Sample records for bond cleavage reactions

  1. Development and application of bond cleavage reactions in bioorthogonal chemistry. (United States)

    Li, Jie; Chen, Peng R


    Bioorthogonal chemical reactions are a thriving area of chemical research in recent years as an unprecedented technique to dissect native biological processes through chemistry-enabled strategies. However, current concepts of bioorthogonal chemistry have largely centered on 'bond formation' reactions between two mutually reactive bioorthogonal handles. Recently, in a reverse strategy, a collection of 'bond cleavage' reactions has emerged with excellent biocompatibility. These reactions have expanded our bioorthogonal chemistry repertoire, enabling an array of exciting new biological applications that range from the chemically controlled spatial and temporal activation of intracellular proteins and small-molecule drugs to the direct manipulation of intact cells under physiological conditions. Here we highlight the development and applications of these bioorthogonal cleavage reactions. Furthermore, we lay out challenges and propose future directions along this appealing avenue of research.

  2. Carbon-Carbon Bond Cleavage Reaction: Synthesis of Multisubstituted Pyrazolo[1,5-a]pyrimidines. (United States)

    Saikia, Pallabi; Gogoi, Sanjib; Boruah, Romesh C


    A new carbon-carbon bond cleavage reaction was developed for the efficient synthesis of multisubstituted pyrazolo[1,5-a]pyrimidines. This base induced reaction of 1,3,5-trisubstituted pentane-1,5-diones and substituted pyrazoles afforded good yields of the pyrazolo[1,5-a]pyrimidines.

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

    Energy Technology Data Exchange (ETDEWEB)

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


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

  4. Exploring Regioselective Bond Cleavage and Cross-Coupling Reactions using a Low-Valent Nickel Complex. (United States)

    Desnoyer, Addison N; Friese, Florian W; Chiu, Weiling; Drover, Marcus W; Patrick, Brian O; Love, Jennifer A


    Recently, esters have received much attention as transmetalation partners for cross-coupling reactions. Herein, we report a systematic study of the reactivity of a series of esters and thioesters with [{(dtbpe)Ni}2(μ-η(2):η(2)-C6H6)] (dtbpe=1,2-bis(di-tert-butyl)phosphinoethane), which is a source of (dtbpe)nickel(0). Trifluoromethylthioesters were found to form η(2)-carbonyl complexes. In contrast, acetylthioesters underwent rapid Cacyl-S bond cleavage followed by decarbonylation to generate methylnickel complexes. This decarbonylation could be pushed backwards by the addition of CO, allowing for regeneration of the thioester. Most of the thioester complexes were found to undergo stoichiometric cross-coupling with phenylboronic acid to yield sulfides. While ethyl trifluoroacetate was also found to form an η(2)-carbonyl complex, phenyl esters were found to predominantly undergo Caryl-O bond cleavage to yield arylnickel complexes. These could also undergo transmetalation to yield biaryls. Attempts to render the reactions catalytic were hindered by ligand scrambling to yield nickel bis(acetate) complexes, the formation of which was supported by independent syntheses. Finally, 2-naphthyl acetate was also found to undergo clean Caryl-O bond cleavage, and although stoichiometric cross-coupling with phenylboronic acid proceeded with good yield, catalytic turnover has so far proven elusive.

  5. Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis. (United States)

    Roca, Maite; De Maria, Leonardo; Wodak, Shoshana J; Moliner, Vicente; Tuñón, Iñaki; Giraldo, Jesús


    To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gchi) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 '. Similar energetic profiles featuring two minima corresponding to the anti and syn Gchi regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of approximately 4 kcal/mol were obtained for the anti --> syn transition. Structural analysis showed a remarkable sensitivity of the phosphate moiety to the conformation of the Gchi angle, suggesting a possible connection between this conformation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O2 '--P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O2'. The simulations revealed that the O2 ' attack along the syn Gchi was more favorable than that along the anti Gchi: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O--P bond formation; structurally, a lesser O2 '--P initial distance, and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the catalytically competent conformation of barnase-ribonucleotide complex, which requires a guanine syn conformation of the substrate to enable abstraction of the ribose H2 ' proton by the general base Glu73, thereby suggesting a coupling between the reactive substrate conformation and enzyme structure

  6. Extended reaction scope of thiamine diphosphate dependent cyclohexane-1,2-dione hydrolase: from C-C bond cleavage to C-C bond ligation. (United States)

    Loschonsky, Sabrina; Wacker, Tobias; Waltzer, Simon; Giovannini, Pier Paolo; McLeish, Michael J; Andrade, Susana L A; Müller, Michael


    ThDP-dependent cyclohexane-1,2-dione hydrolase (CDH) catalyzes the CC bond cleavage of cyclohexane-1,2-dione to 6-oxohexanoate, and the asymmetric benzoin condensation between benzaldehyde and pyruvate. One of the two reactivities of CDH was selectively knocked down by mutation experiments. CDH-H28A is much less able to catalyze the CC bond formation, while the ability for CC bond cleavage is still intact. The double variant CDH-H28A/N484A shows the opposite behavior and catalyzes the addition of pyruvate to cyclohexane-1,2-dione, resulting in the formation of a tertiary alcohol. Several acyloins of tertiary alcohols are formed with 54-94 % enantiomeric excess. In addition to pyruvate, methyl pyruvate and butane-2,3-dione are alternative donor substrates for CC bond formation. Thus, the very rare aldehyde-ketone cross-benzoin reaction has been solved by design of an enzyme variant.

  7. Investigations on organolead compounds V. Lead---lead bond cleavage reactions of hexaphenyldilead

    NARCIS (Netherlands)

    Willemsens, L.C.; Kerk, G.J.M. van der


    It has been shown that a number of nucleophilic and weakly electrophilic reagents (organolithium and organomagnesium compounds, metallic lithium, potassium permanganate, sodium ethoxide, diaryl disulphides, sulphur, ozone, hypochlorous acid and iodine/iodide) selectively cleave the lead---lead bond

  8. A novel N-N bond cleavage reaction of 4-amino-1,2,4-triazole derivatives

    Institute of Scientific and Technical Information of China (English)

    YANG, Guang- Fu(杨光富); YANG, Hua- Zheng(杨华铮)


    5-Substituted-4amino-3thiol-1, 2, 4-triazoles (1a-b) react with ortho nitrochloro-benzene or para-nitrochlorobenzene to give N-N bond cleavage products 2a-d, one structure of which (2b) has been unambiguously confirmed by an X-ray structural analysis.

  9. Bond cleavage reactions of the bridge structure in coal in the presence of hydrogen donating compounds; Suiso kyoyosei kagobutsu sonzaika deno sekitanchu no kakyo kozo no kairetsu hanno

    Energy Technology Data Exchange (ETDEWEB)

    Bando, N.; Kidena, K.; Murata, S.; Nomura, M. [Osaka University, Osaka (Japan). Faculty of Engineering


    In this paper, bond cleavage reactions are discussed in relation to the softening and solubilization of coal. Were used 9,10-dihydroanthracene (DHA) and 9,10-dihydrophenanthrene (DHP) as models of hydrogen donating compounds in coal, and bibenzyl, 1,2-diethane, benzylphenylether, and 1,5-dibenzylnaphthalene were used as models of bridge structure compounds. They were compared mutually, as to reactivity of coal against DHA and DHP. For the homolytic cleavage of bridges, DHA with excellent radical supplement performance provided excellent hydrogen donating performance. While, for the ipso-position cleavage of bridges, it was found that DHP can act as an effective hydrogen donor. For the reaction between coal and hydrogenated aromatic compounds, cleavage of relatively weak bonds, such as ether linkage and dimethylene linkage, occurred at about 380{degree}C, and hydrogen from DHA or DHP was consumed. On the other hand, the results suggested that the cleavage reaction at ipso-position affected by hydrogen donating solvent is also important at temperature range around 420{degree}C. 2 refs., 3 figs., 1 tab.

  10. Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ. (United States)

    Klvaňa, Martin; Bren, Urban; Florián, Jan


    Human X-family DNA polymerases β (Polβ) and λ (Polλ) catalyze the nucleotidyl-transfer reaction in the base excision repair pathway of the cellular DNA damage response. Using empirical valence bond and free-energy perturbation simulations, we explore the feasibility of various mechanisms for the deprotonation of the 3'-OH group of the primer DNA strand, and the subsequent formation and cleavage of P-O bonds in four Polβ, two truncated Polλ (tPolλ), and two tPolλ Loop1 mutant (tPolλΔL1) systems differing in the initial X-ray crystal structure and nascent base pair. The average calculated activation free energies of 14, 18, and 22 kcal mol(-1) for Polβ, tPolλ, and tPolλΔL1, respectively, reproduce the trend in the observed catalytic rate constants. The most feasible reaction pathway consists of two successive steps: specific base (SB) proton transfer followed by rate-limiting concerted formation and cleavage of the P-O bonds. We identify linear free-energy relationships (LFERs) which show that the differences in the overall activation and reaction free energies among the eight studied systems are determined by the reaction free energy of the SB proton transfer. We discuss the implications of the LFERs and suggest pKa of the 3'-OH group as a predictor of the catalytic rate of X-family DNA polymerases.

  11. Catalytic diastereoselective tandem conjugate addition-elimination reaction of Morita-Baylis-Hillman C adducts by C-C bond cleavage

    KAUST Repository

    Yang, Wenguo


    Through the cleavage of the C-C bond, the first catalytic tandem conjugate addition-elimination reaction of Morita-Baylis-Hillman C adducts has been presented. Various S N2′-like C-, S-, and P-allylic compounds could be obtained with exclusive E configuration in good to excellent yields. The Michael product could also be easily prepared by tuning the β-C-substituent group of the α-methylene ester under the same reaction conditions. Calculated relative energies of various transition states by DFT methods strongly support the observed chemoselectivity and diastereoselectivity. © 2012 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim.

  12. Demonstration of the heterolytic O-O bond cleavage of putative nonheme iron(II)-OOH(R) complexes for Fenton and enzymatic reactions. (United States)

    Bang, Suhee; Park, Sora; Lee, Yong-Min; Hong, Seungwoo; Cho, Kyung-Bin; Nam, Wonwoo


    One-electron reduction of mononuclear nonheme iron(III) hydroperoxo (Fe(III)-OOH) and iron(III) alkylperoxo (Fe(III)-OOR) complexes by ferrocene (Fc) derivatives resulted in the formation of the corresponding iron(IV) oxo complexes. The conversion rates were dependent on the concentration and oxidation potentials of the electron donors, thus indicating that the reduction of the iron(III) (hydro/alkyl)peroxo complexes to their one-electron reduced iron(II) (hydro/alkyl)peroxo species is the rate-determining step, followed by the heterolytic O-O bond cleavage of the putative iron(II) (hydro/alkyl)peroxo species to give the iron(IV) oxo complexes. Product analysis supported the heterolytic O-O bond-cleavage mechanism. The present results provide the first example showing the one-electron reduction of iron(III) (hydro/alkyl)peroxo complexes and the heterolytic O-O bond cleavage of iron(II) (hydro/alkyl)peroxo species to form iron(IV) oxo intermediates which occur in nonheme iron enzymatic and Fenton reactions.

  13. Metal ion-promoted cleavage of nucleoside diphosphosugars: a model for reactions of phosphodiester bonds in carbohydrates. (United States)

    Dano, Meisa; Elmeranta, Marjukka; Hodgson, David R W; Jaakkola, Juho; Korhonen, Heidi; Mikkola, Satu


    Cleavage of five different nucleoside diphosphosugars has been studied in the presence of Cu(2+) and Zn(2+) complexes. The results show that metal ion catalysts promote the cleavage via intramolecular transesterification whenever a neighbouring HO group can adopt a cis-orientation with respect to the phosphate. The HO group attacks the phosphate and two monophosphate products are formed. If such a nucleophile is not available, Cu(2+) complexes are able to promote a nucleophilic attack of an external nucleophile, e.g. a water molecule or metal ion coordinated HO ligand, on phosphate. With the Zn(2+) complex, this was not observed.

  14. Discovery and synthetic applications of novel silicon-carbon bond cleavage reactions based on the coordination number change of organosilicon compounds


    Tamao, Kohei


    Some synthetically useful transformations of organosilicon compounds have been developed since the mid 1970s, based on the new concept that the silicon-carbon bonds are activated toward electrophilic cleavage via the formation of penta- and hexa-coordinate species. This review mainly consists of the following aspects: (1) a general concept for the activation of the silicon-carbon bond via penta- and hexa-coordinate species, (2) synthetic application of hexa-coordinate organopentafluorosilicat...

  15. Electron-deficient ruthenium and osmium complexes: From 14-electron species to C-F bond cleavage reactions (United States)

    Huang, Dejian


    Stepwise removal of the fluoride from RuRF(CO)L2 gives [RuR(CO)L 2]BAr'4 (L = PtBu 2Me, R = H, CH3, Ph, Ar' = 3,5- bis(trifluoromethyl)phenyl). This 14-electron cation has a saw-horse shape with two bulky L trans and CO and R cis. The two vacant sites are in fact occupied weakly by C-H bonds from the phosphines. [RuH(CO)L2] + has a strong Lewis acidic but weakened π- basic Ru center as it is illustrated by its reactivity pattern towards olefins and alkynes. While organic fluorocarbon is notorious for its inertness due to the strong C-F bond, the α-C-F bond of a transition metal fluorocarbyl complex is activated. The chemistry in Chapter 3 illustrates this argument. Attempts to replace fluoride of MHF(CO)L2 with CF3 using Me 3SiCF3 do not give MH(CF3)(CO)L2, instead, M[HF(CF2)(CO)L2 is isolated. Fast equilibrium exists between RuHF(CF2)(CO)L2 and RuH(CF3)(CO)L 2 but not for OsHF(CF2)(CO)L2, which is converted to OsF2(CFH)(CO)L2 upon heating. In contrast, isomerization of RuHF(CF2)(CO)L2 gives RUF(CF2H)(CO)L 2.

  16. Regioselectivity in the Reductive Bond Cleavage of Diarylalkylsulfonium Salts

    DEFF Research Database (Denmark)

    Kampmeier, Jack; Mansurul Hoque, AKM; D. Saeva, Franklin;


    This investigation was stimulated by reports that one-electron reductions of monoaryldialkylsulfonium salts never give aryl bond cleavage whereas reductions of diarylmonoalkylsulfonium salts preferentially give aryl bond cleavage. We studied the product ratios from the reductive cleavage of di-4-...

  17. Exchanging Alkyl Groups through Unstrained C-C Bond Cleavage in the Presence of a Copper Catalyst. (United States)

    Wada, Masaru; Noda, Yushi; Nishikata, Takashi


    Although numerous reports exist on strained C-C bond cleavage reactions in aryl substitutions, the cleavage methodology for unstrained C-C bonds in alkylation reactions has not yet been established. We found that unstrained allylic C-C bonds can be cleaved using α-radicals to form C(sp(3) )-C(sp(3) ) bonds in the presence of a copper catalyst. In this reaction, the property of leaving and loading radicals is very important for radical fragmentations. In this paper, we investigated the effects of these properties in cleavage reactions for unstrained C-C bonds.

  18. Carbon-carbon bond cleavage in activation of the prodrug nabumetone

    DEFF Research Database (Denmark)

    Varfaj, Fatbardha; Zulkifli, Siti N A; Park, Hyoung-Goo;


    Carbon-carbon bond cleavage reactions are catalyzed by, among others, lanosterol 14-demethylase (CYP51), cholesterol side-chain cleavage enzyme (CYP11), sterol 17β-lyase (CYP17), and aromatase (CYP19). Because of the high substrate specificities of these enzymes and the complex nature of their su...

  19. Carbon-carbon bond cleavage in activation of the prodrug nabumetone. (United States)

    Varfaj, Fatbardha; Zulkifli, Siti N A; Park, Hyoung-Goo; Challinor, Victoria L; De Voss, James J; Ortiz de Montellano, Paul R


    Carbon-carbon bond cleavage reactions are catalyzed by, among others, lanosterol 14-demethylase (CYP51), cholesterol side-chain cleavage enzyme (CYP11), sterol 17β-lyase (CYP17), and aromatase (CYP19). Because of the high substrate specificities of these enzymes and the complex nature of their substrates, these reactions have been difficult to characterize. A CYP1A2-catalyzed carbon-carbon bond cleavage reaction is required for conversion of the prodrug nabumetone to its active form, 6-methoxy-2-naphthylacetic acid (6-MNA). Despite worldwide use of nabumetone as an anti-inflammatory agent, the mechanism of its carbon-carbon bond cleavage reaction remains obscure. With the help of authentic synthetic standards, we report here that the reaction involves 3-hydroxylation, carbon-carbon cleavage to the aldehyde, and oxidation of the aldehyde to the acid, all catalyzed by CYP1A2 or, less effectively, by other P450 enzymes. The data indicate that the carbon-carbon bond cleavage is mediated by the ferric peroxo anion rather than the ferryl species in the P450 catalytic cycle. CYP1A2 also catalyzes O-demethylation and alcohol to ketone transformations of nabumetone and its analogs.

  20. Cleavage of an amide bond by a ribozyme (United States)

    Dai, X.; De Mesmaeker, A.; Joyce, G. F.; Miller, S. L. (Principal Investigator)


    A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, kcat, is 0.1 x 10(-5) min-1 to 1 x 10(-5) min-1 for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10(3) as compared with the uncatalyzed reaction.

  1. Carbon-Oxygen Bond Cleavage by Bis(imino)pyridine Iron Compounds : Catalyst Deactivation Pathways and Observation of Acyl C-O Bond Cleavage in Esters

    NARCIS (Netherlands)

    Trovitch, Ryan J.; Lobkovsky, Emil; Bouwkamp, Marco W.; Chirik, Paul J.


    Investigations into the substrate scope of bis(imino)pyridine iron-catalyzed hydrogenation and [2 pi + 2 pi]. diene cyclization reactions identified C-O bond cleavage as a principal deactivation pathway. Addition of diallyl or allyl ethyl ether to the bis(imino)pyridine iron dinitrogen complex, ((iP

  2. Aerobic dehydrogenative α-diarylation of benzyl ketones with aromatics through carbon-carbon bond cleavage. (United States)

    More, Nagnath Yadav; Jeganmohan, Masilamani


    Substituted benzyl ketones reacted with aromatics in the presence of K2S2O8 in CF3COOH at room temperature, yielding α-diaryl benzyl ketones through a carbon-carbon bond cleavage. In the reaction, two new carbon-carbon bonds were formed and one carbon-carbon bond was cleaved. It is very interesting that two different nucleophiles such as benzyl ketones and aromatics were coupled together without metal, which is unusual in organic synthesis.

  3. C-S bond cleavage by a polyketide synthase domain. (United States)

    Ma, Ming; Lohman, Jeremy R; Liu, Tao; Shen, Ben


    Leinamycin (LNM) is a sulfur-containing antitumor antibiotic featuring an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. The 1,3-dioxo-1,2-dithiolane moiety is essential for LNM's antitumor activity, by virtue of its ability to generate an episulfonium ion intermediate capable of alkylating DNA. We have previously cloned and sequenced the lnm gene cluster from Streptomyces atroolivaceus S-140. In vivo and in vitro characterizations of the LNM biosynthetic machinery have since established that: (i) the 18-membered macrolactam backbone is synthesized by LnmP, LnmQ, LnmJ, LnmI, and LnmG, (ii) the alkyl branch at C-3 of LNM is installed by LnmK, LnmL, LnmM, and LnmF, and (iii) leinamycin E1 (LNM E1), bearing a thiol moiety at C-3, is the nascent product of the LNM hybrid nonribosomal peptide synthetase (NRPS)-acyltransferase (AT)-less type I polyketide synthase (PKS). Sulfur incorporation at C-3 of LNM E1, however, has not been addressed. Here we report that: (i) the bioinformatics analysis reveals a pyridoxal phosphate (PLP)-dependent domain, we termed cysteine lyase (SH) domain (LnmJ-SH), within PKS module-8 of LnmJ; (ii) the LnmJ-SH domain catalyzes C-S bond cleavage by using l-cysteine and l-cysteine S-modified analogs as substrates through a PLP-dependent β-elimination reaction, establishing l-cysteine as the origin of sulfur at C-3 of LNM; and (iii) the LnmJ-SH domain, sharing no sequence homology with any other enzymes catalyzing C-S bond cleavage, represents a new family of PKS domains that expands the chemistry and enzymology of PKSs and might be exploited to incorporate sulfur into polyketide natural products by PKS engineering.

  4. Glutamic Acid Selective Chemical Cleavage of Peptide Bonds. (United States)

    Nalbone, Joseph M; Lahankar, Neelam; Buissereth, Lyssa; Raj, Monika


    Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.

  5. Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond (United States)

    Rožman, Marko


    Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

  6. Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase. (United States)

    Wang, Miao; Warncke, Kurt


    Adenosylcobalamin-dependent enzymes accelerate the cleavage of the cobalt-carbon (Co-C) bond of the bound coenzyme by >10(10)-fold. The cleavage-generated 5'-deoxyadenosyl radical initiates the catalytic cycle by abstracting a hydrogen atom from substrate. Kinetic coupling of the Co-C bond cleavage and hydrogen-atom-transfer steps at ambient temperatures has interfered with past experimental attempts to directly address the factors that govern Co-C bond cleavage catalysis. Here, we use time-resolved, full-spectrum electron paramagnetic resonance spectroscopy, with temperature-step reaction initiation, starting from the enzyme-coenzyme-substrate ternary complex and (2)H-labeled substrate, to study radical pair generation in ethanolamine ammonia-lyase from Salmonella typhimurium at 234-248 K in a dimethylsulfoxide/water cryosolvent system. The monoexponential kinetics of formation of the (2)H- and (1)H-substituted substrate radicals are the same, indicating that Co-C bond cleavage rate-limits radical pair formation. Analysis of the kinetics by using a linear, three-state model allows extraction of the microscopic rate constant for Co-C bond cleavage. Eyring analysis reveals that the activation enthalpy for Co-C bond cleavage is 32 ± 1 kcal/mol, which is the same as for the cleavage reaction in solution. The origin of Co-C bond cleavage catalysis in the enzyme is, therefore, the large, favorable activation entropy of 61 ± 6 cal/(mol·K) (relative to 7 ± 1 cal/(mol·K) in solution). This represents a paradigm shift from traditional, enthalpy-based mechanisms that have been proposed for Co-C bond-breaking in B12 enzymes. The catalysis is proposed to arise from an increase in protein configurational entropy along the reaction coordinate.

  7. Carbon–carbon bond cleavage for Cu-mediated aromatic trifluoromethylations and pentafluoroethylations

    Directory of Open Access Journals (Sweden)

    Tsuyuka Sugiishi


    Full Text Available This short review highlights the copper-mediated fluoroalkylation using perfluoroalkylated carboxylic acid derivatives. Carbon–carbon bond cleavage of perfluoroalkylated carboxylic acid derivatives takes place in fluoroalkylation reactions at high temperature (150–200 °C or under basic conditions to generate fluoroalkyl anion sources for the formation of fluoroalkylcopper species. The fluoroalkylation reactions, which proceed through decarboxylation or tetrahedral intermediates, are useful protocols for the synthesis of fluoroalkylated aromatics.

  8. Thermodynamic Strategies for C-O Bond Formation and Cleavage via Tandem Catalysis. (United States)

    Lohr, Tracy L; Li, Zhi; Marks, Tobin J


    To reduce global reliance on fossil fuels, new renewable sources of energy that can be used with the current infrastructure are required. Biomass represents a major source of renewable carbon based fuel; however, the high oxygen content (∼40%) limits its use as a conventional fuel. To utilize biomass as an energy source, not only with current infrastructure, but for maximum energy return, the oxygen content must be reduced. One method to achieve this is to develop selective catalytic methods to cleave C-O bonds commonly found in biomass (aliphatic and aromatic ethers and esters) for the eventual removal of oxygen in the form of volatile H2O or carboxylic acids. Once selective methods of C-O cleavage are understood and perfected, application to processing real biomass feedstocks such as lignin can be undertaken. This Laboratory previously reported that recyclable "green" lanthanide triflates are excellent catalysts for C-O bond-forming hydroalkoxylation reactions. Based on the virtues of microscopic reversibility, the same lanthanide triflate catalyst should catalyze the reverse C-O cleavage process, retrohydroalkoxylation, to yield an alcohol and an alkene. However, ether C-O bond-forming (retrohydroalkoxylation) to form an alcohol and alkene is endothermic. Guided by quantum chemical analysis, our strategy is to couple endothermic, in tandem, ether C-O bond cleavage with exothermic alkene hydrogenation, thereby leveraging the combined catalytic cycles thermodynamically to form an overall energetically favorable C-O cleavage reaction. This Account reviews recent developments on thermodynamically leveraged tandem catalysis for ether and more recently, ester C-O bond cleavage undertaken at Northwestern University. First, the fundamentals of lanthanide-catalyzed hydroelementation are reviewed, with particular focus on ether C-O bond formation (hydroalkoxylation). Next, the reverse C-O cleavage/retrohydroalkoxylation processes enabled by tandem catalysis are

  9. Reactivity of mononuclear alkylperoxo copper(II) complex. O-O bond cleavage and C-H bond activation. (United States)

    Kunishita, Atsushi; Ishimaru, Hirohito; Nakashima, Satoru; Ogura, Takashi; Itoh, Shinobu


    A detailed reactivity study has been carried out for the first time on a new mononuclear alkylperoxo copper(II) complex, which is generated by the reaction of copper(II) complex supported by the bis(pyridylmethyl)amine tridentate ligand containing a phenyl group at the 6-position of the pyridine donor groups and cumene hydroperoxide (CmOOH) in CH3CN. The cumylperoxo copper(II) complex thus obtained has been found to undergo homolytic cleavage of the O-O bond and induce C-H bond activation of exogenous substrates, providing important insights into the catalytic mechanism of copper monooxygenases.

  10. New insight into the cleavage reaction of Nostoc sp. strain PCC 7120 carotenoid cleavage dioxygenase in natural and nonnatural carotenoids. (United States)

    Heo, Jinsol; Kim, Se Hyeuk; Lee, Pyung Cheon


    Carotenoid cleavage dioxygenases (CCDs) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. In this study, we investigated the activity and substrate preferences of NSC3, a CCD of Nostoc sp. strain PCC 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. NSC3 cleaved β-apo-8'-carotenal at 3 positions, C-13 C-14, C-15 C-15', and C-13' C-14', revealing a unique cleavage pattern. NSC3 cleaves the natural structure of carotenoids 4,4'-diaponeurosporene, 4,4'-diaponeurosporen-4'-al, 4,4'-diaponeurosporen-4'-oic acid, 4,4'-diapotorulene, and 4,4'-diapotorulen-4'-al to generate novel cleavage products (apo-14'-diaponeurosporenal, apo-13'-diaponeurosporenal, apo-10'-diaponeurosporenal, apo-14'-diapotorulenal, and apo-10'-diapotorulenal, respectively). The study of carotenoids with natural or nonnatural structures produced by using synthetic modules could provide information valuable for understanding the cleavage reactions or substrate preferences of other CCDs in vivo and in vitro.

  11. Transition metal-catalyzed oxidative double bond cleavage of simple and bio-derived alkenes and unsaturated fatty acids

    NARCIS (Netherlands)

    Spannring, Peter; Bruijnincx, Pieter C. A.; Weckhuysen, Bert. M.; Klein Gebbink, Bert


    The oxidative cleavage of the C=C double bond in unsaturated fatty acids into aldehydes or carboxylic acids is a reaction of current interest in biomass valorization. The products of this reaction, which is currently being performed on an industrial scale by means of ozonolysis, can be applied for t

  12. Heterolytic OO bond cleavage: Functional role of Glu113 during bis-Fe(IV) formation in MauG. (United States)

    Geng, Jiafeng; Huo, Lu; Liu, Aimin


    The diheme enzyme MauG utilizes H2O2 to perform oxidative posttranslational modification on a protein substrate. A bis-Fe(IV) species of MauG was previously identified as a key intermediate in this reaction. Heterolytic cleavage of the OO bond of H2O2 drives the formation of the bis-Fe(IV) intermediate. In this work, we tested a hypothesis that a glutamate residue, Glu113 in the distal pocket of the pentacoordinate heme of MauG, facilitates heterolytic OO bond cleavage, thereby leading to bis-Fe(IV) formation. This hypothesis was proposed based on sequence alignment and structural comparison with other H2O2-utilizing hemoenzymes, especially those from the diheme enzyme superfamily that MauG belongs to. Electron paramagnetic resonance (EPR) characterization of the reaction between MauG and H2O2 revealed that mutation of Glu113 inhibited heterolytic OO bond cleavage, in agreement with our hypothesis. This result was further confirmed by the HPLC study in which an analog of H2O2, cumene hydroperoxide, was used to probe the pattern of OO bond cleavage. Together, our data suggest that Glu113 functions as an acid-base catalyst to assist heterolytic OO bond cleavage during the early stage of the catalytic reaction. This work advances our mechanistic understanding of the H2O2-activation process during bis-Fe(IV) formation in MauG.

  13. Enantioselective epoxidation and carbon-carbon bond cleavage catalyzed by Coprinus cinereus peroxidase and myeloperoxidase. (United States)

    Tuynman, A; Spelberg, J L; Kooter, I M; Schoemaker, H E; Wever, R


    We demonstrate that myeloperoxidase (MPO) and Coprinus cinereus peroxidase (CiP) catalyze the enantioselective epoxidation of styrene and a number of substituted derivatives with a reasonable enantiomeric excess (up to 80%) and in a moderate yield. Three major differences with respect to the chloroperoxidase from Caldariomyces fumago (CPO) are observed in the reactivity of MPO and CiP toward styrene derivatives. First, in contrast to CPO, MPO and CiP produced the (S)-isomers of the epoxides in enantiomeric excess. Second, for MPO and CiP the H(2)O(2) had to be added very slowly (10 eq in 16 h) to prevent accumulation of catalytically inactive enzyme intermediates. Under these conditions, CPO hardly showed any epoxidizing activity; only with a high influx of H(2)O(2) (300 eq in 1.6 h) was epoxidation observed. Third, both MPO and CiP formed significant amounts of (substituted) benzaldehydes as side products as a consequence of C-alpha-C-beta bond cleavage of the styrene derivatives, whereas for CPO and cytochrome c peroxidase this activity is not observed. C-alpha-C-beta cleavage was the most prominent reaction catalyzed by CiP, whereas with MPO the relative amount of epoxide formed was higher. This is the first report of peroxidases catalyzing both epoxidation reactions and carbon-carbon bond cleavage. The results are discussed in terms of mechanisms involving ferryl oxygen transfer and electron transfer, respectively.

  14. Efficient Synthesis of Functionalized Benzimidazoles and Perimidines: Ytterbium Chloride Catalyzed CmC Bond Cleavage%Efficient Synthesis of Functionalized Benzimidazoles and Perimidines: Ytterbium Chloride Catalyzed CmC Bond Cleavage

    Institute of Scientific and Technical Information of China (English)

    Cai, Lijian; Ji, Xiaofeng; Yao, Zhigang; Xu, Fan; Shen, Qi


    An efficient method is developed for the synthesis of functionalized benzimidazoles and perimidines by the condensation of aryl diamines with β-carbonyl compounds catalyzed by ytterbium chloride. The reactions give good yields under mild conditions. A mechanism involving a lanthanide activated C--C bond cleavage is proposed.

  15. Oxidative cleavage of benzylic C-N bonds under metal-free conditions. (United States)

    Gong, Jin-Long; Qi, Xinxin; Wei, Duo; Feng, Jian-Bo; Wu, Xiao-Feng


    An interesting procedure for the oxidative cleavage of benzylic C-N bonds has been developed. Using TBAI as the catalyst and H2O2 as the oxidant, various benzylamines were transformed into their corresponding aromatic aldehydes in moderate to good yields. Notably, this is the first example of an oxidative cleavage of benzylic C-N bonds under metal-free conditions.

  16. NMR-spectroscopic characterization of phosphodiester bond cleavage catalyzed by the minimal hammerhead ribozyme. (United States)

    Fürtig, Boris; Richter, Christian; Schell, Peter; Wenter, Philipp; Pitsch, Stefan; Schwalbe, Harald


    In order to relate the conformational dynamics of the hammerhead ribozyme to its biological function the cleavage reaction catalyzed by the hammerhead ribozyme was monitored by time-resolved nuclear magnetic resonance (NMR) spectroscopy. For this purpose, the two nucleosides around the scissile phosphodiester bond were selectively (13)C labelled in multi-step organic syntheses starting from uniformly (13)C-labelled glucose. The phosphoamidites were incorporated using phosphoamidite chemistry in the hammerhead substrate strand. In addition, the 2'-OH group on the 5'-side of the hammerhead substrate strand was labelled with a photolabile protecting group. This labelling strategy enabled a detailed characterisation of the nucleotides around the scissile phosphodiester bond in the ground state conformation of the hammerhead ribozyme in the absence and presence of Mg(2+) ions as well as of the product state. Photochemical induction of the reaction in situ was further characterized by time-resolved NMR spectroscopy. The detailed structural and dynamic investigations revealed that the conformation of the hammerhead ribozyme is significantly affected by addition of Mg(2+) leading to an ensemble of conformations where dynamic transitions between energetically similar conformations occur on the ms-timescale in the presence of Mg(2+). The dynamic transitions are localized around the catalytic core. Cleavage from this ensemble cannot be described by mono-exponential kinetics but follows bi-exponential kinetics. A model is described to take into account these experimental data.

  17. Facile P-C/C-H Bond-Cleavage Reactivity of Nickel Bis(diphosphine) Complexes. (United States)

    Zhang, Shaoguang; Li, Haixia; Appel, Aaron M; Hall, Michael B; Bullock, R Morris


    Unusual cleavage of P-C and C-H bonds of the P2 N2 ligand, in heteroleptic [Ni(P2 N2 )(diphosphine)](2+) complexes under mild conditions, results in the formation of an iminium formyl nickelate featuring a C,P,P-tridentate coordination mode. The structures of both the heteroleptic [Ni(P2 N2 )(diphosphine)](2+) complexes and the resulting iminium formyl nickelate have been characterized by NMR spectroscopy and single-crystal X-ray diffraction analysis. Density functional theory (DFT) calculations were employed to investigate the mechanism of the P-C/C-H bond cleavage, which involves C-H bond cleavage, hydride rotation, Ni-C/P-H bond formation, and P-C bond cleavage.

  18. Cleavage of a specific bond in troponin C by thrombin. (United States)

    Leavis, P C; Rosenfeld, S; Lu, R C


    Limited proteolysis of rabbit skeletal troponin C with bovine thrombin yielded two fragments, TH1 (Mr = 11000) containing Ca2+ binding regions I--III and TH2 (Mr = 6000) containing region IV. Determination of the partial sequences of the fragments established the site of cleavage at Arg120-Ala121. Secondary cleavage by thrombin at other arginyl or lysyl residues in troponin C was ruled out by the sequence data and by the amino acid compositions of the two fragments.

  19. Reaction between radicals and N-alkoxyamines As coordinated cleavage with fragmentation (United States)

    Denisov, E. T.; Shestakov, A. F.


    Quantum chemical calculations of the enthalpy and activation energy of two reactions with MeO{2/⊙} attacking the CH- and CH2-groups of 2,2,6,6-tetramethylpiperidineoxy-2'-butane are performed. It is shown that the cleavage of hydrogen atoms is accompanied by coordinated breaking of N-O-bonds in the former case and C-O-bonds in the latter. Based on the obtained results, a new scheme is proposed for the cyclic mechanism behind the cleavage of chains on nitroxyl radicals in oxidizing hydrocarbons and polymers that agrees with experimental data. At the center of this cyclic mechanism lies the fast exothermic reaction between peroxyl radicals and N-alkoxyamine with the cleavage of H atoms and the coordinated fragmentation of molecules. Using the model of intersecting parabolas, an algorithm for calculating the enthalpies, activation energies, and rate constants of these reactions with the participation of alkyl, alkoxy, aminyl, peroxyl, phenoxyl, thiyl, and hydroxyl radicals is proposed.

  20. Photocatalytic C-C Bond Cleavage and Amination of Cycloalkanols by Cerium(III) Chloride Complex. (United States)

    Guo, Jing-Jing; Hu, Anhua; Chen, Yilin; Sun, Jianfeng; Tang, Haoming; Zuo, Zhiwei


    A general strategy for the cleavage and amination of C-C bonds of cycloalkanols has been achieved through visible-light-induced photoredox catalysis utilizing a cerium(III) chloride complex. This operationally simple methodology has been successfully applied to a wide array of unstrained cyclic alcohols, and represents the first example of catalytic C-C bond cleavage and functionalization of unstrained secondary cycloalkanols.

  1. Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. (United States)

    Zaug, A J; Grabowski, P J; Cech, T R

    The intervening sequence (IVS) of the Tetrahymena ribosomal RNA precursor is excised as a linear RNA molecule which subsequently cyclizes itself in a protein-independent reaction. Cyclization involves cleavage of the linear IVS RNA 15 nucleotides from its 5' end and formation of a phosphodiester bond between the new 5' phosphate and the original 3'-hydroxyl terminus of the IVS. This recombination mechanism is analogous to that by which splicing of the precursor RNA is achieved. The circular molecules appear to have no direct function in RNA splicing, and we propose the cyclization serves to prevent unwanted RNA from driving the splicing reactions backwards.

  2. Aliphatic C-C Bond Cleavage in α-Hydroxy Ketones by a Dioxygen-Derived Nucleophilic Iron-Oxygen Oxidant. (United States)

    Bhattacharya, Shrabanti; Rahaman, Rubina; Chatterjee, Sayanti; Paine, Tapan K


    A nucleophilic iron-oxygen oxidant, formed in situ in the reaction between an iron(II)-benzilate complex and O2 , oxidatively cleaves the aliphatic C-C bonds of α-hydroxy ketones. In the cleavage reaction, α-hydroxy ketones without any α-C-H bond afford a 1:1 mixture of carboxylic acid and ketone. Isotope labeling studies established that one of the oxygen atoms from dioxygen is incorporated into the carboxylic acid product. Furthermore, the iron(II) complex cleaves an aliphatic C-C bond of 17-α-hydroxyprogesterone affording androstenedione and acetic acid. The O2 -dependent aliphatic C-C bond cleavage of α-hydroxy ketones containing no α-C-H bond bears similarity to the lyase activity of the heme enzyme, cytochrome P450 17A1 (CYP17A1).

  3. Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons. (United States)

    Bythell, Benjamin J; Suhai, Sándor; Somogyi, Arpád; Paizs, Béla


    The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

  4. Facile C-S, S-H, and S-S bond cleavage using a nickel(0) NHC complex. (United States)

    Schaub, Thomas; Backes, Marc; Plietzsch, Oliver; Radius, Udo


    [Ni2(iPr2Im)4(COD)] 1 (iPr2Im = 1,3-di(isopropyl)-imidazol-2-ylidene) reacts at room temperature with the thioethers methyl para-tolyl sulfide, ethyl phenyl sulfide, benzothiophene and dibenzothiophene to afford the C-S bond cleavage products [Ni(iPr2Im)2(4-CH3-C6H4)(SMe)] 2, [Ni(iPr2Im)2(C6H5)(SEt)] 3, [Ni(iPr2Im)2(1,8-benzothiophenylato)] 4 and [Ni(iPr2Im)2(C,S-dibenzothiophenylato)] 5. In contrast to the reaction of thioethers or sulfoxides (reported earlier), no C-S bond cleavage was observed for the reaction of 1 with the sulfones bezothiophene-1,1-dioxide and methyl phenyl sulfone. In those cases the stable compounds [Ni(iPr2Im)2(eta2-2,3-benzothiophene-1,1-dioxide)] 6 and [Ni(iPr2Im)2(eta2-MeSO2C6H5)] 7 with a eta2-coordinated sulfone ligand have been isolated. Compound 6 has been structurally characterized. S-H bond cleavage was observed using 2-methyl-2-propanthiol to afford [Ni(iPr2Im)2(H)(StBu)] 8. The reaction of 1 with disulfides led to the dithiolato complexes [Ni(iPr2Im)2(SR)2] (R = tBu 9, Me 10, Ph 11) by S-S bond scission.

  5. Carbon-carbon bond cleavage of 1,2-hydroxy ethers b7 vanadium(V) dipicolinate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Susan K [Los Alamos National Laboratory; Gordon, John C [Los Alamos National Laboratory; Thorn, David L [Los Alamos National Laboratory; Scott, Brian L [Los Alamos National Laboratory; Baker, R Tom [Los Alamos National Laboratory


    The development of alternatives to current petroleum-based fuels and chemicals is becoming increasingly important due to concerns over climate change, growing world energy demand, and energy security issues. Using non-food derived biomass to produce renewable feedstocks for chemicals and fuels is a particularly attractive possibility. However, the majority of biomass is in the form of lignocellulose, which is often not fully utilized due to difficulties associated with breaking down both lignin and cellulose. Recently, a number of methods have been reported to transform cellulose directly into more valuable materials such as glucose, sorbitol, 5-(chloromethyl)furfural, and ethylene glycol. Less progress has been made with selective transformations of lignin, which is typically treated in paper and forest industries by kraft pulping (sodium hydroxide/sodium sulfide) or incineration. Our group has begun investigating aerobic oxidative C-C bond cleavage catalyzed by dipicolinate vanadium complexes, with the idea that a selective C-C cleavage reaction of this type could be used to produce valuable chemicals or intermediates from cellulose or lignin. Lignin is a randomized polymer containing methoxylated phenoxy propanol units. A number of different linkages occur naturally; one of the most prevalent is the {beta}-O-4 linkage shown in Figure 1, containing a C-C bond with 1,2-hydroxy ether substituents. While the oxidative C-C bond cleavage of 1,2-diols has been reported for a number of metals, including vanadium, iron, manganese, ruthenium, and polyoxometalate complexes, C-C bond cleavage of 1,2-hydroxy ethers is much less common. We report herein vanadium-mediated cleavage of C-C bonds between alcohol and ether functionalities in several lignin model complexes. In order to explore the scope and potential of vanadium complexes to effect oxidative C-C bond cleavage in 1,2-hydroxy ethers, we examined the reactivity of the lignin model complexes pinacol monomethyl ether (A

  6. Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane II


    The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.

  7. Scandium(iii) triflate-promoted serine/threonine-selective peptide bond cleavage. (United States)

    Ni, Jizhi; Sohma, Youhei; Kanai, Motomu


    The site-selective cleavage of peptide bonds is an important chemical modification that is useful not only for the structural determination of peptides, but also as an artificial modulator of peptide/protein function and properties. Here we report site-selective hydrolysis of peptide bonds at the Ser and Thr positions with a high conversion yield. This chemical cleavage relies on Sc(iii)-promoted N,O-acyl rearrangement and subsequent hydrolysis. The method is applicable to a broad scope of polypeptides with various functional groups, including a post-translationally modified peptide that is unsuitable for enzymatic hydrolysis. The system was further extended to site-selective cleavage of a native protein, Aβ1-42, which is closely related to the onset of Alzheimer's disease.

  8. Facile P-C/C-H Bond-Cleavage Reactivity of Nickel Bis(diphosphine) Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shaoguang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Li, Haixia [Texas A & M Univ., College Station, TX (United States). Dept. of Chemistry; Appel, Aaron M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hall, Michael B. [Texas A & M Univ., College Station, TX (United States). Dept. of Chemistry; Bullock, R. Morris [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)


    Unusual cleavage of P-C and C-H bonds of the P2N2 ligand in heteroleptic [Ni(P2N2)(diphosphine)]2+ complexes results in the formation of an iminium formyl nickelate featuring a C,P,P-tridentate coordination mode.

  9. Probing Electron-Induced Bond Cleavage at the Single-Molecule Level Using DNA Origami Templates

    DEFF Research Database (Denmark)

    Keller, Adrian Clemens; Bald, Ilko; Rotaru, Alexandru;


    specifically designed oligonucleotide targets that are attached to DNA origami templates. In this way, we use a highly selective approach to compare the efficiency of the electron-induced dissociation of a single disulfide bond with the more complex cleavage of the DNA backbone within a TT dinucleotide...

  10. Biotic and abiotic carbon to sulfur bond cleavage. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Frost, J.W.


    The microbial desulfurization of organosulfur compounds occurs by unprecedented and largely unexplored biochemical processes. A study of such biotic desulfurizations can be expected to give rise to new and useful chemistry and enzymology. The potential value of understanding and harnessing these processes is seen in relation to the need for methods for the removal of organically bound sulfur from coal and the degradation of organic sulfur-containing pollutants. This research effort has been directed towards an examination of desulfurization ability in well characterized microorganisms, the isolation of bacteria with desulfurization ability from natural sources, the characterization and mechanistic evaluation of the observed biocatalytic processes, the development of biomimetic synthetic organic chemistry based on biotic desulfurization mechanisms and the design and preparation of improved coal model compounds for use in microbial selection processes. A systematic approach to studying biodesulfurizations was undertaken in which organosulfur compounds have been broken down into classes based on the oxidation state of the sulfur atom and the structure of the rest of the organic material. Microbes have been evaluated in terms of ability to degrade organosulfur compounds with sulfur in its sulfonic acid oxidation state. These compounds are likely intermediates in coal desulfurization and are present in the environment as persistent pollutants in the form of detergents. It is known that oxygen bonded to sulfur lowers the carbon-sulfur bond energy, providing a thermodynamic basis for starting with this class of compounds.

  11. Efficient nickel mediated carbon-carbon bond cleavage of organonitriles. (United States)

    Schaub, Thomas; Döring, Christian; Radius, Udo


    The reactions of the nickel complex [Ni(2)(iPr(2)Im)4(COD)] 1 with organonitriles smoothly and irreversibly proceed via intermediates with eta(2)-coordinated organonitrile ligands such as [Ni(iPr(2)Im)2(eta(2)-(CN)-PhCN)] 2 and [Ni(iPr(2)Im)2(eta(2)-(CN)-pTolCN)] 4 to yield aryl cyanide complexes of the type trans-[Ni(iPr(2)Im)2(CN)(Ar)] (Ar = Ph 3, pTol 5, 4-CF(3)C(6)H(4) 6, 2,4-(OMe)2C(6)H(3) 7, 2-C(4)H(3)O 8, 2-C(5)H(4)N 9). The compounds 3, 7, 9 and have been structurally characterized. For the conversion of 2 to 3 a free activation enthalpy DeltaG++(328 K) of 103.47 +/- 0.79 kJ mol(-1) was calculated from time dependent NMR spectroscopy. The analogous reaction of arylnitriles with electron releasing substituents or heteroaromatic organonitriles is significantly faster compared to the reaction with benzonitrile or toluonitrile. The reactions of 1 with acetonitrile or trimethylsilyl cyanide afforded [Ni(iPr(2)Im)2(CN)(Me)] 10 and structurally characterized [Ni(iPr(2)Im)2(CN)(SiMe(3))] 11. The usage of an organonitrile with a longer alkyl chain, adiponitrile, yielded [Ni(iPr(2)Im)2(eta(2)-(CN)-NCC(4)H(8)CN)] 12 as well as the C-CN activation product [Ni(iPr(2)Im)2(CN)(C(4)H(8)CN)]13 in thermal and photochemical reactions, although this pathway seems to be significantly interfered with by decomposition pathways under the formation of the dicyanide complex [Ni(iPr(2)Im)(2)(CN)(2)] 14.

  12. From polymer to monomer: cleavage and rearrangement of Si-O-Si bonds after oxidation yielded an ordered cyclic crystallized structure. (United States)

    Zuo, Yujing; Gou, Zhiming; Cao, Jinfeng; Yang, Zhou; Lu, Haifeng; Feng, Shengyu


    Polymerization reactions are very common in the chemical industry, however, the reaction in which monomers are obtained from polymers is rarely invesitgated. This work reveals for the first time that oxone can break the Si-O-Si bond and induce further rearrangement to yield an ordered cyclic structure. The oxidation of P1, which is obtained by reaction of 2,2'-1,2-ethanediylbis(oxy)bis(ethanethiol) (DBOET) with 1,3-divinyl-1,1,3,3-tetramethyldisiloxane (MM(Vi)), with oxone yielded cyclic crystallized sulfone-siloxane dimer (P1-ox) after unexpected cleavage and rearrangement of the Si-O-Si bond.

  13. Substituent-controlled selective synthesis of N-acyl 2-aminothiazoles by intramolecular Zwitterion-mediated C-N bond cleavage. (United States)

    Wang, Yang; Zhao, Fei; Chi, Yue; Zhang, Wen-Xiong; Xi, Zhenfeng


    The cleavage of C-N bonds is an interesting and challenging subject in modern organic synthesis. We have achieved the first zwitterion-controlled C-N bond cleavage in the MCR reaction among lithium alkynethiolates, bulky carbodiimides, and acid chlorides to construct N-acyl 2-aminothiazoles. This is a simple, highly efficient, and general method for the preparation of N-acyl 2-aminothiazoles with a broad range of substituents. The selective synthesis of N-acyl 2-aminothiazoles significantly depends on the steric hindrance of carbodiimides. The result is in striking contrast with our previous convergent reaction giving 5-acyl-2-iminothiazolines via 1,5-acyl migration. It is indeed interesting that the slight change of the substituents on the carbodiimides can completely switch the product structure. Experimental and theoretical results demonstrate the reason why the C-N bond cleavage in the present system is prior to the acyl migration. The intramolecular hydrogen relay via unprecedented Hofmann-type elimination is essential for this totally new zwitterion-controlled C-N bond cleavage.

  14. Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Hao-Bo [ORNL; Parks, Jerry M [ORNL; Johs, Alexander [ORNL; Smith, Jeremy C [ORNL


    In this chapter, we summarize recent work from our laboratory and provide new perspective on two important aspects of bacterial mercury resistance: the molecular mechanism of transcriptional regulation by MerR, and the enzymatic cleavage of the Hg-C bond in methylmercury by the organomercurial lyase, MerB. Molecular dynamics (MD) simulations of MerR reveal an opening-and-closing dynamics, which may be involved in initiating transcription of mercury resistance genes upon Hg(II) binding. Density functional theory (DFT) calculations on an active-site model of the enzyme reveal how MerB catalyzes the Hg-C bond cleavage using cysteine coordination and acid-base chemistry. These studies provide insight into the detailed mechanisms of microbial gene regulation and defense against mercury toxicity.

  15. Ionic S(N)i-Si Nucleophilic Substitution in N-Methylaniline-Induced Si-Si Bond Cleavages of Si2Cl6. (United States)

    Zhang, Jie; Xie, Ju; Lee, Myong Euy; Zhang, Lin; Zuo, Yujing; Feng, Shengyu


    N-Methylaniline-induced Si-Si bond cleavage of Si2Cl6 has been theoretically studied. All calculations were performed by using DFT at the MPWB1K/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) levels. An ionic SN i-Si nucleophilic substitution mechanism, which is a newly found nucleophilic substitution in silicon-containing compounds, is proposed in the N-methylaniline-induced Si-Si bond cleavage in Si2Cl6. Unlike general S(N)i-Si nucleophilic substitutions that go through a pentacoordinated silicon transition state, ionic nucleophilic substitution goes through a tetracoordinated silicon transition state, in which the Si-Si bond is broken and siliconium ions are formed. Special cleavage of the Si-Si bond is presumably due to the good bonding strength between Si and N atoms, which leads to polarization of the Si-Si bond and eventually to heterolytic cleavage. Calculation results show that, in excess N-methylaniline, the final products of the reaction, including (NMePh)(3-n) SiHCl(n) (n=0-2) and (NMePh)(4-n) SiCl(n) (n=2-3), are the Si-Si cleavage products of Si2Cl6 and the corresponding amination products of the former. The ionic S(N)i-Si nucleophilic substitution mechanism can also be employed to describe the amination of chlorosilane by N-methylaniline. The suggested mechanisms are consistent with experimental data.

  16. Metal-catalyzed C-C bond cleavage in alkanes: effects of methyl substitution on transition-state structures and stability. (United States)

    Flaherty, David W; Hibbitts, David D; Iglesia, Enrique


    Methyl substituents at C-C bonds influence hydrogenolysis rates and selectivities of acyclic and cyclic C2-C8 alkanes on Ir, Rh, Ru, and Pt catalysts. C-C cleavage transition states form via equilibrated dehydrogenation steps that replace several C-H bonds with C-metal bonds, desorb H atoms (H*) from saturated surfaces, and form λ H2(g) molecules. Activation enthalpies (ΔH(‡)) and entropies (ΔS(‡)) and λ values for (3)C-(x)C cleavage are larger than for (2)C-(2)C or (2)C-(1)C bonds, irrespective of the composition of metal clusters or the cyclic/acyclic structure of the reactants. (3)C-(x)C bonds cleave through α,β,γ- or α,β,γ,δ-bound transition states, as indicated by the agreement between measured activation entropies and those estimated for such structures using statistical mechanics. In contrast, less substituted C-C bonds involve α,β-bound species with each C atom bound to several surface atoms. These α,β configurations weaken C-C bonds through back-donation to antibonding orbitals, but such configurations cannot form with (3)C atoms, which have one C-H bond and thus can form only one C-M bond. (3)C-(x)C cleavage involves attachment of other C atoms, which requires endothermic C-H activation and H* desorption steps that lead to larger ΔH(‡) values but also larger ΔS(‡) values (by forming more H2(g)) than for (2)C-(2)C and (2)C-(1)C bonds, irrespective of alkane size (C2-C8) or cyclic/acyclic structure. These data and their mechanistic interpretation indicate that low temperatures and high H2 pressures favor cleavage of less substituted C-C bonds and form more highly branched products from cyclic and acyclic alkanes. Such interpretations and catalytic consequences of substitution seem also relevant to C-X cleavage (X = S, N, O) in desulfurization, denitrogenation, and deoxygenation reactions.


    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane II


    The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project was focused on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate deaminase. The objective of the final phase of the project will be to develop derivative C-N bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments resulted in the isolation of microbial cultures that utilize aromatic amides as sole nitrogen sources, several amidase genes were cloned and were included in directed evolution experiments to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. During the second year of the project (October, 2003-September, 2004) enrichment culture experiments succeeded in isolating a mixed bacterial culture that can utilize 2-aminobiphenyl as a sole nitrogen source, directed evolution experiments were focused on the aniline dioxygenase enzyme that is capable of deaminating aniline, and expression vectors were constructed to enable the expression of genes encoding C-N bond cleaving enzymes in Rhodococcus hosts. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the

  18. Rh-Catalyzed C–C Bond Cleavage by Transfer Hydroformylation (United States)

    Murphy, Stephen K.; Park, Jung-Woo; Cruz, Faben A.; Dong, Vy M.


    The dehydroformylation of aldehydes to generate olefins occurs during the biosynthesis of various sterols, including cholesterol in humans. Here, we implement a synthetic version that features the transfer of a formyl group and hydride from an aldehyde substrate to a strained olefin acceptor. A Rh(Xantphos)(benzoate) catalyst activates aldehyde C–H bonds with high chemoselectivity to trigger C–C bond cleavage and generate olefins at low loadings (0.3 to 2 mol%) and temperatures (22 to 80 °C). This mild protocol can be applied to various natural products and was used to achieve a three step synthesis of (+)-yohimbenone. A study of the mechanism reveals that the benzoate counterion acts as a proton-shuttle to enable transfer hydroformylation. PMID:25554782


    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane III


    The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project will focus on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate amidase. The objective of the final phase of the project will be to develop derivative CN bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. The project is on schedule and no major difficulties have been encountered. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments have resulted in the isolation of promising cultures that may be capable of cleaving C-N bonds in aromatic amides, several amidase genes have been cloned and are currently undergoing directed evolution to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. Future research will address expression of these genes in Rhodococcus erythropolis. Enrichment culture experiments and directed evolution experiments continue to be a main focus of research activity and further work is required to obtain an appropriate amidase that will selectively cleave C-N bonds in aromatic substrates. Once an appropriate amidase gene is obtained it must be combined with genes encoding an enzyme capable of converting carbazole to 2'aminobiphenyl-2,3-diol: specifically carA genes. The carA genes from two sources have been cloned and are ready for construction of C-N bond cleavage

  20. A copper complex supported by an N2S-tridentate ligand inducing efficient heterolytic O-O bond cleavage of alkylhydroperoxide. (United States)

    Tano, Tetsuro; Mieda, Kaoru; Sugimoto, Hideki; Ogura, Takashi; Itoh, Shinobu


    We have recently reported a copper(II)-superoxide complex supported by an N3-tridentate ligand (L(N3)), which exhibits a similar structure and reactivity to those of a putative reactive intermediate involved in the catalytic reactions of copper monooxygenases such as peptidylglycine α-hydroxylating monooxygenase (PHM) and dopamine β-monooxygenase (DβM). In this study, we have synthesised and characterised copper complexes supported by a related sulphur-containing ligand (L(N2S)) to get insight into the notable electronic effect of the sulphur donor atom in the reaction with cumene hydroperoxide, inducing efficient heterolytic O-O bond cleavage.

  1. Mechanistic aspects of dinitrogen cleavage and hydrogenation to produce ammonia in catalysis and organometallic chemistry: relevance of metal hydride bonds and dihydrogen. (United States)

    Jia, Hong-Peng; Quadrelli, Elsje Alessandra


    Dinitrogen cleavage and hydrogenation by transition-metal centers to produce ammonia is central in industry and in Nature. After an introductory section on the thermodynamic and kinetic challenges linked to N2 splitting, this tutorial review discusses three major classes of transition-metal systems (homogeneous, heterogeneous and biological) capable of achieving dissociation and hydrogenation of dinitrogen. Molecular complexes, solid-state Haber-Bosch catalytic systems, silica-supported tantalum hydrides and nitrogenase will be discussed. Emphasis is focused on the reaction mechanisms operating in the process of dissociation and hydrogenation of dinitrogen, and in particular on the key role played by metal hydride bonds and by dihydrogen in such reactions.

  2. Mechanisms of Bond Cleavage during Manganese Oxide and UV Degradation of Glyphosate: Results from Phosphate Oxygen Isotopes and Molecular Simulations. (United States)

    Jaisi, Deb P; Li, Hui; Wallace, Adam F; Paudel, Prajwal; Sun, Mingjing; Balakrishna, Avula; Lerch, Robert N


    Degradation of glyphosate in the presence of manganese oxide and UV light was analyzed using phosphate oxygen isotope ratios and density function theory (DFT). The preference of C-P or C-N bond cleavage was found to vary with changing glyphosate/manganese oxide ratios, indicating the potential role of sorption-induced conformational changes on the composition of intermediate degradation products. Isotope data confirmed that one oxygen atom derived solely from water was incorporated into the released phosphate during glyphosate degradation, and this might suggest similar nucleophilic substitution at P centers and C-P bond cleavage both in manganese oxide- and UV light-mediated degradation. The DFT results reveal that the C-P bond could be cleaved by water, OH(-) or (•)OH, with the energy barrier opposing bond dissociation being lowest in the presence of the radical species, and that C-N bond cleavage is favored by the formation of both nitrogen- and carbon-centered radicals. Overall, these results highlight the factors controlling the dominance of C-P or C-N bond cleavage that determines the composition of intermediate/final products and ultimately the degradation pathway.

  3. Mechanism and Thermodynamics of Reductive Cleavage of Carbon-Halogen Bonds in the Polybrominated Aliphatic Electrophiles. (United States)

    Rosokha, Sergiy V; Lukacs, Emoke; Ritzert, Jeremy T; Wasilewski, Adam


    Quantum-mechanical computations revealed that, despite the presence of electron-withdrawing and/or π-acceptor substituents, the lowest unoccupied molecular orbitals (LUMO) of the polybromosubstituted aliphatic molecules R-Br (R-Br = C3Br2F6, CBr3NO2, CBr3CN, CBr3CONH2, CBr3CO2H, CHBr3, CFBr3, CBr4, CBr3COCBr3) are delocalized mostly over their bromine-containing fragments. The singly occupied molecular orbitals in the corresponding vertically excited anion radicals (R-Br(•-))* are characterized by essentially the same shapes and show nodes in the middle of the C-Br bonds. An injection of an electron into the antibonding LUMO results in the barrierless dissociation of the anion-radical species and the concerted reductive cleavages of C-Br bonds leading to the formation of the loosely bonded {R(•)···Br(-)} associates. The interaction energies between the fragments of these ion-radical pairs vary from ∼10 to 20 kcal mol(-1) in the gas phase and from 1 to 3 kcal mol(-1) in acetonitrile. In accord with the concerted mechanism of reductive cleavage, all R-Br molecules showed completely irreversible reduction waves in the voltammograms in the whole range of the scan rates employed (from 0.05 to 5 V s(-1)). Also, the transfer coefficients α, established from the width of these waves and dependence of reduction peak potentials Ep on the scan rates, were significantly lower than 0.5. The standard reduction potentials of the R-Br electrophiles, E(o)R-Br/R·+X(-), and the corresponding R(•) radicals, E(o)R(•)/R(-), were calculated in acetonitrile using the appropriate thermodynamic cycles. In agreement with these calculations, which indicated that the R(•) radicals resulting from the reductive cleavage of the R-Br molecules are stronger oxidants than their parents, the reduction peaks' currents in cyclic voltammograms were consistent with the two-electron transfer processes.

  4. Alcohol-Induced C-N Bond Cleavage of Cyclometalated N-Heterocyclic Carbene Ligands with a Methylene-Linked Pendant Imidazolium Ring. (United States)

    Zhong, Wei; Fei, Zhaofu; Scopelliti, Rosario; Dyson, Paul J


    Reaction of the pentamethylcyclopentadienyl rhodium iodide dimer [Cp*RhI2 ]2 with 1,1'-diphenyl-3,3'-methylenediimidazolium diiodide in non-alcohol solvents, in the presence of base, led to the formation of bis-carbene complex [Cp*Rh(bis-NHC)I]I (bis-NHC=1,1'-diphenyl-4,4'-methylenediimidazoline-5,5'-diylidene). In contrast, when employing alcohols as the solvent in the same reaction, cleavage of a methylene C-N bond is observed, affording ether-functionalized (cyclometalated) carbene ligands coordinated to the metal center and the concomitant formation of complexes with a coordinated imidazole ligand. Studies employing other 1,1'-diimidazolium salts indicate that the cyclometalation step is a prerequisite for the activation/scission of the C-N bond and, based on additional experimental data, a SN 2 mechanism for the reaction is tentatively proposed.

  5. Pyramidalization of the Glycosidic Nitrogen Provides the Way for Efficient Cleavage of the N‑Glycosidic Bond of 8‑OxoG with the hOGG1 DNA Repair Protein

    NARCIS (Netherlands)

    Sebera, J.; Trantirek, L.; Tanaka, Y.; Sychrovský, V.


    A mechanistic pathway for cleavage of the N-glycosidic bond of 8-oxo-2′-deoxyguanosine (oxoG) catalyzed with the human 8-oxoguanine glycosylase 1 DNA repair protein (hOGG1) is proposed in this theoretical study. The reaction scheme suggests direct proton addition to the glycosidic nitrogen N9 of oxo

  6. On the viability of heterolytic peptide N-C(α) bond cleavage in electron capture and transfer dissociation mass spectrometry. (United States)

    Wodrich, Matthew D; Zhurov, Konstantin O; Corminboeuf, Clémence; Tsybin, Yury O


    While frequently employed as an experimental technique, the mechanistic picture surrounding the gas-phase dissociation of peptides carrying multiple positive charges during electron capture and electron transfer dissociation tandem mass spectrometry remains incomplete. Despite this mechanistic uncertainty, most proposals agree that the peptide backbone N-Cα bond located to the C-terminal (right) side of an aminoketyl radical formed in a peptide backbone during the electron capture process is homolytically cleaved. Recently, we introduced the "enol" mechanism, which proposes that a backbone N-Cα bond located to the N-terminal (left) side of an aminoketyl radical is cleaved heterolytically. Here, we further validate this mechanism using replica-exchange molecular dynamics to create unbiased representative sets of low-energy conformers for several model tryptic peptide systems (H-Alax-Lys-OH(2+), x = 3-5). Transition state barrier enthalpies for the cleavage of N-Cα bonds proceeding via the homolytic (right-side) and heterolytic (left-side) pathways, determined by density functional computations, identify the preferred cleavage route for each conformer. These findings support our original hypothesis that heterolytic N-Cα cleavage can exist in a competitive balance with homolytic cleavages, independent of the relative energy of the precursor dication species. Smaller peptide systems see decreased heterolytic N-Cα cleavage probabilities, likely resulting from an insufficient hydrogen-bonding network needed to stabilize and ultimately annihilate the transition state zwitterion. This observation may explain the early dismissal of left-side cleavage pathways based on computational studies employing small model systems.

  7. Alkene cleavage catalysed by heme and nonheme enzymes: reaction mechanisms and biocatalytic applications. (United States)

    Mutti, Francesco G


    The oxidative cleavage of alkenes is classically performed by chemical methods, although they display several drawbacks. Ozonolysis requires harsh conditions (-78°C, for a safe process) and reducing reagents in a molar amount, whereas the use of poisonous heavy metals such as Cr, Os, or Ru as catalysts is additionally plagued by low yield and selectivity. Conversely, heme and nonheme enzymes can catalyse the oxidative alkene cleavage at ambient temperature and atmospheric pressure in an aqueous buffer, showing excellent chemo- and regioselectivities in certain cases. This paper focuses on the alkene cleavage catalysed by iron cofactor-dependent enzymes encompassing the reaction mechanisms (in case where it is known) and the application of these enzymes in biocatalysis.

  8. Mechanism of SN2 disulfide bond cleavage by phosphorus nucleophiles. Implications for biochemical disulfide reducing agents. (United States)

    Dmitrenko, Olga; Thorpe, Colin; Bach, Robert D


    The B3LYP variant of DFT has been used to study the mechanism of S-S bond scission in dimethyl disulfide by a phosphorus nucleophile, trimethylphospine (TMP). The reaction is highly endothermic in the gas phase and requires significant external stabilization of the charged products. DFT calculations (B3LYP) were performed with explicit (water molecules added) and implicit solvent corrections (COSMO model). The transition structures for this SN2 displacement reaction in a number of model systems have been located and fully characterized. The reaction barriers calculated with different approaches for different systems are quite close (around 11 kcal/mol). Remarkably, the calculations suggest that the reaction is almost barrierless with respect to the preorganized reaction complex and that most of the activation energy is required to rearrange the disulfide and TMP to its most effective orientation for the SMe group transfer way. Different reactivities of different phosphorus nucleophiles were suggested to be the result of steric effects, as manifested largely by varying amounts of hindrance to solvation of the initial product phosphonium ion. These data indicate that the gas-phase addition of a phosphine to the disulfide moiety will most likely form a phosphonium cation-thiolate anion salt, in the presence of four or more water molecules, that provide sufficient H-bonding stabilization to allow displacement of the thiolate anion, a normal uncomplicated SN2 transition state is to be expected.

  9. Reaction kinetics of bond rotations in graphene

    KAUST Repository

    Skowron, Stephen T.


    The formation and healing processes of the fundamental topological defect in graphitic materials, the Stone-Wales (SW) defect, are brought into a chemical context by considering the rotation of a carbon-carbon bond as chemical reaction. We investigate the rates and mechanisms of these SW transformations in graphene at the atomic scale using transmission electron microscopy. We develop a statistical atomic kinetics formalism, using direct observations obtained under different conditions to determine key kinetic parameters of the reactions. Based on the obtained statistics we quantify thermally and irradiation induced routes, identifying a thermal process of healing with an activation energy consistent with predicted adatom catalysed mechanisms. We discover exceptionally high rates for irradiation induced SW healing, incompatible with the previously assumed mechanism of direct knock-on damage and indicating the presence of an efficient nonadiabatic coupling healing mechanism involving beam induced electronic excitations of the SW defect.

  10. Photoinitiated reactions in weakly bonded complexes

    Energy Technology Data Exchange (ETDEWEB)

    Wittig, C.


    This paper discusses photoinitiated reactions in weakly bonded binary complexes in which the constituents are only mildly perturbed by the intermolecular bond. Such complexes, with their large zero point excursions, set the stage for events that occur following electronic excitation of one of the constituents. This can take several forms, but in all cases, entrance channel specificity is imposed by the character of the complex as well as the nature of the photoinitiation process. This has enabled us to examine aspects of bimolecular processes: steric effects, chemical branching ratios, and inelastic scattering. Furthermore, monitoring reactions directly in the time domain can reveal mechanisms that cannot be inferred from measurements of nascent product excitations. Consequently, we examined several systems that had been studied previously by our group with product state resolution. With CO{sub 2}/HI, in which reaction occurs via a HOCO intermediate, the rates agree with RRKM predictions. With N{sub 2}O/HI, the gas phase single collision reaction yielding OH + N{sub 2} has been shown to proceed mainly via an HNNO intermediate that undergoes a 1,3-hydrogen shift to the OH + N{sub 2} channel. With complexes, ab initio calculations and high resolution spectroscopic studies of analogous systems suggest that the hydrogen, while highly delocalized, prefers the oxygen to the nitrogen. We observe that OH is produced with a fast risetime (< 250 fs) which can be attributed to either direct oxygen-side attack or rapid HNNO decomposition and/or a termolecular contribution involving the nearby iodine.

  11. Implications of protonation and substituent effects for C-O and O-P bond cleavage in phosphate monoesters. (United States)

    Loncke, Paul G; Berti, Paul J


    A recent study of phosphate monoesters that broke down exclusively through C-O bond cleavage and whose reactivity was unaffected by protonation of the nonbridging oxygens (Byczynski et al. J. Am. Chem. Soc. 2003, 125, 12541) raised several questions about the reactivity of phosphate monoesters, R-O-P(i). Potential catalytic strategies, particularly with regard to selectively promoting C-O or O-P bond cleavage, were investigated computationally through simple alkyl and aryl phosphate monoesters. Both C-O and O-P bonds lengthened upon protonating the bridging oxygen, R-O(H(+))-P(i), and heterolytic bond dissociation energies, DeltaH(C)(-)(O) and DeltaH(O)(-)(P), decreased. Which bond will break depends on the protonation state of the phosphoryl moiety, P(i), and the identity of the organosubstituent, R. Protonating the bridging oxygen when the nonbridging oxygens were already protonated favored C-O cleavage, while protonating the bridging oxygen of the dianion form, R-O-PO(3)(2)(-), favored O-P cleavage. Alkyl R groups capable of forming stable cations were more prone to C-O bond cleavage, with tBu > iPr > F(2)iPr > Me. The lack of effect on the C-O cleavage rate from protonating nonbridging oxygens could arise from two precisely offsetting effects: Protonating nonbridging oxygens lengthens the C-O bond, making it more reactive, but also decreases the bridging oxygen proton affinity, making it less likely to be protonated and, therefore, less reactive. The lack of effect could also arise without bridging oxygen protonation if the ratio of rate constants with different protonation states precisely matched the ratio of acidity constants, K(a). Calculations used hybrid density functional theory (B3PW91/6-31++G) methods with a conductor-like polarizable continuum model (CPCM) of solvation. Calculations on Me-phosphate using MP2/aug-cc-pVDZ and PBE0/aug-cc-pVDZ levels of theory, and variations on the solvation model, confirmed the reproducibility with different

  12. Effect of copper-sulphur bond on the DNA photo-cleavage activity of 2-(methylthio)ethylpyridine-2-carbaldimine copper(II) complexes

    Indian Academy of Sciences (India)

    Tarkeshwar Gupta; Ashis K Patra; Shanta Dhar; Munirathinam Nethaji; Akhil R Chakravarty


    The binding and photo-induced DNA cleavage activity of a binary complex [CuL2](ClO4)2 (1) and the in situ generated ternary complexes [CuLB](ClO4)2 from 1 (B: 1,10-phenanthroline, phen, 2; dipyrido[3,2-: 2',3'-]quinoxaline, dpq, 3) are studied, where L is a N2S-donor tridentate Schiff base 2-(methylthio)ethylpyridine-2-carbaldimine. Complex 1, structurally characterized by X-ray diffraction study, has six-coordinate meridional geometry showing CuN4S2 coordination. The Cu-N bond lengths are in the range of 1.968(3) to 2.158(4) Å. The Cu-S bond lengths of 2.599(2) and 2.705(2) Å are significantly long indicating weak covalent interaction between copper and sulphur atoms. The thiomethyl groups are cis to each other giving S-Cu-S angle of 75.82(5)°. The Cu-N(pyridyl) bond distances are longer than the Cu-N(imine) bonds. The complexes are redox active and display a quasi-reversible cyclic voltammetric response assignable to the Cu(II)/Cu(I) couple near 0.0 V vs SCE in DMF-Tris buffer (1 : 4 /) using 0.1 M KCl as supporting electrolyte. Electronic spectra of the complexes show a - band in the range 630 to 700 nm in DMF along with higher energy charge transfer bands. While complex 1 is a poor binder to DNA, the ternary complexes show good DNA binding propensity. The photo-nuclease activity of 1-3 is studied using UV and visible wavelengths. The DNA cleavage activity at 365 nm follows the order: 3 > 2 > 1. The cleavage reaction involves the formation of singlet oxygen as the reactive species in a type-II process.

  13. Substituent Directed Phototransformations of BN-Heterocycles: Elimination vs Isomerization via Selective B-C Bond Cleavage. (United States)

    Yang, Deng-Tao; Mellerup, Soren K; Peng, Jin-Bao; Wang, Xiang; Li, Quan-Song; Wang, Suning


    Electron-rich and -poor BN-heterocycles with benzyl-pyridyl backbones and two bulky aryls on the boron (Ar = tipp, BN-1, Ar = MesF, BN-2) have been found to display distinct molecular transformations upon irradiation by UV light. BN-1 undergoes an efficient photoelimination reaction forming a BN-phenanthrene with ΦPE = 0.25, whereas BN-2 undergoes a thermally reversible, stereoselective, and quantitative isomerization to a dark colored BN-1,3,5-cyclooctatriene (BN-1,3,5-COT, BN-2a). This unusual photoisomerization persists for other BN-heterocycles with electron-deficient aryls such as BN-3 with a benzyl-benzothiazolyl backbone and Mes(F) substituents or BN-4 with a benzyl-pyridyl backbone and two C6F5 groups on the boron. The photoisomerization of BN-4 goes beyond BN-1,3,5-COT (BN-4a), forming a new species (BN-1,3,6-COT, BN-4b) via C-F bond cleavage and [1,3]-F atom sigmatropic migration. Computational studies support that BN-4a is an intermediate in the formation of BN-4b. This work establishes that steric and electronic factors can effectively control the transformations of BN-heterocycles, allowing access to important and previously unknown BN-embedded species.

  14. Facile Access to Fluoroaromatic Molecules by Transition-Metal-Free C-F Bond Cleavage of Polyfluoroarenes: An Efficient, Green, and Sustainable Protocol. (United States)

    Liu, Cuibo; Zhang, Bin


    The creation of new bonds via C-F bond cleavage of polyfluoroarenes has proven to be an important and powerful tool in synthetic chemistry. Using such a strategy, a myriad of valuable partially fluoroaromatic molecules and building blocks can be obtained. The transition-metal-free nucleophilic aromatic substitution (SN Ar) strategy has aroused the continuing interest of researchers due to its simple, mild, economical, and environmentally benign characteristics, which have been successfully applied to C-F bond functionalizations. In this account, we present a summary of the recent investigations of polyfluoroarenes involving SN Ar reactions and discuss some of our recent endeavors in the construction of partially fluoroaromatic molecules. Through this strategy, many new bonds including C-C, C-N, C-O, C-S, and C-H bonds can be created. Additionally, brief discussions on the transformation mechanisms are also provided. Finally, we discuss the existing limitations of the SN Ar reactions of polyfluoroarenes as well as our perspective on the future development of this chemistry.

  15. The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing. (United States)

    Deweese, Joseph E; Osheroff, Neil


    Topoisomerase II is an essential enzyme that is required for virtually every process that requires movement of DNA within the nucleus or the opening of the double helix. This enzyme helps to regulate DNA under- and overwinding and removes knots and tangles from the genetic material. In order to carry out its critical physiological functions, topoisomerase II generates transient double-stranded breaks in DNA. Consequently, while necessary for cell survival, the enzyme also has the capacity to fragment the genome. The DNA cleavage/ligation reaction of topoisomerase II is the target for some of the most successful anticancer drugs currently in clinical use. However, this same reaction also is believed to trigger chromosomal translocations that are associated with specific types of leukemia. This article will familiarize the reader with the DNA cleavage/ligation reaction of topoisomerase II and other aspects of its catalytic cycle. In addition, it will discuss the interaction of the enzyme with anticancer drugs and the mechanisms by which these agents increase levels of topoisomerase II-generated DNA strand breaks. Finally, it will describe dietary and environmental agents that enhance DNA cleavage mediated by the enzyme.

  16. Carbon kinetic isotope effects at natural abundances during iron-catalyzed photolytic cleavage of Csbnd C bonds in aqueous phase α,ω-dicarboxylic acids (United States)

    Irei, Satoshi


    Carbon kinetic isotope effects (KIEs) at natural abundances during photolysis of Fe3+-oxalato, malonato, and succinato complexes in aqueous solution were studied to identify the Csbnd C bond cleaving mechanism of Fe3+-oxalato complexes under sunlight irradiation. Observed overall KIEs were 5.9‰, 11.5‰, and 8.4‰, respectively. This variation is inconsistent with secondary carbon KIEs for the Fesbnd O bond cleavage, but consistent with primary carbon KIEs for sequential cleavage of Fesbnd O and Csbnd C bonds. Position-specific probability of 13C content estimated KIEs of 5.9‰, 17.2‰, and 17‰ for 12Csbnd 13C bond cleavage, respectively, indicating the different KIEs for carboxyl-carboxyl and methyl-carboxyl cleavage.

  17. Amide bond cleavage initiated by coordination with transition metal ions and tuned by an auxiliary ligand. (United States)

    Yang, Yongpo; Lu, Chunxin; Wang, Hailong; Liu, Xiaoming


    The reaction of ligand , N,N-bis(pyridin-2-ylmethyl)acetamide, with five transition metal salts, FeCl3·6H2O, CuCl2·2H2O, Cu(ClO4)2·6H2O, ZnCl2 and K2PtCl4/KI, produced five metal complexes, [(μ-O)(FeClL')(FeCl3)] (), [CuLCl2] (), [CuBPA(ClO4)(CHCN)] ClO4 (), [ZnLCl2] () and [PtLI2] (), where = 1-(2,4,5-tri(pyridin-2-yl)-3-(pyridin-2-ylmethyl)imidazolidin-1-yl)ethanone which formed in situ, and BPA = bis(pyridin-2-ylmethyl)amine. The ligand and complexes were characterized by a variety of spectroscopic techniques including X-ray single crystal diffraction where applicable. Depending on the metal ion and auxiliary ligand of the complex, the acetyl group of the ligand could be either intact or cleaved. When ferric chloride hexahydrate was used, the deacetylation proceeded even further and a novel heterocyclic compound () was formed in situ. A possible mechanism was proposed for the formation of the heterocyclic compound found in complex . Our results indicate that to cleave effectively an amide bond, it is essential for a metal centre to bind to the amide bond and the metal centre is of sufficient Lewis acidity.

  18. Highly Efficient Oxidative Cleavage of Carbon-Carbon Double Bond over meso-Tetraphenyl Cobalt Porphyrin Catalyst in the Presence of Molecular Oxygen

    Institute of Scientific and Technical Information of China (English)

    周贤太; 纪红兵


    Highly efficient and selective carbon-carbon double bond aerobic cleavage of olefins catalyzed by metallopor- phyrins was investigated, and carbonyl compounds and epoxide were produced as the main products. CoTPP (co- balt meso-tetraphenyl porphyrin) showed excellent activity for the oxidative cleavage of carbon-carbon double bond by using styrene as model compound, in which the TOF (turnover frequency) and selectivity toward benzaldehyde was obtained with 2×10^4h-1 and 86%,respectively.

  19. Selective cleavage of an azaGly peptide bond by copper(II). Long-range effect of histidine residue. (United States)

    Mhidia, Reda; Melnyk, Oleg


    Several reports have highlighted the interest of replacing Gly, a frequent amino acid within bioactive peptides, by azaGly (Agly) to improve their stability, activity or for the design of prodrugs. Because metal catalysis is increasingly used for tailoring peptide molecules, we have studied the stability of Agly peptides in the presence of metal ions. In this study, we show that Cu(II), unlike other metal ions such as Fe(II), Fe(III), Pd(II), or Pt(II), induces the cleavage of Agly peptides at room temperature and pH 7.3. The cleavage occurred in the absence of an anchoring His residue within the peptide but it was accelerated when this amino acid was present in the sequence. The influence of His residue on the cleavage rate was minimal when His and Agly were adjacent, whereas large effects were observed for distant His residues. The reaction between Cu(II) and Agly peptides induced the formation of Cu(I) species, which could be detected using bicinchoninic acid as a probe. The nature of products formed in this reaction allowed suggesting a mechanism for the Cu(II)-induced cleavage of Agly peptides.

  20. Structural Characterization of N-Alkylated Twisted Amides: Consequences for Amide Bond Resonance and N-C Cleavage. (United States)

    Hu, Feng; Lalancette, Roger; Szostak, Michal


    Herein, we describe the first structural characterization of N-alkylated twisted amides prepared directly by N-alkylation of the corresponding non-planar lactams. This study provides the first experimental evidence that N-alkylation results in a dramatic increase of non-planarity around the amide N-C(O) bond. Moreover, we report a rare example of a molecular wire supported by the same amide C=O-Ag bonds. Reactivity studies demonstrate rapid nucleophilic addition to the N-C(O) moiety of N-alkylated amides, indicating the lack of n(N) to π*(C=O) conjugation. Most crucially, we demonstrate that N-alkylation activates the otherwise unreactive amide bond towards σ N-C cleavage by switchable coordination.

  1. The action of the bacterial toxin microcin B17. Insight into the cleavage-religation reaction of DNA gyrase. (United States)

    Pierrat, Olivier A; Maxwell, Anthony


    We have examined the effects of the bacterial toxin microcin B17 (MccB17) on the reactions of Escherichia coli DNA gyrase. MccB17 slows down but does not completely inhibit the DNA supercoiling and relaxation reactions of gyrase. A kinetic analysis of the cleavage-religation equilibrium of gyrase was performed to determine the effect of the toxin on the forward (cleavage) and reverse (religation) reactions. A simple mechanism of two consecutive reversible reactions with a nicked DNA intermediate was used to simulate the kinetics of cleavage and religation. The action of MccB17 on the kinetics of cleavage and religation was compared with that of the quinolones ciprofloxacin and oxolinic acid. With relaxed DNA as substrate, only a small amount of gyrase cleavage complex is observed with MccB17 in the absence of ATP, whereas the presence of the nucleotide significantly enhances the effect of the toxin on both the cleavage and religation reactions. In contrast, ciprofloxacin, oxolinic acid, and Ca2+ show lesser dependence on ATP to stabilize the cleavage complex. MccB17 enhances the overall rate of DNA cleavage by increasing the forward rate constant (k2) of the second equilibrium. In contrast, ciprofloxacin increases the amount of cleaved DNA by a combined effect on the forward and reverse rate constants of both equilibria. Based on these results and on the observations that MccB17 only slowly inhibits the supercoiling and relaxation reactions, we suggest a model of the interaction of MccB17 with gyrase.

  2. Escherichia coli DNA helicase I catalyzes a sequence-specific cleavage/ligation reaction at the F plasmid origin of transfer. (United States)

    Sherman, J A; Matson, S W


    Recent studies have shown that the Escherichia coli F plasmid-encoded traI gene product (TraIp), also known as DNA helicase I, catalyzes the formation of the site- and strand-specific nick that initiates F plasmid DNA transfer. Scission of the phosphodiester bond at the nic site within the origin of transfer (oriT) is accompanied by the covalent attachment of TraIp to the 5'-phosphate of the nicked DNA strand. This mechanism suggests that TraIp may also be capable of catalyzing a DNA ligation reaction using the energy stored in the protein-DNA intermediate. To test this possibility, an in vitro assay was designed that utilized short single-stranded DNA oligonucleotides of different lengths derived from the region within oriT that spanned the nic site. Purified TraIp was capable of efficiently cleaving single-stranded DNA that contained a nic site, and upon cleavage, the protein became covalently linked to the 5'-end of the nic site. When TraIp was incubated with two oligonucleotides of different length that contained the nic site, there was formation of novel recombinant products resulting from a TraIp-catalyzed cleavage/ligation reaction. Furthermore, the cleavage and ligation reactions were both sequence-specific. These data suggest that TraIp plays an important role in the initiation and termination of conjugative DNA transfer.


    Directory of Open Access Journals (Sweden)

    Yuji Matsumoto


    Full Text Available The beta-O-4 bond cleavage of a non-phenolic β-O-4 type dimeric lignin model compound, 2-(2-methoxyphenoxy-1-(3,4-dimethoxyphenyl-ethanol (III, was examined in systems using potassium tert-butoxide as a base (0.5 mol/l and tert-butanol (tBuOH, dimethylsulfoxide, 1,4-dioxane, or tetrahydrofuran as a solvent. The β-O-4 bond of compound III was cleaved in any system at 30°C, and 2-methoxyphenol (II was liberated. The amount of compound II liberated was close to the quantitative yield on the basis of the amount of compound III that disappeared, except for the treatment in the t-BuOH system. The reaction rate was dependent on what solvent was used. Half-life periods for these systems were roughly about 6.0, 3.0, 0.7, and 0.2h, respectively. It seemed that the rates were very high when the polarity of the solvents was low. Two reaction products generated from the aromatic ring with two methoxyl groups of compound III, 4-acetyl-1,2-dimethoxybenzene and 3,4-dimethoxybenzoic acid, were detected in all the systems. A peculiar reaction product, 1,2-dimethoxybenzene, was detected in a fairly large quantity, only when the latter two solvents with low polarities were applied.

  4. Anaerobic DNA cleavage in red light by dicopper(II) complexes on disulphide bond activation

    Indian Academy of Sciences (India)

    Debojyoti Lahiri; Ritankar Majumdar; Ashis K Patra; Akhil R Chakravarty


    Binuclear complexes [Cu(-RSSR)]2 (1) and [M2(-PDS)(H2O)]2 (M = Cu(II), 2; Fe(II), 3), where H2RSSR is a reduced Schiff base derived from 2-(thioethyl)salicylaldimine having a disulphide moiety and H2PDS is derived from dimerization of D-penicillamine, have been prepared, structurally characterized, and their photo-induced DNA cleavage activity studied. The crystal structure of 1 shows the complex as a discrete binuclear species with each metal in a CuN2O2 square-planar geometry (Cu…Cu, 6.420 Å). The tetradentate RSSR2- acts as a bridging ligand. The sulphur atoms in the disulphide unit do not interact with the metal ions. Complexes 1-3 do not show any DNA cleavage activity in darkness. The copper(II) complexes exhibit chemical nuclease activity in the presence of 3-mercaptopropionic acid. Cleavage of supercoiled DNA has been observed in UV-A light of 365 nm for 1 and red light of 647.1 nm for both 1 and 2 in air. Mechanistic data reveal the involvement of the disulphide unit as photosensitizer generating hydroxyl radicals ($^{\\bullet}$OH) as the reactive species. Photo-induced DNA cleavage in red light seems to involve sulphide radicals in a type-I process and hydroxyl radicals. The dicopper(II) complexes show significant anaerobic photo-induced DNA cleavage activity in red light under argon following type-I pathway without involving any reactive oxygen species.

  5. Cleavage of carbon-nitrogen bond in 1,3,5-tri-tert-butyl-1,3,5-triazacyclohexane by copper(I) bromide (United States)

    Khatua, Suman; Majumdar, Amit


    Reactions of CuCl, CuCl2 and CuBr2 with 1,3,5-tri-tert-butyl-1,3,5-triazacyclohexane (tBu3tach) resulted in the formation of [(tBu3tach-H)+(CuCl2)] (1), [(tBu3tach)(CuCl2)] (2) and [(tBu3tach-H)+(CuBr2)] (3) respectively. Interestingly, CuBr was found to mediate the cleavage of the C-N bonds of tBu3tach in a vast range of solvents, namely, chloroform, dichloromethane, tetrahydrofuran, acetonitrile and methanol to yield [Cu4Br4(tBuNCH2)4] (4) and stands as an example of C-N bond cleavage of 1,3,5-triazacyclohexane rings by copper salts. Compounds 1 and 3 contains amidinium cations and are unstable in solution towards the release of copper. The release of copper from 3 in solution was confirmed by the isolation of the compound, [CuBr(MeCN)] (5). Formation of the amidinium cations [(tBu3tach-H)+] in 1 and 3 may be avoided by the use of PPh3 to yield [(tBu3tach)Cu(PPh3)](PF6) (6), while the coordinated N-tert-butylmethanimine (tBuNCH2) in 4 could be replaced by PPh3 to yield [Cu4Br4(PPh3)4] (7). Complexes 1-7 are characterized by a combination of single crystal X-ray structure determination and/or elemental analysis, NMR, IR, and UV-Vis spectroscopy, and Mass spectrometry.

  6. {{text{C}}_{α }} - {text{C}} Bond Cleavage of the Peptide Backbone in MALDI In-Source Decay Using Salicylic Acid Derivative Matrices (United States)

    Asakawa, Daiki; Takayama, Mitsuo


    The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H]+. The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H]+ to that of non-oxidized protonated molecule [M + H]+ of peptide was of the order 5-NSA > 5-FSA > 5-aminosalicylic acid (5-ASA) ≒ 2,5-dihydroxyl benzoic acid (2,5-DHB) ≒ 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the {{{C}}_{α }} - {{C}} bond, leading to the formation of a- and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the {{{C}}_{α }} - {{C}} bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides.

  7. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin* (United States)

    Helmich, Kate E.; Pereira, Jose Henrique; Gall, Daniel L.; Heins, Richard A.; McAndrew, Ryan P.; Bingman, Craig; Deng, Kai; Holland, Keefe C.; Noguera, Daniel R.; Simmons, Blake A.; Sale, Kenneth L.; Ralph, John; Donohue, Timothy J.; Adams, Paul D.; Phillips, George N.


    Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin. PMID:26637355

  8. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. (United States)

    Helmich, Kate E; Pereira, Jose Henrique; Gall, Daniel L; Heins, Richard A; McAndrew, Ryan P; Bingman, Craig; Deng, Kai; Holland, Keefe C; Noguera, Daniel R; Simmons, Blake A; Sale, Kenneth L; Ralph, John; Donohue, Timothy J; Adams, Paul D; Phillips, George N


    Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50-70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.

  9. Room temperature ring expansion of N-heterocyclic carbenes and B-B bond cleavage of diboron(4) compounds. (United States)

    Pietsch, Sabrina; Paul, Ursula; Cade, Ian A; Ingleson, Michael J; Radius, Udo; Marder, Todd B


    We report the isolation and detailed structural characterization, by solid-state and solution NMR spectroscopy, of the neutral mono- and bis-NHC adducts of bis(catecholato)diboron (B2 cat2 ). The bis-NHC adduct undergoes thermally induced rearrangement, forming a six-membered -B-C=N-C=C-N-heterocyclic ring via C-N bond cleavage and ring expansion of the NHC, whereas the mono-NHC adduct is stable. Bis(neopentylglycolato)diboron (B2 neop2 ) is much more reactive than B2 cat2 giving a ring expanded product at room temperature, demonstrating that ring expansion of NHCs can be a very facile process with significant implications for their use in catalysis.

  10. Hydrogen and Dihydrogen Bonds in the Reactions of Metal Hydrides. (United States)

    Belkova, Natalia V; Epstein, Lina M; Filippov, Oleg A; Shubina, Elena S


    The dihydrogen bond-an interaction between a transition-metal or main-group hydride (M-H) and a protic hydrogen moiety (H-X)-is arguably the most intriguing type of hydrogen bond. It was discovered in the mid-1990s and has been intensively explored since then. Herein, we collate up-to-date experimental and computational studies of the structural, energetic, and spectroscopic parameters and natures of dihydrogen-bonded complexes of the form M-H···H-X, as such species are now known for a wide variety of hydrido compounds. Being a weak interaction, dihydrogen bonding entails the lengthening of the participating bonds as well as their polarization (repolarization) as a result of electron density redistribution. Thus, the formation of a dihydrogen bond allows for the activation of both the MH and XH bonds in one step, facilitating proton transfer and preparing these bonds for further transformations. The implications of dihydrogen bonding in different stoichiometric and catalytic reactions, such as hydrogen exchange, alcoholysis and aminolysis, hydrogen evolution, hydrogenation, and dehydrogenation, are discussed.

  11. Experimental and theoretical investigations of copper (I/II) complexes with triazine-pyrazole derivatives as ligands and their in situ C-N bond cleavage (United States)

    Wang, Ji-Xiao; Wang, Che; Wang, Xuan; Wang, Xin-Yu; Xing, Yong-Heng; Sun, Qiao


    Two copper complexes, Cu(SCN)(Mpz∗T-(EtO)2) (1) (Mpz∗T-(EtO)2 = L3) and CuCl(H2O)(Mpz∗T-O2) (2) (Mpz∗T-O2 = L4) were synthesized by the reaction of 2,4,6-tri(3,5-dimethylpyrazol-1-yl)-1,3,5-triazine (L1) or 2,4,6-tri(1H-pyrazol-1-yl)-1,3,5-triazine (L2) with CuCl2·2H2O in anhydrous ethanol and methanol, respectively. The complexes were characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single crystal X-ray diffraction and X-ray powder diffraction. The structural characterizations and quantum mechanical calculations of the two complexes were analyzed in detail. It was found that an in site reaction occurred during the synthesis process of complexes 1 and 2, likely due to catalytic property of copper ions which leads to the C-N bond cleavage to generate new organic species, namely, Mpz∗T-(EtO)2 (L3) and Mpz∗T-O2 (L4).

  12. FeCl2-promoted cleavage of the unactivated C-C bond of alkylarenes and polystyrene: direct synthesis of arylamines. (United States)

    Qin, Chong; Shen, Tao; Tang, Conghui; Jiao, Ning


    Ironing it out: an efficient and convenient nitrogenation strategy involving C-C bond cleavage for the straightforward synthesis of versatile arylamines is presented. Various alkyl azides and alkylarenes, including the common industrial by-product cumene, react using this protocol. Moreover, this method provides a potential strategy for the degradation of polystyrene.

  13. Enzymology of the carotenoid cleavage dioxygenases: reaction mechanisms, inhibition and biochemical roles. (United States)

    Harrison, Peter J; Bugg, Timothy D H


    Carotenoid cleavage dioxygenases (CCDs) are a large family of non-heme iron (II) dependent enzymes. CCDs catalyse the selective oxidative cleavage of carotenoids to produce apocarotenoids. Apocarotenoid derived molecules form important signalling molecules in plants in the form of abscisic acid and strigolactone and in mammals in the form of retinal. Very little is known biochemically about the CCDs and only a handful of CCDs have been biochemically characterised. Mechanistically, debate surrounds whether CCDs utilise a mono or dioxygenase mechanism. Here, we review the biochemical roles of CCDs, discuss the mechanisms by which CCD cleavage is proposed to occur, and discuss recent reports of selective CCD enzyme inhibitors.

  14. An elusive vinyl radical isolated as an appended unit in a five-coordinate Co(iii)-bis(iminobenzosemiquinone) complex formed via ligand-centered C-S bond cleavage. (United States)

    Sarkar, Prasenjit; Tiwari, Archana; Sarmah, Amrit; Bhandary, Subhrajyoti; Roy, Ram Kinkar; Mukherjee, Chandan


    Redox-active ligand H4Pra(edt(AP/AP)) experienced C-S bond cleavage during complexation reaction with Co(OAc)2·2H2O in the presence of Et3N in CH3OH in air. Thus, formed complex 1 was composed of two iminobenzosemiquinone radicals in its coordination sphere and an unprecedented stable tethered-vinyl radical. The complex has been characterized by mass, X-ray single crystal, X-band EPR, variable-temperature magnetic moment measurements and DFT based computational study.

  15. Spontaneous Si-C bond cleavage in (Triphos(Si))-nickel complexes. (United States)

    Petuker, Anette; Mebs, Stefan; Schuth, Nils; Gerschel, Philipp; Reback, Matthew L; Mallick, Bert; van Gastel, Maurice; Haumann, Michael; Apfel, Ulf-Peter


    Herein, we report on the versatile reactions of CH3C(CH2PPh2)3 as well as CH3Si(CH2PPh2)3 derived Ni-complexes. While Ni[CH3C(CH2PPh2)3] complexes reveal high stability, the Ni[CH3Si(CH2PPh2)3] analogs show rapid decomposition at room temperature and afford the unprecedented pseudo-tetrahedral phosphino methanide complex 5. We provide a detailed electronic structure of 5 from X-ray absorption and emission spectroscopy data analysis in combination with DFT calculations, as well as from comparison with structurally related complexes. A mechanistic study for the formation of complex 5 by reaction with BF4(-) is presented, based on a comparison of experimental data with quantum chemical calculations. We also show a simple route towards isolable Ni(i)-complexes on the gram scale.

  16. Photolytic Cleavage and Condensation Reactions of Cyclohexa-2,4-dienones with Diamines

    Directory of Open Access Journals (Sweden)

    Sung Kee Chung


    Full Text Available Cyclohexa-2,4-diene-1-one sulfone derivate undergoes ring cleavage to afford bis-amides containing a diene moiety on irradiation with visible light in the presence of various diamines.

  17. Formation of a dinuclear copper(II) complex through the cleavage of CBond' name='Single-Bond' value='Single-Bond'/>N bond of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole

    Energy Technology Data Exchange (ETDEWEB)

    Shardin, Rosidah; Pui, Law Kung; Yamin, Bohari M. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia); Kassim, Mohammad B. [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor, Malaysia and Fuel Cell Institute, Universiti Kebangsaan Malaysia, UKM 43600 Bangi, Selangor (Malaysia)


    A simple mononuclear octahedral copper(II) complex was attempted from the reaction of three moles of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole and one mole of copper(II) perchlorate hexahydrate in methanol. However, the product of the reaction was confirmed to be a dinuclear copper(II) complex with μ-(3-(pyridin-2-yl)-pyrazolato) and 3-(pyridin-2-yl)-1H-pyrazole ligands attached to each of the Cu(II) centre atom. The copper(II) ion assisted the cleavage of the C{sub benzoyl}Bond' name='Single-Bond' value='Single-Bond'/>N bond afforded a 3-(pyridin-2-yl)-1H-pyrazole molecule. Deprotonation of the 3-(pyridin-2-yl)-1H-pyrazole gave a 3-(pyridin-2-yl)-pyrazolato, which subsequently reacted with the Cu(II) ion to give the (3-(pyridin-2-yl)-pyrazolato)(3-(pyridin-2-yl)-1H-pyrazole)Cu(II) product moiety. The structure of the dinuclear complex was confirmed by x-ray crystallography. The complex crystallized in a monoclinic crystal system with P2(1)/n space group and cell dimensions of a = 12.2029(8) Å, b = 11.4010(7) Å, c = 14.4052(9) Å and β = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (ε = 116 dm{sup 3} mol{sup −1} cm{sup −1}) supports the presence of Cu(II) centres.

  18. Unusual C-C bond cleavage in the formation of amine-bis(phenoxy) group 4 benzyl complexes: Mechanism of formation and application to stereospecific polymerization

    KAUST Repository

    Gowda, Ravikumar R.


    Group 4 tetrabenzyl compounds MBn4 (M = Zr, Ti), upon protonolysis with an equimolar amount of the tetradentate amine-tris(phenol) ligand N[(2,4-tBu2C6H2(CH 2)OH]3 in toluene from -30 to 25 °C, unexpectedly lead to amine-bis(phenoxy) dibenzyl complexes, BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn2 (M = Zr (1), Ti (2)) in 80% (1) and 75% (2) yields. This reaction involves an apparent cleavage of the >NCH2-ArOH bond (loss of the phenol in the ligand) and formation of the >NCH 2-CH2Bn bond (gain of the benzyl group in the ligand). Structural characterization of 1 by X-ray diffraction analysis confirms that the complex formed is a bis(benzyl) complex of Zr coordinated by a newly derived tridentate amine-bis(phenoxy) ligand arranged in a mer configuration in the solid state. The abstractive activation of 1 and 2 with B(C6F 5)3·THF in CD2Cl2 at room temperature generates the corresponding benzyl cations {BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn(THF)}+[BnB(C6F5) 3]- (M = Zr (3), Ti, (4)). These cationic complexes, along with their analogues derived from (imino)phenoxy tri- and dibenzyl complexes, [(2,6-iPr2C6H3)N=C(3,5- tBu2C6H2)O]ZrBn3 (5) and [2,4-Br2C6H2(O)(6-CH2(NC 5H9))CH2N=CH(2-adamantyl-4-MeC 6H2O)]ZrBn2 (6), have been found to effectively polymerize the biomass-derived renewable β-methyl-α-methylene- γ-butyrolactone (βMMBL) at room temperature into the highly stereoregular polymer PβMMBL with an isotacticity up to 99% mm. A combined experimental and DFT study has yielded a mechanistic pathway for the observed unusual C-C bond cleavage in the present protonolysis reaction between ZrBn4 and N[(2,4-tBu2C 6H2(CH2)OH]3 for the formation of complex 1, which involves the benzyl radical and the Zr(III) species, resulting from thermal and photochemical decomposition of ZrBn4, followed by a series of reaction sequences consisting of protonolysis, tautomerization, H-transfer, oxidation, elimination, and radical coupling. © 2014 American Chemical Society.

  19. Alkali metal mediated C-C bond coupling reaction. (United States)

    Tachikawa, Hiroto


    Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2](-) was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

  20. Synthesis of diorganoplatinum(IV) complexes by the Ssbnd S bond cleavage with platinum(II) complexes (United States)

    Niroomand Hosseini, Fatemeh; Rashidi, Mehdi; Nabavizadeh, S. Masoud


    Reaction of [PtR2(NN)] (R = Me, p-MeC6H4 or p-MeOC6H4; NN = 2,2‧-bipyridine, 4,4‧-dimethyl-2,2‧-bipyridine, 1,10-phenanthroline or 2,9-dimethyl-1,10-phenanthroline) with MeSSMe gives the platinum(IV) complexes cis,trans-[PtR2(SMe)2(NN)]. They are characterized by NMR spectroscopy and elemental analysis. The geometries and the nature of the frontier molecular orbitals of Pt(IV) complexes containing Ptsbnd S bonds are studied by means of the density functional theory.

  1. Formation of a dinuclear copper(II) complex through the cleavage of CN bond of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole (United States)

    Shardin, Rosidah; Pui, Law Kung; Yamin, Bohari M.; Kassim, Mohammad B.


    A simple mononuclear octahedral copper(II) complex was attempted from the reaction of three moles of 1-benzoyl-3-(pyridin-2-yl)-1H-pyrazole and one mole of copper(II) perchlorate hexahydrate in methanol. However, the product of the reaction was confirmed to be a dinuclear copper(II) complex with μ-{3-(pyridin-2-yl)-pyrazolato} and 3-(pyridin-2-yl)-1H-pyrazole ligands attached to each of the Cu(II) centre atom. The copper(II) ion assisted the cleavage of the CbenzoylN bond afforded a 3-(pyridin-2-yl)-1H-pyrazole molecule. Deprotonation of the 3-(pyridin-2-yl)-1H-pyrazole gave a 3-(pyridin-2-yl)-pyrazolato, which subsequently reacted with the Cu(II) ion to give the {3-(pyridin-2-yl)-pyrazolato}{3-(pyridin-2-yl)-1H-pyrazole}Cu(II) product moiety. The structure of the dinuclear complex was confirmed by x-ray crystallography. The complex crystallized in a monoclinic crystal system with P2(1)/n space group and cell dimensions of a = 12.2029(8) Å, b = 11.4010(7) Å, c = 14.4052(9) Å and β = 102.414(2)°. The compound was further characterized by mass spectrometry, CHN elemental analysis, infrared and UV-visible spectroscopy and the results concurred with the x-ray structure. The presence of d-d transition at 671 nm (ɛ = 116 dm3 mol-1 cm-1) supports the presence of Cu(II) centres.

  2. Evidence for the powerful catalytic ability of imidozirconocene complex from its epoxide ring cleavage reactions - A DFT mechanistic view

    Indian Academy of Sciences (India)

    Dhurairajan Senthilnathan; Rajadurai Vijay Solomon; Ponnambalam Venuvanalingam


    Imidozirconocene complex is known for its bifunctional reactivity and catalytic ability and this complex mediates ring cleavage of epoxides. Cyclooctene oxide (1) Norbornene oxide (2) and 2,5-dimethyl cyclohexene oxide (3) undergo ring cleavage in the presence of imidozirconocene complex. Epoxide 1 has accessible -hydrogens (type I) while epoxide 2 and 3 do not have them (type II). Normally type I epoxides undergo elimination while type II epoxides prefer insertion. All the insertion reactions lead to five-membered metallacycle formation and elimination results in thermodynamically stable allyl-alkoxy product. The insertion is a two-step process following either diradical or zwitterionic pathway, while elimination is a one-step concerted reaction. DFT (density functional theory) modelling of these reactions at B3LYP/LANL2DZ level show that epoxide 1 undergoes elimination in agreement with experiment. However, calculations indicate that epoxide (2) proceeds through diradical intermediate in contrast to experimental observations. Surprisingly, epoxide (3) that has both the positions blocked by methyl groups undergoes elimination rather than insertion. AIM and EDA analyses offer further insights on the reaction mechanism and bifunctional reactivity of imidozirconozene complex.

  3. Oxidative Cleavage of C=S and P=S Bonds at an Al(I) Center: Preparation of Terminally Bound Aluminum Sulfides. (United States)

    Chu, Terry; Vyboishchikov, Sergei F; Gabidullin, Bulat; Nikonov, Georgii I


    The treatment of cyclic thioureas with the aluminum(I) compound NacNacAl (1; NacNac=[ArNC(Me)CHC(Me)NAr](-) , Ar=2,6-Pr(i)2 C6 H3 ) resulted in oxidative cleavage of the C=S bond and the formation of 3 and 5, the first monomeric aluminum complexes with an Al=S double bond stabilized by N-heterocyclic carbenes. Compound 1 also reacted with triphenylphosphine sulfide in a similar manner, which resulted in cleavage of the P=S bond and production of the adduct [NacNacAl=S(S=PPh3 )] (8). The Al=S double bond in 3 can react with phenyl isothiocyanate to furnish the cycloaddition product 9 and zwitterion 10 as a result of coupling between the liberated carbene and PhN=C=S. All novel complexes were characterized by multinuclear NMR spectroscopy, and the structures of 5, 9, and 10 were confirmed by X-ray diffraction analysis. The nature of the Al=S bond in 5 was also probed by DFT calculations.

  4. Unexpected cleavage of 2-azido-2-(hydroxymethyl)oxetanes: conformation determines reaction pathway? (United States)

    Farber, Elisa; Herget, Jackson; Gascón, José A; Howell, Amy R


    An unanticipated cleavage of 2-azido-2-(hydroxymethyl)oxetanes is reported. In attempts to oxidize the title oxetanyl alcohols to the corresponding carboxylic acids with RuO4, cleaved nitriles were formed as the sole isolable products, while a closely related tetrahydrofuran gave solely the expected carboxylic acid. Quantum chemical calculations suggest that the divergent outcomes are governed by conformational differences in the azidoalcohols.

  5. Purification, molecular cloning, and expression of 2-hydroxyphytanoyl- CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during à-oxidation of 3- methyl-branched fatty acids

    CERN Document Server

    Foulon, V; Croes, K; Waelkens, E


    Purification, molecular cloning, and expression of 2-hydroxyphytanoyl- CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during à-oxidation of 3- methyl-branched fatty acids

  6. Allenes and computational chemistry: from bonding situations to reaction mechanisms. (United States)

    Soriano, Elena; Fernández, Israel


    The present review is focused on the application of computational/theoretical methods to the wide and rich chemistry of allenes. Special emphasis is made on the interplay and synergy between experimental and computational methodologies, rather than on recent developments in methods and algorithms. Therefore, this review covers the state-of-the-art applications of computational chemistry to understand and rationalize the bonding situation and vast reactivity of allenes. Thus, the contents of this review span from the most fundamental studies on the equilibrium structure and chirality of allenes to recent advances in the study of complex reaction mechanisms involving allene derivatives in organic and organometallic chemistry.

  7. Irida-β-ketoimines Derived from Hydrazines To Afford Metallapyrazoles or N-N Bond Cleavage: A Missing Metallacycle Disclosed by a Theoretical and Experimental Study. (United States)

    Zumeta, Itziar; Mendicute-Fierro, Claudio; Bustos, Itxaso; Huertos, Miguel A; Rodríguez-Diéguez, Antonio; Seco, José M; San Sebastian, Eider; Garralda, María A


    Unprecedented metallapyrazoles [IrH2{Ph2P(o-C6H4)CNNHC(o-C6H4)PPh2}] (3) and [IrHCl{Ph2P(o-C6H4)CNNHC(o-C6H4)PPh2}] (4) were obtained by the reaction of the irida-β-ketoimine [IrHCl{(PPh2(o-C6H4CO))(PPh2(o-C6H4CNNH2))H}] (2) in MeOH heated at reflux in the presence and absence of KOH, respectively. In solution, iridapyrazole 3 undergoes a dynamic process due to prototropic tautomerism with an experimental barrier for the exchange of ΔGcoal(⧧) = 53.7 kJ mol(-1). DFT calculations agreed with an intrapyrazole proton transfer process assisted by two water molecules (ΔG = 63.1 kJ mol(-1)). An X-ray diffraction study on 4 indicated electron delocalization in the iridapyrazole ring. The reaction of the irida-β-diketone [IrHCl{(PPh2(o-C6H4CO))2H}] (1) with H2NNRR' in aprotic solvents gave irida-β-ketoimines [IrHCl{(PPh2(o-C6H4CO))(PPh2(o-C6H4CNNRR'))H}] (R = R' = Me (5); R = H, R' = Ph (8)), which can undergo N-N bond cleavage to afford the acyl-amide complex [IrHCl(PPh2(o-C6H4CO))(PPh2(o-C6H4C(O)N(CH3)2))-κP,κO] (6) or [IrHCl(PPh2(o-C6H4CO))(PPh2(o-C6H4CN)-κP)(NH2NHPh-κNH2)] (9) containing o-(diphenylphosphine)benzonitrile and phenylhydrazine, respectively. From a CH2Cl2/CH3OH solution of 9 kept at -18 °C, single crystals of [IrHCl(PPh2(o-C6H4CO))(PPh2(o-C6H4CN)-κP))(HN═NPh-κNH)] (10) containing o-(diphenylphosphine)benzonitrile and phenyldiazene were formed, as shown by X-ray diffraction. The reaction of 1 with methylhydrazine in methanol gave the hydrazine complex [IrCl(PPh2(o-C6H4CO))2(NH2NH(CH3)-κNH2)] (7). Single-crystal X-ray diffraction analysis was performed on 6 and 7.

  8. A Cobalt(I) Pincer Complex with an η(2) -C(aryl)-H Agostic Bond: Facile C-H Bond Cleavage through Deprotonation, Radical Abstraction, and Oxidative Addition. (United States)

    Murugesan, Sathiyamoorthy; Stöger, Berthold; Pittenauer, Ernst; Allmaier, Günter; Veiros, Luis F; Kirchner, Karl


    The synthesis and reactivity of a Co(I) pincer complex [Co(ϰ(3) P,CH,P-P(CH)P(NMe) -iPr)(CO)2](+) featuring an η(2)-C(aryl)-H agostic bond is described. This complex was obtained by protonation of the Co(I) complex [Co(PCP(NMe) -iPr)(CO)2]. The Co(III) hydride complex [Co(PCP(NMe) -iPr)(CNtBu)2(H)](+) was obtained upon protonation of [Co(PCP(NMe) -iPr)(CNtBu)2]. Three ways to cleave the agostic C-H bond are presented. First, owing to the acidity of the agostic proton, treatment with pyridine results in facile deprotonation (C-H bond cleavage) and reformation of [Co(PCP(NMe) -iPr)(CO)2]. Second, C-H bond cleavage is achieved upon exposure of [Co(ϰ(3)P,CH,P-P(CH)P(NMe) -iPr)(CO)2](+) to oxygen or TEMPO to yield the paramagnetic Co(II) PCP complex [Co(PCP(NMe) -iPr)(CO)2](+). Finally, replacement of one CO ligand in [Co(ϰ(3) P,CH,P-P(CH)P(NMe) -iPr)(CO)2](+) by CNtBu promotes the rapid oxidative addition of the agostic η(2) -C(aryl)-H bond to give two isomeric hydride complexes of the type [Co(PCP(NMe) -iPr)(CNtBu)(CO)(H)](+).

  9. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

    Energy Technology Data Exchange (ETDEWEB)

    Sutton, Kristin A. [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States); Black, Paul J.; Mercer, Kermit R. [University of Rochester Medical Center, Rochester, NY 14642 (United States); Garman, Elspeth F. [University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QU (United Kingdom); Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Snell, Edward H., E-mail: [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States); SUNY Buffalo Medical School, 700 Ellicott Street, Buffalo, NY 14203 (United States); Bernhard, William A. [University of Rochester Medical Center, Rochester, NY 14642 (United States); Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086 (United States)


    Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage, to confirm a multi-track radiation-damage process and to develop a model of that process. Electron paramagnetic resonance (EPR) and online UV–visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV–visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5–0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.

  10. Unique features of monoclonal IgG2b in the cleavage reaction with pepsin.

    Directory of Open Access Journals (Sweden)



    Full Text Available Preparations of IgG2b purified from several mouse hybridoma clones were highly susceptible, compared to other subclasses, to peptic digestion under conditions usually used to prepare F (ab'2 fragments. Analyses of the digestion products revealed that no F (ab'2 was produced and that the main product was a Fab-like fragment. Demonstration of the hinge disulfides in the Fc portion clearly indicated that in IgG2b the primary peptic cleavage occurs on the NH2-terminal side of the inter-heavy chain disulfide bridge. The resulting Fab failed to bind with antigen, suggesting the importance of the CH1-hinge region in maintaining the native conformation of the antigen-binding site.

  11. Organometallic Modeling of the Hydrodesulfurization (HDS) Process: Rhenium Carbonyl-promoted C-S Bond Cleavage and Hydrogenation of Thiophenes and Benozothiophenes

    Energy Technology Data Exchange (ETDEWEB)

    Reynolds, Michael A. [Iowa State Univ., Ames, IA (United States)


    Organometallic modeling of the HDS process at single or multiple metal centers is one approach to better understanding the mechanism that govern commercial HDS. Therefore, we have currently been investigating the use of Re2(CO)10 as a potential model system for catalytic HDS with respect to S-binding, ring-opening, and hydrogenation of thiophenes andbenzothiophenes. We have also been investigating the use of UV-light as a method for activating thiophenic molecules towards C-S and C-H bond cleavage.

  12. Tomato carotenoid cleavage dioxygenases 1A and 1B: Relaxed double bond specificity leads to a plenitude of dialdehydes, mono-apocarotenoids and isoprenoid volatiles

    KAUST Repository

    Ilg, Andrea


    The biosynthetic processes leading to many of the isoprenoid volatiles released by tomato fruits are still unknown, though previous reports suggested a clear correlation with the carotenoids contained within the fruit. In this study, we investigated the activity of the tomato (Solanum lycopersicum) carotenoid cleavage dioxygenase (SlCCD1B), which is highly expressed in fruits, and of its homolog SlCCD1A. Using in vitro assays performed with purified recombinant enzymes and by analyzing products formed by the two enzymes in carotene-accumulating Escherichia coli strains, we demonstrate that SlCCD1A and, to a larger extent, SlCCD1B, have a very relaxed specificity for both substrate and cleavage site, mediating the oxidative cleavage of cis- and all-. trans-carotenoids as well as of different apocarotenoids at many more double bonds than previously reported. This activity gives rise to a plenitude of volatiles, mono-apocarotenoids and dialdehyde products, including cis-pseudoionone, neral, geranial, and farnesylacetone. Our results provide a direct evidence for a carotenoid origin of these compounds and point to CCD1s as the enzymes catalyzing the formation of the vast majority of tomato isoprenoid volatiles, many of which are aroma constituents. © 2014 The Authors.

  13. Diversification of ortho-Fused Cycloocta-2,5-dien-1-one Cores and Eight- to Six-Ring Conversion by σ Bond C-C Cleavage. (United States)

    Eccleshare, Lee; Lozada-Rodríguez, Leticia; Cooper, Phillippa; Burroughs, Laurence; Ritchie, John; Lewis, William; Woodward, Simon


    Sequential treatment of 2-C6 H4 Br(CHO) with LiC≡CR(1) (R(1) =SiMe3 , tBu), nBuLi, CuBr⋅SMe2 and HC≡CCHClR(2) [R(2) =Ph, 4-CF3 Ph, 3-CNPh, 4-(MeO2 C)Ph] at -50 °C leads to formation of an intermediate carbanion (Z)-1,2-C6 H4 {CA (=O)C≡CB R(1) }{CH=CH(CH(-) )R(2) } (4). Low temperatures (-50 °C) favour attack at CB leading to kinetic formation of 6,8-bicycles containing non-classical C-carbanion enolates (5). Higher temperatures (-10 °C to ambient) and electron-deficient R(2) favour retro σ-bond C-C cleavage regenerating 4, which subsequently closes on CA providing 6,6-bicyclic alkoxides (6). Computational modelling (CBS-QB3) indicated that both pathways are viable and of similar energies. Reaction of 6 with H(+) gave 1,2-dihydronaphthalen-1-ols, or under dehydrating conditions, 2-aryl-1-alkynylnaphthlenes. Enolates 5 react in situ with: H2 O, D2 O, I2 , allylbromide, S2 Me2 , CO2 and lead to the expected C-E derivatives (E=H, D, I, allyl, SMe, CO2 H) in 49-64 % yield directly from intermediate 5. The parents (E=H; R(1) =SiMe3 , tBu; R(2) =Ph) are versatile starting materials for NaBH4 and Grignard C=O additions, desilylation (when R(1) =SiMe) and oxime formation. The latter allows formation of 6,9-bicyclics via Beckmann rearrangement. The 6,8-ring iodides are suitable Suzuki precursors for Pd-catalysed C-C coupling (81-87 %), whereas the carboxylic acids readily form amides under T3P® conditions (71-95 %).

  14. Studies on a New Usage of Hypophosphorous Acid-iodine System in N-C Bond Cleavage

    Institute of Scientific and Technical Information of China (English)


    A mixture of hypophosphorous acid (H3PO2) and iodine in acetic acid can cleave theN-alkyl bond in a variety of N-1 substituted pyrimidine derivative in relatively high yields, withoutany damage to the amido bond in the non-nucleosides pyrimidine base skeleton.

  15. Resonance Raman spectroscopy reveals pH-dependent active site structural changes of lactoperoxidase compound 0 and its ferryl heme O-O bond cleavage products. (United States)

    Mak, Piotr J; Thammawichai, Warut; Wiedenhoeft, Dennis; Kincaid, James R


    The first step in the enzymatic cycle of mammalian peroxidases, including lactoperoxidase (LPO), is binding of hydrogen peroxide to the ferric resting state to form a ferric-hydroperoxo intermediate designated as Compound 0, the residual proton temporarily associating with the distal pocket His109 residue. Upon delivery of this "stored" proton to the hydroperoxo fragment, it rapidly undergoes O-O bond cleavage, thereby thwarting efforts to trap it using rapid mixing methods. Fortunately, as shown herein, both the peroxo and the hydroperoxo (Compound 0) forms of LPO can be trapped by cryoradiolysis, with acquisition of their resonance Raman (rR) spectra now permitting structural characterization of their key Fe-O-O fragments. Studies were conducted under both acidic and alkaline conditions, revealing pH-dependent differences in relative populations of these intermediates. Furthermore, upon annealing, the low pH samples convert to two forms of a ferryl heme O-O bond-cleavage product, whose ν(Fe═O) frequencies reflect substantially different Fe═O bond strengths. In the process of conducting these studies, rR structural characterization of the dioxygen adduct of LPO, commonly called Compound III, has also been completed, demonstrating a substantial difference in the strengths of the Fe-O linkage of the Fe-O-O fragment under acidic and alkaline conditions, an effect most reasonably attributed to a corresponding weakening of the trans-axial histidyl imidazole linkage at lower pH. Collectively, these new results provide important insight into the impact of pH on the disposition of the key Fe-O-O and Fe═O fragments of intermediates that arise in the enzymatic cycles of LPO, other mammalian peroxidases, and related proteins.

  16. Microstructure and Mechanical Properties of Reaction-Formed Joints in Reaction Bonded Silicon Carbide Ceramics (United States)

    Singh, M.


    A reaction-bonded silicon carbide (RB-SiC) ceramic material (Carborundum's Cerastar RB-SIC) has been joined using a reaction forming approach. Microstructure and mechanical properties of three types of reaction-formed joints (350 micron, 50-55 micron, and 20-25 micron thick) have been evaluated. Thick (approximately 350 micron) joints consist mainly of silicon with a small amount of silicon carbide. The flexural strength of thick joints is about 44 plus or minus 2 MPa, and fracture always occurs at the joints. The microscopic examination of fracture surfaces of specimens with thick joints tested at room temperature revealed the failure mode to be typically brittle. Thin joints (<50-55 micron) consist of silicon carbide and silicon phases. The room and high temperature flexural strengths of thin (<50-55 micron) reaction-formed joints have been found to be at least equal to that of the bulk Cerastar RB-SIC materials because the flexure bars fracture away from the joint regions. In this case, the fracture origins appear to be inhomogeneities inside the parent material. This was always found to be the case for thin joints tested at temperatures up to 1350C in air. This observation suggests that the strength of Cerastar RB-SIC material containing a thin joint is not limited by the joint strength but by the strength of the bulk (parent) materials.

  17. Peptide Bond Synthesis by a Mechanism Involving an Enzymatic Reaction and a Subsequent Chemical Reaction. (United States)

    Abe, Tomoko; Hashimoto, Yoshiteru; Zhuang, Ye; Ge, Yin; Kumano, Takuto; Kobayashi, Michihiko


    We recently reported that an amide bond is unexpectedly formed by an acyl-CoA synthetase (which catalyzes the formation of a carbon-sulfur bond) when a suitable acid and l-cysteine are used as substrates. DltA, which is homologous to the adenylation domain of nonribosomal peptide synthetase, belongs to the same superfamily of adenylate-forming enzymes, which includes many kinds of enzymes, including the acyl-CoA synthetases. Here, we demonstrate that DltA synthesizes not only N-(d-alanyl)-l-cysteine (a dipeptide) but also various oligopeptides. We propose that this enzyme catalyzes peptide synthesis by the following unprecedented mechanism: (i) the formation of S-acyl-l-cysteine as an intermediate via its "enzymatic activity" and (ii) subsequent "chemical" S → N acyl transfer in the intermediate, resulting in peptide formation. Step ii is identical to the corresponding reaction in native chemical ligation, a method of chemical peptide synthesis, whereas step i is not. To the best of our knowledge, our discovery of this peptide synthesis mechanism involving an enzymatic reaction and a subsequent chemical reaction is the first such one to be reported. This new process yields peptides without the use of a thioesterified fragment, which is required in native chemical ligation. Together with these findings, the same mechanism-dependent formation of N-acyl compounds by other members of the above-mentioned superfamily demonstrated that all members most likely form peptide/amide compounds by using this novel mechanism. Each member enzyme acts on a specific substrate; thus, not only the corresponding peptides but also new types of amide compounds can be formed.

  18. Effect of water on hydrolytic cleavage of non-terminal α-glycosidic bonds in cyclodextrins to generate monosaccharides and their derivatives in a dimethyl sulfoxide-water mixture. (United States)

    Kimura, Hiroshi; Hirayama, Masaki; Yoshida, Ken; Uosaki, Yasuhiro; Nakahara, Masaru


    Hydrolytic cleavage of the non-terminal α-1,4-glycosidic bonds in α-, β-, and γ-cyclodextrins and the anomeric-terminal one in d-maltose was investigated to examine how the cleavage rate for α-, β-, and γ-cyclodextrins is slower than that for d-maltose. Effects of water and temperature were studied by applying in situ (13)C NMR spectroscopy and using a dimethyl sulfoxide (DMSO)-water mixture over a wide range of water mole fraction, xw = 0.004-1, at temperatures of 120-180 °C. The cleavage rate constant for the non-anomeric glycosidic bond was smaller by a factor of 6-10 than that of the anomeric-terminal one. The glycosidic-bond cleavage is significantly accelerated through the keto-enol tautomerization of the anomeric-terminal d-glucose unit into the d-fructose one. The smaller the size of the cyclodextrin, the easier the bond cleavage due to the ring strain. The remarkable enhancement in the cleavage rate with decreasing water content was observed for the cyclodextrins and d-maltose as well as d-cellobiose. This shows the important effect of the solitary water whose hydrogen bonding to other water molecules is prohibited by the presence of the organic dipolar aprotic solvent, DMSO, and which has more naked partial charges and higher reactivity. A high 5-hydroxymethyl-2-furaldehyde (5-HMF) yield of 64% was attained in a non-catalytic conversion by tuning the water content to xw = 0.30, at which the undesired polymerization by-paths can be most effectively suppressed. This study provides a step toward designing a new optimal, earth-benign generation process of 5-HMF starting from biomass.

  19. Peptide bond cleavage site determination of novel proteolytic enzymes found in ROS 17/2.8 cell lysates. (United States)

    Guidon, P T; Perrin, D; Harrison, P


    We have identified proteolytic activities in the rat osteoblastic osteosarcoma cell line ROS 17/2.8 which are capable of cleaving a peptide substrate for protein kinase C-mediated phosphorylation (PSPKC, Pro-Leu-Ser-Arg-Thr-Leu-Ser-Val-Ala-Ala-Lys). Using polyacrylamide gel electrophoresis conditions similar to those used to resolve small molecular weight proteins, the peptide bonds of PSPKC which are cleaved by the proteolytic activities present in ROS 17/2.8 cell lysates have been determined. These activities cleave the Ser-Arg, Thr-Leu, and Ser-Val peptide bonds. To date, no proteolytic activities present in osteoblast cell lysates have been described with the aforementioned peptide bond specificities, suggesting that these activities are novel. The PSPKC-cleaved peptide fragment pattern generated was similar for several different osteoblast cell lysates. Lysates generated from different rat tissues were also able to cleave PSPKC, but the peptide fragment pattern generated by ROS 17/2.8 cell lysates appeared to be unique amongst these tissues.

  20. Chemical reactions in dense monolayers: in situ thermal cleavage of grafted esters for preparation of solid surfaces functionalized with carboxylic acids. (United States)

    Dugas, Vincent; Chevalier, Yves


    The thermodynamics of a chemical reaction confined at a solid surface was investigated through kinetic measurements of a model unimolecular reaction. The thermal cleavage of ester groups grafted at the surface of solid silica was investigated together with complementary physicochemical characterization of the grafted species. The ester molecules were chemically grafted to the silica surface and subsequently cleaved into the carboxylic acids. A grafting process of a reproducible monolayer was designed using the reaction of monofunctional organosilane from its gas phase. The thermal deprotection step of the ester end-group was investigated. The thermal deprotection reaction behaves in quite a specific manner when it is conducted at a surface in a grafted layer. Different organosilane molecules terminated by methyl, isopropyl and tert-butyl ester groups were grafted to silica surface; such functionalized materials were characterized by elemental analysis, IR and NMR spectroscopy, and thermogravimetric analysis, and the thermodynamic parameters of the thermal elimination reaction at the surface were measured. The limiting factor of such thermal ester cleavage reaction is the thermal stability of grafted ester group according to the temperature order: tert-butyl groups were not selectively cleaved by temperature. The thermal deprotection of i-propyl ester groups took place at a temperature close to the thermal degradation of the organofunctional tail of the silane. The low thermolysis temperature of the grafted tert-butyl esters allowed their selective cleavage. There is a definite influence of the surface on the reaction. The enthalpy of activation is lower than in the gas phase because of the polarity of the reaction site. The major contribution is entropic; the negative entropy of activation comes from lateral interactions with the neighbor grafted molecules because of the high grafting density. Such reaction is an original strategy to functionalize the silica

  1. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies. (United States)

    Sutton, Kristin A; Black, Paul J; Mercer, Kermit R; Garman, Elspeth F; Owen, Robin L; Snell, Edward H; Bernhard, William A


    Electron paramagnetic resonance (EPR) and online UV-visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV-visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5-0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.

  2. Mode specificity in bond selective reactions F + HOD → HF + OD and DF + OH

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hongwei; Guo, Hua, E-mail: [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)


    The influence of vibrational excitations in the partially deuterated water (HOD) reactant on its bond selective reactions with F is investigated using a full-dimensional quantum wave packet method on an accurate global potential energy surface. Despite the decidedly early barrier of the F + H{sub 2}O reaction, reactant vibrational excitation in each local stretching mode of HOD is found to significantly enhance the reaction which breaks the excited bond. In the mean time, excitation of the HOD bending mode also enhances the reaction, but with much lower efficacy and weaker bond selectivity. Except for low collision energies, all vibrational modes are more effective in promoting the bond selective reactions than the translational energy. These results are compared with the predictions of the recently proposed sudden vector projection model.

  3. Mode specificity in bond selective reactions F + HOD → HF + OD and DF + OH (United States)

    Song, Hongwei; Guo, Hua


    The influence of vibrational excitations in the partially deuterated water (HOD) reactant on its bond selective reactions with F is investigated using a full-dimensional quantum wave packet method on an accurate global potential energy surface. Despite the decidedly early barrier of the F + H2O reaction, reactant vibrational excitation in each local stretching mode of HOD is found to significantly enhance the reaction which breaks the excited bond. In the mean time, excitation of the HOD bending mode also enhances the reaction, but with much lower efficacy and weaker bond selectivity. Except for low collision energies, all vibrational modes are more effective in promoting the bond selective reactions than the translational energy. These results are compared with the predictions of the recently proposed sudden vector projection model.

  4. A computational study on the N-heterocyclic carbene-catalyzed Csp(2)-Csp(3) bond activation/[4+2] cycloaddition cascade reaction of cyclobutenones with imines: a new application of the conservation principle of molecular orbital symmetry. (United States)

    Wang, Yang; Wu, Bohua; Zhang, Haoyang; Wei, Donghui; Tang, Mingsheng


    A comprehensive density functional theory (DFT) investigation has been performed to interrogate the mechanisms and stereoselectivities of the Csp(2)-Csp(3) single bond activation of cyclobutenones and their [4+2] cycloaddition reaction with imines via N-heterocyclic carbene (NHC) organocatalysis. According to our calculated results, the fundamental reaction pathway contains four steps: nucleophilic addition of NHC to cyclobutenone, C-C bond cleavage for the formation of an enolate intermediate, [4+2] cycloaddition of the enolate intermediate with isatin imine, and the elimination of the NHC catalyst. In addition, the calculated results also reveal that the second reaction step is the rate-determining step, whereas the third step is the regio- and stereo-selectivity determining step. For the regio- and stereo-selectivity determining step, all four possible attack modes were considered. The addition of the C[double bond, length as m-dash]N bond in isatin imine to the dienolate intermediate is more energy favorable than the addition of the C[double bond, length as m-dash]O bond to a dienolate intermediate. Moreover, the Re face addition of the C[double bond, length as m-dash]N bond in isatin imine to the Re face of the dienolate intermediate leading to the SS configuration N-containing product was demonstrated to be most energy favorable, which is mainly due to the stronger second-order perturbation energy value in the corresponding transition state. Furthermore, by tracking the frontier molecular orbital (FMO) changes in the rate-determining C-C bond cleavage step, we found that the reaction obeys the conservation principle of molecular orbital symmetry. We believe that the present work would provide valuable insights into this kind of reaction.

  5. Temperature dependent structural variation from 2D supramolecular network to 3D interpenetrated metal–organic framework: In situ cleavage of S–S and C–S bonds

    Energy Technology Data Exchange (ETDEWEB)

    Ugale, Bharat; Singh, Divyendu; Nagaraja, C.M., E-mail:


    Two new Zn(II)–organic compounds, [Zn(muco)(dbds){sub 2}(H{sub 2}O){sub 2}] (1) and [Zn(muco)(dbs)] (2) (where, muco=trans, trans-muconate dianion, dbds=4,4′-dipyridyldisulfide and dbs=4,4′-dipyridylsulfide) have been synthesized from same precursors but at two different temperatures. Both the compounds have been characterized by single-crystal X-ray diffraction, powder X-ray diffraction, elemental analysis, IR spectroscopy, thermal analysis and photoluminescence studies. Compound 1 prepared at room temperature possesses a molecular structure extended to 2D supramolecular network through (H–O…H) hydrogen-bonding interactions. Compound 2, obtained at high temperature (100 °C) shows a 3-fold interpenetrating 3D framework constituted by an in situ generated dbs linker by the cleavage of S–S and C–S bonds of dbds linker. Thus, the influence of reaction temperature on the formation of two structural phases has been demonstrated. Both 1 and 2 exhibit ligand based luminescence emission owing to n→π⁎ and π→π⁎ transitions and also high thermal stabilities. - Graphical abstract: The influence of temperature on the formation of two structural phases, a 2D supramolecular network and a 3D 3-fold interpenetrating framework has been demonstrated and their luminescence emission is measured. - Highlights: • Two new Zn(II)–organic compounds were synthesized by tuning reaction temperatures. • Temperature induced in situ generation of dbs linker has been observed. • The compounds exhibit high thermal stability and luminescence emission properties. • The effect of temperature on structure, dimension and topology has been presented.

  6. SN2-like reaction in hydrogen-bonded complexes: a theoretical study. (United States)

    Wang, Weizhou; Zhang, Yu; Huang, Kaixun


    S(N)2-like reactions in hydrogen-bonded complexes have been investigated in this paper at a correlated MP2(full)/6-311++G(3df,3pd) level, employing FH...NH(3)...HF and ClH...NH(3)...HCl as model systems. The unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond can coexist in one complex which is taken as the reactant of the S(N)2-like reaction. The S(N)2-like reaction occurs along with the inversion of NH(3) and the interconversion of the unconventional F(Cl)-H...N noncovalent bond and the conventional F(Cl)-H...N hydrogen bond. In comparison with that of the isolated NH(3), the inversion barriers of the two complexes both are significantly reduced. The effect of carbon nanotube confinement on the inversion barrier is also discussed.

  7. Reaction dynamics and statistical theory for the growth of hydrogen bonding clusters

    Institute of Scientific and Technical Information of China (English)

    WANG; Haijun; BA; Xinwu(巴信武); ZHAO; Min(赵敏)


    The similarities between the formation of hydrogen bonds and polycondensation reactions are stated from the statistical viewpoint, and then taking the hydrogen bonding system of AaDd type as an example, the growing process of hydrogen bonding clusters is investigated in terms of the theory of reaction dynamics and statistical theory for polymeric reactions. The two methods lead to the same conclusions, stating that the statistical theory for polymerization is applicable to the hydrogen bonding systems. Based on this consideration, the explicit relationship between the conversions of proton-donors and proton-acceptors and the Gibbs free energy of the system under study is given. Furthermore, the sol-gel phase transition is predicted to take place in some hydrogen bonding systems, and the corresponding generalized scaling laws describing this kind of phase transition are obtained.

  8. Molecular Basis of C–N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase

    Energy Technology Data Exchange (ETDEWEB)

    Bodea, Smaranda; Funk, Michael A.; Balskus, Emily P.; Drennan, Catherine L.


    We report that deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. Lastly, this work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.

  9. Palladium-catalyzed Suzuki-Miyaura coupling of amides by carbon-nitrogen cleavage: general strategy for amide N-C bond activation. (United States)

    Meng, Guangrong; Szostak, Michal


    The first palladium-catalyzed Suzuki-Miyaura cross-coupling of amides with boronic acids for the synthesis of ketones by sterically-controlled N-C bond activation is reported. The transformation is characterized by operational simplicity using bench-stable, commercial reagents and catalysts, and a broad substrate scope, including substrates with electron-donating and withdrawing groups on both coupling partners, steric-hindrance, heterocycles, halides, esters and ketones. The scope and limitations are presented in the synthesis of >60 functionalized ketones. Mechanistic studies provide insight into the catalytic cycle of the cross-coupling, including the first experimental evidence for Pd insertion into the amide N-C bond. The synthetic utility is showcased by a gram-scale cross-coupling and cross-coupling at room temperature. Most importantly, this process provides a blueprint for the development of a plethora of metal catalyzed reactions of typically inert amide bonds via acyl-metal intermediates. A unified strategy for amide bond activation to enable metal insertion into N-C amide bond is outlined ().

  10. Ordered cleavage of myeloperoxidase ester bonds releases active site heme leading to inactivation of myeloperoxidase by benzoic acid hydrazide analogs. (United States)

    Huang, Jiansheng; Smith, Forrest; Panizzi, Peter


    Myeloperoxidase (MPO) catalyzes the breakdown of hydrogen peroxide and the formation of the potent oxidant hypochlorous acid. We present the application of the fluorogenic peroxidase substrate 10-acetyl-3,7-dihydroxyphenoxazine (ADHP) in steady-state and transient kinetic studies of MPO function. Using initial kinetic parameters for the MPO system, we characterized under the same conditions a number of gold standards for MPO inhibition, namely 4-amino benzoic acid hydrazide (4-ABAH), isoniazid and NaN3 before expanding our focus to isomers of 4-ABAH and benzoic acid hydrazide analogs. We determined that in the presence of hydrogen peroxide that 4-ABAH and its isomer 2-ABAH are both slow-tight binding inhibitors of MPO requiring at least two steps, whereas NaN3 and isoniazid-based inhibition has a single observable step. We also determined that MPO inhibition by benzoic acid hydrazide and 4-(trifluoromethyl) benzoic acid hydrazide was due to hydrolysis of the ester bond between MPO heavy chain Glu 242 residue and the heme pyrrole A ring, freeing the light chain and heme b fragment from the larger remaining MPO heavy chain. This new mechanism would essentially indicate that the benzoic acid hydrazide analogs impart inhibition through initial ejection of the heme catalytic moiety without prior loss of the active site iron.

  11. The cleavage of the aryl-O-CH/sub 3/ bond using anisole as a model compound

    Energy Technology Data Exchange (ETDEWEB)

    Afifi, A.I.; Hindermann, J.P.; Chornet, E.; Overend, R.P.


    The thermal decomposition of anisole as a prototype of the aryl-methyl-ether linkage of lignin and coals has been studied under supercritical conditions using tetralin as hydrogen donor solvent. The effect of homogenous Lewis acid catalysts have also been studied under the same conditions. The main reaction products are phenol, benzene, toluene and cresols. At high tetralin to anisole ratios the selectivity to phenol is almost 80% with little or no cresol production. This selective conversion can be carried out rapidly and cleanly at high temperature (>450 degrees C). Kinetic studies were undertaken using pyrolytic, donor solvent hydrogenolytic and Lewis acid catalysed regimes in the temperature range 400-500 degrees C. The kinetics of anisole decomposition in a large excess of tetralin have been found to be in good agreement with those published in the literature. The Lewis acid catalysts lower the activation energy relative to the pyrolytic and hydrogenolytic cases. The kinetic studies and their mechanistic interpretation lead to a mechanism involving surprisingly few radical species: methyl, phenoxy, phenoxymethyl and phenyl radicals. In the presence of FeCl/sub 3/, the selectivity towards phenols and cresols is enhanced, though a side reaction leads to polymerization at low (400-420 degrees C) temperatures. It is concluded that the aryl-O-methyl ether linkage in anisole can easily be broken at high temperatures, 450-500 degrees C, in supercritical hydrogen donor solvent to give phenol in high yield and selectivity. 23 refs., 4 figs., 5 tabs.

  12. Direct evidence for preferential {beta} C-H bond cleavage resulting from 248 nm photolysis of the n-propyl radical using selectively-deuterated 1-bromopropane precursors

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Z.; Mathews, M.G.; Koplitz, B. [Tulane Univ., New Orleans, LA (United States)


    A series of selectively deuterated 1-bromopropane precursors have been used to study site-specific photolysis in the n-propyl radical. A two-color photolysis approach (222 nm followed by 248 nm radiation) is used to create an intermediate photofragment and produce an H or a D atom, which is detected by 1 + 1 resonance ionization through Lyman-{alpha}. Target precursors are BrCH{sub 2}CD{sub 2}CD{sub 3}, BrCD{sub 2}CH{sub 2}CD{sub 3}, and BrCD{sub 2}CD{sub 2}CH{sub 3} as well as BrCD{sub 2}CH{sub 2}CH{sub 3}, BrCH{sub 2}CD{sub 2}CH{sub 3}, and BrCH{sub 2}CH{sub 2}CD{sub 3}. The `enhanced` H (or D) atom signals clearly demonstrate that C-H (or C-D) bond cleavage at the {beta} position is strongly favored. The net enhancement process undoubtedly involves photolysis of an intermediate, almost certainly the n-propyl radical. A comparison with systems involving ethyl and isopropyl radical photolysis is also presented. 14 refs., 4 figs.

  13. The mechanism and kinetics of the electrochemical cleavage of azo bond of 2-hydroxy-5-sulfophenyl-azo-benzoic acids

    Energy Technology Data Exchange (ETDEWEB)

    Mandic, Zoran; Nigovic, Biljana; Simunic, Branimir


    The electrochemical reduction of 2-hydroxy-5-[(4-sulfophenyl)azo]benzoic acid, 2-hydroxy-5-[(3-sulfophenyl)azo]benzoic acid, 2-hydroxy-5-[(2-sulfophenyl)azo]benzoic acid and 2-hydroxy-5-azo-benzoic acid has been carried out in aqueous solutions at glassy carbon electrode using cyclic voltammetry and chronoamperometry. The position of sulfo substituent relative to azo bridge as well as pH of the solution have significant impact on the electrochemical behavior of these compounds. It has been proposed that these compounds are reduced predominantly as hydrazone tautomers resulting in corresponding hydrazo compounds. The overall electrochemical reduction follows DISP2 mechanism, ultimately leading to the 5-amino salicylic acid and sulfanilic acid. The rate determining step is the homogenous redox reaction between intermediate hydrazo compound and 5-amino salicylic acid quinoneimine. The mechanism is proposed in which activated complex of 5-amino salicylic acid quinoneimine and intermediate hydrazo compound is formed with the simultaneous loss of one proton.

  14. Oxygen atom transfer reactions from Mimoun complexes to sulfides and sulfoxides. A bonding evolution theory analysis. (United States)

    González-Navarrete, Patricio; Sensato, Fabricio R; Andrés, Juan; Longo, Elson


    In this research, a comprehensive theoretical investigation has been conducted on oxygen atom transfer (OAT) reactions from Mimoun complexes to sulfides and sulfoxides. The joint use of the electron localization function (ELF) and Thom's catastrophe theory (CT) provides a powerful tool to analyze the evolution of chemical events along a reaction pathway. The progress of the reaction has been monitored by structural stability domains from ELF topology while the changes between them are controlled by turning points derived from CT which reveal that the reaction mechanism can be separated in several steps: first, a rupture of the peroxo O1-O2 bond, then a rearrangement of lone pairs of the sulfur atom occurs and subsequently the formation of S-O1 bond. The OAT process involving the oxidation of sulfides and sulfoxides is found to be an asynchronous process where O1-O2 bond breaking and S-O1 bond formation processes do not occur simultaneously. Nucleophilic/electrophilic characters of both dimethyl sulfide and dimethyl sulfoxide, respectively, are sufficiently described by our results, which hold the key to unprecedented insight into the mapping of electrons that compose the bonds while the bonds change.

  15. Bond selectivity in electron-induced reaction due to directed recoil on an anisotropic substrate (United States)

    Anggara, Kelvin; Huang, Kai; Leung, Lydie; Chatterjee, Avisek; Cheng, Fang; Polanyi, John C.


    Bond-selective reaction is central to heterogeneous catalysis. In heterogeneous catalysis, selectivity is found to depend on the chemical nature and morphology of the substrate. Here, however, we show a high degree of bond selectivity dependent only on adsorbate bond alignment. The system studied is the electron-induced reaction of meta-diiodobenzene physisorbed on Cu(110). Of the adsorbate's C-I bonds, C-I aligned `Along' the copper row dissociates in 99.3% of the cases giving surface reaction, whereas C-I bond aligned `Across' the rows dissociates in only 0.7% of the cases. A two-electronic-state molecular dynamics model attributes reaction to an initial transition to a repulsive state of an Along C-I, followed by directed recoil of C towards a Cu atom of the same row, forming C-Cu. A similar impulse on an Across C-I gives directed C that, moving across rows, does not encounter a Cu atom and hence exhibits markedly less reaction.

  16. Reduction reaction analysis of nanoparticle copper oxide for copper direct bonding using formic acid (United States)

    Fujino, Masahisa; Akaike, Masatake; Matsuoka, Naoya; Suga, Tadatomo


    Copper direct bonding is required for electronics devices, especially power devices, and copper direct bonding using formic acid is expected to lower the bonding temperature. In this research, we analyzed the reduction reaction of copper oxide using formic acid with a Pt catalyst by electron spin resonance analysis and thermal gravimetry analysis. It was found that formic acid was decomposed and radicals were generated under 200 °C. The amount of radicals generated was increased by adding the Pt catalyst. Because of these radicals, both copper(I) oxide and copper(II) oxide start to be decomposed below 200 °C, and the reduction of copper oxide is accelerated by reactants such as H2 and CO from the decomposition of formic acid above 200 °C. The Pt catalyst also accelerates the reaction of copper oxide reduction. Herewith, it is considered that the copper surface can be controlled more precisely by using formic acid to induce direct bonding.

  17. Correlation between carbon-carbon bond length and the ease of retro Diels-Alder reaction

    Indian Academy of Sciences (India)

    Sambasivarao Kotha; Shaibal Banerjee; Mobin Shaikh


    The bond length between C8-C9 in (1′R,4′S,4a′R,8a′S)-6′,7′-dimethyl-1′,4′,4a′,8a′-tetrahydrospiro [cyclopropane-1,9′-[1,4]methanonaphthalene]-5′,8′-dione is 1.571 (2) Å and between C7-C12 is 1.567 (2) Å which are longer than the corresponding bond length for saturated bicyclic systems (1.531-1.535Å). This paper reports the correlation between bond length and the ease of retro Diels−Alder reaction.

  18. Covalently Bonded Chitosan on Graphene Oxide via Redox Reaction

    Directory of Open Access Journals (Sweden)

    Víctor M. Castaño


    Full Text Available Carbon nanostructures have played an important role in creating a new field of materials based on carbon. Chemical modification of carbon nanostructures through grafting has been a successful step to improve dispersion and compatibility in solvents, with biomolecules and polymers to form nanocomposites. In this sense carbohydrates such as chitosan are extremely valuable because their functional groups play an important role in diversifying the applications of carbon nanomaterials. This paper reports the covalent attachment of chitosan onto graphene oxide, taking advantage of this carbohydrate at the nanometric level. Grafting is an innovative route to modify properties of graphene, a two-dimensional nanometric arrangement, which is one of the most novel and promising nanostructures. Chitosan grafting was achieved by redox reaction using different temperature conditions that impact on the morphology and features of graphene oxide sheets. Transmission Electron Microscopy, Fourier Transform Infrared, Raman and Energy Dispersive spectroscopies were used to study the surface of chitosan-grafted-graphene oxide. Results show a successful modification indicated by the functional groups found in the grafted material. Dispersions of chitosan-grafted-graphene oxide samples in water and hexane revealed different behavior due to the chemical groups attached to the graphene oxide sheet.

  19. Empirical valence bond model of an SN2 reaction in polar and nonpolar solvents (United States)

    Benjamin, Ilan


    A new model for the substitution nucleophilic reaction (SN2) in solution is described using the empirical valence bond (EVB) method. The model includes a generalization to three dimensions of a collinear gas phase EVB model developed by Mathis et al. [J. Mol. Liq. 61, 81 (1994)] and a parametrization of solute-solvent interactions of four different solvents (water, ethanol, chloroform, and carbon tetrachloride). The model is used to compute (in these four solvents) reaction free energy profiles, reaction and solvent dynamics, a two-dimensional reaction/solvent free energy map, as well as a number of other properties that in the past have mostly been estimated.

  20. Recent Progress in the Research of Transition-Metal-Catalyzed C-CN Bond Cleavage%过渡金属催化的C—CN键断裂的研究进展

    Institute of Scientific and Technical Information of China (English)

    寇学振; 范佳骏; 童晓峰; 沈增明


    有机氰化物是一种重要的合成中间体,在药物、农药、染料和活性物质中都有应用.使用廉价、简单、低毒的氰基化合物在过渡金属的催化下通过C-CN键断裂生成复杂的氰化物是合成有机氰化物的重要手段之一.综述了不同过渡金属(如Ni,Pd,Rh,Cu,Ru,Fe,Mo,Co等)催化不同种类的氰基化合物C-CN键断裂的最新研究进展,如含C(sp1)-CN键化合物、C(sp2)-CN键化合物以及C(sp3)-CN键化合物,并对有关的反应机理及C-CN键断裂机理的进展进行了探讨.%Nitriles are an important class of organic compounds which can be found in pharmaceuticals,agrochemicals,dyes,and bioactive compounds.Transition-metal-catalyzed C-CN bond cleavage using inexpensive,simple and less toxic nitriles is one of the most attractive modem methods for the synthesis of complicated organic cyanides.Research progress of transition-metal-catalyzed (Ni,Pd,Rh,Cu,Ru,Fe,Mo,Co) different types of C-CN bond cleavage is reviewed,which includes some organic cyanides containing C(sp1)—CN bond,C(sp2)—CN bond and C(sp3)—CN bond.The C-CN cleavage mechanisms are also discussed in this review.

  1. Phase Evolution in Boride-Based Cermets and Reaction Bonding onto Plain Low Carbon Steel Substrate (United States)

    Palanisamy, B.; Upadhyaya, A.


    Reaction sinter bonding is a process that aims to bond two materials for improvement in properties through reactive sintering technique. The process has been effectively used to sinter hard materials like borides in situ which not only possess excellent oxidation resistance, good corrosion resistance but also resistant to abrasive wear. Sinter bonding is a unique surface modification process achieved through powder metallurgy and is competent with other techniques like boronizing sintering and sinter-brazing since it eliminates the additional operations of heat treatment and assembly and removes the inherent setbacks with these processes. This study focuses on identifying the phase evolution mechanism using characterization tools like x-ray diffractometry and energy dispersive spectroscopy and study of sinter bonding of the boron containing precursors (Mo-Cr-Fe-Ni-FeB-MoB) onto plain carbon steel. A microstructure containing Fe-based matrix dispersed with complex borides develops with temperature in the tape cast sheets. A fivefold increase in hardness between plain carbon steel in wrought condition and sinter bonded steel was observed. The multilayer consisted of a reaction zone adjacent to the interface and was investigated with the composition profile and hardness measurements. A model of sinter bonding between the cermet and the steel has also been proposed.

  2. Transition-metal-catalyzed C-N bond forming reactions using organic azides as the nitrogen source: a journey for the mild and versatile C-H amination. (United States)

    Shin, Kwangmin; Kim, Hyunwoo; Chang, Sukbok


    Owing to the prevalence of nitrogen-containing compounds in functional materials, natural products and important pharmaceutical agents, chemists have actively searched for the development of efficient and selective methodologies allowing for the facile construction of carbon-nitrogen bonds. While metal-catalyzed C-N cross-coupling reactions have been established as one of the most general protocols for C-N bond formation, these methods require starting materials equipped with functional groups such as (hetero)aryl halides or their equivalents, thus generating stoichiometric amounts of halide salts as byproducts. To address this aspect, a transition-metal-catalyzed direct C-H amination approach has emerged as a step- and atom-economical alternative to the conventional C-N cross-coupling reactions. However, despite the significant recent advances in metal-mediated direct C-H amination reactions, most available procedures need harsh conditions requiring stoichiometric external oxidants. In this context, we were curious to see whether a transition-metal-catalyzed mild C-H amination protocol could be achieved using organic azides as the amino source. We envisaged that a dual role of organic azides as an environmentally benign amino source and also as an internal oxidant via N-N2 bond cleavage would be key to develop efficient C-H amination reactions employing azides. An additional advantage of this approach was anticipated: that a sole byproduct is molecular nitrogen (N2) under the perspective catalytic conditions. This Account mainly describes our research efforts on the development of rhodium- and iridium-catalyzed direct C-H amination reactions with organic azides. Under our initially optimized Rh(III)-catalyzed amination conditions, not only sulfonyl azides but also aryl- and alkyl azides could be utilized as facile amino sources in reaction with various types of C(sp(2))-H bonds bearing such directing groups as pyridine, amide, or ketoxime. More recently, a new

  3. Serine-selective aerobic cleavage of peptides and a protein using a water-soluble copper-organoradical conjugate. (United States)

    Seki, Yohei; Tanabe, Kana; Sasaki, Daisuke; Sohma, Youhei; Oisaki, Kounosuke; Kanai, Motomu


    The site-specific cleavage of peptide bonds is an important chemical modification of biologically relevant macromolecules. The reaction is not only used for routine structural determination of peptides, but is also a potential artificial modulator of protein function. Realizing the substrate scope beyond the conventional chemical or enzymatic cleavage of peptide bonds is, however, a formidable challenge. Here we report a serine-selective peptide-cleavage protocol that proceeds at room temperature and near neutral pH value, through mild aerobic oxidation promoted by a water-soluble copper-organoradical conjugate. The method is applicable to the site-selective cleavage of polypeptides that possess various functional groups. Peptides comprising D-amino acids or sensitive disulfide pairs are competent substrates. The system is extendable to the site-selective cleavage of a native protein, ubiquitin, which comprises more than 70 amino acid residues.

  4. QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer. (United States)

    Elsässer, Brigitta; Fels, Gregor; Weare, John H


    The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.

  5. QM/MM Simulation (B3LYP) of the RNase A Cleavage-Transesterification Reaction Supports a Triester AN+DN Associative Mechanism with an O2´ H Internal Proton Transfer

    Energy Technology Data Exchange (ETDEWEB)

    Elsasser, Brigitta M.; Fels, Gregor; Weare, John H.


    The mechanism of the backbone cleavage transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report QM/MM free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2? oxygen on the neighboring diester phosphate bond and both reach the same product state (PS) (a O3??O2? cyclic phosphate and a O5? hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition state (TS) general acid (His 119)/base (His 12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2? migrates to the non-bridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN+DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 1011 difference in rate strongly supporting the less accepted triester mechanism.

  6. Effect of Carbon Containing Materials on Pure Carbon Reaction-bonded SiC

    Institute of Scientific and Technical Information of China (English)

    JI Xiaoli; WEI Lei; SUN Feng


    Petroleum coke, graphite, gas carbon and lower sulfur carbon black were used to prepare reaction-bonded silicon carbide. The influences of different carbon containing materials on properties of carbonaceous precursors, sintering process, and microstructure of the prepared SiC were researched. The results show that:(1)With the density of carbon containing materials increasing, the porosity of carbonaceous precursors decreases and the infiltrating process of liquid silicon is more difficult.(2)The reaction between carbon containing materials and liquid silicon, the volume effect is more obvious with the density of carbon containing materials increasing.(3)As the carbon containing materials density decreasing, residual carbon in reaction bonded SiC also decreases.

  7. Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques (United States)

    Fernandez, Julio M.


    The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule

  8. Palladium(II)-Catalyzed C-H Bond Activation/C-C and C-O Bond Formation Reaction Cascade: Direct Synthesis of Coumestans. (United States)

    Neog, Kashmiri; Borah, Ashwini; Gogoi, Pranjal


    A palladium catalyzed cascade reaction of 4-hydroxycoumarins and in situ generated arynes has been developed for the direct synthesis of coumestans. This cascade strategy proceeds via C-H bond activation/C-O and C-C bond formations in a single reaction vessel. This methodology affords moderate to good yields of coumestans and is tolerant of a variety of functional groups including halide. The methodology was applied to the synthesis of natural product flemichapparin C.

  9. Cleavage of the Fe—Fe Bond of (Me2SiSiMe2) [η5-C5H4Fe(CO)2]2 with Na/Hg and Molecular Structure of the Ring-Opened Complex

    Institute of Scientific and Technical Information of China (English)

    周秀中; 张怀林; 张振生


    The reaction of the rifle cyclic complex (1) with sodium amalgam in THF resulted in the expected cleavage of the Fe-Fe bond to afford his-sodium salt ( Me2SiSiMe2 ) [η5-C5H4Fe(CO)2]2 (4). The latter was not isolated and was used directly to react with MeI, PhCH2Cl, CH3C(O)Cl, PhC(O)Cl,Cy3SnCl (Cy= cyclohexyl) or Ph3SnCl to afford corresponding ring-opened derivatives (Me2SiSiMe2) [η5-C5H4Fe(CO)2]2 [5, R=Me; 6, R=PhCH2; 7, R=CH3C(O); 8, R=PhC(O); 9, R = Cy3Sn or 10, R = Ph3Sn ]. The crystal and molecular structures of 10 were determined by X-ray diffraction analysis. The molecule took the desired ant/ conformation around the Si-Si bond. The length of the Si--Si bond is 0.2343(3)nm, which is essentially identical to that in the cyclic structure of 1[0.2346(4) tun]. This result unambiguously demonstrates that the Si--Si bond in the cyclic structure of 1 is not subject to obvious strain.

  10. Ultrafast α -CC bond cleavage of acetone upon excitation to 3p and 3d Rydberg states by femtosecond time-resolved photoelectron imaging (United States)

    Hüter, O.; Temps, F.


    The radiationless electronic relaxation and α -CC bond fission dynamics of jet-cooled acetone in the S1 (n π* ) state and in high-lying 3p and 3d Rydberg states have been investigated by femtosecond time-resolved mass spectrometry and photoelectron imaging. The S1 state was accessed by absorption of a UV pump photon at selected wavelengths between λ = 320 and 250 nm. The observed acetone mass signals and the S1 photoelectron band decayed on sub-picosecond time scales, consistent with a recently proposed ultrafast structural relaxation of the molecules in the S1 state away from the Franck-Condon probe window. No direct signatures could be observed by the experiments for CC dissociation on the S1 potential energy hypersurface in up to 1 ns. The observed acetyl mass signals at all pump wavelengths turned out to be associated with absorption by the molecules of one or more additional pump and/or probe photons. In particular, absorption of a second UV pump photon by the S1 (n π* ) state was found to populate a series of high-lying states belonging to the n = 3 Rydberg manifold. The respective transitions are favored by much larger cross sections compared to the S1 ← S0 transition. The characteristic energies revealed by the photoelectron images allowed for assignments to the 3p and 3dyz states. At two-photon excitation energies higher than 8.1 eV, an ultrafast reaction pathway for breaking the α -CC bond in 50-90 fs via the 3dyz Rydberg state and the elusive π π* state was observed, explaining the formation of acetyl radicals after femtosecond laser excitation of acetone at these wavelengths.

  11. A simulation of the reaction bonding of Si3N4 to generate porous microstructures (United States)

    Haubensak, F. G.; Bulatov, V. V.; Argon, A. S.


    A stochastic numerical technique is presented that has been used to study the formation of reaction-bonded porous silicon nitride (RBSN). Like many reaction-bonded materials, RBSN is a structural ceramic that has a naturally occurring porosity of approximately 25% resulting from the unique kinetics of formation. Since such porosity is usually unavoidable, it is of interest to discover its relevant measures, such as the size distribution and degree of homogeneity of pores, and the factors that govern the formation of these pores, in order to understand and optimize the crack propagation resistance of such materials. The probing of the fracture toughness of the generated microstructures by computational means is described in the companion paper [E G. Haubensak, V V Bulatov and A.S. Argon, J. Comput.-Aided Mater. Design, 2 (1995) 205]. The primary purpose of the simulated reaction was the generation of realistic microstructures incorporating the major features of reaction bonding. In this manner it is possible to generate objective, systematic variations of similar microstructures. With such microstructures, crack nucleation and propagation mechanisms can be observed, and processing parameters, which control fracture toughness, can be identified. In the present study, we outline the details of the reaction kinetics model, demonstrate its ability to generate realistic microstructures, and report some additional observations on some topological phenomena resulting from the reaction, such as those controlling the formation of large pores in the final structure. In yet a separate communication of a related experimental study we present the microstructures of the actual RBSN. We will use the findings of the latter study here for making some comparisons.

  12. Irreversible bonding of polyimide and polydimethylsiloxane (PDMS) based on a thiol-epoxy click reaction (United States)

    Hoang, Michelle V.; Chung, Hyun-Joong; Elias, Anastasia L.


    Polyimide is one of the most popular substrate materials for the microfabrication of flexible electronics, while polydimethylsiloxane (PDMS) is the most widely used stretchable substrate/encapsulant material. These two polymers are essential in fabricating devices for microfluidics, bioelectronics, and the internet of things; bonding these materials together is a crucial challenge. In this work, we employ click chemistry at room temperature to irreversibly bond polyimide and PDMS through thiol-epoxy bonds using two different methods. In the first method, we functionalize the surfaces of the PDMS and polyimide substrates with mercaptosilanes and epoxysilanes, respectively, for the formation of a thiol-epoxy bond in the click reaction. In the second method, we functionalize one or both surfaces with mercaptosilane and introduce an epoxy adhesive layer between the two surfaces. When the surfaces are bonded using the epoxy adhesive without any surface functionalization, an extremely small peel strength (0.3 N mm-1 (method 2) are observed, and failure occurs by tearing of the PDMS layer. We envision that the novel processing route employing click chemistry can be utilized in various cases of stretchable and flexible device fabrication.

  13. Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries. (United States)

    Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario


    DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.

  14. B-H bond activation using an electrophilic metal complex: insights into the reaction pathway. (United States)

    Kumar, Rahul; Jagirdar, Balaji R


    A highly electrophilic ruthenium center in the [RuCl(dppe)(2)][OTf] complex brings about the activation of the B-H bond in ammonia borane (H(3)N·BH(3), AB) and dimethylamine borane (Me(2)HN·BH(3), DMAB). At room temperature, the reaction between [RuCl(dppe)(2)][OTf] and AB or DMAB results in trans-[RuH(η(2)-H(2))(dppe)(2)][OTf], trans-[RuCl(η(2)-H(2))(dppe)(2)][OTf], and trans-[RuH(Cl)(dppe)(2)], as noted in the NMR spectra. Mixing the ruthenium complex and AB or DMAB at low temperature (198/193 K) followed by NMR spectral measurements as the reaction mixture was warmed up to room temperature allowed the observation of various species formed enroute to the final products that were obtained at room temperature. On the basis of the variable-temperature multinuclear NMR spectroscopic studies of these two reactions, the mechanistic insights for B-H bond activation were obtained. In both cases, the reaction proceeds via an η(1)-B-H moiety bound to the metal center. The detailed mechanistic pathways of these two reactions as studied by NMR spectroscopy are described.

  15. Dinitrogen cleavage and hydrogenation by a trinuclear titanium polyhydride complex. (United States)

    Shima, Takanori; Hu, Shaowei; Luo, Gen; Kang, Xiaohui; Luo, Yi; Hou, Zhaomin


    Both the Haber-Bosch and biological ammonia syntheses are thought to rely on the cooperation of multiple metals in breaking the strong N≡N triple bond and forming an N-H bond. This has spurred investigations of the reactivity of molecular multimetallic hydrides with dinitrogen. We report here the reaction of a trinuclear titanium polyhydride complex with dinitrogen, which induces dinitrogen cleavage and partial hydrogenation at ambient temperature and pressure. By (1)H and (15)N nuclear magnetic resonance, x-ray crystallographic, and computational studies of some key reaction steps and products, we have determined that the dinitrogen (N2) reduction proceeds sequentially through scission of a N2 molecule bonded to three Ti atoms in a μ-η(1):η(2):η(2)-end-on-side-on fashion to give a μ2-N/μ3-N dinitrido species, followed by intramolecular hydrogen migration from Ti to the μ2-N nitrido unit.

  16. Method for producing bio-fuel that integrates heat from carbon-carbon bond-forming reactions to drive biomass gasification reactions (United States)

    Cortright, Randy D.; Dumesic, James A.


    A low-temperature catalytic process for converting biomass (preferably glycerol recovered from the fabrication of bio-diesel) to synthesis gas (i.e., H.sub.2/CO gas mixture) in an endothermic gasification reaction is described. The synthesis gas is used in exothermic carbon-carbon bond-forming reactions, such as Fischer-Tropsch, methanol, or dimethylether syntheses. The heat from the exothermic carbon-carbon bond-forming reaction is integrated with the endothermic gasification reaction, thus providing an energy-efficient route for producing fuels and chemicals from renewable biomass resources.

  17. Method for producing bio-fuel that integrates heat from carbon-carbon bond-forming reactions to drive biomass gasification reactions (United States)

    Cortright, Randy D [Madison, WI; Dumesic, James A [Verona, WI


    A low-temperature catalytic process for converting biomass (preferably glycerol recovered from the fabrication of bio-diesel) to synthesis gas (i.e., H.sub.2/CO gas mixture) in an endothermic gasification reaction is described. The synthesis gas is used in exothermic carbon-carbon bond-forming reactions, such as Fischer-Tropsch, methanol, or dimethylether syntheses. The heat from the exothermic carbon-carbon bond-forming reaction is integrated with the endothermic gasification reaction, thus providing an energy-efficient route for producing fuels and chemicals from renewable biomass resources.

  18. A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus. (United States)

    Han Du, Wen-Ge; Götz, Andreas W; Yang, Longhua; Walker, Ross C; Noodleman, Louis


    Broken-symmetry density functional calculations have been performed on the [Fea3, CuB] dinuclear center (DNC) of ba3 cytochrome c oxidase from Thermus thermophilus in the states of [Fea3(3+)-(HO2)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of CuB. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] have also been calculated. The transition of [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] → [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O2 binds to Fea3(2+)) to state PM ([Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutral-Asp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.

  19. Terminal Uranium(V/VI) Nitride Activation of Carbon Dioxide and Carbon Disulfide: Factors Governing Diverse and Well-Defined Cleavage and Redox Reactions. (United States)

    Cleaves, Peter A; Kefalidis, Christos E; Gardner, Benedict M; Tuna, Floriana; McInnes, Eric J L; Lewis, William; Maron, Laurent; Liddle, Stephen T


    The reactivity of terminal uranium(V/VI) nitrides with CE2 (E=O, S) is presented. Well-defined C=E cleavage followed by zero-, one-, and two-electron redox events is observed. The uranium(V) nitride [U(Tren(TIPS) )(N)][K(B15C5)2 ] (1, Tren(TIPS) =N(CH2 CH2 NSiiPr3 )3 ; B15C5=benzo-15-crown-5) reacts with CO2 to give [U(Tren(TIPS) )(O)(NCO)][K(B15C5)2 ] (3), whereas the uranium(VI) nitride [U(Tren(TIPS) )(N)] (2) reacts with CO2 to give isolable [U(Tren(TIPS) )(O)(NCO)] (4); complex 4 rapidly decomposes to known [U(Tren(TIPS) )(O)] (5) with concomitant formation of N2 and CO proposed, with the latter trapped as a vanadocene adduct. In contrast, 1 reacts with CS2 to give [U(Tren(TIPS) )(κ(2) -CS3 )][K(B15C5)2 ] (6), 2, and [K(B15C5)2 ][NCS] (7), whereas 2 reacts with CS2 to give [U(Tren(TIPS) )(NCS)] (8) and "S", with the latter trapped as Ph3 PS. Calculated reaction profiles reveal outer-sphere reactivity for uranium(V) but inner-sphere mechanisms for uranium(VI); despite the wide divergence of products the initial activation of CE2 follows mechanistically related pathways, providing insight into the factors of uranium oxidation state, chalcogen, and NCE groups that govern the subsequent divergent redox reactions that include common one-electron reactions and a less-common two-electron redox event. Caution, we suggest, is warranted when utilising CS2 as a reactivity surrogate for CO2 .

  20. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study. (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan


    A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.

  1. Zn/ ZrCl4 System Induced Reductive Cleavage of Se-Se Bond in Diaryl Diselenides: A Novel Method for the Systhesis of Selenoesters

    Institute of Scientific and Technical Information of China (English)


    The Se-Se bond in diaryl diselenides was reduced by Zn/ZrCl4 system to produce selenide anions, which react with acyl chlorides or acid anhydrides to afford selenoesters in THF under mild and neutral conditions.

  2. Selective molecular recognition, C-H bond activation, and catalysis in nanoscale reaction vessels

    Energy Technology Data Exchange (ETDEWEB)

    Fiedler, Dorothea; Leung, Dennis H.; Raymond, Kenneth N.; Bergman, Robert G.


    Supramolecular chemistry represents a way to mimic enzyme reactivity by using specially designed container molecules. We have shown that a chiral self-assembled M{sub 4}L{sub 6} supramolecular tetrahedron can encapsulate a variety of cationic guests, with varying degrees of stereoselectivity. Reactive iridium guests can be encapsulated and the C-H bond activation of aldehydes occurs, with the host cavity controlling the ability of substrates to interact with the metal center based upon size and shape. In addition, the host container can act as a catalyst by itself. By restricting reaction space and preorganizing the substrates into reactive conformations, it accelerates the sigmatropic rearrangement of enammonium cations.

  3. Formation and densification of SiAlON materials by reaction bonding and silicothermal reduction routes (United States)

    Rouquié, Yann; Jones, Mark I.


    Samples of β and O-sialon with different levels of substitution (i.e. z = 1 and 4 for β-sialon and x = 0.05 and 0.2 for O-sialon) have been synthesized by both reaction bonding and silicothermal reduction techniques in a nitrogen atmosphere. The possibility of obtaining dense sialon materials by these lower cost production methods has been investigated using a statistical design methodology. The influence of different parameters (temperature, gas pressure and additive type) on the densification and decomposition has been studied and will be discussed in this presentation.

  4. Formation and densification of SiAlON materials by reaction bonding and silicothermal reduction routes

    Energy Technology Data Exchange (ETDEWEB)

    Rouquie, Yann; Jones, Mark I, E-mail: [Department of Material and Chemicals Engineering, University of Auckland, New Zealand Private bag 92019, Auckland Mail Center, Auckland, 1142 (New Zealand)


    Samples of {beta} and O-sialon with different levels of substitution (i.e. z = 1 and 4 for {beta}-sialon and x = 0.05 and 0.2 for O-sialon) have been synthesized by both reaction bonding and silicothermal reduction techniques in a nitrogen atmosphere. The possibility of obtaining dense sialon materials by these lower cost production methods has been investigated using a statistical design methodology. The influence of different parameters (temperature, gas pressure and additive type) on the densification and decomposition has been studied and will be discussed in this presentation.

  5. Innovative Catalysis in Organic Synthesis Oxidation, Hydrogenation, and C-X Bond Forming Reactions

    CERN Document Server

    Andersson, Pher G


    Authored by a European team of leaders in the field, this book compiles innovative approaches for C-X bond forming processes frequently applied in organic synthesis. It covers all key types of catalysis, including homogeneous, heterogeneous, and organocatalysis, as well as mechanistic and computational studies. Special attention is focused on the improvement of efficiency and sustainability of important catalytic processes, such as selective oxidations, hydrogenation and cross-coupling reactions.The result is a valuable resource for both advanced researchers in academia and industry, as well a

  6. Theoretical Study on the Kinetics of Electron Transfer for Bond-breaking Reaction

    Institute of Scientific and Technical Information of China (English)

    XING,Yu-Mei(邢玉梅); ZHOU,Zheng-Yu(周正宇); GAO,Hong-Wei(高洪伟)


    To test the theory of dissociative electron transfer, a simple model describing the kinetics of electron transfer bond-breaking reactions was used. The Hamiltonian of the system was given.The homogeneous and heterogeneous kinetic data fit reasonably well with an activation-driving force relatiobship derived from the Marcus quadratic theory. In the heterogeneous case, there is a good agreement between the theoretical calculation amd the experimental result, while in the homogeneous case, a good a greement is only observed for the tertiary halides. This is due to the stability of tertiary radical resulting from the sterical effect.

  7. Crystal Structure of the VP4 Protease from Infectious Pancreatic Necrosis Virus Reveals the acyl-enzyme Complex for an Intermolecular Self-Cleavage Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Lee,J.; Feldman, A.; Delmas, B.; Paetzel, M.


    Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH{sub 2}-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-{angstrom} resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser{sup 633}O{gamma} forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala{sup 716}, of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-{angstrom} resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ({approx}19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.

  8. Raman spectroscopic characterization of the core-rim structure in reaction bonded boron carbide ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Jannotti, Phillip; Subhash, Ghatu, E-mail: [Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, Florida 32611 (United States); Zheng, James Q.; Halls, Virginia [Program Executive Office—Soldier Protection and Individual Equipment, US Army, Fort Belvoir, Virginia 22060 (United States); Karandikar, Prashant G.; Salamone, S.; Aghajanian, Michael K. [M-Cubed Technologies, Inc., Newark, Delaware 19711 (United States)


    Raman spectroscopy was used to characterize the microstructure of reaction bonded boron carbide ceramics. Compositional and structural gradation in the silicon-doped boron carbide phase (rim), which develops around the parent boron carbide region (core) due to the reaction between silicon and boron carbide, was evaluated using changes in Raman peak position and intensity. Peak shifting and intensity variation from the core to the rim region was attributed to changes in the boron carbide crystal structure based on experimental Raman observations and ab initio calculations reported in literature. The results were consistent with compositional analysis determined by energy dispersive spectroscopy. The Raman analysis revealed the substitution of silicon atoms first into the linear 3-atom chain, and then into icosahedral units of the boron carbide structure. Thus, micro-Raman spectroscopy provided a non-destructive means of identifying the preferential positions of Si atoms in the boron carbide lattice.

  9. Catalysis of Heterocyclic Azadiene Cycloaddition Reactions by Solvent Hydrogen Bonding: Concise Total Synthesis of Methoxatin. (United States)

    Glinkerman, Christopher M; Boger, Dale L


    Although it has been examined for decades, no general approach to catalysis of the inverse electron demand Diels-Alder reactions of heterocyclic azadienes has been introduced. Typically, additives such as Lewis acids lead to nonproductive consumption of the electron-rich dienophiles without productive activation of the electron-deficient heterocyclic azadienes. Herein, we report the first general method for catalysis of such cycloaddition reactions by using solvent hydrogen bonding of non-nucleophilic perfluoroalcohols, including hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE), to activate the electron-deficient heterocyclic azadienes. Its use in promoting the cycloaddition of 1,2,3-triazine 4 with enamine 3 as the key step of a concise total synthesis of methoxatin is described.

  10. Preparation of Al- AlN Bonded Corundum Based Refractories by in-situ Reaction

    Institute of Scientific and Technical Information of China (English)

    ZHU Boquan; FANG Binxiang; ZHANG Wenjie


    The Al-AlN bonded corundum based refractories was synthesized with the starting materials of fused alu-mina and metallic aluminium in nitrogen atmosphere through in-situ reaction. The study indicated that with the addition of 14% metallic aluminium (13% of Al powder and 1% of Al fiber) , the material nitridized at 1 100 ℃ for 3 h has excellent physical properties. It is found that a massive quantity of AlN in the forms of both whiskers" and hexagon pellet particles is formed, and a large quantity of Al remained in the matrix. This multiple bonding system resulted in the excellent me-chanical properties of the material. It is also found that the hydration tendency of the prepared material is inhib-ited, and the material exhibited excellent thermal shock resistance. The nature of protective oxidation of the bonding system is characterized. Thus, this material may become a new candidate of carbon-free sliding plate material for continuous casting.

  11. Organometallic Bonding in an Ullmann-Type On-Surface Chemical Reaction Studied by High-Resolution Atomic Force Microscopy. (United States)

    Kawai, Shigeki; Sadeghi, Ali; Okamoto, Toshihiro; Mitsui, Chikahiko; Pawlak, Rémy; Meier, Tobias; Takeya, Jun; Goedecker, Stefan; Meyer, Ernst


    The on-surface Ullmann-type chemical reaction synthesizes polymers by linking carbons of adjacent molecules on solid surfaces. Although an organometallic compound is recently identified as the reaction intermediate, little is known about the detailed structure of the bonded organometallic species and its influence on the molecule and the reaction. Herein atomic force microscopy at low temperature is used to study the reaction with 3,9-diiododinaphtho[2,3-b:2',3'-d]thiophene (I-DNT-VW), which is polymerized on Ag(111) in vacuum. Thermally sublimated I-DNT-VW picks up a Ag surface atom, forming a CAg bond at one end after removing an iodine. The CAg bond is usually short-lived, and a CAgC organometallic bond immediately forms with an adjacent molecule. The existence of the bonded Ag atoms strongly affects the bending angle and adsorption height of the molecular unit. Density functional theory calculations reveal the bending mechanism, which reveals that charge from the terminus of the molecule is transferred via the Ag atom into the organometallic bond and strengths the local adsorption to the substrate. Such deformations vanish when the Ag atoms are removed by annealing and CC bonds are established.

  12. Observation of Spontaneous C=C Bond Breaking in the Reaction between Atomic Boron and Ethylene in Solid Neon. (United States)

    Jian, Jiwen; Lin, Hailu; Luo, Mingbiao; Chen, Mohua; Zhou, Mingfei


    A ground-state boron atom inserts into the C=C bond of ethylene to spontaneously form the allene-like compound H2 CBCH2 on annealing in solid neon. This compound can further isomerize to the propyne-like HCBCH3 isomer under UV light excitation. The observation of this unique spontaneous C=C bond insertion reaction is consistent with theoretical predictions that the reaction is thermodynamically exothermic and kinetically facile. This work demonstrates that the stronger C=C bond, rather than the less inert C-H bond, can be broken to form organoboron species from the reaction of a boron atom with ethylene even at cryogenic temperatures.

  13. Thermomechanics of a temperature sensitive covalent adaptable polymer with bond exchange reactions. (United States)

    Sun, XiaoHao; Wu, HengAn; Long, Rong


    We study a covalent adaptable polymer that can rearrange its network topology through thermally activated bond exchange reactions. When the polymer is deformed, such a network rearrangement leads to macroscopic stress relaxation, which allows the polymer to be thermoformed without a mold. Based on a previously developed constitutive model, we investigate thermal-mechanical behaviors of this material under a non-uniform and evolving temperature field through numerical simulations. Our focus is on the complex coupling between mechanical deformation, heat conduction and bond exchange reactions. Several examples are presented to illustrate the effects of non-uniform heating: uniaxial tension under heat conduction, torsion of a thin strip with local heating and thermal imprinting. Our results show that during non-uniform heating the material in the high temperature region creeps. This causes a redistribution of the deformation field and thus results in a final shape that deviates from the prescribed shape. The final shapes after thermoforming can be tuned by controlling the extent of heat conduction through different combinations of heating temperature and time. For example, with high temperature and a short heating time, it is possible to approximately confine stress relaxation and thus shape fixity within the local heating region. This is not the case if low temperature and a long heating time are used. These results can be utilized to design the temporal and spatial sequences of local heating during thermoforming to achieve various complex final shapes.

  14. Fabrication and test of reaction bond silicon carbide for optical applications

    Institute of Scientific and Technical Information of China (English)

    YAO Wang; ZHANG Yu-min; HAN Jie-cai; ZUO Hong-bo


    A reaction bonding fabrication process using various grain size of SiC powder was investigated. The properties such as mechanical, thermal and physic property were tested and analyzed. RBSiC produced using this process is a polycrystalline material and has high specific stiffness (density of 3.09 g/cm3 with elastic modulus of 362.39 GPa), strength (269.64 MPa) and hardness (19.43 GPa). At room temperature its low CTE (3.47×10-6/K), combined with relatively high thermal conductivity (161.14 W/mK)and specific heat capacity (593.86 J/kg.K) can minimize the bothersome thermal distortion. This advantage is outstanding even at higher temperature of test range. Two d250 mm RBSiC mirror were polished. Surface roughness value less than 5 nm was obtained.Results prove that this reaction bonding process is a feasible method to produced high quality RBSiC optical mirror.

  15. Bite angle effects of diphosphines in C-C and C-X bond forming cross coupling reactions

    NARCIS (Netherlands)

    Birkholz, M.N.; Freixa, Z.; van Leeuwen, P.W.N.M.


    Catalytic reactions of C-C and C-X bond formation are discussed in this critical review with particular emphasis on cross coupling reactions catalyzed by palladium and wide bite angle bidentate diphosphine ligands. Especially those studies have been collected that allow comparison of the ligand bite

  16. Hydrolysis of Surfactants Containing Ester Bonds: Modulation of Reaction Kinetics and Important Aspects of Surfactant Self-Assembly (United States)

    Lundberg, Dan; Stjerndahl, Maria


    The effects of self-assembly on the hydrolysis kinetics of surfactants that contain ester bonds are discussed. A number of examples on how reaction rates and apparent reaction orders can be modulated by changes in the conditions, including an instance of apparent zero-order kinetics, are presented. Furthermore, it is shown that the examples on…

  17. PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a carbon-phosphorus bond

    DEFF Research Database (Denmark)

    McSorley, Fern R.; Wyatt, Peter W.; Martinez, Ascuncion;


    The sequential activities of PhnY, an α-ketoglutarate/Fe(II)-dependent dioxygenase, and PhnZ, a Fe(II)-dependent enzyme of the histidine-aspartate motif hydrolase family, cleave the carbon-phosphorus bond of the organophosphonate natural product 2-aminoethylphosphonic acid. PhnY adds a hydroxyl g...

  18. The specific cleavage of lactone linkage to open-loop in cyclic lipopeptide during negative ESI tandem mass spectrometry: the hydrogen bond interaction effect of 4-ethyl guaiacol.

    Directory of Open Access Journals (Sweden)

    Mengzhe Guo

    Full Text Available Mass spectrometry is a valuable tool for the analysis and identification of chemical compounds, particularly proteins and peptides. Lichenysins G, the major cyclic lipopeptide of lichenysin, and the non-covalent complex of lichenysins G and 4-ethylguaiacol were investigated with negative ion ESI tandem mass spectrometry. The different fragmentation mechanisms for these compounds were investigated. Our study shows the 4-ethylguaiacol hydrogen bond with the carbonyl oxygen of the ester group in the loop of lichenysins G. With the help of this hydrogen bond interaction, the ring structure preferentially opens in lactone linkage rather than O-C bond of the ester-group to produce alcohol and ketene. Isothermal titration 1H-NMR analysis verified the hydrogen bond and determined the proportion of subject and ligand in the non-covalent complex to be 1∶1. Theoretical calculations also suggest that the addition of the ligand can affect the energy of the transition structures (TS during loop opening.

  19. Preparing (Multi)Fluoroarenes as Building Blocks for Synthesis: Nickel-Catalyzed Borylation of Polyfluoroarenes via C-F Bond Cleavage. (United States)

    Zhou, Jing; Kuntze-Fechner, Maximilian W; Bertermann, Rüdiger; Paul, Ursula S D; Berthel, Johannes H J; Friedrich, Alexandra; Du, Zhenting; Marder, Todd B; Radius, Udo


    The [Ni(IMes)2]-catalyzed transformation of fluoroarenes into arylboronic acid pinacol esters via C-F bond activation and transmetalation with bis(pinacolato)diboron (B2pin2) is reported. Various partially fluorinated arenes with different degrees of fluorination were converted into their corresponding boronate esters.

  20. Ostensible enzyme promiscuity: alkene cleavage by peroxidases. (United States)

    Mutti, Francesco G; Lara, Miguel; Kroutil, Markus; Kroutil, Wolfgang


    Enzyme promiscuity is generally accepted as the ability of an enzyme to catalyse alternate chemical reactions besides the 'natural' one. In this paper peroxidases were shown to catalyse the cleavage of a C=C double bond adjacent to an aromatic moiety for selected substrates at the expense of molecular oxygen at an acidic pH. It was clearly shown that the reaction occurs due to the presence of the enzyme; furthermore, the reactivity was clearly linked to the hemin moiety of the peroxidase. Comparison of the transformations catalysed by peroxidase and by hemin chloride revealed that these two reactions proceed equally fast; additional experiments confirmed that the peptide backbone was not obligatory for the reaction and only a single functional group of the enzyme was required, namely in this case the prosthetic group (hemin). Consequently, we propose to define such a promiscuous activity as 'ostensible enzyme promiscuity'. Thus, we call an activity that is catalysed by an enzyme 'ostensible enzyme promiscuity' if the reactivity can be tracked back to a single catalytic site, which on its own can already perform the reaction equally well in the absence of the peptide backbone.

  1. Site and bond-specific dynamics of reactions at the gas-liquid interface. (United States)

    Tesa-Serrate, Maria A; King, Kerry L; Paterson, Grant; Costen, Matthew L; McKendrick, Kenneth G


    The dynamics of the interfacial reactions of O((3)P) with the hydrocarbon liquids squalane (C30H62, 2,6,10,15,19,23-hexamethyltetracosane) and squalene (C30H50, trans-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene) have been studied experimentally. Laser-induced fluorescence (LIF) was used to detect the nascent gas-phase OH products. The O((3)P) atoms are acutely sensitive to the chemical differences of the squalane and squalene surfaces. The larger exothermicity of abstraction from allylic C-H sites in squalene is reflected in markedly hotter OH rotational and vibrational distributions. There is a more modest increase in translational energy release. A larger fraction of the available energy is deposited in the liquid for squalene than for squalane, consistent with a more extensive geometry change on formation of the allylic radical co-product. Although the dominant reaction mechanism is direct, impulsive scattering, there is some evidence for OH being accommodated at both liquid surfaces, resulting in thermalised translation and rotational distributions. Despite the H-abstraction reaction being strongly favoured energetically for squalene, the yield of OH is substantially lower than for squalane. This is very likely due to competitive addition of O((3)P) to the unsaturated sites in squalene, implying that double bonds are extensively exposed at the liquid surface.

  2. Unique cleavage of 2-acetamido-2-deoxy-D-glucose from the reducing end of biantennary complex type oligosaccharides. (United States)

    Murase, Takefumi; Kajihara, Yasuhiro


    Basic treatment of a biantennary complex-type sialyloligosaccharide, as well as its asialo form, was found to lead to the specific cleavage of 2-acetamido-2-deoxy-d-glucose (GlcNAc) from the reducing end. The resultant oligosaccharides were identical to those prepared by treatment with endo-beta-glycosidase-M, which cleaves the glycosidic bond between two GlcNAc residues at the reducing end of N-linked oligosaccharides. In addition, mechanistic studies suggested that an elimination reaction in the reducing-end terminal GlcNAc residue causes this specific cleavage reaction.

  3. Experimental investigation on material migration phenomena in micro-EDM of reaction-bonded silicon carbide

    Energy Technology Data Exchange (ETDEWEB)

    Liew, Pay Jun [Department of Mechanical Systems and Design, Tohoku University, Aramaki Aoba 6-6-01, Aoba-ku, Sendai, 980-8579 (Japan); Manufacturing Process Department, Faculty of Manufacturing Engineering, Universiti Teknikal Malaysia Melaka, Hang Tuah Jaya, 76100, Durian Tunggal, Melaka (Malaysia); Yan, Jiwang, E-mail: [Department of Mechanical Engineering, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Kohoku-ku, Yokohama, 223-8522 (Japan); Kuriyagawa, Tsunemoto [Department of Mechanical Systems and Design, Tohoku University, Aramaki Aoba 6-6-01, Aoba-ku, Sendai, 980-8579 (Japan)


    Material migration between tool electrode and workpiece material in micro electrical discharge machining of reaction-bonded silicon carbide was experimentally investigated. The microstructural changes of workpiece and tungsten tool electrode were examined using scanning electron microscopy, cross sectional transmission electron microscopy and energy dispersive X-ray under various voltage, capacitance and carbon nanofibre concentration in the dielectric fluid. Results show that tungsten is deposited intensively inside the discharge-induced craters on the RB-SiC surface as amorphous structure forming micro particles, and on flat surface region as a thin interdiffusion layer of poly-crystalline structure. Deposition of carbon element on tool electrode was detected, indicating possible material migration to the tool electrode from workpiece material, carbon nanofibres and dielectric oil. Material deposition rate was found to be strongly affected by workpiece surface roughness, voltage and capacitance of the electrical discharge circuit. Carbon nanofibre addition in the dielectric at a suitable concentration significantly reduced the material deposition rate.

  4. Hydroacylation of N=N bonds via aerobic C-H activation of aldehydes, and reactions of the products thereof


    Akhbar, A. R.


    The development of methods to construct new chemical bonds efficiently and selectively whilst minimising energy usage and waste production is of high importance in organic chemistry. Many current methods employ inefficient, costly and often toxic multi step protocols to generate new chemical bonds. The hydroacylation reaction is one method of reducing such inefficiencies. The development of an aerobic hydroacylation protocol in the Caddick group has recently allowed the functionalisation of a...

  5. Thermodynamic properties, decomposition kinetics and reaction models of BCHMX and its Formex bonded explosive

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Qi-Long, E-mail: [Institute of Energetic Materials, Faculty of Chemical technology, University of Pardubice, 532 10 Pardubice (Czech Republic); Zeman, Svatopluk, E-mail: [Institute of Energetic Materials, Faculty of Chemical technology, University of Pardubice, 532 10 Pardubice (Czech Republic); Svoboda, Roman [Department of Physical Chemistry, Faculty of Chemical technology, University of Pardubice, 532 10 Pardubice (Czech Republic); Elbeih, Ahmed [Military Technical College, Cairo (Egypt)


    As an attractive new energetic material, cis-1,3,4,6-tetranitrooctahydroimidazo-[4,5-d]imidazole (BCHMX) and its polymer bonded explosive (PBX) with styrene-butadiene rubber (SBR) binder (Formex type) have been investigated with regard to its thermal decomposition kinetics and reaction models by using DSC, TG and SEM techniques. It was found that the decomposition of BCHMX in dynamic nitrogen could be divided into two steps, while there is only one step for its Formex bonded explosive. The activation energy for decomposition of BCHMX/Formex was obtained to be 221.7 {+-} 4.99 kJ mol{sup -1} by modified KAS method, while the mean activation energies for pure BCHMX are calculated as 233.0 {+-} 2.1 kJ mol{sup -1} for first step and 186.0 {+-} 0.92 kJ mol{sup -1} for the second step. It was further proved that the first decomposition step of BCHMX is autocatalytic, during which the crystal of BCHMX could dissolve in the liquid phase of its thermolysis products on the surface. Besides, the JMA and AC models were found to be appropriate to interpret the two-step decomposition of pure BCHMX and JMA model for BCHMX/Formex, the parameterized reaction models for BCHMX could be established as f({alpha}) = {alpha}{sup 0.45}(1 - {alpha}){sup 1.51} and f({alpha}) = 2.33 Multiplication-Sign (1 - {alpha})[-ln(1 - {alpha})]{sup 0.57}, while for BCHMX/Formex as f({alpha}) = 2 Multiplication-Sign (1 - {alpha})[-ln(1 - {alpha})]{sup 1/2}.

  6. Acid-base bifunctional catalysis of silica-alumina-supported organic amines for carbon-carbon bond-forming reactions. (United States)

    Motokura, Ken; Tomita, Mitsuru; Tada, Mizuki; Iwasawa, Yasuhiro


    Acid-base bifunctional heterogeneous catalysts were prepared by the reaction of an acidic silica-alumina (SA) surface with silane-coupling reagents possessing amino functional groups. The obtained SA-supported amines (SA-NR2) were characterized by solid-state 13C and 29Si NMR spectroscopy, FT-IR spectroscopy, and elemental analysis. The solid-state NMR spectra revealed that the amines were immobilized by acid-base interactions at the SA surface. The interactions between the surface acidic sites and the immobilized basic amines were weaker than the interactions between the SA and free amines. The catalytic performances of the SA-NR2 catalysts for various carbon-carbon bond-forming reactions, such as cyano-ethoxycarbonylation, the Michael reaction, and the nitro-aldol reaction, were investigated and compared with those of homogeneous and other heterogeneous catalysts. The SA-NR2 catalysts showed much higher catalytic activities for the carbon-carbon bond-forming reactions than heterogeneous amine catalysts using other supports, such as SiO2 and Al2O3. On the other hand, homogeneous amines hardly promoted these reactions under similar reaction conditions, and the catalytic behavior of SA-NR2 was also different from that of MgO, which was employed as a typical heterogeneous base. An acid-base dual-activation mechanism for the carbon-carbon bond-forming reactions is proposed.

  7. Variational RRKM calculation of thermal rate constant for C–H bond fission reaction of nitro methane

    Directory of Open Access Journals (Sweden)

    Afshin Taghva Manesh


    Full Text Available The present work provides quantitative results for the rate constants of unimolecular C–H bond fission reactions in the nitro methane at elevated temperatures up to 2000 K. In fact, there are three different hydrogen atoms in the nitro methane. The potential energy surface for each C–H bond fission reaction of nitro methane was investigated by ab initio calculations. The geometry and vibrational frequencies of the species involved in this process were optimized at the MP2 level of theory, using the cc-pvdz basis set. Since C–H bond fission channel is a barrierless reaction, we have used variational RRKM theory to predict rate coefficients. By means of calculated rate coefficients at different temperatures, the Arrhenius expression of the channel over the temperature range of 100–2000 K is k(T = 5.9E19∗exp(−56274.6/T.

  8. Stability and Reactivity of Cyclometallated Naphthylamine Complexes in Pd-C Bond Insertion Reactions with Coordinated Alkynylphosphanes

    KAUST Repository

    Chen, Shuli


    Phenylbis(phenylethynyl)phosphane PhP(C≡CPh)2 coordinates regiospecifically to the α-methyl-chiral ortho-platinated and -palladated naphthylamine units at the positions trans to the nitrogen donors. The P→Pt coordination bond is kinetically inert, whereas the P→Pd bond is labile. Upon heating of these phosphane complexes at 70 °C, one of the C≡C bonds in the coordinated PhP(C≡CPh)2 was activated towards an intermolecular Pd-C bond insertion reaction with an external ortho-palladated naphthylamine ring. No intramolecular insertion reaction occurred. In contrast to its palladium analogue, the ortho-platinated ring is not reactive towards coordinated PhP(C≡CPh)2, although it can promote the Pd-C bond insertion reaction. However, despite the high kinetic stability of the P→Pt coordination, the organoplatinum unit is a noticeably weaker activator than its organopalladium counterpart. The chirality of the reacting ortho-metallated naphthylamine ligand exhibited high stereochemical influence on the formation of the new stereogenic phosphorus center during the course of these C-C bond-formation reactions. The coordination chemistry and the absolute stereochemistry of the dimetallic products were determined by single-crystal X-ray crystallographic analysis. The asymmetric monoinsertion of PhP(C≡CPh)2 coordinated to a cyclometallated N,N-dimethyl naphthyl/benzylamine template into the Pd-C bonds of N,N-dimethylnaphthylamine palladacycles has been demonstrated for the synthesis of a variety of new P-stereogenic homo- or heterodimetallic complexes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Reactions of the cumyloxyl and benzyloxyl radicals with strong hydrogen bond acceptors. Large enhancements in hydrogen abstraction reactivity determined by substrate/radical hydrogen bonding. (United States)

    Salamone, Michela; DiLabio, Gino A; Bietti, Massimo


    A kinetic study on hydrogen abstraction from strong hydrogen bond acceptors such as DMSO, HMPA, and tributylphosphine oxide (TBPO) by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out in acetonitrile. The reactions with CumO(•) were described in terms of a direct hydrogen abstraction mechanism, in line with the kinetic deuterium isotope effects, k(H)/k(D), of 2.0 and 3.1 measured for reaction of this radical with DMSO/DMSO-d(6) and HMPA/HMPA-d(18). Very large increases in reactivity were observed on going from CumO(•) to BnO(•), as evidenced by k(H)(BnO(•))/k(H)(CumO(•)) ratios of 86, 4.8 × 10(3), and 1.6 × 10(4) for the reactions with HMPA, TBPO, and DMSO, respectively. The k(H)/k(D) of 0.91 and 1.0 measured for the reactions of BnO(•) with DMSO/DMSO-d(6) and HMPA/HMPA-d(18), together with the k(H)(BnO(•))/k(H)(CumO(•)) ratios, were explained on the basis of the formation of a hydrogen-bonded prereaction complex between the benzyloxyl α-C-H and the oxygen atom of the substrates followed by hydrogen abstraction. This is supported by theoretical calculations that show the formation of relatively strong prereaction complexes. These observations confirm that in alkoxyl radical reactions specific hydrogen bond interactions can dramatically influence the hydrogen abstraction reactivity, pointing toward the important role played by structural and electronic effects.

  10. Pd/C-mediated dual C-C bond forming reaction in water: synthesis of 2,4-dialkynylquinoline

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Ellanki A.; Islam, Aminul; Venu, Bolla K. [Dr. Reddy' s Laboratories Limited, Hyderabad, Andhra Pradesh (India); Mukkanti, K. [JNT University, Hyderabad, Andhra Pradesh (India). Inst. of Science and Technology. Chemistry Division; Pal, Manojit, E-mail: [Matrix Laboratories Ltd., Medak District, Andra Pradesh (India). New Drug Discovery. R and D Center


    Pd/C facilitated dual C-C bond forming reaction between 2,4-diiodoquinoline and terminal alkynes in water providing a practical and one-step synthesis of 2,4-dialkynylquinolines. A number of related quinoline derivatives were prepared in good to excellent yields using this water-based methodology. The use of other palladium catalysts and solvents was examined and the mechanism of the reaction has been discussed. (author)

  11. Chiral BINOL-derived phosphoric acids: privileged Brønsted acid organocatalysts for C-C bond formation reactions. (United States)

    Zamfir, Alexandru; Schenker, Sebastian; Freund, Matthias; Tsogoeva, Svetlana B


    BINOL-derived phosphoric acids have emerged during the last five years as powerful chiral Brønsted acid catalysts in many enantioselective processes. The most successful transformations carried out with chiral BINOL phosphates include C-C bond formation reactions. The recent advances have been reviewed in this article with a focus being placed on hydrocyanations, aldol-type, Mannich, Friedel-Crafts, aza-ene-type, Diels-Alder, as well as cascade and multi-component reactions.

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

    Zhang, Xiangfei; Cao, Zexing


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

  13. Communication: Energetics of reaction pathways for reactions of ethenol with the hydroxyl radical: the importance of internal hydrogen bonding at the transition state. (United States)

    Tishchenko, Oksana; Ilieva, Sonia; Truhlar, Donald G


    We find high multireference character for abstraction of H from the OH group of ethenol (also called vinyl alcohol); therefore we adopt a multireference approach to calculate barrier heights for the various possible reaction channels of OH+C(2)H(3)OH. The relative barrier heights of ten possible saddle points for reaction of OH with ethenol are predicted by multireference Møller-Plesset perturbation theory with active spaces based on correlated participating orbitals (CPOs) and CPO plus a correlated pi orbital (CPO+pi). Six barrier heights for abstracting H from a C-H bond range from 3.1 to 7.7 kcal/mol, two barrier heights for abstracting H from an O-H bond are both 6.0 kcal/mol, and two barrier heights for OH addition to the double bond are -1.8 and -2.8 kcal/mol. Thus we expect abstraction at high-temperature and addition at low temperature. The factor that determines which H is most favorable to abstract is an internal hydrogen bond that constitutes part of a six-membered ring at one of the abstraction saddle points; the hydrogen bond contributes about 3 kcal/mol stabilization.

  14. Magnesium-induced copper-catalyzed synthesis of unsymmetrical diaryl chalcogenide compounds from aryl iodide via cleavage of the Se-Se or S-S bond. (United States)

    Taniguchi, Nobukazu; Onami, Tetsuo


    The methodology for a copper-catalyzed preparation of diaryl chalcogenide compounds from aryl iodides and diphenyl dichalcogenide molecules is reported. Unsymmetrical diaryl sulfide or diaryl selenide can be synthesized from aryl iodide and PhYYPh (Y = S, Se) with a copper catalyst (CuI or Cu(2)O) and magnesium metal in one pot. This reaction can be carried out under neutral conditions according to an addition of magnesium metal as the reductive reagent. Furthermore, it is efficiently available for two monophenylchalcogenide groups generated from diphenyl dichalcogenide.

  15. Generation, Characterization, and Reactivity of a Cu(II)-Alkylperoxide/Anilino Radical Complex: Insight into the O-O Bond Cleavage Mechanism. (United States)

    Paria, Sayantan; Ohta, Takehiro; Morimoto, Yuma; Ogura, Takashi; Sugimoto, Hideki; Fujieda, Nobutaka; Goto, Kei; Asano, Kaori; Suzuki, Takeyuki; Itoh, Shinobu


    The reaction of [Cu(I)(TIPT3tren) (CH3CN)]ClO4 (1) and cumene hydroperoxide (C6H5C(CH3)2OOH, ROOH) at -60 °C in CH2Cl2 gave a Cu(II)-alkylperoxide/anilino radical complex 2, the formation of which was confirmed by UV-vis, resonance Raman, EPR, and CSI-mass spectroscopy. The mechanism of formation of 2, as well as its reactivity, has been explored.

  16. Influences of bracket bonding on mutans streptococcus in plaque detected by real time fluorescence-quantitative polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    AI Hong; LU Hong-fei; LIANG Huan-you; WU Jian; LI Ruo-lan; LIU Guo-ping; XI Yun


    Background Enamel demineralization occurs frequently during orthodontic treatment. In this study, we evaluated the changes of the density of mutans streptococcus (MS) in plaque after bracket bonding and using fluoride adhesive on maxillary incisors by real time fluorescence-quantitative polymerase chain reaction (RT-FQ PCR).Methods The study was designed as a self-paired test. Brackets were bonded with fluoride adhesive on the left side, while non-fluoride adhesive on the right side for each patient. Plaque samples were taken from the surfaces around the brackets of four maxillary incisors before brackets bonding and after the bonding 4 weeks later. The amount of MS was measured by RT-FQ PCR. The data obtained were analyzed statistically using the SPSS 11.5 version and the alpha level was set at 0.05 (2-tailed).Results The amount of MS in plaque increased significantly after bracket bonding (P0.05), and among the incisors using and not using fluoride adhesive (P>0.05).Conclusions The increase of the density of MS in plaque after bracket bonding is one of the etiological factors for enamel demineralization in orthodontic patients. The result of this study did not support what we observed clinically that the incidence of enamel demineralization for lateral incisors was higher than that for central incisors. Using fluoride adhesive for bonding did not affect the amount of MS in plaque in our study. Further study is needed.

  17. Synthesis of tetranuclear, four-coordinate manganese clusters with "pinned butterfly" geometry formed by metal-mediated N-N bond cleavage in diphenylhydrazine. (United States)

    Hamilton, Clifton R; Baglia, Regina A; Gordon, Alexander D; Zdilla, Michael J


    The preparation of four-coordinate tetramanganese-amide-hydrazide clusters is described. Reaction of Mn(NR(2))(2) (R = SiMe(3)) with N,N'-diphenylhydrazine resulted in the formation of a black intermediary mixture that converted to a four-coordinate tetranuclear "pinned butterfly" cluster, Mn(4)(μ(3)-N(2)Ph(2))(2)(μ-N(2)Ph(2))(μ-NHPh)(2)(THF)(4). This compound was isolated in ~90% yield and identified by single-crystal X-ray diffraction analysis. In pyridine, the THF ligands were replaced, giving the pyridyl complex Mn(4)(μ(3)-N(2)Ph(2))(2)(μ-N(2)Ph(2))(μ-NHPh)(2)(py)(4). Charge counting considerations indicate that the clusters had gained two protons and two electrons in addition to the formative fragments. Isolation of the black mixture was achieved by extraction techniques from a reaction with a decreased loading of hydrazine run at low temperatures with decreased solvent polarity. The black mixture was characterized by FT-IR, UV-vis, and (1)H NMR spectroscopy. In addition, an isolable, colorless dimer, Mn(2)(μ-NHPh)(2)(NR(2))(2)(THF)(2), was present in the mixture and identified by single-crystal X-ray diffraction. These intermediates are discussed in light of possible mechanisms for formation of the tetranuclear cluster.

  18. Palladium- and copper-mediated N-aryl bond formation reactions for the synthesis of biological active compounds

    Directory of Open Access Journals (Sweden)

    Burkhard Koenig


    Full Text Available N-Arylated aliphatic and aromatic amines are important substituents in many biologically active compounds. In the last few years, transition-metal-mediated N-aryl bond formation has become a standard procedure for the introduction of amines into aromatic systems. While N-arylation of simple aromatic halides by simple amines works with many of the described methods in high yield, the reactions may require detailed optimization if applied to the synthesis of complex molecules with additional functional groups, such as natural products or drugs. We discuss and compare in this review the three main N-arylation methods in their application to the synthesis of biologically active compounds: Palladium-catalysed Buchwald–Hartwig-type reactions, copper-mediated Ullmann-type and Chan–Lam-type N-arylation reactions. The discussed examples show that palladium-catalysed reactions are favoured for large-scale applications and tolerate sterically demanding substituents on the coupling partners better than Chan–Lam reactions. Chan–Lam N-arylations are particularly mild and do not require additional ligands, which facilitates the work-up. However, reaction times can be very long. Ullmann- and Buchwald–Hartwig-type methods have been used in intramolecular reactions, giving access to complex ring structures. All three N-arylation methods have specific advantages and disadvantages that should be considered when selecting the reaction conditions for a desired C–N bond formation in the course of a total synthesis or drug synthesis.

  19. Thermochemical benchmarking of hydrocarbon bond separation reaction energies: Jacob's ladder is not reversed! (United States)

    Krieg, Helge; Grimme, Stefan


    We reinvestigate the performance of Kohn-Sham density functional (DF) methods for a thermochemical test set of bond separation reactions of alkanes (BSR36) published recently by Steinmann et al. [J. Chem. Theory Comput. 5, 2950 (2009)]. According to our results, the tested approximations perform for this rather special benchmark as usual. We show that the choice of reference enthalpies plays a crucial role in the assessment. Due to the large stoichiometric factors involved, errors of various origin are strongly amplified. Inconsistent reference data are avoided by computing reference energies at the CCSD(T)/CBS level. These are compared to results for a variety of standard DFs. Two different versions of London dispersion corrections (DFT-D2 and DFT-D3) are applied and found to be very significant. The most accurate results are obtained with B2GPPLYP-D2 (MAD = 0.4 kcal mol-1) B2PLYP-D2 (MAD = 0.5 kcal mol-1) and B97-D2 (MAD = 0.9 kcal mol-1 methods. Dispersion corrections not only improve the computed BSR energies but also diminish the accuracy differences between the DFs. The previous DFT-D2 version performs better due to error compensation of medium-range correlation effects between the semi-classical and the density-based description. We strongly recommend not to overinterpret results regarding DF accuracy when based on a single set of chemical reactions and to use high-level theoretical data for benchmarking purposes.

  20. Kinetic solvent effects on hydrogen abstraction reactions from carbon by the cumyloxyl radical. The role of hydrogen bonding. (United States)

    Bietti, Massimo; Salamone, Michela


    A kinetic study of the H-atom abstraction reactions from 1,4-cyclohexadiene and triethylamine by the cumyloxyl radical has been carried out in different solvents. Negligible effects are observed with 1,4-cyclohexadiene, whereas with triethylamine a significant decrease in rate constant (k(H)) is observed on going from benzene to MeOH. A good correlation between log k(H) and the solvent hydrogen bond donor parameter alpha is observed, indicative of an H-bonding interaction between the amine lone pair and the solvent.

  1. Phase reaction of Au/Sn solder bonding for GaN-based vertical structure light emitting diodes

    Institute of Scientific and Technical Information of China (English)


    Au/Sn solder bonding on Si substrates was used to fabricate the GaN-based vertical structure light emitting diodes (VSLEDs). The phase reaction of Au/Sn solder under different bonding conditions was investigated by the measurement of electron back scattering diffraction (EBSD), and the characteristics of VSLED were analyzed by scanning acoustic microscope (SAM), Raman scattering, current-voltage (I-V) and light output-current (L-I) curves. After the bonding process, horizontal stripes of Au/Sn phase (δ phase) and Au5Sn phase (ζ phase) were redirected to vertical stripes, and δ phase tended to move to the solder joint. Sn interstitial diffusion led to the distribution of δ phase and voids in Au/Sn solder, which could be seen in SAM and SEM images. Vertical distribution of the δ phase and ζ phase with proper voids in the Au/Sn bonding layer showed the best bonding quality. Good bonding quality led to little shift of the E2-high mode of Raman spectra peak in GaN after laser lift off (LLO). It also caused more light extraction and forward bias reduction to 2.9 V at 20 mA.

  2. Co-C binding cleavage by the hydrolysis reaction of the Vitamins B{sub 12} coenzyme; Bitamin B{sub 12} hokoso no kasui bunkai hanno ni yoru Co-C setsugo kairetsu

    Energy Technology Data Exchange (ETDEWEB)

    Yonemura, T. [Kochi Univ., Kochi (Japan)


    Vitamin B{sub 12} isolated as antineoplastic anemia agent in 1948 were organometallic complex found in the nature at first, and it was noticed as a metal compound with the unique cobalt-carbon sigma (Co-C{sigma}) combination. Halpern et al. had estimated the dissociation energy to be 26-31kcal/mol when the Co-C combination of the segregated adenosylcobalamin clove in the homolysis, and Finke et al. reported that the cleavage speed is hastened over 10 {sup 10} times under the enzymatic reaction condition inside such a protein. Based on this important factor, the contribution of the electro-donicity of the shaft configuration base was indicated, and other factors to cause the Co-C binding cleavage were recently examined by Halpern and Finke et al. According to the research by Halpern, homolysis reaction and heterolysis reaction were competitively generated, and pH value, temperature, type of the alkyl ligand had a great influence. Especially, it has been clarified that the difference due to the substituent is remarkable. (NEDO)

  3. Bipodal surface organometallic complexes with surface N-donor ligands and application to the catalytic cleavage of C-H and C-C bonds in n -Butane

    KAUST Repository

    Bendjeriou-Sedjerari, Anissa


    We present a new generation of "true vicinal" functions well-distributed on the inner surface of SBA15: [(Sî - Si-NH 2)(≡Si-OH)] (1) and [(≡Si-NH2)2] (2). From these amine-modified SBA15s, two new well-defined surface organometallic species [(≡Si-NH-)(≡Si-O-)]Zr(CH2tBu) 2 (3) and [(≡Si-NH-)2]Zr(CH2tBu) 2 (4) have been obtained by reaction with Zr(CH2tBu) 4. The surfaces were characterized with 2D multiple-quantum 1H-1H NMR and infrared spectroscopies. Energy-filtered transmission electron microscopy (EFTEM), mass balance, and elemental analysis unambiguously proved that Zr(CH2tBu)4 reacts with these vicinal amine-modified surfaces to give mainly bipodal bis(neopentyl)zirconium complexes (3) and (4), uniformly distributed in the channels of SBA15. (3) and (4) react with hydrogen to give the homologous hydrides (5) and (6). Hydrogenolysis of n-butane catalyzed by these hydrides was carried out at low temperature (100 C) and low pressure (1 atm). While (6) exhibits a bis(silylamido)zirconium bishydride, [(≡Si-NH-)2]Zr(H) 2 (6a) (60%), and a bis(silylamido)silyloxozirconium monohydride, [(≡Si-NH-)2(≡Si-O-)]ZrH (6b) (40%), (5) displays a new surface organometallic complex characterized by an 1H NMR signal at 14.46 ppm. The latter is assigned to a (silylimido)(silyloxo)zirconium monohydride, [(≡Si-Nî)(≡Si-O-)]ZrH (5b) (30%), coexistent with a (silylamido)(silyloxo)zirconium bishydride, [(≡Si-NH-)(≡Si-O-)] Zr(H)2 (5a) (45%), and a silylamidobis(silyloxo)zirconium monohydride, [(≡Si-NH-)(≡Si-O-)2]ZrH (5c) (25%). Surprisingly, nitrogen surface ligands possess catalytic properties already encountered with silicon oxide surfaces, but interestingly, catalyst (5) with chelating [N,O] shows better activity than (6) with chelating [N,N]. © 2013 American Chemical Society.

  4. Ab initio study of the solvent H-bonding effect on ESIPT reaction and electronic transitions of 3-hydroxychromone derivatives. (United States)

    Kenfack, Cyril A; Klymchenko, Andrey S; Duportail, Guy; Burger, Alain; Mély, Yves


    The electronic transitions occurring in 4-(N,N-dimethylamino)-3-hydroxyflavone (DMAF) and 2-furanyl-3-hydroxychromone (FHC) were investigated using the TDDFT method in aprotic and protic solvents. The solvent effect was incorporated into the calculations via the PCM formalism. The H-bonding between solute and protic solvent was taken into account by considering a molecular complex between these molecules. To examine the effect of the H-bond on the ESIPT reaction, the absorption and emission wavelengths as well as the energies of the different states that intervene during these electronic transitions were calculated in acetonitrile, ethanol and methanol. The calculated positions of the absorption and emission wavelengths in various solvents were in excellent agreement with the experimental spectra, validating our approach. We found that in DMAF, the hydrogen bonding with protic solvents makes the ESIPT reaction energetically unfavourable, which explains the absence of the ESIPT tautomer emission in protic solvents. In contrast, the excited tautomer state of FHC remains energetically favourable in both aprotic and protic solvents. Comparing our calculations with the previously reported time-resolved fluorescence data, the ESIPT reaction of DMAF in aprotic solvents is reversible because the emitting states are energetically close, whereas in FHC, ESIPT is irreversible because the tautomer state is below the corresponding normal state. Therefore, the ESIPT reaction in DMAF is controlled by the relative energies of the excited states (thermodynamic control), while in FHC the ESIPT is controlled probably by the energetic barrier (kinetic control).

  5. Mechanochemistry: One Bond at a Time (United States)

    Liang, Jian; Fernández, Julio M.


    Single-molecule force clamp spectroscopy offers a novel platform for mechanically denaturing proteins by applying a constant force to a polyprotein. A powerful emerging application of the technique is that, by introducing a disulfide bond in each protein module, the chemical kinetics of disulfide bond cleavage under different stretching forces can be probed at the single-bond level. Even at forces much lower than that can rupture the chemical bond, the breaking of the S-S bond at the presence of various chemical reducing agents is significantly accelerated. Our previous work demonstrated that the rate of thiol/disulfide exchange reaction is force-dependent, and well described by an Arrhenius term of the form: r = A(exp((FΔxr-Ea)/kBT)[nucleophile]). From Arrhenius fits to the force dependency of the reduction rate we measured the bond elongation parameter, Δxr, along the reaction coordinate to the transition state of the SN2 reaction cleaved by different nucleophiles and enzymes, never before observed by any other technique. For S-S cleavage by various reducing agents, obtaining the Δxr value can help depicting the energy landscapes and elucidating the mechanisms of the reactions at the single-molecule level. Small nucleophiles, such as 1, 4-DL-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP) and L-cysteine, react with the S-S bond with monotonically increasing rates under the applied force; while thioredoxin enzymes exhibit both stretching-favored and —resistant reaction-rate regimes. These measurements demonstrate the power of single-molecule force clamp spectroscopy approach in providing unprecedented access to chemical reactions. PMID:19572737

  6. Reaction of Laser-Ablated Uranium and Thorium Atoms with H2Se: A Rare Example of Selenium Multiple Bonding. (United States)

    Vent-Schmidt, Thomas; Andrews, Lester; Thanthiriwatte, K Sahan; Dixon, David A; Riedel, Sebastian


    The compounds H2ThSe and H2USe were synthesized by the reaction of laser-ablated actinide metal atoms with H2Se under cryogenic conditions following the procedures used to synthesize H2AnX (An = Th, U; X = O, S). The molecules were characterized by infrared spectra in an argon matrix with the aid of deuterium substitution and electronic structure calculations at the density functional theory level. The main products, H2ThSe and H2USe, are shown to have a highly polarized actinide-selenium triple bond, as found for H2AnS on the basis of electronic structure calculations. There is an even larger back-bonding of the Se with the An than found for the corresponding sulfur compounds. These molecules are of special interest as rare examples of multiple bonding of selenium to a metal, particularly an actinide metal.

  7. An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane. (United States)

    Song, Lingchun; Mo, Yirong; Gao, Jiali


    An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix element H(12) such that the computed energy of reaction from the EH-MOVB method is in agreement with the target value. The scaling factor is very close to unity, resulting in minimal alteration of the potential energy surface of the original MOVB model. Furthermore, the relative energy between the reactant and product diabatic states in the EH-MOVB method can be improved to match the experimental energy of reaction. A key ingredient in the EH-MOVB theory is that the off-diagonal matrix elements are functions of all degrees of freedom of the system and the overlap matrix is explicitly evaluated. The EH-MOVB method has been applied to the nucleophilic substitution reaction between hydrosulfide and chloromethane to illustrate the methodology and the results were matched to reproduce the results from ab initio valence bond self-consistent valence bond (VBSCF) calculations. The diabatic coupling (the off-diagonal matrix element in the generalized secular equation) has small variations along the minimum energy reaction path in the EH-MOVB model, whereas it shows a maximum value at the transition state and has nearly zero values in the regions of the ion-dipole complexes from VBSCF calculations. The difference in the diabatic coupling stabilization is attributed to the large overlap integral in the computationally efficient MOVB method.

  8. Bridging silyl groups in sigma-bond metathesis and [1, 2] shifts. An experimental and computational study of the reaction between cerium metallocenes and MeOSiMe3

    Energy Technology Data Exchange (ETDEWEB)

    Werkema, Evan; Yahia, Ahmed; Maron, Laurent; Eisenstein, Odile; Andersen, Richard


    The reaction of Cp'2CeH (Cp' = 1,2,4-(Me3C)3C5H2 ) with MeOSiMe3 gives Cp'2CeOMe and HSiMe3 and the reaction of the metallacycle, Cp'[(Me3C)2C5H2C(Me) 2CH2]Ce, with MeOSiMe3 yields Cp'2CeOCH2SiMe3, formed from hypothetical Cp'2CeCH2OSiMe3 by a [1, 2] shift also known as a silyl-Wittig rearrangement. Although both cerium products are alkoxides, they are formed by different pathways. DFT calculations on the reaction of the model metallocene, Cp2CeH, and MeOSiMe3 show that the lowest energy pathway is a H for OMe exchange at Ce that occurs by way of a sigma-bond metathesis transition state as SiMe3 exchanges partners. The formation of Cp2CeOCH2SiMe3 occurs by way of a low activation barrier [1, 2]shift of the SiMe3 group in Cp2CeCH2OSiMe3. Calculations on a model metallacycle, Cp[C5H4C(Me)2CH2]Ce, show that the metallacycle favors CH bond activation over sigma-bond metathesis involving the transfer of the SiMe3 group in good agreement with experiment. The sigma-bond metathesis involving the transfer of SiMe3 and the [1, 2]shift of SiMe3 reactions have in common a pentacoordinate silicon at the transition states. A molecular orbital analysis illustrates the connection between these two Si-O bond cleavage reactions and traces the reason why they occur for a silyl but not for an alkyl group to the difference in energy required to form a pentacoordinate silicon or carbon atom in the transition state. This difference clearly distinguishes a silyl from an alkyl group as shown in the study of"Pyrolysis of Tetramethylsilane Yielding Free d-orbitals by Seyferth and Pudvin in ChemTech 1981, 11, 230-233".

  9. Methandiide as a non-innocent ligand in carbene complexes: from the electronic structure to bond activation reactions and cooperative catalysis. (United States)

    Becker, Julia; Modl, Tanja; Gessner, Viktoria H


    The synthesis of a ruthenium carbene complex based on a sulfonyl-substituted methandiide and its application in bond activation reactions and cooperative catalysis is reported. In the complex, the metal-carbon interaction can be tuned between a Ru-C single bond with additional electrostatic interactions and a Ru=C double bond, thus allowing the control of the stability and reactivity of the complex. Hence, activation of polar and non-polar bonds (O-H, H-H) as well as dehydrogenation reactions become possible. In these reactions the carbene acts as a non-innocent ligand supporting the bond activation as nucleophilic center in the 1,2-addition across the metal-carbon double bond. This metal-ligand cooperativity can be applied in the catalytic transfer hydrogenation for the reduction of ketones. This concept opens new ways for the application of carbene complexes in catalysis.

  10. Enantio- and periselective nitroalkene Diels-Alder reactions catalyzed by helical-chiral hydrogen bond donor catalysts. (United States)

    Peng, Zhili; Narcis, Maurice J; Takenaka, Norito


    Helical-chiral double hydrogen bond donor catalysts promote the nitroalkene Diels-Alder reaction in an enantio- and periselective manner. This represents the first asymmetric catalytic nitroalkene Diels-Alder reaction via LUMO-lowering catalysis. To gain an insight into this new process, the substrate scope of our catalyst was investigated by exploiting readily available 5-substituted pentamethylcyclopentadienes. The catalyst was found to tolerate dienes with different steric demands as well as dienes substituted with heteroatoms. The synthetic utility of 5-substituted pentamethylcyclopentadienes is rather limited, and thus we have developed a three-step route to 1,4,5,5-tetrasubstituted cyclopentadienes from commercially available ketones.

  11. Enantio- and Periselective Nitroalkene Diels-Alder Reactions Catalyzed by Helical-Chiral Hydrogen Bond Donor Catalysts

    Directory of Open Access Journals (Sweden)

    Zhili Peng


    Full Text Available Helical-chiral double hydrogen bond donor catalysts promote the nitroalkene Diels-Alder reaction in an enantio- and periselective manner. This represents the first asymmetric catalytic nitroalkene Diels-Alder reaction via LUMO-lowering catalysis. To gain an insight into this new process, the substrate scope of our catalyst was investigated by exploiting readily available 5-substituted pentamethylcyclopentadienes. The catalyst was found to tolerate dienes with different steric demands as well as dienes substituted with heteroatoms. The synthetic utility of 5-substituted pentamethylcyclopentadienes is rather limited, and thus we have developed a three-step route to 1,4,5,5-tetrasubstituted cyclopentadienes from commercially available ketones.

  12. Can laccases catalyze bond cleavage in lignin?

    DEFF Research Database (Denmark)

    Munk, Line; Sitarz, Anna Katarzyna; Kalyani, Dayanand


    Modification of lignin is recognized as an important aspect of the successful refining of lignocellulosic biomass, and enzyme-assisted processing and upcycling of lignin is receiving significant attention in the literature. Laccases (EC 1.103.2) are taking the centerstage of this attention, since...... is proposed. (C) 2015 Elsevier Inc. All rights reserved....

  13. Chemical Reactions of Metal-Metal Bonded Compounds of the Transition Elements. (United States)


    methanol, has led to the isolation ot solvento complexes , e.g. Mo2 Cl4 (PPh3 )2 (MeOH)2, in which onc ot the ligands L in XLI is replaced by a solvent...Hexa- and Other Polynuclear Complexes .... 8 2. Formation of Metal-Metal Bonds.................... .................... 11 2.1. From Mononuclear...17 2.3. By Addition of a Metal Complex or Fragment Across an M-X Multiple Bond

  14. Intein-Promoted Cyclization of Aspartic Acid Flanking the Intein Leads to Atypical N-Terminal Cleavage. (United States)

    Minteer, Christopher J; Siegart, Nicolle M; Colelli, Kathryn M; Liu, Xinyue; Linhardt, Robert J; Wang, Chunyu; Gomez, Alvin V; Reitter, Julie N; Mills, Kenneth V


    Protein splicing is a post-translational reaction facilitated by an intein, or intervening protein, which involves the removal of the intein and the ligation of the flanking polypeptides, or exteins. A DNA polymerase II intein from Pyrococcus abyssi (Pab PolII intein) can promote protein splicing in vitro on incubation at high temperature. Mutation of active site residues Cys1, Gln185, and Cys+1 to Ala results in an inactive intein precursor, which cannot promote the steps of splicing, including cleavage of the peptide bond linking the N-extein and intein (N-terminal cleavage). Surprisingly, coupling the inactivating mutations to a change of the residue at the C-terminus of the N-extein (N-1 residue) from the native Asn to Asp reactivates N-terminal cleavage at pH 5. Similar "aspartic acid effects" have been observed in other proteins and peptides but usually only occur at lower pH values. In this case, however, the unusual N-terminal cleavage is abolished by mutations to catalytic active site residues and unfolding of the intein, indicating that this cleavage effect is mediated by the intein active site and the intein fold. We show via mass spectrometry that the reaction proceeds through cyclization of Asp resulting in anhydride formation coupled to peptide bond cleavage. Our results add to the richness of the understanding of the mechanism of protein splicing and provide insight into the stability of proteins at moderately low pH. The results also explain, and may help practitioners avoid, a side reaction that may complicate intein applications in biotechnology.

  15. Hydrogen bond driven chemical reactions: Beckmann rearrangement of cyclohexanone oxime into epsilon-caprolactam in supercritical water. (United States)

    Boero, Mauro; Ikeshoji, Tamio; Liew, Chee Chin; Terakura, Kiyoyuki; Parrinello, Michele


    Recent experiments have shown that supercritical water (SCW) has the ability to accelerate and make selective synthetic organic reactions, thus replacing the common but environmentally harmful acid and basic catalysts. In an attempt to understand the intimate mechanism behind this observation, we analyze, via first-principles molecular dynamics, the Beckmann rearrangement of cyclohexanone oxime into epsilon-caprolactam in supercritical water, for which accurate experimental evidence has been reported. Differences in the wetting of the hydrophilic parts of the solute, enhanced by SCW, and the disrupted hydrogen bond network are shown to be crucial in triggering the reaction and in making it selective. Furthermore, the enhanced concentrations of H(+) in SCW play an important role in starting the reaction.

  16. Consequences of metal-oxide interconversion for C-H bond activation during CH4 reactions on Pd catalysts. (United States)

    Chin, Ya-Huei Cathy; Buda, Corneliu; Neurock, Matthew; Iglesia, Enrique


    Mechanistic assessments based on kinetic and isotopic methods combined with density functional theory are used to probe the diverse pathways by which C-H bonds in CH4 react on bare Pd clusters, Pd cluster surfaces saturated with chemisorbed oxygen (O*), and PdO clusters. C-H activation routes change from oxidative addition to H-abstraction and then to σ-bond metathesis with increasing O-content, as active sites evolve from metal atom pairs (*-*) to oxygen atom (O*-O*) pairs and ultimately to Pd cation-lattice oxygen pairs (Pd(2+)-O(2-)) in PdO. The charges in the CH3 and H moieties along the reaction coordinate depend on the accessibility and chemical state of the Pd and O centers involved. Homolytic C-H dissociation prevails on bare (*-*) and O*-covered surfaces (O*-O*), while C-H bonds cleave heterolytically on Pd(2+)-O(2-) pairs at PdO surfaces. On bare surfaces, C-H bonds cleave via oxidative addition, involving Pd atom insertion into the C-H bond with electron backdonation from Pd to C-H antibonding states and the formation of tight three-center (H3C···Pd···H)(‡) transition states. On O*-saturated Pd surfaces, C-H bonds cleave homolytically on O*-O* pairs to form radical-like CH3 species and nearly formed O-H bonds at a transition state (O*···CH3(•)···*OH)(‡) that is looser and higher in enthalpy than on bare Pd surfaces. On PdO surfaces, site pairs consisting of exposed Pd(2+) and vicinal O(2-), Pd(ox)-O(ox), cleave C-H bonds heterolytically via σ-bond metathesis, with Pd(2+) adding to the C-H bond, while O(2-) abstracts the H-atom to form a four-center (H3C(δ-)···Pd(ox)···H(δ+)···O(ox))(‡) transition state without detectable Pd(ox) reduction. The latter is much more stable than transition states on *-* and O*-O* pairs and give rise to a large increase in CH4 oxidation turnover rates at oxygen chemical potentials leading to Pd to PdO transitions. These distinct mechanistic pathways for C-H bond activation, inferred from theory

  17. Consequences of Metal–Oxide Interconversion for C–H Bond Activation during CH₄ Reactions on Pd Catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Ya-Huei; Buda, Corneliu; Neurock, Matthew; Iglesia, Enrique


    Mechanistic assessments based on kinetic and isotopic methods combined with density functional theory are used to probe the diverse pathways by which C-H bonds in CH₄ react on bare Pd clusters, Pd cluster surfaces saturated with chemisorbed oxygen (O*), and PdO clusters. C-H activation routes change from oxidative addition to Habstraction and then to σ-bond metathesis with increasing O-content, as active sites evolve from metal atom pairs (*-*) to oxygen atom (O*-O*) pairs and ultimately to Pd cationlattice oxygen pairs (Pd2+-O2-) in PdO. The charges in the CH₃ and H moieties along the reaction coordinate depend on the accessibility and chemical state of the Pd and O centers involved. Homolytic C-H dissociation prevails on bare (*-*) and O*- covered surfaces (O*-O*), while C-H bonds cleave heterolytically on Pd2+-O2- pairs at PdO surfaces. On bare surfaces, C-H bonds cleave via oxidative addition, involving Pd atom insertion into the C-H bond with electron backdonation from Pd to C-H antibonding states and the formation of tight three-center (H₃C···Pd···H)‡ transition states. On O*-saturated Pd surfaces, C-H bonds cleave homolytically on O*-O* pairs to form radical-like CH3 species and nearly formed O-H bonds at a transition state (O*···CH3 •···*OH)‡ that is looser and higher in enthalpy than on bare Pd surfaces. On PdO surfaces, site pairs consisting of exposed Pd2+ and vicinal O2-, Pdox-Oox, cleave C-H bonds heterolytically via σ-bond metathesis, with Pd2+ adding to the C-H bond, while O2- abstracts the H-atom to form a four-center (H3Cδ-···Pdox···Hδ+···Oox) transition state without detectable Pdox reduction. The latter is much more stable than transition states on *-* and O*-O* pairs and give rise to a large increase in CH₄ oxidation turnover rates at oxygen chemical

  18. Reaction dynamics. Extremely short-lived reaction resonances in Cl + HD (v = 1) → DCl + H due to chemical bond softening. (United States)

    Yang, Tiangang; Chen, Jun; Huang, Long; Wang, Tao; Xiao, Chunlei; Sun, Zhigang; Dai, Dongxu; Yang, Xueming; Zhang, Dong H


    The Cl + H2 reaction is an important benchmark system in the study of chemical reaction dynamics that has always appeared to proceed via a direct abstraction mechanism, with no clear signature of reaction resonances. Here we report a high-resolution crossed-molecular beam study on the Cl + HD (v = 1, j = 0) → DCl + H reaction (where v is the vibrational quantum number and j is the rotational quantum number). Very few forward scattered products were observed. However, two distinctive peaks at collision energies of 2.4 and 4.3 kilocalories per mole for the DCl (v' = 1) product were detected in the backward scattering direction. Detailed quantum dynamics calculations on a highly accurate potential energy surface suggested that these features originate from two very short-lived dynamical resonances trapped in the peculiar H-DCl (v' = 2) vibrational adiabatic potential wells that result from chemical bond softening. We anticipate that dynamical resonances trapped in such wells exist in many reactions involving vibrationally excited molecules.

  19. Synthesis and characterization of the dimercury(I)-linked compound [PPn]4[(Re7C(CO)21Hg)2]. Oxidative cleavage of the mercury-mercury bond leading to carbidoheptarhenate complexes of mercury(II), including [PPN][Re7C(CO)21Hg(S=C(NME2)2)]. (United States)

    Wright, C A; Brand, U; Shapley, J R


    The reaction of [PPN](3)[Re(7)C(CO)(21)] with Hg(2)(NO(3))(2).2H(2)O in dichloromethane formed the complex [PPN](4)[(Re(7)C(CO)(21)Hg)(2)] ([PPN](4)[1]), isolated in 60% yield. Analogous salts of [1](4-) with [PPh(4)](+) and [NEt(4)](+) were also prepared. The crystal structure of [PPN](4)[1] showed that two carbidoheptarhenate cores are linked by a dimercury(I) unit (d(Hg-Hg) = 2.610(4) A), with each individual mercury atom face-bridging. Oxidative cleavage of the Hg-Hg bond in [1](4-) was effected by 4-bromophenyl disulfide to form [Re(7)C(CO)(21)HgSC(6)H(4)Br](2-) ([4](2-)), by I(2) to form [Re(7)C(CO)(21)HgI](2-) ([5](2-)), and by Br(2) to form [Re(7)C(CO)(21)HgBr](2-) ([6](2-)). Oxidation of [1](4-) by ferrocenium ion (2 equiv) in the presence of tetramethylthiourea resulted in the derivative [Re(7)C(CO)(21)HgSC(NMe(2))(2)](-) ([7](-)). The molecular structure of [PPN][7] was determined by X-ray crystallography. This is the first example of a carbidoheptarhenate-mercury complex with a neutral ligand on mercury, and ligand exchange was demonstrated by displacement with triethylphosphine. Complex [7](-) can also be prepared by protonating [Re(7)C(CO)(21)HgO(2)CCH(3)](2-) in the presence of tetramethylthiourea. Cyclic voltammetry data to calibrate and compare the redox properties of compounds [1](4-) and [7](-) have been measured.

  20. Theoretical study on the reaction mechanism of ozone addition to the double bonds of keto-limonene

    Institute of Scientific and Technical Information of China (English)

    Lei Jiang; Yisheng Xu; Baohui Yin; Zhipeng Bai


    The reaction mechanism of ozone (O3) addition to the double bonds of gas phase keto-limonene was investigated using ab initio methods.Two different possibilities for O3 addition to the double bond were considered and two corresponding van der Waais complexes (Complex 1 and Complex 2) were found for 1-endo and 2-endo.The rate constants were calculated using the transition state theory at the CCSD(T)/6-31G(d) + CF//B3LYP/6-31G(d,p) level.The high-pressure limit of the total rate constant at 298 K was 3.51 × 10-16cm3/(molecule.sec),which was in a good agreement with the experimental data.

  1. Mechanistic Insights into Ring Cleavage and Contraction of Benzene over a Titanium Hydride Cluster. (United States)

    Kang, Xiaohui; Luo, Gen; Luo, Lun; Hu, Shaowei; Luo, Yi; Hou, Zhaomin


    Carbon-carbon bond cleavage of benzene by transition metals is of great fundamental interest and practical importance, as this transformation is involved in the production of fuels and other important chemicals in the industrial hydrocracking of naphtha on solid catalysts. Although this transformation is thought to rely on cooperation of multiple metal sites, molecular-level information on the reaction mechanism has remained scarce to date. Here, we report the DFT studies of the ring cleavage and contraction of benzene by a molecular trinuclear titanium hydride cluster. Our studies suggest that the reaction is initiated by benzene coordination, followed by H2 release, C6H6 hydrometalation, repeated C-C and C-H bond cleavage and formation to give a MeC5H4 unit, and insertion of a Ti atom into the MeC5H4 unit with release of H2 to give a metallacycle product. The C-C bond cleavage and ring contraction of toluene can also occur in a similar fashion, though some details are different due to the presence of the methyl substituent. Obviously, the facile release of H2 from the metal hydride cluster to provide electrons and to alter the charge population at the metal centers, in combination with the flexible metal-hydride connections and dynamic redox behavior of the trimetallic framework, has enabled this unusual transformation to occur. This work has not only provided unprecedented insights into the activation and transformation of benzene over a multimetallic framework but it may also offer help in the design of new molecular catalysts for the activation and transformation of inactive aromatics.

  2. Cleavage of an RNA model catalyzed by dinuclear Zn(II) complexes containing rate-accelerating pendants. Comparison of the catalytic benefits of H-bonding and hydrophobic substituents. (United States)

    Mohamed, Mark F; Brown, R Stan


    The transesterification of a simple RNA model, 2-hydroxypropyl p-nitrophenyl phosphate (2, HpNPP) promoted by seven dinuclear Zn(II) catalysts (3,4,5,6,7,8,9:Zn(II)2:(-OCH3)) based on the bis[bis(2-substituted-pyridinyl-6-methyl)]amine ligand system was investigated in methanol under sspH-controlled conditions at 25.0 ± 0.1 °C. The two metal complexing ligands were joined together via the amino N connected to a m-xylyl linker (3, 4, 5, 6, 7) where the 2-pyridinyl substituent = H, CH3, (CH)4, NH2, and NH(C═O)CH3, respectively, and a propyl linker (8, 9) where the ring substituent = H and CH3. All of the dinuclear complexes except 8:Zn(II)2 exhibit saturation kinetics for the kobs versus [catalyst] plots from which one can determine catalyst:substrate binding constants (KM), the catalytic rate constants for their decomposition (kcat), and the second order catalytic rate constants (k2cat = kcat/KM). In the case of 8:Zn(II)2, the plots of kobs versus [catalyst] as a function of sspH are linear, and the catalytic rate constants (k2cat) are defined as the gradients of the plots. Analysis of all of the data at the sspH optimum for each reaction indicates that the presence of the amino and acetamido H-bonding groups and the CH3 group provides similar increases of the kcat terms of 25−50 times that exhibited by the parent complex 3:Zn(II)2. However, in terms of substrate catalyst binding (KM), there is no clear trend that H-bonding groups or the CH3 group provides stronger binding than the parent complex. In terms of the overall second order catalytic rate constant, the CH3, amino, and NH(C═O)CH3 groups provide 20, 10, and 68 times the k2cat observed for the parent complex. In the case of 9:Zn(II)2, the presence of the methyl groups provides a 1000-fold increase in activity (judged by k2cat) over the parent complex 8:Zn(II)2. The results are interpreted to indicate that H-bonding effects may be important for catalysis and less so for substrate binding, but the

  3. Mechanism and Stereoselectivity in an Asymmetric N-Heterocyclic Carbene-Catalyzed Carbon-Carbon Bond Activation Reaction. (United States)

    Pareek, Monika; Sunoj, Raghavan B


    The mechanism and origin of stereoinduction in a chiral N-heterocyclic carbene (NHC) catalyzed C-C bond activation of cyclobutenone has been established using B3LYP-D3 density functional theory computations. The activation of cyclobutenone as an NHC-bound vinyl enolate and subsequent reaction with the electrophilic sulfonyl imine leads to the lactam product. The most preferred stereocontrolling transition state exhibits a number of noncovalent interactions rendering additional stabilization. The computed enantio- and diastereoselectivities are in good agreement with the previous experimental observations.

  4. Reactions of the alkoxy radicals formed following OH-addition to alpha-pinene and beta-pinene. C-C bond scission reactions. (United States)

    Dibble, T S


    The atmospheric degradation pathways of the atmospherically important terpenes alpha-pinene and beta-pinene are studied using density functional theory. We employ the correlation functional of Lee, Yang, and Parr and the three-parameter HF exchange functional of Becke (B3LYP) together with the 6-31G(d) basis set. The C-C bond scission reactions of the beta-hydroxyalkoxy radicals that are formed after OH addition to alpha-pinene and beta-pinene are investigated. Both of the alkoxy radicals formed from the alpha-pinene-OH adduct possess a single favored C-C scission pathway with an extremely low barrier (approximately 3 kcal/mol) leading to the formation of pinonaldehyde. Neither of these pathways produces formaldehyde, and preliminary computational results offer some support for suggestions that 1,5 or 1,6 H-shift (isomerization) reactions of alkoxy radicals contribute to formaldehyde production. In the case of the alkoxy radical formed following OH addition to the methylene group of beta-pinene, there exists two C-C scission reactions with nearly identical barrier heights (approximately 7.5 kcal/mol); one leads to known products (nopinone and formaldehyde) but the ultimate products of the competing reaction are unknown. The single C-C scission pathway of the other alkoxy radical from beta-pinene possesses a very low (approximately 4 kcal/mol) barrier. The kinetically favored C-C scission reactions of all four alkoxy radicals appear to be far faster than expected rates of reaction with O2. The rearrangement of the alpha-pinene-OH adduct, a key step in the proposed mechanism of formation of acetone from alpha-pinene, is determined to possess a barrier of 11.6 kcal/mol. This value is consistent with another computational result and is broadly consistent with the modest acetone yields observed in product yield studies.

  5. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening. (United States)

    Dalvit, Claudio; Vulpetti, Anna


    It is known that strong hydrogen-bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen-bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen-bond complexes involving the fluorine moieties CH2 F, CHF2 , and CF3 , and have compared them with the well-known hydrogen-bond complex formed between acetophenone and the strong hydrogen-bond donor p-fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5-fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein (19) F NMR screening are analyzed through experiments and theoretical simulations.

  6. Solvent effects on a Diels-Alder reaction involving a cationic diene: Consequences of the absence of hydrogen-bond interactions for accelerations in aqueous media

    NARCIS (Netherlands)

    van der Wel, Gerben K.; Wijnen, Jan W.; Engberts, Jan B.F.N.


    In order to study the influence of hydrogen-bond interactions on the accelerations of Diels-Alder reactions in water and highly aqueous mixed solvent systems, second-order rate constants for the Diels-Alder reaction of acridizinium bromide (1a) with cyclopentadiene (CP) have been measured in aqueous

  7. Solvent effects on a Diels-Alder reaction involving a cationic diene : Consequences of the absence of hydrogen-bond interactions for accelerations in aqueous media

    NARCIS (Netherlands)

    Wel, Gerben K. van der; Wijnen, Jan W.; Engberts, Jan B.F.N.


    In order to study the influence of hydrogen-bond interactions on the accelerations of Diels-Alder reactions in water and highly aqueous mixed solvent systems, second-order rate constants for the Diels-Alder reaction of acridizinium bromide (1a) with cyclopentadiene (CP) have been measured in aqueous

  8. Entrance Channel Stereospecificity of Photoinitiated H-Atom Reactions in Weakly Bonded Complexes (United States)

    Shin, Seung Koo; Chen, Y.; Oh, D.; Wittig, C.


    Hot H-atom reactions photoinitiated in T-shaped CO2-HBr and nearly-linear CO2-HCl complexes show remarkably different reaction probabilities. Broadside H-atom approaches in CO2-HBr complexes are greatly favoured over the relatively endon approaches of CO2-HCl complexes, a striking steric effect. Photoinitiated hot H-atom reactions with N2O result in a much lower [NH]/[OH] ratio with N2O-HI complexes than under single-collision conditions at the same photolysis wavelength. In addition, OH rotational distributions differ markedly between bulk and complexed conditions, while NH rotational distributions are similar. These results can be interpreted in terms of entrance channel stereospecificity influencing chemically distinct product channels.

  9. Intramolecular C-N bond activation and ring-expansion reactions of N-heterocyclic carbenes. (United States)

    Hemberger, Patrick; Bodi, Andras; Berthel, Johannes H J; Radius, Udo


    Intramolecular ring-expansion reactions (RER) of the N-heterocyclic carbene 1,3-dimethylimidazolin-2-ylidene were observed upon vacuum ultraviolet (VUV) photoexcitation. Similarly to RERs reported in the solvent phase, for the reaction of NHCs with main-group-element hydrides, hydrogen transfer to the NHC carbon atom is the crucial initial step. In an ionization-mediated protonation, 1,3-dimethylimidazolin-2-ylidene forms an imidazolium ion, which is the rate-limiting step on the pathway to two six-membered ring products, namely, methylpyrimidinium and -pyrazinium ions. To unravel the reaction path, we have used imaging photoelectron photoion coincidence spectroscopy with VUV synchrotron radiation, as well as high-level composite method calculations. Similarities and differences between the mechanism in the gas phase and in the condensed phase are discussed.

  10. Solid-state Photochemical [2+2] Cycloaddition Reaction of Hydrogen-Bonded Zn(II) Metal Complex Containing Several Parallel C=C Bonds

    Indian Academy of Sciences (India)



    A 2D hydrogen-bonded dinuclear Zn(II) complex, [{Zn(H₂O) ₃ (bpe) ₂} ₂ (bpe)](NO₃) ₄・3bpe・14H₂O,1 (bpe = 4,4_-bipyridylethylene) containing coordination complex cations, [{Zn(H₂O) ₃ (bpe) ₂} ₂ (μ-bpe)] ⁴⁺and free bpe and lattice water molecules shows face-to-face, π ・ ・ ・ π stacking of two of the four free bpemolecules with coordinated bpe ligands. Out of eight bpe molecules, six are aligned in parallel fashion withshort C・ ・ ・ C distances of 3.663–3.814Å and they undergo photochemical [2+2] cycloaddition reaction. The photoreaction conducted on ground sample of 1 in the solid-state affords rctt-tetrakis(4-pyridyl)cyclobutane (rctt-tpcb) product in 75% yield. The molecular movement of free bpe molecules was tested by conducting thephotoreaction in ground sample and heated sample of single crystals. The photoreactivity study of 1 indicates that the free bpe molecules are locked between the cationic [{Zn(H₂O) ₃ (bpe) ₂} ₂ (bpe)] ⁴⁺ layers.

  11. Design and Synthesis of Chiral Zn2+ Complexes Mimicking Natural Aldolases for Catalytic C–C Bond Forming Reactions in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Susumu Itoh


    Full Text Available Extending carbon frameworks via a series of C–C bond forming reactions is essential for the synthesis of natural products, pharmaceutically active compounds, active agrochemical ingredients, and a variety of functional materials. The application of stereoselective C–C bond forming reactions to the one-pot synthesis of biorelevant compounds is now emerging as a challenging and powerful strategy for improving the efficiency of a chemical reaction, in which some of the reactants are subjected to successive chemical reactions in just one reactor. However, organic reactions are generally conducted in organic solvents, as many organic molecules, reagents, and intermediates are not stable or soluble in water. In contrast, enzymatic reactions in living systems proceed in aqueous solvents, as most of enzymes generally function only within a narrow range of temperature and pH and are not so stable in less polar organic environments, which makes it difficult to conduct chemoenzymatic reactions in organic solvents. In this review, we describe the design and synthesis of chiral metal complexes with Zn2+ ions as a catalytic factor that mimic aldolases in stereoselective C–C bond forming reactions, especially for enantioselective aldol reactions. Their application to chemoenzymatic reactions in aqueous solution is also presented.

  12. Evolution of chemical bonding and electron density rearrangements during D(3h) → D(3d) reaction in monolayered TiS2: a QTAIM and ELF study. (United States)

    Ryzhikov, Maxim R; Slepkov, Vladimir A; Kozlova, Svetlana G; Gabuda, Svyatoslav P


    Monolayered titanium disulfide TiS2, a prospective nanoelectronic material, was previously shown to be subject to an exothermic solid-state D3h -D3d reaction that proceeds via a newly discovered transition state. Here, we study the reaction in detail using topological methods of quantum chemistry (quantum theory of atoms in molecules and electron localization function analysis) and show how electron density and chemical bonding between the atoms change in the course of the reaction. The reaction is shown to undergo a series of topological catastrophes, associated with elementary chemical events such as break and formation of bonds (including the unexpected formation of S-S bonding between sulfur layers), and rearrangement of electron density of outer valence and core shells.

  13. Diels-Alder Reactions in Water. Effects of Hydrophobicity and Hydrogen Bonding

    NARCIS (Netherlands)

    Otto, Sijbren; Blokzijl, Wilfried; Engberts, Jan B.F.N.


    In order to check whether the activated complex for the Diels-Alder reactions of 5-substituted 1,4-naphthoquinones with cyclopentadiene is more polar in water than in other solvents, we have determined the substituent effects in seven different solvents. The substituent effects gradually decrease wi

  14. Transition Metal Catalyzed Reactions for Forming Carbon–Oxygen and Carbon–Carbon Bonds

    DEFF Research Database (Denmark)

    Sølvhøj, Amanda Birgitte

    of hydrogen per formed mol of ester as assumed. Furthermore a disproportionation mechanism (Tishchenko) could be ruled out due to the fact that free aldehydes did not enter the catalytic cycle. Fast deuterium/hydrogen exchange in the reaction with benzyl alcohol points towards a ruthenium dihydride species...... eliminates a bromo radical and forms the product....

  15. In Pursuit of an Ideal C-C Bond-Forming Reaction (United States)

    RajanBabu, T. V.


    Attempts to introduce the highly versatile vinyl group into other organic molecules in a chemo-, regio- and stereoselective fashion via catalytic activation of ethylene provided challenging opportunities to explore new ligand and salt effects in homogeneous catalysis. This review provides a personal account of the development of enantioselective reactions involving ethylene. PMID:19606231

  16. Fully Borylated Methane and Ethane by Ruthenium-Mediated Cleavage and Coupling of CO. (United States)

    Batsanov, Andrei S; Cabeza, Javier A; Crestani, Marco G; Fructos, Manuel R; García-Álvarez, Pablo; Gille, Marie; Lin, Zhenyang; Marder, Todd B


    Many transition-metal complexes and some metal-free compounds are able to bind carbon monoxide, a molecule which has the strongest chemical bond in nature. However, very few of them have been shown to induce the cleavage of its C-O bond and even fewer are those that are able to transform CO into organic reagents with potential in organic synthesis. This work shows that bis(pinacolato)diboron, B2pin2, reacts with ruthenium carbonyl to give metallic complexes containing borylmethylidyne (CBpin) and diborylethyne (pinBC≡CBpin) ligands and also metal-free perborylated C1 and C2 products, such as C(Bpin)4 and C2 (Bpin)6, respectively, which have great potential as building blocks for Suzuki-Miyaura cross-coupling and other reactions. The use of (13)CO-enriched ruthenium carbonyl has demonstrated that the boron-bound carbon atoms of all of these reaction products arise from CO ligands.

  17. Theoretical Study on Catalyst Activation of Palladacycles in Heck Reaction

    Institute of Scientific and Technical Information of China (English)

    WANG Chen; FU Yao; LI Zhe; GUO Qing-Xiang


    A computational study with the B3PW91 density functional theory was carried out on the activation process of palladacycles as catalysts in the Heck reaction.Two possible pathways (i.e.anion reductive cleavage of the Pd-C bond,and olefin insertion into the Pd-C bond followed by β-H elimination)were taken into consideration.Computational results indicate that the palladacycles are activated via olefin insertion into the Pd-C bond followed by β-H elimination in the reaction conditions.

  18. Heterolytic cleavage of ammonia N-H bond by bifunctional activation in silica-grafted single site Ta(V) imido amido surface complex. Importance of the outer sphere NH3 assistance

    KAUST Repository

    Gouré, Eric


    Ammonia N-H bond is cleaved at room temperature by the silica-supported tantalum imido amido complex [(≡SiO)2Ta(NH)(-NH2)], 2, if excess ammonia is present, but requires 150 °C to achieve the same reaction if only one equivalent NH3 is added to 2. MAS solid-state 15N NMR and in situ IR spectroscopic studies of the reaction of either 15N or 2H labeled ammonia with 2 show that initial coordination of the ammonia is followed by scrambling of either 15N or 2H among ammonia, amido and imido groups. Density functional theory (DFT) calculations with a cluster model [{(μ-O)[(H3SiO) 2SiO]2}Ta(NH)(-NH2)(NH3)], 2 q·NH3, show that the intramolecular H transfer from Ta-NH2 to TaNH is ruled out, but the H transfers from the coordinated ammonia to the amido and imido groups have accessible energy barriers. The energy barrier for the ammonia N-H activation by the Ta-amido group is energetically preferred relative to the Ta-imido group. The importance of excess NH3 for getting full isotope scrambling is rationalized by an outer sphere assistance of ammonia acting as proton transfer agent, which equalizes the energy barriers for H transfer from coordinated ammonia to the amido and imido groups. In contrast, additional coordinated ammonia does not favor significantly the H transfer. These results rationalize the experimental conditions used. © The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2011.

  19. Structural and medium effects on the reactions of the cumyloxyl radical with intramolecular hydrogen bonded phenols. The interplay between hydrogen-bonding and acid-base interactions on the hydrogen atom transfer reactivity and selectivity. (United States)

    Salamone, Michela; Amorati, Riccardo; Menichetti, Stefano; Viglianisi, Caterina; Bietti, Massimo


    A time-resolved kinetic study on the reactions of the cumyloxyl radical (CumO(•)) with intramolecularly hydrogen bonded 2-(1-piperidinylmethyl)phenol (1) and 4-methoxy-2-(1-piperidinylmethyl)phenol (2) and with 4-methoxy-3-(1-piperidinylmethyl)phenol (3) has been carried out. In acetonitrile, intramolecular hydrogen bonding protects the phenolic O-H of 1 and 2 from attack by CumO(•) and hydrogen atom transfer (HAT) exclusively occurs from the C-H bonds that are α to the piperidine nitrogen (α-C-H bonds). With 3 HAT from both the phenolic O-H and the α-C-H bonds is observed. In the presence of TFA or Mg(ClO4)2, protonation or Mg(2+) complexation of the piperidine nitrogen removes the intramolecular hydrogen bond in 1 and 2 and strongly deactivates the α-C-H bonds of the three substrates. Under these conditions, HAT to CumO(•) exclusively occurs from the phenolic O-H group of 1-3. These results clearly show that in these systems the interplay between intramolecular hydrogen bonding and Brønsted and Lewis acid-base interactions can drastically influence both the HAT reactivity and selectivity. The possible implications of these findings are discussed in the framework of the important role played by tyrosyl radicals in biological systems.

  20. Evolution mechanism of the interfacial reaction layers in the joints of diffusion bonded Mo and Ai foils

    Institute of Scientific and Technical Information of China (English)

    LI Jinglong; ZHAO Fengkuan; YANG Weihua; XIONG Jiangtao; ZHANG Fusheng; Lü Xuechao


    Mo foil (10-20 μm in thickness) and Al foil (20-60 μm in thickness) were vacuum diffusion bonded at 600-640 ℃ under 20 MPa for 54 min-6 h. The joints were examined by scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) to study the evolution mechanism of the reaction layers. The results show that Al atoms diffuse into Mo grain boundaries and form reaction products as Mo3Als, MoAl4, MoAl5 and MoAl12. The surface oxide film is eroded by the growths of the reaction products that plow into the lamellar texture of Mo grain boundaries. Mo3Al8 layer grows by "taking root" downwards and transforms into MoAl4 and MoAl5 phases upwards by absorbing Al atoms. MoAl12 layer grows up from MoAl5 layer in the same way. When the supplement of Al atoms ceases, MoAl12 transforms reversely into MoAl5 and MoAl3 into MoAl4 via the loss of Al atoms. However, MoAl4 continues to precipitate from Mo3Al8 layer. At last, there are MoAl4 and Mo3Al8 remained on the joint interface.

  1. Efficient C-O and C-N bond forming cross-coupling reactions catalyzed by core-shell structured Cu/Cu2O nanowires

    KAUST Repository

    Elshewy, Ahmed M.


    Oxygen and Nitrogen containing compounds are of utmost importance due to their interesting and diverse biological activities. The construction of the C-O and C–N bonds is of significance as it opens avenues for the introduction of ether and amine linkages in organic molecules. Despite significant advancements in this field, the construction of C-O and C–N bonds is still a major challenge for organic chemists, due to the involvement of harsh reaction conditions or the use of expensive catalysts or ligands in many cases. Thus, it is a challenge to develop alternative, milder, cheaper and more reproducible methodologies for the construction of these types of bonds. Herein, we introduce a new efficient ligand free catalytic system for C-O and C-N bond formation reactions.

  2. The first chiral diene-based metal-organic frameworks for highly enantioselective carbon-carbon bond formation reactions

    Energy Technology Data Exchange (ETDEWEB)

    Sawano, Takahiro; Ji, Pengfei; McIsaac, Alexandra R.; Lin, Zekai; Abney, Carter W.; Lin, Wenbin [UC


    We have designed the first chiral diene-based metal–organic framework (MOF), E₂-MOF, and postsynthetically metalated E₂-MOF with Rh(I) complexes to afford highly active and enantioselective single-site solid catalysts for C–C bond formation reactions. Treatment of E₂-MOF with [RhCl(C₂H₄)₂]₂ led to a highly enantioselective catalyst for 1,4-additions of arylboronic acids to α,β-unsaturated ketones, whereas treatment of E₂-MOF with Rh(acac)(C₂H₄)₂ afforded a highly efficient catalyst for the asymmetric 1,2-additions of arylboronic acids to aldimines. Interestingly, E₂-MOF·Rh(acac) showed higher activity and enantioselectivity than the homogeneous control catalyst, likely due to the formation of a true single-site catalyst in the MOF. E₂-MOF·Rh(acac) was also successfully recycled and reused at least seven times without loss of yield and enantioselectivity.

  3. Electrochemical and Reaction Bonding Processing of Thick ZrO2/Al2O3 Composite Coatings

    Institute of Scientific and Technical Information of China (English)

    WANGZhou-cheng; XIAOPing


    A novel technique combining electrophoretic deposition (EPD) and reaction bonding process (RBP) is developed to fabricate thick ZrO2/Al2O3 composite coatings. Mixed organic solvents are used here to make suspension containing yttria stablised zirconia (YSZ) and aluminium (Al). The results show that densely packed green form coatings are deposited using a mixture of ethanol and acetylacetone as suspension medium and ball milling for 48 hours. On subsequent heat treatment, melting and oxidation of aluminium in the green forms promote densification during sintering. By these means,thick, uniform and crack-free ZrO2/Al2O3 composite coatings have been fabricated on metal substrate.

  4. Electrochemical and Reaction Bonding Processing of Thick ZrO2/Al2O3 Composite Coatings

    Institute of Scientific and Technical Information of China (English)

    WANG Zhou-cheng; XIAO Ping


    A novel technique combining electrophoretic deposition (EPD) and reaction bonding process (RBP) is developed to fabricate thick ZrO2/Al2O3 composite coatings. Mixed organic solvents are used here to make suspension containing yttria stablised zirconia (YSZ) and aluminium (Al). The results show that densely packed green form coatings are deposited using a mixture of ethanol and acetylacetone as suspension medium and ball milling for 48 hours. On subsequent heat treatment, melting and oxidation of aluminium in the green forms promote densification during sintering. By these means,thick, uniform and crack-free ZrO2/Al2O3 composite coatings have been fabricated on metal substrate.

  5. Role of bonding mechanisms during transfer hydrogenation reaction on heterogeneous catalysts of platinum nanoparticles supported on zinc oxide nanorods (United States)

    Al-Alawi, Reem A.; Laxman, Karthik; Dastgir, Sarim; Dutta, Joydeep


    For supported heterogeneous catalysis, the interface between a metal nanoparticle and the support plays an important role. In this work the dependency of the catalytic efficiency on the bonding chemistry of platinum nanoparticles supported on zinc oxide (ZnO) nanorods is studied. Platinum nanoparticles were deposited on ZnO nanorods (ZnO NR) using thermal and photochemical processes and the effects on the size, distribution, density and chemical state of the metal nanoparticles upon the catalytic activities are presented. The obtained results indicate that the bonding at Pt-ZnO interface depends on the deposition scheme which can be utilized to modulate the surface chemistry and thus the activity of the supported catalysts. Additionally, uniform distribution of metal on the catalyst support was observed to be more important than the loading density. It is also found that oxidized platinum Pt(IV) (platinum hydroxide) provided a more suitable surface for enhancing the transfer hydrogenation reaction of cyclohexanone with isopropanol compared to zero valent platinum. Photochemically synthesized ZnO supported nanocatalysts were efficient and potentially viable for upscaling to industrial applications.

  6. Reaction mechanism of the acidic hydrolysis of highly twisted amides: Rate acceleration caused by the twist of the amide bond. (United States)

    Mujika, Jon I; Formoso, Elena; Mercero, Jose M; Lopez, Xabier


    We present an ab initio study of the acid hydrolysis of a highly twisted amide and a planar amide analogue. The aim of these studies is to investigate the effect that the twist of the amide bond has on the reaction barriers and mechanism of acid hydrolysis. Concerted and stepwise mechanisms were investigated using density functional theory and polarizable continuum model calculations. Remarkable differences were observed between the mechanism of twisted and planar amide, due mainly to the preference for N-protonation of the former and O-protonation of the latter. In addition, we were also able to determine that the hydrolytic mechanism of the twisted amide will be pH dependent. Thus, there is a preference for a stepwise mechanism with formation of an intermediate in the acid hydrolysis, whereas the neutral hydrolysis undergoes a concerted-type mechanism. There is a nice agreement between the characterized intermediate and available X-ray data and a good agreement with the kinetically estimated rate acceleration of hydrolysis with respect to analogous undistorted amide compounds. This work, along with previous ab initio calculations, describes a complex and rich chemistry for the hydrolysis of highly twisted amides as a function of pH. The theoretical data provided will allow for a better understanding of the available kinetic data of the rate acceleration of amides upon twisting and the relation of the observed rate acceleration with intrinsic differential reactivity upon loss of amide bond resonance.

  7. Efficient second strand cleavage during Holliday junction resolution by RuvC requires both increased junction flexibility and an exposed 5' phosphate.

    Directory of Open Access Journals (Sweden)

    Fekret Osman

    Full Text Available BACKGROUND: Holliday junction (HJ resolution is a critical step during homologous recombination. In Escherichia coli this job is performed by a member of the RNase H/Integrase superfamily called RuvC, whereas in Schizosaccharomyces pombe it has been attributed to the XPF family member Mus81-Eme1. HJ resolution is achieved through the sequential cleavage of two strands of like polarity at or close to the junction crossover point. RuvC functions as a dimer, whereas Mus81-Eme1 is thought to function as a dimer of heterodimers. However, in both cases the multimer contains two catalytic sites, which act independently and sequentially during the resolution reaction. To ensure that both strands are cleaved before the nuclease dissociates from the junction, the rate of second strand cleavage is greatly enhanced compared to that of the first. The enhancement of second strand cleavage has been attributed to the increased flexibility of the nicked HJ, which would facilitate rapid engagement of the second active site and scissile bond. Here we have investigated whether other properties of the nicked HJ are important for enhancing second strand cleavage. PRINCIPAL FINDINGS: A comparison of the efficiency of cleavage of nicked HJs with and without a 5' phosphate at the nick site shows that a 5' phosphate is required for most of the enhancement of second strand cleavage by RuvC. In contrast Mus81-Eme1 cleaves nicked HJs with and without a 5' phosphate with equal efficiency, albeit there are differences in cleavage site selection. CONCLUSIONS: Our data show that efficient HJ resolution by RuvC depends on the 5' phosphate revealed by incision of the first strand. This is a hitherto unappreciated factor in promoting accelerated second strand cleavage. However, a 5' phosphate is not a universal requirement since efficient cleavage by Mus81-Eme1 appears to depend solely on the increased junction flexibility that is developed by the first incision.

  8. Energetics and Dynamics of the Fragmentation Reactions of Protonated Peptides Containing Methionine Sulfoxide or Aspartic Acid via Energy- and Time-Resolved Surface Induced Dissociation

    Energy Technology Data Exchange (ETDEWEB)

    Lioe, Hadi; Laskin, Julia; Reid, Gavin E.; O' Hair, Richard Aj


    The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility on these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (non-mobile proton conditions) to lysine (partially-mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFEC) reveals that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1–2 orders of magnitude lower than non-selective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to non-selective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these

  9. Elementary Steps of Syngas Reactions on Mo2C(001): Adsorption Thermochemistry and Bond Dissociation

    Energy Technology Data Exchange (ETDEWEB)

    Medford, Andrew


    Density functional theory (DFT) and ab initio thermodynamics are applied in order to investigate the most stable surface and subsurface terminations of Mo{sub 2}C(001) as a function of chemical potential and in the presence of syngas. The Mo-terminated (001) surface is then used as a model surface to evaluate the thermochemistry and energetic barriers for key elementary steps in syngas reactions. Adsorption energy scaling relations and Broensted-Evans-Polanyi relationships are established and used to place Mo{sub 2}C into the context of transition metal surfaces. The results indicate that the surface termination is a complex function of reaction conditions and kinetics. It is predicted that the surface will be covered by either C{sub 2}H{sub 2} or O depending on conditions. Comparisons to transition metals indicate that the Mo-terminated Mo{sub 2}C(001) surface exhibits carbon reactivity similar to transition metals such as Ru and Ir, but is significantly more reactive towards oxygen.

  10. Carbon-carbon bond activation of cyclobutenones enabled by the addition of chiral organocatalyst to ketone. (United States)

    Li, Bao-Sheng; Wang, Yuhuang; Jin, Zhichao; Zheng, Pengcheng; Ganguly, Rakesh; Chi, Yonggui Robin


    The activation of carbon-carbon (C-C) bonds is an effective strategy in building functional molecules. The C-C bond activation is typically accomplished via metal catalysis, with which high levels of enantioselectivity are difficult to achieve due to high reactivity of metal catalysts and the metal-bound intermediates. It remains largely unexplored to use organocatalysis for C-C bond activation. Here we describe an organocatalytic activation of C-C bonds through the addition of an NHC to a ketone moiety that initiates a C-C single bond cleavage as a key step to generate an NHC-bound intermediate for chemo- and stereo-selective reactions. This reaction constitutes an asymmetric functionalization of cyclobutenones using organocatalysts via a C-C bond activation process. Structurally diverse and multicyclic compounds could be obtained with high optical purities via an atom and redox economic process.

  11. Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site. (United States)

    Martin, Erik; Samoilova, Rimma I; Narasimhulu, Kupala V; Lin, Tzu-Jen; O'Malley, Patrick J; Wraight, Colin A; Dikanov, Sergei A


    In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q

  12. Hydrogen bonding and spin density distribution in the QB semiquinone of bacterial reaction centers and comparison with the QA site (United States)

    Martin, Erik; Samoilova, Rimma I.; Narasimhulu, Kupala V.; Lin, Tzu-Jen; O’Malley, Patrick J.; Wraight, Colin A.; Dikanov, Sergei A.


    In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (QA) and secondary (QB) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the QA and QB sites, using samples of 15N-labeled reaction centers, with the native high spin Fe2+ exchanged for diamagnetic Zn2+, prepared in 1H2O and 2H2O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the QA SQ by Flores et al. (Biophys. J. 2007, 92, 671–682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6–5.4 MHz. HYSCORE was then applied to the QB SQ where we found proton lines corresponding to T~5.2, 3.7 MHz and T~1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the QB site, were used to assign the observed couplings to specific hydrogen bonding interactions with the QB SQ. These calculations allow us to assign the T=5.2 MHz proton to the His-L190 NδH…O4 (carbonyl) hydrogen bonding interaction. The T =3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the QB site show less asymmetric distribution of unpaired spin density over the SQ than seen for the QA site, consistent with available experimental data for 13C and 17O carbonyl hyperfine couplings. The implications of these interactions for QB function and comparisons with the QA site are discussed

  13. Singular characteristics and unique chemical bond activation mechanisms of photocatalytic reactions on plasmonic nanostructures (United States)

    Christopher, Phillip; Xin, Hongliang; Marimuthu, Andiappan; Linic, Suljo


    The field of heterogeneous photocatalysis has almost exclusively focused on semiconductor photocatalysts. Herein, we show that plasmonic metallic nanostructures represent a new family of photocatalysts. We demonstrate that these photocatalysts exhibit fundamentally different behaviour compared with semiconductors. First, we show that photocatalytic reaction rates on excited plasmonic metallic nanostructures exhibit a super-linear power law dependence on light intensity (rate ∝intensityn, with n > 1), at significantly lower intensity than required for super-linear behaviour on extended metal surfaces. We also demonstrate that, in sharp contrast to semiconductor photocatalysts, photocatalytic quantum efficiencies on plasmonic metallic nanostructures increase with light intensity and operating temperature. These unique characteristics of plasmonic metallic nanostructures suggest that this new family of photocatalysts could prove useful for many heterogeneous catalytic processes that cannot be activated using conventional thermal processes on metals or photocatalytic processes on semiconductors.

  14. Reaction heats and bond strengths based on a series of lectures given to postgraduate students at the University of Keele, 1960

    CERN Document Server

    Mortimer, C T


    Reaction Heats and Bond Strengths presents the variations in the heats of particular types of reaction. This book covers a variety of topics, including the hydrogenation and polymerization of olefinic compounds, the dissociation of organic and organo-metallic compounds, and the molecular-addition compounds. Organized into 10 chapters, this book begins with an overview of the concept of bond energy that can be very useful where a comparison is being made between two dissimilar molecules. This text then examines the strain in cyclopropane and cyclobutane, which is largely a result of angular str

  15. Mullite fiber reinforced reaction bonded Si{sub 3}N{sub 4} composites

    Energy Technology Data Exchange (ETDEWEB)

    Saleh, T.; Lightfoot, A.; Haggerty, J. [Massachusetts Institute of Technology, Cambridge, MA (United States); Sayir, A. [NASA Lewis Research Center, Cleveland, OH (United States)


    Fracture toughnesses of brittle ceramic materials have been improved by introducing reinforcements and carefully tailored interface layers. Silicon carbide and Si{sub 3}N{sub 4} have been emphasized as matrices of structural composites intended for high temperature service because they combine excellent mechanical, chemical, thermal and physical properties. Both matrices have been successfully toughened with SiC fibers, whiskers and particles for ceramic matrix composite (CMC) parts made by sintering, hot pressing or reaction forming processes. These SiC reinforced CMCs have exhibited significantly improved toughnesses at low and intermediate temperature levels, as well as retention of properties at high temperatures for selected exposures; however, they are vulnerable to attack from elevated temperature dry and wet oxidizing atmospheres after the matrix has cracked. Property degradation results from oxidation of interface layers and/or reinforcements. The problem is particularly acute for small diameter ({approximately}20 {mu}m) polymer derived SiC fibers used for weavable toes. This research explored opportunities for reinforcing Si{sub 3}N{sub 4} matrices with fibers having improved environmental stability; the finding should also be applicable to SiC matrix CMCs.

  16. Preparation of different amides via Ritter reaction from alcohols and nitriles in the presence of silica-bonded N- propyl sulphamic acid (SBNPSA) under solvent-free conditions

    Indian Academy of Sciences (India)

    Maryam-Sadat Shakeri; Hassan Tajik; Khodabakhsh Niknam


    A number of methods have been proposed for the modification of the Ritter reaction. However, many of these methods involve the use of strongly acidic conditions, stoichiometric amounts of reagents, harsh reaction conditions and extended reaction times. Therefore, the development of mild, efficient, convenient and benign reagents for the Ritter reaction is desirable. In this research, we have developed a clean and environmentally friendly protocol for the synthesis of amides by using different benzylic or tertiary alcohols and different nitriles in the presence of silica-bonded N- propyl sulphamic acid (SBNPSA) as catalyst under solvent-free conditions in high yields.

  17. Enthalpies of hydrogen bonding of quinoline with o-phenylphenol and of hydrogen-bonding reactions involving the acid and base components of a coal-derived asphaltene

    Energy Technology Data Exchange (ETDEWEB)

    Dietz, A.G.; Blaha, C.; Li, N.C.


    Calorimetric studies are reported of hydrogen bonding between quinoline (Qu) and o-phenylphenol (OPP). The enthalpies of hydrogen-bonding of the acid and base components of a coal-derived asphaltene with OPP and Qu are also reported. The results provide strong evidence that the acid and base components of asphaltene function substantially as hydrogen donor and acceptor, respectively. 1 figure, 1 table.

  18. SiC-Si interfacial thermal and mechanical properties of reaction bonded SiC/Si ceramic composites (United States)

    Hsu, Chun-Yen; Deng, Fei; Karandikar, Prashant; Ni, Chaoying

    Reaction bonded SiC/Si (RBSC) ceramic composites are broadly utilized in military, semiconductor and aerospace industries. RBSC affords advanced specific stiffness, hardness and thermal. Interface is a key region that has to be considered when working with any composites. Both thermal and mechanical behaviors of the RBSC are highly dependent on the SiC-Si interface. The SiC-Si interface had been found to act as a thermal barrier in restricting heat transferring at room temperature and to govern the energy absorption ability of the RBSC. However, up to present, the role of the SiC-Si interface to transport heat at higher temperatures and the interfacial properties in the nanoscale have not been established. This study focuses on these critically important subjects to explore scientific phenomena and underlying mechanisms. The RBSC thermal conductivity with volume percentages of SiC at 80 and 90 vol% was measured up to 1,200 °C, and was found to decrease for both samples with increasing environmental temperature. The RBSC with 90 vol% SiC has a higher thermal conductivity than that of the 80 vol%; however, is still significantly lower than that of the SiC. The interfacial thermal barrier effect was found to decrease at higher temperatures close 1200 °C. A custom-made in-situ tensile testing device which can be accommodated inside a ZEISS Auriga 60 FIB/SEM has been setup successfully. The SiC-Si interfacial bonding strength was measured at 98 MPa. The observation and analysis of crack propagation along the SiC-Si interface was achieved with in-situ TEM.

  19. Transition metal-promoted synthesis of 2-aryl/heteroaryl-thioquinazoline: C-S Bond formation by “Chan-Lam Cross-Coupling” Reaction

    Indian Academy of Sciences (India)



    An efficient method for the synthesis of S-aryl/heteroaryl-quinazoline has been developed through the cross-coupling of 1,4-dihydroquinazoline with a variety of aryl and heteroaryl boronic acids assisted by [Cu(OAc)₂] as the catalyst for the formation of carbon-sulfur bonds. This newly developed method demonstratesthat the conditions of the traditional copper-catalyzed Chan-Lam reaction can be improved. Optimized reaction involves base, solvent and catalyst.

  20. Properties and reactions of manganese methylene complexes in the gas phase. The importance of strong metal: carbene bonds for effective olefin metathesis catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, A.E.; Beauchamp, J.L.


    In this communication the formation, properties and reactions of the gas phase carbenes MnCH/sub 2//sup +/, (CO)/sub 5/MnCH/sub 2//sup +/, and (CO)/sub 4/MnCH/sub 2//sup +/ are described. Reported results include observation of metathesis and abstraction reactions of the methylene ligand with olefins and the first experimental determination of metal-carbene bond dissociation energies. Important points are that: (a) metal-methylene bond energies are extremely strong; and (b) the Mn/sup +/-methylene bond energy is decreased substantially on addition of five carbonyls to the metal center. If the metal-carbene bond energy exceeds 100 kcal/mol, then transfer of the carbene to an olefin to give a cyclopropane or new olefin will be endothermic and thus will not compete with the metathesis reaction. In order to avoid low turnover numbers resulting from consumption of carbene intermediates, strong metal-carbene bonds are a desirable feature of practical metathesis catalysts. (DP)

  1. Kinetic solvent effects on the reactions of the cumyloxyl radical with tertiary amides. Control over the hydrogen atom transfer reactivity and selectivity through solvent polarity and hydrogen bonding. (United States)

    Salamone, Michela; Mangiacapra, Livia; Bietti, Massimo


    A laser flash photolysis study on the role of solvent effects on hydrogen atom transfer (HAT) from the C-H bonds of N,N-dimethylformamide (DMF), N,N-dimethylacetamide (DMA), N-formylpyrrolidine (FPRD), and N-acetylpyrrolidine (APRD) to the cumyloxyl radical (CumO(•)) was carried out. From large to very large increases in the HAT rate constant (kH) were measured on going from MeOH and TFE to isooctane (kH(isooctane)/kH(MeOH) = 5-12; kH(isooctane)/kH(TFE) > 80). This behavior was explained in terms of the increase in the extent of charge separation in the amides determined by polar solvents through solvent-amide dipole-dipole interactions and hydrogen bonding, where the latter interactions appear to play a major role with strong HBD solvents such as TFE. These interactions increase the electron deficiency of the amide C-H bonds, deactivating these bonds toward HAT to an electrophilic radical such as CumO(•), indicating that changes in solvent polarity and hydrogen bonding can provide a convenient method for deactivation of the C-H bond of amides toward HAT. With DMF, a solvent-induced change in HAT selectivity was observed, suggesting that solvent effects can be successfully employed to control the reaction selectivity in HAT-based procedures for the functionalization of C-H bonds.

  2. Effects of Thermal Cycling on Thermal Expansion and Mechanical Properties of Sic Fiber-reinforced Reaction-bonded Si3n4 Composites (United States)

    Bhatt, R. T.; Palczer, A. R.


    Thermal expansion curves for SiC fiber-reinforced reaction-bonded Si3N4 matrix composites (SiC/RBSN) and unreinforced RBSN were measured from 25 to 1400 C in nitrogen and in oxygen. The effects of fiber/matrix bonding and cycling on the thermal expansion curves and room-temperature tensile properties of unidirectional composites were determined. The measured thermal expansion curves were compared with those predicted from composite theory. Predicted thermal expansion curves parallel to the fiber direction for both bonding cases were similar to that of the weakly bonded composites, but those normal to the fiber direction for both bonding cases resulted in no net dimensional changes at room temperature, and no loss in tensile properties from the as-fabricated condition. In contrast, thermal cycling in oxygen for both composites caused volume expansion primarily due to internal oxidation of RBSN. Cyclic oxidation affected the mechanical properties of the weakly bonded SiC/RBSN composites the most, resulting in loss of strain capability beyond matrix fracture and catastrophic, brittle fracture. Increased bonding between the SiC fiber and RBSN matrix due to oxidation of the carbon-rich fiber surface coating and an altered residual stress pattern in the composite due to internal oxidation of the matrix are the main reasons for the poor mechanical performance of these composites.

  3. A Photo-Triggered Traceless Staudinger-Bertozzi Ligation Reaction. (United States)

    Hu, Peng; Feng, Tianshi; Yeung, Chi-Chung; Koo, Chi-Kin; Lau, Kai-Chung; Lam, Michael H W


    The use of light to control the course of a chemical/biochemical reaction is an attractive idea because of its ease of administration with high precision and fine spatial resolution. Staudinger ligation is one of the commonly adopted conjugation processes that involve a spontaneous reaction between azides and arylphosphines to form iminophosphoranes, which further hydrolyze to give stable amides. We designed an anthracenylmethyl diphenylphosphinothioester (1) that showed promising Staudinger ligation reactivity upon photo-excitation. Broadband photolysis at 360-400 nm in aqueous organic solvents induced heterolytic cleavage of its anthracenylmethyl-phosphorus bond, releasing a diphenylphosphinothioester (2) as an efficient traceless Staudinger-Bertozzi ligation reagent. The quantum yield of such a photo-induced heterolytic bond-cleavage at the optimal wavelength of photolysis (376 nm) at room temperature is ≥0.07. This work demonstrated the feasibility of photocaging arylphosphines to realize the photo-triggering of the Staudinger ligation reaction.

  4. Hydrogen bonds between nitrogen donors and the semiquinone in the QB-site of bacterial reaction centers (United States)

    Martin, Erik; Samoilova, Rimma I.; Narasimhulu, Kupala V.; Wraight, Colin A.; Dikanov, Sergei A.


    Photosynthetic reaction centers from Rhodobacter sphaeroides have identical ubiquinone-10 molecules functioning as primary (QA) and secondary (QB) electron acceptors. X-band 2D pulsed EPR spectroscopy, called HYSCORE, was applied to study the interaction of the QB site semiquinone with nitrogens from the local protein environment in natural and 15N uniformly labeled reactions centers. 14N and 15N HYSCORE spectra of the QB semiquinone show the interaction with two nitrogens carrying transferred unpaired spin density. Quadrupole coupling constants estimated from 14N HYSCORE spectra indicate them to be a protonated nitrogen of an imidazole residue and amide nitrogen of a peptide group. 15N HYSCORE spectra allowed estimation of the isotropic and anisotropic couplings with these nitrogens. From these data, we calculated the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen, and analyzed the contribution of different factors to the anisotropic hyperfine tensors. The hyperfine coupling of other protein nitrogens with the semiquinone is weak (<0.1 MHz). These results clearly indicate that the QB semiquinone forms hydrogen bonds with two nitrogens, and provide quantitative characteristics of the hyperfine couplings with these nitrogens, which can be used in theoretical modeling of the QB site. Based on the quadrupole coupling constant, one nitrogen can only be assigned to Nδ of His-L190, consistent with all existing structures. However, we cannot specify between two candidates the residue corresponding to the second nitrogen. Further work employing multifrequency spectroscopic approaches or selective isotope labeling would be desirable for unambiguous assignment of this nitrogen. PMID:20672818

  5. Effect of SiO2 on the Preparation and Properties of Pure Carbon Reaction Bonded Silicon Carbide Ceramics

    Institute of Scientific and Technical Information of China (English)

    WU Qi-de; GUO Bing-jian; YAN Yong-gao; ZHAO Xiu-jian; HONG Xiao-lin


    Effect of SiO2 content and sintering process on the composition and properties of Pure CarbonReaction Bonded Silicon Carbide (PCRBSC) ceramics prepared with C - SiO2 green body by infiltrating siliconwas presented. The infiltrating mechanism of C - SiO2 preform was also explored. The experimental results indicatethat the shaping pressure increases with the addition of SiO2 to the preform, and the pore size of the body turnedfiner and distributed in a narrower range, which is beneficial to decreasing the residual silicon content in the sin-tered materials and to avoiding shock off, thus increasing the conversion rate of SiC. SiO2 was deoxidized by car-bon at a high temperature and the gaseous SiO and CO produced are the main reason to the crack of the body atan elevated temperature. If the green body is deposited at 1800℃ in vacuum before infiltration crack will not beproduced in the preform and fully dense RBSC can be obtained. The ultimate material has the following properties:a density of3.05-3.12g/cm3 ,a strength of 580±32MPa and a hardness of (HRA)91-92.3.

  6. Chiral Pd aqua complex-catalyzed asymmetric C-C bond-forming reactions: a Brønsted acid-base cooperative system. (United States)

    Sodeoka, Mikiko; Hamashima, Yoshitaka


    Chiral cationic Pd aqua complexes can function as acid-base catalysts, effectively activating active methylene and methine compounds to give chiral Pd enolates. It is noteworthy that such enolate formation occurs with concomitant formation of a strong protic acid. Although the reactivity of the Pd enolate itself is not sufficient for reactions with carbon-based electrophiles, its cooperative action with the protic acid to activate the electrophiles allows the desired C-C bond-forming reactions to proceed smoothly in a highly enantioselective manner. Based on this mechanistic feature, reactions with acetals have been developed; these are difficult to achieve using conventional basic enolate chemistry.

  7. Theoretical Study of Sodium-Water Surface Reaction Mechanism (United States)

    Kikuchi, Shin; Kurihara, Akikazu; Ohshima, Hiroyuki; Hashimoto, Kenro

    Computational study of the sodium-water reaction at the gas (water) - liquid (sodium) interface has been carried out using the ab initio (first-principle) method. A possible reaction channel has been identified for the stepwise OH bond dissociations of a single water molecule. The energetics including the binding energy of a water molecule on the sodium surface, the activation energies of the bond cleavages, and the reaction energies, have been evaluated, and the rate constants of the first and second OH bond-breakings have been compared. It was found that the estimated rate constant of the former was much larger than the latter. The results are the basis for constructing the chemical reaction model used in a multi-dimensional sodium-water reaction code, SERAPHIM, being developed by Japan Atomic Energy Agency (JAEA) toward the safety assessment of the steam generator (SG) in a sodium-cooled fast reactor (SFR).

  8. Preparation of fluorescence quenched libraries containing interchain disulphide bonds for studies of protein disulphide isomerases

    DEFF Research Database (Denmark)

    Spetzler, J C; Westphal, V; Winther, Jakob R.


    Protein disulphide isomerase is an enzyme that catalyses disulphide redox reactions in proteins. In this paper, fluorogenic and interchain disulphide bond containing peptide libraries and suitable substrates, useful in the study of protein disulphide isomerase, are described. In order to establish...... the quenching chromophore (Tyr(NO2)) and Cys(pNpys) activated for reaction with a second thiol. The formation and cleavage of the interchain disulphide bonds in the library were monitored under a fluorescence microscope. Substrates to investigate the properties of protein disulphide isomerase in solution were...

  9. An Iron-Catalyzed Bond-Making/Bond-Breaking Cascade Merges Cycloisomerization and Cross-Coupling Chemistry. (United States)

    Echeverria, Pierre-Georges; Fürstner, Alois


    Treatment of readily available enynes with alkyl-Grignard reagents in the presence of catalytic amounts of Fe(acac)3 engenders a remarkably facile and efficient reaction cascade that results in the net formation of two new C-C bonds while a C-Z bond in the substrate backbone is broken. Not only does this new manifold lend itself to the extrusion of heteroelements (Z=O, NR), but it can even be used for the cleavage of activated C-C bonds. The reaction likely proceeds via metallacyclic intermediates, the iron center of which gains ate character before reductive elimination occurs. The overall transformation represents a previously unknown merger of cycloisomerization and cross-coupling chemistry. It provides ready access to highly functionalized 1,3-dienes comprising a stereodefined tetrasubstituted alkene unit, which are difficult to make by conventional means.

  10. Activation of C-H Bonds in Pt(+) + x CH4 Reactions, where x = 1-4: Identification of the Platinum Dimethyl Cation. (United States)

    Wheeler, Oscar W; Salem, Michelle; Gao, Amanda; Bakker, Joost M; Armentrout, P B


    Activation of C-H bonds in the sequential reactions of Pt(+) + x(CH4/CD4), where x = 1-4, have been investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and theoretical calculations. Pt(+) cations are formed by laser ablation and exposed to controlled amounts of CH4/CD4 leading to [Pt,xC,(4x-2)H/D](+) dehydrogenation products. Irradiation of these products in the 400-2100 cm(-1) range leads to CH4/CD4 loss from the x = 3 and 4 products, whereas PtCH2(+)/PtCD2(+) products do not decompose at all, and x = 2 products dissociate only when formed from a higher order product. The structures of these complexes were explored theoretically at several levels of theory with three different basis sets. Comparison of the experimental and theoretical results indicate that the species formed have a Pt(CH3)2(+)(CH4)x-2/Pt(CD3)2(+)(CD4)x-2 binding motif for x = 2-4. Thus, reaction of Pt(+) with methane occurs by C-H bond activation to form PtCH2(+), which reacts with an additional methane molecule by C-H bond activation to form the platinum dimethyl cation. This proposed reaction mechanism is consistent with theoretical explorations of the potential energy surface for reactions of Pt(+) with one and two methane molecules.

  11. The Effect of Ti on Microstructural Characteristics and Reaction Mechanism in Bonding of Al-Ceramic Composite (United States)

    Juan, Li; Kehong, Wang; Deku, Zhang


    The effect of Ti on microstructural characteristics and reaction mechanism in bonding of Al-Ceramic composite was studied. Ti and Al-Ceramic composite were diffusion welded at 550, 600, 700, 800, and 900 °C in a vacuum furnace. The microstructures and compositions of the interface layers were analyzed, and the mechanical properties and fracture morphology of the joints were examined. The results indicated that there was a systematic switch from Ti/Ti7Al5Si12/composite at 600 °C and Ti/TiAl3/Ti7Al5Si12/composite at 700 °C to Ti/Ti7Al5Si12/TiAl3/Ti7Al5Si12/composite at 800 °C and Ti/Ti7Al5Si12/TiAl3/composite at 900 °C. The formation of TiAl3 at 700 and 800 °C depended on Al segregation, which was an uphill diffusion driven by chemical potential. The maximum shear strength was 40.9 MPa, found in the joint welded at 700 °C. Most joints fractured between Ti7Al5Si12 and Al-Ceramic composite. In any case, Ti7Al5Si12 was favorable for Al-Ceramic composite welding, which attached to Al-Ceramic composite, reducing the differences in physiochemical properties between SiC and metal, improving the mechanical properties of the joints and increasing the surface wettability of Al-Ceramic composite.

  12. A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Lyubimov, Artem Y. [Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Sinsheimer Laboratories, 1156 High Street, Santa Cruz, CA 95064 (United States); Chen, Lin; Sampson, Nicole S. [Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400 (United States); Vrielink, Alice, E-mail: [School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 (Australia); Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Sinsheimer Laboratories, 1156 High Street, Santa Cruz, CA 95064 (United States)


    The importance of active-site electrostatics for oxidative and reductive half-reactions in a redox flavoenzyme (cholesterol oxidase) have been investigated by a combination of biochemistry and atomic resolution crystallography. A detailed examination of active-site dynamics demonstrates that the oxidation of substrate and the re-oxidation of the flavin cofactor by molecular oxygen are linked by a single active-site asparagine. Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3β-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH⋯π interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k{sub cat}. Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 Å resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH⋯π interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.

  13. Protein and peptide alkoxyl radicals can give rise to C-terminal decarboxylation and backbone cleavage

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan


    when the free amino acid does not, and that hydroperoxides can be formed on both the backbone (at alpha-carbon positions) and the side chain. Decomposition of alpha-carbon hydroperoxides by Fe(II)-EDTA gives initially an alkoxyl radical via a pseudo-Fenton reaction; these radicals fragment rapidly...... with k estimated as > or = 10(7) s(-1). With N-acetyl amino acids and dipeptides beta-scission of an alkoxyl radical at the C-terminal alpha-carbon results in C-terminal decarboxylation, with release of CO2.-; the corresponding amides undergo deamidation with release of .C(O)NH2. Cyclic dipeptides...... undergo analogous reactions with cleavage of the alpha-carbon to carbonyl-carbon bond and formation of .C(O)NHR radicals. With substrates with large aliphatic side chains, radicals from side-chain hydroperoxides are also observed. C-terminal decarboxylation and backbone fragmentation are also observed...

  14. Metal compound-mediated hydrolytic cleavage of oxidized insulin B chain: Regioselectivity and influence of peptide secondary structure

    Institute of Scientific and Technical Information of China (English)

    罗雪梅; 何卫江; 张宇; 郭子建; 朱龙根


    The interaction of oxidized insulin B chain (B) with cis-[Pd-(en) Cl2] (en= ethylendiamine), cis-[Pd-(dtco-3-OH)Cl2](dtc o-3-OH= dithiacyclooctan-3-ol) and CuCl2 was studied by electrospray mass spectrometry. It is discovered that the binding of Pd(Ⅱ) complexes and the sites of cleavage are highly dependent on the secondary structure and local e nvironment of B. The hydrolytic cleavage of denatured B by Pd (Ⅱ) complexes was monitored by HPLC. The reaction is regioselective and follows first order kinetics with half-life of 4.8 days at 40°C. Two a mide bonds, i.e. at Leu6-Cys7 and at Gly8-Ser9, which are close to the two potential Pd(Ⅱ) binding sites His5 and His10, are selectively cleaved. In the case of Cu(Ⅱ) ion as promoter, only one cleavage site was observed which is located at Gly8-Ser9 bond. These results provide improved understanding on the deign of artificial metallopeptidase.

  15. Hydrogen bonding between the QB site ubisemiquinone and Ser-L223 in the bacterial reaction centre – a combined spectroscopic and computational perspective^ (United States)

    Martin, Erik; Baldansuren, Amgalanbaatar; Lin, Tzu-Jen; Samoilova, Rimma I.; Wraight, Colin A.; Dikanov, Sergei A.; O’Malley, Patrick J.


    In the QB site of the Rba. sphaeroides photosynthetic reaction centre the donation of a hydrogen bond from the hydroxyl group of Ser-L223 to the ubisemiquinone formed after the first flash is debatable. In this study we use a combination of spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations to comprehensively explore this topic. We show that ENDOR, ESEEM and HYSCORE spectroscopic differences between the mutant L223SA and the wild type sample (WT) are negligible, indicating only minor perturbations in the ubisemiquinone spin density for the mutant sample. Qualitatively this suggests that a strong hydrogen bond does not exist in the WT between the Ser-L223 hydroxyl group and the semiquinone O1 atom, as removal of this hydrogen bond in the mutant should cause a significant redistribution of spin density in the semiquinone. We show quantitatively, using QM/MM calculations, that a WT model in which the Ser-L223 hydroxyl group is rotated to prevent hydrogen bond formation with the O1 atom of the semiquinone predicts negligible change for the L223SA mutant. This, together with the better agreement between key QM/MM calculated and experimental hyperfine couplings for the non-hydrogen bonded model, leads us to conclude that no strong hydrogen bond is formed between the Ser-L223 hydroxyl group and the semiquinone O1 atom after the first flash. The implications of this finding for quinone reduction in photosynthetic reaction centres are discussed. PMID:23016832

  16. Alkali metal control over N-N cleavage in iron complexes. (United States)

    Grubel, Katarzyna; Brennessel, William W; Mercado, Brandon Q; Holland, Patrick L


    Though N2 cleavage on K-promoted Fe surfaces is important in the large-scale Haber-Bosch process, there is still ambiguity about the number of Fe atoms involved during the N-N cleaving step and the interactions responsible for the promoting ability of K. This work explores a molecular Fe system for N2 reduction, particularly focusing on the differences in the results obtained using different alkali metals as reductants (Na, K, Rb, Cs). The products of these reactions feature new types of Fe-N2 and Fe-nitride cores. Surprisingly, adding more equivalents of reductant to the system gives a product in which the N-N bond is not cleaved, indicating that the reducing power is not the most important factor that determines the extent of N2 activation. On the other hand, the results suggest that the size of the alkali metal cation can control the number of Fe atoms that can approach N2, which in turn controls the ability to achieve N2 cleavage. The accumulated results indicate that cleaving the triple N-N bond to nitrides is facilitated by simultaneous approach of least three low-valent Fe atoms to a single molecule of N2.

  17. Non-innocent additives in a palladium(II)-catalyzed C-H bond activation reaction: insights into multimetallic active catalysts. (United States)

    Anand, Megha; Sunoj, Raghavan B; Schaefer, Henry F


    The role of a widely employed additive (AgOAc) in a palladium acetate-catalyzed ortho-C-H bond activation reaction has been examined using the M06 density functional theory. A new hetero-bimetallic Pd-(μ-OAc)3-Ag is identified as the most likely active species. This finding could have far-reaching implications with respect to the notion of the active species in palladium catalysis in the presence of other metal salt additives.

  18. Rh-Catalyzed Decarbonylation of Conjugated Ynones via Carbon–Alkyne Bond Activation: Reaction Scope and Mechanistic Exploration via DFT Calculations (United States)

    Dermenci, Alpay; Whittaker, Rachel E.; Gao, Yang; Cruz, Faben A.; Yu, Zhi-Xiang; Dong, Guangbin


    In this full article, detailed development of a catalytic decarbonylation of conjugated monoynones to synthesize disubstituted alkynes is described. The reaction scope and limitation has been thoroughly investigated, and a broad range of functional groups including heterocycles were compatible under the catalytic conditions. Mechanistic exploration via DFT calculations has also been executed. Through the computational study, a proposed catalytic mechanism has been carefully evaluated. These efforts are expected to serve as an important exploratory study for developing catalytic alkyne-transfer reactions via carbon−alkyne bond activation. PMID:26229587

  19. Pd-catalyzed autotandem C-C/C-C bond-forming reactions with tosylhydrazones: synthesis of spirocycles with extended π-conjugation. (United States)

    Barroso, Raquel; Valencia, Rocío A; Cabal, María-Paz; Valdés, Carlos


    A new Pd-catalyzed autotandem process is presented by the reaction of tosylhydrazones of cyclic ketones and 2,2'-dibromobiphenyls and related systems. The process involves cross-coupling with tosylhydrazone followed by an intramolecular Heck reaction and gives rise to spirocyclic structures. Noteworthy, two C-CAr bonds are formed on the hydrazonic carbon during the process. Depending on the starting dibromide, an array of spirofluorenes, spirodibenzofluorenes, spiroacridines, and spiroanthracenes have been prepared. Thus, this methodology may be applied for the preparation of interesting structures useful in the development of optoelectronic materials.

  20. The origin of enantioselectivity in the l-threonine-derived phosphine-sulfonamide catalyzed aza-Morita-Baylis-Hillman reaction: Effects of the intramolecular hydrogen bonding

    KAUST Repository

    Lee, Richmond


    l-Threonine-derived phosphine-sulfonamide 4 was identified as the most efficient catalyst to promote enantioselective aza-Morita-Baylis-Hillman (MBH) reactions, affording the desired aza-MBH adducts with excellent enantioselectivities. Density functional theory (DFT) studies were carried out to elucidate the origin of the observed enantioselectivity. The importance of the intramolecular N-H⋯O hydrogen-bonding interaction between the sulfonamide and enolate groups was identified to be crucial in inducing a high degree of stereochemical control in both the enolate addition to imine and the subsequent proton transfer step, affording aza-MBH reactions with excellent enantioselectivity. © 2013 The Royal Society of Chemistry.

  1. Density Functional Studies of the Reaction of Ytterbium Monocation with Fluoromethane: C-F Bond Activation and Electron-Transfer Reactivity

    Institute of Scientific and Technical Information of China (English)


    The potential energy surface and reaction mechanism corresponding to the reaction of ytterbium monocation with fluoromethane,which represents a prototype of the activation of C-F bond in fluorohydrocarbons by bare lanthanide cations,have been investigated for the first time by using density functional theory.A direct fluorine abstraction mechanism was revealed,and the related thermochemistry data were determined.The electron-transfer reactivity of the reaction was analyzed using the two-state model,and a strongly avoided crossing behavior on the transition state region was shown.The present results support the reaction mechanism inferred from early experimental data and the related thermochemistry data can provide a guide for further experimental researches.

  2. Chromium(VI) reduction by catechol(amine)s results in DNA cleavage in vitro

    DEFF Research Database (Denmark)

    Pattison, D I; Davies, Michael Jonathan; Levina, A;


    ) or 4-tert-butylcatechol (5) do not damage DNA. The Cr(VI)/catechol(amine) reactions have been studied at low added H(2)O(2) concentrations, which lead to enhanced DNA cleavage with 1 and induce DNA cleavage with 4. The Cr(V) and organic intermediates generated by the reactions of Cr(VI) with 1 or 4...

  3. Functionalization of N2 to NH3 via direct N ≡ N bond cleavage using M(III)(NMe2)3 (M=W/Mo): A theoretical study

    Indian Academy of Sciences (India)

    Sambath Baskaran; Perumal Balu; Chinnappan Sivasankar


    Atmospheric N2 can be cleaved directly to yield metal-nitride (before proceeding to the functionalization of N of coordinated N2) and subsequently functionalized to ammonia using M(III)(NMe2)3 (M = W/Mo) as a catalyst, and suitable proton and electron sources. The calculated energies of thermodynamic and kinetic states of the various intermediates and transition states in the reaction coordinate to yield ammonia confirmed the viability of the proposed reaction pathway. Rationale of different pathways have been examined and discussed in detail. Changes in the structural features of the catalyst and some important intermediates and transition states have also been examined.

  4. Role of cluster size and substrate in the gas phase CC bond coupling reactions of allyl halides mediated by Agn+ and Agn-1H+ cluster cations (United States)

    Wang, Farrah Qiuyun; Khairallah, George N.; O'Hair, Richard A. J.


    Previous studies have demonstrated that the silver hydride cluster cation Ag4H+ promotes CC bond coupling of allylbromide [G.N. Khairallah, R.A.J. O'Hair, Angewandte Chemie International Edition 44 (2005) 728]. Here the influence of both the nature and the size of the silver cluster cation and the substrate on CC bond coupling are examined. Thus each of the cations Ag2H+, Ag4H+, Ag3+, and Ag5+ were allowed to react with three different halides: allyl chloride, allyl bromide and allyl iodide. No CC bond coupling is observed in the reactions of the cluster cations with allyl chloride. There are four main reaction sequences that result in CC bond coupling for allyl bromide and allyl iodide mediated by Agn+ and Agn-1H+ clusters: (i) A sequence involving the reactions of silver cluster cations with two molecules of C3H5X: Agn+ --> Agn(C3H5X)+ --> AgnX2+. This only occurs in the cases of: n = 3 and X = I; n = 5 and X = Br. (ii) A sequence involving the reactions of silver cluster cations with two molecules of C3H5X via an organometallic intermediate: Agn+ --> Agn-1(C3H5)+ --> Agn-1X+. This only occurs in the cases of: n = 5 and X = Br and I. (iii) A sequence involving the reactions of silver hydride cluster cations with three molecules of C3H5X: Agn-1H+ --> Agn-1X+ --> Agn-1X(C3H5X)+ --> Ag(C3H5)2+ and Agn-1X3+. This only occurs in the cases of: n = 5 and X = Br and I. (iv) A sequence involving the reactions of silver hydride cluster cations with three molecules of C3H5X via an organometallic intermediate: Agn-1H+ --> Agn-1X+ --> Agn-3(C3H5)+ --> Ag(C3H5)2+ and Agn-3X+. This only occurs in the cases of: n = 5 and X = I.

  5. Design and synthesis of quasi-diastereomeric molecules with unchanging central, regenerating axial and switchable helical chirality via cleavage and formation of Ni(II–O and Ni(II–N coordination bonds

    Directory of Open Access Journals (Sweden)

    Vadim A. Soloshonok


    Full Text Available We describe herein the design and synthesis of asymmetric, pentadentate ligands, which are able to coordinate to Ni(II cations leading to quasi-diastereomeric complexes displaying two new elements of chirality: stereogenic axis and helix along with configurational stabilization of the stereogenic center on the nitrogen. Due to the stereocongested structural characteristics of the corresponding Ni(II complexes, the formation of quasi-diastereomeric products is highly stereoselective providing formation of only two, (Ra*,Mh*,Rc* and (Ra*,Ph*,Rc*, out of the four possible stereochemical combinations. The reversible quasi-diastereomeric transformation between the products (Ra*,Mh*,Rc* and (Ra*,Ph*,Rc* occurs by intramolecular trans-coordination of Ni–NH and Ni–O bonds providing a basis for a chiral switch model.

  6. Reactions of the cumyloxyl and benzyloxyl radicals with tertiary amides. Hydrogen abstraction selectivity and the role of specific substrate-radical hydrogen bonding. (United States)

    Salamone, Michela; Milan, Michela; DiLabio, Gino A; Bietti, Massimo


    A time-resolved kinetic study in acetonitrile and a theoretical investigation of hydrogen abstraction reactions from N,N-dimethylformamide (DMF) and N,N-dimethylacetamide (DMA) by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out. CumO(•) reacts with both substrates by direct hydrogen abstraction. With DMF, abstraction occurs from the formyl and N-methyl C-H bonds, with the formyl being the preferred abstraction site, as indicated by the measured kH/kD ratios and by theory. With DMA, abstraction preferentially occurs from the N-methyl groups, whereas abstraction from the acetyl group represents a minor pathway, in line with the computed C-H BDEs and the kH/kD ratios. The reactions of BnO(•) with both substrates were best described by the rate-limiting formation of hydrogen-bonded prereaction complexes between the BnO(•) α-C-H and the amide oxygen, followed by intramolecular hydrogen abstraction. This mechanism is consistent with the very large increases in reactivity measured on going from CumO(•) to BnO(•) and with the observation of kH/kD ratios close to unity in the reactions of BnO(•). Our modeling supports the different mechanisms proposed for the reactions of CumO(•) and BnO(•) and the importance of specific substrate/radical hydrogen bond interactions, moreover providing information on the hydrogen abstraction selectivity.

  7. Structure and Reactivity of Homocysteine Radical Cation in the Gas Phase Studied by Ion-Molecule Reactions and Infrared Multiple Photon Dissociation

    NARCIS (Netherlands)

    Osburn, S.; Burgie, T.; G. Berden,; Oomens, J.; O' Hair, R. A. J.; Ryzhov, V.


    The reactivity of the cysteine (Cys) and homocysteine (Hcy) radical cation was studied using ion molecule reactions. The radical cations were generated via collision-induced dissociation (CID) of their S-nitrosylated precursors. Cleavage of the S-NO bond led to the formation of the radical initially

  8. Kinetic solvent effects on hydrogen abstraction reactions from carbon by the cumyloxyl radical. The importance of solvent hydrogen-bond interactions with the substrate and the abstracting radical. (United States)

    Salamone, Michela; Giammarioli, Ilaria; Bietti, Massimo


    A kinetic study of the hydrogen atom abstraction reactions from propanal (PA) and 2,2-dimethylpropanal (DMPA) by the cumyloxyl radical (CumO•) has been carried out in different solvents (benzene, PhCl, MeCN, t-BuOH, MeOH, and TFE). The corresponding reactions of the benzyloxyl radical (BnO•) have been studied in MeCN. The reaction of CumO• with 1,4-cyclohexadiene (CHD) also has been investigated in TFE solution. With CHD a 3-fold increase in rate constant (k(H)) has been observed on going from benzene, PhCl, and MeCN to TFE. This represents the first observation of a sizable kinetic solvent effect for hydrogen atom abstraction reactions from hydrocarbons by alkoxyl radicals and indicates that strong HBD solvents influence the hydrogen abstraction reactivity of CumO•. With PA and DMPA a significant decrease in k(H) has been observed on going from benzene and PhCl to MeOH and TFE, indicative of hydrogen-bond interactions between the carbonyl lone pair and the solvent in the transition state. The similar k(H) values observed for the reactions of the aldehydes in MeOH and TFE point toward differential hydrogen bond interactions of the latter solvent with the substrate and the radical in the transition state. The small reactivity ratios observed for the reactions of CumO• and BnO• with PA and DMPA (k(H)(BnO•)/k(H)(CumO•) = 1.2 and 1.6, respectively) indicate that with these substrates alkoxyl radical sterics play a minor role.

  9. Computational Study of Bond Dissociation Enthalpies for Lignin Model Compounds. Substituent Effects in Phenethyl Phenyl Ethers

    Energy Technology Data Exchange (ETDEWEB)

    Beste, Ariana [ORNL; Buchanan III, A C [ORNL


    Lignin is an abundant natural resource that is a potential source of valuable chemicals. Improved understanding of the pyrolysis of lignin occurs through the study of model compounds for which phenethyl phenyl ether (PhCH2CH2OPh, PPE) is the simplest example representing the dominant -O-4 ether linkage. The initial step in the thermal decomposition of PPE is the homolytic cleavage of the oxygen-carbon bond. The rate of this key step will depend on the bond dissociation enthalpy, which in turn will depend on the nature and location of relevant substituents. We used modern density functional methods to calculate the oxygen-carbon bond dissociation enthalpies for PPE and several oxygen substituted derivatives. Since carbon-carbon bond cleavage in PPE could be a competitive initial reaction under high temperature pyrolysis conditions, we also calculated substituent effects on these bond dissociation enthalpies. We found that the oxygen-carbon bond dissociation enthalpy is substantially lowered by oxygen substituents situated at the phenyl ring adjacent to the ether oxygen. On the other hand, the carbon-carbon bond dissociation enthalpy shows little variation with different substitution patterns on either phenyl ring.

  10. Symmetrical P4 cleavage at cobalt: characterization of intermediates on the way from P4 to coordinated P2 units. (United States)

    Dürr, Simon; Ertler, Daniel; Radius, Udo


    Degradation of white phosphorus (P(4)) in the coordination sphere of transition metals is commonly divided into two major pathways depending on the P(x) ligands obtained. Consecutive metal-assisted P-P bond cleavage of four bonds of the P(4) tetrahedron leads to complexes featuring two P(2) ligands (symmetric cleavage) or one P(3) and one P(1) ligand (asymmetric cleavage). A systematic investigation of the degradation of white phosphorus P(4) to coordinated μ,η(2:2)-bridging diphosphorus ligands in the coordination sphere of cobalt is presented herein as well as isolation of each of the decisive intermediates on the reaction pathway. The olefin complex [Cp*Co((i)Pr(2)Im)(η(2)-C(2)H(4))], 1 (Cp* = η(5)-C(5)Me(5), (i)Pr(2)Im = 1,3-di-isopropylimidazolin-2-ylidene), reacts with P(4) to give [Cp*Co((i)Pr(2)Im)(η(2)-P(4))], 2, the insertion product of [Cp*Co((i)Pr(2)Im)] into one of the P-P bonds. Addition of a further equivalent of the Co(I) complex [Cp*Co((i)Pr(2)Im)(η(2)-C(2)H(4))], 1, induces cleavage of a second P-P bond to yield the dinuclear complex [{Cp*Co((i)Pr(2)Im)}(2)(μ,η(2:2)-P(4))], 3, in which a kinked cyclo-P(4)(4-) ligand bridges two cobalt atoms. Consecutive dissociation of the N-heterocyclic carbene with concomitant rearrangement of the cyclo-P(4) ligand and P-P dissociation leads to complexes [Cp*Co(μ,η(4:2)-P(4))Co((i)Pr(2)Im)Cp*], 4, featuring a P(4) chain, and [{Cp*Co(μ,η(2:2)-P(2))}(2)], 5, in which two isolated P(2)(2-) ligands bridge two [Cp*Co] fragments. Each of these reactions is quantitative if performed on an NMR scale, and each compound can be isolated in high yields and large quantities.

  11. Hydrogen atom abstraction reactions from tertiary amines by benzyloxyl and cumyloxyl radicals: influence of structure on the rate-determining formation of a hydrogen-bonded prereaction complex. (United States)

    Salamone, Michela; DiLabio, Gino A; Bietti, Massimo


    A time-resolved kinetic study on the hydrogen atom abstraction reactions from a series of tertiary amines by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out. With the sterically hindered triisobutylamine, comparable hydrogen atom abstraction rate constants (k(H)) were measured for the two radicals (k(H)(BnO(•))/k(H)(CumO(•)) = 2.8), and the reactions were described as direct hydrogen atom abstractions. With the other amines, increases in k(H)(BnO(•))/k(H)(CumO(•)) ratios of 13 to 2027 times were observed. k(H) approaches the diffusion limit in the reactions between BnO(•) and unhindered cyclic and bicyiclic amines, whereas a decrease in reactivity is observed with acyclic amines and with the hindered cyclic amine 1,2,2,6,6-pentamethylpiperidine. These results provide additional support to our hypothesis that the reaction proceeds through the rate-determining formation of a C-H/N hydrogen-bonded prereaction complex between the benzyloxyl α-C-H and the nitrogen lone pair wherein hydrogen atom abstraction occurs, and demonstrate the important role of amine structure on the overall reaction mechanism. Additional mechanistic information in support of this picture is obtained from the study of the reactions of the amines with a deuterated benzyloxyl radical (PhCD(2)O(•), BnO(•)-d(2)) and the 3,5-di-tert-butylbenzyloxyl radical.

  12. Wire bonding in microelectronics

    CERN Document Server

    Harman, George G


    Wire Bonding in Microelectronics, Third Edition, has been thoroughly revised to help you meet the challenges of today's small-scale and fine-pitch microelectronics. This authoritative guide covers every aspect of designing, manufacturing, and evaluating wire bonds engineered with cutting-edge techniques. In addition to gaining a full grasp of bonding technology, you'll learn how to create reliable bonds at exceedingly high yields, test wire bonds, solve common bonding problems, implement molecular cleaning methods, and much more. Coverage includes: Ultrasonic bonding systems and technologies, including high-frequency systems Bonding wire metallurgy and characteristics, including copper wire Wire bond testing Gold-aluminum intermetallic compounds and other interface reactions Gold and nickel-based bond pad plating materials and problems Cleaning to improve bondability and reliability Mechanical problems in wire bonding High-yield, fine-pitch, specialized-looping, soft-substrate, and extreme-temperature wire bo...

  13. Peptide bond formation through gas-phase reactions in the interstellar medium: formamide and acetamide as prototypes

    Energy Technology Data Exchange (ETDEWEB)

    Redondo, Pilar; Barrientos, Carmen; Largo, Antonio, E-mail: [Computational Chemistry Group, Departamento de Química Física, Facultad de Ciencias, Universidad de Valladolid, E-47011 Valladolid (Spain)


    A theoretical study of the reactions of NH{sub 4}{sup +} with formaldehyde and CH{sub 5}{sup +} with formamide is carried out. The viability of these gas-phase ion-molecule reactions as possible sources of formamide and acetamide under the conditions of interstellar medium is evaluated. We report a theoretical estimation of the reaction enthalpies and an analysis of their potential energy surfaces. Formation of protonated formamide from the reaction between ammonium cation and formaldehyde is an exothermic process, but all the channels located on the potential energy surface leading to this product present net activation energies. For the reaction between methanium and formamide, different products are possible from a thermodynamic point of view. An analysis of its potential energy surface showed that formation of protonated acetamide and amino acetaldehyde takes place through barrier-free paths. Therefore, this reaction could be a feasible source of acetamide and amino acetaldehyde in space.

  14. Experimental and theoretical evaluation of the reactions leading to formation of internal double bonds in suspension PVC

    NARCIS (Netherlands)

    Purmova, Jindra; Pauwels, Kim F. D.; Agostini, Michela; Bruinsma, Maarten; Vorenkamp, Eltio J.; Schouten, Arend J.; Coote, Michelle L.


    The number of internal double bonds in poly(vinyl chloride) (PVC) samples was studied as a function of molecular weight at various monomer conversions. These defect structures were found to exhibit end-group-like characteristics: their concentration per chain was largely constant as a function of mo

  15. Surfaces. [characterization of surface properties for predicting bond quality (United States)

    Buckley, D. H.


    Techniques for the characterization of surface cleanliness and roughness for predicting the quality of an adhesive bond are outlined. Generally, smooth surfaces are only available from cleavage of crystalline materials along a natural cleavage plane. Films must be deposited on metal surfaces to achieve the same smoothness. Once the surfaces are clean, however, reaction with the ambient atmosphere becomes likely through diffusive and absorption processes, producing asperities. Electron diffraction, Auger electron, and X ray emission spectroscopy are used to characterize surface condition. Once the surface is observed to be clean, the application of an adhesive will usually prohibit separation along the adhesive; separation is then confined to the weaker of the two materials. Finally, the use of polytetrafluorothylene adhesive to test the adhesion between polymers and metal surfaces is described.

  16. Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure, phosphate activation and montmorillonite composition on phosphodiester bond formation (United States)

    Ferris, James P.; KAMALUDDIN; Ertem, Gozen


    The 2(prime)-d-5(prime)-GMP and 2(prime)-d-5(prime)-AMP bind 2 times more strongly to montmorillonite 22A than do 2(prime)-d-5(prime)-CMP and 5(prime)-TMP. The dinucleotide d(pG)2 forms in 9.2 percent yield and the cyclic dinucleotide c(dpG)2 in 5.4 percent yield in the reaction of 2(prime)-d-5(prime)-GMP with EDAC in the presence of montmorillonite 22A. The yield of dimers which contain the phosphodiester bond decreases as the reaction medium is changed from 0.2 M NaCl to a mixture of 0.2 M NaCl and 0.075 M MgCl2. A low yield of d(pA)2 was observed in the condensation reaction of 5(prime)-ImdpA on montmorillonite 22A. The yield of d(pA)2 obtained when EDAC is used as the condensing agent increases with increasing iron content of the Na(+)-montmorillonite used as catalyst. Evidence is presented which shows that the acidity of the Na(+)-montmorillonite is a necessary but not sufficient factor for the montmorillonite catalysis of phosphodiester bond formation.

  17. Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity. (United States)

    Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G


    In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.

  18. Identification of an imino group indispensable for cleavage by a small ribozyme. (United States)

    Spitale, Robert C; Volpini, Rosaria; Heller, Moriah G; Krucinska, Jolanta; Cristalli, Gloria; Wedekind, Joseph E


    The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.

  19. Copper-Catalyzed Carbenoid Insertion Reactions of α-Diazoesters and α-Diazoketones into Si-H and S-H Bonds. (United States)

    Keipour, Hoda; Jalba, Angela; Delage-Laurin, Léo; Ollevier, Thierry


    An efficient copper-catalyzed carbenoid insertion reaction of α-diazo carbonyl compounds into Si-H and S-H bonds was developed. A wide range of α-silylesters and α-thioesters was obtained in high yields (up to 98%) from α-diazoesters using 5 mol % of a simple copper(I) salt as catalyst. Using 0.05 mol % of the same catalyst, α-diazoketones led to α-silylketones in low to good yields (up to 70%).

  20. The new C-C bond formation in the reaction of o-amidophenolate indium(III) complex with alkyl iodides. (United States)

    Piskunov, Alexandr V; Meshcheryakova, Irina N; Fukin, Georgy K; Shavyrin, Andrei S; Cherkasov, Vladimir K; Abakumov, Gleb A


    The reaction of bis(4,6-di-tert-butyl-N-(2,6-di-iso-propylphenyl)-o-amidophenolato)indium(III) anion with alkyl iodides is reported. This process includes oxidative addition of two RI (R = Me, Et) molecules to the non-transition metal complex and results in an alkyl transfer to ring carbon atoms with the formation of two new C-C bonds. The interaction proceeds at mild conditions and gives new indium(III) derivatives containing iminocyclohexa-1,4-dienolate type ligands.

  1. Redox control and hydrogen bonding networks: proton-coupled electron transfer reactions and tyrosine Z in the photosynthetic oxygen-evolving complex. (United States)

    Keough, James M; Zuniga, Ashley N; Jenson, David L; Barry, Bridgette A


    In photosynthetic oxygen evolution, redox active tyrosine Z (YZ) plays an essential role in proton-coupled electron transfer (PCET) reactions. Four sequential photooxidation reactions are necessary to produce oxygen at a Mn(4)CaO(5) cluster. The sequentially oxidized states of this oxygen-evolving cluster (OEC) are called the S(n) states, where n refers to the number of oxidizing equivalents stored. The neutral radical, YZ•, is generated and then acts as an electron transfer intermediate during each S state transition. In the X-ray structure, YZ, Tyr161 of the D1 subunit, is involved in an extensive hydrogen bonding network, which includes calcium-bound water. In electron paramagnetic resonance experiments, we measured the YZ• recombination rate, in the presence of an intact Mn(4)CaO(5) cluster. We compared the S(0) and S(2) states, which differ in Mn oxidation state, and found a significant difference in the YZ• decay rate (t(1/2) = 3.3 ± 0.3 s in S(0); t(1/2) = 2.1 ± 0.3 s in S(2)) and in the solvent isotope effect (SIE) on the reaction (1.3 ± 0.3 in S(0); 2.1 ± 0.3 in S(2)). Although the YZ site is known to be solvent accessible, the recombination rate and SIE were pH independent in both S states. To define the origin of these effects, we measured the YZ• recombination rate in the presence of ammonia, which inhibits oxygen evolution and disrupts the hydrogen bond network. We report that ammonia dramatically slowed the YZ• recombination rate in the S(2) state but had a smaller effect in the S(0) state. In contrast, ammonia had no significant effect on YD•, the stable tyrosyl radical. Therefore, the alterations in YZ• decay, observed with S state advancement, are attributed to alterations in OEC hydrogen bonding and consequent differences in the YZ midpoint potential/pK(a). These changes may be caused by activation of metal-bound water molecules, which hydrogen bond to YZ. These observations document the importance of redox control in proton

  2. Ultrafast infrared studies of chemical reaction dynamics in room-temperature liquids

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Haw [Univ. of California, Berkeley, CA (United States)


    Femtosecond infrared spectroscopy provides sufficient spectral and temporal resolution to support a detailed investigation of the early events of a photochemical reaction. Previously unreported transient species that arise as intermediates during the course of a reaction may have lifetimes that are too short for conventional characterization. For these species, quantum-mechanical (density functional theoretical and ab initio) electronic structure calculations provide invaluable insight into chemical properties including molecular structure and energetic. With the combination of experimental and theoretical results, it is possible to assemble a comprehensive picture of the reaction dynamics of a system that is intricately influenced by the surrounding solvent molecules. The mechanisms of several important organometallic reactions, such as alkane C– H bond activation by η3-Tp*Rh(CO), silane Si–H bond activation by η5-CpMn(CO)2 and η5-CpRe(CO)2, as well as chlorinated methane C–Cl bond cleavage by the Re(CO)5 radical are elucidated. The results demonstrate the importance of molecular morphology change (C–H and Si–H act ivat ion), solvent rearrangement (Si–H activation), intersystem crossing (Si–H activation), and solvent caging (C–Cl cleavage) in understanding the reactivity of the organometallic species, The nature of the apparent free-energy barrier for C–H, Si–H, and C–Cl bond activation reaction is found to be- cleavage of an alkane C–H bond, rearrangement of a silane molecule HSiR3 (R = alkyl group) from a nonreactive alkyl site to the reactive Si–H bond, and Cl atom transfer from a chlorinated methane molecule to Re(CO)5, respectively. These results support previous d initio calculations for C–H and Si–H bond activation reaction profiles which suggest that cleavage of an alkane C–H bond by a transition metal center, unlike that of a silane

  3. Hydrogen atom abstraction selectivity in the reactions of alkylamines with the benzyloxyl and cumyloxyl radicals. The importance of structure and of substrate radical hydrogen bonding. (United States)

    Salamone, Michela; DiLabio, Gino A; Bietti, Massimo


    A time-resolved kinetic study on the hydrogen abstraction reactions from a series of primary and secondary amines by the cumyloxyl (CumO(•)) and benzyloxyl (BnO(•)) radicals was carried out. The results were compared with those obtained previously for the corresponding reactions with tertiary amines. Very different hydrogen abstraction rate constants (k(H)) and intermolecular selectivities were observed for the reactions of the two radicals. With CumO(•), k(H) was observed to decrease on going from the tertiary to the secondary and primary amines. The lowest k(H) values were measured for the reactions with 2,2,6,6-tetramethylpiperidine (TMP) and tert-octylamine (TOA), substrates that can only undergo N-H abstraction. The opposite behavior was observed for the reactions of BnO(•), where the k(H) values increased in the order tertiary < secondary < primary. The k(H) values for the reactions of BnO(•) were in all cases significantly higher than those measured for the corresponding reactions of CumO(•), and no significant difference in reactivity was observed between structurally related substrates that could undergo exclusive α-C-H and N-H abstraction. This different behavior is evidenced by the k(H)(BnO(•))/k(H)(CumO(•)) ratios that range from 55-85 and 267-673 for secondary and primary alkylamines up to 1182 and 3388 for TMP and TOA. The reactions of CumO(•) were described in all cases as direct hydrogen atom abstractions. With BnO(•) the results were interpreted in terms of the rate-determining formation of a hydrogen-bonded prereaction complex between the radical α-C-H and the amine lone pair wherein hydrogen abstraction occurs. Steric effects and amine HBA ability play a major role, whereas the strength of the substrate α-C-H and N-H bonds involved appears to be relatively unimportant. The implications of these different mechanistic pictures are discussed.

  4. Structural and Mechanistic Insights into C-P Bond Hydrolysis by Phosphonoacetate Hydrolase

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Vinayak; Borisova, Svetlana A.; Metcalf, William W.; van der Donk, Wilfred A.; Nair, Satish K. (UIUC)


    Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 {angstrom} resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformate inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.

  5. Site-specifically Hydrolytic Cleavage of Oxidized Insulin B Chain With Cu(II) Ion

    Institute of Scientific and Technical Information of China (English)


    Electrospray mass spectrometry investigation shows that denatured oxidized insulin B chain can be selectively cleaved by simple Cu(II) ion and the site of cleavage is at Gly8-Ser9 bond which is second amide bond left from His 10 in the sequence of oxidized insulin B chain.

  6. Reductive cleavage of nitrite to form terminal uranium mono-oxo complexes. (United States)

    Lewis, Andrew J; Carroll, Patrick J; Schelter, Eric J


    Uranium terminal mono-oxo complexes are prepared with a unique activation of nitrite following reductive cleavage of an N-O bond with loss of nitric oxide. The thermodynamic driving force of U═O bond formation differentiates this reactivity from known mechanisms of nitrite reduction, which are typically mediated by proton transfer. Mechanistic details are explored by DFT supporting a simple homolytic cleavage pathway from a κ(1)-ONO bound intermediate. Complexes of the formula U(VI)OX[N(SiMe(3))(2)](3) are formed providing a trigonal bipyramidal framework into which ligands trans to the U═O bond may be installed.

  7. 4-Dimethylaminoazobenzenes: carcinogenicities and reductive cleavage by microsomal azo reductase. (United States)

    Lambooy, J P; Koffman, B M


    Twenty-four 4-dimethylaminoazobenzenes (DABs) in which systematic structural modifications have been made in the prime ring have been studied for substrate specificity for microsomal azo reductase. The DABs were also evaluated for carcinogenicity and it was found that there was no correlation between carcinogenicity and extent of azo bond cleavage by azo reductase. While any substituent in the prime ring reduces the rate of cleavage of the azo bond relative to the unsubstituted dye, there is a correlation between substituent size and susceptibility to the enzyme. Substituent size was also found to be a significant factor in the induction of hepatomas by the dyes. Preliminary studies have shown that there appears to be a positive correlation between microsomal riboflavin content and the activity of the azo reductase.

  8. Tetrel bond of pseudohalide anions with XH3F (X = C, Si, Ge, and Sn) and its role in SN2 reaction (United States)

    Liu, Mingxiu; Li, Qingzhong; Cheng, Jianbo; Li, Wenzuo; Li, Hai-Bei


    The complexes of XH3F⋯ N3-/OCN-/SCN- (X = C, Si, Ge, and Sn) have been investigated at the MP2/aug-cc-pVTZ(PP) level. The σ-hole of X atom in XH3F acts as a Lewis acid forming a tetrel bond with pseudohalide anions. Interaction energies of these complexes vary from -8 to -50 kcal/mol, mainly depending on the nature of X and pseudohalide anions. Charge transfer from N/O/S lone pair to X-F and X-H σ* orbitals results in the stabilization of these complexes, and the former orbital interaction is responsible for the large elongation of X-F bond length and the remarkable red shift of its stretch vibration. The tetrel bond in the complexes of XH3F (X = Si, Ge, and Sn) exhibits a significant degree of covalency with XH3F distorted significantly in these complexes. A breakdown of the individual forces involved attributes the stability of the interaction to mainly electrostatic energy, with a relatively large contribution from polarization. The transition state structures that connect the two minima for CH3Br⋯ N3-complexhave been localized and characterized. The energetic, geometrical, and topological parameters of the complexes were analyzed in the different stages of the SN2 reaction N3- + CH3Br → Br- + CH3N3.

  9. Breaking down the reactivity of λ(3)-iodanes: the impact of structure and bonding on competing reaction mechanisms. (United States)

    Pinto de Magalhães, Halua; Lüthi, Hans Peter; Togni, Antonio


    The functionalization of arenes via diaryliodonium salts has gained considerable attention in synthesis, as these compounds react under mild conditions. Mechanistic studies have shown that the formation of corresponding λ(3)-iodane intermediates takes a key role, as they determine the course and selectivity of the reaction. Bridged diaryliodonium salts, featuring a heterocyclic moiety involving the iodine atom, were shown to exhibit a distinctly different reactivity, leading to different products. These products are not just the result of reductive elimination reactions but may also arise via radical mechanisms. Our quantum chemical calculations reveal that the λ(3)-iodane intermediate is also the "gateway" for reactions that are observed only for strained bridged systems. At the same time, we find a remarkable affinity of the hypervalent region to planarity for all reaction mechanisms. This also explains the correlation between the size of the bridge connecting the aryl groups and the reaction products observed. Furthermore, the energetics of these competing reactions are examined by analysis of the mechanisms. Finally, using model compounds, some of the basic features governing the reactivity of λ(3)-iodanes are discussed.

  10. Bonds broken and formed during the mixed-linkage glucan : xyloglucan endotransglucosylase reaction catalysed by Equisetum hetero-trans-β-glucanase (United States)

    Simmons, Thomas J.


    Mixed-linkage glucan∶xyloglucan endotransglucosylase (MXE) is one of the three activities of the recently characterised hetero-trans-β-glucanase (HTG), which among land plants is known only from Equisetum species. The biochemical details of the MXE reaction were incompletely understood — details that would promote understanding of MXE's role in vivo and enable its full technological exploitation. We investigated HTG's site of attack on one of its donor substrates, mixed-linkage (1→3),(1→4)-β-d-glucan (MLG), with radioactive oligosaccharides of xyloglucan as the acceptor substrate. Comparing three different MLG preparations, we showed that the enzyme favours those with a high content of cellotetraose blocks. The reaction products were analysed by enzymic digestion, thin-layer chromatography (TLC), high-pressure liquid chromatography (HPLC) and gel-permeation chromatography (GPC). Equisetum HTG consistently cleaved the MLG at the third consecutive β-(1→4)-bond following (towards the reducing terminus) a β-(1→3)-bond. It then formed a β-(1→4)-bond between the MLG and the non-reducing terminal glucose residue of the xyloglucan oligosaccharide, consistent with its xyloglucan endotransglucosylase/hydrolase subfamily membership. Using size-homogeneous barley MLG as the donor substrate, we showed that HTG does not favour any particular region of the MLG chain relative to the polysaccharide's reducing and non-reducing termini; rather, it selects its target cellotetraosyl unit stochastically along the MLG molecule. This work improves our understanding of how enzymes can exhibit promiscuous substrate specificities and provides the foundations to explore strategies for engineering novel substrate specificities into transglycanases. PMID:28108640

  11. A single molecule assay for measuring site-specific DNA cleavage. (United States)

    Gambino, Stefano; Mousley, Briana; Cathcart, Lindsay; Winship, Janelle; Loparo, Joseph J; Price, Allen C


    Sequence-specific DNA cleavage is a key step in a number of genomic transactions. Here, we report a single-molecule technique that allows the simultaneous measurement of hundreds of DNAs, thereby collecting significant statistics in a single experiment. Microbeads are tethered with single DNA molecules in a microfluidic channel. After the DNA cleavage reaction is initiated, the time of cleavage of each DNA is recorded using video microscopy. We demonstrate the utility of our method by measuring the cleavage kinetics of NdeI, a type II restriction endonuclease.

  12. Polymer-pendant ligand chemistry. 1. Reactions of organoarsonic acids and arsenic acid with catechol ligands bonded to polystryene-divinylbenzene and regeneration of the ligand site by a simple hydrolysis procedure

    Energy Technology Data Exchange (ETDEWEB)

    Fish, R.H.; Tannous, R.S.


    A novel method is reported for reactions of organoarsonic acids and arsenic acid, known to be present in oil shale and its pyrolysis products, with catechol ligands bonded to either 2% or 20% cross-linked methylated polystyrene-divinylbenzene (PS-DVB) resins. A previous study with catechol-bonded ligands on PS-DVB resins dealt with their reactions with metal ions in aqueous solution and showed a selectivity toward Hg/sup 2 +/ ions. As far as we have been able to determine, reactions of this polymer-supported ligand with organometallic compounds or inorganic anions have not been reported. 9 references, 2 figures, 1 table.

  13. In Pursuit of an Ideal C-C Bond-Forming Reaction: Development and Applications of the Hydrovinylation of Olefins. (United States)

    Rajanbabu, T V


    Attempts to introduce the highly versatile vinyl group into other organic molecules in a chemo-, regio- and stereoselective fashion via catalytic activation of ethylene provided challenging opportunities to explore new ligand and salt effects in homogeneous catalysis. This review provides a personal account of the development of enantioselective reactions involving ethylene.

  14. Ultrasonic and micromechanical study of damage and elastic properties of SiC/RBSN ceramic composites. [Reaction Bonded Silicon Nitride (United States)

    Chu, Y. C.; Hefetz, M.; Rokhlin, S. I.; Baaklini, G. Y.


    Ultrasonic techniques are employed to develop methods for nondestructive evaluation of elastic properties and damage in SiC/RBSN composites. To incorporate imperfect boundary conditions between fibers and matrix into a micromechanical model, a model of fibers having effective anisotropic properties is introduced. By inverting Hashin's (1979) microstructural model for a composite material with microscopic constituents the effective fiber properties were found from ultrasonic measurements. Ultrasonic measurements indicate that damage due to thermal shock is located near the surface, so the surface wave is most appropriate for estimation of the ultimate strength reduction and critical temperature of thermal shock. It is concluded that bonding between laminates of SiC/RBSN composites is severely weakened by thermal oxidation. Generally, nondestructive evaluation of thermal oxidation effects and thermal shock shows good correlation with measurements previously performed by destructive methods.

  15. Regioselective borylation of the C-H bonds in alkylamines and alkyl ethers. Observation and origin of high reactivity of primary C-H bonds beta to nitrogen and oxygen. (United States)

    Li, Qian; Liskey, Carl W; Hartwig, John F


    Borylation of aliphatic C-H bonds in alkylamines and alkyl ethers to form primary aminoalkyl and alkoxyalkyl boronate esters and studies on the origin of the regioselectivity of these reactions are reported. The products of these reactions can be used directly in Suzuki-Miyaura cross-coupling reactions or isolated as air-stable potassium trifluoroborate salts. Selective borylation of the terminal C-H bond at the positions β to oxygen and nitrogen occurs in preference to borylation of the other terminal C-H bonds. Experimental studies and computational results show that C-H bond cleavage is the rate-determining step of the current borylation reactions. The observed higher reactivity of C-H bonds at the terminal position of ethylamines and ethers results from a combination of attractive Lewis acid-base and hydrogen-bonding interactions, as well as typical repulsive steric interactions, in the transition state. In this transition state, the heteroatom lies directly above the boron atom of one boryl ligand, creating a stabilizing interaction between the weak Lewis acid and Lewis base, and a series of C-H bonds of the substrate lie near the oxygen atoms of the boryl ligands, participating in a set of weak C-H···O interactions that lead to significant stabilization of the transition state forming the major product.

  16. Centralspindlin in Rappaport's cleavage signaling. (United States)

    Mishima, Masanori


    Cleavage furrow in animal cell cytokinesis is formed by cortical constriction driven by contraction of an actomyosin network activated by Rho GTPase. Although the role of the mitotic apparatus in furrow induction has been well established, there remain discussions about the detailed molecular mechanisms of the cleavage signaling. While experiments in large echinoderm embryos highlighted the role of astral microtubules, data in smaller cells indicate the role of central spindle. Centralspindlin is a constitutive heterotetramer of MKLP1 kinesin and the non-motor CYK4 subunit and plays crucial roles in formation of the central spindle and recruitment of the downstream cytokinesis factors including ECT2, the major activator of Rho during cytokinesis, to the site of division. Recent reports have revealed a role of this centralspindlin-ECT2 pathway in furrow induction both by the central spindle and by the astral microtubules. Here, a unified view of the stimulation of cortical contractility by this pathway is discussed. Cytokinesis, the division of the whole cytoplasm, is an essential process for cell proliferation and embryonic development. In animal cells, cytokinesis is executed using a contractile network of actin filaments driven by a myosin-II motor that constricts the cell cortex (cleavage furrow ingression) into a narrow channel between the two daughter cells, which is resolved by scission (abscission) [1-3]. The anaphase-specific organization of the mitotic apparatus (MA, spindle with chromosomes plus asters) positions the cleavage furrow and plays a major role in spatial coupling between mitosis and cytokinesis [4-6]. The nucleus and chromosomes are dispensable for furrow specification [7-10], although they contribute to persistent furrowing and robust completion in some cell types [11,12]. Likewise, centrosomes are not essential for cytokinesis, but they contribute to the general fidelity of cell division [10,13-15]. Here, classical models of cleavage furrow

  17. Reaction pathways of the dissociation of methylal: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Frey, H.-M.; Beaud, P.; Gerber, T.; Mischler, B.; Radi, P.P.; Tzannis, A.-P. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)


    Schemata for modelling combustion processes do not yet include reaction rates for oxygenated fuels like methylal (DMM) which is considered as an additive or replacement for diesel due to its low sooting propensity. Density functional theory (DFT) studies of the possible reaction pathways for different dissociation steps of methylal are presented. Cleavage of a hydrogen bond to the methoxy group or the central carbon atom were simulated at the BLYP/6-311++G{sup **} level of theory. The results are compared to the experiment when dissociating and/or ionising DMM with femtosecond pulses. (author) 1 fig., 1 tab., 1 ref.

  18. Ruthenium(III)/phosphine/pyridine complexes applied in the hydrogenation reactions of polar and apolar double bonds (United States)

    Rodrigues, Claudia; Delolo, Fábio G.; Ferreira, Lucas M.; da S. Maia, Pedro I.; Deflon, Victor M.; Rabeah, Jabor; Brückner, Angelika; Norinder, Jakob; Börner, Armin; Bogado, André L.; Batista, Alzir A.


    In this work, five ruthenium(III) complexes containing phosphine and pyridine based ligands with general formula mer-[RuCl3(dppb)(N)] [where dppb = 1,4-bis(diphenylphosphino)butane and N = pyridine (py), 4-methylpyridine (4-Mepy), 4-vinylpyridine (4-Vpy), 4-tert-butylpyridine (4-tBupy) and 4-phenylpyridine (4-Phpy)] were synthesized and characterized using spectroscopic and electrochemical techniques, as well as magnetic susceptibility to check the paramagnetism of these compounds. These complexes were tested as catalytic precursors in hydrogenation reactions with cyclohexene, undecanal and cyclohexanecarboxaldehyde, as compounds bearing Cdbnd C and Cdbnd O groups. Broad screening was carried out in order to find the optimal reaction conditions with the highest conversion. It was found that by using a ratio of Ru-catalyst/substrate = 1:530 at 80 °C and 15 bar of H2 for 24 h, cyclohexene can be reduced. Hydrogenation of undecanal was possible using a Ru-catalyst/substrate ratio of 1:100 at 160 °C and 100 bar for 24 h, and for the reduction of cyclohexanecarboxaldehyde the reaction conditions were Ru-catalyst/substrate ratio of 1:100 at 160 °C and 50 bar for 24 h.

  19. Thermochemical properties and bond dissociation energies of C3-C5 cycloalkyl hydroperoxides and peroxy radicals: cycloalkyl radical + (3)O2 reaction thermochemistry. (United States)

    Auzmendi-Murua, Itsaso; Bozzelli, Joseph W


    Cyclic aliphatic hydrocarbons are major components in modern fuels; they can be present in the reactants, and they can be formed during the gas-phase oxidation processes. In combustion and thermal oxidation processes, these cyclics will form radicals that react with (3)O(2) to form peroxy radicals. In this study, density functional theory and higher level ab initio calculations are used to calculate thermochemical properties and bond dissociation energies of 3-5-membered cycloalkanes, corresponding hydroperoxides, hydroperoxycycloalkyl radicals, and cycloalkyl radicals that occur in these reaction systems. Geometries, vibration frequencies, and thermochemical properties, ΔH(f 298)°, are calculated with the B3LYP/6-31 g(d,p), B3LYP/6-31 g(2d,2p), composite CBS-QB3, and G3MP2B3 methods. Standard enthalpies of formation at 298 K are evaluated using isodesmic reaction schemes with several work reactions for each species. Group additivity contributions are developed, and application of group additivity with comparison to calculated values is illustrated. Entropy and heat capacities, S°(T) and C(p)°(T) (5 K ≤ T ≤ 5000), are determined using geometric parameters and frequencies from the B3LYP/6-31 g(d,p) calculations.

  20. Synthesis of Bioactive 2-(Arylaminothiazolo[5,4-f]-quinazolin-9-ones via the Hügershoff Reaction or Cu- Catalyzed Intramolecular C-S Bond Formation

    Directory of Open Access Journals (Sweden)

    Damien Hédou


    Full Text Available A library of thirty eight novel thiazolo[5,4-f]quinazolin-9(8H-one derivatives (series 8, 10, 14 and 17 was prepared via the Hügershoff reaction and a Cu catalyzed intramolecular C-S bond formation, helped by microwave-assisted technology when required. The efficient multistep synthesis of the key 6-amino-3-cyclopropylquinazolin-4(3H-one (3 has been reinvestigated and performed on a multigram scale from the starting 5-nitroanthranilic acid. The inhibitory potency of the final products was evaluated against five kinases involved in Alzheimer’s disease and showed that some molecules of the 17 series described in this paper are particularly promising for the development of novel multi-target inhibitors of kinases.

  1. Gadolinium (Gd) Oxide, Carbide, and Carbonyl Cation Bond Energies and Evaluation of the Gd + O → GdO(+) + e(-) Chemi-Ionization Reaction Enthalpy. (United States)

    Demireva, Maria; Kim, JungSoo; Armentrout, P B


    Guided ion beam mass spectrometry (GIBMS) is used to measure the kinetic energy dependent product ion cross sections for reactions of the lanthanide metal gadolinium cation (Gd(+)) with O2, CO2, and CO and for reactions of GdO(+) with CO, O2, and Xe. GdO(+) is formed through barrierless and exothermic processes in the reactions of Gd(+) with O2 and CO2. All other reactions observed are endothermic, and analyses of their kinetic energy dependent cross sections yield 0 K bond dissociation energies (BDEs) for GdO(+), GdC(+), and GdCO(+). The 0 K BDE for GdO(+) is determined from five different reactions to be 7.69 ± 0.10 eV, and this value is combined with literature data to derive the ionization energy (IE) of GdO as 5.82 ± 0.16 eV. Additionally, GdC(+) and GdCO(+) BDEs of 3.18 ± 0.18 eV and 0.65 ± 0.06 eV are obtained from analysis of the Gd(+) reactions with CO and CO2, respectively. Theoretical GdO(+), GdC(+), and GdCO(+) BDEs are calculated for comparison with experiment using various Gd basis sets with an effective core potential and several levels of theory. For calculations that correctly predict a (10)D ground state for Gd(+), good agreement between theoretical and measured GdC(+) and GdCO(+) BDEs is obtained, whereas the GdO(+) BDE is underestimated in these calculations by about 0.8 eV. Additional BDEs for GdO(+) and GdC(+) are calculated using triple- and quadruple-ζ correlation consistent all-electron basis sets for Gd. Calculations with these basis sets provide better agreement with experiment for GdO(+) but not for GdC(+). The measured Gd(+) oxide, carbide, and carbonyl BDEs are similar to those for the group 3 metal ions, Sc(+) and Y(+). This is attributed to similarities in the ground state electronic configurations of these metal ions leading to similar interaction strengths. The experimental GdO(+) BDE measured here combined with the known IE of Gd is used to determine an exothermicity of 1.54 ± 0.10 eV for the Gd chemi-ionization reaction

  2. Free-Radical Triggered Ordered Domino Reaction: An Approach to C-C Bond Formation via Selective Functionalization of α-Hydroxyl-(sp(3))C-H in Fluorinated Alcohols. (United States)

    Xu, Zhengbao; Hang, Zhaojia; Liu, Zhong-Quan


    A free-radical mediated highly ordered radical addition/cyclization/(sp(3))C-C(sp(3)) formation domino reaction is developed. Three new C-C bonds are formed one by one in a mixed system. Furthermore, it represents the first example of cascade C-C bond formation via selective functionalization of α-hydroxyl-C(sp(3))-H in fluorinated alcohols.

  3. Effects of Sm2O3 Content on the Microstructure and Mechanical Properties of Post-Sintered Reaction-Bonded β-SiAlON (United States)

    Li, Yanjun; Liu, Donghua; Zeng, Cunfeng; Shi, Zhongqi; Jin, Zhihao


    β-SiAlON materials were fabricated by a reaction bonding combining post-sintering route using raw materials of Si, Al2O3, AlN, etc. Sm2O3 was used as sintering additive with the content of 0, 2, 4, and 6 wt.%, respectively. The reaction-bonded β-SiAlON (RB-β-SiAlON) were post sintered at 1750 °C for 6 h. XRD results showed that the phase composition of both RB-β-SiAlON and post-sintered RB-β-SiAlON (PSRB-β-SiAlON) was β-SiAlON. For RB-β-SiAlON, the apparent porosity was decreased with the increase of Sm2O3 content, while the bending strength (σf) and Vicker's hardness (HV10) was increased accordingly. After the post-sintering procedure, nearly full densified PSRB-β-SiAlON was obtained and the mechanical properties were significantly improved with the addition of Sm2O3 additive. The σf and HV10 of the PSRB-β-SiAlON (4 wt.% Sm2O3) achieved 520 MPa and 16.4 GPa, respectively, which were as 3.5 and 6.3 times high as those of the corresponding RB-β-SiAlON. The Young's modulus (E) and the fracture toughness (K IC) of the dense PSRB-β-SiAlON were increased with the increase of the Sm2O3 content.

  4. Mutational analysis of bacteriophage T4 RNA ligase 1. Different functional groups are required for the nucleotidyl transfer and phosphodiester bond formation steps of the ligation reaction. (United States)

    Wang, Li Kai; Ho, C Kiong; Pei, Yi; Shuman, Stewart


    T4 RNA ligase 1 (Rnl1) exemplifies an ATP-dependent RNA ligase family that includes fungal tRNA ligase (Trl1) and a putative baculovirus RNA ligase. Rnl1 acts via a covalent enzyme-AMP intermediate generated by attack of Lys-99 N zeta on the alpha phosphorus of ATP. Mutation of Lys-99 abolishes ligase activity. Here we tested the effects of alanine mutations at 19 conserved positions in Rnl1 and thereby identified 9 new residues essential for ligase activity: Arg-54, Lys-75, Phe-77, Gly-102, Lys-119, Glu-227, Gly-228, Lys-240, and Lys-242. Seven of the essential residues are located within counterparts of conserved nucleotidyltransferase motifs I (99KEDG102), Ia (118SK119), IV (227EGYVA231), and V (238HFKIK242) that comprise the active sites of DNA ligases, RNA capping enzymes, and T4 RNA ligase 2. Three other essential residues, Arg-54, Lys-75 and Phe-77, are located upstream of the AMP attachment site within a conserved domain unique to the Rnl1-like ligase family. We infer a shared evolutionary history and active site architecture in Rnl1 (a tRNA repair enzyme) and Trl1 (a tRNA splicing enzyme). We determined structure-activity relationships via conservative substitutions and examined mutational effects on the isolated steps of Rnl1 adenylylation (step 1) and phosphodiester bond formation (step 3). Lys-75, Lys-240, and Lys-242 were found to be essential for step 1 and overall ligation of 5'-phosphorylated RNA but not for phosphodiester bond formation. These results suggest that the composition of the Rnl1 active site is different during steps 1 and 3. Mutations at Arg-54 and Lys-119 abolished the overall RNA ligation reaction without affecting steps 1 and 3. Arg-54 and Lys-119 are thereby implicated as specific catalysts of the RNA adenylation reaction (step 2) of the ligation pathway.

  5. The amide C-N bond of isatins as the directing group and the internal oxidant in Ru-catalyzed C-H activation and annulation reactions: access to 8-amido isocoumarins. (United States)

    Kaishap, Partha Pratim; Sarma, Bipul; Gogoi, Sanjib


    The N-O, N-N and O-O bonds are the frequently used internally oxidative directing groups used in various redox-neutral coupling reactions. The sole use of the C-N bond as the oxidizing directing group was reported recently by Li X. and co-workers for the Rh(iii)-catalyzed C-H activation of phenacyl ammonium salts. Herein, we report the use of the amide C-N bond of isatins as the oxidizing directing group for the Ru(ii)-catalyzed redox-neutral C-H activation and annulation reactions with alkynes which afford 8-amido isocoumarins. The reaction also features excellent regioselectivity with alkyl aryl substituted alkynes.

  6. Reactivity and selectivity patterns in hydrogen atom transfer from amino acid C-H bonds to the cumyloxyl radical: polar effects as a rationale for the preferential reaction at proline residues. (United States)

    Salamone, Michela; Basili, Federica; Bietti, Massimo


    Absolute rate constants for hydrogen atom transfer (HAT) from the C-H bonds of N-Boc-protected amino acids to the cumyloxyl radical (CumO(•)) were measured by laser flash photolysis. With glycine, alanine, valine, norvaline, and tert-leucine, HAT occurs from the α-C-H bonds, and the stability of the α-carbon radical product plays a negligible role. With leucine, HAT from the α- and γ-C-H bonds was observed. The higher kH value measured for proline was explained in terms of polar effects, with HAT that predominantly occurs from the δ-C-H bonds, providing a rationale for the previous observation that proline residues represent favored HAT sites in the reactions of peptides and proteins with (•)OH. Preferential HAT from proline was also observed in the reactions of CumO(•) with the dipeptides N-BocProGlyOH and N-BocGlyGlyOH. The rate constants measured for CumO(•) were compared with the relative rates obtained previously for the corresponding reactions of different hydrogen-abstracting species. The behavior of CumO(•) falls between those observed for the highly reactive radicals Cl(•) and (•)OH and the significantly more stable Br(•). Taken together, these results provide a general framework for the description of the factors that govern reactivity and selectivity patterns in HAT reactions from amino acid C-H bonds.

  7. Reaction pathways of 2-iodoacetic acid on Cu(100): coverage-dependent competition between C-I bond scission and COOH deprotonation and identification of surface intermediates. (United States)

    Lin, Yi-Shiue; Lin, Jain-Shiun; Liao, Yung-Hsuan; Yang, Che-Ming; Kuo, Che-Wei; Lin, Hong-Ping; Fan, Liang-Jen; Yang, Yaw-Wen; Lin, Jong-Liang


    The chemistry of 2-iodoacetic acid on Cu(100) has been studied by a combination of reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), temperature-programmed reaction/desorption (TPR/D), and theoretical calculations based on density functional theory for the optimized intermediate structures. In the thermal decomposition of ICH(2)COOH on Cu(100) with a coverage less than a half monolayer, three surface intermediates, CH(2)COO, CH(3)COO, and CCOH, are generated and characterized spectroscopically. Based on their different thermal stabilities, the reaction pathways of ICH(2)COOH on Cu(100) at temperatures higher than 230 K are established to be ICH(2)COOH --> CH(2)COO + H + I, CH(2)COO + H --> CH(3)COO, and CH(3)COO --> CCOH. Theoretical calculations suggest that the surface CH(2)COO has the skeletal plane, with delocalized pi electrons, approximately parallel to the surface. The calculated Mulliken charges agree with the detected binding energies for the two carbon atoms in CH(2)COO on Cu(100). The CCOH derived from CH(3)COO decomposition has a CC stretching frequency at 2025 cm(-1), reflecting its triple-bond character which is consistent with the calculated CCOH structure on Cu(100). Theoretically, CCOH at the bridge and hollow sites has a similar stability and is adsorbed with the molecular axis approximately perpendicular to the surface. The TPR/D study has shown the evolution of the products of H(2), CH(4), H(2)O, CO, CO(2), CH(2)CO, and CH(3)COOH from CH(3)COO decomposition between 500 and 600 K and the formation of H(2) and CO from CCOH between 600 and 700 K. However, at a coverage near one monolayer, the major species formed at 230 and 320 K are proposed to be ICH(2)COO and CH(3)COO. CH(3)COO becomes the only species present on the surface at 400 K. That is, there are two reaction pathways of ICH(2)COOH --> ICH(2)COO + H and ICH(2)COO + H --> CH(3)COO + I (possibly via CH(2)COO), which are different from those

  8. The aryl ether bond reactions with H-donor solvents: guaiacol and tetralin in the presence of catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Afifi, A.I.; Thring, R.W.; Overend, R.P. [Universite de Sherbrooke, Sherbrooke, PQ (Canada). Dept. de Genie Chimique


    The effect of homogenous catalysis by Fe and Ru, on the conversion of guaiacol in tetralin to catechol and phenol has been investigated as a model for the behaviour of the aryl-oxy linkage that is found in wood, peat and younger coals. In the absence of catalyst and at low ratios of guaiacol to tetralin, the primary product is catechol. Kinetic analysis has confirmed that the rate constant for this primary and rate determining step is given by an Arrhenius pre-exponential factor of 10{sup 13.8} s{sup -1} with an activation energy of 215 kJ mol{sup -1}. The activation energy found is in good agreement with those of other investigators and lies between the values proposed for homolytic fission ({gt} 240 kJ mol{sup -1}) and for a concerted or pericyclic reaction (188 kJ mol{sup -1}). In the presence of catalysts the rate is not changed; however, the yield of a secondary product phenol is increased with both Fe and Ru. Separate experiments confirmed that the selectivity of catechol to phenol conversion was markedly increased in the presence of these catalysts. There is strong evidence for the formation of catecholato-iron complexes and this suggests that in pyrolysis and liquefaction of biomass and young coals there may well be a role of homogeneous catalysts in directing the product slate towards useful intermediate chemicals such as phenols. 14 refs., 9 figs., 4 tabs.

  9. Time-resolved spectroscopic characterization of a novel photodecarboxylation reaction mediated by homolysis of a carbon α-bond in flurbiprofen. (United States)

    Su, Tao; Ma, Jiani; Wong, Naikei; Phillips, David Lee


    Flurbiprofen (Fp), a nonsteroidal anti-inflammatory drug (NSAID) currently in use for arthritis pain relief and in clinical trials for metastatic prostate cancer, can induce photosensitization and phototoxicity upon exposure to sunlight. The mechanisms responsible for Fp phototoxicity are poorly understood and deserve investigation. In this study, the photodecarboxylation reaction of Fp, which has been assumed to underpin its photoinduced side effects, was explored by femtosecond transient absorption (fs-TA), nanosecond transient absorption (ns-TA), and nanosecond time-resolved resonance Raman (ns-TR(3)) spectroscopic techniques in pure acetonitrile (MeCN) solvent. Density functional theory (DFT) calculations were also performed to facilitate the assignments of transient species. The resonance Raman and DFT calculation results reveal that the neutral form of Fp was the predominant species present in MeCN. Analysis of the ultraviolet/visible absorption spectrum and results from TD-DFT calculations indicate that the second excited singlet (S2) can be excited by 266 nm light. Due to its intrinsic instability, S2 rapidly underwent internal conversion (IC) to decay to the lowest lying excited singlet (S1), which was observed in the fs-TA spectra at very early delay times. Intriguingly, three distinct pathways for S1 decay seem to coexist. Specifically, other than fluorescence emission back to the ground state and transformation to the lowest triplet state T1 through intersystem crossing (ISC), the homolysis of the carbon α-bond decarboxylation reaction proceeded simultaneously to give rise to two radical species, one being carboxyl and another being the residual, denoted as FpR. The coexistence of the triplet Fp (T1) and FpR species was verified by means of TR(3) spectra along with ns-TA spectra. As a consequence of its apparent high reactivity, the FpR intermediate was observed to undergo oxidation under oxygen-saturated conditions to yield another radical species

  10. A RhIII-N-heterocyclic carbene complex from metal-metal singly bonded [RhII−RhII] precursor

    Indian Academy of Sciences (India)

    Arup Sinha; Abir Sarbajna; Shrabani dinda; Jitendra K Bera


    Metal-metal singly bonded [Rh2(CO)4(acac)2][OTf]2 (1) has been synthesized and characterized by spectroscopic and analytical techniques. A density functional theory (DFT) optimized structure has been computed for the unbridged centro-symmetric structure. Reaction of 1 with PIN.HBr results in the [Rh(PIN)2(H2O)Br][OTf]2 (2) in high yield. The reaction involves metal-oxidation from RhII to RhIII accompanied by the metal-metal bond cleavage. The X-ray structure of 2 has been determined which reveals the incorporation of two N-heterocyclic carbene (NHC) ligands to each rhodium. This work demonstrates the general utility of the metal-metal bonded compounds for the easy synthesis of metal-NHC compounds.

  11. Real-time monitoring of DNAzyme cleavage process using fluorescent assay

    Institute of Scientific and Technical Information of China (English)

    Xiang Xian Meng; Xiao Hai Yang; Ke Min Wang; Wei Hong Tan; Qiu Ping Guo


    Detection of deoxyribozyme (DNAzyme) cleavage process usually needs complex and time-consuming radial labeling, gel electrophoresis and autoradiography. This paper reported an approach to detect DNAzyme cleavage process in real time using a fluorescence probe. The probe was employed as DNAzyme substrate to convert directly the cleavage information into fluorescence signal in real time. Compared with traditional approach, this non-isotope method not only brought a convenient means to monitor the DNAzyme cleavage reaction, but also offered abundant dynamic data for choosing potential gene therapeutic agents. It provides a new tool for DNAzyme research, as well as a new insight into research on human disease diagnosis. Based on this method, 8-17deoxyribozyme (8-17DNAzyme) against hepatitis C virus RNA (HCV-RNA) was designed and the cleavage process was studied in real time.

  12. Ultrasensitive monitoring of ribozyme cleavage product using molecular-beacon-ligation system

    Institute of Scientific and Technical Information of China (English)

    MENG XiangXian; TANG ZhiWen; WANG KeMin; TAN WeiHong; YANG XiaoHai; LI Jun; GUO QiuPing


    This paper reports a new approach to detect ribozyme cleavage product based on the molecular- beacon-ligation system. The molecular beacon, designed in such a way that one-half of its loop is complementary to ribozyme cleavage product, is used to monitor ligation process of RNA/DNA complex in a homogeneous solution and to convert directly cleavage product information into fluorescence signal. The method need not label ribozyme and ribozyme substrate, which is fast, simple and ultrasensitive for detection of cleavage product. Detection limit of the assay is 0.05 nmol/L. The cleavage product of hammerhead ribozyme against hepatitis C virus RNA (HCV-RNA) was detected perfectly based on this assay. Owing to its ultrasensitivity, excellent specificity, convenience and fidelity, this method might hold out great promise in ribozyme reaction and ribozyme gene therapy.

  13. Identification of the Active Species in Photochemical Hole Scavenging Reactions of Methanol on TiO2

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Mingmin; Henderson, Michael A.


    Molecular and dissociative methanol adsorption species were prepared on rutile TiO2(110) surfaces to study photocatalytic oxidation of methanol in ultrahigh vacuum (UHV) using temperature-programmed desorption (TPD). Adsorbed methoxy groups (CH3O-) were found to be the photoactive form of adsorbed methanol converted to adsorbed formaldehyde and a surface OH group by hole-mediated C-H bond cleavage. These results suggest that adsorbed methoxy is the effective hole scavenger in photochemical reactions involving methanol.

  14. C-H bond activation by metal-superoxo species: what drives high reactivity? (United States)

    Ansari, Azaj; Jayapal, Prabha; Rajaraman, Gopalan


    Metal-superoxo species are ubiquitous in metalloenzymes and bioinorganic chemistry and are known for their high reactivity and their ability to activate inert C-H bonds. The comparative oxidative abilities of M-O2(.-) species (M = Cr(III), Mn(III), Fe(III), and Cu(II)) towards C-H bond activation reaction are presented. These superoxo species generated by oxygen activation are found to be aggressive oxidants compared to their high-valent metal-oxo counterparts generated by O⋅⋅⋅O bond cleavage. Our calculations illustrate the superior oxidative abilities of Fe(III)- and Mn(III)-superoxo species compared to the others and suggest that the reactivity may be correlated to the magnetic exchange parameter.

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

    Kraka, Elfi; Cremer, Dieter


    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

  16. Bulk gold catalyzed oxidation reactions of amines and isocyanides and iron porphyrin catalyzed N-H and O-H bond insertion/cyclization reactions of diamines and aminoalcohols

    Energy Technology Data Exchange (ETDEWEB)

    Klobukowski, Erik [Iowa State Univ., Ames, IA (United States)


    conditions, it was found that the oxidative dehydrogenation of dibenzylamine to Nbenzylidenebenzylamine, with N-methylmorpholine N-oxide (NMMO), was nearly quantitative (96%) within 24 h. However, the reaction with oxygen was much slower, with only a 52% yield of imine product over the same time period. Moreover, the rate of reaction was found to be influenced by the nature of the amine N-oxide. For example, the use of the weakly basic pyridine N-oxide (PyNO) led to an imine yield of only 6% after 24 h. A comparison of amine N-oxide and O2 was also examined in the oxidation of PhCH{sub 2}OH to PhCHO catalyzed by bulk gold. In this reaction, a 52% yield of the aldehyde was achieved when NMMO was used, while only a 7% product yield was afforded when O{sub 2} was the oxidant after 48 h. The bulk gold-catalyzed oxidative dehydrogenation of cyclic amines generates amidines, which upon treatment with Aerosil and water were found to undergo hydrolysis to produce lactams. Moreover, 5-, 6-, and 7-membered lactams could be prepared through a one-pot reaction of cyclic amines by treatment with oxygen, water, bulk gold, and Aerosil. This method is much more atom economical than industrial processes, does not require corrosive acids, and does not generate undesired byproducts. Additionally, the gold and Aerosil catalysts can be readily separated from the reaction mixture. The second project involved studying iron(III) tetraphenylporphyrin chloride, Fe(TPP)Cl, as a homogeneous catalyst for the generation of carbenes from diazo reagents and their reaction with heteroatom compounds. Fe(TPP)Cl, efficiently catalyzed the insertion of carbenes derived from methyl 2-phenyldiazoacetates into O-H bonds of aliphatic and aromatic alcohols. Fe(TPP)Cl was also found to be an effective catalyst for tandem N-H and O-H insertion/cyclization reactions when 1,2-diamines and 1,2-alcoholamines were treated with diazo reagents. This approach provides a one-pot process for synthesizing piperazinones and

  17. Electrochemical Protein Cleavage in a Microfluidic Cell with Integrated Boron Doped Diamond Electrodes

    NARCIS (Netherlands)

    van den Brink, Floris T G; Zhang, Tao; Ma, Liwei; Bomer, Johan; Odijk, Mathieu; Olthuis, Wouter; Permentier, Hjalmar P; Bischoff, Rainer; van den Berg, Albert


    Specific electrochemical cleavage of peptide bonds at the C-terminal side of tyrosine and tryptophan generates peptides amenable to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis for protein identification. To this end we developed a microfluidic electrochemical cell of 160 nL vo

  18. Unusual nickel-mediated C-S cleavage of alkyl and aryl sulfoxides. (United States)

    Schaub, Thomas; Backes, Marc; Radius, Udo


    The first examples of transition metal mediated C-S cleavage of sulfoxides containing sp2- and sp3-hybridized carbon bonds attached to the sulfur atom and the first example of a structurally characterized complex featuring an oxygen-bound sulfinyl ligand are presented.

  19. Guest-host interactions in the cleavage of phenylphenyl acetates by -cyclodextrin in alkaline medium

    Indian Academy of Sciences (India)

    V Raj; T Chandrakala; K Rajasekaran


    Kinetics of cleavage of phenylphenyl acetates (PPA) and several para-substituted PPAs in basic aqueous sodium carbonate-bicarbonate buffer containing -cyclodextrin (CD) have been studied. The reaction exhibits saturation type kinetics and CD accelerates the rate of cleavage by the formation of 1G : 1H inclusion complex. The kinetic results indicate that aryloxy moiety of PPA is included in the hydrophobic cavity of CD. The overall rate constants for the cleavage of the [CD-ester] complex correlate with the Hammett -constants and Hansch hydrophobicity parameters . At higher concentrations of CD, there is an additional catalysis due to the formation of weak 1G : 2H complex.

  20. Study on join method of reaction bonded silicon carbide green body%RBSiC陶瓷素坯连接研究

    Institute of Scientific and Technical Information of China (English)



    The join slurry is composed by silicon carbide (SiC) powder, phenolic resin and carbon black. Joining SiC green body after deairing, and then the reaction bonded SiC(RBSiC) joining mirror blank was prepared by reaction sintering. The relationship of the slurry formula and the microstructure of weld were discussed. The bending strength and the coefficient of thermal expansion of joining RBSiC ceramic were tested. The research shows that PEG200 and PVP can make carbon black dispersing homogeneous in the join slurry, and there is no residual carbon black in the weld after reaction sintering, so the microstructure of RBSiC ceramic is no different from the weld. The blending strength of joining green body and joining RBSiC ceramic are 24.9 MPa and 322.9 MP arespectively, and the fracture occurred in the base material. The ΔCTE of base and weld material is only 0.011 4 ppm during - 100- 400℃.%将碳化硅( Si C )微粉、酚醛树脂和炭黑等均匀混合,配置成连接浆料,真空除泡后连接SiC陶瓷素坯,高温反应烧结后得到反应烧结SiC(RBSiC)连接镜坯。讨论了浆料配方对焊缝显微结构的影响,测试了RBSiC连接坯体的力学性能和线膨胀系数。研究表明:连接浆料中加入聚乙二醇200(PEG200)和聚乙烯醇吡咯烷酮(PVP),能够有效分散炭黑,保证反应烧结过程中炭黑与硅完全反应,无残余碳存在,实现焊缝与基材之间显微结构的一致性;SiC连接坯体素坯和反应烧结后的抗弯强度值分别24.9 MPa和322.9 MPa,而且断裂位置在基材上;在-100~400℃范围内,RBSiC连接坯体与基体线膨胀系数差异仅为0.0114 ppm。

  1. Kinetics of acid-catalyzed cleavage of cumene hydroperoxide. (United States)

    Levin, M E; Gonzales, N O; Zimmerman, L W; Yang, J


    The cleavage of cumene hydroperoxide, in the presence of sulfuric acid, to form phenol and acetone has been examined by adiabatic calorimetry. As expected, acid can catalyze cumene hydroperoxide reaction at temperatures below that of thermally-induced decomposition. At elevated acid concentrations, reactivity is also observed at or below room temperature. The exhibited reactivity behavior is complex and is significantly affected by the presence of other species (including the products). Several reaction models have been explored to explain the behavior and these are discussed.

  2. Fracto—emissions in Catastrophic Cleavage Process

    Institute of Scientific and Technical Information of China (English)

    HonglaiTAN; WeiYANG


    Fracto-emissions accompanying crack propagation are observed in the recent experiments.The energy impulses during and after fracture stimulate the fracto-emissions.Model concerning atomic scale cleavage processes is proposed to formulate a catastrophic fracure theory relevant to these phenomena.A criterion for catastrophic jump of the cleavage potential is applied to representative crystals.

  3. Catalytic activation of carbohydrates as formaldehyde equivalents for Stetter reaction with enones. (United States)

    Zhang, Junmin; Xing, Chong; Tiwari, Bhoopendra; Chi, Yonggui Robin


    We disclose the first catalytic activation of carbohydrates as formaldehyde equivalents to generate acyl anions as one-carbon nucleophilic units for a Stetter reaction. The activation involves N-heterocyclic carbene (NHC)-catalyzed C-C bond cleavage of carbohydrates via a retro-benzoin-type process to generate the acyl anion intermediates. This Stetter reaction constitutes the first success in generating formal formaldehyde-derived acyl anions as one-carbon nucleophiles for non-self-benzoin processes. The renewable nature of carbohydrates, accessible from biomass, further highlights the practical potential of this fundamentally interesting catalytic activation.

  4. Can main group systems act as superior catalysts for dihydrogen generation reactions? A computational investigation. (United States)

    Kuriakose, Nishamol; Vanka, Kumar


    The protolytic cleavage of the O-H bond in water and alcohols is a very important reaction, and an important method for producing dihydrogen. Full quantum chemical studies with density functional theory (DFT) reveal that germanium based complexes, such as HC{CMeArB}2GeH (Ar = 2,6-(i)Pr2C6H3), with the assistance of silicon based compounds such as SiF3H, can perform significantly better than the existing state-of-the-art post-transition metal based systems for catalyzing dihydrogen generation from water and alcohols through the protolysis reaction.

  5. Formation of diphenylphosphanylbutadienyl complexes by insertion of two P-coordinated alkynylphosphanes into a PtbondC6F5 bond: detection of intermediate and reaction products. (United States)

    Ara, Irene; Forniés, Juan; García, Ana; Gómez, Julio; Lalinde, Elena; Moreno, M Teresa


    The reactions between cis-[M(C(6)F(5))(2)(PPh(2)CtriplebondCR)(2)] (M=Pt, Pd; R=Ph, tBu, Tol 2, 3) or cis-[Pt(C(6)F(5))(2)(PPh(2)CtriplebondCR)(PPh(2)CtriplebondCtBu)] (R=Ph 4, Tol 5) and cis-[Pt(C(6)F(5))(2)(thf)(2)] 1 have been investigated. Whereas [M](PPh(2)CtriplebondCtBu)(2) ([M]=cis-M(C(6)F(5))(2)) is inert towards 1, the analogous reactions starting from [M](PPh(2)CtriplebondCR)(2) or [Pt](PPh(2)CtriplebondCR)(PPh(2)CtriplebondCtBu) (R=Ph, Tol) afford unusual binuclear species [Pt(C(6)F(5))(S)mu-[C(R')dbondC(PPh(2))C(PPh(2))doublebondC(R)(C(6)F(5))]M(C(6)F(5))(2)] (R=R'=Ph, Tol, M=Pt 6 a,c, M=Pd 7 a,c; M=Pt, R'=tBu, R=Ph 8, Tol 9) containing a bis(diphenylphosphanyl)butadienyl bridging ligand formed by an unprecedented sequential insertion reaction of two P-coordinated PPh(2)CtriplebondCR ligands into a PtbondC(6)F(5) bond. Although in solution the presence of coordinated solvent S (S=(thf)(x)(H(2)O)(y)) in 6, 7 is suggested by NMR spectroscopy, X-ray diffraction analyses of different crystals of the mixed complex [Pt(C(6)F(5))mu-[C(tBu)doublebondC(PPh(2))C(PPh(2))doublebondC(Tol)(C(6)F(5))]Pt(C(6)F(5))(2)] 9 unequivocally establish that in the solid state the steric crowding of the new diphenylbutadienyl ligand formed stabilizes an unusual coordinatively unsaturated T-shaped 3-coordinated platinum(II) center. Structure determinations of the mononuclear precursors cis-[Pt(C(6)F(5))(2)(PPh(2)CtriplebondCR)(2)] (R=Ph, tBu, Tol) have been carried out to evaluate the factors affecting the insertion processes. The reactions of the platinum complexes 6 towards neutral ligands (L=CO, py, PPh(2)H, CNtBu) in a 1:1 molar ratio afford related diplatinum derivatives 10-13, whereas treatment with CNtBu (1:2 molar ratio) or 2,2'-bipy (1:1 molar ratio) results in the opening of the chelating ring to give cis,cis-[Pt(C(6)F(5))(L)(2)mu-[1-kappaC(1):2-kappaPP'-C(R)doublebondC(PPh(2))C(PPh(2))doublebondC(R)(C(6)F(5))]Pt(C(6)F(5))(2)] (14, 15). The unsaturated or solvento

  6. Microstructure and cleavage in lath martensitic steels

    Directory of Open Access Journals (Sweden)

    John W Morris Jr, Chris Kinney, Ken Pytlewski and Y Adachi


    Full Text Available In this paper we discuss the microstructure of lath martensitic steels and the mechanisms by which it controls cleavage fracture. The specific experimental example is a 9Ni (9 wt% Ni steel annealed to have a large prior austenite grain size, then examined and tested in the as-quenched condition to produce a relatively coarse lath martensite. The microstructure is shown to approximate the recently identified 'classic' lath martensite structure: prior austenite grains are divided into packets, packets are subdivided into blocks, and blocks contain interleaved laths whose variants are the two Kurjumov–Sachs relations that share the same Bain axis of the transformation. When the steel is fractured in brittle cleavage, the laths in the block share {100} cleavage planes and cleave as a unit. However, cleavage cracks deflect or blunt at the boundaries between blocks with different Bain axes. It follows that, as predicted, the block size governs the effective grain size for cleavage.

  7. Proton Mobility in b2 Ion Formation and Fragmentation Reactions of Histidine-Containing Peptides (United States)

    Nelson, Carissa R.; Abutokaikah, Maha T.; Harrison, Alex G.; Bythell, Benjamin J.


    A detailed energy-resolved study of the fragmentation reactions of protonated histidine-containing peptides and their b2 ions has been undertaken. Density functional theory calculations were utilized to predict how the fragmentation reactions occur so that we might discern why the mass spectra demonstrated particular energy dependencies. We compare our results to the current literature and to synthetic b2 ion standards. We show that the position of the His residue does affect the identity of the subsequent b2 ion (diketopiperazine versus oxazolone versus lactam) and that energy-resolved CID can distinguish these isomeric products based on their fragmentation energetics. The histidine side chain facilitates every major transformation except trans-cis isomerization of the first amide bond, a necessary prerequisite to diketopiperazine b2 ion formation. Despite this lack of catalyzation, trans-cis isomerization is predicted to be facile. Concomitantly, the subsequent amide bond cleavage reaction is rate-limiting.

  8. Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor (United States)

    Jepsen, Morten Leth; Harmsen, Charlotte; Godbole, Adwait Anand; Nagaraja, Valakunja; Knudsen, Birgitta R.; Ho, Yi-Ping


    We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes. Electronic supplementary information (ESI) available: Characterization of the QD-based DNA Nanosensor. See DOI: 10.1039/c5nr06326d

  9. Intermetallic Reactions during the Solid-Liquid Interdiffusion Bonding of Bi2Te2.55Se0.45 Thermoelectric Material with Cu Electrodes Using a Sn Interlayer

    Directory of Open Access Journals (Sweden)

    Chien-Hsun Chuang


    Full Text Available The intermetallic compounds formed during the diffusion soldering of a Bi2Te2.55Se0.45 thermoelectric material with a Cu electrode are investigated. For this bonding process, Bi2Te2.55Se0.45 was pre-coated with a 1 μm Sn thin film on the thermoelectric element and pre-heated at 250 °C for 3 min before being electroplated with a Ni barrier layer and a Ag reaction layer. The pre-treated thermoelectric element was bonded with a Ag-coated Cu electrode using a 4 μm Sn interlayer at temperatures between 250 and 325 °C. The results indicated that a multi-layer of Bi–Te–Se/Sn–Te–Se–Bi/Ni3Sn4 phases formed at the Bi2Te2.55Se0.45/Ni interface, ensuring sound cohesion between the Bi2Te2.55Se0.45 thermoelectric material and Ni barrier. The molten Sn interlayer reacted rapidly with both Ag reaction layers to form an Ag3Sn intermetallic layer until it was completely exhausted and the Ag/Sn/Ag sandwich transformed into a Ag/Ag3Sn/Ag joint. Satisfactory shear strengths ranging from 19.3 and 21.8 MPa were achieved in Bi2Te2.55Se0.45/Cu joints bonded at 250 to 300 °C for 5 to 30 min, dropping to values of about 11 MPa for 60 min, bonding at 275 and 300 °C. In addition, poor strengths of about 7 MPa resulted from bonding at a higher temperature of 325 °C for 5 to 60 min.

  10. Secologanin synthase which catalyzes the oxidative cleavage of loganin into secologanin is a cytochrome P450. (United States)

    Yamamoto, H; Katano, N; Ooi, A; Inoue, K


    Secologanin synthase, an enzyme catalyzing the oxidative cleavage of the cyclopentane ring in loganin to form secologanin, was detected in microsomal preparations from cell suspension cultures of Lonicera japonica. The reaction required NADPH and molecular oxygen, and was blocked by carbon monoxide as well as by several other cytochrome P450 inhibitors, indicating that the reaction was mediated by cytochrome P450. Of the substrates examined, only specificity for loganin was demonstrated. A possible reaction mechanism is described.

  11. Disulphide bond formation in food protein aggregation and gelation

    NARCIS (Netherlands)

    Visschers, R.W.; Jongh, de H.H.J.


    In this short review we discuss the role of cysteine residues and cystine bridges for the functional aggregation of food proteins. We evaluate how formation and cleavage of disulphide bonds proceeds at a molecular level, and how inter- and intramolecular disulfide bonds can be detected and modified.

  12. Binding of hydrocarbons and other extremely weak ligands to transition metal complexes that coordinate hydrogen: Investigation of cis-interactions and delocalized bonding involving sigma bonds

    Energy Technology Data Exchange (ETDEWEB)

    Kubas, G.J.; Eckert, J.; Luo, X.L. [and others


    This is the final report of a three-year Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). At the forefront of chemistry are efforts to catalytically transform the inert C-H bonds in alkanes to more useful products using metal compounds. The goal is to observe binding and cleavage of alkane C-H bonds on metals or to use related silane Si-H bonding as models, analogous to the discovery of hydrogen (H{sub 2}) binding to metals. Studies of these unique sigma complexes (M{hor_ellipsis}H-Y; Y{double_bond}H, Si, C) will aid in developing new catalysts or technologies relevant to DOE interest, e.g., new methods for tritium isotope separation. Several transition metals (Mo, W, Mn, and Pt) were found to reversibly bind and cleave H{sub 2}, silanes, and halocarbons. The first metal-SiH{sub 4} complexes, thus serving as a model for methane reactions. A second goal is to study the dynamics and energetics of H-Y bonds on metals by neutron scattering, and evidence for interactions between bound H-Y and nearby H atoms on metal complexes has been found.

  13. Ultrafast studies of organometallic photochemistry: The mechanism of carbon-hydrogen bond activation in solution

    Energy Technology Data Exchange (ETDEWEB)

    Bromberg, S.E.


    When certain organometallic compounds are photoexcited in room temperature alkane solution, they are able to break or activate the C-H bonds of the solvent. Understanding this potentially practical reaction requires a detailed knowledge of the entire reaction mechanism. Because of the dynamic nature of chemical reactions, time-resolved spectroscopy is commonly employed to follow the important events that take place as reactants are converted to products. For the organometallic reactions examined here, the electronic/structural characteristics of the chemical systems along with the time scales for the key steps in the reaction make ultrafast UV/Vis and IR spectroscopy along with nanosecond Step-Scan FTIR spectroscopy the ideal techniques to use for this study. An initial study of the photophysics of (non-activating) model metal carbonyls centering on the photodissociation of M(CO){sub 6} (M = Cr, W, Mo) was carried out in alkane solutions using ultrafast IR spectroscopy. Next, picosecond UV/vis studies of the C-H bond activation reaction of Cp{sup *}M(CO){sub 2} (M = Rh, Ir), conducted in room temperature alkane solution, are described in an effort to investigate the origin of the low quantum yield for bond cleavage ({approximately}1%). To monitor the chemistry that takes place in the reaction after CO is lost, a system with higher quantum yield is required. The reaction of Tp{sup *}Rh(CO){sub 2} (Tp{sup *} = HB-Pz{sub 3}{sup *}, Pz{sup *} = 3,5-dimethylpyrazolyl) in alkanes has a quantum yield of {approximately}30%, making time resolved spectroscopic measurements possible. From ultrafast IR experiments, two subsequently formed intermediates were observed. The nature of these intermediates are discussed and the first comprehensive reaction mechanism for a photochemical C-H activating organometallic complex is presented.

  14. Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection. (United States)

    Sinapah, Sylvie; Wu, Shiying; Chen, Yu; Pettersson, B M Fredrik; Gopalan, Venkat; Kirsebom, Leif A


    RNase P is a catalytic ribonucleoprotein primarily involved in tRNA biogenesis. Archaeal RNase P comprises a catalytic RNase P RNA (RPR) and at least four protein cofactors (RPPs), which function as two binary complexes (POP5•RPP30 and RPP21• RPP29). Exploiting the ability to assemble a functional Pyrococcus furiosus (Pfu) RNase P in vitro, we examined the role of RPPs in influencing substrate recognition by the RPR. We first demonstrate that Pfu RPR, like its bacterial and eukaryal counterparts, cleaves model hairpin loop substrates albeit at rates 90- to 200-fold lower when compared with cleavage by bacterial RPR, highlighting the functionally comparable catalytic cores in bacterial and archaeal RPRs. By investigating cleavage-site selection exhibited by Pfu RPR (±RPPs) with various model substrates missing consensus-recognition elements, we determined substrate features whose recognition is facilitated by either POP5•RPP30 or RPP21•RPP29 (directly or indirectly via the RPR). Our results also revealed that Pfu RPR + RPP21•RPP29 displays substrate-recognition properties coinciding with those of the bacterial RPR-alone reaction rather than the Pfu RPR, and that this behaviour is attributable to structural differences in the substrate-specificity domains of bacterial and archaeal RPRs. Moreover, our data reveal a hierarchy in recognition elements that dictates cleavage-site selection by archaeal RNase P.

  15. Reaction pathways of proton transfer in hydrogen-bonded phenol-carboxylate complexes explored by combined UV-vis and NMR spectroscopy. (United States)

    Koeppe, Benjamin; Tolstoy, Peter M; Limbach, Hans-Heinrich


    Combined low-temperature NMR/UV-vis spectroscopy (UVNMR), where optical and NMR spectra are measured in the NMR spectrometer under the same conditions, has been set up and applied to the study of H-bonded anions A··H··X(-) (AH = 1-(13)C-2-chloro-4-nitrophenol, X(-) = 15 carboxylic acid anions, 5 phenolates, Cl(-), Br(-), I(-), and BF(4)(-)). In this series, H is shifted from A to X, modeling the proton-transfer pathway. The (1)H and (13)C chemical shifts and the H/D isotope effects on the latter provide information about averaged H-bond geometries. At the same time, red shifts of the π-π* UV-vis absorption bands are observed which correlate with the averaged H-bond geometries. However, on the UV-vis time scale, different tautomeric states and solvent configurations are in slow exchange. The combined data sets indicate that the proton transfer starts with a H-bond compression and a displacement of the proton toward the H-bond center, involving single-well configurations A-H···X(-). In the strong H-bond regime, coexisting tautomers A··H···X(-) and A(-)···H··X are observed by UV. Their geometries and statistical weights change continuously when the basicity of X(-) is increased. Finally, again a series of single-well structures of the type A(-)···H-X is observed. Interestingly, the UV-vis absorption bands are broadened inhomogeneously because of a distribution of H-bond geometries arising from different solvent configurations.

  16. Bond Issues. (United States)

    Pollack, Rachel H.


    Notes trends toward increased borrowing by colleges and universities and offers guidelines for institutions that are considering issuing bonds to raise money for capital projects. Discussion covers advantages of using bond financing, how use of bonds impacts on traditional fund raising, other cautions and concerns, and some troubling aspects of…


    Energy Technology Data Exchange (ETDEWEB)

    Abu-Omar, Mahdi M.


    The 2013 Gordon Conference on Inorganic Reaction Mechanisms will present cutting-edge research on the molecular aspects of inorganic reactions involving elements from throughout the periodic table and state-of-the art techniques that are used in the elucidation of reaction mechanisms. The Conference will feature a wide range of topics, such as homogeneous and heterogeneous catalysis, metallobiochemistry, electron-transfer in energy reactions, polymerization, nitrogen fixation, green chemistry, oxidation, solar conversion, alkane functionalization, organotransition metal chemistry, and computational chemistry. The talks will cover themes of current interest including energy, materials, and bioinorganic chemistry. Sections cover: Electron-Transfer in Energy Reactions; Catalytic Polymerization and Oxidation Chemistry; Kinetics and Spectroscopy of Heterogeneous Catalysts; Metal-Organic Chemistry and its Application in Synthesis; Green Energy Conversion;Organometallic Chemistry and Activation of Small Molecules; Advances in Kinetics Modeling and Green Chemistry; Metals in Biology and Disease; Frontiers in Catalytic Bond Activation and Cleavage.

  18. Detection and characterization of chlorinated-dioxin ether cleavage function in the bacterium geobacillus midousuji SH2B-J2

    Energy Technology Data Exchange (ETDEWEB)

    Otsuka, Y.; Hoshina, S. [Jikei Univ. School of Medicine, Tokyo (Japan). Dept. of Laboratory Medicine; Nakamura, M.; Hishiyama, S. [Forestry and Forest Products Research Institute, Ibaraki (Japan); Katayama, Y. [Tokyo Univ. of Agriculture and Technology, Koganei (Japan)


    As of now, there are no dioxin degrading microorganism reported that can be applied to bioremediation. The reasons for this are that degrading function acquired from comprehensive screening of bacteria that can be grown with a single carbon source using non-chlorinated dioxin does not function against highly chlorinated dioxins, and that although white rot fungus capable of degrading lignin, a plant polyphenol substance, have been reported to reduce chlorinated dioxins, degrading enzyme remain unclear. Geobacillus midousuji SH2B-J2 (J2 strain) that have been separated by Hoshina et al. have shown to reduce highly chlorinated dioxins in incineration fly ash, as well as octa-chlorinated dioxins (OCDD). However, details of its degrading mechanisms remain unclear. Since the J2 strain is capable of reducing even OCDD, it was hypothesized that the initial degradation reaction is intramolecular ether bond cleavage, so J2 strain dioxin degradation mechanism was analyzed for verification.

  19. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization. (United States)

    Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders


    Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

  20. Palladium-Catalyzed Cross-Coupling Reactions of Perfluoro Organic Compounds

    Directory of Open Access Journals (Sweden)

    Masato Ohashi


    Full Text Available In this review, we summarize our recent development of palladium(0-catalyzed cross-coupling reactions of perfluoro organic compounds with organometallic reagents. The oxidative addition of a C–F bond of tetrafluoroethylene (TFE to palladium(0 was promoted by the addition of lithium iodide, affording a trifluorovinyl palladium(II iodide. Based on this finding, the first palladium-catalyzed cross-coupling reaction of TFE with diarylzinc was developed in the presence of lithium iodide, affording α,β,β-trifluorostyrene derivatives in excellent yield. This coupling reaction was expanded to the novel Pd(0/PR3-catalyzed cross-coupling reaction of TFE with arylboronates. In this reaction, the trifluorovinyl palladium(II fluoride was a key reaction intermediate that required neither an extraneous base to enhance the reactivity of organoboronates nor a Lewis acid additive to promote the oxidative addition of a C–F bond. In addition, our strategy utilizing the synergetic effect of Pd(0 and lithium iodide could be applied to the C–F bond cleavage of unreactive hexafluorobenzene (C6F6, leading to the first Pd(0-catalyzed cross-coupling reaction of C6F6 with diarylzinc compounds.

  1. Reaction of cytochrome P450 with cumene hydroperoxide: ESR spin-trapping evidence for the homolytic scission of the peroxide O-O bond by ferric cytochrome P450 1A2. (United States)

    Barr, D P; Martin, M V; Guengerich, F P; Mason, R P


    ESR spin trapping was used to investigate the reaction of rabbit cytochrome P450 (P450) 1A2 with cumene hydroperoxide. Cumene hydroperoxide-derived peroxyl, alkoxyl, and carbon-centered radicals were formed and trapped during the reaction. The relative contributions of each radical adduct to the composite ESR spectrum were influenced by the concentration of the spin trap. Computer simulation of the experimental data obtained at various 5,5-dimethyl-1-pyrroline N-oxide (DMPO) concentrations was used to quantitate the contributions of each radical adduct to the composite ESR spectrum. The alkoxyl radical was the initial radical produced during the reaction. Experiments with 2-methyl-2-nitrosopropane identified the carbon-centered adducts as those of the methyl radical, hydroxymethyl radical, and a secondary carbon-centered radical. The reaction did not require NADPH-cytochrome P450 reductase or NADPH. It is concluded that the reaction involves the initial homolytic scission of the peroxide O-O bond to produce the cumoxyl radical. Methyl radicals were produced from the beta-scission of the cumoxyl radical. The peroxyl adduct was not observed in the absence of molecular oxygen. We conclude that the DMPO peroxyl radical adduct detected in the presence of oxygen was due to the methylperoxyl radical formed by the reaction of the methyl radical with oxygen. At a higher P450 concentration, a protein-derived radical adduct was also detected.

  2. Carotenoid-cleavage activities of crude enzymes from Pandanous amryllifolius. (United States)

    Ningrum, Andriati; Schreiner, Matthias


    Carotenoid degradation products, known as norisoprenoids, are aroma-impact compounds in several plants. Pandan wangi is a common name of the shrub Pandanus amaryllifolius. The genus name 'Pandanus' is derived from the Indonesian name of the tree, pandan. In Indonesia, the leaves from the plant are used for several purposes, e.g., as natural colorants and flavor, and as traditional treatments. The aim of this study was to determine the cleavage of β-carotene and β-apo-8'-carotenal by carotenoid-cleavage enzymes isolated from pandan leaves, to investigate dependencies of the enzymatic activities on temperature and pH, to determine the enzymatic reaction products by using Headspace Solid Phase Microextraction Gas Chromatography/Mass Spectrophotometry (HS-SPME GC/MS), and to investigate the influence of heat treatment and addition of crude enzyme on formation of norisoprenoids. Crude enzymes from pandan leaves showed higher activity against β-carotene than β-apo-8'-carotenal. The optimum temperature of crude enzymes was 70°, while the optimum pH value was 6. We identified β-ionone as the major volatile reaction product from the incubations of two different carotenoid substrates, β-carotene and β-apo-8'-carotenal. Several treatments, e.g., heat treatment and addition of crude enzymes in pandan leaves contributed to the norisoprenoid content. Our findings revealed that the crude enzymes from pandan leaves with carotenoid-cleavage activity might provide a potential application, especially for biocatalysis, in natural-flavor industry.

  3. Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes. (United States)

    Simons, Michelle; Szczelkun, Mark D


    The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM that form a methyltransferase (MTase) and HsdR that associates with the MTase and catalyses Adenosine-5'-triphosphate (ATP)-dependent DNA translocation and cleavage. Here, we examine whether the MTase and HsdR components can 'turnover' in vitro, i.e. whether they can catalyse translocation and cleavage events on one DNA molecule, dissociate and then re-bind a second DNA molecule. Translocation termination by both EcoKI and EcoR124I leads to HsdR dissociation from linear DNA but not from circular DNA. Following DNA cleavage, the HsdR subunits appear unable to dissociate even though the DNA is linear, suggesting a tight interaction with the cleaved product. The MTases of EcoKI and EcoAI can dissociate from DNA following either translocation or cleavage and can initiate reactions on new DNA molecules as long as free HsdR molecules are available. In contrast, the MTase of EcoR124I does not turnover and additional cleavage of circular DNA is not observed by inclusion of RecBCD, a helicase-nuclease that degrades the linear DNA product resulting from Type I cleavage. Roles for Type I restriction endonuclease subunit dynamics in restriction alleviation in the cell are discussed.

  4. Potential-modulated DNA cleavage by (N-salicylideneglycinato)copper(II) complex. (United States)

    Yang, Zhou-Sheng; Wang, Yan-Ling; Liu, Yun-Chun; Zhao, Guang-Chao


    The interaction of aqua (N-salicylideneglycinato)copper(II) (Cu(salgly)2+) complex with calf thymus DNA has been investigated by cyclic voltammetry. Potential-modulated DNA cleavage in the presence of Cu(salgly)2+ complex was performed at a gold electrode in a thin layer cell. DNA can be efficiently cleaved by electrochemically reducing Cu(salgly)2+ complex to Cu(salgly)+ complex at -0.7 V (vs. Ag/AgCl). When the solution was aerated with a small flow of O2 during electrolysis, the extent of DNA cleavage was dramatically enhanced, and hydroxyl radical scavengers inhibited DNA cleavage. These results suggested that O2 and hydroxyl radical were involved in potential-modulated DNA cleavage reaction. The percentage of DNA cleavage was enhanced as the working potential was shifted to more negative values and the electrolysis time was increased. It was also dependent on the ratio of Cu(salgly)2+ complex to DNA concentration. The cleaved DNA fragments were separated by high performance liquid chromatography (HPLC). The experimental results indicated that the method for potential-modulated DNA cleavage by Cu(salgly)2+ complex was simple and efficient.

  5. Cleavage of resveratrol in fungi: characterization of the enzyme Rco1 from Ustilago maydis. (United States)

    Brefort, Thomas; Scherzinger, Daniel; Limón, M Carmen; Estrada, Alejandro F; Trautmann, Danika; Mengel, Carina; Avalos, Javier; Al-Babili, Salim


    Ustilago maydis, the causative agent of corn smut disease, contains two genes encoding members of the carotenoid cleavage oxygenase family, a group of enzymes that cleave double bonds in different substrates. One of them, Cco1, was formerly identified as a β-carotene cleaving enzyme. Here we elucidate the function of the protein encoded by the second gene, termed here as Ustilago maydis Resveratrol cleavage oxygenase 1 (Um Rco1). In vitro incubations of heterologously expressed and purified UM Rco1 with different carotenoid and stilbene substrates demonstrate that it cleaves the interphenyl Cα-Cβ double bond of the phytoalexin resveratrol and its derivative piceatannol. Um Rco1 exhibits a high degree of substrate specificity, as suggested by the lack of activity on carotenoids and the other resveratrol-related compounds tested. The activity of Um Rco1 was confirmed by incubation of U. maydis rco1 deletion and over-expression strains with resveratrol. Furthermore, treatment with resveratrol resulted in striking alterations of cell morphology. However, pathogenicity assays indicated that Um rco1 is largely dispensable for biotrophic development. Our work reveals Um Rco1 as the first eukaryotic resveratrol cleavage enzyme identified so far. Moreover, Um Rco1 represents a subfamily of fungal enzymes likely involved in the degradation of stilbene compounds, as suggested by the cleavage of resveratrol by homologs from Aspergillus fumigatus, Chaetomium globosum and Botryotinia fuckeliana.

  6. Relaxase DNA binding and cleavage are two distinguishable steps in conjugative DNA processing that involve different sequence elements of the nic site. (United States)

    Lucas, María; González-Pérez, Blanca; Cabezas, Matilde; Moncalian, Gabriel; Rivas, Germán; de la Cruz, Fernando


    TrwC, the relaxase of plasmid R388, catalyzes a series of concerted DNA cleavage and strand transfer reactions on a specific site (nic) of its origin of transfer (oriT). nic contains the cleavage site and an adjacent inverted repeat (IR(2)). Mutation analysis in the nic region indicated that recognition of the IR(2) proximal arm and the nucleotides located between IR(2) and the cleavage site were essential for supercoiled DNA processing, as judged either by in vitro nic cleavage or by mobilization of a plasmid containing oriT. Formation of the IR(2) cruciform and recognition of the distal IR(2) arm and loop were not necessary for these reactions to take place. On the other hand, IR(2) was not involved in TrwC single-stranded DNA processing in vitro. For single-stranded DNA nic cleavage, TrwC recognized a sequence embracing six nucleotides upstream of the cleavage site and two nucleotides downstream. This suggests that TrwC DNA binding and cleavage are two distinguishable steps in conjugative DNA processing and that different sequence elements are recognized by TrwC in each step. IR(2)-proximal arm recognition was crucial for the initial supercoiled DNA binding. Subsequent recognition of the adjacent single-stranded DNA binding site was required to position the cleavage site in the active center of the protein so that the nic cleavage reaction could take place.

  7. Relaxase DNA Binding and Cleavage Are Two Distinguishable Steps in Conjugative DNA Processing That Involve Different Sequence Elements of the nic Site* (United States)

    Lucas, María; González-Pérez, Blanca; Cabezas, Matilde; Moncalian, Gabriel; Rivas, Germán; de la Cruz, Fernando


    TrwC, the relaxase of plasmid R388, catalyzes a series of concerted DNA cleavage and strand transfer reactions on a specific site (nic) of its origin of transfer (oriT). nic contains the cleavage site and an adjacent inverted repeat (IR2). Mutation analysis in the nic region indicated that recognition of the IR2 proximal arm and the nucleotides located between IR2 and the cleavage site were essential for supercoiled DNA processing, as judged either by in vitro nic cleavage or by mobilization of a plasmid containing oriT. Formation of the IR2 cruciform and recognition of the distal IR2 arm and loop were not necessary for these reactions to take place. On the other hand, IR2 was not involved in TrwC single-stranded DNA processing in vitro. For single-stranded DNA nic cleavage, TrwC recognized a sequence embracing six nucleotides upstream of the cleavage site and two nucleotides downstream. This suggests that TrwC DNA binding and cleavage are two distinguishable steps in conjugative DNA processing and that different sequence elements are recognized by TrwC in each step. IR2-proximal arm recognition was crucial for the initial supercoiled DNA binding. Subsequent recognition of the adjacent single-stranded DNA binding site was required to position the cleavage site in the active center of the protein so that the nic cleavage reaction could take place. PMID:20061574

  8. Reactivity of the metal-->BX3 dative sigma-bond: 1,2-addition reactions of the Fe-->BX3 moiety of the ferraboratrane complex [kappa4-B(mimBu t)3]Fe(CO)2. (United States)

    Figueroa, Joshua S; Melnick, Jonathan G; Parkin, Gerard


    The ferraboratrane [kappa4-B(mim(Bu)t)3]Fe(CO)2 (mim(Bu)t = 2-mercapto-1-tert-butylimidazolyl), the first example of a complex which possesses a retrodative (i.e., metal-to-ligand) Fe-->B bond, is obtained via reaction of the tris(2-mercapto-1-tert-butylimidazolyl)hydroborato complex [Tm(Bu)t]FeCl with LiCH2SiMe3 followed by treatment with CO. Significantly, [kappa4-B(mim(Bu)t)3]Fe(CO)2 exhibits novel reactivity towards a variety of reagents that results in eradication of the Fe-->B bond via a formal 1,2-addition process and the formation of B-functionalized tris(mercaptoimidazolyl)borate derivatives, [XTm(Bu)t]FeY.

  9. Distinct mechanisms for DNA cleavage by myoglobin with a designed heme active center. (United States)

    Zhao, Yuan; Du, Ke-Jie; Gao, Shu-Qin; He, Bo; Wen, Ge-Bo; Tan, Xiangshi; Lin, Ying-Wu


    Heme proteins perform diverse biological functions, of which myoglobin (Mb) is a representative protein. In this study, the O2 carrier Mb was shown to cleave double stranded DNA upon aerobic dithiothreitol-induced reduction, which is fine-tuned by an additional distal histidine, His29 or His43, engineered in the heme active center. Spectroscopic (UV-vis and EPR) and inhibition studies suggested that free radicals including singlet oxygen and hydroxyl radical are responsible for efficient DNA cleavage via an oxidative cleavage mechanism. On the other hand, L29E Mb, with a distinct heme active center involving three water molecules in the met form, was found to exhibit an excellent DNA cleavage activity that was not depending on O2. Inhibition and ligation studies demonstrated for the first time that L29E Mb cleaves double stranded DNA into both the nicked circular and linear forms via a hydrolytic cleavage mechanism, which resembles native endonucleases. This study provides valuable insights into the distinct mechanisms for DNA cleavage by heme proteins, and lays down a base for creating artificial DNA endonucleases by rational design of heme proteins. Moreover, this study suggests that the diverse functions of heme proteins can be fine-tuned by rational design of the heme active center with a hydrogen-bonding network.

  10. Determination of binding constants and stoichiometries of short-range, hydrogen-bonding solvation by use of a proton-transfer indicator reaction (United States)

    Schullery, Stephen E.; Wojdyla, Stephen M.; Ostroski, Robert A.; Scott, Ronald M.


    A recent method for determination of stoichiometries and binding constants for short-range, hydrogen bonding solvation is reviewed and new results are presented. The method exploits the sensitivity of a proton-transfer equilibrium, KPT to changes in solvent composition. Solvation numbers and binding constants for primary and secondary stages of solvation of an aminephenol proton-transfer adduct and the phenol and amine are determined as adjustable parameters when model isotherms are fitted to KPT versus [ S] data, where [ S] is the concentration of a hydrogen-bonding minor component of a mixed solvent, Results for most of the twenty-three aprotic solvents investigated are modeled by bifurcation-type hydrogen bonding of two or more electron pairs to a single polar hydrogen. Results for the seven protic solvents studied, including new data for ethanol, 2-choloroethanol, and 2,2-dichloroethanol, are modeled by two, or possibly three, successive stages of solvation, assumed to involve hydrogen-bonded chains. Preliminary results indicate that solvation by water is amenable to this analysis.

  11. ENDOR Spectroscopy Reveals A Light Induced Movement of the H-Bond from Ser-L223 Upon Forming the Semiquinone (QB−•) in Reaction Centers from Rhodobacter sphaeroides (United States)

    Paddock, M. L.; Flores, M.; Isaacson, R.; Chang, C.; Abresch, E. C.; Okamura, M.Y.


    Proton ENDOR spectroscopy was used to monitor local conformational changes in bacterial reaction centers (RC) associated with the electron transfer reaction DQB → D+•QB−• using mutant RCs capable of photo-reducing QB at cryogenic temperatures. The charge separated state D+•QB−• was studied in mutant RCs formed by either (i) illuminating at low temperature (77K) a sample frozen in the dark (ground state protein conformation) or (ii) illuminating at room temperature prior to and during the freezing (charge separated state protein conformation). The charge recombination rates from the two states differed greatly (>106 fold) as shown previously, indicating a structural change (Paddock et al (2006) Biochemistry 45, 14032 - 14042). ENDOR spectra of QB−• from both samples (35 GHz, 77K) showed three nearly identical sets of hyperfine couplings due to exchangeable protons that were similar to those for QB−• in native RCs indicating that in all RCs, QB−• was located at the proximal position near the metal site. In contrast, one set of H-bond couplings was observed only in the sample frozen under illumination in which the protein can relax prior to freezing. This H-bond was assigned to an interaction between the Ser-L223 hydroxyl and QB−• based on its absence in Ser L223 → Ala mutant RCs. The Ser-L223 hydroxyl H-bond was also observed in the native RCs frozen under illumination. Thus, part of the protein relaxation in response to light induced charge separation involves the formation of an H-bond between the OH group of Ser-L223 and the anionic semiquinone QB−•. This proton movement serves to stabilize the charge separated state and facilitate proton transfer to reduced QB. PMID:17590017

  12. Low energy electron induced reactions in fluorinated acetamide - probing negative ions and neutral stable counterparts* (United States)

    Kopyra, Janina; König-Lehmann, Constanze; Illenberger, Eugen; Warneke, Jonas; Swiderek, Petra


    Electron impact to trifluoroacetamide (CF3CONH2, TFAA) in the energy range 0-12 eV leads to a variety of negative fragment ions which are formed via dissociative electron attachment (DEA). The underlying reactions range from single bond cleavages to remarkably complex reactions that lead to loss of the neutral units HF, H2O and HNCO as deduced from their directly observed ionic counterparts (M - H2O)-, (M - HF)- and (M - HNCO)-. Also formed are the pseudo-halogen ions CN- and OCN-. All these reactions proceed dominantly via a resonance located near 1 eV, i.e., electrons at subexcitation energies trigger reactions involving multiple bond cleavages. The electron induced generation of the neutral molecules HF, H2O and HNCO in condensed TFAA films is probed by temperature controlled thermal desorption spectrometry (TDS) which can be viewed as a complementary techniques to gas-phase experiments in DEA to directly probe the neutral counterparts. Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.

  13. Mixed chloride/phosphine complexes of the dirhenium core. 10. Redox reactions of an edge-sharing dirhenium(III) non-metal-metal-bonded complex, Re(2)(mu-Cl)(2)Cl(4)(PMe(3))(4). (United States)

    Cotton, F A; Dikarev, E V; Petrukhina, M A


    Reduction and oxidation reactions of the dirhenium(III) non-metal-metal-bonded edge-sharing complex, Re(2)(mu-Cl)(2)Cl(4)(PMe(3))(4) (1), have been studied. Several new mono- and dinuclear rhenium compounds have been isolated and structurally characterized in the course of this study. Reductions of 1 with 1 and 2 equiv of KC(8) result in an unusual face-sharing complex having an Re(2)(5+) core, Re(2)(mu-Cl)(3)Cl(2)(PMe(3))(4) (2), and a triply bonded Re(II) compound, 1,2,7,8-Re(2)Cl(4)(PMe(3))(4) (3), respectively. Two-electron reduction of 1 in the presence of tetrabutylammonium chloride affords a new triply bonded complex of the Re(2)(4+) core, [Bu(n)()(4)N][1,2,7-Re(2)Cl(5)(PMe(3))(3)] (4). Oxidation of 1 with NOBF(4) yields a Re(IV) mononuclear compound, trans-ReCl(4)(PMe(3))(2) (5). Two isomers of the monomeric Re(III) anion, [ReCl(4)(PMe(3))(2)](-) (6, 7), have been isolated as side products. The crystal structures of compounds 2 and 4-7 have been determined by X-ray crystallography. The Re-Re distance in the face-sharing complex 2 of 2.686(1) A is relatively short. The metal-metal bond length in anion 4 of 2.2354(7) A is consistent with the usual values for the triply bonded Re(2)(4+) core compounds. In addition, a cis arrangement of trimethylphosphine ligands in the starting material 1 is retained upon reduction in the dinuclear products 2-4.


    The microwave reactions of InX3 with [Q]Y produce a series of tetrahaloindate(III)-based ionic liquids (ILs) with a general formula of [Q][InX3Y] (Q = imidazolium, phosphonium, ammonium, and pyridinium; X = Cl, Br, I; Y = Cl, Br). The reaction of CO2

  15. Adduct Formation, B-H Activation and Ring Expansion at Room Temperature from Reactions of HBcat with NHCs. (United States)

    Würtemberger-Pietsch, Sabrina; Schneider, Heidi; Marder, Todd B; Radius, Udo


    We report the reactions of catecholborane (HBcat; 1) with unsaturated and saturated NHCs as well as CAAC(Me) . Mono-NHC adducts of the type HBcat⋅NHC (NHC=nPr2 Im, iPr2 Im, iPr2 Im(Me) , and Dipp2 Im) were obtained by stoichiometric reactions of HBcat with the unsaturated NHCs. The reaction of CAAC(Me) with HBcat yielded the B-H activated product CAAC(Me) (H)Bcat via insertion of the carbine-carbon atom into the B-H bond. The saturated NHC Dipp2 SIm reacted in a 2:2 ratio yielding an NHC ring-expanded product at room temperature forming a six-membered -B-C=N-C=C-N- ring via C-N bond cleavage and further migration of the hydrides from two HBcat molecules to the former carbene-carbon atom.

  16. The potato carotenoid cleavage dioxygenase 4 catalyzes a single cleavage of β-ionone ring-containing carotenes and non-epoxidated xanthophylls

    KAUST Repository

    Bruno, Mark


    Down-regulation of the potato carotenoid cleavage dioxygenase 4 (StCCD4) transcript level led to tubers with altered morphology and sprouting activity, which also accumulated higher levels of violaxanthin and lutein leading to elevated carotenoid amounts. This phenotype indicates a role of this enzyme in tuber development, which may be exerted by a cleavage product. In this work, we investigated the enzymatic activity of StCCD4, by expressing the corresponding cDNA in carotenoid accumulating Escherichia coli strains and by performing in vitro assays with heterologously expressed enzyme. StCCD4 catalyzed the cleavage of all-. trans-β-carotene at the C9\\'-C10\\' double bond, leading to β-ionone and all-. trans-β-apo-10\\'-carotenal, both in vivo and in vitro. The enzyme also cleaved β,β-cryptoxanthin, zeaxanthin and lutein either at the C9\\'-C10\\' or the C9-C10 double bond in vitro. In contrast, we did not observe any conversion of violaxanthin and only traces of activity with 9-. cis-β-carotene, which led to 9-. cis-β-apo-10\\'-carotenal. Our data indicate that all-. trans-β-carotene is the likely substrate of StCCD4 in planta, and that this carotene may be precursor of an unknown compound involved in tuber development.

  17. Dataset of cocoa aspartic protease cleavage sites

    Directory of Open Access Journals (Sweden)

    Katharina Janek


    Full Text Available The data provide information in support of the research article, “The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors” (Janek et al., 2016 [1]. Three different protein substrates were partially digested with the aspartic protease isolated from cocoa beans and commercial pepsin, respectively. The obtained peptide fragments were analyzed by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS/MS and identified using the MASCOT server. The N- and C-terminal ends of the peptide fragments were used to identify the corresponding in-vitro cleavage sites by comparison with the amino acid sequences of the substrate proteins. The same procedure was applied to identify the cleavage sites used by the cocoa aspartic protease during cocoa fermentation starting from the published amino acid sequences of oligopeptides isolated from fermented cocoa beans.

  18. Limited caspase cleavage of human BAP31. (United States)

    Määttä, J; Hallikas, O; Welti, S; Hildén, P; Schröder, J; Kuismanen, E


    Human BAP31 was cleaved at both of its two identical caspase cleavage sites in two previously reported models of apoptosis. We show here that only the most carboxy-terminal site is cleaved during apoptosis induced in HeLa cells by tunicamycin, tumor necrosis factor and cycloheximide, or staurosporine. Similar results were obtained in HL-60 cells using Fas/APO-1 antibodies, or cycloheximide. This limited cleavage, which is inhibited by several caspase inhibitors, removes eight amino acids from human BAP31 including the KKXX coat protein I binding motif. Ectopic expression of the resulting cleavage product induces redistribution of mannosidase II from the Golgi and prevents endoplasmic reticulum to Golgi transport of virus glycoproteins.

  19. C-Terminally modified peptides via cleavage of the HMBA linker by O-, i>N>- or S-nucleophiles

    DEFF Research Database (Denmark)

    Hansen, Jonas; Diness, Frederik; Meldal, Morten Peter


    A large variety of C-terminally modified peptides was obtained by nucleophilic cleavage of the ester bond in solid phase linked peptide esters of 4-hydroxymethyl benzamide (HMBA). The developed methods provided peptides, C-terminally functionalized as esters, amides and thioesters, with high puri...

  20. Parental Bonding

    Directory of Open Access Journals (Sweden)

    T. Paul de Cock


    Full Text Available Estimating the early parent–child bonding relationship can be valuable in research and practice. Retrospective dimensional measures of parental bonding provide a means for assessing the experience of the early parent–child relationship. However, combinations of dimensional scores may provide information that is not readily captured with a dimensional approach. This study was designed to assess the presence of homogeneous groups in the population with similar profiles on parental bonding dimensions. Using a short version of the Parental Bonding Instrument (PBI, three parental bonding dimensions (care, authoritarianism, and overprotection were used to assess the presence of unobserved groups in the population using latent profile analysis. The class solutions were regressed on 23 covariates (demographics, parental psychopathology, loss events, and childhood contextual factors to assess the validity of the class solution. The results indicated four distinct profiles of parental bonding for fathers as well as mothers. Parental bonding profiles were significantly associated with a broad range of covariates. This person-centered approach to parental bonding has broad utility in future research which takes into account the effect of parent–child bonding, especially with regard to “affectionless control” style parenting.

  1. Comprehensive mechanistic study of ion pair SN2 reactions of lithium isocyanate and methyl halides (United States)

    Sun, Ying-Xin; Ren, Yi; Wong, Ning-Bew; Chu, San-Yan; Xue, Ying

    The anionic SN2 reactions NCO- + CH3X and ion pair SN2 reactions LiNCO + CH3X (X = F, Cl, Br, and I) at saturated carbon with inversion and retention mechanisms were investigated at the level of MP2/6-311+G(d,p). There are two possible reaction pathways in the anionic SN2 reactions, but eight in the ion pair SN2 reactions. Calculated results suggest that the previously reported T-shaped isomer of lithium isocyanate does not exist. All the retention pathways are not favorable based on the analysis of transition structures. Two possible competitive reaction pathways proceed via two six-member ring inversion transition structures. It is found that there are two steps in the most favorable pathway, in which less stable lithium cyanate should be formed through the isomerization of lithium isocyanate and nucleophilic site (N) subsequently attacks methyl halides from the backside. The thermodynamically and kinetically favorable methyl isocyanate is predicted as major product both in the gas phase anionic and the ion pair SN2 reactions. In addition, good correlations between the overall barriers relative to separated reactants, ?H?ovr , with geometrical looseness parameter %L? and the heterolytic cleavage energies of the C bond X and Li bond N (or Li bond O) bonds are observed for the anionic and ion pair SN2 reactions. The trend of variation of the overall barriers predicts the leaving ability of X increase in the order: F reactions of LiNCO + CH3X. The calculations in solution indicate that solvent effects will retard the rate of reactions and the predicted product, methyl isocyanate, is same as the one in the gas phase.

  2. Photoassisted reaction of chemical warfare agent VX droplets under UV light irradiation. (United States)

    Zuo, Guo-Min; Cheng, Zhen-Xing; Li, Guo-Wen; Wang, Lian-Yuan; Chen, Hong


    A photoassisted reaction of O-ethyl S-[2-(diisopropylamino) ethyl] methylphosphonothioate (VX) droplets in air was carried out. The experimental results indicated that VX droplets could be easily and chemically transformed into other compounds under irradiation of a germicidal lamp over sufficient time. Quantum chemical calculation results demonstrated that UV light less than 278 nm wavelength could possibly initiate photoreaction of VX and that both P-S and P=O bonds in the VX molecule were lengthened. The identification of reaction products by gas and liquid chromatography mass spectroscopy and NMR revealed that the VX molecule in air under UV light irradiation could undergo isomerization of S-esters to O-esters, cleavage of P-S, S-C, and C-N bonds, and ozonation of tertiary amines.

  3. Crystal structures of triazine-3-thione derivatives by reaction with copper and cobalt salts. (United States)

    López-Torres, Elena; Mendiola, Maria Antonia; Pastor, César J


    The reaction of 5-methoxy-5,6-diphenyl-4,5-dihydro-2H-[1,2,4]triazine-3-thione L1H2OCH3 with copper(II) chloride leads to the formation of an organic molecule L2 containing two triazine rings linked by a new S-S bond. A binuclear copper(II) complex, 1, containing L1 is also isolated. The reaction of L1H2OCH3 with copper(I) chloride yields a hexanuclear cluster of copper(I), 2, in which the copper atoms form a distorted octahedron with the ligand L1 acting as an NS chelate and sulfur bridge, giving to the copper ion a trigonal geometry by one N and two S atoms. In any reaction of the disulfide L2 with metal salts, complexes containing this molecule are isolated. Reactions with copper(I) and copper(II) chloride and nickel(II) and cadmium(II) nitrate produce the S-S bond cleavage, giving complexes containing the triazine L1 behaving as the NS anion, which show spectroscopic characteristics identical with those formed by reaction with L1H2OCH3. However, the reaction with cobalt(II) nitrate gives a low-spin octahedral cobalt(III) complex, in which an asymmetric rupture of the disulfide L2 has been produced, giving an unexpected complex with a new ligand and keeping the S-S bond.

  4. Overexpression of Crocus carotenoid cleavage dioxygenase, CsCCD4b, in Arabidopsis imparts tolerance to dehydration, salt and oxidative stresses by modulating ROS machinery. (United States)

    Baba, Shoib Ahmad; Jain, Deepti; Abbas, Nazia; Ashraf, Nasheeman


    Apocarotenoids modulate vital physiological and developmental processes in plants. These molecules are formed by the cleavage of carotenoids, a reaction catalyzed by a family of enzymes called carotenoid cleavage dioxygenases (CCDs). Apocarotenoids like β-ionone and β-cyclocitral have been reported to act as stress signal molecules during high light stress in many plant species. In Crocus sativus, these two apocarotenoids are formed by enzymatic cleavage of β-carotene at 9, 10 and 7, 8 bonds by CsCCD4 enzymes. In the present study three isoforms of CsCCD4 were subjected to molecular modeling and docking analysis to determine their substrate specificity and all the three isoforms displayed high substrate specificity for β-carotene. Further, expression of these three CsCCD4 isoforms investigated in response to various stresses revealed that CsCCD4a and CsCCD4b exhibit enhanced expression in response to dehydration, salt and methylviologen, providing a clue towards their role in mediating plant defense response. This was confirmed by overexpressing CsCCD4b in Arabidopsis. The transgenic plants developed longer roots and possessed higher number of lateral roots. Further, overexpression of CsCCD4b imparted enhanced tolerance to salt, dehydration and oxidative stresses as was evidenced by higher survival rate, increased relative root length and biomass in transgenic plants as compared to wild type. Transgenic plants also displayed higher activity and expression of reactive oxygen species (ROS) metabolizing enzymes. This indicates that β-ionone and β-cyclocitral which are enzymatic products of CsCCD4b may act as stress signals and mediate reprogramming of stress responsive genes which ultimately leads to plant defense.

  5. LAMMPS Framework for Directional Dynamic Bonding

    DEFF Research Database (Denmark)


    and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework.......We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled...... to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead...

  6. Halogen Bonding in Organic Synthesis and Organocatalysis. (United States)

    Bulfield, David; Huber, Stefan M


    Halogen bonding is a noncovalent interaction similar to hydrogen bonding, which is based on electrophilic halogen substituents. Hydrogen-bonding-based organocatalysis is a well-established strategy which has found numerous applications in recent years. In light of this, halogen bonding has recently been introduced as a key interaction for the design of activators or organocatalysts that is complementary to hydrogen bonding. This Concept features a discussion on the history and electronic origin of halogen bonding, summarizes all relevant examples of its application in organocatalysis, and provides an overview on the use of cationic or polyfluorinated halogen-bond donors in halide abstraction reactions or in the activation of neutral organic substrates.

  7. Three methods to measure RH bond energies

    Energy Technology Data Exchange (ETDEWEB)

    Berkowitz, J. [Argonne National Lab., IL (United States); Ellison, G.B. [Univ. of Colorado, Boulder, CO (United States). Dept. of Chemistry and Biochemistry; Gutman, D. [Catholic Univ. of America, Washington, DC (United States). Dept. of Chemistry


    In this paper the authors compare and contrast three powerful methods for experimentally measuring bond energies in polyatomic molecules. The methods are: radical kinetics; gas phase acidity cycles; and photoionization mass spectroscopy. The knowledge of the values of bond energies are a basic piece of information to a chemist. Chemical reactions involve the making and breaking of chemical bonds. It has been shown that comparable bonds in polyatomic molecules, compared to the same bonds in radicals, can be significantly different. These bond energies can be measured in terms of bond dissociation energies.

  8. B-B bond activation and NHC ring-expansion reactions of diboron(4) compounds, and accurate molecular structures of B2(NMe2)4, B2eg2, B2neop2 and B2pin2. (United States)

    Eck, Martin; Würtemberger-Pietsch, Sabrina; Eichhorn, Antonius; Berthel, Johannes H J; Bertermann, Rüdiger; Paul, Ursula S D; Schneider, Heidi; Friedrich, Alexandra; Kleeberg, Christian; Radius, Udo; Marder, Todd B


    In this detailed study we report on the structures of the widely employed diboron(4) compounds bis(pinacolato)diboron (B2pin2) and bis(neopentyl glycolato)diboron (B2neop2), as well as bis(ethylene glycolato)diboron (B2eg2) and tetrakis(dimethylamino)diboron (B2(NMe2)4), and their reactivity, along with that of bis(catecholato)diboron (B2cat2) with backbone saturated and backbone unsaturared N-heterocyclic carbenes (NHCs) of different steric demand. Depending on the nature of the diboron(4) compound and the NHC used, Lewis-acid/Lewis-base adducts or NHC ring-expansion products stemming from B-B and C-N bond activation have been observed. The corresponding NHC adducts and NHC ring-expanded products were isolated and characterised via solid-state and solution NMR spectroscopy and X-ray diffraction. In general, we observed B-B bond and C-N bond activation at low temperature for B2eg2, at room temperature for B2neop2 and at higher temperature for B2cat2. The reactivity strongly depends on steric effects of the NHCs and the diboron(4) compounds, as well as on the corresponding Lewis-basicity and Lewis-acidity. Our results provide profound insight into the chemistry of these diboron(4) reagents with the nowadays ubiquitous NHCs, the stability of the corresponding NHC adducts and on B-B bond activation using Lewis-bases in general. We demonstrate that B-B bond activation may be triggered even at temperatures as low as -40 °C to -30 °C without any metal species involved. For example, the reactions of B2eg2 with sterically less demanding NHCs such as Me2Im(Me) and iPr2Im in solution led to the corresponding ring-expanded products at low temperatures. Furthermore, boronium [L2B(OR)2](+) and borenium [LB(OR)2](+) cations have been observed from the reaction of the bis-borate B2eg3 with the NHCs iPr2Im and Me2Im(Me), which led to the conclusion that the activation of bis-borates with NHCs (or Lewis-bases in general) might be a facile and simple route to access such species.

  9. Low-Temperature Bonding of Bi0.5Sb1.5Te3 Thermoelectric Material with Cu Electrodes Using a Thin-Film In Interlayer (United States)

    Lin, Yan-Cheng; Yang, Chung-Lin; Huang, Jing-Yi; Jain, Chao-Chi; Hwang, Jen-Dong; Chu, Hsu-Shen; Chen, Sheng-Chi; Chuang, Tung-Han


    A Bi0.5Sb1.5Te3 thermoelectric material electroplated with a Ni barrier layer and a Ag reaction layer was bonded with a Ag-coated Cu electrode at low temperatures of 448 K (175 °C) to 523 K (250 °C) using a 4- μm-thick In interlayer under an external pressure of 3 MPa. During the bonding process, the In thin film reacted with the Ag layer to form a double layer of Ag3In and Ag2In intermetallic compounds. No reaction occurred at the Bi0.5Sb1.5Te3/Ni interface, which resulted in low bonding strengths of about 3.2 MPa. The adhesion of the Bi0.5Sb1.5Te3/Ni interface was improved by precoating a 1- μm Sn film on the surface of the thermoelectric element and preheating it at 523 K (250 °C) for 3 minutes. In this case, the bonding strengths increased to a range of 9.1 to 11.5 MPa after bonding at 473 K (200 °C) for 5 to 60 minutes, and the shear-tested specimens fractured with cleavage characteristics in the interior of the thermoelectric material. The bonding at 448 K (175 °C) led to shear strengths ranging from 7.1 to 8.5 MPa for various bonding times between 5 and 60 minutes, which were further increased to the values of 10.4 to 11.7 MPa by increasing the bonding pressure to 9.8 MPa. The shear strengths of Bi0.5Sb1.5Te3/Cu joints bonded with the optimized conditions of the modified solid-liquid interdiffusion bonding process changed only slightly after long-term exposure at 473 K (200 °C) for 1000 hours.

  10. Single-molecule chemical reactions on DNA origami

    DEFF Research Database (Denmark)

    Voigt, Niels Vinther; Tørring, Thomas; Rotaru, Alexandru


    as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position...... on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally......DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve...

  11. Cleavage site analysis in picornaviral polyproteins

    DEFF Research Database (Denmark)

    Blom, Nikolaj; Hansen, Jan; Blaas, Dieter;


    are indeed cleaved awaits experimental verification. Additionally, we report several errors detected in the protein databases. A computer server for prediction of cleavage sites by picornaviral proteinases is publicly available at the e-mail address or via WWW at

  12. Aromatic C-H Bond Functionalization Induced by Electrochemically in Situ Generated Tris(p-bromophenyl)aminium Radical Cation: Cationic Chain Reactions of Electron-Rich Aromatics with Enamides. (United States)

    Li, Long-Ji; Jiang, Yang-Ye; Lam, Chiu Marco; Zeng, Cheng-Chu; Hu, Li-Ming; Little, R Daniel


    An effective Friedel-Crafts alkylation reaction of electron-rich aromatics with N-vinylamides, induced by electrochemically in situ-generated TBPA radical cation, has been developed; the resulting adducts are produced in good to excellent yields. In the "ex-cell" type electrolysis, TBPA is transformed to its oxidized form in situ and subsequently employed as an electron transfer reagent to initiate a cationic chain reaction. An easily recoverable and reusable polymeric ionic liquid-carbon black (PIL-CB) composite was also utilized as a supporting electrolyte for the electrochemical generation of TBPA cation radical, without sacrificing efficiency or stability after four electrolyses. Cyclic voltammetry analysis and the results of control experiments demonstrate that the reaction of electron-rich aromatics and N-vinylamides occurs via a cationic chain reaction, which takes place though an oxidative activation of a C-H bond of electron-rich aromatics instead of oxidation of the N-vinylamide as previously assumed.

  13. Computational prediction of cleavage using proteasomal in vitro digestion and MHC I ligand data

    Institute of Scientific and Technical Information of China (English)

    Yu-feng LU; Hao SHENG; Yi ZHANG; Zhi-yang LI


    Proteasomes are responsible for the production of the majority of cytotoxic T lymphocyte (CTL) epitopes.Hence,it is important to identify correctly which peptides will be generated by proteasomes from an unknown protein.However,the pool of proteasome cleavage data used in the prediction algorithms,whether from major histocompatibility complex (MHC) I ligand or in vitro digestion data,is not identical to in vivo proteasomal digestion products.Therefore,the accuracy and reliability of these models still need to be improved.In this paper,three types of proteasomal cleavage data,constitutive proteasome (cCP),immunoproteasome (iCP) in vitro cleavage,and MHC I ligandv data,were used for training cleave-site predictive methods based on the kernel-function stabilized matrix method (KSMM).The predictive accuracies of the KSMM+pair coefficients were 75.0%,72.3%,and 83.1% for cCP,iCP,and MHC I ligand data,respectively,which were comparable to the results from support vector machine (SVM).The three proteasomal cleavage methods were combined in turn with MHC I-peptide binding predictions to model MHC I-peptide processing and the presentation pathway.These integrations markedly improved MHC I peptide identification,increasing area under the receiver operator characteristics (ROC) curve (AUC) values from 0.82 to 0.91.The results suggested that both MHC I ligand and proteasomal in vitro degradation data can give an exact simulation of in vivo processed digestion.The information extracted from cCP and iCP in vitro cleavage data demonstrated that both cCP and iCP are selective in their usage of peptide bonds for cleavage.

  14. A domino palladium-catalyzed C-C and C-O bonds formation via dual O-H bond activation: synthesis of 6,6-dialkyl-6H-benzo[c]chromenes. (United States)

    Mahendar, Lodi; Krishna, Jonnada; Reddy, Alavala Gopi Krishna; Ramulu, Bokka Venkat; Satyanarayana, Gedu


    An efficient Pd-catalyzed domino reaction of α,α-dialkyl-(2-bromoaryl)methanols to 6,6-dialkyl-6H-benzo[c]chromenes is presented. Their formation can be explained via a five membered Pd(II)-cycle that efficiently involves a domino homocoupling with the second molecule, β-carbon cleavage, and finally intramolecular Buchwald-Hartwig cyclization. This domino process effectively involves breaking of five σ-bonds (2C-Br, 2O-H, and a C-C) and formation of two new σ-bonds (C-C and C-O). This mechanistic pathway is unprecedented and further illustrates the power of transition metal catalysis.

  15. Unusual products in the reactions of phosphorus(III) compounds with N=N, C≡C or conjugated double-bonded systems

    Indian Academy of Sciences (India)

    K C Kumara Swamy; E Balaraman; K Praveen Kumar; N Satish Kumar


    The diversity of products in the reaction of diethyl azodicarboxylate (DEAD)/diisopropyl azodicarboxylate (DIAD) and activated acetylenes with PIII compounds bearing oxygen or nitrogen substituents is discussed. New findings that are useful in understanding the nature of intermediates involved in the Mitsunobu reaction are highlighted. X-ray structures of two new compounds (2--Bu-4-MeC6H3O)P (-N--Bu)2P+[(NH--Bu){N[(CO2--Pr)(HNCO2--Pr)]}](Cl-)(2--Bu-4-MeC6H3OH) (23) and [CH2(6--Bu-4-Me-C6H2O)2P(O)C(CO2Me)C-(CO2Me)CClNC(O)Cl] (33) are also reported. The structure of 23 is close to one of the intermediates proposed in the Mitsunobu reaction.

  16. Force-activated reactivity switch in a bimolecular chemical reaction at the single molecule level (United States)

    Szoszkiewicz, Robert; Garcia-Manyes, Sergi; Liang, Jian; Kuo, Tzu-Ling; Fernandez, Julio M.


    Mechanical force can deform the reacting molecules along a well-defined direction of the reaction coordinate. However, the effect of mechanical force on the free-energy surface that governs a chemical reaction is still largely unknown. The combination of protein engineering with single-molecule AFM force-clamp spectroscopy allows us to study the influence of mechanical force on the rate at which a protein disulfide bond is reduced by some reducing agents in a bimolecular substitution reaction (so-called SN2). We found that cleavage of a protein disulfide bond by hydroxide anions exhibits an abrupt reactivity ``switch'' at 500 pN, after which the accelerating effect of force on the rate of an SN2 chemical reaction greatly diminishes. We propose that an abrupt force-induced conformational change of the protein disulfide bond shifts its ground state, drastically changing its reactivity in SN2 chemical reactions. Our experiments directly demonstrate the action of a force-activated switch in the chemical reactivity of a single molecule. References: Sergi Garcia-Manyes, Jian Liang, Robert Szoszkiewicz, Tzu-Ling Kuo and Julio M. Fernandez, Nature Chemistry, 1, 236-242, 2009.

  17. Bond Boom

    Institute of Scientific and Technical Information of China (English)


    The Ministry of Finance recently kick-started a pilot program allowing local governments of Shanghai and Shenzhen,and Zhejiang and Guangdong provinces to issue bonds for the first time.How will the new policy affect fiscal capacities of local governments and the broader economy? What else should the country do to build a healthy bond market? Economists and experts discussed these issues in an interview with the Shanghai Securities Journal.Edited excerpts follow.

  18. Bond Boom

    Institute of Scientific and Technical Information of China (English)


    The Ministry of Finance recently kick-started a pilot program allowing local governments of Shanghai and Shenzhen, and Zhejiang and Guangdong provinces to issue bonds for the first time. How will the new policy affect fiscal capacities of local governments and the broader economy? What else should the country do to build a healthy bond market? Economists and experts discussed these issues in an interview with the ShanghaiSecuritiesJournal. Edited excerpts follow:

  19. Insight into the Mechanism of the Michael Reaction. (United States)

    Giraldo, Carolina; Gómez, Sara; Weinhold, Frank; Restrepo, Albeiro


    The mechanism for the nucleophilic addition step of the Michael reaction between methanethiol as a model Michael donor and several α-substituted methyl acrylates (X=F, Cl, Me, H, CN, NO2 ) as model Michael acceptors is described in detail. We suggest a novel way to condense electrophilic Fukui functions at specific atoms in terms of the contributions from the atomic orbitals to the LUMO or, more generally, to the orbital controlling the reaction. This procedure correctly associates activation energies to local electrophilic Fukui indices for the cases treated in this work. The calculated reaction barriers strongly depend on the nature of the substituent. As a general rule, activation energies are governed by structural changes, although electronic factors are significant for electron-withdrawing groups. Nucleophilic addition to Michael receptors is best described as a highly nonsynchronous process, in which the geometry of the transition state comprises a nonplanar six-membered ring. Formation of the S⋅⋅⋅C bond, which defines the interaction between the reactants, progresses ahead of all other primitive processes in the early stages of the transformation. In view of our results, we postulate that highly complex chemical reactions, as is the case for the nucleophilic addition step studied herein, that involve cleavage/formation of a total of six bonds, lower their activation energies by favoring nonsynchronicity, that is, for these types of systems, primitive changes should advance at different rates.

  20. Lignin-derived oxygenate reforming on a bimetallic surface: The reaction of benzaldehyde on Zn/Pt(111) (United States)

    Shi, Daming; Vohs, John M.


    Temperature programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS) were used to characterize the adsorption and reaction of benzaldehyde (C6H5CHO) on hydrogen-covered Pt(111) and Zn-modified Pt(111) surfaces. Benzaldehyde was found to interact with Pt(111) via both the phenyl ring and carbonyl of the aldehyde group. This bonding configuration facilitates unselective decomposition of the benzaldehyde to produce CO, H2, and small hydrocarbon fragments at relatively low temperatures. On the other hand, benzaldehyde was found to bond to Zn-decorated Pt(111) surface exclusively via the carbonyl group in an η2(C, O) configuration, with the phenyl ring tilted away from the surface. This configuration weakens Csbnd O bond in the carbonyl facilitating its cleavage and helps prevent hydrogenation of the phenyl ring.

  1. Hydrogen bonding in cyclic imides and amide carboxylic acid derivatives from the facile reaction of cis-cyclohexane-1,2-carboxylic anhydride with o- and p-anisidine and m- and p-aminobenzoic acids. (United States)

    Smith, Graham; Wermuth, Urs D


    The structures of the open-chain amide carboxylic acid rac-cis-2-[(2-methoxyphenyl)carbamoyl]cyclohexane-1-carboxylic acid, C(15)H(19)NO(4), (I), and the cyclic imides rac-cis-2-(4-methoxyphenyl)-3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione, C(15)H(17)NO(3), (II), chiral cis-3-(1,3-dioxo-3a,4,5,6,7,7a-hexahydroisoindol-2-yl)benzoic acid, C(15)H(15)NO(4), (III), and rac-cis-4-(1,3-dioxo-3a,4,5,6,7,7a-hexahydroisoindol-2-yl)benzoic acid monohydrate, C(15)H(15)NO(4)·H(2)O, (IV), are reported. In the amide acid (I), the phenylcarbamoyl group is essentially planar [maximum deviation from the least-squares plane = 0.060 (1) Å for the amide O atom] and the molecules form discrete centrosymmetric dimers through intermolecular cyclic carboxy-carboxy O-H···O hydrogen-bonding interactions [graph-set notation R(2)(2)(8)]. The cyclic imides (II)-(IV) are conformationally similar, with comparable benzene ring rotations about the imide N-C(ar) bond [dihedral angles between the benzene and isoindole rings = 51.55 (7)° in (II), 59.22 (12)° in (III) and 51.99 (14)° in (IV)]. Unlike (II), in which only weak intermolecular C-H···O(imide) hydrogen bonding is present, the crystal packing of imides (III) and (IV) shows strong intermolecular carboxylic acid O-H···O hydrogen-bonding associations. With (III), these involve imide O-atom acceptors, giving one-dimensional zigzag chains [graph-set C(9)], while with the monohydrate (IV), the hydrogen bond involves the partially disordered water molecule which also bridges molecules through both imide and carboxy O-atom acceptors in a cyclic R(4)(4)(12) association, giving a two-dimensional sheet structure. The structures reported here expand the structural database for compounds of this series formed from the facile reaction of cis-cyclohexane-1,2-dicarboxylic anhydride with substituted anilines, in which there is a much larger incidence of cyclic imides compared to amide carboxylic acids.

  2. Enzymic Pathways for Formation of Carotenoid Cleavage Products (United States)

    Fleischmann, Peter; Zorn, Holger

    Degraded carotenoids (apocarotenoids, norisoprenoids) have been a subject of intensive research for several decades. From the perspective of human physiology and nutrition, the retinoids, acting as vitamins, signalling molecules, and visual pigments, attracted the greatest attention (Chapters 15 and 16). Plant scientists, however, detected a wealth of different apocarotenoids, presumably derived by the excentric cleavage of carotenoids in various species, the plant hormone abscisic acid (1, Scheme 6) being the best-investigated example. With the onset of fruit ripening, flower opening or senescence of green tissues, carotenoids are degraded oxidatively to smaller, volatile compounds. The natural biological functions of the reaction products are outlined in Chapter 15. As many of these apocarotenoids act as potent flavour compounds, food chemists and flavourists worldwide have investigated meticulously their structural and sensory properties. Many aspects of carotenoid metabolites and breakdown products as aroma compounds are presented in a comprehensive book [1].

  3. Cleavage specificity analysis of six type II transmembrane serine proteases (TTSPs using PICS with proteome-derived peptide libraries.

    Directory of Open Access Journals (Sweden)

    Olivier Barré

    Full Text Available BACKGROUND: Type II transmembrane serine proteases (TTSPs are a family of cell membrane tethered serine proteases with unclear roles as their cleavage site specificities and substrate degradomes have not been fully elucidated. Indeed just 52 cleavage sites are annotated in MEROPS, the database of proteases, their substrates and inhibitors. METHODOLOGY/PRINCIPAL FINDING: To profile the active site specificities of the TTSPs, we applied Proteomic Identification of protease Cleavage Sites (PICS. Human proteome-derived database searchable peptide libraries were assayed with six human TTSPs (matriptase, matriptase-2, matriptase-3, HAT, DESC and hepsin to simultaneously determine sequence preferences on the N-terminal non-prime (P and C-terminal prime (P' sides of the scissile bond. Prime-side cleavage products were isolated following biotinylation and identified by tandem mass spectrometry. The corresponding non-prime side sequences were derived from human proteome databases using bioinformatics. Sequencing of 2,405 individual cleaved peptides allowed for the development of the family consensus protease cleavage site specificity revealing a strong specificity for arginine in the P1 position and surprisingly a lysine in P1' position. TTSP cleavage between R↓K was confirmed using synthetic peptides. By parsing through known substrates and known structures of TTSP catalytic domains, and by modeling the remainder, structural explanations for this strong specificity were derived. CONCLUSIONS: Degradomics analysis of 2,405 cleavage sites revealed a similar and characteristic TTSP family specificity at the P1 and P1' positions for arginine and lysine in unfolded peptides. The prime side is important for cleavage specificity, thus making these proteases unusual within the tryptic-enzyme class that generally has overriding non-prime side specificity.

  4. Temperature and chemical bonding-directed self-assembly of cobalt phosphide nanowires in reaction solutions into vertical and horizontal alignments. (United States)

    Zhang, Shuang-Yuan; Ye, Enyi; Liu, Shuhua; Lim, Suo Hon; Tee, Si Yin; Dong, Zhili; Han, Ming-Yong


    The preparation of vertically or horizontally aligned self-assemblies of CoP nanowires is demonstrated for the first time by aging them in the reaction solution for a sufficient time at 20 or 0 °C. This strategy opens up a way for exploring the controlled self-assembly of various highly anisotropic nanostructures into long-range ordered structures with collective properties.

  5. Palladium nanoparticles bonded to two-dimensional iron oxide graphene nanosheets: a synergistic and highly reusable catalyst for the Tsuji-Trost reaction in water and air. (United States)

    Liu, Jian; Huo, Xing; Li, Tianrong; Yang, Zhengyin; Xi, Pinxian; Wang, Zhiyi; Wang, Baodui


    Low cost, high activity and selectivity, convenient separation, and increased reusability are the main requirements for noble-metal-nanocatalyst-catalyzed reactions. Despite tremendous efforts, developing noble-metal nanocatalysts to meet the above requirements remains a significant challenge. Here we present a general strategy for the preparation of strongly coupled Fe(3)O(4) and palladium nanoparticles (PdNPs) to graphene sheets by employing polyethyleneimine as the coupling linker. Transmission electron microscopic images show that Pd and Fe(3)O(4) nanoparticles are highly dispersed on the graphene surface, and the mean particle size of Pd is around 3 nm. This nanocatalyst exhibits synergistic catalysis by Pd nanoparticles supported on reduced graphene oxide (rGO) and a tertiary amine of polyethyleneimine (Pd/Fe(3)O(4)/PEI/rGO) for the Tsuji-Trost reaction in water and air. For example, the reaction of ethyl acetoacetate with allyl ethyl carbonate afforded the allylated product in more than 99 % isolated yield, and the turnover frequency reached 2200 h(-1). The yield of allylated products was 66 % for Pd/rGO without polyethyleneimine. The catalyst could be readily recycled by a magnet and reused more than 30 times without appreciable loss of activity. In addition, only about 7.5 % of Pd species leached off after 20 cycles, thus rendering this catalyst safer for the environment.

  6. Ultrarapid mutation detection by multiplex, solid-phase chemical cleavage

    Energy Technology Data Exchange (ETDEWEB)

    Rowley, G.; Saad, S.; Giannelli, F.; Green, P.M. [Guy`s & St. Thomas`s Hospitals, London (United Kingdom)


    The chemical cleavage of mismatches in heteroduplexes formed by probe and test DNA detects and locates any sequence change in long DNA segments ({approximately}1.8 kb), and its efficiency has been well tested in the analysis of both average (e.g., coagulation factor IX) and large, complex genes (e.g., coagulation factor VIII and dystrophin). In the latter application RT/PCR products allow the examination of all essential sequences of the gene in a minimum number of reactions. We use two specific chemical reactants (hydroxylamine and osmium tetroxide) and piperidine cleavage of the above procedure to develop a very fast mutation screening method. This is based on: (1) 5{prime} or internal fluorescent labeling to allow concurrent screening of three to four DNA fragments and (2) solid-phase chemistry to use a microliter format and reduce the time required for the procedure, from amplification of sequence to gel loading inclusive, to one person-working-day. We test the two variations of the method, one entailing 5{prime} labeling of probe DNA and the other uniform labeling of both probe and target DNA, by detecting 114 known hemophilia B (coagulation factor IX) mutations and by analyzing 129 new patients. Uniform labeling of both probe and target DNA prior to formation of the heteroduplexes leads to almost twofold redundancy in the ability to detect mutations. Alternatively, the latter procedure may offer very efficient though less than 100% screening for sequence changes with only hydroxylamine. The full method with two chemical reactions (hydroxylamine and osmium tetroxide) should allow one person to screen with virtually 100% accuracy more than 300 kb of sequence in three ABI 373 gels in 1 day. 26 refs., 7 figs., 1 tab.

  7. The cleavage of phosphoenolpyruvate by vanadate. (United States)

    Aureliano, M; Leta, J; Madeira, V M; de Meis, L


    Vanadate rapidly promotes the cleavage of phosphoenolpyruvate with phosphate liberation. This was not observed when ATP, glucose-6-phosphate and acetyl phosphate were incubated with vanadate. 51V NMR spectra shows that phosphoenolpyruvate and acetyl phosphate broadened and shifted upfield the monomeric vanadate signal at -561 ppm, indicative of vanadate/phosphate interactions. Comparatively, smaller changes were detected when glucose-6-phosphate was added to the vanadate solution. The shift behavior was not observed in the presence of ATP, ADP or pyruvate.

  8. Synthesis and characterization of mononuclear iron silanethiolato complexes containing an unsupported Fe-S-Si bond system: X-ray crystal structure of CpFe(CO)2SSiPh3 and its reaction with SO2. (United States)

    Kovács, István; Bélanger-Gariépy, Francine; Shaver, Alan


    Mononuclear iron silanethiolato complexes of the type CpFe(CO)(2)SSiR(3), where R = Ph (1a) and (i)()Pr (1b), were prepared via treatment of [CpFe(CO)(2)(THF)]BF(4) with LiSSiPh(3).Et(2)O and NaSSi(i)()Pr(3), respectively. The molecular structure of 1a was determined by X-ray crystallography. Complex 1a was reacted with 1 equiv of SO(2) to give the corresponding O-silyl thiosulfite, CpFe(CO)(2)SS(O)OSiPh(3) (2), via 1,2-insertion of SO(2) into the S-Si bond. This reaction models the activation of SO(2) in the homogeneously catalyzed Claus process.

  9. Theoretical study of the mechanism for C-H bond activation in spin-forbidden reaction between Ti+ and C2H4

    Institute of Scientific and Technical Information of China (English)


    The mechanism of the spin-forbidden reaction Ti+(4F, 3d24s1) + C2H4 → TiC2H2+ (2A2) + H2 on both doublet and quartet potential energy surfaces has been investigated at the B3LYP level of theory. Crossing points between the potential energy surfaces and the possible spin inversion process are discussed by means of spin-orbit coupling (SOC) calculations. The strength of the SOC between the low-lying quartet state and the doublet state is 59.3 cm-1 in the intermediate complex IM1-4B2. Thus, the changes of its spin multiplicity may occur from the quartet to the doublet surface to form IM1- 2A1, leading to a sig-nificant decrease in the barrier height on the quartet PES. After the insertion intermediate IM2, two dis-tinct reaction paths on the doublet PES have been found, i.e., a stepwise path and a concerted path. The latter is found to be the lowest energy path on the doublet PES to exothermic TiC2H2+ (2A2) + H2 products, with the active barrier of 4.52 kcal/mol. In other words, this reaction proceeds in the following way: Ti++C2H4 →4IC→IM1-4B2→4,2ISC→IM1- 2A1→[2TSins]→IM2→[2TSMCTS]→IM5→TiC2H2+(2A2)+H2.

  10. In vivo analysis of the Notch receptor S1 cleavage.

    Directory of Open Access Journals (Sweden)

    Robert J Lake

    Full Text Available A ligand-independent cleavage (S1 in the extracellular domain of the mammalian Notch receptor results in what is considered to be the canonical heterodimeric form of Notch on the cell surface. The in vivo consequences and significance of this cleavage on Drosophila Notch signaling remain unclear and contradictory. We determined the cleavage site in Drosophila and examined its in vivo function by a transgenic analysis of receptors that cannot be cleaved. Our results demonstrate a correlation between loss of cleavage and loss of in vivo function of the Notch receptor, supporting the notion that S1 cleavage is an in vivo mechanism of Notch signal control.

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

    Energy Technology Data Exchange (ETDEWEB)

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


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

  12. VAMP/synaptobrevin cleavage by tetanus and botulinum neurotoxins is strongly enhanced by acidic liposomes. (United States)

    Caccin, Paola; Rossetto, Ornella; Rigoni, Michela; Johnson, Eric; Schiavo, Giampietro; Montecucco, Cesare


    Tetanus and botulinum neurotoxins (TeNT and BoNTs) block neuroexocytosis via specific cleavage and inactivation of SNARE proteins. Such activity is exerted by the N-terminal 50 kDa light chain (L) domain, which is a zinc-dependent endopeptidase. TeNT, BoNT/B, /D, /F and /G cleave vesicle associated membrane protein (VAMP), a protein of the neurotransmitter-containing small synaptic vesicles, at different single peptide bonds. Since the proteolytic activity of these metalloproteases is higher on native VAMP inserted in synaptic vesicles than on recombinant VAMP, we have investigated the influence of liposomes of different lipid composition on this activity. We found that the rate of VAMP cleavage with all neurotoxins tested here is strongly enhanced by negatively charged lipid mixtures. This effect is at least partially due to the binding of the metalloprotease to the lipid membranes, with electrostatic interactions playing an important role.

  13. Cyclodiphosphazanes as synthetic probes: P-C/P-N bond formation from the reaction with functionalized propargyl alcohols and -hydroxy substrates

    Indian Academy of Sciences (India)

    G Gangadhararao; K C Kumara Swamy


    Phosphano-indoles were synthesized in a fairly straightforward route from the reaction of simple cyclodiphosphazanes [XP(-N-t-Bu)2PY] [X=Y=NH--Bu (1a); X=Y=NH-i-Pr (1b)] with o-aminophenyl functionalized propargyl alcohols. The reaction occurs via an allene intermediate formed by PIII-O-C→PV(O)-C rearrangement, followed by cyclization utilizing the central allenic carbon and the –NH2 functionality. In a similar way, cyclodiphosphazanes [XP(-N-t-Bu)2PY] [X=Y=Cl (1c); X=Cl, Y=NH--Bu(1d)] have been treated with N-hydroxy substrates to obtain novel PIII-O-N→PV(O)-N rearranged products.X-ray structures of the four products, 2-(1-phenyl-ethyl)-3-[(t-Bu)NH)P(-N--Bu)2P(O)]-indole [14], cis-{[-C(=O)-C6H4-C(=O)-]-N-P(=O)-N-t-Bu}2[cis-18], trans-{[-C(=O)-C6H4-C(=O)-]-N-P(=O)-N--Bu}2 [trans-18] and cis-[(-BuNH)P(-N-t−Bu)2P(=O)-N{-C(=O)-CH2-CH2-C(=O)-}] [cis-19] are also reported

  14. SVM-based prediction of caspase substrate cleavage sites

    Directory of Open Access Journals (Sweden)

    Ranganathan Shoba


    Full Text Available Abstract Background Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of such cleavage sites will complement structural and functional studies on substrates cleavage as well as discovery of new substrates. Recently, different computational methods have been developed to predict the cleavage sites of caspase substrates with varying degrees of success. As the support vector machines (SVM algorithm has been shown to be useful in several biological classification problems, we have implemented an SVM-based method to investigate its applicability to this domain. Results A set of unique caspase substrates cleavage sites were obtained from literature and used for evaluating the SVM method. Datasets containing (i the tetrapeptide cleavage sites, (ii the tetrapeptide cleavage sites, augmented by two adjacent residues, P1' and P2' amino acids and (iii the tetrapeptide cleavage sites with ten additional upstream and downstream flanking sequences (where available were tested. The SVM method achieved an accuracy ranging from 81.25% to 97.92% on independent test sets. The SVM method successfully predicted the cleavage of a novel caspase substrate and its mutants. Conclusion This study presents an SVM approach for predicting caspase substrate cleavage sites based on the cleavage sites and the downstream and upstream flanking sequences. The method shows an improvement over existing methods and may be useful for predicting hitherto undiscovered cleavage sites.

  15. Cleavage crystallography of liquid metal embrittled aluminum alloys (United States)

    Reynolds, A. P.; Stoner, G. E.


    The crystallography of liquid metal-induced transgranular cleavage in six aluminum alloys having a variety of microstructures has been determined via Laue X-ray back reflection. The cleavage crystallography was independent of alloy microstructure, and the cleavage plane was 100-plane oriented in all cases. It was further determined that the cleavage crystallography was not influenced by alloy texture. Examination of the fracture surface indicated that there was not a unique direction of crack propagation. In addition, the existence of 100-plane cleavage on alloy 2024 fracture surfaces was inferred by comparison of secondary cleavage crack intersection geometry on the 2024 surfaces with the geometry of secondary cleavage crack intersections on the test alloys.

  16. Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics. (United States)

    Shemesh, Dorit; Nizkorodov, Sergey A; Gerber, R Benny


    Photochemistry of carbonyl compounds is of major importance in atmospheric and organic chemistry. The photochemistry of cyclohexanone is studied here using on-the-fly molecular dynamics simulations on a semiempirical multireference configuration interaction potential-energy surface to predict the distribution of photoproducts and time scales for their formation. Rich photochemistry is predicted to occur on a picosecond time scale following the photoexcitation of cyclohexanone to the first singlet excited state. The main findings include: (1) Reaction channels found experimentally are confirmed by the theoretical simulations, and a new reaction channel is predicted. (2) The majority (87%) of the reactive trajectories start with a ring opening via C-Cα bond cleavage, supporting observations of previous studies. (3) Mechanistic details, time scales, and yields are predicted for all reaction channels. These benchmark results shed light on the photochemistry of isolated carbonyl compounds in the atmosphere and can be extended in the future to photochemistry of more complex atmospherically relevant carbonyl compounds in both gaseous and condensed-phase environments.

  17. Theoretical Study on Reaction Pathways Leading to CO and CO2 in the Pyrolysis of Resorcinol. (United States)

    Furutani, Yuki; Kudo, Shinji; Hayashi, Jun-Ichiro; Norinaga, Koyo


    Possible pathways for the pyrolysis of resorcinol with the formation of CO and CO2 as final products were proposed and evaluated using ab initio calculations. Our experimental study revealed that large quantities of CO2 are generated in the pyrolysis of 1,3-dihydroxybenzene (resorcinol), while the pyrolysis of the dihydroxybenzene isomers 1,2-dihydroxybenzene (catechol) and 1,4-dihydroxybenzene (hydroquinone) produces little CO2. The fate of oxygen atoms in catechol and hydroquinone was essentially the formation of CO. In the proposed pathways, the triplet ground state m-benzoquinone was generated initially from simultaneous cleavage of the two O-H bonds in resorcinol. Subsequently, the direct cleavage of a C-C bond of the m-benzoquinone diradical yields 2-oxidanylcyclopenta-2,4-dien-1-yl-methanone, which can be converted via two channels: release of CO from the aldehyde radical group and combination of the ketone radical and carbon atom in the aldehyde radical group to form the 6-oxabicyclo[3.2.0]hepta-2,4-dien-7-one, resulting in the release of CO2. Potential energy surfaces along the proposed reaction pathways were calculated employing the CBS-QB3 method, and the rate constants at the high-pressure limit were also evaluated based on transition-state theory to assess the feasibility of the proposed reaction pathways.

  18. Photoinduced hydrogen-bonding dynamics. (United States)

    Chu, Tian-Shu; Xu, Jinmei


    Hydrogen bonding dynamics has received extensive research attention in recent years due to the significant advances in femtolaser spectroscopy experiments and quantum chemistry calculations. Usually, photoexcitation would cause changes in the hydrogen bonding formed through the interaction between hydrogen donor and acceptor molecules on their ground electronic states, and such transient strengthening or weakening of hydrogen bonding could be crucial for the photophysical transformations and the subsequent photochemical reactions that occurred on a time scale from tens of femtosecond to a few nanoseconds. In this article, we review the combined experimental and theoretical studies focusing on the ultrafast electronic and vibrational hydrogen bonding dynamics. Through these studies, new mechanisms and proposals and common rules have been put forward to advance our understanding of the hydrogen bondings dynamics in a variety of important photoinduced phenomena like photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer processes, chemosensor fluorescence sensing, rearrangements of the hydrogen-bond network including forming and breaking hydrogen bond in water. Graphical Abstract We review the recent advances on exploring the photoinduced hydrogen bonding dynamics in solutions through a joint approach of laser spectroscopy and theoretical calculation. The reviewed studies have put forward a new mechanism, new proposal, and new rule for a variety of photoinduced phenomena such as photosynthesis, dual fluorescence emission, rotational reorientation, excited-state proton transfer and charge transfer, chemosensor fluorescence sensing, and rearrangements of the hydrogen-bond network in water.

  19. Mechanism of arylboronic acid-catalyzed amidation reaction between carboxylic acids and amines. (United States)

    Wang, Chen; Yu, Hai-Zhu; Fu, Yao; Guo, Qing-Xiang


    Arylboronic acids were found to be efficient catalysts for the amidation reactions between carboxylic acids and amines. Theoretical calculations have been carried out to investigate the mechanism of this catalytic process. It is found that the formation of the acyloxyboronic acid intermediates from the carboxylic acid and the arylboronic acid is kinetically facile but thermodynamically unfavorable. Removal of water (as experimentally accomplished by using molecular sieves) is therefore essential for overall transformation. Subsequently C-N bond formation between the acyloxyboronic acid intermediates and the amine occurs readily to generate the desired amide product. The cleavage of the C-O bond of the tetracoordinate acyl boronate intermediates is the rate-determining step in this process. Our analysis indicates that the mono(acyloxy)boronic acid is the key intermediate. The high catalytic activity of ortho-iodophenylboronic acid is attributed to the steric effect as well as the orbital interaction between the iodine atom and the boron atom.

  20. Synthesis and DNA cleavage activities of mononuclear macrocyclic polyamine zinc(II), copper(II), cobalt(II) complexes which linked with uracil. (United States)

    Wang, Xiao-Yan; Zhang, Ji; Li, Kun; Jiang, Ning; Chen, Shan-Yong; Lin, Hong-Hui; Huang, Yu; Ma, Li-Jian; Yu, Xiao-Qi


    Mononuclear macrocyclic polyamine zinc(II), copper(II), cobalt(II) complexes, which could attach to peptide nucleic acid (PNA), were synthesized as DNA cleavage agents. The structures of these new mononuclear complexes were identified by MS and (1)H NMR spectroscopy. The catalytic activities on DNA cleavage of these mononuclear complexes with different central metals were subsequently studied, which showed that copper complex was better catalyst in the DNA cleavage process than zinc and cobalt complexes. The effects of reaction time, concentration of complexes were also investigated. The results indicated that the copper(II) complexes could catalyze the cleavage of supercoiled DNA (pUC 19 plasmid DNA) (Form I) under physiological conditions to produce selectively nicked DNA (Form II, no Form III produced) with high yields. The mechanism of the cleavage process was also studied.

  1. Efficient and specific internal cleavage of a retroviral palindromic DNA sequence by tetrameric HIV-1 integrase.

    Directory of Open Access Journals (Sweden)

    Olivier Delelis

    Full Text Available BACKGROUND: HIV-1 integrase (IN catalyses the retroviral integration process, removing two nucleotides from each long terminal repeat and inserting the processed viral DNA into the target DNA. It is widely assumed that the strand transfer step has no sequence specificity. However, recently, it has been reported by several groups that integration sites display a preference for palindromic sequences, suggesting that a symmetry in the target DNA may stabilise the tetrameric organisation of IN in the synaptic complex. METHODOLOGY/PRINCIPAL FINDINGS: We assessed the ability of several palindrome-containing sequences to organise tetrameric IN and investigated the ability of IN to catalyse DNA cleavage at internal positions. Only one palindromic sequence was successfully cleaved by IN. Interestingly, this symmetrical sequence corresponded to the 2-LTR junction of retroviral DNA circles-a palindrome similar but not identical to the consensus sequence found at integration sites. This reaction depended strictly on the cognate retroviral sequence of IN and required a full-length wild-type IN. Furthermore, the oligomeric state of IN responsible for this cleavage differed from that involved in the 3'-processing reaction. Palindromic cleavage strictly required the tetrameric form, whereas 3'-processing was efficiently catalysed by a dimer. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that the restriction-like cleavage of palindromic sequences may be a general physiological activity of retroviral INs and that IN tetramerisation is strongly favoured by DNA symmetry, either at the target site for the concerted integration or when the DNA contains the 2-LTR junction in the case of the palindromic internal cleavage.

  2. Abyssal fiction: common shares, colonial cleavages

    Directory of Open Access Journals (Sweden)

    Alexandre Montaury


    Full Text Available The paper aims to develop a reflection on the interaction between the legacies of colonialism and traditional symbolic and cultural practices in African Portuguese-speaking spaces. From a preliminary analysis of fictional texts of wide circulation in Brazil, aims to examine the cleavages, or “abyssal lines” that constitute experiences printed in the daily life of the former Portuguese colony of Cape Verde, Mozambique and Angola.---DOI:

  3. Task-Specific Ionic Liquids Catalyzed Carbon-Heteroatom Bond Formation Reactions%功能化离子液体催化碳-杂键形成反应

    Institute of Scientific and Technical Information of China (English)

    李满; 杨磊; 韩峰; 陈静; 夏春谷


    离子液体独特的溶剂性能使它在合成和催化领域得到了广泛的应用.然而,离子液体的经济问题和可能的环境友好性问题使得人们逐渐把目光投向了离子液体自身的催化性能.人们通过对离子液体结构的修饰设计出了各种具有特定催化性能的功能化离子液体.近年来功能化离子液体在催化碳-杂键形成反应方面有了相当多的应用.本文以形成的碳-杂原子键类型为主线,综述了功能化离子液体在催化碳-杂键形成反应方面的最新研究进展,涉及到了酸性离子液体、碱性离子液体、金属有机功能化离子液体、酸碱双功能离子液体、手性离子液体等多种类型的功能化离子液体.%Ionic liquids have emerged as excellent solvents for synthesis and catalysis in the past decades due to their special properties.However,their relatively high cost and potential risks to human health and environment make their function as catalysts rather than solvents more popular.Incorporating specific functional group(s) into one or both ions of ionic liquids to make them catalytic is highly important.Numerous so-called task-specific or functionalized ionic liquids are designed and successfully applied in catalyzing various reactions.In this review,we present the latest achievements in the carbon-heteroatom bond formation reactions catalyzed by task-specific ionic liquids.The contents are arranged according to the specific types of carbon-heteroatom bond formation reactions.As for the type of task-specific ionic liquids,this review focuses on acidic ionic liquids,basic ionic liquids,organometallic ionic liquids,acid-base bifunctional ionic liquids and chiral ionic liquids.

  4. Computational Study of Metal-Dinitrogen Keggin-Type Polyoxometalate Complexes [PW11O39M(II)N2)](5-) (M = Ru, Os, Re, Ir): Bonding Nature and Dinitrogen Splitting. (United States)

    Liu, Chun-Guang; Liu, Shuang; Zheng, Ting


    Molecular geometry, electronic structure, and metal-dinitrogen bonding nature of a series of metal-dinitrogen derivatives of Keggin-type polyoxometalates (POMs) [PW11O39M(II)N2)](5-) (M = Ru, Os, Re, Ir) have been studied by using a density functional theory (DFT) method with the M06L functional. Among these Keggin-type POM complexes, Os- and Re-substituted POM complexes are the most active for N2 adsorption with considerable adsorption energy. The electronic structure analysis shows that Os(II) and Re(II) centers in their metal-dinitrogen POM complexes possess π(2)xzπ(2)yzπ(2)xy and π(2)xzπ(2)yzπ(1)xy configurations, respectively. DFT-M06L calculations show that the possible synthesis routes proposed in this work for the Ru-, Os-, and Re-dinitrogen POM complexes are thermodynamically feasible under various solvent environments. Meanwhile, the Re-dinitrogen POM complex was assessed for the direct cleavage of dinitrogen molecule. In the reaction mechanism, a dimeric Keggin-type POM derivative of rhenium could represent the intermediate which undergoes N-N bond scission. The calculated free energy barrier (ΔG(⧧)) for a transition state with a zigzag conformation is 16.05 kcal mol(-1) in tetrahydrofuran, which is a moderate barrier for the cleavage of the N-N bond when compared with the literature values. In conclusion, regarding the direct cleavage of the dinitrogen molecule, the findings would be very useful to guide the search for a potential N2 cleavage compound into totally inorganic POM fields.

  5. A regioselective synthesis of benzopinacolones through aerobic dehydrogenative α-arylation of the tertiary sp3 C-H bond of 1,1-diphenylketones with aromatic and heteroaromatic compounds. (United States)

    More, Nagnath Yadav; Jeganmohan, Masilamani


    A regioselective synthesis of symmetrical and unsymmetrical benzopinacolones through aerobic dehydrogenative α-arylation at the tertiary sp(3) C-H bond of substituted 1,1-diphenylketones with aromatic and heteroaromatic compounds, in the presence of K2S2O8 in CF3COOH at room temperature, is described. The reaction is proposed to go via a carbocation intermediate, which could be generated directly from cleavage of the sp(3) C-H bond of 1,1-diphenylketone. Subsequent α-arylation was achieved at the methene sp(3) carbon atom of the substituted ketone. A variety of substituted aromatic and heteroaromatic compounds were compatible with this reaction. In addition, benzopinacolones were converted into sterically hindered, tetrasubstituted alkenes and polycyclic aromatic compounds.

  6. Novel insights into the fungal oxidation of monoaromatic and biarylic environmental pollutants by characterization of two new ring cleavage enzymes. (United States)

    Schlüter, Rabea; Lippmann, Ramona; Hammer, Elke; Gesell Salazar, Manuela; Schauer, Frieder


    The phenol-degrading yeast Trichosporon mucoides can oxidize and detoxify biarylic environmental pollutants such as dibenzofuran, diphenyl ether and biphenyl by ring cleavage. The degradation pathways are well investigated, but the enzymes involved are not. The high similarity of hydroxylated biphenyl derivatives and phenol raised the question if the enzymes of the phenol degradation are involved in ring cleavage or whether specific enzymes are necessary. Purification of enzymes from T. mucoides with catechol cleavage activity demonstrated the existence of three different enzymes: a classical catechol-1,2-dioxygenase (CDO), not able to cleave the aromatic ring system of 3,4-dihydroxybiphenyl, and two novel enzymes with a high affinity towards 3,4-dihydroxybiphenyl. The comparison of the biochemical characteristics and mass spectrometric sequence data of these three enzymes demonstrated that they have different substrate specificities. CDO catalyzes the ortho-cleavage of dihydroxylated monoaromatic compounds, while the two novel enzymes carry out a similar reaction on biphenyl derivatives. The ring fission of 3,4-dihydroxybiphenyl by the purified enzymes results in the formation of (5-oxo-3-phenyl-2,5-dihydrofuran-2-yl)acetic acid. These results suggest that the ring cleavage enzymes catalyzing phenol degradation are not involved in the ring cleavage of biarylic compounds by this yeast, although some intermediates of the phenol metabolism may function as inducers.

  7. Bond energies of ThO+ and ThC+: A guided ion beam and quantum chemical investigation of the reactions of thorium cation with O2 and CO (United States)

    Cox, Richard M.; Citir, Murat; Armentrout, P. B.; Battey, Samuel R.; Peterson, Kirk A.


    Kinetic energy dependent reactions of Th+ with O2 and CO are studied using a guided ion beam tandem mass spectrometer. The formation of ThO+ in the reaction of Th+ with O2 is observed to be exothermic and barrierless with a reaction efficiency at low energies of k/kLGS = 1.21 ± 0.24 similar to the efficiency observed in ion cyclotron resonance experiments. Formation of ThO+ and ThC+ in the reaction of Th+ with CO is endothermic in both cases. The kinetic energy dependent cross sections for formation of these product ions were evaluated to determine 0 K bond dissociation energies (BDEs) of D0(Th+-O) = 8.57 ± 0.14 eV and D0(Th+-C) = 4.82 ± 0.29 eV. The present value of D0 (Th+-O) is within experimental uncertainty of previously reported experimental values, whereas this is the first report of D0 (Th+-C). Both BDEs are observed to be larger than those of their transition metal congeners, TiL+, ZrL+, and HfL+ (L = O and C), believed to be a result of lanthanide contraction. Additionally, the reactions were explored by quantum chemical calculations, including a full Feller-Peterson-Dixon composite approach with correlation contributions up to coupled-cluster singles and doubles with iterative triples and quadruples (CCSDTQ) for ThC, ThC+, ThO, and ThO+, as well as more approximate CCSD with perturbative (triples) [CCSD(T)] calculations where a semi-empirical model was used to estimate spin-orbit energy contributions. Finally, the ThO+ BDE is compared to other actinide (An) oxide cation BDEs and a simple model utilizing An+ promotion energies to the reactive state is used to estimate AnO+ and AnC+ BDEs. For AnO+, this model yields predictions that are typically within experimental uncertainty and performs better than density functional theory calculations presented previously.

  8. Mechanistic information on the reductive elimination from cationic trimethylplatinum(IV) complexes to form carbon-carbon bonds. (United States)

    Procelewska, Joanna; Zahl, Achim; Liehr, Günter; van Eldik, Rudi; Smythe, Nicole A; Williams, B Scott; Goldberg, Karen I


    Cationic complexes of the type fac-[(L(2))Pt(IV)Me(3)(pyr-X)][OTf] (pyr-X = 4-substituted pyridines; L(2) = diphosphine, viz., dppe = bis(diphenylphosphino)ethane and dppbz = o-bis(diphenylphosphino)benzene; OTf = trifluoromethanesulfonate) undergo C-C reductive elimination reactions to form [L(2)Pt(II)Me(pyr-X)][OTf] and ethane. Detailed studies indicate that these reactions proceed by a two-step pathway, viz., initial reversible dissociation of the pyridine ligand from the cationic complex to generate a five-coordinate Pt(IV) intermediate, followed by irreversible concerted C-C bond formation. The reaction is inhibited by pyridine. The highly positive values for DeltaS()(obs) = +180 +/- 30 J K(-1) mol(-1), DeltaH(obs) = 160 +/- 10 kJ mol(-1), and DeltaV()(obs) = +16 +/- 1 cm(3) mol(-1) can be accounted for in terms of significant bond cleavage and/or partial reduction from Pt(IV) to Pt(II) in going from the ground to the transition state. These cationic complexes have provided the first opportunity to carry out detailed studies of C-C reductive elimination from cationic Pt(IV) complexes in a variety of solvents. The absence of a significant solvent effect for this reaction provides strong evidence that the C-C reductive coupling occurs from an unsaturated five-coordinate Pt(IV) intermediate rather than from a six-coordinate Pt(IV) solvento species.

  9. Oxidative cleavage of erucic acid for the synthesis of brassylic acid

    Energy Technology Data Exchange (ETDEWEB)

    Mohammed J. Nasrullah; Pooja Thapliyal; Erica N. Pfarr; Nicholas S. Dusek; Kristofer L. Schiele; James A. Bahr


    The main focus of this work is to synthesize Brassylic Acid (BA) using oxidative cleavage of Erucic Acid (EA). Crambe (Crambe abyssinica) is an industrial oilseed grown in North Dakota. Crambe has potential as an industrial fatty acid feedstock as a source of Erucic acid (EA). It has approximately 50-60 % of EA, a C{sub 22} monounsaturated fatty acid. Oxidative cleavage of unsaturated fatty acids derived from oilseeds produces long chain (9, 11, and 13 carbon atoms) dibasic and monobasic acids. These acids are known commercial feedstocks for the preparation of nylons, polyesters, waxes, surfactants, and perfumes. Other sources of EA are Rapeseed seed oil which 50-60 % of EA. Rapeseed is grown outside USA. The oxidative cleavage of EA was done using a high throughput parallel pressure reactor system. Kinetics of the reaction shows that BA yields reach a saturation at 12 hours. H{sub 2}WO{sub 4} was found to be the best catalyst for the oxidative cleavage of EA. High yields of BA were obtained at 80 C with bubbling of O{sub 2} or 10 bar of O{sub 2} for 12 hours.

  10. Stereoelectronic Control of Cleavage of Dioxolane Five-membered Ring on Carbohydrates

    Institute of Scientific and Technical Information of China (English)

    PAN Xiao-liang; ZHOU Yi-xuan; LIU Wei; LIU Jing-yao; DONG Hai


    A mechanism about the origin of the selectivities for the cleavage of dioxolane five-membered rings on pyranoside rings was suggested.Quantum chemical studies were performed to testify the rationality of the mechanism.It is thus suggested that the selectivities should be dependent on the differences of the free energy at the transition states when the five-membered ring cleaves.Natural bond orbital(NBO) analysis was further made to assess the influence of stereoelectronic effects on the selectivities.

  11. Intratree Variability of Cleavage Resistance of Chinese Fir from Plantation

    Institute of Scientific and Technical Information of China (English)

    XU Ming; REN Haiqing; LUO Xiuqin; YIN Yafang


    This paper studied the variation of cleavage resistance of Chinese fir wood from plantation.Six trees of 36 years old were investigated,and the cleavage resistance properties for 672 samples made of the trees were tested.The samples were cut from the sapwood and heartwood at different directions (south and north) and heights (1.3,3.3,5.3 and 7.3 m) of the trees.The result showed that:tangential cleavage resistance was higher than radial one, and cleavage resistance of sapwood was higher than that of heartwood,but there was no significant difference in cleavage resistances between sections of the north and the south of the trees.There was a little variation in cleavage resistance between the radial and tangential from butt to top log,which shows alittle decrease with the height from 1.3 to 5.3 m,but a rise in the top of the trees.

  12. Coupling and Reactions of 5-Hydroxyconiferyl Alcohol in Lignin Formation

    Energy Technology Data Exchange (ETDEWEB)

    Elder, Thomas; Berstis, Laura; Beckham, Gregg T.; Crowley, Michael F.


    The catechol alcohols, caffeyl and 5-hydroxyconiferyl alcohol, may be incorporated into lignin either naturally or through genetic manipulation. Due to the presence of o-OH groups, these compounds form benzodioxanes, a departure from the interunit connections found in lignins derived from the cinnamyl alcohols. In nature, lignins composed of caffeyl and 5-hydroxyconiferyl alcohol are linear homopolymers and, as such, may have properties that make them amenable for use in value-added products, such as lignin-based carbon fibers. In the current work, results from density functional theory calculations for the reactions of 5-hydroxyconiferyl alcohol, taking stereochemistry into account, are reported. Dehydrogenation and quinone methide formation are found to be thermodynamically favored for 5-hydroxyconiferyl alcohol, over coniferyl alcohol. The comparative energetics of the rearomatization reactions suggest that the formation of the benzodioxane linkage is under kinetic control. Ring-opening reactions of the benzodioxane groups show that the bond dissociation enthalpy of the ..alpha..-O cleavage reaction is lower than that of the ..beta..-O reaction. The catechol lignins represent a novel form of the polymer that may offer new opportunities for bioproducts and genetic targets.

  13. DNA Cleavage Promoted by Cu2+ Complex of N,N'-Bis(2-aminoethyl)-2,6-pyridinedicarboxamide

    Institute of Scientific and Technical Information of China (English)

    LI, Ying; SHENG, Xin; SHAO, Ying; LU, Guo-Yuan


    The interaction of Cu2+ complex of N,N'-bis(2-aminoethyl)-2,6-pyridinedicarboxamide (BAP) with DNA was studied by agarose gel electrophoresis analysis. The results indicate that the BAP-Cu2+ complex can promote the cleavage of phosphodiester bond of supercoiled DNA at physiological condition, which is 3.2×106 times higher than DNA natural degradation. A hydrolytic cleaving mechanism through the cooperation of copper ions and functional amino groups was proposed.

  14. New insights into the catalytic cleavage of the lignin β-O-4 linkage in multifunctional ionic liquid media

    NARCIS (Netherlands)

    Scott, Martin; Deuss, Peter J.; de Vries, Johannes; Prechtl, Martin H. G.; Barta, Katalin


    Ionic liquids are attractive reaction media for the solubilisation and depolymerisation of lignin into value-added products. However, mechanistic insight related to the cleavage of specific linkages relevant for efficient lignin depolymerisation in such solvents is still lacking. This study presents

  15. Primary retention following nuclear recoil in β-decay: Proposed synthesis of a metastable rare gas oxide ((38)ArO4) from ((38)ClO4(-)) and the evolution of chemical bonding over the nuclear transmutation reaction path. (United States)

    Timm, Matthew J; Matta, Chérif F


    Argon tetroxide (ArO4) is the last member of the N=50 e(-) isoelectronic and isosteric series of ions: SiO4(4-), PO4(3-), SO4(2-), and ClO4(-). A high level computational study demonstrated that while ArO4 is kinetically stable it has a considerable positive enthalpy of formation (of ~298kcal/mol) (Lindh et al., 1999. J. Phys. Chem. A 103, pp. 8295-8302) confirming earlier predictions by Pyykkö (1990. Phys. Scr. 33, pp. 52-53). ArO4 can be expected to be difficult to synthesize by traditional chemistry due to its metastability and has not yet been synthesized at the time of writing. A computational investigation of the changes in the chemical bonding of chlorate (ClO4(-)) when the central chlorine atom undergoes a nuclear transmutation from the unstable artificial chlorine isotope (38)Cl to the stable rare argon isotope (38)Ar through β-decay, hence potentially leading to the formation of ArO4, is reported. A mathematical model is presented that allows for the prediction of yields following the recoil of a nucleus upon ejecting a β-electron. It is demonstrated that below a critical angle between the ejected β-electron and that of the accompanying antineutrino their respective linear momentums can cancel to such an extent as imparting a recoil to the daughter atom insufficient for breaking the Ar-O bond. As a result, a primary retention yield of ~1% of ArO4 is predicted following the nuclear disintegration. The study is conducted at the quadratic configuration interaction with single and double excitations [QCISD/6-311+G(3df)] level of theory followed by an analysis of the electron density by the quantum theory of atoms in molecules (QTAIM). Crossed potential energy surfaces (PES) were used to construct a PES from the metastable ArO4 ground singlet state to the Ar-O bond dissociation product ArO3+O((3)P) from which the predicted barrier to dissociation is ca. 22kcal/mol and the exothermic reaction energy is ca. 28kcal/mol [(U)MP2/6-311+G(d)].

  16. Amino acid sequence requirements in the human IgA1 hinge for cleavage by streptococcal IgA1 proteases

    DEFF Research Database (Denmark)

    Senior, BW; Batten, MR; Kilian, Mogens;


    All the IgA1 proteases of the different pathogenic species of Streptococcus cleave the hinge of the alpha chain of human IgA1 only at one proline-threonine peptide bond. In order to study the importance of these amino acids for cleavage, several hinge mutant recombinant IgA1 antibodies were...

  17. Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions (United States)

    Molina-Espíritu, M.; Esquivel, R. O.; Dehesa, J. S.

    We investigate the complexity of selected elementary chemical reactions (namely, the hydrogenic-abstraction reaction and the identity SN2 exchange reaction) by means of the following single and composite information-theoretic measures: disequilibrium (D), exponential entropy(L), Fisher information (I), power entropy (J), I-D, D-L and I-J planes and Fisher-Shannon (FS) and Lopez-Mancini-Calbet (LMC) shape complexities. These quantities, which are functionals of the one-particle density, are computed in both position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of these reactions can be identified through most of the single information-theoretic measures and the two-component planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the abstraction reaction bears the same information-theoretical features of the LMC and FS measures, however for the identity SN2 exchange reaction does not hold a simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.

  18. Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses. (United States)

    Eckhard, Ulrich; Huesgen, Pitter F; Schilling, Oliver; Bellac, Caroline L; Butler, Georgina S; Cox, Jennifer H; Dufour, Antoine; Goebeler, Verena; Kappelhoff, Reinhild; Keller, Ulrich Auf dem; Klein, Theo; Lange, Philipp F; Marino, Giada; Morrison, Charlotte J; Prudova, Anna; Rodriguez, David; Starr, Amanda E; Wang, Yili; Overall, Christopher M


    leucine locked in S1'. Similar negative cooperativity between P3 proline and the novel preference for asparagine in P1 cements our conclusion that non-prime side flexibility greatly impacts MMP binding affinity and cleavage efficiency. Thus, unexpected sequence cooperativity consequences were revealed by PICS that uniquely encompasses both the non-prime and prime sides flanking the proteomic-pinpointed scissile bond.

  19. Structural Basis for Accelerated Cleavage of Bovine Pancreatic Trypsin Inhibitor (BPTI) by Human Mesotrypsin

    Energy Technology Data Exchange (ETDEWEB)

    Salameh,M.; Soares, A.; Hockla, A.; Radisky, E.


    Human mesotrypsin is an isoform of trypsin that displays unusual resistance to polypeptide trypsin inhibitors and has been observed to cleave several such inhibitors as substrates. Whereas substitution of arginine for the highly conserved glycine 193 in the trypsin active site has been implicated as a critical factor in the inhibitor resistance of mesotrypsin, how this substitution leads to accelerated inhibitor cleavage is not clear. Bovine pancreatic trypsin inhibitor (BPTI) forms an extremely stable and cleavage-resistant complex with trypsin, and thus provides a rigorous challenge of mesotrypsin catalytic activity toward polypeptide inhibitors. Here, we report kinetic constants for mesotrypsin and the highly homologous (but inhibitor sensitive) human cationic trypsin, describing inhibition by, and cleavage of BPTI, as well as crystal structures of the mesotrypsin-BPTI and human cationic trypsin-BPTI complexes. We find that mesotrypsin cleaves BPTI with a rate constant accelerated 350-fold over that of human cationic trypsin and 150,000-fold over that of bovine trypsin. From the crystal structures, we see that small conformational adjustments limited to several side chains enable mesotrypsin-BPTI complex formation, surmounting the predicted steric clash introduced by Arg-193. Our results show that the mesotrypsin-BPTI interface favors catalysis through (a) electrostatic repulsion between the closely spaced mesotrypsin Arg-193 and BPTI Arg-17, and (b) elimination of two hydrogen bonds between the enzyme and the amine leaving group portion of BPTI. Our model predicts that these deleterious interactions accelerate leaving group dissociation and deacylation.

  20. Structural effects on the beta-scission reaction of alkoxyl radicals. Direct measurement of the absolute rate constants for ring opening of benzocycloalken-1-oxyl radicals. (United States)

    Bietti, Massimo; Lanzalunga, Osvaldo; Salamone, Michela


    [reaction: see text] The absolute rate constants for beta-scission of a series of benzocycloalken-1-oxyl radicals and of the 2-(4-methylphenyl)-2-butoxyl radical have been measured directly by laser flash photolysis. The benzocycloalken-1-oxyl radicals undergo ring opening with rates which parallel the ring strain of the corresponding cycloalkanes. In the 1-X-indan-1-oxyl radical series, ring opening is observed when X = H, Me, whereas exclusive C-X bond cleavage occurs when X = Et. The factors governing the fragmentation regioselectivity are discussed.

  1. Computational Investigation and Hydrogen/Deuterium Exchange of the Fixed Charge Derivative Tris(2,4,6-Trimethoxyphenyl)Phosphonium: Implications for the Aspartic Acid Cleavage Mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Herrmann, Kristin A.; Wysocki, Vicki H.; Vorpagel, Erich R.


    Aspartic acid (Asp)-containing peptides with the fixed charge derivative tris(2,4,6-trimethoxyphenyl) phosphonium (tTMP-P+) were explored computationally and experimentally by H/D exchange and fragmentation studies in order to probe the phenomenon of selective cleavage C-terminal to Asp in the absence of a ''mobile'' proton. Ab initio modeling of the tTMP-P+ electrostatic potential demonstrates the positive charge is distributed on the phosphonium group and therefore is not initiating or directing fragmentation as would a ''mobile'' proton. Geometry optimizations and vibrational analyses of different aspartic acid conformations show the aspartic acid structure with a hydrogen bond between the side chain hydroxy and backbone carbonyl lies 2.8 kcal/mol above the lowest energy conformer. In reactions with D2O, the phosphonium-derived doubly charged peptide (H+)P+LDIFSDF rapidly exchanges all 12 of its exchangeable hydrogens for deuterium and also displays a non-exchanging population. With no added proton, P+LDIFSDF exchanges a maximum of four of eleven exchangeable hydrogens for deuterium. No exchange is observed when all acidic groups are converted to the corresponding methyl esters. Together, these H/D exchange results indicate that the acidic hydrogens are ''mobile locally'' because they are able to participate in exchange even in the absence of an added proton. Fragmentation of two distinct (H+)P+LDIFSDF ion populations shows the non-exchanging population displays selective cleavage, while the exchanging population fragments more evenly across the peptide backbone. This result demonstrates that H/D exchange can sometimes distinguish between and provide a means of separation of different protonation motifs, and that these protonation motifs can have an effect on the fragmentation.

  2. Molecular simulations of RNA 2'-O-transesterification reaction models in solution. (United States)

    Radak, Brian K; Harris, Michael E; York, Darrin M


    We employ quantum mechanical/molecular mechanical umbrella sampling simulations to probe the free energy surfaces of a series of increasingly complex reaction models of RNA 2'-O-transesterification in aqueous solution under alkaline conditions. Such models are valuable for understanding the uncatalyzed processes underlying catalytic cleavage of the phosphodiester backbone of RNA, a reaction of fundamental importance in biology. The chemically reactive atoms are modeled by the AM1/d-PhoT quantum model for phosphoryl transfer, whereas the aqueous solvation environment is modeled with a molecular mechanics force field. Several simulation protocols were compared that used different ionic conditions and force field models. The results provide insight into how variation of the structural environment of the nucleophile and leaving group affects the free energy profile for the transesterification reaction. Results for a simple RNA backbone model are compared with recent experiments by Harris et al. on the specific base-catalyzed cleavage of a UpG dinucleotide. The calculated and measured free energies of activation match extremely well (ΔF(‡) = 19.9-20.8 vs 19.9 kcal/mol). Solvation is seen to play a crucial role and is characterized by a network of hydrogen bonds that envelopes the pentacoordinate dianionic phosphorane transition state and provides preferential stabilization relative to the reactant state.

  3. Reactions of Dinuclear Platinum(II) Complexes with Peptides. (United States)

    Rajković, Snežana; Živković, Marija D; Djuran, Miloš I


    The present review article highlights recent findings in the reactions between different dinuclear Pt(II) complexes with peptides containing cysteine, methionine and histidine residues. The reactions of {trans-[Pt(NH3)2Cl]2(μ-X)}(2+) and {trans-[Pt(NH3)2(H2O)]2(μ-X)}(4+) type complexes with different bridging ligands (X) (X = pyrazine, 4,4'-bipyridyl and 1,2-bis(4-pyridyl)ethane) with the tripeptide glutathione proceeded in two steps. In the first step, one water or chlorido ligand of the dinuclear Pt(II) complex was substituted by the sulfhydryl group of GSH, while in the second step, the remaining water or chlorido ligand from the dinuclear Pt(II)-peptide complex was replaced by the second molecule of glutathione, finally leading to the formation of the {trans-[Pt(NH3)2(GS)]2(μ-X)}(2+) complex. It was shown that the bridging ligand had an important influence on the reactivity of these complexes with glutathione. No hydrolytic cleavage of any amide bond was observed in the reactions between these complexes and glutathione. However, in reactions performed in acidic media (2.0 complexes with the general formulae {[Pt(L)(H2O)]2(μ-diazine)}(4+) (L is different bidentate coordinated diamine ligands and diazine is a pyrazine- or pyridazine-bridging ligand) and Nacetylated peptides containing L-methionine and L-histidine amino acids in the side chains (Ac-L-Met-Gly, Ac-L-His-Gly and Ac-L-Met-Gly-L-His-GlyNH2), regioselective cleavage of these peptides occurred. The mechanism of these hydrolytic reactions was discussed in relation to the structure of the diazine-bridged Pt(II) complex and the investigated peptides. A systematic summary of these results could contribute to the future design of new dinuclear Pt(II) complexes as potential reagents for regioselective cleavage of peptides and proteins.

  4. Effect of Si-H bond on the gas-phase chemistry of trimethylsilane in the hot wire chemical vapor deposition process. (United States)

    Shi, Y J; Li, X M; Toukabri, R; Tong, L


    The effect of the Si-H bond on the gas-phase reaction chemistry of trimethylsilane in the hot-wire chemical vapor deposition (HWCVD) process has been studied by examining its decomposition on a hot tungsten filament and the secondary gas-phase reactions in a reactor using a soft laser ionization source coupled with mass spectrometry. Trimethylsilane decomposes on the hot filament via Si-H and Si-CH(3) bond cleavages. A short-chain mechanism is found to dominate in the secondary reactions in the reactor. It has been shown that the hydrogen abstractions of both Si-H and C-H occur simultaneously, with the abstraction of Si-H being favored. Tetramethylsilane and hexamethyldisilane are the two major products formed from the radical recombination reactions in the termination steps. Three methyl-substituted disilacyclobutane molecules, i.e., 1,3-dimethyl-1,3-disilacyclobutane, 1,1,3-trimethyl-1,3-disilacyclobutane, and 1,1,3,3-tetramethyl-1,3-disilacyclobutane are also produced in reactor from the cycloaddition reactions of methyl-substituted silene species. Compared to tetramethylsilane and hexamethyldisilane, a common feature with trimethylsilane is that the short-chain mechanism still dominates. However, a more active involvement of the reactive silene intermediates has been found with trimethylsilane.

  5. Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps

    NARCIS (Netherlands)

    J.F. McBlane; D.C. van Gent (Dik); D.A. Ramsden; C. Romeo; C.A. Cuomo; M. Gellert; M.A. Oettinger


    textabstractFormation of double-strand breaks at recombination signal sequences is an early step in V(D)J recombination. Here we show that purified RAG1 and RAG2 proteins are sufficient to carry out this reaction. The cleavage reaction can be divided into two distinct steps. First,

  6. Presence of Meiotic Spindles Indicates Early Cleavage of Embryos

    Institute of Scientific and Technical Information of China (English)


    Objective To assess whether the detection of the meiotic spindle could anticipate the appearance of early cleavage.Methods Oocytes were obtained from stimulated ovaries of consenting patients undergoing oocytes retrieval for ICSI.Spindles were imaged with the Polscope.After ICSI,oocytes with or without spindles were cultured for examination of early cleavage and embryo development.A total of 328 oocytes from 50 cycles were examined with the Polscope and inseminated by ICSI.Results Spindles were imaged in 81.7% of oocytes.After ICSI,more oocytes with spindles (78.4%) fertilized normally than oocytes without spindles (53.3%)(P<0.001).At 25-27 h post ICSI.more fertilized oocytes developed from oocytes with spindles (81.9%) were detected early cleavage than those from oocytes without spindles(28.1%)(P<0.001).Significantly more embryos with early cleavage (82.2%) developed to high quality embryos at d 3 compared with the embryos without early cleavage(48.3%)(P=0.001).The value of rs related to the relationship between spindles and early cleavage was 0.420(P<0.0001).Conclusion The existing of the early cleavage may have a predictive value on the opportunity of high quality embryos and the existing of the spindle may have a predictive value in the appearance of early cleavage.

  7. The Oxygenase CAO-1 of Neurospora crassa Is a Resveratrol Cleavage Enzyme

    KAUST Repository

    Diaz-Sanchez, V.


    The genome of the ascomycete Neurospora crassa encodes CAO-1 and CAO-2, two members of the carotenoid cleavage oxygenase family that target double bonds in different substrates. Previous studies demonstrated the role of CAO-2 in cleaving the C40 carotene torulene, a key step in the synthesis of the C35 apocarotenoid pigment neurosporaxanthin. In this work, we investigated the activity of CAO-1, assuming that it may provide retinal, the chromophore of the NOP-1 rhodopsin, by cleaving β-carotene. For this purpose, we tested CAO-1 activity with carotenoid substrates that were, however, not converted. In contrast and consistent with its sequence similarity to family members that act on stilbenes, CAO-1 cleaved the interphenyl Cα-Cβ double bond of resveratrol and its derivative piceatannol. CAO-1 did not convert five other similar stilbenes, indicating a requirement for a minimal number of unmodified hydroxyl groups in the stilbene background. Confirming its biological function in converting stilbenes, adding resveratrol led to a pronounced increase in cao-1 mRNA levels, while light, a key regulator of carotenoid metabolism, did not alter them. Targeted Δcao-1 mutants were not impaired by the presence of resveratrol, a phytoalexin active against different fungi, which did not significantly affect the growth and development of wild-type Neurospora. However, under partial sorbose toxicity, the Δcao-1 colonies exhibited faster radial growth than control strains in the presence of resveratrol, suggesting a moderate toxic effect of resveratrol cleavage products.

  8. A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigments

    KAUST Repository

    Rodrigo, María J.


    Citrus is the first tree crop in terms of fruit production. The colour of Citrus fruit is one of the main quality attributes, caused by the accumulation of carotenoids and their derivative C30 apocarotenoids, mainly ?-citraurin (3-hydroxy-?-apo-8?-carotenal), which provide an attractive orange-reddish tint to the peel of oranges and mandarins. Though carotenoid biosynthesis and its regulation have been extensively studied in Citrus fruits, little is known about the formation of C30 apocarotenoids. The aim of this study was to the identify carotenoid cleavage enzyme(s) [CCD(s)] involved in the peel-specific C30 apocarotenoids. In silico data mining revealed a new family of five CCD4-type genes in Citrus. One gene of this family, CCD4b1, was expressed in reproductive and vegetative tissues of different Citrus species in a pattern correlating with the accumulation of C30 apocarotenoids. Moreover, developmental processes and treatments which alter Citrus fruit peel pigmentation led to changes of ?-citraurin content and CCD4b1 transcript levels. These results point to the involvement of CCD4b1 in ?-citraurin formation and indicate that the accumulation of this compound is determined by the availability of the presumed precursors zeaxanthin and ?-cryptoxanthin. Functional analysis of CCD4b1 by in vitro assays unequivocally demonstrated the asymmetric cleavage activity at the 7?,8? double bond in zeaxanthin and ?-cryptoxanthin, confrming its role in C30 apocarotenoid biosynthesis. Thus, a novel plant carotenoid cleavage activity targeting the 7?,8? double bond of cyclic C40 carotenoids has been identified. These results suggest that the presented enzyme is responsible for the biosynthesis of C30 apocarotenoids in Citrus which are key pigments in fruit coloration. The Author 2013.

  9. C-H bond activation of methane in aqueous solution: a hybrid quantum mechanical/effective fragment potential study. (United States)

    Da Silva, Júlio C S; Rocha, Willian R


    In this study, we investigated the C-H bond activation of methane catalyzed by the complex [PtCl(4)](2-), using the hybrid quantum mechanical/effective fragment potential (EFP) approach. We analyzed the structures, energetic properties, and reaction mechanism involved in the elementary steps that compose the catalytic cycle of the Shilov reaction. Our B3LYP/SBKJC/cc-pVDZ/EFP results show that the methane activation may proceed through two pathways: (i) electrophilic addition or (ii) direct oxidative addition of the C-H bond of the alkane. The electrophilic addition pathway proceeds in two steps with formation of a σ-methane complex, with a Gibbs free energy barrier of 24.6 kcal mol(-1), followed by the cleavage of the C-H bond, with an energy barrier of 4.3 kcal mol(-1) . The activation Gibbs free energy, calculated for the methane uptake step was 24.6 kcal mol(-1), which is in good agreement with experimental value of 23.1 kcal mol(-1) obtained for a related system. The results shows that the activation of the C-H bond promoted by the [PtCl(4)](2-) catalyst in aqueous solution occurs through a direct oxidative addition of the C-H bond, in a single step, with an activation free energy of 25.2 kcal mol(-1), as the electrophilic addition pathway leads to the formation of a σ-methane intermediate that rapidly undergoes decomposition. The inclusion of long-range solvent effects with polarizable continuum model does not change the activation energies computed at the B3LYP/SBKJC/cc-pVDZ/EFP level of theory significantly, indicating that the large EFP water cluster used, obtained from Monte Carlo simulations and analysis of the center-of-mass radial pair distribution function, captures the most important solvent effects.

  10. Site specificity of DSP-PP cleavage by BMP1. (United States)

    Yang, Robert T; Lim, Glendale L; Yee, Colin T; Fuller, Robert S; Ritchie, Helena H


    Bone morphogenic protein 1 (BMP1), a metalloproteinase, is known to cleave a wide variety of extracellular matrix proteins, suggesting that a consensus substrate cleavage amino acid sequence might exist. However, while such a consensus sequence has been proposed based on P4 to P4' (i.e. the four amino acids flanking either side of the BMP1 cleavage site; P4P3P2P1|P1'P2'P3'P4') sequence homologies between two BMP1 substrates, dentin matrix protein 1 and dentin sialoprotein phosphophoryn (DSP-PP) (i.e. xMQx|DDP), no direct testing has so far been attempted. Using an Sf9 cell expression system, we have been able to produce large amounts of uncleaved DSP-PP. Point mutations introduced into this recombinant DSP-PP were then tested for their effects on DSP-PP cleavage by either Sf9 endogenous tolloid-related protein 1 (TLR-1) or by its human homolog, BMP1. Here, we have measured DSP-PP cleavage efficiencies after modifications based on P4-P4' sequence comparisons with dentin matrix protein 1, as well as for prolysyl oxidase and chordin, two other BMP1 substrates. Our results demonstrate that any mutations within or outside of the DSP-PP P4 to P4' cleavage site can block, impair or accelerate DSP-PP cleavage, and suggest that its BMP1 cleavage site is highly conserved in order to regulate its cleavage efficiency, possibly with additional assistance from its conserved exosites. Thus, BMP1 cleavage cannot be based on a consensus substrate cleavage site.

  11. Mechanistic Insights on C-O and C-C Bond Activation and Hydrogen Insertion during Acetic Acid Hydrogenation Catalyzed by Ruthenium Clusters in Aqueous Medium

    Energy Technology Data Exchange (ETDEWEB)

    Shangguan, Junnan; Olarte, Mariefel V.; Chin, Ya-Huei [Cathy


    Catalytic pathways for acetic acid (CH3COOH) and hydrogen (H2) reactions on dispersed Ru clusters in the aqueous medium and the associated kinetic requirements for C-O and C-C bond cleavages and hydrogen insertion are established from rate and isotopic assessments. CH3COOH reacts with H2 in steps that either retain its carbon backbone and lead to ethanol, ethyl acetate, and ethane (47-95 %, 1-23 %, and 2-17 % carbon selectivities, respectively) or break its C-C bond and form methane (1-43 % carbon selectivities) at moderate temperatures (413-523 K) and H2 pressures (10-60 bar, 298 K). Initial CH3COOH activation is the kinetically relevant step, during which CH3C(O)-OH bond cleaves on a metal site pair at Ru cluster surfaces nearly saturated with adsorbed hydroxyl (OH*) and acetate (CH3COO*) intermediates, forming an adsorbed acetyl (CH3CO*) and hydroxyl (OH*) species. Acetic acid turnover rates increase proportionally with both H2 (10-60 bar) and CH3COOH concentrations at low CH3COOH concentrations (<0.83 M), but decrease from first to zero order as the CH3COOH concentration and the CH3COO* coverages increase and the vacant Ru sites concomitantly decrease. Beyond the initial CH3C(O)-OH bond activation, sequential H-insertions on the surface acetyl species (CH3CO*) lead to C2 products and their derivative (ethanol, ethane, and ethyl acetate) and the competitive C-C bond cleavage of CH3CO* causes the eventual methane formation. The instantaneous carbon selectivities towards C2 species (ethanol, ethane, and ethyl acetate) increase linearly with the concentration of proton-type Hδ+ (derived from carboxylic acid dissociation) and chemisorbed H*. The selectivities towards C2 products decrease with increasing temperature, because of higher observed barriers for C-C bond cleavage than H-insertion. This study offers an interpretation of mechanism and energetics and provides kinetic evidence of carboxylic acid assisted proton-type hydrogen (Hδ+) shuffling during H

  12. Theoretical investigation of hyperthermal reactions at the gas-liquid interface: O (3P) and squalane. (United States)

    Kim, Dongwook; Schatz, George C


    Hyperthermal collisions (5 eV) of ground-state atomic oxygen [O ((3)P)] with a liquid-saturated hydrocarbon, squalane (C(30)H(62)), have been studied using QM/MM hybrid "on-the-fly" direct dynamics. The surface structure of the liquid squalane is obtained from a classical molecular dynamics simulation using the OPLS-AA force field. The MSINDO semiempirical Hamiltonian is combined with OPLS-AA for the QM/MM calculations. In order to achieve a more consistent and efficient simulation of the collisions, we implemented a dynamic partitioning of the QM and MM atoms in which atoms are assigned to QM or MM regions based on their proximity to "seed" (open-shell) atoms that determine where bond making/breaking can occur. In addition, the number of seed atoms is allowed to increase or decrease as time evolves so that multiple reactive events can be described. The results show that H abstraction is the most important process for all incident angles, with H elimination, double H abstraction, and C-C bond cleavage also being important. A number of properties of these reactive channels, as well as inelastic nonreactive scattering, are investigated, including angular and translational energy distributions, the effect of incident collision angle, variation with depth of the reactive event within the liquid, with the reaction site on the hydrocarbon, and the effect of dynamics before and after reaction (direct reaction versus trapping reaction-desorption).

  13. Amide-directed photoredox-catalysed C-C bond formation at unactivated sp3 C-H bonds (United States)

    Chu, John C. K.; Rovis, Tomislav


    Carbon-carbon (C-C) bond formation is paramount in the synthesis of biologically relevant molecules, modern synthetic materials and commodity chemicals such as fuels and lubricants. Traditionally, the presence of a functional group is required at the site of C-C bond formation. Strategies that allow C-C bond formation at inert carbon-hydrogen (C-H) bonds enable access to molecules that would otherwise be inaccessible and the development of more efficient syntheses of complex molecules. Here we report a method for the formation of C-C bonds by directed cleavage of traditionally non-reactive C-H bonds and their subsequent coupling with readily available alkenes. Our methodology allows for amide-directed selective C-C bond formation at unactivated sp3 C-H bonds in molecules that contain many such bonds that are seemingly indistinguishable. Selectivity arises through a relayed photoredox-catalysed oxidation of a nitrogen-hydrogen bond. We anticipate that our findings will serve as a starting point for functionalization at inert C-H bonds through a strategy involving hydrogen-atom transfer.

  14. A cleavage toughness master curve model (United States)

    Odette, G. R.; He, M. Y.


    Development of fusion power will require a fracture toughness database, derived largely from small specimen tests, closely integrated with methods to assess first wall and blanket structural integrities. A master curve-shift (MC-ΔT) method has been proposed as an engineering expedient to treat the effects of structural geometry, irradiation, loading rates and safety margins. However, a number of issues related to the MC-ΔT method remain to be resolved, including the universality of MC shapes. A new micromechanical model of fracture toughness in the cleavage transition regime is proposed that combines analytical representations of finite element analysis simulations of crack-tip stress fields with a local critical stress-critical stressed area (σ∗-A∗) fracture criterion. This model, has been successful in predicting geometry effects, as well as high loading rate and irradiation hardening-induced Charpy shifts. By incorporating a modest temperature dependence in σ∗(T), an inconsistency between model predictions and an observed universal-type MC shape is resolved.

  15. Redox-controlled hydrogen bonding: turning a superbase into a strong hydrogen-bond donor. (United States)

    Wild, Ute; Neuhäuser, Christiane; Wiesner, Sven; Kaifer, Elisabeth; Wadepohl, Hubert; Himmel, Hans-Jörg


    Herein the synthesis, structures and properties of hydrogen-bonded aggregates involving redox-active guanidine superbases are reported. Reversible hydrogen bonding is switched on by oxidation of the hydrogen-donor unit, and leads to formation of aggregates in which the hydrogen-bond donor unit is sandwiched by two hydrogen-bond acceptor units. Further oxidation (of the acceptor units) leads again to deaggregation. Aggregate formation is associated with a distinct color change, and the electronic situation could be described as a frozen stage on the way to hydrogen transfer. A further increase in the basicity of the hydrogen-bond acceptor leads to deprotonation reactions.

  16. Quantification of DNA cleavage specificity in Hi-C experiments. (United States)

    Meluzzi, Dario; Arya, Gaurav


    Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonuclease. Although this cleavage should happen specifically at the enzyme's recognition sequence, an unknown proportion of cleavage events may involve other sequences, owing to the enzyme's star activity or to random DNA breakage. A quantitative estimation of these non-specific cleavages may enable simulating realistic Hi-C read pairs for validation of downstream analyses, monitoring the reproducibility of experimental conditions and investigating biophysical properties that correlate with DNA cleavage patterns. Here we describe a computational method for analyzing Hi-C read pairs to estimate the fractions of cleavages at different possible targets. The method relies on expressing an observed local target distribution downstream of aligned reads as a linear combination of known conditional local target distributions. We validated this method using Hi-C read pairs obtained by computer simulation. Application of the method to experimental Hi-C datasets from murine cells revealed interesting similarities and differences in patterns of cleavage across the various experiments considered.

  17. Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase (United States)

    Saen-oon, Suwipa; Schramm, Vern L.; Schwartz, Steven D.


    The Transition Path Sampling (TPS) method is a powerful technique for studying rare events in complex systems, that allows description of reactive events in atomic detail without prior knowledge of reaction coordinates and transition states. We have applied TPS in combination with a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) method to study the enzyme human purine nucleoside phosphorylase (hPNP). This enzyme catalyzes the reversible phosphorolysis of 6-oxypurine (deoxy)nucleosides to generate the corresponding purine base and (deoxy)ribose 1-phosphate. Hundreds of reactive trajectories were generated. Analysis of this transition path ensembles provides insight into the detailed mechanistic dynamics of reaction in the enzyme. Our studies have indicated a reaction mechanism involving the cleavage of the N-ribosidic bond to form transition states with substantial ribooxacarbenium ion character, that is then followed by conformational changes in the enzyme and the ribosyl group leading to migration of the anomeric carbon of the ribosyl group toward phosphate to form the product ribose 1-phosphate. This latter process is crucial in PNP, because several strong H-bonds form between active site residues in order to capture and align the phosphate nucleophile. Calculations of the commitment probability along reactive paths demonstrated the presence of a broad energy barrier at the transition state. Analysis of these transition state structures showed that bond-breaking and bond-forming distances are not a good choice for the reaction coordinate, but that the pseudorotational phase of the ribose ring is also a significant variable. PMID:20664707

  18. Nuclear Hyperfine and Quadrupole Tensor Characterization of the Nitrogen Hydrogen Bond Donors to the Semiquinone of the QB Site in Bacterial Reaction Centers: A Combined X- and S-Band 14,15N ESEEM and DFT Study (United States)


    The secondary quinone anion radical QB– (SQB) in reaction centers of Rhodobacter sphaeroides interacts with Nδ of His-L190 and Np (peptide nitrogen) of Gly-L225 involved in hydrogen bonds to the QB carbonyls. In this work, S-band (∼3.6 GHz) ESEEM was used with the aim of obtaining a complete characterization of the nuclear quadrupole interaction (nqi) tensors for both nitrogens by approaching the cancelation condition between the isotropic hyperfine coupling and 14N Zeeman frequency at lower microwave frequencies than traditional X-band (9.5 GHz). By performing measurements at S-band, we found a dominating contribution of Nδ in the form of a zero-field nqi triplet at 0.55, 0.92, and 1.47 MHz, defining the quadrupole coupling constant K = e2qQ/4h = 0.4 MHz and associated asymmetry parameter η = 0.69. Estimates of the hyperfine interaction (hfi) tensors for Nδ and Np were obtained from simulations of 1D and 2D 14,15N X-band and three-pulse 14N S-band spectra with all nuclear tensors defined in the SQB g-tensor coordinate system. From simulations, we conclude that the contribution of Np to the S-band spectrum is suppressed by its strong nqi and weak isotropic hfi comparable to the level of hyperfine anisotropy, despite the near-cancelation condition for Np at S-band. The excellent agreement between our EPR simulations and DFT calculations of the nitrogen hfi and nqi tensors to SQB is promising for the future application of powder ESEEM to full tensor characterizations. PMID:24437652

  19. Nuclear hyperfine and quadrupole tensor characterization of the nitrogen hydrogen bond donors to the semiquinone of the QB site in bacterial reaction centers: a combined X- and S-band (14,15)N ESEEM and DFT study. (United States)

    Taguchi, Alexander T; O'Malley, Patrick J; Wraight, Colin A; Dikanov, Sergei A


    The secondary quinone anion radical QB(-) (SQB) in reaction centers of Rhodobacter sphaeroides interacts with Nδ of His-L190 and Np (peptide nitrogen) of Gly-L225 involved in hydrogen bonds to the QB carbonyls. In this work, S-band (∼3.6 GHz) ESEEM was used with the aim of obtaining a complete characterization of the nuclear quadrupole interaction (nqi) tensors for both nitrogens by approaching the cancelation condition between the isotropic hyperfine coupling and (14)N Zeeman frequency at lower microwave frequencies than traditional X-band (9.5 GHz). By performing measurements at S-band, we found a dominating contribution of Nδ in the form of a zero-field nqi triplet at 0.55, 0.92, and 1.47 MHz, defining the quadrupole coupling constant K = e(2)qQ/4h = 0.4 MHz and associated asymmetry parameter η = 0.69. Estimates of the hyperfine interaction (hfi) tensors for Nδ and Np were obtained from simulations of 1D and 2D (14,15)N X-band and three-pulse (14)N S-band spectra with all nuclear tensors defined in the SQB g-tensor coordinate system. From simulations, we conclude that the contribution of Np to the S-band spectrum is suppressed by its strong nqi and weak isotropic hfi comparable to the level of hyperfine anisotropy, despite the near-cancelation condition for Np at S-band. The excellent agreement between our EPR simulations and DFT calculations of the nitrogen hfi and nqi tensors to SQB is promising for the future application of powder ESEEM to full tensor characterizations.

  20. Synthesis, spectral characterization, electrochemical, anti-microbial, DNA binding and cleavage studies of new binuclear Schiff base metal(II complexes derived from o-hydroxyacetophenone

    Directory of Open Access Journals (Sweden)

    P. Jayaseelan


    Full Text Available A new tetradentate binucleating ligand [H2L] has been synthesized by condensation between 3, 3′-diaminobenzidine and o-hydroxyacetophenone in the molar ratio 1:4. The reaction of the ligand with metal chelation leads to bimolecular complexes of the general formula [M2(L]. The ligand and metal complexes have been characterized by elemental analysis, UV, IR,…1H NMR, 13C NMR, conductivity measurements and magnetic studies. In conductivity experiments, all metal chelates showed to be non-electrolytic in nature. The bonding sites are the nitrogen atoms of the azomethine and the oxygen atoms of the phenolic groups. The anti-microbial activities were screened against one Gram-positive bacterium (Streptococcus pyogenes and one Gram-negative bacterium (Klebsella pneumoniae. The anti-fungal activity was screened against Asperigillus flavus. All complexes showed significant anti-bacterial and anti-fungal activities. The DNA binding studies were performed by electronic spectroscopy, cyclic voltammetry studies and viscosity measurements. The cleavage studies of these complexes are investigated by gel electrophoresis method in the presence of peroxide. All complexes cleaved efficiently and the complex interacts with DNA through an intercalating way.

  1. Rubber oxygenase and latex clearing protein cleave rubber to different products and use different cleavage mechanisms. (United States)

    Birke, Jakob; Jendrossek, Dieter


    Two types of enzyme for oxidative cleavage of poly(cis-1,4-isoprene) are known. One is rubber oxygenase (RoxA) that is secreted by Xanthomonas sp. strain 35Y and a few other Gram-negative rubber-degrading bacteria during growth on polyisoprene. RoxA was studied in the past, and the recently solved structure showed a structural relationship to bacterial cytochrome c peroxidases (J. Seidel et al., Proc. Natl. Acad. Sci. U. S. A. 110:13833-13838, 2013, The other enzyme is latex-clearing protein (Lcp) that is secreted by rubber-degrading actinomycetes, but Lcp has not yet been purified. Here, we expressed Lcp of Streptomyces sp. strain K30 in a ΔroxA background of Xanthomonas sp. strain 35Y and purified native (untagged) Lcp. The specific activities of Lcp and RoxA were 0.70 and 0.48 U/mg, respectively. Lcp differed from RoxA in the absence of heme groups and other characteristics. Notably, Lcp degraded polyisoprene via endo-type cleavage to tetra-C20 and higher oligo-isoprenoids with aldehyde and keto end groups, whereas RoxA used an exo-type cleavage mechanism to give the main end product 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD). RoxA was able to cleave isolated Lcp-derived oligo-isoprenoid molecules to ODTD. Inhibitor studies, spectroscopic investigations and metal analysis gave no indication for the presence of iron, other metals, or cofactors in Lcp. Our results suggest that Lcp could be a member of the growing group of cofactor-independent oxygenases and differs in the cleavage mechanism from heme-dependent RoxA. In conclusion, RoxA and Lcp represent two different answers to the same biochemical problem, the cleavage of polyisoprene, a polymer that has carbon-carbon double bonds as the only functional groups for enzymatic attack.

  2. Effects of 2'-O-methyl nucleotide substitution on EcoRI endonuclease cleavage activities.

    Directory of Open Access Journals (Sweden)

    Guojie Zhao

    Full Text Available To investigate the effect of sugar pucker conformation on DNA-protein interactions, we used 2'-O-methyl nucleotide (2'-OMeN to modify the EcoRI recognition sequence -TGAATTCT-, and monitored the enzymatic cleavage process using FRET method. The 2'-O-methyl nucleotide has a C3'-endo sugar pucker conformation different from the C2'-endo sugar pucker conformation of native DNA nucleotides. The initial reaction velocities were measured and the kinetic parameters, Km and Vmax were derived using Michaelis-Menten equation. Experimental results showed that 2'-OMeN substitutions for the EcoRI recognition sequence decreased the cleavage efficiency for A2, A3 and T4 substitutions significantly, and 2'-OMeN substitution for T5 residue inhibited the enzymatic activity completely. In contrast, substitutions for G1 and C6 could maintain the original activity. 2'-fluoro nucleic acid (2'-FNA and locked nucleic acid (LNA having similar C3'-endo sugar pucker conformation also demonstrated similar enzymatic results. This position-dependent enzymatic cleavage property might be attributed to the phosphate backbone distortion caused by the switch from C2'-endo to C3'-endo sugar pucker conformation, and was interpreted on the basis of the DNA-EcoRI structure. These 2'-modified nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property will have potential applications in genetic engineering and biomedicine.

  3. Synthesis, characterization, and photoactivated DNA cleavage by copper (II)/cobalt (II) mediated macrocyclic complexes. (United States)

    Naik, H R Prakash; Naik, H S Bhojya; Aravinda, T; Lamani, D S


    We report the synthesis of new photonuclease consisting of two Co(II)/Cu(II) complexes of macrocyclic fused quinoline. Metal complexes are [MLX(2)], type where M = Co(II) (5), Cu(II) (6), and X = Cl, and are well characterized by elemental analysis, Fourier transform infrared spectroscopy, (1)H-NMR and electronic spectra. We have shown that photocleavage of plasmid DNA is markedly enhanced when this ligand is irradiated in the presence of Cu(II), and more so than that of cobalt. The chemistry of ternary and binary Co(II) complexes showing efficient light induced (360 nm) DNA cleavage activity is summarized. The role of the metal in photoinduced DNA cleavage reactions is explored by designing complex molecules having macrocyclic structure. The mechanistic pathways are found to be concentration dependent on Co(II)/Cu(II) complexes and the photoexcitation energy photoredox chemistry. Highly effective DNA cleavage ability of 6 is attributed to the effective cooperation of the metal moiety.

  4. TD-DFT Insight into Photodissociation of Co-C Bond in Coenzyme B12 (United States)

    Kozlowski, Pawel; Liu, Hui; Kornobis, Karina; Lodowski, Piotr; Jaworska, Maria


    Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo-C → σ*Co-C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a MLCT (metal-to-ligand charge transfer) and a σ bonding-ligand charge transfer (SBLCT) states.

  5. Evaluation of the Wedge Cleavage Test for Assessment of Durability of Adhesive Bonded Joints. (United States)


    applied to the adherends. Exposures of hundreds or thousands of hours are necessary to discriminate between pretreatments if conventional lap shear or peel ...was preceded by additional degreasing in a conventional non- caustic proprietary alkaline cleaning solution. Pickling was for 30 minutes at 62-65°C in...consistent with the lower peel strength given by anodised surfaces5 (c) Adhesive FMIOOO Crack lengths are shown in Table 3 and Fig 5. Fracture energies were

  6. Catalytic C-C Bond Cleavage for the Production of Chemicals from Lignin

    NARCIS (Netherlands)

    Jastrzebski, R.


    Lignin is a major component of lignocellulosic biomass and could be an important renewable feedstock in industry for the production of (aromatic) bulk and fine chemicals. To this end, the development of new catalytic processes is required; both to depolymerise the biopolymer into small aromatic buil

  7. Enantioselective epoxidation and carbon-carbon bond cleavage catalyzed by Coprinus cinereus peroxidase and myeloperoxidase

    NARCIS (Netherlands)

    Tuynman, A; Lutje Spelberg, Jeffrey; Kooter, IM; Schoemaker, HE; Wever, R


    We demonstrate that myeloperoxidase (MPO) and Coprinus cinereus peroxidase (CiP) catalyze the enantioselective epoxidation of styrene and a number of substituted derivatives with a reasonable enantiomeric excess (up to 80%) and in a moderate yield. Three major differences with respect to the chlorop

  8. Specificity of the proteasome cleavage to the antigen protein

    Institute of Scientific and Technical Information of China (English)


    In the MHC classⅠmolecule binding antigenic peptides processing and presentation pathway,the ubiquitin-proteasome system plays a key role in degrading the protein substrate.For the purpose of studying the specificities of proteasomal cleavage sites,partial least squares method is used to predict the proteasomal cleavage sites,and the predictive accuracy of the model is 82.8%.The specificities of the cleavage sites and the adjacent positions come from the contribution of the amino acids of the samples to the cleavage sites,showing the information of proteasome interacting with antigen protein.It demonstrates that the proteasome cleaving to target protein is selective,but not random.

  9. Synthesis and Cleavage Activity of Artifical Minic Polypeptides

    Institute of Scientific and Technical Information of China (English)

    Yong YE; Xiao Lian HU; Ping LI; Ming Yu NIU; Li Feng CAO; Yu Fen ZHAO


    Two artificial minic polypeptides which are synthetic analogues of natural products with DNA affinity were synthesized, and theirs cleavage activity with DNA were examined. The structures of these compounds was confirmed by 1H NMR, MS and IR.

  10. Implementation of a combinatorial cleavage and deprotection scheme

    DEFF Research Database (Denmark)

    Nielsen, John; Rasmussen, Palle H.


    Phthalhydrazide libraries are synthesized in solution from substituted hydrazines and phthalimides in several different library formats including single compounds, indexed sub-libraries and a full library. When carried out during solid-phase synthesis, this combinatorial cleavage and deprotection...

  11. Study on Fabrication Technology of Reaction Bonded Silicon Carbide Mirror Blank for Space%空间用反应烧结碳化硅反射镜坯体制备技术研究

    Institute of Scientific and Technical Information of China (English)

    张舸; 赵汝成; 赵文兴


    Silicon Carbide (SiC) is a new type of candidate material for large-scale lightweight space born mirror.Its low thermal distortion, high stiffness, high optical quality, and its dimensional stability are better than other traditional optical substrate materials such as ULE, Zerodure, Beryllium (Be) and so on.In this paper, the lightweight silicon carbide space mirror blank was fabricated by reaction sintering.Lots of large scale SiC green bodies were prepared by a gel-casting method with the lost mould technology.And the size of the largest SiC green body with sandwich structure is 1080 mm × 820 mm now.After drying, burning out the organic elements and reaction sintering, the reaction bonded SiC (RB-SiC) mirror blanks were fabricated.The test results of ground mirrors show that the structure of RB-SiC is fully solid, and the mechanical and thermal properties of RBSiC are excellent in elastic modulus of 330 GPa, bending strength of 340 MPa, fracture toughness of 4.0 MPa·m1/2 and Coefficient of Thermal Expansion (CTE) of 2.6 × 10-6 K-1.The surface roughness (RMS) of the polished mirror is better than 3 nm, which means SiC is a fine candidate material for the spaceborne mirror.%采用凝胶注模(gel-casting)成型工艺并结合一种先进的消失模技术,制备了具有各种不同轻量化结构形式的碳化硅(SiC)陶瓷素坯,目前制备的背部半封闭素坯最大尺寸为1080mm×820 mm;素坯经过脱模、干燥、脱脂和反应烧结等,可得到空间用SiC反射镜坯体.对反应烧结碳化硅(RB-SiC)反射镜坯体的表面进行了光学加工,并且测试了其各项性能.结果表明,所制备的RB-SiC陶瓷内部结构均匀致密;力学性能和热学性能优异,弹性模量、抗弯强度、断裂韧性和热膨胀系数分别达到了330 GPa,340 MPa,4.0 MPa.m1/2和2.6×10-6K-1;镜体经抛光后的表面粗糙度RMS值优于3 nm,可作为空间用反射镜的候选材料.

  12. Mechanisms for ribotoxin-induced ribosomal RNA cleavage

    Energy Technology Data Exchange (ETDEWEB)

    He, Kaiyu [Department of Microbiology and Molecular Genetics (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States); Zhou, Hui-Ren [Food Science and Human Nutrition (United States); Pestka, James J., E-mail: [Department of Microbiology and Molecular Genetics (United States); Food Science and Human Nutrition (United States); Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824 (United States)


    The Type B trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin known to contaminate cereal-based foods, induces ribosomal RNA (rRNA) cleavage in the macrophage via p38-directed activation of caspases. Here we employed the RAW 264.7 murine macrophage model to test the hypothesis that this rRNA cleavage pathway is similarly induced by other ribotoxins. Capillary electrophoresis confirmed that the antibiotic anisomycin (≥ 25 ng/ml), the macrocylic trichothecene satratoxin G (SG) (≥ 10 ng/ml) and ribosome-inactivating protein ricin (≥ 300 ng/ml) induced 18s and 28s rRNA fragmentation patterns identical to that observed for DON. Also, as found for DON, inhibition of p38, double-stranded RNA-activated kinase (PKR) and hematopoietic cell kinase (Hck) suppressed MAPK anisomycin-induced rRNA cleavage, while, in contrast, their inhibition did not affect SG- and ricin-induced rRNA fragmentation. The p53 inhibitor pifithrin-μ and pan caspase inhibitor Z-VAD-FMK suppressed rRNA cleavage induced by anisomycin, SG and ricin, indicating that these ribotoxins shared with DON a conserved downstream pathway. Activation of caspases 8, 9 and 3 concurrently with apoptosis further suggested that rRNA cleavage occurred in parallel with both extrinsic and intrinsic pathways of programmed cell death. When specific inhibitors of cathepsins L and B (lysosomal cysteine cathepsins active at cytosolic neutral pH) were tested, only the former impaired anisomycin-, SG-, ricin- and DON-induced rRNA cleavage. Taken together, the data suggest that (1) all four ribotoxins induced p53-dependent rRNA cleavage via activation of cathepsin L and caspase 3, and (2) activation of p53 by DON and anisomycin involved p38 whereas SG and ricin activated p53 by an alternative mechanism. Highlights: ► Deoxynivalenol (DON) anisomycin, satratoxin G (SG) and ricin are ribotoxins. ► Ribotoxins induce 18s and 28s rRNA cleavage in the RAW 264.7 macrophage model. ► Ribotoxins induce rRNA cleavage via

  13. Cross Shear Roll Bonding

    DEFF Research Database (Denmark)

    Bay, Niels; Bjerregaard, Henrik; Petersen, Søren. B;


    The present paper describes an investigation of roll bonding an AlZn alloy to mild steel. Application of cross shear roll bonding, where the two equal sized rolls run with different peripheral speed, is shown to give better bond strength than conventional roll bonding. Improvements of up to 20......-23% in bond strength are found and full bond strength is obtained at a reduction of 50% whereas 65% is required in case of conventional roll bonding. Pseudo cross shear roll bonding, where the cross shear effect is obtained by running two equal sized rolls with different speed, gives the same results....

  14. Cell-surface acceleration of urokinase-catalyzed receptor cleavage

    DEFF Research Database (Denmark)

    Høyer-Hansen, G; Ploug, M; Behrendt, N;


    937 cell lysates, had the same amino termini as uPAR(2+3), generated by uPA in a purified system. In both cases cleavage had occurred at two positions in the hinge region connecting domain 1 and 2, between Arg83-Ala84 and Arg89-Ser90, respectively. The uPA-catalyzed cleavage of uPAR is a new negative...

  15. Cleavage events and sperm dynamics in chick intrauterine embryos.

    Directory of Open Access Journals (Sweden)

    Hyung Chul Lee

    Full Text Available This study was undertaken to elucidate detailed event of early embryogenesis in chicken embryos using a noninvasive egg retrieval technique before oviposition. White Leghorn intrauterine eggs were retrieved from 95 cyclic hens aged up to 54-56 weeks and morphogenetic observation was made under both bright field and fluorescent image in a time course manner. Differing from mammals, asymmetric cleavage to yield preblastodermal cells was observed throughout early embryogenesis. The first two divisions occurred synchronously and four polarized preblastodermal cells resulted after cruciform cleavage. Then, asynchronous cleavage continued in a radial manner and overall cell size in the initial cleavage region was smaller than that in the distal area. Numerous sperms were visible, regardless of zygotic nuclei formation. Condensed sperm heads were present mainly in the perivitelline space and cytoplasm, and rarely in the yolk region, while decondensed sperm heads were only visible in the yolk. In conclusion, apparent differences in sperm dynamics and early cleavage events compared with mammalian embryos were detected in chick embryo development, which demonstrated polarized cleavage with penetrating supernumerary sperm into multiple regions.

  16. Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage (United States)


    Background Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg2+ ions in efficient self-cleavage are of crucial interest. Results We report the first Raman characterization of the structure and activity of ASBVd, for plus and minus viroid strands. Both strands exhibit a typical A-type RNA conformation with an ordered double-helical content and a C3′-endo/anti sugar pucker configuration, although small but specific differences are found in the sugar puckering and base-stacking regions. The ASBVd(-) is shown to self-cleave 3.5 times more actively than ASBVd(+). Deuteration and temperature increase perturb differently the double-helical content and the phosphodiester conformation, as revealed by corresponding characteristic Raman spectral changes. Our data suggest that the structure rigidity and stability are higher and the D2O accessibility to H-bonding network is lower for ASBVd(+) than for ASBVd(-). Remarkably, the Mg2+-activated self-cleavage of the viroid does not induce any significant alterations of the secondary viroid structure, as evidenced from the absence of intensity changes of Raman marker bands that, however exhibit small but noticeable frequency downshifts suggesting several minor changes in phosphodioxy, internal loops and hairpins of the cleaved viroids. Conclusions Our results demonstrate the sensitivity of Raman spectroscopy in monitoring structural and conformational changes of the viroid and constitute the basis for further studies of its interactions with therapeutic agents and cell membranes. PMID:24655924

  17. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

    KAUST Repository

    Frusciante, Sarah


    Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7′,8′ double bonds adjacent to a 3-OH-β-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-β-apo-8′-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-β-apo-8′-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the β-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope.

  18. Thermodynamic and kinetic studies of the equilibration reaction between the sulfur and carbon bonded forms of a cobalt(III) complex with the ligands 2-aminoethyl-3-aminopropylsulfide and 1,1,1-tris(aminomethyl)ethane

    DEFF Research Database (Denmark)

    Springborg, J.; Kjellerup, S.; Kofod, Pauli


    A thermodn. and kinetic study of the equilibration between the Co-S bonded complex Co(tame)(S-aeaps)3+ and the Co-C bonded complex Co(tame)(C-aeaps)2+ is reported (tame = 1,1,1-tris(aminomethyl)ethane, aeaps = 2-aminoethyl-3-aminopropyl sulfide = 3-thiahexane-1,6-diamine and C-aeaps = 1,6-diamine-3...

  19. Prevalence of Bimolecular Routes in the Activation of Diatomic Molecules with Strong Chemical Bonds (O2, NO, CO, N2) on Catalytic Surfaces. (United States)

    Hibbitts, David; Iglesia, Enrique


    Dissociation of the strong bonds in O2, NO, CO, and N2 often involves large activation barriers on low-index planes of metal particles used as catalysts. These kinetic hurdles reflect the noble nature of some metals (O2 activation on Au), the high coverages of co-reactants (O2 activation during CO oxidation on Pt), or the strength of the chemical bonds (NO on Pt, CO and N2 on Ru). High barriers for direct dissociations from density functional theory (DFT) have led to a consensus that "defects", consisting of low-coordination exposed atoms, are required to cleave such bonds, as calculated by theory and experiments for model surfaces at low coverages. Such sites, however, bind intermediates strongly, rendering them unreactive at the high coverages prevalent during catalysis. Such site requirements are also at odds with turnover rates that often depend weakly on cluster size or are actually higher on larger clusters, even though defects, such as corners and edges, are most abundant on small clusters. This Account illustrates how these apparent inconsistencies are resolved through activations of strong bonds assisted by co-adsorbates on crowded low-index surfaces. Catalytic oxidations occur on Au clusters at low temperatures in spite of large activation barriers for O2 dissociation on Au(111) surfaces, leading to proposals that O2 activation requires low-coordination Au atoms or Au-support interfaces. When H2O is present, however, O2 dissociation proceeds with low barriers on Au(111) because chemisorbed peroxides (*OOH* and *HOOH*) form and weaken O-O bonds before cleavage, thus allowing activation on low-index planes. DFT-derived O2 dissociation barriers are much lower on bare Pt surfaces, but such surfaces are nearly saturated with CO* during CO oxidation. A dearth of vacant sites causes O2* to react with CO* to form *OOCO* intermediates that undergo O-O cleavage. NO-H2 reactions occur on Pt clusters saturated with NO* and H*; direct NO* dissociation requires vacant

  20. Addition of Carbon–Fluorine Bonds to a Mg(I)–Mg(I) Bond: An Equivalent of Grignard Formation in Solution (United States)


    Addition of the carbon–fluorine bond of a series of perfluorinated and polyfluorinated arenes across the Mg–Mg bond of a simple coordination complex proceeds rapidly in solution. The reaction results in the formation of a new carbon–magnesium bond and a new fluorine–magnesium bond and is analogous to Grignard formation in homogeneous solution. PMID:27636244

  1. Successive heterolytic cleavages of H2 achieve N2 splitting on silica-supported tantalum hydrides: A DFT proposed mechanism

    KAUST Repository

    Soláns, Xavier Luis


    DFT(B3PW91) calculations have been carried out to propose a pathway for the N2 cleavage by H2 in the presence of silica-supported tantalum hydride complexes [(≡ SiO)2TaHx] that forms [(≡SiO)2Ta(NH)(NH2)] (Science2007, 317, 1056). The calculations, performed on the cluster models {μ-O[(HO)2SiO] 2}TaH1 and {μ-O[(HO)2SiO] 2}TaH3, labelled as (≡SiO)2TaH x (x = 1, 3), show that the direct hydride transfers to coordinated N-based ligands in (≡SiO)2TaH(η2-N2) and (≡SiO)2TaH(η2-HNNH) have high energy barrier barriers. These high energy barriers are due in part to a lack of energetically accessible empty orbitals in the negatively charged N-based ligands. It is shown that a succession of proton transfers and reduction steps (hydride transfer or 2 electron reduction by way of dihydride reductive coupling) to the nitrogen-based ligands leads to more energetically accessible pathways. These proton transfers, which occur by way of heterolytic activation of H2, increase the electrophilicity of the resulting ligand (diazenido, N 2H-, and hydrazido, NHNH2-, respectively) that can thus accept a hydride with a moderate energy barrier. In the case of (≡SiO)2TaH(η2-HNNH), the H 2 molecule that is adding across the Ta-N bond is released after the hydride transfer step by heterolytic elimination from (≡SiO) 2TaH(NH2)2, suggesting that dihydrogen has a key role in assisting the final steps of the reaction without itself being consumed in the process. This partly accounts for the experimental observation that the addition of H2 is needed to convert an intermediate, identified as a diazenido complex [(≡SiO)2TaH(η 2-HNNH)] from its ν(N-H) stretching frequency of 3400 cm -1, to the final product. Throughout the proposed mechanism, the tantalum remains in its preferred high oxidation state and avoids redox-type reactions, which are more energetically demanding. © 2012 American Chemical Society.

  2. Cleavage entropy as quantitative measure of protease specificity.

    Directory of Open Access Journals (Sweden)

    Julian E Fuchs


    Full Text Available A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity.

  3. Cleavage entropy as quantitative measure of protease specificity. (United States)

    Fuchs, Julian E; von Grafenstein, Susanne; Huber, Roland G; Margreiter, Michael A; Spitzer, Gudrun M; Wallnoefer, Hannes G; Liedl, Klaus R


    A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity.

  4. Microstructure and properties of hot roll bonding layer of dissimilar metals. 2. Bonding interface microstructure of Zr/stainless steel by hot roll bonding and its controlling

    Energy Technology Data Exchange (ETDEWEB)

    Yasuyama, Masanori; Ogawa, Kazuhiro; Taka, Takao; Nakasuji, Kazuyuki [Sumitomo Metal Industries Ltd., Osaka (Japan); Nakao, Yoshikuni; Nishimoto, Kazutoshi


    The hot roll bonding of zirconium and stainless steel inserted with tantalium was investigated using the newly developed rolling mill. The effect of hot rolling temperatures of zirconium/stainless steel joints on bonding interface structure was evaluated. Intermetallic compound layer containing cracks was observed at the bonding interface between stainless steel and tantalium when the rolling temperature was above 1373K. The hardness of the bonding layer of zirconium and tantalium bonded above 1273K was higher than tantalium or zirconium base metal in spite of absence of intermetallic compound. The growth of reaction layer at the stainless steel and tantalium interface and at the tantalium and zirconium interface was conforming a parabolic low when that was isothermally heated after hot roll bonding, and the growth rate was almost same as that of static diffusion bonding without using hot roll bonding process. It is estimated that the strain caused by hot roll bonding gives no effect on the growth of reaction layer. It was confirmed that the dissimilar joint of zirconium and stainless steel with insert of tantalium having the sound bonding interface were obtained at the suitable bonding temperature of 1173K by the usage of the newly developed hot roll bonding process. (author)

  5. Developing mononuclear copper-active-oxygen complexes relevant to reactive intermediates of biological oxidation reactions. (United States)

    Itoh, Shinobu


    Active-oxygen species generated on a copper complex play vital roles in several biological and chemical oxidation reactions. Recent attention has been focused on the reactive intermediates generated at the mononuclear copper active sites of copper monooxygenases such as dopamine β-monooxygenase (DβM), tyramine β-monooxygenase (TβM), peptidylglycine-α-hydroxylating monooxygenase (PHM), and polysaccharide monooxygenases (PMO). In a simple model system, reaction of O2 and a reduced copper(I) complex affords a mononuclear copper(II)-superoxide complex or a copper(III)-peroxide complex, and subsequent H(•) or e(-)/H(+) transfer, which gives a copper(II)-hydroperoxide complex. A more reactive species such as a copper(II)-oxyl radical type species could be generated via O-O bond cleavage of the peroxide complex. However, little had been explored about the chemical properties and reactivity of the mononuclear copper-active-oxygen complexes due to the lack of appropriate model compounds. Thus, a great deal of effort has recently been made to develop efficient ligands that can stabilize such reactive active-oxygen complexes in synthetic modeling studies. In this Account, I describe our recent achievements of the development of a mononuclear copper(II)-(end-on)superoxide complex using a simple tridentate ligand consisting of an eight-membered cyclic diamine with a pyridylethyl donor group. The superoxide complex exhibits a similar structure (four-coordinate tetrahedral geometry) and reactivity (aliphatic hydroxylation) to those of a proposed reactive intermediate of copper monooxygenases. Systematic studies based on the crystal structures of copper(I) and copper(II) complexes of the related tridentate supporting ligands have indicated that the rigid eight-membered cyclic diamine framework is crucial for controlling the geometry and the redox potential, which are prerequisites for the generation of such a unique mononuclear copper(II)-(end-on)superoxide complex

  6. Reactions of Cyclohexyl Isocyanide with η5-Substituted Cyclo pentadienyl Mo=Mo Triply Bonded Complexes.Crystal Structure of[Mo(CO)2(η5-C5sH4CO2CH3)]2(μ-η2-CNC6H11)

    Institute of Scientific and Technical Information of China (English)

    LI Qingshan; LUO Chuncheng; SONG Licheng


    Reactions of one or two equiv,of cyclohexyl isocyanide in THF at room temperature with Mo=Mo triply bonded complexes[Mo(CO)2(η5-C5H4R)]2(R=COCH3,CO2CH3)gave the isocyanide coordinated Mo-Mo singly bonded complexes with functionally substituted cyclopentadienyl ligands,[Mo(CO)2(η5-C5H4R)]2(μ-η2-CNC611)(1a,R=COCH3;1b,R=CO2CH3)and[Mo(CO)2(η5-C5H4R)(CNC6H11)]2(2a,R=COCH3;2b,R=CO2CH3),respectively.Complexes 1a,1b and 2a,2b could be more conveniently prepared by thermal decarbonylation of MoMo singly bonded complexes[Mo(CO)3(η5-C5H4R)]2(R=COCH3,CO2CH3)in toluene at reflux,followed by treatment of the resulting Mo=Mo triply bonded complexes[Mo(CO)2(η5-C5H4R)]2(R=COCH3,CO2CH3)in situ with cyclohexyl isocyanide.While 1a,1b and 2a,2b were characterized by elemental analysis and spectroscopy,1b was further characterized by X-ray crystallography.

  7. Microwave-Accelerated Organic Reactions

    Institute of Scientific and Technical Information of China (English)

    LU TaJung


    @@ The use of microwave technology in accelerating organic reactions has received intense attention leading to immense growth recently. Accordingly, we have been interested in improving the efficacy of organic processes by microwave irradiation. Here we report our results on the microwave assisted 1,3-dipolar cycloaddition reaction of nitrile oxides with allylic alcohols, the cleavage reaction of 1,3-diketones under alkaline conditions, and the formation of carbamates from isocyanates with alcohols. The reactions carried out under microwave irradiation, in general, required considerably less reaction time and afforded the desired products in higher yields than those under classical conditions. In all the cases we have studied, the procedures are simplified, the purity of the products are higher, and the cost of reaction is greatly reduced employing microwave.

  8. Microwave-Accelerated Organic Reactions

    Institute of Scientific and Technical Information of China (English)

    LU; TaJung


    The use of microwave technology in accelerating organic reactions has received intense attention leading to immense growth recently. Accordingly, we have been interested in improving the efficacy of organic processes by microwave irradiation. Here we report our results on the microwave assisted 1,3-dipolar cycloaddition reaction of nitrile oxides with allylic alcohols, the cleavage reaction of 1,3-diketones under alkaline conditions, and the formation of carbamates from isocyanates with alcohols. The reactions carried out under microwave irradiation, in general, required considerably less reaction time and afforded the desired products in higher yields than those under classical conditions. In all the cases we have studied, the procedures are simplified, the purity of the products are higher, and the cost of reaction is greatly reduced employing microwave.  ……

  9. A new cultural cleavage in post-modern society

    Directory of Open Access Journals (Sweden)

    Jan-Erik Lane


    Full Text Available The attitudes towards gender and homosexuality tend to be linked at the micro level (individuals, which explains the political saliency of this newly emerging cleavage. At the macro level (country, the main finding is that the value orientations towards gender and homosexuality are strongly embedded in the basic cultural or civilisation differences among countries. As developing countries modernise and enter post-modernity, they will also experience the gender cleavage, especially when they adhere to an individualistic culture. Cultural cleavages in the post-modern society, whether in rich or developing countries, can only be properly researched by the survey method. It opens up a large area for both micro and macro analyses in the social sciences.

  10. Variable context Markov chains for HIV protease cleavage site prediction. (United States)

    Oğul, Hasan


    Deciphering the knowledge of HIV protease specificity and developing computational tools for detecting its cleavage sites in protein polypeptide chain are very desirable for designing efficient and specific chemical inhibitors to prevent acquired immunodeficiency syndrome. In this study, we developed a generative model based on a generalization of variable order Markov chains (VOMC) for peptide sequences and adapted the model for prediction of their cleavability by certain proteases. The new method, called variable context Markov chains (VCMC), attempts to identify the context equivalence based on the evolutionary similarities between individual amino acids. It was applied for HIV-1 protease cleavage site prediction problem and shown to outperform existing methods in terms of prediction accuracy on a common dataset. In general, the method is a promising tool for prediction of cleavage sites of all proteases and encouraged to be used for any kind of peptide classification problem as well.

  11. Water as a green solvent for efficient synthesis of isocoumarins through microwave-accelerated and Rh/Cu-catalyzed C-H/O-H bond functionalization

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qiu; Yan, Yunnan; Wang, Xiaowei; Gong, Binwei; Tang, Xiaobo; Shi, JingJing; Xu, H. Eric; Yi, Wei [Shenyang; (Gannan); (Van Andel); (UST - China); (Chinese Aca. Sci.)


    Green chemistry that uses water as a solvent has recently received great attention in organic synthesis. Here we report an efficient synthesis of biologically important isocoumarins through direct cleavage of C–H/O–H bonds by microwave-accelerated and Rh/Cu-catalyzed oxidative annulation of various substituted benzoic acids, where water is used as the only solvent in the reactions. The remarkable features of this “green” methodology include high product yields, wide tolerance of various functional groups as substrates, and excellent region-/site-specificities, thus rendering this methodology a highly versatile and eco-friendly alternative to the existing methods for synthesizing isocoumarins and other biologically important derivatives such as isoquinolones.

  12. Hydrogen Bonds in Excited State Proton Transfer (United States)

    Horke, D. A.; Watts, H. M.; Smith, A. D.; Jager, E.; Springate, E.; Alexander, O.; Cacho, C.; Chapman, R. T.; Minns, R. S.


    Hydrogen bonding interactions between biological chromophores and their surrounding protein and solvent environment significantly affect the photochemical pathways of the chromophore and its biological function. A common first step in the dynamics of these systems is excited state proton transfer between the noncovalently bound molecules, which stabilizes the system against dissociation and principally alters relaxation pathways. Despite such fundamental importance, studying excited state proton transfer across a hydrogen bond has proven difficult, leaving uncertainties about the mechanism. Through time-resolved photoelectron imaging measurements, we demonstrate how the addition of a single hydrogen bond and the opening of an excited state proton transfer channel dramatically changes the outcome of a photochemical reaction, from rapid dissociation in the isolated chromophore to efficient stabilization and ground state recovery in the hydrogen bonded case, and uncover the mechanism of excited state proton transfer at a hydrogen bond, which follows sequential hydrogen and charge transfer processes.

  13. Synthesis of o-Carboxyarylacrylic Acids by Room Temperature Oxidative Cleavage of Hydroxynaphthalenes and Higher Aromatics with Oxone. (United States)

    Parida, Keshaba Nanda; Moorthy, Jarugu Narasimha


    A simple procedure for the synthesis of a variety of o-carboxyarylacrylic acids has been developed with Oxone (2KHSO5·KHSO4·K2SO4); the oxidation reaction involves the stirring of methoxy/hydroxy-substituted naphthalenes, phenanthrenes, anthracenes, etc. with Oxone in an acetonitrile-water mixture (1:1, v/v) at rt. Mechanistically, the reaction proceeds via initial oxidation of naphthalene to o-quinone, which undergoes cleavage to the corresponding o-carboxyarylacrylic acid. The higher aromatics are found to yield carboxymethyl lactones derived from the initially formed o-carboxyarylacrylic acids.

  14. Prediction of proteasome cleavage motifs by neural networks

    DEFF Research Database (Denmark)

    Kesimir, C.; Nussbaum, A.K.; Schild, H.


    physiological conditions. Our algorithm has been trained not only on in vitro data, but also on MHC Class I ligand data, which reflect a combination of immunoproteasome and constitutive proteasome specificity. This feature, together with the use of neural networks, a non-linear classification technique, make...... the prediction of MHC Class I ligand boundaries more accurate: 65% of the cleavage sites and 85% of the non-cleavage sites are correctly determined. Moreover, we show that the neural networks trained on the constitutive proteasome data learns a specificity that differs from that of the networks trained on MHC...

  15. 叔丁醇钾促进的形成碳—碳及碳—杂键的偶联反应的研究进展%Recent Progress in the Research of the t-BuOK-Mediated Coupling Reactions to Form Carbon-Carbon and Carbon-Heteroatom Bonds

    Institute of Scientific and Technical Information of China (English)

    王良贵; 严国兵; 张鑫燕


    Potassium tert-butoxide has wide application as a strong base and weak nucleophilie in organic chemistry. In this paper, the newest development of the t-BuOK-mediated coupling reactions is reviewed. The main focuses are the formation of carbon-carbon, carbon-ziitrogen and carbon-oxygen bonds. The formation mechanisms of these bonds are discussed in details.%叔丁醇钾由于其碱性强而亲核性相对较弱在有机合成中得到广泛应用.综述了近年来叔丁醇钾促进的交叉偶联反应的研究进展,主要包括碳-碳、碳-氮及碳-氧键的形成及其反应机理的探讨.

  16. Bonding with Your Baby (United States)

    ... in infant massage in your area. Breastfeeding and bottle-feeding are both natural times for bonding. Infants respond ... activities include: participating together in labor and delivery feeding ( breast or bottle ); sometimes dad forms a special bond with baby ...

  17. Structure and reactivity of bis(silyl) dihydride complexes (PMe(3))(3)Ru(SiR(3))(2)(H)(2): model compounds and real intermediates in a dehydrogenative C-Si bond forming reaction. (United States)

    Dioumaev, Vladimir K; Yoo, Bok R; Procopio, Leo J; Carroll, Patrick J; Berry, Donald H


    A series of stable complexes, (PMe(3))(3)Ru(SiR(3))(2)(H)(2) ((SiR(3))(2) = (SiH(2)Ph)(2), 3a; (SiHPh(2))(2), 3b; (SiMe(2)CH(2)CH(2)SiMe(2)), 3c), has been synthesized by the reaction of hydridosilanes with (PMe(3))(3)Ru(SiMe(3))H(3) or (PMe(3))(4)Ru(SiMe(3))H. Compounds 3a and 3c adopt overall pentagonal bipyramidal geometries in solution and the solid state, with phosphine and silyl ligands defining trigonal bipyramids and ruthenium hydrides arranged in the equatorial plane. Compound 3a exhibits meridional phosphines, with both silyl ligands equatorial, whereas the constraints of the chelate in 3c result in both axial and equatorial silyl environments and facial phosphines. Although there is no evidence for agostic Si-H interactions in 3a and 3b, the equatorial silyl group in 3c is in close contact with one hydride (1.81(4) A) and is moderately close to the other hydride (2.15(3) A) in the solid state and solution (nu(Ru.H.Si) = 1740 cm(-)(1) and nu(RuH) = 1940 cm(-)(1)). The analogous bis(silyl) dihydride, (PMe(3))(3)Ru(SiMe(3))(2)(H)(2) (3d), is not stable at room temperature, but can be generated in situ at low temperature from the 16e(-) complex (PMe(3))(3)Ru(SiMe(3))H (1) and HSiMe(3). Complexes 3b and 3d have been characterized by multinuclear, variable temperature NMR and appear to be isostructural with 3a. All four complexes exhibit dynamic NMR spectra, but the slow exchange limit could not be observed for 3c. Treatment of 1 with HSiMe(3) at room temperature leads to formation of (PMe(3))(3)Ru(SiMe(2)CH(2)SiMe(3))H(3) (4b) via a CH functionalization process critical to catalytic dehydrocoupling of HSiMe(3) at higher temperatures. Closer inspection of this reaction between -110 and -10 degrees C by NMR reveals a plethora of silyl hydride phosphine complexes formed by ligand redistribution prior to CH activation. Above ca. 0 degrees C this mixture converts cleanly via silane dehydrogenation to the very stable tris(phosphine) trihydride carbosilyl complex 4b

  18. Changes in antioxidant capacity and colour associated with the formation of β-carotene epoxides and oxidative cleavage derivatives. (United States)

    Gurak, Poliana D; Mercadante, Adriana Z; González-Miret, M L; Heredia, Francisco J; Meléndez-Martínez, Antonio J


    In this study HPLC-DAD-MS/MS was applied for the identification of compounds derived from (all-E)-β-carotene following epoxidation and oxidative cleavage. The consequences on the CIELAB colour parameters and antioxidant capacity (AC) were also evaluated. Five apocarotenoids, three secocarotenoids, seven Z isomers and two epoxides were detected as a result of the oxidative cleavage. Four epoxides and three Z isomers were detected as a consequence of the epoxidation reaction. Some compounds were detected for the first time as a result of oxidation reactions. Both treatments led to a marked decrease in b(∗) and Cab(∗) values, indicating that these colour parameters can be used for the rapid assessment of β-carotene oxidation. The oxidative cleavage of β-carotene resulted in increased capacity to both scavenge ABTS(+) and quench singlet oxygen. These results suggest that the study of the AC of these oxidative derivatives and their possible usefulness as food ingredients deserves further attention.

  19. Acrylic mechanical bond tests

    Energy Technology Data Exchange (ETDEWEB)

    Wouters, J.M.; Doe, P.J.


    The tensile strength of bonded acrylic is tested as a function of bond joint thickness. 0.125 in. thick bond joints were found to posses the maximum strength while the acceptable range of joints varied from 0.063 in. to almost 0.25 in. Such joints are used in the Sudbury Neutrino Observatory.

  20. Bond percolation in films (United States)

    Korneta, W.; Pytel, Z.


    Bond percolation in films with simple cubic structure is considered. It is assumed that the probability of a bond being present between nearest-neighbor sites depends on the distances to surfaces. Based on the relation between the Potts model and the bond percolation model, and using the mean-field approximation, the phase diagram and profiles of the percolation probability have been obtained.