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Studying Reaction Intermediates Formed at Graphenic Surfaces  

NASA Astrophysics Data System (ADS)

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

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



The (neutron, Proton) Reaction at Intermediate Energies.  

NASA Astrophysics Data System (ADS)

In nuclei with N >=q Z the (n,p) charge exchange reaction can only excite isovector transitions to the T^> states, i.e. states with isospin T + 1 where T is the isospin of the parent state. At intermediate energies (600 MeV > E_{rm n} > 100 MeV), the reaction is dominated by the spin -isospin reaction mode, so it is a good probe to explore spin excitations. If it is possible to measure cross sections down to 0^circ, the (n,p) reaction can be studied at small momentum transfer to enhance the search for the Gamow-Teller (GT) resonances. In this work, the (n,p) reaction ^{13} C(n,p)^{13}B at 65 MeV has been studied at the Crocker Nuclear Laboratory (CNL), U.C. Davis, and the (n,p) reaction ^6 Li(n,p)^6He at 118 MeV has been studied at the Indiana University Cyclotron Facility (IUCF). Prominent peaks corresponding to the GT transitions to the ground states of ^{13} B and ^6He are observed. Spin -dipole transitions to the excited states of ^ {13}B are also identified. Cross sections at 0^circ and various angles out to 40^circ at CNL, and out to 20^circ at IUCF, were measured. The angular distributions of the cross sections were obtained, and compared with the Distorted Wave Approximation (DWA) calculations. The cross sections at 0^circ are: dsigma/dOmega (0^circ) = 3.11 +/- 0.24 mb/sr for ^{13 }C(n,p)^{13}B(g.s.) at E_{rm n} = 65 MeV; dsigma/dOmega (0^circ) = 11.74 +/- 0.21 mb/sr for ^6Li(n,p) ^6He(g.s.) at E_{ rm n} = 118 MeV. Using the DWA calculations for dsigma/dOmega at 0^circ and the measured cross sections, we can extract the volume integrals of the N-N effective interaction. They are in good agreement with the theoretical predictions from Franey and Love:(UNFORMATTED TABLE OR EQUATION FOLLOWS)vbox{ halign{hfil#hfil&&quadhfil#; hfilcr E_{rm n} & (V_sp{sigmatau }{rm c})_{rm exp. } (MeV - fm^3)& (V _sp{sigmatau}{rm c})_{rm th.} (MeV - fm^3)crnoalign{ vskip4pt} 65 MeV& 179 +/- 19& 178.2cr 118 MeV& 161 +/- 17& 161cr}}(TABLE/EQUATION ENDS).

Wang, Kebin



Microsoft Academic Search

Intermediates from the oxidation of phosphorothioates, (RO)3PS, were studied previously at low temperature using, P NMR, UV and Raman spectra. Now reported is further information about the structure of intermediates and about their reactions, both of which afford significant clues as to how phosphorothioates may produce adverse biological reactions after they have been oxidized biologically. Mass spectra identified intermediates corresponding

Joel Swinson; Lamar Field; Norman E. Heimer; Michael P. Stone; John R. Van Wazer



A new intermediate in the Prins reaction  

PubMed Central

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

Fukuda, Takeshi; Yamazaki, Shoko



Reactions of nitrogen heterocycle-organolithium intermediates with lead halides  

E-print Network

REACTIONS OF NITROGEN HETEROCYCLE- ORGANOLITHIUM INTERMEDIATES WITH LEAD HALIDES A Thesis by JERRY HEAL KINNEY Submitted to the Graduate College of Texas ALM University In partial fulfillment of the requirement for the degree ot MASTER...) (Mem er) December 1970 ABSTRACT Reactions of Nitrogen Heterocycle-Organollthium intermediates With Lead Halides. (December l970) Jerry Neal Kinney, B. S. , Texas AE, M University Directed by: Dr. Choo-Seng Giam Reactions of nitrogen heterocycle...

Kinney, Jerry Neal



Reaction intermediates discovered in crystal structures of enzymes.  


Crystal structures of enzymes have provided valuable information for the reaction mechanisms. Structures of the enzyme complex with different reaction intermediates are particularly valuable. In several cases, these structures of intermediates were discovered accidently, presumably by trapping in the crystal during freezing prior to X-ray data collection. High to atomic resolution structures reveal the detailed geometry of the reaction intermediate and its interactions within the enzyme active site. In other cases, the protein can be crystallized with its substrate, including examples of protease precursors that represent their own substrates. Examples are described of an FAD-dependent dehydrogenase, HIV protease and caspases, where the structures provide snapshots of steps in the reaction and the conformational changes occurring during the reaction. Complementary techniques such as computational chemistry, neutron crystallography, Laue crystallography, and time-resolved spectroscopy can give a more complete picture of the reaction. PMID:22607752

Weber, Irene T; Agniswamy, Johnson; Fu, Guoxing; Shen, Chen-Hsiang; Harrison, Robert W



Novel five-membered ring intermediates in gas phase reactions  

Microsoft Academic Search

This review considers the role of closed-ring intermediates in chemistry, in general, and focuses on recent experimental and\\u000a theoretical works that provide compelling evidence for a fivemembered ring intermediate in the gas phase. The reactions of\\u000a oxygen atoms with ethyl iodide and larger alkyl iodides produce HOI and a corresponding ethylenic compound via attack of the\\u000a oxygen atom at the

Richard A. Loomis; Stephen R. Leone; Mary K. Gilles



Intermediate Phenotypes Identify Divergent Pathways to Alzheimer's Disease  

PubMed Central

Background Recent genetic studies have identified a growing number of loci with suggestive evidence of association with susceptibility to Alzheimer's disease (AD). However, little is known of the role of these candidate genes in influencing intermediate phenotypes associated with a diagnosis of AD, including cognitive decline or AD neuropathologic burden. Methods/Principal Findings Thirty-two single nucleotide polymorphisms (SNPs) previously implicated in AD susceptibility were genotyped in 414 subjects with both annual clinical evaluation and completed brain autopsies from the Religious Orders Study and the Rush Memory and Aging Project. Regression analyses evaluated the relation of SNP genotypes to continuous measures of AD neuropathology and cognitive function proximate to death. A SNP in the zinc finger protein 224 gene (ZNF224, rs3746319) was associated with both global AD neuropathology (p?=?0.009) and global cognition (p?=?0.002); whereas, a SNP at the phosphoenolpyruvate carboxykinase locus (PCK1, rs8192708) was selectively associated with global cognition (p?=?3.57×10?4). The association of ZNF224 with cognitive impairment was mediated by neurofibrillary tangles, whereas PCK1 largely influenced cognition independent of AD pathology, as well as Lewy bodies and infarcts. Conclusions/Significance The findings support the association of several loci with AD, and suggest how intermediate phenotypes can enhance analysis of susceptibility loci in this complex genetic disorder. PMID:20574532

Shulman, Joshua M.; Chibnik, Lori B.; Aubin, Cristin; Schneider, Julie A.; Bennett, David A.; De Jager, Philip L.



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

NASA Astrophysics Data System (ADS)

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

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



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


Computational approaches to understanding chemical reaction mechanisms generally begin by establishing the relative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening species via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by-step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an efficient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mechanism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase. In this Account, we examine mechanistic analysis with URVA in detail, focusing on recent theoretical insights (with a variety of reaction types) from our laboratories. Through the utilization of the concept of localized adiabatic vibrational modes that are associated with the internal coordinates, q(n)(s), of the reaction complex, the chemical character of each reaction phase can be identified via the adiabatic curvature coupling coefficients, A(n,s)(s). These quantities reveal whether a local adiabatic vibrational mode supports (A(n,s) > 0) or resists (A(n,s) < 0) the curving of the path, and thus the structural changes of the reaction complex. URVA can show the mechanism of a reaction expressed in terms of reaction phases, revealing the sequence of chemical processes in the reaction complex and making it possible to determine those electronic factors that control the mechanism and energetics of the reaction. The magnitude of adiabatic curvature coupling coefficients is related to strength and polarizability of the bonds being broken. Transient points along the reaction path are associated with hidden intermediates and hidden transition states, which can be converted into real intermediates and transition states when the reaction conditions or the substitution pattern of the reaction complex are appropriately changed. Accordingly, URVA represents a theoretical tool with tremendous experimental potential, offering the chemist the ability to assert greater control over reactions. PMID:20232791

Kraka, Elfi; Cremer, Dieter



Kaon production in heavy ion reactions at intermediate energies  

E-print Network

The article reviews the physics related to kaon and antikaon production in heavy ion reactions at intermediate energies. Chiral dynamics predicts substantial modifications of the kaon properties in a dense nuclear environment. The status of the theoretical predictions as well as experimental evidences for medium effects such as repulsive/attractive mass shifts for $K^+/K^-$ are reviewed. In the vicinity of the thresholds, and even more pronounced below threshold, the production of strangeness is a highly collective process. Starting from elementary reaction channels the phenomenology of $K^+$ and $K^-$ production, i.e. freeze-out densities, time scales etc. as derived from experiment and theoretical transport calculations is presented. Below threshold kaon production shows a high sensitivity on the nuclear compression reached in heavy ion reactions. This allows to put constraints on the nuclear equation-of-state which are finally discussed.

Christian Fuchs



Characterization of Anionic Cluster Nucleophilic Substitution Reaction Intermediates  

NASA Astrophysics Data System (ADS)

Recent theoretical and experimental developments in the arena of the gas phase S_{rm N}2 reaction (X^- + RY to RX + Y^-) has rekindled interest in this classic chemical reaction. Consideration of the gas phase S_{rm N} 2 double minima potential surface from a valence bond perspective, advocated by Shaik et. al., predicts the presence of a low lying excited electronic state corresponding to electron transfer. In this work we take advantage of long range ion-molecule induced forces to stabilize the S_{rm N}2 reactants in a complex, X^-cdot RY, allowing us to search for this charge transfer excited state from the well defined location on the potential energy surface. Photoelectron spectroscopy of X^ - cdot RY confirms the identification of the species as essentially charge-localized. Vibrational fine structure observed in the case of I^- cdot CH_3I is found to be consistent with small distortions of the CH_3I neutral upon complexation to form a stable intermediate in the S_{rm N}2 identity reaction. A narrow photofragmentation band lies just below the vertical electron detachment energy and is assigned to the X^- cdot RY to X cdotcdot (RY) ^- charge transfer excited state. More detailed study of the photofragmentation band reveals the photoexcitation mechanism is not direct charge transfer but is mediated by a weakly bound negative ion state. The excited state photochemistry of the X ^- cdot RY reaction intermediates is characterized by the formation of the endothermic halide abstraction product XY^-. Trends in the formation of the dihalide product are strongly dependent of the nature of the R group and these results are consistent with a preferential ion binding site in the complex. Search for the XY^- dihalide product in the bimolecular ground state reaction at supra-thermal collision energies revealed halide abstraction as a competitive product channel to the well known Walden inversion mechanism. All of these results are integrated in the development a picture of the X^- cdot RY photofragmentation dynamics in the context of the diabatic (charge-localized) states invoked to interpret the structure of the (ground state) S_{rm N}2 potential surface.

Cyr, Donna Marie


Aqueous-phase hydrodeoxygenation of sorbitol with Pt\\/SiO 2–Al 2O 3: Identification of reaction intermediates  

Microsoft Academic Search

Aqueous-phase hydrodeoxygenation of sugar and sugar-derived molecules can be used to produce a range of alkanes and oxygenates. In this paper, we have identified the reaction intermediates and reaction chemistry for the aqueous-phase hydrodeoxygenation of sorbitol over a bifunctional catalyst (Pt\\/SiO2–Al2O3) that contains both metal (Pt) and acid (SiO2–Al2O3) sites. A wide variety of reactions occur in this process including

Ning Li; George W. Huber



Silyloxyazadienes: one intermediate and two competitive pericyclic reactions.  


The two competing mechanisms in the reaction of 3-trialkylsilyloxy-2-aza-1,3 dienes to form beta-lactams through a [2+2] electrocyclic ring closure or tetrahydrooxazinan-4-ones via a [4+2] hetero-Diels-Alder reaction were studied using Density Functional computations. Although the [2+2] and [4+2] mechanisms are typical of dienes, their competition, starting from the same diene intermediate, has not yet been observed and analyzed. This competition is governed by a delicate interplay between temperature and substituents at the diene and dienophile, respectively. Clearly, entropy tends to favor the [4+2] hetero-Diels-Alder at low temperatures and the [2+2] electrocyclic ring closure at high temperatures, but simple substituent modifications at the diene and dienophile, can make the [4+2] competitive at high temperatures and sometimes even transform the [4+2] concerted mechanism into a two-step Mukaiyama-type process. Moreover, a study of the global electrophilicity values showed that charge transfer in the hetero-Diels-Alder transition states is driven by chemical hardness rather than by chemical potential. PMID:20445910

Bongini, Alessandro; Panunzio, Mauro; Venturini, Alessandro



Kinetics and mechanisms of reactions involving small aromatic reactive intermediates  

SciTech Connect

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

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



Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction  

SciTech Connect

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

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



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

SciTech Connect

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

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



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

PubMed Central

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

Ermert, Johannes



A transient intermediate in the reaction catalyzed by (S)-mandelate dehydrogenase from Pseudomonas putida.  


(S)-Mandelate dehydrogenase from Pseudomonas putida is a member of a FMN-dependent enzyme family that oxidizes (S)-alpha-hydroxyacids to alpha-ketoacids. The reductive half-reaction consists of the steps involved in substrate oxidation and FMN reduction. In this study, we investigated the mechanism of this half-reaction in detail. At low temperatures, a transient intermediate was formed in the course of the FMN reduction reaction. This intermediate is characteristic of a charge-transfer complex of oxidized FMN and an electron-rich donor and is formed prior to full reduction of the flavin. The intermediate was not due to binding of anionic substrates or inhibitors. It was only observed with efficient substrates that have high k(cat) values. At higher temperatures, it was formed within the dead time of the stopped-flow instrument. The rate of formation of the intermediate was 3-4-fold faster than its rate of disappearance; the former had a larger isotope effect. This suggests that the charge-transfer donor is an electron-rich carbanion/enolate intermediate that is generated by the base-catalyzed abstraction of the substrate alpha-proton. This is consistent with the observation that the intermediate was not observed with the R277K and R277G mutants, which have been shown to destabilize the carbanion intermediate (Lehoux, I. E., and Mitra, B. (2000) Biochemistry 39, 10055-10065). Thus, the MDH reaction has two rate-limiting steps of similar activation energies: the formation and breakdown of a distinct intermediate, with the latter step being slightly more rate limiting. We also show that MDH is capable of catalyzing the reverse reaction, the reoxidation of reduced MDH by the product ketoacid, benzoylformate. The transient intermediate was observed during the reverse reaction as well, confirming that it is indeed a true intermediate in the MDH reaction pathway. PMID:14596603

Dewanti, Asteriani R; Mitra, Bharati



Compound nuclei, binary decay, and multifragmentation in intermediate-energy heavy-ion reactions  

SciTech Connect

Hot compound nuclei, frequently produced in intermediate-energy reactions through a variety of processes, are shown to be an important and at times dominant source of complex fragments. 13 refs., 12 figs.

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




EPA Science Inventory

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


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

PubMed Central

The mechanism of the chemical reaction of H2O with three stabilized Criegee intermediates (stabCI-OO, stabCI-CH3-OO and stabCIx-OO) produced via the limonene ozonolysis reaction has been investigated using ab initio and DFT (Density Functional Theory) methods. It has been shown that the formation of the hydrogen-bonded complexes is followed by two different reaction pathways, leading to the formation of either OH radicals via water-catalyzed H migration or of ?-hydroxy hydroperoxide. Both pathways were found to be essential sources of atmospheric OH radical and H2O2 making a significant contribution to the formation of secondary aerosols in the Earth’s atmosphere. The activation energies at the CCSD(T)/6-31G(d) + CF level of theory were found to be in the range of 14.70–21.98 kcal mol?1. The formation of ?-hydroxy hydroperoxide for the reaction of stabCIx-OO and H2O with the activation energy of 14.70 kcal mol?1 is identified as the most favorable pathway. PMID:23481640

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



Two-Neutron Interferometry in Low- and Intermediate-Energy Heavy-Ion Reactions  

SciTech Connect

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

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



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

SciTech Connect

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

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



Mössbauer and EPR Study of Reaction Intermediates of Cytochrome P450  

NASA Astrophysics Data System (ADS)

We present a complementary Mössbauer and EPR study on reaction intermediates of substrate-free and substrate-bound cytochrome P450cam from Pseudomonas putida prepared by the freeze-quench method from 57Fe-labeled P450cam using peroxy acetic acid as oxidizing agent. When reacting the substrate-free P450cam for 8 ms reaction time the reaction mixture consists of ˜85% of ferric low-spin iron (Fe(III)) with g-factors and hyperfine parameters of the starting material; the remaining ˜15% are identified as ferryl iron (Fe(IV); S Fe=1) by its Mössbauer signature. Parallel to the ferryl iron a tyrosine radical ( S rad=1/2) is formed. The two paramagnetic species are not exchange-coupled; however, they are close enough to significantly influence the (EPR) relaxation behavior of the radical spin. In the case of substrate-bound P450cam only trace amounts of the tyrosine radical are formed within 8 ms (<3%); within the accuracy of Mössbauer spectroscopy (5%) iron(IV) can not be detected. The results point to Tyr-96, which is hydrogen-bonded to the substrate camphor, as the candidate for the observed tyrosine radical.

Schünemann, V.; Trautwein, A. X.; Jung, C.; Terner, J.



Trapping Conformational Intermediate States in the Reaction Center Protein from Photosynthetic Bacteria  

E-print Network

at cryogenic temperature and is similar to the rate at room temperature, as expected for an exothermic of reaction rates (12, 13). Other studies have characterized unrelaxed product states (14). In additionTrapping Conformational Intermediate States in the Reaction Center Protein from Photosynthetic

Gunner, Marilyn


Recent developments in methods for identifying reaction coordinates  

PubMed Central

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

Li, Wenjin; Ma, Ao



International chemical identifier for reactions (RInChI)  

PubMed Central

The IUPAC International Chemical Identifier (InChI) provides a method to generate a unique text descriptor of molecular structures. Building on this work, we report a process to generate a unique text descriptor for reactions, RInChI. By carefully selecting the information that is included and by ordering the data carefully, different scientists studying the same reaction should produce the same RInChI. If differences arise, these are most likely the minor layers of the InChI, and so may be readily handled. RInChI provides a concise description of the key data in a chemical reaction, and will help enable the rapid searching and analysis of reaction databases. PMID:24152584



Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome  

SciTech Connect

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

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



Detection of Reaction Intermediates during Human Cystathionine ?-Synthase-monitored Turnover and H2S Production*  

PubMed Central

Human cystathionine ?-synthase (CBS), a novel heme-containing pyridoxal 5?-phosphate enzyme, catalyzes the condensation of homocysteine and serine or cysteine to produce cystathionine and H2O or H2S, respectively. The presence of heme in CBS has limited spectrophotometric characterization of reaction intermediates by masking the absorption of the pyridoxal 5?-phosphate cofactor. In this study, we employed difference stopped-flow spectroscopy to characterize reaction intermediates formed under catalytic turnover conditions. The reactions of l-serine and l-cysteine with CBS resulted in the formation of a common aminoacrylate intermediate (kobs = 0.96 ± 0.02 and 0.38 ± 0.01 mm?1 s?1, respectively, at 24 °C) with concomitant loss of H2O and H2S and without detectable accumulation of the external aldimine or other intermediates. Homocysteine reacted with the aminoacrylate intermediate with kobs = 40.6 ± 3.8 s?1 and re-formed the internal aldimine. In the reverse direction, CBS reacted with cystathionine, forming the aminoacrylate intermediate with kobs = 0.38 ± 0.01 mm?1 s?1. This study provides the first insights into the pre-steady-state kinetic mechanism of human CBS and indicates that the reaction is likely to be limited by a conformational change leading to product release. PMID:23124209

Yadav, Pramod Kumar; Banerjee, Ruma



Population of bound excited states in intermediate-energy fragmentation reactions  

E-print Network

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

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



Neutron Spectra from Intermediate-Energy Nucleus-Nucleus Reactions  

SciTech Connect

Double-differential cross sections of neutron production at angles from 0 to 110 degrees from many reactions induced by light and medium nuclei on targets from 12C to 208Pb, at several incident energies from 95 to 600 MeV/nucleon have been measured recently at the Institute of Physical and Chemical Research (RIKEN) Ring Cyclotron in Japan and at the Heavy-Ion Medical Accelerator of the National Institute of Radiological Science in Chiba, Japan using the time-of-flight technique. We have analyzed all these new measurements using the Quantum Molecular Dynamics (QMD) model, the Oak Ridge intranuclear cascade model HIC, the ISABEL intranuclear cascade model from LAHET, and the Los Alamos version of the Quark-Gluon String Model code LAQGSM03. On the whole, all four models used here describe reasonably well most of the measured neutron spectra, although different models agree differently with data from specific reactions and some serious discrepances are observed for some reactions. We present here some illustrative results from our study, discuss possible reasons for some of the observed discrepancies and try to outline ways to further improve the tested codes in order to address these problems.

Iwase, Hiroshi [GSI, Planckstr. 1, 64291 Darmstadt (Germany); Iwata, Yoshiyuki [National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage, Chiba 263-8555 (Japan); Nakamura, Takashi [Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Gudima, Konstantin [Institute of Applied Physics, Academy of Science of Moldova, Chisinau, MD-2028 (Moldova, Republic of); Mashnik, Stepan; Sierk, Arnold; Prael, Richard [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)



Use of intermediate partitioning to calculate intrinsic isotope effects for the reaction catalyzed by malic enzyme  

Microsoft Academic Search

For those enzymes that proceed via a stepwise reaction mechanism with a discrete chemical intermediate and where deuterium and ¹³C isotope effects are on separate steps, a new method has been developed to solve for the intrinsic deuterium and ¹³C kinetic isotope effects that relies on directly observing the partitioning of the intermediate between the forward and reverse directions. This

Charles B. Grissom; W. W. Cleland



Structures of reaction intermediates of bovine cytochrome c oxidase probed by time-resolved vibrational spectroscopy.  


Structures of reaction intermediates of bovine cytochrome c oxidase (CcO) in the reactions of its fully reduced form with O2 and fully oxidized form with H2O2 were investigated with time-resolved resonance Raman (RR) and infrared spectroscopy. Six oxygen-associated RR bands were observed for the reaction of CcO with O2. The isotope shifts for an asymmetrically labeled dioxygen, (16)O(18)O, has established that the primary intermediate of cytochrome a3 is an end-on type dioxygen adduct and the subsequent intermediate (P) is an oxoiron species with Fe=O stretch (nu(Fe=O)) at 804/764 cm(-1) for (16)O2/(18)O2 derivatives, although it had been long postulated to be a peroxy species. The P intermediate is converted to the F intermediate with nu(Fe=O) at 785/751 cm(-1) and then to a ferric hydroxy species with nu(Fe-OH) at 450/425 cm(-1) (443/417 cm(-1) in D2O). The rate of reaction from P to F intermediates is significantly slower in D2O than in H2O. The reaction of oxidized CcO with H2O2 yields the same oxygen isotope-sensitive bands as those of P and F, indicating the identity of intermediates. Time-resolved infrared spectroscopy revealed that deprotonation of carboxylic acid side chain takes place upon deligation of a ligand from heme a3. UV RR spectrum gave a prominent band due to cis C=C stretch of phospholipids tightly bound to purified CcO. PMID:11132644

Kitagawa, T



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


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

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



Synthesis of a potential intermediate for TMC-95A via an organocatalyzed aldol reaction.  


N-Prolinylanthranilamide-based pseudopeptide organocatalyst 14 was shown to promote enantioselective direct aldol reaction of 7-iodoisatin and 2,2-dimethyl-1,3-dioxan-5-one with 90% conversion (75% isolated yield), 90% enantioselectivity, and 23:1 diastereoselectivity. To demonstrate the synthetic utility of this chemistry, the racemic aldol reaction product was converted in five steps to a potential intermediate for construction of the natural product TMC-95A. PMID:24024913

Pearson, Anthony J; Panda, Santanu; Bunge, Scott D



Preparation of tetrasubstituted furans via intramolecular Wittig reactions with phosphorus ylides as intermediates.  


Novel preparation of tetrasubstituted furans, starting from the Michael acceptors, tributylphosphine, and acyl chlorides, is realized. A broad range of highly functional furans can be efficiently generated in one step at room temperature within 10 min to 21 h in moderate to high yields (60-99%). The reaction was proposed to proceed via intramolecular Wittig-type reactions, using phosphorus ylides as intermediates. PMID:20521775

Kao, Tzu-Ting; Syu, Siang-en; Jhang, Yi-Wun; Lin, Wenwei



Reaction cross sections of intermediate energy ? particles within a relativistic optical model  

NASA Astrophysics Data System (ADS)

The suggestion made recently by H. Abele et al. that relativistic effects in the interaction of alpha particles with various nuclei at intermediate energies may remove the existing discrepancy between the theoretical predictions and the experimental data for the reaction cross section is investigated. We use a relativistic model based on the Kemmer-Duffin-Petiau equation and find that relativistic effects do not lead to a reduction in the reaction cross section within the present approach. Alternative explanations are discussed.

Ait-Tahar, S.; Nedjadi, Y.



Analysis of hard two-photon correlations measured in heavy-ion reactions at intermediate energies  

E-print Network

hypersurfaces, e.g., one describes the correlation as function of the quantities q q1 q2 , q0 E1 E2 1 , or QinvAnalysis of hard two-photon correlations measured in heavy-ion reactions at intermediate energies H Recently reported measurements of hard photon correlations in the reactions 36 Ar on 27 Al at 95A MeV, 86

Bauer, Wolfgang


Diastereoselectivity in nucleophilic displacement reactions at phosphorus; isolation and characterization of a pentacoordinated intermediate  

Microsoft Academic Search

Reaction of the axially substituted trans-3-chloro-2,4-dioxa-3?5-phosphabicyclo[4.4.0]decan-3-one ((±)-1) with O- and S-nucleophiles in the presence of DBN preferentially proceeds with retention at P, whereas the epimeric ration is reversed with DBU as the auxiliary base. N-nucleophiles exclusively react with inversion; in the presence of DBN, a pentacoordinated compound (5), which is considered to be a reaction intermediate, was isolated as the

Franco Alberto Merckling; Peter Rfiedi



Crystal Structure of the Plant PPC Decarboxylase AtHAL3a Complexed with an Ene-thiol Reaction Intermediate  

Microsoft Academic Search

The Arabidopsis thaliana protein AtHAL3a decarboxylates 4?-phosphopantothenoylcysteine to 4?-phosphopantetheine, a step in coenzyme A biosynthesis. Surprisingly, this decarboxylation reaction is carried out as an FMN-dependent redox reaction. In the first half-reaction, the side-chain of the cysteine residue of 4?-phosphopantothenoylcysteine is oxidised and the thioaldehyde intermediate decarboxylates spontaneously to the 4?-phosphopantothenoyl-aminoethenethiol intermediate. In the second half-reaction this compound is reduced to

Stefan Steinbacher; Pilar Hernández-Acosta; Bastian Bieseler; Michael Blaesse; Robert Huber; Francisco Antonio Culiáñez-Macià; Thomas Kupke



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

EPA Science Inventory

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


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

PubMed Central

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

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



An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects  

PubMed Central

Many of the enzymes that catalyze reactions at nucleotide glycosidic linkages proceed through either a reactive oxocarbenium-ion intermediate or a transition state with considerable oxocarbenium character. To investigate how an RNA active site deals with the catalytic challenge of nucleotide synthesis, we probed the transition state of a ribozyme able to promote the formation of a pyrimidine nucleotide. Primary and secondary kinetic isotope effects indicate that this ribozyme stabilizes a highly dissociative reaction with considerable sp2 hybridization and negligible bond order between the departing pyrophosphate leaving group and the anomeric carbon. The small primary 13C isotope effect of 1.002 ± 0.003 indicates that the reaction is likely to be less concerted than that observed for protein nucleotide synthesis enzymes, which typically have primary 13C isotope effects of 1.02–1.03. The dissociative nature of the ribozyme reaction most resembles the reaction of some hydrolytic enzymes, such as uracil DNA glycosylase, which uses the negative charges found in the phosphodiester backbone of its DNA substrate to transiently stabilize an oxocarbenium ion during hydrolysis. The detectable hydrolysis observed in the ribozyme reaction indicates that shielding of this reactive intermediate from water is a significant challenge for RNA, which protein enzymes that synthesize nucleotides have managed to overcome during evolution, apparently by the utilization of more concerted chemistry. PMID:14668444

Unrau, Peter J.; Bartel, David P.



Carboxylation and decarboxylation reactions. Anaplerotic flux and removal of citrate cycle intermediates in skeletal muscle.  


A system for in situ perfusion of rat hindquarters using a fluorocarbon for oxygen and CO2 exchange, and a polyol to provide oncotic pressure is described. Perfusion with glucose plus insulin resulted in no significant change in the tissue level of citrate cycle intermediates, phosphocreatine, ATP, ADP, AMP, and glycogen. Glucose was consumed at a linear rate, and lactate, pyruvate, alanine, glutamine, glutamate, and citrate were released into the perfusing medium. Inclusion of pyruvate resulted in elevation of citrate cycle intermediates and alanine, whereas acetate elevated the level of cycle intermediates without significant effect on tissue alanine or its release. Radioactivity from NaH[14C]O3 was incorporated into citrate cycle intermediates, glutamate, aspartate, and lactate by glucose-perfused hindquarters, the extent of which was markedly elevated as the tissue pyruvate was increased. When pyruvate was in the physiological range, acetate caused elevation in incorporation of CO2 into these metabolites, increased the concentration of citrate, and doubled the concentration of acetyl-CoA. Thirty-five to forty-four per cent of 14C incorporated into citrate was retained after enzymic degradation to 2-oxoglutarate. Perfusion with [2-14C-]propionate led to elevation in the level of citrate cycle intermediates, and radioactivity was incorporated into the latter, as well as glutamate, aspartate, lactate, pyruvate, alanine, and CO2. Two independent calculations estimated the rate of flux of 4-carbon cycle intermediates to 3-carbon metabolites of about 68 mumol/h (approximately 38 nmol/min/g of tissue), a rate in excess of those reported for alanine release from human or rat muscle during starvation. Arsenite blocked carbohydrate flux through the citrate cycle and effected accumulation of lactate, pyruvate, alanine, and 2-oxoglutarate. Flux from 4- to 3-carbon acids was diminished by arsenite, apparently as a result of lowered substrate concentration for decarboxylation. 3-Mercaptopicolinic acid, an inhibitor of phosphoenolpyruvate carboxykinase, was without effect on the parameters studied, suggesting that this enzyme is not involved in the decarboxylation reaction. It is concluded that (a) a constant level of citrate cycle intermediates is maintained in part by continuous flux of carbon into and out of the cycle by carboxylation and decarboxylation reactions; (b) the carbon skeleton of alanine released from skeletal muscle is derived in part from other amino acids which are catabolized to cycle intermediates; and (c) the subsequent removal of these intermediates is probably mediated by malic enzyme(s) (EC, or, or both. PMID:762069

Lee, S H; Davis, E J



A modular array for neutron spectroscopy in low- and intermediate-energy heavy-ion reactions  

Microsoft Academic Search

An array for neutron spectroscopy in low and intermediate-energy heavy-ion reactions is here described. The array is made of cylindrical liquid scintillator cells 6.3 cm in radius and 12.7 cm thick. The detectors are mounted on a mechanical structure that allows to easily position the detectors in a wide range of angles and distances from the target. The performances of

N. Colonna; L. Celano; G. D'Erasmo; E. M. Fiore; L. Fiore; V. Paticchio; G. Tagliente; G. Antuofermo; G. Iacobelli; M. Sacchetti; P. Vasta; A. Pantaleo



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

SciTech Connect

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

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



A new paramagnetic intermediate formed during the reaction of nitrite with deoxyhemoglobin  

PubMed Central

The reduction of nitrite by deoxygenated hemoglobin chains has been implicated in red cell induced vasodilation, although the mechanism for this process has not been established. We have previously demonstrated that the reaction of nitrite with deoxyhemoglobin produces a hybrid intermediate with properties of Hb(II)NO+ and Hb(III)NO that builds up during the reaction retaining potential NO bioactivity. To explain the unexpected stability of this intermediate, which prevents NO release from the Hb(III)NO component, we had implicated the transfer of an electron from the ?-93 thiol to NO+ producing •SHb(II)NO. In order to determine if this species is formed and to characterize its properties, we have investigated the electron paramagnetic resonance (EPR) changes taking place during the nitrite reaction. The EPR effects of blocking the thiol group with N-ethyl-maleimide and using carboxypeptidase-A to stabilize the R-quaternary conformation have demonstrated that •SHb(II)NO is formed and that it has the EPR spectrum expected for NO bound to the heme in the ?-chain plus that of a thiyl radical. This new NO-related paramagnetic species is in equilibrium with the hybrid intermediate “Hb(II)NO+ ? Hb(III)NO” thereby further inhibiting the release of NO from Hb(III)NO. The formation of an NO-related paramagnetic species other than the tightly bound NO in Hb(II)NO was also confirmed by a decrease in the EPR signal by ?20°C incubation, which shifts the equilibrium back to the “Hb(II)NO+ ? Hb(III)NO” intermediate. This previously unrecognized NO hemoglobin species explains the stability of the intermediates and the buildup of a pool of potentially bioactive NO during nitrite reduction. It also provides a pathway for the formation of ?-93 cysteine S-nitrosylated hemoglobin [SNOHb:S-nitrosohemoglobin], which has been shown to induce vasodilation, by a rapid radical-radical reaction of any free NO with the thiyl radical of this new paramagnetic intermediate. PMID:21755997

Salgado, Maria T.; Ramasamy, Somasundaram; Tsuneshige, Antonio; Manoharan, Periakaruppan T.; Rifkind, Joseph M.



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


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

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



Kinetics of and intermediates in a photocycle branching reaction of the photoactive yellow protein from Ectothiorhodospira halophila  

E-print Network

/Vis spectroscopy. As compared to the parallel dark recovery reaction of the presumed blue-shifted signaling state pKinetics of and intermediates in a photocycle branching reaction of the photoactive yellow protein Abstract We have studied the kinetics of the blue light-induced branching reaction in the photocycle

van Stokkum, Ivo


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


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

Dai, Susie Y; Fitzgerald, Michael C



Infrared-driven unimolecular reaction of CH?CHOO Criegee intermediates to OH radical products.  


Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the troposphere, proceeds through energized Criegee intermediates that undergo unimolecular decay to produce OH radicals. Here, we used infrared (IR) activation of cold CH3CHOO Criegee intermediates to drive hydrogen transfer from the methyl group to the terminal oxygen, followed by dissociation to OH radicals. State-selective excitation of CH3CHOO in the CH stretch overtone region combined with sensitive OH detection revealed the IR spectrum of CH3CHOO, effective barrier height for the critical hydrogen transfer step, and rapid decay dynamics to OH products. Complementary theory provides insights on the IR overtone spectrum, as well as vibrational excitations, structural changes, and energy required to move from the minimum-energy configuration of CH3CHOO to the transition state for the hydrogen transfer reaction. PMID:25258077

Liu, Fang; Beames, Joseph M; Petit, Andrew S; McCoy, Anne B; Lester, Marsha I



Macroscopic/microscopic simulation of nuclear reactions at intermediate energies. Denis Lacroix, Aymeric Van Lauwe and Dominique Durand  

E-print Network

Macroscopic/microscopic simulation of nuclear reactions at intermediate energies. Denis Lacroix- tion of nuclear collisions in the intermediate energy range is presented. The model simulates events the classical equation of motion of the two partners in their mutual interaction potential. At that time, using

Boyer, Edmond


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

Microsoft Academic Search

The heterogeneous reactions of O3 with aerosol particles are of central importance to air quality. They are studied extensively, but the molecular mechanisms and kinetics remain unresolved. Based on new experimental data and calculations, we show that long-lived reactive oxygen intermediates (ROIs) are formed. The chemical lifetime of these intermediates exceeds 100 seconds, which is much longer than the surface

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



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

NASA Astrophysics Data System (ADS)

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

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



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

NASA Astrophysics Data System (ADS)

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

Zimányi, László; Khoroshyy, Petro; Mair, Thomas



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


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

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




PubMed Central

Hyperuricemia is associated with hypertension, metabolic syndrome, preeclampsia, cardiovascular disease and renal disease, all conditions associated with oxidative stress. We hypothesized that uric acid, a known antioxidant, might become prooxidative following its reaction with oxidants; and, thereby contribute to the pathogenesis of these diseases. Uric acid and 1,3-15N2-uric acid were reacted with peroxynitrite in different buffers and in the presence of alcohols, antioxidants and in human plasma. The reaction products were identified using liquid chromatography-mass spectrometry (LC-MS) analyses. The reactions generate reactive intermediates that yielded triuret as their final product. We also found that the antioxidant, ascorbate, could partially prevent this reaction. Whereas triuret was preferentially generated by the reactions in aqueous buffers, when uric acid or 1,3-15N2-uric acid was reacted with peroxynitrite in the presence of alcohols, it yielded alkylated alcohols as the final product. By extension, this reaction can alkylate other biomolecules containing OH groups and others containing labile hydrogens. Triuret was also found to be elevated in the urine of subjects with preeclampsia, a pregnancy-specific hypertensive syndrome that is associated with oxidative stress, whereas very little triuret is produced in normal healthy volunteers. We conclude that under conditions of oxidative stress, uric acid can form reactive intermediates, including potential alkylating species, by reacting with peroxynitrite. These reactive intermediates could possibly explain how uric acid contributes to the pathogenesis of diseases such as the metabolic syndrome and hypertension. PMID:19219741

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



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


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

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



Identifying the Role of Specific Motifs in the Lens Fiber Cell–Specific Intermediate Filament Phakosin  

PubMed Central

Purpose Phakosin and filensin are lens fiber cell–specific intermediate filament (IF) proteins. Unlike every other cytoplasmic IF protein, they assemble into a beaded filament (BF) rather than an IF. Why the lens fiber cell requires two unique IF proteins and why and how they assemble into a structure other than an IF are unknown. In this report we test specific motifs/domains in phakosin to identify changes that that have adapted phakosin to lens-specific structure and function. Methods Phakosin shows the highest level of sequence identity to K18, whose natural assembly partner is K8. We therefore exchanged conserved keratin motifs between phakosin and K18 to determine whether phakosin's divergent motifs could redirect the assembly of chimeric K18 and K8. Modified proteins were bacterially expressed and purified. Assembly competence was assessed by electron microscopy. Results Substitution of the phakosin helix initiation motif (HIM) into K18 does not alter assembly with K8, establishing that the radical divergence in phakosin HIM is not by itself the mechanism by which IF assembly is redirected to BF assembly. Unexpectedly, K18 bearing phakosin HIM resulted in normal IF assembly, despite the presence of an otherwise disease-causing R-C substitution, and two helix-disrupting glycines. This disproves the widely held belief that mutation of the R is catastrophic to IF assembly. Additional data are presented that suggest normal IF assembly is dependent on sequence-specific interactions between the IF head domain and the HIM. Conclusions In the lens fiber cell, two members of the IF family have evolved to produce BFs instead of IFs, a change that presumably adapts the IF to a fiber cell–specific function. The authors establish here that the most striking divergence seen in phakosin is not, as hypothesized, the cause of this altered assembly outcome. The authors further establish that the HIM of IFs is far more tolerant of mutations, such as those that cause some corneal dystrophies and Alexander disease, than previously hypothesized and that normal assembly involves sequence-specific interactions between the head domain and the HIM. PMID:17962466

Pittenger, Joshua T.; Hess, John F.; FitzGerald, Paul G.



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

SciTech Connect

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

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



First-Principles Prediction of Crystal Structures, Reaction Pathways, and Intermediate Products in Hydrogen Storage Reactions  

NASA Astrophysics Data System (ADS)

Practical hydrogen storage for mobile applications requires materials that exhibit high hydrogen densities, low decomposition temperatures, and fast kinetics for absorption and desorption. Unfortunately, no reversible materials are currently known that possess all of these attributes. Here we present an overview of our recent efforts aimed at developing a first-principles computational approach to the discovery of novel hydrogen storage materials. We have developed computational tools which enable accurate prediction of decomposition thermodynamics, crystal structures for unknown hydrides, and thermodynamically preferred decomposition pathways. We present examples that illustrate each of these three capabilities. Specifically, we focus on recent work on crystal structure and dehydriding reactions of (i) borohydride materials, such as Ca(BH4)2 and Mg(BH4)2, (ii) amidoboranes and their decomposition products, and (iii) mixtures of complex hydrides. [4pt] [1] J. Yang, A. Sudik, C. Wolverton, and D. J. Siegel, Chem. Soc. Rev. 39, 656 (2010). [0pt] [2] D. E. Farrell, D. Shin, and C. Wolverton, Phys. Rev. B 80, 224201 (2009). [0pt] [3] C. Weidenthaler, A. Pommerin, M. Felderhoff, W. Sun, C. Wolverton, B. Bogdanovic, and F. Schuth, J. Amer. Chem. Soc. 131, 16735 (2009). [0pt] [4] A. R. Akbarzadeh, C. Wolverton, and V. Ozolins, Phys. Rev. B 79, 184102 (2009). [0pt] [5] Y. S. Lee, Y. Kim, Y. W. Cho, D. Shapiro, C. Wolverton, and V. Ozolins, Phys. Rev. B 79, 104107 (2009). [0pt] [6] V. Ozolins, E. H. Majzoub, and C. Wolverton, J. Amer. Chem. Soc. 131, 230 (2009). [0pt] [7] V. Ozolins, E. H. Majzoub, and C. Wolverton, Phys. Rev. Lett. 100, 135501 (2008). [0pt] [8] Y. Zhang, E. Majzoub, V. Ozolins, and C. Wolverton, Phys. Rev. B 82, 174107 (2010).

Wolverton, Chris



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

Microsoft Academic Search

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

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



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

SciTech Connect

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

Tso, Kin



General aspect of catalytic hydrogenation and isomerization reactions on oxide catalyst. Characteristics of the reactions via ionic and nonionic intermediates  

SciTech Connect

An analysis of new and available data, mostly published by Tanaka and Okuhara, on the hydrogenation of alkenes and conjugated dienes and the hydrogen-deuterium exchange on the oxides of cadmium, magnesium, zinc, cobalt, chromium, thorium, zirconium, and lanthanum, and on molybdenum disulfide suggested that the partial hydrogenation of conjugated dienes catalyzed by cadmium and magnesium oxide proceeds by a mechanism which is similar to that of diene hydrogenation on supported alkali metals or on alkali metal hydride and involves allyl carbanion intermediates. The same ionic mechanism apparently also occurs in the double-bond migration of n-alkenes on cadmium oxide, and the isomerization catalyzed by molybdenum disulfide. The nonionic reaction mechanism via o-alkyl and o- or m-allyl intermediates apparently proceeds on active sites of a definite structure, i.e., a specific degree of coordination, but the ionic mechanism seems to depend only on the acidity or basicity of the sites. The nonspecific nature of the site for the ionic mechanism may result in high resistance to poisoning.

Tanaka, K.; Okuhara, T.



Reaction of coordinated dinitrogen. 12. Identification of intermediates in the conversion of molybdenum-bound dinitrogen into ammonia and hydrazine. Factors affecting the ammonia-forming reaction  

SciTech Connect

When bis(dinitrogen) complexes of molybdenum and tungsten are treated with an excess of strong acid, with few exceptions, a complex containing the hydrazido(2-) ligand has been identified either as a product in the reaction or as an intermediate on the way to the formation of ammonia and hydrazine. In the case of those molybdenum complexes that produce ammonia, the stoichiometry of the reaction can be represented by eq 1 and 2: (1) )Mo/sup 0/(N/sub 2/)/sub 2/) ..-->../sup H/sup +// )Mo(NNH/sub 2/)) + N/sub 2/, (2) )Mo(NNH/sub 2/)) ..-->../sup H/sup +// 1/2N/sub 2/ + HN/sub 4//sup +/ + )Mo(III)), with a molybdenum(III) complex as the final molybdenum-containing product. Here the identification of two isomeric hydrazido(2-) complexes are reported upon, that are formed as a mixture in the reaction of excess HBr in tetrahydrofuran (THF) solution with trans-(Mo(N/sub 2/)/sub 2/(triphos)(PPh/sub 3/)), where triphos = PhP(CH/sub 2/CH/sub 2/PPh/sub 2/)/sub 2/. From this mixture of hydrazido(2-) complexes ammonia and a trace of hydrazine are produced in THF solution, but in benzene or toluene solution more hydrazine than ammonia is produced. On the basis of data presented, reversible phosphine dissociation is the next recognizable step toward ammonia formation.

Bossard, G.E.; George, T.A.; Howell, D.B.; Koczon, L.M.; Lester, R.K.



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

SciTech Connect

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

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



Effects of ZSM-5 zeolite confinement on reaction intermediates during dioxygen activation by enclosed dicopper cations.  


We investigate how nanospaces surrounded by a 10-membered ring of ZSM-5 zeolite affect the reaction intermediates formed during dioxygen activation by enclosed dicopper cations. Two types of dioxygen intermediates are considered: one is an O(2)...Cu(2) complex, where dioxygen binds to the two Cu cations, and the other is a bis(mu-oxo)dicopper complex converted from an O(2)...Cu(2) complex by the cleavage of the O-O bond. We employ large-scale density functional theory (DFT) calculations with the B3LYP functional to examine the energetics of the two dioxygen intermediates inside a 10-membered ring of ZSM-5 with double Si --> Al substitutions at variable locations. The properties of the O(2)...Cu(2) complexes, such as the dioxygen bridging modes and dioxygen activation, are strongly affected by the locations of the two Al atoms within the 10-membered ring. In particular, the O(2)...Cu(2) complexes have either end-on or side-on bridging modes depending on the substituted Al positions. On the other hand, the steric hindrances of a ZSM-5 cavity play crucial roles in determining the properties of the bis(mu-oxo)dicopper complexes containing a diamond Cu(2)O(2) core. By restricting its Cu(2)O(2) core to a 10-membered ring of ZSM-5 in which the two Al atoms are second-nearest neighbors, each Cu cation is tetrahedral four-coordinate. On the other hand, the Cu cations have almost square planar coordination inside a ZSM-5 where the Al atoms are fourth-nearest neighbors. The different Cu coordination environments are responsible for the different levels of stability; the planar diamond Cu(2)O(2) core is 30.7 kcal/mol more stable relative to the tetrahedral case. Since the ZSM-5 nanospaces directly influence the stability of the bis(mu-oxo)dicopper complexes by changing the Cu coordination environments, zeolite confinement effects on the bis(mu-oxo)dicopper complexes are more noticeable than those in the O(2)...Cu(2) cases. The DFT findings are important in terms of catalytic functions, because the spatial constraint from the ZSM-5 should significantly contribute to the stability of the reaction intermediates formed during the dioxygen activation. PMID:19093853

Yumura, Takashi; Takeuchi, Mina; Kobayashi, Hisayoshi; Kuroda, Yasushige



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

SciTech Connect

Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2{alpha}-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2{alpha}-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 {angstrom} (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.

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



Radical Intermediates in Photoinduced Reactions on TiO2 (An EPR Spin Trapping Study).  


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

Dvoranová, Dana; Barbieriková, Zuzana; Brezová, Vlasta



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


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

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



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

NSDL National Science Digital Library

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

Ambrose, Bradley S.



Acyl intermediates in penicillopepsin-catalysed reactions and a discussion of the mechanism of action of pepsins.  

PubMed Central

Penicillopepsin catalyses transpeptidation reactions involving the transfer of the N-terminal amino acids of suitable substrates via covalent acyl intermediates to acceptor peptides, usually the substrate. The major products obtained when Phe-Tyr-Thr-Pro-Lys-Ala and Met-Leu-Gly were used as substrates were Phe-Phe and Met-Met respectively. With Met-Leu-Gly the tetrapeptide Met-Met-Leu-Gly was observed as probable intermediate. Co-incubation of Leu-Tyr-Leu and Phe-Tyr-Thr-Pro-Lys-Ala led to the formation of Leu-Phe and Phe-Leu as well as Leu-Leu and Phe-Phe. No reaction was observed with tripeptides in which the first or second amino acid is glycine. It appears that two amino aicds with large hydrophobic residues are needed for the transpeptidation reaction. Nucleophilic compounds other than peptides, such as hydroxylamine, aliphatic alcohols and dinitrophenylhydrazine, were not acceptors for the acyl group. Leucine, phenylalanine and leucine methyl ester also had no effect on the reaction. The transpeptidation reaction proceeded readily at pH 3.6 and 4.7. At pH 6.0 the reaction was slow and at pH 1.9 little or no transpeptidation was observed. Porcine pepsin catalyses similar transpeptidation reactions. Sequence studies show that porcine pepsin and penicillopepsin are homologous. The present study also suggests that they have a very similar mechanism. Evidence available at this time indicates that the mechanism of these enzymes is complex and may be modulated by secondary substrate-enzyme interactions. A hypothesis is presented which proposes that pepsin-catalysed reactions proceed via different covalent intermediates (amino-intermediates or acylintermediates) depending on the nature of the substrate. The possibility that some reactions do not involve covalent intermediates is also discussed. PMID:1172664

Takahashi, M; Hofmann, T



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

PubMed Central

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

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



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

PubMed Central

Background Development of cells with minimal metabolic functionality is gaining importance due to their efficiency in producing chemicals and fuels. Existing computational methods to identify minimal reaction sets in metabolic networks are computationally expensive. Further, they identify only one of the several possible minimal reaction sets. Results In this paper, we propose an efficient graph theory based recursive optimization approach to identify all minimal reaction sets. Graph theoretical insights offer systematic methods to not only reduce the number of variables in math programming and increase its computational efficiency, but also provide efficient ways to find multiple optimal solutions. The efficacy of the proposed approach is demonstrated using case studies from Escherichia coli and Saccharomyces cerevisiae. In case study 1, the proposed method identified three minimal reaction sets each containing 38 reactions in Escherichia coli central metabolic network with 77 reactions. Analysis of these three minimal reaction sets revealed that one of them is more suitable for developing minimal metabolism cell compared to other two due to practically achievable internal flux distribution. In case study 2, the proposed method identified 256 minimal reaction sets from the Saccharomyces cerevisiae genome scale metabolic network with 620 reactions. The proposed method required only 4.5 hours to identify all the 256 minimal reaction sets and has shown a significant reduction (approximately 80%) in the solution time when compared to the existing methods for finding minimal reaction set. Conclusions Identification of all minimal reactions sets in metabolic networks is essential since different minimal reaction sets have different properties that effect the bioprocess development. The proposed method correctly identified all minimal reaction sets in a both the case studies. The proposed method is computationally efficient compared to other methods for finding minimal reaction sets and useful to employ with genome-scale metabolic networks. PMID:24594118



Identifying of meat species using polymerase chain reaction (PCR)  

SciTech Connect

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

Foong, Chow Ming; Sani, Norrakiah Abdullah [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor (Malaysia)



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

NASA Astrophysics Data System (ADS)

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

Wujcik, Kevin; Balsara, Nitash



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

SciTech Connect

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

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



Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.  


o-Succinylbenzoyl-CoA (OSB-CoA) synthetase (EC catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered bi uni uni bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first half-reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the "F" form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered bi uni uni bi iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogues with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogues tested as none were active except 4-[2-(trifluoromethyl)phenyl]-4-oxobutyric acid which exhibited a 100-fold decrease in k(cat)/K(m). On the basis of an understanding of OSB-CoA synthetase's kinetic mechanism and substrate specificity, a reaction intermediate analogue of OSB-AMP, 5'-O-{N-[2-(trifluoromethyl)phenyl]-4-oxobutyl}adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of enzymes. PMID:18973344

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D



A Combined DFT and NMR Investigation of the Zinc Organometallic Intermediate Proposed in the Syn-Selective Tandem Chain Extension-Aldol Reaction of ?-Keto Esters  

PubMed Central

The tandem chain extension-aldol (TCA) reaction of ?-keto esters provides a ?-substituted ?-keto ester with an average syn:anti selectivity of 10:1. It is proposed that the reaction proceeds via a carbon-zinc bound organometallic intermediate potentially bearing mechanistic similarity to the Reformatsky reaction. Evidence, derived from control Reformatsky reactions and a study of the structure of the TCA intermediate utilizing DFT methods and NMR-spectroscopy, suggests the ?-keto group of the TCA intermediate plays a significant role in diastereoselectivity observed in this reaction. Such coordination effects have design implications for future zinc mediated reactions. PMID:22703563

Aiken, Karelle S.; Eger, Wilhelm A.; Williams, Craig M.; Spencer, Carley M.



Observation of all the intermediate steps of a chemical reaction on an oxide surface by scanning tunneling microscopy.  


By means of high-resolution scanning tunneling microscopy (STM), we have revealed unprecedented details about the intermediate steps for a surface-catalyzed reaction. Specifically, we studied the oxidation of H adatoms by O(2) molecules on the rutile TiO(2)(110) surface. O(2) adsorbs and successively reacts with the H adatoms, resulting in the formation of water species. Using time-lapsed STM imaging, we have unraveled the individual reaction intermediates of HO(2), H(2)O(2), and H(3)O(2) stoichiometry and the final reaction product-pairs of water molecules, [H(2)O](2). Because of their different appearance and mobility, these four species are discernible in the time-lapsed STM images. The interpretation of the STM results is corroborated by density functional theory calculations. The presented experimental and theoretical results are discussed with respect to previous reports where other reaction mechanisms have been put forward. PMID:19309169

Matthiesen, Jesper; Wendt, Stefan; Hansen, Jonas Ø; Madsen, Georg K H; Lira, Estephania; Galliker, Patrick; Vestergaard, Ebbe K; Schaub, Renald; Laegsgaard, Erik; Hammer, Bjørk; Besenbacher, Flemming



Organic chemistry on cold molecular films: kinetic stabilization of SN1 and SN2 intermediates in the reactions of ethanol and 2-methylpropan-2-ol with hydrogen bromide.  


We prepared thin molecular films of ethanol and 2-methylpropan-2-ol on Ru(001) substrates at temperature of 100-150 K and examined their reactivity toward HBr. The reaction intermediates and products formed at the surfaces were unambiguously identified by the techniques of Cs(+) reactive ion scattering (RIS) and low-energy sputtering. The reaction on the ethanol surface produced protonated ethanol, which is stabilized on the surface and does not proceed to further reactions. On the 2-methylpropan-2-ol surface, protonated alcohol [(CH(3))(3)COH(2) (+)] and carbocation [(CH(3))(3)C(+)] were formed with the respective yield of 20 and 78 %. Alkyl bromides, which are the final products of the corresponding reactions in liquid solvents, have extremely small yields on these surfaces (< 0.3 % for ethyl bromide and 2 % for tert-butyl bromide). The results indicate that the reactions on frozen films are characterized by kinetic control, stabilization of ionic intermediates (protonated alcohols and tert-butyl cation), and effective blocking of the charge recombination steps in S(N)1 and S(N)2 paths. The implication of these findings for the molecular evolution process in interstellar medium is also discussed. PMID:12698428

Park, Seong-Chan; Maeng, Kye-Won; Kang, Heon



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


The realization of common materials transformations in nanocrystalline systems is fostering the development of novel nanostructures and allowing a deep look into the atomistic mechanisms involved. Galvanic corrosion is one such transformation. We studied galvanic replacement within individual metal nanoparticles by using a combination of plasmonic spectroscopy and scanning transmission electron microscopy. Single-nanoparticle reaction trajectories showed that a Ag nanoparticle exposed to Au³? makes an abrupt transition into a nanocage structure. The transition is limited by a critical structural event, which we identified by electron microscopy to comprise the formation of a nanosized void. Trajectories also revealed a surprisingly strong nonlinearity of the reaction kinetics, which we explain by a model involving the critical coalescence of vacancies into a growing void. The critical void size for galvanic exchange to spontaneously proceed was found to be 20 atomic vacancies. PMID:24677345

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



ENDOR studies of the intermediate electron acceptor radical anion I-. in Photosystem II reaction centers.  


The EPR and ENDOR characteristics of the intermediate electron acceptor radical anion I-. in Photosystem II (PS II) are shown to be identical in membrane particles and in the D1D2 cytochrome b-559 complex (Nanba, O. and Satoh, K. (1987) Proc. Natl. Acad. Sci. USA 84, 109-112). These findings provide further evidence that the D1D2 complex is the reaction center of PS II and show that the pheophytin binding site is intact. A hydrogen bond between I-. and the protein (GLU D1-130) is postulated on the basis of D2O exchange experiments. The ENDOR data of I-. and of the pheophytin a radical anion in different organic solvents are compared and the observed differences are related to structural changes of the molecule on the basis of molecular orbital calculations (RHF-INDO/SP). The importance of the orientation of the vinyl group (attached to ring I) on electron transfer is discussed. PMID:2553112

Lubitz, W; Isaacson, R A; Okamura, M Y; Abresch, E C; Plato, M; Feher, G



Methanol synthesis on ZnO({{000overline{1}}}). II. Structure, energetics, and vibrational signature of reaction intermediates  

NASA Astrophysics Data System (ADS)

A rigorous characterization of a wealth of molecular species adsorbed at oxygen defects on ZnO(000overline{1}) is given. These defects represent the putative active sites in methanol synthesis from CO and H2. The oxidation state of the ZnO catalyst and thus the preferred charge state and the reactivity of the oxygen vacancies depend on the gas phase temperature and pressure conditions. Considering charge states of oxygen vacancies relevant at the reducing conditions of the industrial process, i.e., F++/H2, F0, F0/H2, and F-, as well as the F++ center which is abundant at UHV conditions and therefore important to allow for comparison with surface science experiments, we have investigated the structure, energetics, and vibrational frequencies of an exhaustive catalog of reaction intermediates using electronic structure calculations. After having identified the characteristic adsorption modes of CO, formate, formic acid, hydroxymethylene, formyl, formaldehyde, dioxomethylene, hydroxymethyl, hydroxymethoxide, methoxide, as well as methanol itself, the thermodynamic stability of all species with respect to the charge state of the oxygen vacancy and their electronic stabilization is discussed in detail and summarized in an energy level diagram.

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



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


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

Lietzan, Adam D; St Maurice, Martin



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

SciTech Connect

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

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



Using first principles calculations to identify new destabilized metal hydride reactions for reversible hydrogen storage.  


Hydrides of period 2 and 3 elements are promising candidates for hydrogen storage, but typically have heats of reaction that are too high to be of use for fuel cell vehicles. Recent experimental work has focused on destabilizing metal hydrides through mixing metal hydrides with other compounds. A very large number of possible destabilized metal hydride reaction schemes exist, but the thermodynamic data required to assess the enthalpies of these reactions are not available in many cases. We have used density functional theory calculations to predict the reaction enthalpies for more than 300 destabilization reactions that have not previously been reported. The large majority of these reactions are predicted not to be useful for reversible hydrogen storage, having calculated reaction enthalpies that are either too high or too low, and hence these reactions need not be investigated experimentally. Our calculations also identify multiple promising reactions that have large enough hydrogen storage capacities to be useful in practical applications and have reaction thermodynamics that appear to be suitable for use in fuel cell vehicles and are therefore promising candidates for experimental work. PMID:17356751

Alapati, Sudhakar V; Karl Johnson, J; Sholl, David S



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

NASA Astrophysics Data System (ADS)

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

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



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


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

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



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

NASA Astrophysics Data System (ADS)

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

Somorjai, G. A.



Modelling the formation of maillard reaction intermediates for the generation of flavour  

Microsoft Academic Search

The Maillard reaction comprises a very complex, thermally-driven, set of reactions that leads to the formation of colour and flavour. In producing flavours, it is important to be able to quantitatively follow the course of this reaction system and thence control it by manipulating key input parameters, such as temperature, pH, type and concentration of the sugar and amino acid.

Guillaume Desclaux; Tahir I. Malik; Chris Winkel; D. Leo Pyle; Donald S. Mottram



Direct femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO to 2CH3 CO: Resolving  

E-print Network

devoted to answer such a question, and the issue in different reactions pericyclic, SN2, elimination, etcDirect femtosecond observation of the transient intermediate in the -cleavage reaction of (CH3)2CO, California 91125 Received 17 April 1995; accepted 2 May 1995 When a reaction involving two equivalent bonds

Kim, Sang Kyu


Detailed mechanism of the CH2I + O2 reaction: Yield and self-reaction of the simplest Criegee intermediate CH2OO  

NASA Astrophysics Data System (ADS)

The application of a new reaction scheme using CH2I + O2 to generate the simplest Criegee intermediate, CH2OO, has stimulated lively research; the Criegee intermediates are extremely important in atmospheric chemistry. The detailed mechanism of CH2I + O2 is hence important in understanding kinetics involving CH2OO. We employed ultraviolet absorption to probe simultaneously CH2I2, CH2OO, CH2I, and IO in the reaction system of CH2I + O2 upon photolysis at 248 nm of a flowing mixture of CH2I2, O2, and N2 (or SF6) in the pressure range 7.6-779 Torr to investigate the reaction kinetics. With a detailed mechanism to model the observed temporal profiles of CH2I, CH2OO, and IO, we found that various channels of the reaction CH2I + O2 and CH2OO + I play important roles; an additional decomposition channel of CH2I + O2 to form products other than CH2OO or ICH2OO becomes important at pressure less than 60 Torr. The pressure dependence of the derived rate coefficients of various channels of reactions of CH2I + O2 and CH2OO + I has been determined. We derived a rate coefficient also for the self-reaction of CH2OO as k = (8 ± 4) × 10-11 cm3 molecule-1 s-1 at 295 K. The yield of CH2OO from CH2I + O2 was found to have a pressure dependence on N2 and O2 smaller than in previous reports; for air under 1 atm, the yield of ˜30% is about twice of previous estimates.

Ting, Wei-Lun; Chang, Chun-Hung; Lee, Yu-Fang; Matsui, Hiroyuki; Lee, Yuan-Pern; Lin, Jim-Min, Jr.



Momentum dependence of spin polarization for beta emitting nuclei produced through charge exchange reaction at intermediate energy  

NASA Astrophysics Data System (ADS)

In order to investigate the polarization process in charge exchange reactions, we observed the momentum and angular distribution as well as the nuclear polarization of a proton-rich beta-emitting nucleus, 28P ( I ? = 3 + , T 1/2 = 270 msec), produced through the reaction 28Si+ 9Be at E = 100 MeV/u, by selecting the momentum and the ejection angle. An analysis by using double Gaussian functions resolved the observed momentum distribution into two reaction components, nucleon knockout and pick-up abrasion reactions, as suggested in a previous study. The behavior of the observed angular distribution and nuclear polarization implies the influence of those two components. The momentum dependence of the observed nuclear polarization of 28P could be consistently reproduced by a simple model, in which two reaction components are considered. The present study also shows that the charge exchange reaction at intermediate energy is a useful method to produce polarized beta-emitting nuclei, especially for proton-rich nuclei.

Momota, S.; Mihara, M.; Nishimura, D.; Fukuda, M.; Kamisho, Y.; Wakabayashi, M.; Matsuta, K.; Suzuki, S.; Nagashima, M.; Zhu, Shengyun; Yuan, Daqing; Zheng, Yongnan; Yi, Zuo; Fan, Ping; Izumikawa, T.; Kitagawa, A.; Sato, S.; Kanazawa, M.; Torikoshi, M.; Minamisono, T.; Nakamura, Y.; Tashiro, K.; Honma, A.; Yoshida, N.; Shirai, H.; Ohtsubo, T.; Nagatomo, T.; Uenishi, H.; Iwamoto, K.; Yaguchi, M.; Ogura, T.; Ito, T.; Yamamura, K.; Ichikawa, Y.; Nojiri, Y.; Alonso, J. R.; Symons, T. J. M.



Identification and characterization of monomeric, volatile SiCl3NH2 as product of the reaction between SiCl4 and NH3: an important intermediate on the way to silicon nitride?  


We studied the reaction of SiCl(4) with NH(3) by mass spectrometry and IR spectroscopy. By means of mass spectrometry, SiCl(3)NH(2) was for the first time identified as an intermediate generated in significant amounts in the course of the reaction. In additional experiments, SiCl(3)NH(2) was formed as a stable gaseous product of the ammonolysis of SiCl(4), and the product was identified and characterized in detail by IR spectroscopic methods (gas phase and matrix isolation) in combination with quantum-chemical calculations. The calculations also gave access to important thermodynamical data. PMID:12645028

Himmel, Hans-Jörg; Schiefenhövel, Nils; Binnewies, Michael



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


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

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



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

PubMed Central

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

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



A New Reaction Manifold for the Barton Radical Intermediates: Synthesis of N-Heterocyclic Furanosides and Pyranosides via the Formation of the C1-C2  

E-print Network

A New Reaction Manifold for the Barton Radical Intermediates: Synthesis of N in the deoxygenation process is the collapse of the intermediate 1. Under carefully controlled conditions to deoxygenation.10 These expecta- tions have been borne out, and in this communication we report our initial

RajanBabu, T. V. "Babu"


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

PubMed Central

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

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



Target Mass Dependency of Light Mass Fragment Energy Spectra for Intermediate Energy Proton Induced Reactions  

NASA Astrophysics Data System (ADS)

Double differential fragment production cross sections were measured for intermediate energy protons using a specially designed Bragg Curve Counter. Target mass dependency of Lithium and Beryllium energy spectra were obtained by fitting of the equation describing a Maxwellian distribution with a Coulomb barrier effect. Two parameters of the equation, s and T, which corresponds to absolute normalization and temperature of the Maxwellian respectively, show clear dependency on target mass.

Sanami, T.; Hagiwara, M.



Reaction between atomic fluorine and CF3Br: Evidence for a pseudotrihalogen radical intermediate  

Microsoft Academic Search

The kinetics of the reaction between atomic fluorine and CF3Br has been investigated in the temperature range 188–373 °K using molecular beam analysis in conjunction with an H2 titration to measure the concentration of atomic fluorine in a flow reactor. The effective second order rate constant for this reaction varies from 2.5 × 108 cm3?mole · sec at 373 °K

Joseph W. Bozzelli; C. E. Kolb; M. Kaufman



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

NASA Technical Reports Server (NTRS)

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

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



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


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

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



High resolution reaction intermediates of rabbit muscle fructose-1,6-bisphosphate aldolase: substrate cleavage and induced fit.  


Crystal structures were determined to 1.8 A resolution of the glycolytic enzyme fructose-1,6-bis(phosphate) aldolase trapped in complex with its substrate and a competitive inhibitor, mannitol-1,6-bis(phosphate). The enzyme substrate complex corresponded to the postulated Schiff base intermediate and has reaction geometry consistent with incipient C3-C4 bond cleavage catalyzed Glu-187, which is adjacent by to the Schiff base forming Lys-229. Atom arrangement about the cleaved bond in the reaction intermediate mimics a pericyclic transition state occurring in nonenzymatic aldol condensations. Lys-146 hydrogen-bonds the substrate C4 hydroxyl and assists substrate cleavage by stabilizing the developing negative charge on the C4 hydroxyl during proton abstraction. Mannitol-1,6-bis(phosphate) forms a noncovalent complex in the active site whose binding geometry mimics the covalent carbinolamine precursor. Glu-187 hydrogen-bonds the C2 hydroxyl of the inhibitor in the enzyme complex, substantiating a proton transfer role by Glu-187 in catalyzing the conversion of the carbinolamine intermediate to Schiff base. Modeling of the acyclic substrate configuration into the active site shows Glu-187, in acid form, hydrogen-bonding both substrate C2 carbonyl and C4 hydroxyl, thereby aligning the substrate ketose for nucleophilic attack by Lys-229. The multifunctional role of Glu-187 epitomizes a canonical mechanistic feature conserved in Schiff base-forming aldolases catalyzing carbohydrate metabolism. Trapping of tagatose-1,6-bis(phosphate), a diastereoisomer of fructose 1,6-bis(phosphate), displayed stereospecific discrimination and reduced ketohexose binding specificity. Each ligand induces homologous conformational changes in two adjacent alpha-helical regions that promote phosphate binding in the active site. PMID:15870069

St-Jean, Miguel; Lafrance-Vanasse, Julien; Liotard, Brigitte; Sygusch, Jurgen



Hydrogen bonding to the cysteine ligand of superoxide reductase: acid-base control of the reaction intermediates.  


Superoxide reductase (SOR) is a non-heme iron metalloenzyme that detoxifies superoxide radical in microorganisms. Its active site consists of an unusual non-heme Fe(2+) center in a [His4Cys1] square pyramidal pentacoordination, with the axial cysteine ligand proposed to be an essential feature in catalysis. Two NH peptide groups from isoleucine 118 and histidine 119 establish hydrogen bonds involving the sulfur ligand (Desulfoarculus baarsii SOR numbering). To investigate the catalytic role of these hydrogen bonds, the isoleucine 118 residue of the SOR from Desulfoarculus baarsii was mutated into alanine, aspartate, or serine residues. Resonance Raman spectroscopy showed that the mutations specifically induced an increase of the strength of the Fe(3+)-S(Cys) and S-C?(Cys) bonds as well as a change in conformation of the cysteinyl side chain, which was associated with the alteration of the NH hydrogen bonding involving the sulfur ligand. The effects of the isoleucine mutations on the reactivity of SOR with O2 (•-) were investigated by pulse radiolysis. These studies showed that the mutations induced a specific increase of the pK a of the first reaction intermediate, recently proposed to be an Fe(2+)-O2 (•-) species. These data were supported by density functional theory calculations conducted on three models of the Fe(2+)-O2 (•-) intermediate, with one, two, or no hydrogen bonds involving the sulfur ligand. Our results demonstrated that the hydrogen bonds between the NH (peptide) and the cysteine ligand tightly control the rate of protonation of the Fe(2+)-O2 (•-) reaction intermediate to form an Fe(3+)-OOH species. PMID:23917995

Tremey, Emilie; Bonnot, Florence; Moreau, Yohann; Berthomieu, Catherine; Desbois, Alain; Favaudon, Vincent; Blondin, Geneviève; Houée-Levin, Chantal; Nivière, Vincent



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

PubMed Central

The reaction of fully reduced soluble bovine heart cytochrome oxidase with O2 at 173K was investigated by low-temperature optical and e.p.r. spectroscopy, and the kinetics of the reaction were analysed by non-linear optimization techniques. The only e.p.r. signals seen during the course of the reaction are those attributable to low-spin cytochrome a3+ and CuA2+. Quantitative analysis of e.p.r. signals shows that, at the end point of the reaction at 173K, nearly 100% of CuA is in the cupric state but only about 40% of cytochrome a is in the ferric low-spin state. The optical spectra recorded at this stage of the reaction show incomplete oxidation of haem and the absence of a 655 nm absorption band. The only reaction scheme that accounts for both the e.p.r. and optical data is a four-intermediate mechanism involving a branching pathway. The reaction is initiated when fully reduced cytochrome oxidase reacts with O2 to form intermediate I. This is then converted into either intermediate IIA or intermediate IIB. Of these, intermediate IIB is a stable end product at 173 K, but intermediate IIA is converted into intermediate III, which is the stable state at 173 K in this branch of the mechanism. The kinetic analysis of the e.p.r. data allows the unambiguous assignments of the valence states of cytochrome a and CuA in the intermediates. Intermediate I contains cytochrome a2+ and CuA+, intermediate IIA contains low-spin cytochroma a3+ and CuA+, intermediate IIB contains cytochrome a2+ and CuA2+, and intermediate III contains low-spin cytochrome a3+ and CuA2+. The electronic state of the O2-binding CuBa3 couple during the reoxidation of cytochrome oxidase is discussed in terms of an integrated structure containing CuB, cytochrome a3 and O2. PMID:6246874

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



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

SciTech Connect

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

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



Neutron proton bremsstrahlung from intermediate energy heavy-ion reactions as a probe of the nuclear symmetry energy?  

NASA Astrophysics Data System (ADS)

Hard photons from neutron-proton bremsstrahlung in intermediate energy heavy-ion reactions are examined as a potential probe of the nuclear symmetry energy within a transport model. Effects of the symmetry energy on the yields and spectra of hard photons are found to be generally smaller than those due to the currently existing uncertainties of both the in-medium nucleon-nucleon cross sections and the photon production probability in the elementary process pn?pn?. Very interestingly, nevertheless, the ratio of hard photon spectra R(?) from two reactions using isotopes of the same element is not only approximately independent of these uncertainties but also quite sensitive to the symmetry energy. For the head-on reactions of 132Sn + 124Sn and 112Sn + 112Sn at E/A=50 MeV, for example, the R(?) displays a rise up to 15% when the symmetry energy is reduced by about 20% at ?=1.3? which is the maximum density reached in these reactions.

Yong, Gao-Chan; Li, Bao-An; Chen, Lie-Wen



Vector and tensor analysing powers in deuteron-proton breakup reactions at intermediate energies  

E-print Network

Vector and tensor analysing powers of the d(pol)p->(pp)n (charge-exchange) and d(pol)p->(pn)p (non-charge-exchange) breakup reactions have been measured with the ANKE spectrometer at the COSY ring at a deuteron beam energy of 1170 MeV for small momentum transfers to the low excitation energy (pp) or (pn) systems. A quantitative understanding of the values of A_xx and A_yy for the charge-exchange reaction is provided by impulse approximation calculations. The data suggest that spin-flip isospin-flip transitions, which dominate the charge-exchange breakup of the deuteron, are also important in the non-charge-exchange reaction.

D. Chiladze; J. Carbonell; S. Dymov; V. Glagolev; M. Hartmann; V. Hejny; A. Kacharava; I. Keshelashvili; A. Khoukaz; H. R. Koch; V. Komarov; P. Kulessa; A. Kulikov; G. Macharashvili; Y. Maeda; T. Mersmann; S. Merzliakov; S. Mikirtytchiants; A. Mussgiller; M. Nioradze; H. Ohm; F. Rathmann; R. Schleichert; H. J. Stein; H. Stroeher; Yu. Uzikov; S. Yaschenko; C. Wilkin



Deflection Functions for Heavy-ion Induced Reactions at Intermediate Bombarding Energies  

NASA Astrophysics Data System (ADS)

Exclusive measurements of projectile-like fragments (PLFs) have been performed near the grazing angles for the reactions ^112Sn + ^40Ca, ^112Sn + ^48Ca, ^197Au + ^86Kr at E_lab/A = 35MeV, and for the reactions ^209Bi + ^136Xe at E_lab/A = 28 and 55MeV. The primary character of these reactions is dissipative. The angular distributions of the projectile-like fragments as functions of dissipated energy (deflection functions) for the above systems have been analyzed in the framework of the Nucleon Exchange model (NEM), accounting for the statistical decay of these fragments using the code EVAP. On average, model calculations with the "modified" proximity potential reproduce the experimental deflection functions well. Supported by U.S. DOE grant number DE-FG02-88ER40414.

Agnihotri, D. K.; Baldwin, S. P.; Djerroud, B.; Skulski, W.; Tõke, J.; Schröder, W. U.; Davin, B.; Cornell, E.; Desouza, R. T.; Lott, B.; Dempsey, J.; Charity, R. J.; Sobotka, L. G.; Sarantites, D. G.; Kunde, G. J.; Gaff, S.; Gelbke, C. K.; Glasmacher, T.; Huang, M. J.; Lemon, R.; Lynch, W. G.; Manduci, L.; Martin, L.; Tsang, M. B.



JOURNAL DE PHYSIQUE Colloque C5, supplment au n 11, Tome 37., Novembre 1976, page C5-177 INTERMEDIATE STRUCTURE IN LIGHT ION REACTIONS  

E-print Network

-177 INTERMEDIATE STRUCTURE IN LIGHT ION REACTIONS H. Feshbach Massachusetts Institute of Technology, Cambridge and doorway states which have been discovered in the reactions induced by collision of the light ions 12 C-sections for the colli- sion of light ions is presented. This paper will present a review of the inter- mediate structure

Paris-Sud XI, Université de


Observation of Organometallic and Radical Intermediates Formed during the Reaction of Methyl-Coenzyme M Reductase with Bromoethanesulfonate†  

PubMed Central

Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the final step of methane formation, in which methyl-coenzyme M (2-methylthioethane sulfonate, methyl-SCoM) is reduced with coenzyme B (N-7-mercaptoheptanolyl-threonine phosphate, CoBSH) to form methane and the heterodisulfide CoBS-SCoM. The active dimeric form of MCR contains two Ni(I)-F430 prosthetic groups, one in each monomer. This manuscript describes studies of the reaction of the active Ni(I) state of MCR (MCRred1) with BES (2-bromoethanesulfonate) and CoBSH or its analog, CoB6SH (N-6-mercaptohexanolyl-threonine phosphate), by transient kinetic measurements using EPR and UV-visible spectroscopy and by global fits of the data. This reaction is shown to lead to the formation of three intermediates, the first of which is assigned as an alkyl-Ni(III) species that forms as the active Ni(I)-MCRred1 state of the enzyme decays. Subsequently, a radical (MCRBES radical) is formed that was characterized by multifrequency electron paramagnetic resonance (EPR) studies at X (~ 9 GHz)-, Q (~35 GHz)- and D (~135 GHz)-bands and by electron-nuclear double resonance (ENDOR) spectroscopy. The MCRBES radical is characterized by g-values at 2.00340 and 1.99832 and includes a strongly coupled non-exchangeable proton with a hyperfine coupling constant of 50 MHz. Based on transient kinetic measurements, the formation and decay of the radical coincides with a species that exhibits absorption peaks at 426 nm and 575 nm. Isotopic substitution, multifrequency EPR and ENDOR spectroscopic experiments rule out the possibility that MCRBES is a tyrosyl radical and indicate that if a tyrosyl radical is formed during the reaction, it does not accumulate to detectable levels. The results provide support for a hybrid mechanism of methanogenesis by MCR that includes both alkyl-Ni and radical intermediates. PMID:20597483

Li, Xianghui; Telser, Joshua; Hoffman, Brian M.; Gerfen, Gary; Ragsdale, Stephen W.



Neutral Current Neutrino-{sup 116}Cd Reaction Cross Sections at Low and Intermediate Energies  

SciTech Connect

Differential and integrated cross sections for inelastic scattering of electron neutrinos from a {sup 116}Cd target at low and intermediate neutrino energies ({epsilon}{sub i}{<=}100 MeV) are presented. The nuclear wave functions for the initial and final nuclear states are constructed in the context of quasiparticle random phase approximation (QRPA). By exploiting the results of these cross sections, we study the response of {sup 116}Cd to supernova neutrino spectra by utilizing the folding procedure and employing a two-parameter Fermi-Dirac distribution for the supernova neutrino spectra. Our results show that, this isotope may play a significant role in supernova neutrino detection, in addition to its use in double-beta-decay experiments (COBRA, etc)

Balasi, K. G.; Kosmas, T. S.; Divari, P. C.; Chasioti, V. C. [Theoretical Physics Section, University of Ioannina, GR 45110 Ioannina (Greece)



Perceptions of Macomb County teachers toward professional staff development opportunities as identified by Macomb Intermediate School District's Management Training Center  

Microsoft Academic Search

The purpose of this study was to investigate the perceptions of public school teachers in Macomb County, Michigan toward professional development training offered trough Macomb Intermediate School District's Management Training programs. ^ The study investigated the perceptions of elementary, middle school, and high school teaching staff, to include ancillary personnel in both regular education and special education classrooms in Macomb

Hannah Worley



Sensitivity of the Blue Loops of Intermediate-Mass Stars to Nuclear Reactions  

E-print Network

We investigate the effects of a modification of the $^{14}$N(p,{\\gamma})$^{15}$O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the mass range 5M$_{\\odot}$ to 12M$_{\\odot}$. We show that the blue loops of stars in the mass range 5M$_{\\odot}$ to 8M$_{\\odot}$, that is the range of super ABG stars, are severely affected by a modification of the important $^{14}$N(p,{\\gamma})$^{15}$O reaction rate. We also show that the blue loops can be restored if envelope overshooting is included, which is necessary to explain the observations of the Cepheid stars.

Halabi, Ghina M



Sensitivity of the blue loops of intermediate-mass stars to nuclear reactions  

SciTech Connect

We investigate the effects of a modification of the {sup 14}N(p,{gamma}){sup 15}O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the mass range 5M{sub Circled-Dot-Operator} to 12M{sub Circled-Dot-Operator }. We show that the blue loops of stars in the mass range 5M{sub Circled-Dot-Operator} to 8M{sub Circled-Dot-Operator }, that is the range of super ABG stars, are severely affected by a modification of the important {sup 14}N(p,{gamma}){sup 15}O reaction rate. We also show that the blue loops can be restored if envelope overshooting is included, which is necessary to explain the observations of the Cepheid stars.

Halabi, Ghina M.; El Eid, Mounib [American University of Beirut, Department of Physics, P.O. Box 11-0236, Riad El-Solh, Beirut (Lebanon)



Mechanism of protein modification by glyoxal and glycolaldehyde, reactive intermediates of the Maillard reaction.  


The role of glyoxal and glycolaldehyde in protein cross-linking and N epsilon-(carboxymethyl)lysine (CML) formation during Maillard reaction under physiological conditions was investigated. Incubation of bovine serum albumin with these reagents lead to rapid formation of C-2-imine cross-links and CML. Initial CML formation rate from glyoxal was not dependent on oxidation, suggesting an intramolecular Cannizzaro reaction. CML formation from glucose/lysine or Amadori product of both was strongly dependent on oxidation. Blocking of Amadori product by boric acid totally suppressed CML formation from Amadori product, but only by 37% in the glucose/lysine system. Trapping of glyoxal with aminoguanidine hardly suppressed CML formation from Amadori product, whereas it blocked 50% of CML production in the glucose/lysine system. While these results would support a significant role for glucose autoxidation in CML formation, the addition of lysine to a glucose/aminoguanidine incubation system catalyzed glyoxal-triazine formation 7-fold, thereby strongly suggesting that glucose autoxidation is not a factor for glyoxal-mediated CML formation. Based on these results, it can be estimated that approximately 50% of the CML forming in a glucose/lysine system originates from oxidation of Amadori product, and 40-50% originates from a pre-Amadori stage largely independent from glucose autoxidation. This step may be related to the so-called Namiki pathway of the Maillard reaction. PMID:7730303

Glomb, M A; Monnier, V M



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

SciTech Connect

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

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



A study of stopping power in nuclear reactions at intermediate energies  

E-print Network

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

G. Lehaut; D. Durand; O. Lopez



Proximity Effects in Nucleophilic Addition Reactions to Medium-Bridged Twisted Lactams: Remarkably Stable Tetrahedral Intermediates  

PubMed Central

The reactions of a series of strained bicyclic and tricyclic one-carbon bridged lactams with organometallic reagents have been investigated. These amides permit isolation of a number of remarkably stable hemiaminals upon nucleophilic addition to the twisted amide bonds present in the lactam precursors. The factors that affect the stability of the resulting bridged hemiaminals are presented. In some cases, the hemiaminals were found to collapse to the open-form amino ketones in a manner expected for traditional carboxylic acid derivatives. Transannular N?C=O interactions were also observed in some 9-membered amino ketones. Additionally, tricyclic bridged lactams were found to react with some nucleophiles that typically react with ketones but not with planar amides. The effect of geometry on the reactivity of amide bonds and the amide bond distortion range that marks the boundary of amide-like and ketone-like carbonyl reactivity of lactams are also discussed. PMID:20095610

Szostak, Michal; Yao, Lei; Aubé, Jeffrey



Production of neutron-unbound states in intermediate-mass fragments from sup 14 N+Ag reactions at E / A =35 MeV  

SciTech Connect

The populations of neutron-unbound states and of bound states in intermediate-mass fragments have been measured at 15{degree}, 31{degree}, and 64{degree} from the {sup 14}N+Ag reaction at {ital E}/{ital A}=35 MeV. We did this for eleven neutron-unbound states in seven isotopes whose bound-state populations we were also able to measure. The data are identified in terms of the reaction mechanism producing them, which is either a deep-inelastic mechanism or a quasielastic mechanism. In order to test the assumption that the deep-inelastic data are produced from a thermal source, the unbound-state--bound-state population ratios of deep-inelastic fragments are compared to the predictions of a thermal sequential decay model. Most, but not all, of the deep-inelastic population ratios are fitted with model calculations that assume a source temperature between 2.5 and 3.5 MeV. In the case of {sup 13}C we were able to measure four deep-inelastic populations, and in the case of {sup 12}B we were able to measure three such populations. To further test the assumption of emission from a thermal source, attempts were made to fit all of the populations from each of these two isotopes with the sequential decay model using a single temperature.

Heilbronn, L.; Galonsky, A.; Gelbke, C.K.; Lynch, W.G.; Murakami, T.; Sackett, D.; Schelin, H.; Tsang, M.B. (National Superconducting Cyclotron Laboratory and Department of Physics Astronomy, Michigan State University, East Lansing, Michigan 48824 (USA)); Deak, F.; Kiss, A. (Department of Atomic Physics, Eoetvoes University, Puskin utca 5-7, H-1088 Budapest, Hungary (HU)); Seres, Z. (Central Research Institute for Physics, H-1525 Budapest 114, Hungary (HU)); Kasagi, J. (Tokyo Institute of Technology, O-Okayama, Meguro-ku, Tokyo 152, Japan (JP)); Remington, B.A. (Lawrence Livermore National Laboratory, Livermore, California 94550 (USA))



Mechanistic Origins of Chemo- and Regioselectivity of Ru(II)-Catalyzed Reactions Involving ortho-Alkenylarylacetylene, Alkyne, and Methanol: The Crucial Role of a Chameleon-like Intermediate.  


M06-DFT computations have been applied to understand four catalytic systems which involved [Ru(Cp*)(MeCN)3]PF6 or [Ru(Tp)(PPh3)(MeCN)2]PF6 as mediator and ortho-alkenylarylacetylene, terminal alkyne, and methanol as reactants. Potentially, the products of these systems could be dihydrobiphenylenes, 1,3-dienyl ether, and naphthalene. Remarkably, each system afforded product selectively. Our computed mechanisms successfully account for the chemo- and regioselectivities of these systems. Furthermore, the study demonstrates that the chameleon-like mono(carbene) intermediates formed via the intermolecular alkyne-alkyne oxidative coupling play a crucial role to complete the reactions. According to their geometric and electronic structures, three resonance structures were introduced to characterize their reactivity properties, which address the features of the classical alkyne-alkyne oxidative coupling intermediates, mono(carbene) species, and electrophilicity of the intermediates, respectively. The reactivity properties lead to three channels isomerizing the intermediates to three isomers. Surprisingly, the bis(carbene) isomers, which are similar to the bis(carbene) intermediates generally considered to be crucial in the neutral RuCp*Cl-catalyzed systems, are accessible but not reactive enough to continue the subsequent reaction steps partially due to aromaticity. The other two isomers continue subsequent reaction steps. These findings may help not only to understand the four specific catalytic reactions but also to advance the [2 + 2 + 2] synthetic methodology. PMID:25222525

Dang, Yanfeng; Qu, Shuanglin; Tao, Yuan; Song, Chunyu; Wang, Zhi-Xiang



Preverbal infants identify emotional reactions that are incongruent with goal outcomes.  


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

Skerry, Amy E; Spelke, Elizabeth S



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


The present study investigates for the first time the reduction of nitrite by biogenic hydroxycarbonate green rusts, bio-GR(CO3), produced from the bioreduction of ferric oxyhydroxycarbonate (Fohc), a poorly crystalline solid phase, and of lepidocrocite, a well-crystallized Fe(III)-oxyhydroxide mineral. Results show a fast Fe(II) production from Fohc, which leads to the precipitation of bio-GR(CO3) particles that were roughly 2-fold smaller (2.3 ± 0.4 ?m) than those obtained from the bioreduction of lepidocrocite (5.0 ± 0.4 ?m). The study reveals that both bio-GR(CO3) are capable of reducing nitrite ions into gaseous nitrogen species such as NO, N2O, or N2 without ammonium production at neutral initial pH and that nitrite reduction proceeded to a larger extent with smaller particles than with larger ones. On the basis of the identification of intermediates and end-reaction products using X-ray diffraction and X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge, our study shows the formation of hydroxy-nitrite green rust, GR(NO2), a new type of green rust 1, and suggests that the reduction of nitrite by biogenic GR(CO3) involves both external and internal reaction sites and that such a mechanism could explain the higher reactivity of green rust with respect to nitrite, compared to other mineral substrates possessing only external reactive sites. PMID:24708473

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



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


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

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



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

NASA Astrophysics Data System (ADS)

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

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



Nonclassical aryl radicals: Intermediates or transition states for the hydrogen shift reactions?  

SciTech Connect

Electronic properties of aryl radicals obtained by removing single hydrogen atoms from the sterically congested regions of benzo[c]phenanthrene, biphenyl, triphenylene, phenanthrene, and perylene are studied at the UBLYP/6-311G** level of theory. Two structures are considered by each radical, the classical one involving a C-H{hor_ellipsis}C arrangement of atoms and the nonclassical one possessing a three-center C-H-C linkage. The five nonclassical radicals under study are found to be transition states for degenerate 1,4- and 1,5-hydrogen shift reactions that interconvert the classical species. However, the results of the present calculations indicate that the nonclassical structures with the C-H distances in the C-H-C linkages shorter than 1.34 {angstrom} should be energy minima representing potentially observable chemical systems. The predicted energy barrier to the 1,5-hydrogen shift in the 1-benzo[c]phenanthrenyl radical is only 9.3 kcal/mol with the zero-point energies included, making the hydrogen migration in this system facile at relatively low temperatures. Rigorous analysis of the computed electronic wave functions provides a clear-cut picture of bonding in both the classical and nonclassical aryl radicals. 2 figs., 4 tabs.

Cioslowski, J.; Liu, G.; Moncrieff, D. [Florida State Univ., Tallahassee, FL (United States)] [Florida State Univ., Tallahassee, FL (United States)



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

NASA Astrophysics Data System (ADS)

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

Ben Belgacem, Faker



Discovery of a reaction intermediate of aliphatic aldoxime dehydratase involving heme as an active center  

PubMed Central

Recently, we discovered an intriguing hemoprotein [aliphatic aldoxime dehydratase (OxdA)] that catalyzes the dehydration of aliphatic aldoximes [R–CH=N–OH] to the corresponding nitriles [R–C?N] in the industrial Pseudomonas chlororaphis B23 strain. Unlike the utilization of H2O2 or O2 as a mediator of the catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron, experimental evidence of which was obtained here by means of resonance Raman (RR) analysis with an isotope technique. We found that the addition of a large amount of butyraldoxime (final concentration, 200 mM) to ferrous OxdA with a low enzyme concentration (final concentration, 5 ?M) yields a long-lived OxdA–substrate complex (named OS-II), whose UV-vis spectrum is different from the corresponding spectra of the OxdA–substrate complex I and CO-bound, ferrous, and ferric forms of OxdA. Intriguingly, the RR analysis demonstrated that OS-II includes a highly oxidized heme with strong bonding between a substrate and the heme iron, as judged from the heme oxidation state marker ?4 band at 1,379 cm–1 and the 15N-isotope-substituted butyraldoxime sensitive band at 857 cm–1 in the RR spectra. It is noteworthy that OS-II has a highly oxidized heme like the ferryl-oxo heme species (e.g., compound II) formed by some general hemoproteins, although the function of OxdA is different from those (transport of electrons, transport of oxygen, sensing of oxygen or carbon monoxide, and catalysis of redox reactions) of general hemoproteins. PMID:16407114

Konishi, Kazunobu; Ohta, Takehiro; Oinuma, Ken-Ichi; Hashimoto, Yoshiteru; Kitagawa, Teizo; Kobayashi, Michihiko



Crystal structure of bifunctional aldos-2-ulose dehydratase/isomerase from Phanerochaete chrysosporium with the reaction intermediate ascopyrone M.  


The enzyme aldos-2-ulose dehydratase/isomerase (AUDH) participates in carbohydrate secondary metabolism, catalyzing the conversion of glucosone and 1,5-d-anhydrofructose to the secondary metabolites cortalcerone and microthecin, respectively. AUDH is a homo-dimeric enzyme with subunits of 900 amino acids. The subunit consists of a seven-bladed ?-propeller domain, two cupin folds and a C-terminal lectin domain. AUDH contains a structural Zn(2+) and Mg(2+) located in loop regions and two zinc ions at the bottom of two putative active-site clefts in the propeller and the cupin domain, respectively. Catalysis is dependent on these two zinc ions, as their specific removal led to loss of enzymatic activity. The structure of the Zn(2)(+)-depleted enzyme is very similar to that of native AUDH, and structural changes upon metal removal as the cause for the catalytic deficiencies can be excluded. The complex with the reaction intermediate ascopyrone M shows binding of this compound at two different sites, with direct coordination to Zn(2+) in the propeller domain and as second sphere ligand of the metal ion in the cupin domain. These observations suggest that the two reactions of AUDH might be catalyzed in two different active sites, about 60 Å apart. The dehydration reaction most likely follows an elimination mechanism, where Zn(2+) acts as a Lewis acid polarizing the C2 keto group of 1,5-d-anhydrofructose. Abstraction of the proton at the C3 carbon atom and protonation of the leaving group, the C4 hydroxyl moiety, could potentially be catalyzed by the side chain of the suitably positioned residue His155. PMID:22330145

Claesson, Magnus; Lindqvist, Ylva; Madrid, Susan; Sandalova, Tatyana; Fiskesund, Roland; Yu, Shukun; Schneider, Gunter



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

NASA Astrophysics Data System (ADS)

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

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



Mechanism of the Schiff base forming fructose-1,6-bisphosphate aldolase: structural analysis of reaction intermediates.  


The glycolytic enzyme fructose-1,6-bisphosphate aldolase (FBPA) catalyzes the reversible cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Catalysis of Schiff base forming class I FBPA relies on a number of intermediates covalently bound to the catalytic lysine. Using active site mutants of FBPA I from Thermoproteus tenax, we have solved the crystal structures of the enzyme covalently bound to the carbinolamine of the substrate fructose 1,6-bisphosphate and noncovalently bound to the cyclic form of the substrate. The structures, determined at a resolution of 1.9 A and refined to crystallographic R factors of 0.148 and 0.149, respectively, represent the first view of any FBPA I in these two stages of the reaction pathway and allow detailed analysis of the roles of active site residues in catalysis. The active site geometry of the Tyr146Phe FBPA variant with the carbinolamine intermediate supports the notion that in the archaeal FBPA I Tyr146 is the proton donor catalyzing the conversion between the carbinolamine and Schiff base. Our structural analysis furthermore indicates that Glu187 is the proton donor in the eukaryotic FBPA I, whereas an aspartic acid, conserved in all FBPA I enzymes, is in a perfect position to be the general base facilitating carbon-carbon cleavage. The crystal structure of the Trp144Glu, Tyr146Phe double-mutant substrate complex represents the first example where the cyclic form of beta-fructose 1,6-bisphosphate is noncovalently bound to FBPA I. The structure thus allows for the first time the catalytic mechanism of ring opening to be unraveled. PMID:15766250

Lorentzen, Esben; Siebers, Bettina; Hensel, Reinhard; Pohl, Ehmke



Trapping the tetrahedral intermediate in the alkaline phosphatase reaction by substitution of the active site serine with threonine.  


We report here the construction of a mutant version of Escherichia coli alkaline phosphatase (AP) in which the active site Ser was replaced by Thr (S102T), in order to investigate whether the enzyme can utilize Thr as the nucleophile and whether the rates of the critical steps in the mechanism are altered by the substitution. The mutant AP with Thr at position 102 exhibited an approximately 4000-fold decrease in k(cat) along with a small decrease in Km. The decrease in catalytic efficiency of approximately 2000-fold was a much smaller drop than that observed when Ala or Gly were substituted at position 102. The mechanism by which Thr can substitute for Ser in AP was further investigated by determining the X-ray structure of the S102T enzyme in the presence of the Pi (S102T_Pi), and after soaking the crystals with substrate (S102T_sub). In the S102T_Pi structure, the Pi was coordinated differently with its position shifted by 1.3 A compared to the structure of the wild-type enzyme in the presence of Pi. In the S102T_sub structure, a covalent Thr-Pi intermediate was observed, instead of the expected bound substrate. The stereochemistry of the phosphorus in the S102T_sub structure was inverted compared to the stereochemistry in the wild-type structure, as would be expected after the first step of a double in-line displacement mechanism. We conclude that the S102T mutation resulted in a shift in the rate-determining step in the mechanism allowing us to trap the covalent intermediate of the reaction in the crystal. PMID:17008720

Wang, Jie; Kantrowitz, Evan R



Reaction-intermediate analogues binding by ribulose bisphosphate carboxylase/oxygenase causes specific changes in proteolytic sensitivity: the amino-terminal residue of the large subunit is acetylated proline  

SciTech Connect

Trypsin rapidly inactivated the catalytic activities of spinach ribulose bisphosphate carboxylase/oxygenase but the stoichiometry of binding of the reaction-intermediate analogue carboxyarabinitol bisphosphate was only slightly reduced after proteolysis. Electrophoretic analysis indicated that several forms of the large subunit were generated during proteolysis but that the small subunit was resistant. Three tryptic peptides were isolated and characterized after digestion of the activated enzyme; the tryptic-sensitive sites were identified at Lys-8, Lys-14, and Lys-466 of the large subunit. Tryptic digestion of the enzyme complexed with the reaction-intermediate analogue released only two peptides by hydrolysis at Lys-8 and at Lys-14. The loss of susceptibility of Lys-466 to trypsin may be the result of a conformational change that limits the accessibility of the carboxyl-terminal region after binding of the reaction-intermediate analogue. Analysis of the amino-terminal tryptic peptide by composition and fast atom bombardment mass spectrometry demonstrated that the actual amino-terminal residue is proline at position 3 of the DNA-deduced sequence and that this proline is blocked with an N-acetyl moiety. Thus, posttranslational processing of the chloroplast-encoded large subunit of the enzyme must occur to remove Met-1 and Ser-2 and to acetylate the amino terminus.

Mulligan, R.M.; Houtz, R.L.; Tolbert, N.E.



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

NASA Technical Reports Server (NTRS)

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

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



Chiral iminoesters derived from D-glyceraldehyde in [3 + 2] cycloaddition reactions. Asymmetric synthesis of a key intermediate in the synthesis of neuramidinase inhibitors.  


Silver-catalyzed endo-selective and copper-catalyzed exo-selective asymmetric [3 + 2] cycloadditions of acrylates to chiral iminoesters derived from D-glyceraldehyde have been investigated. The reaction diastereoselectively provides highly functionalized pyrrolidines. This approach was used to develop the first asymmetric synthesis of a key intermediate in the synthesis of pyrrolidine influenza neuramidinase inhibitors. PMID:24143968

Gálvez, José A; Díaz-de-Villegas, María D; Alías, Miriam; Badorrey, Ramón



The Role of Odd-Electron Intermediates and In-Cage Electron Transfer in Ultrafast Photochemical Disproportionation Reactions in Lewis Bases  

E-print Network

and photoproducts.7 Figure 1 shows transient difference spectra recorded after 400 nm photolysis of Cp2W2(CO)6Cl2. The reaction is initiated by a laser pulse at 400 nm, and transient intermediates) with transient absorptions at 1880 and 1995 cm-1 (transient difference spectra in neat CH2Cl2 solutions were

Harris, Charles B.


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

NASA Astrophysics Data System (ADS)

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

Kaufmann, Royi; Yadid, Itamar; Goldfarb, Daniella



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

SciTech Connect

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

Isied, Stephan S.



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


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

Murali Manoj, Kelath



[Intermediate states formed during discharge separation in the reaction centers of Rhodospirillum rubrum in the presence of a low-redox potential].  


The intermediate short-lived states arising in reaction centre preparations (RC) of purple bacterium Rhodospirillum rubrum are investigated under the conditions of low redox potential. Excitation by 353 and 530 nm laser pulses produced two states characterized by optical absorption changes in the range of 350--650 nm and lifetimes: 10--30 ns for the first state and 2.5 +/- 0.5 microseconds for the second one. The first state is similar to the state PF, described previously by Parson et al. for RC from Rps. sphaeroides. Carotenoid extraction with isooctane resulted in changing the spectrum with tau = 2.5 microseconds and in the appearance of new absorption changes similar to those for the R state observed before in carotenoidless bacterial strains within microsecond time range. The comparison of the microsecond spectra with difference spectra (continuous light minus dark) of RC from R. rubrum in the range of 350--650 nm made it possible to identify the states with tau = 2.5 microseconds as carotenoid triplet states. The ratio of quantum yields of PR and carotenoid triplet states production was determined as being 1 : 1. The conclusion was made that triplet-triplet energy transfer from state PR to carotenoid is responsible for the production of carotenoid triplet states. PMID:418326

Godik, V I; Samuilov, V D; Borisov, A Iu



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

NASA Astrophysics Data System (ADS)

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

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



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

SciTech Connect

The ubiquitous presence of phosphoryl transfer as central step in many metabolic, signaling, energy storage, etc. enzymatic reactions requires that the details of the reaction mechanisms (e.g. reaction paths, transition state stabilization and structure, etc.) that leads to their remarkable rates in protein catalytic environments be understood1. It is expected that most of these reactions proceed through a pathway that includes a penta- coordinated phosphorane species. However, the nature of the bonding and the protonation of the structure in this region and the possibility of stable intermediates as the system passes along the reaction path through the transitions state (TS) are currently topics of considerable debate1a,b,c. Typically nucleophilic substitution reactions are classified in terms of extremes of two bonding situations along the reaction path: in a dissociative mechanism the substrate phosphate bridging bond is broken and the bond to the entering nucleophilic group is not yet formed leaving a metastable metaphosphate (PO3?) intermediate (a DN+AN reaction); in an associative mechanism in the extreme case a metastable pentacoordinated phosphorane species with nearly equivalent bonds is present in the TS, whose subsequent dissociation leads to the product state (an AN+DN reaction). Recently we published a computational study of the phosphoryl transfer step of a major class of enzymes, the serine kinases2a,b involved in signal transduction. These calculations2b support a dissociative mechanism (DNAN,) for this family of enzymes with unstable metaphosphate structure in loose transition state with total bond order of 22%.

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



Measurements of identified particles at intermediate transverse momentum in the STAR experiment from Au+Au collisions at sqrt{s_{NN}}=200 GeV  

E-print Network

Data for Au+Au collisions at sqrt{s_{NN}}=200 GeV are analyzed to determine the ratios of identified hadrons ($\\pi$, $K$, $p$, $\\Lambda$) as functions of collision centrality and transverse momentum ($p_T$). We find that ratios of anti-baryon to baryon yields are independent of $p_T$ up to 5 GeV/c, a result inconsistent with results of theoretical pQCD calculations that predict a decrease due to a stronger contribution from valence quark scattering. For both strange and non-strange species, strong baryon enhancements relative to meson yields are observed as a function of collision centrality in the intermediate $p_T$ region, leading to $p/\\pi$ and $\\Lambda$/K ratios greater than unity. The increased $p_T$ range offered by the $\\Lambda$/K$^{0}_{S}$ ratio allows a test of the applicability of various models developed for the intermediate $p_{T}$ region. The physics implications of these measurements are discussed with regard to different theoretical models.

Adams, J; Ahammed, Z; Amonett, J; Anderson, B D; Anderson, M; Arkhipkin, D; Averichev, G S; Badyal, S K; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Bezverkhny, B I; Bharadwaj, S; Bhasin, A; Bhati, A K; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Blyth, C O; Blyth, S L; Bonner, B E; Botje, M; Bouchet, J; Braem, André; Brandin, A V; Bravar, A; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca-Sanchez, M; Castillo, J; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, Y; Cheng, J; Cherney, M; Chikanian, A; Choi, H A; Christie, W; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Das, S; Daugherity, M; Davenport, M; De Cataldo, G; De Moura, M M; De Phillips, M; Dedovich, T G; Derevshchikov, A A; Di Bari, D; Di Mauro, A; Didenko, L; Dietel, T; Djawotho, P; Dogra, S M; Dong, W J; Dong, X; Draper, J E; Du, F; Dunin, V B; Dunlop, J C; Dutta-Majumdar, M R; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Fatemi, R; Fedorisin, J; Filimonov, K; Filip, P; Finch, E; Fine, V; Fisyak, Yu; Fornazier, K S F; Fu, J; Gagliardi, C A; Gaillard, L; Gans, J; Ganti, M S; Ghazikhanian, V; Ghosh, P; González, J E; Gorbunov, Y G; Gos, H; Grebenyuk, O; Grosnick, D P; Guertin, S M; Guo, Y; Gupta, N; Gutíerrez, T D; Haag, B; Hallman, T J; Hamed, A; Harris, J W; He, W; Heinz, M; Henry, T W; Hepplemann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horner, M J; Huang, H Z; Huang, S L; Hughes, E W; Humanic, T J; Igo, G; Jacobs, P; Jacobs, W W; Jakl, P; Jia, F; Jiang, H; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kapitan, J; Kaplan, M; Keane, D; Kechechyan, A; Khodyrev, V Yu; Kim, B C; Kiryluk, J; Kisiel, A; Kislov, E M; Klein, S R; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kouchpil, V; Kowalik, K L; Kravtsov, P; Kravtsov, V I; Krämer, M; Krüger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kunde, G J; Kuznetsov, A A; La Pointe, S; Lamont, M A C; Landgraf, J M; Lange, S; Laue, F; Lauret, J; Le Vine, M J; Lebedev, A; Lednicky, R; Lee, C H; Lehocka, S; Li, C; Li, Q; Li, Y; Lin, G; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Liu, Z; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Love, W A; Lu, Y; Ludlam, T; Lynn, D; López-Noriega, M; Ma, G L; Ma, J G; Ma, Y G; Magestro, D; Mahajan, S; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Martinengo, P; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Melnik, Yu M; Meschanin, A; Miller, M L; Milos, M; Minaev, N G; Mioduszewski, S; Mironov, C; Mischke, A; Mishra, D K; Mitchell, J; Mohanty, B; Molnár, L; Moore, C F; Morozov, D A; Munhoz, M G; Nandi, B K; Nappi, E; Nayak, S K; Nayak, T K; Nelson, J M; Netrakanti, P K; Nikitin, V A; Nogach, L V; Nurushev, S B; Odyniec, Grazyna Janina; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Paic, G; Pal, S K; Panebratsev, Yu A; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevozchikov, V; Perkins, C; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Piuz, François; Planinic, M; Pluta, J; Poljak, N; Porile, N; Porter, J; Posa, E; Poskanzer, A M; Potekhin, M V; Potrebenikova, E V; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rakness, G; Raniwala, R; Raniwala, S; Ray, R L; Razin, S V; Reinnarth, J; Relyea, D; Retière, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevski, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M J; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Sarsour, M; Savin, I; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Schweda, K; Schyns, E; Seger, J; Selyuzhenkov, I; Sen-Gupta, A; Seyboth, P; Shabetai, A; Shahaliev, E; Shao, M; Sharma, M; Shen, W Q; Shimansky, S S; Sichtermann, E P; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sood, G; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M N; Stringfellow, B C; Suaide, A A P; Sugarbaker, E R; Sumbera, M; Sun, Z; Surrow, B; Swanger, M; Symons, T J M; Szanto de Toledo, A; Sørensen, P; Tai, A; Takahashi, J; Tang, A H; Tarnowsky, T J; Thein, D; Thomas, J H; Timmins, A R; Timoshenko, S; Tokarev, M; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Van Buren, G; Van Leeuwen, M; Van der Kolk, N; Van der Molen, A M; Varma, R; Vasilev, A N; Vasilevski, I M; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, J S; Wang, X L; Wang, Y; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Q H; Xu, Z; Yepes, P; Yoo, I K; Yurevich, V I; Zborovský, I; Zhan, W; Zhang, H; Zhang, W M



Heterogeneous Reactions of Epoxides in Acidic Media  

E-print Network

Epoxides have been recently identified as one of the intermediate species in the gas phase oxidation of alkenes. This study investigates the reaction of isoprene oxide and alpha-pinene oxide with sulfuric acid to identify the potential of epoxides...

Lal, Vinita



Developing species-specific primers to identify Bulinus truncatus and Bulinus beccari, the intermediate hosts of Schistosoma haematobium in Saudi Arabia.  


This work aimed to determine the inter- and intra-specific variations in populations of Bulinus truncatus and Bulinus beccari, the intermediate hosts of Schistosoma haematobium in Saudi Arabia, and to develop species-specific primers to identify these snails as a first step in the development of multiplex PCR for simultaneously identifying the snails and diagnosing its infections in a single step. Two populations of B. truncatus were collected from Asser and Bisha (A and B), and two B. beccari populations were collected from Mahial Asser and Merba (C and D). The snails' genomic DNA was extracted and amplified using 5 different primers. The primers displayed variable intra- and inter-specific differences across the populations. The largest RAPD-PCR fragments were cloned into a vector as a preparatory step for sequencing. Similarity searches for the sequenced cloned inserts revealed no similar sequences in the GenBank database or its associated databases. Specific primers used to target the B. truncatus and B. beccari genomes were designed using the Gene Runner program and based on the DNA sequences obtained from RAPD fragment sequence analyses. Using these primers for specific PCRs resulted in expected single-band PCR products of 536 bp for B. beccari and 478 bp for B. truncatus. These results will be helpful for simultaneously identifying B. truncatus and B. beccari snails and diagnosing S. haematobium infections within the snails using single step multiplex PCR. PMID:22441124

Mostafa, Osama M S; Bin Dajem, Saad M; Al-Qahtani, Ahmed; Ibrahim, Essam H; Al-Quraishy, Saleh A S




SciTech Connect

We present a catalog of 1439 young stellar objects (YSOs) spanning the 1.42 deg{sup 2} field surveyed by the Chandra Carina Complex Project (CCCP), which includes the major ionizing clusters and the most active sites of ongoing star formation within the Great Nebula in Carina. Candidate YSOs were identified via infrared (IR) excess emission from dusty circumstellar disks and envelopes, using data from the Spitzer Space Telescope (the Vela-Carina survey) and the Two-Micron All Sky Survey. We model the 1-24 {mu}m IR spectral energy distributions of the YSOs to constrain physical properties. Our Pan-Carina YSO Catalog (PCYC) is dominated by intermediate-mass (2 M{sub sun} < m {approx}< 10 M{sub sun}) objects with disks, including Herbig Ae/Be stars and their less evolved progenitors. The PCYC provides a valuable complementary data set to the CCCP X-ray source catalogs, identifying 1029 YSOs in Carina with no X-ray detection. We also catalog 410 YSOs with X-ray counterparts, including 62 candidate protostars. Candidate protostars with X-ray detections tend to be more evolved than those without. In most cases, X-ray emission apparently originating from intermediate-mass, disk-dominated YSOs is consistent with the presence of low-mass companions, but we also find that X-ray emission correlates with cooler stellar photospheres and higher disk masses. We suggest that intermediate-mass YSOs produce X-rays during their early pre-main-sequence evolution, perhaps driven by magnetic dynamo activity during the convective atmosphere phase, but this emission dies off as the stars approach the main sequence. Extrapolating over the stellar initial mass function scaled to the PCYC population, we predict a total population of >2 x 10{sup 4} YSOs and a present-day star formation rate (SFR) of >0.008 M{sub sun} yr{sup -1}. The global SFR in the Carina Nebula, averaged over the past {approx}5 Myr, has been approximately constant.

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



Composition of reaction intermediates for stoichiometric and fuel-rich dimethyl ether flames: flame-sampling mass spectrometry and modeling studies.  


Molecular-beam synchrotron photoionization mass spectrometry and electron-ionization mass spectrometry are used for measurements of species mole fraction profiles for low-pressure premixed dimethyl ether (DME) flames with equivalence ratios ranging from near-stoichiometric conditions (Phi = 0.93) to fuel-rich flames near the limits of flat-flame stability (Phi = 1.86). The results are compared with predictions of a recently modified kinetic model for DME combustion [Zhao et al., Int. J. Chem. Kinet., 2008, 40, 1-18] that has been extensively tested against laminar flame speed measurements, jet-stirred reactor experiments, pyrolysis and oxidation experiments in flow reactors, species measurements for burner-stabilized flames and ignition delay measurements in shock tubes. The present comprehensive measurements of the composition of reaction intermediates over a broad range of equivalence ratios considerably extends the range of the previous experiments used for validation of this model and allows for an accurate determination of contributions of individual reactions to the formation or destruction of any given flame species. The excellent agreement between measurements and predictions found for all major and most intermediate species over the entire range of equivalence ratios provides a uniquely sensitive test of details of the kinetic model. The dependence on equivalence ratio of the characteristic reaction paths in DME flames is examined within the framework of reaction path analyses. PMID:19224033

Wang, Juan; Chaos, Marcos; Yang, Bin; Cool, Terrill A; Dryer, Fred L; Kasper, Tina; Hansen, Nils; Osswald, Patrick; Kohse-Höinghaus, Katharina; Westmoreland, Phillip R



Food Allergy Disclaimer UMD Dining makes every attempt to identify ingredients that may cause reactions in people with food  

E-print Network

Food Allergy Disclaimer UMD Dining makes every attempt to identify ingredients that may cause reactions in people with food allergies. We make every effort to instruct our food production staff on the severity of food allergies. In addition we label items with possible allergencontaining ingredients

Hill, Wendell T.


Atmospheric Reaction Systems as Null-Models to Identify Structural Traces of Evolution in Metabolism  

PubMed Central

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection. PMID:21573072

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



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

PubMed Central

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

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



Calculated and measured battery voltages - thermodynamics aids in identifying electrochemical reactions. Final report, March-June 1984  

SciTech Connect

Both the open- and closed-circuit voltages of a battery depend on the thermodynamic conditions inside the cell. When the actual electrochemical reaction of a particular battery is unknown, thermodynamic calculations can help to identify it. Using thermodynamics data, the open-circuit voltages for alternatively electrochemical reactions can be calculated. When accurate data are available, the calculated voltage for the correct electrochemical reaction will agree to within millivolts with the measured value. For the Cl/sub 2/-Li molten salt system, the calculated and measured values are both 3.612V. For alkaline zinc batteries, the data indicate that Zn0 is the discharge product at the anode under ambient conditions. For the acid Mn02-Zn system, under the thermodynamic conditions, a two-electron reduction of MnO/sub 2/ occurs. Initially, in the alkaline MnO/sub 2/-Zn system. Mn(OH)/sub 4/ is the discharge product at the cathode.

DeVries, L.E.



Isolation, Characterization of an Intermediate in an Oxygen Atom-Transfer Reaction, and the Determination of the Bond Dissociation Energy  

SciTech Connect

Redox reactions coupled with the formal loss or gain of an oxygen atom are ubiquitous in chemical processes. Such reactions proceed through the reduction of the donor center (XO) and the oxidation of the acceptor (Y) molecule. Among many examples of the metal centered oxygen atom transfer (OAT) reactivity, those involving molybdenum complexes have been widely investigated due to their involvement in mononuclear molybdenum enzymes. The heat of reaction of the overall atom transfer process can be expressed as a difference between the bond dissociation energies (BDEs) of the oxygen-donor(X) and oxygen-acceptor(Y) bond, i.e., H=DX=o-DY=O.

Nemykin, Victor N.; Laskin, Julia; Basu, Partha



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

PubMed Central

Background Enzymes belonging to mechanistically diverse superfamilies often display similar catalytic mechanisms. We previously observed such an association in the case of the cyclic amidohydrolase superfamily whose members play a role in related steps of purine and pyrimidine metabolic pathways. To establish a possible link between enzyme homology and chemical similarity, we investigated further the neighbouring steps in the respective pathways. Results We identified that successive reactions of the purine and pyrimidine pathways display similar chemistry. These mechanistically-related reactions are often catalyzed by homologous enzymes. Detection of series of similar catalysis made by succeeding enzyme families suggested some modularity in the architecture of the central metabolism. Accordingly, we introduce the concept of a reaction module to define at least two successive steps catalyzed by homologous enzymes in pathways alignable by similar chemical reactions. Applying such a concept allowed us to propose new function for misannotated paralogues. In particular, we discovered a putative ureidoglycine carbamoyltransferase (UGTCase) activity. Finally, we present experimental data supporting the conclusion that this UGTCase is likely to be involved in a new route in purine catabolism. Conclusions Using the reaction module concept should be of great value. It will help us to trace how the primordial promiscuous enzymes were assembled progressively in functional modules, as the present pathways diverged from ancestral pathways to give birth to the present-day mechanistically diversified superfamilies. In addition, the concept allows the determination of the actual function of misannotated proteins. PMID:24093154



[Use of the polymerase chain reaction to identify Helicobacter pylori in clinical material].  


A new system for the detection of Helicobacter pylori DNA, based on the method of directed amplification, has been developed. Primers for specific detection of H. pylori were selected from a nucleotide sequence of 16 S-p RNA. The sequences of the primers had a few nucleotide substitutions as compared with the sequences of closely related microorganisms. An essential condition for the attainment of reaction specificity was the rise of annealing step temperature to 66 degrees C. Sensitivity of the system was in the range of 3 to 30 fg of DNA, or 20 to 100 bacterial cells. Using the proposed system for the detection of H. pylori DNA clinical specimens (stomach biopsy sample, gastric juice and wash-offs of oral cavity), obtained from 49 patients with antral gastritis, were analyzed. The method of H. pylori detection in clinical specimens using polymerase chain reaction (PCR) turned out to be more sensitive compared with microbiological tests. By application of PCR H. pylori DNA was detected in subgingival pockets. PMID:8133843

Markova, G A; Boshnakov, R Kh; Petrov, P K; Katsarov, K V; Gintsburg



Intermediate mass fragments and isospin dependence in 124 Sn , 124 Xe + 124 Sn , 112 Sn reactions at 28 MeV/nucleon  

NASA Astrophysics Data System (ADS)

Intermediate mass fragment ( Z>2 ) emission in 124 Sn , 124 Xe + 124 Sn , 112 Sn reactions at 28 MeV/nucleon were studied using neutron ion multidetector for reaction oriented dynamics, a 4? charged particle detection system. A number of observables, such as isotopic yield distributions, energy spectra of light charged particles and intermediate mass fragments, isotopic and isobaric yield ratios, and average neutron to proton ratios are investigated. These observables show significant dependence on the isospin N/Z of the reacting system. It is observed that the formation of neutron-rich clusters are correlated with the excess neutrons in the composite system and depends on the temperature of the emitting source. The origin of light particles and fragments was studied through observations of rapidity distribution as a function of collision violence. With increasing centrality, the heavier 6He isotope is found to be emitted closer to the midrapidity region than the lighter 3He isotope. The emission of heavy fragments from the midrapidity region becomes increasingly favorable for fragments with higher charge Z . The results suggest that the midrapidity region is not only neutron rich but also a rich source of heavy fragment (cluster) formation.

Shetty, D. V.; Keksis, A.; Martin, E.; Ruangma, A.; Souliotis, G. A.; Veselsky, M.; Winchester, E. M.; Yennello, S. J.; Hagel, K.; Ma, Y. G.; Makeev, A.; Marie, N.; Murray, M.; Natowitz, J. B.; Qin, L.; Smith, P.; Wada, R.; Wang, J.; Cinausero, M.; Fioretto, E.; Prete, G.; Fabris, D.; Lunardon, M.; Nebbia, G.; Rizzi, V.; Viesti, G.; Cibor, J.; Majka, Z.; Staszel, P.; Alfaro, R.; Martinez-Davalos, A.; Menchaca-Rocha, A.; El Masri, Y.; Keutgen, T.



Reaction dynamics of photosubstitution intermediates of the triruthenium cluster Ru sub 3 (CO) sub 12 as studied by flash photolysis with infrared detection  

SciTech Connect

The reaction dynamics of intermediates formed by 308-nm XeCl excimer-laser excitation of the triruthenium cluster Ru{sub 3}(CO){sub 12} in room-temperature isooctane solution were studied by using a flash-photolysis apparatus with a tunable infrared laser probe source and Hg/Cd/Te fast-risetime ir detector. The primary photoreaction is the dissociation of CO to give Ru{sub 3}(CO){sub 11}, which is rapidly trapped in second-order reactions by CO or by an added nucleophile such as tetrahydrofuran. The rate constants for such trapping are shown t be 2.4 {times} 10{sup 9} and 6.1 {times} 10{sup 9} M{sup {minus}1} s{sup {minus}1} for CO and THF, respectively. The intermediate Ru{sub 3}(CO){sub 11}(THF) reacts with CO to re-form Ru{sub 3}(CO){sub 12} via an apparent first-order dissociation of the THF with a rate constant about 2 {times} 10{sup 6} s{sup {minus}1}. The flash-photolysis apparatus with the ir detection system is described in detail. 17 refs., 6 figs.

DiBenedetto, J.A.; Ryba, D.W.; Ford, P.C. (Univ. of California, Santa Barbara (USA))



Microscopic differential cell counting to identify inflammatory reactions in dairy cow quarter milk samples.  


The diagnosis of intramammary infections is mostly based on somatic cell count (SCC) and bacteriological analysis. As an alternative, differential cell counting (DCC) could be a useful method, because it identifies changes in the relative cell populations before the increase in total cell number occurs. The aim of the study was to identify cytological parameters that could be used in the field to classify mammary quarters as healthy or diseased, comparing cyto-bacteriological results with DCC. Overall, 48 cows were randomly selected from 3 herds in Lombardy region of Italy. Herd A was characterized by the absence of contagious microorganisms; in herds B and C, the prevalence of Staphylococcus aureus was 20 and 50%, respectively. Foremilk samples were aseptically collected from 188 quarters and submitted to bacteriological analysis, SCC, and DCC. For statistical analysis, the samples were clustered into 4 health groups, and DCC results were compared in each group. Ninety-six samples were classified as normal secretions (N), 30 as mastitis (M), 15 as latent mastitis (LM), and 47 as unspecific mastitis (UM) based on SCC and bacteriological results. Single percentages of lymphocytes, polymorphonuclear neutrophilic leukocytes (PMNL), or macrophages were first evaluated to established variables capable of identifying healthy and inflamed quarters. Then, combinations of cell populations were tested to increase the discrimination power of DCC: phagocytes, logarithmic PMNL:lymphocyte ratio, and logarithmic phagocyte:lymphocyte ratio. The mean percentage of lymphocytes was significantly higher in group N than in groups LM, UM, and M. The mean percentage of PMNL was significantly lower in group N than in groups UM and M, but not LM. Mean percentages of macrophages were not significantly influenced by the 4 groups. The mean value of phagocytes was significantly lower in group N than in the other groups. Both the logarithmic PMNL:lymphocyte and the logarithmic phagocyte:lymphocyte ratios were significantly lower in group N than in groups LM, UM, and M. Fisher (F-)values were calculated, and the highest F-value was that of log PMNL:lymphocytes ratio (48.23). The explanation for this could be that log PMNL:Lym is the only variable that involved both cell populations statistically influenced by health groups but excluded macrophages. Microscopic DCC has potential as a tool to identify cows affected by any inflammatory process of the mammary gland, with the best results being achieved using log PMNL:lymphocyte as variable. PMID:22818454

Pilla, R; Schwarz, D; König, S; Piccinini, R



Reaction times identify a Pavlovian component in a two-choice discrimination.  


Six pigeons discriminated on discrete trials between two colors. In Experiment 1, two luminous spots were both either blue or green and the reinforced responses were "peck left" for blue and "peck right" for green. In Experiment 2, the hue of a center spot controlled subsequent choice pecks to left or right. In both experiments response bias was manipulated in two ways. During stimulus frequency ("SF") sessions correct responses brought food on 40% of trials; in "imbalanced" blocks of sessions one hue appeared on 80% of trials and the other on 20%. During reinforcement probability ("RNF") sessions the hues appeared equally often, but in imbalanced blocks the hues signaled different reinforcement probabilities, either 64% or 16%. In "balanced" control blocks the hues appeared equally often and were both reinforced at 40%. The experiments gave similar results. When bias was computed from choice percentages the imbalanced conditions yielded substantial response bias, and the amount of bias was about the same under RNF and SF treatments. However, reaction times (RTs) gave a different outcome. RNF imbalance slowed responses directed at the less reinforced stimulus, but SF imbalance had little RT effect (Experiment 1) or no effect (Experiment 2). These results suggest that choice was controlled by an instrumental stimulus-response-reinforcement association, whereas RTs were controlled by a Pavlovian stimulus-reinforcement association. PMID:19429212

Blough, Donald S



Volatile Reaction Products From Silicon-Based Ceramics in Combustion Environments Identified  

NASA Technical Reports Server (NTRS)

Silicon-based ceramics and composites are prime candidates for use as components in the hot sections of advanced aircraft engines. These materials must have long-term durability in the combustion environment. Because water vapor is always present as a major product of combustion in the engine environment, its effect on the durability of silicon-based ceramics must be understood. In combustion environments, silicon-based ceramics react with water vapor to form a surface silica (SiO2) scale. This SiO2 scale, in turn, has been found to react with water vapor to form volatile hydroxides. Studies to date have focused on how water vapor reacts with high-purity silicon carbide (SiC) and SiO2 in model combustion environments. Because the combustion environment in advanced aircraft engines is expected to contain about 10-percent water vapor at 10-atm total pressure, the durability of SiC and SiO2 in gas mixtures containing 0.1- to 1-atm water vapor is of interest. The reactions of SiC and SiO2 with water vapor were monitored by measuring weight changes of sample coupons in a 0.5-atm water vapor/0.5-atm oxygen gas mixture with thermogravimetric analysis.

Opila, Elizabeth J.



Intermediates in Reactions of Copper(I) Complexes with N-Oxides: From Formation of Stable Adducts to Oxo Transfer  

PubMed Central

Reactions of Cu(I) complexes of bidentate N-donor supporting ligands with pyridine- and trimethylamine-N-oxides or PhIO were explored. Key results include the identification of novel Cu(I)-N-oxide adducts, aryl substituent hydroxylation, and bis(?-oxo)dicopper complex formation via a route involving oxo transfer. PMID:19425587

Hong, Sungjun; Gupta, Aalo K.; Tolman, William B.



Direct Detection and Kinetic Analysis of Covalent Intermediate Formation in the 4-Amino-4-deoxychorismate Synthase Catalyzed Reaction  

E-print Network

ReceiVed February 13, 2006 ABSTRACT: Chorismate-utilizing enzymes catalyze diverse reactions, providing activity. Acetate is a poor chemical rescue agent for E258D but an excellent one for E258A, with a 20000-fold and 3000-fold rate increase for Gln-dependent and NH4 +-dependent activities, respectively. Lastly

Toney, Michael


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


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

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



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


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

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



Acceleration of secondary dark reactions of intermediates derived from adsorbed dyes on irradiated TiO 2 powders  

Microsoft Academic Search

Time-resolved diffuse reflectance flash photolysis has been used to characterize the kinetic behaviors of transients derived from several dyes (cosin Y, thionine, oxazine 725, and nile blue A) adsorbed on titanium dioxide powder (Degussa P-25) suspended in aqueous solutions of various pH. Secondary reaction rates on these powders were compared with those observed on analogous colloidal TiO2 suspensions. Faster secondary

M. A. Fox; M. T. Dulay



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

Microsoft Academic Search

The inclusive cross sections for 38 different reaction products produced in the interaction of Ca48, S40, and S42 beams around 100 MeV\\/nucleon with a liquid deuterium target are reported. The cross sections for the Ca48 +H2 products are compared to those with Ca48 incident on the commonly used fragmentation targets Be9 and Ta181 and also to global calculations for fragmentation

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



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

Microsoft Academic Search

The inclusive cross sections for 38 different reaction products produced in the interaction of ⁴⁸Ca, ⁴°S, and ⁴²S beams around 100 MeV\\/nucleon with a liquid deuterium target are reported. The cross sections for the ⁴⁸Ca +²H products are compared to those with ⁴⁸Ca incident on the commonly used fragmentation targets ⁹Be and ¹⁸¹Ta and also to global calculations for fragmentation

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



On the origin of cytotoxicity of the natural product varacin. A novel example of a pentathiepin reaction that provides evidence for a triatomic sulfur intermediate.  


A density functional theoretical study is presented, which implicates a novel S(3)-cleavage in the decomposition of a pentathiepin. This study predicts an interconversion between a pentathiepin and an open-chain polysulfur ion intermediate from which a key determinant in the chemistry then follows. Expulsion of diatomic sulfur, S(2), is unlikely from the unimolecular collapse of the open-chain polysulfur ion. Instead, S(3) can dissociate due to an unusually long and weak sulfur-sulfur (S4-S5) bond. A mechanistic picture now emerges which predicts that the novel S-S cleavage reaction and the unanticipated S(3) fragmentation are a result of delocalization of the negative charge within the remaining carbon-sulfur fragment. The computed results presented here reveal a new aspect to the chemistry of pentathiepins, that of S(3) unit transfer, which is proposed to have significance in the mechanism of cytotoxicity of the natural product varacin, 1. PMID:11603989

Greer, A



Characterization of nanoparticles of LiMn2O4 synthesized by a one-step intermediate-temperature solid-state reaction.  


Nanoparticles of lithium manganese oxide (LiMn2O4) with a spinel structure have been synthesized by a one-step intermediate temperature solid-state reaction. The influence of the molar ratio of citric acid to the metal ions on the physicochemical properties of LiMn2O4 powders in air has been analyzed by means of X-ray diffraction and electron microscope techniques. The electrochemical behavior of the material has been examined by charge/discharge tests and cyclic voltammetry. Test results reveal that LiMn2O4 particles with lower molar ratios of citric acid to metal ions (1:2) are highly crystalline and highly electrochemically reversible, with better cycle capabilities when compared with a sample with a higher molar ratio (2:1). The LiMn2O4 powders obtained by this method have a uniform morphology with a narrow size distribution. PMID:15112561

Guo, Z P; Ahn, J H; Liu, H K; Dou, S X



Direct Detection of the Oxygen Rebound Intermediates, Ferryl Mb and NO2, in the Reaction of metMyoglobin with Peroxynitrite  

PubMed Central

Oxygenated hemoproteins are known to react rapidly with nitric oxide (NO) to produce peroxynitrite (PN) at the heme site. This process could lead either to attenuation of the effects of NO or to nitrosative protein damage. Peroxynitrite is a powerful nitrating and oxidizing agent that has been implicated in a variety of cell injuries. Accordingly, it is important to delineate the nature and variety of reaction mechanisms of PN reactions with heme proteins. Here we present direct evidence that ferrylMb and NO2 are both produced during the reaction of PN and metmyolgobin (metMb). Kinetic evidence indicates that these products evolve from initial formation of a caged radical intermediate [FeIV=O ·NO2]. This caged pair reacts mainly via internal return with a rate constant kr to form metMb and nitrate in an oxygen rebound scenario. Detectable amounts of ferrylMb are observed by stopped-flow spectrophotometry, appearing at a rate consistent with the rate, kobs, of heme-mediated PN decomposition. Freely-diffusing NO2, which is liberated concomitantly from the radical pair (ke), preferentially nitrates Tyr103 in horse heart myoglobin. The ratio of the rates of in-cage rebound and cage escape, kr/ke, was found to be ?10 by examining the nitration yields of fluorescein, an external NO2 trap. This rebound/escape model for the metMb/PN interaction is analogous to the behavior of alkyl hyponitrites and the well-studied geminate recombination processes of deoxymyoglobin with O2, CO and NO. The scenario is also similar to the step-wise events of substrate hydroxylation by cytochrome P450 and other oxygenases. It is likely, therefore, that the reaction of metMb with ONOO- and that of oxyMb with NO proceed through the same [FeIV=O ·NO2] caged radical intermediate and lead to similar outcomes. The results indicate that while oxyMb may reduce the concentration of intracellular NO, it would not eliminate the formation of NO2 as a decomposition product of peroxynitrite. PMID:19705829

Su, Jia; Groves, John T.



Detection of intermediates in the oxidative half-reaction of the FAD-dependent thymidylate synthase from Thermotoga maritima: carbon transfer without covalent pyrimidine activation.  


Thymidylate, a vital DNA precursor, is synthesized by thymidylate synthases (TSs). A second class of TSs, encoded by the thyX gene, is found in bacteria and a few other microbes and is especially widespread in anaerobes. TS encoded by thyX requires a flavin adenine dinucleotide prosthetic group for activity. In the oxidative half-reaction, the reduced flavin is oxidized by 2'-deoxyuridine 5'-monophosphate (dUMP) and (6R)-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2THF), synthesizing 2'-deoxythymidine 5'-monophosphate (dTMP). dTMP synthesis is a complex process, requiring the enzyme to promote carbon transfer, probably by increasing the nucleophilicity of dUMP and the electrophilicity of CH2THF, and reduction of the transferred carbon. The mechanism of the oxidative half-reaction was investigated by transient kinetics. Two intermediates were detected, the first by a change in the flavin absorbance spectrum in stopped-flow experiments and the second by the transient disappearance of deoxynucleotide in acid quenching experiments. The effects of substrate analogues and the behavior of mutated enzymes on these reactions lead to the conclusion that activation of dUMP does not occur through a Michael-like addition, the mechanism for the activation analogous with that of the flavin-independent TS. Rather, we propose that the nucleophilicity of dUMP is enhanced by electrostatic polarization upon binding to the active site. This conclusion rationalizes many of our observations, for instance, the markedly slower reactions when two arginine residues that hydrogen bond with the uracil moiety of dUMP were mutated to alanine. The activation of dUMP by polarization is consistent with the majority of the published data on ThyX and provides a testable mechanistic hypothesis. PMID:25068636

Conrad, John A; Ortiz-Maldonado, Mariliz; Hoppe, Samuel W; Palfey, Bruce A



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

SciTech Connect

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

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



Carbamazepine-induced cutaneous reactions: A simple assay to identify patients carrying the HLA-A*31:01 allele.  


Abstract Aims. Treatment with the first-line antiepileptic drug, carbamazepine (CBZ), is associated with adverse cutaneous reactions in up to 10% of patients. One predisposition to these side-effects has been linked to the HLA-A*31:01 allele. HLA-typing is costly and time-consuming. A single nucleotide polymorphism (SNP, rs1061235A > T) has been suggested as a marker for the HLA-A*31:01 allele. We sought to develop and validate a simple, fast and inexpensive assay for rs1061235 to apply in the Norwegian population. Methods. We designed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay for the SNP and tested it on a set of 16 samples with known HLA-A alleles. Results. The assay identified all HLA-A*31:01 alleles present, but also marked for HLA-A*33:03. In a second set of 204 samples from Norwegian epilepsy patients with unknown HLA alleles, nine samples heterozygous for the rs1061235 were found. Subsequent HLA-typing showed that one sample was HLA-A*33:01, whereas the other eight were identified as HLA-A*31:01. The remaining 195 samples were correctly identified as neither carrying the rs1061235 SNP nor HLA-A*31:01. The sensitivity and specificity of the rs1061235 SNP test was 100% and 99.5%, respectively. Misinterpretation of the rare HLA-A*33 variants as HLA-A*31:01 has minor consequence, as it only would result in choosing an alternative drug to CBZ. Conclusion. We have designed and validated a simple, fast and inexpensive test for the rs1061235A> T SNP as a marker for HLA-A*31:01 in the Norwegian population for potential use in a personalized treatment approach to patients planned to receive CBZ. PMID:24882392

Thorstensen, Ketil; Kvitland, Mona; Shirzadi, Maryam; Helde, Grethe; Moen, Torolf; Brodtkorb, Eylert



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

PubMed Central

Transition-metal peroxos have been implicated as key intermediates in a variety of critical biological processes involving O2. Due to their highly reactive nature, very few metal-peroxos have been characterized. The dioxygen chemistry of manganese remains largely unexplored despite the proposed involvement of a binuclear Mn-peroxo, either as a precursor to O2, or derived from O2, in both photosynthetic H2O oxidation and DNA biosynthesis, arguably two of the most fundamental processes of life. Neither of these biological intermediates has been observed. Herein we describe the dioxygen chemistry of coordinatively unsaturated [MnII(SMe2N4(6-MeDPEN))] +(1), and the characterization of intermediates formed en route to a binuclear mono-oxo bridged Mn(III) product {[MnIII(SMe2N4(6-MeDPEN)]2-(?-O)}2+ (2), the oxo atom of which is derived from 18O2. At low-temperatures, a dioxygen intermediate, [Mn(SMe2N4(6-MeDPEN))(O2)]+ (4), is observed (by stopped-flow) to rapidly and irreversibly form in this reaction (k1(?10 °C)= 3780±180M?1s?1, ?H1‡ = 26.4±1.7 kJ mol?1, ?S1‡ = ? 75.6±6.8 J mol?1K?1), and then convert more slowly (k2(?10 °C)= 417±3.2 M?1s?1, ?H2‡ = 47.1±1.4 kJ mol?1, ?S2‡ = ? 15.0±5.7 J mol?1K?1) to a species 3 with isotopically sensitive stretches at ?o-o (?18O) = 819(47) cm?1, kO–O= 3.02 mdyn/Å, and ?Mn-O(?18O) = 611(25) cm?1 consistent with a peroxo. Intermediate 3 releases approximately 0.5 equiv of H2O2 per Mn ion upon protonation, and the rate of conversion of 4 to 3 is dependent on [Mn(II)] concentration, consistent with the formation of a binuclear Mn-peroxo. This was verified by X-ray crystallography, where the peroxo of {[MnIII(SMe2N4(6-Me-DPEN)]2(trans–?–1,2–O2)}2+ (3) is shown to be bridging between two Mn(III) ions in an end-on trans-?-1,2-fashion. This represents the first characterized example of a binuclear Mn(III)-peroxo, and a rare case in which more than one intermediate is observed en route to a binuclear ?–oxo bridged product derived from O2. Vibrational and metrical parameters for binuclear Mn-peroxo 3 are compared with those of related binuclear Fe- and Cu-peroxo compounds. PMID:23470101

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



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

NASA Astrophysics Data System (ADS)

For the double exponential fluorescence decays of the locally excited (LE) and intramolecular charge transfer (ICT) states of 4-(dimethylamino)benzonitrile (DMABN) in acetonitrile (MeCN) the same times ?1 and ?2 are observed. This means that the reversible LE?ICT reaction, starting from the initially excited LE state, can be adequately described by a two state mechanism. The most important factor responsible for the sometimes experimentally observed differences in the nanosecond decay time, with ?1(LE)intermediate in the ICT reaction of DMABN are discussed. From the appearance of an excited state absorption (ESA) band in the spectral region between 700 and 800 nm in MeCN for N,N-dimethylanilines with CN, Br, F, CF3, and C(=O)OC2H2 p-substituents, it is concluded that this ESA band cannot be attributed to a ??* state, as only the C-CtrpbndN group can undergo the required 120° bending.

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



endo/exo Stereoselectivity in Diels?Alder Reactions of ?,?-Dialkylated Conjugated Enals to Cyclic 1,3-Dienes: Intermediates in the Synthesis of (-)-?-Santalol and Its Analogs.  


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

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



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


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

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



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


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

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



Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap.  


A method is presented to quantify intermediate-abundance proteins in human serum using a single-quadrupole linear ion trap mass spectrometer-in contrast, for example, to a triple-quadrupole mass spectrometer. Stable-isotope-labeled (tryptic) peptides are spiked into digested protein samples as internal standards, aligned with the traditional isotope dilution approach. As a proof-of-concept experiment, four proteins of intermediate abundance were selected, coagulation factor V, adiponectin, C-reactive protein (CRP), and thyroxine binding globulin. Stable-isotope-labeled peptides were synthesized with one tryptic sequence from each of these proteins. The normal human serum concentration ranges of these proteins are from 1 to 30 microg/mL (or 20 to 650 pmol/mL). These labeled peptides and their endogenous counterparts were analyzed by LC-MS/MS using multiple reaction monitoring, a multiplexed form of the selected reaction monitoring technique. For these experiments, only one chromatographic dimension (on-line reversed-phase capillary column) was used. Improved limits of detection will result with multidimensional chromatographic methods utilizing more material per sample. Standard curves of the spiked calibrants were generated with concentrations ranging from 3 to 700 pmol/mL using both neat solutions and peptides spiked into the complex matrix of digested serum protein solution where ion suppression effects and interferences are common. Endogenous protein concentrations were determined by comparing MS/MS peak areas of the endogenous peptides to the isotopically labeled internal calibrants. The derived concentrations from a normal human serum pool (neglecting loss of material during sample processing) were 9.2, 110, 120, and 246 pmol/mL for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. These concentrations generally agree with the reported normal ranges for these proteins. As a measure of analytical reproducibility of this single-quadrupole assay, the coefficients of variance based on 12 repeated measurements for each of the endogenous tryptic peptides were 17.0, 25.4, 24.2, and 14.0% for coagulation factor V, adiponectin, CRP, and thyroxine binding globulin, respectively. PMID:16906721

Lin, Shanhua; Shaler, Thomas A; Becker, Christopher H



Imino-oxy acetic acid dealkylation as evidence for an inner-sphere alcohol intermediate in the reaction catalyzed by peptidylglycine alpha-hydroxylating monooxygenase.  


Peptidylglycine alpha-hydroxylating monooxygenase (PHM, EC catalyzes the stereospecific hydroxylation of a glycyl alpha-carbon in a reaction that requires O(2) and ascorbate. Subsequent dealkylation of the alpha-hydroxyglycine by another enzyme, peptidylamidoglycolate lyase (PAL. EC, yields a bioactive amide and glyoxylate. PHM is a noncoupled, type II dicopper monooxygenase which activates O(2) at only a single copper atom, Cu(M). In this study, the PHM mechanism was probed using a non-natural substrate, benzaldehyde imino-oxy acetic acid (BIAA). PHM catalyzes the O-oxidative dealkylation of BIAA to benzaldoxime and glyoxylate with no involvement of PAL. The minimal kinetic mechanism for BIAA was shown to be steady-state ordered using primary deuterium kinetic isotope effects. The (D)(V/K)(APPARENT, BIAA) decreased from 14.7 +/- 1.0 as [O(2)] --> 0 to 1.0 +/- 0.2 as [O(2)] --> infinity suggesting the dissociation rate constant from the PHM x BIAA complex decreases as [O(2)] increases; thereby, reducing the steady-state concentration of [PHM](free). BIAA was further used to differentiate between potential oxidative Cu/O species using a QM/MM reaction coordinate simulation to determine which species could yield product O-dealkylation that matched our experimental data. The results of this study provided compelling evidence for the presence of a covalently linked Cu(II)-alkoxide intermediate with a quartet spin state responsible BIAA oxidation. PMID:19569683

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



Organic Chemistry Jasperse Acid-Base Practice Problems A. Identify each chemical as either an "acid" or a "base" in the following reactions, and  

E-print Network

Organic Chemistry Jasperse Acid-Base Practice Problems A. Identify each chemical as either an "acid" or a "base" in the following reactions, and identify "conjugate" relationships. -You should have one acid the More Acidic for Each of the Following Pairs: Single Variable Problems 16. 17. 18. 19. 20. 21. O O O OH

Jasperse, Craig P.


A restriction fragment length polymorphism-based polymerase chain reaction as an alternative to serotyping for identifying Salmonella serotypes.  


The phase 1 (fliC) and phase 2 (fljB) Salmonella flagella genes were analyzed by restriction fragment length polymorphism (RFLP)-polymerase chain reaction (PCR) to aid in the identification of different Salmonella serotypes. Twenty-four phase 1 flagellin and eight phase 2 flagellin genes could be differentiated among each other with restriction endonucleases Sau3A and HhaI in RFLP-PCR analysis. These flagellin genes comprise the major antigenic formulas for 52 serotypes of Salmonella sp., which include the common serotypes found in poultry and other important food animal species. With the knowledge of the O antigen composition determined from conventional O serotyping, 90% of the Salmonella serotypes could be identified by this double restriction enzyme RFLP analysis of fliC and fljB genes. This RFLP-PCR flagellar typing scheme was successfully applied to the identification of serotype for 112 Salmonella isolates obtained from poultry environment. There was a significant correlation between RFLP-PCR and conventional serotyping (chi-square, P < 0.001). Overall, PCR-RFLP proved to be a fast, accurate, and economical alternative approach to serotyping Salmonella sp. PMID:12887198

Hong, Yang; Liu, Tongrui; Hofacre, Charles; Maier, Marie; White, David G; Ayers, Sherry; Wang, Lihua; Maurer, John J



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.  


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

Yazawa, Kenjiro; Furusawa, Hiroyuki; Okahata, Yoshio



Multicomponent Reactions of Phosphines, Diynedioates, and Aryl Aldehydes Generated Furans Appending Reactive Phosphorus Ylides through Cumulated Trienoates as Key Intermediates: A Phosphine ?-Addition-?-Evolvement of an Anion Pathway.  


Multicomponent reactions of phosphines, diynedioates, and aryl aldehydes have been demonstrated, providing trisubstituted furans appending reactive phosphorus ylides, through cumulated trienoates as key intermediates. The proposed trienoate intermediates, 1,5-dipolar species formed via nucleophilic ?-attack of phosphines toward diynedioates (?-addition-?-evolvement of an anion, abbreviated ?A?E), undergo addition to aryl aldehydes followed by 5-endo-dig cyclization, proton transfer, and resonance to give trisubstituted furans. Furthermore, the phosphorus ylides are oxidized to ?-keto ester furans and utilized as Wittig reagents. PMID:25338301

Deng, Jie-Cheng; Chuang, Shih-Ching



Crystal structure of activated tobacco rubisco complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate.  

PubMed Central

The crystal structure of activated tobacco rubisco, complexed with the reaction-intermediate analogue 2-carboxy-arabinitol 1,5-bisphosphate (CABP) has been determined by molecular replacement, using the structure of activated spinach rubisco (Knight, S., Andersson, I., & Brändén, C.-I., 1990, J. Mol. Biol. 215, 113-160) as a model. The R-factor after refinement is 21.0% for 57,855 reflections between 9.0 and 2.7 A resolution. The local fourfold axis of the rubisco hexadecamer coincides with a crystallographic twofold axis. The result is that the asymmetric unit of the crystals contains half of the L8S8 complex (molecular mass 280 kDa in the asymmetric unit). The activated form of tobacco rubisco is very similar to the activated form of spinach rubisco. The root mean square difference is 0.4 A for 587 equivalent C alpha atoms. Analysis of mutations between tobacco and spinach rubisco revealed that the vast majority of mutations concerned exposed residues. Only 7 buried residues were found to be mutated versus 54 residues at or near the surface of the protein. The crystal structure suggests that the Cys 247-Cys 247 and Cys 449-Cys 459 pairs are linked via disulfide bridges. This pattern of disulfide links differ from the pattern of disulfide links observed in crystals of unactivated tobacco rubisco (Curmi, P.M.G., et al., 1992, J. Biol. Chem. 267, 16980-16989) and is similar to the pattern observed for activated spinach tobacco. PMID:8358296

Schreuder, H. A.; Knight, S.; Curmi, P. M.; Andersson, I.; Cascio, D.; Sweet, R. M.; Branden, C. I.; Eisenberg, D.



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

PubMed Central

N-Hydroxy-N-isopropyloxamate (IpOHA) is known to inhibit extremely tightly (Ki of 22 pM) the bacterial acetohydroxy acid isomeroreductase (EC [Aulabaugh and Schloss (1990) Biochemistry 29, 2824-2830], the second enzyme of the branched-chain-amino-acid-biosynthetic pathway. Yet, although the same pathway exists in plant cells, this compound presents only very poor herbicidal action. Towards the goal of gaining a better understanding of this behaviour, we have studied the mechanism of interaction of this compound with a highly purified acetohydroxy acid isomeroreductase of plant origin, i.e. the spinach (Spinacia oleracea) chloroplast enzyme. IpOHA behaved as a nearly irreversible inhibitor of the enzyme. Encounter complex formation was very slow (association rate constant 1.9 x 10(3) M-1.s-1) and involved a single bimolecular step. Since inhibition was competitive with respect to acetohydroxy acid substrates, the time needed to achieve substantial (90%) inhibition in vitro of enzyme activity in the simultaneous presence of substrates and inhibitors was extremely long (for example of the order of hours at 1 microM IpOHA and 100 microM acetohydroxy acid substrates). Thus, under in vivo conditions, binding of the inhibitor may be so slow that it may delay considerably the time required for inhibition of the target enzyme. Simialr kinetic behaviour was observed with another reaction intermediate analogue described by Schulz, Spönemann, Köcher and Wengenmayer [(1988) FEBS Lett. 238, 375-378], 2-dimethyl-phosphinoyl-2-hydroxyacetic acid (Hoe 704), which displays a higher herbicide activity than IpOHA. The herbicidal potency of these two compounds appeared to be correlated with their rates of association with the plant acetohydroxy acid isomeroreductase, since the bimolecular rate constant for Hoe 704 (2.2 x 10(4) M-1.s-1) was higher than that for IpOHA. PMID:8053906

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



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

SciTech Connect

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

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



Diminished CAGE Effect in {p}-H2: IR Identification of Intermediates in Addition Reactions of CL Atom with Unsaturated Hydrocarbons  

NASA Astrophysics Data System (ADS)

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 ?-complex of ClC6H6 (chlorocyclohexadienyl radical), rather than the previously proposed ?-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.

Lee, Yuan-Pern; Bahou, Mohammed; Golec, Barbara



Formation of the TiSi2 C40 as an intermediate phase during the reaction of the Si\\/Ta\\/Ti system  

Microsoft Academic Search

The effect of a thin Ta layer at the Si\\/Ti interface on the intermediate phase formation has been studied in detail by in situ sheet resistance, x-ray diffraction, transmission electron microscopy and Rutherford backscattering spectroscopy of partially reacted samples. When a Ta layer is deposited at the Si\\/Ti interface, a new intermediate phase has been detected, i.e. the hexagonal TiSi2

F. La Via; F. Mammoliti; G. Corallo; M. G. Grimaldi; D. B. Migas; Leo Miglio



An efficient synthesis of anhydrides of 2-monosubstituted succinic acid monoesters and their application to the Dakin–West reaction: Isolation of some 5-succinyloxyoxazole intermediates  

Microsoft Academic Search

A rapid and versatile synthesis of 2-monosubstituted monosuccinates and their bimolecular anhydrides is described. The reaction of these anhydrides with N-Fmoc-protected dipeptides under the modified Dakin–West reaction affords mainly the corresponding 5-succinyloxyoxazoles.

Joseph Richard Casimir; Laurent Ettouati; Joëlle Paris



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

PubMed Central

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

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



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


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

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



An efficient synthesis of anhydrides of 2-monosubstituted succinic acid monoesters and their application to the Dakin-West reaction: Isolation of some 5-succinyloxyoxazole intermediates  

Microsoft Academic Search

Summary  A rapid and versatile synthesis of 2-monosubstituted monosuccinates and their bimolecular anhydrides is described. The reaction\\u000a of these anhydrides withN-Fmoc-protected dipeptides under the modified Dakin-West reaction affords mainly the corresponding 5-succinyloxyoxazoles.

Joseph Richard Casimir; Laurent Ettouati; Joëlle Paris



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

PubMed Central

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

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



Intermediate Accounting I Spring 2013  

E-print Network

Kimbro Intermediate Accounting I Spring 2013 1 ACCT 311 INTERMEDIATE ACCOUNTING I PIGT 305 - Spring framework underlying Financial Accounting and Financial Statements. To review the process of accumulating, identifying, measuring and recording financial information. To understand the accounting equation and its

Carter, John


Evaluation of the partitioning of bound inorganic phosphate during medium and intermediate phosphate in equilibrium water oxygen exchange reactions of yeast inorganic pyrophosphatase.  

PubMed Central

During the rapid exchange of oxygens of Pi with water catalyzed by yeast inorganic pyrophosphatase, Pi at the catalytic site may either dissociate or undergo reversible loss of an oxygen to water. The effective partitioning of bound Pi during exchange starting with medium Pi containing 18O in all four oxygens has been evaluated by mass spectral analysis of the change in the distribution of Pi species containing zero to four 18O oxygens per Pi. This analysis indicates that the rate of Pi release from the enzyme is only 1.4 times faster than the rate of reformation of the anhydrous intermediate. A similar partitioning of bound Pi is observed during PPi hydrolysis, indicating that hydrolysis and medium exchange have common intermediates. The approach should be applicable to study of related phosphate oxygen exchanges. PMID:356047

Hackney, D D; Boyer, P D



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.  


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

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



Intermediates in reactions of copper(I) complexes with N-oxides: from the formation of stable adducts to oxo transfer.  


Reactions of copper(I) complexes of bidentate N-donor supporting ligands with pyridine- and trimethylamine-N-oxides or PhIO were explored. Key results include the identification of novel copper(I) N-oxide adducts, aryl substituent hydroxylation, and bis(mu-oxo)dicopper complex formation via a route involving oxo transfer. PMID:19425587

Hong, Sungjun; Gupta, Aalo K; Tolman, William B



The Reaction with Oxygen of Cytochrome Oxidase (Cytochrome d) in Escherichia coli K12: Optical Studies of Intermediate Species and Cytochrome b Oxidation at Sub-zero Temperatures  

Microsoft Academic Search

Optical changes in d- and b-type cytochromes, following initiation of the reaction of cytochrome oxidase d with 02, have been studied in cells and derived membrane particles from oxygen- limited cultures of Escherichia coli K 12. At successively higher temperatures between - 132 and - 88 \\




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

PubMed Central

The inappropriate immune response to foods, such as peanut, wheat and milk may be the basis in the pathogenesis of enteropathies like coeliac and Crohn disease, which present small intestinal malabsorption. A number of recent studies have utilized d-xylose absorption as an investigative tool to study small intestinal function in a variety of clinical settings. Thus, the aim of this experimental study was to evaluate the intestinal absorption of d-xylose in an antigen-specific gut inflammatory reaction rat model. Animals of the experimental group were inoculated with peanut protein extract before their exposure to a challenge diet containing exclusively peanut seeds to induce the gut inflammatory reaction caused by peanut allergy. Our results show that systemic inoculation with peanut protein extract renders significantly higher antibody titres (5.085 ± 0.126 units) (P < 0.0001) than control rats (0.905 ± 0.053 units) and that the antibody titres correlate positively to an inflammatory alteration of the gut morphology (P < 0.0001). Animals pertaining to the experimental group showed an intestinal absorption of d-xylose lower than control rats (P < 0.0001). We also observed that d-xylose absorption correlates negatively with IgG titres and positively with morphometric parameters (Pearson correlation). In conclusion, the use of serum d-xylose test was useful to identify the presence of small intestinal malabsorption in our antigen specific gut inflammatory reaction rat model. PMID:19335552

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



Intermediate inputs and economic productivity.  


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

Baptist, Simon; Hepburn, Cameron



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


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

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



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

PubMed Central

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

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



The role of carbonate as a catalyst of Fenton-like reactions in AOP processes: CO3?(-) as the active intermediate.  


Kinetic and DFT results for the carbonate catalysed Co(H2O)6(2+) + H2O2 Fenton-like reaction suggest a mechanism involving the formation of a cyclic transient, cyclic-(CO4)Co(II)(OOH)(H2O)2(-) that decomposes into Co(II)(H2O)(OOH)(OH)2 + CO3?(-), i.e. no OH? radicals are involved. Plausible biological implications are pointed out. PMID:25223650

Burg, Ariela; Shamir, Dror; Shusterman, Inna; Kornweitz, Haya; Meyerstein, Dan



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

PubMed Central

Enantiomerically pure (S)-tributylstannyl[D1]methanol and (R)- and (S)-tributylstannyl[D1]methyl benzoates were Stille-coupled with bromobenzene and benzoyl chloride in 1,4-dioxane and toluene using [(Ph3P)4Pd] or [(Ph3P)2PdCl2] either alone or in combination with CuCN as cocatalyst at temperatures up to 80 °C. The products were found to be enantiomerically pure. (R)- and (S)-N-(tributylstannyl[D1]methyl)phthalimides gave enantiomerically pure products with benzoyl chloride, but with bromobenzene protected phenyl[D1]methylamines gave products of only 52–69?% ee depending on the solvent used. Tributyl(thio[D1]methyl)stannanes could not be Stille-coupled with benzoyl chloride or with bromobenzene. Similarly, dimethyl phenyl[D1]methylboronate underwent a Suzuki–Miyaura coupling with bromobenzene to give phenyl[D1]methylsilane with 99?% ee. All couplings followed a retentive course and, except in one case, the intermediate [XCHDPdLn] complexes were found to be microscopically configurationally stable. PMID:24115906

Malova Krizkova, Petra; Hammerschmidt, Friedrich



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

PubMed Central

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

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



Catalase vs peroxidase activity of a manganese(II) compound: identification of a Mn(III)-(mu-O)(2)-Mn(IV) reaction intermediate by electrospray ionization mass spectrometry and electron paramagnetic resonance spectroscopy.  


Herein, we report reactivity studies of the mononuclear water-soluble complex [Mn(II)(HPClNOL)(eta(1)-NO(3))(eta(2)-NO(3))] 1, where HPClNOL = 1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol, toward peroxides (H(2)O(2) and tert-butylhydroperoxide). Both the catalase (in aqueous solution) and peroxidase (in CH(3)CN) activities of 1 were evaluated using a range of techniques including electronic absorption spectroscopy, volumetry (kinetic studies), pH monitoring during H(2)O(2) disproportionation, electron paramagnetic resonance (EPR), electrospray ionization mass spectrometry in the positive ion mode [ESI(+)-MS], and gas chromatography (GC). Electrochemical studies showed that 1 can be oxidized to Mn(III) and Mn(IV). The catalase-like activity of 1 was evaluated with and without pH control. The results show that the pH decreases when the reaction is performed in unbuffered media. Furthermore, the activity of 1 is greater in buffered than in unbuffered media, demonstrating that pH influences the activity of 1 toward H(2)O(2). For the reaction of 1 with H(2)O(2), EPR and ESI(+)-MS have led to the identification of the intermediate [Mn(III)Mn(IV)(mu-O)(2)(PClNOL)(2)](+). The peroxidase activity of 1 was also evaluated by monitoring cyclohexane oxidation, using H(2)O(2) or tert-butylhydroperoxide as the terminal oxidants. Low yields (<7%) were obtained for H(2)O(2), probably because it competes with 1 for the catalase-like activity. In contrast, using tert-butylhydroperoxide, up to 29% of cyclohexane conversion was obtained. A mechanistic model for the catalase activity of 1 that incorporates the observed lag phase in O(2) production, the pH variation, and the formation of a Mn(III)-(mu-O)(2)-Mn(IV) intermediate is proposed. PMID:19425615

Lessa, Josane A; Horn, Adolfo; Bull, Erika S; Rocha, Michelle R; Benassi, Mario; Catharino, Rodrigo R; Eberlin, Marcos N; Casellato, Annelise; Noble, Christoper J; Hanson, Graeme R; Schenk, Gerhard; Silva, Giselle C; Antunes, O A C; Fernandes, Christiane



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

SciTech Connect

The heaviest isotopes of elements Z=117 to Z=105, {sup 294}117, {sup 293}117, {sup 290}115, {sup 289}115, {sup 286}113, {sup 285}113, {sup 282}Rg, {sup 281}Rg, {sup 278}Mt, {sup 274}Bh, and {sup 270}Db, were identified by means of the Dubna gas-filled recoil separator among the products of the {sup 249}Bk + {sup 48}Ca reaction. The details of the observed six decay chains, indicating the production and decay of isotopes {sup 293}117 and {sup 294}117, are presented and discussed. The decay energies and resulting half-lives of these new nuclei show a strong rise of stability with increasing neutron number, validating the concept of the island of enhanced stability for superheavy nuclei [Oganessian et al., Phys. Rev. Lett. 104, 142502 (2010)].

Oganessian, Yu. Ts.; Abdullin, F. Sh.; Dmitriev, S. N.; Itkis, M. G.; Lobanov, Yu. V.; Mezentsev, A. N.; Polyakov, A. N.; Sagaidak, R. N.; Shirokovsky, I. V.; Subbotin, V. G.; Sukhov, A. M.; Tsyganov, Yu. S.; Utyonkov, V. K.; Voinov, A. A.; Vostokin, G. K. [Joint Institute for Nuclear Research, RU-141980 Dubna (Russian Federation); Bailey, P. D.; Benker, D. E.; Ezold, J. G.; Porter, C. E.; Riley, F. D. [Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States)



Reactions of nitrogen oxides with the five-coordinate Fe(III)(porphyrin) nitrito intermediate Fe(Por)(ONO) in sublimed solids.  


Detailed experimental studies are described for reactions of several nitrogen oxides with iron porphyrin models for heme/NxOy systems. It is shown by FTIR and optical spectroscopy and by isotope labeling experiments that reaction of small increments of NO2 with sublimed thin layers of the iron(II) complex Fe(Por) (Por = meso-tetraphenylporphyrinato dianion, TPP, or meso-tetra-p-tolylporphyrinato dianion, TTP) leads to formation of the 5-coordinate nitrito complexes Fe(Por)(eta1-ONO) (1), which are fairly stable but very slowly decompose under vacuum giving mostly the corresponding nitrosyl complexes Fe(Por)(NO). Further reaction of 1 with new NO2 increments leads to formation of the nitrato complex Fe(Por)(eta2-O2NO) (2). The interaction of NO with 1 at low temperature involves ligand addition to give the nitrito-nitrosyl complexes Fe(Por)(eta1-ONO)(NO) (3); however, these isomerize to the nitro-nitrosyl analogs Fe(Por)(eta1-NO2)(NO) (4) upon warming. Experiments with labeled nitrogen oxides argue for an intramolecular isomerization ("flipping") mechanism rather than one involving dissociation and rebinding of NO2. The Fe(III) centers in the 6-coordinate species 3 and 4 are low spin in contrast to 1, which appears to be high-spin, although DFT computations of the porphinato models Fe(P)(nitrite) suggest that the doublet nitro species and the quartet and sextet nitrito complexes are all relatively close in energy. The nitro-nitrosyl complex 4 is stable under an NO atmosphere but decomposes under intense pumping to give a mixture of the ferrous nitrosyl complex Fe(Por)(NO) and the ferric nitrito complex Fe(Por)(eta1-ONO) indicating the competitive dissociation of NO and NO2. Hence, loss of NO from 4 is accompanied with nitro --> nitrito isomerization consistent with 1 being the more stable of the 5-coordinate NO2 complexes of iron porphyrins. PMID:17338521

Kurtikyan, Tigran S; Hovhannisyan, Astghik A; Hakobyan, Manya E; Patterson, James C; Iretskii, Alexei; Ford, Peter C




SciTech Connect

We present stellar evolutionary sequences of stars in the mass range 5-12 M{sub Sun }, having solar-like initial composition. The stellar models are obtained using updated input physics, including recent rates of thermonuclear reactions. We investigate the effects of a modification of the {sup 14}N(p, {gamma}){sup 15}O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the above mass range. We find that a reduced {sup 14}N(p, {gamma}){sup 15}O rate, as described in the text, has a striking impact on the physical conditions of burning and mixing during shell hydrogen burning when the blue loops are formed. In particular, we find that the efficiency of shell hydrogen burning is crucial for the formation of an extended blue loop. We show that a significantly reduced {sup 14}N(p, {gamma}){sup 15}O rate affects severely the extension of the blue loops and the time spent by the star in the blue part of the Hertzsprung-Russell diagram in the mass range 5-7 M{sub Sun} if the treatment of convection is based on the Schwarzschild criterion only. In this case, envelope overshooting helps to restore well-extended blue loops as supported by the observations of the Cepheid stars. If core overshooting is included during the core hydrogen and core helium burning phases, the loop formation and its properties depend on how this overshooting is treated for a given stellar mass range, as well as on its efficiency.

Halabi, Ghina M.; El Eid, Mounib F. [Department of Physics, American University of Beirut, Beirut (Lebanon); Champagne, Arthur [Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC (United States)



Time-resolved observations of water oxidation intermediates on a cobalt oxide nanoparticle catalyst.  


In any artificial photosynthetic system, the oxidation of water to molecular oxygen provides the electrons needed for the reduction of protons or carbon dioxide to a fuel. Understanding how this four-electron reaction works in detail is important for the development of improved robust catalysts made of Earth-abundant materials, like first-row transition-metal oxides. Here, using time-resolved Fourier-transform infrared spectroscopy and under reaction conditions, we identify intermediates of water oxidation catalysed by an abundant metal-oxide catalyst, cobalt oxide (Co3O4). One intermediate is a surface superoxide (three-electron oxidation intermediate absorbing at 1,013 cm(-1)), whereas a second observed intermediate is attributed to an oxo Co(IV) site (one-electron oxidation intermediate absorbing at 840 cm(-1)). The temporal behaviour of the intermediates reveals that they belong to different catalytic sites. Knowledge of the structure and kinetics of surface intermediates will enable the design of improved metal-oxide materials for more efficient water oxidation catalysis. PMID:24651205

Zhang, Miao; de Respinis, Moreno; Frei, Heinz



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


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

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



Partial methylation of two adjacent adenosines in ribosomes from Euglena gracilis chloroplasts suggests evolutionary loss of an intermediate stage in the methyl-transfer reaction.  


Bacterial, cytoplasmic and organellar ribosomes from a wide phylogenetic spectrum of organisms have a characteristic m6(2)Am6(2)A structure near the 3' end of the RNA of the small ribosomal subunit (SSU). We have studied one of the few exceptions to this extremely conserved post-transcriptionally modified sequence, i.e. dimethylation of only one of the two A's in chloroplasts from Euglena gracilis. It was established that only the A closest to the 5' end is dimethylated, the other one being unmodified. The methylation reaction was studied in vitro using ribosomes from a kasugamycin resistant mutant (ksgA) of Escherichia coli and purified methyl-transferase. Using limited amounts of the methyl donor S-adenosylmethionine (SAM) a partial level of methylation (50% of control) was attained. It is shown that in this case the 3' proximal A is dimethylated while the other is not. This suggests that dimethylation takes place in two successive stages. Apparently in E. gracilis chloroplasts the first stage of methylation does not occur. PMID:6440121

Van Buul, C P; Hamersma, M; Visser, W; Van Knippenberg, P H



On the mechanism of cyclization of 5-hexenylchromate intermediates in the reactions of Fischer carbene complexes with a lithium enolate and allylmagnesium bromide.  


The mechanisms for the evolution of pentacarbonyl-5-hexenylchromate complexes, unsubstituted and methyl substituted at C2, formed from a pentacarbonyl(alkoxy)carbene complex of chromium, the corresponding ketone lithium enolate, and allylmagnesium bromide, were theoretically investigated by using DFT (Density Functional Theory) at the B3PW91/6-31G* level (LANL2DZ for Cr and Br) taking into account the effect of THF solvent through the PCM model (Polarizable Continuum Model). Methyl substitution at C2 provokes a shortening of about 5 degrees in the C1-C2-C3 angle that favors the formation of the pentacyclic product. Also, the presence of this methyl substituent at C2 sterically disfavors the formation of the hexacyclic product. Thus, our results yield the hexacyclic system as the most favored product for the evolution of the unsubstituted alkylpentacarbonylchromate complex, and the pentacyclic product in the case of the substituted system, in good agreement with the experimental findings. The stereochemistry of the products experimentally observed is determined at the transition state for the migration of the Cr(CO)(5) fragment from C1 to C6 and the conformational rearrangement of the C1-C6 skeleton. Amine molecules, present in the reaction medium, can play a catalytic role by assisting the 1,2-H migration in the last step for the formation of hexacyclic products. PMID:19689118

Campomanes, Pablo; Flórez, Josefa; Pérez-Sánchez, Iván; Suero, Marcos G; Sordo, Tomás L; Menéndez, M Isabel



Carbenium ion intermediates in catalytic cracking  

E-print Network

at room temperature. Oligomerization results in longer hydrocarbon chains. However, these results are inconclusive as evidence for the formation of carbocations which are proposed intermediates in the polymerization reaction. Recently, there have been... at room temperature. Oligomerization results in longer hydrocarbon chains. However, these results are inconclusive as evidence for the formation of carbocations which are proposed intermediates in the polymerization reaction. Recently, there have been...

Zardkoohi, Minoo



Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K.  


The decay kinetics of the aminoethanol-generated Co(II)-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10(5) s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 < or = T < or = 207 K: the decay is biexponential with constant fast (0.57 +/- 0.04) and slow (0.43 +/- 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T > or = 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k(obs,m)) and the fast phase of the biexponential decay (k(obs,f)) adhere to the same linear relation on an lnk versus T(-1) (Arrhenius) plot. Thus, k(obs,m) and k(obs,f) correspond to the same apparent Arrhenius prefactor and activation energy (logA(app,f) (s(-1)) = 13.0, E(a,app,f) = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k(obs,m) and k(obs,f) represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k(obs,s)) for 190 < or = T < or = 207 K obeys a different linear Arrhenius relation (logA(app,s) (s(-1)) = 13.9, E(a,app,s) = 16.6 kcal/mol). In the transition temperature range, k(obs,s) displays a super-Arrhenius increase with increasing temperature. The change in E(a,app,s) with temperature and the narrow range over which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the Co(II)-substrate radical pair lies below 190 K. PMID:18805934

Zhu, Chen; Warncke, Kurt



The aromatic ene reaction  

NASA Astrophysics Data System (ADS)

The ene reaction is a pericyclic process in which an alkene with an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed ?-bond. The aromatic ene reaction, in which the alkene component is embedded in an aromatic ring, has only been reported in a few (four) instances and has proceeded in low yield (?6%). Here, we show efficient aromatic ene reactions in which a thermally generated aryne intermediate engages a pendant m-alkylarene substituent to produce a dearomatized isotoluene, itself another versatile but rare reactive intermediate. Our experiments were guided by computational studies that revealed structural features conducive to the aromatic ene process. We proceeded to identify a cascade comprising three reactions: (1) hexadehydro-Diels-Alder (for aryne generation), (2) intramolecular aromatic ene and (3) bimolecular Alder ene. The power of this cascade is evident from the structural complexity of the final products, the considerable scope, and the overall efficiency of these multistage, reagent- and by-product-free, single-pot transformations.

Niu, Dawen; Hoye, Thomas R.



The aromatic ene reaction.  


The ene reaction is a pericyclic process in which an alkene with an allylic hydrogen atom (the ene donor) reacts with a second unsaturated species (the enophile) to form a new product with a transposed ?-bond. The aromatic ene reaction, in which the alkene component is embedded in an aromatic ring, has only been reported in a few (four) instances and has proceeded in low yield (?6%). Here, we show efficient aromatic ene reactions in which a thermally generated aryne intermediate engages a pendant m-alkylarene substituent to produce a dearomatized isotoluene, itself another versatile but rare reactive intermediate. Our experiments were guided by computational studies that revealed structural features conducive to the aromatic ene process. We proceeded to identify a cascade comprising three reactions: (1) hexadehydro-Diels-Alder (for aryne generation), (2) intramolecular aromatic ene and (3) bimolecular Alder ene. The power of this cascade is evident from the structural complexity of the final products, the considerable scope, and the overall efficiency of these multistage, reagent- and by-product-free, single-pot transformations. PMID:24345944

Niu, Dawen; Hoye, Thomas R



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

PubMed Central

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

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



Use of automated sequencing of polymerase chain reaction-generated amplicons to identify three types of cholera toxin subunit B in Vibrio cholerae O1 strains.  

PubMed Central

Cholera toxin is the principal factor causing the profuse intestinal fluid secretion that is characteristic of cholera. The DNA sequences of the cholera toxin subunit B structural genes from 45 Vibrio cholerae O1 strains isolated in 29 countries over a period of 70 years were determined by automated DNA sequencing of polymerase chain reaction-generated amplicons. Three types of cholera toxin B subunit gene (ctxB) were identified. Genotype 1 was found in strains of classical biotype worldwide and El Tor biotype strains associated with the U.S. Gulf Coast, genotype 2 was found in El Tor biotype strains from Australia, and genotype 3 was found in El Tor biotype strains from the seventh pandemic and the recent Latin American epidemic. All base changes correspond to an amino acid substitution in the B subunit of the cholera toxin. Heterogenicity in the B subunit could have implications for vaccine development and diagnostic tests for cholera toxin and antitoxin. We conclude that this technology provides timely and potentially useful epidemiological information. PMID:7678018

Olsvik, O; Wahlberg, J; Petterson, B; Uhlen, M; Popovic, T; Wachsmuth, I K; Fields, P I



Detection of unusual reaction intermediates during the conversion of W(N2)2(dppe)2 to W(H)4(dppe)2 and of H2O into H2.  


W(N(2))(2)(dppe-?(2)P)(2) reacts with H(2) to form WH(3){Ph(C(6)H(4))PCH(2)CH(2)PPh(2)-?(2)P}(dppe-?(2)P) and then W(H)(4)(dppe-?(2)P)(2). When para-hydrogen is used in this study, polarized hydride signals are seen for these two species. The reaction is complicated by the fact that trace amounts of water lead to the formation of H(2), PPh(2)CH(2)CH(2)Ph(2)P(O) and W(H)(3)(OH)(dppe-?(2)P)(2), the latter of which reacts further via H(2)O elimination to form W(H)(4)(dppe-?(2)P)(2) and [WH(3){Ph(C(6)H(4))PCH(2)CH(2)PPh(2)-?(2)P}(dppe-?(2)P)]. These studies demonstrate a role for the 14-electron intermediate W(dppe-?(2)P)(2) in the CH activation reaction pathway leading to [WH(3){Ph(C(6)H(4))PCH(2)CH(2)PPh(2)-k(2)P}(dppe-k(2)P)]. UV irradiation of W(H)(4)(dppe-?(2)P)(2) under H(2) led to phosphine dechelation and the formation of W(H)(6)(dppe-k(2)P)(dppe-k(1)P) rather than H(2) loss and W(H)(2)(dppe-?(2)P)(2) as expected. Parallel DFT studies using the simplified model system W(N(2))(2)((Ph)HPCH(2)CH(2)PH(2)-?(2)P)(H(2)PCH(2)CH(2)PH(2)-?(2)P) confirm that ortho-metalation is viable via both W(dppe-?(2)P)(2) and W(H)(2)(dppe-?(2)P)(2) with explicit THF solvation being necessary to produce the electronic singlet-based reaction pathway that matches with the observation of para-hydrogen induced polarization in the hydride signals of [WH(3){Ph(C(6)H(4))PCH(2)CH(2)PPh(2)-?(2)P}(dppe-?(2)P)], W(H)(3)(OH)(dppe-?(2)P)(2) and W(H)(4)(dppe-?(2)P)(2) during this study. These studies therefore reveal the existence of differentiated and previously unsuspected thermal and photochemical reaction pathways in the chemistry of both W(N(2))(2)(dppe-?(2)P)(2) and W(H)(4)(dppe-?(2)P)(2) which have implications for their reported role in N(2) fixation. PMID:23072491

Eguillor, Beatriz; Caldwell, Patrick J; Cockett, Martin C R; Duckett, Simon B; John, Richard O; Lynam, Jason M; Sleigh, Christopher J; Wilson, Ian



Communications: Elementary oxygen electrode reactions in the aprotic Li-air battery  

Microsoft Academic Search

We discuss the electrochemical reactions at the oxygen electrode of an aprotic Li-air battery. Using density functional theory to estimate the free energy of intermediates during the discharge and charge of the battery, we introduce a reaction free energy diagram and identify possible origins of the overpotential for both processes. We also address the question of electron conductivity through the

J. S. Hummelshøj; J. Blomqvist; S. Datta; T. Vegge; J. Rossmeisl; K. S. Thygesen; A. C. Luntz; K. W. Jacobsen; J. K. Nørskov



Water-Shale interactions in bench-top and high pressure/high temperature autoclave experiments: Identifying geochemical reaction controlling flow back water chemistry  

NASA Astrophysics Data System (ADS)

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

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



Surprisingly high activity for oxygen reduction reaction of selected oxides lacking long oxygen-ion diffusion paths at intermediate temperatures: a case study of cobalt-free BaFeO(3-?).  


The widespread application of solid oxide fuel cell technology requires the development of innovative electrodes with high activity for oxygen reduction reaction (ORR) at intermediate temperatures. Here, we demonstrate that a cobalt-free parent oxide BaFeO(3-?) (BF), which lacks long-range oxygen-ion diffusion paths, has surprisingly high electrocatalytic activity for ORR. Both in situ high-temperature X-ray diffraction analysis on room-temperature powder and transmission electron microscopy on quenched powder are applied to investigate the crystal structure of BF. Despite the lack of long oxygen-ion diffusion paths, the easy redox of iron cations as demonstrated by thermal gravimetric analysis (TGA) and oxygen temperature-programmed desorption and the high oxygen vacancy concentration as supported by iodometric titration and TGA benefit the reduction of oxygen to oxygen ions. Moreover, the electrical conductivity relaxation technique in conjunction with a transient thermogravimetric study reveals very high surface exchange kinetics of BF oxide. At 700 °C, the area specific resistance of BF cathode, as expressed by a symmetrical cell configuration, is only ?0.021 ? cm(2), and the derived single fuel cell achieves high power output with a peak power density of 870 mW cm(-2). It suggests that an undoped BF parent oxide can be used as a high-efficiency catalyst for ORR. PMID:24978102

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



Autocatalytic Networks with Intermediates I: Irreversible Reactions  

E-print Network

Happel a Peter Schuster a;b;c and Peter F. Stadler a;b;\\Lambda a Theoretische Biochemie, Institut f \\Lambda Mailing Address: Peter F Stadler, Inst. f. Theoretische Chemie, Univ. Wien W¨ahringerstr. 17, A RNA and evolution in vitro initiated a great number of investigations dealing with the design of self

Stadler, Peter F.


Some Intermediate-Level Violin Concertos.  

ERIC Educational Resources Information Center

Contends that many violin students attempt difficult concertos before they are technically or musically prepared. Identifies a variety of concertos at the intermediate and advanced intermediate-level for students to study and master before attempting the advanced works by Bach and Mozart. Includes concertos by Vivaldi, Leclair, Viotti, Haydn,…

Abramson, Michael



Identification of combustion intermediates in a low-pressure premixed laminar 2,5-dimethylfuran/oxygen/argon flame with tunable synchrotron photoionization  

SciTech Connect

Low-pressure (4.0 kPa) premixed laminar 2,5-dimethylfuran (DMF)/oxygen/argon flame with an equivalence ratio of 2.0 was studied with tunable vacuum ultraviolet (VUV) synchrotron radiation photoionization and molecular-beam mass spectrometry. Photoionization mass spectra of DMF/O{sub 2}/Ar flame were recorded and the photoionization efficiency curves of the combustion intermediates were measured. Flame species, including isomeric intermediates, are identified by comparing the measured ionization energies with those reported in literatures or those calculated with Gaussian-3 procedure. More than 70 species have been detected, including furan and its derivatives, aromatics, and free radicals. Possible reaction pathways of DMF, 2-methylfuran, and furan are proposed based on the intermediates identified. DMF can be consumed by H-abstraction and pyrolysis reactions. 2-Methylfuran and furan can be consumed by H-abstraction, H-addition and pyrolysis reactions. (author)

Wu, Xuesong; Huang, Zuohua; Wei, Lixia [State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); Yuan, Tao; Zhang, Kuiwen [National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029 (China)



On MHD intermediate shocks  

Microsoft Academic Search

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

C. C. Wu



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

SciTech Connect

Understanding the mechanisms of catalytic processes requires the identification of reaction centers and key intermediates, both of which are often achieved by the use of spectroscopic characterization tools. Due to the heterogeneity of active centers in heterogeneous catalysts, it is frequently difficult to identify the specific sites that are responsible for the overall activity. Furthermore, the simultaneous presence of a large number of surface species on the catalyst surface often poses a great challenge for the unambiguous determination of the relevant species in the reaction mechanism. In contrast, enzymes possess catalytically active centers with precisely defined coordination environments that are only able to accommodate intermediates relevant to the specific catalytic process. Here we show that side-on Cu+-NO+ complexes characterized by high magnetic field solid state magic angle spinning nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopies are the key intermediates in the selective catalytic reduction of NO over Cu-SSZ-13 zeolite catalysts. Analogous intermediates have been observed and characterized in nitrite reductase enzymes, and shown to be the critical intermediates in the formation of N2 for anaerobic ammonium oxidation reactions.[1] The identification of this key reaction intermediate, combined with the results of our prior kinetic studies, allows us to propose a new reaction mechanism for the selective catalytic reduction of NO with NH3 under oxygen-rich environments over Cu-SSZ-13 zeolites, a key reaction in automotive emission control. The authors acknowledge the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy/Vehicle Technologies Program for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle Memorial Institute.

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



Interception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds.  


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

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



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

Microsoft Academic Search

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

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



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

Microsoft Academic Search

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

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



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


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

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



Allergic Reactions  


... For instance, if you have an allergy to pollen, your immune system identifies pollen as an invader or allergen . Your immune system ... it can affect a child's speech and language development. Diagnosing and Treating Allergic Reactions An allergist / immunologist, ...


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


The soot combustion mechanism over potassium-supported oxides (MgO, CeO2 and ZrO2) was studied to clarify the active sites and discover unified reaction intermediates in this typical gas-solid-solid catalytic reaction. The catalytically active sites were identified as free K(+) rather than K2CO3, which can activate gaseous oxygen. The active oxygen spills over to soot and forms a common intermediate, ketene, before it was further oxidized into the end product CO2. The existence of ketene species was confirmed by density functional theory (DFT) calculations. The oxygen spillover mechanism is proposed, which is explained as an electron transfer from soot to gaseous oxygen through the active K(+) sites. The latter mechanism is confirmed for the first time since it was put forward in 1950, not only by ultraviolet photoelectron spectroscopy (UPS) results but also by semi-empirical theoretical calculations. PMID:24740213

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



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


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

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



Intermediates in the Formation of Aromatics in Hydrocarbon Combustion  

NASA Technical Reports Server (NTRS)

The formation of the first benzene ring is believed to be the rate limiting step in soot formation. Two different mechanisms have been proposed for formation of cyclic C6 species. The first involves the reaction of two acetylenes to give CH2CHCCH (vinyl acetylene), the loss of a H to give CHCHCCH (n-C41-13) or CH2CCCH (iso-C4H3), and addition of another acetylene to n-C4H3, followed by ring closure to give phenyl radical. Miller and Melius argue that only n-C4H3 leads to phenyl radical and since iso-C4H3 is more stable than n-C4H3 this mechanism is unlikely. An alternative mechanism proposed by them is formation of benzene from the dimerization of two CH2CCH (propargyl) radicals (formed by the reaction of singlet methylene with C2H2). We report reaction pathways and accurate energetics (from CASSCF/internally contracted CI calculations) for the reactions of CH(pi-2) and CH2-1 with acetylene, the reaction of vinylidene with acetylene, and the reaction of n-C4H3 and iso-C4H3 with acetylene. These calculations identify two new reactive intermediates CHCHCH ( a A"-2 ground state in Cs symmetry; spin coupling is a doublet from three singly occupied orbitals) and CHCCH (B-3 ground state in C2 symmetry) from the reaction of CH with acetylene. These species dimerize with no barrier to form benzene and para-benzyne, respectively. CHCCH is proposed as a reactive intermediate which can add to benzene to give higher polynuclear aromatic hydrocarbons or fullerenes. The addition of a C3H2 unit releases two C-C bond energies and thus the resulting addition product contains sufficient energy to break several CH bonds leading to a reduction in the H to C ratio as the cluster size increases. It is found that iso-C4H3 adds to acetylene to initially give a fulvene radical but that this species rearranges to phenyl radical. Thus, the reaction of acetylene with iso-C4H3 does lead to phenyl radical and the cyclization pathway may also contribute to formation of the initial benzene ring.

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



Mössbauer- and EPR-Snapshots of an Enzymatic Reaction: The Cytochrome P450 Reaction Cycle  

NASA Astrophysics Data System (ADS)

In this communication we present a complimentary Mössbauer- and EPR-study of the time dependance of the reaction of substrate free P450cam with peracetic acid within a time region ranging from 8 ms up to 5 min. An Fe(IV) species as well as a tyrosyl radical residing on the amino acid residue Tyr96 have been identified as reaction intermediates. These species possibly are formed by the reduction of compound I by means of transferring an electron from Tyr 96 to the heme moiety.

Schünemann, V.; Jung, C.; Lendzian, F.; Barra, A.-L.; Teschner, T.; Trautwein, A. X.



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


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

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



Using Systems Biology-based Analysis Approaches to Identify Mechanistically Significant Adverse Drug Reactions: Pulmonary Complications from Combined Use of Anti-TNF? Agents and Corticosteroids  

PubMed Central

Anti-TNF drugs are frequently associated with serious Adverse Events (AEs), which necessitates an improved understanding of individual factors that determine efficacy and safety of anti-TNF agents. We mined the US FDA’s Adverse Event Reporting System (AERS) for anti-TNF-associated AEs to identify and stratify patient subgroups and drug combinations that exhibit specifically correlated complications. We demonstrate the existence of patient subgroup and anti-TNF agent-specific associations for relative risks of developing known and novel AEs including infections, edema, and organ damage associated processes. Concomitant use of anti-TNFs with corticosteroids significantly increased risk of AEs (p < 0.001) including pulmonary fibrosis and pulmonary edema. Using these tightly correlated phenotypes, we mined mouse phenotype data to identify the molecular basis of these AEs. Multiple pathways and networks that regulate injury response, fluid regulation, and wound healing were implicated suggesting modification of anti-TNF-based therapeutic strategies to minimize corticosteroid-based combinatorial risk of severe AEs. PMID:24303326

Sarangdhar, Mayur; Kushwaha, Akash; Dahlquist, Jeanine; Jegga, Anil; Aronow, Bruce



Identifying resonance structures in a scattering cross section using the N3+ + H ? NH3+ ? N2+ + H+ reaction as an example  

NASA Astrophysics Data System (ADS)

The many-channel partial wave S-matrix is shown to have a meromorphic continuation into the fourth quadrant of the complex momentum plane. This allows one to expand this S-matrix in terms of its poles, inside a contour, and an integral along this contour. The contribution of a resonance is defined in terms of the corresponding residue. A reduced partial wave S-matrix as well as a reduced partial wave cross section are defined and used to identify if a given structure in a cross section can be associated with an S-matrix pole. The theory presented contains both short-range and Coulomb interactions. The formalism is applied to a realistic two-channel model of a charge transfer process.

Shilyaeva, Ksenia; Yarevsky, Evgeny; Elander, Nils



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


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

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



Mesoscopic statistical properties of multistep enzyme-mediated reactions.  


Enzyme-mediated reactions may proceed through multiple intermediate conformational states before creating a final product molecule, and one often wishes to identify such intermediate structures from observations of the product creation. In this study, the authors address this problem by solving the chemical master equations for various enzymatic reactions. A perturbation theory analogous to that used in quantum mechanics allows the determination of the first (n) and the second (?2) cumulants of the distribution of created product molecules as a function of the substrate concentration and the kinetic rates of the intermediate processes. The mean product flux V=d(n)/dt (or 'dose-response' curve) and the Fano factor F= ?2/(n) are both realistically measurable quantities, and whereas the mean flux can often appear the same for different reaction types, the Fano factor can be quite different. This suggests both qualitative and quantitative ways to discriminate between different reaction schemes, and the authors explore this possibility in the context of four sample multistep enzymatic reactions. Measuring both the mean flux and the Fano factor can not only discriminate between reaction types, but can also provide some detailed information about the internal, unobserved kinetic rates, and this can be done without measuring single-molecule transition events. PMID:21028932

de Ronde, W H; Daniels, B C; Mugler, A; Sinitsyn, N A; Nemenman, I



Communications: Elementary oxygen electrode reactions in the aprotic Li-air battery  

NASA Astrophysics Data System (ADS)

We discuss the electrochemical reactions at the oxygen electrode of an aprotic Li-air battery. Using density functional theory to estimate the free energy of intermediates during the discharge and charge of the battery, we introduce a reaction free energy diagram and identify possible origins of the overpotential for both processes. We also address the question of electron conductivity through the Li2O2 electrode and show that in the presence of Li vacancies Li2O2 becomes a conductor.

Hummelshøj, J. S.; Blomqvist, J.; Datta, S.; Vegge, T.; Rossmeisl, J.; Thygesen, K. S.; Luntz, A. C.; Jacobsen, K. W.; Nørskov, J. K.



Impact of sulfur dioxide oxidation by Stabilized Criegee Intermediate on sulfate  

EPA Science Inventory

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



Microsoft Academic Search

There is an ever-growing amount of information that must be covered in intermediate accounting courses. Recently this expansion of the body of knowledge has been accelerated by two main factors. The first factor is the increasing scrutiny of the accounting profession by regulators as a result of the financial failure of many large corporations during the past decade. The second

Lesley H. Davidson; William H. Francisco


Intermediate Pashto. Teachers' Manual.  

ERIC Educational Resources Information Center

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

Tegey, Habibullah; Robson, Barbara


Intermediate Pashto. Textbook.  

ERIC Educational Resources Information Center

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

Tegey, Habibullah; Robson, Barbara


Intermediate Pashto. Workbook.  

ERIC Educational Resources Information Center

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

Tegey, Habibullah; Robson, Barbara


SPACE: Intermediate Level Modules.  

ERIC Educational Resources Information Center

These modules were developed to assist teachers at the intermediate level to move away from extensive skill practice and toward more meaningful interdisciplinary learning. This packet, to be used by teachers in the summer Extended Learning Program, provides detailed thematic lesson plans matched to the Indiana Curriculum Proficiency Guide. The…

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


Financial networks with intermediation  

Microsoft Academic Search

In this paper, we develop a framework for the modelling, analysis, and computation of solutions to financial network problems in the presence of intermediation. Specifically, we consider an economy consisting of three types of agents: those with sources of funds, such as households and firms; intermediary ones, such as banks, savings institutions, insurance companies, investment companies, etc, and, finally, the

Anna Nagurney; Ke Ke



Photoelectron-photoion coincidence spectroscopy for multiplexed detection of intermediate species in a flame.  


Complex reactive processes in the gas phase often proceed via numerous reaction steps and intermediate species that must be identified and quantified to develop an understanding of the reaction pathways and establish suitable reaction mechanisms. Here, photoelectron-photoion coincidence (PEPICO) spectroscopy has been applied to analyse combustion intermediates present in a premixed fuel-rich (? = 1.7) ethene-oxygen flame diluted with 25% argon, burning at a reduced pressure of 40 mbar. For the first time, multiplexing fixed-photon-energy PEPICO measurements were demonstrated in a chemically complex reactive system such as a flame in comparison with the scanning "threshold" TPEPICO approach used in recent pioneering combustion investigations. The technique presented here is capable of detecting and identifying multiple species by their cations' vibronic fingerprints, including radicals and pairs or triplets of isomers, from a single time-efficient measurement at a selected fixed photon energy. Vibrational structures for these species have been obtained in very good agreement with scanning-mode threshold photoelectron spectra taken under the same conditions. From such spectra, the temperature in the ionisation volume was determined. Exemplary analysis of species profiles and mole fraction ratios for isomers shows favourable agreement with results obtained by more common electron ionisation and photoionisation mass spectrometry experiments. It is expected that the multiplexing fixed-photon-energy PEPICO technique can contribute effectively to the analysis of chemical reactivity and kinetics in and beyond combustion. PMID:25237782

Krüger, Julia; Garcia, Gustavo A; Felsmann, Daniel; Moshammer, Kai; Lackner, Alexander; Brockhinke, Andreas; Nahon, Laurent; Kohse-Höinghaus, Katharina



Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8, as revealed by X-ray crystallography.  


The alpha(2)beta(2) tetrameric E1 component of the branched-chain 2-oxo acid (BCOA) dehydrogenase multienzyme complex is a thiamin diphosphate (ThDP)-dependent enzyme. E1 catalyzes the decarboxylation of a BCOA concomitant with the formation of the alpha-carbanion/enamine intermediate, 2-(1-hydroxyalkyl)-ThDP, followed by transfer of the 1-hydroxyalkyl group to the distal sulfur atom on the lipoamide of the E2 component. In order to elucidate the catalytic mechanism of E1, the alpha- and beta-subunits of E1 from Thermus thermophilus HB8 have been co-expressed in Escherichia coli, purified and crystallized as a stable complex, and the following crystal structures have been analyzed: the apoenzyme (E1(apo)), the holoenzyme (E1(holo)), E1(holo) in complex with the substrate analogue 4-methylpentanoate (MPA) as an ES complex model, and E1(holo) in complex with 4-methyl-2-oxopentanoate (MOPA) as the alpha-carbanion/enamine intermediate (E1(ceim)). Binding of cofactors to E1(apo) induces a disorder-order transition in two loops adjacent to the active site. Furthermore, upon binding of MPA to E1(holo), the loop comprised of Gly121beta-Gln131beta moves close to the active site and interacts with MPA. The carboxylate group of MPA is recognized mainly by Tyr86beta and N4' of ThDP. The hydrophobic moiety of MPA is recognized by Phe66alpha, Tyr95alpha, Met128alpha and His131alpha. As an intermediate, MOPA is decarboxylated and covalently linked to ThDP, and the conformation of the protein loop is almost the same as in the substrate-free (holoenzyme) form. These results suggest that E1 undergoes an open-closed conformational change upon formation of the ES complex with a BCOA, and the mobile region participates in the recognition of the carboxylate group of the BCOA. ES complex models of E1(holo).MOPA and of E1(ceim).lipoamide built from the above structures suggest that His273alpha and His129beta' are potential proton donors to the carbonyl group of a BCOA and to the proximal sulfur atom on the lipoamide, respectively. PMID:15033367

Nakai, Tadashi; Nakagawa, Noriko; Maoka, Nobuko; Masui, Ryoji; Kuramitsu, Seiki; Kamiya, Nobuo



Intermediate water recovery system  

NASA Technical Reports Server (NTRS)

A water recovery system for collecting, storing, and processing urine, wash water, and humidity condensates from a crew of three aboard a spacecraft is described. The results of a 30-day test performed on a breadboard system are presented. The intermediate water recovery system produced clear, sterile, water with a 96.4 percent recovery rate from the processed urine. Recommendations for improving the system are included.

Deckman, G.; Anderson, A. R. (editor)



Oxide-supported PtCo alloy catalyst for intermediate temperature polymer electrolyte fuel cells  

E-print Network

1 Oxide-supported PtCo alloy catalyst for intermediate temperature polymer electrolyte fuel cells, Fuel cells, Oxygen reduction reaction, Doped Ti-oxide support, Intermediate temperature reduction reaction in a polymer electrolyte fuel cell (PEMFC) operating between 80° and 110 °C at different

Boyer, Edmond


Synthesis of a key intermediate for the preparation of FTY720 analogs.  


A concise synthesis of a useful intermediate 10 for the preparation of fingolimod (FTY-720) analogs was achieved by utilizing a chemoselective Sonogashira reaction of trihalobenzene 12 with alkyne 13. The reaction proceeded with high selectivity to give alkyne 11 containing the dihalobenzene moiety in good yield. Compound 11 was converted into intermediate 10 by hydrogenation without reduction of the halogen atoms. PMID:23124563

Hamada, Maiko; Adachi, Kunitomo; Hikawa, Hidemasa; Yokoyama, Yuusaku



Modeling DNA Replication Intermediates  

SciTech Connect

While there is now available a great deal of information on double stranded DNA from X-ray crystallography, high resolution NMR and computer modeling, very little is known about structures that are representative of the DNA core of replication intermediates. DNA replication occurs at a single strand/double strand junction and bulged out intermediates near the junction can lead to frameshift mutations. The single stranded domains are particularly challenging. Our interest is focused on strategies for modeling the DNA of these types of replication intermediates. Modeling such structures presents special problems in addressing the multiple minimum problem and in treating the electrostatic component of the force field. We are testing a number of search strategies for locating low energy structures of these types and we are also investigating two different distance dependent dielectric functions in the coulombic term of the force field. We are studying both unmodified DNA and DNA damaged by aromatic amines, carcinogens present in the environment in tobacco smoke, barbecued meats and automobile exhaust. The nature of the structure adopted by the carcinogen modified DNA at the replication fork plays a key role in determining whether the carcinogen will cause a mutation during replication that can initiate the carcinogenic process. In the present work results are presented for unmodified DNA.

Broyde, S.; Roy, D.; Shapiro, R.



Exemplary Dissemination Programs for Intermediate Units Serving Rural Schools.  

ERIC Educational Resources Information Center

Utilizing information derived from documents, site visits, correspondence, and personal interviews re: 6 intermediate education units serving rural schools which were initially identified via a mail survey, this report describes intermediate education units with exemplary information dissemination programs. Varying considerably, each program is…

Edington, Everett; Hays, Leonard


Intermediate inflation from rainbow gravity  

NASA Astrophysics Data System (ADS)

It is possible to dualize theories based on deformed dispersion relations and Einstein gravity so as to map them into theories with trivial dispersion relations and rainbow gravity. This often leads to “dual inflation” without the usual breaking of the strong energy condition. We identify the dispersion relations in the original frame which map into “intermediate” inflationary models. These turn out to be particularly simple: power-laws modulated by powers of a logarithm. The fluctuations predicted by these scenarios are near, but not exactly scale-invariant, with a red running spectral index. These dispersion relations deserve further study within the context of quantum gravity and the phenomenon of dimensional reduction in the ultraviolet.

Barrow, John D.; Magueijo, João



Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin  

Microsoft Academic Search

X-ray and electron diffraction studies of specific reac- tion intermediates, or reaction intermediate analogues, have produced a consistent picture of the structural mechanism of light-driven proton pumping by bacteri- orhodopsin. Of central importance within this picture is the structure of the L-intermediate, which follows the retinal all-trans to 13-cis photoisomerization step of the K-intermediate and sets the stage for the

Karl Edman; Antoine Royant; Gisela Larsson; Frida Jacobson; Tom Taylor; David van der Spoel; Ehud M. Landau; Eva Pebay-Peyroula; Richard Neutzea



Intermediates of stigmasterol metabolism in Spodoptera littoralis  

SciTech Connect

Stigmasterol-24,28-epoxide, 22E-stigmasta-5,22,24(28E)-trien-3 beta-ol, and 22E-cholesta-5,22,24-trien-3 beta-ol were identified as normal metabolites of (3H)stigmasterol in Spodoptera littoralis larvae. Relative concentrations of all three of these metabolites increased when a diazasterol inhibitor was fed in combination with stigmasterol in the artificial diet. Identification of these sterols as intermediates in the conversion of stigmasterol to cholesterol in this insect indicates that intermediates analogous to fucosterol and fucosterol-24,28-epoxide in the conversion of sitosterol to cholesterol are produced in the metabolism of stigmasterol. This is the first published identification of stigmasterol-24,28-epoxide and 22E-stigmasta-5,22,24(28E)-trien-3 beta-ol as intermediates in this pathway in an insect.

Svoboda, J.A.; Rees, H.H.; Thompson, M.J.; Hoggard, N. (Insect and Nematode Hormone Laboratory, Beltsville, MD (USA))



Formation of ammonia and hydrazine from the reactions of acids with bis(dinitrogen) complexes of molybdenum. Identification and isolation of intermediates. Possible analogy with the hydrazine-forming property of nitrogenase  

SciTech Connect

The reactions of anhydrous HBr and HCl with trans-(Mo(N/sub 2/)/sub 2/(triphos)(PR/sub 3/)), where triphos = PhP(CH/sub 2/CH/sub 2/PPh/sub 2/)/sub 2/(PR/sub 3/ = PPh/sub 3/(1), PMePh/sub 2/ (2)), in tetrahydrofuran (THF) solution to produce ammonia and in benzene solution to produce hydrazine and ammonia have been examined. Complex 1 reacted with HBr in THF to produce 1.5 mol of N/sub 2//mol of 1 and routinely ca. 0.72 mol of NH/sub 3//mol of 1, respectively, and MoBr/sub 3/(triphos) (greater than or equal to94% yield). No more than a trace of hydrazine was detected. Total nitrogen balance was increased to 100% when amounts of HBr were added periodically during the reaction. The reaction of 1 or 2 with HBr or HCl led to the rapid loss of 1 mol of N/sub 2/ and the formation of a pair of isomeric hydrazido(2-) complexes, (MoX(NNH/sub 2/)(triphos)(PR/sub 3/))X (PR/sub 3/ = PPh/sub 3/ for 1 A(X) and 1 B(X), PPh/sub 2/Me for 2A(X) and 2B(X); X = Br, Cl). The same mixtures were formed in the absence of solvent. The presence of two isomers was the result of the position of the phenyl group on the central phosphorus atom of the triphos ligand relative to the hydrazido(2-) ligand. 48 references, 3 figures, 3 tables.

Baumann, J.A.; Bossard, G.E.; George, T.A.; Howell, D.B.; Koczon, L.M.; Lester, R.K.; Noddings, C.M.



Kinetics and product studies of the reaction ClO + BrO using discharge-flow mass spectrometry  

NASA Technical Reports Server (NTRS)

The kinetics and product branching ratios of the reaction between ClO and BrO were studied at 1 torr pressure over the temperature range 220-400 K, using the method of discharge-flow mass spectrometry. Three product channels were identified and quantified: Br + ClOO, Br + OClO, and BrCl + O2, indicating that the reaction mechanism of ClO + BrO involves metastable intermediates. The overall reaction rate coefficient and the rate coefficients for the three channel reactions are given.

Friedl, Randall R.; Sander, Stanley P.



Pyrolysis of 9-methylenespiro(3. 5)nona-5,7-diene: A route to benzo-2-hexene-1,6-diyl, a putative intermediate in the retro-Diels-Alder reaction of tetralin  

SciTech Connect

A precursor to the 1,6-biradical potentially formed in the retro-Diels-Alder reaction of tetralin, namely, 5-methylenespiro(bicyclo(2.2.1)hept-2-ene-6,1{prime}-cyclobutan)-7-one (9) has been prepared and found to give tetralin and o-allyltoluene upon pyrolysis in solution below 100C and upon flash vacuum pyrolysis around 250C. The product ratio changes from 1:1 to 6:1 at higher temperatures. Rate-determining loss of CO from 9 to give 9-methylenespiro(3.5)nona-5,7-diene, 2, has been demonstrated by trapping the triene with N-methyl- and N-phenyltriazolinedione in a reaction whose rate is independent of trapping agent concentration. The kinetics for loss of ketone, 9, gave log k (s{sup {minus}1}) = 14.628 {plus minus} 0.038-(30.554 {plus minus} 0.064)/2.3RT. Pyrolysis of cis-cyn(to methylene)- and trans-1,2-dimethyl-9-methylenespiro(3.5)nona-5,7-diene gives the vinylcyclobutane rearrangement product, 2,3-dimethyltetralin, with a 4:1 and 2.7:1, respectively, preference for retention over inversion at the migrating carbon. Hydrogen shift products are also formed and by highly ordered transition states. One of these hydrogen shifts involves an unprecedented shift from the carbon remote from the vinyl group.

Gajewski, J.J.; Paul, G.C. (Indiana Univ., Bloomington (United States))



Photooxidation of dicarboxylic acids—Part II: Kinetics, intermediates and field observations  

NASA Astrophysics Data System (ADS)

Among C 2-C 9 dicarboxylic acids (DCAs), succinic acid (C 4 DCA) exhibits the lowest photooxidation rate, while oxalic acid has the highest photooxidation rate in a liquid-phase reaction system. Twenty-seven identified intermediates are classified into six classes: secondary DCAs, oxo-DCAs, methyl-DCAs, hydroxy-DCAs, hydroxy-monocarboxylic acids (hydroxy-MCAs), and oxo-MCAs. Concentration profiles of the identified intermediates affirm two hypotheses: (1) longer DCAs can be the precursors of shorter DCAs and (2) succinic acid can be oxidized to malonic acid with malic acid as an intermediate. Ambient DCAs can also be precursors of substituted DCAs and MCAs; methyl-, oxo-, and hydroxy-substituents consistently position at the center carbon of the base DCA molecules, while hydroxy- and oxo-substituents favor the ? or ( ?-1) position of the base MCAs. A comparison of field observations with the experimental data obtained in this study indicates that oxo-DCAs, having a higher concentration than methyl- and hydroxy-DCAs in ambient particulates, may characterize an atmosphere under prevailing photooxidation with little influence of anthropogenic pollution.

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


Experiments in intermediate energy physics  

SciTech Connect

Research in experimental nuclear physics was done from 1979 to 2002 primarily at intermediate energy facilities that provide pion, proton, and kaon beams. Particularly successful has been the work at the Los Alamos Meson Physics Facility (LAMPF) on unraveling the neutron and proton contributions to nuclear ground state and transition densities. This work was done on a wide variety of nuclei and with great detail on the carbon, oxygen, and helium isotopes. Some of the investigations involved the use of polarized targets which allowed the extraction of information on the spin-dependent part of the triangle-nucleon interaction. At the Indiana University Cyclotron Facility (IUCF) we studied proton-induced charge exchange reactions with results of importance to astrophysics and the nuclear few-body problem. During the first few years, the analysis of heavy-ion nucleus scattering data that had been taken prior to 1979 was completed. During the last few years we created hypernuclei by use of a kaon beam at Brookhaven National Laboratory (BNL) and an electron beam at Jefferson Laboratory (JLab). The data taken at BNL for a study of the non-mesonic weak decay of the A particle in a nucleus are still under analysis by our collaborators. The work at JLab resulted in the best resolution hypernuclear spectra measured thus far with magnetic spectrometers.

Dehnhard, D.



Noncanonical Reactions of Flavoenzymes  

PubMed Central

Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the protein environment modulates the reactivity of the flavin to perform novel chemistries. Recent mechanistic and structural data supporting novel flavin functionalities in reactions catalyzed by chorismate synthase, type II isopentenyl diphosphate isomerase, UDP-galactopyranose mutase, and alkyl-dihydroxyacetonephosphate synthase are presented in this review. In these enzymes, the flavin plays either a direct role in acid/base reactions or as a nucleophile or electrophile. In addition, the flavin cofactor is proposed to function as a “molecular scaffold” in the formation of UDP-galactofuranose and alkyl-dihydroxyacetonephosphate by forming a covalent adduct with reaction intermediates. PMID:23203060

Sobrado, Pablo



Cycloaddition reactions of ICNO  

NASA Astrophysics Data System (ADS)

The mechanism and selectivity of cycloaddition reactions of iodonitrile oxide, ICNO, have been studied with theoretical methods for the first time using MR-AQCC coupled-cluster and B3LYP DFT methods. Calculations have predicted that the favoured ICNO dimerisation process is a multi-step reaction to diiodofuroxan involving dinitrosoethylene-like intermediates. The ICNO cycloaddition with nitriles and ethynyl derivatives is a synchronous process favouring the formation of 1,2,4-oxadiazole and 1,2-oxazole derivatives, respectively. The cycloaddition reactions of ICNO have been studied experimentally by generating ICNO from AgCNO and iodine. Diiodofuroxan is obtained, however, even at the presence of nitriles.

Pasinszki, Tibor; Krebsz, Melinda; Hajgató, Balázs



Identification of the Intermediate Charge-Separated State P+?L? in a Leucine M214 to Histidine Mutant of the Rhodobacter sphaeroides Reaction Center Using Femtosecond Midinfrared Spectroscopy  

PubMed Central

Abstract Energy and electron transfer in a Leu M214 to His (LM214H) mutant of the Rhodobacter sphaeroides reaction center (RC) were investigated by applying time-resolved visible pump/midinfrared probe spectroscopy at room temperature. This mutant replacement of the Leu at position M214 resulted in the incorporation of a bacteriochlorophyll (BChl) in place of the native bacteriopheophytin in the L-branch of cofactors (denoted ?L). Purified LM214H RCs were excited at 600 nm (unselective excitation), at 800 nm (direct excitation of the monomeric BChl cofactors BL and BM), and at 860 nm (direct excitation of the primary donor (P) BChl pair (PL/PM)). Absorption changes associated with carbonyl (C=O) stretch vibrational modes (9-keto, 10a-ester, and 2a-acetyl) of the cofactors and of the protein were recorded in the region between 1600 cm?1 and 1770 cm?1, and the data were subjected to both a sequential analysis and a simultaneous target analysis. After photoexcitation of the LM214H RC, P? decayed on a timescale of ?6.3 ps to P+BL?. The decay of P+BL? occurred with a lifetime of ?2 ps, ?3 times slower than that observed in wild-type and R-26 RCs (?0.7 ps). Further electron transfer to the ?L BChl resulted in formation of the P+?L? state, and its infrared absorbance difference spectrum is reported for the first time, to our knowledge. The fs midinfrared spectra of P+BL? and P+?L? showed clear differences related to the different environments of the two BChls in the mutant RC. PMID:19527655

Pawlowicz, Natalia P.; van Stokkum, Ivo H.M.; Breton, Jacques; van Grondelle, Rienk; Jones, Michael R.



Kinetics, intermediates and acute toxicity of arsanilic acid photolysis.  


Arsanilic acid (4-amino phenyl arsenic acid, ASA) is widely used in poultry production as feed additives, while most of ASA in the feed is excreted in the animal manure and released into the environment. However, the environmental behaviors of ASA were not well understood. In the present study, the photolysis behaviors of ASA and the toxicity of its metabolites to luminescent bacterium were studied. The results showed that ASA could be photodegraded and this process was strongly affected by solution pH, humic acid and dissolved oxygen. Upon UV irradiation for 360 min, ASA could be completely eliminated, but the reduction of total organic carbon (TOC) was not significant. In addition, NH4(+) ions and inorganic arsenic including arsenite and arsenate were identified as the predominant end-products. The conversion of ASA included both direct and indirect photolysis involving radicals, and its possible photolysis pathways were proposed on the basis of the identified intermediates. Unfortunately, higher adverse effects of the conversion products of ASA on bacteria were observed during the photolysis reaction. The results of present study might be helpful for assessing the environmental persistence and risks of ASA. PMID:24405966

Zhu, Xiang-Dong; Wang, Yu-Jun; Liu, Cun; Qin, Wen-Xiu; Zhou, Dong-Mei



Conformational dynamics through an intermediate  

NASA Astrophysics Data System (ADS)

The self-assembly of biological and synthetic nanostructures commonly proceeds via intermediate states. In living systems in particular, the intermediates have the capacity to tilt the balance between functional and potentially fatal behavior. This work develops a statistical mechanical treatment of conformational dynamics through an intermediate under a variable force. An analytical solution is derived for the key experimentally measurable quantity—the distribution of forces at which a conformational transition occurs. The solution reveals rich kinetics over a broad range of parameters and enables one to locate the intermediate and extract the activation barriers and rate constants.

Garai, Ashok; Zhang, Yaojun; Dudko, Olga K.



Pulsed-EPR evidence of a manganese(II) hydroxycarbonyl intermediate in the electrocatalytic reduction of carbon dioxide by a manganese bipyridyl derivative.  


A key intermediate in the electroconversion of carbon dioxide to carbon monoxide, catalyzed by a manganese tris(carbonyl) complex, is characterized. Different catalytic pathways and their potential reaction mechanisms are investigated using a large range of experimental and computational techniques. Sophisticated spectroscopic methods including UV/Vis absorption and pulsed-EPR techniques (2P-ESEEM and HYSCORE) were combined together with DFT calculations to successfully identify a key intermediate in the catalytic cycle of CO2 reduction. The results directly show the formation of a metal-carboxylic acid-CO2 adduct after oxidative addition of CO2 and H(+) to a Mn(0) carbonyl dimer, an unexpected intermediate. PMID:24259443

Bourrez, Marc; Orio, Maylis; Molton, Florian; Vezin, Hervé; Duboc, Carole; Deronzier, Alain; Chardon-Noblat, Sylvie



Observation of a short, strong hydrogen bond in the active site of hydroxynitrile lyase from Hevea brasiliensis explains a large pKa shift of the catalytic base induced by the reaction intermediate.  


The hydroxynitrile lyase from Hevea brasiliensis (HbHNL) uses a catalytic triad consisting of Ser(80)-His(235)-Asp(207) to enhance the basicity of Ser(80)-O gamma for abstracting a proton from the OH group of the substrate cyanohydrin. Following the observation of a relatively short distance between a carboxyl oxygen of Asp(207) and the N delta(1)(His(235)) in a 1.1 A crystal structure of HbHNL, we here show by (1)H and (15)N-NMR spectroscopy that a short, strong hydrogen bond (SSHB) is formed between the two residues upon binding of the competitive inhibitor thiocyanate to HbHNL: the proton resonance of H-N delta 1(His(235)) moves from 15.41 ppm in the free enzyme to 19.35 ppm in the complex, the largest downfield shift observed so far upon inhibitor binding. Simultaneously, the D/H fractionation factor decreases from 0.98 to 0.35. In the observable pH range, i.e. between pH 4 and 10, no significant changes in chemical shifts (and therefore hydrogen bond strength) were observed for free HbHNL. For the complex with thiocyanate, the 19.35 ppm signal returned to 15.41 ppm at approximately pH 8, which indicates a pK(a) near this value for the H-N epsilon(2)(His(235)). These NMR results were analyzed on the basis of finite difference Poisson-Boltzmann calculations, which yielded the relative free energies of four protonation states of the His(235)-Asp(207) pair in solution as well as in the protein environment with and without bound inhibitor. The calculations explain all the NMR features, i.e. they suggest why a short, strong hydrogen bond is formed upon inhibitor binding and why this short, strong hydrogen bond reverts back to a normal one at approximately pH 8. Importantly, the computations also yield a shift of the free energy of the anionic state relative to the zwitterionic reference state by about 10.6 kcal/mol, equivalent to a shift in the apparent pK(a) of His(235) from 2.5 to 10. This huge inhibitor-induced increase in basicity is a prerequisite for His(235) to act as general base in the HbHNL-catalyzed cyanohydrin reaction. PMID:14597632

Stranzl, Gudrun R; Gruber, Karl; Steinkellner, Georg; Zangger, Klaus; Schwab, Helmut; Kratky, Christoph



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


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

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



Time dependence of the catalytic intermediates in cytochrome c oxidase.  


Cytochrome c oxidase, the terminal enzyme in the electron transfer chain, catalyzes the reduction of oxygen to water in a multiple step process by utilizing four electrons from cytochrome c. To study the reaction mechanism, the resonance Raman spectra of the intermediate states were measured during single turnover of the enzyme after catalytic initiation by photolysis of CO from the fully reduced CO-bound enzyme. By measuring the change in intensity of lines associated with heme a, the electron transfer steps were determined and found to be biphasic with apparent rate constants of approximately 40 x 10(3) s(-1) and approximately 1 x 10(3) s(-1). The time dependence for the oxidation of heme a and for the measured formation and decay of the oxy, the ferryl ("F"), and the hydroxy intermediates could be simulated by a simple reaction scheme. In this scheme, the presence of the "peroxy" ("P") intermediate does not build up a sufficient population to be detected because its decay rate is too fast in buffered H(2)O at neutral pH. A comparison of the change in the spin equilibrium with the formation of the hydroxy intermediate demonstrates that this intermediate is high spin. We also confirm the presence of an oxygen isotope-sensitive line at 355 cm(-1), detectable in the spectrum from 130 to 980 micros, coincident with the presence of the F intermediate. PMID:10636892

Han, S; Takahashi, S; Rousseau, D L



Cyclization of ?(3)-Benzylpalladium Intermediates Derived from Carbene Insertion.  


Migratory insertion of benzylidene carbene ligands into arylpalladium(II) species generates ?(3)-benzylpalladium intermediates that can cyclize to generate five- and six-membered rings with new sp(3) centers. The reaction tolerates a range of arene functional groups and stabilized enolates. The products generated through this reaction are 1-arylindanes and 1-aryltetralins that are common to a range of natural products. PMID:25279856

Gutman, Eugene S; Arredondo, Vanessa; Van Vranken, David L



Masonry. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of 13 terminal objectives for an intermediate masonry course. These materials, developed for a two-semester (3 hours daily) course, are designed to provide the student with the skills and knowledge necessary for entry level employment in the field…

Thompson, Moses


Bank and Nonbank Financial Intermediation  

Microsoft Academic Search

Conglomerates, trade credit arrangements, and banks are all instances of financial intermediation. However, these institutions differ significantly in the extent to which the projects financed absorb aggregate intermediary risk, in whether or not intermediation is carried out by a financial specialist, in the type of projects they fund and in the type of claims they issue to investors. The paper




Photoreactions of cyclic sulfite esters: Evidence for diradical intermediates  

PubMed Central

Summary The photochemistry of a phenyl and 1,2-diphenyl substituted sulfite ester is reported. The performance of photoreactions under relatively mild reaction conditions enables the detection of products that have not been observed in previous studies. It is concluded that, complementary to the initially proposed carbene intermediates, diradicals may also be considered. PMID:23019449

Arney, Benny E; Ihmels, Heiko



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

Microsoft Academic Search

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

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



Hydroxo-bridged dicopper(II,III) and -(III,III) complexes: models for putative intermediates in oxidation catalysis.  


A macrocyclic ligand (L(4-)) comprising two pyridine(dicarboxamide) donors was used to target reactive copper species relevant to proposed intermediates in catalytic hydrocarbon oxidations by particulate methane monooxygenase and heterogeneous zeolite systems. Treatment of LH4 with base and Cu(OAc)2·H2O yielded (Me4N)2[L2Cu4(?4-O)] (1) or (Me4N)[LCu2(?-OH)] (2), depending on conditions. Complex 2 was found to undergo two reversible 1-electron oxidations via cyclic voltammetry and low-temperature chemical reactions. On the basis of spectroscopy and theory, the oxidation products were identified as novel hydroxo-bridged mixed-valent Cu(II)Cu(III) and symmetric Cu(III)2 species, respectively, that provide the first precedence for such moieties as oxidation catalysis intermediates. PMID:24821432

Halvagar, Mohammad Reza; Solntsev, Pavlo V; Lim, Hyeongtaek; Hedman, Britt; Hodgson, Keith O; Solomon, Edward I; Cramer, Christopher J; Tolman, William B



Intermediate neutron spectrum problems and the intermediate neutron spectrum experiment  

SciTech Connect

Criticality benchmark data for intermediate energy spectrum systems does not exist. These systems are dominated by scattering and fission events induced by neutrons with energies between 1 eV and 1 MeV. Nuclear data uncertainties have been reported for such systems which can not be resolved without benchmark critical experiments. Intermediate energy spectrum systems have been proposed for the geological disposition of surplus fissile materials. Without the proper benchmarking of the nuclear data in the intermediate energy spectrum, adequate criticality safety margins can not be guaranteed. The Zeus critical experiment now under construction will provide this necessary benchmark data.

Jaegers, P.J.; Sanchez, R.G.



BB Seminar: Prediction of Survival Incorporating Intermediate Event Info

In recent years, an increasing number of predictive markers have been identified as useful for risk prediction. When interest lies in predicting long term survival, it has often been argued that intermediate event information may be very helpful in improving the prediction. Most existing methods for incorporating potentially censored intermediate event information in predicting long term survival focus on modeling the disease process and are derived under restrictive parametric models in a multi-state survival setting.


Site Seeing: Intermediate  

NSDL National Science Digital Library

This field activity introduces students to the concept of a system. Students identify the components, inputs and outputs of the local system at a range of biometry study sites, as well as the boundaries of their investigations at these sites in terms of space and time. Collected data from the different sites are analyzed and compared. The activity includes a student worksheet and data charts. Equipment needed to do this activity includes a compass and camera. This is a learning activity associated with the GLOBE Land Cover/Biology investigations and is supported by the GLOBE Teacher's Guide, Land Cover/Biology.


Reactions & Rates  

NSDL National Science Digital Library

Explore what makes a reaction happen by colliding atoms and molecules. Design experiments with different reactions, concentrations, and temperatures. When are reactions reversible? What affects the rate of a reaction?

Simulations, Phet I.; Koch, Linda; Lemaster, Ron; Loeblein, Trish; Perkins, Kathy; Gratny, Mindy



Gas Producing Micro-Reaction  

NSDL National Science Digital Library

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

House, The S.



Plasticity of Intermediate Filament Subunits  

E-print Network

Intermediate filaments (IFs) assembled in vitro from recombinantly expressed proteins have a diameter of 8–12 nm and can reach several micrometers in length. IFs assemble from a soluble pool of subunits, tetramers in the ...

Kirmse, Robert


The reaction of Fe and Ni at intermediate energies  

E-print Network

at the Texas A&M University Cyclotron Institute. Differing beams of the above materials were created and impinged on the different targets. The resulting fragments were detected in combinations of cesium iodide detectors, silicon detectors and the neutron...

Liddick, Sean Nicholas



Spectroscopy of Reaction Intermediates in Nitramine Decomposition and Combustion.  

National Technical Information Service (NTIS)

The infrared spectra of a number of free radicals and molecular ions which are expected to be important in nitramine decomposition and combustion have been obtained in solid neon. The molecular ion studies resulted in the first infrared spectral detection...

M. E. Jacox



Capturing fleeting intermediates in a catalytic CH amination reaction cycle  

E-print Network

the catalyst bis [rhodium(,,,-tetramethyl-1,3-benzenedipropionic acid)], hereafter designated as Rh2(esp)2 the mechanism for Rh-catalyzed C­H amination depicted in Fig. 1. Sulfamate 2 and iodine oxidant 3 condense of adamantane by 6 gives the sulfonamide product 7 and regenerates the dirhodium catalyst 1. The structures

Zare, Richard N.


Kinetic intermediates in amyloid assembly.  


In contrast to an expected Ostwald-like ripening of amyloid assemblies, the nucleating core of the Dutch mutant of the A? peptide of Alzheimer's disease assembles through a series of conformational transitions. Structural characterization of the intermediate assemblies by isotope-edited IR and solid-state NMR reveals unexpected strand orientation intermediates and suggests new nucleation mechanisms in a progressive assembly pathway. PMID:25313920

Liang, Chen; Ni, Rong; Smith, Jillian E; Childers, W Seth; Mehta, Anil K; Lynn, David G



The critical iron-oxygen intermediate in human aromatase  

SciTech Connect

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

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



Steady-State and Transient Kinetic Analyses of Taurine\\/?-Ketoglutarate Dioxygenase:  Effects of Oxygen Concentration, Alternative Sulfonates, and Active-Site Variants on the Fe IV -oxo Intermediate †  

Microsoft Academic Search

Taurine\\/R-ketoglutarate (RKG) dioxygenase (TauD), an archetype RKG-dependent hydroxylase, is a non-heme mononuclear FeII enzyme that couples the oxidative decarboxylation of RKG with the conversion of taurine to aminoacetaldehyde and sulfite. The crystal structure of taurine- RKG-FeIITauD is known, and spectroscopic studies have kinetically defined the early steps in catalysis and identified a high-spin FeIV-oxo reaction intermediate. The present analysis extends

Piotr K. Grzyska; Matthew J. Ryle; Greta R. Monterosso; Jian Liu; David P. Ballou; Robert P. Hausinger



Time-resolved heme protein intermediates  

NASA Astrophysics Data System (ADS)

To determine the enzymatic mechanisms of heme proteins, it is necessary to identify the intermediates along the catalytic pathway and measure the times of their formation and decay. Resonance Raman scattering spectra are especially powerful for obtaining such information as the electronic structure of the heme group and the nature of the ligand coordinated to the heme iron atom may be monitored. The oxygen intermediates of two physiologically important enzymes will be presented. Nitric oxide synthase (NOS) uses oxygen to convert arginine to NO and citrulline; and cytochrome c oxidase (CcO) reduces oxygen to water to support oxidative phosphorylation. The fate or the oxygen in each of these enzymes has been followed by resonance Raman scattering. In NOS the oxygen is slowly converted to an activated species that then reacts fast, whereas in CcO the oxygen is rapidly converted to a reactive species that subsequently reacts slowly. The properties of the intermediates and the origin of the differences between these enzymes will be discussed.

Rousseau, Denis



Intermediate-sized filaments of human endothelial cells  

PubMed Central

Human endothelial cells prepared from unbilical cords are characterized in parallel by electron microscopy and indirect immunofluorescence microscopy using specific antibodies against different classes of intermediate-sized filaments. The strongly developed, loose bundles of intermediate-sized filaments typically found in these cells are not decorated by antibodies against prekeratin or antibodies against smooth muscle desmin. They are, however, strongly decorated by antibodies directed against murine "vimentin," i.e., the 57,000 mol wt polypeptide which is the major protein of the intermediate-sized filaments predominant in various cells of mesenchymal origin. Cytoskeletal preparations greatly enriched in intermediate-sized filaments show the enrichment of a polypeptide band comigrating with murine vimentin. This shows that the intermediate-sized filaments that are abundant in human endothelial cells are predominantly of the vimentin type and can be demonstrated by their cross-reaction with the vimentin of rodents. These data also strengthen the evidence for several subclasses of intermediate-sized filaments, which can be distinguished by immunological procedures. PMID:379021



ChemTeacher: Decomposition Reactions  

NSDL National Science Digital Library

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



Unusual spin-trap chemistry for the reaction of hydroxyl radical with the carcinogen N-nitrosodimethylamine  

NASA Astrophysics Data System (ADS)

The reaction of the potent carcinogen N-nitrosodimethylamine (NDMA) with hydroxyl radical generated via radiolysis was studied using EPR techniques. Attempts to spin trap NDMA radical intermediates with 3,5-dibromo-4-nitrosobenzene sulfonate (DBNBS) produced only unusual DBNBS radicals. One of these radicals was shown to be generated by both reaction of DBNBS with nitric oxide, and direct oxidation of DBNBS with an inorganic oxidant ( .Br -2). Another DBNBS radical was identified as a sulfite spin adduct resulting from the degradation of DBNBS by a NDMA reactive intermediate. In the absence of DBNBS, hydroxyl radical reaction with NDMA gave the dimethylnitroxide radical. Unexpectedly, addition of DBNBS to a solution containing dimethylnitroxide produced an EPR spectrum nearly identical to that of NDMA solutions with DBNBS added before radiolysis. A proposed mechanism accounting for these observations is presented.

Wink, David A.; Desrosiers, Marc F.


Analysis of dynein intermediate chains, light intermediate chains and light chains in a cohort of hereditary peripheral neuropathies.  


The cytoplasmic dynein heavy chain (DYNC1H1) gene has been increasingly associated with neurodegenerative disorders including axonal Charcot-Marie-Tooth disease (CMT2), intellectual disability and malformations of cortical development. In addition, evidence from mouse models (Loa, catabolite repressor-activator (Cra) and Sprawling (Swl)) has shown that mutations in Dync1h1 cause a range of neurodegenerative phenotypes with motor and sensory neuron involvement. In this current study, we examined the possible contribution of other cytoplasmic dynein subunits that bind to DYNC1H1 as a cause of inherited peripheral neuropathy. We focused on screening the cytoplasmic dynein intermediate, light intermediate and light chain genes in a cohort of families with inherited peripheral neuropathies. Nine genes were screened and ten variants were detected, but none was identified as pathogenic, indicating that cytoplasmic dynein intermediate, light intermediate and light chains are not a cause of neuropathy in our cohort. PMID:25028179

Tey, Shelisa; Ahmad-Annuar, Azlina; Drew, Alexander P; Shahrizaila, Nortina; Nicholson, Garth A; Kennerson, Marina L



Compact intermediates in RNA folding  

SciTech Connect

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

Woodson, S.A. (JHU)



Mineral catalyzed hydrothermal reactions as precursors to extant anabolic pathways  

NASA Astrophysics Data System (ADS)

Investigations into hydrothermal reactions under conditions of moderate hydrostatic pressure and in the presence of transition metal sulfides reveal reaction pathways the bear remarkable similarity with extant anabolic reactions. First, it is seen that most common transition metal sulfides are capable of promoting all of the key reactions at the core of Acetyl Co-A synthesis. These include CO reduction to methyl groups and carbonyl insertion to form transferable acetyl groups. The synthesis of alpha-keto acids are also promoted, presumably by double carbonylation. A pathway starting with CO2 and H2 has been identified leading to the synthesis of citric acid. Citric acid provides a crucial abiotic, anabolic, branch point to the prebiotic synthesis of various amino acids, as well. As the pyrimidines, orotic acid and uracil. In many cases the abiotic reaction pathways differ slightly from extant anabolic pathways by shunting past particularly reactive intermediates, e.g. oxaloacetic acid. These reactions have the capacity to provide the prebiotic world with many, but not all, of the molecular constituents to aid the emergence of an RNA world.

Cody, G. D.


Study of solid-phase reaction between CsNO 3 AND V 2 O 5 in the molar ratio 6:5  

Microsoft Academic Search

Using DTA, DTG and TG methods, the solid-phase reaction between CsNO3 and V2O5 in the molar ratio 6?5 has been studied in oxygen and air streams in the temperature range 20–550°. The reaction proceeds stepwise and CsV3O8 has been identified as an intermediate. A mixture of CsVO3 and Cs2V4O11 is formed as final product of the reaction at 520°. The

?. Žúrková; K. Gáplovská; V. Suchá



[New intermediates in the photochemical transformation of rhodopsin].  


The conditions of preferential accumulation of intermediates of the photochemical reaction cycle of bacteriorhodopsin (BR) P550 and P419 at low temperature are found. Upon illumination P550 and P419 undergo photochemical conversions into the light-adapted form of BR (P570), forming during this conversions a number of new intermediates: P550 leads to P560-- -- -- leads to P570; P419 leads to P421-- -- -- leads to P565-- -- -- leads to P585-- -- -- leads to P570; P419 leads to P470-- -- -- leads to P570. All intermediates are photoactive. All light reactions are photoreversible and give formation to the products with absorption maximum shifted to the red as compared to the initial state. The absorption spectra of intermediates are complex and include several bands which are more pronounced in the spectrum of P419 (maxima at 442, 419, 398 nm, a shoulder at 375 nm) and P421, less in the spectrum of P570 (maximum at 578 nm, shoulders at 540 and 608 nm) and others. PMID:588617

Litvin, F F; Balashov, S P



Selective insertion of sulfur dioxide reduction intermediates on graphene oxide.  


Graphite microparticles (d50 6.20 ?m) were oxidized by strong acids, and the resultant graphite oxide was thermally exfoliated to graphene oxide sheets (MPGO, C/O 1.53). Graphene oxide was treated with nonthermal plasma under a SO2 atmosphere at room temperature. The XPS spectrum showed that SO2 was inserted only as the oxidized intermediate at 168.7 eV in the S 2p region. Short thermal shocks at 600 and 400 °C, under an Ar atmosphere, produced reduced sulfur and carbon dioxide as shown by the XPS spectrum and TGA analysis coupled to FTIR. MPGO was also submitted to thermal reaction with SO2 at 630 °C, and the XPS spectrum in the S 2p region at 164.0 eV showed that this time only the nonoxidized episulfide intermediate was inserted. Plasma and thermal treatment produced a partial reduction of MPGO. The sequence of thermal reaction followed by plasma treatment inserted both sulfur intermediates. Because oxidized and nonoxidized intermediates have different reactivities, this selective insertion would allow the addition of selective types of organic fragments to the surface of graphene oxide. PMID:24605942

Humeres, Eduardo; Debacher, Nito A; Smaniotto, Alessandra; de Castro, Karen M; Benetoli, Luís O B; de Souza, Eduardo P; Moreira, Regina de F P M; Lopes, Cristiane N; Schreiner, Wido H; Canle, Moisés; Santaballa, J Arturo



Photocrystallographic observation of halide-bridged intermediates in halogen photoeliminations.  


Polynuclear transition metal complexes, which frequently constitute the active sites of both biological and chemical catalysts, provide access to unique chemical transformations that are derived from metal-metal cooperation. Reductive elimination via ligand-bridged binuclear intermediates from bimetallic cores is one mechanism by which metals may cooperate during catalysis. We have established families of Rh2 complexes that participate in HX-splitting photocatalysis in which metal-metal cooperation is credited with the ability to achieve multielectron photochemical reactions in preference to single-electron transformations. Nanosecond-resolved transient absorption spectroscopy, steady-state photocrystallography, and computational modeling have allowed direct observation and characterization of Cl-bridged intermediates (intramolecular analogues of classical ligand-bridged intermediates in binuclear eliminations) in halogen elimination reactions. On the basis of these observations, a new class of Rh2 complexes, supported by CO ligands, has been prepared, allowing for the isolation and independent characterization of the proposed halide-bridged intermediates. Direct observation of halide-bridged structures establishes binuclear reductive elimination as a viable mechanism for photogenerating energetic bonds. PMID:25264809

Powers, David C; Anderson, Bryce L; Hwang, Seung Jun; Powers, Tamara M; Pérez, Lisa M; Hall, Michael B; Zheng, Shao-Liang; Chen, Yu-Sheng; Nocera, Daniel G



Expanded Substrate Scope and Improved Reactivity of Ether-forming Cross-Coupling Reactions of Organotrifluoroborates and Acetals  

PubMed Central

Mixed acetals and organotrifluoroborates undergo BF3•OEt2 promoted cross-couplings to give dialkyl ethers under simple, mild conditions. A survey of reaction partners identified a hydroxamate leaving group that improves the regioselectivity and product yield in the BF3•OEt2-promoted coupling reaction of mixed acetals and potassium alkynyl-, alkenyl-, aryl- and heteroaryltrifluoroborates to access substituted dialkyl ethers. This leaving group enables reaction to proceed rapidly under mild conditions (0 °C, 5–60 min) and permits reactions with electron-deficient potassium aryltrifluoroborates that were less reactive with other acetal substrates. A study of the reaction mechanism and characterization of key intermediates by NMR and X-ray crystallography identified a role for the hydroxamate moiety as a reversible leaving group that serves to stabilize the key oxocarbenium intermediate and the need for a slight excess of organodifluoroborane to serve as a catalyst. A secondary role as an activating ligand for the boron nucleophile is also considered. These studies provide the basis for a general class of reagents that lead to dialkyl ethers by a simple, predictable cross-coupling reaction. PMID:21776986

Vo, Cam-Van T.; Mitchell, T. Andrew; Bode, Jeffrey W.



Cestina pro Pokrocile (Intermediate Czech).  

ERIC Educational Resources Information Center

The textbook in intermediate Czech is designed for second-year students of the language and those who already have a basic knowledge of Czech grammar and vocabulary. It is appropriate for use in a traditional college language classroom, the business community, or a government language school. It can be covered in a year-long conventional…

Kabat, Grazyna; And Others


Learning through Literature: Geography, Intermediate.  

ERIC Educational Resources Information Center

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

Sterling, Mary Ellen


Intermediate Filaments: A Historical Perspective  

PubMed Central

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

Oshima, Robert G.



Nuclear photoabsorption and Compton scattering at intermediate energy  

Microsoft Academic Search

Intermediate energy nuclear photoabsorption and Compton scattering within the approach are studied. The same dynamics used to describe a variety of pion-induced reactions are employed. A dynamical model for the photon-nucleon amplitude is constructed, including both resonant-channel and nonresonant backgrounds in addition to Medium corrections to the full amplitude are included for nuclear scattering. A doorway state

J. H. Koch; E. J. Moniz; N. Ohtsuka



Molluscicidal saponins from Anagallis arvensis against schistosome intermediate hosts.  


The molluscicidal activity of saponins isolated from the plant Anagallis arvensis (Primulaceae) was studied against schistosome intermediate hosts, Biomphalaria glabrata and Oncomelania quadrasi. @Strong molluscicidal activity was found in two compounds called desglucoanagalloside B and anagalloside B. Their structures were identified on the basis of chemical and spectroscopic analyses and their activities are comparable to that of the synthetic molluscicide, niclosamide. PMID:10777853

Abdel-Gawad, M M; El-Amin, S M; Ohigashi, H; Watanabe, Y; Takeda, N; Sugiyama, H; Kawanaka, M



Error Analysis in Composition of Iranian Lower Intermediate Students  

ERIC Educational Resources Information Center

Learners make errors during the process of learning languages. This study examines errors in writing task of twenty Iranian lower intermediate male students aged between 13 and 15. A subject was given to the participants was a composition about the seasons of a year. All of the errors were identified and classified. Corder's classification (1967)…

Taghavi, Mehdi



Lexical Patterns in the Eyes of Intermediate EFL Readers  

ERIC Educational Resources Information Center

Hoey (1991) claims that lexical patterns, which are a network of repetitious and synonymous words of a text, can be identified even by elementary foreign language readers. The present study investigates whether intermediate Japanese EFL readers can actually find elements of lexical patterns of a text Hoey uses in his book to demonstrate the…

Yamada, Kyoko



Alder-ene reactions of arynes.  


Efficient Alder-ene reactions of various arynes generated directly from bis-1,3-diynes are described. The reactivity of ene donors with different tethers was examined under thermal and metal-catalyzed conditions, which indicates that both the formation of aryne intermediates and their ene reactions are less sensitive to the catalyst than to the structural features of the substrates. PMID:23540274

Karmakar, Rajdip; Mamidipalli, Phani; Yun, Sang Young; Lee, Daesung



Ketonic decarboxylation reaction mechanism: a combined experimental and DFT study.  


The ketonic decarboxylation of carboxylic acids has been carried out experimentally and studied theoretically by DFT calculations. In the experiments, monoclinic zirconia was identified as a good catalyst, giving high activity and high selectivity when compared with other potential catalysts, such as silica, alumina, or ceria. It was also shown that it could be used for a wide range of substrates, namely, for carboxylic acids with two to eighteen carbon atoms. The reaction mechanism for the ketonic decarboxylation of acetic acid over monoclinic zirconia was investigated by using a periodic DFT slab model. A reaction pathway with the formation of a ?-keto acid intermediate was considered, as well as a concerted mechanism, involving simultaneous carbon-carbon bond formation and carbon dioxide elimination. DFT results showed that the mechanism with the ?-keto acid was the kinetically favored one and this was further supported by an experiment employing a mixture of isomeric (linear and branched) pentanoic acids. PMID:23203990

Pulido, Angeles; Oliver-Tomas, Borja; Renz, Michael; Boronat, Mercedes; Corma, Avelino



Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines).  


Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process. PMID:20508855

Klink, Vincent P; Overall, Christopher C; Alkharouf, Nadim W; Macdonald, Margaret H; Matthews, Benjamin F



Photo-fenton degradation of diclofenac: identification of main intermediates and degradation pathway.  


In recent years, the presence of pharmaceuticals in the aquatic environment has been of growing interest. These new contaminants are important because many of them are not degraded under the typical biological treatments applied in the wastewater treatment plants and represent a continuous input into the environment. Thus, compounds such as diclofenac are present in surface waters in all Europe and a crucial need for more enhanced technologies that can reduce its presence in the environment has become evident. In this sense, advanced oxidation processes (AOPs) represent a good choice for the treatment of hazardous nonbiodegradable pollutants. This work deals with the solar photodegradation of diclofenac, an antiinflammatory drug, in aqueous solutions by photo-Fenton reaction. A pilot-scale facility using a compound parabolic collector (CPC) reactor was used for this study. Results obtained show rapid and complete oxidation of diclofenac after 60 min, and total mineralization (disappearance of dissolved organic carbon, DOC) after 100 min of exposure to sunlight. Although diclofenac precipitates during the process at low pH, its degradation takes place in the homogeneous phase governed by a precipitation-redissolution-degradation process. Establishment of the reaction pathway was made possible by a thorough analysis of the reaction mixture identifying the main intermediate products generated. Gas chromatography-mass spectrometry (GC/ MS) and liquid chromatography coupled with time-of-flight mass spectrometry (LC/TOF-MS) were used to identify 18 intermediates, in two tentative degradation routes. The main one was based on the initial hydroxylation of the phenylacetic acid moiety in the C-4 position and subsequent formation of a quinone imine derivative that was the starting point for further multistep degradation involving hydroxylation, decarboxylation, and oxidation reactions. An alternative route was based on the transient preservation of the biphenyl amino moiety that underwent a similar oxidative process of C-N bond cleavage. The proposed degradation route differs from those previously reported involving alternative degradation processes (ozonization, UV/H2O2, or photolysis), indicating that diclofenac degradation follows different pathways, depending on the treatment applied. PMID:16294867

Pérez-Estrada, Leónidas A; Malato, Sixto; Gernjak, Wolfgang; Agüera, Ana; Thurman, E Michael; Ferrer, Imma; Fernández-Alba, Amadeo R



Supramolecular Non-Amyloid Intermediates in the Early Stages of ?-Synuclein Aggregation  

PubMed Central

The aggregation of ?-synuclein is associated with progression of Parkinson's disease. We have identified submicrometer supramolecular structures that mediate the early stages of the overall mechanism. The sequence of structural transformations between metastable intermediates were captured and characterized by atomic force microscopy guided by a fluorescent probe sensitive to preamyloid species. A novel ?0.3–0.6 ?m molecular assembly, denoted the acuna, nucleates, expands, and liberates fibers with distinctive segmentation and a filamentous fuzzy fringe. These fuzzy fibers serve as precursors of mature amyloid fibrils. Cryo-electron tomography resolved the acuna inner structure as a scaffold of highly condensed colloidal masses interlinked by thin beaded threads, which were perceived as fuzziness by atomic force microscopy. On the basis of the combined data, we propose a sequential mechanism comprising molecular, colloidal, and fibrillar stages linked by reactions with disparate temperature dependencies and distinct supramolecular forms. We anticipate novel diagnostic and therapeutic approaches to Parkinson's and related neurodegenerative diseases based on these new insights into the aggregation mechanism of ?-synuclein and intermediates, some of which may act to cause and/or reinforce neurotoxicity. PMID:22404935

Fauerbach, Jonathan A.; Yushchenko, Dmytro A.; Shahmoradian, Sarah H.; Chiu, Wah; Jovin, Thomas M.; Jares-Erijman, Elizabeth A.



Nuclear data uncertainties in intermediate neutron spectrum problems and the intermediate neutron spectrum experiment  

SciTech Connect

During the investigation of various surplus fissile material disposition proposals, uncertainties in the data of SiO{sub 2}/Pu mixtures were discovered. These uncertainties were detected for Si/Pu ratios ranging from approximately 20:1 to 200:1. Additionally, it has been reported that metal/U{sup 235} mixtures also have data uncertainties. These problems with large data uncertainties are typically intermediate spectrum problems, i.e. problems which are dominated by scattering and fissions occurring in the energy range of 10 eV to 1 MeV. ANSI/ANS-8.1-1983 states that the ``bias shall be established by correlating the results of criticality experiments with the results obtained for these same systems by the method being validated``. There is however, a definite lack of critical experiments with an intermediate neutron spectrum. We have identified two potential areas from which these uncertainties may arise. The first potential source of uncertainty in the nuclear data is due to fact that the cross-sections of the fissile material have not been tested in an intermediate energy spectrum. The second potential source of uncertainty is that the non-fissile material in the mixture may not have been appropriately tested in a critical experiment. To provide this benchmark data a critical experiment is necessary.

Jaegers, P.J.; Hayes, D.; Sanchez, R.G.; Kimpland, R.H.



A Caged, Destabilized Free Radical Intermediate in the Q Cycle  

PubMed Central

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

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




PubMed Central

Sebek, Oldrich K. (The Upjohn Company, Kalamazoo, Mich.), Lester M. Reineke, and Durey H. Peterson. Intermediates in the metabolism of steroids by Penicillium lilacinum. J. Bacteriol. 83:1327–1331. 1962—Nonproliferating cells of Penicillium lilacinum (Thom) metabolized progesterone successively to 20-?-hydroxy-4-pregnen-3-one, testosterone, androstenedione, and testololactone. Testosterone and androstenedione were readily interconvertible. 11-?-Hydroxyprogesterone was transformed in an analogous way and its intermediate, 11-?, 20-?-dihydroxy-4-pregnen-3-one, was isolated and identified by a combination of microbiological and chemical methods. PMID:16561948

Sebek, Oldrich K.; Reineke, Lester M.; Peterson, Durey H.



Mechanics of vimentin intermediate filaments  

NASA Technical Reports Server (NTRS)

It is increasingly evident that the cytoskeleton of living cells plays important roles in mechanical and biological functions of the cells. Here we focus on the contribution of intermediate filaments (IFs) to the mechanical behaviors of living cells. Vimentin, a major structural component of IFs in many cell types, is shown to play an important role in vital mechanical and biological functions such as cell contractility, migration, stiffness, stiffening, and proliferation.

Wang, Ning; Stamenovic, Dimitrijie



Price Theory: An Intermediate Text  

NSDL National Science Digital Library

David D. Friedman, Professor of Law at Santa Clara University, has made his textbook, "Price Theory: An Intermediate Text" available on the web. The book focuses on trying to teach students the "economic way of thinking" and the "analytical core of economics -- price theory." Topics covered include consumer choice, market structure and economic efficiency. Price Theory also contains chapters on less conventional topics such as the political marketplace, the economics of law and law breaking; and the economics of love and marriage.

Friedman, David D.



Fundamentals of flight, intermediate text  

NSDL National Science Digital Library

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

Aerospace, Cislunar



A Unified Theory of Chemical Reactions  

E-print Network

We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent. Our theory reveals the existence of an intermediate situation between ionic and covalent which may be almost barrierless and isoenegetic and which should be of high interest for understanding biochemistry.

Aubry, S



MCNP6 fragmentation of light nuclei at intermediate energies  

NASA Astrophysics Data System (ADS)

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

Mashnik, Stepan G.; Kerby, Leslie M.



MCNP6 fragmentation of light nuclei at intermediate energies  

E-print Network

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

Stepan G. Mashnik; Leslie M. Kerby



Intermediate Level Science Core Curriculum, Grades 5-8  

NSDL National Science Digital Library

This guide is intended to assist teachers and supervisors for grades 5-8 as they prepare curriculum, instruction, and assessment for intermediate-level content and skills of the New York State Learning Standards for Mathematics, Science, and Technology. This Core Curriculum is not a syllabus. It addresses only the content and skills to be tested by the Intermediate Level Science Assessment. The document identifies process skills and describes their alignments with standards, key ideas, and performance indicators. It includes a description of the content of the Intermediate Level Science Examination and a set of examples of activities intended to build skills to support standards on scientific inquiry, the living environment, and the physical setting.


Microfabricated electrochemiluminescence cell for chemical reaction detection  


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

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



Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction  

SciTech Connect

The reaction of the ground state methylidyne radical CH (X2Pi) with pyrrole (C4H5N) has been studied in a slow flow tube reactor using Multiplexed Photoionization Mass Spectrometry coupled to quasi-continuous tunable VUV synchrotron radiation at room temperature (295 K) and 90 oC (363 K), at 4 Torr (533 Pa). Laser photolysis of bromoform (CHBr3) at 248 nm (KrF excimer laser) is used to produce CH radicals that are free to react with pyrrole molecules in the gaseous mixture. A signal at m/z = 79 (C5H5N) is identified as the product of the reaction and resolved from 79Br atoms, and the result is consistent with CH addition to pyrrole followed by Helimination. The Photoionization Efficiency curve unambiguously identifies m/z = 79 as pyridine. With deuterated methylidyne radicals (CD), the product mass peak is shifted by +1 mass unit, consistent with the formation of C5H4DN and identified as deuterated pyridine (dpyridine). Within detection limits, there is no evidence that the addition intermediate complex undergoes hydrogen scrambling. The results are consistent with a reaction mechanism that proceeds via the direct CH (CD) cycloaddition or insertion into the five-member pyrrole ring, giving rise to ring expansion, followed by H atom elimination from the nitrogen atom in the intermediate to form the resonance stabilized pyridine (d-pyridine) molecule. Implications to interstellar chemistry and planetary atmospheres, in particular Titan, as well as in gas-phase combustion processes, are discussed.

Soorkia, Satchin; Taatjes, Craig A.; Osborn, David L.; Selby, Talitha M.; Trevitt, Adam J.; Wilson, Kevin R.; Leone, Stephen R.



Direct detection of pyridine formation by the reaction of CH (CD) with pyrrole: a ring expansion reaction.  


The reaction of the ground state methylidyne radical CH (X(2)Pi) with pyrrole (C(4)H(5)N) has been studied in a slow flow tube reactor using Multiplexed Photoionization Mass Spectrometry coupled to quasi-continuous tunable VUV synchrotron radiation at room temperature (295 K) and 363 K, at 4 Torr (533 Pa). Laser photolysis of bromoform (CHBr(3)) at 248 nm (KrF excimer laser) is used to produce CH radicals that are free to react with pyrrole molecules in the gaseous mixture. A signal at m/z = 79 (C(5)H(5)N) is identified as the product of the reaction and resolved from (79)Br atoms, and the result is consistent with CH addition to pyrrole followed by H-elimination. The photoionization efficiency curve unambiguously identifies m/z = 79 as pyridine. With deuterated methylidyne radicals (CD), the product mass peak is shifted by +1 mass unit, consistent with the formation of C(5)H(4)DN and identified as deuterated pyridine (d-pyridine). Within detection limits, there is no evidence that the addition intermediate complex undergoes hydrogen scrambling. The results are consistent with a reaction mechanism that proceeds via the direct CH (CD) cycloaddition or insertion into the five-member pyrrole ring, giving rise to ring expansion, followed by H atom elimination from the nitrogen atom in the intermediate to form the resonance stabilized pyridine (d-pyridine) molecule. Implications to interstellar chemistry and planetary atmospheres, in particular Titan, as well as gas-phase combustion processes, are discussed. PMID:20463997

Soorkia, Satchin; Taatjes, Craig A; Osborn, David L; Selby, Talitha M; Trevitt, Adam J; Wilson, Kevin R; Leone, Stephen R



PETER POULAY SPECIAL ISSUE, editor in charge H. F. SCAEFER The Mechanism of a Barrierless Reaction  

E-print Network

of those encountered in TSs of CC bond forming reactions; c) a nucleophilic attack phase, in which charge Reaction: Hidden Transition State and Hidden Intermediates in the Reaction of Methylene with Ethene Hyun: The chelotropic addition reaction of singlet methylene to ethene yielding cyclopropane (reaction 1

Quapp, Wolfgang


Special Reactions  

NSDL National Science Digital Library

The basics of chemical reactions were covered in the first chemistry book, including how to write and balance chemical equations that represent those reactions. There is also a quick review of chemical reactions in Chapter 1 of this book. We're going to d

Robertson, William C.



Enzyme Reactions  

NSDL National Science Digital Library

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

School, Minerva D.



Chemical Reactions  

NSDL National Science Digital Library

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

National Science Teachers Association (NSTA)



Reversible Reactions  

NSDL National Science Digital Library

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

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



Nuclear Reactions  

Microsoft Academic Search

Nuclear reactions generate energy in nuclear reactors, in stars, and are responsible for the existence of all elements heavier than hydrogen in the universe. Nuclear reactions denote reactions between nuclei, and between nuclei and other fundamental particles, such as electrons and photons. A short description of the conservation laws and the definition of basic physical quantities is presented, followed by

C. A. Bertulani



Ozone dissociation to oxygen affected by Criegee intermediate.  


The detailed potential energy surfaces for the reactions of Criegee intermediate (CI, H2COO) and formaldehyde (H2CO) with ozone (O3) have been investigated at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311++G(2d,2p) level of theory, respectively. New alternative reaction mechanisms, to the one previously proposed (J. Phys. Chem. Lett. 2013, 4, 2525) have been found. The lower barrier of the new mechanism shows that it is easy for H2COO + O3 to dissociate to formaldehyde and oxygen. For the reactions of H2CO with O3 to produce H2COO and O2, we find relatively high energy barriers, which makes the ozone dissociation to oxygen unlikely to be catalyzed by CI. PMID:24527808

Wei, Wen-Mei; Zheng, Ren-Hui; Pan, Yue-Li; Wu, Yun-Kai; Yang, Fan; Hong, Shi



A photochromic diode with a continuum of intermediate states: towards high density multilevel storage.  


A continuum of intermediate states (current levels) is demonstrated for an organic diode utilizing a photochromic (dithienylethene) switching layer. Specific intermediate states can be attained by controlling the fraction of closed isomer (X) in the transduction layer, affording a novel methodology for multilevel storage applications. The analog response of the device is discussed in terms of the concentration and morphology of closed dithienylethene isomer, which can be accessed via optical and electrical switching reactions. PMID:23847026

Shallcross, R Clayton; Körner, Peter O; Maibach, Eduard; Köhnen, Anne; Meerholz, Klaus



Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis  

PubMed Central

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

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



Intermediate Filaments as Signaling Platforms  

NSDL National Science Digital Library

Intermediate filaments (IFs) are cytoskeletal structures that are crucial for maintaining the structural and mechanical integrity of cells and tissues. Intriguingly, a wide range of previously unknown nonmechanical roles for the IF cytoskeleton are emerging: Recent studies have linked IFs to the integration of signals related to the determination of cell size, the regulation of cell migration and cell survival, and the buffering of the effects of stress-activated kinases. The characteristic structural features and expression patterns of the different members of this diverse family of highly abundant proteins make them well suited to act as cell- and tissue-specific modifiers and organizers of signaling.

Hanna-Mari Pallari (University of Turku and Abo Akademi University;Turku Centre for Biotechnology REV); John E. Eriksson (University of Turku and Abo Akademi University;Turku Centre for Biotechnology REV)



Reaction of Carbohydrates and Pentacoordinate Oxaphosphorane and Their Biomimetic Mechanism  

Microsoft Academic Search

The reaction of D-hexoses, D-pentose and organic pentacoordinate 1,3,2-dioxaphospholene were investigated. The observation showed that there were obvious differences of reaction ratio. Intermediate, and final products in the reactions between hexoses and pentose via pentacoordinate phosphorus compound. The results should give significant clue to the metabolic mechanism of carbohydrate phosphate in nature.

Yong Ju; Jian-Jun Hu; Yu-Fen Zhao



Spectral observation of an acyl-enzyme intermediate of lipoprotein lipase.  


There have been several studies indicating that hydrolysis reactions of fatty acid esters catalyzed by lipases proceed through an acyl-enzyme intermediate typical of serine proteases. In particular, one careful kinetic study with the physiologically important enzyme lipoprotein lipase (LPL) is consistent with rate-limiting deacylation of such an intermediate. To observe the spectrum of acyl-enzyme and study the mechanism of LPL-catalyzed hydrolysis of substrate, we have used a variety of furylacryloyl substrates including 1,2-dipalmitoyl-3-[(beta-2-furylacryloyl)triacyl]glyceride (DPFATG) to study the intermediates formed during the hydrolysis reaction catalyzed by the enzyme. After isolation and characterization of the molecular weight of adipose LPL, we determined its extinction coefficient at 280 nm to quantitate the formation of any acyl-enzyme intermediate formed during substrate hydrolysis. We observed an intermediate at low pH during the enzyme-catalyzed hydrolysis of (furylacryloyl)imidazole. This intermediate builds early in the reaction when a substantial amount of substrate has hydrolyzed but no product, furylacrylate, has been formed. The acyl-enzyme has a lambda max = 305 nm and a molar extinction coefficient of 22,600 M-1 cm-1; these parameters are similar to those for furylacryloyl esters including the serine ester. These data provide the first spectral evidence for a serine acyl-enzyme in lipase-catalyzed reactions. The LPL hydrolysis reaction is base catalyzed, exhibiting two pKa values; the more acidic of these is 6.5, consistent with base catalysis by histidine. The biphasic rates for substrate disappearance or product appearance and the absence of leaving group effect indicate that deacylation of intermediate is rate limiting. PMID:2765496

Rojas, C; Wang, H H; Lively, C R; Gustafson, W G; Schulz, L O; McFarland, J T



Reaction of zirconium alkoxides with tert -butyl hydroperoxide. Oxidative ability of the Zr(OBu- t ) 4 - t -BuOOH system  

Microsoft Academic Search

Oxidation of the isopropoxy group in the Zr(i-PrO)4i-PrOH complex involves both direct reaction with tert-butyl hydroperoxide and intermediate formation of zirconium peroxy compound. Zirconium tetra-tert-butoxide reacts with tert-bytyl hydroperoxide to form metal-containing peroxide and trioxide. Decomposition of the latter leads to oxygen evolution\\u000a and is accompanied by radical formation. The alkoxyl and peroxyl radicals formed were identified by ESR spectroscopy.

M. V. Gulenova; L. P. Stepovik; V. K. Cherkasov



Storage Stability and Improvement of Intermediate Moisture Foods, Phase 3  

NASA Technical Reports Server (NTRS)

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

Labuza, T. P.



Azoxy rearrangement reactions  

NASA Astrophysics Data System (ADS)

The mechanisms of several types of azoxy compound (XN(O)NY) rearrangement reactions have been studied using density functional theory (DFT) with the B3LYP exchange-correlation potential. The substituents X and Y are taken from the set H, CH , F, C H , Cl and CN. The 6-311 + G(d,p) basis set was used to optimize up to ten equilibrium and transition state structures for a given pair of X and Y substituents; except for azoxybenzene where a 6- 311(+)G(d) basis set was used. All geometric structures were characterized by a frequency calculation. The reaction path for converting XN (O)N Y to XN N (O)Y via a concerted intramolecular shift of the oxygen atom from N to N involves three equilibrium and two saddle-point structures. The relatively high (about 70-80 kcalmol1) calculated barrier height to reaction and its independence of the nature of the X and Y substituents is attributed to characteristic orbital, atomic charge and structural factors along the reaction path. Cis trans isomerization across N-- N in the NH(O)NH azoxy compound and across N-N in the ring XNONY oxadiaziridine intermediate is found to have a barrier height of at least - 1 about 30 kcalmol . Single-point CCSD(T)/DFT energy differences are found to be somewhat smaller than the DFT calculated values. 3 6 5

Basch, Harold; Hoz, Tova


Intermediate Accounting II Spring 2012  

E-print Network

allocation processes. To learn the conceptual framework underlying Financial Accounting and Financial recognition. To learn basic "forensic accounting", by identifying the areas susceptible to earnings

Carter, John


Biasing a transition state search to locate multiple reaction pathways  

NASA Astrophysics Data System (ADS)

A variety of chemical systems exhibit multiple reaction pathways that adjoin to a common reactant state. In fact, any reaction producing side products or proceeding via a stable intermediate involves a species possessing at least two reaction pathways. Despite improvements in ab initio transition-state search algorithms it remains difficult to detect multiple reaction pathways. Typically, multiple reaction pathways can only be detected by intuitively varying the initial point in the transition-state search trajectory. This reliance on intuition limits the ability to discover new and unexpected chemistry using ab initio methods. This paper proposes a systematic and intuition-free method for biasing a transition-state search to identify multiple reaction pathways originating from a common reactant state. The method allows the successive location of transition states, with each successful search contributing to a cumulative bias potential for the following search. The method is applicable to all psuedo-Newton-Raphson-type transition-state searches. The procedure was tested for a model potential energy surface and for the thermal rearrangement of trans-1,4-dimethylcyclobutene. In the latter case, four reaction pathways were discovered: two exothermic conrotatory ring openings leading to hexadienes, an endothermic methyl migration pathway leading to a carbene, and an exothermic rearrangement leading to 3-methyl-1,4-pentadiene. In accordance with experiment, the calculations predict that the conrotatory pathway leading to trans,trans-2,4-hexadiene is the kinetically dominant pathway. The methodology was also used to compute selectivities for competitive pathways producing trans and cis triflouropentadiene products in the thermal rearrangement of 3-triflouromethyl-cyclobutene. Again, results were in accord with experimental observations.

Peters, Baron; Liang, WanZhen; Bell, Alexis T.; Chakraborty, Arup



Transient state kinetic investigation of 5-aminolevulinate synthase reaction mechanism.  


5-Aminolevulinate synthase (ALAS), a pyridoxal 5'-phosphate-dependent enzyme, catalyzes the first, and regulatory, step of the heme biosynthetic pathway in nonplant eukaryotes and some bacteria. 5-Aminolevulinate synthase is a dimeric protein having an ordered kinetic mechanism with glycine binding before succinyl-CoA and with aminolevulinate release after CoA and carbon dioxide. Rapid scanning stopped-flow absorption spectrophotometry in conjunction with multiple turnover chemical quenched-flow kinetic analyses and a newly developed CoA detection method were used to examine the ALAS catalytic reaction and identify the rate-determining step. The reaction of glycine with ALAS follows a three-step kinetic process, ascribed to the formation of the Michaelis complex and the pyridoxal 5'-phosphate-glycine aldimine, followed by the abstraction of the glycine pro-R proton from the external aldimine. Significantly, the rate associated with this third step (k(3) = 0.002 s(-1)) is consistent with the rate determined for the ALAS-catalyzed removal of tritium from [2-(3)H(2)]glycine. Succinyl-CoA and acetoacetyl-CoA increased the rate of glycine proton removal approximately 250,000- and 10-fold, respectively, supporting our previous proposal that the physiological substrate, succinyl-CoA, promotes a protein conformational change, which accelerates the conversion of the external aldimine into the initial quinonoid intermediate (Hunter, G. A., and Ferreira, G. C. (1999) J. Biol. Chem. 274, 12222-12228). Rapid scanning stopped-flow and quenched-flow kinetic analyses of the ALAS reaction under single turnover conditions lend evidence for two quinonoid reaction intermediates and a model of the ALAS kinetic mechanism in which product release is at least the partially rate-limiting step. Finally, the carbonyl and carboxylate groups of 5-aminolevulinate play a major protein-interacting role by inducing a conformational change in ALAS and, thus, possibly modulating product release. PMID:12191993

Zhang, Junshun; Ferreira, Gloria C



Production and Characterization of Polymeric Lignin Degradation Intermediates from Two Different Streptomyces spp. †  

PubMed Central

Previous investigations have identified a quantitatively major intermediate of lignin degradation by Streptomyces viridosporus. The intermediate, a modified lignin polymer, acid-precipitable polymeric lignin (APPL), is released as a water-soluble catabolite and has been recovered in amounts equivalent to 30% of the lignin originally present in a corn stover lignocellulose substrate after degradation by this actinomycete. In the present work, APPLs were collected at various time intervals from cultures of two highly ligninolytic Streptomyces sp. strains, S. viridosporus T7A and S. badius 252, growing on corn stover lignocellulose. APPL production was measured over time, and the chemistry of APPLs produced by each organism after different time intervals was compared. Chemical characterizations included assays for lignin, carbohydrate, and ash contents, molecular weight distributions by gel permeation chromatography, and chemical degradation analyses by permanganate oxidation, acidolysis, and alkaline ester hydrolysis. Differences between the organisms were observed in the cultural conditions required for APPL production and in the time courses of APPL accumulation. S. viridosporus produced APPL in solid-state fermentation over a 6- to 8-week incubation period, whereas S. badius produced as much or more APPL, but only in liquid culture and over a 7- to 8-day incubation period. The chemistry of the APPLs produced also differed. S. viridosporus APPL was more lignin-like than that of S. badius and was slowly modified further over time, although no change in molecular weight distribution over time was observed. In contrast, S. badius APPL was less lignin-like and increased substantially in average molecular weight over time. Results indicated that differing mechanisms of lignin metabolism may exist in these two Streptomyces sp. strains. S. viridosporus APPL probably originates from the heart of the lignin and is released largely as the result of ?-ether cleavage and other oxidative reactions. S. badius APPL probably originates in the same manner; however, after release as a water-soluble catabolite, lower-molecular-weight intermediates of lignin degradation are repolymerized with APPL in a reaction catalyzed by an extracellular phenol oxidase. The chemical analyses and the presence of extracellular phenol oxidase in S. badius, but not in S. viridosporus, support this conclusion. PMID:16346714

Borgmeyer, Jeffry R.; Crawford, Don L.



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

PubMed Central

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

Xu, Hai-Chao; Moeller, Kevin D.



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


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

Xu, Hai-Chao; Moeller, Kevin D



Intermediate-Luminosity Red Transients  

NASA Astrophysics Data System (ADS)

Intermediate-luminosity red transients (ILRTs) are a recently recognized class of stellar eruptions with maximum luminosities between those of classical novae and supernovae. During their outbursts, which generally last a few months, they typically evolve to extremely red colors, completely unlike novae. Prototypes include the M31 "Red Variable" of 1988, V838 Mon, SN 2008S, V1309 Sco, the M99 optical transient of 2010, and the 2008 and 2010 ILRTs in the nearby spiral NGC 300. I will present recent developments in the study of ILRTs. At present, it appears that there are (at least) two separate evolutionary channels leading to ILRT outbursts: mergers of close binaries (accounting for ILRTs in old populations and possibly V838 Mon), and eruptions on stars of about 8-12 Msun, possibly due to electron-capture SNe (accounting for ILRTs in young populations).

Bond, Howard E.; Humphreys, R. M.; Bedin, L. R.; Bonanos, A.; Davidson, K.; Monard, B.; Prieto, J.; Walter, F.



Thermal Runaway during Intermediate-Depth Earthquake Rupture  

NASA Astrophysics Data System (ADS)

Intermediate-depth earthquakes occur at depths of 50 to 300 km in subducting lithosphere. Despite their ubiquity in earthquake catalogs, their physical mechanism remains unclear because ambient temperatures and pressures are expected to lead to ductile, rather than brittle deformation. There are two leading explanations for the physical mechanism that enables these earthquakes. In the first, high pore pressure from metamorphic dehydration reactions in the subducting slab reduces the effective normal stress sufficiently to enable frictional failure. In the second, slow deformation generates heat, which leads to weakening, further deformation, and a self-localizing thermal shear runaway. We use the nest of intermediate-depth earthquakes under Bucaramanga, Colombia as recorded by the digital RSNC (Red Sísmica Nacional de Colombia) regional seismic network to explore these two possibilities. We observe a combination of high stress drop and low radiation efficiency for Mw 4-5 earthquakes in the Bucaramanga Nest that points to the importance of thermal effects. If we assume a cm-scale fault-zone width, this combination implies a temperature increase of 600-1,000ºC during earthquake failure, which suggests that substantial shear heating, and possibly partial melting, occurs during intermediate-depth earthquake failure. Our observations support thermal shear runaway as the mechanism for intermediate-depth earthquakes. This mechanism could help explain differences in their behavior, such as the paucity of aftershocks, compared to shallow earthquakes. Although we have inferred these mechanisms for intermediate depth earthquakes, it's likely that they would apply for rapid deformation on the deep extensions of fault zones as well - particularly during large earthquakes, such as the 2012 Mw 8.6 strike-slip event off Sumatra, which is inferred to have ruptured well into the oceanic mantle.

Prieto, German; Florez, Manuel; Barrett, Sarah; Beroza, Gregory; Pedraza, Patricia; Blanco, Jose; Poveda, Esteban



Nuclear Reactions  

Microsoft Academic Search

Nuclear reactions generate energy in nuclear reactors, in stars, and are\\u000aresponsible for the existence of all elements heavier than hydrogen in the\\u000auniverse. Nuclear reactions denote reactions between nuclei, and between nuclei\\u000aand other fundamental particles, such as electrons and photons. A short\\u000adescription of the conservation laws and the definition of basic physical\\u000aquantities is presented, followed by

C. A. Bertulani; B. Kinematics



On the Presence of Limit-Cycles in a Model Exothermic Chemical Reaction: Sal'nikov's Oscillator with Two Temperature-Dependent Reaction Rates  

Microsoft Academic Search

This paper investigates a model chemical reaction in which a single substance undergoes a two-stage process of decay, first producing an intermediate species and finally giving a product chemical. Each of the two stages involves only simple first-order reaction kinetics, but the governing rate parameter for each of the two reactions is temperature dependent. The reaction vessel is assumed to

Lawrence K. Forbes; Mary R. Myerscough; Brian F. Gray



Stepwise conversion of a single source precursor into crystalline AlN by transamination reaction  

SciTech Connect

Ammonolysis of the monomeric, base-stabilized trisaminoalane Me{sub 3}N-Al[N(H)Dipp)]{sub 3} (Dipp=2,6-{sup i}Pr{sub 2}-C{sub 6}H{sub 3}) yielded Al-N oligomers, which were characterized in detail by solid state NMR spectroscopy ({sup 1}H, {sup 13}C, {sup 15}N, {sup 27}Al) and TGA/DTA. Pyrolysis of as-prepared oligomers at different temperatures in an argon steam yielded carbon-containing black solids, whereas pyrolysis under a steady flow of NH{sub 3} produced pure aluminum nitride (AlN). The role of the pyrolysis temperature and the influence of NH{sub 3} on the formation of crystalline materials were investigated. As-prepared AlN was characterized by solid state NMR spectroscopy ({sup 15}N, {sup 27}Al), X-ray diffraction (XRD), transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). Theoretical calculations were performed in order to identify potential reaction intermediates. - Graphical abstract: Ammonolysis reactions of Me{sub 3}N-Al(NHDipp){sub 3} in liquid NH{sub 3} yielded Al-N oligomers, which can be transformed into nanocrystalline aluminum nitride particles under thermolysis conditions at 1000 deg. C. Theoretical calculations were performed in order to identify potential reaction intermediates.

Schulz, Stephan [Institute of Inorganic Chemistry, University of Duisburg-Essen, Universitaetsstrasse 5-7, 45141 Essen (Germany)], E-mail:; Bauer, Tillmann; Hoffbauer, Wilfried [Institute of Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn (Germany); Schmedt auf der Guenne, Joern [Department of Chemistry and Biochemistry, University of Munich (LMU), Butenandtstr. 5-13, D2.076, 81377 Munich (Germany); Doerr, Markus; Marian, Christel M. [Institute of Theoretical and Computational Chemistry, University of Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf (Germany); Assenmacher, Wilfried [Institute of Inorganic Chemistry, University of Bonn, Roemerstr. 164, 53117 Bonn (Germany)




PubMed Central

An important problem in realizing personalized medicine is the development of methods for identifying disease subtypes using quantitative proteomics. Recently we found that bronchoalveolar lavage (BAL) cytokine patterns contain information about dynamic lung responsiveness. In this study, we examined physiological data from 1048 subjects enrolled in the US Severe Asthma Research Program (SARP) to identify four largely separable, quantitative intermediate phenotypes. Upper extremes in the study population were identified for eosinophil- or neutrophil- predominant inflammation, bronchodilation in response to albuterol treatment, or methacholine sensitivity. We evaluated four different statistical (“machine”) learning methods to predict each intermediate phenotypes using BAL cytokine measurements on a 76 subject subset. Comparison of these models using area under the ROC curve and overall classification accuracy indicated that logistic regression and multivariate adaptive regression splines produced the most accurate methods to predict intermediate asthma phenotypes. These robust classification methods will aid future translational studies in asthma targeted at specific intermediate phenotypes. PMID:20718815

Brasier, Allan R.; Victor, Sundar; Ju, Hyunsu; Busse, William W.; Curran-Everett, Douglas; Bleecker, Eugene; Castro, Mario; Chung, Kian Fan; Gaston, Benjamin; Israel, Elliot; Wenzel, Sally E.; Erzurum, Serpil C.; Jarjour, Nizar N.; Calhoun, William J.



Predicting intermediate phenotypes in asthma using bronchoalveolar lavage-derived cytokines.  


An important problem in realizing personalized medicine is the development of methods for identifying disease subtypes using quantitative proteomics. Recently we found that bronchoalveolar lavage (BAL) cytokine patterns contain information about dynamic lung responsiveness. In this study, we examined physiological data from 1,048 subjects enrolled in the US Severe Asthma Research Program (SARP) to identify four largely separable, quantitative intermediate phenotypes. Upper extremes in the study population were identified for eosinophil- or neutrophil-predominant inflammation, bronchodilation in response to albuterol treatment, or methacholine sensitivity. We evaluated four different statistical ("machine") learning methods to predict each intermediate phenotype using BAL A-cytokine measurements on a 76 subject subset. Comparison of these models using area under the ROC curve and overall classification accuracy indicated that logistic regression and multivariate adaptive regression splines produced the most accurate methods to predict intermediate asthma phenotypes. These robust classification methods will aid future translational studies in asthma targeted at specific intermediate phenotypes. PMID:20718815

Brasier, Allan R; Victor, Sundar; Ju, Hyunsu; Busse, William W; Curran-Everett, Douglas; Bleecker, Eugene; Castro, Mario; Chung, Kian Fan; Gaston, Benjamin; Israel, Elliot; Wenzel, Sally E; Erzurum, Serpil C; Jarjour, Nizar N; Calhoun, William J



Reaction Time  

NSDL National Science Digital Library

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

Science, New Y.



Chemical Reactions  

NSDL National Science Digital Library

We are going go over a general view of reactions to prepare us for our unit on Chemical Reactions! Have fun learning! WARNING: If you are caught looking at ANY other site, without permission, you will be sent to the ALC, and you will not participate in any other computer activities for the rest of the year. Get your worksheet and begin! Overview Take this quiz and have me come over and sign off on your worksheet when you have completed the quiz! Overview Quiz Next let's take a look at what effect the rate of a chemical reaction. Rates of Reactions Another quiz, another check off by me! Rates of Reactions Quiz Now how do we measure how fast a ...

Hicken, Mrs.



ChemTeacher: Single Replacement Reactions  

NSDL National Science Digital Library

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



Expression of intermediate filaments at muscle insertions in human fetuses  

PubMed Central

Desmin and vimentin are intermediate filaments that play crucial roles in the maturation, maintenance and recovery of muscle fibers and mesenchymal cells. The expression of these proteins has not been investigated extensively in human fetuses. In the present study, we examined the immunohistochemical expression of intermediate filaments in skeletal muscles of the head, neck and thorax in 12 mid-term human fetuses at 9–18 weeks of gestation. We also used immunohistochemistry to localize the expression of the myosin heavy chain and silver impregnation to identify the fetal endomysium. Expression of desmin and vimentin was already detectable in intercostal muscle at 9 weeks, especially at sites of muscle attachment to the perichondrium. At this stage, myosin heavy chain was expressed throughout the muscle fibers and the endomysium had already developed. Beginning with punctate expression, the positive areas became diffusely distributed in the muscle fibers. At 15–18 weeks, intermediate filament proteins were extensively expressed in all of the muscles examined. Expression at the bone–muscle interface was continuous with expression along the intramuscular tendon fibres. These results suggest that the development of intermediate filaments begins in areas of mechanical stress due to early muscle contraction. Their initially punctate distribution, as observed here, probably corresponds to the earliest stage of fetal enthesis formation. PMID:20500537

Abe, Shinichi; Rhee, Sun-ki; Osonoi, Makoto; Nakamura, Takuo; Cho, Baik Hwan; Murakami, Gen; Ide, Yoshinobu



Reversible potentials for steps in methanol and formic acid oxidation to CO2; adsorption energies of intermediates on the ideal electrocatalyst for methanol oxidation and CO2 reduction.  


Quantum chemical theory is used to identify the reasons for platinum's limitations as an electrocatalyst for oxidizing methanol at fuel cell anodes. The linear Gibbs energy relation (LGER) method is employed to predict reversible potentials for reaction steps for intermediates on the electrode surface. In this procedure, standard reversible potentials are calculated for the reactions in bulk solution phase and then they are perturbed using calculated adsorption bond strengths to the electrode surface, yielding the equilibrium potentials for each electron transfer step for adsorbed intermediates. Adsorption properties of ideal electrocatalysts for the methanol oxidation are found by imposing the condition that the reversible potential of each electron transfer step equals that for the overall reaction. The adsorption bond strengths that provide the ideal properties also apply to formic acid oxidation and carbon dioxide reduction. It is instructive to think of the ideal electrocatalyst as a lens that focusses the reversible potentials for the n individual electron transfer steps to the reversible potential for the n-electron process. It is found that the ideal catalyst will adsorb many intermediates, including HOOC, CO, OCH, HOC, HOCH, HOCH2, and OCH3 more weakly than platinum, and OOCH and OH more strongly. For example, for one possible pathway it is necessary to weaken adsorption bond strengths for HOCH2, HOCH, OCH, HOOC by about 0.5 eV, weaken adsorption CO by about 1.1 eV and strengthen OH adsorption by about 0.6 eV. These results imply a need for developing new multi-component catalysts. PMID:24741672

Anderson, Alfred B; Asiri, Haleema Aied



Copper-Catalyzed Oxidative Heck Reactions between Alkyltrifluoroborates and Vinylarenes  

PubMed Central

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

Liwosz, Timothy W.; Chemler, Sherry R.



Development of an HPLC assay for Staphylococcus aureus sortase: Evidence for the formation of the kinetically competent acyl enzyme intermediate  

Microsoft Academic Search

Many bacterial surface proteins containing an LPXTG motif are anchored to the cell wall peptidoglycan by catalysis with the thiol transpeptidase sortase. The transpeptidation and hydrolysis reactions of sortase have been proposed to proceed through a common acyl enzyme intermediate. The reactions of Staphylococcus aureus sortase with fluorogenic substrate Abz-LPETG-Dnp in the presence or absence of triglycine were characterized in

Ann Aulabaugh; Weidong Ding; Bhupesh Kapoor; Keiko Tabei; Lefa Alksne; Russ Dushin; Tracy Zatz; George Ellestad; Xinyi Huang



The heterogeneous photocatalytic degradation, intermediates and mineralization for the aqueous solution of cresols and nitrophenols  

Microsoft Academic Search

This investigation was initiated to study the heterogeneous photocatalytic reactions of cresols and nitrophenols with ultraviolet light\\/titanium dioxide (UV\\/TiO2) system. The experimental parts consisted of pH effect, determination of intermediates and mineralization. At pH 7 and a concentration of 0.1 mM, cresols and nitrophenols nearly disappeared after 2.5 h of reaction time. Under various pH levels, the pseudo first order

Kuo-Hua Wang; Yung-Hsu Hsieh; Lih-Jinn Chen



Possible Observation of the ^3A' - ^1A' Electronic Transition of the Methylene Peroxy Criegee Intermediate  

NASA Astrophysics Data System (ADS)

It is possible that we have observed for the first time the transition from the ground ^1A' state to the low lying ^3A' state of the methylene peroxy Criegee intermediate, CH_2O_2, which is otherwise known as carbonyl or formaldehyde oxide. Criegee intermediates are reactive intermediates that are formed in the ozonolysis of olefins in both liquid and gaseous phases with the methylene peroxy intermediate being formed specifically from the ozonolysis of ethene. In the atmosphere Criegee intermediates are formed in reactions that lead to secondary organic aerosols and participate in reactions with SO_2 and NO_2. A peroxy-like spectrum was observed in the near-IR using cavity ringdown spectroscopy after photolysis of a diiodomethane precursor at 248 nm followed by a reaction with O_2. Possible assignment of the spectrum to CH_2O_2 is based on a strong analogy between the electronic structure of methylene peroxy and ozone. However experiments and electronic structure calculations are continuing to positively attribute the spectrum to either CH_2O_2 or CH_2IO_2 which could also be formed by this chemistry.

Kline, Neal D.; Miller, Terry A.; Coons, Marc; Herbert, John



Time sequence and time scale of intermediate mass fragment emission  

SciTech Connect

Semiperipheral collisions in the {sup 124}Sn+{sup 64}Ni reaction at 35 MeV/nucleon were studied using the forward part of the Charged Heavy Ion Mass and Energy Resolving Array. Nearly completely determined ternary events involving projectilelike fragments (PLF), targetlike fragments (TLF), and intermediate mass fragments (IMF) were selected. A new method of studying the reaction mechanism, focusing on the analysis of the correlations between relative velocities in the IMF+PLF and IMF+TLF subsystems, is proposed. The relative velocity correlations provide information on the time sequence and time scale of the neck fragmentation processes leading to production of IMFs. It is shown that the majority of light IMFs are produced within 40-80 fm/c after the system starts to reseparate. Heavy IMFs are formed at times of about 120 fm/c or later and can be viewed as resulting from two-step (sequential) neck rupture processes.

De Filippo, E.; Pagano, A.; Cardella, G.; Lanzano, G.; Papa, M.; Pirrone, S.; Politi, G. [INFN, Sezione di Catania and Dipartimento di Fisica e Astronomia, Universita di Catania (Italy); Wilczynski, J. [A. Soltan Institute for Nuclear Studies, Swierk/Warsaw (Poland); Amorini, F.; Anzalone, A.; Baran, V.; Bonasera, A.; Cavallaro, S.; Colonna, M.; Di Toro, M.; Giustolisi, F.; Iacono-Manno, M.; La Guidara, E.; Lanzalone, G.; Maiolino, C. [INFN, Laboratori Nazionali del Sud and Dipartimento di Fisica e Astronomia, Universita di Catania (Italy)] [and others



Chromospheric Activity at Intermediate Ages  

NASA Astrophysics Data System (ADS)

The calibration of the empirical relation between Ca II chromospheric strength and stellar age between 0.6 Gyr (Hyades) and 4.0 - 5 Gyr (M67 and the Sun) relies on the uncertain determination of ages for individual field stars in the solar neighborhood. We therefore propose to obtain WIYN/Hydra spectra of ~ 100 solar-type dwarf stars in the 1.8 Gyr old open cluster, NGC 752. This cluster contains a sample of solar-type dwarfs that is homogeneous in age and chemical composition. Furthermore, NGC 752 is the nearest-and hence brightest- cluster at an age ~ 2 Gyr. The results will yield an improved calibration of the age-activity relation at intermediate ages. In addition, we will determine if the chromospheric Ca II strengths for the solar-type stars in NGC 752 lie in the so-called "Vaughan-Preston Gap''- an apparent discontinuity in the Ca II H& K strength-(B-V) diagram found for field stars in the solar neighborhood. Our data will yield insight on the two proposed origins for the gap, namely, that it is a result of two different modes of dynamo action or that it is actually an artifact of a discontinuity in the local star formation rate. This is a resubmission of a previously approved proposal that was allocated two nights in 2004 November. The time was lost to instrument problems (Hydra gripper malfunctions) and weather. No usable data were obtained.

Giampapa, Mark; Stauffer, John; Deliyannis, Constantine; Sherry, William



Modeling of intermediate phase growth  

SciTech Connect

We introduced a continuum method for modeling of intermediate phase growth and numerically simulated three common experimental situations relevant to the physical metallurgy of soldering: growth of intermetallic compound layer from an unlimited amount of liquid and solid solders and growth of the compound from limited amounts of liquid solder. We found qualitative agreements with the experimental regimes of growth in all cases. For instance, the layer expands in both directions with respect to the base line when it grows from solid solder, and grows into the copper phase when the solder is molten. The quantitative agreement with the sharp-interface approximation was also achieved in these cases. In the cases of limited amounts of liquid solder we found the point of turnaround when the compound/solder boundary changed the direction of its motion. Although such behavior had been previously observed experimentally, the simulations revealed important information: the turnaround occurs approximately at the time of complete saturation of solder with copper. This result allows us to conclude that coarsening of the intermetallic compound structure starts only after the solder is practically saturated with copper.

Umantsev, A. [Department of Natural Sciences, Fayetteville State University, 1200 Murchison Road, Fayetteville, North Carolina 28301 (United States)



Modeling of intermediate phase growth  

NASA Astrophysics Data System (ADS)

We introduced a continuum method for modeling of intermediate phase growth and numerically simulated three common experimental situations relevant to the physical metallurgy of soldering: growth of intermetallic compound layer from an unlimited amount of liquid and solid solders and growth of the compound from limited amounts of liquid solder. We found qualitative agreements with the experimental regimes of growth in all cases. For instance, the layer expands in both directions with respect to the base line when it grows from solid solder, and grows into the copper phase when the solder is molten. The quantitative agreement with the sharp-interface approximation was also achieved in these cases. In the cases of limited amounts of liquid solder we found the point of turnaround when the compound/solder boundary changed the direction of its motion. Although such behavior had been previously observed experimentally, the simulations revealed important information: the turnaround occurs approximately at the time of complete saturation of solder with copper. This result allows us to conclude that coarsening of the intermetallic compound structure starts only after the solder is practically saturated with copper.

Umantsev, A.



Heterogeneous reactions of epoxides in acidic media.  


Epoxides have recently been identified as important intermediates in the gas phase oxidation of hydrocarbons, and their hydrolysis products have been observed in ambient aerosols. To evaluate the role of epoxides in the formation of secondary organic aerosols (SOA), the kinetics and mechanism of heterogeneous reactions of two model epoxides, isoprene oxide and ?-pinene oxide, with sulfuric acid, ammonium bisulfate, and ammonium sulfate have been investigated using complementary experimental techniques. Kinetic experiments using a fast flow reactor coupled to an ion drift-chemical ionization mass spectrometer (ID-CIMS) show a fast irreversible loss of the epoxides with the uptake coefficients (?) of (1.7 ± 0.1) × 10(-2) and (4.6 ± 0.3) × 10(-2) for isoprene oxide and ?-pinene oxide, respectively, for 90 wt % H(2)SO(4) and at room temperature. Experiments using attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) reveal that diols are the major products in ammonium bisulfate and dilute H(2)SO(4) (<25 wt %) solutions for both epoxides. In concentrated H(2)SO(4) (>65 wt %), acetals are formed from isoprene oxide, whereas organosulfates are produced from ?-pinene oxide. The reaction of the epoxides with ammonium sulfate is slow and no products are observed. The epoxide reactions using bulk samples and Nuclear Magnetic Resonance (NMR) spectroscopy reveal the presence of diols as the major products for isoprene oxide, accompanied by aldehyde formation. For ?-pinene oxide, organosulfate formation is observed with a yield increasing with the acidity. Large yields of organosulfates in all NMR experiments with ?-pinene oxide are attributed to the kinetic isotope effect (KIE) from the use of deuterated sulfuric acid and water. Our results suggest that acid-catalyzed hydrolysis of epoxides results in the formation of a wide range of products, and some of the products have low volatility and contribute to SOA growth under ambient conditions prevailing in the urban atmosphere. PMID:22309032

Lal, Vinita; Khalizov, Alexei F; Lin, Yun; Galvan, Maria D; Connell, Brian T; Zhang, Renyi



Atomic resolution study of reversible conversion reaction in metal oxide electrodes for lithium-ion battery.  


Electrode materials based on conversion reactions with lithium ions have shown much higher energy density than those based on intercalation reactions. Here, nanocubes of a typical metal oxide (Co3O4) were grown on few-layer graphene, and their electrochemical lithiation and delithiation were investigated at atomic resolution by in situ transmission electron microscopy to reveal the mechanism of the reversible conversion reaction. During lithiation, a lithium-inserted Co3O4 phase and a phase consisting of nanosized Co-Li-O clusters are identified as the intermediate products prior to the subsequent formation of Li2O crystals. In delithiation, the reduced metal nanoparticles form a network and breakdown into even smaller clusters that act as catalysts to prompt reduction of Li2O, and CoO nanoparticles are identified as the product of the deconversion reaction. Such direct real-space, real-time atomic-scale observations shed light on the phenomena and mechanisms in reaction-based electrochemical energy conversion and provide impetus for further development in electrochemical charge storage devices. PMID:25337887

Luo, Langli; Wu, Jinsong; Xu, Junming; Dravid, Vinayak P



Understanding side reactions in k-o2 batteries for improved cycle life.  


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

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



Stochastic operator-splitting method for reaction-diffusion systems  

NASA Astrophysics Data System (ADS)

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

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



Intermediates and the folding of proteins L and G  

SciTech Connect

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

Brown, Scott; Head-Gordon, Teresa



Dynamic Effects in Nucleophilic Substitution Reactions  

E-print Network

selectivities that are determined by dynamic effects. Those with poorer leaving groups are more likely to do so in a stepwise fashion via a tetrahedral intermediate. Experimental Section General All reactions were carried out in oven dried glassware... and in most cases; freshly purified, dry solvents were used. All chemicals used were obtained commercially and 4.5 ? molecular sieves were added to solvents to maintain dryness when necessary. The reaction vessels were purged with N2 prior to use. Bis...

Bogle, Xavier Sheldon



Gold(I)-catalyzed enantioselective cycloaddition reactions  

PubMed Central

Summary In recent years there have been extraordinary developments of gold(I)-catalyzed enantioselective processes. This includes progress in the area of cycloaddition reactions, which are of particular interest due to their potential for the rapid construction of optically active cyclic products. In this article we will summarize some of the most remarkable examples, emphasizing reaction mechanisms and key intermediates involved in the processes. PMID:24204438



Magnetic properties of intermediate-mass stars  

E-print Network

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

G. A. Wade




ERIC Educational Resources Information Center




Air Conditioning. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

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

Long, William


Appliance Services. Intermediate Course. Career Education.  

ERIC Educational Resources Information Center

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

Killough, Joseph


Automotive Body Repair. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

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

Lang, Thomas


Diesel Mechanics. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

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

Tidwell, Joseph


Marine Engine Mechanics. Performance Objectives. Intermediate Course.  

ERIC Educational Resources Information Center

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

Jones, Marion


Radio and Television Servicing. Intermediate Course.  

ERIC Educational Resources Information Center

Several intermediate performance objectives and corresponding criterion measures are listed for each of 32 terminal objectives for an intermediate (second year) radio/TV servicing course. This 1-year course (3 hours daily) was designed to provide the student with the basic skills and knowledges necessary for entry level employment in the Radio/TV…

Campbell, Guy; And Others


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

Microsoft Academic Search

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

H. Smit; T. Li



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

EPA Science Inventory

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


doubly dehydrated (6) while still tethered to the protein. The complex intermediates were  

E-print Network

intermediates, both two-part combination reactions gave remarkably similar outcomes (Fig. 4). Elaboration strategy for engineering these enzymes to synthesize alter- native products. References and Notes 1. J. Keatinge-Clay, D. A. Maltby, K. F. Medzihradszky, C. Khosla, R. M. Stroud, Nat. Struct. Mol. Biol. 11, 888

La Rosa, Andres H.


Intermediate temperature electrolytes for SOFC  

SciTech Connect

The objective of this work is to identify a new set of materials that would allow the operation of the solid oxide fuel cell in the 600--800{sup degrees}C temperature range. The approach that is being used is to start with a systematic evaluation of new electrolyte materials and then to develop compatible electrode and interconnect materials.

Bloom, I.; Krumpelt, M.; Hash, M.C.; Zebrowski, J.P.; Zurawski, D.



Intermediate temperature electrolytes for SOFC  

SciTech Connect

The objective of this work is to identify a new set of materials that would allow the operation of the solid oxide fuel cell in the 600--800{sup degrees}C temperature range. The approach that is being used is to start with a systematic evaluation of new electrolyte materials and then to develop compatible electrode and interconnect materials.

Bloom, I.; Krumpelt, M.; Hash, M.C.; Zebrowski, J.P.; Zurawski, D.



Drug Reactions  


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


A QM/MM study on the reaction pathway leading to 2-aceto-2-hydroxybutyrate in the catalytic cycle of AHAS.  


The reaction between the intermediate 2-hydroxyethyl-thiamin diphosphate (HEThDP(-) ) and 2-ketobutyrate, in the third step of the catalytic cycle of acetodydroxy acid synthase, is addressed from a theoretical point of view by means of hybrid quantum/molecular mechanical calculations. The QM region includes one molecule of 2-ketobutyrate, the HEThDP(-) intermediate, and the residues Arg 380 y Glu 139; whereas the MM region includes the rest of the protein. The study includes potential energy surface scans to identify and characterize critical points on it, transition state search and activation barrier calculations. The results show that the reaction occurs via a two-step mechanism corresponding to the carboligation and proton transfer in the first stage; and the product release in the second step. PMID:24395707

Sánchez, Leslie; Jaña, Gonzalo A; Delgado, Eduardo J



C3-C4 Intermediate Species in Alternanthera (Amaranthaceae) 1  

PubMed Central

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

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



Nuclear structure at intermediate energies  

SciTech Connect

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

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



Enzyme Reactions  

NSDL National Science Digital Library

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

School, Maryland V.


Activation of the immune response against Infectious Bursal Disease Virus after intramuscular inoculation of an intermediate strain.  


Infectious bursal disesase is a highly contagious, wide spread immunosuppressive chicken disease caused by the Infectious Bursal Disease Virus (IBDV). IBDV is a two segmented double-strand RNA virus, member of the Birnaviridae family. In order to study the interaction between IBDV and the immune system, chickens were exposed to an intermediate IBDV strain by intramuscular route, and using Real Time PCR the expression of a panel of avian cytokines and chemokines in duodenum, spleen and bursa of Fabricius was analyzed. Also, splenic nitrite (NO?) production and the frequencies of different mononuclear cell populations were evaluated by Griess reaction and flow cytometry, respectively. Intramuscular (i.m.) IBDV inoculation promoted an over expression of proinflammatory cytokines IL-6, IL-15 and gIFN in spleen, which correlated with an increase of gIFN plasma concentration measured by ELISA, together with an increment of NO? concentration in splenocyte supernatants at 1dpi. Results obtained in the present work showed that IBDV of intermediate virulence, given i.m., induced similar effects to those previously described for highly virulent IBDV in early innate immune responses. Considering that the i.m. route is the route of choice for the delivery of new generation vaccines, and that the use of recombinant antigens also requires the addition of adjuvants for proper immune stimulation, results presented here could contribute to identify suitable cytokines to be used or to be stimulated when utilizing subunit vaccines, for the improvement of prevention tools for avian health. PMID:21514000

Carballeda, Juan Manuel; Zoth, Silvina Chimeno; Gómez, Evangelina; Gravisaco, María José; Berinstein, Analía



Multiple Scattering and Plasmon Resonance in the Intermediate Regime  

E-print Network

The collective excitation of the conduction electrons in subwavelength structures gives rise to the Localized Surface Plasmon(LSP). The system consisting of two such LSPs, known as the dimer system,is of fundamental interest and is being actively investigated in the literature. Three regimes have been previously identified and they are the photonic regime, the strong coupling regime and the quantum tunneling regime. In this Letter, we propose a new regime for this intriguing systems, the intermediate regime. In this new regime, the quasistatic approximation, which is widely used to study such LSP systems, fails to capture the main physics: the multiple scattering of the electromagnetic waves between the two LSPs, which significantly modifies the properties of the resonant modes in the system. This intermediate regime provides a new route to explore in plasmonics, where controlling both the excited plasmon modes and the damping rates are of paramount significance.

Liu, Bo



Wittig Reaction 33 Reaction: Synthesis of Alkenes  

E-print Network

elimination reactions (E1 or E2 reactions from alcohols or alkyl halides, for example), in eliminationWittig Reaction 33 The Wittig Reaction: Synthesis of Alkenes Intro The "Wittig Reaction" is one reactions the carbon skeleton is already pre-assembled. In the Wittig reaction, however, two smaller carbon

Jasperse, Craig P.


Double barred galaxies at intermediate redshifts: A feasibility study  

E-print Network

Despite the increasing number of studies of barred galaxies at intermediate and high redshifts, double-barred (S2B) systems have only been identified in the nearby (z<0.04) universe thus far. In this feasibility study we demonstrate that the detection and analysis of S2Bs is possible at intermediate redshifts (0.1 < z < 0.5) with the exquisite resolution of the Hubble Space Telescope Advanced Camera for Surveys (HST/ACS). We identify barred galaxies in the HST/ACS data of the Great Observatories Origins Deep Survey (GOODS) using a novel method. The radial profile of the Gini coefficient -- a model-independent structure parameter -- is able to detect bars in early-type galaxies that are large enough that they might host an inner bar of sufficient angular size. Using this method and subsequent examination with unsharp masks and ellipse fits we identified the two most distant S2Bs currently known (at redshifts z=0.103 and z=0.148). We investigate the underlying stellar populations of these two galaxies through a detailed colour analysis, in order to demonstrate the analysis that could be performed on a future sample of intermediate-redshift S2Bs. We also identify two S2Bs and five S2B candidates in the HST/ACS data of the Cosmic Evolution Survey (COSMOS). Our detections of distant S2Bs show that deep surveys like GOODS and COSMOS have the potential to push the limit for S2B detection and analysis out by a factor of ten in redshift and lookback time (z=0.5, t=5Gyr) compared to the previously known S2Bs. This in turn would provide new insight into the formation of these objects.

Thorsten Lisker; Victor P. Debattista; Ignacio Ferreras; Peter Erwin



Computational perspective on Pd-catalyzed C-C cross-coupling reaction mechanisms.  


Palladium-catalyzed C-C cross-coupling reactions (Suzuki-Miyaura, Negishi, Stille, Sonogashira, etc.) are among the most useful reactions in modern organic synthesis because of their wide scope and selectivity under mild conditions. The many steps involved and the availability of competing pathways with similar energy barriers cause the mechanism to be quite complicated. In addition, the short-lived intermediates are difficult to detect, making it challenging to fully characterize the mechanism of these reactions using purely experimental techniques. Therefore, computational chemistry has proven crucial for elucidating the mechanism and shaping our current understanding of these processes. This mechanistic elucidation provides an opportunity to further expand these reactions to new substrates and to refine the selectivity of these reactions. During the past decade, we have applied computational chemistry, mostly using density functional theory (DFT), to the study of the mechanism of C-C cross-coupling reactions. This Account summarizes the results of our work, as well as significant contributions from others. Apart from a few studies on the general features of the catalytic cycles that have highlighted the existence of manifold competing pathways, most studies have focused on a specific reaction step, leading to the analysis of the oxidative addition, transmetalation, and reductive elimination steps of these processes. In oxidative addition, computational studies have clarified the connection between coordination number and selectivity. For transmetalation, computation has increased the understanding of different issues for the various named reactions: the role of the base in the Suzuki-Miyaura cross-coupling, the factors distinguishing the cyclic and open mechanisms in the Stille reaction, the identity of the active intermediates in the Negishi cross-coupling, and the different mechanistic alternatives in the Sonogashira reaction. We have also studied the closely related direct arylation process and highlighted the role of an external base as proton abstractor. Finally, we have also rationalized the effect of ligand substitution on the reductive elimination process. Computational chemistry has improved our understanding of palladium-catalyzed cross-coupling processes, allowing us to identify the mechanistic complexity of these reactions and, in a few selected cases, to fully clarify their mechanisms. Modern computational tools can deal with systems of the size and complexity involved in cross-coupling and have a continuing role in solving specific problems in this field. PMID:23848308

García-Melchor, Max; Braga, Ataualpa A C; Lledós, Agustí; Ujaque, Gregori; Maseras, Feliu



Enantioselective aldol reactions catalyzed by chiral phosphine oxides.  


The development of enantioselective aldol reactions catalyzed by chiral phosphine oxides is described. The aldol reactions presented herein do not require the prior preparation of the masked enol ethers from carbonyl compounds as aldol donors. The reactions proceed through a trichlorosilyl enol ether intermediate, formed in situ from carbonyl compounds, which then acts as the aldol donor. Phosphine oxides activate the trichlorosilyl enol ethers to afford the aldol adducts with high stereoselectivities. This procedure was used to realize a directed cross-aldol reaction between ketones and two types of double aldol reactions (a reaction at one/two ? position(s) of a carbonyl group) with high diastereo- and enantioselectivities. PMID:23828817

Kotani, Shunsuke; Sugiura, Masaharu; Nakajima, Makoto



Snapshots of a protein folding intermediate  

PubMed Central

We have investigated the folding dynamics of Thermus thermophilus cytochrome c552 by time-resolved fluorescence energy transfer between the heme and each of seven site-specific fluorescent probes. We have found both an equilibrium unfolding intermediate and a distinct refolding intermediate from kinetics studies. Depending on the protein region monitored, we observed either two-state or three-state denaturation transitions. The unfolding intermediate associated with three-state folding exhibited native contacts in ?-sheet and C-terminal helix regions. We probed the formation of a refolding intermediate by time-resolved fluorescence energy transfer between residue 110 and the heme using a continuous flow mixer. The intermediate ensemble, a heterogeneous mixture of compact and extended polypeptides, forms in a millisecond, substantially slower than the ?100-?s formation of a burst-phase intermediate in cytochrome c. The surprising finding is that, unlike for cytochrome c, there is an observable folding intermediate, but no microsecond burst phase in the folding kinetics of the structurally related thermostable protein. PMID:23319660

Yamada, Seiji; Bouley Ford, Nicole D.; Keller, Gretchen E.; Ford, William C.; Gray, Harry B.; Winkler, Jay R.



Taxol reactions.  


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

Price, Kursteen S; Castells, Mariana C



Identifying opportunities Overcoming barriers  

E-print Network

of localised culling on neighbouring populations and on woodlands. · deer-related road traffic accidents management involves and affects many people with diverse aims and values. Our objective is to understand issues and management, and identify those involved and who is affected. · identify opportunities


Identifiability of Finite Mixtures  

Microsoft Academic Search

In general, the class of mixtures of the family of normal distributions or of Gamma (Type III) distributions or binomial distributions is not identifiable (see [3], [4] or Section 2 below for the meaning of this statement). In [4] it was shown that the class of all mixtures of a one-parameter additively-closed family of distributions is identifiable. Here, attention will

Henry Teicher



Use of diethyldithiocarbamate as a probe to detect stable intermediates during the decomposition of several mutagenic and nonmutagenic N-nitroso compounds.  


By showing that methyldiethyldithiocarbamate is formed from the reaction of methylnitrosourea and disulfiram, we demonstrated in previous experiments that one of the anticarcinogenic/antimutagenic mechanisms of disulfiram is the scavenging of reactive species. We propose that this reaction may be employed additionally as a model for elucidating the following: (a) possible reactions between alkylating species and nucleophilic sites within the cell, and (b) the existence of stable intermediates during the metabolism of N-nitroso compounds. With structurally related pairs of nitrosoureas (n-propyl/isopropyl; cyclopropyl/allyl; 2-phenylethyl/l-phenylethyl), for which each alkylating group of the first compound can spontaneously rearrange to form the alkylating group of the second isomer, we investigated whether the alkylation proceeds via a monomolecular (sn1) or a bimolecular substitution (sn2). For this, we comparatively determined the relative mutagenic activities of each isomer in Salmonella typhimurium TA 1535, as well as their reactivities towards diethyldithiocarbamate (DDTC) by identifying the reaction products. These studies were aimed at revealing the possible formation of a free carbonium ion in the decomposition of several nitrosoureas in the rat liver supernatant fraction. Our system showed that DDTC reacts by two competing mechanisms: attack at the diazonium ion and at the free carbonium ion. Therefore the striking differences which were observed in the mutagenic potency of cyclopropylnitrosourea and N-nitrosoallylurea as well as of N-nitroso-2-phenylethylurea and N-nitroso-1-phenylethylurea cannot be explained only by the different electrophilic reactivities of the respective intermediates. PMID:3009486

Wiessler, M; Tacchi, A M; Pool, B L; Bertram, B



A Multistep Screening Method to Identify Genes Using Evolutionary Transcriptome of Plants  

PubMed Central

We introduced a multistep screening method to identify the genes in plants using microarrays and ribonucleic acid (RNA)-seq transcriptome data. Our method describes the process for identifying genes using the salt-tolerance response pathways of the potato (Solanum tuberosum) plant. Gene expression was analyzed using microarrays and RNA-seq experiments that examined three potato lines (high, intermediate, and low salt tolerance) under conditions of salt stress. We screened the orthologous genes and pathway genes involved in salinity-related biosynthetic pathways, and identified nine potato genes that were candidates for salinity-tolerance pathways. The nine genes were selected to characterize their phylogenetic reconstruction with homologous genes of Arabidopsis thaliana, and a Circos diagram was generated to understand the relationships among the selected genes. The involvement of the selected genes in salt-tolerance pathways was verified by reverse transcription polymerase chain reaction analysis. One candidate potato gene was selected for physiological validation by generating dehydration-responsive element-binding 1 (DREB1)-overexpressing transgenic potato plants. The DREB1 overexpression lines exhibited increased salt tolerance and plant growth when compared to that of the control. Although the nine genes identified by our multistep screening method require further characterization and validation, this study demonstrates the power of our screening strategy after the initial identification of genes using microarrays and RNA-seq experiments. PMID:24812480

Kim, Chang-Kug; Lim, Hye-Min; Na, Jong-Kuk; Choi, Ji-Weon; Sohn, Seong-Han; Park, Soo-Chul; Kim, Young-Hwan; Kim, Yong-Kab; Kim, Dool-Yi



{gamma} induced multiparticle emissions of medium mass nuclei at intermediate energies  

SciTech Connect

A comprehensive analysis of multiparticle emissions following photon induced reactions at intermediate energies is provided. Photon induced reaction is described in the energy range of {approx}30-140 MeV with an approach based on the quasideuteron nuclear photoabsorption model followed by the process of competition between light particle evaporation and fission for the excited nucleus. The evaporation-fission process of the compound nucleus is simulated in a Monte-Carlo framework. The study shows almost no fission events for the medium mass nuclei and reproduces the available experimental data of photonuclear reaction cross sections satisfactorily at energies {approx}30-140 MeV.

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



Long-lived trifluoromethanide anion: a key intermediate in nucleophilic trifluoromethylations.  


The trifluoromethanide anion is the postulated key intermediate in nucleophilic trifluoromethylation reactions. However, for more than six decades, the trifluoromethanide anion was widely believed to exist only as a short-lived transient species in the condensed phase. It has now been prepared in bulk for the first time in THF solution. The trifluoromethanide anion with the [K(18-crown-6)](+) cation was unequivocally characterized by low-temperature (19) F and (13) C?NMR spectroscopy. Its intermediacy in nucleophilic trifluoromethylation reactions was directly evident by its reaction chemistry with various electrophilic substrates. Variable-temperature NMR spectroscopy, along with quantum mechanical calculations, support the persistence of the trifluoromethanide anion. PMID:25146595

Prakash, G K Surya; Wang, Fang; Zhang, Zhe; Haiges, Ralf; Rahm, Martin; Christe, Karl O; Mathew, Thomas; Olah, George A



Test Rankings and Selection Procedures for Identifying Gifted Intermediate Elementary Children.  

ERIC Educational Resources Information Center

This study attempts to determine the relative ranking value of information gathering devices that could be substituted for tests of mental maturity. Results indicate that the three best devices are: a standardized test of academic achievement, a test of personality, and a self-concept inventory, all of which are easily administered, scored, and…

Doughty, Earl


Carrot-specific features of the phenylpropanoid pathway identified by feeding cultured cells with defined intermediates.  


Plants produce a vast array of secondary metabolites, many of which have important biological properties in animals when consumed as part of the diet. Interestingly, although the activities and benefits of plant secondary metabolites in animals are well established, comparatively little is known about the endogenous functions of these compounds in plants. One way to investigate the role of secondary products in plants is to modify the secondary metabolome and investigate the impact of such modifications on the phenotype. We have designed a novel feeding approach using different hydroxycinnamic acids (HCAs) and the cyanidin precursor dihydroquercetin (DHQ) to modify the metabolome of carrot R3M suspension cells. This strategy increased the accumulation of specific metabolites in a predictable way, and provided novel insights into the carrot phenylpropanoid pathway, suggesting that (a) cells use HCA hexose esters as substrates in the biosynthetic pathway leading to the accumulation of the various HCA derivatives and (b) p-coumaric acid derivative levels play a key roles in the regulation the flux of HCAs along the pathway. Moreover, this rapid strategy for metabolome modification does not depend on the availability of molecular tools or knowledge and can therefore be applied to any plant species. PMID:23759106

Toffali, Ketti; Ceoldo, Stefania; Stocchero, Matteo; Levi, Marisa; Guzzo, Flavia



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

E-print Network

], Autosomal dominant leukodystrophy (LMNB1) [46], acquired partial lipodystrophy (LMNB2) [47], and various other lipodystrophies and cardiomyopa- ments or microtubules. Therefore, truncated APC found in the majority of colorectal cancers and also in other can...

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



Formate ester synthesis via reaction of 2-bromoethylamines with dimethylformamide  

Microsoft Academic Search

2-Bromoethylamines are converted to the corresponding formate esters in the presence of DMF. Both primary and secondary bromides are smoothly transformed to the esters in satisfactory yields. The reaction mechanism involves the formation of an aziridinium ion, which upon reaction with DMF forms a Vilsmeier-type intermediate that is further hydrolyzed to the corresponding formates. Participation of the ?-amino group appears

Marianna Dakanali; George K. Tsikalas; Harald Krautscheid; Haralambos E. Katerinopoulos



Electrochemical and spectroscopic studies of fuel cell reactions  

Microsoft Academic Search

Fuel cells, especially proton exchange membrane fuel cells (PEMFCs) are expected soon to become a major source of clean energy. However, the sluggish kinetics of the fuel cell reactions, i.e., the fuel oxidation and oxygen reduction, hinders the wide-spread application of PEMFCs. These problems prompted our studies to focus on elucidating the nature of the reaction intermediates during the oxidation

Minhua Shao



Computational studies on glyceraldehyde and glycine Maillard reaction-II  

Microsoft Academic Search

Density functional theory calculations have been performed on the proposed mechanism for the intermediate stage of glyceraldehyde and glycine Maillard reaction under different pH conditions at the standard state. By following the total mass balance, possibility of the formation of different compounds in the proposed mechanism has been tested by estimating the Gibb's free energy changes of the reaction. Electronic




EPA Science Inventory

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


Visualizing solution-phase reaction dynamics with time-resolved X-ray liquidography.  


Most chemical reactions occur in solution, and complex interactions between solute and solvent influence the rich chemistry of these processes. To track time-dependent processes in such reactions, researchers often use time-resolved spectroscopy. In these experiments, an optical pulse (pump) initiates a reaction, and another time-delayed optical pulse (probe) monitors the progress of the reaction. However, because of the wavelength range of the probe light used in these experiments, from infrared to ultraviolet, researchers cannot directly determine detailed structural information such as the bond lengths and bond angles of reaction intermediates. In addition, not all intermediates might be sensitive to the spectroscopic signal chosen for the experiment. This Account describes time-resolved X-ray liquidography (TRXL), a technique that overcomes these problems. In this technique, we replace the optical probe with the diffraction of hard X-ray pulses emitted from a synchrotron source. In TRXL, diffraction signals are sensitive to all chemical species simultaneously. In addition, each chemical species has a characteristic diffraction signal, a fingerprint, that we calculate from its three-dimensional atomic coordinates. Because, X-rays scatter from all atoms in the solution sample, including both the solute and the solvent, the analysis of TRXL data can track not only the reaction pathways of the solute molecules but also the solvent behavior and the solute-solvent arrangement, thus providing a global picture of the reactions. We have used TRXL to study structural dynamics and spatiotemporal kinetics of many molecular systems including diatomic molecules, haloalkanes, organometallic complexes, and protein molecules over timescales from picoseconds to milliseconds. We have observed that TRXL data adds to and, in some cases, contradicts results from time-resolved spectroscopy. For example, TRXL has shown that the reaction intermediates upon C-I bond dissociation in C(2)H(4)I(2) and C(2)F(4)I(2) have completely different structures and corresponding subsequent reaction pathways, underscoring the dramatic effect of the fluorine substitution. We have also used TRXL to identify a new reaction intermediate of the photolysis of Ru(3)(CO)(12) that has no bridging carbonyl groups. Though not detected by time-resolved infrared spectroscopy, this intermediate predominates based on the TRXL data. In looking at the quaternary conformational changes of hemoglobin, TRXL analysis suggests a faster transition than was suggested by optical spectroscopy. The time resolution of TRXL is currently limited by the X-ray pulse width available from synchrotron sources ( approximately 100 ps). The resolution should improve to 100 fs or better with X-ray free electron lasers. With this higher resolution, real time observation of ultrafast chemical events such as bond-breaking and bond-making will be possible. PMID:19117426

Ihee, Hyotcherl



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

SciTech Connect

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

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