WorldWideScience

Sample records for hammerhead ribozyme catalysis

  1. Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

    Science.gov (United States)

    Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

    2014-09-01

    The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential

  2. Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site.

    Science.gov (United States)

    Han, Joonhee; Burke, John M

    2005-05-31

    We have used nucleobase substitution and kinetic analysis to test the hypothesis that hammerhead catalysis occurs by a general acid-base mechanism, in which nucleobases are directly involved in deprotonation of the attacking 2'-hydroxyl group and protonation of the 5'-oxygen that serves as the leaving group in the cleavage reaction. We demonstrate that simultaneous substitution of two important nucleobases, G8 and G12, with 2,6-diaminopurine shifts the pH optimum of the cleavage reaction from greater than 9.5 to approximately 6.8 in two different hammerhead constructs. Controls involving substitution with other nucleobases and combinations of nucleobases at G5, G8, and/or G12 do not show this behavior. The observed changes in the pH-rate behavior are consistent with a mechanism in which N1 protonation-deprotonation events of guanine or 2,6-diaminopurine at positions 8 and 12 are essential for catalysis. Further support for the participation of G8 and G12 comes from photochemical cross-linking experiments, which show that G8 and G12 can stack upon the two substrate nucleobases at the reactive linkage, G(or U)1.1 and C17 (Heckman, J. E., Lambert, D., and Burke, J. M. (2005) Photocrosslinking detects a compact active structure of the hammerhead ribozyme, Biochemistry 44, 4148-4156). Together, these results support a model in which the hammerhead undergoes a transient conformational change into a catalytically active structure, in which stacking of G8 and G12 upon the nucleobases spanning the cleavage site provides an appropriate architecture for general acid-base catalysis. The hammerhead and hairpin ribozymes may share similarities in the organization of their active sites and their catalytic mechanism.

  3. Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations.

    Science.gov (United States)

    Lee, Tai-Sung; York, Darrin M

    2008-06-11

    A series of ten 60 ns molecular dynamics (MD) simulations of the native and mutated full length hammerhead ribozymes in the reactant state and in an activated precursor state (G8:2'OH deprotonated) are reported. Mutant simulations include the C3U, G8A, and G8I single mutants and a C3U/G8A double mutant that exhibits an experimental rescue effect. The results provide critical details into the origin of the observed mutation effects and support a mechanism where the 2'OH of G8 acts as a general acid catalyst that is held in position through Watson-Crick hydrogen bonding between G8 and C3.

  4. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity

    Science.gov (United States)

    De la Peña, Marcos; Gago, Selma; Flores, Ricardo

    2003-01-01

    Natural hammerhead ribozymes are mostly found in some viroid and viroid-like RNAs and catalyze their cis cleavage during replication. Hammerheads have been manipulated to act in trans and assumed to have a similar catalytic behavior in this artificial context. However, we show here that two natural cis-acting hammerheads self-cleave much faster than trans-acting derivatives and other reported artificial hammerheads. Moreover, modifications of the peripheral loops 1 and 2 of one of these natural hammerheads induced a >100-fold reduction of the self-cleavage constant, whereas engineering a trans-acting artificial hammerhead into a cis derivative by introducing a loop 1 had no effect. These data show that regions external to the central conserved core of natural hammerheads play a role in catalysis, and suggest the existence of tertiary interactions between these peripheral regions. The interactions, determined by the sequence and size of loops 1 and 2 and most likely of helices I and II, must result from natural selection and should be studied in order to better understand the hammerhead requirements in vivo. PMID:14532128

  5. Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers.

    Science.gov (United States)

    Lünse, Christina E; Weinberg, Zasha; Breaker, Ronald R

    2016-11-18

    Hammerhead ribozymes represent the most common of the nine natural classes of self-cleaving RNAs. The hammerhead catalytic core includes 11 highly-conserved nucleotides located largely within the unpaired regions of a junction formed by stems I, II and III. The vast majority of previously reported examples carry an additional pseudoknot or other tertiary interactions between nucleotides that precede stem I and nucleotides in the loop of stem II. These extra contacts are critical for high-speed RNA catalysis. Herein, we report the discovery of ∼150,000 additional variant hammerhead representatives that exhibit diminished stem III substructures. These variants are frequently associated with Penelope-like retrotransposons, which are a type of mobile genetic element. Kinetic analyses indicate that these RNAs form dimers to cleave RNA.

  6. Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes.

    Science.gov (United States)

    Ren, Aiming; Micura, Ronald; Patel, Dinshaw J

    2017-12-01

    Small self-cleaving ribozymes are widely distributed in nature and are essential for rolling-circle-based replication of satellite and pathogenic RNAs. Earlier structure-function studies on the hammerhead, hairpin, glmS, hepatitis delta virus and Varkud satellite ribozymes have provided insights into their overall architecture, their catalytic active site organization, and the role of nearby nucleobases and hydrated divalent cations in facilitating general acid-base and electrostatic-mediated catalysis. This review focuses on recent structure-function research on active site alignments and catalytic mechanisms of the Rzb hammerhead ribozyme, as well as newly-identified pistol, twister and twister-sister ribozymes. In contrast to an agreed upon mechanistic understanding of self-cleavage by Rzb hammerhead and pistol ribozymes, there exists a divergence of views as to the cleavage site alignments and catalytic mechanisms adopted by twister and twister-sister ribozymes. One approach to resolving this conundrum would be to extend the structural studies from currently available pre-catalytic conformations to their transition state mimic vanadate counterparts for both ribozymes. Copyright © 2017. Published by Elsevier Ltd.

  7. Eukaryotic Penelope-Like Retroelements Encode Hammerhead Ribozyme Motifs

    Science.gov (United States)

    Cervera, Amelia; De la Peña, Marcos

    2014-01-01

    Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes. PMID:25135949

  8. LNA nucleotides improve cleavage efficiency of singular and binary hammerhead ribozymes

    DEFF Research Database (Denmark)

    Christiansen, Janne K; Lobedanz, Sune; Arar, Khalil

    2007-01-01

    Variants of trans-acting hammerhead ribozymes were modified with Locked Nucleic Acid (LNA) nucleotides to reduce their size, to improve access to their RNA target and to explore combinational properties of binary constructs. Using low Mg(2+) concentrations and low substrate and ribozyme concentra......Variants of trans-acting hammerhead ribozymes were modified with Locked Nucleic Acid (LNA) nucleotides to reduce their size, to improve access to their RNA target and to explore combinational properties of binary constructs. Using low Mg(2+) concentrations and low substrate and ribozyme...... molecules with each half binding to the substrate. Efficient, binary hammerhead ribozymes were pursued in a combinatorial approach using a 6-times 5 library, which was analysed concerning the best combinations, buffer conditions and fragment ratios....

  9. Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-01-01

    Full Text Available Nucleic acids are useful for biomedical targeting and sensing applications in which the molecular environment is different from that of a dilute aqueous solution. In this study, the influence of various types of mixed solutions of water and water-soluble organic compounds on RNA was investigated by measuring the catalytic activity of the hammerhead ribozyme and the thermodynamic stability of an oligonucleotide duplex. The compounds with a net neutral charge, such as poly(ethylene glycol, small primary alcohols, amide compounds, and aprotic solvent molecules, added at high concentrations changed the ribozyme-catalyzed RNA cleavage rate, with the magnitude of the effect dependent on the NaCl concentration. These compounds also changed the thermodynamic stability of RNA base pairs of an oligonucleotide duplex and its dependence on the NaCl concentration. Specific interactions with RNA molecules and reduced water activity could account for the inhibiting effects on the ribozyme catalysis and destabilizing effects on the duplex stability. The salt concentration dependence data correlated with the dielectric constant, but not with water activity, viscosity, and the size of organic compounds. This observation suggests the significance of the dielectric constant effects on the RNA reactions under molecular crowding conditions created by organic compounds.

  10. Experimental cancer gene therapy by multiple anti-survivin hammerhead ribozymes.

    Science.gov (United States)

    Fei, Qi; Zhang, Hongyu; Fu, Lili; Dai, Xinlan; Gao, Baomei; Ni, Min; Ge, Chao; Li, Jinjun; Ding, Xia; Ke, Yuwen; Yao, Xuebiao; Zhu, Jingde

    2008-06-01

    To improve the efficacy of gene therapy for cancer, we designed four hammerhead ribozyme adenoviruses (R1 to R4) targeting the exposed regions of survivin mRNA. In addition to the in vitro characterization, which included a determination of the sequence specificity of cleavage by primer extension, assays for cell proliferation and for in vivo tumor growth were used to score for ribozyme efficiency. The resulting suppression of survivin expression induced mitotic catastrophe and cell death via the caspase-3-dependent pathway. Importantly, administration of the ribozyme adenoviruses inhibited tumor growth in a hepatocellular carcinoma xenograft mouse model. Co-expression of R1, R3 and R4 ribozymes synergistically suppressed survivin and, as this combination targets all major forms of the survivin transcripts, produced the most potent anti-cancer effects. The adenoviruses carrying the multiple hammerhead ribozymes described in this report offered a robust gene therapy strategy against cancer.

  11. Effective suppression of Dengue fever virus in mosquito cell cultures using retroviral transduction of hammerhead ribozymes targeting the viral genome

    Directory of Open Access Journals (Sweden)

    Mohammed Ahmed

    2009-06-01

    Full Text Available Abstract Outbreaks of Dengue impose a heavy economic burden on developing countries in terms of vector control and human morbidity. Effective vaccines against all four serotypes of Dengue are in development, but population replacement with transgenic vectors unable to transmit the virus might ultimately prove to be an effective approach to disease suppression, or even eradication. A key element of the refractory transgenic vector approach is the development of transgenes that effectively prohibit viral transmission. In this report we test the effectiveness of several hammerhead ribozymes for suppressing DENV in lentivirus-transduced mosquito cells in an attempt to mimic the transgenic use of these effector molecules in mosquitoes. A lentivirus vector that expresses these ribozymes as a fusion RNA molecule using an Ae. aegypti tRNAval promoter and terminating with a 60A tail insures optimal expression, localization, and activity of the hammerhead ribozyme against the DENV genome. Among the 14 hammerhead ribozymes we designed to attack the DENV-2 NGC genome, several appear to be relatively effective in reducing virus production from transduced cells by as much as 2 logs. Among the sequences targeted are 10 that are conserved among all DENV serotype 2 strains. Our results confirm that hammerhead ribozymes can be effective in suppressing DENV in a transgenic approach, and provide an alternative or supplementary approach to proposed siRNA strategies for DENV suppression in transgenic mosquitoes.

  12. Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities

    Directory of Open Access Journals (Sweden)

    Burke Donald H

    2005-08-01

    Full Text Available Abstract Background Low concentrations of free magnesium in the intracellular environment can present critical limitations for hammerhead ribozymes, especially for those that are designed for intermolecular (trans cleavage of a host or pathogen RNA. Tertiary stabilizing motifs (TSM's from natural and artificial ribozymes with a "type I" topology have been exploited to stabilize trans-cleaving hammerheads. Ribozymes with "type II" or "type III" topologies might seem incompatible with conversion to trans-cleavage designs, because opening the loop at the end of stem 1 or stem 2 to accommodate substrate binding is expected to disrupt the TSM and eliminate tertiary stabilization. Results Stem 1, together with single-stranded segments capping or internal to this stem, contains both the substrate-binding and tertiary stabilization functions. This stem was made discontinuous within the sTRSV hammerhead ribozyme, thereby separating the two functions into discrete structural segments. The resulting ribozyme, designated "RzC," cleaved its 13 nucleotide target substrate at MgCl2 concentrations as low as 0.2 mM at 25°C and 0.5 mM at 37°C. Under multiple-turnover conditions, nearly thirty turnovers were observed at the highest substrate:RzC ribozyme ratios. Similar stabilization was observed for several derivatives of RzC. Catalytic activity was diminished or eliminated at sub-millimolar MgCl2 concentrations for ribozymes with weakened or deleted tertiary interactions. Eadie-Hofstee analysis revealed that the stabilized and non-stabilized ribozymes bind their substrates with equivalent affinities, suggesting that differences in observed activity are not the result of diminished binding. Some of the stabilized and non-stabilized ribozymes appear to fold into a heterogeneous collection of conformers, only a subset of which are catalytically active. Conclusion Hammerhead ribozymes with the "type III" topology can be converted to a tertiary, trans

  13. Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.

    Science.gov (United States)

    Hermann, T; Auffinger, P; Scott, W G; Westhof, E

    1997-09-01

    In the presence of magnesium ions, cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash-freezing of crystals under conditions where the ribozyme is active, provide evidence that a mu-bridging OH-ion is located between two Mg2+ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'- endo to the C2'- endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorous atom and the mu-bridging OH-ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a mu-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH-ion that is able to activate the 2'-hydroxyl nucleophile after a minor and localized conformational change in the RNA.

  14. Antiviral Hammerhead Ribozymes Are Effective for Developing Transgenic Suppression of Chikungunya Virus in Aedes aegypti Mosquitoes

    Directory of Open Access Journals (Sweden)

    Priya Mishra

    2016-06-01

    Full Text Available The chikungunya virus (CHIKV is an emerging pathogen with widespread distribution in regions of Africa, India, and Asia that threatens to spread into temperate climates with the introduction of its major vector, Aedes albopictus. CHIKV causes a disease frequently misdiagnosed as dengue fever, with potentially life-threatening symptoms that can result in a longer-term debilitating arthritis. The increasing risk of spread from endemic regions via human travel and commerce and the current absence of a vaccine put a significant proportion of the world population at risk for this disease. In this study we designed and tested hammerhead ribozymes (hRzs targeting CHIKV structural protein genes of the RNA genome as potential antivirals both at the cellular and in vivo level. We employed the CHIKV strain 181/25, which exhibits similar infectivity rates in both Vero cell cultures and mosquitoes. Virus suppression assay performed on transformed Vero cell clones of all seven hRzs demonstrated that all are effective at inhibiting CHIKV in Vero cells, with hRz #9 and #14 being the most effective. piggyBac transformation vectors were constructed using the Ae. aegypti t-RNAval Pol III promoted hRz #9 and #14 effector genes to establish a total of nine unique transgenic Higgs White Eye (HWE Ae. aegypti lines. Following confirmation of transgene expression by real-time polymerase chain reaction (RT-PCR, comparative TCID50-IFA analysis, in situ Immuno-fluorescent Assays (IFA and analysis of salivary CHIKV titers demonstrated effective suppression of virus replication at 7 dpi in heterozygous females of each of these transgenic lines compared with control HWE mosquitoes. This report provides a proof that appropriately engineered hRzs are powerful antiviral effector genes suitable for population replacement strategies

  15. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).

    Science.gov (United States)

    Martinsen, Lene; Johnsen, Arild; Venanzetti, Federica; Bachmann, Lutz

    2010-01-04

    The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat. We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

  16. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae

    Directory of Open Access Journals (Sweden)

    Venanzetti Federica

    2010-01-01

    Full Text Available Abstract Background The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH ribozyme structure and activity embedded within each repeat. Results We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. Conclusions The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

  17. Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation.

    Science.gov (United States)

    Gaines, Colin S; York, Darrin M

    2016-03-09

    We present results from molecular dynamics simulations and free energy calculations of the twister ribozyme at different stages along the reaction path to gain insight into its mechanism. The results, together with recent biochemical experiments, provide support for a mechanism involving general-acid catalysis by a conserved adenine residue in the active site. Although adenine has been previously implicated as a general acid acting through the N1 position in other ribozymes such as the hairpin and VS ribozymes, in the twister ribozyme there may be a twist. Biochemical experiments suggest that general acid catalysis may occur through the N3 position, which has never before been implicated in this role; however, currently, there is a lack of a detailed structural model for the active state of the twister ribozyme in solution that is consistent with these and other experiments. Simulations in a crystalline environment reported here are consistent with X-ray crystallographic data, and suggest that crystal packing contacts trap the RNA in an inactive conformation with U-1 in an extruded state that is incompatible with an in-line attack to the scissile phosphate. Simulations in solution, on the other hand, reveal this region to be dynamic and able to adopt a conformation where U-1 is stacked with G33. In this state, the nucleophile is in line with the scissile phosphate, and the N1 position of G33 and N3 position of A1 are poised to act as a general base and acid, respectively, as supported by mutational experiments. Free energy calculations further predict the electrostatic environment causes a shift of the microscopic pKa at the N3 position of A1 toward neutrality by approximately 5 pKa units. These results offer a unified interpretation of a broad range of currently available experimental data that points to a novel mode of general acid catalysis through the N3 position of an adenine nucleobase, thus expanding the repertoire of known mechanistic strategies employed by

  18. Catalytic strategies of self-cleaving ribozymes.

    Science.gov (United States)

    Cochrane, Jesse C; Strobel, Scott A

    2008-08-01

    [Structure: see text]. Five naturally occurring nucleolytic ribozymes have been identified: the hammerhead, hairpin, glmS, hepatitis delta virus (HDV), and Varkud satellite (VS) ribozymes. All of these RNA enzymes catalyze self-scission of the RNA backbone using a chemical mechanism equivalent to that of RNase A. RNase A uses four basic strategies to promote this reaction: geometric constraints, activation of the nucleophile, transition-state stabilization, and leaving group protonation. In this Account, we discuss the current thinking on how nucleolytic ribozymes harness RNase A's four sources of catalytic power. The geometry of the phosphodiester cleavage reaction constrains the nucleotides flanking the scissile phosphate so that they are unstacked from a canonical A-form helix and thus require alternative stabilization. Crystal structures and mutational analysis reveal that cross-strand base pairing, along with unconventional stacking and tertiary hydrogen-bonding interactions, work to stabilize the splayed conformation in nucleolytic ribozymes. Deprotonation of the 2'-OH nucleophile greatly increases its nucleophilicity in the strand scission reaction. Crystal structures of the hammerhead, hairpin, and glmS ribozymes reveal the N1 of a G residue within hydrogen-bonding distance of the 2'-OH. In each case, this residue has also been shown to be important for catalysis. In the HDV ribozyme, a hydrated magnesium has been implicated as the general base. Catalysis by the VS ribozyme requires both an A and a G, but the precise role of either has not been elucidated. Enzymes can lower the energy of a chemical reaction by binding more tightly to the transition state than to the ground states. Comparison of the hairpin ground- and transition-state mimic structures reveal greater hydrogen bonding to the transition-state mimic structure, suggesting transition-state stabilization as a possible catalytic strategy. However, the hydrogen-bonding pattern in the glmS ribozyme

  19. K(+)-Responsive off-to-on switching of hammerhead ribozyme through dual G-quadruplex formation requiring no heating and cooling treatment.

    Science.gov (United States)

    Yamaoki, Yudai; Nagata, Takashi; Mashima, Tsukasa; Katahira, Masato

    Functional RNAs that switch their activities in response to K(+) may sense the intracellular (100 mM) and extracellular (5 mM) K(+) concentrations and regulate their functions accordingly. Previously, we developed a quadruplex hammerhead ribozyme (QHR) whose conformational change, from a duplex to a G-quadruplex, triggered by K(+) results in expression of the activity. However, this QHR required heating and cooling treatment (annealing) to induce the K(+)-responsive conformational change and activity. Here, we developed a new quadruplex hammerhead ribozyme (QHR) system that does not require annealing to induce the K(+)-responsive conformational change and activity. This system is composed of QHR and a G-quadruplex-forming complementary DNA strand (QCS). In the absence of K(+), QCS formed a duplex with QHR, which suppressed the residual activity. Upon elevation of the K(+) concentration, QCS dissociated from QHR was trapped in a G-quadruplex, and then QHR could form a G-quadruplex and exerted the activity. The 11.6-fold higher activity was induced by K(+) with an EC50 value of 23 mM, but not by Na(+), which is desirable when the activity switching between the intra-/extracellular environment is aimed at. This is the first report of the activation of functional RNA through a 'dual G-quadruplex formation system'. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water

    Science.gov (United States)

    Sarma, R. H.; Sarma, M. H.; Rein, R.; Shibata, M.; Setlik, R. S.; Ornstein, R. L.; Kazim, A. L.; Cairo, A.; Tomasi, T. B.

    1995-01-01

    Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.

  1. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Yamaguchi, Shota; Oyama, Yui; Deshimaru, Masanobu

    2014-01-01

    Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state–dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites. PMID:24448449

  2. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing.

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Yamaguchi, Shota; Oyama, Yui; Deshimaru, Masanobu

    2014-03-01

    Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state-dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites.

  3. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis

    Czech Academy of Sciences Publication Activity Database

    Mlýnský, V.; Kührová, P.; Jurečka, P.; Šponer, Jiří; Otyepka, M.; Banáš, Pavel

    2017-01-01

    Roč. 121, č. 48 (2017), s. 10828-10840 ISSN 1520-6106 R&D Projects: GA ČR GAP208/12/1878 Institutional support: RVO:68081707 Keywords : delta-virus ribozyme * self-cleaving ribozymes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.177, year: 2016

  4. Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis.

    Science.gov (United States)

    Pereira, Miguel J B; Harris, Dinari A; Rueda, David; Walter, Nils G

    2002-01-22

    The hepatitis delta virus (HDV), an infectious human pathogen and satellite of hepatitis B virus, leads to intensified disease symptoms, including progression to liver cirrhosis. Both the circular RNA genome of HDV and its complementary antigenome contain the same cis-cleaving catalytic RNA motif that plays a crucial role in virus replication. Previously, the high-resolution crystal structure of the product form of a cis-acting genomic HDV ribozyme has been determined, while a trans-acting version of the ribozyme was used to dissect the cleavage reaction pathway. Using fluorescence resonance energy transfer (FRET) on a synthetic trans-cleaving form of the ribozyme, we are able to directly observe substrate binding (at a rate constant k(on) of 7.8 x 10(6) M(-1) min(-1) at pH 7.5, 11 mM MgCl(2), and 25 degrees C) and dissociation (at 0.34 min(-1)). Steady-state and time-resolved FRET experiments in solution and in nondenaturing gels reveal that the substrate (precursor) complex is slightly more compact (by approximately 3 A) than the free ribozyme, yet becomes significantly extended (by approximately 15 A) upon cleavage and product complex formation. We also find that trans cleavage is characterized by a high transition-state entropy (-26 eu). We propose that the significant global conformational change that we observe between the precursor and product structures occurs on the reaction trajectory into a constrained product complex-like transition state. Our observations may present the structural basis of the recently described utilization of intrinsic substrate binding energy to the overall catalytic rate enhancement by the trans-acting HDV ribozyme.

  5. Structural investigation of a high-affinity MnII binding site in the hammerhead ribozyme by EPR spectroscopy and DFT calculations. Effects of neomycin B on metal-ion binding.

    Science.gov (United States)

    Schiemann, Olav; Fritscher, Jörg; Kisseleva, Natalja; Sigurdsson, Snorri Th; Prisner, Thomas F

    2003-10-06

    Electron paramagnetic resonance spectroscopy and density functional theory methods were used to study the structure of a single, high-affinity Mn(II) binding site in the hammerhead ribozyme. This binding site exhibits a dissociation constant Ke of 4.4 microM in buffer solutions containing 1 M NaCl, as shown by titrations monitored by continuous wave (cw) EPR. A combination of electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) experiments revealed that the paramagnetic manganese(II) ion in this binding site is coupled to a single nitrogen atom with a quadrupole coupling constant kappa of 0.7 MHz, an asymmetry parameter eta of 0.4, and an isotropic hyperfine coupling constant of Aiso(14N)=2.3 MHz. All three EPR parameters are sensitive to the arrangement of the Mn(II) ligand sphere and can therefore be used to determine the structure of the binding site. A possible location for this binding site may be at the G10.1, A9 site found to be occupied by Mn(II) in crystals (MacKay et al., Nature 1994, 372, 68 and Scott et al., Science 1996, 274, 2065). To determine whether the structure of the binding site is the same in frozen solution, we performed DFT calculations for the EPR parameters, based on the structure of the Mn(II) site in the crystal. Computations with the BHPW91 density function in combination with a 9s7p4d basis set for the manganese(II) center and the Iglo-II basis set for all other atoms yielded values of kappa(14N)=+0.80 MHz, eta=0.324, and Aiso(14N)=+2.7 MHz, in excellent agreement with the experimentally obtained EPR parameters, which suggests that the binding site found in the crystal and in frozen solution are the same. In addition, we demonstrated by EPR that Mn(II) is released from this site upon binding of the aminoglycoside antibiotic neomycin B (Kd=1.2 microM) to the hammerhead ribozyme. Neomycin B has previously been shown to inhibit the catalytic activity of this ribozyme (Uhlenbeck et al., Biochemistry

  6. Structural principles of RNA catalysis in a 2'-5' lariat-forming ribozyme.

    Science.gov (United States)

    Carlomagno, Teresa; Amata, Irene; Codutti, Luca; Falb, Melanie; Fohrer, Jörg; Masiewicz, Pawel; Simon, Bernd

    2013-03-20

    RNA-catalyzed lariat formation is present in both eukaryotes and prokaryotes. To date we lack structural insights into the catalytic mechanism of lariat-forming ribozymes. Here, we study an artificial 2'-5' AG1 lariat-forming ribozyme that shares the sequence specificity of lariat formation with the pre-mRNA splicing reaction. Using NMR, we solve the structure of the inactive state of the ribozyme in the absence of magnesium. The reaction center 5'-guanosine appears to be part of a helix with an exceptionally widened major groove, while the lariat-forming A48 is looped out at the apex of a pseudoknot. The model of the active state built by mutational analysis, molecular modeling, and small-angle X-ray scattering suggests that A48 is recognized by a conserved adenosine, juxtaposed to the 5'-guanosine in one base-pair step distance, while the G1-N7 coordinates a magnesium ion essential for the activation of the nucleophile. Our findings offer implications for lariat formation in RNA enzymes including the mechanism of the recognition of the branch-site adenosine.

  7. Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo?

    Directory of Open Access Journals (Sweden)

    Eliza Wyszko

    Full Text Available With the discovery of small non-coding RNA (ncRNA molecules as regulators for cellular processes, it became intriguing to develop technologies by which these regulators can be applied in molecular biology and molecular medicine. The application of ncRNAs has significantly increased our knowledge about the regulation and functions of a number of proteins in the cell. It is surprising that similar successes in applying these small ncRNAs in biotechnology and molecular medicine have so far been very limited. The reasons for these observations may lie in the high complexity in which these RNA regulators function in the cells and problems with their delivery, stability and specificity. Recently, we have described mirror-image hammerhead ribozymes and DNAzymes (Spiegelzymes® which can sequence-specifically hydrolyse mirror-image nucleic acids, such as our mirror-image aptamers (Spiegelmers discovered earlier. In this paper, we show for the first time that Spiegelzymes are capable of recognising complementary enantiomeric substrates (D-nucleic acids, and that they efficiently hydrolyse them at submillimolar magnesium concentrations and at physiologically relevant conditions. The Spiegelzymes are very stable in human sera, and do not require any protein factors for their function. They have the additional advantages of being non-toxic and non-immunogenic. The Spiegelzymes can be used for RNA silencing and also as therapeutic and diagnostic tools in medicine. We performed extensive three-dimensional molecular modelling experiments with mirror-image hammerhead ribozymes and DNAzymes interacting with D-RNA targets. We propose a model in which L/D-double helix structures can be formed by natural Watson-Crick base pairs, but where the nucleosides of one of the two strands will occur in an anticlinal conformation. Interestingly enough, the duplexes (L-RNA/D-RNA and L-DNA/D-RNA in these models can show either right- or left-handedness. This is a very new

  8. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

    Czech Academy of Sciences Publication Activity Database

    Banáš, Pavel; Rulíšek, Lubomír; Hánošová, V.; Svozil, Daniel; Walter, N.G.; Šponer, Jiří; Otyepka, Michal

    2008-01-01

    Roč. 112, č. 35 (2008), s. 11177-11187 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA MŠk(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA AV ČR 1QS500040581 Grant - others:NIH(US) GM62357 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : HDV ribozyme * catalysis * QM/MM calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.189, year: 2008

  9. Catalysis of splicing-related reactions between dinucleotides by a ribozyme.

    Science.gov (United States)

    Kay, P S; Inoue, T

    Certain intervening sequence (IVS) RNAs catalyse their own excision from a primary transcript to yield mature RNA in a reaction termed self-splicing. These Group I IVS RNAs contain several conserved sequences and possess a common secondary structure. The Tetrahymena precursor ribosomal RNA possesses an IVS of this group that is known to self-splice in vitro. The nature of this IVS is of great interest to both biology and chemistry, because understanding its catalytic activity should shed new light on the function of RNA in biological systems and the evolution of RNA which might be relevant to the early stages of life on Earth. We have analysed the minimum requirement for this reaction as one approach to understanding the mechanism of this RNA catalysis. We now show that a fragment of the IVS RNA of Tetrahymena can mediate a simple transesterification reaction between the substrate GpN (where N is A, C, G or U) and the nucleophile CpU. This newly discovered reaction and its reverse reaction represent the fundamental catalytic activity of the self-splicing Group I IVSs.

  10. Thirty-five years of research into ribozymes and nucleic acid catalysis: where do we stand today?

    Science.gov (United States)

    Müller, Sabine; Appel, Bettina; Balke, Darko; Hieronymus, Robert; Nübel, Claudia

    2016-01-01

    Since the discovery of the first catalytic RNA in 1981, the field of ribozyme research has developed from the discovery of catalytic RNA motifs in nature and the elucidation of their structures and catalytic mechanisms, into a field of engineering and design towards application in diagnostics, molecular biology and medicine. Owing to the development of powerful protocols for selection of nucleic acid catalysts with a desired functionality from random libraries, the spectrum of nucleic acid supported reactions has greatly enlarged, and importantly, ribozymes have been accompanied by DNAzymes. Current areas of research are the engineering of allosteric ribozymes for artificial regulation of gene expression, the design of ribozymes and DNAzymes for medicinal and environmental diagnostics, and the demonstration of RNA world relevant ribozyme activities. In addition, new catalytic motifs or novel genomic locations of known motifs continue to be discovered in all branches of life by the help of high-throughput bioinformatic approaches. Understanding the biological role of the catalytic RNA motifs widely distributed in diverse genetic contexts belongs to the big challenges of future RNA research.

  11. A 1.9 Å Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jui-Hui; Yajima, Rieko; Chadalavada, Durga M.; Chase, Elaine; Bevilacqua, Philip C.; Golden, Barbara L. (Purdue); (Penn)

    2010-11-01

    The hepatitis delta virus (HDV) ribozyme and HDV-like ribozymes are self-cleaving RNAs found throughout all kingdoms of life. These RNAs fold into a double-nested pseudoknot structure and cleave RNA, yielding 2{prime},3{prime}-cyclic phosphate and 5{prime}-hydroxyl termini. The active site nucleotide C75 has a pK{sub a} shifted >2 pH units toward neutrality and has been implicated as a general acid/base in the cleavage reaction. An active site Mg{sup 2+} ion that helps activate the 2{prime}-hydroxyl for nucleophilic attack has been characterized biochemically; however, this ion has not been visualized in any previous structures. To create a snapshot of the ribozyme in a state poised for catalysis, we have crystallized and determined the structure of the HDV ribozyme bound to an inhibitor RNA containing a deoxynucleotide at the cleavage site. This structure includes the wild-type C75 nucleotide and Mg{sup 2+} ions, both of which are required for maximal ribozyme activity. This structure suggests that the position of C75 does not change during the cleavage reaction. A partially hydrated Mg{sup 2+} ion is also found within the active site where it interacts with a newly resolved G {center_dot} U reverse wobble. Although the inhibitor exhibits crystallographic disorder, we modeled the ribozyme-substrate complex using the conformation of the inhibitor strand observed in the hammerhead ribozyme. This model suggests that the pro-RP oxygen of the scissile phosphate and the 2{prime}-hydroxyl nucleophile are inner-sphere ligands to the active site Mg{sup 2+} ion. Thus, the HDV ribozyme may use a combination of metal ion Lewis acid and nucleobase general acid strategies to effect RNA cleavage.

  12. Technology evaluation: HIV ribozyme gene therapy, Gene Shears Pty Ltd.

    Science.gov (United States)

    de Feyter, R; Li, P

    2000-06-01

    Ribozymes (catalytic RNAs) can be made to specifically cleave target RNAs that are involved in disease conditions and therefore have potential as therapeutic agents. Gene Shears Pty Ltd is developing hammerhead ribozyme technology for therapy against HIV infection, targeting either the tat gene or the RNA packaging sequence (Psi) of HIV. These ribozymes have been expressed from constructs that were introduced into hematopoietic cells in culture, thereby protecting the cells against viral infection. Two phase I clinical trials are underway to test the safety and feasibility of the approach with the anti-tat ribozyme in human subjects.

  13. Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

    Science.gov (United States)

    Ojha, R. P.; Dhingra, M. M.; Sarma, M. H.; Myer, Y. P.; Setlik, R. F.; Shibata, M.; Kazim, A. L.; Ornstein, R. L.; Rein, R.; Turner, C. J.; hide

    1997-01-01

    The structure of an anti-HIV-1 ribozyme-DNA abortive substrate complex was investigated by 750 MHz NMR and computer modeling experiments. The ribozyme was a chimeric molecule with 30 residues-18 DNA nucleotides, and 12 RNA residues in the conserved core. The DNA substrate analog had 17 residues. The chimeric ribozyme and the DNA substrate formed a shortened ribozyme-abortive substrate complex of 47 nucleotides with two DNA stems (stems I and III) and a loop consisting of the conserved core residues. Circular dichroism spectra showed that the DNA stems assume A-family conformation at the NMR concentration and a temperature of 15 degrees C, contrary to the conventional wisdom that DNA duplexes in aqueous solution populate entirely in the B-form. It is proposed that the A-family RNA residues at the core expand the A-family initiated at the core into the DNA stems because of the large free energy requirement for the formation of A/B junctions. Assignments of the base H8/H6 protons and H1' of the 47 residues were made by a NOESY walk. In addition to the methyl groups of all T's, the imino resonances of stems I and III and AH2's were assigned from appropriate NOESY walks. The extracted NMR data along with available crystallographic data, were used to derive a structural model of the complex. Stems I and III of the final model displayed a remarkable similarity to the A form of DNA; in stem III, a GC base pair was found to be moving into the floor of the minor groove defined by flanking AT pairs; data suggest the formation of a buckled rhombic structure with the adjacent pair; in addition, the base pair at the interface of stem III and the loop region displayed deformed geometry. The loop with the catalytic core, and the immediate region of the stems displayed conformational multiplicity within the NMR time scale. A catalytic mechanism for ribozyme action based on the derived structure, and consistent with biochemical data in the literature, is proposed. The complex

  14. 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

    2007-01-01

    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.

  15. Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing

    OpenAIRE

    Fong, Nova; Ohman, Marie; Bentley, David L.

    2009-01-01

    SUMMARY We investigated whether a continuous transcript is necessary for co-transcriptional pre-mRNA processing. Cutting an intron with the fast-cleaving hepatitis ? ribozyme, but not the slower hammerhead, inhibited splicing. Exon tethering to RNA pol II therefore cannot rescue splicing of a transcript severed by a ribozyme that cleaves rapidly relative to splicing. Ribozyme cutting also released cap-binding complex (CBC) from the gene, suggesting that exon 1 is not tethered. Unexpectedly, c...

  16. Thirty-five years of research into ribozymes and nucleic acid catalysis: where do we stand today? [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Sabine Müller

    2016-06-01

    Full Text Available Since the discovery of the first catalytic RNA in 1981, the field of ribozyme research has developed from the discovery of catalytic RNA motifs in nature and the elucidation of their structures and catalytic mechanisms, into a field of engineering and design towards application in diagnostics, molecular biology and medicine. Owing to the development of powerful protocols for selection of nucleic acid catalysts with a desired functionality from random libraries, the spectrum of nucleic acid supported reactions has greatly enlarged, and importantly, ribozymes have been accompanied by DNAzymes. Current areas of research are the engineering of allosteric ribozymes for artificial regulation of gene expression, the design of ribozymes and DNAzymes for medicinal and environmental diagnostics, and the demonstration of RNA world relevant ribozyme activities. In addition, new catalytic motifs or novel genomic locations of known motifs continue to be discovered in all branches of life by the help of high-throughput bioinformatic approaches. Understanding the biological role of the catalytic RNA motifs widely distributed in diverse genetic contexts belongs to the big challenges of future RNA research.

  17. Hairpin Ribozyme Genes Curtail Alcohol Drinking: from Rational Design to in vivo Effects in the Rat

    Directory of Open Access Journals (Sweden)

    Amalia Sapag

    2016-01-01

    Full Text Available Ribozyme genes were designed to reduce voluntary alcohol drinking in a rat model of alcohol dependence. Acetaldehyde generated from alcohol in the liver is metabolized by the mitochondrial aldehyde dehydrogenase (ALDH2 such that diminishing ALDH2 activity leads to the aversive effects of blood acetaldehyde upon alcohol intake. A stepwise approach was followed to design genes encoding ribozymes targeted to the rat ALDH2 mRNA. In vitro studies of accessibility to oligonucleotides identified suitable target sites in the mRNA, one of which fulfilled hammerhead and hairpin ribozyme requirements (CGGUC. Ribozyme genes delivered in plasmid constructs were tested in rat cells in culture. While the hairpin ribozyme reduced ALDH2 activity 56% by cleavage and blockade (P < 0.0001, the hammerhead ribozyme elicited minor effects by blockade. The hairpin ribozyme was tested in vivo by adenoviral gene delivery to UChB alcohol drinker rats. Ethanol intake was curtailed 47% for 34 days (P < 0.0001, while blood acetaldehyde more than doubled upon ethanol administration and ALDH2 activity dropped 25% in liver homogenates, not affecting other ALDH isoforms. Thus, hairpin ribozymes targeted to 16 nt in the ALDH2 mRNA provide durable and specific effects in vivo, representing an improvement on previous work and encouraging development of gene therapy for alcoholism.

  18. Studying Hammerheads in Hawaii

    Science.gov (United States)

    Handler, Alex; Duncan, Kanesa

    2006-01-01

    In this article, the author discusses the High School Scalloped Hammerhead Shark Tagging Program in Hawaii which is an example of a successful partnership research collaboration. High school students and teachers worked with biologists from the University of Hawaii-Manoa (UHM) to conduct research on the life history of scalloped hammerhead sharks…

  19. Efficient transfer of synthetic ribozymes into cells using hemagglutinating virus of Japan (HVJ)-cationic liposomes. Application for ribozymes that target human t-cell leukemia virus type I tax/rex mRNA.

    Science.gov (United States)

    Kitajima, I; Hanyu, N; Soejima, Y; Hirano, R; Arahira, S; Yamaoka, S; Yamada, R; Maruyama, I; Kaneda, Y

    1997-10-24

    We investigated the usefulness of ribozymes in inhibiting the expression of human T-cell leukemia virus type I (HTLV-I) gene. Two hammerhead ribozymes that were against HTLV-I rex (RR) and tax (TR) mRNA were synthesized. Both ribozymes were sequence-specific in the in vitro cleavage analysis of run-off transcripts from tax/rex cDNA. Intracellular activities of the ribozymes were studied in HTLV-I tax cDNA-transfected rat embryonic fibroblasts (Rat/Tax cells), which expressed the Tax but not Rex. Ribozymes were delivered into cells using anionic or cationic liposomes fused with hemagglutinating virus of Japan (HVJ). Cellular uptake of ribozymes complexed with HVJ-cationic liposomes was 15-20 times higher cellular uptake than naked ribozymes, and 4-5 times higher than that of ribozymes complexed with HVJ-anionic liposomes. HVJ-cationic liposomes promoted accumulation of ribozymes in cytoplasm and accelerated transport to the nucleus. Tax protein levels were decreased about 95% and were five times lower when the same amount of TR was introduced into the cells using HVJ-cationic, rather than HVJ-anionic liposomes. Inactive ribozyme and tax antisense oligodeoxynucleotides reduced Tax expression by about 20%, whereas RR and tax sense oligodeoxynucleotides had no effect. These results suggest that the ribozymes' effect against tax mRNA was sequence-specific, and HVJ-cationic liposomes can be useful for intracellular introduction of ribozymes.

  20. Group I intron ribozymes

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2012-01-01

    Group I intron ribozymes constitute one of the main classes of ribozymes and have been a particularly important model in the discovery of key concepts in RNA biology as well as in the development of new methods. Compared to other ribozyme classes, group I intron ribozymes display considerable......, the intronic products of these pathways have the potential to integrate into targets and to form various types of circular RNA molecules. Thus, group I intron ribozymes and associated elements found within group I introns is a rich source of biological phenomena. This chapter provides a strategy and protocols...

  1. RNA folding and catalysis mediated by iron (II.

    Directory of Open Access Journals (Sweden)

    Shreyas S Athavale

    Full Text Available Mg²⁺ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg²⁺ in RNA folding and function can indeed be served by Fe²⁺. The results of quantum mechanical calculations show that the geometry of coordination of Fe²⁺ by RNA phosphates is similar to that of Mg²⁺. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4-P6 domain RNA is conserved between complexes with Fe²⁺ or Mg²⁺. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg²⁺, and the hammerhead ribozyme are enhanced in the presence of Fe²⁺ compared to Mg²⁺. All chemical footprinting and ribozyme assays in the presence of Fe²⁺ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe²⁺. The combined biochemical and paleogeological data are consistent with a role for Fe²⁺ in an RNA World. RNA and Fe²⁺ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg²⁺ alone.

  2. Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes.

    Science.gov (United States)

    Lee, Ki-Young; Lee, Bong-Jin

    2017-04-24

    Fourteen well-defined ribozyme classes have been identified to date, among which nine are site-specific self-cleaving ribozymes. Very recently, small self-cleaving ribozymes have attracted renewed interest in their structure, biochemistry, and biological function since the discovery, during the last three years, of four novel ribozymes, termed twister, twister sister, pistol, and hatchet. In this review, we mainly address the structure, biochemistry, and catalytic mechanism of the novel ribozymes. They are characterized by distinct active site architectures and divergent, but similar, biochemical properties. The cleavage activities of the ribozymes are highly dependent upon divalent cations, pH, and base-specific mutations, which can cause changes in the nucleotide arrangement and/or electrostatic potential around the cleavage site. It is most likely that a guanine and adenine in close proximity of the cleavage site are involved in general acid-base catalysis. In addition, metal ions appear to play a structural rather than catalytic role although some of their crystal structures have shown a direct metal ion coordination to a non-bridging phosphate oxygen at the cleavage site. Collectively, the structural and biochemical data of the four newest ribozymes could contribute to advance our mechanistic understanding of how self-cleaving ribozymes accomplish their efficient site-specific RNA cleavages.

  3. Ionic interactions and the global conformations of the hammerhead ribozyme

    DEFF Research Database (Denmark)

    Bassi, G S; Møllegaard, N E; Murchie, A I

    1995-01-01

    by the remaining helix I. In the probable active conformation, a small angle is subtended between helices I and II. Using uranyl photocleavage, an ion binding site has been detected in the long single-stranded region. The folded conformation could generate a preactivation of the scissile bond to permit in...

  4. A Faster Triphosphorylation Ribozyme.

    Directory of Open Access Journals (Sweden)

    Gregory F Dolan

    Full Text Available In support of the RNA world hypothesis, previous studies identified trimetaphosphate (Tmp as a plausible energy source for RNA world organisms. In one of these studies, catalytic RNAs (ribozymes that catalyze the triphosphorylation of RNA 5'-hydroxyl groups using Tmp were obtained by in vitro selection. One ribozyme (TPR1 was analyzed in more detail. TPR1 catalyzes the triphosphorylation reaction to a rate of 0.013 min-1 under selection conditions (50 mM Tmp, 100 mM MgCl2, 22°C. To identify a triphosphorylation ribozyme that catalyzes faster triphosphorylation, and possibly learn about its secondary structure TPR1 was subjected to a doped selection. The resulting ribozyme, TPR1e, contains seven mutations relative to TPR1, displays a previously unidentified duplex that constrains the ribozyme's structure, and reacts at a 24-fold faster rate than the parent ribozyme. Under optimal conditions (150 mM Tmp, 650 mM MgCl2, 40°C, the triphosphorylation rate of TRP1e reaches 6.8 min-1.

  5. Eggplant Latent Viroid, the Candidate Type Species for a New Genus within the Family Avsunviroidae (Hammerhead Viroids)

    Science.gov (United States)

    Fadda, Z.; Daròs, J. A.; Fagoaga, C.; Flores, R.; Duran-Vila, N.

    2003-01-01

    Viroids, small circular RNAs that replicate independently and in most cases incite diseases in plants, are classified into the families Pospiviroidae, composed of species with a central conserved region (CCR) and without hammerhead ribozymes, and Avsunviroidae, composed of three members lacking CCR but able to self-cleave in both polarity strands through hammerhead ribozymes. Here we report the biological and molecular properties of Eggplant latent viroid (ELVd). Purified circular ELVd induces symptomless infections when inoculated into eggplant seedlings. ELVd can be transmitted horizontally and through seed. Sequencing 10 complete cDNA clones showed that ELVd is a circular RNA of 332 to 335 nucleotides with high variability. This RNA can adopt a quasi-rod-like secondary structure of minimal free energy and alternative foldings that permit formation of stable hammerhead structures in plus and minus strands. The ribozymes are active in vitro and, most likely, in vivo. Considering the ELVd properties to be intermediate between those of the two genera of family Avsunviroidae, we propose ELVd as the type species of a third genus with the name Elaviroid. PMID:12743309

  6. Distribution and movement of scalloped hammerhead Sphryna ...

    African Journals Online (AJOL)

    Knowledge of population distribution and movement is crucial for the conservation and management of shark species occurring in coastal waters. From 1984 to 2009, 641 scalloped hammerheads Sphyrna lewini, 1 342 smooth hammerheads Sphyrna zygaena and 1 352 unspecified hammerheads Sphyrna spp. were ...

  7. Metals induce transient folding and activation of the twister ribozyme.

    Science.gov (United States)

    Panja, Subrata; Hua, Boyang; Zegarra, Diego; Ha, Taekjip; Woodson, Sarah A

    2017-10-01

    Twister is a small ribozyme present in almost all kingdoms of life that rapidly self-cleaves in variety of divalent metal ions. We used activity assays, bulk FRET and single-molecule FRET (smFRET) to understand how different metal ions promote folding and self-cleavage of the Oryza sativa twister ribozyme. Although most ribozymes require additional Mg2+ for catalysis, twister inverts this expectation, requiring 20-30 times less Mg2+ to self-cleave than to fold. Transition metals such as Co2+, Ni2+ and Zn2+ activate twister more efficiently than Mg2+ ions. Although twister is fully active in ≤ 0.5 mM MgCl2, smFRET experiments showed that the ribozyme visits the folded state infrequently under these conditions. Comparison of folding and self-cleavage rates indicates that most folding events lead to catalysis, which correlates with metal bond strength. Thus, the robust activity of twister reports on transient metal ion binding under physiological conditions.

  8. Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

    Science.gov (United States)

    Manchester, John I.; Shibata, Masayuki; Setlik, Robert F.; Ornstein, Rick L.; Rein, Robert

    1993-01-01

    A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

  9. Active site labeling of G8 in the hairpin ribozyme: implications for structure and mechanism.

    Science.gov (United States)

    Thomas, Jason M; Perrin, David M

    2006-12-27

    There is mounting evidence that suggests that general acid/base catalysis is operative in the hairpin ribozyme, with analogy to the protein enzyme RNaseA. Nevertheless, the extent of general base catalysis as well as the identity of the specific chemical groups responsible remains the subject of some controversy. An affinity label has previously been used to alkylate histidine 12 (His12), the active general base in RNaseA. To date, no such experiment has been applied to a ribozyme. We have synthesized the analogous affinity label for the hairpin ribozyme with an electrophilic 2'-bromoacetamide group in lieu of the 2'-hydroxyl (2'OH) at the substrate cleavage site and show that guanosine 8 (G8) of the hairpin ribozyme is specifically alkylated, most likely at the N1 position. This evidence strongly implicates N1 of G8 in active site chemistry. By direct analogy to RNase A, these findings could be consistent with the hypothesis that deprotonated G8 residue functions as a general base in the hairpin ribozyme. Other mechanistic possibilities for N1 of G8 such as indirect general base catalysis mediated by a water molecule or transition state stabilization could also be consistent with our findings.

  10. Catalytic Activities of Ribozymes and DNAzymes in Water and Mixed Aqueous Media

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2017-11-01

    Full Text Available Catalytic nucleic acids are regarded as potential therapeutic agents and biosensors. The catalytic activities of nucleic acid enzymes are usually investigated in dilute aqueous solutions, although the physical properties of the reaction environment inside living cells and that in the area proximal to the surface of biosensors in which they operate are quite different from those of pure water. The effect of the molecular environment is also an important focus of research aimed at improving and expanding nucleic acid function by addition of organic solvents to aqueous solutions. In this study, the catalytic activities of RNA and DNA enzymes (hammerhead ribozyme, 17E DNAzyme, R3C ribozyme, and 9DB1 DNAzyme were investigated using 21 different mixed aqueous solutions comprising organic compounds. Kinetic measurements indicated that these enzymes can display enhanced catalytic activity in mixed solutions with respect to the solution containing no organic additives. Correlation analyses revealed that the turnover rate of the reaction catalyzed by hammerhead ribozyme increased in a medium with a lower dielectric constant than water, and the turnover rate of the reaction catalyzed by 17E DNAzyme increased in conditions that increased the strength of DNA interactions. On the other hand, R3C ribozyme and 9DB1 DNAzyme displayed no significant turnover activity, but their single-turnover rates increased in many mixed solutions. Our data provide insight into the activity of catalytic nucleic acids under various conditions that are applicable to the medical and technology fields, such as in living cells and in biosensors.

  11. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

    Czech Academy of Sciences Publication Activity Database

    Sripathi, K.N.; Banáš, P.; Réblová, K.; Šponer, Jiří; Otyepka, M.; Walter, Nils G.

    2015-01-01

    Roč. 17, č. 8 (2015), s. 5887-5900 ISSN 1463-9076 R&D Projects: GA ČR GAP208/12/1878 Institutional support: RVO:68081707 Keywords : HEPATITIS-DELTA-VIRUS * SELF-CLEAVING RIBOZYMES * ACID-BASE CATALYSIS Subject RIV: BO - Biophysics Impact factor: 4.449, year: 2015

  12. The Novel Chemical Mechanism of the Twister Ribozyme.

    Science.gov (United States)

    Wilson, Timothy J; Liu, Yijin; Domnick, Christof; Kath-Schorr, Stephanie; Lilley, David M J

    2016-05-18

    We describe the multifactorial origins of catalysis by the twister ribozyme. We provide evidence that the adenine immediately 3' to the scissile phosphate (A1) acts as a general acid. Substitution of ring nitrogen atoms indicates that very unusually the N3 of A1 is the proton donor to the oxyanion leaving group. A1 is accommodated in a specific binding pocket that raises its pKa toward neutrality, juxtaposes its N3 with the O5' to be protonated, and helps create the in-line trajectory required for nucleophilic attack. A1 performs general acid catalysis while G33 acts as a general base. A 100-fold stereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stabilization of the transition state by the ribozyme, and functional group substitution at G33 indicates that its exocyclic N2 interacts directly with the scissile phosphate. A model of the ribozyme active site is proposed that accommodates these catalytic strategies.

  13. Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments.

    Science.gov (United States)

    Veeraraghavan, Narayanan; Bevilacqua, Philip C; Hammes-Schiffer, Sharon

    2010-09-10

    The hepatitis delta virus ribozyme is a small, self-cleaving RNA with a compact tertiary structure and buried active site that is important in the life cycle of the virus. The ribozyme's function in nature is to cleave an internal phosphodiester bond and linearize concatemers during rolling circle replication. Crystal structures of the ribozyme have been solved in both pre-cleaved and post-cleaved (product) forms and reveal an intricate network of interactions that conspire to catalyze bond cleavage. In addition, extensive biochemical studies have been performed to work out a mechanism for bond cleavage in which C75 and a magnesium ion catalyze the reaction by general acid-base chemistry. One issue that has remained unclear in this ribozyme and in other ribozymes is the nature of long-distance communication between peripheral regions of the RNA and the buried active site. We performed molecular dynamics simulations on the hepatitis delta virus ribozyme in the product form and assessed communication between a distal structural portion of the ribozyme-the protonated C41 base triple-and the active site containing the critical C75. We varied the ionization state of C41 in both the wild type and a C41 double mutant variant and determined the impact on the active site. In all four cases, effects at the active site observed in the simulations agree with experimental studies on ribozyme activity. Overall, these studies indicate that small functional RNAs have the potential to communicate interactions over long distances and that wild-type RNAs may have evolved ways to prevent such interactions from interfering with catalysis. Copyright 2010 Elsevier Ltd. All rights reserved.

  14. Enhanced visual fields in hammerhead sharks.

    Science.gov (United States)

    McComb, D M; Tricas, T C; Kajiura, S M

    2009-12-01

    Several factors that influence the evolution of the unusual head morphology of hammerhead sharks (family Sphyrnidae) are proposed but few are empirically tested. In this study we tested the 'enhanced binocular field' hypothesis (that proposes enhanced frontal binocularity) by comparison of the visual fields of three hammerhead species: the bonnethead shark, Sphyrna tiburo, the scalloped hammerhead shark, Sphyrna lewini, and the winghead shark, Eusphyra blochii, with that of two carcharhinid species: the lemon shark, Negaprion brevirostris, and the blacknose shark, Carcharhinus acronotus. Additionally, eye rotation and head yaw were quantified to determine if species compensate for large blind areas anterior to the head. The winghead shark possessed the largest anterior binocular overlap (48 deg.) and was nearly four times larger than that of the lemon (10 deg.) and blacknose (11 deg.) sharks. The binocular overlap in the scalloped hammerhead sharks (34 deg.) was greater than the bonnethead sharks (13 deg.) and carcharhinid species; however, the bonnethead shark did not differ from the carcharhinids. These results indicate that binocular overlap has increased with lateral head expansion in hammerhead sharks. The hammerhead species did not demonstrate greater eye rotation in the anterior or posterior direction. However, both the scalloped hammerhead and bonnethead sharks exhibited greater head yaw during swimming (16.9 deg. and 15.6 deg., respectively) than the lemon (15.1 deg.) and blacknose (15.0 deg.) sharks, indicating a behavioral compensation for the anterior blind area. This study illustrates the larger binocular overlap in hammerhead species relative to their carcharhinid sister taxa and is consistent with the 'enhanced binocular field' hypothesis.

  15. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

    Science.gov (United States)

    Serganov, Alexander; Keiper, Sonja; Malinina, Lucy; Tereshko, Valentina; Skripkin, Eugene; Höbartner, Claudia; Polonskaia, Anna; Phan, Anh Tuân; Wombacher, Richard; Micura, Ronald; Dauter, Zbigniew; Jäschke, Andres; Patel, Dinshaw J

    2015-01-01

    The majority of structural efforts addressing RNA’s catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions. PMID:15723077

  16. Hooking mortality of scalloped hammerhead Sphyrna lewini and great hammerhead Sphyrna mokarran sharks caught on bottom longlines

    National Research Council Canada - National Science Library

    Gulak, SJB; de Ron Santiago, AJ; Carlson, JK

    2015-01-01

    The scalloped hammerhead Sphyrna lewini and the great hammerhead S. mokarran are typically caught as bycatch in a variety of fisheries and are listed as globally Endangered by the International Union for the Conservation of Nature...

  17. Hooking mortality of scalloped hammerhead Sphyrna lewini and ...

    African Journals Online (AJOL)

    When these data are considered for potential management strategies to reduce the mortality of hammerhead sharks, a limitation on gear soak time would probably improve hammerhead shark survivorship. However, it may ... hammerheads. Keywords: bycatch, hook timer, logistic regression, soak time, time on the hook ...

  18. Crystal structure of Pistol, a class of self-cleaving ribozyme

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Laura A.; Wang, Jimin; Steitz, Thomas A. (Yale)

    2017-01-17

    Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction. The guanine G40 is in close proximity to serve as the general base for activating the nucleophile by deprotonating the 2'-hydroxyl to initiate the reaction (phosphoester transfer). Furthermore, G40 can also establish hydrogen bonding interactions with the nonbridging oxygen of the scissile phosphate. The proximity of G32 to the O5' leaving group suggests that G32 may putatively serve as the general acid. The RNA structure of Pistol also contains A-minor interactions, which seem to be important to maintain its tertiary structure and compact fold. Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutionary mechanism used by ribozymes for catalysis.

  19. Supramolecular catalysis: Refocusing catalysis

    NARCIS (Netherlands)

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

    2008-01-01

    This chapter contains sections titled: * Introduction: A Brief Personal History * Secondary Phosphines or Phosphites as Supramolecular Ligands * Host-Guest Catalysis * Ionic Interactions as a Means to Form Heterobidentate Assembly Ligands * Ditopic Ligands for the Construction of Bidentate Phosphine

  20. Virgin birth in a hammerhead shark

    OpenAIRE

    Chapman, D. D.; Shivji, M.S.; Louis, E.; Sommer, J; Fletcher, Hugh; PRODOHL Paulo

    2007-01-01

    Parthenogenesis has been documented in all major jawed vertebrate lineages except mammals and cartilaginous fishes (class Chondrichthyes: sharks, batoids and chimeras). Reports of captive female sharks giving birth despite being held in the extended absence of males have generally been ascribed to prior matings coupled with long-term sperm storage by the females. Here, we provide the first genetic evidence for chondrichthyan parthenogenesis, involving a hammerhead shark (Sphyrna tiburo). This...

  1. Electronic Structure Rearrangements in Hybrid Ribozyme/Protein Catalysis

    Science.gov (United States)

    Kang, Jiyoung; Kino, Hiori; Field, Martin J.; Tateno, Masaru

    2017-04-01

    We analyzed the electronic structural changes that occur in the reaction cycle of a biological catalyst composed of RNA and protein, and elucidated the dynamical rearrangements of the electronic structure that was obtained from our previous study in which ab initio quantum mechanics/molecular mechanics molecular dynamics simulations were performed. Notable results that we obtained include the generation of a reactive HOMO that is responsible for bond formation in the initial stages of the reaction, and the appearance of a reactive LUMO that is involved in the bond rupture that leads to products. We denote these changes as dynamical induction of the reactive HOMO (DIRH) and LUMO (DIRL), respectively. Interestingly, we also find that the induction of the reactive HOMO is enhanced by the formation of a low-barrier hydrogen bond (LBHB), which, to the best of our knowledge, represents a novel role for LBHBs in enzymatic systems.

  2. Mechanistic Debris Generated by Twister Ribozymes.

    Science.gov (United States)

    Breaker, Ronald R

    2017-04-21

    Twister RNAs represent a recently discovered class of natural ribozymes that promote rapid cleaving of RNA backbones. Although an abundance of theoretical, biochemical, and structural data exist for several members of the twister class, disagreements about the architecture and mechanism of its active site have emerged. Historically, such storms regarding mechanistic details typically occur soon after each new self-cleaving ribozyme class is reported, but paths forward exist to quickly reach calmer conditions.

  3. Heterogeneous Catalysis.

    Science.gov (United States)

    Vannice, M. A.

    1979-01-01

    Described is a graduate course in catalysis offered at Penn State University. A detailed course outline with 30 lecture topics is presented. A list of 42 references on catalysis used in place of a textbook is provided. (BT)

  4. Virgin birth in a hammerhead shark.

    Science.gov (United States)

    Chapman, Demian D; Shivji, Mahmood S; Louis, Ed; Sommer, Julie; Fletcher, Hugh; Prodöhl, Paulo A

    2007-08-22

    Parthenogenesis has been documented in all major jawed vertebrate lineages except mammals and cartilaginous fishes (class Chondrichthyes: sharks, batoids and chimeras). Reports of captive female sharks giving birth despite being held in the extended absence of males have generally been ascribed to prior matings coupled with long-term sperm storage by the females. Here, we provide the first genetic evidence for chondrichthyan parthenogenesis, involving a hammerhead shark (Sphyrna tiburo). This finding also broadens the known occurrence of a specific type of asexual development (automictic parthenogenesis) among vertebrates, extending recently raised concerns about the potential negative effect of this type of facultative parthenogenesis on the genetic diversity of threatened vertebrate species.

  5. Unwinding the twister ribozyme: from structure to mechanism.

    Science.gov (United States)

    Gebetsberger, Jennifer; Micura, Ronald

    2017-05-01

    The twister ribozyme motif has been identified by bioinformatic means very recently. Currently, four crystal structures with ordered active sites together with a series of chemical and biochemical data provide insights into how this RNA accomplishes its efficient self-cleavage. Of particular interest for a mechanistic proposal are structural distinctions observed in the active sites that concern the conformation of the U-A cleavage site dinucleotide (in-line alignment of the attacking 2'-O nucleophile to the to-be-cleaved PO5' bond versus suboptimal alignments) as well as the presence/absence of Mg2+ ions at the scissile phosphate. All structures support the notion that an active site guanine and the conserved adenine at the cleavage site are important contributors to cleavage chemistry, likely being involved in general acid base catalysis. Evidence for innersphere coordination of a Mg2+ ion to the pro-S nonbridging oxygen of the scissile phosphate stems from two of the four crystal structures. Together with the finding of thio/rescue effects for phosphorothioate substrates, this suggests the participation of divalent ions in the overall catalytic strategy employed by twister ribozymes. In this context, it is notable that twister retains wild-type activity when the phylogenetically conserved stem P1 is deleted, able to cleave a single nucleotide only. WIREs RNA 2017, 8:e1402. doi: 10.1002/wrna.1402 For further resources related to this article, please visit the WIREs website. © 2016 The Authors. WIREs RNA published by Wiley Periodicals, Inc.

  6. Diet of scalloped hammerhead shark in eastern Gulf of Mexico

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Juvenile scalloped hammerhead sharks, Sphyrna lewini, were collected in northwest Florida to examine foraging ecology, bioenergetics, and trophic level (30-60 cm FL...

  7. Chemical fidelity of an RNA polymerase ribozyme

    DEFF Research Database (Denmark)

    Attwater, J.; Tagami, S.; Kimoto, M.

    2013-01-01

    The emergence of catalytically active RNA enzymes (ribozymes) is widely believed to have been an important transition in the origin of life. In the context of a likely heterogeneous chemical environment, substrate specificity and selectivity of these primordial enzymes would have been critical...... for function. Here we have explored the chemical fidelity, i.e. substrate selectivity and specificity for both single and multiple catalytic steps of the Z RNA polymerase ribozyme-a modern day analogue of the primordial RNA replicase. Using a wide range of nucleotide analogues and ionic conditions, we observe...

  8. Application of computational technologies to ribozyme biotechnology products

    Science.gov (United States)

    Christoffersen, Ralph E.; McSwiggen, James; Konings, Danielle

    1994-07-01

    Ribozymes are RNA molecules that act enzymatically to cleave other RNA molecules. The cleavage reaction requires the binding of ribozyme to specific sites on the target RNA through (mostly) Watson-Crick base-pairing interactions. Association of ribozyme with target completes a three-dimensional ribozyme/target complex which results in cleavage of the target RNA. We are employing both computational and experimental approaches to identify sites on target RNA molecules that are open to ribozyme attack and to determine which ribozymes are most active against those sites. Two types of computational technologies are available for aiding in the identification of target sites and design of active ribozymes. First, DNA/RNA sequence analysis software is employed to identify sequence motifs necessary for ribozyme cleavage and to look for sequence conservation between different sources of the target organism so that ribozymes with the broadest possible target range can be designed. Second, RNA folding algorithms are employed to predict the secondary structure of both ribozyme and target RNA in an attempt to identify combinations of ribozyme and target site that will successfully associate prior to ribozyme cleavage. The RNA folding algorithms utilize a set of thermodynamic parameters obtained from measurements on short RNA duplexes; while these rules give reasonable predictions of secondary structure for a small set of highly structured RNAs, they remain largely untested for predicting the structure of messenger RNAs. This paper outlines the current status of designing ribozymes that fold correctly and of locating target sites that are sufficiently unfolded to allow ribozyme cleavage.

  9. Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.

    Science.gov (United States)

    Eiler, Daniel; Wang, Jimin; Steitz, Thomas A

    2014-09-09

    Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-Å resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage site. A second crystal structure of twister from Orzyza sativa determined at 3.1-Å resolution exhibits a disordered scissile phosphate and nucleotide 5' to the cleavage site. The core of twister is stabilized by base pairing, a large network of stacking interactions, and two pseudoknots. We observe three nucleotides that appear to mediate catalysis: a guanosine that we propose deprotonates the 2'-hydroxyl of the nucleotide 5' to the cleavage site and a conserved adenosine. We suggest the adenosine neutralizes the negative charge on a nonbridging phosphate oxygen atom at the cleavage site. The active site also positions the labile linkage for in-line nucleophilic attack, and thus twister appears to simultaneously use three strategies proposed for small self-cleaving ribozymes. The twister crystal structures (i) show its global structure, (ii) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for enhanced catalysis, and (iv) illuminate the roles of all 10 highly conserved nucleotides of twister that participate in the formation of its small and stable catalytic pocket.

  10. In-line alignment and Mg²⁺ coordination at the cleavage site of the env22 twister ribozyme.

    Science.gov (United States)

    Ren, Aiming; Košutić, Marija; Rajashankar, Kanagalaghatta R; Frener, Marina; Santner, Tobias; Westhof, Eric; Micura, Ronald; Patel, Dinshaw J

    2014-11-20

    Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-Å crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modelled 2'-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5' bond. Both an invariant guanosine and a Mg(2+) are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site.

  11. Heterogeneous Catalysis.

    Science.gov (United States)

    Miranda, R.

    1989-01-01

    Described is a heterogeneous catalysis course which has elements of materials processing embedded in the classical format of catalytic mechanisms and surface chemistry. A course outline and list of examples of recent review papers written by students are provided. (MVL)

  12. Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site.

    Science.gov (United States)

    Ucisik, Melek N; Bevilacqua, Philip C; Hammes-Schiffer, Sharon

    2016-07-12

    The recently discovered twister ribozyme is thought to utilize general acid-base catalysis in its self-cleavage mechanism, but the roles of nucleobases and metal ions in the mechanism are unclear. Herein, molecular dynamics simulations of the env22 twister ribozyme are performed to elucidate the structural and equilibrium dynamical properties, as well as to examine the role of Mg(2+) ions and possible candidates for the general base and acid in the self-cleavage mechanism. The active site region and the ends of the pseudoknots were found to be less mobile than other regions of the ribozyme, most likely providing structural stability and possibly facilitating catalysis. A purported catalytic Mg(2+) ion and the closest neighboring Mg(2+) ion remained chelated and relatively immobile throughout the microsecond trajectories, although removal of these Mg(2+) ions did not lead to any significant changes in the structure or equilibrium motions of the ribozyme on the microsecond time scale. In addition, a third metal ion, a Na(+) ion remained close to A1(O5'), the leaving group atom, during the majority of the microsecond trajectories, suggesting that it might stabilize the negative charge on A1(O5') during self-cleavage. The locations of these cations and their interactions with key nucleotides in the active site suggest that they may be catalytically relevant. The P1 stem is partially melted at its top and bottom in the crystal structure and further unwinds in the trajectories. The simulations also revealed an interconnected network comprised of hydrogen-bonding and π-stacking interactions that create a relatively rigid network around the self-cleavage site. The nucleotides involved in this network are among the highly conserved nucleotides in twister ribozymes, suggesting that this interaction network may be important to structure and function.

  13. Assembly and activation of a kinase ribozyme.

    Science.gov (United States)

    Burke, Donald H; Rhee, Steven S

    2010-12-01

    RNA activities can be regulated by modulating the relative energies of all conformations in a folding landscape; however, it is often unknown precisely how peripheral elements perturb the overall landscape in the absence of discrete alternative folds (inactive ensemble). This work explores the effects of sequence and secondary structure in governing kinase ribozyme activity. Kin.46 catalyzes thiophosphoryl transfer from ATPγS onto the 5' hydroxyl of polynucleotide substrates, and is regulated 10,000-fold by annealing an effector oligonucleotide to form activator helix P4. Transfer kinetics for an extensive series of ribozyme variants identified several dispensable internal single-stranded segments, in addition to a potential pseudoknot at the active site between segments J1/4 and J3/2 that is partially supported by compensatory rescue. Standard allosteric mechanisms were ruled out, such as formation of discrete repressive structures or docking P4 into the rest of the ribozyme via backbone 2' hydroxyls. Instead, P4 serves both to complete an important structural element (100-fold contribution to the reaction relative to a P4-deleted variant) and to mitigate nonspecific, inhibitory effects of the single-stranded tail (an additional 100-fold contribution to the apparent rate constant, k(obs)). Thermodynamic activation parameters ΔH(‡) and ΔS(‡), calculated from the temperature dependence of k(obs), varied with tail length and sequence. Inhibitory effects of the unpaired tail are largely enthalpic for short tails and are both enthalpic and entropic for longer tails. These results refine the structural view of this kinase ribozyme and highlight the importance of nonspecific ensemble effects in conformational regulation by peripheral elements.

  14. High-Throughput Mutational Analysis of a Twister Ribozyme.

    Science.gov (United States)

    Kobori, Shungo; Yokobayashi, Yohei

    2016-08-22

    Recent discoveries of new classes of self-cleaving ribozymes in diverse organisms have triggered renewed interest in the chemistry and biology of ribozymes. Functional analysis and engineering of ribozymes often involve performing biochemical assays on multiple ribozyme mutants. However, because each ribozyme mutant must be individually prepared and assayed, the number and variety of mutants that can be studied are severely limited. All of the single and double mutants of a twister ribozyme (a total of 10 296 mutants) were generated and assayed for their self-cleaving activity by exploiting deep sequencing to count the numbers of cleaved and uncleaved sequences for every mutant. Interestingly, we found that the ribozyme is highly robust against mutations such that 71 % and 30 % of all single and double mutants, respectively, retain detectable activity under the assay conditions. It was also observed that the structural elements that comprise the ribozyme exhibit distinct sensitivity to mutations. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  15. Helium ion beam induced growth of hammerhead AFM probes

    NARCIS (Netherlands)

    Nanda, G.; Van Veldhoven, E.; Maas, D.; Sadeghian, H.; Alkemade, P.F.A.

    2015-01-01

    The authors report the direct-write growth of hammerhead atomic force microscope(AFM) probes by He+beam induced deposition of platinum-carbon. In order to grow a thin nanoneedle on top of a conventional AFM probe, the authors move a focused He+beam during exposure to a PtC precursor gas. In the

  16. Helium ion beam induced growth of hammerhead AFM probes

    NARCIS (Netherlands)

    Nanda, G.; Veldhoven, E. van; Maas, D.J.; Sadeghian Marnani, H.; Alkemade, P.F.A.

    2015-01-01

    The authors report the direct-write growth of hammerhead atomic force microscope (AFM) probes by He+ beam induced deposition of platinum-carbon. In order to grow a thin nanoneedle on top of a conventional AFM probe, the authors move a focused He+ beam during exposure to a PtC precursor gas. In the

  17. Enantioconvergent catalysis

    Directory of Open Access Journals (Sweden)

    Justin T. Mohr

    2016-09-01

    Full Text Available An enantioconvergent catalytic process has the potential to convert a racemic starting material to a single highly enantioenriched product with a maximum yield of 100%. Three mechanistically distinct approaches to effecting enantioconvergent catalysis are identified, and recent examples of each are highlighted. These processes are compared to related, non-enantioconvergent methods.

  18. Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

    DEFF Research Database (Denmark)

    Beckert, Bertrand Dominique; Nielsen, Henrik; Einvik, Christer

    2008-01-01

    related to group I ribozymes raising the question about how two closely related ribozymes can carry out very different reactions. Modelling of GIR1 based on new biochemical and mutational data shows an extended substrate domain containing a GoU pair distinct from the nucleophilic residue that dock onto...

  19. Extensive Molecular Dynamics Simulations Show That Canonical G8 and Protonated A38H+ Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

    Science.gov (United States)

    Mlýnský, Vojtěch; Banáš, Pavel; Hollas, Daniel; Réblová, Kamila; Walter, Nils G.; Šponer, Jiří; Otyepka, Michal

    2010-01-01

    The hairpin ribozyme is a prominent member of the group of small catalytic RNAs (RNA enzymes or ribozymes) because it does not require metal ions to achieve catalysis. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants in cleavage and ligation catalyzed by the hairpin ribozyme, yet their exact role in catalysis remains disputed. To gain insight into dynamics in the active site of a minimal self-cleaving hairpin ribozyme, we have performed extensive classical, explicit-solvent molecular dynamics (MD) simulations on timescales of 50-150 ns. Starting from the available X-ray crystal structures, we investigated the structural impact of the protonation states of G8 and A38, and the inactivating A−1(2′-methoxy) substitution employed in crystallography. Our simulations reveal that a canonical G8 agrees well with the crystal structures while a deprotonated G8 profoundly distorts the active site. Thus MD simulations do not support a straightforward participation of the deprotonated G8 in catalysis. By comparison, the G8 enol tautomer is structurally well tolerated, causing only local rearrangements in the active site. Furthermore, a protonated A38H+ is more consistent with the crystallography data than a canonical A38. The simulations thus support the notion that A38H+ is the dominant form in the crystals, grown at pH 6. In most simulations, the canonical A38 departs from the scissile phosphate and substantially perturbs the structures of active site and S-turn. Yet, we occasionally also observe formation of a stable A−1(2′-OH)…A38(N1) hydrogen bond, which documents the ability of the ribozyme to form this hydrogen bond, consistent with a potential role of A38 as general base catalyst. The presence of this hydrogen bond is, however, incompatible with the expected in-line attack angle necessary for self-cleavage, requiring a rapid transition of the deprotonated 2′-oxyanion to a position more favorable for

  20. Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

    Science.gov (United States)

    Mlýnský, Vojtech; Banás, Pavel; Hollas, Daniel; Réblová, Kamila; Walter, Nils G; Sponer, Jirí; Otyepka, Michal

    2010-05-20

    The hairpin ribozyme is a prominent member of the group of small catalytic RNAs (RNA enzymes or ribozymes) because it does not require metal ions to achieve catalysis. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants in cleavage and ligation catalyzed by the hairpin ribozyme, yet their exact role in catalysis remains disputed. To gain insight into dynamics in the active site of a minimal self-cleaving hairpin ribozyme, we have performed extensive classical, explicit-solvent molecular dynamics (MD) simulations on time scales of 50-150 ns. Starting from the available X-ray crystal structures, we investigated the structural impact of the protonation states of G8 and A38, and the inactivating A-1(2'-methoxy) substitution employed in crystallography. Our simulations reveal that a canonical G8 agrees well with the crystal structures while a deprotonated G8 profoundly distorts the active site. Thus MD simulations do not support a straightforward participation of the deprotonated G8 in catalysis. By comparison, the G8 enol tautomer is structurally well tolerated, causing only local rearrangements in the active site. Furthermore, a protonated A38H(+) is more consistent with the crystallography data than a canonical A38. The simulations thus support the notion that A38H(+) is the dominant form in the crystals, grown at pH 6. In most simulations, the canonical A38 departs from the scissile phosphate and substantially perturbs the structures of the active site and S-turn. Yet, we occasionally also observe formation of a stable A-1(2'-OH)...A38(N1) hydrogen bond, which documents the ability of the ribozyme to form this hydrogen bond, consistent with a potential role of A38 as general base catalyst. The presence of this hydrogen bond is, however, incompatible with the expected in-line attack angle necessary for self-cleavage, requiring a rapid transition of the deprotonated 2'-oxyanion to a position more favorable for

  1. Regional variation in undulatory kinematics of two hammerhead species: the bonnethead (Sphyrna tiburo) and the scalloped hammerhead (Sphyrna lewini).

    Science.gov (United States)

    Hoffmann, Sarah L; Warren, Steven M; Porter, Marianne E

    2017-09-15

    Hammerhead sharks (Sphyrnidae) exhibit a large amount of morphological variation within the family, making them the focus of many studies. The size of the laterally expanded head, or cephalofoil, is inversely correlated with pectoral fin area. The inverse relationship between cephalofoil and pectoral fin size in this family suggests that they might serve a complementary role in lift generation. The cephalofoil is also hypothesized to increase olfaction, electroreception and vision; however, little is known about how morphological variation impacts post-cranial swimming kinematics. Previous studies demonstrate that the bonnethead and scalloped hammerhead have significantly different yaw amplitude, and we hypothesized that these species utilize varied frequency and amplitude of undulation along the body. We analyzed video of free-swimming sharks to examine kinematics and 2D morphological variables of the bonnethead and scalloped hammerhead. We also examined the second moment of area along the length of the body and over a size range of animals to determine whether there were shape differences along the body of these species and whether those changed over ontogeny. We found that both species swim with the same standardized velocity and Strouhal number, but there was no correlation between two-dimensional morphology and swimming kinematics. However, the bonnethead has a dorso-ventrally compressed anterior trunk and undulates with greater amplitude, whereas the scalloped hammerhead has a laterally compressed anterior trunk and undulates with lower amplitude. We propose that differences in cross-sectional trunk morphology account for interspecific differences in undulatory amplitude. We also found that for both species, undulatory frequency is significantly greater in the anterior body compared with all other body regions. We hypothesize that the bonnethead and scalloped hammerhead swim with a double oscillation system. © 2017. Published by The Company of Biologists Ltd.

  2. Molecular characterization of a new member of the lariat capping twin-ribozyme introns

    DEFF Research Database (Denmark)

    Tang, Yunjia; Nielsen, Henrik; Masquida, Benoît

    2014-01-01

    BACKGROUND: Twin-ribozyme introns represent a complex class of mobile group I introns that harbour a lariat capping (LC) ribozyme and a homing endonuclease gene embedded in a conventional self-splicing group I ribozyme (GIR2). Twin-ribozyme introns have so far been confined to nucleolar DNA...... splicing and homing endonuclease mRNA maturation. We found Allovahlkampfia GIR2 to be a typical group IC1 splicing ribozyme responsible for addition of the exogenous guanosine cofactor (exoG), exon ligation and circularization of intron RNA. The Allovahlkampfia LC ribozyme, by contrast, represents...... an efficient self-cleaving ribozyme that generates a small 2',5' lariat cap at the 5' end of the homing endonuclease mRNA, and thus contributes to intron mobility. CONCLUSIONS: The discovery of a twin-ribozyme intron in a member of Heterolobosea expands the distribution pattern of LC ribozymes. We identify...

  3. The mitochondrial genome of the hammerhead Sphyrna zygaena.

    Science.gov (United States)

    Bolaño-Martínez, Nataly; Bayona-Vasquez, Natalia; Uribe-Alcocer, Manuel; Díaz-Jaimes, Píndaro

    2016-05-01

    The hammerhead shark (Sphyrna zygaena) is listed as a "Vulnerable" species for the International Union for Conservation of Nature (IUCN). Here we report the complete sequence for the mitochondrial genome of the hammerhead shark of a specimen collected from the eastern Pacific Ocean. The genome structure is quite similar to other reported mtDNA shark species. It has a total length of 16,731 base pairs (bp); the base composition was A (31.54%), T (30.23%) C (25.03%) and G: 13.20, contains 13 protein-coding genes, 2 rRNA genes; 21 tRNA genes. In addition, most of the starting (ATG) and ending codons (TAA) for the mtDNA gene regions were registered.

  4. Functional morphology of the nasal region of a hammerhead shark.

    Science.gov (United States)

    Abel, Richard L; Maclaine, James S; Cotton, Ross; Xuan, Viet Bui; Nickels, Timothy B; Clark, Thomas H; Wang, Zhijin; Cox, Jonathan P L

    2010-04-01

    We describe several novel morphological features in the nasal region of the hammerhead shark Sphyrna tudes. Unlike the open, rounded incurrent nostril of non-hammerhead shark species, the incurrent nostril of S. tudes is a thin keyhole-like aperture. We discovered a groove running anterior and parallel to the incurrent nostril. This groove, dubbed the minor nasal groove to distinguish it from the larger, previously described, (major) nasal groove, is common to all eight hammerhead species. Using life-sized plastic models generated at 200 microm resolution from an X-ray scan, we also investigated flow in the nasal region. Even modest oncoming flow speeds stimulate extensive, but not complete, circulation within the model olfactory chamber, with flow passing through the two main olfactory channels. Flow crossed from one channel to another via a gap in the olfactory array, sometimes guided by the interlamellar channels. Major and minor nasal grooves, as well as directing flow into the olfactory chamber, can, in conjunction with the nasal bridge separating incurrent and excurrent nostrils, limit flow passing into the olfactory chamber, possibly to protect the delicate nasal structures. This is the first simulation of internal flow within the olfactory chamber of a shark.

  5. Electroreception in juvenile scalloped hammerhead and sandbar sharks.

    Science.gov (United States)

    Kajiura, Stephen M; Holland, Kim N

    2002-12-01

    The unique head morphology of sphyrnid sharks might have evolved to enhance electrosensory capabilities. The 'enhanced electroreception' hypothesis was tested by comparing the behavioral responses of similarly sized carcharhinid and sphyrnid sharks to prey-simulating electric stimuli. Juvenile scalloped hammerhead sharks Sphyrna lewini and sandbar sharks Carcharhinus plumbeus oriented to dipole electric fields from the same maximum distance (approximately 30 cm) and thus demonstrated comparable behavioral-response thresholds (hammerheads typically demonstrated a pivot orientation in which the edge of the cephalofoil closest to the dipole remained stationary while the shark bent its trunk to orient to the center of the dipole. By contrast, sandbars swam in a broader arc towards the center of the dipole. The different orientation patterns are attributed to the hydrodynamic properties of the cephalofoil, which enables the hammerheads to execute sharp turns at high speed. The greater trunk width of the sandbar sharks prevented them from demonstrating the same degree of flexibility. Therefore, although the sphyrnid head morphology does not appear to confer a greater sensitivity to prey-simulating dipole electric fields, it does provide (1). a greater lateral search area, which may increase the probability of prey encounter, and (2). enhanced maneuverability, which may aid in prey capture.

  6. Twister ribozymes as highly versatile expression platforms for artificial riboswitches.

    Science.gov (United States)

    Felletti, Michele; Stifel, Julia; Wurmthaler, Lena A; Geiger, Sophie; Hartig, Jörg S

    2016-09-27

    The utilization of ribozyme-based synthetic switches in biotechnology has many advantages such as an increased robustness due to in cis regulation, small coding space and a high degree of modularity. The report of small endonucleolytic twister ribozymes provides new opportunities for the development of advanced tools for engineering synthetic genetic switches. Here we show that the twister ribozyme is distinguished as an outstandingly flexible expression platform, which in conjugation with three different aptamer domains, enables the construction of many different one- and two-input regulators of gene expression in both bacteria and yeast. Besides important implications in biotechnology and synthetic biology, the observed versatility in artificial genetic control set-ups hints at possible natural roles of this widespread ribozyme class.

  7. Ribozyme genes protecting transgenic melon plants against potyviruses

    National Research Council Canada - National Science Library

    Huttner, E; Tucker, W; Vermeulen, A; Ignart, F; Sawyer, B; Birch, R

    2001-01-01

    Potyviruses are the most important viral pathogens of crops worldwide. Under a contract with Gene Shears Pty Limited, we are using ribozyme genes to protect melon plants against two potyviruses: WMV2 and ZYMV...

  8. Bimetallic catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Beuken, E.K. van den; Leeuwen, P.W.N.M. van; Budzelaar, P.H.M.; Feringa, B.L. [Univ. of Groningen (Netherlands)

    1995-12-31

    The field of binucleating ligand systems and their bimetallic complexes has developed considerably in recent years. When two metals are in close proximity the formation of metal-metal bonds, insertion of small molecules into a metal-metal bond, ligand mobility from terminal to bridging site and the transfer of ligands from one metal centre to the other can be observed. A prominent example is the cooperative effect of two metal centres in the hydroformylation reaction of 1-hexene with a dinuclear rhodium phosphine complex. Following interest in bimetallic catalysis, the authors now report the synthesis, molecular structure determination and application in catalysis of a new dinuclear rhodium phosphate complex. A relatively simple synthetic route to diphosphite ligand 1 and tetraphosphite ligand 2 and their corresponding mononuclear complex Rh(acac) and dinuclear complex Rh{sub 2}(acac){sub 2} was developed. Rh{sub 2}(acac){sub 2}, which is the precursor of the catalyst was characterised by X-ray analysis. The active catalysts derived from 1 and 2 are studied by high pressure NMR. Hydroformylation of various alkenes under mild conditions (20 mmol substate, 4 {mu}mol Rh(acac)(CO){sub 2}, 20 bar CO/H{sub 2}, 80{degrees}C) with diphosphite 1 and tetraphosphite 2 will be reported.

  9. 76 FR 23794 - Stock Status Determination for Atlantic Highly Migratory Scalloped Hammerhead Shark

    Science.gov (United States)

    2011-04-28

    ... Scalloped Hammerhead Shark AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... an Atlantic highly migratory species (HMS) scalloped hammerhead shark, and the stock is overfished... sharks in U.S. waters. Based on this paper, in 2005, the population was estimated to be at 45 percent of...

  10. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

    Science.gov (United States)

    Pinard, Robert; Hampel, Ken J.; Heckman, Joyce E.; Lambert, Dominic; Chan, Philip A.; Major, Francois; Burke, John M.

    2001-01-01

    The catalytic determinants for the cleavage and ligation reactions mediated by the hairpin ribozyme are integral to the polyribonucleotide chain. We describe experiments that place G8, a critical guanosine, at the active site, and point to an essential role in catalysis. Cross-linking and modeling show that formation of a catalytic complex is accompanied by a conformational change in which N1 and O6 of G8 become closely apposed to the scissile phosphodiester. UV cross-linking, hydroxyl-radical footprinting and native gel electrophoresis indicate that G8 variants inhibit the reaction at a step following domain association, and that the tertiary structure of the inactive complex is not measurably altered. Rate–pH profiles and fluorescence spectroscopy show that protonation at the N1 position of G8 is required for catalysis, and that modification of O6 can inhibit the reaction. Kinetic solvent isotope analysis suggests that two protons are transferred during the rate-limiting step, consistent with rate-limiting cleavage chemistry involving concerted deprotonation of the attacking 2′-OH and protonation of the 5′-O leaving group. We propose mechanistic models that are consistent with these data, including some that invoke a novel keto–enol tautomerization. PMID:11707414

  11. Speciation of a group I intron into a lariat capping ribozyme

    DEFF Research Database (Denmark)

    Meyer, Mélanie; Nielsen, Henrik; Oliéric, Vincent

    2014-01-01

    The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes ...

  12. Modulation of Group I Ribozyme Activity by Cationic Porphyrins

    Science.gov (United States)

    Matsumura, Shigeyoshi; Ito, Tatsunobu; Tanaka, Takahiro; Furuta, Hiroyuki; Ikawa, Yoshiya

    2015-01-01

    The effects of cationic porphyrins on the catalytic activities of four group I ribozymes were investigated. A cationic porphyrin possessing four pyridinium moieties (pPyP) inhibited two group IC3 ribozymes (Syn Rz and Azo Rz) and a group IC1 ribozyme (Tet Rz). In the case of a group IA2 ribozyme (Td Rz), however, pPyP served not only as an inhibitor but also as an activator, and the effects of pPyP were dependent on its concentration. To analyze the structural and electronic factors determining the effects of pPyP on group I ribozymes, three cationic porphyrins (pPyNCP, pPyF4P, and TMPyP) were also examined. As interactions between small organic molecules and nucleic acids are attractive and important issues in biochemistry and biotechnology, this study contributes to the development of porphyrin-based molecules that can modulate functions of structured RNA molecules. PMID:25811638

  13. Modulation of Group I Ribozyme Activity by Cationic Porphyrins

    Directory of Open Access Journals (Sweden)

    Shigeyoshi Matsumura

    2015-03-01

    Full Text Available The effects of cationic porphyrins on the catalytic activities of four group I ribozymes were investigated. A cationic porphyrin possessing four pyridinium moieties (pPyP inhibited two group IC3 ribozymes (Syn Rz and Azo Rz and a group IC1 ribozyme (Tet Rz. In the case of a group IA2 ribozyme (Td Rz, however, pPyP served not only as an inhibitor but also as an activator, and the effects of pPyP were dependent on its concentration. To analyze the structural and electronic factors determining the effects of pPyP on group I ribozymes, three cationic porphyrins (pPyNCP, pPyF4P, and TMPyP were also examined. As interactions between small organic molecules and nucleic acids are attractive and important issues in biochemistry and biotechnology, this study contributes to the development of porphyrin-based molecules that can modulate functions of structured RNA molecules.

  14. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  15. Catalysis of Photochemical Reactions.

    Science.gov (United States)

    Albini, A.

    1986-01-01

    Offers a classification system of catalytic effects in photochemical reactions, contrasting characteristic properties of photochemical and thermal reactions. Discusses catalysis and sensitization, examples of catalyzed reactions of excepted states, complexing ground state substrates, and catalysis of primary photoproducts. (JM)

  16. Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

    Directory of Open Access Journals (Sweden)

    Nico Rublack

    2014-08-01

    Full Text Available Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated.

  17. Screening of Genetic Switches Based on the Twister Ribozyme Motif.

    Science.gov (United States)

    Felletti, Michele; Klauser, Benedikt; Hartig, Jörg S

    2016-01-01

    The recent description of a new class of small endonucleolytic ribozymes termed twister opened new avenues into the development of artificial riboswitches, providing new tools for the development of artificial genetic circuits in bacteria. Here we present a method to develop new ligand-dependent riboswitches, employing the newly described catalytic motif as an expression platform in conjugation with naturally occurring or in vitro-selected aptameric domains. The twister motif is an outstandingly flexible tool for the development of highly active ribozyme-based riboswitches able to control gene expression in a ligand-dependent manner in Escherichia coli.

  18. Scalloped hammerhead shark Sphyrna lewini, utilizes deep-water, hypoxic zone in the Gulf of California.

    Science.gov (United States)

    Jorgensen, S J; Klimley, A P; Muhlia-Melo, A F

    2009-05-01

    A hammerhead shark Sphyrna lewini tracked for 74 days revealed an expansion of the range of vertical distribution for the species to include the extreme hypoxic environment of the oxygen minimum layer in the Gulf of California.

  19. Maneuvering in juvenile carcharhinid and sphyrnid sharks: the role of the hammerhead shark cephalofoil.

    Science.gov (United States)

    Kajiura, Stephen M; Forni, Jesica B; Summers, Adam P

    2003-01-01

    The peculiar head morphology of hammerhead sharks has spawned a variety of untested functional hypotheses. One of the most intuitively appealing ideas is that the anterior foil acts, as in canard-winged aircraft, to increase maneuverability. We tested this hypothesis by determining whether juveniles of two hammerhead species (Sphyrna tiburo and S. lewini) turn more sharply, more often, and with greater velocity than a juvenile carcharhinid shark (Carcharhinus plumbeus). Although the hammerheads were more maneuverable, further investigation revealed that they do not roll their body during turns, suggesting that the cephalofoil does not act as a steering wing. We also show that hammerhead sharks demonstrate greater lateral flexure in a turn than carcharhinids, and that this flexibility may be due to cross sectional shape rather than number of vertebrae.

  20. Reproductive biology of the scalloped Hammerhead shark Sphyrna lewini (Chondrichthyes: Sphyrnidae) off southwest Mexico

    OpenAIRE

    Bejarano-Álvarez, Marcela; Galván Magaña, Felipe; Ochoa Báez, Rosa Isabel

    2011-01-01

    The scalloped hammerhead shark Sphyrna lewini is the most important species in the artisanal shark fishery in the Gulf of Tehuantepec, Mexico. The knowledge about their reproductive biology in the area is nonexistent, despite their being listed worldwide as endangered by the IUCN. To determine the basic biology of reproduction in this shark would give important data to establish management or conservation plans for this species in Mexico. Samples were collected of 991 hammerhead sharks (342 f...

  1. Advances in catalysis

    CERN Document Server

    Gates, Bruce C

    2012-01-01

    Advances in Catalysis fills the gap between the journal papers and the textbooks across the diverse areas of catalysis research. For more than 60 years Advances in Catalysis has been dedicated to recording progress in the field of catalysis and providing the scientific community with comprehensive and authoritative reviews. This series in invaluable to chemical engineers, physical chemists, biochemists, researchers and industrial chemists working in the fields of catalysis and materials chemistry. * In-depth, critical, state-of-the-art reviews * Comprehensive, covers of all as

  2. Constructional morphology within the head of hammerhead sharks (sphyrnidae).

    Science.gov (United States)

    Mara, Kyle R; Motta, Philip J; Martin, Andrew P; Hueter, Robert E

    2015-05-01

    The study of functional trade-offs is important if a structure, such as the cranium, serves multiple biological roles, and is, therefore, shaped by multiple selective pressures. The sphyrnid cephalofoil presents an excellent model for investigating potential trade-offs among sensory, neural, and feeding structures. In this study, hammerhead shark species were chosen to represent differences in head form through phylogeny. A combination of surface-based geometric morphometrics, computed tomography (CT) volumetric analysis, and phylogenetic analyses were utilized to investigate potential trade-offs within the head. Hammerhead sharks display a diversity of cranial morphologies where the position of the eyes and nares vary among species, with only minor changes in shape, position, and volume of the feeding apparatus through phylogeny. The basal winghead shark, Eusphyra blochii, has small anteriorly positioned eyes. Through phylogeny, the relative size and position of the eyes change, such that derived species have larger, more medially positioned eyes. The lateral position of the external nares is highly variable, showing no phylogenetic trend. Mouth size and position are conserved, remaining relatively unchanged. Volumetric CT analyses reveal no trade-offs between the feeding apparatus and the remaining cranial structures. The few trade-offs were isolated to the nasal capsule volume's inverse correlation with braincase, chondrocranial, and total cephalofoil volume. Eye volume also decreased as cephalofoil width increased. These data indicate that despite considerable changes in head shape, much of the head is morphologically conserved through sphyrnid phylogeny, particularly the jaw cartilages and their associated feeding muscles, with shape change and morphological trade-offs being primarily confined to the lateral wings of the cephalofoil and their associated sensory structures. © 2015 Wiley Periodicals, Inc.

  3. Multicatalyst system in asymmetric catalysis

    CERN Document Server

    Zhou, Jian

    2014-01-01

    This book introduces multi-catalyst systems by describing their mechanism and advantages in asymmetric catalysis.  Helps organic chemists perform more efficient catalysis with step-by-step methods  Overviews new concepts and progress for greener and economic catalytic reactions  Covers topics of interest in asymmetric catalysis including bifunctional catalysis, cooperative catalysis, multimetallic catalysis, and novel tandem reactions   Has applications for pharmaceuticals, agrochemicals, materials, and flavour and fragrance

  4. Crystal structure and mechanistic investigation of the twister ribozyme.

    Science.gov (United States)

    Liu, Yijin; Wilson, Timothy J; McPhee, Scott A; Lilley, David M J

    2014-09-01

    We present a crystal structure at 2.3-Å resolution of the recently described nucleolytic ribozyme twister. The RNA adopts a previously uncharacterized compact fold based on a double-pseudoknot structure, with the active site at its center. Eight highly conserved nucleobases stabilize the core of the ribozyme through the formation of one Watson-Crick and three noncanonical base pairs, and the highly conserved adenine 3' of the scissile phosphate is bound in the major groove of an adjacent pseudoknot. A strongly conserved guanine nucleobase directs its Watson-Crick edge toward the scissile phosphate in the crystal structure, and mechanistic evidence supports a role for this guanine as either a general base or acid in a concerted, general acid-base-catalyzed cleavage reaction.

  5. Catalysis seen in action

    NARCIS (Netherlands)

    Tromp, M.

    2015-01-01

    Synchrotron radiation techniques are widely applied in materials research and heterogeneous catalysis. In homogeneous catalysis, its use so far is rather limited despite its high potential. Here, insights in the strengths and limitations of X-ray spectroscopy technique in the field of homogeneous

  6. Prebiotic Factors Influencing the Activity of a Ligase Ribozyme

    Directory of Open Access Journals (Sweden)

    Fabrizio Anella

    2017-04-01

    Full Text Available An RNA-lipid origin of life scenario provides a plausible route for compartmentalized replication of an informational polymer and subsequent division of the container. However, a full narrative to form such RNA protocells implies that catalytic RNA molecules, called ribozymes, can operate in the presence of self-assembled vesicles composed of prebiotically relevant constituents, such as fatty acids. Hereby, we subjected a newly engineered truncated variant of the L1 ligase ribozyme, named tL1, to various environmental conditions that may have prevailed on the early Earth with the objective to find a set of control parameters enabling both tL1-catalyzed ligation and formation of stable myristoleic acid (MA vesicles. The separate and concurrent effects of temperature, concentrations of Mg2+, MA, polyethylene glycol and various solutes were investigated. The most favorable condition tested consists of 100 mM NaCl, 1 mM Mg2+, 5 mM MA, and 4 °C temperature, whereas the addition of Mg2+-chelating solutes, such as citrate, tRNAs, aspartic acid, and nucleoside triphosphates severely inhibits the reaction. These results further solidify the RNA-lipid world hypothesis and stress the importance of using a systems chemistry approach whereby a wide range of prebiotic factors interfacing with ribozymes are considered.

  7. Reconciling Ligase Ribozyme Activity with Fatty Acid Vesicle Stability

    Directory of Open Access Journals (Sweden)

    Fabrizio Anella

    2014-12-01

    Full Text Available The “RNA world” and the “Lipid world” theories for the origin of cellular life are often considered incompatible due to the differences in the environmental conditions at which they can emerge. One obstacle resides in the conflicting requirements for divalent metal ions, in particular Mg2+, with respect to optimal ribozyme activity, fatty acid vesicle stability and protection against RNA strand cleavage. Here, we report on the activity of a short L1 ligase ribozyme in the presence of myristoleic acid (MA vesicles at varying concentrations of Mg2+. The ligation rate is significantly lower at low-Mg2+ conditions. However, the loss of activity is overcompensated by the increased stability of RNA leading to a larger amount of intact ligated substrate after long reaction periods. Combining RNA ligation assays with fatty acid vesicles we found that MA vesicles made of 5 mM amphiphile are stable and do not impair ligase ribozyme activity in the presence of approximately 2 mM Mg2+. These results provide a scenario in which catalytic RNA and primordial membrane assembly can coexist in the same environment.

  8. An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Westhof, Eric; Johansen, Steinar

    2005-01-01

    Twin-ribozyme introns are formed by two ribozymes belonging to the group I family and occur in some ribosomal RNA transcripts. The group I-like ribozyme, GIR1, liberates the 5' end of a homing endonuclease messenger RNA in the slime mold Didymium iridis. We demonstrate that this cleavage occurs...

  9. Global phylogeography of the scalloped hammerhead shark (Sphyrna lewini).

    Science.gov (United States)

    Duncan, K M; Martin, A P; Bowen, B W; DE Couet, H G

    2006-07-01

    Large marine fishes typically have little population genetic structure. The exceptions are associated with sedentary behaviour, disjunct distributions, or reproductive philopatry. Scalloped hammerhead sharks (Sphyrna lewini) incorporate the contrasting traits of oceanic habitat (usually associated with high dispersal) and possible fidelity to nursery grounds (for reproductive females). To evaluate the expectations of these contrasting behaviours, we examined the global genetic structure of S. lewini based on collections (n = 271 individuals) from 20 nursery areas. A 548-bp fragment of mitochondrial DNA control region revealed 22 polymorphic sites, 24 haplotypes, and three lineages distinguished by 2.56-3.77% sequence divergence. Coalescence analyses based on a provisional molecular clock indicate an origin in the Indo-West Pacific with late Pleistocene radiations into the central Pacific (Hawaii) and eastern Pacific (Central America), as well as recent interchange between oceans via southern Africa. Population subdivisions are strong (overall Phi(ST) = 0.749, P 10). We conclude that nursery populations linked by continuous coastline have high connectivity, but that oceanic dispersal by females is rare. Although we cannot rule out philopatry to natal nurseries, oceanic barriers appear to have a much stronger influence on the genetic architecture of this species and may indicate a mechanism for recent evolutionary radiations in the genus Sphyrna.

  10. Kinematics and critical swimming speed of juvenile scalloped hammerhead sharks

    Science.gov (United States)

    Lowe

    1996-01-01

    Kinematics and critical swimming speed (Ucrit) of juvenile scalloped hammerhead sharks Sphyrna lewini were measured in a Brett-type flume (635 l). Kinematic parameters were also measured in sharks swimming in a large pond for comparison with those of sharks swimming in the flume. Sharks in the flume exhibited a mean Ucrit of 65±11 cm s-1 (± s.d.) or 1.17±0.21 body lengths per second (L s-1), which are similar to values for other species of sharks. In both the flume and pond, tailbeat frequency (TBF) and stride length (LS) increased linearly with increases in relative swimming speed (Urel=body lengths traveled per second). In the flume, tailbeat amplitude (TBA) decreased with increasing speed whereas TBA did not change with speed in the pond. Differences in TBF and LS between sharks swimming in the flume and the pond decreased with increases in Urel. Sharks swimming at slow speeds (e.g. 0.55 L s-1) in the pond had LS 19 % longer and TBF 21 % lower than sharks in the flume at the same Urel. This implies that sharks in the flume expended more energy while swimming at comparable velocities. Comparative measurements of swimming kinematics from sharks in the pond can be used to correct for effects of the flume on shark swimming kinematics and energetics.

  11. Engineering integrated digital circuits with allosteric ribozymes for scaling up molecular computation and diagnostics.

    Science.gov (United States)

    Penchovsky, Robert

    2012-10-19

    Here we describe molecular implementations of integrated digital circuits, including a three-input AND logic gate, a two-input multiplexer, and 1-to-2 decoder using allosteric ribozymes. Furthermore, we demonstrate a multiplexer-decoder circuit. The ribozymes are designed to seek-and-destroy specific RNAs with a certain length by a fully computerized procedure. The algorithm can accurately predict one base substitution that alters the ribozyme's logic function. The ability to sense the length of RNA molecules enables single ribozymes to be used as platforms for multiple interactions. These ribozymes can work as integrated circuits with the functionality of up to five logic gates. The ribozyme design is universal since the allosteric and substrate domains can be altered to sense different RNAs. In addition, the ribozymes can specifically cleave RNA molecules with triplet-repeat expansions observed in genetic disorders such as oculopharyngeal muscular dystrophy. Therefore, the designer ribozymes can be employed for scaling up computing and diagnostic networks in the fields of molecular computing and diagnostics and RNA synthetic biology.

  12. A widespread self-cleaving ribozyme class is revealed by bioinformatics.

    Science.gov (United States)

    Roth, Adam; Weinberg, Zasha; Chen, Andy G Y; Kim, Peter B; Ames, Tyler D; Breaker, Ronald R

    2014-01-01

    Ribozymes are noncoding RNAs that promote chemical transformations with rate enhancements approaching those of protein enzymes. Although ribozymes are likely to have been abundant during the RNA world era, only ten classes are known to exist among contemporary organisms. We report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. Nearly 2,700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. Two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs.

  13. Generation and Development of RNA Ligase Ribozymes with Modular Architecture Through “Design and Selection”

    Directory of Open Access Journals (Sweden)

    Yuki Fujita

    2010-08-01

    Full Text Available In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed “design and selection,” new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

  14. Surface and nanomolecular catalysis

    CERN Document Server

    Richards, Ryan

    2006-01-01

    Using new instrumentation and experimental techniques that allow scientists to observe chemical reactions and molecular properties at the nanoscale, the authors of Surface and Nanomolecular Catalysis reveal new insights into the surface chemistry of catalysts and the reaction mechanisms that actually occur at a molecular level during catalysis. While each chapter contains the necessary background and explanations to stand alone, the diverse collection of chapters shows how developments from various fields each contributed to our current understanding of nanomolecular catalysis as a whole. The

  15. Molecular water oxidation catalysis

    CERN Document Server

    Llobet, Antoni

    2014-01-01

    Photocatalytic water splitting is a promising strategy for capturing energy from the sun by coupling light harvesting and the oxidation of water, in order to create clean hydrogen fuel. Thus a deep knowledge of the water oxidation catalysis field is essential to be able to come up with useful energy conversion devices based on sunlight and water splitting. Molecular Water Oxidation Catalysis: A Key Topic for New Sustainable Energy Conversion Schemes presents a comprehensive and state-of-the-art overview of water oxidation catalysis in homogeneous phase, describing in detail the most importan

  16. How the discovery of ribozymes cast RNA in the roles of both chicken and egg in origin-of-life theories.

    Science.gov (United States)

    Sankaran, Neeraja

    2012-12-01

    Scientific theories about the origin-of-life theories have historically been characterized by the chicken-and-egg problem of which essential aspect of life was the first to appear, replication or self-sustenance. By the 1950s the question was cast in molecular terms and DNA and proteins had come to represent the carriers of the two functions. Meanwhile, RNA, the other nucleic acid, had played a capricious role in origin theories. Because it contained building blocks very similar to DNA, biologists recognized early that RNA could store information in its linear sequences. With the discovery in the 1980s that RNA molecules were capable of biological catalysis, a function hitherto ascribed to proteins alone, RNA took on the role of the single entity that could act as both chicken and egg. Within a few years of the discovery of these catalytic RNAs (ribozymes) scientists had formulated an RNA World hypothesis that posited an early phase in the evolution of life where all key functions were performed by RNA molecules. This paper traces the history the role of RNA in origin-of-life theories with a focus on how the discovery of ribozymes influenced the discourse. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Research on Catalysis.

    Science.gov (United States)

    Bartholomew, Calvin H.; Hecker, William C.

    1984-01-01

    The objectives and philosophy of the Catalysis Laboratory at Brigham Young University are discussed. Also discusses recent and current research activities at the laboratory as well as educational opportunities, research facilities, and sources of research support. (JN)

  18. Hammerhead Shark Research Immersion Program: Experiential Learning Leads to Lasting Educational Benefits

    Science.gov (United States)

    Handler, Alex; Duncan, Kanesa

    2006-01-01

    High school students (n = 45) participated in a 5-day research immersion study on juvenile scalloped hammerhead sharks in Kaneohe Bay, Oahu, Hawaii. Self-surveys were used to evaluate scientific concepts and skills taught during the program. There was a significant shift in students' perceived level of understanding for all categories of concepts…

  19. Variability in multiple paternity rates for grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini).

    Science.gov (United States)

    Green, M E; Appleyard, S A; White, W; Tracey, S; Ovenden, J

    2017-05-08

    This study assessed the presence and prevalence of multiple paternity (MP) in litters of grey reef sharks (Carcharhinus amblyrhynchos) and scalloped hammerheads (Sphyrna lewini) opportunistically caught in Papua New Guinea (PNG). Litter size between species were significantly different with an average of 3.3 pups for grey reef sharks and 17.2 pups for scalloped hammerhead. Using 14 and 10 microsatellite loci respectively, we identified MP in 66% of grey reef sharks (4 out of 6 litters) and 100% MP in scalloped hammerheads (5 litters). We found high paternal skew (the uneven contribution of sires per litter) and a positive correlation between female adult size and litter size in scalloped hammerheads but not in grey reef sharks. Differences in the frequency of MP between species and the identification of paternal skew may be linked with mating strategies and post-copulatory mechanisms. Multiple paternity is thought to benefit populations by enhancing genetic diversity therefore increasing the population's genetic resilience to extrinsic pressures. The identification of MP in two shark species reported here, further elucidates the complex breeding strategies elasmobranchs undertake.

  20. Design principles for ligand-sensing, conformation-switching ribozymes.

    Directory of Open Access Journals (Sweden)

    Xi Chen

    2009-12-01

    Full Text Available Nucleic acid sensor elements are proving increasingly useful in biotechnology and biomedical applications. A number of ligand-sensing, conformational-switching ribozymes (also known as allosteric ribozymes or aptazymes have been generated by some combination of directed evolution or rational design. Such sensor elements typically fuse a molecular recognition domain (aptamer with a catalytic signal generator (ribozyme. Although the rational design of aptazymes has begun to be explored, the relationships between the thermodynamics of aptazyme conformational changes and aptazyme performance in vitro and in vivo have not been examined in a quantitative framework. We have therefore developed a quantitative and predictive model for aptazymes as biosensors in vitro and as riboswitches in vivo. In the process, we have identified key relationships (or dimensionless parameters that dictate aptazyme performance, and in consequence, established equations for precisely engineering aptazyme function. In particular, our analysis quantifies the intrinsic trade-off between ligand sensitivity and the dynamic range of activity. We were also able to determine how in vivo parameters, such as mRNA degradation rates, impact the design and function of aptazymes when used as riboswitches. Using this theoretical framework we were able to achieve quantitative agreement between our models and published data. In consequence, we are able to suggest experimental guidelines for quantitatively predicting the performance of aptazyme-based riboswitches. By identifying factors that limit the performance of previously published systems we were able to generate immediately testable hypotheses for their improvement. The robust theoretical framework and identified optimization parameters should now enable the precision design of aptazymes for biotechnological and clinical applications.

  1. Design and Experimental Evolution of trans-Splicing Group I Intron Ribozymes

    Directory of Open Access Journals (Sweden)

    Ulrich F. Müller

    2017-01-01

    Full Text Available Group I intron ribozymes occur naturally as cis-splicing ribozymes, in the form of introns that do not require the spliceosome for their removal. Instead, they catalyze two consecutive trans-phosphorylation reactions to remove themselves from a primary transcript, and join the two flanking exons. Designed, trans-splicing variants of these ribozymes replace the 3′-portion of a substrate with the ribozyme’s 3′-exon, replace the 5′-portion with the ribozyme’s 5′-exon, or insert/remove an internal sequence of the substrate. Two of these designs have been evolved experimentally in cells, leading to variants of group I intron ribozymes that splice more efficiently, recruit a cellular protein to modify the substrate’s gene expression, or elucidate evolutionary pathways of ribozymes in cells. Some of the artificial, trans-splicing ribozymes are promising as tools in therapy, and as model systems for RNA evolution in cells. This review provides an overview of the different types of trans-splicing group I intron ribozymes that have been generated, and the experimental evolution systems that have been used to improve them.

  2. Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate.

    Science.gov (United States)

    Vušurović, Nikola; Altman, Roger B; Terry, Daniel S; Micura, Ronald; Blanchard, Scott C

    2017-06-21

    The twister RNA is a recently discovered nucleolytic ribozyme that is present in both bacteria and eukarya. While its biological role remains unclear, crystal structure analyses and biochemical approaches have revealed critical features of its catalytic mechanism. Here, we set out to explore dynamic aspects of twister RNA folding along the cleavage reaction coordinate. To do so, we have employed both bulk and single-molecule fluorescence resonance energy transfer (FRET) methods to investigate a set of twister RNAs with labels strategically positioned at communicating segments. The data reveal that folding of the central pseudoknot (T1), the most crucial structural determinant to promote cleavage, exhibits reversible opening and closing dynamics at physiological Mg2+ concentration. Uncoupled folding, in which T1 formation precedes structuring for closing of stem P1, was confirmed using pre-steady-state three-color smFRET experiments initiated by Mg2+ injection. This finding suggests that the folding path of twister RNA requires proper orientation of the substrate prior to T1 closure such that the U5-A6 cleavage site becomes embraced to achieve its cleavage competent conformation. We also find that the cleaved 3'-fragment retains its compacted pseudoknot fold, despite the absence of the phylogenetically conserved stem P1, rationalizing the poor turnover efficiency of the twister ribozyme.

  3. Homogeneous, Heterogeneous, and Enzymatic Catalysis.

    Science.gov (United States)

    Oyama, S. Ted; Somorjai, Gabor A.

    1988-01-01

    Discusses three areas of catalysis: homegeneous, heterogeneous, and enzymatic. Explains fundamentals and economic impact of catalysis. Lists and discusses common industrial catalysts. Provides a list of 107 references. (MVL)

  4. Catalysis for alternative energy generation

    CERN Document Server

    2012-01-01

    Summarizes recent problems in using catalysts in alternative energy generation and proposes novel solutions  Reconsiders the role of catalysis in alternative energy generation  Contributors include catalysis and alternative energy experts from across the globe

  5. Preface: Catalysis Today

    DEFF Research Database (Denmark)

    Li, Yongdan

    2016-01-01

    This special issue of Catalysis Today with the theme “Sustain-able Energy” results from a great success of the session “Catalytic Technologies Accelerating the Establishment of Sustainable and Clean Energy”, one of the two sessions of the 1st International Symposium on Catalytic Science and Techn......This special issue of Catalysis Today with the theme “Sustain-able Energy” results from a great success of the session “Catalytic Technologies Accelerating the Establishment of Sustainable and Clean Energy”, one of the two sessions of the 1st International Symposium on Catalytic Science...... and Technology in Sustainable Energy and Environment, held in Tianjin, China during October8–10, 2014. This biennial symposium offers an international forum for discussing and sharing the cutting-edge researches and the most recent breakthroughs in energy and environmental technologies based on catalysis...

  6. Catalysis seen in action.

    Science.gov (United States)

    Tromp, Moniek

    2015-03-06

    Synchrotron radiation techniques are widely applied in materials research and heterogeneous catalysis. In homogeneous catalysis, its use so far is rather limited despite its high potential. Here, insights in the strengths and limitations of X-ray spectroscopy technique in the field of homogeneous catalysis are given, including new technique developments. A relevant homogeneous catalyst, used in the industrially important selective oligomerization of ethene, is taken as a worked-out example. Emphasis is placed on time-resolved operando X-ray absorption spectroscopy with outlooks to novel high energy resolution and emission techniques. All experiments described have been or can be done at the Diamond Light Source Ltd (Didcot, UK). © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  7. Isotopes in heterogeneous catalysis

    CERN Document Server

    Hargreaves, Justin SJ

    2006-01-01

    The purpose of this book is to review the current, state-of-the-art application of isotopic methods to the field of heterogeneous catalysis. Isotopic studies are arguably the ultimate technique in in situ methods for heterogeneous catalysis. In this review volume, chapters have been contributed by experts in the field and the coverage includes both the application of specific isotopes - Deuterium, Tritium, Carbon-14, Sulfur-35 and Oxygen-18 - as well as isotopic techniques - determination of surface mobility, steady state transient isotope kinetic analysis, and positron emission profiling.

  8. Group I Intron Internal Guide Sequence Binding Strength as a Component of Ribozyme Network Formation

    Directory of Open Access Journals (Sweden)

    Laura Elizabeth Satterwhite

    2016-09-01

    Full Text Available Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations. We provide evidence that the binding strength (KD between the 3-nucleotide internal guide sequence (IGS of one ribozyme and its complement in another is correlated to the catalytic ability of the ribozyme. This work demonstrates that one can begin to deconstruct the thermodynamic basis of information in prebiotic RNA systems.

  9. Pressure modulates the self-cleavage step of the hairpin ribozyme

    Science.gov (United States)

    Schuabb, Caroline; Kumar, Narendra; Pataraia, Salome; Marx, Dominik; Winter, Roland

    2017-03-01

    The ability of certain RNAs, denoted as ribozymes, to not only store genetic information but also catalyse chemical reactions gave support to the RNA world hypothesis as a putative step in the development of early life on Earth. This, however, might have evolved under extreme environmental conditions, including the deep sea with pressures in the kbar regime. Here we study pressure-induced effects on the self-cleavage of hairpin ribozyme by following structural changes in real-time. Our results suggest that compression of the ribozyme leads to an accelerated transesterification reaction, being the self-cleavage step, although the overall process is retarded in the high-pressure regime. The results reveal that favourable interactions between the reaction site and neighbouring nucleobases are strengthened under pressure, resulting therefore in an accelerated self-cleavage step upon compression. These results suggest that properly engineered ribozymes may also act as piezophilic biocatalysts in addition to their hitherto known properties.

  10. Pressure modulates the self-cleavage step of the hairpin ribozyme

    Science.gov (United States)

    Schuabb, Caroline; Kumar, Narendra; Pataraia, Salome; Marx, Dominik; Winter, Roland

    2017-01-01

    The ability of certain RNAs, denoted as ribozymes, to not only store genetic information but also catalyse chemical reactions gave support to the RNA world hypothesis as a putative step in the development of early life on Earth. This, however, might have evolved under extreme environmental conditions, including the deep sea with pressures in the kbar regime. Here we study pressure-induced effects on the self-cleavage of hairpin ribozyme by following structural changes in real-time. Our results suggest that compression of the ribozyme leads to an accelerated transesterification reaction, being the self-cleavage step, although the overall process is retarded in the high-pressure regime. The results reveal that favourable interactions between the reaction site and neighbouring nucleobases are strengthened under pressure, resulting therefore in an accelerated self-cleavage step upon compression. These results suggest that properly engineered ribozymes may also act as piezophilic biocatalysts in addition to their hitherto known properties. PMID:28358002

  11. Catalysis for Sustainable Development

    Indian Academy of Sciences (India)

    Issue front cover thumbnail. Volume 126, Issue 2. March 2014, pages 309-532. Catalysis for Sustainable Development. pp 309-309. Foreword · M Lakshmi Kantam K S Rama Rao · More Details Fulltext PDF. pp 311-317. Concept and progress in coupling of dehydrogenation and hydrogenation reactions through catalysts.

  12. Pollution Control by Catalysis

    DEFF Research Database (Denmark)

    Eriksen, Kim Michael; Fehrmann, Rasmus

    1998-01-01

    The report summarises the results of two years of collaboration supported by INTAS between Department of Chemistry,DTU,DK , IUSTI,Universite de Provence,FR, ICE/HT University 6of Patras,GR, and Boreskov Institute of Catalysis,RU.The project has been concerned with mechanistic studies of deNOx and...

  13. Anion-π catalysis.

    Science.gov (United States)

    Zhao, Yingjie; Beuchat, César; Domoto, Yuya; Gajewy, Jadwiga; Wilson, Adam; Mareda, Jiri; Sakai, Naomi; Matile, Stefan

    2014-02-05

    The introduction of new noncovalent interactions to build functional systems is of fundamental importance. We here report experimental and theoretical evidence that anion-π interactions can contribute to catalysis. The Kemp elimination is used as a classical tool to discover conceptually innovative catalysts for reactions with anionic transition states. For anion-π catalysis, a carboxylate base and a solubilizer are covalently attached to the π-acidic surface of naphthalenediimides. On these π-acidic surfaces, transition-state stabilizations up to ΔΔGTS = 31.8 ± 0.4 kJ mol(-1) are found. This value corresponds to a transition-state recognition of KTS = 2.7 ± 0.5 μM and a catalytic proficiency of 3.8 × 10(5) M(-1). Significantly increasing transition-state stabilization with increasing π-acidity of the catalyst, observed for two separate series, demonstrates the existence of "anion-π catalysis." In sharp contrast, increasing π-acidity of the best naphthalenediimide catalysts does not influence the more than 12 000-times weaker substrate recognition (KM = 34.5 ± 1.6 μM). Together with the disappearance of Michaelis-Menten kinetics on the expanded π-surfaces of perylenediimides, this finding supports that contributions from π-π interactions are not very important for anion-π catalysis. The linker between the π-acidic surface and the carboxylate base strongly influences activity. Insufficient length and flexibility cause incompatibility with saturation kinetics. Moreover, preorganizing linkers do not improve catalysis much, suggesting that the ideal positioning of the carboxylate base on the π-acidic surface is achieved by intramolecular anion-π interactions rather than by an optimized structure of the linker. Computational simulations are in excellent agreement with experimental results. They confirm, inter alia, that the stabilization of the anionic transition states (but not the neutral ground states) increases with the π-acidity of the

  14. Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme

    Science.gov (United States)

    Hiley, Shawna L.; Collins, Richard A.

    2001-01-01

    We have used hydroxyl radicals generated by decomposition of peroxynitrous acid to study Mg2+-dependent structure and folding of the Varkud satellite (VS) ribozyme. Protection from radical cleavage shows the existence of a solvent-inaccessible core, which includes nucleotides near two three-helix junctions, the kissing interaction between stem–loops I and V and other nucleotides, most of which have also been implicated as important for folding or activity. Kinetic folding experiments showed that the ribozyme folds very quickly, with the observed protections completely formed within 2 s of addition of MgCl2. In mutants that disrupt the kissing interaction or entirely remove stem–loop I, which contains the cleavage site, nucleotides in the three-helix junctions and a subset of those elsewhere remain protected. Unlike smaller ribozymes, the VS ribozyme retains a significant amount of structure in the absence of its substrate. Protections that depend on proper interaction between the substrate and the rest ribozyme map to a region previously proposed as the active site of the ribozyme and along both sides of helix II, identifying candidate sites of docking for the substrate helix. PMID:11574478

  15. Hotspots within hotspots? Hammerhead shark movements around Wolf Island, Galapagos Marine Reserve

    OpenAIRE

    Hearn, Alex; Ketchum, James; Klimley, A. Peter; Espinoza, Eduardo; Peñaherrera, Cesar

    2010-01-01

    Are pelagic species such as sharks and tuna distributed homogenously or heterogeneously in the oceans? Large assemblages of these species have been observed at seamounts and offshore islands in the eastern tropical Pacific, which are considered hotspots of pelagic biodiversity. Is the species distribution uniform at these hotspots or do species aggregate at a finer spatial scale at these sites? We employed three techniques to demonstrate that the aggregations of scalloped hammerhead sharks, S...

  16. Hotspots within hotspots? Hammerhead shark movements around Wolf Island, Galapagos Marine Reserve.

    Science.gov (United States)

    Hearn, Alex; Ketchum, James; Klimley, A Peter; Espinoza, Eduardo; Peñaherrera, Cesar

    2010-01-01

    Are pelagic species such as sharks and tuna distributed homogenously or heterogeneously in the oceans? Large assemblages of these species have been observed at seamounts and offshore islands in the eastern tropical Pacific, which are considered hotspots of pelagic biodiversity. Is the species distribution uniform at these hotspots or do species aggregate at a finer spatial scale at these sites? We employed three techniques to demonstrate that the aggregations of scalloped hammerhead sharks, Sphyrna lewini, and other pelagic species were confined to the southeastern corner of Wolf Island in the Galapagos Marine Reserve. Coded ultrasonic transmitters were placed on individuals at this site and at another aggregation site at Darwin Island, separated from Wolf by 40 km, and they were detected by monitors moored at the southeastern corner of Wolf Island and rarely by monitors deployed at other sites around the island. Hammerhead sharks, carrying depth-sensing continual transmitters, were tracked for two-day periods in a vessel and shown to reside a disproportionately large fraction of their time at the southeastern corner. Visual censuses were carried out seasonally at the eight monitor sites at Wolf Island, recording the abundance of one species of tuna, four species of jacks, and a number of other species. The highest diversity and abundance of these species occurred in the southeastern corner of the island. Our results support the use of hammerhead sharks as indicator and umbrella species for pelagic hotspots on a fine scale.

  17. The Hydrodynamics and Odorant Transport Phenomena of Olfaction in the Hammerhead Shark

    Science.gov (United States)

    Rygg, Alex; Craven, Brent

    2013-11-01

    The hammerhead shark possesses a unique head morphology that is thought to facilitate enhanced olfactory performance. The olfactory organs, located at the distal ends of the cephalofoil, contain numerous lamellae that increase the surface area for olfaction. Functionally, for the shark to detect chemical stimuli, water-borne odors must reach the olfactory sensory epithelium that lines these lamellae. Thus, odorant transport from the aquatic environment to the sensory epithelium is the first critical step in olfaction. Here we investigate the hydrodynamics and odorant transport phenomena of olfaction in the hammerhead shark based on an anatomically-accurate reconstruction of the head and olfactory chamber from high-resolution micro-CT and MRI scans of a cadaver specimen. Computational fluid dynamics (CFD) simulations of water flow in the reconstructed model reveal the external and internal hydrodynamics of olfaction during swimming. Odorant transport in the olfactory organ is investigated using a multi-scale approach, whereby molecular dynamics (MD) simulations are used to calculate odorant partition coefficients that are subsequently utilized in macro-scale CFD simulations of odorant deposition. The hydrodynamic and odorant transport results are used to elucidate several important features of olfactory function in the hammerhead shark.

  18. Response of the hammerhead shark olfactory epithelium to amino acid stimuli.

    Science.gov (United States)

    Tricas, Timothy C; Kajiura, Stephen M; Summers, Adam P

    2009-10-01

    Sharks and rays are highly sensitive to chemical stimuli in their natural environment but several hypotheses predict that hammerhead sharks, with their expanded head and enlarged olfactory epithelium, have particularly acute olfactory systems. We used the electro-olfactogram (EOG) technique to compare the relative response of the scalloped hammerhead shark (Sphyrna lewini) olfactory epithelium to 20 proteinogenic amino acids and determine the sensitivity for 6 amino acids. At micromolar concentrations, cysteine evoked the greatest EOG response which was approximately twice as large as that of alanine. The weakest response was obtained for proline followed by aspartic acid and isoleucine. The olfactory epithelium showed adaptation to sequential stimulation, and recovery was related to the inter-stimulus time period. Estimated EOG response thresholds were in the sub-nanomolar range for both alanine (9.2 x 10(-11) M) and cysteine (8.4 x 10(-10) M) and in the micromolar range for proline and serine. These thresholds from 10(-10) to 10(-6) M for the scalloped hammerhead shark are comparable or lower than those reported for other teleost and elasmobranch species. Future work should focus on binary and more complex compounds to test for competition and cross-adaptation for different classes of peripheral receptors, and their responses to molecules found in biologically relevant stimuli.

  19. Crossing lines: a multidisciplinary framework for assessing connectivity of hammerhead sharks across jurisdictional boundaries

    Science.gov (United States)

    Chin, A.; Simpfendorfer, C. A.; White, W. T.; Johnson, G. J.; McAuley, R. B.; Heupel, M. R.

    2017-04-01

    Conservation and management of migratory species can be complex and challenging. International agreements such as the Convention on Migratory Species (CMS) provide policy frameworks, but assessments and management can be hampered by lack of data and tractable mechanisms to integrate disparate datasets. An assessment of scalloped (Sphyrna lewini) and great (Sphyrna mokarran) hammerhead population structure and connectivity across northern Australia, Indonesia and Papua New Guinea (PNG) was conducted to inform management responses to CMS and Convention on International Trade in Endangered Species listings of these species. An Integrated Assessment Framework (IAF) was devised to systematically incorporate data across jurisdictions and create a regional synopsis, and amalgamated a suite of data from the Australasian region. Scalloped hammerhead populations are segregated by sex and size, with Australian populations dominated by juveniles and small adult males, while Indonesian and PNG populations included large adult females. The IAF process introduced genetic and tagging data to produce conceptual models of stock structure and movement. Several hypotheses were produced to explain stock structure and movement patterns, but more data are needed to identify the most likely hypothesis. This study demonstrates a process for assessing migratory species connectivity and highlights priority areas for hammerhead management and research.

  20. Crossing lines: a multidisciplinary framework for assessing connectivity of hammerhead sharks across jurisdictional boundaries.

    Science.gov (United States)

    Chin, A; Simpfendorfer, C A; White, W T; Johnson, G J; McAuley, R B; Heupel, M R

    2017-04-21

    Conservation and management of migratory species can be complex and challenging. International agreements such as the Convention on Migratory Species (CMS) provide policy frameworks, but assessments and management can be hampered by lack of data and tractable mechanisms to integrate disparate datasets. An assessment of scalloped (Sphyrna lewini) and great (Sphyrna mokarran) hammerhead population structure and connectivity across northern Australia, Indonesia and Papua New Guinea (PNG) was conducted to inform management responses to CMS and Convention on International Trade in Endangered Species listings of these species. An Integrated Assessment Framework (IAF) was devised to systematically incorporate data across jurisdictions and create a regional synopsis, and amalgamated a suite of data from the Australasian region. Scalloped hammerhead populations are segregated by sex and size, with Australian populations dominated by juveniles and small adult males, while Indonesian and PNG populations included large adult females. The IAF process introduced genetic and tagging data to produce conceptual models of stock structure and movement. Several hypotheses were produced to explain stock structure and movement patterns, but more data are needed to identify the most likely hypothesis. This study demonstrates a process for assessing migratory species connectivity and highlights priority areas for hammerhead management and research.

  1. RNA catalysis through compartmentalization

    Science.gov (United States)

    Strulson, Christopher A.; Molden, Rosalynn C.; Keating, Christine D.; Bevilacqua, Philip C.

    2012-11-01

    RNA performs important cellular functions in contemporary life forms. Its ability to act both as a catalyst and a storage mechanism for genetic information is also an important part of the RNA world hypothesis. Compartmentalization within modern cells allows the local concentration of RNA to be controlled and it has been suggested that this was also important in early life forms. Here, we mimic intracellular compartmentalization and macromolecular crowding by partitioning RNA in an aqueous two-phase system (ATPS). We show that the concentration of RNA is enriched by up to 3,000-fold in the dextran-rich phase of a polyethylene glycol/dextran ATPS and demonstrate that this can lead to approximately 70-fold increase in the rate of ribozyme cleavage. This rate enhancement can be tuned by the relative volumes of the two phases in the ATPS. Our observations support the importance of compartmentalization in the attainment of function in an RNA World as well as in modern biology.

  2. Magnetic Catalysis in Graphene

    CERN Document Server

    Winterowd, Christopher; Zafeiropoulos, Savvas

    2015-01-01

    One of the most important developments in condensed matter physics in recent years has been the discovery and characterization of graphene. A two-dimensional layer of Carbon arranged in a hexagonal lattice, graphene exhibits many interesting electronic properties, most notably that the low energy excitations behave as massless Dirac fermions. These excitations interact strongly via the Coulomb interaction and thus non-perturbative methods are necessary. Using methods borrowed from lattice QCD, we study the graphene effective theory in the presence of an external magnetic field. Graphene, along with other $(2+1)$-dimensional field theories, has been predicted to undergo spontaneous breaking of flavor symmetry including the formation of a gap as a result of the external magnetic field. This phenomenon is known as magnetic catalysis. Our study investigates magnetic catalysis using a fully non-perturbative approach.

  3. Catalysis and biocatalysis program

    Science.gov (United States)

    Ingham, J. D.

    1993-01-01

    This final report presents a summary of research activities and accomplishments for the Catalysis and Biocatalysis Program, which was renamed the Biological and Chemical Technologies Research (BCTR) Program, currently of the Advanced Industrial Concepts Division (AICD), Office of Industrial Technologies of the Department of Energy (DOE). The Program was formerly under the Division of Energy Conversion and Utilization Technologies (ECUT) until the DOE reorganization in April, 1990. The goals of the BCTR Program are consistent with the initial ECUT goals, but represent an increased effort toward advances in chemical and biological technology transfer. In addition, the transition reflects a need for the BCTR Program to assume a greater R&D role in chemical catalysis as well as a need to position itself for a more encompassing involvement in a broader range of biological and chemical technology research. The mission of the AICD is to create a balanced Program of high risk, long-term, directed interdisciplinary research and development that will improve energy efficiency and enhance fuel flexibility in the industrial sector. Under AICD, the DOE Catalysis and Biocatalysis Program sponsors research and development in furthering industrial biotechnology applications and promotes the integrated participation of universities, industrial companies, and government research laboratories.

  4. Inducible knockdown of Plasmodium gene expression using the glmS ribozyme.

    Directory of Open Access Journals (Sweden)

    Parichat Prommana

    Full Text Available Conventional reverse genetic approaches for study of Plasmodium malaria parasite gene function are limited, or not applicable. Hence, new inducible systems are needed. Here we describe a method to control P. falciparum gene expression in which target genes bearing a glmS ribozyme in the 3' untranslated region are efficiently knocked down in transgenic P. falciparum parasites in response to glucosamine inducer. Using reporter genes, we show that the glmS ribozyme cleaves reporter mRNA in vivo leading to reduction in mRNA expression following glucosamine treatment. Glucosamine-induced ribozyme activation led to efficient reduction of reporter protein, which could be rapidly reversed by removing the inducer. The glmS ribozyme was validated as a reverse-genetic tool by integration into the essential gene and antifolate drug target dihydrofolate reductase-thymidylate synthase (PfDHFR-TS. Glucosamine treatment of transgenic parasites led to rapid and efficient knockdown of PfDHFR-TS mRNA and protein. PfDHFR-TS knockdown led to a growth/arrest mutant phenotype and hypersensitivity to pyrimethamine. The glmS ribozyme may thus be a tool for study of essential genes in P. falciparum and other parasite species amenable to transfection.

  5. A novel chimeric ribozyme vector produces potent inhibition of ICAM-1 expression on ischemic vascular endothelium.

    Science.gov (United States)

    Sonnenday, Christopher J; Warren, Daniel S; Cooke, Sara K; Dietz, Harry C; Montgomery, Robert A

    2004-12-01

    Inhibition of intercellular adhesion molecule-1 (ICAM-1) expression can ameliorate the inflammation induced by ischemia-reperfusion injury (IRI) in animal models. However, current strategies to reduce ICAM-1 expression have been limited by the lack of stability, poor specificity, and the transient nature of synthesized regulatory molecules (antisense/ribozyme). A chimeric expression vector was generated by fusing a ribozyme targeting sequence against ICAM-1 to stabilizing stem-loop structures and nuclear localization signals that are components of endogenous U1 small nuclear RNA. Oligonucleotide scanning was used to predict accessible sites for targeting within the rat ICAM-1 transcript. Efficacy of the chimeric ribozyme vector was tested by transfection of rat aortic endothelial (RAE) cells (in vitro) and intraportal delivery in a rat hepatic IRI model (in vivo). Transfection of RAE cells with the chimeric ribozyme vector produced potent and specific inhibition of ICAM-1 mRNA and protein levels by >65%. This reduction in ICAM-1 expression was accompanied by a proportional decrease in neutrophil adhesion to RAE cells. In vivo intraportal delivery of the chimeric targeting vector to rats sustaining hepatic IRI produced a marked reduction in ICAM-1 expression on liver endothelium after reperfusion. A chimeric ribozyme vector effectively inhibited ICAM-1 expression in vascular endothelial cells and in rat liver following IRI, demonstrating a novel gene targeting technique that may be ideally suited to clinical applications aimed at ameliorating IRI. Copyright 2004 John Wiley & Sons, Ltd.

  6. Flanking sequences with an essential role in hydrolysis of a self-cleaving group I-like ribozyme

    DEFF Research Database (Denmark)

    Einvik, C; Nielsen, Henrik; Nour, R

    2000-01-01

    DiGIR1 is a group I-like ribozyme derived from the mobile twin ribozyme group I intron DiSSU1 in the nuclear ribosomal DNA of the myxomycete Didymium iridis. This ribozyme is responsible for intron RNA processing in vitro and in vivo at two internal sites close to the 5'-end of the intron endo......-nuclease open reading frame and is a unique example of a group I ribozyme with an evolved biological function. DiGIR1 is the smallest functional group I ribozyme known from nature and has an unusual core organization including the 6 bp P15 pseudoknot. Here we report results of functional and structural analyses...

  7. Identification of young-of-the-year great hammerhead shark Sphyrna mokarran in northern Florida and South Carolina.

    Science.gov (United States)

    Barker, A M; Frazier, B S; Bethea, D M; Gold, J R; Portnoy, D S

    2017-08-01

    Two sharks, visually identified in the field as young-of-the-year (YOY) scalloped hammerhead Sphyrna lewini, were identified as great hammerhead Sphyrna mokarran based on nuclear-encoded single nucleotide polymorphisms (SNP) and sequences of mtDNA. Individuals were captured and released in Bulls Bay, SC, and Saint Joseph Bay, FL, in 2013 and 2014, respectively. These findings indicate S. mokarran may be pupping in or around these areas and highlight new regions that may be a productive focus for future research on early life history of S. mokarran. © 2017 The Fisheries Society of the British Isles.

  8. Zeolite catalysis: technology

    Energy Technology Data Exchange (ETDEWEB)

    Heinemann, H.

    1980-07-01

    Zeolites have been used as catalysts in industry since the early nineteen sixties. The great majority of commercial applications employ one of three zeolite types: zeolite Y; Mordenite; ZSM-5. By far the largest use of zeolites is in catalytic cracking, and to a lesser extent in hydrocracking. This paper reviews the rapid development of zeolite catalysis and its application in industries such as: the production of gasoline by catalytic cracking of petroleum; isomerization of C/sub 5/ and C/sub 6/ paraffin hydrocarbons; alkylation of aromatics with olefins; xylene isomerization; and conversion of methanol to gasoline.

  9. Advances in Catalysis by Heteropolyacids

    Science.gov (United States)

    Kozhevnikov, I. V.

    1987-09-01

    The advances in acid catalysis by heteropolyacids are examined and data on the acidity of heteropolyacids are surveyed. The characteristics of homogeneous and heterogeneous acid catalysis by heteropolyacids are discussed and its applied aspects are noted. The bibliography includes 116 references.

  10. Catalysis and prebiotic RNA synthesis

    Science.gov (United States)

    Ferris, James P.

    1993-01-01

    The essential role of catalysis for the origins of life is discussed. The status of the prebiotic synthesis of 2',5'- and 3'5'-linked oligomers of RNA is reviewed. Examples of the role of metal ion and mineral catalysis in RNA oligomer formation are discussed.

  11. DNA-based hybrid catalysis

    NARCIS (Netherlands)

    Rioz-Martínez, Ana; Roelfes, Gerard

    In the past decade, DNA-based hybrid catalysis has merged as a promising novel approach to homogeneous (asymmetric) catalysis. A DNA hybrid catalysts comprises a transition metal complex that is covalently or supramolecularly bound to DNA. The chiral microenvironment and the second coordination

  12. Maternal offloading of organochlorine contaminants in the yolk-sac placental scalloped hammerhead shark (Sphyrna lewini).

    Science.gov (United States)

    Lyons, Kady; Adams, Douglas H

    2015-04-01

    Elasmobranchs are a group of animals that typically occupy upper trophic levels in food webs and have a propensity to accumulate high contaminant concentrations. To date, few studies have investigated maternal offloading processes in sharks, despite the fact that this process represents a substantial source of exposure for young sharks and is a significant pathway for contaminant redistribution within marine ecosystems. Comparable to mammalian systems, scalloped hammerhead sharks (Sphyrna lewini) utilize a yolk-sac placental strategy to nourish young in utero, which may allow females to transfer contaminants to young. Organic contaminants (PCBs and chlorinated pesticides) were measured in livers of both females and males from several age classes that were collected from U.S. Atlantic waters, including two near-term pregnant females and their embryos. Adult female hammerheads (n = 3) were found to have lower levels of PCBs compared to the younger, adult male (mean ± SD, 11.1 ± 1.0 vs. 22.8 μg g(-1) lw), but had substantially higher concentrations of pesticides (4.1 ± 0.9 vs. 1.9 μg g(-1) lw). Embryos from the two litters (n = 36) had similar levels of summed organic contaminant concentrations (4.6 ± 0.9 μg g(-1) lw) and pregnant females were estimated to offload approximately 0.03-2.3% of their hepatic contaminant load to offspring. While the potential health impacts of these transferred contaminants is unknown, this is the first study to demonstrate that scalloped hammerheads are exposed to a substantial amount of contaminants prior to birth and document maternal offloading of organochlorines in a pseudo-placental shark species. Therefore, future research should continue to investigate the potential adverse effects these contaminants have on elasmobranch physiology.

  13. Purification and Identification of Antioxidant Peptides from Protein Hydrolysate of Scalloped Hammerhead (Sphyrna lewini Cartilage

    Directory of Open Access Journals (Sweden)

    Xue-Rong Li

    2017-03-01

    Full Text Available The aim of this study was to purify and identify peptides with antioxidant properties from protein hydrolysate of scalloped hammerhead (Sphyrna lewini cartilage. Cartilaginous proteins of the scalloped hammerhead were extracted by guanidine hydrochloride, and three antioxidant peptides, named enzymolysis peptide of scalloped hammerhead cartilage A (SCPE-A, SCPE-B and SCPE-C, were subsequently isolated from the hydrolysate of the cartilaginous proteins using ultrafiltration and chromatography. The amino acid sequences of SCPE-A, SCPE-B and SCPE-C were identified as Gly-Pro-Glu (GPE, Gly-Ala-Arg-Gly-Pro-Gln (GARGPQ, and Gly-Phe-Thr-Gly-Pro-Pro-Gly-Phe-Asn-Gly (GFTGPPGFNG, with molecular weights of 301.30 Da, 584.64 Da and 950.03 Da, respectively. As per in vitro activity testing, SCPE-A, SCPE-B and SCPE-C exhibited strong scavenging activities on 2,2-diphenyl-1-picrylhydrazyl radicals (DPPH• (half elimination ratio (EC50 2.43, 2.66 and 1.99 mg/mL, hydroxyl radicals (HO• (EC50 0.28, 0.21 and 0.15 mg/mL, 2,2′-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radicals (ABTS+• (EC50 0.24, 0.18 and 0.29 mg/mL, and superoxide anion radicals ( O 2 − • (EC50 0.10, 0.14 and 0.11 mg/mL. In addition, SCPE-A showed inhibition activity similar to butylated hydroxytoluene (BHT in lipid peroxidation in a linoleic acid model system. The amino acid residues of Gly, Pro and Phe could positively influence the antioxidant activities of GPE, GARGPQ and GFTGPPGFNG. These results suggested that GPE, GARGPQ and GFTGPPGFNG might serve as potential antioxidants and be used as food additives and functional foods.

  14. Long distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments

    OpenAIRE

    Veeraraghavan, Narayanan; Bevilacqua, Philip C.; Hammes-Schiffer, Sharon

    2010-01-01

    The hepatitis delta virus (HDV) ribozyme is a small self-cleaving RNA with a compact tertiary structure and buried active site that is important in the life cycle of the virus. The ribozyme’s function in nature is to cleave an internal phosphodiester bond and linearize concatemers during rolling circle replication. Crystal structures of the ribozyme have been solved in both pre-cleaved and post-cleaved (product) forms and reveal an intricate network of interactions that conspire to catalyze b...

  15. The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

    Czech Academy of Sciences Publication Activity Database

    Šefčíková, J.; Krasovská, Maryna V.; Šponer, Jiří; Walter, N.G.

    2007-01-01

    Roč. 35, č. 6 (2007), s. 1933-1946 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400550701; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : hepatitis delta virus * molecular dynamics * self-cleavage Subject RIV: BO - Biophysics Impact factor: 6.954, year: 2007

  16. 76 FR 72891 - Endangered and Threatened Wildlife; 90-Day Finding on a Petition To List the Scalloped Hammerhead...

    Science.gov (United States)

    2011-11-28

    ... standards on extinction risk and impacts or threats discussed above. Distribution and Life History of the... WildEarth Guardians and Friends of Animals to list the scalloped hammerhead shark (Sphyrna lewini) as..., or DPS is ``endangered'' if it is in danger of extinction throughout all or a significant portion of...

  17. 78 FR 24701 - Endangered and Threatened Wildlife; 90-Day Finding on Petitions To List the Great Hammerhead...

    Science.gov (United States)

    2013-04-26

    ... indicate that hypoxic occurrences and dead zones, a result of growing human populations, urban pollution... dead zones (Driggers and Hoffmayer, personal communication, 2013). In addition, both petitions assert... al., 2011; Bester, n.d.). In the western Atlantic Ocean, the great hammerhead range extends from...

  18. Simulations of chemical catalysis

    Science.gov (United States)

    Smith, Gregory K.

    This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows. Project 1 - Bacterial Enzyme SpvC The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a beta-elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31 G(d,p) level of theory. The truncated model suggested the reaction proceeds via a single transition state. After including the enzyme environment in ab initio QM/MM studies, it was found to proceed via an E1cB-like pathway, in which the carbanion intermediate is stabilized by an enzyme oxyanion hole provided by Lys104 and Tyr158 of SpvC. Project 2 - Human Enzyme CDK2 Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensable role in cellular signaling, and their malfunctioning is implicated in many diseases. Ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a

  19. Population and individual foraging patterns of two hammerhead sharks using carbon and nitrogen stable isotopes.

    Science.gov (United States)

    Loor-Andrade, P; Galván-Magaña, F; Elorriaga-Verplancken, F R; Polo-Silva, C; Delgado-Huertas, A

    2015-05-15

    Individual foraging behavior is an important variable of predators commonly studied at the population level. Some hammerhead shark species play a significant role in the marine ecosystem as top consumers. In this context, stable isotope analysis allows us to infer some ecological metrics and patterns that cannot usually be obtained using traditional methods. We determined the isotopic composition (δ(13)C and δ(15)N values) of dorsal muscle and vertebrae of Sphyrna lewini and Sphyrna zygaena using a continuous-flow system consisting of an elemental analyzer combined with a Delta Plus XL mass spectrometer. Foraging variability by sex and by individual was inferred from the isotopic values. There were no significant differences in the isotopic values of muscle samples between sexes, but there were differences between species. The trophic niche breadth of the two species was similar and overlap was low. A low niche overlap was observed between S. lewini individual vertebrae. We found differences in the δ(15)N values of S. zygaena vertebrae, with lower values in the first group of samples. Despite these hammerhead shark species inhabiting the same area, there was low trophic niche overlap between species and individuals, due to different individual foraging strategies, according to the carbon and nitrogen isotopic profiles obtained. The use of tissues that retain lifetime isotopic information is useful to complement studies on trophic ecology. Copyright © 2015 John Wiley & Sons, Ltd.

  20. Fishers' ecological knowledge of smalleye hammerhead, Sphyrna tudes , in a tropical estuary

    Directory of Open Access Journals (Sweden)

    Vinicius J. Giglio

    Full Text Available ABSTRACT Coastal hammerheads have suffered from overexploitation and environmental degradation. We interviewed 79 artisanal fishers to verify fishery aspects, temporal changes in catches and biological aspects of the smalleye hammerhead, Sphyrna tudes , in a marine protected area on Abrolhos Bank, Brazil. Data were compared between three generations of fishers: young, middle-aged and old. Fishers' age varied between 17 and 88 years. We verified significant reductions in the weight of individuals caught by younger fishers. The main types of fishing gear used to catch S. tudes were gill nets and longlines. Overfishing through gill nets and trawl fisheries were mentioned as the cause of S. tudes population collapse in the region. The shark's diet as reported by fishers consisted of fish, crab and shrimp; austral summer was the reproductive season. A strong similarity was verified between fishers' knowledge and biological data. We suggest as plausible strategies to conserve the local population of S. tudes the reduction of net fisheries impact through zoning and establishment of no take areas. These steps can help to initiate the recovery of this depleted species.

  1. Conservation Genetics of the Scalloped Hammerhead Shark in the Pacific Coast of Colombia.

    Science.gov (United States)

    Quintanilla, Sonia; Gómez, Alberto; Mariño-Ramírez, Camila; Sorzano, Carolina; Bessudo, Sandra; Soler, German; Bernal, Jaime E; Caballero, Susana

    2015-01-01

    Previous investigations of the population genetics of the scalloped hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have lacked information about nursery areas. Such areas are key to promoting conservation initiatives that can protect young sharks from threats such as overfishing. Here, we investigated the genetic diversity, phylogeography, and connectivity of S. lewini found in 3 areas of Colombia's Pacific coast: around Malpelo Island and in 2 National Natural Parks on the Colombian Pacific mainland (Sanquianga and Ensenada de Utría). We analyzed mtDNA control region (CR) sequences and genotyped 15 microsatellite loci in 137 samples of adults and juveniles. The mtDNA analyses showed haplotypes shared between the Colombian Pacific individuals sampled in this investigation and other areas in the Eastern Tropical Pacific, the Indo-Pacific, and with sequences previously reported in Colombia (Buenaventura Port), as well as 4 unique haplotypes. Population assignment and paternity analyses detected 3 parent-offspring pairs between Malpelo and Sanquianga and 1 between Malpelo and Utría. These results indicate high genetic connectivity between Malpelo Island and the Colombian Pacific coast, suggesting that these 2 areas are nurseries for S. lewini. This is, to our knowledge, the first evidence of nursery areas identified for the scalloped hammerhead shark anywhere in the world. Additional conservation planning may be required to protect these nursery habitats of this endangered shark species. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. The complement system of elasmobranches revealed by liver transcriptome analysis of a hammerhead shark, Sphyrna zygaena.

    Science.gov (United States)

    Goshima, Masayuki; Sekiguchi, Reo; Matsushita, Misao; Nonaka, Masaru

    2016-08-01

    Comprehensive studies of the complement genes in basal vertebrates have revealed that cyclostomes have apparently primitive complement systems whereas bony fish have well-developed complement systems comparable to those of mammals. Here we have performed liver transcriptome analysis of a hammerhead shark, Sphyrna zygaeana, to elucidate the early history of vertebrate complement evolution. Identified genes were; one C1qB, one C1r, one C1s, one MASP-1/-3, one MASP-2, two factor B/C2, one C3, three C4, one C5, one C6, one C7, one C8A, three C8B, one C8G, one C9, two factor I and one S protein. No MBL, ficolin, C1qA or C1qC were found. These results indicate that the lectin, classical, alternative and lytic pathways were established in the common ancestor of jawed vertebrates. In addition to the absence of MBL and ficolin, the MASP transcripts lacked the serine protease domain, suggesting that the lectin pathway was lost in the hammerhead shark lineage. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Asymmetric trienamine catalysis: new opportunities in amine catalysis.

    Science.gov (United States)

    Kumar, Indresh; Ramaraju, Panduga; Mir, Nisar A

    2013-02-07

    Amine catalysis, through HOMO-activating enamine and LUMO-activating iminium-ion formation, is receiving increasing attention among other organocatalytic strategies, for the activation of unmodified carbonyl compounds. Particularly, the HOMO-raising activation concept has been applied to the greatest number of asymmetric transformations through enamine, dienamine, and SOMO-activation strategies. Recently, trienamine catalysis, an extension of amine catalysis, has emerged as a powerful tool for synthetic chemists with a novel activation strategy for polyenals/polyenones. In this review article, we discuss the initial developments of trienamine catalysis for highly asymmetric Diels-Alder reactions with different dienophiles and emerging opportunities for other types of cycloadditions and cascade reactions.

  4. Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics.

    Science.gov (United States)

    Bingaman, Jamie L; Messina, Kyle J; Bevilacqua, Philip C

    2017-05-01

    Reaction kinetics on the millisecond timescale pervade the protein and RNA fields. To study such reactions, investigators often perturb the system with abiological solution conditions or substrates in order to slow the rate to timescales accessible by hand mixing; however, such perturbations can change the rate-limiting step and obscure key folding and chemical steps that are found under biological conditions. Mechanical methods for collecting data on the millisecond timescale, which allow these perturbations to be avoided, have been developed over the last few decades. These methods are relatively simple and can be conducted on affordable and commercially available instruments. Here, we focus on using the rapid quench-flow technique to study the fast reaction kinetics of RNA enzymes, or ribozymes, which often react on the millisecond timescale under biological conditions. Rapid quench of ribozymes is completely parallel to the familiar hand-mixing approach, including the use of radiolabeled RNAs and fractionation of reactions on polyacrylamide gels. We provide tips on addressing and preventing common problems that can arise with the rapid-quench technique. Guidance is also offered on ensuring the ribozyme is properly folded and fast-reacting. We hope that this article will facilitate the broader use of rapid-quench instrumentation to study fast-reacting ribozymes under biological reaction conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. The glmS Ribozyme Cofactor is a General Acid-Base Catalyst

    Science.gov (United States)

    Viladoms, Julia; Fedor, Martha J.

    2012-01-01

    The glmS ribozyme is the first natural self-cleaving ribozyme known to require a cofactor. The D-glucosamine-6-phosphate (GlcN6P) cofactor has been proposed to serve as a general acid, but its role in the catalytic mechanism has not been established conclusively. We surveyed GlcN6P-like molecules for their ability to support self-cleavage of the glmS ribozyme and found a strong correlation between the pH dependence of the cleavage reaction and the intrinsic acidity of the cofactors. For cofactors with low binding affinities the contribution to rate enhancement was proportional to their intrinsic acidity. This linear free-energy relationship between cofactor efficiency and acid dissociation constants is consistent with a mechanism in which the cofactors participate directly in the reaction as general acid-base catalysts. A high value for the Brønsted coefficient (β ~ 0.7) indicates that a significant amount of proton transfer has already occurred in the transition state. The glmS ribozyme is the first self-cleaving RNA to use an exogenous acid-base catalyst. PMID:23113700

  6. The structure of a nucleolytic ribozyme that employs a catalytic metal ion.

    Science.gov (United States)

    Liu, Yijin; Wilson, Timothy J; Lilley, David M J

    2017-05-01

    The TS ribozyme (originally called "twister sister") is a catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasihelical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an inner-sphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose that the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.

  7. DNA-based hybrid catalysis.

    Science.gov (United States)

    Rioz-Martínez, Ana; Roelfes, Gerard

    2015-04-01

    In the past decade, DNA-based hybrid catalysis has merged as a promising novel approach to homogeneous (asymmetric) catalysis. A DNA hybrid catalysts comprises a transition metal complex that is covalently or supramolecularly bound to DNA. The chiral microenvironment and the second coordination sphere interactions provided by the DNA are key to achieve high enantioselectivities and, often, additional rate accelerations in catalysis. Nowadays, current efforts are focused on improved designs, understanding the origin of the enantioselectivity and DNA-induced rate accelerations, expanding the catalytic scope of the concept and further increasing the practicality of the method for applications in synthesis. Herein, the recent developments will be reviewed and the perspectives for the emerging field of DNA-based hybrid catalysis will be discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. A Survey Course in Catalysis.

    Science.gov (United States)

    Skaates, J. M.

    1982-01-01

    Describes a 10-week survey course in catalysis for chemical engineering and chemistry students designed to show how modern chemistry and chemical engineering interact in the ongoing development of industrial catalysts. Includes course outline and instructional strategies. (Author/JN)

  9. Editorial: Nanoscience makes catalysis greener

    KAUST Repository

    Polshettiwar, Vivek

    2012-01-09

    Green chemistry by nanocatalysis: Catalysis is a strategic field of science because it involves new ways of meeting energy and sustainability challenges. The concept of green chemistry, which makes the science of catalysis even more creative, has become an integral part of sustainability. This special issue is at the interface of green chemistry and nanocatalysis, and features excellent background articles as well as the latest research results. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Investigating single and multiple species fisheries management: stock status evaluation of hammerhead (Sphyrna spp.) sharks in the western North Atlantic Ocean and Gulf of Mexico.

    OpenAIRE

    Hayes, Christopher Glenn

    2007-01-01

    Three hammerhead sharks (Sphyrna spp.) are currently managed as part of the large coastal shark complex in the United States. Including multiple species in an assessment ignores the different stock dynamics of each individual species within the complex due to different life histories. This study completed individual assessments of scalloped (S. lewini), great (S. mokarran), and smooth (S. zygaena) hammerhead sharks in the U.S. Atlantic Ocean and Gulf of Mexico. Combined data for all three ...

  11. Enhanced Micellar Catalysis LDRD.

    Energy Technology Data Exchange (ETDEWEB)

    Betty, Rita G.; Tucker, Mark D; Taggart, Gretchen; Kinnan, Mark K.; Glen, Crystal Chanea; Rivera, Danielle; Sanchez, Andres; Alam, Todd Michael

    2012-12-01

    The primary goals of the Enhanced Micellar Catalysis project were to gain an understanding of the micellar environment of DF-200, or similar liquid CBW surfactant-based decontaminants, as well as characterize the aerosolized DF-200 droplet distribution and droplet chemistry under baseline ITW rotary atomization conditions. Micellar characterization of limited surfactant solutions was performed externally through the collection and measurement of Small Angle X-Ray Scattering (SAXS) images and Cryo-Transmission Electron Microscopy (cryo-TEM) images. Micellar characterization was performed externally at the University of Minnesotas Characterization Facility Center, and at the Argonne National Laboratory Advanced Photon Source facility. A micellar diffusion study was conducted internally at Sandia to measure diffusion constants of surfactants over a concentration range, to estimate the effective micelle diameter, to determine the impact of individual components to the micellar environment in solution, and the impact of combined components to surfactant phase behavior. Aerosolized DF-200 sprays were characterized for particle size and distribution and limited chemical composition. Evaporation rates of aerosolized DF-200 sprays were estimated under a set of baseline ITW nozzle test system parameters.

  12. Complete mitochondrial genome of the scalloped hammerhead Sphyrna lewini (Carcharhiniformes: Sphyrnidae).

    Science.gov (United States)

    Chen, Xiao; Xiang, Dan; Xu, Yuziwei; Shi, Xiaofang

    2015-08-01

    The complete mitochondrial genome of the endangered scalloped hammerhead Sphyrna lewini was firstly determined in this study. It is 16,726 bp in length with the typical gene composition and orders in vertebrates. The overall base composition is 31.4% A, 26.3% C, 13.2% G and 29.1% T. Two start codon (ATG and GTG) and three stop codon (TAG, AGA and TAA/TA/T) patterns were found in protein-coding genes. Except for the tRNA-Ser2, the remaining 21 tRNAs can be folded into the typical cloverleaf structure. The control region possess the highest A + T content (66.1%) and lowest G content (12.6%) among all mitochondrial partitions.

  13. Great hammerhead sharks swim on their side to reduce transport costs.

    Science.gov (United States)

    Payne, Nicholas L; Iosilevskii, Gil; Barnett, Adam; Fischer, Chris; Graham, Rachel T; Gleiss, Adrian C; Watanabe, Yuuki Y

    2016-07-26

    Animals exhibit various physiological and behavioural strategies for minimizing travel costs. Fins of aquatic animals play key roles in efficient travel and, for sharks, the functions of dorsal and pectoral fins are considered well divided: the former assists propulsion and generates lateral hydrodynamic forces during turns and the latter generates vertical forces that offset sharks' negative buoyancy. Here we show that great hammerhead sharks drastically reconfigure the function of these structures, using an exaggerated dorsal fin to generate lift by swimming rolled on their side. Tagged wild sharks spend up to 90% of time swimming at roll angles between 50° and 75°, and hydrodynamic modelling shows that doing so reduces drag-and in turn, the cost of transport-by around 10% compared with traditional upright swimming. Employment of such a strongly selected feature for such a unique purpose raises interesting questions about evolutionary pathways to hydrodynamic adaptations, and our perception of form and function.

  14. New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewini.

    Science.gov (United States)

    Nance, Holly A; Daly-Engel, Toby S; Marko, Peter B

    2009-05-01

    We isolated 15 microsatellite markers for the scalloped hammerhead shark, Sphyrna lewini. Loci were tested on 80 specimens of S. lewini from four Eastern Pacific samples. The number of alleles per locus ranged from 6 to 31 (mean = 14). Observed and expected levels of heterozygosity per locus ranged from 0.39 to 0.91 (mean = 0.70) and from 0.54 to 0.90 (mean = 0.76), respectively. No pairs of loci were in gametic disequilibrium after Bonferroni correction of α. One locus showed significantly lower heterozygosity than expected under Hardy-Weinberg proportions in two populations, possibly caused by null alleles. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

  15. Magnetic catalysis in flavored ABJM

    Energy Technology Data Exchange (ETDEWEB)

    Jokela, Niko; Ramallo, Alfonso V. [Departamento de Física de Partículas, Universidade de Santiago de Compostela and Instituto Galego de Física de Altas Enerxías (IGFAE), E-15782 Santiago de Compostela (Spain); Zoakos, Dimitrios [Centro de Física do Porto and Departamento de Física e Astronomia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal)

    2014-02-05

    We study the magnetic catalysis of chiral symmetry breaking in the ABJM Chern-Simons matter theory with unquenched flavors in the Veneziano limit. We consider a magnetized D6-brane probe in the background of a flavored black hole which includes the backreaction of massless smeared flavors in the ABJM geometry. We find a holographic realization for the running of the quark mass due to the dynamical flavors. We compute several thermodynamic quantities of the brane probe and analyze the effects of the dynamical quarks on the fundamental condensate and on the phase diagram of the model. The dynamical flavors have an interesting effect on the magnetic catalysis. At zero temperature and fixed magnetic field, the magnetic catalysis is suppressed for small bare quark masses whereas it is enhanced for large values of the mass. When the temperature is non-zero there is a critical magnetic field, above which the magnetic catalysis takes place. This critical magnetic field decreases with the number of flavors, which we interpret as an enhancement of the catalysis.

  16. Fundamental insights into interfacial catalysis.

    Science.gov (United States)

    Gong, Jinlong; Bao, Xinhe

    2017-04-03

    Surface and interfacial catalysis plays a vital role in chemical industries, electrochemistry and photochemical reactions. The challenges of modern chemistry are to optimize the chemical reaction processes and understand the detailed mechanism of chemical reactions. Since the early 1960s, the foundation of surface science systems has allowed the study of surface and interfacial phenomena on atomic/molecular level, and thus brought a number of significant developments to fundamental and technological processes, such as catalysis, material science and biochemistry, just to name a few. This themed issue describes the recent advances and developments in the fundamental understanding of surface and interfacial catalysis, encompassing areas of knowledge from metal to metal oxide, carbide, graphene, hexagonal boron nitride, and transition metal dichalcogenides under ultrahigh vacuum conditions, as well as under realistic reaction conditions.

  17. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    The employment of metal salts is quite limited in asymmetric catalysis, although it would provide an additional arsenal of safe and inexpensive reagents to create molecular functions with high optical purity. Cation chelation by polyethers increases the salts' solubility in conventional organic...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...... and KCN, are selectively bound to the catalyst, providing exceptionally high enantioselectivities for kinetic resolutions, elimination reactions (fluoride base), and Strecker synthesis (cyanide nucleophile). Asymmetric cation-binding catalysis was recently expanded to silicon-based reagents, enabling...

  18. Operando research in heterogeneous catalysis

    CERN Document Server

    Groot, Irene

    2017-01-01

    This book is devoted to the emerging field of techniques for visualizing atomic-scale properties of active catalysts under actual working conditions, i.e. high gas pressures and high temperatures. It explains how to understand these observations in terms of the surface structures and dynamics and their detailed interplay with the gas phase. This provides an important new link between fundamental surface physics and chemistry, and applied catalysis. The book explains the motivation and the necessity of operando studies, and positions these with respect to the more traditional low-pressure investigations on the one hand and the reality of industrial catalysis on the other. The last decade has witnessed a rapid development of new experimental and theoretical tools for operando studies of heterogeneous catalysis. The book has a strong emphasis on the new techniques and illustrates how the challenges introduced by the harsh, operando conditions are faced for each of these new tools. Therefore, one can also read th...

  19. Fusarium solani fungal infection of the lateral line canal system in captive scalloped hammerhead sharks (Sphyrna lewini) in Hawaii.

    Science.gov (United States)

    Crow, G L; Brock, J A; Kaiser, S

    1995-10-01

    Two of five scalloped hammerhead sharks (Sphyrna lewini) captured May 1987 in Hawaii (USA) developed granulomatous exudative mycotic dermatitis localized in the lateral line canal system. The lesion initially was noted in the cephalic canals, but over a period of months extended into the lateral canal. Fusarium solani and Vibrio spp. were isolated from the canal exudate of both sharks. Bacterial colonies were not observed in the canal walls or surrounding tissues. Fusarium solani infection resulted in a chronic physical and behavioral deterioration of the two sharks; one shark was euthanized in September 1988 and the other in July 1989. This is the first report of Fusarium solani infection in the lateral line canal system and the third account in hammerhead sharks.

  20. Stress Controlled Catalysis via Engineered Nanostructures

    Science.gov (United States)

    2016-03-02

    fields on catalysis : “Stress Controlled Catalysis via Engineered Nanostructures.” For this effort a workshop was organized and held at Brown... Catalysis via Engineered Nanostructures" The views, opinions and/or findings contained in this report are those of the author(s) and should not contrued...Support for current award "Stress Controlled Catalysis via Engineered Nanostructures" Report Title This is the final report of the ARO project of

  1. Catalysis and sustainable (green) chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Centi, Gabriele; Perathoner, Siglinda [Dipartimento di Chimica Industriale ed Ingegneria dei Materiali, University of Messina, Salita Sperone 31, 98166 Messina (Italy)

    2003-01-15

    Catalysis is a key technology to achieve the objectives of sustainable (green) chemistry. After introducing the concepts of sustainable (green) chemistry and a brief assessment of new sustainable chemical technologies, the relationship between catalysis and sustainable (green) chemistry is discussed and illustrated via an analysis of some selected and relevant examples. Emphasis is also given to the concept of catalytic technologies for scaling-down chemical processes, in order to develop sustainable production processes which reduce the impact on the environment to an acceptable level that allows self-depuration processes of the living environment.

  2. Photoredox Catalysis in Organic Chemistry

    Science.gov (United States)

    2016-01-01

    In recent years, photoredox catalysis has come to the forefront in organic chemistry as a powerful strategy for the activation of small molecules. In a general sense, these approaches rely on the ability of metal complexes and organic dyes to convert visible light into chemical energy by engaging in single-electron transfer with organic substrates, thereby generating reactive intermediates. In this Perspective, we highlight the unique ability of photoredox catalysis to expedite the development of completely new reaction mechanisms, with particular emphasis placed on multicatalytic strategies that enable the construction of challenging carbon–carbon and carbon–heteroatom bonds. PMID:27477076

  3. Aromatic Chlorosulfonylation by Photoredox Catalysis.

    Science.gov (United States)

    Májek, Michal; Neumeier, Michael; Jacobi von Wangelin, Axel

    2017-01-10

    Visible-light photoredox catalysis enables the efficient synthesis of arenesulfonyl chlorides from anilines. The new protocol involves the convenient in situ preparation of arenediazonium salts (from anilines) and the reactive gases SO 2 and HCl (from aqueous SOCl 2 ). The photocatalytic chlorosulfonylation operates at mild conditions (room temperature, acetonitrile/water) with low catalyst loading. Various functional groups are tolerated (e.g., halides, azides, nitro groups, CF 3 , SF 5 , esters, heteroarenes). Theoretical and experimental studies support a photoredox-catalysis mechanism. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Vulnerability to longline fisheries of three hammerhead shark Sphyrna species in the south-western and equatorial Atlantic Ocean.

    Science.gov (United States)

    Bezerra, N P A; Travassos, P; Hazin, F H V

    2016-08-01

    Catch and effort data from 29 418 longline sets from Brazilian tuna longline vessels operating in the south-western and equatorial Atlantic Ocean between 2004 and 2011 were analysed to investigate the distribution, catch rate and size of three species of hammerhead sharks (Sphyrna lewini, Sphyrna mokarran and Sphyrna zygaena). During that period, 6172 hammerhead sharks were caught. Among the elasmobranchs, the highest percentage of hammerhead sharks were caught in 2007, when they accounted for 3·90% of the group, while the lowest value of 0·40% was recorded in 2010. In general, the spatial distribution of the mean catch per unit effort (CPUE) by years and quarters showed a trend of higher catches near the equatorial region and in southern Brazil. The nominal mean CPUE was 0·12 Sphyrna spp. 1000(-1) hooks, with the highest value being recorded in 2007 (0·30 Sphyrna spp. 1000(-1) hooks). The standardized yearly CPUE estimated by a generalized linear model assuming a zero inflated negative binomial (ZINB) distribution were not much different from nominal values. Of the 205 sexed specimens, 117 were females and 88 were males, resulting in a sex ratio with a predominance of females (1·30:1·00), although not statistically significant. The total length of females ranged from 1200 to 2800 mm and of males from 1100 to 3100 mm. Juvenile hammerhead sharks represented 82 and 54% of the sexed female and male specimens, respectively. © 2016 The Fisheries Society of the British Isles.

  5. Feeding strategy of the night shark (Carcharhinus signatus) and scalloped hammerhead shark (Sphyrna lewini) near seamounts off northeastern Brazil

    OpenAIRE

    Teodoro Vaske Júnior; Carolus Maria Vooren; Rosangela Paula Lessa

    2009-01-01

    A total of 425 stomachs of night shark (Carcharhinus signatus), and 98 stomachs of scalloped hammerhead shark (Sphyrna lewini), from longline and surface gillneters near seamounts off northeastern Brazil, were analysed between 1992 and 1999. Both predators prey upon reef and benthopelagic fishes, migrant cephalopods and deep water crustaceans, showing similar feeding niches (Schoener Index T=0.75). The great prey richness of the diets may reflect the fact that the marine food web for these sp...

  6. Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme

    OpenAIRE

    Hiley, Shawna L.; Collins, Richard A.

    2001-01-01

    We have used hydroxyl radicals generated by decomposition of peroxynitrous acid to study Mg2+-dependent structure and folding of the Varkud satellite (VS) ribozyme. Protection from radical cleavage shows the existence of a solvent-inaccessible core, which includes nucleotides near two three-helix junctions, the kissing interaction between stem–loops I and V and other nucleotides, most of which have also been implicated as important for folding or activity. Kinetic folding experiments showed t...

  7. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

    Czech Academy of Sciences Publication Activity Database

    Sripathi, K.N.; Tay, W.W.; Banáš, P.; Otyepka, M.; Šponer, Jiří; Walter, N. G.

    2014-01-01

    Roč. 20, č. 7 (2014), s. 1112-1128 ISSN 1355-8382 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : time-resolved FRET * steady-state FRET * small ribozyme Subject RIV: BO - Biophysics Impact factor: 4.936, year: 2014

  8. Spliceozymes: ribozymes that remove introns from pre-mRNAs in trans.

    Directory of Open Access Journals (Sweden)

    Zhaleh N Amini

    Full Text Available Group I introns are pre-mRNA introns that do not require the spliceosome for their removal. Instead, they fold into complex three-dimensional structures and catalyze two transesterification reactions, thereby excising themselves and joining the flanking exons. These catalytic RNAs (ribozymes have been modified previously to work in trans, whereby the ribozymes can recognize a splice site on a substrate RNA and replace the 5'- or 3'-portion of the substrate. Here we describe a new variant of the group I intron ribozyme from Tetrahymena that recognizes two splice sites on a substrate RNA, removes the intron sequences between the splice sites, and joins the flanking exons, analogous to the action of the spliceosome. This 'group I spliceozyme' functions in vitro and in vivo, and it is able to mediate a growth phenotype in E. coli cells. The intron sequences of the target pre-mRNAs are constrained near the splice sites but can carry a wide range of sequences in their interior. Because the splice site recognition sequences can be adjusted to different splice sites, the spliceozyme may have the potential for wide applications as tool in research and therapy.

  9. Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

    Science.gov (United States)

    White, Neil A; Hoogstraten, Charles G

    2017-09-01

    The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Molecular Mechanism of Heterogeneous Catalysis

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 6. Molecular Mechanism of Heterogeneous Catalysis - The 2007 Nobel Prize in Chemistry. R S Swathi K L Sebastian. General Article Volume 13 Issue 6 June 2008 pp 548-560 ...

  11. Catalysis in Molten Ionic Media

    DEFF Research Database (Denmark)

    Boghosian, Soghomon; Fehrmann, Rasmus

    2013-01-01

    This chapter deals with catalysis in molten salts and ionic liquids, which are introduced and reviewed briefly, while an in-depth review of the oxidation catalyst used for the manufacturing of sulfuric acid and cleaning of flue gas from electrical power plants is the main topic of the chapter...

  12. Cyclopalladated complexes in enantioselective catalysis

    Science.gov (United States)

    Dunina, Valeria V.; Gorunova, Olga N.; Zykov, P. A.; Kochetkov, Konstantin A.

    2011-01-01

    The results of the use of optically active palladacycles in enantioselective catalysis of [3,3]-sigmatropic rearrangements, aldol condensation, the Michael reaction and cross-coupling are analyzed. Reactions with allylic substrates or reagents and some other transformations are considered.

  13. Transition Metal Complexes and Catalysis

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 4; Issue 9. Transition Metal Complexes and Catalysis. Balaji R Jagirdar. General Article Volume 4 Issue 9 September 1999 pp 63-81. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/004/09/0063-0081 ...

  14. Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme.

    Science.gov (United States)

    Zheng, Luqian; Mairhofer, Elisabeth; Teplova, Marianna; Zhang, Ye; Ma, Jinbiao; Patel, Dinshaw J; Micura, Ronald; Ren, Aiming

    2017-10-30

    Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg2+ cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme.

  15. Molecular catalysis science: Perspective on unifying the fields of catalysis.

    Science.gov (United States)

    Ye, Rong; Hurlburt, Tyler J; Sabyrov, Kairat; Alayoglu, Selim; Somorjai, Gabor A

    2016-05-10

    Colloidal chemistry is used to control the size, shape, morphology, and composition of metal nanoparticles. Model catalysts as such are applied to catalytic transformations in the three types of catalysts: heterogeneous, homogeneous, and enzymatic. Real-time dynamics of oxidation state, coordination, and bonding of nanoparticle catalysts are put under the microscope using surface techniques such as sum-frequency generation vibrational spectroscopy and ambient pressure X-ray photoelectron spectroscopy under catalytically relevant conditions. It was demonstrated that catalytic behavior and trends are strongly tied to oxidation state, the coordination number and crystallographic orientation of metal sites, and bonding and orientation of surface adsorbates. It was also found that catalytic performance can be tuned by carefully designing and fabricating catalysts from the bottom up. Homogeneous and heterogeneous catalysts, and likely enzymes, behave similarly at the molecular level. Unifying the fields of catalysis is the key to achieving the goal of 100% selectivity in catalysis.

  16. Ribozyme Mediated gRNA Generation for In Vitro and In Vivo CRISPR/Cas9 Mutagenesis

    Science.gov (United States)

    Ng, Ashley Shu Mei; Ingham, Philip W.

    2016-01-01

    CRISPR/Cas9 is now regularly used for targeted mutagenesis in a wide variety of systems. Here we report the use of ribozymes for the generation of gRNAs both in vitro and in zebrafish embryos. We show that incorporation of ribozymes increases the types of promoters and number of target sites available for mutagenesis without compromising mutagenesis efficiency. We have tested this by comparing the efficiency of mutagenesis of gRNA constructs with and without ribozymes and also generated a transgenic zebrafish expressing gRNA using a heat shock promoter (RNA polymerase II-dependent promoter) that was able to induce mutagenesis of its target. Our method provides a streamlined approach to test gRNA efficiency as well as increasing the versatility of conditional gene knock out in zebrafish. PMID:27832146

  17. Ribozyme Mediated gRNA Generation for In Vitro and In Vivo CRISPR/Cas9 Mutagenesis.

    Directory of Open Access Journals (Sweden)

    Raymond Teck Ho Lee

    Full Text Available CRISPR/Cas9 is now regularly used for targeted mutagenesis in a wide variety of systems. Here we report the use of ribozymes for the generation of gRNAs both in vitro and in zebrafish embryos. We show that incorporation of ribozymes increases the types of promoters and number of target sites available for mutagenesis without compromising mutagenesis efficiency. We have tested this by comparing the efficiency of mutagenesis of gRNA constructs with and without ribozymes and also generated a transgenic zebrafish expressing gRNA using a heat shock promoter (RNA polymerase II-dependent promoter that was able to induce mutagenesis of its target. Our method provides a streamlined approach to test gRNA efficiency as well as increasing the versatility of conditional gene knock out in zebrafish.

  18. Electric Fields and Enzyme Catalysis.

    Science.gov (United States)

    Fried, Stephen D; Boxer, Steven G

    2017-06-20

    What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.

  19. Catalysis in the Primordial World

    Directory of Open Access Journals (Sweden)

    Nenad Raos

    2017-11-01

    Full Text Available Catalysis provides orderly prebiotic synthesis and eventually its evolution into autocatalytic (self-reproduction systems. Research on homogeneous catalysis is concerned mostly with random peptide synthesis and the chances to produce catalytic peptide oligomers. Synthesis of ribose via formose reaction was found to be catalysed by B(OH4−, presumably released by weathering of borate minerals. Oxide and clay mineral surfaces provide catalytic sites for the synthesis of oligopeptides and oligonucleotides. Chemoautotrophic or iron-sulphur-world theory assumes that the first (pioneer organisms developed by catalytic processes on (Fe/NiS particles formed near/close hydrothermal vents. The review provides an overlay of possible catalytic reactions in prebiotic environment, discussing their selectivity (regioselectivity, stereoselectivity as well as geological availability of catalytic minerals and geochemical conditions enabling catalytic reactions on early Earth.

  20. Phylogeny of hammerhead sharks (Family Sphyrnidae) inferred from mitochondrial and nuclear genes.

    Science.gov (United States)

    Lim, Douglas D; Motta, Philip; Mara, Kyle; Martin, Andrew P

    2010-05-01

    Hammerhead sharks (Family Sphyrnidae) get their name from their laterally expanded, dorsal-ventrally compressed head, a structure referred to as the cephalofoil. Species within the family vary for head size and shape and for body size in ways that are functionally significant. Here we infer the phylogeny for all species within the family based on analysis of mitochondrial and nuclear genes amounting to 6292 base pairs. Mixed model Bayesian analysis of the concatenated data and Bayesian estimation of the species tree (BEST) converged on the same topology of the relationships. Shimodaira-Hasegawa tests revealed that all previously proposed hypotheses could be refuted by the data. The new hypothesis for the group suggests that the ancestor of all extant sharks was large (>200 cms) and that small body size probably evolved twice at different times and places. Moreover, the results suggest that once the cephalofoil evolved, it underwent divergent evolution in different lineages presumably in response to unique selective regimes. Copyright 2010 Elsevier Inc. All rights reserved.

  1. Asymmetric hemoglobins, their thiol content, and blood glutathione of the scalloped hammerhead shark, Sphyrna lewini.

    Science.gov (United States)

    Dafré, A L; Reischl, E

    1997-03-01

    Starch gel electrophoresis pH 8.6, or PAGE pH 8.9, of the scalloped hammerhead shark hemolysates showed three hemoglobins (Hb). An additional Hb between the two most mobile electrophoretic components was seen in starch gel electrophoresis, pH 8.1, and also in highly loaded PAGE gels. The relative concentration of these Hbs was variable among individuals, when accessed at pH 8.1. Dilution of hemolysates led to a redistribution of the Hb tetramer subunits. Under denaturing conditions, the unfractionated hemolysate was resolved in 3 Hb subunits. Isolated Hbs, named SL I-SL IV, showed unusual subunit compositions: SL I, the least mobile, is "b3c"; SL II is "a2bc"; SL III and SL IV are composed only by "a" subunits. Hemoglobins in the whole hemolysate have an average of two reactive cysteines per tetramer, which were not easily S-thiolated by glutathione, as is the case for related species. After hemoglobin denaturation, six additional -SH groups were titrated by Ellman's reagent. Methemoglobin content was low in the erythrocytes of nine examined specimens, 1.13 +/- 1.90%. High values for total erythrocyte glutathione (GSH) were found: 4.5 +/- 0.7 mM; n = 7. The ratio of 1.4 +/- 0.4 GSH/Hb is higher than usually reported for mammalians.

  2. Effects of fasting and refeeding on intestinal cell proliferation and apoptosis in hammerhead shark (Sphyrna lewini

    Directory of Open Access Journals (Sweden)

    Hideya Takahashi

    2014-04-01

    Full Text Available Objective: To examine the effects of fasting and refeeding on intestinal cell proliferation and apoptosis in an opportunistic predator, hammerhead shark (Sphyrna lewini of elasmobranch fishes which are among the earliest known extant groups of vertebrates to have the valvular intestine typical for the primitive species. Methods: Animals were euthanized after 5-10 d of fasting or feeding, or after 10-day fasting and 5-day refeeding. Intestinal apoptosis and cell proliferation were assessed by using oligonucleotide detection assay, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and immunohistochemistry of proliferating cells nuclear antigen. Results: Plasma levels of cholesterol and glucose were reduced by fasting. Intestinal apoptosis generally decreased during fasting. Numerous apoptotic cells were observed around the tips of the villi, primarily in the epithelium in the fed sharks, whereas fewer labeled nuclei were detected in the epithelium of fasted sharks. Refeeding returned intestinal apoptosis to the level in the fed sharks. Proliferating cells were observed in the epithelium around the troughs of the villi and greater in number in fed sharks, whereas fewer labeled nuclei were detected in fasted sharks. Conclusions: The cell turnover is modified in both intestinal epithelia of the shark and the murines by fasting/feeding, but in opposite directions. The difference may reflect the feeding ecology of the elasmobranchs, primitive intermittent feeders.

  3. Asymmetric Ion-Pairing Catalysis

    Science.gov (United States)

    Brak, Katrien

    2014-01-01

    Charged intermediates and reagents are ubiquitous in organic transformations. The interaction of these ionic species with chiral neutral, anionic, or cationic small molecules has emerged as a powerful strategy for catalytic, enantioselective synthesis. This review describes developments in the burgeoning field of asymmetric ion-pairing catalysis with an emphasis on the insights that have been gleaned into the structural and mechanistic features that contribute to high asymmetric induction. PMID:23192886

  4. Reaction Selectivity in Heterogeneous Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, Gabor A.; Kliewer, Christopher J.

    2009-02-02

    The understanding of selectivity in heterogeneous catalysis is of paramount importance to our society today. In this review we outline the current state of the art in research on selectivity in heterogeneous catalysis. Current in-situ surface science techniques have revealed several important features of catalytic selectivity. Sum frequency generation vibrational spectroscopy has shown us the importance of understanding the reaction intermediates and mechanism of a heterogeneous reaction, and can readily yield information as to the effect of temperature, pressure, catalyst geometry, surface promoters, and catalyst composition on the reaction mechanism. DFT calculations are quickly approaching the ability to assist in the interpretation of observed surface spectra, thereby making surface spectroscopy an even more powerful tool. HP-STM has revealed three vitally important parameters in heterogeneous selectivity: adsorbate mobility, catalyst mobility, and selective site-blocking. The development of size controlled nanoparticles from 0.8 to 10 nm, of controlled shape, and of controlled bimetallic composition has revealed several important variables for catalytic selectivity. Lastly, DFT calculations may be paving the way to guiding the composition choice for multi-metallic heterogeneous catalysis for the intelligent design of catalysts incorporating the many factors of selectivity we have learned.

  5. Inhibition of gene expression in human cells using RNase P-derived ribozymes and external guide sequences

    OpenAIRE

    Kim, Kihoon; Liu, Fenyong

    2007-01-01

    Ribonuclease P (RNase P) complexed with an external guide sequence (EGS) represents a novel nucleic acid-based gene interference approach to modulate gene expression. This enzyme is a ribonucleoprotein complex for tRNA processing. In E. coli, RNase P contains a catalytic RNA subunit (M1 ribozyme) and a protein subunit (C5 cofactor). EGSs, which are RNAs derived from natural tRNAs, bind to a target mRNA and render the mRNA susceptible to hydrolysis by RNase P and M1 ribozyme. When covalently l...

  6. Nanometallic chemistry: deciphering nanoparticle catalysis from the perspective of organometallic chemistry and homogeneous catalysis.

    Science.gov (United States)

    Yan, Ning; Yuan, Yuan; Dyson, Paul J

    2013-10-07

    Nanoparticle (NP) catalysis is traditionally viewed as a sub-section of heterogeneous catalysis. However, certain properties of NP catalysts, especially NPs dispersed in solvents, indicate that there could be benefits from viewing them from the perspective of homogeneous catalysis. By applying the fundamental approaches and concepts routinely used in homogeneous catalysis to NP catalysts it should be possible to rationally design new nanocatalysts with superior properties to those currently in use.

  7. Cosmic strings and baryon decay catalysis

    Science.gov (United States)

    Gregory, Ruth; Perkins, W. B.; Davis, A.-C.; Brandenberger, R. H.

    1989-01-01

    Cosmic strings, like monopoles, can catalyze proton decay. For integer charged fermions, the cross section for catalysis is not amplified, unlike in the case of monopoles. The catalysis processes are reviewed both in the free quark and skyrmion pictures and the implications for baryogenesis are discussed. A computation of the cross section for monopole catalyzed skyrmion decay is presented using classical physics. Also discussed are some effects which can screen catalysis processes.

  8. Cooperative catalysis designing efficient catalysts for synthesis

    CERN Document Server

    Peters, René

    2015-01-01

    Written by experts in the field, this is a much-needed overview of the rapidly emerging field of cooperative catalysis. The authors focus on the design and development of novel high-performance catalysts for applications in organic synthesis (particularly asymmetric synthesis), covering a broad range of topics, from the latest progress in Lewis acid / Br?nsted base catalysis to e.g. metal-assisted organocatalysis, cooperative metal/enzyme catalysis, and cooperative catalysis in polymerization reactions and on solid surfaces. The chapters are classified according to the type of cooperating acti

  9. Solid acid catalysis from fundamentals to applications

    CERN Document Server

    Hattori, Hideshi

    2014-01-01

    IntroductionTypes of solid acid catalystsAdvantages of solid acid catalysts Historical overviews of solid acid catalystsFuture outlookSolid Acids CatalysisDefinition of acid and base -Brnsted acid and Lewis acid-Acid sites on surfacesAcid strengthRole of acid sites in catalysisBifunctional catalysisPore size effect on catalysis -shape selectivity-Characterization of Solid Acid Catalysts Indicator methodTemperature programmed desorption (TPD) of ammoniaCalorimetry of adsorption of basic moleculesInfrare

  10. Mercury and selenium bioaccumulation in the smooth hammerhead shark, Sphyrna zygaena Linnaeus, from the Mexican Pacific Ocean

    OpenAIRE

    Escobar Sánchez, Ofelia; Galván Magaña, Felipe; Rosiles Martínez, R.

    2010-01-01

    We analyzed total mercury and selenium bioaccumulation in muscle tissue and cartilage fibers (fins) from smooth hammerhead shark, Sphyrna zygaena, caught off Baja California Sur, Mexico. In muscle tissue, the mercury concentration ranged from 0.005 to 1.93 μg g−1 ww (wet weight), which falls within the safety limits for food set by international agencies (Hg > 1.0 μg g−1 ww). Only one specimen showed a mercury value that exceeded this limit. In fins, the mercury bioaccumulation was lower (...

  11. Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini.

    Science.gov (United States)

    Nance, Holly A; Klimley, Peter; Galván-Magaña, Felipe; Martínez-Ortíz, Jimmy; Marko, Peter B

    2011-01-01

    Genetic diversity (θ), effective population size (N(e)), and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP) range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in N(e) (θ = 4N(e)μ), where μ is the mutation rate. Application of the isolation-with-migration (IM) model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1-16.7), with divergence times (t) among all populations significantly greater than zero. Using a conservative (i.e., slow) fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs) for the onset of the decline in N(e) predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.

  12. Demographic processes underlying subtle patterns of population structure in the scalloped hammerhead shark, Sphyrna lewini.

    Directory of Open Access Journals (Sweden)

    Holly A Nance

    Full Text Available Genetic diversity (θ, effective population size (N(e, and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of θ are at least an order of magnitude smaller than ancestral θ, indicating large decreases in N(e (θ = 4N(eμ, where μ is the mutation rate. Application of the isolation-with-migration (IM model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm = 0.1-16.7, with divergence times (t among all populations significantly greater than zero. Using a conservative (i.e., slow fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs for the onset of the decline in N(e predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.

  13. Fundamental concepts in heterogeneous catalysis

    CERN Document Server

    Norskov, Jens K; Abild-Pedersen, Frank; Bligaard, Thomas

    2014-01-01

    This book is based on a graduate course and suitable as a primer for any newcomer to the field, this book is a detailed introduction to the experimental and computational methods that are used to study how solid surfaces act as catalysts.   Features include:First comprehensive description of modern theory of heterogeneous catalysisBasis for understanding and designing experiments in the field   Allows reader to understand catalyst design principlesIntroduction to important elements of energy transformation technologyTest driven at Stanford University over several semesters

  14. Melanoma Angiogenesis and Metastasis Modulated by Ribozyme Targeting of the Secreted Growth Factor Pleiotrophin

    Science.gov (United States)

    Czubayko, Frank; Schulte, Anke M.; Berchem, Guy J.; Wellstein, Anton

    1996-12-01

    Clinical and experimental evidence suggests that spreading of malignant cells from a localized tumor (metastasis) is directly related to the number of microvessels in the primary tumor. This tumor angiogenesis is thought to be mediated by tumor-cell-derived growth factors. However, most tumor cells express a multitude of candidate angiogenesis factors and it is difficult to decipher which of these are rate-limiting factors in vivo. Herein we use ribozyme targeting of pleiotrophin (PTN) in metastatic human melanoma cells to assess the significance of this secreted growth factor for angiogenesis and metastasis. As a model we used human melanoma cells (1205LU) that express high levels of PTN and metastasize from subcutaneous tumors to the lungs of experimental animals. In these melanoma cells, we reduced PTN mRNA and growth factor activity by transfection with PTN-targeted ribozymes and generated cell lines expressing different levels of PTN. We found that the reduction of PTN does not affect growth of the melanoma cells in vitro. In nude mice, however, tumor growth and angiogenesis were decreased in parallel with the reduced PTN levels and apoptosis in the tumors was increased. Concomitantly, the metastatic spread of the tumors from the subcutaneous site to the lungs was prevented. These studies support a direct link between tumor angiogenesis and metastasis through a secreted growth factor and identify PTN as a candidate factor that may be rate-limiting for human melanoma metastasis.

  15. Characterization of the Tetrahymena ribozyme folding pathway using the kinetic footprinting reagent peroxynitrous acid.

    Science.gov (United States)

    Chaulk, S G; MacMillan, A M

    2000-01-11

    Large RNAs fold into complex structures which determine their biological activities. A full understanding of both RNA structure and dynamics will include the description of the pathways by which these structures are formed. Kinetic footprinting [Sclavi, B., et al. (1997) J. Mol. Biol. 266, 144-159] has been shown to be a powerful method for the study of dynamic processes involving RNA. Here we describe the use of a readily available reagent, peroxynitrous acid, as a kinetic footprinting tool for the study of RNA folding. Hydroxyl radicals generated from this reagent were used to footprint the Tetrahymena ribozyme during its magnesium-dependent folding-in agreement with synchroton X-ray footprinting [Sclavi, B., et al. (1998) Science 279, 1940-1943] and oligonucleotide/hybridization cleavage experiments [Zarrinkar, P. P., and Williamson, J. R. (1994) Science 265, 918-924], this work suggests an ordered, hierarchical folding pathway for the ribozyme. Several slow steps in the folding pathway were observed in the peroxynitrous acid footprinting, but none of these corresponded to the rate-determining step of folding. This suggests that the formation of the global, protected structure is followed by one or more slow local rearrangements to yield the final active structure. These studies illustrate the utility of peroxynitrous acid as a reagent for the elucidation of RNA folding pathways and the study of RNA dynamics.

  16. Dissecting human cytomegalovirus gene function and capsid maturation by ribozyme targeting and electron cryomicroscopy.

    Science.gov (United States)

    Yu, Xuekui; Trang, Phong; Shah, Sanket; Atanasov, Ivo; Kim, Yong-Hwan; Bai, Yong; Zhou, Z Hong; Liu, Fenyong

    2005-05-17

    Human CMV (HCMV) is the leading viral cause of birth defects and causes one of the most common opportunistic infections among transplant recipients and AIDS patients. Cleavage of internal scaffolding proteins by the viral protease (Pr) occurs during HCMV capsid assembly. To gain insight into the mechanism of HCMV capsid maturation and the roles of the Pr in viral replication, an RNase P ribozyme was engineered to target the Pr mRNA and down-regulate its expression by >99%, generating premature Pr-minus capsids. Furthermore, scaffolding protein processing and DNA encapsidation were inhibited by 99%, and viral growth was reduced by 10,000-fold. 3D structural comparison of the Pr-minus and wild-type B capsids by electron cryomicroscopy, at an unprecedented 12.5-angstroms resolution, unexpectedly revealed that the structures are identical in their overall shape and organization. However, the Pr-minus capsid contains tenuous connections between the scaffold and the capsid shell, whereas the wild-type B capsid has extra densities in its core that may represent the viral Pr. Our findings indicate that cleavage of the scaffolding protein is not associated with the morphological changes that occur during capsid maturation. Instead, the protease appears to be required for DNA encapsidation and the subsequent maturation steps leading to infectious progeny. These results therefore provide key insights into an essential step of HCMV infection using an RNase P ribozyme-based inhibition strategy.

  17. Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites

    DEFF Research Database (Denmark)

    Einvik, C; Nielsen, Henrik; Westhof, E

    1998-01-01

    available GIR1 sequences and propose a common RNA secondary structure resembling that of group I splicing-ribozymes, but with some important differences. The GIR1s lack most peripheral sequence components, as well as a P1 segment, and, at approximately 160-190 nt, they are the smallest functional group I...

  18. Inhibition of gene expression in human cells using RNase P-derived ribozymes and external guide sequences.

    Science.gov (United States)

    Kim, Kihoon; Liu, Fenyong

    2007-01-01

    Ribonuclease P (RNase P) complexed with an external guide sequence (EGS) represents a novel nucleic acid-based gene interference approach to modulate gene expression. This enzyme is a ribonucleoprotein complex for tRNA processing. In Escherichia coli, RNase P contains a catalytic RNA subunit (M1 ribozyme) and a protein subunit (C5 cofactor). EGSs, which are RNAs derived from natural tRNAs, bind to a target mRNA and render the mRNA susceptible to hydrolysis by RNase P and M1 ribozyme. When covalently linked with a guide sequence, M1 can be engineered into a sequence-specific endonuclease, M1GS ribozyme, which cleaves any target RNAs that base pair with the guide sequence. Studies have demonstrated efficient cleavage of mRNAs by M1GS and RNase P complexed with EGSs in vitro. Moreover, highly active M1GS and EGSs were successfully engineered using in vitro selection procedures. EGSs and M1GS ribozymes are effective in blocking gene expression in both bacteria and human cells, and exhibit promising activity for antimicrobial, antiviral, and anticancer applications. In this review, we highlight some recent results using the RNase P-based technology, and offer new insights into the future of using EGS and M1GS RNA as tools for basic research and as gene-targeting agents for clinical applications.

  19. Kinetics of HIV-1 long terminal repeat trans-activation. Use of intragenic ribozyme to assess rate-limiting steps

    NARCIS (Netherlands)

    Jeang, K. T.; Berkhout, B.

    1992-01-01

    We have examined, using self-cleaving ribozymes, the intracellular trans-activation kinetics of the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) by viral protein Tat. Experiments were designed to effect a competition (during RNA chain elongation) between cleavage of a

  20. A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class.

    Science.gov (United States)

    Košutić, Marija; Neuner, Sandro; Ren, Aiming; Flür, Sara; Wunderlich, Christoph; Mairhofer, Elisabeth; Vušurović, Nikola; Seikowski, Jan; Breuker, Kathrin; Höbartner, Claudia; Patel, Dinshaw J; Kreutz, Christoph; Micura, Ronald

    2015-12-07

    Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pKa value of 5.1 was determined for a (13) C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg(2+) ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn(2+) or Cd(2+) accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 Å X-ray structure of a 2'-OCH3 -U5 modified twister ribozyme. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. catalysis of chemical processes: particular teaching aspects

    African Journals Online (AJOL)

    IICBA01

    ABSTRACT. The paper is devoted to two main issues of catalysis from the viewpoint of teaching and learning activities. The first part deals with positive catalysis which treats the general features of catalytic processes and textbook imperfections. The second part focuses on decelerating or stopping-down chemical processes ...

  2. DOE Laboratory Catalysis Research Symposium - Abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Dunham, T.

    1999-02-01

    The conference consisted of two sessions with the following subtopics: (1) Heterogeneous Session: Novel Catalytic Materials; Photocatalysis; Novel Processing Conditions; Metals and Sulfides; Nuclear Magnetic Resonance; Metal Oxides and Partial Oxidation; Electrocatalysis; and Automotive Catalysis. (2) Homogeneous Catalysis: H-Transfer and Alkane Functionalization; Biocatalysis; Oxidation and Photocatalysis; and Novel Medical, Methods, and Catalyzed Reactions.

  3. SOME BIOLOGICAL ASPECTS OF SCALLOPED HAMMERHEAD SHARKS (Sphyrna lewini Griffith & Smith, 1834 CAUGHT FROM COASTAL FISHERIES IN THE EASTERN INDIAN OCEAN

    Directory of Open Access Journals (Sweden)

    Umi Chodrijah

    2015-12-01

    Full Text Available Indonesia has the largest chondrichthyan fishery in the world, with a reported of 105,000 and 118,000 tonnes landed in 2002 and 2003 respectively. Scalloped hammerhead shark was either targeted or by-catch from this fishery, mostly for its fins. Despite of the growing concern around the world, the availability of biological data of this species, especially in the Eastern Indian Ocean is still lacking. The objectives of this paper are to present some biological information (size composition and sex ratio of the scalloped hammerhead, from coastal fisheries in Eastern Indian Ocean. The data used for the analysis comprised of two components, i.e. survey data in 2010 (February, March, June, August, October and December and data from daily monitoring shark landing in 2013 (January to December. Substantially lower mean size, more immature sharks and more frequent of female caught over years showed that scalloped hammerhead shark in the Eastern Indian Ocean are facing intensive fishing pressure which could lead to overfishing. This could harm the sustainability of scalloped hammerhead shark resource in the long run. The relationship between clasper length and total length was positively correlated where every 5 cmTL increment on clasper length adding 51 cmTL on total length.

  4. Age and growth of the Scalloped Hammerhead shark, Sphyrna lewini (Griffith and Smith, 1834), from the southern Brazilian coast.

    Science.gov (United States)

    Kotas, J E; Mastrochirico, V; Petrere Junior, M

    2011-08-01

    Age and growth studies for the scalloped hammerhead shark, Sphyrna lewini (Griffith and Smith, 1834) caught along the southern Brazilian coast, were based on ring measurements of vertebrae sections of 115 males, 116 females and 14 unknown sexed sharks between 48 and 344 cm total length (TL). The von Bertalanffy growth models were best fit using back-calculated data. The growth parameters obtained for males, were L∞ = 266 cm; K = 0.05/year; L0 = 47 cm. For females, L∞ = 300 cm; K = 0.05/year; L0 = 51 cm. An adult female reached 217 cm TL and was 31.5 years old. On the other hand, an adult male was 29.5 years old and measured 234 cm TL. Longevity estimate for males and females was 55 years. Therefore, S. lewini is a long-lived fish. Ageing precision, based on the IAPE index, was 5.6%. Marginal Increment analysis based on MIR index from hammerheads smaller than 105 cm, compared with the percentual of opaque and hyaline bands found per month ageing whole vertebrae, showed an annual ring formation, i.e., in winter.

  5. "Nanocrystal bilayer for tandem catalysis"

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Yusuke; Tsung, Chia Kuang; Huang, Wenyu; Huo, Ziyang; E.Habas, Susan E; Soejima, Tetsuro; Aliaga, Cesar E; Samorjai, Gabor A; Yang, Peidong

    2011-01-24

    Supported catalysts are widely used in industry and can be optimized by tuning the composition and interface of the metal nanoparticles and oxide supports. Rational design of metal-metal oxide interfaces in nanostructured catalysts is critical to achieve better reaction activities and selectivities. We introduce here a new class of nanocrystal tandem catalysts that have multiple metal-metal oxide interfaces for the catalysis of sequential reactions. We utilized a nanocrystal bilayer structure formed by assembling platinum and cerium oxide nanocube monolayers of less than 10 nm on a silica substrate. The two distinct metal-metal oxide interfaces, CeO2-Pt and Pt-SiO2, can be used to catalyse two distinct sequential reactions. The CeO2-Pt interface catalysed methanol decomposition to produce CO and H2, which were subsequently used for ethylene hydroformylation catalysed by the nearby Pt-SiO2 interface. Consequently, propanal was produced selectively from methanol and ethylene on the nanocrystal bilayer tandem catalyst. This new concept of nanocrystal tandem catalysis represents a powerful approach towards designing high-performance, multifunctional nanostructured catalysts

  6. The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis

    DEFF Research Database (Denmark)

    Vader, Anna; Johansen, Steinar; Nielsen, Henrik

    2002-01-01

    During starvation induced encystment, cells of the myxomycete Didymium iridis accumulate a 7.5-kb RNA that is the result of alternative processing of pre-rRNA. The 5' end corresponds to an internal processing site cleaved by the group I-like ribozyme DiGIR1, located within the twin-ribozyme intron...... context, and presents a new example of the cost to the host of intron load. This is because the formation of the 7.5-kb RNA is incompatible with the formation of functional ribosomal RNA from the same transcript. In the formation of the 7.5-kb RNA, DiGIR1 catalysed cleavage takes place without prior...... splicing performed by DiGIR2. This contrasts with the processing order leading to mature rRNA and I-DirI mRNA in growing cells, suggesting an interplay between the two ribozymes of a twin-ribozyme intron....

  7. A Comparison of the foraging ecology and bioenergetics of the early life-stages of two sympatric hammerhead sharks from 1998-07-12 to 2005-07-27 (NCEI Accession 0163192)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This Archival Information Package (AIP) contains basic biological information on bonnethead and scalloped hammerhead sharks with specific (by stomach and prey item)...

  8. The life histories of endangered hammerhead sharks (Carcharhiniformes, Sphyrnidae) from the east coast of Australia.

    Science.gov (United States)

    Harry, A V; Macbeth, W G; Gutteridge, A N; Simpfendorfer, C A

    2011-06-01

    The life histories of two globally endangered hammerhead sharks, Sphyrna lewini and Sphyrna mokarran, were examined using samples collected from a range of commercial fisheries operating along the east coast of Australia. The catch of S. lewini was heavily biased towards males, and there were significant differences in von Bertalanffy growth parameters (L(∞) and k) and maturity [stretched total length (L(ST)) and age (A) at which 50% are mature, L(ST50) and A(50)] between those caught in the tropics (L(∞) = 2119 mm, k = 0·163, L(ST50) = 1471 mm, A(50) = 5·7 years) and those caught in temperate waters (L(∞) = 3199 mm, k = 0·093, L(ST50) = 2043 mm, A(50) = 8·9 years). The best-fit estimates for a three-parameter von Bertalanffy growth curve fit to both sexes were L(∞) = 3312 mm, L(0) = 584 mm and k = 0·076. Males attained a maximum age of 21 years and grew to at least 2898 mm L(ST). The longevity, maximum length and maturity of females could not be estimated as mature animals could not be sourced from any fishery. Length at birth inferred from neonates with open umbilical scars was 465-563 mm L(ST). There was no significant difference in length and age at maturity of male and female S. mokarran, which reached 50% maturity at 2279 mm L(ST) and 8·3 years. Sphyrna mokarran grew at a similar rate to S. lewini and the best-fit estimates for a two-parameter von Bertalanffy equation fit to length-at-age data for sexes combined with an assumed mean length-at-birth of 700 mm were L(∞) = 4027 mm and k = 0·079. Females attained a maximum age of 39·1 years and grew to at least 4391 mm L(ST). The oldest male S. mokarran was 31·7 years old and 3691 mm L(ST). Validation of annual growth-band deposition in S. mokarran was achieved through a mark, tag and recapture study. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

  9. Age, growth and maturity of the pelagic thresher Alopias pelagicus and the scalloped hammerhead Sphyrna lewini.

    Science.gov (United States)

    Drew, M; White, W T; Dharmadi; Harry, A V; Huveneers, C

    2015-01-01

    Indonesia has the greatest reported chondrichthyan catches worldwide, with c.110,000 t caught annually. The pelagic thresher (Alopias pelagicus) and scalloped hammerhead (Sphryna lewini) together comprise about 25% of the total catches of sharks landed in Indonesia. Age and growth parameters were estimated for A. pelagicus and S. lewini from growth-band counts of thin-cut vertebral sections. Alopias pelagicus (n = 158) and S. lewini (n = 157) vertebrae were collected from three Indonesian fish markets over a 5 year period. A multi-model analysis was used to estimate growth parameters for both species. The models of best fit for males and females for A. pelagicus was the three-parameter logistic (L∞ = 3169 mm LT , k = 0·2) and the two-parameter von Bertalanffy models (L∞ = 3281 mm LT , k = 0·12). Age at maturity was calculated to be 10·4 and 13·2 years for males and females, respectively, and these are the oldest estimated for this species. The samples of S. lewini were heavily biased towards females, and the model of best fit for males and females was the three-parameter Gompertz (L∞ = 2598 mm LT , k = 0·15) and the two-parameter Gompertz (L∞ = 2896 mm LT , k= 0·16). Age at maturity was calculated to be 8·9 and 13·2 years for males and females, respectively. Although numerous age and growth studies have previously been undertaken on S. lewini, few studies have been able to obtain adequate samples from all components of the population because adult females, adult males and juveniles often reside in different areas. For the first time, sex bias in this study was towards sexually mature females, which are commonly lacking in previous biological studies on S. lewini. Additionally, some of the oldest aged specimens and highest age at maturity for both species were observed in this study. Both species exhibit slow rates of growth and late age at maturity, highlighting the need for a re-assessment of the relative resilience of these two

  10. Extensive use of mesopelagic waters by a Scalloped hammerhead shark (Sphyrna lewini) in the Red Sea

    KAUST Repository

    Spät, Julia L.Y.

    2017-09-06

    Background Despite being frequently landed in fish markets along the Saudi Arabian Red Sea coast, information regarding fundamental biology of the Scalloped hammerhead shark (Sphyrna lewini) in this region is scarce. Satellite telemetry studies can generate important data on life history, describe critical habitats, and ultimately redefine management strategies for sharks. To better understand the horizontal and vertical habitat use of S. lewini in the Red Sea and to aid with potential future development of zoning and management plans for key habitats, we deployed a pop-up satellite archival transmitting tag to track a single female specimen (240 cm total length) for a tracking period of 182 days. Results The tag was physically recovered after a deployment period of 6 months, thus providing the complete archived dataset of more than one million depth and temperature records. Based on a reconstructed, most probable track, the shark travelled a circular distance of approximately 1000 km from the central Saudi Arabian Red Sea southeastward into Sudanese waters, returning to the tagging location toward the end of the tracking period. Mesopelagic excursions to depths between 650 and 971 m occurred on 174 of the 182 days of the tracking period. Intervals between such excursions were characterized by constant oscillatory diving in the upper 100 m of the water column. Conclusions This study provides evidence that mesopelagic habitats might be more commonly used by S. lewini than previously suggested. We identified deep diving behavior throughout the 24-h cycle over the entire 6-month tracking period. In addition to expected nightly vertical habitat use, the shark exhibited frequent mesopelagic excursions during daytime. Deep diving throughout the diel cycle has not been reported before and, while dive functionality remains unconfirmed, our study suggests that mesopelagic excursions may represent foraging events within and below deep scattering layers. Additional research

  11. Palladium catalysis for energy applications

    Energy Technology Data Exchange (ETDEWEB)

    Pfefferle, L. D.; Datye, Abhaya

    2001-03-01

    Palladium (Pd) is an attractive catalyst for a range of new combustion applications comprising primary new technologies for future industrial energy needs, including gas turbine catalytic combustion, auto exhaust catalysts, heating and fuel cells. Pd poses particular challenges because it changes both chemical state and morphology as a function of temperature and reactant environment and those changes result in positive and negative changes in activity. Interactions with the support, additives, water, and contaminants as well as carbon formation have also been observed to affect Pd catalyst performance. This report describes the results of a 3.5 year project that resolves some of the conflicting reports in the literature about the performance of Pd-based catalysis.

  12. Nanocrystal assembly for tandem catalysis

    Science.gov (United States)

    Yang, Peidong; Somorjai, Gabor; Yamada, Yusuke; Tsung, Chia-Kuang; Huang, Wenyu

    2014-10-14

    The present invention provides a nanocrystal tandem catalyst comprising at least two metal-metal oxide interfaces for the catalysis of sequential reactions. One embodiment utilizes a nanocrystal bilayer structure formed by assembling sub-10 nm platinum and cerium oxide nanocube monolayers on a silica substrate. The two distinct metal-metal oxide interfaces, CeO.sub.2--Pt and Pt--SiO.sub.2, can be used to catalyze two distinct sequential reactions. The CeO.sub.2--Pt interface catalyzed methanol decomposition to produce CO and H.sub.2, which were then subsequently used for ethylene hydroformylation catalyzed by the nearby Pt--SiO.sub.2 interface. Consequently, propanal was selectively produced on this nanocrystal bilayer tandem catalyst.

  13. Evaluation of a Petition Requesting National Marine Fisheries Service (NMFS) to List the Smooth Hammerhead Shark (Sphryna zygaena) as a Threatened or Endangered Species Under the Endangered Species Act (ESA)

    Science.gov (United States)

    Sturm, A. B.

    2016-12-01

    The wildlife conservation organization, Defenders of Wildlife, petitioned NMFS to list the smooth hammerhead shark, Sphryna zygaena, as endangered or threatened throughout its range under the ESA. The petition was critically evaluated to determine if the petitioners presented substantial scientific or commercial information indicating that the smooth hammerhead shark may warrant listing under the ESA. The petition and the cited scientific literature (as well as scientific literature readily available in NMFS files) were evaluated to determine if the smooth hammerhead shark may be threatened or endangered because of any one or a combination of the following five ESA section 4(a)(1) factors: (1) present or threatened destruction, modification, or curtailment of its habitat or range; (2) over utilization for commercial, recreational, scientific, or educational purposes; (3) disease or predation; (4) inadequacy of existing regulatory mechanisms; (5) or other natural or manmade factors affecting its continued existence. The available scientific literature indicates that the smooth hammerhead shark populations have declined in multiple regions. Smooth hammerhead sharks may warrant listing due to ongoing threats of over utilization for commercial purposes by global fisheries that target and retain incidental catch of these species to obtain their high-value fins, possible inadequacies in global regulatory mechanisms to control this level of exploitation, and natural factors (such as inherent biological vulnerabilities) that may be exacerbating these threats. Based on these findings, the smooth hammerhead shark may warrant listing as a threatened or endangered species under the ESA and a status review of the species is currently being conducted.

  14. Relation between Hydrogen Evolution and Hydrodesulfurization Catalysis

    DEFF Research Database (Denmark)

    Šaric, Manuel; Moses, Poul Georg; Rossmeisl, Jan

    2016-01-01

    A relation between hydrogen evolution and hydrodesulfurization catalysis was found by density functional theory calculations. The hydrogen evolution reaction and the hydrogenation reaction in hydrodesulfurization share hydrogen as a surface intermediate and, thus, have a common elementary step...

  15. Current trends of surface science and catalysis

    CERN Document Server

    Park, Jeong Young

    2014-01-01

    Including detail on applying surface science in renewable energy conversion, this book covers the latest results on model catalysts including single crystals, bridging "materials and pressure gaps", and hot electron flows in heterogeneous catalysis.

  16. Special section on Nano-Catalysis

    CSIR Research Space (South Africa)

    Makgwane, PR

    2013-01-01

    Full Text Available This special issue on nano-catalysis was devoted to the development and application of nanosized structured catalysts materials in various fields such as chemical transformation, environmental cleaning and energy generation supply as a concept tool...

  17. Faraday Discussions meeting Catalysis for Fuels.

    Science.gov (United States)

    Fischer, Nico; Kondrat, Simon A; Shozi, Mzamo

    2017-05-02

    Welcome to Africa was the motto when after more than 100 years the flag ship conference series of the Royal Society of Chemistry, the Faraday Discussions was hosted for the first time on the African Continent. Under the fitting topic 'Catalysis for Fuels' over 120 delegates followed the invitation by the conference chair Prof. Graham Hutchings FRS (Cardiff Catalysis Institute), his organizing committee and the co-organizing DST-NRF Centre of Excellence in Catalysis c*change (). In the presentations of 21 invited speakers and 59 posters, cutting edge research in the field of catalysis for fuels, designing new catalysts for synthetic fuels, hydrocarbon conversion in the production of synthetic fuels and novel photocatalysis was presented over the two-day meeting. The scene was set by the opening lecture of Prof. Enrique Iglesias (UC Berkeley) and wrapped-up with the concluding remarks by Philip Gibson (SASOL).

  18. Loop residues and catalysis in OMP synthase

    DEFF Research Database (Denmark)

    Wang, Gary P.; Hansen, Michael Riis; Grubmeyer, Charles

    2012-01-01

    (preceding paper in this issue, DOI 10.1021/bi300083p)]. The full expression of KIEs by H105A and E107A may result from a less secure closure of the catalytic loop. The lower level of expression of the KIE by K103A suggests that in these mutant proteins the major barrier to catalysis is successful closure...... of the catalytic loop, which when closed, produces rapid and reversible catalysis....

  19. Advancing Sustainable Catalysis with Magnetite Surface ...

    Science.gov (United States)

    This article surveys the recent developments in the synthesis, surface modification, and synthetic applications of magnetitenanoparticles. The emergence of iron(II,III) oxide (triiron tetraoxide or magnetite; Fe3O4, or FeO•Fe2O3) nanoparticles as a sustainable support in heterogeneous catalysis is highlighted. Use of an oxide of earth-abundant iron for various applications in catalysis and environmental remediation.

  20. Contributions to the tooth morphology in early embryos of three species of hammerhead sharks (Elasmobranchii: Sphyrnidae) and their evolutionary implications.

    Science.gov (United States)

    Mello, Waldiney; Brito, Paulo Marques Machado

    2013-09-01

    The tooth types in the embryos of the hammerhead sharks Sphyrna tiburo, Sphyrna tudes and Eusphyra blochii are here described in labial and lingual views, and, in some cases, in additional views. The presence of cusplets was observed in the anterior teeth of S. tiburo and S. tudes, which is secondarily lost after early embryonic stages. Many aligned root foramina were detected in the sphyrnids, which, as the cusplets, are shared by many phylogenetic-related carcharhinids. Other anatomic features, related to the root and central cusp, are presented for the first time. Such characters represent the first step to compare the teeth of extant and fossil species. Copyright © 2013. Published by Elsevier SAS.

  1. Mercury and selenium bioaccumulation in the smooth hammerhead shark, Sphyrna zygaena Linnaeus, from the Mexican Pacific Ocean.

    Science.gov (United States)

    Escobar-Sánchez, O; Galván-Magaña, F; Rosíles-Martínez, R

    2010-04-01

    We analyzed total mercury and selenium bioaccumulation in muscle tissue and cartilage fibers (fins) from smooth hammerhead shark, Sphyrna zygaena, caught off Baja California Sur, Mexico. In muscle tissue, the mercury concentration ranged from 0.005 to 1.93 microg g(-1) ww (wet weight), which falls within the safety limits for food set by international agencies (Hg > 1.0 microg g(-1) ww). Only one specimen showed a mercury value that exceeded this limit. In fins, the mercury bioaccumulation was lower (<0.05). Selenium in muscle ranged from 0.11 to 1.63 microg g(-1) ww, while in fins it ranged from 0.13 to 0.56 microg g(-1) ww.

  2. A computational study of the hydrodynamics in the nasal region of a hammerhead shark (Sphyrna tudes: implications for olfaction.

    Directory of Open Access Journals (Sweden)

    Alex D Rygg

    Full Text Available The hammerhead shark possesses a unique head morphology that is thought to facilitate enhanced olfactory performance. The olfactory chambers, located at the distal ends of the cephalofoil, contain numerous lamellae that increase the surface area for olfaction. Functionally, for the shark to detect chemical stimuli, water-borne odors must reach the olfactory sensory epithelium that lines these lamellae. Thus, odorant transport from the aquatic environment to the sensory epithelium is the first critical step in olfaction. Here we investigate the hydrodynamics of olfaction in Sphyrna tudes based on an anatomically-accurate reconstruction of the head and olfactory chamber from high-resolution micro-CT and MRI scans of a cadaver specimen. Computational fluid dynamics simulations of water flow in the reconstructed model reveal the external and internal hydrodynamics of olfaction during swimming. Computed external flow patterns elucidate the occurrence of flow phenomena that result in high and low pressures at the incurrent and excurrent nostrils, respectively, which induces flow through the olfactory chamber. The major (prenarial nasal groove along the cephalofoil is shown to facilitate sampling of a large spatial extent (i.e., an extended hydrodynamic "reach" by directing oncoming flow towards the incurrent nostril. Further, both the major and minor nasal grooves redirect some flow away from the incurrent nostril, thereby limiting the amount of fluid that enters the olfactory chamber. Internal hydrodynamic flow patterns are also revealed, where we show that flow rates within the sensory channels between olfactory lamellae are passively regulated by the apical gap, which functions as a partial bypass for flow in the olfactory chamber. Consequently, the hammerhead shark appears to utilize external (major and minor nasal grooves and internal (apical gap flow regulation mechanisms to limit water flow between the olfactory lamellae, thus protecting these

  3. Purification, characterization, and biological activity of insulins from the spotted dogfish, Scyliorhinus canicula, and the hammerhead shark, Sphyrna lewini.

    Science.gov (United States)

    Anderson, W Gary; Ali, Mohamed F; Einarsdóttir, Ingibjörg E; Schäffer, Lauge; Hazon, Neil; Conlon, J Michael

    2002-03-01

    Insulin was purified from pancreatic extracts of two elasmobranch species belonging to different families in the order Carcharhiniformes, the European spotted dogfish, Scyliorhinus canicula (Scyliorhinidae), and the hammerhead shark, Sphyrna lewini (Carcharhinidae). The amino acid sequence of dogfish insulin was established as A-chain GIVDHCCRNT(10)CSLYDLEGYC(20)NQ and B-chain LPSQHLCGSH(10)LVETLYFVCG(20)QKGFYYVPKV(30). The primary structure of hammerhead shark insulin was similar to that of dogfish insulin with only 2 amino acid substitutions at A8 (R --> H) and B30 (V --> I). The elasmobranch insulins were markedly different from human insulin (17 amino acid substitutions) but all the residues in human insulin that are believed to be important in determining the receptor binding conformation (B6, B8, B11, B13, B23, B24, B25, A2, A3, and A19) have been conserved in the elasmobranch insulins with the exception of the conservative substitution Phe --> Tyr at B25. Consistent with this, dogfish and human insulin showed almost identical binding affinity to the recombinant solubilized human insulin receptor (K(D) values of 14.0 and 18.6 pM, respectively; relative potency 133%). Previous studies have shown that bovine insulin produces severe and sustained hypoglycemia in elasmobranchs but the effect is of slow onset. Bolus arterial injections of dogfish insulin (10 nmol x kg(-1)) into unanesthetized, fasting dogfish (n = 9) produced no changes in blood glucose, 3-hydroxybutyrate, and acetoacetate concentrations over a 4-h period. In a second series of experiments (n = 7), dogfish insulin (10 nmol x kg(-1)) produced a significant (P < 0.05) fall in blood glucose after 12 h that persisted for at least 48 h, but no change in ketone body concentrations. The data indicate that the metabolic actions of an endogenous elasmobranch insulin in an elasmobranch are similar to those previously described for mammalian insulin.

  4. A computational study of the hydrodynamics in the nasal region of a hammerhead shark (Sphyrna tudes): implications for olfaction.

    Science.gov (United States)

    Rygg, Alex D; Cox, Jonathan P L; Abel, Richard; Webb, Andrew G; Smith, Nadine B; Craven, Brent A

    2013-01-01

    The hammerhead shark possesses a unique head morphology that is thought to facilitate enhanced olfactory performance. The olfactory chambers, located at the distal ends of the cephalofoil, contain numerous lamellae that increase the surface area for olfaction. Functionally, for the shark to detect chemical stimuli, water-borne odors must reach the olfactory sensory epithelium that lines these lamellae. Thus, odorant transport from the aquatic environment to the sensory epithelium is the first critical step in olfaction. Here we investigate the hydrodynamics of olfaction in Sphyrna tudes based on an anatomically-accurate reconstruction of the head and olfactory chamber from high-resolution micro-CT and MRI scans of a cadaver specimen. Computational fluid dynamics simulations of water flow in the reconstructed model reveal the external and internal hydrodynamics of olfaction during swimming. Computed external flow patterns elucidate the occurrence of flow phenomena that result in high and low pressures at the incurrent and excurrent nostrils, respectively, which induces flow through the olfactory chamber. The major (prenarial) nasal groove along the cephalofoil is shown to facilitate sampling of a large spatial extent (i.e., an extended hydrodynamic "reach") by directing oncoming flow towards the incurrent nostril. Further, both the major and minor nasal grooves redirect some flow away from the incurrent nostril, thereby limiting the amount of fluid that enters the olfactory chamber. Internal hydrodynamic flow patterns are also revealed, where we show that flow rates within the sensory channels between olfactory lamellae are passively regulated by the apical gap, which functions as a partial bypass for flow in the olfactory chamber. Consequently, the hammerhead shark appears to utilize external (major and minor nasal grooves) and internal (apical gap) flow regulation mechanisms to limit water flow between the olfactory lamellae, thus protecting these delicate

  5. A Computational Study of the Hydrodynamics in the Nasal Region of a Hammerhead Shark (Sphyrna tudes): Implications for Olfaction

    Science.gov (United States)

    Rygg, Alex D.; Cox, Jonathan P. L.; Abel, Richard; Webb, Andrew G.; Smith, Nadine B.; Craven, Brent A.

    2013-01-01

    The hammerhead shark possesses a unique head morphology that is thought to facilitate enhanced olfactory performance. The olfactory chambers, located at the distal ends of the cephalofoil, contain numerous lamellae that increase the surface area for olfaction. Functionally, for the shark to detect chemical stimuli, water-borne odors must reach the olfactory sensory epithelium that lines these lamellae. Thus, odorant transport from the aquatic environment to the sensory epithelium is the first critical step in olfaction. Here we investigate the hydrodynamics of olfaction in Sphyrna tudes based on an anatomically-accurate reconstruction of the head and olfactory chamber from high-resolution micro-CT and MRI scans of a cadaver specimen. Computational fluid dynamics simulations of water flow in the reconstructed model reveal the external and internal hydrodynamics of olfaction during swimming. Computed external flow patterns elucidate the occurrence of flow phenomena that result in high and low pressures at the incurrent and excurrent nostrils, respectively, which induces flow through the olfactory chamber. The major (prenarial) nasal groove along the cephalofoil is shown to facilitate sampling of a large spatial extent (i.e., an extended hydrodynamic “reach”) by directing oncoming flow towards the incurrent nostril. Further, both the major and minor nasal grooves redirect some flow away from the incurrent nostril, thereby limiting the amount of fluid that enters the olfactory chamber. Internal hydrodynamic flow patterns are also revealed, where we show that flow rates within the sensory channels between olfactory lamellae are passively regulated by the apical gap, which functions as a partial bypass for flow in the olfactory chamber. Consequently, the hammerhead shark appears to utilize external (major and minor nasal grooves) and internal (apical gap) flow regulation mechanisms to limit water flow between the olfactory lamellae, thus protecting these delicate

  6. Specific acid catalysis and Lewis acid catalysis of Diels-Alder reactions in aqueous media

    NARCIS (Netherlands)

    Mubofu, E.B.; Engberts, J.B.F.N.

    A comparative study of specific acid catalysis and Lewis acid catalysis of Diells-Alder reactions between dienophiles (1, 4 and 6) and cyclopentadiene (2) in water and mixed aqueous media is reported. The reactions were performed in water with copper(II) nitrate as the Lewis acid catalyst whereas

  7. Specific acid catalysis and Lewis acid catalysis of Diels–Alder reactions in aqueous media

    NARCIS (Netherlands)

    Mubofu, Egid B.; Engberts, Jan B.F.N.

    2004-01-01

    A comparative study of specific acid catalysis and Lewis acid catalysis of Diels–Alder reactions between dienophiles (1, 4 and 6) and cyclopentadiene (2) in water and mixed aqueous media is reported. The reactions were performed in water with copper(II) nitrate as the Lewis acid catalyst whereas

  8. ISOTOPE METHODS IN HOMOGENEOUS CATALYSIS.

    Energy Technology Data Exchange (ETDEWEB)

    BULLOCK,R.M.; BENDER,B.R.

    2000-12-01

    The use of isotope labels has had a fundamentally important role in the determination of mechanisms of homogeneously catalyzed reactions. Mechanistic data is valuable since it can assist in the design and rational improvement of homogeneous catalysts. There are several ways to use isotopes in mechanistic chemistry. Isotopes can be introduced into controlled experiments and followed where they go or don't go; in this way, Libby, Calvin, Taube and others used isotopes to elucidate mechanistic pathways for very different, yet important chemistries. Another important isotope method is the study of kinetic isotope effects (KIEs) and equilibrium isotope effect (EIEs). Here the mere observation of where a label winds up is no longer enough - what matters is how much slower (or faster) a labeled molecule reacts than the unlabeled material. The most careti studies essentially involve the measurement of isotope fractionation between a reference ground state and the transition state. Thus kinetic isotope effects provide unique data unavailable from other methods, since information about the transition state of a reaction is obtained. Because getting an experimental glimpse of transition states is really tantamount to understanding catalysis, kinetic isotope effects are very powerful.

  9. Comparison of total lipids and fatty acids from liver, heart and abdominal muscle of scalloped (Sphyrna lewini) and smooth (Sphyrna zygaena) hammerhead sharks.

    Science.gov (United States)

    Davidson, Bruce Clement; Nel, Wynand; Rais, Afsha; Namdarizandi, Vahid; Vizarra, Scott; Cliff, Geremy

    2014-01-01

    Liver, heart and abdominal muscle samples from scalloped (Sphyrna lewini) and smooth (Sphyrna zygaena) hammerhead sharks were analysed to characterise their lipid and fatty acid profiles. Samples were compared both between and within species, but there were no significant differences in total lipids for either comparison, although much greater total amounts were found in the liver samples. Within the individual fatty acids, the only significant differences were greater amounts of 22:6n-3, total n-3 polyunsaturates and total polyunsaturates in smooth, when compared to scalloped, hammerhead liver. This may reflect the more wide spread distribution of this species into cooler waters. Within both species the liver levels of the same fatty acid fractions decreased from spring to summer, which may correlate with changes in fatty acid profile to adapt to any differences in amount or species of prey consumed, or other considerations, eg. buoyancy, however there was no data to clarify this.

  10. The electrosensorial pore system of the cephalofoil in the four most common species of hammerhead shark (Elasmobranchii: Sphyrnidae) from the Southwestern Atlantic.

    Science.gov (United States)

    Mello, Waldiney

    2009-04-01

    The laterally expanded head is the principal character distinguishing hammerhead sharks, and its morphology is important for interpreting their ontogeny and species diversity. Because their head shape changes during its ontogeny, it is vital to evaluate it in order to establish other taxonomical characteristics to correctly identify Sphyrna species. This study examines the distribution of electrosensorial pore regions on the ventral surface of the cephalofoil (VSC) in Sphyrna lewini, S. tiburo, S. tudes and S. zygaena from the Southwestern Atlantic Ocean. The pore distribution patterns in the VSC can distinguish these species. Use of those patterns, with the head shape, confirms the identification of the four most common species of hammerhead sharks in the Southwestern Atlantic.

  11. Advanced Resources for Catalysis Science; Recommendations for a National Catalysis Research Institute

    Energy Technology Data Exchange (ETDEWEB)

    Peden, Charles HF.; Ray, Douglas

    2005-10-05

    Catalysis is one of the most valuable contributors to our economy and historically an area where the United States has enjoyed, but is now losing, international leadership. While other countries are stepping up their work in this area, support for advanced catalysis research and development in the U.S. has diminished. Yet, more than ever, innovative and improved catalyst technologies are imperative for new energy production processes to ease our dependence on imported resources, for new energy-efficient and environmentally benign chemical production processes, and for new emission reduction technologies to minimize the environmental impact of an active and growing economy. Addressing growing concerns about the future direction of U.S. catalysis science, experts from the catalysis community met at a workshop to determine and recommend advanced resources needed to address the grand challenges for catalysis research and development. The workshop's primary conclusion: To recapture our position as the leader in catalysis innovation and practice, and promote crucial breakthroughs, the U.S. must establish one or more well-funded and well-equipped National Catalysis Research Institutes competitively selected, centered in the national laboratories and, by charter, networked to other national laboratories, universities, and industry. The Institute(s) will be the center of a national collaboratory that gives catalysis researchers access to the most advanced techniques available in the scientific enterprise. The importance of catalysis to our energy, economic, and environmental security cannot be overemphasized. Catalysis is a vital part of our core industrial infrastructure, as it is integral to chemical processing and petroleum refining, and is critical to proposed advances needed to secure a sustainable energy future. Advances in catalysis could reduce our need for foreign oil by making better use of domestic carbon resources, for example, allowing cost-effective and

  12. SOME BIOLOGICAL ASPECTS OF SCALLOPED HAMMERHEAD SHARKS (Sphyrna lewini Griffith & Smith, 1834) CAUGHT FROM COASTAL FISHERIES IN THE EASTERN INDIAN OCEAN

    OpenAIRE

    Umi Chodrijah; Bram Setyadji

    2015-01-01

    Indonesia has the largest chondrichthyan fishery in the world, with a reported of 105,000 and 118,000 tonnes landed in 2002 and 2003 respectively. Scalloped hammerhead shark was either targeted or by-catch from this fishery, mostly for its fins. Despite of the growing concern around the world, the availability of biological data of this species, especially in the Eastern Indian Ocean is still lacking. The objectives of this paper are to present some biological information (size composition an...

  13. Operando chemistry of catalyst surfaces during catalysis.

    Science.gov (United States)

    Dou, Jian; Sun, Zaicheng; Opalade, Adedamola A; Wang, Nan; Fu, Wensheng; Tao, Franklin Feng

    2017-04-03

    Chemistry of a catalyst surface during catalysis is crucial for a fundamental understanding of mechanism of a catalytic reaction performed on the catalyst in the gas or liquid phase. Due to the pressure- or molecular density-dependent entropy contribution of gas or liquid phase of the reactants and the potential formation of a catalyst surface during catalysis different from that observed in an ex situ condition, the characterization of the surface of a catalyst under reaction conditions and during catalysis can be significant and even necessary for understanding the catalytic mechanism at a molecular level. Electron-based analytical techniques are challenging for studying catalyst nanoparticles in the gas or liquid phase although they are necessary techniques to employ. Instrumentation and further development of these electron-based techniques have now made in situ/operando studies of catalysts possible. New insights into the chemistry and structure of catalyst nanoparticles have been uncovered over the last decades. Herein, the origin of the differences between ex situ and in situ/operando studies of catalysts, and the technical challenges faced as well as the corresponding instrumentation and innovations utilized for characterizing catalysts under reaction conditions and during catalysis, are discussed. The restructuring of catalyst surfaces driven by the pressure of reactant(s) around a catalyst, restructuring in reactant(s) driven by reaction temperature and restructuring during catalysis are also reviewed herein. The remaining challenges and possible solutions are briefly discussed.

  14. Application of Artificial Neural Networks for Catalysis: A Review

    National Research Council Canada - National Science Library

    Hao Li; Zhien Zhang; Zhijian Liu

    2017-01-01

    .... However, their applications for catalysis were not well-studied until recent decades. In this review, we aim to summarize the applications of ANNs for catalysis research reported in the literature...

  15. Green chemistry by nano-catalysis

    KAUST Repository

    Polshettiwar, Vivek

    2010-01-01

    Nano-materials are important in many diverse areas, from basic research to various applications in electronics, biochemical sensors, catalysis and energy. They have emerged as sustainable alternatives to conventional materials, as robust high surface area heterogeneous catalysts and catalyst supports. The nano-sized particles increase the exposed surface area of the active component of the catalyst, thereby enhancing the contact between reactants and catalyst dramatically and mimicking the homogeneous catalysts. This review focuses on the use of nano-catalysis for green chemistry development including the strategy of using microwave heating with nano-catalysis in benign aqueous reaction media which offers an extraordinary synergistic effect with greater potential than these three components in isolation. To illustrate the proof-of-concept of this "green and sustainable" approach, representative examples are discussed in this article. © 2010 The Royal Society of Chemistry.

  16. Progress towards bioorthogonal catalysis with organometallic compounds.

    Science.gov (United States)

    Völker, Timo; Dempwolff, Felix; Graumann, Peter L; Meggers, Eric

    2014-09-22

    The catalysis of bioorthogonal transformations inside living organisms is a formidable challenge--yet bears great potential for future applications in chemical biology and medicinal chemistry. We herein disclose highly active organometallic ruthenium complexes for bioorthogonal catalysis under biologically relevant conditions and inside living cells. The catalysts uncage allyl carbamate protected amines with unprecedented high turnover numbers of up to 270 cycles in the presence of water, air, and millimolar concentrations of thiols. By live-cell imaging of HeLa cells and with the aid of a caged fluorescent probe we could reveal a rapid development of intense fluorescence within the cellular cytoplasm and therefore support the proposed bioorthogonality of the catalysts. In addition, to illustrate the manifold applications of bioorthogonal catalysis, we developed a method for catalytic in-cell activation of a caged anticancer drug, which efficiently induced apoptosis in HeLa cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Request for Symposia Support: Advances in Olefin Polymerization Catalysis

    Science.gov (United States)

    2014-11-24

    included, but were not limited to, heterogeneous catalysis , homogeneous catalysis , advances in catalyst activation, methods for polymer topological...SECURITY CLASSIFICATION OF: This Advances in Olefin Polymerization Catalysis symposium was held at the 247th ACS National Meeting and Exposition...March 19, 2014 in Dallas, Texas and consisted of twelve (12) invited/contributed talks. The hosting ACS division was the Division of Catalysis Science

  18. Next-Generation Catalysis for Renewables: Combining Enzymatic with Inorganic Heterogeneous Catalysis for Bulk Chemical Production

    DEFF Research Database (Denmark)

    Vennestrøm, Peter Nicolai Ravnborg; Christensen, C.H.; Pedersen, S.

    2010-01-01

    chemical platform under different conditions than those conventionally employed. Indeed, new process and catalyst concepts need to be established. Both enzymatic catalysis (biocatalysis) and heterogeneous inorganic catalysis are likely to play a major role and, potentially, be combined. One type...... of combination involves one-pot cascade catalysis with active sites from bio- and inorganic catalysts. In this article the emphasis is placed specifically on oxidase systems involving the coproduction of hydrogen peroxide, which can be used to create new in situ collaborative oxidation reactions for bulk...

  19. Ionic Liquids: Synthesis and Applications in Catalysis

    Directory of Open Access Journals (Sweden)

    Rajni Ratti

    2014-01-01

    Full Text Available Ionic liquids have emerged as an environmentally friendly alternative to the volatile organic solvents. Being designer solvents, they can be modulated to suit the reaction conditions, therefore earning the name “task specific ionic liquids.” Though primarily used as solvents, they are now finding applications in various fields like catalysis, electrochemistry, spectroscopy, and material science to mention a few. The present review is aimed at exploring the applications of ionic liquids in catalysis as acid, base, and organocatalysts and as soluble supports for catalysts.

  20. RNA catalysis and the origins of life

    Science.gov (United States)

    Orgel, Leslie E.

    1986-01-01

    The role of RNA catalysis in the origins of life is considered in connection with the discovery of riboszymes, which are RNA molecules that catalyze sequence-specific hydrolysis and transesterification reactions of RNA substrates. Due to this discovery, theories positing protein-free replication as preceding the appearance of the genetic code are more plausible. The scope of RNA catalysis in biology and chemistry is discussed, and it is noted that the development of methods to select (or predict) RNA sequences with preassigned catalytic functions would be a major contribution to the study of life's origins.

  1. A molecular view of heterogeneous catalysis

    DEFF Research Database (Denmark)

    Christensen, Claus H.; Nørskov, Jens Kehlet

    2008-01-01

    The establishment of a molecular view of heterogeneous catalysis has been hampered for a number of reasons. There are, however, recent developments, which show that we are now on the way towards reaching a molecular-scale picture of the way solids work as catalysts. By a combination of new...... by enabling a rational design of new catalysts. We illustrate this important development in heterogeneous catalysis by highlighting recent examples of catalyst systems for which it has been possible to achieve such a detailed understanding. In particular, we emphasize examples where this progress has made...

  2. Keynotes in energy-related catalysis

    CERN Document Server

    Kaliaguine, S

    2011-01-01

    Catalysis by solid acids, which includes (modified) zeolites, is of special relevance to energy applications. Acid catalysis is highly important in modern petroleum refining operations - large-scale processes such as fluid catalytic cracking, catalytic reforming, alkylation and olefin oligomerization rely on the transformation of hydrocarbons by acid catalysts. (Modified) zeolites are therefore essential for the improvement of existing processes and for technical innovations in the conversion of crude. There can be little doubt that zeolite-based catalysts will play a major role in the futu

  3. Catalysis by nonmetals rules for catalyst selection

    CERN Document Server

    Krylov, Oleg V

    1970-01-01

    Catalysis by Non-metals: Rules of Catalyst Selection presents the development of scientific principles for the collection of catalysts. It discusses the investigation of the mechanism of chemosorption and catalysis. It addresses a series of properties of solid with catalytic activity. Some of the topics covered in the book are the properties of a solid and catalytic activity in oxidation-reduction reactions; the difference of electronegativities and the effective charges of atoms; the role of d-electrons in the catalytic properties of a solid; the color of solids; and proton-acid and proton-ba

  4. Heterogeneous catalysis at nanoscale for energy applications

    CERN Document Server

    Tao, Franklin (Feng); Kamat, Prashant V

    2015-01-01

    This book presents both the fundamentals concepts and latest achievements of a field that is growing in importance since it represents a possible solution for global energy problems.  It focuses on an atomic-level understanding of heterogeneous catalysis involved in important energy conversion processes. It presents a concise picture for the entire area of heterogeneous catalysis with vision at the atomic- and nano- scales, from synthesis, ex-situ and in-situ characterization, catalytic activity and selectivity, to mechanistic understanding based on experimental exploration and theoretical si

  5. Chiral fullerenes from asymmetric catalysis.

    Science.gov (United States)

    Maroto, Enrique E; Izquierdo, Marta; Reboredo, Silvia; Marco-Martínez, Juan; Filippone, Salvatore; Martín, Nazario

    2014-08-19

    Fullerenes are among the most studied molecules during the last three decades, and therefore, a huge number of chemical reactions have been tested on these new carbon allotropes. However, the aim of most of the reactions carried out on fullerenes has been to afford chemically modified fullerenes that are soluble in organic solvents or even water in the search for different mechanical, optical, or electronic properties. Therefore, although a lot of effort has been devoted to the chemical functionalization of these molecular allotropes of carbon, important aspects in the chemistry of fullerenes have not been properly addressed. In particular, the synthesis of chiral fullerenes at will in an efficient manner using asymmetric catalysis has not been previously addressed in fullerene science. Thus, despite the fact that the chirality of fullerenes has always been considered a fundamental issue, the lack of a general stereoselective synthetic methodology has restricted the use of enantiopure fullerene derivatives, which have usually been obtained only after highly expensive HPLC isolation on specific chiral columns or prepared from a pool of chiral starting materials. In this Account, we describe the first stereodivergent catalytic enantioselective syntheses in fullerene science, which have allowed the highly efficient synthesis of enantiomerically pure derivatives with total control of the stereochemical result using metallic catalysts and/or organocatalysts under very mild conditions. Density functional theory calculations strongly support the experimental findings for the assignment of the absolute configuration of the new stereocenters, which has also been ascertained by application of the sector rule and single-crystal X-ray diffraction. The use of the curved double bond of fullerene cages as a two-π-electron component in a variety of stereoselective cycloaddition reactions represents a challenging goal considering that, in contrast to most of the substituted

  6. Intermetallic: A Pseudoelement for Catalysis.

    Science.gov (United States)

    Tsai, A P; Kameoka, S; Nozawa, K; Shimoda, M; Ishii, Y

    2017-12-19

    A clear correlation between electronic structure and CO2 selectivity for steam reforming of methanol (SRM) was obtained with PdZn, PtZn, NiZn, and PdCd intermetallics on the basis of experiments and calculations. In order to rule out the effects of oxide supports, the intermetallic powders were simply prepared by alloying in an arc furnace followed by crushing in a mortar. PdZn and PdCd exhibit valence electronic densities of states similar to that of Cu and significant chemical shifts (larger than 1 eV) of Pd 3d states with respect to pure Pd, as verified by high-resolution hard X-ray photoelectron spectroscopy (HXPS) measurements and density functional theory (DFT) calculations. Consequently, they show the similar high selectivity of CO2 for the SRM reaction. However, this is not the case for PtZn and NiZn because of the slight differences in their valence electronic structures from that of PdZn. The interval between the Fermi level and the top of the d band is closely related to the selectivity of CO2 for the SRM: the larger the interval is, the higher is the selectivity of CO2. According to DFT calculations for bulk PdZn performed by Chen et al. ( Phys. Rev. B 2003 , 68 , 075417 ), the (111) and (100) surfaces exposing Zn and Pd in an equimolar ratio are more stable than the (001) or (110) surfaces terminated by alternative Zn or Pd layers. First-principles slab calculations for PdZn, PtZn, and NiZn show that bond breaking on the surface leads to a reduction in the d bandwidth but that the d band for stable (111) or (100) surfaces remains essentially unchanged from that of the bulk. It is intriguing that PdZn and PdCd do not contain Cu but show similar valence electronic structure and catalytic selectivity, and hence, a concept is proposed where PdZn and PdCd are regarded as pseudoelements of Cu. The basis of this concept is like electronic structure, like catalysis, which has been demonstrated by experiments and calculations. This is a logical way to enable us

  7. Simple peptides derived from the ribosomal core potentiate RNA polymerase ribozyme function

    Science.gov (United States)

    Tagami, Shunsuke; Attwater, James; Holliger, Philipp

    2017-04-01

    The emergence of functional interactions between nucleic acids and polypeptides was a key transition in the origin of life and remains at the heart of all biology. However, how and why simple non-coded peptides could have become critical for RNA function is unclear. Here, we show that putative ancient peptide segments from the cores of both ribosomal subunits enhance RNA polymerase ribozyme (RPR) function, as do derived homopolymeric peptides comprising lysine or the non-proteinogenic lysine analogues ornithine or, to a lesser extent, diaminobutyric acid, irrespective of chirality or chiral purity. Lysine decapeptides enhance RPR function by promoting holoenzyme assembly through primer-template docking, accelerate RPR evolution, and allow RPR-catalysed RNA synthesis at near physiological (≥1 mM) Mg2+ concentrations, enabling templated RNA synthesis within membranous protocells. Our results outline how compositionally simple, mixed-chirality peptides may have augmented the functional potential of early RNAs and promoted the emergence of the first protocells.

  8. Phase 2 gene therapy trial of an anti-HIV ribozyme in autologous CD34+ cells.

    Science.gov (United States)

    Mitsuyasu, Ronald T; Merigan, Thomas C; Carr, Andrew; Zack, Jerome A; Winters, Mark A; Workman, Cassy; Bloch, Mark; Lalezari, Jacob; Becker, Stephen; Thornton, Lorna; Akil, Bisher; Khanlou, Homayoon; Finlayson, Robert; McFarlane, Robert; Smith, Don E; Garsia, Roger; Ma, David; Law, Matthew; Murray, John M; von Kalle, Christof; Ely, Julie A; Patino, Sharon M; Knop, Alison E; Wong, Philip; Todd, Alison V; Haughton, Margaret; Fuery, Caroline; Macpherson, Janet L; Symonds, Geoff P; Evans, Louise A; Pond, Susan M; Cooper, David A

    2009-03-01

    Gene transfer has potential as a once-only treatment that reduces viral load, preserves the immune system and avoids lifetime highly active antiretroviral therapy. This study, which is to our knowledge the first randomized, double-blind, placebo-controlled, phase 2 cell-delivered gene transfer clinical trial, was conducted in 74 HIV-1-infected adults who received a tat-vpr-specific anti-HIV ribozyme (OZ1) or placebo delivered in autologous CD34+ hematopoietic progenitor cells. There were no OZ1-related adverse events. There was no statistically significant difference in viral load between the OZ1 and placebo group at the primary end point (average at weeks 47 and 48), but time-weighted areas under the curve from weeks 40-48 and 40-100 were significantly lower in the OZ1 group. Throughout the 100 weeks, CD4+ lymphocyte counts were higher in the OZ1 group. This study indicates that cell-delivered gene transfer is safe and biologically active in individuals with HIV and can be developed as a conventional therapeutic product.

  9. Direct sp(3)C-H acroleination of N-aryl-tetrahydroisoquinolines by merging photoredox catalysis with nucleophilic catalysis.

    Science.gov (United States)

    Feng, Zhu-Jia; Xuan, Jun; Xia, Xu-Dong; Ding, Wei; Guo, Wei; Chen, Jia-Rong; Zou, You-Quan; Lu, Liang-Qiu; Xiao, Wen-Jing

    2014-04-07

    Sequence catalysis merging photoredox catalysis (PC) and nucleophilic catalysis (NC) has been realized for the direct sp(3) C-H acroleination of N-aryl-tetrahydroisoquinoline (THIQ). The reaction was performed under very mild conditions and afforded products in 50-91% yields. A catalytic asymmetric variant was proved to be successful with moderate enantioselectivities (up to 83 : 17 er).

  10. Homogeneous and heterogeneous catalysis production and ...

    African Journals Online (AJOL)

    Temperature and methanol characteristics (oil molar ratio; catalyst type, concentration and agitation) controlled the ester convers-ion. ... The fuel properties of biodiesels and blends were analysed quantitati-vely, and the biodiesel produced by homogeneous catalysis compared favourably with conventional diesel fuel.

  11. µ-reactors for Heterogeneous Catalysis

    DEFF Research Database (Denmark)

    Jensen, Robert

    is described in detail. Since heating and temperature measurement is an extremely important point in heterogeneous catalysis an entire chapter is dedicated to this subject. Three different types of heaters have been implemented and tested both for repeatability and homogeneity of the heating as well...

  12. Supported ionic liquid-phase (SILP) catalysis

    DEFF Research Database (Denmark)

    Riisager, Anders; Fehrmann, Rasmus; Wasserscheid, P.

    2005-01-01

    The concept of supported ionic liquid-phase (SILP) catalysis has been demonstrated for gas- and liquid-phase continuous fixed-bed reactions using rhodium phosphine catalyzed hydroformylation of propene and 1-octene as examples. The nature of the support had important influence on both the catalytic...

  13. Diffusion and Surface Reaction in Heterogeneous Catalysis

    Science.gov (United States)

    Baiker, A.; Richarz, W.

    1978-01-01

    Ethylene hydrogenation on a platinum catalyst, electrolytically applied to a tube wall, is a good system for the study of the interactions between diffusion and surface reaction in heterogeneous catalysis. Theoretical background, apparatus, procedure, and student performance of this experiment are discussed. (BB)

  14. Confined catalysis under two-dimensional materials

    Science.gov (United States)

    Li, Haobo; Xiao, Jianping; Bao, Xinhe

    2017-01-01

    Confined microenvironments formed in heterogeneous catalysts have recently been recognized as equally important as catalytically active sites. Understanding the fundamentals of confined catalysis has become an important topic in heterogeneous catalysis. Well-defined 2D space between a catalyst surface and a 2D material overlayer provides an ideal microenvironment to explore the confined catalysis experimentally and theoretically. Using density functional theory calculations, we reveal that adsorption of atoms and molecules on a Pt(111) surface always has been weakened under monolayer graphene, which is attributed to the geometric constraint and confinement field in the 2D space between the graphene overlayer and the Pt(111) surface. A similar result has been found on Pt(110) and Pt(100) surfaces covered with graphene. The microenvironment created by coating a catalyst surface with 2D material overlayer can be used to modulate surface reactivity, which has been illustrated by optimizing oxygen reduction reaction activity on Pt(111) covered by various 2D materials. We demonstrate a concept of confined catalysis under 2D cover based on a weak van der Waals interaction between 2D material overlayers and underlying catalyst surfaces. PMID:28533413

  15. Predictive modeling in homogeneous catalysis: a tutorial

    NARCIS (Netherlands)

    Maldonado, A.G.; Rothenberg, G.

    2010-01-01

    Predictive modeling has become a practical research tool in homogeneous catalysis. It can help to pinpoint ‘good regions’ in the catalyst space, narrowing the search for the optimal catalyst for a given reaction. Just like any other new idea, in silico catalyst optimization is accepted by some

  16. Hydroxide catalysis bonding of silicon carbide

    NARCIS (Netherlands)

    Veggel, A.A. van; Ende, D.A. van den; Bogenstahl, J.; Rowan, S.; Cunningham, W.; Gubbels, G.H.M.; Nijmeijer, H.

    2008-01-01

    For bonding silicon carbide optics, which require extreme stability, hydroxide catalysis bonding is considered [Rowan, S., Hough, J. and Elliffe, E., Silicon carbide bonding. UK Patent 040 7953.9, 2004. Please contact Mr. D. Whiteford for further information: D.Whiteford@admin.gla.ac.uk]. This

  17. Supported Ionic Liquid Phase (SILP) catalysis

    DEFF Research Database (Denmark)

    Riisager, Anders; Fehrmann, Rasmus; Haumann, Marco

    2006-01-01

    Applications of ionic liquids to replace conventional solvents in homogeneous transition-metal catalysis have increased significantly during the last decade. Biphasic ionic liquid/organic liquid systems offer advantages with regard to product separation, catalyst stability, and recycling but util...

  18. Surface temperature excess in heterogeneous catalysis

    NARCIS (Netherlands)

    Zhu, L.

    2005-01-01

    In this dissertation we study the surface temperature excess in heterogeneous catalysis. For heterogeneous reactions, such as gas-solid catalytic reactions, the reactions take place at the interfaces between the two phases: the gas and the solid catalyst. Large amount of reaction heats are released

  19. Robust Sub-harmonic Mixer at 340 GHz Using Intrinsic Resonances of Hammer-Head Filter and Improved Diode Model

    Science.gov (United States)

    Wang, Cheng; He, Yue; Lu, Bin; Jiang, Jun; Miao, Li; Deng, Xian-Jin; Xiong, Yong-zhong; Zhang, Jian

    2017-11-01

    This paper presents a sub-harmonic mixer at 340 GHz based on anti-parallel Schottky diodes (SBDs). Intrinsic resonances in low-pass hammer-head filter have been adopted to enhance the isolation for different harmonic components, while greatly minimizing the transmission loss. The application of new DC grounding structure, impedance matching structure, and suspended micro-strip mitigates the negative influences of fabrication errors from metal cavity, quartz substrate, and micro-assembly. An improved lumped element equivalent circuit model of SBDs guarantees the accuracy of simulation, which takes current-voltage (I/V) behavior, capacitance-voltage (C/V) behavior, carrier velocity saturation, DC series resistor, plasma resonance, skin effect, and four kinds of noise generation mechanisms into consideration thoroughly. The measurement indicates that with local oscillating signal of 2 mW, the lowest double sideband conversion loss is 5.5 dB at 339 GHz; the corresponding DSB noise temperature is 757 K. The 3 dB bandwidth of conversion loss is 50 GHz from 317 to 367 GHz.

  20. Bimetallic redox synergy in oxidative palladium catalysis.

    Science.gov (United States)

    Powers, David C; Ritter, Tobias

    2012-06-19

    Polynuclear transition metal complexes, which are embedded in the active sites of many metalloenzymes, are responsible for effecting a diverse array of oxidation reactions in nature. The range of chemical transformations remains unparalleled in the laboratory. With few noteworthy exceptions, chemists have primarily focused on mononuclear transition metal complexes in developing homogeneous catalysis. Our group is interested in the development of carbon-heteroatom bond-forming reactions, with a particular focus on identifying reactions that can be applied to the synthesis of complex molecules. In this context, we have hypothesized that bimetallic redox chemistry, in which two metals participate synergistically, may lower the activation barriers to redox transformations relevant to catalysis. In this Account, we discuss redox chemistry of binuclear Pd complexes and examine the role of binuclear intermediates in Pd-catalyzed oxidation reactions. Stoichiometric organometallic studies of the oxidation of binuclear Pd(II) complexes to binuclear Pd(III) complexes and subsequent C-X reductive elimination from the resulting binuclear Pd(III) complexes have confirmed the viability of C-X bond-forming reactions mediated by binuclear Pd(III) complexes. Metal-metal bond formation, which proceeds concurrently with oxidation of binuclear Pd(II) complexes, can lower the activation barrier for oxidation. We also discuss experimental and theoretical work that suggests that C-X reductive elimination is also facilitated by redox cooperation of both metals during reductive elimination. The effect of ligand modification on the structure and reactivity of binuclear Pd(III) complexes will be presented in light of the impact that ligand structure can exert on the structure and reactivity of binuclear Pd(III) complexes. Historically, oxidation reactions similar to those discussed here have been proposed to proceed via mononuclear Pd(IV) intermediates, and the hypothesis of mononuclear Pd

  1. Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life.

    Science.gov (United States)

    Dhar, Nisha; Weinberg, Marc S; Michod, Richard E; Durand, Pierre M

    2017-09-01

    In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3' end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life.

  2. Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

    Science.gov (United States)

    Dhar, Nisha; Weinberg, Marc S.; Michod, Richard E.; Durand, Pierre M.

    2017-09-01

    In the RNA world hypothesis complex, self-replicating ribozymes were essential. For the emergence of an RNA world, less is known about the early processes that accounted for the formation of complex, long catalysts from small passively formed molecules. The functional role of small sequences has not been fully explored and, here, a possible role for smaller ligases is demonstrated. An established RNA polymerase model, the R18, was truncated from the 3' end to generate smaller molecules. All the molecules were investigated for self-ligation functions with a set of oligonucleotide substrates without predesigned base pairing. The smallest molecule that exhibited self-ligation activity was a 40-nucleotide RNA. It also demonstrated the greatest functional flexibility as it was more general in the kinds of substrates it ligated to itself although its catalytic efficiency was the lowest. The largest ribozyme (R18) ligated substrates more selectively and with greatest efficiency. With increase in size and predicted structural stability, self-ligation efficiency improved, while functional flexibility decreased. These findings reveal that molecular size could have increased from the activity of small ligases joining oligonucleotides to their own end. In addition, there is a size-associated molecular-level trade-off that could have impacted the evolution of RNA-based life.

  3. Transition metal catalysis in confined spaces.

    Science.gov (United States)

    Leenders, Stefan H A M; Gramage-Doria, Rafael; de Bruin, Bas; Reek, Joost N H

    2015-01-21

    Transition metal catalysis plays an important role in both industry and in academia where selectivity, activity and stability are crucial parameters to control. Next to changing the structure of the ligand, introducing a confined space as a second coordination sphere around a metal catalyst has recently been shown to be a viable method to induce new selectivity and activity in transition metal catalysis. In this review we focus on supramolecular strategies to encapsulate transition metal complexes with the aim of controlling the selectivity via the second coordination sphere. As we will discuss, catalyst confinement can result in selective processes that are impossible or difficult to achieve by traditional methods. We will describe the template-ligand approach as well as the host-guest approach to arrive at such supramolecular systems and discuss how the performance of the catalyst is enhanced by confining it in a molecular container.

  4. ELECTROCHEMICAL PROMOTED CATALYSIS: TOWARDS PRACTICAL UTILIZATION

    Directory of Open Access Journals (Sweden)

    DIMITRIOS TSIPLAKIDES

    2008-07-01

    Full Text Available Electrochemical promotion (EP of catalysis has already been recognized as “a valuable development in catalytic research” (J. Pritchard, 1990 and as “one of the most remarkable advances in electrochemistry since 1950” (J. O’M. Bockris, 1996. Laboratory studies have clearly elucidated the phenomenology of electrochemical promotion and have proven that EP is a general phenomenon at the interface of catalysis and electrochemistry. The major progress toward practical utilization of EP is surveyed in this paper. The focus is given on the electropromotion of industrial ammonia synthesis catalyst, the bipolar EP and the development of a novel monolithic electropromoted reactor (MEPR in conjunction with the electropromotion of thin sputtered metal films. Future perspectives of electrochemical promotion applications in the field of hydrogen technologies are discussed.

  5. Predictive Modeling in Actinide Chemistry and Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Ping [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-16

    These are slides from a presentation on predictive modeling in actinide chemistry and catalysis. The following topics are covered in these slides: Structures, bonding, and reactivity (bonding can be quantified by optical probes and theory, and electronic structures and reaction mechanisms of actinide complexes); Magnetic resonance properties (transition metal catalysts with multi-nuclear centers, and NMR/EPR parameters); Moving to more complex systems (surface chemistry of nanomaterials, and interactions of ligands with nanoparticles); Path forward and conclusions.

  6. Catalysis in micellar and macromoleular systems

    CERN Document Server

    Fendler, Janos

    1975-01-01

    Catalysis in Micellar and Macromolecular Systems provides a comprehensive monograph on the catalyses elicited by aqueous and nonaqueous micelles, synthetic and naturally occurring polymers, and phase-transfer catalysts. It delineates the principles involved in designing appropriate catalytic systems throughout. Additionally, an attempt has been made to tabulate the available data exhaustively. The book discusses the preparation and purification of surfactants; the physical and chemical properties of surfactants and micelles; solubilization in aqueous micellar systems; and the principles of

  7. Cosmic string catalysis of skyrmion decay

    Science.gov (United States)

    Gregory, Ruth; Davis, Anne-Christine; Brandenberger, Robert

    1988-01-01

    The Callan-Witten picture is developed for monopole catalyzed skyrmion decay in order to analyze the corresponding cosmic string scenario. It is discovered that cosmic strings (both ordinary and superconducting) can catalyze proton decay, but that this catalysis only occurs on the scale of the core of the string. In order to do this we have to develop a vortex model for the superconducting string. An argument is also given for the difference in the enhancement factors for monopoles and strings.

  8. Nanoheterogeneous catalysis in electrochemically induced olefin perfluoroalkylation.

    Science.gov (United States)

    Dudkina, Yulia B; Gryaznova, Tatyana V; Osin, Yuri N; Salnikov, Vadim V; Davydov, Nikolay A; Fedorenko, Svetlana V; Mustafina, Asia R; Vicic, David A; Sinyashin, Oleg G; Budnikova, Yulia H

    2015-05-21

    Ni-catalyzed electroreductive olefin perfluoroalkylation affords both monomeric and dimeric products depending on the reaction media. Recycling of the catalyst can be achieved by immobilization of a (bpy)NiBr2 complex on silica nanoparticles decorated with anchoring amino-groups. Switching the homogeneous and heterogeneous catalysts is found to be one more factor to control the product ratio. This catalytic technique is both green and atom economical and combines the advantages of nanoheterogeneous catalysis and electrocatalysis.

  9. Nanoscale Advances in Catalysis and Energy Applications

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yimin; Somorjai, Gabor A.

    2010-05-12

    In this perspective, we present an overview of nanoscience applications in catalysis, energy conversion, and energy conservation technologies. We discuss how novel physical and chemical properties of nanomaterials can be applied and engineered to meet the advanced material requirements in the new generation of chemical and energy conversion devices. We highlight some of the latest advances in these nanotechnologies and provide an outlook at the major challenges for further developments.

  10. USD Catalysis Group for Alternative Energy

    Energy Technology Data Exchange (ETDEWEB)

    Hoefelmeyer, James D.; Koodali, Ranjit; Sereda, Grigoriy; Engebretson, Dan; Fong, Hao; Puszynski, Jan; Shende, Rajesh; Ahrenkiel, Phil

    2012-03-13

    The South Dakota Catalysis Group (SDCG) is a collaborative project with mission to develop advanced catalysts for energy conversion with two primary goals: (1) develop photocatalytic systems in which polyfunctionalized TiO2 are the basis for hydrogen/oxygen synthesis from water and sunlight (solar fuels group), (2) develop new materials for hydrogen utilization in fuel cells (fuel cell group). In tandem, these technologies complete a closed chemical cycle with zero emissions.

  11. Hybrid Amyloid Membranes for Continuous Flow Catalysis.

    Science.gov (United States)

    Bolisetty, Sreenath; Arcari, Mario; Adamcik, Jozef; Mezzenga, Raffaele

    2015-12-29

    Amyloid fibrils are promising nanomaterials for technological applications such as biosensors, tissue engineering, drug delivery, and optoelectronics. Here we show that amyloid-metal nanoparticle hybrids can be used both as efficient active materials for wet catalysis and as membranes for continuous flow catalysis applications. Initially, amyloid fibrils generated in vitro from the nontoxic β-lactoglobulin protein act as templates for the synthesis of gold and palladium metal nanoparticles from salt precursors. The resulting hybrids possess catalytic features as demonstrated by evaluating their activity in a model catalytic reaction in water, e.g., the reduction of 4-nitrophenol into 4-aminophenol, with the rate constant of the reduction increasing with the concentration of amyloid-nanoparticle hybrids. Importantly, the same nanoparticles adsorbed onto fibrils surface show improved catalytic efficiency compared to the same unattached particles, pointing at the important role played by the amyloid fibril templates. Then, filter membranes are prepared from the metal nanoparticle-decorated amyloid fibrils by vacuum filtration. The resulting membranes serve as efficient flow catalysis active materials, with a complete catalytic conversion achieved within a single flow passage of a feeding solution through the membrane.

  12. Feeding strategy of the night shark (Carcharhinus signatus and scalloped hammerhead shark (Sphyrna lewini near seamounts off northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Teodoro Vaske Júnior

    2009-06-01

    Full Text Available A total of 425 stomachs of night shark (Carcharhinus signatus, and 98 stomachs of scalloped hammerhead shark (Sphyrna lewini, from longline and surface gillneters near seamounts off northeastern Brazil, were analysed between 1992 and 1999. Both predators prey upon reef and benthopelagic fishes, migrant cephalopods and deep water crustaceans, showing similar feeding niches (Schoener Index T=0.75. The great prey richness of the diets may reflect the fact that the marine food web for these species is very extensive in this region. Due to the concentration for feeding of both predators in the seamounts, intense fisheries should be monitored to avoid localised depletions.Um total de 425 estômagos de tubarão-toninha (Carcharhinus signatus e 98 estômagos de tubarão-martelo-entalhado (Sphyrna lewini, oriundos da pesca de espinhel e pesca com rede de emalhe nas adjacências dos bancos oceânicos do nordeste do Brasil, foi analisado entre 1992 e 1999. Ambas as espécies predam sobre peixes bento-pelágicos e recifais, cefalópodes migradores, e crustáceos de águas profundas, apresentando nichos alimentares similares (Índice de Schoener T=0.75. A alta riqueza de presas nas dietas deve ser um reflexo de que as teias alimentares para estas espécies são consideravelmente longas nessa região. Devido à concentração alimentar de ambos predadores nos bancos oceânicos, a pescaria intensa deve ser monitorada para evitar depleções locais.

  13. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini).

    Science.gov (United States)

    Daly-Engel, Toby S; Seraphin, Kanesa D; Holland, Kim N; Coffey, John P; Nance, Holly A; Toonen, Robert J; Bowen, Brian W

    2012-01-01

    The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA) markers demonstrated strong genetic partitioning overall (global Φ(ST) = 0.749) and significant population separations across oceans and between discontinuous continental coastlines. We surveyed the same global range with increased sample coverage (N = 403) and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (F(ST) = 0.035) over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (Φ(ST) = 0.749). Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific. These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.

  14. Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini.

    Directory of Open Access Journals (Sweden)

    Toby S Daly-Engel

    Full Text Available The scalloped hammerhead shark, Sphyrna lewini, is a large endangered predator with a circumglobal distribution, observed in the open ocean but linked ontogenetically to coastal embayments for parturition and juvenile development. A previous survey of maternal (mtDNA markers demonstrated strong genetic partitioning overall (global Φ(ST = 0.749 and significant population separations across oceans and between discontinuous continental coastlines.We surveyed the same global range with increased sample coverage (N = 403 and 13 microsatellite loci to assess the male contribution to dispersal and population structure. Biparentally inherited microsatellites reveal low or absent genetic structure across ocean basins and global genetic differentiation (F(ST = 0.035 over an order of magnitude lower than the corresponding measures for maternal mtDNA lineages (Φ(ST = 0.749. Nuclear allelic richness and heterozygosity are high throughout the Indo-Pacific, while genetic structure is low. In contrast, allelic diversity is low while population structure is higher for populations at the ends of the range in the West Atlantic and East Pacific.These data are consistent with the proposed Indo-Pacific center of origin for S. lewini, and indicate that females are philopatric or adhere to coastal habitats while males facilitate gene flow across oceanic expanses. This study includes the largest sampling effort and the most molecular loci ever used to survey the complete range of a large oceanic predator, and findings emphasize the importance of incorporating mixed-marker analysis into stock assessments of threatened and endangered shark species.

  15. Neutrons for Catalysis: A Workshop on Neutron Scattering Techniques for Studies in Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Overbury, Steven {Steve} H [ORNL; Coates, Leighton [ORNL; Herwig, Kenneth W [ORNL; Kidder, Michelle [ORNL

    2011-10-01

    This report summarizes the Workshop on Neutron Scattering Techniques for Studies in Catalysis, held at the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) on September 16 and 17, 2010. The goal of the Workshop was to bring experts in heterogeneous catalysis and biocatalysis together with neutron scattering experimenters to identify ways to attack new problems, especially Grand Challenge problems in catalysis, using neutron scattering. The Workshop locale was motivated by the neutron capabilities at ORNL, including the High Flux Isotope Reactor (HFIR) and the new and developing instrumentation at the SNS. Approximately 90 researchers met for 1 1/2 days with oral presentations and breakout sessions. Oral presentations were divided into five topical sessions aimed at a discussion of Grand Challenge problems in catalysis, dynamics studies, structure characterization, biocatalysis, and computational methods. Eleven internationally known invited experts spoke in these sessions. The Workshop was intended both to educate catalyst experts about the methods and possibilities of neutron methods and to educate the neutron community about the methods and scientific challenges in catalysis. Above all, it was intended to inspire new research ideas among the attendees. All attendees were asked to participate in one or more of three breakout sessions to share ideas and propose new experiments that could be performed using the ORNL neutron facilities. The Workshop was expected to lead to proposals for beam time at either the HFIR or the SNS; therefore, it was expected that each breakout session would identify a few experiments or proof-of-principle experiments and a leader who would pursue a proposal after the Workshop. Also, a refereed review article will be submitted to a prominent journal to present research and ideas illustrating the benefits and possibilities of neutron methods for catalysis research.

  16. Special Issue: Coinage Metal (Copper, Silver, and Gold Catalysis

    Directory of Open Access Journals (Sweden)

    Sónia Alexandra Correia Carabineiro

    2016-06-01

    Full Text Available The subject of catalysis by coinage metals (copper, silver, and gold comes up increasingly day-by-day. This Special Issue aims to cover the numerous aspects of the use of these metals as catalysts for several reactions. It deals with synthesis and characterization of copper, silver and gold based catalysis, their characterization and use, both for heterogeneous and homogeneous catalysis, and some of their potential applications.

  17. Special Issue: Coinage Metal (Copper, Silver, and Gold) Catalysis

    OpenAIRE

    Sónia Alexandra Correia Carabineiro

    2016-01-01

    The subject of catalysis by coinage metals (copper, silver, and gold) comes up increasingly day-by-day. This Special Issue aims to cover the numerous aspects of the use of these metals as catalysts for several reactions. It deals with synthesis and characterization of copper, silver and gold based catalysis, their characterization and use, both for heterogeneous and homogeneous catalysis, and some of their potential applications.

  18. Exactly Embedded Wavefunction Methods for Characterizing Nitrogen Reduction Catalysis

    Science.gov (United States)

    2015-01-15

    SUBTITLE Exactly Embedded Wavefunction Methods for Characterizing Nitrogen Reduction Catalysis 5a. CONTRACT NUMBER N/A 5b. GRANT NUMBER FA9550... catalysis , such as hydrogen and nitrogen reduction. In a significant methodological advance from the past year, we developed an accurate and...1-0288), the Miller group developed new electronic structure embedding methods for the investigation of small- molecular activation catalysis , such as

  19. Special Issue: Coinage Metal (Copper, Silver, and Gold) Catalysis.

    Science.gov (United States)

    Carabineiro, Sónia Alexandra Correia

    2016-06-08

    The subject of catalysis by coinage metals (copper, silver, and gold) comes up increasingly day-by-day. This Special Issue aims to cover the numerous aspects of the use of these metals as catalysts for several reactions. It deals with synthesis and characterization of copper, silver and gold based catalysis, their characterization and use, both for heterogeneous and homogeneous catalysis, and some of their potential applications.

  20. Controllable Catalysis with Nanoparticles: Bimetallic Alloy Systems and Surface Adsorbates

    KAUST Repository

    Chen, Tianyou

    2016-05-16

    Transition metal nanoparticles are privileged materials in catalysis due to their high specific surface areas and abundance of active catalytic sites. While many of these catalysts are quite useful, we are only beginning to understand the underlying catalytic mechanisms. Opening the “black box” of nanoparticle catalysis is essential to achieve the ultimate goal of catalysis by design. In this Perspective we highlight recent work addressing the topic of controlled catalysis with bimetallic alloy and “designer” adsorbate-stabilized metal nanoparticles.

  1. Synergistic Catalysis: A Powerful Synthetic Strategy for New Reaction Development

    Science.gov (United States)

    Allen, Anna E.; MacMillan, David W. C.

    2012-01-01

    Synergistic catalysis is a synthetic strategy wherein both the nucleophile and the electrophile are simultaneously activated by two separate and distinct catalysts to afford a single chemical transformation. This powerful catalysis strategy leads to several benefits, specifically synergistic catalysis can (i) introduce new, previously unattainable chemical transformations, (ii) improve the efficiency of existing transformations, and (iii) create or improve catalytic enantioselectivity where stereocontrol was previously absent or challenging. This perspective aims to highlight these benefits using many of the successful examples of synergistic catalysis found in the literature. PMID:22518271

  2. Catalysis in electrochemistry: from fundamentals to strategies for fuel cell development

    National Research Council Canada - National Science Library

    Santos, Elizabeth; Schmickler, Wolfgang

    2011-01-01

    "Catalysis in Electrochemistry: From Fundamentals to Strategies for Fuel Cell Development is a modern, comprehensive reference work on catalysis in electrochemistry, including principles, methods, strategies, and applications...

  3. Shape-controlled nanostructures in heterogeneous catalysis.

    Science.gov (United States)

    Zaera, Francisco

    2013-10-01

    Nanotechnologies have provided new methods for the preparation of nanomaterials with well-defined sizes and shapes, and many of those procedures have been recently implemented for applications in heterogeneous catalysis. The control of nanoparticle shape in particular offers the promise of a better definition of catalytic activity and selectivity through the optimization of the structure of the catalytic active site. This extension of new nanoparticle synthetic procedures to catalysis is in its early stages, but has shown some promising leads already. Here, we survey the major issues associated with this nanotechnology-catalysis synergy. First, we discuss new possibilities associated with distinguishing between the effects originating from nanoparticle size versus those originating from nanoparticle shape. Next, we survey the information available to date on the use of well-shaped metal and non-metal nanoparticles as active phases to control the surface atom ensembles that define the catalytic site in different catalytic applications. We follow with a brief review of the use of well-defined porous materials for the control of the shape of the space around that catalytic site. A specific example is provided to illustrate how new selective catalysts based on shape-defined nanoparticles can be designed from first principles by using fundamental mechanistic information on the reaction of interest obtained from surface-science experiments and quantum-mechanics calculations. Finally, we conclude with some thoughts on the state of the field in terms of the advances already made, the future potentials, and the possible limitations to be overcome. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Surface Science Foundations of Catalysis and Nanoscience

    CERN Document Server

    Kolasinski, Kurt K

    2012-01-01

    Surface science has evolved from being a sub-field of chemistry or physics, and has now established itself as an interdisciplinary topic. Knowledge has developed sufficiently that we can now understand catalysis from a surface science perspective. No-where is the underpinning nature of surface science better illustrated than with nanoscience. Now in its third edition, this successful textbook aims to provide students with an understanding of chemical transformations and the formation of structures at surfaces. The chapters build from simple to more advanced principles with each featuring exerc

  5. Concepts of Modern Catalysis and Kinetics

    CERN Document Server

    Chorkendorff, I

    2003-01-01

    Until now, the literature has offered a rather limited approach to the use of fundamental kinetics and their application to catalytic reactions. Subsequently, this book spans the full range from fundamentals of kinetics and heterogeneous catalysis via modern experimental and theoretical results of model studies to their equivalent large-scale industrial production processes. The result is key knowledge for students at technical universities and professionals already working in industry. "...such an enterprise will be of great value to the community, to professionals as well as graduate an

  6. Heterogeneous Catalysis with Renewed Attention: Principles, Theories, and Concepts

    Science.gov (United States)

    Dumeignil, Franck; Paul, Jean-Francois; Paul, Sebastien

    2017-01-01

    With the development of a strong bioeconomy sector related to the creation of next-generation biorefineries, heterogeneous catalysis is receiving renewed attention. Indeed, catalysis is at the core of biorefinery design, and many new catalysts and catalytic processes are being developed. On the one hand, they are based on knowledge acquired during…

  7. The nature of the active site in heterogeneous metal catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk

    2008-01-01

    This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced...

  8. Comparative study of acid and basic catalysis in microwave ...

    African Journals Online (AJOL)

    Furthermore, yields of 81% and 74% respectively for the synthesis of thioamides 1 and 2 in basic catalysis with 4-methylmorpholine allows to confirm that this reaction is more advantageous in basic catalysis. The structures of thioamides synthesized were characterized and confirmed by spectroscopy Infrared (IR), nuclear ...

  9. Chemical Synthesis of Complex Molecules Using Nanoparticle Catalysis

    OpenAIRE

    Cong, Huan; Porco, John A.

    2012-01-01

    Nanoparticle catalysis has emerged as an active topic in organic synthesis. Of particular interest is the development of enabling methodologies to efficiently assemble complex molecules using nanoparticle catalysis. This Viewpoint highlights recent developments and discusses future perspectives in this emerging field.

  10. Tandem Catalysis Utilizing Olefin Metathesis Reactions.

    Science.gov (United States)

    Zieliński, Grzegorz K; Grela, Karol

    2016-07-04

    Since olefin metathesis transformation has become a favored synthetic tool in organic synthesis, more and more distinct non-metathetical reactions of alkylidene ruthenium complexes have been developed. Depending on the conditions applied, the same olefin metathesis catalysts can efficiently promote isomerization reactions, hydrogenation of C=C double bonds, oxidation reactions, and many others. Importantly, these transformations can be carried out in tandem with olefin metathesis reactions. Through addition of one portion of a catalyst, a tandem process provides structurally advanced products from relatively simple substrates without the need for isolation of the intermediates. These aspects not only make tandem catalysis very attractive from a practical point of view, but also open new avenues in (retro)synthetic planning. However, in the literature, the term "tandem process" is sometimes used improperly to describe other types of multi-reaction sequences. In this Concept, a number of examples of tandem catalysis involving olefin metathesis are discussed with an emphasis on their synthetic value. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Mechanical catalysis on the centimetre scale.

    Science.gov (United States)

    Miyashita, Shuhei; Audretsch, Christof; Nagy, Zoltán; Füchslin, Rudolf M; Pfeifer, Rolf

    2015-03-06

    Enzymes play important roles in catalysing biochemical transaction paths, acting as logical machines through the morphology of the processes. A key challenge in elucidating the nature of these systems, and for engineering manufacturing methods inspired by biochemical reactions, is to attain a comprehensive understanding of the stereochemical ground rules of enzymatic reactions. Here, we present a model of catalysis that can be performed magnetically by centimetre-sized passive floating units. The designed system, which is equipped with permanent magnets only, passively obeys the local causalities imposed by magnetic interactions, albeit it shows a spatial behaviour and an energy profile analogous to those of biochemical enzymes. In this process, the enzyme units trigger physical conformation changes of the target by levelling out the magnetic potential barrier (activation potential) to a funnel type and, thus, induce cascading conformation changes of the targeted substrate units reacting in parallel. The inhibitor units, conversely, suppress such changes by increasing the potential. Because the model is purely mechanical and established on a physics basis in the absence of turbulence, each performance can be explained by the morphology of the unit, extending the definition of catalysis to systems of alternative scales.

  12. A conformational switch in the DiGIR1 ribozyme involved in release and folding of the downstream I-DirI mRNA

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Einvik, Christer; Lentz, Thomas E

    2009-01-01

    DiGIR1 is a group I-like cleavage ribozyme found as a structural domain within a nuclear twin-ribozyme group I intron. DiGIR1 catalyzes cleavage by branching at an Internal Processing Site (IPS) leading to formation of a lariat cap at the 5'-end of the 3'-cleavage product. The 3'-cleavage product...... reaction, thus giving it directionality. Furthermore, the release of the mRNA is a consequence of branching rather than hydrolytic cleavage. A model is put forward that explains the release of the I-DirI mRNA with a lariat cap and a structured 5'-UTR as a direct consequence of the DiGIR1 branching reaction...

  13. A new species of Phoreiobothrium (Cestoidea:Tetraphyllidea) from the great hammerhead shark Sphyrna mokarran and its implications for the evolution of the onchobothriid scolex.

    Science.gov (United States)

    Caira, J N; Healy, C J; Swanson, J

    1996-06-01

    Phoreiobothrium manirei n. sp. is described from the spiral intestines of 3 immature individuals of the great hammerhead shark Sphyrna mokarran collected off of the west coast of Florida. This cestode is unusual in that it possesses 4 muscular papillae on the anterior margin of the accessory sucker. Numerous small protrusions with central cilium-like projections were conspicuous throughout the posterior margin of each bothridium. This species possesses the unique combination of bothridia posteriorly subdivided into subloculi and hooks with extended bases and 2 rather than 3 prongs. In fact, the hooks are strikingly like those of species in the genera Dicranobothrium and Platybothrium. This combination of characters suggests that the bifid hook condition is plesiomorphic with respect to the trifid hook condition within the Onchobothriidae. These data further suggest that the triloculated bothridial condition is plesiomorphic relative to the biloculated condition.

  14. A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA

    Directory of Open Access Journals (Sweden)

    Robert J Scarborough

    2014-01-01

    Full Text Available Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.

  15. Electronic structure and catalysis on metal surfaces.

    Science.gov (United States)

    Greeley, Jeff; Nørskov, Jens K; Mavrikakis, Manos

    2002-01-01

    The powerful computational resources available to scientists today, together with recent improvements in electronic structure calculation algorithms, are providing important new tools for researchers in the fields of surface science and catalysis. In this review, we discuss first principles calculations that are now capable of providing qualitative and, in many cases, quantitative insights into surface chemistry. The calculations can aid in the establishment of chemisorption trends across the transition metals, in the characterization of reaction pathways on individual metals, and in the design of novel catalysts. First principles studies provide an excellent fundamental complement to experimental investigations of the above phenomena and can often allow the elucidation of important mechanistic details that would be difficult, if not impossible, to determine from experiments alone.

  16. Heterogeneous Organo-Catalysis: Sustainable Pathways to ...

    Science.gov (United States)

    Glucose and fructose are among the most abundant plant-derived materials1 and have been converted into useful building units often used in the drug discovery and polymer architecture.2 Unfortunately, most of these conversions require mineral acids and complex heterogeneous catalysis systems which suffer from the diminished activity and recyclability issues.3 Herein, we report a highly reactive and inexpensive heterogeneous sulfonated graphitic carbon nitride (Sg-CN), endowed with strong acidity that readily transforms carbohydrates to furanics. The ready availability and benign nature of the material and its stability over the several reaction cycles renders this catalyst very useful in organic synthesis, polymer industry and in the preparation of drug precursors. Poster presentation at the 253rd American Chemical Society (ACS) National meeting in San Francisco, CA

  17. Multiple roles of graphene in heterogeneous catalysis.

    Science.gov (United States)

    Fan, Xiaobin; Zhang, Guoliang; Zhang, Fengbao

    2015-05-21

    Scientific interest in graphene as a catalyst and as a catalyst support in heterogeneous catalytic reactions has grown dramatically over the past several years. The present critical review summarizes the multiple roles of graphene in heterogeneous catalysis and highlights the influence of defects, heteroatom-containing functionalities, and graphene's two-dimensional structure on catalytic performance. We first discuss the role and advantages of graphene as a catalyst support, with emphasis on its interactions with the catalytic phases and the influence of mass transfer processes. We then clarify the origin of the intrinsic catalytic activity of graphene in heterogeneous catalytic reactions. Finally we suggest challenges and potential practical applications for graphene in industrial processes.

  18. Linking Protein Motion to Enzyme Catalysis

    Directory of Open Access Journals (Sweden)

    Priyanka Singh

    2015-01-01

    Full Text Available Enzyme motions on a broad range of time scales can play an important role in various intra- and intermolecular events, including substrate binding, catalysis of the chemical conversion, and product release. The relationship between protein motions and catalytic activity is of contemporary interest in enzymology. To understand the factors influencing the rates of enzyme-catalyzed reactions, the dynamics of the protein-solvent-ligand complex must be considered. The current review presents two case studies of enzymes—dihydrofolate reductase (DHFR and thymidylate synthase (TSase—and discusses the role of protein motions in their catalyzed reactions. Specifically, we will discuss the utility of kinetic isotope effects (KIEs and their temperature dependence as tools in probing such phenomena.

  19. Microbial biofilms: a concept for industrial catalysis?

    Science.gov (United States)

    Rosche, Bettina; Li, Xuan Zhong; Hauer, Bernhard; Schmid, Andreas; Buehler, Katja

    2009-11-01

    Biofilm reactors have long been commercially used in the treatment of wastewater and off-gas. New opportunities are arising with the rapid expansion of our understanding of biofilm biology over the last few years. Biofilms have great potential as industrial workhorses for the sustainable production of chemicals because of their inherent characteristics of self-immobilization, high resistance to reactants and long-term activity, which all facilitate continuous processing. A variety of biofilm reactor configurations have been explored for productive catalysis and some reactors have been operated continuously for months. Sectors that might particularly benefit from this biofilm approach include synthetic chemistry (ranging from specialty to bulk chemicals), bioenergy, biologics and the food industry.

  20. One-dimensional metal oxide nanostructures for heterogeneous catalysis.

    Science.gov (United States)

    Zhang, Qian; Wang, Hsin-Yi; Jia, Xinli; Liu, Bin; Yang, Yanhui

    2013-08-21

    Metal oxides are of paramount importance in heterogeneous catalysis as either supports or active phases. Controlled synthesis of one-dimensional (1D) metal oxide nanostructures has received enormous attention in heterogeneous catalysis due to the possibility of tailoring the properties of metal oxides by tuning their shapes, sizes, and compositions. This feature article highlights recent advances in shape controlled synthesis of 1D metal oxide nanostructures and their applications in heterogeneous catalysis, with the aim of introducing new insights into the heterogeneous catalyst design.

  1. Iminium and enamine catalysis in enantioselective photochemical reactions

    Science.gov (United States)

    Hörmann, Fabian M.

    2018-01-01

    Although enantioselective catalysis under thermal conditions has been well established over the last few decades, the enantioselective catalysis of photochemical reactions is still a challenging task resulting from the complex enantiotopic face differentiation in the photoexcited state. Recently, remarkable achievements have been reported by a synergistic combination of organocatalysis and photocatalysis, which have led to the expedient construction of a diverse range of enantioenriched molecules which are generally not easily accessible under thermal conditions. In this tutorial review, we summarize and highlight the most significant advances in iminium and enamine catalysis of enantioselective photochemical reactions, with an emphasis on catalytic modes and reaction types. PMID:29155908

  2. Titanium dioxide photo catalysis: present situation and future approaches

    Energy Technology Data Exchange (ETDEWEB)

    Akira, Fujishima; Xintong, Zhang [Kanagawa Academy of Science and Technology, Takatsu-ku, Kanagawa (Japan)

    2006-05-15

    Scientific studies on photo-catalysis started about three decades ago. Titanium dioxide (TiO{sub 2}), which is one of the most basic materials in our daily life, has emerged as an excellent photo-catalyst material for environmental purification. In this short account, we will briefly discuss some fundamental studies on TiO{sub 2} photo-catalysis, summarize the present commercialization of TiO{sub 2}-based products, and highlight several points for the future development of TiO{sub 2} photo-catalysis. (authors)

  3. A new era of catalysis: efficiency, value, and sustainability.

    Science.gov (United States)

    Cheng, Soofin; Lin, Shawn D

    2014-06-01

    Value proposition: Global warming and climate change urge the chemical industry to develop new processes, in which sustainability is a necessity and requirement. Catalysis is recognized to be one of the key technologies in enabling sustainability. This special issue, assembled by guest editors Soofing Chen and Shawn D. Lin, highlights some of the best work presented at "The 6th Asia-Pacific Congress on Catalysis (APCAT-6)", with as major theme "New Era of Catalysis: Efficiency, Value, and Sustainability". © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Prebiotic RNA Synthesis by Montmorillonite Catalysis

    Science.gov (United States)

    Jheeta, Sohan; Joshi, Prakash C.

    2014-08-01

    This review summarizes our recent findings on the role of mineral salts in prebiotic RNA synthesis, which is catalyzed by montmorillonite clay minerals. The clay minerals not only catalyze the synthesis of RNA but also facilitate homochiral selection. Preliminary data of these findings have been presented at the "Horizontal Gene Transfer and the Last Universal Common Ancestor (LUCA)" conference at the Open University, Milton Keynes, UK, 5-6 September 2013. The objective of this meeting was to recognize the significance of RNA in LUCA. We believe that the prebiotic RNA synthesis from its monomers must have been a simple process. As a first step, it may have required activation of the 5'-end of the mononucleotide with a leaving group, e.g., imidazole in our model reaction (Figure 1). Wide ranges of activating groups are produced from HCN under plausible prebiotic Earth conditions. The final step is clay mineral catalysis in the presence of mineral salts to facilitate selective production of functional RNA. Both the clay minerals and mineral salts would have been abundant on early Earth. We have demonstrated that while montmorillonite (pH 7) produced only dimers from its monomers in water, addition of sodium chloride (1 M) enhanced the chain length multifold, as detected by HPLC. The effect of monovalent cations on RNA synthesis was of the following order: Li+ > Na+ > K+. A similar effect was observed with the anions, enhancing catalysis in the following order: Cl- > Br- > I-. The montmorillonite-catalyzed RNA synthesis was not affected by hydrophobic or hydrophilic interactions. We thus show that prebiotic synthesis of RNA from its monomers was a simple process requiring only clay minerals and a small amount of salt.

  5. Density functional theory studies of transition metal nanoparticles in catalysis

    DEFF Research Database (Denmark)

    Greeley, Jeffrey Philip; Rankin, Rees; Zeng, Zhenhua

    2013-01-01

    Periodic Density Functional Theory calculations are capable of providing powerful insights into the structural, energetics, and electronic phenomena that underlie heterogeneous catalysis on transition metal nanoparticles. Such calculations are now routinely applied to single crystal metal surfaces...... and to subnanometer metal clusters. Descriptions of catalysis on truly nanosized structures, however, are generally not as well developed. In this talk, I will illustrate different approaches to analyzing nanocatalytic phenomena with DFT calculations. I will describe case studies from heterogeneous catalysis...... and electrocatalysis, in which single crystal models are combined with Wulff construction-based ideas to produce descriptions of average nanocatalyst behavior. Then, I will proceed to describe explicitly DFT-based descriptions of catalysis on truly nanosized particles (

  6. Applications of metal-organic frameworks in heterogeneous supramolecular catalysis.

    Science.gov (United States)

    Liu, Jiewei; Chen, Lianfen; Cui, Hao; Zhang, Jianyong; Zhang, Li; Su, Cheng-Yong

    2014-08-21

    This review summarizes the use of metal-organic frameworks (MOFs) as a versatile supramolecular platform to develop heterogeneous catalysts for a variety of organic reactions, especially for liquid-phase reactions. Following a background introduction about catalytic relevance to various metal-organic materials, crystal engineering of MOFs, characterization and evaluation methods of MOF catalysis, we categorize catalytic MOFs based on the types of active sites, including coordinatively unsaturated metal sites (CUMs), metalloligands, functional organic sites (FOS), as well as metal nanoparticles (MNPs) embedded in the cavities. Throughout the review, we emphasize the incidental or deliberate formation of active sites, the stability, heterogeneity and shape/size selectivity for MOF catalysis. Finally, we briefly introduce their relevance into photo- and biomimetic catalysis, and compare MOFs with other typical porous solids such as zeolites and mesoporous silica with regard to their different attributes, and provide our view on future trends and developments in MOF-based catalysis.

  7. Selective Oxidation and Ammoxidation of Olefins by Heterogeneous Catalysis.

    Science.gov (United States)

    Grasselli, Robert K.

    1986-01-01

    Shows how the ammoxidation of olefins can be understood in terms of free radicals and surface bound organometallic intermediates. Also illustrates the close intellectual relationships between heterogeneous catalysis and organometallic chemistry. (JN)

  8. Toward an Understanding of Catalysis by Supported Metal Nanoclusters

    Energy Technology Data Exchange (ETDEWEB)

    D. W. Goodman; J. Wang; B. K. Min; E. Ozensoy; F. Yang

    2002-01-01

    OAK (B204) The goal of this program is an atomic-level understanding of catalysis by supported metal nanoclusters, especially the surface intermediates in selective oxidation by noble metal nanocatalysts.

  9. Bridging heterogeneous and homogeneous catalysis concepts, strategies, and applications

    CERN Document Server

    Li, Can

    2014-01-01

    This unique handbook fills the gap in the market for an up-to-date work that links both homogeneous catalysis applied to organic reactions and catalytic reactions on surfaces of heterogeneous catalysts.

  10. Catalysis of Radical Reactions: A Radical Chemistry Perspective.

    Science.gov (United States)

    Studer, Armido; Curran, Dennis P

    2016-01-04

    The area of catalysis of radical reactions has recently flourished. Various reaction conditions have been discovered and explained in terms of catalytic cycles. These cycles rarely stand alone as unique paths from substrates to products. Instead, most radical reactions have innate chains which form products without any catalyst. How do we know if a species added in "catalytic amounts" is a catalyst, an initiator, or something else? Herein we critically address both catalyst-free and catalytic radical reactions through the lens of radical chemistry. Basic principles of kinetics and thermodynamics are used to address problems of initiation, propagation, and inhibition of radical chains. The catalysis of radical reactions differs from other areas of catalysis. Whereas efficient innate chain reactions are difficult to catalyze because individual steps are fast, both inefficient chain processes and non-chain processes afford diverse opportunities for catalysis, as illustrated with selected examples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Enantioselective Fluorination of Spirocyclic β-Prolinals Using Enamine Catalysis

    DEFF Research Database (Denmark)

    Fjelbye, Kasper; Marigo, Mauro; Clausen, Rasmus Prætorius

    2017-01-01

    A series of spirocyclic carbaldehydes were successfully fluorinated using enamine catalysis, furnishing the corresponding tertiary fluorides in both high yields and enantioselectivities. The fluorinated spirocycles provide a set of novel building blocks interesting from a medicinal chemistry point...

  12. Nanostructured Membranes for Enzyme Catalysis and Green Synthesis of Nanoparticles

    Science.gov (United States)

    Macroporous membranes functionalized with ionizable macromolecules provide promising applications in toxic metal capture at high capacity, nanoparticle synthesis, and catalysis. Our low-pressure membrane approach is marked by reaction and separation selectivity and their tunabil...

  13. Nanostructured Membranes for Green Synthesis of Nanoparticles and Enzyme Catalysis

    Science.gov (United States)

    Macroporous membranes functionalized with ionizable macromolecules provide promising applications in toxic metal capture at high capacity, nanoparticle synthesis, and catalysis. Our low‐pressure membrane approach is marked by reaction and separation selectivity and their tunabili...

  14. 3. International conference on catalysis in membrane reactors

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-09-01

    The 3. International Conference on Catalysis in Membrane Reactors, Copenhagen, Denmark, is a continuation of the previous conferences held in Villeurbanne 1994 and Moscow 1996 and will deal with the rapid developments taking place within membranes with emphasis on membrane catalysis. The approx. 80 contributions in form of plenary lectures and posters discuss hydrogen production, methane reforming into syngas, selectivity and specificity of various membranes etc. The conference is organised by the Danish Catalytic Society under the Danish Society for Chemical Engineering. (EG)

  15. Intermetallic compounds in heterogeneous catalysis-a quickly developing field.

    Science.gov (United States)

    Armbrüster, Marc; Schlögl, Robert; Grin, Yuri

    2014-06-01

    The application of intermetallic compounds for understanding in heterogeneous catalysis developed in an excellent way during the last decade. This review provides an overview of concepts and developments revealing the potential of intermetallic compounds in fundamental as well as applied catalysis research. Intermetallic compounds may be considered as platform materials to address current and future catalytic challenges, e.g. in respect to the energy transition.

  16. Dedicated Beamline Facilities for Catalytic Research. Synchrotron Catalysis Consortium (SCC)

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jingguang [Columbia Univ., New York, NY; Frenkel, Anatoly [Yeshiva Univ., New York, NY (United States); Rodriguez, Jose [Brookhaven National Lab. (BNL), Upton, NY (United States); Adzic, Radoslav [Brookhaven National Lab. (BNL), Upton, NY (United States); Bare, Simon R. [UOP LLC, Des Plaines, IL (United States); Hulbert, Steve L. [Brookhaven National Lab. (BNL), Upton, NY (United States); Karim, Ayman [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mullins, David R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Overbury, Steve [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-03-04

    Synchrotron spectroscopies offer unique advantages over conventional techniques, including higher detection sensitivity and molecular specificity, faster detection rate, and more in-depth information regarding the structural, electronic and catalytic properties under in-situ reaction conditions. Despite these advantages, synchrotron techniques are often underutilized or unexplored by the catalysis community due to various perceived and real barriers, which will be addressed in the current proposal. Since its establishment in 2005, the Synchrotron Catalysis Consortium (SCC) has coordinated significant efforts to promote the utilization of cutting-edge catalytic research under in-situ conditions. The purpose of the current renewal proposal is aimed to provide assistance, and to develop new sciences/techniques, for the catalysis community through the following concerted efforts: Coordinating the implementation of a suite of beamlines for catalysis studies at the new NSLS-II synchrotron source; Providing assistance and coordination for catalysis users at an SSRL catalysis beamline during the initial period of NSLS to NSLS II transition; Designing in-situ reactors for a variety of catalytic and electrocatalytic studies; Assisting experimental set-up and data analysis by a dedicated research scientist; Offering training courses and help sessions by the PIs and co-PIs.

  17. Infrared Spectroscopy and Catalysis Research: Infrared spectra of adsorbed molecules provide important information in the study of catalysis.

    Science.gov (United States)

    Eischens, R P

    1964-10-23

    The examples discussed here represent only a small part of the published work relating to infrared spectra of adsorbed molecules. The publications in this field indicate that infrared spectroscopy is being used for surface chemistry research in about 50 laboratories throughout the world. This effort is mainly devoted to problems related to catalysis, and in this field infrared spectroscopy is the most widely used physical tool for surface chemistry studies. The general acceptance of infrared spectroscopy is primarily due to the fact that it provides information which is pertinent to the understanding of surface reactions on an atomic scale. During the last decade significant progress has also been made in the classical chemical techniques of catalysis study and in utilization of physical tools which depend on phenomena of magnetism, conductivity, low-energy electron diffraction, and electron emission. Probably the most important progress has been in the field of inorganic chemistry, where dramatic advances have been made in knowledge of metal coordination compounds. Such knowledge is vital to the understanding of catalysis on metal surfaces. I believe this progress has produced an attitude of sophisticated optimism among catalysis researchers with regard to eventual understanding of heterogeneous catalysis. This attitude is closely related to the realization that there is no "secret of catalysis" which places catalytic action beyond the limits of ordinary chemical knowledge (22). This view implies that the chemical aspects of heterogeneous catalysis are not unique and that the use of solid catalysts merely provides a highly effective exposure of catalytic atoms and facilitates separation of the products from the catalyst. Many capable catalysis researchers believe that studies of homogeneous catalysis provide the most direct route for the study of heterogeneous catalysis. Obviously homogeneous reactions catalyzed by compounds containing only one or two metal atoms

  18. Towards an atomic level understanding of niobia based catalysts and catalysis by combining the science of catalysis with surface science

    OpenAIRE

    Martin Schmal; Hans-Joachim Freund

    2009-01-01

    The science of catalysis and surface science have developed, independently, key information for understanding catalytic processes. One might argue: is there anything fundamental to be discovered through the interplay between catalysis and surface science? Real catalysts of monometallic and bimetallic Co/Nb2O5 and Pd-Co/Nb2O5 catalysts showed interesting selectivity results on the Fischer-Tropsch synthesis (Noronha et al. 1996, Rosenir et al. 1993). The presence of a noble metal increased the ...

  19. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

    Czech Academy of Sciences Publication Activity Database

    Mlýnský, V.; Kuehrova, P.; Zgarbová, M.; Jurečka, P.; Walter, Nils G.; Otyepka, M.; Šponer, Jiří; Banáš, Pavel

    2015-01-01

    Roč. 119, č. 11 (2015), s. 4220-4229 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GAP208/12/1878 Institutional support: RVO:68081707 Keywords : ACID-BASE CATALYSIS * NUCLEIC-ACIDS * RNA CATALYSIS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015

  20. Sulfurized hematite for photo-Fenton catalysis

    Directory of Open Access Journals (Sweden)

    Yaping Zhang

    2017-08-01

    Full Text Available A hematite/amorphous sulfur composite was prepared via simple heating hematite and α-sulfur in Teflon-lined autoclave at low temperature. The composite was characterized by X-ray diffraction (XRD, Raman spectrum, Thermal Gravity Analysis (TGA, Transmission Electron Microscopy (TEM and X-ray photoelectron spectroscopy (XPS. The results revealed that an allotrope sulfur at 5–37% weight percent was found in the composite. After sulfuration, Sn2- or S22- was doped in the lattice of hematite, large amounts of OH and SO4 were adsorbed on the surface of hematite. Hematite/amorphous sulfur composite had superior photo-Fenton activities than pure hematite. This work also demonstrated that amorphous sulfur also had the activity of photo-Fenton catalysis. OH- and SO4 radicals facilitated dye adsorption and acted as a bridge to link H2O2. Moreover, SO4 radicals on hematite served as electron trapping center that can receive photo-induced electron from conduction band of hematite and transfer it to the adsorbed H2O2, increasing the rate of photo-Fenton reaction eventually.

  1. Conjugated Microporous Polymers for Heterogeneous Catalysis.

    Science.gov (United States)

    Zhou, Yun-Bing; Zhan, Zhuang-Ping

    2018-01-04

    Conjugated microporous polymers (CMPs) are a class of crosslinked polymers that combine permanent micropores with π-conjugated skeletons and possess three-dimensional (3D) networks. Compared with conventional materials such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), CMPs usually have superior chemical and thermal stability. CMPs have made significant progress in heterogeneous catalysis in the past seven years. With a bottom-up strategy, catalytic moieties can be directly introduced into in the framework to produce heterogeneous CMP catalysts. Higher activity, stability, and selectivity can be obtained with heterogeneous CMP catalysts in comparison with their homogeneous analogs. In addition, CMP catalysts can be easily isolated and recycled. In this review, we focus on CMPs as an intriguing platform for developing various highly efficient and recyclable heterogeneous catalysts in organic reactions. The design, synthesis, and structure of these CMP catalysts are also discussed in this focus review. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Tumor-specific expression of anti-mdr1 ribozyme selectively restores chemosensitivity in multidrug-resistant colon-adenocarcinoma cells.

    Science.gov (United States)

    Gao, Z; Gao, Z; Fields, J Z; Boman, B M

    1999-07-30

    P-glycoprotein (Pgp)-conferred multidrug resistance (MDR) is expressed in cancer and in normal colon tissues and has important physiological functions. In order to selectively reverse MDR in malignant tissue without disrupting the function of normal colonocytes, a retroviral vector (pCEAMR) containing anti-mdr1 ribozyme coupled to the carcino-embryonic-antigen (CEA) promoter was constructed and introduced into resistant colon-cancer cells (SW1116R) that produce CEA and into control resistant cells (HeLaK) that do not produce CEA. Anti-mdr1 ribozyme was expressed in SW1116R cells but not in HeLaK cells. Subsequently, the expression of mdr1 mRNA and Pgp decreased significantly in the transfected SW1116R cells, and was even lower than in parent non-resistant SW1116 cells. The functional ability of Pgp to facilitate rhodamine 123 (Rh123) efflux showed that the transfected SW1116R cells with low Pgp expression retained Rh123, whereas non-transfected SW1116R cells with high Pgp expression released the dye quickly. There was no difference in mdr1 mRNA or in Pgp between non-transfected and transfected HeLaK cells. Drug resistance to doxorubicin (DOX) decreased 93.1% in the transfected SW1116R cells, while no change in drug resistance occurred in the infected HeLaK cells. DOX could clearly inhibit the growth of transfected SW1116R tumors but had no effect on untransfected and on transfected HeLaK cells in vivo. These results indicate that our anti-mdr1 ribozyme is expressed only in CEA-producing colon-cancer cells and reverses their drug resistance selectively.

  3. Reduction of stromal fibroblast-induced mammary tumor growth, by retroviral ribozyme transgenes to hepatocyte growth factor/scatter factor and its receptor, c-MET.

    Science.gov (United States)

    Jiang, Wen G; Grimshaw, David; Martin, Tracey A; Davies, Gaynor; Parr, Christian; Watkins, Gareth; Lane, Jane; Abounader, Roger; Laterra, John; Mansel, Robert E

    2003-09-15

    Hepatocyte growth factor/scatter factor (HGF/SF) is known to increase the invasiveness and migration of cancer cells in vitro and induce angiogenesis. This study examined if inhibition of HGF/SF receptor expression by cancer cells and HGF/SF expression by stromal fibroblasts affects the growth of mammary cancer. Transgenes encoding ribozymes to specifically target human HGF/SF receptor (pLXSN-MET) or HGF/SF (pLXSN-HGF) were constructed using a pLXSN retroviral vector. Human mammary cancer cells MDA MB 231 was transduced with pLXSN-MET (MDA(+/+)). A human fibroblast cell line MRC5, which produces bioactive HGF/SF, was transduced with pLXSN-HGF (MRC5(+/+)). These cells were used in a nude mice breast tumor model. HGF receptor in MDA(+/+) cells and HGF in MRC5(+/+)cells were successfully removed with respective ribozymes as shown by reverse transcription-PCR and Western blotting, respectively. MDA(+/+) was found to have reduced invasiveness when stimulated with HGF/SF. MRC5(+/+) exhibited a significant reduction in HGF/SF production. When injected into athymic nude mice, MDA(+/+) exhibited a slower rate of growth, compared with the wild type (MDA(-/-)), and the cells transduced with control viral vector (MDA(+/-)). The growth of MDA(-/-) tumor was significantly enhanced when coimplanted with wild-type MRC5 (MRC5(-/-)), and the stimulatory effect was reduced when MRC5(+/+) cells were coimplanted instead of MRC5(-/-). The reduction of tumor growth was accompanied by reduction of angiogenesis, as demonstrated by the staining of VE-cadherin in primary tumor tissues. Retroviral ribozyme transgenes targeting HGF/SF in fibroblasts or its receptor cMET in mammary cancer cells can reduce the growth of mammary cancer and associated angiogenesis by inhibiting paracrine stromal-tumor cell interactions.

  4. Center for Catalysis at Iowa State University

    Energy Technology Data Exchange (ETDEWEB)

    Kraus, George A.

    2006-10-17

    The overall objective of this proposal is to enable Iowa State University to establish a Center that enjoys world-class stature and eventually enhances the economy through the transfer of innovation from the laboratory to the marketplace. The funds have been used to support experimental proposals from interdisciplinary research teams in areas related to catalysis and green chemistry. Specific focus areas included: • Catalytic conversion of renewable natural resources to industrial materials • Development of new catalysts for the oxidation or reduction of commodity chemicals • Use of enzymes and microorganisms in biocatalysis • Development of new, environmentally friendly reactions of industrial importance These focus areas intersect with barriers from the MYTP draft document. Specifically, section 2.4.3.1 Processing and Conversion has a list of bulleted items under Improved Chemical Conversions that includes new hydrogenation catalysts, milder oxidation catalysts, new catalysts for dehydration and selective bond cleavage catalysts. Specifically, the four sections are: 1. Catalyst development (7.4.12.A) 2. Conversion of glycerol (7.4.12.B) 3. Conversion of biodiesel (7.4.12.C) 4. Glucose from starch (7.4.12.D) All funded projects are part of a soybean or corn biorefinery. Two funded projects that have made significant progress toward goals of the MYTP draft document are: Catalysts to convert feedstocks with high fatty acid content to biodiesel (Kraus, Lin, Verkade) and Conversion of Glycerol into 1,3-Propanediol (Lin, Kraus). Currently, biodiesel is prepared using homogeneous base catalysis. However, as producers look for feedstocks other than soybean oil, such as waste restaurant oils and rendered animal fats, they have observed a large amount of free fatty acids contained in the feedstocks. Free fatty acids cannot be converted into biodiesel using homogeneous base-mediated processes. The CCAT catalyst system offers an integrated and cooperative catalytic

  5. Direct arylation and heterogeneous catalysis; ever the twain shall meet.

    Science.gov (United States)

    Cano, Rafael; Schmidt, Alexander F; McGlacken, Gerard P

    2015-10-01

    The formation of aryl-aryl bonds and heteroaryl analogues is one of the most important C-C bond forming processes in organic chemistry. Recently, a methodology termed Direct Arylation (DA) has emerged as an attractive alternative to traditional cross-coupling reactions (Suzuki-Miyaura, Stille, Negishi, etc. ). A parallel focus of the pharmaceutical and other chemical industries has been on the use heterogeneous catalysis as a favourable substitute for its homogeneous counterpart in cross-coupling reactions. Only very recently has heterogeneous catalysis been proposed and applied, to DA reactions. In this perspective, we consider the terms 'heterogeneous' and 'homogeneous' and the problems associated with their delineation in transition-metal catalysed reactions. We highlight the reports at the interface of DA and heterogeneous catalysis and we comment briefly on the methods used which attempt to classify reaction types as homo- or heterogeneous. In future work we recommend an emphasis be placed on kinetic methods which provide an excellent platform for analysis. In addition two analytical techniques are described which if developed to run in situ with DA reactions would illuminate our understanding of the catalysis. Overall, we provide an entry point, and bring together the mature, yet poorly-understood, subject of heterogeneous catalysis with the rapidly expanding area of DA, with a view towards the acceleration of catalyst design and the understanding of catalyst behaviour.

  6. High-Spin Cobalt Hydrides for Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Holland, Patrick L. [Univ. of Rochester, NY (United States)

    2013-08-29

    Organometallic chemists have traditionally used catalysts with strong-field ligands that give low-spin complexes. However, complexes with a weak ligand field have weaker bonds and lower barriers to geometric changes, suggesting that they may lead to more rapid catalytic reactions. Developing our understanding of high-spin complexes requires the use of a broader range of spectroscopic techniques, but has the promise of changing the mechanism and/or selectivity of known catalytic reactions. These changes may enable the more efficient utilization of chemical resources. A special advantage of cobalt and iron catalysts is that the metals are more abundant and cheaper than those currently used for major industrial processes that convert unsaturated organic molecules and biofeedstocks into useful chemicals. This project specifically evaluated the potential of high-spin cobalt complexes for small-molecule reactions for bond rearrangement and cleavage reactions relevant to hydrocarbon transformations. We have learned that many of these reactions proceed through crossing to different spin states: for example, high-spin complexes can flip one electron spin to access a lower-energy reaction pathway for beta-hydride elimination. This reaction enables new, selective olefin isomerization catalysis. The high-spin cobalt complexes also cleave the C-O bond of CO2 and the C-F bonds of fluoroarenes. In each case, the detailed mechanism of the reaction has been determined. Importantly, we have discovered that the cobalt catalysts described here give distinctive selectivities that are better than known catalysts. These selectivities come from a synergy between supporting ligand design and electronic control of the spin-state crossing in the reactions.

  7. Catalysis-by-design impacts assessment

    Energy Technology Data Exchange (ETDEWEB)

    Fassbender, L L; Young, J K [Pacific Northwest Lab., Richland, WA (USA); Sen, R K [Sen (R.K.) and Associates, Washington, DC (USA)

    1991-05-01

    Catalyst researchers have always recognized the need to develop a detailed understanding of the mechanisms of catalytic processes, and have hoped that it would lead to developing a theoretical predictive base to guide the search for new catalysts. This understanding allows one to develop a set of hierarchical models, from fundamental atomic-level ab-initio models to detailed engineering simulations of reactor systems, to direct the search for optimized, efficient catalyst systems. During the last two decades, the explosions of advanced surface analysis techniques have helped considerably to develop the building blocks for understanding various catalytic reactions. An effort to couple these theoretical and experimental advances to develop a set of hierarchical models to predict the nature of catalytic materials is a program entitled Catalysis-by-Design (CRD).'' In assessing the potential impacts of CBD on US industry, the key point to remember is that the value of the program lies in developing a novel methodology to search for new catalyst systems. Industrial researchers can then use this methodology to develop proprietary catalysts. Most companies involved in catalyst R D have two types of ongoing projects. The first type, what we call market-driven R D,'' are projects that support and improve upon a company's existing product lines. Project of the second type, technology-driven R D,'' are longer term, involve the development of totally new catalysts, and are initiated through scientists' research ideas. The CBD approach will impact both types of projects. However, this analysis indicates that the near-term impacts will be on market-driven'' projects. The conclusions and recommendations presented in this report were obtained by the authors through personal interviews with individuals involved in a variety of industrial catalyst development programs and through the three CBD workshops held in the summer of 1989. 34 refs., 7 figs., 7 tabs.

  8. Transglutaminase catalysis of modified whey protein dispersions.

    Science.gov (United States)

    Clare, Debra A; Daubert, Christopher R

    2010-05-01

    Transglutaminase (TGase) cross-linking reactions were accomplished using a heat-modified whey protein concentrate (mWPC) substrate after pH adjustment to 8. Based on earlier reports, the degree of lactosylation with respect to beta-lactoglobulin was lower in mWPC dispersions than measured in commercial whey concentrate (cWPC) protein solutions. In this study, a higher concentration of free sulfhydryl groups was detected in soluble supernatant fractions. Both factors potentially impact the availability of reactive lysine/glutaminyl residues required for TGase reactivity. The addition of 10 mM dithiothreitol (DTT) to the substrate mix, CBZ-glutaminyl glycine and hydroxylamine, revealed a 3.6-fold increase in TGase activity, likely due in part to maintenance of the catalytic cysteine residue in a reduced state. Furthermore, inclusion of DTT to mWPC dispersions significantly raised the apparent viscosity, independently of enzyme modification, while the rate of polymerization increased 2-fold based on OPA assay measurements. Limited cross-linking slightly increased the apparent viscosity, whereas extensive coupling lowered these values compared to equivalent nonenzyme-treated mWPC samples. Carbohydrate-staining revealed formation of glyco-polymers due to covalent linkages between glucosamine and mWPC proteins after TGase processing. Again, the apparent viscosity decreased after extensive enzymatic modification. Larger particles, sized 11.28 mum, were observed in the structural matrix of TGase-mWPC-fixed samples compared to 8 mum particles in control mWPC samples as viewed in scanning electron micrographs. Ultimately, the functional characteristics of TGase-mWPC ingredients may be custom-designed to deliver alternative functional attributes by adjusting the experimental reaction conditions under which catalysis is achieved. Taken together, these results suggest that unique TGase-mWPC and/or TGase-mWPC-glucosamine ingredients may be designed to provide novel, value

  9. Biodiesel forming reactions using heterogeneous catalysis

    Science.gov (United States)

    Liu, Yijun

    Biodiesel synthesis from biomass provides a means for utilizing effectively renewable resources, a way to convert waste vegetable oils and animal fats to a useful product, a way to recycle carbon dioxide for a combustion fuel, and production of a fuel that is biodegradable, non-toxic, and has a lower emission profile than petroleum-diesel. Free fatty acid (FFA) esterification and triglyceride (TG) transesterification with low molecular weight alcohols constitute the synthetic routes to prepare biodiesel from lipid feedstocks. This project was aimed at developing a better understanding of important fundamental issues involved in heterogeneous catalyzed biodiesel forming reactions using mainly model compounds, representing part of on-going efforts to build up a rational base for assay, design, and performance optimization of solid acids/bases in biodiesel synthesis. As FFA esterification proceeds, water is continuously formed as a byproduct and affects reaction rates in a negative manner. Using sulfuric acid (as a catalyst) and acetic acid (as a model compound for FFA), the impact of increasing concentrations of water on acid catalysis was investigated. The order of the water effect on reaction rate was determined to be -0.83. Sulfuric acid lost up to 90% activity as the amount of water present increased. The nature of the negative effect of water on esterification was found to go beyond the scope of reverse hydrolysis and was associated with the diminished acid strength of sulfuric acid as a result of the preferential solvation by water molecules of its catalytic protons. The results indicate that as esterification progresses and byproduct water is produced, deactivation of a Bronsted acid catalyst like H2SO4 occurs. Using a solid composite acid (SAC-13) as an example of heterogeneous catalysts and sulfuric acid as a homogeneous reference, similar reaction inhibition by water was demonstrated for homogeneous and heterogeneous catalysis. This similarity together with

  10. A ribozyme transcribed by a ribozyme

    DEFF Research Database (Denmark)

    Bentin, Thomas

    2011-01-01

    Prominent current ideas on how life emerged on Earth include an RNA world hypothesis in which RNA performed informational as well as catalytic functions in the absence of both DNA and protein. Demonstration of a self-replicative system based on ribonucleic acid polymers as both information carrie...

  11. Tachykinins with unusual structural features from a urodele, the amphiuma, an elasmobranch, the hammerhead shark, and an agnathan, the river lamprey.

    Science.gov (United States)

    Waugh, D; Bondareva, V; Rusakov, Y; Bjenning, C; Nielsen, P F; Conlon, J M

    1995-01-01

    Tachykinins were purified from extracts of gastrointestinal tissues of the urodele, Amphiuma tridactylum (three-toed amphiuma), and the elasmobranch Sphyrna lewini (hammerhead shark), and from the brain of the agnathan Lampetra fluviatilis (river lamprey). The amphiuma substance P (SP) (DNPSVGQFYGLM-NH2) contains 12 amino residues compared with 11 for mammalian SP and lacks the Arg/Lys-Pro-Xaa-Pro motif that is characteristic of NK1 receptor-selective agonists. Lampetra SP (RKPHPKEFVGLM-NH2) is identical to SP from the sea lamprey and the shark SP-related peptide (AKFDKFYGLM-NH2) is identical to dogfish scyliorhinin I. Amphiuma neurokinin A (NKA) (HKDAFIGLM-NH2) and lamprey NKA (HFDEFVGLM-NH2) contain 9 amino acid residues compared with 10 for mammalian NKA. The shark NKA-related peptide (ASGPTQAGIV10GRKRQKGEMF20VGLM-NH2) shows limited structural similarity to mammalian neuropeptide gamma and the teleost tachykinin, carassin but contains 24 rather than 21 amino acid residues. The data show that the primary structures of the tachykinins have been very poorly conserved during vertebrate evolution and that pressure has acted only to maintain the functionally important sequence -Phe-Xaa-Gly Leu-Met-NH2 at the COOH-termini of the peptides.

  12. Metal-free heterogeneous catalysis for sustainable chemistry.

    Science.gov (United States)

    Su, Dang Sheng; Zhang, Jian; Frank, Benjamin; Thomas, Arne; Wang, Xinchen; Paraknowitsch, Jens; Schlögl, Robert

    2010-02-22

    The current established catalytic processes used in chemical industries use metals, in many cases precious metals, or metal oxides as catalysts. These are often energy-consuming and not highly selective, wasting resources and producing greenhouse gases. Metal-free heterogeneous catalysis using carbon or carbon nitride is an interesting alternative to some current industrialized chemical processes. Carbon and carbon nitride combine environmental acceptability with inexhaustible resources and allow a favorable management of energy with good thermal conductivity. Owing to lower reaction temperatures and increased selectivity, these catalysts could be candidates for green chemistry with low emission and an efficient use of the chemical feedstock. This Review highlights some recent promising activities and developments in heterogeneous catalysis using only carbon and carbon nitride as catalysts. The state-of-the-art and future challenges of metal-free heterogeneous catalysis are also discussed.

  13. Catalysis induced by radiations; Catalisis inducida por radiaciones

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez B, J.; Gonzalez J, J. C., E-mail: jaime.jimenez@inin.gob.m [ININ, Departamento de Quimica, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico)

    2010-07-01

    In Mexico is generated a great quantity of residuals considered as dangerous, for its capacity of corrosion, reactivity, toxicity to the environment, inflammability and biological-infectious potential. It is important to mention that the toxic compounds cannot be discharged to the sewerage systems and much less to the receiving bodies of water. The usual treatment that receives the dangerous residuals is the incineration and the bordering. The incineration is an efficient form of treating the residuals, but it can be dioxins source and benzofurans, being the phenol and chloro phenol the precursors of these compounds. At the present time the radiolytic degradation of organic compounds has been broadly studied, especially the 4-chloro phenol and of same form the photo catalysis of organic compounds. However the combination of both processes, called radio catalysis is barely reported. In this work the results of the experiments realized for to degrade the 4-chloro phenol by means of radio catalysis are reported. (Author)

  14. KCC1: First Nanoparticle developed by KAUST Catalysis Center

    KAUST Repository

    Basset, Jean-Marie

    2010-08-01

    KCC1 is the first Nanoparticle developed by KAUST Catalysis Center. Director of KAUST Catalysis Center, Dr. Jean-Marie Basset, Senior Research Scientist at KCC, Dr. Vivek Polshettiwar, and Dr. Dongkyu Cha of the Advanced Nanofabrication Imaging & Characterization Core Laboratory discuss the details of this recent discovery. This video was produced by KAUST Visualization Laboratory and KAUST Technology Transfer and Innovation - Terence McElwee, Director, Technology Transfer and Innovation - IP@kaust.edu.sa This technology is part of KAUST\\'s technology commercialization program that seeks to stimulate development and commercial use of KAUST-developed technologies. For more information email us at ip@kaust.edu.sa.

  15. New and future developments in catalysis activation of carbon dioxide

    CERN Document Server

    Suib, Steven L

    2013-01-01

    New and Future Developments in Catalysis is a package of books that compile the latest ideas concerning alternate and renewable energy sources and the role that catalysis plays in converting new renewable feedstock into biofuels and biochemicals. Both homogeneous and heterogeneous catalysts and catalytic processes will be discussed in a unified and comprehensive approach. There will be extensive cross-referencing within all volumes. This volume presents a complete picture of all carbon dioxide (CO2) sources, outlines the environmental concerns regarding CO2, and critica

  16. The Development of Visible-Light Photoredox Catalysis in Flow.

    Science.gov (United States)

    Garlets, Zachary J; Nguyen, John D; Stephenson, Corey R J

    2014-04-01

    Visible-light photoredox catalysis has recently emerged as a viable alternative for radical reactions otherwise carried out with tin and boron reagents. It has been recognized that by merging photoredox catalysis with flow chemistry, slow reaction times, lower yields, and safety concerns may be obviated. While flow reactors have been successfully applied to reactions carried out with UV light, only recent developments have demonstrated the same potential of flow reactors for the improvement of visible-light-mediated reactions. This review examines the initial and continuing development of visible-light-mediated photoredox flow chemistry by exemplifying the benefits of flow chemistry compared with conventional batch techniques.

  17. Mechanistic Studies on ADAMTS13 Catalysis

    Science.gov (United States)

    Di Stasio, Enrico; Lancellotti, Stefano; Peyvandi, Flora; Palla, Roberta; Mannucci, Pier Mannuccio; De Cristofaro, Raimondo

    2008-01-01

    The zinc-protease a disintegrin-like and metalloprotease with thrombospondin type I repeats (ADAMTS13) cleaves the Tyr1605-Met1606 peptide bond of von Willebrand factor (VWF), avoiding the accumulation of ultra large VWF multimers. Hydrolysis by ADAMTS13 of a VWF analog (Asp1596-Arg1668 peptide, fluorescence energy transfer substrate [FRETS]-VWF73) was investigated by a fluorescence quenching method (FRETS method) from 15°C to 45°C and pH values from 4.5 to 10.5. The catalysis was influenced by two ionizable groups, whose pKa values were equal to 6.41 ± 0.08 (ionization enthalpy = 32.6 ± 1.7 kJ/mol) and 4 ± 0.1 (ionization enthalpy = 3.8 ± 0.4 kJ/mol), whereas these values were equal to 6 ± 0.1 and 4.1 ± 0.1, respectively, in Co2+-substituted ADAMTS13. The catalytic process of FRETS-VWF73 hydrolysis showed negative activation entropy (−144 kJ/mol), suggesting that the transition state becomes more ordered than the ground state of the reactants. The kcat/Km values were not linearly correlated with temperature, as expression of change of the kinetic “stickiness” of the substrate. The Met1606-Arg1668 peptide product acted as hyperbolic mixed-type inhibitor of FRETS-VWF73 hydrolysis. Asp1653, Glu1655, Glu1660, Asp1663, together with the hydrophilic side chain of Thr1656 were shown to form a “hot spot” in the VWF A2 sequence, which drives the molecular recognition and allosteric regulation of binding to ADAMTS13. The interaction of the Met1606-Arg1668 region of VWF with ADAMTS13 involves basic residues of the protease and is thus progressively inhibited at pH values >8.50. A molecular model of the FRETS-VWF73 showed that the substrate can fit into the active site only if ADAMTS13 assumes a C-like shape and, interacting with the acidic 1653–1668 region of VWF, properly orients the Tyr1605-Met1606 peptide bond for the cleavage by the zinc-aquo complex in the active site. PMID:18502798

  18. Isoporphyrin Intermediate in Heme Oxygenase Catalysis

    Science.gov (United States)

    Evans, John P.; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

    2008-01-01

    Human heme oxygenase-1 (hHO-1) catalyzes the O2- and NADPH-dependent oxidation of heme to biliverdin, CO, and free iron. The first step involves regiospecific insertion of an oxygen atom at the α-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin π-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of α-meso-phenylheme-IX, α-meso-(p-methylphenyl)-mesoheme-III, and α-meso-(p-trifluoromethylphenyl)-mesoheme-III. In agreement with previous experiments (Wang, J., Niemevz, F., Lad, L., Huang, L., Alvarez, D. E., Buldain, G., Poulos, T. L., and Ortiz de Montellano, P. R. (2004) J. Biol. Chem. 279, 42593–42604), only the α-biliverdin isomer is produced with concomitant formation of the corresponding benzoic acid. The transient intermediate observed in the NADPH-P450 reductase-catalyzed reaction accumulated when the reaction was supported by H2O2 and exhibited the absorption maxima at 435 and 930 nm characteristic of an isoporphyrin. Product analysis by reversed phase high performance liquid chromatography and liquid chromatography electrospray ionization mass spectrometry of the product generated with H2O2 identified it as an isoporphyrin that, on quenching, decayed to benzoylbiliverdin. In the presence of H218O2, one labeled oxygen atom was incorporated into these products. The hHO-1-isoporphyrin complexes were found to have half-lives of 1.7 and 2.4 h for the p-trifluoromethyl- and p-methyl-substituted phenylhemes, respectively. The addition of NADPH-P450 reductase to the H2O2-generated hHO-1-isoporphyrin complex produced α-biliverdin, confirming its role as a reaction intermediate. Identification of an isoporphyrin intermediate in the catalytic sequence of hHO-1, the first such intermediate observed in hemoprotein catalysis, completes our understanding of the critical first step of heme oxidation. PMID:18487208

  19. Enantioselective conjugate additions of α-amino radicals via cooperative photoredox and Lewis acid catalysis.

    Science.gov (United States)

    Ruiz Espelt, Laura; McPherson, Iain S; Wiensch, Eric M; Yoon, Tehshik P

    2015-02-25

    We report the highly enantioselective addition of photogenerated α-amino radicals to Michael acceptors. This method features a dual-catalyst protocol that combines transition metal photoredox catalysis with chiral Lewis acid catalysis. The combination of these two powerful modes of catalysis provides an effective, general strategy to generate and control the reactivity of photogenerated reactive intermediates.

  20. Seventh BES (Basic Energy Sciences) catalysis and surface chemistry research conference

    Energy Technology Data Exchange (ETDEWEB)

    1990-03-01

    Research programs on catalysis and surface chemistry are presented. A total of fifty-seven topics are included. Areas of research include heterogeneous catalysis; catalysis in hydrogenation, desulfurization, gasification, and redox reactions; studies of surface properties and surface active sites; catalyst supports; chemical activation, deactivation; selectivity, chemical preparation; molecular structure studies; sorption and dissociation. Individual projects are processed separately for the data bases. (CBS)

  1. A conceptual translation of homogeneous catalysis into heterogeneous catalysis: homogeneous-like heterogeneous gold nanoparticle catalyst induced by ceria supporter.

    Science.gov (United States)

    Li, Zhen-Xing; Xue, Wei; Guan, Bing-Tao; Shi, Fu-Bo; Shi, Zhang-Jie; Jiang, Hong; Yan, Chun-Hua

    2013-02-07

    Translation of homogeneous catalysis into heterogeneous catalysis is a promising solution to green and sustainable development in chemical industry. For this purpose, noble metal nanoparticles represent a new frontier in catalytic transformations. Many challenges remain for researchers to transform noble metal nanoparticles of heterogeneous catalytic active sites into ionic species of homogeneous catalytic active sites. We report here a successful design on translating homogeneous gold catalysis into a heterogeneous system with a clear understanding of the catalytic pathway. This study initiates a novel concept to immobilize a homogeneous catalyst based on electron transfer between supporting base and supported nanoparticles. Meanwhile, on the basis of theoretical calculation, it has deepened the understanding of the interactions between noble metal nanoparticles and the catalyst support.

  2. Catalysis of the electrochemical water oxidation to oxygen

    NARCIS (Netherlands)

    Díaz Morales, Oscar Alfonso

    2015-01-01

    This thesis discusses the parameters affecting the catalysis for the electrochemical conversion of water into oxygen. The slow kinetics for the oxygen evolution reaction (OER) is one of the major bottlenecks in the solar energy-to-fuels conversion process, which reduces the efficiency for the

  3. Heterogeneous Catalysis: On Bathroom Mirrors and Boiling Stones

    Science.gov (United States)

    Philipse, Albert P.

    2011-01-01

    Though heterogeneous nucleation of liquid droplets on a smooth surface (such as a bathroom mirror) is a classical topic in nucleation theory, it is not well-known that this topic is actually a pedagogical example of heterogeneous catalysis: the one and only effect of the surface is to lower the activation Gibbs energy of droplet formation. In…

  4. Surface Chemistry in Heterogeneous Catalysis: An Emerging Discipline.

    Science.gov (United States)

    White, J. M.; Campbell, Charles T.

    1980-01-01

    Provides background data on surface chemistry as an emerging discipline. Highlights the important role which surfaces play in catalysis by focusing on the catalyzed oxidation of carbon monoxide. Provides a demonstration of how surfaces exert their influences in heterogeneous phenomena and illustrates how experimental problems in this field are…

  5. Density functional theory in surface science and heterogeneous catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Scheffler, M.; Toulhoat, H.

    2006-01-01

    Solid surfaces are used extensively as catalysts throughout the chemical industry, in the energy sector, and in environmental protection. Recently, density functional theory has started providing new insight into the atomic-scale mechanisms of heterogeneous catalysis, helping to interpret the large...

  6. A Course in Heterogeneous Catalysis Involving Video-Based Seminars.

    Science.gov (United States)

    White, Mark G.

    1984-01-01

    A video-based format was used during a graduate seminar course designed to educate students on the nature of catalysis, to help transfer information among students working on similar problems, and to improve communication skills. The mechanics of and student reaction to this seminar course are discussed. (JN)

  7. Heterogeneous Catalysis: A Central Science for a Sustainable Future.

    Science.gov (United States)

    Friend, Cynthia M; Xu, Bingjun

    2017-03-21

    Developing active, selective, and energy efficient heterogeneous catalytic processes is key to a sustainable future because heterogeneous catalysis is at the center of the chemicals and energy industries. The design, testing, and implementation of robust and selective heterogeneous catalytic processes based on insights from fundamental studies could have a tremendous positive impact on the world.

  8. New trends in (heterogeneous) catalysis for the fine chemicals industry.

    Science.gov (United States)

    Bonrath, Werner

    2014-01-01

    New catalytic methods and modern trends for the synthesis of fine chemicals, especially vitamins, carotenoids, flavoring and fragrance compounds are presented. In particular the application of heterogeneous catalysis in the formation and production on industrial scale of these classes of organic compounds will be highlighted and its use in the replacement of former stoichiometric processes.

  9. Understanding Ziegler–Natta Catalysis Through Your Laptop

    Indian Academy of Sciences (India)

    responsible for the industrial production of millions of tons of polyolefins annually. They are, without question, the most essen- tial heterogeneous catalysis process in the industry today. There- fore, there is a constant .... modeling the surface would be to employ a 'cluster model' where. RESONANCE | November 2017. 1029 ...

  10. Robustness of the rotary catalysis mechanism of F1-ATPase.

    Science.gov (United States)

    Watanabe, Rikiya; Matsukage, Yuki; Yukawa, Ayako; Tabata, Kazuhito V; Noji, Hiroyuki

    2014-07-11

    F1-ATPase (F1) is the rotary motor protein fueled by ATP hydrolysis. Previous studies have suggested that three charged residues are indispensable for catalysis of F1 as follows: the P-loop lysine in the phosphate-binding loop, GXXXXGK(T/S); a glutamic acid that activates water molecules for nucleophilic attack on the γ-phosphate of ATP (general base); and an arginine directly contacting the γ-phosphate (arginine finger). These residues are well conserved among P-loop NTPases. In this study, we investigated the role of these charged residues in catalysis and torque generation by analyzing alanine-substituted mutants in the single-molecule rotation assay. Surprisingly, all mutants continuously drove rotary motion, even though the rotational velocity was at least 100,000 times slower than that of wild type. Thus, although these charged residues contribute to highly efficient catalysis, they are not indispensable to chemo-mechanical energy coupling, and the rotary catalysis mechanism of F1 is far more robust than previously thought. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Magnetic Catalysis of Chiral Symmetry Breaking: A Holographic Prospective

    Directory of Open Access Journals (Sweden)

    Veselin Filev

    2010-01-01

    Zeeman splitting of the energy levels, and the existence of pseudo, Goldstone modes. An analytic derivation of the Gell-Mann-Oaks-Renner relation for the D3/D7 set up is reviewed. In the D3/D5 case, the pseudo-Goldstone modes satisfy nonrelativistic dispersion relation. The studies reviewed confirm the universal nature of the magnetic catalysis of mass generation.

  12. Nitrogen doped carbon nanotubes : synthesis, characterization and catalysis

    NARCIS (Netherlands)

    van Dommele, S.

    2008-01-01

    Nitrogen containing Carbon Nanotubes (NCNT) have altered physical- and chemical properties with respect to polarity, conductivity and reactivity as compared to conventional carbon nanotubes (CNT) and have potential for use in electronic applications or catalysis. In this thesis the incorporation of

  13. Examining the role of glutamic acid 183 in chloroperoxidase catalysis

    NARCIS (Netherlands)

    Yi, X.; Conesa, A.; Punt, P.J.; Hager, L.P.

    2003-01-01

    Site-directed mutagenesis has been used to investigate the role of glutamic acid 183 in chloroperoxidase catalysis. Based on the x-ray crystallographic structure of chloroperoxidase, Glu-183 is postulated to function on distal side of the heme prosthetic group as an acid-base catalyst in

  14. Cooperative catalysis with first-row late transition metals

    NARCIS (Netherlands)

    van der Vlugt, J.I.

    2012-01-01

    Cooperative catalysis with first-row transition metals holds much promise for future developments regarding sustainable, selective transformations, including e.g. alkenes, dienes and a variety of small molecules such as CO2, N2 and water. This non-exhaustive analysis of the current state-of-the-art

  15. Pincer-porphyrin hybrids : Synthesis, self-assembly, and catalysis

    NARCIS (Netherlands)

    Suijkerbuijk, B.M.J.M.

    2007-01-01

    Metal complexes play an important role in established research areas such as catalysis and materials chemistry as well as in emerging fields of chemical exploration such as bioinorganic chemistry. Changes in the metal center's ligand environment, i.e., the nature and number of the Lewis basic atoms

  16. Counterion Binding Effects on the Micellar Catalysis of the Base ...

    African Journals Online (AJOL)

    The effects of counterion binding on micellar catalysis of the base hydrolysis of FE(phen) has been investaged. Pseudo first order rate constant, k , incrases with increase in the concentrations of ME NCI and (But) NC1 at any fixed Sodium dodecyl sulphate (SDS) concentration while the reserve is the case with NH CL.

  17. EPR spectroscopy as a tool in homogeneous catalysis research

    NARCIS (Netherlands)

    Goswami, M.; Chirila, A.; Rebreyend, C.; de Bruin, B.

    2015-01-01

    In the context of homogeneous catalysis, open-shell systems are often quite challenging to characterize. Nuclear magnetic resonance (NMR) spectroscopy is the most frequently applied tool to characterize organometallic compounds, but NMR spectra are usually broad, difficult to interpret and often

  18. Chemometric Optimization Studies in Catalysis Employing High-Throughput Experimentation

    NARCIS (Netherlands)

    Pereira, S.R.M.

    2008-01-01

    The main topic of this thesis is the investigation of the synergies between High-Throughput Experimentation (HTE) and Chemometric Optimization methodologies in Catalysis research and of the use of such methodologies to maximize the advantages of using HTE methods. Several case studies were analysed

  19. Robustness of the Rotary Catalysis Mechanism of F1-ATPase*

    Science.gov (United States)

    Watanabe, Rikiya; Matsukage, Yuki; Yukawa, Ayako; Tabata, Kazuhito V.; Noji, Hiroyuki

    2014-01-01

    F1-ATPase (F1) is the rotary motor protein fueled by ATP hydrolysis. Previous studies have suggested that three charged residues are indispensable for catalysis of F1 as follows: the P-loop lysine in the phosphate-binding loop, GXXXXGK(T/S); a glutamic acid that activates water molecules for nucleophilic attack on the γ-phosphate of ATP (general base); and an arginine directly contacting the γ-phosphate (arginine finger). These residues are well conserved among P-loop NTPases. In this study, we investigated the role of these charged residues in catalysis and torque generation by analyzing alanine-substituted mutants in the single-molecule rotation assay. Surprisingly, all mutants continuously drove rotary motion, even though the rotational velocity was at least 100,000 times slower than that of wild type. Thus, although these charged residues contribute to highly efficient catalysis, they are not indispensable to chemo-mechanical energy coupling, and the rotary catalysis mechanism of F1 is far more robust than previously thought. PMID:24876384

  20. Excess mutual catalysis is required for effective evolvability.

    Science.gov (United States)

    Markovitch, Omer; Lancet, Doron

    2012-01-01

    It is widely accepted that autocatalysis constitutes a crucial facet of effective replication and evolution (e.g., in Eigen's hypercycle model). Other models for early evolution (e.g., by Dyson, Gánti, Varela, and Kauffman) invoke catalytic networks, where cross-catalysis is more apparent. A key question is how the balance between auto- (self-) and cross- (mutual) catalysis shapes the behavior of model evolving systems. This is investigated using the graded autocatalysis replication domain (GARD) model, previously shown to capture essential features of reproduction, mutation, and evolution in compositional molecular assemblies. We have performed numerical simulations of an ensemble of GARD networks, each with a different set of lognormally distributed catalytic values. We asked what is the influence of the catalytic content of such networks on beneficial evolution. Importantly, a clear trend was observed, wherein only networks with high mutual catalysis propensity (p(mc)) allowed for an augmented diversity of composomes, quasi-stationary compositions that exhibit high replication fidelity. We have reexamined a recent analysis that showed meager selection in a single GARD instance and for a few nonstationary target compositions. In contrast, when we focused here on compotypes (clusters of composomes) as targets for selection in populations of compositional assemblies, appreciable selection response was observed for a large portion of the networks simulated. Further, stronger selection response was seen for high p(mc) values. Our simulations thus demonstrate that GARD can help analyze important facets of evolving systems, and indicate that excess mutual catalysis over self-catalysis is likely to be important for the emergence of molecular systems capable of evolutionlike behavior.

  1. Characterization of cis-Acting RNA Elements of Zika Virus by Using a Self-Splicing Ribozyme-Dependent Infectious Clone.

    Science.gov (United States)

    Liu, Zhong-Yu; Yu, Jiu-Yang; Huang, Xing-Yao; Fan, Hang; Li, Xiao-Feng; Deng, Yong-Qiang; Ji, Xue; Cheng, Meng-Li; Ye, Qing; Zhao, Hui; Han, Jian-Feng; An, Xiao-Ping; Jiang, Tao; Zhang, Bo; Tong, Yi-Gang; Qin, Cheng-Feng

    2017-11-01

    Zika virus (ZIKV) has caused significant outbreaks and epidemics in the Americas recently, raising global concern due to its ability to cause microcephaly and other neurological complications. A stable and efficient infectious clone of ZIKV is urgently needed. However, the instability and toxicity of flavivirus cDNA clones in Escherichia coli hosts has hindered the development of ZIKV infectious clones. Here, using a novel self-splicing ribozyme-based strategy, we generated a stable infectious cDNA clone of a contemporary ZIKV strain imported from Venezuela to China in 2016. The constructed clone contained a modified version of the group II self-splicing intron P.li.LSUI2 near the junction between the E and NS1 genes, which were removed from the RNA transcripts by an easy-to-establish in vitro splicing reaction. Transfection of the spliced RNAs into BHK-21 cells led to the production of infectious progeny virus that resembled the parental virus. Finally, potential cis-acting RNA elements in ZIKV genomic RNA were identified based on this novel reverse genetics system, and the critical role of 5'-SLA promoter and 5'-3' cyclization sequences were characterized by a combination of different assays. Our results provide another stable and reliable reverse genetics system for ZIKV that will help study ZIKV infection and pathogenesis, and the novel self-splicing intron-based strategy could be further expanded for the construction of infectious clones from other emerging and reemerging flaviviruses.IMPORTANCE The ongoing Zika virus (ZIKV) outbreaks have drawn global concern due to the unexpected causal link to fetus microcephaly and other severe neurological complications. The infectious cDNA clones of ZIKV are critical for the research community to study the virus, understand the disease, and inform vaccine design and antiviral screening. A panel of existing technologies have been utilized to develop ZIKV infectious clones. Here, we successfully generated a stable

  2. Molecular-Level Design of Heterogeneous Chiral Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Francisco Zaera

    2012-03-21

    The following is a proposal to continue our multi-institutional research on heterogeneous chiral catalysis. Our team combines the use of surface-sensitive analytical techniques for the characterization of model systems with quantum and statistical mechanical calculations to interpret experimental data and guide the design of future research. Our investigation focuses on the interrelation among the three main mechanisms by which enantioselectivity can be bestowed to heterogeneous catalysts, namely: (1) by templating chirality via the adsorption of chiral supramolecular assemblies, (2) by using chiral modifiers capable of forming chiral complexes with the reactant and force enantioselective surface reactions, and (3) by forming naturally chiral surfaces using imprinting chiral agents. Individually, the members of our team are leaders in these various aspects of chiral catalysis, but the present program provides the vehicle to generate and exploit the synergies necessary to address the problem in a comprehensive manner. Our initial work has advanced the methodology needed for these studies, including an enantioselective titration procedure to identify surface chiral sites, infrared spectroscopy in situ at the interface between gases or liquids and solids to mimic realistic catalytic conditions, and DFT and Monte Carlo algorithms to simulate and understand chirality on surfaces. The next step, to be funded by the monies requested in this proposal, is to apply those methods to specific problems in chiral catalysis, including the identification of the requirements for the formation of supramolecular surface structures with enantioselective behavior, the search for better molecules to probe the chiral nature of the modified surfaces, the exploration of the transition from supramolecular to one-to-one chiral modification, the correlation of the adsorption characteristics of one-to-one chiral modifiers with their physical properties, in particular with their configuration

  3. Long-term survival and concomitant gene expression of ribozyme-transduced CD4+ T-lymphocytes in HIV-infected patients.

    Science.gov (United States)

    Macpherson, Janet L; Boyd, Maureen P; Arndt, Allison J; Todd, Alison V; Fanning, Gregory C; Ely, Julie A; Elliott, Fiona; Knop, Alison; Raponi, Mitch; Murray, John; Gerlach, Wayne; Sun, Lun-Quan; Penny, Ronald; Symonds, Geoff P; Carr, Andrew; Cooper, David A

    2005-05-01

    An anti-HIV-1 tat ribozyme, termed Rz2, has been shown to inhibit HIV-1 infection/replication and to decrease HIV-1-induced pathogenicity in T-lymphocyte cell lines and normal peripheral blood T-lymphocytes. We report here the results of a phase I gene transfer clinical trial using Rz2. Apheresis was used to obtain a peripheral blood cell population from each of four HIV-negative donors. After enrichment for CD4+ T-lymphocytes, ex vivo expansion and genetic manipulation (approximately equal aliquots of the cells were transduced with the ribozyme-containing (RRz2) and the control (LNL6) retroviral vector), these cells were infused into the corresponding HIV-1-positive twin recipient. Marking was assessed over an initial 24-week period and in total over an approximate 4-year period. The gene transfer procedure was shown to be safe, and technically feasible. Both RRz2- and LNL6-gene-containing peripheral blood mononuclear cells (PBMC) were detected at all time points examined to 4 years. There was concomitant gene construct expression in the absence of the need for ex vivo peripheral blood cell stimulation and there was no evidence of immune elimination of the neoR T-lymphocytes nor of silencing of the Moloney murine leukemia virus long terminal repeat. The proof of principle results reported here demonstrate safety and feasibility of this type of gene transfer approach. While not specifically tested, T-lymphocytes containing an anti-HIV gene construct may impact on HIV-1 viral load and CD4+ T-lymphocyte count, potentially representing a new therapeutic modality for HIV-1 infection. Copyright (c) 2005 John Wiley & Sons, Ltd.

  4. Carbon mediated catalysis:A review on oxidative dehydrogenation

    Institute of Scientific and Technical Information of China (English)

    De Chen; Anders Holmen; Zhijun Sui; Xinggui Zhou

    2014-01-01

    Carbon mediated catalysis has gained an increasing attention in both areas of nanocatalysis and nanomaterials. The progress in carbon nanomaterials provides many new opportunities to manip-ulate the types and properties of active sites of catalysts through manipulating structures, function-alities and properties of carbon surfaces. The present review focuses on progresses in carbon medi-ated oxidative dehydrogenation reactions of ethylbenzene, propane, and butane. The state-of-the-art of the developments of carbon mediated catalysis is discussed in terms of fundamental studies on adsorption of oxygen and hydrocarbons, reaction mechanism as well as effects of carbon nano-material structures and surface functional groups on the catalytic performance. We highlight the importance and challenges in tuning of the electron density of carbon and oxygen on carbon surfac-es for improving selectivity in oxidative dehydrogenation reactions.

  5. Protein dynamics and enzyme catalysis: insights from simulations.

    Science.gov (United States)

    McGeagh, John D; Ranaghan, Kara E; Mulholland, Adrian J

    2011-08-01

    The role of protein dynamics in enzyme catalysis is one of the most active and controversial areas in enzymology today. Some researchers claim that protein dynamics are at the heart of enzyme catalytic efficiency, while others state that dynamics make no significant contribution to catalysis. What is the biochemist - or student - to make of the ferocious arguments in this area? Protein dynamics are complex and fascinating, as molecular dynamics simulations and experiments have shown. The essential question is: do these complex motions have functional significance? In particular, how do they affect or relate to chemical reactions within enzymes, and how are chemical and conformational changes coupled together? Biomolecular simulations can analyse enzyme reactions and dynamics in atomic detail, beyond that achievable in experiments: accurate atomistic modelling has an essential part to play in clarifying these issues. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. Heterogeneous Catalysis of Polyoxometalate Based Organic–Inorganic Hybrids

    Science.gov (United States)

    Ren, Yuanhang; Wang, Meiyin; Chen, Xueying; Yue, Bin; He, Heyong

    2015-01-01

    Organic–inorganic hybrid polyoxometalate (POM) compounds are a subset of materials with unique structures and physical/chemical properties. The combination of metal-organic coordination complexes with classical POMs not only provides a powerful way to gain multifarious new compounds but also affords a new method to modify and functionalize POMs. In parallel with the many reports on the synthesis and structure of new hybrid POM compounds, the application of these compounds for heterogeneous catalysis has also attracted considerable attention. The hybrid POM compounds show noteworthy catalytic performance in acid, oxidation, and even in asymmetric catalytic reactions. This review summarizes the design and synthesis of organic–inorganic hybrid POM compounds and particularly highlights their recent progress in heterogeneous catalysis. PMID:28788017

  7. Heterogeneous Catalysis of Polyoxometalate Based Organic–Inorganic Hybrids

    Directory of Open Access Journals (Sweden)

    Yuanhang Ren

    2015-03-01

    Full Text Available Organic–inorganic hybrid polyoxometalate (POM compounds are a subset of materials with unique structures and physical/chemical properties. The combination of metal-organic coordination complexes with classical POMs not only provides a powerful way to gain multifarious new compounds but also affords a new method to modify and functionalize POMs. In parallel with the many reports on the synthesis and structure of new hybrid POM compounds, the application of these compounds for heterogeneous catalysis has also attracted considerable attention. The hybrid POM compounds show noteworthy catalytic performance in acid, oxidation, and even in asymmetric catalytic reactions. This review summarizes the design and synthesis of organic–inorganic hybrid POM compounds and particularly highlights their recent progress in heterogeneous catalysis.

  8. Heterogeneous Catalysis of Polyoxometalate Based Organic-Inorganic Hybrids.

    Science.gov (United States)

    Ren, Yuanhang; Wang, Meiyin; Chen, Xueying; Yue, Bin; He, Heyong

    2015-03-31

    Organic-inorganic hybrid polyoxometalate (POM) compounds are a subset of materials with unique structures and physical/chemical properties. The combination of metal-organic coordination complexes with classical POMs not only provides a powerful way to gain multifarious new compounds but also affords a new method to modify and functionalize POMs. In parallel with the many reports on the synthesis and structure of new hybrid POM compounds, the application of these compounds for heterogeneous catalysis has also attracted considerable attention. The hybrid POM compounds show noteworthy catalytic performance in acid, oxidation, and even in asymmetric catalytic reactions. This review summarizes the design and synthesis of organic-inorganic hybrid POM compounds and particularly highlights their recent progress in heterogeneous catalysis.

  9. The energy landscape of adenylate kinase during catalysis

    Science.gov (United States)

    Kerns, S. Jordan; Agafonov, Roman V.; Cho, Young-Jin; Pontiggia, Francesco; Otten, Renee; Pachov, Dimitar V.; Kutter, Steffen; Phung, Lien A.; Murphy, Padraig N.; Thai, Vu; Alber, Tom; Hagan, Michael F.; Kern, Dorothee

    2014-01-01

    Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, MD simulations, and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events, phosphoryl transfer (>105-fold) and lid-opening (103-fold). In contrast, mutation of an essential active-site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid-opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a pre-organized active site. PMID:25580578

  10. Homogeneous Catalysis with Metal Complexes Fundamentals and Applications

    CERN Document Server

    Duca, Gheorghe

    2012-01-01

    The book about homogeneous catalysis with metal complexes deals with the description of the reductive-oxidative, metal complexes  in a liquid phase (in polar solvents, mainly in water, and less in nonpolar solvents). The exceptional importance of the redox processes in chemical systems, in the reactions occuring in living organisms, the environmental processes, atmosphere, water, soil, and in industrial technologies (especially in food-processing industries) is discussed. The detailed practical aspects of the established regularities are explained for solving the specific practical tasks in various fields of industrial chemistry, biochemistry, medicine, analytical chemistry and ecological chemistry. The main scope of the book is the survey and systematization of the latest advances in homogeneous catalysis with metal complexes. It gives an overview of the research results and practical experience accumulated by the author during the last decade.

  11. Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis

    Science.gov (United States)

    Hammes, Gordon G.; Benkovic, Stephen J.; Hammes-Schiffer, Sharon

    2011-01-01

    This brief review discusses our current understanding of the molecular basis of enzyme catalysis. A historical development is presented, beginning with steady state kinetics and progressing through modern fast reaction methods, NMR, and single molecule fluorescence techniques. Experimental results are summarized for ribonuclease, aspartate aminotransferase, and especially dihydrofolate reductase (DHFR). Multiple intermediates, multiple conformations, and cooperative conformational changes are shown to be an essential part of virtually all enzyme mechanisms. In the case of DHFR, theoretical investigations have provided detailed information about the movement of atoms within the enzyme-substrate complex as the reaction proceeds along the collective reaction coordinate for hydride transfer. A general mechanism is presented for enzyme catalysis that includes multiple intermediates and a complex, multidimensional standard free energy surface. Protein flexibility, diverse protein conformations, and cooperative conformational changes are important features of this model. PMID:22029278

  12. Advantages of Catalysis in Self-Assembled Molecular Capsules.

    Science.gov (United States)

    Catti, Lorenzo; Zhang, Qi; Tiefenbacher, Konrad

    2016-06-27

    Control over the local chemical environment of a molecule can be achieved by encapsulation in supramolecular host systems. In supramolecular catalysis, this control is used to gain advantages over classical homogeneous catalysis in bulk solution. Two of the main advantages concern influencing reactions in terms of substrate and product selectivity. Due to size and/or shape recognition, substrate selective conversion can be realized. Additionally, noncovalent interactions with the host environment facilitate alternative reaction pathways and can yield unusual products. This Concept article discusses and highlights literature examples utilizing self-assembled molecular capsules to achieve catalytic transformations displaying a high degree of substrate and/or product selectivity. Furthermore, the advantage of supramolecular hosts in multicatalyst tandem reactions is covered. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. XAFCA: a new XAFS beamline for catalysis research.

    Science.gov (United States)

    Du, Yonghua; Zhu, Yi; Xi, Shibo; Yang, Ping; Moser, Herbert O; Breese, Mark B H; Borgna, Armando

    2015-05-01

    A new X-ray absorption fine-structure (XAFS) spectroscopy beamline for fundamental and applied catalysis research, called XAFCA, has been built by the Institute of Chemical and Engineering Sciences, and the Singapore Synchrotron Light Source. XAFCA covers the photon energy range from 1.2 to 12.8 keV, making use of two sets of monochromator crystals, an Si (111) crystal for the range from 2.1 to 12.8 keV and a KTiOPO4 crystal [KTP (011)] for the range between 1.2 and 2.8 keV. Experiments can be carried out in the temperature range from 4.2 to 1000 K and pressures up to 30 bar for catalysis research. A safety system has been incorporated, allowing the use of flammable and toxic gases such as H2 and CO.

  14. Protruding interfacial OH groups and 'on-water' heterogeneous catalysis.

    Science.gov (United States)

    Jung, Yousung; Marcus, R A

    2010-07-21

    The key aspect of the remarkable organic catalysis that is observed to occur at the organic/water phase boundary, the so-called 'on-water' catalysis (Narayan et al 2005 Angew. Chem. 44 3275), was recently proposed to be the protruding OH groups of water molecules at the interface that interact with the transition state (TS) via hydrogen bonding and lower activation barriers (Jung and Marcus 2007 J. Am. Chem. Soc. 129 5492). In particular, the cycloaddition reaction of quadricyclane (Q) with dimethyl azodicarboxylate (DMAD) on-water was calculated to be more than 100,000 times more efficient in terms of rate constant than the neat reaction. In this paper, we review and consider a related reaction of Q with dimethyl acetylenedicarboxylate, where nitrogen, a good H-bond acceptor, in DMAD is replaced by carbon, a poor H-bond acceptor. A very low rate acceleration of acetylenedicarboxylate on-water relative to the neat reaction is obtained theoretically, as compared to DMAD on-water, due to the relatively low H-bonding ability of acetylenedicarboxylate with water at the TS relative to the reactants. We suggest that there may also be an 'intrinsic steric effect' or orientational advantage in the on-water catalysis in general, and both electronic and steric effects may be in operation for the smaller on-water catalysis for the cycloaddition reaction of quadricyclane and acetylenedicarboxylate. A preliminary quantum mechanical/molecular mechanical (QM/MM) simulation including 1264 water molecules for the on-water reaction of DMAD + Q also suggests that there are indeed approximately two-four more H-bonds between the TS and the dangling OH groups than between the reactants and the surface.

  15. Observations of exoelectron emission associated with heterogeneous catalysis

    Science.gov (United States)

    Hoenig, S. A.; Utter, M. G.

    1977-01-01

    It is suggested that the exoelectron emission from the catalyst may be used to monitor the rate of oxidation of CO and CH4 over palladium catalysts. Indirect heating of the catalyst and atmospheric pressure have no effect upon this monitoring system. Although the mechanism relating catalysis to exoelectron emission is not clear, it is considered possible that electron emission is triggered by the adsorption-desorption cycle.

  16. Engaging Alkenyl Halides with Alkylsilicates via Photoredox Dual Catalysis

    OpenAIRE

    Patel, Niki R.; Kelly, Christopher B.; Jouffroy, Matthieu; Molander, Gary A.

    2016-01-01

    Single-electron transmetalation via photoredox/nickel dual catalysis provides the opportunity for the construction of Csp3 ?Csp2 bonds through the transfer of alkyl radicals under very mild reaction conditions. A general procedure for the cross-coupling of primary and secondary (bis-catecholato)alkylsilicates with alkenyl halides is presented. The developed method allows not only alkenyl bromides and iodides but also previously underexplored alkenyl chlorides to be employed.

  17. Pacific Northwest National Laboratory Catalysis Highlights for FY2007

    Energy Technology Data Exchange (ETDEWEB)

    Garrett, Bruce C.

    2007-11-15

    To reduce the nation’s dependence on imported oil, the U.S. Department of Energy (DOE) and other federal and private agencies are investing in understanding catalysis. This report focuses on catalysis research conducted by Pacific Northwest National Laboratory (PNNL) and its collaborators. Using sophisticated instruments in DOE’s Environmental Molecular Sciences Laboratory, a national scientific user facility, research was conducted to answer key questions related to the nation’s use of automotive fuels. Research teams investigated how hydrogen can be safely stored and efficiently released, critical questions to use this alternative fuel. Further, they are answering key questions to design molecular catalysts to control the transfer of hydrogen atoms, hydrides, and protons important to hydrogen production. In dealing with today’s fuels, researchers examined adsorption of noxious nitrous oxides in automotive exhaust. Beyond automotive fuel, researchers worked on catalysts to harness solar power. These catalysts include the rutile and anatase forms of titanium dioxide. Basic research was conducted on designing catalysts for these and other applications. Our scientists examined how to build catalysts with the desired properties atom by atom and molecule by molecule. In addition, this report contains brief descriptions of the outstanding accomplishments of catalysis experts at PNNL.

  18. Quantifying ligand effects in high-oxidation-state metal catalysis

    Science.gov (United States)

    Billow, Brennan S.; McDaniel, Tanner J.; Odom, Aaron L.

    2017-09-01

    Catalysis by high-valent metals such as titanium(IV) impacts our lives daily through reactions like olefin polymerization. In any catalysis, optimization involves a careful choice of not just the metal but also the ancillary ligands. Because these choices dramatically impact the electronic structure of the system and, in turn, catalyst performance, new tools for catalyst development are needed. Understanding ancillary ligand effects is arguably one of the most critical aspects of catalyst optimization and, while parameters for phosphines have been used for decades with low-valent systems, a comparable system does not exist for high-valent metals. A new electronic parameter for ligand donation, derived from experiments on a high-valent chromium species, is now available. Here, we show that the new parameters enable quantitative determination of ancillary ligand effects on catalysis rate and, in some cases, even provide mechanistic information. Analysing reactions in this way can be used to design better catalyst architectures and paves the way for the use of such parameters in a host of high-valent processes.

  19. Electrochemically responsive heterogeneous catalysis for controlling reaction kinetics.

    Science.gov (United States)

    Mao, Xianwen; Tian, Wenda; Wu, Jie; Rutledge, Gregory C; Hatton, T Alan

    2015-01-28

    We report a method to control reaction kinetics using electrochemically responsive heterogeneous catalysis (ERHC). An ERHC system should possess a hybrid structure composed of an electron-conducting porous framework coated with redox-switchable catalysts. In contrast to other types of responsive catalysis, ERHC combines all the following desired characteristics for a catalysis control strategy: continuous variation of reaction rates as a function of the magnitude of external stimulus, easy integration into fixed-bed flow reactors, and precise spatial and temporal control of the catalyst activity. Herein we first demonstrate a facile approach to fabricating a model ERHC system that consists of carbon microfibers with conformal redox polymer coating. Second, using a Michael reaction whose kinetics depends on the redox state of the redox polymer catalyst, we show that use of different electrochemical potentials permits continuous adjustment of the reaction rates. The dependence of the reaction rate on the electrochemical potential generally agrees with the Nernstian prediction, with minor discrepancies due to the multilayer nature of the polymer film. Additionally, we show that the ERHC system can be employed to manipulate the shape of the reactant concentration-time profile in a batch reactor through applying customized potential-time programs. Furthermore, we perform COMSOL simulation for an ERHC-integrated flow reactor, demonstrating highly flexible manipulation of reactant concentrations as a function of both location and time.

  20. Switching on elusive organometallic mechanisms with photoredox catalysis.

    Science.gov (United States)

    Terrett, Jack A; Cuthbertson, James D; Shurtleff, Valerie W; MacMillan, David W C

    2015-08-20

    Transition-metal-catalysed cross-coupling reactions have become one of the most used carbon-carbon and carbon-heteroatom bond-forming reactions in chemical synthesis. Recently, nickel catalysis has been shown to participate in a wide variety of C-C bond-forming reactions, most notably Negishi, Suzuki-Miyaura, Stille, Kumada and Hiyama couplings. Despite the tremendous advances in C-C fragment couplings, the ability to forge C-O bonds in a general fashion via nickel catalysis has been largely unsuccessful. The challenge for nickel-mediated alcohol couplings has been the mechanistic requirement for the critical C-O bond-forming step (formally known as the reductive elimination step) to occur via a Ni(III) alkoxide intermediate. Here we demonstrate that visible-light-excited photoredox catalysts can modulate the preferred oxidation states of nickel alkoxides in an operative catalytic cycle, thereby providing transient access to Ni(III) species that readily participate in reductive elimination. Using this synergistic merger of photoredox and nickel catalysis, we have developed a highly efficient and general carbon-oxygen coupling reaction using abundant alcohols and aryl bromides. More notably, we have developed a general strategy to 'switch on' important yet elusive organometallic mechanisms via oxidation state modulations using only weak light and single-electron-transfer catalysts.

  1. Probing the chemistry of thioredoxin catalysis with force

    Science.gov (United States)

    Wiita, Arun P.; Perez-Jimenez, Raul; Walther, Kirstin A.; Gräter, Frauke; Berne, B. J.; Holmgren, Arne; Sanchez-Ruiz, Jose M.; Fernandez, Julio M.

    2014-01-01

    Thioredoxins are enzymes that catalyse disulphide bond reduction in all living organisms1. Although catalysis is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction1,2, the role of the enzyme in modulating this chemical reaction is unknown. Here, using single-molecule force-clamp spectroscopy3,4, we investigate the catalytic mechanism of Escherichia coli thioredoxin (Trx). We applied mechanical force in the range of 25–600 pN to a disulphide bond substrate and monitored the reduction of these bonds by individual enzymes. We detected two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulphide bond, causing a shortening of the substrate polypeptide by 0.79 ± 0.09 Å (± s.e.m.), and the second elongating the substrate disulphide bond by 0.17 ± 0.02 Å (±s.e.m.). These results support the view that the Trx active site regulates the geometry of the participating sulphur atoms with sub-ångström precision to achieve efficient catalysis. Our results indicate that substrate conformational changes may be important in the regulation of Trx activity under conditions of oxidative stress and mechanical injury, such as those experienced in cardiovascular disease5,6. Furthermore, single-molecule atomic force microscopy techniques, as shown here, can probe dynamic rearrangements within an enzyme’s active site during catalysis that cannot be resolved with any other current structural biological technique. PMID:17972886

  2. Crown ethers and phase transfer catalysis in polymer science

    CERN Document Server

    Carraher, Charles

    1984-01-01

    Phase transfer catalysis or interfacial catalysis is a syn­ thetic technique involving transport of an organic or inorganic salt from a solid or aqueous phase into an organic liquid where reaction with an organic-soluble substrate takes place. Over the past 15 years there has been an enormous amount of effort invested in the development of this technique in organic synthe­ sis. Several books and numerous review articles have appeared summarizing applications in which low molecular weight catalysts are employed. These generally include either crown ethers or onium salts of various kinds. While the term phase transfer catalysis is relatively new, the concept of using a phasetrans­ fer agent (PTA) is much older~ Both Schnell and Morgan employed such catalysts in synthesis of polymeric species in the early 1950's. Present developments are really extensions of these early applications. It has only been within the last several years that the use of phase transfer processes have been employed in polymer synthesis...

  3. Catalysis in electrochemistry from fundamental aspects to strategies for fuel cell development

    CERN Document Server

    Santos, Elizabeth

    2011-01-01

    Catalysis in Electrochemistry: From Fundamental Aspects to Strategies for Fuel Cell Development is a modern, comprehensive reference work on catalysis in electrochemistry, including principles, methods, strategies, and applications. It points out differences between catalysis at gas/surfaces and electrochemical interfaces, along with the future possibilities and impact of electrochemical science on energy problems. This book contributes both to fundamental science; experience in the design, preparation, and characterization of electrocatalytic materials; and the industrial application o

  4. Revitalizing the aromatic aza-Claisen rearrangement: implications for the mechanism of 'on-water' catalysis.

    Science.gov (United States)

    Beare, Kaitlin D; McErlean, Christopher S P

    2013-04-21

    For too long the aromatic aza-Claisen rearrangement has been the poor relation of its oxygen counterpart. We demonstrate that on-water catalysis facilitates the rearrangement of reverse N-prenylated naphthylamines and anilines, and transforms the aromatic aza-Claisen rearrangement into a synthetically viable reaction. We use this reaction to probe the mechanism of on-water catalysis, and provide compelling support for the acid-catalysis hypothesis.

  5. Catalysis by Atomic-Sized Centers: Methane Activation for Partial Oxidation and Combustion

    Science.gov (United States)

    2015-07-21

    AFRL-OSR-VA-TR-2015-0195 CATALYSIS BY ATOMIC-SIZED CENTERS: METHANE ACTIVATION FOR PARTIAL OXIDATION AND COMBUSTION Horia Metiu UNIVERSITY OF...To) 01-04-2012 to 31-03-2015 4. TITLE AND SUBTITLE CATALYSIS BY ATOMIC-SIZED CENTERS: METHANE ACTIVATION FOR PARTIAL OXIDATION AND COMBUSTION 5a...livelink/llisapi.dll DISTRIBUTION A: Distribution approved for public release. Final Technical Report, FA9550-12-1-0147 “ CATALYSIS BY ATOMIC-SIZED

  6. Support for U.S. Participants at the 15th International Congress on Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Wachs, Israel E.

    2013-08-05

    The grant was used to partially assist the travel expenses of U.S. academic scientists to attend the 15th International Congress on Catalysis. The conference was held in Munich, Germany from July 1-6, 2012. The importance of the International Congress was to bring together the international community of faculty members who participate in catalysis research, and to share information that would lead to further developments and directions in the field of study. Graduate students and Post Docs were invited to apply for travel assistance based on criteria established by the North American Catalysis Society (NACS) and the local Catalysis Clubs.

  7. RNA Catalysis, Thermodynamics and the Origin of Life

    Directory of Open Access Journals (Sweden)

    William G. Scott

    2014-04-01

    Full Text Available The RNA World Hypothesis posits that the first self-replicating molecules were RNAs. RNA self-replicases are, in general, assumed to have employed nucleotide 5ʹ-polyphosphates (or their analogues as substrates for RNA polymerization. The mechanism by which these substrates might be synthesized with sufficient abundance to supply a growing and evolving population of RNAs is problematic for evolutionary hypotheses because non-enzymatic synthesis and assembly of nucleotide 5ʹ-triphosphates (or other analogously activated phosphodiester species is inherently difficult. However, nucleotide 2ʹ,3ʹ-cyclic phosphates are also phosphodiesters, and are the natural and abundant products of RNA degradation. These have previously been dismissed as viable substrates for prebiotic RNA synthesis. We propose that the arguments for their dismissal are based on a flawed assumption, and that nucleotide 2ʹ,3ʹ-cyclic phosphates in fact possess several significant, advantageous properties that indeed make them particularly viable substrates for prebiotic RNA synthesis. An RNA World hypothesis based upon the polymerization of nucleotide 2ʹ,3ʹ-cyclic phosphates possesses additional explanatory power in that it accounts for the observed ribozyme “fossil record”, suggests a viable mechanism for substrate transport across lipid vesicle boundaries of primordial proto-cells, circumvents the problems of substrate scarcity and implausible synthetic pathways, provides for a primitive but effective RNA replicase editing mechanism, and definitively explains why RNA, rather than DNA, must have been the original catalyst. Finally, our analysis compels us to propose that a fundamental and universal property that drives the evolution of living systems, as well as pre-biotic replicating molecules (be they composed of RNA or protein, is that they exploit chemical reactions that already possess competing kinetically-preferred and thermodynamically-preferred pathways in a

  8. Catalysis as a foundational pillar of green chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Anastas, Paul T. [White House Office of Science and Technology Policy, Department of Chemistry, University of Nottingham Nottingham, (United Kingdom); Kirchhoff, Mary M. [U.S. Environmental Protection Agency and Trinity College, Washington, DC (United States); Williamson, Tracy C. [U.S. Environmental Protection Agency, Washington, DC (United States)

    2001-11-30

    Catalysis is one of the fundamental pillars of green chemistry, the design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances. The design and application of new catalysts and catalytic systems are simultaneously achieving the dual goals of environmental protection and economic benefit. Green chemistry, the design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances, is an overarching approach that is applicable to all aspects of chemistry. From feedstocks to solvents, to synthesis and processing, green chemistry actively seeks ways to produce materials in a way that is more benign to human health and the environment. The current emphasis on green chemistry reflects a shift away from the historic 'command-and-control' approach to environmental problems that mandated waste treatment and control and clean up through regulation, and toward preventing pollution at its source. Rather than accepting waste generation and disposal as unavoidable, green chemistry seeks new technologies that are cleaner and economically competitive. Utilizing green chemistry for pollution prevention demonstrates the power and beauty of chemistry: through careful design, society can enjoy the products on which we depend while benefiting the environment. The economic benefits of green chemistry are central drivers in its advancement. Industry is adopting green chemistry methodologies because they improve the corporate bottom line. A wide array of operating costs are decreased through the use of green chemistry. When less waste is generated, environmental compliance costs go down. Treatment and disposal become unnecessary when waste is eliminated. Decreased solvent usage and fewer processing steps lessen the material and energy costs of manufacturing and increase material efficiency. The environmental, human health, and the economic advantages realized through green chemistry

  9. Organocatalysis: Fundamentals and Comparisons to Metal and Enzyme Catalysis

    Directory of Open Access Journals (Sweden)

    Pierre Vogel

    2016-08-01

    Full Text Available Catalysis fulfills the promise that high-yielding chemical transformations will require little energy and produce no toxic waste. This message is carried by the study of the evolution of molecular catalysis of some of the most important reactions in organic chemistry. After reviewing the conceptual underpinnings of catalysis, we discuss the applications of different catalysts according to the mechanism of the reactions that they catalyze, including acyl group transfers, nucleophilic additions and substitutions, and C–C bond forming reactions that employ umpolung by nucleophilic additions to C=O and C=C double bonds. We highlight the utility of a broad range of organocatalysts other than compounds based on proline, the cinchona alkaloids and binaphthyls, which have been abundantly reviewed elsewhere. The focus is on organocatalysts, although a few examples employing metal complexes and enzymes are also included due to their significance. Classical Brønsted acids have evolved into electrophilic hands, the fingers of which are hydrogen donors (like enzymes or other electrophilic moieties. Classical Lewis base catalysts have evolved into tridimensional, chiral nucleophiles that are N- (e.g., tertiary amines, P- (e.g., tertiary phosphines and C-nucleophiles (e.g., N-heterocyclic carbenes. Many efficient organocatalysts bear electrophilic and nucleophilic moieties that interact simultaneously or not with both the electrophilic and nucleophilic reactants. A detailed understanding of the reaction mechanisms permits the design of better catalysts. Their construction represents a molecular science in itself, suggesting that sooner or later chemists will not only imitate Nature but be able to catalyze a much wider range of reactions with high chemo-, regio-, stereo- and enantioselectivity. Man-made organocatalysts are much smaller, cheaper and more stable than enzymes.

  10. The structural basis for specificity in lipoxygenase catalysis.

    Science.gov (United States)

    Newcomer, Marcia E; Brash, Alan R

    2015-03-01

    Many intriguing facets of lipoxygenase (LOX) catalysis are open to a detailed structural analysis. Polyunsaturated fatty acids with two to six double bonds are oxygenated precisely on a particular carbon, typically forming a single chiral fatty acid hydroperoxide product. Molecular oxygen is not bound or liganded during catalysis, yet it is directed precisely to one position and one stereo configuration on the reacting fatty acid. The transformations proceed upon exposure of substrate to enzyme in the presence of O2 (RH + O2 → ROOH), so it has proved challenging to capture the precise mode of substrate binding in the LOX active site. Beginning with crystal structures with bound inhibitors or surrogate substrates, and most recently arachidonic acid bound under anaerobic conditions, a picture is consolidating of catalysis in a U-shaped fatty acid binding channel in which individual LOX enzymes use distinct amino acids to control the head-to-tail orientation of the fatty acid and register of the selected pentadiene opposite the non-heme iron, suitably positioned for the initial stereoselective hydrogen abstraction and subsequent reaction with O2 . Drawing on the crystal structures available currently, this review features the roles of the N-terminal β-barrel (C2-like, or PLAT domain) in substrate acquisition and sensitivity to cellular calcium, and the α-helical catalytic domain in fatty acid binding and reactions with O2 that produce hydroperoxide products with regio and stereospecificity. LOX structures combine to explain how similar enzymes with conserved catalytic machinery differ in product, but not substrate, specificities. © 2014 The Protein Society.

  11. Plasma Chemistry and Catalysis in Gases and Liquids

    CERN Document Server

    Parvulescu, Vasile I; Lukes, Petr

    2012-01-01

    Filling the gap for a book that not only covers gases but also plasma methods in liquids, this is all set to become the standard reference on the topic. It considers the central aspects in plasma chemistry and plasma catalysis by focusing on the green and environmental applications, while also taking into account their practical and economic viability. With the topics addressed by an international group of major experts, this is a must-have for researchers, PhD students and postdocs specializing in the field.

  12. Pd/C Catalysis under Microwave Dielectric Heating

    Directory of Open Access Journals (Sweden)

    Elena Cini

    2017-03-01

    Full Text Available Microwave-assisted organic synthesis (MAOS provides a novel and efficient means of achieving heat organic reactions. Nevertheless, the potential arcing phenomena via microwave (MW interaction with solid metal catalysts has limited its use by organic chemists. As arcing phenomena are now better understood, new applications of Pd/C-catalyzed reactions under MW dielectric heating are now possible. In this review, the state of the art, benefits, and challenges of coupling MW heating with heterogeneous Pd/C catalysis are discussed to inform organic chemists about their use with one of the most popular heterogeneous catalysts.

  13. Inorganic Chemistry in Hydrogen Storage and Biomass Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Thorn, David [Los Alamos National Laboratory

    2012-06-13

    Making or breaking C-H, B-H, C-C bonds has been at the core of catalysis for many years. Making or breaking these bonds to store or recover energy presents us with fresh challenges, including how to catalyze these transformations in molecular systems that are 'tuned' to minimize energy loss and in molecular and material systems present in biomass. This talk will discuss some challenging transformations in chemical hydrogen storage, and some aspects of the inorganic chemistry we are studying in the development of catalysts for biomass utilization.

  14. Direct synthesis of macrodiolides via hafnium(IV) catalysis.

    Science.gov (United States)

    de Léséleuc, Mylène; Collins, Shawn K

    2015-07-04

    Efficient direct synthesis of macrodiolides via catalysis using Hf(OTf)4 is possible in high yields, forming water as the sole by-product. The first protocol for the direct synthesis of macrodiolides from equimolar mixtures of diols and dicarboxylic acids was developed (58-96%). In addition, modification of the reaction concentration allows for the synthesis of head-to-tail macrodiolides from the corresponding seco acids. The catalytic preparation of the macrodiolides using a commercially available catalyst without the need for slow addition or azeotropic condition provides an operationally simple alternative to protocols which employ toxic tin catalysts or stoichiometric activation strategies.

  15. Charge Transfer and Catalysis at the Metal Support Interface

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Lawrence Robert [Univ. of California, Berkeley, CA (United States)

    2012-07-31

    Kinetic, electronic, and spectroscopic characterization of model Pt–support systems are used to demonstrate the relationship between charge transfer and catalytic activity and selectivity. The results show that charge flow controls the activity and selectivity of supported metal catalysts. This dissertation builds on extensive existing knowledge of metal–support interactions in heterogeneous catalysis. The results show the prominent role of charge transfer at catalytic interfaces to determine catalytic activity and selectivity. Further, this research demonstrates the possibility of selectively driving catalytic chemistry by controlling charge flow and presents solid-state devices and doped supports as novel methods for obtaining electronic control over catalytic reaction kinetics.

  16. Mechanism of catalysis of the thio-Claisen rearrangement

    Energy Technology Data Exchange (ETDEWEB)

    Kwart, H.; Miles, W.H.; Horgan, A.G.; Kwart, L.D.

    1981-04-08

    The cyclization-induced rearrangement mechanism proposed by Overman to account for nucleophilic catalysis of the thio-Claisen rearrangement has been tested by application of two criteria, viz., the secondary kinetic deuterium isotope effect at the ..beta.. (side chain) carbon in phenyl allyl sulfide and the substituent rate effect. The results (k/sub H/k/sub D/ = 1.05 and log k/sub xp/k/sub H/ = 0.25 sigma/sup +/) do not support the mechanism. Instead, they can be construed to support the previously validated mechanism of nucleophilic triggering of sigmatropic rearrangement.

  17. Oxy-Allyl Cation Catalysis: An Enantioselective Electrophilic Activation Mode

    Science.gov (United States)

    Liu, Chun; Oblak, E. Zachary; Vander Wal, Mark N.; Dilger, Andrew K.; Almstead, Danielle K.; MacMillan, David W. C.

    2016-01-01

    A generic activation mode for asymmetric LUMO-lowering catalysis has been developed using the long-established principles of oxy-allyl cation chemistry. Here, the enantioselective conversion of racemic α-tosyloxy ketones to optically enriched α-indolic carbonyls has been accomplished using a new amino alcohol catalyst in the presence of electron-rich indole nucleophiles. Kinetic studies reveal that the rate-determining step in this SN1 pathway is the catalyst-mediated α-tosyloxy ketone deprotonation step to form an enantiodiscriminant oxy-allyl cation prior to the stereodefining nucleophilic addition event. PMID:26797012

  18. Development of catalysts and ligands for enantioselective gold catalysis.

    Science.gov (United States)

    Wang, Yi-Ming; Lackner, Aaron D; Toste, F Dean

    2014-03-18

    During the past decade, the use of Au(I) complexes for the catalytic activation of C-C π-bonds has been investigated intensely. Over this time period, the development of homogeneous gold catalysis has been extraordinarily rapid and has yielded a host of mild and selective methods for the formation of carbon-carbon and carbon-heteroatom bonds. The facile formation of new bonds facilitated by gold naturally led to efforts toward rendering these transformations enantioselective. In this Account, we survey the development of catalysts and ligands for enantioselective gold catalysis by our research group as well as related work by others. We also discuss some of our strategies to address the challenges of enantioselective gold(I) catalysis. Early on, our work with enantioselective gold-catalyzed transformations focused on bis(phosphinegold) complexes derived from axially chiral scaffolds. Although these complexes were highly successful in some reactions like cyclopropanation, the careful choice of the weakly coordinating ligand (or counterion) was necessary to obtain high levels of enantioselectivity for the case of allene hydroamination. These counterion effects led us to use the anion itself as a source of chirality, which was successful in the case of allene hydroalkoxylation. In general, these tactics enhance the steric influence around the reactive gold center beyond the two-coordinate ligand environment. The use of binuclear complexes allowed us to use the second gold center and its associated ligand (or counterion) to exert a further steric influence. In a similar vein, we employed a chiral anion (in place of or in addition to a chiral ligand) to move the chiral information closer to the reactive center. In order to expand the scope of reactions amenable to enantioselective gold catalysis to cycloadditions and other carbocyclization processes, we also developed a new class of mononuclear phosphite and phosphoramidite ligands to supplement the previously widely

  19. Decarboxylative Fluorination of Aliphatic Carboxylic Acids via Photoredox Catalysis

    Science.gov (United States)

    Ventre, Sandrine; Petronijevic, Filip R.; MacMillan, David W. C.

    2016-01-01

    The direct conversion of aliphatic carboxylic acids to the corresponding alkyl fluorides has been achieved via visible light-promoted photoredox catalysis. This operationally simple, redox-neutral fluorination method is amenable to a wide variety of carboxylic acids. Photon-induced oxidation of carboxylates leads to the formation of carboxyl radicals, which upon rapid CO2-extrusion and F• transfer from a fluorinating reagent yield the desired fluoroalkanes with high efficiency. Experimental evidence indicates that an oxidative quenching pathway is operable in this broadly applicable fluorination protocol. PMID:25881929

  20. High-Valent Organometallic Copper and Palladium in Catalysis

    Science.gov (United States)

    Hickman, Amanda J.; Sanford, Melanie S.

    2015-01-01

    Preface Copper and palladium catalysts are critically important for numerous commercial chemical processes. Improvements in the activity, selectivity, and scope of these catalysts have the potential to dramatically reduce the environmental impact and increase the sustainability of chemical reactions. One rapidly emerging strategy to achieve these goals is to exploit “high-valent” copper and palladium intermediates in catalysis. This review describes exciting recent advances involving both the fundamental chemistry and the applications of these high-valent metal complexes in numerous synthetically useful catalytic transformations. PMID:22498623

  1. Probing the chemistry of thioredoxin catalysis with force

    OpenAIRE

    Wiita, Arun P.; Perez-Jimenez, Raul; Walther, Kirstin A.; Gräter, Frauke; Berne, B. J.; Holmgren, Arne; Sanchez-Ruiz, Jose M.; Fernandez, Julio M.

    2007-01-01

    Thioredoxins are enzymes that catalyse disulphide bond reduction in all living organisms1. Although catalysis is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction1,2, the role of the enzyme in modulating this chemical reaction is unknown. Here, using single-molecule force-clamp spectroscopy3,4, we investigate the catalytic mechanism of Escherichia coli thioredoxin (Trx). We applied mechanical force in the range of 25–600 pN to a disulphide bond substrate and mo...

  2. Catalysis science and technology for cleaner transportation fuels

    Energy Technology Data Exchange (ETDEWEB)

    Kaufmann, T.G. [Exxon Research and Engineering, PO Box 101, 07932 Florham Park, NJ (United States); Kaldor, A.; Stuntz, G.F.; Kerby, M.C.; Ansell, L.L. [Exxon Research and Development Laboratories, PO Box 2226, 70821 Baton Rouge, LA (United States)

    2000-09-25

    The production of liquid transportation fuels such as gasoline, diesel and jet fuel from petroleum involves the use of a variety of catalytic processes. Although the petroleum refining industry is quite mature, fuel composition requirements continue to evolve with time in response to environmental legislation and changes in engine design. In addition, petroleum feedstocks are becoming heavier and more sour with time. New technology is emerging that allows efficient conversion of natural gas to liquid hydrocarbon fuels. Taken together, these changes pose considerable challenges to the refining industry and significant advances in catalysis are needed to meet the challenge.

  3. USD Catalysis Group for Alternative Energy - Final report

    Energy Technology Data Exchange (ETDEWEB)

    Hoefelmeyer, James

    2014-10-03

    I. Project Summary Catalytic processes are a major technological underpinning of modern society, and are essential to the energy sector in the processing of chemical fuels from natural resources, fine chemicals synthesis, and energy conversion. Advances in catalyst technology are enormously valuable since these lead to reduced chemical waste, reduced energy loss, and reduced costs. New energy technologies, which are critical to future economic growth, are also heavily reliant on catalysts, including fuel cells and photo-electrochemical cells. Currently, the state of South Dakota is underdeveloped in terms of research infrastructure related to catalysis. If South Dakota intends to participate in significant economic growth opportunities that result from advances in catalyst technology, then this area of research needs to be made a high priority for investment. To this end, a focused research effort is proposed in which investigators from The University of South Dakota (USD) and The South Dakota School of Mines and Technology (SDSMT) will contribute to form the South Dakota Catalysis Group (SDCG). The multidisciplinary team of the (SDCG) include: (USD) Dan Engebretson, James Hoefelmeyer, Ranjit Koodali, and Grigoriy Sereda; (SDSMT) Phil Scott Ahrenkiel, Hao Fong, Jan Puszynski, Rajesh Shende, and Jacek Swiatkiewicz. The group is well suited to engage in a collaborative project due to the resources available within the existing programs. Activities within the SDCG will be monitored through an external committee consisting of three distinguished professors in chemistry. The committee will provide expert advice and recommendations to the SDCG. Advisory meetings in which committee members interact with South Dakota investigators will be accompanied by individual oral and poster presentations in a materials and catalysis symposium. The symposium will attract prominent scientists, and will enhance the visibility of research in the state of South Dakota. The SDCG requests

  4. Recent advances in the cycloisomerizations of methylenecyclopropanes under gold catalysis.

    Science.gov (United States)

    Shi, Min; Fang, Wei

    2018-02-21

    During the past decades, cycloisomerizations of methylenecyclopropanes under gold catalysis have attracted much attention from organic chemists. The different patterns of cycloisomerizations have been developed from gold(I)-catalyzed ring-opening and ring-expansion of methylenecyclopropanes. This synthetic methodology provides a new approach to novel cyclic- or polycyclic compounds and even polycyclic aromatic hydrocarbons, organic light emitting materials and biologically active substances. The corresponding products have great potential for material science, medicinal chemistry and total synthesis. This Concept article will mainly focus on the recent advances in the cycloisomerizations of methylenecyclopropanes in the past four year. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase

    OpenAIRE

    Ferreira,Patricia; Hernández-Ortega, Aitor; Lucas, Fatima; Carro, Juan; Herguedas, Beatriz; Borrelli, Kenneth W.; Guallar, Víctor; Martínez, Angel T.; Medina, Milagros

    2015-01-01

    This is the peer reviewed version of the following article: [Ferreira, P., Hernández-Ortega, A., Lucas, F., Carro, J., Herguedas, B., Borrelli, K. W., Guallar, V., Martínez, A. T. and Medina, M. (2015), Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase. FEBS J, 282: 3091–3106. doi:10.1111/febs.13221], which has been published in final form at [10.1111/febs.13221]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-...

  6. Elucidation of mechanisms in manganese and iron based oxidation catalysis : Mechanistic insights and development of novel approaches applied to transition metal catalyzed oxidations catalysis

    NARCIS (Netherlands)

    Angelone, Davide

    2016-01-01

    Oxidation chemistry is central to life and to the modern chemical industry and hence understanding chemical oxidation is essential to developing new processes and elucidating biological oxidation mechanisms. Elucidating mechanisms in inorganic oxidation catalysis and simultaneously developing new

  7. Asymmetric fluorination of α-branched cyclohexanones enabled by a combination of chiral anion phase-transfer catalysis and enamine catalysis using protected amino acids.

    Science.gov (United States)

    Yang, Xiaoyu; Phipps, Robert J; Toste, F Dean

    2014-04-09

    We report a study involving the successful merger of two separate chiral catalytic cycles: a chiral anion phase-transfer catalysis cycle to activate Selectfluor and an enamine activation cycle, using a protected amino acid as organocatalyst. We have demonstrated the viability of this approach with the direct asymmetric fluorination of α-substituted cyclohexanones to generate quaternary fluorine-containing stereocenters. With these two chiral catalytic cycles operating together in a matched sense, high enantioselectivites can be achieved, and we envisage that this dual catalysis method has the potential to be more broadly applicable, given the breadth of enamine catalysis. It also represents a rare example of chiral enamine catalysis operating successfully on α-branched ketones, substrates commonly inert to this activation mode.

  8. Homogeneous vs heterogeneous polymerization catalysis revealed by single-particle fluorescence microscopy.

    Science.gov (United States)

    Esfandiari, N Melody; Blum, Suzanne A

    2011-11-16

    A high-sensitivity and high-resolution single-particle fluorescence microscopy technique differentiated between homogeneous and heterogeneous metathesis polymerization catalysis by imaging the location of the early stages of polymerization. By imaging single polymers and single crystals of Grubbs II, polymerization catalysis was revealed to be solely homogeneous rather than heterogeneous or both.

  9. Final technical report, Symposium on New Theoretical Concepts and Directions in Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Metiu, Horia [University of California, Santa Barbara

    2014-08-22

    We organized in August 2013 a “Symposium on New Theoretical Concepts and Directions in Catalysis” with the participation of 20 invited distinguished quantum chemists and other researchers who use computations to study catalysis. Symposium website; http://catalysis.cnsi.ucsb.edu/

  10. Lewis-acid catalysis of carbon carbon bond forming reactions in water

    NARCIS (Netherlands)

    Engberts, JBFN; Feringa, BL; Keller, E; Otto, S

    1996-01-01

    In this article, we review the recent progress that has been made in the field of Lewis-acid catalysis of carbon carbon-bond-forming reactions in aqueous solution. Since water hampers the hard hard interactions between the catalyst and the reactant, it often complicates catalysis. However, once

  11. Asymmetric Aldol Additions: A Guided-Inquiry Laboratory Activity on Catalysis

    Science.gov (United States)

    King, Jorge H. Torres; Wang, Hong; Yezierski, Ellen J.

    2018-01-01

    Despite the importance of asymmetric catalysis in both the pharmaceutical and commodity chemicals industries, asymmetric catalysis is under-represented in undergraduate chemistry laboratory curricula. A novel guided-inquiry experiment based on the asymmetric aldol addition was developed. Students conduct lab work to compare the effectiveness of…

  12. New tools for the Baeyer-Villiger oxidation of ketones: Phase transfer catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Ricci, Marco; Battistel, Ezio [EniChem SpA, Centro Ricerche Novara, Novara (Italy). Ist. Guido Donegani

    1997-09-01

    The Baeyer-Villiger reaction, allowing the oxidation of ketones to esters, is an important reaction which has found a number of applications in organic synthesis. Some recent, improved procedures, involving either phase-transfer or enzymatic catalysis, will be discussed. This first part will deal with phase-transfer catalysis.

  13. Ir/Sn dual-reagent catalysis towards highly selective alkylation of ...

    Indian Academy of Sciences (India)

    Wintec

    *For correspondence. Ir/Sn dual-reagent catalysis towards highly selective alkylation of arenes and heteroarenes with benzyl alcohols. SUJIT ROY*, SUSMITA PODDER and JOYANTA CHOUDHURY. Organometallics and Catalysis Laboratory, Department of Chemistry, Indian Institute of Technology,. Kharagpur 721 302.

  14. Conduction and Reactivity in Heterogeneous-Molecular Catalysis: New Insights in Water Oxidation Catalysis by Phosphate Cobalt Oxide Films.

    Science.gov (United States)

    Costentin, Cyrille; Porter, Thomas R; Savéant, Jean-Michel

    2016-05-04

    Cyclic voltammetry of phosphate cobalt oxide (CoPi) films catalyzing O2-evolution from water oxidation as a function of scan rate, phosphate concentration and film thickness allowed for new insights into the coupling between charge transport and catalysis. At pH = 7 and low buffer concentrations, the film is insulating below 0.8 (V vs SHE) but becomes conductive above 0.9 (V vs SHE). Between 1.0 to 1.3 (V vs SHE), the mesoporous structure of the film gives rise to a large thickness-dependent capacitance. At higher buffer concentrations, two reversible proton-coupled redox couples appear over the capacitive response with 0.94 and 1.19 (V vs SHE) pH = 7 standard potentials. The latter is, at most, very weakly catalytic and not responsible for the large catalytic current observed at higher potentials. CV-response analysis showed that the amount of redox-active cobalt-species in the film is small, less than 10% of total. The catalytic process involves a further proton-coupled-electron-transfer and is so fast that it is controlled by diffusion of phosphate, the catalyst cofactor. CV-analysis with newly derived relationships led to a combination of the catalyst standard potential with the catalytic rate constant and a lower-limit estimation of these parameters. The large currents resulting from the fast catalytic reaction result in significant potential losses related to charge transport through the film. CoPi films appear to combine molecular catalysis with semiconductor-type charge transport. This mode of heterogeneous molecular catalysis is likely to occur in many other catalytic films.

  15. Characterization techniques for graphene-based materials in catalysis

    Directory of Open Access Journals (Sweden)

    Maocong Hu

    2017-06-01

    Full Text Available Graphene-based materials have been studied in a wide range of applications including catalysis due to the outstanding electronic, thermal, and mechanical properties. The unprecedented features of graphene-based catalysts, which are believed to be responsible for their superior performance, have been characterized by many techniques. In this article, we comprehensively summarized the characterization methods covering bulk and surface structure analysis, chemisorption ability determination, and reaction mechanism investigation. We reviewed the advantages/disadvantages of different techniques including Raman spectroscopy, X-ray photoelectron spectroscopy (XPS, Fourier transform infrared spectroscopy (FTIR and Diffuse Reflectance Fourier Transform Infrared Spectroscopy (DRIFTS, X-Ray diffraction (XRD, X-ray absorption near edge structure (XANES and X-ray absorption fine structure (XAFS, atomic force microscopy (AFM, scanning electron microscopy (SEM, transmission electron microscopy (TEM, high-resolution transmission electron microscopy (HRTEM, ultraviolet-visible spectroscopy (UV-vis, X-ray fluorescence (XRF, inductively coupled plasma mass spectrometry (ICP, thermogravimetric analysis (TGA, Brunauer–Emmett–Teller (BET, and scanning tunneling microscopy (STM. The application of temperature-programmed reduction (TPR, CO chemisorption, and NH3/CO2-temperature-programmed desorption (TPD was also briefly introduced. Finally, we discussed the challenges and provided possible suggestions on choosing characterization techniques. This review provides key information to catalysis community to adopt suitable characterization techniques for their research.

  16. Catalysis of heat-to-work conversion in quantum machines

    Science.gov (United States)

    Ghosh, A.; Latune, C. L.; Davidovich, L.; Kurizki, G.

    2017-11-01

    We propose a hitherto-unexplored concept in quantum thermodynamics: catalysis of heat-to-work conversion by quantum nonlinear pumping of the piston mode which extracts work from the machine. This concept is analogous to chemical reaction catalysis: Small energy investment by the catalyst (pump) may yield a large increase in heat-to-work conversion. Since it is powered by thermal baths, the catalyzed machine adheres to the Carnot bound, but may strongly enhance its efficiency and power compared with its noncatalyzed counterparts. This enhancement stems from the increased ability of the squeezed piston to store work. Remarkably, the fraction of piston energy that is convertible into work may then approach unity. The present machine and its counterparts powered by squeezed baths share a common feature: Neither is a genuine heat engine. However, a squeezed pump that catalyzes heat-to-work conversion by small investment of work is much more advantageous than a squeezed bath that simply transduces part of the work invested in its squeezing into work performed by the machine.

  17. Looking Back on 35 Years of Industrial Catalysis.

    Science.gov (United States)

    Blaser, Hans-Ulrich

    2015-08-19

    This article is an account of my 35 years in the Basel Chemical Industry, starting in 1976 as a young research chemist in the Central Research Laboratories of Ciba-Geigy until my retirement as Chief Scientific Officer of Solvias in 2011. In the first section, important aspects of industrial research are commented from my personal point of view with particular emphasis on the importance of team work and the situation of catalysis in the (Swiss) fine chemicals industry. In the next sections, the three most important areas of catalytic research are described where my colleagues and I could not only solve specific Ciba-Geigy / Novartis / Solvias problems, but also developed industrially relevant, generally applicable catalytic methodologies and contributed to the understanding of these complex catalytic transformations: i) Catalytic C-C and C-N coupling catalysis where we developed highly efficient catalysts for the Heck, Suzuki, Buchwald-Hartwig reactions; ii) Hydrogenations using modified heterogeneous catalysts, especially the chemoselective reduction of functionalized nitro arenes and the enantioselective hydrogenation of substituted ketones using Pt catalysts modified with chinchona alkaloids where mechanistic studies led to a working understanding of this fascinating reaction; iii) Enantioselective homogeneous hydrogenation and chiral ligands. The process development for the production of (S)-metolachlor, an important herbicide via an iridium-Josiphos catalyzed C=N hydrogenation is described in some detail, followed by a brief description how the Solvias Ligand Portfolio was developed.

  18. Conformational dynamics of Thermus aquaticus DNA polymerase I during catalysis.

    Science.gov (United States)

    Xu, Cuiling; Maxwell, Brian A; Suo, Zucai

    2014-08-12

    Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been performed to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a de novo disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Oxidase catalysis via aerobically generated hypervalent iodine intermediates

    Science.gov (United States)

    Maity, Asim; Hyun, Sung-Min; Powers, David C.

    2018-02-01

    The development of sustainable oxidation chemistry demands strategies to harness O2 as a terminal oxidant. Oxidase catalysis, in which O2 serves as a chemical oxidant without necessitating incorporation of oxygen into reaction products, would allow diverse substrate functionalization chemistry to be coupled to O2 reduction. Direct O2 utilization suffers from intrinsic challenges imposed by the triplet ground state of O2 and the disparate electron inventories of four-electron O2 reduction and two-electron substrate oxidation. Here, we generate hypervalent iodine reagents—a broadly useful class of selective two-electron oxidants—from O2. This is achieved by intercepting reactive intermediates of aldehyde autoxidation to aerobically generate hypervalent iodine reagents for a broad array of substrate oxidation reactions. The use of aryl iodides as mediators of aerobic oxidation underpins an oxidase catalysis platform that couples substrate oxidation directly to O2 reduction. We anticipate that aerobically generated hypervalent iodine reagents will expand the scope of aerobic oxidation chemistry in chemical synthesis.

  20. Structural basis for catalysis at the membrane-water interface.

    Science.gov (United States)

    Dufrisne, Meagan Belcher; Petrou, Vasileios I; Clarke, Oliver B; Mancia, Filippo

    2017-11-01

    The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Laser Pyrolysis Techniques: Application To Catalysis, Combustion Diagnostics, And Kinetics

    Science.gov (United States)

    Smith, Gregory P.

    1984-05-01

    A pulsed laser pyrolysis method has been developed to study kinetic processes at high temperatures. A CO2 laser is used to irradiate a 100 torr mixture of an infrared absorber (SF6), bath gas (N2), and reactants. Rapid heating to 700-1400 K occurs, followed by two-stage cooling. Unimolecular reactions are studied by competitive kinetics with a known standard, using mass-spectrometric or gas-chromatographic analysis. Bimolecular processes are examined using laser-induced fluorescence (LIF). The technique offers great advantages in reaching reactive temperatures in a fast and time-resolved manner, without the complications of hot surfaces. It is thus an ideal tool for analyzing and measuring some of the basic processes occurring in more complicated, real, hot systems. Our recent applications of the laser pyrolysis method in the areas of catalysis and combustion are summarized here. Several transition metal-carbonyl bond dissociation energies have been measured, and catalysis by the hot metal particulate products was observed. Since the use of LIF as a flame diagnotic requires some knowledge of the fluorescence quenching rates at high temperatures, the laser pyrolysis method was used to measure these rates for the important OH radical. Its reaction rate with acetylene was also measured, with implications for flame modeling and the mechanism of soot formation. Finally, this method can be used to ignite low concentrations of fuel and oxidant, and then study the time-resolved evolution of the flame chemistry by LIF and chemiluminescence observations.

  2. Role of dynamics in enzyme catalysis: substantial versus semantic controversies.

    Science.gov (United States)

    Kohen, Amnon

    2015-02-17

    CONSPECTUS: The role of the enzyme's dynamic motions in catalysis is at the center of heated contemporary debates among both theoreticians and experimentalists. Resolving these apparent disputes is of both intellectual and practical importance: incorporation of enzyme dynamics could be critical for any calculation of enzymatic function and may have profound implications for structure-based drug design and the design of biomimetic catalysts. Analysis of the literature suggests that while part of the dispute may reflect substantial differences between theoretical approaches, much of the debate is semantic. For example, the term "protein dynamics" is often used by some researchers when addressing motions that are in thermal equilibrium with their environment, while other researchers only use this term for nonequilibrium events. The last cases are those in which thermal energy is "stored" in a specific protein mode and "used" for catalysis before it can dissipate to its environment (i.e., "nonstatistical dynamics"). This terminology issue aside, a debate has arisen among theoreticians around the roles of nonstatistical vs statistical dynamics in catalysis. However, the author knows of no experimental findings available today that examined this question in enzyme catalyzed reactions. Another source of perhaps nonsubstantial argument might stem from the varying time scales of enzymatic motions, which range from seconds to femtoseconds. Motions at different time scales play different roles in the many events along the catalytic cascade (reactant binding, reprotonation of reactants, structural rearrangement toward the transition state, product release, etc.). In several cases, when various experimental tools have been used to probe catalytic events at differing time scales, illusory contradictions seem to have emerged. In this Account, recent attempts to sort the merits of those questions are discussed along with possible future directions. A possible summary of current

  3. Heterogeneous Molecular Catalysis of Electrochemical Reactions: Volcano Plots and Catalytic Tafel Plots.

    Science.gov (United States)

    Costentin, Cyrille; Savéant, Jean-Michel

    2017-06-14

    We analyze here, in the framework of heterogeneous molecular catalysis, the reasons for the occurrence or nonoccurrence of volcanoes upon plotting the kinetics of the catalytic reaction versus the stabilization free energy of the primary intermediate of the catalytic process. As in the case of homogeneous molecular catalysis or catalysis by surface-active metallic sites, a strong motivation of such studies relates to modern energy challenges, particularly those involving small molecules, such as water, hydrogen, oxygen, proton, and carbon dioxide. This motivation is particularly pertinent for what concerns heterogeneous molecular catalysis, since it is commonly preferred to homogeneous molecular catalysis by the same molecules if only for chemical separation purposes and electrolytic cell architecture. As with the two other catalysis modes, the main drawback of the volcano plot approach is the basic assumption that the kinetic responses depend on a single descriptor, viz., the stabilization free energy of the primary intermediate. More comprehensive approaches, investigating the responses to the maximal number of experimental factors, and conveniently expressed as catalytic Tafel plots, should clearly be preferred. This is more so in the case of heterogeneous molecular catalysis in that additional transport factors in the supporting film may additionally affect the current-potential responses. This is attested by the noteworthy presence of maxima in catalytic Tafel plots as well as their dependence upon the cyclic voltammetric scan rate.

  4. Supramolecular phosphate transfer catalysis by pillar[5]arene.

    Science.gov (United States)

    Liz, Daiane G; Manfredi, Alex M; Medeiros, Michelle; Montecinos, Rodrigo; Gómez-González, Borja; Garcia-Rio, Luis; Nome, Faruk

    2016-02-21

    A kinetic study on dinitrophenylphosphate monoester hydrolysis in the presence of a cationic pillararene, P5A, has been carried out. Formation of the supramolecular complex between phosphate ester and P5A has been studied by NMR showing complexation-induced upfield proton shifts indicative of aromatic ring inclusion in the pillararene cavity. Molecular dynamic calculations allow structure characterization for the 1 : 1 and 1 : 2 complexes. As a result of the supramolecular interaction both the acidity of DNPP and its hydrolysis rate constants are increased. Catalysis results from combination of both electrostatic stabilization reducing the negative electron density on the PO3(=) oxygens and monoester dianion destabilization by the steric effects of close NMe3(+) groups hindering the hydrogen-bonding with water and destabilising the monoester dianion.

  5. Protein dynamics and enzyme catalysis: the ghost in the machine?

    Science.gov (United States)

    Glowacki, David R; Harvey, Jeremy N; Mulholland, Adrian J

    2012-06-01

    One of the most controversial questions in enzymology today is whether protein dynamics are significant in enzyme catalysis. A particular issue in these debates is the unusual temperature-dependence of some kinetic isotope effects for enzyme-catalysed reactions. In the present paper, we review our recent model [Glowacki, Harvey and Mulholland (2012) Nat. Chem. 4, 169-176] that is capable of reproducing intriguing temperature-dependences of enzyme reactions involving significant quantum tunnelling. This model relies on treating multiple conformations of the enzyme-substrate complex. The results show that direct 'driving' motions of proteins are not necessary to explain experimental observations, and show that enzyme reactivity can be understood and accounted for in the framework of transition state theory.

  6. Nanoscale magnetic stirring bars for heterogeneous catalysis in microscopic systems.

    Science.gov (United States)

    Yang, Shuliang; Cao, Changyan; Sun, Yongbin; Huang, Peipei; Wei, Fangfang; Song, Weiguo

    2015-02-23

    Nanometer-sized magnetic stirring bars containing Pd nanoparticles (denoted as Fe3 O4 -NC-PZS-Pd) for heterogeneous catalysis in microscopic system were prepared through a facile two-step process. In the hydrogenation of styrene, Fe3 O4 -NC-PZS-Pd showed an activity similar to that of the commercial Pd/C catalyst, but much better stability. In microscopic catalytic systems, Fe3 O4 -NC-PZS-Pd can effectively stir the reaction solution within microdrops to accelerate mass transfer, and displays far better catalytic activity than the commercial Pd/C for the hydrogenation of methylene blue in an array of microdroplets. These results suggested that the Fe3 O4 -NC-PZS-Pd could be used as nanoscale stirring bars in nanoreactors. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Shape-Controlled Metal Nanocrystals for Heterogeneous Catalysis.

    Science.gov (United States)

    Ruditskiy, Aleksey; Peng, Hsin-Chieh; Xia, Younan

    2016-06-07

    The ability to control the shape of metal nanocrystals allows us to not only maneuver their physicochemical properties but also optimize their activity in a variety of applications. Heterogeneous catalysis, in particular, would benefit tremendously from the availability of metal nanocrystals with controlled shapes and well-defined facets or surface structures. The immediate benefits may include significant enhancements in catalytic activity and/or selectivity along with reductions in the materials cost. We provide a brief account of recent progress in the development of metal nanocrystals with controlled shapes and thereby enhanced catalytic performance for several reactions, including formic acid oxidation, oxygen reduction, and hydrogenation. In addition to monometallic nanocrystals, we also cover a bimetallic system, in which the two metals are formulated as alloyed, core-shell, or core-frame structures. We hope this article will provide further impetus for the development of next-generation heterogeneous catalysts essential to a broad range of applications.

  8. A solvable two-species catalysis-driven aggregation model

    CERN Document Server

    Ke Jian Hong

    2003-01-01

    We study the kinetics of a two-species catalysis-driven aggregation system, in which an irreversible aggregation between any two clusters of one species occurs only with the catalytic action of another species. By means of a generalized mean-field rate equation, we obtain the asymptotic solutions of the cluster mass distributions in a simple process with a constant rate kernel. For the case without any consumption of the catalyst, the cluster mass distribution of either species always approaches a conventional scaling law. However, the evolution behaviour of the system in the case with catalyst consumption is complicated and depends crucially on the relative data of the initial concentrations of the two species.

  9. Advanced electron microscopy characterization of nanomaterials for catalysis

    Directory of Open Access Journals (Sweden)

    Dong Su

    2017-04-01

    Full Text Available Transmission electron microscopy (TEM has become one of the most powerful techniques in the fields of material science, inorganic chemistry and nanotechnology. In terms of resolutions, advanced TEM may reach a high spatial resolution of 0.05 nm, a high energy-resolution of 7 meV. In addition, in situ TEM can help researchers to image the process happened within 1 ms. This paper reviews the recent technical progresses of applying advanced TEM characterization on nanomaterials for catalysis. The text is organized based on the perspective of application: for example, size, composition, phase, strain, and morphology. The electron beam induced effect and in situ TEM are also introduced. I hope this review can help the scientists in related fields to take advantage of advanced TEM to their own researches. Keywords: Advanced TEM, Nanomaterials, Catalysts, In situ

  10. Dynamic control of chirality in phosphine ligands for enantioselective catalysis.

    Science.gov (United States)

    Zhao, Depeng; Neubauer, Thomas M; Feringa, Ben L

    2015-03-25

    Chirality plays a fundamental role in biology and chemistry and the precise control of chirality in a catalytic conversion is a key to modern synthesis most prominently seen in the production of pharmaceuticals. In enantioselective metal-based catalysis, access to each product enantiomer is commonly achieved through ligand design with chiral bisphosphines being widely applied as privileged ligands. Switchable phosphine ligands, in which chirality is modulated through an external trigger signal, might offer attractive possibilities to change enantioselectivity in a catalytic process in a non-invasive manner avoiding renewed ligand synthesis. Here we demonstrate that a photoswitchable chiral bisphosphine based on a unidirectional light-driven molecular motor, can be used to invert the stereoselectivity of a palladium-catalysed asymmetric transformation. It is shown that light-induced changes in geometry and helicity of the switchable ligand enable excellent selectivity towards the racemic or individual enantiomers of the product in a Pd-catalysed desymmetrization reaction.

  11. Taking Ockham's razor to enzyme dynamics and catalysis

    Science.gov (United States)

    Glowacki, David R.; Harvey, Jeremy N.; Mulholland, Adrian J.

    2012-03-01

    The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution -- where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.

  12. Quantifying the limits of transition state theory in enzymatic catalysis.

    Science.gov (United States)

    Zinovjev, Kirill; Tuñón, Iñaki

    2017-11-21

    While being one of the most popular reaction rate theories, the applicability of transition state theory to the study of enzymatic reactions has been often challenged. The complex dynamic nature of the protein environment raised the question about the validity of the nonrecrossing hypothesis, a cornerstone in this theory. We present a computational strategy to quantify the error associated to transition state theory from the number of recrossings observed at the equicommittor, which is the best possible dividing surface. Application of a direct multidimensional transition state optimization to the hydride transfer step in human dihydrofolate reductase shows that both the participation of the protein degrees of freedom in the reaction coordinate and the error associated to the nonrecrossing hypothesis are small. Thus, the use of transition state theory, even with simplified reaction coordinates, provides a good theoretical framework for the study of enzymatic catalysis. Copyright © 2017 the Author(s). Published by PNAS.

  13. Enantioselective Polyene Cyclization via Organo-SOMO Catalysis

    Science.gov (United States)

    Rendler, Sebastian; MacMillan, David W. C.

    2010-01-01

    The first organocatalytic enantioselective radical polycyclization has been accomplished using singly occupied molecular orbital (SOMO) catalysis. The presented strategy relies on a selective single-electron oxidation of chiral enamines formed by condensation of polyenals with an imidazolidinone catalyst employing a suitable copper(II) oxidant. The reaction proceeds under mildly acidic conditions at room temperature and shows compatibility with an array of electron-poor as well as electron-rich functional groups. Upon termination by radical arylation, followed by subsequent oxidation and rearomatization, a range of polycyclic aldehydes has been accessed (12 examples, 54-77% yield, 85-93% ee). The enantioselective formation of up to six new carbocycles in a single catalyst-controlled cascade is described. Evidence for a radical-based cascade mechanism is indicated by a series of experimental results. PMID:20334384

  14. Collective synthesis of natural products by means of organocascade catalysis

    Science.gov (United States)

    Jones, Spencer B.; Simmons, Bryon; Mastracchio, Anthony; MacMillan, David W. C.

    2012-01-01

    Organic chemists are now able to synthesize small quantities of almost any known natural product, given sufficient time, resources and effort. However, translation of the academic successes in total synthesis to the large-scale construction of complex natural products and the development of large collections of biologically relevant molecules present significant challenges to synthetic chemists. Here we show that the application of two nature-inspired techniques, namely organocascade catalysis and collective natural product synthesis, can facilitate the preparation of useful quantities of a range of structurally diverse natural products from a common molecular scaffold. The power of this concept has been demonstrated through the expedient, asymmetric total syntheses of six well-known alkaloid natural products: strychnine, aspidospermidine, vincadifformine, akuammicine, kopsanone and kopsinine. PMID:21753848

  15. Cooperative catalysis with block copolymer micelles: a combinatorial approach.

    Science.gov (United States)

    Bukhryakov, Konstantin V; Desyatkin, Victor G; O'Shea, John-Paul; Almahdali, Sarah R; Solovyeva, Vera; Rodionov, Valentin O

    2015-02-09

    A rapid approach to identifying complementary catalytic groups using combinations of functional polymers is presented. Amphiphilic polymers with "clickable" hydrophobic blocks were used to create a library of functional polymers, each bearing a single functionality. The polymers were combined in water, yielding mixed micelles. As the functional groups were colocalized in the hydrophobic microphase, they could act cooperatively, giving rise to new modes of catalysis. The multipolymer "clumps" were screened for catalytic activity, both in the presence and absence of metal ions. A number of catalyst candidates were identified across a wide range of model reaction types. One of the catalytic systems discovered was used to perform a number of preparative-scale syntheses. Our approach provides easy access to a range of enzyme-inspired cooperative catalysts.

  16. Catalysis by Dust Grains in the Solar Nebula

    Science.gov (United States)

    Kress, Monika E.; Tielens, Alexander G. G. M.

    1996-01-01

    In order to determine whether grain-catalyzed reactions played an important role in the chemistry of the solar nebula, we have applied our time-dependent model of methane formation via Fischer-Tropsch catalysis to pressures from 10(exp -5) to 1 bar and temperatures from 450 to 650 K. Under these physical conditions, the reaction 3H2 + CO yields CH4 + H2O is readily catalyzed by an iron or nickel surface, whereas the same reaction is kinetically inhibited in the gas phase. Our model results indicate that under certain nebular conditions, conversion of CO to methane could be extremely efficient in the presence of iron-nickel dust grains over timescales very short compared to the lifetime of the solar nebula.

  17. Value-added Chemicals from Biomass by Heterogeneous Catalysis

    DEFF Research Database (Denmark)

    Voss, Bodil

    been implemented. The subject on chemical production has received less attention. This thesis describes and evaluates the quest for an alternative conversion route, based on a biomass feedstock and employing a heterogeneous catalyst capable of converting the feedstock, to a value-added chemical...... feedstock, having retained one C-C bond originating from the biomass precursor, the aspects of utilising heterogeneous catalysis for its conversion to value added chemicals is investigated. Through a simple analysis of known, but not industrialised catalytic routes, the direct conversion of ethanol...... deactivation of the Cu spinel catalyst may be concluded to be attributed to the formation of high molecular carbonaceous compounds covering the catalytic surface, being catalysed by acidic alumina sites present during and after catalyst activation. This theory explains several phenomena observed...

  18. Gravitational catalysis of merons in Einstein-Yang-Mills theory

    Science.gov (United States)

    Canfora, Fabrizio; Oh, Seung Hun; Salgado-Rebolledo, Patricio

    2017-10-01

    We construct regular configurations of the Einstein-Yang-Mills theory in various dimensions. The gauge field is of meron-type: it is proportional to a pure gauge (with a suitable parameter λ determined by the field equations). The corresponding smooth gauge transformation cannot be deformed continuously to the identity. In the three-dimensional case we consider the inclusion of a Chern-Simons term into the analysis, allowing λ to be different from its usual value of 1 /2 . In four dimensions, the gravitating meron is a smooth Euclidean wormhole interpolating between different vacua of the theory. In five and higher dimensions smooth meron-like configurations can also be constructed by considering warped products of the three-sphere and lower-dimensional Einstein manifolds. In all cases merons (which on flat spaces would be singular) become regular due to the coupling with general relativity. This effect is named "gravitational catalysis of merons".

  19. Catalysis of Transesterification Reactions by a Self-Assembled Nanosystem

    Directory of Open Access Journals (Sweden)

    Davide Zaramella

    2013-01-01

    Full Text Available Histidine-containing peptides self-assemble on the surface of monolayer protected gold nanoparticles to form a catalytic system for transesterification reactions. Self-assembly is a prerequisite for catalysis, since the isolated peptides do not display catalytic activity by themselves. A series of catalytic peptides and substrates are studied in order to understand the structural parameters that are of relevance to the catalytic efficiency of the system. It is shown that the distance between the His-residue and the anionic tail does not affect the catalytic activity. On the other hand, the catalytic His-residue is sensitive to the chemical nature of the flanking amino acid residues. In particular, the presence of polar Ser-residues causes a significant increase in activity. Finally, kinetic studies of a series of substrates reveal that substrates with a hydrophobic component are very suitable for this catalytic system.

  20. Structural Models for Cytochrome P450�Mediated Catalysis

    Directory of Open Access Journals (Sweden)

    David F.V. Lewis

    2003-01-01

    Full Text Available This review focuses on the structural models for cytochrome P450 that are improving our knowledge and understanding of the P450 catalytic cycle, and the way in which substrates bind to the enzyme leading to catalytic conversion and subsequent formation of mono-oxygenated metabolites. Various stages in the P450 reaction cycle have now been investigated using X-ray crystallography and electronic structure calculations, whereas homology modelling of mammalian P450s is currently revealing important aspects of pharmaceutical and other xenobiotic metabolism mediated by P450 involvement. These features are explored in the current review on P450-based catalysis, which emphasises the importance of structural modelling to our understanding of this enzyme's function. In addition, the results of various QSAR analyses on series of chemicals, which are metabolised via P450 enzymes, are presented such that the importance of electronic and other structural factors in explaining variations in rates of metabolism can be appreciated.

  1. Catalysis and Sulfa Drug Resistance in Dihydropteroate Synthase

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Mi-Kyung; Wu, Yinan; Li, Zhenmei; Zhao, Ying; Waddell, M. Brett; Ferreira, Antonio M.; Lee, Richard E.; Bashford, Donald; White, Stephen W. (SJCH)

    2013-04-08

    The sulfonamide antibiotics inhibit dihydropteroate synthase (DHPS), a key enzyme in the folate pathway of bacteria and primitive eukaryotes. However, resistance mutations have severely compromised the usefulness of these drugs. We report structural, computational, and mutagenesis studies on the catalytic and resistance mechanisms of DHPS. By performing the enzyme-catalyzed reaction in crystalline DHPS, we have structurally characterized key intermediates along the reaction pathway. Results support an S{sub N}1 reaction mechanism via formation of a novel cationic pterin intermediate. We also show that two conserved loops generate a substructure during catalysis that creates a specific binding pocket for p-aminobenzoic acid, one of the two DHPS substrates. This substructure, together with the pterin-binding pocket, explains the roles of the conserved active-site residues and reveals how sulfonamide resistance arises.

  2. Metal Carbonyl-Hydrosilane Reactions and Hydrosilation Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Cutler, A. R.

    2001-04-14

    Manganese carbonyl complexes serve as hydrosilation precatalysts for selectively transforming a carbonyl group into a siloxy methylene or a fully reduced methylene group. Substrates of interest include (1) aldehydes, ketones, carboxylic acids, silyl esters, and esters, and (2) their organometallic acyl counterparts. Three relevant catalytic reactions are shown. Two types of manganese precatalysts have been reported: (a) alkyl and acyl complexes (L)(C0){sub 4}MnR [L = CO, PPh{sub 3}; R = COCH{sub 3}, COPh, CH{sub 3}] and (b) halides (CO){sub 5}MnX and [(CO){sub 4}MnX]{sub 2} (X = Br, I). The former promote hydrosilation and deoxygenation catalysis; the latter promote dehydrogenative silation of alcohols and carboxylic acids as well as hydrosilation and deoxygenation of some metallocarboxylic acid derivatives. In every case studied, these Mn precatalysts are far more reactive or selective than traditional Rh(I) precatalysts.

  3. Cooperative catalysis with block copolymer micelles: A combinatorial approach

    KAUST Repository

    Bukhryakov, Konstantin V.

    2015-02-09

    A rapid approach to identifying complementary catalytic groups using combinations of functional polymers is presented. Amphiphilic polymers with "clickable" hydrophobic blocks were used to create a library of functional polymers, each bearing a single functionality. The polymers were combined in water, yielding mixed micelles. As the functional groups were colocalized in the hydrophobic microphase, they could act cooperatively, giving rise to new modes of catalysis. The multipolymer "clumps" were screened for catalytic activity, both in the presence and absence of metal ions. A number of catalyst candidates were identified across a wide range of model reaction types. One of the catalytic systems discovered was used to perform a number of preparative-scale syntheses. Our approach provides easy access to a range of enzyme-inspired cooperative catalysts.

  4. Vanadium-modified molecular sieves: preparation, characterization and catalysis

    Directory of Open Access Journals (Sweden)

    Ângela A. Teixeira-Neto

    2009-01-01

    Full Text Available Vanadium-containing molecular sieves are redox catalysts and are good candidates as substitutes for oxide-supported V2O5 in a number of reactions. These materials have the advantage of presenting better dispersion of vanadium species, as well as shape-selective properties and controllable acidities. They may be prepared by one-pot synthesis or by post-synthesis methods and a number of techniques such as diffuse reflectance UV-visible spectroscopy, 51V nuclear magnetic resonance and electron paramagnetic resonance, to name but a few, have been used to characterize these materials. In this review, methods of preparation of vanadium-modified molecular sieves, their characterization and applications in catalysis are discussed.

  5. Contrast and Synergy between Electrocatalysis and Heterogeneous Catalysis

    Directory of Open Access Journals (Sweden)

    Andrzej Wieckowski

    2011-01-01

    Full Text Available The advances in spectroscopy and theory that have occurred over the past two decades begin to provide detailed in situ resolution of the molecular transformations that occur at both gas/metal as well as aqueous/metal interfaces. These advances begin to allow for a more direct comparison of heterogeneous catalysis and electrocatalysis. Such comparisons become important, as many of the current energy conversion strategies involve catalytic and electrocatalytic processes that occur at fluid/solid interfaces and display very similar characteristics. Herein, we compare and contrast a few different catalytic and electrocatalytic systems to elucidate the principles that cross-cut both areas and establish characteristic differences between the two with the hope of advancing both areas.

  6. Advances in Nucleophilic Phosphine Catalysis of Alkenes, Allenes, Alkynes, and MBHADs

    Science.gov (United States)

    Fan, Yi Chiao

    2014-01-01

    In nucleophilic phosphine catalysis, tertiary phosphines undergo conjugate additions to activated carbon–carbon multiple bonds to form β-phosphonium enolates, β-phosphonium dienolates, β-phosphonium enoates, and vinyl phosphonium ylides as intermediates. When these reactive zwitterionic species react with nucleophiles and electrophiles, they may generate carbo- and heterocycles with multifarious molecular architectures. This Article describes the reactivities of these phosphonium zwitterions, the applications of phosphine catalysis in the syntheses of biologically active compounds and natural products, and recent developments in the enantioselective phosphine catalysis. PMID:24196409

  7. Activation of arene-heteroatom bonds by photoredox catalysis with visible light

    OpenAIRE

    Majek, Michal

    2016-01-01

    Aim of this thesis is the use of photo-redox catalysis for the activation of Ar-X bonds, and development of new synthetic methods based on this approach. In the beginning, the evolution that led to the development of modern photo-redox catalysis is discussed. Explanation of basic theories and definitions, which are encountered in the field of photo-redox catalysis is given. This is followed by a short overview of common photocatalysts, and the most important photocatalytic reactions discov...

  8. Effect of variable surface catalysis on heating near the stagnation point of a blunt body

    Science.gov (United States)

    Stewart, D. A.; Leiser, D. B.; Kolodziej, P.

    1985-01-01

    This paper describes arc-jet data obtained on the performance of glass coated thermal protection systems in a convectively heated environment. These data confirm earlier flight and arc-jet data that show an increased surface catalysis with salt contamination and a decreased surface catalysis near the softening point temperature of the glass. In addition, surface temperature distributions along sphere-cones with abruptly changing surface catalysis were measured near the stagnation point and compared well with computations using a reacting boundary layer code.

  9. Predicting template-based catalysis rates in a simple catalytic reaction model.

    Science.gov (United States)

    Hordijk, Wim; Steel, Mike

    2012-02-21

    We show that in a particular model of catalytic reaction systems, known as the binary polymer model, there is a mathematical concordance between two versions of the model: (1) random catalysis and (2) template-based catalysis. In particular, we derive an analytical calculation that allows us to accurately predict the (observed) required level of catalysis in one version of the model from that in the other version, for a given probability of having self-sustaining autocatalytic sets exist in instances of both model versions. This provides a tractable connection between two models that have been investigated in theoretical origin-of-life studies. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Catalysis Science Initiative: Catalyst Design by Discovery Informatics

    Energy Technology Data Exchange (ETDEWEB)

    Delgass, William Nicholas [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Abu-Omar, Mahdi [Purdue Univ., West Lafayette, IN (United States) Department of Chemistry; Caruthers, James [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Ribeiro, Fabio [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Thomson, Kendall [Purdue Univ., West Lafayette, IN (United States). Chemical Engineering; Schneider, William [Univ. of Notre Dame, IN (United States)

    2016-07-08

    Catalysts selectively enhance the rates of chemical reactions toward desired products. Such reactions provide great benefit to society in major commercial sectors such as energy production, protecting the environment, and polymer products and thereby contribute heavily to the country’s gross national product. Our premise is that the level of fundamental understanding of catalytic events at the atomic and molecular scale has reached the point that more predictive methods can be developed to shorten the cycle time to new processes. The field of catalysis can be divided into two regimes: heterogeneous and homogeneous. For the heterogeneous catalysis regime, we have used the water-gas shift (WGS) reaction (CO + H2O + CO2 + H2O) over supported metals as a test bed. Detailed analysis and strong coupling of theory with experiment have led to the following conclusions: • The sequence of elementary steps goes through a COOH intermediate • The CO binding energy is a strong function of coverage of CO adsorbed on the surface in many systems • In the case of Au catalysts, the CO adsorption is generally too weak on surface with close atomic packing, but the enhanced binding at corner atoms (which are missing bonding partners) of cubo-octahedral nanoparticles increases the energy to a near optimal value and produces very active catalysts. • Reaction on the metal alone cannot account for the experimental results. The reaction is dual functional with water activation occurring at the metal-support interface. It is clear from our work that the theory component is essential, not only for prediction of new systems, but also for reconciling data and testing hypotheses regarding potential descriptors. Particularly important is the finding that the interface between nano-sized metal particles and the oxides that are used to support them represent a new state of matter in the sense that the interfacial bonding perturbs the chemical state of both metals atoms and the support

  11. Core–shell nanoparticles: synthesis and applications in catalysis and electrocatalysis

    Science.gov (United States)

    Core–shell nanoparticles (CSNs) are a class of nanostructured materials that have recently received increased attention owing to their interesting properties and broad range of applications in catalysis, biology, materials chemistry and sensors. By rationally tuning the cores as ...

  12. A Course in Heterogeneous Catalysis: Principles, Practice, and Modern Experimental Techniques.

    Science.gov (United States)

    Wolf, Eduardo E.

    1981-01-01

    Outlines a multidisciplinary course which comprises fundamental, practical, and experimental aspects of heterogeneous catalysis. The course structure is a combination of lectures and demonstrations dealing with the use of spectroscopic techniques for surface analysis. (SK)

  13. Support for U.S. Participants at the 16th International Congress on Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Wachs, Israel E. [Lehigh Univ., Bethlehem, PA (United States)

    2017-01-17

    The enclosed report highlights the travel grant awarded to offset the cost of foreign travel of several faculty and students to attend the 16th International Congress on Catalysis (ICC) held in Beijing, China, July 3-8, 2016.

  14. Lewis acidic zn(ii) schiff base complexes in homogeneous catalysis

    OpenAIRE

    Anselmo, Daniele

    2013-01-01

    The work described in this thesis shows studies towards new applications of Schiff base complexes in homogeneous catalysis . Specifically, we investigated “salen” ligands (including N2S2 chelating systems) and also examined other aspects that are generally considered important in the context of increasing the sustainability of chemical processes. Studies on the use of these Lewis acidic compounds in the catalysis of the fixation of carbon dioxide, multicomponent reactions for the synthesis of...

  15. Liquid phase oxidation via heterogeneous catalysis organic synthesis and industrial applications

    CERN Document Server

    Clerici, Mario G

    2013-01-01

    Sets the stage for environmentally friendly industrial organic syntheses From basic principles to new and emerging industrial applications, this book offers comprehensive coverage of heterogeneous liquid-phase selective oxidation catalysis. It fully examines the synthesis, characterization, and application of catalytic materials for environmentally friendly organic syntheses. Readers will find coverage of all the important classes of catalysts, with an emphasis on their stability and reusability. Liquid Phase Oxidation via Heterogeneous Catalysis features contributions from an internation

  16. Combination of sunlight irradiated oxidative processes for landfill leachate: heterogeneous catalysis (TiO2 versus homogeneous catalysis (H2O2

    Directory of Open Access Journals (Sweden)

    Oswaldo Luiz Cobra Guimarães

    2013-04-01

    Full Text Available The objective of this work was to study the treatment of landfill leachate liquid in nature, after the use of a combination of advanced oxidation processes. More specifically, it compared heterogeneous catalysis with TiO2 to homogeneous catalysis with H2O2, both under photo-irradiated sunlight. The liquid used for the study was the leachate from the landfill of the city of Cachoeira Paulista, São Paulo State, Brazil. The experiments were conducted in a semi-batch reactor open to the absorption of solar UV radiation, with 120 min reaction time. The factors and their respective levels (-1, 0 and 1 were distributed in a experimental design 24-1 with duplicate and triplicate in the central point, resulting in an array with 19 treatment trials. The studied factors in comparing the two catalytic processes were: liquid leachate dilution, TiO2 concentration on the reactor plate, the H2O2 amount and pH level. The leachate had low photo-catalytic degradability, with NOPC reductions ranging from 1% to a maximum of 24.9%. When considering each factor alone, neither homogeneous catalysis with H2O2, nor heterogeneous catalysis with TiO2, could degrade the percolated liquid without significant reductions (5% level in total NOPC. On the other hand, the combined use of homogenous catalysis with H2O2 and heterogeneous catalysis H2O2 resulted in the greatest reductions in NOPC. The optimum condition for the NOPC reduction was obtained at pH 7, dilution of percolated:water at 1:1 (v v-1 rate; excess of 12.5% H2O2 and coating plate reactor with 0.025 g cm-2 TiO2.

  17. Combination of sunlight irradiated oxidative processes for landfill leachate: heterogeneous catalysis (TiO2) versus homogeneous catalysis (H2O2)

    OpenAIRE

    Oswaldo Luiz Cobra Guimarães; Hélcio José Izário Filho; Alessandro Sampaio Cavalcanti; João Victor Serafim Pancotto; Marco Aurélio Kondracki de Alcântara; Mariana Pereira Demarchi Costa

    2013-01-01

    The objective of this work was to study the treatment of landfill leachate liquid in nature, after the use of a combination of advanced oxidation processes. More specifically, it compared heterogeneous catalysis with TiO2 to homogeneous catalysis with H2O2, both under photo-irradiated sunlight. The liquid used for the study was the leachate from the landfill of the city of Cachoeira Paulista, São Paulo State, Brazil. The experiments were conducted in a semi-batch reactor open to the absorptio...

  18. Effect of Water Vapor on Toluene Removal in Catalysis-DBD Plasma Reactors

    Science.gov (United States)

    Wang, Jingting; Cao, Xu; Zhang, Renxi; Gong, Ting; Hou, Huiqi; Chen, Shanping; Zhang, Ruina

    2016-04-01

    The experiment was carried out in a cylindrical dielectric barrier discharge (DBD) reactor assisted with a catalyst to decompose toluene under different humidity. In order to explore the synergistic effect on removing toluene in the catalysis-DBD reactor, this paper investigated the decomposition efficiency and the energy consumption in the catalysis-DBD and the non-catalyst DBD reactors under different humidity. The results showed that the catalysis-DBD reactor had a better performance than the non-catalysis one at the humidity ratio of 0.4%, and the removal efficiency of toluene could reach 88.6% in the catalysis-DBD reactor, while it was only 59.9% in the non-catalytic reactor. However, there was no significant difference in the removal efficiency of toluene between the two reactors when the humidities were 1.2% and 2.4%. Additionally, the degradation products were also analyzed in order to gain a better understanding of the mechanism of decomposing toluene in a catalysis-DBD reactor. supported by the Key Project which is sponsored by the Science and Technology Commission of Shanghai Municipality (No. 13231201903), the Key Programs for Science and Technology Development sponsored by the Science and Technology Commission of Shanghai Municipality (Nos. 13231201901 and 14DZ1208401), and the Key Project sponsored by the State-owned Assets Supervision and Administration Commission of Shanghai, China (No. 2013019)

  19. Mercury and Selenium in Muscle and Target Organs of Scalloped Hammerhead Sharks Sphyrna lewini of the SE Gulf of California: Dietary Intake, Molar Ratios, Loads, and Human Health Risks.

    Science.gov (United States)

    Bergés-Tiznado, Magdalena E; Márquez-Farías, Fernando; Lara-Mendoza, Raúl E; Torres-Rojas, Yassir E; Galván-Magaña, Felipe; Bojórquez-Leyva, Humberto; Páez-Osuna, Federico

    2015-11-01

    Selenium and mercury were evaluated in muscle, liver, kidney, brain, and the stomach contents of juvenile scalloped hammerhead shark Sphyrna lewini. Se:Hg molar ratios were calculated. The average Hg levels in muscle ranged from 0.12 to 1.17 μg/g (wet weight); Hg was 1. Correlations were found for Hg in muscle with size, age, and weight, and also for Hg in liver with size, age, and weight. Hg in muscle was significantly positive correlated to Hg in brain as well as Hg in liver was correlated to Hg in kidney. The highest Hg in preys was for carangid fishes; scombrid and carangid fishes contributed with the highest Se levels. Results suggest that more than 98 % of the total Hg and 62 % of Se end up in muscle and might be affected by factors, such as geographical area, age, size, and feeding habits. The muscle of S. lewini should be consumed by people cautiously so as not to exceed the recommended intake per week.

  20. Supercritical fluid technology for enhanced drug delivery and heterogeneous catalysis

    Science.gov (United States)

    Pathak, Pankaj

    In recent years there has been great interest in the properties of supercritical fluids (SCFs) and applications of supercritical fluid technology in chemistry, material sciences and many other areas. In our laboratory, we have applied supercritical fluid namely CO2, as a medium for pharmaceutical processing and also for heterogeneous catalysis. The method used for pharmaceutical processing is based on the Rapid Expansion of supercritical solutions into a liquid SOLVent (RESOLV). We have used this method for the preparation of nanoparticles from various anti-inflammatory (Ibuprofen and Naproxen), anti-fungal (Amphotericin B) and anti-cancer (Paclitaxel) drugs. The anticancer drug nanoparticle formulations were further used for in vitro biological evaluation. In this dissertation, results from the preparation, characterization and biological evaluation of nanoscale drug particles are reported. The effect of experimental conditions on the properties of the nanoparticles prepared via our RESOLV method is discussed. In addition we have used supercritical CO2 as a medium for photoreduction of CO2 using dispersed TiO 2 or metal coated-TiO2 nanoparticles encapsulated in nanoscale cavities of perfluorinated ionomer membranes. These catalytic films are also stable chemically and photochemically, reusable in repeated reactions. The results from the characterization of the nanoparticles and the use of films using different catalysts are presented and discussed.

  1. Integration of chemical catalysis with extractive fermentation to produce fuels.

    Science.gov (United States)

    Anbarasan, Pazhamalai; Baer, Zachary C; Sreekumar, Sanil; Gross, Elad; Binder, Joseph B; Blanch, Harvey W; Clark, Douglas S; Toste, F Dean

    2012-11-08

    Nearly one hundred years ago, the fermentative production of acetone by Clostridium acetobutylicum provided a crucial alternative source of this solvent for manufacture of the explosive cordite. Today there is a resurgence of interest in solventogenic Clostridium species to produce n-butanol and ethanol for use as renewable alternative transportation fuels. Acetone, a product of acetone-n-butanol-ethanol (ABE) fermentation, harbours a nucleophilic α-carbon, which is amenable to C-C bond formation with the electrophilic alcohols produced in ABE fermentation. This functionality can be used to form higher-molecular-mass hydrocarbons similar to those found in current jet and diesel fuels. Here we describe the integration of biological and chemocatalytic routes to convert ABE fermentation products efficiently into ketones by a palladium-catalysed alkylation. Tuning of the reaction conditions permits the production of either petrol or jet and diesel precursors. Glyceryl tributyrate was used for the in situ selective extraction of both acetone and alcohols to enable the simple integration of ABE fermentation and chemical catalysis, while reducing the energy demand of the overall process. This process provides a means to selectively produce petrol, jet and diesel blend stocks from lignocellulosic and cane sugars at yields near their theoretical maxima.

  2. Theoretical Heterogeneous Catalysis: Scaling Relationships and Computational Catalyst Design.

    Science.gov (United States)

    Greeley, Jeffrey

    2016-06-07

    Scaling relationships are theoretical constructs that relate the binding energies of a wide variety of catalytic intermediates across a range of catalyst surfaces. Such relationships are ultimately derived from bond order conservation principles that were first introduced several decades ago. Through the growing power of computational surface science and catalysis, these concepts and their applications have recently begun to have a major impact in studies of catalytic reactivity and heterogeneous catalyst design. In this review, the detailed theory behind scaling relationships is discussed, and the existence of these relationships for catalytic materials ranging from pure metal to oxide surfaces, for numerous classes of molecules, and for a variety of catalytic surface structures is described. The use of the relationships to understand and elucidate reactivity trends across wide classes of catalytic surfaces and, in some cases, to predict optimal catalysts for certain chemical reactions, is explored. Finally, the observation that, in spite of the tremendous power of scaling relationships, their very existence places limits on the maximum rates that may be obtained for the catalyst classes in question is discussed, and promising strategies are explored to overcome these limitations to usher in a new era of theory-driven catalyst design.

  3. Towards Rational Design of Nanoparticle Catalysis in Ionic Liquids

    Directory of Open Access Journals (Sweden)

    Ning Yan

    2013-06-01

    Full Text Available This feature article introduces the strategies on the design of highly efficient nanoparticle (NP catalytic systems in ionic liquids (ILs. The employment of functional ILs as the media for NP preparation and catalysis could prove advantageous in terms of enhancing both NP stability and catalytic activity. Hydroxyl group functionalized ILs, in particular, exhibited a remarkable promotion effect on a variety of reactions catalyzed by NPs, such as hydrogenation over Rh NPs, hydrodehalogenation over Pt NPs and Suzuki reaction over Pd NPs. In some cases, tailor-made stabilizer is used in addition to keep the NPs sufficiently stable. For example, a carboxylic group modified polyvinylpyrrolidone endows NPs three-fold stabilization, including steric, electrostatic and ligand stabilizations, which leads to excellent stability of the NPs. The catalytic activities of these NPs, on the other hand, are not compromised, as each of these stabilizations is not too strong. Following that, the article describes our recent work on the rational design of bimetallic NPs in ILs and the development of multifunctional systems involving NPs for a tandem reaction sequence that convert lignin-derived phenolic compounds into fuels.

  4. Ferroelectrics: A pathway to switchable surface chemistry and catalysis

    Science.gov (United States)

    Kakekhani, Arvin; Ismail-Beigi, Sohrab; Altman, Eric I.

    2016-08-01

    It has been known for more than six decades that ferroelectricity can affect a material's surface physics and chemistry thereby potentially enhancing its catalytic properties. Ferroelectrics are a class of materials with a switchable electrical polarization that can affect surface stoichiometry and electronic structure and thus adsorption energies and modes; e.g., molecular versus dissociative. Therefore, ferroelectrics may be utilized to achieve switchable surface chemistry whereby surface properties are not fixed but can be dynamically controlled by, for example, applying an external electric field or modulating the temperature. Several important examples of applications of ferroelectric and polar materials in photocatalysis and heterogeneous catalysis are discussed. In photocatalysis, the polarization direction can control band bending at water/ferroelectric and ferroelectric/semiconductor interfaces, thereby facilitating charge separation and transfer to the electrolyte and enhancing photocatalytic activity. For gas-surface interactions, available results suggest that using ferroelectrics to support catalytically active transition metals and oxides is another way to enhance catalytic activity. Finally, the possibility of incorporating ferroelectric switching into the catalytic cycle itself is described. In this scenario, a dynamic collaboration of two polarization states can be used to drive reactions that have been historically challenging to achieve on surfaces with fixed chemical properties (e.g., direct NOx decomposition and the selective partial oxidation of methane). These predictions show that dynamic modulation of the polarization can help overcome some of the fundamental limitations on catalytic activity imposed by the Sabatier principle.

  5. Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

    Science.gov (United States)

    Luk, Louis Y. P.; Javier Ruiz-Pernía, J.; Dawson, William M.; Roca, Maite; Loveridge, E. Joel; Glowacki, David R.; Harvey, Jeremy N.; Mulholland, Adrian J.; Tuñón, Iñaki; Moliner, Vicent; Allemann, Rudolf K.

    2013-01-01

    Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy (15N, 13C, 2H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for “promoting motions” in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate. PMID:24065822

  6. The Applications of Morphology Controlled ZnO in Catalysis

    Directory of Open Access Journals (Sweden)

    Yuhai Sun

    2016-11-01

    Full Text Available Zinc oxide (ZnO, with the unique chemical and physical properties of high chemical stability, broad radiation absorption range, high electrochemical coupling coefficient, and high photo-stability, is an attractive multifunctional material which has promoted great interest in many fields. What is more, its properties can be tuned by controllable synthesized morphologies. Therefore, after the success of the abundant morphology controllable synthesis, both the morphology-dependent ZnO properties and their related applications have been extensively investigated. This review concentrates on the properties of morphology-dependent ZnO and their applications in catalysis, mainly involved reactions on green energy and environmental issues, such as CO2 hydrogenation to fuels, methanol steam reforming to generate H2, bio-diesel production, pollutant photo-degradation, etc. The impressive catalytic properties of ZnO are associated with morphology tuned specific microstructures, defects or abilities of electron transportation, etc. The main morphology-dependent promotion mechanisms are discussed and summarized.

  7. Preparative semiconductor photoredox catalysis: An emerging theme in organic synthesis.

    Science.gov (United States)

    Manley, David W; Walton, John C

    2015-01-01

    Heterogeneous semiconductor photoredox catalysis (SCPC), particularly with TiO2, is evolving to provide radically new synthetic applications. In this review we describe how photoactivated SCPCs can either (i) interact with a precursor that donates an electron to the semiconductor thus generating a radical cation; or (ii) interact with an acceptor precursor that picks up an electron with production of a radical anion. The radical cations of appropriate donors convert to neutral radicals usually by loss of a proton. The most efficient donors for synthetic purposes contain adjacent functional groups such that the neutral radicals are resonance stabilized. Thus, ET from allylic alkenes and enol ethers generated allyl type radicals that reacted with 1,2-diazine or imine co-reactants to yield functionalized hydrazones or benzylanilines. SCPC with tertiary amines enabled electron-deficient alkenes to be alkylated and furoquinolinones to be accessed. Primary amines on their own led to self-reactions involving C-N coupling and, with terminal diamines, cyclic amines were produced. Carboxylic acids were particularly fruitful affording C-centered radicals that alkylated alkenes and took part in tandem addition cyclizations producing chromenopyrroles; decarboxylative homo-dimerizations were also observed. Acceptors initially yielding radical anions included nitroaromatics and aromatic iodides. The latter led to hydrodehalogenations and cyclizations with suitable precursors. Reductive SCPC also enabled electron-deficient alkenes and aromatic aldehydes to be hydrogenated without the need for hydrogen gas.

  8. State of Supported Nanoparticle Ni during Catalysis in Aqueous Media

    Energy Technology Data Exchange (ETDEWEB)

    Chase, Zizwe; Vjunov, Aleksei; Fulton, John; Camaioni, Donald; Balasubramanian, Mahalingam; Lercher, Johannes

    2015-11-09

    The state of Ni supported on HZSM-5 zeolite, silica, and sulfonated carbon was studied during aqueous-phase catalysis of phenol hydrodeoxygenation using in situ extended X-ray absorption fine structure spectroscopy. On sulfonated carbon and HZSM-5 supports, NiO and Ni(OH)(2) were readily reduced to Ni-0 under reaction conditions (approximate to 35bar H-2 in aqueous phenol solutions containing up to 0.5wt.% phosphoric acid at 473K). In contrast, Ni supported on SiO2 was not stable in a fully reduced Ni-0 state. Water enables the formation of Ni-II phyllosilicate, which is more stable, that is, difficult to reduce, than either -Ni(OH)(2) or NiO. Leaching of Ni from the supports was not observed over a broad range of reaction conditions. Ni-0 particles on HZSM-5 were stable even in presence of 15wt.% acetic acid at 473K and 35bar H-2.

  9. Controlling energy flow in multimetallic nanostructures for plasmonic catalysis

    Science.gov (United States)

    Aslam, Umar; Chavez, Steven; Linic, Suljo

    2017-10-01

    It has been shown that photoexcitation of plasmonic metal nanoparticles (Ag, Au and Cu) can induce direct photochemical reactions. However, the widespread application of this technology in catalysis has been limited by the relatively poor chemical reactivity of noble metal surfaces. Despite efforts to combine plasmonic and catalytic metals, the physical mechanisms that govern energy transfer from plasmonic metals to catalytic metals remain unclear. Here we show that hybrid core-shell nanostructures in which a core plasmonic metal harvests visible-light photons can selectively channel that energy into catalytically active centres on the nanostructure shell. To accomplish this, we developed a synthetic protocol to deposit a few monolayers of Pt onto Ag nanocubes. This model system allows us to conclusively separate the optical and catalytic functions of the hybrid nanomaterial and determine that the flow of energy is strongly biased towards the excitation of energetic charge carriers in the Pt shell. We demonstrate the utility of these nanostructures for photocatalytic chemical reactions in the preferential oxidation of CO in excess H2. Our data demonstrate that the reaction occurs exclusively on the Pt surface.

  10. Anatomy of the magnetic catalysis by renormalization-group method

    Directory of Open Access Journals (Sweden)

    Koichi Hattori

    2017-12-01

    Full Text Available We first examine the scaling argument for a renormalization-group (RG analysis applied to a system subject to the dimensional reduction in strong magnetic fields, and discuss the fact that a four-Fermi operator of the low-energy excitations is marginal irrespective of the strength of the coupling constant in underlying theories. We then construct a scale-dependent effective four-Fermi interaction as a result of screened photon exchanges at weak coupling, and establish the RG method appropriately including the screening effect, in which the RG evolution from ultraviolet to infrared scales is separated into two stages by the screening-mass scale. Based on a precise agreement between the dynamical mass gaps obtained from the solutions of the RG and Schwinger–Dyson equations, we discuss an equivalence between these two approaches. Focusing on QED and Nambu–Jona-Lasinio model, we clarify how the properties of the interactions manifest themselves in the mass gap, and point out an importance of respecting the intrinsic energy-scale dependences in underlying theories for the determination of the mass gap. These studies are expected to be useful for a diagnosis of the magnetic catalysis in QCD.

  11. Interpreting single turnover catalysis measurements with constrained mean dwell times.

    Science.gov (United States)

    Ochoa, Maicol A; Zhou, Xiaochun; Chen, Peng; Loring, Roger F

    2011-11-07

    Observation of a chemical transformation at the single-molecule level yields a detailed view of kinetic pathways contributing to the averaged results obtained in a bulk measurement. Studies of a fluorogenic reaction catalyzed by gold nanoparticles have revealed heterogeneous reaction dynamics for these catalysts. Measurements on single nanoparticles yield binary trajectories with stochastic transitions between a dark state in which no product molecules are adsorbed and a fluorescent state in which one product molecule is present. The mean dwell time in either state gives information corresponding to a bulk measurement. Quantifying fluctuations from mean kinetics requires identifying properties of the fluorescence trajectory that are selective in emphasizing certain dynamic processes according to their time scales. We propose the use of constrained mean dwell times, defined as the mean dwell time in a state with the constraint that the immediately preceding dwell time in the other state is, for example, less than a variable time. Calculations of constrained mean dwell times for a kinetic model with dynamic disorder demonstrate that these quantities reveal correlations among dynamic fluctuations at different active sites on a multisite catalyst. Constrained mean dwell times are determined from measurements of single nanoparticle catalysis. The results indicate that dynamical fluctuations at different active sites are correlated, and that especially rapid reaction events produce particularly slowly desorbing product molecules.

  12. Redox, haem and CO in enzymatic catalysis and regulation

    Science.gov (United States)

    Ragsdale, Stephen W.; Yi, Li; Bender, Güneş; Gupta, Nirupama; Kung, Yan; Yan, Lifen; Stich, Troy A.; Doukov, Tzanko; Leichert, Lars; Jenkins, Paul M.; Bianchetti, Christopher M.; George, Simon J.; Cramer, Stephen P.; Britt, R. David; Jakob, Ursula; Martens, Jeffrey R.; Phillips, George N.; Drennan, Catherine L.

    2013-01-01

    The present paper describes general principles of redox catalysis and redox regulation in two diverse systems. The first is microbial metabolism of CO by the Wood–Ljungdahl pathway, which involves the conversion of CO or H2/CO2 into acetyl-CoA, which then serves as a source of ATP and cell carbon. The focus is on two enzymes that make and utilize CO, CODH (carbon monoxide dehydrogenase) and ACS (acetyl-CoA synthase). In this pathway, CODH converts CO2 into CO and ACS generates acetyl-CoA in a reaction involving Ni·CO, methyl-Ni and acetyl-Ni as catalytic intermediates. A 70 Å (1 Å = 0.1 nm) channel guides CO, generated at the active site of CODH, to a CO ‘cage’ near the ACS active site to sequester this reactive species and assure its rapid availability to participate in a kinetically coupled reaction with an unstable Ni(I) state that was recently trapped by photolytic, rapid kinetic and spectroscopic studies. The present paper also describes studies of two haem-regulated systems that involve a principle of metabolic regulation interlinking redox, haem and CO. Recent studies with HO2 (haem oxygenase-2), a K+ ion channel (the BK channel) and a nuclear receptor (Rev-Erb) demonstrate that this mode of regulation involves a thiol–disulfide redox switch that regulates haem binding and that gas signalling molecules (CO and NO) modulate the effect of haem. PMID:22616859

  13. General base-general acid catalysis by terpenoid cyclases.

    Science.gov (United States)

    Pemberton, Travis A; Christianson, David W

    2016-07-01

    Terpenoid cyclases catalyze the most complex reactions in biology, in that more than half of the substrate carbon atoms often undergo changes in bonding during the course of a multistep cyclization cascade that proceeds through multiple carbocation intermediates. Many cyclization mechanisms require stereospecific deprotonation and reprotonation steps, and most cyclization cascades are terminated by deprotonation to yield an olefin product. The first bacterial terpenoid cyclase to yield a crystal structure was pentalenene synthase from Streptomyces exfoliatus UC5319. This cyclase generates the hydrocarbon precursor of the pentalenolactone family of antibiotics. The structures of pentalenene synthase and other terpenoid cyclases reveal predominantly nonpolar active sites typically lacking amino acid side chains capable of serving general base-general acid functions. What chemical species, then, enables the Brønsted acid-base chemistry required in the catalytic mechanisms of these enzymes? The most likely candidate for such general base-general acid chemistry is the co-product inorganic pyrophosphate. Here, we briefly review biological and nonbiological systems in which phosphate and its derivatives serve general base and general acid functions in catalysis. These examples highlight the fact that the Brønsted acid-base activities of phosphate derivatives are comparable to the Brønsted acid-base activities of amino acid side chains.

  14. Anion-π Catalysis of Diels-Alder Reactions.

    Science.gov (United States)

    Liu, Le; Cotelle, Yoann; Bornhof, Anna-Bea; Besnard, Céline; Sakai, Naomi; Matile, Stefan

    2017-10-09

    Among concerted cycloadditions, the Diels-Alder reaction is the grand old classic, which is usually achieved with acid catalysis. In this report, hydroxypyrones, oxa-, and thiazolones are explored because they provide access to anionic dienes. Their [4+2] cycloaddition with cyclic and acyclic dienophiles, such as maleimides and fumarates, affords bicyclic products with four new stereogenic centers. Bifunctional anion-π catalysts composed of amine bases next to the π surface of naphthalenediimides (NDIs) are shown to selectively stabilize the "open", fully accessible anionic exo transition state on the π-acidic aromatic surface. Our results also include reactivities that are hard to access with conventional organocatalysts, such as the exo-specific and highly enantioselective Diels-Alder reaction of thiazolones and maleimides with complete suppression of the otherwise dominant Michael addition. With increasing π acidity of the anion-π catalysts, the rates, chemo-, diastereo-, and enantioselectivities increase consistently. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Electrophilic catalysis in triosephosphate isomerase: The role of histidine-95

    Energy Technology Data Exchange (ETDEWEB)

    Komives, E.A.; Chang, L.C.; Knowles, J.R. (Harvard Univ., Cambridge, MA (USA)); Lolis, E.; Tilton, R.F.; Petsko, G.A. (Massachusetts Inst. of Tech., Cambridge, MA (USA))

    1991-03-26

    Electrophilic catalysis by histidine-95 in triosephosphate isomerase has been probed by using Fourier transform infrared spectroscopy and X-ray crystallography. The carbonyl stretching frequency of dihydroxyacetone phosphate bound to the wild-type enzyme is known to be lower than that of dihydroxyacetone phosphate free in solution, and this decrease in stretching frequency has been ascribed to an enzymic electrophile that polarizes the substrate carbonyl group toward the transition state for the enolization. Infrared spectra of substrate bound to two site-directed mutants of yeast triosephosphate isomerase in which histidine-95 has been changed to glutamine or to asparagine show unperturbed carbonyl stretching frequencies between 1,732 and 1,742 cm{sup {minus}1}. The lack of carbonyl polarization when histidine-95 is removed suggests that histidine-95 is indeed the catalytic electrophile, at least for dihydroxyacetone phosphate. Kinetic studies of the glutamine mutant (H95Q) have shown that the enzyme follows a subtly different mechanism of proton transfers involving only a single acid-base catalytic group. These findings suggest an additional role for histidine-95 as a general acid-base catalyst in the wild-type enzyme. The X-ray crystal structure of the H95Q mutant with an intermediate analogue, phosphoglycolohydroxamate, bound at the active site has been solved to 2.8-{angstrom} resolution, and this structure clearly implicates glutamate-165, the catalytic base in the wild-type isomerase, as the sole acid-base catalyst for the mutant enzyme.

  16. Recent advances in heterogeneous selective oxidation catalysis for sustainable chemistry.

    Science.gov (United States)

    Guo, Zhen; Liu, Bin; Zhang, Qinghong; Deng, Weiping; Wang, Ye; Yang, Yanhui

    2014-05-21

    Oxidation catalysis not only plays a crucial role in the current chemical industry for the production of key intermediates such as alcohols, epoxides, aldehydes, ketones and organic acids, but also will contribute to the establishment of novel green and sustainable chemical processes. This review is devoted to dealing with selective oxidation reactions, which are important from the viewpoint of green and sustainable chemistry and still remain challenging. Actually, some well-known highly challenging chemical reactions involve selective oxidation reactions, such as the selective oxidation of methane by oxygen. On the other hand some important oxidation reactions, such as the aerobic oxidation of alcohols in the liquid phase and the preferential oxidation of carbon monoxide in hydrogen, have attracted much attention in recent years because of their high significance in green or energy chemistry. This article summarizes recent advances in the development of new catalytic materials or novel catalytic systems for these challenging oxidation reactions. A deep scientific understanding of the mechanisms, active species and active structures for these systems are also discussed. Furthermore, connections among these distinct catalytic oxidation systems are highlighted, to gain insight for the breakthrough in rational design of efficient catalytic systems for challenging oxidation reactions.

  17. Anatomy of the magnetic catalysis by renormalization-group method

    Science.gov (United States)

    Hattori, Koichi; Itakura, Kazunori; Ozaki, Sho

    2017-12-01

    We first examine the scaling argument for a renormalization-group (RG) analysis applied to a system subject to the dimensional reduction in strong magnetic fields, and discuss the fact that a four-Fermi operator of the low-energy excitations is marginal irrespective of the strength of the coupling constant in underlying theories. We then construct a scale-dependent effective four-Fermi interaction as a result of screened photon exchanges at weak coupling, and establish the RG method appropriately including the screening effect, in which the RG evolution from ultraviolet to infrared scales is separated into two stages by the screening-mass scale. Based on a precise agreement between the dynamical mass gaps obtained from the solutions of the RG and Schwinger-Dyson equations, we discuss an equivalence between these two approaches. Focusing on QED and Nambu-Jona-Lasinio model, we clarify how the properties of the interactions manifest themselves in the mass gap, and point out an importance of respecting the intrinsic energy-scale dependences in underlying theories for the determination of the mass gap. These studies are expected to be useful for a diagnosis of the magnetic catalysis in QCD.

  18. Site selectivity of specific reaction steps important for catalysis

    DEFF Research Database (Denmark)

    Nielsen, Kenneth

    This thesis presents the results of two dierent projects, both focused on catalysis. The main part is about the investigation of the structure sensitivity of the CO dissociation reaction with STM on a Ru(0 1 54) single crystal and the second part concerns the STM structure study of the Bi/Pt(111......) overlayer system. In the STM study of the structure sensitivity of the CO dissociation reaction on the Ru(0 1 54) sample, it was determined that after cooling the sample from 700K to 400K in 10-8Torr of CO or in the CO that was left after a TPD, the sample displayed periodic decorations on every other...... with simulated STM images and DFT based reaction energy level calculation, it was furthermore determined that it is the B-step conguration that is active for the CO dissociation and that a conguration with the oxygen atom occupying the hcp 3-fold hollow site on top of the step, right next to the dissociation...

  19. Preparative semiconductor photoredox catalysis: An emerging theme in organic synthesis

    Directory of Open Access Journals (Sweden)

    David W. Manley

    2015-09-01

    Full Text Available Heterogeneous semiconductor photoredox catalysis (SCPC, particularly with TiO2, is evolving to provide radically new synthetic applications. In this review we describe how photoactivated SCPCs can either (i interact with a precursor that donates an electron to the semiconductor thus generating a radical cation; or (ii interact with an acceptor precursor that picks up an electron with production of a radical anion. The radical cations of appropriate donors convert to neutral radicals usually by loss of a proton. The most efficient donors for synthetic purposes contain adjacent functional groups such that the neutral radicals are resonance stabilized. Thus, ET from allylic alkenes and enol ethers generated allyl type radicals that reacted with 1,2-diazine or imine co-reactants to yield functionalized hydrazones or benzylanilines. SCPC with tertiary amines enabled electron-deficient alkenes to be alkylated and furoquinolinones to be accessed. Primary amines on their own led to self-reactions involving C–N coupling and, with terminal diamines, cyclic amines were produced. Carboxylic acids were particularly fruitful affording C-centered radicals that alkylated alkenes and took part in tandem addition cyclizations producing chromenopyrroles; decarboxylative homo-dimerizations were also observed. Acceptors initially yielding radical anions included nitroaromatics and aromatic iodides. The latter led to hydrodehalogenations and cyclizations with suitable precursors. Reductive SCPC also enabled electron-deficient alkenes and aromatic aldehydes to be hydrogenated without the need for hydrogen gas.

  20. Sequential rhodium/palladium catalysis: enantioselective formation of dihydroquinolinones in the presence of achiral and chiral ligands.

    Science.gov (United States)

    Zhang, Lei; Qureshi, Zafar; Sonaglia, Lorenzo; Lautens, Mark

    2014-12-08

    Compatible combinations of achiral and chiral ligands can be used in rhodium/palladium catalysis to achieve highly enantioselective domino reactions. The difference in rates of catalysis and minimal effects of ligand interference confer control in the domino sequence. The "all-in-one" 1,4-conjugate arylation and C-N cross-coupling through sequential Rh/Pd catalysis provides access to enantioenriched dihydroquinolinone building blocks. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.