of the transition metal-containing fragment to one terminus of the polymer chain. Chain growth characteristics are therefore favored when the metal does not dissociate from the newly formed reductive elimination product. We have proposed that dissociation is disfavored by the formation of a -complex, in which the metal can sample various locations of the electronically delocalized framework, a process that we term ring-walking , and find the functionality where oxidative addition takes place. Success has been achieved in the nickel-mediated cross coupling reaction of Grignard reagents with aromatic halides by using bromo[1,2-bis(diphenylphosphino)ethane]phenylnickel. This reagent can yield poly(thiophene)s (one of the most widely used type of polymer in plastic solar cells) with excellent

  9. Imaging Proton Transfer and Dihalide Formation Pathways in Reactions of F– + CH3I

    PubMed Central

    2016-01-01

    Ion–molecule reactions of the type X– + CH3Y are commonly assumed to produce Y– through bimolecular nucleophilic substitution (SN2). Beyond this reaction, additional reaction products have been observed throughout the last decades and have been ascribed to different entrance channel geometries differing from the commonly assumed collinear approach. We have performed a crossed beam velocity map imaging experiment on the F– + CH3I reaction at different relative collision energies between 0.4 and 2.9 eV. We find three additional channels competing with nucleophilic substitution at high energies. Experimental branching ratios and angle- and energy differential cross sections are presented for each product channel. The proton transfer product CH2I– is the main reaction channel, which competes with nucleophilic substitution up to 2.9 eV relative collision energy. At this level, the second additional channel, the formation of IF– via halogen abstraction, becomes more efficient. In addition, we present the first evidence for an [FHI]− product ion. This [FHI]− product ion is present only for a narrow range of collision energies, indicating possible dissociation at high energies. All three products show a similar trend with respect to their velocity- and scattering angle distributions, with isotropic scattering and forward scattering of the product ions occurring at low and high energies, respectively. Reactions leading to all three reaction channels present a considerable amount of energy partitioning in product internal excitation. The internally excited fraction shows a collision energy dependence only for CH2I–. A similar trend is observed for the isoelectronic OH– + CH3I system. The comparison of our experimental data at 1.55 eV collision energy with a recent theoretical calculation for the same system shows a slightly higher fraction of internal excitation than predicted, which is, however, compatible within the experimental accuracy. PMID:26799548

  10. Imaging Proton Transfer and Dihalide Formation Pathways in Reactions of F(-) + CH3I.

    PubMed

    Carrascosa, Eduardo; Michaelsen, Tim; Stei, Martin; Bastian, Björn; Meyer, Jennifer; Mikosch, Jochen; Wester, Roland

    2016-07-14

    Ion-molecule reactions of the type X(-) + CH3Y are commonly assumed to produce Y(-) through bimolecular nucleophilic substitution (SN2). Beyond this reaction, additional reaction products have been observed throughout the last decades and have been ascribed to different entrance channel geometries differing from the commonly assumed collinear approach. We have performed a crossed beam velocity map imaging experiment on the F(-) + CH3I reaction at different relative collision energies between 0.4 and 2.9 eV. We find three additional channels competing with nucleophilic substitution at high energies. Experimental branching ratios and angle- and energy differential cross sections are presented for each product channel. The proton transfer product CH2I(-) is the main reaction channel, which competes with nucleophilic substitution up to 2.9 eV relative collision energy. At this level, the second additional channel, the formation of IF(-) via halogen abstraction, becomes more efficient. In addition, we present the first evidence for an [FHI](-) product ion. This [FHI](-) product ion is present only for a narrow range of collision energies, indicating possible dissociation at high energies. All three products show a similar trend with respect to their velocity- and scattering angle distributions, with isotropic scattering and forward scattering of the product ions occurring at low and high energies, respectively. Reactions leading to all three reaction channels present a considerable amount of energy partitioning in product internal excitation. The internally excited fraction shows a collision energy dependence only for CH2I(-). A similar trend is observed for the isoelectronic OH(-) + CH3I system. The comparison of our experimental data at 1.55 eV collision energy with a recent theoretical calculation for the same system shows a slightly higher fraction of internal excitation than predicted, which is, however, compatible within the experimental accuracy. PMID:26799548

  11. FORMATION OF POLYCYCLIC AROMATIC HYDROCARBONS AND THEIR GROWTH TO SOOT -A REVIEW OF CHEMICAL REACTION PATHWAYS. (R824970)

    EPA Science Inventory

    The generation by combustion processes of airborne species of current health concern such as polycyclic aromatic hydrocarbons (PAH) and soot particles necessitates a detailed understanding of chemical reaction pathways responsible for their formation. The present review discus...

  12. Reaction pathways in the coadsorption of carbon monoxide and nitric oxide at caesium surfaces

    NASA Astrophysics Data System (ADS)

    Carley, A. F.; Roberts, M. W.; Santra, A. K.

    2002-09-01

    The reactivity of caesium surfaces to nitric oxide, carbon monoxide and mixtures of NO and CO at low temperatures (90-220 K) has been studied by X-ray photoelectron spectroscopy. Reaction pathways for CO-NO mixtures are controlled by oxygen transients generated by the dissociative chemisorption of NO emphasising the limitations of evidence that might be deduced from the reactivity of the individual molecules, CO on its own not being adsorbed at a caesium surface. Spectroscopic evidence for the formation of CO 2δ- , CO 3, and NO 2 species is discussed.

  13. Theoretical study of addition reactions of carbene, silylene, and germylene to carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chu, Ying-Ying; Su, Ming-Der

    2004-08-01

    A theoretical study of the mechanism of the reaction of a single-walled carbon nanotube (SWCNT) with carbene (H 2C), silylene (H 2Si), and germylene (H 2Ge) has been carried out using a two-layered ONIOM(B3LYP/6-311G ∗:PM3) approach. The main findings are as follows: (1) The computational results based on the method used in this work are in good agreement with recent theoretical findings [Angew. Chem. Int. Ed. 41 (2002) 1853]. That is, SWCNTs with H 2C, H 2Si, and H 2Ge addends favor opened structures rather than three-membered rings. (2) The greater the atomic number of the carbene center, the larger the activation energy and the less exothermic (or the more endothermic) the cycloaddition reaction becomes. Therefore, addition to the C dbnd C bond of a SWCNT is more difficult the heavier the carbene center. (3) The theoretical observations suggest that the singlet-triplet splitting of a carbene can be used as a guide to its reactivity during the SWCNT cycloaddition process.

  14. The reaction of nitroso oxides with olefins: Concerted or nonconcerted addition?

    NASA Astrophysics Data System (ADS)

    Talipov, M. R.; Khursan, S. L.; Safiullin, R. L.

    2011-03-01

    The mechanism of the interaction of nitroso oxides (RNOO) with olefins was studied at MCQDPT2/6-311+G(3 df, 2 p)//CASSCF(10; 9)/6-311G( d) level of theory. The following reaction channels were considered: ( 1) (3 + 2)-cycloaddition and nonconcerted biradical addition of nitroso oxide ( 2) through the terminal oxygen atom and ( 3) through the nitrogen atom to the C=C multiple bond. It was shown for the cases of ( A) cis/trans-HNOO + C2H4, ( B) cis/trans-HNOO + C2F4, ( C) cis/trans-PhNOO + C2H4, and ( D) cis/trans-PhNOO + C2H3CH3 model systems that the typical reaction of nitroso oxides with alkenes was cycloaddition. For olefins with a decreased electron density at the multiple bond, as in system B, a substantial contribution of the one-center mechanism with the formation of biradical intermediates is possible.

  15. Parameterization of phosphine ligands reveals mechanistic pathways and predicts reaction outcomes.

    PubMed

    Niemeyer, Zachary L; Milo, Anat; Hickey, David P; Sigman, Matthew S

    2016-06-01

    The mechanistic foundation behind the identity of a phosphine ligand that best promotes a desired reaction outcome is often non-intuitive, and thus has been addressed in numerous experimental and theoretical studies. In this work, multivariate correlations of reaction outcomes using 38 different phosphine ligands were combined with classic potentiometric analyses to study a Suzuki reaction, for which the site selectivity of oxidative addition is highly dependent on the nature of the phosphine. These studies shed light on the generality of hypotheses regarding the structural influence of different classes of phosphine ligands on the reaction mechanism(s), and deliver a methodology that should prove useful in future studies of phosphine ligands. PMID:27219707

  16. Helical-Peptide-Catalyzed Enantioselective Michael Addition Reactions and Their Mechanistic Insights.

    PubMed

    Ueda, Atsushi; Umeno, Tomohiro; Doi, Mitsunobu; Akagawa, Kengo; Kudo, Kazuaki; Tanaka, Masakazu

    2016-08-01

    Helical peptide foldamer catalyzed Michael addition reactions of nitroalkane or dialkyl malonate to α,β-unsaturated ketones are reported along with the mechanistic considerations of the enantio-induction. A wide variety of α,β-unsaturated ketones, including β-aryl, β-alkyl enones, and cyclic enones, were found to be catalyzed by the helical peptide to give Michael adducts with high enantioselectivities (up to 99%). On the basis of X-ray crystallographic analysis and depsipeptide study, the amide protons, N(2)-H and N(3)-H, at the N terminus in the α-helical peptide catalyst were crucial for activating Michael donors, while the N-terminal primary amine activated Michael acceptors through the formation of iminium ion intermediates. PMID:27384597

  17. Dextran-based hydrogel formed by thiol-Michael addition reaction for 3D cell encapsulation.

    PubMed

    Liu, Zhen Qi; Wei, Zhao; Zhu, Xv Long; Huang, Guo You; Xu, Feng; Yang, Jian Hai; Osada, Yoshihito; Zrínyi, Miklós; Li, Jian Hui; Chen, Yong Mei

    2015-04-01

    Cell encapsulation in three-dimensional (3D) hydrogels can mimic native cell microenvironment and plays a major role in cell-based transplantation therapies. In this contribution, a novel in situ-forming hydrogel, Dex-l-DTT hydrogel ("l" means "linked-by"), by cross-linking glycidyl methacrylate derivatized dextran (Dex-GMA) and dithiothreitol (DTT) under physiological conditions, has been developed using thiol-Michael addition reaction. The mechanical properties, gelation process and degree of swelling of the hydrogel can be easily adjusted by changing the pH of phosphate buffer saline. The 3D cell encapsulation ability is demonstrated by encapsulating rat bone marrow mesenchymal stem cells (BMSCs) and NIH/3T3 fibroblasts into the in situ-forming hydrogel with maintained high viability. The BMSCs also maintain their differentiation potential after encapsulation. These results demonstrate that the Dex-l-DTT hydrogel holds great potential for biomedical field. PMID:25744162

  18. Ab initio calculations of the reaction pathways for methane decomposition over the Cu (111) surface.

    PubMed

    Gajewski, Grzegorz; Pao, Chun-Wei

    2011-08-14

    Growth of large-area, few-layer graphene has been reported recently through the catalytic decomposition of methane (CH(4)) over a Cu surface at high temperature. In this study, we used ab initio calculations to investigate the minimum energy pathways of successive dehydrogenation reactions of CH(4) over the Cu (111) surface. The geometries and energies of all the reaction intermediates and transition states were identified using the climbing image nudged elastic band method. The activation barriers for CH(4) decomposition over this Cu surface are much lower than those in the gas phase; furthermore, analysis of electron density differences revealed significant degrees of charge transfer between the adsorbates and the Cu atoms along the reaction path; these features reveal the role of Cu as the catalytic material for graphene growth. All the dehydrogenation reactions are endothermic, except for carbon dimer (C(2)) formation, which is, therefore, the most critical step for subsequent graphene growth, in particular, on Cu (111) surface. PMID:21842949

  19. Secondary Pollutants from Ozone Reaction with Ventilation Filters and Degradation of Filter Media Additives

    SciTech Connect

    Destaillats, Hugo; Chen, Wenhao; Apte, Michael; Li, Nuan; Spears, Michael; Almosni, Jérémie; Brunner, Gregory; Zhang, Jianshun; Fisk, William J.

    2011-05-01

    Prior research suggests that chemical processes taking place on the surface of particle filters employed in buildings may lead to the formation of harmful secondary byproducts. We investigated ozone reactions with fiberglass, polyester, cotton/polyester and polyolefin filter media, as well as hydrolysis of filter media additives. Studies were carried out on unused media, and on filters that were installed for 3 months in buildings at two different locations in the San Francisco Bay Area. Specimens from each filter media were exposed to {approx}150 ppbv ozone in a flow tube under a constant flow of dry or humidified air (50percent RH). Ozone breakthrough was recorded for each sample over periods of {approx}1000 min; the ozone uptake rate was calculated for an initial transient period and for steady-state conditions. While ozone uptake was observed in all cases, we did not observe significant differences in the uptake rate and capacity for the various types of filter media tested. Most experiments were performed at an airflow rate of 1.3 L/min (face velocity = 0.013 m/s), and a few tests were also run at higher rates (8 to 10 L/min). Formaldehyde and acetaldehyde, two oxidation byproducts, were quantified downstream of each sample. Those aldehydes (m/z 31 and 45) and other volatile byproducts (m/z 57, 59, 61 and 101) were also detected in real-time using Proton-Transfer Reaction - Mass Spectrometry (PTR-MS). Low-ppbv byproduct emissions were consistently higher under humidified air than under dry conditions, and were higher when the filters were loaded with particles, as compared with unused filters. No significant differences were observed when ozone reacted over various types of filter media. Fiberglass filters heavily coated with impaction oil (tackifier) showed higher formaldehyde emissions than other samples. Those emissions were particularly high in the case of used filters, and were observed even in the absence of ozone, suggesting that hydrolysis of additives

  20. Competing retention pathways of uranium upon reaction with Fe(II)

    NASA Astrophysics Data System (ADS)

    Massey, Michael S.; Lezama-Pacheco, Juan S.; Jones, Morris E.; Ilton, Eugene S.; Cerrato, José M.; Bargar, John R.; Fendorf, Scott

    2014-10-01

    Biogeochemical retention processes, including adsorption, reductive precipitation, and incorporation into host minerals, are important in contaminant transport, remediation, and geologic deposition of uranium. Recent work has shown that U can become incorporated into iron (hydr)oxide minerals, with a key pathway arising from Fe(II)-induced transformation of ferrihydrite, (Fe(OH)3·nH2O) to goethite (α-FeO(OH)); this is a possible U retention mechanism in soils and sediments. Several key questions, however, remain unanswered regarding U incorporation into iron (hydr)oxides and this pathway’s contribution to U retention, including: (i) the competitiveness of U incorporation versus reduction to U(IV) and subsequent precipitation of UO2; (ii) the oxidation state of incorporated U; (iii) the effects of uranyl aqueous speciation on U incorporation; and, (iv) the mechanism of U incorporation. Here we use a series of batch reactions conducted at pH ∼7, [U(VI)] from 1 to 170 μM, [Fe(II)] from 0 to 3 mM, and [Ca] at 0 or 4 mM coupled with spectroscopic examination of reaction products of Fe(II)-induced ferrihydrite transformation to address these outstanding questions. Uranium retention pathways were identified and quantified using extended X-ray absorption fine structure (EXAFS) spectroscopy, X-ray powder diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy. Analysis of EXAFS spectra showed that 14-89% of total U was incorporated into goethite, upon reaction with Fe(II) and ferrihydrite. Uranium incorporation was a particularly dominant retention pathway at U concentrations ⩽50 μM when either uranyl-carbonato or calcium-uranyl-carbonato complexes were dominant, accounting for 64-89% of total U. With increasing U(VI) and Fe(II) concentrations, U(VI) reduction to U(IV) became more prevalent, but U incorporation remained a functioning retention pathway. These findings highlight the potential importance of U(V) incorporation within iron

  1. Competing retention pathways of uranium upon reaction with Fe(II)

    SciTech Connect

    Massey, Michael S.; Lezama Pacheco, Juan S.; Jones, Morris; Ilton, Eugene S.; Cerrato, Jose M.; Bargar, John R.; Fendorf, Scott

    2014-10-01

    Biogeochemical retention processes, including adsorption, reductive precipitation, and incorporation into host minerals, are important in contaminant transport, remediation, and geologic deposition of uranium. Recent work has shown that U can become incorporated into iron (hydr)oxide minerals, with a key pathway arising from Fe(II)-induced transformation of ferrihydrite, (Fe(OH)3•nH2O) to goethite (α-FeO(OH)); this is a possible U retention mechanism in soils and sediments. Several key questions, however, remain unanswered regarding U incorporation into iron (hydr)oxides and this pathway’s contribution to U retention, including: (i) the competitiveness of U incorporation versus reduction to U(IV) and subsequent precipitation of UO2; (ii) the oxidation state of incorporated U; (iii) the effects of uranyl aqueous speciation on U incorporation; and, (iv) the mechanism of U incorporation. Here we use a series of batch reactions conducted at pH ~7, [U(VI)] from 1 to 170 μM, [Fe(II)] from 0 to 3 mM, and [Ca] at 0 or 4 mM) coupled with spectroscopic examination of reaction products of Fe(II)-induced ferrihydrite transformation to address these outstanding questions. Uranium retention pathways were identified and quantified using extended x-ray absorption fine structure (EXAFS) spectroscopy, x-ray powder diffraction, x-ray photoelectron spectroscopy, and transmission electron microscopy. Analysis of EXAFS spectra showed that 14 to 89% of total U was incorporated into goethite, upon reaction with Fe(II) and ferrihydrite. Uranium incorporation was a particularly dominant retention pathway at U concentrations ≤ 50 μM when either uranyl-carbonato or calcium-uranyl-carbonato complexes were dominant, accounting for 64 to 89% of total U. With increasing U(VI) and Fe(II) concentrations, U(VI) reduction to U(IV) became more prevalent, but U incorporation remained a functioning retention pathway. These findings highlight the potential importance of U(V) incorporation within

  2. Cinchona Alkaloid Catalyzed Sulfa-Michael Addition Reactions Leading to Enantiopure β-Functionalized Cysteines.

    PubMed

    Breman, Arjen C; Telderman, Suze E M; van Santen, Roy P M; Scott, Jamie I; van Maarseveen, Jan H; Ingemann, Steen; Hiemstra, Henk

    2015-11-01

    Sulfa-Michael additions to α,β-unsaturated N-acylated oxazolidin-2-ones and related α,β-unsaturated α-amino acid derivatives have been enantioselectively catalyzed by Cinchona alkaloids functionalized with a hydrogen bond donating group at the C6' position. The series of Cinchona alkaloids includes known C6' (thio)urea and sulfonamide derivatives and several novel species with a benzimidazole, squaramide or a benzamide group at the C6' position. The sulfonamides were especially suited as bifunctional organocatalysts as they gave the products in very good diastereoselectivity and high enantioselectivity. In particular, the C6' sulfonamides catalyzed the reaction with the α,β-unsaturated α-amino acid derivatives to afford the products in a diastereomeric ratio as good as 93:7, with the major isomer being formed in an ee of up to 99%. The products of the organocatalytic sulfa-Michael addition to α,β-unsaturated α-amino acid derivatives were subsequently converted in high yields to enantiopure β-functionalized cysteines suitable for native chemical ligation. PMID:26451627

  3. [Adaptive reactions of dehydrogenation processes in root voles during additional impacts of the physical nature].

    PubMed

    Kudiasheva, A G; Taskaev, A I

    2011-01-01

    Variations of the dehydrogenation enzyme activity (succinate dehydrogenase, pyruvate dehydrogenase, lactate dehydrogenase) in the heart muscle, liver and brain of root voles (Microtus oeconomus Pall.) and their progeny associated with additional stress effects (chronic low-level gamma-irradiation, short-term exposure to cold) have been studied. Root voles (parents) were caught in the areas with a normal and high-level natural radioactivity in the Republic of Komi. It has been revealed that the direction of shifts of the dehydrogenation enzyme activity in response to the factors of the physical nature is determined by the initial level of the oxidation process in tissues of root voles and their progeny that haven't been subjected to these actions. The reaction of root voles and their progeny (1-3 generations) from the radium zone has lower reserve functional possibilities in relation to the additional exposure as compared with the animals from the control zone. In some cases, chronic low-level irradiation and short-term cooling lead to leveling of differences between groups of animals which initially varied from each other in biochemical indexes. PMID:22279768

  4. Seeding the Pregenetic Earth: Meteoritic Abundances of Nucleobases and Potential Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Pearce, Ben K. D.; Pudritz, Ralph E.

    2015-07-01

    Carbonaceous chondrites are a class of meteorite known for having high contents of water and organics. In this study, the abundances of the nucleobases, i.e., the building blocks of RNA and DNA, found in carbonaceous chondrites are collated from a variety of published data and compared across various meteorite classes. An extensive review of abiotic chemical reactions producing nucleobases is then performed. These reactions are then reduced to a list of 15 individual reaction pathways that could potentially occur within meteorite parent bodies. The nucleobases guanine, adenine, and uracil are found in carbonaceous chondrites in amounts of 1–500 ppb. It is currently unknown which reaction is responsible for their synthesis within the meteorite parent bodies. One class of carbonaceous meteorite dominates the abundances of both amino acids and nucleobases—the so-called CM2 (e.g., Murchison meteorite). CR2 meteorites (e.g., Graves Nunataks) also dominate the abundances of amino acids, but are the least abundant in nucleobases. The abundances of total nucleobases in these two classes are 330 ± 250 and 16 ± 13 ppb, respectively. Guanine most often has the greatest abundances in carbonaceous chondrites with respect to the other nucleobases, but is 1–2 orders of magnitude less abundant in CM2 meteorites than glycine (the most abundant amino acid). Our survey of the reaction mechanisms for nucleobase formation suggests that Fischer–Tropsch synthesis (i.e., CO, H2, and NH3 gases reacting in the presence of a catalyst such as alumina or silica) is the most likely candidate for conditions that characterize the early states of planetesimals.

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

    PubMed

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

    2016-07-27

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

  6. Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase.

    PubMed

    Cornish, Adam J; Ginovska, Bojana; Thelen, Adam; da Silva, Julio C S; Soares, Thereza A; Raugei, Simone; Dupuis, Michel; Shaw, Wendy J; Hegg, Eric L

    2016-06-01

    The proton pathway of [FeFe]-hydrogenase is essential for enzymatic H2 production and oxidation and is composed of four residues and a water molecule. A computational analysis of this pathway in the [FeFe]-hydrogenase from Clostridium pasteurianum revealed that the solvent-exposed residue of the pathway (Glu282) forms hydrogen bonds to two residues outside of the pathway (Arg286 and Ser320), implying that these residues could function in regulating proton transfer. In this study, we show that substituting Arg286 with leucine eliminates hydrogen bonding with Glu282 and results in an ∼3-fold enhancement of H2 production activity when methyl viologen is used as an electron donor, suggesting that Arg286 may help control the rate of proton delivery. In contrast, substitution of Ser320 with alanine reduces the rate ∼5-fold, implying that it either acts as a member of the pathway or influences Glu282 to permit proton transfer. Interestingly, quantum mechanics/molecular mechanics and molecular dynamics calculations indicate that Ser320 does not play a structural role or indirectly influence the barrier for proton movement at the entrance of the channel. Rather, it may act as an additional proton acceptor for the pathway or serve in a regulatory role. While further studies are needed to elucidate the role of Ser320, collectively these data provide insights into the complex proton transport process. PMID:27186945

  7. Computerized pathway elucidation for hydroxyl radical-induced chain reaction mechanisms in aqueous phase advanced oxidation processes.

    PubMed

    Li, Ke; Crittenden, John

    2009-04-15

    The radical reaction mechanism that is involved in advanced oxidation processes is complex. An increasing number of trace contaminants and stringent drinking water standards call for a rule-based model to provide insight to the mechanism of the processes. A model was developed to predict the pathway of contaminant degradation and byproduct formation during advanced oxidation. The model builds chemical molecules as graph objects, which enables mathematic abstraction of chemicals and preserves chemistry information. The model algorithm enumerates all possible reaction pathways according to the elementary reactions (built as reaction rules) established from experimental observation. The method can predict minor pathways that could lead to toxic byproducts so that measures can be taken to ensure drinking water treatment safety. The method can be of great assistance to water treatment engineers and chemists who appreciate the mechanism of treatment processes. PMID:19475958

  8. HIGHLY DIASTEREOSELECTIVE MICHAEL REACTION UNDER SOLVENT-FREE CONDITIONS USING MICROWAVES: CONJUGATE ADDITION OF FLAVANONE TO ITS CHALCONE PRECURSOR

    EPA Science Inventory

    Microwave-assisted reaction of 2'-hydroxychalcones in the presence of DBU resulted in the formation of hitherto unknown dimers by conjugate addition of the intermediate cyclic ketone to the starting enone.

  9. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    PubMed Central

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  10. The molecular basis for the post-translational addition of amino acids by L/F transferase in the N-end rule pathway.

    PubMed

    Fung, Angela Wai S; Fahlman, Richard P

    2015-01-01

    The N-end rule pathway is a conserved targeted proteolytic process observed in organisms ranging from eubacteria to mammals. The N-end rule relates the metabolic stability of a protein to its N-terminal amino acid residue. The identity of the N-terminal amino acid residue is a primary degradation signal, often referred to as an N-degron, which is recognized by the components of the N-end rule when it is a destabilizing N-terminus. N-degrons may be exposed by non-processive proteolytic cleavages or by post-translational modifications. One modification is the post-translational addition of amino acids to the N-termini of proteins, a reaction catalyzed by aminoacyl-tRNA protein transferases. The aminoacyl-tRNA protein transferase in eubacteria like Escherichia coli is L/F transferase. Recent investigations have reported unexpected observations regarding the L/F transferase catalytic mechanism and its mechanisms of substrate recognition. Additionally, recent proteome-wide identification of putative in vivo substrates facilitates hypothesis into the yet elusive biological functions of the prokaryotic N-end rule pathway. Here we summarize the recent findings on the molecular mechanisms of catalysis and substrate recognition by the E. coli L/F transferase in the prokaryotic N-end rule pathway. PMID:25692952

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

    NASA Astrophysics Data System (ADS)

    Pimentel, Carlos; Pina, Carlos M.

    2016-04-01

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

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

    SciTech Connect

    Vikas, E-mail: qlabspu@yahoo.com; Kaur, Gurpreet

    2013-12-14

    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.

  13. Reaction pathways for ethanol on model Co/ZnO(0001) catalysts.

    PubMed

    Martono, Eddie; Hyman, Matthew P; Vohs, John M

    2011-05-28

    The pathways for the reaction of ethanol on model catalysts consisting of Co and CoO films and particles supported on single crystal ZnO(0001) surfaces were studied using X-ray Photoelectron Spectroscopy (XPS) and Temperature Programmed Desorption (TPD). On supported metallic Co films and particles ethanol was found to primarily undergo decarbonylation forming CO, H(2), and adsorbed methyl groups. In contrast, supported CoO particles were found to be largely unreactive toward ethanol. High selectivity to the dehydrogenation product, acetaldehyde, was only observed when the supported Co was partially oxidized and contained both Co(0) and Co(2+). Since acetaldehyde is thought to be a critical intermediate during steam reforming of ethanol (SRE) to produce H(2) and CO(2), the results of this study suggest that partially oxidized Co species provide the active sites for this reaction. This result is consistent with studies of high surface area Co/ZnO catalysts which also suggest that both Co(0) and Co(2+) species are present under typical SRE reaction conditions. PMID:21475754

  14. Additive Runge-Kutta Schemes for Convection-Diffusion-Reaction Equations

    NASA Technical Reports Server (NTRS)

    Kennedy, Christopher A.; Carpenter, Mark H.

    2002-01-01

    Additive Runge-Kutta (ARK) methods are investigated for application to the spatially discretized one- dimensional convection-diffusion-reaction (CDR) equations. Accuracy, stability, conservation, and dense-output are first considered for the general case when N different Runge-Kutta methods are grouped into a single composite method. Then, implicit-explicit, (N = 2), additive Runge-Kutta (ARK(sub 2)) methods from third- to fifth-order are presented that allow for integration of stiff terms by an L-stable, stiffly-accurate explicit, singly diagonally implicit Runge-Kutta (ESDIRK) method while the nonstiff terms are integrated with a traditional explicit Runge-Kutta method (ERK). Coupling error terms of the partitioned method are of equal order to those of the elemental methods. Derived ARK(sub 2) methods have vanishing stability functions for very large values of the stiff scaled eigenvalue, z['] yields -infinity, and retain high stability efficiency in the absence of stiffness, z['] yield 0. Extrapolation-type stage- value predictors are provided based on dense-output formulae. Optimized methods minimize both leading order ARK(sub 2) error terms and Butcher coefficient magnitudes as well as maximize conservation properties. Numerical tests of the new schemes on a CDR problem show negligible stiffness leakage and near classical order convergence rates. However, tests on three simple singular-perturbation problems reveal generally predictable order reduction. Error control is best managed with a PID-controller. While results for the fifth-order method are disappointing, both the new third- and fourth-order methods are at least as efficient as existing ARK(sub 2) methods.

  15. Additive Runge-Kutta Schemes for Convection-Diffusion-Reaction Equations

    NASA Technical Reports Server (NTRS)

    Kennedy, Christopher A.; Carpenter, Mark H.

    2001-01-01

    Additive Runge-Kutta (ARK) methods are investigated for application to the spatially discretized one-dimensional convection-diffusion-reaction (CDR) equations. First, accuracy, stability, conservation, and dense output are considered for the general case when N different Runge-Kutta methods are grouped into a single composite method. Then, implicit-explicit, N = 2, additive Runge-Kutta ARK2 methods from third- to fifth-order are presented that allow for integration of stiff terms by an L-stable, stiffly-accurate explicit, singly diagonally implicit Runge-Kutta (ESDIRK) method while the nonstiff terms are integrated with a traditional explicit Runge-Kutta method (ERK). Coupling error terms are of equal order to those of the elemental methods. Derived ARK2 methods have vanishing stability functions for very large values of the stiff scaled eigenvalue, z(exp [I]) goes to infinity, and retain high stability efficiency in the absence of stiffness, z(exp [I]) goes to zero. Extrapolation-type stage-value predictors are provided based on dense-output formulae. Optimized methods minimize both leading order ARK2 error terms and Butcher coefficient magnitudes as well as maximize conservation properties. Numerical tests of the new schemes on a CDR problem show negligible stiffness leakage and near classical order convergence rates. However, tests on three simple singular-perturbation problems reveal generally predictable order reduction. Error control is best managed with a PID-controller. While results for the fifth-order method are disappointing, both the new third- and fourth-order methods are at least as efficient as existing ARK2 methods while offering error control and stage-value predictors.

  16. Position-specific isotope modeling of organic micropollutants transformations through different reaction pathways

    NASA Astrophysics Data System (ADS)

    Jin, Biao; Rolle, Massimo

    2016-04-01

    Organic compounds are produced in vast quantities for industrial and agricultural use, as well as for human and animal healthcare [1]. These chemicals and their metabolites are frequently detected at trace levels in fresh water environments where they undergo degradation via different reaction pathways. Compound specific stable isotope analysis (CSIA) is a valuable tool to identify such degradation pathways in different environmental systems. Recent advances in analytical techniques have promoted the fast development and implementation of multi-element CSIA. However, quantitative frameworks to evaluate multi-element stable isotope data and incorporating mechanistic information on the degradation processes [2,3] are still lacking. In this study we propose a mechanism-based modeling approach to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. We validate the proposed approach with the concentration and multi-element isotope data of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model precisely captures the dual element isotope trends characteristic of different reaction pathways and their range of variation consistent with observed multi-element (C, N) bulk isotope fractionation. The proposed approach can also be used as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. [1] Schwarzenbach, R.P., Egli, T., Hofstetter, T.B., von Gunten, U., Wehrli, B., 2010. Global Water Pollution and Human Health. Annu. Rev. Environ. Resour. doi:10.1146/annurev-environ-100809-125342. [2] Jin, B., Haderlein, S.B., Rolle, M

  17. Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study.

    PubMed

    Kumari, Manju; Kozmon, Stanislav; Kulhánek, Petr; Štepán, Jakub; Tvaroška, Igor; Koča, Jaroslav

    2015-03-26

    The inverting O-GlcNAc glycosyltransferase (OGT) is an important post-translation enzyme, which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to the hydroxyl group of the Ser/Thr of cytoplasmic, nuclear, and mitochondrial proteins. In the past, three different catalytic bases were proposed for the reaction: His498, α-phosphate, and Asp554. In this study, we used hybrid quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello molecular dynamics to investigate reaction paths using α-phosphate and Asp554 as the catalytic bases. The string method was used to calculate the free-energy reaction profiles of the tested mechanisms. During the investigations, an additional mechanism was observed. In this mechanism, a proton is transferred to α-phosphate via a water molecule. Our calculations show that the mechanism with α-phosphate acting as the base is favorable. This reaction has a rate-limiting free-energy barrier of 23.5 kcal/mol, whereas reactions utilizing Asp554 and water-assisted α-phosphate have barriers of 41.7 and 40.9 kcal/mol, respectively. Our simulations provide a new insight into the catalysis of OGT and may thus guide rational drug design of transition-state analogue inhibitors with potential therapeutic use. PMID:25731954

  18. Reactions of Propylene Oxide on Supported Silver Catalysts: Insights into Pathways Limiting Epoxidation Selectivity

    SciTech Connect

    Kulkarni, Apoorva; Bedolla-Pantoja, Marco; Singh, Suyash; Lobo, Raul F.; Mavrikakis, Manos; Barteau, Mark A.

    2012-02-04

    The reactions of propylene oxide (PO) on silver catalysts were studied to understand the network of parallel and sequential reactions that may limit the selectivity of propylene epoxidation by these catalysts. The products of the anaerobic reaction of PO on Ag/a-Al2O3 were propanal, acetone and allyl alcohol for PO conversions below 2–3%. As the conversion of PO was increased either by increasing the temperature or the contact time, acrolein was formed at the expense of propanal, indicating that acrolein is a secondary reaction product in PO decomposition. With addition of oxygen to the feedstream the conversion of PO increased moderately. In contrast to the experiments in absence of oxygen, CO2 was a significant product while the selectivity to propanal decreased as soon as oxygen was introduced in the system. Allyl alcohol disappeared completely from the product stream in the presence of oxygen, reacting to form acrolein and CO2. The product distribution may be explained by a network of reactions involving two types of oxametallacycles formed by ring opening of PO: one with the oxygen bonded to C1 (OMC1, linear) and the other with oxygen bonded to C2 (OMC2, branched). OMC1 reacts to form PO, propanal, and allyl alcohol.

  19. Evidence of additional excitation energy transfer pathways in the phycobiliprotein antenna system of Acaryochloris marina.

    PubMed

    Nganou, A C; David, L; Adir, N; Pouhe, D; Deen, M J; Mkandawire, M

    2015-02-01

    To improve the energy conversion efficiency of solar organic cells, the clue may lie in the development of devices inspired by an efficient light harvesting mechanism of some aquatic photosynthetic microorganisms that are adapted to low light intensity. Consequently, we investigated the pathways of excitation energy transfer (EET) from successive light harvesting pigments to the low energy level inside the phycobiliprotein antenna system of Acaryochloris marina, a cyanobacterium, using a time resolved absorption difference spectroscopy with a resolution time of 200 fs. The objective was to understand the actual biochemical process and pathways that determine the EET mechanism. Anisotropy of the EET pathway was calculated from the absorption change trace in order to determine the contribution of excitonic coupling. The results reveal a new electron energy relaxation pathway of 14 ps inside the phycocyanin component, which runs from phycocyanin to the terminal emitter. The bleaching of the 660 nm band suggests a broader absorption of the terminal emitter between 660 nm and 675 nm. Further, there are trimer depolarization kinetics of 450 fs and 500 fs in high and low ionic strength, respectively, which arise from the relaxation of the β84 and α84 in adjacent monomers of phycocyanin. Under conditions of low ionic strength buffer solution, the evolution of the kinetic amplitude during the depolarization of the trimer is suggestive of trimer conservation within the phycocyanin hexamer. The anisotropy values were 0.38 and 0.40 in high and in low ionic strength, respectively, indicating that there is no excitonic delocalization in the high energy level of phycocyanin hexamers. PMID:25470281

  20. Addition reaction of alkyl radical to C60 fullerene: Density functional theory study

    NASA Astrophysics Data System (ADS)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-02-01

    Functionalized fullerenes are known as a high-performance molecules. In this study, the alkyl-functionalized fullerenes (denoted by R-C60) have been investigated by means of the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of fullerene. Also, the reaction mechanism of alkyl radicals with C60 was investigated. The methyl, ethyl, propyl, and butyl radicals (denoted by n = 1-4, where n means the number of carbon atoms in the alkyl radical) were examined as alkyl radicals. The DFT calculation showed that the alkyl radical binds to the carbon atom of C60 at the on-top site, and a strong C-C single bond is formed. The binding energies of alkyl radicals to C60 were distributed in the range of 31.8-35.1 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists before alkyl addition, the barrier heights were calculated to be 2.1-2.8 kcal mol-1. The electronic states of R-C60 complexes were discussed on the basis of the theoretical results.

  1. Synthesis of the Hemoglobin-Conjugated Polymer Micelles by Thiol Michael Addition Reactions.

    PubMed

    Qi, Yanxin; Li, Taihang; Wang, Yupeng; Wei, Xing; Li, Bin; Chen, Xuesi; Xie, Zhigang; Jing, Xiabin; Huang, Yubin

    2016-06-01

    Amphiphilic triblock copolymers mPEG-b-PMAC-b-PCL are synthesized using methoxyl poly(ethylene glycol), cyclic carbonic ester monomer including acryloyl group, and ε-caprolactone. Copolymers are self-assembled into core-shell micelles in aqueous solution. Thiolated hemoglobin (Hb) is conjugated with micelles sufficiently through thiol Michael addition reaction to form hemoglobin nanoparticles (HbNs) with 200 nm in diameter. The conjugation of Hb onto the micelle surface is further confirmed by X-ray photoelectron spectroscopy. Feeding ratio of copolymer micelles to Hb at 1:3 would lead to the highest hemoglobin loading efficiency 36.7 wt%. The UV results demonstrate that the gas transporting capacity of HbNs is well remained after Hb is conjugated with polymeric micelles. Furthermore, the obtained HbNs have no obvious detrimental effects on blood components in vitro. This system may thus have great potential as one of the candidates to be developed as oxygen carriers and provide a reference for the modification of protein drugs. PMID:26938024

  2. Pathway and kinetic analysis on the iso-propyl radical + O{sub 2} reaction system

    SciTech Connect

    Bozzelli, J.W.; Pitz, W.J.

    1997-04-07

    We analyze the isopropyl + 02 reaction system using thermochemical Transition State Theory (TST), molecular thermodynamic properties, analysis (quantum RRK) for k(E) and modified strong collision analyze Cyclic transition states for both hydrogen transfer and concerted propylene from isopropylperoxy are calculated using semi-empirical theory in addition to transition states for H02 elimination from hydroperoxy-isopropyl. Computed rate constants are compared to constant measurements of for isopropyl + H02.

  3. Fundamental Reaction Pathway and Free Energy Profile for Butyrylcholinesterase-Catalyzed Hydrolysis of Heroin

    PubMed Central

    Qiao, Yan; Han, Keli; Zhan, Chang-Guo

    2013-01-01

    The pharmacological function of heroin requires an activation process which transforms heroin into 6-monoacetylmorphine (6-MAM) which is the most active form. The primary enzyme responsible for this activation process in human plasma is butyrylcholinesterase (BChE). The detailed reaction pathway of the activation process via BChE-catalyzed hydrolysis has been explored computationally, for the first time, in the present study by performing molecular dynamics simulation and first-principles quantum mechanical/molecular mechanical free energy calculations. It has been demonstrated that the whole reaction process includes acylation and deacylation stages. The acylation consists of two reaction steps, i.e. the nucleophilic attack on the carbonyl carbon of 3-acetyl group of heroin by the hydroxyl oxygen of Ser198 side chain and the dissociation of 6-MAM. The deacylation also consists of two reaction steps, i.e. the nucleophilic attack on the carbonyl carbon of the acyl-enzyme intermediate by a water molecule and the dissociation of the acetic acid from Ser198. The calculated free energy profile reveals that the second transition state (TS2) should be rate-determining. The structural analysis reveals that the oxyanion hole of BChE plays an important role in the stabilization of the rate-determining transition state TS2. The free energy barrier (15.9±0.2 or 16.1±0.2 kcal/mol) calculated for the rate-determining step is in good agreement with the experimentally-derived activation free energy (~16.2 kcal/mol), suggesting that the mechanistic insights obtained from the present computational study are reliable. The obtained structural and mechanistic insights could be valuable for use in future rational design of a novel therapeutic treatment of heroin abuse. PMID:23992153

  4. Noble metal-free hydrazine fuel cell catalysts: EPOC effect in competing chemical and electrochemical reaction pathways.

    PubMed

    Sanabria-Chinchilla, Jean; Asazawa, Koichiro; Sakamoto, Tomokazu; Yamada, Koji; Tanaka, Hirohisa; Strasser, Peter

    2011-04-13

    We report the discovery of a highly active Ni-Co alloy electrocatalyst for the oxidation of hydrazine (N(2)H(4)) and provide evidence for competing electrochemical (faradaic) and chemical (nonfaradaic) reaction pathways. The electrochemical conversion of hydrazine on catalytic surfaces in fuel cells is of great scientific and technological interest, because it offers multiple redox states, complex reaction pathways, and significantly more favorable energy and power densities compared to hydrogen fuel. Structure-reactivity relations of a Ni(60)Co(40) alloy electrocatalyst are presented with a 6-fold increase in catalytic N(2)H(4) oxidation activity over today's benchmark catalysts. We further study the mechanistic pathways of the catalytic N(2)H(4) conversion as function of the applied electrode potential using differentially pumped electrochemical mass spectrometry (DEMS). At positive overpotentials, N(2)H(4) is electrooxidized into nitrogen consuming hydroxide ions, which is the fuel cell-relevant faradaic reaction pathway. In parallel, N(2)H(4) decomposes chemically into molecular nitrogen and hydrogen over a broad range of electrode potentials. The electroless chemical decomposition rate was controlled by the electrode potential, suggesting a rare example of a liquid-phase electrochemical promotion effect of a chemical catalytic reaction ("EPOC"). The coexisting electrocatalytic (faradaic) and heterogeneous catalytic (electroless, nonfaradaic) reaction pathways have important implications for the efficiency of hydrazine fuel cells. PMID:21425793

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

    PubMed

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

    2016-07-11

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

  6. Oxidation of Annelated Diarylamines: Analysis of Reaction Pathways to Nitroxide Diradical and Spirocyclic Products

    SciTech Connect

    Rajca, Andrzej; Shiraishi, Kouichi; Boraty; #324; ski, Przemyslaw J.; Pink, Maren; Miyasaka, Makoto; Rajca, Suchada

    2012-02-06

    Oxidation of diaryldiamine 2, a tetrahydrodiazapentacene derivative, provides diarylnitroxide diradical 1 accompanied by an intermediate nitroxide monoradical and a multitude of isolable diamagnetic products. DFT-computed tensors for EPR spectra and paramagnetic {sup 1}H NMR isotropic shifts for nitroxide diradical 1 show good agreement with the experimental EPR spectra in rigid matrices and paramagnetic {sup 1}H NMR spectra in solution, respectively. Examination of the diamagnetic products elucidates their formation via distinct pathways involving C-O bond-forming reactions, including Baeyer-Villiger-type oxidations. An unusual diiminoketone structure and two spirocyclic structures of the predominant diamagnetic products are confirmed by either X-ray crystallography or correlations between DFT-computed and experimental spectroscopic data such as {sup 1}H, {sup 13}C, and {sup 15}N NMR chemical shifts and electronic absorption spectra.

  7. Catalysts and Reaction Pathways for the Electrochemical Reduction of Carbon Dioxide.

    PubMed

    Kortlever, Ruud; Shen, Jing; Schouten, Klaas Jan P; Calle-Vallejo, Federico; Koper, Marc T M

    2015-10-15

    The electrochemical reduction of CO2 has gained significant interest recently as it has the potential to trigger a sustainable solar-fuel-based economy. In this Perspective, we highlight several heterogeneous and molecular electrocatalysts for the reduction of CO2 and discuss the reaction pathways through which they form various products. Among those, copper is a unique catalyst as it yields hydrocarbon products, mostly methane, ethylene, and ethanol, with acceptable efficiencies. As a result, substantial effort has been invested to determine the special catalytic properties of copper and to elucidate the mechanism through which hydrocarbons are formed. These mechanistic insights, together with mechanistic insights of CO2 reduction on other metals and molecular complexes, can provide crucial guidelines for the design of future catalyst materials able to efficiently and selectively reduce CO2 to useful products. PMID:26722779

  8. Locating all transition states and studying the reaction pathways of potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Westerberg, K. M.; Floudas, C. A.

    1999-05-01

    We propose a new method for calculating all stationary states, including saddle points of all orders, of a potential energy surface based on the αBB deterministic branch and bound global optimization algorithm. This method is based on rigorous optimization methods and offers a theoretical guarantee of enclosing all solutions to the equation ∇V=0. We apply this method to Murrel-Sorbie analytic potential energy surfaces of HCN, HSiN, HBO, and CS2, and to the Empirical Conformational Energy Program for Peptides (ECEPP/3) potential energy surfaces of alanine, alanine dipeptide, and tetra-alanine. For alanine, alanine dipeptide, and tetra-alanine, we proceed to analyze the topography of the potential energy surface by calculating reaction pathways, transition rate matrices, time-evolution of occupation probabilities, and rate disconnectivity graphs.

  9. Kinetics and reaction pathways of formaldehyde degradation using the UV-fenton method.

    PubMed

    Liu, Xiangxuan; Liang, Jiantao; Wang, Xuanjun

    2011-05-01

    This study was based on the purpose of investigating the reaction rules of formaldehyde (HCHO) as an intermediate product in the degradation of many other organic wastewaters. The process conditions of UV-Fenton method for the degradation of the low concentrations of HCHO were studied in a batch photochemical reactor. The results showed that, when the original HCHO concentration was 30 mg/L, at an operating temperature of 23 degrees C, pH = 3, an H202 dosage of 68 mg/L, and an H2O2-to-Fe2+ mole ratio (H2O2:Fe2+) of 5, 91.89% of the HCHO was removed after 30 minutes. The degradation of HCHO in the UV-Fenton system was basically in accordance with the exponential decay. The kinetic study results showed that the reaction orders of HCHO, Fe2+, and H2O2 in the system were 1.054, 0.510, and 0.728, respectively, and the activation energy (Ea) was 9.85 kJ/mol. The comparison of UV/H2O2, Fenton, and UV-Fenton systems for the degradation of HCHO, and the results of iron catalyst tests showed that the mechanism of UV-Fenton on the degradation of HCHO was through a synergistic effect of Fe2+ and UV light to catalyze the decomposition of H2O2. The introduction of UV irradiation to the Fenton system largely increased the degradation rate of HCHO, mainly as a result of the accelerating effect on the formation of the Fe2+/Fe3+ cycle. The reaction products were analyzed by gas chromatography-mass spectrometry and a chemical oxygen demand (COD) analyzer. The effluent gases also were analyzed by gas chromatography. Based on those results, the reaction pathways of HCHO in the UV-Fenton system were proposed. The qualitative and quantitative analysis of the reaction products and the COD showed that the main intermediate product of the reaction was formic acid, and the further oxidation of it was the rate-limiting step for the degradation of HCHO. PMID:21657193

  10. Modeling reaction histories to study chemical pathways in condensed phase detonation

    NASA Astrophysics Data System (ADS)

    Scott Stewart, D.; Hernández, Alberto; Lee, Kibaek

    2016-03-01

    The estimation of pressure and temperature histories, which are required to understand chemical pathways in condensed phase explosives during detonation, is discussed. We argue that estimates made from continuum models, calibrated by macroscopic experiments, are essential to inform modern, atomistic-based reactive chemistry simulations at detonation pressures and temperatures. We present easy to implement methods for general equation of state and arbitrarily complex chemical reaction schemes that can be used to compute reactive flow histories for the constant volume, the energy process, and the expansion process on the Rayleigh line of a steady Chapman-Jouguet detonation. A brief review of state-of-the-art of two-component reactive flow models is given that highlights the Ignition and Growth model of Lee and Tarver [Phys. Fluids 23, 2362 (1980)] and the Wide-Ranging Equation of State model of Wescott, Stewart, and Davis [J. Appl. Phys. 98, 053514 (2005)]. We discuss evidence from experiments and reactive molecular dynamic simulations that motivate models that have several components, instead of the two that have traditionally been used to describe the results of macroscopic detonation experiments. We present simplified examples of a formulation for a hypothetical explosive that uses simple (ideal) equation of state forms and detailed comparisons. Then, we estimate pathways computed from two-component models of real explosive materials that have been calibrated with macroscopic experiments.

  11. Chemistry of Zerumbone. 1. Simplified Isolation, Conjugate Addition Reactions, and a Unique Ring Contracting Transannular Reaction of Its Dibromide.

    PubMed

    Kitayama, Takashi; Okamoto, Tadashi; Hill, Richard K.; Kawai, Yasushi; Takahashi, Sho; Yonemori, Shigetomo; Yamamoto, Yukio; Ohe, Kouichi; Uemura, Sakae; Sawada, Seiji

    1999-04-16

    Zerumbone (1) was isolated from fresh rhizomes of Zingiber zerumbet Smith in yields of 0.3-0.4% by simple steam distillation and recrystallization. 1 accepted 2 equiv of hydrogen cyanide at the C6 and C9 double bonds of the cross-conjugated dienone system to give a mixture of diastereomers 3a-d. In the presence of potassium cyanide, the dominant isomer 3a was isomerized to a mixture of 3a-d. Under controlled conditions, 1 added one mole of methanol regio- and stereoselectively at the C6 double bond to give adduct 4a. With potassium cyanide, 4a was transformed to the mixture of 3a-d. 1 took up one mole of bromine at C6 double bond to give a diastereomeric mixture of adducts 5a and 5b. Treatment of 5a with potassium cyanide gave a mixture of cyclopropanecarboxylic acid 6a and 6b. This unique ring-contracting cyclopropane formation is pictured as a sequential Favorskii type reaction. alpha-Cyclodextrin improved the selectivity and yields of the reactions conducted in an aqueous medium. PMID:11674334

  12. Atmospheric transport and deposition, an additional input pathway for triazine herbicides to surface waters

    SciTech Connect

    Muir, D.C.G.; Rawn, D.F.

    1996-10-01

    Although surface runoff from treated fields is regarded as the major route of entry of triazine herbicides to surface waters, other pathways such as deposition via precipitation, gas absorption and dryfall may also be important. Triazine herbicides have been detected in precipitation but there has been only a very limited amount of work on gas phase and aerosols. To examine the importance of atmospheric inputs concentrations of atrazine, cyanazine and terbuthylazine in gas phase/aerosols, precipitation, and surface waters were determined (along with other herbicides) using selected ion GC-MS. Atrazine was detected at low ng/L concentrations in surface waters (<0.04-5.3 ng/L) and precipitation (0.1-53 ng/L), and at 0.02-0.1 ng/m{sup 3} in air. Cyanazine and terbuthylazine were detected in air and infrequently in water. Highest atrazine concentrations in air were found during June each year on both gas phase and particles. Concentrations of atrazine in surface waters at both locations increased during June, even in the absence of precipitation or overland flow, presumably due to inputs from dryfall and to gas areas and boreal forest lakes due to transport and deposition. Ecological risk assessment of triazines, especially for pristine aquatic environments should include consideration of this atmospheric pathway.

  13. The NBS Reaction: A Simple Explanation for the Predominance of Allylic Substitution over Olefin Addition by Bromine at Low Concentrations.

    ERIC Educational Resources Information Center

    Wamser, Carl C.; Scott, Lawrence T.

    1985-01-01

    Examines mechanisms related to use of N-bromosuccinimide (NBS) for bromination at an allylic position. Also presents derived rate laws for three possible reactions of molecular bromine with an alkene: (1) free radical substitution; (2) free radical addition; and (3) electrophilic addition. (JN)

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

    PubMed

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

    2005-05-27

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

  15. Structural Snapshots of Escherichia coli Histidinol Phosphate Phosphatase along the Reaction Pathway

    SciTech Connect

    Rangarajan,E.; Proteau, A.; Wagner, J.; Hung, M.; Matte, A.; Cygler, M.

    2006-01-01

    HisB from Escherichia coli is a bifunctional enzyme catalyzing the sixth and eighth steps of L-histidine biosynthesis. The N-terminal domain (HisB-N) possesses histidinol phosphate phosphatase activity, and its crystal structure shows a single domain with fold similarity to the haloacid dehalogenase (HAD) enzyme family. HisB-N forms dimers in the crystal and in solution. The structure shows the presence of a structural Zn{sup 2+} ion stabilizing the conformation of an extended loop. Two metal binding sites were also identified in the active site. Their presence was further confirmed by isothermal titration calorimetry. HisB-N is active in the presence of Mg{sup 2+}, Mn{sup 2+}, Co{sup 2+}, or Zn{sup 2+}, but Ca{sup 2+} has an inhibitory effect. We have determined structures of several intermediate states corresponding to snapshots along the reaction pathway, including that of the phosphoaspartate intermediate. A catalytic mechanism, different from that described for other HAD enzymes, is proposed requiring the presence of the second metal ion not found in the active sites of previously characterized HAD enzymes, to complete the second half-reaction. The proposed mechanism is reminiscent of two-Mg{sup 2+} ion catalysis utilized by DNA and RNA polymerases and many nucleases. The structure also provides an explanation for the inhibitory effect of Ca{sup 2+}.

  16. In search of a viable reaction pathway in the chelation of a metallo-protein

    NASA Astrophysics Data System (ADS)

    Rose, Frisco; Hodak, Miroslav; Bernholc, Jerry

    2010-03-01

    Misfolded metallo-proteins are potential causal agents in the onset of neuro-degenerative diseases, such as Alzheimer's and Parkinson's Diseases (PD). Experimental results involving metal chelation have shown significant promise in symptom reduction and misfolding reversal. We explore, through atomistic simulations, potential reaction pathways for the chelation of Cu^2+ from the metal binding site in our representation of a partially misfolded α-synuclein, the protein implicated in PD. Our ab initio simulations use Density Functional Theory (DFT) and nudged elastic band to obtain the minimized energy coordinates of this reaction. Our simulations include ab initio water at the interaction site and in its first solvation shells, while the remainder is fully solvated with orbital-free DFT water representation [1]. Our ongoing studies of viable chelation agents include nicotine, caffeine and other potential reagents, we will review the best case agents in this presentation. [4pt] [1] Hodak M, Lu W, Bernholc J. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J. Chem. Phys. 2008 Jan;128(1):014101-9.

  17. Reaction pathway in vapour phase hydrogenation of maleic anhydride and its esters to {gamma}-butyrolactone

    SciTech Connect

    Messori, M.; Vaccari, A.

    1994-11-01

    The catalytic reactivity of maleic anhydride (MA), succinic anhydride (SA) and their dimethyl esters (dimethyl maleate and dimethyl succinate) in the vapour phase hydrogenation to {gamma}-butyrolacetone (GBL) was investigated. In order to obtain general data, both a multicomponent catalyst (CAT 1: Cu/Zn/Mg/Cr = 40:5:5:50, atomic ratio %), obtained by reduction of a nonstoichiometric spinel-type precursor, and a commercial catalyst (CAT 2: Cu/Mn/Ba/Cr = 44:8:1:47, atomic ratio %) were used. The MA/GBL solution exhibited the highest GBL production, while the SA/GBL solution was converted only partially due to a competitive adsorption of GBL on the active sites, as evidenced by the similar reactivities observed with pure anhydrides. The best carbon balances were observed with the esters, probably the result of lowest light hydrocarbon synthesis and tar formation. With all the feedstocks, the activity of CAT 2 is higher than that of CAT 1, which, however, gives the best yield in GBL due its lower activity in the overhydrogenation and hydrogenolysis reaction. It was found that n-butanol (BuOH) and butyric acid (BuA) derived mainly from GBL. On this basis, the reactivities of the main products observed were investigated separately, confirming the stability of tetrahydrofuran (THF), which reacted only at high temperature with low conversions to ethanol. On the other hand, GBL gave rise to overhydrogenation and/or hydrogenolysis, with high conversion (mainly with CAT 2), confirming its key role in both reactions. Furthermore, the formation in the catalytic tests with BuA and BuOH of n-butanal, notwithstanding the high H{sub 2}/organic ratio, implies that it is the main intermediate in the hydrogenolysis reactions. A new reaction scheme is proposed, pointing out the key role of GBL as the {open_quotes}intersection{close_quotes} of two possible reaction pathways, giving rise to THF or overhydrogenation and hydrogenolysis products, respectively. 44 refs., 4 figs., 6 tabs.

  18. Reactions of a sulfonamide antimicrobial with model humic constituents: assessing pathways and stability of covalent bonding.

    PubMed

    Gulkowska, Anna; Krauss, Martin; Rentsch, Daniel; Hollender, Juliane

    2012-02-21

    The mechanism of covalent bond formation of the model sulfonamide sulfathiazole (STZ) and the stronger nucleophile para-ethoxyaniline was studied in reactions with model humic acid constituents (quinones and other carbonyl compounds) in the absence and presence of laccase. As revealed by high resolution mass spectrometry, the initial bonding of STZ occurred by 1,2- and 1,4-nucleophilic additions of the aromatic amino group to quinones resulting in imine and anilinoquinone formation, respectively. Experiments using the radical scavenger tert-butyl-alcohol provided the same products and similar formation rates as those without scavenger indicating that probably not radical coupling reactions were responsible for the initial covalent bond formation. No addition with nonquinone carbonyl compounds occurred within 76 days except for a slow 1,4-addition to the β-unsaturated carbonyl 1-penten-3-one. The stability of covalent bonds against desorption and pressurized liquid extraction (PLE) was assessed. The recovery rates showed no systematic differences in STZ extractability between the two product types. This suggests that the strength of bonding is not controlled by the initial type of bond, but by the extent of subsequent incorporation of the reaction product into the formed polymer. This incorporation was monitored for (15)N aniline by (1)H-(15)N HMBC NMR spectroscopy. The initial 1,2- and 1,4-addition bonds were replaced by stronger heterocyclic forms with increasing incubation time. These processes could also hold true for soils, and a slow nonextractable residue formation with time could be related to a slow increase of the amount of covalently bound sulfonamide and the strength of bonding. PMID:22260423

  19. Asymmetric N-heterocyclic carbene catalyzed addition of enals to nitroalkenes: controlling stereochemistry via the homoenolate reactivity pathway to access δ-lactams.

    PubMed

    White, Nicholas A; DiRocco, Daniel A; Rovis, Tomislav

    2013-06-12

    An asymmetric intermolecular reaction between enals and nitroalkenes to yield δ-nitroesters has been developed, catalyzed by a novel chiral N-heterocyclic carbene. Key to this work was the development of a catalyst that favors the δ-nitroester pathway over the established Stetter pathway. The reaction proceeds in high stereoselectivity and affords the previously unreported syn diastereomer. We also report an operationally facile two-step, one-pot procedure for the synthesis of δ-lactams. PMID:23713683

  20. Examining the robustness of first-principles calculations for metal hydride reaction thermodynamics by detection of metastable reaction pathways.

    PubMed

    Kim, Ki Chul; Kulkarni, Anant D; Johnson, J Karl; Sholl, David S

    2011-12-28

    First principles calculations have played a useful role in screening mixtures of complex metal hydrides to find systems suitable for H(2) storage applications. Standard methods for this task efficiently identify the lowest energy reaction mechanisms among all possible reactions involving collections of materials for which DFT calculations have been performed. The resulting mechanism can potentially differ from physical reality due to inaccuracies in the DFT functionals used, or due to other approximations made in estimating reaction free energies. We introduce an efficient method to probe the robustness of DFT-based predictions that relies on identifying reactions that are metastable relative to the lowest energy reaction path predicted with DFT. An important conclusion of our calculations is that in many examples DFT cannot unambiguously predict a single reaction mechanism for a well defined metal hydride mixture because two or more mechanisms have reaction energies that differ by a small amount. Our approach is illustrated by analyzing a series of single step reactions identified in our recent work that examined reactions with a large database of solids [Kim et al., Phys. Chem. Chem. Phys. 2011, 13, 7218]. PMID:22068383

  1. Reaction pathways and mechanisms of the electrochemical degradation of phenol on different electrodes.

    PubMed

    Li, Xiao-Yan; Cui, Yu-Hong; Feng, Yu-Jie; Xie, Zhao-Ming; Gu, Ji-Dong

    2005-05-01

    Laboratory experiments were carried out on the kinetics and pathways of the electrochemical (EC) degradation of phenol at three different types of anodes, Ti/SnO2-Sb, Ti/RuO2, and Pt. Although phenol was oxidised by all of the anodes at a current density of 20 mA/cm2 or a cell voltage of 4.6 V, there was a considerable difference between the three anode types in the effectiveness and performance of EC organic degradation. Phenol was readily mineralized at the Ti/SnO2-Sb anode, but its degradation was much slower at the Ti/RuO2 and Pt anodes. The analytical results of high-performance liquid chromatography (HPLC) and gas chromatography coupled with mass spectrometry (GC/MS) indicated that the intermediate products of EC phenol degradation, including benzoquinone and organic acids, were subsequently oxidised rapidly by the Ti/SnO2-Sb anode, but accumulated in the cells of Ti/RuO2 and Pt. There was also a formation of dark-coloured polymeric compounds and precipitates in the solutions electrolyzed by the Ti/RuO2 and Pt anodes, which was not observed for the Ti/SnO2-Sb cells. It is argued that anodic property not only affects the reaction kinetics of various steps of EC organic oxidation, but also alters the pathway of phenol electrolysis. Favourable surface treatment, such as the SnO2-Sb coating, provides the anode with an apparent catalytic function for rapid organic oxidation that is probably brought about by hydroxyl radicals generated from anodic water electrolysis. PMID:15882890

  2. Unification of reaction pathway and kinetic scheme for N2 reduction catalyzed by nitrogenase

    PubMed Central

    Lukoyanov, Dmitriy; Yang, Zhi-Yong; Barney, Brett M.; Dean, Dennis R.; Seefeldt, Lance C.; Hoffman, Brian M.

    2012-01-01

    Nitrogenase catalyzes the reduction of N2 and protons to yield two NH3 and one H2. Substrate binding occurs at a complex organo-metallocluster called FeMo-cofactor (FeMo-co). Each catalytic cycle involves the sequential delivery of eight electrons/protons to this cluster, and this process has been framed within a kinetic scheme developed by Lowe and Thorneley. Rapid freezing of a modified nitrogenase under turnover conditions using diazene, methyldiazene (HN = N-CH3), or hydrazine as substrate recently was shown to trap a common intermediate, designated I. It was further concluded that the two N-atoms of N2 are hydrogenated alternately (“Alternating” (A) pathway). In the present work, Q-band CW EPR and 95Mo ESEEM spectroscopy reveal such samples also contain a common intermediate with FeMo-co in an integer-spin state having a ground-state “non-Kramers” doublet. This species, designated H, has been characterized by ESEEM spectroscopy using a combination of 14,15N isotopologs plus 1,2H isotopologs of methyldiazene. It is concluded that: H has NH2 bound to FeMo-co and corresponds to the penultimate intermediate of N2 hydrogenation, the state formed after the accumulation of seven electrons/protons and the release of the first NH3; I corresponds to the final intermediate in N2 reduction, the state formed after accumulation of eight electrons/protons, with NH3 still bound to FeMo-co prior to release and regeneration of resting-state FeMo-co. A proposed unification of the Lowe-Thorneley kinetic model with the “prompt” alternating reaction pathway represents a draft mechanism for N2 reduction by nitrogenase. PMID:22460797

  3. Effects of aluminum additions to gas atomized reaction synthesis produced oxide dispersion strengthened alloys

    NASA Astrophysics Data System (ADS)

    Spicher, Alexander Lee

    The production of an aluminum containing ferritic oxide dispersion strengthened (ODS) alloy was investigated. The production method used in this study was gas atomization reaction synthesis (GARS). GARS was chosen over the previously commercial method of mechanical alloying (MA) process due to complications from this process. The alloy compositions was determined from three main components; corrosion resistance, dispersoid formation, and additional elements. A combination of Cr and Al were necessary in order to create a protective oxide in the steam atmosphere that the boiler tubing in the next generation of coal-fired power plants would be exposed to. Hf and Y were chosen as dispersoid forming elements due to their increased thermal stability and potential to avoid decreased strength caused by additions of Al to traditional ODS materials. W was used as an additive due to benefits as a strengthener as well as its benefits for creep rupture time. The final composition chosen for the alloy was Fe-16Cr-12Al-0.9W-0.25Hf-0.2Y at%. The aforementioned alloy, GA-1-198, was created through gas atomization with atomization gas of Ar-300ppm O2. The actual composition created was found to be Fe-15Cr-12.3Al-0.9W-0.24Hf-0.19Y at%. An additional alloy that was nominally the same without the inclusion of aluminum was created as a comparison for the effects on mechanical and corrosion properties. The actual composition of the comparison alloy, GA-1-204, was Fe-16Cr-0Al-0.9W-0.25Hf-0.24Y at%. An investigation on the processing parameters for these alloys was conducted on the GA-1-198 alloy. In order to predict the necessary amount of time for heat treatment, a diffusion study was used to find the diffusion rate of oxygen in cast alloys with similar composition. The diffusion rate was found to be similar to that of other GARS compositions that have been created without the inclusion of aluminum. The effect of heat treatment time was investigated with temperatures of 950°C, 1000

  4. Pathway and kinetic analysis on the propyl radical + 02 reaction system

    SciTech Connect

    Bozzelli, J.W.; Pitz, W.J.

    1997-05-01

    In this study of the reaction of alkyl radicals with molecular oxygen, we analyze the propyl + 02 reaction system using thermochemical kinetics, Transition State Theory (TST), molecular thermodynamic properties, quantum Kassel analysis (quantum RRK) for k(E) and modified strong collision analysis for fall off. Cyclic transition states for both hydrogen transfer and the H02 concerted elimination from propylperoxy are calculated using semi-empirical (MOPAC PM3) calculations [8] in addition to transition states for H02 elimination and epoxide formation from hydroperoxy-isopropyl. Computed rate constants for propyl + 02 are compared to the values of Gulati and Walker who measured the rate constants at 50 torr and over a temperature range of 653 to 773 K. Computed rate constants are also used in a detailed chemical kinetic mechanism and compared to the n- propyl + 02 data of Slagle. They measured the rate of disappearance of n-propyl by reaction with 02 over a temperature range of 297 to 635 K and a pressure range of 0.4 to 7 Torr, as well as the fall off data of the Kaiser and Wallington.

  5. Effects of a Protic Ionic Liquid on the Reaction Pathway during Non-Aqueous Sol–Gel Synthesis of Silica: A Raman Spectroscopic Investigation

    PubMed Central

    Martinelli, Anna

    2014-01-01

    The reaction pathway during the formation of silica via a two-component “non-aqueou” sol-gel synthesis is studied by in situ time-resolved Raman spectroscopy. This synthetic route is followed with and without the addition of the protic ionic liquid 1-ethylimidazolium bis(trifluoromethanesulfonyl)imide (C2HImTFSI) in order to investigate its effect on the reaction pathway. We demonstrate that Raman spectroscopy is suitable to discriminate between different silica intermediates, which are produced and consumed at different rates with respect to the point of gelation. We find that half-way to gelation monomers and shorter chains are the most abundant silica species, while the formation of silica rings strongly correlates to the sol-to-gel transition. Thus, curling up of linear chains is here proposed as a plausible mechanism for the formation of small rings. These in turn act as nucleation sites for the condensation of larger rings and thus the formation of the open and polymeric silica network. We find that the protic ionic liquid does not change the reaction pathway per se, but accelerates the cyclization process, intermediated by the faster inclusion of monomeric species. PMID:24743891

  6. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-08-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of a similar magnitude, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity-dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  7. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-12-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  8. Nucleophilic lewis base dependent addition reactions of allenoates with trifluoromethylated cyclic ketimines.

    PubMed

    Yang, Li-Jun; Li, Shen; Wang, Shuai; Nie, Jing; Ma, Jun-An

    2014-04-18

    A detailed investigation on the different reactivity patterns shown by phosphorus- and nitrogen-containing Lewis base catalysts in the reactions of allenoates with cyclic trifluoromethyl ketimines was accomplished. With PPh3, [3 + 2] annulations proceeded smoothly to afford dihydropyrrole derivatives in excellent yields. Under the catalysis of DABCO, [2 + 2] annulations occurred, producing azetidine derivatives in good to high yields. However, in the presence of pyridine, α,α'-disubstituted allenoates were obtained in very high yields via aza-Morita-Baylis-Hillman reactions. These studies provide an opportunity for diverse synthesis of a variety of N-heterocyclic compounds from the same starting materials. PMID:24693927

  9. Additional markers for the type I reactional states of borderline leprosy.

    PubMed

    Lazaro-Medina, A; Tianco, E A; Avila, J M

    1990-08-01

    The histological course of reaction in borderline leprosy has been described by Ridley and Radia. They are dermal edema, dilatation of the lymphatics, swelling of the granulomas, changes in the concentration and distribution of lymphocytes and giant cells, maturity of the histiocytes, and presence of neutrophils. New markers for the condition are spongiosis of the epidermal and follicular epithelium with exocytosis of mononuclear cells, parakeratosis, focal interface changes with occasional individual cell necrosis of keratinocytes, and lastly, follicular mucinosis. Recognition of this reaction is vital in the prevention of deformities secondary to nerve damage. PMID:2393071

  10. p53 and ATF4 mediate distinct and additive pathways to skeletal muscle atrophy during limb immobilization

    PubMed Central

    Fox, Daniel K.; Ebert, Scott M.; Bongers, Kale S.; Dyle, Michael C.; Bullard, Steven A.; Dierdorff, Jason M.; Kunkel, Steven D.

    2014-01-01

    Immobilization causes skeletal muscle atrophy via complex signaling pathways that are not well understood. To better understand these pathways, we investigated the roles of p53 and ATF4, two transcription factors that mediate adaptations to a variety of cellular stresses. Using mouse models, we demonstrate that 3 days of muscle immobilization induces muscle atrophy and increases expression of p53 and ATF4. Furthermore, muscle fibers lacking p53 or ATF4 are partially resistant to immobilization-induced muscle atrophy, and forced expression of p53 or ATF4 induces muscle fiber atrophy in the absence of immobilization. Importantly, however, p53 and ATF4 do not require each other to promote atrophy, and coexpression of p53 and ATF4 induces more atrophy than either transcription factor alone. Moreover, muscle fibers lacking both p53 and ATF4 are more resistant to immobilization-induced atrophy than fibers lacking only p53 or ATF4. Interestingly, the independent and additive nature of the p53 and ATF4 pathways allows for combinatorial control of at least one downstream effector, p21. Using genome-wide mRNA expression arrays, we identified p21 mRNA as a skeletal muscle transcript that is highly induced in immobilized muscle via the combined actions of p53 and ATF4. Additionally, in mouse muscle, p21 induces atrophy in a manner that does not require immobilization, p53 or ATF4, and p21 is required for atrophy induced by immobilization, p53, and ATF4. Collectively, these results identify p53 and ATF4 as essential and complementary mediators of immobilization-induced muscle atrophy and discover p21 as a critical downstream effector of the p53 and ATF4 pathways. PMID:24895282

  11. Reactivity of CHI3 with OH radicals: X-abstraction reaction pathways (X = H, I), atmospheric chemistry, and nuclear safety.

    PubMed

    Sudolská, Mária; Louis, Florent; Cernušák, Ivan

    2014-10-01

    The X-abstraction (X = H, I) pathways in the reaction of CHI3 with OH radical, a possible iodoform removal process relevant to the Earth's atmosphere and conditions prevailing in the case of a nuclear accident, have been studied applying highly correlated ab initio quantum chemistry methods and canonical transition-state theory to obtain reaction energy profiles and rate constants. Geometry optimizations of reactants, products, molecular complexes, and transition states determined at the MP2/cc-pVTZ level of theory have been followed by DK-CCSD(T)/ANO-RCC single-point energy calculations. Further improvement of electronic energies has been achieved by applying spin-orbit coupling, corrections toward full configuration interaction, vibration contributions, and tunneling corrections. Calculated reaction enthalpies at 0 K are -108.2 and -5.1 kJ mol(-1) for the H- and I-abstraction pathways, respectively; the strongly exothermic H-abstraction pathway is energetically favored over the modestly exothermic I-abstraction one. The overall rate constant at 298 K based on our ab initio calculations is 4.90 × 10(-11) cm(3) molecule(-1) s(-1), with the I-abstraction pathway being the major channel over the temperature range of 250-2000 K. The CHI3 atmospheric lifetime with respect to the removal reaction with OH radical is predicted to be about 6 h, very short compared to that of other halomethanes. PMID:25207959

  12. EFFECT OF RELATIVE HUMIDITY AND ADDITIVES ON THE REACTION OF SULFUR DIOXIDE WITH CALCIUM HYDROXIDE

    EPA Science Inventory

    The paper gives results of a study of the reaction of SO2 with Ca(OH)2 at conditions similar to those of commercial-scale bag filters: 19-74 percent relative humidity (RH), 30.4-95 C, and 300-4000 ppm SO2. The study was carried out in a bench-scale reactor with powder reagent Ca(...

  13. Energetics of addition versus insertion mechanisms in the Si +( 2P) + HCOOH reaction

    NASA Astrophysics Data System (ADS)

    González, A. I.; Yáñez, M.

    1996-01-01

    High-level ab initio calculations have been performed to investigate the preference of insertion processes with respect to the formation of adducts in the Si + + formic acid reaction in the gas phase. We have found that the reactivity patterns shown by Si + in reactions with methanol and formaldehyde are significantly different from those exhibited with formic acid, which has both functional groups. The most stable product of the reaction between Si + and HCOOH corresponds to the insertion of the monocation into the COH bond of the neutral. Mostly importantly, the Si + association to the carbonyl oxygen atom is only 4.9 kcal/mol less favourable. All investigated local minima lie below the reactants in energy. In agreement with the experimental evidence, the formation of SiOH + as a possible product of the Si + + HCOOH reaction is predicted to be exothermic by 41.7 kcal/mol. The distonic character of the products is discussed as well as the harmonic vibrational frequencies of the global minimum.

  14. Reactivity of Single-Walled Carbon Nanotubes in the Diels-Alder Cycloaddition Reaction: Distortion-Interaction Analysis along the Reaction Pathway.

    PubMed

    Li, Yingzi; Osuna, Sílvia; Garcia-Borràs, Marc; Qi, Xiaotian; Liu, Song; Houk, Kendall N; Lan, Yu

    2016-08-26

    Diels-Alder cycloaddition is one of the most powerful tools for the functionalization of single-walled carbon nanotubes (SWCNTs). Density functional theory at the B3-LYP level of theory has been used to investigate the reactivity of different-diameter SWCNTs (4-9,5) in Diels-Alder reactions with 1,3-butadiene; the reactivity was found to decrease with increasing SWCNT diameter. Distortion/interaction analysis along the whole reaction pathway was found to be a better way to explore the reactivity of this type of reaction. The difference in interaction energy along the reaction pathway is larger than that of the corresponding distortion energy. However, the distortion energy plots for these reactions show the same trend. Therefore, the formation of the transition state can be determined from the interaction energy. A lower interaction energy leads to an earlier transition state, which indicates a lower activation energy. The computational results also indicate that the original distortion of the SWCNTs leads to an increase in the reactivity of the SWCNTs. PMID:27465519

  15. Muonium Addition Reactions and Kinetic Isotope Effects in the Gas Phase: k∞ Rate Constants for Mu + C2H2.

    PubMed

    Arseneau, Donald J; Garner, David M; Reid, Ivan D; Fleming, Donald G

    2015-07-16

    The kinetics of the addition reaction of muonium (Mu) to acetylene have been studied in the gas phase at N2 moderator pressures mainly from ∼800 to 1000 Torr and over the temperature range from 168 to 446 K, but also down to 200 Torr at 168 K and over a much higher range of pressures, from 10 to 44 bar at 295 K, demonstrating pressure-independent rate constants, kMu(T). Even at 200 Torr moderator pressure, the kinetics for Mu + C2H2 addition behave as if effectively in the high-pressure limit, giving k∞ = kMu due to depolarization of the muon spin in the MuC2H2 radical formed in the addition step. The rate constants kMu(T) exhibit modest Arrhenius curvature over the range of measured temperatures. Comparisons with data and with calculations for the corresponding H(D) + C2H2 addition reactions reveal a much faster rate for the Mu reaction at the lowest temperatures, by 2 orders of magnitude, in accord with the propensity of Mu to undergo quantum tunneling. Moreover, isotopic atom exchange, which contributes in a major way to the analogous D atom reaction, forming C2HD + H, is expected to be unimportant in the case of Mu addition, a consequence of the much higher zero-point energy and hence weaker C-Mu bond that would form, meaning that the present report of the Mu + C2H2 reaction is effectively the only experimental study of kinetic isotope effects in the high-pressure limit for H-atom addition to acetylene. PMID:25664674

  16. Rate and pathways for the reaction of OH with the biogenic p-cymene, an alkylated aromatic

    NASA Astrophysics Data System (ADS)

    Strekowski, R.; Rayez, M.-T.; Rayez, J.-C.; Zetzsch, C.

    2009-04-01

    Aromatics are known to contribute strongly to tropospheric formation of ozone, and p-cymene (4-isopropyltoluene) is one of only a few biogenic, volatile aromatic hydrocarbons. In spite of its symmetry, this molecule (CH3 - °-CH(CH3)2) has a multitude of potential pathways of its reaction with OH radicals. Addition of OH is well-known to be the predominating primary step in the tropospheric transformation of aromatic hydrocarbons. The addition is expected to occur preferably at a non-occupied position, where four positions are available: two equivalent ones ortho to the methyl group and two equivalent ones ortho to the isopropyl group. Furthermore, various C-H bonds (4 aromatic and 10 aliphatic) are available for abstraction, leading to benzyl-type radicals in two cases. The present study combines theoretical calculations with kinetic experiments in the gas phase. The theoretical calculations are based on electronic quantum chemistry DFT method for the investigation of the possible pathways in the potential energy surface of the reaction. The experiments are carried out by the flash photolysis/resonance fluorescence technique. OH radicals are produced by pulsed vacuum-UV photolysis of H2O (> 115 nm) in the presence of p-cymene in a slow flow of He as carrier gas. Their pseudo-first-order decays are monitored by resonance fluorescence, storing the photon counts by multichannel scaling in a PC and accumulating 50 decays each; see Koch et al. (2007) for details of the technique and evaluation of data. The temperature was varied between room temperature (295 K) and 345K, the He pressure was 250 mbar, and the level of p-cymene was increased stepwise, up to 3 x 1013 molecules/cm3. The decays of OH were observed to be exponential at room temperature, becoming clearly biexponential at higher temperatures, thus indicating reversible addition of OH according to the equilibration OH + p-cymene ⇔ p-cymene-OH (1, -1) These reactions might be accompanied by various

  17. From formamide to purine: a self-catalyzed reaction pathway provides a feasible mechanism for the entire process.

    PubMed

    Wang, Jing; Gu, Jiande; Nguyen, Minh Tho; Springsteen, Greg; Leszczynski, Jerzy

    2013-08-15

    A formamide self-catalyzed mechanistic pathway that transforms formamide to purine through a five-membered ring intermediate has been explored by density functional theory calculations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest and lowest energy reaction pathway. All necessary reactants, including catalysts, are generated from a single initial compound, formamide. The most catalytically effective form of formamide is found to be the imidic acid isomer. The catalytic effect of formamide has been found to be much more significant than that of water. The self-catalytic mechanism revealed here provides a pathway with the lowest energy barriers among all reaction routes previously published. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-member ring-closing, and deamination. Overall, a five-membered ring-closing is the rate-determining step in the present catalytic route, which is consistent with our previous mechanistic investigations. The activation energy of this rate-controlling step (ca. 27 kcal/mol) is significantly lower than the rate-determining step (ca. 34 kcal/mol) in the pathway from 4-aminoimidazole-5-carboxamidine described by Schleyer's group (Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 17272-17277) and in the pyrimidine pathway (ca. 44 kcal/mol) reported by Sponer et al. (J. Phys. Chem. A 2012, 116, 720-726). The self-catalyzed mechanistic pathway reported herein is less energetically demanding than previously proposed routes. PMID:23902343

  18. Addition of CFCl3 to Aromatic Aldehydes via in Situ Grignard Reaction.

    PubMed

    Barkakaty, Balaka; Talukdar, Bandana; Lokitz, Bradley S

    2015-01-01

    Synthetic modification of trichlorofluoromethane (CFCl3) to non-volatile and useful fluorinated precursors is a cost-effective and an environmentally benign strategy for the safe consumption/destruction of the ozone depleting potential of the reagent. In this report, we present a novel method for in situ Grignard reaction using magnesium powder and CFCl3 for synthesis of dichlorofluoromethyl aromatic alcohols. PMID:26295221

  19. Addition of CFCl3 to Aromatic Aldehydes via in Situ Grignard Reaction

    DOE PAGESBeta

    Barkakaty, Balaka; Talukdar, Bandana; Lokitz, Bradley

    2015-08-18

    In the case of synthetic modification of trichlorofluoromethane (CFCl3) to non-volatile and useful fluorinated precursors, we realized that it is a cost-effective and an environmentally benign strategy for the safe consumption/destruction of the ozone depleting potential of the reagent. In our report, we present a novel method for in situ Grignard reaction using magnesium powder and CFCl3 for synthesis of dichlorofluoromethyl aromatic alcohols.

  20. Addition of CFCl3 to Aromatic Aldehydes via in Situ Grignard Reaction

    SciTech Connect

    Barkakaty, Balaka; Talukdar, Bandana; Lokitz, Bradley

    2015-08-18

    In the case of synthetic modification of trichlorofluoromethane (CFCl3) to non-volatile and useful fluorinated precursors, we realized that it is a cost-effective and an environmentally benign strategy for the safe consumption/destruction of the ozone depleting potential of the reagent. In our report, we present a novel method for in situ Grignard reaction using magnesium powder and CFCl3 for synthesis of dichlorofluoromethyl aromatic alcohols.

  1. Reaction pathways for bio-active species in a He/H2O atmospheric pressure capacitive discharge

    NASA Astrophysics Data System (ADS)

    Ding, Ke; Lieberman, M. A.

    2015-01-01

    Helium/trace gas atmospheric pressure radio-frequency (rf) capacitive discharges have increasing biomedical applications. We have performed a principal pathway analysis for a chemically complex, bounded He/H2O atmospheric pressure, planar capacitive discharge, with a discharge gap of 0.5 mm and a power of 0.85 W cm-2 at 13.56 MHz (ne ≈ 1.6 × 1017 m-3). The discharge is embedded in a larger volume in which the H2O fraction is controlled to be 0.001. The generation and loss pathways for eleven species of interest for discharge maintenance and biomedical applications have been determined. The production and consumption pathways of He*, H2O, {{\\text{H}}11}\\text{O}5+ and electrons are found to be tightly coupled. The metastable He* generated by electron impact excitation of He is mostly consumed by Penning reactions with H2O, followed by subsequent three-body association reactions with H2O, to form the dominant positive ion, {{\\text{H}}11}\\text{O}5+ . The main loss pathways for {{\\text{H}}11}\\text{O}5+ are ion cluster fragmentations at the wall, which are important generation pathways for H2O. The generation and loss pathways for electrons are almost the same as for {{\\text{H}}11}\\text{O}5+ . OH and H2O2 generation and loss are strongly coupled, and they are important intermediate species in the generation pathways for the purely O-containing bio-active species: O2(a), O, O3 and O*. The generation and loss pathways for the latter four species were found to be strongly coupled by volume and surface processes, with O2 as an important precursor. The generation of O2 from H2O involves H2O2 as a key long-lived intermediate.

  2. Effect of Reaction Pathway on the Extent and Mechanism of Uranium(VI) Immobilization with Calcium and Phosphate.

    PubMed

    Mehta, Vrajesh S; Maillot, Fabien; Wang, Zheming; Catalano, Jeffrey G; Giammar, Daniel E

    2016-03-15

    Phosphate addition to subsurface environments contaminated with uranium can be used as an in situ remediation approach. Batch experiments were conducted to evaluate the dependence of the extent and mechanism of uranium uptake on the pathway for reaction with calcium phosphates. At pH 4.0 and 6.0 uranium uptake from solution occurred via autunite (Ca(UO2)2(PO4)2) precipitation irrespective of the starting forms of calcium and phosphate. At pH 7.5, a condition at which calcium phosphate solids could form, the uptake mechanism depended on the nature of the calcium and phosphate as determined by X-ray absorption spectroscopy and laser-induced fluorescence spectroscopy. When dissolved uranium, calcium, and phosphate were added simultaneously, uranium was structurally incorporated into a newly formed amorphous calcium phosphate solid. Adsorption was the dominant removal mechanism for uranium contacted with preformed amorphous calcium phosphate solids. When U(VI) was added to a suspension containing amorphous calcium phosphate solids as well as dissolved calcium and phosphate, then removal occurred through precipitation (57 ± 4%) of autunite and adsorption (43 ± 4%) onto calcium phosphate. Dissolved uranium, calcium, and phosphate concentrations with saturation index calculations helped identify removal mechanisms and determine thermodynamically favorable solid phases. PMID:26934085

  3. Characterizing the Mechanistic Pathways of the Instant Blood-Mediated Inflammatory Reaction in Xenogeneic Neonatal Islet Cell Transplantation

    PubMed Central

    Liuwantara, David; Chew, Yi Vee; Favaloro, Emmanuel J.; Hawkes, Joanne M.; Burns, Heather L.; O'Connell, Philip J.; Hawthorne, Wayne J.

    2016-01-01

    Introduction The instant blood-mediated inflammatory reaction (IBMIR) causes major loss of islets after transplantation and consequently represents the initial barrier to survival of porcine neonatal islet cell clusters (NICC) after xenotransplantation. Methods This study used novel assays designed to characterize the various immunologic components responsible for xenogeneic IBMIR to identify initiators and investigate processes of IBMIR-associated coagulation, complement activation and neutrophil infiltration. The IBMIR was induced in vitro by exposing NICC to platelet-poor or platelet-rich human plasma or isolated neutrophils. Results We found that xenogeneic IBMIR was characterized by rapid, platelet-independent thrombin generation, with addition of platelets both accelerating and exacerbating this response. Platelet-independent complement activation was observed as early as 30 minutes after NICC exposure to plasma. However, membrane attack complex formation was not observed in NICC histopathology sections until after 60 minutes. We demonstrated for the first time that NICC-mediated complement activation was necessary for neutrophil activation in the xenogeneic IBMIR setting. Finally, using the Seahorse extracellular flux analyzer, we identified substantial loss of islet function (up to 40%) after IBMIR with surviving NICC showing evidence of mitochondrial damage. Conclusions This study used novel assays to describe multiple key pathways by which xenogeneic IBMIR causes islet destruction, allowing further refinement of future interventions aimed at resolving the issue of IBMIR in xenotransplantation. PMID:27500267

  4. Fluid flow pathways through the oceanic crust: reaction permeability and isotopic tracing

    NASA Astrophysics Data System (ADS)

    McCaig, Andrew; Castelain, Teddy; Klein, Frieder

    2013-04-01

    It is generally assumed that the dominant means of creating permeability in ocean floor hydrothermal systems is fracturing, induced either by cooling or by tectonic stress. Here we show textural evidence that metamorphic reactions can create a hierarchy of permeable pathways through gabbroic rocks similar to a fracture hierarchy. Isotopic microsampling shows that just as with fractures, most flow occurs through the larger channelways, and that even at the microscale, flow can be extremely heterogeneous with alteration affecting only certain minerals in the framework, leaving others untouched. Reaction permeability is created in three ways; dissolution creating open porosity, microcracking due to volume increase reactions involving olivine, and expansion of water due to rapid heating in dyke margins, particularly when intruded into brecciated rocks. Our data comes from IODP Hole U1309D, which was drilled to 1400 mbsf in the footwall of the Atlantis Massif detachment fault at the Mid-Atlantic Ridge 30°N. The core is composed of gabbroic rocks interlayered with olivine rich troctolites, with several basalt/diabase sills in the top 130 m. The dominant alteration occurred in the greenschist facies, at depths at least 1 km below seafloor, and decreases in intensity downhole. Whole rock oxygen isotope values range from +5.5 permil to +1.5 permil, indicating variable degrees of interaction with seawater at temperatures generally > 250 °C. Gabbroic rocks and diabases exhibit a range of Sr isotope ratios from MORB values (0.70261) to intermediate ratios (0.70429). Microsampling shows that amphiboles are often more radiogenic than coexisting plagioclase and can sometimes be isotopically altered in the same rock as completely unaltered primary minerals. Large (10 cm) amphibole-filled vugs show values ranging up to 0.708, close to seawater. In some cases however the secondary minerals are virtually unaltered indicating low fluid fluxes in pervasive alteration. SEM textures in

  5. Monitoring Wnt Protein Acylation Using an In Vitro Cyclo-Addition Reaction

    PubMed Central

    Tuladhar, Rubina; Yarravarapu, Nageswari; Lum, Lawrence

    2016-01-01

    We describe here a technique for visualizing the lipidation status of Wnt proteins using azide-alkyne cycloaddition chemistry (click chemistry) and SDS-PAGE. This protocol incorporates in vivo labeling of a Wnt-IgG Fc fusion protein using an alkynylated palmitate probe but departs from a traditional approach by incorporating a secondary cycloaddition reaction performed on single-step purified Wnt protein immobilized on protein A resin. This approach mitigates experimental noise by decreasing the contribution of labeling from other palmitoylated proteins and by providing a robust method for normalizing labeling efficiency based on protein abundance. PMID:27590147

  6. Monitoring Wnt Protein Acylation Using an In Vitro Cyclo-Addition Reaction.

    PubMed

    Tuladhar, Rubina; Yarravarapu, Nageswari; Lum, Lawrence

    2016-01-01

    We describe here a technique for visualizing the lipidation status of Wnt proteins using azide-alkyne cycloaddition chemistry (click chemistry) and SDS-PAGE. This protocol incorporates in vivo labeling of a Wnt-IgG Fc fusion protein using an alkynylated palmitate probe but departs from a traditional approach by incorporating a secondary cycloaddition reaction performed on single-step purified Wnt protein immobilized on protein A resin. This approach mitigates experimental noise by decreasing the contribution of labeling from other palmitoylated proteins and by providing a robust method for normalizing labeling efficiency based on protein abundance. PMID:27590147

  7. Tandem bis-aza-Michael addition reaction of amines in aqueous medium promoted by polystyrenesulfonic Acid

    EPA Science Inventory

    An efficient and environmentally benign tandem bis-aza-Michael addition of amines catalyzed by polystyrene sulfonic acid (PSSA) is described. This operationally simple high yielding microwave assisted synthetic protocol proceeded in water in the absence of any organic solvent.

  8. Insight into the reaction mechanisms for oxidative addition of strong σ bonds to an Al(i) center.

    PubMed

    Zhang, Xiangfei; Cao, Zexing

    2016-06-21

    The oxidation addition of a series of σ H-X bonds (X = H, B, C, Si, N, P, and O) to a single Al(i) supported by a (NacNac)(-) bidentate ligand ((NacNac)(-) = [ArNC(Me)CHC(Me)NAr](-) and Ar = 2,6-(i)Pr2C6H3) has been explored through extensive DFT calculations. The presented results show that activation and addition of these σ bonds follow various reaction mechanisms, in which hydride transfer, proton transfer, and Al-X bond coupling steps are involved. The predicted free energy barriers for these oxidative additions range from 8 to 32 kcal mol(-1), and all the reactions are remarkably favorable thermodynamically. However, sterically hindered ligands, for most reactants, make the formation of the initial reactant complex difficult and may reduce the efficiency of the reaction. Calculations reveal a strong dependence of the reaction mechanism and low-energy channel on the bonding features of X-H and the local structural environments. PMID:27249667

  9. Organocatalytic Domino Oxa-Michael/1,6-Addition Reactions: Asymmetric Synthesis of Chromans Bearing Oxindole Scaffolds.

    PubMed

    Zhao, Kun; Zhi, Ying; Shu, Tao; Valkonen, Arto; Rissanen, Kari; Enders, Dieter

    2016-09-19

    An asymmetric organocatalytic domino oxa-Michael/1,6-addition reaction of ortho-hydroxyphenyl-substituted para-quinone methides and isatin-derived enoates has been developed. In the presence of 5 mol % of a bifunctional thiourea organocatalyst, this scalable domino reaction affords 4-phenyl-substituted chromans bearing spiro-connected oxindole scaffolds and three adjacent stereogenic centers in good to excellent yields (up to 98 %) and with very high stereoselectivities (up to >20:1 d.r., >99 % ee). PMID:27600477

  10. Time-dependent insulin oligomer reaction pathway prior to fibril formation: Cooling and seeding

    PubMed Central

    Sorci, Mirco; Grassucci, Robert A.; Hahn, Ingrid; Frank, Joachim; Belfort, Georges

    2009-01-01

    The difficulty in identifying the toxic agents in all amyloid-related diseases is likely due to the complicated kinetics and thermodynamics of the nucleation process and subsequent fibril formation. The slow progression of these diseases suggests that the formation, incorporation and/or action of toxic agents is possibly rate limiting. Candidate toxic agents include precursors (some at very low concentrations), also called oligomers and protofibrils, and the fibrils. Here, we investigate the kinetic and thermodynamic behavior of human insulin oligomers (imaged by cryo-EM) under fibril forming conditions (pH 1.6 and 65°C) by probing the reaction pathway to insulin fibril formation using two different types of experiments – cooling and seeding – and confirm the validity of the nucleation model and its effect on fibril growth. The results from both the cooling and seeding studies confirm the existence of a time-changing oligomer reaction process prior to fibril formation that likely involves a rate-limiting nucleation process followed by structural rearrangements of intermediates (into β-sheet rich entities) to form oligomers that then form fibrils. The latter structural rearrangement step occurs even in the absence of nuclei (i.e. with added heterologous seeds). Nuclei are formed at the fibrillation conditions (pH 1.6 and 65°C) but are also continuously formed during cooling at pH 1.6 and 25°C. Within the time-scale of the experiments, only after increasing the temperature to 65°C are the trapped insulin nuclei and resultant structures able to induce the structural rearrangement step and overcome the energy barrier to form fibrils. This delay in fibrillation and accumulation of nuclei at low temperature (25°C), result in a decrease in the mean length of the fibers when placed at 65°C. Fits of an empirical model to the data provide quantitative measures of the delay in the lag-time during the nucleation process and subsequent reduction in fibril growth rate

  11. Evaluation of lead anode reactions in acid sulfate electrolytes. 1: Lead alloys with cobalt additives

    SciTech Connect

    Yu, P.; O`Keefe, T.J.

    1999-04-01

    Lead alloys, such as lead-calcium-tin and lead-silver, are the primary insoluble anodes used in the electrowinning of metals. While some difficulties are encountered in their use, there is no obvious replacement that is economically and technically competitive. Two of the specific problems with lead include decreased cathode purity due to incorporation from corrosion products and the relatively high overpotential which increases cell voltage. To gain an improved understanding of the fundamental behavior of lead anodes, the polarization behavior of six different alloys in sulfuric acid was evaluated. Some tests were also made with Co(II) in the acid sulfate electrolyte. Notable differences were found in the multiple activation-passivation cycles, stability, and relative activity for oxygen evolution for the alloys, and the relative trends in behavior were established. Electrochemical impedance spectroscopy studies were also conducted at selected potentials. Overall, the data show that the electrochemical response, particularly the degree of polarization for the oxygen evolution reaction, of the lead alloy anodes are dependent on the surface phases and structures present. The ability to depolarize the anode reaction using Co(II) was particularly sensitive to the lead composition.

  12. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

    PubMed Central

    Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng; Gao, Xin

    2016-01-01

    To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/. PMID:27131375

  13. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.

    PubMed

    Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng; Gao, Xin

    2016-07-01

    To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/. PMID:27131375

  14. Heterogeneous versus homogeneous copper(II) catalysis in enantioselective conjugate-addition reactions of boron in water.

    PubMed

    Kitanosono, Taku; Xu, Pengyu; Kobayashi, Shū

    2014-01-01

    We have developed Cu(II)-catalyzed enantioselective conjugate-addition reactions of boron to α,β-unsaturated carbonyl compounds and α,β,γ,δ-unsaturated carbonyl compounds in water. In contrast to the previously reported Cu(I) catalysis that required organic solvents, chiral Cu(II) catalysis was found to proceed efficiently in water. Three catalyst systems have been exploited: cat. 1: Cu(OH)2 with chiral ligand L1; cat. 2: Cu(OH)2 and acetic acid with ligand L1; and cat. 3: Cu(OAc)2 with ligand L1. Whereas cat. 1 is a heterogeneous system, cat. 2 and cat. 3 are homogeneous systems. We tested 27 α,β-unsaturated carbonyl compounds and an α,β-unsaturated nitrile compound, including acyclic and cyclic α,β-unsaturated ketones, acyclic and cyclic β,β-disubstituted enones, acyclic and cyclic α,β-unsaturated esters (including their β,β-disubstituted forms), and acyclic α,β-unsaturated amides (including their β,β-disubstituted forms). We found that cat. 2 and cat. 3 showed high yields and enantioselectivities for almost all substrates. Notably, no catalysts that can tolerate all of these substrates with high yields and high enantioselectivities have been reported for the conjugate addition of boron. Heterogeneous cat. 1 also gave high yields and enantioselectivities with some substrates and also gave the highest TOF (43,200 h(-1) ) for an asymmetric conjugate-addition reaction of boron. In addition, the catalyst systems were also applicable to the conjugate addition of boron to α,β,γ,δ-unsaturated carbonyl compounds, although such reactions have previously been very limited in the literature, even in organic solvents. 1,4-Addition products were obtained in high yields and enantioselectivities in the reactions of acyclic α,β,γ,δ-unsaturated carbonyl compounds with diboron 2 by using cat. 1, cat. 2, or cat. 3. On the other hand, in the reactions of cyclic α,β,γ,δ-unsaturated carbonyl compounds with compound 2, whereas 1,4-addition products

  15. Well-to-Wheels analysis of landfill gas-based pathways and their addition to the GREET model.

    SciTech Connect

    Mintz, M.; Han, J.; Wang, M.; Saricks, C.; Energy Systems

    2010-06-30

    Today, approximately 300 million standard cubic ft/day (mmscfd) of natural gas and 1600 MW of electricity are produced from the decomposition of organic waste at 519 U.S. landfills (EPA 2010a). Since landfill gas (LFG) is a renewable resource, this energy is considered renewable. When used as a vehicle fuel, compressed natural gas (CNG) produced from LFG consumes up to 185,000 Btu of fossil fuel and generates from 1.5 to 18.4 kg of carbon dioxide-equivalent (CO{sub 2}e) emissions per million Btu of fuel on a 'well-to-wheel' (WTW) basis. This compares with approximately 1.1 million Btu and 78.2 kg of CO{sub 2}e per million Btu for CNG from fossil natural gas and 1.2 million Btu and 97.5 kg of CO{sub 2}e per million Btu for petroleum gasoline. Because of the additional energy required for liquefaction, LFG-based liquefied natural gas (LNG) requires more fossil fuel (222,000-227,000 Btu/million Btu WTW) and generates more GHG emissions (approximately 22 kg CO{sub 2}e /MM Btu WTW) if grid electricity is used for the liquefaction process. However, if some of the LFG is used to generate electricity for gas cleanup and liquefaction (or compression, in the case of CNG), vehicle fuel produced from LFG can have no fossil fuel input and only minimal GHG emissions (1.5-7.7 kg CO{sub 2}e /MM Btu) on a WTW basis. Thus, LFG-based natural gas can be one of the lowest GHG-emitting fuels for light- or heavy-duty vehicles. This report discusses the size and scope of biomethane resources from landfills and the pathways by which those resources can be turned into and utilized as vehicle fuel. It includes characterizations of the LFG stream and the processes used to convert low-Btu LFG into high-Btu renewable natural gas (RNG); documents the conversion efficiencies and losses of those processes, the choice of processes modeled in GREET, and other assumptions used to construct GREET pathways; and presents GREET results by pathway stage. GREET estimates of well-to-pump (WTP), pump

  16. Synthesis of Diverse Heterocyclic Scaffolds via Tandem Additions to Imine Derivatives and Ring-Forming Reactions

    PubMed Central

    Sunderhaus, James D.; Dockendorff, Chris; Martin, Stephen F.

    2009-01-01

    A novel strategy has been developed for the efficient syntheses of diverse arrays of heterocyclic compounds. The key elements of the approach comprise a Mannich-type, multicomponent coupling reaction in which functionalized amines, aromatic aldehydes, acylating agents, and π- and organometallic nucleophiles are combined to generate intermediates that are then further transformed into diverse heterocyclic scaffolds via a variety of cyclization manifolds. Significantly, many of these scaffolds bear functionality that may be exploited by further manipulation to create diverse collections of compounds having substructures found in biologically active natural products and clinically useful drugs. The practical utility of this strategy was exemplified by its application to the first, and extraordinarily concise synthesis of the isopavine alkaloid roelactamine. PMID:20625454

  17. Addition-Elimination or Nucleophilic Substitution? Understanding the Energy Profiles for the Reaction of Chalcogenolates with Dichalcogenides.

    PubMed

    Bortoli, Marco; Wolters, Lando P; Orian, Laura; Bickelhaupt, F Matthias

    2016-06-14

    We have quantum chemically explored the mechanism of the substitution reaction between CH3X(-) and the homo- and heterodichalcogenides CH3X'X″CH3 (X, X', X″ = S, Se, Te) using relativistic density functional theory at ZORA-OLYP/TZ2P and COSMO for simulating the effect of aqueous solvation. In the gas phase, all substitution reactions proceed via a triple-well addition-elimination mechanism that involves a stable three-center intermediate. Aqueous solvation, in some cases, switches the character of the mechanism to double-well SN2 in which the stable three-center intermediate has become a labile transition state. We rationalize reactivity trends and some puzzling aspects of these elementary reactions, in particular, vanishing activation energies and ghost three-center intermediates, using the activation strain model (ASM). PMID:27096625

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

    ERIC Educational Resources Information Center

    Latimer, Devin

    2007-01-01

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

  19. Synthesis of a Fluorescent Acridone Using a Grignard Addition, Oxidation, and Nucleophilic Aromatic Substitution Reaction Sequence

    ERIC Educational Resources Information Center

    Goodrich, Samuel; Patel, Miloni; Woydziak, Zachary R.

    2015-01-01

    A three-pot synthesis oriented for an undergraduate organic chemistry laboratory was developed to construct a fluorescent acridone molecule. This laboratory experiment utilizes Grignard addition to an aldehyde, alcohol oxidation, and iterative nucleophilic aromatic substitution steps to produce the final product. Each of the intermediates and the…

  20. Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Walch, Stephen P.

    2002-01-01

    As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.

  1. Anhydride formation is not a valid mechanism for peptide cleavage by carboxypeptidase-A: a semiempirical reaction pathway study

    NASA Astrophysics Data System (ADS)

    Vardi-Kilshtain, Alexandra; Shoham, Gil; Goldblum, Amiram

    The mechanism of action of zinc metalloproteinases has been studied by following the direct nucleophilic pathway, which has been frequently suggested but not yet examined by computational methods, and comparing it to other pathways. We computed the reaction enthalpies for the direct nucleophilic attack by Glu270 in the active site model of carboxypeptidase-A on a model substrate's peptide carbonyl and followed this pathway through mixed anhydride formation and subsequent anhydride cleavage by water. The starting molecular coordinates originate in our own high-resolution crystal structure and the computations have been conducted with the minimal neglect of differential overlap (MNDO) Hamiltonian, modified to include the d-orbitals of zinc and the effects of multiple hydrogen bonding, thus labelled MNDO/d/H. Compared to our recent results for two other candidate pathways for this mechanism, both of the General-Acid-General-Base type, we conclude that the direct nucleophilic or 'anhydride' pathway has a much higher energy barrier at the rate determining step, which is a proton transfer, than previously calculated paths. We argue that the 'anhydride' pathway is thus not a valid one for the cleavage of peptides by carboxypeptidase-A.

  2. Convergent Synthesis of Diverse Nitrogen Heterocycles via Rh(III)-Catalyzed C-H Conjugate Addition/Cyclization Reactions.

    PubMed

    Weinstein, Adam B; Ellman, Jonathan A

    2016-07-01

    The development of Rh(III)-catalyzed C-H conjugate addition/cyclization reactions that provide access to synthetically useful fused bi- and tricyclic nitrogen heterocycles is reported. A broad scope of C-H functionalization substrates and electrophilic olefin coupling partners is effective, and depending on the nature of the directing group, cyclic imide, amide, or heteroaromatic products are obtained. An efficient synthesis of a pyrrolophenanthridine alkaloid natural product, oxoassoanine, highlights the utility of this method. PMID:27337641

  3. C-C Bond Formation via Copper-Catalyzed Conjugate Addition Reactions to Enones in Water at Room Temperature

    PubMed Central

    Lipshutz, Bruce H.; Huang, Shenlin; Leong, Wendy Wen Yi; Isley, Nicholas A.

    2013-01-01

    Conjugate addition reactions to enones can now be done in water at room temperature with in situ-generated organocopper reagents. Mixing an enone, zinc powder, TMEDA, and an alkyl halide in a micellar environemnt containing catalytic amounts of Cu(I), Ag(I), and Au(III), leads to 1,4-adducts in good isolated yields: no organometallic precursor is involved. PMID:23190029

  4. Theoretical and kinetic study of the reaction of ethyl methyl ketone with HO2 for T = 600-1600 K. Part II: addition reaction channels.

    PubMed

    Zhou, Chong-Wen; Mendes, Jorge; Curran, Henry J

    2013-06-01

    The temperature and pressure dependence of the addition reaction of ethyl methyl ketone (EMK) with HO2 radical has been calculated using the master equation method employing conventional transition state theory estimates for the microcanonical rate coefficients in the temperature range of 600-1600 K. Geometries, frequencies, and hindrance potentials were obtained at the B3LYP/6-311G(d,p) level of theory. A modified G3(MP2,CC) method has been used to calculate accurate electronic energies for all of the species involved in the reactions. The rigid-rotor harmonic oscillator approximation has been used for all of the vibrations except for the torsional degrees of freedom which are being treated as 1D hindered rotors. Asymmetric Eckart barriers were used to model tunneling effect in a one-dimensional reaction coordinate through saddle points. Our calculated results show that the four reaction channels forming 1-buten-2-ol + HO2 radical (R5), 2-buten-2-ol + HO2 radical (R10), acetic acid + ethylene + OH radical (R13), and 2-methyl-2-oxetanol + OH radical (R15) are the dominant channels. When the temperature is below 1000 K, the reaction R15 forming the cyclic ether, 2-methyl-2-oxetanol, is dominant while the reaction R13 forming acetic acid + ethylene + OH radical becomes increasingly dominant at temperatures above 1000 K. The other two channels forming 1-buten-2-ol, 2-buten-2-ol, and HO2 radical are not dominant but are still important product channels over the whole temperature range investigated here. No pressure dependence has been found for the reaction channels forming 2-methyl-2-oxetanol + OH radical and acetic acid + ethylene + OH radical. A slightly negative pressure dependence has been found for the reaction channels producing the two butenols. Rate constants for the four important reaction channels at 1 atm (in cm(3) mol(-1) s(-1)) are k(R5) = 2.67 × 10(15) × T(-1.32)exp(-16637/T), k(R10) = 1.62 × 10(8) × T(0.57)exp(-13142/T), k(R13) = 2.29 × 10(17) × T

  5. Effect of temperature on the reaction pathway of calcium carbonate formation via precursor phases

    NASA Astrophysics Data System (ADS)

    Purgstaller, Bettina; Mavromatis, Vasileios; Konrad, Florian; Dietzel, Martin

    2016-04-01

    It has been earlier postulated that some biogenic and sedimentary calcium carbonate (CaCO3) minerals (e.g. calcite and aragonite) are secondary in origin and have originally formed via a metastable calcium carbonate precursor phase (e.g. amorphous CaCO3, [1-2]). Such formation pathways are likely affected by various physicochemical parameters including aqueous Mg and temperature. In an effort to improve our understanding on the formation mechanism of CaCO3 minerals, precipitation experiments were carried out by the addition of a 0.6 M (Ca,Mg)Cl2 solution at distinct Mg/Ca ratios (1/4 and 1/8) into a 1 M NaHCO3 solution under constant pH conditions(8.3 ±0.1). The formation of CaCO3 was systematically examined as a function of temperature (6, 12, 18 and 25 ±0.3° C). During the experimental runs mineral precipitation was monitored by in situ Raman spectroscopy as well as by continuous sampling and analyzing of precipitates and reactive solutions. The results revealed two pathways of CaCO3 formation depending on the initial Mg/Ca ratio and temperature: (i) In experiments with a Mg/Ca ratio of 1/4 at ≤ 12° C as well as in experiments with a Mg/Ca ratio of 1/8 at ≤ 18° C, ikaite (CaCO3 6H2O) acts as a precursor phase for aragonite formation. (ii) In contrast higher temperatures induced the formation of Mg-rich amorphous CaCO3 (Mg-ACC) which was subsequently transformed to Mg-rich calcite. In situ Raman spectra showed that the transformation of Mg-ACC to Mg-calcite occurs at a higher rate (˜ 8 min) compared to that of ikaite to aragonite (> 2 h). Thus, the formation of aragonite rather than of Mg-calcite occurs due to the slower release of Ca2+and CO32‑ ions into the Mg-rich reactive solution during retarded ikaite dissolution. This behavior is generally consistent with the observation that calcite precipitation is inhibited at elevated aqueous Mg/Ca ratios. [1] Addadi L., Raz S. and Weiner S. (2003) Advanced Materials 15, 959-970. [2] Rodriguez-Blanco J. D

  6. Lewis base activation of Lewis acids. Vinylogous aldol addition reactions of conjugated N,O-silyl ketene acetals to aldehydes.

    PubMed

    Denmark, Scott E; Heemstra, John R

    2006-02-01

    N,O-Silyl dienyl ketene acetals derived from unsaturated morpholine amides have been developed as highly useful reagents for vinylogous aldol addition reactions. In the presence of SiCl4 and the catalytic action of chiral phosphoramide (R,R)-3, N,O-silyl dienyl ketene acetal 8 undergoes high-yielding and highly site-selective addition to a wide variety of aldehydes with excellent enantioselectivity. Of particular note is the high yields and selectivities obtained from aliphatic aldehydes. Low catalyst loadings (2-5 mol %) can be employed. The morpholine amide serves as a useful precursor for further synthetic manipulation. PMID:16433495

  7. Pathway development and pilot library realization in diversity-oriented synthesis: exploring Ferrier and Pauson-Khand reactions on a glycal template.

    PubMed

    Kubota, Hideki; Lim, Jongwon; Depew, Kristopher M; Schreiber, Stuart L

    2002-02-01

    Through a correlation of the ability of small molecules to bind biological macromolecules and their ability to modulate cellular and organismal processes, chemistry can inform biology and vice versa. Diversity-oriented organic synthesis (DOS), which aims to provide structurally complex and diverse small molecules efficiently, can play a key role in such chemical genetic studies. Here we illustrate the trial-and-error experimentation that can refine an initial pathway-planning exercise and result eventually in an effective diversity pathway. By exploring Ferrier and Pauson-Khand reactions on a glycal template, we have developed efficient and stereoselective syntheses of tricyclic compounds. In this pathway, diversity results from the substituents and their spatial relationships about the tricyclic rings. A pilot split-pool library synthesis of 2500 tricyclic compounds highlights the use of planning considerations in DOS and a "one-bead, one-stock solution" technology platform. Additionally, it illustrates a promising synthetic pathway for future chemical genetic studies. PMID:11880041

  8. Modifying structure-sensitive reactions by addition of Zn to Pd

    SciTech Connect

    Childers, David J.; Schweitzer, Neil M.; Kamali Shahari, Seyed Mehdi; Rioux, Robert M.; Miller, Jeffrey T.; Meyer, Randall J.

    2014-10-01

    Silica-supported Pd and PdZn nanoparticles of a similar size were evaluated for neopentane hydrogenolysis/isomerization and propane hydrogenolysis/dehydrogenation. Monometallic Pd showed high neopentane hydrogenolysis selectivity. Addition of small amounts of Zn to Pd lead Pd–Zn scatters in the EXAFS spectrum and an increase in the linear bonded CO by IR. In addition, the neopentane turnover rate decreased by nearly 10 times with little change in the selectivity. Increasing amounts of Zn lead to greater Pd–Zn interactions, higher linear-to-bridging CO ratios by IR and complete loss of neopentane conversion. Pd NPs also had high selectivity for propane hydrogenolysis and thus were poorly selective for propylene. The PdZn bimetallic catalysts, however, were able to preferentially catalyze dehydrogenation, were not active for propane hydrogenolysis, and thus were highly selective for propylene formation. The decrease in hydrogenolysis selectivity was attributed to the isolation of active Pd atoms by inactive metallic Zn,demonstrating that hydrogenolysis requires a particular reactive ensemble whereas propane dehydrogenation does not.

  9. Pathways of nitrobenzene degradation in horizontal subsurface flow constructed wetlands: Effect of intermittent aeration and glucose addition.

    PubMed

    Kirui, Wesley K; Wu, Shubiao; Kizito, Simon; Carvalho, Pedro N; Dong, Renjie

    2016-01-15

    Intermittent aeration and addition of glucose were applied to horizontal subsurface flow constructed wetlands in order to investigate the effect on pathways of nitrobenzene (NB) degradation and interactions with microbial nitrogen and sulphur transformations. The experiment was carried out in three phases A, B and C consisting of different NB loading and glucose dosing. For each phase, the effect of aeration was assessed by intermittently aerating one wetland and leaving one unaerated. Regardless of whether or not the wetland was aerated, at an influent NB concentration of 140 mg/L, both wetlands significantly reduced NB to less than 2 mg/L, a reduction efficiency of 98%. However, once the influent NB concentration was increased to 280 mg/L, the aerated wetland had a higher removal performance 82% compared to that of the unaerated wetland 71%. Addition of glucose further intensified the NB removal to 95% in the aerated wetlands and 92% in the unaerated. Aeration of wetlands enhanced NB degradation, but also resulted in higher NB volatilization of 6 mg m(-2) d(-1). The detected high concentration of sulphide 20-60 mg/L in the unaerated wetland gave a strong indication that NB may act as an electron donor to sulphate-reducing bacteria, but this should be further investigated. Aeration positively improved NB removal in constructed wetlands, but resulted in higher NB volatilization. Glucose addition induced co-metabolism to enhance NB degradation. PMID:26468606

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

    PubMed

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

    2013-04-01

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

  11. The Unfolding and Refolding Reactions of Triosephosphate Isomerase from Trypanosoma Cruzi Follow Similar Pathways. Guanidinium Hydrochloride Studies

    NASA Astrophysics Data System (ADS)

    Vázquez-Contreras, Edgar; Pérez Hernández, Gerardo; Sánchez-Rebollar, Brenda Guadalupe; Chánez-Cárdenas, María Elena

    2005-04-01

    The unfolding and refolding reactions of Trypanosoma cruzi triosephosphate isomerase (TcTIM) was studied under equilibrium conditions at increasing guanidinium hydrochloride concentrations. The changes in activity intrinsic fluorescence and far-ultraviolet circular dichroism as a function of denaturant were used as a quaternary, tertiary and secondary structural probes respectively. The change in extrinsic ANS fluorescence intensity was also investigated. The results show that the transition between the homodimeric native enzyme to the unfolded monomers (unfolding), and its inverse reaction (refolding) are described by similar pathways and two equilibrium intermediates were detected in both reactions. The mild denaturant concentrations intermediate is active and contains significant amount of secondary and tertiary structures. The medium denaturant concentrations intermediate is inactive and able to bind the fluorescent dye. This intermediates are maybe related with those observed in the denaturation pattern of TIMs from other species; the results are discussed in this context.

  12. Rh(I) -Catalyzed Cyclizative Addition Reaction of 1,6-Enyne and Sulfonyl Chloride by Carbophilic Activation.

    PubMed

    Dang, Mengyao; Hou, Longlei; Tong, Xiaofeng

    2016-06-01

    The π-acid-catalyzed cyclizations of 1,n-enynes by carbophilic activation have been extensively studied and appear as highly attractive processes, yet the cases within a catalytic cycle based on redox principle are rare. Herein, we report the cyclizative addition reactions of 1,6-enynes and sulfonyl chlorides by using a [Rh(cod)Cl/dppf] (dppf=1,1'-bis(diphenylphosphino)ferrocene) catalyst system. The process features the involvement of oxidative addition of sulfonyl chloride to Rh(I) catalyst, which generates [(dppf)(RSO2 )RhCl2 ] as a π-acid species to trigger cyclizative addition in a 6-endo-dig manner by carbophilic activation. Moreover, the catalytic protocol is also applicable to 1,6-diene analogues. PMID:27016845

  13. Semifluorinated polymers via cycloaddition and nucleophilic addition reactions of aromatic trifluorovinyl ethers

    NASA Astrophysics Data System (ADS)

    Iacono, Scott Thomas

    This dissertation encompasses the synthesis, characterization, and properties of semifluorinated polymers derived from thermal polymerization of aryl trifluorovinyl ether (TFVE) monomers. This work is divided into two parts based on the methodology of thermal polymerization using aryl TFVE monomers. The first part of this work involves the thermal [2 + 2] cyclodimerization of aryl TFVE monomers affording perfluorocyclobutyl (PFCB) aryl ether polymers. Chapter 1 provides an overview of PFCB aryl ether polymers as a next-generation class of high performance fluoropolymers that have been successfully employed for a myriad of technologies. PFCB aryl ether polymers are highly desired because of their high thermal stability, processability, and tailorability for specific material applications. Chapter 2 introduces a general perspective of polyhedral oligomeric silsesquioxanes (POSS) that were modified with PFCB aryl ether polymer for property enhancement, specifically for low surface energy materials. Chapter 3 and 4 show the synthesis, characterization, and properties of POSS modified PFCB aryl ether polymers as blends and a variety of copolymer architectures, respectively. The second portion of this dissertation focuses on the development of a new, facile step-growth polymerization of diols/bisphenols and aryl TFVEs to afford fluoroethylene/vinylene alkyl/aryl ether (FAE) polymers. Chapter 5 is a prelude to the development of FAE polymers which entails optimizing the methodology and mechanistic rationale of nucleophile addition to aryl TFVEs. Chapter 6 details the FAE polymerization kinetics, physical properties, and strategy for functionalization. Chapter 7 illustrates the modular modification of FAE polymers for the development of tunable light emissive materials for potential use as transport layer material for organic light emitting diodes (OLEDs) and also chemical sensors. Chapter 8 introduces postfunctionaliztion of FAE polymers resulting with sulfonated biaryl

  14. Trigonal pyramidal carbon geometry as model for electrophilic addition-substitution and elimination reactions and its significance in enzymatic processes

    NASA Astrophysics Data System (ADS)

    Buck, Henk M.

    Various examples are given in which compounds are characterized as products or intermediates in a (distorted) trigonal pyramidal (TP) geometry. These observations have taken place mainly in the field of carbocation chemistry. Special attention is given to carbenium ions formed by halogen addition to 1,1-diarylsubstituted ethylenes focused on the electronic effects of the C-halogen bond as axial bond in a TP geometry with regard to the ?-distribution in the rest of the molecular system. The experimental verification is accompanied by quantum chemical calculations. We also used the TP structure as a reactive model for specific enzymatic reactions. The relevance of this geometry is shown for the dehalogenation reaction of the nucleophilic displacement in dichloroethane catalyzed by haloalkane dehalogenase and for the decarboxylation of L-ornithine with ornithine decarboxylase under loss of carbon dioxide.

  15. An additive interaction between the NFκB and estrogen receptor signalling pathways in human endometrial epithelial cells

    PubMed Central

    King, A.E.; Collins, F.; Klonisch, T.; Sallenave, J.-M.; Critchley, H.O.D.; Saunders, P.T.K.

    2010-01-01

    BACKGROUND Human embryo implantation is regulated by estradiol (E2), progesterone and locally produced mediators including interleukin-1β (IL-1β). Interactions between the estrogen receptor (ER) and NF kappa B (NFκB) signalling pathways have been reported in other systems but have not been detailed in human endometrium. METHODS AND RESULTS Real-time PCR showed that mRNA for the p65 and p105 NFκB subunits is maximally expressed in endometrium from the putative implantation window. Both subunits are localized in the endometrial epithelium throughout the menstrual cycle. Reporter assays for estrogen response element (ERE) activity were used to examine functional interactions between ER and NFκB in telomerase immortalized endometrial epithelial cells (TERT-EEC). E2 and IL-1β treatment of TERT-EECs enhances ERE activity by a NFκB and ER dependent mechanism; this effect could be mediated by ERα or ERβ. E2 and IL-1β also positively interact to increase endogenous gene expression of prostaglandin E synthase and c-myc. This is a gene-dependent action as there is no additive effect on cyclin D1 or progesterone receptor expression. CONCLUSION In summary, we have established that NFκB signalling proteins are expressed in normal endometrium and report that IL-1β can enhance the actions of E2 in a cell line derived from healthy endometrium. This mechanism may allow IL-1β, possibly from the developing embryo, to modulate the function of the endometrial epithelium to promote successful implantation, for example by regulating prostaglandin production. Aberrations in the interaction between the ER and NFκB signalling pathways may have a negative impact on implantation contributing to pathologies such as early pregnancy loss and infertility. PMID:19955102

  16. Influence of a Dopamine Pathway Additive Genetic Efficacy Score on Smoking Cessation: Results from Two Randomized Clinical Trials of Bupropion

    PubMed Central

    David, Sean P.; Strong, David R.; Leventhal, Adam M.; Lancaster, Molly A.; McGeary, John E.; Munafò, Marcus R.; Bergen, Andrew W.; Swan, Gary E.; Benowitz, Neal L.; Tyndale, Rachel F.; Conti, David V.; Brown, Richard A.; Lerman, Caryn; Niaura, Raymond

    2013-01-01

    Aims To evaluate associations of treatment and an ‘additive genetic efficacy score’ (AGES) based on dopamine functional polymorphisms with time to first smoking lapse and point prevalence abstinence at end of treatment among participants enrolled in two randomized clinical trials of smoking cessation therapies. Design Double-blind pharmacogenetic efficacy trials randomizing participants to active or placebo bupropion. Study 1 also randomized participants to cognitive-behavioral smoking cessation treatment (CBT) or this treatment with CBT for depression. Study 2 provided standardized behavioural support. Setting Two Hospital-affiliated clinics (Study 1), and two University-affiliated clinics (Study 2). Participants N=792 self-identified white treatment-seeking smokers aged ≥18 years smoking ≥10 cigarettes per day over the last year. Measurements Age, gender, Fagerström Test for Nicotine Dependence, dopamine pathway genotypes (rs1800497 [ANKK1 E713K], rs4680 [COMT V158M], DRD4 exon 3 Variable Number of Tandem Repeats polymorphism [DRD4 VNTR], SLC6A3 3' VNTR) analyzed both separately and as part of an AGES, time to first lapse, and point prevalence abstinence at end of treatment. Findings Significant associations of the AGES (hazard ratio = 1.10, 95% Confidence Interval [CI] = 1.06–1.14], p=0.0099) and of the DRD4 VNTR (HR = 1.29, 95%CI 1.17–1.41, p=0.0073) were observed with time to first lapse. A significant AGES by pharmacotherapy interaction was observed (β [SE]=−0.18 [0.07], p=0.016), such that AGES predicted risk for time to first lapse only for individuals randomized to placebo. Conclusions A score based on functional polymorphisms relating to dopamine pathways appears to predict lapse to smoking following a quit attempt, and the association is mitigated in smokers using bupropion. PMID:23941313

  17. Charting an Alternate Pathway to Reaction Orders and Rate Laws in Introductory Chemistry Courses

    ERIC Educational Resources Information Center

    Rushton, Gregory T.; Criswell, Brett A.; McAllister, Nicole D.; Polizzi, Samuel J.; Moore, Lamesha A.; Pierre, Michelle S.

    2014-01-01

    Reaction kinetics is an axiomatic topic in chemistry that is often addressed as early as the high school course and serves as the foundation for more sophisticated conversations in college-level organic, physical, and biological chemistry courses. Despite the fundamental nature of reaction kinetics, students can struggle with transforming their…

  18. Probing the Additional Capacity and Reaction Mechanism of the RuO2 Anode in Lithium Rechargeable Batteries.

    PubMed

    Kim, Yunok; Muhammad, Shoaib; Kim, Hyunchul; Cho, Yong-Hun; Kim, Hansu; Kim, Ji Man; Yoon, Won-Sub

    2015-07-20

    The structural changes and electrochemical behavior of RuO2 are investigated by using in situ XRD, X-ray absorption spectroscopy, and electrochemical techniques to understand the electrochemical reaction mechanism of this metal oxide anode material. Intermediate phase-assisted transformation of RuO2 to LiRuO2 takes place at the start of discharge. Upon further lithiation, LiRuO2 formed by intercalation decomposes to nanosized Ru metal and Li2 O by a conversion reaction. A reversible capacity in addition to its theoretical capacity is observed on discharging below 0.5 V during which no redox activity involving Ru is observed. TEM, X-ray photoelectron spectroscopy, and the galvanostatic intermittent titration technique are used to probe this additional capacity. The results show that the additional capacity is a result of Li storage in the grain boundary between nanosized Ru metal and Li2 O. Findings of this study provide a better understanding of the quantitative share of capacity by a unique combination of intercalation, conversion, and interfacial Li storage in a RuO2 anode. PMID:26130378

  19. New Insights on the Reaction Pathway Leading to Lactyl-ThDP: A Theoretical Approach.

    PubMed

    Lizana, Ignacio; Jaña, Gonzalo A; Delgado, Eduardo J

    2015-08-24

    In all ThDP-dependent enzymes, the catalytic cycle is initiated with the attack of the C2 atom of the ylide intermediate on the Cα atom of a pyruvate molecule to form the lactyl-ThDP (L-ThDP) intermediate. In this study, the reaction between the ylide intermediate and pyruvate leading to the formation of L-ThDP is addressed from a theoretical point of view. The study includes molecular dynamics, exploration of the potential energy surface by means of QM/MM calculations, and reactivity analysis on key centers. The results show that the reaction occurs via a concerted mechanism in which the carboligation and the proton transfers occur synchronically. It is also observed that during the reaction the protonation state of the N1' atom changes: the reaction starts with the ylide having the N1' atom deprotonated and reaches a transition state showing the N1' atom protonated. This conversion leads to the reaction path of minimum energy, with an activation energy of about 20 kcal mol(-1). On the other hand, it is also observed that the approaching distance between the pyruvate and the ylide, i.e., the Cα-C2 distance, plays a fundamental role in the reaction mechanism since it determines the nucleophilic character of key atoms of the ylide, which in turn trigger the elemental reactions of the mechanism. PMID:26222831

  20. Concise Enantioselective Synthesis of Oxygenated Steroids via Sequential Copper(II)-Catalyzed Michael Addition/Intramolecular Aldol Cyclization Reactions

    PubMed Central

    Cichowicz, Nathan R.; Kaplan, Will; Khomutnyk, Yaroslav; Bhattarai, Bijay; Sun, Zhankui; Nagorny, Pavel

    2015-01-01

    A new scalable enantioselective approach to functionalized oxygenated steroids is described. This strategy is based on chiral bis(oxazoline) copper(II) complex-catalyzed enantioselective and diastereoselective Michael reactions of cyclic ketoesters and enones to install vicinal quaternary and tertiary stereocenters. In addition, the utility of copper(II) salts as highly active catalysts for the Michael reactions of traditionally unreactive ββ′-enones and substituted ββ′-ketoesters that results in unprecedented Michael adducts containing vicinal all-carbon quaternary centers is also demonstrated. The Michael adducts subsequently undergo base-promoted diastereoselective aldol cascade reactions resulting in the natural or unnatural steroid skeletons. The experimental and computational studies suggest that the torsional strain effects arising from the presence of the Δ5-unsaturation are key controling elements for the formation of the natural cardenolide scaffold. The described method enables expedient generation of polycyclic molecules including modified steroidal scaffolds as well as challenging-to-synthesize Hajos-Parrish and Wieland-Miescher ketones. PMID:26491886

  1. Selectivity in the Addition Reactions of Organometallic Reagents to Aziridine-2-carboxaldehydes: The Effects of Protecting Groups and Substitution Patterns

    PubMed Central

    Kulshrestha, Aman; Schomaker, Jennifer M.; Holmes, Daniel; Staples, Richard J.; Jackson, James E.; Borhan, Babak

    2014-01-01

    Good to excellent stereo-selectivity has been found in the addition reactions of Grignard and organo-zinc reagents to N-protected aziridine-2-carboxaldehydes. Specifically, high syn selectivity was obtained with benzyl-protected cis, tert-butyloxycar-bonyl-protected trans, and tosyl-pro-tected 2,3-disubstituted aziridine-2-car-boxaldehydes. Furthermore, rate and selectivity effects of ring substituents, temperature, solvent, and Lewis acid and base modifiers were studied. The diastereomeric preference of addition is dominated by the substrate aziri-dines’ substitution pattern and especially the electronic character and conformational preferences of the nitrogen protecting groups. To help rationalize the observed stereochemical outcomes, conformational and electronic structural analyses of a series of model systems representing the various substitution patterns have been explored by density functional calculations at the B3LYP/6–31G* level of theory with the SM8 solvation model to account for solvent effects. PMID:21928447

  2. The IgE-dependent pathway in allergic transfusion reactions: involvement of donor blood allergens other than plasma proteins.

    PubMed

    Matsuyama, Nobuki; Yasui, Kazuta; Amakishi, Etsuko; Hayashi, Tomoya; Kuroishi, Ayumu; Ishii, Hiroyuki; Matsukura, Harumichi; Tani, Yoshihiko; Furuta, Rika A; Hirayama, Fumiya

    2015-07-01

    On transfusion, several plasma proteins can cause anaphylaxis in patients deficient in the corresponding plasma proteins. However, little is known about other allergens, which are encountered much more infrequently. Although it has been speculated that an allergen-independent pathway underlying allergic transfusion reactions (ATRs) is elicited by biological response modifiers accumulated in blood components during storage, the exact mechanisms remain unresolved. Furthermore, it is difficult even to determine whether ATRs are induced via allergen-dependent or allergen-independent pathways. To distinguish these two pathways in ATR cases, we established a basophil activation test, in which the basophil-activating ability of supernatants of residual transfused blood of ATR cases to whole blood basophils was assessed in the presence or absence of dasatinib, an inhibitor of IgE-mediated basophil activation. Three of 37 supernatants from the platelet concentrates with ATRs activated panel blood basophils in the absence, but not in the presence, of dasatinib. The basophil activation was inhibited by treatment of anti-fish collagen I MoAb in one case, suggesting that the involvement of fish allergens may have been present in donor plasma. We concluded that unknown non-plasma proteins, some of which had epitopes similar to fish antigens, in blood component may be involved in ATRs via an allergen/IgE-dependent pathway. PMID:25840771

  3. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths

    NASA Astrophysics Data System (ADS)

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-06-01

    Photodissociation pathways of nitromethane following π → π* electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH3 and NO2 (2B2) is formed by direct dissociation from the S1 state. Important pathways involving S1 and S0 states for production of various dissociation products CH3NO + O (1D), CH3O(X2E) + NO (X2Π), CH2NO + OH, and CH2O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH3NO2, the OH radical roaming in OH dissociation from CH2N(O)(OH), and the NO roaming in NO dissociation from CH3ONO.

  4. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths.

    PubMed

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-06-28

    Photodissociation pathways of nitromethane following π → π(*) electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH3 and NO2 ((2)B2) is formed by direct dissociation from the S1 state. Important pathways involving S1 and S0 states for production of various dissociation products CH3NO + O ((1)D), CH3O(X(2)E) + NO (X(2)Π), CH2NO + OH, and CH2O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH3NO2, the OH radical roaming in OH dissociation from CH2N(O)(OH), and the NO roaming in NO dissociation from CH3ONO. PMID:24985641

  5. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths

    SciTech Connect

    Isegawa, Miho; Liu, Fengyi; Morokuma, Keiji; Maeda, Satoshi

    2014-06-28

    Photodissociation pathways of nitromethane following π → π{sup *} electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH{sub 3} and NO{sub 2} ({sup 2}B{sub 2}) is formed by direct dissociation from the S{sub 1} state. Important pathways involving S{sub 1} and S{sub 0} states for production of various dissociation products CH{sub 3}NO + O ({sup 1}D), CH{sub 3}O(X{sup 2}E) + NO (X{sup 2}Π), CH{sub 2}NO + OH, and CH{sub 2}O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH{sub 3}NO{sub 2}, the OH radical roaming in OH dissociation from CH{sub 2}N(O)(OH), and the NO roaming in NO dissociation from CH{sub 3}ONO.

  6. Graphene Facilitated Removal of Labetalol in Laccase-ABTS System: Reaction Efficiency, Pathways and Mechanism

    PubMed Central

    Dong, Shipeng; Xiao, Huifang; Huang, Qingguo; Zhang, Jian; Mao, Liang; Gao, Shixiang

    2016-01-01

    The widespread occurrence of the beta-blocker labetalol causes environmental health concern. Enzymatic reactions are highly efficient and specific offering biochemical transformation of trace contaminants with short reaction time and little to none energy consumption. Our experiments indicate that labetalol can be effectively transformed by laccase-catalyzed reaction using 2, 2-Azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as a mediator, while no significant removal of labetalol can be achieved in the absence of ABTS. A total of three products were identified. It is interesting that the presence of graphene greatly increased the reaction rate while not changed the products. In the presence of 100 μg/L graphene, the pseudo-first-order reaction rate constant was increased ~50 times. We found that the enhancement of graphene is probably attributed to the formation and releasing of ABTS2+ which has a much greater reactivity towards labetalol when graphene is present. This study provides fundamental information for laccase-ABTS mediated labetalol reactions and the effect of graphene, which could eventually lead to development of novel methods to control beta-blocker contamination. PMID:26891761

  7. Graphene Facilitated Removal of Labetalol in Laccase-ABTS System: Reaction Efficiency, Pathways and Mechanism

    NASA Astrophysics Data System (ADS)

    Dong, Shipeng; Xiao, Huifang; Huang, Qingguo; Zhang, Jian; Mao, Liang; Gao, Shixiang

    2016-02-01

    The widespread occurrence of the beta-blocker labetalol causes environmental health concern. Enzymatic reactions are highly efficient and specific offering biochemical transformation of trace contaminants with short reaction time and little to none energy consumption. Our experiments indicate that labetalol can be effectively transformed by laccase-catalyzed reaction using 2, 2-Azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as a mediator, while no significant removal of labetalol can be achieved in the absence of ABTS. A total of three products were identified. It is interesting that the presence of graphene greatly increased the reaction rate while not changed the products. In the presence of 100 μg/L graphene, the pseudo-first-order reaction rate constant was increased ~50 times. We found that the enhancement of graphene is probably attributed to the formation and releasing of ABTS2+ which has a much greater reactivity towards labetalol when graphene is present. This study provides fundamental information for laccase-ABTS mediated labetalol reactions and the effect of graphene, which could eventually lead to development of novel methods to control beta-blocker contamination.

  8. Functional Organosulfide Electrolyte Promotes an Alternate Reaction Pathway to Achieve High Performance in Lithium-Sulfur Batteries.

    PubMed

    Chen, Shuru; Dai, Fang; Gordin, Mikhail L; Yu, Zhaoxin; Gao, Yue; Song, Jiangxuan; Wang, Donghai

    2016-03-18

    Lithium-sulfur (Li-S) batteries have recently received great attention because they promise to provide energy density far beyond current lithium ion batteries. Typically, Li-S batteries operate by conversion of sulfur to reversibly form different soluble lithium polysulfide intermediates and insoluble lithium sulfides through multistep redox reactions. Herein, we report a functional electrolyte system incorporating dimethyl disulfide as a co-solvent that enables a new electrochemical reduction pathway for sulfur cathodes. This pathway uses soluble dimethyl polysulfides and lithium organosulfides as intermediates and products, which can boost cell capacity and lead to improved discharge-charge reversibility and cycling performance of sulfur cathodes. This electrolyte system can potentially enable Li-S batteries to achieve high energy density. PMID:26918660

  9. Densification of Reaction Bonded Silicon Nitride with the Addition of Fine Si Powder Effects on the Sinterability and Mechanical Properties

    SciTech Connect

    Lee, Sea-Hoon; Cho, Chun-Rae; Park, Young-Jo; Ko, Jae-Woong; Kim, Hai-Doo; Lin, Hua-Tay; Becher, Paul F

    2013-01-01

    The densification behavior and strength of sintered reaction bonded silicon nitrides (SRBSN) that contain Lu2O3-SiO2 additives were improved by the addition of fine Si powder. Dense specimens (relative density: 99.5%) were obtained by gas-pressure sintering (GPS) at 1850oC through the addition of fine Si. In contrast, the densification of conventional specimens did not complete at 1950oC. The fine Si decreased the onset temperature of shrinkage and increased the shrinkage rate because the additive helped the compaction of green bodies and induced the formation of fine Si3N4 particles after nitridation and sintering at and above 1600oC. The amount of residual SiO2 within the specimens was not strongly affected by adding fine Si powder because most of the SiO2 layer that had formed on the fine Si particles decomposed during nitridation. The maximum strength and fracture toughness of the specimens were 991 MPa and 8.0 MPa m1/2, respectively.

  10. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity.

    PubMed

    Boesenberg, Ulrike; Marcus, Matthew A; Shukla, Alpesh K; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-01-01

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, is likely to apply to other transition metal oxide systems. The presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale. PMID:25410966

  11. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity

    PubMed Central

    Boesenberg, Ulrike; Marcus, Matthew A.; Shukla, Alpesh K.; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-01-01

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, is likely to apply to other transition metal oxide systems. The presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale. PMID:25410966

  12. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity

    SciTech Connect

    Boesenberg, Ulrike; Marcus, Matthew A.; Shukla, Alpesh K.; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-11-20

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, is likely to apply to other transition metal oxide systems. Lastly, the presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale.

  13. Identification of metabolites of dalfampridine (4-aminopyridine) in human subjects and reaction phenotyping of relevant cytochrome P450 pathways

    PubMed Central

    Caggiano, Anthony; Blight, Andrew

    2013-01-01

    Objectives An extended release formulation of dalfampridine (4-aminopyridine; 4-AP), a potassium channel blocker is available in the USA to improve walking in patients with multiple sclerosis. This study investigated the human metabolites of 4-AP and the cytochrome P450 (CYP450) pathways responsible for 4-AP metabolism. Methods Metabolites were identified, using thin layer chromatography, high performance liquid chromatography, and gas chromatography/mass spectroscopy, in plasma and urine samples obtained during an excretion balance study of four subjects who were administered a single oral 15-mg dose of 14C-4-AP. Samples were compared with authentic standards of 4-AP, 2-hydroxy-4AP, 3-hydroxy-4AP, and 4-AP-N-oxide. Reaction phenotyping was performed in vitro using human liver microsomes and recombinant CYP450 enzymes with incubation in the presence of direct and time-dependent inhibitors to determine the CYP450 pathways involved in metabolite formation. Results While most (∼70%) of the radioactivity detected in plasma at each time point corresponded to unchanged 4-AP, two major metabolites were recovered. One metabolite co-localized with the authentic reference standard of 3-hydroxy-4-AP, and the other metabolite was identified as the sulfate conjugate of 3-hydroxy-4-AP. Two minor components were observed, one accounting for 2% of radioactivity and the other below the level of quantitation. Reaction phenotyping showed moderate correlations for conversion of 4-AP to 3-hydroxy-4AP with both CYP2E1 (r = 0.596; p < 0.001) and CYP2C8 (r = 0.608; p < 0.001). Use of a CYP2E1 metabolism-dependent inhibitor inhibited formation of 3-hydroxy-4-AP with and without pre-incubation (higher inhibition with pre-incubation), further supporting the likelihood of CYP2E1 as a metabolic pathway. The main limitation of this study was the inability to identify the CYP enzymes responsible for the 3-hydroxylation of 4-AP, although this conversion represents only a minor

  14. Directing reaction pathways by catalyst active-site selection using self-assembled monolayers.

    PubMed

    Pang, Simon H; Schoenbaum, Carolyn A; Schwartz, Daniel K; Medlin, J Will

    2013-01-01

    One key route for controlling reaction selectivity in heterogeneous catalysis is to prepare catalysts that exhibit only specific types of sites required for desired product formation. Here we show that alkanethiolate self-assembled monolayers with varying surface densities can be used to tune selectivity to desired hydrogenation and hydrodeoxygenation products during the reaction of furfural on supported palladium catalysts. Vibrational spectroscopic studies demonstrate that the selectivity improvement is achieved by controlling the availability of specific sites for the hydrogenation of furfural on supported palladium catalysts through the selection of an appropriate alkanethiolate. Increasing self-assembled monolayer density by controlling the steric bulk of the organic tail ligand restricts adsorption on terrace sites and dramatically increases selectivity to desired products furfuryl alcohol and methylfuran. This technique of active-site selection simultaneously serves both to enhance selectivity and provide insight into the reaction mechanism. PMID:24025780

  15. Exploring reaction pathways with transition path and umbrella sampling: Application to methyl maltoside

    NASA Astrophysics Data System (ADS)

    Dimelow, Richard J.; Bryce, Richard A.; Masters, Andrew J.; Hillier, Ian H.; Burton, Neil A.

    2006-03-01

    The transition path sampling (TPS) method is a powerful approach to study chemical reactions or transitional properties on complex potential energy landscapes. One of the main advantages of the method over potential of mean force methods is that reaction rates can be directly accessed without knowledge of the exact reaction coordinate. We have investigated the complementary nature of these two differing approaches, comparing transition path sampling with the weighted histogram analysis method to study a conformational change in a small model system. In this case study, the transition paths for a transition between two rotational conformers of a model disaccharide molecule, methyl β-D-maltoside, were compared with a free energy surface constrained by the two commonly used glycosidic (ϕ,ψ) torsional angles. The TPS method revealed a reaction channel that was not apparent from the potential of mean force method, and the suitability of ϕ and ψ as reaction coordinates to describe the isomerization in vacuo was confirmed by examination of the transition path ensemble. Using both transition state theory and transition path sampling methods, the transition rate was estimated. We have estimated a characteristic time between transitions of approximately 160 ns for this rare isomerization event between the two conformations of the carbohydrate. We conclude that transition path sampling can extract subtle information about the dynamics not apparent from the potential of mean force method. However, in calculating the reaction rate, the transition path sampling method required 27.5 times the computational effort than was needed by the potential of mean force method.

  16. Theoretical study on the CuH + H. -->. Cu + H/sub 2/ reaction pathway

    SciTech Connect

    Ruiz, M.E.; Garcia-Prieto, J.; Poulain, E.; Ozin, G.A.; Poirier, R.A.; Matta, S.M.; Czismadia, I.G.; Gracie, C.; Novaro, O.

    1986-01-16

    Quite recently, experimental results on the CuH + H ..-->.. Cu + H/sub 2/ thermal matrix phase reaction were reported, indicating that it proceeds with no activation barrier, and no evidence exists for an intermediate CuH/sub 2/ species at 10-13 K. Here the authors present a theoretical study of this reaction using variational and perturbational configuration interaction calculations with a relativistic pseudopotential (PSHONDO-CIPSI) set of programs. The results confirm the lack of a barrier and provide an explanation as to why the CuH/sub 2/ species may not be observed. 11 references, 3 figures, 3 tables.

  17. Towards quantum-based modeling of enzymatic reaction pathways: Application to the acetylholinesterase catalysis

    NASA Astrophysics Data System (ADS)

    Polyakov, Igor V.; Grigorenko, Bella L.; Moskovsky, Alexander A.; Pentkovski, Vladimir M.; Nemukhin, Alexander V.

    2013-01-01

    We apply computational methods aiming to approach a full quantum mechanical treatment of chemical reactions in proteins. A combination of the quantum mechanical - molecular mechanical methodology for geometry optimization and the fragment molecular orbital approach for energy calculations is examined for an example of acetylcholinesterase catalysis. The codes based on the GAMESS(US) package operational on the 'RSC Tornado' computational cluster are applied to determine that the energy of the reaction intermediate upon hydrolysis of acetylcholine is lower than that of the enzyme-substrate complex. This conclusion is consistent with the experiments and it is free from the empirical force field contributions.

  18. Fundamental kinetics and mechanistic pathways for oxidation reactions in supercritical water

    NASA Technical Reports Server (NTRS)

    Webley, Paul A.; Tester, Jefferson W.

    1988-01-01

    Oxidation of the products of human metabolism in supercritical water has been shown to be an efficient way to accomplish the on-board water/waste recycling in future long-term space flights. Studies of the oxidation kinetics of methane to carbon dioxide in supercritical water are presented in this paper in order to enhance the fundamental understanding of the oxidation of human waste compounds in supercritical water. It is concluded that, although the elementary reaction models remain the best hope for simulating oxidation in supercritical water, several modifications to existing mechanisms need to be made to account for the role of water in the reaction mechanism.

  19. Mechanisms and reaction pathways for simultaneous oxidation of NOx and SO₂ by ozone determined by in situ IR measurements.

    PubMed

    Sun, Chenglang; Zhao, Nan; Zhuang, Zhuokai; Wang, Haiqiang; Liu, Yue; Weng, Xiaole; Wu, Zhongbiao

    2014-06-15

    Ozone (O3) oxidation combined with wet scrubbing is a promising method for the simultaneous removal of SO2 and NOx in flue gas. In this study, the O3 oxidation processes of NO and SO2, as well as their coexistence, were investigated using an in situ IR spectrometer. Experimental results showed that the O3 concentration and the reaction temperature played critical roles in the O3 oxidation process of NO. Around 80°C, when inlet molar ratio of O3/NO was less than 1, NO was mainly oxidized to NO2, while when the ratio was greater than 1, NO would be further oxidized to NO3, N2O5, and HNO3. NO3 was the key intermediate product for the formation of N2O5 and HNO3. However, the subsequent reactions of NO3 were temperature dependence. With the increase of reaction temperature above 100°C, the concentration of NO2 increased whereas the concentrations of N2O5 and HNO3 decreased. The oxidation of SO2 by O3 was negligible and SO2 had little influence on the oxidation of NO in the simultaneous oxidation of NO and SO2. Finally, based on the in situ IR results, the oxidation mechanism is discussed and the reaction pathways are proposed. PMID:24801895

  20. Vitamin B6 nutritional status and cellular availability of pyridoxal 5'-phosphate govern the function of the transsulfuration pathway's canonical reactions and hydrogen sulfide production via side reactions.

    PubMed

    Gregory, Jesse F; DeRatt, Barbara N; Rios-Avila, Luisa; Ralat, Maria; Stacpoole, Peter W

    2016-07-01

    The transsulfuration pathway (TS) acts in sulfur amino acid metabolism by contributing to the regulation of cellular homocysteine, cysteine production, and the generation of H2S for signaling functions. Regulation of TS pathway kinetics involves stimulation of cystathionine β-synthase (CBS) by S-adenosylmethionine (SAM) and oxidants such as H2O2, and by Michaelis-Menten principles whereby substrate concentrations affect reaction rates. Although pyridoxal phosphate (PLP) serves as coenzyme for both CBS and cystathionine γ-lyase (CSE), CSE exhibits much greater loss of activity than CBS during PLP insufficiency. Thus, cellular and plasma cystathionine concentrations increase in vitamin B6 deficiency mainly due to the bottleneck caused by reduced CSE activity. Because of the increase in cystathionine, the canonical production of cysteine (homocysteine → cystathionine → cysteine) is largely maintained even during vitamin B6 deficiency. Typical whole body transsulfuration flux in humans is 3-7 μmol/h per kg body weight. The in vivo kinetics of H2S production via side reactions of CBS and CSE in humans are unknown but they have been reported for cultured HepG2 cells. In these studies, cells exhibit a pronounced reduction in H2S production capacity and rates of lanthionine and homolanthionine synthesis in deficiency. In humans, plasma concentrations of lanthionine and homolanthionine exhibit little or no mean change due to 4-wk vitamin B6 restriction, nor do they respond to pyridoxine supplementation of subjects in chronically low-vitamin B6 status. Wide individual variation in responses of the H2S biomarkers to such perturbations of human vitamin B6 status suggests that the resulting modulation of H2S production may have physiological consequences in a subset of people. Supported by NIH grant DK072398. This paper refers to data from studies registered at clinicaltrials.gov as NCT01128244 and NCT00877812. PMID:26765812

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

    SciTech Connect

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

    2004-04-12

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

  2. Coal thermolysis modeling: The effects of restricted diffusion on thermal reaction pathways

    SciTech Connect

    Buchanan, A.C. III; Britt, P.F.; Biggs, C.A.

    1989-01-01

    The technique of model compound immobilization by covalent surface attachment is being employed to investigate the potential impact of restricted diffusional mobility on the thermal reactivity of coal. This restricted mobility may be imposed in coal as a consequence of its cross-linked, macromolecular structure. A detailed study of the thermolysis of surface-immobilized bibenzyl showed that the rate of unimolecular C-C homolysis is similar to that in fluid phases. Recent studies have foucused on the thermally induced, free radical chain decomposition reactions for surface-immobilized 1,3-diphenylpropane and 1,4-diphenylbutane. For 1,4-diphenylbutane both the reaction rate and product composition are strongly dependent on surface coverage and, hence, the proximity of 1.4-diphenylbutane molecules and hydrogen abstracting radicals on the surface. The rates and selectivities of these key bimolecular reaction steps on the surface might also be affected by the structure of neighboring molecules. In the current study, we are beginning to probe this feature by examining the influence of the structure of co-attached aromatic molecules such as biphenyl and diphenylmethane on the reaction rate and regioselectivity in the thermolysis of 1,4-diphenylbutane. 7 refs. , 1 fig., 2 tabs.

  3. Urea degradation by electrochemically generated reactive chlorine species: products and reaction pathways.

    PubMed

    Cho, Kangwoo; Hoffmann, Michael R

    2014-10-01

    This study investigated the transformation of urea by electrochemically generated reactive chlorine species (RCS). Solutions of urea with chloride ions were electrolyzed using a bismuth doped TiO2 (BiOx/TiO2) anode coupled with a stainless steel cathode at applied anodic potentials (Ea) of either +2.2 V or +3.0 V versus the normal hydrogen electrode. In NaCl solution, the current efficiency of RCS generation was near 30% at both potentials. In divided cell experiments, the pseudo-first-order rate of total nitrogen decay was an order of magnitude higher at Ea of +3.0 V than at +2.2 V, presumably because dichlorine radical (Cl2(-)·) ions facilitate the urea transformation primary driven by free chlorine. Quadrupole mass spectrometer analysis of the reactor headspace revealed that N2 and CO2 are the primary gaseous products of the oxidation of urea, whose urea-N was completely transformed into N2 (91%) and NO3(-) (9%). The higher reaction selectivity with respect to N2 production can be ascribed to a low operational ratio of free available chlorine to N. The mass-balance analysis recovered urea-C as CO2 at 77%, while CO generation most likely accounts for the residual carbon. In light of these results, we propose a reaction mechanism involving chloramines and chloramides as reaction intermediates, where the initial chlorination is the rate-determining step in the overall sequence of reactions. PMID:25219459

  4. A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease

    PubMed Central

    Holmans, Peter; Moskvina, Valentina; Jones, Lesley; Sharma, Manu; Vedernikov, Alexey; Buchel, Finja; Sadd, Mohamad; Bras, Jose M.; Bettella, Francesco; Nicolaou, Nayia; Simón-Sánchez, Javier; Mittag, Florian; Gibbs, J. Raphael; Schulte, Claudia; Durr, Alexandra; Guerreiro, Rita; Hernandez, Dena; Brice, Alexis; Stefánsson, Hreinn; Majamaa, Kari; Gasser, Thomas; Heutink, Peter; Wood, Nicholas W.; Martinez, Maria; Singleton, Andrew B.; Nalls, Michael A.; Hardy, John; Morris, Huw R.; Williams, Nigel M.; Arepalli, Sampath; Barker, Roger; Barrett, Jeffrey; Ben-Shlomo, Yoav; Berendse, Henk W.; Berg, Daniela; Bhatia, Kailash; de Bie, Rob M.A.; Biffi, Alessandro; Bloem, Bas; Brice, Alexis; Bochdanovits, Zoltan; Bonin, Michael; Bras, Jose M.; Brockmann, Kathrin; Brooks, Janet; Burn, David J.; Charlesworth, Gavin; Chen, Honglei; Chinnery, Patrick F.; Chong, Sean; Clarke, Carl E.; Cookson, Mark R.; Cooper, Jonathan M.; Corvol, Jen-Christophe; Counsell, Carl; Damier, Philippe; Dartigues, Jean Francois; Deloukas, Panagiotis; Deuschl, Günther; Dexter, David T.; van Dijk, Karin D.; Dillman, Allissa; Durif, Frank; Durr, Alexandra; Edkins, Sarah; Evans, Jonathan R.; Foltynie, Thomas; Gao, Jianjun; Gardner, Michelle; Gasser, Thomas; Gibbs, J. Raphael; Goate, Alison; Gray, Emma; Guerreiro, Rita; Gústafsson, Ómar; Hardy, John; Harris, Clare; Hernandez, Dena G.; Heutink, Peter; van Hilten, Jacobus J.; Hofman, Albert; Hollenbeck, Albert; Holmans, Peter; Holton, Janice; Hu, Michele; Huber, Heiko; Hudson, Gavin; Hunt, Sarah E.; Huttenlocher, Johanna; Illig, Thomas; Langford, Cordelia; Lees, Andrew; Lesage, Suzanne; Lichtner, Peter; Limousin, Patricia; Lopez, Grisel; Lorenz, Delia; Martinez, Maria; McNeill, Alisdair; Moorby, Catriona; Moore, Matthew; Morris, Huw; Morrison, Karen E.; Moskvina, Valentina; Mudanohwo, Ese; Nalls, Michael A.; Pearson, Justin; Perlmutter, Joel S.; Pétursson, Hjörvar; Plagnol, Vincent; Pollak, Pierre; Post, Bart; Potter, Simon; Ravina, Bernard; Revesz, Tamas; Riess, Olaf; Rivadeneira, Fernando; Rizzu, Patrizia; Ryten, Mina; Saad, Mohamad; Sawcer, Stephen; Schapira, Anthony; Scheffer, Hans; Sharma, Manu; Shaw, Karen; Sheerin, Una-Marie; Shoulson, Ira; Schulte, Claudia; Sidransky, Ellen; Simón-Sánchez, Javier; Singleton, Andrew B.; Smith, Colin; Stefánsson, Hreinn; Stefánsson, Kári; Steinberg, Stacy; Stockton, Joanna D.; Sveinbjornsdottir, Sigurlaug; Talbot, Kevin; Tanner, Carlie M.; Tashakkori-Ghanbaria, Avazeh; Tison, François; Trabzuni, Daniah; Traynor, Bryan J.; Uitterlinden, André G.; Velseboer, Daan; Vidailhet, Marie; Walker, Robert; van de Warrenburg, Bart; Wickremaratchi, Mirdhu; Williams, Nigel; Williams-Gray, Caroline H.; Winder-Rhodes, Sophie; Wood, Nicholas

    2013-01-01

    Parkinson's disease (PD) is the second most common neurodegenerative disease affecting 1–2% in people >60 and 3–4% in people >80. Genome-wide association (GWA) studies have now implicated significant evidence for association in at least 18 genomic regions. We have studied a large PD-meta analysis and identified a significant excess of SNPs (P < 1 × 10−16) that are associated with PD but fall short of the genome-wide significance threshold. This result was independent of variants at the 18 previously implicated regions and implies the presence of additional polygenic risk alleles. To understand how these loci increase risk of PD, we applied a pathway-based analysis, testing for biological functions that were significantly enriched for genes containing variants associated with PD. Analysing two independent GWA studies, we identified that both had a significant excess in the number of functional categories enriched for PD-associated genes (minimum P = 0.014 and P = 0.006, respectively). Moreover, 58 categories were significantly enriched for associated genes in both GWA studies (P < 0.001), implicating genes involved in the ‘regulation of leucocyte/lymphocyte activity’ and also ‘cytokine-mediated signalling’ as conferring an increased susceptibility to PD. These results were unaltered by the exclusion of all 178 genes that were present at the 18 genomic regions previously reported to be strongly associated with PD (including the HLA locus). Our findings, therefore, provide independent support to the strong association signal at the HLA locus and imply that the immune-related genetic susceptibility to PD is likely to be more widespread in the genome than previously appreciated. PMID:23223016

  5. Distinctive Reaction Pathways at Base Metals in High-Spin Organometallic Catalysts.

    PubMed

    Holland, Patrick L

    2015-06-16

    Inexpensive "base" metals are more affordable and sustainable than precious metals and also offer opportunities to discover new mechanisms for selective catalytic reactions. Base metal complexes can have high-spin electronic configurations that are rare in precious metal complexes. This Account describes some concepts relevant to high-spin organometallic complexes, focusing on our recent work with β-diketiminate complexes of iron and cobalt. Even though high-spin organometallic complexes have some unfamiliar spectroscopic properties, they can be studied using NMR spectroscopy as well as techniques that focus on the magnetism brought about by the unpaired electrons. Understanding the mechanisms of reactions using these complexes can be complicated, because complexes with a high-spin electronic configuration may need to change spin states to avoid high barriers for reaction. These spin-state changes can be rapid, and the ability of an excited spin state to "cut through" the barrier for a reaction can lead to spin acceleration. These concepts, originally developed by Poli, Shaik, Schwarz, and Harvey, are applied here to the fundamental organometallic reaction of β-hydride elimination (BHE). Experimentally validated density-functional calculations show spin acceleration in BHE using three-coordinate iron(II) and cobalt(II) complexes. A square-planar transition state is particularly beneficial for accelerating BHE when a high-spin iron(II) complex goes from an S = 2 ground state to an S = 1 transition state or when a high-spin cobalt(II) complex goes from an S = 3/2 ground state to an S = 1/2 transition state. The relative energies of the spin states can be controlled with the choice of the supporting ligand. Using an appropriate ligand, isomerization of 1-alkenes to their Z-2 isomers can be catalyzed in high yields using the cobalt(II) alkyl complexes as catalysts. Though an earlier paper attributed the regioselectivity and stereoselectivity to the preferred geometry

  6. Citrus Peel Additives for One-Pot Triazole Formation by Decarboxylation, Nucleophilic Substitution, and Azide-Alkyne Cycloaddition Reactions

    ERIC Educational Resources Information Center

    Mendes, Desiree E.; Schoffstall, Allen M.

    2011-01-01

    This undergraduate organic laboratory experiment consists of three different reactions occurring in the same flask: a cycloaddition reaction, preceded by decarboxylation and nucleophilic substitution reactions. The decarboxylation and cycloaddition reactions occur using identical Cu(I) catalyst and conditions. Orange, lemon, and other citrus fruit…

  7. Design of Selective Gas Sensors Using Additive-Loaded In2O3 Hollow Spheres Prepared by Combinatorial Hydrothermal Reactions

    PubMed Central

    Kim, Sun-Jung; Hwang, In-Sung; Kang, Yun Chan; Lee, Jong-Heun

    2011-01-01

    A combinatorial hydrothermal reaction has been used to prepare pure and additive (Sb, Cu, Nb, Pd, and Ni)-loaded In2O3 hollow spheres for gas sensor applications. The operation of Pd- and Cu-loaded In2O3 sensors at 371 °C leads to selective H2S detection. Selective detection of CO and NH3 was achieved by the Ni-In2O3 sensor at sensing temperatures of 371 and 440 °C, respectively. The gas responses of six different sensors to NH3, H2S, H2, CO and CH4 produced unique gas sensing patterns that can be used for the artificial recognition of these gases. PMID:22346661

  8. Hydrogenation of O and OH on Pt(111): A comparison between the reaction rates of the first and the second hydrogen addition steps

    SciTech Connect

    Näslund, L.-Å.

    2014-03-14

    The formation of water through hydrogenation of oxygen on platinum occurs at a surprisingly low reaction rate. The reaction rate limited process for this catalytic reaction is, however, yet to be settled. In the present work, the reaction rates of the first and the second hydrogen addition steps are compared when hydrogen is obtained through intense synchrotron radiation that induces proton production in a water overlayer on top of the adsorbed oxygen species. A substantial amount of the produced hydrogen diffuses to the platinum surface and promotes water formation at the two starting conditions O/Pt(111) and (H{sub 2}O+OH)/Pt(111). The comparison shows no significant difference in the reaction rate between the first and the second hydrogen addition steps, which indicates that the rate determining process of the water formation from oxygen on Pt(111) is neither the first nor the second H addition step or, alternatively, that both H addition steps exert rate control.

  9. Mechanism and Reaction Pathways for Microcystin-LR Degradation through UV/H2O2 Treatment.

    PubMed

    Liu, Yafeng; Ren, Jing; Wang, Xiangrong; Fan, Zhengqiu

    2016-01-01

    Microcystin-LR (MCLR) is the most common cyanotoxin in contaminated aquatic systems. MCLR inhibits protein phosphatases 1 and 2A, leading to liver damage and tumor formation. MCLR is relatively stable owing to its cyclic structures. The combined UV/H2O2 technology can degrade MCLR efficiently. The second-order rate constant of the reaction between MCLR and hydroxyl radical (·OH) is 2.79(±0.23)×1010 M-1 s-1 based on the competition kinetics model using nitrobenzene as reference compound. The probable degradation pathway was analyzed through liquid chromatography mass spectrometry. Results suggested that the major destruction pathways of MCLR were initiated by ·OH attack on the benzene ring and diene of the Adda side chain. The corresponding aldehyde or ketone peptide residues were formed through further oxidation. Another minor destruction pathway involved ·OH attack on the methoxy group of the Adda side chain, followed by complete removal of the methoxy group. The combined UV/H2O2 system is a promising technology for MCLR removal in contaminated aquatic systems. PMID:27281173

  10. Mechanism and Reaction Pathways for Microcystin-LR Degradation through UV/H2O2 Treatment

    PubMed Central

    Liu, Yafeng; Ren, Jing; Wang, Xiangrong; Fan, Zhengqiu

    2016-01-01

    Microcystin-LR (MCLR) is the most common cyanotoxin in contaminated aquatic systems. MCLR inhibits protein phosphatases 1 and 2A, leading to liver damage and tumor formation. MCLR is relatively stable owing to its cyclic structures. The combined UV/H2O2 technology can degrade MCLR efficiently. The second-order rate constant of the reaction between MCLR and hydroxyl radical (·OH) is 2.79(±0.23)×1010 M−1 s−1 based on the competition kinetics model using nitrobenzene as reference compound. The probable degradation pathway was analyzed through liquid chromatography mass spectrometry. Results suggested that the major destruction pathways of MCLR were initiated by ·OH attack on the benzene ring and diene of the Adda side chain. The corresponding aldehyde or ketone peptide residues were formed through further oxidation. Another minor destruction pathway involved ·OH attack on the methoxy group of the Adda side chain, followed by complete removal of the methoxy group. The combined UV/H2O2 system is a promising technology for MCLR removal in contaminated aquatic systems. PMID:27281173

  11. Oxidation of elemental mercury by chlorine: Gas phase, Surface,and Photo-induced reaction pathways

    SciTech Connect

    Yan, Nai-Qiang; Liu, Shou-Heng; Chang, Shih-Ger

    2004-10-22

    Accurate oxidation rate constants of mercury gas are needed for determining its dispersion and lifetime in the atmosphere. They would also help in developing a technology for the control of mercury emissions from coal-fired power plants. However, it is difficult to establish the accurate rate constants primarily due to the fact that mercury easily adsorbs on solid surface and its reactions can be catalyzed by the surface. We have demonstrated a procedure that allows the determination of gas phase, surface-induced, and photo-induced contributions in the kinetic study of the oxidation of mercury by chlorine gas. The kinetics was studied using reactors with various surface to volume ratios. The effect of the surface and the photo irradiation on the reaction was taken into consideration. The pressure dependent study revealed that the gas phase oxidation was a three-body collision process. The third order rate constant was determined to be 7.5({+-}0.2) x 10{sup -39} mL{sup 2} molecules{sup -2}s{sup -1} with N{sub 2} as the third body at 297 {+-} 1 K. The surface induced reaction on quartz window was second order and the rate constant was 2.7 x 10{sup -17} mL{sup 2} molecules{sup -1} cm{sup -2} sec. Meanwhile, the 253.7 nm photon employed for mercury detection was found to accelerate the reaction. The utilization efficiency of 253.7 nm photon for Hg{sup 0} oxidation was 6.7 x 10{sup -4} molecules photon{sup -1} under the conditions employed in this study.

  12. Fundamental Reaction Pathways for Cytochrome P450-catalyzed 5′-Hydroxylation and N-Demethylation of Nicotine

    PubMed Central

    Li, Dongmei; Wang, Yong; Han, Keli; Zhan, Chang-Guo

    2010-01-01

    The reaction pathways for 5′-hydroxylation and N-demethylation of nicotine catalyzed by cytochrome P450 were investigated by performing a series of first-principle electronic structure calculations on a catalytic reaction model system. The computational results indicate that 5′-hydroxylation of nicotine occurs through a two-state stepwise process, i.e. an initial hydrogen atom transfer from nicotine to Cpd I (i.e. the HAT step) followed by a recombination of the nicotine moiety with the iron-bound hydroxyl group (i.e. the rebound step) on both the high-spin (HS) quartet and low-spin (LS) doublet states. The HAT step is the rate-determining one. This finding represents the first case that exhibits genuine rebound transition state species on both the HS and the LS states for Cα-H hydroxylation of amines. N-demethylation of nicotine involves a N-methylhydroxylation to form N-(hydroxymethyl)nornicotine, followed by N-(hydroxymethyl)nornicotine decomposition to nornicotine and formaldehyde. The N-methylhydroxylation step is similar to 5′-hydroxylation, namely that a rate-determining HAT step followed by a rebound step. The decomposition process occurs on the deprotonated state of N-(hydroxymethyl)nornicotine assisted by a water molecule and the energy barrier is significantly lower than that of the N-methylhydroxylation process. Comparison of the rate-determining free energy barriers for the two reaction pathways predicts a preponderance of 5′-hydroxylation over the N-demethylation by roughly a factor of 18:1, which is in excellent agreement with the factor of 19:1 derived from available experimental data. PMID:20572647

  13. Noble reaction features of bromoborane in oxidative addition of B-Br σ-bond to [M(PMe3)2] (M=Pt or Pd): theoretical study.

    PubMed

    Zeng, Guixiang; Sakaki, Shigeyoshi

    2011-06-01

    Through detailed calculations by density functional theory and second-order Møller-Plesset perturbation theory (MP2) to fourth-order Møller-Plesset perturbation theory including single, double, and quadruple excitations [MP4(SDQ)] methods, we investigated the oxidative addition of the B-Br bond of dibromo(trimethylsiloxy)borane [Br(2)B(OSiMe(3))] to Pt(0) and Pd(0) complexes [M(PMe(3))(2)] (M = Pt or Pd) directly yielding a trans bromoboryl complex trans-[MBr{BBr(OSiMe(3))}(PMe(3))(2)]. Two reaction pathways are found for this reaction: One is a nucleophilic attack pathway which directly leads to the trans product, and the other is a stepwise reaction pathway which occurs through successive cis oxidative addition of the B-Br bond to [M(PMe(3))(2)] and thermal cis-trans isomerization. In the Pt system, the former course occurs with a much smaller energy barrier (E(a) = 5.8 kcal/mol) than the latter one (E(a) = 20.7 kcal/mol), where the DFT-calculated E(a) value is presented hereafter. In the Pd system, only the latter course is found in which the rate-determining steps is the cis-trans isomerization with the E(a) of 15.1 kcal/mol. Interestingly, the thermal cis-trans isomerization occurs on the singlet potential energy surface against our expectation. This unexpected result is understood in terms of the strong donation ability of the boryl group. Detailed analyses of electronic processes in all these reaction steps as well as remarkable characteristic features of [Br(2)B(OSiMe(3))] are also provided. PMID:21557562

  14. Effects of the method of apatite seed crystals addition on setting reaction of α-tricalcium phosphate based apatite cement.

    PubMed

    Tsuru, Kanji; Ruslin; Maruta, Michito; Matsuya, Shigeki; Ishikawa, Kunio

    2015-10-01

    Appropriate setting time is an important parameter that determines the effectiveness of apatite cement (AC) for clinical application, given the issues of crystalline inflammatory response phenomena if AC fails to set. To this end, the present study analyzes the effects of the method of apatite seed crystals addition on the setting reaction of α-tricalcium phosphate (α-TCP) based AC. Two ACs, both consisting of α-TCP and calcium deficient hydroxyapatite (cdHAp), were analyzed in this study. In one AC, cdHAp was added externally to α-TCP and this AC was abbreviated as AC(EA). In the other AC, α-TCP was partially hydrolyzed to form cdHAp on the surface of α-TCP. This AC was referred to as AC(PH). Results indicate a decrease in the setting time of both ACs with the addition of cdHAp. Among them, for the given amount of added cdHAp, AC(PH) showed relatively shorter setting time than AC(EA). Besides, the mechanical strength of the set AC(PH) was also higher than that of set AC(EA). These properties of AC(PH) were attributed to the predominant crystal growth of cdHAp in the vicinity of the α-TCP particle surface. Accordingly, it can be concluded that the partial hydrolysis of α-TCP may be a better approach to add low crystalline cdHAp onto α-TCP based AC. PMID:26411440

  15. A DFT study of addition reaction between fragment ion (CH₂) units and fullerene (C₆₀) molecule.

    PubMed

    Zaragoza, Irineo Pedro; Vergara, Jaime; Pérez-Manríquez, Liliana; Salcedo, Roberto

    2011-05-01

    The theoretical study of the interaction between CH(2) and fullerene (C(60)) suggests the existence of an addition reaction mechanism; this feature is studied by applying an analysis of electronic properties. Several different effects are evident in this interaction as a consequence of the particular electronic transfer which occurs during the procedure. The addition or insertion of the methylene group results in a process, where the inclusion of CH(2) into a fullerene bond produces the formation of several geometric deformations. A simulation of these procedures was carried out, taking advantage of the dynamic semi-classical Born-Oppenheimer approximation. Dynamic aspects were analyzed at different speeds, for the interaction between the CH(2) group and the two bonds: CC (6, 6) and CC (6, 5) respectively on the fullerene (C(60)) rings. All calculations which involved electrons employed DFT as well as exchange and functional correlation. The results indicate a tendency for the CH(2) fragment to attack the CC (6, 5) bond. PMID:20658255

  16. Sintered-reaction Bonded Silicon Nitride Densified by a Gas Pressure Sintering Process Effects of Rare Earth Oxide Sintering Additives

    SciTech Connect

    Lee, S. H.; Ko, J. W.; Park, Y. J.; Kim, H. D.; Lin, Hua-Tay; Becher, Paul F

    2012-01-01

    Reaction-bonded silicon nitrides containing rare-earth oxide sintering additives were densified by gas pressure sintering. The sintering behavior, microstructure and mechanical properties of the resultant specimens were analyzed. For that purpose, Lu2O3-SiO2 (US), La2O3-MgO (AM) and Y2O3-Al2O3 (YA) additive systems were selected. Among the tested compositions, densification of silicon nitride occurred at the lowest temperature when using the La2O3-MgO system. Since the Lu2O3-SiO2 system has the highest melting temperature, full densification could not be achieved after sintering at 1950oC. However, the system had a reasonably high bending strength of 527 MPa at 1200oC in air and a high fracture toughness of 9.2 MPa m1/2. The Y2O3-Al2O3 system had the highest room temperature bending strength of 1.2 GPa

  17. Impact of organic-mineral matter interactions on thermal reaction pathways for coal model compounds

    SciTech Connect

    Buchanan, A.C. III; Britt, P.F.; Struss, J.A.

    1995-07-01

    Coal is a complex, heterogeneous solid that includes interdispersed mineral matter. However, knowledge of organic-mineral matter interactions is embryonic, and the impact of these interactions on coal pyrolysis and liquefaction is incomplete. Clay minerals, for example, are known to be effective catalysts for organic reactions. Furthermore, clays such as montmorillonite have been proposed to be key catalysts in the thermal alteration of lignin into vitrinite during the coalification process. Recent studies by Hatcher and coworkers on the evolution of coalified woods using microscopy and NMR have led them to propose selective, acid-catalyzed, solid state reaction chemistry to account for retained structural integrity in the wood. However, the chemical feasibility of such reactions in relevant solids is difficult to demonstrate. The authors have begun a model compound study to gain a better molecular level understanding of the effects in the solid state of organic-mineral matter interactions relevant to both coal formation and processing. To satisfy the need for model compounds that remain nonvolatile solids at temperatures ranging to 450 C, model compounds are employed that are chemically bound to the surface of a fumed silica (Si-O-C{sub aryl}linkage). The organic structures currently under investigation are phenethyl phenyl ether (C{sub 6}H{sub 5}CH{sub 2}CH{sub 2}OC{sub 6}H{sub 5}) derivatives, which serve as models for {beta}-alkyl aryl ether units that are present in lignin and lignitic coals. The solid-state chemistry of these materials at 200--450 C in the presence of interdispersed acid catalysts such as small particle size silica-aluminas and montmorillonite clay will be reported. Initial focus will be on defining the potential impact of these interactions on coal pyrolysis and liquefaction.

  18. Influence of surface defects and local structure on oxygenate reaction pathways over metal oxide surfaces

    NASA Astrophysics Data System (ADS)

    Cox, D. F.

    1993-07-01

    Complete thermal desorption and photoemission studies of seven molecules (methanol, formaldehyde, formic acid, isopropanol, acetone, water, and carbon monoxide) were completed on four different SnO2(110) surfaces (stoichiometric, reduced, slightly-defective, and highly-defective). Initial thermal desorption studies of acetic acid and propene were also done. Results indicate that different initial surface conditions can dramatically affect: (1) probability for heterolytic dissociation of Bronsted acids, (2) reaction kinetics for unimolecular decomposition of oxygenated surface intermediates, and (3) product selectivity.

  19. Evidence for Different Reaction Pathways for Liquid and Granular Micronutrients in a Calcareous Soil

    SciTech Connect

    Hettiarachchi, Ganga M.; McLaughlin, Mike J.; Scheckel, Kirk G.; Chittleborough, David J.; Newville, Mathew; Sutton, Steve; Lombi, Enzo

    2008-06-16

    The benefits of Mn and Zn fluid fertilizers over conventional granular products in calcareous sandy loam soils have been agronomically demonstrated. We hypothesized that the differences in the effectiveness between granular and fluid Mn and Zn fertilizers is due to different Mn and Zn reaction processes in and around fertilizer granules and fluid fertilizer bands. We used a combination of several synchrotron-based x-ray techniques, namely, spatially resolved micro-x-ray fluorescence (?-XRF), micro-x-ray absorption near edge structure spectroscopy (?-XANES), and bulk-XANES and -extended x-ray absorption fine structure (EXAFS) spectroscopy, along with several laboratory-based x-ray techniques to speciate different fertilizer-derived Mn and Zn species in highly calcareous soils to understand the chemistry underlying the observed differential behavior of fluid and granular micronutrient forms. Micro-XRF mapping of soil-fertilizer reactions zones indicated that the mobility of Mn and Zn from liquid fertilizer was greater than that observed for equivalent granular sources of these micronutrients in soil. After application of these micronutrient fertilizers to soil, Mn and Zn from liquid fertilizers were found to remain in comparatively more soluble solid forms, such as hydrated Mn phosphate-like, Mn calcite-like, adsorbed Zn-like, and Zn silicate-like phases, whereas Mn and Zn from equivalent granular sources tended to transform into comparatively less soluble solid forms such as Mn oxide-like, Mn carbonate-like, and Zn phosphate-like phases.

  20. Mechanism for the Direct Synthesis of H2O2 on Pd Clusters: Heterolytic Reaction Pathways at the Liquid-Solid Interface.

    PubMed

    Wilson, Neil M; Flaherty, David W

    2016-01-20

    Direct synthesis (H2 + O2 → H2O2) is a promising reaction for producing H2O2, which can replace chlorinated oxidants in industrial processes. The mechanism of this reaction and the reasons for the importance of seemingly unrelated factors (e.g., Pd cluster size and solvent pH) remain unclear despite significant research. We propose a mechanism for H2O2 formation on Pd clusters consistent with steady-state H2O2 and H2O formation rates measured as functions of reactant pressures and temperature and the interpretations of proton concentration effects. H2O2 forms by sequential proton-electron transfer to O2 and OOH surface intermediates, whereas H2O forms by O-O bond rupture within OOH surface species. Direct synthesis, therefore, does not proceed by the Langmuir-Hinshelwood mechanism often invoked. Rather, H2O2 forms by heterolytic reaction pathways resembling the two-electron oxygen reduction reaction (ORR); however, the chemical potential of H2 replaces an external electrical potential as the thermodynamic driving force. Activation enthalpies (ΔH(⧧)) for H2O formation increase by 14 kJ mol(-1) when Pd cluster diameters increase from 0.7 to 7 nm because changes in the electronic structure of Pd surface atoms decrease their propensity to cleave O-O bonds. ΔH(⧧) values for H2O2 remain nearly constant because barriers for proton-electron transfer depend weakly on the coordinative saturation of Pd surface atoms. Collectively, these results provide a self-consistent mechanism, which clarifies many studies in which H2O2 rates and selectivities were shown to depend on the concentration of acid/halide additives and Pd cluster size. These findings will guide the rational design of selective catalysts for direct synthesis. PMID:26597848

  1. Neutron Reactions in Accreting Neutron Stars: A New Pathway to Efficient Crust Heating

    SciTech Connect

    Gupta, Sanjib S.; Kawano, Toshihiko; Moeller, Peter

    2008-12-05

    In our calculation of neutron star crust heating we include several key new model features. In earlier work electron capture (EC) only allowed neutron emission from the daughter ground state; here we calculate, in a deformed quasi-random-phase approximation (QRPA) model, EC decay rates to all states in the daughter that are allowed by Gamow-Teller selection rules and energetics. The subsequent branching ratios between the 1n,...,xn channels and the competing {gamma} decay are calculated in a Hauser-Feshbach model. In our multicomponent plasma model a single (EC, xn) reaction step can produce several neutron-deficient nuclei, each of which can further decay by (EC, xn). Hence, the neutron emission occurs more continuously with increasing depth as compared to that in a one-component plasma model.

  2. The reaction pathway of membrane-bound rat liver mitochondrial monoamine oxidase

    PubMed Central

    Houslay, Miles D.; Tipton, Keith F.

    1973-01-01

    1. A preparation of a partly purified mitochondrial outer-membrane fraction suitable for kinetic investigations of monoamine oxidase is described. 2. An apparatus suitable for varying the O2 concentration in a spectrophotometer cuvette is described. 3. The reaction catalysed by the membrane-bound enzyme is shown to proceed by a double-displacement (Ping Pong) mechanism, and a formal mechanism is proposed. 4. KCN, NaN3, benzyl cyanide and 4-cyanophenol are shown to be reversible inhibitors of the enzyme. 5. The non-linear reciprocal plot obtained with impure preparations of benzylamine, which is typical of high substrate inhibition, is shown to be due to aldehyde contamination of the substrate. PMID:4778271

  3. Kinetic and Reaction Pathway Analysis in the Application of Botulinum Toxin A for Wound Healing

    PubMed Central

    Lebeda, Frank J.; Dembek, Zygmunt F.; Adler, Michael

    2012-01-01

    A relatively new approach in the treatment of specific wounds in animal models and in patients with type A botulinum toxin is the focus of this paper. The indications or conditions include traumatic wounds (experimental and clinical), surgical (incision) wounds, and wounds such as fissures and ulcers that are signs/symptoms of disease or other processes. An objective was to conduct systematic literature searches and take note of the reactions involved in the healing process and identify corresponding pharmacokinetic data. From several case reports, we developed a qualitative model of how botulinum toxin disrupts the vicious cycle of muscle spasm, pain, inflammation, decreased blood flow, and ischemia. We transformed this model into a minimal kinetic scheme for healing chronic wounds. The model helped us to estimate the rate of decline of this toxin's therapeutic effect by calculating the rate of recurrence of clinical symptoms after a wound-healing treatment with this neurotoxin. PMID:22174710

  4. 1/f Noise Through Retino-Cortical Pathways Assessed By Reaction Times

    NASA Astrophysics Data System (ADS)

    Medina, José M.; Díaz, José A.

    2009-04-01

    Certain process in the brain exhibits intrinsic fluctuations that follow flicker noise close to 1/f Fourier spectra. Examples are found from ion-channels to visual psychophysics. In the latter, modern mental chronometry plays a central role by reaction times (RT). Here we examine the existence of flicker noise in RT taking into account the first stages of color coding. Stimuli were isolated along the cardinal directions in the color space. Although the power spectral density of the RT series scales inversely with the cell size, in all cases the exponent was close to unity. Our results suggest that 1/f long-term correlations share a common mechanism from photoreceptors to the visual cortex.

  5. Competitive reaction pathways in vibrationally induced photodissociation of H2SO4.

    PubMed

    Yosa Reyes, Juvenal; Nagy, Tibor; Meuwly, Markus

    2014-09-14

    Vibrationally induced photodissociation of sulfuric acid into H2O + SO3 is investigated based on reactive molecular dynamics (MD) simulations. Multisurface adiabatic reactive MD simulations allow us to follow both, H-transfer and water elimination after excitation of the ν9 OH-stretching mode. Analysis of several thousand trajectories finds that the H2O and SO3 fragments have distinct final state distributions with respect to translational, rotational, and vibrational degrees of freedom. Rotational distributions peak at quantum numbers j ≤ 5 for water and j ≈ 60 for SO3. The final state distributions should be useful in identifying products in forthcoming experiments. Based on the MD trajectories, a kinetic scheme has been developed which is able to explain most of the trajectory data and suggests that IVR is very rapid. Typical lifetimes of the excited complex range from several 10 picoseconds to hundreds of nanoseconds, depending on the excitation level. Including temperature and pressure profiles characteristic for the stratosphere in the kinetic model shows that excitations higher than ν9 = 4 can significantly contribute to the photolysis rate. This extends and specifies earlier work in that multi-level modeling is required to understand the significance of vibrationally induced decomposition pathways of sulfuric acid in the middle atmosphere. PMID:25072517

  6. Mixed N-Heterocyclic Carbene-Bis(oxazolinyl)borato Rhodium and Iridium Complexes in Photochemical and Thermal Oxidative Addition Reactions

    SciTech Connect

    Xu, Songchen; Manna, Kuntal; Ellern, Arkady; Sadow, Aaron D

    2014-12-08

    In order to facilitate oxidative addition chemistry of fac-coordinated rhodium(I) and iridium(I) compounds, carbene–bis(oxazolinyl)phenylborate proligands have been synthesized and reacted with organometallic precursors. Two proligands, PhB(OxMe2)2(ImtBuH) (H[1]; OxMe2 = 4,4-dimethyl-2-oxazoline; ImtBuH = 1-tert-butylimidazole) and PhB(OxMe2)2(ImMesH) (H[2]; ImMesH = 1-mesitylimidazole), are deprotonated with potassium benzyl to generate K[1] and K[2], and these potassium compounds serve as reagents for the synthesis of a series of rhodium and iridium complexes. Cyclooctadiene and dicarbonyl compounds {PhB(OxMe2)2ImtBu}Rh(η4-C8H12) (3), {PhB(OxMe2)2ImMes}Rh(η4-C8H12) (4), {PhB(OxMe2)2ImMes}Rh(CO)2 (5), {PhB(OxMe2)2ImMes}Ir(η4-C8H12) (6), and {PhB(OxMe2)2ImMes}Ir(CO)2 (7) are synthesized along with ToMM(η4-C8H12) (M = Rh (8); M = Ir (9); ToM = tris(4,4-dimethyl-2-oxazolinyl)phenylborate). The spectroscopic and structural properties and reactivity of this series of compounds show electronic and steric effects of substituents on the imidazole (tert-butyl vs mesityl), effects of replacing an oxazoline in ToM with a carbene donor, and the influence of the donor ligand (CO vs C8H12). The reactions of K[2] and [M(μ-Cl)(η2-C8H14)2]2 (M = Rh, Ir) provide {κ4-PhB(OxMe2)2ImMes'CH2}Rh(μ-H)(μ-Cl)Rh(η2-C8H14)2 (10) and {PhB(OxMe2)2ImMes}IrH(η3-C8H13) (11). In the former compound, a spontaneous oxidative addition of a mesityl ortho-methyl to give a mixed-valent dirhodium species is observed, while the iridium compound forms a monometallic allyl hydride. Photochemical reactions of dicarbonyl compounds 5 and 7 result in C–H bond oxidative addition providing the compounds {κ4-PhB(OxMe2)2ImMes'CH2}RhH(CO) (12) and {PhB(OxMe2)2ImMes}IrH(Ph)CO (13). In 12, oxidative addition results in cyclometalation of the mesityl ortho-methyl similar to 10, whereas the iridium compound reacts with the benzene solvent to give a rare crystallographically characterized cis

  7. Anaerobic Oxidation of n-Dodecane by an Addition Reaction in a Sulfate-Reducing Bacterial Enrichment Culture

    PubMed Central

    Kropp, Kevin G.; Davidova, Irene A.; Suflita, Joseph M.

    2000-01-01

    We identified trace metabolites produced during the anaerobic biodegradation of H26- and D26-n-dodecane by an enrichment culture that mineralizes these compounds in a sulfate-dependent fashion. The metabolites are dodecylsuccinic acids that, in the case of the perdeuterated substrate, retain all of the deuterium atoms. The deuterium retention and the gas chromatography-mass spectrometry fragmentation patterns of the derivatized metabolites suggest that they are formed by C—H or C—D addition across the double bond of fumarate. As trimethylsilyl esters, two nearly coeluting metabolites of equal abundance with nearly identical mass spectra were detected from each of H26- and D26-dodecane, but as methyl esters, only a single metabolite peak was detected for each parent substrate. An authentic standard of protonated n-dodecylsuccinic acid that was synthesized and derivatized by the two methods had the same fragmentation patterns as the metabolites of H26-dodecane. However, the standard gave only a single peak for each ester type and gas chromatographic retention times different from those of the derivatized metabolites. This suggests that the succinyl moiety in the dodecylsuccinic acid metabolites is attached not at the terminal methyl group of the alkane but at a subterminal position. The detection of two equally abundant trimethylsilyl-esterified metabolites in culture extracts suggests that the analysis is resolving diastereomers which have the succinyl moiety located at the same subterminal carbon in two different absolute configurations. Alternatively, there may be more than one methylene group in the alkane that undergoes the proposed fumarate addition reaction, giving at least two structural isomers in equal amounts. PMID:11097919

  8. Facile preparation and biological imaging of luminescent polymeric nanoprobes with aggregation-induced emission characteristics through Michael addition reaction.

    PubMed

    Lv, Qiulan; Wang, Ke; Xu, Dazhuang; Liu, Meiying; Wan, Qing; Huang, Hongye; Liang, Shangdong; Zhang, Xiaoyong; Wei, Yen

    2016-09-01

    Water dispersion aggregation-induced emission (AIE) dyes based nanomaterials have recently attracted increasing attention in the biomedical fields because of their unique optical properties, outstanding performance as imaging and therapeutic agents. The methods to conjugate hydrophilic polymers with AIE dyes to solve the hydrophobic nature of AIE dyes and makeS them widely used in biomedicine, which have been extensively explored and paid great effort previously. Although great advance has been made in the fabrication and biomedical applications of AIE-active polymeric nanoprobes, facile and efficient strategies for fabrication of biodegradable AIE-active nanoprobes are still high desirable. In this work, amphiphilic biodegradable fluorescent organic nanoparticles (PLL-TPE-O-E FONs) have been fabricated for the first time by conjugation of AIE dye tetraphenylethene acrylate (TPE-O-E) with Poly-l-Lysine (PLL) through a facile one-step Michael addition reaction, which was carried out under rather mild conditions, included air atmosphere, near room temperature and absent of metal catalysts or hazardous reagents. Due to the unique AIE properties, these amphiphilic copolymers tend to self-assemble into high luminescent water dispersible nanoparticles with size range from 400 to 600nm. Laser scanning microscope and cytotoxicity results revealed that PLL-TPE-O-E FONs can be internalized into cytoplasm with negative cytotoxicity, which implied that PLL-TPE-O-E FONs are promising for biological applications. PMID:27311129

  9. Interleukin-13 Activates Distinct Cellular Pathways Leading to Ductular Reaction, Steatosis, and Fibrosis.

    PubMed

    Gieseck, Richard L; Ramalingam, Thirumalai R; Hart, Kevin M; Vannella, Kevin M; Cantu, David A; Lu, Wei-Yu; Ferreira-González, Sofía; Forbes, Stuart J; Vallier, Ludovic; Wynn, Thomas A

    2016-07-19

    Fibroproliferative diseases are driven by dysregulated tissue repair responses and are a major cause of morbidity and mortality because they affect nearly every organ system. Type 2 cytokine responses are critically involved in tissue repair; however, the mechanisms that regulate beneficial regeneration versus pathological fibrosis are not well understood. Here, we have shown that the type 2 effector cytokine interleukin-13 simultaneously, yet independently, directed hepatic fibrosis and the compensatory proliferation of hepatocytes and biliary cells in progressive models of liver disease induced by interleukin-13 overexpression or after infection with Schistosoma mansoni. Using transgenic mice with interleukin-13 signaling genetically disrupted in hepatocytes, cholangiocytes, or resident tissue fibroblasts, we have revealed direct and distinct roles for interleukin-13 in fibrosis, steatosis, cholestasis, and ductular reaction. Together, these studies show that these mechanisms are simultaneously controlled but distinctly regulated by interleukin-13 signaling. Thus, it may be possible to promote interleukin-13-dependent hepatobiliary expansion without generating pathological fibrosis. VIDEO ABSTRACT. PMID:27421703

  10. Cobalt catalyzed peroxymonosulfate oxidation of tetrabromobisphenol A: Kinetics, reaction pathways, and formation of brominated by-products.

    PubMed

    Ji, Yuefei; Kong, Deyang; Lu, Junhe; Jin, Hao; Kang, Fuxing; Yin, Xiaoming; Zhou, Quansuo

    2016-08-01

    Degradation of tetrabromobisphenol A (TBBPA), a flame retardant widely spread in the environment, in Co(II) catalyzed peroxymonosulfate (PMS) oxidation process was systematically explored. The second-order-rate constant for reaction of sulfate radical (SO4(-)) with TBBPA was determined to be 5.27×10(10)M(-1)s(-1). Apparently, degradation of TBBPA showed first-order kinetics to the concentrations of both Co(II) and PMS. The presence of humic acid (HA) and bicarbonate inhibited TBBPA degradation, most likely due to their competition for SO4(-). Degradation of TBBPA was initiated by an electron abstraction from one of the phenolic rings. Detailed transformation pathways were proposed, including β-scission of isopropyl bridge, phenolic ring oxidation, debromination and coupling reactions. Further oxidative degradation of intermediates in Co(II)/PMS process yielded brominated disinfection by-products (Br-DBPs) such as bromoform and brominated acetic acids. Evolution profile of Br-DBPs showed an initially increasing and then decreasing pattern with maximum concentrations occurring around 6-10h. The presence of HA enhanced the formation of Br-DBPs significantly. These findings reveal potentially important, but previously unrecognized, formation of Br-DBPs during sulfate radical-based oxidation of bromide-containing organic compounds that may pose toxicological risks to human health. PMID:27107323

  11. Dexmedetomidine attenuates inflammatory reaction in the lung tissues of septic mice by activating cholinergic anti-inflammatory pathway.

    PubMed

    Liu, Zhaoguo; Wang, Yueping; Wang, Yaoqi; Ning, Qiaoqing; Zhang, Yong; Gong, Chunzhi; Zhao, Wenxiang; Jing, Guangjian; Wang, Qianqian

    2016-06-01

    Dexmedetomidine (Dex) is a highly selective α2-adrenergic receptor agonist that is widely used for sedation in intensive care units and in clinical anesthesia. Dex has also been shown to possess anti-inflammatory benefits. However, the underlying mechanism by which Dex relieves the inflammatory reaction in the lung tissues of septic mice has not been fully elucidated. In this study, we aimed to evaluate the protective effects and possible mechanism of Dex on the sepsis-induced lung inflammatory response in mice. Sepsis was induced in mice models through the intraperitoneal injection of lipopolysaccharide (LPS). The preemptive administration of Dex substantially abated sepsis-induced pulmonary edema, pulmonary histopathological changes, and NF-κB p65 activity. The production of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) at both the mRNA and protein levels was also reduced. Moreover, these effects were significantly blocked by the α7 nicotinic acetylcholine receptor (α7nAChR) antagonist α-bungarotoxin (α-Bgt). α-Bgt aggravated pulmonary edema and pulmonary histopathological changes, as well as increased NF-κB p65 activity and TNF-α and IL-6 expression at both the mRNA and protein levels. The overall results demonstrate that Dex inhibits the LPS-induced inflammatory reaction in the lung tissues of septic mice partly through the α7nAChR-dependent cholinergic anti-inflammatory pathway. PMID:27074053

  12. Temperature-dependent reaction pathways for the anomalous hydrocracking of triglycerides in the presence of sulfided Co-Mo-catalyst.

    PubMed

    Anand, Mohit; Sinha, Anil K

    2012-12-01

    Kinetic studies and product profiling was done to understand the anomalous cracking of jathropha oil triglycerides in the presence of sulfided Co-Mo/Al(2)O(3) catalyst. At temperatures between 320 and 340 °C, only deoxygenation and oligomerization reactions took place whereas at temperatures above 340 °C, internal conversions between the products and direct conversion to lighter and middle distillates were favored High pressures (80 bar) and H(2)/feed ratios (>1500) were necessary to minimize oligomerization of the products and to increase the lifespan of the catalyst. Lumped kinetic models were validated with experimental results. Activation energies for the formation of lighter (83 kJ/mol) and middle fractions (126 kJ/mol) were higher than those for the heavy (47 kJ/mol) and deoxygenated (47 kJ/mol) products. Jatropha oil triglycerides hydroconversion pathways were dependent on temperature and the triglycerides could be hydrocracked to lower range hydrocarbons (C5-C14) by increasing the reaction temperatures. PMID:23073102

  13. Photo-Wolff Rearrangement of 2-Diazo-1,2-naphthoquinone: Stern-Volmer Analysis of the Stepwise Reaction Pathway.

    PubMed

    Ladinig, Manfred; Ramseier, Markus; Wirz, Jakob

    2015-01-01

    2-Diazo-1,2-naphthoquinone (1) and its derivatives are the photoactive components in Novolak photoresists. A femtosecond infrared study has established that the photoreaction of 1 proceeds largely by a concerted Wolff rearrangement yielding the ketene 1H-inden-1-ylidene-methanone (3) within 300 fs after excitation, but earlier trapping studies gave evidence for a minor reaction path via a carbene intermediate 1-oxo-2(1H)-naphthalenylidene (2) with a lifetime of about 10 ps. Here, we provide a quantitative assessment of the stepwise pathway by Stern-Volmer analysis of the trapping of 2 by methanol to yield 2-methoxy-1-naphthol (4). We conclude that the lifetime of the carbene 2 is at least 200 ps. Moreover, [3 + 2]cycloaddition of 2 and acetonitrile yielding 2-methylnaphth[2,1-d]oxazole (5) was observed. A comparison of the yields of 5 formed upon photolysis and upon thermolysis of 1 in acetonitrile provides evidence that a substantial part of the hot nascent carbene 2 formed photolytically rearranges to the ketene 3 during its vibrational relaxation (hot ground-state reaction). PMID:25196741

  14. Selective Blockade of Herpesvirus Entry Mediator–B and T Lymphocyte Attenuator Pathway Ameliorates Acute Graft-versus-Host Reaction

    PubMed Central

    del Rio, Maria-Luisa; Jones, Nick D.; Buhler, Leo; Norris, Paula; Shintani, Yasushi; Ware, Carl F.; Rodriguez-Barbosa, Jose-Ignacio

    2013-01-01

    The cosignaling network mediated by the herpesvirus entry mediator (HVEM; TNFRSF14) functions as a dual directional system that involves proinflammatory ligand, lymphotoxin that exhibits inducible expression and competes with HSV glycoprotein D for HVEM, a receptor expressed by T lymphocytes (LIGHT; TNFSF14), and the inhibitory Ig family member B and T lymphocyte attenuator (BTLA). To dissect the differential contributions of HVEM/BTLA and HVEM/LIGHT interactions, topographically-specific, competitive, and nonblocking anti-HVEM Abs that inhibit BTLA binding, but not LIGHT, were developed. We demonstrate that a BTLA-specific competitor attenuated the course of acute graft-versus-host reaction in a murine F1 transfer semiallogeneic model. Selective HVEM/BTLA blockade did not inhibit donor T cell infiltration into graft-versus-host reaction target organs, but decreased the functional activity of the alloreactive T cells. These results highlight the critical role of HVEM/BTLA pathway in the control of the allogeneic immune response and identify a new therapeutic target for transplantation and autoimmune diseases. PMID:22490863

  15. Asymmetric pathways in the electrochemical conversion reaction of NiO as battery electrode with high storage capacity

    DOE PAGESBeta

    Boesenberg, Ulrike; Marcus, Matthew A.; Shukla, Alpesh K.; Yi, Tanghong; McDermott, Eamon; Teh, Pei Fen; Srinivasan, Madhavi; Moewes, Alexander; Cabana, Jordi

    2014-11-20

    Electrochemical conversion reactions of transition metal compounds create opportunities for large energy storage capabilities exceeding modern Li-ion batteries. However, for practical electrodes to be envisaged, a detailed understanding of their mechanisms is needed, especially vis-à-vis the voltage hysteresis observed between reduction and oxidation. Here, we present such insight at scales from local atomic arrangements to whole electrodes. NiO was chosen as a simple model system. The most important finding is that the voltage hysteresis has its origin in the differing chemical pathways during reduction and oxidation. This asymmetry is enabled by the presence of small metallic clusters and, thus, ismore » likely to apply to other transition metal oxide systems. Lastly, the presence of nanoparticles also influences the electrochemical activity of the electrolyte and its degradation products and can create differences in transport properties within an electrode, resulting in localized reactions around converted domains that lead to compositional inhomogeneities at the microscale.« less

  16. Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

    SciTech Connect

    Torres, Rodrigo; Lan, Benson; Latif, Yama; Chim, Nicholas; Goulding, Celia W.

    2014-04-01

    The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully

  17. Revisiting the mechanism of dioxygen activation in soluble methane monooxygenase from M. capsulatus (Bath): evidence for a multi-step, proton-dependent reaction pathway.

    PubMed

    Tinberg, Christine E; Lippard, Stephen J

    2009-12-29

    Stopped-flow kinetic investigations of soluble methane monooxygenase (sMMO) from M. capsulatus (Bath) have clarified discrepancies that exist in the literature regarding several aspects of catalysis by this enzyme. The development of thorough kinetic analytical techniques has led to the discovery of two novel oxygenated iron species that accumulate in addition to the well-established intermediates H(peroxo) and Q. The first intermediate, P*, is a precursor to H(peroxo) and was identified when the reaction of reduced MMOH and MMOB with O(2) was carried out in the presence of >or=540 microM methane to suppress the dominating absorbance signal due to Q. The optical properties of P* are similar to those of H(peroxo), with epsilon(420) = 3500 M(-1) cm(-1) and epsilon(720) = 1250 M(-1) cm(-1). These values are suggestive of a peroxo-to-iron(III) charge-transfer transition and resemble those of peroxodiiron(III) intermediates characterized in other carboxylate-bridged diiron proteins and synthetic model complexes. The second identified intermediate, Q*, forms on the pathway of Q decay when reactions are performed in the absence of hydrocarbon substrate. Q* does not react with methane, forms independently of buffer composition, and displays a unique shoulder at 455 nm in its optical spectrum. Studies conducted at different pH values reveal that rate constants corresponding to P* decay/H(peroxo) formation and H(peroxo) decay/Q formation are both significantly retarded at high pH and indicate that both events require proton transfer. The processes exhibit normal kinetic solvent isotope effects (KSIEs) of 2.0 and 1.8, respectively, when the reactions are performed in D(2)O. Mechanisms are proposed to account for the observations of these novel intermediates and the proton dependencies of P* to H(peroxo) and H(peroxo) to Q conversion. PMID:19921958

  18. Detonation of highly dilute porous explosives; II: Influence of inert additives on the structure of the front, the parameters, and the reaction time

    SciTech Connect

    Shvedov, K.K.; Aniskin, A.I.; Dremin, A.N.; Il'in, A.N.

    1982-06-01

    For the detonation of porous explosives with inert additives, as for the detonation of individual porous explosives, the basic postulates and conclusions of the modern gasdynamic theory of detonation are valid. The influence of solid, refractory inert additives on the decomposition mechanism of porous explosives depends on the individual properties of the explosives and mainly on the dispersity of the additives. With the elimination of pronounced heating of the additives in mixtures with TNT, a certain positive influence on the appearance of decomposition sources and the total reaction time is observed. In cases with hexogen, no such influence is observed, which is evidently the result of physical inhomogeneity of the porous structure of the charge and the sufficiently high detonation pressures of the mixtures. The basic influence of inert additives on the critical diameter, front structure, detonation parameters, and reaction time of porous explosives is exerted through processes of energy absorption in the reaction region and factors leading to energy losses may lead to ambiguity of the detonation conditions in a system with specified chemical potential energy. The state of the additive in the reaction region must be taken into account for reliable theoretical description of the detonation conditions of porous explosives with a large content of inert additives.

  19. Physical Properties and CO2 Reaction Pathway of 1-Ethyl-3-Methylimidazolium Ionic Liquids with Aprotic Heterocyclic Anions

    SciTech Connect

    Seo, S; DeSilva, MA; Brennecke, JF

    2014-12-25

    Ionic liquids (ILs) with aprotic heterocyclic anions (AHA) are attractive candidates for CO2 capture technologies. In this study, a series of AHA ILs with 1-ethyl-3-methylimidazolium ([emim](+)) cations were synthesized, and their physical properties (density, viscosity, and ionic conductivity) were measured. In addition, CO2 solubility in each IL was determined at room temperature using a volumetric method at pressures between 0 and 1 bar. The AHAs are basic anions that are capable of reacting stoichiometrically with CO2 to form carbamate species. An interesting CO2 uptake isotherm behavior was observed, and this may be attributed to a parallel, equilibrium proton exchange process between the imidazolium cation and the basic AHA in the presence of CO2, followed by the formation of "transient" carbene species that react rapidly with CO2. The presence of the imidazolium-carboxylate species and carbamate anion species was verified using H-1 and C-13 NMR spectroscopy. While the reaction between CO2 and the proposed transient carbene resulted in cation-CO2 binding that is stronger than the anion-CO2 reaction, the reactions of the imidazolium AHA ILs were fully reversible upon regeneration at 80 degrees C with nitrogen purging. The presence of water decreased the CO2 uptake due to the inhibiting effect of the neutral species (protonated form of AHA) that is formed.

  20. Complete active space second order perturbation theory (CASPT2) study of N(²D) + H₂O reaction paths on D₁ and D₀ potential energy surfaces: direct and roaming pathways.

    PubMed

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-10-21

    We report reaction paths starting from N((2)D) + H2O for doublet spin states, D0 and D1. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H2ON → H-O(H)N → H-HON → NO((2)Π) + H2, (2) cis-HNOH → HNO-H → H-HNO → NO + H2, (3) H2NO → H-HNO → HNO-H → trans-HNOH, are confirmed on the D0 surface. PMID:25338892

  1. Complete active space second order perturbation theory (CASPT2) study of N(2D) + H2O reaction paths on D1 and D0 potential energy surfaces: Direct and roaming pathways

    NASA Astrophysics Data System (ADS)

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-10-01

    We report reaction paths starting from N(2D) + H2O for doublet spin states, D0 and D1. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H2ON → H-O(H)N → H-HON → NO(2Π) + H2, (2) cis-HNOH → HNO-H → H-HNO → NO + H2, (3) H2NO → H-HNO → HNO-H → trans-HNOH, are confirmed on the D0 surface.

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

    SciTech Connect

    Huggins, John Mitchell

    1980-06-01

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

  3. Pyridine Group-Assisted Addition of Diazo-Compounds to Imines in the 3-CC Reaction of 2-Aminopyridines, Aldehydes, and Diazo-Compounds

    PubMed Central

    Gulevich, Anton V.; Helan, Victoria; Wink, Donald J.

    2013-01-01

    A novel three-component (3-CC) coupling reaction of 2-aminoazines, aromatic aldehydes and diazo-compounds producing polyfunctional β-amino-α-diazo-compounds has been developed. The reaction features an unprecedented heterocycle-assisted addition of a diazo-compound to an imine. The obtained diazoesters were efficiently converted into valuable heterocycles, as well as to β-amino acid derivatives. PMID:23373731

  4. Methyl iodide oxidative addition to [Rh(acac)(CO)(PPh3)]: an experimental and theoretical study of the stereochemistry of the products and the reaction mechanism.

    PubMed

    Conradie, Marrigje M; Conradie, Jeanet

    2011-08-28

    Density functional theory was used to investigate the oxidative addition and subsequent carbonyl insertion and deinsertion steps of the reaction of methyl iodide to a rhodium(I) acetylacetonato complex of the formula [Rh(acac)(CO)(PPh(3))] (Hacac = acetylacetone). This process has been studied experimentally for many rhodium β-diketonato complexes, but, to the best of our knowledge, this is the first systematic computational study of the complete reaction sequence. Experimental (1)H techniques complement the theoretical results on the stereochemistry of the reaction intermediates and products. (1)H NMR also revealed the existence of a second rhodium(III)-acyl product, which has not been previously observed in this reaction. The calculated Gibbs free energy of activation of the oxidative addition reaction is 71 kJ mol(-1), which is in agreement with the experimental value of 82(1) kJ mol(-1). The DFT-calculated oxidative addition corresponds to an associative S(N)2 nucleophilic attack by the rhodium metal centre on the methyl iodide, which is in agreement with calculated and experimental (in brackets) activation parameters of the reaction, 27 (38.8) kJ mol(-1) for ΔH((≠)) and -147 (-146) J K(-1) mol(-1) for ΔS((≠)). PMID:21761056

  5. Activation of Aryl Halides by Nickel(I) Pincer Complexes: Reaction Pathways of Stoichiometric and Catalytic Dehalogenations.

    PubMed

    Rettenmeier, Christoph A; Wenz, Jan; Wadepohl, Hubert; Gade, Lutz H

    2016-08-15

    Homolytic C-X bond cleavage of organohalides by the T-shaped nickel(I) complexes [LigNi(I)] 1 bearing the iso-PyrrMeBox ligand had been found previously to be the crucial activation step in the asymmetric hydrodehalogenation of geminal dihalides. Here, this mechanistic investigation is extended to aryl halides, which allowed a systematic study of the activation process by a combination of experimental data and density functional theory modeling. While the activation of both aryl chlorides and geminal dichlorides appears to proceed via an analogous transition state, the generation of a highly stabile nickel(II)aryl species in the reaction of the aryl chlorides for the former represents a major difference in the reactive behavior. This difference was found to have a crucial impact on the activity of these nickel pincer systems as catalysts in the dehalogenation of aryl chlorides compared to geminal dichlorides and highlights the importance of the regulatory pathways controlling the nickel(I) concentration throughout the catalysis. These results along with the identification and characterization of novel nickel(II)aryl species are presented. PMID:27483018

  6. Biomimetic oxidative dimerization of anodically generated stilbene radical cations: effect of aromatic substitution on product distribution and reaction pathways.

    PubMed

    Hong, Fong-Jiao; Low, Yun-Yee; Chong, Kam-Weng; Thomas, Noel F; Kam, Toh-Seok

    2014-05-16

    A systematic study of the electrochemical oxidation of 1,2-diarylalkenes was carried out with the focus on detailed product studies and variation of product type as a function of aromatic substitution. A reinvestigation of the electrochemical oxidation of 4,4'-dimethoxystilbene under various conditions was first carried out, and all products formed were fully characterized and quantitated. This was followed by a systematic investigation of the effect of aromatic substitution on the nature and distribution of the products. The aromatic substituents were found to fall into three main categories, viz., substrates in which the nature and position of the aromatic substituents gave rise to essentially the same products as 4,4'-dimethoxystilbene, for example, tetraaryltetrahydrofurans, dehydrotetralins, and aldehydes (p-MeO or p-NMe2 on one ring and X on the other ring, where X = o-MeO or p-alkyl, or m- or p-EWG; e.g., 4-methoxy-4'-trifluoromethylstilbene); those that gave rise to a mixture of indanyl (or tetralinyl) acetamides and dehydrotetralins (or pallidols) (both or one ring substituted by alkyl groups, e.g., 4,4'-dimethylstilbene); and those where strategic placement of donor groups, such as OMe and OH, led to the formation of ampelopsin F and pallidol-type carbon skeletons (e.g., 4,3',4'-trimethoxystilbene). Reaction pathways to rationalize the formation of the different products are presented. PMID:24754525

  7. Stereoselective reaction of 2-carboxythioesters-1,3-dithiane with nitroalkenes: an organocatalytic strategy for the asymmetric addition of a glyoxylate anion equivalent.

    PubMed

    Massolo, Elisabetta; Benaglia, Maurizio; Genoni, Andrea; Annunziata, Rita; Celentano, Giuseppe; Gaggero, Nicoletta

    2015-05-28

    An efficient organocatalytic methodology has been developed to perform the stereoselective addition of 2-carboxythioesters-1,3-dithiane to nitroalkenes. Under mild reaction conditions γ-nitro-β-aryl-α-keto esters with up to 92% ee were obtained, realizing a formal catalytic stereoselective conjugate addition of the glyoxylate anion synthon. The reaction products are versatile starting materials for further synthetic transformations; for example, the simultaneous reduction of the nitro group and removal of the dithiane ring was accomplished, allowing the preparation of a GABAB receptor agonist baclofen. PMID:25883074

  8. Addition of water, methanol, and ammonia to Al3O3- clusters: Reaction products, transition states, and electron detachment energies

    NASA Astrophysics Data System (ADS)

    Guevara-García, Alfredo; Martínez, Ana; Ortiz, J. V.

    2005-06-01

    Products of reactions between the book and kite isomers of Al3O3- and three important molecules are studied with electronic structure calculations. Dissociative adsorption of H2O or CH3OH is highly exothermic and proton-transfer barriers between anion-molecule complexes and the products of these reactions are low. For NH3, the reaction energies are less exothermic and the corresponding barriers are higher. Depending on experimental conditions, Al3O3- (NH3) coordination complexes or products of dissociative adsorption may be prepared. Vertical electron detachment energies of stable anions are predicted with ab initio electron propagator calculations and are in close agreement with experiments on Al3O3- and its products with H2O and CH3OH. Changes in the localization properties of two Al-centered Dyson orbitals account for the differences between the photoelectron spectra of Al3O3- and those of the product anions.

  9. Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

    PubMed Central

    Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo

    2013-01-01

    Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489

  10. Mechanistic investigations of CO-photoextrusion and oxidative addition reactions of early transition-metal carbonyls: (η(5)-C5H5)M(CO)4 (M = V, Nb, Ta).

    PubMed

    Su, Shih-Hao; Su, Ming-Der

    2016-06-28

    The mechanisms for the photochemical Si-H bond activation reaction are studied theoretically using a model system of the group 5 organometallic compounds, η(5)-CpM(CO)4 (M = V, Nb, and Ta), with the M06-2X method and the Def2-SVPD basis set. Three types of reaction pathways that lead to final insertion products are identified. The structures of the intersystem crossings, which play a central role in these photo-activation reactions, are determined. The intermediates and transitional structures in either the singlet or triplet states are also calculated to provide a mechanistic explanation of the reaction pathways. All of the potential energy surfaces for the group 5 η(5)-CpM(CO)4 complexes are quite similar. In particular, the theoretical evidence suggests that after irradiation using light, η(5)-CpM(CO)4 quickly loses one CO ligand to yield two tricarbonyls, in either the singlet or the triplet states. The triplet tricarbonyl 16-electron intermediates, ([η(5)-CpM(CO)3](3)), play a key role in the formation of the final oxidative addition product, η(5)-CpM(CO)3(H)(SiMe3). However, the singlet counterparts, ([η(5)-CpM(CO)3](1)), play no role in the formation of the final product molecule, but their singlet metal centers interact weakly with solvent molecules ((Me3)SiH) to produce alkyl-solvated organometallic complexes, which are observable experimentally. This theoretical evidence is in accordance with the available experimental observations. PMID:27265245

  11. Elucidating the Pseudomonas aeruginosa fatty acid degradation pathway: identification of additional fatty acyl-CoA synthetase homologues.

    PubMed

    Zarzycki-Siek, Jan; Norris, Michael H; Kang, Yun; Sun, Zhenxin; Bluhm, Andrew P; McMillan, Ian A; Hoang, Tung T

    2013-01-01

    The fatty acid (FA) degradation pathway of Pseudomonas aeruginosa, an opportunistic pathogen, was recently shown to be involved in nutrient acquisition during BALB/c mouse lung infection model. The source of FA in the lung is believed to be phosphatidylcholine, the major component of lung surfactant. Previous research indicated that P. aeruginosa has more than two fatty acyl-CoA synthetase genes (fadD; PA3299 and PA3300), which are responsible for activation of FAs using ATP and coenzyme A. Through a bioinformatics approach, 11 candidate genes were identified by their homology to the Escherichia coli FadD in the present study. Four new homologues of fadD (PA1617, PA2893, PA3860, and PA3924) were functionally confirmed by their ability to complement the E. coli fadD mutant on FA-containing media. Growth phenotypes of 17 combinatorial fadD mutants on different FAs, as sole carbon sources, indicated that the four new fadD homologues are involved in FA degradation, bringing the total number of P. aeruginosa fadD genes to six. Of the four new homologues, fadD4 (PA1617) contributed the most to the degradation of different chain length FAs. Growth patterns of various fadD mutants on plant-based perfumery substances, citronellic and geranic acids, as sole carbon and energy sources indicated that fadD4 is also involved in the degradation of these plant-derived compounds. A decrease in fitness of the sextuple fadD mutant, relative to the ΔfadD1D2 mutant, was only observed during BALB/c mouse lung infection at 24 h. PMID:23737986

  12. Lewis acid-base 1,2-addition reactions: synthesis of pyrylium borates from en-ynoate precursors.

    PubMed

    Wilkins, Lewis C; Hamilton, Hugh B; Kariuki, Benson M; Hashmi, A Stephen K; Hansmann, Max M; Melen, Rebecca L

    2016-03-30

    Treatment of methyl (Z)-2-alken-4-ynoates with the strong Lewis acid tris(pentafluorophenyl) borane, B(C6F5)3, yield substituted zwitterionic pyrylium borate species via an intramolecular 6-endo-dig cyclisation reaction. PMID:26435394

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

    PubMed

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

    2016-07-01

    A previous work showed that the night period is important for the occurrence of Fenton-like oxidation of small aromatic acids from biomass burning in atmospheric waters, which originate new chromophoric compounds apparently more complex than the precursors, although the chemical transformations involved in the process are still unknown. In this work were identified by gas chromatography-mass spectrometry (GC-MS) and by electrospray mass spectrometry (ESI-MS) the organic intermediate compounds formed during the Fenton-like oxidation of three aromatic acids from biomass burning (benzoic, 4-hydroxybenzoic and 3,5-dihydroxybenzoic acids), the same compounds evaluated in the previous study, in water and in the absence of light, which in turns allows to disclose the chemical reaction pathways involved. The oxidation intermediate compounds found for benzoic acid were 2-hydroxybenzoic, 3-hydroxybenzoic, 4-hydroxybenzoic, 2,3-dihydroxybenzoic, 2,5-dihydroxybenzoic, 2,6-dihydroxybenzoic and 3,4-dihydroxybenzoic acids. The oxidation intermediates for 4-hydroxybenzoic acid were 3,4-hydroxybenzoic acid and hydroquinone, while for 3,5-dihydroxybenzoic acid were 2,4,6-trihydroxybenzoic and 3,4,5-trihydroxybenzoic acids, and tetrahydroxybenzene. The results suggested that the hydroxylation of the three small aromatic acids is the main step of Fenton-like oxidation in atmospheric waters during the night, and that the occurrence of decarboxylation is also an important step during the oxidation of the 4-dihydroxybenzoic and 3,5-dihydroxybenzoic acids. In addition, it is important to highlight that the compounds produced are also small aromatic compounds with potential adverse effects on the environment, besides becoming available for further chemical reactions in atmospheric waters. PMID:27088537

  14. Involvement of mitogen-activated protein kinase and NF-κB signaling pathways in perfluorooctane sulfonic acid-induced inflammatory reaction in BV2 microglial cells.

    PubMed

    Zhu, Jingying; Qian, Wenyi; Wang, Yixin; Gao, Rong; Wang, Jun; Xiao, Hang

    2015-12-01

    Microglial activation is closely related to the pathogenesis of neurodegenerative diseases by producing proinflammatory cytokines. Perfluorooctane sulfonic acid (PFOS), known as an emerging persistent organic pollutant, is reported to disturb human immune homeostasis; however, whether it affects cytokine production or the immune response in the central nervous system remains unclear. The present study was aimed to explore whether PFOS contributed to inflammatory action and to investigate the corresponding mechanisms in BV2 microglia. PFOS-mediated morphologic changes, cytokine responses and signaling events were examined by light microscopy, real-time polymerase chain reaction, enzyme-linked immunosorbent assay and Western blot assays. Our results indicated that PFOS increased BV2 cells activation and simultaneously increased tumor necrosis factor alpha and interleukin-6 expression. In addition, the c-Jun N-terminal protein kinase inhibitor (SP600125), as well as ERK1/2 blocker (PD98059), transcriptionally at least, displayed anti-inflammatory properties on PFOS-elicited cytokine responses. Moreover, the inflammatory transcription factor NF-κB was specifically activated by PFOS as well. These results, taken together, suggested that PFOS exerts its functional effects on the response of microglial cell activation via, in part, the c-Jun N-terminal protein kinase, ERK and NF-κB signaling pathways with its subsequent influence on proinflammatory action. PMID:25677194

  15. An Experiment To Demonstrate How a Catalyst Affects the Rate of a Reaction.

    ERIC Educational Resources Information Center

    Copper, Christine L.; Koubeck, Edward

    1999-01-01

    Describes a chemistry experiment that allows students to calculate rates of reaction, orders of reaction, and activation energies. The activity demonstrates that to increase a reaction's rate, a catalyst need only provide any additional pathway for the reaction, not necessarily a pathway having lower activation energy. (WRM)

  16. Double-addition reaction of aryl methyl sulfones with N-tert-butylsulfinyl imines: diastereoselective and concise synthesis of 2-sulfonylated 1,3-diamines.

    PubMed

    Li, Ya; Li, Desheng; Zheng, Tao; Li, Hongsen; Ren, Xinfeng

    2014-11-10

    We report a double-addition reaction of methyl phenyl sulfone and methyl 2-pyridyl sulfone with N-tert-butylsulfinyl imines. This method provides concise access to 2-sulfonylated 1,3-anti diamines with good to excellent diastereoselectivities. This protocol has the benefit of using readily accessible starting materials and is operationally simple. PMID:25288374

  17. Visible-Light-Promoted Dual C-C Bond Formations of Alkynoates via a Domino Radical Addition/Cyclization Reaction: A Synthesis of Coumarins.

    PubMed

    Feng, Shangbiao; Xie, Xingang; Zhang, Weiwei; Liu, Lin; Zhong, Zhuliang; Xu, Dengyu; She, Xuegong

    2016-08-01

    A visible-light-promoted, mild, and direct difunctionalization of alkynoates has been accomplished. This procedure provides a new strategy toward synthesis of the coumarin core structure by photoredox-mediated oxidation to generate the α-oxo radical, which supervenes a domino radical addition/cyclization reaction in moderate to good yields with high regioselectivity at ambient temperature. PMID:27443889

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  19. The Wnt and Delta-Notch signalling pathways interact to direct pair-rule gene expression via caudal during segment addition in the spider Parasteatoda tepidariorum.

    PubMed

    Schönauer, Anna; Paese, Christian L B; Hilbrant, Maarten; Leite, Daniel J; Schwager, Evelyn E; Feitosa, Natália Martins; Eibner, Cornelius; Damen, Wim G M; McGregor, Alistair P

    2016-07-01

    In short-germ arthropods, posterior segments are added sequentially from a segment addition zone (SAZ) during embryogenesis. Studies in spiders such as Parasteatoda tepidariorum have provided insights into the gene regulatory network (GRN) underlying segment addition, and revealed that Wnt8 is required for dynamic Delta (Dl) expression associated with the formation of new segments. However, it remains unclear how these pathways interact during SAZ formation and segment addition. Here, we show that Delta-Notch signalling is required for Wnt8 expression in posterior SAZ cells, but represses the expression of this Wnt gene in anterior SAZ cells. We also found that these two signalling pathways are required for the expression of the spider orthologues of even-skipped (eve) and runt-1 (run-1), at least in part via caudal (cad). Moreover, it appears that dynamic expression of eve in this spider does not require a feedback loop with run-1, as is found in the pair-rule circuit of the beetle Tribolium Taken together, our results suggest that the development of posterior segments in Parasteatoda is directed by dynamic interactions between Wnt8 and Delta-Notch signalling that are read out by cad, which is necessary but probably not sufficient to regulate the expression of eve and run-1 Our study therefore provides new insights towards better understanding the evolution and developmental regulation of segmentation in other arthropods, including insects. PMID:27287802

  20. Light-induced conformational changes in photosynthetic reaction centers: redox-regulated proton pathway near the dimer.

    PubMed

    Deshmukh, Sasmit S; Williams, JoAnn C; Allen, James P; Kálmán, László

    2011-04-26

    The influence of the hydrogen bonds on the light-induced structural changes were studied in the wild type and 11 mutants with different hydrogen bonding patterns of the primary electron donor of reaction centers from Rhodobacter sphaeroides. Previously, using the same set of mutants at pH 8, a marked light-induced change of the local dielectric constant in the vicinity of the dimer was reported in wild type and in mutants retaining Leu L131 that correlated with the recovery kinetics of the charge-separated state [ Deshmukh et al. (2011) Biochemistry, 50, 340-348]. In this work after prolonged illumination the recovery of the oxidized dimer was found to be multiphasic in all mutants. The fraction of the slowest phase, assigned to a recovery from a conformationally altered state, was strongly pH dependent and found to be extremely long at room temperature, at pH 6, with rate constants of ∼10(-3) s(-1). In wild type and in mutants with Leu at L131 the very long recovery kinetics was coupled to a large proton release at pH 6 and a decrease of up to 79 mV of the oxidation potential of the dimer. In contrast, in the mutants carrying the Leu to His mutation at the L131 position, only a negligible fraction of the dimer exhibited lowered potential, the large proton release was not observed, the oxidized dimer recovered 1 or 2 orders of magnitude faster depending on the pH, and the very long-lived state was not or barely detectable. These results are modeled as arising from the loss of a proton pathway from the bacteriochlorophyll dimer to the solvent when His is present at the L131 position. PMID:21410139

  1. Ligand addition versus substitution in the slow reaction of 13CO with Mn(CO)-4 in a flowing afterglow apparatus

    NASA Astrophysics Data System (ADS)

    McDonald, Richard N.; Schmidt, Myron A.

    1992-09-01

    The gas-phase reactions of Mn(CO)-4 with CO and 13CO are reported. Only addition was observed with CO producing Mn(CO)-5 (kapp = (2.5±0.2) × 10-12 cm3 molecule-1 s-1). Both addition (kadd = (3.2 ±0.4) × 10-12 cm3 molecule-1 s-1) and substitution (ksub = (1.2 ± 0.4) × 10-12 cm3 molecule-1 s-1) product-forming channels were observed in the reaction with 13CO. The average branching fractions for addition and thermoneutral substitution are 0.74 and 0.26 respectively. These branching fractions and the 70% collisional quenching efficiency of the excited addition intermediates [Mn(13CO)(CO)-4]* with the helium buffer gas are essentially the same values as those previously obtained for the quenching/decomposition of [Fe(13CO)(CO)[radical sign]-3]*. The ground electronic state of Mn(CO)-4 is believed to be the triplet because the negative ion is isoelectronic with Fe(CO)4, a known ground state triplet complex. Thus, the slow rate of the Mn(CO)-4/CO reaction (reaction EFFICIENCY = 0.0036) is considered to be the result of the spin-forbidden curve crossing of the triplet Mn(CO)-4 + CO inlet surface to the attractive singlet Mn(CO)-4 + CO --> singlet Mn(CO)-5 product surface. Comparisons with the results from the fast spin-allowed addition/substitution reactions of Fe(CO)[radical sign]-3 with 13CO are given.

  2. Influence of the reaction medium on enzyme activity in bio-organic synthesis: behaviour of lipase from Candida rugosa in the presence of polar additives.

    PubMed

    Triantafyllou, A O; Adlercreutz, P; Mattiasson, B

    1993-04-01

    Lipase from Candida rugosa immobilized on Celite was employed as the biocatalyst in order to examine the effect of the reaction medium upon enzymic activity and selectivity. As the model reaction, transesterification between tributyrin and pentan-2-ol in iso-octane (2,2,4-trimethylpentane) was chosen. A small amount of water (0.05%, v/v) was added to the reaction medium. Enhanced transesterification yields and increased selectivity of the lipase could be obtained by manipulating the microenvironment of the catalyst. Addition of 0.2% NN-dimethylformamide allowed a 93% higher ester yield compared with that obtained when no extra addition was made. Under the same conditions, the ratio of the amount of transesterification product over the amount of hydrolysis product after 48 h, became 52% higher than the ratio determined in the absence of additives. It was concluded that addition of compounds that have low logP3 (P is the partition coefficient in the octanol/water two-phase system) values and high dielectric constant was advantageous in order to favour transesterification over hydrolytic processes. PMID:8484905

  3. Asymmetric Catalytic Enantio- and Diastereoselective Boron Conjugate Addition Reactions of α-Functionalized α,β-Unsaturated Carbonyl Substrates.

    PubMed

    Xie, Jian-Bo; Lin, Siqi; Qiao, Shuo; Li, Guigen

    2016-08-01

    An efficient catalytic system has been established for the asymmetric boron conjugate addition of B2pin2 onto α-functionalized (involving C, N, O, and Cl) α,β-unsaturated carbonyls under mild, neutral conditions involving Cu[(S)-(R)-ppfa]Cl, AgNTf2, and alcohols. The dual additives of AgNTf2 and alcohols were found to play crucial roles for achieving high catalytic activity and enantio- and diastereoselectivity (up to 98% ee and 70:1 dr). PMID:27434500

  4. Diallyl Trisulfide Is a Fast H2S Donor, but Diallyl Disulfide Is a Slow One: The Reaction Pathways and Intermediates of Glutathione with Polysulfides.

    PubMed

    Liang, Dong; Wu, Haixia; Wong, Ming Wah; Huang, Dejian

    2015-09-01

    Diallyl trisulfide (DATS) reacts rapidly with glutathione (GSH) to release H2S through thiol-disulfide exchange followed by allyl perthiol reduction by GSH. Yet diallyl disulfide (DADS) only releases a minute amount of H2S via a sluggish reaction with GSH through an α-carbon nucleophilic substitution pathway. The results clarify the misunderstanding of DADS as a rapid H2S donor, which is attributed to its DATS impurity. PMID:26301500

  5. Multifunctional Electrochemical Platforms Based on the Michael Addition/Schiff Base Reaction of Polydopamine Modified Reduced Graphene Oxide: Construction and Application.

    PubMed

    Huang, Na; Zhang, Si; Yang, Liuqing; Liu, Meiling; Li, Haitao; Zhang, Youyu; Yao, Shouzhuo

    2015-08-19

    In this paper, a new strategy for the construction of multifunctional electrochemical detection platforms based on the Michael addition/Schiff base reaction of polydopamine modified reduced graphene oxide was first proposed. Inspired by the mussel adhesion proteins, 3,4-dihydroxyphenylalanine (DA) was selected as a reducing agent to simultaneously reduce graphene oxide and self-polymerize to obtain the polydopamine-reduced graphene oxide (PDA-rGO). The PDA-rGO was then functionalized with thiols and amines by the reaction of thiol/amino groups with quinine groups of PDA-rGO via the Michael addition/Schiff base reaction. Several typical compounds containing thiol and/or amino groups such as 1-[(4-amino)phenylethynyl] ferrocene (Fc-NH2), cysteine (cys), and glucose oxidase (GOx) were selected as the model molecules to anchor on the surface of PDA-rGO using the strategy for construction of multifunctional electrochemical platforms. The experiments revealed that the composite grafted with ferrocene derivative shows excellent catalysis activity toward many electroactive molecules and could be used for individual or simultaneous detection of dopamine hydrochloride (DA) and uric acid (UA), or hydroquinone (HQ) and catechol (CC), while, after grafting of cysteine on PDA-rGO, simultaneous discrimination detection of Pb(2+) and Cd(2+) was realized on the composite modified electrode. In addition, direct electron transfer of GOx can be observed when GOx-PDA-rGO was immobilized on glassy carbon electrode (GCE). When glucose was added into the system, the modified electrode showed excellent electric current response toward glucose. These results inferred that the proposed multifunctional electrochemical platforms could be simply, conveniently, and effectively regulated through changing the anchored recognition or reaction groups. This study would provide a versatile method to design more detection or biosensing platforms through a chemical reaction strategy in the future. PMID

  6. Adult neuron addition to the zebra finch song motor pathway correlates with the rate and extent of recovery from botox-induced paralysis of the vocal muscles

    PubMed Central

    Pytte, Carolyn; Yu, Yi-Lo; Wildstein, Sara; George, Shanu; Kirn, John

    2011-01-01

    In adult songbirds, neurons are continually incorporated into the telencephalic nucleus HVC, a pre-motor region necessary for the production of learned vocalizations. Previous studies have demonstrated that neuron addition to HVC is highest when song is most variable: in juveniles during song learning, in seasonally singing adults during peaks in plasticity that precede the production of new song components, or during seasonal re-establishment of a previously learned song. These findings suggest that neuron addition provides motor flexibility for the transition from a variable song to a target song. Here we test the association between the quality of song structure and HVC neuron addition by experimentally manipulating syringeal muscle control with botox, which produces a transient partial paralysis. We show that the quality of song structure co-varies with new neuron addition to HVC. Both the magnitude of song distortion and the rate of song recovery following syringeal botox injections were correlated with the number of new neurons incorporated into HVC. We suggest that the quality of song structure is either a cause or consequence of the number of new neurons added to HVC. Birds with naturally high rates of neuron addition may have had the greatest success in recovering song. Alternatively, or in addition, new neuron survival in the song motor pathway may be regulated by the quality of song-generated feedback as song regains its original stereotyped structure. Present results are the first to show a relationship between peripheral muscle control and adult neuron addition to cortical pre-motor circuits. PMID:22114266

  7. Reaction Pathways and Excited States in H2O2+OH → HO2+H2O : A New ab initio Investigation

    SciTech Connect

    Ginovska, Bojana; Camaioni, Donald M.; Dupuis, Michel

    2007-08-28

    The mechanism of the hydrogen abstraction reaction H2O2+OH→ HO2+H2O in gas phase was studied, using DFT (MPW1K) level of theory. We located 2 pathways for the reaction, both going through the same intermediate complex OH-H2O2, but via two distinct transition state structures that differ by the orientation of the hydroxyl hydrogen relative to the incipient hydroperoxy hydrogen. In one case, these hydrogens are on same side of the plane made by the 3 oxygen atoms and in the other these hydrogens are on opposite sides of the plane. The first two excited states were calculated for selected points of both pathways using time-dependent DFT, multiconfigurational quasi-degenerate-perturbation theory (MCQDPT2/ CASSCF) and equation of motion coupled cluster singles, doubles model (EOM-CCSD) EOMCCSD energies and completely renormalized EOM-CCSD(T)(IA) correction. An avoided crossing between the two excited states was found on both reaction pathways, on the product side of the barrier to H-transfer on the ground state surface, near the transition states. Further more, we report on the calculation of the rate of the reaction in the gas phase for temperatures in the range of 250-500 K, and suggest that the strong temperature dependence of the rate at high temperatures is due to reaction on the low-lying excited state surface over a barrier that is much larger than on the ground state surface. This work was supported in part by the Office of Basic Energy Sciences of the Department of Energy (DOE), Chemical Sciences program (BG and MD) and in part by the U.S. Department of Energy’s Office of Biological and Environmental Research, Environmental Management Science Program (BG and DMC). The Pacific Northwest National Laboratory is operated for DOE by Battelle Memorial Institute.

  8. The stereochemical outcome of electrophilic addition reactions on the 5,6-double bond in the spinosyns.

    PubMed

    De Amicis, C V; Graupner, P R; Erickson, J A; Paschal, J W; Kirst, H A; Creemer, L C; Fanwick, P E

    2001-12-14

    The electrophilic addition of reagents to the 5,6-double bond in spinosyn A and spinosyn D systems occurred with high pi-diastereofacial selectivity. Addition occurred preferentially from the beta face of the molecule with selectivities ranging from 5:1 to better than 30:1. Various NMR properties were investigated in order to distinguish the beta and alpha isomers with the help of theoretical models of the products. These NMR properties include a (13)C gamma effect to C-11 and vicinal coupling between H-4 and H-5. To help rationalize the selectivity, computational studies on the transition states for epoxidation were calculated using density functional theory. The results indicate that beta epoxidation is favored and that the geometries of the transition structures are consistent with torsional steering being the source of the selectivity. PMID:11735521

  9. Thermochemical treatment of sewage sludge ash with sodium salt additives for phosphorus fertilizer production--Analysis of underlying chemical reactions.

    PubMed

    Stemann, Jan; Peplinski, Burkhard; Adam, Christian

    2015-11-01

    Stocks of high grade phosphate rock are becoming scarce, and there is growing concern about potentially harmful impurities in conventional phosphorus fertilizers. Sewage sludge ash is a promising secondary phosphorus source. However, to remove heavy metals and convert the phosphorus contained in sewage sludge ash into mineral phases available to plants, an after-treatment is required. Laboratory-scale calcination experiments of sewage sludge ash blended with sodium salts using dried sewage sludge as a reducing agent were carried out at 1000°C. Thus, the Ca3(PO4)2 or whitlockite component of raw sewage sludge ash, which is not readily plant available, was converted to CaNaPO4 (buchwaldite). Consequently, nearly complete phosphorus solubility in ammonium citrate (a well-established indicator for plant availability) was achieved. Moreover, it was shown that Na2CO3 may be replaced by moderately priced Na2SO4. However, molar ratios of Na/P>2 were required to achieve >80% phosphorus solubility. Such over-stoichiometric Na consumption is largely caused by side reactions with the SiO2 component of the sewage sludge ash - an explanation for which clear evidence is provided for the first time. PMID:26219587

  10. Evidence for the formation of an enamine species during aldol and Michael-type addition reactions promiscuously catalyzed by 4-oxalocrotonate tautomerase.

    PubMed

    Poddar, Harshwardhan; Rahimi, Mehran; Geertsema, Edzard M; Thunnissen, Andy-Mark W H; Poelarends, Gerrit J

    2015-03-23

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which has a catalytic N-terminal proline residue (Pro1), can promiscuously catalyze various carbon-carbon bond-forming reactions, including aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde, and Michael-type addition of acetaldehyde to a wide variety of nitroalkenes to yield valuable γ-nitroaldehydes. To gain insight into how 4-OT catalyzes these unnatural reactions, we carried out exchange studies in D2 O, and X-ray crystallography studies. The former established that H-D exchange within acetaldehyde is catalyzed by 4-OT and that the Pro1 residue is crucial for this activity. The latter showed that Pro1 of 4-OT had reacted with acetaldehyde to give an enamine species. These results provide evidence of the mechanism of the 4-OT-catalyzed aldol and Michael-type addition reactions in which acetaldehyde is activated for nucleophilic addition by Pro1-dependent formation of an enamine intermediate. PMID:25728471

  11. Effects of N{sub 2}O gas addition on the properties of ZnO films grown by catalytic reaction-assisted chemical vapor deposition

    SciTech Connect

    Yasui, Kanji Morioka, Makoto; Kanauchi, Shingo; Ohashi, Yuki; Kato, Takahiro; Tamayama, Yasuhiro

    2015-11-15

    The influence of N{sub 2}O gas addition on the properties of zinc oxide (ZnO) films grown on a-plane (11–20) sapphire (a-Al{sub 2}O{sub 3}) substrates was investigated, using a chemical vapor deposition method based on the reaction between dimethylzinc and high-temperature H{sub 2}O produced by a catalytic H{sub 2}-O{sub 2} reaction on platinum (Pt) nanoparticles. The addition of N{sub 2}O was found to increase the size of the crystalline facets and to improve the crystal orientation along the c-axis. The electron mobility at 290 K was also increased to 234 cm{sup 2}/Vs following the addition of N{sub 2}O gas at a pressure of 3.2 × 10{sup −3 }Pa. In addition, the minimum full width at half maximum of the most intense photoluminescence peak derived from neutral donor bound excitons at 10 K decreased to 0.6 meV by the addition of N{sub 2}O gas at a pressure of 3.1 × 10{sup −2 }Pa.

  12. Mechanisms for the inversion of chirality: global reaction route mapping of stereochemical pathways in a probable chiral extraterrestrial molecule, 2-aminopropionitrile.

    PubMed

    Kaur, Ramanpreet; Vikas

    2015-02-21

    2-Aminopropionitrile (APN), a probable candidate as a chiral astrophysical molecule, is a precursor to amino-acid alanine. Stereochemical pathways in 2-APN are explored using Global Reaction Route Mapping (GRRM) method employing high-level quantum-mechanical computations. Besides predicting the conventional mechanism for chiral inversion that proceeds through an achiral intermediate, a counterintuitive flipping mechanism is revealed for 2-APN through chiral intermediates explored using the GRRM. The feasibility of the proposed stereochemical pathways, in terms of the Gibbs free-energy change, is analyzed at the temperature conditions akin to the interstellar medium. Notably, the stereoinversion in 2-APN is observed to be more feasible than the dissociation of 2-APN and intermediates involved along the stereochemical pathways, and the flipping barrier is observed to be as low as 3.68 kJ/mol along one of the pathways. The pathways proposed for the inversion of chirality in 2-APN may provide significant insight into the extraterrestrial origin of life. PMID:25702015

  13. Mechanisms for the inversion of chirality: Global reaction route mapping of stereochemical pathways in a probable chiral extraterrestrial molecule, 2-aminopropionitrile

    SciTech Connect

    Kaur, Ramanpreet; Vikas E-mail: qlabspu@yahoo.com

    2015-02-21

    2-Aminopropionitrile (APN), a probable candidate as a chiral astrophysical molecule, is a precursor to amino-acid alanine. Stereochemical pathways in 2-APN are explored using Global Reaction Route Mapping (GRRM) method employing high-level quantum-mechanical computations. Besides predicting the conventional mechanism for chiral inversion that proceeds through an achiral intermediate, a counterintuitive flipping mechanism is revealed for 2-APN through chiral intermediates explored using the GRRM. The feasibility of the proposed stereochemical pathways, in terms of the Gibbs free-energy change, is analyzed at the temperature conditions akin to the interstellar medium. Notably, the stereoinversion in 2-APN is observed to be more feasible than the dissociation of 2-APN and intermediates involved along the stereochemical pathways, and the flipping barrier is observed to be as low as 3.68 kJ/mol along one of the pathways. The pathways proposed for the inversion of chirality in 2-APN may provide significant insight into the extraterrestrial origin of life.

  14. Evaluation of gold nanoparticles as the additive in real-time polymerase chain reaction with SYBR Green I dye

    NASA Astrophysics Data System (ADS)

    Yang, Wenchao; Mi, Lijuan; Cao, Xueyan; Zhang, Xiaodong; Fan, Chunhai; Hu, Jun

    2008-06-01

    Gold nanoparticles (AuNPs) have been proven to be able to improve the specificity or increase the efficiency of a polymerase chain reaction (PCR) when a suitable amount of AuNPs was used. However, there is still a lack of systematic evaluation of AuNPs in real-time PCR. In this study, DNA degradation and the fluorescence quenching effect of AuNPs were first tested in real-time PCR. Then two different kinds of Taq DNA polymerase, native and recombinant Taq polymerase, were employed to evaluate the AuNPs' effect on the threshold cycle (CT) values, standard curves and melting curves in real-time PCR. Different ratios of the amount of native Taq DNA polymerase to the amount of AuNPs were also tested. It was found that AuNPs could be applied in real-time PCR with correlation coefficient R2>0.989. The combination of 2.09 nM AuNPs with 3.75 U of native Taq DNA polymerase could make the amplification curves shift to the left and enhance the efficiency of the real-time PCR (0.628 39 without AuNPs compared with 0.717 89 with 2.09 nM AuNPs), thus enabling faster detection in comparison with those of control samples. However, no improvement ability of AuNPs was found in real-time PCR based on recombinant rTaq DNA polymerase. Besides, the results suggest that a complex interaction exists between AuNPs and native Taq DNA polymerase.

  15. Addition-fragmentation reaction of thionoesters compounds in free-radical polymerisation (methyl, cyanomethyl and styryl): a theoretical interpretation

    NASA Astrophysics Data System (ADS)

    Hannachi, Douniazed; Ouddai, Nadia; Arotçaréna, Michel; Chermette, Henry

    2015-07-01

    A joint experimental and theoretical study has been carried out on reversible addition-fragmentation chain transfer polymerisation (RAFT). We have performed density functional theory calculations at the (Perdew-Burke-Ernzerhof) PBE/triple zeta plus polarisation level to analyse the RAFT mechanisms corresponding to these compounds. Global and local reactivity indices have been calculated to investigate the effect of the addition of methyl, cyanomethyl and styryl radicals on the double bond C=S of thionoester compounds producing an adduct radical. This mechanism is shown to be difficult when the cyanomethyl is used contrarily to the methyl and styryl radicals, in agreement with experimental results. The activation barrier of fragmentation of adduct radicals does not correlate well with the length of fragmented bond (O-Cα). The bond topological analysis of radical adduct predicts that the distance between the oxygen and a critical point (O-CP) in the fragment bond is a good parameter to estimate the activation energy of the fragmentation mechanism. It is shown that the nature of the free radicals is more selective than that of the thionoester compounds. With an overall large agreement with experiments, these theoretical results afford an explanation of the efficiency for the RAFT mechanism.

  16. Study of the effects of potassium addition to supported iron catalysts in the Fischer-Tropsch reaction

    SciTech Connect

    Miller, D.G.; Moskovits, M.

    1988-10-20

    The Fischer-Tropsch activity of supported iron catalysts prepared via electrochemical techniques has been evaluated as a function of potassium addition. Catalyst pretreatment in 0.09, 0.18, and 0.27 M K/sub 2/CO/sub 3/ solutions generated potassium levels of 1.7, 2.8, and 3.9 wt %, respectively. Pretreatment in 0.18 M KOH provided a catalyst with 2.3 wt% potassium and facilitated comparison of the effects of the basicity of the pretreatment solution upon catalyst activity. A maximum in catalyst activity and CO conversion was noted upon increasing K content, followed by a sharp decline in activity at potassium levels in excess of the maximum. The hydrogenation ability of the catalyst decreased, and a shift to higher molecular weight products was observed, with increasing potassium content. The type of pretreatment solution had little effect on the catalyst activity or the product selectivity.

  17. Interfacial Reactions of Zn-Al Alloys with Na Addition on Cu Substrate During Spreading Test and After Aging Treatments

    NASA Astrophysics Data System (ADS)

    Gancarz, Tomasz; Pstruś, Janusz; Berent, Katarzyna

    2016-04-01

    Spreading tests for Cu substrate with Zn-Al eutectic-based alloys with 0.2, 0.5, and 1.0 wt.% of Na were studied using the sessile drop method in the presence of QJ201 flux. Spreading tests were performed for 1, 3, 8, 15, 30, and 60 min of contact, at the temperatures of 475, 500, 525, and 550 °C. After cleaning the flux residue from solidified samples, the spreading area of Zn-Al + Na on Cu was determined in accordance with ISO 9455-10:2013-03. Selected, solidified solder-substrate couples were cross-sectioned and subjected to scanning electron microscopy of the interfacial microstructure. The experiment was designed to demonstrate the effect of Na addition on the kinetics of formation and growth of CuZn, Cu5Zn8, and CuZn4 phases, which were identified using x-ray diffraction and energy-dispersive spectroscopy analysis. The addition of Na to eutectic Zn-Al caused the spreading area to decrease and the thickness of intermetallic compound layers at the interface to reduce. Samples after the spreading test at 500 °C for 1 min were subjected to aging for 1, 10, and 30 days at 120,170, and 250 °C. The greater thicknesses of IMC layers were obtained for a temperature of 250 °C. With increasing Na content in Zn-Al + Na alloys, the thickness reduced, which correlates to the highest value of activation energy for Zn-Al with 1% Na.

  18. Structural and rate studies of the 1,2-additions of lithium phenylacetylide to lithiated quinazolinones: influence of mixed aggregates on the reaction mechanism.

    PubMed

    Briggs, Timothy F; Winemiller, Mark D; Collum, David B; Parsons, Rodney L; Davulcu, Akin H; Harris, Gregory D; Fortunak, Joseph M; Confalone, Pat N

    2004-05-01

    The 1,2-addition of lithium phenylacetylide (PhCCLi) to quinazolinones was investigated using a combination of structural and rate studies. (6)Li, (13)C, and (19)F NMR spectroscopies show that deprotonation of quinazolinones and phenylacetylene in THF/pentane solutions with lithium hexamethyldisilazide affords a mixture of lithium quinazolinide/PhCCLi mixed dimer and mixed tetramer along with PhCCLi dimer. Although the mixed tetramer dominates at high mixed aggregate concentrations and low temperatures used for the structural studies, the mixed dimer is the dominant form at the low total mixed aggregate concentrations, high THF concentrations, and ambient temperatures used to investigate the 1,2-addition. Monitoring the reaction rates using (19)F NMR spectroscopy revealed a first-order dependence on mixed dimer, a zeroth-order dependence on THF, and a half-order dependence on the PhCCLi concentration. The rate law is consistent with the addition of a disolvated PhCCLi monomer to the mixed dimer. Investigation of the 1,2-addition of PhCCLi to an O-protected quinazolinone implicates reaction via trisolvated PhCCLi monomers. PMID:15113214

  19. Embedding the Ni-SOD mimetic Ni-NCC within a polypeptide sequence alters specificity of the reaction pathway

    PubMed Central

    Krause, Mary E.; Glass, Amanda M.; Jackson, Timothy A.; Laurence, Jennifer S.

    2013-01-01

    The unique metal abstracting peptide (MAP) asparagine-cysteine-cysteine (NCC) binds nickel in a square planar 2N:2S geometry and acts as a mimic of the enzyme nickel superoxide dismutase (Ni-SOD). The Ni-NCC tripeptide complex undergoes rapid, site-specific chiral inversion to DLD-NCC in the presence of oxygen. Superoxide scavenging activity increases proportionally with the degree of chiral inversion. Characterization of the NCC sequence within longer peptides with absorption, circular dichroism (CD), and magnetic CD (MCD) spectroscopies and mass spectrometry (MS) shows that the geometry of metal coordination is maintained, though the electronic properties of the complex are varied to a small extent due to bis-amide, rather than amine/amide, coordination. In addition, both the Ni-tripeptides and Ni-pentapeptides have a −2 charge. The study here demonstrates that the chiral inversion chemistry does not occur when NCC is embedded in a longer polypeptide sequence. Nonetheless, the superoxide scavenging reactivity of the embedded Ni-NCC module is similar to that of the chirally inverted tripeptide complex, which is consistent with a minor change in reduction potential for the Ni-pentapeptide. Together, this suggests that the charge of the complex could affect the SOD activity as much as a change in primary coordination sphere. In Ni-NCC and other Ni-SOD mimics, changes in chirality, superoxide scavenging activity, and oxidation of the peptide itself all depend on the presence of dioxygen or its reduced derivatives (e.g., superoxide), and the extent to which each of these distinct reactions occurs is ruled by electronic and steric effects that emenate from the organization of ligands around the metal center. PMID:23214928

  20. Expanding Mg-Zn hybrid chemistry: inorganic salt effects in addition reactions of organozinc reagents to trifluoroacetophenone and the implications for a synergistic lithium-magnesium-zinc activation.

    PubMed

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

    2011-07-18

    Numerous organic transformations rely on organozinc compounds made through salt-metathesis (exchange) reactions from organolithium or Grignard reagents with a suitable zinc precursor. By combining X-ray crystallography, NMR spectroscopy and DFT calculations, this study sheds new light on the constitution of the organometallic species involved in this important synthetic tool. Investigations into the metathesis reactions of equimolar amounts of Grignard reagents (RMgX) and ZnCl(2) in THF led to the isolation of novel magnesium-zinc hybrids, [{(thf)(2)Mg(μ-Cl)(3)ZnR}(2)] (R=Et, tBu, nBu or o-OMe-C(6)H(4)), which exhibit an unprecedented structural motif in mixed magnesium-zinc chemistry. Furthermore, theoretical modelling of the reaction of EtMgCl with ZnCl(2) reveals that formation of the mixed-metal compound is thermodynamically preferred to that of the expected homometallic products, RZnCl and MgCl(2). This study also assesses the alkylating ability of hybrid 3 towards the sensitive ketone trifluoroacetophenone, revealing a dramatic increase in the chemoselectivity of the reaction when LiCl is introduced as an additive. This observation, combined with recent related breakthroughs in synthesis, points towards the existence of a trilateral Li/Mg/Zn synergistic effect. PMID:21656589

  1. Molecular weight growth in Titan's atmosphere: branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes.

    PubMed

    Kirk, Benjamin B; Savee, John D; Trevitt, Adam J; Osborn, David L; Wilson, Kevin R

    2015-08-28

    The reaction of small hydrocarbon radicals (i.e.˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC[triple bond, length as m-dash]C˙), a likely product from the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (-H = 27%, -CH3 = 73%) and (-H = 14%, -CH3 = 86%), respectively. Together, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions. PMID:26204935

  2. Pathways for the OH + Cl2 → HOCl + Cl and HOCl + Cl → HCl + ClO Reactions.

    PubMed

    Wang, Hongyan; Qiu, Yudong; Czakó, Gábor; Schaefer, Henry F

    2015-07-16

    High level coupled-cluster theory, with spin-orbit coupling evaluated via the Breit-Pauli operator in the interacting-states approach, is used to investigate the OH radical reaction with Cl2 and the subsequent reaction HOCl + Cl. The entrance complex, transition state, and exit complex for both reactions have been determined using the CCSD(T) method with correlation consistent basis sets up to cc-pV6Z. Also reported are CCSDT computations. The OH + Cl2 reaction is predicted to be endothermic by 2.2 kcal/mol, compared to the best experiments, 2.0 kcal/mol. The above theoretical results include zero-point vibrational energy corrections and spin-orbit contributions. The activation energy (Ea) of the OH + Cl2 reaction predicted here, 2.3 kcal/mol, could be as much as 1 kcal/mol too high, but it falls among the four experimental Ea values, which span the range 1.1-2.5 kcal/mol. The exothermicity of the second reaction HOCl + Cl → HCl + ClO is 8.4 kcal/mol, compared to experiment 8.7 kcal/mol. The activation energy for latter reaction is unknown experimentally, but predicted here to be large, 11.5 kcal/mol. There are currently no experiments relevant to the theoretical entrance and exit complexes predicted here. PMID:25965106

  3. Bis(trifluoromethyl)methylene Addition to Vinyl-Terminated SAMs: A Gas-Phase C–C Bond-Forming Reaction on a Surface

    PubMed Central

    2014-01-01

    Vinyl-terminated self-assembled monolayers (SAMs) on silicon oxide substrates were chemically modified by the addition of a bis(trifluoromethyl)methylene group in a rare gas-phase C–C bond-forming reaction to directly generate films carrying terminal CF3 groups. The vinyl-terminated films were treated with hexafluoroacetone azine (HFAA) for modification. The films were characterized with ellipsometry, contact angle measurements, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). In this study, we find that for optimized conditions clean reactions occur on a surface between SAMs with terminal olefins and HFAA, and the product is consistent with bis(trifluoromethyl)cyclopropanation formation after nitrogen extrusion. PMID:24806554

  4. Bis(trifluoromethyl)methylene addition to vinyl-terminated SAMs: a gas-phase C-C bond-forming reaction on a surface.

    PubMed

    Adamkiewicz, Malgorzata; O'Hagan, David; Hähner, Georg

    2014-05-20

    Vinyl-terminated self-assembled monolayers (SAMs) on silicon oxide substrates were chemically modified by the addition of a bis(trifluoromethyl)methylene group in a rare gas-phase C-C bond-forming reaction to directly generate films carrying terminal CF3 groups. The vinyl-terminated films were treated with hexafluoroacetone azine (HFAA) for modification. The films were characterized with ellipsometry, contact angle measurements, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). In this study, we find that for optimized conditions clean reactions occur on a surface between SAMs with terminal olefins and HFAA, and the product is consistent with bis(trifluoromethyl)cyclopropanation formation after nitrogen extrusion. PMID:24806554

  5. Transmetalation from B to Rh in the course of the catalytic asymmetric 1,4-addition reaction of phenylboronic acid to enones: a computational comparison of diphosphane and diene ligands.

    PubMed

    Li, You-Gui; He, Gang; Qin, Hua-Li; Kantchev, Eric Assen B

    2015-02-14

    Transmetalation is a key elementary reaction of many important catalytic reactions. Among these, 1,4-addition of arylboronic acids to organic acceptors such as α,β-unsaturated ketones has emerged as one of the most important methods for asymmetric C-C bond formation. A key intermediate for the B-to-Rh transfer arising from quaternization on a boronic acid by a Rh-bound hydroxide (the active catalyst) has been proposed. Herein, DFT calculations (IEFPCM/PBE0/DGDZVP level of theory) establish the viability of this proposal, and characterize the associated pathways. The delivery of phenylboronic acid in the orientation suited for the B-to-Rh transfer from the very beginning is energetically preferable, and occurs with expulsion of Rh-coordinated water molecules. For the bulkier binap ligand, the barriers are higher (particularly for the phenylboronic acid activation step) due to a less favourable entropy term to the free energy, in accordance with the experimentally observed slower transmetalation rate. PMID:25422851

  6. The kinetics of consecutive enzyme reactions. The design of coupled assays and the temporal response of pathways.

    PubMed Central

    Easterby, J S

    1984-01-01

    A regime is proposed for the design of coupled enzyme assays in which auxiliary enzymes are added at concentrations proportional to their Km values. Under these conditions it is possible to calculate the complete time course of the assay including the time required for the system to approach its steady state. The consequence of increasing the number of coupling enzymes is shown to be a considerable decrease in time required to reach the steady state provided that the overall transient time remains the same. The method is extended to the general consideration of pathways and shows that pathways of the same length exhibit identical temporal responses provided that the units of concentration and time used are based on the steady-state concentration of intermediates and the transient time respectively. An unexpected finding is that increasing the number of intermediates in a pathway can decrease the time required to enter a steady state. PMID:6743248

  7. Reaction pathways by quantum Monte Carlo: Insight on the torsion barrier of 1,3-butadiene, and the conrotatory ring opening of cyclobutene

    NASA Astrophysics Data System (ADS)

    Barborini, Matteo; Guidoni, Leonardo

    2012-12-01

    Quantum Monte Carlo (QMC) methods are used to investigate the intramolecular reaction pathways of 1,3-butadiene. The ground state geometries of the three conformers s-trans, s-cis, and gauche, as well as the cyclobutene structure are fully optimised at the variational Monte Carlo (VMC) level, obtaining an excellent agreement with the experimental results and other quantum chemistry high level calculations. Transition state geometries are also estimated at the VMC level for the s-trans to gauche torsion barrier of 1,3-butadiene and for the conrotatory ring opening of cyclobutene to the gauche-1,3-butadiene conformer. The energies of the conformers and the reaction barriers are calculated at both variational and diffusional Monte Carlo levels providing a precise picture of the potential energy surface of 1,3-butadiene and supporting one of the two model profiles recently obtained by Raman spectroscopy [Boopalachandran et al., J. Phys. Chem. A 115, 8920 (2011), 10.1021/jp2051596]. Considering the good scaling of QMC techniques with the system's size, our results also demonstrate how variational Monte Carlo calculations can be applied in the future to properly investigate the reaction pathways of large and correlated molecular systems.

  8. The effect of chemical additives on the synthesis of ethanol

    SciTech Connect

    Chuang, S.S.C.

    1992-03-06

    The objective of this research was to investigate the reaction mechanism of higher alcohol and aldehyde synthesis from syngas and the role of additives in the synthesis. An in situ IR reaction system and probe molecule technique were developed to study adsorbed species, active sites, and reaction pathway during reaction. The catalysts used for this study included silica-supported Rh, Ru, and Ni. (VC)

  9. Chelating σ-Aryl Post-Metallocenes: Probing Intramolecular [C-H···F-C] Interactions and Unusual Reaction Pathways.

    PubMed

    Liu, Cham-Chuen; Chan, Michael C W

    2015-06-16

    -[O,C,N] and [O,N,C] complexes, which occurs with chemical connectivity across intramolecular C-H···F-C interactions. This result is important because the applicability of weak attractive ligand-polymer interactions in catalysis is feasible only if the observed coupling and hence the noncovalent interaction is genuine. The verified intramolecular C-H···F-C contacts in these complexes can therefore be considered as synthetic models for ligand-polymer interactions in olefin polymerization processes. Significantly, reports concerning late transition metal systems have appeared that hint at the generality of the WALPI concept for modulating polymerization reactions. We evaluated the olefin polymerization reactivity of Ti-[O,N,C] catalysts through judicious substitution. DFT calculations, which revealed diverse kinetically competitive reaction pathways and active sites (including unusual ethylene-assimilated species) in addition to normal chain propagation, were also employed to rationalize polymerization efficiencies. Further developments in catalytic applications of multidentate σ-aryl ligand systems and novel reactivity of the corresponding complexes can be envisaged. PMID:25993345

  10. A chemical bonding model for photo-induced defects in hydrogenated amorphous silicon (a-Si:H): Intrinsic and extrinsic reaction pathways

    SciTech Connect

    Lucovsky, G.; Yang, H.

    1997-07-01

    In device grade a-Si:H photo- or light-induced defect generation is an intrinsic effect for impurity concentrations of oxygen and nitrogen below about 10{sup 19} to 10{sup 20} cm{sup {minus}3}; however, at higher concentrations it increases with increasing impurity content. Charged defect configurations are identified by empirical chemistry and are studied by ab initio calculations. This paper addresses: (1) the chemical stability of charged defects; (2) the reaction pathways for defect metastability; and (3) the transition between extrinsic and intrinsic behavior.

  11. Ge/Si and 87Sr/86Sr tracers of weathering reactions and hydrologic pathways in a tropical granitoid system

    USGS Publications Warehouse

    Derry, L.A.; Pett-Ridge, J. C.; Kurtz, A.C.; Troester, J.W.

    2006-01-01

    Ge/Si and 87Sr/86Sr data from primary and secondary minerals, soil waters, and stream waters in a tropical granitoid catchment quantitatively reflect mineral alteration reactions that occur at different levels within the bedrock-saprolite-soil zone. Near the bedrock-saprolite interface, plagioclase to kaolinite reaction yields low Ge/Si and 87Sr/86Sr. Higher in the regolith column, biotite weathering and kaolinite dissolution drive Ge/Si and 87Sr/86Sr to high values. Data from streams at base flow sample the bedrock-saprolite interface zone, while at high discharge solutes are derived from upper saprolite-soil zone. Coupled Ge/Si and 87Sr/86Sr can be effective tools for quantifying the importance of specific weathering reactions, and for geochemical hydrograph separation. ?? 2005 Elsevier B.V. All rights reserved.

  12. Elucidating the Reaction Pathways in the Synthesis of Organolead Trihalide Perovskite for High-Performance Solar Cells

    PubMed Central

    Wang, Baohua; Young Wong, King; Xiao, Xudong; Chen, Tao

    2015-01-01

    The past two years have witnessed unprecedentedly rapid development of organic–inorganic halide perovskite–based solar cells. The solution–processability and high efficiency make this technology extraordinarily attractive. The intensive investigations have accumulated rich experiences in the perovskite fabrication; while the mechanism of the chemical synthesis still remains unresolved. Here, we set up the chemical equation of the synthesis and elucidate the reactions from both thermodynamic and kinetic perspectives. Our study shows that gaseous products thermodynamically favour the reaction, while the activation energy and “collision” probability synergistically determine the reaction rate. These understandings enable us to finely tune the crystal size for high-quality perovskite film, leading to a record fill factor among similar device structures in the literature. This investigation provides a general strategy to explore the mechanism of perovskite synthesis and benefits the fabrication of high–efficiency perovskite photoactive layer. PMID:26020476

  13. Relevance of the H2 + O reaction pathway for the surface formation of interstellar water. Combined experimental and modeling study

    NASA Astrophysics Data System (ADS)

    Lamberts, T.; Cuppen, H. M.; Fedoseev, G.; Ioppolo, S.; Chuang, K.-J.; Linnartz, H.

    2014-10-01

    The formation of interstellar water is commonly accepted to occur on the surfaces of icy dust grains in dark molecular clouds at low temperatures (10-20 K), involving hydrogenation reactions of oxygen allotropes. As a result of the large abundances of molecular hydrogen and atomic oxygen in these regions, the reaction H2 + O has been proposed to contribute significantly to the formation of water as well. However, gas-phase experiments and calculations, as well as solid-phase experimental work contradict this hypothesis. Here, we use precisely executed temperature-programmed desorption (TPD) experiments in an ultra-high vacuum setup combined with kinetic Monte Carlo simulations to establish an upper limit of the water production starting from H2 and O. These reactants were brought together in a matrix of CO2 in a series of (control) experiments at different temperatures and with different isotopological compositions. The water detected with the quadrupole mass spectrometer upon TPD was found to originate mainly from contamination in the chamber itself. However, if water is produced in small quantities on the surface through H2 + O, this can only be explained by a combined classical and tunneled reaction mechanism. An absolutely conservative upper limit for the reaction rate was derived with a microscopic kinetic Monte Carlo model that converts the upper limit into the highest possible reaction rate. Incorporating this rate into simulation runs for astrochemically relevant parameters shows that the upper limit to the contribution of the reaction H2 + O in OH, and hence water formation, is 11% in dense interstellar clouds. Our combined experimental and theoretical results indicate, however, that this contribution is most likely much lower.

  14. Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

    PubMed

    Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

    2016-02-11

    The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br. PMID:26766412

  15. Effects of Interface Coating and Nitride Enhancing Additive on Properties of Hi-Nicalon SiC Fiber Reinforced Reaction-Bonded Silicon Nitride Composites

    NASA Technical Reports Server (NTRS)

    Bhatt, Ramakrishana T.; Hull, David R.; Eldridge, Jeffrey I.; Babuder, Raymond

    2000-01-01

    Strong and tough Hi-Nicalon SiC fiber reinforced reaction-bonded silicon nitride matrix composites (SiC/ RBSN) have been fabricated by the fiber lay-up approach. Commercially available uncoated and PBN, PBN/Si-rich PBN, and BN/SiC coated SiC Hi-Nicalon fiber tows were used as reinforcement. The composites contained approximately 24 vol % of aligned 14 micron diameter SiC fibers in a porous RBSN matrix. Both one- and two-dimensional composites were characterized. The effects of interface coating composition, and the nitridation enhancing additive, NiO, on the room temperature physical, tensile, and interfacial shear strength properties of SiC/RBSN matrix composites were evaluated. Results indicate that for all three coated fibers, the thickness of the coatings decreased from the outer periphery to the interior of the tows, and that from 10 to 30 percent of the fibers were not covered with the interface coating. In the uncoated regions, chemical reaction between the NiO additive and the SiC fiber occurs causing degradation of tensile properties of the composites. Among the three interface coating combinations investigated, the BN/SiC coated Hi-Nicalon SiC fiber reinforced RBSN matrix composite showed the least amount of uncoated regions and reasonably uniform interface coating thickness. The matrix cracking stress in SiC/RBSN composites was predicted using a fracture mechanics based crack bridging model.

  16. Muonium addition reactions in the gas phase: Quantum tunneling in Mu+C2H4 and Mu+C2D4

    NASA Astrophysics Data System (ADS)

    Garner, David M.; Fleming, Donald G.; Arseneau, Donald J.; Senba, Masayoshi; Reid, Ivan D.; Mikula, Randall J.

    1990-08-01

    The reaction kinetics for the addition of the muonium (Mu=μ+e-) atom to C2H4 and C2D4 have been measured over the temperature range 150-500 K at (N2) moderator pressures near 1 atm. A factor of about 8 variation in moderator pressure was carried out for C2H4, with no significant change seen in the apparent rate constant kapp, which is therefore taken to be at the high pressure limit, yielding the bimolecular rate constant kMu for the addition step. This is also expected from the nature of the μSR technique employed, which, in favorable cases, gives kapp=kMu at any pressure. Comparisons with the H atom data of Lightfoot and Pilling, and Sugawara et al. and the D atom data of Sugawara et al. reveal large isotope effects. Only at the highest temperatures, near 500 K, is kMu/kH given by its classical value of 2.9, from the mean velocity dependence of the collision rate but at the lowest temperatures kMu/kH≳30/1 is seen, reflecting the pronounced tunneling of the much lighter Mu atom (mμ=1/9 mp). The present Mu results should provide accurate tests of reaction theories on currently available ab initio surfaces.

  17. Complete active space second order perturbation theory (CASPT2) study of N({sup 2}D) + H{sub 2}O reaction paths on D{sub 1} and D{sub 0} potential energy surfaces: Direct and roaming pathways

    SciTech Connect

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-10-21

    We report reaction paths starting from N({sup 2}D) + H{sub 2}O for doublet spin states, D{sub 0} and D{sub 1}. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H{sub 2}ON → H–O(H)N → H–HON → NO({sup 2}Π) + H{sub 2}, (2) cis-HNOH → HNO–H → H–HNO → NO + H{sub 2}, (3) H{sub 2}NO → H–HNO → HNO–H → trans-HNOH, are confirmed on the D{sub 0} surface.

  18. First-principles molecular dynamics simulations of condensed-phase V-type nerve agent reaction pathways and energy barriers.

    PubMed

    Gee, Richard H; Kuo, I-Feng W; Chinn, Sarah C; Raber, Ellen

    2012-03-14

    Computational studies of condensed-phase chemical reactions are challenging in part because of complexities in understanding the effects of the solvent environment on the reacting chemical species. Such studies are further complicated due to the demanding computational resources required to implement high-level ab initio quantum chemical methods when considering the solvent explicitly. Here, we use first-principles molecular dynamics simulations to examine condensed-phase decontamination reactions of V-type nerve agents in an explicit aqueous solvent. Our results include a detailed study of hydrolysis, base-hydrolysis, and nucleophilic oxidation of both VX and R-VX, as well as their protonated counterparts (i.e., VXH(+) and R-VXH(+)). The decontamination mechanisms and chemical reaction energy barriers, as determined from our simulations, are found to be in good agreement with experiment. The results demonstrate the applicability of using such simulations to assist in understanding new decontamination technologies or other applications that require computational screening of condensed-phase chemical reaction mechanisms. PMID:22298156

  19. A crossed molecular beam and ab initio investigation of the exclusive methyl loss pathway in the gas phase reaction of boron monoxide (BO; X2Σ+) with dimethylacetylene (CH3CCCH3; X1A(1g)).

    PubMed

    Kaiser, Ralf I; Maity, Surajit; Dangi, Beni B; Su, Yuan-Siang; Sun, B J; Chang, Agnes H H

    2014-01-21

    The crossed molecular beam reaction of boron monoxide ((11)BO; X(2)Σ(+)) with dimethylacetylene (CH3CCCH3; X(1)A(1g)) was investigated at a collision energy of 23.9 ± 1.5 kJ mol(-1). The scattering dynamics were suggested to be indirect (complex forming reaction) and were initiated by the addition of (11)BO(X(2)Σ(+)) with the radical center located at the boron atom to the π electron density at the acetylenic carbon-carbon triple bond without entrance barrier leading to cis-trans(11)BOC4H6 doublet radical intermediates. cis-(11)BOC4H6 underwent cis-trans isomerization followed by unimolecular decomposition via a methyl group (CH3) loss forming 1-propynyl boron monoxide (CH3CC(11)BO) in an overall exoergic reaction (experimental: -91 ± 22 kJ mol(-1); theoretical: -105 ± 9 kJ mol(-1); NIST: -104 ± 12 kJ mol(-1)) via a tight exit transition state; trans-(11)BOC4H6 was found to lose a methyl group instantaneously. Neither atomic nor molecular hydrogen loss pathways were detectable. The experimental finding of an exclusive methyl loss pathway gains full support from our computational study predicting a methyl group versus atomic hydrogen loss branching ratio of 99.99% to 0.01% forming 1-propynyl boron monoxide (CH3CC(11)BO) and 1-methyl-propadienyl boron monoxide (CH3((11)BO)CCCH2), respectively. PMID:24281672

  20. The preparation of large surface area lanthanum based perovskite supports for AuPt nanoparticles: tuning the glycerol oxidation reaction pathway by switching the perovskite B site.

    PubMed

    Evans, Christopher D; Kondrat, Simon A; Smith, Paul J; Manning, Troy D; Miedziak, Peter J; Brett, Gemma L; Armstrong, Robert D; Bartley, Jonathan K; Taylor, Stuart H; Rosseinsky, Matthew J; Hutchings, Graham J

    2016-07-01

    Gold and gold alloys, in the form of supported nanoparticles, have been shown over the last three decades to be highly effective oxidation catalysts. Mixed metal oxide perovskites, with their high structural tolerance, are ideal for investigating how changes in the chemical composition of supports affect the catalysts' properties, while retaining similar surface areas, morphologies and metal co-ordinations. However, a significant disadvantage of using perovskites as supports is their high crystallinity and small surface area. We report the use of a supercritical carbon dioxide anti-solvent precipitation methodology to prepare large surface area lanthanum based perovskites, making the deposition of 1 wt% AuPt nanoparticles feasible. These catalysts were used for the selective oxidation of glycerol. By changing the elemental composition of the perovskite B site, we dramatically altered the reaction pathway between a sequential oxidation route to glyceric or tartronic acid and a dehydration reaction pathway to lactic acid. Selectivity profiles were correlated to reported oxygen adsorption capacities of the perovskite supports and also to changes in the AuPt nanoparticle morphologies. Extended time on line analysis using the best oxidation catalyst (AuPt/LaMnO3) produced an exceptionally high tartronic acid yield. LaMnO3 produced from alternative preparation methods was found to have lower activities, but gave comparable selectivity profiles to that produced using the supercritical carbon dioxide anti-solvent precipitation methodology. PMID:27074316

  1. Dissociation pathways of a single dimethyl disulfide on Cu(111): Reaction induced by simultaneous excitation of two vibrational modes

    SciTech Connect

    Motobayashi, Kenta; Kim, Yousoo; Arafune, Ryuichi; Ohara, Michiaki; Ueba, Hiromu; Kawai, Maki

    2014-05-21

    We present a novel reaction mechanism for a single adsorbed molecule that proceeds via simultaneous excitation of two different vibrational modes excited by inelastic tunneling electrons from a scanning tunneling microscope. Specifically, we analyze the dissociation of a single dimethyl disulfide (DMDS, (CH{sub 3}S){sub 2}) molecule on Cu(111) by using a versatile theoretical method, which permits us to simulate reaction rates as a function of sample bias voltage. The reaction is induced by the excitation of C-H stretch and S-S stretch modes by a two-electron process at low positive bias voltages. However, at increased voltages, the dissociation becomes a single-electron process that excites a combination mode of these stretches, where excitation of the C-H stretch is the energy source and excitation of the S-S stretch mode enhances the anharmonic coupling rate. A much smaller dissociation yield (few orders of magnitude) at negative bias voltages is understood in terms of the projected density of states of a single DMDS on Cu(111), which reflects resonant excitation through the molecular orbitals.

  2. A general mechanism for the copper- and silver-catalyzed olefin aziridination reactions: concomitant involvement of the singlet and triplet pathways.

    PubMed

    Maestre, Lourdes; Sameera, W M C; Díaz-Requejo, M Mar; Maseras, Feliu; Pérez, Pedro J

    2013-01-30

    The olefin aziridination reactions catalyzed by copper and silver complexes bearing hydrotris(pyrazolyl)borate (Tp(x)) ligands have been investigated from a mechanistic point of view. Several mechanistic probe reactions were carried out, specifically competition experiments with p-substituted styrenes, stereospecificity of olefins, effects of the radical inhibitors, and use of a radical clock. Data from these experiments seem to be contradictory, as they do not fully support the previously reported concerted or stepwise mechanisms. But theoretical calculations have provided the reaction profiles for both the silver and copper systems with different olefins to satisfy all experimental data. A mechanistic proposal has been made on the basis of the information that we collected from experimental and theoretical studies. In all cases, the reaction starts with the formation of a metal-nitrene species that holds some radical character, and therefore the aziridination reaction proceeds through the radical mechanism. The silver-based systems however hold a minimum energy crossing point (MECP) between the triplet and closed-shell singlet surfaces, which induce the direct formation of the aziridines, and stereochemistry of the olefin is retained. In the case of copper, a radical intermediate is formed, and this intermediate constitutes the starting point for competition steps involving ring-closure (through a MECP between the open-shell singlet and triplet surfaces) or carbon-carbon bond rotation, and explains the loss of stereochemistry with a given substrate. Overall, all the initially contradictory experimental data fit in a mechanistic proposal that involves both the singlet and the triplet pathways. PMID:23276287

  3. Mixtures of l-Amino Acids as Reaction Medium for Formation of Iron Nanoparticles: The Order of Addition into a Ferrous Salt Solution Matters

    PubMed Central

    Šišková, Karolína M.; Machala, Libor; Tuček, Jiři; Kašlík, Josef; Mojzeš, Peter; Zbořil, Radek

    2013-01-01

    Owing to Mössbauer spectroscopy, an advanced characterization technique for iron-containing materials, the present study reveals previously unknown possibilities using l-amino acids for the generation of magnetic particles. Based on our results, a simple choice of the order of l-amino acids addition into a reaction mixture containing ferrous ions leads to either superparamagnetic ferric oxide/oxyhydroxide particles, or magnetically strong Fe0-Fe2O3/FeOOH core-shell particles after chemical reduction. Conversely, when ferric salts are employed with the addition of selected l-amino acids, only Fe0-Fe2O3/FeOOH core-shell particles are observed, regardless of the addition order. We explain this phenomenon by a specific transient/intermediate complex formation between Fe2+ and l-glutamic acid. This type of complexation prevents ferrous ions from spontaneous oxidation in solutions with full air access. Moreover, due to surface-enhanced Raman scattering spectroscopy we show that the functional groups of l-amino acids are not destroyed during the borohydride-induced reduction. These functionalities can be further exploited for (i) attachment of l-amino acids to the as-prepared magnetic particles, and (ii) for targeted bio- and/or environmental applications where the surface chemistry needs to be tailored and directed toward biocompatible species. PMID:24071943

  4. Addition Reactions of Me3 SiCN with Aldehydes Catalyzed by Aluminum Complexes Containing in their Coordination Sphere O, S, and N Ligands.

    PubMed

    Yang, Zhi; Yi, Yafei; Zhong, Mingdong; De, Sriman; Mondal, Totan; Koley, Debasis; Ma, Xiaoli; Zhang, Dongxiang; Roesky, Herbert W

    2016-05-10

    The reaction of one equivalent of LAlH2 (1; L=HC(CMeNAr)2 , Ar=2,6-iPr2 C6 H3 , β-diketiminate ligand) with two equivalents of 2-mercapto-4,6-dimethylpyrimidine hydrate resulted in LAl[(μ-S)(m-C4 N2 H)(CH2 )2 ]2 (2) in good yield. Similarly, when N-2-pyridylsalicylideneamine, N-(2,6-diisopropylphenyl)salicylaldimine, and ethyl 3-amino-4,5,6,7-tetrahydrobenzo[b]thiophene-2-carboxylate were used as starting materials, the corresponding products LAl[(μ-O)(o-C6 H4 )CN(C5 NH4 )]2 (3), LAlH[(μ-O)(o-C4 H4 )CN(2,6-iPr2 C6 H3 )] (4), and LAl[(μ-NH)(o-C8 SH8 )(COOC2 H5 )]2 (5) were isolated. Compounds 2-5 were characterized by (1) H and (13) C NMR spectroscopy as well as by single-crystal X-ray structural analysis. Surprisingly, compounds 2-5 exhibit good catalytic activity in addition reactions of aldehydes with trimethylsilyl cyanide (TMSCN). PMID:27062461

  5. Decolorization of azo dye C.I. Reactive Black 5 by ozonation in aqueous solution: influencing factors, degradation products, reaction pathway and toxicity assessment.

    PubMed

    Zheng, Qing; Dai, Yong; Han, Xiangyun

    2016-01-01

    In this study, ozonation treatment of C.I. Reactive Black 5 (RB5) was investigated at various operating parameters. The results showed that the aqueous solution initially containing 200 mg/L RB5 was quickly decolorized at pH 8.0 with an ozone dose of 3.2 g/h. Reaction intermediates with m/z 281, 546, 201, 350, 286 and 222 were elucidated using liquid chromatography-mass spectrometry, while sulfate ion, nitrate ion and three carboxylic acids (i.e., oxalic acid, formic acid, and acetic acid) were identified by ion exchange chromatography. Thus, the cleavage of the azo bond and the introduction of OH groups in the corresponding positions were proposed as the predominant reaction pathway. The detachment of sulfonic groups was also commonly observed during the ozonation treatment. The proposed degradation mechanism was confirmed by frontier electron density calculations, suggesting the feasibility of predicting the major events in the whole ozonation process with the computational method. Compared with RB5 degradation, the reduction of total organic carbon (TOC) proceeded much more slowly, and approximately 54% TOC was removed after 4 h of ozonation. Acute toxicity tests with Photobacterium phosphoreum showed that the toxicity of reaction solution was firstly increased and then decreased to a negligible level after 160 min. PMID:27054721

  6. 15N electron nuclear double resonance of the primary donor cation radical P+.865 in reaction centers of Rhodopseudomonas sphaeroides: additional evidence for the dimer model.

    PubMed Central

    Lubitz, W; Isaacson, R A; Abresch, E C; Feher, G

    1984-01-01

    Four 15N hyperfine coupling constants, including signs, have been measured by electron nuclear double resonance (ENDOR) and electron nuclear nuclear triple resonance (TRIPLE) for the bacteriochlorophyll a radical cation, BChla+., in vitro and for the light-induced primary donor radical cation, P+.865, in reaction centers of Rhodopseudomonas sphaeroides R-26. A comparison of the data shows that the hyperfine coupling constants have the same sign in both radicals and are, on the average, smaller by a factor of 2 in P+.865. These results provide additional evidence that P+.865 is a bacteriochlorophyll dimer and are in contradiction with the monomer structure of P+.865 recently proposed by O'Malley and Babcock. The reduction factors of the individual 15N couplings, together with the evidence from proton ENDOR data and molecular orbital calculations, indicate a dimer structure in which only two rings (either I and I or III and III) of the bacteriochlorophyll macrocycles overlap. PMID:6096857

  7. Quantum Chemistry Study of Cycloaddition Pathways for the Reaction of o-Benzyne with Fullerenes and Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Han, Jie; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Functionalization of fullerenes via the [2+2] cycloaddition reaction with o-benzyne has been demonstrated in the laboratory. In contrast, [2+4) cycloaddition products are formed when benzyne reacts with planar polycyclic aromatic hydrocarbons. Using density functional theory (DFT) calculations with Becke's hybrid functional and small contracted gaussian basis sets, we are able to reproduce these product preferences. The objective of this work is to explore the functionalization of carbon nanotubes. We have studied o-benzyne cycloaddition products with a [14,0] single-walled nanotube. We find both the [2+2] and [2+4] adducts to be stable, with the latter product being somewhat favored.

  8. 2,4,6,8-Tetrachlorodibenzothiophene in the Newark Bay Estuary: the likely source and reaction pathways.

    PubMed

    Parette, Robert; Pearson, Wendy N

    2014-09-01

    Historic industrial activity along the Newark Bay Estuary has resulted in pollution from a number of contaminants; one of which is 2,4,6,8-tetrachlorodibenzothiophene (2,4,6,8-TCDT), a unique chemical contaminant whose origins have not been adequately explained. This research demonstrates that the probable source of 2,4,6,8-TCDT was the chlorination of phenol produced via the sulfonation method. Thiophenol, the major impurity in this type of phenol, was likely converted to 2,4,6,8-TCDT through one or more pathways during the production of 2,4-dichlorophenol, 2,4-dichlorophenoxyacetic acid (2,4-D), or 2,4,6-trichlorophenol. From a mass balance standpoint, production of these chemicals at an industrial plant along the Passaic River could account for the 2,4,6,8-TCDT in the Newark Bay Estuary. PMID:24997913

  9. Diminished CAGE Effect in {p}-H2: IR Identification of Intermediates in Addition Reactions of CL Atom with Unsaturated Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Lee, Yuan-Pern; Bahou, Mohammed; Golec, Barbara

    2011-06-01

    We report infrared absorption spectra of several free radicals produced upon reaction of Cl atoms with unsaturated hydrocarbons isolated in solid {p}-H2. Cl atoms were produced by in situ photodissociation of Cl2 isolated in solid {p}-H2 at 365 nm. In experiments with the Cl2/C6H6/{p}-H2 matrices, intense absorption features at 617.0, 719.8, 956.0, and 1430.5 Cm-1 and weaker ones at 577.1, 833.6, 876.8, 833.6, 983.0, 993.5, 1008.0, 1026.4, 1112.5, 1118.5, 1179.0, 1406.5, 1509.4, 2967.2, 3054.3, 3063.4, 3070.9, and 3083.9 Cm-1 appeared upon irradiation of the matrix at 365 nm and increased in intensity upon subsequent annealing of the matrix at 4.8 K for a few minutes. By comparison of vibrational wavenumbers and deuterium isotopic shifts predicted with the B3PW91 and MPW1PW91/aug-cc-pVTZ methods, these features are readily assigned to the σ-complex of ClC6H6 (chlorocyclohexadienyl radical), rather than the previously proposed π-complex. In experiments with the Cl2/C2H2/{p}-H2 matrices, the 1-chloroethyl radicals (CHClCH3) and chloroethene (C2H3Cl) are identified as the main products of the Cl + C2H2 reaction in solid {p}-H2. The assignments of IR absorption lines at 738.2, 1027.6, 1283.4, 1377.1, 1426.6, 1442.6, and 2861.2 Cm-1 to 1-chloroethyl radicals are based on comparison of the observed vibrational wavenumbers and 13C- and D-isotopic shifts with those predicted with the B3LYP and MP2/aug-cc-pVDZ methods. These results indicate that the primary products of the addition reaction Cl + C2H2, the 2-chlorovinyl radicals, are unstable; they react readily with {p}-H2 to form CHClCH3 and C2H3Cl. If time permits, other examples such as Cl + 1, 3-butadien and H + C6H6 or C6H5Cl will be discussed. These results serve as excellent examples to demonstrate that the diminished cage effect of solid {p}-H2 makes production of free radicals via bimolecular reactions feasible.

  10. Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations

    PubMed Central

    2015-01-01

    AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N1-methyl adenine (1-meA) catalyzed by AlkB after the formation of FeIV–oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH– has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH– ligand on the hydrogen abstraction by the FeIV–oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH– ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe–O–C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H2O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme FeII and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB. PMID:25400523

  11. Coprecipitation of (14)C and Sr with carbonate precipitates: The importance of reaction kinetics and recrystallization pathways.

    PubMed

    Hodkin, David J; Stewart, Douglas I; Graham, James T; Burke, Ian T

    2016-08-15

    This study investigated the simultaneous removal of Sr(2+) and (14)CO3(2-) from pH>12 Ca(OH)2 solution by the precipitation of calcium carbonate. Initial Ca(2+):CO3(2-) ratios ranged from 10:1 to 10:100 (mM:mM). Maximum removal of (14)C and Sr(2+) both occurred in the system containing 10mM Ca(2+) and 1mM CO3(2-) (99.7% and 98.6% removal respectively). A kinetic model is provided that describes (14)C and Sr removal in terms of mineral dissolution and precipitation reactions. The removal of (14)C was achieved during the depletion of the initial TIC in solution, and was subsequently significantly affected by recrystallization of the calcite precipitate from an elongate to isotropic morphology. This liberated >46% of the (14)C back to solution. Sr(2+) removal occurred as Ca(2+) became depleted in solution and was not significantly affected by the recrystallization process. The proposed reaction could form the basis for low cost remediation scheme for (90)Sr and (14)C in radioactively contaminated waters (<$0.25 reagent cost per m(3) treated). PMID:27104491

  12. PSI Mehler reaction is the main alternative photosynthetic electron pathway in Symbiodinium sp., symbiotic dinoflagellates of cnidarians.

    PubMed

    Roberty, Stéphane; Bailleul, Benjamin; Berne, Nicolas; Franck, Fabrice; Cardol, Pierre

    2014-10-01

    Photosynthetic organisms have developed various photoprotective mechanisms to cope with exposure to high light intensities. In photosynthetic dinoflagellates that live in symbiosis with cnidarians, the nature and relative amplitude of these regulatory mechanisms are a matter of debate. In our study, the amplitude of photosynthetic alternative electron flows (AEF) to oxygen (chlororespiration, Mehler reaction), the mitochondrial respiration and the Photosystem I (PSI) cyclic electron flow were investigated in strains belonging to three clades (A1, B1 and F1) of Symbiodinium. Cultured Symbiodinium strains were maintained under identical environmental conditions, and measurements of oxygen evolution, fluorescence emission and absorption changes at specific wavelengths were used to evaluate PSI and PSII electron transfer rates (ETR). A light- and O2 -dependent ETR was observed in all strains. This electron transfer chain involves PSII and PSI and is insensitive to inhibitors of mitochondrial activity and carbon fixation. We demonstrate that in all strains, the Mehler reaction responsible for photoreduction of oxygen by the PSI under high light, is the main AEF at the onset and at the steady state of photosynthesis. This sustained photosynthetic AEF under high light intensities acts as a photoprotective mechanism and leads to an increase of the ATP/NADPH ratio. PMID:24975027

  13. Combined crossed molecular beam and ab initio investigation of the multichannel reaction of boron monoxide (BO; X2Σ+) with Propylene (CH3CHCH2; X1A'): competing atomic hydrogen and methyl loss pathways.

    PubMed

    Maity, Surajit; Dangi, Beni B; Parker, Dorian S N; Kaiser, Ralf I; An, Yi; Sun, Bing-Jian; Chang, A H H

    2014-10-16

    The reaction dynamics of boron monoxide ((11)BO; X(2)Σ(+)) with propylene (CH(3)CHCH(2); X(1)A') were investigated under single collision conditions at a collision energy of 22.5 ± 1.3 kJ mol(-1). The crossed molecular beam investigation combined with ab initio electronic structure and statistical (RRKM) calculations reveals that the reaction follows indirect scattering dynamics and proceeds via the barrierless addition of boron monoxide radical with its radical center located at the boron atom. This addition takes place to either the terminal carbon atom (C1) and/or the central carbon atom (C2) of propylene reactant forming (11)BOC(3)H(6) intermediate(s). The long-lived (11)BOC(3)H(6) doublet intermediate(s) underwent unimolecular decomposition involving at least three competing reaction mechanisms via an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group elimination to form cis-/trans-1-propenyl-oxo-borane (CH(3)CHCH(11)BO), 3-propenyl-oxo-borane (CH(2)CHCH(2)(11)BO), and ethenyl-oxo-borane (CH(2)CH(11)BO), respectively. Utilizing partially deuterated propylene (CD(3)CHCH(2) and CH(3)CDCD(2)), we reveal that the loss of a vinyl hydrogen atom is the dominant hydrogen elimination pathway (85 ± 10%) forming cis-/trans-1-propenyl-oxo-borane, compared to the loss of a methyl hydrogen atom (15 ± 10%) leading to 3-propenyl-oxo-borane. The branching ratios for an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group loss are experimentally derived to be 26 ± 8%:5 ± 3%:69 ± 15%, respectively; these data correlate nicely with the branching ratios calculated via RRKM theory of 19%:5%:75%, respectively. PMID:25238644

  14. Effect of sodium acetate additive in successive ionic layer adsorption and reaction on the performance of CdS quantum-dot-sensitized solar cells

    NASA Astrophysics Data System (ADS)

    Liu, I.-Ping; Chen, Liang-Yih; Lee, Yuh-Lang

    2016-09-01

    Sodium acetate (NaAc) is utilized as an additive in cationic precursors of the successive ionic layer adsorption and reaction (SILAR) process to fabricate CdS quantum-dot (QD)-sensitized photoelectrodes. The effects of the NaAc concentration on the deposition rate and distribution of QDs in mesoporous TiO2 films, as well as on the performance of CdS-sensitized solar cells are studied. The experimental results show that the presence of NaAc can significantly accelerate the deposition of CdS, improve the QD distribution across photoelectrodes, and thereby, increase the performance of solar cells. These results are mainly attributed to the pH-elevation effect of NaAc to the cationic precursors which increases the electrostatic interaction of the TiO2 film to cadmium ions. The light-to-energy conversion efficiency of the CdS-sensitized solar cell increases with increasing concentration of the NaAc and approaches a maximum value (3.11%) at 0.05 M NaAc. Additionally, an ionic exchange is carried out on the photoelectrode to transform the deposited CdS into CdS1-xSex ternary QDs. The light-absorption range of the photoelectrode is extended and an exceptional power conversion efficiency of 4.51% is achieved due to this treatment.

  15. Stabilization of nickel by aluminum- and iron-rich ceramic materials: Reaction pathways and product leaching behavior

    NASA Astrophysics Data System (ADS)

    Shih, Kaimin

    The feasibility of stabilizing nickel-laden sludge with commonly available ceramic precursors was investigated. Nickel aluminate spinel (NiAl2O 4) was the immobilization phase produced when NiO was sintered with aluminum-rich precursors, including gamma-Al2O3, corundum, kaolinite and mullite. Analogously, nickel ferrite spinel (NiFe2O 4) was the stable phase produced by firing NiO with hematite, as an iron-rich precursor. By using gamma-Al2O3 as the precursor, the NiAl2O4 formation mechanism was a reaction between NiO and gamma-Al2O3 at lower temperatures (990°C), while the reaction was between NiO and corundum at higher temperatures. When sintering NiO with kaolinite, nickel can be efficiently incorporated in NiAl2O4 by two mechanisms: (i) a low temperature reaction with a defect spinel, and (ii) a high temperature reaction with mullite. Nickel-incorporation efficiency was quantitatively estimated by powder X-ray Diffraction (XRD) analysis. With 3-hours sintering, NiFe2O 4 (trevorite) formation took place above 600°C with more than 95% nickel incorporation efficiency achieved above 1000°C; while NiAl 2O4 crystallized above 1000°C with an efficiency >90% above 1250°C. In using kaolinite and mullite as precursors, nickel is not incorporated in any silicon-containing phase. The kinetic factors responsible for nickel incorporation efficiency from different precursors were revealed through investigation of product microstructures. Moreover, four raw material mixing procedures were compared, with the ball-milled slurries demonstrating the highest nickel incorporation efficiency. Prolonged leach tests of NiO, NiAl2O4, NiFe 2O4 and sintered kaolinite + NiO samples were carried out using the TCLP extraction fluids #1 and #2 to evaluate the durability of sintered products. Over longer leaching periods, spinel proved superior to NiO for immobilization of nickel, although NiFe2O4 appears slightly more leachable than NiAl2O4. With TCLP extraction fluid #1 (pH 4.9), the

  16. Brønsted acid-base reactions with anhydrous sulfamates as a pathway to [SO3N]3--containing compounds: Preparation of Li3SO3N

    NASA Astrophysics Data System (ADS)

    Kurzman, Joshua A.; Jouan, Gauthier; Courty, Matthieu; Palacín, M. Rosa; Armand, Michel; Recham, Nadir

    2013-11-01

    Li3SO3N has been prepared by the mechanochemical reaction between lithium sulfamate (LiSO3NH2) and lithium amide or lithium hydride. This is the first example of an anhydrous compound containing the rare [SO3N]3- polyanion. Li3SO3N adopts the low-temperature Pmn2β structure of isoelectronic Li3PO4. Structural refinement from neutron powder diffraction data supports disordering of nitrogen over two of the three anion sites, although a fully disordered model cannot be conclusively refuted. While the compound is a poor ionic conductor, it is electrochemically stable to at least 5 V vs. Li+/Li0. This simple mechanochemical pathway should be suitable for preparing a host of other alkali-rich nitrogen-containing polyanionic compounds.

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

    PubMed

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

    2014-12-31

    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

  18. Two pathways of proton transfer reaction to (triphos)Cu(η(1)-BH4) via a dihydrogen bond [triphos = 1,1,1-tris(diphenylphosphinomethyl)ethane].

    PubMed

    Golub, I E; Filippov, O A; Belkova, N V; Epstein, L M; Rossin, A; Peruzzini, M; Shubina, E S

    2016-05-31

    The interaction of the η(1)-tetrahydroborate copper(i) complex (triphos)Cu(η(1)-BH4) () with proton donors [CF3CH2OH (TFE), (CF3)2CHOH (HFIP), (CF3)3COH (PFTB), PhOH, p-NO2C6H4OH (PNP), p-NO2C6H4N[double bond, length as m-dash]NC6H4OH (PNAP), CF3OH] was a subject of a combined IR spectroscopic and theoretical investigation. Spectral (Δν) and thermodynamic (ΔH) parameters of dihydrogen bond (DHB) formation were determined experimentally. The terminal hydride ligand (characterized by the basicity factor Ej(BH) = 0.87 ± 0.01) is found to be a site of proton transfer which begins with nucleophilic substitution of BH4(-) by the alcohol oxygen atom on the copper center (BH pathway). The activation barrier computed for (CF3)2CHOH in CH2Cl2 - ΔG = 20.6 kcal mol(-1) - is in good agreement with the experimental value (ΔG = 20.0 kcal mol(-1)). An abnormal dependence of the reaction rate on the proton donor strength found experimentally in dichloromethane is explained computationally on the basis of the variation of the structural and energetic details of this process with the proton donor strength. In the second reaction mechanism found (CuH pathway), DHB complexes with the initial ROH coordination to the bridging hydride lead to B-Hbr bond cleavage with BH3 elimination. "Copper assistance" via the CuO interaction is not involved. This mechanism can be evoked to explain the occurrence of proton transfer in coordinating solvents. PMID:27163554

  19. The electrochemical reactions of pure In with Li and Na: anomalous electrolyte decomposition, benefits of FEC additive, phase transitions and electrode performance

    SciTech Connect

    Hawks, Samantha A; Baggetto, Loic; Bridges, Craig A; Veith, Gabriel M

    2014-01-01

    Indium thin films are evaluated as an anode material for Li-ion and Na-ion batteries (theoretical capacities of 1012 mAh g-1 for Li and 467 mAh g-1 for Na). The native surface oxides are responsible for the anomalous electrolyte decomposition during the first cycle while oxidized In species are found to be responsible for the electrolyte decomposition during the subsequent cycles. The presence of 5wt% FEC electrolyte additive suppresses the occurrence of the anomalous electrolyte decomposition during the first cycle but is not sufficient to prevent the decomposition upon further cycling from 0 to 2 V. Prevention of the anomalous decomposition can be achieved by restricting the charge cut-off, for instance at 1.1 V, or by using larger amounts of FEC. The In films show moderately good capacity retention with storage capacities when cycled with Li (950 mAh g-1) but significantly less when cycled with Na (125 mAh g-1). XRD data reveal that several known Li-In phases (i.e LiIn, Li3In2, LiIn2 and Li13In3) form during the electrochemical reaction. In contrast, the reaction with Na is severely limited. The largest amount of inserted Na is evidenced for cells short-circuited 40 hrs at 65C, for which the XRD data show the coexistence of NaIn, In, and an unknown phase. During cycling, mechanical degradation due to repeated expansion/shrinkage, evidenced by SEM, coupled with SEI formation is the primary source of the capacity fade. Finally, we show that the In thin films exhibit very high rate capability for both Li (100 C) and Na (30 C).

  20. Reactions of D-glucose with phenolic amino acids: further insights into the competition between Maillard and Pictet-Spengler condensation pathways.

    PubMed

    Manini, Paola; Napolitano, Alessandra; d'Ischia, Marco

    2005-12-30

    The reactions of 5-S-cysteinyldopa, L-alpha-methyldopa and DL-m-tyrosine with D-glucose were investigated at 90 degrees C in phosphate buffer at pH ranging from 5.0 to 9.0. Whereas gave mainly the double Maillard condensation product N,N'-bis(1''-deoxy-D-fructos-1''-yl)-5-S-cysteinyldopa, as an inseparable mixture of beta-D-fructopyranosyl and alpha,beta-D-fructofuranosyl derivatives, 2 and 3 gave both Maillard and Pictet-Spengler products, although to different extents and with different regio- and stereochemistry. A peculiar pattern of reactivity was displayed by which gave, besides the Maillard product and the expected 6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline C-1 diastereoisomeric pairs, the unprecedented 7,8-dihydroxy-1,2,3,4-tetrahydroisoquinoline derivative via the ortho cyclization pathway. Pictet-Spengler cyclization of 2 and 3 proceeded with Felkin-Anh-type asymmetric induction, favouring the 1R isomer throughout the pH range 5.0-9.0. These results, which highlight the first example of carbohydrate-derived 7,8-dihydroxytetrahydroisoquinoline, provide new insights into the factors governing competition between Maillard and Pictet-Spengler condensation pathways. PMID:16229826

  1. Poly-pathway model, a novel approach to simulate multiple metabolic states by reaction network-based model - Application to amino acid depletion in CHO cell culture.

    PubMed

    Hagrot, Erika; Oddsdóttir, Hildur Æsa; Gonzalez Hosta, Joan; Jacobsen, Elling W; Chotteau, Véronique

    2016-06-20

    Mammalian cell lines are characterized by a complex and flexible metabolism. A single model that could describe the variations in metabolic behavior triggered by variations in the culture conditions would be a precious tool in bioprocess development. In this paper, we introduce an approach to generate a poly-pathway model and use it to simulate diverse metabolic states triggered in response to removal, reduction or doubling of amino acids in the culture medium of an antibody-producing CHO cell line. Macro-reactions were obtained from a metabolic network via elementary flux mode enumeration and the fluxes were modeled by kinetic equations with saturation and inhibition effects from external medium components. Importantly, one set of kinetic parameters was estimated using experimental data of the multiple metabolic states. A good fit between the model and the data was obtained for the majority of the metabolites and the experimentally observed flux variations. We find that the poly-pathway modeling approach is promising for the simulation of multiple metabolic states. PMID:27060554

  2. Mechanism of the Iron(II)-Catalyzed Hydrosilylation of Ketones: Activation of Iron Carboxylate Precatalysts and Reaction Pathways of the Active Catalyst.

    PubMed

    Bleith, Tim; Gade, Lutz H

    2016-04-13

    A detailed mechanistic study of the catalytic hydrosilylation of ketones with the highly active and enantioselective iron(II) boxmi complexes as catalysts (up to >99% ee) was carried out to elucidate the pathways for precatalyst activation and the mechanism for the iron-catalyzed hydrosilylation. Carboxylate precatalysts were found to be activated by reduction of the carboxylate ligand to the corresponding alkoxide followed by entering the catalytic cycle for the iron-catalyzed hydrosilylation. An Eyring-type analysis of the temperature dependence of the enantiomeric ratio established a linear relationship of ln(S/R) and T(-1), indicating a single selectivity-determining step over the whole temperature range from -40 to +65 °C (ΔΔG(‡)sel, 233 K = 9 ± 1 kJ/mol). The rate law as well as activation parameters for the rate-determining step were derived and complemented by a Hammett analysis, radical clock experiments, kinetic isotope effect (KIE) measurements (kH/kD = 3.0 ± 0.2), the isolation of the catalytically active alkoxide intermediate, and DFT-modeling of the whole reaction sequence. The proposed reaction mechanism is characterized by a rate-determining σ-bond metathesis of an alkoxide complex with the silane, subsequent coordination of the ketone to the iron hydride complex, and insertion of the ketone into the Fe-H bond to regenerate the alkoxide complex. PMID:27013140

  3. Electron Paramagnetic Resonance Spectroscopic Study on Nonequilibrium Reaction Pathways in the Photolysis of Solid Nitromethane (CH3NO2) and D3-Nitromethane (CD3NO2).

    PubMed

    Tsegaw, Yetsedaw Andargie; Sander, Wolfram; Kaiser, Ralf I

    2016-03-10

    Thin films of nitromethane (CH3NO2) along with its isotopically labeled counterpart D3-nitromethane (CD3NO2) were photolyzed at discrete wavelength between 266 nm (4.7 eV) and 121 nm (10.2 eV) to explore the underlying mechanisms involved in the decomposition of model compounds of energetic materials in the condensed phase at 5 K. The chemical modifications of the ices were traced in situ via electron paramagnetic resonance, thus focusing on the detection of (hitherto elusive) reaction intermediates and products with unpaired electrons. These studies revealed the formation of two carbon-centered radicals [methyl (CH3), nitromethyl (CH2NO2)], one oxygen-centered radical [methoxy (CH3O)], two nitrogen-centered radicals [nitrogen monoxide (NO), nitrogen dioxide (NO2)], as well as atomic hydrogen (H). The decomposition products of these channels and the carbon-centered nitromethyl (CH2NO2) radical in particular represent crucial reaction intermediates leading via sequential molecular mass growth processes in the exposed nitromethane samples to complex organic molecules as predicted previously by dynamics calculations. The detection of the nitromethyl (CH2NO2) radical along with atomic hydrogen (H) demonstrated the existence of a high-energy decomposition pathway, which is closed under collisionless conditions in the gas phase. PMID:26863093

  4. Shift of reaction pathway by added chloride ions in the oxidation of aromatic ketones by dichloroisocyanuric acid—A kinetic study

    NASA Astrophysics Data System (ADS)

    Kumar, Y. Lakshman; Nadh, R. Venkata; Radhakrishnamurti, P. S.

    2016-03-01

    Role of added chloride ions on the shift of reaction pathway of oxidation of aromatic ketones (acetophenone, desoxybenzoin) by dichloroisocyanuric acid (DCICA) was studied in aqueous acetic acid—perchloric acid medium. Participation of enolic and protonated forms of ketones in the rate determining steps is manifested from zero and first orders with respect to the oxidant in absence and presence of added chloride ions, respectively. Positive and negative effects of acid and dielectric constant on the reaction rate were observed. The observations deduce plausible mechanisms involving (i) rate-determining formation of enol from the conjugate acid of the ketone (SH+) in the absence of added chloride ions and (ii) rapid formation of molecular chlorine species from HOCl (hydrolytic species of DCICA) in the presence of added chloride ions, which then interacts with SH+ in a rate-determining step prior to the rapid steps of product formation. The order of Arrhenius parameters substantiate the proposed plausible mechanisms based on order of reactants both in presence and absence of added chloride ions.

  5. Ab initio study of the reaction pathways for OH + C/sub 2/H/sub 4/. -->. HOCH/sub 2/CH/sub 2/. -->. products

    SciTech Connect

    Sosa, C.; Schlegel, H.B.

    1987-11-11

    The energetically favorable reaction paths for the unimolecular decomposition of the primary addition product of OH + C/sub 2/H/sub 4/ have been studied with ab initio techniques. Equilibrium geometries and transition structures were fully optimized with 3-21G and 6-31G* basis sets at the Hartree-Fock level. Heats of reaction and barrier heights have been computed with Moeller-Plesset perturbation theory up to fourth order, with and without annihilation of spin contamination. At the MP4 level barrier heights are lowered by 2-7 kcal/mol when the largest spin contaminant is removed. After the addition of OH + C/sub 2/H/sub 4/ to form the 2-hydroxyethyl radical, the most favorable reaction path (other than decomposition to reactants) is the (1,3)-hydrogen shift to form ethoxy radical followed by a dissociation into CH/sub 3/ + CH/sub 2/O. Other slightly higher energy paths include dissociation of ethoxy into H + CH/sub 3/CHO and decomposition of the 2-hydroxyethyl radical into H + HOCHCH/sub 2/.

  6. Thermodynamic and kinetic modeling of mineralogical evolution in the Soultz-sous-Forêts geothermal system: insights into the reaction pathways

    NASA Astrophysics Data System (ADS)

    Van Ngo, Viet; Lucas, Yann; Clément, Alain; Fritz, Bertrand

    2015-04-01

    The energy production from hot fractured rocks has been investigated at the Soultz-sous-Forêts EGS (Alsace, France) from nearly three decades. Three wells have been drilled up to the depth of about 5000 m in which two wells are served as the fluid production and the third as a fluid re-injection. The circulation of geothermal fluids through the fractured reservoir leads to a strong chemical nonequilibrium of the solid and aqueous phases, which potentially cause changes in porosity, permeability, and flow pathways of the geothermal reservoir. Numerous experimental and modeling studies (e.g., Dubois et al., 2000; Baldeyrou et al., 2003; Ledésert et al., 2009; Fritz et al., 2010; Ledésert et al., 2010) carried out within the framework of the Soultz-sous-Forêts system have reported that quartz, calcite and illites are formed as the major secondary phases in the main fractures. Some contributions among the above publications further indicated that calcite plays an important role in the reduction of permeability of the fractured zones and illites are considered as a characteristic product of the hydrothermal vein alteration. Therefore, it is important to predict the evolution of minerals (especially for quartz, calcite, and illites), which may potentially modify the transport properties of the geothermal reservoir (e.g., Ledésert et al., 2009; Fritz et al., 2010). Understanding the changes in mineralogy in the fractured zones is also useful to choose the reagents in order to improve the permeability of the geothermal reservoir via the chemical stimulation. The overall objectives of the current study are to (i) investigate the long-term evolution of mineralogy in the geothermal Soultz-sous-Forêts Enhanced Geothermal System (EGS), (ii) establish the relationship between different mineral groups, (iii) study the reaction pathways, and (iv) compare the thermodynamic and kinetic approaches. The numerical calculations carried out using the KINDIS numerical code were

  7. A Dual Colorimetric/Fluorescence System for Determining pH Based on the Nucleophilic Addition Reaction of an o-Hydroxymerocyanine Dye.

    PubMed

    Yue, Yongkang; Huo, Fangjun; Lee, Songyi; Yin, Caixia; Yoon, Juyoung; Chao, Jianbin; Zhang, Yongbin; Cheng, Fangqin

    2016-01-22

    Owing to their ability to monitor pH in a precise and rapid manner, optical probes have widely been developed for biological and nonbiological applications. The strategies thus far employed to determine pH rely on two types of processes including reversible protonation of amine nitrogen atoms and deprotonation of phenols. We have developed a novel dual, colorimetric/fluorescence system for determining the pH of a solution. This system utilizes an o-hydroxymerocyanine dye that undergoes a nucleophilic addition reaction that subsequently causes reversible structural changes interconverting a merocyanine to a spirocyanine and a spirocyanine to a spiropyran. It was demonstrated that the dye can be employed to measure the pH of solutions in the 2.5-5.75 and 9.6-11.8 ranges with color changes from yellow to dark blue and then to lavender. Moreover, the fluorescence response associated with the spirocyanine-spiropyran transformation of the dye occurring in alkaline solutions provides a precise method. PMID:26603952

  8. Market surveillance on non-halal additives incorporated in surimi based products using polymerase chain reaction (PCR)-southern hybridization analysis

    NASA Astrophysics Data System (ADS)

    Aravindran, S.; Sahilah, A. M.; Aminah, A.

    2014-09-01

    Halal surveillance on halal ingredients incorporated in surimi based products were studied using polymerase chain reaction (PCR)-southern hybridization on chip analysis. The primers used in this technique were targeted on mitochondria DNA (mtDNA) of cytochrome b (cyt b) gene sequence which able to differentiate 7 type (beef, chicken, duck, goat, buffalo, lamb and pork) of species on a single chip. 17 (n = 17*3) different brands of surimi-based product were purchased randomly from Selangor local market in January 2013. Of 17 brands, 3 (n = 3*3) brands were positive for chicken DNA, 1 (n = 1*3) brand was positive for goat DNA, and the remainder 13 brands (n = 13*3) have no DNA species detected. The sensitivity of PCR-southern hybridization primers to detect each meat species was 0.1 ng. In the present study, it is evidence that PCR-Southern Hybridization analysis offered a reliable result due to its highly specific and sensitive properties in detecting non-halal additive such as plasma protein incorporation in surimi-based product.

  9. The azomethine ylide route to amine C-H functionalization: redox-versions of classic reactions and a pathway to new transformations.

    PubMed

    Seidel, Daniel

    2015-02-17

    Conspectus Redox-neutral methods for the functionalization of amine α-C-H bonds are inherently efficient because they avoid external oxidants and reductants and often do not generate unwanted byproducts. However, most of the current methods for amine α-C-H bond functionalization are oxidative in nature. While the most efficient variants utilize atmospheric oxygen as the terminal oxidant, many such transformations require the use of expensive or toxic oxidants, often coupled with the need for transition metal catalysts. Redox-neutral amine α-functionalizations that involve intramolecular hydride transfer steps provide viable alternatives to certain oxidative reactions. These processes have been known for some time and are particularly well suited for tertiary amine substrates. A mechanistically distinct strategy for secondary amines has emerged only recently, despite sharing common features with a range of classic organic transformations. Among those are such widely used reactions as the Strecker, Mannich, Pictet-Spengler, and Kabachnik-Fields reactions, Friedel-Crafts alkylations, and iminium alkynylations. In these classic processes, condensation of a secondary amine with an aldehyde (or a ketone) typically leads to the formation of an intermediate iminium ion, which is subsequently attacked by a nucleophile. The corresponding redox-versions of these transformations utilize identical starting materials but incorporate an isomerization step that enables α-C-H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-functionalization, generating water as the only byproduct. Reactions are promoted by simple carboxylic acids and in some cases require no additives. Azomethine ylides, dipolar species whose usage is predominantly in [3 + 2] cycloadditions and other pericyclic processes, have been

  10. The Azomethine Ylide Route to Amine C–H Functionalization: Redox-Versions of Classic Reactions and a Pathway to New Transformations

    PubMed Central

    2016-01-01

    Conspectus Redox-neutral methods for the functionalization of amine α-C–H bonds are inherently efficient because they avoid external oxidants and reductants and often do not generate unwanted byproducts. However, most of the current methods for amine α-C–H bond functionalization are oxidative in nature. While the most efficient variants utilize atmospheric oxygen as the terminal oxidant, many such transformations require the use of expensive or toxic oxidants, often coupled with the need for transition metal catalysts. Redox-neutral amine α-functionalizations that involve intramolecular hydride transfer steps provide viable alternatives to certain oxidative reactions. These processes have been known for some time and are particularly well suited for tertiary amine substrates. A mechanistically distinct strategy for secondary amines has emerged only recently, despite sharing common features with a range of classic organic transformations. Among those are such widely used reactions as the Strecker, Mannich, Pictet–Spengler, and Kabachnik–Fields reactions, Friedel–Crafts alkylations, and iminium alkynylations. In these classic processes, condensation of a secondary amine with an aldehyde (or a ketone) typically leads to the formation of an intermediate iminium ion, which is subsequently attacked by a nucleophile. The corresponding redox-versions of these transformations utilize identical starting materials but incorporate an isomerization step that enables α-C–H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-functionalization, generating water as the only byproduct. Reactions are promoted by simple carboxylic acids and in some cases require no additives. Azomethine ylides, dipolar species whose usage is predominantly in [3 + 2] cycloadditions and other pericyclic

  11. The effect of chemical additives on the synthesis of ethanol

    SciTech Connect

    Chuang, S.S.C.

    1990-07-01

    The objective of this research is to elucidate the role of various chemical additives on ethanol synthesis over Rh- and Ni-based catalysts. Chemical additives used for this study will include S, P, Ag, Cu, Mn, and Na which have different electronegativities. The effect of additives on the surface state of the catalysts, heat of adsorption of reactant molecules, reaction intermediates, reaction pathways, reaction kinetics, and product distributions is/will be investigated by a series of experimental studies of NO adsorption, reaction probing, study state rate measurement, and transient kinetic study. A better understanding of the role of additive on the synthesis reaction may allow us to sue chemical additives to manipulate the catalytic properties of Rh- and Ni-based catalysts for producing high yields of ethanol from syngas. (VC)

  12. The effect of chemical additives on the synthesis of ethanol

    SciTech Connect

    Chuang, S.S.C.

    1990-07-01

    The objective of this research is to elucidate the role of various chemical additives on ethanol synthesis over Rh- and Ni-based catalysts. Chemical additives used for this study will include S, P, Ag, Cu, Mn, and Na which have different electronegativities. The effect of additives on the surface state of the catalysts, heat of adsorption of reactant molecules, reaction intermediates, reaction pathways, reaction kinetics, and product distributions is/will be investigated by a series of experimental studies of NO adsorption, reaction probing, study state rate measurement, and transient kinetic study. A better understanding of the role of additive on the synthesis reaction may allow us to use chemical additives to manipulate the catalytic properties of Rh- and Ni-based catalysts for producing high yields of ethanol from syngas.

  13. The effect of chemical additives on the synthesis of ethanol

    SciTech Connect

    Chuang, S.S.C.

    1990-11-01

    The objective of this research is to elucidate the role of additives on the ethanol synthesis over Rh- and Ni-based catalysts. Chemical additives used for this study will include S, P, Ag, Cu, Mn, and Na which have different electronegativities. The effect of additives on the surface state of the catalysts, heat of adsorption of reactant molecules, reaction intermediates, reaction pathways, reaction kinetics, and product distributions is/will be investigated by a series of experimental studies of NO adsorption, reaction probing, study state rate measurement, and transient kinetic study. A better understanding of the role of additive on the synthesis reaction may allow them to use chemical additives to manipulate the catalytic properties of Rh- and Ni-based catalysts for producing high yields of ethanol from syngas. 49 refs., 6 figs., 3 tabs.

  14. The effect of chemical additives on the synthesis of ethanol

    SciTech Connect

    Chuang, S.S.C.; Balakos, M.W.

    1991-09-20

    The objective of this research is to elucidate the role of various chemical additives on ethanol synthesis over Rh- and Ni-based catalysts. Chemical additives used for this study will include S, P, Ag, Cu, Mn, and Na which have different electronegativities. The effect of additives on the surface state of the catalysts, heat of adsorption of reactant molecules, reaction intermediates, reaction pathways, reaction kinetics, and product distributions is/will be investigated by a series of experimental studies of NO adsorption, reaction probing, study state rate measurement, and transient kinetic study. A better understanding of the role of additives on the synthesis reaction may allow us to use chemical additives to manipulate the catalytic properties of Rh- and Ni-based catalysts for producing high yields of ethanol from syngas. 27 refs. 7 figs., 2 tabs.

  15. The effect of additional noradrenergic and serotonergic depletion on a lateralised choice reaction time task in rats with nigral 6-OHDA lesions.

    PubMed

    Lindgren, Hanna S; Demirbugen, Merve; Bergqvist, Filip; Lane, Emma L; Dunnett, Stephen B

    2014-03-01

    Parkinson's disease (PD) patients often suffer from visuospatial deficits, which have been considered a disruption of the representation of external space. The lateralised choice reaction time (CRT) task is an operant task for rodents in which similar deficits can be assessed. It has been demonstrated that specific parameters in this task is disrupted after unilateral injections of 6-hydroxydopamine (6-OHDA), which have been associated with the dopamine (DA) depletion that inevitably follows this type of lesion. However, studies have demonstrated that this type of lesion also affects the serotonergic (5HT) and noradrenergic (NA) systems. However, the impact of these systems on parameters in the CRT task had not yet been investigated. To this end, rats were pretrained on the CRT task before receiving selective lesions of the DAergic system, either alone or in combination with depletion of the NA or 5HT system. All rats with a 6-OHDA lesion displayed a gradual decline in the selection, initiation and execution of lateralised movements compared to sham-lesion controls on the side contralateral to the lesion. They also displayed a reduced number of useable trials as well as an increased number of procedural errors. Interestingly, the group with an additional noradrenergic lesion was significantly slower in reacting to lateralised stimuli throughout the testing period compared to the other two groups with a 6-OHDA lesion. There was however no difference between the three different lesion groups in the other parameters assessed in the task. These data confirm previous findings demonstrating that the majority of the parameters assessed in the lateralised CRT task are strongly dependent on DA. However, this study has also shown that the NAergic system may play an important role in contributing to the attentive performance influencing the capacity to react to the presented lateralised stimuli. PMID:24333808

  16. Laboratory studies of carbon kinetic isotope effects on the production mechanism of particulate phenolic compounds formed by toluene photooxidation: a tool to constrain reaction pathways.

    PubMed

    Irei, Satoshi; Rudolph, Jochen; Huang, Lin; Auld, Janeen; Collin, Fabrice; Hastie, Donald

    2015-01-01

    In this study, we examined compound-specific stable carbon isotope ratios for phenolic compounds in secondary organic aerosol (SOA) formed by photooxidation of isotope-label-free toluene. SOA generated by photooxidation of toluene using a continuous-flow reactor and an 8 m(3) indoor smog chamber was collected on filters, which were extracted with acetonitrile for compound-specific analysis. Eight phenolic compounds were identified in the extracts using a gas chromatograph coupled with a mass spectrometer, and their compound-specific stable carbon isotope ratios were determined using a gas chromatograph coupled with a combustion furnace followed by an isotope ratio mass spectrometer. The majority of products, including methylnitrophenols and methylnitrocatechols, were isotopically depleted by 5-6‰ compared to the initial isotope ratio of toluene, whereas the isotope ratio for 4-nitrophenol remained identical to that of toluene. On the basis of the reaction mechanisms proposed in previous reports, stable carbon isotope ratios of these products were calculated. By comparing the observed isotope ratios with the predicted isotope ratios, we explored possible production pathways for the particulate phenolic compounds. PMID:25490235

  17. Excitation functions for production of 46Sc by deuteron and proton beams in natTi: A basis for additional monitor reactions

    NASA Astrophysics Data System (ADS)

    Hermanne, A.; Tárkányi, F.; Takács, S.; Ditrói, F.; Amjed, N.

    2014-11-01

    An objective of a new Coordinated Research Program launched recently by IAEA is to strengthen and broaden the cross section database for monitoring of charged particle beams given in IAEA-TECDOC-1211. One of the suggestions is to complement the widely used natTi(d,x)48V monitor reaction by the natTi(d,x)46Sc reaction having a maximum in a somewhat higher energy. After compilation of the data sets for this reaction available in literature and unpublished data from our earlier experiments, a selection of 20 sets is proposed for statistical fitting and extraction of recommended values. A similar analysis is presented for the natTi(p,x)46Sc reaction where 16 datasets are finally selected.

  18. High performance addition-type thermoplastics (ATTs) - Evidence for the formation of a Diels-Alder adduct in the reaction of an acetylene-terminated material and a bismaleimide

    NASA Technical Reports Server (NTRS)

    Pater, R. H.; Soucek, M. D.; Chang, A. C.; Partos, R. D.

    1991-01-01

    Recently, the concept and demonstration of a new versatile synthetic reaction for making a large number of high-performance addition-type thermoplastics (ATTs) were reported. The synthesis shows promise for providing polymers having an attractive combination of easy processability, good toughness, respectable high temperature mechanical performance, and excellent thermo-oxidative stability. The new chemistry involves the reaction of an acetylene-terminated material with a bismaleimide or benzoquinone. In order to clarify the reaction mechanism, model compound studies were undertaken in solutions as well as in the solid state. The reaction products were purified by flash chromatography and characterized by conventional analytical techniques including NMR, FT-IR, UV-visible, mass spectroscopy, and high pressure liquid chromatography. The results are presented of the model compound studies which strongly support the formation of a Diels-Alder adduct in the reaction of an acetylene-terminated compound and a bismaleimide or benzoquinone.

  19. Incorporation of additional radionuclides and the external exposure pathway into the BECAMP (Basic Environmental Compliance and Monitoring Program) radiological assessment model

    SciTech Connect

    Ng, Yook C.; Rodean, H.C.; Anspaugh, L.R.

    1988-11-01

    The Nevada Applied Ecology Group (NAEG) Model of transport and dose for transuranic radionuclides was modified and expanded for the analysis of radionuclides other than pure alpha-emitters. Doses from internal and external exposures were estimated for the inventories and soil distributions of the individual radionuclides quantified in Areas 2 and 4 of the Nevada Test Site (NTS). We found that the dose equivalents via inhalation to liver, lungs, bone marrow, and bone surface from the plutonium isotopes and /sup 241/Am, those via ingestion to bone marrow and bone surfaces from /sup 90/Sr, and those via ingestion to all the target organs from /sup 137/Cs were the highest from internal exposures. The effective dose equivalents from /sup 137/Cs, /sup 152/Eu, and /sup 154/Eu were the highest from the external exposures. The /sup 60/Co, /sup 152/Eu, /sup 154/Eu, and /sup 155/Eu dose estimates for external exposures greatly exceeded those for internal exposures. The /sup 60/Co, /sup 90/Sr, and /sup 137/Cs dose equivalents from internal exposures were underestimated due to the adoption of some of the foodchain parameter values originally selected for /sup 239/Pu. Nonetheless, the ingestion pathway contributed significantly to the dose estimates for /sup 90/Sr and /sup 137/Cs, but contributed very much less than external exposures to the dose estimates for /sup 60/Co. Therefore, the use of more appropriate values would not alter the identification of important radionuclides, pathways, target organs, and exposure modes in this analysis. 19 refs., 13 figs., 12 tabs.

  20. Chemical pathways for the formation of ammonia in Hanford wastes

    SciTech Connect

    Stock, L.M.; Pederson, L.R.

    1997-09-01

    This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important). Reduction of nitrite ions is believed to be the most important source of ammonia. Whether by radiolytic or thermal routes, nitrite reduction reactions proceed through nitrogen dioxide, nitric oxide, the nitrosyl anion, and the hyponitrite anion. Nitrite ion is also converted into hydroxylamine, another important intermediate on the pathway to form ammonia. These reaction pathways additionally result in the formation of nitrous oxide and molecular nitrogen, whereas hydrogen formation is produced in a separate reaction sequence.

  1. Food additives.

    PubMed

    Berglund, F

    1978-01-01

    The use of additives to food fulfils many purposes, as shown by the index issued by the Codex Committee on Food Additives: Acids, bases and salts; Preservatives, Antioxidants and antioxidant synergists; Anticaking agents; Colours; Emulfifiers; Thickening agents; Flour-treatment agents; Extraction solvents; Carrier solvents; Flavours (synthetic); Flavour enhancers; Non-nutritive sweeteners; Processing aids; Enzyme preparations. Many additives occur naturally in foods, but this does not exclude toxicity at higher levels. Some food additives are nutrients, or even essential nutritents, e.g. NaCl. Examples are known of food additives causing toxicity in man even when used according to regulations, e.g. cobalt in beer. In other instances, poisoning has been due to carry-over, e.g. by nitrate in cheese whey - when used for artificial feed for infants. Poisonings also occur as the result of the permitted substance being added at too high levels, by accident or carelessness, e.g. nitrite in fish. Finally, there are examples of hypersensitivity to food additives, e.g. to tartrazine and other food colours. The toxicological evaluation, based on animal feeding studies, may be complicated by impurities, e.g. orthotoluene-sulfonamide in saccharin; by transformation or disappearance of the additive in food processing in storage, e.g. bisulfite in raisins; by reaction products with food constituents, e.g. formation of ethylurethane from diethyl pyrocarbonate; by metabolic transformation products, e.g. formation in the gut of cyclohexylamine from cyclamate. Metabolic end products may differ in experimental animals and in man: guanylic acid and inosinic acid are metabolized to allantoin in the rat but to uric acid in man. The magnitude of the safety margin in man of the Acceptable Daily Intake (ADI) is not identical to the "safety factor" used when calculating the ADI. The symptoms of Chinese Restaurant Syndrome, although not hazardous, furthermore illustrate that the whole ADI

  2. Bi(OTf)3-catalyzed addition of isocyanides to 2H-chromene acetals: an efficient pathway for accessing 2-carboxamide-2H-chromenes.

    PubMed

    Lyu, Longyun; Jin, Ming Yu; He, Qijie; Xie, Han; Bian, Zhaoxiang; Wang, Jun

    2016-09-14

    Bismuth triflate (Bi(OTf)3) is identified as an efficient catalyst for the direct addition of isocyanides to 2H-chromene acetals. The large scope of isocyanides and chromene acetals makes them suitable substrates in this catalytic system. By this synthetic strategy, a polyfunctional molecular scaffold, 2-carboxamide-2H-chromenes could be prepared efficiently in one step up to 95% yield. In addition, this efficient and practical protocol proceeded smoothly in the gram scale even when the catalytic loading was reduced to 2 mol%. PMID:27503764

  3. The effect of chemical additives on the synthesis of ethanol

    SciTech Connect

    Chuang, S.S.C.

    1988-11-14

    The objective of this research is to elucidate the role of various chemical additives on ethanol synthesis over Rh- and Ni-based catalysts. Chemical additives used for this study will include S, P, Ag, Cu, Mn, and Na which have different electronegativities. The effect of additives on the surface state of the catalysts, heat of adsorption of reactant molecules, reaction intermediates, reaction pathways, reaction kinetics, and product distributions is/will be investigated by a series of experimental studies including temperature programmed desorption, infrared study of NO adsorption, reactive probing, steady state rate measurement, and transient kinetic study. A better understanding of the role of additive on the synthesis reaction may allow us to use chemical additives to manipulate the catalytic properties of Rh- and Ni-based catalysts for producing high yields of ethanol from syngas.

  4. G-Quadruplex Folds of the Human Telomere Sequence Alter the Site Reactivity and Reaction Pathway of Guanine Oxidation Compared to Duplex DNA

    PubMed Central

    Fleming, Aaron M.; Burrows, Cynthia J.

    2013-01-01

    Telomere shortening occurs during oxidative and inflammatory stress with guanine (G) as the major site of damage. In this work, a comprehensive profile of the sites of oxidation and structures of products observed from G-quadruplex and duplex structures of the human telomere sequence was studied in the G-quadruplex folds (hybrid (K+), basket (Na+), and propeller (K+ + 50% CH3CN)) resulting from the sequence 5’-(TAGGGT)4T-3’ and in an appropriate duplex containing one telomere repeat. Oxidations with four oxidant systems consisting of riboflavin photosensitization, carbonate radical generation, singlet oxygen, and the copper Fenton-like reaction were analyzed under conditions of low product conversion to determine relative reactivity. The one-electron oxidants damaged the 5’-G in G-quadruplexes leading to spiroiminodihydantoin (Sp) and 2,2,4-triamino-2H-oxazol-5-one (Z) as major products as well as 8-oxo-7,8-dihydroguanine (OG) and 5-guanidinohydantoin (Gh) in low relative yields, while oxidation in the duplex context produced damage at the 5’- and middle-Gs of GGG sequences and resulted in Gh being the major product. Addition of the reductant N-acetylcysteine (NAC) to the reaction did not alter the riboflavin-mediated damage sites, but decreased Z by 2-fold and increased OG by 5-fold, while not altering the hydantoin ratio. However, NAC completely quenched the CO3•− reactions. Singlet oxygen oxidations of the G-quadruplex showed reactivity at all Gs on the exterior faces of G-quartets and furnished the product Sp, while no oxidation was observed in the duplex context under these conditions, and addition of NAC had no effect. Because a long telomere sequence would have higher-order structures of G-quadruplexes, studies were also conducted with 5’-(TAGGGT)8-T-3’, and it provided similar oxidation profiles to the single G-quadruplex. Lastly, CuII/H2O2-mediated oxidations were found to be indiscriminate in the damage patterns, and 5-carboxamido-5

  5. Analysing the Temperature Effect on the Competitiveness of the Amine Addition versus the Amidation Reaction in the Epoxidized Oil/Amine System by MCR-ALS of FTIR Data

    PubMed Central

    del Río, Vanessa; Callao, M. Pilar; Larrechi, M. Soledad

    2011-01-01

    The evaluation of the temperature effect on the competitiveness between the amine addition and the amidation reaction in a model cure acid-catalysed reaction between the epoxidized methyl oleate (EMO), obtained from high oleic sunflower oil, and aniline is reported. The study was carried out analysing the kinetic profiles of the chemical species involved in the system, which were obtained applying multivariate curve resolution-alternating least squares (MCR-ALS) to the Fourier transform infrared spectra data obtained from the reaction monitoring at two different temperatures (60°C and 30°C). At both experimental temperatures, two mechanisms were postulated: non-autocatalytic and autocatalytic. The different behaviour was discussed considering not only the influence of the temperature on the amidation reaction kinetic, but also the presence of the homopolymerization of the EMO reagent. PMID:21765830

  6. Experience in using the covariances of some ENDF/B-V dosimetry cross sections: proposed improvements and addition of cross-reaction covariances

    SciTech Connect

    Fu, C.Y.; Hetrick, D.M.

    1982-01-01

    Recent ratio data, with carefully evaluated covariances, were combined with eleven of the ENDF/B-V dosimetry cross sections using the generalized least-squares method. The purpose was to improve these evaluated cross sections and covariances, as well as to generate values for the cross-reaction covariances. The results represent improved cross sections as well as realistic and usable covariances. The latter are necessary for meaningful intergral-differential comparisons and for spectrum unfolding.

  7. Discovery-Oriented Approach To Organic Synthesis: Tandem Aldol Condensation-Michael Addition Reactions. Identifying Diastereotopic Hydrogens in an Achiral Molecule by NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wachter-Jurcsak, Nanette; Reddin, Kendra

    2001-09-01

    We have found a beautiful example of anisochrony of diastereotopic acyclic methylene hydrogens in a symmetric diketone, synthesized by techniques traditionally performed in an introductory organic laboratory course. Synthesis of the diketone is high-yielding and easy to carry out, and the products can be directly isolated with a good degree of purity with no need of further manipulation. The reaction can be accomplished in a single laboratory session.

  8. Simvastatin and Dipentyl Phthalate Lower Ex Vivo Testicular Testosterone Production and Exhibit Additive Effects on Testicular Testosterone and Gene Expression Via Distinct Mechanistic Pathways in the Fetal Rat

    PubMed Central

    Beverly, Brandiese E. J.; Lambright, Christy S.; Furr, Johnathan R.; Sampson, Hunter; Wilson, Vickie S.; McIntyre, Barry S.; Foster, Paul M. D.; Travlos, Gregory; Gray, L. Earl

    2014-01-01

    Sex differentiation of the male reproductive tract in mammals is driven, in part, by fetal androgen production. In utero, some phthalate esters (PEs) alter fetal Leydig cell differentiation, reducing the expression of several genes associated with steroid synthesis/transport, and consequently, lowering fetal androgen and Insl3 hormone levels. Simvastatin (SMV) is a cholesterol-lowering drug that directly inhibits HMG-CoA reductase. SMV may also disrupt steroid biosynthesis, but through a different mode of action (MOA) than the PEs. As cholesterol is a precursor of steroid hormone biosynthesis, we hypothesized that in utero exposure to SMV during the critical period of sex differentiation would lower fetal testicular testosterone (T) production without affecting genes involved in cholesterol and androgen synthesis and transport. Secondly, we hypothesized that a mixture of SMV and a PE, which may have different MOAs, would reduce testosterone levels in an additive manner. Pregnant Sprague Dawley rats were dosed orally with SMV, dipentyl phthalate (DPeP), or SMV plus DPeP from gestational days 14-18, and fetuses were evaluated on GD18. On GD18, SMV lowered fetal T production and serum triglycerides, low density lipoprotein, high density lipoprotein, and total cholesterol levels, and downregulated two genes in the fetal testis that were different from those altered by PEs. When SMV and DPeP were administered as a mixture, fetal T production was significantly reduced in an additive manner, thus demonstrating that a mixture of chemicals can induce additive effects on fetal T production even though they display different MOAs. PMID:25055962

  9. Impact of Pt additives on the surface reactions between SnO2, water vapour, CO and H2; an operando investigation.

    PubMed

    Großmann, Katharina; Wicker, Susanne; Weimar, Udo; Barsan, Nicolae

    2013-11-28

    The impact of Pt doping on the surface reactions between tin dioxide, water vapour, CO and H2 was investigated by a combination of simultaneously performed operando DRIFT (Diffuse Reflectance Infrared Fourier Transform) spectroscopy, DC resistance measurements and analysis of the reaction products by using a MS (Mass Spectrometer). Both undoped and Pt doped tin dioxide sensors were exposed to different test gases in synthetic air or in N2 backgrounds. The approach made it possible to identify the differences between the two materials with respect to their surface chemistry and their impact on the gas sensing performance. The main finding is that the presence of Pt changes the reaction partners' nature for water vapour and H2 on the one hand, and CO on the other hand when the sensors are operated in air. In this way the cross interference effect of humidity, which is responsible for the loss of CO sensing performance for the sensors based on undoped SnO2, is reversed. PMID:24105035

  10. Reactions of vinyl amido ligands in Tp`(CO){sub 2}W[N(R`)CH=CHR] complexes prepared from addition of primary amines to coordinated alkynes

    SciTech Connect

    Feng, S.G.; White, P.S.; Templeton, J.L.

    1995-11-01

    Reaction of the ytterbium-benzophenone dianion complex (1), which was formed by reaction of Yb metal with benzophenone in THF/HMPA, with 2,6-di-tert-butyl-4-methylphenol, yielded the ytterbium(II) aryloxide complex Yb(OAr){sub 2}(HMPA){sub 2} (2, Ar= C{sub 6}H{sub 2} -{sup t}Bu{sub 2}-2,6-Me-4) as a major product (80%) and the ytterbium(III) enolate complex (3) as a minor one (ca. 5% yield). The mechanisms of these reactions are discussed. X-ray crystallographic studies reveal that 3, 4a, and 7b are isostructural, and so are 5a and 6. The central metal ions in these complexes are all five-coordinated in a trigonal bipyramid form (highly distorted in the case of 5a and 6) with two HMPA ligands at the apical and three anionic oxygen ligands at the equatorial positions. 20 refs., 2 figs., 7 tabs.

  11. Journey on greener pathways: from the use of alternate energy inputs and benign reaction media to sustainable applications of nano-catalysts in synthesis and environmental remediation

    EPA Science Inventory

    Sustainable synthetic processes developed during the past two decades involving the use of alternate energy inputs and greener reaction media are summarized. These processes include examples of coupling reactions, the synthesis of heterocyclic compounds, and a variety of reactio...

  12. The formation of cyclo-addition adducts in the reaction of an acetylene-terminated material with a bismaleimide: A model compound study for addition-type thermoplastics (ATTs) using metal catalysts

    SciTech Connect

    Soucek, M.D., Pater, R.H.; Ritenour, S.L.

    1993-12-31

    A model compound study using an acetylene-terminated material and a bismaleimide has provided evidence that a diruthenium complex Ru{sub 2}(CO){sub 6}[1,2-({mu}-PPh){sub 2}C{sub 6}H{sub 4}] and a rhodium complex Rh(PPh{sub 3}){sub 3}Cl can catalyze a Diels-Alder type cycloaddition in which acetylene-terminated material acts as a diene and the bismaleimide is a dieneophile. The molten state reaction of N-(3-ethynylphenyl) phthalimide and N-(4-phenoxyphenyl) maleimide with Ru{sub 2}(CO){sub 6}[{mu}-(PhP){sub 2}C{sub 6}H{sub 4}] or Rh(PPh{sub 3}){sub 3}Cl heated to 170{degrees}C led to two major products. The spectral data for the first major product is consistent with a 2:1 Diels-Alder adduct formed from two molecules of the acetylene compound and one molecule of the maleimide. The spectral data for the second major product is consistent with a 2:2 Diels-Alder adduct formed from two molecules of each reactant.

  13. Graphene Layer Growth Chemistry: Five-Six-Ring Flip Reaction

    SciTech Connect

    Whitesides, Russell; Domin, Dominik; Lester Jr., William A.; Frenklach, Michael

    2007-03-24

    A theoretical study revealed a new reaction pathway, in which a fused five and six-membered ring complex on the zigzag edge of a graphene layer isomerizes to reverse its orientation, or 'flips,' after activation by a gaseous hydrogen atom. The process is initiated by hydrogen addition to or abstraction from the surface complex. The elementary steps of the migration pathway were analyzed using density-functional theory (DFT) calculations to examine the region of the potential energy surface associated with the pathway. The DFT calculations were performed on substrates modeled by the zigzag edges of tetracene and pentacene. Rate constants for the flip reaction were obtained by the solution of energy master equation utilizing the DFT energies, frequencies, and geometries. The results indicate that this reaction pathway is competitive with other pathways important to the edge evolution of aromatic species in high temperature environments.

  14. Copper- and Silver-Catalyzed Diastereo- and Enantioselective Conjugate Addition Reaction of 1-Pyrroline Esters to Nitroalkenes: Diastereoselectivity Switch by Chiral Metal Complexes.

    PubMed

    Koizumi, Akihiro; Kimura, Midori; Arai, Yuri; Tokoro, Yuichiro; Fukuzawa, Shin-ichi

    2015-11-01

    syn-Diastereoselective conjugate addition of 1-pyrroline esters to nitroalkenes in good yields with an excellent enantioselectivity by using CuOAc/Me-FcPHOX catalyst in the presence of pyridine. In contrast, AgOAc/tBu-ThioClickFerrophos catalyzed the anti diastereoselective conjugate addition with a high enantioselectivity without additional base. Thus, the preparation of chiral 1-pyrroline derivatives bearing diverse stereochemistry could be achieved. The diastereoselective reduction of the imine group in the conjugate adduct could afford the 2,5-cis-proline ester derivative. PMID:26426827

  15. Elucidation of metabolic pathways from enzyme classification data.

    PubMed

    McDonald, Andrew G; Tipton, Keith F

    2014-01-01

    The IUBMB Enzyme List is widely used by other databases as a source for avoiding ambiguity in the recognition of enzymes as catalytic entities. However, it was not designed for metabolic pathway tracing, which has become increasingly important in systems biology. A Reactions Database has been created from the material in the Enzyme List to allow reactions to be searched by substrate/product, and pathways to be traced from any selected starting/seed substrate. An extensive synonym glossary allows searches by many of the alternative names, including accepted abbreviations, by which a chemical compound may be known. This database was necessary for the development of the application Reaction Explorer ( http://www.reaction-explorer.org ), which was written in Real Studio ( http://www.realsoftware.com/realstudio/ ) to search the Reactions Database and draw metabolic pathways from reactions selected by the user. Having input the name of the starting compound (the "seed"), the user is presented with a list of all reactions containing that compound and then selects the product of interest as the next point on the ensuing graph. The pathway diagram is then generated as the process iterates. A contextual menu is provided, which allows the user: (1) to remove a compound from the graph, along with all associated links; (2) to search the reactions database again for additional reactions involving the compound; (3) to search for the compound within the Enzyme List. PMID:24218216

  16. Tandem Esterification/1,4-Addition-Type Friedel-Crafts Alkylation Reactions of Phenols/Naphthols with Olefinic Thioazlactones: Access to Functionalized 1,2-Dihydrobenzo[f]chromen-3-ones and 3,4-Dihydrochromen-2-ones.

    PubMed

    Ziyaei Halimehjani, Azim; Khoshdoun, Maryam

    2016-07-01

    An efficient approach for the synthesis of novel alkyl 2,3-dihydro-3-oxo-1-aryl-1H-benzo[f]chromen-2-ylcarbamodithioates and alkyl 3,4-dihydro-2-oxo-4-aryl-2H-chromen-3-ylcarbamodithioates from 2-(alkylthio)thioazlactones (thioazlactones) and phenols or naphthols catalyzed by PTSA was developed. The reaction proceeds via a domino esterification/intramolecular 1,4-addition-type Friedel-Crafts alkylation reaction to afford interesting complex molecules by a simple procedure with high yields and diastereoselectivity. An X-ray analysis was carried out to firmly establish the stereochemistry of the products. PMID:27310869

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

    PubMed

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

    2016-06-22

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

  18. New insights in understanding plasma-catalysis reaction pathways: study of the catalytic ozonation of an acetaldehyde saturated Ag/TiO2/SiO2 catalyst

    NASA Astrophysics Data System (ADS)

    Sauce, Sonia; Vega-González, Arlette; Jia, Zixian; Touchard, Sylvain; Hassouni, Khaled; Kanaev, Andrei; Duten, Xavier

    2015-07-01

    This paper is a preliminary study intended to straighten out the role of reactive oxygen species in the activation mechanisms occurring in a plasma driven catalysis process for acetaldehyde decomposition. For this purpose, the interaction between the surface, the pollutant and one of the main oxidative species generated by non-thermal plasma, namely ozone, was studied. Acetaldehyde catalytic ozonation over a nanostructured Ag/TiO2/SiO2 catalyst is carried out at room temperature and atmospheric pressure, and followed by diffuse reflectance infrared fourier transform spectroscopy (DRIFTS). For this, the catalyst is firstly saturated with acetaldehyde. At the end of the saturation, acetaldehyde and crotonaldehyde, its condensation product, are identified as the major adsorbed species. In a second step, the surface ozonation is carried out and three additional intermediates are identified, namely, acetone, formic acid and acetic acid. Gaseous CO, CO2, methyl formate and methyl acetate are detected at the DRIFTS outlet, evidencing the partial mineralization of the adsorbed species. A global reaction scheme is proposed for explaining the formation of those adsorbed intermediates and gaseous products. This proposed heterogeneous ozone induced chemistry has to be taken into account when associating non-thermal plasma in air to a catalyst. Contribution to the topical issue "The 14th International Symposium on High Pressure Low Temperature Plasma Chemistry (HAKONE XIV)", edited by Nicolas Gherardi, Ronny Brandenburg and Lars Stollenwark

  19. Chemical pathways for the formation of ammonia in Hanford wastes

    SciTech Connect

    Stock, L.M.; Pederson, L.R.

    1997-12-01

    This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important).

  20. Inverse Thio Effects in the Hepatitis Delta Virus Ribozyme Reveal that the Reaction Pathway Is Controlled by Metal Ion Charge Density

    PubMed Central

    2015-01-01

    The hepatitis delta virus (HDV) ribozyme self-cleaves in the presence of a wide range of monovalent and divalent ions. Prior theoretical studies provided evidence that self-cleavage proceeds via a concerted or stepwise pathway, with the outcome dictated by the valency of the metal ion. In the present study, we measure stereospecific thio effects at the nonbridging oxygens of the scissile phosphate under a wide range of experimental conditions, including varying concentrations of diverse monovalent and divalent ions, and combine these with quantum mechanical/molecular mechanical (QM/MM) free energy simulations on the stereospecific thio substrates. The RP substrate gives large normal thio effects in the presence of all monovalent ions. The SP substrate also gives normal or no thio effects, but only for smaller monovalent and divalent cations, such as Li+, Mg2+, Ca2+, and Sr2+; in contrast, sizable inverse thio effects are found for larger monovalent and divalent cations, including Na+, K+, NH4+, and Ba2+. Proton inventories are found to be unity in the presence of the larger monovalent and divalent ions, but two in the presence of Mg2+. Additionally, rate–pH profiles are inverted for the low charge density ions, and only imidazole plus ammonium ions rescue an inactive C75Δ variant in the absence of Mg2+. Results from the thio effect experiments, rate–pH profiles, proton inventories, and ammonium/imidazole rescue experiments, combined with QM/MM free energy simulations, support a change in the mechanism of HDV ribozyme self-cleavage from concerted and metal ion-stabilized to stepwise and proton transfer-stabilized as the charge density of the metal ion decreases. PMID:25799319

  1. New sterically-hindered o-quinones annelated with metal-dithiolates: regiospecificity in oxidative addition reactions of a bifacial ligand to the Pd and Pt complexes.

    PubMed

    Martyanov, K A; Cherkasov, V K; Abakumov, G A; Samsonov, M A; Khrizanforova, V V; Budnikova, Y H; Kuropatov, V A

    2016-04-25

    An unusual reactivity of sterically hindered o-quinones with an annelated dithiete ring towards coordination at a dithiolene site has been discovered. New Pd and Pt dithiolate complexes have been synthesized. The reaction proceeds regioselectively, and the quinone site of the parent ligand is not affected even while using an excess of the metal complex. Both Pt and Pd complexes display a square planar surrounding for the metal ion and have very similar NMR, IR and UV/Vis spectra. Surprisingly, being coordinated at the dithiolene site to the metal, the ligand exhibits activity like an o-quinone, it could be reduced with different metals resulting in the corresponding o-semiquinonates which were confirmed by EPR spectroscopy. It was shown that an unpaired electron exhibits HFC with the phosphorus nuclei of phosphine ligands coordinated to the metal ions at the dithiolene site of the molecule. PMID:27040038

  2. Promotion of oxygen reduction reaction durability of carbon-supported PtAu catalysts by surface segregation and TiO₂ addition.

    PubMed

    Liu, Chen-Wei; Chen, Hong-Shuo; Lai, Chien-Ming; Lin, Jiunn-Nan; Tsai, Li-Duan; Wang, Kuan-Wen

    2014-02-12

    Highly effective carbon supported-Pt75Au25 catalysts for oxygen reduction reaction (ORR) are prepared though titanium dioxide modification and post heat treatment. After accelerated durability test (ADT) of 1700 cycles, the ORR activity of PtAu/C catalysts modified by TiO2 and air heat treatment is 3 times higher than that of the commercial Pt/C. The enhancement of ORR activity is attributed to surface and structural alteration by air-induced Pt surface segregation and lower unfilled d states. On the contrary, for TiO2 modified and H2 treated PtAu/C catalysts, the deterioration of the ORR activity may be due to the loss of electrochemical surface area after ADT and the increase of d-band vacancy. PMID:24447040

  3. Enzymatic redox chemistry: A proposed reaction pathway for the six-electron reduction of SO sub 3 sup 2 minus to S sup 2 minus by the assimilatory-type sulfite reductase from Desulfovibrio vulgaris (Hildenborough)

    SciTech Connect

    Tan, Jian; Cowan, J.A. )

    1991-09-10

    A detailed reaction pathway for the six-electron reduction of SO{sub 3}{sup 2{minus}} to S{sup 2{minus}} by the assimilatory-type sulfite reductase (SiR) from Desulfovibrio vulgaris (Hildenborough) has been deduced from experiments with {sup 35}S-labeled enzyme and the relative reaction rates of nitrogenous substrates. The ligand bridging the prosthetic (Fe{sub 4}S{sub 4})-siroheme center is apparently exchanged by {sup 35}S{sup 2{minus}} in both oxidized and reduced enzyme. This {sup 35}S{sup 2{minus}} label was retained in the course of SO{sub 3}{sup 2{minus}} reduction, implicating substrate binding to the nonbridging axial site of the siroheme. A reaction mechanism is proposed in which SO{sub 3}{sup 2{minus}} binds to Fe{sup 2+} through the sulfur atom, followed by a series of two-electron reductive cleavages of S-O bonds. Protonation of oxygen facilitates bond cleavage, giving hydroxide as leaving group. The bridge remains intact throughout the course of the reaction, providing an efficient coupling pathway for electron transfer between the cluster and siroheme.

  4. The effect of chemical additives on the synthesis of ethanol. Final technical report, September 15, 1987--March 15, 1992

    SciTech Connect

    Chuang, S.S.C.

    1992-03-06

    The objective of this research was to investigate the reaction mechanism of higher alcohol and aldehyde synthesis from syngas and the role of additives in the synthesis. An in situ IR reaction system and probe molecule technique were developed to study adsorbed species, active sites, and reaction pathway during reaction. The catalysts used for this study included silica-supported Rh, Ru, and Ni. (VC)

  5. Different pathways of radical translocation in yeast cytochrome c peroxidase and its W191F mutant on reaction with H(2)O(2) suggest an antioxidant role.

    PubMed

    Tsaprailis, George; English, Ann M

    2003-02-01

    In the absence of exogenous donors, turnover of 10 molar equivalents of H(2)O(2) by wild-type recombinant cytochrome c peroxidase [CCP(MI)] and its W191F mutant at pH 7.0 occurs by oxidation of endogenous donors on the polypeptide. No O(2) evolution was observed with either enzyme on reaction with 10 molar equivalents of H(2)O(2), eliminating catalase-like activity, but O(2) evolution was observed when 100 molar equivalents of H(2)O(2) were added to the enzymes. Protein dimers were observed by SDS-PAGE following H(2)O(2) turnover by the peroxidases, and dimeric forms of CCP(MI) and CCP(W191) were isolated by gel-permeation chromatography. LC-ESI-MS analysis of the tryptic digests of the dimers revealed the previously reported T(6)-T(6) crosslink and a new crosslink between T(6)-T(26), but no T(26)-T(26) crosslink. The crosslinked tryptic peptides contain the exposed tyrosine residues Tyr36, Tyr39 and Tyr42 (T(6)), and Tyr229 and Tyr236 (T(26)). Addition of a spin trap, 2-methyl-2-nitrosopropane (MNP), to the CCP(MI)/H(2)O(2) reaction resulted in MNP labeling of peptides T(6), T(21) (which contains Tyr153) and T(26). MNP labeling of Tyr236 was found by sequencing peptide T(26). MNP labeling did not compete with dimerization of H(2)O(2)-oxidized CCP(W191F), suggesting that dityrosine formation in this mutant is very rapid owing to the high reactivity of radicals formed on T(6). H(2)O(2)-dependent formation of CCP-cytochrome c heterodimers was observed for both CCP(MI) and W191F in the presence of ferricytochrome c, the oxidized form of CCP's donor substrate. Interestingly, no H(2)O(2)-dependent cytochrome crosslinking to the W51F mutant was observed, even though this mutant underwent extensive homocrosslinking. The translocation of oxidizing equivalents from the heme to the surface residues of CCP is discussed in terms of an antioxidant role for CCP. PMID:12589560

  6. Signal Transduction Reaction Monitoring Deciphers Site-Specific PI3K-mTOR/MAPK Pathway Dynamics in Oncogene-Induced Senescence.

    PubMed

    de Graaf, Erik L; Kaplon, Joanna; Mohammed, Shabaz; Vereijken, Lisette A M; Duarte, Daniel P; Redondo Gallego, Laura; Heck, Albert J R; Peeper, Daniel S; Altelaar, A F Maarten

    2015-07-01

    We report a straightforward strategy to comprehensively monitor signal transduction pathway dynamics in mammalian systems. Combining targeted quantitative proteomics with highly selective phosphopeptide enrichment, we monitor, with great sensitivity, phosphorylation dynamics of the PI3K-mTOR and MAPK signaling networks. Our approach consists of a single enrichment step followed by a single targeted proteomics experiment, circumventing the need for labeling and immune purification while enabling analysis of selected phosphorylation nodes throughout signaling pathways. The need for such a comprehensive pathway analysis is illustrated by highlighting previously uncharacterized phosphorylation changes in oncogene-induced senescence, associated with diverse biological phenotypes and pharmacological intervention of the PI3K-mTOR pathway. PMID:26011226

  7. Theoretical study on the initial reaction mechanisms of ansa-metallocene zirconium precursor on hydroxylated Si(1 0 0) surface.

    PubMed

    Zhou, Guangfen; Ren, Jie; Zhang, Shaowen

    2016-05-01

    The initial reaction mechanisms for depositing ZrO2 thin films using ansa-metallocene zirconium (Cp2CMe2)ZrMe2 precursor were studied by density functional theory (DFT) calculations. The (Cp2CMe2)ZrMe2 precursor could be absorbed on the hydroxylated Si(1 0 0) surface via physisorption. Possible reaction pathways of (Cp2CMe2)ZrMe2 were proposed. For each reaction, the activation energies and reaction energies were compared, and stationary points along the reaction pathways were shown. In addition, the influence of dispersion effects on the reactions was evaluated by non-local dispersion corrected DFT calculations. PMID:27138945

  8. Synthesis of 9H-Pyrrolo[1,2-a]indole and 3H-Pyrrolizine Derivatives via a Phosphine-Catalyzed Umpolung Addition/Intramolecular Wittig Reaction.

    PubMed

    Saleh, Nidal; Voituriez, Arnaud

    2016-05-20

    The first umpolung addition/intramolecular Wittig reaction, catalytic in phosphine, is described. The in situ phosphine oxide reduction was accomplished by the use of silane and a catalytic amount of bis(4-nitrophenyl)phosphate. This catalytic protocol is applicable to the synthesis of a wide range of functionalized 9H-pyrrolo[1,2-a]indoles and pyrrolizines (18 examples, 70-98% yields). PMID:27080174

  9. The Fate of Carbon Draining Permafrost Soils is Controlled by Photochemical Reactions in Addition to Microbial Degradation in Arctic Surface Waters

    NASA Astrophysics Data System (ADS)

    Kling, G. W.; Dobkowski, J.; Ward, C. P.; Crump, B. C.; Neilson, B. T.; Cory, R. M.

    2013-12-01

    Perhaps the unknown of greatest potential consequence in determining the arc of climate change in this century is the role of thawing permafrost carbon. Arctic soil temperatures are increasing and large areas of permafrost have thawed, but not all soils will thaw quietly in place. Destabilization from melting ice has caused an increase in thermokarst failures that expose buried C and release dissolved organic C (DOC) to surface waters. We found that this exposure to sunlight and surface conditions increases the reactivity of permafrost C to microbial attack by 40% compared to soil DOC held in the dark. The range of lability to microbes depends on microbial community composition and especially on prior light exposure, implying that sunlight may act as an amplification factor in converting frozen C to gases in the atmosphere. We also found that photochemical degradation accounted for the majority (up to 80%) of the degradation of DOC in the water column of lakes and streams. This was based on concurrent measurements of (1) respiration of DOM to CO2 by bacteria in the dark, (2) O2 consumed in DOM photo-oxidation, (3) CO2 produced by DOM photo-mineralization, and (4) photo-stimulated bacterial respiration. Using in-situ UV light profiles and surveys of ~70 surface waters on the North Slope of Alaska, we found that depth-integrated water column rates of photochemical DOM degradation equaled or exceeded dark bacterial respiration, by up to 7x depending on the mean depth of the water column. The total dark and light processing of DOM in these waters was estimated to be roughly 20% of the DOM exported from major rivers on the North Slope of Alaska to the Arctic Ocean. The dominant degradation pathway was the partial photo-oxidation of DOC, which was at least 2x greater than complete photo-mineralization of DOC to CO2 or than bacterial respiration to CO2. This means that the dominant fate of permafrost C released as DOC is to be partially degraded and transported through

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

    PubMed Central

    2015-01-01

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

  11. A Novel Testosterone Catabolic Pathway in Bacteria ▿ ‡

    PubMed Central

    Leu, Yann-Lii; Wang, Po-Hsiang; Shiao, Ming-Shi; Ismail, Wael; Chiang, Yin-Ru

    2011-01-01

    Forty years ago, Coulter and Talalay (A. W. Coulter and P. Talalay, J. Biol. Chem. 243:3238–3247, 1968) established the oxygenase-dependent pathway for the degradation of testosterone by aerobes. The oxic testosterone catabolic pathway involves several oxygen-dependent reactions and is not available for anaerobes. Since then, a variety of anaerobic bacteria have been described for the ability to degrade testosterone in the absence of oxygen. Here, a novel, oxygenase-independent testosterone catabolic pathway in such organisms is described. Steroidobacter denitrificansDSMZ18526 was shown to be capable of degrading testosterone in the absence of oxygen and was selected as the model organism in this study. In a previous investigation, we identified the initial intermediates involved in an anoxic testosterone catabolic pathway, most of which are identical to those of the oxic pathway demonstrated in Comamonas testosteroni. In this study, five additional intermediates of the anoxic pathway were identified. We demonstrated that subsequent steps of the anoxic pathway greatly differ from those of the established oxic pathway, which suggests that a novel pathway for testosterone catabolism is present. In the proposed anoxic pathway, a reduction reaction occurs at C-4 and C-5 of androsta-1,4-diene-3,17-dione, the last common intermediate of both the oxic and anoxic pathways. After that, a novel hydration reaction occurs and a hydroxyl group is thus introduced to the C-1α position of C19steroid substrates. To our knowledge, an enzymatic hydration reaction occurring at the A ring of steroid compounds has not been reported before. PMID:21725000

  12. The additional loss of Bak and not the lack of the protein tyrosine kinase p56/Lck in one JCaM1.6 subclone caused pronounced apoptosis resistance in response to stimuli of the intrinsic pathway.

    PubMed

    Rudner, J; Mueller, A-C; Matzner, N; Huber, S M; Handrick, R; Belka, C; Jendrossek, V

    2009-05-01

    Ionising radiation, hypoxia, and the cyclooxygenase-2 inhibitor Celecoxib are known agonists of the intrinsic apoptosis pathway that involves mitochondrial damage upstream of caspase activation. Mitochondrial integrity is regulated by the pro-apoptotic Bcl-2 protein family members Bak and Bax. Upstream of the mitochondria, many kinases and phosphatases control the apoptotic response. However, the role of the non-receptor tyrosine kinase p56/Lck during apoptosis is controversial. The present investigation demonstrate the existence of two JCaM1.6 subclones, one expressing and one deficient for Bak. The lack of p56/Lck expression in JCaM1.6 cells per se did hardly affect apoptosis induced by ionising radiation, hypoxia, or Celecoxib. Only the additional loss of Bak expression, as observed in one JCaM1.6 subclone, rendered the cells resistant. siRNA-mediated downregulation of Bak and p56/Lck mimicked the observed effects in the subclones. Earlier experiments performed with the Bak-negative clone might have lead to the wrong assumption that lack of p56/Lck alone, and not the additonal loss of Bak, was responsible for reduced sensitivity towards stimuli of the intrinsic apoptosis pathway. PMID:19343496

  13. A highly active recyclable gold-graphene nanocomposite material for oxidative esterification and Suzuki cross-coupling reactions in green pathway.

    PubMed

    Mondal, Paramita; Salam, Noor; Mondal, Avijit; Ghosh, Kajari; Tuhina, K; Islam, Sk Manirul

    2015-12-01

    A graphene based composite with gold nanoparticles has been synthesized via a simple chemical route and the structure and compositions of nanocomposite has been characterized. The catalyst was found to be remarkably stable and active for the oxidative esterification of alcohols under present reaction conditions using molecular oxygen as green oxidant and Suzuki cross-coupling reactions between aryl halides and phenylboronic acids using environmentally friendly water as solvent. The versatility of both the protocols was demonstrated by taking a number of substrates. This protocol offers several advantages like high yields, clean reactions, recyclability of the catalyst, reaction in water and use of green oxidant. This study suggests graphene, as an economical substitute for carbon nanotubes, could act as a prominent support in heterogeneous catalysis. PMID:26275502

  14. Growth of Thin, Anisotropic, π-Conjugated Molecular Films by Stepwise "Click" Assembly of Molecular Building Blocks: Characterizing Reaction Yield, Surface Coverage, and Film Thickness versus Addition Step Number.

    PubMed

    Demissie, Abel T; Haugstad, Greg; Frisbie, C Daniel

    2015-07-15

    We report the systematic characterization of anisotropic, π-conjugated oligophenyleneimine (OPI) films synthesized using stepwise imine condensation, or "click" chemistry. Film synthesis began with a self-assembled monolayer (SAM) of 4-formylthiophenol or 4-aminothiophenol on Au, followed by repetitive, alternate addition of terephthalaldehyde (benzene-1,4-dicarbaldehyde) or 1,4-benzenediamine to form π-conjugated films ranging from 0.6-5.5 nm in thickness. By systematically capping the OPI films with a redox or halogen label, we were able to measure the relative surface coverage after each monomer addition via Rutherford backscattering spectrometry, X-ray photoelectron spectroscopy, spectroscopic ellipsometry, reflection-absorption infrared spectroscopy, and cyclic voltammetry. Nuclear reaction analysis was also employed for the first time on a SAM to calculate the surface coverage of carbon atoms after each stepwise addition. These six different analysis methods indicate that the average extent of reaction is 99% for each addition step. The high yield and molecular surface coverage confirm the efficacy of Schiff base chemistry, at least with the terephthalaldehyde and 1,4-benzenediamine monomers, for preparing high-quality molecular films with π conjugation normal to the substrate. PMID:26098519

  15. Oxidative addition of allylic halides to ruthenium(II) compounds. Preparation, reactions, and X-ray crystallographic structure of ruthenium(IV)-allyl complexes

    SciTech Connect

    Nagashima, Hideo; Mukai, Katsunori; Shiota, Yusuke; Yamaguchi, Keitaro; Ara, Kenichi; Fukahori, Takahiko; Itoh, Kenji ); Suzuki, Hiroharu; Akita, Munetaka; Moro-oka, Yoshihiko )

    1990-03-01

    The oxidative addition of allylic halides to (C{sub 5}R{sub 5})RuL{sub 2}X (R = H, Me; L = CO, PPh{sub 3}) gave new Ru(IV)-{eta}{sup 3}-allyl complexes, (C{sub 5}R{sub 5})RuX{sub 2}({eta}{sup 3}-allyl). An X-ray structure determination was carried out on (C{sub 5}Me{sub 5})RuBr{sub 2}({eta}{sup 3}-C{sub 3}H{sub 5}), indicating a pseudo-piano-stool structure having two Br atoms and two terminal carbons of the endo-{eta}{sup 3}-allyl ligand located at the basal positions. There is a crystal mirror plane bisecting the pentamethylcyclopentadienyl and the {pi}-allyl ligands. Crystal data: orthorhombic, space group P2{sub 1}2{sub 1}2{sub 1}, a = 22.738 (1) {angstrom}, b = 13.367 (7) {angstrom}, c = 9.383 (1) {angstrom}, Z = 4., data refined to R = 0.0695. Its {sup 1}H and {sup 13}C NMR spectra showed symmetric allyl signals, supporting that the above-described piano-stool structure is maintained even in solution.

  16. Multiple Pathways Linking Racism to Health Outcomes

    PubMed Central

    Harrell, Camara Jules P.; Burford, Tanisha I.; Cage, Brandi N.; Nelson, Travette McNair; Shearon, Sheronda; Thompson, Adrian; Green, Steven

    2012-01-01

    This commentary discusses advances in the conceptual understanding of racism and selected research findings in the social neurosciences. The traditional stress and coping model holds that racism constitutes a source of aversive experiences that, when perceived by the individual, eventually lead to poor health outcomes. Current evidence points to additional psychophysiological pathways linking facets of racist environments with physiological reactions that contribute to disease. The alternative pathways emphasize prenatal experiences, subcortical emotional neural circuits, conscious and preconscious emotion regulation, perseverative cognitions, and negative affective states stemming from racist cognitive schemata. Recognition of these pathways challenges change agents to use an array of cognitive and self-controlling interventions in mitigating racism’s impact. Additionally, it charges policy makers to develop strategies that eliminate deep-seated structural aspects of racism in society. PMID:22518195

  17. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

    PubMed Central

    Caspi, Ron; Altman, Tomer; Dreher, Kate; Fulcher, Carol A.; Subhraveti, Pallavi; Keseler, Ingrid M.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Ong, Quang; Paley, Suzanne; Pujar, Anuradha; Shearer, Alexander G.; Travers, Michael; Weerasinghe, Deepika; Zhang, Peifen; Karp, Peter D.

    2012-01-01

    The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains more than 1800 pathways derived from more than 30 000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc (http://biocyc.org/) is a collection of more than 1700 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups. PMID:22102576

  18. The role of acidic sites and the catalytic reaction pathways on the Rh/ZrO2 catalysts for ethanol steam reforming.

    PubMed

    Zhong, Ziyi; Ang, Hanwee; Choong, Catherine; Chen, Luwei; Huang, Lin; Lin, Jianyi

    2009-02-01

    Rh catalysts supported on ZrO(2)-based oxides were studied for ethanol steam reforming (SR) reaction. Pure ZrO(2) as the support resulted in higher H(2) production yield compared to the ZrO(2) oxide decorated with CeO(2), Al(2)O(3), La(2)O(3) or Li(2)O at the reaction temperature of 300 degrees C. Above 450 degrees C, all the catalysts exhibited similar catalytic activity. However, at low reaction temperatures (below 400 degrees C), a significant enhancement in the catalytic activity, selectivity and stability was achieved by replacing the ZrO(2) support prepared by a precipitation method (ZrO(2)-CP) with that prepared by a hydrothermal method (ZrO(2)-HT). A deactivation was observed during the EtOH SR reaction at 300 degrees C on the two catalysts of Rh/ZrO(2)-CP and Rh/ZrO(2)-HT. NH(3)-TPD experiments confirmed that the ZrO(2)-HT support had two types of acidic sites while the ZrO(2)-CP support had only one type of weak acidic sites. DRIFTS studies showed that the absorption of EtOH molecules was strong on the Rh/ZrO(2)-HT catalyst and a number of C(2) oxygenates were accumulated on the catalyst surface. Meanwhile, the EtOH absorption on the Rh/ZrO(2)-CP catalyst was weak and the accumulation of CO, carbonate and CH(x) was observed. It is concluded that the relatively strong Lewis acidic sites in the Rh/ZrO(2)-HT catalyst is responsible for the strong absorption of EtOH molecules, and the subsequent C-H breakage step (formation of acetaldehyde or called as dehydrogenation reaction) is a fast reaction on it; on the Rh/ZrO(2)-CP catalyst, the EtOH adsorption was weak and the C-C breakage was the dominating reaction which led to the accumulation of surface CO, CH(x) and CO(2) species. Therefore, it is believed that, in order to promote the absorption of EtOH molecules and to reduce the formation of metastable carbonaceous species (C(2) oxygenates) during the reaction, the catalyst should be enhanced both with Lewis acidity and with C-C bond breakage function. Also

  19. A phase field approach with a reaction pathways-based potential to model reconstructive martensitic transformations with a large number of variants

    NASA Astrophysics Data System (ADS)

    Denoual, C.; Vattré, A.

    2016-05-01

    A pathway tree is constructed by recursively duplicating a single reconstructive martensitic transformation path with respect to lattice symmetries and point-group rotations. An energy potential built on this pathway is implemented in a phase-field technique in large strain framework, with the transformational strain as the order parameter. A specific splitting between non-dissipative elastic behavior and the dissipative evolution of the order parameter allows for the modeling of acoustic waves during rapid transformations. A simple toy-model transition from hexa- to square-lattice successfully demonstrates the possibility to model reconstructive martensitic transformations for a large number of variants (more than one hundred). Pure traction applied to our toy-model shows that variants can nucleate into previously created variants, with a hierarchical nucleation of variants spanning over five levels of transformation.

  20. Reaction Mechanism of the Symmetry-Forbidden [2+2] Addition of Ethylene and Acetylene to Amido-Substituted Digermynes and Distannynes Ph2N-EE-NPh2, (E = Ge, Sn): A Theoretical Study.

    PubMed

    Zhao, Lili; Jones, Cameron; Frenking, Gernot

    2015-08-24

    Quantum chemical calculations of reaction mechanisms for the formal [2+2] addition of ethylene and acetylene to the amido-substituted digermyne and distannyne Ph2N-EE-NPh2 (E = Ge, Sn) have been carried out by using density functional theory at the BP86/def2-TZVPP level. The nature and bonding situations were studied with the NBO method and with the charge and energy decomposition analysis EDA-NOCV. The addition of ethylene to Ph2N-EE-NPh2 takes place through an initial [2+1] addition to one metal atom and consecutive rearrangement to four-membered cyclic species, which feature a weak E-E bond. Rotation about the C-C bond with concomitant rupture of the E-E bond leads to the 1,2-disubstituted ethanes, which have terminal E(NPh2) groups. The overall reaction Ph2N-EE-NPh2+C2H4→(Ph2N)E-C2H4-E(NPh2) has very low activation barriers and is slightly exergonic for E = Ge but slightly endergonic for E = Sn. The analysis of the electronic structure shows that there is charge donation of nearly one electron to the ethylene moiety already in the first part of the reaction. The energy partitioning analysis suggests that the HOMO(Ph2N-EE-NPh2)→LUMO(C2H4) interaction has a similar strength as the HOMO(C2H4)→LUMO(Ph2N-EE-NPh2) interaction. The [2+2] addition of acetylene to Ph2N-EE-NPh2 also takes place through an initial [2+1] approach, which eventually leads to 1,2-disubstituted olefins (Ph2N)E-C2H2-E(NPh2). The formation of the energetically lowest lying conformations of cis-(Ph2N)E-C2H2-E(NPh2), which occurs with very low activation barriers, is clearly exergonic for the germanium and the tin compound. The trans-coordinated isomers of (Ph2N)E-C2H2-E(NPh2) are slightly lower in energy than the cis form but they are separated by a substantial energy barrier for the rotation about the C-C bond. The energy decomposition analysis indicates that the initial reaction takes place under formation of electron-sharing bonds between triplet fragments rather than HOMO

  1. MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information

    PubMed Central

    2013-01-01

    Background A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information. The dominant paradigm in metabolic reconstruction is to assign functional annotations using BLAST. Functional annotations are then projected onto symbolic representations of metabolism in the form of KEGG pathways or SEED subsystems. Results Here we present MetaPathways, an open source pipeline for pathway inference that uses the PathoLogic algorithm to map functional annotations onto the MetaCyc collection of reactions and pathways, and construct environmental Pathway/Genome Databases (ePGDBs) compatible with the editing and navigation features of Pathway Tools. The pipeline accepts assembled or unassembled nucleotide sequences, performs quality assessment and control, predicts and annotates noncoding genes and open reading frames, and produces inputs to PathoLogic. In addition to constructing ePGDBs, MetaPathways uses MLTreeMap to build phylogenetic trees for selected taxonomic anchor and functional gene markers, converts General Feature Format (GFF) files into concatenated GenBank files for ePGDB construction based on third-party annotations, and generates useful file formats including Sequin files for direct GenBank submission and gene feature tables summarizing annotations, MLTreeMap trees, and ePGDB pathway coverage summaries for statistical comparisons. Conclusions MetaPathways provides users with a modular annotation and analysis pipeline for predicting metabolic interaction networks from environmental sequence information using an alternative to KEGG pathways and SEED subsystems mapping. It is extensible to genomic and transcriptomic datasets from a wide range of sequencing platforms, and generates useful data products for microbial community structure and function analysis. The MetaPathways software package

  2. D5h [PhSiO1.5]10 synthesis via F(-) catalyzed rearrangement of [PhSiO1.5]n. An experimental/computational analysis of likely reaction pathways.

    PubMed

    Furgal, Joseph C; Goodson, Theodore; Laine, Richard M

    2016-01-21

    We describe here the synthesis and analysis of the reaction pathways leading to formation of the rare D5h decaphenylsilsesquioxane (SQ) [PhSiO1.5]10via F(-) catalyzed rearrangement of [PhSiO1.5]nn = 8, 12, and oligomers initially synthesized from PhSi(OEt)3. Isolated yields of ∼50% [PhSiO1.5]10 are obtained via rearrangement of all starting materials. The recovered starting materials can be re-equilibrated using catalytic F(-) to generate similar yields in second batches. These yields arise because [PhSiO1.5]10 exhibits higher solubility and better energy stabilization (10 kcal mol(-1) theory) in CH2Cl2 compared to [PhSiO1.5]8 or [PhSiO1.5]12. Reaction intermediates were identified using time dependent (19)F NMR and MALDI-ToF mass spectrometry eventually equilibrating to form the 8 : 10 : 12 cages in a 1 : 3 : 1.3 equilibrium in CH2Cl2. Experimental results coupled with modeling using the Gamess computational package provide multiple reasonable pathways for SQ rearrangements to [RSiO1.5]10, starting from [RSiO1.5]8. Heats of reaction for interconversion of the model intermediates [HSiO1.5]x determined computationally, were used to select the most reasonable reaction pathways. The findings support a mechanism involving activation and cleavage of a T8 cage corner by F(-) attachment, followed by the corners stepwise removal as [i.e. RSi(OH)3], followed thereafter by reinsertion forming [RSiO1.5]9-OH followed by, insertion of another corner to form [RSiO1.5]10-(OH)2 and finally condensation to give [RSiO1.5]10. The most enthalpically favorable path (-24 kcal mol(-1)) involves a hybrid mechanism. PMID:26648403

  3. Chemical pathway analysis of the Martian atmosphere: CO2-formation pathways

    NASA Astrophysics Data System (ADS)

    Stock, Joachim W.; Boxe, Christopher S.; Lehmann, Ralph; Grenfell, J. Lee; Patzer, A. Beate C.; Rauer, Heike; Yung, Yuk L.

    2012-05-01

    The chemical composition of a planetary atmosphere plays an important role for atmospheric structure, stability, and evolution. Potentially complex interactions between chemical species do not often allow for an easy understanding of the underlying chemical mechanisms governing the atmospheric composition. In particular, trace species can affect the abundance of major species by acting in catalytic cycles. On Mars, such cycles even control the abundance of its main atmospheric constituent CO2. The identification of catalytic cycles (or more generally chemical pathways) by hand is quite demanding. Hence, the application of computer algorithms is beneficial in order to analyze complex chemical reaction networks. Here, we have performed the first automated quantified chemical pathways analysis of the Martian atmosphere with respect to CO2-production in a given reaction system. For this, we applied the Pathway Analysis Program (PAP) to output data from the Caltech/JPL photochemical Mars model. All dominant chemical pathways directly related to the global CO2-production have been quantified as a function of height up to 86 km. We quantitatively show that CO2-production is dominated by chemical pathways involving HOx and Ox. In addition, we find that NOx in combination with HOx and Ox exhibits a non-negligible contribution to CO2-production, especially in Mars' lower atmosphere. This study reveals that only a small number of chemical pathways contribute significantly to the atmospheric abundance of CO2 on Mars; their contributions to CO2-production vary considerably with altitude. This analysis also endorses the importance of transport processes in governing CO2-stability in the Martian atmosphere. Lastly, we identify a previously unknown chemical pathway involving HOx, Ox, and HO2-photodissociation, contributing 8% towards global CO2-production by chemical pathways using recommended up-to-date values for reaction rate coefficients.

  4. Structural Milestones in the Reaction Pathway of an Amide Hydrolase: Substrate, Acyl, and Product Complexes of Cephalothin with AmpC [beta]-Lactamase

    SciTech Connect

    Beadle, Beth M.; Trehan, Indi; Focia, Pamela J.; Shoichet, Brian K.

    2010-03-05

    {beta}-lactamases hydrolyze {beta}-lactam antibiotics and are the leading cause of bacterial resistance to these drugs. Although {beta}-lactamases have been extensively studied, structures of the substrate-enzyme and product-enzyme complexes have proven elusive. Here, the structure of a mutant AmpC in complex with the {beta}-lactam cephalothin in its substrate and product forms was determined by X-ray crystallography to 1.53 {angstrom} resolution. The acyl-enzyme intermediate between AmpC and cephalothin was determined to 2.06 {angstrom} resolution. The ligand undergoes a dramatic conformational change as the reaction progresses, with the characteristic six-membered dihydrothiazine ring of cephalothin rotating by 109{sup o}. These structures correspond to all three intermediates along the reaction path and provide insight into substrate recognition, catalysis, and product expulsion.

  5. Low-T, Fluid-Ashflow-Tuff Interactions: How Rock Textures, Chemistry and Mineralogy Reflect Reaction Pathways and Influence Rock Response to Heating

    SciTech Connect

    Sorena S. Sorensen

    2002-04-01

    Near-surface,low-temperature,K-metasomatism of rhyolitic to dacitic ash-flow tuffs is a volumetrically and petrologically significant feature of the western United States and may be a primary alteration path in arid lands. Cathodoluminesence (CL) petrography of K-metasomatized ash-flow tuffs quickly yields information about the mineralogical changes and reaction mechanisms during alteration of large sample suites. Such changes can be linked to geochemical changes of major, minor and trace elements and of oxygen isotope values.

  6. A theoretical study on the reaction pathways and the mechanism of 1,3- dipolar cycloaddition of vinyl acetylene and methyl azide.

    PubMed

    Siadati, Seyyed Amir; Mahboobifar, Ali; Nasiri, Ramin

    2014-01-01

    1,3-dipolar cycloaddition procedure is one of the most widely practiced methods in order to synthesize heterocyclic compounds. Although, it seems very simple, but, there are numerous precursors of heterocyclic molecules who have more than one positions to react with a 1,3-dipole species. As a result, while using a precursor with more than one position for reaction, it is probable to synthesize several products with different structures. This paper studies all possible interactions of vinyl acetylene, which has two positions for reaction, with methyl azide. This reaction could lead to the emergence of any 1,3-dipolar cycloaddition products. Our ultimate goal is to help researchers to find out how precursors containing both carbon-carbon double, and the triple bonds interact with 1,3- dipolar species. The present study used the DFT calculations at B3LYP/6-311++G(3df,pd) level to check all probable interactions between vinyl acetylene and methyl azide, and determined Potential Energy Surface, and optimized all species. PMID:24852164

  7. Reactions of CF3-enones with arenes under superelectrophilic activation: a pathway to trans-1,3-diaryl-1-CF3-indanes, new cannabinoid receptor ligands.

    PubMed

    Iakovenko, Roman O; Kazakova, Anna N; Muzalevskiy, Vasiliy M; Ivanov, Alexander Yu; Boyarskaya, Irina A; Chicca, Andrea; Petrucci, Vanessa; Gertsch, Jürg; Krasavin, Mikhail; Starova, Galina L; Zolotarev, Andrey A; Avdontceva, Margarita S; Nenajdenko, Valentine G; Vasilyev, Aleksander V

    2015-09-01

    4-Aryl-1,1,1-trifluorobut-3-en-2-ones ArCH[double bond, length as m-dash]CHCOCF3 (CF3-enones) react with arenes in excess of Brønsted superacids (TfOH, FSO3H) to give, stereoselectively, trans-1,3-diaryl-1-trifluoromethyl indanes in 35-85% yields. The reaction intermediates, the O-protonated ArCH[double bond, length as m-dash]CHC(OH(+))CF3 and the O,C-diprotonated ArHC(+)CH2C(OH(+))CF3 species, have been studied by means of (1)H, (13)C, (19)F NMR, and DFT calculations. Both types of the cations may participate in the reaction, depending on their electrophilicity and electron-donating properties of the arenes. The formation of CF3-indanes is a result of cascade reaction of protonated CF3-enones to form chemo-, regio- and stereoselectively three new C-C bonds. The obtained trans-1,3-diaryl-1-trifluoromethyl indanes were investigated as potential ligands for cannabinoid receptors CB1 and CB2 types. The most potent compound showed sub-micromolar affinity for both receptor subtypes with a 6-fold selectivity toward the CB2 receptor with no appreciable cytotoxicity toward SHSY5Y cells. PMID:26186675

  8. Palladium-catalyzed oxidative carbonylation reactions.

    PubMed

    Wu, Xiao-Feng; Neumann, Helfried; Beller, Matthias

    2013-02-01

    Palladium-catalyzed coupling reactions have become a powerful tool for advanced organic synthesis. This type of reaction is of significant value for the preparation of pharmaceuticals, agrochemicals, as well as advanced materials. Both, academic as well as industrial laboratories continuously investigate new applications of the different methodologies. Clearly, this area constitutes one of the major topics in homogeneous catalysis and organic synthesis. Among the different palladium-catalyzed coupling reactions, several carbonylations have been developed and widely used in organic syntheses and are even applied in the pharmaceutical industry on ton-scale. Furthermore, methodologies such as the carbonylative Suzuki and Sonogashira reactions allow for the preparation of interesting building blocks, which can be easily refined further on. Although carbonylative coupling reactions of aryl halides have been well established, palladium-catalyzed oxidative carbonylation reactions are also interesting. Compared with the reactions of aryl halides, oxidative carbonylation reactions offer an interesting pathway. The oxidative addition step could be potentially avoided in oxidative reactions, but only few reviews exist in this area. In this Minireview, we summarize the recent development in the oxidative carbonylation reactions. PMID:23307763

  9. Food additives

    MedlinePlus

    Food additives are substances that become part of a food product when they are added during the processing or making of that food. "Direct" food additives are often added during processing to: Add nutrients ...

  10. Real-time Monitoring of Intermediates Reveals the Reaction Pathway in the Thiol-Disulfide Exchange between Disulfide Bond Formation Protein A (DsbA) and B (DsbB) on a Membrane-immobilized Quartz Crystal Microbalance (QCM) System*

    PubMed Central

    Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

    2013-01-01

    Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

  11. Real-time monitoring of intermediates reveals the reaction pathway in the thiol-disulfide exchange between disulfide bond formation protein A (DsbA) and B (DsbB) on a membrane-immobilized quartz crystal microbalance (QCM) system.

    PubMed

    Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio

    2013-12-13

    Disulfide bond formation protein B (DsbBS-S,S-S) is an inner membrane protein in Escherichia coli that has two disulfide bonds (S-S, S-S) that play a role in oxidization of a pair of cysteine residues (SH, SH) in disulfide bond formation protein A (DsbASH,SH). The oxidized DsbAS-S, with one disulfide bond (S-S), can oxidize proteins with SH groups for maturation of a folding preprotein. Here, we have described the transient kinetics of the oxidation reaction between DsbASH,SH and DsbBS-S,S-S. We immobilized DsbBS-S,S-S embedded in lipid bilayers on the surface of a 27-MHz quartz crystal microbalance (QCM) device to detect both formation and degradation of the reaction intermediate (DsbA-DsbB), formed via intermolecular disulfide bonds, as a mass change in real time. The obtained kinetic parameters (intermediate formation, reverse, and oxidation rate constants (kf, kr, and kcat, respectively) indicated that the two pairs of cysteine residues in DsbBS-S,S-S were more important for the stability of the DsbA-DsbB intermediate than ubiquinone, an electron acceptor for DsbBS-S,S-S. Our data suggested that the reaction pathway of almost all DsbASH,SH oxidation processes would proceed through this stable intermediate, avoiding the requirement for ubiquinone. PMID:24145032

  12. Developmentally regulated interconversions between end product-inhibitable and noninhibitable forms of a first pathway-specific enzyme activity can be mimicked in vitro by protein dephosphorylation-phosphorylation reactions.

    PubMed

    Frisa, P S; Sonneborn, D R

    1982-10-01

    During the life cycle of Blastocladiella emersonii, dramatic shifts occur in the sensitivity of the first hexosamine biosynthetic pathway-specific enzyme [amidotransferase; 2-amino-2-deoxy-D-glucose-6-phosphate ketol-isomerase (amino-transferring), EC 5.3.1.19] to end product inhibition. These shifts are developmentally correlated with changes in the utilization of the end product (uridine-5'-diphospho-N-acetylglucosamine) for chitin synthesis [Selitrennikoff, C. P., Dalley, N. E. & Sonneborn, D. R. (1980) Proc. Natl. Acad. Sci. USA 77, 5998-6002]. Alterations in amidotransferase sensitivity to end product inhibition can be mimicked by in vitro protein dephosphorylation-phosphorylation reactions, as follows: (i) Zoospore end product-inhibitable amidotransferase activity can be converted to a noninhibitable form by an endogenous (zoospore) protein phosphatase (phosphoprotein phosphohydrolase EC 3.1.3.16) reaction; this noninhibitable form can be converted back to an inhibitable form either by an endogenous cAMP-independent protein kinase (ATP:protein phosphotransferase, EC 2.7.1.37) reaction or with an added cAMP-dependent protein kinase. (ii) Noninhibitable amidotransferase activity from growing cells can also be converted to the inhibitable form with added protein kinase. PMID:6959119

  13. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  14. Acetic Acid Reforming over Rh Supported on La2O3/CeO2-ZrO2: Catalytic Performance and Reaction Pathway Analysis

    SciTech Connect

    Lemonidou, Angeliki A.; Vagia, Ekaterini C.; Lercher, Johannes A.

    2013-07-11

    Reforming of acetic acid was investigated on Rh supported on CeO2-ZrO2 modified with 3 wt % La. The active catalyst converted acetic acid to H-2-rich gas and hardly formed coke. The low rate of coke formation is concluded to be related to the presence of redox-active oxygen limiting the concentration of coke precursors. Temperature-programmed O-18(2)) isotope exchange measurements showed that the La2O3 and Rh enhanced the mobility of lattice oxygen compared with that of the parent CeO2-ZrO2. Ketonization and decarboxylation of acetic acid are the dominating reactions over the latter up to 600 degrees C, whereas above 600 degrees C, steam reforming and water gas shift also contribute. Over 0.5 wt % Rh on La2O3/CeO2-ZrO2, reforming and water gas shift reactions dominate, even below 300 degrees C, producing mostly H-2 and CO2. Using isotope labeling, it is shown that acetic acid adsorbs dissociatively on Rh, forming acetates, which sequentially decarboxylate and form surface methyl groups. The latter are in turn converted to CO, CO2, and H-2.

  15. Why did Italians protest against Berlusconi's sexist behaviour? The role of sexist beliefs and emotional reactions in explaining women and men's pathways to protest.

    PubMed

    Paladino, Maria-Paola; Zaniboni, Sara; Fasoli, Fabio; Vaes, Jeroen; Volpato, Chiara

    2014-06-01

    By taking advantage of the Italian protest in 2009 in reaction to the behaviour of then Prime Minister Berlusconi, in this research, we investigated the role of sexist beliefs (i.e., hostile sexism, complementary gender differentiation, protective paternalism, and heterosexual intimacy) and group-based emotional reactions (i.e., anger, humiliation, and sadness) to women's and men's action mobilization against public forms of sexism. The findings of this study suggest that women and men engaged in this protest for different reasons. Women mobilized to express their anger at Berlusconi's sexist behaviour, an emotion related to the condemnation of hostile sexist views and benevolent sexist beliefs about heterosexual intimacy. In contrast, the strength of men's participation in the protest was affected by humiliation, an emotion related to the condemnation of hostile sexist beliefs and support for complementary gender differentiation. This emotional path suggests that men likely protested to restore their reputations. These findings underline the role of sexist beliefs and group-based emotions in transforming the condemnation of a sexist event into action mobilization against sexism for both women and men. PMID:23330650

  16. Reaction of carboranyl boron-centered radicals with phosphites and the addition of carborane-containing and some other phosphoranyl radicals to 3,6-di-tert-butyl-ortho-benzoquinone

    SciTech Connect

    Tumanskii, B.L.; Kampel', V.Ts.; Bregadze, VI.; Bubnov, N.N.; Solodovnikov, S.P.; Prokof'ev, A.I.; Kozlov, E.S.; Godovikov, N.N.; Kabachnik, M.I.

    1986-08-20

    The preparative photolysis of bis(m-carboran-9-yl)mercury and bis(p-carboran-2-yl)-mercury with trimethyl phosphite leads to the dimethyl esters of m- and p-B-carboranylphosphonic acids. The reaction of carboranyl boron-centered radicals with phosphites occurs through the formation of a phosphoranyl radical. The addition of the phosphoranyl radicals derived from 2,6,7-tris(trichloromethyl)-3,5,8-trioxo-1,4-diphosphabicyclo(2.2.2)octane to 3,6-di-tert-butyl-ortho-benzoquinone was detected. ESR spectroscopy was used to observe the tautomeric transfers of the phosphoranyl group between the ortho-benzoquinone oxygen atoms.

  17. Energy-transfer and charge-separation pathways in the reaction center of photosystem II revealed by coherent two-dimensional optical spectroscopy

    PubMed Central

    Abramavicius, Darius; Mukamel, Shaul

    2010-01-01

    The excited state dynamics and relaxation of electrons and holes in the photosynthetic reaction center of photosystem II are simulated using a two-band tight-binding model. The dissipative exciton and charge carrier motions are calculated using a transport theory, which includes a strong coupling to a harmonic bath with experimentally determined spectral density, and reduces to the Redfield, the Förster, and the Marcus expressions in the proper parameter regimes. The simulated third order two-dimensional signals, generated in the directions −k1+k2+k3, k1−k2+k3, and k1+k2−k3, clearly reveal the exciton migration and the charge-separation processes. PMID:21073225

  18. A New Bioinspired Perchlorate Reduction Catalyst with Significantly Enhanced Stability via Rational Tuning of Rhenium Coordination Chemistry and Heterogeneous Reaction Pathway.

    PubMed

    Liu, Jinyong; Han, Mengwei; Wu, Dimao; Chen, Xi; Choe, Jong Kwon; Werth, Charles J; Strathmann, Timothy J

    2016-06-01

    Rapid reduction of aqueous ClO4(-) to Cl(-) by H2 has been realized by a heterogeneous Re(hoz)2-Pd/C catalyst integrating Re(O)(hoz)2Cl complex (hoz = oxazolinyl-phenolato bidentate ligand) and Pd nanoparticles on carbon support, but ClOx(-) intermediates formed during reactions with concentrated ClO4(-) promote irreversible Re complex decomposition and catalyst deactivation. The original catalyst design mimics the microbial ClO4(-) reductase, which integrates Mo(MGD)2 complex (MGD = molybdopterin guanine dinucleotide) for oxygen atom transfer (OAT). Perchlorate-reducing microorganisms employ a separate enzyme, chlorite dismutase, to prevent accumulation of the destructive ClO2(-) intermediate. The structural intricacy of MGD ligand and the two-enzyme mechanism for microbial ClO4(-) reduction inspired us to improve catalyst stability by rationally tuning Re ligand structure and adding a ClOx(-) scavenger. Two new Re complexes, Re(O)(htz)2Cl and Re(O)(hoz)(htz)Cl (htz = thiazolinyl-phenolato bidentate ligand), significantly mitigate Re complex decomposition by slightly lowering the OAT activity when immobilized in Pd/C. Further stability enhancement is then obtained by switching the nanoparticles from Pd to Rh, which exhibits high reactivity with ClOx(-) intermediates and thus prevents their deactivating reaction with the Re complex. Compared to Re(hoz)2-Pd/C, the new Re(hoz)(htz)-Rh/C catalyst exhibits similar ClO4(-) reduction activity but superior stability, evidenced by a decrease of Re leaching from 37% to 0.25% and stability of surface Re speciation following the treatment of a concentrated "challenge" solution containing 1000 ppm of ClO4(-). This work demonstrates the pivotal roles of coordination chemistry control and tuning of individual catalyst components for achieving both high activity and stability in environmental catalyst applications. PMID:27182602

  19. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

    PubMed Central

    Caspi, Ron; Billington, Richard; Ferrer, Luciana; Foerster, Hartmut; Fulcher, Carol A.; Keseler, Ingrid M.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Ong, Quang; Paley, Suzanne; Subhraveti, Pallavi; Weaver, Daniel S.; Karp, Peter D.

    2016-01-01

    The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service. PMID:26527732

  20. Tougher Addition Polyimides Containing Siloxane

    NASA Technical Reports Server (NTRS)

    St. Clair, T. L.; Maudgal, S.

    1986-01-01

    Laminates show increased impact resistances and other desirable mechanical properties. Bismaleamic acid extended by reaction of diaminosiloxane with maleic anhydride in 1:1 molar ratio, followed by reaction with half this molar ratio of aromatic dianhydride. Bismaleamic acid also extended by reaction of diaminosiloxane with maleic anhydride in 1:2 molar ratio, followed by reaction with half this molar ratio of aromatic diamine (Michael-addition reaction). Impact resistances improved over those of unmodified bismaleimide, showing significant increase in toughness. Aromatic addition polyimides developed as both matrix and adhesive resins for applications on future aircraft and spacecraft.

  1. Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO-LCMO approach

    NASA Astrophysics Data System (ADS)

    Nishioka, Hirotaka; Ando, Koji

    2011-05-01

    By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], 10.1016/j.cplett.2009.05.069, we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling TDA of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate TDA. Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable TDA for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.

  2. Controlling Catalytic Selectivity via Adsorbate Orientation on the Surface: From Furfural Deoxygenation to Reactions of Epoxides.

    PubMed

    Pang, Simon H; Medlin, J Will

    2015-04-16

    Specificity to desired reaction products is the key challenge in designing solid catalysts for reactions involving addition or removal of oxygen to/from organic reactants. This challenge is especially acute for reactions involving multifunctional compounds such as biomass-derived aromatic molecules (e.g., furfural) and functional epoxides (e.g., 1-epoxy-3-butene). Recent surface-level studies have shown that there is a relationship between adsorbate surface orientation and reaction selectivity in the hydrogenation pathways of aromatic oxygenates and the ring-opening or ring-closing pathways of epoxides. Control of the orientation of reaction intermediates on catalytic surfaces by modifying the surface or near-surface environment has been shown to be a promising method of affecting catalytic selectivity for reactions of multifunctional molecules. In this Perspective, we review recent model studies aimed at understanding the surface chemistry for these reactions and studies that utilize this insight to rationally design supported catalysts. PMID:26263134

  3. Curation and Computational Design of Bioenergy-Related Metabolic Pathways

    SciTech Connect

    Karp, Peter D.

    2014-09-12

    . The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.

  4. Reactions of C{sub 2}H{sub 5} radicals with O, O{sub 3}, and NO{sub 3}: Decomposition pathways of the intermediate C{sub 2}H{sub 5}O radical

    SciTech Connect

    Hoyermann, K.; Seeba, J.; Olzmann, M.; Viskolcz

    1999-07-22

    Alkoxy radicals are important species in the atmospheric degradation of hydrocarbons as well as in combustion processes. Additionally, they play a crucial role in the pyrolysis of oxygen-containing hydrocarbons. The reactions of C{sub 2}H{sub 5} with O, O{sub 3}, and NO{sub 3} have been investigated in a discharge flow reactor at room temperature and pressures between 1 and 3 mbar. The reaction products were detected by mass spectrometry with electron-impact ionization. The product pattern observed is explained in terms of the decomposition of an intermediately formed, chemically activated ethoxy radical. It is shown that, with this assumption, the experimentally determined branching ratios of the different product channels can be reproduced nearly quantitatively by RRKM calculations based on ab initio results for the stationary points of the potential energy surface of C{sub 2}H{sub 5}O. For C{sub 2}H{sub 5} + O and C{sub 2}H{sub 5} + O{sub 3}, the existence of an additional, parallel channel leading to OH has to be assumed.. High-pressure Arrhenius parameters for the unimolecular reactions of the ethoxy radical are given and discussed.

  5. Detecting a quasi-stable imine species on the reaction pathway of SHV-1 β-lactamase and 6β-(hydroxymethyl)penicillanic acid sulfone.

    PubMed

    Che, Tao; Rodkey, Elizabeth A; Bethel, Christopher R; Shanmugam, Sivaprakash; Ding, Zhe; Pusztai-Carey, Marianne; Nottingham, Michael; Chai, Weirui; Buynak, John D; Bonomo, Robert A; van den Akker, Focco; Carey, Paul R

    2015-01-27

    For the class A β-lactamase SHV-1, the kinetic and mechanistic properties of the clinically used inhibitor sulbactam are compared with the sulbactam analog substituted in its 6β position by a CH2OH group (6β-(hydroxymethyl)penicillanic acid). The 6β substitution improves both in vitro and microbiological inhibitory properties of sulbactam. Base hydrolysis of both compounds was studied by Raman and NMR spectroscopies and showed that lactam ring opening is followed by fragmentation of the dioxothiazolidine ring leading to formation of the iminium ion within 3 min. The iminium ion slowly loses a proton and converts to cis-enamine (which is a β-aminoacrylate) in 1 h for sulbactam and in 4 h for 6β-(hydroxymethyl) sulbactam. Rapid mix-rapid freeze Raman spectroscopy was used to follow the reactions between the two sulfones and SHV-1. Within 23 ms, a 10-fold excess of sulbactam was entirely hydrolyzed to give a cis-enamine product. In contrast, the 6β-(hydroxymethyl) sulbactam formed longer-lived acyl-enzyme intermediates that are a mixture of imine and enamines. Single crystal Raman studies, soaking in and washing out unreacted substrates, revealed stable populations of imine and trans-enamine acyl enzymes. The corresponding X-ray crystallographic data are consonant with the Raman data and also reveal the role played by the 6β-hydroxymethyl group in retarding hydrolysis of the acyl enzymes. The 6β-hydroxymethyl group sterically hinders approach of the water molecule as well as restraining the side chain of E166 that facilitates hydrolysis. PMID:25536850

  6. Detecting a Quasi-stable Imine Species on the Reaction Pathway of SHV-1 β-Lactamase and 6β-(Hydroxymethyl)penicillanic Acid Sulfone

    PubMed Central

    2015-01-01

    For the class A β-lactamase SHV-1, the kinetic and mechanistic properties of the clinically used inhibitor sulbactam are compared with the sulbactam analog substituted in its 6β position by a CH2OH group (6β-(hydroxymethyl)penicillanic acid). The 6β substitution improves both in vitro and microbiological inhibitory properties of sulbactam. Base hydrolysis of both compounds was studied by Raman and NMR spectroscopies and showed that lactam ring opening is followed by fragmentation of the dioxothiazolidine ring leading to formation of the iminium ion within 3 min. The iminium ion slowly loses a proton and converts to cis-enamine (which is a β-aminoacrylate) in 1 h for sulbactam and in 4 h for 6β-(hydroxymethyl) sulbactam. Rapid mix–rapid freeze Raman spectroscopy was used to follow the reactions between the two sulfones and SHV-1. Within 23 ms, a 10-fold excess of sulbactam was entirely hydrolyzed to give a cis-enamine product. In contrast, the 6β-(hydroxymethyl) sulbactam formed longer-lived acyl–enzyme intermediates that are a mixture of imine and enamines. Single crystal Raman studies, soaking in and washing out unreacted substrates, revealed stable populations of imine and trans-enamine acyl enzymes. The corresponding X-ray crystallographic data are consonant with the Raman data and also reveal the role played by the 6β-hydroxymethyl group in retarding hydrolysis of the acyl enzymes. The 6β-hydroxymethyl group sterically hinders approach of the water molecule as well as restraining the side chain of E166 that facilitates hydrolysis. PMID:25536850

  7. Detailed Chemical Kinetic Reaction Mechanism for Biodiesel Components Methyl Stearate and Methyl Oleate

    SciTech Connect

    Naik, C; Westbrook, C K; Herbinet, O; Pitz, W J; Mehl, M

    2010-01-22

    New chemical kinetic reaction mechanisms are developed for two of the five major components of biodiesel fuel, methyl stearate and methyl oleate. The mechanisms are produced using existing reaction classes and rules for reaction rates, with additional reaction classes to describe other reactions unique to methyl ester species. Mechanism capabilities were examined by computing fuel/air autoignition delay times and comparing the results with more conventional hydrocarbon fuels for which experimental results are available. Additional comparisons were carried out with measured results taken from jet-stirred reactor experiments for rapeseed methyl ester fuels. In both sets of computational tests, methyl oleate was found to be slightly less reactive than methyl stearate, and an explanation of this observation is made showing that the double bond in methyl oleate inhibits certain low temperature chain branching reaction pathways important in methyl stearate. The resulting detailed chemical kinetic reaction mechanism includes more approximately 3500 chemical species and more than 17,000 chemical reactions.

  8. A crossed molecular beam and ab-initio investigation of the reaction of boron monoxide (BO; X2Σ+) with methylacetylene (CH3CCH; X1A1): competing atomic hydrogen and methyl loss pathways.

    PubMed

    Maity, Surajit; Parker, Dorian S N; Dangi, Beni B; Kaiser, Ralf I; Fau, Stefan; Perera, Ajith; Bartlett, Rodney J

    2013-11-21

    The gas-phase reaction of boron monoxide ((11)BO; X(2)Σ(+)) with methylacetylene (CH3CCH; X(1)A1) was investigated experimentally using crossed molecular beam technique at a collision energy of 22.7 kJ mol(-1) and theoretically using state of the art electronic structure calculation, for the first time. The scattering dynamics were found to be indirect (complex forming reaction) and the reaction proceeded through the barrier-less formation of a van-der-Waals complex ((11)BOC3H4) followed by isomerization via the addition of (11)BO(X(2)Σ(+)) to the C1 and/or C2 carbon atom of methylacetylene through submerged barriers. The resulting (11)BOC3H4 doublet radical intermediates underwent unimolecular decomposition involving three competing reaction mechanisms via two distinct atomic hydrogen losses and a methyl group elimination. Utilizing partially deuterated methylacetylene reactants (CD3CCH; CH3CCD), we revealed that the initial addition of (11)BO(X(2)Σ(+)) to the C1 carbon atom of methylacetylene was followed by hydrogen loss from the acetylenic carbon atom (C1) and from the methyl group (C3) leading to 1-propynyl boron monoxide (CH3CC(11)BO) and propadienyl boron monoxide (CH2CCH(11)BO), respectively. Addition of (11)BO(X(2)Σ(+)) to the C1 of methylacetylene followed by the migration of the boronyl group to the C2 carbon atom and/or an initial addition of (11)BO(X(2)Σ(+)) to the sterically less accessible C2 carbon atom of methylacetylene was followed by loss of a methyl group leading to the ethynyl boron monoxide product (HCC(11)BO) in an overall exoergic reaction (78 ± 23 kJ mol(-1)). The branching ratios of these channels forming CH2CCH(11)BO, CH3CC(11)BO, and HCC(11)BO were derived to be 4 ± 3%, 40 ± 5%, and 56 ± 15%, respectively; these data are in excellent agreement with the calculated branching ratios using statistical RRKM theory yielding 1%, 38%, and 61%, respectively. PMID:23651442

  9. Multifunctional fuel additives

    SciTech Connect

    Baillargeon, D.J.; Cardis, A.B.; Heck, D.B.

    1991-03-26

    This paper discusses a composition comprising a major amount of a liquid hydrocarbyl fuel and a minor low-temperature flow properties improving amount of an additive product of the reaction of a suitable diol and product of a benzophenone tetracarboxylic dianhydride and a long-chain hydrocarbyl aminoalcohol.

  10. Radical Additions to Aromatic Residues in Peptides Facilitate Unexpected Side Chain and Backbone Losses

    NASA Astrophysics Data System (ADS)

    Zhang, Xing; Julian, Ryan R.

    2014-04-01

    Accurate identification of fragments in tandem mass spectrometry experiments is aided by knowledge of relevant fragmentation mechanisms. Herein, novel radical addition reactions that direct unexpected side-chain dissociations at tryptophan and tyrosine residues are reported. Various mechanisms that can account for the observed dissociation channels are investigated by experiment and theory. The propensity for radical addition at a particular site is found to be primarily under kinetic control, which is largely dictated by molecular structure. In certain peptides, intramolecular radical addition reactions are favored, which leads to the observation of numerous unexpected fragments. In one pathway, radical addition leads to migration of an aromatic side chain to another residue. Alternatively, radical addition followed by hydrogen atom loss leads to cyclization of the peptide and increased observation of internal sequence fragments. Radical addition reactions should be considered when assigning fragmentation spectra obtained from activation of hydrogen deficient peptides.

  11. Simultaneous synthesis of 2-phenylethanol and L-homophenylalanine using aromatic transaminase with yeast Ehrlich pathway.

    PubMed

    Hwang, Joon-Young; Park, Jihyang; Seo, Joo-Hyun; Cha, Minho; Cho, Byung-Kwan; Kim, Juhan; Kim, Byung-Gee

    2009-04-01

    2-Phenylethanol is a widely used aroma compound with rose-like fragrance and L-homophenylalanine is a building block of angiotensin-converting enzyme (ACE) inhibitor. 2-phenylethanol and L-homophenylalanine were synthesized simultaneously with high yield from 2-oxo-4-phenylbutyric acid and L-phenylalanine, respectively. A recombinant Escherichia coli harboring a coupled reaction pathway comprising of aromatic transaminase, phenylpyruvate decarboxylase, carbonyl reductase, and glucose dehydrogenase (GDH) was constructed. In the coupled reaction pathway, the transaminase reaction was coupled with the Ehrlich pathway of yeast; (1) a phenylpyruvate decarboxylase (YDR380W) as the enzyme to generate the substrate for the carbonyl reductase from phenylpyruvate (i.e., byproduct of the transaminase reaction) and to shift the reaction equilibrium of the transaminase reaction, and (2) a carbonyl reductase (YGL157W) to produce the 2-phenylethanol. Selecting the right carbonyl reductase showing the highest activity on phenylacetaldehyde with narrow substrate specificity was the key to success of the constructing the coupling reaction. In addition, NADPH regeneration was achieved by incorporating the GDH from Bacillus subtilis in the coupled reaction pathway. Based on 40 mM of L-phenylalanine used, about 96% final product conversion yield of 2-phenylethanol was achieved using the recombinant E. coli. PMID:19016485

  12. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  13. Phosphazene additives

    SciTech Connect

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  14. Effect of core-shell structure and chitosan addition on catalytic activities of copper-containing silica-aluminosilicate composites in deNO(x) reaction by H2.

    PubMed

    Chamnankid, Busaya; Samanpratan, Rattanaporn; Kongkachuichay, Paisan

    2012-12-01

    Mesoporous silica-aluminosilicate composites were used as supports for selective catalytic reduction of NO by H2 using copper catalyst. Effect of loading techniques and structures of the supports on the catalytic performance were investigated. The nature, the oxidation state of copper, the structural properties and the morphology of the catalysts were characterized by means of UV-vis spectra, Fourier Transform Infrared Spectroscopy (FTIR), nitrogen sorption, and transmission electron microscopy, respectively. By using substitution technique, the copper(II) species were introduced into the silica-aluminosilicate framework by replacing aluminum atoms that located in the tetrahedral coordination. On the other hand, by using incipient wetness impregnation method, the copper species were deposited on the surface of composite materials. Upon testing their performances in deNO(x) reaction, the catalysts prepared by incipient wetness impregnation method showed higher catalytic activity than those prepared by substitution technique in any copper content. The core-shell structure was able to enhance the catalytic performance. It was found that, among the tested catalysts, the 1.5% Cu loaded core-shell mesoporous silica aluminosilicate composites prepared by an incipient wetness impregnation yielded the highest NO conversion of approximately 59%. However, the addition of chitosan creating macroporosity and controlling the uniform small clusters did not improve the catalytic performance. PMID:23447996

  15. Elucidation of the pathway to astaxanthin in the flowers of Adonis aestivalis.

    PubMed

    Cunningham, Francis X; Gantt, Elisabeth

    2011-08-01

    A few species in the genus Adonis are the only land plants known to produce the valuable red ketocarotenoid astaxanthin in abundance. Here, we ascertain the pathway that leads from the β-rings of β-carotene, a carotenoid ubiquitous in plants, to the 3-hydroxy-4-keto-β-rings of astaxanthin (3,3'-dihydroxy-β,β-carotene-4,4'-dione) in the blood-red flowers of Adonis aestivalis, an ornamental and medicinal plant commonly known as summer pheasant's eye. Two gene products were found to catalyze three distinct reactions, with the first and third reactions of the pathway catalyzed by the same enzyme. The pathway commences with the activation of the number 4 carbon of a β-ring in a reaction catalyzed by a carotenoid β-ring 4-dehydrogenase (CBFD), continues with the further dehydrogenation of this carbon to yield a carbonyl in a reaction catalyzed by a carotenoid 4-hydroxy-β-ring 4-dehydrogenase, and concludes with the addition of an hydroxyl group at the number 3 carbon in a reaction catalyzed by the erstwhile CBFD enzyme. The A. aestivalis pathway is both portable and robust, functioning efficiently in a simple bacterial host. Our elucidation of the pathway to astaxanthin in A. aestivalis provides enabling technology for development of a biological production process and reveals the evolutionary origin of this unusual plant pathway, one unrelated to and distinctly different from those used by bacteria, green algae, and fungi to synthesize astaxanthin. PMID:21862704

  16. The reaction of an iridium PNP complex with parahydrogen facilitates polarisation transfer without chemical change† †Electronic supplementary information (ESI) available: Sample preparation, signal enhancements and raw data. CCDC 1026865. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4dt03088e Click here for additional data file. Click here for additional data file.

    PubMed Central

    Holmes, Arthur J.; Rayner, Peter J.; Cowley, Michael J.; Green, Gary G. R.; Whitwood, Adrian C.

    2015-01-01

    The short lived pincer complex [(C5H3N(CH2P(tBu)2)2)Ir(H)2(py)]BF4 is shown to be active for signal amplification by reversible exchange. This catalyst formulation enables the efficient transfer of polarization from parahydrogen to be placed into just a single molecule of the hyperpolarisation target, pyridine. When the catalysts 1H nuclei are replaced by 2H, increased levels of substrate hyperpolarization result and when the reverse situation is examined the catalyst itself is clearly visible through hyperpolarised signals. The ligand exchange pathways of [(C5H3N(CH2P(tBu)2)2)Ir(H)2(py)]BF4 that are associated with this process are shown to involve the formation of 16-electron [(C5H3N(CH2P(tBu)2)2)Ir(H)2]BF4 and the 18-electron H2 addition product [(C5H3N(CH2P(tBu)2)2)Ir(H)2(H2)]BF4. PMID:25410259

  17. Fuel Dependence of Benzene Pathways

    SciTech Connect

    Zhang, H; Eddings, E; Sarofim, A; Westbrook, C

    2008-07-14

    The relative importance of formation pathways for benzene, an important precursor to soot formation, was determined from the simulation of 22 premixed flames for a wide range of equivalence ratios (1.0 to 3.06), fuels (C{sub 1}-C{sub 12}), and pressures (20 to 760 torr). The maximum benzene concentrations in 15 out of these flames were well reproduced within 30% of the experimental data. Fuel structural properties were found to be critical for benzene production. Cyclohexanes and C{sub 3} and C{sub 4} fuels were found to be among the most productive in benzene formation; and long-chain normal paraffins produce the least amount of benzene. Other properties, such as equivalence ratio and combustion temperatures, were also found to be important in determining the amount of benzene produced in flames. Reaction pathways for benzene formation were examined critically in four premixed flames of structurally different fuels of acetylene, n-decane, butadiene, and cyclohexane. Reactions involving precursors, such as C{sub 3} and C{sub 4} species, were examined. Combination reactions of C{sub 3} species were identified to be the major benzene formation routes with the except