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Reaction Site (reaction + site)
Selected AbstractsA Practical Procedure for the Synthesis of Multifunctional Aldehydes Through the Fukuyama Reduction and Elucidation of the Reaction Site and Mechanism.CHEMINFORM, Issue 30 2004Mayumi Kimura Abstract For Abstract see ChemInform Abstract in Full Text. [source] Tuning the Reaction Site for Enzyme-Free Primer-Extension Reactions through Small Molecule SubstituentsCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2006Jan A. Rojas Stütz Dr. Abstract The replication of genetic information relies on the template-directed extension of DNA primers catalyzed by polymerases. The active sites of polymerases accept four different substrates and ensure fidelity and processivity for each of them. Because of the pivotal role of catalyzed primer extension for life, it is important to better understand this reaction on a molecular level. Here we present results from primer-extension reactions performed with chemical systems that show high reactivity in the absence of polymerases. Small molecular caps linked to the 5,-terminus of templates are shown to enhance the rate and selectivity of primer extension driven by 2-methylimidazolides as activated monomers for any of the four different templating bases (A, C, G, and T). The most consistent effect is provided by a stilbene carboxamide residue, rather than larger aromatic or aliphatic substituents. Up to 20-fold rate enhancements were achieved for the reactions at the terminus of the template. The preference for a medium size cap can be explained by competing interactions with both the oligonucleotides and the incoming deoxynucleotide. The data also show that there is no particularly intractable problem in combining promiscuity with fidelity. Exploratory experiments involving a longer template and a downstream-binding strand with a 5,-cap show up to 38-fold rate acceleration over the same reaction templated by a single overhanging nucleotide. [source] Homogeneous Two-Component Polycondensation Without Strict Stoichiometric Balance via the Tsuji,Trost Reaction: Remote Control of Two Reaction Sites by Catalysis.CHEMINFORM, Issue 33 2004Nobuyoshi Nomura No abstract is available for this article. [source] Phosphonylation of 2-Amino- and 2-Amido-3-bromopyridines and 2-Amino-3-chloroquinoxalines with Triethyl PhosphiteEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 27 2009M. Shaker S. Adam Abstract The Tavs reaction of 2-amino- and 2-acylamido-3-bromopyridines 1 and 2 with triethyl phosphite in the presence of palladium acetate or chloride allows the synthesis of 2-amino- and 2-acylamidopyridine-3-phosphonates 3 and 4. A second ring nitrogen atom causes strong activation and leads to excellent yields in the phosphonylation of 2-amino-3-chloroquinoxalines. 2,3-Dichloroquinoxaline does not need a catalyst and undergoes double phosphonylation with sodium diethyl phosphite under Michaelis,Becker conditions. The results show an activating influence of pyridine nitrogen (,M) and deactivating influence of the amino group (+M). The reactivity of 1 and 2 in the Tavs coupling is compared with that of the 3-NH-2-bromopyridine position isomers and 2-bromoanilines and discussed in terms of the opposite effects of pyridine and amino(amido) nitrogen and different position of the N atoms towards the reaction site. The advantage of the Tavs reaction is the easy optimization because neither auxiliary ligands are required nor a base to trap the halide or a solvent. Triethyl phosphite itself acts as ligand and forms Pd0{P(OEt)3}n in the initial phase of the reaction. The structures of the products and the expected intramolecular N,H···O=P hydrogen bridging bonds were proven by solution NMR and by X-ray crystal structure analysis of single crystalline 3c.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Micellar catalysis on the redox reaction of glycolic acid with chromium(VI)INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 6 2001Kabir-ud-Din Chromium(VI) oxidation of glycolic acid in the absence and presence of cetyltrimethylammonium bromide (CTAB) and cetylpyridinium bromide (CPB) followed the same mechanism as shown by kinetic study. The reaction followed second-order kinetics, first-order in each reactant. The oxidation is strongly catalyzed by manganese(II) and cationic micelles of CTAB or CPB. The catalytic effect of micelles can be fitted to a model in which the reaction rate depends upon the concentration of both reactants in the micellar pseudophase. Some added inorganic salts (NaCl, NaBr, NaNO3, and Na2SO4) reduce the micellar catalysis by excluding glycolic acid from the reaction site. The reactivity of glycolic acid towards chromium(VI) has been discussed and also compared with those obtained previously for the reaction between chromium(VI) and the reductants oxalic and lactic acids. On the basis of the observed results, probable mechanisms have been proposed. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 377,386, 2001 [source] Intelligent structure design of membrane cathode assembly for direct methanol fuel cellINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 12 2005K. Furukawa Abstract The performance and the structural model of membrane electrode assembly (MEA) have been developed and experimentally verified with fundamental calculations of the direct methanol fuel cell (DMFC). The model provides information concerning the influence of the operating and structural parameters. The composition and performance optimization of MEA structure in DMFC has been investigated by including both electrochemical reaction and mass transport process. In the experimentation, the effect of Nafion content and loading method in the catalyst layer of cathode for DMFC was investigated. For the spray method electrode (SME), the cell performance and cathode performance using a dynamic hydrogen electrode (DHE) as a reference electrode was improved in comparison with those of the PME electrode by decreasing cathode potential. From ac impedance measurements of the cathode, the adsorption resistance of the SME electrode was decreased compared with that of the PME electrode. The higher cell performance was mostly dependent on the adsorption resistance. In the modelling, the cathode overpotential was decreased with increasing ionomer content, due to increasing ionic conductivity for proton transfer and the larger reaction site. The resistance to oxygen transport was increased at the same time, and became dominant at higher ionomer loadings, leading to an increase in the voltage loss. The ratio of ionomer to void space in the cathode affected the cathode polarization, which had the lowest resistance of oxygen diffusion at the ratio of 0.1,0.2. Copyright © 2005 John Wiley & Sons, Ltd. [source] FI Catalysts: A Molecular Zeolite for Olefin PolymerizationADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 10 2010Haruyuki Makio Abstract A bis(phenoxyimine) group 4 transition metal catalyst (now known as FI catalysts) can discern ethylene from a mixture of ethylene and propylene at more than 99% selectivity. Denisty function theory (DFT) calculations revealed a spatially confined reaction site in the transition states of the migratory insertion which is just the right size for an ethylene molecule but too small for a propylene one. The substituents adjacent to the phenoxy-oxygens are of crucial importance in developing the size/shape-selectivity. [source] Palladium(II) Complexes of C2 -Bridged Chiral Diphosphines: Application to Enantioselective Carbonyl-Ene ReactionsADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 8 2010He-Kuan Luo Abstract (11bR,11,bR)-4,4,-(1,2-Phenylene)bis[4,5-dihydro-3H -dinaphtho[2,1- c:1,,2,- e]phosphepin] [abbreviated as (R)-BINAPHANE], (3R,3,R,4S,4,S,11bS,11,bS)-4,4,-bis(1,1-dimethylethyl)-4,4,,5,5,-tetrahydro-3,3,-bi-3H -dinaphtho[2,1- c:1,,2,- e]phosphepin [(S)-BINAPINE], (1S,1,S,2R,2,R)-1,1,-bis(1,1-dimethylethyl)-2,2,-biphospholane [(S,S,R,R)-TANGPHOS] and (2R,2,R,5R,5,R)-1,1,-(1,2-phenylene)bis[2,5-bis(1-methylethyl)phospholane] [(R,R) -i- Pr-DUPHOS] are C2 -bridged chiral diphosphines that form stable complexes with palladium(II) and platinum(II) containing a five-membered chelate ring. The Pd(II)-BINAPHANE catalyst displayed good to excellent enantioselectivities with ee values as high as 99.0% albeit in low yields for the carbonyl-ene reaction between phenylglyoxal and alkenes. Its Pt(II) counterpart afforded improved yields while retaining satisfactory enantioselectivity. For the carbonyl-ene reaction between ethyl trifluoropyruvate and alkenes, the Pd(II)-BINAPHANE catalyst afforded both good yields and extremely high enantioselectivities with ees as high as 99.6%. A comparative study on the Pd(II) catalysts of the four C2 -bridged chiral diphosphines revealed that Pd(II)-BINAPHANE afforded the best enantioselectivity. The ee values derived from Pd(II)-BINAPHANE are much higher than those derived from the other three Pd(II) catalysts. A comparison of the catalyst structures shows that the Pd(II)-BINAPHANE catalyst is the only one that has two bulky (R)-binaphthyl groups close to the reaction site. Hence it creates a deep chiral space that can efficiently control the reaction behavior in the carbonyl-ene reactions resulting in excellent enantioselectivity. [source] Photo-induced cross-linking mechanism in azide,novolac negative photoresists: molecular level investigation using NMR spectroscopyMAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2003Debmalya Roy Abstract Negative photoresists are composed of a photoactive component (aromatic azides/bisazides) and cyclized rubber or novolac resin dissolved in an organic solvent. Hydrogen abstraction and/or insertion reaction of the reactive nitrene intermediate formed during photoirradiation of the azide result in a cross-linked network of the novolac resin. The molecular weight of novolac resin in the exposed part of the photoresist film thus increases compared with that of the unexposed part. This makes the exposed part insoluble in the alkaline developer. Exploiting this change in physical property, a pattern can be transferred to a substrate from a mask. A better understanding of the exact mechanism of cross-linking reactions is very important to the design of a high-performing negative photoresist. A quinone,imine-type complex has been proposed earlier involving the aromatic moiety of novolac resin as the reaction site. A more recent study focuses the attack of nitrene on the methylenic bridge and hydroxyl group of novolac resins, which were found to be responsible for the cross-linking reaction along with the aromatic moiety of novolac resin. However, in our study no evidence was found for the involvement of a methylenic hydrogen or aromatic moiety of novolac resin in the cross-linking reaction. The 1H NMR, 13C NMR and DEPT-135 spectra before and after photolysis indicate that the cross-linking site is predominantly the hydroxyl group of novolac resin. Multiple reaction sites of attack for the nitrene intermediate have been demonstrated in cashew nut shell liquid (CNSL)-based novolac resin by 1H NMR spectroscopy, which in turn further increases the cross-linked network in the exposed part of a negative photoresist. Copyright © 2003 John Wiley & Sons, Ltd. [source] Adjustment of leaf photosynthesis to shade in a natural canopy: rate parametersPLANT CELL & ENVIRONMENT, Issue 3 2005A. LAISK ABSTRACT The present study was performed to investigate the adjustment of the rate parameters of the light and dark reactions of photosynthesis to the natural growth light in leaves of an overstorey species, Betula pendula Roth, a subcanopy species, Tilia cordata P. Mill., and a herb, Solidago virgaurea L., growing in a natural plant community in Järvselja, Estonia. Shoots were collected from the site and individual leaves were measured in a laboratory applying a standardized routine of kinetic gas exchange, Chl fluorescence and 820 nm transmittance measurements. These measurements enabled the calculations of the quantum yield of photosynthesis and rate constants of excitation capture by photochemical and non-photochemical quenchers, rate constant for P700+ reduction via the cytochrome b6f complex with and without photosynthetic control, actual maximum and potential (uncoupled) electron transport rate, stomatal and mesophyll resistances for CO2 transport, Km(CO2) and Vm of ribulose-bisphosphate carboxylase-oxygenase (Rubisco) in vivo. In parallel, N, Chl and Rubisco contents were measured from the same leaves. No adjustment toward higher quantum yield in shade compared with sun leaves was observed, although relatively more N was partitioned to the light-harvesting machinery in shade leaves (H. Eichelmann et al., 2004). The electron transport rate through the Cyt b6f complex was strongly down-regulated under saturating light compared with darkness, and this was observed under atmospheric, as well as saturating CO2 concentration. In vivo Vm measurements of Rubisco were lower than corresponding reported measurements in vitro, and the kcat per reaction site varied widely between leaves and growth sites. The correlation between Rubisco Vm and the photosystem I density was stronger than between Vm and the density of Rubisco active sites. The results showed that the capacity of the photosynthetic machinery decreases in shade-adjusted leaves, but it still remains in excess of the actual photosynthetic rate. The photosynthetic control systems that are targeted to adjust the photosynthetic rate to meet the plant's needs and to balance the partial reactions of photosynthesis, down-regulate partial processes of photosynthesis: excess harvested light is quenched non-photochemically; excess electron transport capacity of Cyt b6f is down-regulated by ,pH-dependent photosynthetic control; Rubisco is synthesized in excess, and the number of activated Rubisco molecules is controlled by photosystem I-related processes. Consequently, the nitrogen contained in the components of the photosynthetic machinery is not used at full efficiency. The strong correlation between leaf nitrogen and photosynthetic performance is not due to the nitrogen requirements of the photosynthetic apparatus, but because a certain amount of energy must be captured through photosynthesis to maintain this nitrogen within a leaf. [source] Reductive transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine, and methylenedinitramine with elemental ironENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2005Seok-Young Oh Abstract Reductive (pre)treatment with elemental iron is a potentiallyuseful method for degrading nitramine explosives in water and soil. In the present study, we examined the kinetics, products, and mechanisms of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) degradation with elemental iron. Both RDX and HMX were transformed with iron to formaldehyde, NH, N2O, and soluble products. The yields of formaldehyde were relatively constant (71% ± 5%), whereas the yields of NH and N2O varied, depending on the nitramine and the mechanism. The reactions most likely were controlled by a surface process rather than by external mass transfer. Methylenedinitramine (MDNA) was an intermediate of both RDX and HMX and was transformed quantitatively to formaldehyde with iron. However, product distributions and kinetic modeling results suggest that MDNA represented a minor reaction path and accounted for only 30% of the RDX reacted and 14% of the formaldehyde produced. Additional experiments showed that RDX reduction with elemental iron could be mediated by graphite and Fe2+ sorbed to magnetite, as demonstrated previously for nitroaromatics and nitrate esters. Methylenedinitramine was degraded primarily through reduction in the presence of elemental iron, because its hydrolysis was slow compared to its reactions with elemental iron and surface-bound Fe2+. Our results show that in a cast iron-water system, RDX may be transformed via multiple mechanisms involving different reaction paths and reaction sites. [source] Diffusion of strongly sorbed solutes in soil: a dual-porosity model allowing for slow access to sorption sites and time-dependent sorption reactionsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 1 2010M. Ptashnyk We use homogenization techniques to derive a dual (or double) porosity model of solute diffusion and reaction in soil, allowing for slow access to sorption sites within micro-aggregates and time-dependent sorption reactions. We give a means for determining the conditions in which micro-scale concentration gradients affect macro-scale gradients and fluxes. We present equations for a unit volume of soil represented as a series of uniformly-spaced, porous spherical particles, containing and surrounded by solution through which solutes diffuse. The methods we use can, in principle, be applied to more complex geometries. We compare the model's predictions with those of the equivalent single porosity model for commonly used boundary conditions. We show that failure to allow for slow access to reaction sites can lead to seriously erroneous results. Slow access has the effect of decreasing the sorption of solute into soil from a source or desorption from soil to a sink. As a result of slow access, the diffusion coefficients of strongly-sorbed solutes measured at the macro-scale will be time-dependent and will depend on the method of measurement. We also show that slow access is more often likely to limit macro-scale diffusion than rates of slow chemical reactions per se. In principle, the unimportance of slow reactions except at periods longer than several weeks of diffusion simplifies modelling because, if slow access is correctly allowed for, sorption can be described with equilibrium relations with an understanding of speciation and rapid sorption-desorption reactions. [source] Modelling CO poisoning and O2 bleeding in a PEM fuel cell anodeINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 12 2003J.J. Baschuk Abstract Fuel gas containing carbon monoxide severely degrades the performance of a polymer electrolyte membrane (PEM) fuel cell. However, CO poisoning can be mitigated by introducing oxygen into the fuel (oxygen bleeding). A mathematical PEM fuel cell model is developed that simulates both CO poisoning and oxygen bleeding, and obtains excellent agreement with published, experimental data. Modelling efforts indicate that CO adsorption and desorption follow a Temkin model. Increasing operating pressure or temperature mitigates CO poisoning, while use of reformate fuel increases the severity of the poisoning effect. Although oxygen bleeding mitigates CO poisoning, an unrecoverable performance loss exists at high current densities due to competition for reaction sites between hydrogen adsorption and the heterogeneous catalysis of CO. Copyright © 2003 John Wiley & Sons, Ltd. [source] Nucleation and growth of myrmekite during ductile shear deformation in metagranitesJOURNAL OF METAMORPHIC GEOLOGY, Issue 7 2006L. MENEGON Abstract Myrmekite is extensively developed along strain gradients of continuous, lower amphibolite facies shear zones in metagranites of the Gran Paradiso unit (Western Alps). To evaluate the role of stress, strain energy and fluid phase in the formation of myrmekite, we studied a sample suite consisting of weakly deformed porphyric granites (WDGs), foliated granites (FGs) representative of intermediate strains, and mylonitic granites (MGs). In the protolith, most K-feldspar is microcline with different sets of perthite lamellae and fractures. In the WDGs, abundant quartz-oligoclase myrmekite developed inside K-feldspar only along preexisting perthite lamellae and fractures oriented at a high angle to the incremental shortening direction. In the WDGs, stress played a direct role in the nucleation of myrmekites along interfaces already characterized by high stored elastic strain because of lattice mismatch between K-feldspar and albite. In the FGs and MGs, K-feldspar was progressively dismembered along the growing network of microshear zones exploiting the fine-grained recrystallized myrmekite and perthite aggregates. This was accompanied by a more pervasive fluid influx into the reaction surfaces, and myrmekite occurs more or less pervasively along all the differently oriented internal perthites and fractures independently of the kinematic framework of the shear zone. In the MGs, myrmekite forms complete rims along the outer boundary of the small K-feldspar porphyroclasts, which are almost completely free of internal reaction interfaces. Therefore, we infer that the role of fluid in the nucleation of myrmekite became increasingly important as deformation progressed and outweighed that of stress. Mass balance calculations indicate that, in Al,Si-conservative conditions, myrmekite growth was associated with a volume loss of 8.5%. This resulted in microporosity within myrmekite that enhanced the diffusion of chemical components to the reaction sites and hence the further development of myrmekite. [source] Photo-induced cross-linking mechanism in azide,novolac negative photoresists: molecular level investigation using NMR spectroscopyMAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2003Debmalya Roy Abstract Negative photoresists are composed of a photoactive component (aromatic azides/bisazides) and cyclized rubber or novolac resin dissolved in an organic solvent. Hydrogen abstraction and/or insertion reaction of the reactive nitrene intermediate formed during photoirradiation of the azide result in a cross-linked network of the novolac resin. The molecular weight of novolac resin in the exposed part of the photoresist film thus increases compared with that of the unexposed part. This makes the exposed part insoluble in the alkaline developer. Exploiting this change in physical property, a pattern can be transferred to a substrate from a mask. A better understanding of the exact mechanism of cross-linking reactions is very important to the design of a high-performing negative photoresist. A quinone,imine-type complex has been proposed earlier involving the aromatic moiety of novolac resin as the reaction site. A more recent study focuses the attack of nitrene on the methylenic bridge and hydroxyl group of novolac resins, which were found to be responsible for the cross-linking reaction along with the aromatic moiety of novolac resin. However, in our study no evidence was found for the involvement of a methylenic hydrogen or aromatic moiety of novolac resin in the cross-linking reaction. The 1H NMR, 13C NMR and DEPT-135 spectra before and after photolysis indicate that the cross-linking site is predominantly the hydroxyl group of novolac resin. Multiple reaction sites of attack for the nitrene intermediate have been demonstrated in cashew nut shell liquid (CNSL)-based novolac resin by 1H NMR spectroscopy, which in turn further increases the cross-linked network in the exposed part of a negative photoresist. Copyright © 2003 John Wiley & Sons, Ltd. [source] Kinetics of TmHU binding to DNA as observed by optical tweezersMICROSCOPY RESEARCH AND TECHNIQUE, Issue 11 2007Mathias Salomo Abstract The kinetics of binding for the histone-like protein TmHU (from Thermotoga maritima) to DNA is analyzed on a single molecule level by use of optical tweezers. For the reaction rate a pronounced concentration-dependence is found with an "all or nothing"-limit which suggests the cooperative nature of the binding-reaction. By analyzing the statistics of mechanically induced dissociation-events of TmHU from DNA multiple reaction sites are observed to become more likely with increasing TmHU concentration. This is interpreted as a hint for a secondary organizational level of the TmHU/DNA complex. The reaction rate of TmHU binding to DNA is remarkably higher than that of the HU protein from Escherichia coli which will be discussed. Microsc. Res. Tech., 2007. © 2007 Wiley-Liss, Inc. [source] False labelling due to quenching failure of N -hydroxy-succinimide,ester-coupled dyesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2010Weiqun Wang Abstract In comparative fluorescence gel electrophoresis experiments, cross-talk was detected. It was traced back to a failure in the quenching process in typical labelling protocols. Despite a huge excess of potential reaction sites for the N -hydroxy-succinimide,ester-coupled dye, sufficient active dye molecules were available after the quenching step to label protein molecules un-specifically. It could be shown that only a 100-fold increase in the amount of quencher will silence residual dye to such an extent that no artificial signals are detected. [source] | ||||||||||||||||